Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002008.1 Kokia drynarioides strain JFW-HI SEQ_113871, 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: 62563
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Warning! 114 characters in sequence are not A, C, G, or T
Found at i:5734 original size:2 final size:2
Alignment explanation
Indices: 5727--5751 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5717 ACAACCCCTT
5727 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
5752 CTAGTCTGAT
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:8329 original size:15 final size:15
Alignment explanation
Indices: 8309--8355 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
8299 AGGTGATTTG
8309 TTAAAAAAACATAAA
1 TTAAAAAAACATAAA
*
8324 TT-AAAAAACAAAAAA
1 TTAAAAAAAC-ATAAA
8339 TTAAATAAAACACTAAA
1 TTAAA-AAAACA-TAAA
8356 ATAACTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 7 0.27
15 8 0.31
16 3 0.12
17 8 0.31
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (15 bp):
TTAAAAAAACATAAA
Found at i:17528 original size:33 final size:33
Alignment explanation
Indices: 17471--17533 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
17461 CATAATAATG
* *
17471 AAATGGTAGCAAAACAATGAGAAAACAACAAGA
1 AAATAGTAGCAAAACAATCAGAAAACAACAAGA
*
17504 AAATAGTAGCAAAACAA-CATGAAAATAACA
1 AAATAGTAGCAAAACAATCA-GAAAACAACA
17534 TTTTTTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 1 0.04
33 25 0.96
ACGTcount: A:0.62, C:0.13, G:0.14, T:0.11
Consensus pattern (33 bp):
AAATAGTAGCAAAACAATCAGAAAACAACAAGA
Found at i:18277 original size:11 final size:11
Alignment explanation
Indices: 18277--18328 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
18267 TTATTTTAAA
*
18277 TTTAAATTTGT
1 TTTAAATTTAT
*
18288 TTTAAATTTAAA
1 TTTAAATTT-AT
* *
18300 TTTAAATTAAG
1 TTTAAATTTAT
18311 TTTAAATTTACT
1 TTTAAATTTA-T
18323 TTTAAA
1 TTTAAA
18329 ATTAAAATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 19 0.58
12 14 0.42
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:18282 original size:6 final size:6
Alignment explanation
Indices: 18261--18347 Score: 65
Period size: 6 Copynumber: 15.2 Consensus size: 6
18251 TATTATAAGA
* **
18261 TTAAAT TT-ATT TTAAAT TTAAAT TT-GTT TTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* ** * * *
18306 TTAAGT TTAAAT TTACTT TTAAAA TTAAAA TT-ATT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T
18348 AAAAAAAAGT
Statistics
Matches: 61, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
5 14 0.23
6 47 0.77
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:18297 original size:23 final size:23
Alignment explanation
