Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 187 of 204
Found at i:55627409 original size:16 final size:16
Alignment explanation
Indices: 55627388--55627426 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
55627378 ATTTCACCTA
55627388 CAAGCATCATAAAACT
1 CAAGCATCATAAAACT
55627404 CAAGCATCATAAAACT
1 CAAGCATCATAAAACT
55627420 CAAGCAT
1 CAAGCAT
55627427 TCATCAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.49, C:0.26, G:0.08, T:0.18
Consensus pattern (16 bp):
CAAGCATCATAAAACT
Found at i:55636864 original size:15 final size:15
Alignment explanation
Indices: 55636844--55636873 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55636834 TATAATTTTA
55636844 ATATTTTAATAATTT
1 ATATTTTAATAATTT
55636859 ATATTTTAATAATTT
1 ATATTTTAATAATTT
55636874 TTAAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATTTTAATAATTT
Found at i:55636952 original size:16 final size:18
Alignment explanation
Indices: 55636928--55636964 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
55636918 ACATTTATCA
*
55636928 TTATTAATT-TAAAA-TT
1 TTATAAATTATAAAAGTT
55636944 TTATAAATTATAAAAGTT
1 TTATAAATTATAAAAGTT
55636962 TTA
1 TTA
55636965 AATAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 5 0.28
18 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTATAAATTATAAAAGTT
Found at i:55648570 original size:19 final size:19
Alignment explanation
Indices: 55648534--55648571 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
55648524 TTGGATTAGA
*
55648534 TTTATATTATTATAAATTT
1 TTTATATTATTAAAAATTT
55648553 TTTATATT-TTAAATAATTT
1 TTTATATTATTAAA-AATTT
55648572 AAAAGTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTATATTATTAAAAATTT
Found at i:55660526 original size:15 final size:15
Alignment explanation
Indices: 55660503--55660534 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
55660493 GTCGAATCAT
*
55660503 ATAATCCTTAACTGA
1 ATAACCCTTAACTGA
55660518 ATAACCCTTAACTGA
1 ATAACCCTTAACTGA
55660533 AT
1 AT
55660535 TGAAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (15 bp):
ATAACCCTTAACTGA
Found at i:55663091 original size:17 final size:18
Alignment explanation
Indices: 55663061--55663107 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
55663051 TAGATTTTAA
**
55663061 AATATTTTCGTATTT-TT
1 AATATTTTAATATTTATT
55663078 AATATTTTAATATTTATT
1 AATATTTTAATATTTATT
* *
55663096 ATTTTTTTAATA
1 AATATTTTAATA
55663108 AATTATAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
AATATTTTAATATTTATT
Found at i:55666735 original size:19 final size:20
Alignment explanation
Indices: 55666711--55666756 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
55666701 TACAAAATAA
*
55666711 TCAAAATAATTT-TTAAAA-T
1 TCAAAAT-ATTTATAAAAATT
55666730 TCAAAATATTTATAAAAATT
1 TCAAAATATTTATAAAAATT
55666750 TCAAAAT
1 TCAAAAT
55666757 TTATATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 12 0.50
20 8 0.33
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (20 bp):
TCAAAATATTTATAAAAATT
Found at i:55671157 original size:19 final size:19
Alignment explanation
Indices: 55671133--55671171 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
55671123 TTACATCCCA
*
55671133 GCAACTGAACATCTAATTT
1 GCAACTGAACATCCAATTT
55671152 GCAACTGAACATCCAATTT
1 GCAACTGAACATCCAATTT
55671171 G
1 G
55671172 ACATTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (19 bp):
GCAACTGAACATCCAATTT
Found at i:55689799 original size:22 final size:23
Alignment explanation
Indices: 55689746--55689800 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
55689736 ATTTGTCATT
*
55689746 ATAA-AAATAAAACAAATTTAGA
1 ATAATAAATATAACAAATTTAGA
* *
55689768 TTAATGAATATAACAAATTT-GA
1 ATAATAAATATAACAAATTTAGA
55689790 ATAATAAATAT
1 ATAATAAATAT
55689801 CTAAAATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.31
Consensus pattern (23 bp):
ATAATAAATATAACAAATTTAGA
Found at i:55691976 original size:125 final size:125
Alignment explanation
Indices: 55691731--55691987 Score: 338
Period size: 125 Copynumber: 2.1 Consensus size: 125
55691721 AAATAGTGGG
** * * * *
55691731 AAATCGCTTCTACTAGGATGCTATTTGAGAAGAAATTGTGAAATCGTGGCCTCGTGGACGCGATT
1 AAATCGCTGATACAAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGACT
* **
55691796 TCGCTACAGTGGTCATGTAAGAAATAATTTTTTTTTGATGTTTTCTGAGCAAATAGTATA
66 TCGCTACAGTAGTCATGTAAGAAATAATTTTTTTTTGATCATTTCTGAGCAAATAGTATA
* * *
55691856 AAATCGCTGATACAAGGATGCTATATTGGGCAGAAATTGTTAAATCGCGCCCTCGTGGACGCGAC
1 AAATCGCTGATACAAGGATGCTAT-TTGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGAC
** * *
55691921 TTCGCTACAGTTAGTCATGTTGGAAATAATTTTTTTTT-A-CATTTCTGAGCAAATAGTGTC
65 TTCGCTACAG-TAGTCATGTAAGAAATAATTTTTTTTTGATCATTTCTGAGCAAATAGTATA
55691981 AAATCGC
1 AAATCGC
55691988 GCCCTCGTGG
Statistics
Matches: 114, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
125 45 0.39
126 45 0.39
127 24 0.21
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (125 bp):
AAATCGCTGATACAAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGACT
TCGCTACAGTAGTCATGTAAGAAATAATTTTTTTTTGATCATTTCTGAGCAAATAGTATA
Found at i:55695206 original size:7 final size:7
Alignment explanation
Indices: 55695190--55695224 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
55695180 CTGTTGTATG
55695190 TTAGGG-
1 TTAGGGT
55695196 TTAGGGT
1 TTAGGGT
55695203 TTAGGGT
1 TTAGGGT
55695210 TTAGGGT
1 TTAGGGT
55695217 TTAGGGT
1 TTAGGGT
55695224 T
1 T
55695225 AAGAGTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
TTAGGGT
Found at i:55695222 original size:21 final size:20
Alignment explanation
Indices: 55695190--55695233 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
55695180 CTGTTGTATG
* *
55695190 TTAGGGTTAGGGTTTAGGGT
1 TTAGGGTTAGGGTTAAGAGT
55695210 TTAGGGTTTAGGGTTAAGAGT
1 TTAGGG-TTAGGGTTAAGAGT
55695231 TTA
1 TTA
55695234 TAATTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (20 bp):
TTAGGGTTAGGGTTAAGAGT
Found at i:55695267 original size:24 final size:23
Alignment explanation
Indices: 55695240--55695285 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
55695230 TTTATAATTA
*
55695240 AATTAAGTTAGGGTTAAGGTTTAT
1 AATTAAATTA-GGTTAAGGTTTAT
*
55695264 AATTAAATTAGGTTAGGGTTTA
1 AATTAAATTAGGTTAAGGTTTA
55695286 GTGTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (23 bp):
AATTAAATTAGGTTAAGGTTTAT
Found at i:55695268 original size:29 final size:29
Alignment explanation
Indices: 55695217--55696005 Score: 966
Period size: 30 Copynumber: 27.3 Consensus size: 29
55695207 GGTTTAGGGT
*
55695217 TTAGGGTTAAGAGTTTATAATTAAATTAAG
1 TTAGGGTT-AGGGTTTATAATTAAATTAAG
* *
55695247 TTAGGGTTAAGGTTTATAATTAAATTAGG
1 TTAGGGTTAGGGTTTATAATTAAATTAAG
* *
55695276 TTAGGGTTTAGTGTTTTTAATTAAATTAAG
1 TTAGGG-TTAGGGTTTATAATTAAATTAAG
* *
55695306 TTAGGGTTAGTGTTTATAATTAAATTAGG
1 TTAGGGTTAGGGTTTATAATTAAATTAAG
* *
55695335 TTAGGGTTTAGAGTTTTTAATTAAATTAAG
1 TTAGGG-TTAGGGTTTATAATTAAATTAAG
*
55695365 TTAGGGTTAGGGTTTATAATTAAATTAGG
1 TTAGGGTTAGGGTTTATAATTAAATTAAG
*
55695394 TTAGGGTTTAGGGTTTTTAATTAAATTAAG
1 TTAGGG-TTAGGGTTTATAATTAAATTAAG
*
55695424 TTAGGGTTTAGGGTTTATAATTAAATTAGG
1 TTAGGG-TTAGGGTTTATAATTAAATTAAG
55695454 TTAGGGTTTAGGGTTTATAATTAAATTAAG
1 TTAGGG-TTAGGGTTTATAATTAAATTAAG
* *
55695484 TTAGGGTTAGGGTTTGTAATTAAATTAGG
1 TTAGGGTTAGGGTTTATAATTAAATTAAG
* * *
55695513 TCAGGGTTTAGGGTTTGTAATTAAGTTAAG
1 TTAGGG-TTAGGGTTTATAATTAAATTAAG
55695543 TTAGGGTTTAGGGTTTATAATTAAATTAAG
1 TTAGGG-TTAGGGTTTATAATTAAATTAAG
*
55695573 TTAGGGTTTAGGGTTTTTAATTAAATTAAG
1 TTAGGG-TTAGGGTTTATAATTAAATTAAG
*
55695603 TTAGGGTTTAGGGTTTATAATTAAATTAGG
1 TTAGGG-TTAGGGTTTATAATTAAATTAAG
*
55695633 TTAGGGTTAGGGTTTTTAATTAAATTAAG
1 TTAGGGTTAGGGTTTATAATTAAATTAAG
*
55695662 TTAGGGTTAGGGTTTATAATTAAATTAGG
1 TTAGGGTTAGGGTTTATAATTAAATTAAG
*
55695691 TTAGAGTTAGGGTTTATAATTAAA-T---
1 TTAGGGTTAGGGTTTATAATTAAATTAAG
55695716 TTAGGGTTTAGGGTTTATAATTAAATTAAG
1 TTAGGG-TTAGGGTTTATAATTAAATTAAG
* *
55695746 TTAGGGTTATGGTTTATAATTAAATTAGG
1 TTAGGGTTAGGGTTTATAATTAAATTAAG
*
55695775 TTAGGGTTAGGGTTTTTAATTAAATTAAG
1 TTAGGGTTAGGGTTTATAATTAAATTAAG
* *
55695804 TTA-GGTTAGGGGTTT-TAATTCAATTAGG
1 TTAGGGTTA-GGGTTTATAATTAAATTAAG
* *
55695832 TTAGGTTTTAGGGTTTATAATTACATTAAG
1 TTAGG-GTTAGGGTTTATAATTAAATTAAG
* * * *
55695862 TTA-AGTTAGGGTTTTTAATTCAATTAGG
1 TTAGGGTTAGGGTTTATAATTAAATTAAG
*
55695890 TTA-GGTTAGGGTTT-TCAATTCAATTAAG
1 TTAGGGTTAGGGTTTAT-AATTAAATTAAG
55695918 TTAGGG-T----TTT-TAATTAAATTAAG
1 TTAGGGTTAGGGTTTATAATTAAATTAAG
* *
55695941 TTA-GGTTAGGGGTTT-TAATTCAATTAGG
1 TTAGGGTTA-GGGTTTATAATTAAATTAAG
* *
55695969 TTA-GGTTAGGGTTTTTTAATTCAATTAAG
1 TTAGGGTTAGGG-TTTATAATTAAATTAAG
55695998 TTAGGGTT
1 TTAGGGTT
55696006 TTTAATTAAA
Statistics
Matches: 675, Mismatches: 60, Indels: 48
0.86 0.08 0.06
Matches are distributed among these distances:
22 2 0.00
23 15 0.02
24 4 0.01
25 5 0.01
26 18 0.03
27 5 0.01
28 92 0.14
29 254 0.38
30 280 0.41
ACGTcount: A:0.31, C:0.01, G:0.24, T:0.44
Consensus pattern (29 bp):
TTAGGGTTAGGGTTTATAATTAAATTAAG
Found at i:55695300 original size:59 final size:58
Alignment explanation
Indices: 55695217--55696005 Score: 1036
Period size: 59 Copynumber: 13.6 Consensus size: 58
55695207 GGTTTAGGGT
* * *
55695217 TTAGGGTTAAGAGTTTATAATTAAATTAAGTTAGGGTTAAGGTTTATAATTAAATTAGG
1 TTAGGGTT-AGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTATAATTAAATTAGG
* *
55695276 TTAGGGTTTAGTGTTTTTAATTAAATTAAGTTAGGGTTAGTGTTTATAATTAAATTAGG
1 TTAGGG-TTAGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTATAATTAAATTAGG
*
55695335 TTAGGGTTTAGAGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTATAATTAAATTAGG
1 TTAGGG-TTAGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTATAATTAAATTAGG
55695394 TTAGGGTTTAGGGTTTTTAATTAAATTAAGTTAGGGTTTAGGGTTTATAATTAAATTAGG
1 TTAGGG-TTAGGGTTTTTAATTAAATTAAGTTAGGG-TTAGGGTTTATAATTAAATTAGG
* *
55695454 TTAGGGTTTAGGGTTTATAATTAAATTAAGTTAGGGTTAGGGTTTGTAATTAAATTAGG
1 TTAGGG-TTAGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTATAATTAAATTAGG
* * * *
55695513 TCAGGGTTTAGGGTTTGTAATTAAGTTAAGTTAGGGTTTAGGGTTTATAATTAAATTAAG
1 TTAGGG-TTAGGGTTTTTAATTAAATTAAGTTAGGG-TTAGGGTTTATAATTAAATTAGG
55695573 TTAGGGTTTAGGGTTTTTAATTAAATTAAGTTAGGGTTTAGGGTTTATAATTAAATTAGG
1 TTAGGG-TTAGGGTTTTTAATTAAATTAAGTTAGGG-TTAGGGTTTATAATTAAATTAGG
55695633 TTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTATAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTATAATTAAATTAGG
* * *
55695691 TTAGAGTTAGGGTTTATAATTAAA-T---TTAGGGTTTAGGGTTTATAATTAAATTAAG
1 TTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGG-TTAGGGTTTATAATTAAATTAGG
* * * * *
55695746 TTAGGGTTATGGTTTATAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAG
1 TTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTATAATTAAATTAGG
* * * * * *
55695804 TTA-GGTTAGGGGTTTTAATTCAATTAGGTTAGGTTTTAGGGTTTATAATTACATTAAG
1 TTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGG-GTTAGGGTTTATAATTAAATTAGG
* * * *
55695862 TTA-AGTTAGGGTTTTTAATTCAATTAGGTTA-GGTTAGGGTTT-TCAATTCAATTA--
1 TTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTAT-AATTAAATTAGG
*
55695916 --A--GTTAGGGTTTTTAATTAAATTAAGTTA-GGTTAGGGGTTT-TAATTCAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTA-GGGTTTATAATTAAATTAGG
*
55695969 TTA-GGTTAGGGTTTTTTAATTCAATTAAGTTAGGGTT
1 TTAGGGTTAGGG-TTTTTAATTAAATTAAGTTAGGGTT
55696006 TTTAATTAAA
Statistics
Matches: 673, Mismatches: 39, Indels: 37
0.90 0.05 0.05
Matches are distributed among these distances:
51 40 0.06
52 8 0.01
54 6 0.01
55 46 0.07
56 25 0.04
57 47 0.07
58 124 0.18
59 234 0.35
60 143 0.21
ACGTcount: A:0.31, C:0.01, G:0.24, T:0.44
Consensus pattern (58 bp):
TTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTATAATTAAATTAGG
Found at i:55695326 original size:24 final size:23
Alignment explanation
Indices: 55695299--55695344 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
55695289 TTTTTAATTA
* *
55695299 AATTAAGTTAGGGTTAGTGTTTAT
1 AATTAAATTA-GGTTAGGGTTTAT
55695323 AATTAAATTAGGTTAGGGTTTA
1 AATTAAATTAGGTTAGGGTTTA
55695345 GAGTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (23 bp):
AATTAAATTAGGTTAGGGTTTAT
Found at i:55696011 original size:23 final size:25
Alignment explanation
Indices: 55695580--55696021 Score: 205
Period size: 29 Copynumber: 16.0 Consensus size: 25
55695570 AAGTTAGGGT
*
55695580 TTAGGGTTTTTAATTAAATTAAGTTAGGG
1 TTAGGGTTTTTAATTCAATT-A--TA-GG
* *
55695609 TTTAGGGTTTATAATTAAATTAGGTTAGGG
1 -TTAGGGTTTTTAATTCAATTA---TA-GG
*
55695639 TTAGGGTTTTTAATTAAATTAAGTTAGGG
1 TTAGGGTTTTTAATTCAATT-A--TA-GG
* *
55695668 TTAGGGTTTATAATTAAATTAGGTTAGAG
1 TTAGGGTTTTTAATTCAATTA---TAG-G
* *
55695697 TTAGGGTTTATAATTAAATT-TAGGG
1 TTAGGGTTTTTAATTCAATTATA-GG
* *
55695722 TTTAGGGTTTATAATTAAATTAAGTTAGGG
1 -TTAGGGTTTTTAATTCAATT-A--TA-GG
* * *
55695752 TTATGGTTTATAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTCAATTA---TA-GG
*
55695781 TTAGGGTTTTTAATTAAATTAAGTTAGG
1 TTAGGGTTTTTAATTCAATT-A--TAGG
*
55695809 TTAGGGGTTTTAATTCAATTAGGTTAGG
1 TTAGGGTTTTTAATTCAATTA---TAGG
* *
55695837 TTTTAGGGTTTATAATT-ACATTAAGTTAAG
1 --TTAGGGTTTTTAATTCA-ATT-A--TAGG
55695867 TTAGGGTTTTTAATTCAATTAGGTTAGG
1 TTAGGGTTTTTAATTCAATTA---TAGG
*
55695895 TTAGGGTTTTCAATTCAATTA-A-G
1 TTAGGGTTTTTAATTCAATTATAGG
*
55695918 TTAGGGTTTTTAATTAAATTAAGTTAGG
1 TTAGGGTTTTTAATTCAATT-A--TAGG
*
55695946 TTAGGGGTTTTAATTCAATTAGGTTAGG
1 TTAGGGTTTTTAATTCAATTA---TAGG
55695974 TTAGGGTTTTTTAATTCAATTA-A-G
1 TTAGGG-TTTTTAATTCAATTATAGG
*
55695998 TTAGGGTTTTTAATTAAATT-TAGG
1 TTAGGGTTTTTAATTCAATTATAGG
55696022 GGTTTTAATC
Statistics
Matches: 364, Mismatches: 20, Indels: 62
0.82 0.04 0.14
Matches are distributed among these distances:
23 33 0.09
24 10 0.03
25 4 0.01
26 21 0.06
27 4 0.01
28 102 0.28
29 135 0.37
30 54 0.15
31 1 0.00
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.45
Consensus pattern (25 bp):
TTAGGGTTTTTAATTCAATTATAGG
Found at i:55696014 original size:18 final size:19
Alignment explanation
