Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014879.1 Kokia drynarioides strain JFW-HI SEQ_129922, whole genome shotgun sequence
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: 283654
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 221 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:3502 original size:21 final size:21
Alignment explanation
Indices: 3478--3520 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3468 AAATGCCTTG
** *
3478 CGTGGCATGACACACGATGTC
1 CGTGGCACAACACACAATGTC
3499 CGTGGCACAACACACAATGTC
1 CGTGGCACAACACACAATGTC
3520 C
1 C
3521 ATATTGCAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.33, G:0.23, T:0.16
Consensus pattern (21 bp):
CGTGGCACAACACACAATGTC
Found at i:3590 original size:21 final size:21
Alignment explanation
Indices: 3533--3593 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
3523 ATTGCAACAC
* *
3533 ACAACCTTGTGTTAAGCCACA
1 ACAACCTTGTGTTGAGCTACA
*
3554 ACAACCCTGTGTTGAGCTACA
1 ACAACCTTGTGTTGAGCTACA
*
3575 ACAACCTTGTGGTGAGCTA
1 ACAACCTTGTGTTGAGCTA
3594 TAGCCTGAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (21 bp):
ACAACCTTGTGTTGAGCTACA
Found at i:17954 original size:23 final size:23
Alignment explanation
Indices: 17922--17969 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
17912 ATTAAGATTG
* *
17922 TTTGGGTTATGTCACTGATGAGT
1 TTTGGATTATGCCACTGATGAGT
17945 TTTGGATTATGCCACTGATGAGT
1 TTTGGATTATGCCACTGATGAGT
17968 TT
1 TT
17970 ATGTAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.19, C:0.10, G:0.27, T:0.44
Consensus pattern (23 bp):
TTTGGATTATGCCACTGATGAGT
Found at i:18770 original size:17 final size:19
Alignment explanation
Indices: 18731--18772 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
18721 ATAATTCTAG
18731 TAAAA-TAACTTCAATTCT
1 TAAAATTAACTTCAATTCT
18749 TAAAATTAACTT-AATT-T
1 TAAAATTAACTTCAATTCT
18766 TAAAATT
1 TAAAATT
18773 CTAAAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.35
18 9 0.39
19 6 0.26
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAAATTAACTTCAATTCT
Found at i:19590 original size:16 final size:16
Alignment explanation
Indices: 19565--19610 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
19555 GGGGAATGTG
19565 TAAA-AAACAT-AAATA
1 TAAATAAACATGAAA-A
19580 TAAATAAACATGAAAA
1 TAAATAAACATGAAAA
*
19596 TAAATAAAGATGAAA
1 TAAATAAACATGAAA
19611 TAAGCATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 4 0.14
16 21 0.75
17 3 0.11
ACGTcount: A:0.70, C:0.04, G:0.07, T:0.20
Consensus pattern (16 bp):
TAAATAAACATGAAAA
Found at i:20041 original size:24 final size:24
Alignment explanation
Indices: 20014--20094 Score: 144
Period size: 24 Copynumber: 3.4 Consensus size: 24
20004 CAAAATGGTA
20014 TGGTGGAACGCAAGCATAGACAGG
1 TGGTGGAACGCAAGCATAGACAGG
*
20038 TGGTGGAACGCAAGCATAGATAGG
1 TGGTGGAACGCAAGCATAGACAGG
20062 TGGTGGAACGCAAGCATAGACAGG
1 TGGTGGAACGCAAGCATAGACAGG
*
20086 TGGTTGAAC
1 TGGTGGAAC
20095 TTGGTCTTAC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.32, C:0.15, G:0.37, T:0.16
Consensus pattern (24 bp):
TGGTGGAACGCAAGCATAGACAGG
Found at i:26860 original size:40 final size:42
Alignment explanation
Indices: 26800--26917 Score: 132
Period size: 47 Copynumber: 2.7 Consensus size: 42
26790 TTAAATTTAA
26800 GGTATAAGACTGGATGTGATGGCTTCAATTT-ACCT-TTTGG
1 GGTATAAGACTGGATGTGATGGCTTCAATTTCACCTATTTGG
* * * * *
26840 GGTATAAGATTGGATATGATGACTTAAATTTTCCCATCTAGATTTGG
1 GGTATAAGACTGGATGTGATGGCTTCAA-TTT--CACCT--ATTTGG
26887 GGTATAAGACTGGATGTGATGGCTTCAATTT
1 GGTATAAGACTGGATGTGATGGCTTCAATTT
26918 GCCCTTTAGT
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
40 24 0.39
41 3 0.05
44 3 0.05
46 3 0.05
47 29 0.47
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.37
Consensus pattern (42 bp):
GGTATAAGACTGGATGTGATGGCTTCAATTTCACCTATTTGG
Found at i:27083 original size:45 final size:45
Alignment explanation
Indices: 26885--27111 Score: 236
Period size: 46 Copynumber: 5.0 Consensus size: 45
26875 ATCTAGATTT
* * *
26885 GGGGTATAAGACTGGATGTGATGGCTTCAATT-TGCCCT-TT-AGTTA
1 GGGGTAAAAGATTGGATG-G-TGGCTTCAATTGT-CCCTCTTGACTTA
* * *
26930 -CGGTAAAAGATTGAATGGTGACTTCAATCTG-CCCTTCTTGACTTA
1 GGGGTAAAAGATTGGATGGTGGCTTCAAT-TGTCCC-TCTTGACTTA
* * *
26975 AGGGTAAAAGATTGGATGGTGGATTCAATATGTCCCTCTTAACTTA
1 GGGGTAAAAGATTGGATGGTGGCTTCAAT-TGTCCCTCTTGACTTA
*
27021 GGGGTAAAAGATTGGATGGTGGCTTCAATTTTCCCCTCTTGAC-TA
1 GGGGTAAAAGATTGGATGGTGGCTTCAATTGT-CCCTCTTGACTTA
27066 GGGGTAAAAGATTGGATGGT--CTTCAAATTGTCCCTCTTGACTTA
1 GGGGTAAAAGATTGGATGGTGGCTTC-AATTGTCCCTCTTGACTTA
27110 GG
1 GG
27112 CCCTCCTAAC
Statistics
Matches: 155, Mismatches: 17, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
42 12 0.08
43 17 0.11
44 24 0.15
45 28 0.18
46 71 0.46
47 3 0.02
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (45 bp):
GGGGTAAAAGATTGGATGGTGGCTTCAATTGTCCCTCTTGACTTA
Found at i:27539 original size:17 final size:18
Alignment explanation
Indices: 27519--27552 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
27509 AAAAAAAGAG
27519 AAAAAAAGG-GAAAAAAA
1 AAAAAAAGGAGAAAAAAA
*
27536 AAAAGAAGGAGAAAAAA
1 AAAAAAAGGAGAAAAAA
27553 GTGAAGAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAAAAGGAGAAAAAAA
Found at i:27549 original size:18 final size:18
Alignment explanation
Indices: 27519--27572 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
27509 AAAAAAAGAG
27519 AAAAA-AAGG-GAAAAAA
1 AAAAAGAAGGAGAAAAAA
27535 AAAAAGAAGGAGAAAAAA
1 AAAAAGAAGGAGAAAAAA
***
27553 GTGAAGAAGGAGGAAAAAA
1 AAAAAGAAGGA-GAAAAAA
27572 A
1 A
27573 GGAAAAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 5 0.16
17 4 0.13
18 15 0.48
19 7 0.23
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (18 bp):
AAAAAGAAGGAGAAAAAA
Found at i:28436 original size:21 final size:23
Alignment explanation
Indices: 28393--28436 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 23
28383 AAAAAATGGT
28393 ATTAATTTAAAAAACATAAAAAG
1 ATTAATTTAAAAAACATAAAAAG
28416 ATTAATTT-AAAAA-ATAAAAAG
1 ATTAATTTAAAAAACATAAAAAG
28437 GGCAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.38
22 5 0.24
23 8 0.38
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (23 bp):
ATTAATTTAAAAAACATAAAAAG
Found at i:28443 original size:21 final size:22
Alignment explanation
Indices: 28396--28451 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
28386 AAATGGTATT
**
28396 AATTTAAAAAACATAAAAAGATT
1 AATTT-AAAAACATAAAAAGAGC
*
28419 AATTTAAAAA-ATAAAAAGGGC
1 AATTTAAAAACATAAAAAGAGC
*
28440 AATTTTAAAACA
1 AATTTAAAAACA
28452 AAACAATGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 17 0.61
22 6 0.21
23 5 0.18
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (22 bp):
AATTTAAAAACATAAAAAGAGC
Found at i:41587 original size:200 final size:200
Alignment explanation
Indices: 41276--42266 Score: 1251
Period size: 200 Copynumber: 5.0 Consensus size: 200
41266 CAATGAAACG
* * *
41276 AGGCTCAAAGCGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGATATTGAGAAGCAAGGCGAAG
1 AGGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGGCGAAG
*
41341 CAATAAAATGGTTAGCTT-CTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGA
66 CAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGA
* * **
41405 TACAAAGAAGTGGATTGAAACAAGTAAGGCATTCATCTTCCTGATGAGATACAGAGAAGAATACC
131 TACAAAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACC
41470 AACTC
196 AACTC
* *
41475 GAGGCACAATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGGCGAA
1 -AGGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGGCGAA
* * * * * * *
41540 GCAATAAAA-GGTTATCTTCCTAATGAGAAACTGAGAAGTGGACCAAATTTGTCTTCTTGATAAG
65 GCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAG
* * * * *
41604 GTATAGAGAAGCGGATTGAAACAAGTAAGGCGGTCATCTTCCTGATGAGATACAGAGAAAAATAC
130 ATACAAAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATAC
41669 CAACTC
195 CAACTC
* * * *
41675 AGGGCTCGATGCGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATATTAAGAAGCAGGTCGAA
1 A-GGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGGCGAA
* *
41740 GCAATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGAATCAAATTCGTCTTCCTGATGAG
65 GCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAG
* * * ** *
41805 ATACAGAGAAGCAGATTGAAACAAGCGATACGGTCACCTTCCTGATGAGATACTGAGAAGAAGAC
130 ATACAAAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATAC--AG-AGAAGA-
* * *
41870 CAAATCAAACCC
191 -ATA-CCAACTC
* * * * *
41882 ACGCTCAATGCGAGCAAATCTTTGAACCCCAGCTTCTTGACGAGATAATGAGAAGCAGGGCGAAG
1 AGGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGGCGAAG
* * * * **
41947 CAATAAAATGTTTAGCTTCCTGATGAGATACTGAGAAGAGGACCGAATTTTTCTTCCTGATGAGA
66 CAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGA
* * *
42012 TACAAAGAAGCGGATTGAAACAAGTGAGGCGGTCATATTCCTGATGAGATACAGAAAAGTATACC
131 TACAAAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACC
42077 AACTC
196 AACTC
* * * *
42082 A--AT-AA---GAACAAATCTTCGACCCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAG
1 AGGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGGCGAAG
* * *
42141 CAATAAAAAGGTTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAATTCGTCTTCCTGATGAAA
66 CAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGA
* * * ** * * * *
42206 CACTAAGAAGTGGATCAAAACAAGTGATGCAGTCATGTTCCTGATGAGATACTGAGAAGAA
131 TACAAAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAA
42267 GGCCAAGTCA
Statistics
Matches: 679, Mismatches: 103, Indels: 24
0.84 0.13 0.03
Matches are distributed among these distances:
194 154 0.23
197 2 0.00
198 1 0.00
199 9 0.01
200 242 0.36
201 93 0.14
203 6 0.01
204 7 0.01
206 159 0.23
207 6 0.01
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (200 bp):
AGGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGGCGAAG
CAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGA
TACAAAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACC
AACTC
Found at i:42229 original size:194 final size:194
Alignment explanation
Indices: 41896--42257 Score: 526
Period size: 194 Copynumber: 1.9 Consensus size: 194
41886 TCAATGCGAG
* * * *
41896 CAAATCTTTGAACCCCAGCTTCTTGACGAGATAATGAGAAGCAGGGCGAAGCAATAAAATGTTTA
1 CAAATCTTCGAACCCCAGCTTCCTGACGAGATAATGAGAAGCAGGGCGAAGCAATAAAAAGGTTA
* * * ** * *
41961 GCTTCCTGATGAGATACTGAGAAGAGGACCGAATTTTTCTTCCTGATGAGATACAAAGAAGCGGA
66 GCTTCCTGATGAGATACGGAGAAGAGAACCAAATTCGTCTTCCTGATGAAACACAAAGAAGCGGA
** *
42026 TTGAAACAAGTGAGGCGGTCATATTCCTGATGAGATACAGAAAAGTATACCAACTCAATAAGAA
131 TCAAAACAAGTGAGGCAGTCATATTCCTGATGAGATACAGAAAAGTATACCAACTCAATAAGAA
* * *
42090 CAAATCTTCGACCCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTA
1 CAAATCTTCGAACCCCAGCTTCCTGACGAGATAATGAGAAGCAGGGCGAAGCAATAAAAAGGTTA
* * *
42155 GCTTCCTGATGAGATACGGAGAAGTGAACCAAATTCGTCTTCCTGATGAAACACTAAGAAGTGGA
66 GCTTCCTGATGAGATACGGAGAAGAGAACCAAATTCGTCTTCCTGATGAAACACAAAGAAGCGGA
* *
42220 TCAAAACAAGTGATGCAGTCATGTTCCTGATGAGATAC
131 TCAAAACAAGTGAGGCAGTCATATTCCTGATGAGATAC
42258 TGAGAAGAAG
Statistics
Matches: 146, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
194 146 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (194 bp):
CAAATCTTCGAACCCCAGCTTCCTGACGAGATAATGAGAAGCAGGGCGAAGCAATAAAAAGGTTA
GCTTCCTGATGAGATACGGAGAAGAGAACCAAATTCGTCTTCCTGATGAAACACAAAGAAGCGGA
TCAAAACAAGTGAGGCAGTCATATTCCTGATGAGATACAGAAAAGTATACCAACTCAATAAGAA
Found at i:42684 original size:7 final size:6
Alignment explanation
Indices: 42644--42710 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
42634 ATTGATTTTG
* **
42644 AATTTA AATTT- ATTTTA AATTTA AATTT- GTTTTAA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
* *
42691 GATTTA TATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AA
42711 ACTTTAAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.14
6 39 0.80
7 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
AATTTA
Found at i:42684 original size:24 final size:24
Alignment explanation
Indices: 42644--42719 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 24
42634 ATTGATTTTG
* *
42644 AATTTAAATTT-ATTTTAAATTTA
1 AATTTATATTTAAATTTAAATTTA
*
42667 AATTTGT-TTTAAAATTTAAATTTA
1 AATTTATATTT-AAATTTAAATTTA
*
42691 GATTTATATTTAAATTTAAAACTTTA
1 AATTTATATTTAAATTT-AAA-TTTA
42717 AAT
1 AAT
42720 ATTGAATGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
22 3 0.07
23 5 0.12
24 22 0.52
25 6 0.14
26 6 0.14
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (24 bp):
AATTTATATTTAAATTTAAATTTA
Found at i:42708 original size:18 final size:18
Alignment explanation
Indices: 42611--42708 Score: 98
Period size: 17 Copynumber: 5.6 Consensus size: 18
42601 TTAAACCCAT
42611 TTTAAGATTTA-TTTTAAGA
1 TTTAA-ATTTAGTTTTAA-A
* *
42630 -TTAAATTGA-TTTTGAA
1 TTTAAATTTAGTTTTAAA
42646 TTTAAATTTA-TTTTAAA
1 TTTAAATTTAGTTTTAAA
42663 TTTAAATTT-GTTTTAAAA
1 TTTAAATTTAGTTTT-AAA
* *
42681 TTTAAATTTAGATTTATA
1 TTTAAATTTAGTTTTAAA
42699 TTTAAATTTA
1 TTTAAATTTA
42709 AAACTTTAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
16 1 0.01
17 36 0.52
18 28 0.41
19 4 0.06
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (18 bp):
TTTAAATTTAGTTTTAAA
Found at i:43363 original size:3 final size:3
Alignment explanation
Indices: 43355--43399 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
43345 TCAAATGTTT
* *
43355 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43400 CTTTTTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:44521 original size:30 final size:29
Alignment explanation
Indices: 44467--44580 Score: 108
Period size: 29 Copynumber: 3.9 Consensus size: 29
44457 AAGGTTCCTA
44467 AACTGTCCAAAAATTACATTTTTACCCTCG
1 AACTGTCCAAAAATTACATTTTTACCC-CG
*
44497 AACT-TCCAAAAATTCCATTTTTTACCCCG
1 AACTGTCCAAAAATTACA-TTTTTACCCCG
** *
44526 AA-TGTCCAAAAATTTTATTTTTATCCCG
1 AACTGTCCAAAAATTACATTTTTACCCCG
** * *
44554 ATTTTTCTAAAAATTAC-TGTTTTACCC
1 AACTGTCCAAAAATTACAT-TTTTACCC
44581 TTGAATGTCT
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
28 13 0.19
29 44 0.63
30 13 0.19
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (29 bp):
AACTGTCCAAAAATTACATTTTTACCCCG
Found at i:46029 original size:22 final size:21
Alignment explanation
Indices: 46003--46049 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
45993 AATTCAAGAG
*
46003 TATAGGGACTGTTTGGAAATTA
1 TATAGGAACTG-TTGGAAATTA
*
46025 TATAGGAATTGTTGGAAATTA
1 TATAGGAACTGTTGGAAATTA
46046 TATA
1 TATA
46050 TATATACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.38
Consensus pattern (21 bp):
TATAGGAACTGTTGGAAATTA
Found at i:46516 original size:34 final size:34
Alignment explanation
Indices: 46478--46546 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
46468 GTTGGGCGTA
*
46478 ACTTTCGTTAGTTAATCTGACTAATGCTGGGCAC
1 ACTTTCGTCAGTTAATCTGACTAATGCTGGGCAC
* * * * *
46512 ACTTTTGTCGGTTTATCTGACTAGTGTTGGGCAC
1 ACTTTCGTCAGTTAATCTGACTAATGCTGGGCAC
46546 A
1 A
46547 AAACCGTTGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (34 bp):
ACTTTCGTCAGTTAATCTGACTAATGCTGGGCAC
Found at i:47858 original size:21 final size:21
Alignment explanation
Indices: 47832--47903 Score: 126
Period size: 21 Copynumber: 3.4 Consensus size: 21
47822 TGTGAATGAG
47832 GGCACACGAGCGTGTGTTTGA
1 GGCACACGAGCGTGTGTTTGA
47853 GGCACACGAGCGTGTGTTTGA
1 GGCACACGAGCGTGTGTTTGA
*
47874 GGCACACGAGCATGTGTTTGA
1 GGCACACGAGCGTGTGTTTGA
*
47895 GACACACGA
1 GGCACACGA
47904 CCATGTGACC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.24, C:0.21, G:0.35, T:0.21
Consensus pattern (21 bp):
GGCACACGAGCGTGTGTTTGA
Found at i:50287 original size:15 final size:15
Alignment explanation
Indices: 50267--50295 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
50257 AATAAACAAA
50267 TAAGAACTCAAAAAT
1 TAAGAACTCAAAAAT
50282 TAAGAACTCAAAAA
1 TAAGAACTCAAAAA
50296 GACAAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.14, G:0.07, T:0.17
Consensus pattern (15 bp):
TAAGAACTCAAAAAT
Found at i:54665 original size:17 final size:16
Alignment explanation
Indices: 54645--54700 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 16
54635 ATTGTCCCTA
54645 CATTATTAATGTCATTG
1 CATT-TTAATGTCATTG
*
54662 CATTTTTATTGTCATTG
1 CA-TTTTAATGTCATTG
*
54679 TA-TTTACATTGTCATTG
1 CATTTTA-A-TGTCATTG
54696 CATTT
1 CATTT
54701 CCATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 4 0.13
17 23 0.74
18 4 0.13
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.54
Consensus pattern (16 bp):
CATTTTAATGTCATTG
Found at i:55266 original size:15 final size:14
Alignment explanation
Indices: 55246--55275 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
55236 TCAGTCACAT
55246 AAAAAGAAAGAAAAA
1 AAAAAGAAA-AAAAA
55261 AAAAAGAAAAAAAA
1 AAAAAGAAAAAAAA
55275 A
1 A
55276 CAATATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAA
Found at i:55270 original size:10 final size:11
Alignment explanation
Indices: 55246--55275 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
55236 TCAGTCACAT
*
55246 AAAAAGAAAGA
1 AAAAAAAAAGA
55257 AAAAAAAAAGA
1 AAAAAAAAAGA
55268 AAAAAAAA
1 AAAAAAAA
55276 CAATATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:55945 original size:37 final size:37
Alignment explanation
Indices: 55865--55956 Score: 91
Period size: 36 Copynumber: 2.5 Consensus size: 37
55855 GCACTTCTAG
* * *
55865 ATTGCACCCTAAG-TTGTCGTCGTATTATTATTTTCGA
1 ATTGCA-CCTAAGAATGTCGTCGTATAAGTATTTTCGA
* *
55902 A-TGCACCTAAGACTGTCGTTGTATAAGTATTCTTC-A
1 ATTGCACCTAAGAATGTCGTCGTATAAGTATT-TTCGA
*
55938 ATTGCACCTAGGAATGTCG
1 ATTGCACCTAAGAATGTCG
55957 CTATATTCAG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
35 6 0.13
36 21 0.46
37 19 0.41
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (37 bp):
ATTGCACCTAAGAATGTCGTCGTATAAGTATTTTCGA
Found at i:55984 original size:13 final size:13
Alignment explanation
Indices: 55966--55990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55956 GCTATATTCA
55966 GTATCAATTTTAC
1 GTATCAATTTTAC
55979 GTATCAATTTTA
1 GTATCAATTTTA
55991 TGCCTAAGGT
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:0.12, G:0.08, T:0.48
Consensus pattern (13 bp):
GTATCAATTTTAC
Found at i:60349 original size:19 final size:19
Alignment explanation
Indices: 60327--60371 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
60317 TTTTATTAGG
60327 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
60346 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
60365 ATTTAAT
1 ATTTAAT
60372 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:63964 original size:12 final size:13
Alignment explanation
Indices: 63927--63964 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
63917 GGCAACCTAA
63927 TTATTTTTATT-T
1 TTATTTTTATTAT
63939 TTATTTTTATTTAT
1 TTATTTTTA-TTAT
63953 TTA-TTTTATTAT
1 TTATTTTTATTAT
63965 ATGTCCAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 13 0.54
13 7 0.29
14 4 0.17
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTATTTTTATTAT
Found at i:65432 original size:19 final size:19
Alignment explanation
Indices: 65410--65454 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
65400 TTTTATTAGG
65410 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
65429 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
65448 ATTTAAT
1 ATTTAAT
65455 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:66289 original size:21 final size:21
Alignment explanation
Indices: 66263--66308 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
66253 TTTTTATTTC
66263 TTTTAATTCTATTTCTTTTAT
1 TTTTAATTCTATTTCTTTTAT
66284 TTTTAATTCTATTTCTTTTAT
