Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 8 of 182
Found at i:2938600 original size:3 final size:3
Alignment explanation
Indices: 2938592--2938623 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2938582 ATAAGTCTGT
2938592 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
2938624 TCTCTCTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:2940462 original size:21 final size:22
Alignment explanation
Indices: 2940432--2940472 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2940422 ATAGGTAATG
*
2940432 ATTTTAAATTTTAT-GAATAAA
1 ATTTTAAATTGTATAGAATAAA
*
2940453 ATTTTTAATTGTATAGAATA
1 ATTTTAAATTGTATAGAATA
2940473 TTTAAAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (22 bp):
ATTTTAAATTGTATAGAATAAA
Found at i:2940960 original size:20 final size:19
Alignment explanation
Indices: 2940907--2940960 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2940897 TTTAACACTT
* *
2940907 TTAAATTAAAAGAATGAAA
1 TTAAATTAAAAAAATCAAA
2940926 TTAAATTATAAAAAATCAAA
1 TTAAATTA-AAAAAATCAAA
*
2940946 TTTAATTAAATAAAA
1 TTAAATTAAA-AAAA
2940961 AAAATTAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (19 bp):
TTAAATTAAAAAAATCAAA
Found at i:2946957 original size:33 final size:33
Alignment explanation
Indices: 2946915--2946981 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
2946905 GTCAAAGTTT
2946915 ATGTATAAATATGATATTTATCCCTTAAAATAA
1 ATGTATAAATATGATATTTATCCCTTAAAATAA
2946948 ATGTATAAATATGATATTTATCCCTTAAAATAA
1 ATGTATAAATATGATATTTATCCCTTAAAATAA
2946981 A
1 A
2946982 CTAATTTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (33 bp):
ATGTATAAATATGATATTTATCCCTTAAAATAA
Found at i:2947649 original size:12 final size:12
Alignment explanation
Indices: 2947632--2947671 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2947622 TCTTATAAAA
2947632 ATTAAAAAATAT
1 ATTAAAAAATAT
2947644 ATTAAAAAATAT
1 ATTAAAAAATAT
* **
2947656 TTTAGTAAATAT
1 ATTAAAAAATAT
2947668 ATTA
1 ATTA
2947672 GAAACCCAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (12 bp):
ATTAAAAAATAT
Found at i:2953994 original size:5 final size:6
Alignment explanation
Indices: 2953977--2954001 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2953967 ATATGTATAT
2953977 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
2954002 ACACCATACG
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:2971001 original size:18 final size:19
Alignment explanation
Indices: 2970974--2971010 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2970964 CATTTAAATC
*
2970974 ATTATTTTTATTA-ATATA
1 ATTATATTTATTATATATA
2970992 ATTATATTTATTATATATA
1 ATTATATTTATTATATATA
2971011 TTAATTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTATATTTATTATATATA
Found at i:2982767 original size:19 final size:17
Alignment explanation
Indices: 2982736--2982779 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 17
2982726 ATATAATCTA
2982736 AAAAAATCTAAAATTAT
1 AAAAAATCTAAAATTAT
2982753 AAAAAATCATAAAAATTAT
1 AAAAAATC-T-AAAATTAT
2982772 ATAAAAAT
1 A-AAAAAT
2982780 ACAATAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.33
18 1 0.04
19 9 0.38
20 6 0.25
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAAATCTAAAATTAT
Found at i:2982858 original size:28 final size:27
Alignment explanation
Indices: 2982833--2982885 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
2982823 AAAAAAATAT
*
2982833 TATTAGA-AACAAT-TTTTTATTTAAA
1 TATTAGAGAACAATGTTTATATTTAAA
2982858 TATTAGAGAACAATGTTTATATTTAAA
1 TATTAGAGAACAATGTTTATATTTAAA
2982885 T
1 T
2982886 CGTATTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 7 0.28
26 6 0.24
27 12 0.48
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (27 bp):
TATTAGAGAACAATGTTTATATTTAAA
Found at i:2982890 original size:80 final size:81
Alignment explanation
Indices: 2982796--2982959 Score: 303
Period size: 80 Copynumber: 2.0 Consensus size: 81
2982786 AGTTGGAACA
*
2982796 ATATTTATATCGTATTGAAAGAAAATAAAAAAAATATTATTAGAAACAA-TTTTTTATTTAAATA
1 ATATTTAAATCGTATTGAAAGAAAATAAAAAAAATATTATTAGAAACAATTTTTTTATTTAAATA
2982860 TTAGAGAACAATGTTT
66 TTAGAGAACAATGTTT
*
2982876 ATATTTAAATCGTATTGAAAGAAAATAAAAAAAATATTTTTAGAAACAATTTTTTTATTTAAATA
1 ATATTTAAATCGTATTGAAAGAAAATAAAAAAAATATTATTAGAAACAATTTTTTTATTTAAATA
2982941 TTAGAGAACAATGTTT
66 TTAGAGAACAATGTTT
2982957 ATA
1 ATA
2982960 AGAAACTGAA
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
80 47 0.58
81 34 0.42
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.39
Consensus pattern (81 bp):
ATATTTAAATCGTATTGAAAGAAAATAAAAAAAATATTATTAGAAACAATTTTTTTATTTAAATA
TTAGAGAACAATGTTT
Found at i:2985723 original size:15 final size:15
Alignment explanation
Indices: 2985703--2985756 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
2985693 ATACTACAAA
2985703 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
2985718 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
2985735 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
2985752 ATATT
1 ATATT
2985757 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:2985815 original size:15 final size:16
Alignment explanation
Indices: 2985795--2985824 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2985785 AGTATATTAC
2985795 TTAAAA-TTATTATTT
1 TTAAAATTTATTATTT
2985810 TTAAAATTTATTATT
1 TTAAAATTTATTATT
2985825 AAAATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAAAATTTATTATTT
Found at i:2990770 original size:22 final size:24
Alignment explanation
Indices: 2990718--2990772 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
2990708 AGCAATTCAT
* * *
2990718 TATATATTAAATAAAATCACATAT
1 TATACATTAAATAAAATAACATAC
2990742 TAT-CATTAAA-AAAA-AACATAC
1 TATACATTAAATAAAATAACATAC
2990763 TATACATTAA
1 TATACATTAA
2990773 CTATATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 8 0.30
22 10 0.37
23 6 0.22
24 3 0.11
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (24 bp):
TATACATTAAATAAAATAACATAC
Found at i:3010184 original size:21 final size:23
Alignment explanation
Indices: 3010160--3010208 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
3010150 AATTTATATT
3010160 TTTAAAAAAATT-A-TTTAAAAA
1 TTTAAAAAAATTAATTTTAAAAA
3010181 TTT-AAAAAATTAATTTTTAAAAA
1 TTTAAAAAAATTAA-TTTTAAAAA
3010204 TTTAA
1 TTTAA
3010209 TCATATCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 8 0.33
21 4 0.17
23 11 0.46
24 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTAAAAAAATTAATTTTAAAAA
Found at i:3011318 original size:16 final size:18
Alignment explanation
Indices: 3011297--3011343 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 18
3011287 ACATACCTTG
3011297 AAATAATTTAAAT-T-CA
1 AAATAATTTAAATCTACA
3011313 AAATAATTTAAATCTAACA
1 AAATAATTTAAATCT-ACA
3011332 AAAT-ATTTAAAT
1 AAATAATTTAAAT
3011344 GTAAATTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 13 0.46
17 1 0.04
18 8 0.29
19 6 0.21
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATAATTTAAATCTACA
Found at i:3018832 original size:16 final size:17
Alignment explanation
Indices: 3018801--3018839 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3018791 GTAATACGTG
*
3018801 TATAAATATATAATTTA
1 TATAAAAATATAATTTA
3018818 TATAAAAAT-TAATTTA
1 TATAAAAATATAATTTA
3018834 -ATAAAA
1 TATAAAA
3018840 TAAAATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
16 7 0.33
17 8 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAAAAATATAATTTA
Found at i:3042396 original size:32 final size:29
