Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 5 of 135
Found at i:1841866 original size:29 final size:30
Alignment explanation
Indices: 1841816--1841875 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
1841806 ATCATAATTT
1841816 TAAAATTTTAAAGAAATGTATAA-AATAAA
1 TAAAATTTTAAAGAAATGTATAATAATAAA
*
1841845 TAAATATTTTCAAGAAA-GTATAATAATAAA
1 TAAA-ATTTTAAAGAAATGTATAATAATAAA
1841875 T
1 T
1841876 TTAAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAAATTTTAAAGAAATGTATAATAATAAA
Found at i:1841921 original size:26 final size:25
Alignment explanation
Indices: 1841839--1841924 Score: 72
Period size: 26 Copynumber: 3.4 Consensus size: 25
1841829 AAATGTATAA
*
1841839 AATAAATAAATATTTTCAAGAAAGTAT
1 AATAAA-AAAT-TTTTCAAGAAAATAT
*
1841866 AATAATAAA--TTT-AA-AAATATAT
1 AATAAAAAATTTTTCAAGAAA-ATAT
1841888 AAAATAAAAAATGTTTTCAAGAAAATAT
1 --AATAAAAAAT-TTTTCAAGAAAATAT
1841916 AATAAAAAA
1 AATAAAAAA
1841925 AATAAAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
21 3 0.06
22 5 0.10
23 3 0.06
24 8 0.17
26 12 0.25
27 8 0.17
28 6 0.12
29 3 0.06
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (25 bp):
AATAAAAAATTTTTCAAGAAAATAT
Found at i:1841931 original size:50 final size:51
Alignment explanation
Indices: 1841829--1841932 Score: 147
Period size: 50 Copynumber: 2.1 Consensus size: 51
1841819 AATTTTAAAG
* * * **
1841829 AAATGTATAAAATAAATAAATATTTTCAAGAAAGTATAATAATAAATTTAA
1 AAATATATAAAATAAATAAATATTTTCAAGAAAATATAATAAAAAAAATAA
*
1841880 AAATATATAAAATAAA-AAATGTTTTCAAGAAAATATAATAAAAAAAATAA
1 AAATATATAAAATAAATAAATATTTTCAAGAAAATATAATAAAAAAAATAA
1841930 AAA
1 AAA
1841933 AAAATGAGAC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 32 0.68
51 15 0.32
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (51 bp):
AAATATATAAAATAAATAAATATTTTCAAGAAAATATAATAAAAAAAATAA
Found at i:1841933 original size:51 final size:51
Alignment explanation
Indices: 1841824--1841933 Score: 141
Period size: 51 Copynumber: 2.1 Consensus size: 51
1841814 TTTAAAATTT
* * * *
1841824 TAAAGAAATGTATAAAATAAATAAATATTTTCAAGAAAGTATAATAATAAAT
1 TAAA-AAATATATAAAATAAATAAATATTTTCAAGAAAATATAATAAAAAAA
* *
1841876 TTAAAAATATATAAAATAAA-AAATGTTTTCAAGAAAATATAATAAAAAAAA
1 TAAAAAATATATAAAATAAATAAATATTTTCAAGAAAATATAAT-AAAAAAA
1841927 TAAAAAA
1 TAAAAAA
1841934 AAATGAGACT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
50 21 0.42
51 26 0.52
52 3 0.06
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (51 bp):
TAAAAAATATATAAAATAAATAAATATTTTCAAGAAAATATAATAAAAAAA
Found at i:1843060 original size:46 final size:46
Alignment explanation
Indices: 1842952--1843060 Score: 114
Period size: 46 Copynumber: 2.4 Consensus size: 46
1842942 GAGGGACAGA
* *
1842952 ATTAAATTATATATTTTTATAATAATAAAAATATAATTTTATAATT
1 ATTAAATTATATATTTTTATAATAATAAAAATATAATTTTAAAATG
* ** * * *
1842998 ATAATAATT-TATATTTTTATAATTTTTAAATTATTACTTTTAAAATG
1 ATTA-AATTATATATTTTTATAATAATAAAAATA-TAATTTTAAAATG
1843045 ATTAAATTATA-ATTTT
1 ATTAAATTATATATTTT
1843061 ATCATTATTA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
46 32 0.63
47 19 0.37
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (46 bp):
ATTAAATTATATATTTTTATAATAATAAAAATATAATTTTAAAATG
Found at i:1843068 original size:37 final size:36
Alignment explanation
Indices: 1843014--1843092 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
1843004 ATTTATATTT
*
1843014 TTATAATTTTTAAATTATTACTTTTAAAATGAT-TAAA
1 TTATAATTTTTAAATTATTA-ATTTAAAAT-ATATAAA
* *
1843051 TTATAA-TTTTATCATTATTAATTTAAAATTTATAAA
1 TTATAATTTTTA-AATTATTAATTTAAAATATATAAA
1843087 TTATAA
1 TTATAA
1843093 AAAAATCTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 1 0.03
36 23 0.62
37 13 0.35
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (36 bp):
TTATAATTTTTAAATTATTAATTTAAAATATATAAA
Found at i:1843070 original size:22 final size:22
Alignment explanation
Indices: 1842952--1843090 Score: 109
Period size: 22 Copynumber: 6.1 Consensus size: 22
1842942 GAGGGACAGA
*
1842952 ATTAAATTATATATTTTTATAATA
1 ATTAAATTATA-A-TTTTATAATT
* *
1842976 ATAAAAATATAATTTTATAATT
1 ATTAAATTATAATTTTATAATT
* *
1842998 ATAATAATTTATATTTTTATAATT
1 AT--TAAATTATAATTTTATAATT
* * * *
1843022 TTTAAATTATTACTTTTAAAATG
1 ATTAAATTA-TAATTTTATAATT
*
1843045 ATTAAATTATAATTTTATCATT
1 ATTAAATTATAATTTTATAATT
* *
1843067 ATTAATTTA-AAATTTATAAATT
1 ATTAAATTATAATTTTAT-AATT
1843089 AT
1 AT
1843091 AAAAAAATCT
Statistics
Matches: 91, Mismatches: 20, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
21 7 0.08
22 39 0.43
23 19 0.21
24 26 0.29
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (22 bp):
ATTAAATTATAATTTTATAATT
Found at i:1844006 original size:3 final size:3
Alignment explanation
Indices: 1843998--1844028 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
1843988 TTGAGGAGTG
1843998 TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
1844029 GTAGGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1849762 original size:18 final size:18
Alignment explanation
Indices: 1849739--1849773 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1849729 AATGTTAATT
* *
1849739 TTTTAGTATTTATTTGAG
1 TTTTAGAATTGATTTGAG
1849757 TTTTAGAATTGATTTGA
1 TTTTAGAATTGATTTGA
1849774 CAAAAACTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (18 bp):
TTTTAGAATTGATTTGAG
Found at i:1851503 original size:36 final size:36
Alignment explanation
Indices: 1851435--1851503 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 36
1851425 AAAATAGTGG
* * ** *
1851435 AAATATTAACAATAAAATAAGAGTTATGTAATATTC
1 AAATAATAACAACAAAATAAGAGCAATATAATATTC
*
1851471 AAATAATAACAACAAAATAATAGCAATATAATA
1 AAATAATAACAACAAAATAAGAGCAATATAATA
1851504 GCGAAACAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 27 1.00
ACGTcount: A:0.59, C:0.07, G:0.06, T:0.28
Consensus pattern (36 bp):
AAATAATAACAACAAAATAAGAGCAATATAATATTC
Found at i:1852351 original size:23 final size:23
Alignment explanation
Indices: 1852325--1852373 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1852315 TTAGTAATTA
1852325 AAAAACAAT-ATTTATAAATTAAT
1 AAAAACAATAATTTA-AAATTAAT
**
1852348 AAAAAGTATAATTTAAAATTAAT
1 AAAAACAATAATTTAAAATTAAT
1852371 AAA
1 AAA
1852374 TAAATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAACAATAATTTAAAATTAAT
Found at i:1859037 original size:21 final size:22
Alignment explanation
Indices: 1859005--1859047 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1858995 TAAGTTTGTA
* *
1859005 ATATATTATATTTTGTTATTTT
1 ATATATTATATTATGTAATTTT
1859027 ATATA-TATATTATGTAATTTT
1 ATATATTATATTATGTAATTTT
1859048 TACACTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (22 bp):
ATATATTATATTATGTAATTTT
Found at i:1860798 original size:4 final size:4
Alignment explanation
Indices: 1860791--1860829 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
1860781 ATATATATAT
* *
1860791 ATAG ATAG ATAG ATAG ATAG ATAG AGAG ATAG AGAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1860830 AGGAGATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.28, T:0.21
Consensus pattern (4 bp):
ATAG
Found at i:1867451 original size:121 final size:118
Alignment explanation
Indices: 1867319--1867563 Score: 386
Period size: 121 Copynumber: 2.1 Consensus size: 118
1867309 AAGAGTTAAA
* *
1867319 ATATTAAATGTTAAAGTA-AAGATATTCGACAATTAACATTGAAATAAATAGTTATAGTTATTGT
1 ATATTAAATGTTAAAGTACAA-ATATTAGACAATTAACATTGAAATAAATAGTTATAATTATTGT
*
1867383 CAACTGTTTCCGTAAATTCAATTCATTAGGAGAAAAACCATTAATACAATAT-TAGTT
65 CAACTGTTTCCGTAAATTCAATTCATTAGGAG-AAAACAATTAATA-AAT-TGTA-TT
*
1867440 ATATTAAATGTTAAAGTACAAATATTAGACAATTAATATTGAAATAAATAGTTATAATTATTGTC
1 ATATTAAATGTTAAAGTACAAATATTAGACAATTAACATTGAAATAAATAGTTATAATTATTGTC
*
1867505 AACTTTTTCCGTAAATTCAATTCATTAGGAGAAAACAATTAATAAATTGTATT
66 AACTGTTTCCGTAAATTCAATTCATTAGGAGAAAACAATTAATAAATTGTATT
1867558 ATATTA
1 ATATTA
1867564 TATTAAAATA
Statistics
Matches: 117, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
118 9 0.08
119 5 0.04
120 12 0.10
121 89 0.76
122 2 0.02
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (118 bp):
ATATTAAATGTTAAAGTACAAATATTAGACAATTAACATTGAAATAAATAGTTATAATTATTGTC
AACTGTTTCCGTAAATTCAATTCATTAGGAGAAAACAATTAATAAATTGTATT
Found at i:1868506 original size:21 final size:19
Alignment explanation
Indices: 1868455--1868529 Score: 66
Period size: 19 Copynumber: 3.9 Consensus size: 19