Indices: 55695991--55696030 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
55695981 TTTTTAATTC
*
55695991 AATT-AAGTTAGGGTTTTT
1 AATTAAAGTTAGGGGTTTT
*
55696009 AATTAAATTTAGGGGTTTT
1 AATTAAAGTTAGGGGTTTT
55696028 AAT
1 AAT
55696031 CAAATAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (19 bp):
AATTAAAGTTAGGGGTTTT
Found at i:55696022 original size:19 final size:19
Alignment explanation
Indices: 55695998--55696035 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55695988 TTCAATTAAG
* *
55695998 TTAGGGTTTTTAATTAAAT
1 TTAGGGGTTTTAATCAAAT
55696017 TTAGGGGTTTTAATCAAAT
1 TTAGGGGTTTTAATCAAAT
55696036 AATGTCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (19 bp):
TTAGGGGTTTTAATCAAAT
Found at i:55698187 original size:14 final size:15
Alignment explanation
Indices: 55698170--55698203 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
55698160 AATAAATATC
55698170 TAAAAATA-CATAAA
1 TAAAAATAGCATAAA
*
55698184 TAAAAATAGCTTAAA
1 TAAAAATAGCATAAA
55698199 TAAAA
1 TAAAA
55698204 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (15 bp):
TAAAAATAGCATAAA
Found at i:55698429 original size:22 final size:22
Alignment explanation
Indices: 55698399--55698440 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
55698389 ATTTGGAGAT
*
55698399 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
55698421 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
55698441 TTTGAGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:55698508 original size:21 final size:22
Alignment explanation
Indices: 55698442--55698518 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
55698432 ATTTGAGAGT
* * *
55698442 TTGAGATAATTTTGGAAGGAAT
1 TTGAGAGAATTTTTGAAGGAAA
* *
55698464 TTGAGAGAACTTTTGAAGGGAA
1 TTGAGAGAATTTTTGAAGGAAA
55698486 TTGAGAGAATTTTTGAA-GAAA
1 TTGAGAGAATTTTTGAAGGAAA
55698507 TTGAGAGAATTT
1 TTGAGAGAATTT
55698519 GTTTGTGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 15 0.31
22 33 0.69
ACGTcount: A:0.38, C:0.01, G:0.27, T:0.34
Consensus pattern (22 bp):
TTGAGAGAATTTTTGAAGGAAA
Found at i:55701875 original size:112 final size:111
Alignment explanation
Indices: 55701654--55701881 Score: 341
Period size: 112 Copynumber: 2.0 Consensus size: 111
55701644 GTCTGTTCAA
55701654 TTCAATTAAAAAATATTAAAAATTTAGTTCACCCAATCTATATTGCTTCCCAAGTCAATTGTTTC
1 TTCAATTAAAAAATATTAAAAATTTAGTTCACCCAATCTATATTGCTTCCCAAGTCAATTGTTTC
* * * * *
55701719 AATGCCCTTTTCTGGAATAGTACCTCTGCTCAAGTGGTCGGTCCAG
66 AATGCCCTTTTCTGGAACAGTACATCTGATCAAGCGGTCAGTCCAG
* *
55701765 TTCAATTAAAAAAATATTAAAAATTTAGTTCACCCAATCTATATTGTTTTCCAAGTCAATTGTTT
1 TTCAATT-AAAAAATATTAAAAATTTAGTTCACCCAATCTATATTGCTTCCCAAGTCAATTGTTT
* * *
55701830 CAATGTCCTTTTCTGGAACGGTACAT-TGGATCGAGCGGTCAGTCCAG
65 CAATGCCCTTTTCTGGAACAGTACATCT-GATCAAGCGGTCAGTCCAG
55701877 TTCAA
1 TTCAA
55701882 ACAACCTTGA
Statistics
Matches: 105, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
111 8 0.08
112 97 0.92
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36
Consensus pattern (111 bp):
TTCAATTAAAAAATATTAAAAATTTAGTTCACCCAATCTATATTGCTTCCCAAGTCAATTGTTTC
AATGCCCTTTTCTGGAACAGTACATCTGATCAAGCGGTCAGTCCAG
Found at i:55709092 original size:24 final size:22
Alignment explanation
Indices: 55709035--55709098 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 22
55709025 CAAAATATTA
*
55709035 ATAAAATTA-TTTTATATTAAT
1 ATAAAAATATTTTTATATTAAT
*
55709056 ATATAAATATTTTTATAATTAAAT
1 ATAAAAATATTTTTAT-ATT-AAT
*
55709080 TTAAAAATATTTTT-TATTA
1 ATAAAAATATTTTTATATTA
55709099 TTTAAATCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 8 0.22
22 9 0.25
23 4 0.11
24 15 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATAAAAATATTTTTATATTAAT
Found at i:55709471 original size:12 final size:11
Alignment explanation
Indices: 55709444--55709504 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
55709434 ATTTTTTTAA
55709444 TTTTAAAATAT
1 TTTTAAAATAT
55709455 TTTTAAAATACT
1 TTTTAAAATA-T
55709467 TTTT-AAAT-T
1 TTTTAAAATAT
* *
55709476 TTTT---TTAA
1 TTTTAAAATAT
55709484 TTTTAAAATAT
1 TTTTAAAATAT
55709495 TTTTAAAATA
1 TTTTAAAATA
55709505 AATATTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 1 0.02
8 4 0.10
9 5 0.12
11 26 0.63
12 5 0.12
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:55709521 original size:40 final size:40
Alignment explanation
Indices: 55709421--55709523 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 40
55709411 GCCCGAATAT
55709421 AATAAATA-TTTTTATTTTTTTAATTTTAAAATATTTTTAA
1 AATAAATATTTTTTA-TTTTTTAATTTTAAAATATTTTTAA
*
55709461 AAT-ACT-TTTTAAATT-TTTTTTAATTTTAAAATATTTTTAA
1 AATAAATATTTT---TTATTTTTTAATTTTAAAATATTTTTAA
*
55709501 AATAAATATTTTTTAATTTTTAA
1 AATAAATATTTTTTATTTTTTAA
55709524 AATAAATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
39 7 0.13
40 38 0.72
41 2 0.04
42 6 0.11
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (40 bp):
AATAAATATTTTTTATTTTTTAATTTTAAAATATTTTTAA
Found at i:55709545 original size:23 final size:23
Alignment explanation
Indices: 55709493--55709548 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
55709483 ATTTTAAAAT
**
55709493 ATTTTTAAAATAAATATTTTTTA
1 ATTTTTAAAATAAATATTTGATA
55709516 ATTTTTAAAATAAAT-TTTGATA
1 ATTTTTAAAATAAATATTTGATA
*
55709538 TTTATTTAAAA
1 ATT-TTTAAAA
55709549 AACGGGCCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 7 0.24
23 22 0.76
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTTTTAAAATAAATATTTGATA
Found at i:55713484 original size:21 final size:20
Alignment explanation
Indices: 55713458--55713504 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
55713448 TGAATGCTGA
* *
55713458 TTTTTGGTTAAGATTTTTCAT
1 TTTTTGGATAAGAATTTT-AT
55713479 TTTTTGGATAAGAATTTTAT
1 TTTTTGGATAAGAATTTTAT
*
55713499 TGTTTG
1 TTTTTG
55713505 ATTTGTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.21, C:0.02, G:0.17, T:0.60
Consensus pattern (20 bp):
TTTTTGGATAAGAATTTTAT
Found at i:55717771 original size:26 final size:25
Alignment explanation
Indices: 55717741--55717790 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
55717731 TACAATTGTG
*
55717741 TTAAAATCATTAATAAAAAATATTTT
1 TTAAAAT-ACTAATAAAAAATATTTT
* *
55717767 TTAAAATACTAATTACAAATATTT
1 TTAAAATACTAATAAAAAATATTT
55717791 AAATATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (25 bp):
TTAAAATACTAATAAAAAATATTTT
Found at i:55718084 original size:13 final size:13
Alignment explanation
Indices: 55718068--55718117 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
55718058 TTTAAGCCAA
55718068 ACTTTTCAAAATC
1 ACTTTTCAAAATC
*
55718081 ACTTCTCAAAATC
1 ACTTTTCAAAATC
*
55718094 ACTTTTTCACAA-C
1 AC-TTTTCAAAATC
55718107 ACTTTTCAAAA
1 ACTTTTCAAAA
55718118 GCAACGAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 8 0.25
13 17 0.53
14 7 0.22
ACGTcount: A:0.38, C:0.26, G:0.00, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAATC
Found at i:55718464 original size:20 final size:19
Alignment explanation
Indices: 55718434--55718484 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
55718424 AGTAAAGTAT
55718434 AAATA-ATTAAATGAAAAC
1 AAATACATTAAATGAAAAC
*
55718452 GAAATACATTAAACG-AAAC
1 -AAATACATTAAATGAAAAC
55718471 AAA-AC-TTAAATGAA
1 AAATACATTAAATGAA
55718485 TTAAATTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 6 0.21
17 3 0.11
18 3 0.11
19 9 0.32
20 7 0.25
ACGTcount: A:0.63, C:0.10, G:0.08, T:0.20
Consensus pattern (19 bp):
AAATACATTAAATGAAAAC
Found at i:55722566 original size:26 final size:28
Alignment explanation
Indices: 55722530--55722587 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
55722520 CTCAAATAAA
*
55722530 AAATAATAATATT-TTATAATTAAAT-T
1 AAATAAGAATATTATTATAATTAAATAT
* *
55722556 AAATAAGAATATTATTGTTATTAAATAT
1 AAATAAGAATATTATTATAATTAAATAT
55722584 AAAT
1 AAAT
55722588 TCCAAGGCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 12 0.44
27 10 0.37
28 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (28 bp):
AAATAAGAATATTATTATAATTAAATAT
Found at i:55725281 original size:132 final size:132
Alignment explanation
Indices: 55725030--55725424 Score: 664
Period size: 132 Copynumber: 3.0 Consensus size: 132
55725020 CACGAGCATA
55725030 TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTTCTCCCATGCCAGGATTAAT
1 TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTTCTCCCATGCCAGGATTAAT
* * * * * *
55725095 TTCATCAACTTGTGGGGTTTCTACGGTTGATAAAGTAGCCGCAAGGGAAACTTCCTCCGACCTAG
66 TTCAACAACTTGAGGGTTTTCTACGGTTGATAAAGTAGCCACGAGGGTAACTTCCTCCGACCTAG
55725160 CC
131 CC
* *
55725162 TCTCCTTGATTGGAGGGATGAAGCTGAGAACATTCTTCAAAATTTTCTCCCACGCCAGGATTAAT
1 TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTTCTCCCATGCCAGGATTAAT
*
55725227 TTCAACAACTTGAGGGTTTTCTACGGTTGATAAAGTAGCCACGAGGGTACCTTCCTCCGACCTAG
66 TTCAACAACTTGAGGGTTTTCTACGGTTGATAAAGTAGCCACGAGGGTAACTTCCTCCGACCTAG
55725292 CC
131 CC
*
55725294 TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTACTCCCATGCCAGGATTAAT
1 TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTTCTCCCATGCCAGGATTAAT
* * * *
55725359 TTCAACAACTTCAGGGTTTTCTATGGTTGATAAAGTAGCCACGAAGGTAACTGCCTCCGACCTAG
66 TTCAACAACTTGAGGGTTTTCTACGGTTGATAAAGTAGCCACGAGGGTAACTTCCTCCGACCTAG
55725424 C
131 C
55725425 TTGTTCTTCT
Statistics
Matches: 246, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 246 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (132 bp):
TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTTCTCCCATGCCAGGATTAAT
TTCAACAACTTGAGGGTTTTCTACGGTTGATAAAGTAGCCACGAGGGTAACTTCCTCCGACCTAG
CC
Found at i:55729529 original size:30 final size:30
Alignment explanation
Indices: 55729493--55729554 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
55729483 TCCCAATAGG
*
55729493 CATAAACTATAACTATTGTCGAACTTGGAA
1 CATAAACTATAACTATTGTCGAACTCGGAA
55729523 CATAAACTATAACTATTGTCGAACTCGGAA
1 CATAAACTATAACTATTGTCGAACTCGGAA
55729553 CA
1 CA
55729555 CCTTCATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.27
Consensus pattern (30 bp):
CATAAACTATAACTATTGTCGAACTCGGAA
Found at i:55733915 original size:48 final size:49
Alignment explanation
Indices: 55733836--55733949 Score: 124
Period size: 48 Copynumber: 2.3 Consensus size: 49
55733826 GTGGTATGAA
*
55733836 ACTTGAACTCGTGACTGCATAATAATCATCAACT-GGAGCCCGAGTTAT
1 ACTTGAACTCGTGACTGCATAACAATCATCAACTGGGAGCCCGAGTTAT
* * * * **
55733884 ACTTGAACTTGTGACTGCATAGCCA-CTATCAATTGGGAGCCTTAGTTAT
1 ACTTGAACTCGTGACTGCATAACAATC-ATCAACTGGGAGCCCGAGTTAT
* *
55733933 ATTTCAACTCGTGACTG
1 ACTTGAACTCGTGACTG
55733950 TATCCACCAT
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
47 1 0.02
48 27 0.50
49 26 0.48
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (49 bp):
ACTTGAACTCGTGACTGCATAACAATCATCAACTGGGAGCCCGAGTTAT
Found at i:55735123 original size:30 final size:30
Alignment explanation
Indices: 55735084--55735171 Score: 99
Period size: 30 Copynumber: 2.9 Consensus size: 30
55735074 AAATTTTAAA
* *
55735084 TTAATAATGATAAAATTATATTTTAAATTT
1 TTAAAAATGATAAAATTATATTTTAAACTT
*
55735114 TTAAAAATGATAAAAATT-TAATTTAAACTT
1 TTAAAAATGAT-AAAATTATATTTTAAACTT
*
55735144 TTAAAAATAAT-AAATATATATTATTAAA
1 TTAAAAATGATAAAAT-TATATT-TTAAA
55735172 ATGATAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
28 4 0.08
29 1 0.02
30 33 0.67
31 11 0.22
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.43
Consensus pattern (30 bp):
TTAAAAATGATAAAATTATATTTTAAACTT
Found at i:55736220 original size:33 final size:33
Alignment explanation
Indices: 55736178--55736282 Score: 112
Period size: 33 Copynumber: 3.3 Consensus size: 33
55736168 TTACTTTACA
55736178 TTCATGTTTATTGTAGGTATTTAAACTGTGGGT
1 TTCATGTTTATTGTAGGTATTTAAACTGTGGGT
* ** ****
55736211 TTCATGTTTA-T-AATTTATTT--ACT-TTACA
1 TTCATGTTTATTGTAGGTATTTAAACTGTGGGT
55736239 TTCATGTTTATTGTAGGTATTTAAACTGTGGGT
1 TTCATGTTTATTGTAGGTATTTAAACTGTGGGT
55736272 TTCATGTTTAT
1 TTCATGTTTAT
55736283 AATTTAAGAA
Statistics
Matches: 53, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
28 11 0.21
29 4 0.08
30 6 0.11
31 6 0.11
32 4 0.08
33 22 0.42
ACGTcount: A:0.23, C:0.08, G:0.17, T:0.52
Consensus pattern (33 bp):
TTCATGTTTATTGTAGGTATTTAAACTGTGGGT
Found at i:55736262 original size:61 final size:61
Alignment explanation
Indices: 55736167--55736288 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
55736157 TTTTTTTTTT
55736167 TTTACTTTACATTCATGTTTATTGTAGGTATTTAAACTGTGGGTTTCATGTTTATAATTTA
1 TTTACTTTACATTCATGTTTATTGTAGGTATTTAAACTGTGGGTTTCATGTTTATAATTTA
55736228 TTTACTTTACATTCATGTTTATTGTAGGTATTTAAACTGTGGGTTTCATGTTTATAATTTA
1 TTTACTTTACATTCATGTTTATTGTAGGTATTTAAACTGTGGGTTTCATGTTTATAATTTA
55736289 AGAAAATGGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.52
Consensus pattern (61 bp):
TTTACTTTACATTCATGTTTATTGTAGGTATTTAAACTGTGGGTTTCATGTTTATAATTTA
Found at i:55753948 original size:21 final size:20
Alignment explanation
Indices: 55753912--55753950 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
55753902 TTATTGATAT
*
55753912 TTAAAAAATTATATATAAGA
1 TTAAAAAATTAAATATAAGA
55753932 TTAAAAAATTTAAATATAA
1 TTAAAAAA-TTAAATATAA
55753951 AATATCTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
TTAAAAAATTAAATATAAGA
Found at i:55757977 original size:23 final size:24
Alignment explanation
Indices: 55757919--55757983 Score: 89
Period size: 23 Copynumber: 2.7 Consensus size: 24
55757909 ATAATTTCAT
*
55757919 ATTTATATTAATTATATTAATATA
1 ATTTATATTAATTATATCAATATA
55757943 ATTATATATTAATTATATCAA-A-A
1 ATT-TATATTAATTATATCAATATA
55757966 ATATTATATTAATTATAT
1 AT-TTATATTAATTATAT
55757984 ATGTTAAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
23 17 0.45
24 5 0.13
25 16 0.42
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTTATATTAATTATATCAATATA
Found at i:55757980 original size:9 final size:9
Alignment explanation
Indices: 55757921--55757960 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
55757911 AATTTCATAT
55757921 TTATATTAA
1 TTATATTAA
55757930 TTATATTAA
