Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011048.1 Kokia drynarioides strain JFW-HI SEQ_126019, 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: 54506
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1445 original size:142 final size:142
Alignment explanation
Indices: 1272--1532 Score: 468
Period size: 142 Copynumber: 1.8 Consensus size: 142
1262 AAATACAAAT
* * * *
1272 AAAAGAAGAAAAAATTGCAACTCCGCTGCTTGGAATTACTGAGTACGTCAGCAGCACTTTGTTTG
1 AAAAGAAGAAAAAACTGCAACTCCACAGCTTGGAATTACTGAGTACATCAGCAGCACTTTGTTTG
1337 CTCCATCGTGTTGTTGATGAGAAAGGTGAATCTAAGTAAGAGTGTTTTGTAAAAATAAAAAATAA
66 CTCCATCGTGTTGTTGATGAGAAAGGTGAATCTAAGTAAGAGTGTTTTGTAAAAATAAAAAATAA
1402 AAGAAAAACAGA
131 AAGAAAAACAGA
*
1414 AAAAGAAGAAAAGACTGCAACTCCACAGCTTGGAATTACTGAGTACATCAGCAGCACTTTGTTTG
1 AAAAGAAGAAAAAACTGCAACTCCACAGCTTGGAATTACTGAGTACATCAGCAGCACTTTGTTTG
*
1479 CTTCATCGTGTTGTTGATGAGAAAGGTGAATCTAAGTAAGAGTGTTTTGTAAAA
66 CTCCATCGTGTTGTTGATGAGAAAGGTGAATCTAAGTAAGAGTGTTTTGTAAAA
1533 GAAAAACAGA
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
142 113 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (142 bp):
AAAAGAAGAAAAAACTGCAACTCCACAGCTTGGAATTACTGAGTACATCAGCAGCACTTTGTTTG
CTCCATCGTGTTGTTGATGAGAAAGGTGAATCTAAGTAAGAGTGTTTTGTAAAAATAAAAAATAA
AAGAAAAACAGA
Found at i:2325 original size:15 final size:15
Alignment explanation
Indices: 2307--2346 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2297 TTTTGTAAAT
*
2307 TTTAATTTTAGCGGA
1 TTTAATTTAAGCGGA
* *
2322 TTTAATTTAATCGTA
1 TTTAATTTAAGCGGA
2337 TTTAATTTAA
1 TTTAATTTAA
2347 AATCAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.53
Consensus pattern (15 bp):
TTTAATTTAAGCGGA
Found at i:2656 original size:19 final size:20
Alignment explanation
Indices: 2616--2666 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
2606 CATAAAACGG
2616 ATATGTATAA-TATAAAAAAA
1 ATAT-TATAATTATAAAAAAA
*
2636 ATGTTATAATTAT-AAAAAA
1 ATATTATAATTATAAAAAAA
*
2655 ATATTACAATTA
1 ATATTATAATTA
2667 ATGTTTTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (20 bp):
ATATTATAATTATAAAAAAA
Found at i:4526 original size:10 final size:10
Alignment explanation
Indices: 4511--4535 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4501 AGAAAAGAAT
4511 AATAATAAAA
1 AATAATAAAA
4521 AATAATAAAA
1 AATAATAAAA
4531 AATAA
1 AATAA
4536 AGAAAGGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AATAATAAAA
Found at i:17460 original size:20 final size:21
Alignment explanation
Indices: 17423--17463 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
17413 TTCATAAAGT
*
17423 TTTTTTTTTCTATCTATTTTA
1 TTTTCTTTTCTATCTATTTTA
*
17444 TTTTCTTTT-TATTTATTTTA
1 TTTTCTTTTCTATCTATTTTA
17464 AAAAAGAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTCTTTTCTATCTATTTTA
Found at i:18119 original size:96 final size:95
Alignment explanation
Indices: 17945--18136 Score: 273
Period size: 96 Copynumber: 2.0 Consensus size: 95
17935 ATTTTGGGAA
17945 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCACAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAA-GTTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
18010 GAATCGAAGATAAAGAAAACATTGCCTCGATT
65 GAATCGAAGATAAA-AAAACATTACCTCGATT
* *
18042 AAGGGTATTCGATTATTTCGATTTGAAGGAAA-TTGCACCTAGTAAGTTAAGGCACAA-ATTTCA
1 AAGGATATTCGATTATCTCGATTTGAA-GAAAGTTGCACCTAGTAAGTTAAGGCACAATATTTCA
* *
18105 GAAACTCGAA-ATAAAAGAATATTACCTCGATT
65 G-AA-TCGAAGATAAAAAAACATTACCTCGATT
18137 TTAAAGTCTT
Statistics
Matches: 87, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
95 21 0.24
96 32 0.37
97 30 0.34
98 4 0.05
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (95 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAGTTGCACCTAGTAAGTTAAGGCACAATATTTCAG
AATCGAAGATAAAAAAACATTACCTCGATT
Found at i:18437 original size:30 final size:28
