Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 119 of 297
Found at i:42405330 original size:52 final size:52
Alignment explanation
Indices: 42405252--42405355 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
42405242 AGAAGTGGCT
*
42405252 GACCACTTGCAAACATTAGCAGTACAAGCCGATATGATGAGTTTAAAATACG
1 GACCACTTGCAAACATTAGCAGTACAAGCCGATATGATGAATTTAAAATACG
42405304 GACCACTTGCAAACATTAGCAGTACAAGCCGATATGATGAATTTAAAATACG
1 GACCACTTGCAAACATTAGCAGTACAAGCCGATATGATGAATTTAAAATACG
42405356 AGTCAGAATC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.23
Consensus pattern (52 bp):
GACCACTTGCAAACATTAGCAGTACAAGCCGATATGATGAATTTAAAATACG
Found at i:42405528 original size:9 final size:9
Alignment explanation
Indices: 42405514--42405545 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
42405504 CAACGCTTTT
42405514 TTGCATTCA
1 TTGCATTCA
42405523 TTGCATTCA
1 TTGCATTCA
42405532 TTGCATTCA
1 TTGCATTCA
42405541 -TGCAT
1 TTGCAT
42405546 CGGCATTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.22
9 18 0.78
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (9 bp):
TTGCATTCA
Found at i:42410148 original size:48 final size:48
Alignment explanation
Indices: 42410072--42410169 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
42410062 TGCTATAAGG
42410072 TGATGCCGTTTGGATTGAAAAATACGGGAGCAACATATTAGAGAGCCA
1 TGATGCCGTTTGGATTGAAAAATACGGGAGCAACATATTAGAGAGCCA
* *
42410120 TGATGTCGTTTGGATTGAAAAATGCGGGAGCAACATATTAGAGAGCCA
1 TGATGCCGTTTGGATTGAAAAATACGGGAGCAACATATTAGAGAGCCA
42410168 TG
1 TG
42410170 GTAACCCTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.24
Consensus pattern (48 bp):
TGATGCCGTTTGGATTGAAAAATACGGGAGCAACATATTAGAGAGCCA
Found at i:42413654 original size:64 final size:64
Alignment explanation
Indices: 42413577--42413700 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 64
42413567 TCATTCGTGA
* **
42413577 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTGGTTATTTGACATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
* * * * *
42413641 CACATTTAGTTAGGATCATTTGATTCATTTCAATGATAGCGTCCTAATTATTTGGCATAA
1 CACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAA
42413701 ACATAGTTAC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
Found at i:42413912 original size:44 final size:44
Alignment explanation
Indices: 42413764--42414161 Score: 273
Period size: 44 Copynumber: 9.1 Consensus size: 44
42413754 GTGGAATTGG
*
42413764 TGAATTCACAAG-CCTTAAACCCCTAAGCAGTAGGGTAACAGGC
1 TGAATTTACAAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGC
* * * * * *
42413807 TGAATTTACAA-ATCTTAACCCCCTAAGCAGTAAGGAAATA-GA
1 TGAATTTACAAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGC
* * ** * *
42413849 TCGAAGATGA-TGGGCCTTAAAACCCTAAGCAGTAGGGTAACAGGC
1 T-GAA-TTTACAAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGC
* * * *
42413894 TGAATTTACAAGATCTTAACCCCCTAAGCAGTAGGGAAACA-GA
1 TGAATTTACAAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGC
** * *
42413937 TCGAA--GGCGATGAACCTTAAACCCTTAAGCAGTAGGGTAACAGGC
1 T-GAATTTAC-AAG-ACCTTAAACCCCTAAGCAGTAGGGTAACAGGC
* * * *
42413982 TGAATTTACAAGATCTTAACCCCCTAAGCAGTAGGGAAACA-GA
1 TGAATTTACAAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGC
** * *
42414025 TCGAA--GGCGATGAACCTTAAACCCTTAAGCAGTAGGGTAACAGGC
1 T-GAATTTAC-AAG-ACCTTAAACCCCTAAGCAGTAGGGTAACAGGC
* * * * *
42414070 TGAATTTACAAGATCTTAACCCCCTAAGCAGTAGGGAAATA-GA
1 TGAATTTACAAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGC
** *
42414113 TCGAA--GGCGATGGACCTTAAACCCCTAAGCAGTAGGGTAACAGGC
1 T-GAATTTAC-A-AGACCTTAAACCCCTAAGCAGTAGGGTAACAGGC
42414158 TGAA
1 TGAA
42414162 AATTATAGAT
Statistics
Matches: 263, Mismatches: 70, Indels: 43
0.70 0.19 0.11
Matches are distributed among these distances:
42 5 0.02
43 49 0.19
44 195 0.74
45 12 0.05
46 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (44 bp):
TGAATTTACAAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGC
Found at i:42413938 original size:88 final size:88
Alignment explanation
Indices: 42413776--42414161 Score: 643
Period size: 88 Copynumber: 4.4 Consensus size: 88
42413766 AATTCACAAG
* *
42413776 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAA-ATCTTAACCCCCTAAGCAGTAA
1 CCTTAAAACCCTAAGCAGTAGGGTAACAGGCTGAATTTACAAGATCTTAACCCCCTAAGCAGTAG
* ** **
42413840 GGAAATAGATCGAAGATGATGGG
66 GGAAACAGATCGAAGGCGATGAA
42413863 CCTTAAAACCCTAAGCAGTAGGGTAACAGGCTGAATTTACAAGATCTTAACCCCCTAAGCAGTAG
1 CCTTAAAACCCTAAGCAGTAGGGTAACAGGCTGAATTTACAAGATCTTAACCCCCTAAGCAGTAG
42413928 GGAAACAGATCGAAGGCGATGAA
66 GGAAACAGATCGAAGGCGATGAA
42413951 CCTT-AAACCCTTAAGCAGTAGGGTAACAGGCTGAATTTACAAGATCTTAACCCCCTAAGCAGTA
1 CCTTAAAACCC-TAAGCAGTAGGGTAACAGGCTGAATTTACAAGATCTTAACCCCCTAAGCAGTA
42414015 GGGAAACAGATCGAAGGCGATGAA
65 GGGAAACAGATCGAAGGCGATGAA
42414039 CCTT-AAACCCTTAAGCAGTAGGGTAACAGGCTGAATTTACAAGATCTTAACCCCCTAAGCAGTA
1 CCTTAAAACCC-TAAGCAGTAGGGTAACAGGCTGAATTTACAAGATCTTAACCCCCTAAGCAGTA
* *
42414103 GGGAAATAGATCGAAGGCGATGGA
65 GGGAAACAGATCGAAGGCGATGAA
*
42414127 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAA
1 CCTTAAAACCCTAAGCAGTAGGGTAACAGGCTGAA
42414162 AATTATAGAT
Statistics
Matches: 286, Mismatches: 10, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
87 47 0.16
88 234 0.82
89 5 0.02
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (88 bp):
CCTTAAAACCCTAAGCAGTAGGGTAACAGGCTGAATTTACAAGATCTTAACCCCCTAAGCAGTAG
GGAAACAGATCGAAGGCGATGAA
Found at i:42414956 original size:12 final size:12
Alignment explanation
Indices: 42414941--42414988 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
42414931 TATTTATCTC
42414941 TTTATATTTATG
1 TTTATATTTATG
42414953 TTTATATTTTATG
1 TTTATA-TTTATG
** *
42414966 TATTATACATATC
1 T-TTATATTTATG
42414979 TTTATATTTA
1 TTTATATTTA
42414989 CACATGAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 13 0.45
13 11 0.38
14 5 0.17
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (12 bp):
TTTATATTTATG
Found at i:42415169 original size:22 final size:22
Alignment explanation
Indices: 42415141--42415182 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
42415131 TAACGTGCTA
* *
42415141 TTATTACTATTATTTTTATTTT
1 TTATTACCATTATTGTTATTTT
42415163 TTATTACCATTATTGTTATT
1 TTATTACCATTATTGTTATT
42415183 GTACTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTACCATTATTGTTATTTT
Found at i:42416414 original size:96 final size:96
Alignment explanation
Indices: 42416250--42416460 Score: 422
Period size: 96 Copynumber: 2.2 Consensus size: 96
42416240 ACGAGGTGTT
42416250 GTGCCCTAACTTACTGGGTACGACATTTTGTCACCTCGAAATAAGAATTTGTTTAAAAATAAAGG
1 GTGCCCTAACTTACTGGGTACGACATTTTGTCACCTCGAAATAAGAATTTGTTTAAAAATAAAGG
42416315 CAATATTTGGTATTAGGAAATTCGAGAAAAC
66 CAATATTTGGTATTAGGAAATTCGAGAAAAC
42416346 GTGCCCTAACTTACTGGGTACGACATTTTGTCACCTCGAAATAAGAATTTGTTTAAAAATAAAGG
1 GTGCCCTAACTTACTGGGTACGACATTTTGTCACCTCGAAATAAGAATTTGTTTAAAAATAAAGG
42416411 CAATATTTGGTATTAGGAAATTCGAGAAAAC
66 CAATATTTGGTATTAGGAAATTCGAGAAAAC
42416442 GTGCCCTAACTTACTGGGT
1 GTGCCCTAACTTACTGGGT
42416461 TTCGACTTTT
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 115 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (96 bp):
GTGCCCTAACTTACTGGGTACGACATTTTGTCACCTCGAAATAAGAATTTGTTTAAAAATAAAGG
CAATATTTGGTATTAGGAAATTCGAGAAAAC
Found at i:42417860 original size:126 final size:126
Alignment explanation
Indices: 42417635--42417885 Score: 475
Period size: 126 Copynumber: 2.0 Consensus size: 126
42417625 GGATAAAGTG
42417635 TTTCACAGAAGATTGATGACTGTTGATACACTGTTGTTCCATTCTAAAATGAGAGCTTTGATAGA
1 TTTCACAGAAGATTGATGACTGTTGATACACTGTTGTTCCATTCTAAAATGAGAGCTTTGATAGA
***
42417700 GGCAAGGGCGGCTCATGATGTCTGTTAATTTTTGGAAGGATAATGGTGGTGCTGGCCTATA
66 GGCAAGGAAAGCTCATGATGTCTGTTAATTTTTGGAAGGATAATGGTGGTGCTGGCCTATA
42417761 TTTCACAGAAGATTGATGACTGTTGATACACTGTTGTTCCATTCTAAAATGAGAGCTTTGATAGA
1 TTTCACAGAAGATTGATGACTGTTGATACACTGTTGTTCCATTCTAAAATGAGAGCTTTGATAGA
42417826 GGCAAGGAAAGCTCATGATGTCTGTTAATTTTTGGAAGGATAATGGTGGTGCTGGCCTAT
66 GGCAAGGAAAGCTCATGATGTCTGTTAATTTTTGGAAGGATAATGGTGGTGCTGGCCTAT
42417886 GAAATGTAGT
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 122 1.00
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.33
Consensus pattern (126 bp):
TTTCACAGAAGATTGATGACTGTTGATACACTGTTGTTCCATTCTAAAATGAGAGCTTTGATAGA
GGCAAGGAAAGCTCATGATGTCTGTTAATTTTTGGAAGGATAATGGTGGTGCTGGCCTATA
Found at i:42418655 original size:327 final size:327
Alignment explanation
Indices: 42418054--42418708 Score: 1274
Period size: 327 Copynumber: 2.0 Consensus size: 327
42418044 TGTTCTCTAG
*
42418054 GCCGATTGAAGCTACAGGATTGGGAAAAGCAGAGGTAAGAGCCATAAAAATAGTCGTGGAGATGT
1 GCCGATTGAAGCTACAGGATTAGGAAAAGCAGAGGTAAGAGCCATAAAAATAGTCGTGGAGATGT
42418119 TTATGAGTATAGGTTGGCATGAAAAAGTTCCTCTAGTTATTGAGTCTAGCTTGAGTGTTGTTCTG
66 TTATGAGTATAGGTTGGCATGAAAAAGTTCCTCTAGTTATTGAGTCTAGCTTGAGTGTTGTTCTG
*
42418184 GAGGGGTTGTTGGATAGGAGCTATAGACCATGGATGTTTCGGAATCTATTCATTAGTATCGGTTG
131 GAGGGGTTGTTGGATAGGAGCTATAGACCATGGATGTTGCGGAATCTATTCATTAGTATCGGTTG
42418249 TGATATTAATCTATTGTTGCGTGCTCAATTCACAATTATTCAATGACAAGGTAATATTATAGCTA
196 TGATATTAATCTATTGTTGCGTGCTCAATTCACAATTATTCAATGACAAGGTAATATTATAGCTA
42418314 ATGCTCCAACAAAAGTAGGTATAAGGAGACCTTTGCTATTTAAAGTCTGATGGTGATTATTGTGA
261 ATGCTCCAACAAAAGTAGGTATAAGGAGACCTTTGCTATTTAAAGTCTGATGGTGATTATTGTGA
42418379 TT
326 TT
42418381 GCCGATTGAAGCTACAGGATTAGGAAAAGCAGAGGTAAGAGCCATAAAAATAGTCGTGGAGATGT
1 GCCGATTGAAGCTACAGGATTAGGAAAAGCAGAGGTAAGAGCCATAAAAATAGTCGTGGAGATGT
42418446 TTATGAGTATAGGTTGGCATGAAAAAGTTCCTCTAGTTATTGAGTCTAGCTTGAGTGTTGTTCTG
66 TTATGAGTATAGGTTGGCATGAAAAAGTTCCTCTAGTTATTGAGTCTAGCTTGAGTGTTGTTCTG
*
42418511 GAGGGGTTGTTGGATAGGAGCTATAGACCATGGATGTTGCGGAATCTATTCATTGGTATCGGTTG
131 GAGGGGTTGTTGGATAGGAGCTATAGACCATGGATGTTGCGGAATCTATTCATTAGTATCGGTTG
42418576 TGATATTAATCTATTGTTGCGTGCTCAATTCACAATTATTCAATGACAAGGTAATATTATAGCTA
196 TGATATTAATCTATTGTTGCGTGCTCAATTCACAATTATTCAATGACAAGGTAATATTATAGCTA
*
42418641 ATGCTCCGACAAAAGTAGGTATAAGGAGACCTTTGCTATTTAAAGTCTGATGGTGATTATTGTGA
261 ATGCTCCAACAAAAGTAGGTATAAGGAGACCTTTGCTATTTAAAGTCTGATGGTGATTATTGTGA
42418706 TT
326 TT
42418708 G
1 G
42418709 TTTGAATTGT
Statistics
Matches: 324, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
327 324 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (327 bp):
GCCGATTGAAGCTACAGGATTAGGAAAAGCAGAGGTAAGAGCCATAAAAATAGTCGTGGAGATGT
TTATGAGTATAGGTTGGCATGAAAAAGTTCCTCTAGTTATTGAGTCTAGCTTGAGTGTTGTTCTG
