Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 53 of 427
Found at i:12828759 original size:16 final size:15
Alignment explanation
Indices: 12828734--12828769 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
12828724 TAAAAGTGTG
12828734 CATAATATATAAATA
1 CATAATATATAAATA
*
12828749 CATATATATATACATA
1 CATA-ATATATAAATA
12828765 CATAA
1 CATAA
12828770 CATAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (15 bp):
CATAATATATAAATA
Found at i:12828982 original size:21 final size:21
Alignment explanation
Indices: 12828944--12829001 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
12828934 ATAATAGTAC
*
12828944 AATAT-TAAAAGATATATACGT
1 AATATATAAAA-ATATATACAT
*
12828965 AATATATAAAAATGTATACAT
1 AATATATAAAAATATATACAT
12828986 AATATATAGAAAATAT
1 AATATATA-AAAATAT
12829002 GATATTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (21 bp):
AATATATAAAAATATATACAT
Found at i:12829540 original size:21 final size:22
Alignment explanation
Indices: 12829505--12829546 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
12829495 AAGATTATAA
12829505 GAAAATATAATTAATA-ATATT
1 GAAAATATAATTAATATATATT
12829526 GAAAATAT-ATATAATATATAT
1 GAAAATATAAT-TAATATATAT
12829547 AACATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 13 0.68
22 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (22 bp):
GAAAATATAATTAATATATATT
Found at i:12829585 original size:24 final size:25
Alignment explanation
Indices: 12829539--12829602 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 25
12829529 AATATATATA
* *
12829539 ATATATATAACATAATATTAAAACA-C
1 ATATATATAATAT-ATA-TAAAAAATC
*
12829565 ATATATATAATATATA-AAAAAATT
1 ATATATATAATATATATAAAAAATC
*
12829589 ACATATATAATATA
1 ATATATATAATATA
12829603 ATACATAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 5 0.15
24 13 0.39
25 3 0.09
26 12 0.36
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (25 bp):
ATATATATAATATATATAAAAAATC
Found at i:12829686 original size:9 final size:9
Alignment explanation
Indices: 12829656--12829708 Score: 65
Period size: 9 Copynumber: 6.0 Consensus size: 9
12829646 ACACTAAGAC
12829656 ATATAATAA
1 ATATAATAA
*
12829665 ATACAATAA
1 ATATAATAA
12829674 ATATAATAA
1 ATATAATAA
12829683 ATATAA-ATA
1 ATATAATA-A
*
12829692 TTATAATAA
1 ATATAATAA
12829701 ATA-AATAA
1 ATATAATAA
12829709 CAGAAAATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
8 6 0.16
9 31 0.82
10 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (9 bp):
ATATAATAA
Found at i:12831181 original size:13 final size:13
Alignment explanation
Indices: 12831163--12831189 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12831153 CTCTTTAGAA
12831163 TTTTTTTAAAATT
1 TTTTTTTAAAATT
12831176 TTTTTTTAAAATT
1 TTTTTTTAAAATT
12831189 T
1 T
12831190 GAATTTTTTA
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTTTAAAATT
Found at i:12831196 original size:19 final size:21
Alignment explanation
Indices: 12831172--12831221 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 21
12831162 ATTTTTTTAA
12831172 AATTTTTTTTTAAA-A-TTTG
1 AATTTTTTTTTAAATATTTTG
*
12831191 AA-TTTTTTATAAATATTTTG
1 AATTTTTTTTTAAATATTTTG
*
12831211 ATTTTTTTTTT
1 AATTTTTTTTT
12831222 GTAATTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 10 0.40
19 3 0.12
20 5 0.20
21 7 0.28
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (21 bp):
AATTTTTTTTTAAATATTTTG
Found at i:12832900 original size:14 final size:14
Alignment explanation
Indices: 12832881--12832907 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12832871 ACATAAGTAA
12832881 ATAAATAAATAAAT
1 ATAAATAAATAAAT
12832895 ATAAATAAATAAA
1 ATAAATAAATAAA
12832908 ACATGGCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAATAAATAAAT
Found at i:12832982 original size:15 final size:15
Alignment explanation
Indices: 12832953--12832984 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12832943 CGATAATAAT
12832953 AATAATAATAATATA
1 AATAATAATAATATA
*
12832968 AATAATAATAGTATA
1 AATAATAATAATATA
12832983 AA
1 AA
12832985 ACGATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AATAATAATAATATA
Found at i:12832994 original size:3 final size:3
Alignment explanation
Indices: 12832945--12832977 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
12832935 AACAAAAACG
12832945 ATA ATA ATA ATA ATA ATA AT- ATAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
12832978 GTATAAAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.86
4 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12833405 original size:21 final size:23
Alignment explanation
Indices: 12833373--12833419 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
12833363 ACTATTAATA
12833373 ATATTACAT-AA-ATATATACAT
1 ATATTACATAAAGATATATACAT
12833394 ATATT-CATTAAAGATATATACAT
1 ATATTACA-TAAAGATATATACAT
12833417 ATA
1 ATA
12833420 ATAAAACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.09
21 6 0.26
22 2 0.09
23 13 0.57
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (23 bp):
ATATTACATAAAGATATATACAT
Found at i:12836165 original size:26 final size:26
Alignment explanation
Indices: 12836129--12836237 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
12836119 CATGAAATTC
12836129 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
12836155 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
12836181 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
12836207 TTATCATG-AACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
12836232 TTATCA
1 TTATCA
12836238 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 21 0.27
26 57 0.73
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:12841870 original size:26 final size:26
Alignment explanation
Indices: 12841834--12841943 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
12841824 CATGAAATTC
12841834 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
12841860 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
12841886 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
12841912 TTGTCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
12841938 TTATCA
1 TTATCA
12841944 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:12842575 original size:25 final size:25
Alignment explanation
Indices: 12842543--12842604 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
12842533 TGGGATAATA
*
12842543 TAAAAATATATGA-ATAATGT-GATAT
1 TAAAAATATAT-ACATAATATAG-TAT
12842568 TAAAAATATATACATAATATAGTAT
1 TAAAAATATATACATAATATAGTAT
*
12842593 TAAATATATATA
1 TAAAAATATATA
12842605 TAATACATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 1 0.03
25 31 0.94
26 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (25 bp):
TAAAAATATATACATAATATAGTAT
Found at i:12842789 original size:3 final size:3
Alignment explanation
Indices: 12842781--12842866 Score: 59
Period size: 3 Copynumber: 28.7 Consensus size: 3
12842771 CATATAAGAG
* * *
12842781 TAA TAA TAA TAA TTA TAA CAC TAA TAA TAA TAA TAA -ATA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
* * * * * *
12842826 TAG TAG TAA AAA TAA -ATA CAA TAA TAA TCA TAA AAA TAA TA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TA
12842867 TAAATAATGT
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
2 2 0.03
3 60 0.94
4 2 0.03
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:12842839 original size:24 final size:24
Alignment explanation
Indices: 12842783--12842874 Score: 80
Period size: 24 Copynumber: 3.8 Consensus size: 24
12842773 TATAAGAGTA
* * * * *
12842783 ATAATAATAATTATAACACTAATA
1 ATAAAAATAAATATAATAATAATC
* *
12842807 ATAATAATAAATATAATAATAGT-
1 ATAAAAATAAATATAATAATAATC
*
12842830 AGTAAAAATAAATACAATAATAATC
1 A-TAAAAATAAATATAATAATAATC
12842855 ATAAAAAT-AATATAAATAAT
1 ATAAAAATAAATAT-AATAAT
12842875 GTGCACATGA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
23 5 0.09
24 51 0.89
25 1 0.02
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (24 bp):
ATAAAAATAAATATAATAATAATC
Found at i:12844645 original size:18 final size:18
Alignment explanation
Indices: 12844609--12844644 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12844599 TTTGAAATTT
12844609 ATTAAATTTTATTTCAAA
1 ATTAAATTTTATTTCAAA
*
12844627 ATTAAGTTTTA-TTCAAA
1 ATTAAATTTTATTTCAAA
12844644 A
1 A
12844645 ACATTATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTAAATTTTATTTCAAA
Found at i:12844905 original size:22 final size:22
Alignment explanation
Indices: 12844879--12844924 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
12844869 TAAAAATATA
12844879 AAACAATGAAGAACAAAGAATT
1 AAACAATGAAGAACAAAGAATT
