Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013312.1 Kokia drynarioides strain JFW-HI SEQ_128334, 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: 100858
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 135 characters in sequence are not A, C, G, or T
Found at i:2418 original size:18 final size:18
Alignment explanation
Indices: 2395--2431 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2385 TTTGTGATCA
2395 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
2413 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
2431 A
1 A
2432 TATGAATTGT
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:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:4879 original size:24 final size:26
Alignment explanation
Indices: 4851--4899 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
4841 AGCACAATTT
*
4851 ACTTTTATAT-TT-TGTTTTCTTTTA
1 ACTTTTAAATCTTATGTTTTCTTTTA
*
4875 ACTTTTAAATCTTATGTTTTTTTTT
1 ACTTTTAAATCTTATGTTTTCTTTT
4900 TCTTTCCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 2 0.10
26 10 0.48
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.69
Consensus pattern (26 bp):
ACTTTTAAATCTTATGTTTTCTTTTA
Found at i:4955 original size:2 final size:2
Alignment explanation
Indices: 4950--4974 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4940 TTCAGAGATC
4950 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 T
4975 GTTTTGAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8837 original size:41 final size:42
Alignment explanation
Indices: 8780--8863 Score: 161
Period size: 41 Copynumber: 2.0 Consensus size: 42
8770 AACTAATAAA
8780 TAGTATGTAATTAGATAAATGCAGGGCGAAGCTGGAA-TTTT
1 TAGTATGTAATTAGATAAATGCAGGGCGAAGCTGGAACTTTT
8821 TAGTATGTAATTAGATAAATGCAGGGCGAAGCTGGAACTTTT
1 TAGTATGTAATTAGATAAATGCAGGGCGAAGCTGGAACTTTT
8863 T
1 T
8864 TTTTTTTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 37 0.88
42 5 0.12
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.32
Consensus pattern (42 bp):
TAGTATGTAATTAGATAAATGCAGGGCGAAGCTGGAACTTTT
Found at i:9051 original size:18 final size:19
Alignment explanation
Indices: 9028--9065 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
9018 ATTAAACAAC
*
9028 TTAAAA-CGAATTTTAAAA
1 TTAAAATCGAATTTGAAAA
*
9046 TTAAAATCGGATTTGAAAA
1 TTAAAATCGAATTTGAAAA
9065 T
1 T
9066 AATTGAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (19 bp):
TTAAAATCGAATTTGAAAA
Found at i:12641 original size:18 final size:18
Alignment explanation
Indices: 12612--12663 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
12602 TTATTATGGA
* **
12612 GAACTGTGTTAATTTGGT
1 GAACTGTATTAATTTGAC
* *
12630 GATCTGTATTAATATGAC
1 GAACTGTATTAATTTGAC
12648 GAACTGTATTAATTTG
1 GAACTGTATTAATTTG
12664 CCAAACAGTG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (18 bp):
GAACTGTATTAATTTGAC
Found at i:13622 original size:15 final size:15
Alignment explanation
Indices: 13602--13631 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
13592 TGATGATTGT
13602 TGGGATTTAGAATTA
1 TGGGATTTAGAATTA
13617 TGGGATTTAGAATTA
1 TGGGATTTAGAATTA
13632 GCACTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.40
Consensus pattern (15 bp):
TGGGATTTAGAATTA
Found at i:21380 original size:24 final size:25
Alignment explanation
Indices: 21353--21403 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
