Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009609.1 Kokia drynarioides strain JFW-HI SEQ_124325, whole genome shotgun sequence
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: 132609
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1197 original size:15 final size:15
Alignment explanation
Indices: 1172--1246 Score: 87
Period size: 15 Copynumber: 5.0 Consensus size: 15
1162 TTGGGCTTTC
*
1172 GGGCAATTTGTAATT
1 GGGCCATTTGTAATT
* *
1187 GGGTCATTTGTATTT
1 GGGCCATTTGTAATT
* * *
1202 GGGTCATCTGTAACT
1 GGGCCATTTGTAATT
*
1217 GGGCCATTTGTTATT
1 GGGCCATTTGTAATT
1232 GGGCCATTTGTAATT
1 GGGCCATTTGTAATT
1247 TGGACTTTTG
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 49 1.00
ACGTcount: A:0.19, C:0.12, G:0.27, T:0.43
Consensus pattern (15 bp):
GGGCCATTTGTAATT
Found at i:1308 original size:17 final size:17
Alignment explanation
Indices: 1286--1331 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
1276 TGGACTTTTC
*
1286 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
1303 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
1320 TAAACTTAAATT
1 TAAATTTAAATT
1332 CAATTTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:2467 original size:45 final size:45
Alignment explanation
Indices: 2384--2713 Score: 240
Period size: 45 Copynumber: 7.3 Consensus size: 45
2374 TGGAGGGTGT
* * * * * *
2384 ATAAACTAGTGGTTTAGGCTCAGGTTTCTCTTTCTTTGGTGGTTC
1 ATAAACTGGTGGCTTGGGTTCAGGCTTCTCTTTTTTTGGTGGTTC
* * * *
2429 ATACACAGGTGGCTTGGATTCATGCTTCTCTTTTTTTGGTGGTGT-
1 ATAAACTGGTGGCTTGGGTTCAGGCTTCTCTTTTTTTGGTGGT-TC
* * * *
2474 ATAAACTGGTGG-TTAAGGCTCAGGCTTCTCCTTTTTTGGTGTTTC
1 ATAAACTGGTGGCTT-GGGTTCAGGCTTCTCTTTTTTTGGTGGTTC
* * * * *
2519 ATACACTAGTGGCTAGGGTTCAGGATTCTTTTTTTTTGGTGGTGT-
1 ATAAACTGGTGGCTTGGGTTCAGGCTTCTCTTTTTTTGGTGGT-TC
* * *
2564 ATAAACTGATGGCTTAGGTTCAGGCTTCTC--TCTTTGGTGGTTC
1 ATAAACTGGTGGCTTGGGTTCAGGCTTCTCTTTTTTTGGTGGTTC
* * * * * * *
2607 ATACACTGGGGGCTTGGGCTCAAGCTTTTCTTTCTAATTGGAGGTAT-
1 ATAAACTGGTGGCTTGGGTTCAGGCTTCTCTTT-T-TTTGGTGGT-TC
** * * *
2654 ATAAACTGGTGATTTGGGTTCAGACTTCTCATTCTTTGGTGGTTC
1 ATAAACTGGTGGCTTGGGTTCAGGCTTCTCTTTTTTTGGTGGTTC
* *
2699 ATAGACAGGTGGCTT
1 ATAAACTGGTGGCTT
2714 ATGTTCATAT
Statistics
Matches: 212, Mismatches: 61, Indels: 24
0.71 0.21 0.08
Matches are distributed among these distances:
42 1 0.00
43 33 0.16
44 4 0.02
45 139 0.66
46 3 0.01
47 31 0.15
48 1 0.00
ACGTcount: A:0.17, C:0.16, G:0.26, T:0.41
Consensus pattern (45 bp):
ATAAACTGGTGGCTTGGGTTCAGGCTTCTCTTTTTTTGGTGGTTC
Found at i:2493 original size:90 final size:90
Alignment explanation
Indices: 2379--2713 Score: 372
Period size: 90 Copynumber: 3.7 Consensus size: 90
2369 TTCTTTGGAG
* *
2379 GGTGTATAAACTAGTGGTTTAGGCTCAGGTTTCTCTTTCTTTGGTGGTTCATACACAGGTGGCTT
1 GGTGTATAAACTGGTGGTTTAGGCTCAGGCTTCTCTTTCTTTGGTGGTTCATACACAGGTGGCTT
* *
2444 GGATTCATGCTTCTCTTTTTTTGGT
66 GGGTTCAAGCTTCTCTTTTTTTGGT
* *
2469 GGTGTATAAACTGGTGGTTAAGGCTCAGGCTTCTCCTTT-TTTGGTGTTTCATACACTA-GTGGC
1 GGTGTATAAACTGGTGGTTTAGGCTCAGGCTTCT-CTTTCTTTGGTGGTTCATACAC-AGGTGGC
* * * *
2532 TAGGGTTCAGGATTCTTTTTTTTTGGT
64 TTGGGTTCAAGCTTCTCTTTTTTTGGT
* * * * *
2559 GGTGTATAAACTGATGGCTTAGGTTCAGGCTTCTC--TCTTTGGTGGTTCATACACTGGGGGCTT
1 GGTGTATAAACTGGTGGTTTAGGCTCAGGCTTCTCTTTCTTTGGTGGTTCATACACAGGTGGCTT
* * * *
2622 GGGCTCAAGCTTTTCTTTCTAATTGGA
66 GGGTTCAAGCTTCTCTTT-T-TTTGGT
* * * * * * *
2649 GGTATATAAACTGGTGATTTGGGTTCAGACTTCTCATTCTTTGGTGGTTCATAGACAGGTGGCTT
1 GGTGTATAAACTGGTGGTTTAGGCTCAGGCTTCTCTTTCTTTGGTGGTTCATACACAGGTGGCTT
2714 ATGTTCATAT
Statistics
Matches: 204, Mismatches: 33, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
87 1 0.00
88 34 0.17
89 2 0.01
90 137 0.67
91 5 0.02
92 25 0.12
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.41
Consensus pattern (90 bp):
GGTGTATAAACTGGTGGTTTAGGCTCAGGCTTCTCTTTCTTTGGTGGTTCATACACAGGTGGCTT
GGGTTCAAGCTTCTCTTTTTTTGGT
Found at i:6370 original size:29 final size:28
Alignment explanation
Indices: 6338--6421 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 28
6328 TAGACACCTG
*
6338 GGGATAAAATGGTAATTTTTAGGAAAATC
1 GGGATAAAATGGTAATTTTT-GGAAAATA
**
6367 GGGATTAAAAATGG-AATTTTTGGACATTTA
1 GGGA-T-AAAATGGTAATTTTTGGA-AAATA
* *
6397 GGGGTAAAAGGGTAATTTTTGGAAA
1 GGGATAAAATGGTAATTTTTGGAAA
6422 TTTTAAGGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
28 7 0.16
29 18 0.40
30 13 0.29
31 7 0.16
ACGTcount: A:0.38, C:0.02, G:0.27, T:0.32
Consensus pattern (28 bp):
GGGATAAAATGGTAATTTTTGGAAAATA
Found at i:6446 original size:59 final size:58
Alignment explanation
Indices: 6373--6564 Score: 226
Period size: 59 Copynumber: 3.3 Consensus size: 58
6363 AATCGGGATT
** * *
6373 AAAAATGGAATTTTTGGACATTT-AGGGGTAAAAGGGTAATTTTTGGAAATTTTAAGGTC
1 AAAAATGGAATTTTTGGA-ATTTGA-GGGTAAAAATGTGATTTTTGGAAGTTTTAAGGTC
* *
6432 -AAAATGGAATTTTTTGGAAGTTTGTGGGTAAAAATGTGATTTTTGGAAGTTTTAGGGTC
1 AAAAATGGAA-TTTTTGGAA-TTTGAGGGTAAAAATGTGATTTTTGGAAGTTTTAAGGTC
* * * **
6491 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTGCTTTTTGGAGGTTTCGAGGTC
1 AAAAATGGAATTTTTGGAA-TTTGAGGGTAAAAATGTGATTTTTGGAAGTTTTAAGGTC
6550 AAAAATGGAATTTTT
1 AAAAATGGAATTTTT
6565 TGAAGTTTTA
Statistics
Matches: 116, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
58 10 0.09
59 97 0.84
60 9 0.08
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAATTTGAGGGTAAAAATGTGATTTTTGGAAGTTTTAAGGTC
Found at i:6584 original size:59 final size:58
Alignment explanation
Indices: 6373--6621 Score: 215
Period size: 59 Copynumber: 4.2 Consensus size: 58
6363 AATCGGGATT
* ** * * *
6373 AAAAATGGAATTTTTGGACA--TTTAGGGGTAAAAGGGTAATTTTTGGAAATTTTAAGGTC
1 AAAAATGGAATTTTTTGA-AGTTTTA-GGGTAAAAATGTGATTTTTGG-AAGTTTGAGGTC
*
6432 -AAAATGGAATTTTTTGGAAGTTTGT-GGGTAAAAATGTGATTTTTGGAAGTTTTAGGGTC