Alignment explanation
Indices: 3042317--3042402 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 29
3042307 TAAAATTAAT
* * *
3042317 AAAA-ATAAAATTATACTTTGATCTCTTTA
1 AAAATATAAAATTATAATTTAAT-TTTTTA
*
3042346 AAAATATAAAATTTTAATTTAATTTTTTA
1 AAAATATAAAATTATAATTTAATTTTTTA
3042375 AAAATTATTAAAAATTATAATTTAATTT
1 AAAA-TA-T-AAAATTATAATTTAATTT
3042403 CGATCCTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
29 13 0.27
30 17 0.35
31 1 0.02
32 17 0.35
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (29 bp):
AAAATATAAAATTATAATTTAATTTTTTA
Found at i:3043076 original size:12 final size:12
Alignment explanation
Indices: 3043059--3043083 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3043049 ATATTTAAAA
3043059 TAAAAAAATATT
1 TAAAAAAATATT
3043071 TAAAAAAATATT
1 TAAAAAAATATT
3043083 T
1 T
3043084 TTTAAAACTA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAAAAATATT
Found at i:3046172 original size:11 final size:11
Alignment explanation
Indices: 3046158--3046254 Score: 61
Period size: 11 Copynumber: 8.5 Consensus size: 11
3046148 TAAATACCTT
3046158 TAAAATAATAA
1 TAAAATAATAA
3046169 TAAAATTAATAA
1 TAAAA-TAATAA
* *
3046181 TAAAATAAGAG
1 TAAAATAATAA
* *
3046192 TTATATAAT-A
1 TAAAATAATAA
3046202 TCCAAATAATAATAA
1 T---AA-AATAATAA
*
3046217 TAAAATAATAG
1 TAAAATAATAA
*
3046228 TAATATAATAA
1 TAAAATAATAA
* *
3046239 TGAAATGATAA
1 TAAAATAATAA
*
3046250 CAAAA
1 TAAAA
3046255 AATGAGAAAA
Statistics
Matches: 64, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
10 1 0.02
11 42 0.66
12 13 0.20
13 1 0.02
14 5 0.08
15 2 0.03
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:3046180 original size:12 final size:12
Alignment explanation
Indices: 3046158--3046186 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3046148 TAAATACCTT
3046158 TAAAA-TAATAA
1 TAAAATTAATAA
3046169 TAAAATTAATAA
1 TAAAATTAATAA
3046181 TAAAAT
1 TAAAAT
3046187 AAGAGTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:3046222 original size:14 final size:14
Alignment explanation
Indices: 3046161--3046239 Score: 54
Period size: 14 Copynumber: 5.2 Consensus size: 14
3046151 ATACCTTTAA
3046161 AATAATAATAAAAT
1 AATAATAATAAAAT
3046175 --TAATAATAAAAT
1 AATAATAATAAAAT
3046187 AAGAGTTATATAATATCCAAAT
1 -A-A--TA-ATAATA---AAAT
3046209 AATAATAATAAAAT
1 AATAATAATAAAAT
* *
3046223 AATAGTAATATAAT
1 AATAATAATAAAAT
3046237 AAT
1 AAT
3046240 GAAATGATAA
Statistics
Matches: 53, Mismatches: 2, Indels: 20
0.71 0.03 0.27
Matches are distributed among these distances:
12 12 0.23
14 19 0.36
17 6 0.11
18 4 0.08
19 6 0.11
20 1 0.02
21 1 0.02
22 4 0.08
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.32
Consensus pattern (14 bp):
AATAATAATAAAAT
Found at i:3050486 original size:14 final size:14
Alignment explanation
Indices: 3050463--3050496 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3050453 TATATAAATT
3050463 TAATTA-TAATATA
1 TAATTATTAATATA
3050476 TAATTATTAATATA
1 TAATTATTAATATA
*
3050490 AAATTAT
1 TAATTAT
3050497 ATTTATGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATTATTAATATA
Found at i:3064760 original size:29 final size:29
Alignment explanation
Indices: 3064718--3064785 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
3064708 ACTACAAAAA
3064718 TAGTCACTTATGTTTGAAATGTTACATTT
1 TAGTCACTTATGTTTGAAATGTTACATTT
*
3064747 TAGTCACTTATGTTTGAAATGTTACGTTT
1 TAGTCACTTATGTTTGAAATGTTACATTT
3064776 TAGTCACTTA
1 TAGTCACTTA
3064786 AATTAGTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (29 bp):
TAGTCACTTATGTTTGAAATGTTACATTT
Found at i:3066241 original size:14 final size:15
Alignment explanation
Indices: 3066211--3066242 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3066201 ATTTTAAGTT
3066211 AATTTTATTTTTCAA
1 AATTTTATTTTTCAA
3066226 AATTTTATTTTT-AA
1 AATTTTATTTTTCAA
3066240 AAT
1 AAT
3066243 AAACTATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTTTATTTTTCAA
Found at i:3073963 original size:21 final size:21
Alignment explanation
Indices: 3073931--3073972 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3073921 TTTTTATTTT
3073931 ATTTTATTTTAAAT-TTTTTAA
1 ATTTTATTTT-AATGTTTTTAA
3073952 ATTTT-TTATTAATGTTTTTAA
1 ATTTTATT-TTAATGTTTTTAA
3073973 CATATCAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTTATTTTAATGTTTTTAA
Found at i:3075715 original size:31 final size:31
Alignment explanation
Indices: 3075680--3075741 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
3075670 CTTAACAGTC
3075680 TAATGACTTAAATAAAAACTTTCGAATAATT
1 TAATGACTTAAATAAAAACTTTCGAATAATT
* *
3075711 TAATGACTTAAATGAAAACTTTTGAATAATT
1 TAATGACTTAAATAAAAACTTTCGAATAATT
3075742 CAATAACTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (31 bp):
TAATGACTTAAATAAAAACTTTCGAATAATT
Found at i:3076440 original size:5 final size:5
Alignment explanation
Indices: 3076430--3076454 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3076420 TATCACTTTT
3076430 TTAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA
3076455 AATAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:3089263 original size:2 final size:2
Alignment explanation
Indices: 3089256--3089283 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3089246 TTTATTTATT
3089256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3089284 AAAGGCTTGT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3093228 original size:19 final size:18
Alignment explanation
Indices: 3093206--3093268 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 18
3093196 AAATTACAAA
*
3093206 AAAAATCAAAATAATTTTC
1 AAAAATAAAAAT-ATTTTC
*
3093225 AAAAATTAAAAATGATTTTT
1 AAAAA-TAAAAAT-ATTTTC
* *
3093245 AAAATTAAAAATATTTAC
1 AAAAATAAAAATATTTTC
3093263 AAAAAT
1 AAAAAT
3093269 TCTAAAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 9 0.25
19 12 0.33
20 15 0.42
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAAATAAAAATATTTTC
Found at i:3093269 original size:19 final size:19
Alignment explanation
Indices: 3093213--3093269 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
3093203 AAAAAAAATC
3093213 AAAATAATTTTCAAAAATTA
1 AAAATAA-TTTCAAAAATTA
* **
3093233 AAAATGATTTTTAAAATTA
1 AAAATAATTTCAAAAATTA
3093252 AAAAT-ATTTACAAAAATT
1 AAAATAATTT-CAAAAATT
3093270 CTAAAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 4 0.13
19 21 0.68
20 6 0.19
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAATAATTTCAAAAATTA
Found at i:3108896 original size:6 final size:6
Alignment explanation
Indices: 3108885--3108911 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3108875 TTACCGCTGT
3108885 GCGATG GCGATG GCGATG GCGATG GCG
1 GCGATG GCGATG GCGATG GCGATG GCG
3108912 GAAATGGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.19, G:0.52, T:0.15
Consensus pattern (6 bp):
GCGATG
Found at i:3118019 original size:20 final size:20
Alignment explanation
Indices: 3117977--3118020 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3117967 ACATCAGTTG
* *
3117977 TTTATATTCTTCAATGTTTT
1 TTTATATACTTCAATGTTAT
3117997 TTTATATACTTC-ATGTTCAT
1 TTTATATACTTCAATGTT-AT
3118017 TTTA
1 TTTA
3118021 CGATCCATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.23, C:0.11, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTATATACTTCAATGTTAT
Found at i:3124133 original size:5 final size:6
Alignment explanation
Indices: 3124118--3124142 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3124108 TAATTGCCTT
