Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 10 of 19
Found at i:2073390 original size:26 final size:26
Alignment explanation
Indices: 2073361--2073416 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
2073351 TAATTATATA
* * *
2073361 AATTTAAAATGAAACTTATTTTAAAT
1 AATTGAAAATAAAACTTATTTCAAAT
*
2073387 AATTGAAAATAAAATTTATTTCAAAT
1 AATTGAAAATAAAACTTATTTCAAAT
2073413 AATT
1 AATT
2073417 CATACAGCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (26 bp):
AATTGAAAATAAAACTTATTTCAAAT
Found at i:2078389 original size:16 final size:16
Alignment explanation
Indices: 2078368--2078399 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2078358 CACATCTAAA
*
2078368 TTCGAATCTCAGTAAC
1 TTCGAATCCCAGTAAC
2078384 TTCGAATCCCAGTAAC
1 TTCGAATCCCAGTAAC
2078400 ATAAATTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.28
Consensus pattern (16 bp):
TTCGAATCCCAGTAAC
Found at i:2081409 original size:16 final size:17
Alignment explanation
Indices: 2081390--2081421 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2081380 TTTATGTTAA
2081390 TATTTTTTAA-TAATAT
1 TATTTTTTAATTAATAT
2081406 TATTTTTTAATTAATA
1 TATTTTTTAATTAATA
2081422 ATTAAGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTTTTAATTAATAT
Found at i:2081410 original size:48 final size:45
Alignment explanation
Indices: 2081325--2081417 Score: 100
Period size: 48 Copynumber: 2.0 Consensus size: 45
2081315 AAAATAACAA
* *
2081325 TATTATTTTTATTAGATATTTTTATTTATATGATATTTAATTTAATTT
1 TATTATTTTTATTAGATATTTTTAATAATAT-ATATTT--TTTAATTT
2081373 TATTATTTTTATGTTA-ATATTTTTTAATAATAT-TATTTTTTAATT
1 TATTATTTTTA--TTAGATA-TTTTTAATAATATATATTTTTTAATT
2081418 AATAATTAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
46 7 0.17
48 16 0.40
49 3 0.08
50 14 0.35
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (45 bp):
TATTATTTTTATTAGATATTTTTAATAATATATATTTTTTAATTT
Found at i:2081441 original size:6 final size:6
Alignment explanation
Indices: 2081430--2081460 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2081420 TAATTAAGTT
2081430 ATATAA ATATAA ATATAA ATATAA A-ATAA AT
1 ATATAA ATATAA ATATAA ATATAA ATATAA AT
2081461 TTTATCTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:2081527 original size:20 final size:20
Alignment explanation
Indices: 2081481--2081527 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
2081471 TTAATTTTAC
* *
2081481 GAAACAATATTATATTAAGT
1 GAAAAAATATTATAATAAGT
*
2081501 -AACAAAATATTATAATAATT
1 GAA-AAAATATTATAATAAGT
2081521 GAAAAAA
1 GAAAAAA
2081528 ATATGAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.09
20 18 0.82
21 2 0.09
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (20 bp):
GAAAAAATATTATAATAAGT
Found at i:2102940 original size:24 final size:26
Alignment explanation
Indices: 2102913--2102976 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
2102903 AAATCTATAC
2102913 ATTTTTAATAAAT-AAAATTATTTA-
1 ATTTTTAATAAATAAAAATTATTTAT
*
2102937 A-TTTTATTAAAATAAAAATTATTTAT
1 ATTTTTAAT-AAATAAAAATTATTTAT
*
2102963 ATTTATTAAAAAAT
1 ATTT-TTAATAAAT
2102977 TAATTAGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 6 0.19
24 5 0.16
25 11 0.34
26 1 0.03
27 6 0.19
28 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTTTTAATAAATAAAAATTATTTAT
Found at i:2102982 original size:25 final size:25
Alignment explanation
Indices: 2102922--2102973 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
2102912 CATTTTTAAT
2102922 AAAT-AAAATTATTTAATTTTATTA
1 AAATAAAAATTATTTAATTTTATTA
2102946 AAATAAAAATTATTT-ATATTTATTA
1 AAATAAAAATTATTTAAT-TTTATTA
2102971 AAA
1 AAA
2102974 AATTAATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATAAAAATTATTTAATTTTATTA
Found at i:2103448 original size:9 final size:9
Alignment explanation
Indices: 2103387--2103488 Score: 54
Period size: 9 Copynumber: 11.3 Consensus size: 9
2103377 TATTAGATGT
*
2103387 TATAATTTA
1 TATATTTTA
*
2103396 TATATTTTT
1 TATATTTTA
*
2103405 TATTATTTTT
1 TA-TATTTTA
*
2103415 TATATTATA
1 TATATTTTA
*
2103424 -ATTATGTTA
1 TA-TATTTTA
2103433 -ATA--TTA
1 TATATTTTA
2103439 TATATTTTA
1 TATATTTTA
2103448 TATAATTTT-
1 TAT-ATTTTA
2103457 TAATATATTTA
1 T-ATAT-TTTA
2103468 TATA-TTTA
1 TATATTTTA
*
2103476 TATTATATTA
1 TA-TATTTTA
2103486 TAT
1 TAT
2103489 TTTAATTTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
6 3 0.04
7 3 0.04
8 9 0.12
9 32 0.43
10 27 0.36
11 1 0.01
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (9 bp):
TATATTTTA
Found at i:2103453 original size:19 final size:21
Alignment explanation
Indices: 2103430--2103483 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
2103420 TATAATTATG
2103430 TTAATATTATATATTT-TATA
1 TTAATATTATATATTTATATA
*
2103450 -TAATTTTTAATATATTTATATA
1 TTAA-TATT-ATATATTTATATA
*
2103472 TTTATATTATAT
1 TTAATATTATAT
2103484 TATATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
19 3 0.11
20 3 0.11
21 12 0.44
22 7 0.26
23 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTAATATTATATATTTATATA
Found at i:2103501 original size:53 final size:52
Alignment explanation
Indices: 2103370--2103497 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
2103360 TTTTGTCAGG
* * * *
2103370 TAATATATATTAGATGTTATA-A-TTTATATATTTTTTATTATTTTTTATATTA
1 TAAT-TATATTA-ATATTATATATTTTATATAATTTTTAATATTTTATATATTA
*
2103422 TAATTATGTTAATATTATATATTTTATATAATTTTTAATATATTTATATATT-
1 TAATTATATTAATATTATATATTTTATATAATTTTTAATAT-TTTATATATTA
*
2103474 TATATTATATT-ATATTTTA-ATTTT
1 TA-ATTATATTAATATTATATATTTT
2103498 TTATGTTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
50 7 0.11
51 12 0.18
52 30 0.46
53 16 0.25
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (52 bp):
TAATTATATTAATATTATATATTTTATATAATTTTTAATATTTTATATATTA
Found at i:2103687 original size:18 final size:18
Alignment explanation
Indices: 2103666--2103700 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2103656 TGATTTAAAA
2103666 AAAATCAAA-TTAATTAAT
1 AAAAT-AAATTTAATTAAT
2103684 AAAATAAATTTAATTAA
1 AAAATAAATTTAATTAA
2103701 AAATTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATAAATTTAATTAAT
Found at i:2103717 original size:23 final size:24
Alignment explanation
Indices: 2103677--2103727 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 24
2103667 AAATCAAATT
2103677 AATTAATAAAATAAATTTAATTAAA
1 AATTAAT-AAATAAATTTAATTAAA
*
2103702 AATTAAT-AATATATTTAATTAAA
1 AATTAATAAATAAATTTAATTAAA
2103725 AAT
1 AAT
2103728 AAATTATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 18 0.72
25 7 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AATTAATAAATAAATTTAATTAAA
Found at i:2103980 original size:3 final size:3
Alignment explanation
Indices: 2103972--2104006 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2103962 GGTAATAGAT
* *
2103972 ATA ATA ATA CTA ATA ATA CTA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2104007 TTGACAAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2103985 original size:9 final size:9
Alignment explanation
Indices: 2103964--2104006 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
2103954 CACTATAAGG
2103964 TAATAGATA-
1 TAATA-ATAC
2103973 TAATAATAC
1 TAATAATAC
2103982 TAATAATAC
1 TAATAATAC
*
2103991 TAATAATAA
1 TAATAATAC
2104000 TAATAAT
1 TAATAAT
2104007 TTGACAAGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 3 0.09