GAGGGGTTGTTGGATAGGAGCTATAGACCATGGATGTTGCGGAATCTATTCATTAGTATCGGTTG
TGATATTAATCTATTGTTGCGTGCTCAATTCACAATTATTCAATGACAAGGTAATATTATAGCTA
ATGCTCCAACAAAAGTAGGTATAAGGAGACCTTTGCTATTTAAAGTCTGATGGTGATTATTGTGA
TT
Found at i:42423316 original size:74 final size:74
Alignment explanation
Indices: 42423195--42423345 Score: 293
Period size: 74 Copynumber: 2.0 Consensus size: 74
42423185 GAACATTTTG
42423195 ATTATCACGCTAACACACGGAATTTTATGATATAGTGATTATTAATTGCCAAATCTTAAAAATTG
1 ATTATCACGCTAACACACGGAATTTTATGATATAGTGATTATTAATTGCCAAATCTTAAAAATTG
42423260 TAATAAGCA
66 TAATAAGCA
42423269 ATTATCACGCTAACACACGGAATTTTATGATATAGTGATTATTAATTGCCAAATCTTAAAAATTG
1 ATTATCACGCTAACACACGGAATTTTATGATATAGTGATTATTAATTGCCAAATCTTAAAAATTG
*
42423334 TAATAAGTA
66 TAATAAGCA
42423343 ATT
1 ATT
42423346 TGGCTACAAT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (74 bp):
ATTATCACGCTAACACACGGAATTTTATGATATAGTGATTATTAATTGCCAAATCTTAAAAATTG
TAATAAGCA
Found at i:42424416 original size:130 final size:130
Alignment explanation
Indices: 42424183--42424441 Score: 500
Period size: 130 Copynumber: 2.0 Consensus size: 130
42424173 ATTTCTCAAG
*
42424183 CCCAAAACTCTCCAAAATCATCTTCAAAATTGTCTTTTCTAACTTTGATGTTAGTTGAATGAAAG
1 CCCAAAACTCTCCAAAATCATCTTCAAAATTGTCTTTTCTAACTCTGATGTTAGTTGAATGAAAG
*
42424248 ATGCCAGAGTTTCACTGCCAAACACAAAGCAAATAATTAATAAAAACCAAGTTTACTAATTTTGA
66 ATGCCAGAGTTTCACTGCCAAACACAAAGCAAATAATTAATAAAAACCAAGTCTACTAATTTTGA
42424313 CCCAAAACTCTCCAAAATCATCTTCAAAATTGTCTTTTCTAACTCTGATGTTAGTTGAATGAAAG
1 CCCAAAACTCTCCAAAATCATCTTCAAAATTGTCTTTTCTAACTCTGATGTTAGTTGAATGAAAG
42424378 ATGCCAGAGTTTCACTGCCAAACACAAAGCAAATAATTAATAAAAACCAAGTCTACTAATTTTG
66 ATGCCAGAGTTTCACTGCCAAACACAAAGCAAATAATTAATAAAAACCAAGTCTACTAATTTTG
42424442 TTAAAGGGCT
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 127 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (130 bp):
CCCAAAACTCTCCAAAATCATCTTCAAAATTGTCTTTTCTAACTCTGATGTTAGTTGAATGAAAG
ATGCCAGAGTTTCACTGCCAAACACAAAGCAAATAATTAATAAAAACCAAGTCTACTAATTTTGA
Found at i:42430601 original size:9 final size:9
Alignment explanation
Indices: 42430587--42430618 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
42430577 CAACGCTTTT
42430587 TTGCATTCA
1 TTGCATTCA
42430596 TTGCATTCA
1 TTGCATTCA
42430605 TTGCATTCA
1 TTGCATTCA
42430614 -TGCAT
1 TTGCAT
42430619 CGGCATTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.22
9 18 0.78
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (9 bp):
TTGCATTCA
Found at i:42439370 original size:26 final size:26
Alignment explanation
Indices: 42439339--42439446 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
42439329 TGAAATGCCC
*
42439339 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
42439365 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
42439391 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
42439417 ATCATAGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
42439443 ATCA
1 ATCA
42439447 ATTTGAATCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:42447446 original size:57 final size:57
Alignment explanation
Indices: 42447358--42447471 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
42447348 AGTCAGGACA
42447358 CAAGTTGCGCCAAAGGTCGTAATCCAGAAGCCCGTTGCTTTCCCTTATAAAGATAGC
1 CAAGTTGCGCCAAAGGTCGTAATCCAGAAGCCCGTTGCTTTCCCTTATAAAGATAGC
42447415 CAAGTTGCGCCAAAGGTCGTAATCCAGAAGCCCGTTGCTTTCCCTTATAAAGATAGC
1 CAAGTTGCGCCAAAGGTCGTAATCCAGAAGCCCGTTGCTTTCCCTTATAAAGATAGC
42447472 AAAAGGGTAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (57 bp):
CAAGTTGCGCCAAAGGTCGTAATCCAGAAGCCCGTTGCTTTCCCTTATAAAGATAGC
Found at i:42447751 original size:73 final size:73
Alignment explanation
Indices: 42447669--42447815 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
42447659 CGGGACCTAA
42447669 ACCAACTGTTAATGAGCCAGTGACTGAAAAAGAAGCAAAAGAATTCTTAAAATTCTTGAAGCACA
1 ACCAACTGTTAATGAGCCAGTGACTGAAAAAGAAGCAAAAGAATTCTTAAAATTCTTGAAGCACA
42447734 GCGAATAT
66 GCGAATAT
*
42447742 ACCAACTGTTAATGAGCCAGTGACTGAAAAAGAAGCAAAAGAATTCTTAAAATTCTTGAAGCACC
1 ACCAACTGTTAATGAGCCAGTGACTGAAAAAGAAGCAAAAGAATTCTTAAAATTCTTGAAGCACA
42447807 GCGAATAT
66 GCGAATAT
42447815 A
1 A
42447816 GTGTCATAGA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.44, C:0.17, G:0.18, T:0.22
Consensus pattern (73 bp):
ACCAACTGTTAATGAGCCAGTGACTGAAAAAGAAGCAAAAGAATTCTTAAAATTCTTGAAGCACA
GCGAATAT
Found at i:42449002 original size:82 final size:82
Alignment explanation
Indices: 42448906--42449068 Score: 308
Period size: 82 Copynumber: 2.0 Consensus size: 82
42448896 TTAACGCCGT
* *
42448906 ATATAAAGAAAGGAATGGAGTTGAAGATTTGTCGGGCATTCGTCCTTATGAGCCAGAAAGTGTTC
1 ATATAAAGAAAGGAATAGAGTTGAAGATTTGTCGGGCATTCGCCCTTATGAGCCAGAAAGTGTTC
42448971 TGAATAATTGGACTGCC
66 TGAATAATTGGACTGCC
42448988 ATATAAAGAAAGGAATAGAGTTGAAGATTTGTCGGGCATTCGCCCTTATGAGCCAGAAAGTGTTC
1 ATATAAAGAAAGGAATAGAGTTGAAGATTTGTCGGGCATTCGCCCTTATGAGCCAGAAAGTGTTC
42449053 TGAATAATTGGACTGC
66 TGAATAATTGGACTGC
42449069 GAAAGAGATT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (82 bp):
ATATAAAGAAAGGAATAGAGTTGAAGATTTGTCGGGCATTCGCCCTTATGAGCCAGAAAGTGTTC
TGAATAATTGGACTGCC
Found at i:42458180 original size:26 final size:26
Alignment explanation
Indices: 42458134--42458190 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
42458124 ATATACATAT
* * *
42458134 TAAAAATAATTATAATGAAATACTAA
1 TAAAAAAAATAATAATGAAATAATAA
*
42458160 TAAAAAAAATAATAGAT-AAATAATAT
1 TAAAAAAAATAATA-ATGAAATAATAA
42458186 TAAAA
1 TAAAA
42458191 TGAAAGTAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (26 bp):
TAAAAAAAATAATAATGAAATAATAA
Found at i:42459594 original size:13 final size:14
Alignment explanation
Indices: 42459570--42459598 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42459560 CATAAATCAA
42459570 TTTAATTAAAAAAT
1 TTTAATTAAAAAAT
42459584 TTTAATTAAAAAAT
1 TTTAATTAAAAAAT
42459598 T
1 T
42459599 GAAATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAATTAAAAAAT
Found at i:42459658 original size:18 final size:19
Alignment explanation
Indices: 42459637--42459677 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 19
42459627 CGATTTTAAT
42459637 TAAAATATAATTT-AA-GGA
1 TAAAAT-TAATTTAAAGGGA
42459655 T-AAATTAATTTAAAGGGA
1 TAAAATTAATTTAAAGGGA
42459673 TAAAA
1 TAAAA
42459678 ATAGGAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 6 0.30
17 6 0.30
18 5 0.25
19 3 0.15
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (19 bp):
TAAAATTAATTTAAAGGGA
Found at i:42459670 original size:17 final size:18
Alignment explanation
Indices: 42459639--42459676 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42459629 ATTTTAATTA
42459639 AAATATAATTTAA-GGAT
1 AAATATAATTTAAGGGAT
42459656 AAAT-TAATTTAAAGGGAT
1 AAATATAATTT-AAGGGAT
42459674 AAA
1 AAA
42459677 AATAGGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 6 0.32
18 7 0.37
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (18 bp):
AAATATAATTTAAGGGAT
Found at i:42459708 original size:23 final size:23
Alignment explanation
Indices: 42459682--42459756 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
42459672 ATAAAAATAG
*
42459682 GAATTAAAGTAATTTAAACTAAT
1 GAATTAAAGTAATTTAAAATAAT
* * *
42459705 GAATGAATAG-ATTTTAAAAAAAT
1 GAATTAA-AGTAATTTAAAATAAT
* *
42459728 GGGATTTAAAGTAATTTAAAGTAAT
1 --GAATTAAAGTAATTTAAAATAAT
42459753 GAAT
1 GAAT
42459757 AGGAATTTAA
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
23 19 0.50
24 4 0.11
25 15 0.39
ACGTcount: A:0.51, C:0.01, G:0.15, T:0.33
Consensus pattern (23 bp):
GAATTAAAGTAATTTAAAATAAT
Found at i:42461198 original size:61 final size:60
Alignment explanation
Indices: 42461125--42461271 Score: 156
Period size: 61 Copynumber: 2.4 Consensus size: 60
42461115 ACCCTAGTAC
* * *
42461125 TAGATTTAAAAAAAACAATATTTTTTT-AGTGGTGTGACATTAATTGCTGACATCTCAATA-
1 TAGATTTTAAAAAAA-AATATTTTTTTGAGTAGTGGGACATTAATTGCTGACATC-CAATAG
* * * **
42461185 TCATATTTTAAAAAAAAATATTTTTTTGATTATTGGGACATTAATTTTTGACATCCAATAG
1 T-AGATTTTAAAAAAAAATATTTTTTTGAGTAGTGGGACATTAATTGCTGACATCCAATAG
*
42461246 TAGA-TTTAAAAAAATATATATTTTTT
1 TAGATTTTAAAAAAAAATAT-TTTTTT
42461272 AGTTGTTAGG
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
59 14 0.19
60 25 0.34
61 34 0.47
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.43
Consensus pattern (60 bp):
TAGATTTTAAAAAAAAATATTTTTTTGAGTAGTGGGACATTAATTGCTGACATCCAATAG
Found at i:42466912 original size:44 final size:41
Alignment explanation
Indices: 42466835--42466918 Score: 107
Period size: 44 Copynumber: 2.0 Consensus size: 41
42466825 GAAAAAGGAA
42466835 TAAATGAAAAAAATTAAATAAAATATAAAATTTTATAAATT
1 TAAATGAAAAAAATTAAATAAAATATAAAATTTTATAAATT
* *
42466876 TAAATGAAAAGAAATACTAAAATGAAA-ATAAAATTTTTTAAAT
1 TAAATGAAAA-AAAT--T-AAATAAAATATAAAATTTTATAAAT
42466919 GAATTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
41 10 0.27
42 4 0.11
44 16 0.43
45 7 0.19
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (41 bp):
TAAATGAAAAAAATTAAATAAAATATAAAATTTTATAAATT
Found at i:42466992 original size:46 final size:46
Alignment explanation
Indices: 42466911--42467011 Score: 143
Period size: 46 Copynumber: 2.2 Consensus size: 46
42466901 AAATAAAATT
42466911 TTTTAAATGAATTTTTTTTAAAATCGAAATGAGATTTTTTTAGACAAA
1 TTTTAAATGAA-TTTTTTTAAAATCGAAATGAGATTTTTTTA-ACAAA
*
42466959 TTTTAAATGAGA-TTTTTT-AAATTGAAATGAGATTTTTTTAACAAA
1 TTTTAAATGA-ATTTTTTTAAAATCGAAATGAGATTTTTTTAACAAA
*
42467004 TTTAAAAT
1 TTTTAAAT
42467012 TTAAATTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
45 12 0.24
46 21 0.42
47 6 0.12
48 10 0.20
49 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.47
Consensus pattern (46 bp):
TTTTAAATGAATTTTTTTAAAATCGAAATGAGATTTTTTTAACAAA
Found at i:42467154 original size:11 final size:12
Alignment explanation
Indices: 42467127--42467159 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
42467117 TAAATTGAAA
42467127 AAAAACAATATG
1 AAAAACAATATG
42467139 AAAAACAATATG
1 AAAAACAATATG
42467151 AAAAA-AATA
1 AAAAACAATA
42467160 ATATGAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.15
Consensus pattern (12 bp):
AAAAACAATATG
Found at i:42467169 original size:28 final size:26
Alignment explanation
Indices: 42467108--42467181 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
42467098 AATTTGATAA
*
42467108 AATATGAAATA-AAT-TGAAAAAAAAC
1 AATATGAAAAACAATATG-AAAAAAAC
*
