Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 6 of 230
Found at i:1779072 original size:29 final size:30
Alignment explanation
Indices: 1779028--1779086 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1779018 AATTTTAAAA
1779028 TTAAAAAAAATT-AAAAAAGTATTTTAAAA
1 TTAAAAAAAATTAAAAAAAGTATTTTAAAA
1779057 TT-AAAAAAATTAAAAAAAAGTATTTTAAAA
1 TTAAAAAAAATT-AAAAAAAGTATTTTAAAA
1779087 GTATTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.32
29 2 0.07
30 17 0.61
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (30 bp):
TTAAAAAAAATTAAAAAAAGTATTTTAAAA
Found at i:1779086 original size:11 final size:11
Alignment explanation
Indices: 1779072--1779097 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1779062 AAAATTAAAA
1779072 AAAAGTATTTT
1 AAAAGTATTTT
1779083 AAAAGTATTTT
1 AAAAGTATTTT
1779094 AAAA
1 AAAA
1779098 TTAAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:1779811 original size:29 final size:29
Alignment explanation
Indices: 1779737--1779812 Score: 71
Period size: 31 Copynumber: 2.5 Consensus size: 29
1779727 TGATTGAATA
*
1779737 CAAATTAAAGTTTCATGTATATATTTAAAC
1 CAAATTAAAG-TTCATGTATATAATTAAAC
* * * **
1779767 CACGATCAAAATTTCATGTATATAATTGCAC
1 CA-AAT-TAAAGTTCATGTATATAATTAAAC
1779798 CAAATTAAAGTTCAT
1 CAAATTAAAGTTCAT
1779813 ATGTGAAATT
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
29 8 0.23
30 4 0.11
31 20 0.57
32 3 0.09
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (29 bp):
CAAATTAAAGTTCATGTATATAATTAAAC
Found at i:1781489 original size:50 final size:50
Alignment explanation
Indices: 1781378--1781505 Score: 129
Period size: 50 Copynumber: 2.6 Consensus size: 50
1781368 ATGCATGTAT
* * * * * *
1781378 GCTCATACGAGCTGTA-AACGGGAAGCTCTTTCGAGCCACATAATGGGAA
1 GCTCATAAGAGCTGTATATCGGGAAGCTCCTGCGAACCAAATAATGGGAA
*
1781427 GCTCATATGAGCTGTATATCGGGAAGCTCCTGCGAACCAAAT-ATCGGGAA
1 GCTCATAAGAGCTGTATATCGGGAAGCTCCTGCGAACCAAATAAT-GGGAA
*
1781477 GCTCA-AGAGAGCTGT-TAATCAGGAAGCTC
1 GCTCATA-AGAGCTGTAT-ATCGGGAAGCTC
1781506 ATGAGAGTCA
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
49 19 0.28
50 48 0.72
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (50 bp):
GCTCATAAGAGCTGTATATCGGGAAGCTCCTGCGAACCAAATAATGGGAA
Found at i:1785039 original size:19 final size:18
Alignment explanation
Indices: 1785017--1785077 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
1785007 GAAATAAAAT
1785017 TTAAATATTAAATAATTTA
1 TTAAATATT-AATAATTTA
*
1785036 TTAAA-AATAATAAATTATA
1 TTAAATATTAAT-AATT-TA
1785055 TTAATTATATTAATAATTTA
1 TTAA--ATATTAATAATTTA
1785075 TTA
1 TTA
1785078 TATGATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 3 0.09
18 6 0.17
19 11 0.31
20 5 0.14
21 5 0.14
22 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAATATTAATAATTTA
Found at i:1785172 original size:10 final size:9
Alignment explanation
Indices: 1785143--1785168 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1785133 ATTTTATATT
1785143 AATATTTTA
1 AATATTTTA
1785152 AATATTTTA
1 AATATTTTA
1785161 AATATTTT
1 AATATTTT
1785169 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTTTA
Found at i:1795824 original size:21 final size:23
Alignment explanation
Indices: 1795798--1795845 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
1795788 TTTTAAGAAG
*
1795798 ATTATAAA-ATTATA-AAAAAAT
1 ATTATAAATAGTATATAAAAAAT
1795819 ATTATAAATAGTATATAAAAAAT
1 ATTATAAATAGTATATAAAAAAT
1795842 -TTAT
1 ATTAT
1795846 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 9 0.38
23 7 0.29
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
ATTATAAATAGTATATAAAAAAT
Found at i:1796429 original size:24 final size:23
Alignment explanation
Indices: 1796381--1796433 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
1796371 TATGAGAGTG
* *
1796381 AATACTCATTTTTATATAATTAA
1 AATATTCATTTTTATATAATAAA
1796404 AATATTCATATTTTATATTAA-AAA
1 AATATTCAT-TTTTATA-TAATAAA
1796428 AATATT
1 AATATT
1796434 ATTAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 8 0.31
24 15 0.58
25 3 0.12
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (23 bp):
AATATTCATTTTTATATAATAAA
Found at i:1797306 original size:37 final size:37
Alignment explanation
Indices: 1797242--1797335 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
1797232 ATTTTTGGAG
* * * * *
1797242 AGAATTGTTACTGTTGATCTTCGTCTTTTTTTTACAA
1 AGAATTGTTACTATTCATCTCCATCTTTTCTTTACAA
* *
1797279 AGAATTGTTACTATTCATCTCCATCTTTTCTTTGCAG
1 AGAATTGTTACTATTCATCTCCATCTTTTCTTTACAA
**
1797316 AGAATCATTACTATTCATCT
1 AGAATTGTTACTATTCATCT
1797336 ATGCTTTTGT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (37 bp):
AGAATTGTTACTATTCATCTCCATCTTTTCTTTACAA
Found at i:1798075 original size:37 final size:37
Alignment explanation
Indices: 1798025--1798114 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
1798015 CTTGGAAGAT
* * * * **
1798025 AAAAGACGGAGATGAACAATAATGATTCTTTGCAAAG
1 AAAACACGAAGATGAACAACAACGATTCCCTGCAAAG
* *
1798062 AAAACACGAAGATGAATAGCAACGATTCCCTGCAAAG
1 AAAACACGAAGATGAACAACAACGATTCCCTGCAAAG
*
1798099 AAAATACGAAGATGAA
1 AAAACACGAAGATGAA
1798115 TAGTAATCAT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.49, C:0.14, G:0.20, T:0.17
Consensus pattern (37 bp):
AAAACACGAAGATGAACAACAACGATTCCCTGCAAAG
Found at i:1798527 original size:17 final size:17
Alignment explanation
Indices: 1798505--1798537 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1798495 TAATATTCTA
1798505 TTTT-AATATTATAATAT
1 TTTTAAATATTA-AATAT
1798522 TTTTAAATATTAAATA
1 TTTTAAATATTAAATA
1798538 AAAAAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTAAATATTAAATAT
Found at i:1798532 original size:18 final size:21
Alignment explanation
Indices: 1798488--1798537 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
1798478 AAGAATATTG
*
1798488 AATATTATAATATTCTATTTT
1 AATATTATAATATTCTATTTA
1798509 AATATTATAATA-T-T-TTTA
1 AATATTATAATATTCTATTTA
1798527 AATATTA-AATA
1 AATATTATAATA
1798538 AAAAAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 4 0.14
18 10 0.36
19 1 0.04
20 1 0.04
21 12 0.43
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
AATATTATAATATTCTATTTA
Found at i:1806468 original size:28 final size:28
Alignment explanation
Indices: 1806428--1806481 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
1806418 GTGTGATTCA
1806428 ATTTTTTTACTGTTTTTTTACAATGACG
1 ATTTTTTTACTGTTTTTTTACAATGACG
1806456 ATTTTTTTACTGTTTTTTTACAATGA
1 ATTTTTTTACTGTTTTTTTACAATGA
1806482 GAGTTAGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.59
Consensus pattern (28 bp):
ATTTTTTTACTGTTTTTTTACAATGACG
Found at i:1810398 original size:12 final size:12
Alignment explanation
Indices: 1810381--1810414 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1810371 GAAGGGTAGA
*
1810381 GAGAAAGAAATC
1 GAGAAAAAAATC
*
1810393 GAGAAAAAAATT
1 GAGAAAAAAATC
1810405 GAGAAAAAAA
1 GAGAAAAAAA
1810415 AAAAGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.03, G:0.21, T:0.09
Consensus pattern (12 bp):
GAGAAAAAAATC
Found at i:1810710 original size:33 final size:33
Alignment explanation
Indices: 1810669--1810739 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1810659 CAGTGAATTA
* *
1810669 TTTTTTCACTATCACTACTATCAAGTTAAAAGT
1 TTTTTTCACTATCACTACAATCAAGTTAAAAAT
*
1810702 TTTTTTCACTATTACTACAATCAAGTTAAAAAT
1 TTTTTTCACTATCACTACAATCAAGTTAAAAAT
1810735 TTTTT
1 TTTTT
1810740 AATAGGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.46
Consensus pattern (33 bp):
TTTTTTCACTATCACTACAATCAAGTTAAAAAT
Found at i:1810754 original size:20 final size:21
Alignment explanation
Indices: 1810729--1810778 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1810719 CAATCAAGTT
1810729 AAAAATTTTTTAATAGG-TGA
1 AAAAATTTTTTAATAGGTTGA
**
1810749 AAAAATAATTTAATAGGTTGA
1 AAAAATTTTTTAATAGGTTGA
*
1810770 AAATATTTT
1 AAAAATTTT
1810779 AACTGGTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (21 bp):
AAAAATTTTTTAATAGGTTGA
Found at i:1821251 original size:11 final size:11
Alignment explanation
Indices: 1821235--1821265 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1821225 AAGTATGGGT
1821235 AGGTATGGGAA
1 AGGTATGGGAA
*
1821246 AGGTATGGGCA
1 AGGTATGGGAA
1821257 AGGTATGGG
1 AGGTATGGG
1821266 GTATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:1825336 original size:18 final size:18
Alignment explanation
Indices: 1825313--1825369 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
1825303 CCCAACTACT
**
1825313 GTATACGTGAGCAGTACC
1 GTATACGTGAATAGTACC
*
1825331 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
1825349 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
1825367 GTA
1 GTA
1825370 AACGGTCGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:1825931 original size:11 final size:11
Alignment explanation
Indices: 1825915--1825945 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1825905 AAATATGGGT
1825915 AGGTATGGGAA
1 AGGTATGGGAA
*
1825926 AGGTATGGGCA
1 AGGTATGGGAA
1825937 AGGTATGGG
1 AGGTATGGG
1825946 GTATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:1832920 original size:40 final size:40
Alignment explanation
Indices: 1832865--1832941 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
1832855 GACTATAGGG
*
1832865 TTTAACTAAGAGAAGAAACCTGGTTAAGTGGTGAACACAA
1 TTTAACTAAGAGAAGAAACCTGGTTAAGTGGGGAACACAA
*
1832905 TTTAACTAAGAGAAGAAATCTGGTTAAGTGGGGAACA
1 TTTAACTAAGAGAAGAAACCTGGTTAAGTGGGGAACA
1832942 TGTTGCCAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.23
