Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold329
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: 4121247
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 5938 characters in sequence are not A, C, G, or T
File 21 of 25
Found at i:3309918 original size:16 final size:17
Alignment explanation
Indices: 3309894--3309926 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3309884 TAACAGTTTC
3309894 AAATATTAATTTATATA
1 AAATATTAATTTATATA
*
3309911 AAAT-TTAATTTTTATA
1 AAATATTAATTTATATA
3309927 TACTGACATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAATATTAATTTATATA
Found at i:3310573 original size:28 final size:28
Alignment explanation
Indices: 3310524--3310577 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
3310514 ATAATATTAA
* *
3310524 TATAATTTGTGTCCTAAACGTGTTTTTG
1 TATAATTCGTATCCTAAACGTGTTTTTG
* *
3310552 TATAATTCGTATCTTAATCGTGTTTT
1 TATAATTCGTATCCTAAACGTGTTTT
3310578 CATGTTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.52
Consensus pattern (28 bp):
TATAATTCGTATCCTAAACGTGTTTTTG
Found at i:3311506 original size:11 final size:11
Alignment explanation
Indices: 3311458--3311511 Score: 65
Period size: 11 Copynumber: 4.9 Consensus size: 11
3311448 ATCAGTATCA
*
3311458 AAATAAAATAT
1 AAATATAATAT
*
3311469 ATAATATGATAT
1 A-AATATAATAT
*
3311481 AAAAATAATAT
1 AAATATAATAT
3311492 AAATATAATAT
1 AAATATAATAT
3311503 AAATA-AATA
1 AAATATAATA
3311512 AATATTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
10 4 0.11
11 24 0.65
12 9 0.24
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
AAATATAATAT
Found at i:3311578 original size:15 final size:15
Alignment explanation
Indices: 3311558--3311620 Score: 54
Period size: 15 Copynumber: 3.8 Consensus size: 15
3311548 CTTAAATTTT
3311558 AATATATAAATATAA
1 AATATATAAATATAA
3311573 AATATAATTATAACCTACTAA
1 AATAT-A-TA-AA--TA-TAA
3311594 AATATATAAATATAA
1 AATATATAAATATAA
* *
3311609 TATAAATAAATA
1 AATATATAAATA
3311621 AATTATCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
15 18 0.45
16 3 0.08
17 2 0.05
18 4 0.10
19 2 0.05
20 3 0.08
21 8 0.20
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (15 bp):
AATATATAAATATAA
Found at i:3314611 original size:42 final size:41
Alignment explanation
Indices: 3314532--3314613 Score: 103
Period size: 43 Copynumber: 2.0 Consensus size: 41
3314522 TTTTATTGAT
3314532 TTTTATTTAATTTTAATTTAAAAATTAATTAAATATAATTTA
1 TTTTATTTAATTTTAATTTAAAAATTAA-TAAATATAATTTA
* * *
3314574 TTTTATTTTATTTTTGATTTATAAATTAA-AAATTATAATT
1 TTTTA-TTTAATTTTAATTTAAAAATTAATAAA-TATAATT
3314614 ATTCAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 3 0.09
42 12 0.34
43 20 0.57
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (41 bp):
TTTTATTTAATTTTAATTTAAAAATTAATAAATATAATTTA
Found at i:3314735 original size:45 final size:46
Alignment explanation
Indices: 3314657--3314745 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 46
3314647 TAATTAGTTT
* *
3314657 TTTATAGTATAATAATAAATATTTTATTTTTAAATTATTAAAAAAAA
1 TTTAAAGTATAATAATAAATATTATATTTTTAAATT-TTAAAAAAAA
*
3314704 TTTAAAGTATTATAA-AAATA-TATATTTTTAAATTTTAAAAAA
1 TTTAAAGTATAATAATAAATATTATATTTTTAAATTTTAAAAAA
3314746 TTAATAAGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
44 8 0.21
45 13 0.33
46 5 0.13
47 13 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (46 bp):
TTTAAAGTATAATAATAAATATTATATTTTTAAATTTTAAAAAAAA
Found at i:3316185 original size:17 final size:18
Alignment explanation
Indices: 3316153--3316196 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
3316143 TATATAAAAA
3316153 TAAATATAACATAAATATT
1 TAAATATAACATAAAT-TT
*
3316172 T-AATATAATA-AAATTT
1 TAAATATAACATAAATTT
3316188 TAAATATAA
1 TAAATATAA
3316197 ATATAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 3 0.13
17 11 0.48
18 8 0.35
19 1 0.04
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAATATAACATAAATTT
Found at i:3316189 original size:16 final size:19
Alignment explanation
Indices: 3316153--3316216 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 19
3316143 TATATAAAAA
3316153 TAAATATAACATAAATATT
1 TAAATATAACATAAATATT
*
3316172 T-AATATAATA-AAAT-TT
1 TAAATATAACATAAATATT
*
3316188 TAAATATAAATATAATATATAT
1 TAAATAT-AACATAA-ATAT-T
3316210 TAAATAT
1 TAAATAT
3316217 GTCAGGAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
16 3 0.08
17 9 0.24
18 12 0.32
19 3 0.08
20 2 0.05
21 1 0.03
22 8 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATATAACATAAATATT
Found at i:3316799 original size:587 final size:572
Alignment explanation
Indices: 3315824--3316962 Score: 1698
Period size: 589 Copynumber: 2.0 Consensus size: 572
3315814 GAACCAGCAA
3315824 TTATTAAAAAATTATTTTTATATTAATATTATATATTTATAATTAAATTAAAATATATTATTTTC
1 TTATTAAAAAATTATTTTTATATTAATATTATATATTTATAATTAAATTAAAATATATTATTTTC
* *
3315889 ATAAAAAATTATTCTGAGCAAGCTAAGCTAAAATAAAAAATAAAAAATTAAATTAATTCAATTTA
66 ATAAAAAATTATTCTGAACAAGCTAAACTAAAATAAAAAATAAAAAATTAAATTAATTCAATTTA
* * *
3315954 AATTTATCAAATTAAATAAATAATTTAACTTATGAGCAAATTTACCTTACATATTTCTTTCTAAG
131 AATTTACCAAATCAAATAAATAATTTAACTTATGAGCAAATTTACCTTACATATTTCTTTCCAAG
* * *
3316019 TTAGTTTACATACATATGAAAACTAATGTTAATTAAATGAAGAGAGGAAAAAAAATGGAATCCTA
196 TAAGTTTACATACATATGAAAACTAATATTAATTAAATGAAGAGAAGAAAAAAAATGGAATCCTA
* *
3316084 TGAGCTTTTCCCATGCCACAAATTCACACTTATTTTGTATTTTATATTTTTTTATTAATTATATA
261 TGAACTTTTCCCATGCCACAAATTCACACTTATTTTGTATTTTATATTTTTTTAGTAATTATATA
* *
3316149 AAAATAAATATAACATAAATATTTAATATAATAAAATTTTAAATATAAATATAATATATATTAAA
326 AAAATAAATATAACATAAATATTTAATATAATAAAATTTTAAATACAAATAT-AGATATATTAAA
* *
3316214 TATGTCAGGAAATTTTTAATATATTA-TTTTTTATTTATTAAACATATTACATTTAAGTCATTTT
390 TATGTCAAGAAATATTTAATATATTATTTTTTTATTTATTAAACATATTACATTTAAGTCATTTT
* *
3316278 TTTAATAGCGT-CCAAAATATAGGCATTGGTTTTCCAGTTGAAAAACAACAAAAGTAGTCCAAAA
455 TTTAATAGCATCCCAAAATATAGGCATTGATTTTCCAGTTGAAAAACAACAAAAGTAGTCCAAAA
3316342 TCATAGGAAAAACATTTCGAAGATTCCAACTTGTAGACCTAAATTTACCATTTAC
520 TCATAGGAAAAACA-TTCGAAGATTCCAA-TTGTAGACCTAAATTTACCATTTAC
* *
3316397 TTATTAAAAATTTATTTTTATATTAATATTTATATATTTGTAATTAAATTAAAATATATTATTTT
1 TTATTAAAAAATTATTTTTATATTAATA-TTATATATTTATAATTAAATTAAAATATATTATTTT
* * *
3316462 TATTAAAAAATTATTCTGAACAAGTTAAACTAAAATAAAATAAT-AAAAATCTAAATTAACTT-G
65 CA-TAAAAAATTATTCTGAACAAGCTAAACTAAAATAAAA-AATAAAAAAT-TAAATTAA-TTCA
* *
3316525 ATTTAAATTTACCAAATCGAATAAATAATTTAACTTATGAGTAAATTTACTCATGAACTTACCAA
126 ATTTAAATTTACCAAATCAAATAAATAATTTAACTTATGAGCAAATTTA--C-----CTTA-C-A
* * *
3316590 GCTATTTCTTTCCAAGTAAGTTTGCATACATATGAAAACTAATATTAATTAAATGCAGAGAAG-T
182 --TATTTCTTTCCAAGTAAGTTTACATACATATGAAAACTAATATTAATTAAATGAAGAGAAGAA
3316654 AAAAAATGGAATCCTATGAAC-TTTCCGCATGCCACAAATTCATACACTTATTTTGTATTTTATA
245 AAAAAATGGAATCCTATGAACTTTTCC-CATGCCACAAATTC--ACACTTATTTTGTATTTTATA
* *
3316718 TTTTTTATAGTAGTTGTATAAAAATAAATATAACATAAATATTTAATATAATAAAATTTTAAATA
307 TTTTTT-TAGTAATTATATAAAAATAAATATAACATAAATATTTAATATAATAAAATTTTAAATA
* *
3316783 CAAATAT-GATATATTAAATATTTCAAGTAATATTTAATATATTATTTTTTTATTTATTAAACAT
371 CAAATATAGATATATTAAATATGTCAAGAAATATTTAATATATTATTTTTTTATTTATTAAACAT
* * *
3316847 ATTAGATTTAAGTCATTTTTTTAATAGCATCCCAAATTATAGGCATTGATTTTCCCGTTGAAAAA
436 ATTACATTTAAGTCATTTTTTTAATAGCATCCCAAAATATAGGCATTGATTTTCCAGTTGAAAAA
* * *
3316912 CAACATAATTAGTCCAAAATCATAGGAAAAACATTCTAAGATTCCAATTGT
501 CAACAAAAGTAGTCCAAAATCATAGGAAAAACATTCGAAGATTCCAATTGT
3316963 CCCTCCACAG
Statistics
Matches: 508, Mismatches: 36, Indels: 30
0.89 0.06 0.05
Matches are distributed among these distances:
573 27 0.05
574 36 0.07
575 40 0.08
576 56 0.11
577 2 0.00
578 1 0.00
583 4 0.01
584 1 0.00
585 6 0.01
586 34 0.07
587 91 0.18
588 87 0.17
589 123 0.24
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (572 bp):
TTATTAAAAAATTATTTTTATATTAATATTATATATTTATAATTAAATTAAAATATATTATTTTC
ATAAAAAATTATTCTGAACAAGCTAAACTAAAATAAAAAATAAAAAATTAAATTAATTCAATTTA
AATTTACCAAATCAAATAAATAATTTAACTTATGAGCAAATTTACCTTACATATTTCTTTCCAAG
TAAGTTTACATACATATGAAAACTAATATTAATTAAATGAAGAGAAGAAAAAAAATGGAATCCTA
TGAACTTTTCCCATGCCACAAATTCACACTTATTTTGTATTTTATATTTTTTTAGTAATTATATA
AAAATAAATATAACATAAATATTTAATATAATAAAATTTTAAATACAAATATAGATATATTAAAT
ATGTCAAGAAATATTTAATATATTATTTTTTTATTTATTAAACATATTACATTTAAGTCATTTTT
TTAATAGCATCCCAAAATATAGGCATTGATTTTCCAGTTGAAAAACAACAAAAGTAGTCCAAAAT
CATAGGAAAAACATTCGAAGATTCCAATTGTAGACCTAAATTTACCATTTAC
Found at i:3316822 original size:28 final size:27
Alignment explanation
Indices: 3316755--3316826 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
3316745 ATATAACATA
* *
3316755 AATATTTAATATAATAAAATTTTAAAT
1 AATATTTAATATATTAAAATTTCAAAT
* * * *
3316782 ACAAATATGATATATTAAATATTTCAAGT
1 A-ATATTTAATATATTAAA-ATTTCAAAT
3316811 AATATTTAATATATTA
1 AATATTTAATATATTA
3316827 TTTTTTTATT
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
27 1 0.03
28 25 0.74
29 8 0.24
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (27 bp):
AATATTTAATATATTAAAATTTCAAAT
Found at i:3319769 original size:33 final size:33
Alignment explanation
Indices: 3319724--3319791 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
3319714 AACATCTTCT
3319724 TTATCTTAAATTTAATAGTATTAGGGAT-AAATA
1 TTATCTTAAATTTAATAGTATTAGGG-TCAAATA
*
3319757 TTATCTTTAATTTAATAGTATTAGGGTCAAATA
1 TTATCTTAAATTTAATAGTATTAGGGTCAAATA
3319790 TT
1 TT
3319792 GTAGATATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
32 1 0.03
33 32 0.97
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (33 bp):
TTATCTTAAATTTAATAGTATTAGGGTCAAATA
Found at i:3320156 original size:23 final size:23
Alignment explanation
Indices: 3320122--3320166 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3320112 TGTAACTTGA
*
3320122 TCATCATATATTTTTATCGATAC
1 TCATCATATATTTATATCGATAC
*
3320145 TCAT-ATAGTATTTATGTCGATA
1 TCATCATA-TATTTATATCGATA
3320167 TACTTTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (23 bp):
TCATCATATATTTATATCGATAC
Found at i:3321049 original size:16 final size:15
Alignment explanation
Indices: 3321025--3321054 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3321015 TTATTATAAA
3321025 AAAATTAAAATTTTC
1 AAAATTAAAATTTTC
3321040 AAAATATAAAATTTT
1 AAAAT-TAAAATTTT
3321055 ATAAGCGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTAAAATTTTC
Found at i:3325889 original size:28 final size:28
Alignment explanation
Indices: 3325858--3325911 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
3325848 GACTATTCAC
* *
3325858 TCAGAAATGGTGAGGTTGGAGTATCCCT
1 TCAGAAATGATGAGGATGGAGTATCCCT
*
3325886 TCAGAGATGATGAGGATGGAGTATCC
1 TCAGAAATGATGAGGATGGAGTATCC
3325912 TCAGAGATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.28, C:0.13, G:0.33, T:0.26
