Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 129 of 211
Found at i:40908896 original size:12 final size:12
Alignment explanation
Indices: 40908879--40908903 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40908869 CTTTTCCATC
40908879 TATCTTCTTTAT
1 TATCTTCTTTAT
40908891 TATCTTCTTTAT
1 TATCTTCTTTAT
40908903 T
1 T
40908904 GTTCCAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (12 bp):
TATCTTCTTTAT
Found at i:40910776 original size:225 final size:226
Alignment explanation
Indices: 40910360--40910812 Score: 838
Period size: 225 Copynumber: 2.0 Consensus size: 226
40910350 CCAATTGCCT
*
40910360 TCTTGAATTTCTTCAAGACATCAATCAGCTTCTATTCTTGATTCTCGGTTAATTCAACTGAAATA
1 TCTTGAATTTCTTCAAGACATCAATCAGCTTCTATTCTTGATTCTCGGTTAATTCAACTAAAATA
* *
40910425 ATCACAGGTAAAGTAGAAGAGTTACCCAAAAAAAAACATATTTAAGGTTAAATGGTAGTACCTTT
66 ATCACAAGTAAAGTAGAAGAGTTACCCAAAAAAAAACATATTTAAGGTGAAATGGTAGTACCTTT
40910490 AACTCTAACTTGGGTGGTTCTTCAGTTGAGGCTTTCAACTGCTTATACTTATGGTATTCTAAATC
131 AACTCTAACTTGGGTGGTTCTTCAGTTGAGGCTTTCAACTGCTTATACTTATGGTATTCTAAATC
40910555 TAAAGACTTGGAATGGGATTTGTGAAGTGAA
196 TAAAGACTTGGAATGGGATTTGTGAAGTGAA
*
40910586 TCTTGAATTTCTTCAAGACATCAATCAGCTTCTATTCTTGATTCTCGGTTAATTGAACTAAAATA
1 TCTTGAATTTCTTCAAGACATCAATCAGCTTCTATTCTTGATTCTCGGTTAATTCAACTAAAATA
40910651 ATCACAAGTAAAGTAGAAGAGTTACCC-AAAAAAAACATATTTAAGGTGAAATGGTAGTACCTTT
66 ATCACAAGTAAAGTAGAAGAGTTACCCAAAAAAAAACATATTTAAGGTGAAATGGTAGTACCTTT
*
40910715 AACTCTAACTTGGGTGGTTCTTCAGTTGAGTCTTTCAACTGCTTATACTTATAGG-ATTCTAAAT
131 AACTCTAACTTGGGTGGTTCTTCAGTTGAGGCTTTCAACTGCTTATACTTAT-GGTATTCTAAAT
40910779 CTAAAGACTTGGAATGGGATTTGTGAAGTGAA
195 CTAAAGACTTGGAATGGGATTTGTGAAGTGAA
40910811 TC
1 TC
40910813 CCTTCAATTC
Statistics
Matches: 221, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
225 130 0.59
226 91 0.41
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (226 bp):
TCTTGAATTTCTTCAAGACATCAATCAGCTTCTATTCTTGATTCTCGGTTAATTCAACTAAAATA
ATCACAAGTAAAGTAGAAGAGTTACCCAAAAAAAAACATATTTAAGGTGAAATGGTAGTACCTTT
AACTCTAACTTGGGTGGTTCTTCAGTTGAGGCTTTCAACTGCTTATACTTATGGTATTCTAAATC
TAAAGACTTGGAATGGGATTTGTGAAGTGAA
Found at i:40922686 original size:12 final size:12
Alignment explanation
Indices: 40922653--40922687 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
40922643 TATATGCCCG
*
40922653 TGTGCCAAGCCA
1 TGTGCCAGGCCA
40922665 TGTGCCAGGCCA
1 TGTGCCAGGCCA
*
40922677 TGTGCTAGGCC
1 TGTGCCAGGCC
40922688 GTGTAACAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.20
Consensus pattern (12 bp):
TGTGCCAGGCCA
Found at i:40927934 original size:249 final size:250
Alignment explanation
Indices: 40927473--40927978 Score: 1005
Period size: 249 Copynumber: 2.0 Consensus size: 250
40927463 CCTCATTGAA
40927473 TAAGCTGTTGAGGAAGAACACTCCTTTTAAATGGGGTGAACAGCAATAAGCTAGTTTTATGAAGT
1 TAAGCTGTTGAGGAAGAACACTCCTTTTAAATGGGGTGAACAGCAATAAGCTAGTTTTATGAAGT
40927538 TAAAATCCGTGTTGAAAGAAGCTCCTGTTCTAATTCAACCAGAAACTGGTAAGGTGTATGTGGTG
66 TAAAATCCGTGTTGAAAGAAGCTCCTGTTCTAATTCAACCAGAAACTGGTAAGGTGTATGTGGTG
40927603 TACAGCGATGCTTTGCATGACAGACTTGGATGTGTCTTAAAGTATGATGGTAAGGTTGTAGCCTA
131 TACAGCGATGCTTTGCATGACAGACTTGGATGTGTCTTAAAGTATGATGGTAAGGTTGTAGCCTA
40927668 TGCTTTAAGACAACTTAGGCCACATGAATTCAATTACCCTACTCATGATTTGGAG
196 TGCTTTAAGACAACTTAGGCCACATGAATTCAATTACCCTACTCATGATTTGGAG
40927723 TAAGCTGTTGAGGAAGAACACT-CTTTTAAATGGGGTGAACAGCAATAAGCTAGTTTTATGAAGT
1 TAAGCTGTTGAGGAAGAACACTCCTTTTAAATGGGGTGAACAGCAATAAGCTAGTTTTATGAAGT
40927787 TAAAATCCGTGTTGAAAGAAGCTCCTGTTCTAATTCAACCAGAAACTGGTAAGGTGTATGTGGTG
66 TAAAATCCGTGTTGAAAGAAGCTCCTGTTCTAATTCAACCAGAAACTGGTAAGGTGTATGTGGTG
40927852 TACAGCGATGCTTTGCATGACAGACTTGGATGTGTCTTAAAGTATGATGGTAAGGTTGTAGCCTA
131 TACAGCGATGCTTTGCATGACAGACTTGGATGTGTCTTAAAGTATGATGGTAAGGTTGTAGCCTA
40927917 TGCTTTAAGACAACTTAGGCCACATGAATTCAATTACCCTACTCATGATTTGGAG
196 TGCTTTAAGACAACTTAGGCCACATGAATTCAATTACCCTACTCATGATTTGGAG
40927972 TAAGCTG
1 TAAGCTG
40927979 CTGTTTTTTT
Statistics
Matches: 256, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
249 234 0.91
250 22 0.09
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (250 bp):
TAAGCTGTTGAGGAAGAACACTCCTTTTAAATGGGGTGAACAGCAATAAGCTAGTTTTATGAAGT
TAAAATCCGTGTTGAAAGAAGCTCCTGTTCTAATTCAACCAGAAACTGGTAAGGTGTATGTGGTG
TACAGCGATGCTTTGCATGACAGACTTGGATGTGTCTTAAAGTATGATGGTAAGGTTGTAGCCTA
TGCTTTAAGACAACTTAGGCCACATGAATTCAATTACCCTACTCATGATTTGGAG
Found at i:40931635 original size:16 final size:16
Alignment explanation
Indices: 40931614--40931645 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40931604 AATAGAATTA
40931614 AATGGGAAAAAGATGG
1 AATGGGAAAAAGATGG
40931630 AATGGGAAAAAGATGG
1 AATGGGAAAAAGATGG
40931646 CAAAATATGC
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:0.50, C:0.00, G:0.38, T:0.12
Consensus pattern (16 bp):
AATGGGAAAAAGATGG
Found at i:40940666 original size:24 final size:24
Alignment explanation
Indices: 40940634--40940695 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
40940624 GTGCTTCCCT
40940634 TTAAGTGCT-TTTCGGAGCTACCCG
1 TTAAGTGCTCTTT-GGAGCTACCCG
40940658 TTAAGTGCTCTTTGGAGCTACCCG
1 TTAAGTGCTCTTTGGAGCTACCCG
40940682 TTATAG-GCTCTTTG
1 TTA-AGTGCTCTTTG
40940696 TAAGCTTCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
24 31 0.86
25 5 0.14
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (24 bp):
TTAAGTGCTCTTTGGAGCTACCCG
Found at i:40940710 original size:25 final size:24
Alignment explanation
Indices: 40940649--40940711 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
40940639 TGCTTTTCGG
*
40940649 AGCTACCCGTTA-AGTGCTCTTTGG
1 AGCTACCCGTTATAG-GCTCTTTGA
40940673 AGCTACCCGTTATAGGCTCTTTGTA
1 AGCTACCCGTTATAGGCTCTTTG-A
* *
40940698 AGCTTCCCTTTATA
1 AGCTACCCGTTATA
40940712 TTGCCCGGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.59
25 14 0.41
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (24 bp):
AGCTACCCGTTATAGGCTCTTTGA
Found at i:40946682 original size:24 final size:24
Alignment explanation
Indices: 40946655--40946702 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40946645 AAATTAGTAA
40946655 GTCAAATAAACTACACTAATAAAT
1 GTCAAATAAACTACACTAATAAAT
* * *
40946679 GTCAAATATATTATACTAATAAAT
1 GTCAAATAAACTACACTAATAAAT
40946703 ACTAAATCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.31
Consensus pattern (24 bp):
GTCAAATAAACTACACTAATAAAT
Found at i:40948642 original size:24 final size:24
Alignment explanation
Indices: 40948615--40948662 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40948605 AAATTAGTAA
40948615 GTCAAATAAACTACACTAATAAAT
1 GTCAAATAAACTACACTAATAAAT
* * *
40948639 GTCAAATATATTATACTAATAAAT
1 GTCAAATAAACTACACTAATAAAT
40948663 ACTAAATCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.31
Consensus pattern (24 bp):
GTCAAATAAACTACACTAATAAAT
Found at i:40950602 original size:24 final size:24
Alignment explanation
Indices: 40950575--40950622 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40950565 AAATTAGTAA
40950575 GTCAAATAAACTACACTAATAAAT
1 GTCAAATAAACTACACTAATAAAT
* * *
40950599 GTCAAATATATTATACTAATAAAT
1 GTCAAATAAACTACACTAATAAAT
40950623 ACTAAATCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.31
Consensus pattern (24 bp):
GTCAAATAAACTACACTAATAAAT
Found at i:40951782 original size:20 final size:20
Alignment explanation
Indices: 40951723--40951805 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 20
40951713 CAAGCAATTC
*
40951723 TAACTTGTTTGAAAATCATTT
1 TAACTTGGTT-AAAATCATTT
* *
40951744 TGA--TGTGTTAAAATGATTT
1 TAACTTG-GTTAAAATCATTT
*
40951763 TAACTTGGTTGAAATCATTT
1 TAACTTGGTTAAAATCATTT
* *
40951783 TGACTAGGTTAAAATCATTT
1 TAACTTGGTTAAAATCATTT
40951803 TAA
1 TAA
40951806 ATTGATTTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.27
20 32 0.65
21 4 0.08
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (20 bp):
TAACTTGGTTAAAATCATTT
Found at i:40951794 original size:40 final size:40
Alignment explanation
Indices: 40951723--40951805 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
40951713 CAAGCAATTC
* *
40951723 TAACTTGTTTGAAAATCATTTTGATGTGTTAAAATGATTT
1 TAACTTGGTTGAAAATCATTTTGATGTGTTAAAATCATTT
40951763 TAACTTGGTTG-AAATCATTTTGACTAG-GTTAAAATCATTT
1 TAACTTGGTTGAAAATCATTTTGA-T-GTGTTAAAATCATTT
40951803 TAA
1 TAA
40951806 ATTGATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
39 12 0.31
40 26 0.67
41 1 0.03
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (40 bp):
TAACTTGGTTGAAAATCATTTTGATGTGTTAAAATCATTT
Found at i:40953607 original size:27 final size:27
Alignment explanation
Indices: 40953577--40953638 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
40953567 CCTATCAGGT
40953577 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
*
40953604 AGGCGCCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
40953631 AGGCGCCA
1 AGGCGCCA
40953639 TTACTAGACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.34, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:40953820 original size:22 final size:22
Alignment explanation
Indices: 40953795--40953853 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
40953785 AATAAACACC
40953795 AAAAAAT-TTTTAAAAATAAAA
1 AAAAAATATTTTAAAAATAAAA
*
40953816 AAAAAGTATTTTAAAAATAAAAA
1 AAAAAATATTTTAAAAAT-AAAA
40953839 ATAAAAATATATTTA
1 A-AAAAATAT-TTTA
40953854 TTGTATTCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 6 0.19
22 10 0.31
23 5 0.16
24 7 0.22
25 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAAAATATTTTAAAAATAAAA
Found at i:40954023 original size:19 final size:19
Alignment explanation
Indices: 40954001--40954038 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40953991 AATTTAATTT
*
40954001 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
40954020 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