1 AAAAATGGAATTTTTT-GAAGTTT-TAGGGTAAAAATGTGATTTTTGGAAGTTTGA-GGTC
* ** * *
6491 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTGCTTTTTGGAGGTTTCGAGGTC
1 AAAAATGGAATTTTTTGAAGTTTTAGGGTAAAAATGTGATTTTTGGAAGTTT-GAGGTC
* * *
6550 AAAAATGGAATTTTTTGAAGTTTTAAGGTCAAAATG-GAATTTTTAGG-AGTTCGAGGAT-
1 AAAAATGGAATTTTTTGAAGTTTTAGGGTAAAAATGTG-ATTTTT-GGAAGTTTGAGG-TC
*
6608 AAAAATGTAATTTT
1 AAAAATGGAATTTT
6622 CGAACAGTTT
Statistics
Matches: 158, Mismatches: 21, Indels: 23
0.78 0.10 0.11
Matches are distributed among these distances:
58 39 0.25
59 99 0.63
60 19 0.12
61 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (58 bp):
AAAAATGGAATTTTTTGAAGTTTTAGGGTAAAAATGTGATTTTTGGAAGTTTGAGGTC
Found at i:6600 original size:29 final size:29
Alignment explanation
Indices: 6374--6593 Score: 193
Period size: 30 Copynumber: 7.5 Consensus size: 29
6364 ATCGGGATTA
6374 AAAATGGAATTTTTGGACA--TTTAGGGGT-
1 AAAATGGAATTTTTGGA-AGTTTTA-GGGTC
* * *
6402 AAAAGGGTAATTTTTGGAAATTTTAAGGTC
1 AAAATGG-AATTTTTGGAAGTTTTAGGGTC
*
6432 AAAATGGAATTTTTTGGAAGTTTGT-GGGTA
1 AAAATGGAA-TTTTTGGAAGTTT-TAGGGTC
6462 AAAATGTG-ATTTTTGGAAGTTTTAGGGTC
1 AAAATG-GAATTTTTGGAAGTTTTAGGGTC
** *
6491 AAAAATGGAATTTTTGGAAGTTCGAGGGTA
1 -AAAATGGAATTTTTGGAAGTTTTAGGGTC
* * *
6521 AAAATGTG-CTTTTTGG-AGGTTTCGAGGTC
1 AAAATG-GAATTTTTGGAAGTTTTAG-GGTC
* *
6550 AAAAATGGAATTTTTTGAAGTTTTAAGGTC
1 -AAAATGGAATTTTTGGAAGTTTTAGGGTC
6580 AAAATGGAATTTTT
1 AAAATGGAATTTTT
6594 AGGAGTTCGA
Statistics
Matches: 156, Mismatches: 21, Indels: 29
0.76 0.10 0.14
Matches are distributed among these distances:
28 12 0.08
29 64 0.41
30 73 0.47
31 7 0.04
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTTAGGGTC
Found at i:6612 original size:29 final size:29
Alignment explanation
Indices: 6372--6621 Score: 188
Period size: 29 Copynumber: 8.5 Consensus size: 29
6362 AAATCGGGAT
* *
6372 TAAAAATGGAATTTTTGGACATTTAG-GGG
1 TAAAAATGGAATTTTTGGA-AGTTCGAGGG
* * ** *
6401 T-AAAAGGGTAATTTTTGGAAATTTTAAGG
1 TAAAAATGG-AATTTTTGGAAGTTCGAGGG
* * *
6430 TCAAAATGGAATTTTTTGGAAGTTTGTGGG
1 TAAAAATGGAA-TTTTTGGAAGTTCGAGGG
**
6460 TAAAAATGTG-ATTTTTGGAAGTTTTAGGG
1 TAAAAATG-GAATTTTTGGAAGTTCGAGGG
6489 TCAAAAATGGAATTTTTGGAAGTTCGAGGG
1 T-AAAAATGGAATTTTTGGAAGTTCGAGGG
* *
6519 TAAAAATGTG-CTTTTTGGAGGTTTCGA-GG
1 TAAAAATG-GAATTTTTGGAAG-TTCGAGGG
* ** *
6548 TCAAAAATGGAATTTTTTGAAGTTTTAAGG
1 T-AAAAATGGAATTTTTGGAAGTTCGAGGG
* *
6578 TCAAAATGGAATTTTTAGG-AGTTCGAGGA
1 TAAAAATGGAATTTTT-GGAAGTTCGAGGG
*
6607 TAAAAATGTAATTTT
1 TAAAAATGGAATTTT
6622 CGAACAGTTT
Statistics
Matches: 178, Mismatches: 30, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
28 9 0.05
29 90 0.51
30 78 0.44
31 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTCGAGGG
Found at i:7785 original size:12 final size:13
Alignment explanation
Indices: 7740--7789 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 13
7730 TTGACTCCCT
7740 TTATTTATT--TA
1 TTATTTATTAATA
*
7751 TTA-TTAATAATA
1 TTATTTATTAATA
7763 TTATTTATTAATA
1 TTATTTATTAATA
*
7776 TT-TTTTTTAATA
1 TTATTTATTAATA
7788 TT
1 TT
7790 CATTATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
10 4 0.12
11 3 0.09
12 16 0.48
13 10 0.30
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTTATTAATA
Found at i:8515 original size:6 final size:6
Alignment explanation
Indices: 8492--8575 Score: 68
Period size: 6 Copynumber: 14.3 Consensus size: 6
8482 GTTCTAAATC
* * **
8492 AATTTG AATTTT AA-TTA AATTTA AATTTA AA-GCA AATTTA AATTTAA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A
**
8539 AAGATA AATTTA AATTTA AGA--TA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA A-ATTTA AATTTA AATTTA AA
8576 AATAAATTTG
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
4 1 0.02
5 10 0.16
6 46 0.74
7 5 0.08
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:8518 original size:17 final size:18
Alignment explanation
Indices: 8507--8584 Score: 115
Period size: 17 Copynumber: 4.4 Consensus size: 18
8497 GAATTTTAAT
8507 TAAATTTAAATTTAAAG-
1 TAAATTTAAATTTAAAGA
*
8524 CAAATTTAAATTTAAAAGA
1 TAAATTTAAATTT-AAAGA
8543 TAAATTTAAATTT-AAGA
1 TAAATTTAAATTTAAAGA
*
8560 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAAGA
8578 TAAATTT
1 TAAATTT
8585 GAATCAATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
17 29 0.53
18 14 0.25
19 12 0.22
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (18 bp):
TAAATTTAAATTTAAAGA
Found at i:8554 original size:36 final size:35
Alignment explanation
Indices: 8507--8584 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 35
8497 GAATTTTAAT
8507 TAAATTTAAATTTAA-AGCAAATTTAAATTTAAAAGA
1 TAAATTTAAATTTAAGA-CAAATTTAAATTTAAAA-A
*
8543 TAAATTTAAATTTAAGATAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAGACAAATTTAAATTTAAAAA
8578 TAAATTT
1 TAAATTT
8585 GAATCAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 8 0.20
36 31 0.77
37 1 0.03
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (35 bp):
TAAATTTAAATTTAAGACAAATTTAAATTTAAAAA
Found at i:9703 original size:45 final size:45
Alignment explanation
Indices: 9659--9893 Score: 264
Period size: 45 Copynumber: 5.2 Consensus size: 45
9649 TTCAAGTTTT
* * * *
9659 TCTTTCTTTGGTGGTGTATAAATTGGTGGTTTAGGCTCAGGTTTT
1 TCTTTCTTTGGAGGTGTATAAACTGGTGGTTTAGGCTCAGGCTTC
* * * * *
9704 TCCTTCTTTGGAGGT-TCATATACTGGTGGTTTCGGTTCGGGCTTC
1 TCTTTCTTTGGAGGTGT-ATAAACTGGTGGTTTAGGCTCAGGCTTC
9749 TCTTTCTTTGGAGGTGTATAAACTGGTGGTTTAGGCTCAGGCTT-
1 TCTTTCTTTGGAGGTGTATAAACTGGTGGTTTAGGCTCAGGCTTC
* * * * *
9793 TTTCTTCTTTGGAGGT-TCATATACTGGTGGTTTCGGTTCGGGCTTC
1 TCT-TTCTTTGGAGGTGT-ATAAACTGGTGGTTTAGGCTCAGGCTTC
9839 TCTATT-TTTGGAGGTGTATAAACTGGTGG-TTAGGCTCAGGCTTC
1 TCT-TTCTTTGGAGGTGTATAAACTGGTGGTTTAGGCTCAGGCTTC
*
9883 TCCTTCTTTGG
1 TCTTTCTTTGG
9894 TGGTTCATAG
