Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013308.1 Kokia drynarioides strain JFW-HI SEQ_128330, 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: 74313
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Warning! 141 characters in sequence are not A, C, G, or T
Found at i:3014 original size:96 final size:95
Alignment explanation
Indices: 2826--3017 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 95
2816 TTTTTGGGAA
* *
2826 AAGGATATTCGATTATATCGATTTGAAAAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATATCGATTTGAAAAAAGATTGCACCTAGTAAGTTAAGGCACAATATTTCA
* * *
2891 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAACAAAAGG-AACATTACCTCGATT
* *
2922 AAGGGTATTCGATTATTTCGATTTGAAGAAAA-ATTGCACCTAGTAAGTTAAGGCACGAAT-TTT
1 AAGGATATTCGATTATATCGATTTGAA-AAAAGATTGCACCTAGTAAGTTAAGGCAC-AATATTT
*
2985 C-GAAACTCGAAACAAAAGG-ATATTACCTCGATT
64 CAG-AA-TCG-AACAAAAGGAACATTACCTCGATT
3018 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
95 1 0.01
96 65 0.78
97 10 0.12
98 7 0.08
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (95 bp):
AAGGATATTCGATTATATCGATTTGAAAAAAGATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAACAAAAGGAACATTACCTCGATT
Found at i:3357 original size:29 final size:28
Alignment explanation
Indices: 3241--3357 Score: 64
Period size: 29 Copynumber: 4.1 Consensus size: 28
3231 TTCGGATACC
*
3241 CGGGGGTAAAATGGTAATTTTG-GATTCT
1 CGGGGGTAAAAGGGTAATTTTGAGATT-T
*
3269 C-GGGG-AAAAGTGGTAATTTTTGGAAAATTT
1 CGGGGGTAAAAG-GGTAA-TTTT-G-AGATTT
* ** * *
3299 -GGGGTTAAAA-ATTGAATTTTTAGACATT
1 CGGGGGTAAAAGGGT-AATTTTGAGA-TTT
3327 CGGGGGTAAAAGGGTAATTTTGAGAGTTT
1 CGGGGGTAAAAGGGTAATTTTGAGA-TTT
3356 CG
1 CG
3358 AGGTCGAAAT
Statistics
Matches: 64, Mismatches: 14, Indels: 21
0.65 0.14 0.21
Matches are distributed among these distances:
26 4 0.06
27 11 0.17
28 7 0.11
29 28 0.44
30 7 0.11
31 7 0.11
ACGTcount: A:0.30, C:0.05, G:0.31, T:0.34
Consensus pattern (28 bp):
CGGGGGTAAAAGGGTAATTTTGAGATTT
Found at i:3368 original size:57 final size:58
Alignment explanation
Indices: 3307--3415 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 58
3297 TTGGGGTTAA
* * *
3307 AAATTGAATTTTTAGACATTCGGGGGTAAAAGGGTAA-TTTTGAGAGTTTCGAGGTCG
1 AAATTGAATTTTTAGACATTCGAGGGAAAAAGGGTAATTTTTGAAAGTTTCGAGGTCG
* * *
3364 AAATTGAGTTTTTGGACATTCGAGGGAAAAATGGTAATTTTTGAAAGTTTCG
1 AAATTGAATTTTTAGACATTCGAGGGAAAAAGGGTAATTTTTGAAAGTTTCG
3416 GGGGTAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
57 32 0.71
58 13 0.29
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.35
Consensus pattern (58 bp):
AAATTGAATTTTTAGACATTCGAGGGAAAAAGGGTAATTTTTGAAAGTTTCGAGGTCG
Found at i:3404 original size:29 final size:28
Alignment explanation
Indices: 3243--3437 Score: 80
Period size: 28 Copynumber: 6.8 Consensus size: 28
3233 CGGATACCCG
* *
3243 GGGGTAAAATGGTAA-TTTTGG-ATTCTC
1 GGGGAAAAATGGTAATTTTTGGAAAT-TC
* *
3270 GGGGAAAAGTGGTAATTTTTGGAAAATTT
1 GGGGAAAAATGGTAATTTTTGG-AAATTC
* * *
3299 GGGGTTAAAAATTG-AATTTTTAGACATTC
1 GGGG--AAAAATGGTAATTTTTGGAAATTC
* * **
3328 GGGGGTAAAAGGGTAA-TTTTGAGAGTTTC
1 -GGGGAAAAATGGTAATTTTTG-GAAATTC
