Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014548.1 Kokia drynarioides strain JFW-HI SEQ_129587, 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: 28773
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Found at i:1180 original size:19 final size:20
Alignment explanation
Indices: 1144--1186 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1134 GTCTTTGAAT
*
1144 TTTTTAAAATTGATAAATTA
1 TTTTTAAAATTGATAAATAA
* *
1164 TTTTTATAATTTA-AAATAA
1 TTTTTAAAATTGATAAATAA
1183 TTTT
1 TTTT
1187 ACATTTAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAAAATTGATAAATAA
Found at i:2980 original size:31 final size:31
Alignment explanation
Indices: 2945--3035 Score: 87
Period size: 31 Copynumber: 2.9 Consensus size: 31
2935 TGATAAATAT
*
2945 ATTTTAATTTCGATTCAATTATACATATTAA
1 ATTTTAATTTTGATTCAATTATACATATTAA
* * *
2976 ATTTTTATTTTGGTTCAAATGTATA-A-ATAAA
1 ATTTTAATTTTGATTC-AAT-TATACATATTAA
* * *
3007 ACTTTGATTTTGATTCAATTGTACATATT
1 ATTTTAATTTTGATTCAATTATACATATT
3036 TAAAGAAATG
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
29 3 0.06
30 4 0.09
31 32 0.68
32 4 0.09
33 4 0.09
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (31 bp):
ATTTTAATTTTGATTCAATTATACATATTAA
Found at i:14200 original size:59 final size:59
Alignment explanation
Indices: 14072--14373 Score: 486
Period size: 59 Copynumber: 5.2 Consensus size: 59
14062 CAAAAATGAG
* *
14072 ATTTTTGGAA-GTTCGGGGTCAAAAATGGGA-TTTTGGAAGTTTAGGGGTAAAATGGTG
1 ATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTA
*
14129 ATTTTTGGAAGGTTCGGGGTAAAAAATGGTGATTTTTGGAAGTTCAGGGGTAAAAT-GTA
1 ATTTTTGGAAGGTTCGGGGTCAAAAATGG-GATTTTTGGAAGTTCAGGGGTAAAATGGTA
* *
14188 ATTTTTGGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTTAGGGGTAAAATGGTA
1 ATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTA
*
14247 ATTTTTGGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC-GAGGGTAAAATGGTA
1 ATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAG-GGGTAAAATGGTA
*
14306 ATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAAGGGTAAAATGGTA
1 ATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTA
*
14365 ACTTTTGGA
1 ATTTTTGGA
14374 TAGTTTAGGG
Statistics
Matches: 227, Mismatches: 12, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
57 10 0.04
58 43 0.19
59 152 0.67
60 22 0.10
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.33
Consensus pattern (59 bp):
ATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTA
Found at i:14359 original size:29 final size:29
Alignment explanation
Indices: 14053--14349 Score: 342
Period size: 29 Copynumber: 10.1 Consensus size: 29
14043 ACTTTTAGAT
*
14053 GTTCGGGGTCAAAAATGAGATTTTTGGAA
1 GTTCGGGGTCAAAAATGGGATTTTTGGAA
14082 GTTCGGGGTCAAAAATGGGA-TTTTGGAA
1 GTTCGGGGTCAAAAATGGGATTTTTGGAA
*
14110 GTTTAGGGGT--AAAATGGTGATTTTTGGAA
1 G-TTCGGGGTCAAAAATGG-GATTTTTGGAA
*
14139 GGTTCGGGGTAAAAAATGGTGATTTTTGGAA
1 -GTTCGGGGTCAAAAATGG-GATTTTTGGAA
**
14170 GTTCAGGGGT--AAAATGTAATTTTTGGAA
1 GTTC-GGGGTCAAAAATGGGATTTTTGGAA
*
14198 GGTTCGGGGTCAAAAATGAGATTTTTGGAA
1 -GTTCGGGGTCAAAAATGGGATTTTTGGAA
* *
14228 GTTTAGGGGT--AAAATGGTAATTTTTGGAAA
1 G-TTCGGGGTCAAAAATGG-GATTTTTGG-AA
14258 GTTCGGGGTCAAAAATGGGATTTTTGGAA
1 GTTCGGGGTCAAAAATGGGATTTTTGGAA
