Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008199.1 Hibiscus syriacus cultivar Beakdansim tig00110819_pilon, whole genome shotgun sequence
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: 2638622
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1575494 original size:18 final size:18
Alignment explanation
Indices: 1575473--1575509 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1575463 GTAATTGGAG
1575473 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1575491 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1575509 T
1 T
1575510 ATAAATTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1575516 original size:24 final size:24
Alignment explanation
Indices: 1575465--1575517 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1575455 TTTCATATGT
* * *
1575465 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
1575489 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1575513 AATTT
1 AATTT
1575518 CAGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1575821 original size:39 final size:39
Alignment explanation
Indices: 1575778--1575864 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
1575768 TCTGATGCTC
* *
1575778 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCACATATAGTGCCAAGCAAAAGGAA
*
1575817 ATCAAAATCCAAATCACATATAGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCACATATAGTGCCAAGCAAAAGGAA
1575856 ATCAAAATC
1 ATCAAAATC
1575865 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.49, C:0.21, G:0.14, T:0.16
Consensus pattern (39 bp):
ATCAAAATCCAAAGCACATATAGTGCCAAGCAAAAGGAA
Found at i:1577812 original size:21 final size:21
Alignment explanation
Indices: 1577778--1577831 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1577768 CTTCTTCGAT
* *
1577778 GATGTTAGGGGCCTATTGAAC
1 GATGATAGGTGCCTATTGAAC
* *
1577799 GAT-ATGAGGTGCCTCTTGAAT
1 GATGAT-AGGTGCCTATTGAAC
1577820 GATGATAGGTGC
1 GATGATAGGTGC
1577832 ACCGGGCTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 24 0.89
22 2 0.07
ACGTcount: A:0.24, C:0.13, G:0.33, T:0.30
Consensus pattern (21 bp):
GATGATAGGTGCCTATTGAAC
Found at i:1577987 original size:12 final size:12
Alignment explanation
Indices: 1577968--1578009 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1577958 GGGCCACTGA
1577968 AAATAAATTAAT
1 AAATAAATTAAT
* *
1577980 ATATAAATTAGT
1 AAATAAATTAAT
*
1577992 AAATAAATAAAT
1 AAATAAATTAAT
1578004 AAATAA
1 AAATAA
1578010 TGCCGAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (12 bp):
AAATAAATTAAT
Found at i:1580306 original size:22 final size:22
Alignment explanation
Indices: 1580278--1580321 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1580268 GGAGATAGAA
1580278 GGATTTCGTCGGAAATGGGGAC
1 GGATTTCGTCGGAAATGGGGAC
*
1580300 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCGTCGGAAATGGGGAC
1580322 AGATGTCGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.14, G:0.43, T:0.23
Consensus pattern (22 bp):
GGATTTCGTCGGAAATGGGGAC
Found at i:1588221 original size:16 final size:16
Alignment explanation
Indices: 1588200--1588231 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1588190 TTGTTTGTAG
1588200 GAATTGTTTAAGTGTT
1 GAATTGTTTAAGTGTT
1588216 GAATTGTTTAAGTGTT
1 GAATTGTTTAAGTGTT
1588232 CATTGTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (16 bp):
GAATTGTTTAAGTGTT
Found at i:1589805 original size:16 final size:16
Alignment explanation
Indices: 1589786--1589816 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1589776 GTTATTGAAC
1589786 TGATATGATATTTACT
1 TGATATGATATTTACT
*
1589802 TGATTTGATATTTAC
1 TGATATGATATTTAC
1589817 CTAATTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (16 bp):
TGATATGATATTTACT
Found at i:1590337 original size:16 final size:16
Alignment explanation
Indices: 1590316--1590357 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
1590306 AATTTTTTAG
1590316 ATTTTATTATTTATTA
1 ATTTTATTATTTATTA
*
1590332 ATTTTA-TA-TAATTA
1 ATTTTATTATTTATTA
1590346 ATTTT-TTATTTA
1 ATTTTATTATTTA
1590358 AAATATGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
14 12 0.55
15 4 0.18
16 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTATTATTTATTA
Found at i:1590567 original size:29 final size:29
Alignment explanation
Indices: 1590535--1590652 Score: 125
Period size: 29 Copynumber: 4.1 Consensus size: 29
1590525 TATATGTATA
* *
1590535 ATGTGTGTATAATTTATTAAAATGTATGT
1 ATGTGCGTATAATTAATTAAAATGTATGT
* *
1590564 ATGTACGTATAATTAATT--AATGTAT-A
1 ATGTGCGTATAATTAATTAAAATGTATGT
* *
1590590 ATGTGTGTATAATTTATTAAAATGTATGT
1 ATGTGCGTATAATTAATTAAAATGTATGT
* **
1590619 ATGTGCATATAATTAATTAATGTGTAATGT
1 ATGTGCGTATAATTAATTAAAATGT-ATGT
1590649 ATGT
1 ATGT
1590653 ATGATATATG
Statistics
Matches: 72, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
26 15 0.21
27 7 0.10
28 7 0.10
29 35 0.49
30 8 0.11
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.46
Consensus pattern (29 bp):
ATGTGCGTATAATTAATTAAAATGTATGT
Found at i:1590587 original size:55 final size:55
Alignment explanation
Indices: 1590528--1590654 Score: 218
Period size: 55 Copynumber: 2.3 Consensus size: 55
1590518 ATTGATATAT
*
1590528 ATGTATAATGTGTGTATAATTTATTAAAATGTATGTATGTACGTATAATTAATTA
1 ATGTATAATGTGTGTATAATTTATTAAAATGTATGTATGTACATATAATTAATTA
*
1590583 ATGTATAATGTGTGTATAATTTATTAAAATGTATGTATGTGCATATAATTAATTA
1 ATGTATAATGTGTGTATAATTTATTAAAATGTATGTATGTACATATAATTAATTA
* *
1590638 ATGTGTAATGTATGTAT
1 ATGTATAATGTGTGTAT
1590655 GATATATGTA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 68 1.00
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.46
Consensus pattern (55 bp):
ATGTATAATGTGTGTATAATTTATTAAAATGTATGTATGTACATATAATTAATTA
Found at i:1590956 original size:26 final size:25
Alignment explanation
Indices: 1590927--1591035 Score: 106
Period size: 22 Copynumber: 4.5 Consensus size: 25
1590917 GTATGTATGT
1590927 ATGTATATATGTATAATTAATATATA
1 ATGTATA-ATGTATAATTAATATATA
1590953 ATG--T-ATGTATAATT-A-AT-TA
1 ATGTATAATGTATAATTAATATATA
*
1590972 ATGTATAATGTATGAATTGATATAT-
1 ATGTATAATGTAT-AATTAATATATA
* * *
1590997 ATGCATAATGTATAAATAATTTATTA
1 ATGTATAATGTATAATTAATATA-TA
1591023 ATGTATAATGTAT
1 ATGTATAATGTAT
1591036 GCATGCGTGC
Statistics
Matches: 69, Mismatches: 5, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
19 5 0.07
20 2 0.03
21 2 0.03
22 16 0.23
23 4 0.06
24 9 0.13
25 15 0.22
26 16 0.23
ACGTcount: A:0.43, C:0.01, G:0.11, T:0.45
Consensus pattern (25 bp):
ATGTATAATGTATAATTAATATATA
Found at i:1591074 original size:2 final size:2
Alignment explanation
Indices: 1591067--1591105 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1591057 ATTTATACTT
* *
1591067 TA TA TA TA TA TA TA TA TA TA TA TA TA CA CA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1591106 CATGCATCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1604270 original size:135 final size:135
Alignment explanation
Indices: 1604023--1604278 Score: 374
Period size: 135 Copynumber: 1.9 Consensus size: 135
1604013 TCTGGAAAGG
*
1604023 AAGTAGAGGAAAGCAAGCCTTCAAAGTATATTGAAGAACATACTCGAACCCTAAACGAGCATAAA
1 AAGTAGAGGAAAGCAAGCCTTCAAAGTATATTGAAGAACATACTCGAAACCTAAACGAGCATAAA
* * *
1604088 ACTATAGATGCACCAAATGCAGTTCAAAGAAGAGACAACTTAGAATCTGTTCCAGAAATTATAGT
66 ACTAGAGATGCACCAAAAGCAGTTCAAAGAAGAGACAACTTAAAATCTGTTCCAGAAATTATAGT
1604153 GGATC
131 GGATC
* * *
1604158 AAGTAGAGGAAAGCCAA-CCTTCAAAGTATATTGAAGAAGATACTC-AAACCTTAACTGAGCTTA
1 AAGTAGAGGAAAG-CAAGCCTTCAAAGTATATTGAAGAACATACTCGAAACCTAAAC-GAGCATA
* * *
1604221 ACACTAGAGATGCACCAAACAG-AGTTCAAAGCAGTGACAACTTAAAATCTGTTCCAGA
64 AAACTAGAGATGCACCAAA-AGCAGTTCAAAGAAGAGACAACTTAAAATCTGTTCCAGA
1604279 TACTAAAGTT
Statistics
Matches: 108, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
134 8 0.07
135 96 0.89
136 4 0.04
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.21
Consensus pattern (135 bp):
AAGTAGAGGAAAGCAAGCCTTCAAAGTATATTGAAGAACATACTCGAAACCTAAACGAGCATAAA
ACTAGAGATGCACCAAAAGCAGTTCAAAGAAGAGACAACTTAAAATCTGTTCCAGAAATTATAGT
GGATC
Found at i:1605220 original size:150 final size:150
Alignment explanation
Indices: 1604944--1605228 Score: 455
Period size: 150 Copynumber: 1.9 Consensus size: 150
1604934 AGGTAATGGT
* ** *
1604944 GAATCCCTATTCTTAATCAGACCGGAAGGCATCAGCAGGTTTGGAAAATCAAATGAACAAGAAGC
1 GAATCCCTATTCTTAATCAGACCGGAAGACATCAGCAGGCCTGAAAAATCAAATGAACAAGAAGC
*
1605009 TGATATGAACAAAACAGAAACAATTGAAAGCGATTGTACAAGAGTTGTTGAAAGTGAAAAAGAAA
66 TGATATGAACAAAACAGAAACAATTGAAAGCGATTATACAAGAGTTGTTGAAAGTGAAAAAGAAA
1605074 GAGAGACAGCTAATGAAGGC
131 GAGAGACAGCTAATGAAGGC
*
1605094 GAATCCCTATTCTTAATCAGACCGGAAGACATCAGCGGGCCTGAAAAATCAAATGAACAAGAAGC