Alignment explanation
Indices: 18401--18780 Score: 182
Period size: 29 Copynumber: 12.9 Consensus size: 28
18391 GGATTCACGA
* *
18401 GGGTAAAATGGTATTTTTGGGAAAATTAAG
1 GGGTAAAATGG-ATTTTT-GGAAATTTTAG
* *
18431 GGGTAAAAATGGATTTTTTGG-AAGTTTCG
1 GGGT-AAAATGGA-TTTTTGGAAATTTTAG
* * *
18460 GGGTCAAATGGAATTTTTGG-AAGTTTCG
1 GGGTAAAATGG-ATTTTTGGAAATTTTAG
* * **
18488 GGGTCAAATGGAATTTTTGGAAGTTTCGG
1 GGGTAAAATGG-ATTTTTGGAAATTTTAG
* * *
18517 GGGTAAAAATGATATTTTTGGAAGTTTGA-
1 GGGT-AAAATG-GATTTTTGGAAATTTTAG
*
18546 GGGTAAAAATGGAATTTTTGGAAGTTTT-G
1 GGGT-AAAATGG-ATTTTTGGAAATTTTAG
* *
18575 GGGTAAAAATGGATTTTTTGGAAGTTTTGG
1 GGGT-AAAATGGA-TTTTTGGAAATTTTAG
*
18605 GGGTAAAATTGGATTTTTTGGAAGTTTTAG
1 GGGTAAAA-TGGA-TTTTTGGAAATTTTAG
* ***
18635 GGGTAAATATGGTATTTTTGG-AAGTACGG
1 GGGTAAA-ATGG-ATTTTTGGAAATTTTAG
* *
18664 GGGTAAAAATGGAATTTTTGG-AAGTTTCG
1 GGGT-AAAATGG-ATTTTTGGAAATTTTAG
* * **
18693 AGGGTAAAAATGGTATTTTTTGAAGTTCGA-
1 -GGGT-AAAATGG-ATTTTTGGAAATTTTAG
* *
18723 GGGTAAAAATGGAATTTTTGGAAGTTTCA-
1 GGGT-AAAATGG-ATTTTTGGAAATTTTAG
* *
18752 AGGTCAAAAATGGAATTTTTGGAAGTTTT
1 GGGT--AAAATGG-ATTTTTGGAAATTTT
18781 GGGACCTTCT
Statistics
Matches: 296, Mismatches: 37, Indels: 34
0.81 0.10 0.09
Matches are distributed among these distances:
28 42 0.14
29 125 0.42
30 113 0.38
31 16 0.05
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.37
Consensus pattern (28 bp):
GGGTAAAATGGATTTTTGGAAATTTTAG
Found at i:18463 original size:29 final size:29
Alignment explanation
Indices: 18430--18779 Score: 433
Period size: 30 Copynumber: 12.0 Consensus size: 29
18420 GGAAAATTAA
*
18430 GGGGTAAAAATGGATTTTTTGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
*
18459 GGGGT-CAAATGGAATTTTTGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
*
18487 GGGGT-CAAATGGAATTTTTGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
18515 GGGGGTAAAAAT-GATATTTTTGGAAGTTT-
1 -GGGGTAAAAATGGA-ATTTTTGGAAGTTTC
*
18544 GAGGGTAAAAATGGAATTTTTGGAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTC
* *
18574 GGGGTAAAAATGGATTTTTTGGAAGTTTTG
1 GGGGTAAAAATGGAATTTTTGGAAG-TTTC
* * *
18604 GGGGTAAAATTGGATTTTTTGGAAGTTTTA
1 GGGGTAAAAATGGAATTTTTGGAAG-TTTC
* * *
18634 GGGGTAAATATGGTATTTTTGGAAG-TAC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
18662 GGGGGTAAAAATGGAATTTTTGGAAGTTTC
1 -GGGGTAAAAATGGAATTTTTGGAAGTTTC
* *
18692 GAGGGTAAAAATGGTATTTTTTGAAG-TTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTC
18721 GAGGGTAAAAATGGAATTTTTGGAAGTTTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTC
**
18751 AAGGTCAAAAATGGAATTTTTGGAAGTTT
1 GGGGT-AAAAATGGAATTTTTGGAAGTTT
18780 TGGGACCTTC
Statistics
Matches: 287, Mismatches: 22, Indels: 23
0.86 0.07 0.07
Matches are distributed among these distances:
28 51 0.18
29 113 0.39
30 123 0.43
ACGTcount: A:0.30, C:0.03, G:0.31, T:0.37
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTC
Found at i:18777 original size:59 final size:58
Alignment explanation
Indices: 18431--18778 Score: 416
Period size: 59 Copynumber: 5.9 Consensus size: 58
18421 GAAAATTAAG
* * *
18431 GGGTAAAAATGGATTTTTTGGAAGTTTCGGGGT-CAAATGGAATTTTTGGAAGTTTCG-
1 GGGTAAAAATGGAATTTTTGGAAGTTTCAGGGTAAAAATGGAATTTTTGGAAG-TTCGA
* * *
18488 GGGT-CAAATGGAATTTTTGGAAGTTTCGGGGGTAAAAAT-GATATTTTTGGAAGTTTGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTC-AGGGTAAAAATGGA-ATTTTTGGAAGTTCGA
** * * *
18546 GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTAAAAATGGATTTTTTGGAAGTTTTGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCAGGGTAAAAATGGAATTTTTGGAAG-TTCGA
* * * * * * *
18605 GGGTAAAATTGGATTTTTTGGAAGTTTTAGGGGTAAATATGGTATTTTTGGAAGTACGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCA-GGGTAAAAATGGAATTTTTGGAAGTTCGA
* *
18664 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGGTATTTTTTGAAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTC-AGGGTAAAAATGGAATTTTTGGAAGTTCGA
