Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012938.1 Kokia drynarioides strain JFW-HI SEQ_127956, 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: 89200
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:3963 original size:44 final size:44
Alignment explanation
Indices: 3844--3965 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 44
3834 TTTGAAAATT
* **
3844 GGAACATTGTTTCCCTATTATTGAAAGTATGTGATTGATTGAGA
1 GGAACATTGTTTCCTTATTATTGAAAGTATGTGATCAATTGAGA
** * *
3888 GTTACACTGTTT-CTTATTATTGAAATTATGTGATCAATTGAGA
1 GGAACATTGTTTCCTTATTATTGAAAGTATGTGATCAATTGAGA
3931 GGAACATTGTTTCCTTATTATTGAAAGTATGTGAT
1 GGAACATTGTTTCCTTATTATTGAAAGTATGTGAT
3966 TGACTAAGAG
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
43 36 0.55
44 30 0.45
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.42
Consensus pattern (44 bp):
GGAACATTGTTTCCTTATTATTGAAAGTATGTGATCAATTGAGA
Found at i:4000 original size:13 final size:13
Alignment explanation
Indices: 3982--4015 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
3972 AGAGCATGTT
*
3982 GAATATGCCAAAA
1 GAATATGACAAAA
3995 GAATATGACAAAA
1 GAATATGACAAAA
4008 GAATATGA
1 GAATATGA
4016 AAAGTATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.56, C:0.09, G:0.18, T:0.18
Consensus pattern (13 bp):
GAATATGACAAAA
Found at i:9520 original size:343 final size:343
Alignment explanation
Indices: 8889--9578 Score: 1236
Period size: 343 Copynumber: 2.0 Consensus size: 343
8879 TGATATAGAT
* *
8889 TTTGCTATATACATTTAATGTTATTGATTTGATATGTTTTAGGTATCCTAATACGTCATTCTATA
1 TTTGCTATATACATGTAATGTTATTGATTTGATATGTTTTAGGTATCCTAATACATCATTCTATA
** *
8954 TTGTGTATACATGTTTTGACATGTGTGACTATGAATCATAAAGGTGTGAATTGGTTGCCCTATTT
66 TTGTGTATACATGTTTTGACATACGTGACTATGAATCATAAAGGTGTAAATTGGTTGCCCTATTT
*
9019 CGAAACTTGAAATAGGTATCAAATGGCTCAAATTTTACCAAAAATGGAGCACACGTCCTGACAAG
131 CGAAACTTGAAATAGGTATCAAATGGCTCAAATTTTACCAAAAATAGAGCACACGTCCTGACAAG
9084 CATTCTTTCTCATCACAACATCGTCCGACATGACTCATGTCACAACATTGAGTGATCTGAAGTAA
196 CATTCTTTCTCATCACAACATCGTCCGACATGACTCATGTCACAACATTGAGTGATCTGAAGTAA
* *
9149 AGACGTGACAAAATTTTTGGCGAAGTCACGACGTTGAGGAAGTGACATCATGACGTCGACCCTGA
261 AGACGCGACAAAATTTTTGGCAAAGTCACGACGTTGAGGAAGTGACATCATGACGTCGACCCTGA
9214 GATTTTAAAACTTTACAA
326 GATTTTAAAACTTTACAA
*
9232 TTTGCTATATACATGTAATGTTATTGATTTGATATGTTTTAGGTATCCTAATACATCGTTCTATA
1 TTTGCTATATACATGTAATGTTATTGATTTGATATGTTTTAGGTATCCTAATACATCATTCTATA
*
9297 TTGTGTATACATGTTTTGACATACGTGACTATGAATCATAAAGGTGTAAATTGGTTGCCTTATTT
66 TTGTGTATACATGTTTTGACATACGTGACTATGAATCATAAAGGTGTAAATTGGTTGCCCTATTT
*
9362 CGAAACTTGAAATTGGTATCAAATGGCTCAAATTTTACCAAAAATAGAGCACACGTCCTGACAAG
131 CGAAACTTGAAATAGGTATCAAATGGCTCAAATTTTACCAAAAATAGAGCACACGTCCTGACAAG
* * * *
9427 CATTTTTTCTCGTCACAACATCGTCCGACATGACTCATGTCGCAACATTGAGTGGTCTGAAGTAA
196 CATTCTTTCTCATCACAACATCGTCCGACATGACTCATGTCACAACATTGAGTGATCTGAAGTAA
*
9492 AGACGCGACAAAATTTTTGGCAAAGTCACGACGTTGAGGAAGTGACGTCATGACGTCGACCCTGA
261 AGACGCGACAAAATTTTTGGCAAAGTCACGACGTTGAGGAAGTGACATCATGACGTCGACCCTGA
9557 GATTTTAAAACTTTACAA
326 GATTTTAAAACTTTACAA
9575 TTTG
1 TTTG
9579 ATCCTATTTC
Statistics
Matches: 331, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
343 331 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (343 bp):
