Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012714.1 Kokia drynarioides strain JFW-HI SEQ_127725, 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: 116671
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 122 characters in sequence are not A, C, G, or T
Found at i:1557 original size:212 final size:210
Alignment explanation
Indices: 1086--1623 Score: 614
Period size: 212 Copynumber: 2.5 Consensus size: 210
1076 TGCTCGGATT
* *** * *
1086 CTTCATTCTTTTTGAAGTACCTTCTGTCTGACATTAGTGTTTGATATGTGGGTATGGAGATATGA
1 CTTCATTCTTTTTGAAGTACC-CCTGTCTGACATTAGTGTTTGATACACGGATATGGAGACATGA
* * *
1151 CCTTCAAAGATCCCTTAATATATGGAAAAACTTGAGAAAGTCTAATCATACCCATGTCGGGGATA
65 CCTCCAAAGATCCCTTAATATATGG-AAAACTTGGGAAAGTCTAATCATACCCATGCCGGGGATA
* * * * * * * * * *
1216 TTCACACCTGAGTCCAGTAACATGTGAACAATGCCGGTGCAACGAAGAACTAAAATGAAAATCCA
129 CTCAAACCCGAGTCAAGAAACATATGAACAATGACGATGCAACCAAGAACTAAAATGAAAAACCA
*
1281 TCTGCCCCAATTGTTGG
194 TCTGCCCCAATTGTTGA
* * * *
1298 CTTCATTCTTCTTGAAGTACCCCTGCCCGACATTAGTGTTTGATACACGGATATGGAGACATTAC
1 CTTCATTCTTTTTGAAGTACCCCTGTCTGACATTAGTGTTTGATACACGGATATGGAGACATGAC
* * * *
1363 CCCCAAAGATCCCTTAATATATGGAAAACCTTGGGAAAATCTAATCATACTCGTGCCGGGGACT-
66 CTCCAAAGATCCCTTAATATATGGAAAA-CTTGGGAAAGTCTAATCATACCCATGCCGGGGA-TA
* *
1427 CTCAAACCCGAGTCTAAGCAAACCTATG-ACAATGACGATGTAACCAAGAACTTAAAA-GAAAAA
129 CTCAAACCCGAGTC-AAG-AAACATATGAACAATGACGATGCAACCAAGAAC-TAAAATGAAAAA
* *
1490 CTATCTGCCCCCATTGTTGA
191 CCATCTGCCCCAATTGTTGA
* * * * * *
1510 CTTCATTCTTTTTGAAGTACCCCAGTTTAACATTAGTGTTCGATACACGAATATCGAGACATGAC
1 CTTCATTCTTTTTGAAGTACCCCTGTCTGACATTAGTGTTTGATACACGGATATGGAGACATGAC
* **
1575 CTCCAAAGAACCCCCAATATATGAGAAAACTTGGGAAAGTCTAATCATA
66 CTCCAAAGATCCCTTAATATATG-GAAAACTTGGGAAAGTCTAATCATA
1624 TCCGTGTCAG
Statistics
Matches: 273, Mismatches: 47, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
210 4 0.01
211 96 0.35
212 157 0.58
213 16 0.06
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (210 bp):
CTTCATTCTTTTTGAAGTACCCCTGTCTGACATTAGTGTTTGATACACGGATATGGAGACATGAC
CTCCAAAGATCCCTTAATATATGGAAAACTTGGGAAAGTCTAATCATACCCATGCCGGGGATACT
CAAACCCGAGTCAAGAAACATATGAACAATGACGATGCAACCAAGAACTAAAATGAAAAACCATC
TGCCCCAATTGTTGA
Found at i:7638 original size:80 final size:80
Alignment explanation
Indices: 7538--7700 Score: 317
Period size: 80 Copynumber: 2.0 Consensus size: 80
7528 GTCACAAAGA
7538 AAAAAAAAGACCAAATTATACAATGTGTAAACATTAGGAGTTCATTTTTTTAGAATCAAGACTAA
1 AAAAAAAAGACCAAATTATACAATGTGTAAACATTAGGAGTTCATTTTTTTAGAATCAAGACTAA
7603 ATAAACACAACATAT
66 ATAAACACAACATAT
7618 AAAAAAAAGACCAAATTATACAATGTGTAAACATTAGGAGTTCATTTTTTTAGAATCAAGACTAA
1 AAAAAAAAGACCAAATTATACAATGTGTAAACATTAGGAGTTCATTTTTTTAGAATCAAGACTAA
*
7683 ATAAACACAACGTAT
66 ATAAACACAACATAT
7698 AAA
1 AAA
7701 TGTCAAGGCT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.27
Consensus pattern (80 bp):
AAAAAAAAGACCAAATTATACAATGTGTAAACATTAGGAGTTCATTTTTTTAGAATCAAGACTAA
ATAAACACAACATAT
Found at i:11131 original size:31 final size:30
Alignment explanation
Indices: 11070--11132 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 30
11060 AGTCTATATC
* * * *
11070 TTTATGATTTTTAAAAATTTAAATTAAATT
1 TTTATCATTTTTAAAAAATCAAATGAAATT
*
11100 TTTATCATTTTTAAAAAAATCAAATGCAATT
1 TTTATCATTTTT-AAAAAATCAAATGAAATT
11131 TT
1 TT
11133 ACCTTTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (30 bp):
TTTATCATTTTTAAAAAATCAAATGAAATT
Found at i:15624 original size:26 final size:26
Alignment explanation
Indices: 15595--15655 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
15585 CCTCATTTGT
*
15595 TTTTTTTTAATGAATATATACATATA