1 TTATATTAA
55757939 -TATAATT-A
1 TTAT-ATTAA
55757947 -TATATTAA
1 TTATATTAA
55757955 TTATAT
1 TTATAT
55757961 CAAAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 3 0.11
8 8 0.29
9 17 0.61
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TTATATTAA
Found at i:55758042 original size:85 final size:84
Alignment explanation
Indices: 55757873--55758029 Score: 241
Period size: 85 Copynumber: 1.9 Consensus size: 84
55757863 TATATTATGT
55757873 TATCAAAAATATTATATTAATTATATATGTTAAATAATAATTTCATATTTATATTAATTATATTA
1 TATCAAAAATATTATATTAATTATATATGTTAAATAATAATTTCATATTTATATT-ATTATATTA
* *
55757938 ATATAATTATATATTAATTA
65 ATATAATAATATAATAATTA
55757958 TATCAAAAATATTATATTAATTATATATGTTAAATAATAATTAT-ATATTTATA-T-TTATATTA
1 TATCAAAAATATTATATTAATTATATATGTTAAATAATAATT-TCATATTTATATTATTATATTA
55758020 A-ATAACTAAT
65 ATATAA-TAAT
55758030 CCAGTAATAA
Statistics
Matches: 69, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
81 4 0.06
82 12 0.17
84 1 0.01
85 51 0.74
86 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (84 bp):
TATCAAAAATATTATATTAATTATATATGTTAAATAATAATTTCATATTTATATTATTATATTAA
TATAATAATATAATAATTA
Found at i:55765810 original size:44 final size:42
Alignment explanation
Indices: 55765759--55765869 Score: 132
Period size: 44 Copynumber: 2.5 Consensus size: 42
55765749 GATCTGCTCT
*
55765759 CTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCACTCCA
1 CTGCAACTTCAG-GAGATAAGATCC-AGGCTTTAATCCACTCCA
* * **
55765803 CTGCAACTTCAGGAAGATAGGATTCCCGGCTTTAATCTGCTCCA
1 CTGCAACTTCAGG-AGATAAGA-TCCAGGCTTTAATCCACTCCA
55765847 CTGCAACTTCAGGGAGATAAGAT
1 CTGCAACTTCA-GGAGATAAGAT
55765870 TTGCCATCTT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
43 2 0.03
44 51 0.88
45 5 0.09
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (42 bp):
CTGCAACTTCAGGAGATAAGATCCAGGCTTTAATCCACTCCA
Found at i:55766083 original size:87 final size:86
Alignment explanation
Indices: 55765977--55766257 Score: 266
Period size: 87 Copynumber: 3.3 Consensus size: 86
55765967 ATATGCTTTC
* * * * *
55765977 TGCAACTTCAGAGATATAAGATCAAAGGTTTTATTTTGCCCACTGTAACTTCAGCGGGATAGGAT
1 TGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCTGCCCACTGCAACTTCAGCGGGATAGGAT
55766042 TACCGACTTTAATCTGCTCCAT
66 TACCGA-TTTAATCTGCTCCAT
* * **** * * *
55766064 TGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAG-GGAGATAA
1 TGCAACTTCAGAGAGATAAGATCTAAGGT-TTTAATCTGCC-CACTGCAACTTCAGCGG-GATAG
* ***
55766128 GACTA--GATGCGATCTGCT-C-T
63 GATTACCGATTTAATCTGCTCCAT
* * *
55766148 CTGCAATTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCCCACTGCAACTTCAGCGAGATAGGA
1 -TGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCTGCCCACTGCAACTTCAGCGGGATAGGA
*
55766213 TTACCGGATTTAATCTGCTCCAC
65 TTACC-GATTTAATCTGCTCCAT
*
55766236 TGCAACTTCAGGGAGATAAGAT
1 TGCAACTTCAGAGAGATAAGAT
55766258 TTGCCATCTT
Statistics
Matches: 148, Mismatches: 36, Indels: 20
0.73 0.18 0.10
Matches are distributed among these distances:
83 22 0.15
84 10 0.07
85 23 0.16
86 18 0.12
87 44 0.30
88 10 0.07
89 21 0.14
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (86 bp):
TGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCTGCCCACTGCAACTTCAGCGGGATAGGAT
TACCGATTTAATCTGCTCCAT
Found at i:55766127 original size:172 final size:172
Alignment explanation
Indices: 55765833--55766303 Score: 600
Period size: 172 Copynumber: 2.7 Consensus size: 172
55765823 GATTCCCGGC
* * * * *
55765833 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCC--ATCTTCAGTCTGC-CTCACTG
1 TTTAATCCGC-CCACTGCAACTTCAGCGAGATAGGA-TTACCGGAT-TT-AATCTGCTC-CACTG
* * * *
55765895 CAACTTCA-GGAGGATAAGACTTG-CTTACTT-AGTCCG-CTCCACTGCAACTTTAGAGAGATAA
61 CAACTTCAGGGA-GATAAGATTTGCCAT-CTTCAGTCTGCCT-CACTGCAACTTCAGAGAGATAA
* *
55765956 GACTAGATGCGATATGCTTTCTGCAACTTCAGAGATATAAGATCAAAGGT
123 GACTAGATGCGATATGCTCTCTGCAACTTCAGAGAGATAAGATCAAAGGT
* ** * * *
55766006 TTTATTTTGCCCACTGTAACTTCAGCGGGATAGGATTACC-GACTTTAATCTGCTCCATTGCAAC
1 TTTAATCCGCCCACTGCAACTTCAGCGAGATAGGATTACCGGA-TTTAATCTGCTCCACTGCAAC
*
55766070 TTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGGAGATAAGACTAGA
65 TTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGAGAGATAAGACTAGA
* * *
55766135 TGCGATCTGCTCTCTGCAATTTCAGAGAGATAAGATCTAAGGT
130 TGCGATATGCTCTCTGCAACTTCAGAGAGATAAGATCAAAGGT
55766178 TTTAATCCGCCCACTGCAACTTCAGCGAGATAGGATTACCGGATTTAATCTGCTCCACTGCAACT
1 TTTAATCCGCCCACTGCAACTTCAGCGAGATAGGATTACCGGATTTAATCTGCTCCACTGCAACT
55766243 TCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGA-AGGATAAGACT
66 TCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGAGA-GATAAGACT
55766304 TGCTTACTTA
Statistics
Matches: 263, Mismatches: 26, Indels: 19
0.85 0.08 0.06
Matches are distributed among these distances:
171 36 0.14
172 214 0.81
173 13 0.05
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (172 bp):
TTTAATCCGCCCACTGCAACTTCAGCGAGATAGGATTACCGGATTTAATCTGCTCCACTGCAACT
TCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGAGAGATAAGACTAGAT
GCGATATGCTCTCTGCAACTTCAGAGAGATAAGATCAAAGGT
Found at i:55766209 original size:83 final size:83
Alignment explanation
Indices: 55765927--55766209 Score: 244
Period size: 83 Copynumber: 3.3 Consensus size: 83
55765917 GCTTACTTAG
* * * * *
55765927 TCCGCTCCACTGCAACTTTAGAGAGATAAGACTAGATGCGATATGCTTTCTGCAACTTCAGAGAT
1 TCCGC-CCACTGCAACTTCAGCGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
* *
55765992 ATAAGATCAAAGGTTTTAT
65 ATAAGATCTAAGGTTTTAA
** * * * * ***
55766011 TTTGCCCACTGTAACTTCAGCGGGATAGGATTACCGACTTTAATCTGCTC-CATTGCAACTTCAG
1 TCCGCCCACTGCAACTTCAGCGAGATAAGACTA--GA-TGCGATCTGCTCTC--TGCAACTTCAG
* * **** * *
55766075 GGAGATAAGATTTGCCATCTTCAG
61 AGAGATAAGATCTAAGGT-TTTAA
* * *
55766099 TCTGCCTCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAATTTCAGAGAG
1 TCCGCC-CACTGCAACTTCAGCGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
55766164 ATAAGATCTAAGGTTTTAA
65 ATAAGATCTAAGGTTTTAA
55766183 TCCGCCCACTGCAACTTCAGCGAGATA
1 TCCGCCCACTGCAACTTCAGCGAGATA
55766210 GGATTACCGG
Statistics
Matches: 148, Mismatches: 43, Indels: 17
0.71 0.21 0.08
Matches are distributed among these distances:
83 42 0.28
84 11 0.07
85 25 0.17
86 16 0.11
87 24 0.16
88 8 0.05
89 22 0.15
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (83 bp):
TCCGCCCACTGCAACTTCAGCGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGA
TAAGATCTAAGGTTTTAA
Found at i:55766245 original size:216 final size:213
Alignment explanation
Indices: 55765759--55766474 Score: 729
Period size: 216 Copynumber: 3.3 Consensus size: 213
55765749 GATCTGCTCT
** *
55765759 CTGCAACTTCAGAGAGATAAGA-T-CCAAGGTTTTAATCCACTCCACTGCAACTTCAGGAAGATA
1 CTGCAACTTCAGAGAGATAAGATTACC--GGTTTTAATCTGCTCCACTGCAACTTCAGG-GGATA
* *
55765822 GGATTCCCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTG
63 GGATTACCGACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTG
* * * * * *
55765887 CCTCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAGTCCGCTCCACTGCAACTTTAGAGA
128 CCTCACTGCAACTTCAGGGA-GATAAGACTAG-ATGC-GA-TCTGCT-CTCTGCAA-TTTAGAGA
* *** ***
55765951 GATAAGA-CT-AGATGCGATAT-GCTTT
187 GATAAGATCTAAGGTTTTA-ATCGCCCA
* * ** * * *
55765976 CTGCAACTTCAGAGATATAAGATCAAAGGTTTTATTTTGC-CCACTGTAACTTCAGCGGGATAGG
1 CTGCAACTTCAGAGAGATAAGATTACCGGTTTTAATCTGCTCCACTGCAACTTCAG-GGGATAGG
*
55766040 ATTACCGACTTTAATCTGCTCCATTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCC
65 ATTACCGACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCC
55766105 TCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAATTTCAGAGAGATAAGA
130 TCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAATTT-AGAGAGATAAGA
55766170 TCTAAGGTTTTAATCCGCCCA
194 TCTAAGGTTTTAAT-CGCCCA
* * * *
55766191 CTGCAACTTCAGCGAGATAGGATTACCGGATTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
1 CTGCAACTTCAGAGAGATAAGATTACCGGTTTTAATCTGCTCCACTGCAACTTCAGGG-GATAGG
* * * * * *
55766256 ATTTGCC-ATCTTCAGTCTGC-CTCACTGCAACTTCA-GAAGGATAAGACTTG-CTTACTT-AGT
65 A-TTACCGA-CTTTAATCTGCTC-CACTGCAACTTCAGGGA-GATAAGATTTGCCAT-CTTCAGT
* * *
55766316 CTG-CTCCACTGCAACTTCAGGGAGATAAGACTAAATGCGATCTCCTCTCTACAATTTTAGAGAG
125 CTGCCT-CACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAA-TTTAGAGAG
55766380 ATAAGATCTAAGGTTTTAATTCGCCCA
188 ATAAGATCTAAGGTTTTAA-TCGCCCA
* * * * * *
55766407 CTGCAACTTCAGCGAGATAGGATTACCGGCTTTAATCTGCTCCATTGTAACTTCAGGGAGATAAG
1 CTGCAACTTCAGAGAGATAAGATTACCGGTTTTAATCTGCTCCACTGCAACTTCAGGG-GATAGG
55766472 ATT
65 ATT
55766475 TGTCATCTTC
Statistics
Matches: 430, Mismatches: 50, Indels: 40
0.83 0.10 0.08
Matches are distributed among these distances:
211 3 0.01
212 19 0.04
213 9 0.02
214 5 0.01
215 41 0.10
216 277 0.64
217 76 0.18
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (213 bp):
CTGCAACTTCAGAGAGATAAGATTACCGGTTTTAATCTGCTCCACTGCAACTTCAGGGGATAGGA
TTACCGACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCT
CACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAATTTAGAGAGATAAGATC
TAAGGTTTTAATCGCCCA
Found at i:55766340 original size:89 final size:88
Alignment explanation
Indices: 55766053--55766345 Score: 294
Period size: 89 Copynumber: 3.4 Consensus size: 88
55766043 ACCGACTTTA
*
55766053 ATCTGCTCCATTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
* * * *
55766118 AGGGAGATAAGACTAG-ATGC-G
66 AGAGAGATAAGACTTGCATACTT
* * * * **** * * *
55766139 ATCTGCT-CTCTGCAATTTCAGAGAGATAAGATCTAAGGT-TTTAATCCGCC-CACTGCAACTTC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
* * * ** *
55766201 AGCGAGATAGGA-TTACCGGATTT
66 AGAGAGATAAGACTT-GCATACTT
55766224 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
1 -ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
*
55766289 CAGA-AGGATAAGACTTGCTTACTT
65 CAGAGA-GATAAGACTTGCATACTT
55766313 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 A-TCTGCTCCACTGCAACTTCAGGGAGATAAGA
55766346 CTAAATGCGA
Statistics
Matches: 159, Mismatches: 38, Indels: 17
0.74 0.18 0.08
Matches are distributed among these distances:
82 1 0.01
83 22 0.14
84 8 0.05
85 23 0.14
86 14 0.09
87 24 0.15
88 10 0.06
89 55 0.35
90 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (88 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
AGAGAGATAAGACTTGCATACTT
Found at i:55766410 original size:172 final size:172
Alignment explanation
Indices: 55766049--55766680 Score: 503
Period size: 172 Copynumber: 3.7 Consensus size: 172
55766039 GATTACCGAC
*
55766049 TTTAA-TCTGCTCCATTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCA
1 TTTAATTC-GCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCA
* * * * * * *
55766113 ACTTCAGGGAGATAAGACTAGATGC-GA-TCTGCT-CTCTGCAATTTCAGAGAGATAAGATCTAA
65 ACTTCAGGGAGATAAGACTTGTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTAA
* *** * * * * * *
55766175 GGTTTTAATC-CGCCCACTGCAACTTCAGCGAGATAGGAT-TACCGGA
129 --ATGCGATCTC-CTCTCTGCAACTTCAGAGAGATAAGATCTA-AGGT
55766221 TTTAA-TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCA
1 TTTAATTC-GCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCA
*
55766285 ACTTCA-GAAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
65 ACTTCAGGGA-GATAAGACTTG-TTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
* * *
55766349 AATGCGATCTCCTCTCTACAATTTTAGAGAGATAAGATCTAAGGT
128 AATGCGATCTCCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGT
* * * ** * * * *
55766394 TTTAATTCGC-CCACTGCAACTTCAGCGAGATAGGA-TTACCGGCTTTAATCTG-CTCCATTGTA
1 TTTAATTCGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCT-CACTGCA
* * * * *
55766456 ACTTCAGGGAGATAAGATTTGTCATCTTCAGTTTGC-CTCACTACAACTTCA-GAAGAATAAGAC
65 ACTTCAGGGAGATAAGACTTGTTA-CTT-AGTCTGCTC-CACTGCAACTTCAGGGAG-ATAAGAC
* * * * * *
55766519 TAAATGGGATATGCTCTTTGCAACTTCAGAGAGATAATATCCAAGGT
126 TAAATGCGATCTCCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGT
* * * *
55766566 TGTAATTCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGC-T-TT-AATCTG-CTCCACTG
1 TTTAATTCGCTCCACTGCAACTTCAGGGAGATAAGATT-T-GCCATCTTCAGTCTGCCT-CACTG
*
55766627 CAACTTTAGGGAGATAAGA-TT-TTCCATCTTCAGTCTGC-CTCACTGCAACTTCAG
63 CAACTTCAGGGAGATAAGACTTGTT--A-CTT-AGTCTGCTC-CACTGCAACTTCAG
55766681 AAGGATAAGA
Statistics
Matches: 382, Mismatches: 57, Indels: 40
0.80 0.12 0.08
Matches are distributed among these distances:
170 4 0.01
171 43 0.11
172 178 0.47
173 115 0.30
174 9 0.02
175 11 0.03
176 22 0.06
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (172 bp):
TTTAATTCGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAA
CTTCAGGGAGATAAGACTTGTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAAAT
GCGATCTCCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGT
Found at i:55766442 original size:388 final size:388
Alignment explanation
Indices: 55765722--55766736 Score: 1611
Period size: 388 Copynumber: 2.6 Consensus size: 388
55765712 ACCCCTGGCT
* *
55765722 CAACTTCAGGGAGATAACACTAAATACGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAG
1 CAACTTCAGGGAGATAAGACTAAATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAG
* *
55765787 GTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTCCCGGCTTTAATCTGCTCCACTGCA
66 GTTTTAATCCGCTCCACTGCAACTTCAGG-AGATAGGATTACCGGCTTTAATCTGCTCCACTGCA
*
55765852 ACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTT
130 ACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGAAGGATAAGACTT
* * * * * * *
55765917 GCTTACTTAGTCCGCTCCACTGCAACTTTAGAGAGATAAGACTAGATGCGATATGCTTTCTGCAA
195 GCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAAATGCGATATCCTCTCTACAA
* * * * *
55765982 CTTCAGAGATATAAGATCAAAGGTTTTATTTTGCCCACTGTAACTTCAGCGGGATAGGATTACCG
260 CTTCAGAGAGATAAGATCAAAGGTTTTAATTCGCCCACTGCAACTTCAGCGAGATAGGATTACCG
*
55766047 ACTTTAATCTGCTCCATTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTG
325 ACTTTAATCTGCTCCATTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTA
* * *
55766111 CAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAATTTCAGAGAGATAAGATCTAAG