Consensus pattern (40 bp):
TTTAACTAAGAGAAGAAACCTGGTTAAGTGGGGAACACAA
Found at i:1835775 original size:19 final size:21
Alignment explanation
Indices: 1835736--1835775 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1835726 TTGATGAAAC
1835736 AAGAAGTTTAAAAACTCAATT
1 AAGAAGTTTAAAAACTCAATT
*
1835757 AAGAA-TTTAGAAA-TCAATT
1 AAGAAGTTTAAAAACTCAATT
1835776 TGAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
AAGAAGTTTAAAAACTCAATT
Found at i:1839977 original size:60 final size:60
Alignment explanation
Indices: 1839907--1840025 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 60
1839897 ATGAACTTAG
* * *
1839907 CTTTAAGGTTCAAATTGGTA-TCTAATATTTTTTTTGGTTCAATTA-AGTACTTAAACTTGC
1 CTTTAAGGTTCAAATTGGTACT-TAAAATTTATTTTGGTCCAATTAGA-TACTTAAACTTGC
* * *
1839967 CTTTAGGGTTCAATTTGGTACTTAAAATTTATTTTGGTCCAATTAGATACTTGAACTTG
1 CTTTAAGGTTCAAATTGGTACTTAAAATTTATTTTGGTCCAATTAGATACTTAAACTTG
1840026 GCTTCTTAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
60 49 0.96
61 2 0.04
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (60 bp):
CTTTAAGGTTCAAATTGGTACTTAAAATTTATTTTGGTCCAATTAGATACTTAAACTTGC
Found at i:1848656 original size:15 final size:15
Alignment explanation
Indices: 1848636--1848679 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
1848626 ACCAAATTAC
1848636 AAAAAAATTAAATCT
1 AAAAAAATTAAATCT
1848651 AAAAAAA-TAGAATCT
1 AAAAAAATTA-AATCT
1848666 AAAAAAATTGAAAT
1 AAAAAAATT-AAAT
1848680 AAAAGCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 2 0.08
15 19 0.73
16 4 0.15
17 1 0.04
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (15 bp):
AAAAAAATTAAATCT
Found at i:1849895 original size:16 final size:15
Alignment explanation
Indices: 1849856--1849898 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
1849846 AAAGTGCAGG
1849856 GATTAAAATATTAAC
1 GATTAAAATATTAAC
** *
1849871 TTTTCAAATATATAAC
1 GATTAAAATAT-TAAC
1849887 GATTAAAATATT
1 GATTAAAATATT
1849899 CCTTTTAATA
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (15 bp):
GATTAAAATATTAAC
Found at i:1850761 original size:16 final size:16
Alignment explanation
Indices: 1850740--1850773 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1850730 TGCATACCGT
* *
1850740 TTATTTTTATTTTTTA
1 TTATTTTCATTTTCTA
1850756 TTATTTTCATTTTCTA
1 TTATTTTCATTTTCTA
1850772 TT
1 TT
1850774 CCTTCCATTA
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:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCATTTTCTA
Found at i:1851638 original size:27 final size:27
Alignment explanation
Indices: 1851582--1851872 Score: 327
Period size: 27 Copynumber: 10.8 Consensus size: 27
1851572 GACCCCAAAC
*
1851582 TGTTATAAAATAACTGTTATG-ACCTCA
1 TGTTATAAAATAACTGTTATGCCCCT-A
** *
1851609 TGTGGTAAAATAACTATTATGCCCCTA
1 TGTTATAAAATAACTGTTATGCCCCTA
*
1851636 TGTTATAAAATAACGGTTATGCCCCTA
1 TGTTATAAAATAACTGTTATGCCCCTA
* *
1851663 TGTTATAAAATTACAGTTATGCCCCTA
1 TGTTATAAAATAACTGTTATGCCCCTA
*
1851690 TGTTATAAAATAACTGTTATGCCCTTA
1 TGTTATAAAATAACTGTTATGCCCCTA
*
1851717 TGTTATAAAATGACTGTTATG-CCCTCA
1 TGTTATAAAATAACTGTTATGCCCCT-A
* ** ** *
1851744 CGTGGTAAAATGGCTATTATGCCCCTA
1 TGTTATAAAATAACTGTTATGCCCCTA
* * *
1851771 TGTTATAAAATGACGGCTATGCCCCTA
1 TGTTATAAAATAACTGTTATGCCCCTA
* *
1851798 TGTTATAAAATGACTGTTATGCCCTTA
1 TGTTATAAAATAACTGTTATGCCCCTA
*
1851825 TGTTATAAAATAACTGTTATGCCCTTA
1 TGTTATAAAATAACTGTTATGCCCCTA
** *
1851852 TGTGGTAAAATGACTG-TATGC
1 TGTTATAAAATAACTGTTATGC
1851873 TTAATGCTAT
Statistics
Matches: 227, Mismatches: 34, Indels: 7
0.85 0.13 0.03
Matches are distributed among these distances:
26 8 0.04
27 212 0.93
28 7 0.03
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (27 bp):
TGTTATAAAATAACTGTTATGCCCCTA
Found at i:1852190 original size:34 final size:32
Alignment explanation
Indices: 1852152--1852214 Score: 108
Period size: 34 Copynumber: 1.9 Consensus size: 32
1852142 TTACTGTCAC
1852152 TGTAATGGGCTAAGGCCCACACTGATACTGATAT
1 TGTAATGGGCTAAGGCCCA-ACTGA-ACTGATAT
1852186 TGTAATGGGCTAAGGCCCAACTGAACTGA
1 TGTAATGGGCTAAGGCCCAACTGAACTGA
1852215 ACTGTTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 5 0.17
33 5 0.17
34 19 0.66
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (32 bp):
TGTAATGGGCTAAGGCCCAACTGAACTGATAT
Found at i:1855970 original size:39 final size:38
Alignment explanation
Indices: 1855918--1856063 Score: 177
Period size: 39 Copynumber: 3.7 Consensus size: 38
1855908 ATATATTTAT
1855918 TTTTTTAACTTTTTTTAATTTTAAAATATTTTTAAAATA
1 TTTTTTAA-TTTTTTTAATTTTAAAATATTTTTAAAATA
*
1855957 TTTTTTTA-TTTTTTAATTTTAAAATATTTTTAAAATA
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATA
* **
1855994 CTTTTTAAATTTTTTTAATTTTAAAGCATTTTTAAAATA
1 -TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATA
**
1856033 TTGTTAAAATATTTTTTTAATTTTTAAAATA
1 TT-TT-TTA-ATTTTTTTAA-TTTTAAAATA
1856064 AAATTTTGGT
Statistics
Matches: 93, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
37 29 0.31
38 8 0.09
39 36 0.39
40 2 0.02
41 10 0.11
42 8 0.09
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (38 bp):
TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATA
Found at i:1855975 original size:37 final size:38
Alignment explanation
Indices: 1855919--1856063 Score: 184
Period size: 37 Copynumber: 3.7 Consensus size: 38
1855909 TATATTTATT
*
1855919 TTTTTAACTTTTTTTAATTTTAAAATATTTTTAAAATA
1 TTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATA
**
1855957 TTTTTTTA-TTTTTTAATTTTAAAATATTTTTAAAATA
1 TTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATA
**
1855994 CTTTTTAAATTTTTTTAATTTTAAAGCATTTTTAAAATA
1 -TTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATA
*
1856033 TTGTTAAAATATTTTTTTAATTTTTAAAATA
1 TT-TT-TAA-ATTTTTTTAA-TTTTAAAATA
1856064 AAATTTTGGT
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
37 29 0.32
38 13 0.14
39 29 0.32
40 2 0.02
41 10 0.11
42 8 0.09
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (38 bp):
TTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATA
Found at i:1856000 original size:12 final size:11
Alignment explanation
Indices: 1855936--1856048 Score: 72
Period size: 11 Copynumber: 11.4 Consensus size: 11
1855926 CTTTTTTTAA
1855936 TTTTAAAATAT
1 TTTTAAAATAT
1855947 TTTTAAAATAT
1 TTTTAAAATAT
*
1855958 TTTT---TTAT
1 TTTTAAAATAT
*
1855966 TTTT----TAA
1 TTTTAAAATAT
1855973 TTTTAAAATAT
1 TTTTAAAATAT
1855984 TTTTAAAATACT
1 TTTTAAAATA-T
1855996 TTTT-AAAT-T
1 TTTTAAAATAT
*
1856005 TTTT----TAA
1 TTTTAAAATAT
**
1856012 TTTTAAAGCAT
1 TTTTAAAATAT
1856023 TTTTAAAATAT
1 TTTTAAAATAT
*
1856034 TGTTAAAATAT
1 TTTTAAAATAT
1856045 TTTT
1 TTTT
1856049 TTAATTTTTA
Statistics
Matches: 82, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
6 1 0.01
7 10 0.12
8 7 0.09
9 5 0.06
11 54 0.66
12 5 0.06
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:1862856 original size:111 final size:111
Alignment explanation
Indices: 1862720--1862940 Score: 361
Period size: 111 Copynumber: 2.0 Consensus size: 111
1862710 TAAATAATCG
* * *
1862720 AAAATTTTCTACAATCAAAGCGCATAAACCAAAAACTCACTTTCAGGAATTCGATACGTCGTGTC
1 AAAATTTTCTACAACCAAAACGCATAAACCAAAAACTCACTTTCAGGAATTCGATACGCCGTGTC
* * *
1862785 CTATTGTATTGGATGTGATGTGTCGTTTTCTTGAAATGAAGATTTT
66 CTAATGTATTGGATGTGACGTGTCGTTTTCTCGAAATGAAGATTTT
* * *
1862831 AAAATTTTCTACAACCAAAATGCATAAACCAAAAACTCACTTTCGGGAATTCGATATGCCGTGTC
1 AAAATTTTCTACAACCAAAACGCATAAACCAAAAACTCACTTTCAGGAATTCGATACGCCGTGTC
1862896 CTAATGTATTGGATGTGACGTGTCGTTTTCTCGAAATGAAGATTT
66 CTAATGTATTGGATGTGACGTGTCGTTTTCTCGAAATGAAGATTT
1862941 AAATAATAAG
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
111 101 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (111 bp):
AAAATTTTCTACAACCAAAACGCATAAACCAAAAACTCACTTTCAGGAATTCGATACGCCGTGTC
CTAATGTATTGGATGTGACGTGTCGTTTTCTCGAAATGAAGATTTT
Found at i:1874888 original size:44 final size:44
Alignment explanation
Indices: 1874704--1874875 Score: 254
Period size: 44 Copynumber: 3.9 Consensus size: 44
1874694 AATCACAAAA
* * *
1874704 CCTAGCTCCCTGACCAGCAGTGGAATAGGTTAAAGATCGTAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
* * *
1874748 CCTATCTCCCTGACCAGCAGAGGAATAGGTAGAAGATTGCAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
* * *
1874792 CCTAACTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTATGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
*
1874836 CCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATTGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGT
1874876 GGATCCTGTC
Statistics
Matches: 114, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 114 1.00
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.24
Consensus pattern (44 bp):
CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
Found at i:1875490 original size:22 final size:22
Alignment explanation
Indices: 1875448--1875491 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1875438 TACAGAAATA
* *
1875448 AAATAATAAAAATGAACAATTG
1 AAATAATAAAAAGGAAAAATTG
1875470 AAATAA-AAAAAGGATAAAATTG
1 AAATAATAAAAAGGA-AAAATTG
1875492 GAATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.66, C:0.02, G:0.11, T:0.20
Consensus pattern (22 bp):
AAATAATAAAAAGGAAAAATTG
Found at i:1882706 original size:77 final size:77
Alignment explanation
Indices: 1882579--1882731 Score: 270
Period size: 77 Copynumber: 2.0 Consensus size: 77
1882569 TAATAAAAGT
*
1882579 AAATCACTATCCTATACACATTTCAATCACATCATCTTTACGACTTATCATAATTAATAGATTAA