Statistics
Matches: 157, Mismatches: 26, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
43 2 0.01
44 23 0.15
45 126 0.80
46 6 0.04
ACGTcount: A:0.12, C:0.15, G:0.29, T:0.44
Consensus pattern (45 bp):
TCTTTCTTTGGAGGTGTATAAACTGGTGGTTTAGGCTCAGGCTTC
Found at i:9754 original size:90 final size:90
Alignment explanation
Indices: 9659--9902 Score: 404
Period size: 90 Copynumber: 2.7 Consensus size: 90
9649 TTCAAGTTTT
* *
9659 TCTTTCTTTGGTGGTGTATAAATTGGTGGTTTAGGCTCAGGTTTTTCCTTCTTTGGAGGTTCATA
1 TCTTTCTTTGGAGGTGTATAAACTGGTGGTTTAGGCTCAGGTTTTTCCTTCTTTGGAGGTTCATA
9724 TACTGGTGGTTTCGGTTCGGGCTTC
66 TACTGGTGGTTTCGGTTCGGGCTTC
9749 TCTTTCTTTGGAGGTGTATAAACTGGTGGTTTAGGCTCAGGCTTTTT-CTTCTTTGGAGGTTCAT
1 TCTTTCTTTGGAGGTGTATAAACTGGTGGTTTAGGCTCAGG-TTTTTCCTTCTTTGGAGGTTCAT
9813 ATACTGGTGGTTTCGGTTCGGGCTTC
65 ATACTGGTGGTTTCGGTTCGGGCTTC
* * *
9839 TCTATT-TTTGGAGGTGTATAAACTGGTGG-TTAGGCTCAGGCTTCTCCTTCTTTGGTGGTTCAT
1 TCT-TTCTTTGGAGGTGTATAAACTGGTGGTTTAGGCTCAGGTTTTTCCTTCTTTGGAGGTTCAT
9902 A
65 A
9903 GACCGGAGGT
Statistics
Matches: 146, Mismatches: 5, Indels: 7
0.92 0.03 0.04
Matches are distributed among these distances:
88 3 0.02
89 28 0.19
90 108 0.74
91 7 0.05
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.44
Consensus pattern (90 bp):
TCTTTCTTTGGAGGTGTATAAACTGGTGGTTTAGGCTCAGGTTTTTCCTTCTTTGGAGGTTCATA
TACTGGTGGTTTCGGTTCGGGCTTC
Found at i:16914 original size:17 final size:17
Alignment explanation
Indices: 16892--16924 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16882 TAGATATATT
16892 TTTAAAATTAAATTTAC
1 TTTAAAATTAAATTTAC
*
16909 TTTAAATTTAAATTTA
1 TTTAAAATTAAATTTA
16925 AATTCATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAAAATTAAATTTAC
Found at i:16915 original size:11 final size:12
Alignment explanation
Indices: 16892--17002 Score: 79
Period size: 11 Copynumber: 9.5 Consensus size: 12
16882 TAGATATATT
*
16892 TTTAAAATTAAA
1 TTTAAATTTAAA
*
16904 TTT-ACTTTAAA
1 TTTAAATTTAAA
16915 TTTAAATTTAAA
1 TTTAAATTTAAA
* **
16927 TTCATTTTTTAAA
1 TTTA-AATTTAAA
*
16940 TTTAAATTT-AT
1 TTTAAATTTAAA
16951 TTTAAATTTAAA
1 TTTAAATTTAAA
*
16963 TTT-AGTTTAAA
1 TTTAAATTTAAA
*
16974 TTTGAAA--TAAT
1 TTT-AAATTTAAA
* *
16985 TTTGAACTTAAA
1 TTTAAATTTAAA
16997 TTTAAA
1 TTTAAA
17003 ATCAATTACA
Statistics
Matches: 75, Mismatches: 17, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
10 2 0.03
11 35 0.47
12 28 0.37
13 10 0.13
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:16918 original size:6 final size:6
Alignment explanation
Indices: 16892--17002 Score: 79
Period size: 6 Copynumber: 19.0 Consensus size: 6
16882 TAGATATATT
* * * **
16892 TTTAAA ATTAAA TTT-AC TTTAAA TTTAAA TTTAAA TTCATTT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA
* * *
16940 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AG TTTAAA TTTGAAA --TAAT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
* *
16985 TTTGAA CTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
17003 ATCAATTACA
Statistics
Matches: 78, Mismatches: 20, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
4 2 0.03
5 13 0.17
6 57 0.73
7 6 0.08
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:16955 original size:17 final size:17
Alignment explanation
Indices: 16915--17000 Score: 93
Period size: 17 Copynumber: 4.9 Consensus size: 17
16905 TTACTTTAAA
*
16915 TTTAAATTTAAATTCATTT
1 TTTAAATTTAAATT--TAT
16934 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
16951 TTTAAATTTAAATTTAG
1 TTTAAATTTAAATTTAT
*
16968 TTTAAATTTGAAA-TAAT
1 TTTAAATTT-AAATTTAT
* *
16985 TTTGAACTTAAATTTA
1 TTTAAATTTAAATTTA
17001 AAATCAATTA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
16 3 0.05
17 38 0.66
18 3 0.05
19 14 0.24
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:18840 original size:29 final size:29
Alignment explanation
Indices: 18803--18862 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
18793 TACCCCCCGA
*
18803 AACTTCCAAAAACTCCATTTTTATCC-TCG
1 AACTACCAAAAACTCCATTTTTA-CCTTCG
*
18832 AACTACCAAAAATTCCATTTTTACCTTCG
1 AACTACCAAAAACTCCATTTTTACCTTCG
18861 AA
1 AA
18863 ACTTTTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (29 bp):
AACTACCAAAAACTCCATTTTTACCTTCG
Found at i:18881 original size:60 final size:61
Alignment explanation
Indices: 18817--18947 Score: 139
Period size: 60 Copynumber: 2.2 Consensus size: 61
18807 TCCAAAAACT
* * * *
18817 CCATTTTTATCCTCGA-ACTACC-AAAAATTCCATTTTT-ACCTTCGAAACTTTTGAAAA-TTA
1 CCATTTTTACCCTC-ATACTACCAAAAAAATCCATTTTTGACC-CCAAAACTTTT-AAAAGTTA
* *
18877 CCA-TTTTACCCTCATATTTCCAAAAAAATCCATTTTTGACCCCAAAACTTTTAAAAGTTA
1 CCATTTTTACCCTCATACTACCAAAAAAATCCATTTTTGACCCCAAAACTTTTAAAAGTTA
18937 CCA-TTTTACCC
1 CCATTTTTACCC
18948 CTGGATGTCC
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
58 1 0.02
59 17 0.28
60 40 0.66
61 3 0.05
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.37
Consensus pattern (61 bp):
CCATTTTTACCCTCATACTACCAAAAAAATCCATTTTTGACCCCAAAACTTTTAAAAGTTA
Found at i:19043 original size:60 final size:61
Alignment explanation
Indices: 18927--19044 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 61
18917 CCCAAAACTT
* * * * *
18927 TTAAAAGTTACCATTTTACCCCTGGATGTCCAAAATTTTCGTTTTTGATCCTAATTTTTTC
1 TTAAAAGTTACCATTTTACCCCTGGATGTCCAAAATTGTCATTTTTAACCCAAATTTTTTC
* *
18988 TTAAAA-TTACCTTTTTACCCCTGGATGTCTAAAA-TGTCATTTTTAACCCCAAATTTT
1 TTAAAAGTTACCATTTTACCCCTGGATGTCCAAAATTGTCATTTTTAA-CCCAAATTTT
19045 CTCAAAATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 9 0.18
60 34 0.69
61 6 0.12
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.44
Consensus pattern (61 bp):
TTAAAAGTTACCATTTTACCCCTGGATGTCCAAAATTGTCATTTTTAACCCAAATTTTTTC
Found at i:22579 original size:22 final size:20
Alignment explanation