40954039 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:40954168 original size:27 final size:27
Alignment explanation
Indices: 40954137--40954208 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
40954127 TACCGACATT
* *
40954137 CAATATTCATACAAAATTATAATATTA
1 CAATATTCATACAAAATTACAAAATTA
40954164 CAATATTCATACAAAATTACAAAATTA
1 CAATATTCATACAAAATTACAAAATTA
*
40954191 CAATATTCATATAAAATT
1 CAATATTCATACAAAATT
40954209 GCAATATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (27 bp):
CAATATTCATACAAAATTACAAAATTA
Found at i:40954281 original size:22 final size:24
Alignment explanation
Indices: 40954248--40954420 Score: 157
Period size: 22 Copynumber: 7.1 Consensus size: 24
40954238 ATAAATTATC
*
40954248 TATATTTAGTATGAATATTGTAAT
1 TATATTTTGTATGAATATTGTAAT
40954272 T-T-TTTTGTATGAATATTGTAATAT
1 TATATTTTGTATGAATATTGT-A-AT
*
40954296 TATAATTTTGTATGAATATTGCAAT
1 TAT-ATTTTGTATGAATATTGTAAT
40954321 T-T-TTTTGTATGAATATTGTAATAT
1 TATATTTTGTATGAATATTGT-A-AT
40954345 TATAATTTTGTATGAATATTGTAATGT
1 TAT-ATTTTGTATGAATATTGTAA--T
*
40954372 CGGTATATATTG--T-AATATTGTAAT
1 ---TATATTTTGTATGAATATTGTAAT
40954396 T-T-TTTTGTATGAATATTGTAAT
1 TATATTTTGTATGAATATTGTAAT
40954418 TAT
1 TAT
40954421 TTTATAATTA
Statistics
Matches: 125, Mismatches: 5, Indels: 39
0.74 0.03 0.23
Matches are distributed among these distances:
19 4 0.03
20 1 0.01
21 2 0.02
22 44 0.35
23 4 0.03
24 9 0.07
25 6 0.05
26 12 0.10
27 35 0.28
29 5 0.04
30 3 0.02
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.53
Consensus pattern (24 bp):
TATATTTTGTATGAATATTGTAAT
Found at i:40954310 original size:49 final size:49
Alignment explanation
Indices: 40954251--40954423 Score: 228
Period size: 49 Copynumber: 3.6 Consensus size: 49
40954241 AATTATCTAT
*
40954251 ATTTAGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
*
40954300 ATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTATA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
* ** *
40954349 ATTTTGTATGAATATTGTAA--TGTCGGTAT--ATATTGTAATATTGTA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
*
40954394 ATTTTTTTGTATGAATATTGTAATTATTTT
1 A---TTTTGTATGAATATTGTAATTTTTTT
40954424 ATAATTAATT
Statistics
Matches: 108, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
45 16 0.15
47 6 0.06
48 19 0.18
49 66 0.61
50 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (49 bp):
ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
Found at i:40954436 original size:22 final size:22
Alignment explanation
Indices: 40954384--40954436 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
40954374 GTATATATTG
* *
40954384 TAATATTGTAATTTTTTTGTAT
1 TAATATTGTAATTATTTTATAT
*
40954406 GAATATTGTAATTATTTTATAAT
1 TAATATTGTAATTATTTTAT-AT
40954429 TAAT-TTGT
1 TAATATTGT
40954437 TAGTAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.58
Consensus pattern (22 bp):
TAATATTGTAATTATTTTATAT
Found at i:40954488 original size:19 final size:19
Alignment explanation
Indices: 40954466--40954503 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40954456 TATAAATTTA
*
40954466 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
40954485 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
40954504 AAATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:40954762 original size:27 final size:28
Alignment explanation
Indices: 40954724--40954800 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 28
40954714 CCGGCCCGGC
*
40954724 CCATTGGCGCCTCTCAGAAT-GGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
*
40954751 CCATTGGCGCCTCCCAG-GTAGGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
40954778 CCATTGGCGCCTCCCAG-ATAGGC
1 CCATTGGCGCCTCCCAGAATAGGC
40954801 GCCAATACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.17
Consensus pattern (28 bp):
CCATTGGCGCCTCCCAGAATAGGCACCA
Found at i:40956694 original size:14 final size:14
Alignment explanation
Indices: 40956675--40956717 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
40956665 AATATTAATT
40956675 ATTTAAATAATTAA
1 ATTTAAATAATTAA
*
40956689 ATTTAATTAATT-A
1 ATTTAAATAATTAA
**
40956702 ATTTAACCAATTAA
1 ATTTAAATAATTAA
40956716 AT
1 AT
40956718 AATTTTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTTAAATAATTAA
Found at i:40963029 original size:21 final size:19
Alignment explanation
Indices: 40962982--40963024 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
40962972 TTTTATTTTT
*
40962982 TTCTTA-TTTTTAATATTTA
1 TTCTTAGTTTTTAA-ATTTC
40963001 TTCTTAGTTTTTAAATTTC
1 TTCTTAGTTTTTAAATTTC
40963020 TTCTT
1 TTCTT
40963025 TTAGTGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.67
Consensus pattern (19 bp):
TTCTTAGTTTTTAAATTTC
Found at i:40964194 original size:63 final size:62
Alignment explanation
Indices: 40964123--40964326 Score: 169
Period size: 63 Copynumber: 3.2 Consensus size: 62
40964113 ATTGTTCATT
*
40964123 ATCGTAAATCAATGAACTTAGGTTGTGATCATAAATCAGCGAACCTTATTAATAACAGTTGTG
1 ATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAACCTTA-TAATAACAGTTGTG
* * * * * * * * *
40964186 ATCATAAATTAACGAGCTATTTGGAGTTGCGATCGTAAATCAGCTAA-CTTAGAA-AAGATTGTT
1 ATCGTAAATCAATGA---ACTTAG-GTTGTGATCGTAAATCAGCGAACCTTATAATAACA--G-T
40964249 TGTG
59 TGTG
* * * * **
40964253 ATCGTAAATCAATGAACTTAGGCTGTGATCGTAAATCAGGGAGCCTTAATAATATCAAATGTG
1 ATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAACCTT-ATAATAACAGTTGTG
40964316 ATCGTAAATCA
1 ATCGTAAATCA
40964327 GCAAGTTGTT
Statistics
Matches: 106, Mismatches: 25, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
63 44 0.42
64 10 0.09
65 5 0.05
66 11 0.10
67 36 0.34
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (62 bp):
ATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAACCTTATAATAACAGTTGTG
Found at i:40964257 original size:130 final size:130
Alignment explanation
Indices: 40964040--40964422 Score: 496
Period size: 130 Copynumber: 2.9 Consensus size: 130
40964030 CAGTGTTACA
* * *
40964040 AATAATATCAGTTGTGATTGTAAATCAGCGAGCTATTTGGAATTGCGATTGTAAATCAGCTAACT
1 AATAATATCAGTTGTGATCGTAAATCAGCGAGCTATTTGGAGTTGCGATCGTAAATCAGCTAACT
* * *
40964105 CAAAAAAGATTGTTCATTATCGTAAATCAATGAACTTAGGTTGTGATCATAAATCAGCGAACCTT
66 CAGAAAAGATTGTTCATGATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAACCTT
* * * * *
40964170 ATTAATAACAGTTGTGATCATAAATTAACGAGCTATTTGGAGTTGCGATCGTAAATCAGCTAACT
1 AATAATATCAGTTGTGATCGTAAATCAGCGAGCTATTTGGAGTTGCGATCGTAAATCAGCTAACT
* ** * * *
40964235 TAGAAAAGATTGTTTGTGATCGTAAATCAATGAACTTAGGCTGTGATCGTAAATCAGGGAGCCTT
66 CAGAAAAGATTGTTCATGATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAACCTT
** * * * **
40964300 AATAATATCAAATGTGATCGTAAATCAGCAAGTTGTTTGGAGTTATGATCGTAAATCAGCTAACT
1 AATAATATCAGTTGTGATCGTAAATCAGCGAGCTATTTGGAGTTGCGATCGTAAATCAGCTAACT
* * * * * *
40964365 CGGAGAAGATTGTTCCTGATCGTTAATCAATGAACTTAGCTTGTGAACGTAAATCAGC
66 CAGAAAAGATTGTTCATGATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGC
40964423 AAGCTATTTG
Statistics
Matches: 214, Mismatches: 39, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
130 214 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (130 bp):
AATAATATCAGTTGTGATCGTAAATCAGCGAGCTATTTGGAGTTGCGATCGTAAATCAGCTAACT
CAGAAAAGATTGTTCATGATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAACCTT
Found at i:40964515 original size:94 final size:94
Alignment explanation
Indices: 40964312--40964495 Score: 242
Period size: 94 Copynumber: 2.0 Consensus size: 94
40964302 TAATATCAAA
* * * ** * * *
40964312 TGTGATCGTAAATCAGCAAGTTGTTTGGAGTTATGATCGTAAATCAGCTAACTCGGAGAAGATTG
1 TGTGAACGTAAATCAGCAAGCTATTTGGAGTTACAATCATAAATAAGCTAACTCAGAGAAGATTG
* *
40964377 TTCCTGATCGTTAATCAATGAACTTAGCT
66 TTCCTGATCATAAATCAATGAACTTAGCT
* *
40964406 TGTGAACGTAAATCAGCAAGCTATTTGGAGTTGCAATCATAAATAAGCTAACTTAGAGAAGATTG
1 TGTGAACGTAAATCAGCAAGCTATTTGGAGTTACAATCATAAATAAGCTAACTCAGAGAAGATTG
**
40964471 TTTGTGATCATAAATCAATGAACTT
66 TTCCTGATCATAAATCAATGAACTT
40964496 GGGTTGTAAT
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
94 76 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.32
Consensus pattern (94 bp):
TGTGAACGTAAATCAGCAAGCTATTTGGAGTTACAATCATAAATAAGCTAACTCAGAGAAGATTG
TTCCTGATCATAAATCAATGAACTTAGCT
Found at i:40967986 original size:25 final size:27
Alignment explanation
Indices: 40967955--40968017 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
40967945 GGCGGCTAGG
40967955 GAAAAGAAAAAGAA-GAAAAT-AAAAA
1 GAAAAGAAAAAGAAGGAAAATGAAAAA
** *
40967980 GGGAAGAAAATGAAGGAAAATGAAAAA
1 GAAAAGAAAAAGAAGGAAAATGAAAAA
40968007 GAAAAGAAAAA
1 GAAAAGAAAAA
40968018 AGAAAAAGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 11 0.37
26 6 0.20
27 13 0.43
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (27 bp):
GAAAAGAAAAAGAAGGAAAATGAAAAA
Found at i:40976392 original size:28 final size:28
Alignment explanation
Indices: 40976360--40976413 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
40976350 GACATTACCG
*
40976360 TAAATGTAAAAGTCTGTCAAGACTATCA
1 TAAATGTAAAAGTCTATCAAGACTATCA
** *
40976388 TAAATGTGGAAGTCTATCAGGACTAT
1 TAAATGTAAAAGTCTATCAAGACTAT
40976414 TGTATATCTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.30
Consensus pattern (28 bp):
TAAATGTAAAAGTCTATCAAGACTATCA
Found at i:40976469 original size:24 final size:24
Alignment explanation
Indices: 40976404--40976470 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
40976394 TGGAAGTCTA
* * *
40976404 TCAGGACTATTGTATATCTGGAAG
1 TCAGAACTATCGTATATGTGGAAG
*
40976428 TCAGAACTATCATATATGTGGAAG
1 TCAGAACTATCGTATATGTGGAAG
* *
40976452 TTAGTACTATCGTATATGT
1 TCAGAACTATCGTATATGT
40976471 CGAGGTCCGT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (24 bp):
TCAGAACTATCGTATATGTGGAAG
Found at i:40976488 original size:28 final size:28
Alignment explanation
Indices: 40976451--40976517 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