Indices: 18271--18320 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
18261 TTAAATTTAT
*
18271 TTTAAATTTAAATT-TGTTTTAAA
1 TTTAAATTTAAATTAAG-TTTAAA
18294 TTTAAATTTAAATTAAGTTTAAA
1 TTTAAATTTAAATTAAGTTTAAA
18317 TTTA
1 TTTA
18321 CTTTTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
TTTAAATTTAAATTAAGTTTAAA
Found at i:18320 original size:29 final size:29
Alignment explanation
Indices: 18288--18347 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
18278 TTAAATTTGT
*
18288 TTTAAATTT-AAATTTAAATTAAGTTTAAA
1 TTTAAATTTAAAATTAAAATT-AGTTTAAA
** *
18317 TTTACTTTTAAAATTAAAATTATTTTAAA
1 TTTAAATTTAAAATTAAAATTAGTTTAAA
18346 TT
1 TT
18348 AAAAAAAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (29 bp):
TTTAAATTTAAAATTAAAATTAGTTTAAA
Found at i:18326 original size:23 final size:24
Alignment explanation
Indices: 18271--18333 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
18261 TTAAATTTAT
*
18271 TTTAAATTT-AAATT-TGTTTTAAA
1 TTTAAATTTAAAATTAAG-TTTAAA
18294 TTTAAATTT-AAATTAAGTTTAAA
1 TTTAAATTTAAAATTAAGTTTAAA
**
18317 TTTACTTTTAAAATTAA
1 TTTAAATTTAAAATTAA
18334 AATTATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 27 0.77
24 8 0.23
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (24 bp):
TTTAAATTTAAAATTAAGTTTAAA
Found at i:18352 original size:17 final size:17
Alignment explanation
Indices: 18243--18347 Score: 122
Period size: 17 Copynumber: 6.1 Consensus size: 17
18233 TGAATTCCTT
*
18243 TTTAAATTTATTATAAGA
1 TTTAAATTTATTTTAA-A
18261 -TTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
18277 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
** *
18294 TTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAA
18311 TTTAAATTTACTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
18329 ATTAAAATTATTTTAAA
1 TTTAAATTTATTTTAAA
18346 TT
1 TT
18348 AAAAAAAAGT
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
16 1 0.01
17 60 0.82
18 12 0.16
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:19441 original size:87 final size:89
Alignment explanation
Indices: 19308--19474 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 89
19298 CCCCTAAAGT
* *
19308 TTTCAAAAACTACATTTTGACCCTCGAACTTCACAAAAATTACATTTTT-ACCCTTGAA-CTTCT
1 TTTCAAAAACTACATTTTGACCCTCAAACTTCACAAAAATTACATTTTTAACCCCT-AATCTTCT
*
19371 AAAAAATTACATTTTTAACTCCAAAC
65 -AAAAATTACAATTTTAACTCCAAAC
* * *
19397 TTTCAAAAATTATATTTT-ACCC-CTAAACTTC-CAAAAATTACATTTTTAACCCCTAATTTTCT
1 TTTCAAAAACTACATTTTGACCCTC-AAACTTCACAAAAATTACATTTTTAACCCCTAATCTTCT
19459 AAAAATTACAATTTTA
65 AAAAATTACAATTTTA
19475 CCCCCAGATG
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
87 34 0.49
88 19 0.28
89 16 0.23