21343 ATCATAAATT
*
21353 TTTTATAAATATTT-TAATTATTTA
1 TTTTATAAATATTTAAAATTATTTA
*
21377 TTTTATAATTATTTAAAATTATTTA
1 TTTTATAAATATTTAAAATTATTTA
21402 TT
1 TT
21404 ACATTGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTATAAATATTTAAAATTATTTA
Found at i:23519 original size:24 final size:24
Alignment explanation
Indices: 23492--23543 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
23482 TTCGTAGGTG
* *
23492 AAATAAATTATATTAATATATATT
1 AAATAAATTATACTAATAAATATT
*
23516 AAATATATTATACTAATAAATATT
1 AAATAAATTATACTAATAAATATT
23540 AAAT
1 AAAT
23544 TTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATATT
Found at i:27638 original size:25 final size:26
Alignment explanation
Indices: 27610--27663 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
27600 TGTATCATCA
27610 TATTTTTATAAAT-ATTT-TAATTATT
1 TATTTTTAT-AATCATTTATAATTATT
27635 TA-TTTTATAATCATTTATAATTATT
1 TATTTTTATAATCATTTATAATTATT
27660 TATT
1 TATT
27664 ATATTAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.12
24 10 0.38
25 12 0.46
26 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (26 bp):
TATTTTTATAATCATTTATAATTATT
Found at i:29993 original size:64 final size:64
Alignment explanation
Indices: 29892--30020 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
29882 AAAAGAAAAG
29892 AAAGGTGGAGTTGTAATCCTCCATTGAAAAAGTAAGCTTAACATCCAATCATTTATCATAGTAT
1 AAAGGTGGAGTTGTAATCCTCCATTGAAAAAGTAAGCTTAACATCCAATCATTTATCATAGTAT
29956 AAAGGTGGAGTTGTAATCCTCCATTGAAAAAGTAAGCTTAACATCCAATCATTTATCATAGTAT
1 AAAGGTGGAGTTGTAATCCTCCATTGAAAAAGTAAGCTTAACATCCAATCATTTATCATAGTAT
30020 A
1 A
30021 TAATGTTTTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (64 bp):
AAAGGTGGAGTTGTAATCCTCCATTGAAAAAGTAAGCTTAACATCCAATCATTTATCATAGTAT
Found at i:32174 original size:18 final size:18
Alignment explanation
Indices: 32134--32185 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
32124 TTTTCAGTTG
*
32134 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
*
32152 CAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
32170 TAATTAA--AAATTTATT
1 TAATTAATTAAATTTATT
32186 CTCATTCTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:34242 original size:22 final size:19
Alignment explanation
Indices: 34202--34244 Score: 50
Period size: 22 Copynumber: 2.1 Consensus size: 19
34192 ATTTTATAAA
*
34202 ATTATTACAAAATTTATAT
1 ATTATTACAAAATTCATAT
34221 ATTATTATCAATACATTCATAT
1 ATTATTA-CAA-A-ATTCATAT
34243 AT
1 AT
34245 ATATGTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 7 0.35
20 3 0.15
21 1 0.05
22 9 0.45
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTATTACAAAATTCATAT
Found at i:34488 original size:26 final size:28
Alignment explanation
Indices: 34446--34513 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 28
34436 TTAAAAATAT
*
34446 TTATATTATAT-TATTTTAATTT-TT-AA
1 TTATTTTATATAT-TTTTAATTTATTGAA
*
34472 TTATTTTATATATTTTTTATTTATTGAA
1 TTATTTTATATATTTTTAATTTATTGAA
*
34500 -AATTTTATATATTT
1 TTATTTTATATATTT
34514 ATTTTAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 18 0.50
27 16 0.44
28 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (28 bp):
TTATTTTATATATTTTTAATTTATTGAA
Found at i:34523 original size:12 final size:12
Alignment explanation
Indices: 34447--34529 Score: 52