1 AAATCACTATCCTATACACATTTCAATCACATCATCTTTACGACTTATCATAATTAATAAATTAA
1882644 ACATTGAAATTC
66 ACATTGAAATTC
* * *
1882656 AAATCATTATCGTATACACATTTCAATCATATCATCTTTACGACTTATCATAATTAATAAATTAA
1 AAATCACTATCCTATACACATTTCAATCACATCATCTTTACGACTTATCATAATTAATAAATTAA
1882721 ACATTGAAATT
66 ACATTGAAATT
1882732 AAACTGTGAA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 72 1.00
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.37
Consensus pattern (77 bp):
AAATCACTATCCTATACACATTTCAATCACATCATCTTTACGACTTATCATAATTAATAAATTAA
ACATTGAAATTC
Found at i:1883212 original size:16 final size:17
Alignment explanation
Indices: 1883175--1883213 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1883165 AGTAAAAATT
1883175 TAATTTTATTATTTTAA
1 TAATTTTATTATTTTAA
*
1883192 T-ATTTTA-TATTTTTA
1 TAATTTTATTATTTTAA
1883207 TAATTTT
1 TAATTTT
1883214 TACTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 8 0.40
16 11 0.55
17 1 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TAATTTTATTATTTTAA
Found at i:1883220 original size:21 final size:22
Alignment explanation
Indices: 1883196--1883238 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1883186 TTTTAATATT
*
1883196 TTATATT-TTTATAATTTTTAC
1 TTATATTATTTAAAATTTTTAC
1883217 TTATATTAATTTAAAATTTTTA
1 TTATATT-ATTTAAAATTTTTA
1883239 TTAAATACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATATTATTTAAAATTTTTAC
Found at i:1890335 original size:12 final size:12
Alignment explanation
Indices: 1890318--1890342 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1890308 CAGAGGCTAT
1890318 TAACAATATTTA
1 TAACAATATTTA
1890330 TAACAATATTTA
1 TAACAATATTTA
1890342 T
1 T
1890343 GTTATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:1898613 original size:76 final size:76
Alignment explanation
Indices: 1898327--1898797 Score: 387
Period size: 76 Copynumber: 6.2 Consensus size: 76
1898317 TCATTTAAGA
* * * * * * * *** * **
1898327 TAACAGTTTACTTGTTTTAATATCGCGATTATCATCTTTACGATCCACTGATTTAATATCGTGAC
1 TAACAGTTTGCTTGATTTAATCTTGCGACTATCATTTTTATGATCTGTTGATTTAAGATCGCAAC
* * *
1898392 TTTCAATTTTT
66 CTTCAGTTTTC
* * * * * *
1898403 TAACAATTCGCTTGATTTAATCTCGTGACTGTCATTTTTATAATCTGTTGATTTAAGATCG-AGA
1 TAACAGTTTGCTTGATTTAATCTTGCGACTATCATTTTTATGATCTGTTGATTTAAGATCGCA-A
* *
1898467 CCATCGGTTTTC
65 CCTTCAGTTTTC
* * * * * *
1898479 TAACAGTTTGC-TGATTTAATATTGCAACTGTCATTTTTACGATCCGCTT-ATCTAAGATCGCAA
1 TAACAGTTTGCTTGATTTAATCTTGCGACTATCATTTTTATGATCTG-TTGATTTAAGATCGCAA
1898542 CCTTCAGTTTTC
65 CCTTCAGTTTTC
* * * **
1898554 TAACAGTTTGCTTGATTTAATCTTGTGACTATCATTTTTATGGTTTGTTGATTTAAGATCGTGAC
1 TAACAGTTTGCTTGATTTAATCTTGCGACTATCATTTTTATGATCTGTTGATTTAAGATCGCAAC
*
1898619 CTTCGGTTTTC
66 CTTCAGTTTTC
* * * * * * * *
1898630 TAACAATTTGCTTGATTTAATCTTGCGACTATCGTTTTTACGATCCGCTAATTTAATATCGCAGC
1 TAACAGTTTGCTTGATTTAATCTTGCGACTATCATTTTTATGATCTGTTGATTTAAGATCGCAAC
*
1898695 CTTCAATTTTC
66 CTTCAGTTTTC
* * * * * * * *
1898706 TAATAGTTTGCTTGATTTAATCTCGCAACTTTCATTTTTATG-GCTTGTTGATTTAATAGCACAA
1 TAACAGTTTGCTTGATTTAATCTTGCGACTATCATTTTTATGATC-TGTTGATTTAAGATCGCAA
1898770 CCTTC-GATTTTC
65 CCTTCAG-TTTTC
1898782 TAACAGTTTGC-TGATT
1 TAACAGTTTGCTTGATT
1898798 CACGATCACG
Statistics
Matches: 312, Mismatches: 76, Indels: 15
0.77 0.19 0.04
Matches are distributed among these distances:
75 68 0.22
76 244 0.78
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (76 bp):
TAACAGTTTGCTTGATTTAATCTTGCGACTATCATTTTTATGATCTGTTGATTTAAGATCGCAAC
CTTCAGTTTTC
Found at i:1898625 original size:151 final size:151
Alignment explanation
Indices: 1898327--1898797 Score: 530
Period size: 152 Copynumber: 3.1 Consensus size: 151
1898317 TCATTTAAGA
* * * * * * * * * * **
1898327 TAACAGTTTACTTGTTTTAATATCGCGATTATCATCTTTACGATCCACTGATTTAATATCGTGAC
1 TAACAGTTTGC-TGATTTAATATTGCAACTATCATTTTTACGATCCGCTAATCTAAGATCGCAAC
* * * * * ** *
1898392 TTTCAATTTTTTAACAATTCGCTTGATTTAATCTCGTGACTGTCATTTTTATAATCTGTTGATTT
65 CTTCAATTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTTTTATGGTTTGTTGATTT
*
1898457 AAGATCGAGACCATCGGTTTTC
130 AAGATCGAGACCTTCGGTTTTC
* *
1898479 TAACAGTTTGCTGATTTAATATTGCAACTGTCATTTTTACGATCCGCTTATCTAAGATCGCAACC
1 TAACAGTTTGCTGATTTAATATTGCAACTATCATTTTTACGATCCGCTAATCTAAGATCGCAACC
* *
1898544 TTCAGTTTTCTAACAGTTTGCTTGATTTAATCTTGTGACTATCATTTTTATGGTTTGTTGATTTA
66 TTCAATTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTTTTATGGTTTGTTGATTTA
*
1898609 AGATCGTGACCTTCGGTTTTC
131 AGATCGAGACCTTCGGTTTTC
* * * * * * *
1898630 TAACAATTTGCTTGATTTAATCTTGCGACTATCGTTTTTACGATCCGCTAATTTAATATCGCAGC
1 TAACAGTTTGC-TGATTTAATATTGCAACTATCATTTTTACGATCCGCTAATCTAAGATCGCAAC
* ** * *
1898695 CTTCAATTTTCTAATAGTTTGCTTGATTTAATCTCGCAACTTTCATTTTTATGGCTTGTTGATTT
65 CTTCAATTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTTTTATGGTTTGTTGATTT
* * * *
1898760 AATAGC-ACAACCTTCGATTTTC
130 AAGATCGA-GACCTTCGGTTTTC
1898782 TAACAGTTTGCTGATT
1 TAACAGTTTGCTGATT
1898798 CACGATCACG
Statistics
Matches: 270, Mismatches: 47, Indels: 5
0.84 0.15 0.02
Matches are distributed among these distances:
151 131 0.49
152 139 0.51
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (151 bp):
TAACAGTTTGCTGATTTAATATTGCAACTATCATTTTTACGATCCGCTAATCTAAGATCGCAACC
TTCAATTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTTTTATGGTTTGTTGATTTA
AGATCGAGACCTTCGGTTTTC
Found at i:1898727 original size:152 final size:151
Alignment explanation
Indices: 1898327--1898820 Score: 551
Period size: 151 Copynumber: 3.3 Consensus size: 151
1898317 TCATTTAAGA
* * * * * * * *
1898327 TAACAGTTTACTTGTTTTAATATCGCGATTATCATCTTTACGATCCACTGATTTAATATCG-TGA
1 TAACAGTTTGC-TGATTTAATATTGCGACTATCATTTTTACGATCCGCTAATTTAATATCGCAG-
* * * * * ** *
1898391 CTTTCAATTTTTTAACAATTCGCTTGATTTAATCTCGTGACTGTCATTTTTATAATCTGTTGATT
64 CCTTCAATTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTTTTATGGTTTGTTGATT
*
1898456 TAAGATCGAGACCATCGGTTTTC
129 TAAGATCGAGACCTTCGGTTTTC
* * * * * *
1898479 TAACAGTTTGCTGATTTAATATTGCAACTGTCATTTTTACGATCCGCTTATCTAAGATCGCAACC
1 TAACAGTTTGCTGATTTAATATTGCGACTATCATTTTTACGATCCGCTAATTTAATATCGCAGCC
* *
1898544 TTCAGTTTTCTAACAGTTTGCTTGATTTAATCTTGTGACTATCATTTTTATGGTTTGTTGATTTA
66 TTCAATTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTTTTATGGTTTGTTGATTTA
*
1898609 AGATCGTGACCTTCGGTTTTC
131 AGATCGAGACCTTCGGTTTTC
* * *
1898630 TAACAATTTGCTTGATTTAATCTTGCGACTATCGTTTTTACGATCCGCTAATTTAATATCGCAGC
1 TAACAGTTTGC-TGATTTAATATTGCGACTATCATTTTTACGATCCGCTAATTTAATATCGCAGC
* ** * *
1898695 CTTCAATTTTCTAATAGTTTGCTTGATTTAATCTCGCAACTTTCATTTTTATGGCTTGTTGATTT
65 CTTCAATTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTTTTATGGTTTGTTGATTT
* * * *
1898760 AATAGC-ACAACCTTCGATTTTC
130 AAGATCGA-GACCTTCGGTTTTC
* ** **
1898782 TAACAGTTTGCTGATTCACGATCACGACTATCATTTTTA
1 TAACAGTTTGCTGATTTAATATTGCGACTATCATTTTTA
1898821 AAGCTCGCTA
Statistics
Matches: 285, Mismatches: 54, Indels: 7
0.82 0.16 0.02
Matches are distributed among these distances:
151 146 0.51
152 139 0.49
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (151 bp):
TAACAGTTTGCTGATTTAATATTGCGACTATCATTTTTACGATCCGCTAATTTAATATCGCAGCC
TTCAATTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTTTTATGGTTTGTTGATTTA
AGATCGAGACCTTCGGTTTTC
Found at i:1899206 original size:18 final size:19
Alignment explanation
Indices: 1899180--1899217 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1899170 CTCTCTTTGT
*
1899180 TTTTGAAATTTTAAA-ATA
1 TTTTAAAATTTTAAATATA
1899198 TTTTAAAATTTTAAATATA
1 TTTTAAAATTTTAAATATA
1899217 T
1 T
1899218 ATATATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTTAAAATTTTAAATATA
Found at i:1901646 original size:13 final size:13
Alignment explanation
Indices: 1901612--1901653 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1901602 AAAGTCAAAT
*
1901612 TAAATAA-AAAAT
1 TAAATAATAAAAA
1901624 TAAAATTAATAAAAA
1 T-AAA-TAATAAAAA
1901639 TAAATAATAAAAA
1 TAAATAATAAAAA
1901652 TA
1 TA
1901654 TATTGATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 1 0.04
13 14 0.54
14 6 0.23
15 5 0.19
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAATAATAAAAA
Found at i:1905554 original size:19 final size:20
Alignment explanation
Indices: 1905530--1905568 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
1905520 AAATTGGTTA
1905530 GTGTAATTTA-ATTTTTTTC
1 GTGTAATTTAGATTTTTTTC
1905549 GTGTAATTTAGTATTTTTTT
1 GTGTAATTTAG-ATTTTTTT
1905569 ATAACTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.21, C:0.03, G:0.13, T:0.64
Consensus pattern (20 bp):
GTGTAATTTAGATTTTTTTC
Found at i:1906505 original size:12 final size:12
Alignment explanation
Indices: 1906488--1906518 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1906478 TATGTATCCA
1906488 TCCGAGTTCGAG
1 TCCGAGTTCGAG
1906500 TCCGAGTTCGAG
1 TCCGAGTTCGAG
1906512 TCCGAGT
1 TCCGAGT
1906519 CTAAGTTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.32, T:0.26
Consensus pattern (12 bp):
TCCGAGTTCGAG
Found at i:1907389 original size:15 final size:15
Alignment explanation
Indices: 1907334--1907390 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
1907324 TTTATACTAC
*
1907334 AAAATATTTAGTATT
1 AAAATATTTATTATT
* *
1907349 AATATATTTATAATTGT
1 AAAATATTTATTA-T-T
1907366 AATAAATATTTATTATT
1 -A-AAATATTTATTATT
1907383 AAAATATT
1 AAAATATT
1907391 AATATTGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.30
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:1907590 original size:10 final size:10
Alignment explanation
