Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 39 of 145
Found at i:12518809 original size:100 final size:100
Alignment explanation
Indices: 12518684--12519063 Score: 600
Period size: 100 Copynumber: 3.8 Consensus size: 100
12518674 TCAGGGAAGC
* * * * * * * * *
12518684 AAGATTCGCCGTTGTAGTTTAAATCTGTTCCACTGC-GCTGCTGGGGAAATATGATTCGCCGTTG
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATC-ACCGGAGAAGTAAGATTCGCCATTG
* *
12518748 TGGCCTCAATCTTTTTTATTGCAATGTTGGGGAAAG
65 TGGCTTCAATCTTTTTGATTGCAATGTTGGGGAAAG
12518784 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCACCGGAGAAGTAAGATTCGCCATTGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCACCGGAGAAGTAAGATTCGCCATTGT
12518849 GGCTTCAATCTTTTTGATTGCAATGTTGGGGAAAG
66 GGCTTCAATCTTTTTGATTGCAATGTTGGGGAAAG
* * *
12518884 AAGATTCGCCGTTGCAACTTCAATCTGTTCCACTGCATCACCGGAGAAGTAAGATTCGCCGTTGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCACCGGAGAAGTAAGATTCGCCATTGT
12518949 GGCTTCAATCTTTTTGATTGCAATGTTGGGGAAAG
66 GGCTTCAATCTTTTTGATTGCAATGTTGGGGAAAG
* *
12518984 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCGCCGGAGAAGTAAGATTCGTCATTGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCACCGGAGAAGTAAGATTCGCCATTGT
12519049 GGCTTCAATCTTTTT
66 GGCTTCAATCTTTTT
12519064 AATTACAAAC
Statistics
Matches: 260, Mismatches: 19, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
100 259 1.00
101 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (100 bp):
AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCACCGGAGAAGTAAGATTCGCCATTGT
GGCTTCAATCTTTTTGATTGCAATGTTGGGGAAAG
Found at i:12528643 original size:3 final size:3
Alignment explanation
Indices: 12528635--12528668 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
12528625 ATCATTTTCT
12528635 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
12528669 GTTTTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12528993 original size:15 final size:14
Alignment explanation
Indices: 12528969--12529002 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
12528959 TACCTACGTA
*
12528969 TATATGTACATATTT
1 TATATATACATA-TT
12528984 TATATATACATATT
1 TATATATACATATT
12528998 TATAT
1 TATAT
12529003 GTTCTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (14 bp):
TATATATACATATT
Found at i:12536973 original size:88 final size:89
Alignment explanation
Indices: 12536853--12537032 Score: 353
Period size: 88 Copynumber: 2.0 Consensus size: 89
12536843 TTATGCCTTG
12536853 AAATTTTGTAGTATATTTTAATTTTAAAAGTATATTAGTTTATTTAATTTTTAGATTATCTATAA
1 AAATTTTGTAGTATATTTTAATTTTAAAAGTATATTAGTTTATTTAATTTTTAGATTATCTATAA
12536918 TGAAAATTATAAATAATATTTTTA
66 TGAAAATTATAAATAATATTTTTA
12536942 AAATTTTGTAG-ATATTTTAATTTTAAAAGTATATTAGTTTATTTAATTTTTAGATTATCTATAA
1 AAATTTTGTAGTATATTTTAATTTTAAAAGTATATTAGTTTATTTAATTTTTAGATTATCTATAA
12537006 TGAAAATTATAAATAATATTTTTA
66 TGAAAATTATAAATAATATTTTTA
12537030 AAA
1 AAA
12537033 ATTATATAAA
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
88 80 0.88
89 11 0.12
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.51
Consensus pattern (89 bp):
AAATTTTGTAGTATATTTTAATTTTAAAAGTATATTAGTTTATTTAATTTTTAGATTATCTATAA
TGAAAATTATAAATAATATTTTTA
Found at i:12542717 original size:40 final size:40
Alignment explanation
Indices: 12542671--12542811 Score: 246
Period size: 40 Copynumber: 3.5 Consensus size: 40
12542661 AAATGAGCAT
12542671 TACCTACTGAATCTACTGAAACGTATGCGCTATCGAGCCA
1 TACCTACTGAATCTACTGAAACGTATGCGCTATCGAGCCA
* *
12542711 TACCTACTGAATCTACTGAAATGTATGCGCTATCAAGCCA
1 TACCTACTGAATCTACTGAAACGTATGCGCTATCGAGCCA
*
12542751 TACCTACTGAATCTACTGAAACGTATGTGCTATCGAGCCA
1 TACCTACTGAATCTACTGAAACGTATGCGCTATCGAGCCA
*
12542791 TACCTACTGATTCTACTGAAA
1 TACCTACTGAATCTACTGAAA
12542812 GTTGCTCAAA
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 95 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (40 bp):
TACCTACTGAATCTACTGAAACGTATGCGCTATCGAGCCA
Found at i:12551669 original size:23 final size:23
Alignment explanation
Indices: 12551639--12551687 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
12551629 TTGAGAAAAA
12551639 AAACTTAAATTAATTAAAATAAT
1 AAACTTAAATTAATTAAAATAAT
*
12551662 AAACTTAAATTGATTAAAATAAT
1 AAACTTAAATTAATTAAAATAAT
12551685 AAA
1 AAA
12551688 AACAAAAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (23 bp):
AAACTTAAATTAATTAAAATAAT
Found at i:12552256 original size:5 final size:5
Alignment explanation
Indices: 12552246--12552270 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12552236 GGATTAAAAC
12552246 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
12552271 TCCAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:12552845 original size:17 final size:17
Alignment explanation
Indices: 12552823--12552857 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12552813 AGTTTTTCTC
12552823 TTTGTATAACTGTTTGA
1 TTTGTATAACTGTTTGA
12552840 TTTGTATAACTGTTTGA
1 TTTGTATAACTGTTTGA
12552857 T
1 T
12552858 GGGGATGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (17 bp):
TTTGTATAACTGTTTGA
Found at i:12562469 original size:293 final size:293
Alignment explanation
Indices: 12561942--12562517 Score: 1152
Period size: 293 Copynumber: 2.0 Consensus size: 293
12561932 ACAAGTCTCA
12561942 CGACCGCCTAATTTAATTCCACATCGAATAAGTCGACTCAATTAAATTATTTCCAAAGTCGTAGG
1 CGACCGCCTAATTTAATTCCACATCGAATAAGTCGACTCAATTAAATTATTTCCAAAGTCGTAGG
12562007 ATTTTATTCCGATTCAAATAGAGTTTGATAGAGCTTTTTTTGATCTAGCGGTGGGACCAATCAAT
66 ATTTTATTCCGATTCAAATAGAGTTTGATAGAGCTTTTTTTGATCTAGCGGTGGGACCAATCAAT
12562072 CATATACAATTAGGCTCTAGTAATTGTCATTATGTCCAGAAGCATCATTCTGATAATTCGAAATT
131 CATATACAATTAGGCTCTAGTAATTGTCATTATGTCCAGAAGCATCATTCTGATAATTCGAAATT
12562137 CATTTGATCATGGAGTTAGTCTACAAGAAGTACTATGATTGGGAACTCCTTATTGTATACTCTTT
196 CATTTGATCATGGAGTTAGTCTACAAGAAGTACTATGATTGGGAACTCCTTATTGTATACTCTTT
12562202 GAGAAAGCAATTCATCCAACTACAGAACTAGTC
261 GAGAAAGCAATTCATCCAACTACAGAACTAGTC
12562235 CGACCGCCTAATTTAATTCCACATCGAATAAGTCGACTCAATTAAATTATTTCCAAAGTCGTAGG
1 CGACCGCCTAATTTAATTCCACATCGAATAAGTCGACTCAATTAAATTATTTCCAAAGTCGTAGG
12562300 ATTTTATTCCGATTCAAATAGAGTTTGATAGAGCTTTTTTTGATCTAGCGGTGGGACCAATCAAT
66 ATTTTATTCCGATTCAAATAGAGTTTGATAGAGCTTTTTTTGATCTAGCGGTGGGACCAATCAAT
12562365 CATATACAATTAGGCTCTAGTAATTGTCATTATGTCCAGAAGCATCATTCTGATAATTCGAAATT
131 CATATACAATTAGGCTCTAGTAATTGTCATTATGTCCAGAAGCATCATTCTGATAATTCGAAATT
12562430 CATTTGATCATGGAGTTAGTCTACAAGAAGTACTATGATTGGGAACTCCTTATTGTATACTCTTT
196 CATTTGATCATGGAGTTAGTCTACAAGAAGTACTATGATTGGGAACTCCTTATTGTATACTCTTT
12562495 GAGAAAGCAATTCATCCAACTAC
261 GAGAAAGCAATTCATCCAACTAC
12562518 TTTGTCCAAT
Statistics
Matches: 283, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
293 283 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (293 bp):
CGACCGCCTAATTTAATTCCACATCGAATAAGTCGACTCAATTAAATTATTTCCAAAGTCGTAGG
ATTTTATTCCGATTCAAATAGAGTTTGATAGAGCTTTTTTTGATCTAGCGGTGGGACCAATCAAT
CATATACAATTAGGCTCTAGTAATTGTCATTATGTCCAGAAGCATCATTCTGATAATTCGAAATT
CATTTGATCATGGAGTTAGTCTACAAGAAGTACTATGATTGGGAACTCCTTATTGTATACTCTTT
GAGAAAGCAATTCATCCAACTACAGAACTAGTC
Found at i:12563674 original size:41 final size:41
Alignment explanation
Indices: 12563628--12563711 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
12563618 CTTTGTGACG
* *
12563628 CACAACTTATCACTAAGCTCACTAGGAGAGCTTCCCTGATA
1 CACAACTTATCACAAAGCTCACGAGGAGAGCTTCCCTGATA
* *
12563669 CACAACTTATCACAAAGCTCACGAGGGGAGCTTCGCTGATA
1 CACAACTTATCACAAAGCTCACGAGGAGAGCTTCCCTGATA
12563710 CA
1 CA
12563712 TAGCTTGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (41 bp):
CACAACTTATCACAAAGCTCACGAGGAGAGCTTCCCTGATA
Found at i:12564553 original size:27 final size:27
Alignment explanation
Indices: 12564533--12564638 Score: 160
Period size: 27 Copynumber: 3.9 Consensus size: 27
12564523 GAACTCCCAA
12564533 TTCACCTAAACTTTGATGAACACCTAT
1 TTCACCTAAACTTTGATGAACACCTAT
* *
12564560 TTCGCCTAAACTTTCATGAACACCTAT
1 TTCACCTAAACTTTGATGAACACCTAT
*
12564587 TTCGCCTAAACTTTGATGAACACCTAT
1 TTCACCTAAACTTTGATGAACACCTAT
*
12564614 TTCACCTAAAAC-TTGGTGAACACCT
1 TTCACCT-AAACTTTGATGAACACCT
12564639 TGTTCGTCGG
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
27 69 0.95
28 4 0.05
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.32
Consensus pattern (27 bp):
TTCACCTAAACTTTGATGAACACCTAT
Found at i:12574384 original size:27 final size:26
Alignment explanation
Indices: 12574347--12574572 Score: 211
Period size: 27 Copynumber: 8.5 Consensus size: 26
12574337 AGACTCCAAA
* *
12574347 ATAGGGTAAAATGACTGAAATACCCTA
1 ATAGGGTAAAATGACCGAAATACCC-C
* * **
12574374 ATAGGGTAAAATAACCTAAATACCAAT
1 ATAGGGTAAAATGACCGAAATACC-CC
*
12574401 ATAAGGTAAAGA-GACCGAAATACCCCC
1 ATAGGGTAAA-ATGACCGAAATA-CCCC
* * *
12574428 ACAGGATAAAATGACCAAAATAACCCC
1 ATAGGGTAAAATGACCGAAAT-ACCCC
*
12574455 ATAAGGTAAAATGACCGAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCC-C
* * *
12574482 ACAGGGTAAAATGACCGAAATATTCGC
1 ATAGGGTAAAATGACCGAAATA-CCCC
*
12574509 ATAGGGTAAAATGACTGAAATACCCC
1 ATAGGGTAAAATGACCGAAATACCCC
* ** *
12574535 ATAGAGTAGTATGAACGAAATACCCC
1 ATAGGGTAAAATGACCGAAATACCCC
12574561 ATAGGGTAAAAT
1 ATAGGGTAAAAT
12574573 AATTGTTATA
Statistics
Matches: 158, Mismatches: 34, Indels: 15
0.76 0.16 0.07
Matches are distributed among these distances:
26 37 0.23
27 116 0.73
28 5 0.03
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.18
Consensus pattern (26 bp):
ATAGGGTAAAATGACCGAAATACCCC
Found at i:12578212 original size:54 final size:53
Alignment explanation
Indices: 12578136--12578417 Score: 294
Period size: 54 Copynumber: 5.2 Consensus size: 53
12578126 AGACCCCAAA
* *
12578136 ATAGGGTAAAATAATCGAAATACCCTATTAGGGTAAAATGACCGAAATACCCCG
1 ATAGGGTAAAATAACCGAAATACCCTA-TAGGGTAAAATGACCGAAATACCCCC
* *
12578190 AGAGGGTAAAATAACCGAAATACCCTCATAGGGTAAAATGATCGAAATACCCCC
1 ATAGGGTAAAATAACCGAAATACCCT-ATAGGGTAAAATGACCGAAATACCCCC
*** * * *
12578244 ATAGGGTAAAATAACCGAAATACCCCCGCAGGGTAAAATAATCAAAATACCCCC
1 ATAGGGTAAAATAACCGAAATA-CCCTATAGGGTAAAATGACCGAAATACCCCC
* * *** * * *
12578298 ACAGGGTAGAATGGTCGAAATACCCCAATAGGGTAGAATGGCCGAAATACCCCC
1 ATAGGGTAAAATAACCGAAATA-CCCTATAGGGTAAAATGACCGAAATACCCCC
* * * ** * *
12578352 ATAGGGTAAAATGACCTAAATACCCTCATAGAGTAGTATGACTGAGATACCCCC
1 ATAGGGTAAAATAACCGAAATACCCT-ATAGGGTAAAATGACCGAAATACCCCC
12578406 ATAGGGTAAAAT
1 ATAGGGTAAAAT
12578418 GACTATTATA
Statistics
Matches: 191, Mismatches: 34, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
53 3 0.02
54 184 0.96
55 4 0.02
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.18
Consensus pattern (53 bp):
ATAGGGTAAAATAACCGAAATACCCTATAGGGTAAAATGACCGAAATACCCCC
Found at i:12578431 original size:27 final size:26
Alignment explanation
Indices: 12578136--12578420 Score: 257
Period size: 27 Copynumber: 10.6 Consensus size: 26
12578126 AGACCCCAAA
* *
12578136 ATAGGGTAAAATAATCGAAATA-CCCT
1 ATAGGGTAAAATGA-CGAAATACCCCC
*
12578162 ATTAGGGTAAAATGACCGAAATACCCCG
1 A-TAGGGTAAAATGA-CGAAATACCCCC
* * *
12578190 AGAGGGTAAAATAACCGAAATACCCTC
1 ATAGGGTAAAATGA-CGAAATACCCCC
12578217 ATAGGGTAAAATGATCGAAATACCCCC
1 ATAGGGTAAAATGA-CGAAATACCCCC
*
12578244 ATAGGGTAAAATAACCGAAATACCCCC
1 ATAGGGTAAAATGA-CGAAATACCCCC
** * *
12578271 GCAGGGTAAAATAATCAAAATACCCCC
1 ATAGGGTAAAATGA-CGAAATACCCCC