1 GAATCCCTATTCTTAATCAGACCGGAAGACATCAGCAGGCCTGAAAAATCAAATGAACAAGAAGC
* * * *
1605159 TGATATGAACGAAACAGAAACAATTGGAAGTGATTATACAAGCA-TTGTTGAAAGTGCAAAAGAA
66 TGATATGAACAAAACAGAAACAATTGAAAGCGATTATACAAG-AGTTGTTGAAAGTGAAAAAGAA
*
1605223 CGAGAG
130 AGAGAG
1605229 GTAATACATT
Statistics
Matches: 123, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
150 122 0.99
151 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.19
Consensus pattern (150 bp):
GAATCCCTATTCTTAATCAGACCGGAAGACATCAGCAGGCCTGAAAAATCAAATGAACAAGAAGC
TGATATGAACAAAACAGAAACAATTGAAAGCGATTATACAAGAGTTGTTGAAAGTGAAAAAGAAA
GAGAGACAGCTAATGAAGGC
Found at i:1606837 original size:41 final size:41
Alignment explanation
Indices: 1606739--1606864 Score: 173
Period size: 41 Copynumber: 3.0 Consensus size: 41
1606729 TCTGTATTAC
1606739 TCAAGACTCGGAACTAAATATCTTATGTATGTGTGTGTGTGTG
1 TCAAGACTCGGAACTAAATATCTTATGTA--TGTGTGTGTGTG
* * * *
1606782 TCAAGACAT-AGAACTCAATATCTTATGCATGTATGTGTGTG
1 TCAAGAC-TCGGAACTAAATATCTTATGTATGTGTGTGTGTG
*
1606823 TCAAGACTCGGAACTAAATATCTTATGTGTGTGTGTGTGTG
1 TCAAGACTCGGAACTAAATATCTTATGTATGTGTGTGTGTG
1606864 T
1 T
1606865 ATCTAAACTC
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
40 1 0.01
41 46 0.64
43 24 0.33
44 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.37
Consensus pattern (41 bp):
TCAAGACTCGGAACTAAATATCTTATGTATGTGTGTGTGTG
Found at i:1608383 original size:30 final size:30
Alignment explanation
Indices: 1608338--1608395 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1608328 TTTATTTCGA
* *
1608338 GGATTAAATTAAAATTTTAATTAAATTCAG
1 GGATCAAAGTAAAATTTTAATTAAATTCAG
*
1608368 GGATCAAAGTAAAATTTTAATTGAATTC
1 GGATCAAAGTAAAATTTTAATTAAATTC
1608396 GGATCCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (30 bp):
GGATCAAAGTAAAATTTTAATTAAATTCAG
Found at i:1613799 original size:29 final size:29
Alignment explanation
Indices: 1613742--1613809 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
1613732 ATTTTATGAG
*
1613742 TATTGTTTATATGATATTTGATTTACTGTA
1 TATT-TTTATATGATATTTGAGTTACTGTA
*
1613772 TATTTTTGATATGATCTTT-AGTTACTGTA
1 TATTTTT-ATATGATATTTGAGTTACTGTA
*
1613801 TTTTTTTAT
1 TATTTTTAT
1613810 CTTATTTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.06
29 18 0.53
30 14 0.41
ACGTcount: A:0.24, C:0.04, G:0.12, T:0.60
Consensus pattern (29 bp):
TATTTTTATATGATATTTGAGTTACTGTA
Found at i:1615224 original size:16 final size:16
Alignment explanation
Indices: 1615173--1615229 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 16
1615163 GCTTGAATAA
1615173 AAAATAAAATATCAA-AT
1 AAAATAAAA-A-CAACAT
1615190 AAAA-AATAAA-AACAGT
1 AAAATAA-AAACAACA-T
1615206 AAAATAAAAACAACAT
1 AAAATAAAAACAACAT
1615222 AAAATAAA
1 AAAATAAA
1615230 TTAAAATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
14 2 0.06
15 1 0.03
16 20 0.57
17 12 0.34
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (16 bp):
AAAATAAAAACAACAT
Found at i:1615229 original size:21 final size:21
Alignment explanation
Indices: 1615205--1615248 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1615195 ATAAAAACAG
1615205 TAAAATAAAA-ACAACATAAAA
1 TAAAATAAAATA-AACATAAAA
* *
1615226 TAAATTAAAATAAACATATAA
1 TAAAATAAAATAAACATAAAA
1615247 TA
1 TA
1615249 TAAAGATCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAAATAAAATAAACATAAAA
Found at i:1616759 original size:13 final size:13
Alignment explanation
Indices: 1616741--1616770 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1616731 CATTATGATT
1616741 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
1616754 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
1616767 TTTT
1 TTTT
1616771 ACTTGAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:1617324 original size:2 final size:2
Alignment explanation
Indices: 1617317--1617342 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1617307 TGGTTTTCTG
1617317 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
1617343 TTATCGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1618279 original size:37 final size:37
Alignment explanation
Indices: 1618203--1618279 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
1618193 TTTTTATGTT
*
1618203 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
1618240 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
1618277 TTT
1 TTT
1618280 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:1618462 original size:19 final size:18
Alignment explanation
Indices: 1618419--1618462 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
1618409 CCAGTAATTC
*
1618419 TATTCCCTGATAATCTTT
1 TATTCCCTGATAATCTTA
*
1618437 TATTTCCACTGGTAATCTTA
1 TA-TTCC-CTGATAATCTTA
1618457 TATTCC
1 TATTCC
1618463 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 8 0.36
20 12 0.55
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.48
Consensus pattern (18 bp):
TATTCCCTGATAATCTTA
Found at i:1618644 original size:32 final size:29
Alignment explanation
Indices: 1618608--1618666 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 29
1618598 AATATTAATC
* *
1618608 TAATATAAGTTCTAAATAATTAAGAATATAAA
1 TAATAAAAGTT-TAAA-AAATAAG-ATATAAA
1618640 TAATAAAAGTTTAAAAAATAAGATATA
1 TAATAAAAGTTTAAAAAATAAGATATA
1618667 CAAGATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 6 0.24
31 4 0.16
32 10 0.40
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (29 bp):
TAATAAAAGTTTAAAAAATAAGATATAAA
Found at i:1631972 original size:2 final size:2
Alignment explanation
Indices: 1631959--1631996 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1631949 TATAATTGCG
*
1631959 AT AT AA 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
1631997 TCTTTTCCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1633039 original size:5 final size:5
Alignment explanation
Indices: 1633029--1633054 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1633019 ATTCATATAT
1633029 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
1633055 GAAACTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:1633429 original size:252 final size:238
Alignment explanation
Indices: 1632974--1633572 Score: 733
Period size: 252 Copynumber: 2.4 Consensus size: 238
1632964 TTTATTTATA
* *
1632974 TATTGAATAAAAATATTTTTTTTATTATTTCGGGTTGGGTTTCTAATTCATATATTCGGGTCGGG
1 TATTGAATAAAAATA-ATTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATA------T----
* *
1633039 TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTTGGGTTTTTTAACTGTGATATTC
55 TCGGGTCGGGT-GGGTGAAACTTTATTTTGGTCGGGTCGAGTCGGGTTTTTTAACTGTGATATTC
* * *
1633104 GGGTCGGGTCAAGTTTGGGTTTAGGGTGAAAAATACCTGACCCGAAAATTATATAATTTTACCTT
119 GGGTCGGGTC-----TGGGTTAAGGGTGAAAAATACCTGACCCAAAAAATATATAATTTTACCTT
* *
1633169 ATATATTTAGGAATAATTACAATAATAGCCCTCAATATATAATTTTTTTCAATTAAGTCACTGTT
179 ATATATTTAGGAATAATTACAATAATA--CCTC--TATAT-A--TATTCCAATTAAGTCACTGTT
1633234 TT
237 TT
1633236 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGG
1 TATTGAATAAAAATAA-TTTTTTATTATTTCGGGTC--G--GG-TTTCTAATTCATATATTCGGG
* * ** *
1633301 TCGGGTAGGGTGAAATTTTATTTTGCTCGGGTCGAGTCGTTTTTTTTTAAGTGTGATATTCGGGT
60 TCGGGT-GGGTGAAACTTTATTTTGGTCGGGTCGAGTCG-GGTTTTTTAACTGTGATATTCGGGT
1633366 CGGGTC-GGGTTAAGGGTGAAAAATA-CTCGACCCAAAAAATATATAATTTTACCTTATATATTT
123 CGGGTCTGGGTTAAGGGTGAAAAATACCT-GACCCAAAAAATATATAATTTTACCTTATATATTT
1633429 AGGAATAATTACAATAATACCTCTATATATATTCCAATTAAGTCACTGTTTT
187 AGGAATAATTACAATAATACCTCTATATATATTCCAATTAAGTCACTGTTTT
1633481 TATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTC----
1 TATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGT
1633542 GGGTGAAACTTTATTTTGGTCGGGTCGAGTC
66 GGGTGAAACTTTATTTTGGTCGGGTCGAGTC
1633573 TCGGATGGAG
Statistics
Matches: 312, Mismatches: 17, Indels: 44
0.84 0.05 0.12
Matches are distributed among these distances:
234 29 0.09
239 23 0.07
240 2 0.01
242 1 0.00
244 19 0.06
245 37 0.12
247 1 0.00
248 5 0.02
250 4 0.01
251 2 0.01
252 70 0.22
257 39 0.12
258 28 0.09
261 1 0.00
262 33 0.11
264 1 0.00
266 2 0.01
267 15 0.05
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.41
Consensus pattern (238 bp):
TATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGT
GGGTGAAACTTTATTTTGGTCGGGTCGAGTCGGGTTTTTTAACTGTGATATTCGGGTCGGGTCTG
GGTTAAGGGTGAAAAATACCTGACCCAAAAAATATATAATTTTACCTTATATATTTAGGAATAAT
TACAATAATACCTCTATATATATTCCAATTAAGTCACTGTTTT
Found at i:1633969 original size:18 final size:18
Alignment explanation
Indices: 1633924--1634006 Score: 87
Period size: 18 Copynumber: 4.7 Consensus size: 18
1633914 TATGGAATTG
*
1633924 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