9 29 0.91
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (9 bp):
TAATAATAC
Found at i:2104458 original size:25 final size:22
Alignment explanation
Indices: 2104430--2104482 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
2104420 TTGAAGCTGC
2104430 ATTTTTAAAATTAAATAATTTTATT
1 ATTTTTAAAATT--A-AATTTTATT
**
2104455 ATTTTTATCATTAAATTTTATT
1 ATTTTTAAAATTAAATTTTATT
2104477 ATTTTT
1 ATTTTT
2104483 TATAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 15 0.58
23 1 0.04
25 10 0.38
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTTTAAAATTAAATTTTATT
Found at i:2104867 original size:38 final size:40
Alignment explanation
Indices: 2104825--2104905 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
2104815 AAATTATGAA
* **
2104825 AAAAAAT-AAAT-TATAAAATAT-ATTTTTATAATATTAAT
1 AAAAAATAAAATAAATAAAATATAATAATTATAATA-TAAT
2104863 AAAAAATAAAATAAATAAAATATAATAATTATAATATAAT
1 AAAAAATAAAATAAATAAAATATAATAATTATAATATAAT
2104903 AAA
1 AAA
2104906 TATAAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 7 0.19
39 4 0.11
40 16 0.43
41 10 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (40 bp):
AAAAAATAAAATAAATAAAATATAATAATTATAATATAAT
Found at i:2104867 original size:40 final size:40
Alignment explanation
Indices: 2104823--2104917 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 40
2104813 TTAAATTATG
* **
2104823 AAAAAAAATAAAT-TATAAAATAT-ATTTTTATAATATTAAT
1 AAAAAAAA-AAATAAATAAAATATAATAATTATAATA-TAAT
*
2104863 AAAAAATAAAATAAATAAAATATAATAATTATAATATAAT
1 AAAAAAAAAAATAAATAAAATATAATAATTATAATATAAT
* *
2104903 AAATATAAAAATAAA
1 AAAAAAAAAAATAAA
2104918 AATTTCTCAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
39 4 0.09
40 32 0.70
41 10 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (40 bp):
AAAAAAAAAAATAAATAAAATATAATAATTATAATATAAT
Found at i:2104884 original size:14 final size:14
Alignment explanation
Indices: 2104865--2104920 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
2104855 ATATTAATAA
*
2104865 AAAATAAAATAAAT
1 AAAATATAATAAAT
*
2104879 AAAATATAATAATT
1 AAAATATAATAAAT
*
2104893 ATAATATAATAAAT
1 AAAATATAATAAAT
*
2104907 ATAAAAATAA-AAAT
1 A-AAATATAATAAAT
2104921 TTCTCATACT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 29 0.83
15 6 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATATAATAAAT
Found at i:2105525 original size:3 final size:3
Alignment explanation
Indices: 2105517--2105557 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2105507 CCAAAACTCA
2105517 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2105558 ATCAGAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2105879 original size:8 final size:9
Alignment explanation
Indices: 2105854--2105924 Score: 60
Period size: 8 Copynumber: 8.2 Consensus size: 9
2105844 TTATCTTGAT
2105854 TATA-TAAA
1 TATATTAAA
**
2105862 TATAAAAAA
1 TATATTAAA
2105871 TA-ATTAAA
1 TATATTAAA
2105879 TATATTAAA
1 TATATTAAA
2105888 -ATATTAAA
1 TATATTAAA
*
2105896 AATAATTAAA
1 TAT-ATTAAA
*
2105906 TATA-TATA
1 TATATTAAA
*
2105914 TATTTTAAA
1 TATATTAAA
2105923 TA
1 TA
2105925 AGTTATTATT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
8 24 0.47
9 19 0.37
10 8 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TATATTAAA
Found at i:2105880 original size:17 final size:16
Alignment explanation
Indices: 2105858--2105900 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
2105848 CTTGATTATA
2105858 TAAATATAAAAAATAAT
1 TAAATATAAAAAAT-AT
*
2105875 TAAATATATTAAAATAT
1 TAAATATA-AAAAATAT
*
2105892 TAAAAATAA
1 TAAATATAA
2105901 TTAAATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAATATAAAAAATAT
Found at i:2105922 original size:27 final size:27
Alignment explanation
Indices: 2105859--2105910 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
2105849 TTGATTATAT
*
2105859 AAATATAAAAAATAATTAAATATATTA
1 AAATATTAAAAATAATTAAATATATTA
2105886 AAATATTAAAAATAATTAAATATAT
1 AAATATTAAAAATAATTAAATATAT
2105911 ATATATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
AAATATTAAAAATAATTAAATATATTA
Found at i:2106237 original size:20 final size:20
Alignment explanation
Indices: 2106212--2106268 Score: 87
Period size: 22 Copynumber: 2.8 Consensus size: 20
2106202 TAAAAAAGGA
*
2106212 TTTTACTTTTTTATTCATAT
1 TTTTACTTTTTTACTCATAT
2106232 TTTTACTTTTTTTTACTCATAT
1 TTTTAC--TTTTTTACTCATAT
2106254 TTTTACTTTTTTACT
1 TTTTACTTTTTTACT
2106269 GATACATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 15 0.44
22 19 0.56
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTACTTTTTTACTCATAT
Found at i:2106259 original size:12 final size:12
Alignment explanation
Indices: 2106219--2106260 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
2106209 GGATTTTACT
*
2106219 TTTTTATTCATA
1 TTTTTACTCATA
*
2106231 TTTTTACT--TT
1 TTTTTACTCATA
2106241 TTTTTACTCATA
1 TTTTTACTCATA
2106253 TTTTTACT
1 TTTTTACT
2106261 TTTTTACTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
10 9 0.36
12 16 0.64
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTACTCATA
Found at i:2106688 original size:3 final size:3
Alignment explanation
Indices: 2106680--2106711 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2106670 TTTTACCTTT
*
2106680 TTC TTC TTC TTC TTC TTC TTC TTC TTC GTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
2106712 GTTTGTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:2111500 original size:96 final size:96
Alignment explanation
Indices: 2111384--2111581 Score: 387
Period size: 96 Copynumber: 2.1 Consensus size: 96
2111374 GCTGTTGCAA
*
2111384 ATTATTTTTTATATCCATGCACCCTTTTCTGTTGCTTTTTATTTTGATCTTTATCATCATCCTAC
1 ATTAGTTTTTATATCCATGCACCCTTTTCTGTTGCTTTTTATTTTGATCTTTATCATCATCCTAC
2111449 TGTTAAAAGTGTCTAGAATTGAATTAGTGCT
66 TGTTAAAAGTGTCTAGAATTGAATTAGTGCT
2111480 ATTAGTTTTTATATCCATGCACCCTTTTCTGTTGCTTTTTATTTTGATCTTTATCATCATCCTAC
1 ATTAGTTTTTATATCCATGCACCCTTTTCTGTTGCTTTTTATTTTGATCTTTATCATCATCCTAC
2111545 TGTTAAAAGTGTCTAGAATTGAATTAGTGCT
66 TGTTAAAAGTGTCTAGAATTGAATTAGTGCT
2111576 ATTAGT
1 ATTAGT
2111582 GTCCTGAAAA
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 101 1.00
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.48
Consensus pattern (96 bp):
ATTAGTTTTTATATCCATGCACCCTTTTCTGTTGCTTTTTATTTTGATCTTTATCATCATCCTAC
TGTTAAAAGTGTCTAGAATTGAATTAGTGCT
Found at i:2114484 original size:2 final size:2
Alignment explanation
Indices: 2114477--2114505 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2114467 TACAAAAGTG
2114477 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
2114506 GAATGAAATA
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:2117513 original size:21 final size:21
Alignment explanation
Indices: 2117489--2117546 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
2117479 AATTTTGATA
2117489 TAAAATTATATTAAAAGTTAT
1 TAAAATTATATTAAAAGTTAT
*
2117510 TAAAATTACTATT-AATGTTAT
1 TAAAATTA-TATTAAAAGTTAT
* *
2117531 CAAATTTATATTAAAA
1 TAAAATTATATTAAAA
2117547 ACAGAATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.13
21 23 0.74
22 4 0.13
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (21 bp):
TAAAATTATATTAAAAGTTAT
Found at i:2117612 original size:20 final size:21
Alignment explanation
Indices: 2117580--2117752 Score: 114