1 CAACTTCAGGGAGATAAGACTAAATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAG
*
55766176 GTTTTAATCCGC-CCACTGCAACTTCAGCGAGATAGGATTACCGGATTTAATCTGCTCCACTGCA
66 GTTTTAATCCGCTCCACTGCAACTTCAG-GAGATAGGATTACCGGCTTTAATCTGCTCCACTGCA
55766240 ACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGAAGGATAAGACTT
130 ACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGAAGGATAAGACTT
*
55766305 GCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAAATGCGATCTCCTCTCTACAA
195 GCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAAATGCGATATCCTCTCTACAA
* * *
55766370 TTTTAGAGAGATAAGATCTAAGGTTTTAATTCGCCCACTGCAACTTCAGCGAGATAGGATTACCG
260 CTTCAGAGAGATAAGATCAAAGGTTTTAATTCGCCCACTGCAACTTCAGCGAGATAGGATTACCG
* * * *
55766435 GCTTTAATCTGCTCCATTGTAACTTCAGGGAGATAAGATTTGTCATCTTCAGTTTGCCTCACTA
325 ACTTTAATCTGCTCCATTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTA
* * * * *
55766499 CAACTTCA-GAAGAATAAGACTAAATGGGATATGCTCTTTGCAACTTCAGAGAGATAATATCCAA
1 CAACTTCAGGGAG-ATAAGACTAAATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAA
* * *
55766563 GGTTGTAATTCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGC
65 GGTTTTAATCCGCTCCACTGCAACTTCA-GGAGATAGGATTACCGGCTTTAATCTGCTCCACTGC
* *
55766628 AACTTTAGGGAGATAAGATTTTCCATCTTCAGTCTGCCTCACTGCAACTTCAGAAGGATAAGACT
129 AACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGAAGGATAAGACT
*
55766693 TGCTTATTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
194 TGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
55766737 CGATCTGTTA
Statistics
Matches: 577, Mismatches: 45, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
387 3 0.01
388 348 0.60
389 225 0.39
390 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (388 bp):
CAACTTCAGGGAGATAAGACTAAATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAG
GTTTTAATCCGCTCCACTGCAACTTCAGGAGATAGGATTACCGGCTTTAATCTGCTCCACTGCAA
CTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGAAGGATAAGACTTG
CTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAAATGCGATATCCTCTCTACAAC
TTCAGAGAGATAAGATCAAAGGTTTTAATTCGCCCACTGCAACTTCAGCGAGATAGGATTACCGA
CTTTAATCTGCTCCATTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTA
Found at i:55766475 original size:216 final size:216
Alignment explanation
Indices: 55766097--55766519 Score: 722
Period size: 216 Copynumber: 2.0 Consensus size: 216
55766087 TGCCATCTTC
* * *
55766097 AGTCTGCCTCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAATTTCAGAG
1 AGTCTGCCTCACTGCAACTTCAGGGAGATAAGACTAAATGCGATCTCCTCTCTACAATTTCAGAG
55766162 AGATAAGATCTAAGGTTTTAATCCGCCCACTGCAACTTCAGCGAGATAGGATTACCGGATTTAAT
66 AGATAAGATCTAAGGTTTTAATCCGCCCACTGCAACTTCAGCGAGATAGGATTACCGGATTTAAT
*
55766227 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAG
131 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTACAACTTCAG
*
55766292 AAGGATAAGACTTGCTTACTT
196 AAGAATAAGACTTGCTTACTT
*
55766313 AGTCTG-CTCCACTGCAACTTCAGGGAGATAAGACTAAATGCGATCTCCTCTCTACAATTTTAGA
1 AGTCTGCCT-CACTGCAACTTCAGGGAGATAAGACTAAATGCGATCTCCTCTCTACAATTTCAGA
* *
55766377 GAGATAAGATCTAAGGTTTTAATTCGCCCACTGCAACTTCAGCGAGATAGGATTACCGGCTTTAA
65 GAGATAAGATCTAAGGTTTTAATCCGCCCACTGCAACTTCAGCGAGATAGGATTACCGGATTTAA
* * * *
55766442 TCTGCTCCATTGTAACTTCAGGGAGATAAGATTTGTCATCTTCAGTTTGCCTCACTACAACTTCA
130 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTACAACTTCA
55766507 GAAGAATAAGACT
195 GAAGAATAAGACT
55766520 AAATGGGATA
Statistics
Matches: 194, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
215 2 0.01
216 192 0.99
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (216 bp):
AGTCTGCCTCACTGCAACTTCAGGGAGATAAGACTAAATGCGATCTCCTCTCTACAATTTCAGAG
AGATAAGATCTAAGGTTTTAATCCGCCCACTGCAACTTCAGCGAGATAGGATTACCGGATTTAAT
CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTACAACTTCAG
AAGAATAAGACTTGCTTACTT
Found at i:55766618 original size:173 final size:172
Alignment explanation
Indices: 55766313--55766692 Score: 532
Period size: 173 Copynumber: 2.2 Consensus size: 172
55766303 TTGCTTACTT
* * * *
55766313 AGTCTG-CTCCACTGCAACTTCAG-GGAGATAAGACTAAATGCGATCTCCTCTCTACAATTTTAG
1 AGTCTGCCT-CACTGCAACTTCAGAAGA-ATAAGACTAAATGCGATATCCTCTCTACAACTTCAG
* *
55766376 AGAGATAAGATCTAAGGTTTTAATTCGCCCACTGCAACTTCAGCGAGATAGGATTACCGGCTTTA
64 AGAGATAAGATCCAAGGTTGTAATTCGCCCACTGCAACTTCAGCGAGATAGGATTACCGGCTTTA
* *
55766441 ATCTGCTCCATTGTAACTTCAGGGAGATAAGATTTGT-CATCTTC
129 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT-TCCATCTTC
* * * * * *
55766485 AGTTTGCCTCACTACAACTTCAGAAGAATAAGACTAAATGGGATATGCTCTTTGCAACTTCAGAG
1 AGTCTGCCTCACTGCAACTTCAGAAGAATAAGACTAAATGCGATATCCTCTCTACAACTTCAGAG
* * *
55766550 AGATAATATCCAAGGTTGTAATTCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAA
66 AGATAAGATCCAAGGTTGTAATTCGC-CCACTGCAACTTCAGCGAGATAGGATTACCGGCTTTAA
*
55766615 TCTGCTCCACTGCAACTTTAGGGAGATAAGATTTTCCATCTTC
130 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTTCCATCTTC
*
55766658 AGTCTGCCTCACTGCAACTTCAGAAGGATAAGACT
1 AGTCTGCCTCACTGCAACTTCAGAAGAATAAGACT
55766693 TGCTTATTTA
Statistics
Matches: 183, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
172 73 0.40
173 110 0.60
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (172 bp):
AGTCTGCCTCACTGCAACTTCAGAAGAATAAGACTAAATGCGATATCCTCTCTACAACTTCAGAG
AGATAAGATCCAAGGTTGTAATTCGCCCACTGCAACTTCAGCGAGATAGGATTACCGGCTTTAAT
CTGCTCCACTGCAACTTCAGGGAGATAAGATTTTCCATCTTC
Found at i:55766735 original size:44 final size:43
Alignment explanation
Indices: 55765798--55766736 Score: 220
Period size: 44 Copynumber: 21.7 Consensus size: 43
55765788 TTTTAATCCA
* * * * *
55765798 CTCCACTGCAACTTCAGGAAGATAGGA-TTCCCGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTTCC--ATTTAGTCTG
55765842 CTCCACTGCAACTTCAGGGAGATAAGA-TTTGCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTT-CCAT-TT-AGTCTG
* * * *
55765887 C-CTCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAGTCCG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTTC-CATTTAGTCTG
* * ** ** *
55765931 CTCCACTGCAACTTTAGAGAGATAAGAC--TAGA-TGCGATATG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTTCCATTTAG-TCTG
** * * ****** * *
55765972 CT-TTCTGCAACTTCAGAGATATAAGATCAAAGGTTTTATTTTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CTTTCCATTTAGTCTG
* * * *
55766015 C-CCACTGTAACTTCAGCGG-GATAGGA-TTACCGACTTTAATCTG
1 CTCCACTGCAACTTCAG-GGAGATAAGACTTTCC-A-TTTAGTCTG
*
55766058 CTCCATTGCAACTTCAGGGAGATAAGA-TTTGCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTT-CCAT-TT-AGTCTG
** **
55766103 C-CTCACTGCAACTTCAGGGAGATAAGAC--TAGA-TGCGATCTG
1 CTC-CACTGCAACTTCAGGGAGATAAGACTTTCCATTTAG-TCTG
* * * ***** * *
55766144 CT-CTCTGCAATTTCAGAGAGATAAGATCTAAGGTTTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CTTTCCATTTAGTCTG
* * * *
55766187 C-CCACTGCAACTTCAGCGAGATAGGA-TTACCGGATTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTTCC--ATTTAGTCTG
55766230 CTCCACTGCAACTTCAGGGAGATAAGA-TTTGCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTT-CCAT-TT-AGTCTG
* * * *
55766275 C-CTCACTGCAACTTCA-GAAGGATAAGACTTGCTTACTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTTC-CATTTAGTCTG
* * ** *
55766319 CTCCACTGCAACTTCAGGGAGATAAGAC--T-AAATGCGATCTC
1 CTCCACTGCAACTTCAGGGAGATAAGACTTTCCATTTAG-TCTG
* * * * * ***** *
55766360 CT-CTCTACAATTTTAGAGAGATAAGATCTAAGGTTTTAAT-TCG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CTTTCCATTTAGTCT-G
* * * * *
55766403 C-CCACTGCAACTTCAGCGAGATAGGA-TTACCGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTTCC--ATTTAGTCTG
* * * *
55766446 CTCCATTGTAACTTCAGGGAGATAAGA-TTTGTCATCTTCAGTTTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTT-CCAT-TT-AGTCTG
* * * * ** *
55766491 C-CTCACTACAACTTCA-GAAGAATAAGAC--T-AAATGGGATATG
1 CTC-CACTGCAACTTCAGGGAG-ATAAGACTTTCCATTTAG-TCTG
** * * *
55766532 CT-CTTTGCAACTTCAGAGAGAT-A-A-TATCCAAGGTTGTAAT-TCG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTTCC-A--TT-TAGTCT-G
* *
55766575 CTCCACTGCAACTTCAGGGAGATAGGA-TTATCGGC-TTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-TC--CATTTAGTCTG
* *
55766619 CTCCACTGCAACTTTAGGGAGATAAGATTTTCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTTCCAT-TT-AGTCTG
* * *
55766664 C-CTCACTGCAACTTCA-GAAGGATAAGACTTGCTTATTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTTC-CATTTAGTCTG
55766708 CTCCACTGCAACTTCAGGGAGATAAGACT
1 CTCCACTGCAACTTCAGGGAGATAAGACT
55766737 CGATCTGTTA
Statistics
Matches: 656, Mismatches: 151, Indels: 176
0.67 0.15 0.18
Matches are distributed among these distances:
38 1 0.00
39 2 0.00
40 79 0.12
41 32 0.05
42 4 0.01
43 105 0.16
44 261 0.40
45 159 0.24
46 10 0.02
47 2 0.00
49 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTTCCATTTAGTCTG
Found at i:55775919 original size:11 final size:11
Alignment explanation
Indices: 55775902--55775931 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
55775892 TTTTATTTTT
55775902 TAATTTTAAAA
1 TAATTTTAAAA
*
55775913 TACTTTTAAAA
1 TAATTTTAAAA
55775924 TAATTTTA
1 TAATTTTA
55775932 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:55775950 original size:30 final size:31
Alignment explanation
Indices: 55775916--55775991 Score: 136
Period size: 30 Copynumber: 2.5 Consensus size: 31
55775906 TTTAAAATAC
55775916 TTTTAAAATAATTTTATTTTTA-TTTTTTAA
1 TTTTAAAATAATTTTATTTTTATTTTTTTAA
*
55775946 TTTTAAAATAATTTTATTTTTATTTTTTTAT
1 TTTTAAAATAATTTTATTTTTATTTTTTTAA
55775977 TTTTAAAATAATTTT
1 TTTTAAAATAATTTT
55775992 TTAATGTTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 22 0.50
31 22 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (31 bp):
TTTTAAAATAATTTTATTTTTATTTTTTTAA
Found at i:55775971 original size:41 final size:41
Alignment explanation
Indices: 55775884--55775961 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
55775874 TAAATATATA
*
55775884 TATTTTATTTTTATTTTTTAATTTTAAAATACTTTTAAAAT
1 TATTTTATTTTTATTTTTTAATTTTAAAATAATTTTAAAAT
*
55775925 AATTTTATTTTTATTTTTTAATTTTAAAATAATTTTA
1 TATTTTATTTTTATTTTTTAATTTTAAAATAATTTTA
55775962 TTTTTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (41 bp):
TATTTTATTTTTATTTTTTAATTTTAAAATAATTTTAAAAT
Found at i:55779415 original size:17 final size:16
Alignment explanation
Indices: 55779389--55779420 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
55779379 ATATATAATT
55779389 AAAAAATAATTACATA
1 AAAAAATAATTACATA
55779405 AAAATAATAATTACAT
1 AAAA-AATAATTACAT
55779421 CCTAAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAAATAATTACATA
Found at i:55783630 original size:33 final size:33
Alignment explanation
Indices: 55783588--55783925 Score: 137
Period size: 33 Copynumber: 9.7 Consensus size: 33
55783578 ATGTGAAGGG
*
55783588 GGTTGCTAAGTGCTGATTACCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* *
55783621 GGTTGCTAAGTGCTGATTCCACCGTATCTTGAATATAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A-C-T-CAT-T---GGT
*
55783663 GGTTGCTAAGTGCTGATT-CCC--C-CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
*
55783690 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* * * *
55783723 GGTTGCTAAGTGCTGA-TCCGACCGTATTTTAAATGCGAAGGG
1 GGTTGCTAAGTGCTGATTCC--CCG-A--CT-CAT----TGGT
55783765 GGTTGCTAAGTGCTGATTCCTCC-A---A--GG-
1 GGTTGCTAAGTGCTGATTCC-CCGACTCATTGGT
* * *
55783792 GGTTGCTATGTGCTGATTCCCCAAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* * *
55783825 GGTTGCTAAGTGCTGATTCCACGATATCTTTGAATGTGAAAGA
1 GGTTGCTAAGTGCTGATTCCCCG--A-C--T-CAT-TG---GT
* *
55783868 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
*
55783901 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
55783926 TAACAGTTAA
Statistics
Matches: 237, Mismatches: 24, Indels: 87
0.68 0.07 0.25
Matches are distributed among these distances:
26 2 0.01
27 38 0.16
28 7 0.03
30 1 0.00
31 2 0.01
32 7 0.03
33 76 0.32
34 11 0.05
35 3 0.01
36 4 0.02
37 4 0.02
38 6 0.03
39 3 0.01
40 5 0.02
41 2 0.01
42 40 0.17
43 26 0.11
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
Found at i:55783713 original size:102 final size:102
Alignment explanation
Indices: 55783586--55783889 Score: 443
Period size: 102 Copynumber: 3.0 Consensus size: 102
55783576 AAATGTGAAG
* *
55783586 GGGGTTGCTAAGTGCTGATTACCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
1 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
*
55783651 GAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
66 GAATGTAAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
* *
55783688 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGA-TCCGACCGTATTT
1 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCC-ACCGTATCT
* ** *
55783752 TAAATGCGAAGGGGGTTGCTAAGTGCTGATTCCTCCAA
65 TGAATGTAAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
* *
55783790 GGGGTTGCTATGTGCTGATTCCCCAAATCATTGGTGGTTGCTAAGTGCTGATTCCA-CGATATCT
1 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCG-TATC-
*
55783854 TTGAATGTGAAA-GAGGTTGCTAAGTGCTGATTCCCC
64 TTGAATGT-AAAGGGGGTTGCTAAGTGCTGATTCCCC
55783890 GAATCACTGG
Statistics
Matches: 180, Mismatches: 17, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
101 5 0.03
102 142 0.79
103 31 0.17
104 2 0.01
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.32
Consensus pattern (102 bp):
GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
GAATGTAAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:55783799 original size:27 final size:26
Alignment explanation
Indices: 55783763--55783815 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
55783753 AAATGCGAAG
55783763 GGGGTTGCTAAGTGCTGATTCCTCCAA
1 GGGGTTGCTAAGTGCTGATTCC-CCAA
*
55783790 GGGGTTGCTATGTGCTGATTCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCAA
55783816 ATCATTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCAA
Found at i:55786850 original size:57 final size:57
Alignment explanation
Indices: 55786747--55786859 Score: 156
Period size: 57 Copynumber: 2.0 Consensus size: 57
55786737 GGGTGATCCT
* **
55786747 ATCTTGATATAGCCCTCCCGAAGAATATGTGTGAAAAAGATCTAGCCTGGACGGGTG