40976441 ATATGTGGAA
* * *
40976451 GTTAGTACTATCGTATATGTCGAGGTCC
1 GTTAGGACTATCGTAAATGTCGAAGTCC
* * * *
40976479 GTTATGACTATCTTAAATGTGGAAGTTC
1 GTTAGGACTATCGTAAATGTCGAAGTCC
40976507 GTTAGGACTAT
1 GTTAGGACTAT
40976518 ATTTTAAGTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37
Consensus pattern (28 bp):
GTTAGGACTATCGTAAATGTCGAAGTCC
Found at i:40978954 original size:51 final size:50
Alignment explanation
Indices: 40978835--40979019 Score: 192
Period size: 51 Copynumber: 3.7 Consensus size: 50
40978825 TTATCATTCA
* * * *
40978835 ATACACGTAGTAGTCTTCACATAGTACTACACACGTGATCAAACTTTCCG
1 ATACACGTAGTAGTCTGCACATAGTACTACACAAGTGACCAAACCTTCCG
* *
40978885 ATTCACGTAGTAGTCTGCACATAGTACTAAACAAGTGACCAAAGCCTTCCG
1 ATACACGTAGTAGTCTGCACATAGTACTACACAAGTGACCAAA-CCTTCCG
* * * * * * *
40978936 GTACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTATCTAT-TG
1 ATACACGTAGTAGTCTGCACATAGTACTACACAAGTGACCA-AACCT-TCCG
* * *
40978987 ACACACGTAGTAGCCTGCACTTAGTACTACACA
1 ATACACGTAGTAGTCTGCACATAGTACTACACA
40979020 CGTGTTTATA
Statistics
Matches: 113, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
50 38 0.34
51 73 0.65
52 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (50 bp):
ATACACGTAGTAGTCTGCACATAGTACTACACAAGTGACCAAACCTTCCG
Found at i:40982426 original size:16 final size:16
Alignment explanation
Indices: 40982405--40982449 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
40982395 TTTAGGGGCA
40982405 AAAATGTAATTTTGCC
1 AAAATGTAATTTTGCC
40982421 AAAATGTAATTTTGCC
1 AAAATGTAATTTTGCC
*
40982437 AAAATGTGATTTT
1 AAAATGTAATTTT
40982450 TGGACTGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (16 bp):
AAAATGTAATTTTGCC
Found at i:40982837 original size:51 final size:51
Alignment explanation
Indices: 40982672--40982867 Score: 184
Period size: 51 Copynumber: 3.9 Consensus size: 51
40982662 AGTGAAAGTG
** * *
40982672 ATGGTCACGCGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGA-ATGA
1 ATGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGATATTA
* * * * * * *
40982722 AAGGTCGCATGTCTAGTACTATATGCAGGCTACTATGCGTA-CTGGATAGCTT-
1 ATGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTATC-GGATA--TTA
* * * *
40982774 -CGATCACATGTGTAGTACTATGTGTAGGATACTACGTGTATCAGATATTA
1 ATGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGATATTA
* *
40982824 ATGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
1 ATGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTATCG
40982868 AATGATAATA
Statistics
Matches: 113, Mismatches: 26, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
49 3 0.03
50 35 0.31
51 73 0.65
52 1 0.01
53 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGATATTA
Found at i:40989747 original size:51 final size:50
Alignment explanation
Indices: 40989621--40989805 Score: 176
Period size: 51 Copynumber: 3.7 Consensus size: 50
40989611 TATCATTCGA
* * * *
40989621 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAACTTTTCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACATGATCAAACCTTCCGG
* * *
40989671 TTCACGTAGTAGCATGCCCATAGTACTACACACATGA-CGAAAGCCTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACATGATC-AAA-CCTTCCGG
* ** * * * *
40989722 TACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTATCTAT-CGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACATGATCA-AACCT-TCCGG
* *
40989773 TACACGTAGTAGTCTGCACTTAGTACTACACAC
1 TACACGTAGTAGCCTGCACATAGTACTACACAC
40989806 GTGTTTATAG
Statistics
Matches: 110, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
49 1 0.01
50 35 0.32
51 71 0.65
52 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (50 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACATGATCAAACCTTCCGG
Found at i:41000134 original size:19 final size:18
Alignment explanation
Indices: 41000098--41000137 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
41000088 ATGTATATGC
41000098 ATATATTAAAATACGTAT
1 ATATATTAAAATACGTAT
* *
41000116 ATATATGTATAATATGTAT
1 ATATAT-TAAAATACGTAT
41000135 ATA
1 ATA
41000138 AAAATGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (18 bp):
ATATATTAAAATACGTAT
Found at i:41002165 original size:44 final size:44
Alignment explanation
Indices: 41002108--41002261 Score: 154
Period size: 44 Copynumber: 3.6 Consensus size: 44
41002098 TATGCGATCT
* *
41002108 GCTCTACTGCAACTTTAGAGAGATAAGATCTGTGGTTTTAATCC
1 GCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
* * * * * *
41002152 GCTCCACTGCAACTTCAGGGAAATAAGA-C--TGGATATGATCT
1 GCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
** * *
41002193 ATTCTAC-GACAACTTCAGAGAGATGAGATCTGTGGTTTTAATCC
1 GCTCCACTG-CAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
*
41002237 GCTCCACTGCAGCTTCAGAGAGATA
1 GCTCCACTGCAACTTCAGAGAGATA
41002262 GGATTGGTAC
Statistics
Matches: 82, Mismatches: 23, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
40 1 0.01
41 28 0.34
42 1 0.01
43 1 0.01
44 50 0.61
45 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
Found at i:41002192 original size:85 final size:85
Alignment explanation
Indices: 41002067--41002254 Score: 243
Period size: 85 Copynumber: 2.2 Consensus size: 85
41002057 TCTTTTGTCT
* * * * ** * * *
41002067 GCTCTACTACAACTTCATGGAGATAAGACTTTATGCGATCTGCTCTACTG-CAACTTTAGAGAGA
1 GCTCCACTGCAACTTCAGGGAAATAAGACTGGATACGATCTACTCTAC-GACAACTTCAGAGAGA
41002131 TAAGATCTGTGGTTTTAATCC
65 TAAGATCTGTGGTTTTAATCC
* *
41002152 GCTCCACTGCAACTTCAGGGAAATAAGACTGGATATGATCTATTCTACGACAACTTCAGAGAGAT
1 GCTCCACTGCAACTTCAGGGAAATAAGACTGGATACGATCTACTCTACGACAACTTCAGAGAGAT
*
41002217 GAGATCTGTGGTTTTAATCC
66 AAGATCTGTGGTTTTAATCC
*
41002237 GCTCCACTGCAGCTTCAG
1 GCTCCACTGCAACTTCAG
41002255 AGAGATAGGA
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
84 1 0.01
85 88 0.99
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (85 bp):
GCTCCACTGCAACTTCAGGGAAATAAGACTGGATACGATCTACTCTACGACAACTTCAGAGAGAT
AAGATCTGTGGTTTTAATCC
Found at i:41002332 original size:50 final size:50
Alignment explanation
Indices: 41002273--41002430 Score: 183
Period size: 50 Copynumber: 3.2 Consensus size: 50
41002263 GATTGGTACA
* *
41002273 TTCAATCTGTTTAACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGC
1 TTCAATCTGTTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGC
** * ** * * * *
41002323 TTCAATCTGTTCCATTGCACA-GCCGGGGAAGTAAAATTCACCGTTGTGGC
1 TTCAATCTGTTTAATTGCA-ATGTCGGGGAAACAAGATTCGCCGTCGTAGC
* *
41002373 TTCAATCTATTTAATTGCAATGTCGGGGAAACAAGATTCGTCGTCGTAGC
1 TTCAATCTGTTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGC
41002423 TTCAATCT
1 TTCAATCT
41002431 ATTCCACTAC
Statistics
Matches: 84, Mismatches: 22, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
49 1 0.01
50 82 0.98
51 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (50 bp):
TTCAATCTGTTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGC
Found at i:41002452 original size:50 final size:50
Alignment explanation
Indices: 41002296--41002489 Score: 165
Period size: 50 Copynumber: 3.9 Consensus size: 50
41002286 ACTGCAATGT
* * *
41002296 CAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCATTGCAC-AGC
1 CAGGGAAACAAAATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACTA-C
* ** * * * ** * * **
41002346 CGGGGAAGTAAAATTCACCGTTGTGGCTTCAATCTATTTAATTGCAATGT
1 CAGGGAAACAAAATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACTAC
* * * *
41002396 CGGGGAAACAAGATTCGTCGTCGTAGCTTCAATCTATTCCACTACACTAC
1 CAGGGAAACAAAATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACTAC
** * *
41002446 CAGGGAAGTAAAATTCGCCGTTGTGGCTTCAATCTATTCCACTG
1 CAGGGAAACAAAATTCGCCGTCGTAGCTTCAATCTATTCCACTG
41002490 TAATGCCAAA
Statistics
Matches: 108, Mismatches: 35, Indels: 2
0.74 0.24 0.01
Matches are distributed among these distances:
50 108 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (50 bp):
CAGGGAAACAAAATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACTAC
Found at i:41002452 original size:100 final size:100
Alignment explanation
Indices: 41002273--41002483 Score: 325
Period size: 100 Copynumber: 2.1 Consensus size: 100
41002263 GATTGGTACA
* * *
41002273 TTCAATCTGTTTAACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCAT
1 TTCAATCTATTTAACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCAC
* *
41002338 TGCACAGCCGGGGAAGTAAAATTCACCGTTGTGGC
66 TACACAGCCAGGGAAGTAAAATTCACCGTTGTGGC
* * *
41002373 TTCAATCTATTTAATTGCAATGTCGGGGAAACAAGATTCGTCGTCGTAGCTTCAATCTATTCCAC
1 TTCAATCTATTTAACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCAC
*
41002438 TACACTA-CCAGGGAAGTAAAATTCGCCGTTGTGGC
66 TACAC-AGCCAGGGAAGTAAAATTCACCGTTGTGGC
41002473 TTCAATCTATT
1 TTCAATCTATT
41002484 CCACTGTAAT
Statistics
Matches: 101, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
100 100 0.99
101 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (100 bp):
TTCAATCTATTTAACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCAC
TACACAGCCAGGGAAGTAAAATTCACCGTTGTGGC
Found at i:41002774 original size:88 final size:88
Alignment explanation
Indices: 41002662--41002846 Score: 271
Period size: 88 Copynumber: 2.1 Consensus size: 88
41002652 CATTACAACG
* * * * * * *
41002662 TCAAGGCGATAAGACTGGTGTCTTCGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCCA
1 TCAAGGAGACAAGACTGGTATCTTCGATCTACTTCACTGCCAATACAAGAAGACAAGATCTGCCA
*
41002727 TTTTCAACCTACTCCATTGCTGC
66 TTTTCAACCTACTCCACTGCTGC
* * *
41002750 TCAGGGAGACAAGACTGGTATCTTCGATCTACTTCGCTGCCAATACAAGAAGACAAGATCTGCTA
1 TCAAGGAGACAAGACTGGTATCTTCGATCTACTTCACTGCCAATACAAGAAGACAAGATCTGCCA
41002815 TTTTCAACCTACTCCACTGCTGC
66 TTTTCAACCTACTCCACTGCTGC
41002838 TCAAGGAGA
1 TCAAGGAGA
41002847 TAAGGCTGAA
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (88 bp):
TCAAGGAGACAAGACTGGTATCTTCGATCTACTTCACTGCCAATACAAGAAGACAAGATCTGCCA
TTTTCAACCTACTCCACTGCTGC
