Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 4 of 120
Found at i:796349 original size:31 final size:29
Alignment explanation
Indices: 796280--796382 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 29
796270 CTAATTACTT
* * * *
796280 AAATGAAAACTTTTGAATAGTTTAGTAACTT
1 AAATGAAAATTTTTGAATAG-TTAATGAC-C
796311 AAATGAAAATTTTTGAATAGTTCAATGACC
1 AAATGAAAATTTTTGAATAGTT-AATGACC
*
796341 AAATTGAAAATTTTT--TTAGTTAAGTGACC
1 AAA-TGAAAATTTTTGAATAGTTAA-TGACC
796370 AAAATGAAAATTT
1 -AAATGAAAATTT
796383 ACTCATAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
28 2 0.03
29 19 0.30
30 8 0.13
31 34 0.54
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.37
Consensus pattern (29 bp):
AAATGAAAATTTTTGAATAGTTAATGACC
Found at i:796370 original size:29 final size:30
Alignment explanation
Indices: 796311--796382 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
796301 TTAGTAACTT
796311 AAATGAAAATTTTTGAATAGTTCAATGACCA
1 AAATGAAAATTTTT-AATAGTTCAATGACCA
* *
796342 AATTGAAAATTTTT-TTAGTT-AAGTGACCA
1 AAATGAAAATTTTTAATAGTTCAA-TGACCA
796371 AAATGAAAATTT
1 AAATGAAAATTT
796383 ACTCATAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 2 0.05
29 22 0.59
31 13 0.35
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.36
Consensus pattern (30 bp):
AAATGAAAATTTTTAATAGTTCAATGACCA
Found at i:797456 original size:2 final size:2
Alignment explanation
Indices: 797449--797476 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
797439 AGGAATTGGG
797449 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
797477 CGAACTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:798152 original size:6 final size:6
Alignment explanation
Indices: 798143--798167 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
798133 GCTCAGTCAA
798143 AAGCTC AAGCTC AAGCTC AAGCTC A
1 AAGCTC AAGCTC AAGCTC AAGCTC A
798168 TGCCCAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.16, T:0.16
Consensus pattern (6 bp):
AAGCTC
Found at i:811931 original size:66 final size:66
Alignment explanation
Indices: 811850--811982 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
811840 CTATATATGA
811850 TTCTCTTACCGTAAATTTAGACTCTAACTAATTGTGGTTCTTTACAGACAAATGTTTTACCACTG
1 TTCTCTTACCGTAAATTTAGACTCTAACTAATTGTGGTTCTTTACAGACAAATGTTTTACCACTG
811915 C
66 C
811916 TTCTCTTACCGTAAATTTAGACTCTAACTAATTGTGGTTCTTTACAGACAAATGTTTTACCACTG
1 TTCTCTTACCGTAAATTTAGACTCTAACTAATTGTGGTTCTTTACAGACAAATGTTTTACCACTG
811981 C
66 C
811982 T
1 T
811983 ATAGATGCTC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (66 bp):
TTCTCTTACCGTAAATTTAGACTCTAACTAATTGTGGTTCTTTACAGACAAATGTTTTACCACTG
C
Found at i:821048 original size:26 final size:25
Alignment explanation
Indices: 820989--821053 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 25
820979 TTAACATTAT
*
820989 TTTTAAAAAGTGTTTTTGAAAAGTG
1 TTTTAAAAAGTTTTTTTGAAAAGTG
* *
821014 TGGTGAAAAAGTTTTTTTGAGAAA-TAG
1 T-TTTAAAAAGTTTTTTTGA-AAAGT-G
*
821041 TTTTAAAATGTTT
1 TTTTAAAAAGTTT
821054 GGTTAAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
25 1 0.03
26 25 0.81
27 5 0.16
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (25 bp):
TTTTAAAAAGTTTTTTTGAAAAGTG
Found at i:826443 original size:29 final size:29
Alignment explanation
Indices: 826410--826465 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
826400 TATCTTCTAT
*
826410 TAAGAATAGCGTTTTAATATAATAATATA
1 TAAGAATAACGTTTTAATATAATAATATA
* * *
826439 TAAGAATAATGTTTTGATATGATAATA
1 TAAGAATAACGTTTTAATATAATAATA
826466 AAAATGGGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.39
Consensus pattern (29 bp):
TAAGAATAACGTTTTAATATAATAATATA
Found at i:832424 original size:31 final size:30
Alignment explanation
Indices: 832358--832429 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
832348 ATCACATTTA
* * **
832358 ACAAAACAGTCACTCAACTTTGAAAATGTG
1 ACAAAACAGTCACTAAACTTTCAAAAAATG
*
832388 ACAAAACAGTCACTAAAGTTATCAAAAAATG
1 ACAAAACAGTCACTAAACTT-TCAAAAAATG
*
832419 ACAAAATAGTC
1 ACAAAACAGTC
832430 CTCTTATTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 18 0.51
31 17 0.49
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (30 bp):
ACAAAACAGTCACTAAACTTTCAAAAAATG
Found at i:833388 original size:30 final size:31
Alignment explanation
Indices: 833324--833395 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
833314 ACAACAAGAA
* * *
833324 GATTATTTTGTGATTTTTCGATAATTTTAGT
1 GATTATTTTGTCATTTTTCGATAAGTTGAGT
833355 GATTATTTTGTCATATTTTC-A-AAGTTGAGT
1 GATTATTTTGTCAT-TTTTCGATAAGTTGAGT
*
833385 GATTGTTTTGT
1 GATTATTTTGT
833396 TAAATGCAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 17 0.47
31 14 0.39
32 5 0.14
ACGTcount: A:0.22, C:0.04, G:0.18, T:0.56
Consensus pattern (31 bp):
GATTATTTTGTCATTTTTCGATAAGTTGAGT
Found at i:842174 original size:24 final size:23
Alignment explanation
Indices: 842142--842207 Score: 82
Period size: 24 Copynumber: 2.9 Consensus size: 23
842132 GTTTTGATGC
842142 TTTTTTTACTGTTTTGATTGGTG
1 TTTTTTTACTGTTTTGATTGGTG
*
842165 TTTTTTTTACTGTTTTTGA--GTTG
1 -TTTTTTTACTG-TTTTGATTGGTG
*
842188 TTTTTTTATTGTTTTGATTG
1 TTTTTTTACTGTTTTGATTG
842208 CTATTTTCGT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
21 6 0.16
22 10 0.27
23 4 0.11
24 11 0.30
25 6 0.16
ACGTcount: A:0.09, C:0.03, G:0.18, T:0.70
Consensus pattern (23 bp):
TTTTTTTACTGTTTTGATTGGTG
Found at i:842191 original size:22 final size:24
Alignment explanation
Indices: 842142--842202 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 24
842132 GTTTTGATGC
842142 TTTTTTTACTG-TTTTGATTGGTGT
1 TTTTTTTACTGTTTTTGA-TGGTGT
*
842166 TTTTTTTACTGTTTTTGA-GTTG-
1 TTTTTTTACTGTTTTTGATGGTGT
*
842188 TTTTTTTATTGTTTT
1 TTTTTTTACTGTTTT
842203 GATTGCTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 14 0.41
23 3 0.09
24 11 0.32
25 6 0.18
ACGTcount: A:0.08, C:0.03, G:0.16, T:0.72
Consensus pattern (24 bp):
TTTTTTTACTGTTTTTGATGGTGT
Found at i:842268 original size:32 final size:31
Alignment explanation
Indices: 842196--842280 Score: 82
Period size: 32 Copynumber: 2.6 Consensus size: 31
842186 TGTTTTTTTA
* *
842196 TTGTTTTGATTGCTATTTTCGTGTTATTTTTG
1 TTGTTTT-ATTGCTATTTTTGTGTTATTTATG
*
842228 CTGTTTTTATTGCTATTTTTGTTGTT-TTTAATG
1 TTG-TTTTATTGCTATTTTTG-TGTTATTT-ATG
* *
842261 TTGTTTTACTGTTATTTTTG
1 TTGTTTTATTGCTATTTTTG
842281 CTGCTGTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
32 32 0.73
33 12 0.27
ACGTcount: A:0.11, C:0.06, G:0.16, T:0.67
Consensus pattern (31 bp):
TTGTTTTATTGCTATTTTTGTGTTATTTATG
Found at i:842291 original size:44 final size:44
Alignment explanation
Indices: 842238--842323 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
842228 CTGTTTTTAT
*
842238 TGCTATTTTTGTTGTT-TTTAATGTTGTTT-TACTGTTATTTTTGC
1 TGCTATTTTTGTTGTTATTT-ATGTTGTTTGGA-TGTTATTTTTGC
* *
842282 TGCTGTTTTTGTTGTTATTTTTGTTGTTTGGATGTTATTTTT
1 TGCTATTTTTGTTGTTATTTATGTTGTTTGGATGTTATTTTT
842324 TATGCGTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 33 0.89
45 4 0.11
ACGTcount: A:0.09, C:0.05, G:0.19, T:0.67
Consensus pattern (44 bp):
TGCTATTTTTGTTGTTATTTATGTTGTTTGGATGTTATTTTTGC
Found at i:851702 original size:27 final size:26
Alignment explanation
Indices: 851672--851753 Score: 69
Period size: 27 Copynumber: 3.1 Consensus size: 26
851662 GCACCTGCTG
851672 ACGTGGCACTATTTTGTCTTATATGCC
1 ACGTGGCA-TATTTTGTCTTATATGCC
* * * * *
851699 ACGTCAGCATATAATTAT-TT-TTTGCTG
1 ACGT-GGCATAT-TTTGTCTTATATGC-C
851726 ACGTGGCATATTTTGTCTTATATGCC
1 ACGTGGCATATTTTGTCTTATATGCC
851752 AC
1 AC
851754 ATCAGCAGTT
Statistics
Matches: 40, Mismatches: 10, Indels: 11
0.66 0.16 0.18
Matches are distributed among these distances:
25 3 0.08
26 14 0.35
27 17 0.43
28 6 0.15
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (26 bp):
ACGTGGCATATTTTGTCTTATATGCC
Found at i:853160 original size:26 final size:25
Alignment explanation
Indices: 853092--853162 Score: 63
Period size: 26 Copynumber: 2.8 Consensus size: 25
853082 TTTAAAAGGT
* *
853092 ATATATTAATTTTAATCTAATTTATA
1 ATATA-TAATTTTAATTTAATTAATA
** *
853118 ATATATAA-TACAGATTTGATATAATA
1 ATATATAATTTTA-ATTTAAT-TAATA
853144 ATATATAATTTTAATTTAA
1 ATATATAATTTTAATTTAA
853163 AAGGATATTG
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
24 2 0.06
25 8 0.24
26 22 0.65
27 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (25 bp):
ATATATAATTTTAATTTAATTAATA
Found at i:857625 original size:19 final size:19