Period size: 11 Copynumber: 6.9 Consensus size: 12
34437 TAAAAATATT
*
34447 TATATTATATTA
1 TATATTATTTTA
34459 T-T-TTAATTTT-
1 TATATT-ATTTTA
34469 TA-ATTATTTTA
1 TATATTATTTTA
34480 TATATT-TTTTA
1 TATATTATTTTA
*
34491 TTTATTGAAAATTTTA
1 TATATT----ATTTTA
34507 TATATTTATTTTA
1 TATA-TTATTTTA
34520 -ATATTATTTT
1 TATATTATTTT
34530 TATGTTTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 23
0.69 0.04 0.28
Matches are distributed among these distances:
10 8 0.14
11 26 0.46
12 7 0.12
13 6 0.11
16 8 0.14
17 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (12 bp):
TATATTATTTTA
Found at i:35463 original size:75 final size:75
Alignment explanation
Indices: 35374--35523 Score: 273
Period size: 75 Copynumber: 2.0 Consensus size: 75
35364 TTTAATAATT
*
35374 ATTAGAATTTTGATAGTTAAAAGTAAACGGTATAATTTAGTAATTAAAATTTAAAAAATAAGCTT
1 ATTAGAATTTTGATAGTTAAAAGTAAACGGTATAATTTAATAATTAAAATTTAAAAAATAAGCTT
35439 TATCTTTTAA
66 TATCTTTTAA
* *
35449 ATTAGAATTTTGATAGTTAAAAGTAATCGGTATAATTTAATAATTAAATTTTAAAAAATAAGCTT
1 ATTAGAATTTTGATAGTTAAAAGTAAACGGTATAATTTAATAATTAAAATTTAAAAAATAAGCTT
35514 TATCTTTTAA
66 TATCTTTTAA
35524 TTTTAAAATT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (75 bp):
ATTAGAATTTTGATAGTTAAAAGTAAACGGTATAATTTAATAATTAAAATTTAAAAAATAAGCTT
TATCTTTTAA
Found at i:36226 original size:6 final size:6
Alignment explanation
Indices: 36217--36276 Score: 77
Period size: 6 Copynumber: 10.2 Consensus size: 6
36207 GATTTATTTC
* * **
36217 TAAATT TAAATT T-ACTT TAAATT TAAATT TAAATT CATTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
36264 TAAATT TAAATT T
1 TAAATT TAAATT T
36277 TTAAAATTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
5 4 0.09
6 41 0.91
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (6 bp):
TAAATT
Found at i:36239 original size:17 final size:18
Alignment explanation
Indices: 36203--36247 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
36193 TTTAAATTAT
* *
36203 TTTAGATTTATTTCTAAA
1 TTTAAATTTACTTCTAAA
36221 TTTAAATTTACTT-TAAA
1 TTTAAATTTACTTCTAAA
36238 TTTAAATTTA
1 TTTAAATTTA
36248 AATTCATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTAAATTTACTTCTAAA
Found at i:36261 original size:18 final size:20
Alignment explanation
Indices: 36221--36288 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 20
36211 TATTTCTAAA
*
36221 TTTAAATTT-ACTTTAAA--
1 TTTAAATTTAAATTTAAATT
*
36238 TTTAAATTTAAA-TT-CATT
1 TTTAAATTTAAATTTAAATT
36256 TTTAAATTTAAATTTAAATT
1 TTTAAATTTAAATTTAAATT
36276 TTTAAAATTTAAA
1 TTT-AAATTTAAA
36289 GTTAGTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
16 1 0.02
17 11 0.26
18 13 0.31
19 2 0.05
20 6 0.14
21 9 0.21
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAAATTTAAATTTAAATT
Found at i:36264 original size:24 final size:23
Alignment explanation
Indices: 36217--36275 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 23
36207 GATTTATTTC
*
36217 TAAATTTAAATTTACTTTAAATT
1 TAAATTTAAATTCACTTTAAATT
*
36240 TAAATTTAAATTCATTTTTAAATT
1 TAAATTTAAATTCA-CTTTAAATT
36264 TAAATTTAAATT
1 TAAATTTAAATT
36276 TTTAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
23 13 0.39
24 20 0.61
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAATTTAAATTCACTTTAAATT
Found at i:38256 original size:29 final size:29
Alignment explanation
Indices: 38216--38463 Score: 159