*** * * *
3357 GAGGTCGAAATTG-AGTTTTTGGACATTC
1 G-GGGAAAAATGGTAATTTTTGGAAATTC
3385 GAGGGAAAAATGGTAATTTTT-GAAAGTTTC
1 G-GGGAAAAATGGTAATTTTTGGAAA--TTC
3415 GGGGGTAAAAATGG-AATTTTTGG
1 -GGGG-AAAAATGGTAATTTTTGG
3438 GAGTTTCGGG
Statistics
Matches: 123, Mismatches: 29, Indels: 28
0.68 0.16 0.16
Matches are distributed among these distances:
27 13 0.11
28 34 0.28
29 33 0.27
30 27 0.22
31 16 0.13
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (28 bp):
GGGGAAAAATGGTAATTTTTGGAAATTC
Found at i:3435 original size:30 final size:30
Alignment explanation
Indices: 3241--3448 Score: 91
Period size: 30 Copynumber: 7.2 Consensus size: 30
3231 TTCGGATACC
* *
3241 CGGGGGTAAAATGGTAA-TTTTG-GA-TTCT
1 CGGGGGAAAAATGGTAATTTTTGAAAGTT-T
* *
3269 C-GGGGAAAAGTGGTAATTTTTGGAAAATTT
1 CGGGGGAAAAATGGTAATTTTT-GAAAGTTT
* * *
3299 -GGGGTTAAAAATTG-AATTTTTAGACA--TT
1 CGGGG-GAAAAATGGTAATTTTT-GAAAGTTT
* * *
3327 CGGGGGTAAAAGGGTAA-TTTTGAGAGTTT
1 CGGGGGAAAAATGGTAATTTTTGAAAGTTT
* *** * * *
3356 CGAGGTCGAAATTG-AGTTTTTGGACA--TT
1 CGGGGGAAAAATGGTAATTTTT-GAAAGTTT
*
3384 CGAGGGAAAAATGGTAATTTTTGAAAGTTT
1 CGGGGGAAAAATGGTAATTTTTGAAAGTTT
**
3414 CGGGGGTAAAAATGG-AATTTTTGGGAGTTT
1 CGGGGG-AAAAATGGTAATTTTTGAAAGTTT
3444 CGGGG
1 CGGGG
3449 CTCCGGGATA
Statistics
Matches: 134, Mismatches: 30, Indels: 30
0.69 0.15 0.15
Matches are distributed among these distances:
27 16 0.12
28 32 0.24
29 27 0.20
30 43 0.32
31 16 0.12
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.34
Consensus pattern (30 bp):
CGGGGGAAAAATGGTAATTTTTGAAAGTTT
Found at i:5278 original size:17 final size:18
Alignment explanation
Indices: 5256--5298 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5246 GGCTTTATTT
**
5256 ATTTTAAATTT-ATGATA
1 ATTTTAAATTTGAAAATA
5273 ATTTTAAATTTGAAAATA
1 ATTTTAAATTTGAAAATA
5291 ATTTTAAA
1 ATTTTAAA
5299 CTTAAAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
ATTTTAAATTTGAAAATA
Found at i:5293 original size:18 final size:17
Alignment explanation
Indices: 5256--5354 Score: 63
Period size: 17 Copynumber: 5.5 Consensus size: 17
5246 GGCTTTATTT
**
5256 ATTTTAAATTTATGATA
1 ATTTTAAATTTAAAATA
5273 ATTTTAAATTTGAAAATA
1 ATTTTAAATTT-AAAATA
* *
5291 ATTTTAAACTTAAAGTAA
1 ATTTTAAATTTAAAAT-A
* *
5309 ATTAATTTAAATTTTTAAACA
1 A-T--TTTAAA-TTTAAAATA
* *
5330 AATTTAATTTTAAAATA
1 ATTTTAAATTTAAAATA
*
5347 AATTTAAA
1 ATTTTAAA
5355 AGGAATTTGA
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
17 29 0.46
18 21 0.33
19 1 0.02
21 8 0.13
22 4 0.06
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTTTAAATTTAAAATA
Found at i:5336 original size:39 final size:39
Alignment explanation
Indices: 5275--5350 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
5265 TTATGATAAT
* * *
5275 TTTAAATTTGAAAATAATTTTAAACTTAAAGTAAATTAA
1 TTTAAATTTGAAAACAAATTTAAACTTAAAATAAATTAA
** **
5314 TTTAAATTTTTAAACAAATTTAATTTTAAAATAAATT
1 TTTAAATTTGAAAACAAATTTAAACTTAAAATAAATT
5351 TAAAAGGAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (39 bp):
TTTAAATTTGAAAACAAATTTAAACTTAAAATAAATTAA
Found at i:6411 original size:19 final size:19
Alignment explanation
Indices: 6382--6419 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