Period size: 20 Copynumber: 8.3 Consensus size: 21
2117570 CAATAAATAA
2117580 AAAATT-ATC-AAATT-TATT
1 AAAATTAATCAAAATTATATT
2117598 AAAAGTTAAT-AAAATTATATAT
1 AAAA-TTAATCAAAATTATAT-T
* *
2117620 AATATT-ATGAAAATTATATT
1 AAAATTAATCAAAATTATATT
*
2117640 AAAAAT-ATCAAAATTATATT
1 AAAATTAATCAAAATTATATT
*
2117660 AAAAGTTAATCATTAGAATTTTATT
1 AAAA-TTAATCA--A-AATTATATT
* *
2117685 AAAAGTT-ATTAAAATTATATC
1 AAAA-TTAATCAAAATTATATT
*
2117706 AAAATTTATC-AAATT-TATT
1 AAAATTAATCAAAATTATATT
* *
2117725 ATAAATGATATCAAAATTGTA-T
1 A-AAATTA-ATCAAAATTATATT
2117747 AAAATT
1 AAAATT
2117753 TACCAAAACT
Statistics
Matches: 125, Mismatches: 14, Indels: 29
0.74 0.08 0.17
Matches are distributed among these distances:
18 4 0.03
19 6 0.05
20 42 0.34
21 36 0.29
22 16 0.13
23 2 0.02
24 4 0.03
25 15 0.12
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.40
Consensus pattern (21 bp):
AAAATTAATCAAAATTATATT
Found at i:2117658 original size:11 final size:11
Alignment explanation
Indices: 2117608--2117752 Score: 69
Period size: 11 Copynumber: 13.5 Consensus size: 11
2117598 AAAAGTTAAT
2117608 AAAATTATAT-
1 AAAATTATATC
* *
2117618 ATAA-TATTATG
1 AAAATTA-TATC
*
2117629 AAAATTATATT
1 AAAATTATATC
2117640 AAAA--ATATC
1 AAAATTATATC
*
2117649 AAAATTATATT
1 AAAATTATATC
2117660 AAAAGTTA-ATC
1 AAAA-TTATATC
* *
2117671 ATTAGAATTTTATT
1 A--A-AATTATATC
2117685 AAAAGTTAT-T-
1 AAAA-TTATATC
2117695 AAAATTATATC
1 AAAATTATATC
2117706 AAAATT-TATC
1 AAAATTATATC
*
2117716 -AAATT-TATT
1 AAAATTATATC
*
2117725 ATAAATGATATC
1 A-AAATTATATC
*
2117737 AAAATTGTAT-
1 AAAATTATATC
2117747 AAAATT
1 AAAATT
2117753 TACCAAAACT
Statistics
Matches: 105, Mismatches: 14, Indels: 32
0.70 0.09 0.21
Matches are distributed among these distances:
9 22 0.21
10 21 0.20
11 41 0.39
12 13 0.12
13 3 0.03
14 5 0.05
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (11 bp):
AAAATTATATC
Found at i:2117700 original size:21 final size:21
Alignment explanation
Indices: 2117589--2117723 Score: 105
Period size: 21 Copynumber: 6.3 Consensus size: 21
2117579 AAAAATTATC
*
2117589 AAATT-TATTAAAAGTTAATA
1 AAATTATATTAAAAGTTATTA
* *
2117609 AAATTATATATAATA-TTATGA
1 AAATTATAT-TAAAAGTTATTA
* *
2117630 AAATTATATTAAAA-ATATCA
1 AAATTATATTAAAAGTTATTA
2117650 AAATTATATTAAAAGTTAATCATTA
1 AAATTATATTAAAAG-T--T-ATTA
* *
2117675 GAATTTTATTAAAAGTTATTA
1 AAATTATATTAAAAGTTATTA
* * *
2117696 AAATTATATCAAAATTTATCA
1 AAATTATATTAAAAGTTATTA
*
2117717 AATTTAT
1 AAATTAT
2117724 TATAAATGAT
Statistics
Matches: 92, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
20 27 0.29
21 42 0.46
22 5 0.05
24 2 0.02
25 16 0.17
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (21 bp):
AAATTATATTAAAAGTTATTA
Found at i:2117719 original size:9 final size:10
Alignment explanation
Indices: 2117579--2117782 Score: 62
Period size: 11 Copynumber: 19.6 Consensus size: 10
2117569 TCAATAAATA
*
2117579 AAAAATTATC
1 AAAATTTATC
*
2117589 -AAATTTATT
1 AAAATTTATC
*
2117598 AAAAGTTAAT-
1 AAAA-TTTATC
2117608 AAAATTATAT-
1 AAAATT-TATC
* *
2117618 ATAATATTATG
1 AAAAT-TTATC
*
2117629 AAAATTATATT
1 AAAATT-TATC
*
2117640 AAAA-ATATC
1 AAAATTTATC
*
2117649 AAAATTATATT
1 AAAATT-TATC
*
2117660 AAAAGTTAATC
1 AAAA-TTTATC
*
2117671 ATTAGAATTTTATT
1 A--A-AA-TTTATC
* *
2117685 AAAAGTTATT
1 AAAATTTATC
2117695 AAAATTATATC
1 AAAATT-TATC
2117706 AAAATTTATC
1 AAAATTTATC
*
2117716 -AAATTTATT
1 AAAATTTATC
*
2117725 ATAAATGATATC
1 A-AAAT-TTATC
2117737 AAAATTGTAT-
1 AAAATT-TATC
*
2117747 AAAATTTACC
1 AAAATTTATC
* *
2117757 AAAA-CTATT
1 AAAATTTATC
*
2117766 ACAATGTTATC
1 AAAAT-TTATC
2117777 AAAATT
1 AAAATT
2117783 ATTACGAAAG
Statistics
Matches: 143, Mismatches: 31, Indels: 40
0.67 0.14 0.19
Matches are distributed among these distances:
9 31 0.22
10 42 0.29
11 55 0.38
12 7 0.05
13 1 0.01
14 7 0.05
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.39
Consensus pattern (10 bp):
AAAATTTATC
Found at i:2117736 original size:31 final size:31
Alignment explanation
Indices: 2117684--2117754 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
2117674 AGAATTTTAT
* *
2117684 TAAAAGTTATTAAAATTATATCAAAATT-TA
1 TAAAATTTATTAAAATGATATCAAAATTGTA
*
2117714 TCAAATTTATTATAAATGATATCAAAATTGTA
1 TAAAATTTATTA-AAATGATATCAAAATTGTA
2117746 TAAAATTTA
1 TAAAATTTA
2117755 CCAAAACTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 10 0.29
31 15 0.43
32 10 0.29
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (31 bp):
TAAAATTTATTAAAATGATATCAAAATTGTA
Found at i:2119727 original size:27 final size:27
Alignment explanation
Indices: 2119665--2119727 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
2119655 TTTTTTATAT
* *
2119665 TAATATTTAAAATTATATTAAATTAAA
1 TAATATTTTAAATTAAATTAAATTAAA
*
2119692 TAATATTTTAAATTAAATTAATTTAAA
1 TAATATTTTAAATTAAATTAAATTAAA
*
2119719 TAATTTTTT
1 TAATATTTT
2119728 TAAAAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TAATATTTTAAATTAAATTAAATTAAA
Found at i:2120352 original size:16 final size:15
Alignment explanation
Indices: 2120321--2120364 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2120311 TGAAGAACAG
**
2120321 GAAGAGGAAAAGGAA
1 GAAGAGGATGAGGAA
*
2120336 GAAGCGAGATGAGGAA
1 GAAGAG-GATGAGGAA
2120352 GAAGAGGATGAGG
1 GAAGAGGATGAGG
2120365 GACAGGAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.48, C:0.02, G:0.45, T:0.05
Consensus pattern (15 bp):
GAAGAGGATGAGGAA
Found at i:2121003 original size:151 final size:150
Alignment explanation
Indices: 2120708--2121007 Score: 417
Period size: 151 Copynumber: 2.0 Consensus size: 150
2120698 TATCAAGTAC
*
2120708 TTTTGCTTCTTTGAGTGGCTGAATGTGCTTGCCTAGGTTCAATTTTGAAGAGTTTGATGGAAAGG
1 TTTTGCTTCTTTGAGTGGCTGAAGGTGCTTGCCTAGGTTCAATTTTGAAGAGTTTGATGGAAAGG
* * * *
2120773 GTTTTTTGTTTTGATCTCTTAATGCAATTTAGGGTTTTCTGGTATTTACGCTCGTAATGGGGGAG
66 GCTTTTAGTTTTGATCTCTTAATGCAATTTAGGGTTTTATGGTATTTACGCTCGTAATGGGGGAA
2120838 AACTGAAGAGTTTTTTTTTT
131 AACTGAAGAGTTTTTTTTTT
***
2120858 TTTTGGCTTCTTTGAGTGGCTGAAGGTGCTTGCCTAGGTTCAATTTTTTGGAGTTTGATGGAAAG
1 TTTT-GCTTCTTTGAGTGGCTGAAGGTGCTTGCCTAGGTTCAATTTTGAAGAGTTTGATGGAAAG
* * * * * * *
2120923 GGCTTTTAGTTTTGATTTCTTAATGCAATTTTGTGTTTTATGTTATTTAC-CGTTGTTAT-TGGG
65 GGCTTTTAGTTTTGATCTCTTAATGCAATTTAGGGTTTTATGGTATTTACGC-TCGTAATGGGGG
2120986 AAAACT-ATAGAGTTTTTTTTTT
129 AAAACTGA-AGAGTTTTTTTTTT
2121008 GGTTAGTTTT
Statistics
Matches: 132, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
149 1 0.01
150 27 0.20
151 104 0.79
ACGTcount: A:0.19, C:0.09, G:0.25, T:0.47
Consensus pattern (150 bp):
TTTTGCTTCTTTGAGTGGCTGAAGGTGCTTGCCTAGGTTCAATTTTGAAGAGTTTGATGGAAAGG
GCTTTTAGTTTTGATCTCTTAATGCAATTTAGGGTTTTATGGTATTTACGCTCGTAATGGGGGAA
AACTGAAGAGTTTTTTTTTT
Found at i:2126192 original size:3 final size:3
Alignment explanation
Indices: 2126184--2126213 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2126174 CCCTTAAAAT
2126184 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2126214 TAAAAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2126733 original size:2 final size:2
Alignment explanation
Indices: 2126728--2126762 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2126718 ATATATATAT
2126728 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2126763 TGGGCAATAT
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2134819 original size:2 final size:2