*
1633941 GATTTCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
* *
1633959 TATTCCAATTCGTTCACA
1 GATTCCAATTCCTTCACA
* * *
1633977 GTTTCCAATTCATTTACA
1 GATTCCAATTCCTTCACA
*
1633995 GATTTCAATTCC
1 GATTCCAATTCC
1634007 CTCAGAAACA
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 11 0.21
18 42 0.79
ACGTcount: A:0.28, C:0.27, G:0.07, T:0.39
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:1640641 original size:198 final size:197
Alignment explanation
Indices: 1640304--1640686 Score: 522
Period size: 198 Copynumber: 1.9 Consensus size: 197
1640294 ATTAATTTTT
* * * * *
1640304 TTAGCTGATCCTATTTCTATGTGTAATGAGGTAAGGGAGAGGTAGGATAGTAGGATGCCCCAACT
1 TTAGCTGACCCTATTCCCATATGTAATGAGGTAAGGGAGAGGTAGGATAGTAGGATGCCCCAACG
* * * * * * *
1640369 CCAGGTTGAGAGCAGCTTTCGTGGGAGACCTCCGGCAGTCAGAATTATGAATTGTCCACCGTGGG
66 CCAAGTTAAAAGCAACTTTCGTGGAAGACCTCCAGCAGTCAGAATTATGAATTGCCCACCGTGGG
* *
1640434 ACTCGATCCCACGACCACAAGGTTAAGAGCCTTGCACTCTAT-CAACTGAGCTGGACAATCAATT
131 ACACGATCCCACGACCACAAAGTTAAGAGCCTTGCACTCT-TCCAACTGAGCTGGACAATCAATT
1640498 CTA
195 CTA
* *
1640501 TTAGCTGACCCTATTCCCATATGTAATGGGGTGAA-GGAGAGGTAAGG-TAGTAGGCTGCCCCCA
1 TTAGCTGACCCTATTCCCATATGTAATGAGGT-AAGGGAGAGGT-AGGATAGTAGGATG-CCCCA
*
1640564 ACGCCAAGTTAAAAGCAAC-TTCTGTGGAAGACTTCCAGCAGTCAGAATTATGAATTGCCCACCG
63 ACGCCAAGTTAAAAGCAACTTTC-GTGGAAGACCTCCAGCAGTCAGAATTATGAATTGCCCACCG
**
1640628 TGGGACACGATCCCACGACCACAAAGTTAAGAGCCTTGCGTTCTTCCAACTGAGCTGGA
127 TGGGACACGATCCCACGACCACAAAGTTAAGAGCCTTGCACTCTTCCAACTGAGCTGGA
1640687 TGGGCAATTC
Statistics
Matches: 162, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
197 48 0.30
198 114 0.70
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (197 bp):
TTAGCTGACCCTATTCCCATATGTAATGAGGTAAGGGAGAGGTAGGATAGTAGGATGCCCCAACG
CCAAGTTAAAAGCAACTTTCGTGGAAGACCTCCAGCAGTCAGAATTATGAATTGCCCACCGTGGG
ACACGATCCCACGACCACAAAGTTAAGAGCCTTGCACTCTTCCAACTGAGCTGGACAATCAATTC
TA
Found at i:1649502 original size:20 final size:20
Alignment explanation
Indices: 1649440--1649494 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
1649430 GCGATTGTTG
1649440 CGAAAGTCAAATTCGCTACA
1 CGAAAGTCAAATTCGCTACA
1649460 CGAAAGTCAAATTCGCTACA
1 CGAAAGTCAAATTCGCTACA
1649480 CGAAAGTCAAATTCG
1 CGAAAGTCAAATTCG
1649495 TGTTACGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (20 bp):
CGAAAGTCAAATTCGCTACA
Found at i:1651470 original size:65 final size:63
Alignment explanation
Indices: 1651401--1651560 Score: 187
Period size: 65 Copynumber: 2.5 Consensus size: 63
1651391 AATTAAACTG
* * *
1651401 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCATTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-
1651465 A
63 A
* * * * * *
1651466 AACATCGAATGTATTTGATGCATCAATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGA
*
1651530 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
1651561 TCTTAGTGAA
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
63 1 0.01
64 28 0.35
65 47 0.58
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:1659081 original size:21 final size:21
Alignment explanation
Indices: 1659039--1659082 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1659029 ACCCTGGGAG
*
1659039 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
1659060 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
1659081 CT
1 CT
1659083 CCTCCTACAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:1660191 original size:65 final size:63
Alignment explanation
Indices: 1660071--1660280 Score: 190
Period size: 65 Copynumber: 3.3 Consensus size: 63
1660061 ATTTTCAGAG
* * * * * **
1660071 TGATGCACCGATGCACCAATCCATGCATTGATGCACCATGAATTAAATTG-AACATCGAATGCAT
1 TGATGCATCGATGCA-CAA-CCATGCATCGATGCACTAAGGA-TATTTTGAAACATCGAATGCAT
1660135 T
63 T
* * *
1660136 TCATGTATCGATGCACATACCATGCA-CAGATGCACTAAGGATTTTTTGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCATC-GATGCACTAAGGATATTTTG-AAACATCGAATGCAT
1660200 T
63 T
** * ** * *
1660201 TGATGCATCGATATACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCATCGATGCACTAAGGATATTTTGAAACATCGAATGCATT
1660265 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
1660281 TCTTAGTGCA
Statistics
Matches: 117, Mismatches: 22, Indels: 14
0.76 0.14 0.09
Matches are distributed among these distances:
63 5 0.04
64 47 0.40
65 62 0.53
66 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTAAGGATATTTTGAAACATCGAATGCATT
Found at i:1660280 original size:17 final size:19
Alignment explanation
Indices: 1660252--1660300 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1660242 TATTTTGAAA
1660252 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1660270 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1660289 CACCGATGCACT
1 CATCGATGCACT
1660301 GAGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1660296 original size:64 final size:63
Alignment explanation
Indices: 1660121--1660300 Score: 168
Period size: 65 Copynumber: 2.8 Consensus size: 63
1660111 AATTAAATTG
* * * *
1660121 AACATCGAATGCATTTCATGTATCGATGCACATACCA-TGCACAGATGCACTAAGGATTTTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCAC-T--CAGTGCACCGATGCACTAAGGATATTTTGA
1660185 A
63 A
** * ** *
1660186 AACATCGAATGCATTTGATGCATCGATATAC-CAGCCATGCATCGATGCACTCTGGCTATTTTG-
1 AACATCGAATGCATTTGATGCATCGATGCACTCAG---TGCACCGATGCACTAAGGATATTTTGA
1660249 A
63 A
*
1660250 AACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACTC--AGTGCACCGATGCACT
1660301 GAGAGTCCAA
Statistics
Matches: 94, Mismatches: 14, Indels: 15
0.76 0.11 0.12
Matches are distributed among these distances:
61 2 0.02
64 42 0.45
65 48 0.51
67 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAGTGCACCGATGCACTAAGGATATTTTGAA
Found at i:1661029 original size:21 final size:21
Alignment explanation
Indices: 1661003--1661074 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
1660993 TAACTCAACA
* *
1661003 CTCTTGAACGGTGGAAGGGAC
1 CTCTTGAACGATGGAAGGGGC
1661024 CTCTTGAACGAT-GAGAGGGGC
1 CTCTTGAACGATGGA-AGGGGC
*
1661045 CTCTTGAATGATAGG-AGGGGC
1 CTCTTGAACGAT-GGAAGGGGC
1661066 CTCTTGAAC
1 CTCTTGAAC
1661075 TTTGACAGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
20 2 0.05
21 41 0.93
23 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGGAAGGGGC
Found at i:1661522 original size:21 final size:21
Alignment explanation
Indices: 1661493--1661533 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1661483 GTCGTGACGT
* *
1661493 AAAGTACTGACCTCATCACGC
1 AAAGCACTGACCTAATCACGC
1661514 AAAGCACTGACCTAATCACG
1 AAAGCACTGACCTAATCACG
1661534 TAACTCCCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.32, G:0.15, T:0.17
Consensus pattern (21 bp):
AAAGCACTGACCTAATCACGC
Found at i:1663437 original size:22 final size:22
Alignment explanation
Indices: 1663407--1663463 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
1663397 GATGGAGATA
1663407 GACAGATTTCGCCAGAGATGGG
1 GACAGATTTCGCCAGAGATGGG
* * *
1663429 GACGGATTTCGTCGGAGATGGG
1 GACAGATTTCGCCAGAGATGGG
*
1663451 GACAGATGTCGCC
1 GACAGATTTCGCC
1663464 GTAGAGAGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (22 bp):
GACAGATTTCGCCAGAGATGGG
Found at i:1663682 original size:20 final size:20
Alignment explanation
Indices: 1663631--1663682 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
1663621 TGACTTCTGT
** * *
1663631 GTTGCGAATTACAAATTCGT
1 GTTGCGAATTTGAAAATCGC
1663651 GTTGC-AATTTTGAAAATCGC
1 GTTGCGAA-TTTGAAAATCGC
1663671 GTTGCGAATTTG
1 GTTGCGAATTTG
1663683 TTGGTCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATCGC
Found at i:1669448 original size:31 final size:31
Alignment explanation
Indices: 1669412--1669484 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
1669402 GTCACTCTCA
* ** *
1669412 ATTATATAGATTACTTTATATTAGTCCCTCT
1 ATTATATAAATTACTCCAGATTAGTCCCTCT
**
1669443 ATTATATAAATTGGTCCAGATTAGTCCCTCT
1 ATTATATAAATTACTCCAGATTAGTCCCTCT
1669474 ATTAT-TAAATT
1 ATTATATAAATT
1669485 TAGATTAGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 6 0.17
31 30 0.83
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (31 bp):
ATTATATAAATTACTCCAGATTAGTCCCTCT
Found at i:1679874 original size:27 final size:26
Alignment explanation
Indices: 1679830--1679882 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
1679820 CCCTTGCGCA
* *
1679830 TCCATTCCCAATTTCTCCCCTCGCTCG
1 TCCATTCCCAAATCCTCCCCTC-CTCG
*
1679857 TCCATTCCCAAATCCTCCTCTCCTCG
1 TCCATTCCCAAATCCTCCCCTCCTCG
1679883 CCGTTCTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.13, C:0.49, G:0.06, T:0.32
Consensus pattern (26 bp):
TCCATTCCCAAATCCTCCCCTCCTCG
Found at i:1685651 original size:11 final size:10
