Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 101 of 187
Found at i:29856245 original size:53 final size:54
Alignment explanation
Indices: 29856151--29856309 Score: 173
Period size: 53 Copynumber: 3.0 Consensus size: 54
29856141 CGTGAGGTCA
* * *
29856151 ATTAAATAACCGAAATA-CCCATGTAAGGTAAAATGACTGAAATACCCCCGA-AGG
1 ATTAAATGATCGAAATACCCCA-GTAAGGTAAAATAACTGAAATACCCCC-ATAGG
* *
29856205 GTTAAATGATCGAAATACCCCA-TAAGGTAAAATAATTGAAATACCCCCATAGG
1 ATTAAATGATCGAAATACCCCAGTAAGGTAAAATAACTGAAATACCCCCATAGG
* * * **
29856258 ATAAAATGATCGAAATACCCCCG-AAGGGTAAAATGACCAAAATACCCCCATA
1 ATTAAATGATCGAAATACCCCAGTAA-GGTAAAATAACTGAAATACCCCCATA
29856310 TTCTAGAATG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
52 1 0.01
53 48 0.54
54 36 0.40
55 4 0.04
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (54 bp):
ATTAAATGATCGAAATACCCCAGTAAGGTAAAATAACTGAAATACCCCCATAGG
Found at i:29856356 original size:27 final size:27
Alignment explanation
Indices: 29856177--29856359 Score: 174
Period size: 27 Copynumber: 6.8 Consensus size: 27
29856167 ACCCATGTAA
*
29856177 GGTAAAATGACTGAAATACCCCCGA-AG
1 GGTAAAATGATTGAAATACCCCC-ATAG
* * *
29856204 GGTTAAATGATCGAAATA-CCCCATAA
1 GGTAAAATGATTGAAATACCCCCATAG
*
29856230 GGTAAAATAATTGAAATACCCCCATAG
1 GGTAAAATGATTGAAATACCCCCATAG
* *
29856257 GATAAAATGATCGAAATACCCCCGA-AG
1 GGTAAAATGATTGAAATACCCCC-ATAG
*** *
29856284 GGTAAAATGACCAAAATACCCCCATAT
1 GGTAAAATGATTGAAATACCCCCATAG
** * *
29856311 TCTAGAATGACTGAAATACCCCCATAG
1 GGTAAAATGATTGAAATACCCCCATAG
**
29856338 GGTAAAATGATTGTTATACCCC
1 GGTAAAATGATTGAAATACCCC
29856360 TAGAAGATTA
Statistics
Matches: 125, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
25 1 0.01
26 21 0.17
27 102 0.82
28 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (27 bp):
GGTAAAATGATTGAAATACCCCCATAG
Found at i:29861479 original size:40 final size:40
Alignment explanation
Indices: 29861435--29861532 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 40
29861425 CATTTGGATA
29861435 AAAAACGCCGCTAAAAATCAA-TCATTAGCGACGCTTCTAG
1 AAAAACGCCGCTAAAAATCAAGT-ATTAGCGACGCTTCTAG
* * * * * * **
29861475 AAAAATGCCGCTACAGATCAAGTATTCGCGGCGCTTTTCT
1 AAAAACGCCGCTAAAAATCAAGTATTAGCGACGCTTCTAG
29861515 AAAAACGCCGCTAAAAAT
1 AAAAACGCCGCTAAAAAT
29861533 GAGCATTAGC
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
40 45 0.98
41 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.21
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCAAGTATTAGCGACGCTTCTAG
Found at i:29861758 original size:41 final size:41
Alignment explanation
Indices: 29861588--29861746 Score: 255
Period size: 41 Copynumber: 3.9 Consensus size: 41
29861578 CAACGACGTC
29861588 GCGCCGCTAATGCTTGGGTCTTTAGCGGCGCTTTTGAAGAA
1 GCGCCGCTAATGCTTGGGTCTTTAGCGGCGCTTTTGAAGAA
* *
29861629 GTGCCACTAATGCTTGGGTCTTTAGCGGCGCTTTTGAAGAA
1 GCGCCGCTAATGCTTGGGTCTTTAGCGGCGCTTTTGAAGAA
* *
29861670 GCGCCGCTAATGCTTGGGTCTTTAGCAGCGTTTTTGAAGAA
1 GCGCCGCTAATGCTTGGGTCTTTAGCGGCGCTTTTGAAGAA
** *
29861711 GCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTG
1 GCGCCGCTAATGCTTGGGTCTTTAGCGGCGCTTTTG
29861747 GAAAAGAGCC
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 109 1.00
ACGTcount: A:0.17, C:0.21, G:0.30, T:0.31
Consensus pattern (41 bp):
GCGCCGCTAATGCTTGGGTCTTTAGCGGCGCTTTTGAAGAA
Found at i:29862162 original size:7 final size:7
Alignment explanation
Indices: 29862116--29862169 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
29862106 GAGTTACTAT
*
29862116 TTTAAGG
1 TTTATGG
29862123 TTTATGG
1 TTTATGG
*
29862130 ATTATGGG
1 TTTAT-GG
*
29862138 TTTAGGG
1 TTTATGG
* *
29862145 GTTATGA
1 TTTATGG
29862152 TTTATGG
1 TTTATGG
29862159 TTTATGG
1 TTTATGG
29862166 TTTA
1 TTTA
29862170 AAGGTTGGGG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (7 bp):
TTTATGG
Found at i:29862181 original size:21 final size:21
Alignment explanation
Indices: 29862157--29862196 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29862147 TATGATTTAT
*
29862157 GGTTTATGGTTTAAAGGTTGG
1 GGTTTAAGGTTTAAAGGTTGG
*
29862178 GGTTTAAGGTTTAGAGGTT
1 GGTTTAAGGTTTAAAGGTT
29862197 ATGTGTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (21 bp):
GGTTTAAGGTTTAAAGGTTGG
Found at i:29862220 original size:7 final size:7
Alignment explanation
Indices: 29862116--29862241 Score: 51
Period size: 7 Copynumber: 17.7 Consensus size: 7
29862106 GAGTTACTAT
*
29862116 TTTAAGG
1 TTTAGGG
*
29862123 TTTATGG
1 TTTAGGG
*
29862130 ATTATGGG
1 TTTA-GGG
29862138 TTTAGGG
1 TTTAGGG
* * *
29862145 GTTATGA
1 TTTAGGG
*
29862152 TTTATGG
1 TTTAGGG
*
29862159 TTTATGG
1 TTTAGGG
*
29862166 TTTAAAGG
1 TTT-AGGG
*
29862174 -TTGGGG
1 TTTAGGG
*
29862180 TTTAAGG
1 TTTAGGG
29862187 TTTAGAGG
1 TTTAG-GG
*
29862195 -TTATGTG
1 TTTA-GGG
*
29862202 TTAAGGG
1 TTTAGGG
29862209 TTTTAGGG
1 -TTTAGGG
29862217 TTTA-GG
1 TTTAGGG
**
29862223 TTTATAG
1 TTTAGGG
29862230 TTTAGGG
1 TTTAGGG
29862237 TTTAG
1 TTTAG
29862242 ATTAACTAGT
Statistics
Matches: 89, Mismatches: 22, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
6 8 0.09
7 62 0.70
8 19 0.21
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:29862236 original size:28 final size:28
Alignment explanation
Indices: 29862152--29862239 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 28
29862142 GGGGTTATGA
* * * *
29862152 TTTATGGTTTATGGTTTAAAGGTT-GGGG
1 TTTAAGGTTTA-GGTTTATAGTTTAGGGT
*
29862180 TTTAAGGTTTAGAGGTTAT-GTGTTAAGGGT
1 TTTAAGGTTTAG-GTTTATAGT-TT-AGGGT
*
29862210 TTTAGGGTTTAGGTTTATAGTTTAGGGT
1 TTTAAGGTTTAGGTTTATAGTTTAGGGT
29862238 TT
1 TT
29862240 AGATTAACTA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
27 2 0.04
28 23 0.48
29 7 0.15
30 16 0.33
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (28 bp):
TTTAAGGTTTAGGTTTATAGTTTAGGGT
Found at i:29862238 original size:14 final size:14
Alignment explanation
Indices: 29862054--29862240 Score: 53
Period size: 14 Copynumber: 13.1 Consensus size: 14
29862044 TAATTATCAC
*
29862054 TATAGTTTAAGGTT
1 TATAGTTTAGGGTT
* * * *
29862068 TTTGGATTAGGGTA
1 TATAGTTTAGGGTT
* *
29862082 TATGGTTTAGAGTT
1 TATAGTTTAGGGTT
*
29862096 TAAAGTTTAGGAG-T
1 TATAGTTTAGG-GTT
* *
29862110 TACTATTTTAAGGTT
1 TA-TAGTTTAGGGTT
* *
29862125 TATGGATTATGGGTT
1 TATAGTTTA-GGGTT
** * * *
29862140 TAGGGGTTATGATT
1 TATAGTTTAGGGTT
* *
29862154 TATGGTTTATGGTT
1 TATAGTTTAGGGTT
* * *
29862168 TAAAGGTTGGGGTT
1 TATAGTTTAGGGTT
29862182 TA-AGGTTTAGAGG-T
1 TATA-GTTTAG-GGTT
29862196 TAT-GTGTTAAGGGTT
1 TATAGT-TT-AGGGTT
29862211 T-TAGGGTTTA-GGTT
1 TATA--GTTTAGGGTT
29862225 TATAGTTTAGGGTT
1 TATAGTTTAGGGTT
29862239 TA
1 TA
29862241 GATTAACTAG
Statistics
Matches: 125, Mismatches: 33, Indels: 30
0.66 0.18 0.16
Matches are distributed among these distances:
13 8 0.06
14 83 0.66
15 30 0.24
16 2 0.02
17 2 0.02
ACGTcount: A:0.23, C:0.01, G:0.30, T:0.46
Consensus pattern (14 bp):
TATAGTTTAGGGTT
Found at i:29862943 original size:13 final size:15
Alignment explanation
Indices: 29862915--29862946 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
29862905 CTCGTATTAT
29862915 TATTAATTTAATATA
1 TATTAATTTAATATA
29862930 TATTAA-TT-ATATA
1 TATTAATTTAATATA
29862943 TATT
1 TATT
29862947 TTTCATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 2 0.12
15 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTAATTTAATATA
Found at i:29865568 original size:81 final size:80
Alignment explanation
Indices: 29865472--29865622 Score: 293
Period size: 81 Copynumber: 1.9 Consensus size: 80
29865462 AATTTCTATA
29865472 GAGCTATCAAATTGTGTTGCATGAAAATAAGAAAGTTTCTTTTTTTTTTCTTTAATACAAAATTA
1 GAGCTATCAAATTGTGTTGCATGAAAATAAGAAAGTTTC-TTTTTTTTTCTTTAATACAAAATTA
29865537 GCTTTTGTTGTCTTTT
65 GCTTTTGTTGTCTTTT
29865553 GAGCTATCAAATTGTGTTGCATGAAAATAAGAAAGTTTCTTTTTTTTTCTTTAATACAAAATTAG
1 GAGCTATCAAATTGTGTTGCATGAAAATAAGAAAGTTTCTTTTTTTTTCTTTAATACAAAATTAG
29865618 CTTTT
66 CTTTT
29865623 CTATTAATCA
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 31 0.44
81 39 0.56
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.46
Consensus pattern (80 bp):
GAGCTATCAAATTGTGTTGCATGAAAATAAGAAAGTTTCTTTTTTTTTCTTTAATACAAAATTAG
CTTTTGTTGTCTTTT
Found at i:29867769 original size:43 final size:43
Alignment explanation
Indices: 29867713--29867985 Score: 404
Period size: 43 Copynumber: 6.3 Consensus size: 43
29867703 AAAGGTTTGT
* * *
29867713 TCTTTAGCGGCGTTTGCGGGAAAAGCGCCGTTAAAGGTCGTGG
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCGTGG
*
29867756 TCTTTAGCGGCGTTTGT-GGAATAAGCGCCGCTATAGATCGTGG
1 TCTTTAGCGGCGTTTGTGGGAA-AAGCGCCGCTAAAGATCGTGG
* * *
29867799 TCTTTAGCAGCGTTTGTGGGAAAAGCACCGCTATAGATCGTGG
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCGTGG
* * *
29867842 TCTTTAGCGGCGTTTGTGGGAAAAGCGCTGCTATAGATTGTGG
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCGTGG
*
29867885 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGG
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCGTGG
* *
29867928 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCGTGG
*
29867971 TCTTTAGCGGTGTTT
1 TCTTTAGCGGCGTTT
29867986 TTTGCGGCGC
Statistics
Matches: 212, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
42 4 0.02
43 204 0.96
44 4 0.02
ACGTcount: A:0.19, C:0.18, G:0.34, T:0.29
Consensus pattern (43 bp):
TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCGTGG
Found at i:29868058 original size:22 final size:22
Alignment explanation
Indices: 29868030--29868073 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
29868020 TAGCGGTGCT
*
29868030 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
29868052 AAAAAGCACCGCTAAAAGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
29868074 TTTTGGTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:29873709 original size:554 final size:553
Alignment explanation
Indices: 29872660--29873764 Score: 1691
Period size: 554 Copynumber: 2.0 Consensus size: 553
29872650 AAGAGTTATT
* * *
29872660 TTATCTTTTTTATAACAGTCAAACCAACCATTCTAATAGTAAAAGGTTACGGAGAGGCCAAGAAT
1 TTATCTTTTTTATAACAGTCAAACCAACCATTCTAATAGTAAAAAGTAACAGAGAGGCCAAGAAT
* * *
29872725 TTCAAATAAAACAGCATAAGAACTCAATGTCTCAAAATTAAAGTATAGGGGCTAAAATTTAGATT
66 TTCAAATAAAAAAGCATAAGAACTCAATGTCTCAAAATTAAAATATAGGGACTAAAATTTAGATT
* *
29872790 TTAAAAGAATACAATGACCTTTAGCATATTAAACTTCCTTTTTTTTTTCTCACCCAACGATGAAA
131 TTAAAAGAATACAAGGACCTTTAGCATATTAAACTTCCTTTCTTTTTTCTCACCCAACGATGAAA
* **
29872855 GGTTACAAAATGGTCTTTCAACTATTTGATTTTTTCTTTTGTGGTCATCGGTCGTGAAATGGCTA
196 AGTTACAAAATGGTCACTCAACTATTTGATTTTTTCTTTTGTGGTCATCGGTCGTGAAATGGCTA
* * * * * *
29872920 AGTTTCAGCTTTTAAAGTTAGCATAATACCGTATTTAACCCTTAAACATTTGTACATTGCATCAA
261 AGTCTAAGCTTTTAAAATTAGCATAATACCATATTTAACCCTCAAACATTTATACATTGCATCAA
* * *
29872985 TATAGTATTGATTCTAAAAAAATTACCCCTTAGTGTTTTCACAGTATGTAATTTGATCCTTTTTT
326 TATAGTATTGAATCTAAAAAAATTACCCCTCAATGTTTTCACAGTATGTAATTTGATCC-TTTTT
*
29873050 TACAGTTTTGTTCAAACATTATTACAATTTGGTTACTAATTGATCCTTTTCACATTGTGTTAACA
390 TACAATTTTGTTCAAACATTATTACAATTTGGTTACTAATTGATCCTTTTCACATTGTGTTAACA