3124118 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
3124143 AAATTTCTTC
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:3125619 original size:5 final size:5
Alignment explanation
Indices: 3125613--3125650 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
3125603 TACAAAGAGA
*
3125613 TGGGA TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT TGG
1 TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT TGG
3125651 AGAGCACATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.61, T:0.37
Consensus pattern (5 bp):
TGGGT
Found at i:3125800 original size:6 final size:6
Alignment explanation
Indices: 3125786--3125821 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
3125776 TAAAACAAGA
*
3125786 CCAACG CCAATG CCAATG CCAATG CCAATG CCAATG
1 CCAATG CCAATG CCAATG CCAATG CCAATG CCAATG
3125822 GATGAATGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.33, C:0.36, G:0.17, T:0.14
Consensus pattern (6 bp):
CCAATG
Found at i:3135143 original size:22 final size:22
Alignment explanation
Indices: 3135099--3135143 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3135089 TATATAACTC
*
3135099 TAAATTTAATTTATATTTTAAA
1 TAAATTTAATTTATATTTCAAA
*
3135121 TAAATTTAACTTTTTA-TTCAAA
1 TAAATTTAA-TTTATATTTCAAA
3135143 T
1 T
3135144 TTATTTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
TAAATTTAATTTATATTTCAAA
Found at i:3135920 original size:22 final size:24
Alignment explanation
Indices: 3135875--3135920 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
3135865 ATTTGTTCTC
3135875 TATTAAATTCTTAAAAAAAATTAT
1 TATTAAATTCTTAAAAAAAATTAT
* *
3135899 TATT-AATT-TTAAATAAAGTTAT
1 TATTAAATTCTTAAAAAAAATTAT
3135921 GTTAATCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 4 0.20
24 4 0.20
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TATTAAATTCTTAAAAAAAATTAT
Found at i:3136405 original size:22 final size:23
Alignment explanation
Indices: 3136354--3136413 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
3136344 AAATATTTAT
*
3136354 ATATATT-TATA-TATTTTTAAA
1 ATATATTATATATTTTTTTTAAA
*
3136375 ATTTATTAT-TATTTTTTTTGAAA
1 ATATATTATATATTTTTTTT-AAA
3136398 ATAT-TTATATATTTTT
1 ATATATTATATATTTTT
3136414 ATATTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 8 0.25
22 11 0.34
23 13 0.41
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
ATATATTATATATTTTTTTTAAA
Found at i:3136433 original size:29 final size:29
Alignment explanation
Indices: 3136343--3136427 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 29
3136333 CTTTAAGTTT
3136343 AAAATATTTATATA-TATTTATATATTTTT-
1 AAAATATTTATATATTA-TTATAT-TTTTTG
3136372 -AAA-ATTTAT-TATTA-T-T-TTTTTTG
1 AAAATATTTATATATTATTATATTTTTTG
*
3136395 AAAATATTTATATATTTTTATATTTTTT-
1 AAAATATTTATATATTATTATATTTTTTG
3136423 AAAAT
1 AAAAT
3136428 CTTTTAAACT
Statistics
Matches: 47, Mismatches: 1, Indels: 17
0.72 0.02 0.26
Matches are distributed among these distances:
22 5 0.11
23 1 0.02
24 4 0.09
25 7 0.15
26 6 0.13
27 9 0.19
28 9 0.19
29 6 0.13
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (29 bp):
AAAATATTTATATATTATTATATTTTTTG
Found at i:3138239 original size:113 final size:113
Alignment explanation
Indices: 3138041--3138270 Score: 349
Period size: 113 Copynumber: 2.0 Consensus size: 113
3138031 CCATTAACCC
* * *
3138041 AAAGAAATTTAATGGGAAGAAGATATTAGAACCAAAGTTATTGAATTTTTTGGTTAATGGGATTT
1 AAAGAAACTTAACGGGAAGAAGATATTAGAACCAAAGTTATTGAATCTTTTGGTTAATGGGATTT
*
3138106 AAAGAATCAAGCTTTGAGACAAATTTGTAACTAAAGATATTGGAATCA
66 AAAGAATCAAGCTTTAAGACAAATTTGTAACTAAAGATATTGGAATCA
3138154 AAAGAAACTTAACGGGAAGAAGATATT-GAAACCAAA-TATATTGAATCTTTTGGTTAAT-GGAT
1 AAAGAAACTTAACGGGAAGAAGATATTAG-AACCAAAGT-TATTGAATCTTTTGGTTAATGGGA-
* **
3138216 TTTAAAGATTCAAGCTTTAAGACAGTTTTGTAACTAAAGATATTGGAATCA
63 TTTAAAGAATCAAGCTTTAAGACAAATTTGTAACTAAAGATATTGGAATCA
3138267 AAAG
1 AAAG
3138271 GGAAGAAGAA
Statistics
Matches: 107, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
112 5 0.05
113 102 0.95
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (113 bp):
AAAGAAACTTAACGGGAAGAAGATATTAGAACCAAAGTTATTGAATCTTTTGGTTAATGGGATTT
AAAGAATCAAGCTTTAAGACAAATTTGTAACTAAAGATATTGGAATCA
Found at i:3138561 original size:29 final size:29
Alignment explanation
Indices: 3138513--3138583 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
3138503 AAATAATAAT
*
3138513 ATAAGTGACTAAAACGTAACATT-TCAAAC
1 ATAAGTGACTAAAACATAAC-TTGTCAAAC
*
3138542 ATAAGTGACTAAAATATAACTTGAGTCAAAC
1 ATAAGTGACTAAAACATAACTT--GTCAAAC
*
3138573 AAAAGTGACTA
1 ATAAGTGACTA
3138584 TTTTTATAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 2 0.06
29 18 0.50
31 16 0.44
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.24
Consensus pattern (29 bp):
ATAAGTGACTAAAACATAACTTGTCAAAC
Found at i:3149931 original size:30 final size:30
Alignment explanation
Indices: 3149875--3149931 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
3149865 ACAATTCAAC
*
3149875 TATTTTTAAAAAATTAATATTTAAATTATA
1 TATTTTTAAAAAATTAATATTCAAATTATA
**
3149905 TATTTTTTTAAAATTAATGA-TCAAATT
1 TATTTTTAAAAAATTAAT-ATTCAAATT
3149932 TAACTGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 22 0.96
31 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (30 bp):
TATTTTTAAAAAATTAATATTCAAATTATA
Found at i:3150969 original size:14 final size:16
Alignment explanation
Indices: 3150950--3150983 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
3150940 TTAAATAAAA
3150950 ATAATATA-AAA-TTT
1 ATAATATATAAACTTT
3150964 ATAATATATAAACTTT
1 ATAATATATAAACTTT
3150980 ATAA
1 ATAA
3150984 CAAATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 3 0.17
16 7 0.39
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAATATATAAACTTT
Found at i:3150972 original size:16 final size:16
Alignment explanation
Indices: 3150953--3150983 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3150943 AATAAAAATA
3150953 ATATAAAATTTATAAT
1 ATATAAAATTTATAAT
*
3150969 ATATAAACTTTATAA
1 ATATAAAATTTATAA
3150984 CAAATATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAAAATTTATAAT
Found at i:3158135 original size:55 final size:55
Alignment explanation
Indices: 3158049--3158158 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
3158039 TGCAAATAAA
3158049 TTCACAGACAAACTAAATCAAACTTCATGCATCTCATACTTGCCATAATTTATAC
1 TTCACAGACAAACTAAATCAAACTTCATGCATCTCATACTTGCCATAATTTATAC
*
3158104 TTCACAGACAAACTAAATCAAACTTCGTGCATCTCATACTTGCCATAATTTATAC
1 TTCACAGACAAACTAAATCAAACTTCATGCATCTCATACTTGCCATAATTTATAC
3158159 ATGCAATTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.31
Consensus pattern (55 bp):
TTCACAGACAAACTAAATCAAACTTCATGCATCTCATACTTGCCATAATTTATAC
Found at i:3166805 original size:3 final size:3
Alignment explanation
Indices: 3166797--3166836 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3166787 CCCTTTCATC
3166797 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
3166837 TTATATATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:3171925 original size:20 final size:19
Alignment explanation
Indices: 3171900--3171939 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3171890 TAAGTTTATT
3171900 TATATA-AATTT-TAAAATA
1 TATATATAATTTATAAAA-A
3171918 TATATATAATTTATAAAAA
1 TATATATAATTTATAAAAA
3171937 TAT
1 TAT
3171940 TAAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 9 0.45
20 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATATATAATTTATAAAAA
Found at i:3172113 original size:22 final size:22