* * * *
12578298 ACAGGGTAGAATGGTCGAAATACCCCA
1 ATAGGGTAAAAT-GACGAAATACCCCC
* *
12578325 ATAGGGTAGAATGGCCGAAATACCCCC
1 ATAGGGTAAAAT-GACGAAATACCCCC
* *
12578352 ATAGGGTAAAATGACCTAAATACCCTC
1 ATAGGGTAAAATGA-CGAAATACCCCC
* ** *
12578379 ATAGAGTAGTATGACTGAGATACCCCC
1 ATAGGGTAAAATGAC-GAAATACCCCC
12578406 ATAGGGTAAAATGAC
1 ATAGGGTAAAATGAC
12578421 TATTATACCC
Statistics
Matches: 215, Mismatches: 39, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
26 3 0.01
27 208 0.97
28 4 0.02
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.18
Consensus pattern (26 bp):
ATAGGGTAAAATGACGAAATACCCCC
Found at i:12578431 original size:81 final size:81
Alignment explanation
Indices: 12578136--12578420 Score: 340
Period size: 81 Copynumber: 3.5 Consensus size: 81
12578126 AGACCCCAAA
* * * * *
12578136 ATAGGGTAAAATAATCGAAATA-CCCTATTAGGGTAAAATGACCGAAATACCCCGAGAGGGTAAA
1 ATAGGGTAGAATGATCGAAATACCCCCA-TAGGGTAAAATGACCGAAATACCCCCACAGGGTAAA
*
12578200 ATAACCGAAATACCCTC
65 ATAACCAAAATACCCTC
* * *
12578217 ATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATAACCGAAATACCCCCGCAGGGTAAAA
1 ATAGGGTAGAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCACAGGGTAAAA
* *
12578282 TAATCAAAATACCCCC
66 TAACCAAAATACCCTC
* * * * * *
12578298 ACAGGGTAGAATGGTCGAAATACCCCAATAGGGTAGAATGGCCGAAATACCCCCATAGGGTAAAA
1 ATAGGGTAGAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCACAGGGTAAAA
* *
12578363 TGACCTAAATACCCTC
66 TAACCAAAATACCCTC
* * *
12578379 ATAGAGTAGTATGA-CTGAGATACCCCCATAGGGTAAAATGAC
1 ATAGGGTAGAATGATC-GAAATACCCCCATAGGGTAAAATGAC
12578421 TATTATACCC
Statistics
Matches: 172, Mismatches: 30, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
80 1 0.01
81 167 0.97
82 4 0.02
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.18
Consensus pattern (81 bp):
ATAGGGTAGAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCACAGGGTAAAA
TAACCAAAATACCCTC
Found at i:12580135 original size:20 final size:20
Alignment explanation
Indices: 12580107--12580161 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
12580097 AGCAAAAGAA
12580107 AAATT-AAAATATAAAA-ATT
1 AAATTAAAAATA-AAAATATT
12580126 AAATTAAAAATAAAAATATT
1 AAATTAAAAATAAAAATATT
12580146 AAA-TAAAAATAAAAAT
1 AAATTAAAAATAAAAAT
12580162 GGCTAAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 22 0.65
20 12 0.35
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATTAAAAATAAAAATATT
Found at i:12580141 original size:6 final size:6
Alignment explanation
Indices: 12580100--12580161 Score: 61
Period size: 6 Copynumber: 9.8 Consensus size: 6
12580090 AGCATCAAGC
* * * *
12580100 AAAAGA AAAATTA AAATATA AAAATT AAATTA AAAATA AAAATA TTAAATA
1 AAAATA AAAA-TA AAA-ATA AAAATA AAAATA AAAATA AAAATA -AAAATA
12580151 AAAATA AAAAT
1 AAAATA AAAAT
12580162 GGCTAAATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
6 31 0.67
7 14 0.30
8 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (6 bp):
AAAATA
Found at i:12585614 original size:21 final size:21
Alignment explanation
Indices: 12585576--12585615 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12585566 TACGTCAATG
*
12585576 ACAACACTTTGTCATCAATCA
1 ACAACACTTAGTCATCAATCA
12585597 ACAACACATTAGTC-TCAAT
1 ACAACAC-TTAGTCATCAAT
12585616 ACATTATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.40, C:0.28, G:0.05, T:0.28
Consensus pattern (21 bp):
ACAACACTTAGTCATCAATCA
Found at i:12595506 original size:21 final size:20
Alignment explanation
Indices: 12595482--12595522 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12595472 ACCAAAAACG
*
12595482 ATTTATTACTTGGAAAATAAA
1 ATTTA-TACTTAGAAAATAAA
*
12595503 ATTTATCCTTAGAAAATAAA
1 ATTTATACTTAGAAAATAAA
12595523 TTTTCACTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (20 bp):
ATTTATACTTAGAAAATAAA
Found at i:12596120 original size:95 final size:96
Alignment explanation
Indices: 12596002--12596192 Score: 375
Period size: 95 Copynumber: 2.0 Consensus size: 96
12595992 TTAATTATTT
12596002 TAATTTCATTTTCGAACTTCAATTATTTAATTATAATTAATTAAATAATAATTAAAAAATATTAA
1 TAATTTCATTTTCGAACTTCAATTATTTAATTATAATTAATTAAATAATAATTAAAAAATATTAA
12596067 ATTAATTCTTAAGTCATTTTTATACTCAGCG
66 ATTAATTCTTAAGTCATTTTTATACTCAGCG
12596098 TAATTTCA-TTTCGAACTTCAATTATTTAATTATAATTAATTAAATAATAATTAAAAAATATTAA
1 TAATTTCATTTTCGAACTTCAATTATTTAATTATAATTAATTAAATAATAATTAAAAAATATTAA
12596162 ATTAATTCTTAAGTCATTTTTATACTCAGCG
66 ATTAATTCTTAAGTCATTTTTATACTCAGCG
12596193 AGAGAACATA
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 87 0.92
96 8 0.08
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (96 bp):
TAATTTCATTTTCGAACTTCAATTATTTAATTATAATTAATTAAATAATAATTAAAAAATATTAA
ATTAATTCTTAAGTCATTTTTATACTCAGCG
Found at i:12606101 original size:9 final size:9
Alignment explanation
Indices: 12606084--12606120 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
12606074 TGAGTTTTCG
12606084 AATTCGAAT
1 AATTCGAAT
*
12606093 AACTCGAAT
1 AATTCGAAT
12606102 AATTCGAAT
1 AATTCGAAT
12606111 AATTCGAAT
1 AATTCGAAT
12606120 A
1 A
12606121 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:12613671 original size:25 final size:24
Alignment explanation
Indices: 12613642--12613770 Score: 68
Period size: 25 Copynumber: 5.2 Consensus size: 24
12613632 AATAACGGGT
12613642 AGCTCCGAAAAGCCATTAATCAGGA
1 AGCTCC-AAAAGCCATTAATCAGGA
*
12613667 AGCTCCAAATAGCCATATATTCA-GA
1 AGCTCCAAA-AGCCAT-TAATCAGGA
* * *
12613692 A-ATTCAAGCGAGCCA-T-ATCAGGA
1 AGCTCCAA--AAGCCATTAATCAGGA
** * *
12613715 AGCTTCGGAGAGTCATTAATCAGGA
1 AGC-TCCAAAAGCCATTAATCAGGA
* *
12613740 AGCTAACAAAGAGCCTTTAATCAGGA
1 AGCT-CCAAA-AGCCATTAATCAGGA
12613766 AGCTC
1 AGCTC
12613771 ACGAAGAGCC
Statistics
Matches: 76, Mismatches: 17, Indels: 22
0.66 0.15 0.19
Matches are distributed among these distances:
22 3 0.04
23 9 0.12
24 9 0.12
25 33 0.43
26 22 0.29
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (24 bp):
AGCTCCAAAAGCCATTAATCAGGA
Found at i:12613759 original size:26 final size:26
Alignment explanation
Indices: 12613730--12613780 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
12613720 CGGAGAGTCA
12613730 TTAATCAGGAAGCTAACAAAGAGCCT
1 TTAATCAGGAAGCTAACAAAGAGCCT
* *
12613756 TTAATCAGGAAGCTCACGAAGAGCC
1 TTAATCAGGAAGCTAACAAAGAGCC
12613781 ATATATCGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.18
Consensus pattern (26 bp):
TTAATCAGGAAGCTAACAAAGAGCCT
Found at i:12616834 original size:44 final size:44
Alignment explanation
Indices: 12616766--12616883 Score: 114
Period size: 44 Copynumber: 2.7 Consensus size: 44
12616756 ATGGCAAATC
* * * * *
12616766 TTATCTCCTTGAGGTTGCAATGGAGCAGATTGAAGCCGATA-ATA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAATAGATA
* * *
12616810 TTATCTCCCTGAAGTTGTAGTGGAGC-GAATTAAAGTAATAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAGCAATAGATA
* *
12616854 CTATGTCCCTGAAGTTGCAGTGGAGCAGAT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGAT
12616884 CAAACTGATG
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
43 4 0.07
44 55 0.92
45 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAATAGATA
Found at i:12625673 original size:83 final size:81
Alignment explanation
Indices: 12625493--12625673 Score: 193
Period size: 83 Copynumber: 2.2 Consensus size: 81
12625483 TTTTACATTT
* ** * * * * *
12625493 GCGCCGCTAATGGTGGAGGTTTTAGTGGCGTTTTTGGTCAATCGCCGCTAGTGTTAAGGTATTAG
1 GCGCCGCTAATGTTGGAGGTGATAGTGGCGTTTTTAGTAAATCGCCACTAATATTAAGGTATTAG
* * *
12625558 CAGCGTTTTTCTCTTA
66 CAGCGTTTCTATCCTA
* *
12625574 GCGCCACT-ATCGGTTGGTGGTGATAGTGGCGTTTTCTAGTAAATCGCCACTAATATTAAGGTAT
1 GCGCCGCTAAT--GTTGGAGGTGATAGTGGCGTTTT-TAGTAAATCGCCACTAATATTAAGGTA-
*
12625638 TTAGCGGCGTTTCTATCCTA
62 TTAGCAGCGTTTCTATCCTA
12625658 GCGCCGCTAATGTTGG
1 GCGCCGCTAATGTTGG
12625674 GAATTTTCCT
Statistics
Matches: 80, Mismatches: 15, Indels: 8
0.78 0.15 0.08
Matches are distributed among these distances:
80 2 0.03
81 7 0.09
82 19 0.24
83 27 0.34
84 23 0.29
85 2 0.03
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (81 bp):
GCGCCGCTAATGTTGGAGGTGATAGTGGCGTTTTTAGTAAATCGCCACTAATATTAAGGTATTAG
CAGCGTTTCTATCCTA
Found at i:12625722 original size:125 final size:126
Alignment explanation
Indices: 12625574--12625800 Score: 350
Period size: 125 Copynumber: 1.8 Consensus size: 126
12625564 TTTTCTCTTA
*
12625574 GCGCCACTATCGGTTGGTGGTGATAGTGGCGT-TTTCTAGTAAATCGCCACTAATATTAAGGTAT
1 GCGCCACTATCGGTTGGGGGTGATAGTGGCGTGTTT-TAGTAAATCGCCACTAATATTAAGGTAT
12625638 TTAGCGGCGTTTCTATCCTAGCGCCGCTAAT-GTTGGGAATTTTCCTGGCGTTTTTATGTAT
65 TTAGCGGCGTTTCTATCCTAGCGCCGCTAATGGTTGGGAATTTTCCTGGCGTTTTTATGTAT
* * * * *
12625699 GCGCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATT
1 GCGCCACTATCGGTTGGGGGTGATAGTGGCGTGTTTTAGTAAATCGCCACTAATATTAAGGTATT
* * *
12625764 TAGTGGCGTTTCTATCTTAGCGCCGCTATTGGTTGGG
66 TAGCGGCGTTTCTATCCTAGCGCCGCTAATGGTTGGG
12625801 GGTGATAGTG
Statistics
Matches: 91, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
125 82 0.90
126 9 0.10
ACGTcount: A:0.17, C:0.18, G:0.29, T:0.36
Consensus pattern (126 bp):
GCGCCACTATCGGTTGGGGGTGATAGTGGCGTGTTTTAGTAAATCGCCACTAATATTAAGGTATT
TAGCGGCGTTTCTATCCTAGCGCCGCTAATGGTTGGGAATTTTCCTGGCGTTTTTATGTAT
Found at i:12625729 original size:42 final size:43
Alignment explanation
Indices: 12625683--12625819 Score: 110
Period size: 42 Copynumber: 3.3 Consensus size: 43
12625673 GGAATTTTCC
12625683 TGGCGT-TTTTATGTATGCGCCGCTATTGGTTGGGGGTGATAG
1 TGGCGTGTTTTATGTATGCGCCGCTATTGGTTGGGGGTGATAG
* * * **
12625725 TGGCGTGTTTT-GGTCAAT-CGCCACTAAT-GTT-AAGGT-ATTTAG
1 TGGCGTGTTTTATGT--ATGCGCCGCTATTGGTTGGGGGTGA--TAG
* *
12625767 TGGCGT-TTCTATCT-TAGCGCCGCTATTGGTTGGGGGTGATAG
1 TGGCGTGTTTTATGTAT-GCGCCGCTATTGGTTGGGGGTGATAG
12625809 TGGCGTGTTTT
1 TGGCGTGTTTT
12625820 GGTCAATCGC
Statistics
Matches: 70, Mismatches: 13, Indels: 23
0.66 0.12 0.22
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 14 0.20
42 33 0.47
43 18 0.26
44 3 0.04
ACGTcount: A:0.14, C:0.14, G:0.34, T:0.39
Consensus pattern (43 bp):
TGGCGTGTTTTATGTATGCGCCGCTATTGGTTGGGGGTGATAG
Found at i:12625830 original size:209 final size:206
Alignment explanation
Indices: 12625478--12625858 Score: 548
Period size: 209 Copynumber: 1.8 Consensus size: 206
12625468 TACCTTTATC
* ** *
12625478 GGCGTTTTTACATTTGCGCCGCTAATGGTGGAGGTTTTAGTGGCGTTTTTGGTCAATCGCCGCTA
1 GGCGTTTTTACATATGCGCCGCTAATGGTGGAGGTGATAGTGGCGTTTTTGGTCAATCGCCACTA
* * * *
12625543 GTGTTAAGGTATTAGCAGCGTTTTTCTCTTAGCGCCACTATCGGTTGGTGGTGATAGTGGCGTTT
66 ATGTTAAGGTATTAGCAGCGTTTCTATCTTAGCGCCACTATCGGTTGGGGGTGATAGTGGCGTTT
12625608 TCTAGTAAATCGCCACTAATATTAAGGTATTTAGCGGCGTTTCTATCCTAGCGCCGCTAATGTTG
131 TCTAGTAAATCGCCACTAATATTAAGGTATTTAGCGGCGTTTCTATCCTAGCGCCGCTAATGTTG
12625673 GGAATTTTCCT
196 GGAATTTTCCT
** * *
12625684 GGCGTTTTTATGTATGCGCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCAC
1 GGCGTTTTTACATATGCGCCGCTAATGG-TGGAGGTGATAGTGGCGT-TTTTGGTCAATCGCCAC
** * *
12625749 TAATGTTAAGGTATTTAGTGGCGTTTCTATCTTAGCGCCGCTATTGGTTGGGGGTGATAGTGGCG
64 TAATGTTAAGGTA-TTAGCAGCGTTTCTATCTTAGCGCCACTATCGGTTGGGGGTGATAGTGGCG
* * *
12625814 TGTTT-TGGTCAATCGCCACTAATGTTAAGGTATTTAGCGGCGTTT
128 T-TTTCTAGTAAATCGCCACTAATATTAAGGTATTTAGCGGCGTTT
12625859 GGTTTTAAAG
Statistics
Matches: 152, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