Alignment explanation
Indices: 2134812--2134874 Score: 85
Period size: 2 Copynumber: 32.5 Consensus size: 2
2134802 TAGGTTTGTT
* * *
2134812 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T- TA CA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2134853 TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
2134875 TGCGGACCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2135994 original size:63 final size:63
Alignment explanation
Indices: 2135895--2136037 Score: 241
Period size: 63 Copynumber: 2.3 Consensus size: 63
2135885 TTACTCCATC
* * * *
2135895 TATAAATGGTGGAGCTTTGAACCTAACCAACCAGCAAAAGATTTATTCGTGGTTGGAGGGATA
1 TATAAATGGTGGAGCTTTGAACCTAACCAACCAGCAAAAGATTAATTCATGATTGAAGGGATA
*
2135958 TATAAATGGTGGAGCTTTGAACCTGACCAACCAGCAAAAGATTAATTCATGATTGAAGGGATA
1 TATAAATGGTGGAGCTTTGAACCTAACCAACCAGCAAAAGATTAATTCATGATTGAAGGGATA
2136021 TATAAATGGTGGAGCTT
1 TATAAATGGTGGAGCTT
2136038 CTCAGAATGG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 75 1.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.27
Consensus pattern (63 bp):
TATAAATGGTGGAGCTTTGAACCTAACCAACCAGCAAAAGATTAATTCATGATTGAAGGGATA
Found at i:2140865 original size:20 final size:20
Alignment explanation
Indices: 2140837--2140874 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2140827 AAGACCCCAG
* *
2140837 AAAATGAAAACGGAAAAAGA
1 AAAAAGAAAAAGGAAAAAGA
2140857 AAAAAGAAAAAGGAAAAA
1 AAAAAGAAAAAGGAAAAA
2140875 AACTCTGCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAAAGAAAAAGGAAAAAGA
Found at i:2141072 original size:2 final size:2
Alignment explanation
Indices: 2141060--2141093 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2141050 AAAACCAAAC
*
2141060 AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2141094 TACCTGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2144899 original size:14 final size:15
Alignment explanation
Indices: 2144869--2144903 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2144859 AAAAATCAAA
*
2144869 TTAAATTGATTATTT
1 TTAATTTGATTATTT
2144884 TTAATTTGATTA-TT
1 TTAATTTGATTATTT
2144898 TTAATT
1 TTAATT
2144904 ATATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (15 bp):
TTAATTTGATTATTT
Found at i:2145813 original size:2 final size:2
Alignment explanation
Indices: 2145806--2145859 Score: 64
Period size: 2 Copynumber: 29.5 Consensus size: 2
2145796 TAGAATGGTG
2145806 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2145845 T- TT TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
2145860 TTAAAATTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
1 5 0.11
2 41 0.89
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2146386 original size:14 final size:14
Alignment explanation
Indices: 2146367--2146416 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
2146357 CGCTTTGCTA
2146367 TATATAAATATATG
1 TATATAAATATATG
2146381 TATATAAATAT-T-
1 TATATAAATATATG
*
2146393 TATATTAATATTTATG
1 TATA-TAA-ATATATG
2146409 TAT-TAAAT
1 TATATAAAT
2146417 GTAGTTAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
12 4 0.13
13 6 0.19
14 17 0.55
15 1 0.03
16 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (14 bp):
TATATAAATATATG
Found at i:2146404 original size:12 final size:12
Alignment explanation
Indices: 2146367--2146407 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
2146357 CGCTTTGCTA
2146367 TATATAAATATAT
1 TATATAAATAT-T
2146380 GTATATAAATATT
1 -TATATAAATATT
*
2146393 TATATTAATATT
1 TATATAAATATT
2146405 TAT
1 TAT
2146408 GTATTAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 14 0.54
13 1 0.04
14 11 0.42
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
TATATAAATATT
Found at i:2151774 original size:18 final size:20
Alignment explanation
Indices: 2151737--2151774 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
2151727 ACAATTAGAA
*
2151737 TATACAAATATTTCATTATT
1 TATACAAATATTTAATTATT
2151757 TATA-AAATA-TTAATTATT
1 TATACAAATATTTAATTATT
2151775 AACGTATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TATACAAATATTTAATTATT
Found at i:2159677 original size:79 final size:79
Alignment explanation
Indices: 2159546--2159715 Score: 261
Period size: 79 Copynumber: 2.2 Consensus size: 79
2159536 TAAGCATAGC
2159546 GGTGACTTGGCGTCACGGGACGCTAATAACTTGGCATCATGCAGGGTCAATTACGCGCCATGGTG
1 GGTGACTTGGCGTCACGGGACGCTAATAACTTGGCATCATGCAGGGTCAATTACGCGCCATGGTG
2159611 GCGACCAGAGTGAG
66 GCGACCAGAGTGAG
* * * * * *
2159625 GGTGACTTGGCGTCACAGGG-CGTTAATGACTTGGCGTCATGCGGGGTTAATTACGTGCCATGGT
1 GGTGACTTGGCGTCAC-GGGACGCTAATAACTTGGCATCATGCAGGGTCAATTACGCGCCATGGT
*
2159689 GGGGACCAGAGTGAG
65 GGCGACCAGAGTGAG
2159704 GGTGACTTGGCG
1 GGTGACTTGGCG
2159716 CTATGGTGGC
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
79 80 0.96
80 3 0.04
ACGTcount: A:0.20, C:0.20, G:0.38, T:0.22
Consensus pattern (79 bp):
GGTGACTTGGCGTCACGGGACGCTAATAACTTGGCATCATGCAGGGTCAATTACGCGCCATGGTG
GCGACCAGAGTGAG
Found at i:2159851 original size:113 final size:113
Alignment explanation
Indices: 2159608--2159828 Score: 325
Period size: 113 Copynumber: 1.9 Consensus size: 113
2159598 ACGCGCCATG
** * * *
2159608 GTGGCGACCAGAGTGAGGGTGACTTGGCGTCACAGGGCGTTAATGACTTGGCGTCATGCGGGGTT
1 GTGGCGACCAGAGTGAGGGTGACTTAACATCACAGGGCGTTAATGACTTGGCATCATGCGGGGTC
* * **
2159673 AATTACGTGCCATGGTGGGGACCAGAGTGAGGGTGACTTGGCGCTATG
66 AATTACGTGCCATGGTGGCGACCAGAGTGAAGGTGACTTGGCGCTACA
2159721 GTGGCGACCAGAGTGAGGGTGACTTAACATCACAGGGCGTTAATGACTTGGCATCATGCAGGGGT
1 GTGGCGACCAGAGTGAGGGTGACTTAACATCACAGGGCGTTAATGACTTGGCATCATGC-GGGGT
* * *
2159786 CAATTGCGTGCCATGGTGGCGACCGGGGTGAAGGTGACTTGGC
65 CAATTACGTGCCATGGTGGCGACCAGAGTGAAGGTGACTTGGC
2159829 ATCACAGGGC
Statistics
Matches: 97, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
113 55 0.57
114 42 0.43
ACGTcount: A:0.20, C:0.19, G:0.39, T:0.22
Consensus pattern (113 bp):
GTGGCGACCAGAGTGAGGGTGACTTAACATCACAGGGCGTTAATGACTTGGCATCATGCGGGGTC
AATTACGTGCCATGGTGGCGACCAGAGTGAAGGTGACTTGGCGCTACA
Found at i:2159914 original size:15 final size:15
Alignment explanation
Indices: 2159894--2159923 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2159884 GCACTTGCAC
2159894 CCTTCTGGCGAGTAT
1 CCTTCTGGCGAGTAT
*
2159909 CCTTCTGGCGTGTAT
1 CCTTCTGGCGAGTAT
2159924 AGAGAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.27, G:0.27, T:0.37
Consensus pattern (15 bp):
CCTTCTGGCGAGTAT
Found at i:2167548 original size:2 final size:2
Alignment explanation
Indices: 2167541--2167569 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2167531 CCTTAGAGTT
2167541 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2167570 ATTTGAACTT
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2169707 original size:24 final size:25
Alignment explanation
Indices: 2169675--2169724 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
2169665 CTATCAGTTT
2169675 TACAACCTTCATT-GGTTAAGTAAA
1 TACAACCTTCATTAGGTTAAGTAAA
*
2169699 TACAACCTTCATTAGTTTAAGTAAA
1 TACAACCTTCATTAGGTTAAGTAAA
2169724 T
1 T
2169725 TCACTTGTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (25 bp):
TACAACCTTCATTAGGTTAAGTAAA
Found at i:2173675 original size:2 final size:2
Alignment explanation
Indices: 2173668--2173698 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2173658 CATCCATGTT