Consensus pattern (28 bp):
TCAGAAATGATGAGGATGGAGTATCCCT
Found at i:3325958 original size:80 final size:79
Alignment explanation
Indices: 3325868--3326283 Score: 282
Period size: 80 Copynumber: 5.2 Consensus size: 79
3325858 TCAGAAATGG
* * * *
3325868 TGAGGTTGGAGTATCCCTTCAGAGATGATGAGGATGGAGTATCCTCAGAGATGAAAATTTTGATG
1 TGAGGTTGGAGTATCCCTTCAGAGATGATGAGGTTGGAGTATCCTCAGAGATGAAAAATTCGATA
*
3325933 TTTCGGAAGTAAAAA
66 TTT-AGAAGTAAAAA
* * * * **
3325948 TGAGGTTGGAGTATCCC--CATAGAT-AGTGGGGTTGAAATATCC-CAGAGACAAAAAATTCGAT
1 TGAGGTTGGAGTATCCCTTCAGAGATGA-TGAGGTTGGAGTATCCTCAGAGATGAAAAATTCGAT
3326009 ACTTTAGAAGTAAAAA
65 A-TTTAGAAGTAAAAA
* * * * * * * *
3326025 CGTGATTGGAGTTTCTCC-TCAAAGATGGTGAGGTTGGAGTATCTTCAAAGATGAAAAATTCGAT
1 TGAGGTTGGAGTATC-CCTTCAGAGATGATGAGGTTGGAGTATCCTCAGAGATGAAAAATTCGAT
3326089 ATTTTAGAAGTAAAAA
65 A-TTTAGAAGTAAAAA
* * ** * * **
3326105 TTGA-GTTAGAGTATCCTCTT-AGAGATGGT-AGGGTTAAAGTAT--TCAAAAAACAAAAAAATT
1 -TGAGGTTGGAGTATCC-CTTCAGAGATGATGA-GGTTGGAGTATCCTC-AGAGA-TGAAAAATT
* * *
3326165 TGATATTTCAAAATTAAAAA
61 CGATATTT-AGAAGTAAAAA
* *
3326185 T-AGGGTTAGAGTAT-CCTCTCAGAGATGAT-AGGATTGGAGTATCCCCAGAGATGAAAAATTCG
1 TGA-GGTTGGAGTATCCCT-TCAGAGATGATGAGG-TTGGAGTATCCTCAGAGATGAAAAATTCG
*
3326247 ATGTCTTAGAAGTAAAAA
63 ATAT-TTAGAAGTAAAAA
* * *
3326265 CGAGATTGAAGTATCCCTT
1 TGAGGTTGGAGTATCCCTT
3326284 TTTAATGTTT
Statistics
Matches: 258, Mismatches: 55, Indels: 46
0.72 0.15 0.13
Matches are distributed among these distances:
77 37 0.14
78 28 0.11
79 32 0.12
80 149 0.58
81 11 0.04
82 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (79 bp):
TGAGGTTGGAGTATCCCTTCAGAGATGATGAGGTTGGAGTATCCTCAGAGATGAAAAATTCGATA
TTTAGAAGTAAAAA
Found at i:3326224 original size:28 final size:26
Alignment explanation
Indices: 3326184--3326238 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
3326174 AAAATTAAAA
*
3326184 ATAGGGTTAGAGTATCCTCTCAGAGATG
1 ATAGGATTAGAGTATCC-C-CAGAGATG
*
3326212 ATAGGATTGGAGTATCCCCAGAGATG
1 ATAGGATTAGAGTATCCCCAGAGATG
3326238 A
1 A
3326239 AAAATTCGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 9 0.36
27 1 0.04
28 15 0.60
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (26 bp):
ATAGGATTAGAGTATCCCCAGAGATG
Found at i:3326239 original size:160 final size:158
Alignment explanation
Indices: 3325871--3326281 Score: 401
Period size: 160 Copynumber: 2.6 Consensus size: 158
3325861 GAAATGGTGA
* *
3325871 GGTTGGAGTATCC-CTTCAGAGATGATGAGGA-TGGAGTATCCTCAGAGATGAAAATTTTGATGT
1 GGTTGGAGTATCCTC-TCAGAGATGATGAGGATTGGAGTATCCTCAGAGATGAAAAATTCGATGT
** * * * * * *
3325934 TTCGGAAGTAAAAATGAGGTTGGAGTATCCCCATAGATAGTGGGGTTGAAATATCCCAGAGACAA
65 TTTAGAAGTAAAAATGAGGTTAGAGTATCCCCAGAGATAGTAGGGTTGAAATATCCAAAAAACAA
* *
3325999 AAAATTCGATACTTTAGAAGTAAAAACGT
130 AAAATTCGATACTTTAAAAGTAAAAAAGT
* * * * * * *
3326028 GATTGGAGT-TTCTCCTCAAAGATGGTGAGG-TTGGAGTATCTTCAAAGATGAAAAATTCGATAT
1 GGTTGGAGTATCCT-CTCAGAGATGATGAGGATTGGAGTATCCTCAGAGATGAAAAATTCGATGT
* * *
3326091 TTTAGAAGTAAAAATTGA-GTTAGAGTATCCTCTTAGAGATGGTAGGGTT-AAAGTATTCAAAAA
65 TTTAGAAGTAAAAA-TGAGGTTAGAGTATCC-C-CAGAGATAGTAGGGTTGAAA-TATCCAAAAA
* *
3326154 ACAAAAAAATTTGATA-TTTCAAAATTAAAAATAG-
126 AC-AAAAAATTCGATACTTT-AAAAGTAAAAA-AGT
* * *
3326188 GGTTAGAGTATCCTCTCAGAGATGAT-AGGATTGGAGTATCCCCAGAGATGAAAAATTCGATGTC
1 GGTTGGAGTATCCTCTCAGAGATGATGAGGATTGGAGTATCCTCAGAGATGAAAAATTCGATGTT
* *
3326252 TTAGAAGTAAAAACGAGATT-GAAGTATCCC
66 TTAGAAGTAAAAATGAGGTTAG-AGTATCCC
3326282 TTTTTAATGT
Statistics
Matches: 204, Mismatches: 36, Indels: 26
0.77 0.14 0.10
Matches are distributed among these distances:
156 2 0.01
157 71 0.35
158 8 0.04
159 30 0.15
160 89 0.44
161 4 0.02
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.28
Consensus pattern (158 bp):
GGTTGGAGTATCCTCTCAGAGATGATGAGGATTGGAGTATCCTCAGAGATGAAAAATTCGATGTT
TTAGAAGTAAAAATGAGGTTAGAGTATCCCCAGAGATAGTAGGGTTGAAATATCCAAAAAACAAA
AAATTCGATACTTTAAAAGTAAAAAAGT
Found at i:3329829 original size:24 final size:24
Alignment explanation
Indices: 3329742--3329829 Score: 65
Period size: 24 Copynumber: 3.6 Consensus size: 24
3329732 TTTTTTTAAA
*
3329742 AATAATTATTAAAATATT-TTAGAT
1 AATAATTA-TAAAATTTTATTAGAT
* * *
3329766 AATACTTTTAACAATTAATTA-TAAAT
1 AATAATTATAA-AATT--TTATTAGAT
* *
3329792 AA-AATTGTTAAATTTTATTAGAT
1 AATAATTATAAAATTTTATTAGAT
3329815 AATAATTATAAAATT
1 AATAATTATAAAATT
3329830 AGAGCTTACT
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
22 3 0.06
23 9 0.19
24 23 0.48
25 5 0.10
26 8 0.17
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.44
Consensus pattern (24 bp):
AATAATTATAAAATTTTATTAGAT
Found at i:3331142 original size:19 final size:18
Alignment explanation
Indices: 3331105--3331138 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3331095 AACTTTATTT
*
3331105 TTAAGATATAAGATTTTA
1 TTAAAATATAAGATTTTA
3331123 TTAAAATATAAG-TTTT
1 TTAAAATATAAGATTTT
3331139 TTATAATACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (18 bp):
TTAAAATATAAGATTTTA
Found at i:3331272 original size:25 final size:24
Alignment explanation
Indices: 3331244--3331290 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
3331234 AAAATTTCAA
*
3331244 TATTATGATAATTTTAAAAAATAAT
1 TATTATAAT-ATTTTAAAAAATAAT
*
3331269 TATTATAATATTTTAAATAATA
1 TATTATAATATTTTAAAAAATA
3331291 TTTTTAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TATTATAATATTTTAAAAAATAAT
Found at i:3331500 original size:21 final size:21
Alignment explanation
Indices: 3331461--3331501 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3331451 TATGATAAAA
*
3331461 ATATTTTATATTATTATTTAT
1 ATATTTTATATTATAATTTAT
3331482 ATATTTTATAATTA-AATTTA
1 ATATTTTAT-ATTATAATTTA
3331502 AGTTGGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTTTATATTATAATTTAT
Found at i:3333594 original size:17 final size:17
Alignment explanation
Indices: 3333572--3333609 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3333562 TAAAGGAATT
*
3333572 AATTAACCCTTCATTGA
1 AATTAACCCTCCATTGA
*
3333589 AATTAAGCCTCCATTGA
1 AATTAACCCTCCATTGA
3333606 AATT
1 AATT
3333610 CTTTGTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (17 bp):
AATTAACCCTCCATTGA
Found at i:3339838 original size:24 final size:24
Alignment explanation
Indices: 3339810--3339856 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3339800 GCCACTCCAT
* *
3339810 TTCATATTTTTTTTTTCTTTTTTC
1 TTCATATTCTTTCTTTCTTTTTTC
*
3339834 TTCATCTTCTTTCTTTCTTTTTT
1 TTCATATTCTTTCTTTCTTTTTT
3339857 ACCTAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (24 bp):
TTCATATTCTTTCTTTCTTTTTTC
Found at i:3341055 original size:45 final size:48
Alignment explanation
Indices: 3340954--3341059 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 48
3340944 AATGTGCCAT
* *
3340954 TTCAAGGTCAGCGACATTGGGCTAAGGGAAAAGTGGACCAATGTGCTGA
1 TTCAAGGCCAGCGACATTGGGCTAA-GGAAAAGTGGACCAATATGCTGA
* * *
3341003 CTCAAGGCCAGCGACATTGGGCTTA-GAAAGGT-G-CCAATATGCTGA
1 TTCAAGGCCAGCGACATTGGGCTAAGGAAAAGTGGACCAATATGCTGA
3341048 TTCAAGGCCAGC
1 TTCAAGGCCAGC
3341060 AATATCGGAC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
45 22 0.43
46 1 0.02
47 6 0.12
49 22 0.43
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.20
Consensus pattern (48 bp):
TTCAAGGCCAGCGACATTGGGCTAAGGAAAAGTGGACCAATATGCTGA
Found at i:3341141 original size:32 final size:32
Alignment explanation
Indices: 3341092--3341610 Score: 894
Period size: 32 Copynumber: 16.2 Consensus size: 32
3341082 AAAATGGTGA
* ** **
3341092 TTTGAAAAGGGTTGCCACTAACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3341124 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3341156 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
3341188 TTTGGAATGAGTTGCCACCGACTTGTGTGGGT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3341220 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3341252 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3341284 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3341316 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3341348 TTTGAAATGGGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3341380 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3341412 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3341444 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3341476 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3341508 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3341540 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3341572 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3341604 TTGGAAA
1 TTTGAAA
3341611 AGAATGCCAC
Statistics
Matches: 469, Mismatches: 18, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 469 1.00
ACGTcount: A:0.16, C:0.18, G:0.34, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:3341709 original size:27 final size:27
Alignment explanation
Indices: 3341625--3342265 Score: 994
Period size: 27 Copynumber: 23.4 Consensus size: 27
3341615 TGCCACCGCC
*
3341625 TTGTGGACTTAAAAAGGGTGCCACGAAG
1 TTGTGGACTT-AAAAGGGTGCCACGGAG
*
3341653 TTGTGAACTTAAAAGGGATGCCACGGAG
1 TTGTGGACTTAAAAGGG-TGCCACGGAG
3341681 TTGTGGACTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
3341708 TTGTGGACTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
3341735 TTGTGGACTTAAAAGGGATGCCACGGAG
1 TTGTGGACTTAAAAGGG-TGCCACGGAG
*
3341763 TTGTGGACTTAAAAGGATGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
*
3341790 CTGTGGACTTAAAAGGGATGCCACGGAG
1 TTGTGGACTTAAAAGGG-TGCCACGGAG
3341818 TTGTGGACTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
* *
3341845 TTGCGGACTAAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
*
3341872 TTGTGGACTTTAAAAGGGTGCCACAGAG
1 TTGTGGAC-TTAAAAGGGTGCCACGGAG
**
3341900 TTGTGGACTTAAAAAGGGTGCCATAGAG
1 TTGTGGACTT-AAAAGGGTGCCACGGAG
* * *
3341928 TTGTGGACTTAAAAAGATGCCACAGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
* *
3341955 TTGTGGACTTAAAAGGATGCCACAGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
3341982 TTGTGGACTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
*
3342009 TTGTGGACTTAAAAGGGTGCCACGGAT
1 TTGTGGACTTAAAAGGGTGCCACGGAG
3342036 TTGTGGACTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
*
3342063 TTGTGGACTTAAAAGGGATGCCACAGAG
1 TTGTGGACTTAAAAGGG-TGCCACGGAG
*
3342091 TTGTGGACTTAAAAGGGATGCCACAGAG
1 TTGTGGACTTAAAAGGG-TGCCACGGAG
* *
3342119 TTGTGGACTTAAAAAGGTGCCATGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
3342146 TTGTGGACTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
*
3342173 TTGTGGACTTAAAAGAGATGCCACGGAG
1 TTGTGGACTTAAAAG-GGTGCCACGGAG
3342201 TTGTGGACTTAAAAGGGATGCCACGGAG
1 TTGTGGACTTAAAAGGG-TGCCACGGAG
*
3342229 TTGTGGACTTAAAAGGGTGCTACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