206 24 0.16
207 15 0.10
208 28 0.18
209 82 0.54
210 3 0.02
ACGTcount: A:0.17, C:0.17, G:0.29, T:0.37
Consensus pattern (206 bp):
GGCGTTTTTACATATGCGCCGCTAATGGTGGAGGTGATAGTGGCGTTTTTGGTCAATCGCCACTA
ATGTTAAGGTATTAGCAGCGTTTCTATCTTAGCGCCACTATCGGTTGGGGGTGATAGTGGCGTTT
TCTAGTAAATCGCCACTAATATTAAGGTATTTAGCGGCGTTTCTATCCTAGCGCCGCTAATGTTG
GGAATTTTCCT
Found at i:12625883 original size:84 final size:84
Alignment explanation
Indices: 12625699--12625858 Score: 311
Period size: 84 Copynumber: 1.9 Consensus size: 84
12625689 TTTTATGTAT
12625699 GCGCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATT
1 GCGCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATT
*
12625764 TAGTGGCGTTTCTATCTTA
66 TAGCGGCGTTTCTATCTTA
12625783 GCGCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATT
1 GCGCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATT
12625848 TAGCGGCGTTT
66 TAGCGGCGTTT
12625859 GGTTTTAAAG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.16, C:0.16, G:0.33, T:0.36
Consensus pattern (84 bp):
GCGCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATT
TAGCGGCGTTTCTATCTTA
Found at i:12626715 original size:21 final size:21
Alignment explanation
Indices: 12626676--12626791 Score: 78
Period size: 21 Copynumber: 5.6 Consensus size: 21
12626666 CGGGTATGGA
*
12626676 TTAGGGTTT-GGGATTAAGGT
1 TTAGGGTTTGGGGGTTAAGGT
12626696 TTAGGGTTTGGGGGTTAAGGT
1 TTAGGGTTTGGGGGTTAAGGT
* **
12626717 CTAGGG-TTAAGGGTTAAGGAT
1 TTAGGGTTTGGGGGTTAAGG-T
**
12626738 TT-GGGATTT-GGGGTTGGTGGT
1 TTAGGG-TTTGGGGGTT-AAGGT
* * ** *
12626759 TTGGGGTTTGGGGTTTGTGAT
1 TTAGGGTTTGGGGGTTAAGGT
12626780 TTAGGGTTTGGG
1 TTAGGGTTTGGG
12626792 TTTTTGGGGT
Statistics
Matches: 78, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
20 23 0.29
21 43 0.55
22 12 0.15
ACGTcount: A:0.14, C:0.01, G:0.46, T:0.40
Consensus pattern (21 bp):
TTAGGGTTTGGGGGTTAAGGT
Found at i:12626763 original size:14 final size:14
Alignment explanation
Indices: 12626737--12626806 Score: 70
Period size: 14 Copynumber: 4.9 Consensus size: 14
12626727 GGGTTAAGGA
*
12626737 TTTGGGATTTGGGG
1 TTTGGGGTTTGGGG
12626751 -TTGGTGGTTTGGGG
1 TTTGG-GGTTTGGGG
* *
12626765 TTTGGGGTTTGTGA
1 TTTGGGGTTTGGGG
* *
12626779 TTTAGGGTTTGGGTT
1 TTTGGGGTTTGGG-G
12626794 TTTGGGGTTTGGG
1 TTTGGGGTTTGGG
12626807 ATTAAGGTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
13 4 0.09
14 26 0.57
15 16 0.35
ACGTcount: A:0.04, C:0.00, G:0.49, T:0.47
Consensus pattern (14 bp):
TTTGGGGTTTGGGG
Found at i:12627374 original size:16 final size:16
Alignment explanation
Indices: 12627353--12627408 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
12627343 ACTTAGTAAT
12627353 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
12627369 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
* * *
12627385 GAAATAAATA-AATAAA
1 TAAA-AGATACAATTAA
12627401 TAAAAGAT
1 TAAAAGAT
12627409 GTGAGATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 3 0.09
16 27 0.79
17 4 0.12
ACGTcount: A:0.66, C:0.04, G:0.07, T:0.23
Consensus pattern (16 bp):
TAAAAGATACAATTAA
Found at i:12627722 original size:23 final size:23
Alignment explanation
Indices: 12627696--12627740 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
12627686 CACTTAGCCG
12627696 AAATTCCCCCCAAATTATCCCCA
1 AAATTCCCCCCAAATTATCCCCA
* *
12627719 AAATTCCCCCCGAATTTTCCCC
1 AAATTCCCCCCAAATTATCCCC
12627741 CCAAAATCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.44, G:0.02, T:0.24
Consensus pattern (23 bp):
AAATTCCCCCCAAATTATCCCCA
Found at i:12627734 original size:11 final size:11
Alignment explanation
Indices: 12627696--12627752 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
12627686 CACTTAGCCG
12627696 AAATTCCCCCC
1 AAATTCCCCCC
* *
12627707 AAATTATCCCCA
1 AAATT-CCCCCC
12627719 AAATTCCCCCC
1 AAATTCCCCCC
*
12627730 GAATTTTCCCCCC
1 -AA-ATTCCCCCC
*
12627743 AAAATCCCCC
1 AAATTCCCCC
12627753 AATTCTAGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
11 15 0.42
12 13 0.36
13 8 0.22
ACGTcount: A:0.30, C:0.47, G:0.02, T:0.21
Consensus pattern (11 bp):
AAATTCCCCCC
Found at i:12628140 original size:23 final size:24
Alignment explanation
Indices: 12628114--12628170 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
12628104 CACTTAGCCG
12628114 AAATTCCCCCCAAATTAT-CCCAA
1 AAATTCCCCCCAAATTATCCCCAA
* *
12628137 AAATTCCCCCCGAATTTTCCCCCAA
1 AAATTCCCCCCAAATTAT-CCCCAA
12628162 AAA-TCCCCC
1 AAATTCCCCC
12628171 AATTCTAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 16 0.53
24 6 0.20
25 8 0.27
ACGTcount: A:0.33, C:0.44, G:0.02, T:0.21
Consensus pattern (24 bp):
AAATTCCCCCCAAATTATCCCCAA
Found at i:12629622 original size:21 final size:20
Alignment explanation
Indices: 12629598--12629636 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
12629588 CTATATTTAA
12629598 ATATTGTTAATAATAAATTTT
1 ATATTGTTAA-AATAAATTTT
* *
12629619 ATATTTTTAAAATTAATT
1 ATATTGTTAAAATAAATT
12629637 GTACATGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
ATATTGTTAAAATAAATTTT
Found at i:12629761 original size:21 final size:21
Alignment explanation
Indices: 12629737--12629836 Score: 60
Period size: 21 Copynumber: 4.4 Consensus size: 21
12629727 TATTAACATA
*
12629737 TATATTTTCAATAATAAATTT
1 TATATTTTAAATAATAAATTT
*
12629758 TATAATTTTAGAAATAATTGTAAATGT
1 TAT-ATTTT--AAATAA---TAAATTT
* *
12629785 TAT-TTTCTAAATATTAACA-TC
1 TATATTT-TAAATAATAA-ATTT
*
12629806 TATATTTTCAATAATAAATTT
1 TATATTTTAAATAATAAATTT
12629827 TATAATTTTA
1 TAT-ATTTTA
12629837 GAAANNNNNN
Statistics
Matches: 59, Mismatches: 9, Indels: 21
0.66 0.10 0.24
Matches are distributed among these distances:
20 1 0.02
21 21 0.36
22 14 0.24
24 10 0.17
25 3 0.05
26 1 0.02
27 9 0.15
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (21 bp):
TATATTTTAAATAATAAATTT
Found at i:12629840 original size:69 final size:70
Alignment explanation
Indices: 12629598--12629836 Score: 385
Period size: 70 Copynumber: 3.4 Consensus size: 70
12629588 CTATATTTAA
* *
12629598 ATATTGTT-AATAATAAATTTTATATTTTTAAAATTAATTGTACATGTTATTTTTCTAAATATTA
1 ATATT-TTCAATAATAAATTTTATAATTTTAAAACTAATTGTACATGTTATTTTTCTAAATATTA
12629662 ACATAT
65 ACATAT
* *
12629668 ATGTTTTCAATAATAAATTTTATATTTTTAAAACTAATTGTACATGTTATTTTTCTAAATATTAA
1 ATATTTTCAATAATAAATTTTATAATTTTAAAACTAATTGTACATGTTATTTTTCTAAATATTAA
12629733 CATAT
66 CATAT
*
12629738 ATATTTTCAATAATAAATTTTATAATTTTAGAAA-TAATTGTAAATGTTA-TTTTCTAAATATTA
1 ATATTTTCAATAATAAATTTTATAATTTTA-AAACTAATTGTACATGTTATTTTTCTAAATATTA
*
12629801 ACATCT
65 ACATAT
12629807 ATATTTTCAATAATAAATTTTATAATTTTA
1 ATATTTTCAATAATAAATTTTATAATTTTA
12629837 GAAANNNNNN
Statistics
Matches: 161, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
69 51 0.32
70 107 0.66
71 3 0.02
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (70 bp):
ATATTTTCAATAATAAATTTTATAATTTTAAAACTAATTGTACATGTTATTTTTCTAAATATTAA
CATAT
Found at i:12630607 original size:16 final size:16
Alignment explanation
Indices: 12630586--12630649 Score: 92
Period size: 16 Copynumber: 3.9 Consensus size: 16
12630576 CGGACTTGCA
*
12630586 TAACTTATATAATACT
1 TAACTTACATAATACT
12630602 TAACTTACATAACTTACT
1 TAACTTACATAA--TACT
*
12630620 TAACTTACATAATACA
1 TAACTTACATAATACT
12630636 TAACTTACATAATA
1 TAACTTACATAATA
12630650 ACATAATAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
16 28 0.64
18 16 0.36
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (16 bp):
TAACTTACATAATACT
Found at i:12630644 original size:9 final size:9
Alignment explanation
Indices: 12630579--12630944 Score: 80
Period size: 9 Copynumber: 41.3 Consensus size: 9
12630569 AACTTGTCGG
*
12630579 ACTTGCATA
1 ACTTACATA
*
12630588 ACTTATATA
1 ACTTACATA
*
12630597 A--TACTTA
1 ACTTACATA
12630604 ACTTACATA
1 ACTTACATA
*
12630613 ACTTACTTA
1 ACTTACATA
12630622 ACTTACATA
1 ACTTACATA
12630631 A--TACATA
1 ACTTACATA
12630638 ACTTACATA
1 ACTTACATA
*
12630647 A-TAACATAATA
1 ACTTAC---ATA
*
12630658 AGTTACATAA
1 ACTTACAT-A
*
12630668 TATTATACATA
1 -ACT-TACATA
*
12630679 ACTCACATA
1 ACTTACATA
*
12630688 AC-TAAATGA
1 ACTTACAT-A
12630697 A-TTA-AT-
1 ACTTACATA
*
12630703 ATTATACATTA
1 ACT-TACA-TA
* **
12630714 ACTTGTC-GG
1 ACTT-ACATA
*
12630723 ACTTGCATA
1 ACTTACATA
*
12630732 ACTTATATA
1 ACTTACATA
*
12630741 A--TACTTA
1 ACTTACATA
*
12630748 ACTTTCATA
1 ACTTACATA
12630757 ACTTACATA
1 ACTTACATA
12630766 ACTTACATA
1 ACTTACATA
*
12630775 A--TACAGA
1 ACTTACATA
12630782 ACTTACATA
1 ACTTACATA
*
12630791 A-TAACATAATA
1 ACTTAC---ATA
*
12630802 AGTTACATAA
1 ACTTACAT-A
*
12630812 TATTATACATA
1 -ACT-TACATA
*
12630823 ACTCACATA
1 ACTTACATA
*
12630832 AC-TAAATTA
1 ACTTACA-TA
* * *
12630841 ATTTATATT
1 ACTTACATA
12630850 A--TACATTA
1 ACTTACA-TA
* **
12630858 ACTTGTC-GG
1 ACTT-ACATA
* *
12630867 ACTTGCGTA
1 ACTTACATA
*
12630876 ACTTATATA
1 ACTTACATA
*
12630885 A--TACTTA
1 ACTTACATA
12630892 ACTTACATA
1 ACTTACATA
12630901 ACTTACATA
1 ACTTACATA
12630910 A--TACATA
1 ACTTACATA
*
12630917 ACTTACGTA
1 ACTTACATA
12630926 A--TACATA
1 ACTTACATA
12630933 ACTTACATA
1 ACTTACATA
12630942 ACT
1 ACT
12630945 CATATATACT
Statistics
Matches: 257, Mismatches: 56, Indels: 88
0.64 0.14 0.22
Matches are distributed among these distances:
6 1 0.00
7 45 0.18
8 19 0.07
9 146 0.57
10 12 0.05
11 18 0.07
12 16 0.06
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.36
Consensus pattern (9 bp):
ACTTACATA
Found at i:12630751 original size:16 final size:16
Alignment explanation
Indices: 12630728--12630799 Score: 81
Period size: 16 Copynumber: 4.3 Consensus size: 16
12630718 GTCGGACTTG
*
12630728 CATAACTTATATAATA
1 CATAACTTACATAATA
* *
12630744 CTTAACTTTCATAACTTA
1 CATAACTTACATAA--TA
12630762 CATAACTTACATAATA
1 CATAACTTACATAATA
*
12630778 CAGAACTTACATAATAA
1 CATAACTTACATAAT-A
12630795 CATAA
1 CATAA
12630800 TAAGTTACAT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
16 27 0.59
17 5 0.11
18 14 0.30
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.33
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:12630810 original size:144 final size:144
Alignment explanation
Indices: 12630550--12630917 Score: 668
Period size: 144 Copynumber: 2.6 Consensus size: 144
12630540 NNNNNNNNNN
12630550 TGAATTAATATTATACATTAACTTGTCGGACTTGCATAACTTATATAATACTTAACTTACATAAC
1 TGAATTAATATTATACATTAACTTGTCGGACTTGCATAACTTATATAATACTTAACTTACATAAC
* *
12630615 TTACTTAACTTACATAATACATAACTTACATAATAACATAATAAGTTACATAATATTATACATAA
66 TTACATAACTTACATAATACAGAACTTACATAATAACATAATAAGTTACATAATATTATACATAA
12630680 CTCACATAACTAAA
131 CTCACATAACTAAA
*
12630694 TGAATTAATATTATACATTAACTTGTCGGACTTGCATAACTTATATAATACTTAACTTTCATAAC
1 TGAATTAATATTATACATTAACTTGTCGGACTTGCATAACTTATATAATACTTAACTTACATAAC
12630759 TTACATAACTTACATAATACAGAACTTACATAATAACATAATAAGTTACATAATATTATACATAA
66 TTACATAACTTACATAATACAGAACTTACATAATAACATAATAAGTTACATAATATTATACATAA
12630824 CTCACATAACTAAA
131 CTCACATAACTAAA
* * *
12630838 TTAATTTATATTATACATTAACTTGTCGGACTTGCGTAACTTATATAATACTTAACTTACATAAC
1 TGAATTAATATTATACATTAACTTGTCGGACTTGCATAACTTATATAATACTTAACTTACATAAC
12630903 TTACATAA--TACATAA
66 TTACATAACTTACATAA
12630918 CTTACGTAAT
Statistics
Matches: 217, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
142 7 0.03