Alignment explanation
Indices: 1685635--1685744 Score: 60
Period size: 11 Copynumber: 9.9 Consensus size: 10
1685625 TACGATTATG
1685635 TAAAATTATAT
1 TAAAA-TATAT
*
1685646 TAAAATATTT
1 TAAAATATAT
*
1685656 ATAAAATATTT
1 -TAAAATATAT
1685667 TATAAATATATT
1 TA-AAATATA-T
*
1685679 AATAAAATATTT
1 --TAAAATATAT
1685691 TATAAATATATT
1 TA-AAATATA-T
*
1685703 AATAAAATATTT
1 --TAAAATATAT
1685715 TATAAATATAT
1 TA-AAATATAT
*
1685726 TAATAAAATAT
1 TAA-AATATAT
1685737 T-AAATATA
1 TAAAATATA
1685745 AATTTTAATC
Statistics
Matches: 80, Mismatches: 8, Indels: 24
0.71 0.07 0.21
Matches are distributed among these distances:
9 5 0.06
10 12 0.15
11 43 0.54
12 4 0.05
13 12 0.15
14 4 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TAAAATATAT
Found at i:1685753 original size:24 final size:24
Alignment explanation
Indices: 1685646--1685737 Score: 168
Period size: 24 Copynumber: 3.9 Consensus size: 24
1685636 AAAATTATAT
*
1685646 TAAA-ATATTTATAAAATATTTTA
1 TAAATATATTAATAAAATATTTTA
1685669 TAAATATATTAATAAAATATTTTA
1 TAAATATATTAATAAAATATTTTA
1685693 TAAATATATTAATAAAATATTTTA
1 TAAATATATTAATAAAATATTTTA
1685717 TAAATATATTAATAAAATATT
1 TAAATATATTAATAAAATATT
1685738 AAATATAAAT
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
23 4 0.06
24 63 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAAATATATTAATAAAATATTTTA
Found at i:1685753 original size:48 final size:47
Alignment explanation
Indices: 1685639--1685753 Score: 162
Period size: 48 Copynumber: 2.4 Consensus size: 47
1685629 ATTATGTAAA
1685639 ATTATATTAAAATATTT-ATAAAATATTTTATAAATATATTAATAAAAT
1 ATTATA-T-AAATATTTAATAAAATATTTTATAAATATATTAATAAAAT
*
1685687 ATTTTATAAATATATTAATAAAATATTTTATAAATATATTAATAAAAT
1 ATTATATAAATAT-TTAATAAAATATTTTATAAATATATTAATAAAAT
1685735 ATTAAATATAAAT-TTTAAT
1 ATT--ATATAAATATTTAAT
1685754 CGAAGTCTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
46 6 0.10
47 3 0.05
48 44 0.72
49 1 0.02
50 7 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (47 bp):
ATTATATAAATATTTAATAAAATATTTTATAAATATATTAATAAAAT
Found at i:1686023 original size:31 final size:30
Alignment explanation
Indices: 1685986--1686072 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
1685976 AAATATTGCA
* *
1685986 AAATGATTATTATA-TTTATCAGATTGCTAT
1 AAATGATTATTA-AGTTTATCAAATTACTAT
* * *
1686016 GAAATGATCATTAAATTTTATCAAATTATTAT
1 -AAATGATTATT-AAGTTTATCAAATTACTAT
1686048 AAATGATTATTAAGTTTATCAAATT
1 AAATGATTATTAAGTTTATCAAATT
1686073 TTTACAATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
30 13 0.27
31 21 0.44
32 14 0.29
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (30 bp):
AAATGATTATTAAGTTTATCAAATTACTAT
Found at i:1692913 original size:2 final size:2
Alignment explanation
Indices: 1692906--1692931 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1692896 ATTGGAGATT
1692906 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
1692932 AAAGGTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1695269 original size:2 final size:2
Alignment explanation
Indices: 1695262--1695317 Score: 87
Period size: 2 Copynumber: 28.0 Consensus size: 2
1695252 AGTATAACAA
1695262 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
*
1695304 AA AT -T CAT AT AT AT
1 AT AT AT -AT AT AT AT
1695318 TTTTATTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.96
3 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1711986 original size:6 final size:7
Alignment explanation
Indices: 1711966--1711991 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1711956 AGTTAACTTA
1711966 TTATTTT
1 TTATTTT
1711973 TTATTTT
1 TTATTTT
1711980 TTATTTT
1 TTATTTT
1711987 TTATT
1 TTATT
1711992 AATAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTATTTT
Found at i:1714350 original size:18 final size:18
Alignment explanation
Indices: 1714327--1714375 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
1714317 CTCAACTCAA
*
1714327 AGGTATCCAGCATTCTCT
1 AGGTATCCAGCATTCTCG
1714345 AGGTATCCAGCATTCTCG
1 AGGTATCCAGCATTCTCG
*
1714363 AGGCATCCAGCAT
1 AGGTATCCAGCAT
1714376 CCTCCTACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (18 bp):
AGGTATCCAGCATTCTCG
Found at i:1730093 original size:5 final size:5
Alignment explanation
Indices: 1730083--1730109 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1730073 ATCACTCCCT
1730083 AAAAC AAAAC AAAAC AAAAC AAAAC AA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AA
1730110 TGAAGTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:1730133 original size:7 final size:7
Alignment explanation
Indices: 1730121--1730145 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1730111 GAAGTTCTTC
1730121 AAAGCTA
1 AAAGCTA
1730128 AAAGCTA
1 AAAGCTA
1730135 AAAGCTA
1 AAAGCTA
1730142 AAAG
1 AAAG
1730146 ATCCTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.16, T:0.12
Consensus pattern (7 bp):
AAAGCTA
Found at i:1732155 original size:28 final size:27
Alignment explanation
Indices: 1732122--1732175 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 27
1732112 ATATTAGAAA
1732122 TAATTA-AAATATATTTAAAAAATTATTT
1 TAATTATAAAT-T-TTTAAAAAATTATTT
1732150 TAATTATTAAATTTTTAAAAAATTAT
1 TAATTA-TAAATTTTTAAAAAATTAT
1732176 AATTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 19 0.79
29 1 0.04
30 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TAATTATAAATTTTTAAAAAATTATTT
Found at i:1745915 original size:12 final size:12
Alignment explanation
Indices: 1745898--1745934 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1745888 TTAAAAAATA
1745898 TTTAATTTTAAT
1 TTTAATTTTAAT
1745910 TTTAATTTTAAT
1 TTTAATTTTAAT
* *
1745922 TTGAATTTAAAT
1 TTTAATTTTAAT
1745934 T
1 T
1745935 AGTAGAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (12 bp):
TTTAATTTTAAT
Found at i:1745919 original size:18 final size:18
Alignment explanation
Indices: 1745893--1745934 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1745883 TAAATTTAAA
*
1745893 AAATATTTAATTTTAATTT
1 AAAT-TTTAATTTGAATTT
*
1745912 TAATTTTAATTTGAATTT
1 AAATTTTAATTTGAATTT
1745930 AAATT
1 AAATT
1745935 AGTAGAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
AAATTTTAATTTGAATTT
Found at i:1746984 original size:17 final size:17
Alignment explanation
Indices: 1746962--1746999 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1746952 GACCTGTTCC
1746962 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1746979 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1746996 GACC
1 GACC
1747000 GGTGTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:1747073 original size:29 final size:29
Alignment explanation
Indices: 1747000--1747067 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
1746990 ACCGTTGACC
*
1747000 GGTGTTATTTTAGTAATTAATTCGAAATA
1 GGTGTTATTTTAGTAATTAATTCGAAAAA
*
1747029 GGT-TATATTTTAGTAATTAATT-TAAAAA
1 GGTGT-TATTTTAGTAATTAATTCGAAAAA
1747057 GGGTGTTATTT
1 -GGTGTTATTT
1747068 CTGTAAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 5 0.15
29 28 0.82
30 1 0.03
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (29 bp):
GGTGTTATTTTAGTAATTAATTCGAAAAA
Found at i:1753740 original size:21 final size:21
Alignment explanation
Indices: 1753696--1753740 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1753686 GATTTCTGGG
* * *
1753696 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
1753717 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
1753738 CAA
1 CAA
1753741 ACGAACCAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:1753813 original size:23 final size:22
Alignment explanation
Indices: 1753765--1753813 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1753755 ACAGAATGTC
*
1753765 AAGG-GGGAACTGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
1753786 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
1753809 AAGGA
1 AAGGA
1753814 AGAAATGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.14
22 14 0.64
23 5 0.23
ACGTcount: A:0.33, C:0.29, G:0.29, T:0.10
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:1755378 original size:23 final size:23
Alignment explanation
Indices: 1755348--1755430 Score: 148
Period size: 23 Copynumber: 3.6 Consensus size: 23
1755338 CATTTTATAT
*
1755348 GGCACTTCGGTGTAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
1755371 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
1755394 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
1755417 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1755431 TTTATGCGAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:1757147 original size:25 final size:25
Alignment explanation