*
18723 GGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTT
1 GGGTAAAAATGGAATTTTTGGAAGTTTCAGGGT-AAAAATGGAATTTTTGGAAGTT
18779 TTGGGACCTT
Statistics
Matches: 255, Mismatches: 26, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
56 21 0.08
57 14 0.05
58 44 0.17
59 154 0.60
60 22 0.09
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.37
Consensus pattern (58 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTCAGGGTAAAAATGGAATTTTTGGAAGTTCGA
Found at i:19870 original size:18 final size:18
Alignment explanation
Indices: 19847--19888 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 18
19837 GGTATCCTTT
19847 TTATTATTATT--AT-AC
1 TTATTATTATTAAATAAC
19862 TTATTATTATTAAATAAC
1 TTATTATTATTAAATAAC
19880 TTATTATTA
1 TTATTATTA
19889 CCGTTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.46
17 2 0.08
18 11 0.46
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATTATTATTAAATAAC
Found at i:20569 original size:17 final size:17
Alignment explanation
Indices: 20547--20626 Score: 124
Period size: 17 Copynumber: 4.7 Consensus size: 17
20537 TAAATAAATT
*
20547 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
20564 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
20581 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
20598 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
20615 TAAATTTAAATT
1 TAAATTTAAATT
20627 CTGTTGGGCC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:20569 original size:23 final size:23
Alignment explanation
Indices: 20534--20581 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
20524 ATTGGACATT
20534 ATTTAAATAAATTTAAATTT-AA
1 ATTTAAATAAATTTAAATTTCAA
20556 ATTTATAATAAATTTAAATTTCAA
1 ATTTA-AATAAATTTAAATTTCAA
20580 AT
1 AT
20582 AAATTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.21
23 15 0.62
24 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAAATAAATTTAAATTTCAA
Found at i:20584 original size:11 final size:10
Alignment explanation
Indices: 20534--20591 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
20524 ATTGGACATT
20534 ATTTAAATAA
1 ATTTAAATAA
20544 ATTTAAATTTAA
1 ATTTAAA--TAA
20556 ATTTATAATAA
1 ATTTA-AATAA
20567 ATTTAAAT--
1 ATTTAAATAA
*
20575 -TTCAAATAA
1 ATTTAAATAA
20584 ATTTAAAT
1 ATTTAAAT
20592 TTAAAATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 6 0.15
10 16 0.40
11 8 0.20
12 8 0.20
13 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (10 bp):
ATTTAAATAA
Found at i:20590 original size:23 final size:23
Alignment explanation
Indices: 20539--20596 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
20529 ACATTATTTA
**
20539 AATAAATTTAAATTTAAATTTAT
1 AATAAATTTAAATTTAAATAAAT
20562 AATAAATTTAAATTTCAAATAAAT
1 AATAAATTTAAATTT-AAATAAAT
*
20586 -TTAAATTTAAA
1 AATAAATTTAAA
20597 ATAAACTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 25 0.81
24 6 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AATAAATTTAAATTTAAATAAAT
Found at i:20598 original size:7 final size:6
Alignment explanation
Indices: 20541--20626 Score: 76
Period size: 6 Copynumber: 15.0 Consensus size: 6
20531 ATTATTTAAA
20541 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATT TCAAA-- TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT
* * * *
20587 TAAATT TAAA-A TAAACT TAATTT TAAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
20627 CTGTTGGGCC
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
4 5 0.08
5 11 0.17
6 44 0.68
7 5 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:21041 original size:37 final size:37
Alignment explanation
Indices: 20991--21061 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
20981 CATATCACTT
* *
20991 GTTTTGATCCACTTCTCTGTATTTCATCAAGAAGATG
1 GTTTTGATCCACTTCCCCGTATTTCATCAAGAAGATG
* * * *