144 210 0.97
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (144 bp):
TGAATTAATATTATACATTAACTTGTCGGACTTGCATAACTTATATAATACTTAACTTACATAAC
TTACATAACTTACATAATACAGAACTTACATAATAACATAATAAGTTACATAATATTATACATAA
CTCACATAACTAAA
Found at i:12630902 original size:25 final size:25
Alignment explanation
Indices: 12630874--12630944 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 25
12630864 CGGACTTGCG
* *
12630874 TAACTTATATAATACTTAACTTACA
1 TAACTTACATAATACATAACTTACA
*
12630899 TAACTTACATAATACATAACTTACG
1 TAACTTACATAATACATAACTTACA
12630924 TAA--TACATAACTTACATAACT
1 TAACTTACATAA--TACATAACT
12630945 CATATATACT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
23 7 0.17
25 34 0.83
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.35
Consensus pattern (25 bp):
TAACTTACATAATACATAACTTACA
Found at i:12630948 original size:16 final size:16
Alignment explanation
Indices: 12630895--12630942 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
12630885 ATACTTAACT
12630895 TACATAACTTACATAA
1 TACATAACTTACATAA
*
12630911 TACATAACTTACGTAA
1 TACATAACTTACATAA
12630927 TACATAACTTACATAA
1 TACATAACTTACATAA
12630943 CTCATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:12638689 original size:43 final size:43
Alignment explanation
Indices: 12638631--12639075 Score: 236
Period size: 43 Copynumber: 10.5 Consensus size: 43
12638621 CTTCGACTTG
* * **
12638631 CTCCACTACTCCTTAGGGAGATAAGACTGGTGGCTTAAATCTA
1 CTCCACTACTGCTTAGGGAGATAAGACTGGTTGCTTTCATCTA
* * * *
12638674 CTTCACTACTGCTTAGGGAGATAAGA-TCGGTTTCTTTCGTCTG
1 CTCCACTACTGCTTAGGGAGATAAGACT-GGTTGCTTTCATCTA
* * * *
12638717 CTCCACTACTGCTTAGAGAGATAAGAC---TTGATGTGATCTA
1 CTCCACTACTGCTTAGGGAGATAAGACTGGTTGCTTTCATCTA
* * * * *
12638757 CTCTACTACTACTTAGGGAGATAAGA-TCGGTTTCTTTCGTCTG
1 CTCCACTACTGCTTAGGGAGATAAGACT-GGTTGCTTTCATCTA
* * *
12638800 CTCCACTACTGCTTAGGGAGATAAGAC---TTGATGTGATCTA
1 CTCCACTACTGCTTAGGGAGATAAGACTGGTTGCTTTCATCTA
* * * ** *
12638840 CTTCACTACTGTTTAGGGAGATAAGA-TCGGTTTCTTTTGTCTG
1 CTCCACTACTGCTTAGGGAGATAAGACT-GGTTGCTTTCATCTA
* *
12638883 CTCCACTACTGCTTAGGGAGATAAGACTTGG-TGC---GATCTG
1 CTCCACTACTGCTTAGGGAGATAAGAC-TGGTTGCTTTCATCTA
* * * *** * * *
12638923 CTCCACTAGTGCTTAGGGCGATAGGATCTAACAT-CTTTGACCTG
1 CTCCACTACTGCTTAGGGAGATAAGA-CT-GGTTGCTTTCATCTA
* * *** * * * *
12638967 CTCCACTACTGCTTAGAGAGATAGGATCTAACAT-ATTTGACCTG
1 CTCCACTACTGCTTAGGGAGATAAGA-CT-GGTTGCTTTCATCTA
* * ** *
12639011 CTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTG
1 CTCCACTACTGCTTAGGGAGATAAGACTGGTTGCTTTCATCTA
* *
12639054 CTTCACTACTGCTTAGGAAGAT
1 CTCCACTACTGCTTAGGGAGAT
12639076 GAGATTCGCC
Statistics
Matches: 315, Mismatches: 67, Indels: 40
0.75 0.16 0.09
Matches are distributed among these distances:
40 89 0.28
41 2 0.01
42 2 0.01
43 149 0.47
44 72 0.23
45 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.32
Consensus pattern (43 bp):
CTCCACTACTGCTTAGGGAGATAAGACTGGTTGCTTTCATCTA
Found at i:12638778 original size:40 final size:40
Alignment explanation
Indices: 12638517--12639038 Score: 246
Period size: 44 Copynumber: 12.3 Consensus size: 40
12638507 TCGTAACTTC
* * * *
12638517 AGGGAGATAAGACTGGATGCGATCTGCTCTACTATTGCTT
1 AGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTT
* * ** * *
12638557 AGAGAGATAGGATCTACCATCTTTGACCTGCTCCACTACTGCTT
1 AGGGAGATAAGA-CT-TGA--TGTGATCTGCTCCACTACTGCTT
* * ** * *
12638601 AGGGAGATAGGGTCTACCATCTTCGA-CTTGCTCCACTACTCCTT
1 AGGGAGATA-AGACT-TGAT-GT-GATC-TGCTCCACTACTGCTT
* * * *
12638645 AGGGAGATAAGAC-TGGTGGCTTAAATCTACTTCACTACTGCTT
1 AGGGAGATAAGACTTGAT-G--T-GATCTGCTCCACTACTGCTT
** *
12638688 AGGGAGATAAGATCGGTTTCTTTCG-TCTGCTCCACTACTGCTT
1 AGGGAGATAAGA-C--TTGATGT-GATCTGCTCCACTACTGCTT
* * * *
12638731 AGAGAGATAAGACTTGATGTGATCTACTCTACTACTACTT
1 AGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTT
** *
12638771 AGGGAGATAAGATCGGTTTCTTTCG-TCTGCTCCACTACTGCTT
1 AGGGAGATAAGA-C--TTGATGT-GATCTGCTCCACTACTGCTT
* * *
12638814 AGGGAGATAAGACTTGATGTGATCTACTTCACTACTGTTT
1 AGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTT
** *
12638854 AGGGAGATAAGATCGGTTTCTTTTG-TCTGCTCCACTACTGCTT
1 AGGGAGATAAGA-C---TTGATGTGATCTGCTCCACTACTGCTT
* * *
12638897 AGGGAGATAAGACTTGGTGCGATCTGCTCCACTAGTGCTT
1 AGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTT
* * ** * *
12638937 AGGGCGATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTT
1 AGGGAGATAAGA-CT-TGA--TGTGATCTGCTCCACTACTGCTT
* * * *
12638981 AGAGAGATAGGATCTAACAT-ATTTGACCTGCTCCACTACTGCTT
1 AGGGAGATAAGA-CT----TGATGTGATCTGCTCCACTACTGCTT
*
12639025 AGGGAGATAGGACT
1 AGGGAGATAAGACT
12639039 GGTGGCTTAA
Statistics
Matches: 374, Mismatches: 75, Indels: 63
0.73 0.15 0.12
Matches are distributed among these distances:
39 6 0.02
40 98 0.26
41 7 0.02
42 5 0.01
43 119 0.32
44 133 0.36
45 2 0.01
46 1 0.00
47 3 0.01
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (40 bp):
AGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTT
Found at i:12638788 original size:83 final size:83
Alignment explanation
Indices: 12638629--12638950 Score: 459
Period size: 83 Copynumber: 3.8 Consensus size: 83
12638619 ATCTTCGACT
* * *
12638629 TGCTCCACTACTCCTTAGGGAGATAAGAC-TGGTGGCTTAAATCTACTTCACTACTGCTTAGGGA
1 TGCTCCACTACTGCTTAGGGAGATAAGACTTGAT-G--T-GATCTACTTCACTACTGCTTAGGGA
12638693 GATAAGATCGGTTTCTTTCGTC
62 GATAAGATCGGTTTCTTTCGTC
* *
12638715 TGCTCCACTACTGCTTAGAGAGATAAGACTTGATGTGATCTAC-TCTACTACTACTTAGGGAGAT
1 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTACTTC-ACTACTGCTTAGGGAGAT
12638779 AAGATCGGTTTCTTTCGTC
65 AAGATCGGTTTCTTTCGTC
*
12638798 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTACTTCACTACTGTTTAGGGAGATA
1 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTACTTCACTACTGCTTAGGGAGATA
*
12638863 AGATCGGTTTCTTTTGTC
66 AGATCGGTTTCTTTCGTC
* * * * * *
12638881 TGCTCCACTACTGCTTAGGGAGATAAGACTTGGTGCGATCTGCTCCACTAGTGCTTAGGGCGATA
1 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTACTTCACTACTGCTTAGGGAGATA
*
12638946 GGATC
66 AGATC
12638951 TAACATCTTT
Statistics
Matches: 216, Mismatches: 17, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
82 2 0.01
83 180 0.83
84 3 0.01
86 28 0.13
87 3 0.01
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (83 bp):
TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTACTTCACTACTGCTTAGGGAGATA
AGATCGGTTTCTTTCGTC
Found at i:12640319 original size:13 final size:14
Alignment explanation
Indices: 12640291--12640325 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
12640281 ATTTTTACTA
12640291 TTTCATCTTTCATT
1 TTTCATCTTTCATT
*
12640305 TTTCAT-TTTCGTT
1 TTTCATCTTTCATT
12640318 TTTCATCT
1 TTTCATCT
12640326 CTTTTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.11, C:0.20, G:0.03, T:0.66
Consensus pattern (14 bp):
TTTCATCTTTCATT
Found at i:12642622 original size:64 final size:64
Alignment explanation
Indices: 12642543--12642671 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
12642533 GGAAACAACA
*
12642543 TGTGCGTAAAATAAACTATGATACAACTCCTGGTACGACATTGGGATTGGTGCAAATTGAGACT
1 TGTGCGTAAAATAAACTATGATACAACTCCTGGTACGACATTGGGATTGGTACAAATTGAGACT
12642607 TGTGCGTAAAATAAACTATGATACAACTCCTGGTACGACATTGGGATTGGTACAAATTGAGACT
1 TGTGCGTAAAATAAACTATGATACAACTCCTGGTACGACATTGGGATTGGTACAAATTGAGACT
12642671 T
1 T
12642672 CTCAGTACCT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (64 bp):
TGTGCGTAAAATAAACTATGATACAACTCCTGGTACGACATTGGGATTGGTACAAATTGAGACT
Found at i:12648738 original size:43 final size:42
Alignment explanation
Indices: 12648677--12648833 Score: 140
Period size: 43 Copynumber: 3.6 Consensus size: 42
12648667 AAAAGTCAGC
*
12648677 GGCGTTTGTGATTGAAGCGCCGCTAAAGGTCAAGGTCTTTAGT
1 GGCGTTTGT-AATGAAGCGCCGCTAAAGGTCAAGGTCTTTAGT
* * * * * *
12648720 GGCGTTTGTAAATCAAGCGCCGCTATAGG-CTAATGTATTTTGC
1 GGCGTTTGT-AATGAAGCGCCGCTAAAGGTC-AAGGTCTTTAGT
* * *
12648763 GGCGTTTGTAGTGGAAGCGCCGCTAAAAGTCAAGCTCTTTAGT
1 GGCGTTTGTAAT-GAAGCGCCGCTAAAGGTCAAGGTCTTTAGT
12648806 GGCGTTT-T-ATGGTAAAGCGCCGCTAAAG
1 GGCGTTTGTAAT-G--AAGCGCCGCTAAAG
12648834 ATAATAACCT
Statistics
Matches: 90, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
41 3 0.03
42 4 0.04
43 82 0.91
44 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (42 bp):
GGCGTTTGTAATGAAGCGCCGCTAAAGGTCAAGGTCTTTAGT
Found at i:12648851 original size:86 final size:86
Alignment explanation
Indices: 12648674--12648852 Score: 204
Period size: 86 Copynumber: 2.1 Consensus size: 86
12648664 GCTAAAAGTC
* * * *
12648674 AGCGGCGTTTGTGATTGAAGCGCCGCTAAAGGTCAAGGTCTTTAGTGGCGTTTGTAAATCAAGCG
1 AGCGGCGTTTGTGATGGAAGCGCCGCTAAAAGTCAAGCTCTTTAGTGGCGTTTGTAAATAAAGCG
* * *
12648739 CCGCTATAGGCTAATGTATTT
66 CCGCTATAAGATAATGAATTT
* **
12648760 TGCGGCGTTTGT-AGTGGAAGCGCCGCTAAAAGTCAAGCTCTTTAGTGGCGTTT-TATGGTAAAG
1 AGCGGCGTTTGTGA-TGGAAGCGCCGCTAAAAGTCAAGCTCTTTAGTGGCGTTTGTA-AATAAAG
12648823 CGCCGCTA-AAGATAAT-AACCTTT
64 CGCCGCTATAAGATAATGAA--TTT
12648846 AGCGGCG
1 AGCGGCG
12648853 CTTAAGTCAC
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
84 1 0.01
85 9 0.12
86 68 0.87
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (86 bp):
AGCGGCGTTTGTGATGGAAGCGCCGCTAAAAGTCAAGCTCTTTAGTGGCGTTTGTAAATAAAGCG
CCGCTATAAGATAATGAATTT
Found at i:12648870 original size:43 final size:43
Alignment explanation
Indices: 12648823--12649004 Score: 274
Period size: 43 Copynumber: 4.2 Consensus size: 43
12648813 TATGGTAAAG
*** *
12648823 CGCCGCTAAAGATAATAACCTTTAGCGGCGCTTAAGTCACAAA
1 CGCCGCTAAAGAGCTTAACTTTTAGCGGCGCTTAAGTCACAAA
*
12648866 CGCCGCTAAAGAGCTTGACTTTTAGCGGCGCTTAAGTCACAAA
1 CGCCGCTAAAGAGCTTAACTTTTAGCGGCGCTTAAGTCACAAA
* * *
12648909 CGTCGCTAAAGAGCTTAACTTTTAGTGACGCTTAAGTCACAAA
1 CGCCGCTAAAGAGCTTAACTTTTAGCGGCGCTTAAGTCACAAA
* *
12648952 CGCCGCTAAAGAGCTTGACTTTTAGCGGCGCTCAAGTCACAAA
1 CGCCGCTAAAGAGCTTAACTTTTAGCGGCGCTTAAGTCACAAA
12648995 CGCCGCTAAA
1 CGCCGCTAAA
12649005 TACCGTGACC
Statistics
Matches: 125, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 125 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (43 bp):
CGCCGCTAAAGAGCTTAACTTTTAGCGGCGCTTAAGTCACAAA
Found at i:12649019 original size:43 final size:43
Alignment explanation
Indices: 12648843--12649024 Score: 283
Period size: 43 Copynumber: 4.2 Consensus size: 43
12648833 GATAATAACC
12648843 TTTAGCGGCGCTTAAGTCACAAACGCCGCTAAAGAGCTTGACT
1 TTTAGCGGCGCTTAAGTCACAAACGCCGCTAAAGAGCTTGACT
* *
12648886 TTTAGCGGCGCTTAAGTCACAAACGTCGCTAAAGAGCTTAACT
1 TTTAGCGGCGCTTAAGTCACAAACGCCGCTAAAGAGCTTGACT
* *
12648929 TTTAGTGACGCTTAAGTCACAAACGCCGCTAAAGAGCTTGACT
1 TTTAGCGGCGCTTAAGTCACAAACGCCGCTAAAGAGCTTGACT
* * * * *
12648972 TTTAGCGGCGCTCAAGTCACAAACGCCGCTAAATACCGTGACC
1 TTTAGCGGCGCTTAAGTCACAAACGCCGCTAAAGAGCTTGACT
12649015 TTTAGCGGCG
1 TTTAGCGGCG
12649025 TTTTTTGCTA
Statistics
Matches: 126, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 126 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.24
Consensus pattern (43 bp):
TTTAGCGGCGCTTAAGTCACAAACGCCGCTAAAGAGCTTGACT
Found at i:12649504 original size:44 final size:44
Alignment explanation
Indices: 12649454--12649538 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
12649444 TTGTTTTTAG
12649454 TTTCACTCAAACTCTAATTAGTATAAGTTATTTTAATATTAAAT
1 TTTCACTCAAACTCTAATTAGTATAAGTTATTTTAATATTAAAT