1 TTTTTTTCAATGAATATATACATATA
15621 TTTTTTTCAATGAATATATACATATA
1 TTTTTTTCAATGAATATATACATATA
15647 TTTTTTTCA
1 TTTTTTTCA
15656 TCCATATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (26 bp):
TTTTTTTCAATGAATATATACATATA
Found at i:26809 original size:17 final size:17
Alignment explanation
Indices: 26779--26825 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
26769 ATATTTTATC
* *
26779 AATTTGATTCTTTTTTT
1 AATTTGTTTTTTTTTTT
*
26796 ACTCTTGTTTTTTTTTTT
1 AAT-TTGTTTTTTTTTTT
26814 AATTTGTTTTTT
1 AATTTGTTTTTT
26826 AATGAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.74
Consensus pattern (17 bp):
AATTTGTTTTTTTTTTT
Found at i:34003 original size:28 final size:26
Alignment explanation
Indices: 33941--34003 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
33931 AATTAAGTTT
*
33941 ATTTAAAATAAAAATATTAAATTTAA
1 ATTTAAAATAAAAAAATTAAATTTAA
33967 ATTTGAAAATAAAAAAA-TATAATATTAA
1 ATTT-AAAATAAAAAAATTA-AAT-TTAA
33995 ATATTAAAA
1 AT-TTAAAA
34004 AATATTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 6 0.19
27 14 0.44
28 10 0.31
29 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
ATTTAAAATAAAAAAATTAAATTTAA
Found at i:34185 original size:23 final size:23
Alignment explanation
Indices: 34154--34198 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
34144 ATATATAATA
*
34154 TTTTAATAAAGTTTAAAAATATT
1 TTTTAATAAAATTTAAAAATATT
* *
34177 TTTTCATAAAATTTTAAAATAT
1 TTTTAATAAAATTTAAAAATAT
34199 AGAATTATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTTAATAAAATTTAAAAATATT
Found at i:34369 original size:24 final size:24
Alignment explanation
Indices: 34330--34390 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
34320 GAATTATATA
*
34330 TTTATAATTTTATAAAAACTA-TTT
1 TTTAAAATTTT-TAAAAACTATTTT
*
34354 TTTAAAACTTTTT-AAAATTATTTT
1 TTTAAAA-TTTTTAAAAACTATTTT
34378 TTTAAAATTTTTA
1 TTTAAAATTTTTA
34391 CATTTTTAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 11 0.34
24 17 0.53
25 4 0.12
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTAAAATTTTTAAAAACTATTTT
Found at i:39165 original size:17 final size:19
Alignment explanation
Indices: 39129--39165 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
39119 CGGGTTTTAA
*
39129 AATTTTGAGAATTTGAGTT
1 AATTTTGAGAATTCGAGTT
39148 AATTTTG-G-ATTCGAGTT
1 AATTTTGAGAATTCGAGTT
39165 A
1 A
39166 TTTCGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 1 0.06
19 7 0.41
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.46
Consensus pattern (19 bp):
AATTTTGAGAATTCGAGTT
Found at i:40550 original size:58 final size:59
Alignment explanation
Indices: 40458--40572 Score: 155
Period size: 58 Copynumber: 2.0 Consensus size: 59
40448 ATCTCAAGGT
40458 CTAACTTGGAAAAAAAAAAGCTTAAGCCCTAATGTGAGAACAATTGCCAAGTTCAGGGA
1 CTAACTTGGAAAAAAAAAAGCTTAAGCCCTAATGTGAGAACAATTGCCAAGTTCAGGGA
* * * *
40517 CTAACTT-GAACAAAAAAA-CTTTAAG-CCTCAATGTGGGAACACTTGTCAAGTTCAGG
1 CTAACTTGGAAAAAAAAAAGC-TTAAGCCCT-AATGTGAGAACAATTGCCAAGTTCAGG
40573 TCCCAAATAC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
57 4 0.08
58 39 0.78
59 7 0.14
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (59 bp):
CTAACTTGGAAAAAAAAAAGCTTAAGCCCTAATGTGAGAACAATTGCCAAGTTCAGGGA
Found at i:40905 original size:19 final size:17
Alignment explanation
Indices: 40881--40930 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
40871 ATGTGTGAAT
40881 TTTAATTCGAATCTCAAAA
1 TTTAATTC-AAT-TCAAAA
40900 TTTAATTCAATTC-AAA
1 TTTAATTCAATTCAAAA
*
40916 TTTCATTCAATTCAA
1 TTTAATTCAATTCAA
40931 TTTAGTCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 15 0.52