1868445 TAATTGTGCA
*
1868455 TAATAA-TTTT-ATAATAT
1 TAATAATTTTTAAAAATAT
* *
1868472 TAAT-TTTGTTTAAAAATTT
1 TAATAATT-TTTAAAAATAT
1868491 TAATGAATTTCTTAAAAATAT
1 TAAT-AATTT-TTAAAAATAT
*
1868512 TAATAATTTTAAAAAATA
1 TAATAATTTTTAAAAATA
1868530 AATATAATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
17 5 0.11
18 3 0.07
19 17 0.37
20 6 0.13
21 15 0.33
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (19 bp):
TAATAATTTTTAAAAATAT
Found at i:1875514 original size:2 final size:2
Alignment explanation
Indices: 1875507--1875540 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1875497 TTATTTATCA
*
1875507 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1875541 CAATTTGCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1876233 original size:17 final size:17
Alignment explanation
Indices: 1876210--1876253 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1876200 AACAAAAAAT
1876210 AAAATAATAATA-TTTA
1 AAAATAATAATATTTTA
**
1876226 AGAAATAATTTTATTTTA
1 A-AAATAATAATATTTTA
1876244 AAAATAATAA
1 AAAATAATAA
1876254 AAATGCAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
16 1 0.05
17 16 0.73
18 5 0.23
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
AAAATAATAATATTTTA
Found at i:1900214 original size:12 final size:11
Alignment explanation
Indices: 1900188--1900311 Score: 50
Period size: 11 Copynumber: 10.6 Consensus size: 11
1900178 CAAATGCATC
*
1900188 TAAAATAATAG
1 TAAAATAATAA
1900199 TAAAATTAATAA
1 TAAAA-TAATAA
*
1900211 TAAAACAATAA
1 TAAAATAATAA
* *
1900222 TTTTACAATATCTAAA
1 ---TAAAATA-AT-AA
*
1900238 TAATAATAAAAA
1 TAA-AATAATAA
*
1900250 TAAAATAATAG
1 TAAAATAATAA
* * *
1900261 CAATATAATAG
1 TAAAATAATAA
* *
1900272 TAAAATGACAA
1 TAAAATAATAA
* *
1900283 CAAAAAAATAA
1 TAAAATAATAA
*
1900294 GAAAATAATAA
1 TAAAATAATAA
*
1900305 CAAAATA
1 TAAAATA
1900312 GTGGAAAACA
Statistics
Matches: 82, Mismatches: 24, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
11 53 0.65
12 15 0.18
13 2 0.02
14 9 0.11
15 1 0.01
16 2 0.02
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:1901292 original size:28 final size:28
Alignment explanation
Indices: 1901234--1901295 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
1901224 AATCGAATGG
*
1901234 ATTAAATTATTAATTTTTGATTTAATTA
1 ATTAAATTATTAATTTTTGATTTAATAA
1901262 ATTAAATTATTAATTTAATT-ATTTAA-AA
1 ATTAAATTATTAATTT--TTGATTTAATAA
1901290 ATTAAA
1 ATTAAA
1901296 AAATAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 23 0.74
29 6 0.19
30 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (28 bp):
ATTAAATTATTAATTTTTGATTTAATAA
Found at i:1901350 original size:21 final size:21
Alignment explanation
Indices: 1901325--1901367 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1901315 CAATAAGAAC
1901325 GTAAACATCACTTGAATAATT
1 GTAAACATCACTTGAATAATT
1901346 GTAAACATCACTTGAATAATT
1 GTAAACATCACTTGAATAATT
1901367 G
1 G
1901368 AATTAAAGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (21 bp):
GTAAACATCACTTGAATAATT
Found at i:1919578 original size:18 final size:18
Alignment explanation
Indices: 1919555--1919589 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1919545 CGTTGATAGA
1919555 TTCAAACTATATAACTTT
1 TTCAAACTATATAACTTT
1919573 TTCAAACTATATAACTT
1 TTCAAACTATATAACTT
1919590 ATTCGTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (18 bp):
TTCAAACTATATAACTTT
Found at i:1927707 original size:24 final size:24
Alignment explanation
Indices: 1927670--1927715 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1927660 CTTAACTGAA
*
1927670 TTTTAAATAAAATATAATTTTATC
1 TTTTAAATAAAATAAAATTTTATC
1927694 TTTTAAA-AATAATAAAATTTTA
1 TTTTAAATAA-AATAAAATTTTA
1927716 ATTACTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTTAAATAAAATAAAATTTTATC
Found at i:1939557 original size:18 final size:18
Alignment explanation
Indices: 1939534--1939569 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1939524 CTAAAGCTTT
1939534 TTTTAATATTT-TTATACA
1 TTTTAAT-TTTATTATACA
1939552 TTTTAATTTTATTATACA
1 TTTTAATTTTATTATACA
1939570 GACTTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTAATTTTATTATACA
Found at i:1940072 original size:206 final size:204
Alignment explanation
Indices: 1939635--1940191 Score: 851
Period size: 206 Copynumber: 2.7 Consensus size: 204
1939625 AAGTTAACTC
* *
1939635 TATCAACAAATAATAGAGAGCTAAACAAAGTAATTCATACATGTATTTTCATTCATTCATCAGAA
1 TATCAGCAAATAATAGAGAGCTAAACAAAGTAATTCATACTTGTATTTTCATTCATTCATCAGAA
* *
1939700 TATCAGTAGCACACTATTTATACAACTCAAGAACTGCTATACCAAACAATAACA----ACTTACT
66 TATCAGTAGCACACTATTTATACAACTCAAGAACTGCTATACCAAACGATAACAGCTTACTAACT
* * * * *
1939761 TCAGCTAA--CTAACA-CCAACTGACACTAACTGATACTCAGCTAACTGTCAACGACTAACTGCT
131 TCAAC-AATGCT-TCAGCTAACTGACACTAACTGATACTCAACTAACTGTCAACAACTAACTGCT
1939823 AACTGATACCA
194 AACTGATACCA
1939834 TATCAGCAAATAATAGAGAGCTAAACAAAGTAATTCATACTTGTATTTTCATTCATTCATCAGAA
1 TATCAGCAAATAATAGAGAGCTAAACAAAGTAATTCATACTTGTATTTTCATTCATTCATCAGAA
*
1939899 TATCAGTAGCACACTATTTATACAACTCAAGAACTGCTATACCAGACGATAACAGCTTACTAACT
66 TATCAGTAGCACACTATTTATACAACTCAAGAACTGCTATACCAAACGATAACAGCTTACTAACT
* *
1939964 TCAACAATTGGCTTCAGCTAACTGACACTAATTGATACTCAACTAATTGTCAACAACTAACTGCT
131 TCAACAA-T-GCTTCAGCTAACTGACACTAACTGATACTCAACTAACTGTCAACAACTAACTGCT
1940029 AACTGATACCA
194 AACTGATACCA
*
1940040 TATCAGCAAATAACAGAGAGCTAAACAAAGTAATTCATACTTGTATTTTCATTCATTCATCAGAA
1 TATCAGCAAATAATAGAGAGCTAAACAAAGTAATTCATACTTGTATTTTCATTCATTCATCAGAA
* * * *
1940105 TACCAGTAGCACACTATTTATATAACTCAAGAACTACTACACCAAACGATAACAGCTTA-TAACT
66 TATCAGTAGCACACTATTTATACAACTCAAGAACTGCTATACCAAACGATAACAGCTTACTAACT
1940169 TCAACAACTGACTTCAGCTAACT
131 TCAACAA-TG-CTTCAGCTAACT
1940192 AACCTCAACT
Statistics
Matches: 329, Mismatches: 19, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
199 115 0.35
202 2 0.01
203 10 0.03
204 1 0.00
205 27 0.08
206 174 0.53
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (204 bp):
TATCAGCAAATAATAGAGAGCTAAACAAAGTAATTCATACTTGTATTTTCATTCATTCATCAGAA
TATCAGTAGCACACTATTTATACAACTCAAGAACTGCTATACCAAACGATAACAGCTTACTAACT
TCAACAATGCTTCAGCTAACTGACACTAACTGATACTCAACTAACTGTCAACAACTAACTGCTAA
CTGATACCA
Found at i:1948710 original size:18 final size:18
Alignment explanation
Indices: 1948687--1948726 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1948677 TGTGTTAGCA
* *
1948687 GTTATCAGCGGTTGGGTT
1 GTTATCAGCAGTTGAGTT
1948705 GTTATCAGCAGTTGAGTT
1 GTTATCAGCAGTTGAGTT
1948723 GTTA
1 GTTA
1948727 GCAGTTAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.10, G:0.33, T:0.40
Consensus pattern (18 bp):
GTTATCAGCAGTTGAGTT
Found at i:1955347 original size:16 final size:18
Alignment explanation
Indices: 1955326--1955358 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1955316 TGTTTTTAAT
1955326 TTAATT-TAT-TAAAATA
1 TTAATTATATATAAAATA
1955342 TTAATTATATATAAAAT
1 TTAATTATATATAAAAT
1955359 TATAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAATTATATATAAAATA
Found at i:1956604 original size:4 final size:4
Alignment explanation
Indices: 1956595--1956638 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
1956585 ATATCCCTAC
* * * *
1956595 ACAT ACAT ACAT GCAT ACAT ATAT ATAC ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1956639 GATAAACAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:1958522 original size:2 final size:2
Alignment explanation
Indices: 1958515--1958546 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1958505 CAAAGCATTA
1958515 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
1958547 GAGCTTTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1959316 original size:23 final size:22
Alignment explanation
Indices: 1959265--1959317 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
1959255 TATAAATTTT
*
1959265 TTAAAATATAATATAATAAAAAA
1 TTAAAA-ATAATATAAGAAAAAA
* *
1959288 TT-AAAATAATATAAGATTAATA
1 TTAAAAATAATATAAGA-AAAAA
1959310 TTAAAAAT
1 TTAAAAAT
1959318 TATAATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 10 0.40
22 8 0.32
23 7 0.28
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
TTAAAAATAATATAAGAAAAAA
Found at i:1964054 original size:15 final size:16
Alignment explanation
Indices: 1964020--1964056 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1964010 AACAACCAGT
*
1964020 TCAA-ACAATGGGTCA