21028 GTTTTGGTTCACTTCCCCGTATTTCGTCAGGAAG
1 GTTTTGATCCACTTCCCCGTATTTCATCAAGAAG
21062 CTAACCATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (37 bp):
GTTTTGATCCACTTCCCCGTATTTCATCAAGAAGATG
Found at i:21292 original size:193 final size:198
Alignment explanation
Indices: 21058--21416 Score: 507
Period size: 193 Copynumber: 1.8 Consensus size: 198
21048 ATTTCGTCAG
*
21058 GAAGCTAACCATTTTATTACTTCAACCTGCTTCTCAGTATCTTATCAGGAAGTTGGGGTTC-AAG
1 GAAGCTAACCATTTTATTACTTCAACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAA-
* * *
21122 GATTTGCTCACATCGAG-CGTG-G-G-T-TTGATC-AGTGTCTCATCAGGAAGATAACCGCCTCG
65 GATTTGCTCACATCGAGTCCTGAGTGATATTCATCTAGTGTCTCATCAGGAAGATAACCGCCTCA
*
21181 CTTGTTTCAATCCGCTTCTCTGTATCTTATCAGGAAGACAAATTTGGTTCACTTCTCAATATCTC
130 CTTGTTTCAATCCGCTTCTCTG-ATCTCATCAGGAAGACAAATTTGGTTCACTTCTCAATATCTC
21246 ATTAA
194 ATTAA
* *
21251 GAAGCTAACCATTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGCAGTTGGGGTTCGAAG
1 GAAGCTAACCATTTTATTACTTCAACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAG
* * * * * *
21316 ATTTGCTCGCATCGAGTCCTGAGTTGATATTCTTCTTTGTTTCTCATCAGGAAGATGACCGCCTT
66 ATTTGCTCACATCGAGTCCTGAG-TGATATTCATC-TAGTGTCTCATCAGGAAGATAACCGCCTC
*
21381 ACTTTTTTCAATCCGCTTCTCTGATCTCATCAGGAA
129 ACTTGTTTCAATCCGCTTCTCTGATCTCATCAGGAA
21417 ACTCGGATTC
Statistics
Matches: 143, Mismatches: 14, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
193 74 0.52
194 5 0.03
195 1 0.01
197 1 0.01
198 1 0.01
199 4 0.03
200 12 0.08
201 45 0.31
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (198 bp):
GAAGCTAACCATTTTATTACTTCAACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAG
ATTTGCTCACATCGAGTCCTGAGTGATATTCATCTAGTGTCTCATCAGGAAGATAACCGCCTCAC
TTGTTTCAATCCGCTTCTCTGATCTCATCAGGAAGACAAATTTGGTTCACTTCTCAATATCTCAT
TAA
Found at i:21435 original size:115 final size:116
Alignment explanation
Indices: 21271--21652 Score: 344
Period size: 115 Copynumber: 3.3 Consensus size: 116
21261 ATTTTATTGC
* * ** * * *
21271 TTCAA-CCTGCTTCTCAGTATCTCATCAGGCAGTTGGGGTTCGAAGATTTGCTCGCATCGAGTCC
1 TTCAATCC-GCTTCTCTGTATCTCATCAGGAAACTAGGATTCGAAGATTTGCTCACATCGAGTCC
* * *
21335 TGAGTTGATATTCTTCTTTGTTTCTCATCAGGAAGATGACCGCCTTACTTTT
65 TGAGTTGATATTCTTCTTTGTATCTCATCAGGAAGATGACCGCATTACTTAT
* *
21387 TTCAATCCGCTTCTCTG-ATCTCATCAGGAAACTCGGATTCGAAGATTTGATCACATCGA-TCCT
1 TTCAATCCGCTTCTCTGTATCTCATCAGGAAACTAGGATTCGAAGATTTGCTCACATCGAGTCC-
* * * * ****
21450 TGAGTTGGTATACTTCTTTGTATCTCATCAGGAAGCTAACAATTTTA-TTAT
65 TGAGTTGATATTCTTCTTTGTATCTCATCAGGAAGATGACCGCATTACTTAT
* * * * * * *
21501 TTCGA-CCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAGGATTTGCTCATATCGAG-CG
1 TTCAATCC-GCTTCTCTGTATCTCATCAGGAAACTAGGATTCGAAGATTTGCTCACATCGAGTCC
* * * ** *
21564 TGAGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGATCGCATCGCTTGT
65 TGAG-TTGATAT--TCTTCTT-T--GTATCTCATCAGGAAGATGACCGCATTACTTAT
21622 TTCAATCCGCTTCTCTGTATCTCATCAGGAA
1 TTCAATCCGCTTCTCTGTATCTCATCAGGAA
21653 GACGAATTTG
Statistics
Matches: 210, Mismatches: 43, Indels: 21
0.77 0.16 0.08
Matches are distributed among these distances:
113 2 0.01
114 22 0.10
115 115 0.55
116 13 0.06
117 8 0.04
118 1 0.00
120 18 0.09
121 29 0.14
122 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (116 bp):
TTCAATCCGCTTCTCTGTATCTCATCAGGAAACTAGGATTCGAAGATTTGCTCACATCGAGTCCT
GAGTTGATATTCTTCTTTGTATCTCATCAGGAAGATGACCGCATTACTTAT
Found at i:21882 original size:201 final size:204
Alignment explanation
Indices: 21469--22021 Score: 702
Period size: 201 Copynumber: 2.7 Consensus size: 204
21459 ATACTTCTTT
*
21469 GTATCTCATCAGGAAGCTAACAATTTTATTATTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
1 GTATCTCATCAGGAAGCTAACCATTTTATTATTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
* * ** * * *
21534 TAGGGTTCGAGGATTTGCTCATATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAATATCTCATC
66 TGGGGTTCGAAGATTTGCTCGCATCGAGCCTGAGTTTGATAT-GTCTTCTTCT-AATATATCATC
* *
21599 AGGAAGATGATCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGA
129 AGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGA
*
21664 TTCACTTCTTA
194 TTCACTTCTCA
** * *
21675 GTATCTCATCAAAAAGCTAACCATTTTATT-TCTTCGACTTGCTTCTCAGTATCTCGTCAGGAAG
1 GTATCTCATCAGGAAGCTAACCATTTTATTAT-TTCGACCTGCTTCTCAGTATCTCATCAGGAAG
* *
21739 CTGGGGTTCGAAGATTTGCTCGCATCGAGTCCTGAGTTTG-TAT-TCTTCTT-T-GTATATCATT
65 CTGGGGTTCGAAGATTTGCTCGCATCGAG-CCTGAGTTTGATATGTCTTCTTCTAATATATCATC
* * *
21800 AGGAAGATGACCGCCTTACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGG
129 AGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGA
*
21865 TTCACTTCTCC
194 TTCACTTCTCA
* * *
21876 GTATCTCATCAGGAAGCTAACCATTTTATTATTTCGACCTGCTTCTCAGTATCTTAACAGGAAGT
1 GTATCTCATCAGGAAGCTAACCATTTTATTATTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
* * ** * * * *
21941 TGGGGTTCGAAGATTTGCTCGCTTTGAGCCTCGTTTCATTGATTTGGTCTACTTCTCAGTATCTC
66 TGGGGTTCGAAGATTTGCTCGCATCGAGCCT-GAGT--TTGATAT-GTCTTCTTCT-AATATATC
22006 ATCAGGAAGATGACCG
126 ATCAGGAAGATGACCG
22022 TATCGTTGTT
Statistics
Matches: 299, Mismatches: 36, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
200 3 0.01
201 160 0.54
202 1 0.00
203 4 0.01
204 9 0.03
205 1 0.00
206 90 0.30
207 10 0.03
209 21 0.07
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (204 bp):
GTATCTCATCAGGAAGCTAACCATTTTATTATTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
TGGGGTTCGAAGATTTGCTCGCATCGAGCCTGAGTTTGATATGTCTTCTTCTAATATATCATCAG
GAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGATT
CACTTCTCA
Found at i:33778 original size:29 final size:28
Alignment explanation
Indices: 33746--33806 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
33736 AAAATGAGAC
* *
33746 TTTTCGGATACTTGGGGGTAAAATGGTAA
1 TTTT-GGATACTCGAGGGTAAAATGGTAA
* *
33775 TTTTGGATTCTCGAGGGTGAAATGGTAA
1 TTTTGGATACTCGAGGGTAAAATGGTAA
33803 TTTT
1 TTTT
33807 AGGAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.25, C:0.07, G:0.30, T:0.39
Consensus pattern (28 bp):
TTTTGGATACTCGAGGGTAAAATGGTAA
Found at i:33836 original size:30 final size:29
Alignment explanation
Indices: 33794--34142 Score: 430
Period size: 30 Copynumber: 11.7 Consensus size: 29
33784 CTCGAGGGTG
* *
33794 AAATGGTAATTTTAGGAAAATTTAGGGGTAA
1 AAATGG-AATTTTTGG-AAGTTTAGGGGTAA
*
33825 AAATGGAATTTTTGGAAGTTTTAGGGTTAA
1 AAATGGAATTTTTGGAAG-TTTAGGGGTAA
*
33855 AAATGGAATTTTTGGAAGTTTCGAGGGTAA
1 AAATGGAATTTTTGGAAGTTTAG-GGGTAA
*
33885 AAAT-GATATTTTTGGAAGTTTAAGGGTAA
1 AAATGGA-ATTTTTGGAAGTTTAGGGGTAA
*
33914 AAATGGAATTTTTGGAAGTTTTGGGGTAA
1 AAATGGAATTTTTGGAAGTTTAGGGGTAA
* *
33943 AAATGGATTTTTTGGAAGTTTTGGGGGTAA
1 AAATGGAATTTTTGGAAG-TTTAGGGGTAA
*
33973 AAATGGATTTTTTGGAAGTTTTAGGGGTAA
1 AAATGGAATTTTTGGAAG-TTTAGGGGTAA
* * ***
34003 AGATGGTATTTTTGGAAGTACGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTAGGGGTAA
*
34032 AAATGGAATTTTTGGAAGTTTTGGGGTCAA
1 AAATGGAATTTTTGGAAGTTTAGGGGT-AA
*
34062 AAATGGAATTTTTGGAAGTTTCGAGGGTAA
1 AAATGGAATTTTTGGAAGTTTAG-GGGTAA
* * *
34092 AAATGGAATTTTTGGAAGTCTCGAGGTCAA
1 AAATGGAATTTTTGGAAGTTTAGGGGT-AA
34122 AAATGGAATTTTTGGAAGTTT
1 AAATGGAATTTTTGGAAGTTT
34143 CGAGACCTCC
Statistics
Matches: 283, Mismatches: 27, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
29 88 0.31
30 185 0.65
31 10 0.04
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.36
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAGTTTAGGGGTAA
Found at i:33912 original size:89 final size:88
Alignment explanation
Indices: 33760--34146 Score: 434
Period size: 89 Copynumber: 4.4 Consensus size: 88
33750 CGGATACTTG
* * * *
33760 GGGGT-AAAATGGTAA-TTTTGG-A-TTCTCGAGGGT-GAAATGG-TAATTTTAGGAAAATTTAG
1 GGGGTAAAAATGG-AATTTTTGGAAGTT-TCGAGGGTAAAAATGGAT-ATTTTTGG-AAGTTTAA