Indices: 22545--22587 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
22535 TAAACGTAAA
22545 ATTAAATAAATTCATAATTAAC
1 ATTAAATAAATTC-T-ATTAAC
**
22567 ATTAAATTGATTCTATTAAC
1 ATTAAATAAATTCTATTAAC
22587 A
1 A
22588 AAATGATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 1 0.05
22 11 0.58
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (20 bp):
ATTAAATAAATTCTATTAAC
Found at i:29204 original size:6 final size:6
Alignment explanation
Indices: 29193--29217 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29183 CAAATGTGCG
29193 TATACA TATACA TATACA TATACA T
1 TATACA TATACA TATACA TATACA T
29218 GATGTTTGGT
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:0.16, G:0.00, T:0.36
Consensus pattern (6 bp):
TATACA
Found at i:44438 original size:6 final size:6
Alignment explanation
Indices: 44418--44453 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
44408 AATAAAAACA
* *
44418 AGGGAG AGGAAG AGGGGG AGGGAG AGGGAG AGGGAG
1 AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG
44454 GAGAGGTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
AGGGAG
Found at i:44441 original size:18 final size:19
Alignment explanation
Indices: 44418--44456 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
44408 AATAAAAACA
44418 AGGGAGAGGAAGAGGG-GG
1 AGGGAGAGGAAGAGGGAGG
*
44436 AGGGAGAGGGAGAGGGAGG
1 AGGGAGAGGAAGAGGGAGG
44455 AG
1 AG
44457 AGGTTAGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (19 bp):
AGGGAGAGGAAGAGGGAGG
Found at i:54395 original size:18 final size:18
Alignment explanation
Indices: 54374--54411 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54364 AAATTGTTTA
*
54374 AAAAAATAAAAAATAAAT
1 AAAAAACAAAAAATAAAT
*
54392 AAAAAACAAAAAATGAAT
1 AAAAAACAAAAAATAAAT
54410 AA
1 AA
54412 TTAAAGATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (18 bp):
AAAAAACAAAAAATAAAT
Found at i:55296 original size:17 final size:17
Alignment explanation
Indices: 55258--55304 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
55248 CAAGGATAAA
55258 AAATTTA-TATAAACCT
1 AAATTTATTATAAACCT
55274 ATAATTTATTATAAACAC-
1 A-AATTTATTATAAAC-CT
55292 AAATTTATGTATA
1 AAATTTAT-TATA
55305 TTCTCTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 13 0.48
18 12 0.44
19 1 0.04
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (17 bp):
AAATTTATTATAAACCT
Found at i:57708 original size:30 final size:29
Alignment explanation
Indices: 57655--57727 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 29
57645 AAGTTTAAAT
*
57655 TAAAAATATAAAATTACATTTTAATT-TCC
1 TAAAAATATAAAATTACATTTTAATTCT-A
*
57684 TAAAAATAATAAAATTTCGA-TTTAATTCTA
1 TAAAAAT-ATAAAATTAC-ATTTTAATTCTA
57714 TAAAAATTATAAAA
1 TAAAAA-TATAAAA
57728 ATATAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 7 0.18
30 28 0.74
31 3 0.08
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.38
Consensus pattern (29 bp):
TAAAAATATAAAATTACATTTTAATTCTA
Found at i:58404 original size:2 final size:2
Alignment explanation
Indices: 58399--58427 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
58389 ACACACACAC
58399 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 A
58428 AATTTGAATT
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63937 original size:18 final size:18
Alignment explanation
Indices: 63916--63951 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
63906 TTAAAATTGA
63916 ACTTAATTTTTTTTTCTT
1 ACTTAATTTTTTTTTCTT
63934 ACTTAATTTTTTTTTCTT
1 ACTTAATTTTTTTTTCTT
63952 GATAGTGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (18 bp):
ACTTAATTTTTTTTTCTT
Found at i:64168 original size:11 final size:12
Alignment explanation
Indices: 64149--64229 Score: 62
Period size: 11 Copynumber: 7.0 Consensus size: 12
64139 ATTGGACCTC
*
64149 TTTTTAATTT-A
1 TTTTAAATTTAA
64160 TTTTAAATTTAGA
1 TTTTAAATTTA-A
*
64173 -TTT-ATTTTAA
1 TTTTAAATTTAA
*
64183 ATTTAAA-TTAA
1 TTTTAAATTTAA
*
64194 TCTTAAATTTAA
1 TTTTAAATTTAA
* *
64206 ATTTAATTTTAA
1 TTTTAAATTTAA
*
64218 TTTTAAAATTAA
1 TTTTAAATTTAA
64230 AAAGTCCATT
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
10 1 0.02
11 26 0.48
12 26 0.48
13 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (12 bp):
TTTTAAATTTAA
Found at i:64175 original size:6 final size:6
Alignment explanation
Indices: 64161--64230 Score: 65
Period size: 6 Copynumber: 12.0 Consensus size: 6
64151 TTTAATTTAT
* *
64161 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* * *
64207 TTTAAT TTTAAT TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
64231 AAGTCCATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
4 2 0.04
5 5 0.09
6 43 0.81
7 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:64177 original size:17 final size:17
Alignment explanation
Indices: 64154--64224 Score: 97
Period size: 17 Copynumber: 4.1 Consensus size: 17
64144 ACCTCTTTTT
64154 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
64171 GATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
64188 AATTAATCTTAAATTTA
1 AATTTATTTTAAATTTA
*
64205 AATTTAATTTTAATTTTA
1 AATTT-ATTTTAAATTTA
64223 AA
1 AA
64225 ATTAAAAAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
17 34 0.74
18 12 0.26
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:65012 original size:3 final size:3
Alignment explanation
Indices: 65006--65127 Score: 145
Period size: 3 Copynumber: 39.0 Consensus size: 3
64996 AATGTGTTAT
65006 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
65054 TAA TAA TAA TAA TAA TAA TAA GTAA TAA CTGCCA CAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA -T--AA TAA TAA TAA TAA TAA
* **
65103 TAG TAA TGT TAA TAA TTAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA
65128 AAAAATCGAA
Statistics