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.38
Consensus pattern (89 bp):
TTTCAAAAACTACATTTTGACCCTCAAACTTCACAAAAATTACATTTTTAACCCCTAATCTTCTA
AAAATTACAATTTTAACTCCAAAC
Found at i:19451 original size:30 final size:29
Alignment explanation
Indices: 19291--19502 Score: 162
Period size: 30 Copynumber: 7.2 Consensus size: 29
19281 CAGAAATCAT
* * * *
19291 ATTTTGACCCCTAAAGTTTTCAAAAACTAC
1 ATTTTTACCCCTAAA-CTTCCAAAAATTAC
* *
19321 ATTTTGA-CCCTCGAACTTCACAAAAATTAC
1 ATTTTTACCCCT-AAACTTC-CAAAAATTAC
* * *
19351 ATTTTTACCCTTGAACTTCTAAAAAATTAC
1 ATTTTTACCCCTAAACTTC-CAAAAATTAC
* * *
19381 ATTTTTAACTCC-AAACTTTCAAAAATTAT
1 ATTTTT-ACCCCTAAACTTCCAAAAATTAC
19410 A-TTTTACCCCTAAACTTCCAAAAATTAC
1 ATTTTTACCCCTAAACTTCCAAAAATTAC
** *
19438 ATTTTTAACCCCTAATTTTCTAAAAATTAC
1 ATTTTT-ACCCCTAAACTTCCAAAAATTAC
* * * *
19468 AATTTTACCCCCAGA-TGTCCAAAAATTTC
1 ATTTTTACCCCTAAACT-TCCAAAAATTAC
19497 ATTTTT
1 ATTTTT
19503 GATCTCGAAC
Statistics
Matches: 147, Mismatches: 27, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
27 4 0.03
28 21 0.14
29 40 0.27
30 76 0.52
31 6 0.04
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (29 bp):
ATTTTTACCCCTAAACTTCCAAAAATTAC
Found at i:19492 original size:59 final size:59
Alignment explanation
Indices: 19372--19730 Score: 231
Period size: 57 Copynumber: 6.2 Consensus size: 59
19362 TGAACTTCTA
* * * * * *
19372 AAAAATTACATTTTTAACTCCAAACTTTC-AAAAATTA-TATTTTACCCCTAAACT-TCC
1 AAAAATTACATTTTTAACCCCGAATTTTCTAAAAATTACCATTTTACCCCCAGA-TGTCC
* *
19429 AAAAATTACATTTTTAACCCCTAATTTTCTAAAAATTACAATTTTACCCCCAGATGTCC
1 AAAAATTACATTTTTAACCCCGAATTTTCTAAAAATTACCATTTTACCCCCAGATGTCC
* * * * *
19488 AAAAATTTCATTTTTGATCTCGAACTTTT-TGAAAATTACCATTTTACCCCC-GTATGTCC
1 AAAAATTACATTTTTAACCCCGAA-TTTTCTAAAAATTACCATTTTACCCCCAG-ATGTCC
* * * * * * * *
19547 AAAAA-AAAATTTTTGATCCCGAA-CTTCCAAAAATTACCATTTTACCCCCTGATGTCA
1 AAAAATTACATTTTTAACCCCGAATTTTCTAAAAATTACCATTTTACCCCCAGATGTCC
* * *** * * * **
19604 AAAAATTTCATTTTTGATTTCGTATTTTC-CAAAATTATCATTTTA-CGTCAGATGTCC
1 AAAAATTACATTTTTAACCCCGAATTTTCTAAAAATTACCATTTTACCCCCAGATGTCC
* * * * * * *
19661 AAAAA-TACCATTTTT--CCCCTGAAGTGTC-CAAAATTACCGTTTTACCCCCGGGTATCC
1 AAAAATTA-CATTTTTAACCCC-GAATTTTCTAAAAATTACCATTTTACCCCCAGATGTCC
*
19718 AAAAATTGCATTT
1 AAAAATTACATTT
19731 AATCTCGTTT
Statistics
Matches: 240, Mismatches: 49, Indels: 26
0.76 0.16 0.08
Matches are distributed among these distances:
55 1 0.00
56 22 0.09
57 93 0.39
58 52 0.22
59 68 0.28
60 4 0.02
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (59 bp):
AAAAATTACATTTTTAACCCCGAATTTTCTAAAAATTACCATTTTACCCCCAGATGTCC
Found at i:19501 original size:87 final size:88
Alignment explanation
