Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold480
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: 956445
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 6 of 7
Found at i:804881 original size:51 final size:51
Alignment explanation
Indices: 804815--805172 Score: 289
Period size: 51 Copynumber: 6.9 Consensus size: 51
804805 TTAAGTTTCT
* *
804815 CAATTTTTCATAATCGGGGATACTCCAACCCCGGTTATATTTCTAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAC
* * * * * *
804866 TAATTTTTCACAATCGGGGATACTCCAACTCTGATTTTATTTTTGAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAC
* *
804917 CAATTTTCCACAATCGGGGATACTCCAACCACGGTTTTATTT-TCAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACAC
* * * * *
804968 CAA-TTTTCTATAATTGGGGATACTCCAACTCTGATTTTATTT-TCAAAACAC
1 CAATTTTTC-ACAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACAC
* * * * *
805019 CAATTTTTCACAATCGGGGATACTCCAACCTC-G-TTAATCATC-AGGGATACTC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTAT-TTCTA---AAACAC
** * * * *
805071 CAACCCTGTCAC-TTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAATAT
1 CAA-TTTTTCACAAT-C--GGGGATACTCCAACCCCGGTTTTATTTCTAAAACAC
** * * *
805125 TGATTTCTCACAATCGGGGATACTCCAACCCCAGCTTTATTTCTAAAA
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAA
805173 TATAGATTTC
Statistics
Matches: 240, Mismatches: 51, Indels: 32
0.74 0.16 0.10
Matches are distributed among these distances:
49 5 0.02
50 6 0.03
51 176 0.73
52 13 0.05
53 12 0.05
54 4 0.02
55 16 0.07
56 3 0.01
57 5 0.02
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.33
Consensus pattern (51 bp):
CAATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAC
Found at i:804987 original size:102 final size:102
Alignment explanation
Indices: 804815--805048 Score: 355
Period size: 102 Copynumber: 2.3 Consensus size: 102
804805 TTAAGTTTCT
* * *
804815 CAATTTTTCATAATCGGGGATACTCCAACCCCGGTTATATTTCTAAAACACTAATTTTTCACAAT
1 CAATTTTTCACAATCGGGGATACTCCAACCACGGTTATATTTCTAAAACACCAATTTTTCACAAT
**
804880 CGGGGATACTCCAACTCTGATTTTATTTTTGAAACAC
66 CGGGGATACTCCAACTCTGATTTTATTTTCAAAACAC
* * *
804917 CAATTTTCCACAATCGGGGATACTCCAACCACGGTTTTATTT-TCAAAACACCAA-TTTTCTATA
1 CAATTTTTCACAATCGGGGATACTCCAACCACGGTTATATTTCT-AAAACACCAATTTTTC-ACA
*
804980 ATTGGGGATACTCCAACTCTGATTTTATTTTCAAAACAC
64 ATCGGGGATACTCCAACTCTGATTTTATTTTCAAAACAC
805019 CAATTTTTCACAATCGGGGATACTCCAACC
1 CAATTTTTCACAATCGGGGATACTCCAACC
805049 TCGTTAATCA
Statistics
Matches: 120, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
101 6 0.05
102 114 0.95
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (102 bp):
CAATTTTTCACAATCGGGGATACTCCAACCACGGTTATATTTCTAAAACACCAATTTTTCACAAT
CGGGGATACTCCAACTCTGATTTTATTTTCAAAACAC
Found at i:805164 original size:157 final size:158
Alignment explanation
Indices: 804932--805234 Score: 341
Period size: 157 Copynumber: 1.9 Consensus size: 158
804922 TTCCACAATC
* *
804932 GGGGATACTCCAACCACGGTTTTATTTTCAAAACACCAATTTTCTATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCACGGTTTTATTTTCAAAACACCAATTTTCTACAATCGGGGATACTCCAAC
* * * * * *
804997 TCTGATTTTATTT-TCAAAACACCA-ATTTTTCACAATCGGGGATACTCCAACCTCGTTA-ATCA
66 CCAGACTTTATTTCT-AAAACA-CAGATTTCTCACAATCAGAGATACTCCAACCTCGTTATATC-
805059 TCA-GGGATACTCCAACCCTGTCACTTCCGA
128 TCAGGGGATACTCCAACCCTGTCACTTCCGA
* * ***
805089 GGGGATACTCCAACCCCGGTTTTA-TTTCTAAAATATTGA-TTTCTCACAATCGGGGATACTCCA
1 GGGGATACTCCAACCACGGTTTTATTTTC-AAAACACCAATTTTCT-ACAATCGGGGATACTCCA
* * * *
805152 ACCCCAG-CTTTATTTCTAAAATATAGATTTCTCACAATCAGAGATACTTCAACCTCGTTATTTC
64 A-CCCAGACTTTATTTCTAAAACACAGATTTCTCACAATCAGAGATACTCCAACCTCGTTATATC
*
805216 TGAGGGGATACTCCAACCC
128 TCAGGGGATACTCCAACCC
805235 CGGCTTTATT
Statistics
Matches: 121, Mismatches: 18, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
156 10 0.08
157 90 0.74
158 21 0.17
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (158 bp):
GGGGATACTCCAACCACGGTTTTATTTTCAAAACACCAATTTTCTACAATCGGGGATACTCCAAC
CCAGACTTTATTTCTAAAACACAGATTTCTCACAATCAGAGATACTCCAACCTCGTTATATCTCA
GGGGATACTCCAACCCTGTCACTTCCGA
Found at i:805173 original size:51 final size:51
Alignment explanation
Indices: 805089--805205 Score: 180
Period size: 51 Copynumber: 2.3 Consensus size: 51
805079 TCACTTCCGA
* * *
805089 GGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTGATTTCTCACAATC
1 GGGGATACTCCAACCCCAGCTTTATTTCTAAAATATAGATTTCTCACAATC
805140 GGGGATACTCCAACCCCAGCTTTATTTCTAAAATATAGATTTCTCACAATC
1 GGGGATACTCCAACCCCAGCTTTATTTCTAAAATATAGATTTCTCACAATC
* * *
805191 AGAGATACTTCAACC
1 GGGGATACTCCAACC
805206 TCGTTATTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCAGCTTTATTTCTAAAATATAGATTTCTCACAATC
Found at i:805225 original size:79 final size:79
Alignment explanation
Indices: 805140--805312 Score: 258
Period size: 79 Copynumber: 2.2 Consensus size: 79
805130 TCTCACAATC
* *
805140 GGGGATACTCCAACCCCAGCTTTATTTCTAAAATATAGATTTCTCACAATCAGAGATACTTCAAC
1 GGGGATACTCCAACCCCAGCTTTATTCCTAAAATATAGATTTCTCACAATCAGAGATACTCCAAC
*
805205 CTCGTTA-TTTCTGA
66 CCCGTTATTTTC-GA
* * * *
805219 GGGGATACTCCAACCCCGGCTTTATTCCTAAAATATTGATTTCTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCAGCTTTATTCCTAAAATATAGATTTCTCACAATCAGAGATACTCCAAC
*
805284 CCCGTTATTTTCGC
66 CCCGTTATTTTCGA
805298 GGGGATACTCCAACC
1 GGGGATACTCCAACC
805313 TCGTTATTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
79 81 0.95
80 4 0.05
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (79 bp):
GGGGATACTCCAACCCCAGCTTTATTCCTAAAATATAGATTTCTCACAATCAGAGATACTCCAAC
CCCGTTATTTTCGA
Found at i:805309 original size:28 final size:28
Alignment explanation
Indices: 805269--805343 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
805259 TTCTCACAAT
805269 CGGGGATACTCCAACCCCGTTATTTTCG
1 CGGGGATACTCCAACCCCGTTATTTTCG
* *
805297 CGGGGATACTCCAACCTCGTTATTTTTG
1 CGGGGATACTCCAACCCCGTTATTTTCG
*
805325 AGGGGATACTCCAACCCCG
1 CGGGGATACTCCAACCCCG
805344 ATTTTCTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.27
Consensus pattern (28 bp):
CGGGGATACTCCAACCCCGTTATTTTCG
Found at i:805382 original size:79 final size:79
Alignment explanation
Indices: 805299--805467 Score: 241
Period size: 79 Copynumber: 2.1 Consensus size: 79
805289 TATTTTCGCG
*** * *
805299 GGGATACTCCAA-CCTCGTTATTTTTGAGGGGATACTCCAACCCCGATTTTCTTTTCAAAACACC
1 GGGATACTCCAACCCT-GTTATTTCCAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACC
* *
805363 AATTTTCTATAATTA
65 AATTTTCCATAATCA
*
805378 GGGATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCGATTTTATTTCCAGAACACCA
1 GGGATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCA
805443 ATTTTCCATAATCA
66 ATTTTCCATAATCA
*
805457 GGGATCCTCCA
1 GGGATACTCCA
805468 GCCCCGTTGT
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
79 77 0.96
80 3 0.04
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (79 bp):
GGGATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCA
ATTTTCCATAATCA
Found at i:805382 original size:107 final size:107
Alignment explanation
Indices: 805194--805419 Score: 267
Period size: 107 Copynumber: 2.1 Consensus size: 107
805184 CACAATCAGA
* * * ***
805194 GATACTTCAACCTCGTTATTTCTGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATATTGAT
1 GATACTCCAACCTCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATTCCTAAAACACCAAT
* * **
805259 TTCTCACAATCGGGGATACTCCAACCCCGTTATTTTCGCGGG
66 TTCTCACAATCAGGGATACTCCAACCCCGTTATTTCCAAGGG
* * * *
805301 GATACTCCAACCTCGTTATTTTTGAGGGGATACTCCAACCCCGATTTTCTT-TTCAAAACACCAA
1 GATACTCCAACCTCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATTCCT-AAAACACCAA
* * *
805365 TTT-TCTATAATTAGGGATACTCCAACCCTGTTATTTCCAAGGG
65 TTTCTC-ACAATCAGGGATACTCCAACCCCGTTATTTCCAAGGG
805408 GATACTCCAACC
1 GATACTCCAACC
805420 CCGATTTTAT
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
106 3 0.03
107 97 0.97
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (107 bp):
GATACTCCAACCTCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATTCCTAAAACACCAAT
TTCTCACAATCAGGGATACTCCAACCCCGTTATTTCCAAGGG
Found at i:810577 original size:29 final size:29
Alignment explanation
Indices: 810545--810620 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
810535 TTAAATTTTA
*
810545 TTATTTTATTTAAATAAATTTTTATATTT
1 TTATTTTATTTAAATAAACTTTTATATTT
* * * *
810574 TTATTATATTCAAATAAGCTTTTATCTTT
1 TTATTTTATTTAAATAAACTTTTATATTT
* *
810603 TGATTTGTATCTAAATAA
1 TTATTT-TATTTAAATAA
810621 GCCATTATCT
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 28 0.76
30 9 0.24
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.57
Consensus pattern (29 bp):
TTATTTTATTTAAATAAACTTTTATATTT
Found at i:810792 original size:22 final size:23
Alignment explanation
Indices: 810767--810812 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
810757 ATTTTTATTC
810767 AAAT-TTAATTATAAAAAT-ATAT
1 AAATATTAA-TATAAAAATAATAT
810789 AAATATTAATATAAAAATAATAT
1 AAATATTAATATAAAAATAATAT
810812 A
1 A
810813 TTAATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AAATATTAATATAAAAATAATAT
Found at i:810797 original size:23 final size:22
Alignment explanation
Indices: 810767--810818 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
810757 ATTTTTATTC
810767 AAAT-TTAATTATAAAAATATAT
1 AAATATTAATTATAAAAATA-AT
810789 AAATATTAA-TATAAAAATAAT
1 AAATATTAATTATAAAAATAAT
810810 --ATATTAATT
1 AAATATTAATT
810819 TTTTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.25
20 1 0.04
21 2 0.07
22 14 0.50
23 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATTAATTATAAAAATAAT
Found at i:811583 original size:2 final size:2
Alignment explanation
Indices: 811576--811604 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
811566 AAGCAGAAAC
811576 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
811605 AAGATACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:813016 original size:30 final size:30
Alignment explanation
Indices: 812982--813069 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 30
812972 TGGCAAAAGC
* *
812982 TAAAGGTTAAGAGTTTGTTTGAGTGTAAAA
1 TAAAGGTTAAGGGTTTATTTGAGTGTAAAA
* *
813012 TAAAGATT--GGGTTTATTTGAGCGTAAAA
1 TAAAGGTTAAGGGTTTATTTGAGTGTAAAA
* *
813040 TAAAAGTTAAGGGCTTATTTGAGTGTAAAA
1 TAAAGGTTAAGGGTTTATTTGAGTGTAAAA
813070 AAAATATGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 23 0.48
30 25 0.52
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (30 bp):
TAAAGGTTAAGGGTTTATTTGAGTGTAAAA
Found at i:813030 original size:28 final size:29
Alignment explanation
Indices: 812994--813073 Score: 94
Period size: 28 Copynumber: 2.8 Consensus size: 29
812984 AAGGTTAAGA
*
812994 GTTTGTTTGAGTGTAAAAT-AAAGATT-GG
1 GTTTATTTGAGTGTAAAATAAAAG-TTAGG
*
813022 GTTTATTTGAGCGTAAAATAAAAGTTAAGG
1 GTTTATTTGAGTGTAAAATAAAAGTT-AGG
*
813052 GCTTATTTGAGTGTAAAA-AAAA
1 GTTTATTTGAGTGTAAAATAAAA
813074 TATGATGACT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
28 19 0.42
29 8 0.18
30 18 0.40
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.35
Consensus pattern (29 bp):
GTTTATTTGAGTGTAAAATAAAAGTTAGG
Found at i:816873 original size:14 final size:14
Alignment explanation
Indices: 816854--816884 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
816844 TGTCATTAAA
816854 TTTTATTTATTTAT
1 TTTTATTTATTTAT
*
816868 TTTTATTTATTTCT
1 TTTTATTTATTTAT
816882 TTT
1 TTT
816885 AGTTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTATTTATTTAT
Found at i:820333 original size:23 final size:23
Alignment explanation
Indices: 820288--820334 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
820278 TTATGAAAAA
* *
820288 ATATTTATAATTATTATATAATT
1 ATATTAATAATTATTATACAATT
820311 ATATTAATAATATATTAT-CAATT
1 ATATTAATAAT-TATTATACAATT
820334 A
1 A
820335 AAGTAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATTAATAATTATTATACAATT
Found at i:821053 original size:2 final size:2
Alignment explanation
Indices: 821046--821073 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
821036 TATTATATTG
821046 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
821074 CTAATTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:828668 original size:21 final size:22
Alignment explanation
Indices: 828643--828683 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
828633 AACATGCTGT
828643 AAATGCATGAAACAT-AGCTCA
1 AAATGCATGAAACATGAGCTCA
*
828664 AAATGCATGAATCATGAGCT
1 AAATGCATGAAACATGAGCT
828684 GTTATAATGA
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:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (22 bp):
AAATGCATGAAACATGAGCTCA
Found at i:829631 original size:13 final size:13
Alignment explanation
Indices: 829613--829640 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
829603 ATACAAAGAT
829613 CAATGTATCGATA
1 CAATGTATCGATA
829626 CAATGTATCGATA
1 CAATGTATCGATA
829639 CA
1 CA
829641 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:829653 original size:21 final size:21
Alignment explanation
Indices: 829627--829685 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
829617 GTATCGATAC
829627 AATGTATCGATACATTTGAGT
1 AATGTATCGATACATTTGAGT
829648 AATGTATCGATACATTTGAGT
1 AATGTATCGATACATTTGAGT
829669 AATGTATCGATACATTT
1 AATGTATCGATACATTT
829686 TTTGGCAGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (21 bp):
AATGTATCGATACATTTGAGT
Found at i:829728 original size:19 final size:19
Alignment explanation
Indices: 829704--829806 Score: 146
Period size: 19 Copynumber: 5.7 Consensus size: 19
829694 TAGCTTACAT
*
829704 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
829723 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
829742 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
829761 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
829774 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
829794 TGTATCGATACAA
1 TGTATCGATACAA
829807 ATCGTTGAAA
Statistics
Matches: 76, Mismatches: 1, Indels: 13
0.84 0.01 0.14
Matches are distributed among these distances:
13 9 0.12
14 1 0.01
16 6 0.08
19 47 0.62
20 13 0.17
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:829779 original size:13 final size:13
Alignment explanation
Indices: 829761--829785 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
829751 ACAACACTTA
829761 TGTATCGATACAT
1 TGTATCGATACAT
829774 TGTATCGATACA
1 TGTATCGATACA
829786 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:832973 original size:357 final size:357
Alignment explanation
Indices: 832499--833216 Score: 1337
Period size: 357 Copynumber: 2.0 Consensus size: 357
832489 AGCACTAGAG
832499 AGATACCGATACGAAATATCGTTTTGTGATCTTTAAAAATAGTTTTCAAAGCATGAATGCATAAG
1 AGATACCGATACGAAATATCGTTTTGTGATCTTTAAAAATAGTTTTCAAAGCATGAATGCATAAG
* *
832564 GTCTTTACGAAAGGAAATATGTTAGTAAAAAAGAAAAATAATAGACAAAGTTACACAAAATAAAC
66 GTCTCTACGAAAAGAAATATGTTAGTAAAAAAGAAAAATAATAGACAAAGTTACACAAAATAAAC
832629 GAACAAAAATACATAACAAGGAGGGACAATCAAAGTGTGTCTCATGATTATTTTCGATGAATGAT
131 GAACAAAAATACATAACAAGGAGGGACAATCAAAGTGTGTCTCATGATTATTTTCGATGAATGAT
832694 GCATAATCGTGATAACAATGTTGAGACTTGATTGGATTCTGTGAGGTTTTTGAAAATAATCTAGG
196 GCATAATCGTGATAACAATGTTGAGACTTGATTGGATTCTGTGAGGTTTTTGAAAATAATCTAGG
*
832759 GGTTCCCTAGAGAAAAGTTTGAAAAAGAAATTCAAAAAGAAATAAGGTTAGAGTATTTTCCCGAA
261 GGTGCCCTAGAGAAAAGTTTGAAAAAGAAATTCAAAAAGAAATAAGGTTAGAGTATTTTCCCGAA
*
832824 AATAACGGGGTTGGAATATCCCCGGTGGTGAA
326 AATAACGAGGTTGGAATATCCCCGGTGGTGAA
832856 AGATACCGATACGAAATATCGTTTTGTGATCTTTAAAAATAGTTTTCAAAGCATGAATGCATAAG
1 AGATACCGATACGAAATATCGTTTTGTGATCTTTAAAAATAGTTTTCAAAGCATGAATGCATAAG
832921 GTCTCTACGAAAAGAAATATGTTAGTAAAAAAGAAAAATAATAGACAAAGTTACACAAAATAAAC
66 GTCTCTACGAAAAGAAATATGTTAGTAAAAAAGAAAAATAATAGACAAAGTTACACAAAATAAAC
* *
832986 GCACAAAAATATATAACAAGGAGGGACAATCAAAGTGTGTCTCATGATTATTTTCGATGAATGAT
131 GAACAAAAATACATAACAAGGAGGGACAATCAAAGTGTGTCTCATGATTATTTTCGATGAATGAT
*
833051 GCATAATCGTGATAACAATGTTGAGACTTGATTGGATTCTGTGAGGTTTTTGAAAATGATCTAGG
196 GCATAATCGTGATAACAATGTTGAGACTTGATTGGATTCTGTGAGGTTTTTGAAAATAATCTAGG
* * * *
833116 GGTGCCTTAGAGAAAAGTTTGAAAAAGAAATTCAAAAAGAAATAGGGTTAGAGTATTTTTCTGAA
261 GGTGCCCTAGAGAAAAGTTTGAAAAAGAAATTCAAAAAGAAATAAGGTTAGAGTATTTTCCCGAA
833181 AATAACGAGGTTGGAATATCCCCGGTGGTGAA
326 AATAACGAGGTTGGAATATCCCCGGTGGTGAA
833213 AGAT
1 AGAT
833217 TGGTGTTTTA
Statistics
Matches: 350, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
357 350 1.00
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.28
Consensus pattern (357 bp):
AGATACCGATACGAAATATCGTTTTGTGATCTTTAAAAATAGTTTTCAAAGCATGAATGCATAAG
GTCTCTACGAAAAGAAATATGTTAGTAAAAAAGAAAAATAATAGACAAAGTTACACAAAATAAAC
GAACAAAAATACATAACAAGGAGGGACAATCAAAGTGTGTCTCATGATTATTTTCGATGAATGAT
GCATAATCGTGATAACAATGTTGAGACTTGATTGGATTCTGTGAGGTTTTTGAAAATAATCTAGG
GGTGCCCTAGAGAAAAGTTTGAAAAAGAAATTCAAAAAGAAATAAGGTTAGAGTATTTTCCCGAA
AATAACGAGGTTGGAATATCCCCGGTGGTGAA
Found at i:833409 original size:78 final size:78
Alignment explanation
Indices: 833179--833605 Score: 360
Period size: 79 Copynumber: 5.4 Consensus size: 78
833169 TATTTTTCTG
* * * * * * *
833179 AAAATAACGAGGTTGGAATATCCCCGGTGGTGAAAGATTGGTGTTTTAGAAATAAAATTGGGGTT
1 AAAATAACGAGGTTAGAGTAT-CCCGATAGTGAAAAATCGGTGTTTTAGAAATAAAATTGGAGTT
*
833244 GGAGTATCTCCTCA
65 GGAGTATCCCCTCA
* * * * * * **
833258 GAAATAACGGGGTTGGAGTATCCCCGATAGTGAAAAATCGATATTTTAAAAATAAAAACAGG-GT
1 AAAATAACGAGGTTAGAGTAT-CCCGATAGTGAAAAATCGGTGTTTTAGAAAT-AAAATTGGAGT
833322 TGGAGTATCCCCTCA
64 TGGAGTATCCCCTCA
* * * * * *
833337 AAAATAACGGGGTTAGAGTATCCCAATGGTAAAAAATCGGTGTTTTAGAAATAAATTTGGAGCTG
1 AAAATAACGAGGTTAGAGTATCCCGATAGTGAAAAATCGGTGTTTTAGAAATAAAATTGGAGTTG
*
833402 GAGTATCCCTTC-
66 GAGTATCCCCTCA
* * * * ** * *
833414 AAAATAATGAGGTTGGAGCATCCTCGATAATGAAAAATCAATGTTTTAAAAATAAAA-TCGAGAT
1 AAAATAACGAGGTTAGAGTATCC-CGATAGTGAAAAATCGGTGTTTTAGAAATAAAATTGGAG-T
*
833478 TGGAGTATCCCCTCG
64 TGGAGTATCCCCTCA
* * * * **
833493 AAAATAGCGAGATTAAAGTATCCCTGATGGTGAAAAATCGGTGTTTTAGAAATAAAA-TCAAGGT
1 AAAATAACGAGGTTAGAGTATCCC-GATAGTGAAAAATCGGTGTTTTAGAAATAAAATTGGA-GT
* **
833557 TGAAGTAT-CCCTTG
64 TGGAGTATCCCCTCA
* * *
833571 AAAATAACAAGGTTGGAGTATCCTGATAGTGAAAA
1 AAAATAACGAGGTTAGAGTATCCCGATAGTGAAAA
833606 CTGGGTTGGA
Statistics
Matches: 279, Mismatches: 62, Indels: 16
0.78 0.17 0.04
Matches are distributed among these distances:
77 38 0.14
78 101 0.36
79 133 0.48
80 7 0.03
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (78 bp):
AAAATAACGAGGTTAGAGTATCCCGATAGTGAAAAATCGGTGTTTTAGAAATAAAATTGGAGTTG
GAGTATCCCCTCA
Found at i:833594 original size:157 final size:156
Alignment explanation
Indices: 833179--833605 Score: 495
Period size: 156 Copynumber: 2.7 Consensus size: 156
833169 TATTTTTCTG
* * * * * *
833179 AAAATAACGAGGTTGGAA-TATCCCCGGTGGTGAAAGATTGGTGTTTTAGAAATAAAATTGGGGT
1 AAAATAACGAGATT-AAAGTAT-CCCGATGGTGAAAAATCGGTGTTTTAGAAATAAAATTAGGGT
* * *
833243 TGGAGTATCTCC-TCAGAAATAACGGGGTTGGAGTATCCCCGATAGTGAAAAATCGATATTTTAA
64 TGGAGTATC-CCTTCA-AAATAACGAGGTTGGAGTATCCTCGATAGTGAAAAATCAATATTTTAA
*
833307 AAATAAAAACAGGGTTGGAGTATCCCCTCA
127 AAATAAAAACAGGATTGGAGTATCCCCTCA
* * * * * * *
833337 AAAATAACGGGGTTAGAGTATCCCAATGGTAAAAAATCGGTGTTTTAGAAAT-AAATTTGGAGCT
1 AAAATAACGAGATTAAAGTATCCCGATGGTGAAAAATCGGTGTTTTAGAAATAAAATTAGG-GTT
* * * *
833401 GGAGTATCCCTTCAAAATAATGAGGTTGGAGCATCCTCGATAATGAAAAATCAATGTTTTAAAAA
65 GGAGTATCCCTTCAAAATAACGAGGTTGGAGTATCCTCGATAGTGAAAAATCAATATTTTAAAAA
* *
833466 TAAAATC-GAGATTGGAGTATCCCCTCG
130 TAAAAACAG-GATTGGAGTATCCCCTCA
* * *
833493 AAAATAGCGAGATTAAAGTATCCCTGATGGTGAAAAATCGGTGTTTTAGAAATAAAATCAAGGTT
1 AAAATAACGAGATTAAAGTATCCC-GATGGTGAAAAATCGGTGTTTTAGAAATAAAATTAGGGTT
* * *
833558 GAAGTATCCCTTGAAAATAACAAGGTTGGAGTATCCT-GATAGTGAAAA
65 GGAGTATCCCTTCAAAATAACGAGGTTGGAGTATCCTCGATAGTGAAAA
833606 CTGGGTTGGA
Statistics
Matches: 227, Mismatches: 36, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
155 1 0.00
156 105 0.46
157 100 0.44
158 21 0.09
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (156 bp):
AAAATAACGAGATTAAAGTATCCCGATGGTGAAAAATCGGTGTTTTAGAAATAAAATTAGGGTTG
GAGTATCCCTTCAAAATAACGAGGTTGGAGTATCCTCGATAGTGAAAAATCAATATTTTAAAAAT
AAAAACAGGATTGGAGTATCCCCTCA
Found at i:833644 original size:56 final size:56
Alignment explanation
Indices: 833554--833662 Score: 159
Period size: 56 Copynumber: 1.9 Consensus size: 56
833544 ATAAAATCAA
833554 GGTTGAAGTATCCCTTGAAAATAACAAGGTTGGAGTATCCT-GATAGTGAAAACTG
1 GGTTGAAGTATCCCTTGAAAATAACAAGGTTGGAGTATCCTCGATAGTGAAAACTG
* * *
833609 GGTTGGAGTATCCCTTCGAAAATAAC-GGGATTGGAGTATCCTCGATGGTGAAAA
1 GGTTGAAGTATCCCTT-GAAAATAACAAGG-TTGGAGTATCCTCGATAGTGAAAA
833663 ATTGGTGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
55 17 0.35
56 21 0.44
57 10 0.21
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.27
Consensus pattern (56 bp):
GGTTGAAGTATCCCTTGAAAATAACAAGGTTGGAGTATCCTCGATAGTGAAAACTG
Found at i:833674 original size:213 final size:213
Alignment explanation
Indices: 833400--833807 Score: 522
Period size: 213 Copynumber: 1.9 Consensus size: 213
833390 AATTTGGAGC
*
833400 TGGAGTATCCCTTCAAAATAATGAGGTTGGAGCATCCTCGATAATGAAAAATCAATGTTTTAAAA
1 TGGAGTATCCCTTCAAAATAACGAGGTTGGAGCATCCTCGATAATGAAAAATCAATGTTTTAAAA
* * *
833465 ATAAAATC-GAGATTGGAGT-ATCCCCTCGAAAATAGCGAGATTAAAGTATCC-CTGATGGTG-A
66 ATAAAATCGGAG-TTGAAGTAAT-CCCTCGAAAATAACGAGATTAAAGTATCCTC-GATAGTGAA
*
833526 AAAATCGGTGTTTTAGAAATAAAATCAAGGTTGAAGT-ATCCCTTGAAAATAACAAGGTTGGAGT
128 AAAAT-GGTGTTTTAGAAATAAAATCAAGGTTGAAGTAATCCCTCGAAAATAACAAGGTTGGAGT
833590 ATCCTGATAGTGAAAACTGGGT
192 ATCCTGATAGTGAAAACTGGGT
* ** *** *
833612 TGGAGTATCCCTTCGAAAATAACG-GGATTGGAGTATCCTCGATGGTGAAAAATTGGTGTTTTAG
1 TGGAGTATCCCTTC-AAAATAACGAGG-TTGGAGCATCCTCGATAATGAAAAATCAATGTTTTAA
* * * * * *
833676 AAATAAAATCGGAGTTGAAGTAATCCCTCGAACATAATGGGGTTGAAGTATCCTCGGTAGTGAAA
64 AAATAAAATCGGAGTTGAAGTAATCCCTCGAAAATAACGAGATTAAAGTATCCTCGATAGTGAAA
** **
833741 AAATGGTGTTTTAGAAATAAAATCGGGGTTGAAGTAATCCCTCGAAAATAACGGGGTTGGAGTAT
129 AAATGGTGTTTTAGAAATAAAATCAAGGTTGAAGTAATCCCTCGAAAATAACAAGGTTGGAGTAT
833806 CC
194 CC
833808 CCGGTAATAA
Statistics
Matches: 167, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
212 16 0.10
213 111 0.66
214 40 0.24
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (213 bp):
TGGAGTATCCCTTCAAAATAACGAGGTTGGAGCATCCTCGATAATGAAAAATCAATGTTTTAAAA
ATAAAATCGGAGTTGAAGTAATCCCTCGAAAATAACGAGATTAAAGTATCCTCGATAGTGAAAAA
ATGGTGTTTTAGAAATAAAATCAAGGTTGAAGTAATCCCTCGAAAATAACAAGGTTGGAGTATCC
TGATAGTGAAAACTGGGT
Found at i:833731 original size:79 final size:78
Alignment explanation
Indices: 833610--833941 Score: 350
Period size: 79 Copynumber: 4.2 Consensus size: 78
833600 TGAAAACTGG
* * * * *
833610 GTTGGAGTATCCCTTCGAAAATAACGGGATTGGAGTATCCTCGATGGTGAAAAATTGGTGTTTTA
1 GTTGAAGTATCCC-TCGAAAATAACGGGATTGAAGTATCCTCGGTAGTGAAAAATCGGTGTTTTA
833675 GAAATAAAATCGGA