12844901 AAACAATGAAGAACAAAGAATT
1 AAACAATGAAGAACAAAGAATT
12844923 AA
1 AA
12844925 CATTGAGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.65, C:0.09, G:0.13, T:0.13
Consensus pattern (22 bp):
AAACAATGAAGAACAAAGAATT
Found at i:12848922 original size:18 final size:18
Alignment explanation
Indices: 12848899--12848935 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
12848889 TAGTCGCCTG
12848899 CTCCCTTATTCTAATTCA
1 CTCCCTTATTCTAATTCA
12848917 CTCCCTTATTCTAATTCA
1 CTCCCTTATTCTAATTCA
12848935 C
1 C
12848936 CTCAACGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.35, G:0.00, T:0.43
Consensus pattern (18 bp):
CTCCCTTATTCTAATTCA
Found at i:12851781 original size:13 final size:13
Alignment explanation
Indices: 12851743--12851782 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
12851733 TAGTTTCCTT
*
12851743 TTTTTTTTTTTAA
1 TTTTTTTTTTAAA
12851756 TTTTTGTTTTTAAA
1 TTTTT-TTTTTAAA
*
12851770 TTTTTTTATTAAA
1 TTTTTTTTTTAAA
12851783 AAATACAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (13 bp):
TTTTTTTTTTAAA
Found at i:12851928 original size:25 final size:26
Alignment explanation
Indices: 12851886--12851936 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
12851876 ATTAATGGAT
* *
12851886 GAAAAAACATTTTGGATA-CTAATCTA
1 GAAAAAACAATTTAGATATC-AATCTA
12851912 GAAAAAA-AATTTAGATATCAATCTA
1 GAAAAAACAATTTAGATATCAATCTA
12851937 ATAAAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (26 bp):
GAAAAAACAATTTAGATATCAATCTA
Found at i:12857532 original size:26 final size:26
Alignment explanation
Indices: 12857503--12857560 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
12857493 ATAATTTTAA
12857503 AAAAATTAAAATTTAATCTTA-TACTT
1 AAAAATT-AAATTTAATCTTATTACTT
* * * *
12857529 AAAAAATAAATTTTATTTTATTATTT
1 AAAAATTAAATTTAATCTTATTACTT
12857555 AAAAAT
1 AAAAAT
12857561 CTTAATCCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (26 bp):
AAAAATTAAATTTAATCTTATTACTT
Found at i:12857539 original size:25 final size:28
Alignment explanation
Indices: 12857502--12857559 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 28
12857492 TATAATTTTA
12857502 AAAAAATTAAAATTTAATCTTA-TACTT
1 AAAAAATTAAAATTTAATCTTATTACTT
* * *
12857529 AAAAAA-T-AAATTTTATTTTATTATTT
1 AAAAAATTAAAATTTAATCTTATTACTT
12857555 AAAAA
1 AAAAA
12857560 TCTTAATCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 11 0.41
26 10 0.37
27 6 0.22
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (28 bp):
AAAAAATTAAAATTTAATCTTATTACTT
Found at i:12862253 original size:5 final size:5
Alignment explanation
Indices: 12862220--12862252 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
12862210 TATAGGAAGC
*
12862220 ATAAT ATAAT ATAAT ATAAT ATAAT ATAGT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
12862253 GCTTAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:12867101 original size:23 final size:23
Alignment explanation
Indices: 12867075--12867120 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
12867065 TATGGAGAAC
12867075 AACTATTTTCAATCTTTGTCCAA
1 AACTATTTTCAATCTTTGTCCAA
12867098 AACTATTTTCAATCTTTGTCCAA
1 AACTATTTTCAATCTTTGTCCAA
12867121 CTATGGAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.43
Consensus pattern (23 bp):
AACTATTTTCAATCTTTGTCCAA
Found at i:12869212 original size:14 final size:13
Alignment explanation
Indices: 12869186--12869220 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
12869176 CTAGAAATTA
12869186 TAATTTTTGTATT
1 TAATTTTTGTATT
*
12869199 TGATTTTATGTATT
1 TAATTTT-TGTATT
12869213 TAATTTTT
1 TAATTTTT
12869221 AATTAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (13 bp):
TAATTTTTGTATT
Found at i:12870362 original size:59 final size:60
Alignment explanation
Indices: 12870283--12870401 Score: 195
Period size: 59 Copynumber: 2.0 Consensus size: 60
12870273 TTGTTTTTTA
* *
12870283 TAATTATTTTAAAACTAATTTGTTAGTAATTTAGGATTATATTATAAATTTTTGTGTTTG
1 TAATTATTTTAAAACTAATTTATTAGTAATTTAGGATTATATTATAAATTGTTGTGTTTG
* *
12870343 TAATTA-TTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTG
1 TAATTATTTTAAAACTAATTTATTAGTAATTTAGGATTATATTATAAATTGTTGTGTTTG
12870402 GTTTAGTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
59 49 0.89
60 6 0.11
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.53
Consensus pattern (60 bp):
TAATTATTTTAAAACTAATTTATTAGTAATTTAGGATTATATTATAAATTGTTGTGTTTG
Found at i:12870501 original size:72 final size:74
Alignment explanation
Indices: 12870404--12870562 Score: 259
Period size: 72 Copynumber: 2.2 Consensus size: 74
12870394 TGTGTTTGGT
* * *
12870404 TTAGTATTTGGTGAGTTTATAGTAATGTAAAATTATTTTGTTAAATATTTTGTTAGTAA-TTTAT
1 TTAGTGTTTTGTGAGTTTATAGTAATATAAAATTATTTTGTTAAATATTTTGTTAGTAATTTTAT
12870468 TATAAATTA
66 TATAAATTA
*
12870477 TT-GTGTTTTGTGAGTTTTTAGTAATATAAAATTATTTTGTTAAATATTTTGTTAGTAATTTTAT
1 TTAGTGTTTTGTGAGTTTATAGTAATATAAAATTATTTTGTTAAATATTTTGTTAGTAATTTTAT
*
12870541 TATAAATTT
66 TATAAATTA
12870550 TTAGTGTTTTGTG
1 TTAGTGTTTTGTG
12870563 TCTTGTTATA
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
72 52 0.66
73 17 0.22
74 10 0.13
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.55
Consensus pattern (74 bp):
TTAGTGTTTTGTGAGTTTATAGTAATATAAAATTATTTTGTTAAATATTTTGTTAGTAATTTTAT
TATAAATTA
Found at i:12870532 original size:34 final size:34
Alignment explanation
Indices: 12870423--12870535 Score: 120
Period size: 34 Copynumber: 3.2 Consensus size: 34
12870413 GGTGAGTTTA
*
12870423 TAGTAATGTAAAATTATTTTGTTAAATATTTTGT
1 TAGTAATATAAAATTATTTTGTTAAATATTTTGT
* *** *
12870457 TAGTAATTTATTATAAATTATTGTGTTTTGTGAGTTT-T
1 TAGTAA--TA-TA-AAATTATTTTGTTAAAT-ATTTTGT
12870495 TAGTAATATAAAATTATTTTGTTAAATATTTTGT
1 TAGTAATATAAAATTATTTTGTTAAATATTTTGT
12870529 TAGTAAT
1 TAGTAAT
12870536 TTTATTATAA
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
33 4 0.06
34 27 0.44
35 2 0.03
36 3 0.05
37 2 0.03
38 20 0.32
39 4 0.06
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (34 bp):
TAGTAATATAAAATTATTTTGTTAAATATTTTGT
Found at i:12870824 original size:98 final size:102
Alignment explanation
Indices: 12870611--12870864 Score: 317
Period size: 98 Copynumber: 2.5 Consensus size: 102
12870601 ATTAGGTTAC
*
12870611 AAATTGTTAGTGTTTAG-TATAGGATTTTGTGATTTTTTTAGTAATGTAAATTTTTAAAAAAATA
1 AAATTGTTAGTGTTTAGTTATATG-TTTTGTGA-TTTTTTAGTAATGT-AA--TTTAAAAAAATA
* * * * **
12870675 ATTGTACAGTTATTTTGTTAGTACTTTTTGATTAGGTTATAT
61 AATGTACAGTTATTTTATTAGCAATTTACGATTAGGTTATAT
*
12870717 AAATTGTTAGTGTTTAGTTATTTGTTTTGTGATTTTTTAGTAATGT-ATTTAAAAAAA-AAAT-T
1 AAATTGTTAGTGTTTAGTTATATGTTTTGTGATTTTTTAGTAATGTAATTTAAAAAAATAAATGT
*
12870779 ATAGTTATTTTATTAGCAATTTACG-TTAGGTTATAT
66 ACAGTTATTTTATTAGCAATTTACGATTAGGTTATAT
12870815 AAATTGTTAGTGTTTAGTT-TAGTGTTTTGTGATTTTTT--TAATGTAATTTA
1 AAATTGTTAGTGTTTAGTTATA-TGTTTTGTGATTTTTTAGTAATGTAATTTA
12870865 TATATAATGT
Statistics
Matches: 135, Mismatches: 10, Indels: 15
0.84 0.06 0.09
Matches are distributed among these distances:
96 6 0.04
97 6 0.04
98 46 0.34
99 20 0.15
100 3 0.02
101 10 0.07
103 1 0.01
105 14 0.10
106 25 0.19
107 4 0.03
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.52
Consensus pattern (102 bp):
AAATTGTTAGTGTTTAGTTATATGTTTTGTGATTTTTTAGTAATGTAATTTAAAAAAATAAATGT
ACAGTTATTTTATTAGCAATTTACGATTAGGTTATAT
Found at i:12870896 original size:16 final size:16
Alignment explanation
Indices: 12870853--12870896 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
12870843 GTGATTTTTT
*
12870853 TAATGTAATTTATATA
1 TAATGTAATTTTTATA
12870869 TAATGTAATTTTTATA
1 TAATGTAATTTTTATA
*
12870885 TAATATAATTTT
1 TAATGTAATTTT
12870897 ATTTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (16 bp):
TAATGTAATTTTTATA
Found at i:12872814 original size:33 final size:33
Alignment explanation
Indices: 12872777--12872863 Score: 97
Period size: 33 Copynumber: 2.6 Consensus size: 33
12872767 TCCCTGCTTG
* * *
12872777 TATCCACCTCAGTACTCCGCTCCTTCC-GGCCCA
1 TATCCACCACAGTACTCCACTAC-TCCTGGCCCA
12872810 TATCCACCACTA-TACTCCACTACTCCTGGCCCA
1 TATCCACCAC-AGTACTCCACTACTCCTGGCCCA
* *
12872843 TATCCACCGCCGTACTCCACT
1 TATCCACCACAGTACTCCACT
12872864 CATCCAGGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
32 3 0.07
33 42 0.91
34 1 0.02
ACGTcount: A:0.20, C:0.47, G:0.09, T:0.24
Consensus pattern (33 bp):
TATCCACCACAGTACTCCACTACTCCTGGCCCA
Found at i:12873189 original size:77 final size:76
Alignment explanation
Indices: 12873062--12873204 Score: 207
Period size: 78 Copynumber: 1.9 Consensus size: 76
12873052 AATAACTTCA
* *
12873062 TATTTATGTAATGAATTTTTTGCCATTTTATTTATCAATTTAATTTATTTTTTAAAAAATTTAAA