Indices: 19334--19494 Score: 204
Period size: 87 Copynumber: 1.8 Consensus size: 88
19324 TTGACCCTCG
* * *
19334 AACTTCACAAAAATTACATTTTTACCCTTGAACTTCTAAAAAATTACATTTTTAACTCCAAACTT
1 AACTTCACAAAAATTACATTTTTACCCCTGAACTTCTAAAAAATTACAATTTTAACCCCAAACTT
*
19399 TCAAAAATTATATTTTACCCCTA
66 CCAAAAATTATATTTTACCCCTA
* * *
19422 AACTTC-CAAAAATTACATTTTTAACCCCT-AATTTTCT-AAAAATTACAATTTTACCCCCAGA-
1 AACTTCACAAAAATTACATTTTT-ACCCCTGAA-CTTCTAAAAAATTACAATTTTAACCCCAAAC
19483 TGTCCAAAAATT
64 T-TCCAAAAATT
19495 TCATTTTTGA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
86 1 0.02
87 47 0.75
88 15 0.24
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.36
Consensus pattern (88 bp):
AACTTCACAAAAATTACATTTTTACCCCTGAACTTCTAAAAAATTACAATTTTAACCCCAAACTT
CCAAAAATTATATTTTACCCCTA
Found at i:19502 original size:29 final size:30
Alignment explanation
Indices: 19372--19502 Score: 96
Period size: 29 Copynumber: 4.5 Consensus size: 30
19362 TGAACTTCTA
* *
19372 AAAAATTACATTTTTAACTCCAAACTT-T-C
1 AAAAATTACATTTTTAACCCCCAA-TTGTCC
* * *
19401 AAAAATTATA-TTTT-ACCCCTAAACT-TCC
1 AAAAATTACATTTTTAACCCC-CAATTGTCC
* * *
19429 AAAAATTACATTTTTAACCCCTAATTTTCT
1 AAAAATTACATTTTTAACCCCCAATTGTCC
*
19459 AAAAATTACAATTTT-ACCCCCAGA-TGTCC
1 AAAAATTACATTTTTAACCCCCA-ATTGTCC
*
19488 AAAAATTTCATTTTT
1 AAAAATTACATTTTT
19503 GATCTCGAAC
Statistics
Matches: 83, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
27 6 0.07
28 17 0.20
29 38 0.46
30 22 0.27
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAAATTACATTTTTAACCCCCAATTGTCC
Found at i:19617 original size:58 final size:58
Alignment explanation
Indices: 19312--19621 Score: 210
Period size: 59 Copynumber: 5.3 Consensus size: 58
19302 TAAAGTTTTC
* * *
19312 AAAAACTACA-TTTTGACCCTCGAACTTCACAAAAATTA-CATTTTTA-CCCTTGAACT-TCTA
1 AAAAATTACATTTTTGATCC-CGAACTTC-CAAAAATTACCA-TTTTACCCCCTG-A-TGTC-A
* * * * * *
19372 AAAAATTACATTTTT-AACTCCAAACTTTCAAAAATTA-TATTTTA-CCCCTAAACT-TCC
1 AAAAATTACATTTTTGATC-CCGAACTTCCAAAAATTACCATTTTACCCCCT-GA-TGTCA
* * * * * * * *
19429 AAAAATTACATTTTTAACCCCTAATTTTCTAAAAATTACAATTTTACCCCCAGATGTCC
1 AAAAATTACATTTTTGATCCCGAA-CTTCCAAAAATTACCATTTTACCCCCTGATGTCA
* * ***
19488 AAAAATTTCATTTTTGATCTCGAACTTTTTGAAAATTACCATTTTACCCCC-GTATGTCCA
1 AAAAATTACATTTTTGATCCCGAAC-TTCCAAAAATTACCATTTTACCCCCTG-ATGT-CA
*
19548 AAAAA--AAATTTTTGATCCCGAACTTCCAAAAATTACCATTTTACCCCCTGATGTCA
1 AAAAATTACATTTTTGATCCCGAACTTCCAAAAATTACCATTTTACCCCCTGATGTCA
*
19604 AAAAATTTCATTTTTGAT
1 AAAAATTACATTTTTGAT
19622 TTCGTATTTT
Statistics
Matches: 202, Mismatches: 34, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
56 7 0.03
57 45 0.22
58 53 0.26
59 65 0.32
60 27 0.13