Indices: 1757113--1757161 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1757103 ATTTTGAGAT
1757113 AATTTCGATTAGAAAGGATGTATGC
1 AATTTCGATTAGAAAGGATGTATGC
*
1757138 AATTTCGATTGGAAAGGATGTATG
1 AATTTCGATTAGAAAGGATGTATG
1757162 TGATTGGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.33
Consensus pattern (25 bp):
AATTTCGATTAGAAAGGATGTATGC
Found at i:1760432 original size:23 final size:23
Alignment explanation
Indices: 1760364--1760424 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
1760354 ATATTTTCTA
1760364 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1760387 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
1760410 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
1760425 TTTATACGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1761963 original size:17 final size:17
Alignment explanation
Indices: 1761941--1761974 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1761931 TGACCAGTTT
1761941 CGACCCGACCGTTGACC
1 CGACCCGACCGTTGACC
* *
1761958 CGACCCGGCTGTTGACC
1 CGACCCGACCGTTGACC
1761975 GTTGACCGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.44, G:0.26, T:0.15
Consensus pattern (17 bp):
CGACCCGACCGTTGACC
Found at i:1762026 original size:29 final size:30
Alignment explanation
Indices: 1761984--1762050 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 30
1761974 CGTTGACCGA
*
1761984 TGCTATTTTAGTAATTAATTCGAAATA-GG
1 TGCTATTTTAGTAATTAATTCAAAATAGGG
1762013 TGCTATTTTAGTAATTAATTCAAAATAGGG
1 TGCTATTTTAGTAATTAATTCAAAATAGGG
1762043 TGCTATTT
1 TGCTATTT
1762051 CTGTAAAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 26 0.72
30 10 0.28
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.43
Consensus pattern (30 bp):
TGCTATTTTAGTAATTAATTCAAAATAGGG
Found at i:1765049 original size:21 final size:21
Alignment explanation
Indices: 1765023--1765082 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
1765013 CAGAACAAGT
*
1765023 AGTATCGGTACCCCTTCAATG
1 AGTATCGATACCCCTTCAATG
1765044 AGTATCGATACCCCTTCAATG
1 AGTATCGATACCCCTTCAATG
*
1765065 AGTATCGATACCCTTTCA
1 AGTATCGATACCCCTTCA
1765083 TAAAATTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (21 bp):
AGTATCGATACCCCTTCAATG
Found at i:1765243 original size:20 final size:20
Alignment explanation
Indices: 1765220--1765272 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1765210 ACAGTATCAG
1765220 TACTATTCATACAATATTGA
1 TACTATTCATACAATATTGA
*
1765240 TACTATTCATACAATATTGG
1 TACTATTCATACAATATTGA
1765260 TACTATTCATACA
1 TACTATTCATACA
1765273 GTACAATACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.40
Consensus pattern (20 bp):
TACTATTCATACAATATTGA
Found at i:1765296 original size:40 final size:40
Alignment explanation
Indices: 1765219--1765297 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
1765209 CACAGTATCA
** *
1765219 GTACTATTCATACAATATTGATACTATTCATACAATATTG
1 GTACTATTCATACAATATCAATACTATTCATAAAATATTG
*
1765259 GTACTATTCATACAGTA-CAATACTATTCATAAAAATATT
1 GTACTATTCATACAATATCAATACTATTCAT-AAAATATT
1765298 TTTGTGCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 11 0.32
40 23 0.68
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (40 bp):
GTACTATTCATACAATATCAATACTATTCATAAAATATTG
Found at i:1765488 original size:2 final size:2
Alignment explanation
Indices: 1765479--1765524 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1765469 ATTAATCATT
1765479 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1765520 CA TA T
1 TA TA T
1765525 CGTATTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1772597 original size:103 final size:103
Alignment explanation
Indices: 1772413--1772638 Score: 382
Period size: 103 Copynumber: 2.2 Consensus size: 103
1772403 GTCGAGGGTT
*
1772413 TATGTGGTTCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAA
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAA
* *
1772478 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
1772516 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAA
*
1772581 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1772619 TATGTGGTCCTT-ATGGACAT
1 TATGTGGTCCTTCA-GGACAT
1772639 TATTATATGG
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAA
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1772699 original size:23 final size:23
Alignment explanation
Indices: 1772637--1772714 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
1772627 CCTTATGGAC
* * *
1772637 ATTATTATATGGCACTACGATGCA
1 ATTA-TATGTGGCACTTCGGTGCA
* * * *
1772661 ATTCTACGCGGTACTTCGGTGCA
1 ATTATATGTGGCACTTCGGTGCA
1772684 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTTCGGTGCA
1772707 ATTATATG
1 ATTATATG
1772715 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 40 0.93
24 3 0.07
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (23 bp):
ATTATATGTGGCACTTCGGTGCA
Found at i:1779732 original size:27 final size:27
Alignment explanation
Indices: 1779714--1779949 Score: 427
Period size: 27 Copynumber: 8.7 Consensus size: 27
1779704 TGATCTACGT
1779714 CGCCGGATGGGTGATGGTGACCTGCGA
1 CGCCGGATGGGTGATGGTGACCTGCGA
*
1779741 CGTCGGATGGGTGATGGTGACCTGCGA
1 CGCCGGATGGGTGATGGTGACCTGCGA
*
1779768 CGTCGGATGGGTGATGGTGACCTGCGA
1 CGCCGGATGGGTGATGGTGACCTGCGA
*
1779795 CGTCGGATGGGTGATGGTGACCTGCGA
1 CGCCGGATGGGTGATGGTGACCTGCGA
*
1779822 CGTCGGATGGGTGATGGTGACCTGCGA
1 CGCCGGATGGGTGATGGTGACCTGCGA
1779849 CGCCGGATGGGTGATGGTGACCTGCGA
1 CGCCGGATGGGTGATGGTGACCTGCGA
*
1779876 CGCTGGATGGGTGATGGTGACCTGCGA
1 CGCCGGATGGGTGATGGTGACCTGCGA
1779903 CGCCGGATGGGTGATGGTGACCTGCGA
1 CGCCGGATGGGTGATGGTGACCTGCGA
1779930 CGCCGGATGGGTGATGGTGA
1 CGCCGGATGGGTGATGGTGA
1779950 TCTGTATCGA
Statistics
Matches: 205, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 205 1.00
ACGTcount: A:0.15, C:0.19, G:0.45, T:0.21
Consensus pattern (27 bp):
CGCCGGATGGGTGATGGTGACCTGCGA
Found at i:1786791 original size:2 final size:2
Alignment explanation
Indices: 1786784--1786823 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1786774 AATTTTAAGA
1786784 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
1786824 TTATTTATAA
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:1786847 original size:23 final size:23
Alignment explanation
Indices: 1786816--1786859 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1786806 ATATATATAT
* *
1786816 ATATATATTTATTTATAAATAAG
1 ATATATATTTACTTAGAAATAAG
*
1786839 ATATTTATTTACTTAGAAATA
1 ATATATATTTACTTAGAAATA
1786860 TCAGAAAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (23 bp):
ATATATATTTACTTAGAAATAAG
Found at i:1787077 original size:27 final size:26
Alignment explanation
Indices: 1787047--1787130 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 26
1787037 TATTTATATG
*
1787047 AATACATAATAATAACAATAAAAATTA
1 AATAAATAATAATAACAATAAAAA-TA
*
1787074 AATATAT-AT-A-AACATATAAAAATA
1 AATAAATAATAATAACA-ATAAAAATA
* *
1787098 AATAAACAATGACTAA-AATAAAAAATA
1 AATAAATAAT-AATAACAAT-AAAAATA
1787125 AATAAA
1 AATAAA
1787131 ACTATATTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
24 11 0.23
25 10 0.21
26 4 0.09
27 20 0.43
28 2 0.04
ACGTcount: A:0.69, C:0.06, G:0.01, T:0.24
Consensus pattern (26 bp):
AATAAATAATAATAACAATAAAAATA
Found at i:1787102 original size:18 final size:17
Alignment explanation
Indices: 1787063--1787105 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1787053 TAATAATAAC
* *
1787063 AATAAAAATTAAATATA
1 AATAAACATTAAAAATA
*
1787080 TATAAACATATAAAAATA
1 AATAAACAT-TAAAAATA
1787098 AATAAACA
1 AATAAACA
1787106 ATGACTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
AATAAACATTAAAAATA
Found at i:1789015 original size:124 final size:123
Alignment explanation
Indices: 1788698--1789101 Score: 673
Period size: 123 Copynumber: 3.3 Consensus size: 123
1788688 TTAAGATAAG
* * *
1788698 GTTGAACAAGTTCATCTCATTATGAACTTCTTCTTCCTCTTCAGATTAGTTCTTCTCATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAA
* *
1788763 CTTTCTCTAGAAAAGTTGATGTTGATCTATCTCCTTCAGTGATAGAGTCATGCAAAAA
66 CTTTCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAA
* *
1788821 GTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATAAGTTCTTCTCATCATGAA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAA
1788886 CTTTCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAA
66 CTTTCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAA
* * *
1788944 GGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAATTATTCTCATTATAA
1 -GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGA
*
1789009 ACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAA
65 ACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAA
* * *
1789068 GTTAAACAAGTTCTTCTCATTATGAACTTTTTCT
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCT
1789102 GGAAAAGTTG
Statistics
Matches: 264, Mismatches: 16, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
123 147 0.56
124 117 0.44
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (123 bp):
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAA
Found at i:1789103 original size:84 final size:84
Alignment explanation
Indices: 1788997--1789185 Score: 333
Period size: 84 Copynumber: 2.2 Consensus size: 84
1788987 AGATAAATTA
* * *
1788997 TTCTCATTATAAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATG
1 TTCTCATTATGAACTTTTTCTGGAAAAGTTGATGCTGATATATCTCCTTCTGTGATAGAGTCATG
1789062 CAAAAAGTTAAACAAGTTC
66 CAAAAAGTTAAACAAGTTC
1789081 TTCTCATTATGAACTTTTTCTGGAAAAGTTGATGCTGATATATCTCCTTCTGTGATAGAGTCATG
1 TTCTCATTATGAACTTTTTCTGGAAAAGTTGATGCTGATATATCTCCTTCTGTGATAGAGTCATG
**
1789146 CAAAAAGTTGTACAAGTTC
66 CAAAAAGTTAAACAAGTTC
1789165 TTCTCATTATGAACTTTTTCT
1 TTCTCATTATGAACTTTTTCT
1789186 CCTTCTCCAG
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 100 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (84 bp):
TTCTCATTATGAACTTTTTCTGGAAAAGTTGATGCTGATATATCTCCTTCTGTGATAGAGTCATG
CAAAAAGTTAAACAAGTTC
Found at i:1789337 original size:37 final size:37
Alignment explanation
Indices: 1789296--1789480 Score: 149
Period size: 37 Copynumber: 5.1 Consensus size: 37
1789286 GAGACGAATC
1789296 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
* ** ** * * *** *
1789333 TTGTTTCAAGTGAAACTGTCTCAAGCGAAACGCAGT-
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1789369 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
* ** ** ** * *** *
1789406 TTATTTCGAGTGAAACTGTCTCAAGCGAGACGCAGT-
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1789442 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1789479 TT
1 TT
1789481 ATTTGAAAAC
Statistics
Matches: 100, Mismatches: 46, Indels: 4
0.67 0.31 0.03
Matches are distributed among these distances:
36 49 0.49
37 51 0.51
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (37 bp):
TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
Found at i:1789359 original size:73 final size:73
Alignment explanation
Indices: 1789270--1789484 Score: 369
Period size: 73 Copynumber: 2.9 Consensus size: 73
1789260 TTCTTTTTAT
* *
1789270 TGAAACTGTCTTAAGCGAGACG-AATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGT
1 TGAAACTGTCTCAAGCGAGACGCAGT-TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGT
*
1789334 TGTTTCAAG
65 TATTTCAAG
*
1789343 TGAAACTGTCTCAAGCGAAACGCAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTT
1 TGAAACTGTCTCAAGCGAGACGCAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTT
*
1789408 ATTTCGAG
66 ATTTCAAG
1789416 TGAAACTGTCTCAAGCGAGACGCAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTT
1 TGAAACTGTCTCAAGCGAGACGCAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTT
1789481 ATTT
66 ATTT
1789485 GAAAACATCA
Statistics
Matches: 135, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
73 133 0.99
74 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (73 bp):
TGAAACTGTCTCAAGCGAGACGCAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTT
ATTTCAAG
Found at i:1789391 original size:36 final size:37
Alignment explanation
Indices: 1789282--1789480 Score: 125
Period size: 36 Copynumber: 5.5 Consensus size: 37
1789272 AAACTGTCTT
* *
1789282 AAGCGAGACGAA-TCTTGTTTTAAGAAAAACAATCTC
1 AAGCGAGACAAAGTGTTGTTTTAAGAAAAACAATCTC
* * * * ** **
1789318 AAGTGAGATAAATTGTTGTTTCAAGTGAAACTGTCTC
1 AAGCGAGACAAAGTGTTGTTTTAAGAAAAACAATCTC
* **
1789355 AAGCGAAACGCAGT-TTGTTTTAAGAAAAACAATCTC
1 AAGCGAGACAAAGTGTTGTTTTAAGAAAAACAATCTC
* * * * ** ** **
1789391 AAGTGAGATAAATTGTTATTTCGAGTGAAACTGTCTC
1 AAGCGAGACAAAGTGTTGTTTTAAGAAAAACAATCTC
**
1789428 AAGCGAGACGCAGT-TTGTTTTAAGAAAAACAATCTC
1 AAGCGAGACAAAGTGTTGTTTTAAGAAAAACAATCTC
* * *
1789464 AAGTGAGATAAATTGTT
1 AAGCGAGACAAAGTGTT
1789481 ATTTGAAAAC
Statistics
Matches: 110, Mismatches: 50, Indels: 5
0.67 0.30 0.03
Matches are distributed among these distances:
36 58 0.53
37 52 0.47
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (37 bp):
AAGCGAGACAAAGTGTTGTTTTAAGAAAAACAATCTC
Found at i:1790187 original size:22 final size:22
Alignment explanation
Indices: 1790162--1790221 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
1790152 AATAAAGCTT
1790162 TCATCTTTGAAAAGAT-AATCTA
1 TCATCTTTGAAAA-ATGAATCTA
*
1790184 TCATCTTTGAAGAATGAATCTA
1 TCATCTTTGAAAAATGAATCTA
*
1790206 TCATCTTTGAAGAATG
1 TCATCTTTGAAAAATG
1790222 TAGATGTAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 2 0.06
22 34 0.94
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (22 bp):
TCATCTTTGAAAAATGAATCTA
Found at i:1797861 original size:36 final size:36
Alignment explanation
Indices: 1797801--1797872 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
1797791 TCTTGCTGTA
* * *
1797801 GAATGCTTTTGGTATCAATCTAACAGGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTATGTG
*
1797837 GAATACTTTTGGTATTAATATAACAGGATCTATGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTATGTG
1797873 TGCATTGCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATATAACAGGATCTATGTG
Found at i:1798769 original size:2 final size:2
Alignment explanation
Indices: 1798762--1798798 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1798752 ATAAAGAAGA
1798762 AT AT AT AT 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 AT AT AT AT A
1798799 AATAGTATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1799324 original size:2 final size:2
Alignment explanation
Indices: 1799311--1799360 Score: 65
Period size: 2 Copynumber: 27.5 Consensus size: 2
1799301 TTTTAAGAAA
1799311 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT -T A- 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
1799349 AT AT AT AT -T AT A
1 AT AT AT AT AT AT A
1799361 AATAAGATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
1 5 0.12
2 38 0.88
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1799332 original size:18 final size:18
Alignment explanation
Indices: 1799323--1799358 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1799313 ATATTAATAT
1799323 ATATATATATATATATTA
1 ATATATATATATATATTA
1799341 ATATATATATATATATTA
1 ATATATATATATATATTA
1799359 TAAATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATATATATATATTA
Found at i:1799370 original size:18 final size:18
Alignment explanation
Indices: 1799325--1799375 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1799315 ATTAATATAT
* *
1799325 ATATATATATATATTAAT
1 ATATAGATATATATTAAA
*
1799343 ATATATATATATATTATAA
1 ATATAGATATATATTA-AA
*
1799362 ATA-AGATATTTATT
1 ATATAGATATATATT
1799376 TACTTAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
ATATAGATATATATTAAA
Found at i:1799465 original size:118 final size:117
Alignment explanation
Indices: 1799337--1799564 Score: 332
Period size: 118 Copynumber: 1.9 Consensus size: 117
1799327 ATATATATAT
*
1799337 ATTAATATATATATATATATTATAAATAAGATATTTATTTACTT-AGAAATATCAGAAAATGACT
1 ATTAATATATATA-ATTTA-TA-AAATAAGATATTTATTTACTTAAG-AATATCAGAAAATGACT
* * **
1799401 TCTAGGTGCTTTAAGATAATCAATTTCTTAATATTTAAAAATAAATTAATATTAAA
62 TCTAGGTGCTTTAAGACAACCAATTTCTTAATATAAAAAAATAAATTAATATTAAA
* *
1799457 ATTAATATATATAATTTATAAAAATATGATATTTATTTATTTAAGAATATCAGAAAATGACTTCT
1 ATTAATATATATAATTTAT-AAAATAAGATATTTATTTACTTAAGAATATCAGAAAATGACTTCT
*
1799522 AGGTGCTTTAAGACAGCCAATTTCTTAATATAAAAAAATAAAT
65 AGGTGCTTTAAGACAACCAATTTCTTAATATAAAAAAATAAAT
1799565 GGTTGTCCCT
Statistics
Matches: 98, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
118 78 0.80
119 7 0.07
120 13 0.13
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (117 bp):
ATTAATATATATAATTTATAAAATAAGATATTTATTTACTTAAGAATATCAGAAAATGACTTCTA
GGTGCTTTAAGACAACCAATTTCTTAATATAAAAAAATAAATTAATATTAAA
Found at i:1800948 original size:13 final size:14
Alignment explanation
Indices: 1800930--1800977 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
1800920 TAATTATTTT
1800930 TATATATTTAAA-A
1 TATATATTTAAATA
1800943 TATATATTTAAATA
1 TATATATTTAAATA
* *
1800957 TATATATATATATA
1 TATATATTTAAATA
1800971 TAT-TATT
1 TATATATT
1800978 ACTTCATGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
13 15 0.48
14 16 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATATATTTAAATA
Found at i:1800957 original size:12 final size:12
Alignment explanation
Indices: 1800930--1800974 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
1800920 TAATTATTTT