1 TCAATACAATGGGACA
1964035 TCAATACAATGGGACA
1 TCAATACAATGGGACA
1964051 -CAATAC
1 TCAATAC
1964057 GCTCCGGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (16 bp):
TCAATACAATGGGACA
Found at i:1977132 original size:21 final size:18
Alignment explanation
Indices: 1977108--1977150 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 18
1977098 AAGAGTTTTG
1977108 TGTTTAAATCATTTATATATA
1 TGTTTAAAT--TTTATAT-TA
*
1977129 TGTTTTAATTTTATATTA
1 TGTTTAAATTTTATATTA
1977147 TGTT
1 TGTT
1977151 GAGGTTGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 7 0.33
21 8 0.38
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.60
Consensus pattern (18 bp):
TGTTTAAATTTTATATTA
Found at i:1978790 original size:4 final size:4
Alignment explanation
Indices: 1978781--1978808 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1978771 GGAATACTAA
1978781 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
1978809 CACCTTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:1983921 original size:7 final size:7
Alignment explanation
Indices: 1983909--1983936 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1983899 ATATCACCAT
1983909 CAAATTA
1 CAAATTA
1983916 CAAATTA
1 CAAATTA
1983923 CAAATTA
1 CAAATTA
1983930 CAAATTA
1 CAAATTA
1983937 GATTTCACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (7 bp):
CAAATTA
Found at i:1985826 original size:2 final size:2
Alignment explanation
Indices: 1985819--1985856 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1985809 TCTCTAAAAG
1985819 TA 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
1985857 ATTAACTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1994094 original size:14 final size:15
Alignment explanation
Indices: 1994070--1994113 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
1994060 TATGTAAAGG
*
1994070 ATAATATTAAAATAA
1 ATAAAATTAAAATAA
1994085 ATAAAA-TAAAATAA
1 ATAAAATTAAAATAA
1994099 A-AAAATTAAAA-AA
1 ATAAAATTAAAATAA
1994112 AT
1 AT
1994114 TTACATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 7 0.27
14 14 0.54
15 5 0.19
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
ATAAAATTAAAATAA
Found at i:1994114 original size:9 final size:10
Alignment explanation
Indices: 1994070--1994114 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
1994060 TATGTAAAGG
1994070 ATAATATTAAA
1 ATAA-ATTAAA
1994081 ATAAA-TAAA
1 ATAAATTAAA
*
1994090 ATAAAATAAA
1 ATAAATTAAA
1994100 A-AAATTAAA
1 ATAAATTAAA
1994109 A-AAATT
1 ATAAATT
1994115 TACATTAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 22 0.69
10 6 0.19
11 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
ATAAATTAAA
Found at i:2000221 original size:18 final size:17
Alignment explanation
Indices: 2000195--2000228 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2000185 CAGTTTTGGT
*
2000195 TTTGTTTTTCAGTGCTTG
1 TTTGATTTTCAG-GCTTG
2000213 TTTGATTTTCAGGCTT
1 TTTGATTTTCAGGCTT
2000229 TGCTCGTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.59
Consensus pattern (17 bp):
TTTGATTTTCAGGCTTG
Found at i:2001458 original size:27 final size:27
Alignment explanation
Indices: 2001420--2001472 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
2001410 GTTTATTCGT
2001420 TTTTAAGTATGTAACTCAATGAGAAAA
1 TTTTAAGTATGTAACTCAATGAGAAAA
2001447 TTTTAAGTATGTAACTCAATGAGAAA
1 TTTTAAGTATGTAACTCAATGAGAAA
2001473 TTTCCTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (27 bp):
TTTTAAGTATGTAACTCAATGAGAAAA
Found at i:2010789 original size:48 final size:50
Alignment explanation
Indices: 2010688--2010794 Score: 127
Period size: 49 Copynumber: 2.2 Consensus size: 50
2010678 ATCCGAATAA
**
2010688 AAAAAGGT-AAAACTAAGTCGTTTTGATAAATATTTACTTTTCTAAAGTT
1 AAAAAGGTAAAAACTAAGTCGTTTTGATAAATATTTACTCATCTAAAGTT
* *
2010737 -AAAAGGTAAAAATTACA-TCGTTTTGATAAATGTTTACTCAT-T-AAGTT
1 AAAAAGGTAAAAACTA-AGTCGTTTTGATAAATATTTACTCATCTAAAGTT
2010784 AAAAA-GTAAAA
1 AAAAAGGTAAAA
2010795 TCATTATAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
47 11 0.22
48 12 0.24
49 27 0.53
50 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (50 bp):
AAAAAGGTAAAAACTAAGTCGTTTTGATAAATATTTACTCATCTAAAGTT
Found at i:2016701 original size:30 final size:30
Alignment explanation
Indices: 2016667--2016732 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
2016657 ATATTAACAT
*
2016667 CATAAAATATGCATCTTAAGAAGCAAGAAC
1 CATAAAACATGCATCTTAAGAAGCAAGAAC
*
2016697 CATAAACCATGCATCTTAAGAAGCAAGAAC
1 CATAAAACATGCATCTTAAGAAGCAAGAAC
2016727 CATAAA
1 CATAAA
2016733 CCAACTCTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.50, C:0.20, G:0.12, T:0.18
Consensus pattern (30 bp):
CATAAAACATGCATCTTAAGAAGCAAGAAC
Found at i:2016733 original size:30 final size:30
Alignment explanation
Indices: 2016675--2016735 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2016665 ATCATAAAAT
2016675 ATGCATCTTAAGAAGCAAGAACCATAAACC
1 ATGCATCTTAAGAAGCAAGAACCATAAACC
2016705 ATGCATCTTAAGAAGCAAGAACCATAAACC
1 ATGCATCTTAAGAAGCAAGAACCATAAACC
2016735 A
1 A
2016736 ACTCTCAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.48, C:0.23, G:0.13, T:0.16
Consensus pattern (30 bp):
ATGCATCTTAAGAAGCAAGAACCATAAACC
Found at i:2028105 original size:18 final size:17
Alignment explanation
Indices: 2028064--2028106 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2028054 TTTAACTTTA
2028064 TTATATAAATTAATTTT
1 TTATATAAATTAATTTT
* *
2028081 CTA-ATAAATATAGTTTT
1 TTATATAAAT-TAATTTT
2028098 TTATATAAA
1 TTATATAAA
2028107 ATTTTTCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.29
17 10 0.48
18 5 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TTATATAAATTAATTTT
Found at i:2029364 original size:27 final size:29
Alignment explanation
Indices: 2029334--2029393 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
2029324 TTATAATTTT
2029334 TTTTAAGTT-ATG-AATTTAGTCATTATA
1 TTTTAAGTTAATGAAATTTAGTCATTATA
* **
2029361 TTTTAATTTAATGAAATTTAGTTTTTATA
1 TTTTAAGTTAATGAAATTTAGTCATTATA
2029390 TTTT
1 TTTT
2029394 TTGAAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 8 0.29
28 3 0.11
29 17 0.61
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (29 bp):
TTTTAAGTTAATGAAATTTAGTCATTATA
Found at i:2031200 original size:22 final size:21
Alignment explanation
Indices: 2031165--2031210 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
2031155 ATATGATATA
*
2031165 TTTACTTATTTT-AATTTACT
1 TTTACTTATTTTAAATTAACT
2031185 TTTACTTACATTTTAAATTAACT
1 TTTACTT--ATTTTAAATTAACT
2031208 TTT
1 TTT
2031211 TATTTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
22 5 0.23
23 10 0.45
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTACTTATTTTAAATTAACT
Found at i:2032599 original size:15 final size:16
Alignment explanation
Indices: 2032579--2032611 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2032569 GTTAGCATTT
*
2032579 AATT-AAAATTTTAAA
1 AATTAAAAATTATAAA
2032594 AATTAAAAATTATAAA
1 AATTAAAAATTATAAA
2032610 AA
1 AA
2032612 CTATTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTAAAAATTATAAA
Found at i:2032671 original size:38 final size:38
Alignment explanation
Indices: 2032581--2032676 Score: 90
Period size: 38 Copynumber: 2.5 Consensus size: 38
2032571 TAGCATTTAA
*
2032581 TTAAAATTTTAAAAATTAAAAATTATAAAAACTATTCT
1 TTAAAATTTTAAAAATTAAAAATTATAAAAACTATTAT
*** *
2032619 TTAAAATAAAAAAAATCATCAAGAA-TATAAAAA-TA-TAT
1 TTAAAATTTTAAAAAT--T-AAAAATTATAAAAACTATTAT
2032657 TTAAAATTTTAAAAAATTAA
1 TTAAAATTTT-AAAAATTAA
2032677 TTAAATGTTG
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
36 2 0.04
37 1 0.02
38 22 0.48
39 8 0.17
40 9 0.20
41 4 0.09
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (38 bp):
TTAAAATTTTAAAAATTAAAAATTATAAAAACTATTAT
Found at i:2036612 original size:23 final size:24
Alignment explanation
Indices: 2036565--2036612 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2036555 TCGACTTATT
*
2036565 AATAACATTACACAATTTAAAAAA
1 AATAACATTACACAATGTAAAAAA
*
2036589 AATAACATTAC-CAATGTAATAAA
1 AATAACATTACACAATGTAAAAAA
2036612 A
1 A
2036613 TTAAAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.25
Consensus pattern (24 bp):
AATAACATTACACAATGTAAAAAA
Found at i:2041325 original size:26 final size:25
Alignment explanation
Indices: 2041269--2041481 Score: 144
Period size: 26 Copynumber: 9.2 Consensus size: 25