Found at i:41007398 original size:8 final size:8
Alignment explanation
Indices: 41007385--41007410 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
41007375 ATGATGTGGA
41007385 AAAAGAAT
1 AAAAGAAT
41007393 AAAAGAAT
1 AAAAGAAT
41007401 AAAAGAAT
1 AAAAGAAT
41007409 AA
1 AA
41007411 TTACTCGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAGAAT
Found at i:41014836 original size:19 final size:18
Alignment explanation
Indices: 41014800--41014839 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
41014790 ATGTATATGC
41014800 ATATATTAAAATACGTAT
1 ATATATTAAAATACGTAT
* *
41014818 ATATATGTATAATATGTAT
1 ATATAT-TAAAATACGTAT
41014837 ATA
1 ATA
41014840 AAAAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (18 bp):
ATATATTAAAATACGTAT
Found at i:41014848 original size:19 final size:20
Alignment explanation
Indices: 41014828--41014867 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
41014818 ATATATGTAT
*
41014828 AATATGTATATAAAAAAATAA
1 AATATATATAT-AAAAAATAA
41014849 AATATATATATAAAAAATA
1 AATATATATATAAAAAATA
41014868 TTTATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (20 bp):
AATATATATATAAAAAATAA
Found at i:41015363 original size:3 final size:3
Alignment explanation
Indices: 41015355--41015384 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
41015345 ATGACAACAG
*
41015355 TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41015385 CAAACTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:41016738 original size:19 final size:19
Alignment explanation
Indices: 41016714--41016779 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
41016704 AAAAATTATA
41016714 AAAAATATTTTTAAAAATT
1 AAAAATATTTTTAAAAATT
* ** *
41016733 AAAAAT-TATTATAATTATA
1 AAAAATAT-TTTTAAAAATT
* *
41016752 AAAAATGTTTTTAAAATTT
1 AAAAATATTTTTAAAAATT
*
41016771 TAAAATATT
1 AAAAATATT
41016780 AATTAAATAC
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
18 1 0.03
19 32 0.94
20 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
AAAAATATTTTTAAAAATT
Found at i:41016755 original size:37 final size:38
Alignment explanation
Indices: 41016681--41016781 Score: 132
Period size: 38 Copynumber: 2.7 Consensus size: 38
41016671 ACATTTAGTT
* * *
41016681 TATTTTTTAAAATTTATAATTATAAAAATTATAAAAAA
1 TATTTTTAAAAATTTAAAATTATTAAAATTATAAAAAA
* *
41016719 TATTTTTAAAAATTAAAAATTATTATAATTATAAAAAA
1 TATTTTTAAAAATTTAAAATTATTAAAATTATAAAAAA
* *
41016757 TGTTTTTAAAATTTTAAAA-TATTAA
1 TATTTTTAAAAATTTAAAATTATTAA
41016782 TTAAATACTA
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 5 0.09
38 49 0.91
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (38 bp):
TATTTTTAAAAATTTAAAATTATTAAAATTATAAAAAA
Found at i:41017588 original size:9 final size:9
Alignment explanation
Indices: 41017574--41017604 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
41017564 GTTAAACGAA
41017574 TCGAGTTAT
1 TCGAGTTAT
*
41017583 TCGAGTTAA
1 TCGAGTTAT
41017592 TCGAGTTAT
1 TCGAGTTAT
41017601 TCGA
1 TCGA
41017605 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:41019274 original size:9 final size:9
Alignment explanation
Indices: 41019257--41019293 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
41019247 TGAGTTTTCA
41019257 AATTCGAAT
1 AATTCGAAT
*
41019266 AACTCGAAT
1 AATTCGAAT
41019275 AATTCGAAT
1 AATTCGAAT
41019284 AATTCGAAT
1 AATTCGAAT
41019293 A
1 A
41019294 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:41019565 original size:31 final size:31
Alignment explanation
Indices: 41019505--41019565 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
41019495 AAACCTTTTA
*
41019505 TTTTCCCCCAAAATTTTTTTCTCCCTCCCAC
1 TTTTCCCCCAAAATTTTATTCTCCCTCCCAC
* *
41019536 TTTTCCCCTAAAACTTTTATTC-CCTTCCCA
1 TTTTCCCCCAAAA-TTTTATTCTCCCTCCCA
41019566 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.18, C:0.39, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTCCCCCAAAATTTTATTCTCCCTCCCAC
Found at i:41031036 original size:27 final size:27
Alignment explanation
Indices: 41030998--41031083 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
41030988 TATTCTTGGC
41030998 GAACTCTGAAGGTGTAGTAAGTATGGT
1 GAACTCTGAAGGTGTAGTAAGTATGGT
** * *
41031025 GAACTCTGAAGGAATAATATA-TATGGC
1 GAACTCTGAAGGTGTAGTA-AGTATGGT
* * *
41031052 GAACTCTAAAGATGCAGTAAGTATGGT
1 GAACTCTGAAGGTGTAGTAAGTATGGT
41031079 GAACT
1 GAACT
41031084 TTGTAGGAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
26 1 0.02
27 44 0.96
28 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.27
Consensus pattern (27 bp):
GAACTCTGAAGGTGTAGTAAGTATGGT
Found at i:41031071 original size:54 final size:54
Alignment explanation
Indices: 41030994--41031096 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 54
41030984 ATGGTATTCT
* * *
41030994 TGGCGAACTCTGAAGGTGTAGTAAGTATGGTGAACTCTGAAGGAATAATATATA
1 TGGCGAACTCTAAAGATGCAGTAAGTATGGTGAACTCTGAAGGAATAATATATA
* *
41031048 TGGCGAACTCTAAAGATGCAGTAAGTATGGTGAACTTTGTAGGAATAAT
1 TGGCGAACTCTAAAGATGCAGTAAGTATGGTGAACTCTGAAGGAATAAT
41031097 GTGTACAGCG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (54 bp):
TGGCGAACTCTAAAGATGCAGTAAGTATGGTGAACTCTGAAGGAATAATATATA
Found at i:41031108 original size:54 final size:54
Alignment explanation
Indices: 41030996--41031118 Score: 156
Period size: 54 Copynumber: 2.3 Consensus size: 54
41030986 GGTATTCTTG
* * * **
41030996 GCGAACTCTGAAGGTGTAGTAAGTATGGTGAACTCTGAAGGAATAATATATATG
1 GCGAACTCTAAAGATGCAGTAAGTATGGTGAACTCTGAAGGAATAATATATACA
* * * *
41031050 GCGAACTCTAAAGATGCAGTAAGTATGGTGAACTTTGTAGGAATAATGTGTACA
1 GCGAACTCTAAAGATGCAGTAAGTATGGTGAACTCTGAAGGAATAATATATACA
41031104 GCGAACTCTGAAAGA
1 GCGAACTCT-AAAGA
41031119 AAGGCTTCGT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
54 54 0.92
55 5 0.08
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (54 bp):
GCGAACTCTAAAGATGCAGTAAGTATGGTGAACTCTGAAGGAATAATATATACA
Found at i:41033046 original size:19 final size:20
Alignment explanation
Indices: 41033024--41033072 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
41033014 AAGTACAATT
41033024 AAATTAATT-AAATTATTTA-
1 AAATTAATTGAAATT-TTTAG
*
41033043 AAATTAATATGATATTTTTAG
1 AAATTAAT-TGAAATTTTTAG
41033064 AAATTAATT
1 AAATTAATT
41033073 TTCAAGTCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 8 0.31
20 6 0.23
21 12 0.46
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (20 bp):
AAATTAATTGAAATTTTTAG
Found at i:41035664 original size:11 final size:11
Alignment explanation
Indices: 41035647--41035676 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
41035637 CAACATGCGA
41035647 CGACGACTACT
1 CGACGACTACT
*
41035658 TGACGACTACT
1 CGACGACTACT
41035669 CGACGACT
1 CGACGACT
41035677 TTTTATTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (11 bp):
CGACGACTACT
Found at i:41049220 original size:15 final size:16
Alignment explanation
Indices: 41049200--41049236 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
41049190 ATCGTTAAAA
41049200 TTATTATC-ATTGTAT
1 TTATTATCTATTGTAT
41049215 TTATTA-CTATTGTAT
1 TTATTATCTATTGTAT
*
41049230 TTGTTAT
1 TTATTAT
41049237 TACGATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 1 0.05
15 18 0.95
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (16 bp):
TTATTATCTATTGTAT
Found at i:41061143 original size:44 final size:43
Alignment explanation
Indices: 41061091--41061645 Score: 296
Period size: 44 Copynumber: 12.8 Consensus size: 43
41061081 TATCGCATCT
*
41061091 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* * *
41061135 AGTCTTATC-CTCTTGAAGTTGCAGT-GAGGCAGACTGAAGATGGAA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
* * * * *
41061180 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAG-GTTA-AAGCCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * *
41061223 TAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAGGAA
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
*
41061268 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGATTGAAGATAGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
* * * *
41061313 AATCTTATCTCCCTGAAGTTGCAGCGGAGCAG-GTTA-AAGCCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * ** * * *
41061356 TAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAA-AACCTT
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-A
* * * * * * *
41061400 GGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
*
41061441 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* * * * ** * * *
41061485 AATCCTATCTTCATGAAGTTGCAGTGGAGTGGATTAA-AACCTT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-A
* ** * * * * * *
41061528 GGATCTTATCTTTCTGAAGTTGCAG-AGAGTAGA-T-CGCATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
* *
41061569 AGTCTTATCTCCCTGAAGTTGAAGTGGAGCAGACTAAGTAGGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* **
41061613 AGTCTTATCTCTCTGAAGTTGCAGCAGAGCAGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
41061646 TCACATCAAA
Statistics
Matches: 386, Mismatches: 90, Indels: 70
0.71 0.16 0.13
Matches are distributed among these distances:
40 40 0.10
41 19 0.05
42 14 0.04
43 23 0.06
44 217 0.56
45 65 0.17
46 6 0.02
47 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (43 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
Found at i:41061230 original size:89 final size:87
Alignment explanation
Indices: 41061093--41061633 Score: 285
Period size: 89 Copynumber: 6.2 Consensus size: 87
41061083 TCGCATCTAG
* *
41061093 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGTAAGCAAGTCTTATC-CTCTTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAG-AAGCAAATCTTATCTC-CCTGAAGTTGC
41061157 AGT-GAGGCAGACTGAAG-ATGGAAAA
64 AGTGGA-GCAGACT-AAGTA-GGAAAA
* * *
41061182 TCTTATCTCCCTAAAGTTGTAGTGGAGCAG-GTTA-AAGCCGATAATCTTATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGAAG-C-A-AATCTTATCTCCCTGAAGTTG
*
