Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014945.1 Kokia drynarioides strain JFW-HI SEQ_129988, 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: 243659
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 304 characters in sequence are not A, C, G, or T
Found at i:44 original size:7 final size:7
Alignment explanation
Indices: 19--90 Score: 56
Period size: 7 Copynumber: 10.3 Consensus size: 7
9 TGGACCCTAG
*
19 ACCCTAA
1 ACCCCAA
*
26 ACCCTAA
1 ACCCCAA
33 A-CCCAA
1 ACCCCAA
39 ACCCCAA
1 ACCCCAA
*
46 GCCCCAA
1 ACCCCAA
* *
53 GCCACAA
1 ACCCCAA
*
60 ACCCATAA
1 ACCC-CAA
* *
68 ACACTAA
1 ACCCCAA
75 ACCCCAA
1 ACCCCAA
82 ACCCCAA
1 ACCCCAA
89 AC
1 AC
91 TCTCAACACC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
6 5 0.09
7 44 0.81
8 5 0.09
ACGTcount: A:0.44, C:0.47, G:0.03, T:0.06
Consensus pattern (7 bp):
ACCCCAA
Found at i:184 original size:15 final size:14
Alignment explanation
Indices: 136--183 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
126 CCACACCCCG
136 ACCCCTACACCCT-A
1 ACCCCTA-ACCCTCA
*
150 AACCCTAACACCTCA
1 ACCCCTAAC-CCTCA
165 ACCCCTAACCCTCA
1 ACCCCTAACCCTCA
179 ACCCC
1 ACCCC
184 CAAACCCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 2 0.07
14 19 0.63
15 9 0.30
ACGTcount: A:0.31, C:0.56, G:0.00, T:0.12
Consensus pattern (14 bp):
ACCCCTAACCCTCA
Found at i:262 original size:15 final size:15
Alignment explanation
Indices: 244--299 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
234 CCTTAAATCC
244 CAAACCTCAAACCCT
1 CAAACCTCAAACCCT
259 CAAACC-CTAAACCCT
1 CAAACCTC-AAACCCT
* * *
274 CTAGCCTC-AAGCCT
1 CAAACCTCAAACCCT
*
288 CAAACCCCAAAC
1 CAAACCTCAAAC
300 ATAAAAAATA
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
14 11 0.35
15 19 0.61
16 1 0.03
ACGTcount: A:0.38, C:0.46, G:0.04, T:0.12
Consensus pattern (15 bp):
CAAACCTCAAACCCT
Found at i:1548 original size:13 final size:13
Alignment explanation
Indices: 1530--1563 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1520 CATGATTGTC
1530 AAATTAAATGCAG
1 AAATTAAATGCAG
*
1543 AAATTAATTGCAG
1 AAATTAAATGCAG
*
1556 GAATTAAA
1 AAATTAAA
1564 GAGAATGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (13 bp):
AAATTAAATGCAG
Found at i:4149 original size:12 final size:12
Alignment explanation
Indices: 4120--4156 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
4110 TTAGTTTGAT
4120 GTTTCGATTTATG
1 GTTTCGATTTA-G
*
4133 GTTTCGAATTAG
1 GTTTCGATTTAG
4145 GTTTCGATTTAG
1 GTTTCGATTTAG
4157 ATATTAGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.19, C:0.08, G:0.24, T:0.49
Consensus pattern (12 bp):
GTTTCGATTTAG
Found at i:4248 original size:25 final size:25
Alignment explanation
Indices: 4220--4312 Score: 68
Period size: 25 Copynumber: 3.7 Consensus size: 25
4210 TATATTGGGG
4220 TTTTGATTTTGTTTTGAGGTTTCTA
1 TTTTGATTTTGTTTTGAGGTTTCTA
* * * *
4245 TTTTGTTTTTGCGCTTTGA--TCTCGA
1 TTTTGATTTT--GTTTTGAGGTTTCTA
4270 TTTTGATTTTGATTTTG-GGTTT-TA
1 TTTTGATTTTG-TTTTGAGGTTTCTA
*
4294 GTTTTGTATTATGTTTTGA
1 -TTTTG-ATTTTGTTTTGA
4313 TTTGGGGTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
23 1 0.02
24 5 0.10
25 34 0.67
26 5 0.10
27 6 0.12
ACGTcount: A:0.12, C:0.05, G:0.20, T:0.62
Consensus pattern (25 bp):
TTTTGATTTTGTTTTGAGGTTTCTA
Found at i:4446 original size:25 final size:25
Alignment explanation
Indices: 4411--4461 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
4401 GTCGGCTTCA
* *
4411 GTTTTGGTTTGGGGTTACAATTTTG
1 GTTTTGATTTGAGGTTACAATTTTG
* *
4436 GTTTTGATTTGAGTTTTCAATTTTG
1 GTTTTGATTTGAGGTTACAATTTTG
4461 G
1 G
4462 ATTGTGGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.14, C:0.04, G:0.27, T:0.55
Consensus pattern (25 bp):
GTTTTGATTTGAGGTTACAATTTTG
Found at i:4478 original size:25 final size:25
Alignment explanation
Indices: 4428--4488 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
4418 TTTGGGGTTA
*
4428 CAATTTTGGTTTTGATTTGAGTTTT
1 CAATTTTGGTTGTGATTTGAGTTTT
* *
4453 CAATTTTGGATTGTGGTTTTAG-TTT
