Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009819.1 Kokia drynarioides strain JFW-HI SEQ_124540, 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: 53490
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:1439 original size:17 final size:17
Alignment explanation
Indices: 1419--1452 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1409 TTTTACATGA
*
1419 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
1436 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
1453 GATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:1721 original size:19 final size:20
Alignment explanation
Indices: 1690--1734 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
1680 CATGCAGGTA
*
1690 GCAGCATGGGGCAACATACG
1 GCAGCATGGGGCAACACACG
1710 GCAGCA-GGGGCAACACACG
1 GCAGCATGGGGCAACACACG
1729 GCAGCA
1 GCAGCA
1735 AACGGCAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.31, C:0.29, G:0.36, T:0.04
Consensus pattern (20 bp):
GCAGCATGGGGCAACACACG
Found at i:6573 original size:17 final size:17
Alignment explanation
Indices: 6543--6577 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6533 TAACTTTTGC
6543 TTTTACTTTCTATTTTA
1 TTTTACTTTCTATTTTA
6560 TTTTATCTTT-TATTTTA
1 TTTTA-CTTTCTATTTTA
6577 T
1 T
6578 GCTCTCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTACTTTCTATTTTA
Found at i:9686 original size:20 final size:21
Alignment explanation
Indices: 9634--9686 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
9624 TGTGGAGGTT
* *
9634 CTACTAATACAAGTATGACTT
1 CTACCAATACAAGTATGACTA
* *
9655 CTACCAAAACAATTATG-CTA
1 CTACCAATACAAGTATGACTA
*
9675 CTACCGATACAA
1 CTACCAATACAA
9687 CAAACTCCAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.26
Consensus pattern (21 bp):
CTACCAATACAAGTATGACTA
Found at i:12792 original size:35 final size:35
Alignment explanation
Indices: 12721--12793 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 35
12711 GTAATGTGTG
* *
12721 AGAAGGAGTGGTGTTAGATGAAAAAATAAGTGAGA
1 AGAAGAAGTGGTGTTAGATGAAAAAATAAGGGAGA
* *
12756 AGAAGAAGTGTTGTTAGATGGAAAAAT--GGG-GA
1 AGAAGAAGTGGTGTTAGATGAAAAAATAAGGGAGA
12788 AGAAGA
1 AGAAGA
12794 TGAAATTGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 8 0.24
33 2 0.06
35 24 0.71
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.19
Consensus pattern (35 bp):
AGAAGAAGTGGTGTTAGATGAAAAAATAAGGGAGA
Found at i:15592 original size:12 final size:13
Alignment explanation
Indices: 15568--15597 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
15558 ATACATATAT
15568 TTTCACATAACCA
1 TTTCACATAACCA
15581 TTTCACAT-ACCA
1 TTTCACATAACCA
15593 TTTCA
1 TTTCA
15598 TGTGTAGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (13 bp):
TTTCACATAACCA
Found at i:16441 original size:40 final size:40
Alignment explanation
Indices: 16397--16528 Score: 221
Period size: 40 Copynumber: 3.3 Consensus size: 40
16387 TTTTTCGAAT
16397 TTTTCATTTATTATCCTTTCGGATAATATCCTTTTCAACC
1 TTTTCATTTATTATCCTTTCGGATAATATCCTTTTCAACC
* *
16437 TTTTCGTTTATTATCCTTCCGGATAATATCCTTTTCAACC
1 TTTTCATTTATTATCCTTTCGGATAATATCCTTTTCAACC
*
16477 TTTTCATTTATTATCC-TTCTAGATAATATCCTTTTCAACC
1 TTTTCATTTATTATCCTTTC-GGATAATATCCTTTTCAACC
16517 TTTTCATTTATT
1 TTTTCATTTATT
16529 CGAAAATACC
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
39 2 0.02
40 84 0.98