* **
29873115 ATTGGACTTGTGTTTTTAAATTCAAAAAGTAAAGTACTAAATTCTTTGAAATAAAAAGTAAGAGA
455 ATTAGACTTGTACTTTTAAATTCAAAAAGTAAAGTACTAAATTCTTTGAAATAAAAAGTAAGAGA
*
29873180 CTAAATTTCAAATGTACAAATAATATAAAAAAAA
520 CTAAATTTCAAATATACAAATAATATAAAAAAAA
*
29873214 TTATCTTTTTTATAACAGTCAAACCAACCATTCTAATGGTAAAAAGTAACAGAGAGGCCAAGAAT
1 TTATCTTTTTTATAACAGTCAAACCAACCATTCTAATAGTAAAAAGTAACAGAGAGGCCAAGAAT
* * *
29873279 TTCAAATAAAAAAGTATAAGAACTCAATGTCTCACAATTAAAATATAGGGACTAAATTTTAGATT
66 TTCAAATAAAAAAGCATAAGAACTCAATGTCTCAAAATTAAAATATAGGGACTAAAATTTAGATT
* * * *
29873344 TTAAAAGAGGTACAAGGACCTTTGGCATATTTAAGCTTCC-TTCTTTTTTCTCACCTAACGATGA
131 TTAAAAGA-ATACAAGGACCTTTAGCATA-TTAAACTTCCTTTCTTTTTTCTCACCCAACGATGA
* *
29873408 AAAGTTACAAAATGGTCACTCAACTATTTGATTTTTTCTTTAT-TGGTCATTGGTAC-TTAAATG
194 AAAGTTACAAAATGGTCACTCAACTATTTGATTTTTTCTTT-TGTGGTCATCGGT-CGTGAAATG
* *
29873471 GC-AATGTCTAAGCTTTTAAAATTAGTATAATAGCATATTTAACCCTCAAACATTTATACATTGC
257 GCTAA-GTCTAAGCTTTTAAAATTAGCATAATACCATATTTAACCCTCAAACATTTATACATTGC
* * *
29873535 TTCAATATAGTATTGAATCTAAAAAAATTTACCCCTCAATGTTTTCACATTGTGTAATTTGATCC
321 ATCAATATAGTATTGAATCTAAAAAAA-TTACCCCTCAATGTTTTCACAGTATGTAATTTGATCC
*
29873600 -TTTTTACAATTTTGTTCAAACATTTTTA-AAGTTTGGTTACTAATTGATCCTTTTCACATTGTG
385 TTTTTTACAATTTTGTTCAAACATTATTACAA-TTTGGTTACTAATTGATCCTTTTCACATTGTG
* * *
29873663 TTGACAATTAGACTTGTACTTTTAAATTCAGAAAGTAATGTACTAAATTCTTTGAAATAAAAAGT
449 TTAACAATTAGACTTGTACTTTTAAATTCAAAAAGTAAAGTACTAAATTCTTTGAAATAAAAAGT
*
29873728 AGGAGACTAAATTTCAAATATACAAATAATATAAAAA
514 AAGAGACTAAATTTCAAATATACAAATAATATAAAAA
29873765 CTTAAAACAT
Statistics
Matches: 499, Mismatches: 45, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
553 2 0.00
554 282 0.57
555 171 0.34
556 44 0.09
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (553 bp):
TTATCTTTTTTATAACAGTCAAACCAACCATTCTAATAGTAAAAAGTAACAGAGAGGCCAAGAAT
TTCAAATAAAAAAGCATAAGAACTCAATGTCTCAAAATTAAAATATAGGGACTAAAATTTAGATT
TTAAAAGAATACAAGGACCTTTAGCATATTAAACTTCCTTTCTTTTTTCTCACCCAACGATGAAA
AGTTACAAAATGGTCACTCAACTATTTGATTTTTTCTTTTGTGGTCATCGGTCGTGAAATGGCTA
AGTCTAAGCTTTTAAAATTAGCATAATACCATATTTAACCCTCAAACATTTATACATTGCATCAA
TATAGTATTGAATCTAAAAAAATTACCCCTCAATGTTTTCACAGTATGTAATTTGATCCTTTTTT
ACAATTTTGTTCAAACATTATTACAATTTGGTTACTAATTGATCCTTTTCACATTGTGTTAACAA
TTAGACTTGTACTTTTAAATTCAAAAAGTAAAGTACTAAATTCTTTGAAATAAAAAGTAAGAGAC
TAAATTTCAAATATACAAATAATATAAAAAAAA
Found at i:29883276 original size:46 final size:46
Alignment explanation
Indices: 29883216--29883317 Score: 123
Period size: 46 Copynumber: 2.2 Consensus size: 46
29883206 GGTTATGGCT
* * * * *
29883216 TTTCTAAAATGACACTTAATGTTTTAACCTTTCTAAGGTTGTGACC
1 TTTCTGAAACGACACTTAATGTTATAACCTTTCTAAGGTTATAACC
* * * *
29883262 TTTTTGAAACGACACTTAATGTTATGACTTTTTTAAGGTTATAACC
1 TTTCTGAAACGACACTTAATGTTATAACCTTTCTAAGGTTATAACC
29883308 TTTCTGAAAC
1 TTTCTGAAAC
29883318 ATCTCTTAGT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (46 bp):
TTTCTGAAACGACACTTAATGTTATAACCTTTCTAAGGTTATAACC
Found at i:29884267 original size:22 final size:22
Alignment explanation
Indices: 29884212--29884268 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
29884202 GGTGTTTTGC
*
29884212 TATCTCGAGACATAGGTCACTA
1 TATCTCGAGACTTAGGTCACTA
* * *
29884234 TATCTCAAGACTTAGTTCATTA
1 TATCTCGAGACTTAGGTCACTA
*
29884256 TGTCTCGAGACTT
1 TATCTCGAGACTT
29884269 TCTTGATAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (22 bp):
TATCTCGAGACTTAGGTCACTA
Found at i:29884347 original size:21 final size:21
Alignment explanation
Indices: 29884321--29884362 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
29884311 TGGTGAAAAT
29884321 TATTCTTAAGGTCTCGAGACA
1 TATTCTTAAGGTCTCGAGACA
*
29884342 TATTCTTAATGTCTCGAGACA
1 TATTCTTAAGGTCTCGAGACA
29884363 CTAACAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (21 bp):
TATTCTTAAGGTCTCGAGACA
Found at i:29888335 original size:27 final size:27
Alignment explanation
Indices: 29888305--29888360 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
29888295 CAGGAAATCT
* *
29888305 AAGAATAGCTTTTGTGGCAAATTCTGA
1 AAGAATAGCCTTTGTGGAAAATTCTGA
29888332 AAGAATAGCCTTTGTGGAAAATTCTGA
1 AAGAATAGCCTTTGTGGAAAATTCTGA
29888359 AA
1 AA
29888361 ATATTTCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (27 bp):
AAGAATAGCCTTTGTGGAAAATTCTGA
Found at i:29889629 original size:20 final size:20
Alignment explanation
Indices: 29889588--29889630 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
29889578 CTAAGATAAG
*
29889588 GTATCAGTACCTTTAAGGAA
1 GTATCAGTACCTTTAAGCAA
29889608 GTATCAGTACC-TTAAGTCAA
1 GTATCAGTACCTTTAAG-CAA
29889628 GTA
1 GTA
29889631 CCGATAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (20 bp):
GTATCAGTACCTTTAAGCAA
Found at i:29893316 original size:12 final size:11
Alignment explanation
Indices: 29893299--29893355 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
29893289 AACAAATCCT
29893299 CTCTCATATTTC
1 CTCTCA-ATTTC
29893311 CTCTCAA-TTC
1 CTCTCAATTTC
29893321 CTCTCAATTTC
1 CTCTCAATTTC
*
29893332 CT-TCCAAAATT-
1 CTCT-C-AATTTC
29893343 CTCTCAATTTC
1 CTCTCAATTTC
29893354 CT
1 CT
29893356 TCCAAAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 15 0.39
11 12 0.32
12 11 0.29
ACGTcount: A:0.21, C:0.35, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:29893346 original size:22 final size:22
Alignment explanation
Indices: 29893316--29893371 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
29893306 ATTTCCTCTC
29893316 AATTCCTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
29893339 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
29893361 AATTCTCTCAA
1 AATTCTCTCAA
29893372 ATCCATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:29893397 original size:29 final size:29
Alignment explanation
Indices: 29893365--29893451 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
29893355 TTCCAAAATT
29893365 CTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAAATCCATATTTAATTTCAATTTC
* **
29893394 CTCTCAATTTCC-T-TCCAA----AA-TT-
1 CTCTCAA-ATCCATATTTAATTTCAATTTC
29893416 CTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAAATCCATATTTAATTTCAATTTC
29893445 CTCTCAA
1 CTCTCAA
29893452 TTTCCTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 18
0.64 0.09 0.27
Matches are distributed among these distances:
21 3 0.07
22 8 0.19
23 5 0.12
24 2 0.05
27 2 0.05
28 5 0.12
29 15 0.35
30 3 0.07
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.43
Consensus pattern (29 bp):
CTCTCAAATCCATATTTAATTTCAATTTC
Found at i:29893400 original size:51 final size:51
Alignment explanation
Indices: 29893343--29893458 Score: 232
Period size: 51 Copynumber: 2.3 Consensus size: 51
29893333 TTCCAAAATT
29893343 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
29893394 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
29893445 CTCTCAATTTCCTT
1 CTCTCAATTTCCTT
29893459 TTTTAAAATA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 65 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (51 bp):
CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
Found at i:29893403 original size:22 final size:22
Alignment explanation
Indices: 29893378--29893454 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 22
29893368 TCAAATCCAT
29893378 ATTTAATTTCAATTTCCTCTCA
1 ATTTAATTTCAATTTCCTCTCA
** * *
29893400 ATTTCCTTCCAAAATTCTCTCAAATCCA
1 ATTTAATTTC-AATTTC-CTC---T-CA
29893428 TATTTAATTTCAATTTCCTCTCA
1 -ATTTAATTTCAATTTCCTCTCA
29893451 ATTT
1 ATTT
29893455 CCTTTTTTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
22 11 0.28
23 7 0.17
24 4 0.10
27 4 0.10
28 7 0.17
29 7 0.17
ACGTcount: A:0.29, C:0.25, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTAATTTCAATTTCCTCTCA
Found at i:29894232 original size:7 final size:7
Alignment explanation
Indices: 29894222--29894246 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29894212 ATTCGATTGA
29894222 TATTTAG
1 TATTTAG
29894229 TATTTAG
1 TATTTAG
29894236 TATTTAG
1 TATTTAG
29894243 TATT
1 TATT
29894247 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:29894921 original size:18 final size:18
Alignment explanation
Indices: 29894895--29894929 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29894885 AGGTGCGTTT
*
29894895 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
29894913 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
29894930 TCCTTTTCCG
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:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:29895401 original size:44 final size:45
Alignment explanation
Indices: 29895352--29895438 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 45
29895342 ATATTTTGAA
*
29895352 TATTTTGATATTATTTTATGTAAAAAAATAGAAATTT-TTTGAGT
1 TATTTTGATATTATTTGATGTAAAAAAATAGAAATTTATTTGAGT
* *
29895396 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TATTTTGATATTATTTGATGTAAAAAAATAGAAATTTATTTGA
29895439 TGTAATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 34 0.87
45 5 0.13
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAAAAAAATAGAAATTTATTTGAGT
Found at i:29895440 original size:25 final size:25
Alignment explanation
Indices: 29895406--29895473 Score: 136
Period size: 25 Copynumber: 2.7 Consensus size: 25
29895396 TATTTTGATA
29895406 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
29895431 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
29895456 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
29895474 ACTCTAACCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:29895498 original size:23 final size:23
Alignment explanation
Indices: 29895470--29895792 Score: 113
Period size: 23 Copynumber: 13.5 Consensus size: 23
29895460 TTGATGTAAT
*
29895470 AAAAACTCTAACCTAATTTAACC
1 AAAAACCCTAACCTAATTTAACC
** * **
29895493 CTAAACCCTAACCTAAATTAATT
1 AAAAACCCTAACCTAATTTAACC
**
29895516 AAAAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCTAATTTAACC
* *
29895539 AAAAACCCTAAACT-A-TTAACTT
1 AAAAACCCTAACCTAATTTAAC-C
**
29895561 AAAAACCCTAACCTTAACCTAATTTAATT
1 AAAAA--C---CC-TAACCTAATTTAACC
* **
29895590 AAAAACTCTAACCTAATTTAATT
1 AAAAACCCTAACCTAATTTAACC
*
29895613 AAAAACCCTAAACCCTTAACTTAA--
1 AAAAACCCT-AA-CC-TAATTTAACC
* **
29895637 AAACCCTAACCTTAACCTAATTTAATT
1 AAA----AACCCTAACCTAATTTAACC
* *
29895664 AAAAACCCTAAACCCTTAACTTAA-A
1 AAAAACCCT-AA-CC-TAATTTAACC
* * **
29895689 AACATTAACCTTAACCTAAATTAATT
1 AA-A--AACCCTAACCTAATTTAACC
**
29895715 AAAAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCTAATTTAACC
* **
29895738 AAAAACCCTAAACC---CTTAATT
1 AAAAACCCT-AACCTAATTTAACC
**
29895759 AAAAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCTAATTTAACC
29895782 AAAAACCCTAA
1 AAAAACCCTAA
29895793 ACCCTTAACT
Statistics
Matches: 243, Mismatches: 28, Indels: 58
0.74 0.09 0.18
Matches are distributed among these distances:
20 4 0.02
21 19 0.08
22 7 0.03
23 122 0.50
24 13 0.05
25 21 0.09
26 21 0.09
27 10 0.04
28 15 0.06
29 7 0.03
30 4 0.02