Alignment explanation
Indices: 857593--857648 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
857583 TTTTTTAAAA
857593 TATAAATA-TTTGAATTTT
1 TATAAATATTTTGAATTTT
857611 TATAAATATTTTGAA-TTT
1 TATAAATATTTTGAATTTT
*
857629 TAAAAATTATTTTG-ATTTT
1 TATAAA-TATTTTGAATTTT
857648 T
1 T
857649 TTATTTTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 17 0.50
19 17 0.50
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:858352 original size:16 final size:16
Alignment explanation
Indices: 858316--858348 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
858306 GTTTTTTAAT
858316 AATTTAATAATATATA
1 AATTTAATAATATATA
*
858332 AATTTTATAATA-ATA
1 AATTTAATAATATATA
858347 AA
1 AA
858349 ATTTGTATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTTAATAATATATA
Found at i:858526 original size:19 final size:20
Alignment explanation
Indices: 858504--858551 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
858494 ATAATTATTT
*
858504 ATTTTATATATATAATTA-C
1 ATTTTATATATATAATGATC
* * *
858523 ATTTAATATTTTTAATGATC
1 ATTTTATATATATAATGATC
858543 ATTTTATAT
1 ATTTTATAT
858552 TTTATAGATG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTTATATATATAATGATC
Found at i:870817 original size:20 final size:20
Alignment explanation
Indices: 870792--870834 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
870782 TTGTTTGGAA
*
870792 CTTTTTCCAGGATTCTTGAT
1 CTTTTTCCAGGATTCTTCAT
*
870812 CTTTTTCTAGGATTCTTCAT
1 CTTTTTCCAGGATTCTTCAT
870832 CTT
1 CTT
870835 AAAATATTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.21, G:0.12, T:0.53
Consensus pattern (20 bp):
CTTTTTCCAGGATTCTTCAT
Found at i:876162 original size:16 final size:17
Alignment explanation
Indices: 876131--876165 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
876121 AAAAATTTAC
876131 TTTATAAAATAAATAAA
1 TTTATAAAATAAATAAA
*
876148 TTTATATAA-AAATAAA
1 TTTATAAAATAAATAAA
876164 TT
1 TT
876166 AATCTCTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTATAAAATAAATAAA
Found at i:882747 original size:6 final size:6
Alignment explanation
Indices: 882731--882762 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
882721 TTTACACTCT
882731 CAATT- CAATTA CAATTA CAATTA CAATTA CAA
1 CAATTA CAATTA CAATTA CAATTA CAATTA CAA
882763 ATTCCTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (6 bp):
CAATTA
Found at i:887159 original size:18 final size:20
Alignment explanation
Indices: 887120--887165 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
887110 ACTTTTCACA
887120 TTTCATCTTCTTTAACAACC
1 TTTCATCTTCTTTAACAACC
887140 TTTCATCTTCTTT-A-AACC
1 TTTCATCTTCTTTAACAACC
887158 TTTCATCT
1 TTTCATCT
887166 CCTTGTAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 12 0.46
19 1 0.04
20 13 0.50
ACGTcount: A:0.22, C:0.28, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTCATCTTCTTTAACAACC
Found at i:887332 original size:3 final size:3
Alignment explanation
Indices: 887324--887372 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
887314 TGTTCTTTCC
887324 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
887371 AT
1 AT
887373 AACAGAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:888951 original size:22 final size:19
Alignment explanation
Indices: 888926--888993 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 19
888916 TTGGGGGTTT
888926 TTTTTTACTATTTTAGTTG
1 TTTTTTACTATTTTAGTTG
* *
888945 CTATTTTTTGCTGTTTTATGTTG
1 ---TTTTTTACTATTTTA-GTTG
*
888968 TTTTTTACTATTTTGGTTG
1 TTTTTTACTATTTTAGTTG
888987 TTGTTTT
1 TT-TTTT
888994 CGTGTTGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 6 0.15
20 16 0.41
22 13 0.33
23 4 0.10
ACGTcount: A:0.10, C:0.06, G:0.15, T:0.69
Consensus pattern (19 bp):
TTTTTTACTATTTTAGTTG
Found at i:889020 original size:32 final size:31
Alignment explanation
Indices: 888948--889021 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 31
888938 TTAGTTGCTA
*
888948 TTTTTTGCTGTTTTATGTTGTTTTTTACTAT
1 TTTTTTGTTGTTTTATGTTGTTTTTTACTAT
* *
888979 TTTGGTTGTTGTTTTCGTGTTG-TTTTTACTAT
1 TTT-TTTGTTGTTTT-ATGTTGTTTTTTACTAT
889011 TATTTTTGTTG
1 T-TTTTTGTTG
889022 CTATTTTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 3 0.08
32 26 0.72
33 7 0.19
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.69
Consensus pattern (31 bp):
TTTTTTGTTGTTTTATGTTGTTTTTTACTAT
Found at i:889026 original size:12 final size:12
Alignment explanation
Indices: 889011--889035 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
889001 TTTTTACTAT
889011 TATTTTTGTTGC
1 TATTTTTGTTGC
889023 TATTTTTGTTGC
1 TATTTTTGTTGC
889035 T
1 T
889036 TTTAATGTTG
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:0.08, C:0.08, G:0.16, T:0.68
Consensus pattern (12 bp):
TATTTTTGTTGC
Found at i:889033 original size:33 final size:31
Alignment explanation
Indices: 888948--889039 Score: 80
Period size: 32 Copynumber: 2.9 Consensus size: 31
888938 TTAGTTGCTA
* *
888948 TTTTTTGCTG-TTTTATGTTGTTTTTTACTAT
1 TTTTTTGTTGCTTTTTTGTTG-TTTTTACTAT
* *
888979 TTTGGTTGTTG-TTTTCGTGTTGTTTTTACTAT
1 TTT-TTTGTTGCTTTT-TTGTTGTTTTTACTAT
*
889011 TATTTTTGTTGCTATTTTTGTTGCTTTTA
1 T-TTTTTGTTGCT-TTTTTGTTGTTTTTA
889040 ATGTTGTTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
31 3 0.06
32 26 0.52
33 18 0.36
34 3 0.06
ACGTcount: A:0.09, C:0.07, G:0.16, T:0.68
Consensus pattern (31 bp):
TTTTTTGTTGCTTTTTTGTTGTTTTTACTAT
Found at i:889250 original size:25 final size:25
Alignment explanation
Indices: 889221--889293 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 25
889211 AATATAAAAT
* *
889221 TTTTTAATGTATTTTAAATTTATTTA
1 TTTTTAATAT-TTTTAAATGTATTTA
889247 TTTTTAATATTTTTAAATGTATTTGA
1 TTTTTAATATTTTTAAATGTATTT-A
*
889273 TATATTTTATATTTTTTAAAT
1 T-T-TTTAATA-TTTTTAAAT
889294 TTGTTGTATG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
25 13 0.32
26 11 0.28
27 1 0.03
28 6 0.15
29 9 0.22
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (25 bp):
TTTTTAATATTTTTAAATGTATTTA
Found at i:900989 original size:22 final size:22
Alignment explanation
Indices: 900964--901014 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
900954 TATTTGTTTG
900964 TTTTTACA-TATTTATTAAATTA
1 TTTTTACAGT-TTTATTAAATTA
**
900986 TTTTTTTAGTTTTATTAAATTA
1 TTTTTACAGTTTTATTAAATTA
901008 TTATTTA
1 TT-TTTA
901015 AAACCTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTTACAGTTTTATTAAATTA
Found at i:906998 original size:6 final size:6
Alignment explanation
Indices: 906987--907014 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
906977 CAACAGCAGT
906987 ACCAGC ACCAGC ACCAGC ACCAGC ACCA
1 ACCAGC ACCAGC ACCAGC ACCAGC ACCA
907015 ACAACAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.50, G:0.14, T:0.00
Consensus pattern (6 bp):
ACCAGC
Found at i:911748 original size:17 final size:17
Alignment explanation
Indices: 911726--911760 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
911716 GTTAATACAC
911726 TATTTGATGCATGAGTT
1 TATTTGATGCATGAGTT
911743 TATTTGATGCATGAGTT
1 TATTTGATGCATGAGTT
911760 T
1 T
911761 GCCTTCAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.49
Consensus pattern (17 bp):
TATTTGATGCATGAGTT
Found at i:925302 original size:17 final size:17
Alignment explanation
Indices: 925280--925320 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
925270 AGGTGGAGAA
* * *
925280 CTTGTTCGTTGAGAGTT
1 CTTGTTAGTAGAGAATT
925297 CTTGTTAGTAGAGAATT
1 CTTGTTAGTAGAGAATT
925314 CTTGTTA
1 CTTGTTA
925321 AGGTGAAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.24, T:0.46
Consensus pattern (17 bp):
CTTGTTAGTAGAGAATT
Found at i:933734 original size:5 final size:5
Alignment explanation
Indices: 933724--933749 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
933714 CACAAAAAAA
933724 TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT T
933750 GTTATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:934033 original size:3 final size:3
Alignment explanation
Indices: 934027--934059 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
934017 AGGCACGTGC
934027 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
934060 TTTGTAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:936998 original size:21 final size:21
Alignment explanation
Indices: 936963--937028 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
936953 TTAAAAATAG
* * * *
936963 TTGTGACACTAAAATTCATTA
1 TTGTGACAGTGAAATTGAGTA