2041259 CATTAAGGAA
2041269 CACTA-GTGTGCTCTCTGTTT---AG
1 CACTATGTGTGCT-TCTGTTTCCCAG
*
2041291 CACTATGTGTGCTTCTATTTCCCCAG
1 CACTATGTGTGCTTCTGTTT-CCCAG
*
2041317 CACTGTGTGTGCTTCTGTTT---AG
1 CACTATGTGTGCTTCTGTTTCCCAG
*
2041339 CACTATGTGTGTTTCTGTTTCCCTAG
1 CACTATGTGTGCTTCTGTTTCCC-AG
* * *
2041365 CAATGTGTGTGCTTCT-CTT--CAG
1 CACTATGTGTGCTTCTGTTTCCCAG
2041387 CAC--TGTGTGCTTCTG-TT--CAG
1 CACTATGTGTGCTTCTGTTTCCCAG
2041407 CAC--TGTGTGCTTCTG-TT--CAG
1 CACTATGTGTGCTTCTGTTTCCCAG
* *
2041427 CACTGTGTGTGCCTACTGTTTCCCAG
1 CACTATGTGTG-CTTCTGTTTCCCAG
**
2041453 CACT-TACGTGCTTCTGTTTTCCCAG
1 CACTATGTGTGCTTCTG-TTTCCCAG
2041478 CACT
1 CACT
2041482 TATCCGCCTC
Statistics
Matches: 160, Mismatches: 14, Indels: 31
0.78 0.07 0.15
Matches are distributed among these distances:
20 39 0.24
22 41 0.26
23 13 0.08
24 7 0.04
25 18 0.11
26 42 0.26
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.40
Consensus pattern (25 bp):
CACTATGTGTGCTTCTGTTTCCCAG
Found at i:2041344 original size:48 final size:46
Alignment explanation
Indices: 2041269--2041471 Score: 211
Period size: 48 Copynumber: 4.4 Consensus size: 46
2041259 CATTAAGGAA
* *
2041269 CACTAGTGTGCTCTCTGTTTAGCACTATGTGTGCTTCTATTTCCCCAG
1 CACTTGTGTGCT-TCTGTTTAGCACTATGTGTGCTTCTGTTT-CCCAG
*
2041317 CACTGTGTGTGCTTCTGTTTAGCACTATGTGTGTTTCTGTTTCCCTAG
1 CACT-TGTGTGCTTCTGTTTAGCACTATGTGTGCTTCTGTTTCCC-AG
* * *
2041365 CAATGTGTGTGCTTCTCTTCAGCAC--TGTGTGCTTCTG-TT--CAG
1 CACT-TGTGTGCTTCTGTTTAGCACTATGTGTGCTTCTGTTTCCCAG
* * *
2041407 CAC-TGTGTGCTTCTGTTCAGCACTGTGTGTGCCTACTGTTTCCCAG
1 CACTTGTGTGCTTCTGTTTAGCACTATGTGTG-CTTCTGTTTCCCAG
**
2041453 CACTTACGTGCTTCTGTTT
1 CACTTGTGTGCTTCTGTTT
2041472 TCCCAGCACT
Statistics
Matches: 133, Mismatches: 13, Indels: 19
0.81 0.08 0.12
Matches are distributed among these distances:
40 19 0.14
42 10 0.08
43 6 0.05
44 2 0.02
45 2 0.02
46 17 0.13
47 15 0.11
48 55 0.41
49 7 0.05
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (46 bp):
CACTTGTGTGCTTCTGTTTAGCACTATGTGTGCTTCTGTTTCCCAG
Found at i:2041436 original size:22 final size:22
Alignment explanation
Indices: 2041274--2041438 Score: 149
Period size: 20 Copynumber: 7.3 Consensus size: 22
2041264 AGGAACACTA
* *
2041274 GTGTGCTCTCTGTTTAGCACTAT
1 GTGTGCT-TCTGTTCAGCACTGT
*
2041297 GTGTGCTTCTATTTCCCCAGCACTGT
1 GTGTGCTTCT-GTT---CAGCACTGT
* *
2041323 GTGTGCTTCTGTTTAGCACTAT
1 GTGTGCTTCTGTTCAGCACTGT
* *
2041345 GTGTGTTTCTGTTTCCCTAGCAATGT
1 GTGTGCTTCTG-TT--C-AGCACTGT
*
2041371 GTGTGCTTCTCTTCAGCAC--T
1 GTGTGCTTCTGTTCAGCACTGT
2041391 GTGTGCTTCTGTTCAGCAC--T
1 GTGTGCTTCTGTTCAGCACTGT
2041411 GTGTGCTTCTGTTCAGCACTGT
1 GTGTGCTTCTGTTCAGCACTGT
2041433 GTGTGC
1 GTGTGC
2041439 CTACTGTTTC
Statistics
Matches: 118, Mismatches: 14, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
20 39 0.33
22 31 0.26
23 12 0.10
25 4 0.03
26 32 0.27
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.42
Consensus pattern (22 bp):
GTGTGCTTCTGTTCAGCACTGT
Found at i:2043013 original size:25 final size:26
Alignment explanation
Indices: 2042985--2043046 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 26
2042975 AACAGAATCG
2042985 CATAAGTGCTGGAGAAACA-AAAGCA
1 CATAAGTGCTGGAGAAACAGAAAGCA
*
2043010 CATAAGTGCT-GAGAAACAGTAAGCA
1 CATAAGTGCTGGAGAAACAGAAAGCA
*
2043035 CACACAGTGCTG
1 CATA-AGTGCTG
2043047 AACAGAGGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 8 0.25
25 18 0.56
26 6 0.19
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.15
Consensus pattern (26 bp):
CATAAGTGCTGGAGAAACAGAAAGCA
Found at i:2043060 original size:22 final size:22
Alignment explanation
Indices: 2043032--2043076 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2043022 GAAACAGTAA
2043032 GCACACACAGTGCTGAACAGAG
1 GCACACACAGTGCTGAACAGAG
*
2043054 GCACACACAGTGCTGAATAGAG
1 GCACACACAGTGCTGAACAGAG
2043076 G
1 G
2043077 GCACGAAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.24, G:0.29, T:0.11
Consensus pattern (22 bp):
GCACACACAGTGCTGAACAGAG
Found at i:2043089 original size:23 final size:22
Alignment explanation
Indices: 2043032--2043101 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
2043022 GAAACAGTAA
*
2043032 GCACACACAGTGCTGAACAGAG
1 GCACAAACAGTGCTGAACAGAG
* *
2043054 GCACACACAGTGCTGAATAGAGG
1 GCACAAACAGTGCTGAACAGA-G
*
2043077 GCACGAAAC-GTGCTAAACAGTAG
1 GCAC-AAACAGTGCTGAACAG-AG
2043100 GC
1 GC
2043102 GTGCAAGTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 20 0.49
23 17 0.41
24 4 0.10
ACGTcount: A:0.36, C:0.24, G:0.29, T:0.11
Consensus pattern (22 bp):
GCACAAACAGTGCTGAACAGAG
Found at i:2044137 original size:59 final size:59
Alignment explanation
Indices: 2044070--2044188 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
2044060 TCTCTTTTCC
2044070 TTTGTCTTCAGTTTGGTCCCTTTCCTTCTTTCCTTTCTCTTCAATTTCACATAGACACA
1 TTTGTCTTCAGTTTGGTCCCTTTCCTTCTTTCCTTTCTCTTCAATTTCACATAGACACA
2044129 TTTGTCTTCAGTTTGGTCCCTTTCCTTCTTTCCTTTCTCTTCAATTTCACATAGACACA
1 TTTGTCTTCAGTTTGGTCCCTTTCCTTCTTTCCTTTCTCTTCAATTTCACATAGACACA
2044188 T
1 T
2044189 GTAAGCTAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.15, C:0.29, G:0.08, T:0.48
Consensus pattern (59 bp):
TTTGTCTTCAGTTTGGTCCCTTTCCTTCTTTCCTTTCTCTTCAATTTCACATAGACACA
Found at i:2046473 original size:23 final size:22
Alignment explanation
Indices: 2046443--2046567 Score: 106
Period size: 23 Copynumber: 5.5 Consensus size: 22
2046433 ACGCTAGCGC
2046443 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTT-GCACTTTGTGT
*
2046466 GCTTACTGTTTCGCACCTTGTGT
1 GCTTACTGTTT-GCACTTTGTGT
* * * *
2046489 GCCTACTGATTTGCGCTATGTGC
1 GCTTACTG-TTTGCACTTTGTGT
* * **
2046512 GCCTACTGATTGCACTGGGTGT
1 GCTTACTGTTTGCACTTTGTGT
* * *
2046534 GCCTACTGGATTGCACTGTGTGT
1 GCTTACT-GTTTGCACTTTGTGT
2046557 GCTTACTGTTT
1 GCTTACTGTTT
2046568 CCCCAGCACT
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
22 19 0.22
23 64 0.74
24 3 0.03
ACGTcount: A:0.11, C:0.23, G:0.26, T:0.40
Consensus pattern (22 bp):
GCTTACTGTTTGCACTTTGTGT
Found at i:2046564 original size:45 final size:46
Alignment explanation
Indices: 2046446--2046564 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 46
2046436 CTAGCGCGCT
* * *
2046446 TACTG-TTTCGCACTTTGTGTGCTTACTGTTTCGCACCTTGTGTGCC
1 TACTGATTT-GCACTATGTGTGCTTACTGATTCGCACCTGGTGTGCC
* * *
2046492 TACTGATTTGCGCTATGTGCGCCTACTGATT-GCA-CTGGGTGTGCC
1 TACTGATTTGCACTATGTGTGCTTACTGATTCGCACCT-GGTGTGCC
*
2046537 TACTGGA-TTGCACTGTGTGTGCTTACTG
1 TACT-GATTTGCACTATGTGTGCTTACTG
2046565 TTTCCCCAGC
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
44 2 0.03
45 31 0.52
46 24 0.40
47 3 0.05
ACGTcount: A:0.12, C:0.24, G:0.26, T:0.39
Consensus pattern (46 bp):
TACTGATTTGCACTATGTGTGCTTACTGATTCGCACCTGGTGTGCC
Found at i:2049898 original size:141 final size:141
Alignment explanation
Indices: 2049640--2049922 Score: 449
Period size: 141 Copynumber: 2.0 Consensus size: 141
2049630 AGAGGCTCCA
* * * * *
2049640 GGTCTCCACTTATCCTTGATAAAGTTGCGTAAAGCCGGATGCTCAACCCACCTTGCAAGAAATCG
1 GGTCTCCACTTATCCTTGACAAAGTTGCGAAAAGCAGAATGCTCAACCCACCCTGCAAGAAATCG
2049705 AAAAGGCCTTCCTCTTGGTAACACAACTTCTAGTTTGAGAACGAGGAAAAGTGGTCTATGATCGG
66 AAAAGGCCTTCCTCTTGGTAACACAACTTCTAGTTTGAGAACGAGGAAAAGTGGTCTATGATCGG
2049770 ATTTGATCTTC
131 ATTTGATCTTC
* * *
2049781 GGTCTTCACTTATCCTTGACGAAGTTGGGAAAAGCAGAATGCTCAACCCACCCTGCAAGAAATCG
1 GGTCTCCACTTATCCTTGACAAAGTTGCGAAAAGCAGAATGCTCAACCCACCCTGCAAGAAATCG
* * * * *
2049846 AAAAGGCCTTTCTTTTGGTAACACAACTTCTGGTTTGAGAACGAGGAGAAGTGGTCTATGGTCGG
66 AAAAGGCCTTCCTCTTGGTAACACAACTTCTAGTTTGAGAACGAGGAAAAGTGGTCTATGATCGG
2049911 ATTTGATCTTC
131 ATTTGATCTTC
2049922 G
1 G
2049923 AGAGATGAGT
Statistics
Matches: 129, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
141 129 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (141 bp):
GGTCTCCACTTATCCTTGACAAAGTTGCGAAAAGCAGAATGCTCAACCCACCCTGCAAGAAATCG
AAAAGGCCTTCCTCTTGGTAACACAACTTCTAGTTTGAGAACGAGGAAAAGTGGTCTATGATCGG
ATTTGATCTTC
Found at i:2054325 original size:22 final size:22
Alignment explanation
Indices: 2054270--2054359 Score: 99
Period size: 22 Copynumber: 3.9 Consensus size: 22
2054260 TAAATGAACG
* * *
2054270 GAGAGCACCAAGGTACTAAACA
1 GAGAGCACAAATGTGCTAAACA
2054292 GAGAGCACAAATGTGCTAAACA
1 GAGAGCACAAATGTGCTAAACA
*
2054314 GAGAGCACAAATGTGCTAATAATCG
1 GAGAGCACAAATGTGCT-A-AA-CA
*
2054339 GAGAGCACAATACGTGCTAAA
1 GAGAGCACAA-ATGTGCTAAA