Matches: 102, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
3 94 0.92
4 7 0.07
6 1 0.01
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:66118 original size:29 final size:29
Alignment explanation
Indices: 66078--66237 Score: 153
Period size: 30 Copynumber: 5.4 Consensus size: 29
66068 AGGGTCCCTA
66078 AACTGTCCAAAAATCCCATTTTTACCCTCG
1 AACT-TCCAAAAATCCCATTTTTACCCTCG
** * *
66108 AACTTTAAAAAATTCCA-TTTTAACCTCG
1 AACTTCCAAAAATCCCATTTTTACCCTCG
* * **
66136 AAACTTCCAAAAATCTCATTTTTGACCTTAA
1 -AACTTCCAAAAATCCCATTTTT-ACCCTCG
*
66167 AACTTCCAAAAATCCCATTTTTGACCC-CAA
1 AACTTCCAAAAATCCCATTTTT-ACCCTC-G
* * *
66197 AACTTTCAAAAATCTCAATTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTACCCTCG
66226 AACTTCCAAAAA
1 AACTTCCAAAAA
66238 ATTCCGTTTT
Statistics
Matches: 105, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
28 10 0.10
29 38 0.36
30 54 0.51
31 3 0.03
ACGTcount: A:0.38, C:0.28, G:0.04, T:0.31
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTACCCTCG
Found at i:66255 original size:59 final size:59
Alignment explanation
Indices: 66085--66266 Score: 206
Period size: 59 Copynumber: 3.1 Consensus size: 59
66075 CTAAACTGTC
* * * * * *
66085 CAAAAATCCCATTTTTACCCTCGAACTT-TAAAAAATTCCATTTTAACCTCGAAACTTC
1 CAAAAATCTCATTTTTACCCTCGAACTTCCAAAAAATTCCATTTTGACCCCAAAACTTT
* ** *
66143 CAAAAATCTCATTTTTGACCTTAAAACTTCC-AAAAATCCCATTTTTGACCCCAAAACTTT
1 CAAAAATCTCATTTTT-ACCCTCGAACTTCCAAAAAATTCCA-TTTTGACCCCAAAACTTT
* * * *
66203 CAAAAATCTCAATTTTACCCTCGAACTTCCAAAAAATTCCGTTTTGCCCCCAAAACTCT
1 CAAAAATCTCATTTTTACCCTCGAACTTCCAAAAAATTCCATTTTGACCCCAAAACTTT
66262 CAAAA
1 CAAAA
66267 TTACCCTTTT
Statistics
Matches: 102, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
58 15 0.15
59 50 0.49
60 37 0.36
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.31
Consensus pattern (59 bp):
CAAAAATCTCATTTTTACCCTCGAACTTCCAAAAAATTCCATTTTGACCCCAAAACTTT
Found at i:71434 original size:205 final size:199
Alignment explanation
Indices: 70984--71502 Score: 797
Period size: 205 Copynumber: 2.6 Consensus size: 199
70974 TTCGAACTCC
*
70984 AGCTTCCTGATGGGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCAA
1 AGCTTCCTGATGGGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC-A
* *
71049 ATTGAAACAAACAACGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAC
65 ATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
* *
71114 GCTCGAGCAAATCTTCGAACCCCAGCTTCTTGATGAAACACTGAGAAGCAGGTCGAAGCAATAAA
130 GATCGAGCAAATCTTCGAACCCCAGCTTCTTGATGAAACACTGAGAAGCAGGTCAAAGCAATAAA
71179 AGGTT
195 AGGTT
* * *
71184 AGCTTCCTGATGAGATACTGAGAAGTGGACTAAATTCGTCTTCCTGATGAGATACAGAGAGGCAA
1 AGCTTCCTGATGGGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAA
*
71249 GTTGAAACAAACGACGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCGC
66 -TTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAA-CC-C
* * * * * *
71314 ACTCGATGTGAGTAAATCTTTGAACTCCAGCTT-TCTGGTGAGACACTGAGAAGCAGGTCAAAGC
128 A--CGAT-CGAGCAAATCTTCGAACCCCAGCTTCT-TGATGAAACACTGAGAAGCAGGTCAAAGC
71378 AATAAAAGGTT
189 AATAAAAGGTT
*
71389 AGCTTCTTGATGGGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGA
1 AGCTTCCTGATGGGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC-A
*
71454 ATTGAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAG
65 ATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAG
71503 GCCGAGTCAA
Statistics
Matches: 290, Mismatches: 21, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
199 2 0.01
200 115 0.40
201 2 0.01
202 2 0.01
204 4 0.01
205 163 0.56
206 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (199 bp):
AGCTTCCTGATGGGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAA
TTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACG
ATCGAGCAAATCTTCGAACCCCAGCTTCTTGATGAAACACTGAGAAGCAGGTCAAAGCAATAAAA
GGTT
Found at i:71834 original size:11 final size:11
Alignment explanation
Indices: 71817--71897 Score: 76
Period size: 11 Copynumber: 7.3 Consensus size: 11
71807 CGGGCCCCTT
*
71817 TTTAATTT-AT
1 TTTAATTTAAA
*
71827 TTTAAATTTAGA
1 TTT-AATTTAAA
*
71839 TTTATTTTAAA
1 TTTAATTTAAA
*
71850 TTTAAATT-AA
1 TTTAATTTAAA
71860 TCTTAAATTTAAA
1 T-TT-AATTTAAA
71873 TTTAATTTAAA
1 TTTAATTTAAA
*
71884 TTTAATTTCAA
1 TTTAATTTAAA
71895 TTT
1 TTT
71898 TAAAATTAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
10 6 0.10
11 40 0.69
12 9 0.16
13 3 0.05
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:71841 original size:6 final size:6
Alignment explanation
Indices: 71827--71907 Score: 73
Period size: 6 Copynumber: 14.0 Consensus size: 6
71817 TTTAATTTAT
* *
71827 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* *
71873 TTT-AA TTTAAA TTT-AA TTTCAAT TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
71908 AAGTCCATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
4 2 0.03
5 15 0.25
6 37 0.61
7 7 0.11
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:71843 original size:17 final size:16
Alignment explanation
Indices: 71817--71906 Score: 99
Period size: 17 Copynumber: 5.3 Consensus size: 16
71807 CGGGCCCCTT
71817 TTTAATTTATTTTAAA
1 TTTAATTTATTTTAAA
71833 TTTAGATTTATTTTAAA
1 TTTA-ATTTATTTTAAA
* *
71850 TTTAAATTAATCTTAAA
1 TTT-AATTTATTTTAAA
*
71867 TTTAAATTTAATTTAAA
1 TTT-AATTTATTTTAAA
71884 TTTAATTTCAATTTTAAA
1 TTTAATTT--ATTTTAAA
*
71902 ATTAA
1 TTTAA
71907 AAAGTCCATT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
16 9 0.14
17 42 0.67
18 12 0.19
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (16 bp):
TTTAATTTATTTTAAA
Found at i:72688 original size:3 final size:3
Alignment explanation
Indices: 72682--72807 Score: 90
Period size: 3 Copynumber: 39.0 Consensus size: 3
72672 ATAAATGTGC
*
72682 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA GTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