Period size: 29 Copynumber: 8.4 Consensus size: 29
38206 AACTTTTTTG
**
38216 AAAATTACATTTTTATTCCCGAACTTCCA
1 AAAATTACATTTTTAACCCCGAACTTCCA
* *
38245 AAAATTATA-TTTTAACCCCAAAACTTCCA
1 AAAATTACATTTTTAACCCC-GAACTTCCA
*
38274 AAAATTACATTTTTACCCCCGAACTTCCA
1 AAAATTACATTTTTAACCCCGAACTTCCA
** * * * *
38303 AAAATTTTATTCTTGACCTCGAAACTTTCA
1 AAAATTACATTTTTAACCCCG-AACTTCCA
* *
38333 AAAATCACCA-TTTT-ACCCCAAACTTCC-
1 AAAATTA-CATTTTTAACCCCGAACTTCCA
* * *
38360 AAAATTTCATTTTTGACCCCGAAACTTTCA
1 AAAATTACATTTTTAACCCCG-AACTTCCA
*
38390 AAAATTACCA-TTTT-ACCCCTAGA-TGTCCA
1 AAAATTA-CATTTTTAACCCCGA-ACT-TCCA
* * * * *
38419 AAAACTCCATTTTTTGACCCTGAAACTTTCA
1 AAAATTACA-TTTTTAACCCCG-AACTTCCA
38450 AAAATTACCATTTT
1 AAAATTA-CATTTT
38464 ACCCTTGAAT
Statistics
Matches: 167, Mismatches: 35, Indels: 32
0.71 0.15 0.14
Matches are distributed among these distances:
26 2 0.01
27 9 0.05
28 23 0.14
29 71 0.43
30 38 0.23
31 20 0.12
32 4 0.02
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAATTACATTTTTAACCCCGAACTTCCA
Found at i:38296 original size:58 final size:58
Alignment explanation
Indices: 38216--38484 Score: 264
Period size: 58 Copynumber: 4.6 Consensus size: 58
38206 AACTTTTTTG
** * * *
38216 AAAATTA-CATTTTTATTCCCGAACTTCCAAAAATTATATTTTAACCCCAAAACTTCCA
1 AAAATTACCA-TTTTACCCCCGAACTTCCAAAAATTATATTTTGACCCCGAAACTTTCA
* *
38274 AAAATTA-CATTTTTACCCCCGAACTTCCAAAAATTTTATTCTTGACCTCGAAACTTTCA
1 AAAATTACCA-TTTTACCCCCGAACTTCCAAAAATTATATT-TTGACCCCGAAACTTTCA
* * *
38333 AAAATCACCATTTTA-CCCCAAACTTCCAAAATTTCAT-TTTTGACCCCGAAACTTTCA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATT-ATATTTTGACCCCGAAACTTTCA
* * * *
38390 AAAATTACCATTTTA-CCCCTAGA-TGTCCAAAAACTCCATTTTTTGACCCTGAAACTTTCA
1 AAAATTACCATTTTACCCCCGA-ACT-TCCAAAAA-T-TATATTTTGACCCCGAAACTTTCA
**
38450 AAAATTACCATTTTACCCTTGAA-TATCCAAAAATT
1 AAAATTACCATTTTACCCCCGAACT-TCCAAAAATT
38485 CCGTTTTTGA
Statistics
Matches: 180, Mismatches: 22, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
57 37 0.21
58 64 0.36
59 30 0.17
60 46 0.26
61 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAACTTCCAAAAATTATATTTTGACCCCGAAACTTTCA
Found at i:38451 original size:60 final size:57
Alignment explanation
Indices: 38265--38467 Score: 214
Period size: 57 Copynumber: 3.5 Consensus size: 57
38255 TTTAACCCCA
* * * ** *
38265 AAACTTCCAAAAATTA-CATTTTTACCCCCGAACTTCCAAAAATTTTATTCTTGA-CCTCG
1 AAACTTTCAAAAATTACCA-TTTTA-CCCCAAACTTCC-AAAACTCCATTTTTGACCCT-G
* * * *
38324 AAACTTTCAAAAATCACCATTTTACCCCAAACTTCCAAAATTTCATTTTTGACCCCG
1 AAACTTTCAAAAATTACCATTTTACCCCAAACTTCCAAAACTCCATTTTTGACCCTG
*
38381 AAACTTTCAAAAATTACCATTTTACCCCTAGA-TGTCCAAAAACTCCATTTTTTGACCCTG
1 AAACTTTCAAAAATTACCATTTTACCCC-AAACT-TCC-AAAACTCCA-TTTTTGACCCTG
38441 AAACTTTCAAAAATTACCATTTTACCC
1 AAACTTTCAAAAATTACCATTTTACCC
38468 TTGAATATCC
Statistics
Matches: 127, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
57 43 0.34
58 18 0.14
59 26 0.20
60 40 0.31
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (57 bp):
AAACTTTCAAAAATTACCATTTTACCCCAAACTTCCAAAACTCCATTTTTGACCCTG
Found at i:38479 original size:60 final size:57
Alignment explanation
Indices: 38240--38492 Score: 205
Period size: 60 Copynumber: 4.3 Consensus size: 57
38230 ATTCCCGAAC
* * ** * *
38240 TTCCAAAAATT--ATATTTTAACCCCAAAACTTCCAAAAATTA-CATTTTTACCCCCGAA