Alignment explanation
Indices: 3172088--3172141 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
3172078 TATCCAAACA
*
3172088 ATAACAACAAAATAGTAATAAC
1 ATAACAACAAAATAGTAACAAC
* ***
3172110 ATAATAGTGAAATAGTAACAAC
1 ATAACAACAAAATAGTAACAAC
*
3172132 AAAACAACAA
1 ATAACAACAA
3172142 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 10, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.63, C:0.13, G:0.07, T:0.17
Consensus pattern (22 bp):
ATAACAACAAAATAGTAACAAC
Found at i:3181398 original size:16 final size:15
Alignment explanation
Indices: 3181377--3181406 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3181367 TTCGCTAGTA
3181377 CAAATATATATATAAT
1 CAAATATA-ATATAAT
3181393 CAAATATAATATAA
1 CAAATATAATATAA
3181407 AATCTAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (15 bp):
CAAATATAATATAAT
Found at i:3181410 original size:17 final size:16
Alignment explanation
Indices: 3181377--3181410 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3181367 TTCGCTAGTA
*
3181377 CAAATATATATATAAT
1 CAAATATATATAAAAT
3181393 CAAATATAATATAAAAT
1 CAAATAT-ATATAAAAT
3181410 C
1 C
3181411 TAATCAACGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (16 bp):
CAAATATATATAAAAT
Found at i:3181676 original size:27 final size:28
Alignment explanation
Indices: 3181630--3181695 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
3181620 ATTATTAGAC
* * * *
3181630 TTAAATAATATAACTTTATTTTATAT-A
1 TTAAAAAATATAAATATATTTTACATAA
*
3181657 TTATAAAATATAAATATATTTTACATAA
1 TTAAAAAATATAAATATATTTTACATAA
3181685 TTAAAAAATAT
1 TTAAAAAATAT
3181696 TAACTTAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 21 0.66
28 11 0.34
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
TTAAAAAATATAAATATATTTTACATAA
Found at i:3182255 original size:17 final size:16
Alignment explanation
Indices: 3182235--3182272 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
3182225 TAAAAATTCT
*
3182235 AAAATTTATATCTTTAA
1 AAAATATATAT-TTTAA
3182252 AAAATATATATTTTAA
1 AAAATATATATTTTAA
3182268 AAAAT
1 AAAAT
3182273 CTAAAGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAATATATATTTTAA
Found at i:3200489 original size:15 final size:16
Alignment explanation
Indices: 3200469--3200502 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3200459 TTATTTTTTA
*
3200469 AAATTA-TAAATAGAT
1 AAATTATTAAAAAGAT
3200484 AAATTATTAAAAAGAT
1 AAATTATTAAAAAGAT
3200500 AAA
1 AAA
3200503 GTTAGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AAATTATTAAAAAGAT
Found at i:3203105 original size:58 final size:58
Alignment explanation
Indices: 3203036--3203150 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
3203026 AAAGAAGTTG
* *
3203036 TTTATGAGTGTTATTT-AGGAATAAAATTATATTTGAGTTTAAAAATATTTGGGTTTAA
1 TTTATGAGTGTT-TTTGAAGAATAAAATTATATTTGAGTTTAAAAATATTAGGGTTTAA
* *
3203094 TTTATGAGTGTTTTTGAAGAATGAAATTATATTTGGGTTTAAAAATATTAGGGTTTA
1 TTTATGAGTGTTTTTGAAGAATAAAATTATATTTGAGTTTAAAAATATTAGGGTTTA
3203151 GTTTGTTGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 3 0.06
58 49 0.94
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (58 bp):
TTTATGAGTGTTTTTGAAGAATAAAATTATATTTGAGTTTAAAAATATTAGGGTTTAA
Found at i:3204699 original size:23 final size:24
Alignment explanation
Indices: 3204659--3204703 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
3204649 TCAACAAAGC
3204659 AAGATATATCTTTCACTGCTCTGG
1 AAGATATATCTTTCACTGCTCTGG
*
3204683 AAGATATA-CTTTGACTGCTCT
1 AAGATATATCTTTCACTGCTCT
3204704 AATCTTACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (24 bp):
AAGATATATCTTTCACTGCTCTGG
Found at i:3205401 original size:11 final size:11
Alignment explanation
Indices: 3205386--3205533 Score: 97
Period size: 11 Copynumber: 13.1 Consensus size: 11
3205376 TAAATATCTC
3205386 TAAAATAATAA
1 TAAAATAATAA
* *
3205397 CAAAATTAACAA
1 TAAAA-TAATAA
3205409 TAAAATAATAA
1 TAAAATAATAA
* *
3205420 TTATATAAT-A
1 TAAAATAATAA
*
3205430 TCTAAATAATGACAA
1 T-AAAATAAT---AA
* *
3205445 CAAAATAATGA
1 TAAAATAATAA
* *
3205456 TAATATAATAG
1 TAAAATAATAA
*
3205467 TAAAATAGTAA
1 TAAAATAATAA
3205478 TAAAATAATGAA
1 TAAAATAAT-AA
*
3205490 -AAAATAACAA
1 TAAAATAATAA
3205500 TAAAATAATAA
1 TAAAATAATAA
3205511 T-AAATAAGTAA
1 TAAAATAA-TAA
3205522 -AAAAGTAATAA
1 TAAAA-TAATAA
3205533 T
1 T
3205534 TTTTTTGCAA
Statistics
Matches: 105, Mismatches: 20, Indels: 23
0.71 0.14 0.16
Matches are distributed among these distances:
10 10 0.10
11 73 0.70
12 14 0.13
14 7 0.07
15 1 0.01
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.26
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:3205473 original size:36 final size:36
Alignment explanation
Indices: 3205405--3205473 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
3205395 AACAAAATTA
* * *
3205405 ACAATAAAATAATAATTATATAATATCTAAATAATG
1 ACAACAAAATAATAATAATATAATATCAAAATAATG
*
3205441 ACAACAAAATAATGATAATATAATAGT-AAAATA
1 ACAACAAAATAATAATAATATAATA-TCAAAATA
3205474 GTAATAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 27 0.96
37 1 0.04
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.29
Consensus pattern (36 bp):
ACAACAAAATAATAATAATATAATATCAAAATAATG
Found at i:3205650 original size:17 final size:17
Alignment explanation
Indices: 3205595--3205650 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
3205585 CCTGAAATCT
*
3205595 AATTTATTTTTTAAACA
1 AATTTATTTTTTGAACA
* **
3205612 AATTTTATTTTATGTCCA
1 AA-TTTATTTTTTGAACA
*
3205630 AATTTATTTTTTGAACT
1 AATTTATTTTTTGAACA
3205647 AATT
1 AATT
3205651 AAGTGGATTT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.55
Consensus pattern (17 bp):
AATTTATTTTTTGAACA
Found at i:3208036 original size:42 final size:42
Alignment explanation
Indices: 3207977--3208094 Score: 227
Period size: 42 Copynumber: 2.8 Consensus size: 42
3207967 GCCCGGCCCG
3207977 AATCAGTTTATACTTATTCTTTTTGCTGCTGTTTAGCTGCTA
1 AATCAGTTTATACTTATTCTTTTTGCTGCTGTTTAGCTGCTA
3208019 AATCAGTTTATACTTATTCTTTTTGCTGCTGTTTAGCTGCTA
1 AATCAGTTTATACTTATTCTTTTTGCTGCTGTTTAGCTGCTA
*
3208061 AATCAGTTTATACTTACTCTTTTTGCTGCTGTTT
1 AATCAGTTTATACTTATTCTTTTTGCTGCTGTTT
3208095 TATTTATATA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.19, C:0.17, G:0.14, T:0.51
Consensus pattern (42 bp):
AATCAGTTTATACTTATTCTTTTTGCTGCTGTTTAGCTGCTA
Found at i:3217618 original size:29 final size:29
Alignment explanation
Indices: 3217570--3217629 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
3217560 TTAAATTAGT
* *
3217570 AAATATAAAATTATACTTTACTTCTTTAA
1 AAATATAAAATTATACTTTAATCCTTTAA
3217599 AAATATAAAAATT-TGA-TTTAATCCTTTAA
1 AAATAT-AAAATTAT-ACTTTAATCCTTTAA
3217628 AA
1 AA
3217630 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (29 bp):
AAATATAAAATTATACTTTAATCCTTTAA
Found at i:3217654 original size:22 final size:22
Alignment explanation
Indices: 3217629--3217670 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3217619 ATCCTTTAAA
3217629 ATTTTTAAAATAATAAAATTAT
1 ATTTTTAAAATAATAAAATTAT
***
3217651 ATTTTTGTTATAATAAAATT
1 ATTTTTAAAATAATAAAATT
3217671 TTAAATTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTTTTAAAATAATAAAATTAT
Found at i:3219141 original size:2 final size:2
Alignment explanation
Indices: 3219134--3219167 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3219124 TTTCTCTTAG
3219134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3219168 TAGCTTTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3228483 original size:26 final size:28