*
14287 GTTCGAGGGT--AAAATGGTAATTTTTGGAA
1 GTTCG-GGGTCAAAAATGG-GATTTTTGGAA
14316 GGTTCGGGGTCAAAAATGGGATTTTTGGAA
1 -GTTCGGGGTCAAAAATGGGATTTTTGGAA
14346 GTTC
1 GTTC
14350 AAGGGTAAAA
Statistics
Matches: 234, Mismatches: 14, Indels: 40
0.81 0.05 0.14
Matches are distributed among these distances:
27 7 0.03
28 39 0.17
29 92 0.39
30 58 0.25
31 38 0.16
ACGTcount: A:0.29, C:0.05, G:0.33, T:0.33
Consensus pattern (29 bp):
GTTCGGGGTCAAAAATGGGATTTTTGGAA
Found at i:14383 original size:29 final size:28
Alignment explanation
Indices: 14072--14383 Score: 260
Period size: 29 Copynumber: 10.6 Consensus size: 28
14062 CAAAAATGAG
* *
14072 ATTTTTGGAAGTTCGGGGTCAAAAATGG-G
1 ATTTTTGGAAGTTCAGGGT--AAAATGGTA
* *
14101 A-TTTTGGAAGTTTAGGGGTAAAATGGTG
1 ATTTTTGGAAGTTCA-GGGTAAAATGGTA
* *
14129 ATTTTTGGAAGGTTCGGGGTAAAAAATGGTG
1 ATTTTTGGAA-GTTCAGGGT--AAAATGGTA
14160 ATTTTTGGAAGTTCAGGGGTAAAAT-GTA
1 ATTTTTGGAAGTTCA-GGGTAAAATGGTA
*
14188 ATTTTTGGAAGGTTCGGGGTCAAAAAT-G-A
1 ATTTTTGGAA-GTTCAGGGT--AAAATGGTA
*
14217 GATTTTTGGAAGTTTAGGGGTAAAATGGTA
1 -ATTTTTGGAAGTTCA-GGGTAAAATGGTA
* *
14247 ATTTTTGGAAAGTTCGGGGTCAAAAATGG-G
1 ATTTTTGG-AAGTTCAGGGT--AAAATGGTA
14277 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGTTC-AGGGTAAAATGGTA
* *
14306 ATTTTTGGAAGGTTCGGGGTCAAAAATGG-G
1 ATTTTTGGAA-GTTCAGGGT--AAAATGGTA
14336 ATTTTTGGAAGTTCAAGGGTAAAATGGTA
1 ATTTTTGGAAGTTC-AGGGTAAAATGGTA
* *
14365 ACTTTTGGATAGTTTAGGG
1 ATTTTTGGA-AGTTCAGGG
14384 ACCTCCGAGG
Statistics
Matches: 238, Mismatches: 20, Indels: 50
0.77 0.06 0.16
Matches are distributed among these distances:
27 7 0.03
28 48 0.20
29 79 0.33
30 67 0.28
31 37 0.16
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.34
Consensus pattern (28 bp):
ATTTTTGGAAGTTCAGGGTAAAATGGTA
Found at i:15711 original size:17 final size:16
Alignment explanation
Indices: 15691--15767 Score: 82
Period size: 17 Copynumber: 4.6 Consensus size: 16
15681 AAATAAATTT
15691 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
*
15708 TAAATTTAAATTTCAAC
1 TAAATTTAAATTT-AAA
*
15725 CAAATTTAAATTTAGAA
1 TAAATTTAAATTTA-AA
* *
15742 TAAACTTAATTTTAAAA
1 TAAATTTAAATTT-AAA
15759 TAAATTTAA
1 TAAATTTAA
15768 GTTGATTGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
16 1 0.02
17 47 0.94
18 2 0.04
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:15764 original size:34 final size:34
Alignment explanation
Indices: 15691--15767 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 34
15681 AAATAAATTT
* * * *
15691 TAAATTTAAATTTATAATAAATTTAAATTTCAAC
1 TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
* *
15725 CAAATTTAAATTTAGAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
15759 TAAATTTAA
1 TAAATTTAA
15768 GTTGATTGGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (34 bp):
TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
Found at i:16583 original size:2 final size:2
Alignment explanation
Indices: 16576--16607 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16566 TGGTTTTCAA
16576 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
16608 GTTGGATCTT
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:17422 original size:19 final size:21
Alignment explanation