1 TTTTAATTCTATTTCTTTTAT
66305 TTTT
1 TTTT
66309 CCTCAGATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTAATTCTATTTCTTTTAT
Found at i:66293 original size:15 final size:15
Alignment explanation
Indices: 66253--66306 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
66243 ACACCTCTAT
66253 TTTTTATTTCTTTTA
1 TTTTTATTTCTTTTA
* *
66268 ATTCTATTTCTTTTA
1 TTTTTATTTCTTTTA
*
66283 TTTTTAATTCTATTT-
1 TTTTTATTTCT-TTTA
*
66298 CTTTTATTT
1 TTTTTATTT
66307 TTCCTCAGAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
15 28 0.90
16 3 0.10
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTATTTCTTTTA
Found at i:69885 original size:27 final size:27
Alignment explanation
Indices: 69854--69908 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
69844 AAAAATAAAG
*
69854 TAAATTTTTTTAACTTTTAAGCCAAAA
1 TAAATCTTTTTAACTTTTAAGCCAAAA
69881 TAAATCTTTTTAACTTTTAAGCCAAAA
1 TAAATCTTTTTAACTTTTAAGCCAAAA
69908 T
1 T
69909 TTTCATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.44
Consensus pattern (27 bp):
TAAATCTTTTTAACTTTTAAGCCAAAA
Found at i:70350 original size:18 final size:19
Alignment explanation
Indices: 70304--70350 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
70294 ATCAAGTAAG
70304 TTATTAAAAAATATAAAAAT
1 TTATTAAAAAATAT-AAAAT
* **
70324 ATAGAAAAAAATAT-AAAT
1 TTATTAAAAAATATAAAAT
70342 TTATTAAAA
1 TTATTAAAA
70351 TTGGTAGAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
TTATTAAAAAATATAAAAT
Found at i:70578 original size:18 final size:20
Alignment explanation
Indices: 70541--70586 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
70531 TTATTAATAA
*
70541 TATAAAATAATTAAATTTAT
1 TATAAAATAATTAAAATTAT
70561 TATAAAAT-A-TAAAATTAT
1 TATAAAATAATTAAAATTAT
*
70579 AATAAAAT
1 TATAAAAT
70587 CATATAATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 15 0.62
19 1 0.04
20 8 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TATAAAATAATTAAAATTAT
Found at i:71503 original size:25 final size:25
Alignment explanation
Indices: 71470--71535 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 25
71460 ATTTTTATCA
*
71470 ATTTTTATATTTTAAA-ACTTTTCT
1 ATTTTTATATTTTAAATACATTTCT
71494 ATTTTTTATAAATTTTAAATACATTTCT
1 A-TTTTTAT--ATTTTAAATACATTTCT
*
71522 ATTTCTATATTTTA
1 ATTTTTATATTTTA
71536 TATTTTTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
24 1 0.03
25 13 0.36
27 14 0.39
28 8 0.22
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTTTTATATTTTAAATACATTTCT
Found at i:71509 original size:18 final size:17
Alignment explanation
Indices: 71461--71509 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
71451 TTTATAATAA
*
71461 TTTTTATCAATTTTTAT
1 TTTTTATAAATTTTTAT
*
71478 ATTTTA-AAACTTTTCTAT
1 TTTTTATAAA-TTTT-TAT
71496 TTTTTATAAATTTT
1 TTTTTATAAATTTT
71510 AAATACATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 2 0.08
17 9 0.35
18 12 0.46
19 3 0.12
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTATAAATTTTTAT
Found at i:72632 original size:16 final size:17
Alignment explanation
Indices: 72611--72645 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
72601 TTAAAAATGT
*
72611 TATTTAATTTTAAA-AA
1 TATTTAATATTAAATAA
72627 TATTTAATATTAAATAA
1 TATTTAATATTAAATAA
72644 TA
1 TA
72646 CAAAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTTAATATTAAATAA
Found at i:72979 original size:23 final size:23
Alignment explanation
Indices: 72953--73017 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 23
72943 AATAACTTCT
*
72953 TTAAAATAAAGTATAAA-AAATTA
1 TTAAAATAAAGT-TAAAGAAAATA
*
72976 TT-AAACAAAGTTAAAGAAAATA
1 TTAAAATAAAGTTAAAGAAAATA
*
72998 TATAAAAT-AATTTAAAGAAA
1 T-TAAAATAAAGTTAAAGAAA
73018 GTGAAAATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 4 0.11
22 14 0.40
23 14 0.40
24 3 0.09
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.28
Consensus pattern (23 bp):
TTAAAATAAAGTTAAAGAAAATA
Found at i:90965 original size:9 final size:9
Alignment explanation
Indices: 90951--91065 Score: 58
Period size: 9 Copynumber: 12.6 Consensus size: 9
90941 ACATGTGAGA
90951 AAAAATTAT
1 AAAAATTAT
90960 AAAAATTATT
1 AAAAATTA-T
**
90970 AAATTTTAAT
1 AAAAATT-AT
**
90980 AAAAAAGAT
1 AAAAATTAT
90989 AAAAA-TATT
1 AAAAATTA-T
90998 AAAAATTTAT
1 AAAAA-TTAT
*
91008 TAAAA--AT
1 AAAAATTAT
*
91015 AAAAATCAT
1 AAAAATTAT
91024 AAAAA-TAT
1 AAAAATTAT
* *
91032 AAAAAACTGT
1 -AAAAATTAT
*
91042 AAAATTTTAT
1 AAAA-ATTAT
*
91052 AAAAATCAT
1 AAAAATTAT
91061 AAAAA
1 AAAAA
91066 AAAACCTTTA
Statistics
Matches: 80, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
7 6 0.08
8 3 0.04
9 45 0.56
10 23 0.29
11 3 0.04
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:91006 original size:29 final size:29
Alignment explanation
Indices: 90958--91013 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
90948 AGAAAAAATT
*
90958 ATAAAAATTATTAAATTTTAATAAAAAAG
1 ATAAAAATTATTAAAATTTAATAAAAAAG
*
90987 ATAAAAA-TATTAAAAATTTATTAAAAA
1 ATAAAAATTATT-AAAATTTAATAAAAA
91014 TAAAAATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (29 bp):
ATAAAAATTATTAAAATTTAATAAAAAAG
Found at i:95157 original size:25 final size:26
Alignment explanation
Indices: 95129--95199 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 26
95119 TTTTCATCCT
95129 AATTTTACCCTAGTAAAATTTTGA-G
1 AATTTTACCCTAGTAAAATTTTGACG
** *
95154 AATTTTATTCTGGTAAAATTTTGACG
1 AATTTTACCCTAGTAAAATTTTGACG
* *
95180 -ATTTTACCTTAGTAACATTT
1 AATTTTACCCTAGTAAAATTT
95200 CTAAAAAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
25 36 0.97
26 1 0.03
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (26 bp):
AATTTTACCCTAGTAAAATTTTGACG
Found at i:98275 original size:47 final size:47
Alignment explanation
Indices: 98214--98471 Score: 248
Period size: 47 Copynumber: 5.5 Consensus size: 47
98204 CATAATGACG
* *
98214 CGAGCCTTGTGCCTAGCAGGCTTTAATGTCGGTGTATTGTACCGTAT
1 CGAGCCTTGGGCCTAGCAGGCTTTAATGTCGGTGTACTGTACCGTAT
* * * * *
98261 CGAGCCTCGGGCCTAGTAGGCTTTAATGTCGGTGTATTCTATCGTAT
1 CGAGCCTTGGGCCTAGCAGGCTTTAATGTCGGTGTACTGTACCGTAT
* *
98308 CGGGCCTTAGGCCTAGCAGGCTTTAATG-CTGGTGTACTGTACCGTAT
1 CGAGCCTTGGGCCTAGCAGGCTTTAATGTC-GGTGTACTGTACCGTAT
* * * * * * * * *
98355 TGGGCCTCGAGCCTAGCAAGCTTTAATGTCAGTTTACTATATCGTAT
1 CGAGCCTTGGGCCTAGCAGGCTTTAATGTCGGTGTACTGTACCGTAT
* ** * * *
98402 CGAGCCTTAGGCCTAGCAGGCTTTAATACCGATGTACTGTACCATAA
1 CGAGCCTTGGGCCTAGCAGGCTTTAATGTCGGTGTACTGTACCGTAT
* * **
98449 AGGGCCTTTTGCCTAGCAGGCTT
1 CGAGCCTTGGGCCTAGCAGGCTT
98472 CGTGCCGGTG
Statistics
Matches: 169, Mismatches: 40, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
46 1 0.01
47 167 0.99
48 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (47 bp):
CGAGCCTTGGGCCTAGCAGGCTTTAATGTCGGTGTACTGTACCGTAT
Found at i:98454 original size:94 final size:94
Alignment explanation
Indices: 98214--98455 Score: 306
Period size: 94 Copynumber: 2.6 Consensus size: 94
98204 CATAATGACG
* * * * * *
98214 CGAGCCTT-GTGCCTAGCAGGCTTTAATGTCGGTGTATTGTACCGTATCGAGCCTCGGGCCTAGT
1 CGAGCCTTAG-GCCTAGCAGGCTTTAATGCCGGTGTACTGTACCGTATAGGGCCTCGAGCCTAGC
* * * *
98278 AGGCTTTAATGTCGGTGTATTCTATCGTAT
65 AAGCTTTAATGTCAGTGTACTATATCGTAT
* * *
98308 CGGGCCTTAGGCCTAGCAGGCTTTAATGCTGGTGTACTGTACCGTATTGGGCCTCGAGCCTAGCA
1 CGAGCCTTAGGCCTAGCAGGCTTTAATGCCGGTGTACTGTACCGTATAGGGCCTCGAGCCTAGCA
*
98373 AGCTTTAATGTCAGTTTACTATATCGTAT
66 AGCTTTAATGTCAGTGTACTATATCGTAT
* * * *
98402 CGAGCCTTAGGCCTAGCAGGCTTTAATACCGATGTACTGTACCATAAAGGGCCT
1 CGAGCCTTAGGCCTAGCAGGCTTTAATGCCGGTGTACTGTACCGTATAGGGCCT
98456 TTTGCCTAGC
Statistics
Matches: 127, Mismatches: 20, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
94 126 0.99
95 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (94 bp):
CGAGCCTTAGGCCTAGCAGGCTTTAATGCCGGTGTACTGTACCGTATAGGGCCTCGAGCCTAGCA
AGCTTTAATGTCAGTGTACTATATCGTAT
Found at i:98513 original size:40 final size:40
Alignment explanation
Indices: 98458--98564 Score: 160
Period size: 40 Copynumber: 2.7 Consensus size: 40
98448 AAGGGCCTTT
*
98458 TGCCTAGCAGGCTTCGTGCCGGTGTATCTATCAGGCTCAA
1 TGCCTAGCAAGCTTCGTGCCGGTGTATCTATCAGGCTCAA
* * *
98498 TGCCTAACAAGCTTCGTGTCAGTGTATCTATCAGGCTCAA
1 TGCCTAGCAAGCTTCGTGCCGGTGTATCTATCAGGCTCAA
* *
98538 TGCCTAGCAAGCTTCGCGCTGGTGTAT
1 TGCCTAGCAAGCTTCGTGCCGGTGTAT
98565 TTAACGGGCT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.29
Consensus pattern (40 bp):
TGCCTAGCAAGCTTCGTGCCGGTGTATCTATCAGGCTCAA
Found at i:102800 original size:18 final size:19
Alignment explanation
Indices: 102743--102790 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
102733 GACCTGACCT
* *
102743 ATTGACTTTGATCGTTGACC
1 ATTGACTTTGA-CTTTAACC
*
102763 GTTGACTTTGACTTTAACC
1 ATTGACTTTGACTTTAACC
102782 ATTGACTTT
1 ATTGACTTT
102791 TCTTTTACCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.44
Consensus pattern (19 bp):
ATTGACTTTGACTTTAACC
Found at i:112887 original size:23 final size:23
Alignment explanation
Indices: 112843--112887 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
112833 GGAACAGAAT
* **
112843 TGAACACTGCCATAGCTGATAAC
1 TGAACACTGCCAAAGCAAATAAC
112866 TGAACACTGCCAAAGCAAATAA
1 TGAACACTGCCAAAGCAAATAA
112888 ACAGAGAGCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (23 bp):
TGAACACTGCCAAAGCAAATAAC
Found at i:113832 original size:22 final size:22
Alignment explanation
Indices: 113782--113834 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
113772 CAGAGGACAT
* *
113782 CGAAATGCTAAACAGTAAGCAC
1 CGAAGTGCAAAACAGTAAGCAC
*
113804 CGAAGTGCAAAACAGTAGGCAC
1 CGAAGTGCAAAACAGTAAGCAC
*
113826 CGTAGTGCA
1 CGAAGTGCA
113835 TTCACGTAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.13
Consensus pattern (22 bp):
CGAAGTGCAAAACAGTAAGCAC
Found at i:114556 original size:30 final size:30
Alignment explanation