* * * *
12649498 TTTCACTTAAACTCTTATTAGTGTAGGTTATTTTAATATTA
1 TTTCACTCAAACTCTAATTAGTATAAGTTATTTTAATATTA
12649539 TTTGACTTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (44 bp):
TTTCACTCAAACTCTAATTAGTATAAGTTATTTTAATATTAAAT
Found at i:12650470 original size:24 final size:24
Alignment explanation
Indices: 12650442--12650494 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
12650432 TTTCTAGAAG
*
12650442 ATTTAGTATTTATTAGTATAA-TAT
1 ATTTAGTATTTATTAGAATAACT-T
12650466 ATTTAGTATTTATTAGAATAACTT
1 ATTTAGTATTTATTAGAATAACTT
12650490 ATTTA
1 ATTTA
12650495 AATTACAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.53
Consensus pattern (24 bp):
ATTTAGTATTTATTAGAATAACTT
Found at i:12652182 original size:11 final size:11
Alignment explanation
Indices: 12652166--12652191 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12652156 AAAACAATTC
12652166 ATAATAAAACA
1 ATAATAAAACA
12652177 ATAATAAAACA
1 ATAATAAAACA
12652188 ATAA
1 ATAA
12652192 GATCTAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAATAAAACA
Found at i:12663625 original size:20 final size:20
Alignment explanation
Indices: 12663600--12663639 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12663590 CGGAAAATGA
*
12663600 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
12663620 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
12663640 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:12663655 original size:14 final size:15
Alignment explanation
Indices: 12663579--12663655 Score: 61
Period size: 14 Copynumber: 5.0 Consensus size: 15
12663569 GATTGGCAGT
*
12663579 AAAATG-TTTTCCGG
1 AAAATGATTTTCTGG
12663593 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
12663607 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
12663627 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
12663642 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
12663656 TGTTTGATTG
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 26 0.51
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:12664847 original size:32 final size:32
Alignment explanation
Indices: 12664811--12664871 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
12664801 AATCAACCAT
*
12664811 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATACAACAAGCTTAAAACATAATAAA
*
12664843 TTCAATATATAACAAGCTTAAAACATAAT
1 TTCAATATACAACAAGCTTAAAACATAAT
12664872 CAATATGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.28
Consensus pattern (32 bp):
TTCAATATACAACAAGCTTAAAACATAATAAA
Found at i:12664882 original size:27 final size:30
Alignment explanation
Indices: 12664811--12664884 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 30
12664801 AATCAACCAT
**
12664811 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATATAACAAGCTTAAAAC--AATAAA
12664843 TTCAATATATAACAAGCTTAAAAC-AT-AA
1 TTCAATATATAACAAGCTTAAAACAATAAA
*
12664871 -TCAATATGTAACAA
1 TTCAATATATAACAA
12664885 ATTCAATACA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
27 13 0.33
28 2 0.05
29 2 0.05
32 22 0.56
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.27
Consensus pattern (30 bp):
TTCAATATATAACAAGCTTAAAACAATAAA
Found at i:12666949 original size:14 final size:14
Alignment explanation
Indices: 12666932--12666964 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
12666922 GTGAAGGACC
12666932 GGAGGTGGACCGGT
1 GGAGGTGGACCGGT
*
12666946 GGAGGTGGATCGGT
1 GGAGGTGGACCGGT
12666960 GGAGG
1 GGAGG
12666965 ACGGAGGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.09, G:0.61, T:0.15
Consensus pattern (14 bp):
GGAGGTGGACCGGT
Found at i:12669638 original size:20 final size:21
Alignment explanation
Indices: 12669591--12669638 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
12669581 TTTAAAATCC
* * *
12669591 TAAATCTCAAATTCTAGATCA
1 TAAACCTCAAAGTCTAGACCA
*
12669612 TATACCTCAAAGTCTA-ACCA
1 TAAACCTCAAAGTCTAGACCA
12669632 TAAACCT
1 TAAACCT
12669639 TAAACCATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.29
Consensus pattern (21 bp):
TAAACCTCAAAGTCTAGACCA
Found at i:12672927 original size:3 final size:3
Alignment explanation
Indices: 12672921--12672973 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
12672911 TTTTTTTTTG
* * * *
12672921 TTA TTA TTA TCA TTA TTA TTA TT- TTA TGTA TTG TCA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
12672966 TTA TTA TT
1 TTA TTA TT
12672974 TCTATATTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:12673056 original size:2 final size:2
Alignment explanation
Indices: 12673003--12673040 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
12672993 TTTTTATGTG
*
12673003 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12673041 GCAGTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:12673302 original size:20 final size:19
Alignment explanation
Indices: 12673279--12673329 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
12673269 AAATATATAC
12673279 TTATATTTTTAATACATATT
1 TTATATTTTT-ATACATATT
* *
12673299 TTATAATATTTATATATATT
1 TTAT-ATTTTTATACATATT
12673319 TGTATATTTTT
1 T-TATATTTTT
12673330 CTTTATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTATATTTTTATACATATT
Found at i:12673391 original size:33 final size:34
Alignment explanation
Indices: 12673314--12673391 Score: 81
Period size: 33 Copynumber: 2.4 Consensus size: 34
12673304 ATATTTATAT
* * *
12673314 ATATTTGTATATTTTTCTTTATTTTCGTAAATGC
1 ATATTTGTATATTTTTCTTTAATTTCATAAATCC
* *
12673348 AT-TATATATATTTTT-TATTAATTTCAT-AATCC
1 ATATTTGTATATTTTTCT-TTAATTTCATAAATCC
12673380 ATATTTGTATAT
1 ATATTTGTATAT
12673392 ATAAATCCAT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
32 7 0.20
33 26 0.74
34 2 0.06
ACGTcount: A:0.29, C:0.08, G:0.05, T:0.58
Consensus pattern (34 bp):
ATATTTGTATATTTTTCTTTAATTTCATAAATCC
Found at i:12675485 original size:14 final size:15
Alignment explanation
Indices: 12675457--12675485 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12675447 CTAAAATAAG
12675457 GTGGCCCAAATACAA
1 GTGGCCCAAATACAA
12675472 GTGGCCCAAA-ACAA
1 GTGGCCCAAATACAA
12675486 ATGAAGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.41, C:0.28, G:0.21, T:0.10
Consensus pattern (15 bp):
GTGGCCCAAATACAA
Found at i:12684097 original size:21 final size:22
Alignment explanation
Indices: 12684055--12684099 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
12684045 TTTCGAGTAA
* *
12684055 ATATTCTTTCATTACGCCTAAAT
1 ATATTATTTCATTAC-CATAAAT
12684078 ATATTATTTCATTA-CATAAAT
1 ATATTATTTCATTACCATAAAT
12684099 A
1 A
12684100 ATTGTACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
23 13 0.65
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATTATTTCATTACCATAAAT
Found at i:12687582 original size:292 final size:293
Alignment explanation
Indices: 12687051--12687619 Score: 1115
Period size: 292 Copynumber: 1.9 Consensus size: 293
12687041 NNNNNNNNNN
12687051 GCGAATAAAAATATCAAGAAAATCGTGGCGAAAATGGCTGAAACTTACAAAGATTGGCATGAGAA
1 GCGAATAAAAATATCAAGAAAATCGTGGCGAAAATGGCTGAAACTTACAAAGATTGGCATGAGAA
12687116 GTTACCTTTCACTCTTCTTGCTTACCGAACATCTATCAGGACTTCTACTGGGGCAACACCTTTCT
66 GTTACCTTTCACTCTTCTTGCTTACCGAACATCTATCAGGACTTCTACTGGGGCAACACCTTTCT
12687181 CGTTGGTTTATAGAATGGAGGCAGTTTTACCCATTGAGGTTGAAATTCCTTCTCTCCTAGTTTTG
131 CGTTGGTTTATAGAATGGAGGCAGTTTTACCCATTGAGGTTGAAATTCCTTCTCTCCTAGTTTTG
12687246 GCCGAGTTAAAATTGAATGAGGCCGAATGGATCCAATCTCGGTATGATCAACTAAACCTGATTGA
196 GCCGAGTTAAAATTGAATGAGGCCGAATGGATCCAATCTCGGTATGATCAACTAAACCTGATTGA
12687311 AGAGAAAAGATTAAAAGTGGTGCAATGGAAGCG
261 AGAGAAAAGATTAAAAGTGGTGCAATGGAAGCG
12687344 GCGAAT-AAAATATCAAGAAAATCGTGGCGAAAATGGCTGAAACTTACAAAGATTGGCATGAGAA
1 GCGAATAAAAATATCAAGAAAATCGTGGCGAAAATGGCTGAAACTTACAAAGATTGGCATGAGAA
12687408 GTTACCTTTCACTCTTCTTGCTTACCTG-ACATCTATCAGGACTTCTACTGGGGCAACACCTTTC
66 GTTACCTTTCACTCTTCTTGCTTACC-GAACATCTATCAGGACTTCTACTGGGGCAACACCTTTC
12687472 TCGTTGGTTTATAGAATGGAGGCAGTTTTACCCATTGAGGTTGAAATTCCTTCTCTCCTAGTTTT
130 TCGTTGGTTTATAGAATGGAGGCAGTTTTACCCATTGAGGTTGAAATTCCTTCTCTCCTAGTTTT
12687537 GGCCGAGTTAAAATTGAATGAGGCCGAATGGATCCAATCTCGGTATGATCAACTAAACCTGATTG
195 GGCCGAGTTAAAATTGAATGAGGCCGAATGGATCCAATCTCGGTATGATCAACTAAACCTGATTG
12687602 AAGAGAAAAGATTAAAAG
260 AAGAGAAAAGATTAAAAG
12687620 CCATTCGTCA
Statistics
Matches: 275, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
292 268 0.97
293 7 0.03
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (293 bp):
GCGAATAAAAATATCAAGAAAATCGTGGCGAAAATGGCTGAAACTTACAAAGATTGGCATGAGAA
GTTACCTTTCACTCTTCTTGCTTACCGAACATCTATCAGGACTTCTACTGGGGCAACACCTTTCT
CGTTGGTTTATAGAATGGAGGCAGTTTTACCCATTGAGGTTGAAATTCCTTCTCTCCTAGTTTTG
GCCGAGTTAAAATTGAATGAGGCCGAATGGATCCAATCTCGGTATGATCAACTAAACCTGATTGA
AGAGAAAAGATTAAAAGTGGTGCAATGGAAGCG
Found at i:12689288 original size:44 final size:43
Alignment explanation
Indices: 12689235--12689696 Score: 279
Period size: 44 Copynumber: 10.7 Consensus size: 43
12689225 GAAGATGGCA
*
12689235 AGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGAT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-AT
* * *
12689279 AGTCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACC-T
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * * * *** *
12689321 CAGATTTTATCTCTCTGAAGTTGCAG-AGAACAGATCGCA-TC-T
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * * * *
12689363 AGTCTTATCTCTCTAAAGTTGCAGTAGAGTAGACTAAGTAAG-CA-
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCCAT
* * * *
12689407 AGTCTTA-CCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCA-
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGA-TTAA-A-GCCAT
*
12689452 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCGAT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CCAT
* * * * *
12689496 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * * * *** *
12689539 AGATCTTATCTCTCTAAAGTTGTAG-AGAGCAGATCGCA-TC-T
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* *
12689580 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAGGCA-
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AGCCAT
* * *
12689624 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATG-GAA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCAT
*
12689669 AATCTTATCTCCCTGAAGTTGCAGTGGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGA
12689697 ATAGATTGAA
Statistics
Matches: 329, Mismatches: 62, Indels: 52
0.74 0.14 0.12
Matches are distributed among these distances:
40 39 0.12
41 18 0.05
42 8 0.02
43 29 0.09
44 177 0.54
45 53 0.16
46 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
Found at i:12689514 original size:173 final size:172
Alignment explanation
Indices: 12689232--12689703 Score: 448
Period size: 173 Copynumber: 2.7 Consensus size: 172
12689222 ATCGAAGATG
* * * * *
12689232 GCAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGA-TTAA-AGCCGATAGTCCTATCTCCCTGA
1 GCAAGTCTTACCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAGGC-A-AGTCTTATCTCCCTGA
* * *
12689295 AGTTGCAGTGGAGCGGATTAAAACCTCAGAT--T-TTATCTCTCTGAAGTTGCAG-AGAACAGA-
64 AGTTGCAGTGGAGCAGATT-AAA-GTC-GATAATCTTATCTCCCTGAAGTTGCAGTAGAACAGAT
*** * *
12689355 TCGCATC-TAG-TCTTATCTCTCTAAAGTTGCAGTAGAGTAGACTAAGTAA
126 TAAAACCTTAGATCTTATCTCTCTAAAGTTGCAG-AGAGCAGA-T-AG-AA