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAAACCCTAACCTAATTTAACC
Found at i:29895582 original size:51 final size:51
Alignment explanation
Indices: 29895519--29895876 Score: 229
Period size: 51 Copynumber: 7.2 Consensus size: 51
29895509 ATTAATTAAA
*
29895519 AACCCTAACCTAATTTAATTAAAAACCCTAAACT-ATTAACTTAAAAACCCT
1 AACCTTAACCTAATTTAATTAAAAACCCTAAACTAATTAA-TTAAAAACCCT
* *
29895570 AACCTTAACCTAATTTAATTAAAAACTCTAACCTAATTTAATTAAAAACCCT
1 AACCTTAACCTAATTTAATTAAAAACCCTAAACTAA-TTAATTAAAAACCCT
* ***** * *
29895622 AAACCCTTAACTTAA---AAACCCTAACCTTAACCTAATTTAATTAAAAACCCT
1 -AA-CCTTAACCTAATTTAATTAAAAACCCTAAACTAA-TTAATTAAAAACCCT
* ** * *
29895673 AAACCCTTAACTTAA-AAACATT---AACCTTAACCTAAATTAATTAAAAA--C-
1 -AA-CCTTAACCTAATTTA-ATTAAAAACCCTAAACT-AATTAATTAAAAACCCT
**
29895721 --CC-TAACCTAATTTAATTAAAAACCCTAAAC-CCTTAATTAAAAA--C-
1 AACCTTAACCTAATTTAATTAAAAACCCTAAACTAATTAATTAAAAACCCT
**
29895765 --CC-TAACCTAATTTAATTAAAAACCCTAAAC-CCTTAACTTAAAAACCCT
1 AACCTTAACCTAATTTAATTAAAAACCCTAAACTAATTAA-TTAAAAACCCT
* * *
29895813 AACATTAACCTAAATTAATTAAAAACTCTAAACCTAATTTAATTAAAAACCCT
1 AACCTTAACCTAATTTAATTAAAAACCCTAAA-CTAA-TTAATTAAAAACCCT
29895866 AAACCCTTAAC
1 -AA-CCTTAAC
29895877 TTANNNNNNN
Statistics
Matches: 257, Mismatches: 26, Indels: 44
0.79 0.08 0.13
Matches are distributed among these distances:
43 10 0.04
44 51 0.20
45 7 0.03
46 8 0.03
47 1 0.00
49 1 0.00
50 1 0.00
51 122 0.47
52 15 0.06
53 18 0.07
54 17 0.07
55 6 0.02
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.28
Consensus pattern (51 bp):
AACCTTAACCTAATTTAATTAAAAACCCTAAACTAATTAATTAAAAACCCT
Found at i:29895588 original size:74 final size:74
Alignment explanation
Indices: 29895489--29895674 Score: 318
Period size: 74 Copynumber: 2.5 Consensus size: 74
29895479 AACCTAATTT
* * *
29895489 AACCCTAAACCCTAACCTAAATTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACTA
1 AACCCT-AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCA
29895554 TTAACTTAAA
65 TTAACTTAAA
* *
29895564 AACCCTAACCTTAACCTAATTTAATTAAAAACTCTAACCTAATTTAATTAAAAACCCTAAACCCT
1 AACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCAT
29895629 TAACTTAAA
66 TAACTTAAA
29895638 AACCCTAACCTTAACCTAATTTAATTAAAAACCCTAA
1 AACCCTAACCTTAACCTAATTTAATTAAAAACCCTAA
29895675 ACCCTTAACT
Statistics
Matches: 105, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
74 99 0.94
75 6 0.06
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (74 bp):
AACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCAT
TAACTTAAA
Found at i:29895686 original size:125 final size:121
Alignment explanation
Indices: 29895469--29895879 Score: 593
Period size: 125 Copynumber: 3.4 Consensus size: 121
29895459 TTTGATGTAA
**** *
29895469 TAAAAACTCTAACCTAATTTAACCCTAAACCCT-AA-CC-TAAATTAATTAAA-AACCCTAACCT
1 TAAAAACTCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTAA--AAACAA-CCTAACCT
** *
29895530 AATTTAATTAAAAACCCTAAACTATTAACTTAAAAACCCTAACCTTAACCTAATTTAAT
63 AATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAAATTAAT
29895589 TAAAAACTCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACC
1 TAAAAACTCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAA--C-AACC-TAACC
**
29895654 TAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACATTAACCTTAACCTAAATTAAT
62 TAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAAATTAAT
*
29895714 TAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAA-TTAAAAAC--CCTAACCTAAT
1 TAAAAACTCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACAACCTAACCTAAT
*
29895776 TTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACATTAACCTAAATTAAT
66 TTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAAATTAAT
29895832 TAAAAACTCTAAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTA
1 TAAAAACTCT-AACCTAATTTAATTAAAAACCCTAAACCCTTAACTTA
29895880 NNNNNNNNNN
Statistics
Matches: 266, Mismatches: 15, Indels: 20
0.88 0.05 0.07
Matches are distributed among these distances:
118 71 0.27
119 35 0.13
120 32 0.12
121 5 0.02
122 3 0.01
123 7 0.03
124 9 0.03
125 104 0.39
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.28
Consensus pattern (121 bp):
TAAAAACTCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACAACCTAACCTAAT
TTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAAATTAAT
Found at i:29895757 original size:44 final size:44
Alignment explanation
Indices: 29895709--29895815 Score: 205
Period size: 44 Copynumber: 2.4 Consensus size: 44
29895699 TTAACCTAAA
29895709 TTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCC
1 TTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCC
29895753 TTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCC
1 TTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCC
29895797 TTAACTTAAAAACCCTAAC
1 TTAA-TTAAAAACCCTAAC
29895816 ATTAACCTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 48 0.77
45 14 0.23
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (44 bp):
TTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCC
Found at i:29895795 original size:74 final size:74
Alignment explanation
Indices: 29895489--29895872 Score: 302
Period size: 74 Copynumber: 5.2 Consensus size: 74
29895479 AACCTAATTT
* * *
29895489 AACCCTAAACCCTAACCTAAATTAATTAAAAACCCT-AACCTAATTTAATTAAAAACCCTAAACT
1 AACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACC---CTTAATTAAAAACCCTAACCT
29895553 -A-TTAACTTAAA
63 AACTTAA-TTAAA
* * *
29895564 AACCCT-AACCTTAACCTAATTTAATTAAAAACTCT-AACCTAATTTAATTAAAAACCCTAAACC
1 AACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACC---CTTAATTAAAAACCCT-AACC
29895627 ---CTTAACTTAAA
62 TAACTTAA-TTAAA
* **
29895638 AACCCT-AACCTTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACATTAACCTTA
1 AACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAA-TTAAAAACCCTAACC-TA
* *
29895702 ACCTAAATTAATT
64 A-CTTAATTAA-A
*
29895715 AA----AAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACCTAAT
1 AACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACCTAAC
29895776 TTAATTAAA
66 TTAATTAAA
* * * *
29895785 AACCCTAAACCCTTAACTTAA--AAACCCTAACATTAA-CCTAAA---TTAATTAAAAACTCTAA
1 AACCCTAAACCC-TAACCTAATTTAA--TTAA-A--AACCCTAAACCCTTAATTAAAAACCCT-A
*
29895844 ACCTAATTTAATTAAA
59 ACCTAACTTAATTAAA
29895860 AACCCTAAACCCT
1 AACCCTAAACCCT
29895873 TAACTTANNN
Statistics
Matches: 267, Mismatches: 20, Indels: 45
0.80 0.06 0.14
Matches are distributed among these distances:
70 2 0.01
71 7 0.03
72 11 0.04
73 24 0.09
74 152 0.57
75 52 0.19
76 5 0.02
77 12 0.04
78 2 0.01
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (74 bp):
AACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACCTAAC
TTAATTAAA
Found at i:29895808 original size:23 final size:21
Alignment explanation
Indices: 29895709--29895814 Score: 117
Period size: 23 Copynumber: 4.8 Consensus size: 21
29895699 TTAACCTAAA
*
29895709 TTAATTAAAAACCCT-AACCTAAT
1 TTAATTAAAAACCCTAAACC---C
29895732 TTAATTAAAAACCCTAAACCC
1 TTAATTAAAAACCCTAAACCC
*
29895753 TTAATTAAAAACCCT-AACCTAAT
1 TTAATTAAAAACCCTAAACC---C
29895776 TTAATTAAAAACCCTAAACCC
1 TTAATTAAAAACCCTAAACCC
29895797 TTAACTTAAAAACCCTAA
1 TTAA-TTAAAAACCCTAA
29895815 CATTAACCTA
Statistics
Matches: 74, Mismatches: 3, Indels: 13
0.82 0.03 0.14
Matches are distributed among these distances:
20 4 0.05
21 19 0.26
22 13 0.18
23 30 0.41
24 8 0.11
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (21 bp):
TTAATTAAAAACCCTAAACCC
Found at i:29895826 original size:20 final size:22
Alignment explanation
Indices: 29895737--29895826 Score: 73
Period size: 21 Copynumber: 4.2 Consensus size: 22
29895727 CTAATTTAAT
* *
29895737 TAAAAACCCTAAACCCTTAA-T
1 TAAAAACCCTAAACCATTAACC
*
29895758 TAAAAACCCT-AACCTAATTTAA-T
1 TAAAAACCCTAAACC--A-TTAACC
* *
29895781 TAAAAACCCTAAACCCTTAACT
1 TAAAAACCCTAAACCATTAACC
29895803 TAAAAACCCT-AA-CATTAACC
1 TAAAAACCCTAAACCATTAACC
29895823 TAAA
1 TAAA
29895827 TTAATTAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
20 14 0.23
21 16 0.27
22 11 0.18
23 15 0.25
24 4 0.07
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAAAACCCTAAACCATTAACC
Found at i:29896045 original size:23 final size:23
Alignment explanation
Indices: 29896019--29896124 Score: 94
Period size: 23 Copynumber: 4.4 Consensus size: 23
29896009 AGAACAACCA
29896019 AACCTAATTTAATTAAAAACCTT
1 AACCTAATTTAATTAAAAACCTT
*
29896042 AACCTAATTTAATTAAAAACCCTA
1 AACCTAATTTAATTAAAAA-CCTT
*
29896066 AACCCTTAA-TTAA--AAACCCTAACCCT
1 AA-CC-TAATTTAATTAAA----AACCTT
29896092 AACCTAATTTAATTAAAAA-CTCT
1 AACCTAATTTAATTAAAAACCT-T
29896115 AACCTAATTT
1 AACCTAATTT
29896125 TACATAATTT
Statistics
Matches: 68, Mismatches: 4, Indels: 22
0.72 0.04 0.23
Matches are distributed among these distances:
22 1 0.01
23 35 0.51
24 8 0.12
25 12 0.18
26 7 0.10
27 5 0.07
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (23 bp):
AACCTAATTTAATTAAAAACCTT
Found at i:29896076 original size:21 final size:20
Alignment explanation
Indices: 29896027--29896091 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 20
29896017 CAAACCTAAT
* *
29896027 TTAATTAAAAACCTTAACCTAAT
1 TTAATTAAAAACCCTAACC---C
29896050 TTAATTAAAAACCCTAAACCC
1 TTAATTAAAAACCCT-AACCC
29896071 TTAATTAAAAACCCTAACCC
1 TTAATTAAAAACCCTAACCC
29896091 T
1 T
29896092 AACCTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.15
21 15 0.38
23 14 0.36
24 4 0.10
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (20 bp):
TTAATTAAAAACCCTAACCC
Found at i:29896077 original size:44 final size:46
Alignment explanation
Indices: 29896027--29896116 Score: 121
Period size: 50 Copynumber: 1.9 Consensus size: 46
29896017 CAAACCTAAT
29896027 TTAATTAAAAA-CCT-TAACCTAATTTAATTAAAAACCCTAAACCC
1 TTAATTAAAAACCCTCTAACCTAATTTAATTAAAAACCCTAAACCC
*
29896071 TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACTCTAA
1 TTAATTAAAAACCCT----CTAACCTAATTTAATTAAAAACCCTAA
29896117 CCTAATTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
44 11 0.28
45 3 0.08
50 25 0.64
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (46 bp):
TTAATTAAAAACCCTCTAACCTAATTTAATTAAAAACCCTAAACCC
Found at i:29899487 original size:124 final size:126
Alignment explanation
Indices: 29899322--29899673 Score: 534
Period size: 126 Copynumber: 2.8 Consensus size: 126
29899312 CCCAAACATG
*
29899322 CTACTGTAGCAAAAGCGCG-TCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGCTCCACGA-GGCACGATTTCACAAATTCTTCTCAAATAGCATCCTG
*
29899386 CTAGAAGCGATTTTATATTA-TTGATCAGAAACGTCAAAGAAA-AATTATTTCTTACATGAC
65 CTAGAAGCGATTTTATATTATTTGATCAGAAACGTCAAAAAAATAATTATTTCTTACATGAC
* * *
29899446 CTACTGTAGCAAAAGCGCGCT-GACGAGGCCTCGATTTCACAAATTCTTCTCAAATAGCATCCTA
1 CTACTGTAGCAAAAGCGCGCTCCACGAGG-CACGATTTCACAAATTCTTCTCAAATAGCATCCTG
* * * * *
29899510 CTAGAAGCGATTTTATACTATTTGCTTAGAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
65 CTAGAAGCGATTTTATATTATTTGATCAGAAACGTCAAAAAAATAATTATTTCTTACATGAC
*
