Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011260.1 Kokia drynarioides strain JFW-HI SEQ_126239, 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: 74078
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:4647 original size:18 final size:18
Alignment explanation
Indices: 4624--4660 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4614 ACAATTCATA
4624 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
4642 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
4660 T
1 T
4661 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:4990 original size:17 final size:18
Alignment explanation
Indices: 4956--4991 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4946 TGAATTTCTA
4956 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
4974 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
4991 T
1 T
4992 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:12498 original size:17 final size:18
Alignment explanation
Indices: 12476--12510 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
12466 CAAAAATATT
*
12476 AATATTAATTA-ATTAAA
1 AATATTAAATATATTAAA
12493 AATATTAAATATATTAAA
1 AATATTAAATATATTAAA
12511 TAAATCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATTAAATATATTAAA
Found at i:12508 original size:22 final size:23
Alignment explanation
Indices: 12467--12514 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
12457 ATTTGTTAAC
*
12467 AAAAATATTAATATTAATTAATT
1 AAAAATATTAATATTAATTAAAT
12490 AAAAATATTAA-A-TATATTAAAT
1 AAAAATATTAATATTA-ATTAAAT
12512 AAA
1 AAA
12515 TCAATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 2 0.09
22 10 0.43
23 11 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAAATATTAATATTAATTAAAT
Found at i:15821 original size:39 final size:39
Alignment explanation
Indices: 15777--15858 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
15767 TGACAACACC
15777 AAAAATATTTAAAAAATAATCATGATATAATGATTTGGG
1 AAAAATATTTAAAAAATAATCATGATATAATGATTTGGG
15816 AAAAATATTTAAAAAATAATCATGATATAATGATTTGGG
1 AAAAATATTTAAAAAATAATCATGATATAATGATTTGGG
15855 AAAA
1 AAAA
15859 GTTGGGTGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.32
Consensus pattern (39 bp):
AAAAATATTTAAAAAATAATCATGATATAATGATTTGGG
Found at i:23464 original size:37 final size:37
Alignment explanation
Indices: 23414--23487 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
23404 TTTTATTGAC
23414 ATAGTGAAATTAAACATACTGACATAATGAGCAGCAT
1 ATAGTGAAATTAAACATACTGACATAATGAGCAGCAT
23451 ATAGTGAAATTAAACATACTGACATAATGAGCAGCAT
1 ATAGTGAAATTAAACATACTGACATAATGAGCAGCAT
23488 GAGATTTCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (37 bp):
ATAGTGAAATTAAACATACTGACATAATGAGCAGCAT
Found at i:27710 original size:17 final size:17
Alignment explanation
Indices: 27676--27718 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
27666 TTAACTTCGG
* *
27676 TGAGCTCACATATCCAA
1 TGAGCTCGCACATCCAA
*
27693 TGAGCTCGCACATTCAA
1 TGAGCTCGCACATCCAA
*
27710 TGAACTCGC
1 TGAGCTCGC
27719 TGTCATGGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (17 bp):
TGAGCTCGCACATCCAA
Found at i:28502 original size:25 final size:23
Alignment explanation
Indices: 28461--28506 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
28451 CCAATTAAGG
28461 AATTATTGTTTAGATTTAATTCT
1 AATTATTGTTTAGATTTAATTCT
*
28484 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
28507 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCT
Found at i:34190 original size:3 final size:3
Alignment explanation
Indices: 34182--34282 Score: 157
Period size: 3 Copynumber: 33.7 Consensus size: 3
34172 TAAAATACCA
34182 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
34230 AAT AAT AAT AAT ACT AAT ACT AAT ACT AAT ACT AAT ACT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
34278 AAT AA
1 AAT AA
34283 AAGAGAATAT
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:37427 original size:6 final size:6
Alignment explanation