Alignment explanation
Indices: 3228454--3228506 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
3228444 CTAAAAATAA
3228454 TTTTT-AAAAATTT-CAAAATT-TATAT
1 TTTTTAAAAAATTTACAAAATTATATAT
*
3228479 TTTTTAAAAAATTTATAAAATTATATAT
1 TTTTTAAAAAATTTACAAAATTATATAT
3228507 AAAAGTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 5 0.21
26 8 0.33
27 6 0.25
28 5 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTTTAAAAAATTTACAAAATTATATAT
Found at i:3230620 original size:15 final size:16
Alignment explanation
Indices: 3230590--3230628 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
3230580 TAATAAAAAT
3230590 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
3230607 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
3230622 ATAATTT
1 ATAATTT
3230629 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:3230621 original size:24 final size:23
Alignment explanation
Indices: 3230561--3230629 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 23
3230551 AGTTGAAATT
**
3230561 AAATTATATATTTTTATTATAATA
1 AAATT-TATATTTTTATTATTTTA
* *
3230585 AAA-ATATAATTTTATTATTTTA
1 AAATTTATATTTTTATTATTTTA
*
3230607 ATAATTTATATTTTTATAATTTT
1 A-AATTTATATTTTTATTATTTT
3230630 TTTAAAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
22 16 0.44
23 2 0.06
24 18 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
AAATTTATATTTTTATTATTTTA
Found at i:3230667 original size:30 final size:31
Alignment explanation
Indices: 3230618--3230689 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
3230608 TAATTTATAT
* * *
3230618 TTTTATAATTTTTTTAAAAAA-TAAATTAAAA
1 TTTTATTA-TTTTTGAAAAAATTAAAGTAAAA
**
3230649 TTTTATTATTTTTGAAAAAATTAAAGTGTAA
1 TTTTATTATTTTTGAAAAAATTAAAGTAAAA
3230680 TTTTATTATT
1 TTTTATTATT
3230690 ATTAATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (31 bp):
TTTTATTATTTTTGAAAAAATTAAAGTAAAA
Found at i:3231934 original size:26 final size:26
Alignment explanation
Indices: 3231898--3231964 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
3231888 CAAAGTACTT
3231898 AACAGAAGCACACACAATGCTGGGGA
1 AACAGAAGCACACACAATGCTGGGGA
* *
3231924 AACAGAAGCACACATAGTGCTGGGGA
1 AACAGAAGCACACACAATGCTGGGGA
3231950 AACAGAAGCACACAC
1 AACAGAAGCACACAC
3231965 GGTACTGAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.43, C:0.24, G:0.25, T:0.07
Consensus pattern (26 bp):
AACAGAAGCACACACAATGCTGGGGA
Found at i:3260374 original size:12 final size:12
Alignment explanation
Indices: 3260357--3260391 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3260347 GATCAAGGTG
*
3260357 GATGGAGATGGA
1 GATGGAGAAGGA
3260369 GATGGAGAAGGA
1 GATGGAGAAGGA
*
3260381 GAAGGAGAAGG
1 GATGGAGAAGG
3260392 CGACAACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.51, T:0.09
Consensus pattern (12 bp):
GATGGAGAAGGA
Found at i:3268698 original size:30 final size:30
Alignment explanation
Indices: 3268652--3268718 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
3268642 TAATTTATAC
* * *
3268652 TTTTATAATTTTTAAAAAATTAA-ATAAATA
1 TTTTATCATTTATAAAAAATCAATATAAA-A
*
3268682 TTTTATCATTTATAAAAAATCAATATACAA
1 TTTTATCATTTATAAAAAATCAATATAAAA
3268712 TTTTATC
1 TTTTATC
3268719 TAAATTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 28 0.88
31 4 0.12
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (30 bp):
TTTTATCATTTATAAAAAATCAATATAAAA
Found at i:3277876 original size:18 final size:18
Alignment explanation
Indices: 3277853--3277888 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3277843 TTGAACTTTG
3277853 AATCCTAAACCCTAAGCT
1 AATCCTAAACCCTAAGCT
*
3277871 AATCCTAAATCCTAAGCT
1 AATCCTAAACCCTAAGCT
3277889 CTAAACATTT
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:0.39, C:0.31, G:0.06, T:0.25
Consensus pattern (18 bp):
AATCCTAAACCCTAAGCT
Found at i:3285732 original size:25 final size:24
Alignment explanation
Indices: 3285679--3285732 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
3285669 TTCGAATTCC
*
3285679 TTTTTGTTTTATAAAAAAATCTAG
1 TTTTTGTTTTACAAAAAAATCTAG
* * *
3285703 ATTTTGTTTTCCAAAAAAATGTTAG
1 TTTTTGTTTTACAAAAAAAT-CTAG
3285728 TTTTT
1 TTTTT
3285733 TGAGATAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (24 bp):
TTTTTGTTTTACAAAAAAATCTAG
Found at i:3290874 original size:6 final size:6
Alignment explanation
Indices: 3290863--3290897 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
3290853 GAGACGTGAT
3290863 TGCCAA TGCCAA TGCCAA TGCCAA TGCCAA TGCCA
1 TGCCAA TGCCAA TGCCAA TGCCAA TGCCAA TGCCA
3290898 CACTGAAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.17
Consensus pattern (6 bp):
TGCCAA
Found at i:3291451 original size:22 final size:22
Alignment explanation
Indices: 3291423--3291466 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3291413 AACTACTCAA
3291423 AACACCTCAATGCAAAATAGAC
1 AACACCTCAATGCAAAATAGAC
3291445 AACACCTCAATGCAAAATAGAC
1 AACACCTCAATGCAAAATAGAC
3291467 GTTATATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.27, G:0.09, T:0.14
Consensus pattern (22 bp):
AACACCTCAATGCAAAATAGAC
Found at i:3305823 original size:20 final size:20
Alignment explanation
Indices: 3305785--3305823 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3305775 AGAATTGTTT
*
3305785 GGAATGTGTTGTTTGGAGCA
1 GGAATGTGTTGTTTAGAGCA
3305805 GGAATGTTGTTG-TTAGAGC
1 GGAATG-TGTTGTTTAGAGC
3305824 CACTCAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.21, C:0.05, G:0.38, T:0.36
Consensus pattern (20 bp):
GGAATGTGTTGTTTAGAGCA
Found at i:3313738 original size:22 final size:23
Alignment explanation
Indices: 3313687--3313739 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
3313677 GAAAGTATAA
3313687 ATGTTATTTAAAAATTTTAATTT
1 ATGTTATTTAAAAATTTTAATTT
3313710 -T-TATATTT-AAAA-TTTAATGTT
1 ATGT-TATTTAAAAATTTTAAT-TT
3313731 ATGTTATTT
1 ATGTTATTT
3313740 GCATTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
20 6 0.23
21 7 0.27
22 12 0.46
23 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (23 bp):
ATGTTATTTAAAAATTTTAATTT
Found at i:3324383 original size:6 final size:6
Alignment explanation
Indices: 3324372--3324398 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3324362 TGATCAAAAT
3324372 TGAAAG TGAAAG TGAAAG TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGA
3324399 TATGAATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.19
Consensus pattern (6 bp):
TGAAAG
Found at i:3325538 original size:22 final size:22
Alignment explanation
Indices: 3325508--3325556 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
3325498 ATAGAAAATT
* *
3325508 ATATAAAATTATTA-AATATTAA
1 ATATTAAATTAATATAATA-TAA
3325530 ATATTAAATTAATATAATATAA
1 ATATTAAATTAATATAATATAA
3325552 ATATT
1 ATATT
3325557 TTGAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATTAAATTAATATAATATAA
Found at i:3327285 original size:16 final size:17
Alignment explanation
Indices: 3327257--3327302 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
3327247 TGATTTGATA
*
3327257 AAAAAATATAAATTAA-
1 AAAAAATAAAAATTAAT
3327273 AAAAGAA-AAAAATTAAT
1 AAAA-AATAAAAATTAAT
3327290 AAAAAATAAAAAT
1 AAAAAATAAAAAT
3327303 ATATTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAAAATAAAAATTAAT
Found at i:3327294 original size:20 final size:22
Alignment explanation
Indices: 3327256--3327295 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
3327246 GTGATTTGAT
*
3327256 AAAAAAATATAAATTAAAAAAG
1 AAAAAAATATAAATAAAAAAAG
3327278 AAAAAAAT-T-AATAAAAAA