41061245 CAGTGGAGCAGACTAAGTAGGAAAG
63 CAGTGGAGCAGACTAAGTAGGAAAA
* *
41061270 TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTT
1 TCTTATCTC-CCTGAAGTTGTAGTGGA-GCAGACT-AAGA-AGCAAATCTTATCTCCCTGAAGTT
* ** *
41061333 GCAGCGGAGCAGGTTAA--AGCCGATAA
62 GCAGTGGAGCAGACTAAGTAG--GAAAA
* * * ** * * ** *
41061359 TCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAA-AACCTTGGATCTTATCTCTCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGAAGC--AAATCTTATCTCCCTGAAGTTGC
* * * *** *
41061423 AG-AGAGCAGA-T-CGCA-TCTAG
64 AGTGGAGCAGACTAAGTAGGAAAA
* * * * *
41061443 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGCAAATCCTATCTTCATGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAG-AAGCAAATCTTATCTCCCTGAAGTTGCA
** * * *
41061508 GTGGAGTGGATTAAAACCTTGG---A
65 GTGGAGCAGACT--AA-GTAGGAAAA
** * * * * * * * * *
41061531 TCTTATCTTTCTGAAGTTGCAG-AGAGTAGA-T-CGCATCTAGTCTTATCTCCCTGAAGTTGAAG
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGAAGCAAATCTTATCTCCCTGAAGTTGCAG
* *
41061593 TGGAGCAGACTAAGTAGGCAAG
66 TGGAGCAGACTAAGTAGGAAAA
*
41061615 TCTTATCTCTCTGAAGTTG
1 TCTTATCTCCCTGAAGTTG
41061634 CAGCAGAGCA
Statistics
Matches: 348, Mismatches: 72, Indels: 69
0.71 0.15 0.14
Matches are distributed among these distances:
81 3 0.01
82 2 0.01
84 97 0.28
85 6 0.02
86 11 0.03
87 19 0.05
88 78 0.22
89 121 0.35
90 7 0.02
91 2 0.01
92 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (87 bp):
TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGAAGCAAATCTTATCTCCCTGAAGTTGCAG
TGGAGCAGACTAAGTAGGAAAA
Found at i:41061250 original size:133 final size:133
Alignment explanation
Indices: 41061093--41061385 Score: 478
Period size: 133 Copynumber: 2.2 Consensus size: 133
41061083 TCGCATCTAG
* * *
41061093 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCTTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGAAAGTCTTATCCTCCTGAAGTTGCA
* * *
41061158 GTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGGTTAAAGCCGA
66 GTGAGGCAGACTGAAGATAGAAAATCTTATCTCCCTAAAGTTGCAGCGGAGCAGGTTAAAGCCGA
41061223 TAA
131 TAA
*
41061226 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAGGAAAGTCTTATCCTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGAAAGTCTTATCCTCCTGAAGTTGCA
* * *
41061291 GTGAGGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGCGGAGCAGGTTAAAGCCGA
66 GTGAGGCAGACTGAAGATAGAAAATCTTATCTCCCTAAAGTTGCAGCGGAGCAGGTTAAAGCCGA
41061356 TAA
131 TAA
* *
41061359 TCCTATCTTCCTGAAGTTGCAGTGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
41061386 TGGATTAAAA
Statistics
Matches: 148, Mismatches: 12, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
133 148 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (133 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGAAAGTCTTATCCTCCTGAAGTTGCA
GTGAGGCAGACTGAAGATAGAAAATCTTATCTCCCTAAAGTTGCAGCGGAGCAGGTTAAAGCCGA
TAA
Found at i:41061407 original size:133 final size:132
Alignment explanation
Indices: 41061137--41061600 Score: 481
Period size: 128 Copynumber: 3.6 Consensus size: 132
41061127 AGTAAGCAAG
* * * * *
41061137 TCTTATCCTCTTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTAAAGTTGT
1 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGATTGAAGAT-GCAAATCTTATCTCCCTGAAGTTGC
* * ** * * *
41061202 AGTGGAGCAGGTTAAAGCCGATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT--AA-GTA
65 AGTGGAGCAGGTTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCTT
41061264 GGAAA
130 GG--A
41061269 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTG
1 -TCTTATCCTCCTGAAGTTGCAGTGAGGCAGATTGAAGAT-GCAAATCTTATCTCCCTGAAGTTG
*
41061334 CAGCGGAGCAGGTTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCT
64 CAGTGGAGCAGGTTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCT
41061399 TGGA
129 TGGA
* * * * *
41061403 TCTTAT-CTCTCTGAAGTTGCAGAGA-GCAGATCG--CAT-CTAGTCTTATCTCCCTGAAGTTGC
1 TCTTATCCTC-CTGAAGTTGCAGTGAGGCAGATTGAAGATGCAAATCTTATCTCCCTGAAGTTGC
* *
41061463 AGTGGAGCAGGCTAAGTAAG-C-A-AATCCTATCTTCATGAAGTTGCAGTGGAGTGGATTAAAAC
65 AGTGGAGCAGG-TTA--AAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAAC
41061525 CTTGGA
127 CTTGGA
* * * * * * * * *
41061531 TCTTATCTTTCTGAAGTTGCAGAGA-GTAGATCG--CAT-CTAGTCTTATCTCCCTGAAGTTGAA
1 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGATTGAAGATGCAAATCTTATCTCCCTGAAGTTGCA
41061592 GTGGAGCAG
66 GTGGAGCAG
41061601 ACTAAGTAGG
Statistics
Matches: 297, Mismatches: 26, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
128 141 0.47
129 4 0.01
130 3 0.01
131 3 0.01
132 10 0.03
133 130 0.44
134 1 0.00
135 2 0.01
136 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (132 bp):
TCTTATCCTCCTGAAGTTGCAGTGAGGCAGATTGAAGATGCAAATCTTATCTCCCTGAAGTTGCA
GTGGAGCAGGTTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCTTG
GA
Found at i:41061496 original size:128 final size:128
Alignment explanation
Indices: 41061315--41061636 Score: 490
Period size: 128 Copynumber: 2.5 Consensus size: 128
41061305 AGATAGCAAA
* *
41061315 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGG-TTA--AAGCCGATAATCCTATCTTCCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAG-C-A-AATCCTATCTTCCTGAAGTT
41061377 GCAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTA
63 GCAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTA
41061442 G
128 G
*
41061443 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGCAAATCCTATCTTCATGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGCAAATCCTATCTTCCTGAAGTTGCA
* *
41061508 GTGGAGTGGATTAAAACCTTGGATCTTATCTTTCTGAAGTTGCAGAGAGTAGATCGCATCTAG
66 GTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
* * * * *
41061571 TCTTATCTCCCTGAAGTTGAAGTGGAGCAGACTAAGTAGGCAAGTCTTATC-TCTCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGCAAATCCTATCTTC-CTGAAGTTGC
41061635 AG
65 AG
41061637 CAGAGCAGAT
Statistics
Matches: 179, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
127 2 0.01
128 170 0.95
129 3 0.02
130 1 0.01
131 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (128 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGCAAATCCTATCTTCCTGAAGTTGCA
GTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
Found at i:41063145 original size:16 final size:17
Alignment explanation
Indices: 41063124--41063156 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
41063114 TAAATCTATA
41063124 TACATA-TATATTTTTG
1 TACATATTATATTTTTG
41063140 TACATATTTATATTTTT
1 TACATA-TTATATTTTT
41063157 TTTCAACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (17 bp):
TACATATTATATTTTTG
Found at i:41063469 original size:15 final size:16
Alignment explanation
Indices: 41063451--41063487 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
41063441 ATCGTTAAAA
41063451 TTATTATC-ATTGTAT
1 TTATTATCTATTGTAT
41063466 TTATTA-CTATTGTAT
1 TTATTATCTATTGTAT
*
41063481 TTGTTAT
1 TTATTAT
41063488 TACGATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 1 0.05
15 18 0.95
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (16 bp):
TTATTATCTATTGTAT
Found at i:41075852 original size:20 final size:21
Alignment explanation
Indices: 41075821--41075859 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41075811 TTTATGGTTT
41075821 TAAATAATTTTTGGGTAAAAA
1 TAAATAATTTTTGGGTAAAAA
*
41075842 TAAAT-ATTTTTGGTTAAA
1 TAAATAATTTTTGGGTAAA
41075860 TTGAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (21 bp):
TAAATAATTTTTGGGTAAAAA
Found at i:41085653 original size:42 final size:43
Alignment explanation
Indices: 41085541--41085766 Score: 242
Period size: 43 Copynumber: 5.3 Consensus size: 43
41085531 TTTCTTACAT
* ** *
41085541 AAACGCCACTAAAGAACATGATCTTTAGCGGTACTTTTATCAG
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
* * *
41085584 AAACGTCGCTAAAAAACATGA-CATTTAGCGGTGCTTTT-TCAC
1 AAACGCCGCTAAAGAACATGATC-TTTAGCGGCGCTTTTATCAC
* ** * ** *
41085626 AGACGCCGCTAAAGGTCATGTTCTTTAG-TACGCTTTTAACAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
* *
41085668 AAACGCCGCTAAAGAACATGATCTTTAGCGGCACTTTTATCAT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
* * * *
41085711 AAATGCCGCTACAGAACATGATCTTTAGTGGCGTTTTTATCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
41085754 AAACGCCGCTAAA
1 AAACGCCGCTAAA
41085767 AGTACCGTTC
Statistics
Matches: 147, Mismatches: 32, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
41 6 0.04
42 51 0.35
43 90 0.61
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
Found at i:41085686 original size:84 final size:86
Alignment explanation
Indices: 41085541--41085767 Score: 244
Period size: 85 Copynumber: 2.7 Consensus size: 86
41085531 TTTCTTACAT
* * *** * *
41085541 AAACGCCACTAAAGAACATGATCTTTAGCGGTACTTTTATCAGAAACGTCGCTAAAAAACATGA-
1 AAACGCCGCTAAAGAACATGATCTTTAGTGACGCTTTTATCACAAACGCCGCTAAAAAACATGAT
**
41085605 CATTTAGCGGTGCTTTT-TCAC
66 C-TTTAGCGGCACTTTTATCAC
* ** * * *
41085626 AGACGCCGCTAAAGGTCATGTTCTTTAGT-ACGCTTTTAACACAAACGCCGCTAAAGAACATGAT
1 AAACGCCGCTAAAGAACATGATCTTTAGTGACGCTTTTATCACAAACGCCGCTAAAAAACATGAT
*
41085690 CTTTAGCGGCACTTTTATCAT
66 CTTTAGCGGCACTTTTATCAC
* * * *
41085711 AAATGCCGCTACAGAACATGATCTTTAGTGGCGTTTTTATCACAAACGCCGCTAAAA
1 AAACGCCGCTAAAGAACATGATCTTTAGTGACGCTTTTATCACAAACGCCGCTAAAA
41085768 GTACCGTTCT
Statistics
Matches: 113, Mismatches: 26, Indels: 5
0.78 0.18 0.03
Matches are distributed among these distances:
84 40 0.35
85 50 0.44
86 23 0.20
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (86 bp):
AAACGCCGCTAAAGAACATGATCTTTAGTGACGCTTTTATCACAAACGCCGCTAAAAAACATGAT
CTTTAGCGGCACTTTTATCAC
Found at i:41085854 original size:16 final size:16
Alignment explanation
Indices: 41085835--41085868 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41085825 AAATATTAAA
*
41085835 TATTAAAATCAAACAT
1 TATTAAAATCAAAAAT
*
41085851 TATTAATATCAAAAAT
1 TATTAAAATCAAAAAT
41085867 TA
1 TA