936984 TTGTGACAGTGAAATTGAGTA
1 TTGTGACAGTGAAATTGAGTA
*
937005 TTGT-AGAGTGAAATTGAGTA
1 TTGTGACAGTGAAATTGAGTA
937025 TTGT
1 TTGT
937029 AACGGTGAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 19 0.47
21 21 0.52
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (21 bp):
TTGTGACAGTGAAATTGAGTA
Found at i:937016 original size:20 final size:20
Alignment explanation
Indices: 936991--937029 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
936981 TTATTGTGAC
936991 AGTGAAATTGAGTATTGTAG
1 AGTGAAATTGAGTATTGTAG
937011 AGTGAAATTGAGTATTGTA
1 AGTGAAATTGAGTATTGTA
937030 ACGGTGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (20 bp):
AGTGAAATTGAGTATTGTAG
Found at i:950270 original size:21 final size:20
Alignment explanation
Indices: 950222--950296 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
950212 TTAGAGTTTC
* * **
950222 AATCGATTCAAACAATAATG
1 AATCGATTCAAAAAACAAAA
*
950242 AATCGATTTAAAACAACAAAA
1 AATCGATTCAAAA-AACAAAA
* * *
950263 AATTGATTGAAATAAACAAAG
1 AATCGATTCAAA-AAACAAAA
950284 AATCGATTCAAAA
1 AATCGATTCAAAA
950297 GAAGCAATAT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 12 0.28
21 30 0.70
22 1 0.02
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.23
Consensus pattern (20 bp):
AATCGATTCAAAAAACAAAA
Found at i:950345 original size:55 final size:55
Alignment explanation
Indices: 950284--950588 Score: 288
Period size: 55 Copynumber: 5.4 Consensus size: 55
950274 ATAAACAAAG
* * * *
950284 AATCGATTCAAAAGAAGCAATATTCCACCATAACAATCGATTTGAACATATAATC
1 AATCGATTCAAAAGAAGCAATATTCCAACATAACAATCAATTTAAACATATAAAC
*
950339 AATCGATTCAAAAGAAGCAGA-ATTCCAACATGACAATCAATTTAAACATATAAAC
1 AATCGATTCAAAAGAAGCA-ATATTCCAACATAACAATCAATTTAAACATATAAAC
* * * ** * *
950394 AATCGATCCAAAATATGCGGTATTCCAACGTAACAATTAATTTAAACATATAAAC
1 AATCGATTCAAAAGAAGCAATATTCCAACATAACAATCAATTTAAACATATAAAC
* * * * * *
950449 AATCTATTTAAAAGAAGAAAAAACAATATTCTACCATAACAATCGATTTAAACATAAAAAC
1 AATCGATTCAAAAGAAG------CAATATTCCAACATAACAATCAATTTAAACATATAAAC
** * * * * * *
950510 AATATATTCGAAAGAAGCAGTATTTCAACATGACAATCATTTTAAACATAAAAAC
1 AATCGATTCAAAAGAAGCAATATTCCAACATAACAATCAATTTAAACATATAAAC
* *
950565 AATTGATCCAAAAGAAGCAATATT
1 AATCGATTCAAAAGAAGCAATATT
950589 TTTGAGAAAT
Statistics
Matches: 201, Mismatches: 41, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
55 156 0.78
56 1 0.00
61 44 0.22
ACGTcount: A:0.50, C:0.17, G:0.09, T:0.25
Consensus pattern (55 bp):
AATCGATTCAAAAGAAGCAATATTCCAACATAACAATCAATTTAAACATATAAAC
Found at i:950578 original size:116 final size:116
Alignment explanation
Indices: 950371--950581 Score: 253
Period size: 116 Copynumber: 1.8 Consensus size: 116
950361 TTCCAACATG
* * * * * * *
950371 ACAATCAATTTAAACATATAAACAATCGATCCAAAATATGCGGTATTCCAACGTAACAATTAATT
1 ACAATCAATTTAAACATAAAAACAATAGATCCAAAAGAAGCAGTATTCCAACATAACAATCAATT
* **
950436 TAAACATATAAACAATCTATTTAAAAGAAGAAAAAACAATATTCTACCATA
66 TAAACATAAAAACAATCTATCCAAAAGAAGAAAAAACAATATTCTACCATA
* * * * * * *
950487 ACAATCGATTTAAACATAAAAACAATATATTCGAAAGAAGCAGTATTTCAACATGACAATCATTT
1 ACAATCAATTTAAACATAAAAACAATAGATCCAAAAGAAGCAGTATTCCAACATAACAATCAATT
950552 TAAACATAAAAACAAT-TGATCCAAAAGAAG
66 TAAACATAAAAACAATCT-ATCCAAAAGAAG
950582 CAATATTTTT
Statistics
Matches: 77, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
115 1 0.01
116 76 0.99
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.26
Consensus pattern (116 bp):
ACAATCAATTTAAACATAAAAACAATAGATCCAAAAGAAGCAGTATTCCAACATAACAATCAATT
TAAACATAAAAACAATCTATCCAAAAGAAGAAAAAACAATATTCTACCATA
Found at i:968000 original size:24 final size:25
Alignment explanation
Indices: 967954--968003 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
967944 GTTTGTTTAT
*
967954 TATTCATTAATATTGTTCGTGAACA
1 TATTCATTAATATTGTTCATGAACA
967979 TATTCAATT-ATA-TGTTCATGAACA
1 TATTC-ATTAATATTGTTCATGAACA
968003 T
1 T
968004 GTTCGTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 12 0.52
25 8 0.35
26 3 0.13
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (25 bp):
TATTCATTAATATTGTTCATGAACA
Found at i:968078 original size:28 final size:30
Alignment explanation
Indices: 968017--968079 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
968007 CGTGAACATT
* *
968017 AAATAAACGAACATGAACACAAATAATTTT
1 AAATTAACGAACATGAACACAAATAATTTA
968047 AAATTAACGAACATGAACA-AAA-AATTTA
1 AAATTAACGAACATGAACACAAATAATTTA
968075 AAATT
1 AAATT
968080 CTTAAAGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 10 0.32
29 3 0.10
30 18 0.58
ACGTcount: A:0.59, C:0.11, G:0.06, T:0.24
Consensus pattern (30 bp):
AAATTAACGAACATGAACACAAATAATTTA
Found at i:968388 original size:22 final size:24
Alignment explanation
Indices: 968356--968403 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
968346 TGTACTCTCT
*
968356 TTTTTTCCAGTTAAACT-TTATTA
1 TTTTTTCCAGTTAAACTATGATTA
968379 TTTTTT-CAGTTAAACTATGATTA
1 TTTTTTCCAGTTAAACTATGATTA
968402 TT
1 TT
968404 CTCAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.56
Consensus pattern (24 bp):
TTTTTTCCAGTTAAACTATGATTA
Found at i:978896 original size:3 final size:3
Alignment explanation
Indices: 978888--978912 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
978878 AAATAAAATG
978888 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
978913 TAGGCATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:978948 original size:15 final size:15
Alignment explanation
Indices: 978928--978957 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
978918 ATTTTTATTT
978928 TTATTATTGAAAGTA
1 TTATTATTGAAAGTA
978943 TTATTATTGAAAGTA
1 TTATTATTGAAAGTA
978958 GATGCCATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (15 bp):
TTATTATTGAAAGTA
Found at i:980372 original size:9 final size:9
Alignment explanation
Indices: 980358--980383 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
980348 AAATTATCTT
980358 ATTTGGTTC
1 ATTTGGTTC
980367 ATTTGGTTC
1 ATTTGGTTC
980376 ATTTGGTT
1 ATTTGGTT
980384 AGAAGATGAA
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:0.12, C:0.08, G:0.23, T:0.58
Consensus pattern (9 bp):
ATTTGGTTC
Found at i:989763 original size:18 final size:16
Alignment explanation
Indices: 989729--989777 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
989719 TCAGTTGTAA
*
989729 TTAATTTAAAA-TT-T
1 TTAATTAAAAATTTAT
989743 TTAATTAATCAAATTTAT
1 TTAATTAA--AAATTTAT
989761 TTAATTAAAAATTTAT
1 TTAATTAAAAATTTAT
989777 T
1 T
989778 ATCATCCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 7 0.23
16 12 0.40
17 2 0.07
18 9 0.30
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATTAAAAATTTAT
Found at i:996378 original size:15 final size:15
Alignment explanation
Indices: 996342--996379 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
996332 TATTAAGATG
996342 ATTATAT-AATAAAA
1 ATTATATAAATAAAA
*
996356 TTTA-ATAAATAAAA
1 ATTATATAAATAAAA
996370 ATTATATAAA
1 ATTATATAAA
996380 ATTATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 2 0.10
14 13 0.65
15 5 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTATATAAATAAAA
Found at i:998543 original size:19 final size:19
Alignment explanation
Indices: 998503--998567 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 19
998493 TCAAACACAC
*
998503 TTTTGTCTTTTTTGTCT--T
1 TTTTGTCTTTTTT-TCTCAA
998521 TTTTGTCTTTTTTTCTCAA
1 TTTTGTCTTTTTTTCTCAA
* *
998540 TTTTCT-TTTTTTTTTCAA
1 TTTTGTCTTTTTTTCTCAA
998558 TTTT-TCTTTT
1 TTTTGTCTTTT
998568 CGATTTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.10
18 32 0.78
19 5 0.12
ACGTcount: A:0.06, C:0.12, G:0.05, T:0.77
Consensus pattern (19 bp):
TTTTGTCTTTTTTTCTCAA
Found at i:998552 original size:9 final size:9
Alignment explanation
Indices: 998503--998533 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
998493 TCAAACACAC
998503 TTTTGTCTT
1 TTTTGTCTT
998512 TTTTGTCTT
1 TTTTGTCTT
998521 TTTTGTCTT
1 TTTTGTCTT
998530 TTTT
1 TTTT
998534 TCTCAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.81
Consensus pattern (9 bp):
TTTTGTCTT
Found at i:998567 original size:13 final size:12
Alignment explanation
Indices: 998546--998580 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
998536 TCAATTTTCT
998546 TTTTTTTTTCAA
1 TTTTTTTTTCAA
*
998558 TTTTTCTTTTCGA
1 TTTTT-TTTTCAA
998571 TTTTTTTTTC
1 TTTTTTTTTC
998581 TAAACAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.09, C:0.11, G:0.03, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:999511 original size:12 final size:12