1 AAAAAAATATAAATAAAAAA
3327296 TAAAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 1 0.06
22 8 0.47
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (22 bp):
AAAAAAATATAAATAAAAAAAG
Found at i:3350307 original size:16 final size:16
Alignment explanation
Indices: 3350286--3350319 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3350276 TAAAATATAT
3350286 AATTATATTAAATCAA
1 AATTATATTAAATCAA
*
3350302 AATTATATTCAATCAA
1 AATTATATTAAATCAA
3350318 AA
1 AA
3350320 GTAAATTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
AATTATATTAAATCAA
Found at i:3352010 original size:2 final size:2
Alignment explanation
Indices: 3351998--3352028 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
3351988 AGCCCCAGTA
3351998 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
3352029 GCAAGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3353952 original size:21 final size:22
Alignment explanation
Indices: 3353923--3353977 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
3353913 TACATATATT
*
3353923 TTATATAATATTTA-GAATACA
1 TTATTTAATATTTAGGAATACA
3353944 TTATTTAATATTTATGGAATACA
1 TTATTTAATATTTA-GGAATACA
3353967 TT-TTATAATAT
1 TTATT-TAATAT
3353978 GGTGTTGACT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 13 0.43
22 2 0.07
23 15 0.50
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (22 bp):
TTATTTAATATTTAGGAATACA
Found at i:3367901 original size:6 final size:6
Alignment explanation
Indices: 3367890--3367921 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
3367880 TCAGTACGTA
*
3367890 TATATC TATATC TATATC TATATC TGTATC TA
1 TATATC TATATC TATATC TATATC TATATC TA
3367922 ACATAAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.03, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:3369795 original size:9 final size:10
Alignment explanation
Indices: 3369774--3369824 Score: 52
Period size: 11 Copynumber: 4.9 Consensus size: 10
3369764 ATACAAACAA
3369774 AATATTATTTT
1 AATATT-TTTT
3369785 AATA-TTTTT
1 AATATTTTTT
3369794 AATTATTTTTT
1 AA-TATTTTTT
3369805 AATAATTATTTT
1 AAT-ATT-TTTT
3369817 AAT-TTTTT
1 AATATTTTT
3369825 ATAAAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 9 0.25
10 6 0.17
11 14 0.39
12 7 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
AATATTTTTT
Found at i:3369837 original size:22 final size:23
Alignment explanation
Indices: 3369784--3369839 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
3369774 AATATTATTT
* *
3369784 TAATATTTTTAATTATTTTTTAA
1 TAATAATTTTAATTATTTTATAA
*
3369807 TAATTATTTTAATT-TTTTATAA
1 TAATAATTTTAATTATTTTATAA
*
3369829 -AATAAATTTAA
1 TAATAATTTTAA
3369840 ATTACTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 9 0.32
22 7 0.25
23 12 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TAATAATTTTAATTATTTTATAA
Found at i:3369838 original size:21 final size:23
Alignment explanation
Indices: 3369791--3369839 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
3369781 TTTTAATATT
* * *
3369791 TTTAATTATTTTTTAATAATTAT
1 TTTAATTATTTTATAATAATAAA
3369814 TTTAATT-TTTTATAA-AATAAA
1 TTTAATTATTTTATAATAATAAA
3369835 TTTAA
1 TTTAA
3369840 ATTACTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 9 0.39
22 7 0.30
23 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTAATTATTTTATAATAATAAA
Found at i:3370832 original size:21 final size:21
Alignment explanation
Indices: 3370771--3370837 Score: 82
Period size: 20 Copynumber: 3.2 Consensus size: 21
3370761 TTGGTCCTAT
**
3370771 TTTTTACTGTTTTTGTTACTG
1 TTTTTACTGTTTTTGTTGTTG
* *
3370792 TTTTTTGCTATTTTTG-TGTTG
1 -TTTTTACTGTTTTTGTTGTTG
3370813 TTTTTACTGTTTTTGTTGTTG
1 TTTTTACTGTTTTTGTTGTTG
3370834 TTTT
1 TTTT
3370838 CGTGCTATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 13 0.34
21 12 0.32
22 13 0.34
ACGTcount: A:0.06, C:0.06, G:0.16, T:0.72
Consensus pattern (21 bp):
TTTTTACTGTTTTTGTTGTTG
Found at i:3371431 original size:10 final size:10
Alignment explanation
Indices: 3371416--3371444 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3371406 GAGCATAAAA
3371416 TGTTTTTTTG
1 TGTTTTTTTG
3371426 TGTTTTTTTG
1 TGTTTTTTTG
3371436 TGTTTTTTT
1 TGTTTTTTT
3371445 ACAGAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (10 bp):
TGTTTTTTTG
Found at i:3371715 original size:26 final size:26
Alignment explanation
Indices: 3371685--3371754 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 26
3371675 ATACATATTT
3371685 AATTATTTATATTTAGTCA-TATAATA
1 AATTATTTATATTTA-TCATTATAATA
* *
3371711 AATTATTAATATAATTTATTATTTTAATA
1 AATTATT--TAT-ATTTATCATTATAATA
3371740 AATTATTTAATATTT
1 AATTATTT-ATATTT
3371755 CAATTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
26 7 0.19
27 5 0.14
28 7 0.19
29 18 0.49
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (26 bp):
AATTATTTATATTTATCATTATAATA
Found at i:3371724 original size:16 final size:16
Alignment explanation
Indices: 3371703--3371752 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 16
3371693 ATATTTAGTC
3371703 ATATAATAAATTATTA
1 ATATAATAAATTATTA
3371719 ATATAAT---TTATTA
1 ATATAATAAATTATTA
* *
3371732 TTTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
3371749 ATAT
1 ATAT
3371753 TTCAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 11 0.42
16 10 0.38
17 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:3371728 original size:29 final size:30
Alignment explanation
Indices: 3371695--3371752 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
3371685 AATTATTTAT
3371695 ATTTAGTCA-TATAATAAATTA-TTAATATA
1 ATTTA-TCATTATAATAAATTATTTAATATA
* *
3371724 ATTTATTATTTTAATAAATTATTTAATAT
1 ATTTATCATTATAATAAATTATTTAATAT
3371753 TTCAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 16 0.64
30 7 0.28
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
ATTTATCATTATAATAAATTATTTAATATA
Found at i:3372438 original size:14 final size:14
Alignment explanation
Indices: 3372421--3372451 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3372411 AGAGTTTAAA
3372421 AAATTTAATTAATT
1 AAATTTAATTAATT
*
3372435 AAATTTATTTAATT
1 AAATTTAATTAATT
3372449 AAA
1 AAA
3372452 CATTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:3372781 original size:29 final size:30
Alignment explanation
Indices: 3372728--3372786 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
3372718 TATGGTTTAA
* *
3372728 TGTGCAATTGTATACATGAACTTTT-ATTT
1 TGTGCAATTGTATACATAAAATTTTGATTT
* *
3372757 TGTGTAATTTTATACATAAAATTTTGATTT
1 TGTGCAATTGTATACATAAAATTTTGATTT
3372787 GATTTAATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.51
Consensus pattern (30 bp):
TGTGCAATTGTATACATAAAATTTTGATTT
Found at i:3374932 original size:219 final size:219
Alignment explanation
Indices: 3374553--3374991 Score: 806
Period size: 219 Copynumber: 2.0 Consensus size: 219
3374543 ATCACCCCAT
3374553 ACATTTATTGAGAGAGGCGAGGTGTAACTCTCACCATTTTTATAAAGGTATGTATGATTACATCA
1 ACATTTATTGAGAGAGGCGAGGTGTAACTCTCACCATTTTTATAAAGGTATGTATGATTACATCA
*
3374618 CATGGTAACCCCACTTAATAATTAAAAACCATTCAATCAATCACAACATGCCATATGTAATAGCT
66 CATAGTAACCCCACTTAATAATTAAAAACCATTCAATCAATCACAACATGCCATATGTAATAGCT
*
3374683 AACACTTAGTTGGTCTATTGCTTCAAGCCCTCCCTTAACATGAGAAAGGATTGTACGAAATAGAG
131 AACACTTAGTTGGTCTATTGCTTCAAGCCCTCCCTTAACATGAGAAAGGATTGTACGAAATAAAG
*
3374748 ATATTATTTATTTCCAATATTTTA
196 ATATTATCTATTTCCAATATTTTA
* *
3374772 ACATTTATTGAGAGAGGCGATGTGTAACTCTGACCATTTTTATAAAGGTATGTATGATTACATCA