33819 GGGTAAAAATGGAATTTTTGGAAGTTTT
62 GGGTAAAAATGGAATTTTTGGAAG-TTT
*
33847 AGGGTTAAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAAT-GATATTTTTGGAAGTTTAAGGG
1 -GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGGATATTTTTGGAAGTTTAAGGG
33911 TAAAAATGGAATTTTTGGAAGTTTT
65 TAAAAATGGAATTTTTGGAAG-TTT
* * * *
33936 GGGGTAAAAATGGATTTTTTGGAAGTTTTGGGGGTAAAAATGGAT-TTTTTGGAAGTTTTAGGGG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGGATATTTTTGGAAG-TTTAAGGG
* * **
34000 TAAAGATGGTATTTTTGGAAGTACG
65 TAAAAATGGAATTTTTGGAAGT-TT
* *
34025 GGGGTAAAAATGGAATTTTTGGAAGTTTTG-GGGTCAAAAATGGA-ATTTTTGGAAGTTTCGAGG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGT-AAAAATGGATATTTTTGGAAGTTT-AAGG
*
34088 GTAAAAATGGAATTTTTGGAAGTCTC
64 GTAAAAATGGAATTTTTGGAAGT-TT
*
34114 GAGGTCAAAAATGGAATTTTTGGAAGTTTCGAG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTCGAG
34147 ACCTCCTGGG
Statistics
Matches: 261, Mismatches: 24, Indels: 25
0.84 0.08 0.08
Matches are distributed among these distances:
88 61 0.23
89 151 0.58
90 41 0.16
91 8 0.03
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (88 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGGATATTTTTGGAAGTTTAAGGGT
AAAAATGGAATTTTTGGAAGTTT
Found at i:35929 original size:6 final size:6
Alignment explanation
Indices: 35918--35986 Score: 65
Period size: 6 Copynumber: 12.0 Consensus size: 6
35908 ATTATTTAAA
* *
35918 TAAATT TAAATT TAAATT TCAAA-- TAAATT TAAATT TAAA-A TAAACT
1 TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT TAAATT
* *
35964 TAATTT TAAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT
35987 CTGTTGACCT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
4 3 0.06
5 9 0.18
6 36 0.71
7 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:35941 original size:23 final size:22
Alignment explanation
Indices: 35911--35956 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 22
35901 ATTGAACATT
35911 ATTTAAATAAATTTAAATTTAA
1 ATTTAAATAAATTTAAATTTAA
35933 ATTTCAAATAAATTTAAATTTAA
1 ATTT-AAATAAATTTAAATTTAA
35956 A
1 A
35957 ATAAACTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTAAATAAATTTAAATTTAA
Found at i:35946 original size:17 final size:17
Alignment explanation
Indices: 35924--35986 Score: 99
Period size: 17 Copynumber: 3.7 Consensus size: 17
35914 TAAATAAATT
*
35924 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
35941 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
35958 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
35975 TAAATTTAAATT
1 TAAATTTAAATT
35987 CTGTTGACCT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:36615 original size:23 final size:23
Alignment explanation
Indices: 36534--36611 Score: 124
Period size: 23 Copynumber: 3.4 Consensus size: 23
36524 AGATTTAAAC
36534 AAATATTCATATTTATATTATTA
1 AAATATTCATATTTATATTATTA
36557 AAATATTCATATTTATATTATTA
1 AAATATTCATATTTATATTATTA
*
36580 AAATATTCATATTTTATACTA-TA
1 AAATATTCATA-TTTATATTATTA
36603 AAA-ATTCAT
1 AAATATTCAT
36612 TATTAAATAT
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
22 6 0.11
23 39 0.74
24 8 0.15
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (23 bp):
AAATATTCATATTTATATTATTA
Found at i:36710 original size:20 final size:20
Alignment explanation
Indices: 36673--36715 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
36663 ATTTTTTCAA
36673 TAAAATATTAAGAATATTACT
1 TAAAATATTAAGAATATTA-T
36694 TAAAAT-TTAA-AATTATTAT
1 TAAAATATTAAGAA-TATTAT
36713 TAA
1 TAA
36716 TGTTAAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.29
20 9 0.43
21 6 0.29
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
TAAAATATTAAGAATATTAT
Found at i:36772 original size:21 final size:21
Alignment explanation
Indices: 36746--36794 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
36736 ATAAAATCAT