1 ATCTTAATATAGCCCTCCCGAAGAATATGTGTGAAAAAGATCTAGCCCAGACGGGTG
* * *
55786804 ATCTTAATATAGCCCTCCTGAAGAATATGTG-GAAAATGGATTTAGCCCAGACGGGT
1 ATCTTAATATAGCCCTCCCGAAGAATATGTGTGAAAA-AGATCTAGCCCAGACGGGT
55786860 AATTCGAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
56 5 0.10
57 44 0.90
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (57 bp):
ATCTTAATATAGCCCTCCCGAAGAATATGTGTGAAAAAGATCTAGCCCAGACGGGTG
Found at i:55788170 original size:3 final size:3
Alignment explanation
Indices: 55788162--55788211 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
55788152 TTGTTATTTC
* *
55788162 TAT TAT TAT TA- AAT TAGT T-T TAT TAT TAT TAT TATT TAT TAT CAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA-T TAT TAT TAT
55788207 TAT TA
1 TAT TA
55788212 GTTTTATTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 3 0.08
3 31 0.79
4 5 0.13
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:55788201 original size:16 final size:16
Alignment explanation
Indices: 55788180--55788211 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55788170 TTAAATTAGT
*
55788180 TTTATTATTATTATTA
1 TTTATTATCATTATTA
55788196 TTTATTATCATTATTA
1 TTTATTATCATTATTA
55788212 GTTTTATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATTATCATTATTA
Found at i:55788788 original size:12 final size:12
Alignment explanation
Indices: 55788767--55788798 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
55788757 TTTTATAGCC
*
55788767 TTATTCATTTCT
1 TTATTTATTTCT
55788779 TTATTTATTTCT
1 TTATTTATTTCT
55788791 TTATTTAT
1 TTATTTAT
55788799 ATTTTCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (12 bp):
TTATTTATTTCT
Found at i:55791310 original size:28 final size:28
Alignment explanation
Indices: 55791272--55791369 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
55791262 ACAAAGTGCA
*
55791272 AATAACAATAAGCACCAAAGTGCAAAAT
1 AATAACGATAAGCACCAAAGTGCAAAAT
*
55791300 AATAACGATAAGCACCAAAGTGCAAATTTT
1 AATAACGATAAGCACCAAAGTGCAAA--AT
* *
55791330 TACAACGATAAGCACCAAAGTGCAAAAT
1 AATAACGATAAGCACCAAAGTGCAAAAT
55791358 AAT-ACGATAAGC
1 AATAACGATAAGC
55791370 GCACTAATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
27 9 0.15
28 27 0.44
30 25 0.41
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.17
Consensus pattern (28 bp):
AATAACGATAAGCACCAAAGTGCAAAAT
Found at i:55791339 original size:30 final size:28
Alignment explanation
Indices: 55791263--55791369 Score: 125
Period size: 30 Copynumber: 3.9 Consensus size: 28
55791253 TCACTAAACA
55791263 CAAAGTGC-AAATAAC-A--ATAAGCAC
1 CAAAGTGCAAAATAACAACGATAAGCAC
*
55791287 CAAAGTGCAAAATAATAACGATAAGCAC
1 CAAAGTGCAAAATAACAACGATAAGCAC
* *
55791315 CAAAGTGCAAATTTTTACAACGATAAGCAC
1 CAAAGTGCAAA--ATAACAACGATAAGCAC
*
55791345 CAAAGTGCAAAATAA-TACGATAAGC
1 CAAAGTGCAAAATAACAACGATAAGC
55791370 GCACTAATTT
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
24 8 0.11
25 6 0.09
26 1 0.01
27 9 0.13
28 21 0.30
30 25 0.36
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (28 bp):
CAAAGTGCAAAATAACAACGATAAGCAC
Found at i:55809789 original size:6 final size:6
Alignment explanation
Indices: 55809778--55809809 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
55809768 CTGAAAAGTT
55809778 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT
55809810 GAGGCTATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:55813557 original size:13 final size:14
Alignment explanation
Indices: 55813529--55813561 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
55813519 ACTGCCGTAC
*
55813529 ATATATCTACCTGA
1 ATATATATACCTGA
55813543 ATATATATA-CTGA
1 ATATATATACCTGA
55813556 ATATAT
1 ATATAT
55813562 TCTCTATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (14 bp):
ATATATATACCTGA
Found at i:55822381 original size:37 final size:39
Alignment explanation
Indices: 55822314--55822390 Score: 115
Period size: 37 Copynumber: 2.0 Consensus size: 39
55822304 TAAACACCAA
*
55822314 AAAAAGTATTTTAAAAATAAAAAATAAAAAAGTAT-TTT
1 AAAAAGTATTTTAAAAATAAAAAATAAAAAAATATATTT
55822352 AAAAA-TATTTT-AAAATAAAAAATAAAAAAAATATATTT
1 AAAAAGTATTTTAAAAATAAAAAAT-AAAAAAATATATTT
55822390 A
1 A
55822391 TTATATTCGG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
36 12 0.33
37 15 0.42
38 9 0.25
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (39 bp):
AAAAAGTATTTTAAAAATAAAAAATAAAAAAATATATTT
Found at i:55822670 original size:10 final size:10
Alignment explanation
Indices: 55822655--55822724 Score: 56
Period size: 10 Copynumber: 7.2 Consensus size: 10
55822645 TGATAAAAAT
55822655 AAAATTTATA
1 AAAATTTATA
55822665 AAAA-TTATA
1 AAAATTTATA
55822674 AAAA-TTATTA
1 AAAATTTA-TA
* *
55822684 AATATTAATA
1 AAAATTTATA
**
55822694 AAAATAGA-A
1 AAAATTTATA
*
55822703 AAAAATTATA
1 AAAATTTATA
*
55822713 AAATTTTATA
1 AAAATTTATA
55822723 AA
1 AA
55822725 GTCGTAAGAA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
9 18 0.38
10 27 0.57
11 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (10 bp):
AAAATTTATA
Found at i:55822742 original size:19 final size:18
Alignment explanation
Indices: 55822718--55822782 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 18
55822708 TTATAAAATT
*
55822718 TTATAAAGTCGTAAGAAAA
1 TTATAAAATCGTAA-AAAA
** *
55822737 TTATAAAAAAGTAAAGAA
1 TTATAAAATCGTAAAAAA
55822755 TTATAAAATCTGTAAAAAAA
1 TTATAAAATC-GT-AAAAAA
55822775 TTATAAAA
1 TTATAAAA
55822783 ATCATATTGC
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 11 0.30
19 13 0.35
20 13 0.35
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.28
Consensus pattern (18 bp):
TTATAAAATCGTAAAAAA
Found at i:55822778 original size:20 final size:19
Alignment explanation
Indices: 55822718--55822782 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 19
55822708 TTATAAAATT
* *
55822718 TTATAAAGTCGTAAGAAAA
1 TTATAAAATCGTAAAAAAA
** *
55822737 TTATAAAAAAGT-AAAGAA
1 TTATAAAATCGTAAAAAAA
55822755 TTATAAAATCTGTAAAAAAA
1 TTATAAAATC-GTAAAAAAA
55822775 TTATAAAA
1 TTATAAAA
55822783 ATCATATTGC
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
18 12 0.33
19 11 0.31
20 13 0.36
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.28
Consensus pattern (19 bp):
TTATAAAATCGTAAAAAAA
Found at i:55822782 original size:9 final size:9
Alignment explanation
Indices: 55822653--55822784 Score: 65
Period size: 9 Copynumber: 13.9 Consensus size: 9
55822643 TATGATAAAA
*
55822653 ATAAAATTT
1 ATAAAAATT
55822662 ATAAAAATT
1 ATAAAAATT
55822671 ATAAAAATT
1 ATAAAAATT
*
55822680 ATTAAATATT
1 A-TAAAAATT
*
55822690 AATAAAAATAG
1 -ATAAAAAT-T
*
55822701 AAAAAAATT
1 ATAAAAATT
55822710 AT-AAAATT
1 ATAAAAATT
* *
55822718 TTATAAAGTCGT
1 ATA-AAAAT--T
55822730 A-AGAAAATT
1 ATA-AAAATT
55822739 ATAAAAA--
1 ATAAAAATT
55822746 AGTAAAGAATT
1 A-TAAA-AATT
*
55822757 ATAAAATCTGT
1 ATAAAA-AT-T
*
55822768 AAAAAAATT
1 ATAAAAATT
55822777 ATAAAAAT
1 ATAAAAAT
55822785 CATATTGCTA
Statistics
Matches: 93, Mismatches: 16, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
7 1 0.01
8 11 0.12
9 36 0.39
10 31 0.33
11 13 0.14
12 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:55822823 original size:16 final size:16
Alignment explanation
Indices: 55822802--55822832 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55822792 CTAAAAGAAT
55822802 TTTTTTATAATTTTTA
1 TTTTTTATAATTTTTA
*
55822818 TTTTTTATCATTTTT
1 TTTTTTATAATTTTT
55822833 TGCCACATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTATAATTTTTA
Found at i:55824164 original size:34 final size:34
Alignment explanation
Indices: 55824114--55824182 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 34
55824104 AAAATACAGT
* *
55824114 AATTTTTTTTTGAAACAC-AAATATTTTTGAAAC
1 AATTTTTTTTTGAAACACGAAAAATTTTTAAAAC
55824147 AATTTTTTTTTGAAAACACGAAAAATTTTTAAAAC
1 AATTTTTTTTTG-AAACACGAAAAATTTTTAAAAC
55824182 A
1 A
55824183 CGAGAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 12 0.38
34 6 0.19
35 14 0.44
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (34 bp):
AATTTTTTTTTGAAACACGAAAAATTTTTAAAAC
Found at i:55824180 original size:18 final size:18
Alignment explanation
Indices: 55824153--55824222 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
55824143 AAACAATTTT
55824153 TTTTTGAAAACACGAAAAA
1 TTTTT-AAAACACGAAAAA
*
55824172 TTTTTAAAACACG-AGAA
1 TTTTTAAAACACGAAAAA
*
55824189 -TTTTAGAGACAC-AAAAA
1 TTTTTA-AAACACGAAAAA
*
55824206 TTCTTAAAAACACGAAA
1 TT-TTTAAAACACGAAA
55824223 TTTTTTGAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
16 5 0.12
17 11 0.27
18 14 0.34
19 11 0.27
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.26
Consensus pattern (18 bp):
TTTTTAAAACACGAAAAA
Found at i:55824397 original size:18 final size:18
Alignment explanation
Indices: 55824152--55824585 Score: 135
Period size: 17 Copynumber: 24.3 Consensus size: 18
55824142 GAAACAATTT
55824152 TTTTTTGAAAACACGAAAA
1 TTTTTTGAAAACACG-AAA
*
55824171 ATTTTT-AAAACACGAGAA
1 TTTTTTGAAAACACGA-AA
* * *
55824189 -TTTTAG-AGACACAAAA
1 TTTTTTGAAAACACGAAA
* * *
55824205 ATTCTTAAAAACACGAAA
1 TTTTTTGAAAACACGAAA
* * *
55824223 TTTTTTGAAGACGCGACGA
1 TTTTTTGAAAACACGA-AA
*
55824242 --TTTTG-AGACACGAGAAA
1 TTTTTTGAAAACAC--GAAA
*
55824259 TTTTTTGAAAACGCG--A
1 TTTTTTGAAAACACGAAA
***
55824275 TTTTTTG-AAATGTGAAA
1 TTTTTTGAAAACACGAAA
* * *
55824292 ATTTGTG-AAACATGAGAA
1 TTTTTTGAAAACACGA-AA
*
55824310 -TTGTTGAAAACACGCAAA
1 TTTTTTGAAAACACG-AAA
* * *
55824328 -TTTGTG-AAACATGGAAG
1 TTTTTTGAAAACA-CGAAA
* * *
55824345 TCTTTAGAAAACATGAAAA
1 TTTTTTGAAAACACG-AAA
*
55824364 TTTTTTG--ATCATCGAAA
1 TTTTTTGAAAACA-CGAAA
55824381 TTTTTTGAAAACACGAAA
1 TTTTTTGAAAACACGAAA
* *
55824399 TTTTTTG-GAACACCAGAA
1 TTTTTTGAAAACACGA-AA
*
55824417 -TTTTTGAAAACACGAGGA
1 TTTTTTGAAAACACGA-AA
55824435 -TTTTTG-AAACACGAAA
1 TTTTTTGAAAACACGAAA
* * *
55824451 ATTTTTGAAACCATCGGAA
1 TTTTTTGAAAACA-CGAAA
*
55824470 -TTTTTGAAGACACGAAGA
1 TTTTTTGAAAACACGAA-A
**
55824488 -TTTTTG-AAACACTGGATTTT
1 TTTTTTGAAAACAC--GA--AA
55824508 TTTTTTGAAAACACGAAA
1 TTTTTTGAAAACACGAAA
** * *
55824526 -AATTTGAAAA-ATGGAA
1 TTTTTTGAAAACACGAAA
*
55824542 GTTTTTGAAAACACAGGAAA
1 TTTTTTGAAAACAC--GAAA
*
55824562 TTTTTTTGAAAACA-TAAA
1 -TTTTTTGAAAACACGAAA
55824580 TTTTTT
1 TTTTTT
55824586 TTTTGAATTT
Statistics
Matches: 308, Mismatches: 68, Indels: 80
0.68 0.15 0.18
Matches are distributed among these distances:
15 5 0.02
16 20 0.06
17 112 0.36
18 105 0.34
19 33 0.11
20 9 0.03
21 18 0.06
22 6 0.02
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (18 bp):
TTTTTTGAAAACACGAAA
Found at i:55824402 original size:35 final size:33
Alignment explanation
Indices: 55824351--55824496 Score: 116
Period size: 35 Copynumber: 4.1 Consensus size: 33
55824341 GAAGTCTTTA
* *
55824351 GAAAACATGAAAATTTTTTGATCATCGAAATTTTTT
1 GAAAACACG-AAATTTTTTGAACA-CGAAA-TTTTT
*
55824387 GAAAACACGAAATTTTTTGGAACACCAGAATTTTT
1 GAAAACACGAAATTTTTT-GAACACGA-AATTTTT
*
55824422 GAAAACACGAGGA-TTTTTGAAACACGAAAATTTTT
1 GAAAACACGA-AATTTTTTG-AACACG-AAATTTTT
* *
55824457 GAAACCATCGGAA-TTTTTGAAGACACGAAGATTTTT
1 GAAAACA-CGAAATTTTTTG-A-ACACGAA-ATTTTT
55824493 GAAA
1 GAAA
55824497 CACTGGATTT
Statistics
Matches: 94, Mismatches: 8, Indels: 16
0.80 0.07 0.14
Matches are distributed among these distances:
34 1 0.01
35 60 0.64
36 33 0.35
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (33 bp):
GAAAACACGAAATTTTTTGAACACGAAATTTTT
Found at i:55824439 original size:53 final size:54
Alignment explanation
Indices: 55824382--55824496 Score: 162
Period size: 53 Copynumber: 2.2 Consensus size: 54
55824372 TCATCGAAAT
* * *
55824382 TTTTTGAAAACACGAAATTTTTTGGAA-CACCAGAATTTTTGAAAACACGAGGA
1 TTTTTGAAAACACGAAAATTTTTGAAACCACCAGAATTTTTGAAAACACGAAGA
* * *
55824435 TTTTTG-AAACACGAAAATTTTTGAAACCATCGGAATTTTTGAAGACACGAAGA
1 TTTTTGAAAACACGAAAATTTTTGAAACCACCAGAATTTTTGAAAACACGAAGA
55824488 TTTTTGAAA
1 TTTTTGAAA
55824497 CACTGGATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
52 18 0.33
53 34 0.63
54 2 0.04
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (54 bp):
TTTTTGAAAACACGAAAATTTTTGAAACCACCAGAATTTTTGAAAACACGAAGA
Found at i:55824497 original size:53 final size:52
Alignment explanation
Indices: 55824120--55824499 Score: 179
Period size: 52 Copynumber: 7.2 Consensus size: 52
55824110 CAGTAATTTT
*** *
55824120 TTTTTGAAACAC-AAATATTTTTGAAACA--ATTTTTTTTTGAAAACACGAAAAA
1 TTTTTGAAACACGAAA-ATTTTTGAAACACCA-GAATTTTTGAAAACACG-AAGA
* * * * * * * *
55824172 TTTTTAAAACACGAGAATTTTAGAGACACAAAAATTCTTAAAAACACGAA-A
1 TTTTTGAAACACGAAAATTTTTGAAACACCAGAATTTTTGAAAACACGAAGA
* ** * * * *
55824223 TTTTTTGAAGACGCGACGA-TTTTGAGACACGAGAAATTTTTTGAAAACGCG-A-T
1 -TTTTTGAA-ACACGAAAATTTTTGAAACACCAG-AA-TTTTTGAAAACACGAAGA
*** * ** *
55824276 TTTTTGAAATGTGAAAATTTGTGAAACATGAGAATTGTTGAAAACACGCAA-A
1 TTTTTGAAACACGAAAATTTTTGAAACACCAGAATTTTTGAAAACACG-AAGA
* * * * * ** * *
55824328 TTTGTGAAACATGGAAGTCTTTAGAAAACATGAAAATTTTTTG--ATCATCGAA-A
1 TTTTTGAAACACGAAAAT-TTTTG-AAACACCAGAA-TTTTTGAAAACA-CGAAGA
* * *
55824381 TTTTTTGAAAACACGAAATTTTTTGGAACACCAGAATTTTTGAAAACACGAGGA
1 -TTTTTG-AAACACGAAAATTTTTGAAACACCAGAATTTTTGAAAACACGAAGA
* * *
55824435 TTTTTGAAACACGAAAATTTTTGAAACCATCGGAATTTTTGAAGACACGAAGA
1 TTTTTGAAACACGAAAATTTTTGAAA-CACCAGAATTTTTGAAAACACGAAGA
55824488 TTTTTGAAACAC
1 TTTTTGAAACAC
55824500 TGGATTTTTT
Statistics
Matches: 251, Mismatches: 57, Indels: 39
0.72 0.16 0.11
Matches are distributed among these distances:
50 12 0.05
51 8 0.03
52 98 0.39
53 82 0.33
54 37 0.15
55 14 0.06
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.32
Consensus pattern (52 bp):
TTTTTGAAACACGAAAATTTTTGAAACACCAGAATTTTTGAAAACACGAAGA
Found at i:55824510 original size:36 final size:35
Alignment explanation
Indices: 55824376--55824497 Score: 122
Period size: 35 Copynumber: 3.5 Consensus size: 35
55824366 TTTTGATCAT
* * * *
55824376 CGAAATTTTTTGAAAACA-CGAAATTTTTTGGAACA
1 CGAAAATTTTTGAAACCATCGGAA-TTTTTGAAACA
* * * *
55824411 CCAGAATTTTTGAAAACA-CGAGGATTTTTGAAACA