1 CAATTTTGG-TTGTGATTTGAGTTTT
*
4478 CAATTTCGGTT
1 CAATTTTGGTT
4489 TGAAGTTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 2 0.06
25 20 0.65
26 9 0.29
ACGTcount: A:0.16, C:0.07, G:0.21, T:0.56
Consensus pattern (25 bp):
CAATTTTGGTTGTGATTTGAGTTTT
Found at i:10077 original size:2 final size:2
Alignment explanation
Indices: 10065--10097 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
10055 TCAATGGAAA
*
10065 AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
10098 ATGGAAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11340 original size:17 final size:18
Alignment explanation
Indices: 11309--11342 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11299 AATTTAATTC
11309 TAATTAAATTATTTAAAG
1 TAATTAAATTATTTAAAG
*
11327 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
11343 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAG
Found at i:11474 original size:22 final size:23
Alignment explanation
Indices: 11445--11497 Score: 92
Period size: 22 Copynumber: 2.4 Consensus size: 23
11435 ATGTTTAGGT
11445 TTAA-GGTTTATGGTTTTGAGGA
1 TTAAGGGTTTATGGTTTTGAGGA
11467 TT-AGGGTTTATGGTTTTGAGGA
1 TTAAGGGTTTATGGTTTTGAGGA
11489 TTAAGGGTT
1 TTAAGGGTT
11498 AGTGGTCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.03
22 22 0.76
23 6 0.21
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (23 bp):
TTAAGGGTTTATGGTTTTGAGGA
Found at i:21261 original size:18 final size:18
Alignment explanation
Indices: 21240--21274 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21230 TGAGTTTTTG
21240 AATTCAAATAACTCGAAC
1 AATTCAAATAACTCGAAC
* *
21258 AATTCGAATAATTCGAA
1 AATTCAAATAACTCGAA
21275 TATTAAACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.26
Consensus pattern (18 bp):
AATTCAAATAACTCGAAC
Found at i:21332 original size:22 final size:22
Alignment explanation
Indices: 21291--21341 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
21281 ACTATAATAT
*
21291 TTTATA-TTTTTATCCCAAAAC
1 TTTATACTTTTTATCCAAAAAC
*
21312 TTTATACTTTTTTTCCAAAAAC
1 TTTATACTTTTTATCCAAAAAC
21334 TTT-TACTT
1 TTTATACTT
21342 CTTCTCACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTATACTTTTTATCCAAAAAC
Found at i:21562 original size:28 final size:28
Alignment explanation
Indices: 21504--21562 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
21494 TCCCCAAAAA
**
21504 CCCTCAAAACTTTTACTCCCTCTCCTTT
1 CCCTCAAAACTTTTACTCCCTCTCCCAT
*
21532 CCCTCTAAAACTTTTATTCCC-CTCCCAT
1 CCCTC-AAAACTTTTACTCCCTCTCCCAT
21560 CCC
1 CCC
21563 ATCCCATCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.19, C:0.46, G:0.00, T:0.36
Consensus pattern (28 bp):
CCCTCAAAACTTTTACTCCCTCTCCCAT
Found at i:21874 original size:18 final size:18
Alignment explanation
Indices: 21830--21874 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
21820 CATTTTATAC
21830 TATTTATA-T-TATTGAA
1 TATTTATATTATATTGAA
*
21846 T-TTTTTAATTATATTGAA
1 TATTTAT-ATTATATTGAA
21864 TATTTATATTA
1 TATTTATATTA
21875 AAATTGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
15 4 0.17
16 2 0.09
17 1 0.04
18 12 0.52
19 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (18 bp):
TATTTATATTATATTGAA
Found at i:29352 original size:11 final size:11
Alignment explanation
Indices: 29336--29360 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29326 TATAATATTC
29336 TTTTTTCTTTT
1 TTTTTTCTTTT
29347 TTTTTTCTTTT
1 TTTTTTCTTTT
29358 TTT
1 TTT
29361 GAATTTGTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:31738 original size:62 final size:62
Alignment explanation
Indices: 31668--31791 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
31658 TATTAGTACA
31668 AACCAGATATGAAAATACATTGAGACTAATTCCAAATTATCAATTAAACTATGTAAACTAAG
1 AACCAGATATGAAAATACATTGAGACTAATTCCAAATTATCAATTAAACTATGTAAACTAAG
31730 AACCAGATATGAAAATACATTGAGACTAATTCCAAATTATCAATTAAACTATGTAAACTAAG
1 AACCAGATATGAAAATACATTGAGACTAATTCCAAATTATCAATTAAACTATGTAAACTAAG
31792 TTTTTTTTCC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (62 bp):