2054360 GATAACGGAG
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
22 36 0.61
23 1 0.02
24 4 0.07
25 12 0.20
26 6 0.10
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.14
Consensus pattern (22 bp):
GAGAGCACAAATGTGCTAAACA
Found at i:2066155 original size:12 final size:12
Alignment explanation
Indices: 2066140--2066165 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2066130 TAGTAAGATC
2066140 TAGTCAATTTTA
1 TAGTCAATTTTA
2066152 TAGTCAATTTTA
1 TAGTCAATTTTA
2066164 TA
1 TA
2066166 CAAAGAAAAT
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:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (12 bp):
TAGTCAATTTTA
Found at i:2079187 original size:22 final size:21
Alignment explanation
Indices: 2079156--2079196 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2079146 TTTTAATTAA
**
2079156 AATAAATTATTTAAATTGACT
1 AATAAATTATAAAAATTGACT
2079177 AATAACATTATAAAAATTGA
1 AATAA-ATTATAAAAATTGA
2079197 GATATCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (21 bp):
AATAAATTATAAAAATTGACT
Found at i:2082261 original size:7 final size:7
Alignment explanation
Indices: 2082249--2082288 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
2082239 TGAATCCTTT
2082249 ATTCCTA
1 ATTCCTA
2082256 ATTCCTA
1 ATTCCTA
2082263 ATTCCTA
1 ATTCCTA
2082270 ATTCCTA
1 ATTCCTA
2082277 ATTCCTA
1 ATTCCTA
2082284 ATTCC
1 ATTCC
2082289 ATACTTTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.42
Consensus pattern (7 bp):
ATTCCTA
Found at i:2083920 original size:16 final size:16
Alignment explanation
Indices: 2083899--2083932 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2083889 GAGGATGACT
* *
2083899 AAAAAATTTAATTTTA
1 AAAAAATTAAATATTA
2083915 AAAAAATTAAATATTA
1 AAAAAATTAAATATTA
2083931 AA
1 AA
2083933 TTAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAAATTAAATATTA
Found at i:2083936 original size:21 final size:21
Alignment explanation
Indices: 2083912--2083954 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2083902 AAATTTAATT
*
2083912 TTAAAAAAATTAAATA-TTAAA
1 TTAAAAAAAAT-AATAGTTAAA
2083933 TTAAAAAAAATAATAGTTAAA
1 TTAAAAAAAATAATAGTTAAA
2083954 T
1 T
2083955 GATCAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
TTAAAAAAAATAATAGTTAAA
Found at i:2087032 original size:19 final size:19
Alignment explanation
Indices: 2086988--2087032 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 19
2086978 TAATATTTTT
2086988 TTAATAAAAATATCACATC
1 TTAATAAAAATATCACATC
2087007 --AATTAAAAA-ATCACATGC
1 TTAA-TAAAAATATCACAT-C
2087025 TTAATAAA
1 TTAATAAA
2087033 TTCAAATACC
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
17 9 0.41
18 7 0.32
19 4 0.18
20 2 0.09
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.29
Consensus pattern (19 bp):
TTAATAAAAATATCACATC
Found at i:2095296 original size:15 final size:16
Alignment explanation
Indices: 2095280--2095325 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
2095270 AAATTTCAAT
2095280 AAATAAAAAATATATA
1 AAATAAAAAATATATA
**
2095296 AAAGTATTAAATAT-TA
1 AAA-TAAAAAATATATA
2095312 AAATAAAAAATATA
1 AAATAAAAAATATA
2095326 GATATTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
15 8 0.33
16 8 0.33
17 8 0.33
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
AAATAAAAAATATATA
Found at i:2095630 original size:24 final size:25
Alignment explanation
Indices: 2095598--2095645 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
2095588 AAATTCTTTA
2095598 TATTATATAAATTTATTA-TTATAC
1 TATTATATAAATTTATTACTTATAC
* *
2095622 TATTTTATAATTTTATTACTTATA
1 TATTATATAAATTTATTACTTATA
2095646 TAAAAAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTATATAAATTTATTACTTATAC
Found at i:2106498 original size:2 final size:2
Alignment explanation
Indices: 2106491--2106516 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2106481 TGAGTTATTC
2106491 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
2106517 TCTGATTTGT
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:2114332 original size:31 final size:31
Alignment explanation
Indices: 2114287--2114362 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 31
2114277 TTTAAAGACT
* ***
2114287 AAAATAAATTTAATTGTTAAATTCAA-ATATC
1 AAAATAAATATAATTACGAAATTCAAGA-ATC
*
2114318 AAAATACATATAATTACGAAATTCAAGAATC
1 AAAATAAATATAATTACGAAATTCAAGAATC
*
2114349 AAAAT-GATATAATT
1 AAAATAAATATAATT
2114363 CCTTTTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 8 0.21
31 29 0.76
32 1 0.03
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (31 bp):
AAAATAAATATAATTACGAAATTCAAGAATC
Found at i:2114361 original size:30 final size:31
Alignment explanation
Indices: 2114305--2114362 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2114295 TTTAATTGTT
2114305 AAATTCAAATATCAAAATACATATAATTACG
1 AAATTCAAATATCAAAATACATATAATTACG
*
2114336 AAATTCAAGA-ATCAAAAT-GATATAATT
1 AAATTCAA-ATATCAAAATACATATAATT
2114363 CCTTTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 8 0.32
31 16 0.64
32 1 0.04
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.29
Consensus pattern (31 bp):
AAATTCAAATATCAAAATACATATAATTACG
Found at i:2119660 original size:7 final size:7
Alignment explanation
Indices: 2119648--2119674 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2119638 GGTTGATTAC
2119648 TACATGA
1 TACATGA
2119655 TACATGA
1 TACATGA
2119662 TACATGA
1 TACATGA
2119669 TACATG
1 TACATG
2119675 CCCAGTGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (7 bp):
TACATGA
Found at i:2134370 original size:117 final size:117
Alignment explanation
Indices: 2134077--2135028 Score: 1277
Period size: 117 Copynumber: 8.0 Consensus size: 117
2134067 TAGGCTTGGC
* * *
2134077 CTTAAGGGGATCTTCCATTTCAACCCTGATATTACTTAACCCTTCAATGCTCTGTTCACCACCAA
1 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
2134142 TAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGGCTTGG
66 TAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTA-----GG
* * * *
2134199 CCTTAAGGGGATCTTCCATTTCAACCCTGATATTACTTAACCCTTCAATGCTCTGCTCACCACCA
1 -CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCA
2134264 ATAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
65 ATAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
* * *
2134317 CTTAAGGGGTTCTTCCATTTCAGCCTTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
1 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
* * * * *
2134382 CAATTTTCTTCTTCTTC--G----TTGAACCCTTTGGCCAACCATGTTTAGG
66 TAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
* * * * **
2134428 CTTAAGGGGATTTTCCATTTCAACCCAGCTGTCACTTAACCCTACAATACAATGTTCACCACCAA
1 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
** * *
2134493 TAGTTTTCTTCTTCTTGATGTTCATTGTACCCTTTGGCTGACCACATTTAGG
66 TAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
*
2134545 CTTAAGGGGATCTTCCATTTCAACCTTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
1 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
* * * * * * *
2134610 TAGTGTTCTTGTTGTCGTTGTTTTTCTTTGAACCTTTTGGCCGACCACGTTTAGG
66 TAGTTTTCTT-CT-TC-TTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
* *
2134665 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACACTTCAATACTCTGTTCACCAGCAA
1 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
*
2134730 TAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTCTAGG
66 TAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
* *
2134782 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACACTTCAATACGCTGTTCACCACCAA
1 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
2134847 TAGTTTTCTTCTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
66 TAG-----TT-TTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
* * *
2134905 CTTAAGGGGATCTTCCATTTCAACCTTGTTATCACTTAACCCTTCAATAATCTGTTCACCACCAA
1 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
* * * * * *
2134970 TAGTTTTCTTCTTGTTGTTGTTTTTCTTTGTACCCTTTGGCCTACCACGCTTACG
66 TAGTTTTCTTCTTCTTCTTG---TTCATTGTACCCTTTGGCCGACCACGTTTAGG
2135025 CTTA
1 CTTA
2135029 GCCTGCTTAC
Statistics
Matches: 740, Mismatches: 71, Indels: 39
0.87 0.08 0.05
Matches are distributed among these distances:
111 95 0.13
113 1 0.00
115 1 0.00
117 274 0.37
118 7 0.01
119 3 0.00
120 134 0.18
122 2 0.00
123 223 0.30
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (117 bp):
CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
TAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
Found at i:2153013 original size:3 final size:3
Alignment explanation
Indices: 2153005--2153031 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2152995 ATAAATAAGC
2153005 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2153032 CAAAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2156781 original size:20 final size:20
Alignment explanation
Indices: 2156756--2156796 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2156746 ATTAGTCATA
2156756 TTTCAATCTGTCAATGGATT
1 TTTCAATCTGTCAATGGATT
2156776 TTTCAATCTGTCAATGGATT
1 TTTCAATCTGTCAATGGATT
2156796 T
1 T
2156797 ACTTCGTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (20 bp):
TTTCAATCTGTCAATGGATT
Found at i:2157667 original size:12 final size:13
Alignment explanation
Indices: 2157650--2157687 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
2157640 TTTATATCGA
2157650 TATTTTAATTGAT
1 TATTTTAATTGAT
*
2157663 T-TTTTAATTAAT
1 TATTTTAATTGAT
*
2157675 TAATTTAATTGAT
1 TATTTTAATTGAT
2157688 CAATCTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (13 bp):
TATTTTAATTGAT
Found at i:2159501 original size:18 final size:16
Alignment explanation
Indices: 2159478--2159511 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
2159468 AATATTTTAT
2159478 TTATATTAATTCTATATA
1 TTATA-TAATT-TATATA
2159496 TTATATAATTTATATA
1 TTATATAATTTATATA
2159512 ACATAAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATAATTTATATA
Found at i:2171132 original size:17 final size:17
Alignment explanation
Indices: 2171110--2171142 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2171100 TGTTCAGACA
2171110 TATATTTATAATTGTAT
1 TATATTTATAATTGTAT
*
2171127 TATATTTATACTTGTA
1 TATATTTATAATTGTA
2171143 AACTCCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (17 bp):
TATATTTATAATTGTAT
Found at i:2173534 original size:30 final size:30
Alignment explanation
Indices: 2173459--2173534 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
2173449 TTGCTTCTTG
* * *
2173459 ATTAATTTATTTTTATTCTTTTAATGAGATT
1 ATTAA-TTATATTTATTCTTTTAAAGAAATT
* **
2173490 ATTACTTACCTTTATT-TTTTGAAAGAAATT
1 ATTAATTATATTTATTCTTTT-AAAGAAATT
2173520 ATTAATTATATTTAT
1 ATTAATTATATTTAT
2173535 ATAAAGCAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 4 0.11
30 28 0.78
31 4 0.11
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (30 bp):
ATTAATTATATTTATTCTTTTAAAGAAATT
Found at i:2174082 original size:31 final size:30
Alignment explanation
Indices: 2174028--2174115 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 30
2174018 TCATTGTGCT
2174028 CTTCAAAATTTT-GAATATTTTAATTA-AGTC
1 CTTCAAAATTTTAGAA-ATTTTAATTATA-TC
2174058 CTTCAAAATTTTTAGAAATTTTAATTATATC
1 CTTCAAAA-TTTTAGAAATTTTAATTATATC
* * *
2174089 TTTCAAAACTTTCAAAAATTTTAATTA
1 CTTCAAAA-TTTTAGAAATTTTAATTA
2174116 GATCATCCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
30 8 0.16
31 39 0.76
32 4 0.08
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (30 bp):
CTTCAAAATTTTAGAAATTTTAATTATATC
Found at i:2179000 original size:71 final size:71
Alignment explanation
Indices: 2178884--2179025 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 71
2178874 AATAACTCAA
*
2178884 GACACATTGGGTCCAAAGAAGATAAGAGAGATGAAACAAATAGGCAAAATATCATCTCAATCCAT
1 GACACATTGGGTCCAAAGAAGACAAGAGAGATGAAACAAATAGGCAAAATATCATCTCAATCCAT
2178949 AATTTC
66 AATTTC
2178955 GACACATTGGGTCCAAAGAAGACAAGAGAGATGAAACAAATAGGCAAAATATCATCTCAATCCAT
1 GACACATTGGGTCCAAAGAAGACAAGAGAGATGAAACAAATAGGCAAAATATCATCTCAATCCAT
2179020 AATTTC
66 AATTTC
2179026 AAGTCGGTTT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (71 bp):
GACACATTGGGTCCAAAGAAGACAAGAGAGATGAAACAAATAGGCAAAATATCATCTCAATCCAT
AATTTC
Found at i:2189027 original size:2 final size:2
Alignment explanation
Indices: 2189022--2189097 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
2189012 ACAAACCCCG
2189022 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
2189064 TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2189098 CCTTTAAGCC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:2201460 original size:17 final size:17
Alignment explanation
Indices: 2201438--2201472 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2201428 TTTCATGCCT
2201438 TTTTTTTCAA-ATTTTTA
1 TTTTTTT-AATATTTTTA
2201455 TTTTTTTAATATTTTTA
1 TTTTTTTAATATTTTTA
2201472 T
1 T
2201473 AAATTATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTTAATATTTTTA
Found at i:2202509 original size:23 final size:23
Alignment explanation
Indices: 2202466--2202509 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2202456 TAATAAAATA
*
2202466 TACATGTGTAAAAAATTTATTTG
1 TACATGTGTAAAAAATATATTTG
*
2202489 TACATTTGTAAAATAA-ATATT
1 TACATGTGTAAAA-AATATATT
2202510 AATTTACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.89
24 2 0.11
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (23 bp):
TACATGTGTAAAAAATATATTTG
Found at i:2202659 original size:25 final size:25
Alignment explanation
Indices: 2202631--2202680 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2202621 AGGCTCAAAC
** * *
2202631 GAAAAAGGGAAGGAAGAAAGGGAAA
1 GAAAAAGAAAAGGAAAAAAGAGAAA
2202656 GAAAAAGAAAAGGAAAAAAGAGAAA
1 GAAAAAGAAAAGGAAAAAAGAGAAA
2202681 CTAGAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (25 bp):
GAAAAAGAAAAGGAAAAAAGAGAAA
Found at i:2213461 original size:18 final size:16
Alignment explanation
Indices: 2213429--2213472 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
2213419 ATGGGATGAG
2213429 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
2213445 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
2213459 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
2213473 ATTCTAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:2213563 original size:21 final size:22
Alignment explanation
Indices: 2213508--2213563 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
2213498 TTAAACTCAT
2213508 TTCCACATA-CTTCTCTTTTTTA
1 TTCCA-ATATCTTCTCTTTTTTA
* * *
2213530 TCTTCATTTTCTTC-CTTTTTTA
1 T-TCCAATATCTTCTCTTTTTTA
2213552 TTCCAATATCTT
1 TTCCAATATCTT
2213564 TAGTTACAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
21 8 0.31
22 11 0.42
23 7 0.27
ACGTcount: A:0.16, C:0.25, G:0.00, T:0.59
Consensus pattern (22 bp):
TTCCAATATCTTCTCTTTTTTA
Found at i:2215259 original size:28 final size:28
Alignment explanation
Indices: 2215227--2215287 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
2215217 CTTACGAACT
*
2215227 TAAATATGAA-TCGTAAAATAAATATGAA
1 TAAATATGAACT-GTAAAACAAATATGAA
2215255 TAAATATGAACTGTAAAACAAATATGAA
1 TAAATATGAACTGTAAAACAAATATGAA
2215283 -AAATA
1 TAAATA
2215288 CAAAAGAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
27 5 0.16
28 25 0.81
29 1 0.03
ACGTcount: A:0.59, C:0.05, G:0.10, T:0.26
Consensus pattern (28 bp):
TAAATATGAACTGTAAAACAAATATGAA
Found at i:2221221 original size:22 final size:22
Alignment explanation
Indices: 2221195--2221236 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2221185 AATTTTGTAT
2221195 AATTCAAATATATTTTAATTTA
1 AATTCAAATATATTTTAATTTA
**
2221217 AATTCGGATATATTTTAATT
1 AATTCAAATATATTTTAATT
2221237 ATTAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (22 bp):
AATTCAAATATATTTTAATTTA
Found at i:2229040 original size:2 final size:2
Alignment explanation
Indices: 2229033--2229107 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
2229023 GTACAGATGG
2229033 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
2229075 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 A
2229108 GTATTATGGA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2245496 original size:22 final size:23
Alignment explanation
Indices: 2245449--2245497 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
2245439 AACAAGAAAC
* *
2245449 ACAAAACACAAAGAACAAGTTTA
1 ACAAAACACAAAGAACAAATTAA
2245472 ACAAAA-ACAAAG-ACTAAATTAA
1 ACAAAACACAAAGAAC-AAATTAA
2245494 ACAA
1 ACAA
2245498 CAAAACAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 15 0.65
23 6 0.26
ACGTcount: A:0.65, C:0.16, G:0.06, T:0.12
Consensus pattern (23 bp):
ACAAAACACAAAGAACAAATTAA
Found at i:2246213 original size:14 final size:14
Alignment explanation
Indices: 2246194--2246255 Score: 56