TTTGCTATATACATGTAATGTTATTGATTTGATATGTTTTAGGTATCCTAATACATCATTCTATA
TTGTGTATACATGTTTTGACATACGTGACTATGAATCATAAAGGTGTAAATTGGTTGCCCTATTT
CGAAACTTGAAATAGGTATCAAATGGCTCAAATTTTACCAAAAATAGAGCACACGTCCTGACAAG
CATTCTTTCTCATCACAACATCGTCCGACATGACTCATGTCACAACATTGAGTGATCTGAAGTAA
AGACGCGACAAAATTTTTGGCAAAGTCACGACGTTGAGGAAGTGACATCATGACGTCGACCCTGA
GATTTTAAAACTTTACAA
Found at i:11567 original size:23 final size:23
Alignment explanation
Indices: 11515--11569 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
11505 TGACGTGGCG
* *
11515 TCCAGTCAGTAGCTTCTAGAAGA
1 TCCAGTCAGTAGCTTCCAAAAGA
*
11538 TCCAGTCAGTAGCTTCCAAAAGG
1 TCCAGTCAGTAGCTTCCAAAAGA
*
11561 TCTAGTCAG
1 TCCAGTCAG
11570 CAAGGATGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (23 bp):
TCCAGTCAGTAGCTTCCAAAAGA
Found at i:17268 original size:16 final size:14
Alignment explanation
Indices: 17237--17280 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
17227 TTTATTTCGA
*
17237 TTATTTATATTATT
1 TTATTTTTATTATT
17251 TTATTTTTACTTATTT
1 TTATTTTTA-TTA-TT
*
17267 TTATTTTTGTTATT
1 TTATTTTTATTATT
17281 CAGGTATGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 10 0.38
15 6 0.23
16 10 0.38
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (14 bp):
TTATTTTTATTATT
Found at i:17280 original size:15 final size:16
Alignment explanation
Indices: 17237--17274 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
17227 TTTATTTCGA
*
17237 TTATTTATA-TTA-TT
1 TTATTTTTACTTATTT
17251 TTATTTTTACTTATTT
1 TTATTTTTACTTATTT
17267 TTATTTTT
1 TTATTTTT
17275 GTTATTCAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 3 0.14
16 10 0.48
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTTACTTATTT
Found at i:18680 original size:10 final size:11
Alignment explanation
Indices: 18661--18689 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
18651 AATAAAGAAA
18661 AAAAAGAAGAG
1 AAAAAGAAGAG
18672 AAAAA-AAGAG
1 AAAAAGAAGAG
18682 AAAAAGAA
1 AAAAAGAA
18690 AAAAAAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAAGAAGAG
Found at i:19480 original size:23 final size:23
Alignment explanation
Indices: 19427--19481 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
19417 CTGACGTGGC
* * *
19427 ATCCAATCAGCAGCTTTTAGAAG
1 ATCCAGTCAGCAGCTTCTAAAAG
19450 ATCCAGTCAGCAGCTTCTAAAAG
1 ATCCAGTCAGCAGCTTCTAAAAG
* *
19473 GTCTAGTCA
1 ATCCAGTCA
19482 ACAAGGATGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (23 bp):
ATCCAGTCAGCAGCTTCTAAAAG
Found at i:21268 original size:82 final size:80
Alignment explanation
Indices: 21162--21444 Score: 275
Period size: 82 Copynumber: 3.4 Consensus size: 80
21152 TATGTTTCAG
* * *
21162 GATTTATTTCCCGTCGGTTAACAGATTTTATTCTA-TTTGATTTTATTTCCAAAAATGAGAATAT
1 GATTTA-TTCCCG-CCGTTAACAGATTTTATTCTAGTTTGATTTTGTTTCCAAAAAT-A-AATAA
* *
21226 GTAAATAAATCTGTTTCGG
62 GTAAATAAATCTATTTCGA
* * * *
21245 GATTTATTCCCGCCGTTGAACAGATTTAATTTTATATTTTGATTTTGGTTT-CAAATAATAATTA
1 GATTTATTCCCGCCGTT-AACAGATTT--TATTCTAGTTTGATTTT-GTTTCCAAA-AATAAATA
21309 AGTAAATAAATCTATTTCGA
61 AGTAAATAAATCTATTTCGA
* * * *
21329 GATTTATTCCCACCATTTAATAGATTTTATTCAAGTTTGATTTTGTTTCC-AAAATAAAATAAGT
1 GATTTATTCCCGCC-GTTAACAGATTTTATTCTAGTTTGATTTTGTTTCCAAAAAT-AAATAAG-
* *
21393 TGACTAAATCTATTTCGA
63 TAAATAAATCTATTTCGA
* *
21411 GATTTATTCCCGTCGATTAACAGATTATATTCTA