42467133 AATATGAAAAACAATATGAAAAAAAT
1 AATATGAAAAACAATATGAAAAAAAC
*
42467159 AATATGAGAAAAATAATATGAAA
1 AATAT--GAAAAACAATATGAAA
42467182 TGAATTGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 10 0.24
26 15 0.36
27 2 0.05
28 15 0.36
ACGTcount: A:0.68, C:0.03, G:0.09, T:0.20
Consensus pattern (26 bp):
AATATGAAAAACAATATGAAAAAAAC
Found at i:42467233 original size:39 final size:41
Alignment explanation
Indices: 42467145--42467271 Score: 135
Period size: 39 Copynumber: 3.2 Consensus size: 41
42467135 TATGAAAAAC
* *
42467145 AATATGAAAAAAATAATATGAGAA-AAAT--AATATGAAATG
1 AATATGAAAAAAATAATATGAAAAGAAATGAAAAAT-AAATG
42467184 AAT-TGAAAAAAAATAATATGAAAAGAAATGAAAAAT-AAT-
1 AATATG-AAAAAAATAATATGAAAAGAAATGAAAAATAAATG
* *
42467223 AATATGAAAAAAATAATATGAAATGAATTGAAAAA-AAATTG
1 AATATGAAAAAAATAATATGAAAAGAAATGAAAAATAAA-TG
42467264 AA-ATGAAA
1 AATATGAAA
42467272 TAATTGAAAT
Statistics
Matches: 76, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
38 2 0.03
39 52 0.68
40 16 0.21
41 2 0.03
42 4 0.05
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (41 bp):
AATATGAAAAAAATAATATGAAAAGAAATGAAAAATAAATG
Found at i:42467235 original size:64 final size:65
Alignment explanation
Indices: 42467108--42467261 Score: 249
Period size: 64 Copynumber: 2.4 Consensus size: 65
42467098 AATTTGATAA
* * *
42467108 AATATGAAATAAATTGAAAAAAAACAATATGAAAAACAATATGAAAAAAATAATATGAGAAAAAT
1 AATATGAAATGAATTGAAAAAAAATAATATGAAAAACAATATGAAAAAAATAATATGAAAAAAAT
*
42467173 AATATGAAATGAATTGAAAAAAAATAATATG-AAAAGAA-ATGAAAAATAATAATATGAAAAAAA
1 AATATGAAATGAATTGAAAAAAAATAATATGAAAAACAATATGAAAAA-AATAATATGAAAAAAA
42467236 T
65 T
42467237 AATATGAAATGAATTGAAAAAAAAT
1 AATATGAAATGAATTGAAAAAAAAT
42467262 TGAAATGAAA
Statistics
Matches: 84, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
63 8 0.10
64 47 0.56
65 29 0.35
ACGTcount: A:0.67, C:0.01, G:0.10, T:0.21
Consensus pattern (65 bp):
AATATGAAATGAATTGAAAAAAAATAATATGAAAAACAATATGAAAAAAATAATATGAAAAAAAT
Found at i:42467237 original size:14 final size:14
Alignment explanation
Indices: 42467125--42467245 Score: 102
Period size: 14 Copynumber: 9.2 Consensus size: 14
42467115 AATAAATTGA
*
42467125 AAAAAAACAATATG
1 AAAAAAATAATATG
*
42467139 --AAAAACAATATG
1 AAAAAAATAATATG
42467151 AAAAAAATAATATG
1 AAAAAAATAATATG
*
42467165 AGAAAAATAATATG
1 AAAAAAATAATATG
42467179 ----AAATGAAT-TG
1 AAAAAAAT-AATATG
42467189 AAAAAAAATAATATG
1 -AAAAAAATAATATG
*
42467204 ---AAAAGAA-ATG
1 AAAAAAATAATATG
42467214 AAAAATAATAATATG
1 AAAAA-AATAATATG
42467229 AAAAAAATAATATG
1 AAAAAAATAATATG
42467243 AAA
1 AAA
42467246 TGAATTGAAA
Statistics
Matches: 89, Mismatches: 4, Indels: 28
0.74 0.03 0.23
Matches are distributed among these distances:
10 9 0.10
11 9 0.10
12 12 0.13
13 2 0.02
14 43 0.48
15 14 0.16
ACGTcount: A:0.69, C:0.02, G:0.10, T:0.20
Consensus pattern (14 bp):
AAAAAAATAATATG
Found at i:42467270 original size:16 final size:16
Alignment explanation
Indices: 42467246--42467306 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
42467236 TAATATGAAA
*
42467246 TGAATTGAAAAAAAAT
1 TGAAATGAAAAAAAAT
*
42467262 TGAAATG--AAATAAT
1 TGAAATGAAAAAAAAT
**
42467276 TGAAATGAAATTAAAT
1 TGAAATGAAAAAAAAT
*
42467292 TAAAATGAAAAAAAA
1 TGAAATGAAAAAAAA
42467307 AGATTGAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
14 13 0.37
16 22 0.63
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (16 bp):
TGAAATGAAAAAAAAT
Found at i:42467286 original size:25 final size:26
Alignment explanation
Indices: 42467168--42467297 Score: 107
Period size: 25 Copynumber: 5.2 Consensus size: 26
42467158 TAATATGAGA
* *
42467168 AAAATAATATGAAATG-AATTGAAAA
1 AAAATAATATGAAAAGAAATTGAAAT
42467193 AAAATAATATGAAAAGAAA-TGAAA-
1 AAAATAATATGAAAAGAAATTGAAAT
42467217 AATAATAATATGAAAA-AAA-T-AATAT
1 AA-AATAATATGAAAAGAAATTGAA-AT
* *
42467242 GAAATGAAT-TGAAAAAAAATTGAAAT
1 AAAAT-AATATGAAAAGAAATTGAAAT
* *
42467268 GAAATAAT-TGAAATGAAATT-AAATT
1 AAAATAATATGAAAAGAAATTGAAA-T
42467293 AAAAT
1 AAAAT
42467298 GAAAAAAAAA
Statistics
Matches: 91, Mismatches: 5, Indels: 18
0.80 0.04 0.16
Matches are distributed among these distances:
23 2 0.02
24 19 0.21
25 58 0.64
26 10 0.11
27 2 0.02
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.25
Consensus pattern (26 bp):
AAAATAATATGAAAAGAAATTGAAAT
Found at i:42469782 original size:14 final size:14
Alignment explanation
Indices: 42469765--42469843 Score: 72
Period size: 14 Copynumber: 5.6 Consensus size: 14
42469755 AACCTTGTTT
42469765 TTTCATTTTAATTA
1 TTTCATTTTAATTA
42469779 TTTCATTTTAATTA
1 TTTCATTTTAATTA
**
42469793 TTTTTTTTTCAATTCA
1 TTTCATTTT-AATT-A
* * *
42469809 TTTCATATTATTTT
1 TTTCATTTTAATTA
42469823 TTTCATTTT--TTA
1 TTTCATTTTAATTA
*
42469835 TATCATTTT
1 TTTCATTTT
42469844 TCATATTATT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
12 10 0.19
14 29 0.55
15 7 0.13
16 7 0.13
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTCATTTTAATTA
Found at i:42469837 original size:21 final size:23
Alignment explanation
Indices: 42469791--42469844 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
42469781 TCATTTTAAT
42469791 TATT-TTTTTTTCAATTCATTTCA
1 TATTATTTTTTTCAATT-ATTTCA
*
42469814 TATTATTTTTTTC-ATT-TTTTA
1 TATTATTTTTTTCAATTATTTCA
*
42469835 TATCATTTTT
1 TATTATTTTT
42469845 CATATTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 13 0.46
23 7 0.25
24 8 0.29
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTATTTTTTTCAATTATTTCA
Found at i:42469856 original size:58 final size:57
Alignment explanation
Indices: 42469762--42469928 Score: 204
Period size: 58 Copynumber: 3.0 Consensus size: 57
42469752 TTCAACCTTG
42469762 TTTTTTCATTTTAATTATTTCA-TTTT-A-ATTATTTTTTTTTCAATTCATTTCATATTAT
1 TTTTTTCATTTT--TTA-TTCATTTTTCATATTA-TTTTTTTTCAATTCATTTCATATTAT
*
42469820 TTTTTTCATTTTTTATATCATTTTTCATATTATTTTTTTTCAATTCAATTCATATTAT
1 TTTTTTCATTTTTTAT-TCATTTTTCATATTATTTTTTTTCAATTCATTTCATATTAT
* * *
42469878 TTTTCTCA--TATTATT--TTTTTCATATTATTTTTTTTCAATTCATGTCATATT
1 TTTTTTCATTTTTTATTCATTTTTCATATTATTTTTTTTCAATTCATTTCATATT
42469929 TTATCAAATT
Statistics
Matches: 100, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
53 34 0.34
55 2 0.02
56 11 0.11
57 4 0.04
58 45 0.45
59 4 0.04
ACGTcount: A:0.23, C:0.10, G:0.01, T:0.66
Consensus pattern (57 bp):
TTTTTTCATTTTTTATTCATTTTTCATATTATTTTTTTTCAATTCATTTCATATTAT
Found at i:42469910 original size:14 final size:14
Alignment explanation
Indices: 42469809--42469911 Score: 81
Period size: 14 Copynumber: 7.2 Consensus size: 14
42469799 TTTCAATTCA
42469809 TTTCATATTATTTT
1 TTTCATATTATTTT
*
42469823 TTTCATTTTTTATATCATT
1 TTTCA--TATTAT-T--TT
42469842 TTTCATATTATTTTT
1 TTTCATATTA-TTTT
42469857 TTTCA-ATTCA----
1 TTTCATATT-ATTTT
*
42469867 ATTCATATTATTTT
1 TTTCATATTATTTT
*
42469881 TCTCATATTATTTT
1 TTTCATATTATTTT
42469895 TTTCATATTATTTT
1 TTTCATATTATTTT
42469909 TTT
1 TTT
42469912 TCAATTCATG
Statistics
Matches: 71, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
10 5 0.07
11 3 0.04
14 36 0.51
15 8 0.11
16 5 0.07
17 6 0.08
18 1 0.01
19 7 0.10
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTCATATTATTTT
Found at i:42469926 original size:53 final size:55
Alignment explanation
Indices: 42469789--42469928 Score: 187
Period size: 53 Copynumber: 2.5 Consensus size: 55
42469779 TTTCATTTTA
* *
42469789 ATTATTTTTTTTTCAATTCATTTCATATTATTTTTTTCATTTTTTATATCATTTTTCAT
1 ATTA-TTTTTTTTCAATTCA-TTCATATTATTTTTCTCA-TTATTATAT-ATTTTTCAT
42469848 ATTATTTTTTTTCAATTCAATTCATATTATTTTTCTCA-TATTAT-T-TTTTTCAT
1 ATTATTTTTTTTCAATTC-ATTCATATTATTTTTCTCATTATTATATATTTTTCAT
42469901 ATTATTTTTTTTCAATTCATGTCATATT
1 ATTATTTTTTTTCAATTCAT-TCATATT
42469929 TTATCAAATT
Statistics
Matches: 77, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
52 2 0.03
53 33 0.43
55 1 0.01
56 5 0.06
58 31 0.40
59 5 0.06
ACGTcount: A:0.24, C:0.11, G:0.01, T:0.65
Consensus pattern (55 bp):
ATTATTTTTTTTCAATTCATTCATATTATTTTTCTCATTATTATATATTTTTCAT
Found at i:42470394 original size:6 final size:6
Alignment explanation
Indices: 42470381--42470476 Score: 55
Period size: 6 Copynumber: 17.3 Consensus size: 6
42470371 CTTTTTTTTA
* * *
42470381 TTTC-T TTTCAT TTTCA- TTTCAT TTTAAT TTT-A- TTTCA- TTCCAA
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT
* * * * * *
42470424 TTTCA- TTTCAT TCT-AA TTTCAT TTCCAT TTCCAT TTCCAT TTCCA-
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT
42470469 TTTCAT TT
1 TTTCAT TT
42470477 CAATTATATA
Statistics
Matches: 75, Mismatches: 9, Indels: 13
0.77 0.09 0.13
Matches are distributed among these distances:
4 3 0.04
5 27 0.36
6 45 0.60
ACGTcount: A:0.20, C:0.21, G:0.00, T:0.59
Consensus pattern (6 bp):
TTTCAT
Found at i:42470395 original size:11 final size:11
Alignment explanation
Indices: 42470381--42470478 Score: 83
Period size: 11 Copynumber: 8.9 Consensus size: 11
42470371 CTTTTTTTTA
*
42470381 TTTCTTTTCAT
1 TTTCATTTCAT
42470392 TTTCATTTCAT
1 TTTCATTTCAT
* *
42470403 TTTAATTTTA-
1 TTTCATTTCAT
* *
42470413 TTTCATTCCAA
1 TTTCATTTCAT
42470424 TTTCATTTCAT
1 TTTCATTTCAT
* *
42470435 TCTAATTTCAT
1 TTTCATTTCAT
*
42470446 TTCCATTTCCAT
1 TTTCATTT-CAT
*
42470458 TTCCATTTCCA-
1 TTTCATTT-CAT
42470469 TTTCATTTCA
1 TTTCATTTCA
42470479 ATTATATATT
Statistics
Matches: 71, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
10 9 0.13
11 48 0.68
12 14 0.20
ACGTcount: A:0.20, C:0.21, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTCATTTCAT
Found at i:42470399 original size:16 final size:15
Alignment explanation
Indices: 42470368--42470416 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
42470358 ATGTTTCTTT
42470368 TTTCTTTT--TTTTA
1 TTTCTTTTCATTTTA
42470381 TTTCTTTTCATTTTCA
1 TTTCTTTTCATTTT-A
*
42470397 TTTCATTTTAATTTTA
1 TTTC-TTTTCATTTTA
42470413 TTTC
1 TTTC
42470417 ATTCCAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 8 0.26
15 4 0.13
16 10 0.32
17 9 0.29
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTCTTTTCATTTTA
Found at i:42470417 original size:16 final size:16
Alignment explanation
Indices: 42470376--42470453 Score: 77
Period size: 16 Copynumber: 4.8 Consensus size: 16
42470366 TTTTTCTTTT
*
42470376 TTTTATTTC-TTTTCA
1 TTTTATTTCATTTTAA
42470391 TTTTCATTTCATTTTAA
1 TTTT-ATTTCATTTTAA
**
42470408 TTTTATTTCATTCCAA
1 TTTTATTTCATTTTAA
* *
42470424 TTTCATTTCATTCTAA
1 TTTTATTTCATTTTAA
*
42470440 TTTCATTTCCATTT
1 TTTTATTT-CATTT