AACCAGATATGAAAATACATTGAGACTAATTCCAAATTATCAATTAAACTATGTAAACTAAG
Found at i:34436 original size:23 final size:22
Alignment explanation
Indices: 34404--34541 Score: 98
Period size: 23 Copynumber: 5.9 Consensus size: 22
34394 ACACTAGCGC
*
34404 GCCCTTTGTTTAGCACGTTTTGT
1 GCCCTCTGTTTAGCAC-TTTTGT
* *
34427 GCCCTCTGTTCAGCACTGTGTGT
1 GCCCTCTGTTTAGCACT-TTTGT
34450 GCCCTCTGTTATTAGCA-TTTCGTGT
1 GCCCTCTG-T-TTAGCACTTT--TGT
* * *
34475 GCCCTTTGATTAGTACTTTGTGT
1 GCCCTCTGTTTAGCACTTT-TGT
*
34498 GCCCTCTGTTACCTAGCACTTATGT
1 GCCCTCTGTT---TAGCACTTTTGT
* *
34523 GCCCTCTGTTAAGTACTTT
1 GCCCTCTGTTTAGCACTTT
34542 GGTACTTTCT
Statistics
Matches: 91, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
22 7 0.08
23 44 0.48
24 5 0.05
25 28 0.31
26 7 0.08
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.42
Consensus pattern (22 bp):
GCCCTCTGTTTAGCACTTTTGT
Found at i:34474 original size:25 final size:24
Alignment explanation
Indices: 34424--34533 Score: 93
Period size: 25 Copynumber: 4.6 Consensus size: 24
34414 TAGCACGTTT
* *
34424 TGTGCCCTCTG-T-TCAGCACTGTG
1 TGTGCCCTCTGTTATTAGCA-TTTG
34447 TGTGCCCTCTGTTATTAGCATTTCG
1 TGTGCCCTCTGTTATTAGCATTT-G
* *
34472 TGTGCCCT-T-TGATTAGTACTTTG
1 TGTGCCCTCTGTTATTAGCA-TTTG
* * *
34495 TGTGCCCTCTGTTACCTAGCACTTA
1 TGTGCCCTCTGTTA-TTAGCATTTG
34520 TGTGCCCTCTGTTA
1 TGTGCCCTCTGTTA
34534 AGTACTTTGG
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
23 27 0.38
24 8 0.11
25 32 0.45
26 4 0.06
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.41
Consensus pattern (24 bp):
TGTGCCCTCTGTTATTAGCATTTG
Found at i:34538 original size:48 final size:46
Alignment explanation
Indices: 34414--34542 Score: 141
Period size: 48 Copynumber: 2.7 Consensus size: 46
34404 GCCCTTTGTT
* * * *
34414 TAGCACGTTTTGTGCCCTCTGTTCAGCACTGTGTGTGCCCTCTGTTAT
1 TAGCAC-TTATGTGCCCTCTGTT-AGTACTTTGTGTGCCCTCTGTTAC
* * *
34462 TAGCATTTCGTGTGCCCTTTGATTAGTACTTTGTGTGCCCTCTGTTACC
1 TAGCACTT-ATGTGCCCTCTG-TTAGTACTTTGTGTGCCCTCTGTTA-C
34511 TAGCACTTATGTGCCCTCTGTTAAGTACTTTG
1 TAGCACTTATGTGCCCTCTGTT-AGTACTTTG
34543 GTACTTTCTG
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
47 4 0.06
48 55 0.81
49 9 0.13
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.41
Consensus pattern (46 bp):
TAGCACTTATGTGCCCTCTGTTAGTACTTTGTGTGCCCTCTGTTAC
Found at i:43015 original size:314 final size:315
Alignment explanation
Indices: 42445--43078 Score: 1155
Period size: 314 Copynumber: 2.0 Consensus size: 315
42435 GACGGTCCTC
** *
42445 ATTTCTACATTGGGACTTCCAAAGAAAACCATCCATGATCAAAAGACAAAGGCTGGATGTTACCA
1 ATTTCTACATTGGGACTTAAAAAGAAAACCATCAATGATCAAAAGACAAAGGCTGGATGTTACCA
*
42510 AACTACCAATAACAGACTTTAATTTAAAGGCTTTTACTAGCAAATTACTCTACCAAATTAAAGGT
66 AACTACCAATAACAGACTTTAATTTAAAAGCTTTTACTAGCAAATTACTCTACCAAATTAAAGGT
42575 GAAATTTAAACAATATCTAATGCACATGAAGTTGATTTGATTCCCTAATCCTTTAACTTTTTCAC
131 GAAATTTAAACAATATCTAATGCACATGAAGTTGATTTGATTCCCTAATCCTTTAACTTTTTCAC
42640 AGATGAAAAAAATTGCAATAGAGGAATGATATTTTTACACGAAGTAAATTTAACAAACCAAGGTG
196 AGATGAAAAAAATTGCAATAGAGGAATGATATTTTTACACGAAGTAAATTTAACAAACCAAGGTG
*
42705 GGGTGGAGAGACTCAATGATGACTGCAGCATTTTAAGTCTTTAACTTATACCCCT
261 GGGTCGAGAGACTCAATGATGACTGCAGCATTTTAAGTCTTTAACTTATACCCCT
*
42760 ATTTCTACATTGGGACTTAAAAATAAAACCATCAATGATC-AAAGACAAAGGCTGGATGTTACCA
1 ATTTCTACATTGGGACTTAAAAAGAAAACCATCAATGATCAAAAGACAAAGGCTGGATGTTACCA
*
42824 AACTACCAATAACAGACTTTAATTTAAAAGCTTTTACTAGCAAATTACTCTACCAAATTAAGGGT
66 AACTACCAATAACAGACTTTAATTTAAAAGCTTTTACTAGCAAATTACTCTACCAAATTAAAGGT
42889 GAAATTTAAACAATATCTAATGCACATGAAGTTGATTT-ACTTCCCTAATCCTTTAACTTTTTCA
131 GAAATTTAAACAATATCTAATGCACATGAAGTTGATTTGA-TTCCCTAATCCTTTAACTTTTTCA
* *
42953 CAGATGAAAAAAATTGCTATAGAGGAATGATATTTTTACACGAAGTAAATTTCACAAACCAAGGT
195 CAGATGAAAAAAATTGCAATAGAGGAATGATATTTTTACACGAAGTAAATTTAACAAACCAAGGT
*
43018 GGGGTCGTGAGACTCAATGATGACTGCAGCATTTTAAGTCTTTAACTTATACCCCT
260 GGGGTCGAGAGACTCAATGATGACTGCAGCATTTTAAGTCTTTAACTTATACCCCT
43074 ATTTC