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.52
Consensus pattern (40 bp):
TTTTCATTTATTATCCTTTCGGATAATATCCTTTTCAACC
Found at i:16630 original size:2 final size:2
Alignment explanation
Indices: 16623--16657 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16613 TAAATACAAA
16623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16658 ACAATATCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21844 original size:27 final size:27
Alignment explanation
Indices: 21768--21890 Score: 84
Period size: 27 Copynumber: 4.6 Consensus size: 27
21758 GCAAAGGCTT
* * ** *
21768 TCCATTCAGATTACACCACGAAGGCAG
1 TCCATTCAGAATACGCCAAAAAAGCAG
* * *
21795 TCCTTTCAGAATATGCCATAAAAGCAG
1 TCCATTCAGAATACGCCAAAAAAGCAG
* *
21822 TCCATTCAGAATACGCGAAAAAAGCAA
1 TCCATTCAGAATACGCCAAAAAAGCAG
* * * * * *
21849 TTCATTTAGAATACACCACAAAGGCAA
1 TCCATTCAGAATACGCCAAAAAAGCAG
* *
21876 TTCATTCAAAATACG
1 TCCATTCAGAATACG
21891 TCATACAGAC
Statistics
Matches: 75, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.22
Consensus pattern (27 bp):
TCCATTCAGAATACGCCAAAAAAGCAG
Found at i:22525 original size:5 final size:5
Alignment explanation
Indices: 22515--22539 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
22505 ACCATTTAAC
22515 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
22540 CATTATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:24318 original size:44 final size:44
Alignment explanation
Indices: 24259--24343 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
24249 TATAACCAAC
24259 TCCACAAAGACTTGTTGAGAAAAAGTTAACATAATTATATACAT
1 TCCACAAAGACTTGTTGAGAAAAAGTTAACATAATTATATACAT
* * * * *
24303 TCCATAAATACTTGTTGAGAAAAAGTTGACGTACTTATATA
1 TCCACAAAGACTTGTTGAGAAAAAGTTAACATAATTATATA
24344 AATGTATGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (44 bp):
TCCACAAAGACTTGTTGAGAAAAAGTTAACATAATTATATACAT
Found at i:24910 original size:16 final size:18
Alignment explanation
Indices: 24871--24904 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24861 TAAGTTCATA
24871 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
24888 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
24905 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:30965 original size:14 final size:14
Alignment explanation
Indices: 30946--30975 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
30936 TCAATAAATT
30946 AAAAATTAAATATA
1 AAAAATTAAATATA
*
30960 AAAAATTTAATATA
1 AAAAATTAAATATA
30974 AA
1 AA
30976 CTTTTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAAATTAAATATA
Found at i:33127 original size:20 final size:19
Alignment explanation
Indices: 33102--33144 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
33092 TTATTGAGAA
33102 ATATTTAGTAAATTTGTTTT
1 ATATTT-GTAAATTTGTTTT
* *
33122 ATATTTTTAGATTTGTTTT
1 ATATTTGTAAATTTGTTTT
33141 ATAT
1 ATAT
33145 AATATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (19 bp):
ATATTTGTAAATTTGTTTT
Found at i:33545 original size:22 final size:21
Alignment explanation
Indices: 33520--33561 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
33510 CTATGAAATT
33520 TAAACAA-AATAATTATAAGAAC
1 TAAACAAGAA-AATTA-AAGAAC
*
33542 TAAAGAAGAAAATTAAAGAA
1 TAAACAAGAAAATTAAAGAA
33562 AAAGGGAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 5 0.28
22 11 0.61