29899572 CTACTGTAGTAAAAGCGC-CTCCACGAGAGCACGATTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGCTCCACGAG-GCACGATTTCACAAATTCTTCTCAAATAGCATCCTG
*
29899636 CTAGAAGCGATTTTATATTATTTTATCAGAAACGTCAA
65 CTAGAAGCGATTTTATATTATTTGATCAGAAACGTCAA
29899674 CTCGAAATTA
Statistics
Matches: 205, Mismatches: 17, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
123 2 0.01
124 75 0.37
125 22 0.11
126 105 0.51
127 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGCTCCACGAGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATATTATTTGATCAGAAACGTCAAAAAAATAATTATTTCTTACATGAC
Found at i:29900457 original size:10 final size:10
Alignment explanation
Indices: 29900437--29900509 Score: 51
Period size: 11 Copynumber: 7.1 Consensus size: 10
29900427 TCACTTAATT
29900437 AATTTTT-AA
1 AATTTTTAAA
29900446 AATTTTTAAA
1 AATTTTTAAA
** *
29900456 AATTCAATGAA
1 AATT-TTTAAA
*
29900467 AATTATATAAA
1 AATT-TTTAAA
29900478 ATATTTTTAAA
1 A-ATTTTTAAA
*
29900489 AATTATT-AA
1 AATTTTTAAA
29900498 AATTATTTAAA
1 AATT-TTTAAA
29900509 A
1 A
29900510 TGTATAAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
9 13 0.26
10 13 0.26
11 21 0.42
12 3 0.06
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (10 bp):
AATTTTTAAA
Found at i:29900478 original size:31 final size:29
Alignment explanation
Indices: 29900443--29900519 Score: 82
Period size: 33 Copynumber: 2.5 Consensus size: 29
29900433 AATTAATTTT
29900443 TAAAATTTTTAAAAATTCAATGAAAATTATA
1 TAAAATTTTTAAAAATT--ATGAAAATTATA
* *
29900474 TAAAATATTTTTAAAAATTATTAAAATTATT
1 T-AAA-ATTTTTAAAAATTATGAAAATTATA
* *
29900505 TAAAATGTATAAAAA
1 TAAAATTTTTAAAAA
29900520 ATATATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 9 0.22
30 3 0.08
31 12 0.30
32 3 0.08
33 13 0.32
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (29 bp):
TAAAATTTTTAAAAATTATGAAAATTATA
Found at i:29900490 original size:22 final size:21
Alignment explanation
Indices: 29900465--29900528 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
29900455 AAATTCAATG
29900465 AAAATTATATAAAATATTTTT
1 AAAATTATATAAAATATTTTT
*
29900486 AAAAATTAT-TAAAAT-TATTT
1 -AAAATTATATAAAATATTTTT
*
29900506 AAAATGTATAAAAAATATATTTT
1 AAAAT-TATATAAAATAT-TTTT
29900529 TAATATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
19 5 0.14
20 7 0.20
21 11 0.31
22 9 0.26
23 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AAAATTATATAAAATATTTTT
Found at i:29900500 original size:42 final size:42
Alignment explanation
Indices: 29900438--29900528 Score: 105
Period size: 42 Copynumber: 2.1 Consensus size: 42
29900428 CACTTAATTA
* *
29900438 ATTTTTAAAATTTTTAAAAATTCAATGAAAAT-TATATAAAAT
1 ATTTTTAAAATTATTAAAAATT-AATGAAAATGTATAAAAAAT
* *
29900480 ATTTTTAAAAATTATT-AAAATTATTTAAAATGTATAAAAAAT
1 ATTTTT-AAAATTATTAAAAATTAATGAAAATGTATAAAAAAT
29900522 ATATTTT
1 AT-TTTT
29900529 TAATATTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
41 7 0.17
42 23 0.55
43 12 0.29
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (42 bp):
ATTTTTAAAATTATTAAAAATTAATGAAAATGTATAAAAAAT
Found at i:29900510 original size:10 final size:10
Alignment explanation
Indices: 29900437--29900510 Score: 55
Period size: 10 Copynumber: 7.3 Consensus size: 10
29900427 TCACTTAATT
29900437 AATT-TTTAA
1 AATTATTTAA
29900446 AATT-TTTAAA
1 AATTATTT-AA
* *
29900456 AATTCAATGAA
1 AATT-ATTTAA
*
29900467 AATTATATAA
1 AATTATTTAA
*
29900477 AATATTTTTAAA
1 AAT-TATTT-AA
29900489 AATTA-TTAA
1 AATTATTTAA
29900498 AATTATTTAA
1 AATTATTTAA
29900508 AAT
1 AAT
29900511 GTATAAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
9 14 0.27
10 21 0.41
11 10 0.20
12 6 0.12
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (10 bp):
AATTATTTAA
Found at i:29900549 original size:42 final size:40
Alignment explanation
Indices: 29900438--29900551 Score: 104
Period size: 43 Copynumber: 2.7 Consensus size: 40
29900428 CACTTAATTA
* *
29900438 ATTTTTAAAATTTTTAAAAATTCAATGAAAATTATATAAAATAT
1 ATTTTTAAAATTTTT-AAAATT---TTAAAATTATAAAAAATAT
* *
29900482 -TTTTAAAAATTATTAAAATTATTTAAAATGTATAAAAAATAT
1 ATTTTTAAAATTTTTAAAA-T-TTTAAAAT-TATAAAAAATAT
*
29900524 ATTTTTAATATTTTTAAACATTTTAAAA
1 ATTTTTAAAATTTTTAAA-ATTTTAAAA
29900552 ATTAAGTAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
41 6 0.10
42 22 0.38
43 28 0.48
44 2 0.03
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (40 bp):
ATTTTTAAAATTTTTAAAATTTTAAAATTATAAAAAATAT
Found at i:29902406 original size:18 final size:18
Alignment explanation
Indices: 29902385--29902426 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
29902375 TAGAAATTAT
*
29902385 TTTTTATCA-TATTAATAA
1 TTTTTATAATTATTAAT-A
29902403 TTTTTATAATTATTAATA
1 TTTTTATAATTATTAATA
29902421 TTTTTA
1 TTTTTA
29902427 AAAATATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTTATAATTATTAATA
Found at i:29902407 original size:19 final size:19
Alignment explanation
Indices: 29902382--29902425 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
29902372 TTTTAGAAAT
*
29902382 TATTTTTTATCA-TATTAA
1 TATTTTTTATAATTATTAA
*
29902400 TAATTTTTATAATTATTAA
1 TATTTTTTATAATTATTAA
29902419 TATTTTT
1 TATTTTT
29902426 AAAAATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTTTTATAATTATTAA
Found at i:29909786 original size:6 final size:6
Alignment explanation
Indices: 29909777--29909801 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29909767 CCAAATCCAT
29909777 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
29909802 TTGAAAACGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:29912443 original size:50 final size:49
Alignment explanation
Indices: 29912331--29912569 Score: 171
Period size: 49 Copynumber: 4.7 Consensus size: 49
29912321 ATTTGGGTAA
* * **
29912331 AGAGATCCCATGTAAGACCATGTCTAGGACATGACATTGGTATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCT-GGACATGGCATTGG---CACCGAG---ATG
* *
29912387 AGAGGTCCCATGTAAGACCATGTCTGGAACATGGCGTTGGCACCGAGGTG
1 AGAGGTCCCATGTAAGACCATGTCTGG-ACATGGCATTGGCACCGAGATG
* *
29912437 AGAGGTCTCCCA--TAAGACCATGTCTGGACATGGCATGGGCACCGATATG
1 AGAGG--TCCCATGTAAGACCATGTCTGGACATGGCATTGGCACCGAGATG
** * * * * *
29912486 AGAACTCCTATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCT-GGACATGGCATTGGCACCG-AGATG
* **
29912535 AAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCT-GGACATGGC
29912570 TTTAGCATGT
Statistics
Matches: 152, Mismatches: 24, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
47 4 0.03
48 1 0.01
49 65 0.43
50 36 0.24
52 5 0.03
53 5 0.03
55 2 0.01
56 34 0.22
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (49 bp):
AGAGGTCCCATGTAAGACCATGTCTGGACATGGCATTGGCACCGAGATG
Found at i:29916896 original size:42 final size:42
Alignment explanation
Indices: 29916803--29916898 Score: 101
Period size: 40 Copynumber: 2.3 Consensus size: 42
29916793 CAAGTCAGGC
* *
29916803 AGTTACACGGCCTGACACACAGGCGTGTGAGGCCATTTCAAG
1 AGTTACACGGCCTGACACACAGGCGCGTGAGACCATTTCAAG
* * *
29916845 AGTT--ACGGCCT-AGCACGCGGGCGCGTGAGACCATTTTGAA-
1 AGTTACACGGCCTGA-CACACAGGCGCGTGAGACCA-TTTCAAG
29916885 AGTTACACGGCCTG
1 AGTTACACGGCCTG
29916899 GCGTGTTTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
39 1 0.02
40 27 0.61
41 5 0.11
42 11 0.25
ACGTcount: A:0.24, C:0.26, G:0.30, T:0.20
Consensus pattern (42 bp):
AGTTACACGGCCTGACACACAGGCGCGTGAGACCATTTCAAG
Found at i:29924008 original size:45 final size:45
Alignment explanation
Indices: 29923944--29924077 Score: 173
Period size: 45 Copynumber: 3.0 Consensus size: 45
29923934 CGGGTAAATT
29923944 GGGTACCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACC
1 GGGTACCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACC
* * *
29923989 GGGTACCATTGATTTTAAAGGTGGTTTCTATGTGTTGATTCCACC
1 GGGTACCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACC
* * * * * *
29924034 GAGTATCATTGACTATAAGGGTGG-TGTTGTGTGCTGA-TCCACC
1 GGGTACCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACC
29924077 G
1 G
29924078 TGTATCTGTT
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
43 7 0.09
44 9 0.12
45 61 0.79
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.35
Consensus pattern (45 bp):
GGGTACCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACC
Found at i:29929595 original size:27 final size:27
Alignment explanation
Indices: 29929564--29929663 Score: 67
Period size: 27 Copynumber: 3.7 Consensus size: 27
29929554 GCCTCGATGG
*
29929564 ACTAACCCATTTTTACTGTCCTAGTAA
1 ACTAACCCATGTTTACTGTCCTAGTAA
*** * * *
29929591 ACTAACTTGTTTTTACTGT-CTCGATGA
1 ACTAACCCATGTTTACTGTCCTAG-TAA
* * * * *
29929618 ACTAATCTATGTTTACTATCCCAGTAG
1 ACTAACCCATGTTTACTGTCCTAGTAA
*
29929645 ACTACCCCATGTTTACTGT
1 ACTAACCCATGTTTACTGT
29929664 TCCGAAAAAG
Statistics
Matches: 53, Mismatches: 18, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
26 3 0.06
27 48 0.91
28 2 0.04
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (27 bp):
ACTAACCCATGTTTACTGTCCTAGTAA
Found at i:29932852 original size:43 final size:42
Alignment explanation
Indices: 29932799--29932946 Score: 142
Period size: 43 Copynumber: 3.5 Consensus size: 42
29932789 TATCCCATAT
* * * *
29932799 ATGGTATTACATGTTATCACATATCGATGCATGTGTCCCAGAC
1 ATGGTCTTACACGTAATCACATAT-GATGCATATGTCCCAGAC
* *
29932842 A-GTGTCTTACACG-AATCATATATGGTGCCA-ATGTCCCAGAC
1 ATG-GTCTTACACGTAATCACATATGATG-CATATGTCCCAGAC
*
29932883 ATGGTCTTACACGTAATCTCATATTGATGC-TAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACATA-TGATGCAT-ATGTCCCAGAC
* *
29932926 ATGGTCTTACATGAAATCACA
1 ATGGTCTTACACGTAATCACA
29932947 ACTCGGAAGT
Statistics
Matches: 86, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
41 24 0.28
42 20 0.23
43 42 0.49
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (42 bp):
ATGGTCTTACACGTAATCACATATGATGCATATGTCCCAGAC
Found at i:29932881 original size:41 final size:43
Alignment explanation
Indices: 29932832--29932936 Score: 146
Period size: 43 Copynumber: 2.5 Consensus size: 43
29932822 TCGATGCATG
*
29932832 TGTCCCAGACA-GTGTCTTACACG-AA--TCATATATGGTGCCAA
1 TGTCCCAGACATG-GTCTTACACGTAATCTCATAT-TGATGCCAA
*
29932873 TGTCCCAGACATGGTCTTACACGTAATCTCATATTGATGCTAA
1 TGTCCCAGACATGGTCTTACACGTAATCTCATATTGATGCCAA
29932916 TGTCCCAGACATGGTCTTACA
1 TGTCCCAGACATGGTCTTACA
29932937 TGAAATCACA
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
41 21 0.36
42 3 0.05
43 28 0.48
44 6 0.10
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (43 bp):
TGTCCCAGACATGGTCTTACACGTAATCTCATATTGATGCCAA
Found at i:29933369 original size:68 final size:68
Alignment explanation
Indices: 29933284--29933504 Score: 336
Period size: 68 Copynumber: 3.2 Consensus size: 68
29933274 CTGTGAAATC
* * * * *
29933284 AACAGATTCGGATAGCTACATTTATTAAATAAAACAGCATAAATGGTAGTGCATTGAATAATGAA
1 AACACATTCGGACAGCTACATTTACTAAATAAAACAGCATAAATGATAGTGCATTGAATAGTGAA
29933349 TTT
66 TTT
* *
29933352 AACACATTCGGACAGCTACATTTACTAAATGAAACAGCATAAATGATAGTGCATTGAACAGTGAA
1 AACACATTCGGACAGCTACATTTACTAAATAAAACAGCATAAATGATAGTGCATTGAATAGTGAA
29933417 TTT
66 TTT
* *
29933420 AACACATTCGGACAGCTACATTTACTAAATAAAACAGCATAAATGATGGTGCTTTG-ATCAGTGA