1 ATTTC
43079 ATCCCTACAA
Statistics
Matches: 308, Mismatches: 10, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
313 1 0.00
314 271 0.88
315 36 0.12
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (315 bp):
ATTTCTACATTGGGACTTAAAAAGAAAACCATCAATGATCAAAAGACAAAGGCTGGATGTTACCA
AACTACCAATAACAGACTTTAATTTAAAAGCTTTTACTAGCAAATTACTCTACCAAATTAAAGGT
GAAATTTAAACAATATCTAATGCACATGAAGTTGATTTGATTCCCTAATCCTTTAACTTTTTCAC
AGATGAAAAAAATTGCAATAGAGGAATGATATTTTTACACGAAGTAAATTTAACAAACCAAGGTG
GGGTCGAGAGACTCAATGATGACTGCAGCATTTTAAGTCTTTAACTTATACCCCT
Found at i:51325 original size:13 final size:13
Alignment explanation
Indices: 51298--51360 Score: 67
Period size: 13 Copynumber: 4.8 Consensus size: 13
51288 TTAGCATTGC
51298 TTTTGAAAACA-AT
1 TTTTGAAAA-ATAT
*
51311 TTTTAAAAAATAT
1 TTTTGAAAAATAT
*
51324 TTTGGAAAAATGA-
1 TTTTGAAAAAT-AT
*
51337 TTTTGAAAAATAC
1 TTTTGAAAAATAT
51350 TTTTGAAAAAT
1 TTTTGAAAAAT
51361 TTGGTTTAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
12 2 0.05
13 40 0.93
14 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.40
Consensus pattern (13 bp):
TTTTGAAAAATAT
Found at i:51340 original size:26 final size:26
Alignment explanation
Indices: 51311--51360 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
51301 TGAAAACAAT
51311 TTTTAAAAAATA-TTTTGGAAAAATGA
1 TTTTAAAAAATACTTTT-GAAAAATGA
*
51337 TTTTGAAAAATACTTTTGAAAAAT
1 TTTTAAAAAATACTTTTGAAAAAT
51361 TTGGTTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (26 bp):
TTTTAAAAAATACTTTTGAAAAATGA
Found at i:51763 original size:19 final size:21
Alignment explanation
Indices: 51739--51779 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
51729 TTAACATTGC
*
51739 TTTTTAT-TTAAAAGTA-TTT
1 TTTTTATGTCAAAAGTACTTT
51758 TTTTTATGTCAAAAGTACTTT
1 TTTTTATGTCAAAAGTACTTT
51779 T
1 T
51780 AAAAAGCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 8 0.42
21 4 0.21
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.59
Consensus pattern (21 bp):
TTTTTATGTCAAAAGTACTTT
Found at i:54822 original size:6 final size:6
Alignment explanation
Indices: 54811--54839 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
54801 CCTTTCCTCC
54811 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
54840 TTTGTTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCA
Found at i:63034 original size:15 final size:15
Alignment explanation
Indices: 63014--63043 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
63004 CACCACCACA
63014 TCAAAAGAACTCCAG
1 TCAAAAGAACTCCAG
*
63029 TCAAAAGAGCTCCAG
1 TCAAAAGAACTCCAG
63044 ATTTTCTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.17, T:0.13
Consensus pattern (15 bp):
TCAAAAGAACTCCAG
Found at i:69305 original size:235 final size:238
Alignment explanation
Indices: 68880--69357 Score: 719
Period size: 235 Copynumber: 2.0 Consensus size: 238
68870 AAGAAATGGT
* *
68880 TACCAAAGAAAAAAAAGGAACACCATCGCAAAAGATTTAGAAGTTCGAGTAGAGTTTACATGCAG
1 TACCAAAGAAAAAAAAGGAACACCATCGCAAAAGATTTAGAAGTTCGAGAAGAATTTACAT--AG
68945 TAATCAGTAATGGTCTTGGATGTAATTTGAAAAAAATGGTGGACCAATTTGCTCACAAATCTGAT
64 --A-CAGTAATGGTCTTGGATGTAATTTGAAAAAAATGGTGGACCAATTTGCTCACAAATCTGAT
* * * *
69010 TTCAACACATTCAGAAGTTAAGCACCTAGGTGTAAGGAACATTCAAGAGCCAAGAACTCTCGAGA
126 TTCAACACATTCAGAAGTTAAGCACCTAAGTGTAAAGAACACTCAAGAGCCAAGAACTCTCGAAA
* * *
69075 GAAAGGCAAAACAAAGGCATATATGTTGTTATAGCGATGTAATTCATA
191 GAAAGGCAAAACAAAGGAATATATATTGTTATAGCGATGAAATTCATA
* *
69123 TACCAAAGAAAAAAAATGAACACCATCGCAAAAGATTTTGAAGTTCGAGAAGAATTTACAT-G-C
1 TACCAAAGAAAAAAAAGGAACACCATCGCAAAAGATTTAGAAGTTCGAGAAGAATTTACATAGAC
* *
69186 AGTAATGGTCTTGGATGTAATTT-AAAATAATGGTGGACCAATTTGCTCACACATCTGATTTCAA
66 AGTAATGGTCTTGGATGTAATTTGAAAAAAATGGTGGACCAATTTGCTCACAAATCTGATTTCAA
* * * *
69250 CACATTCAGAAGTTATGTACCTAAGTGTAAAGAACACTCCAGAGCCAATAACTCTCGAAAGAAAG
131 CACATTCAGAAGTTAAGCACCTAAGTGTAAAGAACACTCAAGAGCCAAGAACTCTCGAAAGAAAG
* *
69315 GCAAAGCAAAGGAATATATATTGTTATAGTGATGAAATTCATA
196 GCAAAACAAAGGAATATATATTGTTATAGCGATGAAATTCATA