Indices: 17381--17422 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
17371 TTGAATAGGA
* *
17381 AATTTTAATTGTGTAGTGCTT
1 AATTTTAAGTGTGTAGTGATT
17402 AATTTTAAGTGT-TAG-GATT
1 AATTTTAAGTGTGTAGTGATT
17421 AA
1 AA
17423 ATTAAATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 3 0.16
21 11 0.58
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (21 bp):
AATTTTAAGTGTGTAGTGATT
Found at i:22289 original size:23 final size:23
Alignment explanation
Indices: 22263--22404 Score: 95
Period size: 23 Copynumber: 6.4 Consensus size: 23
22253 ACACTAGCGC
22263 GCTCTCTGTTTAGCACTTCGTGT
1 GCTCTCTGTTTAGCACTTCGTGT
*
22286 GCTCTCTGATTAGCACTTCGTGT
1 GCTCTCTGTTTAGCACTTCGTGT
* *
22309 G--CTC-----AGTACTTTGTGT
1 GCTCTCTGTTTAGCACTTCGTGT
* * **
22325 ACTCTCTGTTTAGCATTTTATGT
1 GCTCTCTGTTTAGCACTTCGTGT
* *
22348 GCTCTCTGTTGCCCAGCACTT-ATGT
1 GCTCTCTGTT---TAGCACTTCGTGT
*
22373 GCTCTCTGTTTAGTACTTCG-GT
1 GCTCTCTGTTTAGCACTTCGTGT
*
22395 ACTCTCTGTT
1 GCTCTCTGTT
22405 CCGTTTATCC
Statistics
Matches: 94, Mismatches: 14, Indels: 23
0.72 0.11 0.18
Matches are distributed among these distances:
16 10 0.11
18 3 0.03
21 3 0.03
22 17 0.18
23 41 0.44
25 14 0.15
26 6 0.06
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTTCGTGT
Found at i:22349 original size:39 final size:39
Alignment explanation
Indices: 22277--22351 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
22267 TCTGTTTAGC
* *
22277 ACTTCGTGTGCTCTCTGATTAGCACTTCGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTCATGTGCTCAGT
* * * *
22316 ACTTTGTGTACTCTCTGTTTAGCATTTTATGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTCATGTGCTC
22352 TCTGTTGCCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTCATGTGCTCAGT
Found at i:23560 original size:19 final size:20
Alignment explanation
Indices: 23538--23587 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
23528 AAAATAATAA
23538 ATTTTAATAAATT-ATAAA-C
1 ATTTTAA-AAATTAATAAATC
23557 ATTTTACAAAATTAATAAATC
1 ATTTTA-AAAATTAATAAATC
23578 ATATTTAAAA
1 AT-TTTAAAA
23588 TTTTATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 11 0.41
20 6 0.22
21 6 0.22
22 4 0.15
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTTAAAAATTAATAAATC
Found at i:24268 original size:10 final size:9
Alignment explanation
Indices: 24217--24340 Score: 81
Period size: 10 Copynumber: 13.0 Consensus size: 9
24207 TTATGATTTT
*
24217 TTTTTGTAA
1 TTTTTATAA
*
24226 ATTTTATAA
1 TTTTTATAA
*
24235 GTTTGTATCAA
1 -TTTTTAT-AA
*
24246 TTTTAAT-A
1 TTTTTATAA
24254 TTTTTAATAA
1 TTTTT-ATAA
*
24264 TTTTTATGA
1 TTTTTATAA
24273 TTTTTATAA
1 TTTTTATAA
*
24282 GTTTTTAAGAA
1 -TTTTT-ATAA
* *
24293 TTTGTATATG
1 TTTTTATA-A
24303 TTTTTATAA
1 TTTTTATAA
24312 TATTTTATATA
1 T-TTTTATA-A
24323 TTTTTATTAA
1 TTTTTA-TAA
24333 -TTTTATAA
1 TTTTTATAA
24341 AAAATTATAA
Statistics
Matches: 90, Mismatches: 15, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
8 8 0.09
9 28 0.31
10 45 0.50
11 9 0.10
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:24295 original size:20 final size:19
Alignment explanation
Indices: 24246--24308 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
24236 TTTGTATCAA
*
24246 TTTTAATATTTTTAATAA-T
1 TTTTAAGATTTTT-ATAAGT
*
24265 TTTTATGATTTTTATAAGT
1 TTTTAAGATTTTTATAAGT