Alignment explanation
Indices: 999494--999525 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
999484 TTGCATAATT
999494 AAAATAAAACTA
1 AAAATAAAACTA
999506 AAAATAAAACTA
1 AAAATAAAACTA
*
999518 AATATAAA
1 AAAATAAA
999526 TATAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (12 bp):
AAAATAAAACTA
Found at i:999525 original size:18 final size:18
Alignment explanation
Indices: 999494--999541 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
999484 TTGCATAATT
*
999494 AAAATAAA-ACTAAAAATA
1 AAAATAAATA-TAAATATA
*
999512 AAACTAAATATAAATATA
1 AAAATAAATATAAATATA
*
999530 AATATAAATATA
1 AAAATAAATATA
999542 CTAATTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 24 0.96
19 1 0.04
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATAAATATAAATATA
Found at i:999538 original size:6 final size:6
Alignment explanation
Indices: 999516--999541 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
999506 AAAATAAAAC
999516 TAAATA TAAATA TAAATA TAAATA TA
1 TAAATA TAAATA TAAATA TAAATA TA
999542 CTAATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:1008788 original size:10 final size:10
Alignment explanation
Indices: 1008771--1008828 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
1008761 GCCTAACTAG
1008771 AAATATATAT
1 AAATATATAT
*
1008781 ATATATATAT
1 AAATATATAT
*
1008791 -AATATCATAA
1 AAATAT-ATAT
1008801 AAACTATATAT
1 AAA-TATATAT
*
1008812 AAAAATATAT
1 AAATATATAT
*
1008822 AGATATA
1 AAATATA
1008829 GGATAAAGGG
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
9 4 0.11
10 23 0.61
11 8 0.21
12 3 0.08
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (10 bp):
AAATATATAT
Found at i:1015574 original size:21 final size:21
Alignment explanation
Indices: 1015549--1015596 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1015539 TTTTAGTAAG
*
1015549 AATATA-GAAAATTAATATTTT
1 AATATATGAAAAGTAA-ATTTT
1015570 AATATATGAAAAGTAAATTTT
1 AATATATGAAAAGTAAATTTT
1015591 AA-ATAT
1 AATATAT
1015597 TTTTTAAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.16
21 13 0.52
22 8 0.32
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (21 bp):
AATATATGAAAAGTAAATTTT
Found at i:1015942 original size:17 final size:17
Alignment explanation
Indices: 1015907--1015958 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
1015897 AATAATTGAA
* *
1015907 TTATAACTTTTTATA-T
1 TTATAATTTTTTAAATT
1015923 TTATAATTTTTTAAATT
1 TTATAATTTTTTAAATT
1015940 TTATATATTTTTT-AATT
1 TTATA-ATTTTTTAAATT
1015957 TT
1 TT
1015959 CAAATGATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
16 13 0.41
17 12 0.38
18 7 0.22
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATAATTTTTTAAATT
Found at i:1015951 original size:18 final size:16
Alignment explanation
Indices: 1015907--1015958 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
1015897 AATAATTGAA
*
1015907 TTATAACTTTTT-ATAT
1 TTATAATTTTTTAAT-T
1015923 TTATAATTTTTTAAATT
1 TTATAATTTTTT-AATT
1015940 TTATATATTTTTTAATT
1 TTATA-ATTTTTTAATT
1015957 TT
1 TT
1015959 CAAATGATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 11 0.34
17 12 0.38
18 9 0.28
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATAATTTTTTAATT
Found at i:1015958 original size:25 final size:24
Alignment explanation
Indices: 1015914--1015963 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
1015904 GAATTATAAC
*
1015914 TTTTTATATTTATAATTTTTTAAA
1 TTTTTATATTTATAATTTTTCAAA
*
1015938 TTTTATATATTTTTTAA-TTTTCAAA
1 TTTT-TATA-TTTATAATTTTTCAAA
1015963 T
1 T
1015964 GATGATGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 4 0.18
25 12 0.55
26 6 0.27
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTTTATATTTATAATTTTTCAAA
Found at i:1021140 original size:16 final size:17
Alignment explanation
Indices: 1021119--1021151 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1021109 TTCTTTCTTC
*
1021119 CTATTTCTTTT-TATTT
1 CTATTTATTTTATATTT
1021135 CTATTTATTTTATATTT
1 CTATTTATTTTATATTT
1021152 TACTAGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (17 bp):
CTATTTATTTTATATTT
Found at i:1021344 original size:13 final size:13
Alignment explanation
Indices: 1021326--1021361 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
1021316 TTTTTTAGGC
1021326 TCCTATCTTGTAA
1 TCCTATCTTGTAA
1021339 TCCTATCTTGTAA
1 TCCTATCTTGTAA
1021352 TCCTATCTTG
1 TCCTATCTTG
1021362 ATTACGCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.19, C:0.25, G:0.08, T:0.47
Consensus pattern (13 bp):
TCCTATCTTGTAA
Found at i:1023617 original size:37 final size:37
Alignment explanation
Indices: 1023567--1023638 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
1023557 CCTTTCTACA
1023567 CCTTTATTTAAAAAATTCAAATTCAATTAAAAATATT
1 CCTTTATTTAAAAAATTCAAATTCAATTAAAAATATT
1023604 CCTTTATTTAAAAAATTCAAATTCAATTAAAAATA
1 CCTTTATTTAAAAAATTCAAATTCAATTAAAAATA
1023639 CTAAAAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (37 bp):
CCTTTATTTAAAAAATTCAAATTCAATTAAAAATATT
Found at i:1023637 original size:18 final size:19
Alignment explanation
Indices: 1023574--1023636 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
1023564 ACACCTTTAT
1023574 TTAAAAAATTCAAATTCAA
1 TTAAAAAATTCAAATTCAA
* * *
1023593 TTAAAAATATTC--CTTTAT
1 TTAAAAA-ATTCAAATTCAA
1023611 TTAAAAAATTCAAATTCAA
1 TTAAAAAATTCAAATTCAA
1023630 TTAAAAA
1 TTAAAAA
1023637 TACTAAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 4 0.11
18 10 0.29
19 17 0.49
20 4 0.11
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (19 bp):
TTAAAAAATTCAAATTCAA
Found at i:1044960 original size:24 final size:24
Alignment explanation
Indices: 1044928--1044974 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1044918 CGCAAGTTCA
1044928 ATACATTTACGCTCGTCAGCTAAG
1 ATACATTTACGCTCGTCAGCTAAG
*
1044952 ATACGTTTACGCTCGTCAGCTAA
1 ATACATTTACGCTCGTCAGCTAA
1044975 TATAAGAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (24 bp):
ATACATTTACGCTCGTCAGCTAAG
Found at i:1058719 original size:2 final size:2
Alignment explanation
Indices: 1058712--1058736 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1058702 TAATTTATGT
1058712 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
1058737 TAAAATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1059293 original size:23 final size:23
Alignment explanation
Indices: 1059267--1059310 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1059257 AATATGAATT
1059267 TTAAAATCTACAAAATAAAAGAA
1 TTAAAATCTACAAAATAAAAGAA
* **
1059290 TTAAATTCTTGAAAATAAAAG
1 TTAAAATCTACAAAATAAAAG
1059311 TGTATGGACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (23 bp):
TTAAAATCTACAAAATAAAAGAA
Found at i:1060093 original size:15 final size:15
Alignment explanation
Indices: 1060070--1060103 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1060060 TGTTATGGGG
*
1060070 TTTTCTTTTTTTTTC
1 TTTTCTTTTTTTTGC
*
1060085 TTTTTTTTTTTTTGC
1 TTTTCTTTTTTTTGC
1060100 TTTT
1 TTTT
1060104 GCTGGATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (15 bp):
TTTTCTTTTTTTTGC
Found at i:1081091 original size:13 final size:12
Alignment explanation
Indices: 1081066--1081090 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1081056 TTTTAAAAAA
1081066 TCAAATTTTTTT
1 TCAAATTTTTTT
1081078 TCAAATTTTTTT
1 TCAAATTTTTTT
1081090 T
1 T
1081091 TATGATTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TCAAATTTTTTT
Found at i:1081158 original size:31 final size:33
Alignment explanation
Indices: 1081119--1081187 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 33
1081109 TTATAAAAAT
* * *
1081119 TAAT-TTAAAGTAAACCTAATA-TTATTTTTAA
1 TAATATTAAAATAAACATAATATTTATATTTAA
*
1081150 -AATATTAAAATATACATAATATTTATATTTAA
1 TAATATTAAAATAAACATAATATTTATATTTAA
1081182 TAATAT
1 TAATAT
1081188 AATATATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
30 3 0.10
31 14 0.45
32 9 0.29
33 5 0.16
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (33 bp):
TAATATTAAAATAAACATAATATTTATATTTAA
Found at i:1081195 original size:32 final size:31
Alignment explanation
Indices: 1081135--1081195 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
1081125 AAAGTAAACC
*
1081135 TAATATTATTTTTAAAATATTAAAATATACA
1 TAATATTATATTTAAAATATTAAAATATACA
*
1081166 TAATATTTATATTTAATAATA-TAATATATA
1 TAATA-TTATATTTAA-AATATTAAAATATA