*
3342256 TCGTGGACTT
1 TTGTGGACTT
3342266 TGAAAAGGTC
Statistics
Matches: 574, Mismatches: 31, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
27 331 0.58
28 243 0.42
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (27 bp):
TTGTGGACTTAAAAGGGTGCCACGGAG
Found at i:3341812 original size:110 final size:110
Alignment explanation
Indices: 3341625--3342265 Score: 1024
Period size: 110 Copynumber: 5.8 Consensus size: 110
3341615 TGCCACCGCC
* *
3341625 TTGTGGACTTAAAAAGGG-TGCCACGAAGTTGTGAACTTAAAAGGGATGCCACGGAGTTGTGGAC
1 TTGTGGACTT-AAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGAC
3341689 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
65 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
*
3341735 TTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAA-GGATGCCACGGAGCTGTGGACT
1 TTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACT
3341799 TAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
66 TAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
* * *
3341845 TTGCGGACTAAAAAGGG-TGCCACGGAGTTGTGGACTTTAAAAGGG-TGCCACAGAGTTGTGGAC
1 TTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGAC-TTAAAAGGGATGCCACGGAGTTGTGGAC
** * * *
3341908 TTAAAAAGGGTGCCATAGAGTTGTGGACTTAAAAAGATGCCACAGAG
65 TT-AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
*
3341955 TTGTGGACTTAAAA-GGATGCCACAGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACT
1 TTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACT
*
3342018 TAAAAGGGTGCCACGGATTTGTGGACTTAAAAGGGTGCCACGGAG
66 TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
* *
3342063 TTGTGGACTTAAAAGGGATGCCACAGAGTTGTGGACTTAAAAGGGATGCCACAGAGTTGTGGACT
1 TTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACT
* *
3342128 TAAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
66 TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
*
3342173 TTGTGGACTTAAAAGAGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACT
1 TTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACT
* *
3342238 TAAAAGGGTGCTACGGAGTCGTGGACTT
66 TAAAAGGGTGCCACGGAGTTGTGGACTT
3342266 TGAAAAGGTC
Statistics
Matches: 490, Mismatches: 33, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
108 52 0.11
109 114 0.23
110 315 0.64
111 9 0.02
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (110 bp):
TTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACT
TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
Found at i:3341859 original size:137 final size:136
Alignment explanation
Indices: 3341625--3342264 Score: 1014
Period size: 137 Copynumber: 4.7 Consensus size: 136
3341615 TGCCACCGCC
* *
3341625 TTGTGGACTTAAAAAGGGTGCCACGAAGTTGTGAACTTAAAAGGGATGCCACGGAGTTGTGGACT
1 TTGTGGACTT-AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACT
*
3341690 TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATG
65 TAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TG
3341755 CCACGGAG
129 CCACGGAG
* *
3341763 TTGTGGACTTAAAAGGATGCCACGGAGCTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTT
1 TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTT
*
3341828 AAAAGGGTGCCACGGAGTTGCGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGC
66 AAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGC
*
3341893 CACAGAG
130 CACGGAG
** * *
3341900 TTGTGGACTTAAAAAGGGTGCCATAGAGTTGTGGACTTAAAA-AGATGCCACAGAGTTGTGGACT
1 TTGTGGACTT-AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACT
* * *
3341964 TAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGC
65 TAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGC
*
3342029 CACGGAT
130 CACGGAG
*
3342036 TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACAGAGTTGTGGACTT
1 TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTT
* *
3342101 AAAAGGGATGCCACAGAGTTGTGGACTTAAAAA-GGTGCCATGGAGTTGTGGACTTAAAAGGGTG
66 AAAAGGG-TGCCACGGAGTTGTGGAC-TAAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTG
3342165 CCACGGAG
129 CCACGGAG
*
3342173 TTGTGGACTTAAAAGAGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACT
1 TTGTGGACTTAAAAG-GGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACT
* *
3342238 TAAAAGGGTGCTACGGAGTCGTGGACT
65 TAAAAGGGTGCCACGGAGTTGTGGACT
3342265 TTGAAAAGGT
Statistics
Matches: 465, Mismatches: 31, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
135 29 0.06
136 56 0.12
137 274 0.59
138 106 0.23
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (136 bp):
TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTT
AAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
ACGGAG
Found at i:3349526 original size:23 final size:24
Alignment explanation
Indices: 3349478--3349527 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3349468 ATATTTTTTA
* *
3349478 TTTTTTAAAACAAATAACGATCAT
1 TTTTTTAAAACAAAAAACGATAAT
*
3349502 TTTTTTAAAA-AAAAAACG-TAAA
1 TTTTTTAAAACAAAAAACGATAAT
3349524 TTTT
1 TTTT
3349528 AAACTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 6 0.26
23 7 0.30
24 10 0.43
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (24 bp):
TTTTTTAAAACAAAAAACGATAAT
Found at i:3350099 original size:23 final size:24
Alignment explanation
Indices: 3350073--3350118 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3350063 GCCACTCCAT
*
3350073 TTCATATT-TTTTTTTCTTTTTTC
1 TTCATATTCTTTCTTTCTTTTTTC
*
3350096 TTCATCTTCTTTCTTTCTTTTTT
1 TTCATATTCTTTCTTTCTTTTTT
3350119 ACCTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (24 bp):
TTCATATTCTTTCTTTCTTTTTTC
Found at i:3350504 original size:24 final size:23
Alignment explanation
Indices: 3350476--3350520 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3350466 ACTCAATCGG
3350476 AAAACCCACTTTGGTTTTTTTTGA
1 AAAACCC-CTTTGGTTTTTTTTGA
**
3350500 AAAACCCCTTTTTTTTTTTTT
1 AAAACCCCTTTGGTTTTTTTT
3350521 TTCGACCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.22, C:0.18, G:0.07, T:0.53
Consensus pattern (23 bp):
AAAACCCCTTTGGTTTTTTTTGA
Found at i:3351349 original size:27 final size:27
Alignment explanation
Indices: 3351314--3351367 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
3351304 CAATTTTGAT
3351314 AAAATTTTTACTTTTTAATCTGGTTAA
1 AAAATTTTTACTTTTTAATCTGGTTAA
3351341 AAAATTTTTACTTTTTAATCTGGTTAA
1 AAAATTTTTACTTTTTAATCTGGTTAA
3351368 GTTAACGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (27 bp):
AAAATTTTTACTTTTTAATCTGGTTAA
Found at i:3352831 original size:2 final size:2
Alignment explanation
Indices: 3352824--3352885 Score: 57
Period size: 2 Copynumber: 34.5 Consensus size: 2
3352814 AACTTTGTCT
* *
3352824 AG AG AG AG AG AG AG AG AG AG AA AG AG A- AG AA AG -G AG AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3352863 AG A- AG AG AG AG A- AG A- AG A- AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
3352886 TAGGTGGTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
1 7 0.14
2 42 0.86
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3352835 original size:6 final size:6
Alignment explanation
Indices: 3352824--3352885 Score: 57
Period size: 5 Copynumber: 11.5 Consensus size: 6
3352814 AACTTTGTCT
* *
3352824 AGAGAG AGAGAG AGAGAG AGAAAG AGA-AG AAAG-G AGAG-G AGA-AG
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG
3352868 AGAGAG A-AGA- AGA-AG AGA
1 AGAGAG AGAGAG AGAGAG AGA
3352886 TAGGTGGTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
4 2 0.04
5 23 0.48
6 23 0.48
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (6 bp):
AGAGAG
Found at i:3352873 original size:24 final size:26
Alignment explanation
Indices: 3352831--3352878 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
3352821 TCTAGAGAGA
3352831 GAGAGAGAGAGAGAAAGAGAAGAAAG
1 GAGAGAGAGAGAGAAAGAGAAGAAAG
*
3352857 GAGAG-GAGA-AGAGAGAGAAGAA
1 GAGAGAGAGAGAGAAAGAGAAGAA
3352879 GAAGAGATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.57
25 4 0.19
26 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (26 bp):
GAGAGAGAGAGAGAAAGAGAAGAAAG
Found at i:3356176 original size:32 final size:33
Alignment explanation
Indices: 3356102--3356180 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
3356092 ATAAAAAAAT
* * * * *
3356102 AAAATATATATAATATAAATTTATGAATATTTT
1 AAAATTTATATAAAATAAATTTATGAAGATATA
*
3356135 AAAATTTATATAAAATAAA-TTATTAAGATATA
1 AAAATTTATATAAAATAAATTTATGAAGATATA
3356167 AAAATTTATATAAA
1 AAAATTTATATAAA
3356181 TATATAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 23 0.57
33 17 0.43
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (33 bp):
AAAATTTATATAAAATAAATTTATGAAGATATA
Found at i:3356183 original size:18 final size:18
Alignment explanation
Indices: 3356135--3356184 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
3356125 TGAATATTTT
3356135 AAAATTTATATAAA-AT-
1 AAAATTTATATAAATATA
3356151 -AAA-TTAT-TAAGATATA
1 AAAATTTATATAA-ATATA
3356167 AAAATTTATATAAATATA
1 AAAATTTATATAAATATA
3356185 TAATATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.11
14 5 0.18
15 5 0.18
17 3 0.11
18 9 0.32
19 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAAATTTATATAAATATA
Found at i:3356743 original size:16 final size:17
Alignment explanation
Indices: 3356722--3356759 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3356712 ATTGAAAAAT
*
3356722 AAATTAATAAA-ATAAA
1 AAATTAACAAATATAAA
3356738 AAATTAACAAATATAAA
1 AAATTAACAAATATAAA
*
3356755 TAATT
1 AAATT
3356760 TAAAACTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATTAACAAATATAAA
Found at i:3357479 original size:19 final size:19
Alignment explanation
Indices: 3357453--3357503 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
3357443 ACGTAAGCAT
3357453 AAATAAAATAAAAAAAG-A
1 AAATAAAATAAAAAAAGTA
* *
3357471 AAATGAAAAT-GAAACAGTA
1 AAAT-AAAATAAAAAAAGTA
3357490 AAATAAAAATAAAA
1 AAAT-AAAATAAAA
3357504 TAAAATAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 9 0.35
19 15 0.58
20 2 0.08
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (19 bp):
AAATAAAATAAAAAAAGTA
Found at i:3361401 original size:20 final size:20
Alignment explanation
Indices: 3361378--3361431 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
3361368 TAAAGGAAAA
3361378 GAAAGGAAAGGAAAGTAAAG
1 GAAAGGAAAGGAAAGTAAAG
* **
3361398 GAAAGGAAAGGAAGGTTGAG
1 GAAAGGAAAGGAAAGTAAAG
*
3361418 GATAGGAAAGGAAA
1 GAAAGGAAAGGAAA
3361432 TATGTATCTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.39, T:0.07
Consensus pattern (20 bp):
GAAAGGAAAGGAAAGTAAAG
Found at i:3361431 original size:5 final size:5
Alignment explanation
Indices: 3361369--3361410 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
3361359 AGACAATATT
* *