65 GAAATAAAATCGGA
* * *
833689 GTTGAAGTAATCCCTCGAACATAATGGGGTTGAAGTATCCTCGGTAGTGAAAAAAT-GGTGTTTT
1 GTTGAAGT-ATCCCTCGAAAATAACGGGATTGAAGTATCCTCGGTAGTG-AAAAATCGGTGTTTT
*
833753 AGAAATAAAATCGGG
64 AGAAATAAAATCGGA
* * * * * **
833768 GTTGAAGTAATCCCTCGAAAATAACGGGGTTGGAGTATCCCCGGTAATAAAAAATCAATGTTTTA
1 GTTGAAGT-ATCCCTCGAAAATAACGGGATTGAAGTATCCTCGGTAGTGAAAAATCGGTGTTTTA
* *
833833 GAAATAAAACCAGA
65 GAAATAAAATCGGA
* * * *
833847 GTT-AGAGTATCCCTTC-AGAAACAACGGTATTGAAGTATCCTCGGTGGTGAAAAATCGGTATTT
1 GTTGA-AGTATCCC-TCGA-AAATAACGGGATTGAAGTATCCTCGGTAGTGAAAAATCGGTGTTT
*
833910 TAGAAATAAAA-CTGA
63 TAGAAATAAAATCGGA
833925 GATTGAAGTAT-CCTCGA
1 G-TTGAAGTATCCCTCGA
833942 TAGTGGAAAA
Statistics
Matches: 213, Mismatches: 31, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
77 2 0.01
78 20 0.09
79 179 0.84
80 12 0.06
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (78 bp):
GTTGAAGTATCCCTCGAAAATAACGGGATTGAAGTATCCTCGGTAGTGAAAAATCGGTGTTTTAG
AAATAAAATCGGA
Found at i:833840 original size:292 final size:290
Alignment explanation
Indices: 833312--833841 Score: 670
Period size: 292 Copynumber: 1.8 Consensus size: 290
833302 TTTAAAAATA
*
833312 AAAACAGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTAGAGTATCCCAATGGTAAAAAATCGG
1 AAAACAGGGTTGGAGTATCCCCTCAAAAATAACGGGATTAGAGTATCCCAATGGTAAAAAATCGG
* * * *
833377 TGTTTTAGAAATAAATTTGGAGCTGGAGTATCCCTTCAAAATAATGAGGTTGGAGCATCCTCGAT
66 TGTTTTAGAAATAAAATCGGAGCTGAAGTATCCCTTCAAAATAATGAGGTTGAAGCATCCTCGAT
* *
833442 AATGAAAAATCAATGTTTTAAAAATAAAATCGAGATTGGAGTATCCCCTCGAAAATAGCGAGATT
131 AATGAAAAATCAATGTTTTAAAAATAAAATCGAGATTGAAGTATCCCCTCGAAAATAACGAGATT
* ** * **
833507 AAAGTATCCCTGATGGTGAAAAATCGGTGTTTTAGAAATAAAATCAAGGTTGAAGTATCCCTTGA
196 AAAGTATCCCCGATAATAAAAAATCAATGTTTTAGAAATAAAATCAAGGTTGAAGTATCCCTTGA
833572 AAATAACAAGGTTGGAGTATCCTGATAGTG
261 AAATAACAAGGTTGGAGTATCCTGATAGTG
* * * * * * *
833602 AAAACTGGGTTGGAGTATCCCTTCGAAAATAACGGGATTGGAGTATCCTCGATGGTGAAAAATTG
1 AAAACAGGGTTGGAGTATCCCCTCAAAAATAACGGGATTAGAGTATCC-CAATGGTAAAAAATCG
* * * *
833667 GTGTTTTAGAAATAAAATCGGAGTTGAAGTAATCCC-TCGAACATAATGGGGTTGAAGTATCCTC
65 GTGTTTTAGAAATAAAATCGGAGCTGAAGT-ATCCCTTC-AAAATAATGAGGTTGAAGCATCCTC
* * ** * * *
833731 GGTAGTGAAAAAAT-GGTGTTTTAGAAATAAAATCGGGGTTGAAGTAAT-CCCTCGAAAATAACG
128 GATAATG-AAAAATCAATGTTTTAAAAATAAAATCGAGATTGAAGT-ATCCCCTCGAAAATAACG
* * ** *
833794 GGGTTGGAGTATCCCCGGTAATAAAAAATCAATGTTTTAGAAATAAAA
191 AGATTAAAGTATCCCCGATAATAAAAAATCAATGTTTTAGAAATAAAA
833842 CCAGAGTTAG
Statistics
Matches: 199, Mismatches: 36, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
290 43 0.22
291 41 0.21
292 107 0.54
293 8 0.04
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (290 bp):
AAAACAGGGTTGGAGTATCCCCTCAAAAATAACGGGATTAGAGTATCCCAATGGTAAAAAATCGG
TGTTTTAGAAATAAAATCGGAGCTGAAGTATCCCTTCAAAATAATGAGGTTGAAGCATCCTCGAT
AATGAAAAATCAATGTTTTAAAAATAAAATCGAGATTGAAGTATCCCCTCGAAAATAACGAGATT
AAAGTATCCCCGATAATAAAAAATCAATGTTTTAGAAATAAAATCAAGGTTGAAGTATCCCTTGA
AAATAACAAGGTTGGAGTATCCTGATAGTG
Found at i:833920 original size:371 final size:369
Alignment explanation
Indices: 833239--833937 Score: 857
Period size: 371 Copynumber: 1.9 Consensus size: 369
833229 AATAAAATTG
*
833239 GGGTTGGAGTATCTCCTCAGAAATAACGGGGTTGGAGTATCCCCGATAGTGAAAAATCGATATTT
1 GGGTTGGAGTATCTCCTCAGAAATAACGGGATTGGAGTATCCCCGATAGTGAAAAATCGATATTT
* *
833304 TAAAAATAAAAACAGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTAGAGTATCCCAATGGTAA
66 TAAAAATAAAAACAGGGTTGAAGTATCCCCTCAAAAATAACGGGGTTAGAGTATCCCAATAGTAA
* * * *
833369 AAAATCGGTGTTTTAGAAATAAATTTGGAGCTGGAGTATCCCTTCAAAATAATGAGGTTGGAGCA
131 AAAATCGGTGTTTTAGAAATAAAATCGGAGCTGAAGTATCCCTTCAAAATAACGAGGTTGGAGCA
* * * *
833434 TCCTCGATAATGAAAAATCAATGTTTTAAAAATAAAATCGAGATTGGAGTATCCCCTCGAAAATA
196 TCCCCGATAATAAAAAATCAATGTTTTAAAAATAAAACCGAGATTAGAGTATCCCCTCGAAAATA
* *
833499 GCGAGATTAAAGTATCCCTGATGGTGAAAAATCGGTGTTTTAGAAATAAAA-TCAAGGTTGAAGT
261 GCGAGATTAAAGTATCCCTGATGGTGAAAAATCGGTATTTTAGAAATAAAACT-AAGATTGAAGT
833563 ATCCCTTGAAAATAACAAGGTTGGAGTATCCTGATAGTGAAAACT
325 ATCCCTTGAAAATAACAAGGTTGGAGTATCCTGATAGTGAAAACT
* * * * *
833608 GGGTTGGAGTATC-CCTTC-GAAAATAACGGGATTGGAGTATCCTCGATGGTGAAAAATTGGTGT
1 GGGTTGGAGTATCTCC-TCAG-AAATAACGGGATTGGAGTATCCCCGATAGTGAAAAATCGATAT
* * * * * **
833671 TTTAGAAATAAAATC-GGAGTTGAAGTAAT-CCCTCGAACATAATGGGGTT-GAAGTATCCTCGG
64 TTTAAAAATAAAAACAGG-GTTGAAGT-ATCCCCTCAAAAATAACGGGGTTAG-AGTATCC-CAA
* * *
833733 TAGTGAAAAAAT-GGTGTTTTAGAAATAAAATCGGGGTTGAAGTAATCCC-TCGAAAATAACGGG
125 TAGT-AAAAAATCGGTGTTTTAGAAATAAAATCGGAGCTGAAGT-ATCCCTTC-AAAATAACGAG
* * *
833796 GTTGGAGTATCCCCGGTAATAAAAAATCAATGTTTTAGAAATAAAACC-AGAGTTAGAGTATCCC
187 GTTGGAGCATCCCCGATAATAAAAAATCAATGTTTTAAAAATAAAACCGAGA-TTAGAGTATCCC
* * *
833860 TTCAGAAACA-A-CG-GTATTGAAGTAT-CCTCGGTGGTGAAAAATCGGTATTTTAGAAATAAAA
251 CTC-GAAA-ATAGCGAG-ATTAAAGTATCCCT-GATGGTGAAAAATCGGTATTTTAGAAATAAAA
*
833921 CTGAGATTGAAGTATCC
312 CTAAGATTGAAGTATCC
833938 TCGATAGTGG
Statistics
Matches: 280, Mismatches: 35, Indels: 28
0.82 0.10 0.08
Matches are distributed among these distances:
368 6 0.02
369 96 0.34
370 41 0.15
371 130 0.46
372 6 0.02
373 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.27
Consensus pattern (369 bp):
GGGTTGGAGTATCTCCTCAGAAATAACGGGATTGGAGTATCCCCGATAGTGAAAAATCGATATTT
TAAAAATAAAAACAGGGTTGAAGTATCCCCTCAAAAATAACGGGGTTAGAGTATCCCAATAGTAA
AAAATCGGTGTTTTAGAAATAAAATCGGAGCTGAAGTATCCCTTCAAAATAACGAGGTTGGAGCA
TCCCCGATAATAAAAAATCAATGTTTTAAAAATAAAACCGAGATTAGAGTATCCCCTCGAAAATA
GCGAGATTAAAGTATCCCTGATGGTGAAAAATCGGTATTTTAGAAATAAAACTAAGATTGAAGTA
TCCCTTGAAAATAACAAGGTTGGAGTATCCTGATAGTGAAAACT
Found at i:833936 original size:51 final size:51
Alignment explanation
Indices: 833875--833988 Score: 165
Period size: 51 Copynumber: 2.2 Consensus size: 51
833865 AAACAACGGT
* * *
833875 ATTGAAGTATCCTCGGTGGTGAAAAATCGGTATTTTAGAAATAAAACTGAG
1 ATTGAAGTATCCTCGATAGTGAAAAATCGGTATTTTAGAAATAAAACCGAG
* *
833926 ATTGAAGTATCCTCGATAGTGGAAAATCGGTGTTTTAGAAATAAAACCGAG
1 ATTGAAGTATCCTCGATAGTGAAAAATCGGTATTTTAGAAATAAAACCGAG
* *
833977 GTTGGAGTATCC
1 ATTGAAGTATCC
833989 ACTTGAAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (51 bp):
ATTGAAGTATCCTCGATAGTGAAAAATCGGTATTTTAGAAATAAAACCGAG
Found at i:833961 original size:209 final size:209
Alignment explanation
Indices: 833718--834129 Score: 564
Period size: 209 Copynumber: 2.0 Consensus size: 209
833708 CATAATGGGG
* * *
833718 TTGAAGTATCCTCGGTAGTGAAAAAATGGTGTTTTAGAAATAAAATCGGGGTTGAAGTAATCC-C
1 TTGAAGTATCCTCGATAGTGAAAAAATGGTGTTTTAGAAATAAAACCGAGGTTGAAGT-ATCCAC
*
833782 TCGAAAATAACGGGGTTGGAGTATCCCCGGTAATAAAAAATCAATGTTTTAGAAATAAAACC-AG
65 TCGAAAATAACAGGGTTGGAGTATCCCCGGTAATAAAAAATCAATGTTTTAGAAATAAAACCGA-
* * *
833846 AGTTAGAGTATC-CCTTCAGAAACAAC-GGTATTGAAGTATCCTCGGTGGTGAAAAATCGGTATT
129 AGTTAGAGTATCTCC-TCAGAAACAACAGG-ATTGAAGTATCCTCGATAGTGAAAAATCAGTATT
833909 TTAGAAATAAAACTGAGA
192 TTAGAAATAAAACTGAGA
* *
833927 TTGAAGTATCCTCGATAGTG-GAAAATCGGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCCAC
1 TTGAAGTATCCTCGATAGTGAAAAAAT-GGTGTTTTAGAAATAAAACCGAGGTTGAAGTATCCAC
* * ** * *
833991 TTGAAAATAACAGGGTTGGAGTATCTCCGGTGGTGAAAAATCAATGTTTTAGAAATAAAATCGAA
65 TCGAAAATAACAGGGTTGGAGTATCCCCGGTAATAAAAAATCAATGTTTTAGAAATAAAACCGAA
* * * * *
834056 GTTAGAGTATCTCCTCAGAAATAACAGGGTTGGAGTATTCTCGATAGTGGAAAATCAGTATTTTA
130 GTTAGAGTATCTCCTCAGAAACAACAGGATTGAAGTATCCTCGATAGTGAAAAATCAGTATTTTA
834121 GAAATAAAA
195 GAAATAAAA
834130 ATATCGATGA
Statistics
Matches: 178, Mismatches: 20, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
208 9 0.05
209 164 0.92
210 5 0.03
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (209 bp):
TTGAAGTATCCTCGATAGTGAAAAAATGGTGTTTTAGAAATAAAACCGAGGTTGAAGTATCCACT
CGAAAATAACAGGGTTGGAGTATCCCCGGTAATAAAAAATCAATGTTTTAGAAATAAAACCGAAG
TTAGAGTATCTCCTCAGAAACAACAGGATTGAAGTATCCTCGATAGTGAAAAATCAGTATTTTAG
AAATAAAACTGAGA
Found at i:834064 original size:79 final size:79
Alignment explanation
Indices: 833931--834129 Score: 233
Period size: 79 Copynumber: 2.5 Consensus size: 79
833921 CTGAGATTGA
* * ** * * *
833931 AGTATCCTCGATAGTGGAAAATCGGTGTTTTAGAAATAAAACCGAGGTTGGAGTATC-CACT-TG
1 AGTATTCTCGATAGTGAAAAATCAATGTTTTAGAAATAAAACCGAAGTTAGAGTATCTC-CTCAG
833994 AAAATAACAGGGTTGG
65 -AAATAACAGGGTTGG
* * *
834010 AGTA-TCTCCGGTGGTGAAAAATCAATGTTTTAGAAATAAAATCGAAGTTAGAGTATCTCCTCAG
1 AGTATTCT-CGATAGTGAAAAATCAATGTTTTAGAAATAAAACCGAAGTTAGAGTATCTCCTCAG
834074 AAATAACAGGGTTGG
65 AAATAACAGGGTTGG
* * *
834089 AGTATTCTCGATAGTGGAAAATCAGTATTTTAGAAATAAAA
1 AGTATTCTCGATAGTGAAAAATCAATGTTTTAGAAATAAAA
834130 ATATCGATGA
Statistics
Matches: 101, Mismatches: 15, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
78 2 0.02
79 94 0.93
80 5 0.05
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (79 bp):
AGTATTCTCGATAGTGAAAAATCAATGTTTTAGAAATAAAACCGAAGTTAGAGTATCTCCTCAGA
AATAACAGGGTTGG
Found at i:835393 original size:5 final size:5
Alignment explanation
Indices: 835383--835429 Score: 94
Period size: 5 Copynumber: 9.4 Consensus size: 5
835373 ATTTTTATAC
835383 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
835430 GAACAAATGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:836034 original size:19 final size:19
Alignment explanation
Indices: 836006--836049 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
835996 AAAATATATT
836006 GATACATAAGGGTTGTATC
1 GATACATAAGGGTTGTATC
* **
836025 GATACTTAAGTTTTGTATC
1 GATACATAAGGGTTGTATC
836044 GATACA
1 GATACA
836050 ATGTATCACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.36
Consensus pattern (19 bp):
GATACATAAGGGTTGTATC
Found at i:836103 original size:21 final size:21
Alignment explanation
Indices: 836074--836115 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
836064 AGCTACTGCC
836074 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
*
836095 AAGGGAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
836116 GTATCGATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:836120 original size:13 final size:13
Alignment explanation
Indices: 836102--836127 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
836092 ATTAAGGGAA
836102 TGTATCGATACAT
1 TGTATCGATACAT
836115 TGTATCGATACAT
1 TGTATCGATACAT
836128 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:838525 original size:52 final size:51
Alignment explanation
Indices: 838468--838853 Score: 233
Period size: 52 Copynumber: 7.4 Consensus size: 51
838458 CAATTGTTGA
*
838468 TAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTT
1 TAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCC-T
* * *
838520 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCA
1 TAATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTCCT
* * ** * ***** * * **
838572 CAATCGAGGATACTCCAACCTTGTTATTTCATCGGGGATACTCCAA--CCCCGT
1 TAATCGGGGATACTCCAACCCCG--ATTTTATTTCCAAAACACCAATTTTCC-T
* * ** * ***
838624 TACCTCCGAGGGAATACTCCAACCTCGGCTTTATTTCCAAAATATTGATTTCTCAC-
1 TA-AT-CG-GGG-ATACTCCAACCCCGATTTTATTTCCAAAACACCAATTT-TC-CT
* * * *
838680 -AATCGGGGATAATCCAACCCC-ATTTTTATTTTCAAAACACTAATTTTCCA
1 TAATCGGGGATACTCCAACCCCGA-TTTTATTTCCAAAACACCAATTTTCCT
* * * *
838730 CAATCGGGGATACTCCAACCCTGGTTTTATTTTCAAAACACCAATTTTCCTT
1 TAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCC-T
* * * * *
838782 TAATCGGGGATAATCCAACTCTGATTTTATTTCCAAAAACACCAATTTTTCA
1 TAATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTCCT
* * *
838834 CAATCGAGGATTCTCCAACC
1 TAATCGGGGATACTCCAACC
838854 TCGTTATTTC
Statistics
Matches: 249, Mismatches: 67, Indels: 36
0.71 0.19 0.10
Matches are distributed among these distances:
49 1 0.00
50 2 0.01
51 74 0.30
52 98 0.39
53 40 0.16
54 16 0.06
55 3 0.01
56 13 0.05
57 1 0.00
58 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (51 bp):
TAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCT
Found at i:838708 original size:51 final size:51
Alignment explanation
Indices: 838653--838853 Score: 181
Period size: 51 Copynumber: 3.9 Consensus size: 51
838643 CAACCTCGGC
* * *
838653 TTTATTTCCAAAATATTGA-TTTCTCACAATCGGGGATAATCCAACCCCATT
1 TTTATTTCCAAAACACTAATTTTC-CACAATCGGGGATAATCCAACCCCATT
* * ***
838704 TTTATTTTCAAAACACTAATTTTCCACAATCGGGGATACTCCAACCCTGGT
1 TTTATTTCCAAAACACTAATTTTCCACAATCGGGGATAATCCAACCCCATT
* * ** **
838755 TTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATAATCCAACTCTGA-T
1 TTTATTTCCAAAACACTAATTTTCC-ACAATCGGGGATAATCCAAC-CCCATT
* * * **
838807 TTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATTCTCCAACC
1 TTTATTTCC-AAAACACTAATTTTCCACAATCGGGGATAATCCAACC
838854 TCGTTATTTC
Statistics
Matches: 124, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
51 63 0.51
52 45 0.36
53 16 0.13
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.35
Consensus pattern (51 bp):
TTTATTTCCAAAACACTAATTTTCCACAATCGGGGATAATCCAACCCCATT
Found at i:838977 original size:79 final size:78
Alignment explanation
Indices: 838869--839098 Score: 239
Period size: 79 Copynumber: 2.9 Consensus size: 78
838859 ATTTCGTCGA
** * *
838869 GGAT-CTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGA
1 GGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCC-GTTTTATTTCCAAAATATTGA
* **
838933 TTTCTCGCAATTGG
65 TTTCTCACAACCGG
* ** * *
838947 GGATACTTCAACCCCGTTATTTCTGAGGGGATACTCCAATCCCAATTTTATTTCC-TAATCATCG
1 GGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAA-CCCCGTTTTATTTCCAAAAT-ATTG
* *
839011 ATTTTTCATAACCGG
64 ATTTCTCACAACCGG
* * * *
839026 GGATACTCCAACCCCGTTATTTTTAAGGGGATACTCCAACCCCGTTATTATCTCCAAAATATTAA
1 GGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGTT-TTATTTCCAAAATATT-G
839091 ATTTCTCA
64 ATTTCTCA
839099 TCGGGACATA
Statistics
Matches: 122, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
78 12 0.10
79 97 0.80
80 13 0.11
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.32
Consensus pattern (78 bp):
GGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGTTTTATTTCCAAAATATTGAT
TTCTCACAACCGG
Found at i:843413 original size:2 final size:2
Alignment explanation
Indices: 843406--843447 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
843396 GATGATGATG
843406 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
843448 TTGGCCCTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:845584 original size:2 final size:2
Alignment explanation
Indices: 845577--845604 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
845567 TTTTAACATC
845577 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
845605 GTTTTAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:846236 original size:21 final size:20
Alignment explanation
Indices: 846207--846252 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
846197 AAATATTAAA
846207 AAATATTTTTAAATT-AATATT
1 AAATATTTTT-AATTAAAT-TT
*
846228 AAATTTTTTTAATTAAATTT
1 AAATATTTTTAATTAAATTT
846248 AAATA
1 AAATA
846253 AAAATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAATATTTTTAATTAAATTT
Found at i:846249 original size:20 final size:21
Alignment explanation
Indices: 846207--846252 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
846197 AAATATTAAA
846207 AAATATTTTTAAATTAATATT
1 AAATATTTTTAAATTAATATT
*
846228 AAAT-TTTTTTAATTAA-ATTT
1 AAATATTTTTAAATTAATA-TT
846248 AAATA
1 AAATA
846253 AAAATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 1 0.05
20 17 0.77
21 4 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAATATTTTTAAATTAATATT
Found at i:852933 original size:18 final size:20
Alignment explanation
Indices: 852907--852958 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
852897 ATAATTATAA
* *
852907 ATTTTATTATATGTGA-T-T
1 ATTTAATTATATATGACTAT
852925 ATTTAATTATATATGACTAT
1 ATTTAATTATATATGACTAT
*
852945 TTTTAATTATATAT
1 ATTTAATTATATAT
852959 AAAATTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 14 0.48
19 1 0.03
20 14 0.48
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (20 bp):
ATTTAATTATATATGACTAT
Found at i:852939 original size:20 final size:19
Alignment explanation
Indices: 852908--852958 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
852898 TAATTATAAA
*
852908 TTTT-ATTATATGTGAT-T
1 TTTTAATTATATATGATAT
*
852925 ATTTAATTATATATGACTAT
1 TTTTAATTATATATGA-TAT
852945 TTTTAATTATATAT
1 TTTTAATTATATAT
852959 AAAATTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 3 0.11
18 10 0.36
19 1 0.04
20 14 0.50
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (19 bp):
TTTTAATTATATATGATAT
Found at i:853546 original size:17 final size:16
Alignment explanation
Indices: 853509--853554 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
853499 TTTTTTTGAT
*
853509 ATAATAAAAATATAAG
1 ATAATAAAAAAATAAG
*
853525 ATAATAAAAAAATAAT
1 ATAATAAAAAAATAAG
*
853541 ATTAATAATAAAAT
1 A-TAATAAAAAAAT
853555 TTATAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
ATAATAAAAAAATAAG
Found at i:854424 original size:13 final size:13
Alignment explanation
Indices: 854406--854430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
854396 TACATTGTTC
854406 ATTGTATCGATAT
1 ATTGTATCGATAT
854419 ATTGTATCGATA
1 ATTGTATCGATA
854431 CATTCTGGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGTATCGATAT
Found at i:854507 original size:13 final size:13
Alignment explanation
Indices: 854489--854549 Score: 80
Period size: 13 Copynumber: 5.2 Consensus size: 13
854479 ACATTGCTTG
854489 TTGTATCGATACA
1 TTGTATCGATACA
854502 TTGTATCGATACA
1 TTGTATCGATACA
854515 TTG---C--T-CA
1 TTGTATCGATACA
854522 TTGTATCGATACA
1 TTGTATCGATACA
854535 TTGTATCGATACA
1 TTGTATCGATACA
854548 TT
1 TT
854550 CTGGATTTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
7 5 0.12
8 1 0.02
10 2 0.05
12 1 0.02
13 33 0.79
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:854509 original size:33 final size:33
Alignment explanation
Indices: 854467--854549 Score: 148
Period size: 33 Copynumber: 2.5 Consensus size: 33
854457 ATACATTTTG
**
854467 CATTGTATCGATACATTGCTTGTTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
854500 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
854533 CATTGTATCGATACATT
1 CATTGTATCGATACATT
854550 CTGGATTTAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.41
Consensus pattern (33 bp):
CATTGTATCGATACATTGCTCATTGTATCGATA
Found at i:854523 original size:20 final size:20
Alignment explanation
Indices: 854452--854537 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
854442 TACCCAGATA
*
854452 TATCGATACATT-TTGCATTG
1 TATCGATACATTGCT-CATTG
**
854472 TATCGATACATTGCTTGTTG
1 TATCGATACATTGCTCATTG
854492 TATCGAT--A-----CATTG
1 TATCGATACATTGCTCATTG
854505 TATCGATACATTGCTCATTG
1 TATCGATACATTGCTCATTG
854525 TATCGATACATTG
1 TATCGATACATTG
854538 TATCGATACA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
13 10 0.19
15 1 0.02
18 1 0.02
20 40 0.75
21 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (20 bp):
TATCGATACATTGCTCATTG
Found at i:854596 original size:115 final size:115
Alignment explanation
Indices: 854390--854598 Score: 355
Period size: 115 Copynumber: 1.8 Consensus size: 115
854380 TCACAATTTA
* * *
854390 TATCGATACATTGTTCATTGTATCGATATATTGTATCGATACATTCTGGGTTTACCCAGATATAT
1 TATCGATACATTGCTCATTGTATCGATACATTGTATCGATACATTCTGGATTTACCCAGATATAT
* * *
854455 CGATACATTTTGCATTGTATCGATACATTGCTTGTTGTATCGATACATTG
66 CGATACATTTTACAATGTATCAATACATTGCTTGTTGTATCGATACATTG
854505 TATCGATACATTGCTCATTGTATCGATACATTGTATCGATACATTCTGGATTTACCCAGATATAT
1 TATCGATACATTGCTCATTGTATCGATACATTGTATCGATACATTCTGGATTTACCCAGATATAT
*
854570 CTATACATTTTACAATGTATCAATACATT
66 CGATACATTTTACAATGTATCAATACATT
854599 CAAGTATTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
115 87 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.41
Consensus pattern (115 bp):
TATCGATACATTGCTCATTGTATCGATACATTGTATCGATACATTCTGGATTTACCCAGATATAT
CGATACATTTTACAATGTATCAATACATTGCTTGTTGTATCGATACATTG
Found at i:857049 original size:79 final size:78
Alignment explanation
Indices: 856895--857118 Score: 328
Period size: 79 Copynumber: 2.9 Consensus size: 78
856885 TTTTTATCTC
* *
856895 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATCTTTC---ATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAAT-TTTCATAATCGGGGATACTCCAAC
*
856957 CCCGTTATTTCCGA
65 CCCGTTATCTCCGA
* *
856971 GGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTT-TCATAATCGGGGATACTCCAAC
857036 CCCGTTATCTCCGA
65 CCCGTTATCTCCGA
* * *
857050 GCGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTTCATACTCGGGGATACTCCAAT
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAA-TTTTCATAATCGGGGATACTCCAAC
857115 CCCG
65 CCCG
857119 GTTTTATTTC
Statistics
Matches: 133, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
75 2 0.02
76 38 0.29
79 90 0.68
80 3 0.02
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTCATAATCGGGGATACTCCAACC
CCGTTATCTCCGA
Found at i:857128 original size:51 final size:51
Alignment explanation
Indices: 857052--857271 Score: 260
Period size: 51 Copynumber: 4.3 Consensus size: 51
857042 ATCTCCGAGC
* ** * * * *
857052 GGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTTCATACTCGG
1 GGATACTCCAATCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGG
* *
857103 GGATACTCCAATCCCGGTTTTATTTCTAAAATACTAATTCTCCACAATCGG
1 GGATACTCCAATCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGG
* *
857154 GGATACTCTAATCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGG
1 GGATACTCCAATCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGG
** * * * * * * *
857205 GGATACTCTTACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATCGA
1 GGATACTCCAATCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGG
857256 GGATACTCCAATCCCG
1 GGATACTCCAATCCCG
857272 TTATTTTCTA
Statistics
Matches: 146, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 146 1.00
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (51 bp):
GGATACTCCAATCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGG
Found at i:857294 original size:181 final size:181
Alignment explanation
Indices: 857101--857447 Score: 511
Period size: 181 Copynumber: 1.9 Consensus size: 181
857091 TTTCATACTC
* * *
857101 GGGGATACTCCAATCC-CGGTTTTATTTCTAAAATACTAATTCTCCACAATCGGGGATACTCTAA
1 GGGGATACTCCAA-CCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAA
* * **
857165 -TCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCTTACCCCGATTTTATT
65 CTC-CGATTTTATTTCCAAAACACCAATTCTCCACAATCGGGGATACTCCAACCCCGATTTTATT
* * *
857229 TCTAAAACA-TCAATTTTTCATAATCGAGGATACTCCAATCCCGTTATTTTCTA
129 TCTAAAACACT-AATTCTCCACAATCGAGGATACTCCAATCCCGTTATTTTCTA
*
857282 GGGGATACTCCAACCTTGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
* * *
857347 TCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCGGTTTTATTTC
66 TCCGATTTTATTTCCAAAACACCAATTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTC
*
857412 TAAAACACTAATTCTCCACAATCGGGGATACTCCAA
131 TAAAACACTAATTCTCCACAATCGAGGATACTCCAA
857448 CTCCGATTTT
Statistics
Matches: 148, Mismatches: 15, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
180 2 0.01
181 143 0.97
182 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (181 bp):
GGGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
TCCGATTTTATTTCCAAAACACCAATTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTC
TAAAACACTAATTCTCCACAATCGAGGATACTCCAATCCCGTTATTTTCTA
Found at i:857342 original size:51 final size:52
Alignment explanation
Indices: 857282--857502 Score: 324
Period size: 51 Copynumber: 4.3 Consensus size: 52
857272 TTATTTTCTA
* * *
857282 GGGGATACTCCAACCT-TGGTTTTATTTCTAAAACACCAATTCTCCACAATC
1 GGGGATACTCCAACCTCCGATTTTATTTCCAAAACACCAATTCTCCACAATC
*
857333 GGGGATACTCCAA-CTCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
1 GGGGATACTCCAACCTCCGATTTTATTTCCAAAACACCAATTCTCCACAATC
* * *
857384 GGGGATACTCCAACCT-CGGTTTTATTTCTAAAACACTAATTCTCCACAATC
1 GGGGATACTCCAACCTCCGATTTTATTTCCAAAACACCAATTCTCCACAATC
* * *
857435 GGGGATACTCCAA-CTCCGATTTTATTTCCAAAACACCAATTTTTCATAATC
1 GGGGATACTCCAACCTCCGATTTTATTTCCAAAACACCAATTCTCCACAATC
857486 GGGGATACTCCAACCTC
1 GGGGATACTCCAACCTC
857503 GTTATTTTCG
Statistics
Matches: 152, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
50 4 0.03
51 143 0.94
52 5 0.03
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (52 bp):
GGGGATACTCCAACCTCCGATTTTATTTCCAAAACACCAATTCTCCACAATC
Found at i:857381 original size:232 final size:231
Alignment explanation
Indices: 856971--857633 Score: 977
Period size: 232 Copynumber: 2.9 Consensus size: 231
856961 TTATTTCCGA
** * * *
856971 GGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAA-
* * * ** * * * *
857036 CCCGTTATCTCCGAGCGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTTCATACTC
65 CCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATC
* * * * *
857101 GGGGATACTCCAA-TCCCGGTTTTATTTCTAAAATACTAATTCTCCACAATCGGGGATACTCTAA
130 GGGGATACTCCAACT-CCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCTAA
*
857165 TCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATC
194 CCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATC
** *
857203 GGGGATACTCTTACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATCGAGGATACTCCAAT
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAA-
* **
857268 CCCGTTATTTTCTAGGGGATACTCCAACCTTGGTTTTATTTCTAAAACACCAATTCTCCACAATC
65 CCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATC
*
857333 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCCAAC
130 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCTAAC
*
857398 CTCGGTTTTATTTCTAAAACACTAATTCTCCACAATC
195 CTCGGTTTTATTTCTAAAACACCAATTCTCCACAATC
* * *
857435 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
*
857500 CTCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATT
66 C-CGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATC
* *
857565 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCTAAC
130 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCTAAC
857630 CTCG
195 CTCG
857634 TTATTTCATC
Statistics
Matches: 387, Mismatches: 42, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
231 2 0.01
232 384 0.99
233 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (231 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
CCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCG
GGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCTAACC
TCGGTTTTATTTCTAAAACACCAATTCTCCACAATC
Found at i:857390 original size:130 final size:130
Alignment explanation
Indices: 857152--857396 Score: 391
Period size: 130 Copynumber: 1.9 Consensus size: 130
857142 CTCCACAATC
* * **
857152 GGGGATACTCTAATCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCTTAC
1 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
* * * *
857217 CCCGATTTTATTTCTAAAACATCAATTTTTCATAATCGAGGATACTCCAATCCCGTTATTTTCTA
66 CCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGAGGATACTCCAATCCCGTTATTTTCTA
*
857282 GGGGATACTCCAACCTTGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
* *
857347 TCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCCAA
66 CCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGAGGATACTCCAA
857397 CCTCGGTTTT
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
130 104 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (130 bp):
GGGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
CCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGAGGATACTCCAATCCCGTTATTTTCTA
Found at i:857458 original size:102 final size:102
Alignment explanation
Indices: 857282--857503 Score: 408
Period size: 102 Copynumber: 2.2 Consensus size: 102
857272 TTATTTTCTA
*
857282 GGGGATACTCCAACCTTGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
857347 TCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
66 TCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
*
857384 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACACTAATTCTCCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
* *
857449 TCCGATTTTATTTCCAAAACACCAATTTTTCATAATC
66 TCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
857486 GGGGATACTCCAACCTCG
1 GGGGATACTCCAACCTCG
857504 TTATTTTCGA
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 116 1.00
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (102 bp):
GGGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
TCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:857590 original size:51 final size:51
Alignment explanation
Indices: 857514--857630 Score: 164
Period size: 51 Copynumber: 2.3 Consensus size: 51
857504 TTATTTTCGA
* *
857514 GGGGATACTCCAACCCCGGTTTTA-TTTCTAAAACACCAATTCTCCACAATT
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTCTCCACAATC
* * *
857565 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTCTCCACAATC
*
857616 GGGGATACTCTAACC
1 GGGGATACTCCAACC
857631 TCGTTATTTC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 54 0.93
52 4 0.07
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTCTCCACAATC
Found at i:857617 original size:130 final size:131
Alignment explanation
Indices: 857384--857658 Score: 466
Period size: 130 Copynumber: 2.1 Consensus size: 131
857374 TTCCACAATC
* *
857384 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACACTAATTCTCCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
*
857449 TCCGATTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCCAACCTCGTTATTT-TCG
66 TCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTATCG
857513 A
131 A
*
857514 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
* *
857579 TCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCTAACCTCGTTATTTCATC
66 TCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCTCGTTATTT-ATC
857644 GA
130 GA
857646 --GGATACTCCAACC
1 GGGGATACTCCAACC
857659 TCGTTATTTC
Statistics
Matches: 137, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
130 133 0.97
132 4 0.03
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (131 bp):
GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
TCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTATCG
A
Found at i:857649 original size:28 final size:28
Alignment explanation
Indices: 857613--857686 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 28
857603 ATTTTTCACA
* *
857613 ATCGGGGATACTCTAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCTCGTTATTTC
857641 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCTCGTTATTTC
857669 --CGAGGGGATACTCCAACC
1 ATCGA--GGATACTCCAACC
857687 CCGGCTTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 3 0.07
28 39 0.93
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCTCGTTATTTC
Found at i:857737 original size:51 final size:51
Alignment explanation
Indices: 857672--857790 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
857662 TTATTTCCGA
* *
857672 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATC
1 GGGGATACTCCAACCCCGGCCTTAGTTCCAAAATATTGATTTCTCACAATC
* * * * *
857723 GGGGATACTTCAACCCCGTCCTTAGTTCTAAAATATTGATTTCTCATAATT
1 GGGGATACTCCAACCCCGGCCTTAGTTCCAAAATATTGATTTCTCACAATC
857774 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
857791 ATTATTTTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGCCTTAGTTCCAAAATATTGATTTCTCACAATC
Found at i:857778 original size:158 final size:159
Alignment explanation
Indices: 857483--857810 Score: 387
Period size: 158 Copynumber: 2.1 Consensus size: 159
857473 ATTTTTCATA
* * *
857483 ATCGGGGATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAAC
* * * * *
857548 ACCAATTCTCCACAATTGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCACA
66 ACCAATTCTCCACAATCGGGGATACTCCAACCCCGATCTTATTCTCAAAACACCAATTTCTCACA
* * *
857613 ATCGGGGATACTCTAACCTCGTTA-TTTC
131 ATCGGGGATACTCCAACCCCATTATTTTC
* *
857641 ATCGAGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
1 ATCGGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAAC
*** * * ***
857706 ATTGATT-TCTCACAATCGGGGATACTTCAACCCCG-TCCTTAGTTCT-AAAATATTGATTTCTC
66 ACCAATTCTC-CACAATCGGGGATACTCCAACCCCGAT-CTTA-TTCTCAAAACACCAATTTCTC
* *
857768 ATAATTGGGGATACTCCAACCCCATTATTTTC
128 ACAATCGGGGATACTCCAACCCCATTATTTTC
857800 A-CGGGGATACT
1 ATCGGGGATACT
857811 TCAATCCCGA
Statistics
Matches: 142, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
157 3 0.02
158 131 0.92
159 8 0.06
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (159 bp):
ATCGGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAAC
ACCAATTCTCCACAATCGGGGATACTCCAACCCCGATCTTATTCTCAAAACACCAATTTCTCACA
ATCGGGGATACTCCAACCCCATTATTTTC
Found at i:860112 original size:59 final size:59
Alignment explanation
Indices: 860045--860162 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
860035 ATTCGGTTGT
860045 CCTTTTAAACTTAGATCTTGGGATCTTTAGTCAACTAAGTAGGGTTGTCATTATGTAAC
1 CCTTTTAAACTTAGATCTTGGGATCTTTAGTCAACTAAGTAGGGTTGTCATTATGTAAC
860104 CCTTTTAAACTTAGATCTTGGGATCTTTAGTCAACTAAGTAGGGTTGTCATTATGTAAC
1 CCTTTTAAACTTAGATCTTGGGATCTTTAGTCAACTAAGTAGGGTTGTCATTATGTAAC
860163 TTATAATTTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (59 bp):
CCTTTTAAACTTAGATCTTGGGATCTTTAGTCAACTAAGTAGGGTTGTCATTATGTAAC
Found at i:861606 original size:24 final size:25
Alignment explanation
Indices: 861579--861626 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
861569 GGGTTATATC
861579 AATTCAAATGAAA-AT-AAATAAAAT
1 AATT-AAATGAAAGATAAAATAAAAT
*
861603 AATTAAATTAAAGATAAAATAAAA
1 AATTAAATGAAAGATAAAATAAAA
861627 ATGCAAGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (25 bp):
AATTAAATGAAAGATAAAATAAAAT
Found at i:863316 original size:15 final size:15
Alignment explanation
Indices: 863298--863335 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
863288 TTTTTAATTT
863298 TTTTTACTTTTTTCA
1 TTTTTACTTTTTTCA
*
863313 TTTTTA-TTTTTTTA
1 TTTTTACTTTTTTCA
863327 TTTTTACTT
1 TTTTTACTT
863336 AAAGTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTACTTTTTTCA
Found at i:863316 original size:24 final size:22
Alignment explanation
Indices: 863282--863325 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
863272 TTTAAAATTT
863282 CTTTTTTTTTTAATTTTTTTTA
1 CTTTTTTTTTTAATTTTTTTTA
*
863304 CTTTTTTCATTTTTATTTTTTT
1 CTTTTTT--TTTTAATTTTTTT