*
12689404 GCAAGTCTTACC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAGAT-GGCAAGTCTTATCTCCCTG
1 GCAAGTCTTACCTC-CCTGAAGTTGCAGTGGAGCAGACT-AA-ATAGGCAAGTCTTATCTCCCTG
* * * *
12689467 AAGTTGCAGTGGAGCAGATTAAAGTCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTA
63 AAGTTGCAGTGGAGCAGATTAAAGTCGATAATCTTATCTCCCTGAAGTTGCAGTAGAACAGATTA
* * *
12689532 AAACCTTAGATCTTATCTCTCTAAAGTTGTAGAGAGCAGATCGCA
128 AAACCTTAGATCTTATCTCTCTAAAGTTGCAGAGAGCAGATAGAA
* * *
12689577 TCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAGGCAAGTCTTATC-CTCCTGAA
1 GCAAGTCTTACCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAGGCAAGTCTTATCTC-CCTGAA
* * * * * *
12689641 GTTGCAGT-GAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATT
65 GTTGCAGTGGA-GCAGATTAAAG-TCGATAATCTTATCTCCCTGAAGTTGCAGTAGAACAGATT
12689704 GAAGCACTAG
Statistics
Matches: 250, Mismatches: 33, Indels: 33
0.79 0.10 0.10
Matches are distributed among these distances:
170 3 0.01
171 8 0.03
172 73 0.29
173 119 0.48
174 9 0.04
175 7 0.03
176 10 0.04
177 21 0.08
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (172 bp):
GCAAGTCTTACCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAGGCAAGTCTTATCTCCCTGAAG
TTGCAGTGGAGCAGATTAAAGTCGATAATCTTATCTCCCTGAAGTTGCAGTAGAACAGATTAAAA
CCTTAGATCTTATCTCTCTAAAGTTGCAGAGAGCAGATAGAA
Found at i:12689601 original size:217 final size:217
Alignment explanation
Indices: 12689212--12689696 Score: 783
Period size: 217 Copynumber: 2.2 Consensus size: 217
12689202 ACTAAGCAGT
* *
12689212 AGTGGAGCAGA-TCGAAGATGGCAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCC
1 AGTGGGGCAGACT-GAAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
* * *
12689276 GATAGTCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATTTTATCTCTCTGAAG
65 GATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTAAAG
* * *
12689341 TTGCAGAGAACAGATCGCATCTAGTCTTATCTCTCTAAAGTTGCAGTAGAGTAGACTAAGTAAGC
130 TTGCAGAGAACAGATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTAAATAAGC
12689406 AAGTCTTACCCTCCTGAAGTTGC
195 AAGTCTTACCCTCCTGAAGTTGC
*
12689429 AGTGGGGCAGACTGAAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCG
1 AGTGGGGCAGACTGAAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCG
*
12689494 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTAAAGT
66 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTAAAGT
* * * * *
12689559 TGTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAGGCA
131 TGCAGAGAACAGATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTAAATAAGCA
*
12689624 AGTCTTATCCTCCTGAAGTTGC
196 AGTCTTACCCTCCTGAAGTTGC
* * *
12689646 AGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTTGCAGTGGA
1 AGTGGGGCAGACTGAAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGA
12689697 ATAGATTGAA
Statistics
Matches: 248, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
217 247 1.00
218 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (217 bp):
AGTGGGGCAGACTGAAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCG
ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTAAAGT
TGCAGAGAACAGATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTAAATAAGCA
AGTCTTACCCTCCTGAAGTTGC
Found at i:12689630 original size:84 final size:87
Alignment explanation
Indices: 12689363--12689696 Score: 240
Period size: 89 Copynumber: 3.8 Consensus size: 87
12689353 GATCGCATCT
* * * * * * *
12689363 AGTCTTATCTCTCTAAAGTTGCAGTAGAGTAGA-CTAAGTAAGCAAGTCTTA-CCCTCCTGAAGT
1 AGTCTTATCTCCCTAAAGTTGCAGTAGAGCAGATCAAAGTCA-TAA-TCCTATCTC-CCTGAAGT
*
12689426 TGCAGTGGGGCAGACTGAAGAT-GGCA
63 TGCAGTGGAGCAGACT-AA-ATAGGCA
* * *
12689452 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCGATAATCCTATCTCCCTGAAGTTG
1 AGTCTTATCTCCCTAAAGTTGCAGTAGAGCAGATCAAAGTC-ATAATCCTATCTCCCTGAAGTTG
* * * *
12689517 CAGTGGAGCGGATTAAA-A-CCTT
65 CAGTGGAGCAGACTAAATAGGC-A
* * ** * *
12689539 AGATCTTATCTCTCTAAAGTTGTAG-AGAGCAGATCGCA-TC-TAGTCTTATCTCCCTGAAGTTG
1 AG-TCTTATCTCCCTAAAGTTGCAGTAGAGCAGATCAAAGTCATAATCCTATCTCCCTGAAGTTG
12689601 CAGTGGAGCAGACTAAATAGGCA
65 CAGTGGAGCAGACTAAATAGGCA
* * * * *
12689624 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGA-CTGAAGATGGAAAATCTTATCTCCCTGAA
1 AGTCTTATCTC-CCTAAAGTTGCAGTAGA-GCAGATC-AAAG-T-CATAATCCTATCTCCCTGAA
12689686 GTTGCAGTGGA
61 GTTGCAGTGGA
12689697 ATAGATTGAA
Statistics
Matches: 194, Mismatches: 35, Indels: 32
0.74 0.13 0.12
Matches are distributed among these distances:
83 1 0.01
84 55 0.28
85 10 0.05
86 4 0.02
87 13 0.07
88 21 0.11
89 81 0.42
90 8 0.04
91 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (87 bp):
AGTCTTATCTCCCTAAAGTTGCAGTAGAGCAGATCAAAGTCATAATCCTATCTCCCTGAAGTTGC
AGTGGAGCAGACTAAATAGGCA
Found at i:12689967 original size:14 final size:15
Alignment explanation
Indices: 12689955--12689983 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12689945 CTAAAATACG
12689955 GTGGCCCAAATACAA
1 GTGGCCCAAATACAA
12689970 GTGGCCCAAA-ACAA
1 GTGGCCCAAATACAA
12689984 ATGAAGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.41, C:0.28, G:0.21, T:0.10
Consensus pattern (15 bp):
GTGGCCCAAATACAA
Found at i:12699587 original size:42 final size:42
Alignment explanation
Indices: 12699339--12699640 Score: 121
Period size: 42 Copynumber: 7.1 Consensus size: 42
12699329 TATCTCAATC
* * * * * *
12699339 TGGCATCAT-AGTGCATCATCAAATATACCAAAGGAAAGATAC
1 TGGCA-CATAAGTGCATCATCAGATAAATCAAAGCAAATATAT
* * * * * * *
12699381 TAGCACATATAGTGCATCATCGGGTAAGTCGAAA-TAATTATAC
1 TGGCACATA-AGTGCATCATCAGATAAATC-AAAGCAAATATAT
** * * * * *
12699424 TGGCACACGAGATCCATCATCAGATGAATCGAAGCAATTATAC
1 TGGCACATAAG-TGCATCATCAGATAAATCAAAGCAAATATAT
* ** *
12699467 TAGCATGCAT-AGTGCATCATC-GAATAAA-CATAAGCAACCATGT
1 TGGCA--CATAAGTGCATCATCAG-ATAAATCA-AAGCAAATATAT
* * ** ** * *
12699510 CGGCACGTAAGTGCATCATTTGATGTA-CTGAAGCAAATATAC
1 TGGCACATAAGTGCATCATCAGATAAATC-AAAGCAAATATAT
* * * * * *
12699552 TGGCACGTAAGTGCATTATCAGATATATCAGAGCAATTACAT
1 TGGCACATAAGTGCATCATCAGATAAATCAAAGCAAATATAT
* *
12699594 TGGCATATAGGTGCATCATCAGATAAATCAAAGCAAATATAT
1 TGGCACATAAGTGCATCATCAGATAAATCAAAGCAAATATAT
12699636 TGGCA
1 TGGCA
12699641 TGTGAGTGGA
Statistics
Matches: 189, Mismatches: 58, Indels: 26
0.69 0.21 0.10
Matches are distributed among these distances:
41 5 0.03
42 101 0.53
43 76 0.40
44 5 0.03
45 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (42 bp):
TGGCACATAAGTGCATCATCAGATAAATCAAAGCAAATATAT
Found at i:12699641 original size:42 final size:42
Alignment explanation
Indices: 12699540--12699641 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
12699530 TGATGTACTG
* ** * *
12699540 AAGCAAATATACTGGCACGTAAGTGCATTATCAGATATATCA
1 AAGCAAATATATTGGCATATAAGTGCATCATCAGATAAATCA
* * * *
12699582 GAGCAATTACATTGGCATATAGGTGCATCATCAGATAAATCA
1 AAGCAAATATATTGGCATATAAGTGCATCATCAGATAAATCA
12699624 AAGCAAATATATTGGCAT
1 AAGCAAATATATTGGCAT
12699642 GTGAGTGGAT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (42 bp):
AAGCAAATATATTGGCATATAAGTGCATCATCAGATAAATCA
Found at i:12699654 original size:42 final size:41
Alignment explanation
Indices: 12699540--12699654 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 41
12699530 TGATGTACTG
* * * *
12699540 AAGCAAATATACTGGCACGTAAGTGCATTATCAGATATATCA
1 AAGCAAATATATTGGCATGT-AGTGCATCATCAGATAAATCA
* * * *
12699582 GAGCAATTACATTGGCATATAGGTGCATCATCAGATAAATCA
1 AAGCAAATATATTGGCATGTA-GTGCATCATCAGATAAATCA
*
12699624 AAGCAAATATATTGGCATGTGAGTGGATCAT
1 AAGCAAATATATTGGCATGT-AGTGCATCAT
12699655 TGACTAAACT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
41 1 0.02
42 56 0.97
43 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (41 bp):
AAGCAAATATATTGGCATGTAGTGCATCATCAGATAAATCA
Found at i:12707901 original size:30 final size:30
Alignment explanation
Indices: 12707858--12707919 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
12707848 CTTAATAAGT
*
12707858 AAATGTCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
*
12707888 AAATGCCTTTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
12707918 AA
1 AA
12707920 TAAAATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAC
Found at i:12711069 original size:26 final size:27
Alignment explanation
Indices: 12711009--12711070 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
12710999 TTATTCGTTC
**
12711009 AATTAACAAAAATCATTAAATCAAATTT
1 AATTAA-AAAAATCATTAAATCAAAAAT
*
12711037 AA-CAAAAAAATCATTAAA-CAAAAAT
1 AATTAAAAAAATCATTAAATCAAAAAT
12711062 AATTAAAAA
1 AATTAAAAA
12711071 CCACTTGACT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 7 0.24
26 18 0.62
27 2 0.07
28 2 0.07
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (27 bp):
AATTAAAAAAATCATTAAATCAAAAAT
Found at i:12712672 original size:41 final size:41
Alignment explanation
Indices: 12712526--12712660 Score: 198
Period size: 41 Copynumber: 3.3 Consensus size: 41
12712516 CAACGACACT
* * * * *
12712526 TAGCCTGCTAGAATTATAGCTTAATTCAGATCACCAGCACG
1 TAGCCTGCTAGATTTATAACCTGATTCAGATCACCGGCACG
* *
12712567 TAGCCTGCTAGGTTTATAACCTGAGTCAGATCACCGGCACG
1 TAGCCTGCTAGATTTATAACCTGATTCAGATCACCGGCACG
*
12712608 TAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACG
1 TAGCCTGCTAGATTTATAACCTGATTCAGATCACCGGCACG
12712649 TAGCCTGCTAGA
1 TAGCCTGCTAGA
12712661 CTTAAAGCCT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 85 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (41 bp):
TAGCCTGCTAGATTTATAACCTGATTCAGATCACCGGCACG
Found at i:12713456 original size:2 final size:2
Alignment explanation
Indices: 12713449--12713497 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
12713439 TTCAATAACT
* * *
12713449 TA TA TA TA TA TG TA TA TA TA T- TA -A CA T- TA TA TA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12713488 TA TA TA TA TA
1 TA TA TA TA TA
12713498 CATGCTTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12713481 original size:27 final size:26
Alignment explanation
Indices: 12713444--12713496 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
12713434 CTAATTTCAA
**
12713444 TAACTTATATATATATGTATATATAT
1 TAACTTATATATATACATATATATAT
12713470 TAACATTATATATATACATATATATAT
1 TAAC-TTATATATATACATATATATAT
12713497 ACATGCTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (26 bp):
TAACTTATATATATACATATATATAT
Found at i:12717094 original size:18 final size:18
Alignment explanation
Indices: 12717074--12717107 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12717064 CACATATATA
12717074 AAAATAT-CAAATTTTAC
1 AAAATATGCAAATTTTAC
*
12717091 AAAATATGCATATTTTA
1 AAAATATGCAAATTTTA
12717108 ACTAAAACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (18 bp):
AAAATATGCAAATTTTAC
Found at i:12721566 original size:17 final size:18
Alignment explanation
Indices: 12721537--12721593 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
12721527 TTTTTTCTCC
12721537 AAAACCCTAAAAATCCTA
1 AAAACCCTAAAAATCCTA
*
12721555 AAAACCCTAAAACACCCT-
1 AAAACCCTAAAA-ATCCTA
12721573 -AAACCCT-AAAATCC-A
1 AAAACCCTAAAAATCCTA
12721588 AAAACC
1 AAAACC
12721594 TACAAGTCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 3 0.09
16 8 0.24
17 7 0.21
18 12 0.35
19 4 0.12
ACGTcount: A:0.54, C:0.33, G:0.00, T:0.12
Consensus pattern (18 bp):
AAAACCCTAAAAATCCTA