Indices: 114482--114541 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
114472 GTACAAAGAT
114482 TAAAAATTTATGTATCATACTTATTATAAA
1 TAAAAATTTATGTATCATACTTATTATAAA
114512 TAAAAATTTATGTATCATACTTATTATAAA
1 TAAAAATTTATGTATCATACTTATTATAAA
114542 AGAATCATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (30 bp):
TAAAAATTTATGTATCATACTTATTATAAA
Found at i:116954 original size:3 final size:3
Alignment explanation
Indices: 116946--116976 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
116936 AAAGACCCAA
116946 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
116977 GGGTTTCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:117664 original size:51 final size:50
Alignment explanation
Indices: 117608--117823 Score: 146
Period size: 50 Copynumber: 4.3 Consensus size: 50
117598 TAAAAAGGAG
117608 AGTTTATATTTTTAAAAATAAAAATCACT-TTTTTAGTTATTTTAAAGAAAA
1 AGTTTATATTTTTAAAAATAAAAAT-A-TGTTTTTAGTTATTTTAAAGAAAA
* * ** *
117659 AGTTTA-ATTTTT--AAATAAAATTTTGATTTTTTTAACTATTTCAAA-ATAAA
1 AGTTTATATTTTTAAAAATAAAA--AT-ATGTTTTTAGTTATTTTAAAGA-AAA
* * * * ***
117709 AGTTTGTATTTTT--AAGT-AAAGTAGTGATTTTCA-TTA-AAAAAAGAAAGAA
1 AGTTTATATTTTTAAAAATAAAAATA-TG-TTTTTAGTTATTTTAAAG-AA-AA
*
117758 AATTTATATTTTTAAAAATAAAAATATGTTTTTAGTTATTTTAAAGAAAA
1 AGTTTATATTTTTAAAAATAAAAATATGTTTTTAGTTATTTTAAAGAAAA
*
117808 AGTTTAAATTTTTAAA
1 AGTTTATATTTTTAAA
117824 TAAAATTTTG
Statistics
Matches: 126, Mismatches: 24, Indels: 31
0.70 0.13 0.17
Matches are distributed among these distances:
47 4 0.03
48 13 0.10
49 21 0.17
50 54 0.43
51 25 0.20
52 9 0.07
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (50 bp):
AGTTTATATTTTTAAAAATAAAAATATGTTTTTAGTTATTTTAAAGAAAA
Found at i:117850 original size:52 final size:49
Alignment explanation
Indices: 117645--117890 Score: 144
Period size: 51 Copynumber: 4.9 Consensus size: 49
117635 CTTTTTTAGT
117645 TATTTTAAAGAAAAAGTTT-AATTTTTAAATAAAATTTTGATTTTTTTAAC
1 TATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAATTTTGA--TTTTTAAC
* ** * * ** * *
117695 TATTTCAAA-ATAAAAGTTTGTATTTTTAAGTAAAGTAGTGA-TTTTCAT
1 TATTTTAAAGA-AAAAGTTTAAATTTTTAAATAAAATTTTGATTTTTAAC
*** * * * * **
117743 TA-AAAAAAGAAAGAAAATTTATATTTTTAAAAATAAAAATATG-TTTTTAGT
1 TATTTTAAAG-AA-AAAGTTTAAATTTTT--AAATAAAATTTTGATTTTTAAC
117794 TATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAATTTTGATTCTTTTACAC
1 TATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAATTTTGA-T-TTTTA-AC
* * * **
117846 TATTTCGAAA-AAAAAGTTTAGATTTTTAAGTAAAATAATGATTTT
1 TATTT-TAAAGAAAAAGTTTAAATTTTTAAATAAAATTTTGATTTT
117891 CATTAAAAAA
Statistics
Matches: 148, Mismatches: 34, Indels: 28
0.70 0.16 0.13
Matches are distributed among these distances:
47 3 0.02
48 19 0.13
49 15 0.10
50 33 0.22
51 39 0.26
52 36 0.24
53 3 0.02
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (49 bp):
TATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAATTTTGATTTTTAAC
Found at i:118262 original size:4 final size:4
Alignment explanation
Indices: 118253--118303 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
118243 GTGCCCCAAT
* * * *
118253 TTCA TTCA TTCA TTTA TTCA TTCA TTCG TTCA TTCG TTCA TTTA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
118301 TTC
1 TTC
118304 GCTCATTTGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.20, C:0.22, G:0.04, T:0.55
Consensus pattern (4 bp):
TTCA
Found at i:118300 original size:16 final size:16
Alignment explanation
Indices: 118257--118310 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
118247 CCCAATTTCA
* *
118257 TTCATTCATTTATTCA
1 TTCATTCATTCATTCG
*
118273 TTCATTCGTTCATTCG
1 TTCATTCATTCATTCG
*
118289 TTCATTTATTCATTCG
1 TTCATTCATTCATTCG
*
118305 CTCATT
1 TTCATT
118311 TGTTTATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.19, C:0.22, G:0.06, T:0.54
Consensus pattern (16 bp):
TTCATTCATTCATTCG
Found at i:118309 original size:8 final size:8
Alignment explanation
Indices: 118257--118310 Score: 54
Period size: 8 Copynumber: 6.8 Consensus size: 8
118247 CCCAATTTCA
*
118257 TTCATTCA
1 TTCATTCG
* *
118265 TTTATTCA
1 TTCATTCG
118273 TTCATTCG
1 TTCATTCG
118281 TTCATTCG
1 TTCATTCG
**
118289 TTCATTTA
1 TTCATTCG
118297 TTCATTCG
1 TTCATTCG
*
118305 CTCATT
1 TTCATT
118311 TGTTTATTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.19, C:0.22, G:0.06, T:0.54
Consensus pattern (8 bp):
TTCATTCG
Found at i:127338 original size:27 final size:27
Alignment explanation
Indices: 127308--127363 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
127298 GACGGTGGAG
127308 ATTCAATGATATCTATAATATCTCTTA
1 ATTCAATGATATCTATAATATCTCTTA
127335 ATTCAATGATATCTATAATATCTCTTA
1 ATTCAATGATATCTATAATATCTCTTA
127362 AT
1 AT
127364 CTAAGGAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.45
Consensus pattern (27 bp):
ATTCAATGATATCTATAATATCTCTTA
Found at i:127375 original size:27 final size:27
Alignment explanation
Indices: 127308--127376 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
127298 GACGGTGGAG
* *
127308 ATTCAATGATATCTATAATATCTCTTA
1 ATTCAAGGAGATCTATAATATCTCTTA
* *
127335 ATTCAATGATATCTATAATATCTCTTA
1 ATTCAAGGAGATCTATAATATCTCTTA
127362 A-TCTAAGGAGATCTA
1 ATTC-AAGGAGATCTA
127377 GTCAAACATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 2 0.05
27 37 0.95
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (27 bp):
ATTCAAGGAGATCTATAATATCTCTTA
Found at i:132238 original size:9 final size:8
Alignment explanation
Indices: 132212--132254 Score: 59
Period size: 8 Copynumber: 5.1 Consensus size: 8
132202 TGTTTAAATC
132212 AAGAAAAA
1 AAGAAAAA
*
132220 AATACAAAA
1 AAGA-AAAA
132229 AAGAATAAA
1 AAGAA-AAA
132238 AAGAAAAA
1 AAGAAAAA
132246 AAGAAAAA
1 AAGAAAAA
132254 A
1 A
132255 TATATAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 16 0.52
9 15 0.48
ACGTcount: A:0.84, C:0.02, G:0.09, T:0.05
Consensus pattern (8 bp):
AAGAAAAA
Found at i:132238 original size:17 final size:17
Alignment explanation
Indices: 132216--132256 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
132206 TAAATCAAGA
*
132216 AAAAAATA-CAAAAAAG
1 AAAAAATAGAAAAAAAG
132232 AATAAAA-AGAAAAAAAG
1 AA-AAAATAGAAAAAAAG
132249 AAAAAATA
1 AAAAAATA
132257 TATAGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.83, C:0.02, G:0.07, T:0.07
Consensus pattern (17 bp):
AAAAAATAGAAAAAAAG
Found at i:132256 original size:21 final size:22
Alignment explanation
Indices: 132227--132268 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
132217 AAAAATACAA
132227 AAAAGAATAAAAAGAAAAAAAG
1 AAAAGAATAAAAAGAAAAAAAG
* *
132249 AAAA-AATATATAGAAAAAAA
1 AAAAGAATAAAAAGAAAAAAA
132269 TAGAAAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (22 bp):
AAAAGAATAAAAAGAAAAAAAG
Found at i:132744 original size:42 final size:42
Alignment explanation
Indices: 132676--132840 Score: 206
Period size: 42 Copynumber: 3.9 Consensus size: 42
132666 AAGGAAAGCA
*
132676 TTCATTGAATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * * *
132718 TTCATTGCATTTAGAGGTCTAGGTGTGGA-GACTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTC-CATTTACTT
*
132760 TTCATTGCATTTAGAGGTCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * * * * *
132802 TTTATTACATTTAGACGCCTAGGTGTAGAGGTCCATTTA
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTA
132841 TTCATTTTTT
Statistics
Matches: 106, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
41 2 0.02
42 102 0.96
43 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
Found at i:132840 original size:84 final size:84
Alignment explanation
Indices: 132676--132831 Score: 249
Period size: 84 Copynumber: 1.9 Consensus size: 84
132666 AAGGAAAGCA
* * *
132676 TTCATTGAATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGTCTAGG
1 TTCATTGAATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTACATTTAGACGCCTAGG
*
132741 TGTGGAGACTCATTTACTT
66 TGTAGAGACTCATTTACTT
* * *
132760 TTCATTGCATTTAGAGGTCCAAGTGTGGAGGTCCATTTACTTTTTATTACATTTAGACGCCTAGG
1 TTCATTGAATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTACATTTAGACGCCTAGG
132825 TGTAGAG
66 TGTAGAG
132832 GTCCATTTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 65 1.00
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.38
Consensus pattern (84 bp):
TTCATTGAATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTACATTTAGACGCCTAGG
TGTAGAGACTCATTTACTT
Found at i:133264 original size:11 final size:11
Alignment explanation
Indices: 133242--133273 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
133232 GAGATCGTTA
133242 TTTCTCTTTTCT
1 TTTCT-TTTTCT
133254 TTTCTTTTTCT
1 TTTCTTTTTCT
133265 TTTCTTTTT
1 TTTCTTTTT
133274 TGGGCTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:133302 original size:3 final size:3
Alignment explanation
Indices: 133294--133327 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
133284 AAAGACCCAA
133294 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
133328 GGGTTTCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:133886 original size:19 final size:21
Alignment explanation
Indices: 133864--133910 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 21
133854 TAAAAATCTG
133864 ATTTTTTTAAA-AAAG-TTTA
1 ATTTTTTTAAACAAAGTTTTA
*
133883 A-TTTTTTAAACAAAGTTTTG
1 ATTTTTTTAAACAAAGTTTTA
133903 ATTTTTTT
1 ATTTTTTT
133911 TAACTATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 9 0.38
19 5 0.21
20 4 0.17
21 6 0.25
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.57
Consensus pattern (21 bp):
ATTTTTTTAAACAAAGTTTTA
Found at i:134041 original size:149 final size:146
Alignment explanation
Indices: 133873--134386 Score: 640
Period size: 149 Copynumber: 3.5 Consensus size: 146
133863 GATTTTTTTA
* *
133873 AAAAAGTTTAATTTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGAT
1 AAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAATTTAGAT
133938 TTTTAAG-AAAGTAGTGATTTTCAATAAAAAAGGAGAAAGTTTATATTTTTAAAAATAAATATCT
66 TTTTAAGTAAAGTAGTGATTTTCAATAAAAAA--AGAAAGTTTATATTTTTAAAAATAAA-ATCT
134002 ATTTTTTAGTTATTTTAAAG
128 A-TTTTTAGTTATTTTAAAG
* * *
134022 AAAAAGTTTAAATTTTTAAATAAGGTTTTGATTTTTTTTAACTATTTCGAAATAAAAATTTAAAT
1 AAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAATTTAGAT
*
134087 TTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAGAAAGTTTATA-TTTT--AAA-AAAA---A--
66 TTTTAAGTAAAGTAGTGATTTTCAATAAAAAAAGAAAGTTTATATTTTTAAAAATAAAATCTATT
134143 -TTAGTTATTTTAAAG
131 TTTAGTTATTTTAAAG
* *
134158 AAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTTATCTATTTCGAAATAAAAATTTAGA
1 AAAAAGTTTAAATTTTTAAACAAAGTTTTGA-TTTTTTTTAACTATTTCGAAATAAAAATTTAGA
* * *
134223 TTTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAAAAAGAAAATTTAGATTTTTAAAAAATAAAA
65 TTTTTAAGTAAAGTAGTGATTTTC----AATAAAAAAAGAAAGTTTATATTTTT-AAAAAT-AAA
* *
134288 ATCTGTTTTTAGTGATTTTAAAG
124 ATCTATTTTTAGTTATTTTAAAG
* ** * * *
134311 TGAAAAGTTTAAATTTTTAAACAAAACTTT-AATTTTTTAAACTATTTCAAAATAAAAATTTTA-
1 -AAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAA-TTTAG
*
134374 ATTTTGAAGTAAA
64 ATTTTTAAGTAAA
134387 ATAATGTTTT
Statistics
Matches: 321, Mismatches: 24, Indels: 37
0.84 0.06 0.10
Matches are distributed among these distances:
136 45 0.14
137 55 0.17
140 1 0.00
141 17 0.05
142 4 0.01
143 1 0.00
144 3 0.01
145 6 0.02
147 8 0.02
148 12 0.04
149 67 0.21
150 23 0.07
152 35 0.11
153 19 0.06
154 25 0.08
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.43
Consensus pattern (146 bp):
AAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAATTTAGAT
TTTTAAGTAAAGTAGTGATTTTCAATAAAAAAAGAAAGTTTATATTTTTAAAAATAAAATCTATT
TTTAGTTATTTTAAAG
Found at i:134254 original size:136 final size:136
Alignment explanation
Indices: 134007--134261 Score: 465
Period size: 137 Copynumber: 1.9 Consensus size: 136
133997 TATCTATTTT
*
134007 TTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAATAAGGTTTTGATTTTTTTTAACTATTTCGA
1 TTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGA
134072 AATAAAAATTTAAATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAGAAAGTTTATATTTTAA
66 AATAAAAATTTAAATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAGAAAGTTTATATTTTAA
134137 AAAAAA
131 AAAAAA
*
134143 TTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTTATCTATTTCG
1 TTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTTTTGA-TTTTTTTTAACTATTTCG
* *
134208 AAATAAAAATTTAGATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAAAAAG
65 AAATAAAAATTTAAATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAGAAAG
134262 AAAATTTAGA
Statistics
Matches: 114, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
136 45 0.39
137 69 0.61
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (136 bp):
TTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGA
AATAAAAATTTAAATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAGAAAGTTTATATTTTAA
AAAAAA
Found at i:134341 original size:20 final size:20
Alignment explanation
Indices: 134313--134352 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
134303 TTTTAAAGTG
*
134313 AAAAGTTTAAATTTTTAAAC
1 AAAACTTTAAATTTTTAAAC
*
134333 AAAACTTTAATTTTTTAAAC
1 AAAACTTTAAATTTTTAAAC
134353 TATTTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAACTTTAAATTTTTAAAC
Found at i:134430 original size:289 final size:285
Alignment explanation
Indices: 133873--134431 Score: 748
Period size: 289 Copynumber: 1.9 Consensus size: 285
133863 GATTTTTTTA
* *
133873 AAAAAGTTTAATTTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGAT
1 AAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAATTTAGAT
* ** * * *
133938 TTTTAAGAAAGTAGTGATTTTCAATAAAAAAGGAGAAAGTTTATATTTTTAAAAATAAATATCTA
66 TTTTAAGAAAGTAGTGATTTTCAAAAAAAAAAAAGAAAATTTAGATTTTTAAAAATAAAAATCTA
* * * *** * *
134003 TTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAATAAGGTTTTGATTTTTTTTAACTATT
131 GTTTTTAGTGATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAACTTTGAATTTTTTAAACTATT
* * * * * *
134068 TCGAAATAAAAATTTAAATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAGAAAGTTTATATT
196 TCAAAATAAAAATTTAAATTTTGAAGTAAAATAATGATTTTCATTAAAAAAAGAAACTTTAGATT
*
134133 TTAAAAAAAATTAGTTATTTTAAAG
261 TAAAAAAAAATTAGTTATTTTAAAG
* *
134158 AAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTTATCTATTTCGAAATAAAAATTTAGA
1 AAAAAGTTTAAATTTTTAAACAAAGTTTTGA-TTTTTTTTAACTATTTCGAAATAAAAATTTAGA
134223 TTTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAAAAAGAAAATTTAGATTTTTAAAAAATAAAA
65 TTTTTAAG-AAAGTAGTGATTTTCA--AAAAAAAAAAAGAAAATTTAGATTTTT-AAAAATAAAA
*
134288 ATCT-GTTTTTAGTGATTTTAAAGTGAAAAGTTTAAATTTTTAAACAAAACTTT-AATTTTTTAA
126 ATCTAGTTTTTAGTGATTTTAAAG-AAAAAGTTTAAATTTTTAAACAAAACTTTGAATTTTTTAA
* * *
134351 ACTATTTCAAAATAAAAATTTTAATTTTGAAGTAAAATAATG-TTTT-TTTAATCAAAAGAAAAC
190 ACTATTTCAAAATAAAAATTTAAATTTTGAAGTAAAATAATGATTTTCATTAA-AAAAAG-AAAC
*
134414 TTTCGATTTAAAAAAAAA
253 TTTAGATTTAAAAAAAAA
134432 ATAAAAATTT
Statistics
Matches: 236, Mismatches: 30, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
285 29 0.12
286 39 0.17
287 20 0.08
288 9 0.04
289 102 0.43
290 37 0.16
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (285 bp):
AAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAATTTAGAT
TTTTAAGAAAGTAGTGATTTTCAAAAAAAAAAAAGAAAATTTAGATTTTTAAAAATAAAAATCTA
GTTTTTAGTGATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAACTTTGAATTTTTTAAACTATT
TCAAAATAAAAATTTAAATTTTGAAGTAAAATAATGATTTTCATTAAAAAAAGAAACTTTAGATT
TAAAAAAAAATTAGTTATTTTAAAG
Found at i:135834 original size:242 final size:238
Alignment explanation
Indices: 135413--135892 Score: 699
Period size: 242 Copynumber: 2.0 Consensus size: 238
135403 AAAATCATAA
135413 TAATGATAAAAGATCGAATAAGTTGTAGATAAATTTTAATATTTCTCTTAATTCATTAGTAACTT
1 TAATGATAAAAGATCGAATAAGTTGTAGATAAATTTTAATATTTCTCTTAATTCATTAGTAACTT
* * *
135478 TTAGGTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAATAATTGAAGGCATTTTACTAGAATT
66 TTAGGTTTTTTTTAGGATTCTAAAATAAAATTAATTTTAAGAATTGAAAGCATTTTACTAGAATT
* * * * *
135543 ATTTAAGTATCTTTTAGGATTCTCGTTAGAATTAAAAATCTCTAATTTAAGTTTTAAATTAAATA
131 ACTTAAGTATCCTTTAGGATTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAAGTAAATA
*
135608 ACTTTGGCGAACACATTTTAGTCAAGTTACAAGTAAATCGGAG
196 ACTTTGGCGAACACATCTTAGTCAAGTTACAAGTAAATCGGAG
*
135651 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAATTT
1 TAATGATAAAAGATCGAATAAGTTGTAGATAAATTTTAATATTTCTCTTAATTCATTAGTAA---
* * **
135716 TTTTTTAGGTTTTTTTTAGTATTCTAAAATAAAATTAATTTTAAGAATTGAAATTATTTTACTAG
63 -CTTTTAGGTTTTTTTTAGGATTCTAAAATAAAATTAATTTTAAGAATTGAAAGCATTTTACTAG
* * * * *
135781 AATTACTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATTTCTAATTTAAGTTTTAAAGTA
127 AATTACTTAAGTATCCTTTAGGATTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAAGTA
* * * ** *
135846 GATAAGTTTGGTGAACATGTCTTAGTCAAGTTACAAGTAAATTGGAG
192 AATAACTTTGGCGAACACATCTTAGTCAAGTTACAAGTAAATCGGAG
135893 GCATTTTTTA
Statistics
Matches: 213, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
238 61 0.29
242 152 0.71
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.42
Consensus pattern (238 bp):
TAATGATAAAAGATCGAATAAGTTGTAGATAAATTTTAATATTTCTCTTAATTCATTAGTAACTT
TTAGGTTTTTTTTAGGATTCTAAAATAAAATTAATTTTAAGAATTGAAAGCATTTTACTAGAATT
ACTTAAGTATCCTTTAGGATTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAAGTAAATA
ACTTTGGCGAACACATCTTAGTCAAGTTACAAGTAAATCGGAG
Found at i:136907 original size:22 final size:22
Alignment explanation
Indices: 136882--136923 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
136872 GAATACACAA
* *
136882 CAAAATCAAGGCAAATCATACT
1 CAAAATCAAGCCAAACCATACT
136904 CAAAATCAAGCCAAACCATA
1 CAAAATCAAGCCAAACCATA
136924 GTTATGCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.26, G:0.07, T:0.14
Consensus pattern (22 bp):
CAAAATCAAGCCAAACCATACT
Found at i:137375 original size:26 final size:26
Alignment explanation
Indices: 137341--137405 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
137331 AATAAATTTA
*
137341 GCTCATACGAGCTCAGT-CAGTAAATT
1 GCTCTTACGAGC-CAGTACAGTAAATT
**
137367 GCTCTTACGAGCCAGTACAGTATGTT
1 GCTCTTACGAGCCAGTACAGTAAATT
137393 GCTCTTACGAGCC
1 GCTCTTACGAGCC
137406 TATATCGCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
25 4 0.11
26 31 0.89
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28
Consensus pattern (26 bp):
GCTCTTACGAGCCAGTACAGTAAATT
Found at i:137470 original size:19 final size:19
Alignment explanation
Indices: 137446--137532 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
137436 ACAGTATGTT
137446 GCTCTTACGAGCCTA-TATC
1 GCTCTTACGAGCC-AGTATC
*
137465 GCTCTTACGAGCCAGTATT
1 GCTCTTACGAGCCAGTATC
* *
137484 GCTCTTATGAGCAAGTATC
1 GCTCTTACGAGCCAGTATC
* *
137503 ACTCCTACGAGCCAGTATC
1 GCTCTTACGAGCCAGTATC
137522 GCTCTTACGAG
1 GCTCTTACGAG
137533 ACAACTAAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
18 1 0.02
19 56 0.98
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (19 bp):
GCTCTTACGAGCCAGTATC
Found at i:141439 original size:24 final size:24
Alignment explanation
Indices: 141411--141513 Score: 116
Period size: 24 Copynumber: 4.1 Consensus size: 24
141401 GTATAATGGT
*
141411 TAACCTATTTGGGCTCGTAAGAGC
1 TAACCTATCTGGGCTCGTAAGAGC
* *
141435 TAACCCTTTTTTCTGGTCTCGTAAGAGC
1 TAA-CC---TATCTGGGCTCGTAAGAGC
141463 TAACCTATCTGGGCTCGTAAGAGC
1 TAACCTATCTGGGCTCGTAAGAGC
* * *
141487 TAACCTATCCGGCCTCATAAGAGC
1 TAACCTATCTGGGCTCGTAAGAGC
141511 TAA
1 TAA
141514 ATTTGTCTGG
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
24 44 0.66
25 2 0.03
27 2 0.03
28 19 0.28