2173668 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2173699 AACCTGGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2179356 original size:21 final size:20
Alignment explanation
Indices: 2179328--2179369 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2179318 TTGAATTTAA
2179328 TAAAAATAATATAAAATTTT
1 TAAAAATAATATAAAATTTT
* *
2179348 TAAACAATAATTTAACATTTT
1 TAAA-AATAATATAAAATTTT
2179369 T
1 T
2179370 TAATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAAAATAATATAAAATTTT
Found at i:2179945 original size:40 final size:40
Alignment explanation
Indices: 2179885--2180018 Score: 189
Period size: 40 Copynumber: 3.4 Consensus size: 40
2179875 TGTGTGGGGG
* * *
2179885 AAAACTGTT-ATTTTCATTAAAACTTTCAATTTTGTGAAGC
1 AAAACTATTAATTTTC-TTAAAAATTTCAATTTTATGAAGC
* *
2179925 AAAACTATTAATTTTCTTAAAATTTTCAATTTTATGAACC
1 AAAACTATTAATTTTCTTAAAAATTTCAATTTTATGAAGC
* *
2179965 AAAACTATTAATTTCCTTAAAAATTTTAATTTTATGAAGC
1 AAAACTATTAATTTTCTTAAAAATTTCAATTTTATGAAGC
2180005 AAAACTATTAATTT
1 AAAACTATTAATTT
2180019 CCTTGTGTAT
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
40 79 0.93
41 6 0.07
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.43
Consensus pattern (40 bp):
AAAACTATTAATTTTCTTAAAAATTTCAATTTTATGAAGC
Found at i:2179977 original size:22 final size:21
Alignment explanation
Indices: 2179903--2180018 Score: 59
Period size: 22 Copynumber: 5.7 Consensus size: 21
2179893 TATTTTCATT
*
2179903 AAAACT-TTCAATTTTGTGAAGC
1 AAAACTATT-AATTTTATGAA-C
* *
2179925 AAAACTATTAATTTTCT---T
1 AAAACTATTAATTTTATGAAC
*
2179943 AAAA-TTTTCAATTTTATGAACC
1 AAAACTATT-AATTTTATGAA-C
** *
2179965 AAAACTATTAATTTCCT-TA-
1 AAAACTATTAATTTTATGAAC
*
2179984 AAAA-TTTTAATTTTATGAAGC
1 AAAACTATTAATTTTATGAA-C
2180005 AAAACTATTAATTT
1 AAAACTATTAATTT
2180019 CCTTGTGTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 22
0.66 0.13 0.21
Matches are distributed among these distances:
17 3 0.04
18 20 0.29
19 5 0.07
21 5 0.07
22 31 0.45
23 5 0.07
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.42
Consensus pattern (21 bp):
AAAACTATTAATTTTATGAAC
Found at i:2180576 original size:16 final size:16
Alignment explanation
Indices: 2180555--2180601 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
2180545 TTAAAAAAAT
2180555 TAAATATTTAATTTAA
1 TAAATATTTAATTTAA
* *
2180571 TAAATAATAAATTTAA
1 TAAATATTTAATTTAA
2180587 T--ATATTTATATTTAA
1 TAAATATTTA-ATTTAA
2180602 AATTTATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 5 0.19
15 6 0.23
16 15 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATATTTAATTTAA
Found at i:2181114 original size:25 final size:26
Alignment explanation
Indices: 2181086--2181143 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
2181076 TTATTTAATA
2181086 TATTAAATTT-ATA-AAAAATATTAAC
1 TATTAAATTTAATATAAAAATATT-AC
* *
2181111 TATTATATTTAATATAATAATATTAC
1 TATTAAATTTAATATAAAAATATTAC
2181137 TA-TAAAT
1 TATTAAAT
2181144 AATATATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 13 0.46
26 7 0.25
27 8 0.29
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (26 bp):
TATTAAATTTAATATAAAAATATTAC
Found at i:2181627 original size:23 final size:22
Alignment explanation
Indices: 2181601--2181643 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
2181591 ATCGTTTTAT
2181601 TATTAGACA-TAATATAATAAATA
1 TATTAGA-ATTAATAT-ATAAATA
*
2181624 TATTTGAATTAATATATAAA
1 TATTAGAATTAATATATAAA
2181644 AAAATAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (22 bp):
TATTAGAATTAATATATAAATA
Found at i:2184932 original size:2 final size:2
Alignment explanation
Indices: 2184925--2184961 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2184915 CTACACTCCC
2184925 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2184962 CACGTCTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2185194 original size:2 final size:2
Alignment explanation
Indices: 2185181--2185211 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2185171 TAGTGTTGGG
*
2185181 TA TA TG 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 T
2185212 GTGGAAGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2186790 original size:13 final size:13
Alignment explanation
Indices: 2186756--2186798 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2186746 AATTTAATTT
* *
2186756 AATTAATTTATAT
1 AATTAATTTTTAA
2186769 AATT-ATTTTTAA
1 AATTAATTTTTAA
2186781 AATTAATTTTTAA
1 AATTAATTTTTAA
2186794 TAATT
1 -AATT
2186799 TTTTATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 10 0.38
13 12 0.46
14 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTAATTTTTAA
Found at i:2188040 original size:11 final size:12
Alignment explanation
Indices: 2188019--2188051 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2188009 AAATTTGACA
2188019 ATTTATATATTT
1 ATTTATATATTT
2188031 ATTT-TATATTT
1 ATTTATATATTT
*
2188042 ATATATATAT
1 ATTTATATAT
2188052 ATATATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTATATATTT
Found at i:2195649 original size:15 final size:16
Alignment explanation
Indices: 2195626--2195666 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2195616 TCATACATTA
*
2195626 TAATCTTTATAT-AAT
1 TAATATTTATATAAAT
2195641 TAATATTTA-ATAAAT
1 TAATATTTATATAAAT
2195656 TAACTATTTAT
1 TAA-TATTTAT
2195667 TAGATCAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.09
15 14 0.64
16 6 0.27
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATATTTATATAAAT
Found at i:2195740 original size:14 final size:14
Alignment explanation
Indices: 2195721--2195764 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
2195711 ATTAATTTTA
2195721 TATTTATATAATAT
1 TATTTATATAATAT
*
2195735 TATTTATA-ATTAT
1 TATTTATATAATAT
2195748 TATTT-T-TAATA-
1 TATTTATATAATAT
2195759 TATTTA
1 TATTTA
2195765 ATTATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 5 0.19
12 4 0.15
13 9 0.35
14 8 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTTATATAATAT
Found at i:2195849 original size:41 final size:43
Alignment explanation
Indices: 2195785--2195871 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 43
2195775 TTTTATTAAA
* * ** *
2195785 TAAATAATTAAATATTATTAA-TTTATTAAAGTTATATATAATT
1 TAAATAAATAAATATTATAAATTTTA-TAAAAATATATAAAATT
2195828 TAAATAAATAAA-A-TATAAATTTTATAAAAATATATAAAATT
1 TAAATAAATAAATATTATAAATTTTATAAAAATATATAAAATT
2195869 TAA
1 TAA
2195872 CAACCACTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
41 22 0.58
42 5 0.13
43 11 0.29
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (43 bp):
TAAATAAATAAATATTATAAATTTTATAAAAATATATAAAATT
Found at i:2198967 original size:2 final size:2
Alignment explanation
Indices: 2198960--2198997 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2198950 TCCTTCCTTT
2198960 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2198998 AAACTTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2199141 original size:20 final size:20
Alignment explanation
Indices: 2199118--2199157 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2199108 ATTAAAATAA
*
2199118 AAATTAA-AATATTTAAATTT
1 AAATTAATAAT-TATAAATTT
2199138 AAATTAATAATTATAAATTT
1 AAATTAATAATTATAAATTT
2199158 TTTTAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTAATAATTATAAATTT
Found at i:2204180 original size:30 final size:30