3361369 AAAGG AAAAG AAAGG AAAGG AAAGT AAAGG AAAGG AAAGG AA
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AA
3361411 GGTTGAGGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.02
Consensus pattern (5 bp):
AAAGG
Found at i:3361759 original size:20 final size:20
Alignment explanation
Indices: 3361734--3361774 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3361724 GCTTTAGGAA
*
3361734 TTAAAA-CCAATTTAAGTACC
1 TTAAAAGCCAATATAAG-ACC
3361754 TTAAAAGCCAATATAAGACC
1 TTAAAAGCCAATATAAGACC
3361774 T
1 T
3361775 AATGAACCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.27
Consensus pattern (20 bp):
TTAAAAGCCAATATAAGACC
Found at i:3384467 original size:131 final size:129
Alignment explanation
Indices: 3384292--3384553 Score: 443
Period size: 131 Copynumber: 2.0 Consensus size: 129
3384282 TCTCTTAGTT
*
3384292 TTTGTCTTATTTGTTTTCTTTTGAGCAATATATAAGAGTTTGTGTTAAAGTTACCACTTTGGTCA
1 TTTGTCTTATTTGTTTTCTTTTGAGCAATATATAAGAGTGTGTGTTAAAGTTACCACTTTGGTCA
* *
3384357 TTAGCTCGTAGCACTTGCTATTTCGAAAGAAAAGGTCAGTGCCATGTGTAACTGCATGGTAAGTG
66 TTAGCTCGTAGCACTGGCTATTTCGAAAG-AAA-GTCAGTGACATGTGTAACTGCATGGTAAGTG
3384422 C
129 C
*
3384423 TTTGTCTTATTTGTTTTCTTTTGAGCAATATGTAAGAGTGTGTGTTAAAGTTACCACTTTGGTCA
1 TTTGTCTTATTTGTTTTCTTTTGAGCAATATATAAGAGTGTGTGTTAAAGTTACCACTTTGGTCA
* * *
3384488 TTAGTTCGTAGCACTGGCTATTTCGAAAGAAAGTCAGTGACATTTGTAACTGCATGTTAAGTGC
66 TTAGCTCGTAGCACTGGCTATTTCGAAAGAAAGTCAGTGACATGTGTAACTGCATGGTAAGTGC
3384552 TT
1 TT
3384554 AGTTCTATTT
Statistics
Matches: 124, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
129 31 0.25
130 3 0.02
131 90 0.73
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (129 bp):
TTTGTCTTATTTGTTTTCTTTTGAGCAATATATAAGAGTGTGTGTTAAAGTTACCACTTTGGTCA
TTAGCTCGTAGCACTGGCTATTTCGAAAGAAAGTCAGTGACATGTGTAACTGCATGGTAAGTGC
Found at i:3385463 original size:18 final size:18
Alignment explanation
Indices: 3385440--3385479 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
3385430 AACATAGAAA
3385440 AACCTGATAGTTCTGATC
1 AACCTGATAGTTCTGATC
3385458 AACCTGATAGTTCTGATC
1 AACCTGATAGTTCTGATC
3385476 AACC
1 AACC
3385480 AGGAGCAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (18 bp):
AACCTGATAGTTCTGATC
Found at i:3390703 original size:23 final size:23
Alignment explanation
Indices: 3390673--3390720 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
3390663 TGACTGGGAA
3390673 ATAAAGTGGTCCTACCTTGTGAG
1 ATAAAGTGGTCCTACCTTGTGAG
3390696 ATAAAGTGGTCCTACCTTGTGAG
1 ATAAAGTGGTCCTACCTTGTGAG
3390719 AT
1 AT
3390721 TTAGACTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (23 bp):
ATAAAGTGGTCCTACCTTGTGAG
Found at i:3397726 original size:59 final size:58
Alignment explanation
Indices: 3397551--3397736 Score: 165
Period size: 59 Copynumber: 3.2 Consensus size: 58
3397541 TAGCAGGTAC
* ** * * * *
3397551 AAAACTAACTTAAAAAACTCTTAAATGTATAAAAATTGCATAATGATACATAGATTAT
1 AAAAATAACTTAAATGACTCTAAAATGTATAAAAATTGTATAATAATACTTAGATTAT
* * * * * * * **
3397609 AAAAAGTAACTTAAATGATTTTAAAAAGCACAAAAATAGTATAATAGTTTTTAGATTAT
1 AAAAA-TAACTTAAATGACTCTAAAATGTATAAAAATTGTATAATAATACTTAGATTAT
* * * *
3397668 GAAAAATAGCTTAAATGACTCTAAAATGTATAAAAATTGTATAACAATCCTTAAATTAT
1 -AAAAATAACTTAAATGACTCTAAAATGTATAAAAATTGTATAATAATACTTAGATTAT
3397727 AAAAAATAAC
1 -AAAAATAAC
3397737 CTAATTATCA
Statistics
Matches: 96, Mismatches: 30, Indels: 3
0.74 0.23 0.02
Matches are distributed among these distances:
58 4 0.04
59 87 0.91
60 5 0.05
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.31
Consensus pattern (58 bp):
AAAAATAACTTAAATGACTCTAAAATGTATAAAAATTGTATAATAATACTTAGATTAT
Found at i:3399031 original size:78 final size:78
Alignment explanation
Indices: 3398901--3399055 Score: 197
Period size: 78 Copynumber: 2.0 Consensus size: 78
3398891 TAGTTTAAGA
* ** * *
3398901 TGAAAATATTATTAAAACATCCTTGACATAACTACAAAGTGATTTTCGGTTATTTGGAGTGGTTA
1 TGAAAATATTATTAAAACATCCTTGACATAACTACAAAGTGATTCTAAGTTATTTGGAATGATTA
3398966 GGAA-GGTGAAATG
66 -GAATGGTGAAATG
* * **
3398979 TGAAAATATTGTTAAAACATCTCTT-ATATAACTATGAAGTGATTCTAAGTTATTTGGAATGATT
1 TGAAAATATTATTAAAACATC-CTTGACATAACTACAAAGTGATTCTAAGTTATTTGGAATGATT
3399043 AGAATGGTGAAAT
65 AGAATGGTGAAAT
3399056 ACTAACAAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
77 3 0.05
78 60 0.91
79 3 0.05
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.35
Consensus pattern (78 bp):
TGAAAATATTATTAAAACATCCTTGACATAACTACAAAGTGATTCTAAGTTATTTGGAATGATTA
GAATGGTGAAATG
Found at i:3399120 original size:75 final size:73
Alignment explanation
Indices: 3399020--3399172 Score: 216
Period size: 75 Copynumber: 2.1 Consensus size: 73
3399010 CTATGAAGTG
* * *
3399020 ATTCTAAGTTATTTGGAATGATTAGAATGGTGAAATACTAACAAATTCAAATTGAATAACTTTTT
1 ATTCTAAATTATTTGGAATGATTAGAAAGGTGAAATACTAACAAATTCAAATTAAATAACTTTTT
*
3399085 TGTGCCTAGA
66 TAT--CTAGA
* * * *
3399095 ATTCTAAATTATTTGGAGTGGTTAGAAAGGTGAAATACTAGCAAATTCAGATTAAATAACTTTTT
1 ATTCTAAATTATTTGGAATGATTAGAAAGGTGAAATACTAACAAATTCAAATTAAATAACTTTTT
3399160 TATCTAGA
66 TATCTAGA
3399168 ATTCT
1 ATTCT
3399173 CGTGCAGTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
73 10 0.14
75 60 0.86
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (73 bp):
ATTCTAAATTATTTGGAATGATTAGAAAGGTGAAATACTAACAAATTCAAATTAAATAACTTTTT
TATCTAGA
Found at i:3399820 original size:2 final size:2
Alignment explanation
Indices: 3399779--3399806 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3399769 TGGCTTTTGA
3399779 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3399807 TGCCGTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3399836 original size:19 final size:19
Alignment explanation
Indices: 3399814--3399850 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3399804 GAGTGCCGTA
* *
3399814 AGAGAGAAGAAGAAAGTGC
1 AGAGAAAAGAAAAAAGTGC
3399833 AGAGAAAAGAAAAAAGTG
1 AGAGAAAAGAAAAAAGTG
3399851 AAAAATGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.32, T:0.05
Consensus pattern (19 bp):
AGAGAAAAGAAAAAAGTGC
Found at i:3399941 original size:40 final size:36
Alignment explanation
Indices: 3399894--3399966 Score: 92
Period size: 36 Copynumber: 1.9 Consensus size: 36
3399884 AAAAAGCTAA
* *
3399894 AAATTTTATTTTTATATATTATATAAATATTTTTATATTT
1 AAATTTTA-CTTTATA-A-TAT-TAAATATTTATATATTT
3399934 AAATTTTACTTTATAATATTAAATATTTATATA
1 AAATTTTACTTTATAATATTAAATATTTATATA
3399967 AATGATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 13 0.42
37 3 0.10
38 1 0.03
39 6 0.19
40 8 0.26
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (36 bp):
AAATTTTACTTTATAATATTAAATATTTATATATTT
Found at i:3402400 original size:2 final size:2
Alignment explanation
Indices: 3402388--3402417 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3402378 TGTTTCAATG
*
3402388 TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3402418 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3402422 original size:2 final size:2
Alignment explanation
Indices: 3402417--3402480 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
3402407 ATATATATAT
3402417 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
3402458 AG AG AG AG AA AG AA AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG A
3402481 ACTTACTTCA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3405841 original size:16 final size:17
Alignment explanation
Indices: 3405822--3405854 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3405812 TATTCTTAAA
3405822 AATTATA-ATGTTAATT
1 AATTATATATGTTAATT
*
3405838 AATTATATATTTTAATT
1 AATTATATATGTTAATT
3405855 TTAAAGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AATTATATATGTTAATT
Found at i:3406617 original size:5 final size:5
Alignment explanation
Indices: 3406607--3406638 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
3406597 ATAATAGTTC
3406607 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
3406639 ATAATCATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:3408062 original size:3 final size:3
Alignment explanation
Indices: 3408054--3408082 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3408044 TTAAAAGAAA
3408054 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3408083 ATTTGCATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3410098 original size:16 final size:15
Alignment explanation
Indices: 3410069--3410112 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 15
3410059 AATACATTAT
3410069 ATTT-ATATAT-ATA
1 ATTTGATATATAATA
3410082 ATTTGATATATTAATA
1 ATTTGATATA-TAATA
*
3410098 ATTTTATATATAATA
1 ATTTGATATATAATA
3410113 TATTAAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 4 0.15
14 5 0.19
15 6 0.22
16 12 0.44
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTGATATATAATA
Found at i:3410221 original size:18 final size:18
Alignment explanation
Indices: 3410200--3410237 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3410190 TTGTGTAATT
* *
3410200 TTTTTTTGTGTATTTGTA
1 TTTTTTTATGTATTTATA
3410218 TTTTTTTATGTATTTATA
1 TTTTTTTATGTATTTATA
3410236 TT
1 TT
3410238 ATAATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.11, T:0.74
Consensus pattern (18 bp):
TTTTTTTATGTATTTATA
Found at i:3410351 original size:213 final size:212
Alignment explanation
Indices: 3409940--3410400 Score: 538
Period size: 213 Copynumber: 2.2 Consensus size: 212
3409930 TGGGCGCTAC
* *
3409940 GTGGGCAACTTTTTTCTCTCATGTTTTATTTTTTTATCTTGTGCAATTTTTTTTTTTTGTATTTG
1 GTGGGCAACTTTTTTCTC-CA-GTTTTATTTTTTAATCTTGTGCAATTTTTTTTTTGTGTATTTG
* * *
3410005 TGTTTTTGTGTAATCATAATATAATAATATTATTTTTATACCTTAATTGAATTCAATACATTATA
64 TGTTTTTATGTAATCATAATATAATAATATTATTTTTATACCATAATTGAATTCAAAACATTATA
* * * * * * *
3410070 TTTATATATATAATTTGATATATTAATAATTTTATATATAATATATTAAAGTAATCTTTAAGGAT
129 TTTATATAAAAAATTTGATACATTAATAATTTTATATACAATATATAAAAATAATCTTAAAGGAT
**
3410135 TACTTTTATTGGG-TGCCAT
194 TACTTGCATTGGGTTGCC-T
*
3410154 GTGGGCAACATTTTTTCTCCAGTTTTATTTTTTAAT-TTGTGTAA-TTTTTTTTTGTGTATTTGT
1 GTGGGCAAC-TTTTTTCTCCAGTTTTATTTTTTAATCTTGTGCAATTTTTTTTTTGTGTATTTG-
* * * * * ** * *
3410217 ATTTTTTTATGTATTTATATTATAATTATATTATTTTTATGTCATAATTGAATTTAAAATATTAT
64 -TGTTTTTATGTAATCATAATATAATAATATTATTTTTATACCATAATTGAATTCAAAACATTAT
*
3410282 ATATT-TATAAAAAATTTGATACATTAATAATTTTATATACAATATATAAAAATAAT-TCTAAAT
128 AT-TTATATAAAAAATTTGATACATTAATAATTTTATATACAATATATAAAAATAATCT-TAAAG
*
3410345 GATTACTTGCATTGGGTTTCCT
191 GATTACTTGCATTGGGTTGCCT
*
3410367 GTGAGCAATCTTTTTTC-CCAAGTTTTACTTTTTT
1 GTGGGCAA-CTTTTTTCTCC-AGTTTTA-TTTTTT
3410401 CTATAATTTT
Statistics
Matches: 211, Mismatches: 27, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
211 17 0.08
212 10 0.05
213 152 0.72
214 23 0.11
215 9 0.04