6372 AAAATTGCAT
6382 ATAATTAAAATTTATAAAAA
1 ATAATTAAAATTTA-AAAAA
6402 ATAA-TAAAATTTAAAAAA
1 ATAATTAAAATTTAAAAAA
6420 TTTTAAACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAATTAAAATTTAAAAAA
Found at i:6648 original size:22 final size:22
Alignment explanation
Indices: 6603--6647 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
6593 CTTTTTCATA
6603 TTAATAATCAAAATTTAAAATT
1 TTAATAATCAAAATTTAAAATT
* *
6625 TTAATAAT-GAAATTTATAATT
1 TTAATAATCAAAATTTAAAATT
6646 TT
1 TT
6648 TTTTTCTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TTAATAATCAAAATTTAAAATT
Found at i:7252 original size:27 final size:28
Alignment explanation
Indices: 7222--7278 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
7212 TTTATAATTT
*
7222 ATAAAATTTTAA-ATTAATAATGATAAA
1 ATAAAATTTTAACATTAAAAATGATAAA
* *
7249 ATAATATTTTAACTTTTAAAAATGATAAA
1 ATAAAATTTTAAC-ATTAAAAATGATAAA
7278 A
1 A
7279 ATTTGATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 11 0.44
29 14 0.56
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (28 bp):
ATAAAATTTTAACATTAAAAATGATAAA
Found at i:7652 original size:178 final size:170
Alignment explanation
Indices: 7455--7768 Score: 423
Period size: 170 Copynumber: 1.8 Consensus size: 170
7445 TTAAGTTGTT
*
7455 TAATAATATAAGGAGTTCAATCATTA-AAATATTAAATTAAAATTTTAATAGAGAATTTTTATAT
1 TAATAATATAAGAAGTTCAATCATTATAAATATTAAATTAAAA-TTTAAT--AG--TTTTTATAT
**** * ** * *
7519 AATTTTTTTGAAATATTTTAATAAAGTTATTTTTTTATTTAAAAGAATATTTTAATCAATCACTT
61 AA-AAAATTGAAATATTTTAATAAAATTA--TTTTTACATAAAA-AATATTTTAACCAATCACTC
7584 TTAATAATTTTAGAGTATGAAATAGATTATTTTAATTATTTTAATAAAA
122 TTAATAATTTTAGAGTATGAAATAGATTATTTTAATTATTTTAATAAAA
7633 TAATAATATAAGAAGTTCAATCATTATAAATATTAAATTAAAATTTAATAGTTTTTATATAAAAA
1 TAATAATATAAGAAGTTCAATCATTATAAATATTAAATTAAAATTTAATAGTTTTTATATAAAAA
* * *
7698 ATTGAAATGTTTTAATAAAATTATTTTTACATAAAAAATATTTTAGCCAATCACTCTTAATAGTT
66 ATTGAAATATTTTAATAAAATTATTTTTACATAAAAAATATTTTAACCAATCACTCTTAATAATT
7763 TTAGAG
131 TTAGAG
7769 CTAAACTATA
Statistics
Matches: 122, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
170 31 0.25
171 11 0.09
173 20 0.16
174 11 0.09
176 2 0.02
178 31 0.25
179 16 0.13
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (170 bp):
TAATAATATAAGAAGTTCAATCATTATAAATATTAAATTAAAATTTAATAGTTTTTATATAAAAA
ATTGAAATATTTTAATAAAATTATTTTTACATAAAAAATATTTTAACCAATCACTCTTAATAATT
TTAGAGTATGAAATAGATTATTTTAATTATTTTAATAAAA
Found at i:21481 original size:22 final size:22
Alignment explanation
Indices: 21456--21498 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
21446 AAGCAACTAA
21456 AGCTCTAAGAGGCCAAGGAAGC
1 AGCTCTAAGAGGCCAAGGAAGC
21478 AGCTCTAAGAGGCCAAGGAAG
1 AGCTCTAAGAGGCCAAGGAAG
21499 TACAAACTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.21, G:0.33, T:0.09
Consensus pattern (22 bp):
AGCTCTAAGAGGCCAAGGAAGC
Found at i:28758 original size:32 final size:33
Alignment explanation
Indices: 28700--28776 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
28690 AATTTTCAAT
*
28700 AAATAAAAAATATATAAATTTATT-AAATATTA
1 AAATAAAAAATATATAAATTTATTAAAAAATTA