61 5 0.02
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (58 bp):
AAAAATTACATTTTTGATCCCGAACTTCCAAAAATTACCATTTTACCCCCTGATGTCA
Found at i:19664 original size:58 final size:57
Alignment explanation
Indices: 19460--19665 Score: 195
Period size: 58 Copynumber: 3.6 Consensus size: 57
19450 TAATTTTCTA
* **
19460 AAAATTACAATTTTACCCCCAGATGTCC-AAAAATTTCATTTTTGATCTCGAACTTTTTG
1 AAAATTACCATTTTA-CCCCAGATGTCCAAAAAATTTCATTTTTGATCTCG-A-TTTTCC
* ** * **
19519 AAAATTACCATTTTACCCCCGTATGTCCAAAAAA--AAATTTTTGATCCCGAACTTCC
1 AAAATTACCATTTTACCCCAG-ATGTCCAAAAAATTTCATTTTTGATCTCGATTTTCC
* *
19575 AAAAATTACCATTTTACCCCCTGATGT-CAAAAAATTTCATTTTTGATTTCGTATTTTCC
1 -AAAATTACCATTTTA-CCCCAGATGTCCAAAAAATTTCATTTTTGATCTCG-ATTTTCC
* **
19634 AAAATTATCATTTTACGTCAGATGTCCAAAAA
1 AAAATTACCATTTTACCCCAGATGTCCAAAAA
19666 TACCATTTTT
Statistics
Matches: 119, Mismatches: 20, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
56 9 0.08
57 27 0.23
58 53 0.45
59 25 0.21
60 5 0.04
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.36
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCAGATGTCCAAAAAATTTCATTTTTGATCTCGATTTTCC
Found at i:19968 original size:13 final size:13
Alignment explanation
Indices: 19935--19972 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
19925 CATGCCCTAA
19935 CGTGTGGAAACTT
1 CGTGTGGAAACTT
19948 C--G-GGAAACTT
1 CGTGTGGAAACTT
19958 CGTGTGGAAACTT
1 CGTGTGGAAACTT
19971 CG
1 CG
19973 GGAAATCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.41
11 1 0.05
12 1 0.05
13 11 0.50
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (13 bp):
CGTGTGGAAACTT
Found at i:31209 original size:34 final size:34
Alignment explanation
Indices: 31166--31231 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
31156 TTTTAAATAT
* *
31166 GTTTGAATTTATTTTAAATTCAAATTCATTTTGA
1 GTTTGAATTTACTTGAAATTCAAATTCATTTTGA
* *
31200 GTTTGAATTTACTTGAAATTTAAATTTATTTT
1 GTTTGAATTTACTTGAAATTCAAATTCATTTT
31232 AAATTAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.55
Consensus pattern (34 bp):
GTTTGAATTTACTTGAAATTCAAATTCATTTTGA
Found at i:31961 original size:3 final size:3
Alignment explanation
Indices: 31931--32009 Score: 90
Period size: 3 Copynumber: 26.3 Consensus size: 3
31921 TAAACATTGC
* * *
31931 TAA TAT TAA TAA TAT TAA TAA GT-T TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
*
31976 TAA TAA TAA TAA TAA TAA -AA GTAA TAA TAT TAA T
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA T
32010 CATTAAACCA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
2 3 0.05
3 58 0.91
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:33396 original size:29 final size:29
Alignment explanation