1 AACACATTCGGACAGCTACATTTACTAAATAAAACAGCATAAATGATAGTGCATTGAAT-AGTGA
*
29933484 ATCT
65 ATTT
29933488 AACACATTCGGACAGCT
1 AACACATTCGGACAGCT
29933505 TAATTTTAAG
Statistics
Matches: 140, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
67 1 0.01
68 139 0.99
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (68 bp):
AACACATTCGGACAGCTACATTTACTAAATAAAACAGCATAAATGATAGTGCATTGAATAGTGAA
TTT
Found at i:29936392 original size:19 final size:20
Alignment explanation
Indices: 29936359--29936402 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
29936349 TTATTTTTTT
*
29936359 TAAAATATTTAT-AAATTTG
1 TAAAATATTTATAAAATTTA
29936378 TAAAATA-TTATTAAAATTTA
1 TAAAATATTTA-TAAAATTTA
29936398 TAAAA
1 TAAAA
29936403 AATACTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 8 0.36
20 11 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
TAAAATATTTATAAAATTTA
Found at i:29936916 original size:21 final size:20
Alignment explanation
Indices: 29936883--29936927 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
29936873 AAAAACAGAG
*
29936883 AAAAAATTATAAAAATTATA
1 AAAAAATCATAAAAATTATA
*
29936903 AAAAAATCATTAAAACTTATTA
1 AAAAAATCA-TAAAAATTA-TA
29936925 AAA
1 AAA
29936928 CTTATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 8 0.38
22 5 0.24
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAAATCATAAAAATTATA
Found at i:29936975 original size:28 final size:27
Alignment explanation
Indices: 29936941--29937025 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 27
29936931 ATAATAATTA
29936941 TTAGAAATTAATTAAAAACCATAAAAAT
1 TTAGAAATTAATTAAAAACCA-AAAAAT
* * * *
29936969 TTAGAAAAAAATAATTTATAA--AAAAATT
1 TTAG---AAATTAATTAAAAACCAAAAAAT
*
29936997 TTGGAAATTAATTAAAAACCAAAAAAT
1 TTAGAAATTAATTAAAAACCAAAAAAT
29937024 TT
1 TT
29937026 TATAAAAATA
Statistics
Matches: 43, Mismatches: 9, Indels: 11
0.68 0.14 0.17
Matches are distributed among these distances:
25 11 0.26
27 8 0.19
28 12 0.28
29 1 0.02
31 11 0.26
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (27 bp):
TTAGAAATTAATTAAAAACCAAAAAAT
Found at i:29936986 original size:15 final size:15
Alignment explanation
Indices: 29936966--29936995 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29936956 AAACCATAAA
29936966 AATTTAGAAAAAAAT
1 AATTTAGAAAAAAAT
*
29936981 AATTTATAAAAAAAT
1 AATTTAGAAAAAAAT
29936996 TTTGGAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
AATTTAGAAAAAAAT
Found at i:29937078 original size:24 final size:26
Alignment explanation
Indices: 29937020--29937070 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
29937010 AAAAACCAAA
*
29937020 AAATTTTATAAAAA-TATTTTTTTCC
1 AAATTTTATAAAAATTATTTTTCTCC
29937045 AAAATTTTATAAAAATTATTTTTCTC
1 -AAATTTTATAAAAATTATTTTTCTC
29937071 ATTTTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (26 bp):
AAATTTTATAAAAATTATTTTTCTCC
Found at i:29937171 original size:23 final size:23
Alignment explanation
Indices: 29937145--29937189 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29937135 TATGGTTTTT
29937145 AATTA-ATTTCTAACAATTTTCTA
1 AATTATATTTCTAA-AATTTTCTA
*
29937168 AATTATTTTTCTAAAATTTTCT
1 AATTATATTTCTAAAATTTTCT
29937190 GGTTTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (23 bp):
AATTATATTTCTAAAATTTTCTA
Found at i:29937203 original size:33 final size:34
Alignment explanation
Indices: 29937166--29937233 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
29937156 AACAATTTTC
** * *
29937166 TAAATTATTTTTCTA-AAATTTTCTGGTTTTTAA
1 TAAATTATTTTTAAATAAATTTTATGATTTTTAA
29937199 TAAATTATTTTTAAATAAATTTTATGATTTTTAA
1 TAAATTATTTTTAAATAAATTTTATGATTTTTAA
29937233 T
1 T
29937234 TCATTTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 13 0.43
34 17 0.57
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.57
Consensus pattern (34 bp):
TAAATTATTTTTAAATAAATTTTATGATTTTTAA
Found at i:29937259 original size:29 final size:29
Alignment explanation
Indices: 29937227--29937288 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
29937217 ATTTTATGAT
29937227 TTTTAATTC-ATTTATAAT-AATTATTATAA
1 TTTTAA-TCAATTT-TAATGAATTATTATAA
* *
29937256 TTTTAATCAATTTTAATGACTTTTTATAA
1 TTTTAATCAATTTTAATGAATTATTATAA
29937285 TTTT
1 TTTT
29937289 TATAAACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (29 bp):
TTTTAATCAATTTTAATGAATTATTATAA
Found at i:29937297 original size:20 final size:20
Alignment explanation
Indices: 29937274--29937313 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29937264 AATTTTAATG
29937274 ACTTTT-TATAATTTTTATAA
1 ACTTTTCTAT-ATTTTTATAA
*
29937294 ACTTTTCTATGTTTTTATAA
1 ACTTTTCTATATTTTTATAA
29937314 TTCTAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (20 bp):
ACTTTTCTATATTTTTATAA
Found at i:29937925 original size:31 final size:31
Alignment explanation
Indices: 29937857--29937925 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 31
29937847 ATTAATAAAA
* *
29937857 TTAAAATTTATTTTTATATATTTATTTATTT
1 TTAAAATTTATTTTTATATATTTATATATGT
* *
29937888 TCTAAAATATTTTTTTTATATTTTTATATA-GT
1 T-TAAAAT-TTATTTTTATATATTTATATATGT
29937920 TTAAAA
1 TTAAAA
29937926 GGCACCAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
31 6 0.19
32 8 0.25
33 18 0.56
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (31 bp):
TTAAAATTTATTTTTATATATTTATATATGT
Found at i:29938138 original size:16 final size:17
Alignment explanation
Indices: 29938112--29938144 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
29938102 TTTTAAATGA
*
29938112 TTTTTTATTAATTTTTG
1 TTTTTTATTAACTTTTG
29938129 TTTTTT-TTAACTTTTG
1 TTTTTTATTAACTTTTG
29938145 AATTTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTTTATTAACTTTTG
Found at i:29962482 original size:2 final size:2
Alignment explanation
Indices: 29962477--29962504 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29962467 AAAACCCATG
29962477 TA TA TA 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
29962505 ATTTTAAAGA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29962890 original size:19 final size:19
Alignment explanation
Indices: 29962866--29962904 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
29962856 TGTGATGTGA
29962866 AATTATTGTCTTTATGCGT
1 AATTATTGTCTTTATGCGT
29962885 AATTATTGTCTTTATGCGT
1 AATTATTGTCTTTATGCGT
29962904 A
1 A
29962905 TGGTATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.51
Consensus pattern (19 bp):
AATTATTGTCTTTATGCGT
Found at i:29964609 original size:40 final size:40
Alignment explanation
Indices: 29964469--29964606 Score: 168
Period size: 40 Copynumber: 3.5 Consensus size: 40
29964459 AGCTTGCATA
* * *
29964469 GGGAGTTTCACTGATACACAACTTATCACTAAGCTCACAG
1 GGGAGCTTCGCTGATACACAGCTTATCACTAAGCTCACAG
* * * * * * *
29964509 GGGAGCTTTGTTCATACACAGCTTCTTACTAAGTTCACAA
1 GGGAGCTTCGCTGATACACAGCTTATCACTAAGCTCACAG
* *
29964549 GGGAGCTTCGCTGATACATAGCTTATCACTAAGCTCACGG
1 GGGAGCTTCGCTGATACACAGCTTATCACTAAGCTCACAG
29964589 GGGAGCTTCGCTGATACA
1 GGGAGCTTCGCTGATACA
29964607 TAGGGGTGTG
Statistics
Matches: 79, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.27
Consensus pattern (40 bp):
GGGAGCTTCGCTGATACACAGCTTATCACTAAGCTCACAG
Found at i:29964873 original size:18 final size:18
Alignment explanation
Indices: 29964840--29964892 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
29964830 ATTCACCTAA
*
29964840 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
29964859 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
29964877 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
29964893 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:29964955 original size:19 final size:20
Alignment explanation
Indices: 29964921--29964970 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
29964911 ATTTAATAAA
29964921 TAAAAATAAAATTCTAAAAC
1 TAAAAATAAAATTCTAAAAC
*
29964941 TAAAACTAAAA-TCTAAAAGTC
1 TAAAAATAAAATTCTAAAA--C
29964962 TAAAAATAA
1 TAAAAATAA
29964971 TTTAATTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 7 0.27
20 10 0.38
21 9 0.35
ACGTcount: A:0.64, C:0.10, G:0.02, T:0.24
Consensus pattern (20 bp):
TAAAAATAAAATTCTAAAAC
Found at i:29965008 original size:9 final size:9
Alignment explanation
Indices: 29964990--29965083 Score: 125
Period size: 9 Copynumber: 10.4 Consensus size: 9
29964980 GTAGTGATTC
29964990 AATTCGGTT
1 AATTCGGTT
*
29964999 AATTCAGTT
1 AATTCGGTT
*
29965008 AATTCGGGT
1 AATTCGGTT
29965017 AATTCGGTT
1 AATTCGGTT
*
29965026 AATTCGGGT
1 AATTCGGTT
*
29965035 AATCCGGTT
1 AATTCGGTT
*
29965044 AATTCAGTT
1 AATTCGGTT
*
29965053 AATTCGGGT
1 AATTCGGTT
29965062 AATTCGGTT
1 AATTCGGTT
*
29965071 AATTCAGTT
1 AATTCGGTT
29965080 AATT
1 AATT
29965084 TTTAACCAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 72 1.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:29966832 original size:2 final size:2
Alignment explanation
Indices: 29966816--29966861 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
29966806 TTATGAATAG
* *
29966816 TA TA TA AA TA AA TA TA TA TA 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 TA TA TA TA TA TA
29966858 TA TA
1 TA TA
29966862 CAAATGTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:29968735 original size:18 final size:18
Alignment explanation
Indices: 29968712--29968750 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29968702 TTTAAGTGTG
29968712 TTTAAATAT-ATATATATA
1 TTTAAAT-TCATATATATA
*
29968730 TTTAAATTCATATATTTA
1 TTTAAATTCATATATATA
29968748 TTT
1 TTT
29968751 CGAATACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAATTCATATATATA
Found at i:29971596 original size:23 final size:23
Alignment explanation
Indices: 29971561--29971914 Score: 192
Period size: 23 Copynumber: 15.2 Consensus size: 23
29971551 TATATATACC
*
29971561 AATTTGGATAGCACTTATACACAA
1 AATTT-GACAGCACTTATACACAA
*
29971585 AATTTGACAGCA-TGTATATACAA
1 AATTTGACAGCACT-TATACACAA
* * * *
29971608 AATTGGACAACATTTATTCACCAA
1 AATTTGACAGCACTTATACA-CAA
* * * *
29971632 AATTAGGCAGCA-TATATATAC-C
1 AATTTGACAGCACT-TATACACAA
*
29971654 GATTTGGACAGCACTTATACACAA
1 AATTT-GACAGCACTTATACACAA
*
29971678 AATTTGACAGCA-TGTATATACAA
1 AATTTGACAGCACT-TATACACAA
* * *
29971701 AATTGGACAGCATTTATTCACCAA
1 AATTTGACAGCACTTATACA-CAA
* * *
29971725 AATTGGGCAGCATACATATAC-C--
1 AATTTGACAGC--ACTTATACACAA
*
29971747 AATTTGGACAACACTTATACACAA
1 AATTT-GACAGCACTTATACACAA
29971771 AATTTGACAGCA-TGTATACACAA
1 AATTTGACAGCACT-TATACACAA
* * * *
29971794 AATTGGACAACATTTATTCACCAA
1 AATTTGACAGCACTTATACA-CAA
* * *
29971818 AATTGGGCAGCATACATATAC-C--
1 AATTTGACAGC--ACTTATACACAA
29971840 AATTTGGACAGCACTTATACACAA
1 AATTT-GACAGCACTTATACACAA
*
29971864 AATTTGACAGCA-TGTATATACAA
1 AATTTGACAGCACT-TATACACAA
* * * *
29971887 AATTGGACAACATTTATTCACCAA
1 AATTTGACAGCACTTATACA-CAA
29971911 AATT
1 AATT
29971915 GGGCAGCATG
Statistics
Matches: 255, Mismatches: 47, Indels: 56
0.71 0.13 0.16
Matches are distributed among these distances:
21 14 0.05
22 17 0.07
23 140 0.55
24 74 0.29