1081196 ATATTGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 5 0.19
32 17 0.65
33 4 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (31 bp):
TAATATTATATTTAAAATATTAAAATATACA
Found at i:1085531 original size:23 final size:25
Alignment explanation
Indices: 1085486--1085531 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1085476 ATAAAATTTA
*
1085486 TTATATTATTATAAAGATCAATATT
1 TTATATTATTATAAAGATAAATATT
*
1085511 TTATATT-TTATATA-ATAAATA
1 TTATATTATTATAAAGATAAATA
1085532 AAAAAAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 6 0.32
25 7 0.37
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (25 bp):
TTATATTATTATAAAGATAAATATT
Found at i:1086941 original size:13 final size:13
Alignment explanation
Indices: 1086923--1086963 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1086913 AAGGTGGAGA
1086923 AGAGGAAGAAGAG
1 AGAGGAAGAAGAG
1086936 AGAGG-AG-AGAG
1 AGAGGAAGAAGAG
* *
1086947 AGAAGAAGAAGAA
1 AGAGGAAGAAGAG
1086960 AGAG
1 AGAG
1086964 AACATATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 8 0.35
12 4 0.17
13 11 0.48
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (13 bp):
AGAGGAAGAAGAG
Found at i:1086963 original size:24 final size:23
Alignment explanation
Indices: 1086919--1086963 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1086909 AAATAAGGTG
* *
1086919 GAGAAGAGGAAGAAGAGAGAGGA
1 GAGAAGAAGAAGAAGAAAGAGGA
1086942 GAGAGAGAAGAAGAAGAAAGAG
1 GAGA-AGAAGAAGAAGAAAGAG
1086964 AACATATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (23 bp):
GAGAAGAAGAAGAAGAAAGAGGA
Found at i:1094154 original size:29 final size:28
Alignment explanation
Indices: 1094118--1094281 Score: 168
Period size: 29 Copynumber: 5.7 Consensus size: 28
1094108 TGTAAAAACA
*
1094118 TAATTTTGGAAAAGTTTAGGATCAAAATG
1 TAATTTT-GAAAAGTTTAGGGTCAAAATG
* **
1094147 TGATTTTGGGAAGTTTAGGGTCAAAATG
1 TAATTTTGAAAAGTTTAGGGTCAAAATG
* *
1094175 TTATTTTTGAAAAGTTTAAGGGT-TAAATG
1 -TAATTTTGAAAAGTTT-AGGGTCAAAATG
*
1094204 TAATTTTGAATAAGTTTAGGGTTAAAATG
1 TAATTTTGAA-AAGTTTAGGGTCAAAATG
* * *
1094233 TAATTTTTAAAAGTTCAGGAGTTAAAATG
1 TAATTTTGAAAAGTTTAGG-GTCAAAATG
* *
1094262 TGATTTTAAAAAGTTTAGGG
1 TAATTTTGAAAAGTTTAGGG
1094282 GTTAAAATAT
Statistics
Matches: 114, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
28 41 0.36
29 68 0.60
30 5 0.04
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.39
Consensus pattern (28 bp):
TAATTTTGAAAAGTTTAGGGTCAAAATG
Found at i:1094183 original size:58 final size:57
Alignment explanation
Indices: 1094118--1094281 Score: 181
Period size: 57 Copynumber: 2.9 Consensus size: 57
1094108 TGTAAAAACA
* *
1094118 TAATTTTGGAAAAGTTTAGGATCAAAATGTGATTTTG-GGAAGTTTAGGGTCAAAATG
1 TAATTTTTGAAAAGTTTAGGAT-AAAATGTGATTTTGAAGAAGTTTAGGGTCAAAATG
* * * * * *
1094175 TTATTTTTGAAAAGTTTAAGGGTTAAATGTAATTTTGAATAAGTTTAGGGTTAAAATG
1 TAATTTTTGAAAAGTTT-AGGATAAAATGTGATTTTGAAGAAGTTTAGGGTCAAAATG
* *
1094233 TAATTTTT-AAAAGTTCAGGAGTTAAAATGTGATTTT-AAAAAGTTTAGGG
1 TAATTTTTGAAAAGTTTAGGA--TAAAATGTGATTTTGAAGAAGTTTAGGG
1094282 GTTAAAATAT
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
56 3 0.03
57 46 0.52
58 40 0.45
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.39
Consensus pattern (57 bp):
TAATTTTTGAAAAGTTTAGGATAAAATGTGATTTTGAAGAAGTTTAGGGTCAAAATG
Found at i:1094284 original size:58 final size:57
Alignment explanation
Indices: 1094118--1094301 Score: 185
Period size: 58 Copynumber: 3.2 Consensus size: 57
1094108 TGTAAAAACA
* * * *** *
1094118 TAATTTTGGAAAAGTTTAGGA-TCAAAATGTGATTTTGGGAAGTTTAGGGTCAAAATG
1 TAATTTT-TAAAAGTTAAGGAGTTAAAATGTGATTTTAAAAAGTTTAGGGTTAAAATG
* * *
1094175 TTATTTTTGAAAAGTTTAAGG-GTT-AAATGTAATTTTGAATAAGTTTAGGGTTAAAATG
1 TAATTTTT-AAAAG-TTAAGGAGTTAAAATGTGATTTT-AAAAAGTTTAGGGTTAAAATG
* *
1094233 TAATTTTTAAAAGTTCAGGAGTTAAAATGTGATTTTAAAAAGTTTAGGGGTTAAAATA
1 TAATTTTTAAAAGTTAAGGAGTTAAAATGTGATTTTAAAAAGTTTA-GGGTTAAAATG
*
1094291 TGATTTTTAAA
1 TAATTTTTAAA
1094302 GAAAAGAGGG
Statistics
Matches: 105, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
56 5 0.05
57 39 0.37
58 61 0.58
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.40
Consensus pattern (57 bp):
TAATTTTTAAAAGTTAAGGAGTTAAAATGTGATTTTAAAAAGTTTAGGGTTAAAATG
Found at i:1095704 original size:6 final size:6
Alignment explanation
Indices: 1095693--1095726 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1095683 GAGTCATGGG
* *
1095693 TAAATT TAAATT TAAATC TAAATT TAAAAT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
1095727 ATATTTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:1108158 original size:29 final size:29
Alignment explanation
Indices: 1108124--1108304 Score: 152
Period size: 30 Copynumber: 6.2 Consensus size: 29
1108114 TAAAAATGCA
1108124 ATTTTGGAAAAGTTTAAGGTCAAAATGTG
1 ATTTTGGAAAAGTTTAAGGTCAAAATGTG
* * *
1108153 ACTTTGG-GAAGTTTATGGTCAAAATGTG
1 ATTTTGGAAAAGTTTAAGGTCAAAATGTG
* * * *
1108181 ATTTTTGAAAAGTTTAGGGGTTAAAATGTA
1 ATTTTGGAAAAGTTTA-AGGTCAAAATGTG
* * *
1108211 ATTTT-AAAGAAGTTTAAGGGTCAAAATATA
1 ATTTTGGAA-AAGTTTAA-GGTCAAAATGTG
* * *
1108241 ATTTTAGAGAAGTTTAGGGGTC-AAATGTG
1 ATTTTGGAAAAGTTTA-AGGTCAAAATGTG
* * *
1108270 ATTTTGGAAAAGTTTAGGGGTTAAAATATG
1 ATTTTGGAAAAGTTTA-AGGTCAAAATGTG
1108300 ATTTT
1 ATTTT
1108305 TAAAGAAAAT
Statistics
Matches: 123, Mismatches: 22, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
28 24 0.20
29 39 0.32
30 59 0.48
31 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (29 bp):
ATTTTGGAAAAGTTTAAGGTCAAAATGTG
Found at i:1108209 original size:30 final size:30
Alignment explanation
Indices: 1108110--1108305 Score: 168
Period size: 29 Copynumber: 6.7 Consensus size: 30
1108100 CAAACAATTC
* ** *
1108110 GGGGTAAAAATGCAATTTTGGAAAAGTTTA
1 GGGGTCAAAATGTGATTTTTGAAAAGTTTA
* * **
1108140 -AGGTCAAAATGTGA-CTTTGGGAAGTTTA
1 GGGGTCAAAATGTGATTTTTGAAAAGTTTA
*
1108168 -TGGTCAAAATGTGATTTTTGAAAAGTTTA
1 GGGGTCAAAATGTGATTTTTGAAAAGTTTA
* * *
1108197 GGGGTTAAAATGT-AATTTTAAAGAAGTTTA
1 GGGGTCAAAATGTGATTTTTGAA-AAGTTTA
* * * * *
1108227 AGGGTCAAAATATAATTTTAGAGAAGTTTA
1 GGGGTCAAAATGTGATTTTTGAAAAGTTTA
*
1108257 GGGGTC-AAATGTGATTTTGGAAAAGTTTA
1 GGGGTCAAAATGTGATTTTTGAAAAGTTTA
* *
1108286 GGGGTTAAAATATGATTTTT
1 GGGGTCAAAATGTGATTTTT
1108306 AAAGAAAATA
Statistics
Matches: 130, Mismatches: 31, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
28 23 0.18
29 52 0.40
30 50 0.38
31 5 0.04
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (30 bp):
GGGGTCAAAATGTGATTTTTGAAAAGTTTA
Found at i:1108274 original size:59 final size:61
Alignment explanation
Indices: 1108160--1108304 Score: 172
Period size: 59 Copynumber: 2.4 Consensus size: 61
1108150 GTGACTTTGG
* * *
1108160 GAAGTTT-ATGGTCAAAATGTGATTTTTGAAAAGTTTAGGGGTTAAAATGTAATTTT-AAA
1 GAAGTTTAAGGGTCAAAATATGATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTGAAA
* * * * *
1108219 GAAGTTTAAGGGTCAAAATATAATTTTAGAGAAGTTTAGGGG-TCAAATGTGATTTTGGAA
1 GAAGTTTAAGGGTCAAAATATGATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTGAAA
* *
1108279 -AAGTTTAGGGGTTAAAATATGATTTT
1 GAAGTTTAAGGGTCAAAATATGATTTT
1108305 TAAAGAAAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 42 0.58
60 31 0.42
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (61 bp):
GAAGTTTAAGGGTCAAAATATGATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTGAAA
Found at i:1108282 original size:89 final size:87
Alignment explanation
Indices: 1108110--1108311 Score: 246
Period size: 89 Copynumber: 2.3 Consensus size: 87
1108100 CAAACAATTC
* * * * * * *
1108110 GGGGTAAAAATGCAATTTTGGAA-AAGTTTAAGGTCAAAATGTGACTTTGGGAAGTTTATGGTCA
1 GGGGTTAAAATGTAATTTT-AAAGAAGTTTAAGGTCAAAATATAACTTTGAGAAGTTTAGGGTCA
*
1108174 AAATGTGATTTTTGAAAAGTTTA
65 AAATGTGATTTTGGAAAAGTTTA
*
1108197 GGGGTTAAAATGTAATTTTAAAGAAGTTTAAGGGTCAAAATATAATTTTAGAGAAGTTTAGGGGT
1 GGGGTTAAAATGTAATTTTAAAGAAGTTTAA-GGTCAAAATATAACTTT-GAGAAGTTTA-GGGT
1108262 C-AAATGTGATTTTGGAAAAGTTTA
63 CAAAATGTGATTTTGGAAAAGTTTA
* *
1108286 GGGGTTAAAATATGATTTTTAAAGAA
1 GGGGTTAAAATGT-AATTTTAAAGAA
1108312 AATAAGCAGC
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
86 2 0.02
87 25 0.25
88 14 0.14
89 43 0.43
90 15 0.15
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (87 bp):
GGGGTTAAAATGTAATTTTAAAGAAGTTTAAGGTCAAAATATAACTTTGAGAAGTTTAGGGTCAA
AATGTGATTTTGGAAAAGTTTA
Found at i:1109240 original size:21 final size:21
Alignment explanation