17 3 0.10
18 3 0.10
19 8 0.28
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTAATTCAATTCAAAA
Found at i:48452 original size:18 final size:18
Alignment explanation
Indices: 48413--48450 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
48403 ACATTAAATG
48413 AAAT-TTATTATTATTAA
1 AAATATTATTATTATTAA
48430 AAATATTATTATTAATTAA
1 AAATATTATTATT-ATTAA
48449 AA
1 AA
48451 TAAAAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 8 0.42
19 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATATTATTATTATTAA
Found at i:49643 original size:29 final size:29
Alignment explanation
Indices: 49602--49861 Score: 181
Period size: 29 Copynumber: 8.9 Consensus size: 29
49592 GGAGGTCCCT
**
49602 AAACTATCCAAAAATTACCATTTTACCCTT
1 AAACT-TCCAAAAATTACCATTTTACCCCC
* * **
49632 AAACTT-CAAAAAATCCCAATTTTGACCCTA
1 AAACTTCCAAAAATTACC-ATTTT-ACCCCC
* * * * *
49662 AAACTTCTAAATATTATCGTTTTACCCCT
1 AAACTTCCAAAAATTACCATTTTACCCCC
*
49691 GAACTTCCAAAAATT-CCATTTTTGA-CCCC
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
* *
49720 AAACCTTCTAAAAATTACCATTTTGCCCCC
1 AAA-CTTCCAAAAATTACCATTTTACCCCC
* * *
49750 AAACTCCCAAAAA-T-CCTATTTTAACCTCG
1 AAACTTCCAAAAATTACC-ATTTT-ACCCCC
* *
49779 AAACTTCTAAAAATTATCATTTTACCCCC
1 AAACTTCCAAAAATTACCATTTTACCCCC
* * *
49808 GAACTTCCAAAAA-TCCCATTTTGACCCCG
1 AAACTTCCAAAAATTACCATTTT-ACCCCC
* *
49837 AAACATCCAAAAATTACTATTTTAC
1 AAACTTCCAAAAATTACCATTTTAC
49862 TCCCGGATGT
Statistics
Matches: 177, Mismatches: 39, Indels: 29
0.72 0.16 0.12
Matches are distributed among these distances:
27 2 0.01
28 23 0.13
29 86 0.49
30 56 0.32
31 10 0.06
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.31
Consensus pattern (29 bp):
AAACTTCCAAAAATTACCATTTTACCCCC
Found at i:49794 original size:58 final size:56
Alignment explanation
Indices: 49602--49861 Score: 250
Period size: 59 Copynumber: 4.4 Consensus size: 56
49592 GGAGGTCCCT
* ** * *
49602 AAACTATCCAAAAATTACCATTTTACCCTTAAACTTCAAAAAATCCCAATTTTGACCCTA
1 AAACT-TCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAAT-CC-ATTTTGACCC-G
* * * ** *
49662 AAACTTCTAAATATTATCGTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCC
1 AAACTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAA-TCCA-TTTTGACCCG
* * *
49720 AAACCTTCTAAAAATTACCATTTTGCCCCCAAACTCCCAAAAATCCTATTTTAACCTCG
1 AAA-CTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCC-ATTTTGACC-CG
* *
49779 AAACTTCTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCCATTTTGACCCCG
1 AAACTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAAT-CCATTTTGA-CCCG
* * *
49837 AAACATCCAAAAATTACTATTTTAC
1 AAACTTCTAAAAATTACCATTTTAC
49862 TCCCGGATGT
Statistics
Matches: 167, Mismatches: 26, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
58 79 0.47
59 82 0.49
60 6 0.04
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.31
Consensus pattern (56 bp):
AAACTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCATTTTGACCCG
Found at i:49897 original size:117 final size:117
Alignment explanation
Indices: 49602--49861 Score: 310
Period size: 117 Copynumber: 2.2 Consensus size: 117
49592 GGAGGTCCCT
* ** * * * ** *
49602 AAACTATCCAAAAATTACCATTTTACCCTTAAACTTCAAAAAATCCCAATTTTGACC-CTAAAAC
1 AAACCATCCAAAAATTACCATTTTACCCCCAAACTCCCAAAAAT-CCTATTTCAACCTC-GAAAC
* * * *
49666 TTCTAAATATTATCGTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCC
64 TTCTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * *
49720 AAACCTTCTAAAAATTACCATTTTGCCCCCAAACTCCCAAAAATCCTATTTTAACCTCGAAACTT
1 AAACCATCCAAAAATTACCATTTTACCCCCAAACTCCCAAAAATCCTATTTCAACCTCGAAACTT