26 10 0.04
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (23 bp):
AATTTGACAGCACTTATACACAA
Found at i:29971650 original size:93 final size:93
Alignment explanation
Indices: 29971506--29971937 Score: 756
Period size: 93 Copynumber: 4.6 Consensus size: 93
29971496 CATATATATA
* * * * *
29971506 TATATACAAAACTGGACAGCATTTATTCACCAAAATTGGGCAGTATATATATACCAATTTGGATA
1 TATATACAAAATTGGACAACATTTATTCACCAAAATTGGGCAGCATACATATACCAATTTGGACA
29971571 GCACTTATACACAAAATTTGACAGCATG
66 GCACTTATACACAAAATTTGACAGCATG
* * *
29971599 TATATACAAAATTGGACAACATTTATTCACCAAAATTAGGCAGCATATATATACCGATTTGGACA
1 TATATACAAAATTGGACAACATTTATTCACCAAAATTGGGCAGCATACATATACCAATTTGGACA
29971664 GCACTTATACACAAAATTTGACAGCATG
66 GCACTTATACACAAAATTTGACAGCATG
*
29971692 TATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATACATATACCAATTTGGACA
1 TATATACAAAATTGGACAACATTTATTCACCAAAATTGGGCAGCATACATATACCAATTTGGACA
*
29971757 ACACTTATACACAAAATTTGACAGCATG
66 GCACTTATACACAAAATTTGACAGCATG
*
29971785 TATACACAAAATTGGACAACATTTATTCACCAAAATTGGGCAGCATACATATACCAATTTGGACA
1 TATATACAAAATTGGACAACATTTATTCACCAAAATTGGGCAGCATACATATACCAATTTGGACA
29971850 GCACTTATACACAAAATTTGACAGCATG
66 GCACTTATACACAAAATTTGACAGCATG
*
29971878 TATATACAAAATTGGACAACATTTATTCACCAAAATTGGGCAGCATGCATATACCAATTT
1 TATATACAAAATTGGACAACATTTATTCACCAAAATTGGGCAGCATACATATACCAATTT
29971938 TAGAATACCA
Statistics
Matches: 323, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 323 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.28
Consensus pattern (93 bp):
TATATACAAAATTGGACAACATTTATTCACCAAAATTGGGCAGCATACATATACCAATTTGGACA
GCACTTATACACAAAATTTGACAGCATG
Found at i:29971947 original size:14 final size:14
Alignment explanation
Indices: 29971928--29971955 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29971918 CAGCATGCAT
29971928 ATACCAATTTTAGA
1 ATACCAATTTTAGA
29971942 ATACCAATTTTAGA
1 ATACCAATTTTAGA
29971956 CCGTTAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
ATACCAATTTTAGA
Found at i:29972684 original size:28 final size:28
Alignment explanation
Indices: 29972652--29972773 Score: 167
Period size: 28 Copynumber: 4.4 Consensus size: 28
29972642 AATAAGTTCG
* * *
29972652 CACACTTAGTGCTTAATAATCAAACTCA
1 CACACTTAGTGCTTTACAATTAAACTCA
*
29972680 CACACTTAGTGCTTTACCATTAAACTCA
1 CACACTTAGTGCTTTACAATTAAACTCA
29972708 CACACTTAGTGCTTTACAATT-AACT-A
1 CACACTTAGTGCTTTACAATTAAACTCA
* *
29972734 GCACACTTAGTGCTTTACAATTAAATTCG
1 -CACACTTAGTGCTTTACAATTAAACTCA
29972763 CACACTTAGTG
1 CACACTTAGTG
29972774 TCGAAAGTCA
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
26 1 0.01
27 25 0.30
28 58 0.69
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.32
Consensus pattern (28 bp):
CACACTTAGTGCTTTACAATTAAACTCA
Found at i:29972748 original size:55 final size:56
Alignment explanation
Indices: 29972652--29972773 Score: 167
Period size: 55 Copynumber: 2.2 Consensus size: 56
29972642 AATAAGTTCG
* *
29972652 CACACTTAGTGCTTAATAATCAAACTCACACACTTAGTGCTTTACCATTAAACTCA
1 CACACTTAGTGCTTAACAATCAAACTCACACACTTAGTGCTTTACAATTAAACTCA
* * * *
29972708 CACACTTAGTGCTTTACAAT-TAACT-AGCACACTTAGTGCTTTACAATTAAATTCG
1 CACACTTAGTGCTTAACAATCAAACTCA-CACACTTAGTGCTTTACAATTAAACTCA
29972763 CACACTTAGTG
1 CACACTTAGTG
29972774 TCGAAAGTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
54 1 0.02
55 40 0.68
56 18 0.31
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.32
Consensus pattern (56 bp):
CACACTTAGTGCTTAACAATCAAACTCACACACTTAGTGCTTTACAATTAAACTCA
Found at i:29972834 original size:2 final size:2
Alignment explanation
Indices: 29972827--29972877 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
29972817 CACTACATGC
29972827 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29972869 AT AT AT AT A
1 AT AT AT AT A
29972878 CCATTCAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29979525 original size:70 final size:70
Alignment explanation
Indices: 29978076--29979514 Score: 1614
Period size: 70 Copynumber: 20.6 Consensus size: 70
29978066 CAGCTGACGA
* *
29978076 TTAAGGCTCGCAGGTTCAATACTGTAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
29978141 GTATC
66 GTATC
* * ** **
29978146 TTAAGACTTGCAGGTTCAATACCATAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAATTG
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
29978211 GTATC
66 GTATC
* * * * *
29978216 TTAAGGCTCGCAGGTTCAATACCGTAGCCTCCAAAACAGTTAGTGCAAGCCTACGTTCCTAGCTG
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
*
29978281 ATATC
66 GTATC
* * * *
29978286 CTAAGACTCGCAGGTTTAATACCGCAACCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
*
29978351 ATATC
66 GTATC
* * * * * * * *
29978356 CTAAGGCTCGTAGCTTTAATACCGCTGCCTCCAAAATAATTAGCGCGAGCCTACACTCCCAGCTG
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
*
29978421 ATAT-
66 GTATC
* *** * * * * *
29978425 TCTAAGGCTCGTAGGTTCAATACTATAGCCTCCAAAACAGTTAACGTGAGCTTACGCTCCTAGGT
1 T-TAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCT
29978490 GGTATC
65 GGTATC
* * * ** * *
29978496 ATAAGGCTCGCAGGTTCAATACCGTAACCTCCAAAACAGTTAGCGCGAGTTTATGCTCCCAGCTA
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
29978561 GTATC
66 GTATC
* * * * * **
29978566 TTAAGGCTCACAGGTTCAATATCACAGCCTCCAAAATAGTTAGCGCGAGCTTACGCTCCCAAATG
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
29978631 GTATC
66 GTATC
* * * * * * * *
29978636 CTAAGGCTTGCATGTTCAATACTGCAACCTCTAAAACAGTTAACGCGAGCCTACGCTCCTAGCTG
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
*
29978701 ATATC
66 GTATC
* * * * *
29978706 CTAAGGCTCACAGGTTCAATACCGCAGCCTCCAAAATAGTTAGCGTGAGCCTATGCTCCCAGCTG
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
*
29978771 ATATC
66 GTATC
** * * *
29978776 TTAAGGCTCGCAGGTTCAATACTACAACCTCCAAAA-TGATTAGCGCGAGCTTACGCTCCCAGCT
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAG-TTAGCGCGAGCCTACGCTCCCAGCT
29978840 GGTATC
65 GGTATC
* * * ** * * * * *
29978846 ATAAGGCTCGTAGGTTTAATATTGCAGCTTCCAAAATAGTTAGTGCGAGCTTATGCTCCCAGCTG
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
29978911 GTATC
66 GTATC
* * *
29978916 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGTGCGAACCTACGCTCCCAGTTG
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
29978981 GTATC
66 GTATC
* * * * * * * * *
29978986 CTAAGGCTTGCAGGTTCAATACTGCA-ACTCTAAAACAATTAGCGTGAGCATA--CTCCCAGTTG
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
*
29979048 ATATC
66 GTATC
* * * * *
29979053 TTAAGGCTCCCAGGTTCAATACCGCAGCCTCCAAAACAATTAGCGCGAGCTTATGCTCCCAGTTG
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
*
29979118 GTACC
66 GTATC
* * * *
29979123 TTAAGGCTCACAAGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAACCTACGCTCCCAACTG
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
29979188 GTATC
66 GTATC
* * * * * * *
29979193 CTAAGGCTTGCAGGTTCAATACCGCA-ACTCTAAAACAATTAGCGTGAGCCTACGCTCCCAGTTG
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
*
29979257 ATATC
66 GTATC
* * * * * * * *
29979262 CTAAGGCTCGCAAGTTCAATACCGCAGCATACAAAATAGTTAGTGCGAGCTTACGCTCCCAACTG
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
29979327 GTATC
66 GTATC
* * *
29979332 TTAAGGCTTGCAGATTCAATACCGCAACCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCA-CTT
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGC-T
29979396 GGTATC
65 GGTATC
* * * * * * *
29979402 CTAAGGCTCGCAGGTTCAATATCGCAGCATCCAAAATAGTTAGCGCGAGCTTACACTCCCAGCTA
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
*
29979467 ATATC
66 GTATC
*
29979472 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAATAGTTAG
1 TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAG
29979515 TGCCAACTTA
Statistics
Matches: 1148, Mismatches: 211, Indels: 20
0.83 0.15 0.01
Matches are distributed among these distances:
67 36 0.03
68 22 0.02
69 80 0.07
70 1008 0.88
71 2 0.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (70 bp):
TTAAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAGCTG
GTATC
Found at i:29979994 original size:7 final size:7
Alignment explanation
Indices: 29979982--29980007 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29979972 TTTATATTAA
29979982 TTTATAT
1 TTTATAT
29979989 TTTATAT
1 TTTATAT
29979996 TTTATAT
1 TTTATAT
29980003 TTTAT
1 TTTAT
29980008 TATATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTATAT
Found at i:29980543 original size:30 final size:26
Alignment explanation
Indices: 29980483--29980552 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 26
29980473 AAAATTTCAG
29980483 TAATT-AAATAAAATAAAATTATTAA
1 TAATTAAAATAAAATAAAATTATTAA
*
29980508 T-ATTAAAATAAAATAAATATTTTTAAAAA
1 TAATTAAAATAAAATAAA-ATTATT---AA
*
29980537 TAATTAAAATATAATA
1 TAATTAAAATAAAATA
29980553 TGGGCGGGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
24 3 0.08
25 13 0.35
26 5 0.14
29 3 0.08
30 13 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
TAATTAAAATAAAATAAAATTATTAA
Found at i:29985023 original size:17 final size:18
Alignment explanation
Indices: 29984995--29985031 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
29984985 TCCTTAGTTA
*
29984995 TTGCATATTTTTAATATT
1 TTGCATATTTTTAAAATT
29985013 TTGCA-ATTTTTAAAATT
1 TTGCATATTTTTAAAATT
29985030 TT
1 TT
29985032 AAACAGTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (18 bp):
TTGCATATTTTTAAAATT
Found at i:29990403 original size:15 final size:15
Alignment explanation
Indices: 29990385--29990417 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29990375 TTTCCACTCT
*
29990385 TTTACTTTCTTTTCA
1 TTTAATTTCTTTTCA
29990400 TTTAATTTCTTTTCA
1 TTTAATTTCTTTTCA
29990415 TTT
1 TTT
29990418 CCTACATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTAATTTCTTTTCA
Found at i:29992373 original size:27 final size:27
Alignment explanation
Indices: 29992273--29992373 Score: 96
Period size: 27 Copynumber: 3.7 Consensus size: 27
29992263 CTTTAGAGTG
* *
29992273 CGCCACAAAGGCATTCC-CTTCATAGAT
1 CGCCACAAAGAC-TTCCTTTTCATAGAT
* *
29992300 TGCCACAAAGACTTTCTTTTCATAGAT
1 CGCCACAAAGACTTCCTTTTCATAGAT
** *
29992327 CGCCACAAAGACCACTTTTTCATAGAT
1 CGCCACAAAGACTTCCTTTTCATAGAT
* * *
29992354 CGACGCAAATACTTCCTTTT
1 CGCCACAAAGACTTCCTTTT
29992374 TTCTAGCATG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
26 3 0.05
27 55 0.95
ACGTcount: A:0.30, C:0.29, G:0.12, T:0.30
Consensus pattern (27 bp):
CGCCACAAAGACTTCCTTTTCATAGAT
Found at i:29996605 original size:101 final size:98
Alignment explanation
Indices: 29996489--29996742 Score: 267
Period size: 91 Copynumber: 2.6 Consensus size: 98
29996479 TATTATCAAG
*
29996489 AATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAA
1 AATTTTAT-TAATTATATAT-ATTATTAAA-TATATTTAATATTAATTATTTTAAATTATATAAA
29996554 TTCATATAAGAAAATTTATTA-TCAAGAATT-TTATG-
63 TTCATATAAGAAAATTTATTAGT-AAGAATTATT-TGA
* * *
29996589 AA----ATT-A-TATAT-TATTATTAAATTATATATAATAATAATTATTTTAAATTATACAAATT
1 AATTTTATTAATTATATATATTATTAAA-TATATTTAATATTAATTATTTTAAATTATATAAATT
* * *
29996647 CATATAAGAAAATTTATTAGTTATAATTATTTTA