863326 ATTTTTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (22 bp):
CTTTTTTTTTTAATTTTTTTTA
Found at i:868941 original size:27 final size:27
Alignment explanation
Indices: 868882--868933 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
868872 AATCTAATTG
* *
868882 AATTTTTTTCTTGACTTTTCACCTAAA
1 AATTTTTTTCTGGACTTTTCACATAAA
868909 AATTTTTTATCTGGACTTTT-ACATA
1 AATTTTTT-TCTGGACTTTTCACATA
868934 TTAATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (27 bp):
AATTTTTTTCTGGACTTTTCACATAAA
Found at i:872122 original size:15 final size:15
Alignment explanation
Indices: 872102--872134 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
872092 TTATATATAT
872102 GTATGACACTTTCAC
1 GTATGACACTTTCAC
872117 GTATGACACTTTCAC
1 GTATGACACTTTCAC
872132 GTA
1 GTA
872135 AATTTTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (15 bp):
GTATGACACTTTCAC
Found at i:872570 original size:54 final size:52
Alignment explanation
Indices: 872504--872984 Score: 394
Period size: 54 Copynumber: 9.1 Consensus size: 52
872494 GAAACTATTA
* * * *
872504 AAAAATTTAAAATAGATTTTATATTAAATCTTAAGTTACTATTTAAAAATAAT
1 AAAAA-TTAAAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAAT
*
872557 AAAAATTAAAAAATATTTTATATTAAATCTTAAATTACTA-TT-----TAA-
1 AAAAATTAAAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAAT
* * * *
872602 AAAAATTAAAAAATTCTTTTATATTAAATC-CTGAATTGCTAATTAAAAATAAT
1 AAAAATTAAAAAA-TATTTTATATTAAATCTC-AAATTACTATTTAAAAATAAT
** * * * *
872655 ACAATTTTTAAAAAATATTTTATATTAAATATAAAATTATTTTTTAAAAAATAAT
1 A-AA-AATTAAAAAATATTTTATATTAAATCTCAAATTACTATTT-AAAAATAAT
* ** * *
872710 AAAAATTTAAAATATATTTTATATTAAAT-TCCGGATTACTAGTTAAAAACAAT
1 AAAAA-TTAAAAAATATTTTATATTAAATCT-CAAATTACTATTTAAAAATAAT
* * *
872763 AAAATCTTAAAAAATATTTTATATTAAATC-AAGAATTACAATTTAAAAAATAAT
1 AAAA-ATTAAAAAATATTTTATATTAAATCTCA-AATTACTATTT-AAAAATAAT
* * * *
872817 AAAAATTTATAAAATATTTTATATTAAACCACAAATTACTATTTAAATATAAT
1 AAAAA-TTAAAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAAT
* * * * * *
872870 AAAAAAAATAAAAAGTCTTTTATGTTAAATC-CTGAATTACTTTTTTAAAAAATAAT
1 --AAAAATTAAAAAATATTTTATATTAAATCTC-AAATTAC-TATTT-AAAAATAAT
*
872926 AAAAAGTT-AAAAATATTTTATATTAAATCTCAAATTACTTTTTTAAAAA-AAT
1 AAAAA-TTAAAAAATATTTTATATTAAATCTCAAATTAC-TATTTAAAAATAAT
872978 AAAAATT
1 AAAAATT
872985 TATATTAAAT
Statistics
Matches: 345, Mismatches: 55, Indels: 58
0.75 0.12 0.13
Matches are distributed among these distances:
45 13 0.04
46 25 0.07
47 2 0.01
51 4 0.01
52 43 0.12
53 63 0.18
54 157 0.46
55 30 0.09
56 8 0.02
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (52 bp):
AAAAATTAAAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAAT
Found at i:872626 original size:46 final size:45
Alignment explanation
Indices: 872557--872650 Score: 134
Period size: 46 Copynumber: 2.1 Consensus size: 45
872547 TAAAAATAAT
* *
872557 AAAAATTAAAAAATATTTTATATTAAATCTTAAATTACTATTTAA
1 AAAAATTAAAAAATATTTTATATTAAATCCTAAATTACTAATTAA
* * *
872602 AAAAATTAAAAAATTCTTTTATATTAAATCCTGAATTGCTAATTAA
1 AAAAATTAAAAAA-TATTTTATATTAAATCCTAAATTACTAATTAA
872648 AAA
1 AAA
872651 TAATACAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 13 0.30
46 30 0.70
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.39
Consensus pattern (45 bp):
AAAAATTAAAAAATATTTTATATTAAATCCTAAATTACTAATTAA
Found at i:872982 original size:108 final size:107
Alignment explanation
Indices: 872663--872982 Score: 371
Period size: 107 Copynumber: 3.0 Consensus size: 107
872653 ATACAATTTT
*
872663 TAAAAAATATTTTATATTAAAT-ATAAAATTA-TTTTTTAAAAAATAATAAAAATTTAAAATATA
1 TAAAAAATATTTTATATTAAATCA-AGAATTACTTTTTTAAAAAATAATAAAAATTTAAAA-ATA
** * ***
872726 TTTTATATTAAAT-TCCGGATTACTAGTTAAAAACAAT-AAAATCT
64 TTTTATATTAAATCT-CAAATTACTATTTAAAAA-AATAAAAAAAA
**
872770 TAAAAAATATTTTATATTAAATCAAGAATTAC-AATTTAAAAAATAATAAAAATTTATAAAATAT
1 TAAAAAATATTTTATATTAAATCAAGAATTACTTTTTTAAAAAATAATAAAAATTTA-AAAATAT
* * *
872834 TTTATATTAAACCACAAATTACTATTTAAATATAATAAAAAAAA
65 TTTATATTAAATCTCAAATTACTATTTAAA-AAAATAAAAAAAA
* * * ** *
872878 TAAAAAGTCTTTTATGTTAAATCCTGAATTACTTTTTTAAAAAATAATAAAAAGTTAAAAATATT
1 TAAAAAATATTTTATATTAAATCAAGAATTACTTTTTTAAAAAATAATAAAAATTTAAAAATATT
*
872943 TTATATTAAATCTCAAATTACTTTTTTAAAAAAATAAAAA
66 TTATATTAAATCTCAAATTAC-TATTTAAAAAAATAAAAA
872983 TTTATATTAA
Statistics
Matches: 181, Mismatches: 24, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
107 81 0.45
108 72 0.40
109 28 0.15
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (107 bp):
TAAAAAATATTTTATATTAAATCAAGAATTACTTTTTTAAAAAATAATAAAAATTTAAAAATATT
TTATATTAAATCTCAAATTACTATTTAAAAAAATAAAAAAAA
Found at i:873022 original size:40 final size:41
Alignment explanation
Indices: 872942--873022 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
872932 TTAAAAATAT
* * *
872942 TTTATATTAAATCTCAAATTACTTTTTTAAAAAAATAAAAA
1 TTTATATTAAATCTCAAACTACTTATTTAAAAAAACAAAAA
**
872983 TTTATATTAAATCTTGAACTAC-TATTTAAAAAAACAAAAA
1 TTTATATTAAATCTCAAACTACTTATTTAAAAAAACAAAAA
873023 ATAAAAATAC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
40 16 0.46
41 19 0.54
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.38
Consensus pattern (41 bp):
TTTATATTAAATCTCAAACTACTTATTTAAAAAAACAAAAA
Found at i:873177 original size:17 final size:18
Alignment explanation
Indices: 873151--873187 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
873141 TAATAAAAAT
*
873151 TAAAAGTATATATTT-TA
1 TAAAAATATATATTTATA
873168 TAAAAATATATATTTATA
1 TAAAAATATATATTTATA
873186 TA
1 TA
873188 CTATTATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TAAAAATATATATTTATA
Found at i:873239 original size:22 final size:22
Alignment explanation
Indices: 873211--873309 Score: 60
Period size: 22 Copynumber: 4.6 Consensus size: 22
873201 AATTATATTT
873211 AGTTAAAGTTATATGTACATTC
1 AGTTAAAGTTATATGTACATTC
* * * *
873233 AGTTAAA-ATATTTTTACATAC
1 AGTTAAAGTTATATGTACATTC
** * * *
873254 TTTTAAAGTCATATGCACACT-
1 AGTTAAAGTTATATGTACATTC
* *
873275 A-TTAATGTTATATGTATATTC
1 AGTTAAAGTTATATGTACATTC
* *
873296 AATTAAATTTATAT
1 AGTTAAAGTTATAT
873310 CTATGTATAA
Statistics
Matches: 53, Mismatches: 21, Indels: 6
0.66 0.26 0.08
Matches are distributed among these distances:
20 14 0.26
21 16 0.30
22 23 0.43
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.44
Consensus pattern (22 bp):
AGTTAAAGTTATATGTACATTC
Found at i:873434 original size:53 final size:53
Alignment explanation
Indices: 873341--873753 Score: 374
Period size: 54 Copynumber: 7.9 Consensus size: 53
873331 TGTAAATATG
*
873341 TATTTT-ATTTTTATTATTTTTTAAATAA-CAATT-TGAGATTTAATATAAAATT
1 TATTTTAATTTTTATTA-TTTTTAAA-AAGTAATTCTGAGATTTAATATAAAATT
* * * *
873393 TACTTTTAATTTTTGTTATTTTTAAAAATTAGTTCT-TGATTTAATATAAAA-T
1 TA-TTTTAATTTTTATTATTTTTAAAAAGTAATTCTGAGATTTAATATAAAATT
* * * * * *
873445 AAGTTTTTATTTTAATTATTTTTTAAAAAGCAATTGT-ATGATTTAATATAAAATA
1 TA-TTTTAATTTTTATTA-TTTTTAAAAAGTAATTCTGA-GATTTAATATAAAATT
*
873500 T-TTTTAATTTTTTATTATTTTTAAACAGTAATT-TGAGATTTAATAT--AATT
1 TATTTTAA-TTTTTATTATTTTTAAAAAGTAATTCTGAGATTTAATATAAAATT
* * *
873550 T-TTTTAATTTTTATTATTTTTAAATAGTAATTC-AAGATTTAGTATAAAATAT
1 TATTTTAATTTTTATTATTTTTAAAAAGTAATTCTGAGATTTAATATAAAAT-T
* *
873602 T-TTGTTAATATTTATTATTTTTTAAAAAGTAATT-TGGGATTTAATATAAAATAT
1 TATT-TTAATTTTTATTA-TTTTTAAAAAGTAATTCTGAGATTTAATATAAAAT-T
* * * * * *
873656 GATTTTAATTTTTTATTATTTTGAAATAGTAATTC-AAAATTTAATATAAAATA
1 TATTTTAA-TTTTTATTATTTTTAAAAAGTAATTCTGAGATTTAATATAAAATT
* *
873709 T-TTTTAATTTTTATCATTTTTAAATAGTAATT-TGAGATTTAATAT
1 TATTTTAATTTTTATTATTTTTAAAAAGTAATTCTGAGATTTAATAT
873754 TTTATTATGT
Statistics
Matches: 299, Mismatches: 42, Indels: 41
0.78 0.11 0.11
Matches are distributed among these distances:
49 34 0.11
50 10 0.03
51 36 0.12
52 39 0.13
53 75 0.25
54 95 0.32
55 10 0.03
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (53 bp):
TATTTTAATTTTTATTATTTTTAAAAAGTAATTCTGAGATTTAATATAAAATT
Found at i:873590 original size:208 final size:208
Alignment explanation
Indices: 873343--873753 Score: 523
Period size: 208 Copynumber: 2.0 Consensus size: 208
873333 TAAATATGTA
** *
873343 TTTTATTTTTATTATTTTTTAAATAACAATTTGAGATTTAATATAAAAT-TTACTT-TTAATTTT
1 TTTTATTTTTATTATTTTTTAAATAACAATTCAAGATTTAATATAAAATATT--TTGTTAATATT
* * * * *
873406 TGTTA-TTTTTAAAAATTAGTTCT-TGATTTAATATAAAATAAG-TTTTTATTTTAATTATT-TT
64 TATTATTTTTTAAAAAGTAATT-TGGGATTTAATATAAAATAAGATTTTAATTTT--TTATTATT
* ** *
873467 TT-AAAAAGCAATTGTATGATTTAATATAAAATATTTTTAATTTTTTATTATTTTTAAACAGTAA
126 TTGAAAAAGCAATT-CAAAATTTAATATAAAATATTTTTAA-TTTTTATCATTTTTAAACAGTAA
873531 TTTGAGATTTAATATAATTT
189 TTTGAGATTTAATATAATTT
** *
873551 TTTTAATTTTTATTA-TTTTTAAATAGTAATTCAAGATTTAGTATAAAATATTTTGTTAATATTT
1 TTTT-ATTTTTATTATTTTTTAAATAACAATTCAAGATTTAATATAAAATATTTTGTTAATATTT
*
873615 ATTATTTTTTAAAAAGTAATTTGGGATTTAATATAAAATATGATTTTAATTTTTTATTATTTTGA
65 ATTATTTTTTAAAAAGTAATTTGGGATTTAATATAAAATAAGATTTTAATTTTTTATTATTTTGA
* * *
873680 AATAGTAATTCAAAATTTAATATAAAATATTTTTAATTTTTATCATTTTTAAATAGTAATTTGAG
130 AAAAGCAATTCAAAATTTAATATAAAATATTTTTAATTTTTATCATTTTTAAACAGTAATTTGAG
873745 ATTTAATAT
195 ATTTAATAT
873754 TTTATTATGT
Statistics
Matches: 176, Mismatches: 19, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
207 2 0.01
208 86 0.49
209 70 0.40
210 18 0.10
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (208 bp):
TTTTATTTTTATTATTTTTTAAATAACAATTCAAGATTTAATATAAAATATTTTGTTAATATTTA
TTATTTTTTAAAAAGTAATTTGGGATTTAATATAAAATAAGATTTTAATTTTTTATTATTTTGAA
AAAGCAATTCAAAATTTAATATAAAATATTTTTAATTTTTATCATTTTTAAACAGTAATTTGAGA
TTTAATATAATTT
Found at i:873626 original size:103 final size:103
Alignment explanation
Indices: 873333--873753 Score: 458
Period size: 106 Copynumber: 4.0 Consensus size: 103
873323 TAATAGTATG
** ** *
873333 TAAATATGTATTTT-ATTTTTATTATTTTTTAAATAACAATTTGAGATTTAATATAAAATTTACT
1 TAAATATGT-TTTTAATTTTTATTA-TTTTTAAATAGTAATTCAAGATTTAATATAAAA--TATT
* * * *
873397 TTTAATTTTTGTTATTTTTAAAAATTAGTTCT-TGATTTAATA
62 TTTAATTTTTATTATTTTTAAAAAGTAATT-TGAGATTTAATA
* * * * * *
873439 TAAAATAAGTTTTT-ATTTTAATTATTTTTTAAAAAGCAATTGTATGATTTAATATAAAATATTT
1 T-AAATATGTTTTTAATTTTTATTA-TTTTTAAATAGTAATT-CAAGATTTAATATAAAATATTT
*
873503 TTAATTTTTTATTATTTTTAAACAGTAATTTGAGATTTAATA
63 TTAA-TTTTTATTATTTTTAAAAAGTAATTTGAGATTTAATA
*
873545 T-AAT-T-TTTTTAATTTTTATTATTTTTAAATAGTAATTCAAGATTTAGTATAAAATATTTTGT
1 TAAATATGTTTTTAATTTTTATTATTTTTAAATAGTAATTCAAGATTTAATATAAAATA-TTT-T
* *
873607 TAATATTTATTATTTTTTAAAAAGTAATTTGGGATTTAATA
64 TAATTTTTATTA-TTTTTAAAAAGTAATTTGAGATTTAATA
* * *
873648 TAAAATATGATTTTAATTTTTTATTATTTTGAAATAGTAATTCAAAATTTAATATAAAATATTTT
1 T-AAATATGTTTTTAA-TTTTTATTATTTTTAAATAGTAATTCAAGATTTAATATAAAATATTTT
* *
873713 TAATTTTTATCATTTTTAAATAGTAATTTGAGATTTAATA
64 TAATTTTTATTATTTTTAAAAAGTAATTTGAGATTTAATA
873753 T
1 T
873754 TTTATTATGT
Statistics
Matches: 272, Mismatches: 30, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
101 16 0.06
102 30 0.11
103 40 0.15
104 3 0.01
105 39 0.14
106 72 0.26
107 31 0.11
108 41 0.15
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.53
Consensus pattern (103 bp):
TAAATATGTTTTTAATTTTTATTATTTTTAAATAGTAATTCAAGATTTAATATAAAATATTTTTA
ATTTTTATTATTTTTAAAAAGTAATTTGAGATTTAATA
Found at i:873765 original size:157 final size:155
Alignment explanation
Indices: 873459--873749 Score: 413
Period size: 159 Copynumber: 1.9 Consensus size: 155