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.53
Consensus pattern (212 bp):
GTGGGCAACTTTTTTCTCCAGTTTTATTTTTTAATCTTGTGCAATTTTTTTTTTGTGTATTTGTG
TTTTTATGTAATCATAATATAATAATATTATTTTTATACCATAATTGAATTCAAAACATTATATT
TATATAAAAAATTTGATACATTAATAATTTTATATACAATATATAAAAATAATCTTAAAGGATTA
CTTGCATTGGGTTGCCT
Found at i:3412970 original size:14 final size:14
Alignment explanation
Indices: 3412951--3412985 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3412941 CCCCCGCAGC
3412951 GTCACAAAATGTTT
1 GTCACAAAATGTTT
3412965 GTCACAAAATGTTT
1 GTCACAAAATGTTT
3412979 GTC-CAAA
1 GTCACAAA
3412986 CTGAATGCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31
Consensus pattern (14 bp):
GTCACAAAATGTTT
Found at i:3413341 original size:18 final size:19
Alignment explanation
Indices: 3413294--3413338 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
3413284 TTAAATAAAT
3413294 ATTAAAAATTATTTTTATA
1 ATTAAAAATTATTTTTATA
*
3413313 ATTAAAAATTATTTTTATG
1 ATTAAAAATTATTTTTATA
3413332 ATTAAAA
1 ATTAAAA
3413339 TTAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTAAAAATTATTTTTATA
Found at i:3414160 original size:2 final size:2
Alignment explanation
Indices: 3414125--3414149 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3414115 TAACTGAAAT
3414125 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3414150 TTGAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3414792 original size:16 final size:16
Alignment explanation
Indices: 3414771--3414838 Score: 53
Period size: 15 Copynumber: 4.6 Consensus size: 16
3414761 TAAATATAAC
3414771 ATTTAAAATTATAAAT
1 ATTTAAAATTATAAAT
*
3414787 ATTTAAAA-TAAAAAT
1 ATTTAAAATTATAAAT
3414802 -TCTTAAACA-T-TAAAT
1 AT-TTAAA-ATTATAAAT
3414817 A---AAAATTA-AAAT
1 ATTTAAAATTATAAAT
3414829 ATTTAAAATT
1 ATTTAAAATT
3414839 TAGTAAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 17
0.69 0.03 0.28
Matches are distributed among these distances:
11 1 0.02
12 9 0.21
14 1 0.02
15 21 0.50
16 10 0.24
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTAAAATTATAAAT
Found at i:3414798 original size:21 final size:22
Alignment explanation
Indices: 3414775--3414837 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 22
3414765 TATAACATTT
3414775 AAAATTATAAATATTTAAAATA
1 AAAATTATAAATATTTAAAATA
* *
3414797 AAAATTCTTAAACA-TT-AAATA
1 AAAATT-ATAAATATTTAAAATA
3414818 AAAATTA-AAATATTTAAAAT
1 AAAATTATAAATATTTAAAAT
3414838 TTAGTAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 15 0.44
22 8 0.24
23 5 0.15
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAATTATAAATATTTAAAATA
Found at i:3415434 original size:19 final size:20
Alignment explanation
Indices: 3415396--3415436 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3415386 AATTTACGAA
*
3415396 GATATATCATTACATTTCATT
1 GATATATCAATACA-TTCATT
3415417 GATATATCAATACA-TCATT
1 GATATATCAATACATTCATT
3415436 G
1 G
3415437 GGCTGGGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
21 13 0.68
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (20 bp):
GATATATCAATACATTCATT
Found at i:3416182 original size:10 final size:10
Alignment explanation
Indices: 3416167--3416213 Score: 58
Period size: 10 Copynumber: 4.4 Consensus size: 10
3416157 GAGGGAAACC
3416167 AAAAAAGAAA
1 AAAAAAGAAA
*
3416177 AAAAAAGGAA
1 AAAAAAGAAA
3416187 AAAAAAGAAA
1 AAAAAAGAAA
3416197 AACAAGGAAGAAA
1 AA-AA--AAGAAA
3416210 AAAA
1 AAAA
3416214 TAATGCTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 20 0.62
11 2 0.06
12 2 0.06
13 8 0.25
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:3416192 original size:20 final size:20
Alignment explanation
Indices: 3416167--3416212 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
3416157 GAGGGAAACC
3416167 AAAAAAGAAAAAAAAAGGAA-
1 AAAAAAG-AAAAAAAAGGAAG
*
3416187 AAAAAAGAAAAACAAGGAAG
1 AAAAAAGAAAAAAAAGGAAG
3416207 AAAAAA
1 AAAAAA
3416213 ATAATGCTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAAAAAGGAAG
Found at i:3416946 original size:27 final size:28
Alignment explanation
Indices: 3416909--3416984 Score: 88
Period size: 27 Copynumber: 2.8 Consensus size: 28
3416899 TTAGGGGCCA
3416909 TTTTACA--TTTCATGCATTTTAGGA-G
1 TTTTACATTTTTCATGCATTTTAGGACG
*
3416934 TTTTACATTTTTCACGCATTTTAGGACTG
1 TTTTACATTTTTCATGCATTTTAGGAC-G
3416963 TTTTAGTCATTTTTCATG-ATTT
1 TTTTA--CATTTTTCATGCATTT
3416985 AGAAGCTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
25 7 0.16
27 16 0.37
29 6 0.14
30 4 0.09
31 10 0.23
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.53
Consensus pattern (28 bp):
TTTTACATTTTTCATGCATTTTAGGACG
Found at i:3417024 original size:57 final size:58
Alignment explanation
Indices: 3416963--3417111 Score: 178
Period size: 57 Copynumber: 2.6 Consensus size: 58
3416953 TTTAGGACTG
* * * *
3416963 TTTTAGTCATTTTTCATGATTTAGAAGCTATTATGTAA-TTCATGCATTT-TAGCATCA
1 TTTTAGTCATTTTTCATGATTTAGAAACTATTATATAATTTCACGCATTTCAAG-ATCA
* *
3417020 TTTTAGTAATTTTTCATGATTTAGAAACTATTATATAATTTCACGTATTTCAAGATCA
1 TTTTAGTCATTTTTCATGATTTAGAAACTATTATATAATTTCACGCATTTCAAGATCA
* * **
3417078 TTTTATTC-TTTTTTATGATTTAGGGACTATTATA
1 TTTTAGTCATTTTTCATGATTTAGAAACTATTATA
3417112 CAAATTTATG
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
57 58 0.73
58 19 0.24
59 2 0.03
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.50
Consensus pattern (58 bp):
TTTTAGTCATTTTTCATGATTTAGAAACTATTATATAATTTCACGCATTTCAAGATCA
Found at i:3417058 original size:29 final size:29
Alignment explanation
Indices: 3416971--3417060 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
3416961 TGTTTTAGTC
* *
3416971 ATTTTTCATGATTTAGAAGCTATTATGTA
1 ATTTTTCATGATTTAGAAACTATTATATA
* * *
3417000 A---TTCATGCATTTTAGCATC-ATTTTAGTA
1 ATTTTTCATG-A-TTTAGAAACTATTATA-TA
3417028 ATTTTTCATGATTTAGAAACTATTATATA
1 ATTTTTCATGATTTAGAAACTATTATATA
3417057 ATTT
1 ATTT
3417061 CACGTATTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
26 6 0.13
27 5 0.11
28 10 0.21
29 14 0.30
30 6 0.13
31 6 0.13
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.49
Consensus pattern (29 bp):
ATTTTTCATGATTTAGAAACTATTATATA
Found at i:3417441 original size:20 final size:20
Alignment explanation
Indices: 3417418--3417490 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3417408 ACAATTCAAA
3417418 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3417438 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
3417459 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3417479 GTATCGATACAT
1 GTATCGATACAT
3417491 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3417461 original size:21 final size:21
Alignment explanation
Indices: 3417435--3417511 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
3417425 TACATGTTGC
3417435 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
3417456 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
3417476 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
3417496 AGATGTATCGATACAT
1 A-ATGTATCGATACAT
3417512 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:3417469 original size:41 final size:41
Alignment explanation
Indices: 3417418--3417511 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
3417408 ACAATTCAAA
3417418 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAA-AT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAAGAT
3417459 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3417500 GTATCGATACAT
1 GTATCGATACAT
3417512 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 6 0.12
41 46 0.88
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:3417568 original size:13 final size:13
Alignment explanation
Indices: 3417550--3417575 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3417540 TACAGCAAGT
3417550 ATGTATCGATACA
1 ATGTATCGATACA
3417563 ATGTATCGATACA
1 ATGTATCGATACA
3417576 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3421658 original size:15 final size:15
Alignment explanation
Indices: 3421638--3421668 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3421628 TAAAAATGTC
*
3421638 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3421653 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3421668 C
1 C
3421669 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3423757 original size:13 final size:13
Alignment explanation
Indices: 3423739--3423777 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3423729 ACATTTTTCC
3423739 TTGTATCGATACA
1 TTGTATCGATACA
3423752 TTGTATCGATACA
1 TTGTATCGATACA
*
3423765 CTGTATCGATACA
1 TTGTATCGATACA
3423778 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3426244 original size:20 final size:20
Alignment explanation
Indices: 3426221--3426334 Score: 138
Period size: 20 Copynumber: 5.6 Consensus size: 20
3426211 ACAATTCAAA
3426221 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3426241 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
3426262 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3426282 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
3426303 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3426323 GTATCGATACAT
1 GTATCGATACAT
3426335 AAAAAAGATG
Statistics
Matches: 76, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
20 44 0.58
21 32 0.42
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3426264 original size:21 final size:21
Alignment explanation
Indices: 3426238--3426355 Score: 134
Period size: 21 Copynumber: 5.7 Consensus size: 21
3426228 TACATGTTGC
3426238 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
3426259 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
3426279 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
3426300 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
3426320 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
3426340 AGATGTATCGATACAT
1 A-ATGTATCGATACAT
3426356 TTCTTGGCAG
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
20 32 0.41
21 46 0.59
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:3426272 original size:41 final size:41
Alignment explanation
Indices: 3426221--3426355 Score: 254
Period size: 41 Copynumber: 3.3 Consensus size: 41
3426211 ACAATTCAAA
3426221 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAAAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAAAT
3426262 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAAAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAAAT
3426303 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAA-AT
3426344 GTATCGATACAT
1 GTATCGATACAT
3426356 TTCTTGGCAG
Statistics
Matches: 93, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
40 6 0.06
41 87 0.94
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAAAT
Found at i:3426412 original size:13 final size:13
Alignment explanation
Indices: 3426394--3426419 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3426384 TACAGCAAGT
3426394 ATGTATCGATACA
1 ATGTATCGATACA
3426407 ATGTATCGATACA
1 ATGTATCGATACA
3426420 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3433817 original size:6 final size:6
Alignment explanation
Indices: 3433806--3433843 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
3433796 ATCTAGACTT
3433806 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TT
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TT
3433844 TTAATTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TTAAAA
Found at i:3434776 original size:21 final size:21
Alignment explanation
Indices: 3434747--3434787 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3434737 AAAGGTCAAA
3434747 ACCCTAGAAAGTATCGATACAG
1 ACCCTAG-AAGTATCGATACAG
*
3434769 ACCC-AGAAGTATTGATACA
1 ACCCTAGAAGTATCGATACA
3434788 TATTGCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 2 0.11
22 4 0.22
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (21 bp):
ACCCTAGAAGTATCGATACAG
Found at i:3441131 original size:13 final size:13
Alignment explanation
Indices: 3441109--3441155 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
3441099 TGATCTTAGT
*
3441109 TCGATTCATTGTA
1 TCGATACATTGTA
*
3441122 TCGATACATTATA
1 TCGATACATTGTA
3441135 TCGATACATTGTA
1 TCGATACATTGTA
3441148 TCGATACA
1 TCGATACA
3441156 AGGGCACTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (13 bp):
TCGATACATTGTA
Found at i:3441321 original size:13 final size:14
Alignment explanation
Indices: 3441303--3441331 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3441293 CTCTTCATTT
3441303 TTCATCAAAAA-AC
1 TTCATCAAAAACAC
3441316 TTCATCAAAAACAC
1 TTCATCAAAAACAC
3441330 TT
1 TT
3441332 TTATTTCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (14 bp):
TTCATCAAAAACAC
Found at i:3443801 original size:13 final size:13
Alignment explanation
Indices: 3443783--3443807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3443773 CATATTGCTT
3443783 TGTATCGATACAC
1 TGTATCGATACAC
3443796 TGTATCGATACA
1 TGTATCGATACA
3443808 TGATCTAGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:3444629 original size:14 final size:14
Alignment explanation
Indices: 3444610--3444671 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 14
3444600 TTAATGCATT
3444610 ACTGTTCATGTATC
1 ACTGTTCATGTATC
3444624 ACTGTTC----ATC
1 ACTGTTCATGTATC
*
3444634 ACTGTTTATGTATC
1 ACTGTTCATGTATC
*
3444648 ACTATTC----ATC
1 ACTGTTCATGTATC
3444658 ACTGTTCATGTATC
1 ACTGTTCATGTATC
3444672 GATACAGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
10 18 0.50
14 18 0.50
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.44
Consensus pattern (14 bp):
ACTGTTCATGTATC
Found at i:3444644 original size:24 final size:24
Alignment explanation
Indices: 3444610--3444671 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
3444600 TTAATGCATT
*
3444610 ACTGTTCATGTATCACTGTTCATC
1 ACTGTTCATGTATCACTATTCATC
*
3444634 ACTGTTTATGTATCACTATTCATC
1 ACTGTTCATGTATCACTATTCATC
3444658 ACTGTTCATGTATC
1 ACTGTTCATGTATC
3444672 GATACAGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.44
Consensus pattern (24 bp):
ACTGTTCATGTATCACTATTCATC
Found at i:3445062 original size:24 final size:24
Alignment explanation
Indices: 3445034--3445088 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
3445024 ATTGTTTGTT
3445034 TTGTTTGTAAGGTTGTGTTCAACC
1 TTGTTTGTAAGGTTGTGTTCAACC
3445058 TTGTTTGTAAGGTTGTGTTCAACC
1 TTGTTTGTAAGGTTGTGTTCAACC
3445082 TTGTTTG
1 TTGTTTG
3445089 CAATCACTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.15, C:0.11, G:0.25, T:0.49
Consensus pattern (24 bp):
TTGTTTGTAAGGTTGTGTTCAACC
Found at i:3445191 original size:36 final size:34
Alignment explanation
Indices: 3445129--3445215 Score: 99
Period size: 36 Copynumber: 2.6 Consensus size: 34
3445119 CTAAGTGATT
* *
3445129 GAGAGGTTCTATCTTA-ACCTTCGAAAAAGATAGGG
1 GAGAGGTTCTATCTTAGCCCGTCG-AAAAGATA-GG
3445164 AGAGAGGTTCTATCTTAGCCCGT-GAAAAGATAGG
1 -GAGAGGTTCTATCTTAGCCCGTCGAAAAGATAGG
*
3445198 GAG-GTTTCTATCTTAGCC
1 GAGAGGTTCTATCTTAGCC
3445216 TTGAAAGATA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
32 14 0.30
33 3 0.06
34 2 0.04
35 8 0.17
36 17 0.36
37 3 0.06
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (34 bp):
GAGAGGTTCTATCTTAGCCCGTCGAAAAGATAGG
Found at i:3449926 original size:25 final size:25
Alignment explanation
Indices: 3449892--3449953 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
3449882 TTATTAATTC
3449892 TTAAAATATTAAAAACAATTTATTA
1 TTAAAATATTAAAAACAATTTATTA
3449917 TTAAAATATTAAAAACAATTTATTA
1 TTAAAATATTAAAAACAATTTATTA
3449942 TTAAAATATTAA
1 TTAAAATATTAA
3449954 TATTTTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (25 bp):
TTAAAATATTAAAAACAATTTATTA
Found at i:3449957 original size:14 final size:14
Alignment explanation
Indices: 3449873--3449987 Score: 57
Period size: 14 Copynumber: 8.5 Consensus size: 14
3449863 TATCAACATA
*
3449873 AATATTAAATTATT
1 AATATTAAAATATT
*
3449887 AATTCTTAAAATATT
1 AA-TATTAAAATATT
3449902 AA-A--AACAAT-TT
1 AATATTAA-AATATT
*
3449913 ATTATTAAAATATT
1 AATATTAAAATATT
3449927 AA-A--AACAAT-TT
1 AATATTAA-AATATT
*
3449938 ATTATTAAAATATT
1 AATATTAAAATATT
**
3449952 AATATTTTAATATT
1 AATATTAAAATATT
* * *
3449966 AATTTTCTAAATAGT
1 AATATT-AAAATATT
3449981 AATATTA
1 AATATTA
3449988 TAATCTCAAT
Statistics
Matches: 75, Mismatches: 14, Indels: 24
0.66 0.12 0.21
Matches are distributed among these distances:
11 10 0.13
12 8 0.11
13 7 0.09
14 27 0.36
15 23 0.31
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.45
Consensus pattern (14 bp):
AATATTAAAATATT
Found at i:3450434 original size:35 final size:35
Alignment explanation
Indices: 3450392--3450464 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
3450382 TATAAATATG
3450392 TATGTTTAATAATACTAAAAATTATATTATTAAAA
1 TATGTTTAATAATACTAAAAATTATATTATTAAAA
* *
3450427 TATGTTTAATAATATTAAAAATTATATTATTAAGA
1 TATGTTTAATAATACTAAAAATTATATTATTAAAA
3450462 TAT
1 TAT
3450465 ATTATTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (35 bp):
TATGTTTAATAATACTAAAAATTATATTATTAAAA
Found at i:3450466 original size:48 final size:44
Alignment explanation
Indices: 3450414--3450522 Score: 110
Period size: 45 Copynumber: 2.3 Consensus size: 44
3450404 TACTAAAAAT
* *
3450414 TATATTATTAAAATATGTTTAATAATATTAAAAATTATATTATTAAGA
1 TATATTATTAAAATAT-TTTAAT-AT-TTAAAAATTAAAATATTAA-A
** *
3450462 TATATTATTTTAATATTTTAATATTTTAAAATTAAAATATTAAA
1 TATATTATTAAAATATTTTAATATTTAAAAATTAAAATATTAAA
*
3450506 TATTTTTATTAATAATA
1 TA-TATTATTAA-AATA
3450523 ATATTTGGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
44 3 0.06
45 22 0.43
46 6 0.12
47 6 0.12
48 14 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (44 bp):
TATATTATTAAAATATTTTAATATTTAAAAATTAAAATATTAAA
Found at i:3450515 original size:45 final size:48
Alignment explanation
Indices: 3450414--3450508 Score: 117
Period size: 45 Copynumber: 2.1 Consensus size: 48
3450404 TACTAAAAAT
** * *
3450414 TATATTATTAAAATATGTTTAATAATATTAAAAATTATATTATTAAGA
1 TATATTATTTTAATATGTTTAATAATATTAAAAATTAAAATATTAAGA
*
3450462 TATATTATTTTAATAT-TTTAAT-AT-TTTAAAATTAAAATATTAA-A
1 TATATTATTTTAATATGTTTAATAATATTAAAAATTAAAATATTAAGA
3450506 TAT
1 TAT
3450509 TTTTATTAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
44 4 0.10
45 16 0.38
46 2 0.05
47 6 0.14
48 14 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (48 bp):
TATATTATTTTAATATGTTTAATAATATTAAAAATTAAAATATTAAGA
Found at i:3451399 original size:42 final size:41
Alignment explanation
Indices: 3451311--3451401 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 41
3451301 ATGAAAAATT
*
3451311 TAATTTTG-AAATAATCTATTTAGTTTATTATCTGATAATC
1 TAATTTTGAAAATAATCTATTTAGTTTATTATCTAATAATC
* *
3451351 TGATTTTGAAAATAATCT-TATTAGTTTTATTATTTAATAATAC
1 TAATTTTGAAAATAATCTAT-TTAG-TTTATTATCTAATAAT-C
3451394 -AATTTTGA
1 TAATTTTGA
3451402 TATAGATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
40 8 0.19
41 13 0.30
42 21 0.49
43 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (41 bp):
TAATTTTGAAAATAATCTATTTAGTTTATTATCTAATAATC
Found at i:3456742 original size:51 final size:51
Alignment explanation
Indices: 3456687--3456785 Score: 164
Period size: 51 Copynumber: 1.9 Consensus size: 51
3456677 GAGTGCCCCC
3456687 GATTGTGAGAAATCAATATTTTAGAAAT-AAGGCCGGGGTTGAAGTATCTTT
1 GATTGTGAGAAATCAATATTTTAGAAATGAA-GCCGGGGTTGAAGTATCTTT
* *
3456738 GATTGTGAGAAATCAATATTTTGGAAATGAAGCCGGGGTTGGAGTATC
1 GATTGTGAGAAATCAATATTTTAGAAATGAAGCCGGGGTTGAAGTATC
3456786 CCCTCAGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 43 0.96
52 2 0.04
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.31
Consensus pattern (51 bp):
GATTGTGAGAAATCAATATTTTAGAAATGAAGCCGGGGTTGAAGTATCTTT
Found at i:3456845 original size:28 final size:28
Alignment explanation
Indices: 3456771--3456847 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
3456761 GAAATGAAGC
*
3456771 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
3456799 CGGGGCTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
3456827 CGGGGTTGGAATATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
3456848 TGTGAAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.98
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:3456935 original size:51 final size:49
Alignment explanation
Indices: 3456827--3456940 Score: 129
Period size: 49 Copynumber: 2.3 Consensus size: 49
3456817 GATGAAATAA
* * * *
3456827 CGGGGTTGGAATATCCCCGATTGTGAAAAATTAGTGTTAAAAATAAAAT
1 CGGGGTTGGAGTATACCCGATTATGAAAAATTAGTGTTAAAAATAAAAC
* * * * *
3456876 CGGAGTTGGAGTATACCCGATTATGGAGAATTGGTGTTTTAGAAATAAAAC
1 CGGGGTTGGAGTATACCCGATTATGAAAAATTAGTG--TTAAAAATAAAAC
3456927 CGGGGTTGGAGTAT
1 CGGGGTTGGAGTAT
3456941 CCCCTCGAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 29 0.55
51 24 0.45
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.29
Consensus pattern (49 bp):
CGGGGTTGGAGTATACCCGATTATGAAAAATTAGTGTTAAAAATAAAAC
Found at i:3457014 original size:79 final size:79
Alignment explanation
Indices: 3456880--3457181 Score: 401
Period size: 79 Copynumber: 3.8 Consensus size: 79
3456870 TAAAATCGGA
* * * * * * *
3456880 GTTGGAGTATACCCGATTATGGAGAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATATTTTAGAAATAAAATCGGAGTTGGAGTATCCCC
3456945 TCGAAAATAACGGG
66 TCGAAAATAACGGG
3456959 GTTGGAGTATCCCCGATTATGAAAAATTGATATTTTAGAAATAAAATCGGAGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATATTTTAGAAATAAAATCGGAGTTGGAGTATCCCC