1 TTCCAAAAATTCCATTTTTTGACCCTGAAACTTTCAAAAATTACCA-TTTTA--CCCTAA
** * * *
38297 CTTCCAAAAATTTTA-TTCTTGA-CCTCGAAACTTTCAAAAATCACCATTTTACCCCAAA
1 -TTCCAAAAATTCCATTTTTTGACCCT-GAAACTTTCAAAAATTACCATTTTA-CCCTAA
* *
38355 CTTCC-AAAATTTCA-TTTTTGACCCCGAAACTTTCAAAAATTACCATTTTACCCCTAGA
1 -TTCCAAAAATTCCATTTTTTGACCCTGAAACTTTCAAAAATTACCATTTTA-CCCTA-A
*
38413 TGTCCAAAAACTCCATTTTTTGACCCTGAAACTTTCAAAAATTACCATTTTACCCTTGAA
1 T-TCCAAAAATTCCATTTTTTGACCCTGAAACTTTCAAAAATTACCATTTTACCC-T-AA
*
38473 TATCCAAAAATTCCGTTTTT
1 T-TCCAAAAATTCCATTTTT
38493 GATCTCGATT
Statistics
Matches: 165, Mismatches: 19, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
57 44 0.27
58 30 0.18
59 33 0.20
60 57 0.35
61 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (57 bp):
TTCCAAAAATTCCATTTTTTGACCCTGAAACTTTCAAAAATTACCATTTTACCCTAA
Found at i:38480 original size:29 final size:28
Alignment explanation
Indices: 38388--38484 Score: 74
Period size: 29 Copynumber: 3.3 Consensus size: 28
38378 CCGAAACTTT
*
38388 CAAAAATTACCATTTTACCCCT-AGATGTC
1 CAAAAATTACCATTTTA-CCCTGA-ATATC
* *
38417 CAAAAACT-CCATTTTTTGACCCTGAA-ACTTT
1 CAAAAATTACCA--TTTT-ACCCTGAATA--TC
38448 CAAAAATTACCATTTTACCCTTGAATATC
1 CAAAAATTACCATTTTACCC-TGAATATC
38477 CAAAAATT
1 CAAAAATT
38485 CCGTTTTTGA
Statistics
Matches: 54, Mismatches: 5, Indels: 18
0.70 0.06 0.23
Matches are distributed among these distances:
28 3 0.06
29 20 0.37
30 17 0.31
31 11 0.20
32 3 0.06
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (28 bp):
CAAAAATTACCATTTTACCCTGAATATC
Found at i:42996 original size:21 final size:21
Alignment explanation
Indices: 42972--43018 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
42962 TCCTTTTGAA
* * *
42972 TTTTTGGTATTTACTCATATT
1 TTTTTGCTATTCACTCATAAT
*
42993 TTTTTGCTATTCCCTCATAAT
1 TTTTTGCTATTCACTCATAAT
43014 TTTTT
1 TTTTT
43019 ATACTTATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.17, C:0.15, G:0.06, T:0.62
Consensus pattern (21 bp):
TTTTTGCTATTCACTCATAAT
Found at i:46580 original size:6 final size:6
Alignment explanation
Indices: 46569--46599 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
46559 TGTTCATTCT
*
46569 CGTTCC CGTTCC CGTTCC CGTTCC TGTTCC C
1 CGTTCC CGTTCC CGTTCC CGTTCC CGTTCC C
46600 TTACCTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.16, T:0.35
Consensus pattern (6 bp):
CGTTCC
Found at i:50348 original size:15 final size:15
Alignment explanation
Indices: 50333--50371 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
50323 TATAACCTTA
*
50333 AAATTTTAAACT-TT
1 AAATTTTAAAATATT
*
50347 AAATTCTAAAATATT
1 AAATTTTAAAATATT
50362 AAATTTTAAA
1 AAATTTTAAA
50372 TCTTAATTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATTTTAAAATATT
Found at i:50356 original size:22 final size:22
Alignment explanation
Indices: 50331--50372 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
50321 TCTATAACCT
*
50331 TAAAATTTTAAACTTTAAATTC
1 TAAAATATTAAACTTTAAATTC
*
50353 TAAAATATTAAATTTTAAAT
1 TAAAATATTAAACTTTAAAT
50373 CTTAATTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAAATATTAAACTTTAAATTC
Found at i:50448 original size:2 final size:2
Alignment explanation
Indices: 50412--50436 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50402 AACAGTCGTT
50412 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 T