Indices: 37418--37460 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
37408 AATTAGTACA
*
37418 TTTATT TTTATT TTCATT TTTCATTT TTTATT TTTATT TTTAT
1 TTTATT TTTATT TTTATT TTT-A-TT TTTATT TTTATT TTTAT
37461 GGTTGTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 26 0.79
7 2 0.06
8 5 0.15
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:37470 original size:26 final size:26
Alignment explanation
Indices: 37418--37473 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
37408 AATTAGTACA
**
37418 TTTATTTTTATTTTCATTTTTCATTT
1 TTTATTTTTATTTTCATGGTTCATTT
* **
37444 TTTATTTTTATTTTTATGGTTGTTTT
1 TTTATTTTTATTTTCATGGTTCATTT
37470 TTTA
1 TTTA
37474 GTTGTTATCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.14, C:0.04, G:0.05, T:0.77
Consensus pattern (26 bp):
TTTATTTTTATTTTCATGGTTCATTT
Found at i:38334 original size:13 final size:12
Alignment explanation
Indices: 38308--38352 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
38298 TCTGAATTTT
*
38308 AAAAAAAAA-AG
1 AAAAAAAAATTG
38319 AAAAAAAAAGTTG
1 AAAAAAAAA-TTG
38332 AAAAGAAAAATTG
1 AAAA-AAAAATTG
38345 AAAAAAAA
1 AAAAAAAA
38353 GAGAGAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 9 0.30
12 4 0.13
13 12 0.40
14 5 0.17
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:38379 original size:20 final size:18
Alignment explanation
Indices: 38332--38379 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
38322 AAAAAAGTTG
38332 AAAAGAAAAATTGAAAAAA
1 AAAAG-AAAATTGAAAAAA
38351 AAGAGAGAAAATTGAGAAAAGA
1 AA-A-AGAAAATTGA-AAAA-A
38373 AAAAGAA
1 AAAAGAA
38380 GTATTTGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
19 2 0.08
20 13 0.52
21 7 0.28
22 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (18 bp):
AAAAGAAAATTGAAAAAA
Found at i:39432 original size:23 final size:25
Alignment explanation
Indices: 39406--39451 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39396 CCAATTAGAG
39406 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
39429 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
39452 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:41315 original size:23 final size:23
Alignment explanation
Indices: 41289--41333 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
41279 TGCTACTGTG
*
41289 ACTTGCACCATAGTGCCACTAAC
1 ACTTACACCATAGTGCCACTAAC
**
41312 ACTTACACTGTAGTGCCACTAA
1 ACTTACACCATAGTGCCACTAA
41334 AACATGCATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.24
Consensus pattern (23 bp):
ACTTACACCATAGTGCCACTAAC
Found at i:41347 original size:23 final size:23
Alignment explanation
Indices: 41299--41355 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
41289 ACTTGCACCA
* *
41299 TAGTGCCACTAACACTTACACTG
1 TAGTGCCACTAAAACATACACTG
*
41322 TAGTGCCACTAAAACATGCA-TCG
1 TAGTGCCACTAAAACATACACT-G
*
41345 TAGTGTCACTA
1 TAGTGCCACTA
41356 TAACTTGCGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (23 bp):
TAGTGCCACTAAAACATACACTG
Found at i:52610 original size:17 final size:17
Alignment explanation
Indices: 52588--52624 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
52578 CAATTTTAGC
52588 TTTCTTGAATTTGGATT
1 TTTCTTGAATTTGGATT
**
52605 TTTCTTGGGTTTGGATT
1 TTTCTTGAATTTGGATT
52622 TTT
1 TTT
52625 TTGGGCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.05, G:0.22, T:0.62
Consensus pattern (17 bp):
TTTCTTGAATTTGGATT
Found at i:52628 original size:16 final size:17
Alignment explanation
Indices: 52597--52629 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52587 CTTTCTTGAA
52597 TTTGGATTTTTCTTGGG
1 TTTGGATTTTTCTTGGG
52614 TTTGGATTTTT-TTGGG
1 TTTGGATTTTTCTTGGG
52630 CATAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.06, C:0.03, G:0.30, T:0.61
Consensus pattern (17 bp):
TTTGGATTTTTCTTGGG
Found at i:52776 original size:24 final size:26
Alignment explanation
Indices: 52744--52791 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
52734 ATGTTTTATA
52744 AATTATATTTTT-AAT-ATAATAATT