1 GATTTATTCCCGCCG-TTAACAGATTTTATTCTA
21445 TTTTTTATTT
Statistics
Matches: 165, Mismatches: 24, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
80 3 0.02
81 16 0.10
82 72 0.44
83 6 0.04
84 46 0.28
85 16 0.10
86 6 0.04
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (80 bp):
GATTTATTCCCGCCGTTAACAGATTTTATTCTAGTTTGATTTTGTTTCCAAAAATAAATAAGTAA
ATAAATCTATTTCGA
Found at i:23626 original size:14 final size:14
Alignment explanation
Indices: 23607--23636 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
23597 AAGGTAGATA
23607 ACCATCCTATAACC
1 ACCATCCTATAACC
23621 ACCATCCTATAACC
1 ACCATCCTATAACC
23635 AC
1 AC
23637 TTGAAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.43, G:0.00, T:0.20
Consensus pattern (14 bp):
ACCATCCTATAACC
Found at i:23675 original size:29 final size:29
Alignment explanation
Indices: 23631--23686 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
23621 ACCATCCTAT
*
23631 AACCACTTGAAAATGTGGGGGTGTCTTAC
1 AACCACTTGAAAATGTGGGGGTATCTTAC
*
23660 AACCACTTGAATATGTGGGGGTATCTT
1 AACCACTTGAAAATGTGGGGGTATCTT
23687 GTTAAATGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (29 bp):
AACCACTTGAAAATGTGGGGGTATCTTAC
Found at i:25482 original size:2 final size:2
Alignment explanation
Indices: 25475--25500 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25465 TGGATATTAA
25475 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
25501 TCAGAGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25734 original size:19 final size:19
Alignment explanation
Indices: 25712--25756 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
25702 TTATATTAGG
25712 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
25731 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
25750 ATTTAAT
1 ATTTAAT
25757 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:26601 original size:21 final size:22
Alignment explanation
Indices: 26551--26611 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
26541 TTCAACTTCC
*
26551 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTATTTTTAATT
26573 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
26595 CTA-TTTCTTTTATTTTT
1 CTATTTTCTTTTATTTTT
26612 CCTTAGATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
21 17 0.46
22 20 0.54
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAATT
Found at i:26605 original size:15 final size:16
Alignment explanation
Indices: 26556--26585 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26546 CTTCCCTATT
26556 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
26571 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
26586 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:27251 original size:18 final size:17
Alignment explanation
Indices: 27225--27262 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
27215 ATCAAAGACG
*
27225 ATAACATAATTTAATAAT
1 ATAAAATAATTTAA-AAT
27243 ATAAAATAATTTAAAAT
1 ATAAAATAATTTAAAAT
27260 ATA
1 ATA
27263 TATTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAAAATAATTTAAAAT
Found at i:32599 original size:22 final size:22
Alignment explanation
Indices: 32559--32618 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
32549 CAATCTGAGG
* *
32559 AAAAATAAAAG-AAACAAAATT