23 2 0.11
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (21 bp):
TAAACAAGAAAATTAAAGAAC
Found at i:36329 original size:19 final size:17
Alignment explanation
Indices: 36294--36330 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
36284 GTAATTAATA
36294 TTAATTATTTATAAAAT
1 TTAATTATTTATAAAAT
36311 TTAATTATATTATATAAAT
1 TTAATTAT-TTATA-AAAT
36330 T
1 T
36331 ATATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 5 0.28
19 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAATTATTTATAAAAT
Found at i:36346 original size:33 final size:33
Alignment explanation
Indices: 36263--36379 Score: 91
Period size: 34 Copynumber: 3.5 Consensus size: 33
36253 TATATGAAAT
* *
36263 ATTA-ATTTTAAATATTTCTAAGTA-ATTAATATTA
1 ATTATATTTTAAATA-TT-TAAATATATT-ATATAA
* *
36297 ATTAT-TTATAAA-ATTTAATTATATTATATAA
1 ATTATATTTTAAATATTTAAATATATTATATAA
*
36328 ATTATATTTTAAATATTTAAATATAATCAT-TAA
1 ATTATATTTTAAATATTTAAATAT-ATTATATAA
*
36361 ATATTTATATTTAAATATT
1 AT-TATAT-TTTAAATATT
36380 AACACAGTTG
Statistics
Matches: 69, Mismatches: 7, Indels: 13
0.78 0.08 0.15
Matches are distributed among these distances:
31 15 0.22
32 11 0.16
33 15 0.22
34 18 0.26
35 10 0.14
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (33 bp):
ATTATATTTTAAATATTTAAATATATTATATAA
Found at i:36376 original size:14 final size:14
Alignment explanation
Indices: 36339--36381 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
36329 TTATATTTTA
36339 AATATTTAAATA-T
1 AATATTTAAATATT
36352 AATCA-TTAAATATT
1 AAT-ATTTAAATATT
*
36366 TATATTTAAATATT
1 AATATTTAAATATT
36380 AA
1 AA
36382 CACAGTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATTTAAATATT
Found at i:38247 original size:72 final size:72
Alignment explanation
Indices: 38049--38229 Score: 301
Period size: 72 Copynumber: 2.5 Consensus size: 72
38039 CATACTAAAT
* * *
38049 CAAATATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAGAACATAAATTCAATATC
1 CAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAGATTCAATATC
38114 CAAAAAC
66 CAAAAAC
*
38121 TAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAGATTCAATATC
1 CAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAGATTCAATATC
*
38186 TAAAAAC
66 CAAAAAC
*
38193 CAAACATAAACAACTATTGATAAAACTAGTTTA-ACAT
1 CAAACATAAACAACTATTGATAAAACTAGATTACACAT
38230 TGTTGATTAG
Statistics
Matches: 102, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 4 0.04
72 98 0.96
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.25
Consensus pattern (72 bp):
CAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAGATTCAATATC
CAAAAAC
Found at i:38685 original size:18 final size:18
Alignment explanation
Indices: 38658--38703 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
38648 CATCATTGTT
38658 AACATCATTTGAAATTTG
1 AACATCATTTGAAATTTG
* * *
38676 AACATTATTTGAAGTTTT
1 AACATCATTTGAAATTTG
38694 AACATCATTT
1 AACATCATTT
38704 CTTGCATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (18 bp):
AACATCATTTGAAATTTG
Found at i:42937 original size:37 final size:37
Alignment explanation
Indices: 42896--42967 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 37
42886 CCAGAATTGC
*
42896 GCCC-AAACATGTCGCTGCATGAGCACTTCTAGATTAT
1 GCCCAAAAC-TGTCGCCGCATGAGCACTTCTAGATTAT
42933 GCCCAAAACTGTCGCCGCATGAGCACTTCTAGATT