1 TATTTATGTAATGAATTTTTTACCATTTTATTTATCAATTTAATTGATTTTTT-AAAAATTTAAA
12873127 TAGTCAACTTTG
65 TAGTCAACTTTG
* * * *
12873139 TATTTATGTAATGATTTTTTTTACCATTTTATTTATCAATTTTA-TGATTTTTTTACAATTTAAA
1 TATTTATGTAATGA-ATTTTTTACCATTTTATTTATCAATTTAATTGATTTTTTAAAAATTTAAA
12873203 TA
65 TA
12873205 AATAAATTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
76 11 0.19
77 22 0.37
78 26 0.44
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (76 bp):
TATTTATGTAATGAATTTTTTACCATTTTATTTATCAATTTAATTGATTTTTTAAAAATTTAAAT
AGTCAACTTTG
Found at i:12878100 original size:19 final size:19
Alignment explanation
Indices: 12878082--12878118 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12878072 TGTATTTTAT
*
12878082 TATTAT-TTTAATTAATTA
1 TATTATATTCAATTAATTA
12878100 TATTATATTCAATTAATTA
1 TATTATATTCAATTAATTA
12878119 ATAGCTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTATATTCAATTAATTA
Found at i:12878247 original size:16 final size:15
Alignment explanation
Indices: 12878228--12878298 Score: 58
Period size: 15 Copynumber: 4.7 Consensus size: 15
12878218 ATTATAGGTT
12878228 TTTAAAATAAATAAAA
1 TTTAAAATAAAT-AAA
*
12878244 TTT-AAATAACACAAA
1 TTTAAAATAA-ATAAA
*
12878259 TTT-AAA-AATTAAA
1 TTTAAAATAAATAAA
*
12878272 TATAAAATAAAGTAAA
1 TTTAAAATAAA-TAAA
*
12878288 TTTAAACTAAA
1 TTTAAAATAAA
12878299 AGATAAAATG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
13 5 0.11
14 5 0.11
15 17 0.39
16 17 0.39
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (15 bp):
TTTAAAATAAATAAA
Found at i:12878304 original size:23 final size:23
Alignment explanation
Indices: 12878278--12878321 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
12878268 TAAATATAAA
*
12878278 ATAAAGTAAATTTAAACTAAAAG
1 ATAAAATAAATTTAAACTAAAAG
*
12878301 ATAAAATGAATTTAAACTAAA
1 ATAAAATAAATTTAAACTAAA
12878322 CTGATACAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (23 bp):
ATAAAATAAATTTAAACTAAAAG
Found at i:12881851 original size:6 final size:6
Alignment explanation
Indices: 12881842--12881874 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
12881832 CTCGATAGGT
*
12881842 ATAGAG ATAGAG ATAAAG ATAGAG ATAGAG ATA
1 ATAGAG ATAGAG ATAGAG ATAGAG ATAGAG ATA
12881875 ATCATCATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.27, T:0.18
Consensus pattern (6 bp):
ATAGAG
Found at i:12885551 original size:23 final size:23
Alignment explanation
Indices: 12885525--12885571 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
12885515 ATTTTTTATG
12885525 GGATTGCTTATATAGGCCTTAGA
1 GGATTGCTTATATAGGCCTTAGA
12885548 GGATTGCTTATATAGGCCTTAGA
1 GGATTGCTTATATAGGCCTTAGA
12885571 G
1 G
12885572 CTTTGCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.34
Consensus pattern (23 bp):
GGATTGCTTATATAGGCCTTAGA
Found at i:12885577 original size:23 final size:23
Alignment explanation
Indices: 12885527--12885579 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
12885517 TTTTTATGGG
*
12885527 ATTGCTTATATAGGCCTTAGAGG
1 ATTGCTTATATAGGCCTTAGAGC
12885550 ATTGCTTATATAGGCCTTAGAGC
1 ATTGCTTATATAGGCCTTAGAGC
*
12885573 TTTGCTT
1 ATTGCTT
12885580 TACACTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.40
Consensus pattern (23 bp):
ATTGCTTATATAGGCCTTAGAGC
Found at i:12888659 original size:18 final size:17
Alignment explanation
Indices: 12888631--12888670 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
12888621 CCGCCTCGTG
12888631 GAAAACGATCCCTGCTA
1 GAAAACGATCCCTGCTA
12888648 GAAAAGCGATCCCTGCTA
1 GAAAA-CGATCCCTGCTA
12888666 GAAAA
1 GAAAA
12888671 TTTGCCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (17 bp):
GAAAACGATCCCTGCTA
Found at i:12893438 original size:31 final size:31
Alignment explanation
Indices: 12893402--12893462 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
12893392 TTAACAACTC
12893402 AGTGACTTAAATAAAAACTTTTGAATAGTTT
1 AGTGACTTAAATAAAAACTTTTGAATAGTTT
* *
12893433 AGTGACTTCAATAAAAACTTTTGGATAGTT
1 AGTGACTTAAATAAAAACTTTTGAATAGTT
12893463 CAATGACCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTTTGAATAGTTT
Found at i:12893927 original size:36 final size:36
Alignment explanation
Indices: 12893880--12893948 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
12893870 TCAAAATTAA
12893880 AAACCTTACACAAGTGTAATATTAGCTAAGCGATAG
1 AAACCTTACACAAGTGTAATATTAGCTAAGCGATAG
12893916 AAACCTTACACAAGTGTAATATTAGCTAAGCGA
1 AAACCTTACACAAGTGTAATATTAGCTAAGCGA
12893949 GTCGCAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (36 bp):
AAACCTTACACAAGTGTAATATTAGCTAAGCGATAG
Found at i:12911797 original size:16 final size:16
Alignment explanation
Indices: 12911776--12911815 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12911766 AATACCGATA
*
12911776 CCAATCGAATTAAGCC
1 CCAATCGAATTAAGAC
12911792 CCAATCGAATTAAGAC
1 CCAATCGAATTAAGAC
*
12911808 TCAATCGA
1 CCAATCGA
12911816 CAACTCTATT
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:0.40, C:0.28, G:0.12, T:0.20
Consensus pattern (16 bp):
CCAATCGAATTAAGAC
Found at i:12912637 original size:17 final size:17
Alignment explanation
Indices: 12912617--12912667 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
12912607 TAATTTTTTT
*
12912617 CTTTTATTTTCTTTTAA
1 CTTTCATTTTCTTTTAA
* *
12912634 CTTTCCTTTTTTTTTAA
1 CTTTCATTTTCTTTTAA
*
12912651 CTTATCATTCTCTTTTA
1 CTT-TCATTTTCTTTTA
12912668 TTTCTCCCTC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 17 0.63
18 10 0.37
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.67
Consensus pattern (17 bp):
CTTTCATTTTCTTTTAA
Found at i:12918962 original size:63 final size:63
Alignment explanation
Indices: 12918773--12918965 Score: 210
Period size: 63 Copynumber: 3.1 Consensus size: 63
12918763 ATACAAGACA
* * * * * *
12918773 GAAGAACCTGATCATAGTGAACCCAAAGCTATGGATTTGACTACC-GAACAGCTTCCCATGGAG
1 GAAGAACCTGATCATACTGAAGCCAAAGCTAAGGATTTGAGTACCAG-ACAGCTTCTCGTGGAG
* * * * * * *
12918836 GAAGTACCTGATCCTACTGAAGCCAAAGGTGAGGATTTGAGTACCAGA-ATGCTTGTTGCGGAG
1 GAAGAACCTGATCATACTGAAGCCAAAGCTAAGGATTTGAGTACCAGACA-GCTTCTCGTGGAG
* * *
12918899 GAAGAACCTGAGCATACTGAAGCCAAAGCTAAGGATTCGAGTACCAGACCGCTTCTCGTGGAG
1 GAAGAACCTGATCATACTGAAGCCAAAGCTAAGGATTTGAGTACCAGACAGCTTCTCGTGGAG
12918962 GAAG
1 GAAG
12918966 GAAGCACCGT
Statistics
Matches: 104, Mismatches: 23, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
62 1 0.01
63 102 0.98
64 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.20
Consensus pattern (63 bp):
GAAGAACCTGATCATACTGAAGCCAAAGCTAAGGATTTGAGTACCAGACAGCTTCTCGTGGAG
Found at i:12938285 original size:18 final size:17
Alignment explanation
Indices: 12938262--12938296 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
12938252 AAAATAAAAT
12938262 TTTTAATTAATTAATTAA
1 TTTTAATTAATT-ATTAA
12938280 TTTTAATTAATTATTAA
1 TTTTAATTAATTATTAA
12938297 ATAAAGTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTAATTAATTATTAA
Found at i:12938758 original size:10 final size:10
Alignment explanation
Indices: 12938723--12938770 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
12938713 TTTTTGCATA
12938723 TCTTTCCTTCT
1 TCTTTCC-TCT
*
12938734 TCTTT-CTCA
1 TCTTTCCTCT
12938743 TCTTTCCTCT
1 TCTTTCCTCT
12938753 TCTTTCCCTCT
1 TCTTT-CCTCT
*
12938764 TTTTTCC
1 TCTTTCC
12938771 CTAATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 7 0.22
10 11 0.34
11 14 0.44
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (10 bp):
TCTTTCCTCT
Found at i:12939885 original size:6 final size:6
Alignment explanation
Indices: 12939867--12939913 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
12939857 CTGAAGCAGT
* * *
12939867 GGCTCC AGCTCC GGATCC GGCTCC GGCTCC GGCTCC AGCTCC GGCTC
1 GGCTCC GGCTCC GGCTCC GGCTCC GGCTCC GGCTCC GGCTCC GGCTC
12939914 TGGTTTCGCT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.06, C:0.47, G:0.30, T:0.17
Consensus pattern (6 bp):
GGCTCC
Found at i:12941383 original size:15 final size:15
Alignment explanation
Indices: 12941363--12941398 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
12941353 GAGAGCTTGA
12941363 AAGTGCGTACGCTTC
1 AAGTGCGTACGCTTC
12941378 AAGTGCGTACGCTTC
1 AAGTGCGTACGCTTC
12941393 AAGTGC
1 AAGTGC
12941399 TTCCGACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.25
Consensus pattern (15 bp):
AAGTGCGTACGCTTC
Found at i:12947787 original size:20 final size:20
Alignment explanation
Indices: 12947758--12947815 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
12947748 AAAAAAAAAA
*
12947758 TCAAAGTAATTTTTAAAATT
1 TCAAAATAATTTTTAAAATT
*
12947778 TGAAAATAATTTTTAAAA-T
1 TCAAAATAATTTTTAAAATT
*