28732 AAATAAAACAATATA-AATATTT-TTAAAAAATTA
1 AAATAAAA-AATATATAA-ATTTATTAAAAAATTA
*
28765 AAA-AAATAATAT
1 AAATAAAAAATAT
28777 GAGCAAGCCT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
31 5 0.12
32 15 0.38
33 20 0.50
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (33 bp):
AAATAAAAAATATATAAATTTATTAAAAAATTA
Found at i:28776 original size:31 final size:31
Alignment explanation
Indices: 28683--28776 Score: 81
Period size: 31 Copynumber: 3.1 Consensus size: 31
28673 TAAGATGACT
* * *
28683 ATATAAAAATTTTCAATAAA-T-AAAAAAT-
1 ATATAAATATTTTTAAAAAATTAAAAAAATA
* * *
28711 ATATAAAT-TTATT-AAATATTAAAATAAAACA
1 ATATAAATATTTTTAAAAAATT-AAA-AAAATA
28742 ATATAAATATTTTTAAAAAATTAAAAAAATA
1 ATATAAATATTTTTAAAAAATTAAAAAAATA
28773 ATAT
1 ATAT
28777 GAGCAAGCCT
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
26 3 0.06
27 4 0.08
28 7 0.14
29 2 0.04
30 4 0.08
31 17 0.34
32 7 0.14
33 6 0.12
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (31 bp):
ATATAAATATTTTTAAAAAATTAAAAAAATA
Found at i:31833 original size:18 final size:18
Alignment explanation
Indices: 31800--31863 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
31790 ATCAACAAAT
*
31800 AATTT-AAAAATTATAAA
1 AATTTCAAAAAATATAAA
31817 AATATTCAAAAAA-ATAAA
1 AAT-TTCAAAAAATATAAA
31835 TTCAATTTTCAAAAAATATAAA
1 ---AA-TTTCAAAAAATATAAA
31857 AATTTCA
1 AATTTCA
31864 TAATTTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
17 3 0.08
18 12 0.31
19 7 0.18
21 11 0.28
22 6 0.15
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTTCAAAAAATATAAA
Found at i:36611 original size:17 final size:18
Alignment explanation
Indices: 36589--36623 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
36579 AATGATTATT
36589 TTTATT-TTTTTCTTTCC
1 TTTATTATTTTTCTTTCC
*
36606 TTTATTATTTTTTTTTCC
1 TTTATTATTTTTCTTTCC
36624 AATATCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATTATTTTTCTTTCC
Found at i:38262 original size:2 final size:2
Alignment explanation
Indices: 38255--38292 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
38245 ACTATTGGTT
38255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38293 AACAAAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39116 original size:34 final size:35
Alignment explanation
Indices: 39078--39154 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 35
39068 TGAAACTAAC
39078 AATAATTAAA-TAATTAATTAAAAATTCATAAAAA
1 AATAATTAAACTAATTAATTAAAAATTCATAAAAA
** * **
39112 AATAA-TAAACTGGTTCATTAAAAATTCATAATTA
1 AATAATTAAACTAATTAATTAAAAATTCATAAAAA
39146 AATAATTAA
1 AATAATTAA
39155 TTAAATATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 4 0.11
34 29 0.81
35 3 0.08
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (35 bp):
AATAATTAAACTAATTAATTAAAAATTCATAAAAA
Found at i:39157 original size:26 final size:25
Alignment explanation
Indices: 39128--39184 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
39118 AAACTGGTTC
39128 ATTAAAAATTCATAATTAAA-TAATTA
1 ATTAAAAATTCATAA--AAATTAATTA
*
39154 ATTAAATATTCATAAAAATTAATTA
1 ATTAAAAATTCATAAAAATTAATTA
*
39179 AATAAA
1 ATTAAA
39185 TAAAGCATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 3 0.11