42470454 CCATTTCCAT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
15 4 0.07
16 37 0.69
17 13 0.24
ACGTcount: A:0.21, C:0.17, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTATTTCATTTTAA
Found at i:42470460 original size:12 final size:12
Alignment explanation
Indices: 42470439--42470477 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
42470429 TTTCATTCTA
42470439 ATTT-CATTTCC
1 ATTTCCATTTCC
42470450 ATTTCCATTTCC
1 ATTTCCATTTCC
42470462 ATTTCCATTT-C
1 ATTTCCATTTCC
42470473 ATTTC
1 ATTTC
42470478 AATTATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.18, C:0.28, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTTCCATTTCC
Found at i:42470466 original size:18 final size:17
Alignment explanation
Indices: 42470392--42470478 Score: 69
Period size: 16 Copynumber: 5.3 Consensus size: 17
42470382 TTCTTTTCAT
**
42470392 TTTCATTT-CATTTTAA
1 TTTCATTTCCATTTCCA
*
42470408 TTTTATTT-CA-TTCCAA
1 TTTCATTTCCATTTCC-A
*
42470424 TTTCATTT-CA-TTCTAA
1 TTTCATTTCCATTTC-CA
42470440 TTTCATTTCCATTTCCA
1 TTTCATTTCCATTTCCA
42470457 TTTCCATTTCCATTT-CA
1 TTT-CATTTCCATTTCCA
42470474 TTTCA
1 TTTCA
42470479 ATTATATATT
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
15 2 0.03
16 33 0.55
17 11 0.18
18 14 0.23
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTCATTTCCATTTCCA
Found at i:42470512 original size:22 final size:23
Alignment explanation
Indices: 42470469--42470520 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
42470459 TCCATTTCCA
*
42470469 TTTC-ATTTCAATTATATATTTT
1 TTTCAATTTAAATTATATATTTT
42470491 TTTCAATTTAAATT-TAT-TTTT
1 TTTCAATTTAAATTATATATTTT
42470512 TTCTCAATT
1 TT-TCAATT
42470521 CATTTATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 6 0.22
22 13 0.48
23 8 0.30
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTCAATTTAAATTATATATTTT
Found at i:42470530 original size:22 final size:22
Alignment explanation
Indices: 42470469--42470576 Score: 71
Period size: 21 Copynumber: 5.0 Consensus size: 22
42470459 TCCATTTCCA
42470469 TTTC-ATTTCAATTATATATTTT
1 TTTCAATTTCAATTATAT-TTTT
*
42470491 TTTCAATTTAAATT-TATTTTT
1 TTTCAATTTCAATTATATTTTT
* **
42470512 TTCTCAA-TTCATTTATATTACT
1 TT-TCAATTTCAATTATATTTTT
* * *
42470534 TTTAAATTT-AATTTTAATTTT
1 TTTCAATTTCAATTATATTTTT
* * *
42470555 TTTCTTATTTCATTTAAATTTT
1 TTTC-AATTTCAATTATATTTT
42470577 CTATTTTCAA
Statistics
Matches: 63, Mismatches: 17, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
21 24 0.38
22 24 0.38
23 15 0.24
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTCAATTTCAATTATATTTTT
Found at i:42470642 original size:47 final size:46
Alignment explanation
Indices: 42470463--42470642 Score: 154
Period size: 47 Copynumber: 3.9 Consensus size: 46
42470453 TCCATTTCCA
* *
42470463 TTTC-CATTTCATTTCAATTATATATTTTTTTCAATTTAAATTT-ATTTT
1 TTTCTCATTTCATTTAAATTATCTA---TTTTCAATTT-AATTTAATTTT
* * *
42470511 TTTCTCAATTCATTTATATTA-C--TTTTAAATTTAATTTTAATTTT
1 TTTCTCATTTCATTTAAATTATCTATTTTCAATTTAA-TTTAATTTT
* * **
42470555 TTTCTTATTTCATTTAAATTTTCTATTTTCAATGCAAATTTAATTTT
1 TTTCTCATTTCATTTAAATTATCTATTTTCAAT-TTAATTTAATTTT
* * *
42470602 TTTGTCATTTCTTTTAAATTATCTATCTTTCCATTTAATTT
1 TTTCTCATTTCATTTAAATTATCTAT-TTTCAATTTAATTT
42470643 TTTGCTCATT
Statistics
Matches: 105, Mismatches: 19, Indels: 17
0.74 0.13 0.12
Matches are distributed among these distances:
42 2 0.02
43 12 0.11
44 22 0.21
45 1 0.01
47 43 0.41
48 12 0.11
49 13 0.12
ACGTcount: A:0.27, C:0.11, G:0.01, T:0.61
Consensus pattern (46 bp):
TTTCTCATTTCATTTAAATTATCTATTTTCAATTTAATTTAATTTT
Found at i:42470718 original size:76 final size:74
Alignment explanation
Indices: 42470634--42470843 Score: 251
Period size: 76 Copynumber: 2.7 Consensus size: 74
42470624 CTATCTTTCC
* *
42470634 ATTTAATTTTTTGCTCATTTTATTTAAATTAAAAGTTTCTCTCATTTCATTTAAATTTATCTTTC
1 ATTTAATTTTTTACTCATTTCATTTAAA-TAAAAGTTT-TCTCATTTCATTTAAATTTATCTTTC
42470699 TTTCAAATTTA
64 TTTCAAATTTA
* * **
42470710 ATTTAATTTTTTTCTCATTTCATTTCAATGAAATTTTTTCCTCATTTCATTTAAATTTATCTTTC
1 ATTTAATTTTTTACTCATTTCATTTAAAT-AAAAGTTTT-CTCATTTCATTTAAATTTATCTTTC
* *
42470775 TTTCAATTTTC
64 TTTCAAATTTA
* *
42470786 ATTTAAATTTTGTAC-CATTTCATTTCAAACAAAATTGTTTTCTCATTTCATTTAAATT
1 ATTT-AATTTTTTACTCATTTCATTT-AAATAAAA--GTTTTCTCATTTCATTTAAATT
42470844 ATCAACCTTT
Statistics
Matches: 115, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
75 2 0.02
76 82 0.71
77 27 0.23
78 4 0.03
ACGTcount: A:0.28, C:0.14, G:0.02, T:0.56
Consensus pattern (74 bp):
ATTTAATTTTTTACTCATTTCATTTAAATAAAAGTTTTCTCATTTCATTTAAATTTATCTTTCTT
TCAAATTTA
Found at i:42470783 original size:27 final size:25
Alignment explanation
Indices: 42470669--42470796 Score: 102
Period size: 28 Copynumber: 5.0 Consensus size: 25
42470659 AAATTAAAAG
*
42470669 TTTCTCTCATTTCATTTAAATTTATC
1 TTTCTTTCATTTCATTTAAATTT-TC
* *
42470695 TTTCTTTCAAATTTAATTT-AATTTTT
1 TTTCTTTC--ATTTCATTTAAATTTTC
* *
42470721 TTCTCATTTCATTTCAATGAAA-TTT-
1 TT-TC-TTTCATTTCATTTAAATTTTC
*
42470746 TTTC-CTCATTTCATTTAAATTTATC
1 TTTCTTTCATTTCATTTAAATTT-TC
42470771 TTTCTTTCAATTTTCATTTAAATTTT
1 TTTCTTTC-A-TTTCATTTAAATTTT
42470797 GTACCATTTC
Statistics
Matches: 81, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
22 12 0.15
23 2 0.02
24 3 0.04
25 6 0.07
26 21 0.26
27 11 0.14
28 26 0.32
ACGTcount: A:0.25, C:0.15, G:0.01, T:0.59
Consensus pattern (25 bp):
TTTCTTTCATTTCATTTAAATTTTC
Found at i:42473976 original size:102 final size:103
Alignment explanation
Indices: 42473854--42474100 Score: 313
Period size: 102 Copynumber: 2.4 Consensus size: 103
42473844 TAAGTCTGGA
* *
42473854 GCCGGCCATTGACAAGCCAGCTCTAATTTTTTTTAAATACTGGTACTCTGGTG-CCATCCATTAA
1 GCCGGCCATTGACAGGCCAGCACTAATTTTTTTTAAATACTGGTACTCTGGTGTCCA-CCATTAA
*
42473918 CAGACCAACACAAAAAAA-TGATTTTTTTTGTACTTGGT
65 CAGACCAACACAAAAAAATTGATTTTTTTCGTACTTGGT
* * *
42473956 GCCGGCCATTGACAGGCCAGCACCAAATTTTTTTTAAAATAC--GTACTCTGGTGTCGACCATTG
1 GCCGGCCATTGACAGGCCAGCA-CTAATTTTTTTT-AAATACTGGTACTCTGGTGTCCACCATTA
* * *
42474019 ACAGGCCAGCACAAAAAAATTTATTTTTTTCGTACTTGGT
64 ACAGACCAACACAAAAAAATTGATTTTTTTCGTACTTGGT
** * * *
42474059 GCTTGCCATTGACAGGCCAGAACTGATTTTTTTAAAATACTG
1 GCCGGCCATTGACAGGCCAGCACTAATTTTTTTTAAATACTG
42474101 ATATTTTTGT
Statistics
Matches: 124, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
101 6 0.05
102 62 0.50
103 50 0.40
104 6 0.05
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (103 bp):
GCCGGCCATTGACAGGCCAGCACTAATTTTTTTTAAATACTGGTACTCTGGTGTCCACCATTAAC
AGACCAACACAAAAAAATTGATTTTTTTCGTACTTGGT
Found at i:42474008 original size:52 final size:51
Alignment explanation
Indices: 42473818--42474030 Score: 156
Period size: 52 Copynumber: 4.2 Consensus size: 51
42473808 GCCTGTCAAT
* * *
42473818 GGCCAGCACC-AATTTTTTTTTAATAC-TAAGTCTGGAGCCGGCCATTGACA
1 GGCCAGCACCAAATTTTTTTTAAATACGT-ACTCTGGTGCCGGCCATTGACA
* * * ** *
42473868 AGCCAGC-TCTAATTTTTTTTAAATACTGGTACTCTGGTGCCATCCATTAACA
1 GGCCAGCACCAAATTTTTTTTAAATAC--GTACTCTGGTGCCGGCCATTGACA
* * *
42473920 GACCAACACAAAAAAATGATTTTTTT---T--GTACT-TGGTGCCGGCCATTGACA
1 GGCCAGCAC---CAAAT--TTTTTTTAAATACGTACTCTGGTGCCGGCCATTGACA
* *
42473970 GGCCAGCACCAAATTTTTTTTAAAATACGTACTCTGGTGTCGACCATTGACA
1 GGCCAGCACCAAATTTTTTTT-AAATACGTACTCTGGTGCCGGCCATTGACA
42474022 GGCCAGCAC
1 GGCCAGCAC
42474031 AAAAAAATTT
Statistics
Matches: 124, Mismatches: 22, Indels: 32
0.70 0.12 0.18
Matches are distributed among these distances:
45 7 0.06
47 4 0.03
49 2 0.02
50 43 0.35
51 10 0.08
52 46 0.37
53 1 0.01
55 1 0.01
56 3 0.02
58 7 0.06
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (51 bp):
GGCCAGCACCAAATTTTTTTTAAATACGTACTCTGGTGCCGGCCATTGACA
Found at i:42474981 original size:51 final size:51
Alignment explanation
Indices: 42474945--42475041 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
42474935 TTAAATTTAT
* *
42474945 TTTTTTTTGTTTTAGGG-CACTGATA-GCCGGCACCAACTTTATCAGAATAAA
1 TTTTTTTAGTTTT-GGGACACTGA-AGGCCGACACCAACTTTATCAGAATAAA
*
42474996 TTTTTTTAGTTTTGGGACATTGAAGGCCGACACCAACTTTATCAGA
1 TTTTTTTAGTTTTGGGACACTGAAGGCCGACACCAACTTTATCAGA
42475042 TTTAAAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
50 4 0.10
51 37 0.90
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (51 bp):
TTTTTTTAGTTTTGGGACACTGAAGGCCGACACCAACTTTATCAGAATAAA
Found at i:42482684 original size:27 final size:27
Alignment explanation
Indices: 42482654--42482811 Score: 115
Period size: 27 Copynumber: 5.6 Consensus size: 27
42482644 ATTATTCTCC
42482654 TATATA-TATTTATATTGTATTTTATTA
1 TATATATTATTTATATT-TATTTTATTA
* *
42482681 TATAGCATTTATTATATTTTTACTTTTATTA
1 TATA-TA-TTATT-TATATTTA-TTTTATTA
* *
42482712 TATATATTACTTACTATATTATTTTTTTA
1 TATATATTATTTA-TAT-TTATTTTATTA
* * *
42482741 TTATATATTATGTATATCATATATTATT-
1 -TATATATTATTTATAT-TTATTTTATTA
* *
42482769 TATTATATTATTTATGTTTATATTATTCA
1 TA-TATATTATTTATATTTATTTTATT-A
42482798 T-TATATTATTTATA
1 TATATATTATTTATA
42482812 ATTTTAAGAT
Statistics
Matches: 104, Mismatches: 16, Indels: 22
0.73 0.11 0.15
Matches are distributed among these distances:
27 27 0.26
28 15 0.14
29 24 0.23
30 21 0.20
31 17 0.16
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (27 bp):
TATATATTATTTATATTTATTTTATTA
Found at i:42482789 original size:15 final size:12
Alignment explanation
Indices: 42482687--42482810 Score: 82
Period size: 12 Copynumber: 10.5 Consensus size: 12
42482677 ATTATATAGC
42482687 ATTTATTATATT
1 ATTTATTATATT
*
42482699 -TTTACT-T-TT
1 ATTTATTATATT
42482708 A-TTATATATATT
1 ATTTAT-TATATT
* *
42482720 ACTTACTATATT
1 ATTTATTATATT
*
42482732 ATTT-TTTTATT
1 ATTTATTATATT
* *
42482743 ATATATTAT-GT
1 ATTTATTATATT
*
42482754 ATATCA-TATATT
1 AT-TTATTATATT
42482766 ATTTATTATATT
1 ATTTATTATATT
42482778 ATTTATGTTTATATT
1 ATTTA---TTATATT
*
42482793 ATTCATTATATT
1 ATTTATTATATT
42482805 ATTTAT
1 ATTTAT
42482811 AATTTTAAGA
Statistics
Matches: 85, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
9 5 0.06
10 2 0.02
11 22 0.26
12 42 0.49
13 3 0.04
15 11 0.13
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (12 bp):
ATTTATTATATT
Found at i:42486429 original size:38 final size:38
Alignment explanation
Indices: 42486364--42486489 Score: 189
Period size: 38 Copynumber: 3.3 Consensus size: 38
42486354 ATATTTGATG
*
42486364 TATATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAT
42486404 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* * *