12947797 TCAAAAT-ATTTATAAAATT
1 TCAAAATAATTTTTAAAATT
12947816 CTAAAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 9 0.27
19 8 0.24
20 16 0.48
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (20 bp):
TCAAAATAATTTTTAAAATT
Found at i:12947812 original size:18 final size:18
Alignment explanation
Indices: 12947766--12947827 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
12947756 AATCAAAGTA
* *
12947766 ATTTTTAAAATTTGAAAAT
1 ATTTATAAAA-TTCAAAAT
*
12947785 AATTTTTAAAATTCAAAAT
1 -ATTTATAAAATTCAAAAT
*
12947804 ATTTATAAAATTCTAAA-
1 ATTTATAAAATTCAAAAT
12947821 ATTTATA
1 ATTTATA
12947828 TTTTAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
17 7 0.18
18 15 0.38
19 7 0.18
20 10 0.26
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTTATAAAATTCAAAAT
Found at i:12947821 original size:19 final size:20
Alignment explanation
Indices: 12947764--12947822 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
12947754 AAAATCAAAG
12947764 TAATTTTTAAAATT-TGAAAA
1 TAATTTTTAAAATTCT-AAAA
12947784 TAATTTTTAAAATTC-AAAA
1 TAATTTTTAAAATTCTAAAA
*
12947803 T-ATTTATAAAATTCTAAAA
1 TAATTTTTAAAATTCTAAAA
12947822 T
1 T
12947823 TTATATTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 12 0.33
19 10 0.28
20 14 0.39
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (20 bp):
TAATTTTTAAAATTCTAAAA
Found at i:12948387 original size:54 final size:48
Alignment explanation
Indices: 12948305--12948450 Score: 186
Period size: 47 Copynumber: 2.9 Consensus size: 48
12948295 CAATTCGACT
* * *
12948305 TGACTCGACTCGATCGAATACTCTGTAACTCCCCTAACTCCTCCTGACTCAAT
1 TGACTCGACTCGATCGAATACTTTGTAACACCCCTAACTCCTCC---C-C-AG
*
12948358 TGGACTTGACTCGATCGAATACTTTGTAACACCCCTAACTCCT-CCCAG
1 T-GACTCGACTCGATCGAATACTTTGTAACACCCCTAACTCCTCCCCAG
*
12948406 TCACTCGACTCGATCGAATACTTTGTAACACCCCTAACTCCTCCC
1 TGACTCGACTCGATCGAATACTTTGTAACACCCCTAACTCCTCCC
12948451 AGTCGTCGGA
Statistics
Matches: 85, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
47 39 0.46
48 4 0.05
49 1 0.01
50 1 0.01
53 2 0.02
54 38 0.45
ACGTcount: A:0.25, C:0.36, G:0.12, T:0.27
Consensus pattern (48 bp):
TGACTCGACTCGATCGAATACTTTGTAACACCCCTAACTCCTCCCCAG
Found at i:12948756 original size:15 final size:15
Alignment explanation
Indices: 12948736--12948771 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
12948726 TATTGAACCA
12948736 TACTTCGACTACTAC
1 TACTTCGACTACTAC
12948751 TACTTCGACTACTAC
1 TACTTCGACTACTAC
12948766 TACTTC
1 TACTTC
12948772 TACTTTCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.25, C:0.33, G:0.06, T:0.36
Consensus pattern (15 bp):
TACTTCGACTACTAC
Found at i:12949198 original size:15 final size:15
Alignment explanation
Indices: 12949180--12949216 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
12949170 GTTGTCCGTG
12949180 TGTGACATACAACCA
1 TGTGACATACAACCA
*
12949195 TGTGACATACAGCCA
1 TGTGACATACAACCA
12949210 TGTGACA
1 TGTGACA
12949217 GACCATGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (15 bp):
TGTGACATACAACCA
Found at i:12964008 original size:62 final size:64
Alignment explanation
Indices: 12963893--12964019 Score: 240
Period size: 62 Copynumber: 2.0 Consensus size: 64
12963883 TTTAGCACTC
12963893 GAAATCTGATTTCGAAAAACAATATTACATAATTTTTGAATCTTAAGTCGTAGTCTATTAATCG
1 GAAATCTGATTTCGAAAAACAATATTACATAATTTTTGAATCTTAAGTCGTAGTCTATTAATCG
12963957 GAAATCTGATTTCG-AAAACAATATTACATAA-TTTTGAATCTTAAGTCGTAGTCTATTAATCG
1 GAAATCTGATTTCGAAAAACAATATTACATAATTTTTGAATCTTAAGTCGTAGTCTATTAATCG
12964019 G
1 G
12964020 GTTTCAACTT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
62 32 0.51
63 17 0.27
64 14 0.22
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (64 bp):
GAAATCTGATTTCGAAAAACAATATTACATAATTTTTGAATCTTAAGTCGTAGTCTATTAATCG
Found at i:12969896 original size:15 final size:16
Alignment explanation
Indices: 12969860--12969898 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
12969850 AACATGTGAC
12969860 GGTTTAAATTATTATT
1 GGTTTAAATTATTATT
12969876 --TTTAAATTATT-TT
1 GGTTTAAATTATTATT
12969889 GGTTTAAATT
1 GGTTTAAATT
12969899 TGAAGTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.10
14 11 0.52
15 8 0.38
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (16 bp):
GGTTTAAATTATTATT
Found at i:12976032 original size:14 final size:14
Alignment explanation
Indices: 12976010--12976043 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12976000 CACACCATAC
12976010 ACATATATATATAT
1 ACATATATATATAT
*
12976024 ACATGTATATATAT
1 ACATATATATATAT
*
12976038 ATATAT
1 ACATAT
12976044 TATTACCCAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (14 bp):
ACATATATATATAT
Found at i:12978169 original size:2 final size:2
Alignment explanation
Indices: 12978162--12978190 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12978152 AACTTGTGAG
12978162 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12978191 GTCTATGCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12979595 original size:4 final size:4
Alignment explanation
Indices: 12979586--12979613 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
12979576 GATCAATATG
12979586 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
12979614 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:12984113 original size:23 final size:23
Alignment explanation
Indices: 12984083--12984128 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
12984073 AGATGTCAAT
12984083 CTCGAGAACATAAAAAGAATGAC
1 CTCGAGAACATAAAAAGAATGAC
12984106 CTCGAGAACATAAAAAGAATGAC
1 CTCGAGAACATAAAAAGAATGAC
12984129 TAACTTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.17, G:0.17, T:0.13
Consensus pattern (23 bp):
CTCGAGAACATAAAAAGAATGAC
Found at i:12988732 original size:2 final size:2
Alignment explanation
Indices: 12988727--12988761 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12988717 AAAATCATTT
12988727 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12988762 TTCCAGCTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12993478 original size:31 final size:31
Alignment explanation
Indices: 12993425--12993507 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 31
12993415 TCATTTAACG
* *
12993425 AAAAAAAATAATTTG-GTCACTAAACTATTC
1 AAAAAAATTTATTTGAGTCACTAAACTATTC
*
12993455 -AAAAATTTTCATTTGAGTCACTAAACTATTC
1 AAAAAAATTT-ATTTGAGTCACTAAACTATTC
*
12993486 AAAAAAATTTATTTAAGTCACT
1 AAAAAAATTTATTTGAGTCACT
12993508 TGACTATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 6 0.13
30 5 0.11
31 26 0.58
32 8 0.18
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (31 bp):
AAAAAAATTTATTTGAGTCACTAAACTATTC
Found at i:12996913 original size:18 final size:18
Alignment explanation
Indices: 12996890--12996947 Score: 116
Period size: 18 Copynumber: 3.2 Consensus size: 18
12996880 CTTTGTTTAA
12996890 TCTTAAATTTCTACATTT
1 TCTTAAATTTCTACATTT
12996908 TCTTAAATTTCTACATTT
1 TCTTAAATTTCTACATTT
12996926 TCTTAAATTTCTACATTT
1 TCTTAAATTTCTACATTT
12996944 TCTT
1 TCTT
12996948 TCTTCTTTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (18 bp):
TCTTAAATTTCTACATTT
Found at i:12996945 original size:9 final size:9
Alignment explanation
Indices: 12996897--12996946 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
12996887 TAATCTTAAA
12996897 TTTCTACAT
1 TTTCTACAT
*
12996906 TTTCTTA-AA
1 TTTC-TACAT
12996915 TTTCTACAT
1 TTTCTACAT
*
12996924 TTTCTTA-AA
1 TTTC-TACAT
12996933 TTTCTACAT
1 TTTCTACAT
12996942 TTTCT
1 TTTCT
12996947 TTCTTCTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
8 4 0.12
9 25 0.76
10 4 0.12
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (9 bp):
TTTCTACAT
Found at i:13004093 original size:10 final size:10
Alignment explanation
Indices: 13004078--13004129 Score: 86
Period size: 10 Copynumber: 5.1 Consensus size: 10
13004068 TTAAACTCTA
13004078 AAAGATAAAT
1 AAAGATAAAT
13004088 AAAGATAAAT
1 AAAGATAAAT
13004098 AAAAGATAAAT
1 -AAAGATAAAT
*
13004109 AAGGATAAAT
1 AAAGATAAAT
13004119 AAAGATAAAT
1 AAAGATAAAT
13004129 A
1 A
13004130 CTAAAATTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
10 29 0.74
11 10 0.26
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:13004100 original size:21 final size:21
Alignment explanation
Indices: 13004076--13004129 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
13004066 AATTAAACTC
13004076 TAAAAGATAAATAAAGATAAA
1 TAAAAGATAAATAAAGATAAA
*
13004097 TAAAAGATAAATAAGGATAAA
1 TAAAAGATAAATAAAGATAAA
13004118 T-AAAGATAAATA
1 TAAAAGATAAATA
13004130 CTAAAATTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (21 bp):
TAAAAGATAAATAAAGATAAA