69358 CAATTTATTG
Statistics
Matches: 216, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
235 134 0.62
236 24 0.11
240 1 0.00
243 57 0.26
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (238 bp):
TACCAAAGAAAAAAAAGGAACACCATCGCAAAAGATTTAGAAGTTCGAGAAGAATTTACATAGAC
AGTAATGGTCTTGGATGTAATTTGAAAAAAATGGTGGACCAATTTGCTCACAAATCTGATTTCAA
CACATTCAGAAGTTAAGCACCTAAGTGTAAAGAACACTCAAGAGCCAAGAACTCTCGAAAGAAAG
GCAAAACAAAGGAATATATATTGTTATAGCGATGAAATTCATA
Found at i:78526 original size:6 final size:6
Alignment explanation
Indices: 78515--78545 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
78505 GCATGAAGTT
*
78515 TGAAGG TGAAGG TGAAGG CGAAGG TGAAGG T
1 TGAAGG TGAAGG TGAAGG TGAAGG TGAAGG T
78546 TTGGCACAGA
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:0.32, C:0.03, G:0.48, T:0.16
Consensus pattern (6 bp):
TGAAGG
Found at i:92258 original size:6 final size:6
Alignment explanation
Indices: 92236--92269 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
92226 ATGGCATAAA
92236 TTTTAT TTTAATAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTT--TAT TTTTAT TTTTAT TTTTAT TT
92270 ATACTATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.77
8 6 0.23
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:96704 original size:16 final size:16
Alignment explanation
Indices: 96683--96713 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
96673 GTTGATGTAA
*
96683 TTTTTTTAATTTACTT
1 TTTTTTTAATATACTT
96699 TTTTTTTAATATACT
1 TTTTTTTAATATACT
96714 GGTGTGATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTTTAATATACTT
Found at i:98244 original size:52 final size:52
Alignment explanation
Indices: 98156--98322 Score: 217
Period size: 52 Copynumber: 3.2 Consensus size: 52
98146 AAATGCAAAA
* * *
98156 AGGTTCGATGACTACGTGTCATCGTGAGTACATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTAAGTATATGAATCCTTTACGGATTATG
* **
98208 AGGTCCGATAACTACGTGTCATCGTAAGTATATGAATCCTTTACAAATTATG
1 AGGTCCGATGACTACGTGTCATCGTAAGTATATGAATCCTTTACGGATTATG
* * * * ** *
98260 AGTTCCGATGACTACTTATCACCCAAAATATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTAAGTATATGAATCCTTTACGGATTATG
98312 AGGTCCGATGA
1 AGGTCCGATGA
98323 TTATGTGTTA
Statistics
Matches: 98, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 98 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (52 bp):
AGGTCCGATGACTACGTGTCATCGTAAGTATATGAATCCTTTACGGATTATG
Found at i:98342 original size:52 final size:51
Alignment explanation
Indices: 98156--98342 Score: 178
Period size: 52 Copynumber: 3.6 Consensus size: 51
98146 AAATGCAAAA
* * * * *
98156 AGGTTCGATGACTACGTGTCATCGTGAGTACATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCG-AAATATATGAATCCTTTACGGATTATG
* * * **
98208 AGGTCCGATAACTACGTGTCATCGTAAGTATATGAATCCTTTACAAATTATG
1 AGGTCCGATGACTATGTGTCATCG-AAATATATGAATCCTTTACGGATTATG
* * * *
98260 AGTTCCGATGACTACT-TATCACCCAAAATATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTA-TGTGTCA-TCGAAATATATGAATCCTTTACGGATTATG
* *
98312 AGGTCCGATGATTATGTGTTATCGAGAATAT
1 AGGTCCGATGACTATGTGTCATCGA-AATAT
98343 CAAATGCGAA
Statistics
Matches: 110, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
51 3 0.03
52 106 0.96
53 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (51 bp):
AGGTCCGATGACTATGTGTCATCGAAATATATGAATCCTTTACGGATTATG
Found at i:101812 original size:75 final size:75
Alignment explanation
Indices: 101732--101949 Score: 357
Period size: 75 Copynumber: 2.9 Consensus size: 75
101722 AAACAATAGT
* *
101732 AGAGGAAGCAAATGTGGTAACTGCCACAAGCCAAGTACAAGAAGAAGCGCTGCATGGGGAAAAGG
1 AGAGGAAGCAAATGTGGTAATTGCCACAAACCAAGTACAAGAAGAAGCGCTGCATGGGGAAAAGG
101797 AAACCATTGA
66 AAACCATTGA
101807 AGAGGAAGCAAATGTGGTAATTGCCACAAACCAAGTACAAGAAGAAGCGCTGCATGGGGAAAAGG
1 AGAGGAAGCAAATGTGGTAATTGCCACAAACCAAGTACAAGAAGAAGCGCTGCATGGGGAAAAGG
101872 AAACCATTGA
66 AAACCATTGA
* * * **
101882 AGAAGAAGCAAATGTGGTGATTGCCACAAACCAAGTGCAAGAAGAAGCAATGCAT-GGGAAGAAG