Found at i:12721571 original size:10 final size:9
Alignment explanation
Indices: 12721537--12721583 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
12721527 TTTTTTCTCC
12721537 AAAACCCTA
1 AAAACCCTA
*
12721546 AAAATCCTA
1 AAAACCCTA
12721555 AAAACCCTA
1 AAAACCCTA
12721564 AAACACCCT-
1 AAA-ACCCTA
12721573 -AAACCCTA
1 AAAACCCTA
12721581 AAA
1 AAA
12721584 TCCAAAAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 5 0.15
8 2 0.06
9 21 0.64
10 5 0.15
ACGTcount: A:0.55, C:0.32, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAACCCTA
Found at i:12723084 original size:6 final size:6
Alignment explanation
Indices: 12723073--12723105 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
12723063 GCTAATTAAA
12723073 AATATT AATATT AATATT AATATT AATATT AAT
1 AATATT AATATT AATATT AATATT AATATT AAT
12723106 TAAAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATATT
Found at i:12726522 original size:154 final size:154
Alignment explanation
Indices: 12726241--12726543 Score: 570
Period size: 154 Copynumber: 2.0 Consensus size: 154
12726231 TATTTGCTTT
*
12726241 AAAGCATGCAGATCATCCTCGTTAGTGGAATGGCATCTTGGACACATAAGGTCAATGACGTGAAT
1 AAAGCATGCAGATCATCCTCATTAGTGGAATGGCATCTTGGACACATAAGGTCAATGACGTGAAT
* *
12726306 TCTCCTTGCTATTTTCATCCGAAAGGTAGTATACCATAGCAAGCCTGCCACGAGAATGATTTAAC
66 TCTCCTTGCTATTTTCATCCGAAAGGTAGTATACCATAGCAAGCCTGCCAAGAGAATCATTTAAC
*
12726371 TTTAGGAGGTAGCTCTAAGAAAGC
131 CTTAGGAGGTAGCTCTAAGAAAGC
12726395 AAAGCATGCAGATCATCCTCATTAGTGGAATGGCATCTTGGACACATAAGGTCAATGACGTGAAT
1 AAAGCATGCAGATCATCCTCATTAGTGGAATGGCATCTTGGACACATAAGGTCAATGACGTGAAT
12726460 TCTCCTTGCTATTTTCATCCGAAAGGTAGTATACCATAGCAAGCCTGCCAAGAGAATCATTTAAC
66 TCTCCTTGCTATTTTCATCCGAAAGGTAGTATACCATAGCAAGCCTGCCAAGAGAATCATTTAAC
12726525 CTTAGGAGGTAGCTCTAAG
131 CTTAGGAGGTAGCTCTAAG
12726544 TTCCACAAAG
Statistics
Matches: 145, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 145 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (154 bp):
AAAGCATGCAGATCATCCTCATTAGTGGAATGGCATCTTGGACACATAAGGTCAATGACGTGAAT
TCTCCTTGCTATTTTCATCCGAAAGGTAGTATACCATAGCAAGCCTGCCAAGAGAATCATTTAAC
CTTAGGAGGTAGCTCTAAGAAAGC
Found at i:12732818 original size:4 final size:4
Alignment explanation
Indices: 12732809--12732871 Score: 57
Period size: 4 Copynumber: 16.5 Consensus size: 4
12732799 AAAATTAAGG
12732809 AATA AATA AATGA AATA AATA AA-A CAAGTA AATA AA-A AAT- AA-A AATA
1 AATA AATA AAT-A AATA AATA AATA -AA-TA AATA AATA AATA AATA AATA
12732856 AA-A AATA AA-A AATA AA
1 AATA AATA AATA AATA AA
12732872 AATAAAGGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
3 14 0.28
4 29 0.58
5 6 0.12
6 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (4 bp):
AATA
Found at i:12732850 original size:7 final size:7
Alignment explanation
Indices: 12732838--12732877 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
12732828 TAAAACAAGT
12732838 AAATAAA
1 AAATAAA
12732845 AAAT-AA
1 AAATAAA
12732851 AAATAAA
1 AAATAAA
12732858 AAATAAA
1 AAATAAA
12732865 AAAT-AA
1 AAATAAA
12732871 AAATAAA
1 AAATAAA
12732878 GGTTAATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.39
7 19 0.61
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAATAAA
Found at i:12732850 original size:20 final size:20
Alignment explanation
Indices: 12732813--12732876 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
12732803 TTAAGGAATA
12732813 AATAAATGAAATAAATAAAACA-
1 AATAAAT-AAA-AAATAAAA-AT
*
12732835 AGTAAATAAAAAATAAAAAT
1 AATAAATAAAAAATAAAAAT
*
12732855 AAAAAATAAAAAATAAAAAT
1 AATAAATAAAAAATAAAAAT
12732875 AA
1 AA
12732877 AGGTTAATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 1 0.03
20 28 0.74
21 3 0.08
22 6 0.16
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (20 bp):
AATAAATAAAAAATAAAAAT
Found at i:12732854 original size:13 final size:13
Alignment explanation
Indices: 12732838--12732877 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
12732828 TAAAACAAGT
12732838 AAATAAAAAATAA
1 AAATAAAAAATAA
12732851 AAATAAAAAATAA
1 AAATAAAAAATAA
12732864 AAA-ATAAAAATAA
1 AAATA-AAAAATAA
12732877 A
1 A
12732878 GGTTAATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 1 0.04
13 25 0.96
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:12732877 original size:20 final size:20
Alignment explanation
Indices: 12732838--12732877 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
12732828 TAAAACAAGT
12732838 AAATAAAAAATAAAAATAAA
1 AAATAAAAAATAAAAATAAA
12732858 AAATAAAAAATAAAAATAAA
1 AAATAAAAAATAAAAATAAA
12732878 GGTTAATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (20 bp):
AAATAAAAAATAAAAATAAA
Found at i:12733000 original size:7 final size:6
Alignment explanation
Indices: 12732980--12733018 Score: 60
Period size: 6 Copynumber: 6.2 Consensus size: 6
12732970 TGCTTAAAGT
12732980 AAATAA AAATAA AAATAAA AAATAAA AAATAA AAATAA A
1 AAATAA AAATAA AAAT-AA AAAT-AA AAATAA AAATAA A
12733019 GGTTAATGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 19 0.59
7 13 0.41
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:12733002 original size:13 final size:13
Alignment explanation
Indices: 12732980--12733018 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
12732970 TGCTTAAAGT
12732980 AAATAAAAAT-AA
1 AAATAAAAATAAA
12732992 AAATAAAAAATAAA
1 AAAT-AAAAATAAA
12733006 AAATAAAAATAAA
1 AAATAAAAATAAA
12733019 GGTTAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 4 0.16
13 15 0.60
14 6 0.24
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAATAAAAATAAA
Found at i:12733016 original size:141 final size:142
Alignment explanation
Indices: 12732834--12733117 Score: 561
Period size: 141 Copynumber: 2.0 Consensus size: 142
12732824 TAAATAAAAC
12732834 AAGTAAATAAAAAATAAAAATAAAAAATAAAAAATAAAAATAAAGGTTAATGTAATATTTGGCTT
1 AAGTAAATAAAAAATAAAAATAAAAAATAAAAAATAAAAATAAAGGTTAATGTAATATTTGGCTT
12732899 TGGAATTTGGTAATTAGGTCCATTTTAATATTTGTGTTTTTTGGTCAATCTTACTATCTATAGTT
66 TGGAATTTGGTAATTAGGTCCATTTTAATATTTGTGTTTTTTGGTCAATCTTACTATCTATAGTT
12732964 GTTGTTTGCTTA
131 GTTGTTTGCTTA
12732976 AAGTAAAT-AAAAATAAAAATAAAAAATAAAAAATAAAAATAAAGGTTAATGTAATATTTGGCTT
1 AAGTAAATAAAAAATAAAAATAAAAAATAAAAAATAAAAATAAAGGTTAATGTAATATTTGGCTT
12733040 TGGAATTTGGTAATTAGGTCCATTTTAATATTTGTGTTTTTTGGTCAATCTTACTATCTATAGTT
66 TGGAATTTGGTAATTAGGTCCATTTTAATATTTGTGTTTTTTGGTCAATCTTACTATCTATAGTT
12733105 GTTGTTTGCTTA
131 GTTGTTTGCTTA
12733117 A
1 A
12733118 TATAAAAATT
Statistics
Matches: 142, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
141 134 0.94
142 8 0.06
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (142 bp):
AAGTAAATAAAAAATAAAAATAAAAAATAAAAAATAAAAATAAAGGTTAATGTAATATTTGGCTT
TGGAATTTGGTAATTAGGTCCATTTTAATATTTGTGTTTTTTGGTCAATCTTACTATCTATAGTT
GTTGTTTGCTTA
Found at i:12743135 original size:22 final size:22
Alignment explanation
Indices: 12743108--12743162 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
12743098 CACAAAGTTG
12743108 ATGTTGCGACACACCAGGACCT
1 ATGTTGCGACACACCAGGACCT
*
12743130 ATGTTGTGACACACCAGGACCT
1 ATGTTGCGACACACCAGGACCT
*
12743152 ATGTCGCGACA
1 ATGTTGCGACA
12743163 TAGCAACTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (22 bp):
ATGTTGCGACACACCAGGACCT
Found at i:12749664 original size:8 final size:8
Alignment explanation
Indices: 12749650--12749679 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
12749640 TCAAATGAAC
12749650 AGAAATGG
1 AGAAATGG
*
12749658 TGAAATGG
1 AGAAATGG
12749666 AGAAATGG
1 AGAAATGG
12749674 AGAAAT
1 AGAAAT
12749680 ATGAAACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (8 bp):
AGAAATGG
Found at i:12749729 original size:57 final size:57
Alignment explanation
Indices: 12749668--12749815 Score: 140
Period size: 57 Copynumber: 2.6 Consensus size: 57
12749658 TGAAATGGAG
* **
12749668 AAATGGAGAAATATGAAA-CATTTGGAAATGGTTAAGATTTTCT-CAAAATGAAAATGA
1 AAATGGAG-AA-ATGAAATCATTTGAAAATGAATAAGATTTTCTCCAAAATGAAAATGA
* ** *
12749725 AAATGGAGAAATGAAATTATTTGAAAATGAATGTGGTTTTCTCCAAAATGAAAATGAA
1 AAATGGAGAAATGAAATCATTTGAAAATGAATAAGATTTTCTCCAAAATGAAAATG-A
* * *
12749783 AAAT-GAAAAATGAAAATGACTTGAAAAATGAAT
1 AAATGGAGAAATG-AAATCATTTG-AAAATGAAT
12749816 TTATGTTTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
55 6 0.08
56 20 0.26
57 28 0.37
58 13 0.17
59 9 0.12
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (57 bp):
AAATGGAGAAATGAAATCATTTGAAAATGAATAAGATTTTCTCCAAAATGAAAATGA
Found at i:12749814 original size:7 final size:7
Alignment explanation
Indices: 12749769--12749798 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
12749759 GGTTTTCTCC
12749769 AAAATG-
1 AAAATGA
12749775 AAAATGA
1 AAAATGA
12749782 AAAATGA
1 AAAATGA
12749789 AAAATGA
1 AAAATGA
12749796 AAA
1 AAA
12749799 TGACTTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAATGA
Found at i:12751105 original size:22 final size:22
Alignment explanation
Indices: 12751058--12751105 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
12751048 CAAATTACTA
*
12751058 TCAAATATATAAAAATTATAAT
1 TCAAATATATAAAAATTATAAC
12751080 TCAAATATATAAAAATT-TAAAC
1 TCAAATATATAAAAATTAT-AAC
12751102 TCAA
1 TCAA
12751106 TCATAACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (22 bp):
TCAAATATATAAAAATTATAAC
Found at i:12755654 original size:42 final size:43
Alignment explanation
Indices: 12755574--12755754 Score: 156
Period size: 42 Copynumber: 4.2 Consensus size: 43
12755564 ATTTGGGTTA
* *
12755574 AACCTACACGAGAAATATTAATAGTGCATGGTTACCCTTTCGAGTT
1 AACCTACACGAGAAATA-TAGT-GT-CATGATTACCCTTTCGAGTT
* *
12755620 AACCTACACGAGAAATTTAGTGTC-TGATTACCCTTT-TAGGTT
1 AACCTACACGAGAAATATAGTGTCATGATTACCCTTTCGA-GTT
* * ** * *
12755662 AACCTACACAAGAAATATAGTG-CTTTTTTACCCTTTTGGGTT
1 AACCTACACGAGAAATATAGTGTCATGATTACCCTTTCGAGTT
* * * *
12755704 AACCTACATGAAAAATATAGTGTC-T-AGTTACTCGTTCGAGTT
1 AACCTACACGAGAAATATAGTGTCATGA-TTACCCTTTCGAGTT
12755746 AACCTACAC
1 AACCTACAC
12755755 AACAAAGAGC
Statistics
Matches: 111, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
41 2 0.02
42 86 0.77
43 2 0.02
44 2 0.02
45 3 0.03
46 16 0.14
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (43 bp):
AACCTACACGAGAAATATAGTGTCATGATTACCCTTTCGAGTT
Found at i:12762290 original size:21 final size:21
Alignment explanation
Indices: 12762248--12762289 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12762238 TACTTTCATT
* *
12762248 ATTTTTAAAAATTAATTGAAA
1 ATTTATAAAAAATAATTGAAA
12762269 ATTTATAAAAAAT-ATTGAAA
1 ATTTATAAAAAATAATTGAAA
12762289 A
1 A
12762290 AAATTTGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTTATAAAAAATAATTGAAA
Found at i:12762620 original size:14 final size:14
Alignment explanation
Indices: 12762601--12762630 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12762591 GGTCTAGGTG
12762601 ATTCTACAAGGCCT
1 ATTCTACAAGGCCT
*
12762615 ATTCTACACGGCCT
1 ATTCTACAAGGCCT
12762629 AT
1 AT
12762631 CCACACGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (14 bp):
ATTCTACAAGGCCT
Found at i:12762684 original size:17 final size:16
Alignment explanation
Indices: 12762658--12762691 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
12762648 TCTAATGGCC
*
12762658 TGGCCACATGGCCATG
1 TGGCCACATGGCAATG
12762674 TGGCTCACATGGCAATG
1 TGGC-CACATGGCAATG
12762691 T
1 T