Indices: 1109199--1109243 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1109189 ATGTTTGAAA
*
1109199 ATAATAAATGACATTAATAAT
1 ATAATAAATGAAATTAATAAT
*
1109220 ATAATAAAT-AAATATATTAAT
1 ATAATAAATGAAAT-TAATAAT
1109241 ATA
1 ATA
1109244 TTTAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
ATAATAAATGAAATTAATAAT
Found at i:1111188 original size:12 final size:12
Alignment explanation
Indices: 1111158--1111191 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1111148 TCCCCAGCAG
*
1111158 CAGGACCAGGAC
1 CAGGACGAGGAC
1111170 CAGGACGAGGAC
1 CAGGACGAGGAC
*
1111182 GAGGACGAGG
1 CAGGACGAGG
1111192 GCTTCCTCCA
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:0.32, C:0.24, G:0.44, T:0.00
Consensus pattern (12 bp):
CAGGACGAGGAC
Found at i:1114462 original size:62 final size:62
Alignment explanation
Indices: 1114385--1114509 Score: 214
Period size: 62 Copynumber: 2.0 Consensus size: 62
1114375 GAAAGGAGAG
* *
1114385 TATTTTGAGATGTAAACTAAGGTTGGGAAATGGCTTGAGAAGGAAAGTGAGATGAGGATATC
1 TATTTTGAAATGTAAACTAAGGTTGGGAAATGGCTTGAGAAGGAAAATGAGATGAGGATATC
* *
1114447 TATTTTGAAATGTAAACTAAGGTTGGGAAATGGCTTGAGAAGGAAAATGTGATGAGGGTATC
1 TATTTTGAAATGTAAACTAAGGTTGGGAAATGGCTTGAGAAGGAAAATGAGATGAGGATATC
1114509 T
1 T
1114510 GTATATAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.35, C:0.05, G:0.31, T:0.29
Consensus pattern (62 bp):
TATTTTGAAATGTAAACTAAGGTTGGGAAATGGCTTGAGAAGGAAAATGAGATGAGGATATC
Found at i:1114575 original size:27 final size:27
Alignment explanation
Indices: 1114528--1114596 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 27
1114518 ATTTGTAAAC
*
1114528 ATTTTTTATATTTTATATTTTATTGTA
1 ATTTTATATATTTTATATTTTATTGTA
*
1114555 ATTTTATATCATTTTAT-TTTTTTTGTA
1 ATTTTATAT-ATTTTATATTTTATTGTA
1114582 ATTTTATATTATTTT
1 ATTTTATA-TATTTT
1114597 TTGAATAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 30 0.79
28 8 0.21
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (27 bp):
ATTTTATATATTTTATATTTTATTGTA
Found at i:1114598 original size:20 final size:19
Alignment explanation
Indices: 1114565--1114638 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 19
1114555 ATTTTATATC
1114565 ATTTTAT-T-TTTTTTGTA
1 ATTTTATATATTTTTTGTA
1114582 ATTTTATATTATTTTTTGAATA
1 ATTTTATA-TATTTTTTG--TA
*
1114604 ATTTGTA-ATATTTTTTTGAA
1 ATTT-TATATA-TTTTTTGTA
*
1114624 ATTTTCTATATTTTT
1 ATTTTATATATTTTT
1114639 ATATTTTTGC
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
17 7 0.15
19 7 0.15
20 15 0.32
21 2 0.04
22 14 0.30
23 2 0.04
ACGTcount: A:0.26, C:0.01, G:0.05, T:0.68
Consensus pattern (19 bp):
ATTTTATATATTTTTTGTA
Found at i:1114719 original size:9 final size:9
Alignment explanation
Indices: 1114698--1114748 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
1114688 TATTTTAAAC
*
1114698 AATTTTCAT
1 AATTTTTAT
*
1114707 AATTTTTAC
1 AATTTTTAT
1114716 AATTATTTTAT
1 AA-T-TTTTAT
*
1114727 AATTTATAT
1 AATTTTTAT
1114736 AATTTTTA-
1 AATTTTTAT
1114744 AATTT
1 AATTT
1114749 CTTTTGTGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
8 5 0.14
9 21 0.60
10 2 0.06
11 7 0.20
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (9 bp):
AATTTTTAT
Found at i:1114739 original size:20 final size:21
Alignment explanation
Indices: 1114699--1114739 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1114689 ATTTTAAACA
*
1114699 ATTTTCATAATTTTTACAATT
1 ATTTTCATAATTTATACAATT
*
1114720 ATTTT-ATAATTTATATAATT
1 ATTTTCATAATTTATACAATT
1114740 TTTAAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTCATAATTTATACAATT
Found at i:1114833 original size:44 final size:45
Alignment explanation
Indices: 1114783--1114895 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 45
1114773 TTTGTCTGCA
1114783 ATTTTTTTATA-ATTTATATATTTTGT-CATTTATAATGA-TTTTAT
1 ATTTTTTTATATATTTATATATTTTGTGCATTT-TAAT-ATTTTTAT
*
1114827 ATTTTTTT-TATATTTAT-TATTTTTTGCATTTTAATATTTTTAT
1 ATTTTTTTATATATTTATATATTTTGTGCATTTTAATATTTTTAT
* * *
1114870 AATATTTTATATATTTTTATGATTTT
1 ATTTTTTTATATATTTATAT-ATTTT
1114896 TTAAATATAA
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
42 1 0.02
43 25 0.42
44 27 0.46
45 1 0.02
46 5 0.08
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (45 bp):
ATTTTTTTATATATTTATATATTTTGTGCATTTTAATATTTTTAT
Found at i:1114841 original size:18 final size:18
Alignment explanation
Indices: 1114815--1114888 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
1114805 TTGTCATTTA
1114815 TAATGATTTTATATTTTTT
1 TAAT-ATTTTATATTTTTT
*
1114834 TTATA-TTTATTATTTTTT
1 TAATATTTTA-TATTTTTT
** * *
1114852 GCAT-TTTAATATTTTTA
1 TAATATTTTATATTTTTT
*
1114869 TAATATTTTATATATTTT
1 TAATATTTTATATTTTTT
1114887 TA
1 TA
1114889 TGATTTTTTA
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
17 13 0.31
18 26 0.62
19 3 0.07
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (18 bp):
TAATATTTTATATTTTTT
Found at i:1114874 original size:11 final size:11
Alignment explanation
Indices: 1114858--1114903 Score: 55
Period size: 10 Copynumber: 4.5 Consensus size: 11
1114848 TTTTGCATTT
1114858 TAATATTTTTA
1 TAATATTTTTA
1114869 TAATA-TTTTA
1 TAATATTTTTA
1114879 T-ATATTTTTA
1 TAATATTTTTA
*
1114889 TGAT-TTTTTA
1 TAATATTTTTA
1114899 -AATAT
1 TAATAT
1114904 AAAATACTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
9 5 0.16
10 19 0.61
11 7 0.23
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TAATATTTTTA
Found at i:1114883 original size:20 final size:20
Alignment explanation
Indices: 1114811--1114903 Score: 74
Period size: 20 Copynumber: 5.0 Consensus size: 20
1114801 TATTTTGTCA
1114811 TTTATAATGATTTTATAT-TT
1 TTTATAAT-ATTTTATATATT
*
1114831 TTT-TTATA-TTTAT-TATT
1 TTTATAATATTTTATATATT
**
1114848 TTT-T-GCATTTTA-ATATT
1 TTTATAATATTTTATATATT
1114865 TTTATAATATTTTATATATT
1 TTTATAATATTTTATATATT
* * *
1114885 TTTATGATTTTTTAAATAT
1 TTTATAATATTTTATATAT
1114904 AAAATACTAG
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
16 2 0.03
17 22 0.37
18 2 0.03
19 9 0.15
20 24 0.41
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTATAATATTTTATATATT
Found at i:1114894 original size:18 final size:18
Alignment explanation
Indices: 1114817--1114895 Score: 69
Period size: 17 Copynumber: 4.4 Consensus size: 18
1114807 GTCATTTATA
1114817 ATGATTTTATAT-TTTTT
1 ATGATTTTATATATTTTT
*
1114834 -TTATATTTAT-TATTTTT
1 ATGAT-TTTATATATTTTT
1114851 -TGCATTTTA-ATATTTTT
1 ATG-ATTTTATATATTTTT
*
1114868 ATAATATTTTATATATTTTT
1 AT--GATTTTATATATTTTT
1114888 ATGATTTT
1 ATGATTTT
1114896 TTAAATATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
16 4 0.08
17 22 0.44
18 8 0.16
19 6 0.12
20 10 0.20
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.68
Consensus pattern (18 bp):
ATGATTTTATATATTTTT
Found at i:1116502 original size:58 final size:58
Alignment explanation
Indices: 1116412--1116527 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
1116402 TGAAAACTAT
1116412 TTGAAGGATGAAATTCATATTCACTCTAACTAAGTTCAAGTTAAACAAAACATTAGCA
1 TTGAAGGATGAAATTCATATTCACTCTAACTAAGTTCAAGTTAAACAAAACATTAGCA
1116470 TTGAAGGATGAAATTCATATTCACTCTAACTAAGTTCAAGTTAAACAAAACATTAGCA
1 TTGAAGGATGAAATTCATATTCACTCTAACTAAGTTCAAGTTAAACAAAACATTAGCA
1116528 CTGCATCTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (58 bp):
TTGAAGGATGAAATTCATATTCACTCTAACTAAGTTCAAGTTAAACAAAACATTAGCA
Found at i:1122415 original size:2 final size:2
Alignment explanation
Indices: 1122408--1122433 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1122398 CTAAATGTTC
1122408 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
1122434 GTATGTATGT
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:1128072 original size:15 final size:16
Alignment explanation
Indices: 1128054--1128121 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 16
1128044 TAGGGCTTAA
1128054 GATTTTAAGGTTT-AT
1 GATTTTAAGGTTTCAT
*
1128069 GA-TTCAAGGTTTCAT
1 GATTTTAAGGTTTCAT
* *
1128084 GATTTT-GGGATTTCAA
1 GATTTTAAGG-TTTCAT
* **
1128100 GGTTTTTTGGTTTCAT
1 GATTTTAAGGTTTCAT
1128116 GATTTT
1 GATTTT
1128122 TGGTTTGTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
14 9 0.22
15 8 0.20
16 22 0.54
17 2 0.05
ACGTcount: A:0.21, C:0.06, G:0.22, T:0.51
Consensus pattern (16 bp):
GATTTTAAGGTTTCAT
Found at i:1128113 original size:16 final size:15
Alignment explanation
Indices: 1128076--1128127 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1128066 TATGATTCAA
* *
1128076 GGTTTCATGATTTTG
1 GGTTTCAGGATTTTT
*