873449 TTTTATTTTA
* *
873459 ATTATTTTTTAAAAAGCAATTGTATGATTTAATATAAAATATTTTTAATTTTTTATTATTTTTAA
1 ATTATTTTTTAAAAAGCAATTGTAGGATTTAATATAAAATATTTTTAATTTTTTATTATTTTGAA
** * * *
873524 ACAGTAATTTGAGATTTAATATAATTTTTTTAATTTTTATTATTTTTAAATAGTAATTCAAGATT
66 ACAGTAATTCAAAATTTAATATAATATTTTTAATTTTTATCATTTTTAAATAGTAATTCAAGATT
*
873589 TAGTATAAAATATTTTGTTAATATTT
131 TAG-ATAAAATATTATGTTAATATTT
* *
873615 ATTATTTTTTAAAAAGTAATT-TGGGATTTAATATAAAATATGATTTTAATTTTTTATTATTTTG
1 ATTATTTTTTAAAAAGCAATTGTAGGATTTAATATAAAATAT--TTTTAATTTTTTATTATTTTG
* **
873679 AAATAGTAATTCAAAATTTAATATAAAATATTTTTAATTTTTATCATTTTTAAATAGTAATTTGA
64 AAACAGTAATTCAAAATTTAATAT--AATATTTTTAATTTTTATCATTTTTAAATAGTAATTCAA
873744 GATTTA
127 GATTTA
873750 ATATTTTATT
Statistics
Matches: 119, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
155 18 0.15
156 20 0.17
157 40 0.34
159 41 0.34
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.53
Consensus pattern (155 bp):
ATTATTTTTTAAAAAGCAATTGTAGGATTTAATATAAAATATTTTTAATTTTTTATTATTTTGAA
ACAGTAATTCAAAATTTAATATAATATTTTTAATTTTTATCATTTTTAAATAGTAATTCAAGATT
TAGATAAAATATTATGTTAATATTT
Found at i:874067 original size:13 final size:13
Alignment explanation
Indices: 874049--874074 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
874039 CATATCCAGA
874049 TGTATCGATACAT
1 TGTATCGATACAT
874062 TGTATCGATACAT
1 TGTATCGATACAT
874075 AGGTATTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:874139 original size:104 final size:104
Alignment explanation
Indices: 873959--874178 Score: 422
Period size: 104 Copynumber: 2.1 Consensus size: 104
873949 ATATTTCAAA
*
873959 GTATCGATACATAGGTATTTGTATTGATACATTAGAGTTGACTTAAGCTACAAAGGTCAAAATCC
1 GTATCGATACATAGGTATTTGTATCGATACATTAGAGTTGACTTAAGCTACAAAGGTCAAAATCC
874024 CTGTATGTATTGATACATATCCAGATGTATCGATACATT
66 CTGTATGTATTGATACATATCCAGATGTATCGATACATT
874063 GTATCGATACATAGGTATTTGTATCGATACATTAGAGTTGACTTAAGCTACAAAGGTCAAAATCC
1 GTATCGATACATAGGTATTTGTATCGATACATTAGAGTTGACTTAAGCTACAAAGGTCAAAATCC
*
874128 TTGTATGTATTGATACATATCCAGATGTATCGATACATT
66 CTGTATGTATTGATACATATCCAGATGTATCGATACATT
874167 GTATCGATACAT
1 GTATCGATACAT
874179 GTTCATTTAC
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 114 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (104 bp):
GTATCGATACATAGGTATTTGTATCGATACATTAGAGTTGACTTAAGCTACAAAGGTCAAAATCC
CTGTATGTATTGATACATATCCAGATGTATCGATACATT
Found at i:874171 original size:13 final size:13
Alignment explanation
Indices: 874153--874178 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
874143 CATATCCAGA
874153 TGTATCGATACAT
1 TGTATCGATACAT
874166 TGTATCGATACAT
1 TGTATCGATACAT
874179 GTTCATTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:874520 original size:23 final size:23
Alignment explanation
Indices: 874490--874543 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
874480 CAGCTGAACT
* *
874490 TCAAGAGAAGCGCTCAAGAAACA
1 TCAAGAGAACCACTCAAGAAACA
*
874513 TCAAGAGATCCACTCAAGAAACA
1 TCAAGAGAACCACTCAAGAAACA
874536 TCAAGAGA
1 TCAAGAGA
874544 TCAAAGCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (23 bp):
TCAAGAGAACCACTCAAGAAACA
Found at i:874544 original size:23 final size:23
Alignment explanation
Indices: 874502--874545 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
874492 AAGAGAAGCG
874502 CTCAAGAAACATCAAGAGATCCA
1 CTCAAGAAACATCAAGAGATCCA
874525 CTCAAGAAACATCAAGAGATC
1 CTCAAGAAACATCAAGAGATC
874546 AAAGCATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.25, G:0.14, T:0.14
Consensus pattern (23 bp):
CTCAAGAAACATCAAGAGATCCA
Found at i:880557 original size:21 final size:21
Alignment explanation
Indices: 880528--880567 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
880518 TCTCACATTA
880528 CTTCATCAAACTTTC-TCAAAT
1 CTTCATCAAA-TTTCATCAAAT
*
880549 CTTCTTCAAATTTCATCAA
1 CTTCATCAAATTTCATCAA
880568 TTTTACATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (21 bp):
CTTCATCAAATTTCATCAAAT
Found at i:880567 original size:10 final size:10
Alignment explanation
Indices: 880529--880579 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
880519 CTCACATTAC
880529 TTCATCAAACT
1 TTCATCAAA-T
880540 TTC-TCAAAT
1 TTCATCAAAT
*
880549 CTTCTTCAAAT
1 -TTCATCAAAT
*
880560 TTCATCAATT
1 TTCATCAAAT
880570 TTACATCAAA
1 TT-CATCAAA
880580 AAATCTCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 1 0.03
10 18 0.53
11 15 0.44
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (10 bp):
TTCATCAAAT
Found at i:881975 original size:33 final size:33
Alignment explanation
Indices: 881914--881978 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
881904 TGAGAGTTGA
* * *
881914 TCACTTTACTTTCGCAGCACATGAATGAGCACG
1 TCACTTCACTCTCACAGCACATGAATGAGCACG
* *
881947 TCACTTCACTCTCACAGCGCATGGATGAGCAC
1 TCACTTCACTCTCACAGCACATGAATGAGCAC
881979 TATAGTGCAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (33 bp):
TCACTTCACTCTCACAGCACATGAATGAGCACG
Found at i:882916 original size:19 final size:19
Alignment explanation
Indices: 882873--882941 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 19
882863 TACATCTAGA
*
882873 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
882893 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
882912 TGTATCGATACATGCACAAT
1 TGTATCGATACATGTTC-AT
882932 TGTATCGATA
1 TGTATCGATA
882942 TATGAAACTG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 17 0.39
20 26 0.59
21 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:882987 original size:13 final size:13
Alignment explanation
Indices: 882969--882993 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
882959 CTACCCTGTT
882969 TGTATCGATACAA
1 TGTATCGATACAA
882982 TGTATCGATACA
1 TGTATCGATACA
882994 TGATGAATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:884001 original size:21 final size:21
Alignment explanation
Indices: 883933--884002 Score: 52
Period size: 21 Copynumber: 3.1 Consensus size: 21
883923 TAATTTGAGG
883933 TTTAATATAAAATAATTTTTTA
1 TTTAATATAAAAT-ATTTTTTA
* * * *
883955 -TTATTTTAAAAAATTAATTCGATA
1 TTTAATATAAAATATT--TT--TTA
883979 TTTAATATAAAATATTTTTTA
1 TTTAATATAAAATATTTTTTA
884000 TTT
1 TTT
884003 TTTATTTTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 11
0.65 0.15 0.20
Matches are distributed among these distances:
20 3 0.09
21 14 0.40
22 2 0.06
23 2 0.06
24 2 0.06
25 12 0.34
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (21 bp):
TTTAATATAAAATATTTTTTA
Found at i:884074 original size:54 final size:52
Alignment explanation
Indices: 883755--884099 Score: 305
Period size: 49 Copynumber: 6.9 Consensus size: 52
883745 TGAGCTTTCA
* *
883755 TATTATTTTTTAAAAAATAGTTTGAGATTTAATATAAAATA-TTTTTTA-TTT
1 TATTA-TTTTTAAAAAATAATTTAAGATTTAATATAAAATATTTTTTTATTTT
* ** * *
883806 T-TTATTATTAATTAGTAATTCTAA-ATTTAATATAAAATA-TTTTTAATTTTT
1 TATTATTTTTAAAAAATAATT-TAAGATTTAATATAAAATATTTTTTTA-TTTT
* * * **
883857 TATTAATTTTAAAAAGT-ATTCT-AGATTTAATATAAAATA-TTTTTAAAATT
1 TATTATTTTTAAAAAATAATT-TAAGATTTAATATAAAATATTTTTTTATTTT
* * * *
883907 TATTATTTTTAAATAATAATTTGAGGTTTAATATAAAATA-----AT-TTTT
1 TATTATTTTTAAAAAATAATTTAAGATTTAATATAAAATATTTTTTTATTTT
** *
883953 TATTA-TTTTAAAAAATTAATTCGATATTTAATATAAAATA-TTTTTTA-TTT
1 TATTATTTTTAAAAAA-TAATTTAAGATTTAATATAAAATATTTTTTTATTTT
884003 T-TTATTTTTAAAAAATAATTTAAGATTTAATATAAAATATTTTCTTTAATTTT
1 TATTATTTTTAAAAAATAATTTAAGATTTAATATAAAATATTTT-TTT-ATTTT
* *
884056 TATTATTTTTAAATAATAATATAAGATTTAATATAAAAT-TTTTT
1 TATTATTTTTAAAAAATAATTTAAGATTTAATATAAAATATTTTT
884100 AATTTTATTG
Statistics
Matches: 244, Mismatches: 31, Indels: 37
0.78 0.10 0.12
Matches are distributed among these distances:
45 9 0.04
46 28 0.11
49 56 0.23
50 41 0.17
51 54 0.22
52 13 0.05
53 8 0.03
54 35 0.14
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (52 bp):
TATTATTTTTAAAAAATAATTTAAGATTTAATATAAAATATTTTTTTATTTT
Found at i:884430 original size:17 final size:17
Alignment explanation
Indices: 884410--884448 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
884400 TATATAAATA
884410 TTAAAATAAAATTA-ATT
1 TTAAAAT-AAATTATATT
*
884427 TTAAAATAATTTATATT
1 TTAAAATAAATTATATT
884444 TTAAA
1 TTAAA
884449 TAATAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAAATAAATTATATT
Found at i:884470 original size:26 final size:27
Alignment explanation
Indices: 884434--884492 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
884424 ATTTTAAAAT
*
884434 AATTTATATTTTAAAT-AATAAAATAA
1 AATTTTTATTTTAAATAAATAAAATAA
* * *
884460 AATTTTTATTTTTAATAAATTAAATTA
1 AATTTTTATTTTAAATAAATAAAATAA
884487 AATTTT
1 AATTTT
884493 AAATAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AATTTTTATTTTAAATAAATAAAATAA
Found at i:884472 original size:27 final size:28
Alignment explanation
Indices: 884436--884492 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
884426 TTTAAAATAA
884436 TTTATATTTTAA-ATAATAAAATAAAATT
1 TTTATATTTTAATA-AATAAAATAAAATT
* *
884464 TTTAT-TTTTAATAAATTAAATTAAATT
1 TTTATATTTTAATAAATAAAATAAAATT
884491 TT
1 TT
884493 AAATAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTATATTTTAATAAATAAAATAAAATT
Found at i:884497 original size:21 final size:21
Alignment explanation
Indices: 884467--884506 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
884457 TAAAATTTTT
* *
884467 ATTTTTAATAAATTAAATTAA
1 ATTTTAAATAAATAAAATTAA
884488 ATTTTAAATAAATAAAATT
1 ATTTTAAATAAATAAAATT
884507 TTTTATCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTTAAATAAATAAAATTAA
Found at i:884509 original size:17 final size:17
Alignment explanation
Indices: 884475--884508 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
884465 TTATTTTTAA
*
884475 TAAATTAAATTAAATTT
1 TAAATTAAATAAAATTT
884492 TAAA-TAAATAAAATTT
1 TAAATTAAATAAAATTT
884508 T
1 T
884509 TTATCATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTAAATAAAATTT
Found at i:885729 original size:20 final size:18
Alignment explanation
Indices: 885679--885743 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
885669 CCTTATGCTG
* *
885679 AAAAAATAATACAAAGAAA
1 AAAAAAGAATA-AAGGAAA
*
885698 AAGAAA-AATAAAGGAAA
1 AAAAAAGAATAAAGGAAA
*
885715 GGAAAAAAGAATAAATGAAA
1 --AAAAAAGAATAAAGGAAA
885735 AAAAAAGAA
1 AAAAAAGAA
885744 GAAGAAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 6 0.15
18 13 0.33
19 10 0.26
20 10 0.26
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.08
Consensus pattern (18 bp):
AAAAAAGAATAAAGGAAA
Found at i:885883 original size:36 final size:36
Alignment explanation
Indices: 885843--885925 Score: 166
Period size: 36 Copynumber: 2.3 Consensus size: 36
885833 GGTTTTCGGC
885843 TTATTTACCTTTCCTTTCTAAACCATGGCCTAAATG
1 TTATTTACCTTTCCTTTCTAAACCATGGCCTAAATG
885879 TTATTTACCTTTCCTTTCTAAACCATGGCCTAAATG
1 TTATTTACCTTTCCTTTCTAAACCATGGCCTAAATG
885915 TTATTTACCTT
1 TTATTTACCTT
885926 GAAAAGGCCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.45
Consensus pattern (36 bp):
TTATTTACCTTTCCTTTCTAAACCATGGCCTAAATG
Found at i:887310 original size:117 final size:116
Alignment explanation
Indices: 887143--887357 Score: 292
Period size: 117 Copynumber: 1.8 Consensus size: 116
887133 TTCATAACCC
* * * *
887143 TGTGCAGCATTCACATATTCTGGGCCATGTACATCCATACATTTTGTATCATTCAT-AAGCATAT
1 TGTGCAGCATTCACATATTCCGGGCCATATACATCCATACATTTTATATCATTCATGAA-CACAT
*
887207 GCATCACTTTAATCATGG-CATATGTATCTAAGCATTTGCATTGTTCATGTTGG
65 GCATCA-TTTAATCA-GGTCATATGCATCTAAGCATTTGCATTGTTCATGTTGG