Alignment explanation
Indices: 2204123--2204180 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
2204113 AAATCAACAT
* *
2204123 AAAAACTTATTTGGTTACAAATCAAAGTTA
1 AAAAACTTATTTGGGTACAAATAAAAGTTA
*
2204153 AAAAAGCTTATTTGGGTATAAA-AAAAGT
1 AAAAA-CTTATTTGGGTACAAATAAAAGT
2204181 GCAGCGACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.42
31 14 0.58
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (30 bp):
AAAAACTTATTTGGGTACAAATAAAAGTTA
Found at i:2204302 original size:3 final size:3
Alignment explanation
Indices: 2204294--2204336 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
2204284 TCCTAGAAAT
2204294 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -AA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
2204337 GTAAAGAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2205085 original size:16 final size:18
Alignment explanation
Indices: 2205054--2205086 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2205044 TAATACTCTT
2205054 ATTATATTTAATATTATA
1 ATTATATTTAATATTATA
2205072 ATTAT-TTTAA-ATTAT
1 ATTATATTTAATATTAT
2205087 TATAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTATATTTAATATTATA
Found at i:2205168 original size:18 final size:18
Alignment explanation
Indices: 2205122--2205157 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2205112 ATTAATAATT
2205122 TATTTTATATAAATATTAA
1 TATTTT-TATAAATATTAA
2205141 TATTTTTATAAAT-TTAA
1 TATTTTTATAAATATTAA
2205158 ATTATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTTTATAAATATTAA
Found at i:2210103 original size:17 final size:18
Alignment explanation
Indices: 2210069--2210103 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2210059 TAATTTGATA
*
2210069 GTAATTAAAGATAATTTT
1 GTAATTAAAGAAAATTTT
2210087 GTAATTAAA-AAAATTTT
1 GTAATTAAAGAAAATTTT
2210104 AAGTAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (18 bp):
GTAATTAAAGAAAATTTT
Found at i:2222497 original size:22 final size:23
Alignment explanation
Indices: 2222471--2222521 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
2222461 CATACATATT
**
2222471 TAAAATTTTATTTATAAAATTAA
1 TAAAATTTTATCAATAAAATTAA
*
2222494 -AAAATTTTATCAATAAATTTAA
1 TAAAATTTTATCAATAAAATTAA
2222516 TAAAAT
1 TAAAAT
2222522 AAAATATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAAATTTTATCAATAAAATTAA
Found at i:2223438 original size:22 final size:20
Alignment explanation
Indices: 2223413--2223455 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
2223403 AAAAAGGTAA
2223413 ATTAACAAACAAATATAATATT
1 ATTAACAAA-AAATATAA-ATT
**
2223435 ATTATTAAAAAATATAAATT
1 ATTAACAAAAAATATAAATT
2223455 A
1 A
2223456 CGTGTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTAACAAAAAATATAAATT
Found at i:2224032 original size:6 final size:6
Alignment explanation
Indices: 2224021--2224045 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2224011 TTGCTGTCCC
2224021 TCCAAA TCCAAA TCCAAA TCCAAA T
1 TCCAAA TCCAAA TCCAAA TCCAAA T
2224046 GTTTCACACT
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:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (6 bp):
TCCAAA
Found at i:2226109 original size:21 final size:21
Alignment explanation
Indices: 2226085--2226148 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
2226075 ATATTTGATA
2226085 AATATTTAAATATAAATATAT
1 AATATTTAAATATAAATATAT
*
2226106 AATATTTTTAAATATATTAA-AAAT
1 AATA--TTTAAATATA--AATATAT
2226130 AAT-TTTAAA-ATAAATATAT
1 AATATTTAAATATAAATATAT
2226149 TAGTATCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
18 2 0.06
19 3 0.08
20 3 0.08
21 10 0.28
23 10 0.28
24 6 0.17
25 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATATTTAAATATAAATATAT
Found at i:2226112 original size:32 final size:31
Alignment explanation
Indices: 2226061--2226131 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
2226051 GGTACTCACA
* *
2226061 AAAAAAAAATATTTATATTTGATAAATAT-TT
1 AAAAATAAATATTAATATTT-ATAAATATATT
* *
2226092 AAATATAAATATATAATATTTTTAAATATATT
1 AAAAATAAATAT-TAATATTTATAAATATATT
2226124 AAAAATAA
1 AAAAATAA
2226132 TTTTAAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
31 17 0.52
32 16 0.48
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (31 bp):
AAAAATAAATATTAATATTTATAAATATATT
Found at i:2230463 original size:2 final size:2
Alignment explanation
Indices: 2230456--2230484 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2230446 TGAAGTTGCT
2230456 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
2230485 TATTTAAACA
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:2231625 original size:2 final size:2
Alignment explanation
Indices: 2231618--2231652 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2231608 TGATTACTGC
* *
2231618 AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2231653 AAGTACCCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2234058 original size:24 final size:23
Alignment explanation
Indices: 2234009--2234058 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
2233999 TATCTTTAAA
*
2234009 ATTTTAATAAATTTATATTCTTT
1 ATTTTAATAAATTTATATTCTAT
2234032 ATTTTAAATAAATTTATGATT-TAT
1 ATTTT-AATAAATTTAT-ATTCTAT
2234056 ATT
1 ATT
2234059 AACAGTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 5 0.21
24 16 0.67
25 3 0.12
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
ATTTTAATAAATTTATATTCTAT
Found at i:2234316 original size:2 final size:2
Alignment explanation
Indices: 2234309--2234344 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2234299 AACAATAAAG
2234309 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2234345 GAAAAGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2234703 original size:17 final size:17
Alignment explanation
Indices: 2234681--2234729 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 17
2234671 ATTATCTTAA
2234681 TATTTATTAAAATAATT
1 TATTTATTAAAATAATT
2234698 TATTTA--AAAA-AATT
1 TATTTATTAAAATAATT
*
2234712 TA-GTATTAAAAT-ATT
1 TATTTATTAAAATAATT
2234727 TAT
1 TAT
2234730 AATTACGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
13 2 0.07
14 6 0.22
15 13 0.48
17 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TATTTATTAAAATAATT
Found at i:2234706 original size:14 final size:14
Alignment explanation
Indices: 2234682--2234729 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
2234672 TTATCTTAAT
2234682 ATTTA-TTAAAATA
1 ATTTATTTAAAATA
*
2234695 ATTTATTTAAAAAA
1 ATTTATTTAAAATA
2234709 ATTTAGTATTAAAAT-
1 ATTTA-T-TTAAAATA
2234724 ATTTAT
1 ATTTAT
2234730 AATTACGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 5 0.17
14 13 0.43
15 6 0.20
16 6 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATTTATTTAAAATA
Found at i:2234840 original size:17 final size:17
Alignment explanation
Indices: 2234818--2234859 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
2234808 ATTAAATAAT
* *
2234818 TTAATTTAAATTTTATA
1 TTAATTTAAAATATATA
2234835 TTAATTTAAAATATATA
1 TTAATTTAAAATATATA
2234852 TTAATTTA
1 TTAATTTA
2234860 TTTATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAATTTAAAATATATA
Found at i:2238904 original size:2 final size:2
Alignment explanation
Indices: 2238897--2238922 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2238887 GCCTATGTGA
2238897 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