* *
24284 TTTTAAGAATTTGTATATGT
1 TTTTAAG-ATTTTTATAAGT
24304 TTTTA
1 TTTTA
24309 TAATATTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 4 0.11
19 18 0.49
20 15 0.41
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (19 bp):
TTTTAAGATTTTTATAAGT
Found at i:24337 original size:9 final size:10
Alignment explanation
Indices: 24230--24339 Score: 54
Period size: 9 Copynumber: 11.2 Consensus size: 10
24220 TTGTAAATTT
* *
24230 TATAAGTTTG
1 TATAATTTTA
24240 TATCAATTTTA
1 TAT-AATTTTA
*
24251 -ATATTTTTA
1 TATAATTTTA
24260 -ATAATTTT-
1 TATAATTTTA
*
24268 TATGATTTT-
1 TATAATTTTA
24277 TATAAGTTTT-
1 TATAA-TTTTA
*
24287 TAAGAATTTGTA
1 T-ATAATTT-TA
**
24299 TATGTTTTTA
1 TATAATTTTA
24309 TA-ATATTTTA
1 TATA-ATTTTA
*
24319 TATATTTTTA
1 TATAATTTTA
24329 T-TAATTTTA
1 TATAATTTTA
24338 TA
1 TA
24340 AAAAATTATA
Statistics
Matches: 77, Mismatches: 14, Indels: 18
0.71 0.13 0.17
Matches are distributed among these distances:
9 32 0.42
10 30 0.39
11 14 0.18
12 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (10 bp):
TATAATTTTA
Found at i:24374 original size:20 final size:19
Alignment explanation
Indices: 24325--24385 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 19
24315 TTTATATATT
*
24325 TTTATTAATTTTATAAAAA
1 TTTATTAATTTTATTAAAA
*
24344 ATTA-TAA-TTTATTAAAA
1 TTTATTAATTTTATTAAAA
* *
24361 TTTATTAGATTTTAATAATA
1 TTTATTA-ATTTTATTAAAA
24381 TTTAT
1 TTTAT
24386 CAGTTTTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
17 12 0.35
18 5 0.15
19 4 0.12
20 13 0.38
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TTTATTAATTTTATTAAAA
Found at i:24680 original size:17 final size:17
Alignment explanation
Indices: 24648--24712 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
24638 GTTTATATTA
* *
24648 AATTTAATAATTTTAA-
1 AATTTTATATTTTTAAT
*
24664 AATATTTTTATTTTTAAT
1 AAT-TTTATATTTTTAAT
24682 AATTTTATATTTTT-AT
1 AATTTTATATTTTTAAT
24698 -A-TTTATAATTTTTAA
1 AATTTTAT-ATTTTTAA
24713 GATTTTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
14 5 0.12
15 7 0.17
16 6 0.15
17 20 0.49
18 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTTATATTTTTAAT
Found at i:24682 original size:15 final size:15
Alignment explanation
Indices: 24664--24719 Score: 60
Period size: 15 Copynumber: 3.6 Consensus size: 15
24654 ATAATTTTAA
24664 AATATTTTTATTTTT
1 AATATTTTTATTTTT
24679 AATAATTTTATATTTTT
1 AAT-ATTTT-TATTTTT
*
24696 -ATATTTATAATTTTT
1 AATATTT-TTATTTTT
*
24711 AAGATTTTT
1 AATATTTTT
24720 TAATCATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 14 0.41
16 13 0.38
17 7 0.21
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (15 bp):
AATATTTTTATTTTT
Found at i:24691 original size:23 final size:24
Alignment explanation
Indices: 24649--24719 Score: 83
Period size: 23 Copynumber: 2.9 Consensus size: 24
24639 TTTATATTAA
24649 ATTTAATAATTTTAAAATATTTTTAT
1 ATTTAATAATTTT--AATATTTTTAT
*
24675 TTTTAATAATTTT-ATATTTTTAT
1 ATTTAATAATTTTAATATTTTTAT
*
24698 ATTT-ATAATTTTTAAGATTTTT
1 ATTTAATAA-TTTTAATATTTTT
24720 TAATCATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 4 0.10
23 17 0.43
24 7 0.17
26 12 0.30
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (24 bp):
ATTTAATAATTTTAATATTTTTAT