1 GCCCAAAACTGTCGCCGCATGAGCACTTCTAGATT
42968 TCACCAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
37 29 0.88
38 4 0.12
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (37 bp):
GCCCAAAACTGTCGCCGCATGAGCACTTCTAGATTAT
Found at i:43954 original size:16 final size:16
Alignment explanation
Indices: 43933--43963 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43923 TTGTGGATCC
43933 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
43949 CATTTTATCTTTATT
1 CATTTTACCTTTATT
43964 TTTCACATTA
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:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:45348 original size:127 final size:125
Alignment explanation
Indices: 45143--45369 Score: 339
Period size: 127 Copynumber: 1.8 Consensus size: 125
45133 AGCTGCTCTT
* * *
45143 TGGTTGAGATCCACAAACCCTATAGATAAAAGATGTTAGAGAAAGTTGTGGATACTCCATTCATA
1 TGGTTGAGATCCACAAACCCTATAGATAAAAGATGTCAAAGAAAGTCGTGGATACTCCATTCATA
*
45208 AAGTCGCAGTTGGAATTGACTAATTTGTGAATACATAAAGGGTGCAAACAAGTTATCGTA
66 AAGTCGCAGTTGGAATTGACTAAATTGTGAATACATAAAGGGTGCAAACAAGTTATCGTA
* * *
45268 TGGTTGAGGATCCACAACCCCT-TGCAGATAAAAGCTGTCAAAGAAAGTCGTGGATACTCCGTTC
1 TGGTTGA-GATCCACAAACCCTAT--AGATAAAAGATGTCAAAGAAAGTCGTGGATACTCCATTC
* *
45332 ATAAAGTCGCAGTTGGAATTTACTAAATTGTGAGTACA
63 ATAAAGTCGCAGTTGGAATTGACTAAATTGTGAATACA
45370 CAACAAACGT
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
125 8 0.09
126 13 0.14
127 69 0.77
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (125 bp):
TGGTTGAGATCCACAAACCCTATAGATAAAAGATGTCAAAGAAAGTCGTGGATACTCCATTCATA
AAGTCGCAGTTGGAATTGACTAAATTGTGAATACATAAAGGGTGCAAACAAGTTATCGTA
Found at i:46372 original size:58 final size:58
Alignment explanation
Indices: 46174--46395 Score: 228
Period size: 58 Copynumber: 3.8 Consensus size: 58
46164 TTTTTTTAAG
* * * * * *
46174 AATAGTGGAAAAACAGTAAAATTTAGAAAACTAGTGGAAAAACTATAAAATCTAGAAAAAA
1 AATAGTGGTAGAACTGTAAAATCTAGAAAACTAGTGGCAAAACTGTAAAATCTAG---AAA
* * * ** * *
46235 AATAGTGGTGGAACTGTAAAATATGGAAAACTAGTTTCAAAAACTGTAAAATTTGGAAA
1 AATAGTGGTAGAACTGTAAAATCTAGAAAACTAGTGGC-AAAACTGTAAAATCTAGAAA
* * * *
46294 AATAGTGGCAGAACTATAAAATCTGGAAAACTAGTGGCAAAATTGTAAAATCTAGAAA
1 AATAGTGGTAGAACTGTAAAATCTAGAAAACTAGTGGCAAAACTGTAAAATCTAGAAA
* * *
46352 AGTAGTGGTAGAACTGTAAAATCTAGAAAAATAGTGGCAGAACT
1 AATAGTGGTAGAACTGTAAAATCTAGAAAACTAGTGGCAAAACT
46396 ATAGAATTTG
Statistics
Matches: 132, Mismatches: 28, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
58 54 0.41
59 35 0.27
61 29 0.22
62 14 0.11
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (58 bp):
AATAGTGGTAGAACTGTAAAATCTAGAAAACTAGTGGCAAAACTGTAAAATCTAGAAA
Found at i:46393 original size:29 final size:29
Alignment explanation
Indices: 46174--46395 Score: 183
Period size: 29 Copynumber: 7.5 Consensus size: 29
46164 TTTTTTTAAG
* * *
46174 AATAGTGGAAAAACAGTAAAATTTAGAAA
1 AATAGTGGCAAAACTGTAAAATCTAGAAA
* * *
46203 ACTAGTGGAAAAACTATAAAATCTAGAAAAAA
1 AATAGTGGCAAAACTGTAAAATCTAG---AAA
*** * *
46235 AATAGTGGTGGAACTGTAAAATATGGAAA
1 AATAGTGGCAAAACTGTAAAATCTAGAAA
* ** * *
46264 ACTAGTTTCAAAAACTGTAAAATTTGGAAA
1 AATAGTGGC-AAAACTGTAAAATCTAGAAA
* * *
46294 AATAGTGGCAGAACTATAAAATCTGGAAA
1 AATAGTGGCAAAACTGTAAAATCTAGAAA
* *
46323 ACTAGTGGCAAAATTGTAAAATCTAGAAA
1 AATAGTGGCAAAACTGTAAAATCTAGAAA
* * *
46352 AGTAGTGGTAGAACTGTAAAATCTAGAAA