** * ** *
72728 TAA CTGCC TCAT TAA TAA TAA TAA TAA GTAA TAA CTGCC TCAT TAA TAA
1 TAA -T-AA T-AA TAA TAA TAA TAA TAA -TAA TAA -T-AA T-AA TAA TAA
* *
72777 TAA TAA TAG TAA TAT TAA TAA TTAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
72808 AAAAATCGAA
Statistics
Matches: 98, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
3 83 0.85
4 15 0.15
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:72744 original size:31 final size:31
Alignment explanation
Indices: 72709--72790 Score: 148
Period size: 31 Copynumber: 2.7 Consensus size: 31
72699 ATAATAATAA
*
72709 TAATAATAGTAATAAGTAATAACTGCCTCAT
1 TAATAATAATAATAAGTAATAACTGCCTCAT
72740 TAATAATAATAATAAGTAATAACTGCCTCAT
1 TAATAATAATAATAAGTAATAACTGCCTCAT
72771 TAATAATAATAAT-AGTAATA
1 TAATAATAATAATAAGTAATA
72791 TTAATAATTA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 7 0.14
31 43 0.86
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (31 bp):
TAATAATAATAATAAGTAATAACTGCCTCAT
Found at i:72806 original size:31 final size:30
Alignment explanation
Indices: 72682--72807 Score: 76
Period size: 31 Copynumber: 3.9 Consensus size: 30
72672 ATAAATGTGC
*
72682 TAATAATAATAATAATAA-TAATAATAATAA
1 TAATAGTAAT-ATAATAATTAATAATAATAA
*
72712 TAATAGTAATAAGTAATAACTGCCTCATTAATAATAA
1 TAATAGTAAT-A-TAATAA-T---T-AATAATAATAA
* ** * *
72749 TAATAAGTAATA-ACTGCCTCATTAATAATAA
1 TAAT-AGTAATATAAT-AATTAATAATAATAA
72780 TAATAGTAATATTAATAATTAATAATAA
1 TAATAGTAATA-TAATAATTAATAATAA
72808 AAAAATCGAA
Statistics
Matches: 74, Mismatches: 11, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
30 18 0.24
31 29 0.39
32 2 0.03
35 3 0.04
36 1 0.01
37 15 0.20
38 6 0.08
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (30 bp):
TAATAGTAATATAATAATTAATAATAATAA
Found at i:74928 original size:9 final size:9
Alignment explanation
Indices: 74910--74999 Score: 63
Period size: 9 Copynumber: 10.7 Consensus size: 9
74900 GTCAACAAAT
74910 AATT-TTAA
1 AATTATTAA
74918 AATTATTAA
1 AATTATTAA
74927 AATTATT--
1 AATTATTAA
74934 --TT-TTAA
1 AATTATTAA
*
74940 AAATA-TAA
1 AATTATTAA
*
74948 AATTCTTAA
1 AATTATTAA
74957 AATTATTTAA
1 AATTA-TTAA
*
74967 AATTATTTTTA
1 AATTA--TTAA
74978 AA-TA-TAA
1 AATTATTAA
74985 AATTATTAA
1 AATTATTAA
74994 AATTAT
1 AATTAT
75000 CATCATCTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 21
0.71 0.07 0.23
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
7 4 0.06
8 13 0.20
9 27 0.42
10 11 0.17
11 6 0.09
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (9 bp):
AATTATTAA
Found at i:74994 original size:37 final size:38
Alignment explanation
Indices: 74910--74999 Score: 132
Period size: 37 Copynumber: 2.4 Consensus size: 38
74900 GTCAACAAAT
74910 AATTTTAAAATTA-TTAAAATTATTTTTTAAAAATATAA
1 AATTTTAAAATTATTTAAAATTATTTTTT-AAAATATAA
74948 AATTCTTAAAATTATTTAAAATTA-TTTTT-AAATATAA
1 AATT-TTAAAATTATTTAAAATTATTTTTTAAAATATAA
74985 AATTATTAAAATTAT
1 AATT-TTAAAATTAT
75000 CATCATCTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
37 22 0.45
38 4 0.08
39 14 0.29
40 9 0.18
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (38 bp):
AATTTTAAAATTATTTAAAATTATTTTTTAAAATATAA
Found at i:75572 original size:6 final size:6
Alignment explanation
Indices: 75552--75586 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
75542 TTTTTTTCTA
*
75552 TTCCCC TTCTCCC TTTCCC TTCCCC TTCCCC TTCC
1 TTCCCC TTC-CCC TTCCCC TTCCCC TTCCCC TTCC
75587 AAGAAATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (6 bp):
TTCCCC
Found at i:76022 original size:16 final size:14
Alignment explanation
Indices: 75999--76066 Score: 59
Period size: 16 Copynumber: 4.6 Consensus size: 14
75989 TTGATGATGA
*
75999 TAATTTTAATAATTT
1 TAATTTTAA-AATAT
76014 TATATTTTAAAA-AT
1 TA-ATTTTAAAATAT
*
76028 TAATTTTAAAAATTT
1 TAATTTT-AAAATAT
76043 TATATTTTTAAAA-AT
1 TA-A-TTTTAAAATAT
76058 TAATTTTAA
1 TAATTTTAA
76067 TAATGTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
13 11 0.24
14 8 0.18
15 10 0.22
16 12 0.27
17 4 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TAATTTTAAAATAT
Found at i:76032 original size:29 final size:30
Alignment explanation
Indices: 75999--76070 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
75989 TTGATGATGA
75999 TAATTTTAATAATTTTATA-TTTTAAAAAT
1 TAATTTTAATAATTTTATATTTTTAAAAAT
*
76028 TAATTTTAAAAATTTTATATTTTTAAAAAT
1 TAATTTTAATAATTTTATATTTTTAAAAAT
76058 TAATTTTAATAAT
1 TAATTTTAATAAT
76071 GTTAAAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 18 0.45
30 22 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
TAATTTTAATAATTTTATATTTTTAAAAAT
Found at i:76035 original size:13 final size:13
Alignment explanation
Indices: 76017--76066 Score: 64
Period size: 13 Copynumber: 3.5 Consensus size: 13
76007 ATAATTTTAT
76017 ATTTTAAAAATTA
1 ATTTTAAAAATTA
76030 ATTTTAAAAATTTTA
1 ATTTTAAAAA--TTA
76045 TATTTTTAAAAATTA
1 -A-TTTTAAAAATTA
76060 ATTTTAA
1 ATTTTAA
76067 TAATGTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 16 0.48
14 1 0.03
15 6 0.18
16 1 0.03
17 9 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTAAAAATTA
Found at i:84057 original size:11 final size:11
Alignment explanation
Indices: 84043--84101 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
84033 ATTAATTTTT
84043 TTTAAATTTAA
1 TTTAAATTTAA
*
84054 TTTAAGATTAAA
1 TTTAA-ATTTAA
*
84066 TTT-ATTTTAAA
1 TTTAAATTT-AA
84077 TTTAAATTTAA
1 TTTAAATTTAA
* *
84088 ATTAAGTTTAA
1 TTTAAATTTAA
84099 TTT
1 TTT
84102 TATTTTTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
10 2 0.05
11 24 0.63
12 12 0.32
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:84066 original size:17 final size:17
Alignment explanation