2238923 TTGTTAATTC
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:2242176 original size:17 final size:19
Alignment explanation
Indices: 2242141--2242181 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
2242131 TTTTATCGTA
2242141 TAAAAAATATATAAATA-T
1 TAAAAAATATATAAATATT
2242159 TAAAAAA-AT-TAAATTATT
1 TAAAAAATATATAAA-TATT
2242177 TAAAA
1 TAAAA
2242182 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.19
17 4 0.19
18 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAAAAATATATAAATATT
Found at i:2242204 original size:31 final size:30
Alignment explanation
Indices: 2242162--2242229 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
2242152 TAAATATTAA
*
2242162 AAAAATTAAA-TTATTTAAAATTTAAAATTT
1 AAAAATAAAATTTA-TTAAAATTTAAAATTT
* *
2242192 AATAAATAAAATTTATTAAATTTTAAATTTT
1 AA-AAATAAAATTTATTAAAATTTAAAATTT
2242223 AAAAATA
1 AAAAATA
2242230 TATTTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 7 0.21
31 23 0.70
32 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
AAAAATAAAATTTATTAAAATTTAAAATTT
Found at i:2242806 original size:20 final size:21
Alignment explanation
Indices: 2242783--2242822 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2242773 TTATTTTATT
2242783 TAAAAATTA-ATTTTAAATTA
1 TAAAAATTATATTTTAAATTA
* *
2242803 TAAAACTTATTTTTTAAATT
1 TAAAAATTATATTTTAAATT
2242823 TTTTATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAAAATTATATTTTAAATTA
Found at i:2243202 original size:50 final size:51
Alignment explanation
Indices: 2243115--2243216 Score: 188
Period size: 50 Copynumber: 2.0 Consensus size: 51
2243105 CCCGTTTTAA
2243115 AAATATATTATTTATATATATATATATATTTGAATTTCACTAGAAGAAAAAT
1 AAATATATTA-TTATATATATATATATATTTGAATTTCACTAGAAGAAAAAT
2243167 AAATATATTA-TATATATATATATATATTTGAATTTCACTAGAAGAAAAAT
1 AAATATATTATTATATATATATATATATTTGAATTTCACTAGAAGAAAAAT
2243217 TGCTTGCGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 40 0.80
52 10 0.20
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (51 bp):
AAATATATTATTATATATATATATATATTTGAATTTCACTAGAAGAAAAAT
Found at i:2243652 original size:19 final size:20
Alignment explanation
Indices: 2243608--2243645 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2243598 TTAAGTTAAT
*
2243608 AAATTTATATATTTATTATA
1 AAATTTATATATTTAATATA
2243628 AAATTTA-ATATTTAATAT
1 AAATTTATATATTTAATAT
2243646 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTTATATATTTAATATA
Found at i:2243691 original size:2 final size:2
Alignment explanation
Indices: 2243679--2243714 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2243669 ATGATTTTTG
*
2243679 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2243715 AAAACCTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2244948 original size:29 final size:29
Alignment explanation
Indices: 2244913--2244999 Score: 115
Period size: 29 Copynumber: 3.0 Consensus size: 29
2244903 TTAGATTTGA
2244913 TTTATATTATTATTTAATAAATAAAATAT
1 TTTATATTATTATTTAATAAATAAAATAT
2244942 TTTATATTATTATTTAATAAATAAAAAATAT
1 TTTATATTATTATTTAATAAAT--AAAATAT
** *
2244973 TTTAT-TTAAAATTTAATTAA-AAAATAT
1 TTTATATTATTATTTAATAAATAAAATAT
2245000 AAATATTTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
27 7 0.13
29 22 0.42
30 12 0.23
31 12 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TTTATATTATTATTTAATAAATAAAATAT
Found at i:2245009 original size:33 final size:33
Alignment explanation
Indices: 2244926--2245009 Score: 102
Period size: 31 Copynumber: 2.6 Consensus size: 33
2244916 ATATTATTAT
* **
2244926 TTAATAAATAAAATATTTTATATTATTATTTAA
1 TTAAAAAATAAAATATTTTATATTAAAATTTAA
*
2244959 -TAAATAA-AAAATATTTTAT-TTAAAATTTAA
1 TTAAAAAATAAAATATTTTATATTAAAATTTAA
2244989 TTAAAAAATATAAATATTTTA
1 TTAAAAAATA-AAATATTTTA
2245010 ATATATTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
30 9 0.21
31 18 0.42
32 6 0.14
33 10 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
TTAAAAAATAAAATATTTTATATTAAAATTTAA
Found at i:2245026 original size:29 final size:29
Alignment explanation
Indices: 2244920--2245026 Score: 85
Period size: 29 Copynumber: 3.5 Consensus size: 29
2244910 TGATTTATAT
*
2244920 TATTATTTAATAAATAAAATATTTT-ATA
1 TATTATTAAATAAATAAAATATTTTAATA
* *
2244948 TTATTATTTAATAAATAAAAAATATTTTATTTAA
1 -TATTATTAAATAAAT--AAAATATTTTA-AT-A
*
2244982 AATTTAATTAAA-AAATATAAATATTTTAATA
1 TA-TT-ATTAAATAAATA-AAATATTTTAATA
2245013 TATT-TTAAATAAAT
1 TATTATTAAATAAAT
2245027 TTTTTGAATA
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
28 5 0.08
29 19 0.30
30 2 0.03
31 12 0.19
32 2 0.03
33 12 0.19
34 7 0.11
35 5 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TATTATTAAATAAATAAAATATTTTAATA
Found at i:2245344 original size:3 final size:3
Alignment explanation
Indices: 2245338--2245383 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2245328 TTCAAACATA
2245338 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2245384 CAGTTGAAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2256612 original size:11 final size:11
Alignment explanation
Indices: 2256595--2256641 Score: 67
Period size: 11 Copynumber: 4.1 Consensus size: 11
2256585 TATTAATTTA
2256595 TATATTTATAT
1 TATATTTATAT
*
2256606 CATATTTATAT
1 TATATTTATAT
2256617 TATATTTTTATAT
1 TATA--TTTATAT
2256630 TATATTTATAT
1 TATATTTATAT
2256641 T
1 T
2256642 TAGAGGGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 21 0.66
13 11 0.34
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:2256619 original size:24 final size:23
Alignment explanation
Indices: 2256575--2256641 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 23
2256565 ATTAAATGGG
2256575 TATATATATTTATTAATTTATATATT
1 TATATATATTTA-T-A-TTATATATT
*
2256601 TATATCATATTTATATTATATTTT
1 TATAT-ATATTTATATTATATATT
2256625 TATATTATATTTATATT
1 TATA-TATATTTATATT
2256642 TAGAGGGTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
24 23 0.61
25 2 0.05
26 6 0.16
27 7 0.18
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (23 bp):
TATATATATTTATATTATATATT
Found at i:2256626 original size:13 final size:13
Alignment explanation
Indices: 2256575--2256636 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
2256565 ATTAAATGGG
2256575 TATA-TATATTTAT
1 TATATTATATTT-T
*
2256588 TA-ATTTATATATT
1 TATA-TTATATTTT
*
2256601 TATATCATA--TT
1 TATATTATATTTT
2256612 TATATTATATTTT
1 TATATTATATTTT
2256625 TATATTATATTT
1 TATATTATATTT
2256637 ATATTTAGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
11 10 0.24
12 1 0.02
13 23 0.56
14 7 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (13 bp):
TATATTATATTTT
Found at i:2257015 original size:18 final size:16
Alignment explanation
Indices: 2256994--2257027 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
2256984 TATTTTTATA
2256994 ATTTTATATAAGATTAAT
1 ATTTTA-ATAA-ATTAAT
2257012 ATTTTAATAAATTAAT
1 ATTTTAATAAATTAAT
2257028 TGTTAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTTAATAAATTAAT
Found at i:2262259 original size:2 final size:2
Alignment explanation
Indices: 2262254--2262287 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2262244 TGTGTGTGTG
* *
2262254 TA TA TA CA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2262288 GTTGTATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2270421 original size:3 final size:3