Indices: 1907577--1907608 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
1907567 TTTAAAATAT
1907577 AATATTTTTA
1 AATATTTTTA
1907587 AATATTTTTA
1 AATATTTTTA
1907597 AATATTTTTA
1 AATATTTTTA
1907607 AA
1 AA
1907609 AATAAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
AATATTTTTA
Found at i:1908669 original size:54 final size:54
Alignment explanation
Indices: 1908603--1908708 Score: 149
Period size: 54 Copynumber: 2.0 Consensus size: 54
1908593 TCGTGTGACC
* *
1908603 CAAGTCAGTGAGTTACACGGGCAGGGACACGAGCTGGGACACAATCATGTGTTT
1 CAAGTCAATGAGTTACACGGGCAGAGACACGAGCTGGGACACAATCATGTGTTT
* * * * *
1908657 CAAGTCAATGAGTTACACGGGCAGAGACATGGGTTGGGACACGATCGTGTGT
1 CAAGTCAATGAGTTACACGGGCAGAGACACGAGCTGGGACACAATCATGTGT
1908709 CCCAACTTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.21
Consensus pattern (54 bp):
CAAGTCAATGAGTTACACGGGCAGAGACACGAGCTGGGACACAATCATGTGTTT
Found at i:1909042 original size:48 final size:48
Alignment explanation
Indices: 1908983--1909075 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
1908973 TCAAGAGGGA
*
1908983 ATAAATAGTGATAAGACTGTAGACAGTGGAAGACCAAGCTTAGCAATG
1 ATAAATAGTGATAAGACTGTAGACACTGGAAGACCAAGCTTAGCAATG
* * * *
1909031 ATAAATAGTGATAAGAGTGTAGGCACTGGAAGATCAAGTTTAGCA
1 ATAAATAGTGATAAGACTGTAGACACTGGAAGACCAAGCTTAGCA
1909076 TTGCATAGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.41, C:0.11, G:0.26, T:0.23
Consensus pattern (48 bp):
ATAAATAGTGATAAGACTGTAGACACTGGAAGACCAAGCTTAGCAATG
Found at i:1912250 original size:26 final size:28
Alignment explanation
Indices: 1912184--1912258 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 28
1912174 TATAGATACG
*
1912184 TACATATATGTATGAATAAATTATAAAAAA
1 TACATATATGTAT--ATATATTATAAAAAA
* * *
1912214 TATACACATGTATATATATTA-AAAAAA
1 TACATATATGTATATATATTATAAAAAA
*
1912241 -ACATATATGTGTATATAT
1 TACATATATGTATATATAT
1912259 ATGACTACGA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 14 0.38
27 6 0.16
28 7 0.19
30 10 0.27
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (28 bp):
TACATATATGTATATATATTATAAAAAA
Found at i:1913247 original size:3 final size:3
Alignment explanation
Indices: 1913239--1913268 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1913229 TAATGGTAAT
1913239 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1913269 ATAACATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1922683 original size:18 final size:19
Alignment explanation
Indices: 1922662--1922703 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
1922652 TTACAATTTT
1922662 TTTTATAATTATTAAGTA-
1 TTTTATAATTATTAAGTAG
* *
1922680 TTTTA-AGTTATTTAGTAG
1 TTTTATAATTATTAAGTAG
1922698 TTTTAT
1 TTTTAT
1922704 GTTAACAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (19 bp):
TTTTATAATTATTAAGTAG
Found at i:1922696 original size:17 final size:18
Alignment explanation
Indices: 1922670--1922707 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1922660 TTTTTTATAA
1922670 TTATTAAGTA-TTTTAAG
1 TTATTAAGTAGTTTTAAG
* *
1922687 TTATTTAGTAGTTTTATG
1 TTATTAAGTAGTTTTAAG
1922705 TTA
1 TTA
1922708 ACAAGAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (18 bp):
TTATTAAGTAGTTTTAAG
Found at i:1937263 original size:15 final size:12
Alignment explanation
Indices: 1937230--1937274 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 12
1937220 CACGTATATG
1937230 TATATAAAAATA
1 TATATAAAAATA
1937242 TATATAAAAATTA
1 TATATAAAAA-TA
*
1937255 TAAATATAAAATA
1 TATATA-AAAATA
1937268 TATATAA
1 TATATAA
1937275 GTATGTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 11 0.38
13 14 0.48
14 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TATATAAAAATA
Found at i:1937288 original size:27 final size:26
Alignment explanation
Indices: 1937230--1937291 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
1937220 CACGTATATG
1937230 TATATA-AAAATATATATAAAAATTA
1 TATATATAAAATATATATAAAAATTA
* **
1937255 TAAATATAAAATATATATAAGTATGTA
1 TATATATAAAATATATATAAAAAT-TA
1937282 TATATATAAA
1 TATATATAAA
1937292 TGAGGAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 5 0.16
26 15 0.48
27 11 0.35
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (26 bp):
TATATATAAAATATATATAAAAATTA
Found at i:1942646 original size:49 final size:49
Alignment explanation
Indices: 1942590--1942687 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
1942580 TGTTCACGCG
1942590 TTTAACTCCCACTTTATGCGTCTTAAATATGACCCATAGAGTCAACTGT
1 TTTAACTCCCACTTTATGCGTCTTAAATATGACCCATAGAGTCAACTGT
1942639 TTTAACTCCCACTTTATGCGTCTTAAATATGACCCATAGAGTCAACTGT
1 TTTAACTCCCACTTTATGCGTCTTAAATATGACCCATAGAGTCAACTGT
1942688 CAATGAATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (49 bp):
TTTAACTCCCACTTTATGCGTCTTAAATATGACCCATAGAGTCAACTGT
Found at i:1950786 original size:25 final size:25
Alignment explanation
Indices: 1950758--1950862 Score: 135
Period size: 25 Copynumber: 4.3 Consensus size: 25
1950748 ACCTTAGCGC
*
1950758 GCTCTCTGATTATTAGCACGTTAAT
1 GCTCTCTGATTATTAGCACATTAAT
* *
1950783 GCTCTTTGATTATTAGCACATTAGT
1 GCTCTCTGATTATTAGCACATTAAT
* *
1950808 GCTCTCCGATTATTAGCACATTTAT
1 GCTCTCTGATTATTAGCACATTAAT
*
1950833 GCTCTCTG--TA-TAGCACATTTAT
1 GCTCTCTGATTATTAGCACATTAAT
1950855 GCTCTCTG
1 GCTCTCTG
1950863 TATAACACTT
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
22 20 0.28
23 2 0.03
25 50 0.69
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACATTAAT
Found at i:1950849 original size:22 final size:22
Alignment explanation
Indices: 1950821--1950884 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
1950811 CTCCGATTAT
1950821 TAGCACATTTATGCTCTCTGTA
1 TAGCACATTTATGCTCTCTGTA
1950843 TAGCACATTTATGCTCTCTGTA
1 TAGCACATTTATGCTCTCTGTA
*
1950865 TAACAC-TTTAGTGCTCTCTG
1 TAGCACATTTA-TGCTCTCTG
1950885 CTTAATAGTG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 4 0.10
22 36 0.90
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (22 bp):
TAGCACATTTATGCTCTCTGTA
Found at i:1953554 original size:23 final size:23
Alignment explanation
Indices: 1953511--1953569 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1953501 AAAAATAGTG
*
1953511 AAATTATATATTAATACATAATA
1 AAATTATATATTAATACATAAAA
* * **
1953534 AATTTATATTTTAATTTATAAAA
1 AAATTATATATTAATACATAAAA
1953557 AAATTATA-ATTAA
1 AAATTATATATTAA
1953570 ATACTGACCC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATTATATATTAATACATAAAA
Found at i:1954858 original size:16 final size:16
Alignment explanation
Indices: 1954837--1954869 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1954827 ATTTCGTCCC
1954837 TCTTTATTACCTCAAA
1 TCTTTATTACCTCAAA
1954853 TCTTTATTACCTCAAA
1 TCTTTATTACCTCAAA
1954869 T
1 T
1954870 TTTGCTAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.45
Consensus pattern (16 bp):
TCTTTATTACCTCAAA
Found at i:1962709 original size:13 final size:13
Alignment explanation
Indices: 1962691--1962716 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1962681 ATTTATTGTA
1962691 ATAAATAACAATC
1 ATAAATAACAATC
1962704 ATAAATAACAATC
1 ATAAATAACAATC
1962717 CAGTAAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (13 bp):
ATAAATAACAATC
Found at i:1971759 original size:48 final size:48
Alignment explanation
Indices: 1971670--1971763 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
1971660 TTTCTTGGCT
* * * *
1971670 TAAAAACGCCTAAGTCAGCCTAACTTCCACCCATAATGGATTCAACCG
1 TAAAAACGCCCAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
1971718 TAAAAACGCCCAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCCAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
1971764 AGAATTCCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 4 0.10
48 36 0.90
ACGTcount: A:0.39, C:0.30, G:0.13, T:0.18
Consensus pattern (48 bp):
TAAAAACGCCCAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:1975231 original size:14 final size:14
Alignment explanation
Indices: 1975212--1975245 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1975202 TTGATTCACT
1975212 TGTGACGTTTATGG
1 TGTGACGTTTATGG
1975226 TGTGACGTTTATGG
1 TGTGACGTTTATGG
1975240 TGTGAC
1 TGTGAC
1975246 TTACCTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.15, C:0.09, G:0.35, T:0.41
Consensus pattern (14 bp):
TGTGACGTTTATGG
Found at i:2000459 original size:20 final size:20
Alignment explanation
Indices: 2000431--2000469 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2000421 GTATAATATA
* *
2000431 TTAAGAATATTATTTAAATT
1 TTAAAAATATTATTAAAATT
2000451 TTAAAAATATTATTAAAAT
1 TTAAAAATATTATTAAAAT
2000470 AAAATTGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TTAAAAATATTATTAAAATT
Found at i:2009017 original size:11 final size:11
Alignment explanation
Indices: 2009001--2009042 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
2008991 TAGTTATTTA
2009001 TAATAAAATAT
1 TAATAAAATAT
2009012 TAATAAAATAT
1 TAATAAAATAT
*
2009023 CTCATTAAAATAT
1 -T-AATAAAATAT
2009036 TAATAAA
1 TAATAAA
2009043 GTAATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 16 0.59
12 2 0.07
13 9 0.33
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:2009190 original size:95 final size:95
Alignment explanation
Indices: 2009027--2009217 Score: 382
Period size: 95 Copynumber: 2.0 Consensus size: 95
2009017 AAATATCTCA
2009027 TTAAAATATTAATAAAGTAATATTTATCTAATTAAATAATTATAAAATATCATCAAAATATCTCT
1 TTAAAATATTAATAAAGTAATATTTATCTAATTAAATAATTATAAAATATCATCAAAATATCTCT
2009092 AACATCATCATTGCCTTCTAGATTTCTCTT
66 AACATCATCATTGCCTTCTAGATTTCTCTT