Indices: 84044--84103 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
84034 TTAATTTTTT
84044 TTAAATTTAATTTAAGA
1 TTAAATTTAATTTAAGA
*
84061 TTAAATTTATTTTAA-A
1 TTAAATTTAATTTAAGA
* *
84077 TTTAAATTTAAATTAAGT
1 -TTAAATTTAATTTAAGA
*
84095 TTAATTTTA
1 TTAAATTTA
84104 TTTTTAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 1 0.03
17 35 0.97
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAAATTTAATTTAAGA
Found at i:84080 original size:6 final size:6
Alignment explanation
Indices: 84043--84117 Score: 68
Period size: 6 Copynumber: 13.0 Consensus size: 6
84033 ATTAATTTTT
*
84043 TTTAAA TTT-AA TTTAAGA -TTAAA TTT-AT TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * **
84089 -TTAAG TTTAAT TTTATT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
84118 AATTAAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
5 14 0.25
6 42 0.74
7 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:84097 original size:23 final size:23
Alignment explanation
Indices: 84044--84113 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
84034 TTAATTTTTT
84044 TTAAATTT-AATTTAAGA-TTAAA
1 TTAAATTTAAATTTAA-ATTTAAA
* *
84066 TTTATTTTAAATTTAAATTTAAA
1 TTAAATTTAAATTTAAATTTAAA
* * **
84089 TTAAGTTTAATTTTATTTTTAAA
1 TTAAATTTAAATTTAAATTTAAA
84112 TT
1 TT
84114 TAAAAATTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
22 7 0.18
23 32 0.82
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (23 bp):
TTAAATTTAAATTTAAATTTAAA
Found at i:84117 original size:29 final size:28
Alignment explanation
Indices: 84029--84117 Score: 110
Period size: 29 Copynumber: 3.2 Consensus size: 28
84019 TTGACCGGGC
*
84029 TTAAATT-AATTTTTTTTAAATTT-AAT
1 TTAAATTAAATTTATTTTAAATTTAAAT
84055 TTAAGATTAAATTTATTTTAAATTTAAAT
1 TTAA-ATTAAATTTATTTTAAATTTAAAT
* **
84084 TTAAATTAAGTTTAATTTTATTTTTAAAT
1 TTAAATTAAATTT-ATTTTAAATTTAAAT
84113 TTAAA
1 TTAAA
84118 AATTAAAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
26 4 0.07
27 3 0.05
28 23 0.42
29 25 0.45
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
TTAAATTAAATTTATTTTAAATTTAAAT
Found at i:85723 original size:29 final size:30
Alignment explanation
Indices: 85673--85891 Score: 163
Period size: 30 Copynumber: 7.4 Consensus size: 30
85663 GAAGGTTTCT
* * *
85673 GAACTTTCCAAAAATCATATTTTGACCC-C
1 GAACTTTTCAAAAATTACATTTTGACCCTC
85702 -AATCTTTTCAAAAATTACATTTTGACCCTC
1 GAA-CTTTTCAAAAATTACATTTTGACCCTC
*
85732 GAACTTTTCAAAAATTACATTTT--CCCCC
1 GAACTTTTCAAAAATTACATTTTGACCCTC
* *
85760 GAAC-TTCCAAAATAAATCACATTTTG-CCCTC
1 GAACTTTTC--AA-AAATTACATTTTGACCCTC
* * *
85791 GAAC-TTCCAAAAATTACCATTTTTATCCTC
1 GAACTTTTCAAAAATTA-CATTTTGACCCTC
* *
85821 GAAC-TTCCAAAAATTACTATTTT-ACGCTC
1 GAACTTTTCAAAAATTAC-ATTTTGACCCTC
* * *
85850 GAA-TGTCCATAAATTACAATTTTGA-CCTC
1 GAACTTTTCAAAAATTAC-ATTTTGACCCTC
*
85879 GAACTTTCCAAAA
1 GAACTTTTCAAAA
85892 CCATTTTACC
Statistics
Matches: 159, Mismatches: 18, Indels: 25
0.79 0.09 0.12
Matches are distributed among these distances:
27 3 0.02
28 15 0.09
29 62 0.39
30 65 0.41
31 14 0.09
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.34
Consensus pattern (30 bp):
GAACTTTTCAAAAATTACATTTTGACCCTC
Found at i:85741 original size:30 final size:30
Alignment explanation
Indices: 85673--85983 Score: 203
Period size: 29 Copynumber: 10.8 Consensus size: 30
85663 GAAGGTTTCT
* *
85673 GAACTTTCCAAAAATCATATTTTGACCC-C
1 GAACTTTCCAAAAATTACATTTTGACCCTC
*
85702 -AATCTTTTCAAAAATTACATTTTGACCCTC
1 GAA-CTTTCCAAAAATTACATTTTGACCCTC
* *
85732 GAACTTTTCAAAAATTACATTTT--CCCCC
1 GAACTTTCCAAAAATTACATTTTGACCCTC
*
85760 GAAC-TTCCAAAATAAATCACATTTTG-CCCTC
1 GAACTTTCC--AA-AAATTACATTTTGACCCTC
* *
85791 GAAC-TTCCAAAAATTACCATTTTTATCCTC
1 GAACTTTCCAAAAATTA-CATTTTGACCCTC
*
85821 GAAC-TTCCAAAAATTACTATTTT-ACGCTC
1 GAACTTTCCAAAAATTAC-ATTTTGACCCTC
* *
85850 GAA-TGTCCATAAATTACAATTTTGA-CCTC
1 GAACTTTCCAAAAATTAC-ATTTTGACCCTC
*
85879 GAACTTTCC-AAAA--CCATTTT-ACCC-C
1 GAACTTTCCAAAAATTACATTTTGACCCTC
* * * * *
85904 TAAATGTCCAAAAATTACATTTTGGCCCCC
1 GAACTTTCCAAAAATTACATTTTGACCCTC
** * *
85934 G-TGTGTCCAAAAATTACCATATT-ACCCTC
1 GAACTTTCCAAAAATTA-CATTTTGACCCTC
* *
85963 GAGC-ATCC-AAAATTACATTTT
1 GAACTTTCCAAAAATTACATTTT
85984 TGACTCCGTT
Statistics
Matches: 227, Mismatches: 34, Indels: 44
0.74 0.11 0.14
Matches are distributed among these distances:
25 8 0.04
26 11 0.05
27 9 0.04
28 28 0.12
29 89 0.39
30 68 0.30
31 14 0.06
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.33
Consensus pattern (30 bp):
GAACTTTCCAAAAATTACATTTTGACCCTC
Found at i:85754 original size:59 final size:58
Alignment explanation
Indices: 85673--85890 Score: 162
Period size: 59 Copynumber: 3.7 Consensus size: 58
85663 GAAGGTTTCT
* * * *
85673 GAACTTTCCAAAAATCATATTTTGACCCC-AATCTTTTC-AA-AAATTACATTTTGACCCTC
1 GAACTTTCCAAAAATTACATTTT-ACCCCGAA-C-TTCCAAATAAATCACATTTTG-CCCTC
* *
85732 GAACTTTTCAAAAATTACATTTTCCCCCGAACTTCCAAAATAAATCACATTTTGCCCTC
1 GAACTTTCCAAAAATTACATTTTACCCCGAACTTCC-AAATAAATCACATTTTGCCCTC
* * * *
85791 GAAC-TTCCAAAAATTACCATTTTTATCCTCGAACTTCC-AA-AAATTACTATTTTACGCTC
1 GAACTTTCCAAAAATTA-CA-TTTTA-CCCCGAACTTCCAAATAAATCAC-ATTTTGCCCTC
* * *
85850 GAA-TGTCCATAAATTACAATTTTGACCTCGAACTTTCCAAA
1 GAACTTTCCAAAAATTAC-ATTTT-ACCCCGAAC-TTCCAAA
85891 ACCATTTTAC
Statistics
Matches: 132, Mismatches: 14, Indels: 25
0.77 0.08 0.15
Matches are distributed among these distances:
57 3 0.02
58 35 0.27
59 65 0.49
60 18 0.14
61 11 0.08
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (58 bp):
GAACTTTCCAAAAATTACATTTTACCCCGAACTTCCAAATAAATCACATTTTGCCCTC
Found at i:103759 original size:22 final size:22
Alignment explanation
Indices: 103724--103768 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
103714 AAGTTTCAAC
* *
103724 AATAATCATAATTATAATTATA
1 AATAATCATAATTAAAATGATA