Alignment explanation
Indices: 2270413--2270444 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2270403 AAGCTGAGAT
2270413 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2270445 TTAAAAACTT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2270825 original size:3 final size:3
Alignment explanation
Indices: 2270817--2270851 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2270807 AATAAATTTA
2270817 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2270852 AAAATAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2276138 original size:2 final size:2
Alignment explanation
Indices: 2276131--2276178 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2276121 GATCATCTAG
2276131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2276173 AT AT AT
1 AT AT AT
2276179 TCCTTTTCTA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2277182 original size:13 final size:13
Alignment explanation
Indices: 2277151--2277188 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2277141 AATTAAAGTG
*
2277151 AGAAACAAAG-AA
1 AGAAAAAAAGAAA
*
2277163 GGAAAAAAAGAAA
1 AGAAAAAAAGAAA
2277176 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
2277189 GGCTTCGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:2277189 original size:12 final size:12
Alignment explanation
Indices: 2277151--2277189 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2277141 AATTAAAGTG
*
2277151 AGAAACAAAGAA
1 AGAAAAAAAGAA
*
2277163 GGAAAAAAAGAAA
1 AGAAAAAAAG-AA
2277176 AGAAAAAAAGAA
1 AGAAAAAAAGAA
2277188 AG
1 AG
2277190 GCTTCGAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.77, C:0.03, G:0.21, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAGAA
Found at i:2279642 original size:3 final size:3
Alignment explanation
Indices: 2279634--2279675 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2279624 AATGGATTTT
2279634 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2279676 GTTTTTAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2285528 original size:19 final size:19
Alignment explanation
Indices: 2285501--2285562 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
2285491 TTAAAAAATA
2285501 AATATAAATAATTAAATTTT
1 AATA-AAATAATTAAATTTT
*
2285521 AATAAAATTA-TATAATTTT
1 AATAAAATAATTA-AATTTT
* *
2285540 AATATATTAATATAAATATTT
1 AATAAAATAAT-TAAAT-TTT
2285561 AA
1 AA
2285563 AAAGTAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 2 0.06
19 18 0.53
20 7 0.21
21 7 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATAAAATAATTAAATTTT
Found at i:2285575 original size:13 final size:15
Alignment explanation
Indices: 2285554--2285585 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2285544 TATTAATATA
2285554 AATATTTAAAAAG-T
1 AATATTTAAAAAGTT
2285568 AATA-TTAAAAAGTT
1 AATATTTAAAAAGTT
2285582 AATA
1 AATA
2285586 AACAACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (15 bp):
AATATTTAAAAAGTT
Found at i:2293760 original size:1 final size:1
Alignment explanation
Indices: 2293754--2293818 Score: 76
Period size: 1 Copynumber: 65.0 Consensus size: 1
2293744 TGGCAATTGG
* * * ** *
2293754 AAAAAAAAAAAAAAAACAAAACAAAAAAAAAAGAAAAAAACCAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2293819 GTGAAGATTT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.91, C:0.08, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:2293790 original size:33 final size:33
Alignment explanation
Indices: 2293753--2293819 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
2293743 ATGGCAATTG
2293753 GAAAAAAA-AAAAAAAAACAAAACAAAAAAAAAA
1 GAAAAAAACAAAAAAAAA-AAAACAAAAAAAAAA
*
2293786 GAAAAAAACCAAAAAAAAAAAACAAAAAAAAAA
1 GAAAAAAACAAAAAAAAAAAAACAAAAAAAAAA
2293819 G
1 G
2293820 TGAAGATTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.88, C:0.07, G:0.04, T:0.00
Consensus pattern (33 bp):
GAAAAAAACAAAAAAAAAAAAACAAAAAAAAAA
Found at i:2296915 original size:21 final size:21
Alignment explanation
Indices: 2296891--2296932 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2296881 TGACTCATTC
*
2296891 AATTTATTTA-AATTTAAATTT
1 AATTTAATTATAA-TTAAATTT
2296912 AATTTAATTATAATTAAATTT
1 AATTTAATTATAATTAAATTT
2296933 TTAAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTTAATTATAATTAAATTT
Found at i:2299665 original size:18 final size:16
Alignment explanation
Indices: 2299637--2299684 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 16
2299627 AAAAATATTT
2299637 TTATATA-AATTTTTA
1 TTATATATAATTTTTA
* *
2299652 TTTTATTAATAATTTATA
1 TTATA-T-ATAATTTTTA
2299670 TTATATATAATTTTT
1 TTATATATAATTTTT
2299685 GTTAGTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
15 4 0.15
16 9 0.35
17 2 0.08
18 11 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATATATAATTTTTA
Found at i:2308553 original size:2 final size:2
Alignment explanation
Indices: 2308546--2308571 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2308536 GAAAGATTAA
2308546 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
2308572 CACAAATTAA
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:2311674 original size:2 final size:2
Alignment explanation
Indices: 2311669--2311695 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2311659 ATGTACACAC
2311669 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 A
2311696 GAGGTTTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2316566 original size:2 final size:2
Alignment explanation
Indices: 2316559--2316592 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2316549 TAACTTTGAC
2316559 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
2316593 TGAGCACTGA
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:2323927 original size:25 final size:25
Alignment explanation
Indices: 2323889--2323939 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2323879 TATTTATTTT
2323889 TAAAATATTTTTAATAAAATAAAAA
1 TAAAATATTTTTAATAAAATAAAAA
* *
2323914 TAAAA-ATTTATTAATAATATATAAA
1 TAAAATATTT-TTAATAAAATAAAAA
2323939 T
1 T
2323940 TATATACTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
TAAAATATTTTTAATAAAATAAAAA
Found at i:2324017 original size:34 final size:37
Alignment explanation
Indices: 2323973--2324045 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 37
2323963 TAAATTTTTT
2323973 ATTTTATATTTAA-ATAAA-TTA-TTAA-TATAAATAA
1 ATTTTATATTTAACA-AAATTTATTTAATTATAAATAA
*
2324007 ATTTTTTATTTAACAAAATTTTATTTAATTATAAATAA
1 ATTTTATATTTAACAAAA-TTTATTTAATTATAAATAA
2324045 A
1 A
2324046 CATAATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
34 15 0.45
35 1 0.03
36 3 0.09
37 4 0.12
38 10 0.30
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTTATATTTAACAAAATTTATTTAATTATAAATAA
Found at i:2335423 original size:29 final size:29
Alignment explanation
Indices: 2335380--2335458 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
2335370 GTCACGTAAA
* *
2335380 TAAAATAGTAATATTTTGATAAATAATTT
1 TAAAATAATATTATTTTGATAAATAATTT
* * *
2335409 TAAAATAATATTATTTTAATAATTTATTT
1 TAAAATAATATTATTTTGATAAATAATTT
*
2335438 TAAAATTAAAATTATTTTGAT
1 TAAAA-TAATATTATTTTGAT
2335459 TAATCTACCT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 29 0.69
30 13 0.31
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TAAAATAATATTATTTTGATAAATAATTT
Done.