*
3457024 TCGGAAATAACGGG
66 TCGAAAATAACGGG
* * * *
3457038 GTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAAT-GGGGTTGGAGTGTCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATATTTTAGAAAT-AAAATCGGAGTTGGAGTATCCC
*
3457102 TTC-AGAAATAACGGG
65 CTCGA-AAATAACGGG
* * * * * *
3457117 GTTGGAGTATCCCCGATTGTGAAAAGTCGGTATTTTGGAAATAAAATCGGAGTTAGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATATTTTAGAAATAAAATCGGAGTTGGAGTATCCCC
3457182 GATCATGGAA
Statistics
Matches: 195, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
78 5 0.03
79 185 0.95
80 5 0.03
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (79 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGATATTTTAGAAATAAAATCGGAGTTGGAGTATCCCC
TCGAAAATAACGGG
Found at i:3457111 original size:158 final size:158
Alignment explanation
Indices: 3456880--3457181 Score: 446
Period size: 158 Copynumber: 1.9 Consensus size: 158
3456870 TAAAATCGGA
** * *
3456880 GTTGGAGTATACCCGATTATGGAGAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
1 GTTGGAGTATACCCGATTATGGAGAATTAATATTTTAGAAATAAAAACGGGGTTGGAGTATCCCC
*
3456945 TCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATATTTTAGAAATAAAATCGGA
66 TCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTAGAAATAAAATCGGA
*
3457010 GTTGGAGTATCCCCTCGGAAATAACGGG
131 GTTAGAGTATCCCCTCGGAAATAACGGG
* * *
3457038 GTTGGAGTATCCCCGATTAT-GAGAAATTAATATTTTAGAAATAAAAATGGGGTTGGAGTGTCCC
1 GTTGGAGTATACCCGATTATGGAG-AATTAATATTTTAGAAATAAAAACGGGGTTGGAGTATCCC
* * * * *
3457102 TTC-AGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAGTCGGTATTTTGGAAATAAAATCG
65 CTCGA-AAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTAGAAATAAAATCG
3457166 GAGTTAGAGTATCCCC
129 GAGTTAGAGTATCCCC
3457182 GATCATGGAA
Statistics
Matches: 128, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
157 4 0.03
158 124 0.97
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (158 bp):
GTTGGAGTATACCCGATTATGGAGAATTAATATTTTAGAAATAAAAACGGGGTTGGAGTATCCCC
TCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTAGAAATAAAATCGGA
GTTAGAGTATCCCCTCGGAAATAACGGG
Found at i:3457245 original size:51 final size:51
Alignment explanation
Indices: 3457117--3457296 Score: 202
Period size: 51 Copynumber: 3.5 Consensus size: 51
3457107 AAATAACGGG
* * * *
3457117 GTTGGAGTATCCCCGATTGTGAAAAGTCGGTATTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTGGAAATAAAACCGGA
* * * * *
3457168 GTTAGAGTATCCCCGATCATGGAAAATGGGTGTTTTAGAAATAAAACCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTGGAAATAAAACCGGA
* * * *
3457219 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGAAACCGG-
1 GTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTGGAAATAAAACCGGA
* *
3457269 GATCGGAGTATCCCCGA-GATGAAAAATC
1 G-TTGGAGTATCCCCGATTATGAAAAATC
3457297 TAGAAATTTA
Statistics
Matches: 107, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
50 9 0.08
51 98 0.92
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTGGAAATAAAACCGGA
Found at i:3459601 original size:20 final size:20
Alignment explanation
Indices: 3459576--3459614 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3459566 AAAATGCCTG
* *
3459576 AATGTATTGATACATTGTAA
1 AATGTATCGATACAATGTAA
3459596 AATGTATCGATACAATGTA
1 AATGTATCGATACAATGTA
3459615 TTGATACAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACAATGTAA
Found at i:3459612 original size:13 final size:13
Alignment explanation
Indices: 3459596--3459625 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3459586 TACATTGTAA
3459596 AATGTATCGATAC
1 AATGTATCGATAC
*
3459609 AATGTATTGATAC
1 AATGTATCGATAC
3459622 AATG
1 AATG
3459626 AGCCATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:3459613 original size:33 final size:33
Alignment explanation
Indices: 3459576--3459645 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
3459566 AAAATGCCTG
*
3459576 AATGTATTGATACATTGTA-AAATGTATCGATAC
1 AATGTATTGATACAATG-AGAAATGTATCGATAC
**
3459609 AATGTATTGATACAATGAGCCATGTATCGATAC
1 AATGTATTGATACAATGAGAAATGTATCGATAC
3459642 AATG
1 AATG
3459646 CAAAATGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 1 0.03
33 32 0.97
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (33 bp):
AATGTATTGATACAATGAGAAATGTATCGATAC
Found at i:3459719 original size:13 final size:13
Alignment explanation
Indices: 3459701--3459726 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3459691 ACAAAGATCG
3459701 ATGTATCGATACA
1 ATGTATCGATACA
3459714 ATGTATCGATACA
1 ATGTATCGATACA
3459727 TTGAATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3463376 original size:27 final size:27
Alignment explanation
Indices: 3463338--3463410 Score: 137
Period size: 27 Copynumber: 2.7 Consensus size: 27
3463328 AAGTTTAAAA
3463338 ATGGGGTTGGAGTATCCCCTCGGAGAC
1 ATGGGGTTGGAGTATCCCCTCGGAGAC
3463365 ATGGGGTTGGAGTATCCCCTCGGAGAC
1 ATGGGGTTGGAGTATCCCCTCGGAGAC
*
3463392 ATGGGGTTGGAGTGTCCCC
1 ATGGGGTTGGAGTATCCCC
3463411 GATAATAATA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.16, C:0.22, G:0.38, T:0.23
Consensus pattern (27 bp):
ATGGGGTTGGAGTATCCCCTCGGAGAC
Found at i:3465814 original size:13 final size:13
Alignment explanation
Indices: 3465796--3465821 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3465786 CAGGGTAGCT
3465796 TTGTATCGATACA
1 TTGTATCGATACA
3465809 TTGTATCGATACA
1 TTGTATCGATACA
3465822 ACACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3467737 original size:11 final size:9
Alignment explanation
Indices: 3467711--3467748 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
3467701 TTAAAAATTA
3467711 ATATTTTAT
1 ATATTTTAT
3467720 ATATTTTAT
1 ATATTTTAT
*
3467729 ATATTTTTT
1 ATATTTTAT
3467738 ACT-TTTTAT
1 A-TATTTTAT
3467747 AT
1 AT
3467749 TTCATAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 1 0.04
9 24 0.92
10 1 0.04
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (9 bp):
ATATTTTAT
Found at i:3467761 original size:25 final size:26
Alignment explanation
Indices: 3467714--3467763 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
3467704 AAAATTAATA
* * *
3467714 TTTTATATATTTTATATATTTTTTAC
1 TTTTATATATTTCATAGAATTTTTAC
3467740 TTTT-TATATTTCATAGAATTTTTA
1 TTTTATATATTTCATAGAATTTTTA
3467764 AAATATTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (26 bp):
TTTTATATATTTCATAGAATTTTTAC
Found at i:3468546 original size:55 final size:55
Alignment explanation
Indices: 3468470--3468579 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
3468460 TCCATTTTAA
3468470 ATAATGTATTTTAAAGATTTTGGTCTATATGAAAACTCATGAGTCGATTTAATAC
1 ATAATGTATTTTAAAGATTTTGGTCTATATGAAAACTCATGAGTCGATTTAATAC
3468525 ATAATGTATTTTAAAGATTTTGGTCTATATGAAAACTCATGAGTCGATTTAATAC
1 ATAATGTATTTTAAAGATTTTGGTCTATATGAAAACTCATGAGTCGATTTAATAC
3468580 TCTTACTCGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (55 bp):
ATAATGTATTTTAAAGATTTTGGTCTATATGAAAACTCATGAGTCGATTTAATAC
Found at i:3473143 original size:20 final size:20
Alignment explanation
Indices: 3473118--3473194 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
3473108 GCAAAAGGAT
*
3473118 AGAATGTATAGATACATTGA
1 AGAATGTATCGATACATTGA
*
3473138 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
3473158 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
3473178 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
3473195 CTGGGTACTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:3474014 original size:45 final size:46
Alignment explanation
Indices: 3473894--3474017 Score: 151
Period size: 49 Copynumber: 2.7 Consensus size: 46
3473884 AGATGAGAGG
**
3473894 AGTGCCAATGTGCCAATTCAAGGCCAGCGACATTAGGCTAAGGGAAA
1 AGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGGCTAA-GGAAA
* *
3473941 AGTGGACCAATGTGATGATTCAAGGCCAGCGACATTAGGCTAA-TAAA
1 AGT-G-CCAATGTGCTGATTCAAGGCCAGCGACATTAGGCTAAGGAAA
* * *
3473988 GGTGCCAATATGCTGATTCAATGCCAGCGA
1 AGTGCCAATGTGCTGATTCAAGGCCAGCGA
3474018 TGTTAGACAG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
45 23 0.34
46 1 0.01
47 8 0.12
48 1 0.01
49 34 0.51
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (46 bp):
AGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGGCTAAGGAAA
Found at i:3474248 original size:29 final size:29
Alignment explanation
Indices: 3474079--3474931 Score: 842
Period size: 28 Copynumber: 29.1 Consensus size: 29
3474069 TTTTTTTAAA
* *
3474079 AAAAAAGTGCCACTAACTTGTGTGGGCTTTG
1 AAAAGAGTGCCACTGAC-T-TGTGGGCTTTG
* * *
3474110 AAAAGAGTTACCACCGACTCGTGTGGCCTTTG
1 AAAAGAG-TGCCACTGACT--TGTGGGCTTTG
*
3474142 AAAAGAGTTACCACT-AGCTTGTGGGCTTTG
1 AAAAGAG-TGCCACTGA-CTTGTGGGCTTTG
*
3474172 -AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
3474200 AAAGGA-TGCCACTAATTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
3474228 AAAATAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
3474257 AAATG-GTGCCACTAACTTGCGTGGGCTTTG
1 AAAAGAGTGCCACTGACTT--GTGGGCTTTG
*
3474287 AAAAGAGTGCCACTGACTTGTGGGCTTCG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
3474316 AAAGGA-TGCCACTAACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
3474344 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
3474373 -AAAGGGTGCCACTGACTTGCGTGGGCTTTG
1 AAAAGAGTGCCACTGACTT--GTGGGCTTTG
* * *
3474403 AAAAGA-TACCACTAACTTATGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
3474431 AAAGGA-TGCCACTGACTTGTGGGTTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
3474459 AAAAG-GTGCCACTGACTTATGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
3474487 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
3474516 AAAAGA-TGCCACTAACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
3474544 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
3474573 -AAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * *
3474601 AAAAAAGTGCCACTGATTTATGGGTTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
3474630 -AAAG-GTTGCCACTGACTTGCGTGGGCTTTG
1 AAAAGAG-TGCCACTGACTT--GTGGGCTTTG
* * *
3474660 -AAAGGGTACCACTGACTTGTAGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
3474688 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
**
3474717 AAAAG-GATGCCACTGACTTGTACGCTTTG
1 AAAAGAG-TGCCACTGACTTGTGGGCTTTG
* * * *
3474746 AAATGGGTTGCTACCGACTTGTGTGGGCTTTG
1 AAAAGAG-TGCCACTGAC-T-TGTGGGCTTTG
* * **
3474778 AAATGGGTTGCCACCCACTTGTGTAGGCTTTG
1 AAAAGAG-TGCCACTGACTTGTG--GGCTTTG
* * *
3474810 AAATGGGTTGCCACCGACTTGTGTGGGCTTT-
1 AAAAGAG-TGCCACTGAC-T-TGTGGGCTTTG
* *
3474841 AAAATGGGTTGCCACCGACTTGTGTGGACTTT-
1 AAAA-GAG-TGCCACTGACTTGTG-GG-CTTTG
* * * *
3474873 CAAAGGGTGCCATTGACTTGTGGGCCTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
3474902 -AAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