50437 TAACCCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52362 original size:3 final size:3
Alignment explanation
Indices: 52311--52344 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
52301 TTTGTAACCC
52311 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
52345 TCTTAATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:86270 original size:47 final size:47
Alignment explanation
Indices: 86196--86308 Score: 172
Period size: 47 Copynumber: 2.4 Consensus size: 47
86186 AAAGAGGAAG
* * * *
86196 AAGTGGCAGTTTATCTGTAAAACTGGTGGTTTGTCTACAATATTATT
1 AAGTGACAGTTTATCTGCAAAACTGGTGGCTTGTCCACAATATTATT
*
86243 AAGTGACAGTTTATCTGCAAAATTGGTGGCTTGTCCACAATATTATT
1 AAGTGACAGTTTATCTGCAAAACTGGTGGCTTGTCCACAATATTATT
*
86290 AAGTGACAGTTTATTTGCA
1 AAGTGACAGTTTATCTGCA
86309 TTACTGTGAC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 60 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.38
Consensus pattern (47 bp):
AAGTGACAGTTTATCTGCAAAACTGGTGGCTTGTCCACAATATTATT
Found at i:88860 original size:22 final size:24
Alignment explanation
Indices: 88807--88860 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 24
88797 TTAGAAAAAA
88807 TTTATTTCTATTACTTTAGCCATTT
1 TTTATTT-TATTACTTTAGCCATTT
88832 TTT-TTTTATTA-TTT-G-CATTTT
1 TTTATTTTATTACTTTAGCCA-TTT
88853 TTTATTTT
1 TTTATTTT
88861 TTTCCTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 2 0.07
21 7 0.26
22 7 0.26
23 5 0.19
24 3 0.11
25 3 0.11
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTATTTTATTACTTTAGCCATTT
Found at i:89808 original size:28 final size:28
Alignment explanation
Indices: 89777--89834 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
89767 GTAAAACCTG
*
89777 TGAAGGCAACAGGGATTTATGATGTTGA
1 TGAAGGCAACAGGGATTTATGATATTGA
89805 TGAAGGCAACAGGGATTTATGATATTGA
1 TGAAGGCAACAGGGATTTATGATATTGA
89833 TG
1 TG
89835 TTGTTTCTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.07, G:0.31, T:0.29
Consensus pattern (28 bp):
TGAAGGCAACAGGGATTTATGATATTGA
Found at i:93530 original size:25 final size:23
Alignment explanation
Indices: 93489--93535 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
93479 CCAATTAGAA
93489 AATTATTGTTTAGATTTAATTTT
1 AATTATTGTTTAGATTTAATTTT
*
93512 AATTATCTTTTTAGAATTTAATTT
1 AATTAT-TGTTTAG-ATTTAATTT
93536 GGATCCAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 6 0.29
25 9 0.43
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTTT
Found at i:94049 original size:23 final size:23
Alignment explanation
Indices: 94017--94070 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
94007 TGTGGCATCT
* *
94017 AGTCAACAGCTTCTA-AAAGATCC
1 AGTCAGCAGCTTCCAGAAAG-TCC
*
94040 AGTCAGCAGCTTCCAGAAAGTCT
1 AGTCAGCAGCTTCCAGAAAGTCC
94063 AGTCAGCA
1 AGTCAGCA
94071 ATGATGGACG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (23 bp):
AGTCAGCAGCTTCCAGAAAGTCC
Found at i:96969 original size:9 final size:9
Alignment explanation
Indices: 96957--96998 Score: 57
Period size: 9 Copynumber: 4.3 Consensus size: 9
96947 AAAAGGTTCG
96957 AAAAGAAAA
1 AAAAGAAAA
96966 AAAAGAAAA
1 AAAAGAAAA
96975 AAAAGGAAGAA
1 AAAA-GAA-AA
96986 AAGAAGAAAA
1 AA-AAGAAAA
96996 AAA
1 AAA
96999 CATGGTTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 14 0.47
10 7 0.23
11 7 0.23
12 2 0.07
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Done.