1 AGAGGAAGCAAATGTGGTAATTGCCACAAACCAAGTACAAGAAGAAGCGCTGCATGGGGAA-AAG
101946 GAAA
65 GAAA
101950 TGGCAGCACC
Statistics
Matches: 135, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
74 5 0.04
75 130 0.96
ACGTcount: A:0.43, C:0.16, G:0.29, T:0.12
Consensus pattern (75 bp):
AGAGGAAGCAAATGTGGTAATTGCCACAAACCAAGTACAAGAAGAAGCGCTGCATGGGGAAAAGG
AAACCATTGA
Found at i:103981 original size:2 final size:2
Alignment explanation
Indices: 103974--103998 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
103964 ATTATAAAAC
103974 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
103999 TACATTAATA
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:105407 original size:17 final size:17
Alignment explanation
Indices: 105387--105430 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
105377 AATTAATTTT
105387 TTTTTTAAATTTAAAAA
1 TTTTTTAAATTTAAAAA
**
105404 TTTTAAAAATTTAAAAA
1 TTTTTTAAATTTAAAAA
*
105421 TTATTTAAAT
1 TTTTTTAAAT
105431 AATTTAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTTTAAATTTAAAAA
Found at i:105410 original size:9 final size:9
Alignment explanation
Indices: 105396--105462 Score: 66
Period size: 9 Copynumber: 7.1 Consensus size: 9
105386 TTTTTTTAAA
105396 TTTAAAAAT
1 TTTAAAAAT
105405 TTTAAAAA-
1 TTTAAAAAT
105413 TTTAAAAATT
1 TTTAAAAA-T
105423 ATTTAAATAA-
1 -TTTAAA-AAT
105433 TTTAAAAAT
1 TTTAAAAAT
*
105442 TATATAAAAT
1 TTTA-AAAAT
105452 TTTAAATAAT
1 TTTAAA-AAT
105462 T
1 T
105463 GCTAATGTGG
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
8 10 0.20
9 19 0.39
10 12 0.24
11 6 0.12
12 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TTTAAAAAT
Found at i:105426 original size:20 final size:19
Alignment explanation
Indices: 105393--105462 Score: 90
Period size: 20 Copynumber: 3.7 Consensus size: 19
105383 TTTTTTTTTT
105393 AAATTTAAAAA-T-TTTAA
1 AAATTTAAAAATTATTTAA
105410 AAATTTAAAAATTATTTAA
1 AAATTTAAAAATTATTTAA
*
105429 ATAATTTAAAAATTATATAA
1 A-AATTTAAAAATTATTTAA
*
105449 AATTTTAAATAATT
1 AAATTTAAA-AATT
105463 GCTAATGTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
17 11 0.23
18 1 0.02
19 13 0.28
20 22 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATTTAAAAATTATTTAA
Found at i:105436 original size:28 final size:29
Alignment explanation
Indices: 105395--105462 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
105385 TTTTTTTTAA
105395 ATTTAAA-AATTTTAAAAATT-TA-AAAATT
1 ATTTAAATAA-TTTAAAAATTATATAAAA-T
105423 ATTTAAATAATTTAAAAATTATATAAAAT
1 ATTTAAATAATTTAAAAATTATATAAAAT
105452 -TTTAAATAATT
1 ATTTAAATAATT
105463 GCTAATGTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
28 28 0.76
29 5 0.14
30 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
ATTTAAATAATTTAAAAATTATATAAAAT
Found at i:108899 original size:31 final size:31
Alignment explanation
Indices: 108864--108928 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
108854 TACAATATGA
* *
108864 TCATTAAATTAATTGAGAGTTTTCATTTAAG
1 TCATTAAATCAATTGAAAGTTTTCATTTAAG
* *
108895 TCATTAAATCATTTGAAAGTTTTTATTTAAG
1 TCATTAAATCAATTGAAAGTTTTCATTTAAG
108926 TCA
1 TCA
108929 CTAGACTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (31 bp):
TCATTAAATCAATTGAAAGTTTTCATTTAAG
Found at i:111362 original size:23 final size:22
Alignment explanation
Indices: 111320--111371 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 22
111310 ATTTGCGTTA
*
111320 TGTGCGCCTACTGATTGCACTG
1 TGTGTGCCTACTGATTGCACTG
111342 TGTGTGCCTACTGGATTGCACTG
1 TGTGTGCCTACT-GATTGCACTG
111365 TGTGTGC
1 TGTGTGC
111372 TTATTGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.12, C:0.23, G:0.31, T:0.35
Consensus pattern (22 bp):
TGTGTGCCTACTGATTGCACTG
Found at i:114705 original size:22 final size:20
Alignment explanation
Indices: 114672--114715 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
114662 AAATTGATTA
*
114672 TTTAATTATTTAATTTTATTT
1 TTTAATTATTTAATATT-TTT
*
114693 TTTAGATTTTTTAATATTTTT
1 TTTA-ATTATTTAATATTTTT
114714 TT
1 TT