65 CATATAAGAAAATTTATTAGTAAGAATTATTTGA
* * *
29996681 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATAT
1 AATTTTATT-AATTATATATATT-ATT-AAATATATTTAATATTAATTATTTTAAATTATAT
29996743 TTTATAGTAT
Statistics
Matches: 128, Mismatches: 13, Indels: 25
0.77 0.08 0.15
Matches are distributed among these distances:
91 68 0.53
92 6 0.05
93 5 0.04
94 1 0.01
96 5 0.04
98 1 0.01
99 4 0.03
100 5 0.04
101 30 0.23
102 3 0.02
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (98 bp):
AATTTTATTAATTATATATATTATTAAATATATTTAATATTAATTATTTTAAATTATATAAATTC
ATATAAGAAAATTTATTAGTAAGAATTATTTGA
Found at i:29996684 original size:91 final size:91
Alignment explanation
Indices: 29996393--29996665 Score: 510
Period size: 91 Copynumber: 3.0 Consensus size: 91
29996383 NNNTTGGCAC
29996393 TCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTAT
1 TCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTAT
29996458 ATAAATTCATATAAGAAAATTTATTA
66 ATAAATTCATATAAGAAAATTTATTA
29996484 TCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTAT
1 TCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTAT
29996549 ATAAATTCATATAAGAAAATTTATTA
66 ATAAATTCATATAAGAAAATTTATTA
* * *
29996575 TCAAGAATTTTATGAAATTATATATTATTATTAAATTATATATAATAATAATTATTTTAAATTAT
1 TCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTAT
*
29996640 ACAAATTCATATAAGAAAATTTATTA
66 ATAAATTCATATAAGAAAATTTATTA
29996666 GTTATAATTA
Statistics
Matches: 178, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 178 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (91 bp):
TCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTAT
ATAAATTCATATAAGAAAATTTATTA
Found at i:29996798 original size:37 final size:35
Alignment explanation
Indices: 29996757--29996926 Score: 100
Period size: 38 Copynumber: 4.7 Consensus size: 35
29996747 TAGTATCATA
*
29996757 TATTATGATTTTAGTAAATTCATATAAGAATATTGAT
1 TATTATGATTTTAGTAAATT-ATATAA-AATATTAAT
* * *
29996794 TATTAATAATTTTATTAAATTATAT---ATTTTAAT
1 TATT-ATGATTTTAGTAAATTATATAAAATATTAAT
* * * *
29996827 TATAAT-ATATTTAATAATAATTATGTTAAATTATCT-A-
1 TATTATGAT-TTTAGT-A-AATTAT-ATAAAATAT-TAAT
*
29996864 TATTATGATTTGAGTAAATTCATATAAGAATATTAAT
1 TATTATGATTTTAGTAAATT-ATATAA-AATATTAAT
* *
29996901 TATTAAGAATTTTATTAAATTATATA
1 TATTATG-ATTTTAGTAAATTATATA
29996927 TTTTAATTAT
Statistics
Matches: 101, Mismatches: 17, Indels: 30
0.68 0.11 0.20
Matches are distributed among these distances:
31 2 0.02
32 7 0.07
33 10 0.10
34 6 0.06
35 9 0.09
36 8 0.08
37 28 0.28
38 30 0.30
39 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.49
Consensus pattern (35 bp):
TATTATGATTTTAGTAAATTATATAAAATATTAAT
Found at i:29996809 original size:120 final size:119
Alignment explanation
Indices: 29996681--29997077 Score: 620
Period size: 120 Copynumber: 3.4 Consensus size: 119
29996671 AATTATTTTA
* * *
29996681 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTT-AAATTATATTTT
* *
29996746 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAT
65 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
29996801 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTA--T--GTTA-A----A
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTAAATTATATTTTA
*
29996857 T--TATC-TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 TAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
29996908 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT-TTAAATTATATTTT
*
29996973 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATACTGATTATTAAG
65 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
29997028 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT
29997078 GTTTAAATAT
Statistics
Matches: 254, Mismatches: 10, Indels: 26
0.88 0.03 0.09
Matches are distributed among these distances:
107 92 0.36
108 4 0.02
110 3 0.01
112 3 0.01
113 1 0.00
114 1 0.00
115 3 0.01
117 2 0.01
118 1 0.00
119 4 0.02
120 140 0.55
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (119 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTAAATTATATTTTA
TAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:29996836 original size:16 final size:16
Alignment explanation
Indices: 29996815--29996860 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
29996805 TTATTAAATT
29996815 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
29996831 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
29996846 AT-TATGTTAAATTAT
1 ATATAT-TTTAATTAT
29996861 CTATATTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:29996943 original size:16 final size:16
Alignment explanation
Indices: 29996922--29996968 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
29996912 TTATTAAATT
29996922 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
29996938 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
29996953 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
29996969 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:29996967 original size:227 final size:221
Alignment explanation
Indices: 29996550--29997085 Score: 751
Period size: 227 Copynumber: 2.4 Consensus size: 221
29996540 TTAAATTATA
* * * *
29996550 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATT-ATTA-AATTA
1 TAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATT-TTAATTATAA-TA
* * * *
29996613 TATATAATAATAATTATTTTAAATTATACAAATTCATATAAGAAAATTTATTAGTTATAATTATT
64 TATTTAATAATAATTATGTTAAATTATACAAATTCATATAAGAAAATTTATAAGATATAATTATT
* *
29996678 TTAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATAT
129 TAAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATAT
*
29996743 TTTATAGTATCATATATTATGATTTTAG
194 TTTATAGTATCATATATTATGATTTGAG
*
29996771 TAAATTCATATAAGAATATTGATTATTAATAATTTTATTAAATTATATATTTTAATTATAATATA
1 TAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
* * *
29996836 TTTAATAATAATTATGTTAAATTAT-CTATATT-ATGATTTGAGTAAATTCATATAAGAATATTA
66 TTTAATAATAATTATGTTAAATTATAC-AAATTCAT-A--TAAGAAAATT--TATAAG-ATA-TA
* *
29996899 ATTA-TTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-A
123 ATTATTTAA-AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCA
29996962 AATTATATTTTATAGTATCATATATTATGATTTGAG
186 AATTATATTTTATAGTATCATATATTATGATTTGAG
*
29996998 TAAATTCATATAAGAATACTGATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
1 TAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
29997063 TTTAATAATAATTATGTTTAAAT
66 TTTAATAATAATTATG-TTAAAT
29997086 ATGATTAAAT
Statistics
Matches: 283, Mismatches: 19, Indels: 19
0.88 0.06 0.06
Matches are distributed among these distances:
220 5 0.02
221 82 0.29
222 2 0.01
223 8 0.03
225 5 0.02
226 5 0.02
227 168 0.59
228 8 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (221 bp):
TAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
TTTAATAATAATTATGTTAAATTATACAAATTCATATAAGAAAATTTATAAGATATAATTATTTA
AAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTT
TATAGTATCATATATTATGATTTGAG
Found at i:29997063 original size:16 final size:16
Alignment explanation
Indices: 29997042--29997083 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
29997032 TTATTAAATT
*
29997042 ATATATTTTAATTATA
1 ATATATTTTAATAATA
29997058 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
29997073 AT-TATGTTTAA
1 ATATAT-TTTAA
29997084 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:29997068 original size:15 final size:15
Alignment explanation
Indices: 29997033--29997074 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29997023 TTAAGAATTT
*
29997033 TATTAAATTAT-ATA
1 TATTTAATTATAATA
29997047 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
29997061 TATTTAATAATAAT
1 TATTTAATTATAAT
29997075 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:29999435 original size:9 final size:9
Alignment explanation
Indices: 29999421--29999496 Score: 107
Period size: 9 Copynumber: 8.4 Consensus size: 9
29999411 TTTGGTTAAA
29999421 AATTAACCG
1 AATTAACCG
*
29999430 AATTAACTG
1 AATTAACCG
29999439 AATTAACCG
1 AATTAACCG
* *
29999448 GATTACCCG
1 AATTAACCG
29999457 AATTAACCG
1 AATTAACCG
*
29999466 AATTACCCG
1 AATTAACCG
*
29999475 AATTAACCA
1 AATTAACCG
29999484 AATTAACCG
1 AATTAACCG
29999493 AATT
1 AATT
29999497 GAATCACTAC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 57 1.00
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:29999776 original size:18 final size:18
Alignment explanation
Indices: 29999720--29999767 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
29999710 TCGAAACTGG
***
29999720 TCGGTTAACCGAATTTTT
1 TCGGTTAACCGAAAAATT
*
29999738 TCGGTTAACCGAAAAAAT
1 TCGGTTAACCGAAAAATT
29999756 TCGGTTAACCGA
1 TCGGTTAACCGA
29999768 CCAGTTTCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (18 bp):
TCGGTTAACCGAAAAATT
Found at i:30006949 original size:41 final size:40
Alignment explanation
Indices: 30006890--30007035 Score: 145
Period size: 41 Copynumber: 3.6 Consensus size: 40
30006880 CAGACTTATT
**
30006890 GTCTAGCAGGCTGGATGCCGGTGATATAATTCAGGCTATG
1 GTCTAGCAGGCTTAATGCCGGTGATATAATTCAGGCTATG
* * * *
30006930 TGCCTAGCAGGCTTAATGCCGGTGA-ATTAATTCAGACTTTAC
1 -GTCTAGCAGGCTTAATGCCGGTGATA-TAATTCAGGCTAT-G
* *
30006972 GTCTAGCAGGCTTAATGCCGGTGATACATTTC-GGACTATAG
1 GTCTAGCAGGCTTAATGCCGGTGATATAATTCAGG-CTAT-G
30007013 GTCTAGCAGGCTGTAA-GCCGGTG
1 GTCTAGCAGGCT-TAATGCCGGTG
30007036 TATCGAATCA
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
40 2 0.02
41 82 0.93
42 4 0.05
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (40 bp):
GTCTAGCAGGCTTAATGCCGGTGATATAATTCAGGCTATG
Found at i:30009811 original size:15 final size:16
Alignment explanation
Indices: 30009793--30009822 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30009783 ATTTTTTATT
30009793 GAAAAAT-TTTCAATC
1 GAAAAATGTTTCAATC
30009808 GAAAAATGTTTCAAT
1 GAAAAATGTTTCAAT
30009823 AATCACAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (16 bp):
GAAAAATGTTTCAATC
Found at i:30017951 original size:13 final size:13
Alignment explanation
Indices: 30017928--30017971 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
30017918 AACCCCAATT
30017928 TTTCATTTTCTTTC
1 TTTC-TTTTCTTTC
30017942 TTTCTTTTCTTTC
1 TTTCTTTTCTTTC
*
30017955 TTTC-CTTCTTTC
1 TTTCTTTTCTTTC
*
30017967 ATTCT
1 TTTCT
30017972 CTATTTCGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 10 0.37
13 13 0.48
14 4 0.15
ACGTcount: A:0.05, C:0.25, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTCTTTTCTTTC
Found at i:30018062 original size:13 final size:13
Alignment explanation
Indices: 30018041--30018072 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
30018031 TTTGATTAAT
*
30018041 TAATGTAATATAA
1 TAATATAATATAA
30018054 TAATATAATATAA
1 TAATATAATATAA
30018067 TAATAT
1 TAATAT
30018073 TTTAATCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
TAATATAATATAA
Found at i:30030359 original size:3 final size:3
Alignment explanation
Indices: 30030353--30030396 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