25 11 0.39
26 14 0.50
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (25 bp):
ATTAAAAATTCATAAAAATTAATTA
Found at i:39184 original size:25 final size:25
Alignment explanation
Indices: 39130--39186 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
39120 ACTGGTTCAT
* *
39130 TAAAAATTCATAATTAAATAATTAAT
1 TAAATATTCATAA-TAAATAATTAAA
39156 TAAATATTCATAA-AAATTAATTAAA
1 TAAATATTCATAATAAA-TAATTAAA
39181 TAAATA
1 TAAATA
39187 AAGCATCGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 3 0.11
25 13 0.46
26 12 0.43
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAATATTCATAATAAATAATTAAA
Found at i:47225 original size:18 final size:18
Alignment explanation
Indices: 47196--47291 Score: 101
Period size: 18 Copynumber: 5.3 Consensus size: 18
47186 TTAATTAATT
47196 TTTTAAATATTTTAAAATA
1 TTTT-AATATTTTAAAATA
*
47215 TTTTTATATTTTAAAAT-
1 TTTTAATATTTTAAAATA
47232 TTTTAAAATATTTT--AATA
1 TTTT--AATATTTTAAAATA
*
47250 TTTTAAAATTTTTAAAATA
1 TTTTAATA-TTTTAAAATA
*
47269 TTTTTATATTTTAAAAT-
1 TTTTAATATTTTAAAATA
47286 TTTTAA
1 TTTTAA
47292 AAGTTAATTA
Statistics
Matches: 65, Mismatches: 6, Indels: 14
0.76 0.07 0.16
Matches are distributed among these distances:
16 3 0.05
17 16 0.25
18 25 0.38
19 21 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTAATATTTTAAAATA
Found at i:47226 original size:27 final size:27
Alignment explanation
Indices: 47219--47293 Score: 141
Period size: 27 Copynumber: 2.8 Consensus size: 27
47209 AAAATATTTT
47219 TATATTTTAAAATTTTTAAAATATTTT
1 TATATTTTAAAATTTTTAAAATATTTT
*
47246 AATATTTTAAAATTTTTAAAATATTTT
1 TATATTTTAAAATTTTTAAAATATTTT
47273 TATATTTTAAAATTTTTAAAA
1 TATATTTTAAAATTTTTAAAA
47294 GTTAATTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TATATTTTAAAATTTTTAAAATATTTT
Found at i:47263 original size:54 final size:54
Alignment explanation
Indices: 47190--47293 Score: 183
Period size: 54 Copynumber: 1.9 Consensus size: 54
47180 GTGCAGTTAA
*
47190 TTAATTTTTTAAATATTTTAAAATATTTTTATATTTTAAAATTTTTAAAATATT
1 TTAATTTTTAAAATATTTTAAAATATTTTTATATTTTAAAATTTTTAAAATATT
47244 TTAATATTTTAAAAT-TTTTAAAATATTTTTATATTTTAAAATTTTTAAAA
1 TTAAT-TTTTAAAATATTTTAAAATATTTTTATATTTTAAAATTTTTAAAA
47294 GTTAATTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
54 40 0.83
55 8 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (54 bp):
TTAATTTTTAAAATATTTTAAAATATTTTTATATTTTAAAATTTTTAAAATATT
Found at i:52765 original size:33 final size:36
Alignment explanation
Indices: 52723--52789 Score: 104
Period size: 33 Copynumber: 1.9 Consensus size: 36
52713 TGTTTATATG
*
52723 AAATTGAAGAGAAA-GAGAAGAG-AGA-CAAGGATC
1 AAATTGAAGAGAAAGGAAAAGAGAAGAGCAAGGATC
52756 AAATTGAAGAGAAAGGAAAAGAGAAGAGCAAGGA
1 AAATTGAAGAGAAAGGAAAAGAGAAGAGCAAGGA
52790 GTGAAAAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 14 0.47
34 7 0.23
35 3 0.10
36 6 0.20
ACGTcount: A:0.57, C:0.04, G:0.31, T:0.07
Consensus pattern (36 bp):
AAATTGAAGAGAAAGGAAAAGAGAAGAGCAAGGATC
Found at i:53731 original size:23 final size:23
Alignment explanation
Indices: 53697--53842 Score: 104
Period size: 23 Copynumber: 6.4 Consensus size: 23
53687 ACGCTAGCGC