2009122 TTAAAATATTAATAAAGTAATATTTATCTAATTAAATAATTATAAAATATCATCAAAATATCTCT
1 TTAAAATATTAATAAAGTAATATTTATCTAATTAAATAATTATAAAATATCATCAAAATATCTCT
2009187 AACATCATCATTGCCTTCTAGATTTCTCTT
66 AACATCATCATTGCCTTCTAGATTTCTCTT
2009217 T
1 T
2009218 CTTTCTAATT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.41
Consensus pattern (95 bp):
TTAAAATATTAATAAAGTAATATTTATCTAATTAAATAATTATAAAATATCATCAAAATATCTCT
AACATCATCATTGCCTTCTAGATTTCTCTT
Found at i:2011699 original size:19 final size:19
Alignment explanation
Indices: 2011675--2011740 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
2011665 TCTCTCCCGA
2011675 CAAAATTTTTTAAAAAATT
1 CAAAATTTTTTAAAAAATT
2011694 CAAAATAATTTTT--AAAATT
1 CAAAAT--TTTTTAAAAAATT
* *
2011713 TAAAA-TATTTATAAAAATT
1 CAAAATTTTTTA-AAAAATT
2011732 CCAAAATTT
1 -CAAAATTT
2011741 ATATTTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
16 4 0.11
19 22 0.61
20 4 0.11
21 6 0.17
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (19 bp):
CAAAATTTTTTAAAAAATT
Found at i:2011727 original size:18 final size:19
Alignment explanation
Indices: 2011683--2011738 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
2011673 GACAAAATTT
*
2011683 TTTAAAAAATTCAAAATAA
1 TTTATAAAATTCAAAATAA
* *
2011702 TTTTTAAAATTTAAAAT-A
1 TTTATAAAATTCAAAATAA
2011720 TTTATAAAAATTCCAAAAT
1 TTTAT-AAAATT-CAAAAT
2011739 TTATATTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 5 0.17
19 20 0.67
20 5 0.17
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
TTTATAAAATTCAAAATAA
Found at i:2011775 original size:22 final size:21
Alignment explanation
Indices: 2011750--2011816 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
2011740 TATATTTTTT
2011750 AAATAAATTATAAAAATTTCAA
1 AAATAAATTATAAAAATTT-AA
* *
2011772 AAATAAATTCTAAAAATATAA
1 AAATAAATTATAAAAATTTAA
* *
2011793 AAGA-AAGTTAAAAAAATTTAA
1 AA-ATAAATTATAAAAATTTAA
2011814 AAA
1 AAA
2011817 ATATTCTAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 1 0.03
21 19 0.50
22 18 0.47
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (21 bp):
AAATAAATTATAAAAATTTAA
Found at i:2015877 original size:41 final size:39
Alignment explanation
Indices: 2015752--2015880 Score: 111
Period size: 40 Copynumber: 3.3 Consensus size: 39
2015742 CGGCACTCAA
* * * *
2015752 TGTCTCATCGGATAATTCAAAGTAATAATTTGACATCTAG
1 TGTCTCATCGAATAATCCAAAGTAATAA-TTGACACCCAG
* * * * *
2015792 TGTCTCATC-AGCTAAACCGAAGTAAT--TTGGCACCCTG
1 TGTCTCATCGA-ATAATCCAAAGTAATAATTGACACCCAG
*
2015829 TGCCTCATCGAATTAATCCAAAGTAATAAATTGACACCCAG
1 TGTCTCATCGAA-TAATCCAAAGTAAT-AATTGACACCCAG
2015870 TGTCTCATCGA
1 TGTCTCATCGA
2015881 CTCAAAGTCG
Statistics
Matches: 67, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
37 15 0.22
38 13 0.19
40 20 0.30
41 19 0.28
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (39 bp):
TGTCTCATCGAATAATCCAAAGTAATAATTGACACCCAG
Found at i:2016075 original size:24 final size:24
Alignment explanation
Indices: 2016038--2016084 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2016028 TATATATACC
2016038 AATTCAATCAATA-TAAATTCAATA
1 AATTCAATCAATATTAAA-TCAATA
2016062 AATTC-ATCACATATTAAATCAAT
1 AATTCAATCA-ATATTAAATCAAT
2016085 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (24 bp):
AATTCAATCAATATTAAATCAATA
Found at i:2016916 original size:19 final size:20
Alignment explanation
Indices: 2016892--2016930 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2016882 ATTAATAAGC
2016892 AATACATAT-TTTATTATTA
1 AATACATATGTTTATTATTA
2016911 AATACATATGTTTATTATTA
1 AATACATATGTTTATTATTA
2016931 CACATGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (20 bp):
AATACATATGTTTATTATTA
Found at i:2022830 original size:21 final size:23
Alignment explanation
Indices: 2022804--2022845 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
2022794 AGGGTTTTAG
*
2022804 TTTGTTTCTTT-TT-TTTTAGGT
1 TTTGTTTATTTATTCTTTTAGGT
2022825 TTTGTTTATTTATTCTTTTAG
1 TTTGTTTATTTATTCTTTTAG
2022846 TTCTATAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 2 0.11
23 6 0.33
ACGTcount: A:0.10, C:0.05, G:0.12, T:0.74
Consensus pattern (23 bp):
TTTGTTTATTTATTCTTTTAGGT
Found at i:2023225 original size:3 final size:3
Alignment explanation
Indices: 2023217--2023244 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2023207 ATTTTAATCC
2023217 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2023245 CCTTCTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2026626 original size:208 final size:208
Alignment explanation
Indices: 2026268--2026688 Score: 770
Period size: 208 Copynumber: 2.0 Consensus size: 208
2026258 GGGTTGGACC
2026268 CCTATCAGCCCCATTCCGTCGTCCTGGACACAATTGGTAAAGGCAAAAATCTTGGGTCTTGAATA
1 CCTATCAGCCCCATTCCGTCGTCCTGGACACAATTGGTAAAGGCAAAAATCTTGGGTCTTGAATA
2026333 CCCAAATTCGAGATTTACCATACACAAACAAATGTTGGAATATCTGAATCTCCTTATAAATTGTT
66 CCCAAATTCGAGATTTACCATACACAAACAAATGTTGGAATATCTGAATCTCCTTATAAATTGTT
*
2026398 ATCTTACCATATATAAGTTTGAGACCGAATACCACCATTAAGAAAAGAAAAGGAACGGTATTCTT
131 ACCTTACCATATATAAGTTTGAGACCGAATACCACCATTAAGAAAAGAAAAGGAACGGTATTCTT
* *
2026463 TGTGATTAGGGGG
196 TGTCATTAGGGCG
2026476 CCTATCAGCCCCATTCCGTCGTCCTGGACACAATTGGTAAAGGCAAAAATCTTGGGTCTTGAATA
1 CCTATCAGCCCCATTCCGTCGTCCTGGACACAATTGGTAAAGGCAAAAATCTTGGGTCTTGAATA
* * *
2026541 TCCAAATTCGAGATTTACCGTACACAAACAAATGTTGGGATATCTGAATCTCCTTATAAATTGTT
66 CCCAAATTCGAGATTTACCATACACAAACAAATGTTGGAATATCTGAATCTCCTTATAAATTGTT
* *
2026606 ACCTTACTATATATAAGTTTGAGACCGAATACCACCATTAAGAAAAGAAAAGGAATGGTATTCTT
131 ACCTTACCATATATAAGTTTGAGACCGAATACCACCATTAAGAAAAGAAAAGGAACGGTATTCTT
2026671 TGTCATTAGGGCG
196 TGTCATTAGGGCG
2026684 CCTAT
1 CCTAT
2026689 AACTGAAGAA
Statistics
Matches: 205, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
208 205 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (208 bp):
CCTATCAGCCCCATTCCGTCGTCCTGGACACAATTGGTAAAGGCAAAAATCTTGGGTCTTGAATA
CCCAAATTCGAGATTTACCATACACAAACAAATGTTGGAATATCTGAATCTCCTTATAAATTGTT
ACCTTACCATATATAAGTTTGAGACCGAATACCACCATTAAGAAAAGAAAAGGAACGGTATTCTT
TGTCATTAGGGCG
Found at i:2038510 original size:29 final size:29
Alignment explanation
Indices: 2038478--2038534 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2038468 AATTGTATGT
2038478 TTTTA-AAGGATT-AAATCAAAATTTTATCA
1 TTTTAGAAGG-TTAAAAT-AAAATTTTATCA
*
2038507 TTTTAGAAGGTTAAAATATAATTTTATC
1 TTTTAGAAGGTTAAAATAAAATTTTATC
2038535 TTTACTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (29 bp):
TTTTAGAAGGTTAAAATAAAATTTTATCA
Found at i:2043550 original size:14 final size:15
Alignment explanation
Indices: 2043531--2043563 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2043521 AGATAATGTT
*
2043531 TTATATT-TTAAAAA
1 TTATATTATAAAAAA
2043545 TTATATTATAAAAAA
1 TTATATTATAAAAAA
2043560 TTAT
1 TTAT
2043564 CAATTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTATATTATAAAAAA
Found at i:2046003 original size:57 final size:57
Alignment explanation
Indices: 2045915--2046162 Score: 302
Period size: 57 Copynumber: 4.4 Consensus size: 57
2045905 TTAATGTCCC
* * *
2045915 TTGCCACCAGAACTTGGACCTGAATTGG-GGTTGACAGCATCAGTAAATGCATGACCT
1 TTGCCTCCTGAACTTGGACCTGAATTGGTGG-TGACAGCATCACTAAATGCATGACCT
** * *
2045972 TTGCCTCCTTCACTTGGACCTGAATTGG-GGTTAACAGCATCAGTAAATGCATGACCT
1 TTGCCTCCTGAACTTGGACCTGAATTGGTGG-TGACAGCATCACTAAATGCATGACCT
* * **
2046029 TTGCCTCCTGGACTTGGACCTGAGTTGGTGGTGACAGCATCACTATGTGCATGACCT
1 TTGCCTCCTGAACTTGGACCTGAATTGGTGGTGACAGCATCACTAAATGCATGACCT
* * * * *
2046086 TTGCCACCAGAACTTGGCCCTGAATTGGTGGTGACAGAATCACTAACTGCATGACCT
1 TTGCCTCCTGAACTTGGACCTGAATTGGTGGTGACAGCATCACTAAATGCATGACCT
* *
2046143 TTGCCTCCTGGACTAGGACC
1 TTGCCTCCTGAACTTGGACC
2046163 ACTGGTCTTG
Statistics
Matches: 165, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
57 163 0.99
58 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.27
Consensus pattern (57 bp):
TTGCCTCCTGAACTTGGACCTGAATTGGTGGTGACAGCATCACTAAATGCATGACCT
Found at i:2049811 original size:15 final size:15
Alignment explanation
Indices: 2049793--2049821 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2049783 TGAGTGAGTA
2049793 TGAAAAATCGATTTT
1 TGAAAAATCGATTTT
2049808 TGAAAAATCGATTT
1 TGAAAAATCGATTT
2049822 ACTTTAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (15 bp):
TGAAAAATCGATTTT
Found at i:2050131 original size:3 final size:3
Alignment explanation
Indices: 2050118--2050164 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
2050108 TTCTCATAAG
2050118 AGA AGA A-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
2050165 GAAAGTAGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2052258 original size:43 final size:44
Alignment explanation
Indices: 2052211--2052311 Score: 113
Period size: 44 Copynumber: 2.3 Consensus size: 44
2052201 ACAGATGAGA
*
2052211 TCTTACATGT-AATC-AAATATCGATGCC-ACTGTCCCAGACAGAG
1 TCTTACACGTAAATCTAAAT-TCGATGCCGAC-GTCCCAGACAGAG
* *
2052254 TCTTACACGTAAATCTCAATTCGATGCCGACGTCCCAGAC-GTGG
1 TCTTACACGTAAATCTAAATTCGATGCCGACGTCCCAGACAG-AG
2052298 TCTTACACG-AAATC
1 TCTTACACGTAAATC
2052312 ACATATCAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
43 15 0.29
44 31 0.61
45 5 0.10
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (44 bp):
TCTTACACGTAAATCTAAATTCGATGCCGACGTCCCAGACAGAG
Found at i:2053443 original size:13 final size:13
Alignment explanation
Indices: 2053425--2053451 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2053415 CACAAACTAT
2053425 AAAATTTTCACAC
1 AAAATTTTCACAC
2053438 AAAATTTTCACAC
1 AAAATTTTCACAC
2053451 A
1 A