1128091 GGATTTCAAGGTTTTTT
1 GG-TTTC-AGGATTTTT
*
1128108 GGTTTCATGATTTTT
1 GGTTTCAGGATTTTT
1128123 GGTTT
1 GGTTT
1128128 GTGTTTTGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 14 0.47
16 8 0.27
17 8 0.27
ACGTcount: A:0.13, C:0.06, G:0.25, T:0.56
Consensus pattern (15 bp):
GGTTTCAGGATTTTT
Found at i:1128176 original size:28 final size:27
Alignment explanation
Indices: 1128130--1128182 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
1128120 TTTGGTTTGT
1128130 GTTTTGGGTTTAAGGTTTATGGTTTCAA
1 GTTTTGGGTTTAAGGTTTA-GGTTTCAA
* **
1128158 GTTTTGGTTTTAATTTTTAGGTTTC
1 GTTTTGGGTTTAAGGTTTAGGTTTC
1128183 TTGGTTAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.15, C:0.04, G:0.25, T:0.57
Consensus pattern (27 bp):
GTTTTGGGTTTAAGGTTTAGGTTTCAA
Found at i:1130407 original size:24 final size:23
Alignment explanation
Indices: 1130338--1130408 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
1130328 GTTCATTTAA
*
1130338 ATTAATCAAACATGTCCACGAAC
1 ATTAATCAAACATGTTCACGAAC
**
1130361 ATTAAAT-AAACATGTTCGTGAAC
1 ATT-AATCAAACATGTTCACGAAC
*
1130384 ATATAATCGAACATGTTCACGAAC
1 AT-TAATCAAACATGTTCACGAAC
1130408 A
1 A
1130409 ATGTTAATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 21 0.54
24 18 0.46
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.25
Consensus pattern (23 bp):
ATTAATCAAACATGTTCACGAAC
Found at i:1134651 original size:23 final size:23
Alignment explanation
Indices: 1134625--1134669 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1134615 AAATTCGATT
**
1134625 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
1134648 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
1134670 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:1141662 original size:190 final size:192
Alignment explanation
Indices: 1141334--1141715 Score: 615
Period size: 191 Copynumber: 2.0 Consensus size: 192
1141324 TCCCCATGAA
* *
1141334 GCTTTGTGGTTGTTTTCCCAGTGGTTCTTCTTTATCAAGCATTCTATGATTTGTAAATGAGATTT
1 GCTTTGTGGTTGTTTTCCAAGTGGTTCTTATTTATCAAGCATTCTATGATTTGTAAATGAGATTT
* *
1141399 AACCAGAGTTATCTCACACTACTGCAGCAAATTTCTTCCTATATATTTTTGGGTTTATTTTTGTA
66 AACCAGAGTTATCTCACACTACTGCACCAAATTTCTTCCTATATATTTTTGGGTTTATTTTTGCA
** * * * *
1141464 TAAGCAGGCATGTGGTT-TGGTGTACATTTGTTACTTCTGCATGTGTGAATGAGTTTTGTTG
131 TAAGCAGGCAAATGGTTGGGGTGTACATTTGCTACCTCTGCATGTGTGAATAAGTTTTGTTG
* *
1141525 GCTTTGTGGTTGTTTTCCAAGTGGTTCTTATTTATCAAGCTTTCTATGATTTTTAAATGAG-TTT
1 GCTTTGTGGTTGTTTTCCAAGTGGTTCTTATTTATCAAGCATTCTATGATTTGTAAATGAGATTT
*
1141589 TACCAGAGTTATCTCACACTACTGCACCAAATTTCTTCCTATATATTTTTGGGTTTATTTTTGCA
66 AACCAGAGTTATCTCACACTACTGCACCAAATTTCTTCCTATATATTTTTGGGTTTATTTTTGCA
* *
1141654 TGAGCAGGCAAATGGTTGGGGTGTGCATTTGCTACCTCTGCATGTGTGAATAAGTTTTGTTG
131 TAAGCAGGCAAATGGTTGGGGTGTACATTTGCTACCTCTGCATGTGTGAATAAGTTTTGTTG
1141716 CACAGTTTTT
Statistics
Matches: 175, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
190 79 0.45
191 96 0.55
ACGTcount: A:0.21, C:0.15, G:0.20, T:0.44
Consensus pattern (192 bp):
GCTTTGTGGTTGTTTTCCAAGTGGTTCTTATTTATCAAGCATTCTATGATTTGTAAATGAGATTT
AACCAGAGTTATCTCACACTACTGCACCAAATTTCTTCCTATATATTTTTGGGTTTATTTTTGCA
TAAGCAGGCAAATGGTTGGGGTGTACATTTGCTACCTCTGCATGTGTGAATAAGTTTTGTTG
Found at i:1159444 original size:2 final size:2
Alignment explanation
Indices: 1159439--1159463 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1159429 TTCACTTTTT
1159439 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1159464 AATTTTGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1162255 original size:24 final size:24
Alignment explanation
Indices: 1162227--1162274 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1162217 TTGAATTAAA
* *
1162227 AATATTTGAATTAGGTTTTT-TTTT
1 AATATTTCAA-TACGTTTTTATTTT
1162251 AATATTTCAATACGTTTTTATTTT
1 AATATTTCAATACGTTTTTATTTT
1162275 TTAAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.60
Consensus pattern (24 bp):
AATATTTCAATACGTTTTTATTTT
Found at i:1166661 original size:17 final size:18
Alignment explanation
Indices: 1166632--1166675 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
1166622 GGCCCAAACC
*
1166632 ATTTTGAA-ATTAAATTT
1 ATTTTGAATTTTAAATTT
1166649 ATTTT-AATTTTAAATTT
1 ATTTTGAATTTTAAATTT
1166666 ATTTTGAATT
1 ATTTTGAATT
1166676 CAATTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 2 0.08
17 18 0.75
18 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
ATTTTGAATTTTAAATTT
Found at i:1166669 original size:11 final size:11
Alignment explanation
Indices: 1166638--1166723 Score: 54
Period size: 11 Copynumber: 7.7 Consensus size: 11
1166628 AACCATTTTG
*
1166638 AAATTAAATTT
1 AAATTTAATTT
*
1166649 -ATTTTAATTTT
1 AAATTTAA-TTT
*
1166660 AAATTTATTTT
1 AAATTTAATTT
* *
1166671 GAATTCAATTT
1 AAATTTAATTT
1166682 AAATTTGAATTT
1 AAATTT-AATTT
1166694 -AATTTAAATTT
1 AAATTT-AATTT
1166705 AACA-TT-ATTAT
1 AA-ATTTAATT-T
1166716 AAATTTAA
1 AAATTTAA
1166724 AAATAAAAGC
Statistics
Matches: 57, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
10 9 0.16
11 33 0.58
12 14 0.25
13 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:1166688 original size:17 final size:17
Alignment explanation
Indices: 1166668--1166704 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1166658 TTAAATTTAT
1166668 TTTGAATTCAATTTAAA
1 TTTGAATTCAATTTAAA
*
1166685 TTTGAATTTAATTTAAA
1 TTTGAATTCAATTTAAA
1166702 TTT
1 TTT
1166705 AACATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (17 bp):
TTTGAATTCAATTTAAA
Found at i:1166724 original size:6 final size:6
Alignment explanation
Indices: 1166641--1166706 Score: 50
Period size: 6 Copynumber: 11.7 Consensus size: 6
1166631 CATTTTGAAA
* * * * *
1166641 TTAAAT TT-ATT TTAATT TTAAAT TT-ATT TTGAA- TTCAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
1166686 TTGAAT TT-AAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAA
1166707 CATTATTATA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
5 17 0.35
6 32 0.65
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (6 bp):
TTAAAT
Found at i:1167505 original size:26 final size:25
Alignment explanation
Indices: 1167458--1167515 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
1167448 TAATAAAGGC
* *
1167458 ATTAATAATATTAATATTTATTATTA
1 ATTAATAATAATAATATATATTA-TA
1167484 ATTAATAATAATAAT-TAATATTATA
1 ATTAATAATAATAATAT-ATATTATA
1167509 A-TAATAA
1 ATTAATAA
1167516 AGAAATTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 6 0.21
25 4 0.14
26 19 0.66
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTAATAATAATAATATATATTATA
Found at i:1168708 original size:29 final size:28
Alignment explanation
Indices: 1168664--1168771 Score: 119
Period size: 29 Copynumber: 3.8 Consensus size: 28
1168654 CTAAACAGTC
1168664 CAAAAATTACATTTTAACCCCAAAACTT
1 CAAAAATTACATTTTAACCCCAAAACTT
* *
1168692 CAGAAAATTACATTTTAACCCCGAACCTT
1 CA-AAAATTACATTTTAACCCCAAAACTT
* *
1168721 CCAAAAATTACCGTTTT-ACCCCTAAACTTT
1 -CAAAAATTA-CATTTTAACCCCAAAAC-TT
* *
1168751 CCAAAATTTCATTTTAACCCC
1 CAAAAATTACATTTTAACCCC
1168772 GATTTCACCA
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
28 7 0.10
29 51 0.76
30 9 0.13
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.31
Consensus pattern (28 bp):
CAAAAATTACATTTTAACCCCAAAACTT
Found at i:1168785 original size:29 final size:29
Alignment explanation
Indices: 1168753--1168905 Score: 95
Period size: 29 Copynumber: 5.2 Consensus size: 29
1168743 TAAACTTTCC
*
1168753 AAAATTTCATTTTAACCCCGATTTCACCAA
1 AAAATTCCATTTTAACCCCGATTTCACC-A
* *
1168783 AAAATTACCATTTTACCCCCAAACTTT--CC-
1 AAAATT-CCATTTTAACCCC-GA-TTTCACCA
**
1168812 AAAATTCCATTTTTAACCCTAATTTCACCA
1 AAAATTCCA-TTTTAACCCCGATTTCACCA
*
1168842 AAAATTACCGTTTT-ACCCCTGAACTTT--CC-
1 AAAATT-CCATTTTAACCCC-G-A-TTTCACCA
* *
1168871 AAAATTCTATTTTTAACCCCGATTTCACTA
1 AAAATTCCA-TTTTAACCCCGATTTCACCA
1168901 AAAAT
1 AAAAT
1168906 CACCGTTTTA
Statistics
Matches: 96, Mismatches: 11, Indels: 32
0.69 0.08 0.23
Matches are distributed among these distances:
27 6 0.06
28 7 0.07
29 32 0.33
30 28 0.29
31 16 0.17
32 4 0.04
33 3 0.03
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATTCCATTTTAACCCCGATTTCACCA
Found at i:1168810 original size:59 final size:59
Alignment explanation
Indices: 1168663--1169006 Score: 355
Period size: 59 Copynumber: 5.9 Consensus size: 59
1168653 CCTAAACAGT
* * * * *
1168663 CCAAAAATTA-CATTTTAACCCCAAAAC-TTCAGAAAATTACA-TTTTAACCCCGAACCTT--