53697 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
* *
53720 GCTTACTATTTCACACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
* * *
53743 GTTTACTGTTTCGAACCTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
* *
53766 GCCTATTGATTT-GCACTAT-GTGT
1 GCTTACTG-TTTCGCACT-TCGTGT
* * *
53789 GCCTATTGATT-GCACTGT-GTGT
1 GCTTACTGTTTCGCACT-TCGTGT
** *
53811 GCTTACTGTTAAGTACTTCG-GT
1 GCTTACTGTTTCGCACTTCGTGT
*
53833 ACTTACTGTT
1 GCTTACTGTT
53843 CCGTTTATCC
Statistics
Matches: 99, Mismatches: 20, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
22 31 0.31
23 64 0.65
24 4 0.04
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:53804 original size:22 final size:23
Alignment explanation
Indices: 53762--53812 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 23
53752 TTCGAACCTC
53762 GTGTGCCTATTGATTTGCACTAT
1 GTGTGCCTATTGATTTGCACTAT
*
53785 GTGTGCCTATTGA-TTGCACTGT
1 GTGTGCCTATTGATTTGCACTAT
53807 GTGTGC
1 GTGTGC
53813 TTACTGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.14, C:0.18, G:0.27, T:0.41
Consensus pattern (23 bp):
GTGTGCCTATTGATTTGCACTAT
Found at i:58017 original size:84 final size:84
Alignment explanation
Indices: 57876--58037 Score: 306
Period size: 84 Copynumber: 1.9 Consensus size: 84
57866 CTAAGTCTGC
*
57876 TCATTTCTTACCGGTAAGAACTGATTTCTCAATGGAAAAGTATGCTCAATTGTACATAGATGAAA
1 TCATTTCTTACCGGTAAGAACTGATTTCTCAATGGAAAAGCATGCTCAATTGTACATAGATGAAA
57941 TAGTTAGATTACACCTGTA
66 TAGTTAGATTACACCTGTA
*
57960 TCATTTCTTACCGGTAAGAACTGATTTCTCAATGGAAAAGCATGCTCAATTGTACATAGATGAGA
1 TCATTTCTTACCGGTAAGAACTGATTTCTCAATGGAAAAGCATGCTCAATTGTACATAGATGAAA
58025 TAGTTAGATTACA
66 TAGTTAGATTACA
58038 TGGTGTGCCT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (84 bp):
TCATTTCTTACCGGTAAGAACTGATTTCTCAATGGAAAAGCATGCTCAATTGTACATAGATGAAA
TAGTTAGATTACACCTGTA
Found at i:59722 original size:17 final size:17
Alignment explanation
Indices: 59700--59765 Score: 87
Period size: 17 Copynumber: 3.8 Consensus size: 17
59690 CCCCTTTTTA
*
59700 ATTTTAAATTTAGATTT
1 ATTTTAAATTTAAATTT
*
59717 ATTTTAAATTTAAATTA
1 ATTTTAAATTTAAATTT
*
59734 ATCTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
59751 AATTTTAAAATTAAA
1 -ATTTTAAATTTAAA
59766 AAAGTTCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
17 30 0.71
18 12 0.29
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:59727 original size:11 final size:12
Alignment explanation
Indices: 59696--59765 Score: 65
Period size: 12 Copynumber: 6.0 Consensus size: 12
59686 TGGGCCCCTT
*
59696 TTTAATTTTAAA
1 TTTAAATTTAAA
* *
59708 TTTAGATTT-AT
1 TTTAAATTTAAA
59719 TTTAAATTTAAA
1 TTTAAATTTAAA
59731 -TT-AATCTTAAA
1 TTTAAAT-TTAAA
*
59742 TTTAAATTTAAT
1 TTTAAATTTAAA
*
59754 TTTAAAATTAAA
1 TTTAAATTTAAA
59766 AAAGTTCAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
10 3 0.07
11 16 0.35
12 24 0.52
13 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:60465 original size:15 final size:15
Alignment explanation
Indices: 60445--60573 Score: 63
Period size: 15 Copynumber: 8.5 Consensus size: 15
60435 TTAATAATAG
60445 TAATAATTATT-TTAA
1 TAATAA-TATTATTAA