12762692 ACTTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.21, C:0.26, G:0.29, T:0.24
Consensus pattern (16 bp):
TGGCCACATGGCAATG
Found at i:12765872 original size:45 final size:45
Alignment explanation
Indices: 12765814--12766021 Score: 220
Period size: 45 Copynumber: 4.6 Consensus size: 45
12765804 TGCGATAGCG
* * * *
12765814 TCTTTCAACTATGGTCTTACTTAGTTTTGTCATGATGTCATAGCA
1 TCTTTCAACTATGGTCTTACTCACTTTTATCATGATGTCATAACA
* *
12765859 TCTTTCAACTATGGTTTTACTCACTTTTATCATGATGCCATAACA
1 TCTTTCAACTATGGTCTTACTCACTTTTATCATGATGTCATAACA
**
12765904 TCTTTCAACTATTTTCTTACTCACTTTTATCATGAT-TCCATAACA
1 TCTTTCAACTATGGTCTTACTCACTTTTATCATGATGT-CATAACA
* * * * ** * *
12765949 TCTTTCAACTTTGGTCTTACACACTCTTATGACAATGCCATAGCA
1 TCTTTCAACTATGGTCTTACTCACTTTTATCATGATGTCATAACA
* ** *
12765994 TCTTTTAGTTATGGTCTTACTCATTTTT
1 TCTTTCAACTATGGTCTTACTCACTTTT
12766022 GGCGCATAGT
Statistics
Matches: 134, Mismatches: 27, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
45 134 1.00
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.45
Consensus pattern (45 bp):
TCTTTCAACTATGGTCTTACTCACTTTTATCATGATGTCATAACA
Found at i:12769351 original size:148 final size:148
Alignment explanation
Indices: 12769083--12769354 Score: 411
Period size: 148 Copynumber: 1.8 Consensus size: 148
12769073 TAAGTATGAA
*** * * *
12769083 CCACCACTCTCAACCTTGTTGCAAAGCAAGAACACTAATGACAAACTAAAGTGGTTGCATGGTTT
1 CCACCACTCTCAACCTCACTACAAAGCAAGAACACTAATGACAAACTAAAATGGTTGCATGGTTA
*
12769148 TGTGGTCCTACAAATAATTAATAGTTATGGTTTACGAAAAAAATTATCGGTGGTTAAAGCAGATT
66 TGTGGTCCTACAAATAATTAATAGTTATGATTTACGAAAAAAATTATCGGTGGTTAAAGCAGATT
12769213 GAAAAGGCAAGTTCTGAT
131 GAAAAGGCAAGTTCTGAT
* *
12769231 CCACCACTCTCAACCTCACTACAAAGCGAGAACGCTAA-GCACAAACTAAAATGGTTGCATGGTT
1 CCACCACTCTCAACCTCACTACAAAGCAAGAACACTAATG-ACAAACTAAAATGGTTGCATGGTT
* ** *
12769295 ATGTGGTTCTACAAATAATTAATAGTTATGATTTGTGAAATAAATTATCGGTGGTTAAAG
65 ATGTGGTCCTACAAATAATTAATAGTTATGATTTACGAAAAAAATTATCGGTGGTTAAAG
12769355 GAGGCGTAAT
Statistics
Matches: 110, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
147 1 0.01
148 109 0.99
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (148 bp):
CCACCACTCTCAACCTCACTACAAAGCAAGAACACTAATGACAAACTAAAATGGTTGCATGGTTA
TGTGGTCCTACAAATAATTAATAGTTATGATTTACGAAAAAAATTATCGGTGGTTAAAGCAGATT
GAAAAGGCAAGTTCTGAT
Found at i:12770344 original size:30 final size:30
Alignment explanation
Indices: 12770308--12770368 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
12770298 CAGGTCCTTG
12770308 CGACATCAACTCTGTGACAAGAATAGAACA
1 CGACATCAACTCTGTGACAAGAATAGAACA
12770338 CGACATCAACTCTGTGACAAGAATAGAACA
1 CGACATCAACTCTGTGACAAGAATAGAACA
12770368 C
1 C
12770369 AAAGAAGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.25, G:0.16, T:0.16
Consensus pattern (30 bp):
CGACATCAACTCTGTGACAAGAATAGAACA
Found at i:12773292 original size:116 final size:115
Alignment explanation
Indices: 12773088--12773324 Score: 402
Period size: 116 Copynumber: 2.1 Consensus size: 115
12773078 ATTTCTTGTC
* *
12773088 CACACGGCCTAAGACACGGCATGTGTCTCAGCCGTGTGTGACACATGGCCATGCGACATGACTGT
1 CACACGGCCTAAGACACGGCATGTGTCTCAGCCGTATGTGACACATGGCCATGCAACATGACTGT
*
12773153 GTGTCCCCTGTAGGTTTTTGGGGTTGCAATTCGAAAGTTACATGGCCTAG
66 GTGTCCCCTGTAGGTTTTTGGGGTTGCAATTCGAAAGTTACACGGCCTAG
* * * *
12773203 GACACGGCCTAAGACACGAGCGTGTGTCTCAGCTGTATGTGACACATGGCCATGCAACATGGCTG
1 CACACGGCCTAAGACACG-GCATGTGTCTCAGCCGTATGTGACACATGGCCATGCAACATGACTG
12773268 TGTGTCCCCTGTAGGTTTTTGGGGTTGCAATTCGAAAGTTACACGGCCTAG
65 TGTGTCCCCTGTAGGTTTTTGGGGTTGCAATTCGAAAGTTACACGGCCTAG
12773319 CACACG
1 CACACG
12773325 ACCTGGCACA
Statistics
Matches: 113, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
115 17 0.15
116 96 0.85
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (115 bp):
CACACGGCCTAAGACACGGCATGTGTCTCAGCCGTATGTGACACATGGCCATGCAACATGACTGT
GTGTCCCCTGTAGGTTTTTGGGGTTGCAATTCGAAAGTTACACGGCCTAG
Found at i:12774796 original size:17 final size:17
Alignment explanation
Indices: 12774774--12774809 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12774764 AATTTAGGGG
* *
12774774 CACCATGACAGATGATC
1 CACCATAACAGAGGATC
12774791 CACCATAACAGAGGATC
1 CACCATAACAGAGGATC
12774808 CA
1 CA
12774810 TCGAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.31, G:0.17, T:0.14
Consensus pattern (17 bp):
CACCATAACAGAGGATC
Found at i:12789977 original size:25 final size:25
Alignment explanation
Indices: 12789945--12790009 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
12789935 ACCTAAGCGC
*
12789945 GCTATCTGATTATTAGCACGGTAGT
1 GCTATCTGATTATTAGCACGCTAGT
* * *
12789970 GCTCTCTGATTAATAGCATGCTAGT
1 GCTATCTGATTATTAGCACGCTAGT
12789995 GCTATCTGATTATTA
1 GCTATCTGATTATTA
12790010 AAACATTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (25 bp):
GCTATCTGATTATTAGCACGCTAGT
Found at i:12792728 original size:45 final size:44
Alignment explanation
Indices: 12792660--12792755 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
12792650 GCCGACTATT
*
12792660 GTTACTGTACCGATTCGAAACTTTGTGTGTCGAATACTATTACC
1 GTTACTGTACAGATTCGAAACTTTGTGTGTCGAATACTATTACC
* * *
12792704 GTTACTGTTACAGATTC-AACACTTTGTGTGTTGAATACTGTTACT
1 GTTACTG-TACAGATTCGAA-ACTTTGTGTGTCGAATACTATTACC
12792749 GTTACTG
1 GTTACTG
12792756 CTACCGATAC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
44 9 0.20
45 37 0.80
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.40
Consensus pattern (44 bp):
GTTACTGTACAGATTCGAAACTTTGTGTGTCGAATACTATTACC
Found at i:12795963 original size:16 final size:16
Alignment explanation
Indices: 12795942--12795973 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12795932 TAGCCCTATT
12795942 AGTGTAGAGAGTTAAC
1 AGTGTAGAGAGTTAAC
12795958 AGTGTAGAGAGTTAAC
1 AGTGTAGAGAGTTAAC
12795974 TTAAGTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.31, T:0.25
Consensus pattern (16 bp):
AGTGTAGAGAGTTAAC
Found at i:12807598 original size:5 final size:5
Alignment explanation
Indices: 12807588--12807618 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
12807578 TCTATTACCA
12807588 CATAT CATAT CATAT CATAT CATA- CATAT CA
1 CATAT CATAT CATAT CATAT CATAT CATAT CA
12807619 GAAGGAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (5 bp):
CATAT
Found at i:12808430 original size:9 final size:9
Alignment explanation
Indices: 12808413--12808449 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
12808403 TGAGTTTTCA
12808413 AATTCGAAT
1 AATTCGAAT
*
12808422 AACTCGAAT
1 AATTCGAAT
*
12808431 AATTCAAAT
1 AATTCGAAT
12808440 AATTCGAAT
1 AATTCGAAT
12808449 A
1 A
12808450 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:12808688 original size:102 final size:103
Alignment explanation
Indices: 12808534--12808763 Score: 435
Period size: 102 Copynumber: 2.2 Consensus size: 103
12808524 TCCCACTTTC
*
12808534 CCCCCAAAACTTTTACTCCCCTCCCCTCCCAACCCCCCAATCTACCCAAAATTCATTTCCCACCA
1 CCCCCAAAATTTTTACT-CCCTCCCCTCCCAACCCCCCAATCTACCCAAAATTCATTTCCCACCA
12808599 AAAATTTTACTCCCAAAACCCCTAAAAACCTTTTATTTT
65 AAAATTTTACTCCCAAAACCCCTAAAAACCTTTTATTTT
12808638 CCCCCAAAATTTTTACTCCCTCCCCT-CCAACCCCCCAATCTACCCAAAATTCATTTCCCACCAA
1 CCCCCAAAATTTTTACTCCCTCCCCTCCCAACCCCCCAATCTACCCAAAATTCATTTCCCACCAA
12808702 AAATTTTACTCCCAAAACCCCTAAAAACCTTTTATTTT
66 AAATTTTACTCCCAAAACCCCTAAAAACCTTTTATTTT
12808740 CCCCCAAAATTTTTACTCCCTCCC
1 CCCCCAAAATTTTTACTCCCTCCC
12808764 ACTTTTCCCC
Statistics
Matches: 125, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
102 100 0.80
103 9 0.07
104 16 0.13
ACGTcount: A:0.30, C:0.42, G:0.00, T:0.28
Consensus pattern (103 bp):
CCCCCAAAATTTTTACTCCCTCCCCTCCCAACCCCCCAATCTACCCAAAATTCATTTCCCACCAA
AAATTTTACTCCCAAAACCCCTAAAAACCTTTTATTTT
Found at i:12808923 original size:21 final size:22
Alignment explanation
Indices: 12808894--12808934 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
12808884 TCCCTCAAAC
12808894 TTTTATTCCCCAAAACTTTTTA
1 TTTTATTCCCCAAAACTTTTTA
*
12808916 TTTT-TTCCCCTAAACTTTT
1 TTTTATTCCCCAAAACTTTT
12808935 ACTTCTCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTTATTCCCCAAAACTTTTTA
Found at i:12816342 original size:45 final size:45
Alignment explanation
Indices: 12816286--12816380 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 45
12816276 TACTATGTGA
* *
12816286 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCT-AATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGATATGTGCTGAA-TCC
*
12816331 ACCGGACATCATTGATTAATAAGGTGGTTGATATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGATATGTGCTGAATCC
12816376 ACCGA
1 ACCGA
12816381 GTATCTGTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 43 0.96
46 2 0.04
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGATATGTGCTGAATCC
Found at i:12818899 original size:5 final size:6
Alignment explanation
Indices: 12818863--12818910 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
12818853 GGTTTCTCAT
* * * *
12818863 AATGGA AATGGA AACGAA AATGAA AATGAA AATAAA AATGAGA AATGA
1 AATGAA AATGAA AATGAA AATGAA AATGAA AATGAA AATGA-A AATGA
12818911 TACATTTGCA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
6 30 0.83
7 6 0.17
ACGTcount: A:0.62, C:0.02, G:0.21, T:0.15
Consensus pattern (6 bp):
AATGAA
Found at i:12822585 original size:7 final size:7
Alignment explanation
Indices: 12822573--12822597 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12822563 AAAAGACAGA
12822573 AAAATTT
1 AAAATTT
12822580 AAAATTT
1 AAAATTT
12822587 AAAATTT
1 AAAATTT
12822594 AAAA
1 AAAA
12822598 ACAACCTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATTT
Found at i:12825464 original size:85 final size:84
Alignment explanation
Indices: 12825308--12825699 Score: 291
Period size: 85 Copynumber: 4.6 Consensus size: 84
12825298 AGCCTCCAGT
* * * * * *
12825308 ACCTTGGTGGCTCGGATGTGTGGGAGCCTCGAACACCATTGGAACCTTGGTGGCTCGAATGT-CT
1 ACCTT-GT-GCTCGGATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTGGCACGGATGTGC-
*
12825372 GGGAGCCTTGAGCACCATCGGC
63 GGAAGCCTTGAGCACCATCGGC
* **
12825394 ACCTTAGTGCTCGGATGTGCGAGAGCCTCG-GCCACCATCGGCAACCTTGGT-GCTTGGATGTGC
1 ACCTT-GTGCTCGGATGTGCGGGAGCCTCGAG-CACCATCGGC-ACCTTGGTGGCACGGATGTGC
* *
12825457 GAAAGCCTCGAGCACCATCGGC
63 GGAAGCCTTGAGCACCATCGGC
** * * * *
12825479 ACCTTTGTGC-CTGTCTGTACGGGAGCCTCGAGCAGCATGGGCACCTTGGTGGCACGGATGTACG
1 ACC-TTGTGCTC-GGATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTGGCACGGATGTGCG
* *
12825543 GAAGCC-TCAG-ACGTCATCGGTA
64 GAAGCCTTGAGCAC--CATCGG-C
* *
12825565 ACCTTGATGCTTGGATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGT-GCATGGATGTGCGG
1 ACCTTG-TGCTCGGATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTGGCACGGATGTGCGG
* * * *
12825629 GAGCATCGA-CACCATCAGC
65 AAGCCTTGAGCACCATCGGC
* * * * *
12825648 AAACTAG-GCCCTTGGTTGTGCGGGAGCCTCGGAG-ACCATCGGCACCTCGGTG
1 -ACCTTGTG--CTCGGATGTGCGGGAGCCTC-GAGCACCATCGGCACCTTGGTG
12825700 CTATGATGTG
Statistics
Matches: 245, Mismatches: 42, Indels: 39
0.75 0.13 0.12
Matches are distributed among these distances:
82 1 0.00
83 2 0.01
84 55 0.22
85 126 0.51
86 61 0.25
ACGTcount: A:0.18, C:0.28, G:0.33, T:0.21
Consensus pattern (84 bp):
ACCTTGTGCTCGGATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTGGCACGGATGTGCGGA
AGCCTTGAGCACCATCGGC
Done.