1 AAAAATAAATGAAAATAAAATT
32580 AAAAATAAATGAAAATAAAATT
1 AAAAATAAATGAAAATAAAATT
* *
32602 -GAAAGAAATAGAAAATA
1 AAAAATAAAT-GAAAATA
32619 GGGAATTCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (22 bp):
AAAAATAAATGAAAATAAAATT
Found at i:33445 original size:19 final size:19
Alignment explanation
Indices: 33421--33463 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
33411 AAACATAAAT
33421 TAAATATAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
33440 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
33459 TAAAT
1 TAAAT
33464 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:45084 original size:58 final size:58
Alignment explanation
Indices: 44994--45113 Score: 213
Period size: 58 Copynumber: 2.1 Consensus size: 58
44984 TATCCTCCTG
* *
44994 TAATACAATAAAATATTTATTATATTTATGGTAGTGTTTTTTTAATATTAATACTTTT
1 TAATACAATAAAATATTTATTATATTTATGGTAGTGTTTTTTTAATATAAATACATTT
*
45052 TAATACAATAAAATATTTATTATATTTGTGGTAGTGTTTTTTTAATATAAATACATTT
1 TAATACAATAAAATATTTATTATATTTATGGTAGTGTTTTTTTAATATAAATACATTT
45110 TAAT
1 TAAT
45114 GTGTTAGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (58 bp):
TAATACAATAAAATATTTATTATATTTATGGTAGTGTTTTTTTAATATAAATACATTT
Found at i:47695 original size:27 final size:25
Alignment explanation
Indices: 47644--47700 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
47634 TTAAAAAATT
*
47644 AAATTAATTTTTTTTTTAATTTTTA
1 AAATTAATTTTATTTTTAATTTTTA
47669 AAATATAATTTTATTTTT-ATTAATTTA
1 AAAT-TAATTTTATTTTTAATT--TTTA
47696 AAATT
1 AAATT
47701 TTTAAAAGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 7 0.25
26 13 0.46
27 8 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
AAATTAATTTTATTTTTAATTTTTA
Found at i:50912 original size:30 final size:30
Alignment explanation
Indices: 50850--51406 Score: 545
Period size: 30 Copynumber: 18.9 Consensus size: 30
50840 TTTGAGGTCG
* *
50850 AAAATGGAGA-TTTTGG-AGGTTAAGGG-TA
1 AAAATGGA-ATTTTTGGAAGTTTTAGGGTTA
50878 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
* *
50908 AAAATGGAATTTTTGGAA-ATTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
* *
50937 AAAACT-AAATTTTTGGAAGTTTTGGGGTTA
1 AAAA-TGGAATTTTTGGAAGTTTTAGGGTTA
* * *
50967 AAAATGGGATTTTTGGAA--ATTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
* * * *
50995 AAAATGAAATTTTTAGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
* *
51025 AAAATGGGATTTTTGGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
*
51055 AAAAT-GAGATTTTTGGAAG-TTT-GGGAGTA
1 AAAATGGA-ATTTTTGGAAGTTTTAGGG-TTA
**
51084 AAAATGGAATTTTTGGAAGTTTCGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
* *
51114 AAAATGGAATTTTTGGAA-ATTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
** *
51143 AAAATAAAATTTTTGGAAGTTTT-GAGGTCA
1 AAAATGGAATTTTTGGAAGTTTTAG-GGTTA
* * *
51173 AAAATGGAATTTTTGGAA-ATTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
* * * *
51202 AAAATGGAATTTTTGGAAGTTTCAAGATCA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
* * *
51232 AAAAT-TAGATTTTTGGAAG-TTTGGGGGTA
1 AAAATGGA-ATTTTTGGAAGTTTTAGGGTTA
*
51261 AAAATGGAATTTTTGGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
*
51291 AAAATTGG-ATTTTTGGAAG-TTTAGGGGTA
1 AAAA-TGGAATTTTTGGAAGTTTTAGGGTTA
*
51320 AAAATAGAATTTTTGGAAGTTTTAGGGTTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