49785 CTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTGACCCC
66 CTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
*
49836 GAAA-CATCCAAAAATTACTATTTTAC
1 -AAACCATCCAAAAATTACCATTTTAC
49862 TCCCGGATGT
Statistics
Matches: 121, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
116 28 0.23
117 56 0.46
118 37 0.31
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.31
Consensus pattern (117 bp):
AAACCATCCAAAAATTACCATTTTACCCCCAAACTCCCAAAAATCCTATTTCAACCTCGAAACTT
CTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
Found at i:49919 original size:117 final size:117
Alignment explanation
Indices: 49602--49927 Score: 284
Period size: 117 Copynumber: 2.8 Consensus size: 117
49592 GGAGGTCCCT
* ** * * * ** *
49602 AAACTATCCAAAAATTACCATTTTACCCTTAAACTTCAAAAAATCCCAATTTTGACC-CTAAAAC
1 AAACCATCCAAAAATTACCATTTTACCCCCAAACTCCCAAAAAT-CCTATTTCAACCTC-GAAAC
* * * * * *
49666 TTCTAAATATTATCGTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCC
64 TTCTAAAAATAACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * *
49720 AAACCTTCTAAAAATTACCATTTTGCCCCCAAACTCCCAAAAATCCTATTTTAACCTCGAAACTT
1 AAACCATCCAAAAATTACCATTTTACCCCCAAACTCCCAAAAATCCTATTTCAACCTCGAAACTT
* *
49785 CTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTGACCCC
66 CTAAAAATAACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* ** ** * * * * *
49836 GAAA-CATCCAAAAATTACTATTTTACTCCCGGATGTCCGAAGACTCCGT-TTTCGACCTCGAAG
1 -AAACCATCCAAAAATTACCATTTTAC-CCCCAAACTCCCAAAAATCC-TATTTCAACCTCGAAA
49899 C-TCTAAAAATAACCATTTTTACCCCCGAA
63 CTTCTAAAAATAACCA-TTTTACCCCCGAA
49928 TGTTTAAAAT
Statistics
Matches: 172, Mismatches: 31, Indels: 11
0.80 0.14 0.05
Matches are distributed among these distances:
116 40 0.23
117 94 0.55
118 38 0.22
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.30
Consensus pattern (117 bp):
AAACCATCCAAAAATTACCATTTTACCCCCAAACTCCCAAAAATCCTATTTCAACCTCGAAACTT
CTAAAAATAACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
Found at i:75282 original size:23 final size:24
Alignment explanation
Indices: 75252--75299 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
75242 CCTATGCTAA
75252 AGAGGATCGCGTA-GAAGAT-GTTG
1 AGAGGATC-CGTAGGAAGATGGTTG
*
75275 AGAGGATCCTTAGGAAGATGGTTG
1 AGAGGATCCGTAGGAAGATGGTTG
75299 A
1 A
75300 AAATGGTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 14 0.64
24 5 0.23
ACGTcount: A:0.31, C:0.08, G:0.38, T:0.23
Consensus pattern (24 bp):
AGAGGATCCGTAGGAAGATGGTTG
Found at i:77718 original size:16 final size:16
Alignment explanation
Indices: 77697--77727 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
77687 TATCAGTTAT
77697 AATCAATTCACACAAA
1 AATCAATTCACACAAA
77713 AATCAATTCACACAA
1 AATCAATTCACACAA
77728 CTTAAACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (16 bp):
AATCAATTCACACAAA
Found at i:84001 original size:29 final size:31
Alignment explanation
Indices: 83962--84034 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
83952 AAAATTTACA
83962 AAACGGAGAGACAAATTCATCGGAAAACTCG
1 AAACGGAGAGACAAATTCATCGGAAAACTCG
*
83993 AAACGGAGAGACAAATTCATTGGAAAACTCG
1 AAACGGAGAGACAAATTCATCGGAAAACTCG
84024 AAACGGAGAGA
1 AAACGGAGAGA
84035 TTGGAATTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (31 bp):
AAACGGAGAGACAAATTCATCGGAAAACTCG
Found at i:89224 original size:17 final size:16
Alignment explanation
Indices: 89204--89237 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
89194 TTAACACTAA
89204 ATTTAAATTTGAAATTG
1 ATTTAAATTTG-AATTG
*
89221 ATTTTAATTTGAATTG
1 ATTTAAATTTGAATTG
89237 A
1 A
89238 CCCAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (16 bp):