Found at i:13004772 original size:13 final size:13
Alignment explanation
Indices: 13004754--13004782 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
13004744 TAATACATCA
13004754 TTTCTTCTTTTTT
1 TTTCTTCTTTTTT
13004767 TTTCTTCTTTTTT
1 TTTCTTCTTTTTT
13004780 TTT
1 TTT
13004783 TTTTTCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTCTTCTTTTTT
Found at i:13004780 original size:16 final size:15
Alignment explanation
Indices: 13004754--13004788 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
13004744 TAATACATCA
13004754 TTTCTTCTTTTTTTTT
1 TTTCTT-TTTTTTTTT
*
13004770 CTTCTTTTTTTTTTT
1 TTTCTTTTTTTTTTT
13004785 TTTC
1 TTTC
13004789 ATATATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTCTTTTTTTTTTT
Found at i:13006646 original size:42 final size:44
Alignment explanation
Indices: 13006567--13006667 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 44
13006557 CCTCAATTGA
** *
13006567 GATTTACGTATAAGACCATGTCTGGGACATTGGCATCG-TATTT
1 GATTTACGTATAAGACCATGTCTGGGACAGAGACATCGATATTT
* *
13006610 GATTT-CGTGTAAGACCCTGTCTGGGACAGAGACATCGATA-TT
1 GATTTACGTATAAGACCATGTCTGGGACAGAGACATCGATATTT
* *
13006652 GAATTACATATAAGAC
1 GATTTACGTATAAGAC
13006668 TACGTCCGGG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
42 33 0.69
43 15 0.31
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (44 bp):
GATTTACGTATAAGACCATGTCTGGGACAGAGACATCGATATTT
Found at i:13006942 original size:41 final size:41
Alignment explanation
Indices: 13006896--13006977 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
13006886 AAGTATGAAT
13006896 TATTCTATGAAATGATCATGAATCTTTATGGTTAAATTGTA
1 TATTCTATGAAATGATCATGAATCTTTATGGTTAAATTGTA
*
13006937 TATTCTATGAAATGATTATGAATCTTTATGGTTAAATTGTA
1 TATTCTATGAAATGATCATGAATCTTTATGGTTAAATTGTA
13006978 CTTATATACT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (41 bp):
TATTCTATGAAATGATCATGAATCTTTATGGTTAAATTGTA
Found at i:13009584 original size:5 final size:5
Alignment explanation
Indices: 13009576--13009617 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
13009566 AGTAATAAAT
13009576 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AA
13009618 ATTAAGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:13009627 original size:20 final size:20
Alignment explanation
Indices: 13009584--13009644 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
13009574 ATAATAAAAT
* *
13009584 AAAATAAAAT-AAAATAAAAT
1 AAAATAAAATAAAAAT-TAAG
13009604 AAAATAAAATAAAAATTAAG
1 AAAATAAAATAAAAATTAAG
13009624 AAAA-ATAAATAAAAA-TAAG
1 AAAATA-AAATAAAAATTAAG
13009643 AA
1 AA
13009645 TTAGGTTGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.19
20 25 0.68
21 5 0.14
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAATAAAATAAAAATTAAG
Found at i:13012768 original size:4 final size:4
Alignment explanation
Indices: 13012759--13012847 Score: 88
Period size: 4 Copynumber: 21.8 Consensus size: 4
13012749 CCCTTTTCTA
** * * *
13012759 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TCAC GTTTGC TCTC TGTA
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTT-C TTTC TTTC
** *
13012809 ACTC TTTC TATC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
13012848 TTTAACTTAC
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
4 65 0.94
5 3 0.04
6 1 0.01
ACGTcount: A:0.04, C:0.26, G:0.03, T:0.66
Consensus pattern (4 bp):
TTTC
Found at i:13018967 original size:47 final size:47
Alignment explanation
Indices: 13018858--13018968 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
13018848 CCGGAATAAG
*
13018858 CACATAGTGCTTCATCGGAACAAATCCAGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCAGAACTTTAACAGTATAGTA
* * * *
13018905 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCAGAACTTTAACAGTA-TAGTA
13018952 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
13018969 ACTTAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCAGAACTTTAACAGTATAGTA
Found at i:13019738 original size:4 final size:4
Alignment explanation
Indices: 13019729--13019757 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
13019719 CCCTTTTCTA
13019729 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
13019758 CACGTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:13019854 original size:14 final size:13
Alignment explanation
Indices: 13019826--13019859 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
13019816 TCATAAATCT
13019826 ATATTCAATAAATA
1 ATATT-AATAAATA
13019840 ATATTAATAATATA
1 ATATTAATAA-ATA
13019854 ATATTA
1 ATATTA
13019860 TTCTAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATTAATAAATA
Found at i:13021873 original size:9 final size:9
Alignment explanation
Indices: 13021859--13021885 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
13021849 CTATCCCTAT
13021859 AAAATAATA
1 AAAATAATA
13021868 AAAATAATA
1 AAAATAATA
13021877 AAAATAATA
1 AAAATAATA
13021886 GTATAAGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAATAATA
Found at i:13022771 original size:21 final size:21
Alignment explanation
Indices: 13022747--13022789 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
13022737 AATTAAACTC
13022747 TAAAAGATAAATAAAGATAAA
1 TAAAAGATAAATAAAGATAAA
13022768 TAAAAGATAAATAAAGATAAA
1 TAAAAGATAAATAAAGATAAA
13022789 T
1 T
13022790 GCTAAGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (21 bp):
TAAAAGATAAATAAAGATAAA
Found at i:13022773 original size:11 final size:10
Alignment explanation
Indices: 13022749--13022789 Score: 73
Period size: 10 Copynumber: 4.0 Consensus size: 10
13022739 TTAAACTCTA
13022749 AAAGATAAAT
1 AAAGATAAAT
13022759 AAAGATAAAT
1 AAAGATAAAT
13022769 AAAAGATAAAT
1 -AAAGATAAAT
13022780 AAAGATAAAT
1 AAAGATAAAT
13022790 GCTAAGATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 20 0.67
11 10 0.33
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.20
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:13032007 original size:11 final size:12
Alignment explanation
Indices: 13031992--13032041 Score: 59
Period size: 11 Copynumber: 4.1 Consensus size: 12
13031982 CAAAGTTAAT
13031992 ATTAGTTAATT-
1 ATTAGTTAATTA
13032003 ATTAGTTAATTA
1 ATTAGTTAATTA
13032015 AGTTAGGATTAATTA
1 A-TTA-G-TTAATTA
13032030 ATTAGTT-ATTA
1 ATTAGTTAATTA
13032041 A
1 A
13032042 ACTAAATACT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
11 16 0.46
12 3 0.09
13 4 0.11
14 4 0.11
15 8 0.23
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (12 bp):
ATTAGTTAATTA
Found at i:13032018 original size:30 final size:30
Alignment explanation
Indices: 13031984--13032041 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
13031974 TGATTAATCA
* *
13031984 AAGTTAATATTAGTTAATTA-TTAGTTAATT
1 AAGTTAAGATTAATTAATTAGTTA-TTAATT
*
13032014 AAGTTAGGATTAATTAATTAGTTATTAA
1 AAGTTAAGATTAATTAATTAGTTATTAA
13032042 ACTAAATACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (30 bp):
AAGTTAAGATTAATTAATTAGTTATTAATT
Found at i:13032040 original size:15 final size:15
Alignment explanation
Indices: 13031991--13032041 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
13031981 TCAAAGTTAA
*
13031991 TATTAGTTAATTA-T
1 TATTAATTAATTAGT
13032005 TAGTTAATTAAGTTAG-
1 TA-TTAATTAA-TTAGT
*
13032021 GATTAATTAATTAGT
1 TATTAATTAATTAGT
13032036 TATTAA
1 TATTAA
13032042 ACTAAATACT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
14 6 0.20
15 20 0.67
16 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (15 bp):
TATTAATTAATTAGT
Found at i:13037205 original size:53 final size:53
Alignment explanation
Indices: 13037064--13037214 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
13037054 ACAAGTGTGC
* * **
13037064 CCGTTTAAGATCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
13037117 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
13037170 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
13037215 ACCGTGTAAG
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:13039405 original size:2 final size:2
Alignment explanation
Indices: 13039398--13039436 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
13039388 TATCTTGAGT
13039398 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13039437 TTCATTGCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13045406 original size:2 final size:2
Alignment explanation
Indices: 13045399--13045427 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13045389 TTTATGAATG
13045399 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13045428 GTTTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13046564 original size:17 final size:17
Alignment explanation