*** *
51350 AAAATGGAATTTTTGGAAGTTCGGGGGTAAA
1 AAAATGGAATTTTTGGAAGTTTTAGGGT-TA
* *
51381 AAAATGAAATTTTTGGAAGGTTTAGG
1 AAAATGGAATTTTTGGAAGTTTTAGG
51407 TACCTCCAGG
Statistics
Matches: 430, Mismatches: 75, Indels: 45
0.78 0.14 0.08
Matches are distributed among these distances:
27 1 0.00
28 41 0.10
29 146 0.34
30 214 0.50
31 28 0.07
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.36
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTTAGGGTTA
Found at i:50955 original size:59 final size:60
Alignment explanation
Indices: 50850--51406 Score: 567
Period size: 59 Copynumber: 9.4 Consensus size: 60
50840 TTTGAGGTCG
* * * * *
50850 AAAATGGAGA-TTTTGG-AGGTTAAGGGT-AAAAATGGAATTTTTGGAAGTTTTAGGGTTA
1 AAAATGGA-ATTTTTGGAAGTTTAGGGGTCAAAAATGAAATTTTTGGAAGTTTTGGGGGTA
* *
50908 AAAATGGAATTTTTGGAAATTTAGGGGT-AAAAACT-AAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTCAAAAA-TGAAATTTTTGGAAGTTTTGGGGGTA
* * *
50967 AAAATGGGATTTTTGGAA-ATTAGGGGT-AAAAATGAAATTTTTAGAAGTTTT-GGGGTCA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTCAAAAATGAAATTTTTGGAAGTTTTGGGGGT-A
* * *
51025 AAAATGGGATTTTTGGAAGTTTTA-GGGTCAAAAATGAGATTTTTGGAAG-TTTGGGAGTA
1 AAAATGGAATTTTTGGAAG-TTTAGGGGTCAAAAATGAAATTTTTGGAAGTTTTGGGGGTA
* * * * *
51084 AAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAA-ATTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTCAAAAATGAAATTTTTGGAAGTTTTGGGGGTA
** * * * *
51143 AAAATAAAATTTTTGGAAGTTTTGAGGTCAAAAATGGAATTTTTGGAA-ATTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTCAAAAATGAAATTTTTGGAAGTTTTGGGGGTA
* * * *
51202 AAAATGGAATTTTTGGAAGTTTCA-AGATCAAAAATTAGATTTTTGGAAG-TTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTT-AGGGGTCAAAAATGAAATTTTTGGAAGTTTTGGGGGTA
* *
51261 AAAATGGAATTTTTGGAAGTTTTA-GGGTCAAAAATTG-GATTTTTGGAAG-TTTAGGGGTA
1 AAAATGGAATTTTTGGAAG-TTTAGGGGTCAAAAA-TGAAATTTTTGGAAGTTTTGGGGGTA
* * * *
51320 AAAATAGAATTTTTGGAAGTTTTA-GGGTTAAAAATGGAATTTTTGGAAG-TTCGGGGGTAAA
1 AAAATGGAATTTTTGGAAG-TTTAGGGGTCAAAAATGAAATTTTTGGAAGTTTTGGGGGT--A
*
51381 AAAATGAAATTTTTGGAAGGTTTAGG
1 AAAATGGAATTTTTGGAA-GTTTAGG
51407 TACCTCCAGG
Statistics
Matches: 435, Mismatches: 44, Indels: 36
0.84 0.09 0.07
Matches are distributed among these distances:
57 6 0.01
58 67 0.15
59 309 0.71
60 30 0.07
61 21 0.05
62 2 0.00
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.36
Consensus pattern (60 bp):
AAAATGGAATTTTTGGAAGTTTAGGGGTCAAAAATGAAATTTTTGGAAGTTTTGGGGGTA
Found at i:51155 original size:118 final size:117
Alignment explanation
Indices: 50850--51406 Score: 632
Period size: 118 Copynumber: 4.7 Consensus size: 117
50840 TTTGAGGTCG
* * *
50850 AAAATGGAGA-TTTTGG-AGGTTAAGGG-TAAAAATGGAATTTTTGGAAGTTTTAGGGTTAAAAA
1 AAAATGGA-ATTTTTGGAAGTTTCAGGGTTAAAAATGGAATTTTTGGAAG-TTTAGGGGTAAAAA
* **
50912 TGGAATTTTTGGAA-ATTTAGGGGT-AAAAACTAAATTTTTGGAAGTTTTGGGGTTA
64 TGGAATTTTTGGAAGTTTTA-GGGTCAAAAACTGGATTTTTGGAAG-TTTGGGG-TA
* * * * * *
50967 AAAATGGGATTTTTGGAA-ATT-AGGGGTAAAAATGAAATTTTTAGAAGTTTTGGGGTCAAAAAT
1 AAAATGGAATTTTTGGAAGTTTCAGGGTTAAAAATGGAATTTTTGGAAGTTTAGGGGT-AAAAAT
*
51030 GGGATTTTTGGAAGTTTTAGGGTCAAAAA-TGAGATTTTTGGAAGTTTGGGAGTA
65 GGAATTTTTGGAAGTTTTAGGGTCAAAAACTG-GATTTTTGGAAGTTTGGG-GTA
* * *