60460 TAATAATATTATTAA
1 TAATAATATTATTAA
* *
60475 TGAT-ATCATTAATAA
1 TAATAAT-ATTATTAA
**
60490 TAAATAAGT-TT-TTCT
1 T-AATAA-TATTATTAA
* *
60505 TAATATTCATTAATAA
1 TAATAAT-ATTATTAA
*
60521 TAATAA-ATGT-TTCGA
1 TAATAATAT-TATT-AA
*
60536 TAATAATAATATTAA
1 TAATAATATTATTAA
* *
60551 TAATAATAATAATAA
1 TAATAATATTATTAA
60566 TAATAATA
1 TAATAATA
60574 AAGGAGACAA
Statistics
Matches: 86, Mismatches: 16, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
13 1 0.01
14 13 0.15
15 57 0.66
16 13 0.15
17 1 0.01
18 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (15 bp):
TAATAATATTATTAA
Found at i:60475 original size:12 final size:12
Alignment explanation
Indices: 60435--60491 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
60425 TCAATAATTC
*
60435 TTAATAATAGTA
1 TTAATAATATTA
* * *
60447 ATAATTATTTTA
1 TTAATAATATTA
*
60459 ATAATAATATTA
1 TTAATAATATTA
* *
60471 TTAATGATATCA
1 TTAATAATATTA
60483 TTAATAATA
1 TTAATAATA
60492 AATAAGTTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (12 bp):
TTAATAATATTA
Found at i:60541 original size:3 final size:3
Alignment explanation
Indices: 60535--60574 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
60525 AAATGTTTCG
*
60535 ATA ATA ATA ATA TTA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
60575 AGGAGACAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:61704 original size:90 final size:88
Alignment explanation
Indices: 61568--61748 Score: 222
Period size: 90 Copynumber: 2.0 Consensus size: 88
61558 TTTTACCTTT
* *
61568 AAACTTCCAAAAATCCCATTTTAACTCCAAAACTTCCAAAAATCCCATTTTTACCCTAAAACTTA
1 AAACTTCCAAAAATCCAATTTTAACTCCAAAACTTCCAAAAATCCCATTTTTACCCCAAAACTTA
*
61633 AAAAAATCTCAATT-TTACCCCCA
66 AAAAAATCTC-ATTCTTAACCCCA
* * * **
61656 AAACTTCCAGAAAATCCTAATTTTGAC-CTCGAAACTTCTAAAAATCCCATTTTTACCCCCGAAC
1 AAACTTCCA-AAAATCC-AATTTTAACTC-CAAAACTTCCAAAAATCCCATTTTTACCCCAAAAC
**
61720 TTGCAAAAATCTCATTCTTAACCCCA
63 TTAAAAAAATCTCATTCTTAACCCCA
61746 AAA
1 AAA
61749 ATTACCATTT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
88 9 0.11
89 11 0.14
90 59 0.75
ACGTcount: A:0.40, C:0.29, G:0.03, T:0.28
Consensus pattern (88 bp):
AAACTTCCAAAAATCCAATTTTAACTCCAAAACTTCCAAAAATCCCATTTTTACCCCAAAACTTA
AAAAAATCTCATTCTTAACCCCA
Found at i:61735 original size:29 final size:29
Alignment explanation
Indices: 61538--61747 Score: 168
Period size: 29 Copynumber: 7.1 Consensus size: 29
61528 GAAGGTCCCT
* ***
61538 AAACTGTCCAAAAATCTAATTTTTACCTTT
1 AAACT-TCCAAAAATCTCATTTTTACCCCC
* * * *
61568 AAACTTCCAAAAATCCCATTTTAACTCCA
1 AAACTTCCAAAAATCTCATTTTTACCCCC
* **
61597 AAACTTCCAAAAATCCCATTTTTACCCTA
1 AAACTTCCAAAAATCTCATTTTTACCCCC
** *
61626 AAACTTAAAAAAATCTCAATTTTACCCCC
1 AAACTTCCAAAAATCTCATTTTTACCCCC
* * * *
61655 AAAACTTCCAGAAAATCCTAATTTTGACCTCG
1 -AAACTTCCA-AAAAT-CTCATTTTTACCCCC
* *
61687 AAACTTCTAAAAATCCCATTTTTACCCCC
1 AAACTTCCAAAAATCTCATTTTTACCCCC
* * * *
61716 GAACTTGCAAAAATCTCATTCTTAACCCC
1 AAACTTCCAAAAATCTCATTTTTACCCCC
61745 AAA
1 AAA
61748 AATTACCATT
Statistics
Matches: 141, Mismatches: 36, Indels: 7
0.77 0.20 0.04
Matches are distributed among these distances:
29 101 0.72
30 17 0.12