2053452 TATAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:2053847 original size:11 final size:10
Alignment explanation
Indices: 2053801--2053849 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
2053791 AATATAATTT
2053801 AATATTTTTA
1 AATATTTTTA
*
2053811 TATA-TTTTA
1 AATATTTTTA
2053820 AATATTTTTA
1 AATATTTTTA
*
2053830 AATATTTTTT
1 AATATTTTTA
*
2053840 AATAATTTTA
1 AATATTTTTA
2053850 TTTTTTAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
9 8 0.24
10 25 0.76
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
AATATTTTTA
Found at i:2060872 original size:41 final size:43
Alignment explanation
Indices: 2060806--2060895 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 43
2060796 GTGCATAAGG
*
2060806 TCTCGAGACATAGTTGTATAGTCTCGAGAC-A-TGTTCCAAAA
1 TCTCGAGACATAGTGGTATAGTCTCGAGACAATTGTTCCAAAA
* *
2060847 TCTCGAGACA-AGTGGTCATTA-TCTCGAGACAATTGTTCCTAAG
1 TCTCGAGACATAGTGGT-A-TAGTCTCGAGACAATTGTTCCAAAA
2060890 TCTCGA
1 TCTCGA
2060896 AACAGAAGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
40 5 0.12
41 20 0.48
42 3 0.07
43 14 0.33
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (43 bp):
TCTCGAGACATAGTGGTATAGTCTCGAGACAATTGTTCCAAAA
Found at i:2070753 original size:3 final size:3
Alignment explanation
Indices: 2070745--2070789 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
2070735 AAACAAACCT
2070745 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2070790 AGTTAAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2071613 original size:24 final size:24
Alignment explanation
Indices: 2071586--2071633 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2071576 CCCTTCTCCT
2071586 CTCTATTCTTTTT-TTTTCTTTTTG
1 CTCT-TTCTTTTTGTTTTCTTTTTG
*
2071610 CTCTTTTTTTTTGTTTTCTTTTTG
1 CTCTTTCTTTTTGTTTTCTTTTTG
2071634 TTGTTGGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.77
Consensus pattern (24 bp):
CTCTTTCTTTTTGTTTTCTTTTTG
Found at i:2080798 original size:41 final size:38
Alignment explanation
Indices: 2080753--2080840 Score: 115
Period size: 37 Copynumber: 2.3 Consensus size: 38
2080743 TAAAAAGTAT
* *
2080753 TTATATTAAAAAACACTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAAA-A-TA-AATAAATATAATAAATATATTA
2080794 TTATATT-AAAAAATAAATAAATATAATAAATATATTA
1 TTATATTAAAAAAATAAATAAATATAATAAATATATTA
*
2080831 TTGTATTAAA
1 TTATATTAAA
2080841 TATAATTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
37 26 0.60
38 4 0.09
39 1 0.02
40 5 0.12
41 7 0.16
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.39
Consensus pattern (38 bp):
TTATATTAAAAAAATAAATAAATATAATAAATATATTA
Found at i:2090015 original size:51 final size:52
Alignment explanation
Indices: 2089960--2090076 Score: 134
Period size: 51 Copynumber: 2.3 Consensus size: 52
2089950 TATAAAACTT
* *
2089960 ATATATATATATAAAATACA-TAATGCATTTATGAAAATAAGGAAA-ATATAA
1 ATATATATATATAAAATACATTAATGCATTTA-CAAAAAAAGGAAATATATAA
* * * *
2090011 ATATATACATATAAAATATATTCATGCATTTACAAAAAAATGAAATATATAA
1 ATATATATATATAAAATACATTAATGCATTTACAAAAAAAGGAAATATATAA
*
2090063 GTATA-ATATA-AAAA
1 ATATATATATATAAAA
2090077 CATGGAAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
50 4 0.07
51 32 0.57
52 20 0.36
ACGTcount: A:0.57, C:0.05, G:0.06, T:0.32
Consensus pattern (52 bp):
ATATATATATATAAAATACATTAATGCATTTACAAAAAAAGGAAATATATAA
Found at i:2090338 original size:3 final size:3
Alignment explanation
Indices: 2090330--2090376 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
2090320 ATATGTAGGT
2090330 ATA ATA ATA AT- ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2090376 A
1 A
2090377 CAAAATTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2090633 original size:19 final size:21
Alignment explanation
Indices: 2090595--2090638 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
2090585 TCCCTTTTTT
*
2090595 AAAATCGTAAATAAGTAAAAA
1 AAAATCGTAAATAAGAAAAAA
2090616 AAAATCG-AAA-AAGAAAAAA
1 AAAATCGTAAATAAGAAAAAA
2090635 AAAA
1 AAAA
2090639 GAAAACAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.55
20 3 0.14
21 7 0.32
ACGTcount: A:0.75, C:0.05, G:0.09, T:0.11
Consensus pattern (21 bp):
AAAATCGTAAATAAGAAAAAA
Found at i:2090850 original size:17 final size:17
Alignment explanation
Indices: 2090828--2090880 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 17
2090818 ATTATAAAAT
2090828 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
2090845 CATATCATATCTAAGATTA
1 CATATC-T-TCTAAGATTA
* *
2090864 CATATCCTCGAAGATTA
1 CATATCTTCTAAGATTA
2090881 TATTTTCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 15 0.47
18 1 0.03
19 16 0.50
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.36
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:2096156 original size:3 final size:3
Alignment explanation
Indices: 2096148--2096179 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2096138 ATTTCTGGGC
*
2096148 TGT TGT TGT TGC TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
2096180 GTTTCTTCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.34, T:0.62
Consensus pattern (3 bp):
TGT
Found at i:2098569 original size:30 final size:29
Alignment explanation
Indices: 2098534--2098627 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 29
2098524 AAAAAAATTT
*
2098534 TTTTGACCCCTAA-TTTTTTCCTAAATTTCA
1 TTTTGACCCCTAACTTTCTT--TAAATTTCA
*
2098564 TTTTGACCCTTAAACTTTCTTTAAATTTCA
1 TTTTGACCCCT-AACTTTCTTTAAATTTCA
* * *
2098594 CTTAGACCCCTAAACTTTCATTAAATTTCA
1 TTTTGACCCCT-AACTTTCTTTAAATTTCA
2098624 TTTT
1 TTTT
2098628 AATCCTAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
30 47 0.87
31 2 0.04
32 5 0.09
ACGTcount: A:0.27, C:0.22, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTTGACCCCTAACTTTCTTTAAATTTCA
Found at i:2108957 original size:53 final size:53
Alignment explanation
Indices: 2108804--2109222 Score: 658
Period size: 53 Copynumber: 8.0 Consensus size: 53
2108794 NNNNNTTGCT
* * **
2108804 AAAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTGAAAA-A-ATAGAA
1 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTA
*
2108855 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATAGAAATTA
1 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTA
2108908 AAAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-
1 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTA
2108960 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTA
1 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTA
2109014 AAAGGCTCAACTCACCTCTCGCAATATGAGTTG-TTTTTGAAAACAGAAATTA
1 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTA
2109066 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATTG-AA--A
1 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACA--GAAATTA
*
2109118 AAAGGCTCAACTCACCTCTCGCAATATGAGTTG-TTTTTGAAAAAATGAAATTA
1 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACA-GAAATTA
* *
2109171 AAAGTCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATT
1 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATT
2109223 GAAATACCTC
Statistics
Matches: 347, Mismatches: 9, Indels: 22
0.92 0.02 0.06
Matches are distributed among these distances:
50 2 0.01
51 56 0.16
52 120 0.35
53 123 0.35
54 45 0.13
55 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (53 bp):
AAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTA
Found at i:2108989 original size:105 final size:106
Alignment explanation
Indices: 2108804--2109222 Score: 651
Period size: 105 Copynumber: 4.0 Consensus size: 106
2108794 NNNNNTTGCT
* * *
2108804 AAAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTGAAAAAATAGA--AAAAGGCTCAACT
1 AAAGGCTCAACTCACCTCTCGCAATATGAGTTG-TTTTTGAAAAAAGAAATTAAAAGGCTCAACT
*
2108867 CACCTCTCGCAATATGAGTTGATTTTTG-AAAATAGAAATTA
65 CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTA
2108908 AAAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-AAAGGCTCAAC
1 AAAGGCTCAACTCACCTCTCGCAATATGAGTTG-TTTTTGAAAAA-AGAAATTAAAAGGCTCAAC
2108971 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTA
64 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTA
*
2109014 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGTTTTTGAAAACAGAAATTAAAAGGCTCAACTC
1 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGTTTTTGAAAAAAGAAATTAAAAGGCTCAACTC
2109079 ACCTCTCGCAATATGAGTTGATTTTTG-AAAACATTG-AA--A
66 ACCTCTCGCAATATGAGTTGATTTTTGAAAAACA--GAAATTA
*
2109118 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGTTTTTGAAAAAATGAAATTAAAAGTCTCAACT
1 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGTTTTTGAAAAAA-GAAATTAAAAGGCTCAACT
*
2109183 CACCTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATT
65 CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT
2109223 GAAATACCTC
Statistics
Matches: 295, Mismatches: 8, Indels: 22
0.91 0.02 0.07
Matches are distributed among these distances:
103 31 0.11
104 63 0.21
105 104 0.35
106 78 0.26
107 19 0.06
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (106 bp):
AAAGGCTCAACTCACCTCTCGCAATATGAGTTGTTTTTGAAAAAAGAAATTAAAAGGCTCAACTC
ACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTA
Found at i:2109480 original size:65 final size:67
Alignment explanation
Indices: 2109176--2109780 Score: 504
Period size: 64 Copynumber: 9.4 Consensus size: 67
2109166 AATTAAAAGT
**
2109176 CTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATACCTCAACGTGTC
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTT-AAAACAG-AATTGAAATACCTC-ACGTGTC