1 AATAGTGGCAAAACTGTAAAATCTAGAAA
*
46381 AATAGTGGCAGAACT
1 AATAGTGGCAAAACT
46396 ATAGAATTTG
Statistics
Matches: 154, Mismatches: 35, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
29 109 0.71
30 23 0.15
32 22 0.14
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (29 bp):
AATAGTGGCAAAACTGTAAAATCTAGAAA
Found at i:46837 original size:32 final size:33
Alignment explanation
Indices: 46796--46867 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
46786 AATAAGAAAG
*
46796 TTAAATTCTA-TTAGG-TTTTGAAAATGAGTAAT
1 TTAAATTCTAGTTAGGATTTT-AAAAGGAGTAAT
*
46828 TTAAATTCTAGTTAGGATTTTAAAAGGATTAAT
1 TTAAATTCTAGTTAGGATTTTAAAAGGAGTAAT
*
46861 TTGAATT
1 TTAAATT
46868 TTAAATTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 10 0.29
33 21 0.60
34 4 0.11
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (33 bp):
TTAAATTCTAGTTAGGATTTTAAAAGGAGTAAT
Found at i:47524 original size:23 final size:23
Alignment explanation
Indices: 47474--47524 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
47464 ATTTAACTTT
* *
47474 ATAGTTTTTAATACATTCATATT
1 ATAGTTTTTAATACATTAATATC
*
47497 TTAGTTTTTAATA-ATTAATACTC
1 ATAGTTTTTAATACATTAATA-TC
47520 ATAGT
1 ATAGT
47525 CAAGACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (23 bp):
ATAGTTTTTAATACATTAATATC
Found at i:51407 original size:37 final size:37
Alignment explanation
Indices: 51255--51380 Score: 198
Period size: 37 Copynumber: 3.4 Consensus size: 37
51245 AGTACTATCA
* * **
51255 AGAGCGTAATGTTATATGGAAGGCTTACATCTTGGCT
1 AGAGCGTAATGTTATATGGAAGGCTTACGTCTCGATT
* *
51292 AGAGCATAATGTTATATGGAAGACTTACGTCTCGATT
1 AGAGCGTAATGTTATATGGAAGGCTTACGTCTCGATT
51329 AGAGCGTAATGTTATATGGAAGGCTTACGTCTCGATT
1 AGAGCGTAATGTTATATGGAAGGCTTACGTCTCGATT
51366 AGAGCGTAATGTTAT
1 AGAGCGTAATGTTAT
51381 GTGATTTGTT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 81 1.00
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (37 bp):
AGAGCGTAATGTTATATGGAAGGCTTACGTCTCGATT
Found at i:51816 original size:23 final size:24
Alignment explanation
Indices: 51790--51834 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
51780 TTAATTTTTA
*
51790 CATTTAAA-CAAGATGTATTTACT
1 CATTTAAATCAAAATGTATTTACT
*
51813 CATTTAAATCAAAATTTATTTA
1 CATTTAAATCAAAATGTATTTA
51835 AACAACCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (24 bp):
CATTTAAATCAAAATGTATTTACT
Found at i:52909 original size:22 final size:22
Alignment explanation
Indices: 52862--52926 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
52852 CTAAATAACT
* * *
52862 GAGAGCACCAATGTGCTATATA
1 GAGAGCACAAATGTGCTAAACA
*
52884 GAGAGCACAAATGTGCTAAACG
1 GAGAGCACAAATGTGCTAAACA
*
52906 GAGAGCACTAAACGTGCTAAA
1 GAGAGCAC-AAATGTGCTAAA
52927 TAACGGAGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 26 0.70
23 11 0.30
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (22 bp):
GAGAGCACAAATGTGCTAAACA
Found at i:52926 original size:23 final size:22
Alignment explanation
Indices: 52884--52926 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
52874 GTGCTATATA
*
52884 GAGAGCACAAATGTGCTAAACG
1 GAGAGCACAAACGTGCTAAACG
52906 GAGAGCACTAAACGTGCTAAA
1 GAGAGCAC-AAACGTGCTAAA
52927 TAACGGAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.42, C:0.19, G:0.26, T:0.14
Consensus pattern (22 bp):
GAGAGCACAAACGTGCTAAACG
Done.