1 AATTATATTTTTAAATGATAATAATT
*
52768 AATTTTATTTTTAAATGATAATAA
1 AATTATATTTTTAAATGATAATAA
52792 CACAATACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 3 0.14
26 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
AATTATATTTTTAAATGATAATAATT
Found at i:53018 original size:24 final size:24
Alignment explanation
Indices: 52989--53037 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
52979 ATGTATATGA
* * *
52989 ATTTGTATGTAATATTTTTGGTTT
1 ATTTGTATGGAACATTTATGGTTT
53013 ATTTGTATGGAACATTTATGGTTT
1 ATTTGTATGGAACATTTATGGTTT
53037 A
1 A
53038 ATGATATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.02, G:0.18, T:0.55
Consensus pattern (24 bp):
ATTTGTATGGAACATTTATGGTTT
Found at i:55440 original size:18 final size:18
Alignment explanation
Indices: 55406--55452 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
55396 CACATTGCAT
* *
55406 GAAATGAATGTGTTGGAA
1 GAAATGCATGAGTTGGAA
* *
55424 GAAGTGCATGAGTTGGAT
1 GAAATGCATGAGTTGGAA
55442 GAAATGCATGA
1 GAAATGCATGA
55453 AATAATGCAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.34, T:0.26
Consensus pattern (18 bp):
GAAATGCATGAGTTGGAA
Found at i:56236 original size:21 final size:22
Alignment explanation
Indices: 56206--56257 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
56196 AGCTCAATTC
56206 AAAATTTAATTTAAT-AAAAAT
1 AAAATTTAATTTAATAAAAAAT
*
56227 AAAATATAA-TTAATAAAAAAT
1 AAAATTTAATTTAATAAAAAAT
56248 AAAATTTAAT
1 AAAATTTAAT
56258 AAAATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAATTTAATTTAATAAAAAAT
Found at i:56246 original size:16 final size:17
Alignment explanation
Indices: 56213--56261 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 17
56203 TTCAAAATTT
56213 AATTTAAT-AAAAATAAA
1 AATTTAATAAAAAAT-AA
56230 ATATAATTAATAAAAAATAA
1 A-AT--TTAATAAAAAATAA
56250 AATTTAATAAAA
1 AATTTAATAAAA
56262 TATTTATTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 10 0.36
18 2 0.07
19 2 0.07
20 8 0.29
21 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTTAATAAAAAATAA
Found at i:56330 original size:14 final size:14
Alignment explanation
Indices: 56307--56341 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
56297 CATTTCATTG
* *
56307 AAAATAATTTCTGT
1 AAAATGATTTCTAT
56321 AAAATGATTTCTAT
1 AAAATGATTTCTAT
56335 AAAATGA
1 AAAATGA
56342 CTTGATTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCTAT
Found at i:63642 original size:12 final size:11
Alignment explanation
Indices: 63625--63651 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
63615 TCCATAATTT
63625 AAAAAAAAAAG
1 AAAAAAAAAAG
63636 AAAAAAAAAAG
1 AAAAAAAAAAG
63647 AAAAA
1 AAAAA
63652 TATTTTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:68884 original size:17 final size:17
Alignment explanation
Indices: 68853--68886 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
68843 ATCATTCGCT
**
68853 ATTTCAATAGTATTTTC
1 ATTTCAATAACATTTTC
68870 ATTTCAATAACATTTTC
1 ATTTCAATAACATTTTC
68887 CATATAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTTCAATAACATTTTC
Found at i:69987 original size:14 final size:14
Alignment explanation
Indices: 69965--70022 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
69955 TATTTTTTAC
69965 TTATAATATATTAT
1 TTATAATATATTAT
*
69979 TTATCATATATTA-
1 TTATAATATATTAT
** *
69992 ACACTAATATAATAT
1 TTA-TAATATATTAT
70007 TTATAATATATATAT
1 TTATAATATAT-TAT
70022 T
1 T
70023 ACTTTGACTG
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
13 1 0.03
14 27 0.82
15 5 0.15
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (14 bp):
TTATAATATATTAT
Found at i:70294 original size:22 final size:21
Alignment explanation
Indices: 70268--70317 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
70258 GTGGGTCAAA
70268 GGTGGCCGATGACGGAGTCGAC
1 GGTGGCCGA-GACGGAGTCGAC
* **
70290 GGTGGTCGGAGGTGGAGTCGAC
1 GGTGG-CCGAGACGGAGTCGAC
70312 GGTGGC
1 GGTGGC
70318 TCCCATGGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 20 0.83