1 CGAAAATTTTTGAAACCATCG-GAATTTTTGAAACA
55824446 CGAAAATTTTTGAAACCATCGGAATTTTTGAAGACA
1 CGAAAATTTTTGAAACCATCGGAATTTTTGAA-ACA
*
55824482 CGAAGATTTTTGAAAC
1 CGAAAATTTTTGAAAC
55824498 ACTGGATTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
35 52 0.71
36 21 0.29
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.31
Consensus pattern (35 bp):
CGAAAATTTTTGAAACCATCGGAATTTTTGAAACA
Found at i:55824725 original size:16 final size:15
Alignment explanation
Indices: 55824704--55824757 Score: 63
Period size: 16 Copynumber: 3.5 Consensus size: 15
55824694 TGGCTTATTT
*
55824704 ATTAAAATAATTTAAA
1 ATTAAAATAAATT-AA
*
55824720 ATTAAATTAAATTGAA
1 ATTAAAATAAATT-AA
*
55824736 ATTAAATTAAATTAA
1 ATTAAAATAAATTAA
55824751 ATTAAAA
1 ATTAAAA
55824758 ATATAAATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 8 0.24
16 26 0.76
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
ATTAAAATAAATTAA
Found at i:55824728 original size:5 final size:5
Alignment explanation
Indices: 55824704--55824756 Score: 70
Period size: 5 Copynumber: 10.2 Consensus size: 5
55824694 TGGCTTATTT
* *
55824704 ATTAA AATAA TTTAAA ATTAA ATTAA ATTGAA ATTAA ATTAA ATTAA ATTAA
1 ATTAA ATTAA ATT-AA ATTAA ATTAA ATT-AA ATTAA ATTAA ATTAA ATTAA
55824756 A
1 A
55824757 AATATAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
5 33 0.79
6 9 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (5 bp):
ATTAA
Found at i:55824730 original size:21 final size:21
Alignment explanation
Indices: 55824718--55824757 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55824708 AAATAATTTA
* *
55824718 AAATTAAATTAAATTGAAATT
1 AAATTAAATTAAATTAAAATG
55824739 AAATTAAATTAAATTAAAA
1 AAATTAAATTAAATTAAAA
55824758 ATATAAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
AAATTAAATTAAATTAAAATG
Found at i:55824938 original size:12 final size:12
Alignment explanation
Indices: 55824916--55824961 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 12
55824906 TTGAACCCCT
55824916 TTTTTTCCTTCTC
1 TTTTTT-CTTCTC
55824929 TTTTTTCTTCT-
1 TTTTTTCTTCTC
55824940 TTTTTTC-TC-C
1 TTTTTTCTTCTC
55824950 TTTTTT-TTCTC
1 TTTTTTCTTCTC
55824961 T
1 T
55824962 CTGCTGGGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 10 0.33
11 9 0.30
12 5 0.17
13 6 0.20
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTCTTCTC
Found at i:55824943 original size:11 final size:11
Alignment explanation
Indices: 55824914--55824956 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
55824904 AATTGAACCC
55824914 CTTTTTTTCCTT
1 CTTTTTTT-CTT
55824926 CTCTTTTTTCTT
1 CT-TTTTTTCTT
*
55824938 CTTTTTTTCTC
1 CTTTTTTTCTT
55824949 CTTTTTTT
1 CTTTTTTT
55824957 TCTCTCTGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 16 0.55
12 7 0.24
13 6 0.21
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
CTTTTTTTCTT
Found at i:55824955 original size:23 final size:24
Alignment explanation
Indices: 55824914--55824959 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
55824904 AATTGAACCC
*
55824914 CTTTTTTTCCTTCTCTTTTTTCTT
1 CTTTTTTTCCTCCTCTTTTTTCTT
*
55824938 CTTTTTTT-CTCCTTTTTTTTCT
1 CTTTTTTTCCTCCTCTTTTTTCT
55824960 CTCTGCTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (24 bp):
CTTTTTTTCCTCCTCTTTTTTCTT
Found at i:55825094 original size:19 final size:18
Alignment explanation
Indices: 55825049--55825095 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
55825039 ATTGGCCTGC
55825049 CCTTTTTTTTGCGTTGGG
1 CCTTTTTTTTGCGTTGGG
* * *
55825067 CCCTATTTTTGCTTTGGG
1 CCTTTTTTTTGCGTTGGG
*
55825085 CCTTGTTTTTG
1 CCTTTTTTTTG
55825096 TTTCTTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.02, C:0.19, G:0.23, T:0.55
Consensus pattern (18 bp):
CCTTTTTTTTGCGTTGGG
Found at i:55825250 original size:11 final size:11
Alignment explanation
Indices: 55825209--55825268 Score: 58
Period size: 11 Copynumber: 5.8 Consensus size: 11
55825199 TAAAAAAAAA
55825209 TTCTT-TTTCT
1 TTCTTCTTTCT
55825219 TT-TTCTTT-T
1 TTCTTCTTTCT
**
55825228 TT-TTCCCT-T
1 TTCTTCTTTCT
55825237 TTCTTCTTTCT
1 TTCTTCTTTCT
55825248 TTCTTCTTTCT
1 TTCTTCTTTCT
55825259 TTCTCTCTTT
1 TTCT-TCTTT
55825269 TTCTTCTCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
9 12 0.29
10 9 0.21
11 16 0.38
12 5 0.12
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (11 bp):
TTCTTCTTTCT
Found at i:55825276 original size:11 final size:11
Alignment explanation
Indices: 55825210--55825276 Score: 52
Period size: 11 Copynumber: 6.2 Consensus size: 11
55825200 AAAAAAAAAT
*
55825210 TCTTTTTCTTTT
1 TCTTTTTC-TTC
*
55825222 TCTTTTTTTTC
1 TCTTTTTCTTC
*
55825233 -CCTTTTCTTC
1 TCTTTTTCTTC
55825243 T-TTCTTTCTTC
1 TCTT-TTTCTTC
55825254 T-TTCTTTC-TC
1 TCTT-TTTCTTC
55825264 TCTTTTTCTTC
1 TCTTTTTCTTC
55825275 TC
1 TC
55825277 CTTCGTTCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
10 16 0.35
11 23 0.50
12 7 0.15
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
TCTTTTTCTTC
Found at i:55825681 original size:30 final size:30
Alignment explanation
Indices: 55825644--55825799 Score: 163
Period size: 30 Copynumber: 5.2 Consensus size: 30
55825634 GGGCTGAAAC
* * *
55825644 ATAATTTTGATAAATTTTAGGGGTCAAAAT
1 ATAATTTTGAAAAAGTTTAGGGGTAAAAAT
* * * *
55825674 GTAATTTTGAGAAAGTTTAAGGGTTAAAAT
1 ATAATTTTGAAAAAGTTTAGGGGTAAAAAT
*
55825704 ATAA-TTTCAAAAAGTTTAGGGGTAAAAAAT
1 ATAATTTTGAAAAAGTTTAGGGGT-AAAAAT
* * * *
55825734 ATAATTTTAAAAAATTTTAGGGATCAAAAT
1 ATAATTTTGAAAAAGTTTAGGGGTAAAAAT
* *
55825764 GTAATTTT-AAAAAGTTTAAGGGTAAAAAT
1 ATAATTTTGAAAAAGTTTAGGGGTAAAAAT
55825793 ATAATTT
1 ATAATTT
55825800 AAAAAAATTG
Statistics
Matches: 104, Mismatches: 20, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
29 39 0.38
30 49 0.47
31 16 0.15
ACGTcount: A:0.46, C:0.02, G:0.16, T:0.37
Consensus pattern (30 bp):
ATAATTTTGAAAAAGTTTAGGGGTAAAAAT
Found at i:55825708 original size:60 final size:59
Alignment explanation
Indices: 55825644--55825808 Score: 188
Period size: 59 Copynumber: 2.8 Consensus size: 59
55825634 GGGCTGAAAC
* * * * * * *
55825644 ATAATTTTGATAAATTTTAGGGGTCAAAATGTAATTTTGAGAAAGTTTAAGGG-TTAAAAT
1 ATAATTTT-AAAAAGTTTAGGGGTAAAAATATAATTTT-AAAAAATTTAAGGGATCAAAAT
* *
55825704 ATAATTTCAAAAAGTTTAGGGGTAAAAAATATAATTTTAAAAAATTTTAGGGATCAAAAT
1 ATAATTTTAAAAAGTTTAGGGGT-AAAAATATAATTTTAAAAAATTTAAGGGATCAAAAT
* * *
55825764 GTAATTTTAAAAAGTTTAAGGGTAAAAATATAATTTAAAAAAATT
1 ATAATTTTAAAAAGTTTAGGGGTAAAAATATAATTTTAAAAAATT
55825809 GAGCCGGACA
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
59 45 0.50
60 45 0.50
ACGTcount: A:0.47, C:0.02, G:0.15, T:0.36
Consensus pattern (59 bp):
ATAATTTTAAAAAGTTTAGGGGTAAAAATATAATTTTAAAAAATTTAAGGGATCAAAAT
Found at i:55825726 original size:29 final size:29
Alignment explanation
Indices: 55825659--55825805 Score: 150
Period size: 29 Copynumber: 5.0 Consensus size: 29
55825649 TTTGATAAAT
* * * *
55825659 TTTAGGGGTCAAAATGTAATTTTGAGAAAG
1 TTTAGGGGTAAAAATATAA-TTTAAAAAAG
* * *
55825689 TTTAAGGGTTAAAATATAATTTCAAAAAG
1 TTTAGGGGTAAAAATATAATTTAAAAAAG
*
55825718 TTTAGGGGTAAAAAATATAATTTTAAAAAAT
1 TTTAGGGGT-AAAAATATAA-TTTAAAAAAG
* * * *
55825749 TTTAGGGATCAAAATGTAATTTTAAAAAG
1 TTTAGGGGTAAAAATATAATTTAAAAAAG
*
55825778 TTTAAGGGTAAAAATATAATTTAAAAAA
1 TTTAGGGGTAAAAATATAATTTAAAAAA
55825806 ATTGAGCCGG
Statistics
Matches: 96, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
29 47 0.49
30 33 0.34
31 16 0.17
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (29 bp):
TTTAGGGGTAAAAATATAATTTAAAAAAG
Found at i:55826078 original size:83 final size:76
Alignment explanation
Indices: 55825946--55827611 Score: 1005
Period size: 78 Copynumber: 21.8 Consensus size: 76
55825936 ATAGAAATTG
* * * * *
55825946 AAAATACCTCGCCGTGTGGCCCGAGGCTCAACTCACCTCTAGCATTATGAGTTGATTTTTTTTTT
1 AAAATACCTCGGCATGT-GTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTT
*
55826011 GAAAAACAGAAATATAAA
60 AAAAAACAGAAAT-TAAA
* * **
55826029 AGAAATACCTCGGCATGTGTCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTAAAAAAA
1 A-AAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAA
*
55826094 ACAGAAATT--G
65 ACAGAAATTAAA
* * * *
55826104 AAAATACCTCAG-A-GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTAAAAAA
1 AAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAA
*
55826166 ATAGAAATTTAAA
65 ACAGAAA-TTAAA
* * *
55826179 ATAAATACATCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTGATTTT
1 A-AAATACCTCGGCATGTGTCC-GAGGCTCAACTCACCTCTCGCAATATGA---G--TTGA----
* * ** * *
55826244 TTTTTTAGAAGTAAAAATT-GA
55 TTTTTAAAAAACAGAAATTAAA
* * * * *
55826265 AAAATACCTCGAC-T-TGACTCAAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGCAAA
1 AAAATACCTCGGCATGTGTC-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-AAAA
* * *
55826328 AATAGGAATT--T
64 AACAGAAATTAAA
* * * * *
55826339 AAAATACCTCAGCATGCGACCCGAAGCTCAACTCACCTCTCG-TA-ATGAGTTGATTTTTAAAAA
1 AAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAA
55826402 ACAGAAATTTAAA
65 ACAGAAA-TTAAA
* * * * *
55826415 AGAAATACTTCGGCATGTGTCGGAGGCTCAACTCACCTCTCGCAATATAAGCTGA-TTTAAAAAA
1 A-AAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAA
55826479 ACAGAAATTAAAA
65 ACAGAAATT-AAA
* *
55826492 AGAAATACCTTGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAA
1 A-AAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAA
*
55826557 ACAGAAATT--G
65 ACAGAAATTAAA
* * * * ***
55826567 AAAATACCTCAGC--GTGACTCGAGGCTCAACTCACCTCTCGCAATATAAGTTAATTTTTTTGAA
1 AAAATACCTCGGCATGTGTC-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAA
55826630 A-A-AAA-T--A
65 ACAGAAATTAAA
****** * * * * * * * * * **** ** **
55826637 CCTCGGCGT-GTGACCTGAGGCTC-A-ACTCACCTCTCGCAATAT-G-AGT-TGAAAAAAAATAG
1 AAAATACCTCG-G-CATGTGTC-CGAGGCTCAACTCAC-C--TCTCGCAATATGAGTTGATTTTT
*
55826696 AAATTAA-A-AAA-T--A
60 AAA-AAACAGAAATTAAA
****** * * ** * * * * * * **
55826709 CCTCGGCGTGTGGCCCGAGACTC-A-ACTC-ACTTCTCGCAATAT-G-AGT-TGA-TT--TTTGA
1 AAAATACCT-CGGCATGTGTC-CGAGGCTCAAC-TCAC-C--TCTCGCAATATGAGTTGATTTTT
* * * ** *
55826765 AAAACAGAAATTTAAAA
60 AAAAAACAGAAATTAAA
* * *
55826782 GAAATACCTCGGCATGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAAAAA
1 AAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-AAAAA
55826847 ACAGAAATTAAAA
65 ACAGAAATT-AAA
* * *
55826860 AGAAATACCTCGGCATATGTCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTAAAAAA
1 A-AAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TAAAA
*
55826925 AACAGAAATT--G
64 AACAGAAATTAAA
* * * *
55826936 AAAATACCTCAGC--GTGACCCGATGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTAAAAA
1 AAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAA
55826998 ACAGAAATTTAAA
65 ACAGAAA-TTAAA
* * *
55827011 AGAAATACCTCGACATGTGTCCGAGGCTCAACTTACCTCTCGCAATATGAGTTGA-TTTAAAAAA
1 A-AAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAA
* *
55827075 ACGGAAATT-GA
65 ACAGAAATTAAA
* * * *
55827086 AAAGTACCTCGGGATGTGGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAA
1 AAAATACCTCGGCATGT-GTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAA
* *
55827151 TA-GGAATTTAAAA
65 -ACAGAAATT-AAA
* * * *
55827164 AAAATACCTCGGTATGTGACCCGAAGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT----A
* *
55827229 AAAAATAGAAATT-GA
61 AAAAACAGAAATTAAA
* * * *
55827244 AAAGTACCTCGGCATGTGAGCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAA
*
55827309 ACAAAAATT-AA
65 ACAGAAATTAAA
* ** *
55827320 AAAATACCTCAGCATG-ACCCGAGGCTCAACTCACCTCTCGCAATAT-AGTTGATTTTTTTGAAA
1 AAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTAAAA
*
55827383 AACAAAAATTTAAA
64 AACAGAAA-TTAAA
* * *
55827397 AGAAATACCTCGACATGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
1 A-AAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAA
*
55827462 ACAAAAATTTAAA
65 ACAGAAA-TTAAA
* * * * *
55827475 AAAATACCTCGGCGTGTGACCCGAGGCTTAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAA
55827540 ACAGAAATTTAAA
65 ACAGAAA-TTAAA
55827553 AGAAATACCTCGGCATGTGTCCCGAGGCTCAACTCACCTCTCGC-A-ATGAGTTGATTTTT
1 A-AAATACCTCGGCATGTGT-CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
55827612 GCAAAAATAG
Statistics
Matches: 1276, Mismatches: 217, Indels: 186
0.76 0.13 0.11
Matches are distributed among these distances:
68 1 0.00
69 5 0.00
70 7 0.01
71 19 0.01
72 96 0.08
73 115 0.09
74 131 0.10
75 80 0.06
76 109 0.09
77 175 0.14
78 225 0.18
79 131 0.10
80 62 0.05
81 2 0.00
82 10 0.01
83 67 0.05
84 16 0.01
85 10 0.01
86 2 0.00
87 2 0.00
88 11 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (76 bp):
AAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAA
CAGAAATTAAA
Found at i:55826218 original size:78 final size:79
Alignment explanation
Indices: 55825947--55826623 Score: 551
Period size: 73 Copynumber: 8.7 Consensus size: 79
55825937 TAGAAATTGA
* * * * * **
55825947 AAATACCTCGCCGTGTGGCCCGAGGCTCAACTCACCTCTAGCATTATGAGTTGATTTTTTTTTTG
1 AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTAA
*
55826012 AAAAACAGAAATATAAAAG
61 AAAAACAGAAATTTAAAAG
* * * *
55826031 AAATACCTCGGCATGTG-TCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTAAAAAAAA
1 AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAA
*
55826095 CAGAAA-TT--GA-
66 CAGAAATTTAAAAG
* *
55826105 AAATACCTCAG-A-GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTAAAAAAA
1 AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAA
* *
55826167 TAGAAATTTAAAAT
66 CAGAAATTTAAAAG
* * * ****
55826181 AAATACATCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTGATTTTTT
1 AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TT--TTAAAA
**** * *
55826246 TTTTAG-AAGTAAAAATTG
63 AAACAGAAATTTAAAA--G
* * * * **
55826264 AAAAATACCTCGAC-T-TGACTCAAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGCAA
1 --AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTAAAA
* *
55826327 AAATAGGAATTT---A-
63 AAACAGAAATTTAAAAG
* * * * *
55826340 AAATACCTCAGCATGCGACCCGAAGCTCAACTCACCTCTCG-TA-ATGAGTTGATTTTTAAAAAA