Indices: 33261--33530 Score: 151
Period size: 30 Copynumber: 9.3 Consensus size: 29
33251 ACTTAAAAAT
33261 TTTCCAAAATTACATTTTAACCCTCAAAC
1 TTTCCAAAATTACATTTTAACCCTCAAAC
* * *
33290 TTTTCCAAAACTATATTTTAACCCCCAAAC
1 -TTTCCAAAATTACATTTTAACCCTCAAAC
* * *
33320 TTCTCCAAAATTATATTTTGACACCTCGAAC
1 TT-TCCAAAATTACATTTTAAC-CCTCAAAC
* * * * *
33351 ATTACGAAAATTTCATTTTTACCCTTAAAC
1 -TTTCCAAAATTACATTTTAACCCTCAAAC
* *
33381 TTTCCAAAATTCCATTTTGACCCT-AAAC
1 TTTCCAAAATTACATTTTAACCCTCAAAC
* * **
33409 -TTCATGAAAATTACATTTTTACCCTTGAAC
1 TTTC--CAAAATTACATTTTAACCCTCAAAC
* * * * *
33439 CTTCCAAAA--AAATTTTGACCC-C-GAT
1 TTTCCAAAATTACATTTTAACCCTCAAAC
* * *
33464 TTTCCAAAAAATACCATTTTACCCCT-GAAC
1 TTTCC-AAAATTA-CATTTTAACCCTCAAAC
* * **
33494 TTCCCAAAATTCCATTTTAACCCT-AATT
1 TTTCCAAAATTACATTTTAACCCTCAAAC
33522 TTTCCAAAA
1 TTTCCAAAA
33531 GTTGCCATTT
Statistics
Matches: 185, Mismatches: 42, Indels: 28
0.73 0.16 0.11
Matches are distributed among these distances:
25 5 0.03
26 4 0.02
27 13 0.07
28 25 0.14
29 56 0.30
30 57 0.31
31 23 0.12
32 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
TTTCCAAAATTACATTTTAACCCTCAAAC
Found at i:33601 original size:59 final size:58
Alignment explanation
Indices: 33463--33718 Score: 284
Period size: 59 Copynumber: 4.4 Consensus size: 58
33453 TTGACCCCGA
* *
33463 TTTTCCAAAAAATACCATTTTACCCCTGAACTTCCCAAAATTCCA-TTTTAACCCTAAT
1 TTTTCCAAAAATTACCATTTTACCCC-GAACTTCCAAAAATTCCATTTTTAACCCTAAT
* * * ** * * *
33521 TTTTCCAAAAGTTGCCATTTTACTCCCGAAGTTCCAAAAATTTTATTTTTGACCTTGAT
1 TTTTCCAAAAATTACCATTTTAC-CCCGAACTTCCAAAAATTCCATTTTTAACCCTAAT
* * * *
33580 TTTTCCAAAAATTACCATTTTACCCTCGAATTTTCC-AAAATTCCATTTTTGA-CGTCGAT
1 TTTTCCAAAAATTACCATTTTACCC-CGAA-CTTCCAAAAATTCCATTTTTAACCCT-AAT
* * *
33639 GTCTCGAAAAATTACCATTTTACCTCCGAACTTCCAAAAATTCCATTTTTAACCCTAAT
1 TTTTCCAAAAATTACCATTTTACC-CCGAACTTCCAAAAATTCCATTTTTAACCCTAAT
33698 TTTTCCAAAAATTACCATTTT
1 TTTTCCAAAAATTACCATTTT
33719 TCCCTCGAGT
Statistics
Matches: 164, Mismatches: 26, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
58 42 0.26
59 115 0.70
60 7 0.04
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (58 bp):
TTTTCCAAAAATTACCATTTTACCCCGAACTTCCAAAAATTCCATTTTTAACCCTAAT
Found at i:33629 original size:29 final size:29
Alignment explanation
Indices: 33258--33726 Score: 138
Period size: 30 Copynumber: 16.0 Consensus size: 29
33248 TTGACTTAAA
* * *
33258 AATTTTCCAAAATTACATTTTAACCCTCA
1 AATTTTCCAAAATTCCATTTTTACCCTCG
* ** * * *
33287 AACTTTTCCAAAACTATATTTTAACCCCCA
1 AA-TTTTCCAAAATTCCATTTTTACCCTCG
* ** *
33317 AACTTCTCCAAAATTATATTTTGACACCTCG
1 AA-TTTTCCAAAATTCCATTTTTAC-CCTCG
* * * * **
33348 AACATTACGAAAATTTCATTTTTACCCTTA