1 ACATTTATTGAGAGAGGCGAGGTGTAACTCTCACCATTTTTATAAAGGTATGTATGATTACATCA
3374837 CATAGTAACCCCACTTAATAATTAAAAACCATTCAATCAATCACAACATGCCATATGTAATAGCT
66 CATAGTAACCCCACTTAATAATTAAAAACCATTCAATCAATCACAACATGCCATATGTAATAGCT
* * *
3374902 AACATTTAGTTGGTCTATTGCTTCAAGCCCTCCTTTAACATGAGAAAGGATTGTACGAAATAAAT
131 AACACTTAGTTGGTCTATTGCTTCAAGCCCTCCCTTAACATGAGAAAGGATTGTACGAAATAAAG
3374967 ATATTATCTATTTCCAATATTTTA
196 ATATTATCTATTTCCAATATTTTA
3374991 A
1 A
3374992 TGTCACATAA
Statistics
Matches: 212, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
219 212 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (219 bp):
ACATTTATTGAGAGAGGCGAGGTGTAACTCTCACCATTTTTATAAAGGTATGTATGATTACATCA
CATAGTAACCCCACTTAATAATTAAAAACCATTCAATCAATCACAACATGCCATATGTAATAGCT
AACACTTAGTTGGTCTATTGCTTCAAGCCCTCCCTTAACATGAGAAAGGATTGTACGAAATAAAG
ATATTATCTATTTCCAATATTTTA
Found at i:3384699 original size:17 final size:18
Alignment explanation
Indices: 3384677--3384711 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3384667 ACCGAACAAG
3384677 TCATCCTC-TTAACTTTC
1 TCATCCTCATTAACTTTC
*
3384694 TCATCCTCATTATCTTTC
1 TCATCCTCATTAACTTTC
3384712 CATAAACGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (18 bp):
TCATCCTCATTAACTTTC
Found at i:3386773 original size:16 final size:15
Alignment explanation
Indices: 3386748--3386781 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3386738 TGAGATTGGA
3386748 CTATTACTCGCCCCC
1 CTATTACTCGCCCCC
*
3386763 CTATCTACTCGCTCCC
1 CTAT-TACTCGCCCCC
3386779 CTA
1 CTA
3386782 GCCGTTGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.15, C:0.50, G:0.06, T:0.29
Consensus pattern (15 bp):
CTATTACTCGCCCCC
Found at i:3389245 original size:11 final size:11
Alignment explanation
Indices: 3389229--3389253 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3389219 ATAAACTAAA
3389229 TTATTTAGTTT
1 TTATTTAGTTT
3389240 TTATTTAGTTT
1 TTATTTAGTTT
3389251 TTA
1 TTA
3389254 GTCTTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (11 bp):
TTATTTAGTTT
Found at i:3399018 original size:15 final size:15
Alignment explanation
Indices: 3398998--3399029 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3398988 GCTTTTTTTC
3398998 AACGCTATATTGTGG
1 AACGCTATATTGTGG
3399013 AACGCTATATTGTGG
1 AACGCTATATTGTGG
3399028 AA
1 AA
3399030 TGAATGAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (15 bp):
AACGCTATATTGTGG
Found at i:3430825 original size:21 final size:21
Alignment explanation
Indices: 3430801--3430842 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3430791 ATCGTGAAAG
*
3430801 AAGGATTGGAGACGGCAGAGA
1 AAGGACTGGAGACGGCAGAGA
* *
3430822 AAGGGCTGGAGACGGCGGAGA
1 AAGGACTGGAGACGGCAGAGA
3430843 GAGGGATCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.48, T:0.07
Consensus pattern (21 bp):
AAGGACTGGAGACGGCAGAGA
Found at i:3430847 original size:21 final size:21
Alignment explanation
Indices: 3430807--3430847 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3430797 AAAGAAGGAT
3430807 TGGAGACGGCAGAGAAAGGGC
1 TGGAGACGGCAGAGAAAGGGC
* *
3430828 TGGAGACGGCGGAGAGAGGG
1 TGGAGACGGCAGAGAAAGGG
3430848 ATCTTTACAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.54, T:0.05
Consensus pattern (21 bp):
TGGAGACGGCAGAGAAAGGGC
Found at i:3431919 original size:14 final size:14
Alignment explanation
Indices: 3431896--3431926 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3431886 TTGAAAGTGG
3431896 TTTTTAAAAAATAA
1 TTTTTAAAAAATAA
*
3431910 TTTTTGAAAAATAA
1 TTTTTAAAAAATAA
3431924 TTT
1 TTT
3431927 ATTTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
TTTTTAAAAAATAA
Found at i:3431945 original size:21 final size:18
Alignment explanation
Indices: 3431896--3431953 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
3431886 TTGAAAGTGG
3431896 TTTTT-AAAAAAT-A-AT
1 TTTTTAAAAAAATAATAT
* *
3431911 TTTTGAAAAATAAT-TTAT
1 TTTTTAAAAA-AATAATAT
3431929 TTTTTAAAAAAATTAATAT
1 TTTTTAAAAAAA-TAATAT
3431948 TTTTTA
1 TTTTTA
3431954 GTGTTTGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 4 0.12
16 4 0.12
17 5 0.15
18 12 0.35
19 9 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTTTAAAAAAATAATAT
Found at i:3431948 original size:19 final size:18
Alignment explanation
Indices: 3431909--3431953 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
3431899 TTAAAAAATA
*
3431909 ATTTTTGAAAAATAATTT
1 ATTTTTTAAAAATAATTT
3431927 ATTTTTTAAAAA-AATTAAT
1 ATTTTTTAAAAATAATT--T
3431946 ATTTTTTA
1 ATTTTTTA
3431954 GTGTTTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 11 0.46
19 9 0.38
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTTTTTAAAAATAATTT
Found at i:3432409 original size:16 final size:16
Alignment explanation
Indices: 3432378--3432414 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
3432368 ATGTGGAAAA
3432378 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
3432394 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
3432410 TATTA
1 TATTA
3432415 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:3444964 original size:18 final size:16
Alignment explanation
Indices: 3444935--3444978 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
3444925 AGGTTTAAAT
*
3444935 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
3444952 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
3444966 TTAAAAATTTATT
1 TTAAAAATTTATT
3444979 AGCATTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:3445993 original size:61 final size:59
Alignment explanation
Indices: 3445918--3446304 Score: 346
Period size: 60 Copynumber: 6.3 Consensus size: 59
3445908 AAAAAATTGT
* * *
3445918 ATTTTTTGGGTGTTGGCCATTG-TAT-GTCCGACATCCCTTATTTCTCGAGAAAAAAATTTCAA
1 ATTTTTT--GTGTTGGCCATTGCAATGGT-CGACACCCCCT-TTTCTCGAGAAAAAAA-TTCAA
3445980 ATTTTTTGATGTTGGCCA-TGCAATGGTCGACACCCCCTGTTT-TCGAGAAAAAAATTCAA
1 ATTTTTTG-TGTTGGCCATTGCAATGGTCGACACCCCCT-TTTCTCGAGAAAAAAATTCAA
* * * *
3446039 TTTTTTTTTGTGTTAGCCA-T-CAAATGGCCGGTCGACACCCCCTATTCTCGAGAAAAAAAATTT
1 --ATTTTTTGTGTTGGCCATTGC-AAT----GGTCGACACCCCCTTTTCTCGAG-AAAAAAATTC
3446102 AA
58 AA
* * *
3446104 ATTTTTTTTGTGTTGGTCA-T-CAAATGGCCGACACCTCCC-TTTCTCGAGAAAAAAGTTCAA
1 A--TTTTTTGTGTTGGCCATTGC-AATGGTCGACACC-CCCTTTTCTCGAGAAAAAAATTCAA
* *
3446164 ATTTTTTTAGTGTTGGTCA-TGCAATGGTCGACACCCCCTTTTCTCTAGAAAAAAATTCAA
1 A-TTTTTT-GTGTTGGCCATTGCAATGGTCGACACCCCCTTTTCTCGAGAAAAAAATTCAA
* *
3446224 TTTTTTTTTGTGTTGGCCA-TGCAATGGTCGACACCCCCTGTTCTCGAGAAAAAAAATTCAA
1 --ATTTTTTGTGTTGGCCATTGCAATGGTCGACACCCCCTTTTCTCGAG-AAAAAAATTCAA
3446285 ATTTTTTTGTGTTGGCCATT
1 A-TTTTTTGTGTTGGCCATT
3446305 TTACTCGAAT
Statistics
Matches: 279, Mismatches: 23, Indels: 47
0.80 0.07 0.13
Matches are distributed among these distances:
59 16 0.06
60 132 0.47
61 67 0.24
62 12 0.04
63 2 0.01
64 19 0.07
65 31 0.11
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (59 bp):
ATTTTTTGTGTTGGCCATTGCAATGGTCGACACCCCCTTTTCTCGAGAAAAAAATTCAA
Found at i:3446031 original size:60 final size:57
Alignment explanation
Indices: 3445958--3446303 Score: 372
Period size: 60 Copynumber: 5.7 Consensus size: 57
3445948 ACATCCCTTA
3445958 TTTCTCGAGAAAAAAATTTCAAATTTTTTGATGTTGGCCATGCAATGGTCGACACCCCC
1 TTTCTCGAGAAAAAAA-TTCAAATTTTTTG-TGTTGGCCATGCAATGGTCGACACCCCC
* * *
3446017 TGTTTTCGAGAAAAAAATTCAATTTTTTTTTGTGTTAGCCAT-CAAATGGCCGGTCGACACCCCC
1 T-TTCTCGAGAAAAAAATTCAA--ATTTTTTGTGTTGGCCATGC-AAT----GGTCGACACCCCC
* * *
3446081 TATTCTCGAGAAAAAAAATTTAAATTTTTTTTGTGTTGGTCAT-CAAATGGCCGACACCTCCC