1800930 TATATATTTAAAA
1 TATATATTT-AAA
1800943 TATATATTTAAA
1 TATATATTTAAA
* *
1800955 TATATATATATA
1 TATATATTTAAA
1800967 TATATATT
1 TATATATT
1800975 ATTACTTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 20 0.69
13 9 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TATATATTTAAA
Found at i:1805293 original size:139 final size:139
Alignment explanation
Indices: 1805043--1805303 Score: 513
Period size: 139 Copynumber: 1.9 Consensus size: 139
1805033 AAATTTCGGT
*
1805043 TATCGATTAATTCGGTTCGAAATCTTTTAATTTATCAAATTAACTGAAATTAATAAATATTCAAT
1 TATCGATTAATTCGGTTCGAAATCTGTTAATTTATCAAATTAACTGAAATTAATAAATATTCAAT
1805108 ATATTGTATATATTATTTATTTAGGGGTGTTTAAACTTCATTTGTAGCCAAATTAACAGAATTAA
66 ATATTGTATATATTATTTATTTAGGGGTGTTTAAACTTCATTTGTAGCCAAATTAACAGAATTAA
1805173 CCAAAAACA
131 CCAAAAACA
1805182 TATCGATTAATTCGGTTCGAAATCTGTTAATTTATCAAATTAACTGAAATTAATAAATATTCAAT
1 TATCGATTAATTCGGTTCGAAATCTGTTAATTTATCAAATTAACTGAAATTAATAAATATTCAAT
1805247 ATATTGTATATATTATTTATTTAGGGGTGTTTAAACTTCATTTGTAGCCAAATTAAC
66 ATATTGTATATATTATTTATTTAGGGGTGTTTAAACTTCATTTGTAGCCAAATTAAC
1805304 CAAAAACATT
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 121 1.00
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (139 bp):
TATCGATTAATTCGGTTCGAAATCTGTTAATTTATCAAATTAACTGAAATTAATAAATATTCAAT
ATATTGTATATATTATTTATTTAGGGGTGTTTAAACTTCATTTGTAGCCAAATTAACAGAATTAA
CCAAAAACA
Found at i:1815337 original size:20 final size:21
Alignment explanation
Indices: 1815312--1815363 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1815302 TTTTCCCAAT
*
1815312 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1815332 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1815353 TCGCAATGCGA
1 TCGCAATGCGA
1815364 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1815377 original size:20 final size:20
Alignment explanation
Indices: 1815352--1815486 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
1815342 AATTGGGAAA
1815352 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1815372 ATCGCAATGCGATACTCACT
1 ATCGCAATGCGATACTGACT
* *
1815392 ATCGCAATGCGATAAT-ACAA
1 ATCGCAATGCGATACTGAC-T
* *
1815412 ATTCGCAACGAGATACTGACT
1 A-TCGCAATGCGATACTGACT
* * *
1815433 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
1815453 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
1815473 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1815487 TTTCAAAGCG
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 67 0.70
21 23 0.24
22 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1815396 original size:61 final size:61
Alignment explanation
Indices: 1815349--1815480 Score: 174
Period size: 61 Copynumber: 2.2 Consensus size: 61
1815339 GCGAATTGGG
* * * *
1815349 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTCACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTCACTATCGCAACGCGATAATAC
* * * * *
1815410 AAATTCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTCACTATCGCAACGCGATAATAC
*
1815471 ATAATCGCAA
1 AAAATCGCAA
1815481 TGCGATTTTC
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTCACTATCGCAACGCGATAATAC
Found at i:1815487 original size:41 final size:40
Alignment explanation
Indices: 1815352--1815486 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 40
1815342 AATTGGGAAA
* *
1815352 ATCGCAATGCGATACTGACTATCGCAATGCGATACT-CACT
1 ATCGCAATGCGATACTGACTTTCGCAACGCGATACTACA-T
* * *
1815392 ATCGCAATGCGATAAT-ACAAATTCGCAACGAGATACTGAC-T
1 ATCGCAATGCGATACTGAC--TTTCGCAACGCGATACT-ACAT
* * * *
1815433 TTCGCAACGCGATTCTGACTTTCGCAACGCGATAATACAT
1 ATCGCAATGCGATACTGACTTTCGCAACGCGATACTACAT
1815473 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1815487 TTTCAAAGCG
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
39 4 0.05
40 30 0.41
41 37 0.50
42 2 0.03
43 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (40 bp):
ATCGCAATGCGATACTGACTTTCGCAACGCGATACTACAT
Found at i:1815682 original size:22 final size:22
Alignment explanation
Indices: 1815654--1815697 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1815644 CACTCTCTCA
*
1815654 CCCATCTCTGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1815676 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1815698 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1817359 original size:18 final size:18
Alignment explanation
Indices: 1817338--1817382 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1817328 TCCACTTCGG
*
1817338 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1817356 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1817374 GAGCCATCA
1 GAGCCATCA
1817383 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1817918 original size:19 final size:20
Alignment explanation
Indices: 1817875--1817919 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1817865 AGCAACACGA
1817875 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
1817895 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
1817914 AAATGA
1 AAATGA
1817920 AAATCGTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:1817938 original size:14 final size:14
Alignment explanation
Indices: 1817919--1817976 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1817909 ATGCGAAATG
*
1817919 AAAATCGTAACGAC
1 AAAATCGCAACGAC
*
1817933 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1817949 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1817965 AAAATCGCAACG
1 AAAATCGCAACG
1817977 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1817963 original size:32 final size:33
Alignment explanation
Indices: 1817903--1817993 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1817893 GGAAATGGCT
*
1817903 ATCGCAATGCGAAATGAAAATCGTAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1817936 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1817968 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1817994 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1818029 original size:14 final size:14
Alignment explanation
Indices: 1818010--1818100 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
1818000 TTGTGTTTCG
1818010 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1818024 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1818040 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1818056 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
1818073 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1818089 CGTTGCGATTTT
1 CGTTGCGATTTT
1818101 CATTTCGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 27 0.42
15 3 0.05
16 12 0.19
17 4 0.06
18 12 0.19
19 6 0.09
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1818074 original size:33 final size:33
Alignment explanation
Indices: 1818005--1818116 Score: 208
Period size: 33 Copynumber: 3.4 Consensus size: 33
1817995 GCGATTTGTG
*
1818005 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1818037 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1818070 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1818103 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1818117 AGCCATTTCC
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 26 0.33
33 52 0.67
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1818135 original size:20 final size:20
Alignment explanation
Indices: 1818110--1818156 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1818100 TCATTTCGCA
1818110 TTGCGATAGCCATTTCCGAG
1 TTGCGATAGCCATTTCCGAG
* * *
1818130 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCGAG
1818150 TTGCGAT
1 TTGCGAT
1818157 TTTAAGTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGAG
Found at i:1820046 original size:14 final size:14
Alignment explanation
Indices: 1820027--1820062 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1820017 ATTGTTTAAT
1820027 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1820041 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1820055 TGATTTGT
1 TGATTTGT
1820063 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1820208 original size:14 final size:16
Alignment explanation
Indices: 1820189--1820263 Score: 59
Period size: 19 Copynumber: 4.6 Consensus size: 16
1820179 GAAACAGACT
1820189 ATCGCAATG-A-GAAA
1 ATCGCAATGAATGAAA
1820203 ATCGCAATGCGAAATGAAA
1 ATCGCAAT--G-AATGAAA
1820222 ATCGCAATGCGAAATGAAA
1 ATCGCAAT--G-AATGAAA
*
1820241 ATCGCAACG-A-GAAA
1 ATCGCAATGAATGAAA
1820255 ATCGCAATG
1 ATCGCAATG
1820264 CGATTTTCAT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
14 20 0.37
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 30 0.56
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (16 bp):