1 CCAAAAATTACCGTTTT-ACCCCCAAACTTTC-CAAAATTTCATTTTTAACCCCG-A-TTTCA
*
1168721 CCAAAAATTACCGTTTTACCCCTAAACTTTCCAAAATTTCA-TTTTAACCCCGATTTCA
1 CCAAAAATTACCGTTTTACCCCCAAACTTTCCAAAATTTCATTTTTAACCCCGATTTCA
* * **
1168779 CCAAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCA
1 CC-AAAAATTACCGTTTTACCCCCAAACTTTCCAAAATTTCATTTTTAACCCCGATTTCA
**
1168839 CCAAAAATTACCGTTTTACCCCTGAACTTTCCAAAA-TTCTATTTTTAACCCCGATTTCA
1 CCAAAAATTACCGTTTTACCCCCAAACTTTCCAAAATTTC-ATTTTTAACCCCGATTTCA
* * * * * * *
1168898 CTAAAAATCACCGTTTTACCCTCGAGCTTTCC-AAATCTCATTTTTAACCCCGACTTCA
1 CCAAAAATTACCGTTTTACCCCCAAACTTTCCAAAATTTCATTTTTAACCCCGATTTCA
* * * *
1168956 CCAAAAATTACTGTTTTACCCCTGAACCTTT-CAAAATCTCATTTTTAACCC
1 CCAAAAATTACCGTTTTACCCC-CAAACTTTCCAAAATTTCATTTTTAACCC
1169007 TAAATTTTCC
Statistics
Matches: 246, Mismatches: 30, Indels: 19
0.83 0.10 0.06
Matches are distributed among these distances:
56 2 0.01
57 1 0.00
58 82 0.33
59 144 0.59
60 17 0.07
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (59 bp):
CCAAAAATTACCGTTTTACCCCCAAACTTTCCAAAATTTCATTTTTAACCCCGATTTCA
Found at i:1168872 original size:118 final size:117
Alignment explanation
Indices: 1168704--1169006 Score: 393
Period size: 118 Copynumber: 2.6 Consensus size: 117
1168694 GAAAATTACA
*
1168704 TTTTAACCCCGAACCTT--CCAAAAATTACCGTTTTACCCCTAAACTTTCCAAAATTTCA-TTTT
1 TTTTAACCCC-AA-CTTCACCAAAAATTACCGTTTTACCCCTGAACTTTCCAAAATTTCATTTTT
*
1168766 AACCCCGATTTCACCAAAAAATTACCATTTTACCCCCAAACTTTCCAAAAT-TCCAT
64 AACCCCGATTTCA-CAAAAAATCACCATTTTACCCCCAAACTTTCC-AAATCT-CAT
* *
1168822 TTTTAACCCTAATTTCACCAAAAATTACCGTTTTACCCCTGAACTTTCCAAAA-TTCTATTTTTA
1 TTTTAACCCCAACTTCACCAAAAATTACCGTTTTACCCCTGAACTTTCCAAAATTTC-ATTTTTA
* * * * *
1168886 ACCCCGATTTCACTAAAAATCACCGTTTTACCCTCGAGCTTTCCAAATCTCAT
65 ACCCCGATTTCACAAAAAATCACCATTTTACCCCCAAACTTTCCAAATCTCAT
* * *
1168939 TTTTAACCCCGACTTCACCAAAAATTACTGTTTTACCCCTGAACCTTT-CAAAATCTCATTTTTA
1 TTTTAACCCCAACTTCACCAAAAATTACCGTTTTACCCCTGAA-CTTTCCAAAATTTCATTTTTA
1169003 ACCC
65 ACCC
1169007 TAAATTTTCC
Statistics
Matches: 164, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
116 2 0.01
117 67 0.41
118 78 0.48
119 17 0.10
ACGTcount: A:0.31, C:0.30, G:0.04, T:0.34
Consensus pattern (117 bp):
TTTTAACCCCAACTTCACCAAAAATTACCGTTTTACCCCTGAACTTTCCAAAATTTCATTTTTAA
CCCCGATTTCACAAAAAATCACCATTTTACCCCCAAACTTTCCAAATCTCAT
Found at i:1168890 original size:30 final size:28
Alignment explanation
Indices: 1168695--1168890 Score: 86
Period size: 29 Copynumber: 6.7 Consensus size: 28
1168685 AAAACTTCAG
* *
1168695 AAAATTACA-TTTTAACCCCGAACCTTCC
1 AAAATT-CATTTTTAACCCCTAACTTTCC
**
1168723 AAAAATTACCGTTTT-ACCCCTAAACTTTCC
1 -AAAATT-CATTTTTAACCCCT-AACTTTCC
*
1168753 AAAATTTCA-TTTTAACCCC-GA-TTTCACC
1 AAAA-TTCATTTTTAACCCCTAACTTT--CC
* *
1168781 AAAAAATTACCA-TTTTACCCCCAAACTTTCC
1 --AAAATT--CATTTTTAACCCCTAACTTTCC
1168812 AAAATTCCATTTTTAA-CCCTAA-TTTCACC
1 AAAATT-CATTTTTAACCCCTAACTTT--CC
**
1168841 AAAAATTACCGTTTT-ACCCCTGAACTTTCC
1 -AAAATT-CATTTTTAACCCCT-AACTTTCC
1168871 AAAATTCTATTTTTAACCCC
1 AAAATTC-ATTTTTAACCCC
1168891 GATTTCACTA
Statistics
Matches: 132, Mismatches: 14, Indels: 41
0.71 0.07 0.22
Matches are distributed among these distances:
26 3 0.02
27 4 0.03
28 15 0.11
29 49 0.37
30 39 0.30
31 15 0.11
32 4 0.03
33 3 0.02
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATTCATTTTTAACCCCTAACTTTCC
Found at i:1168973 original size:30 final size:30
Alignment explanation
Indices: 1168762--1168977 Score: 87
Period size: 29 Copynumber: 7.3 Consensus size: 30
1168752 CAAAATTTCA
* **
1168762 TTTTAACCCCGATTTCACCAAAAAATTACCA
1 TTTTAACCCCGACTTCACC-AAAAATTACTG
* * * *
1168793 TTTTACCCCCAAACTT-TCC-AAAATTCCAT-
1 TTTTAACCCC-GACTTCACCAAAAATTAC-TG
** * *
1168822 TTTTAACCCTAATTTCACCAAAAATTACCG
1 TTTTAACCCCGACTTCACCAAAAATTACTG
* *
1168852 TTTT-ACCCCTGAACTT-TCC-AAAATT-CTAT
1 TTTTAACCCC-G-ACTTCACCAAAAATTACT-G
* * * *
1168881 TTTTAACCCCGATTTCACTAAAAATCACCG
1 TTTTAACCCCGACTTCACCAAAAATTACTG
* ** *
1168911 TTTT-ACCCTCGAGCTT-TCCAAATCTCA-T-
1 TTTTAACCC-CGA-CTTCACCAAAAATTACTG
1168939 TTTTAACCCCGACTTCACCAAAAATTACTG
1 TTTTAACCCCGACTTCACCAAAAATTACTG
1168969 TTTT-ACCCC
1 TTTTAACCCC
1168978 TGAACCTTTC
Statistics
Matches: 133, Mismatches: 34, Indels: 38
0.65 0.17 0.19
Matches are distributed among these distances:
27 3 0.02
28 22 0.17
29 47 0.35
30 41 0.31
31 17 0.13
32 3 0.02
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.34
Consensus pattern (30 bp):
TTTTAACCCCGACTTCACCAAAAATTACTG
Found at i:1171273 original size:22 final size:23
Alignment explanation
Indices: 1171233--1171279 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1171223 AATAATTTAA
*
1171233 AAATTATAAAAACAAAAAAT-AT
1 AAATTATAAAAAAAAAAAATCAT
1171255 AAATTA-AAAAATAAAAAAATCAT
1 AAATTATAAAAA-AAAAAAATCAT
1171278 AA
1 AA
1171280 GAATTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 13 0.59
23 4 0.18
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.21
Consensus pattern (23 bp):
AAATTATAAAAAAAAAAAATCAT
Found at i:1173906 original size:80 final size:80
Alignment explanation
Indices: 1173773--1174009 Score: 465
Period size: 80 Copynumber: 3.0 Consensus size: 80
1173763 GGCGAAGTAT
1173773 TTGATACGCCTTTGATTTCTCAAATATTGGTTAATGGTAAAACTCAGAGAGTTGAATATGAACCA
1 TTGATACGCCTTTGATTTCTCAAATATTGGTTAATGGTAAAACTCAGAGAGTTGAATATGAACCA
1173838 TTACCGTCTATACCC
66 TTACCGTCTATACCC
1173853 TTGATACGCCTTTGATTTCTCAAATATTGGTTAATGGTAAAACTCAGAGAGTTGAATATGAACCA
1 TTGATACGCCTTTGATTTCTCAAATATTGGTTAATGGTAAAACTCAGAGAGTTGAATATGAACCA
1173918 TTACCGTCTATACCC
66 TTACCGTCTATACCC
*
1173933 TTGATATGCCTTTGATTTCTCAAATATTGGTTAATGGTAAAACTCAGAGAGTTGAATATGAACCA
1 TTGATACGCCTTTGATTTCTCAAATATTGGTTAATGGTAAAACTCAGAGAGTTGAATATGAACCA
1173998 TTACCGTCTATA
66 TTACCGTCTATA
1174010 TGTTTTTCTT
Statistics
Matches: 156, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 156 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (80 bp):
TTGATACGCCTTTGATTTCTCAAATATTGGTTAATGGTAAAACTCAGAGAGTTGAATATGAACCA
TTACCGTCTATACCC
Found at i:1176247 original size:3 final size:3
Alignment explanation
Indices: 1176239--1176268 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1176229 TATATCCCAA
1176239 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1176269 GAATAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1177328 original size:7 final size:7
Alignment explanation
Indices: 1177316--1177361 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
1177306 TTTCGAAAAA
1177316 GTCAACG
1 GTCAACG
1177323 GTCAACG
1 GTCAACG
*
1177330 GTCAA-A
1 GTCAACG
1177336 GTCAACG
1 GTCAACG
*
1177343 ATCAACG
1 GTCAACG
1177350 GTCAACG
1 GTCAACG
*
1177357 ATCAA
1 GTCAA
1177362 TCAACACCGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
6 5 0.15
7 28 0.85
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:1177338 original size:20 final size:20
Alignment explanation
Indices: 1177313--1177354 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1177303 GTTTTTCGAA
*
1177313 AAAGTCAACGGTCAACGGTC
1 AAAGTCAACGATCAACGGTC
1177333 AAAGTCAACGATCAACGGTC
1 AAAGTCAACGATCAACGGTC
1177353 AA
1 AA
1177355 CGATCAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.14
Consensus pattern (20 bp):
AAAGTCAACGATCAACGGTC
Found at i:1177492 original size:21 final size:21
Alignment explanation
Indices: 1177467--1177532 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1177457 TGGTTCAAAT
1177467 GGTTTGGTTTAAATGAATTTG
1 GGTTTGGTTTAAATGAATTTG
* *
1177488 GGTTTGATTTAAATGAATGTG
1 GGTTTGGTTTAAATGAATTTG
*
1177509 GGTTTGGTTTAAATAGGATTTG
1 GGTTTGGTTTAAAT-GAATTTG
1177531 GG
1 GG
1177533 CTTAATGGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 32 0.82
22 7 0.18
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (21 bp):
GGTTTGGTTTAAATGAATTTG
Found at i:1177934 original size:11 final size:11
Alignment explanation
Indices: 1177909--1177974 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 11
1177899 TTAAAAAAGG
*
1177909 AAGAAAATAGAA
1 AAGAAAAGAG-A
1177921 AAGAAAAGAGA
1 AAGAAAAGAGA
1177932 AAGAAATA-AGA
1 AAGAAA-AGAGA
* *
1177943 AATGAATGAGAAA
1 AA-GAA-AAGAGA
1177956 AAGAAAAGAGA
1 AAGAAAAGAGA
1177967 AAGGAAAA
1 AA-GAAAA
1177975 ATGAGAGGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
11 18 0.41
12 22 0.50
13 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (11 bp):
AAGAAAAGAGA
Done.