* *
36746 AATATTAAATAATTTTATTAA
1 AATATTAAATAATATTAATAA
*
36767 AATATTAAATTATATTAATAA
1 AATATTAAATAATATTAATAA
*
36788 ATTATTA
1 AATATTA
36795 TGTTATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATATTAAATAATATTAATAA
Found at i:38262 original size:19 final size:18
Alignment explanation
Indices: 38229--38274 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
38219 CCTAAAAACA
*
38229 AAAATAATTATAAATAAAAT
1 AAAA-AATTAAAAAT-AAAT
38249 AAAAAATTAAAAATAAAT
1 AAAAAATTAAAAATAAAT
38267 AAACAAAT
1 AAA-AAAT
38275 AAGGTAACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 13 0.54
20 4 0.17
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAAATTAAAAATAAAT
Found at i:45075 original size:18 final size:19
Alignment explanation
Indices: 45038--45075 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
45028 AAGACTATTA
* *
45038 AAACATGTCATCTGAGAAT
1 AAACATGTCAGCTAAGAAT
45057 AAACAT-TCAGCTAAGAAT
1 AAACATGTCAGCTAAGAAT
45075 A
1 A
45076 CTATCTTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (19 bp):
AAACATGTCAGCTAAGAAT
Found at i:47369 original size:20 final size:20
Alignment explanation
Indices: 47316--47370 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
47306 TTTTTTTCAC
* * *
47316 AAAAAATTATTAAAAATCAT
1 AAAAAAATATAAAAAATCAG
** *
47336 AAAAGTATAAAAAAAATCAG
1 AAAAAAATATAAAAAATCAG
47356 AAAAAAATATAAAAA
1 AAAAAAATATAAAAA
47371 TATTAAATAT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (20 bp):
AAAAAAATATAAAAAATCAG
Found at i:47377 original size:9 final size:9
Alignment explanation
Indices: 47358--47394 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
47348 AAAATCAGAA
47358 AAAAATA-T
1 AAAAATATT
47366 AAAAATATT
1 AAAAATATT
47375 --AAATATT
1 AAAAATATT
47382 AAAAATATT
1 AAAAATATT
47391 AAAA
1 AAAA
47395 CCGTTATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.27
8 7 0.27
9 12 0.46
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAAATATT
Found at i:47386 original size:16 final size:15
Alignment explanation
Indices: 47360--47393 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
47350 AATCAGAAAA
47360 AAATATAAAAATATT
1 AAATATAAAAATATT
47375 AAATATTAAAAATATT
1 AAATA-TAAAAATATT
47391 AAA
1 AAA
47394 ACCGTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATATAAAAATATT
Found at i:47422 original size:9 final size:9
Alignment explanation
Indices: 47410--47495 Score: 54
Period size: 10 Copynumber: 9.6 Consensus size: 9
47400 ATAAACTTAT
47410 TAAAAATTA
1 TAAAAATTA
*
47419 TAAAAAAATA
1 T-AAAAATTA
47429 TAAAAACTTA
1 TAAAAA-TTA
*
47439 TAAATATTA
1 TAAAAATTA
*
47448 TAAGAA-TA
1 TAAAAATTA
47456 -AAAAA--A
1 TAAAAATTA
* *
47462 TAGTAAATTC
1 TA-AAAATTA
*
47472 TATTAAATTA
1 TA-AAAATTA
47482 TAAAAATTA
1 TAAAAATTA
47491 TAAAA
1 TAAAA
47496 GTAACAAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
6 1 0.02
7 5 0.08
8 5 0.08
9 24 0.40
10 25 0.42
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:47455 original size:27 final size:29
Alignment explanation
Indices: 47402--47461 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 29
47392 AAACCGTTAT
*
47402 AAACTTATTAAAAATTATAAAAAAATATAA
1 AAACTTATTAAAAATTAT-AAAAAATAAAA
* *
47432 AAACTTA-TAAATATTAT-AAGAATAAAA
1 AAACTTATTAAAAATTATAAAAAATAAAA
47459 AAA
1 AAA
47462 TAGTAAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 11 0.41
29 9 0.33
30 7 0.26
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (29 bp):
AAACTTATTAAAAATTATAAAAAATAAAA
Found at i:47494 original size:26 final size:26
Alignment explanation
Indices: 47425--47494 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 26
47415 ATTATAAAAA
47425 AATATAAAAACTTATAAATATTATAAG
1 AATATAAAAA-TTATAAATATTATAAG
*
47452 AATA-AAAAAATAGTAAAT-TCTATTAA-
1 AATATAAAAATTA-TAAATAT-TA-TAAG
*
47478 ATTATAAAAATTATAAA
1 AATATAAAAATTATAAA