1 AA-TTTTCCAAAATTCCATTTTTACCCTCG
* *
33378 AACTTTCCAAAATTCCATTTTGACCCT--
1 AATTTTCCAAAATTCCATTTTTACCCTCG
** * * *
33405 AAACTTCATGAAAATTACATTTTTACCCTTG
1 AATTTTC--CAAAATTCCATTTTTACCCTCG
** ** *
33436 AACCTTCCAAAA--AAATTTTGACCC-CG
1 AATTTTCCAAAATTCCATTTTTACCCTCG
*
33462 -ATTTTCCAAAAAATACCA-TTTTACCC-CTG
1 AATTTTCC--AAAATTCCATTTTTACCCTC-G
* * *
33491 AACTTCCCAAAATTCCATTTTAACCCT--
1 AATTTTCCAAAATTCCATTTTTACCCTCG
33518 AATTTTTCCAAAAGTTGCCA-TTTTACTCC-CG
1 AA-TTTTCCAAAA-TT-CCATTTTTAC-CCTCG
* ** *
33549 AA-GTTCCAAAAATTTTATTTTTGA-CCTTG
1 AATTTTCC-AAAATTCCATTTTT-ACCCTCG
*
33578 ATTTTTCCAAAAATTACCA-TTTTACCCTCG
1 AATTTTCC-AAAATT-CCATTTTTACCCTCG
*
33608 AATTTTCCAAAATTCCATTTTTGA-CGTCG
1 AATTTTCCAAAATTCCATTTTT-ACCCTCG
* *
33637 -ATGTCTCGAAAAATTACCA-TTTTA-CCTCCG
1 AAT-TTTC-CAAAATT-CCATTTTTACCCT-CG
*
33667 AA-CTTCCAAAAATTCCATTTTTAACCCT--
1 AATTTTCC-AAAATTCCATTTTT-ACCCTCG
33695 AATTTTTCCAAAAATTACCATTTTT-CCCTCG
1 AA-TTTTCC-AAAATT-CCATTTTTACCCTCG
33726 A
1 A
33727 GTATCGAAAA
Statistics
Matches: 335, Mismatches: 62, Indels: 84
0.70 0.13 0.17
Matches are distributed among these distances:
25 5 0.01
26 1 0.00
27 21 0.06
28 37 0.11
29 108 0.32
30 117 0.35
31 46 0.14
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (29 bp):
AATTTTCCAAAATTCCATTTTTACCCTCG
Found at i:36457 original size:3 final size:3
Alignment explanation
Indices: 36449--36516 Score: 55
Period size: 3 Copynumber: 21.7 Consensus size: 3
36439 TAAAAACAAT
* * * *
36449 TAA TAA TAA TAA CAA TAA TAA TAAA TAA TAG TAA TAAA TAA CAT TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA T-AA TAA TAA TAA
* *
36496 TAAA TAT TAA TAA AAA TAA TA
1 T-AA TAA TAA TAA TAA TAA TA
36517 TAAAGAAAGT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
3 41 0.82
4 9 0.18
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:36483 original size:13 final size:13
Alignment explanation
Indices: 36449--36516 Score: 77
Period size: 13 Copynumber: 5.4 Consensus size: 13
36439 TAAAAACAAT
36449 TAATAATAAT-AA
1 TAATAATAATAAA
*
36461 CAATAATAATAAA
1 TAATAATAATAAA
*
36474 TAATAGTAATAAA
1 TAATAATAATAAA
* *
36487 TAACATTAATAAA
1 TAATAATAATAAA
*
36500 TATTAATAA-AAA
1 TAATAATAATAAA
36512 TAATA
1 TAATA
36517 TAAAGAAAGT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
12 16 0.35
13 30 0.65
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:38804 original size:24 final size:22
Alignment explanation
Indices: 38772--38817 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
38762 CCCGATCTGA
*
38772 ATTTATAATAATTATTTTATTTTT
1 ATTTATAAT-ACTATTTT-TTTTT
*
38796 ATTTTTAATACTATTTTTTTTT
1 ATTTATAATACTATTTTTTTTT