1 AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAA
55826403 CAGAAATTTAAAAG
66 CAGAAATTTAAAAG
* * * * *
55826417 AAATACTTCGGCATGTG-TCGGAGGCTCAACTCACCTCTCGCAATATAAGCTGA-TTTAAAAAAA
1 AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAA
*
55826480 CAGAAATTAAAAAG
66 CAGAAATTTAAAAG
* *
55826494 AAATACCTTGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAA
1 AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAA
*
55826558 CAGAAA-TT--GA-
66 CAGAAATTTAAAAG
* * * *
55826568 AAATACCTCAGC--GTGACTCGAGGCTCAACTCACCTCTCGCAATATAAGTTAATTTT
1 AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
55826624 TTTGAAAAAA
Statistics
Matches: 481, Mismatches: 86, Indels: 63
0.76 0.14 0.10
Matches are distributed among these distances:
72 20 0.04
73 87 0.18
74 39 0.08
75 5 0.01
76 51 0.11
77 87 0.18
78 75 0.16
79 1 0.00
80 1 0.00
81 12 0.02
82 8 0.02
83 69 0.14
84 16 0.03
85 10 0.02
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (79 bp):
AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAA
CAGAAATTTAAAAG
Found at i:55826633 original size:78 final size:77
Alignment explanation
Indices: 55826258--55826634 Score: 318
Period size: 77 Copynumber: 5.0 Consensus size: 77
55826248 TTAGAAGTAA
* * * * *
55826258 AAATTGAAAAATACCTCGACT-TGACTCAAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTT
1 AAATTAAAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
* *
55826322 TG-CAAAAATAG
66 TGAAAAAAACAG
* * * * * *
55826333 GAATT-TAAAATACCTCAGCATGCGACCCGAAGCTCAACTCACCTCTCG-TA-ATGAGTTGATTT
1 AAATTAAAAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
55826395 TT--AAAAAACAG
65 TTGAAAAAAACAG
* * * * *
55826406 AAATTTAAAAGAAATACTTCGGCATGTG-TCGGAGGCTCAACTCACCTCTCGCAATATAAGCTGA
1 AAA-TT-AAA-AAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
55826470 --TTT-AAAAAAACAG
62 TTTTTGAAAAAAACAG
* *
55826483 AAATTAAAAAGAAATACCTTGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAATT--AAA-AAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
55826547 -TTTT-AAAAAAACAG
62 TTTTTGAAAAAAACAG
* * * * *
55826561 AAATT-GAAAATACCTCAGC-GTGACTCGAGGCTCAACTCACCTCTCGCAATATAAGTTAATTTT
1 AAATTAAAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TT
55826624 TTTGAAAAAAA
64 TTTGAAAAAAA
55826635 TACCTCGGCG
Statistics
Matches: 251, Mismatches: 35, Indels: 30
0.79 0.11 0.09
Matches are distributed among these distances:
72 3 0.01
73 41 0.16
74 37 0.15
75 7 0.03
76 51 0.20
77 87 0.35
78 25 0.10
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (77 bp):
AAATTAAAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
TGAAAAAAACAG
Found at i:55826822 original size:78 final size:78
Alignment explanation
Indices: 55826688--55827631 Score: 1103
Period size: 78 Copynumber: 12.2 Consensus size: 78
55826678 TGAGTTGAAA
* * * * *
55826688 AAAAATAGAAA-TT-AAA-AAATACCTCGGCGTGTGGCCCGAGACTCAACTCACTTCTCGCAATA
1 AAAAACAGAAATTTAAAAGAAATACCTCGGCATGT-GTCCGAGGCTCAACTCACCTCTCGCAATA
55826750 TGAGTTGATTTTTG
65 TGAGTTGATTTTTG
*
55826764 AAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATAT
*
55826829 GAGTTAATTTTTG
66 GAGTTGATTTTTG
* * *
55826842 AAAAAACAGAAATTAAAAAGAAATACCTCGGCATATGTCCGAGGCTCAACTCACCTCTCGTAATA
1 -AAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATA
**
55826907 TGAGTTGATTTTAAA
65 TGAGTTGATTTT-TG
* * * * *
55826922 AAAAACAGAAA-TT--GA-AAATACCTCAGC--GTGACCCGATGCTCAACTCACCTCTCGCATTA
1 AAAAACAGAAATTTAAAAGAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATA
*
55826981 TGAGTTGA-TTTTA
65 TGAGTTGATTTTTG
* *
55826994 AAAAACAGAAATTTAAAAGAAATACCTCGACATGTGTCCGAGGCTCAACTTACCTCTCGCAATAT
1 AAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATAT
**
55827059 GAGTTGA-TTTAA
66 GAGTTGATTTTTG
* * * *
55827071 AAAAACGGAAATTGAAAAG---TACCTCGGGATGTGGTCTGAGGCTCAACTCACCTCTCGCAATA
1 AAAAACAGAAATTTAAAAGAAATACCTCGGCATGT-GTCCGAGGCTCAACTCACCTCTCGCAATA
55827133 TGAGTTGA-TTTTG
65 TGAGTTGATTTTTG
* * * * * * *
55827146 AAAAATAGGAATTTAAAAAAAATACCTCGGTATGTGACCCGAAGCTCAACTCATCTCTCGCAATA
1 AAAAACAGAAATTTAAAAGAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATA
55827211 TGAGTTGATTTTTG
65 TGAGTTGATTTTTG
** * * *
55827225 AAAAA-A-AAATAGAAATTGAAAAGTACCTCGGCATGTGAGCCGAGGCTCAACTCACCTCTTGCA
1 AAAAACAGAAATTTAAA-AG-AAA-TACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCA
55827288 ATATGAGTTGATTTTTG
62 ATATGAGTTGATTTTTG
* * **
55827305 AAAAACA-AAAATT-AAA-AAATACCTCAGCATG-ACCCGAGGCTCAACTCACCTCTCGCAATAT
1 AAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATAT
55827366 -AGTTGATTTTTTTG
66 GAGTTGA--TTTTTG
* * *
55827380 AAAAACAAAAATTTAAAAGAAATACCTCGACATGTGTCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATAT
55827445 GAGTTGATTTTTG
66 GAGTTGATTTTTG
* * * * *
55827458 AAAAACAAAAATTTAAAA-AAATACCTCGGCGTGTGACCCGAGGCTTAACTCACCTCTTGCAATA
1 AAAAACAGAAATTTAAAAGAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATA
55827522 TGAGTTGATTTTTG
65 TGAGTTGATTTTTG
55827536 AAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCCGAGGCTCAACTCACCTCTCGC-A-A
1 AAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGT-CCGAGGCTCAACTCACCTCTCGCAATA
55827599 TGAGTTGATTTTTG
65 TGAGTTGATTTTTG
*
55827613 CAAAAATAG-AATTTGAAAA
1 -AAAAACAGAAATTT-AAAA
55827632 ATAATTCCTG
Statistics
Matches: 749, Mismatches: 85, Indels: 66
0.83 0.09 0.07
Matches are distributed among these distances:
72 12 0.02
73 13 0.02
74 70 0.09
75 77 0.10
76 37 0.05
77 103 0.14
78 194 0.26
79 174 0.23
80 65 0.09
81 4 0.01
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (78 bp):
AAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTTTTG
Found at i:55827207 original size:153 final size:153
Alignment explanation
Indices: 55826629--55827632 Score: 1107
Period size: 153 Copynumber: 6.5 Consensus size: 153
55826619 ATTTTTTTGA
* * * **
55826629 AAAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----AAAA
1 AAAAGATACCTCGGCATGTG-TCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
* * * * * *
55826690 AAATAGAAATT-AAAAAATACCTCGGCGTGTGGCCCGAGACTCAACTCACTTCTCGCAATATGAG
65 AAACAGAATTTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
** *
55826754 TTGATTTTTGAAAAACAGAAATTT
130 TTGATTTTAAAAAAACAGAAATTG
*
55826778 AAAAGAAATACCTCGGCATGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGA
1 AAAAG--ATACCTCGGCATGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-
* * * *
55826843 AAAAACAGAAATTAAAAAGAAATACCTCGGCATATG-TCCGAGGCTCAACTCACCTCTCGTAATA
63 AAAAACAG-AATTTAAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATA
55826907 TGAGTTGATTTTAAAAAAAACAGAAATTG
126 TGAGTTGATTTT-AAAAAAACAGAAATTG
* * * * * *
55826936 -AAA-ATACCTCAGC--GTGACCCGATGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTAAA
1 AAAAGATACCTCGGCATGTG-TCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
* * *
55826996 AAACAGAAATTTAAAAGAAATACCTCGACATGTG-TCCGAGGCTCAACTTACCTCTCGCAATATG
65 AAACAG-AATTTAAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
*
55827060 AGTTGA-TTTAAAAAAACGGAAATTG
128 AGTTGATTTTAAAAAAACAGAAATTG
*
55827085 AAAAG-TACCTCGGGATGTGGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAA
1 AAAAGATACCTCGGCATGT-GTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
* * * *
55827148 AAATAGGAATTTAAAAAAAATACCTCGGTATGTGACCCGAAGCTCAACTCATCTCTCGCAATATG
65 AAACA-GAATTT-AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
*
55827213 AGTTGATTTTTGAAAAAAAAATAGAAATTG
128 AGTTGA-TTTT---AAAAAAACAGAAATTG
* * *
55827243 AAAAG-TACCTCGGCATGTGAGCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAA
1 AAAAGATACCTCGGCATGTG-TCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
* * *
55827307 AAACAAAAATT-AAAAAATACCTCAGCA--TGACCCGAGGCTCAACTCACCTCTCGCAATAT-AG
65 AAACAGAATTTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
** * *
55827368 TTGATTTTTTTGAAAAACAAAAATTT
130 TTGA--TTTTAAAAAAACAGAAATTG
*
55827394 AAAAGAAATACCTCGACATGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
1 AAAAG--ATACCTCGGCATGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
* * * *
55827459 AAAACAAAAATTTAAAAAAATACCTCGGCGTGTGACCCGAGGCTTAACTCACCTCTTGCAATATG
64 AAAAC-AGAATTTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
** *
55827524 AGTTGATTTTTGAAAAACAGAAATTT
128 AGTTGATTTTAAAAAAACAGAAATTG
*
55827550 AAAAGAAATACCTCGGCATGTGTCCCGAGGCTCAACTCACCTCTCGC-A-ATGAGTTGATTTTTG
1 AAAAG--ATACCTCGGCATGTGT-CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
* *
55827613 CAAAAATAGAATTTGAAAAA
63 -AAAAACAGAATTTAAAAAA
55827633 TAATTCCTGA
Statistics
Matches: 739, Mismatches: 78, Indels: 70
0.83 0.09 0.08
Matches are distributed among these distances:
149 19 0.03
150 47 0.06
151 97 0.13
152 71 0.10
153 120 0.16
154 63 0.09
155 50 0.07
156 64 0.09
157 95 0.13
158 102 0.14
159 11 0.01
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (153 bp):
AAAAGATACCTCGGCATGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
AACAGAATTTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTAAAAAAACAGAAATTG
Found at i:55827439 original size:463 final size:454
Alignment explanation
Indices: 55825965--55827632 Score: 1638
Period size: 463 Copynumber: 3.6 Consensus size: 454
55825955 CGCCGTGTGG
* * ** *
55825965 CCCGAGGCTCAACTCACCTCTAGCATTATGAGTTGATTTTTTTTTTGAAAAACAGAAATATAAAA
1 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTAAAAAAACAGAAATTTAAAA
* * * *
55826030 GAAATACCTCGGCATGTGTCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTAAAAAAAA
62 GAAATACCTCGACATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT-TAAAAAA
* * *
55826095 CAGAAATTGAAAATACCTCAGAGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTT
126 CAGAAATTAAAAATACCTCACAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
* * *
55826160 AAAAAAATAGAAATTTAAAATAAATACATCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAA
191 AAAAAAACAGAAA-TT--AA-AAGTACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAA
**** ** *
55826225 TATGAGTTGATTTGATTTTTTTTTTAGAAGTAAAAATTGAAAAATACCTC-GACT-TGACTC-AA
252 TATGAGTTGATTTGA-----AAAATAGAA-TTTAAA---AAAAATACCTCGGA-TGTGACCCGAA
* * * *
55826287 GGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTG---CAAAAATAGGAATTTAAAATACCTC
307 -GCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTGAAAAAAAAATAGAAATTGAAAATACCTC
* * * * * *
55826349 AGCATGCGACCCGAAGCTCAACTCACCTCTCG-TA-ATGAGTTGATTTTTAAAAAACAGAAATTT
370 GGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA-AAAATT
* *
55826412 AAAAGAAATACTTCGGCATGTG
434 AAAAGAAATACCTCGGCATG-A
* * * * *
55826434 TCGGAGGCTCAACTCACCTCTCGCAATATAAGCTGA--TTTAAAAAAACAGAAATTAAAAAGAAA
1 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAACAGAAATTTAAAAGAAA
* *
55826497 TACCTTGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAACAGA
66 TACCTCGACATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-AAAAAACAGA
* * * *
55826562 AATTGAAAATACCTCAGC-GTGACTCGAGGCTCAACTCACCTCTCGCAATATAAGTTAATTT---
130 AATTAAAAATACCTCA-CAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAAA
****
55826623 --TTTTGAAA--AAAA-TACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGT
194 AAAACAGAAATTAAAAGTACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGT
** * * *
55826683 TGA--AAAAAAATAGAAATT--AAAAAATACCTCGGCGTGTGGCCCG-AGACTCAACTCACTTCT
259 TGATTTGAAAAATAGAATTTAAAAAAAATACCTCGG-ATGTGACCCGAAG-CTCAACTCAC-TCT
** * * *
55826743 CGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAA-AG-AAATACCTCGGCATGTG-TCTGA
321 CGCAATATGAGTTGATTTTTGAAAAA-A-AAATAGAAATTGAAAATACCTCGGCATGTGACCCGA
* *
55826805 GGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAAAAAACAGAAATTAAAAAGAAATACCT
384 GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAAAAATT-AAAAGAAATACCT
55826870 CGGCAT-A
447 CGGCATGA
* * * *
55826877 TGTCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTAAAAAAAACAGAAA-TT--GA-A
1 --CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAACAGAAATTTAAAAGA
* * *
55826938 AATACCTC-AGC--GTGACCCGATGCTCAACTCACCTCTCGCATTATGAGTTGATTTTAAAAAAC
64 AATACCTCGA-CATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAC
* *
55827000 AGAAATTTAAAAGAAATACCTCGACATGTG-TCCGAGGCTCAACTTACCTCTCGCAATATGAGTT
127 AGAAA-TT--AA-AAATACCTC-ACA-GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
* **
55827064 GATTTAAAAAAACGGAAATTGAAAAGTACCTCGG-GATGTGGTCTGAGGCTCAACTCACCTCTCG
186 GATTTAAAAAAACAGAAATT-AAAAGTACCTCGGCG-TGTGACCTGAGGCTCAACTCACCTCTCG
55827128 CAATATGAGTTGATTTTGAAAAATAGGAATTTAAAAAAAATACCTCGGTATGTGACCCGAAGCTC
249 CAATATGAGTTGA-TTTGAAAAATA-GAATTTAAAAAAAATACCTCGG-ATGTGACCCGAAGCTC
55827193 AACTCATCTCTCGCAATATGAGTTGATTTTTGAAAAAAAAATAGAAATTGAAAAGTACCTCGGCA
311 AACTCA-CTCTCGCAATATGAGTTGATTTTTGAAAAAAAAATAGAAATTGAAAA-TACCTCGGCA
* *
55827258 TGTGAGCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAAAAATT-AAA-
374 TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAG
*
55827321 AAATACCTCAGCATGA
439 AAATACCTCGGCATGA
** *
55827337 CCCGAGGCTCAACTCACCTCTCGCAATAT-AGTTGATTTTTTTGAAAAACAAAAATTTAAAAGAA
1 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTAAAAAAACAGAAATTTAAAAGAA
* * *
55827401 ATACCTCGACATGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAA
65 ATACCTCGACATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTAAAAAACAG
* * * *
55827466 AAATTTAAAAAAATACCTCGGCGTGTGACCCGAGGCTTAACTCACCTCTTGCAATATGAGTTGAT
129 AAA-TT--AAAAATACCTC-AC-AGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
** * * *
55827531 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCCGAGGCTCAACTCACCTCTCG
188 TTTAAAAAAACAGAAA-TTAAAAG---TACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCG
*
55827596 C-A-ATGAGTTGATTTTTGCAAAAATAGAATTTGAAAAA
249 CAATATGAGTTGA--TTTG-AAAAATAGAATTTAAAAAA
55827633 TAATTCCTGA
Statistics
Matches: 1007, Mismatches: 120, Indels: 146
0.79 0.09 0.11
Matches are distributed among these distances:
438 11 0.01
439 4 0.00
440 37 0.04
441 16 0.02
442 59 0.06
443 26 0.03
444 25 0.02
445 73 0.07
446 36 0.04
447 18 0.02