3474930 AA
1 AA
3474932 GAGATAAACG
Statistics
Matches: 707, Mismatches: 80, Indels: 72
0.82 0.09 0.08
Matches are distributed among these distances:
27 1 0.00
28 263 0.37
29 195 0.28
30 97 0.14
31 36 0.05
32 110 0.16
33 1 0.00
34 4 0.01
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.29
Consensus pattern (29 bp):
AAAAGAGTGCCACTGACTTGTGGGCTTTG
Found at i:3474254 original size:57 final size:57
Alignment explanation
Indices: 3474086--3474931 Score: 819
Period size: 57 Copynumber: 14.4 Consensus size: 57
3474076 AAAAAAAAAG
* * * *
3474086 TGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTACCACCGACTCGTGTGGCCTTTGAAAAGAGT
1 TGCCACTAAC-T-TGTGGGCTTTGAAAAGAG-TGCCACTGACT--TGTGGGCTTTG-AAAG-GA
* * *
3474150 TACCACTAGCTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
3474206 TGCCACTAATTTGTGGGCTTTGAAAATAGTGCCACTGACTTGTGGGCTTTGAAATGG-
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA-GGA
*
3474263 TGCCACTAACTTGCGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTCGAAAGGA
1 TGCCACTAACTT--GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
*
3474322 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * *
3474379 TGCCACTGACTTGCGTGGGCTTTGAAAAGA-TACCACTAACTTATGGGCTTTGAAAGGA
1 TGCCACTAACTT--GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * *
3474437 TGCCACTGACTTGTGGGTTTTGAAAAG-GTGCCACTGACTTATGGGCTTTGAAAAGA
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
3474493 GTGCCACTGACTTGTGGGCTTTGAAAAGA-TGCCACTAACTTGTGGGCTTTGAAAAGA
1 -TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * **
3474550 GTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAAA
1 -TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * * *
3474607 GTGCCACTGATTTATGGGTTTTG-AAAG-GTTGCCACTGACTTGCGTGGGCTTTGAAAGGG
1 -TGCCACTAACTTGTGGGCTTTGAAAAGAG-TGCCACTGACTT--GTGGGCTTTGAAAGGA
* * *
3474666 TACCACTGACTTGTAGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGA
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGA
* ** * * * * *
3474724 TGCCACTGACTTGTACGCTTTGAAATGGGTTGCTACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACTAACTTGTGGGCTTTGAAAAGAG-TGCCACTGAC-T-TGTGGGCTTTGAAA--GGA
** * * * * *
3474786 TGCCACCCACTTGTGTAGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTAAAATGGGT
1 TGCCACTAACTTGTG--GGCTTTGAAAAGAG-TGCCACTGAC-T-TGTGGGCTTTGAAA--GGA
** * * * * *
3474850 TGCCACCGACTTGTGTGGACTTT-CAAAGGGTGCCATTGACTTGTGGGCCTTGAAAGGG
1 TGCCACTAACTTGTG-GG-CTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
3474908 TGCCACTAACTTGTGGGCTTTGAA
1 TGCCACTAACTTGTGGGCTTTGAA
3474932 GAGATAAACG
Statistics
Matches: 687, Mismatches: 69, Indels: 59
0.84 0.08 0.07
Matches are distributed among these distances:
56 68 0.10
57 248 0.36
58 112 0.16
59 105 0.15
60 26 0.04
61 17 0.02
62 33 0.05
63 8 0.01
64 70 0.10
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (57 bp):
TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
Found at i:3477444 original size:13 final size:13
Alignment explanation
Indices: 3477426--3477450 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3477416 ATTACTCAAA
3477426 TGTATCGATACAT
1 TGTATCGATACAT
3477439 TGTATCGATACA
1 TGTATCGATACA
3477451 CCGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3477515 original size:52 final size:52
Alignment explanation
Indices: 3477459--3477579 Score: 206
Period size: 52 Copynumber: 2.3 Consensus size: 52
3477449 CACCGATCTT
*
3477459 TGTATCGATACATGCAGGCAAACTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAACTTGCCCAGATGTATCGATACACTATAAAA
* * *
3477511 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAACTTGCCCAGATGTATCGATACACTATAAAA
3477563 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
3477580 ATAAATTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAACTTGCCCAGATGTATCGATACACTATAAAA
Found at i:3485800 original size:27 final size:27
Alignment explanation
Indices: 3485761--3485814 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3485751 GGCATTTTTT
* * *
3485761 CTTCAAAGTCCACGACTCTGTGGCACC
1 CTTCAAAGCCCACAACTCCGTGGCACC
*
3485788 CTTCTAAGCCCACAACTCCGTGGCACC
1 CTTCAAAGCCCACAACTCCGTGGCACC
3485815 TTTTTCTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.22, C:0.41, G:0.17, T:0.20
Consensus pattern (27 bp):
CTTCAAAGCCCACAACTCCGTGGCACC
Found at i:3485845 original size:34 final size:33
Alignment explanation
Indices: 3485792--3486349 Score: 210
Period size: 34 Copynumber: 17.8 Consensus size: 33
3485782 GGCACCCTTC
**
3485792 TAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
1 TAAGCCCACAACTCCGTGGCACCTTTTTCCGTT
* * *
3485825 TAAAGCCCACAGCTCTGTGGCACTCTTTTCCCGTT
1 T-AAGCCCACAACTCCGTGGCAC-CTTTTTCCGTT
*
3485860 TAAGCCCACAACTCCGTGGCA-C-----CCTTT
1 TAAGCCCACAACTCCGTGGCACCTTTTTCCGTT
* * * * *
3485887 TAAGTCCACAACTCAGTGGCACC-TTCT-CATC
1 TAAGCCCACAACTCCGTGGCACCTTTTTCCGTT
* * * *
3485918 AAAGTCCACAACTTCGTGGCACC--CTT---TT
1 TAAGCCCACAACTCCGTGGCACCTTTTTCCGTT
* ** * * *
3485946 AAAGCCCACAACTTTGTGGCACTCGTTTTCCCTC
1 TAAGCCCACAACTCCGTGGCAC-CTTTTTCCGTT
* * * *
3485980 TAAGCCCACAGCTCCGTGACACTCTTTTCCCATT
1 TAAGCCCACAACTCCGTGGCAC-CTTTTTCCGTT
*
3486014 TAAGCCCACAACTCCGTGGCA-C-----CCTTT
1 TAAGCCCACAACTCCGTGGCACCTTTTTCCGTT
* * * * *
3486041 TAAGTCCACAACTCAGTGGCACC-TTCT-CATC
1 TAAGCCCACAACTCCGTGGCACCTTTTTCCGTT
* * * *
3486072 AAAGTCCACAACTTCGTGGCACC--CTT---TT
1 TAAGCCCACAACTCCGTGGCACCTTTTTCCGTT
* ** *
3486100 AAAGCCCACAACTTTGTGGCACTCGTTTTCC-TT
1 TAAGCCCACAACTCCGTGGCAC-CTTTTTCCGTT
*
3486133 CTAAGCCCACAGCTCCGTGGCA-CTCTTTTCCTGTT
1 -TAAGCCCACAACTCCGTGGCACCT-TTTTCC-GTT
*
3486168 TAAGCCCACAACTCCGTGGCA-C-----CCTTT
1 TAAGCCCACAACTCCGTGGCACCTTTTTCCGTT
* * * * *
3486195 TAAGTCCACAACTCAGTGGCACC-TTCT-CATC
1 TAAGCCCACAACTCCGTGGCACCTTTTTCCGTT
* * * *
3486226 AAAGTCCACAACTTCGTGGCACC--CTT---TT
1 TAAGCCCACAACTCCGTGGCACCTTTTTCCGTT
* ** *
3486254 AAAGCCCACAACTTTGTGGCACTCGTTTTCC-TT
1 TAAGCCCACAACTCCGTGGCAC-CTTTTTCCGTT
* *
3486287 CTAAGCCCACAGCTCCGTGGCACTCTTTTCCCGTT
1 -TAAGCCCACAACTCCGTGGCAC-CTTTTTCCGTT
*
3486322 TAAGCCCACAACTCCGTGGCACCATTTT
1 TAAGCCCACAACTCCGTGGCACCTTTTT
3486350 AAGTCCACAA
Statistics
Matches: 410, Mismatches: 76, Indels: 78
0.73 0.13 0.14
Matches are distributed among these distances:
27 67 0.16
28 68 0.17
29 3 0.01
30 3 0.01
31 72 0.18
32 3 0.01
33 15 0.04
34 166 0.40
35 13 0.03
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.28
Consensus pattern (33 bp):
TAAGCCCACAACTCCGTGGCACCTTTTTCCGTT
Found at i:3485936 original size:58 final size:56
Alignment explanation
Indices: 3485861--3486275 Score: 207
Period size: 58 Copynumber: 6.9 Consensus size: 56
3485851 TTTCCCGTTT
* *
3485861 AAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCAGTGGCACCTTCTCATCA
1 AAGCCCACAACTTCGTGGCACCCTTTTAAGCCCACAACTCAGTGGCACCTT-TC-TCA
* ** *
3485919 AAGTCCACAACTTCGTGGCACCCTTTTAAAGCCCACAACTTTGTGGCACTCGTTTTCCCTCT
1 AAGCCCACAACTTCGTGGCACCCTTTT-AAGCCCACAACTCAGTGGCAC-C--TTT--CTCA
* * * * *
3485981 AAGCCCACAGCTCCGTGACACTCTTTTCCCATTTAAGCCCACAACTCCGTGGCACCCTTT-T--
1 AAGCCCACAACTTCGTGGCA-------CCCTTTTAAGCCCACAACTCAGTGGCA-CCTTTCTCA
* *
3486042 AAGTCCACAAC-TCAGTGGCA-CCTTCTCATCAAAGTCCACAACTTC-GTGGCACCCTTT-T-A
1 AAGCCCACAACTTC-GTGGCACCCTT-T--T--AAGCCCACAAC-TCAGTGGCA-CCTTTCTCA
* * * *
3486101 AAGCCCACAACTTTGTGGCACTCGTTTTCCTTCTAAGCCCACAGCTCCGTGGCACTCTTTTCCTG
1 AAGCCCACAACTTCGTGGCA--C-----CCTTTTAAGCCCACAACTCAGTGGCAC-C-TTT-C--
**
3486166 TTT
54 TCA
* *
3486169 AAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCAGTGGCACCTTCTCATCA
1 AAGCCCACAACTTCGTGGCACCCTTTTAAGCCCACAACTCAGTGGCACCTT-TC-TCA
* **
3486227 AAGTCCACAACTTCGTGGCACCCTTTTAAAGCCCACAACTTTGTGGCAC
1 AAGCCCACAACTTCGTGGCACCCTTTT-AAGCCCACAACTCAGTGGCAC
3486276 TCGTTTTCCT
Statistics
Matches: 277, Mismatches: 39, Indels: 81
0.70 0.10 0.20
Matches are distributed among these distances:
53 3 0.01
54 1 0.00
56 1 0.00
58 74 0.27
59 57 0.21
60 5 0.02
61 41 0.15
62 36 0.13
63 5 0.02
64 1 0.00
66 4 0.01
67 5 0.02
68 37 0.13
69 7 0.03
ACGTcount: A:0.23, C:0.36, G:0.14, T:0.27
Consensus pattern (56 bp):
AAGCCCACAACTTCGTGGCACCCTTTTAAGCCCACAACTCAGTGGCACCTTTCTCA
Found at i:3486016 original size:154 final size:154
Alignment explanation
Indices: 3485735--3486518 Score: 1255
Period size: 154 Copynumber: 5.1 Consensus size: 154
3485725 TACCTTCTTA
* ** * * * *
3485735 AAGTCCACGACTCAGTGGCATTTTTTCTTCAAAGTCCACGAC-TCTGTGGCACCCTTCT-AAGCC
1 AAGTCCACAACTCAGTGGCACCTTCTCATCAAAGTCCACAACTTC-GTGGCACCCTTTTAAAGCC
** * * * *
3485798 CACAACTCCGTGGCAC-CTTTTTCTTTTTAAAGCCCACAGCTCTGTGGCACTCTTTTCCCGTTTA
65 CACAACTTTGTGGCACTCGTTTTCCTTCT-AAGCCCACAGCTCCGTGGCACTCTTTTCCCGTTTA
3485862 AGCCCACAACTCCGTGGCACCCTTTT
129 AGCCCACAACTCCGTGGCACCCTTTT
3485888 AAGTCCACAACTCAGTGGCACCTTCTCATCAAAGTCCACAACTTCGTGGCACCCTTTTAAAGCCC
1 AAGTCCACAACTCAGTGGCACCTTCTCATCAAAGTCCACAACTTCGTGGCACCCTTTTAAAGCCC
* * *
3485953 ACAACTTTGTGGCACTCGTTTTCCCTCTAAGCCCACAGCTCCGTGACACTCTTTTCCCATTTAAG
66 ACAACTTTGTGGCACTCGTTTTCCTTCTAAGCCCACAGCTCCGTGGCACTCTTTTCCCGTTTAAG
3486018 CCCACAACTCCGTGGCACCCTTTT
131 CCCACAACTCCGTGGCACCCTTTT
3486042 AAGTCCACAACTCAGTGGCACCTTCTCATCAAAGTCCACAACTTCGTGGCACCCTTTTAAAGCCC
1 AAGTCCACAACTCAGTGGCACCTTCTCATCAAAGTCCACAACTTCGTGGCACCCTTTTAAAGCCC
*
3486107 ACAACTTTGTGGCACTCGTTTTCCTTCTAAGCCCACAGCTCCGTGGCACTCTTTTCCTGTTTAAG
66 ACAACTTTGTGGCACTCGTTTTCCTTCTAAGCCCACAGCTCCGTGGCACTCTTTTCCCGTTTAAG
3486172 CCCACAACTCCGTGGCACCCTTTT
131 CCCACAACTCCGTGGCACCCTTTT
3486196 AAGTCCACAACTCAGTGGCACCTTCTCATCAAAGTCCACAACTTCGTGGCACCCTTTTAAAGCCC
1 AAGTCCACAACTCAGTGGCACCTTCTCATCAAAGTCCACAACTTCGTGGCACCCTTTTAAAGCCC
3486261 ACAACTTTGTGGCACTCGTTTTCCTTCTAAGCCCACAGCTCCGTGGCACTCTTTTCCCGTTTAAG
66 ACAACTTTGTGGCACTCGTTTTCCTTCTAAGCCCACAGCTCCGTGGCACTCTTTTCCCGTTTAAG
*
3486326 CCCACAACTCCGTGGCACCATTTT
131 CCCACAACTCCGTGGCACCCTTTT
3486350 AAGTCCACAACTCAGTGGCACCTTCTCATCAAAGTCCACAACTTCGTGGCACCCTTTTAAAGCCC
1 AAGTCCACAACTCAGTGGCACCTTCTCATCAAAGTCCACAACTTCGTGGCACCCTTTTAAAGCCC
* * * * *
3486415 ACAACTTTGTGGTACTCATTTTTCTTCTAAGTCCACAACTCCGTGGCA-------CCCGTTTAAG
66 ACAACTTTGTGGCACTCGTTTTCCTTCTAAGCCCACAGCTCCGTGGCACTCTTTTCCCGTTTAAG
3486473 CCCACAACTCCGTGGCACCCTTTT
131 CCCACAACTCCGTGGCACCCTTTT
* *
3486497 AAGTCCACGACTCCGTGGCACC
1 AAGTCCACAACTCAGTGGCACC
3486519 CTTTTTTCCT
Statistics
Matches: 598, Mismatches: 30, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
147 53 0.09
153 48 0.08
154 489 0.82
155 8 0.01
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.28
Consensus pattern (154 bp):
AAGTCCACAACTCAGTGGCACCTTCTCATCAAAGTCCACAACTTCGTGGCACCCTTTTAAAGCCC
ACAACTTTGTGGCACTCGTTTTCCTTCTAAGCCCACAGCTCCGTGGCACTCTTTTCCCGTTTAAG
CCCACAACTCCGTGGCACCCTTTT
Done.