42486442 TATATCCGGGATAAATCCCGCAGGCCTAGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
42486480 TATATTCGGG
1 TATATCCGGG
42486490 CCTTCGTGCC
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
38 66 0.81
39 5 0.06
40 10 0.12
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
Found at i:42486778 original size:43 final size:43
Alignment explanation
Indices: 42486482--42486765 Score: 559
Period size: 43 Copynumber: 6.6 Consensus size: 43
42486472 GCTGGTATTA
42486482 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
42486525 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
42486568 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
42486611 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
42486654 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
42486697 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
42486740 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
42486766 GTAATGCCGG
Statistics
Matches: 239, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 239 1.00
ACGTcount: A:0.10, C:0.26, G:0.35, T:0.30
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:42499471 original size:19 final size:20
Alignment explanation
Indices: 42499437--42499475 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
42499427 TAGGTGCTTG
42499437 TTTCAGCCCATATAGAGCCTT
1 TTTCAGCCCATATAGA-CCTT
42499458 TTTCAG-CC-TATAGACCTT
1 TTTCAGCCCATATAGACCTT
42499476 GTCTTCTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 2 0.11
21 6 0.33
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (20 bp):
TTTCAGCCCATATAGACCTT
Found at i:42503829 original size:7 final size:6
Alignment explanation
Indices: 42503780--42503836 Score: 51
Period size: 6 Copynumber: 8.8 Consensus size: 6
42503770 ATTCACATGC
* * *
42503780 TTTTAT TTTTCT TTTTACT TTTTGT CTCCTTGAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTA-T TTTTAT -T--TTTAT TTTTAT TTTTAT TTTTAT
42503832 TTTTA
1 TTTTA
42503837 ATTTAAACAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
6 31 0.76
7 6 0.15
8 1 0.02
9 3 0.07
ACGTcount: A:0.12, C:0.09, G:0.04, T:0.75
Consensus pattern (6 bp):
TTTTAT
Found at i:42508368 original size:23 final size:23
Alignment explanation
Indices: 42508341--42508479 Score: 197
Period size: 23 Copynumber: 6.0 Consensus size: 23
42508331 AGTTAGAAGT
42508341 GTGAAGAGACTTGAATATGAAAA
1 GTGAAGAGACTTGAATATGAAAA
* * *
42508364 GTGAAAAAACTTGAATATGAATA
1 GTGAAGAGACTTGAATATGAAAA
42508387 GTGAAGAGACTTGAATATGAAAA
1 GTGAAGAGACTTGAATATGAAAA
* * *
42508410 GTGAAAAAACTTGAATATGAATA
1 GTGAAGAGACTTGAATATGAAAA
*
42508433 GTGAAGAGACTTGAAGATGAAAA
1 GTGAAGAGACTTGAATATGAAAA
* *
42508456 GTTAAGAGGCTTGAATATGAAAA
1 GTGAAGAGACTTGAATATGAAAA
42508479 G
1 G
42508480 ATACACACAT
Statistics
Matches: 100, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 100 1.00
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.23
Consensus pattern (23 bp):
GTGAAGAGACTTGAATATGAAAA
Found at i:42508408 original size:46 final size:46
Alignment explanation
Indices: 42508341--42508476 Score: 227
Period size: 46 Copynumber: 3.0 Consensus size: 46
42508331 AGTTAGAAGT
42508341 GTGAAGAGACTTGAATATGAAAAGTGAAAAAACTTGAATATGAATA
1 GTGAAGAGACTTGAATATGAAAAGTGAAAAAACTTGAATATGAATA
42508387 GTGAAGAGACTTGAATATGAAAAGTGAAAAAACTTGAATATGAATA
1 GTGAAGAGACTTGAATATGAAAAGTGAAAAAACTTGAATATGAATA
* * * **
42508433 GTGAAGAGACTTGAAGATGAAAAGTTAAGAGGCTTGAATATGAA
1 GTGAAGAGACTTGAATATGAAAAGTGAAAAAACTTGAATATGAA
42508477 AAGATACACA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.24
Consensus pattern (46 bp):
GTGAAGAGACTTGAATATGAAAAGTGAAAAAACTTGAATATGAATA
Found at i:42512919 original size:23 final size:23
Alignment explanation
Indices: 42512893--42513032 Score: 199
Period size: 23 Copynumber: 6.1 Consensus size: 23
42512883 AAGTTAGAAG
42512893 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
42512916 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
42512939 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
42512962 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
*
42512985 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
42513008 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
42513031 AG
1 AG
42513033 ATACACACAT
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 101 1.00
ACGTcount: A:0.49, C:0.04, G:0.24, T:0.23
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:42512960 original size:46 final size:46
Alignment explanation
Indices: 42512893--42513029 Score: 229
Period size: 46 Copynumber: 3.0 Consensus size: 46
42512883 AAGTTAGAAG
42512893 AGTGAAGAGACTTGAATATGAAAAGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAAAGTGAAAAAACTTGAATATGAAT
42512939 AGTGAAGAGACTTGAATATGAAAAGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAAAGTGAAAAAACTTGAATATGAAT
* * * **
42512985 AGTGAAGAGACTTGAAGATGAAAAGTTAAGAGGCTTGAATATGAA
1 AGTGAAGAGACTTGAATATGAAAAGTGAAAAAACTTGAATATGAA
42513030 AAGATACACA
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 86 1.00
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.23
Consensus pattern (46 bp):
AGTGAAGAGACTTGAATATGAAAAGTGAAAAAACTTGAATATGAAT
Found at i:42513890 original size:16 final size:17
Alignment explanation
Indices: 42513863--42513895 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
42513853 TGCCTTTCTT
*
42513863 TTTTTATATAAATTATG
1 TTTTTATATAAAATATG
42513880 TTTTTAT-TAAAATATG
1 TTTTTATATAAAATATG
42513896 ATTCACATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTTTATATAAAATATG
Found at i:42513954 original size:5 final size:6
Alignment explanation
Indices: 42513906--42513962 Score: 51
Period size: 6 Copynumber: 8.8 Consensus size: 6
42513896 ATTCACATGC
* * *
42513906 TTTTAT TTTTCT TTTTACT TTTTGT CTCCTTGAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTA-T TTTTAT -T--TTTAT TTTTAT TTTTAT TTTTAT
42513958 TTTTA
1 TTTTA
42513963 ATGTAAACAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
6 31 0.76
7 6 0.15
8 1 0.02
9 3 0.07
ACGTcount: A:0.12, C:0.09, G:0.04, T:0.75
Consensus pattern (6 bp):
TTTTAT
Found at i:42518270 original size:20 final size:21
Alignment explanation
Indices: 42518232--42518270 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
42518222 GGCGGTTTTG
42518232 AGAAATCAAAGTGAAATAGGA
1 AGAAATCAAAGTGAAATAGGA
* *
42518253 AGAAA-CAATGTGATATAG
1 AGAAATCAAAGTGAAATAG
42518271 TAATTATAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.54, C:0.05, G:0.23, T:0.18
Consensus pattern (21 bp):
AGAAATCAAAGTGAAATAGGA
Found at i:42524935 original size:17 final size:17
Alignment explanation
Indices: 42524898--42524935 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
42524888 CAAAATTCCT
*
42524898 TTTTGGCTTTTTTTTTG
1 TTTTGGCTTTTTTTTTA
42524915 TTTTGG-TTTTTTTGTTA
1 TTTTGGCTTTTTTT-TTA
42524932 TTTT
1 TTTT
42524936 TTGATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.03, C:0.03, G:0.16, T:0.79
Consensus pattern (17 bp):
TTTTGGCTTTTTTTTTA
Found at i:42526243 original size:6 final size:6
Alignment explanation
Indices: 42526232--42526261 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
42526222 ATCAAATTTC
42526232 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
42526262 TTCTCCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:42530186 original size:34 final size:34
Alignment explanation
Indices: 42530138--42530204 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
42530128 TGTTACCGAC
*
42530138 ACTGAAATGGGCTAAGGCCC-ACACTGATACTGAT
1 ACTGAAATGGGCTAAGGCCCTA-ACTGAAACTGAT
*
42530172 ACTGTAATGGGCTAAGGCCCTAACTGAAACTGA
1 ACTGAAATGGGCTAAGGCCCTAACTGAAACTGA
42530205 ACTATTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 29 0.97
35 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (34 bp):
ACTGAAATGGGCTAAGGCCCTAACTGAAACTGAT
Found at i:42530960 original size:25 final size:25
Alignment explanation
Indices: 42530944--42531000 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
42530934 GACAGTTTAT
*
42530944 TCTGAAAATACTGTAGATAGCATAC
1 TCTGAAAATACTGTAGACAGCATAC
* ** *
42530969 TCTGAAAATACTATAGTTAGCATCC
1 TCTGAAAATACTGTAGACAGCATAC
42530994 TCTGAAA
1 TCTGAAA
42531001 CTATAGTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (25 bp):
TCTGAAAATACTGTAGACAGCATAC
Found at i:42536387 original size:39 final size:39
Alignment explanation
Indices: 42536340--42536417 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
42536330 TTAGTGTAGT
*
42536340 GTAGTTTCTAATTCTTGTTCTGCAATTGTTGATGTAGGG
1 GTAGTTTCTAATTCTTGTTCTGCAATTGTTGATGGAGGG
42536379 GTAGTTTCTAATTCTTGTTCTGCAATTGTTGATGGAGGG
1 GTAGTTTCTAATTCTTGTTCTGCAATTGTTGATGGAGGG
42536418 AAAGGCTACG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.18, C:0.10, G:0.27, T:0.45
Consensus pattern (39 bp):
GTAGTTTCTAATTCTTGTTCTGCAATTGTTGATGGAGGG
Found at i:42541256 original size:170 final size:167
Alignment explanation
Indices: 42540890--42541291 Score: 479
Period size: 170 Copynumber: 2.4 Consensus size: 167
42540880 ATGGAACTAG
* * * * *
42540890 TCATTACTACCAATAATGGACATTCTAATTTGGAAAAAAAATATTGATGATTGTGAATAATAATA
1 TCATTGCTACCGATAATGGACATCCTAATTTCGAAAAAAAATA-TGATAATTGTGAATAATAATA
* * *
42540955 CTTTGAGTAGTCAAATTTGAATATTTCAAGTAGCGTTGGGAGTGGGAACCCTTTGATATTTGCTT
65 CTTTGAATAGTCAAATTTGAATATTTCAAGAAGCGTTGGGAGTGGGAACCCTTTGATATTTGATT
* * *
42541020 TGACATTTGTCCAAGTTGGAAGCACACGAGGGGATTAG
130 TGACATTTGTCCAAGTTGGAAGCAAACGAGGGAATTAA
** * *
42541058 TCATTGCTACCGGCAATAGACATCCTAATTTCAAGAGAAAAAAATATGAATAATTGTGAATAATG
1 TCATTGCTACCGATAATGGACATCCTAATTTC--GA-AAAAAAATATG-ATAATTGTGAATAATA
* *** * *
42541123 ATACTTTGAATAGTCATATTTGAATATTTTTGGAAGTGTTGGGAGTGGG-ACCCTTTGAT-TTTT
62 ATACTTTGAATAGTCAAATTTGAATATTTCAAGAAGCGTTGGGAGTGGGAACCCTTTGATATTTG
* *
42541186 ATTTCTATATTTGTCCAAGTTGG-AGACAAACGAGGGAATTAA
127 ATTT-GACATTTGTCCAAGTTGGAAG-CAAACGAGGGAATTAA
* *
42541228 TCATTGCTACCGATAGTGGACATCCTAATTTCGACAAGAAAA-ATGATAATTGTGAATAATAATA
1 TCATTGCTACCGATAATGGACATCCTAATTTCGA-AAAAAAATATGATAATTGTGAATAATAATA
42541292 ATAATAATAA
Statistics
Matches: 198, Mismatches: 30, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
166 18 0.09
167 3 0.02
168 33 0.17
169 8 0.04
170 71 0.36
171 65 0.33
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (167 bp):
TCATTGCTACCGATAATGGACATCCTAATTTCGAAAAAAAATATGATAATTGTGAATAATAATAC
TTTGAATAGTCAAATTTGAATATTTCAAGAAGCGTTGGGAGTGGGAACCCTTTGATATTTGATTT