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (24 bp):
TAACCTATCTGGGCTCGTAAGAGC
Found at i:142706 original size:16 final size:16
Alignment explanation
Indices: 142687--142721 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
142677 TAGTAATTTT
142687 AATGTTAAAG-GACTAA
1 AATGTTAAAGTGA-TAA
142703 AATGTTAAAGTGATAA
1 AATGTTAAAGTGATAA
142719 AAT
1 AAT
142722 TACGAGGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.51, C:0.03, G:0.17, T:0.29
Consensus pattern (16 bp):
AATGTTAAAGTGATAA
Found at i:143761 original size:47 final size:47
Alignment explanation
Indices: 143710--143819 Score: 148
Period size: 47 Copynumber: 2.3 Consensus size: 47
143700 GCCTTGTGCT
* * ** *
143710 TAGCAGGCTTTAATGTTGGTGTACTATACTGTATTGGGCCTCGGGCC
1 TAGCAGGCTTTAATGTTGGTATACTATACCGTATTGAACCTCAGGCC
* * *
143757 TAGCAGGCTTTAATGCTGGTATGCTGTACCGTATTGAACCTCAGGCC
1 TAGCAGGCTTTAATGTTGGTATACTATACCGTATTGAACCTCAGGCC
143804 TAGCAGGCTTTAATGT
1 TAGCAGGCTTTAATGT
143820 CGACTTATTG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (47 bp):
TAGCAGGCTTTAATGTTGGTATACTATACCGTATTGAACCTCAGGCC
Found at i:143959 original size:40 final size:40
Alignment explanation
Indices: 143898--144000 Score: 127
Period size: 40 Copynumber: 2.6 Consensus size: 40
143888 GCCTTGTGCT
* *
143898 TAGCAGGCTTCGTGCTGGTGTATTTATCGGGCTCAATGCC
1 TAGCAGGCTTCGTGCTGGTGTATCTATCAGGCTCAATGCC
* *
143938 TAGCAGGCTTCGTGCCT-GTGTATCTATCAGGCTTAATGCT
1 TAGCAGGCTTCGTG-CTGGTGTATCTATCAGGCTCAATGCC
* **
143978 TAACAGGCTTCGCACTGGTGTAT
1 TAGCAGGCTTCGTGCTGGTGTAT
144001 TTAATGAGCT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.04
40 50 0.93
41 2 0.04
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.33
Consensus pattern (40 bp):
TAGCAGGCTTCGTGCTGGTGTATCTATCAGGCTCAATGCC
Found at i:148193 original size:182 final size:182
Alignment explanation
Indices: 147879--148222 Score: 546
Period size: 182 Copynumber: 1.9 Consensus size: 182
147869 CATTCGTCGT
* * *
147879 TTTATCCGACTAGTGCTGGGCGCAAAATCGTTGGTTAATCCAACTAGAGATGGGCTCATTTTTGC
1 TTTATCCGACTAGCGCTGGGCGCAAAACCGTTGGTTAATCCAACTAGAGATGGGCTCATTATTGC
* * *
147944 GGTTTATCTGCTAGGCACTAGGTGCCAAGAATTGACAGACTTTGTTGATTAATCCAACTAGAGCT
66 GGTTTACCCGCTAGACACTAGGTGCCAAGAATTGACAGACTTTGTTGATTAATCCAACTAGAGCT
* *
148009 GGGCTCACTTCT-GCGGTTTATCCGCTAGGCACTAGGTGTCATGATCATCGG
131 GGGCTCACTTATCACGGTTTATCCGCTAGGCACTAGGTGTCATGATCATCGG
*
148060 TTTATCCGACTAGCGCTGGGCGCAAAACCGTTGGTTAATCCAACTAGAGTTGGGCTCACTTATTG
1 TTTATCCGACTAGCGCTGGGCGCAAAACCGTTGGTTAATCCAACTAGAGATGGGCTCA-TTATTG
* * ** *
148125 CGGTTTACCCGCTAGACATTGGGTGCCAAGAATTGATGGACTTTGTTGGTTAATCCAACTAGAGC
65 CGGTTTACCCGCTAGACACTAGGTGCCAAGAATTGACAGACTTTGTTGATTAATCCAACTAGAGC
148190 TGGGCTCACTTATCACGGTTTATCCGCTAGGCA
130 TGGGCTCACTTATCACGGTTTATCCGCTAGGCA
148223 TCGGGTGTCA
Statistics
Matches: 147, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
181 55 0.37
182 74 0.50
183 18 0.12
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (182 bp):
TTTATCCGACTAGCGCTGGGCGCAAAACCGTTGGTTAATCCAACTAGAGATGGGCTCATTATTGC
GGTTTACCCGCTAGACACTAGGTGCCAAGAATTGACAGACTTTGTTGATTAATCCAACTAGAGCT
GGGCTCACTTATCACGGTTTATCCGCTAGGCACTAGGTGTCATGATCATCGG
Found at i:148229 original size:80 final size:80
Alignment explanation
Indices: 148089--148240 Score: 232
Period size: 80 Copynumber: 1.9 Consensus size: 80
148079 GCGCAAAACC
* ** *
148089 GTTGGTTAATCCAACTAGAGTTGGGCTCACTTATTGCGGTTTACCCGCTAGACATTGGGTGCCAA
1 GTTGGTTAATCCAACTAGAGCTGGGCTCACTTATCACGGTTTACCCGCTAGACATCGGGTGCCAA
148154 GAATTGATGGACTTT
66 GAATTGATGGACTTT
* * *
148169 GTTGGTTAATCCAACTAGAGCTGGGCTCACTTATCACGGTTTATCCGCTAGGCATCGGGTGTCAA
1 GTTGGTTAATCCAACTAGAGCTGGGCTCACTTATCACGGTTTACCCGCTAGACATCGGGTGCCAA
*
148234 GATTTGA
66 GAATTGA
148241 CGGGATTTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 64 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (80 bp):
GTTGGTTAATCCAACTAGAGCTGGGCTCACTTATCACGGTTTACCCGCTAGACATCGGGTGCCAA
GAATTGATGGACTTT
Found at i:149686 original size:2 final size:2
Alignment explanation
Indices: 149679--149703 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
149669 TGACATGATT
149679 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
149704 TAATTTTCTC
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:150818 original size:20 final size:20
Alignment explanation
Indices: 150793--150834 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
150783 AACACACGTC
*
150793 TTTCTTTC-TTCTTCTTCTTG
1 TTTCTTTCATT-TCCTTCTTG
150813 TTTCTTTCATTTCCTTCTTG
1 TTTCTTTCATTTCCTTCTTG
150833 TT
1 TT
150835 GTCGCTGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.02, C:0.24, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTCTTTCATTTCCTTCTTG
Found at i:159662 original size:17 final size:19
Alignment explanation
Indices: 159631--159671 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
159621 TATTTATTTT
*
159631 TAATATATTATAAATTACA
1 TAATATATTATAAATAACA
159650 TAATATA-TA-AAATAACA
1 TAATATATTATAAATAACA
159667 TAATA
1 TAATA
159672 AAAATATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.57
18 2 0.10
19 7 0.33
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAATATATTATAAATAACA
Found at i:166061 original size:19 final size:15
Alignment explanation
Indices: 166018--166046 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
166008 TTGTCCTGTA
166018 AATTCAAATCCAACT
1 AATTCAAATCCAACT
166033 AATTCAAATCCAAC
1 AATTCAAATCCAAC
166047 CAATAACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (15 bp):
AATTCAAATCCAACT
Found at i:167854 original size:15 final size:15
Alignment explanation
Indices: 167834--167886 Score: 97
Period size: 15 Copynumber: 3.5 Consensus size: 15
167824 CCCTCCATTA
167834 CTCCTTCCATTTCCT
1 CTCCTTCCATTTCCT
167849 CTCCTTCCATTTCCT
1 CTCCTTCCATTTCCT
167864 CTCCTTCCATTTCCT
1 CTCCTTCCATTTCCT
*
167879 CTTCTTCC
1 CTCCTTCC
167887 CACTACTTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.06, C:0.47, G:0.00, T:0.47
Consensus pattern (15 bp):
CTCCTTCCATTTCCT
Found at i:168400 original size:13 final size:13
Alignment explanation
Indices: 168382--168406 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
168372 TGAGCTATTT
168382 TTGGTTATACCAG
1 TTGGTTATACCAG
168395 TTGGTTATACCA
1 TTGGTTATACCA
168407 AACTAGACAG
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:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGGTTATACCAG
Found at i:169493 original size:20 final size:20
Alignment explanation
Indices: 169470--169517 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
169460 GCCAAAGATT
*
169470 ACAAACATTGGTCAAAAATA
1 ACAAACATTGGTAAAAAATA
**
169490 ACAAATGTTGGTAAAAAATA
1 ACAAACATTGGTAAAAAATA
*
169510 GCAAACAT
1 ACAAACAT
169518 CAATAAAAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.21
Consensus pattern (20 bp):
ACAAACATTGGTAAAAAATA
Found at i:179840 original size:44 final size:44
Alignment explanation
Indices: 179777--179865 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
179767 AAAATTTTTT
179777 TTGGGGGACCGGAATTGAATTCTATATTTTTACAATAATACAAA
1 TTGGGGGACCGGAATTGAATTCTATATTTTTACAATAATACAAA
*
179821 TTGGGGGACCGGAATTGAATTGTATATTTTTACAATAATACAAA
1 TTGGGGGACCGGAATTGAATTCTATATTTTTACAATAATACAAA
179865 T
1 T
179866 GCAATTTCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (44 bp):
TTGGGGGACCGGAATTGAATTCTATATTTTTACAATAATACAAA
Found at i:186459 original size:14 final size:15
Alignment explanation
Indices: 186439--186523 Score: 56
Period size: 15 Copynumber: 5.9 Consensus size: 15
186429 ATATCACAAT
*
186439 AATAATAATAACTAAAA
1 AATAATAATAA--AATA
186456 AATAA-AATAAAATA
1 AATAATAATAAAATA
*
186470 AATAATAAT--GAT-
1 AATAATAATAAAATA
*
186482 AATAA-AATAAAACA
1 AATAATAATAAAATA
**
186496 ACGAATAATAAAATA
1 AATAATAATAAAATA
186511 ACATAA-AATAAAA
1 A-ATAATAATAAAA
186524 ATACAAATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
11 3 0.06
12 5 0.09
13 3 0.06
14 11 0.21
15 19 0.36
16 7 0.13
17 5 0.09
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (15 bp):
AATAATAATAAAATA
Found at i:186459 original size:17 final size:16
Alignment explanation
Indices: 186439--186491 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
186429 ATATCACAAT
186439 AATAATAATAACTAAAA
1 AATAATAATAA-TAAAA
*
186456 AATAA-AATAA-AATA
1 AATAATAATAATAAAA
*
186470 AATAATAATGATAATAA
1 AATAATAATAATAA-AA
186487 AATAA
1 AATAA
186492 AACAACGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 8 0.27
15 4 0.13
16 7 0.23
17 11 0.37
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (16 bp):
AATAATAATAATAAAA
Found at i:186464 original size:5 final size:5
Alignment explanation
Indices: 186454--186533 Score: 58
Period size: 5 Copynumber: 15.4 Consensus size: 5
186444 TAATAACTAA
* *
186454 AAAAT AAAAT AAAAT -AAAT AATAAT GATAAT AAAAT AAAAC AACGAAT
1 AAAAT AAAAT AAAAT AAAAT AA-AAT -AAAAT AAAAT AAAAT AA--AAT
*
186502 --AAT AAAAT AACAT AAAAT AAAAAT ACAAAT AA
1 AAAAT AAAAT AAAAT AAAAT -AAAAT A-AAAT AA
186534 TTAATACATA
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
3 3 0.05
4 4 0.07
5 34 0.57
6 16 0.27
7 3 0.05
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:186470 original size:30 final size:30
Alignment explanation
Indices: 186436--186539 Score: 97
Period size: 31 Copynumber: 3.3 Consensus size: 30
186426 GTAATATCAC
186436 AATAATAATAATAACTAAAAAATAAAATAA
1 AATAATAATAATAACTAAAAAATAAAATAA
* *
186466 AATAAATAATAATGA-TAATAAAATAAAACAA
1 AAT-AATAATAATAACTAA-AAAATAAAATAA
*
186497 CGAATAATAA-AATAAC-ATAAAATAAAAATACA
1 --AATAATAATAATAACTAAAAAAT-AAAATA-A
186529 AATAATTAATA
1 AATAA-TAATA
186540 CATATAAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
30 16 0.27
31 34 0.57
32 7 0.12
33 3 0.05
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (30 bp):