41085869 ATTAGTGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAAAATCAAAAAT
Found at i:41089098 original size:19 final size:19
Alignment explanation
Indices: 41089074--41089117 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
41089064 TTGTCTCGCA
41089074 ATCCGTGCGGCCTTAGGCG
1 ATCCGTGCGGCCTTAGGCG
*
41089093 ATCCGTGTGGCCTTAGGCG
1 ATCCGTGCGGCCTTAGGCG
41089112 ATCCGT
1 ATCCGT
41089118 TCGTCCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.11, C:0.30, G:0.34, T:0.25
Consensus pattern (19 bp):
ATCCGTGCGGCCTTAGGCG
Found at i:41092955 original size:24 final size:23
Alignment explanation
Indices: 41092928--41092972 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
41092918 AATTGGGTCG
41092928 TTTTGCTTTGCTAAAAATTATTTA
1 TTTT-CTTTGCTAAAAATTATTTA
*
41092952 TTTTTTTTGCTAAAAATTATT
1 TTTTCTTTGCTAAAAATTATT
41092973 AGTTAAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.58
Consensus pattern (23 bp):
TTTTCTTTGCTAAAAATTATTTA
Found at i:41093428 original size:36 final size:31
Alignment explanation
Indices: 41093381--41093449 Score: 75
Period size: 36 Copynumber: 2.1 Consensus size: 31
41093371 TTTATTTCTT
*
41093381 TATCAATGTTTTCTTTAAATATAATATTTAAATA
1 TATCAATGTTTTCATTAAATAT--T-TTTAAATA
*
41093415 TATCAAATGGTTTTGATTAAATATTTTTAAATA
1 TATC-AAT-GTTTTCATTAAATATTTTTAAATA
41093448 TA
1 TA
41093450 AAAGCATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
33 10 0.32
34 5 0.16
35 3 0.10
36 13 0.42
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (31 bp):
TATCAATGTTTTCATTAAATATTTTTAAATA
Found at i:41094431 original size:41 final size:41
Alignment explanation
Indices: 41094356--41094627 Score: 307
Period size: 41 Copynumber: 6.7 Consensus size: 41
41094346 TTTTTTGCGA
*
41094356 CGCTTTTTCAAAAACGCTACTAAAGCCCCGAGCATTAGCGG
1 CGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCATTAGCGG
* * * * *
41094397 CGATTTTTCAAAAATGCCATTAAATCCCCTAGCATTAGCGG
1 CGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCATTAGCGG
* * * *
41094438 CGCTTTTTCAAAAACGTCGCTAAATCCCCTAGCATTAGCGG
1 CGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCATTAGCGG
* *
41094479 TGCTTTTTTAAAAACG-CAGCTAAAGCCCCGAGCATTAGCGG
1 CGCTTTTTCAAAAACGCCA-CTAAAGCCCCGAGCATTAGCGG
* * * **
41094520 CACTTTTTTAAAAACGCCTCTAAAGCCCCGAGCA-T-GCAA
1 CGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCATTAGCGG
* * * * *
41094559 TGCTTTTTCAAAAATGCCGCTAAAACCTCGAGCATTAGCGG
1 CGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCATTAGCGG
*
41094600 CGCTTTTTCAAAAACGCCGCTAAAGCCC
1 CGCTTTTTCAAAAACGCCACTAAAGCCC
41094628 TAAAAGGTCA
Statistics
Matches: 193, Mismatches: 34, Indels: 8
0.82 0.14 0.03
Matches are distributed among these distances:
39 29 0.15
40 3 0.02
41 160 0.83
42 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (41 bp):
CGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCATTAGCGG
Found at i:41094606 original size:80 final size:82
Alignment explanation
Indices: 41094356--41094627 Score: 341
Period size: 82 Copynumber: 3.3 Consensus size: 82
41094346 TTTTTTGCGA
** * * **
41094356 CGCTTTTTCAAAAACGCTACTAAAGCCCCGAGCATTAGCGGCGATTTTTCAAAAATGCCATTAAA
1 CGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGTGCTTTTTCAAAAATGCCGCTAAA
* *
41094421 TCCCCTAGCATTAGCGG
66 ACCCCGAGCATTAGCGG
* * * * * *
41094438 CGCTTTTTCAAAAACGTCGCTAAATCCCCTAGCATTAGCGGTGCTTTTTTAAAAACGCAGCTAAA
1 CGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGTGCTTTTTCAAAAATGCCGCTAAA
*
41094503 GCCCCGAGCATTAGCGG
66 ACCCCGAGCATTAGCGG
* * * **
41094520 CACTTTTTTAAAAACGCCTCTAAAGCCCCGAGCA-T-GCAATGCTTTTTCAAAAATGCCGCTAAA
1 CGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGTGCTTTTTCAAAAATGCCGCTAAA
*
41094583 ACCTCGAGCATTAGCGG
66 ACCCCGAGCATTAGCGG
41094600 CGCTTTTTCAAAAACGCCGCTAAAGCCC
1 CGCTTTTTCAAAAACGCCGCTAAAGCCC
41094628 TAAAAGGTCA
Statistics
Matches: 160, Mismatches: 30, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
80 63 0.39
81 1 0.01
82 96 0.60
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (82 bp):
CGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGTGCTTTTTCAAAAATGCCGCTAAA
ACCCCGAGCATTAGCGG
Found at i:41094716 original size:39 final size:40
Alignment explanation
Indices: 41094662--41094786 Score: 121
Period size: 39 Copynumber: 3.1 Consensus size: 40
41094652 TGGGCTTAGG
* *
41094662 TTTTTTGCGGAGTTTTTCGAAAAACG-TCGCTAATGCTC-A
1 TTTTTAGCGGAGTTTTTCAAAAAACGCT-GCTAATGCTCGA
* *
41094701 TTTTTAGCGGCGTTTTTCAAAAAACGCTGTTAATGCTCGA
1 TTTTTAGCGGAGTTTTTCAAAAAACGCTGCTAATGCTCGA
* ** * * *
41094741 TCTTTAGCGGA-AATTTCTATAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGAGTTTTTC-AAAAAACGCTGCTAATGCTCGA
41094781 TTTTTA
1 TTTTTA
41094787 CTGTCGTTTT
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
39 36 0.51
40 34 0.49
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (40 bp):
TTTTTAGCGGAGTTTTTCAAAAAACGCTGCTAATGCTCGA
Found at i:41105838 original size:52 final size:52
Alignment explanation
Indices: 41105781--41105884 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
41105771 ACTTTAATAG
*
41105781 TTAAAATAGGGTGACAAAGATTGAGGTGCAAATCAAATTGCGCTCTTGAGAC
1 TTAAAATAGGGTGACAAAGATTGAGGTGCAAATCAAATTACGCTCTTGAGAC
* *
41105833 TTAAAATAGGGTGACAAAGATTGAGGTGCAGATCAAATTACTCTCTTGAGAC
1 TTAAAATAGGGTGACAAAGATTGAGGTGCAAATCAAATTACGCTCTTGAGAC
41105885 GATACTCGCT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (52 bp):
TTAAAATAGGGTGACAAAGATTGAGGTGCAAATCAAATTACGCTCTTGAGAC
Found at i:41106202 original size:30 final size:27
Alignment explanation
Indices: 41106168--41106232 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
41106158 TAAAATACTC
41106168 TAATATATAATTAAATTAAAATTAATTAAT
1 TAATATATAATTAAA-TAAAATTAA--AAT
* * *
41106198 TAATAGATAATTATATCAAATTAAAAT
1 TAATATATAATTAAATAAAATTAAAAT
41106225 TAATATAT
1 TAATATAT
41106233 CATATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 10 0.32
29 8 0.26
30 13 0.42
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
TAATATATAATTAAATAAAATTAAAAT
Found at i:41116520 original size:36 final size:36
Alignment explanation
Indices: 41116473--41116546 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
41116463 GGAGGAGCGC
* * *
41116473 ATCAGTCAGAATAGATCTGAAAGGCTGCTCAACTGA
1 ATCAGTCAGAATAGACCCGAAAGGCTACTCAACTGA
* *
41116509 ATCAGTCAGAATTGACCCGAAAGGCTACTTAACTGA
1 ATCAGTCAGAATAGACCCGAAAGGCTACTCAACTGA
41116545 AT
1 AT
41116547 AGAGTTTACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (36 bp):
ATCAGTCAGAATAGACCCGAAAGGCTACTCAACTGA
Found at i:41117569 original size:18 final size:17
Alignment explanation
Indices: 41117526--41117570 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
41117516 AATTTTTTTC
* *
41117526 TTTCACTTTATTATTAT
1 TTTCTCTTTATTATTAG
41117543 TTTCTTCTTTATTATTTAG
1 TTTC-TCTTTATTA-TTAG
41117562 TTTCTCTTT
1 TTTCTCTTT
41117571 TATTTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 13 0.54
19 7 0.29
ACGTcount: A:0.16, C:0.13, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTCTCTTTATTATTAG
Found at i:41117574 original size:19 final size:18
Alignment explanation
Indices: 41117531--41117570 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
41117521 TTTTCTTTCA
*
41117531 CTTTATTATTATTTTCTT
1 CTTTATTATTAGTTTCTT
41117549 CTTTATTATTTAGTTTC-T
1 CTTTATTA-TTAGTTTCTT
41117567 CTTT
1 CTTT
41117571 TATTTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.15, C:0.12, G:0.03, T:0.70
Consensus pattern (18 bp):
CTTTATTATTAGTTTCTT
Found at i:41125540 original size:11 final size:11
Alignment explanation
Indices: 41125526--41125551 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41125516 GAAATTAAAC
41125526 AAATAAACAAA
1 AAATAAACAAA
41125537 AAATAAACAAA
1 AAATAAACAAA
41125548 AAAT
1 AAAT
41125552 TAATATCATA
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:0.81, C:0.08, G:0.00, T:0.12
Consensus pattern (11 bp):
AAATAAACAAA
Found at i:41149009 original size:28 final size:26
Alignment explanation
Indices: 41148962--41149022 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
41148952 AGAGGCATTA
41148962 CGGTCA-TTTACCTTACAGGGGTATTT
1 CGGTCATTTTACCTTACA-GGGTATTT
*
41148988 TGGTCATTTTACCCTT-CGAGGGTATTT
1 CGGTCATTTTA-CCTTAC-AGGGTATTT
41149015 CGGTCATT
1 CGGTCATT
41149023 CAACAACCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 5 0.17
27 20 0.67
28 5 0.17
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (26 bp):
CGGTCATTTTACCTTACAGGGTATTT
Found at i:41157196 original size:22 final size:22
Alignment explanation
Indices: 41157168--41157261 Score: 109
Period size: 22 Copynumber: 4.3 Consensus size: 22
41157158 ATACCACAGT
* *
41157168 AGTAGGCACCGAAGTGCTAAAC
1 AGTAGGCACCGAAGTGCGAATC
* *
41157190 AGTAGGCATCAAAGTGCGAATC
1 AGTAGGCACCGAAGTGCGAATC
* *
41157212 AGTAGGCACC-ATAGTGTGAAGC
1 AGTAGGCACCGA-AGTGCGAATC
*
41157234 AATAGGCACCGAAGTGCGAATC
1 AGTAGGCACCGAAGTGCGAATC
41157256 AGTAGG
1 AGTAGG
41157262 TACCACAGTG
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
21 1 0.02
22 57 0.97
23 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.30, T:0.16
Consensus pattern (22 bp):
AGTAGGCACCGAAGTGCGAATC
Found at i:41157271 original size:22 final size:21
Alignment explanation
Indices: 41157168--41157277 Score: 103
Period size: 22 Copynumber: 5.0 Consensus size: 21
41157158 ATACCACAGT
* *
41157168 AGTAGGCACCGAAGTGCTAAAC
1 AGTAGGCACC-AAGTGCGAATC
*
41157190 AGTAGGCATCAAAGTGCGAATC
1 AGTAGGCA-CCAAGTGCGAATC
* *
41157212 AGTAGGCACCATAGTGTGAAGC
1 AGTAGGCACCA-AGTGCGAATC
*
41157234 AATAGGCACCGAAGTGCGAATC
1 AGTAGGCACC-AAGTGCGAATC
* *
41157256 AGTAGGTACCACAGTGCAAATC
1 AGTAGGCACCA-AGTGCGAATC
41157278 CTGTACAAGC
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
21 3 0.04
22 67 0.93
23 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.16
Consensus pattern (21 bp):