Indices: 13046542--13046584 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
13046532 CTGTAGGGGG
*
13046542 TCACACGGCCATGTGAC
1 TCACACGGCCATATGAC
13046559 TCACACGGCCATATGAC
1 TCACACGGCCATATGAC
13046576 TCACACGGC
1 TCACACGGC
13046585 TGAGAGACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.26, C:0.37, G:0.21, T:0.16
Consensus pattern (17 bp):
TCACACGGCCATATGAC
Found at i:13047175 original size:22 final size:22
Alignment explanation
Indices: 13047149--13047193 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
13047139 ATTATGTATA
13047149 TTAATTCATAATATAA-TTAATT
1 TTAATT-ATAATATAATTTAATT
* *
13047171 TTAATTTTAATCTAATTTAATT
1 TTAATTATAATATAATTTAATT
13047193 T
1 T
13047194 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTATAATATAATTTAATT
Found at i:13049979 original size:27 final size:25
Alignment explanation
Indices: 13049869--13049963 Score: 181
Period size: 25 Copynumber: 3.8 Consensus size: 25
13049859 CTGTACATGT
*
13049869 ATGCTCACACGAGCTGTGAATCAGA
1 ATGCTCACACAAGCTGTGAATCAGA
13049894 ATGCTCACACAAGCTGTGAATCAGA
1 ATGCTCACACAAGCTGTGAATCAGA
13049919 ATGCTCACACAAGCTGTGAATCAGA
1 ATGCTCACACAAGCTGTGAATCAGA
13049944 ATGCTCACACAAGCTGTGAA
1 ATGCTCACACAAGCTGTGAA
13049964 AATGGGCCTG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
25 69 1.00
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (25 bp):
ATGCTCACACAAGCTGTGAATCAGA
Found at i:13059775 original size:35 final size:35
Alignment explanation
Indices: 13059736--13059842 Score: 214
Period size: 35 Copynumber: 3.1 Consensus size: 35
13059726 TCAGCTGAAA
13059736 TTACTTCCCCTATTTGATTTTTCAGATCAATTTTT
1 TTACTTCCCCTATTTGATTTTTCAGATCAATTTTT
13059771 TTACTTCCCCTATTTGATTTTTCAGATCAATTTTT
1 TTACTTCCCCTATTTGATTTTTCAGATCAATTTTT
13059806 TTACTTCCCCTATTTGATTTTTCAGATCAATTTTT
1 TTACTTCCCCTATTTGATTTTTCAGATCAATTTTT
13059841 TT
1 TT
13059843 CTCTACCGTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 72 1.00
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.55
Consensus pattern (35 bp):
TTACTTCCCCTATTTGATTTTTCAGATCAATTTTT
Found at i:13061936 original size:24 final size:24
Alignment explanation
Indices: 13061906--13062172 Score: 417
Period size: 24 Copynumber: 11.1 Consensus size: 24
13061896 GAATGTGACT
* *
13061906 ATAGCAAATCGCACACATAGTGCT
1 ATAGTAAATCGCACACATAGTGCC
*
13061930 ATAGCAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
13061954 ATAGTAAATCGCACACATAGTGCT
1 ATAGTAAATCGCACACATAGTGCC
13061978 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
13062002 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
* *
13062026 ATAGTGAATCGCACACCTAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
* *
13062050 ATAGTGAATCGCACACCTAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
13062074 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
13062098 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
* *
13062122 ATAGTGAGTCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
13062146 ATAGTAAACCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
13062170 ATA
1 ATA
13062173 TGGTCTTTGC
Statistics
Matches: 230, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 230 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (24 bp):
ATAGTAAATCGCACACATAGTGCC
Found at i:13066740 original size:10 final size:10
Alignment explanation
Indices: 13066713--13066752 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
13066703 TTAAATTCCA
13066713 AAAGATAAAT
1 AAAGATAAAT
13066723 ACAA-ATAAAT
1 A-AAGATAAAT
*
13066733 AAAGATAATT
1 AAAGATAAAT
13066743 AAAGATAAAT
1 AAAGATAAAT
13066753 CTTAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 2 0.08
10 22 0.85
11 2 0.08
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.23
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:13070635 original size:36 final size:36
Alignment explanation
Indices: 13070595--13070667 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
13070585 CCAAATAAAG
13070595 TACATGTTCATACAACTAATATGCCCAAAAGGCACC
1 TACATGTTCATACAACTAATATGCCCAAAAGGCACC
13070631 TACATGTTCATACAACTAATATGCCCAAAAGGCACC
1 TACATGTTCATACAACTAATATGCCCAAAAGGCACC
13070667 T
1 T
13070668 CAATCACAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.23
Consensus pattern (36 bp):
TACATGTTCATACAACTAATATGCCCAAAAGGCACC
Found at i:13070943 original size:2 final size:2
Alignment explanation
Indices: 13070936--13070961 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13070926 ATAAGGCCAC
13070936 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
13070962 CAATCTAGCC
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:13074895 original size:19 final size:19
Alignment explanation
Indices: 13074861--13074899 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
13074851 ATTGGTTGGA
13074861 TGTTGATATTGAAAATTAT
1 TGTTGATATTGAAAATTAT
13074880 TGTTGGATATTG-AAATTAT
1 TGTT-GATATTGAAAATTAT
13074899 T
1 T
13074900 ATGTTTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (19 bp):
TGTTGATATTGAAAATTAT
Found at i:13075893 original size:16 final size:16
Alignment explanation
Indices: 13075872--13075904 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
13075862 GTAATACTAG
13075872 TTATGCACTTGGATAA
1 TTATGCACTTGGATAA
13075888 TTATGCACTTGGATAA
1 TTATGCACTTGGATAA
13075904 T
1 T
13075905 ACTATAGTTA
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:0.12, G:0.18, T:0.39
Consensus pattern (16 bp):
TTATGCACTTGGATAA
Found at i:13076976 original size:9 final size:7
Alignment explanation
Indices: 13076943--13076968 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
13076933 ACTCATCTCA
13076943 CACACCT
1 CACACCT
13076950 CACACCT
1 CACACCT
13076957 CACACCT
1 CACACCT
13076964 CACAC
1 CACAC
13076969 GTCTCACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.58, G:0.00, T:0.12
Consensus pattern (7 bp):
CACACCT
Found at i:13079919 original size:39 final size:39
Alignment explanation
Indices: 13079875--13079966 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 39
13079865 TATTTAAAAA
*
13079875 AATTTAAAATT-TGGATTATTTTGGTTACATGTTCAAATC
1 AATTTAAAATTAAGGATT-TTTTGGTTACATGTTCAAATC
* * * *
13079914 AATTTATAATTAAAGGATTTTTTTGTTATATGTTCATATC
1 AATTTAAAATT-AAGGATTTTTTGGTTACATGTTCAAATC
* *
13079954 AATTCATAATTAA
1 AATTTAAAATTAA
13079967 ATCATTTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 12 0.27
40 28 0.62
41 5 0.11
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (39 bp):
AATTTAAAATTAAGGATTTTTTGGTTACATGTTCAAATC
Found at i:13079955 original size:40 final size:41
Alignment explanation
Indices: 13079887--13079967 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 41
13079877 TTTAAAATTT
*
13079887 GGATTATTTTGGTTACATGTTCAAATCAATTTATAATTAAA
1 GGATTATTTTGGTTACATGTTCAAATCAATTCATAATTAAA
* * *
13079928 GGATT-TTTTTGTTATATGTTCATATCAATTCATAATTAAA
1 GGATTATTTTGGTTACATGTTCAAATCAATTCATAATTAAA
13079968 TCATTTTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 31 0.86
41 5 0.14
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.47
Consensus pattern (41 bp):
GGATTATTTTGGTTACATGTTCAAATCAATTCATAATTAAA
Found at i:13080002 original size:16 final size:16
Alignment explanation
Indices: 13079963--13080008 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
13079953 CAATTCATAA
*
13079963 TTAAATCATTTTAAGAT
1 TTAAATTATTTT-AGAT
* *
13079980 TTTAATTATTTTATAT
1 TTAAATTATTTTAGAT
13079996 TTAAATTATTTTA
1 TTAAATTATTTTA
13080009 ACTTTTTACG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (16 bp):
TTAAATTATTTTAGAT
Found at i:13087827 original size:5 final size:6
Alignment explanation
Indices: 13087798--13087825 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
13087788 GCTGAATCTT
13087798 TTTTTG TTTTTG TTTTTG TTTTTG TTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTT
13087826 GTGGAACTTG
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:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:13092871 original size:18 final size:18
Alignment explanation
Indices: 13092836--13092871 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
13092826 GTCATTTTTT
*
13092836 GTTAAAAACGAAAAAAAA
1 GTTAAAAACAAAAAAAAA
13092854 GTTAAAAACAAAAAAAAA
1 GTTAAAAACAAAAAAAAA
13092872 TAAAAAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.75, C:0.06, G:0.08, T:0.11
Consensus pattern (18 bp):
GTTAAAAACAAAAAAAAA
Found at i:13092878 original size:18 final size:18
Alignment explanation
Indices: 13092839--13092878 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
13092829 ATTTTTTGTT
* *
13092839 AAAAACGAAAAAAAAGTT