51084 AAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAATTTAGGGGTAAAAATA
1 AAAATGGAATTTTTGGAAGTTTCAGGGTTAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATG
* *
51149 AAATTTTTGGAAGTTTT-GAGGTCAAAAA-TGGAATTTTTGGAAATTTGGGGGTA
66 GAATTTTTGGAAGTTTTAG-GGTCAAAAACTGG-ATTTTTGGAAGTTT-GGGGTA
* * * * *
51202 AAAATGGAATTTTTGGAAGTTTCAAGATCAAAAAT-TAGATTTTTGGAAGTTTGGGGGTAAAAAT
1 AAAATGGAATTTTTGGAAGTTTCAGGGTTAAAAATGGA-ATTTTTGGAAGTTTAGGGGTAAAAAT
*
51266 GGAATTTTTGGAAGTTTTAGGGTCAAAAATTGGATTTTTGGAAGTTTAGGGGTA
65 GGAATTTTTGGAAGTTTTAGGGTCAAAAACTGGATTTTTGGAAGTTT-GGGGTA
* * **
51320 AAAATAGAATTTTTGGAAGTTTTAGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAAAA
1 AAAATGGAATTTTTGGAAGTTTCAGGGTTAAAAATGGAATTTTTGGAAGTTTAGGGGT--AAAAA
* *
51385 TGAAATTTTTGGAAGGTTTAGG
64 TGGAATTTTTGGAAGTTTTAGG
51407 TACCTCCAGG
Statistics
Matches: 379, Mismatches: 42, Indels: 35
0.83 0.09 0.08
Matches are distributed among these distances:
116 12 0.03
117 85 0.22
118 220 0.58
119 37 0.10
120 25 0.07
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.36
Consensus pattern (117 bp):
AAAATGGAATTTTTGGAAGTTTCAGGGTTAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATG
GAATTTTTGGAAGTTTTAGGGTCAAAAACTGGATTTTTGGAAGTTTGGGGTA
Found at i:52406 original size:3 final size:3
Alignment explanation
Indices: 52356--52386 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
52346 TTTTTTTTGT
*
52356 TTA TTA TTA TTA ATA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
52387 CAAAACATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:52429 original size:30 final size:30
Alignment explanation
Indices: 52395--52468 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 30
52385 ATCAAAACAT
52395 TTATTATTATTAATGA-AT-ATTAATAAAAA
1 TTATTATTATTAATGATATCATTAAT-AAAA
**
52424 CTTATTTATTATTAATGATATCATTAATATTA
1 -TTA-TTATTATTAATGATATCATTAATAAAA
52456 TTATTATTATTAA
1 TTATTATTATTAA
52469 AACAGTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 13 0.33
31 16 0.41
32 4 0.10
33 6 0.15
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
TTATTATTATTAATGATATCATTAATAAAA
Found at i:53201 original size:16 final size:16
Alignment explanation
Indices: 53176--53206 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53166 ATTTTAAAAT
*
53176 TAAATTTAAATTTAAA
1 TAAATCTAAATTTAAA
53192 TAAATCTAAATTTAA
1 TAAATCTAAATTTAA
53207 GGTTAAAAAG
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:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATCTAAATTTAAA
Found at i:53212 original size:22 final size:21
Alignment explanation
Indices: 53172--53213 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
53162 TTTAATTTTA
*
53172 AAATTAAATTTAAATTTAAAT
1 AAATTAAATTTAAAGTTAAAT
*
53193 AAATCTAAATTTAAGGTTAAA
1 AAAT-TAAATTTAAAGTTAAA
53214 AAGGGACCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (21 bp):
AAATTAAATTTAAAGTTAAAT
Found at i:58748 original size:21 final size:22
Alignment explanation
Indices: 58718--58758 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
58708 AAACATGATA
*
58718 AAAAACCAC-TCATCACCAAGC
1 AAAAACCACTTCACCACCAAGC
*
58739 AAAAATCACTTCACCACCAA
1 AAAAACCACTTCACCACCAA
58759 ACTTTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.49, C:0.37, G:0.02, T:0.12
Consensus pattern (22 bp):