47495 AGTAACAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
25 3 0.08
26 19 0.53
27 14 0.39
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (26 bp):
AATATAAAAATTATAAATATTATAAG
Found at i:48153 original size:26 final size:26
Alignment explanation
Indices: 48124--48173 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
48114 ATATGTTTTT
48124 TTTATTA-ATTTTATATATTTTTATAA
1 TTTATTAGATTTTATA-ATTTTTATAA
48150 TTTATTAGATTTTATAATTTTTAT
1 TTTATTAGATTTTATAATTTTTAT
48174 TAATGTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (26 bp):
TTTATTAGATTTTATAATTTTTATAA
Found at i:48171 original size:45 final size:44
Alignment explanation
Indices: 48122--48214 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 44
48112 AAATATGTTT
* * *
48122 TTTTTATTAATTTTATATATTTTTATAATTTATTAGA-TTTTATAA
1 TTTTTATTAATGTCATATATTTTTAT-ATTTAATA-ATTTTTATAA
*
48167 TTTTTATTAATGTCATATTTTTTTATATTTAATAATTTTTATAA
1 TTTTTATTAATGTCATATATTTTTATATTTAATAATTTTTATAA
48211 TTTT
1 TTTT
48215 GAGAAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 19 0.44
45 23 0.53
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (44 bp):
TTTTTATTAATGTCATATATTTTTATATTTAATAATTTTTATAA
Found at i:48212 original size:9 final size:9
Alignment explanation
Indices: 48122--48214 Score: 54
Period size: 9 Copynumber: 10.4 Consensus size: 9
48112 AAATATGTTT
48122 TTTTTATTAA
1 TTTTTA-TAA
48132 -TTTTATATA
1 TTTTTATA-A
48141 TTTTTATAA
1 TTTTTATAA
*
48150 TTTATTA-GA
1 TTT-TTATAA
48159 -TTTTATAA
1 TTTTTATAA
48167 TTTTTATTAA
1 TTTTTA-TAA
* *
48177 -TGTCAT-A
1 TTTTTATAA
*
48184 TTTTT-TTA
1 TTTTTATAA
*
48192 TATTTAATAA
1 T-TTTTATAA
48202 TTTTTATAA
1 TTTTTATAA
48211 TTTT
1 TTTT
48215 GAGAAAAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 21
0.68 0.10 0.22
Matches are distributed among these distances:
7 5 0.08
8 10 0.16
9 33 0.52
10 16 0.25
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:48213 original size:17 final size:17
Alignment explanation
Indices: 48124--48213 Score: 58
Period size: 17 Copynumber: 5.2 Consensus size: 17
48114 ATATGTTTTT
* *
48124 TTTATTAATTTTATATAT
1 TTTAATAATTTT-TATAA
* *
48142 TTTTATAATTTATTA-GA
1 TTTAATAATTT-TTATAA
*
48159 TTTTATAATTTTTATTAA
1 TTTAATAATTTTTA-TAA
* * *
48177 TGTCAT-ATTTTTTTATA
1 TTTAATAATTTTTATA-A
48194 TTTAATAATTTTTATAA
1 TTTAATAATTTTTATAA
48211 TTT
1 TTT
48214 TGAGAAAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
16 5 0.09
17 26 0.46
18 24 0.43
19 1 0.02
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTAATAATTTTTATAA
Found at i:52162 original size:19 final size:20
Alignment explanation
Indices: 52140--52181 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
52130 ACACAAAAAT
52140 AAAAAAT-ATT-AATTTATA
1 AAAAAATGATTAAATTTATA
52158 AAAAAATGATTAAAATTTATA
1 AAAAAATGATT-AAATTTATA
52179 AAA
1 AAA
52182 GAAGAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
19 3 0.14
21 11 0.52
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAAAATGATTAAATTTATA
Found at i:54454 original size:23 final size:23
Alignment explanation
Indices: 54337--54458 Score: 67
Period size: 23 Copynumber: 5.2 Consensus size: 23
54327 AGTACTTAAT
54337 AGTAAGCACACA-AGTGCTGGGGAAAC
1 AGTAAGCACACACAGTGCT---G-AAC
54363 AGTAAGCACACACAGTGC--AATC
1 AGTAAGCACACACAGTGCTGAA-C
* * * * *
54385 AGTAGGCGCACATAGCG-TAAATC
1 AGTAAGCACACACAGTGCTGAA-C
* *
54408 AGTAGGCACAC-GAGATGC-GAAAC
1 AGTAAGCACACACAG-TGCTG-AAC
54431 AGTAAGCACACACAGTGCTGAAC
1 AGTAAGCACACACAGTGCTGAAC
54454 AGTAA
1 AGTAA
54459 ACGCGCTAGC
Statistics
Matches: 77, Mismatches: 10, Indels: 21
0.71 0.09 0.19
Matches are distributed among these distances:
21 2 0.03
22 16 0.21
23 37 0.48
24 5 0.06
26 12 0.16
27 5 0.06
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.13
Consensus pattern (23 bp):
AGTAAGCACACACAGTGCTGAAC
Done.