103746 AATAATACAT-ATTAAAATGATA
1 AATAAT-CATAATTAAAATGATA
103768 A
1 A
103769 TAAACTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
AATAATCATAATTAAAATGATA
Found at i:103980 original size:21 final size:22
Alignment explanation
Indices: 103921--103980 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 22
103911 TAAATTATAG
*
103921 AAATTTTTAATATTT-AATATTTT
1 AAATTTTT--TATTTAATTATTTT
*
103944 AAATTTGTTTA-ATAATTATTTT
1 AAATTT-TTTATTTAATTATTTT
103966 -AATTTTTTATTTAAT
1 AAATTTTTTATTTAAT
103981 ATAAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 4 0.13
21 10 0.32
22 9 0.29
23 6 0.19
24 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
AAATTTTTTATTTAATTATTTT
Found at i:113661 original size:18 final size:17
Alignment explanation
Indices: 113620--113666 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
113610 AAAAAGTACA
113620 AATTTAAAAAATATAAT
1 AATTTAAAAAATATAAT
* *
113637 -ATATAAAAAATTTAAT
1 AATTTAAAAAATATAAT
113653 AATTGTAAAAAATA
1 AATT-TAAAAAATA
113667 AAATTTTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 14 0.58
17 2 0.08
18 8 0.33
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AATTTAAAAAATATAAT
Found at i:125683 original size:61 final size:61
Alignment explanation
Indices: 125604--125758 Score: 199
Period size: 61 Copynumber: 2.6 Consensus size: 61
125594 AAATAATTTG
*
125604 GTGTTGGCCATGCATTAGCCGACACC-AC-CTTTTTTATCTGATAAAAAATTCAAATTTTTTT
1 GTGTTGGCCATGCATTAGCCGACACCAACACTTTTTTATCAGATAAAAAA-T-AAATTTTTTT
* * *
125665 GTGTTGGTCATGCGTTAGCCGACACCAACATTTTTTTATCAGATAAAAAATAAATTTTTTT
1 GTGTTGGCCATGCATTAGCCGACACCAACACTTTTTTATCAGATAAAAAATAAATTTTTTT
* * * *
125726 GTATTGACCATGCATTGGTCGACACCAAC-CTTT
1 GTGTTGGCCATGCATTAGCCGACACCAACACTTT
125759 CATCCTTTCT
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
60 3 0.04
61 57 0.70
62 3 0.04
63 18 0.22
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (61 bp):
GTGTTGGCCATGCATTAGCCGACACCAACACTTTTTTATCAGATAAAAAATAAATTTTTTT
Found at i:126629 original size:30 final size:30
Alignment explanation
Indices: 126593--126710 Score: 166
Period size: 30 Copynumber: 3.9 Consensus size: 30
126583 AAAAAATAAT
*
126593 AATTAGAAATGAAATTTAAAATATAAACGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
** *
126623 AATTAGAAATTAAAAATAAAATATACACGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
*
126653 AATTAGAAATTAAATTTAAAATATAAAGGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
*
126683 AATTACAAATTAAATTTGAAAA-ATAAAC
1 AATTAGAAATTAAATTT-AAAATATAAAC
126711 AAAAAAAATC
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
30 73 0.95
31 4 0.05
ACGTcount: A:0.61, C:0.04, G:0.08, T:0.27
Consensus pattern (30 bp):
AATTAGAAATTAAATTTAAAATATAAACGA
Found at i:127995 original size:34 final size:29
Alignment explanation
Indices: 127912--128018 Score: 97
Period size: 34 Copynumber: 3.3 Consensus size: 29
127902 CAATAAATAT
* *
127912 TTCGAAAATATAAAAAATATATGTAAAAAAGTA
1 TTCGAAAATAGAAAAAATAT-TAT-AAAAA--A
*
127945 TTTCAAAAATAGAAAAAATATTATTTTTAAAAAA
1 -TTCGAAAATAGAAAAAATATTA----TAAAAAA
127979 TTCGAAAATAGAAAAAAATATTATAAAAAA
1 TTCGAAAATAG-AAAAAATATTATAAAAAA
128009 TTCGAAAATA
1 TTCGAAAATA
128019 TTTCTTATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
30 17 0.27
33 11 0.17
34 30 0.47
36 5 0.08
37 1 0.02
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.29
Consensus pattern (29 bp):
TTCGAAAATAGAAAAAATATTATAAAAAA
Found at i:129318 original size:93 final size:93
Alignment explanation
Indices: 129202--129616 Score: 665
Period size: 93 Copynumber: 4.5 Consensus size: 93
129192 TAATTTTAAA
129202 ATTTGATAAAAATTGAAATATAATAATAATTTTTTATTTAAATAAATTTAAAATTTAAATTTGAT
1 ATTTGATAAAAATTGAAATATAATAATAATTTTTTATTTAAATAAATTTAAAATTTAAATTTGAT
* *
129267 AAATAATGTATTGTTAAATCAATACATT
66 AAATAATGTATTGTCAAATCAACACATT
* *
129295 ATTTGATAAAAATTGAAATATAATATTAATTTTTTATTTAAATAAATTTAAAATTTAAATTTGGT
1 ATTTGATAAAAATTGAAATATAATAATAATTTTTTATTTAAATAAATTTAAAATTTAAATTTGAT
* *
129360 AAATAATATATTGTGAAATCAACACATT
66 AAATAATGTATTGTCAAATCAACACATT
* * *
129388 ATTTGATAAAAATTAAAATATAATAATAATTTTTTATTTAAATAATTTTAAATTTTAAATTTGAT
1 ATTTGATAAAAATTGAAATATAATAATAATTTTTTATTTAAATAAATTTAAAATTTAAATTTGAT
* *
129453 AAATAATGTATTGTCAAATCAATATATT
66 AAATAATGTATTGTCAAATCAACACATT
* *
129481 ATTTGATAAAAATTGAAATATAATAATAATTTTTTATTTAAATAAATTTAAACGTTT-AATTTGG
1 ATTTGATAAAAATTGAAATATAATAATAATTTTTTATTTAAATAAATTTAAA-ATTTAAATTTGA
*
129545 TAAATAATGTATTATCAAATCAACACATT
65 TAAATAATGTATTGTCAAATCAACACATT
*
129574 ATTTGGTAAAAATTGAAATATAAT--TAATTTTTTATTTAAATAA
1 ATTTGATAAAAATTGAAATATAATAATAATTTTTTATTTAAATAA
129617 TGTTAAATTA
Statistics
Matches: 299, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
91 19 0.06
93 277 0.93
94 3 0.01
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (93 bp):
ATTTGATAAAAATTGAAATATAATAATAATTTTTTATTTAAATAAATTTAAAATTTAAATTTGAT
AAATAATGTATTGTCAAATCAACACATT
Found at i:129642 original size:12 final size:11
Alignment explanation
Indices: 129608--129645 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
129598 TAATTTTTTA
129608 TTTAAA-TAAT
1 TTTAAATTAAT
*
129618 GTTAAATTAAT
1 TTTAAATTAAT
129629 TTTAAATGTAAT
1 TTTAAAT-TAAT
129641 TTTAA
1 TTTAA
129646 TTTCAACTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 5 0.21
11 10 0.42
12 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (11 bp):
TTTAAATTAAT
Found at i:129768 original size:17 final size:16
Alignment explanation
Indices: 129735--129769 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
129725 AATTTGGAAA
*
129735 TTAATTTCAACTTAAT
1 TTAATTTCAAATTAAT
129751 TTAATTTGCAAATTAAT
1 TTAATTT-CAAATTAAT
129768 TT
1 TT
129770 TTACACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (16 bp):
TTAATTTCAAATTAAT
Done.