AAAAACCACTTCACCACCAAGC
Found at i:59370 original size:21 final size:21
Alignment explanation
Indices: 59346--59386 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
59336 TTGAGTCAAA
* *
59346 CATTTTCAAATATGTTAAAAC
1 CATTTTCAAACAAGTTAAAAC
59367 CATTTTCAAACAAGTTAAAA
1 CATTTTCAAACAAGTTAAAA
59387 TTGCTCTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (21 bp):
CATTTTCAAACAAGTTAAAAC
Found at i:59510 original size:58 final size:58
Alignment explanation
Indices: 59443--59561 Score: 211
Period size: 58 Copynumber: 2.1 Consensus size: 58
59433 AATTTGTAAA
59443 ATATCGATACCCCTGTTTTCAAACGAGACCAAGACAGTATTCTGACTTGTAGGTATCG
1 ATATCGATACCCCTGTTTTCAAACGAGACCAAGACAGTATTCTGACTTGTAGGTATCG
* * *
59501 ATATCGATACCCCTGTTTTCGATCGAGACCAAGAGAGTATTCTGACTTGTAGGTATCG
1 ATATCGATACCCCTGTTTTCAAACGAGACCAAGACAGTATTCTGACTTGTAGGTATCG
59559 ATA
1 ATA
59562 CTTTCCATCA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (58 bp):
ATATCGATACCCCTGTTTTCAAACGAGACCAAGACAGTATTCTGACTTGTAGGTATCG
Found at i:60053 original size:37 final size:37
Alignment explanation
Indices: 60012--60089 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
60002 GGGTAGAAAC
* *
60012 CTTAAGGTGTTGTATC-TTATGACTTTGGGGTATAAGT
1 CTTAAGGTGTTGT-CCATTAAGACTTTGGGGTATAAGT
*
60049 CTTAAGGTGTTGTCCATTAAGACTTTGTGGTATAAGT
1 CTTAAGGTGTTGTCCATTAAGACTTTGGGGTATAAGT
60086 CTTA
1 CTTA
60090 TTTGGGTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 1 0.03
37 36 0.97
ACGTcount: A:0.23, C:0.10, G:0.24, T:0.42
Consensus pattern (37 bp):
CTTAAGGTGTTGTCCATTAAGACTTTGGGGTATAAGT
Found at i:62667 original size:16 final size:16
Alignment explanation
Indices: 62648--62692 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
62638 TCATTTTCAT
62648 TTTACTTTTTTTTTTC
1 TTTACTTTTTTTTTTC
*
62664 TTTA-TTTTGCTTTTTC
1 TTTACTTTT-TTTTTTC
62680 -TT-CTTTTTTTTTT
1 TTTACTTTTTTTTTT
62693 TTTCTCTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 5 0.20
15 10 0.40
16 10 0.40
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.82
Consensus pattern (16 bp):
TTTACTTTTTTTTTTC
Found at i:62693 original size:16 final size:16
Alignment explanation
Indices: 62648--62702 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
62638 TCATTTTCAT
*
62648 TTTACTTTTTTTTTTC
1 TTTATTTTTTTTTTTC
**
62664 TTTATTTTGCTTTTTC
1 TTTATTTTTTTTTTTC
*
62680 TTCTTTTTTTTTTTTTC
1 TT-TATTTTTTTTTTTC
*
62697 TCTATT
1 TTTATT
62703 CTCCTTTGTT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
16 18 0.60
17 12 0.40
ACGTcount: A:0.05, C:0.13, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTATTTTTTTTTTTC
Found at i:65607 original size:3 final size:3
Alignment explanation
Indices: 65599--65629 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
65589 GAGGACACCT
65599 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
65630 CGGTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:70656 original size:24 final size:24
Alignment explanation
Indices: 70629--70684 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
70619 ACAATATGAT
70629 ATGGAAGACTTGGTGATATCTTTA
1 ATGGAAGACTTGGTGATATCTTTA
*
70653 ATGGAAGACTTGGTGATTTCTTTA
1 ATGGAAGACTTGGTGATATCTTTA
*
70677 ATAGAAGA
1 ATGGAAGA
70685 GCATACGTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (24 bp):