GACATTTGTCCAAGTTGGAAGCAAACGAGGGAATTAA
Found at i:42541290 original size:3 final size:3
Alignment explanation
Indices: 42541282--42542092 Score: 1622
Period size: 3 Copynumber: 270.3 Consensus size: 3
42541272 GATAATTGTG
42541282 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42541330 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42541378 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42541426 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42541474 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42541522 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42541570 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42541618 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42541666 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42541714 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42541762 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42541810 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42541858 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42541906 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42541954 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42542002 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42542050 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
42542093 GAAGTCAAAT
Statistics
Matches: 808, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 808 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:42560750 original size:45 final size:45
Alignment explanation
Indices: 42560649--42560775 Score: 138
Period size: 45 Copynumber: 2.9 Consensus size: 45
42560639 TTTTCTCAAA
* *
42560649 TCACCGGCATT-TCGCCTGTTAGGCTCG-AGGCCCG-ATATCAGT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
*
42560691 TCACCGTCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGT-A-T
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA-TCAGT
** * *
42560735 CTCACCGGCATTATAGTTTGCTAAGCTCAAAGGCCCGAATA
1 -TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
42560776 ATCAAGTCAA
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
42 10 0.14
43 14 0.19
44 8 0.11
45 39 0.54
46 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
Found at i:42561214 original size:38 final size:38
Alignment explanation
Indices: 42561169--42561248 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
42561159 CAAAGGCCCG
* * * *
42561169 AATATAATACCAGCACTAGGCCTGCGGGATTTATCCCA
1 AATATAATACCAGCACGAAGCCTGCAGGATTTAACCCA
*
42561207 AATATAATACCAGCACGAAGCCTGCAGGATTTAACCCG
1 AATATAATACCAGCACGAAGCCTGCAGGATTTAACCCA
42561245 AATA
1 AATA
42561249 CACATCAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.21
Consensus pattern (38 bp):
AATATAATACCAGCACGAAGCCTGCAGGATTTAACCCA
Found at i:42566303 original size:54 final size:54
Alignment explanation
Indices: 42566227--42566331 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
42566217 AAATGGCATG
* * *
42566227 GGATATGGCATTGAAGATGGGAACCAGTTAGGTACAGCCACTGGATATGGCGTT
1 GGATATGGCATTGAAGAAGGGAACCAGGTAGGTACAGCCACTGGACATGGCGTT
* * *
42566281 GGATATGGCATTGGAGAAGGGAACCAGGTAGGTACAGGCATTGGACATGGC
1 GGATATGGCATTGAAGAAGGGAACCAGGTAGGTACAGCCACTGGACATGGC
42566332 ATGGGAAGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.29, C:0.14, G:0.36, T:0.21
Consensus pattern (54 bp):
GGATATGGCATTGAAGAAGGGAACCAGGTAGGTACAGCCACTGGACATGGCGTT
Found at i:42566363 original size:42 final size:42
Alignment explanation
Indices: 42566279--42566385 Score: 108
Period size: 42 Copynumber: 2.5 Consensus size: 42
42566269 GGATATGGCG
* * *
42566279 TTGGATATGGCATTGGAGAA-GGGAACCAGGTAGGTACAGGCA
1 TTGGACATGGCATGGGA-AATGGGAACCAGGTAGGGACAGGCA
* * **
42566321 TTGGACATGGCATGGGAAGTGGGAACCAGTTAGGGATGGGCA
1 TTGGACATGGCATGGGAAATGGGAACCAGGTAGGGACAGGCA
** *
42566363 TTGGGTATGGCATTGGAAATGGG
1 TTGGACATGGCATGGGAAATGGG
42566386 GATCAATCAG
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
41 1 0.02
42 52 0.98
ACGTcount: A:0.27, C:0.10, G:0.41, T:0.21
Consensus pattern (42 bp):
TTGGACATGGCATGGGAAATGGGAACCAGGTAGGGACAGGCA
Found at i:42566596 original size:42 final size:42
Alignment explanation
Indices: 42566500--42566606 Score: 164
Period size: 42 Copynumber: 2.5 Consensus size: 42
42566490 GGGATATGGC
*
42566500 ATTGGATATGGCACTGGAAATGGGAACCAGTTAGGAACGGGT
1 ATTGGATATGGTACTGGAAATGGGAACCAGTTAGGAACGGGT
42566542 ATTGGATATGGTACTGGAAATGGGAACCAGTTAGGAAAC-GGT
1 ATTGGATATGGTACTGGAAATGGGAACCAGTTAGG-AACGGGT
*
42566584 ATTGGATTTGGTA-TCGGAAATGG
1 ATTGGATATGGTACT-GGAAATGG
42566607 AGGTCAGTCA
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
41 1 0.02
42 57 0.93
43 3 0.05
ACGTcount: A:0.31, C:0.09, G:0.35, T:0.25
Consensus pattern (42 bp):
ATTGGATATGGTACTGGAAATGGGAACCAGTTAGGAACGGGT
Found at i:42574332 original size:1 final size:1
Alignment explanation
Indices: 42574322--42574416 Score: 55
Period size: 1 Copynumber: 95.0 Consensus size: 1
42574312 ATCTTCCCCA
* * * * * * * * * *
42574322 TTTTTATTTTTATTTTTATTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTATTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
42574387 ATTTTTATTTTTATTTTTATTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
42574417 AAAGCTTAAG
Statistics
Matches: 64, Mismatches: 30, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (1 bp):
T
Found at i:42574337 original size:5 final size:6
Alignment explanation
Indices: 42574321--42574417 Score: 149
Period size: 6 Copynumber: 16.2 Consensus size: 6
42574311 AATCTTCCCC
* * * *
42574321 ATTTTT ATTTTT ATTTTT ATTTTT CTTTTT CTTTTT CTTTTT CTTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
*
42574369 CTTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
42574417 A
1 A
42574418 AAGCTTAAGA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 89 1.00
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:42576982 original size:27 final size:27
Alignment explanation
Indices: 42576952--42577025 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
42576942 AGGCGATCCA
42576952 TTCAGAGTT-CGCCACAAAGGCTTTTCT
1 TTCAGA-TTACGCCACAAAGGCTTTTCT
*
42576979 TTCATATTACGCCACAAAGGCTTTTCT
1 TTCAGATTACGCCACAAAGGCTTTTCT
* * *
42577006 TTCATATTACACCATAAAGG
1 TTCAGATTACGCCACAAAGG
42577026 TGTTCCTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 2 0.05
27 41 0.95
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (27 bp):
TTCAGATTACGCCACAAAGGCTTTTCT
Found at i:42577034 original size:27 final size:27
Alignment explanation
Indices: 42576963--42577040 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
42576953 TCAGAGTTCG
* *
42576963 CCACAAAGGCTTTTCTTTCATATTACG
1 CCACAAAGGCTTTCCTTTCATATTACA
*
42576990 CCACAAAGGCTTTTCTTTCATATTACA
1 CCACAAAGGCTTTCCTTTCATATTACA
*
42577017 CCATAAAGG-TGTTCCTTTCATATT
1 CCACAAAGGCT-TTCCTTTCATATT
42577041 GCCTAAGTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 46 0.98
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.38
Consensus pattern (27 bp):
CCACAAAGGCTTTCCTTTCATATTACA
Found at i:42579708 original size:39 final size:39
Alignment explanation
Indices: 42579664--42579743 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
42579654 AAAGAACTCA
42579664 CCAGAAACTCTAACACAAGTCTATAAAGTAGGTCTCTTT
1 CCAGAAACTCTAACACAAGTCTATAAAGTAGGTCTCTTT
*
42579703 CCAGAAACTCTAACACAAGTCTATAAATTAGGTCTCTTT
1 CCAGAAACTCTAACACAAGTCTATAAAGTAGGTCTCTTT
42579742 CC
1 CC
42579744 CTTATCACTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (39 bp):
CCAGAAACTCTAACACAAGTCTATAAAGTAGGTCTCTTT
Found at i:42580673 original size:17 final size:17
Alignment explanation
Indices: 42580651--42580686 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
42580641 ATGGAACACC
42580651 TCTACGTTATCCAAGAA
1 TCTACGTTATCCAAGAA
42580668 TCTACGTTATCCAAGAA
1 TCTACGTTATCCAAGAA
42580685 TC
1 TC
42580687 CTTAGCTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (17 bp):
TCTACGTTATCCAAGAA
Found at i:42602535 original size:18 final size:18
Alignment explanation
Indices: 42602501--42602535 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42602491 AATTAAGAGT
* *
42602501 TATTTTTTTAATTTAATG
1 TATTTTTTAAATATAATG
42602519 TATTTTTTAAATATAAT
1 TATTTTTTAAATATAAT
42602536 TATCTTATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TATTTTTTAAATATAATG
Found at i:42604071 original size:21 final size:21
Alignment explanation
Indices: 42604047--42604087 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42604037 TAGTTTGTAA
* *
42604047 TATATTATATTATGTTATTTT
1 TATATAATATTATGTAATTTT
42604068 TATATAATATTATGTAATTT
1 TATATAATATTATGTAATTT
42604088 ATAACATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
TATATAATATTATGTAATTTT
Found at i:42606171 original size:8 final size:8
Alignment explanation
Indices: 42606157--42606194 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
42606147 TCTAACATTA
42606157 TAATATTT
1 TAATATTT
*
42606165 GAATA--T
1 TAATATTT
42606171 TAATATTT
1 TAATATTT
42606179 TAATATTT
1 TAATATTT
42606187 TAATATTT
1 TAATATTT
42606195 AAAAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
6 5 0.19
8 21 0.81
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (8 bp):
TAATATTT
Found at i:42606276 original size:17 final size:17
Alignment explanation
Indices: 42606230--42606280 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
42606220 GATTCAAATT
*
42606230 AATTTTTATATAAAATGA
1 AATTTTTTTATAAAA-GA
* *
42606248 AA-TTATTCATAAAAGA
1 AATTTTTTTATAAAAGA
42606264 AATTTTTTTATAAAAGA
1 AATTTTTTTATAAAAGA
42606281 TTGTTTATGC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 4 0.15
17 21 0.78
18 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (17 bp):
AATTTTTTTATAAAAGA
Found at i:42614961 original size:38 final size:38
Alignment explanation
Indices: 42614918--42615011 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 38
42614908 CTATCTCCAA
* **
42614918 CCAACCCAACACACCATGTGGGGATAGAATCAACCCA-
1 CCAACCCTACACACCACATGGGGATAGAATCAACCCAT
*
42614955 CTCAACCCTACACACCAAACATGGGGATATAATCAACCCAT
1 C-CAACCCTACACACC--ACATGGGGATAGAATCAACCCAT
42614996 CCAACCCTACACACCA
1 CCAACCCTACACACCA
42615012 AAAGGTACCG
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
37 1 0.02
38 14 0.29
40 33 0.67
41 1 0.02
ACGTcount: A:0.38, C:0.38, G:0.11, T:0.13
Consensus pattern (38 bp):
CCAACCCTACACACCACATGGGGATAGAATCAACCCAT
Found at i:42614990 original size:40 final size:40