AATAATAATAATAACTAAAAAATAAAATAA
Found at i:186490 original size:26 final size:24
Alignment explanation
Indices: 186436--186526 Score: 85
Period size: 26 Copynumber: 3.6 Consensus size: 24
186426 GTAATATCAC
*
186436 AATAATAATAATAACTAA-AAAATAA
1 AATAA-AATAA-AAATAATAAAATAA
*
186461 AATAAAATAAATAATAATGATAATAA
1 AATAAAATAAA-AATAAT-AAAATAA
* *
186487 AATAAAACAACGAATAATAAAATAA
1 AATAAAATAA-AAATAATAAAATAA
*
186512 CATAAAATAAAAATA
1 AATAAAATAAAAATA
186527 CAAATAATTA
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
23 1 0.02
24 13 0.24
25 19 0.35
26 21 0.39
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (24 bp):
AATAAAATAAAAATAATAAAATAA
Found at i:186505 original size:3 final size:3
Alignment explanation
Indices: 186415--186491 Score: 58
Period size: 3 Copynumber: 26.7 Consensus size: 3
186405 GAAATGAGCA
* *
186415 AAT AAT AAT AAGT AAT -AT CAC AAT AAT AAT AAT AACT AA- AA- AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
186459 AA- AAT AA- AAT AAAT AAT AAT GAT AAT AA- AAT AA
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA
186492 AACAACGAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
2 12 0.20
3 40 0.66
4 9 0.15
ACGTcount: A:0.68, C:0.04, G:0.03, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:186548 original size:30 final size:30
Alignment explanation
Indices: 186436--186534 Score: 80
Period size: 30 Copynumber: 3.2 Consensus size: 30
186426 GTAATATCAC
* *
186436 AATAATAATAATAACTAAAAAATAAAA-TA-A
1 AATAATAA-AATAAC-ATAAAATAAAACAACA
*
186466 AATAAATAATAATGATA-ATAAAATAAAACAACG
1 AAT-AATAA-AAT-A-ACATAAAATAAAACAACA
186499 AATAATAAAATAACATAAAATAAAA-ATACA
1 AATAATAAAATAACATAAAATAAAACA-ACA
186529 AATAAT
1 AATAAT
186535 TAATACATAT
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
29 2 0.03
30 23 0.40
31 22 0.38
32 7 0.12
33 4 0.07
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (30 bp):
AATAATAAAATAACATAAAATAAAACAACA
Found at i:187330 original size:75 final size:74
Alignment explanation
Indices: 187170--187337 Score: 210
Period size: 75 Copynumber: 2.2 Consensus size: 74
187160 CCTATATGTC
* * *
187170 CAGGCCGTGTGCCACTTCGAATTAAAACAAAATTATTGCCTAGTGGTCACACGGTCTGGCACATG
1 CAGGCCGTGTACCACTTCGAATTAAAACAAAAATATTACCTAGTGGTCACACGGTCTGGCACATG
**
187235 CTTGTGTGT
66 CCCGTGTGT
* * * * * *
187244 CTAGGCTGTGTATCATTTCGAATTAAAATAAAAATATTACCTTGTGGTCACATGGTCTGGCACAT
1 C-AGGCCGTGTACCACTTCGAATTAAAACAAAAATATTACCTAGTGGTCACACGGTCTGGCACAT
187309 GCCCGTGTGTT
65 GCCCGTGTG-T
*
187320 CAGGCCGTGTACCTCTTC
1 CAGGCCGTGTACCACTTC
187338 AAAAGTCATT
Statistics
Matches: 77, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
74 1 0.01
75 74 0.96
76 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (74 bp):
CAGGCCGTGTACCACTTCGAATTAAAACAAAAATATTACCTAGTGGTCACACGGTCTGGCACATG
CCCGTGTGT
Found at i:191875 original size:42 final size:42
Alignment explanation
Indices: 191809--191931 Score: 165
Period size: 42 Copynumber: 2.9 Consensus size: 42
191799 ATTTTCAAAG
* * * * *
191809 CCATGAAATGATGCTTGTTAATTTTTCACAGTTGTCTCGAGA
1 CCATGAATTGATGCTTGCTGATTTTTCAAAGTTGTCTCAAGA
*
191851 CCATGAATTGATGCTTGCTGATTTTTCAAAGTTGTCTCAAGG
1 CCATGAATTGATGCTTGCTGATTTTTCAAAGTTGTCTCAAGA
* * *
191893 TCATGAATTGATGCTTGCTGATTTTTAAAAGCTGTCTCA
1 CCATGAATTGATGCTTGCTGATTTTTCAAAGTTGTCTCA
191932 TTGTTTTGAA
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (42 bp):
CCATGAATTGATGCTTGCTGATTTTTCAAAGTTGTCTCAAGA
Found at i:193234 original size:14 final size:14
Alignment explanation
Indices: 193215--193246 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
193205 CATAAACAAA
*
193215 TAAAATGGAAAAAT
1 TAAAATAGAAAAAT
193229 TAAAATAGAAAAAT
1 TAAAATAGAAAAAT
193243 TAAA
1 TAAA
193247 TTAAAAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (14 bp):
TAAAATAGAAAAAT
Found at i:197059 original size:22 final size:21
Alignment explanation
Indices: 197010--197059 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
197000 AATAATTTTT
*
197010 TATTT-TTATATATTTTTAAA
1 TATTTATTATATATTTTGAAA
*
197030 TTTATTATTATATATTTTGAATA
1 TAT-TTATTATATATTTTGAA-A
197053 TATTTAT
1 TATTTAT
197060 ATGTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 2 0.08
21 2 0.08
22 17 0.71
23 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTATTATATATTTTGAAA
Found at i:197061 original size:19 final size:20
Alignment explanation
Indices: 197013--197066 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
197003 AATTTTTTAT
*
197013 TTTTATATATTTTTAAATTTA
1 TTTTATATA-TTTTAAATATA
*
197034 TTATTATATATTTTGAATATA
1 TT-TTATATATTTTAAATATA
*
197055 -TTTATATGTTTT
1 TTTTATATATTTT
197067 TTTTATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 10 0.34
20 1 0.03
21 11 0.38
22 7 0.24
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTTATATATTTTAAATATA
Found at i:197850 original size:18 final size:17
Alignment explanation
Indices: 197827--197869 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
197817 GAATAAATTT
*
197827 TTAATTAAATATTTTTAA
1 TTAATTAAA-ATTTTAAA
197845 TTAATTGAAAATTTTAAA
1 TTAATT-AAAATTTTAAA
*
197863 TTTATTA
1 TTAATTA
197870 CAACTGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 18 0.82
19 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TTAATTAAAATTTTAAA
Found at i:198357 original size:24 final size:26
Alignment explanation
Indices: 198330--198386 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
198320 AAATGGGTTG
198330 TACAGAAAAT-TAAAATTTTA-AAAA
1 TACAGAAAATATAAAATTTTATAAAA
*
198354 TACA-AAAATATTAAATTTTATAAAA
1 TACAGAAAATATAAAATTTTATAAAA
*
198379 GA-AGAAAA
1 TACAGAAAA
198387 CACATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 5 0.18
24 14 0.50
25 9 0.32
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (26 bp):
TACAGAAAATATAAAATTTTATAAAA
Found at i:199184 original size:52 final size:51
Alignment explanation
Indices: 199101--199336 Score: 296
Period size: 52 Copynumber: 4.5 Consensus size: 51
199091 ATGTAAAAAT
*
199101 GTTCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGAGTATGAG
1 GTTCCATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGA-TATGAG
*
199153 GTTCCATGACTACATGTCATCGTGAGTATATGAATCCTTTACGGATAATGAG
1 GTTCCATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGAT-ATGAG
* *
199205 G-TCCGATGACTACGTGTCATCGTGATTATATGAATCCCTTACGGATTATGAG
1 GTTCC-ATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGA-TATGAG
* * * * * *
199257 GTTCGATGACTACGTGTCATTGTGAGTATGTGAATCCTTTATGGATTGTGAA
1 GTTCCATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGA-TATGAG
* *
199309 G-TCCGATGACCATGTGTCATCGTGAGTA
1 GTTCC-ATGACTACGTGTCATCGTGAGTA
199337 CTAAATAAAA
Statistics
Matches: 162, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
51 6 0.04
52 153 0.94
53 3 0.02
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (51 bp):
GTTCCATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATATGAG
Found at i:199284 original size:104 final size:104
Alignment explanation
Indices: 199104--199336 Score: 349
Period size: 104 Copynumber: 2.2 Consensus size: 104
199094 TAAAAATGTT
*
199104 CGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGAGTATGAGGTTCCATGACTACATG
1 CGATGACTACGTGTCATCGTGAGTATATGAATCCCTTACGGAGTATGAGGTTCCATGACTACATG
*
199169 TCATCGTGAGTATATGAATCCTTTACGGATAATGAGGTC
66 TCATCGTGAGTATATGAATCCTTTACGGATAATGAAGTC
* * * *
199208 CGATGACTACGTGTCATCGTGATTATATGAATCCCTTACGGATTATGAGGTTCGATGACTACGTG
1 CGATGACTACGTGTCATCGTGAGTATATGAATCCCTTACGGAGTATGAGGTTCCATGACTACATG
* * * **
199273 TCATTGTGAGTATGTGAATCCTTTATGGATTGTGAAGTC
66 TCATCGTGAGTATATGAATCCTTTACGGATAATGAAGTC
* *
199312 CGATGACCATGTGTCATCGTGAGTA
1 CGATGACTACGTGTCATCGTGAGTA
199337 CTAAATAAAA
Statistics
Matches: 115, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
104 115 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (104 bp):
CGATGACTACGTGTCATCGTGAGTATATGAATCCCTTACGGAGTATGAGGTTCCATGACTACATG
TCATCGTGAGTATATGAATCCTTTACGGATAATGAAGTC
Found at i:203310 original size:13 final size:12
Alignment explanation
Indices: 203292--203325 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
203282 AAGGATCACG
203292 CATAGAGACTTA
1 CATAGAGACTTA
203304 TCATAGAGAACTTA
1 -CATAGAG-ACTTA
203318 CATAGAGA
1 CATAGAGA
203326 GTTTTCTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.05
13 14 0.70
14 5 0.25
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.24
Consensus pattern (12 bp):
CATAGAGACTTA
Found at i:208217 original size:16 final size:16
Alignment explanation
Indices: 208196--208229 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
208186 TAAGTAAACC
208196 AATTTTCACCACTAAG
1 AATTTTCACCACTAAG
*
208212 AATTTTTACCACTAAG
1 AATTTTCACCACTAAG
208228 AA
1 AA
208230 AATTGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.32
Consensus pattern (16 bp):
AATTTTCACCACTAAG
Found at i:212815 original size:22 final size:22
Alignment explanation
Indices: 212790--212831 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
212780 AAATTATGAT
212790 AATTTAAGAGAGAATTGAGAAA
1 AATTTAAGAGAGAATTGAGAAA
* *
212812 AATTTGAGAGAGATTTGAGA
1 AATTTAAGAGAGAATTGAGA
212832 GTGTGAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (22 bp):
AATTTAAGAGAGAATTGAGAAA
Found at i:213045 original size:69 final size:68
Alignment explanation
Indices: 212917--213149 Score: 322
Period size: 69 Copynumber: 3.4 Consensus size: 68
212907 GGGGTGGGGG
* * * ** *
212917 GTCCAATGGCTAATTAAATAGTCGTTGGAGAAAGTAGTCGTTAGTTATTGTTAGGGGAAAACACT
1 GTCCAACGGCTAATTAAATAGCCGTTGGAGAAAGTAGTCTTTAGTTACCGTT-GGGGAAAACGCT
212982 TGGA
65 TGGA
* *
212986 GTCCAACGGCTAATTAAATAGCCGTTGGAGAAAGTAGTTTTTATTTACCGTTGGAGGAAAACGCT
1 GTCCAACGGCTAATTAAATAGCCGTTGGAGAAAGTAGTCTTTAGTTACCGTTGG-GGAAAACGCT
213051 TGGA
65 TGGA
* * *