ATGGAAGACTTGGTGATATCTTTA
Found at i:78711 original size:15 final size:15
Alignment explanation
Indices: 78687--78717 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
78677 GACACATCAT
78687 AAAGCCTTTTCAGCA
1 AAAGCCTTTTCAGCA
*
78702 AAAGCTTTTTCAGCA
1 AAAGCCTTTTCAGCA
78717 A
1 A
78718 GAATCGCGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (15 bp):
AAAGCCTTTTCAGCA
Found at i:79839 original size:17 final size:18
Alignment explanation
Indices: 79814--79854 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
79804 AGGTGCCTAA
79814 AAAGAAAGAGAAAGAGAAAGG
1 AAAGAAA-A-AAAGAG-AAGG
79835 AAAGAAAAAAAGAGAAGG
1 AAAGAAAAAAAGAGAAGG
79853 AA
1 AA
79855 GAAGATGCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 6 0.30
20 1 0.05
21 7 0.35
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAAGAGAAGG
Found at i:80860 original size:18 final size:18
Alignment explanation
Indices: 80834--80887 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
80824 ATGCATTGCA
*
80834 TTTAGTTGTCATTACATT
1 TTTAATTGTCATTACATT
*
80852 TTTAATTGTCATTGCA-T
1 TTTAATTGTCATTACATT
* *
80869 TTTAATTGTTAGTACATT
1 TTTAATTGTCATTACATT
80887 T
1 T
80888 GCATTGTAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.56
Consensus pattern (18 bp):
TTTAATTGTCATTACATT
Found at i:80873 original size:17 final size:17
Alignment explanation
Indices: 80827--80877 Score: 68
Period size: 18 Copynumber: 3.0 Consensus size: 17
80817 TAGTTGCATG
*
80827 CATTGCA-TTTAGTTGT
1 CATTGCATTTTAATTGT
*
80843 CATTACATTTTTAATTGT
1 CATTGCA-TTTTAATTGT
80861 CATTGCATTTTAATTGT
1 CATTGCATTTTAATTGT
80878 TAGTACATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.20
17 10 0.33
18 14 0.47
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (17 bp):
CATTGCATTTTAATTGT
Found at i:80886 original size:17 final size:17
Alignment explanation
Indices: 80834--80887 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
80824 ATGCATTGCA
* *
80834 TTTAGTTGTCATTACATT
1 TTTAATTGTCAGTACA-T
* *
80852 TTTAATTGTCATTGCAT
1 TTTAATTGTCAGTACAT
*
80869 TTTAATTGTTAGTACAT
1 TTTAATTGTCAGTACAT
80886 TT
1 TT
80888 GCATTGTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 17 0.55
18 14 0.45
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.56
Consensus pattern (17 bp):
TTTAATTGTCAGTACAT
Found at i:83632 original size:21 final size:23
Alignment explanation
Indices: 83606--83655 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
83596 TTACGTATGA
*
83606 TGATTTAATAC-C-TTTTGTTAT
1 TGATTTAATACTCACTTTGTTAT
*
83627 TGATTTTAGTACTCACTTTGTTAT
1 TGA-TTTAATACTCACTTTGTTAT
83651 TGATT
1 TGATT
83656 AAATTACAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 3 0.12
22 7 0.29
23 3 0.12
24 11 0.46
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.56
Consensus pattern (23 bp):
TGATTTAATACTCACTTTGTTAT
Found at i:89074 original size:24 final size:24
Alignment explanation
Indices: 89031--89076 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
89021 AAGATTTAAT
*
89031 ATTTATTAGTATAATATATTTGGC
1 ATTTATTAGCATAATATATTTGGC
* *
89055 ATTTATTAGCATATTTTATTTG
1 ATTTATTAGCATAATATATTTG
89077 ACTTAAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.54
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTGGC
Done.