ATCGCAATGAATGAAA
Found at i:1820223 original size:19 final size:19
Alignment explanation
Indices: 1820199--1820266 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1820189 ATCGCAATGA
1820199 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1820218 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1820237 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1820251 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1820267 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1820310 original size:20 final size:20
Alignment explanation
Indices: 1820293--1820380 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
1820283 CGATTTTCTA
1820293 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
1820313 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
*
1820333 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
1820353 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
1820373 GTTGCGAT
1 GTTGCGAT
1820381 TTCCCCGTTG
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
19 3 0.05
20 50 0.89
21 3 0.05
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:1820318 original size:34 final size:36
Alignment explanation
Indices: 1820273--1820360 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 36
1820263 GCGATTTTCA
* *
1820273 TTTCGCATTGCGATTTTC-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
1820307 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAGCCAT
1820347 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
1820361 AGCCATTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
34 12 0.26
35 5 0.11
38 1 0.02
39 1 0.02
40 27 0.59
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
Found at i:1820714 original size:20 final size:21
Alignment explanation
Indices: 1820670--1820721 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1820660 ATAGTCAGTA
*
1820670 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1820691 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1820711 TCGCATTGCGA
1 TCGCATTGCGA
1820722 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1820937 original size:12 final size:12
Alignment explanation
Indices: 1820918--1820951 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1820908 CTCTCCGGCG
1820918 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1820930 ATATCCGTTCCT
1 ACATCCGTTCCT
1820942 ACATCC-TTCC
1 ACATCCGTTCC
1820952 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1821533 original size:24 final size:24
Alignment explanation
Indices: 1821506--1821559 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1821496 GTATTCGAAA
*
1821506 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1821530 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1821554 TTTGAT
1 TTTGAT
1821560 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1824072 original size:19 final size:19
Alignment explanation
Indices: 1824050--1824108 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1824040 GGAAATTACT
1824050 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1824069 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1824083 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1824102 ATCGCAA
1 ATCGCAA
1824109 CGCTAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1824256 original size:14 final size:14
Alignment explanation
Indices: 1824237--1824273 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1824227 CATCAATTAA
1824237 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1824251 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1824265 ACAAATCAA
1 ACAAATCAA
1824274 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1825689 original size:42 final size:41
Alignment explanation
Indices: 1825630--1825835 Score: 155
Period size: 42 Copynumber: 4.9 Consensus size: 41
1825620 GTGAATCGGG
* *
1825630 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * * *
1825672 CTCTTGGACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
1825714 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * *
1825756 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
1825798 ATCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
1825836 GCGAGTCGGG
Statistics
Matches: 125, Mismatches: 31, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
41 9 0.07
42 105 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:1825771 original size:84 final size:84
Alignment explanation
Indices: 1825660--1825835 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
1825650 CCTCTTCAAC
* *
1825660 GATGACAGTGGCCTCTTGGACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCATCTTCAACGA
1825725 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1825744 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCATCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCATCTTCAACGA
1825809 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1825828 GATGACAG
1 GATGACAG
1825836 GCGAGTCGGG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCATCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:1826233 original size:91 final size:90
Alignment explanation
Indices: 1826054--1826238 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
1826044 ATTTCAAACT
*
1826054 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
1826119 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
1826147 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACATTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
1826211 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
1826238 T
1 T
1826239 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:1827993 original size:14 final size:14
Alignment explanation
Indices: 1827974--1828065 Score: 76
Period size: 14 Copynumber: 5.9 Consensus size: 14
1827964 GGAAATAACT
1827974 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1827988 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
1828005 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
*
1828021 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
1828040 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1828054 ATCGCAACGAGA
1 ATCGCAACGAGA
1828066 AATGAAAATC
Statistics
Matches: 64, Mismatches: 4, Indels: 20
0.73 0.05 0.23
Matches are distributed among these distances:
14 29 0.45
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 17 0.27
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1828008 original size:33 final size:33
Alignment explanation
Indices: 1827950--1828079 Score: 190
Period size: 33 Copynumber: 3.9 Consensus size: 33
1827940 ACGAGATAAT
* *
1827950 GAGAATCGTAACGCGGAAAT-AACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGAA-AATCGCAACGA
**
1827984 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1828017 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
*
1828050 GAGAATCGCAACGAGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
1828080 TGCGATTTTG
Statistics
Matches: 90, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
33 76 0.84
34 14 0.16
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:1828113 original size:19 final size:19
Alignment explanation
Indices: 1828080--1828160 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
1828070 AAAATCGCAA
**
1828080 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
1828099 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
1828118 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
1828132 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1828152 TGCGATTTT
1 TGCGATTTT
1828161 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1828704 original size:20 final size:20
Alignment explanation
Indices: 1828679--1828731 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1828669 GCGCTATGTA
*
1828679 AATCGCGTTGTGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1828699 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1828719 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1828732 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1828769 original size:20 final size:20
Alignment explanation
Indices: 1828744--1828813 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
1828734 TTGTATTATT
1828744 GCATTGCGATAGTAAGTATC
1 GCATTGCGATAGTAAGTATC
*
1828764 GCATTGCGATAGTCAGTATC
1 GCATTGCGATAGTAAGTATC
1828784 GCATTGCGATAGTTAA-TATC
1 GCATTGCGATAG-TAAGTATC
1828804 GCATTGCGAT
1 GCATTGCGAT
1828814 TTTCCCAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 45 0.96
21 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (20 bp):
GCATTGCGATAGTAAGTATC
Done.