1 AAAAACGAAAAAAAAATA
13092857 AAAAAC-AAAAAAAAATA
1 AAAAACGAAAAAAAAATA
13092874 AAAAA
1 AAAAA
13092879 GAGGGTTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.82, C:0.05, G:0.05, T:0.07
Consensus pattern (18 bp):
AAAAACGAAAAAAAAATA
Found at i:13092927 original size:27 final size:27
Alignment explanation
Indices: 13092897--13092968 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
13092887 TGTGGGTCTC
* *
13092897 AGAGGAGGTACCGGTTGTGCCTCTGGT
1 AGAGGAGGCACCGGTTGTACCTCTGGT
* *
13092924 AGAGGCGGCACCGGTTGTACCTCTGGC
1 AGAGGAGGCACCGGTTGTACCTCTGGT
* * *
13092951 ATAGGCGACACCGGTTGT
1 AGAGGAGGCACCGGTTGT
13092969 TCTATACTAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.17, C:0.24, G:0.38, T:0.22
Consensus pattern (27 bp):
AGAGGAGGCACCGGTTGTACCTCTGGT
Found at i:13093379 original size:152 final size:151
Alignment explanation
Indices: 13093093--13093940 Score: 1150
Period size: 150 Copynumber: 5.7 Consensus size: 151
13093083 TTAGGTTTTT
* * *
13093093 TATATAAAAACACTAAAATAATACATTTGAAACATGATATACTAAAATAATAT---AAA-AAACT
1 TATA-AAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAAT
* * *
13093154 ACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATATTAAAAATACAAACAAAGGGCCAAAA
65 ACAAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTAAAAATACAAAGAAAGGGCCAAAA
* * *
13093219 TTAGGGTTATTTATTAAATTAA
130 TCAAGGTTATTTACTAAATTAA
13093241 TATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAAAT
1 TATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATAT-AAAAAATAAAAT
* *
13093306 ACAAAAATAGTATATTTTAAAAAATAAAATCTGAAAATTTTAAAAATACAAAGAAATGGCCAAAA
65 ACAAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTAAAAATACAAAGAAAGGGCCAAAA
13093371 TCAAGGTTATTTACTAAATTAA
130 TCAAGGTTATTTACTAAATTAA
* * * *
13093393 TATAAAAAATATTAAAATAATATATTTGAAACATTATGTTCTAAAATAATAT-AAAAATAAAATA
1 TATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATA
*
13093457 -AGAAAATAGTATATTTTTAAAAATAAAATCCGAAAATTTTAAAAATACAAAGAAAGGGCCAAAA
66 CA-AAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTAAAAATACAAAGAAAGGGCCAAAA
*
13093521 TCAGGGTTATTTACTAAATTAA
130 TCAAGGTTATTTACTAAATTAA
* * * * *
13093543 TATAAAAAACACTAAAAAAATATATTTAAAATATTATATACTAAAATAATATAAAAAATAAAATA
1 TATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATA
* * * *
13093608 CGAAAATAGTGTATTTTTAAAAATAAAATCCAAAAATTTTAAAAATACAAAGAAAGGGCCAAAAT
66 CAAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTAAAAATACAAAGAAAGGGCCAAAAT
13093673 C-AGGTTATTTACTAAATTAA
131 CAAGGTTATTTACTAAATTAA
13093693 TATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATAT-----A-AAAAT-
1 TATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATA
* * * * * *
13093751 ----AATA-TAT-TTTT-GAAAATAAAATTCAAAAATTTTGAAAATACAAAGAAATGGTCAAAAT
66 CAAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTAAAAATACAAAGAAAGGGCCAAAAT
*
13093809 CAGGGTTATTTACTAAATTAA
131 CAAGGTTATTTACTAAATTAA
* *
13093830 TATAAAAAAATACTAAAATAATATATTTGAAACATTATGTACTAAAAT-A-A-AAAAAATAAAAT
1 TAT-AAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAAT
** *
13093892 ATGAAAATAGTATATATTAAAAAATAAAATCCGAAAATTTTAAAAATAC
65 ACAAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTAAAAATAC
13093941 GAAAATTTTT
Statistics
Matches: 627, Mismatches: 49, Indels: 47
0.87 0.07 0.07
Matches are distributed among these distances:
136 44 0.07
137 26 0.04
138 44 0.07
139 4 0.01
140 1 0.00
141 5 0.01
144 5 0.01
145 1 0.00
146 4 0.01
147 49 0.08
148 7 0.01
149 27 0.04
150 202 0.32
151 77 0.12
152 131 0.21
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (151 bp):
TATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATA
CAAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTAAAAATACAAAGAAAGGGCCAAAAT
CAAGGTTATTTACTAAATTAA
Found at i:13093529 original size:302 final size:297
Alignment explanation
Indices: 13093093--13093940 Score: 1238
Period size: 302 Copynumber: 2.9 Consensus size: 297
13093083 TTAGGTTTTT
* * *
13093093 TATATAAAAACACTAAAATAATACATTTGAAACATGATATACTAAAATAATATAAAAAACTACGA
1 TATA-AAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATA-GA
* * * *
13093158 AAATAGTATATTTTAAAAAATAAAATCCGAAAATATTAAAAATACAAACAAAGGGCCAAAATTAG
64 AAATAGTATATTTTTAAAAATAAAATCCGAAAATTTTAAAAATACAAAGAAAGGGCCAAAATCAG
* *
13093223 GGTTATTTATTAAATTAATATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAAT
129 GGTTATTTACTAAATTAATATAAAAAACACTAAAATAATATATTTGAAACATTATGTACTAAAAT
* *
13093288 AATATAAAAAAATAAAATACAAAAATAGTATATTTTAAAAAATAAAATCTGAAAATTTTAAAAAT
194 AATATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTAAAAAT
*
13093353 ACAAAGAAATGGCCAAAATCAAGGTTATTTACTAAATTAA
259 ACAAAGAAAGGGCCAAAATC-AGGTTATTTACTAAATTAA
* * * *
13093393 TATAAAAAATATTAAAATAATATATTTGAAACATTATGTTCTAAAATAATATAAAAATAAAATAA
1 TATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATAT--AAA-AAAAT-A
13093458 GAAAATAGTATATTTTTAAAAATAAAATCCGAAAATTTTAAAAATACAAAGAAAGGGCCAAAATC
62 GAAAATAGTATATTTTTAAAAATAAAATCCGAAAATTTTAAAAATACAAAGAAAGGGCCAAAATC
* * * *
13093523 AGGGTTATTTACTAAATTAATATAAAAAACACTAAAAAAATATATTTAAAATATTATATACTAAA
127 AGGGTTATTTACTAAATTAATATAAAAAACACTAAAATAATATATTTGAAACATTATGTACTAAA
* * *
13093588 ATAATAT-AAAAAATAAAATACGAAAATAGTGTATTTTTAAAAATAAAATCCAAAAATTTTAAAA
192 ATAATATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTAAAA
13093652 ATACAAAGAAAGGGCCAAAATCAGGTTATTTACTAAATTAA
257 ATACAAAGAAAGGGCCAAAATCAGGTTATTTACTAAATTAA
13093693 TATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATAT--AAAAAT-----
1 TATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAGAAA
* * * * * *
13093751 A-A-TATATTTTTGAAAATAAAATTCAAAAATTTTGAAAATACAAAGAAATGGTCAAAATCAGGG
66 ATAGTATATTTTTAAAAATAAAATCCGAAAATTTTAAAAATACAAAGAAAGGGCCAAAATCAGGG
*
13093814 TTATTTACTAAATTAATATAAAAAAATACTAAAATAATATATTTGAAACATTATGTACT--AA-A
131 TTATTTACTAAATTAATAT-AAAAAACACTAAAATAATATATTTGAAACATTATGTACTAAAATA
* *
13093876 ATA-AAAAAAATAAAATATGAAAATAGTATATATTAAAAAATAAAATCCGAAAATTTTAAAAATA
195 ATATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTAAAAATA
13093940 C
260 C
13093941 GAAAATTTTT
Statistics
Matches: 499, Mismatches: 43, Indels: 27
0.88 0.08 0.05
Matches are distributed among these distances:
285 60 0.12
286 2 0.00
287 74 0.15
288 35 0.07
289 1 0.00
295 5 0.01
296 1 0.00
299 42 0.08
300 71 0.14
301 76 0.15
302 131 0.26
303 1 0.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (297 bp):
TATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAGAAA
ATAGTATATTTTTAAAAATAAAATCCGAAAATTTTAAAAATACAAAGAAAGGGCCAAAATCAGGG
TTATTTACTAAATTAATATAAAAAACACTAAAATAATATATTTGAAACATTATGTACTAAAATAA
TATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTAAAAATAC
AAAGAAAGGGCCAAAATCAGGTTATTTACTAAATTAA
Found at i:13093739 original size:138 final size:138
Alignment explanation
Indices: 13093597--13093940 Score: 449
Period size: 136 Copynumber: 2.4 Consensus size: 138
13093587 AATAATATAA
* *
13093597 AAAATAAAATACGAAAATAGTGTATTTTTAAAAATAAAATCCAAAAATTTTAAAAATACAAAGAA
1 AAAATAAAATA--AAAATAATATATTTTTAAAAATAAAATCCAAAAATTTTAAAAATACAAAGAA
13093662 AGGGCCAAAATCA-GGTTATTTACTAAATTAATAT-AAAAAACACTAAAATAATACATTTGAAAC
64 AGGGCCAAAATCAGGGTTATTTACTAAATTAATATAAAAAAACACTAAAATAATACATTTGAAAC
13093725 ATTATGTACT
129 ATTATGTACT
* * * * *
13093735 AAAATAATATAAAAATAATATATTTTTGAAAATAAAATTCAAAAATTTTGAAAATACAAAGAAAT
1 AAAATAAAATAAAAATAATATATTTTTAAAAATAAAATCCAAAAATTTTAAAAATACAAAGAAAG
* * *
13093800 GGTCAAAATCAGGGTTATTTACTAAATTAATATAAAAAAATACTAAAATAATATATTTGAAACAT
66 GGCCAAAATCAGGGTTATTTACTAAATTAATATAAAAAAACACTAAAATAATACATTTGAAACAT
13093865 TATGTACT
131 TATGTACT
* *
13093873 AAAATAAAAAAAATAAAATATGAAAATAGTATATATTAAAAAATAAAATCCGAAAATTTTAAAAA
1 AAAAT----AAAATAAAA-AT---AATA-TAT-T-TTTAAAAATAAAATCCAAAAATTTTAAAAA
13093938 TAC
55 TAC
13093941 GAAAATTTTT
Statistics
Matches: 177, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
136 58 0.33
137 21 0.12
138 52 0.29
142 8 0.05
143 2 0.01
146 4 0.02
147 3 0.02
148 1 0.01
149 28 0.16
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (138 bp):
AAAATAAAATAAAAATAATATATTTTTAAAAATAAAATCCAAAAATTTTAAAAATACAAAGAAAG
GGCCAAAATCAGGGTTATTTACTAAATTAATATAAAAAAACACTAAAATAATACATTTGAAACAT
TATGTACT
Found at i:13093943 original size:17 final size:17
Alignment explanation
Indices: 13093917--13093949 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13093907 ATTAAAAAAT
*
13093917 AAAATCCGAAAATTTTA
1 AAAATACGAAAATTTTA
13093934 AAAATACGAAAATTTT
1 AAAATACGAAAATTTT
13093950 TTATTTCCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (17 bp):
AAAATACGAAAATTTTA