2109241 TTGAGG
63 TTGA-G
*
2109247 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATACC-AAC--G-CT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTT-AAAACAG-AATTGAAATACCTCACGTGTCT
2109308 TGAG
64 TGAG
*
2109312 CT-AACT-ATTTCTCGC-A-ATGAGTTGAATTTT-GAACA-AATTGAAATTACCT--CGTGTC-T
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTAAAACAGAATTGAAA-TACCTCACGTGTCTT
2109368 GAG
65 GAG
* ** ** * *
2109371 CTCAACTCATTTCTCGCAATTATG-TTTGTTTTTTTATCATAGAATTGAATTACCTCACGTGTCT
1 CTCAACTCATTTCTCGCAA-TATGAGTTG-AATTTTAAAACAGAATTGAAATACCTCACGTGTCT
2109435 TGAG
64 TGAG
* * * * *
2109439 CTCAACTCA-TTCTCGCAATA-GAATTGAATTTTAAAACAGAATTGAAAAAACTCAAGTGTCTAG
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTAAAACAGAATTGAAATACCTCACGTGTCTTG
2109502 -G
66 AG
* * *
2109503 CTCAACTCA-TT-TCGCAATATGAGTTGAATTTGAAAACAGAAATGAAATTACC-AACGTGTCTT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTAAAACAGAATTGAAA-TACCTCACGTGTCTT
2109565 -A-
65 GAG
* * * *
2109566 CT----TC-TTTCTCGCAATATGAGTTGAATTTTGAAGCAAAAATTGAAAATACCTCA-ATGGTC
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTAAAAC-AGAATTG-AAATACCTCACGT-GTC
2109625 TTGAG
63 TTGAG
* * * *
2109630 GTCAACTCATTTCTCGC-AT-TGAG-T--ATTTT-GAAC--AATTG-AATTCCT-AAGTGTCTTG
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTAAAACAGAATTGAAATACCTCACGTGTCTTG
2109685 AG
66 AG
* *
2109687 ACTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAGCA-AATTAAAATACCTCAACGTG-C
1 -CTCAACTCATTTCTCGCAATATGAGTTGAATTTT-AAAACAGAATTGAAATACCTC-ACGTGTC
2109750 TTGAG
63 TTGAG
2109755 CTCAACTCA--TCTCGCAATATGA-TTGA
1 CTCAACTCATTTCTCGCAATATGAGTTGA
2109781 GATAAATGAA
Statistics
Matches: 440, Mismatches: 48, Indels: 99
0.75 0.08 0.17
Matches are distributed among these distances:
57 18 0.04
58 27 0.06
59 17 0.04
60 37 0.08
61 34 0.08
62 11 0.03
63 30 0.07
64 64 0.15
65 55 0.12
66 22 0.05
67 35 0.08
68 23 0.05
69 14 0.03
71 53 0.12
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (67 bp):
CTCAACTCATTTCTCGCAATATGAGTTGAATTTTAAAACAGAATTGAAATACCTCACGTGTCTTG
AG
Found at i:2109533 original size:64 final size:67
Alignment explanation
Indices: 2109176--2109865 Score: 464
Period size: 64 Copynumber: 10.6 Consensus size: 67
2109166 AATTAAAAGT
**
2109176 CTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATACCTCAACGTGTC
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTT-AAAACAG-AATTGAAATACCTCAA-GTGTC
*
2109241 TTGAGG
63 TAGA-G
*
2109247 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATA-C-CAA-CG-CT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTT-AAAACAG-AATTGAAATACCTCAAGTGTCT
*
2109308 TGAG
64 AGAG
*
2109312 CT-AACT-ATTTCTCGC-A-ATGAGTTGAATTTT-GAACA-AATTGAAATTACCTC--GTGTCT-
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTAAAACAGAATTGAAA-TACCTCAAGTGTCTA
2109368 GAG
65 GAG
* ** ** * * *
2109371 CTCAACTCATTTCTCGCAATTATG-TTTGTTTTTTTATCATAGAATTGAATTACCTCACGTGTCT
1 CTCAACTCATTTCTCGCAA-TATGAGTTG-AATTTTAAAACAGAATTGAAATACCTCAAGTGTCT
*
2109435 TGAG
64 AGAG
* * *
2109439 CTCAACTCA-TTCTCGCAATA-GAATTGAATTTTAAAACAGAATTGAAAAAACTCAAGTGTCTAG
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTAAAACAGAATTGAAATACCTCAAGTGTCTAG
2109502 -G
66 AG
* *
2109503 CTCAACTCA-TT-TCGCAATATGAGTTGAATTTGAAAACAGAAATGAAATTA-C-CAACGTGTCT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTAAAACAGAATTGAAA-TACCTCAA-GTGTCT
*
2109564 -TA-
64 AGAG
* * *
2109566 CT----TC-TTTCTCGCAATATGAGTTGAATTTTGAAGCAAAAATTGAAAATACCTCAA-TGGTC
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTAAAAC-AGAATTG-AAATACCTCAAGT-GTC
*
2109625 TTGAG
63 TAGAG
* * * *
2109630 GTCAACTCATTTCTCGC-AT-TGAG-T--ATTTT-GAAC--AATTG-AATTCCT-AAGTGTCTTG
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTAAAACAGAATTGAAATACCTCAAGTGTCTAG
2109685 AG
66 AG
* *
2109687 ACTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAGCA-AATTAAAATACCTCAACGTG-C
1 -CTCAACTCATTTCTCGCAATATGAGTTGAATTTT-AAAACAGAATTGAAATACCTCAA-GTGTC
*
2109750 TTGAG
63 TAGAG
** *
2109755 CTCAACTCA--TCTCGCAATATGA-TTGAGATAAATGAAAAACAAAAATTGAAATTACCTCAGAC
1 CTCAACTCATTTCTCGCAATATGAGTTGA-AT---TTTAAAAC-AGAATTGAAA-TACCTCA-A-
* *
2109817 GTAGCCGAG-G
58 GT-GTCTAGAG
*
2109827 CTCAACTCATCTTCT-GCAATATGAGTTGATTTTTGAAAA
1 CTCAACTCAT-TTCTCGCAATATGAGTTGAATTTT-AAAA
2109866 ACAAAATTAA
Statistics
Matches: 504, Mismatches: 52, Indels: 125
0.74 0.08 0.18
Matches are distributed among these distances:
57 18 0.04
58 25 0.05
59 17 0.03
60 39 0.08
61 32 0.06
62 10 0.02
63 36 0.07
64 64 0.13
65 57 0.11
66 22 0.04
67 39 0.08
68 26 0.05
69 21 0.04
70 8 0.02
71 56 0.11
72 15 0.03
73 2 0.00
74 10 0.02
75 7 0.01
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (67 bp):
CTCAACTCATTTCTCGCAATATGAGTTGAATTTTAAAACAGAATTGAAATACCTCAAGTGTCTAG
AG
Found at i:2109628 original size:191 final size:190
Alignment explanation
Indices: 2109187--2109647 Score: 475
Period size: 191 Copynumber: 2.4 Consensus size: 190
2109177 TCAACTCACC
*
2109187 TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATACCTCAACGTGTCTTGAGGCTCAA
1 TCTCGCAATATGAGTTGAATTTTG-AAACAAAAATTGAAATACCTCAACGTGTCTTGA-GCTCAA
* * *
2109252 CTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATACCAACGCTTGAGCTAAC
64 CTCATTTCTCGCAATATGAATTGAATTTTGAAAACAGAAATTGAAAAACCAACGCTAGAGCTAAC
* *
2109317 TATTTCTCGCAATGAGTTGAATTTTGAACAAATTGAAATTACCTCGTGTCTGAGCTCAACTCATT
129 TATTTCTCGCAATGAGTTGAATTTTGAACAAAATGAAATTACCACGTGTCTGAGCT--A-TCATT
* * ** * * *
2109382 TCTCGCAATTATG-TTTG-TTTTTTTATCATAGAATTGAATTACCTC-ACGTGTCTTGAGCTCAA
1 TCTCGCAA-TATGAGTTGAATTTTGAAACA-AAAATTGAAATACCTCAACGTGTCTTGAGCTCAA
*
2109444 CTCA-TTCTCGCAATA-GAATTGAATTTT-AAAACAG-AATTGAAAAAACTCAAGTGTCTAG-GC
64 CTCATTTCTCGCAATATGAATTGAATTTTGAAAACAGAAATTG-AAAAAC-CAA-CG-CTAGAGC
*
2109504 TCAACTCA-TT-TCGCAATATGAGTTGAA-TTTGAAAACAGAAATGAAATTACCAACGTGTCTTA
125 T-AACT-ATTTCTCGC-A-ATGAGTTGAATTTTG--AACA-AAATGAAATTACC-ACGTGTCTGA
2109566 -CT-TC-TT
182 GCTATCATT
* * *
2109572 TCTCGCAATATGAGTTGAATTTTGAAGCAAAAATTGAAAATACCTCAATG-GTCTTGAGGTCAAC
1 TCTCGCAATATGAGTTGAATTTTGAAACAAAAATTG-AAATACCTCAACGTGTCTTGAGCTCAAC
2109636 TCATTTCTCGCA
65 TCATTTCTCGCA
2109648 TTGAGTATTT
Statistics
Matches: 223, Mismatches: 24, Indels: 41
0.77 0.08 0.14
Matches are distributed among these distances:
188 5 0.02
189 16 0.07
190 33 0.15
191 52 0.23
192 34 0.15
193 25 0.11
194 21 0.09
195 25 0.11
196 12 0.05
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (190 bp):
TCTCGCAATATGAGTTGAATTTTGAAACAAAAATTGAAATACCTCAACGTGTCTTGAGCTCAACT
CATTTCTCGCAATATGAATTGAATTTTGAAAACAGAAATTGAAAAACCAACGCTAGAGCTAACTA
TTTCTCGCAATGAGTTGAATTTTGAACAAAATGAAATTACCACGTGTCTGAGCTATCATT
Found at i:2109872 original size:72 final size:69
Alignment explanation
Indices: 2109688--2109877 Score: 196
Period size: 72 Copynumber: 2.7 Consensus size: 69
2109678 TGTCTTGAGA
* *
2109688 CTCAACTCAT-TTCTCGCAATATGAGTTGAATTTTG-AAAGC-AAATTAAAATACCTCAACGTGC
1 CTCAACTCATCTTCT-GCAATATGAGTTGATTTTTGAAAAACAAAATTAAAATACCTCAACGTGC
*
2109750 TTGAG
65 TCGAG
*** *
2109755 CTCAACTCATC-TC-GCAATATGA-TTGAGATAAATGAAAAACAAAAATTGAAATTACCTCAGAC
1 CTCAACTCATCTTCTGCAATATGAGTT--GATTTTTGAAAAAC-AAAATT-AAAATACCTCA-AC
2109817 GTAGC-CGAGG
61 GT-GCTCGA-G
2109827 CTCAACTCATCTTCTGCAATATGAGTTGATTTTTGAAAAACAAAATTAAAA
1 CTCAACTCATCTTCTGCAATATGAGTTGATTTTTGAAAAACAAAATTAAAA
2109878 GGCTAACTCA
Statistics
Matches: 99, Mismatches: 11, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
64 2 0.02
65 9 0.09
66 4 0.04
67 16 0.16
69 5 0.05
70 10 0.10
71 9 0.09
72 20 0.20
73 13 0.13
74 9 0.09
75 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.28
Consensus pattern (69 bp):
CTCAACTCATCTTCTGCAATATGAGTTGATTTTTGAAAAACAAAATTAAAATACCTCAACGTGCT
CGAG
Found at i:2121703 original size:16 final size:15
Alignment explanation
Indices: 2121651--2121702 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
2121641 AACTTTTCTT
2121651 TTTTGAAAACACGAAAA
1 TTTT-AAAACAC-AAAA
*
2121668 TTTTAAAATACAAGAA
1 TTTTAAAACACAA-AA
2121684 TTTTAGAAACAC-AAA
1 TTTTA-AAACACAAAA
2121699 TTTT
1 TTTT
2121703 TTTTAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 8 0.26
16 14 0.45
17 9 0.29
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.33
Consensus pattern (15 bp):
TTTTAAAACACAAAA
Found at i:2121815 original size:19 final size:19
Alignment explanation
Indices: 2121788--2121824 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2121778 AACACGAAAA
*
2121788 TTTTTAAAACAAAAATTTG
1 TTTTGAAAACAAAAATTTG
*
2121807 TTTTGAAAACATAAATTT
1 TTTTGAAAACAAAAATTT
2121825 TTGATAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (19 bp):
TTTTGAAAACAAAAATTTG
Found at i:2122279 original size:19 final size:19
Alignment explanation
Indices: 2122239--2122280 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2122229 AAACACCATT
* *
2122239 AAATAAATAAAATAAAATA
1 AAATAAATAAAAAAAAAAA
2122258 AAATAAA-AAAAAAAGAAAA
1 AAATAAATAAAAAAA-AAAA
2122277 AAAT
1 AAAT
2122281 TACCCAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.14
Consensus pattern (19 bp):
AAATAAATAAAAAAAAAAA
Found at i:2122392 original size:1 final size:1
Alignment explanation
Indices: 2122386--2122436 Score: 93
Period size: 1 Copynumber: 51.0 Consensus size: 1
2122376 AAATCTGCTA
*
2122386 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2122437 CTTATAAACC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.02, G:0.00, T:0.98
Consensus pattern (1 bp):
T
Found at i:2135147 original size:23 final size:24
Alignment explanation