1 T-TTCTCGAG-AAAAAAATTCAAA--TTTTTTGTGTTGGCCATGC-AATGGTCGACACC-CCC
* *
3446143 TTTCTCGAGAAAAAAGTTCAAATTTTTTTAGTGTTGGTCATGCAATGGTCGACACCCCC
1 TTTCTCGAGAAAAAAATTCAAA-TTTTTT-GTGTTGGCCATGCAATGGTCGACACCCCC
* *
3446202 TTTTCTCTAGAAAAAAATTCAATTTTTTTTTGTGTTGGCCATGCAATGGTCGACACCCCC
1 -TTTCTCGAGAAAAAAATTCAA--ATTTTTTGTGTTGGCCATGCAATGGTCGACACCCCC
3446262 TGTTCTCGAGAAAAAAAATTCAAATTTTTTTGTGTTGGCCAT
1 T-TTCTCGAG-AAAAAAATTCAAA-TTTTTTGTGTTGGCCAT
3446304 TTTACTCGAA
Statistics
Matches: 248, Mismatches: 19, Indels: 39
0.81 0.06 0.13
Matches are distributed among these distances:
59 18 0.07
60 131 0.53
61 43 0.17
62 4 0.02
64 21 0.08
65 31 0.12
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (57 bp):
TTTCTCGAGAAAAAAATTCAAATTTTTTGTGTTGGCCATGCAATGGTCGACACCCCC
Found at i:3446154 original size:185 final size:180
Alignment explanation
Indices: 3445958--3446299 Score: 528
Period size: 185 Copynumber: 1.9 Consensus size: 180
3445948 ACATCCCTTA
*
3445958 TTTCTCGAGAAAAAAATTTCAAATTTTTTGA-TGTTGGCCATGCAATGGTCGACACCCCCTGTTT
1 TTTCTCGAG-AAAAAAGTTCAAATTTTTTGAGTGTTGGCCATGCAATGGTCGACACCCCCT-TTT
3446022 -TCGAGAAAAAAATTCAATTTTTTTTTGTGTTAGCCAT-CAAATGGCCGGTCGACACCCCCTATT
64 CTCGAGAAAAAAATTCAATTTTTTTTTGTGTTAGCCATGC-AAT----GGTCGACACCCCCTATT
*
3446085 CTCGAGAAAAAAAATTTAAATTTTTTTTGTGTTGGTCATCAAATGGCCGACACCTCCC
124 CTCGAGAAAAAAAATTCAAA-TTTTTTTGTGTTGGTCATCAAATGGCCGACACCTCCC
* *
3446143 TTTCTCGAGAAAAAAGTTCAAATTTTTTTAGTGTTGGTCATGCAATGGTCGACACCCCCTTTTCT
1 TTTCTCGAGAAAAAAGTTCAAATTTTTTGAGTGTTGGCCATGCAATGGTCGACACCCCCTTTTCT
* * *
3446208 CTAGAAAAAAATTCAATTTTTTTTTGTGTTGGCCATGCAATGGTCGACACCCCCTGTTCTCGAGA
66 CGAGAAAAAAATTCAATTTTTTTTTGTGTTAGCCATGCAATGGTCGACACCCCCTATTCTCGAGA
3446273 AAAAAAATTCAAATTTTTTTGTGTTGG
131 AAAAAAATTCAAATTTTTTTGTGTTGG
3446300 CCATTTTACT
Statistics
Matches: 147, Mismatches: 7, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
180 14 0.10
181 35 0.24
184 22 0.15
185 75 0.51
186 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.36
Consensus pattern (180 bp):
TTTCTCGAGAAAAAAGTTCAAATTTTTTGAGTGTTGGCCATGCAATGGTCGACACCCCCTTTTCT
CGAGAAAAAAATTCAATTTTTTTTTGTGTTAGCCATGCAATGGTCGACACCCCCTATTCTCGAGA
AAAAAAATTCAAATTTTTTTGTGTTGGTCATCAAATGGCCGACACCTCCC
Found at i:3447237 original size:30 final size:30
Alignment explanation
Indices: 3447177--3447268 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
3447167 TAATAATTAG
* * ** *
3447177 AATATACATGAAATTAGAAAGAAAAATTAA
1 AATATACAAGAAATTCGAAATTAAATTTAA
3447207 AATATACAAGAAATTCGAAATTAAATTTAA
1 AATATACAAGAAATTCGAAATTAAATTTAA
*
3447237 AATA-AAAACGAAATTAC-AAATTAAATTTAA
1 AATATACAA-GAAATT-CGAAATTAAATTTAA
3447267 AA
1 AA
3447269 AGTAAAGGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
29 3 0.06
30 50 0.93
31 1 0.02
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.26
Consensus pattern (30 bp):
AATATACAAGAAATTCGAAATTAAATTTAA
Found at i:3455128 original size:6 final size:6
Alignment explanation
Indices: 3455117--3455150 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
3455107 CTTTTTTCGA
3455117 GAAACT GAAACT GAAACT GAAACT GAAACT GAAA
1 GAAACT GAAACT GAAACT GAAACT GAAACT GAAA
3455151 ACATGAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.53, C:0.15, G:0.18, T:0.15
Consensus pattern (6 bp):
GAAACT
Found at i:3459163 original size:21 final size:22
Alignment explanation
Indices: 3459138--3459199 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 22
3459128 GAGACTAGAT
3459138 TAATTAATTTAATTAATTTCAA
1 TAATTAATTTAATTAATTTCAA
* * **
3459160 -AATTACTGTAACAAATTTCAA
1 TAATTAATTTAATTAATTTCAA
* *
3459181 TAATTTATTTAATTGATTT
1 TAATTAATTTAATTAATTT
3459200 TTATATTTTG
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (22 bp):
TAATTAATTTAATTAATTTCAA
Found at i:3463456 original size:3 final size:3
Alignment explanation
Indices: 3463448--3463485 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3463438 TCAAGCATTA
3463448 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3463486 ACAAAAAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3466806 original size:19 final size:20
Alignment explanation
Indices: 3466784--3466834 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
3466774 TGTTTCATTA
3466784 TTATTTTATTGTC-ACT-TT
1 TTATTTTATTGTCTACTATT
*
3466802 GTTATTATATTG-CTACTATT
1 -TTATTTTATTGTCTACTATT
3466822 TTATTATTATTGT
1 TTATT-TTATTGT
3466835 TCGGATGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 1 0.04
19 18 0.69
20 7 0.27
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.63
Consensus pattern (20 bp):
TTATTTTATTGTCTACTATT
Found at i:3468022 original size:35 final size:34
Alignment explanation
Indices: 3467958--3468033 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 34
3467948 AAAACAATAG
*
3467958 CAAAAATAATAGCAAAATGACAACAAAAATAGCAA
1 CAAAAATAACAGCAAAA-GACAACAAAAATAGCAA
* *
3467993 CAAAAATAACAGTAAAA-ACAACACTAAAATAGTAA
1 CAAAAATAACAGCAAAAGACAACA--AAAATAGCAA
*
3468028 AAAAAA
1 CAAAAA
3468034 GCATCAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
33 6 0.17
35 29 0.83
ACGTcount: A:0.68, C:0.13, G:0.07, T:0.12
Consensus pattern (34 bp):
CAAAAATAACAGCAAAAGACAACAAAAATAGCAA
Found at i:3480009 original size:2 final size:2
Alignment explanation
Indices: 3480002--3480026 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3479992 CTTTGTTAGA
3480002 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3480027 GAAAGTATGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3489166 original size:29 final size:30
Alignment explanation
Indices: 3489133--3489198 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
3489123 ATTGTATTTT
3489133 ATTTTTTATAT-TTAAAAAAAGATAAATTA
1 ATTTTTTATATGTTAAAAAAAGATAAATTA
* * *
3489162 GTTTTTTATATGTTAGAAAAATATAAATTA
1 ATTTTTTATATGTTAAAAAAAGATAAATTA
3489192 ATTTTTT
1 ATTTTTT
3489199 TTAGAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 10 0.31
30 22 0.69
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (30 bp):
ATTTTTTATATGTTAAAAAAAGATAAATTA
Found at i:3489639 original size:19 final size:20
Alignment explanation
Indices: 3489597--3489640 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3489587 ATGAGTTTAG
3489597 AAAAATTATAGAAAAGTATC
1 AAAAATTATAGAAAAGTATC
*
3489617 AAAATATTATTGAAAA-TAT-
1 AAAA-ATTATAGAAAAGTATC
3489636 AAAAA
1 AAAAA
3489641 GGTAATGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.05
19 4 0.18
20 7 0.32
21 10 0.45
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (20 bp):
AAAAATTATAGAAAAGTATC
Found at i:3493195 original size:2 final size:2
Alignment explanation
Indices: 3493188--3493235 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
3493178 GCACGAAAGG
3493188 GA GA GA GA GA GA GA 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 GA GA GA GA GA GA GA
3493230 GA GA GA
1 GA GA GA
3493236 AGGAAACTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3496407 original size:3 final size:3
Alignment explanation
Indices: 3496399--3496434 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3496389 TCCATAGTAC
3496399 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3496435 ATACTCATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3497523 original size:2 final size:2
Alignment explanation
Indices: 3497518--3497554 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3497508 ACACACACAA
3497518 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3497555 AAAGAAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.