30030343 AAAAAGAGAT
30030353 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
30030397 TGAAACCATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:30038130 original size:17 final size:17
Alignment explanation
Indices: 30038110--30038143 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
30038100 ATTAATTGAT
30038110 TTATATAATTAAATCAA
1 TTATATAATTAAATCAA
30038127 TTATATAATTAAATCAA
1 TTATATAATTAAATCAA
30038144 AAAATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
TTATATAATTAAATCAA
Found at i:30038510 original size:23 final size:22
Alignment explanation
Indices: 30038479--30038535 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
30038469 TCCAAGTAAA
*
30038479 TTTTAAATGTTGTCCAAAATATG
1 TTTT-AATGTTATCCAAAATATG
* *
30038502 TTTTGAATGTCATCCAAAGTATG
1 TTTT-AATGTTATCCAAAATATG
30038525 TTTTAATGTTA
1 TTTTAATGTTA
30038536 ATATTGTAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 6 0.21
23 23 0.79
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.46
Consensus pattern (22 bp):
TTTTAATGTTATCCAAAATATG
Found at i:30039460 original size:2 final size:2
Alignment explanation
Indices: 30039453--30039479 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30039443 ATGAAATAAG
30039453 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
30039480 AATGTGGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30045526 original size:18 final size:18
Alignment explanation
Indices: 30045503--30045550 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
30045493 AAAATATGAG
*
30045503 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
30045521 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
30045539 AAATGATGTTCA
1 AAATGATGTTCA
30045551 AATTGATGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:30046074 original size:72 final size:72
Alignment explanation
Indices: 30045979--30046217 Score: 365
Period size: 72 Copynumber: 3.3 Consensus size: 72
30045969 CAATGCTAAA
* *
30045979 CTAGTTTTATCAATAATTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
*
30046044 TTGTAAT
66 CTGTAAT
* *
30046051 CTAGTTGTATCAATGGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
*
30046116 GTGTAAT
66 CTGTAAT
* * *
30046123 CTAGTTTTATTAATAGTTGTTTATGTTCGGTCTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
*
30046188 ACT-AAAT
66 -CTGTAAT
30046195 -TAGTTTTATCAATAGTTGTTTAT
1 CTAGTTTTATCAATAGTTGTTTAT
30046218 ATATGATTTT
Statistics
Matches: 153, Mismatches: 13, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
71 22 0.14
72 130 0.85
73 1 0.01
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.55
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
CTGTAAT
Found at i:30053622 original size:2 final size:2
Alignment explanation
Indices: 30053617--30053646 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30053607 GGTATATAAG
30053617 TA TA TA TA 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
30053647 AATGTTCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30054509 original size:41 final size:41
Alignment explanation
Indices: 30054464--30054593 Score: 176
Period size: 41 Copynumber: 3.2 Consensus size: 41
30054454 TATATTGTCA
*
30054464 GTGAATCAATTCAGGCTAAAAGCCTAGCAGGCTAAGTGCCG
1 GTGAATCAATTCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
*
30054505 GTGAACTGAATT-AGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GTGAA-TCAATTCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
* *
30054546 ATG-ATCTGAA-TCAGGCTTTAAGCCTAGCAGGCTAAGTGCCG
1 GTGAATC--AATTCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
30054587 GTGAATC
1 GTGAATC
30054594 TGTTTAAATT
Statistics
Matches: 78, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
39 1 0.01
40 2 0.03
41 67 0.86
42 8 0.10
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (41 bp):
GTGAATCAATTCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
Found at i:30054852 original size:46 final size:45
Alignment explanation
Indices: 30054758--30054853 Score: 124
Period size: 44 Copynumber: 2.1 Consensus size: 45
30054748 AAATTGTTGG
* *
30054758 ATATATATATGTGTACGCATTCGACATATGTGGATTATAAGTGTAT
1 ATATATATATGTGTA-GCATTCGACACATGTGGATTATAAGTATAT
* *
30054804 ATATATATATGTGT-GCATTCGGCACATGTGG-TTGATAAGTATAA
1 ATATATATATGTGTAGCATTCGACACATGTGGATT-ATAAGTATAT
30054848 ATATAT
1 ATATAT
30054854 GCTTTTGGCA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
43 2 0.04
44 29 0.64
46 14 0.31
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (45 bp):
ATATATATATGTGTAGCATTCGACACATGTGGATTATAAGTATAT
Found at i:30059278 original size:120 final size:120
Alignment explanation
Indices: 30058948--30059397 Score: 694
Period size: 120 Copynumber: 3.8 Consensus size: 120
30058938 TATCTTAATA
* * * * ***
30058948 TTAAAATATA-AAATTATTATTACAATATAAAAAATATATACAATAGTCAAACCAATCTTAATAT
1 TTAAAATATACAAATTATTATTACAATATAAAAAAAACATACACTA-CCAAAATTATCTTAATAT
*
30059012 TACTTTTAACACAAATCTAATCATTCAAACAAAAATATAATGTTGAATGTTATATC
65 TACTTTTAACACAAATCTAATAATTCAAACAAAAATATAATGTTGAATGTTATATC
* * *
30059068 TTAAAATATACAAGTTATTATTACAA-A-AAAAAAGACATACACTACCAAAATTATCTTAATGTT
1 TTAAAATATACAAATTATTATTACAATATAAAAAAAACATACACTACCAAAATTATCTTAATATT
*
30059131 ACTTTTAACACAAATATAATAATTCAAACAAAAATATAATGTTGAATGTTATATC
66 ACTTTTAACACAAATCTAATAATTCAAACAAAAATATAATGTTGAATGTTATATC
30059186 TTAAAATATACAAATTATTATTACAATATAAAAAAAACATACACTACCAAAATTATCTTAATATT
1 TTAAAATATACAAATTATTATTACAATATAAAAAAAACATACACTACCAAAATTATCTTAATATT
* * *
30059251 ACTTTTAACACAATTCTAATAATTCAAACAAAAATATAATATTGAATGCTATATC
66 ACTTTTAACACAAATCTAATAATTCAAACAAAAATATAATGTTGAATGTTATATC
*
30059306 TTAAAATATACAAATTATTATTACAATATATAAAAAAA-A-ACACTACTAAAATTATCTTAATAT
1 TTAAAATATACAAATTATTATTACAATATA-AAAAAAACATACACTACCAAAATTATCTTAATAT
*
30059369 TACTTTTAACACAATTCTAATAATTCAAA
65 TACTTTTAACACAAATCTAATAATTCAAA
30059398 AAATTATAAT
Statistics
Matches: 307, Mismatches: 19, Indels: 9
0.92 0.06 0.03
Matches are distributed among these distances:
118 92 0.30
119 67 0.22
120 127 0.41
121 21 0.07
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (120 bp):
TTAAAATATACAAATTATTATTACAATATAAAAAAAACATACACTACCAAAATTATCTTAATATT
ACTTTTAACACAAATCTAATAATTCAAACAAAAATATAATGTTGAATGTTATATC
Found at i:30059457 original size:16 final size:16
Alignment explanation
Indices: 30059436--30059512 Score: 50
Period size: 16 Copynumber: 4.5 Consensus size: 16
30059426 TTAATAATAA
30059436 TAATAATAATCTAATC
1 TAATAATAATCTAATC
*
30059452 TAATAATATATCAATAAACCTT
1 TAATAATA-ATC--T-AA--TC
* *
30059474 TAACACA-AATCTAATT
1 TAATA-ATAATCTAATC
30059490 TAATAATAATCTAATC
1 TAATAATAATCTAATC
30059506 TAA-AATA
1 TAATAATA
30059513 TAAATAATAC
Statistics
Matches: 49, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
15 5 0.10
16 25 0.51
17 3 0.06
18 2 0.04
19 2 0.04
20 2 0.04
21 3 0.06
22 6 0.12
23 1 0.02
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATAATAATCTAATC
Found at i:30068384 original size:23 final size:23
Alignment explanation
Indices: 30068354--30068401 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
30068344 ACATTTGCTT
30068354 TCTTATGATCATTGTATTAACAA
1 TCTTATGATCATTGTATTAACAA
30068377 TCTTATGATCATTGTATTAACAA
1 TCTTATGATCATTGTATTAACAA
30068400 TC
1 TC
30068402 AAATATATGT
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:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (23 bp):
TCTTATGATCATTGTATTAACAA
Found at i:30068458 original size:31 final size:31
Alignment explanation
Indices: 30068423--30068498 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
30068413 CTCCTCGAAT
*
30068423 GCATATAACTGAATATTGATATACATCAAGA
1 GCATATAACCGAATATTGATATACATCAAGA
* *
30068454 GCATATAACCGAGTATTTATATACATCAAGA
1 GCATATAACCGAATATTGATATACATCAAGA
*
30068485 GCATATACCCGAAT
1 GCATATAACCGAAT
30068499 GTATGCATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (31 bp):
GCATATAACCGAATATTGATATACATCAAGA
Found at i:30069011 original size:40 final size:40
Alignment explanation
Indices: 30068897--30068997 Score: 184
Period size: 40 Copynumber: 2.5 Consensus size: 40
30068887 TGACTCAGAA
30068897 CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAAAAACT
1 CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAAAAACT
* *
30068937 CACCAGCATTAAGCCTGCTAGACATTAAGTCTGAAAAATT
1 CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAAAAACT
30068977 CACCGGCATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
30068998 GCACAGAACC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAAAAACT
Found at i:30069988 original size:29 final size:27
Alignment explanation
Indices: 30069955--30070017 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
30069945 CATTTCATTT
* *
30069955 ATTTCACATTTTAGTCCCTCAAAATT-TTA
1 ATTTCACAATTTAG-CCCT--AAATTCTCA
30069984 ATTTCACAATTTAGCCCTAAATTCTCA
1 ATTTCACAATTTAGCCCTAAATTCTCA
30070011 ATTTCAC
1 ATTTCAC
30070018 CAAAAATTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 5 0.16
27 9 0.29
28 4 0.13
29 13 0.42
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (27 bp):
ATTTCACAATTTAGCCCTAAATTCTCA
Found at i:30075849 original size:17 final size:17
Alignment explanation
Indices: 30075827--30075867 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
30075817 ACCGTACAGA
*
30075827 TAATGCCTCCAGATTTT
1 TAATGCATCCAGATTTT
30075844 TAATGCATCCAGATTTT
1 TAATGCATCCAGATTTT
30075861 TAATGCA
1 TAATGCA
30075868 AAGACTACGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (17 bp):
TAATGCATCCAGATTTT
Found at i:30078847 original size:20 final size:20
Alignment explanation
Indices: 30078822--30078860 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
30078812 GCTACTCATA
30078822 TTTTCA-AAAACTTATCAGAG
1 TTTTCAGAAAACTTA-CAGAG
*
30078842 TTTTCAGAACACTTACAGA
1 TTTTCAGAAAACTTACAGA
30078861 ATCGGTGCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (20 bp):
TTTTCAGAAAACTTACAGAG
Found at i:30084480 original size:28 final size:28
Alignment explanation
Indices: 30084440--30084681 Score: 268
Period size: 28 Copynumber: 8.6 Consensus size: 28
30084430 AGAGTCTGCT
30084440 ACAAAGGCTTATTCTTTCATAGTTCGCC
1 ACAAAGGCTTATTCTTTCATAGTTCGCC
* * *
30084468 ACAAAGGCTTATTCTTTCGTAGTTTGCT
1 ACAAAGGCTTATTCTTTCATAGTTCGCC
* * * *
30084496 ACAAAGGCTTATTTTTTCGTAGTTTGTC
1 ACAAAGGCTTATTCTTTCATAGTTCGCC
30084524 ACAAAGGCTTATTCTTTCATAGTTCGCC
1 ACAAAGGCTTATTCTTTCATAGTTCGCC
**
30084552 ACAAAGGCTTATTCTTTCATAGTTCATC
1 ACAAAGGCTTATTCTTTCATAGTTCGCC
* * * * *
30084580 ACAAAAGTTTATTCTTTTATAGGTCGTC
1 ACAAAGGCTTATTCTTTCATAGTTCGCC
* ** *
30084608 ATAAAGGCTTATTCTTTTTTTGTTCGCC
1 ACAAAGGCTTATTCTTTCATAGTTCGCC
* * ***
30084636 ATAAAGGCTTATTCTTTCGTAGTTCATT
1 ACAAAGGCTTATTCTTTCATAGTTCGCC
*
30084664 AGAAAGGCTTATTCTTTC
1 ACAAAGGCTTATTCTTTC
30084682 CTGATGTGTT
Statistics
Matches: 183, Mismatches: 31, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 183 1.00
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (28 bp):
ACAAAGGCTTATTCTTTCATAGTTCGCC
Done.