Indices: 2135100--2135145 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
2135090 GAAAAATATT
2135100 AAATATATATATTTTTTATTTTTA
1 AAATATATATATTTTTTATTTTTA
2135124 AAATATA-ATAGTTTTTTATTTT
1 AAATATATATA-TTTTTTATTTT
2135146 AAGTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATATATATTTTTTATTTTTA
Found at i:2135274 original size:59 final size:59
Alignment explanation
Indices: 2135211--2135398 Score: 234
Period size: 68 Copynumber: 3.1 Consensus size: 59
2135201 ATCAAGTTTG
*
2135211 TTTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAA
1 TTTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAA
*
2135270 TTTTACTAATTAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGA
1 TTTTACTAATCAAATGTTAGATTTTATT---AC-----A-ACAATTAATACAATTAATAATTTGA
2135335 TAA
57 TAA
* * * *
2135338 ATTTATTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAA-TTAATAA
1 TTTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAA
2135396 TTT
1 TTT
2135399 GATGATTTTA
Statistics
Matches: 112, Mismatches: 8, Indels: 19
0.81 0.06 0.14
Matches are distributed among these distances:
58 8 0.07
59 45 0.40
60 1 0.01
62 2 0.02
65 2 0.02
67 1 0.01
68 53 0.47
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.43
Consensus pattern (59 bp):
TTTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAA
Found at i:2135313 original size:9 final size:9
Alignment explanation
Indices: 2135301--2135328 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2135291 TTTTATTACA
2135301 ACAATTAAT
1 ACAATTAAT
2135310 ACAATTAAT
1 ACAATTAAT
2135319 ACAATTAAT
1 ACAATTAAT
2135328 A
1 A
2135329 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:2135319 original size:68 final size:68
Alignment explanation
Indices: 2135242--2135412 Score: 292
Period size: 68 Copynumber: 2.5 Consensus size: 68
2135232 TTTTGTTACA
*
2135242 ACAATTAATACAATTAATAATTTGATAATTTTACTAATTAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAATTTTACTAATCAAATGTTAGATTTTATTACAACAATT
2135307 AAT
66 AAT
* *
2135310 ACAATTAATACAATTAATAATTTGATAAATTTATTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAATTTTACTAATCAAATGTTAGATTTTATTACAACAATT
2135375 AAT
66 AAT
*
2135378 ACAATT-A-ACAATTAATAATTTGATGATTTTACTAA
1 ACAATTAATACAATTAATAATTTGATAATTTTACTAA
2135413 CAATTAATTT
Statistics
Matches: 97, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
66 25 0.26
67 1 0.01
68 71 0.73
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.42
Consensus pattern (68 bp):
ACAATTAATACAATTAATAATTTGATAATTTTACTAATCAAATGTTAGATTTTATTACAACAATT
AAT
Found at i:2135424 original size:16 final size:16
Alignment explanation
Indices: 2135403--2135442 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
2135393 TAATTTGATG
*
2135403 ATTTTACTAACAATTA
1 ATTTTAATAACAATTA
2135419 ATTTTAATAACAATTA
1 ATTTTAATAACAATTA
*
2135435 GTTTTAAT
1 ATTTTAAT
2135443 TTTATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (16 bp):
ATTTTAATAACAATTA
Found at i:2135443 original size:22 final size:23
Alignment explanation
Indices: 2135416--2135477 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
2135406 TTACTAACAA
* * *
2135416 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
2135438 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
*
2135461 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
2135478 CGGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:2137186 original size:27 final size:27
Alignment explanation
Indices: 2137088--2137183 Score: 97
Period size: 27 Copynumber: 3.4 Consensus size: 27
2137078 TTATTATAAT
2137088 TTAAATAATTTTATTATACATATATTA
1 TTAAATAATTTTATTATACATATATTA
* * *
2137115 TTAAATTAA-TTTATTTTA-ATGTTAAATAA
1 TTAAA-TAATTTTATTATACA---TATATTA
2137144 TTTAAATAATTTTATTATACATATATTA
1 -TTAAATAATTTTATTATACATATATTA
2137172 TTAAATTAATTT
1 TTAAA-TAATTT
2137184 ATTTTAATGT
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
26 1 0.02
27 18 0.33
28 14 0.25
29 8 0.15
30 13 0.24
31 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (27 bp):
TTAAATAATTTTATTATACATATATTA
Found at i:2137229 original size:57 final size:57
Alignment explanation
Indices: 2137083--2137197 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
2137073 ATTAATTATT
2137083 ATAATTTAAATAATTTTATTATACATATATTATTAAATTAATTTATTTTAATGTTAA
1 ATAATTTAAATAATTTTATTATACATATATTATTAAATTAATTTATTTTAATGTTAA
2137140 ATAATTTAAATAATTTTATTATACATATATTATTAAATTAATTTATTTTAATGTTAA
1 ATAATTTAAATAATTTTATTATACATATATTATTAAATTAATTTATTTTAATGTTAA
2137197 A
1 A
2137198 ATTGTTAATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (57 bp):
ATAATTTAAATAATTTTATTATACATATATTATTAAATTAATTTATTTTAATGTTAA
Found at i:2143322 original size:25 final size:23
Alignment explanation
Indices: 2143294--2143339 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
2143284 TTTTGTTTAA
2143294 TTTAAAAATTAGTATTTTTAAAATG
1 TTTAAAAATT--TATTTTTAAAATG
**
2143319 TTTATGAATTTATTTTTAAAA
1 TTTAAAAATTTATTTTTAAAA
2143340 CTATTTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (23 bp):
TTTAAAAATTTATTTTTAAAATG
Found at i:2145345 original size:17 final size:17
Alignment explanation
Indices: 2145323--2145362 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2145313 AAAAACTTAC
*
2145323 ATTAACCCGAACATAAA
1 ATTAACCCAAACATAAA
*
2145340 ATTAACCCAAACTTAAA
1 ATTAACCCAAACATAAA
2145357 A-TAACC
1 ATTAACC
2145363 GAATTTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.53, C:0.25, G:0.03, T:0.20
Consensus pattern (17 bp):
ATTAACCCAAACATAAA
Found at i:2152579 original size:27 final size:27
Alignment explanation
Indices: 2152541--2152594 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2152531 AATATATATA
2152541 TAACATAATTCAGTTTTTCATGGAAAG
1 TAACATAATTCAGTTTTTCATGGAAAG
2152568 TAACATAATTCAGTTTTTCATGGAAAG
1 TAACATAATTCAGTTTTTCATGGAAAG
2152595 CCCAACCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (27 bp):
TAACATAATTCAGTTTTTCATGGAAAG
Found at i:2152876 original size:52 final size:51
Alignment explanation
Indices: 2152798--2152901 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 51
2152788 TGTTCATAAA
2152798 CAACCCTATCAAACAACAACAATATGCTACTTTGGTGTTAGAATTGTGTGAT
1 CAACCCTATCAAACAACAACAATATGCTAC-TTGGTGTTAGAATTGTGTGAT
* *
2152850 CAACCCTATCAAACAATAATAATATGCTACTTGGTGTTAGAATTGTGTGAT
1 CAACCCTATCAAACAACAACAATATGCTACTTGGTGTTAGAATTGTGTGAT
2152901 C
1 C
2152902 TGAATTTCGA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 22 0.44
52 28 0.56
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (51 bp):
CAACCCTATCAAACAACAACAATATGCTACTTGGTGTTAGAATTGTGTGAT
Found at i:2159318 original size:17 final size:18
Alignment explanation
Indices: 2159297--2159332 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
2159287 TCCAATAAAA
2159297 TTTTTTTCCATATTTCATT
1 TTTTTTTCCATATTTCA-T
2159316 TTTTTTTCCATATTTCA
1 TTTTTTTCCATATTTCA
2159333 AAATCTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTTTCCATATTTCAT
Found at i:2160066 original size:16 final size:16
Alignment explanation
Indices: 2160047--2160085 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
2160037 GTCATTTTTG
*
2160047 GTTTGAATTATTTCGA
1 GTTTAAATTATTTCGA
2160063 GTTTAAATTATTTCGA
1 GTTTAAATTATTTCGA
2160079 GTTTAAA
1 GTTTAAA
2160086 CCATTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (16 bp):
GTTTAAATTATTTCGA
Found at i:2160091 original size:16 final size:16
Alignment explanation
Indices: 2160056--2160092 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2160046 GGTTTGAATT
**
2160056 ATTTCGAGTTTAAATT
1 ATTTCGAGTTTAAACC
2160072 ATTTCGAGTTTAAACC
1 ATTTCGAGTTTAAACC
2160088 ATTTC
1 ATTTC
2160093 AAATTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.46
Consensus pattern (16 bp):
ATTTCGAGTTTAAACC
Found at i:2163577 original size:18 final size:18
Alignment explanation
Indices: 2163554--2163599 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2163544 TTTGTTCACA
* * *
2163554 GGTTTTGGTGTTGGGTGT
1 GGTTTTGGAGTTGGATGG
2163572 GGTTTTGGAGTTGGATGG
1 GGTTTTGGAGTTGGATGG
2163590 GGTTTTGGAG
1 GGTTTTGGAG
2163600 GTCTGTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.07, C:0.00, G:0.50, T:0.43
Consensus pattern (18 bp):
GGTTTTGGAGTTGGATGG
Found at i:2171327 original size:20 final size:20
Alignment explanation
Indices: 2171290--2171327 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2171280 ATAGGTATGC
*
2171290 ATGTGTTTGTAATTTGATTT
1 ATGTGTTTGTAATATGATTT
2171310 ATGTGTTT-TAAATATGAT
1 ATGTGTTTGT-AATATGAT
2171328 AAACGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.55
Consensus pattern (20 bp):
ATGTGTTTGTAATATGATTT
Found at i:2171772 original size:43 final size:42
Alignment explanation
Indices: 2171720--2171880 Score: 137
Period size: 43 Copynumber: 3.7 Consensus size: 42
2171710 TGTTGGTCTA
* *
2171720 TAGCGGCGCTTCAACCACAAACGCCACTAAAGAACCTAATCTT
1 TAGCGGCGCTTC-CCCACAAACGCCACTAAAGAACCTGATCTT
* * * *
2171763 TAGCTGCGCTTTCCCCTCAAACGCCAC-AATAGACCCTGATCTA
1 TAGCGGCGC-TTCCCCACAAACGCCACTAA-AGAACCTGATCTT
* *
2171806 TAGCGGCGTTTTCCCCACAAACGCCGCTAAAG-ACCATGATCTT
1 TAGCGGCG-CTTCCCCACAAACGCCACTAAAGAACC-TGATCTT
* * ** *
2171849 TAGTGCCGCTTTTTCCACAAACACCACTAAAG
1 TAGCGGCGC-TTCCCCACAAACGCCACTAAAG
2171881 GCCAACACCT
Statistics
Matches: 93, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
42 4 0.04
43 84 0.90
44 5 0.05
ACGTcount: A:0.29, C:0.34, G:0.15, T:0.22
Consensus pattern (42 bp):
TAGCGGCGCTTCCCCACAAACGCCACTAAAGAACCTGATCTT
Done.