Found at i:13094151 original size:38 final size:38
Alignment explanation
Indices: 13094107--13094203 Score: 99
Period size: 38 Copynumber: 2.5 Consensus size: 38
13094097 ATGCCGGGTG
*
13094107 TATTAAATATATTATATTTTAAATCAAAATATTT-TACT
1 TATTAAATATATTATATTTT-AATAAAAATATTTGTACT
* * * *
13094145 TATTAAATATTTTAAATTATAATAAAAATATTTGTATT
1 TATTAAATATATTATATTTTAATAAAAATATTTGTACT
*
13094183 TGAGTTGAATATATT-TATTTT
1 T-A-TTAAATATATTATATTTT
13094204 TTTAATATAG
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
37 12 0.26
38 21 0.45
39 5 0.11
40 9 0.19
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (38 bp):
TATTAAATATATTATATTTTAATAAAAATATTTGTACT
Found at i:13094275 original size:27 final size:27
Alignment explanation
Indices: 13094237--13094319 Score: 157
Period size: 27 Copynumber: 3.1 Consensus size: 27
13094227 ATGTCGCCTA
13094237 TGCCAGAGGCACGACCGGTGCCACCTC
1 TGCCAGAGGCACGACCGGTGCCACCTC
13094264 TGCCAGAGGCACGACCGGTGCCACCTC
1 TGCCAGAGGCACGACCGGTGCCACCTC
*
13094291 TGCCAGAGGCACAACCGGTGCCACCTC
1 TGCCAGAGGCACGACCGGTGCCACCTC
13094318 TG
1 TG
13094320 GGACCTACAC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.19, C:0.40, G:0.29, T:0.12
Consensus pattern (27 bp):
TGCCAGAGGCACGACCGGTGCCACCTC
Found at i:13095200 original size:6 final size:6
Alignment explanation
Indices: 13095191--13095245 Score: 101
Period size: 6 Copynumber: 9.2 Consensus size: 6
13095181 ATCTTTTTTA
*
13095191 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GCATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
13095239 GTATAT G
1 GTATAT G
13095246 CAAGTGGTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (6 bp):
GTATAT
Found at i:13102668 original size:27 final size:27
Alignment explanation
Indices: 13102630--13102684 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
13102620 TCAACCCAAA
13102630 ATCCGAGTTGAACATTAAAAAACTAAC
1 ATCCGAGTTGAACATTAAAAAACTAAC
13102657 ATCCGAGTTGAACATTAAAAAACTAAC
1 ATCCGAGTTGAACATTAAAAAACTAAC
13102684 A
1 A
13102685 CTTTCACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.49, C:0.18, G:0.11, T:0.22
Consensus pattern (27 bp):
ATCCGAGTTGAACATTAAAAAACTAAC
Found at i:13105325 original size:7 final size:7
Alignment explanation
Indices: 13105315--13105341 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
13105305 TTTCATTTTC
13105315 CATTTGG
1 CATTTGG
13105322 CATTTGG
1 CATTTGG
13105329 CATTTGG
1 CATTTGG
13105336 CATTTG
1 CATTTG
13105342 CTCTTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (7 bp):
CATTTGG
Found at i:13105741 original size:16 final size:19
Alignment explanation
Indices: 13105693--13105754 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
13105683 TTTAGTCATA
13105693 TAATAAATTATTAATATAAT
1 TAATAAATTATTAATAT-AT
13105713 TAATATAATTTATT-AT-T-T
1 TAATA-AA-TTATTAATATAT
*
13105731 TAATAAATTATTTAATATTT
1 TAATAAATTA-TTAATATAT
13105751 TAAT
1 TAAT
13105755 TTTATTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
16 3 0.08
17 4 0.11
18 8 0.22
19 1 0.03
20 11 0.31
21 4 0.11
22 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATAAATTATTAATATAT
Found at i:13106244 original size:18 final size:20
Alignment explanation
Indices: 13106221--13106262 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
13106211 TATATTAAAT
13106221 AAATTATT-AAAAATTTA-A
1 AAATTATTAAAAAATTTATA
13106239 AAATTATTAAAAAATTTATA
1 AAATTATTAAAAAATTTATA
13106259 AAAT
1 AAAT
13106263 CTAATTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.36
19 9 0.41
20 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATTATTAAAAAATTTATA
Found at i:13111504 original size:42 final size:42
Alignment explanation
Indices: 13111449--13111738 Score: 312
Period size: 42 Copynumber: 6.7 Consensus size: 42
13111439 AATCCTCCTG
*
13111449 AAAACATAAATCCTAATTGAGGTGAGATTAAATGAAAAATTA
1 AAAAAATAAATCCTAATTGAGGTGAGATTAAATGAAAAATTA
* *
13111491 AAAAAATGAATCCTAATTGAGGTGAGATTAAATGAAAAAATA
1 AAAAAATAAATCCTAATTGAGGTGAGATTAAATGAAAAATTA
* * * *
13111533 AAAAGATAAATCCTAATTGAGGTGTGATTAAATAAAAAACTA
1 AAAAAATAAATCCTAATTGAGGTGAGATTAAATGAAAAATTA
** * *
13111575 AAAAGGTAAATCTTAACTGAGGTGAGATTAAATGAAAAATTAA
1 AAAAAATAAATCCTAATTGAGGTGAGATTAAATGAAAAATT-A
* * * *
13111618 AAAGATAAGCTTAAATCCTAATTAAGTTGGGATTAAAT-AAAAAGCTA
1 AAA-A-AA---TAAATCCTAATTGAGGTGAGATTAAATGAAAAA-TTA
* * **
13111665 AAAAAGATAAATCCTAATTGAGTTGGGATTAAATGAAATGTTA
1 AAAAA-ATAAATCCTAATTGAGGTGAGATTAAATGAAAAATTA
* *
13111708 AAAAGATAAATCCTAATTGAGGTGGGATTAA
1 AAAAAATAAATCCTAATTGAGGTGAGATTAA
13111739 TTGTGGGGCT
Statistics
Matches: 211, Mismatches: 28, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
42 136 0.64
43 36 0.17
44 4 0.02
45 1 0.00
46 2 0.01
47 9 0.04
48 23 0.11
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (42 bp):
AAAAAATAAATCCTAATTGAGGTGAGATTAAATGAAAAATTA
Found at i:13111571 original size:84 final size:84
Alignment explanation
Indices: 13111449--13111738 Score: 355
Period size: 84 Copynumber: 3.4 Consensus size: 84
13111439 AATCCTCCTG
* * * * *
13111449 AAAACATAAATCCTAATTGAGGTGAGATTAAATGAAAAATTAAAAAAATGAATCCTAATTGAGGT
1 AAAAGATAAATCCTAATTGAGGTGGGATTAAATAAAAAACTAAAAAAATAAATCCTAATTGAGGT
*
13111514 GAGATTAAATGAAAAAATA
66 GAGATTAAATGAAAAATTA
* ** * *
13111533 AAAAGATAAATCCTAATTGAGGTGTGATTAAATAAAAAACTAAAAAGGTAAATCTTAACTGAGGT
1 AAAAGATAAATCCTAATTGAGGTGGGATTAAATAAAAAACTAAAAAAATAAATCCTAATTGAGGT
13111598 GAGATTAAATGAAAAATTA
66 GAGATTAAATGAAAAATTA
* * *
13111617 AAAAGATAAGCTTAAATCCTAATTAAGTTGGGATTAAATAAAAAGCTAAAAAAGATAAATCCTAA
1 AAAAG---A---TAAATCCTAATTGAGGTGGGATTAAATAAAAAACTAAAAAA-ATAAATCCTAA
* * **
13111682 TTGAGTTGGGATTAAATGAAATGTTA
59 TTGAGGTGAGATTAAATGAAAAATTA
13111708 AAAAGATAAATCCTAATTGAGGTGGGATTAA
1 AAAAGATAAATCCTAATTGAGGTGGGATTAA
13111739 TTGTGGGGCT
Statistics
Matches: 175, Mismatches: 24, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
84 79 0.45
85 23 0.13
87 1 0.01
88 1 0.01
90 36 0.21
91 35 0.20
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (84 bp):
AAAAGATAAATCCTAATTGAGGTGGGATTAAATAAAAAACTAAAAAAATAAATCCTAATTGAGGT
GAGATTAAATGAAAAATTA
Found at i:13115865 original size:139 final size:140
Alignment explanation
Indices: 13115493--13115865 Score: 414
Period size: 139 Copynumber: 2.6 Consensus size: 140
13115483 AGATGGGATT
* * * * *
13115493 TGAAAAAACTGAAGTGAATTATTGAACATGATCAAATGGGGTTATAGAGTTGCATATTCTAAATA
1 TGAAGAAACTGAAGTGAATTACTGAACATGATCAAATGGGGTTGTAGAGTTGCTTATTCTACATA
* **
13115558 TGGAAGAAGCTAGGATACATGCCTGGTTTTGATTGTTTGATACATGATCTTGAAGATAGGACTTC
66 TGGAAGAAGC-AGGATAAATGCCTGG-TTTGA-TCATTGATACATGATCTTGAAGATAGGACTTC
*
13115623 AAAGGAGAAAAGC
128 AAAGAAGAAAAGC
* *
13115636 TGAAGAAACTGAAGT-AAGGTACTGAACATGATCAAATGGGGTTGTTA-AGTTGCTTGTTCTACA
1 TGAAGAAACTGAAGTGAA-TTACTGAACATGATCAAATGGGGTTG-TAGAGTTGCTTATTCTACA
* * * * *
13115699 TATGGAAGAAACAGGGTAAATGGCTGGTTT-A-CATTGATACATGATCTTGAA-AGTGGGACTTG
64 TATGGAAGAAGCAGGATAAATGCCTGGTTTGATCATTGATACATGATCTTGAAGA-TAGGACTTC
*
13115761 AAGAGAAGAGAAGC
128 AA-AGAAGAAAAGC
* * * * *
13115775 TTAAGAAACTGAAGTGATTTACTGAAAATGATCAAATGGGGTTGTCGAGTTGCTTATTCCACATA
1 TGAAGAAACTGAAGTGAATTACTGAACATGATCAAATGGGGTTGTAGAGTTGCTTATTCTACATA
* * * *
13115840 TGGAGGAGGCAGAATATATGCCTGGT
66 TGGAAGAAGCAGGATAAATGCCTGGT
13115866 AAAGATGGGA
Statistics
Matches: 193, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
137 1 0.01
138 28 0.15
139 82 0.42
140 2 0.01
141 3 0.02
142 14 0.07
143 61 0.32
144 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.28
Consensus pattern (140 bp):
TGAAGAAACTGAAGTGAATTACTGAACATGATCAAATGGGGTTGTAGAGTTGCTTATTCTACATA
TGGAAGAAGCAGGATAAATGCCTGGTTTGATCATTGATACATGATCTTGAAGATAGGACTTCAAA
GAAGAAAAGC
Found at i:13115961 original size:18 final size:18
Alignment explanation
Indices: 13115934--13115971 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
13115924 TGCTTCTAAG
*
13115934 AAGCATTTTTG-GAACAAA
1 AAGCACTTTTGAG-ACAAA
13115952 AAGCACTTTTGAGACAAA
1 AAGCACTTTTGAGACAAA
13115970 AA
1 AA
13115972 CATTCCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (18 bp):
AAGCACTTTTGAGACAAA
Found at i:13119470 original size:25 final size:26
Alignment explanation
Indices: 13119410--13119470 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
13119400 AAAAAGTGTC
*
13119410 AAAT-TTAAGTAACAAATTGGATAAA
1 AAATATTAAGTAACAAATTAGATAAA
*
13119435 AAA-ATTGAAGTACCAAATTAGA-AAA
1 AAATATT-AAGTAACAAATTAGATAAA
13119460 AAATATTAAGT
1 AAATATTAAGT
13119471 TCAAATGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 15 0.48
26 16 0.52
ACGTcount: A:0.57, C:0.05, G:0.11, T:0.26
Consensus pattern (26 bp):
AAATATTAAGTAACAAATTAGATAAA
Done.