Period size: 13 Copynumber: 4.5 Consensus size: 14
2246184 TAAATCTTAG
2246194 AATTTAATTTTTAT
1 AATTTAATTTTTAT
* *
2246208 AATTT-ATTTTGAG
1 AATTTAATTTTTAT
2246221 AATTTAATTTTT-T
1 AATTTAATTTTTAT
* * *
2246234 ATTTTTATATTTTAA
1 AATTTAAT-TTTTAT
2246249 AATTTAA
1 AATTTAA
2246256 GTTTAAAAGT
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
13 17 0.47
14 14 0.39
15 5 0.14
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (14 bp):
AATTTAATTTTTAT
Found at i:2246240 original size:27 final size:28
Alignment explanation
Indices: 2246192--2246255 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
2246182 TATAAATCTT
2246192 AGAATTTAATTTTTATAATTTAT-TTTG
1 AGAATTTAATTTTTATAATTTATATTTG
* *
2246219 AGAATTTAATTTTT-TATTTTTATATTTT
1 AGAATTTAATTTTTATA-ATTTATATTTG
*
2246247 AAAATTTAA
1 AGAATTTAA
2246256 GTTTAAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 2 0.06
27 19 0.59
28 11 0.34
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (28 bp):
AGAATTTAATTTTTATAATTTATATTTG
Found at i:2253834 original size:41 final size:41
Alignment explanation
Indices: 2253787--2253886 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 41
2253777 CGACCTCGAG
** *
2253787 TCGATGAGACACTGGGTGTCATTATTTTACTTCGGATA-GA
1 TCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAGGA
** *
2253827 TTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAGGA
1 -TCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAGGA
2253866 -CGATGAGACACTGGGTGTCAC
1 TCGATGAGACACTGGGTGTCAC
2253887 TTTATTGCTT
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
37 10 0.21
38 16 0.34
39 6 0.13
40 4 0.09
41 11 0.23
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (41 bp):
TCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAGGA
Found at i:2253879 original size:37 final size:37
Alignment explanation
Indices: 2253812--2253890 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
2253802 GTGTCATTAT
**
2253812 TTTACTTCGGATAGATTCGATGAGGTACTGGGTACCAC
1 TTTACTTCGGATAGA-TCGATGAGACACTGGGTACCAC
* **
2253850 TTTACTTCGGCTAGGA-CGATGAGACACTGGGTGTCAC
1 TTTACTTCGGATA-GATCGATGAGACACTGGGTACCAC
2253887 TTTA
1 TTTA
2253891 TTGCTTCGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
37 21 0.60
38 12 0.34
39 2 0.06
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.32
Consensus pattern (37 bp):
TTTACTTCGGATAGATCGATGAGACACTGGGTACCAC
Found at i:2256429 original size:18 final size:18
Alignment explanation
Indices: 2256397--2256448 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
2256387 TTTTTTCAAC
*
2256397 TTATT-TAATGAAAATTT
1 TTATTATAATGTAAATTT
2256414 TTATTATAATGTAAATTT
1 TTATTATAATGTAAATTT
2256432 TTATTATAATGTAAATT
1 TTATTATAATGTAAATT
2256449 CATATATTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
TTATTATAATGTAAATTT
Found at i:2260463 original size:1 final size:1
Alignment explanation
Indices: 2260457--2260487 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
2260447 TGGATGCTGG
2260457 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2260488 AAATTTAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2261125 original size:28 final size:29
Alignment explanation
Indices: 2261078--2261135 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
2261068 TAATTTTTGC
2261078 TATAACTTTATAAAATATAA-AAAAAATT
1 TATAACTTTATAAAATATAATAAAAAATT
*
2261106 TATAACTTGTATAAAA-ATAATAACAAATT
1 TATAACTT-TATAAAATATAATAAAAAATT
2261135 T
1 T
2261136 GGCCGCTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (29 bp):
TATAACTTTATAAAATATAATAAAAAATT
Found at i:2261654 original size:67 final size:66
Alignment explanation
Indices: 2261465--2261666 Score: 331
Period size: 67 Copynumber: 3.1 Consensus size: 66
2261455 AACATTTGCA
2261465 TTCATTTTAAAACCTTTTTTTAGATAATTACGTTTATTTTCATTAAATTA-AGAGTTA-TTTTTT
1 TTCATTTTAAAA-CTTTTTTTAGATAATTACGTTTATTTTCATTAAATTAGA-AGTTATTTTTTT
2261528 AAT
64 AAT
*
2261531 TTCATTTTAAAACTTTTTTTAGATAA--ACGTTTATTTTCATTAAATTAGGAGTTATTTTTTTAA
1 TTCATTTTAAAACTTTTTTTAGATAATTACGTTTATTTTCATTAAATTAGAAGTTATTTTTTTAA
2261594 T
66 T
*
2261595 TTCATTTTAAAACTTTTTTTAAAATAATTACGTTTATTTTCATTAAATTAGAAGTTATTTTTTTA
1 TTCATTTTAAAACTTTTTTT-AGATAATTACGTTTATTTTCATTAAATTAGAAGTTATTTTTTTA
2261660 AT
65 AT
2261662 TTCAT
1 TTCAT
2261667 GTATGATTTA
Statistics
Matches: 128, Mismatches: 3, Indels: 9
0.91 0.02 0.06
Matches are distributed among these distances:
63 26 0.20
64 29 0.23
65 19 0.15
66 12 0.09
67 42 0.33
ACGTcount: A:0.32, C:0.07, G:0.06, T:0.55
Consensus pattern (66 bp):
TTCATTTTAAAACTTTTTTTAGATAATTACGTTTATTTTCATTAAATTAGAAGTTATTTTTTTAA
T
Found at i:2263865 original size:31 final size:31
Alignment explanation
Indices: 2263830--2263892 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
2263820 TACAAAATGA
*
2263830 TCACTAAACTTTTCAAAAATTTTCATTTAAG
1 TCACTAAACTATTCAAAAATTTTCATTTAAG
** *
2263861 TCACTAAACTATTCAAATTTTTTTATTTAAG
1 TCACTAAACTATTCAAAAATTTTCATTTAAG
2263892 T
1 T
2263893 TATCAGACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (31 bp):
TCACTAAACTATTCAAAAATTTTCATTTAAG
Found at i:2266415 original size:43 final size:42
Alignment explanation
Indices: 2266346--2266428 Score: 98
Period size: 43 Copynumber: 2.0 Consensus size: 42
2266336 TTTATTTAAA
2266346 TTTATTATTTATATAAAATAATAAATATTATTATG-AAAATATT
1 TTTATTATTTATATAAAATAATAAATA-TA-TATGTAAAATATT
* * *
2266389 TTTATTTTTTATATAACAT-CTAAAATATATATGTAAAATA
1 TTTATTATTTATATAAAATAAT-AAATATATATGTAAAATA
2266429 AAAAAAATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
41 4 0.11
42 9 0.26
43 22 0.63
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (42 bp):
TTTATTATTTATATAAAATAATAAATATATATGTAAAATATT
Found at i:2270474 original size:18 final size:19
Alignment explanation
Indices: 2270444--2270480 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2270434 ATAATTTAAT
2270444 TTTTTAAATAAAAAATATA
1 TTTTTAAATAAAAAATATA
*
2270463 TTTTTAAA-AAAAATTATA
1 TTTTTAAATAAAAAATATA
2270481 AACATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTTTAAATAAAAAATATA
Found at i:2270527 original size:9 final size:9
Alignment explanation
Indices: 2270497--2270531 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
2270487 TTTAAAATCA
2270497 TAGAAAAAT
1 TAGAAAAAT
*
2270506 TATAAATAAT
1 TAGAAA-AAT
2270516 TAGAAAAAT
1 TAGAAAAAT
2270525 TAGAAAA
1 TAGAAAA
2270532 CTCTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (9 bp):
TAGAAAAAT
Found at i:2273374 original size:6 final size:6
Alignment explanation
Indices: 2273363--2273397 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2273353 TACTAGAGAA
* *
2273363 GGTGGC GGTGGC GGTGGC GGTGGT GGTGGA GGTGG
1 GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGG
2273398 TTGTGCCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.03, C:0.09, G:0.69, T:0.20
Consensus pattern (6 bp):
GGTGGC
Found at i:2274047 original size:19 final size:19
Alignment explanation
Indices: 2274023--2274061 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2274013 GTGAATATTA
2274023 AAATTTATTATTATACTTT
1 AAATTTATTATTATACTTT
* * *
2274042 AAATTTGTTGTTATATTTT
1 AAATTTATTATTATACTTT
2274061 A
1 A
2274062 TAAATAATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
AAATTTATTATTATACTTT
Found at i:2275322 original size:20 final size:20
Alignment explanation
Indices: 2275247--2275322 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 20
2275237 TTCAACTATA
*
2275247 ATTAAACTTAATCACTTTATT
1 ATTAAA-TTAATCACTTTAAT
*
2275268 ATTAAATGTAATCTAATATTTAAT
1 ATTAAAT-TAATC--A-CTTTAAT
*
2275292 ATTAAGA-TAATCACTTCAAT
1 ATTAA-ATTAATCACTTTAAT
2275312 ATTAAATTAAT
1 ATTAAATTAAT
2275323 AAAATACTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
19 1 0.02
20 15 0.33
21 12 0.27
23 6 0.13
24 10 0.22
25 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (20 bp):
ATTAAATTAATCACTTTAAT
Found at i:2279170 original size:17 final size:17
Alignment explanation
Indices: 2279150--2279196 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
2279140 TTTTTATATA
2279150 TTTAGTTTTTATTTTCT
1 TTTAGTTTTTATTTTCT
2279167 TTTA-TATTTTAATTTTCT
1 TTTAGT-TTTT-ATTTTCT
*
2279185 TCTAGTTTTTAT
1 TTTAGTTTTTAT
2279197 CTATCTTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 1 0.04
17 10 0.38
18 14 0.54
19 1 0.04
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.72