Alignment explanation
Indices: 42614936--42615013 Score: 131
Period size: 40 Copynumber: 1.9 Consensus size: 40
42614926 ACACACCATG
42614936 TGGGGATAGAATCAACCCA-CTCAACCCTACACACCAAACA
1 TGGGGATAGAATCAACCCATC-CAACCCTACACACCAAACA
*
42614976 TGGGGATATAATCAACCCATCCAACCCTACACACCAAA
1 TGGGGATAGAATCAACCCATCCAACCCTACACACCAAA
42615014 AGGTACCGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 35 0.97
41 1 0.03
ACGTcount: A:0.40, C:0.35, G:0.12, T:0.14
Consensus pattern (40 bp):
TGGGGATAGAATCAACCCATCCAACCCTACACACCAAACA
Found at i:42623176 original size:21 final size:21
Alignment explanation
Indices: 42623150--42623189 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42623140 CATGATGAAT
*
42623150 TCAGGTGAGTTTTAATCTGGC
1 TCAGGTGAGTTCTAATCTGGC
42623171 TCAGGTGAGTTCTAATCTG
1 TCAGGTGAGTTCTAATCTG
42623190 CTTGGCATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.15, G:0.28, T:0.38
Consensus pattern (21 bp):
TCAGGTGAGTTCTAATCTGGC
Found at i:42631077 original size:9 final size:9
Alignment explanation
Indices: 42631059--42631116 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
42631049 TTTGGTTAAA
42631059 AATTAACCG
1 AATTAACCG
*
42631068 AATTACCCG
1 AATTAACCG
*
42631077 AATTAATCG
1 AATTAACCG
*
42631086 AATTACCCG
1 AATTAACCG
42631095 AATTAACCG
1 AATTAACCG
*
42631104 AATTAACCA
1 AATTAACCG
42631113 AATT
1 AATT
42631117 GAATCACTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:42631082 original size:18 final size:18
Alignment explanation
Indices: 42631059--42631108 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
42631049 TTTGGTTAAA
42631059 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
42631077 AATTAATCGAATTACCCG
1 AATTAACCGAATTACCCG
42631095 AATTAACCGAATTA
1 AATTAACCGAATTA
42631109 ACCAAATTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.26
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:42633631 original size:12 final size:12
Alignment explanation
Indices: 42633614--42633649 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
42633604 ATTCATTTGA
42633614 CATTCATGCATT
1 CATTCATGCATT
42633626 CATTCATGCATT
1 CATTCATGCATT
*
42633638 CATTCATACATT
1 CATTCATGCATT
42633650 GCATCTCCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:42642023 original size:72 final size:72
Alignment explanation
Indices: 42641947--42642760 Score: 1142
Period size: 72 Copynumber: 11.1 Consensus size: 72
42641937 CTGTTTCAAA
* *
42641947 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
*
42642012 TGTTGTC
66 TGTTTTC
* *
42642019 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAGACGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
*
42642084 TCTGTTTTC
64 TTTGTTTTC
* * *
42642093 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAGACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
42642158 TGTTTTC
66 TGTTTTC
*
42642165 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
42642230 TGTTTTC
66 TGTTTTC
* ** * * * *
42642237 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
42642302 TGTCTTTC
66 TGT-TTTC
*
42642310 AAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
* *
42642375 TCTGTTGTTAA
64 TTTGTT-TT-C
** *
42642386 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
42642451 TGTTTTC
66 TGTTTTC
* ** * * * *
42642458 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA-TTT
42642523 TTGTTTTTC
65 TTG-TTTTC
*
42642532 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
42642597 TTTGTTTTC
64 TTTGTTTTC
* ** * * * *
42642606 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
42642671 TGTCTTTC
66 TGT-TTTC
*
42642679 AAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
42642744 TTTGTTTTC
64 TTTGTTTTC
*
42642753 ACAAATCA
1 AAAAATCA
42642761 CACATGTGGT
Statistics
Matches: 669, Mismatches: 59, Indels: 26
0.89 0.08 0.03
Matches are distributed among these distances:
72 325 0.49
73 15 0.02
74 149 0.22
75 127 0.19
76 53 0.08
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (72 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
TGTTTTC
Found at i:42642721 original size:369 final size:365
Alignment explanation
Indices: 42641940--42642749 Score: 1431
Period size: 369 Copynumber: 2.2 Consensus size: 365
42641930 TTTATTTCTG
42641940 TTTCAAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
1 TTTC-AAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
** * *
42642005 CAATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAGACGCTG
65 CAATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTG
** * **
42642070 AGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGA
130 AGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGA
*
42642135 GACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
195 CACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
42642200 CTCGGGACACGCTGAGGTAATTTCAATTTTTGTTTTCAAAATTCAACTCATATTGCGAGAAATGA
260 CTCGGGACACGCTGAGGTAATTTCAATTTTTGTTTTCAAAATTCAACTCATATTGCGAGAAATGA
42642265 GTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGTC
325 GTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGTC
42642306 TTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
1 TTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
*
42642371 AATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGA
66 AATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGA
*
42642436 GGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGAC
131 GGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGAC
* * *
42642501 ATGCTGAGGTATTTTCAATTTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
196 ACGCTGAGGTAATTTCAA-TTTCTG-TTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTG
42642566 AGCCTCGGGACACGCTGAGGTAATTTCAATTTTTGTTTTCAAAATTCAACTCATATTGCGAGAAA
257 AGCCTCGGGACACGCTGAGGTAATTTCAATTTTTGTTTTCAAAATTCAACTCATATTGCGAGAAA
42642631 TGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGTC
322 TGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGTC
42642675 TTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
1 TTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
*
42642740 AATTTTTGTT
66 AATTTCTGTT
42642750 TTCACAAATC
Statistics
Matches: 424, Mismatches: 16, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
365 195 0.46
366 9 0.02
367 5 0.01
369 215 0.51
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (365 bp):
TTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
AATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGA
GGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGAC
ACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
TCGGGACACGCTGAGGTAATTTCAATTTTTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAG
TTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGTC
Found at i:42644115 original size:23 final size:23
Alignment explanation
Indices: 42644089--42644139 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
42644079 TTAAGAACCC
42644089 TAATTTAATTGAATATATTCATT
1 TAATTTAATTGAATATATTCATT
42644112 TAATTTAATTGAATATATTCATT
1 TAATTTAATTGAATATATTCATT
*
42644135 CAATT
1 TAATT
42644140 GCTTATAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (23 bp):
TAATTTAATTGAATATATTCATT
Found at i:42646018 original size:62 final size:61
Alignment explanation
Indices: 42645857--42646024 Score: 148
Period size: 62 Copynumber: 2.8 Consensus size: 61
42645847 TTAAATTAGT
* * ** *
42645857 TAATATTTAAATAATCTAATATAATTATACAT-AATA-TATATATTTTAAATACTTTTTAA
1 TAATATTTAAATAATTTAATATAATTATACATAAATATTATAAATTTTAAATACTAATAAA
* ** * * * *
42645916 TAATTAATTATTTATTTGTAAATTTAATTCTACATGAAATATTTTAAAATTTTAAATA-TAATAA
1 TAA-TATTTAAATAATT-T-AATATAATTATACAT-AAATATTAT-AAATTTTAAATACTAATAA
42645980 A
61 A
42645981 TAATATTTAAATAATTTAATATAATTATACATAAA-A-TATAAATT
1 TAATATTTAAATAATTTAATATAATTATACATAAATATTATAAATT
42646025 AATTCAAAAA
Statistics
Matches: 83, Mismatches: 19, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
58 5 0.06
59 5 0.06
60 9 0.11
61 4 0.05
62 26 0.31
63 1 0.01
64 13 0.16
65 9 0.11
66 11 0.13
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (61 bp):
TAATATTTAAATAATTTAATATAATTATACATAAATATTATAAATTTTAAATACTAATAAA
Found at i:42647883 original size:33 final size:33
Alignment explanation
Indices: 42647846--42647910 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
42647836 TGTGTTCCAC
*
42647846 ACGGTCAAGGCCAATTTGGGCCGTGTGGGCCAT
1 ACGGTCAAGGCCAATTTGGGCCATGTGGGCCAT
42647879 ACGGTCAAGGCCAATTTGGGCCATGTGGGCCA
1 ACGGTCAAGGCCAATTTGGGCCATGTGGGCCA
42647911 CACAGGTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.25, G:0.35, T:0.20
Consensus pattern (33 bp):
ACGGTCAAGGCCAATTTGGGCCATGTGGGCCAT
Found at i:42650953 original size:19 final size:20
Alignment explanation
Indices: 42650929--42650970 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
42650919 AATTTTTTTT
42650929 ATTTTAAAAAAAACTC-AAA
1 ATTTTAAAAAAAACTCTAAA
* *
42650948 ATTTTAAGAAAAAGTCTAAA
1 ATTTTAAAAAAAACTCTAAA
42650968 ATT
1 ATT
42650971 ACTCCCCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (20 bp):
ATTTTAAAAAAAACTCTAAA
Found at i:42651275 original size:25 final size:25
Alignment explanation
Indices: 42651204--42651265 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
42651194 TTATATATAT
42651204 TCAAATAATTATAATTAGAATTAAA
1 TCAAATAATTATAATTAGAATTAAA
*
42651229 TCAAATAATTAGAATTAGAATTAAA
1 TCAAATAATTATAATTAGAATTAAA
*
42651254 TC-AATAAATATA
1 TCAAATAATTATA
42651266 TAAGTAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 8 0.24
25 26 0.76
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (25 bp):
TCAAATAATTATAATTAGAATTAAA
Found at i:42652992 original size:82 final size:80
Alignment explanation
Indices: 42652809--42652971 Score: 238
Period size: 82 Copynumber: 2.0 Consensus size: 80
42652799 ATATCAATGA
* *
42652809 AATCCATCATTGTTAGGCAACTTGGGATGACAAAGTAAACTAAAAATTATTGATGATAGAATATT
1 AATCCATAATTGTT-GGCAACTCGGGATGACAAAGTAAACTAAAAATTATTGATGATAGAATATT
42652874 AACACAATATGTTTATT
65 AACAC-ATATGTTTATT
* * *
42652891 AATCCATCATTGTTTGGCAACTCGGGATGATAAAGTAAAGTAAAAATTTATTGATGATAGAATAT
1 AATCCATAATTG-TTGGCAACTCGGGATGACAAAGTAAACTAAAAA-TTATTGATGATAGAATAT
42652956 TAACAC-TATGTTTATT
64 TAACACATATGTTTATT
42652972 TAGATTTGCT
Statistics
Matches: 76, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
81 10 0.13
82 40 0.53
83 26 0.34