213055 GTCCAACGACAAATTAAATAGCCGTTGGAGAAAGTAGTCTTTAGTTACCGTTGGGGGAAAATGCT
1 GTCCAACGGCTAATTAAATAGCCGTTGGAGAAAGTAGTCTTTAGTTACCGTT-GGGGAAAACGCT
*
213120 TGGG
65 TGGA
*
213124 GTCCAATGGCTAATTAAATAGCCGTT
1 GTCCAACGGCTAATTAAATAGCCGTT
213150 AATTACCGTT
Statistics
Matches: 145, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
68 2 0.01
69 141 0.97
70 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (68 bp):
GTCCAACGGCTAATTAAATAGCCGTTGGAGAAAGTAGTCTTTAGTTACCGTTGGGGAAAACGCTT
GGA
Found at i:213999 original size:13 final size:13
Alignment explanation
Indices: 213981--214006 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
213971 GGGCCTCAGA
213981 TAGCTCCAGAAAT
1 TAGCTCCAGAAAT
213994 TAGCTCCAGAAAT
1 TAGCTCCAGAAAT
214007 ACAGATAAAT
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:0.23, G:0.15, T:0.23
Consensus pattern (13 bp):
TAGCTCCAGAAAT
Found at i:217790 original size:59 final size:60
Alignment explanation
Indices: 217716--217839 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 60
217706 CTTAAATATA
* * *
217716 AAAAATTTAACAAATTTAGCCCTCAATATTTATAAAATTT-T-AATTTTAGTTCAAATTCT
1 AAAAATTGAACAAATTTAACCCTCAACATTTATAAAATTTATCAA-TTTAGTTCAAATTCT
* * * *
217775 AAAAATTGAATAAATTTAACTCTTAACATTTATAAAATTTATCAATTTAGTTCCAATTCT
1 AAAAATTGAACAAATTTAACCCTCAACATTTATAAAATTTATCAATTTAGTTCAAATTCT
217835 AAAAA
1 AAAAA
217840 AAAATTAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
59 34 0.61
60 20 0.36
61 2 0.04
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.40
Consensus pattern (60 bp):
AAAAATTGAACAAATTTAACCCTCAACATTTATAAAATTTATCAATTTAGTTCAAATTCT
Found at i:219826 original size:24 final size:24
Alignment explanation
Indices: 219799--219853 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
219789 GACCCGACTA
* * *
219799 GTTGACTGGCCTAACTCATTGATC
1 GTTGACTGACCCAACCCATTGATC
* *
219823 GTTGACCGACCCGACCCATTGATC
1 GTTGACTGACCCAACCCATTGATC
219847 GTTGACT
1 GTTGACT
219854 ATTGAATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (24 bp):
GTTGACTGACCCAACCCATTGATC
Found at i:222660 original size:18 final size:18
Alignment explanation
Indices: 222637--222671 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
222627 AAGAGCACAA
*
222637 AATAAATAAAATAATATT
1 AATAAATAAAAAAATATT
222655 AATAAATAAAAAAATAT
1 AATAAATAAAAAAATAT
222672 ATGTATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAAATAAAAAAATATT
Found at i:223684 original size:21 final size:20
Alignment explanation
Indices: 223660--223702 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 20
223650 GATTGTTTTT
223660 TGTTTT-TTCCTATTTTTCTTC
1 TGTTTTCTT-CTA-TTTTCTTC
223681 TGTTTTGCTTCTATTTTCTTC
1 TGTTTT-CTTCTATTTTCTTC
223702 T
1 T
223703 TTGATGCAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 15 0.75
22 3 0.15
23 2 0.10
ACGTcount: A:0.05, C:0.19, G:0.07, T:0.70
Consensus pattern (20 bp):
TGTTTTCTTCTATTTTCTTC
Found at i:224382 original size:40 final size:40
Alignment explanation
Indices: 224329--224446 Score: 148
Period size: 40 Copynumber: 3.0 Consensus size: 40
224319 GACTTCAATT
* *
224329 TACCCTCTGGTTAGGGTAAAAGATCGGGTGGTCTTCAAGC
1 TACCCTCTAGTTAGGGTAAAAGATCGGATGGTCTTCAAGC
* * *
224369 TACCCTTTAGTTAGGGTAAAAGAAT-GGATGATCTTCAATC
1 TACCCTCTAGTTAGGGTAAAAG-ATCGGATGGTCTTCAAGC
** *
224409 TGGCCTCTAGTTAGGGTAAAAGATCGGATGGTCCTCAA
1 TACCCTCTAGTTAGGGTAAAAGATCGGATGGTCTTCAA
224447 TATGCCCCAT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
39 2 0.03
40 62 0.94
41 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (40 bp):
TACCCTCTAGTTAGGGTAAAAGATCGGATGGTCTTCAAGC
Found at i:224596 original size:42 final size:42
Alignment explanation
Indices: 224336--224900 Score: 426
Period size: 42 Copynumber: 13.7 Consensus size: 42
224326 ATTTACCCTC
* * * * **
224336 TGGTTAGGGTAAAAGATCGGGT-G-GTCTTCAAGCTACCCTT
1 TGGTTAGGGTAAGAGATCGGATGGTGTCTTCAATCTGCCCCA
* * * *
224376 TAGTTAGGGTAAAAGAAT-GGAT-G-ATCTTCAATCTGGCCTC-
1 TGGTTAGGGTAAGAG-ATCGGATGGTGTCTTCAATCT-GCCCCA
* * * *
224416 TAGTTAGGGTAAAAGATCGGAT-G-GTCCTCAATATGCCCCA
1 TGGTTAGGGTAAGAGATCGGATGGTGTCTTCAATCTGCCCCA
* * * * *
224456 TGGTTGGGGTAAGAGATCGGA-CG-ATCTTTAATCTGCCTCA
1 TGGTTAGGGTAAGAGATCGGATGGTGTCTTCAATCTGCCCCA
* * ** * *
224496 TGGTTGGGGTAAAAGATC-GA-AATGTCATCAATTTGCCCCA
1 TGGTTAGGGTAAGAGATCGGATGGTGTCTTCAATCTGCCCCA
* * *
224536 TGGTT-GGGCTAAAAGATCGGATGGTGTCTTCAATCTGCCTCG
1 TGGTTAGGG-TAAGAGATCGGATGGTGTCTTCAATCTGCCCCA
* * * * * **
224578 TAGTTAGGGTAAGAGATCGAATGGTGTCTTTAATATGCTCTG
1 TGGTTAGGGTAAGAGATCGGATGGTGTCTTCAATCTGCCCCA
** * *
224620 TGGTT-GGAGTAAGAGATTAGATGGTGTCTTCAA-CTCGCTCGA
1 TGGTTAGG-GTAAGAGATCGGATGGTGTCTTCAATCT-GCCCCA
* * ** * * *
224662 TGGTTGGGGTAAGAGGTCAAATGGTGTCTCCAATATGCCCCG
1 TGGTTAGGGTAAGAGATCGGATGGTGTCTTCAATCTGCCCCA
* *
224704 TGGTTGGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCCA
1 TGGTTAGGGTAAGAGATCGGATGGTGTCTTCAATCTGCCCCA
* * * * **
224746 TGGTTGGGGTATA-AGATTGGATGATGTCTTCAATTTGCCCTG
1 TGGTTAGGGTA-AGAGATCGGATGGTGTCTTCAATCTGCCCCA
* * *
224788 TGGTTAGGGTAAGAGATTGGATGATGTCTTTAATCTGCCCCA
1 TGGTTAGGGTAAGAGATCGGATGGTGTCTTCAATCTGCCCCA
*
224830 TGGTTAGGGTAAGAGATCGAATGGTGTCTTCAATCTGCCCCA
1 TGGTTAGGGTAAGAGATCGGATGGTGTCTTCAATCTGCCCCA
*
224872 TGGTT-GGGTAAGAGATTGGATGGTGTCTT
1 TGGTTAGGGTAAGAGATCGGATGGTGTCTT
224901 TTGTAGTTTC
Statistics
Matches: 430, Mismatches: 79, Indels: 31
0.80 0.15 0.06
Matches are distributed among these distances:
39 11 0.03
40 129 0.30
41 32 0.07
42 251 0.58
43 7 0.02
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.31
Consensus pattern (42 bp):
TGGTTAGGGTAAGAGATCGGATGGTGTCTTCAATCTGCCCCA
Found at i:224685 original size:84 final size:83
Alignment explanation
Indices: 224400--224900 Score: 489
Period size: 84 Copynumber: 6.0 Consensus size: 83
224390 GAATGGATGA
* * * * * *
224400 TCTTCAATCTGGCCTC-TAGTTAGGGTAAAAGATCGGAT-G-GTCCTCAATATGCCCCATGGTTG
1 TCTTCAATCT-GCCCCATGGTTAGGGTAAGAGATCGAATGGTGTCTTCAATATGCCCCGTGGTT-
* * *
224462 GGGTAAGAGATCGGA-CG-A
64 GGGTAAGAGATTGGATGGTG
* * * * * * * *
224480 TCTTTAATCTGCCTCATGGTTGGGGTAAAAGATCGAA--ATGTCATCAATTTGCCCCATGGTTGG
1 TCTTCAATCTGCCCCATGGTTAGGGTAAGAGATCGAATGGTGTCTTCAATATGCCCCGTGGTTGG
* *
224543 GCTAAAAGATCGGATGGTG
66 G-TAAGAGATTGGATGGTG
* * * * * *
224562 TCTTCAATCTGCCTCGTAGTTAGGGTAAGAGATCGAATGGTGTCTTTAATATGCTCTGTGGTTGG
1 TCTTCAATCTGCCCCATGGTTAGGGTAAGAGATCGAATGGTGTCTTCAATATGCCCCGTGGTTGG
*
224627 AGTAAGAGATTAGATGGTG
66 -GTAAGAGATTGGATGGTG
* * * * * *
224646 TCTTCAA-CTCGCTCGATGGTTGGGGTAAGAGGTCAAATGGTGTCTCCAATATGCCCCGTGGTTG
1 TCTTCAATCT-GCCCCATGGTTAGGGTAAGAGATCGAATGGTGTCTTCAATATGCCCCGTGGTT-
224710 GGGTAAGAGATTGGATGGTG
64 GGGTAAGAGATTGGATGGTG
* * * * * *
224730 TCTTCAATCTGCCCCATGGTTGGGGTATA-AGATTGGATGATGTCTTCAATTTGCCCTGTGGTTA
1 TCTTCAATCTGCCCCATGGTTAGGGTA-AGAGATCGAATGGTGTCTTCAATATGCCCCGTGGTT-
*
224794 GGGTAAGAGATTGGATGATG
64 GGGTAAGAGATTGGATGGTG
* * *
224814 TCTTTAATCTGCCCCATGGTTAGGGTAAGAGATCGAATGGTGTCTTCAATCTGCCCCATGGTTGG
1 TCTTCAATCTGCCCCATGGTTAGGGTAAGAGATCGAATGGTGTCTTCAATATGCCCCGTGGTTGG
224879 GTAAGAGATTGGATGGTG
66 GTAAGAGATTGGATGGTG
224897 TCTT
1 TCTT
224901 TTGTAGTTTC
Statistics
Matches: 349, Mismatches: 59, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
79 8 0.02
80 58 0.17
81 1 0.00
82 32 0.09
83 26 0.07
84 218 0.62
85 6 0.02
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (83 bp):
TCTTCAATCTGCCCCATGGTTAGGGTAAGAGATCGAATGGTGTCTTCAATATGCCCCGTGGTTGG
GTAAGAGATTGGATGGTG
Found at i:234645 original size:17 final size:17
Alignment explanation
Indices: 234616--234650 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
234606 TTATTTAGGG
234616 TCTTGGGTCGTTTGGGC
1 TCTTGGGTCGTTTGGGC
234633 TCTTAGGGT-GTTTGGGC
1 TCTT-GGGTCGTTTGGGC
234650 T
1 T
234651 AGGTGGGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.03, C:0.14, G:0.40, T:0.43
Consensus pattern (17 bp):
TCTTGGGTCGTTTGGGC
Found at i:235135 original size:21 final size:21
Alignment explanation
Indices: 235111--235163 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
235101 AATAGTGTTG
235111 CCTTTTAACTTAATGATTTTC
1 CCTTTTAACTTAATGATTTTC
*
235132 CCTTTTAACTTAATGATTTTG
1 CCTTTTAACTTAATGATTTTC
*
235153 ACTTTTAACTT
1 CCTTTTAACTT
235164 TAAAAAGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.53
Consensus pattern (21 bp):
CCTTTTAACTTAATGATTTTC
Found at i:237873 original size:37 final size:38
Alignment explanation
Indices: 237788--237882 Score: 104
Period size: 40 Copynumber: 2.5 Consensus size: 38
237778 CACACCAGAA
237788 TGACACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAG
1 TGACACCCAGTGCCTCATCGGATAGTTCGAAG--ATAAAG
* *
237828 TGACACCCAGTGTCTCATCGGCCTAG-TCGAAG-TAAAG
1 TGACACCCAGTGCCTCATCGG-ATAGTTCGAAGATAAAG
** *
237865 TGGTACCCAGTACCTCAT
1 TGACACCCAGTGCCTCAT
237883 TGAATCTATC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
37 19 0.40
40 26 0.54
41 3 0.06
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.22
Consensus pattern (38 bp):
TGACACCCAGTGCCTCATCGGATAGTTCGAAGATAAAG
Found at i:250574 original size:36 final size:35
Alignment explanation
Indices: 250483--250602 Score: 102
Period size: 36 Copynumber: 3.3 Consensus size: 35
250473 GTAAAATTTT
*
250483 ACAGAAGAAAGAAAGAAGAAATTTTGGTGGTGATTGG
1 ACAGAAGAAAGAAAGAAGAAATTTTGG-GGGGATT-G
* *
250520 A-TGATGAGAAAGTAAAG-A-AAATTTTGGGGGGGTTG
1 ACAGA--AGAAAG-AAAGAAGAAATTTTGGGGGGATTG
* **
250555 ACAGAAGAAAGAAAGAAGAAGTTTTGGGGGTTTTTG
1 ACAGAAGAAAGAAAGAAGAAATTTTGGGGG-GATTG
*
250591 ATAGAAGAAAGA
1 ACAGAAGAAAGA
250603 TTTAGTGTAG
Statistics
Matches: 68, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
33 4 0.06
34 7 0.10
35 13 0.19
36 23 0.34
37 10 0.15
38 7 0.10
39 4 0.06
ACGTcount: A:0.42, C:0.02, G:0.33, T:0.23
Consensus pattern (35 bp):
ACAGAAGAAAGAAAGAAGAAATTTTGGGGGGATTG
Done.