AGTAGGCACCAAGTGCGAATC
Found at i:41162812 original size:10 final size:10
Alignment explanation
Indices: 41162797--41162845 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
41162787 ATTAACATGT
41162797 TTAATTTTAA
1 TTAATTTTAA
41162807 TTAATTTTATAA
1 TTAA-TTT-TAA
* *
41162819 TAAATTTTGA
1 TTAATTTTAA
41162829 TTAATTTTAA
1 TTAATTTTAA
41162839 TT-ATTTT
1 TTAATTTT
41162846 CGACAGATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 5 0.15
10 16 0.48
11 6 0.18
12 6 0.18
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
TTAATTTTAA
Found at i:41165109 original size:17 final size:18
Alignment explanation
Indices: 41165087--41165122 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
41165077 ACAATGTCAT
*
41165087 GTGCTT-AACCATTTTTA
1 GTGCTTAAACCAGTTTTA
41165104 GTGCTTAAACCAGTTTTA
1 GTGCTTAAACCAGTTTTA
41165122 G
1 G
41165123 GTGCCCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (18 bp):
GTGCTTAAACCAGTTTTA
Found at i:41173541 original size:16 final size:16
Alignment explanation
Indices: 41173520--41173550 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41173510 TTCACTATTA
*
41173520 TGTCTTTTTTATTTTC
1 TGTCTTTTATATTTTC
41173536 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
41173551 GCATGCATGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.74
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:41175197 original size:37 final size:39
Alignment explanation
Indices: 41175147--41175224 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 39
41175137 TTTAATAGTT
41175147 TAGTATTAAATTAAATCAA-ATTAAA-T-AGTTATCTTAA
1 TAGTATTAAATTAAATCAATATTAAAGTGA-TTATCTTAA
** * *
41175184 TAGTATTTTATTAATTTAATATTAAAGTGATTATCTTAA
1 TAGTATTAAATTAAATCAATATTAAAGTGATTATCTTAA
41175223 TA
1 TA
41175225 TTAAATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
37 15 0.44
38 6 0.18
39 12 0.35
40 1 0.03
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (39 bp):
TAGTATTAAATTAAATCAATATTAAAGTGATTATCTTAA
Found at i:41175300 original size:16 final size:17
Alignment explanation
Indices: 41175282--41175338 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
41175272 AATAAGATTT
41175282 AATATTAAATTAATAT-
1 AATATTAAATTAATATA
* * *
41175298 AATATT-TATCAAGATA
1 AATATTAAATTAATATA
*
41175314 AATATTATATTAAT-TA
1 AATATTAAATTAATATA
41175330 AATATTAAA
1 AATATTAAA
41175339 GTGATTAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 6 0.18
16 22 0.67
17 5 0.15
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
AATATTAAATTAATATA
Found at i:41194218 original size:20 final size:21
Alignment explanation
Indices: 41194178--41194218 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
41194168 TTGCCCGAGA
*
41194178 TATCGTGATATCTTCCCTTCGG
1 TATCGTGATATC-TACCTTCGG
41194200 TATCGTGATATC-ACCTTCG
1 TATCGTGATATCTACCTTCG
41194219 TCAGTGGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.39
Consensus pattern (21 bp):
TATCGTGATATCTACCTTCGG
Found at i:41196047 original size:16 final size:16
Alignment explanation
Indices: 41196026--41196059 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
41196016 GAAAGAAGCA
41196026 ATAACATTATATTGTG
1 ATAACATTATATTGTG
*
41196042 ATAACATTGTATTGTG
1 ATAACATTATATTGTG
41196058 AT
1 AT
41196060 TATGATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (16 bp):
ATAACATTATATTGTG
Found at i:41198110 original size:39 final size:37
Alignment explanation
Indices: 41198040--41198112 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 37
41198030 ATTGATTTAA
41198040 TATTAAATTAAATTAAATACTTATCTTAATATTATTT
1 TATTAAATTAAATTAAATACTTATCTTAATATTATTT
*
41198077 TATTAATTTAATATTAAAGTGAC-TATCTTAATATTA
1 TATTAAATTAA-ATTAAA-T-ACTTATCTTAATATTA
41198113 AATTTAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 10 0.31
38 6 0.19
39 14 0.44
40 2 0.06
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.49
Consensus pattern (37 bp):
TATTAAATTAAATTAAATACTTATCTTAATATTATTT
Found at i:41211254 original size:11 final size:12
Alignment explanation
Indices: 41211228--41211265 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
41211218 GAAATTAAGG
*
41211228 TTTTAGCGGCGT
1 TTTTAGTGGCGT
41211240 TTTTAGTGGCGT
1 TTTTAGTGGCGT
41211252 TTTTAGTGGCGT
1 TTTTAGTGGCGT
41211264 TT
1 TT
41211266 AGATGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.08, C:0.11, G:0.32, T:0.50
Consensus pattern (12 bp):
TTTTAGTGGCGT
Found at i:41211455 original size:40 final size:41
Alignment explanation
Indices: 41211309--41211467 Score: 203
Period size: 41 Copynumber: 3.9 Consensus size: 41
41211299 GGCGCTAACG
* * * *
41211309 GAAAAATGCCGCAATAGGTAAAGTAGTAGCGGCGTTTATGA
1 GAAAAACGCCGCAAAAGGTCAAGCAGTAGCGGCGTTTATGA
*
41211350 GAAAAACGCCGCAAAAGGTCAAGCAGTAGTGGCGTTTATGA
1 GAAAAACGCCGCAAAAGGTCAAGCAGTAGCGGCGTTTATGA
* * * *
41211391 GGAAAACGCCGCAAAAAGTCAAGCAGTAGCAGCATTTATGA
1 GAAAAACGCCGCAAAAGGTCAAGCAGTAGCGGCGTTTATGA
* * *
41211432 GAAAAATGCTGCAAAAGGT-AAGCAATAGCGGCGTTT
1 GAAAAACGCCGCAAAAGGTCAAGCAGTAGCGGCGTTT
41211468 TAATCATTTT
Statistics
Matches: 101, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 14 0.14
41 87 0.86
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.18
Consensus pattern (41 bp):
GAAAAACGCCGCAAAAGGTCAAGCAGTAGCGGCGTTTATGA
Found at i:41211589 original size:21 final size:22
Alignment explanation
Indices: 41211565--41211608 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
41211555 CCCCTAAAAC
*
41211565 TTTCCCCGAATCCCTTA-ATTT
1 TTTCCCCAAATCCCTTAGATTT
41211586 TTTCCCCAAATCCCTTAGATTT
1 TTTCCCCAAATCCCTTAGATTT
41211608 T
1 T
41211609 CCCGACCGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.20, C:0.32, G:0.05, T:0.43
Consensus pattern (22 bp):
TTTCCCCAAATCCCTTAGATTT
Found at i:41211682 original size:25 final size:25
Alignment explanation
Indices: 41211662--41211747 Score: 102
Period size: 25 Copynumber: 3.4 Consensus size: 25
41211652 ATCGCCTTTG
41211662 ACACTCCTCTGTCACATCGCCGTCA
1 ACACTCCTCTGTCACATCGCCGTCA
* *
41211687 ACACTCCTCTGTCGCATTGCCGTCA
1 ACACTCCTCTGTCACATCGCCGTCA
* * * *
41211712 ACACTCCTTTGCCGCAT-GACCGTCG
1 ACACTCCTCTGTCACATCG-CCGTCA
41211737 ACACTCCTCTG
1 ACACTCCTCTG
41211748 CTGCATCGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
24 1 0.02
25 53 0.98
ACGTcount: A:0.17, C:0.42, G:0.15, T:0.26
Consensus pattern (25 bp):
ACACTCCTCTGTCACATCGCCGTCA
Found at i:41213824 original size:8 final size:8
Alignment explanation
Indices: 41213811--41213838 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
41213801 ATAACTTACA
41213811 TAAACATT
1 TAAACATT
41213819 TAAACATT
1 TAAACATT
41213827 TAAACATT
1 TAAACATT
41213835 TAAA
1 TAAA
41213839 GTTAATGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.36
Consensus pattern (8 bp):
TAAACATT
Found at i:41213881 original size:51 final size:51
Alignment explanation
Indices: 41213779--41213881 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
41213769 TTAACTCTTT
* *
41213779 ACATTTAAAGTTAATGATTATCATAACTTACATAAACATTTAAACATTTAA
1 ACATTTAAAGTTAATGATTATCAGAACTTACATAAACATTTAAACAATTAA
* *
41213830 ACATTTAAAGTTAATGATTATCAGAAGTTACATAAACATTTAAAGAATTAA
1 ACATTTAAAGTTAATGATTATCAGAACTTACATAAACATTTAAACAATTAA
41213881 A
1 A
41213882 AAATGTAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.35
Consensus pattern (51 bp):
ACATTTAAAGTTAATGATTATCAGAACTTACATAAACATTTAAACAATTAA
Found at i:41226779 original size:40 final size:40
Alignment explanation
Indices: 41226695--41226878 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
41226685 TTGAATGTTG
* * * *
41226695 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
41226734 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
41226775 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
41226815 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
41226855 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
41226879 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:41226832 original size:80 final size:81
Alignment explanation
Indices: 41226695--41226875 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
41226685 TTGAATGTTG
* * *
41226695 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
41226759 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
41226775 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
41226836 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
41226855 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
41226876 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:41226899 original size:39 final size:39
Alignment explanation
Indices: 41226763--41226925 Score: 141
Period size: 40 Copynumber: 4.1 Consensus size: 39
41226753 GGTATTTGTG
* * * **
41226763 CGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTG
1 CGAGTTATAAAATCCGGGTTAAGTCCCGAAGG-CATTGAA
* * **
41226803 CGAGATACT-AATTCCGGGTTAAGTCCCGAAGGCATTCGTG
1 CGAGTTA-TAAAATCCGGGTTAAGTCCCGAAGGCATT-GAA
*
41226843 CGAGTTTTAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
1 CGAGTTATAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
* * * *
41226882 TGAGTTAATATAA-CCGGGCTATGTCCCGAAGGCACTTGAA
1 CGAGTT-ATAAAATCCGGGTTAAGTCCCGAAGGCA-TTGAA
41226922 CGAG
1 CGAG
41226926 GAGCTAAATC
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
39 29 0.28
40 75 0.71
41 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (39 bp):
CGAGTTATAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
Found at i:41234875 original size:9 final size:9
Alignment explanation
Indices: 41234861--41234887 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
41234851 AGCTACAGTG
41234861 TTAACTAAC
1 TTAACTAAC
41234870 TTAACTAAC
1 TTAACTAAC
41234879 TTAACTAAC
1 TTAACTAAC
41234888 ATCAAGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (9 bp):
TTAACTAAC
Found at i:41238752 original size:12 final size:12