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (80 bp):
AATCCATAATTGTTGGCAACTCGGGATGACAAAGTAAACTAAAAATTATTGATGATAGAATATTA
ACACATATGTTTATT
Found at i:42653425 original size:20 final size:20
Alignment explanation
Indices: 42653400--42653442 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
42653390 TATGTTATGT
42653400 AAATGATTATATAAATATTG
1 AAATGATTATATAAATATTG
42653420 AAATGATTATATAAATATTG
1 AAATGATTATATAAATATTG
42653440 AAA
1 AAA
42653443 GGTAGTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (20 bp):
AAATGATTATATAAATATTG
Found at i:42664544 original size:21 final size:20
Alignment explanation
Indices: 42664511--42664578 Score: 57
Period size: 21 Copynumber: 3.4 Consensus size: 20
42664501 AAGATGTTAC
*
42664511 TATTATTCATATTTTCAGCAT
1 TATTATT-ATATTTTCAACAT
* *
42664532 TATTATTATTATTATCACCAT
1 TATTATTA-TATTTTCAACAT
** *
42664553 TGCTATTATGTTTT-AACAT
1 TATTATTATATTTTCAACAT
42664572 TATTATT
1 TATTATT
42664579 TTCTATTATC
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
19 9 0.24
20 5 0.14
21 23 0.62
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (20 bp):
TATTATTATATTTTCAACAT
Found at i:42665068 original size:22 final size:22
Alignment explanation
Indices: 42665012--42665069 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
42665002 ATTATTATTA
* *
42665012 CTATTATTCTTTATTGTCATGG
1 CTATTATTTTTTATTGTCATAG
* * *
42665034 TTATTA-TTTTTATTTTTATAG
1 CTATTATTTTTTATTGTCATAG
42665055 CTATTATTTTTTATT
1 CTATTATTTTTTATT
42665070 ACTAATATCA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (22 bp):
CTATTATTTTTTATTGTCATAG
Found at i:42665177 original size:17 final size:18
Alignment explanation
Indices: 42665146--42665179 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42665136 ATGATTTTTC
*
42665146 TTTTATATATTTACATTT
1 TTTTATATATATACATTT
42665164 TTTTATATA-ATACATT
1 TTTTATATATATACATT
42665180 GATTCTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATATATATACATTT
Found at i:42665377 original size:3 final size:3
Alignment explanation
Indices: 42665362--42665397 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
42665352 TACATAATAT
* *
42665362 TTA TTA TTT TTA TTA TCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42665398 AAAAAAACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:42669446 original size:49 final size:49
Alignment explanation
Indices: 42669393--42669492 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
42669383 GGACCGAGGG
42669393 CCTTTTATATAGTAAATCCATAAGACATAACCCATCATAGTGTCAATGT
1 CCTTTTATATAGTAAATCCATAAGACATAACCCATCATAGTGTCAATGT
*
42669442 CCTTTTATATAGTAATTCCATAAGACATAACCCATCATAGTGTCAATGT
1 CCTTTTATATAGTAAATCCATAAGACATAACCCATCATAGTGTCAATGT
42669491 CC
1 CC
42669493 ATGCCCTATT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (49 bp):
CCTTTTATATAGTAAATCCATAAGACATAACCCATCATAGTGTCAATGT
Found at i:42670624 original size:12 final size:12
Alignment explanation
Indices: 42670607--42670631 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42670597 GTTAACGTAC
42670607 TTAATAAATAAA
1 TTAATAAATAAA
42670619 TTAATAAATAAA
1 TTAATAAATAAA
42670631 T
1 T
42670632 CTTTTATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTAATAAATAAA
Found at i:42672812 original size:30 final size:30
Alignment explanation
Indices: 42672776--42672833 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
42672766 TTTTGAAAAA
42672776 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
*
42672806 CAGAAATTAAAAAGCTCAACTCACCTCT
1 CAGAAATTAAAAAGCTCAACTCAACTCT
42672834 TGCAATATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.43, C:0.28, G:0.09, T:0.21
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:42672884 original size:87 final size:84
Alignment explanation
Indices: 42672737--42672894 Score: 244
Period size: 87 Copynumber: 1.8 Consensus size: 84
42672727 GACTGGAGGT
42672737 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACT
42672802 CTCGCAGAAATTAAAAAGC
66 CTCGCAGAAATTAAAAAGC
* * * *
42672821 TCAACTCACCTCTTGCAATATGAGTTGAATTTTTTTTAAAAACAGAAATTAAAAGGCTTAACTCA
1 TCAACTCACCTCTCGCAATATGAGTTG-A--TTTTTGAAAAACAGAAATTAAAAGACTCAACTCA
*
42672886 CCTCTCGCA
63 ACTCTCGCA
42672895 ACATGAGTTG
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
84 26 0.39
85 1 0.02
87 39 0.59
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (84 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACT
CTCGCAGAAATTAAAAAGC
Found at i:42673259 original size:73 final size:72
Alignment explanation
Indices: 42673167--42673356 Score: 247
Period size: 72 Copynumber: 2.6 Consensus size: 72
42673157 ATTAAAAGGT
* * * * *
42673167 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAAAAATTGAAATTACCTCATCCTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATT-TTGAAAAACAAAAATTGAAAATACCTCAGCCTGC
*
42673232 CCTGAGGC
65 CCCGAGGC
* ** *
42673240 TCAACTCACCTCTCGCAATATAAGTTGAAATT-AAAACACAAAAATTGAAAATACCTCAGCGTGC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAA-ACAAAAATTGAAAATACCTCAGCCTGC
42673304 CCCGAGGC
65 CCCGAGGC
* *
42673312 TCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACCAAAAT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAAT
42673357 AAAAAGGCTT
Statistics
Matches: 100, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
71 3 0.03
72 67 0.67
73 30 0.30
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (72 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTGAAAATACCTCAGCCTGCC
CCGAGGC
Found at i:42673825 original size:116 final size:116
Alignment explanation
Indices: 42673287--42673812 Score: 1016
Period size: 116 Copynumber: 4.5 Consensus size: 116
42673277 ACAAAAATTG
42673287 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACC
1 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACC
42673352 AAAATAAAAAGGCTTAACTCACCTCTAGCAATATGAGTCAATTTAAAACTA
66 AAAATAAAAAGGCTTAACTCACCTCTAGCAATATGAGTCAATTTAAAACTA
42673403 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACC
1 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACC
42673468 AAAATAAAAAGGCTTAACTCACCTCTAGCAATATGAGTCAATTTAAAACTA
66 AAAATAAAAAGGCTTAACTCACCTCTAGCAATATGAGTCAATTTAAAACTA
42673519 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACC
1 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACC
42673584 AAAATAAAAAGGCTTAACTCACCTCTAGCAATATGAGTCAATTTAAAACTA
66 AAAATAAAAAGGCTTAACTCACCTCTAGCAATATGAGTCAATTTAAAACTA
42673635 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACC
1 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACC
42673700 AAAATAAAAAGGCTTAACTCACCTCTAGCAATATGAGTCAATTTAAAACTA
66 AAAATAAAAAGGCTTAACTCACCTCTAGCAATATGAGTCAATTTAAAACTA
* * * *
42673751 AAAATACCTCAGCGTGCCCCTAGACTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAA
1 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAA
42673813 CAACAATTAA
Statistics
Matches: 406, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 406 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.25
Consensus pattern (116 bp):
AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACC
AAAATAAAAAGGCTTAACTCACCTCTAGCAATATGAGTCAATTTAAAACTA
Found at i:42682137 original size:12 final size:12
Alignment explanation
Indices: 42682105--42682140 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
42682095 TGGGATATGC
42682105 AATGTATGAATG
1 AATGTATGAATG
**
42682117 AATACATGAATG
1 AATGTATGAATG
42682129 AATGTATGAATG
1 AATGTATGAATG
42682141 TCAAAATGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (12 bp):
AATGTATGAATG
Found at i:42685301 original size:19 final size:19
Alignment explanation
Indices: 42685277--42685345 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
42685267 TAATAATAAT
42685277 ATAAAATAATAGTATGTAC
1 ATAAAATAATAGTATGTAC
* *
42685296 ATAAAAATATATA-TATATGC
1 AT-AAAATA-ATAGTATGTAC
* *
42685316 ATATAATAAAAGTATGTA-
1 ATAAAATAATAGTATGTAC
42685334 ATAATAATAATA
1 ATAA-AATAATA
42685346 TCTACAATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
18 5 0.13
19 17 0.45
20 13 0.34
21 3 0.08
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (19 bp):
ATAAAATAATAGTATGTAC
Found at i:42685986 original size:18 final size:18
Alignment explanation
Indices: 42685963--42686008 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
42685953 TTTCTTGGTT
*
42685963 TTTTTTTGGGGGGTTAGG
1 TTTTTTTGGGGGGTTAAG
***
42685981 TTTTTTTTTTGGGTTAAG
1 TTTTTTTGGGGGGTTAAG
42685999 TTTTTTTGGG
1 TTTTTTTGGG
42686009 AGGGGGCTTA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.07, C:0.00, G:0.33, T:0.61
Consensus pattern (18 bp):
TTTTTTTGGGGGGTTAAG
Found at i:42693290 original size:11 final size:11
Alignment explanation
Indices: 42693276--42693316 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
42693266 ATTTTTTTCC
42693276 CTATTTTGCTA
1 CTATTTTGCTA
*
42693287 CTATTTTACTA
1 CTATTTTGCTA
* *
42693298 TTATGTTGCTA
1 CTATTTTGCTA
42693309 CTATTTTG
1 CTATTTTG
42693317 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:42693364 original size:12 final size:11
Alignment explanation
Indices: 42693345--42693375 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
42693335 TATATAAAAC
42693345 TTATTTTATTA
1 TTATTTTATTA
42693356 TTAATTTTATTA
1 TT-ATTTTATTA
42693368 TTATTTTA
1 TTATTTTA
42693376 AAGACATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:42693414 original size:30 final size:30
Alignment explanation
Indices: 42693357--42693414 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
42693347 ATTTTATTAT
*
42693357 TAATTTTATTATTATTTTAAAGACATTTCC
1 TAATTTTATTATTATTCTAAAGACATTTCC
* * *
42693387 TAATTTTGTTATTATTCTAGAGGCATTT
1 TAATTTTATTATTATTCTAAAGACATTT
42693415 GCTTGTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (30 bp):
TAATTTTATTATTATTCTAAAGACATTTCC
Found at i:42695498 original size:3 final size:3
Alignment explanation
Indices: 42695490--42695523 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
42695480 CAAGAACCAA
42695490 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
42695524 GGTCCTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:42697970 original size:2 final size:2
Alignment explanation
Indices: 42697965--42697989 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42697955 TTGTTTTTTA
42697965 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 A
42697990 AAAAGAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.