38818 GCTTGTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 7 0.35
24 8 0.40
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
ATTTATAATACTATTTTTTTTT
Found at i:44767 original size:12 final size:12
Alignment explanation
Indices: 44750--44775 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44740 AATTTGTTTG
44750 TTGTTTTAATAT
1 TTGTTTTAATAT
44762 TTGTTTTAATAT
1 TTGTTTTAATAT
44774 TT
1 TT
44776 TTAAGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:50752 original size:2 final size:2
Alignment explanation
Indices: 50745--50777 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
50735 ATTTTGATAA
50745 AT AT AT AT AT AT AT AT AT AT GAT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
50778 TTATTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52266 original size:183 final size:181
Alignment explanation
Indices: 51926--52480 Score: 799
Period size: 183 Copynumber: 3.0 Consensus size: 181
51916 GCCTTCTGAG
* * * * * *
51926 ACTGAGGATCATTCGGCAGAGGTCTTAAACCATGAACTAGGCCAAACCACTGCAACTACAACCCC
1 ACTGAGTATCATTTGGCAGACGTCCTGAACCATGAACTAGGTCAAACCACTGCAACTACAACCCC
* * * * *
51991 CGGCTTCGACAAGGAGCCCATACCAACC-ACCAACAGAACTTCCCAAGGTATAGCAAGATACAAG
66 CAGCATC-ACAAGGAGCACATACCAACCAACC-ACAGCACTTCCCAAGATATAGCAAGATACAAG
* *
52055 ACGAAGAGGCCTAGACTGAGTTCAAGTTTAGAATTGACTCTGAAACCAACTACA
129 AAGAAAAGGCCTAGACTGAG-TCAAGTTTAGAATTGACTCTGAAACCAACTACA
** * *
52109 ACTGAGTATCATTTTTCAGACGTCCTGAACCATGAACTAGGTCGAACCACTGCAACTACAATCCC
1 ACTGAGTATCATTTGGCAGACGTCCTGAACCATGAACTAGGTCAAACCACTGCAACTACAACCCC
52174 CAGCATCACCAAGGAGCACATACCAACCAACCACAGCACTTCCCAAGATATAGCAAGATACAAGA
66 CAGCATCA-CAAGGAGCACATACCAACCAACCACAGCACTTCCCAAGATATAGCAAGATACAAGA
*
52239 AGAAAAGGCCTAGCCTGAGTACAAGTTTAGAATTGACTCTGAAACCAACTACA
130 AGAAAAGGCCTAGACTGAGT-CAAGTTTAGAATTGACTCTGAAACCAACTACA
* * * *
52292 GCTGAGTATCATTTGGCAGATGTCCTGAACCATGAACTAGATCAAATCACTGCAACTACAACCCC
1 ACTGAGTATCATTTGGCAGACGTCCTGAACCATGAACTAGGTCAAACCACTGCAACTACAACCCC
52357 CAGCATCAACAAGGAGCACATACCAACCAACCACAGCACTTCCCAAGATATAGCAAGATACAAGA
66 CAGCATC-ACAAGGAGCACATACCAACCAACCACAGCACTTCCCAAGATATAGCAAGATACAAGA
* * *
52422 CA-AAAGGGCCTAGACTGAGTCTGAGTTTAGAATTGACTCTGAAACCAGCTACA
130 -AGAAAAGGCCTAGACTGAGTC-AAGTTTAGAATTGACTCTGAAACCAACTACA
52475 ACTGAG
1 ACTGAG
52481 GGTATGACAG
Statistics
Matches: 335, Mismatches: 31, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
182 3 0.01
183 327 0.98
184 5 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (181 bp):
ACTGAGTATCATTTGGCAGACGTCCTGAACCATGAACTAGGTCAAACCACTGCAACTACAACCCC
CAGCATCACAAGGAGCACATACCAACCAACCACAGCACTTCCCAAGATATAGCAAGATACAAGAA
GAAAAGGCCTAGACTGAGTCAAGTTTAGAATTGACTCTGAAACCAACTACA
Done.