ATTTAAATTTGAATTG
Found at i:96512 original size:12 final size:12
Alignment explanation
Indices: 96495--96528 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
96485 TGTCCTGCAC
96495 CAGCATCAGGTT
1 CAGCATCAGGTT
96507 CAGCATCAGGTT
1 CAGCATCAGGTT
96519 CAGCATCAGG
1 CAGCATCAGG
96529 ACCTTTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (12 bp):
CAGCATCAGGTT
Found at i:102904 original size:20 final size:21
Alignment explanation
Indices: 102872--102910 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
102862 TCCAAAAAAA
102872 AATCAAATCCAACT-TAACCG
1 AATCAAATCCAACTCTAACCG
102892 AATCAAA-CTCAACTCTAAC
1 AATCAAATC-CAACTCTAAC
102911 GATGACATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 12 0.71
21 4 0.24
ACGTcount: A:0.46, C:0.31, G:0.03, T:0.21
Consensus pattern (21 bp):
AATCAAATCCAACTCTAACCG
Found at i:105752 original size:16 final size:16
Alignment explanation
Indices: 105731--105764 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
105721 TCAGATCGTT
*
105731 TGAATTGATCAAGTTA
1 TGAATTCATCAAGTTA
105747 TGAATTCATCAAGTTA
1 TGAATTCATCAAGTTA
105763 TG
1 TG
105765 CCTTTCTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (16 bp):
TGAATTCATCAAGTTA
Found at i:107149 original size:30 final size:29
Alignment explanation
Indices: 107114--107172 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
107104 CTTTTATAGA
* *
107114 AGTTTTAGTGTTCACTTTTTTTTTAGTTTT
1 AGTTTTAGT-TTCACTTTATTTTTAATTTT
*
107144 AGTTTTAGTTTTACTTTATTTTTAATTTT
1 AGTTTTAGTTTCACTTTATTTTTAATTTT
107173 TACTTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.17, C:0.05, G:0.10, T:0.68
Consensus pattern (29 bp):
AGTTTTAGTTTCACTTTATTTTTAATTTT
Found at i:107161 original size:17 final size:18
Alignment explanation
Indices: 107141--107178 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
107131 TTTTTTTAGT
107141 TTTAGTTTT-AGTTTTAC
1 TTTAGTTTTAAGTTTTAC
* *
107158 TTTATTTTTAATTTTTAC
1 TTTAGTTTTAAGTTTTAC
107176 TTT
1 TTT
107179 TTAAAGTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (18 bp):
TTTAGTTTTAAGTTTTAC
Found at i:107174 original size:30 final size:30
Alignment explanation
Indices: 107114--107179 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
107104 CTTTTATAGA
*
107114 AGTTTTAGTGTTCACTTTTTTTTTAGTTTT
1 AGTTTTAGTGTTCACTTTTTTTTAAGTTTT
* *
107144 AGTTTTAGT-TTTACTTTATTTTTAATTTTT
1 AGTTTTAGTGTTCACTTT-TTTTTAAGTTTT
*
107174 ACTTTT
1 AGTTTT
107180 TAAAGTTAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.17, C:0.06, G:0.09, T:0.68
Consensus pattern (30 bp):
AGTTTTAGTGTTCACTTTTTTTTAAGTTTT
Found at i:111672 original size:6 final size:6
Alignment explanation
Indices: 111658--111701 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
111648 AAAAGAGAGA
* * *
111658 GAAAGG GAAAAG GAAAAG GAAAAG GAAAAA GAAAAA GAAAAG GA
1 GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GA
111702 GAGAATAGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
GAAAAG
Found at i:114736 original size:5 final size:6
Alignment explanation
Indices: 114720--114744 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
114710 ATTGTATAAA
114720 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
114745 CGGTTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:115689 original size:6 final size:6
Alignment explanation
Indices: 115678--115705 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
115668 AATGAAACCC
115678 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
115706 TCTTTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Done.