449 1 0.00
451 54 0.05
452 2 0.00
453 2 0.00
454 5 0.00
455 47 0.05
457 6 0.01
458 53 0.05
459 27 0.03
460 6 0.01
461 64 0.06
462 39 0.04
463 223 0.22
464 56 0.06
465 18 0.02
466 11 0.01
467 17 0.02
468 41 0.04
469 30 0.03
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (454 bp):
CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAACAGAAATTTAAAAGAAA
TACCTCGACATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAACAGAA
ATTAAAAATACCTCACAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAAAAA
AACAGAAATTAAAAGTACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTGAAAAATAGAATTTAAAAAAAATACCTCGGATGTGACCCGAAGCTCAACTCACTCTCGCAA
TATGAGTTGATTTTTGAAAAAAAAATAGAAATTGAAAATACCTCGGCATGTGACCCGAGGCTCAA
CTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGAAATACCTCGGCATGA
Found at i:55828515 original size:10 final size:9
Alignment explanation
Indices: 55828496--55828577 Score: 67
Period size: 10 Copynumber: 8.6 Consensus size: 9
55828486 TTGATTTTTC
55828496 TTTTTCTTT
1 TTTTTCTTT
55828505 TCTTTGT-TTT
1 T-TTT-TCTTT
*
55828515 TTTTTGTTGT
1 TTTTTCTT-T
*
55828525 TTTTTGTTGT
1 TTTTTCTT-T
*
55828535 TTTTTATTT
1 TTTTTCTTT
*
55828544 TTTGTCTTT
1 TTTTTCTTT
55828553 TTTTGTCTTT
1 TTTT-TCTTT
55828563 TTTTGTCTTT
1 TTTT-TCTTT
55828573 TTTTT
1 TTTTT
55828578 AGACATAATA
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
8 1 0.02
9 18 0.28
10 44 0.69
11 1 0.02
ACGTcount: A:0.01, C:0.06, G:0.10, T:0.83
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:55828519 original size:20 final size:18
Alignment explanation
Indices: 55828490--55828577 Score: 70
Period size: 19 Copynumber: 4.6 Consensus size: 18
55828480 TTCATCTTGA
55828490 TTTTTCTTTTTCTTTTCTTTG
1 TTTTT-TTTTT-TTTT-TTTG
55828511 TTTTTTTTTGTTGTTTTTTG
1 TTTTTTTTT-TT-TTTTTTG
* *
55828531 -TTGTTTTTTATTTTTTG
1 TTTTTTTTTTTTTTTTTG
*
55828548 TCTTTTTTTGTCTTTTTTTG
1 T-TTTTTTT-TTTTTTTTTG
*
55828568 TCTTTTTTTT
1 TTTTTTTTTT
55828578 AGACATAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
17 7 0.13
18 2 0.04
19 19 0.35
20 18 0.33
21 9 0.16
ACGTcount: A:0.01, C:0.07, G:0.09, T:0.83
Consensus pattern (18 bp):
TTTTTTTTTTTTTTTTTG
Found at i:55828548 original size:37 final size:38
Alignment explanation
Indices: 55828507--55828578 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
55828497 TTTTCTTTTC
*
55828507 TTTGTTTTTTTTTGT-TGTTTTTTGT-TGTTTTTTATTT
1 TTTGTCTTTTTTTGTCT-TTTTTTGTCTGTTTTTTATTT
*
55828544 TTTGTCTTTTTTTGTCTTTTTTTGTCTTTTTTTTA
1 TTTGTCTTTTTTTGTCTTTTTTTGTCTGTTTTTTA
55828579 GACATAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 22 0.71
38 9 0.29
ACGTcount: A:0.03, C:0.04, G:0.11, T:0.82
Consensus pattern (38 bp):
TTTGTCTTTTTTTGTCTTTTTTTGTCTGTTTTTTATTT
Found at i:55828566 original size:27 final size:26
Alignment explanation
Indices: 55828490--55828566 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 26
55828480 TTCATCTTGA
* *
55828490 TTTT-TCTTTTTCTTTTCTTTGTTTTT
1 TTTTGTCTTTTT-TTGTCTTTTTTTTT
55828516 TTTTGT-TGTTTTTTGT-TGTTTTTTATT
1 TTTTGTCT-TTTTTTGTCT-TTTTTT-TT
55828543 TTTTGTCTTTTTTTGTCTTTTTTT
1 TTTTGTCTTTTTTTGTCTTTTTTT
55828567 GTCTTTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
25 1 0.02
26 13 0.30
27 27 0.63
28 2 0.05
ACGTcount: A:0.01, C:0.06, G:0.09, T:0.83
Consensus pattern (26 bp):
TTTTGTCTTTTTTTGTCTTTTTTTTT
Found at i:55836199 original size:18 final size:17
Alignment explanation
Indices: 55836130--55836201 Score: 60
Period size: 16 Copynumber: 4.2 Consensus size: 17
55836120 AATTATTTTT
*
55836130 TTTTGAAAACACGAAAAAA
1 TTTTAAAAACACG--AAAA
*
55836149 TTTT-AAAACACGAGAA
1 TTTTAAAAACACGAAAA
* *
55836165 TTTTAGAGACA--AAAA
1 TTTTAAAAACACGAAAA
55836180 TTATTAAAAACACGAAAA
1 TT-TTAAAAACACGAAAA
55836198 TTTT
1 TTTT
55836202 TGAAGACGCG
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
15 5 0.12
16 14 0.33
17 6 0.14
18 14 0.33
19 4 0.09
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.28
Consensus pattern (17 bp):
TTTTAAAAACACGAAAA
Found at i:55836296 original size:18 final size:18
Alignment explanation
Indices: 55836273--55836537 Score: 232
Period size: 18 Copynumber: 14.9 Consensus size: 18
55836263 AAAATTTGTG
*
55836273 AAACACGAGAATTGTTGA
1 AAACACGAGAATTTTTGA
55836291 AAACACGCA-AATTTTTGA
1 AAACACG-AGAATTTTTGA
55836309 AAACACGCA-AATTTTTG-
1 AAACACG-AGAATTTTTGA
55836326 AAACACGA-AAGTTTTTAGA
1 AAACACGAGAA-TTTTT-GA
*
55836345 AAACACGAAAAATTTTTG-
1 AAACACG-AGAATTTTTGA
*
55836363 -ATCATCGA-AATTTTTTGA
1 AAACA-CGAGAA-TTTTTGA
*
55836381 AAACACGAGGATTTTTG-
1 AAACACGAGAATTTTTGA
* *
55836398 AAACACCATAATTTTTGA
1 AAACACGAGAATTTTTGA
*
55836416 AAACACGAGGATTTTTG-
1 AAACACGAGAATTTTTGA
*
55836433 AAACACGAAAATTTTTGA
1 AAACACGAGAATTTTTGA
*
55836451 AAACACGAGAATTTTTTTA
1 AAACACGAGAA-TTTTTGA
* *
55836470 AAACATGAAAATTTTTGA
1 AAACACGAGAATTTTTGA
55836488 AAACATCG-GAATTTTTGA
1 AAACA-CGAGAATTTTTGA
*
55836506 AGACACGA-AGATTTTTG-
1 AAACACGAGA-ATTTTTGA
*
55836523 AAACACAAG-ATTTTT
1 AAACACGAGAATTTTT
55836538 TTTTTTGAAA
Statistics
Matches: 207, Mismatches: 22, Indels: 38
0.78 0.08 0.14
Matches are distributed among these distances:
16 11 0.05
17 60 0.29
18 99 0.48
19 29 0.14
20 6 0.03
21 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (18 bp):
AAACACGAGAATTTTTGA
Found at i:55836327 original size:36 final size:34
Alignment explanation
Indices: 55836264--55836538 Score: 272
Period size: 35 Copynumber: 7.8 Consensus size: 34
55836254 TGAAATGTGA
* *
55836264 AAATTTGTG-AAACACGAGAATTGTTGAAAACACG
1 AAATTTTTGAAAACACGAGAATTTTTG-AAACACG
55836298 CAAATTTTTGAAAACACGCA-AATTTTTGAAACACG
1 -AAATTTTTGAAAACACG-AGAATTTTTGAAACACG
* *
55836333 AAAGTTTTTAGAAAACACGAAAAATTTTTG-ATCATCG
1 AAA-TTTTT-GAAAACACG-AGAATTTTTGAAACA-CG
* *
55836370 AAATTTTTTGAAAACACGAGGATTTTTGAAACACC
1 AAA-TTTTTGAAAACACGAGAATTTTTGAAACACG
*
55836405 ATAATTTTTGAAAACACGAGGATTTTTGAAACACG
1 A-AATTTTTGAAAACACGAGAATTTTTGAAACACG
* *
55836440 AAAATTTTTGAAAACACGAGAATTTTTTTAAAACATG
1 -AAATTTTTGAAAACACGAGAA--TTTTTGAAACACG
55836477 AAAATTTTTGAAAACATCG-GAATTTTTGAAGACACG
1 -AAATTTTTGAAAACA-CGAGAATTTTTGAA-ACACG
* *
55836513 AAGATTTTTG-AAACACAAGATTTTTT
1 AA-ATTTTTGAAAACACGAGAATTTTT
55836539 TTTTTGAAAA
Statistics
Matches: 208, Mismatches: 17, Indels: 30
0.82 0.07 0.12
Matches are distributed among these distances:
34 4 0.02
35 100 0.48
36 53 0.25
37 49 0.24
38 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.32
Consensus pattern (34 bp):
AAATTTTTGAAAACACGAGAATTTTTGAAACACG
Found at i:55836628 original size:10 final size:10
Alignment explanation
Indices: 55836613--55836639 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
55836603 ACATAAAATT
55836613 TTTTTTTGAA
1 TTTTTTTGAA
55836623 TTTTTTTGAA
1 TTTTTTTGAA
55836633 TTTTTTT
1 TTTTTTT
55836640 CGTTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:55836908 original size:13 final size:13
Alignment explanation
Indices: 55836890--55836922 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
55836880 AACCTTTTTT
55836890 TCTTTTTTCCTTC
1 TCTTTTTTCCTTC
55836903 TCTTTTTT-CTTC
1 TCTTTTTTCCTTC
55836915 T-TTTTTTC
1 TCTTTTTTC
55836923 TCCTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.32
12 5 0.26
13 8 0.42
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TCTTTTTTCCTTC
Found at i:55836914 original size:12 final size:12
Alignment explanation
Indices: 55836890--55836937 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 12
55836880 AACCTTTTTT
55836890 TCTTTTTTCCTTC
1 TCTTTTTT-CTTC
55836903 TCTTTTTTCTTC
1 TCTTTTTTCTTC
55836915 T-TTTTTTC-TC
1 TCTTTTTTCTTC
55836925 -CTTTTTT-TTC
1 TCTTTTTTCTTC
55836935 TCT
1 TCT
55836938 CTGCTGGACC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 10 0.31
11 9 0.28
12 5 0.16
13 8 0.25
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
TCTTTTTTCTTC
Found at i:55836915 original size:23 final size:23
Alignment explanation
Indices: 55836884--55836935 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
55836874 AAATTGAACC
*
55836884 TTTTT-TTCTTTTTTCCTTCTCT
1 TTTTTCTTCTTTTTTCCTCCTCT
* *
55836906 TTTTTCTTCTTTTTTTCTCCTTT
1 TTTTTCTTCTTTTTTCCTCCTCT
55836929 TTTTTCT
1 TTTTTCT
55836936 CTCTGCTGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTCTTCTTTTTTCCTCCTCT
Found at i:55836919 original size:11 final size:11
Alignment explanation
Indices: 55836884--55836932 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
55836874 AAATTGAACC
55836884 TTTTT-TTCTT
1 TTTTTCTTCTT
*
55836894 TTTTCCTTCTCT
1 TTTTTCTTCT-T
55836906 TTTTTCTTCTT
1 TTTTTCTTCTT
*
55836917 TTTTTCTCCTT
1 TTTTTCTTCTT
55836928 TTTTT
1 TTTTT
55836933 TCTCTCTGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
10 4 0.12
11 20 0.59
12 10 0.29
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTCTTCTT
Found at i:55837052 original size:18 final size:18
Alignment explanation
Indices: 55837029--55837063 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
55837019 GCCTGCCCTT
55837029 TTTTTTTGCATTGGGCCC
1 TTTTTTTGCATTGGGCCC
*
55837047 TTTTTTTGCTTTGGGCC
1 TTTTTTTGCATTGGGCC
55837064 TAGTTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.20, G:0.23, T:0.54
Consensus pattern (18 bp):
TTTTTTTGCATTGGGCCC
Found at i:55837070 original size:18 final size:18
Alignment explanation
Indices: 55837031--55837072 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
55837021 CTGCCCTTTT
*
55837031 TTTTTGCATTGGGCCCTT
1 TTTTTGCATTGGGCCCTG
*
55837049 TTTTTGCTTTGGG-CCTAG
1 TTTTTGCATTGGGCCCT-G
55837067 TTTTTG
1 TTTTTG
55837073 TTTCTTATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.05, C:0.17, G:0.24, T:0.55
Consensus pattern (18 bp):
TTTTTGCATTGGGCCCTG
Found at i:55837218 original size:17 final size:16
Alignment explanation
Indices: 55837175--55837222 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
55837165 AAAAAAATTC
55837175 TTTTTCTTTTTCTTCT
1 TTTTTCTTTTTCTTCT
* *
55837191 TTTTCCCTTTTCTTCT
1 TTTTTCTTTTTCTTCT
55837207 TTCTTTCTTTTTCTTC
1 TT-TTTCTTTTTCTTC
55837223 CCCTTCGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 16 0.59
17 11 0.41
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTCTTTTTCTTCT
Found at i:55837219 original size:24 final size:22
Alignment explanation
Indices: 55837176--55837219 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
55837166 AAAAAATTCT
55837176 TTTTCTTTTTCTTCTTTTTCCC
1 TTTTCTTTTTCTTCTTTTTCCC
55837198 TTTTCTTCTTTCTTTCTTTTTC
1 TTTTCTT-TTTC-TTCTTTTTC
55837220 TTCCCCTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 9 0.45
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTCTTTTTCTTCTTTTTCCC
Found at i:55837689 original size:58 final size:57
Alignment explanation
Indices: 55837604--55837754 Score: 160
Period size: 58 Copynumber: 2.6 Consensus size: 57
55837594 TAATTTGGAG
* * * * * *
55837604 AAAGTTTAGTGGTCAAAATGTAATTTTAAGAAAGTTTAAGGGTGAAAATATAATTTTAA
1 AAAGTTTAG-GGT-AAAATGTAATTTTAAAAAAATTTAAGGATCAAAATACAATTTCAA
*
55837663 AAAGTTTAGGAGTAAAATGTAATTTTAAAAAAATTTAAGGATCAAAATGCAATTTCAA
1 AAAGTTTAGG-GTAAAATGTAATTTTAAAAAAATTTAAGGATCAAAATACAATTTCAA
* * *
55837721 AAAGTATAGGGGTAAAA-ATATTATTTAAAAAAAT
1 AAAGTTTA-GGGTAAAATGTAAT-TTTAAAAAAAT
55837755 CGAGGCGAAC
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
57 3 0.04
58 63 0.80
59 13 0.16
ACGTcount: A:0.49, C:0.03, G:0.16, T:0.32
Consensus pattern (57 bp):
AAAGTTTAGGGTAAAATGTAATTTTAAAAAAATTTAAGGATCAAAATACAATTTCAA
Found at i:55837693 original size:29 final size:29
Alignment explanation
Indices: 55837604--55837731 Score: 127
Period size: 30 Copynumber: 4.4 Consensus size: 29
55837594 TAATTTGGAG
*
55837604 AAAGTTTAGTGGTCAAAATGTAATTTTAAG
1 AAAGTTTAG-GGTCAAAATGTAATTTTAAA
* *
55837634 AAAGTTTAAGGGTGAAAATATAATTTT-AA
1 AAAGTTT-AGGGTCAAAATGTAATTTTAAA
55837663 AAAGTTTAGGAGT-AAAATGTAATTTTAAA
1 AAAGTTTAGG-GTCAAAATGTAATTTTAAA
* * * *
55837692 AAAATTTAAGGATCAAAATGCAA-TTTCAA
1 AAAGTTT-AGGGTCAAAATGTAATTTTAAA
*
55837721 AAAGTATAGGG
1 AAAGTTTAGGG
55837732 GTAAAAATAT
Statistics
Matches: 82, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
28 18 0.22
29 29 0.35
30 33 0.40
31 2 0.02
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (29 bp):
AAAGTTTAGGGTCAAAATGTAATTTTAAA
Found at i:55842681 original size:24 final size:23
Alignment explanation
Indices: 55842654--55842719 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 23
55842644 GAATTTTTAA
55842654 AAAAAAACCGAACATCTTTTTATT-
1 AAAAAAACC-AACAT-TTTTTATTC
*
55842678 AAAAAATCCAACATTTTTTTATTC
1 AAAAAAACCAACA-TTTTTTATTC
55842702 AAAAAAACCAACATTTTT
1 AAAAAAACCAACATTTTT
55842720 CGACCGAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
23 17 0.45
24 21 0.55
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAAAAACCAACATTTTTTATTC
Found at i:55843138 original size:25 final size:25
Alignment explanation
Indices: 55843087--55843139 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
55843077 TAATATTATT
**
55843087 TTTAATTTTTTTTATATTATTTTAA
1 TTTAATTTTTTTTATATTATTAAAA
55843112 TTTAATATTTTTTTAT-TTATTAAAA
1 TTTAAT-TTTTTTTATATTATTAAAA
55843137 TTT
1 TTT
55843140 TCTATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTAATTTTTTTTATATTATTAAAA
Found at i:55847921 original size:36 final size:36
Alignment explanation
Indices: 55847880--55848070 Score: 247
Period size: 36 Copynumber: 5.0 Consensus size: 36
55847870 CTAAGGCTAA
*
55847880 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
55847916 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
55847952 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--AG
* * *
55847994 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
55848034 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
55848070 C
1 C
55848071 TAAAGCTACC
Statistics
Matches: 139, Mismatches: 6, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
36 100 0.72
38 3 0.02
40 3 0.02
42 3 0.02
44 2 0.01
46 28 0.20
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Done.