23 3 0.12
ACGTcount: A:0.14, C:0.18, G:0.52, T:0.16
Consensus pattern (21 bp):
GGTGGCCGAGACGGAGTCGAC
Found at i:70836 original size:60 final size:60
Alignment explanation
Indices: 70772--71005 Score: 219
Period size: 60 Copynumber: 3.9 Consensus size: 60
70762 ATCTCCAAAC
*
70772 TTTCTAAAAATGTCATTTTGACCCCTAAACTTTTT-GAAAATGTCATTTTGACCCTTGAAT
1 TTTCTAAAAATGTCATTTTGACCCCTAAACTTTTTAGAAAATGT-ATTTTGACCCTTGAAA
* * * * * *
70832 TTTCTAGAAATGTCATTTTAACCCCTTAACTTTTTAAAAAATATATTTTGACCATTGAAA
1 TTTCTAAAAATGTCATTTTGACCCCTAAACTTTTTAGAAAATGTATTTTGACCCTTGAAA
* * * *
70892 TTTCT-AAAATTTCATTTTTGACCCCTAAACTTTCTTA-AAATTATATTTTGACCCCT-AAA
1 TTTCTAAAAATGTCA-TTTTGACCCCTAAACTTT-TTAGAAAATGTATTTTGACCCTTGAAA
* * * * * *
70951 CTTTCTTAAAAT-TATATTTTGA-CCCTCGAACTTTTTGGAAATTGTATTTTAACCC
1 -TTTCTAAAAATGT-CATTTTGACCCCT-AAACTTTTTAGAAAATGTATTTTGACCC
71006 CAAAACTTTC
Statistics
Matches: 147, Mismatches: 19, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
59 16 0.11
60 116 0.79
61 15 0.10
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (60 bp):
TTTCTAAAAATGTCATTTTGACCCCTAAACTTTTTAGAAAATGTATTTTGACCCTTGAAA
Found at i:70983 original size:30 final size:30
Alignment explanation
Indices: 70747--71037 Score: 187
Period size: 30 Copynumber: 9.7 Consensus size: 30
70737 TGTTTTGTTC
*
70747 TAAAATTATATTTTGATCTCC-AAACTTTCT
1 TAAAATTATATTTTGA-CCCCTAAACTTTCT
* *
70777 AAAAATGT-CATTTTGACCCCTAAACTTT-T
1 TAAAAT-TATATTTTGACCCCTAAACTTTCT
* * * *
70806 TGAAAATGT-CATTTTGACCCTTGAATTTTC-
1 T-AAAAT-TATATTTTGACCCCTAAACTTTCT
* * *
70836 TAGAAATGT-CATTTTAACCCCTTAACTTT-T
1 TA-AAAT-TATATTTTGACCCCTAAACTTTCT
* **
70866 TAAAAAATATATTTTGACCATTGAAA-TTTC-
1 T-AAAATTATATTTTGACCCCT-AAACTTTCT
70896 TAAAATT-TCATTTTTGACCCCTAAACTTTCT
1 TAAAATTAT-A-TTTTGACCCCTAAACTTTCT
70927 TAAAATTATATTTTGACCCCTAAACTTTCT
1 TAAAATTATATTTTGACCCCTAAACTTTCT
*
70957 TAAAATTATATTTTGA-CCCTCGAACTTT-T
1 TAAAATTATATTTTGACCCCT-AAACTTTCT
* * * *
70986 TGGAAATTGTATTTTAACCCCAAAACTTTC-
1 T-AAAATTATATTTTGACCCCTAAACTTTCT
* *
71016 CAAAATTTTGATTTT-ACCCCTA
1 TAAAATTAT-ATTTTGACCCCTA
71038 TTTTCCTTAT
Statistics
Matches: 211, Mismatches: 30, Indels: 41
0.75 0.11 0.15
Matches are distributed among these distances:
28 1 0.00
29 33 0.16
30 161 0.76
31 15 0.07
32 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.42
Consensus pattern (30 bp):
TAAAATTATATTTTGACCCCTAAACTTTCT
Found at i:71006 original size:90 final size:89
Alignment explanation
Indices: 70744--71037 Score: 253
Period size: 90 Copynumber: 3.3 Consensus size: 89
70734 CCTTGTTTTG
* * * *
70744 TTCTAAAATTATATTTTGATCTCC-AAACTTTCTAAAAATGT-CATTTTGACCC-CTAAACTTTT
1 TTCTAAAATTATATTTTGA-CCCCTAAACTTTCTTAAAAT-TATATTTTGACCCTC-GAACTTTT
* * * *
70806 TGAAAATGTCATTTTGACCCTTGAATT
63 TGAAATTGTCATTTTGACCCCTAAACT
* * * * * * * *
70833 TTCTAGAAATGT-CATTTTAACCCCTTAACTTT-TTAAAAAATATATTTTGACCATTGAAATTTC
1 TTCTA-AAAT-TATATTTTGACCCCTAAACTTTCTT-AAAATTATATTTTGACCCTCGAACTTTT
*
70896 TAAAATT-TCATTTTTGACCCCTAAACT
63 TGAAATTGTCA-TTTTGACCCCTAAACT
70923 TTCTTAAAATTATATTTTGACCCCTAAACTTTCTTAAAATTATATTTTGACCCTCGAACTTTTTG
1 TTC-TAAAATTATATTTTGACCCCTAAACTTTCTTAAAATTATATTTTGACCCTCGAACTTTTT-
* *
70988 GAAATTGT-ATTTTAACCCCAAAACT
64 GAAATTGTCATTTTGACCCCTAAACT
* *
71013 TTCCAAAATTTTGATTTT-ACCCCTA
1 TTCTAAAATTAT-ATTTTGACCCCTA
71038 TTTTCCTTAT
Statistics
Matches: 162, Mismatches: 30, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
89 28 0.17
90 122 0.75
91 11 0.07
92 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.43
Consensus pattern (89 bp):
TTCTAAAATTATATTTTGACCCCTAAACTTTCTTAAAATTATATTTTGACCCTCGAACTTTTTGA
AATTGTCATTTTGACCCCTAAACT
Found at i:72615 original size:2 final size:2
Alignment explanation
Indices: 72608--72636 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
72598 AAATTTTCAT
72608 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
72637 TAATTTAATA
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
Done.