* * *
887260 TGTGCAGCTTTCACATAATTCCGGGCCATATTCATCCATGCA-TTTATATCATTCATGAACACAT
1 TGTGCAGCATTCACAT-ATTCCGGGCCATATACATCCATACATTTTATATCATTCATGAACACAT
*
887324 GCATCATTTTATCAGGTCATATGCATCTAAGCAT
65 GCATCATTTAATCAGGTCATATGCATCTAAGCAT
887358 CTATATCATT
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
115 2 0.02
116 23 0.27
117 38 0.44
118 23 0.27
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (116 bp):
TGTGCAGCATTCACATATTCCGGGCCATATACATCCATACATTTTATATCATTCATGAACACATG
CATCATTTAATCAGGTCATATGCATCTAAGCATTTGCATTGTTCATGTTGG
Found at i:888268 original size:122 final size:123
Alignment explanation
Indices: 888069--888299 Score: 295
Period size: 122 Copynumber: 1.9 Consensus size: 123
888059 CTTCAAGAAC
* * *
888069 ATTTCAAAAACATTTCATCAGGGATTTTTTTAGGACATGTATTAGAGATATTCTCCAAAAACCTC
1 ATTTCAAAAACAATTCATCAGGGATTTTTTGAGGACATGTATTAGAGATACTCTCCAAAAACCTC
* *
888134 TGTAGAGGACA-TTAAAAAGCTTTTTTCGAGGACATTTTGAAAACCCTTCTTAATGAT
66 TCTAGAGGACATTTAAAAAGCTTTTTTCAAGGACATTTTGAAAACCCTTCTTAATGAT
* * ** * * *
888191 ATTTCAAAAACAATTGATTAGGGATTTTTTGAGGACATGTATTAGAGATACTCTTTAAAAGCTTT
1 ATTTCAAAAACAATTCATCAGGGATTTTTTGAGGACATGTATTAGAGATACTCTCCAAAAACCTC
* ** *
888256 TCTTG-GGAACATTTCGAAAGCTTTTTTTAAGGACATTTTGAAAA
66 TCTAGAGG-ACATTTAAAAAGCTTTTTTCAAGGACATTTTGAAAA
888300 ACCTCACTCG
Statistics
Matches: 91, Mismatches: 16, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
121 2 0.02
122 61 0.67
123 28 0.31
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (123 bp):
ATTTCAAAAACAATTCATCAGGGATTTTTTGAGGACATGTATTAGAGATACTCTCCAAAAACCTC
TCTAGAGGACATTTAAAAAGCTTTTTTCAAGGACATTTTGAAAACCCTTCTTAATGAT
Found at i:892641 original size:3 final size:3
Alignment explanation
Indices: 892633--892657 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
892623 CTATAATGTA
892633 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
892658 TATTTAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:897346 original size:196 final size:196
Alignment explanation
Indices: 897012--897383 Score: 620
Period size: 196 Copynumber: 1.9 Consensus size: 196
897002 AAGGGCCTAG
*
897012 AAAAATTAAGTGTCTACAAGGATATTTCATTAGATATGTTCTAAAAGCCTATCTTAAGGATATTT
1 AAAAATTAAATGTCTACAAGGATATTTCATTAGATATGTTCTAAAAGCCTATCTTAAGGATATTT
* ** * * *
897077 CAATTAGGATAGTTTTAAATCTTCTTTCAAGGATACCTTCAAAGCTTCCTATAAGGCTTTTTTTT
66 CAATTAGGATAGTTTTAAAACTTCTTTCAAAAATACCTTCAAAGCTTCCCATAAAGCCTTTTTTT
*
897142 AAGGTTAACTCGTTCCCTTAAAAAGGGTTAAGCCTTAAGATTAATGTTTACTCAAAAAAGGCCTG
131 AAGGTTAACTCATTCCCTTAAAAAGGGTTAAGCCTTAAGATTAATGTTTACTCAAAAAAGGCCTG
897207 A
196 A
* *
897208 AAAAATTAAATGTCTACAAGGATATTTCGTTATG-TATGTTTTAAAAGCCTATCTTAAGGATATT
1 AAAAATTAAATGTCTACAAGGATATTTCATTA-GATATGTTCTAAAAGCCTATCTTAAGGATATT
897272 TCAATTAGGATAGTTTTAAAACTTCTTTCAAAAATACCTTCAAAGCTTCCCATAAAGCCTTTTTT
65 TCAATTAGGATAGTTTTAAAACTTCTTTCAAAAATACCTTCAAAGCTTCCCATAAAGCCTTTTTT
* *
897337 TAAGGTTAACTCATTCCCTTAAGAAGGGTTTAGCCTTAAGATTAATG
130 TAAGGTTAACTCATTCCCTTAAAAAGGGTTAAGCCTTAAGATTAATG
897384 CTGAGATATT
Statistics
Matches: 163, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
196 162 0.99
197 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (196 bp):
AAAAATTAAATGTCTACAAGGATATTTCATTAGATATGTTCTAAAAGCCTATCTTAAGGATATTT
CAATTAGGATAGTTTTAAAACTTCTTTCAAAAATACCTTCAAAGCTTCCCATAAAGCCTTTTTTT
AAGGTTAACTCATTCCCTTAAAAAGGGTTAAGCCTTAAGATTAATGTTTACTCAAAAAAGGCCTG
A
Found at i:900793 original size:20 final size:21
Alignment explanation
Indices: 900768--900806 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
900758 TTAAAAATAG
*
900768 AATTTTTAAT-TAAACCTTGA
1 AATTTTCAATATAAACCTTGA
900788 AATTTTCAATATAAACCTT
1 AATTTTCAATATAAACCTT
900807 CACATATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.44
Consensus pattern (21 bp):
AATTTTCAATATAAACCTTGA
Found at i:901651 original size:20 final size:21
Alignment explanation
Indices: 901603--901656 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
901593 TTTACAAATT
*
901603 TGTATCGATACAAACAGTAAA
1 TGTATCGATACATACAGTAAA
* *
901624 TATATCGATACATA-AGTGAA
1 TGTATCGATACATACAGTAAA
901644 TGTATCGATACAT
1 TGTATCGATACAT
901657 GTCTAAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATACAGTAAA
Found at i:901769 original size:20 final size:22
Alignment explanation
Indices: 901724--901775 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
901714 CATTAGTAAA
901724 TGTATCGATACATGCTTACAAT
1 TGTATCGATACATGCTTACAAT
* *
901746 TGTATCGATACAT-TTTTC-AT
1 TGTATCGATACATGCTTACAAT
901766 TGTATCGATA
1 TGTATCGATA
901776 TATTCTGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.43
21 3 0.11
22 13 0.46
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.42
Consensus pattern (22 bp):
TGTATCGATACATGCTTACAAT
Found at i:903045 original size:12 final size:12
Alignment explanation
Indices: 903028--903053 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
903018 GCCTTAATCA
903028 ATGGGAATTAAC
1 ATGGGAATTAAC
903040 ATGGGAATTAAC
1 ATGGGAATTAAC
903052 AT
1 AT
903054 AAACTTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (12 bp):
ATGGGAATTAAC
Found at i:905908 original size:14 final size:13
Alignment explanation
Indices: 905890--905924 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 13
905880 AATTTGACAA
905890 AAAAAAGAGAAAAAG
1 AAAAAA-AG-AAAAG
905905 AAAAAAAGAAAAG
1 AAAAAAAGAAAAG
905918 AAAAAAA
1 AAAAAAA
905925 TTCTAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.60
14 2 0.10
15 6 0.30
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:907993 original size:17 final size:17
Alignment explanation
Indices: 907967--908005 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
907957 TATATTTAGG
907967 AAAATAAAGTATGCATA
1 AAAATAAAGTATGCATA
*
907984 AAAATTAAGTATGCATA
1 AAAATAAAGTATGCATA
908001 AAAAT
1 AAAAT
908006 CCTAAATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.05, G:0.10, T:0.26
Consensus pattern (17 bp):
AAAATAAAGTATGCATA
Found at i:909117 original size:14 final size:14
Alignment explanation
Indices: 909098--909124 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
909088 AGATCCCCGC
909098 CATTTTTTTTTATT
1 CATTTTTTTTTATT
909112 CATTTTTTTTTAT
1 CATTTTTTTTTAT
909125 ATTTATGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (14 bp):
CATTTTTTTTTATT
Found at i:909947 original size:17 final size:16
Alignment explanation
Indices: 909925--909980 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
909915 ATTTAAATTG
909925 ATAATTATAAACATAAT
1 ATAATTATAAA-ATAAT
909942 ATAATTATATAAATAAAT
1 ATAATTATA-AAAT-AAT
*
909960 ACAATGTA-AAATATAAT
1 ATAAT-TATAAA-ATAAT
909977 ATAA
1 ATAA
909981 AAACATGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
17 19 0.58
18 12 0.36
19 2 0.06
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.34
Consensus pattern (16 bp):
ATAATTATAAAATAAT
Found at i:910027 original size:17 final size:16
Alignment explanation
Indices: 910005--910036 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
909995 ATGAAAAGTA
910005 ATATAAATATAATTAAG
1 ATATAAATAT-ATTAAG
910022 ATATAAATATATTAA
1 ATATAAATATATTAA
910037 ATTTTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
ATATAAATATATTAAG
Found at i:910062 original size:17 final size:16
Alignment explanation
Indices: 910004--910086 Score: 62
Period size: 19 Copynumber: 4.9 Consensus size: 16
909994 TATGAAAAGT
910004 AATATAAATATAATTA
1 AATATAAATATAATTA
910020 AGATATAAATAT-ATTA
1 A-ATATAAATATAATTA
**
910036 AAT-TTTATATAATATA
1 AATATAAATATAAT-TA
910052 AATATTAATATATCAATATA
1 AATA-TAA-ATAT-AAT-TA
*
910072 TATATAATATATAAT
1 AATATAA-ATATAAT
910087 AAACTCAACA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
14 5 0.09
15 4 0.07
16 11 0.20
17 10 0.18
18 4 0.07
19 12 0.22
20 9 0.16
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (16 bp):
AATATAAATATAATTA
Found at i:910062 original size:31 final size:31
Alignment explanation
Indices: 910004--910087 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
909994 TATGAAAAGT
*
910004 AATATAAATATAAT-TAAGATATAAATATATTA
1 AATATATATATAATATAA-ATATAAATATA-TA
* * *
910036 AAT-TTTATATAATATAAATATTAATATATC
1 AATATATATATAATATAAATATAAATATATA
910066 AATATATATATAATATATAATA
1 AATATATATATAATATA-AATA
910088 AACTCAACAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
30 4 0.09
31 30 0.68
32 10 0.23
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (31 bp):
AATATATATATAATATAAATATAAATATATA
Found at i:910255 original size:2 final size:2
Alignment explanation
Indices: 910248--910294 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
910238 GCCCATGTCC
*
910248 CT CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
910290 CT CT C
1 CT CT C
910295 ATATATAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:914325 original size:29 final size:29
Alignment explanation
Indices: 914274--914348 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 29
914264 TTTAATCGTA
*
914274 TTAAATA--ATAATTATTTATTTAAATATTT
1 TTAAATATTATAA-TATTTATTT-AATATAT
914303 TTAAATATTATAATATTTA-TTAATATAT
1 TTAAATATTATAATATTTATTTAATATAT
*
914331 TAAAATAATTAT-ATATTT
1 TTAAAT-ATTATAATATTT
914349 GATCGAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 17 0.41
29 14 0.34
30 6 0.15
31 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TTAAATATTATAATATTTATTTAATATAT
Found at i:914332 original size:20 final size:19
Alignment explanation
Indices: 914290--914342 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
914280 AATAATTATT
*
914290 TATTTAAATATTT-TTAAA
1 TATTAAAATATTTATTAAA
*
914308 TATTATAATATTTATTAATA
1 TATTAAAATATTTATTAA-A
*
914328 TATTAAAATAATTAT
1 TATTAAAATATTTAT
914343 ATATTTGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 11 0.38
19 4 0.14
20 14 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTAAAATATTTATTAAA
Found at i:916948 original size:2 final size:2
Alignment explanation
Indices: 916941--916980 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
916931 AGGTATCTTC
916941 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
916981 GCAGCATATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:921014 original size:5 final size:5
Alignment explanation
Indices: 920994--921074 Score: 51
Period size: 5 Copynumber: 16.2 Consensus size: 5
920984 TAAGATAATT
* * * *
920994 ATATA ATTTAA ATATA ATATAA AAATA ATTATA ATATT ATATA AAATA
1 ATATA ATAT-A ATATA ATAT-A ATATA A-TATA ATATA ATATA ATATA
* * *
921042 AT-TA AAATA A-A-A ATAAA ATAAA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
921075 AAAATAATAC
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
3 2 0.03
4 5 0.08
5 41 0.68
6 12 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
ATATA
Found at i:921022 original size:30 final size:29
Alignment explanation
Indices: 920988--921082 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
920978 TAGACATAAG
920988 ATAATTATATAATTTAAATATAATATAAAA
1 ATAATTATA-AATTTAAATATAATATAAAA
*
921018 ATAATTATAATATTATATAAAATAAT-T-AAA
1 ATAATTATAA-ATT-TA-AATATAATATAAAA
** * *
921048 ATAAAAATAAAATAAAATATAATATAAAAA
1 ATAATTATAAATTTAAATATAATAT-AAAA
921078 ATAAT
1 ATAAT
921083 ACAAACACGA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
27 7 0.13
28 2 0.04
29 3 0.06
30 30 0.58
31 3 0.06
32 7 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
ATAATTATAAATTTAAATATAATATAAAA
Done.