114716 ATGTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTAATTATTTAATATTTTT
Found at i:144675 original size:6 final size:6
Alignment explanation
Indices: 144664--144694 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
144654 GTAGTAAGTG
144664 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC C
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC C
144695 CCAATTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CTCTCC
Found at i:145638 original size:31 final size:31
Alignment explanation
Indices: 145600--145674 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 31
145590 TATACTTGTA
* *
145600 GTCATCCAATTA-TTGATAAGTATTTTTTATG
1 GTCATCCAACTATTTG-TAAGTATCTTTTATG
145631 GTCATCCAACTATTTGTAAGTATCTTTTATG
1 GTCATCCAACTATTTGTAAGTATCTTTTATG
145662 GTCATCCAACTAT
1 GTCATCCAACTAT
145675 GAAAAGTTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 38 0.93
32 3 0.07
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (31 bp):
GTCATCCAACTATTTGTAAGTATCTTTTATG
Found at i:148877 original size:8 final size:8
Alignment explanation
Indices: 148840--148911 Score: 60
Period size: 8 Copynumber: 8.8 Consensus size: 8
148830 TAATCACTTA
148840 TTTAAA-T
1 TTTAAATT
148847 TTTAAATT
1 TTTAAATT
*
148855 ATT--ATT
1 TTTAAATT
148861 TTATAAAATT
1 TT-T-AAATT
148871 TTTAAATT
1 TTTAAATT
148879 TTTAAATT
1 TTTAAATT
148887 TTCTATATATT
1 TT-TA-A-ATT
*
148898 TTTATATT
1 TTTAAATT
148906 TTTAAA
1 TTTAAA
148912 AAAAATTATA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
6 4 0.08
7 7 0.13
8 26 0.49
9 3 0.06
10 8 0.15
11 5 0.09
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (8 bp):
TTTAAATT
Found at i:148977 original size:19 final size:19
Alignment explanation
Indices: 148955--149013 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
148945 ACAAATTTAA
148955 AATTTTTATAAA-TATTTTG
1 AATTTTTA-AAATTATTTTG
* *
148974 AATTTTAAAAATTATTTTT
1 AATTTTTAAAATTATTTTG
148993 AATTTTTGAAAATTATTTTG
1 AATTTTT-AAAATTATTTTG
149013 A
1 A
149014 TCATTTTGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 3 0.09
19 19 0.56
20 12 0.35
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
AATTTTTAAAATTATTTTG
Found at i:148999 original size:20 final size:20
Alignment explanation
Indices: 148955--149013 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
148945 ACAAATTTAA
*
148955 AATTTTTATAAA-TATTTTG
1 AATTTTTAAAAATTATTTTG
*
148974 AA-TTTTAAAAATTATTTTT
1 AATTTTTAAAAATTATTTTG
*
148993 AATTTTTGAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
149013 A
1 A
149014 TCATTTTGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.24
19 10 0.29
20 16 0.47
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:169715 original size:2 final size:2
Alignment explanation
Indices: 169710--169741 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
169700 AAATAAATAA
169710 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
169742 TAATAAAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:180123 original size:15 final size:15
Alignment explanation
Indices: 180103--180137 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
180093 TTTGAGGCAA
180103 TTCCTCTTCTTC-TTC
1 TTCCTCTT-TTCTTTC
180118 TTCCTCTTTTCTTTC
1 TTCCTCTTTTCTTTC
180133 TTCCT
1 TTCCT
180138 TCACATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (15 bp):
TTCCTCTTTTCTTTC
Found at i:187066 original size:2 final size:2
Alignment explanation
Indices: 187061--187090 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
187051 AAAAAGAAGC
187061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
187091 CATAGAACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:194211 original size:21 final size:21
Alignment explanation
Indices: 194187--194227 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
194177 GTCATTTTAC
194187 TTTTAGA-TTTAATAATTTAAT
1 TTTTAGATTTTAA-AATTTAAT
*
194208 TTTTATATTTTAAAATTTAA
1 TTTTAGATTTTAAAATTTAA
194228 GTTTATCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTAGATTTTAAAATTTAAT
Found at i:196385 original size:17 final size:17
Alignment explanation
Indices: 196365--196397 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
196355 TCAATTAAAG
*
196365 TTTTATTTG-AATTTTT
1 TTTTTTTTGTAATTTTT
196381 TTTTTTTTGTAATTTTT
1 TTTTTTTTGTAATTTTT
196398 AATTTCCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTTTTTGTAATTTTT
Found at i:209309 original size:32 final size:31
Alignment explanation
Indices: 209237--209311 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
209227 GTCTAATTTT
* *
209237 GTACTCAAACTTGACACTTTTTCTTAATTTG
1 GTACTTAAACTTGACACTTTTTCTTAAGTTG
* * * *
209268 ATTCCTAAACTTGACACTTTTTTTTAAAGTTG
1 GTACTTAAACTTGACACTTTTTCTT-AAGTTG
209300 GTACTTAAACTT
1 GTACTTAAACTT
209312 TTTGGGTCCA
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
31 20 0.59
32 14 0.41
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.45
Consensus pattern (31 bp):
GTACTTAAACTTGACACTTTTTCTTAAGTTG
Found at i:209584 original size:59 final size:59
Alignment explanation
Indices: 209511--209680 Score: 200
Period size: 59 Copynumber: 2.9 Consensus size: 59
209501 ATTTAATAAA
* * *
209511 TTTAGATACCAAATTGAATCTAAAAAAAGCTTAGGCACCAAATTAGGAAAAATGCT-AAG
1 TTTAGGTACCAAATTGGATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAATG-TGAAG
* * **
209570 TTTAGGTACCAAATTGGATCTAAAAAACGTTTAGGTACCAAATTAAAAAAAATGTGAAG
1 TTTAGGTACCAAATTGGATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAATGTGAAG
* * * * *
209629 TTCAAGTACCAAATTGGGTC-AAAAAAAACTTTAGATACCAAATTAGGAAAAA
1 TTTAGGTACCAAATTGGATCTAAAAAAAGC-TTAGGTACCAAATTAGGAAAAA
209681 ATGTCAAATT
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
58 7 0.08
59 86 0.92
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (59 bp):
TTTAGGTACCAAATTGGATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAATGTGAAG
Found at i:209807 original size:28 final size:28
Alignment explanation
Indices: 209775--209833 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
209765 TATTAATTAA
209775 TATTTTAATAATTCC-AACTTTGAAAATT
1 TATTTTAATAATTCCTAACTTT-AAAATT
* * *
209803 TA-TTTATTTATTCCTAACTTTTAAATT
1 TATTTTAATAATTCCTAACTTTAAAATT
209830 TATT
1 TATT
209834 AATTTAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (28 bp):
TATTTTAATAATTCCTAACTTTAAAATT
Found at i:209815 original size:27 final size:27
Alignment explanation
Indices: 209785--209839 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
209775 TATTTTAATA
*
209785 ATTCC-AACTTTGAAAATTTATTTATTT
1 ATTCCTAACTTT-AAAATTTATTAATTT
*
209812 ATTCCTAACTTTTAAATTTATTAATTT
1 ATTCCTAACTTTAAAATTTATTAATTT
209839 A
1 A
209840 ATTAGGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.53
Consensus pattern (27 bp):
ATTCCTAACTTTAAAATTTATTAATTT
Found at i:213887 original size:82 final size:81
Alignment explanation
Indices: 213767--213921 Score: 247
Period size: 82 Copynumber: 1.9 Consensus size: 81
213757 TCCCTTTTTT
* * *
213767 TAAAAAAGATTAGATCATAATTATATATCTCTCTACTCAAAAATTAAATAAGGTCTTTGTTAGTA
1 TAAAAAAGATTAGATCATAATTATATATCGCTCAACTCAAAAATTAAATAAGGTCTTTGGTAGTA
213832 GTATTTTTATTAAAAA
66 GTATTTTTATTAAAAA
* * *
213848 TAAATAAAGATTAGATCATATTTATTTATCGCTCAACTCAAAAATTAATTAAGGTCTTTGGTAGT
1 TAAA-AAAGATTAGATCATAATTATATATCGCTCAACTCAAAAATTAAATAAGGTCTTTGGTAGT
213913 AGTATTTTT
65 AGTATTTTT
213922 CTTCTACTTC
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
81 4 0.06
82 63 0.94
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (81 bp):
TAAAAAAGATTAGATCATAATTATATATCGCTCAACTCAAAAATTAAATAAGGTCTTTGGTAGTA
GTATTTTTATTAAAAA
Found at i:220707 original size:6 final size:6
Alignment explanation
Indices: 220696--220749 Score: 108
Period size: 6 Copynumber: 9.0 Consensus size: 6
220686 AACTATGTGT
220696 TTGGAG TTGGAG TTGGAG TTGGAG TTGGAG TTGGAG TTGGAG TTGGAG
1 TTGGAG TTGGAG TTGGAG TTGGAG TTGGAG TTGGAG TTGGAG TTGGAG
220744 TTGGAG
1 TTGGAG
220750 CATTAGCTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
TTGGAG
Done.