Alignment explanation
Indices: 41238735--41238759 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41238725 GGTGTTCATT
41238735 CGGTTAACCGAC
1 CGGTTAACCGAC
41238747 CGGTTAACCGAC
1 CGGTTAACCGAC
41238759 C
1 C
41238760 CGAAATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:41238883 original size:9 final size:9
Alignment explanation
Indices: 41238871--41238910 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
41238861 CTGTTAACTG
41238871 AATTAACCA
1 AATTAACCA
41238880 AATTAACCA
1 AATTAACCA
* *
41238889 AATTACCCG
1 AATTAACCA
*
41238898 AATTAACCG
1 AATTAACCA
41238907 AATT
1 AATT
41238911 GAATCACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.47, C:0.23, G:0.05, T:0.25
Consensus pattern (9 bp):
AATTAACCA
Found at i:41238885 original size:18 final size:18
Alignment explanation
Indices: 41238864--41238910 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
41238854 ATTCTGTCTG
*
41238864 TTAACTGAATTAACCAAA
1 TTAACCGAATTAACCAAA
* * *
41238882 TTAACCAAATTACCCGAA
1 TTAACCGAATTAACCAAA
41238900 TTAACCGAATT
1 TTAACCGAATT
41238911 GAATCACTAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.28
Consensus pattern (18 bp):
TTAACCGAATTAACCAAA
Found at i:41242113 original size:13 final size:13
Alignment explanation
Indices: 41242095--41242119 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41242085 ATATGATTAT
41242095 GTTTGAAAAACGG
1 GTTTGAAAAACGG
41242108 GTTTGAAAAACG
1 GTTTGAAAAACG
41242120 CAACGAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (13 bp):
GTTTGAAAAACGG
Found at i:41250267 original size:72 final size:68
Alignment explanation
Indices: 41250183--41250319 Score: 193
Period size: 72 Copynumber: 2.0 Consensus size: 68
41250173 TGATTTAACT
* *
41250183 TAATCACTTTAATATTAAATTAATATAATATTTATCTACAAGAGAAACATTAAATTAAATTTAAT
1 TAATCACTTTAATATTAAATTAATAAAATA-CTAT-TA-AA-AGAAACATTAAATTAAATTTAAT
41250248 ATTAGGA
62 ATTAGGA
* **
41250255 TAATCACTTTAATATTAAATTAATAAAATACTATTAAAATAAGTATTAAATTAAATTTAATATTA
1 TAATCACTTTAATATTAAATTAATAAAATACTATTAAAAGAAACATTAAATTAAATTTAATATTA
41250320 AACTATTAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
68 24 0.40
69 2 0.03
70 2 0.03
71 3 0.05
72 29 0.48
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (68 bp):
TAATCACTTTAATATTAAATTAATAAAATACTATTAAAAGAAACATTAAATTAAATTTAATATTA
GGA
Found at i:41250277 original size:11 final size:11
Alignment explanation
Indices: 41250263--41250338 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
41250253 GATAATCACT
41250263 TTAATATTAAA
1 TTAATATTAAA
41250274 TTAATA--AAA
1 TTAATATTAAA
*
41250283 -TACTATTAAA
1 TTAATATTAAA
*
41250293 ATAAGTATTAAA
1 TTAA-TATTAAA
41250305 TTAA-ATTTAATA
1 TTAATA-TTAA-A
41250317 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
41250330 ATAATATTA
1 TTAATATTA
41250339 TTTTTCGAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 4 0.08
11 17 0.33
12 15 0.29
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:41250278 original size:20 final size:18
Alignment explanation
Indices: 41250231--41250337 Score: 60
Period size: 19 Copynumber: 5.8 Consensus size: 18
41250221 CAAGAGAAAC
41250231 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
*
41250248 ATTAGGA-TAATCACTTTAAT
1 ATTA-AATTAAT-A-TTTAAT
** *
41250268 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
*
41250287 ATTAAAATAAGTA-TTAA-
1 ATTAAATTAA-TATTTAAT
*
41250304 ATTAAATTTAATATTAAACT
1 ATTAAA-TTAATATTTAA-T
*
41250324 ATTAAAATAATATT
1 ATTAAATTAATATT
41250338 ATTTTTCGAA
Statistics
Matches: 68, Mismatches: 12, Indels: 18
0.69 0.12 0.18
Matches are distributed among these distances:
17 15 0.22
18 9 0.13
19 22 0.32
20 22 0.32
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:41250325 original size:37 final size:36
Alignment explanation
Indices: 41250263--41250338 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
41250253 GATAATCACT
41250263 TTAATATTAAATTAATAAAATACTATTAAAATAAGTA
1 TTAATATTAAATTAATAAAATACTATTAAAATAA-TA
*
41250300 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAATA
1 TTAATATTAAA-TTAATA-AAATACTATTAAAATAATA
41250336 TTA
1 TTA
41250339 TTTTTCGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 11 0.31
37 23 0.64
38 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAATA
Found at i:41253856 original size:13 final size:13
Alignment explanation
Indices: 41253838--41253864 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41253828 TAATTGAGTT
41253838 AGTGTCACTCATC
1 AGTGTCACTCATC
41253851 AGTGTCACTCATC
1 AGTGTCACTCATC
41253864 A
1 A
41253865 ACCCGATCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.30
Consensus pattern (13 bp):
AGTGTCACTCATC
Found at i:41259919 original size:12 final size:11
Alignment explanation
Indices: 41259894--41259931 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
41259884 GAACATGATG
41259894 AATTTTA-ATT
1 AATTTTATATT
41259904 AATTTTATAGTT
1 AATTTTATA-TT
41259916 AATTTT-TATT
1 AATTTTATATT
41259926 AATTTT
1 AATTTT
41259932 GACTATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 3 0.12
12 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
AATTTTATATT
Found at i:41267393 original size:22 final size:21
Alignment explanation
Indices: 41267368--41267411 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
41267358 TGATAAACTT
41267368 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
41267390 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
41267411 T
1 T
41267412 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:41272913 original size:17 final size:17
Alignment explanation
Indices: 41272883--41272918 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41272873 AGTGTGATAT
41272883 AACTCCAACAAGCTTCC
1 AACTCCAACAAGCTTCC
* *
41272900 AACTCGAACGAGCTTCC
1 AACTCCAACAAGCTTCC
41272917 AA
1 AA
41272919 ATCACTATAA
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:0.36, C:0.36, G:0.11, T:0.17
Consensus pattern (17 bp):
AACTCCAACAAGCTTCC
Found at i:41273427 original size:25 final size:25
Alignment explanation
Indices: 41273397--41273466 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
41273387 CTGTAATCGA
*
41273397 TAAGCTCCTTCAAGCTGAATAACGG
1 TAAGCTCATTCAAGCTGAATAACGG
* * * *
41273422 TAAGCTCATTCGAGCTCAGTATCGG
1 TAAGCTCATTCAAGCTGAATAACGG
41273447 TAAGCTCATAT-AAGCTGAAT
1 TAAGCTCAT-TCAAGCTGAAT
41273467 TGGTAACCCT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
25 35 0.97
26 1 0.03
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (25 bp):
TAAGCTCATTCAAGCTGAATAACGG
Found at i:41276692 original size:14 final size:15
Alignment explanation
Indices: 41276670--41276746 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
41276660 CAATCAAACA
41276670 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
41276684 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
41276699 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
41276719 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
41276733 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
41276747 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:41276711 original size:20 final size:20
Alignment explanation
Indices: 41276686--41276725 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41276676 AATATTTTCC
*
41276686 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
41276706 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
41276726 TCATTTTACG
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:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:41276731 original size:34 final size:35
Alignment explanation
Indices: 41276674--41276740 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
41276664 CAAACACCAG
*
41276674 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
41276709 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
41276741 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:41277196 original size:12 final size:12
Alignment explanation
Indices: 41277179--41277205 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41277169 ATATTAAGCT
41277179 AATGATTCCTAA
1 AATGATTCCTAA
41277191 AATGATTCCTAA
1 AATGATTCCTAA
41277203 AAT
1 AAT
41277206 TAAGATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (12 bp):
AATGATTCCTAA
Found at i:41277539 original size:44 final size:44
Alignment explanation
Indices: 41277476--41277581 Score: 176
Period size: 44 Copynumber: 2.4 Consensus size: 44
41277466 TGTAGGCTTT
* * *
41277476 CAAAAAATGCTCAAATCACCTAAACTCAAAATACTGAGTCATCC
1 CAAAACATGCTCATATCACCTAAACTCAAAATACCGAGTCATCC
41277520 CAAAACATGCTCATATCACCTAAACTCAAAATACCGAGTCATCC
1 CAAAACATGCTCATATCACCTAAACTCAAAATACCGAGTCATCC
41277564 CAAAACATGCTCAATATC
1 CAAAACATGCTC-ATATC
41277582 TCTACTTCTT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
44 53 0.91
45 5 0.09
ACGTcount: A:0.43, C:0.29, G:0.07, T:0.21
Consensus pattern (44 bp):
CAAAACATGCTCATATCACCTAAACTCAAAATACCGAGTCATCC
Found at i:41277869 original size:14 final size:14
Alignment explanation
Indices: 41277852--41277895 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
41277842 GGTGCAGGAC
*
41277852 TGGAGGTGGACCGG
1 TGGAGGTGGATCGG
* *
41277866 TGGAAGTGGATCAG
1 TGGAGGTGGATCGG
41277880 TGGAGGTGGATCGG
1 TGGAGGTGGATCGG
41277894 TG
1 TG
41277896 CTCGGTGGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.18, C:0.09, G:0.52, T:0.20
Consensus pattern (14 bp):
TGGAGGTGGATCGG
Found at i:41278191 original size:14 final size:14
Alignment explanation
Indices: 41278172--41278204 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
41278162 GAGGTAGACC
41278172 GGAGGTGGACCGGT
1 GGAGGTGGACCGGT
*
41278186 GGAGGTGGATCGGT
1 GGAGGTGGACCGGT
41278200 GGAGG
1 GGAGG
41278205 ACGGAGGTAA
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
Done.