31 13 0.09
32 10 0.07
ACGTcount: A:0.39, C:0.28, G:0.03, T:0.30
Consensus pattern (29 bp):
AAACTTCCAAAAATCTCATTTTTACCCCC
Found at i:62167 original size:96 final size:96
Alignment explanation
Indices: 61997--62181 Score: 257
Period size: 96 Copynumber: 1.9 Consensus size: 96
61987 AAAACTTTAA
* * *
61997 AATCGAGGCAATATTCTGTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAATT
1 AATCGAGGCAATATTCTGTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACCAGGTACAATC
*
62062 TTTCTTCAAATCGAAATAATCGAATACCCTT
66 TTTCATCAAATCGAAATAATCGAATACCCTT
* * *
62093 AATCGAGGCAATGTTTCT-TTATCTTCGA-TTTTGAAAATTTTCGCCTTAACTTACCAGGTACAA
1 AATCGAGGCAAT-ATTCTGTTAT-TTCGAGTTTCGAAAATTTGCGCCTTAACTTACCAGGTACAA
**
62156 TCTTTCATCAAATCGGGATAATCGAA
64 TCTTTCATCAAATCGAAATAATCGAA
62182 CATCCTTTTC
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
96 69 0.88
97 9 0.12
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (96 bp):
AATCGAGGCAATATTCTGTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACCAGGTACAATC
TTTCATCAAATCGAAATAATCGAATACCCTT
Found at i:73964 original size:205 final size:205
Alignment explanation
Indices: 73526--74096 Score: 763
Period size: 205 Copynumber: 2.8 Consensus size: 205
73516 CTACGATGCG
* * * * ** * *
73526 GTCATCTTCCTAATAAGATACTGAGAATAAAACCAAATCAATGAAACGAGGCTCAAAGTGAGCAA
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA--ACTC-ACGCTCGAAGTGAGCAA
* * *
73591 ATCTTTGAACCCCAGCTTCCTGATGAGATACGAAGAAGCAGTGTGAAGCAATAAAAGGTTAGCTT
63 ATCTTCGAACCCCAGCTTCCTGATGAGATACGGAGAAGCAGAGTGAAGCAATAAAAGGTTAGCTT
* *
73656 CCTGATGAGATAGCTGAGAAGTGGATCAAATTCGCCTTCTTGATGAGATACAGAGAAGCGAATTG
128 CCTGATGAGATA-CTGAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGAATTG
** *
73721 AAATTAATGACGCA
192 AAACAAACGACGCA
*
73735 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGACGTGAGCAAATC
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGAAGTGAGCAAATC
* * *
73800 CTCGAACCCCAGCTTCCTGGTGAGATACGGAGAAGCAGAGTGAAGCAATAAAGGGTTAGCTTCCT
66 TTCGAACCCCAGCTTCCTGATGAGATACGGAGAAGCAGAGTGAAGCAATAAAAGGTTAGCTTCCT
**
73865 GATGAGATACTGAGAAGTGGACCAAATTCTTCTTCCTGATGAGATACAGAGAAGCGAATTGAAAC
131 GATGAGATACTGAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGAATTGAAAC
73930 AAACGACGCA
196 AAACGACGCA
73940 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGC-CTGATA-TGAGCAAA
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTC-GA-AGTGAGCAAA
* * * *
74003 TCTTCAAACCCCAGCTTCCTGATGAGACACTGAGAAGCA-AGTTGAAGTAATAAAATGGTTAGCT
64 TCTTCGAACCCCAGCTTCCTGATGAGATACGGAGAAGCAGAG-TGAAGCAATAAAA-GGTTAGCT
* * * *
74067 TCTTGGTGAAATAC-GAGGAAGTGAACCAAA
127 TCCTGATGAGATACTGA-GAAGTGGACCAAA
74097 ACCATTTTCT
Statistics
Matches: 323, Mismatches: 34, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
204 3 0.01
205 165 0.51
206 116 0.36
207 2 0.01
209 37 0.11
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (205 bp):
GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGAAGTGAGCAAATC
TTCGAACCCCAGCTTCCTGATGAGATACGGAGAAGCAGAGTGAAGCAATAAAAGGTTAGCTTCCT
GATGAGATACTGAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGAATTGAAAC
AAACGACGCA
Done.