Consensus pattern (17 bp):
TTTAGTTTTTATTTTCT
Found at i:2281271 original size:48 final size:48
Alignment explanation
Indices: 2281216--2281310 Score: 190
Period size: 48 Copynumber: 2.0 Consensus size: 48
2281206 CATGCGAGAG
2281216 GTTCTTGATAAAAGAAGCAGCATTGATCTAATAAACAATTATTCTTTT
1 GTTCTTGATAAAAGAAGCAGCATTGATCTAATAAACAATTATTCTTTT
2281264 GTTCTTGATAAAAGAAGCAGCATTGATCTAATAAACAATTATTCTTT
1 GTTCTTGATAAAAGAAGCAGCATTGATCTAATAAACAATTATTCTTT
2281311 CTTTTCCGGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (48 bp):
GTTCTTGATAAAAGAAGCAGCATTGATCTAATAAACAATTATTCTTTT
Found at i:2281779 original size:29 final size:28
Alignment explanation
Indices: 2281710--2281777 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 28
2281700 TTTTCACAAA
2281710 TTTAAAATTTAATTCTTCTACTTTTATT
1 TTTAAAATTTAATTCTTCTACTTTTATT
**
2281738 TCAAGAAATTTAATTCTTCTACTTTTTATAT
1 TTTA-AAATTTAATTCTTCTAC-TTTTAT-T
2281769 TTTAAAATT
1 TTTAAAATT
2281778 AAAGTCCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 2 0.06
29 17 0.52
30 11 0.33
31 3 0.09
ACGTcount: A:0.32, C:0.10, G:0.01, T:0.56
Consensus pattern (28 bp):
TTTAAAATTTAATTCTTCTACTTTTATT
Found at i:2303405 original size:22 final size:23
Alignment explanation
Indices: 2303356--2303405 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
2303346 TAATATTTAA
*
2303356 TAATTTTATCACTTTAGTCTCTT
1 TAATTTTATCACTTTAGACTCTT
2303379 T--TTTTAATCACTTT-GACT-TT
1 TAATTTT-ATCACTTTAGACTCTT
2303399 TAATTTT
1 TAATTTT
2303406 CAAAATTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
20 3 0.13
21 7 0.30
22 12 0.52
23 1 0.04
ACGTcount: A:0.22, C:0.14, G:0.04, T:0.60
Consensus pattern (23 bp):
TAATTTTATCACTTTAGACTCTT
Found at i:2309245 original size:31 final size:31
Alignment explanation
Indices: 2309210--2309275 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
2309200 ATAAAAAGGA
2309210 TAAATTTATTATTATACCAATTAAAATTATG
1 TAAATTTATTATTATACCAATTAAAATTATG
*
2309241 TAAATTTATTATTATATCAATTAAAATTATG
1 TAAATTTATTATTATACCAATTAAAATTATG
2309272 TAAA
1 TAAA
2309276 ACTAAGGTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (31 bp):
TAAATTTATTATTATACCAATTAAAATTATG
Found at i:2309262 original size:16 final size:16
Alignment explanation
Indices: 2309212--2309262 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
2309202 AAAAAGGATA
*
2309212 AATTTATTATTATACC
1 AATTTATTATTATATC
** * *
2309228 AA-TTAAAATTATGTA
1 AATTTATTATTATATC
2309243 AATTTATTATTATATC
1 AATTTATTATTATATC
2309259 AATT
1 AATT
2309263 AAAATTATGT
Statistics
Matches: 25, Mismatches: 9, Indels: 2
0.69 0.25 0.06
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (16 bp):
AATTTATTATTATATC
Found at i:2312988 original size:20 final size:20
Alignment explanation
Indices: 2312944--2312989 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2312934 TAATAGGTAA
* * *
2312944 TAAAATATTATTTTATTTAT
1 TAAATTATTATTTTAATAAT
*
2312964 AAAATTATTATTTTAATAAT
1 TAAATTATTATTTTAATAAT
2312984 TAAATT
1 TAAATT
2312990 CAATGTGATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAAATTATTATTTTAATAAT
Found at i:2325880 original size:19 final size:19
Alignment explanation
Indices: 2325856--2325892 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2325846 TTGTGTTTAT
2325856 AATTTGATTAATGTGTTTC
1 AATTTGATTAATGTGTTTC
2325875 AATTTGATTAATGTGTTT
1 AATTTGATTAATGTGTTT
2325893 TAAATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.03, G:0.16, T:0.54
Consensus pattern (19 bp):
AATTTGATTAATGTGTTTC
Found at i:2329623 original size:36 final size:37
Alignment explanation
Indices: 2329554--2329636 Score: 141
Period size: 36 Copynumber: 2.3 Consensus size: 37
2329544 AAAGAAGAAA
2329554 GAGAAAAATTCAAGTTTCATGCATAAGATTATAAACT
1 GAGAAAAATTCAAGTTTCATGCATAAGATTATAAACT
2329591 GAGAAAAATTCAAGTTTCATG-ATAAGATTATAAACT
1 GAGAAAAATTCAAGTTTCATGCATAAGATTATAAACT
* *
2329627 TAGATAAATT
1 GAGAAAAATT
2329637 TGTCGTCATA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
36 23 0.52
37 21 0.48
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.31
Consensus pattern (37 bp):
GAGAAAAATTCAAGTTTCATGCATAAGATTATAAACT
Found at i:2346004 original size:6 final size:6
Alignment explanation
Indices: 2345989--2346018 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2345979 TTCCTTTGCT
2345989 TTTTTA -TTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T
2346019 CTGCTTGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:2367074 original size:42 final size:42
Alignment explanation
Indices: 2367015--2367098 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
2367005 CAAATATTTT
* *
2367015 TAAACTCAAATATAATTTCATTCTTCAAA-AATACTCATAAAC
1 TAAACTCAAATATAATTTCATTCCT-AAATAACACTCATAAAC
* *
2367057 TAAACTTAAATATAATTTTATTCCTAAATAACACTCATAAAC
1 TAAACTCAAATATAATTTCATTCCTAAATAACACTCATAAAC
2367099 AACTCCTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 3 0.08
42 34 0.92
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.35
Consensus pattern (42 bp):
TAAACTCAAATATAATTTCATTCCTAAATAACACTCATAAAC
Found at i:2370769 original size:28 final size:27
Alignment explanation
Indices: 2370699--2370779 Score: 103
Period size: 28 Copynumber: 3.0 Consensus size: 27
2370689 GTTAGAGAAT
* *
2370699 TTTTTTTTAAATCTCTTAAAAATTAATA
1 TTTTTTTTAACTCT-TTAAAAATTAAAA
2370727 TTTTTTTT-ACT-TTTAAAAATTAAAA
1 TTTTTTTTAACTCTTTAAAAATTAAAA
*
2370752 TTTTTTTTGAACTCTTTAAAAACTAAAA
1 TTTTTTTT-AACTCTTTAAAAATTAAAA
2370780 AATAATATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 20 0.43
26 1 0.02
27 5 0.11
28 21 0.45
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (27 bp):
TTTTTTTTAACTCTTTAAAAATTAAAA
Found at i:2375763 original size:38 final size:38
Alignment explanation
Indices: 2375709--2375789 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 38
2375699 CCTAGTACTG
2375709 TTCTTTTCTACAAAAAAAAAAAATAGAATAATTGATTA
1 TTCTTTTCTACAAAAAAAAAAAATAGAATAATTGATTA
* *
2375747 TTCTTTTCTACCAAAAAAAGAAATAGAATAATTGATTA
1 TTCTTTTCTACAAAAAAAAAAAATAGAATAATTGATTA
2375785 TTCTT
1 TTCTT
2375790 AAAGAATCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (38 bp):
TTCTTTTCTACAAAAAAAAAAAATAGAATAATTGATTA
Found at i:2385937 original size:31 final size:31
Alignment explanation
Indices: 2385902--2385960 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2385892 CCAACTTCTA
2385902 AAAAAGTGTCAAGGTTAGA-TACCAAATTAGG
1 AAAAAGTGTCAA-GTTAGAGTACCAAATTAGG
*
2385933 AAAAAGTGTCAAGTTTGAGTACCAAATT
1 AAAAAGTGTCAAGTTAGAGTACCAAATT
2385961 GCACCAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.25
Consensus pattern (31 bp):
AAAAAGTGTCAAGTTAGAGTACCAAATTAGG
Found at i:2386012 original size:91 final size:90
Alignment explanation
Indices: 2385831--2386019 Score: 227
Period size: 90 Copynumber: 2.1 Consensus size: 90
2385821 AAAGATTAAG
* **
2385831 TACCAAATTAGAAAAAAGAGTCAAGTTCATGTACCAAATTGGACCCCAAAAAATTTAAGTACCAA
1 TACCAAATTAGAAAAAAGAGTCAAGTTCATGTACCAAATTGCACCAAAAAAAATTTAAGTACCAA
* ** * *
2385896 CTTCTAAAAAAGTGTCAAGGTTAGA
66 ATTAGAAAAAAGTATCAAAGTTAGA
* * *
2385921 TACCAAATTAGGAAAAAGTGTCAAGTTTGA-GTACCAAATTGCACCAAAAAAAAGTTTAAGTACC
1 TACCAAATTAGAAAAAAGAGTCAAG-TTCATGTACCAAATTGCACCAAAAAAAA-TTTAAGTACC
* * *
2385985 AAATTAGGAAAAATTATCAAATTTAGA
64 AAATTAGAAAAAAGTATCAAAGTTAGA
2386012 TACCAAAT
1 TACCAAAT
2386020 GTTATAATTA
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
90 43 0.52
91 40 0.48
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (90 bp):
TACCAAATTAGAAAAAAGAGTCAAGTTCATGTACCAAATTGCACCAAAAAAAATTTAAGTACCAA
ATTAGAAAAAAGTATCAAAGTTAGA
Found at i:2386018 original size:31 final size:31
Alignment explanation
Indices: 2385916--2386019 Score: 80
Period size: 31 Copynumber: 3.5 Consensus size: 31
2385906 AGTGTCAAGG
* *
2385916 TTAGA-TACCAAATTAGGAAAAAGTGTCAAGT
1 TTAGAGTACCAAATTAGGAAAAA-TATCAAAT
*
2385947 TT-GAGTACCAAATT-GCACCAAAA-A--AAAGT
1 TTAGAGTACCAAATTAGGA--AAAATATCAAA-T
2385976 TTA-AGTACCAAATTAGGAAAAATTATCAAAT
1 TTAGAGTACCAAATTAGGAAAAA-TATCAAAT
2386007 TTAGA-TACCAAAT
1 TTAGAGTACCAAAT
2386020 GTTATAATTA
Statistics
Matches: 58, Mismatches: 4, Indels: 22
0.69 0.05 0.26
Matches are distributed among these distances:
28 6 0.10
29 14 0.24
30 7 0.12
31 23 0.40
32 8 0.14
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.26
Consensus pattern (31 bp):
TTAGAGTACCAAATTAGGAAAAATATCAAAT
Done.