Found at i:24697 original size:8 final size:8
Alignment explanation
Indices: 24665--24711 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
24655 TAATTTTAAA
24665 ATATTTTT
1 ATATTTTT
*
24673 AT-TTTTA
1 ATATTTTT
*
24680 ATAATTTT
1 ATATTTTT
24688 ATATTTTT
1 ATATTTTT
*
24696 ATATTTAT
1 ATATTTTT
24704 A-ATTTTT
1 ATATTTTT
24711 A
1 A
24712 AGATTTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
7 12 0.38
8 20 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
ATATTTTT
Found at i:25154 original size:28 final size:29
Alignment explanation
Indices: 25103--25157 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
25093 TGAAAATTGA
** *
25103 TAAAAAAAAAATTTTGAGCCCTTAAAAAC
1 TAAAAAAAAAATTAGGAGCACTTAAAAAC
25132 TAAAAAAAAAATTAGGA-CACTTAAAA
1 TAAAAAAAAAATTAGGAGCACTTAAAA
25158 GTTGATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.60, C:0.11, G:0.07, T:0.22
Consensus pattern (29 bp):
TAAAAAAAAAATTAGGAGCACTTAAAAAC
Found at i:25214 original size:29 final size:29
Alignment explanation
Indices: 25089--25216 Score: 75
Period size: 29 Copynumber: 4.3 Consensus size: 29
25079 TTTTTGAAAT
*
25089 CTCTTGAAAATTGATAAAAAAAAAATTTTGAG-
1 CTCTTAAAAATT-A-AAAAAAAAAA--TTGAGA
* *
25121 CCCTTAAAAACT-AAAAAAAAAATT-AGGA
1 CTCTTAAAAATTAAAAAAAAAAATTGA-GA
* * * * * **
25149 CACTTAAAAGTTGATAAAAAAATTTTTGA
1 CTCTTAAAAATTAAAAAAAAAAATTGAGA
*
25178 CT-TGTAAAAATTAAAAAAAAAAATTGAGC
1 CTCT-TAAAAATTAAAAAAAAAAATTGAGA
25207 CTCTTAAAAA
1 CTCTTAAAAA
25217 AAATTTGGAT
Statistics
Matches: 73, Mismatches: 17, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
26 1 0.01
27 3 0.04
28 10 0.14
29 49 0.67
30 1 0.01
32 9 0.12
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.27
Consensus pattern (29 bp):
CTCTTAAAAATTAAAAAAAAAAATTGAGA
Found at i:26598 original size:10 final size:10
Alignment explanation
Indices: 26565--26623 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
26555 AATGTGTTAA
26565 AAAAATAAAT
1 AAAAATAAAT
*
26575 ATAAATAGACAT
1 AAAAATA-A-AT
26587 AAAAATAAAT
1 AAAAATAAAT
*
26597 AAAGATAAAAT
1 AAAAAT-AAAT
**
26608 AAGGATAAAT
1 AAAAATAAAT
26618 AAAAAT
1 AAAAAT
26624 TATACAAGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
10 21 0.52
11 11 0.28
12 8 0.20
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:26609 original size:21 final size:21
Alignment explanation
Indices: 26565--26621 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
26555 AATGTGTTAA
*
26565 AAAAATAAATATAAATAGACAT
1 AAAAATAAATA-AAATAGAAAT
26587 AAAAATAAATAAAGATA-AAAT
1 AAAAATAAATAAA-ATAGAAAT
**
26608 AAGGATAAATAAAA
1 AAAAATAAATAAAA
26622 ATTATACAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 1 0.03
21 16 0.52
22 14 0.45
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (21 bp):
AAAAATAAATAAAATAGAAAT
Found at i:26849 original size:19 final size:16
Alignment explanation
Indices: 26827--26865 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 16
26817 TTTTAATTTT
26827 AAAATTTTAGATTAAATCA
1 AAAATTTTA-A-TAAA-CA
26846 AAAATTTTAATAAACA
1 AAAATTTTAATAAACA
26862 AAAA
1 AAAA
26866 AGTTACGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 4 0.20
18 1 0.05
19 9 0.45
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (16 bp):
AAAATTTTAATAAACA
Done.