Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006003.1 Kokia drynarioides strain JFW-HI SEQ_120434, 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: 222010
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:13624 original size:26 final size:27
Alignment explanation
Indices: 13579--13629 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
13569 ATTAATGAGG
*
13579 AATACAAATAGGAAATAAA-TATAAGA
1 AATACAAATAGGAAAGAAATTATAAGA
13605 AATAC-AATAGGAAAAGAAATTATAA
1 AATACAAATAGG-AAAGAAATTATAA
13630 AATAGTCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 11 0.50
27 5 0.23
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.20
Consensus pattern (27 bp):
AATACAAATAGGAAAGAAATTATAAGA
Found at i:13726 original size:15 final size:16
Alignment explanation
Indices: 13703--13754 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
13693 AATAAATACG
*
13703 ATATCCATAAAATTAA
1 ATATACATAAAATTAA
*
13719 ATAT-CATAAAATAAA
1 ATATACATAAAATTAA
* *
13734 ACATAAATAAATATTAA
1 ATATACATAAA-ATTAA
13751 ATAT
1 ATAT
13755 TAAATAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 13 0.45
16 9 0.31
17 7 0.24
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (16 bp):
ATATACATAAAATTAA
Found at i:17466 original size:25 final size:26
Alignment explanation
Indices: 17426--17480 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
17416 AAACTAAATT
*
17426 TAAACAAATAAAGAAACGATGAAAAA
1 TAAACAAATAAAGAAACAATGAAAAA
* *
17452 TAAAC-AATAATGAAATAATGAAAAA
1 TAAACAAATAAAGAAACAATGAAAAA
17477 TAAA
1 TAAA
17481 ATAAAGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.69, C:0.05, G:0.09, T:0.16
Consensus pattern (26 bp):
TAAACAAATAAAGAAACAATGAAAAA
Found at i:43381 original size:18 final size:18
Alignment explanation
Indices: 43350--43385 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
43340 TTGTTTAAAG
43350 CATCTATTCATCCTCATC
1 CATCTATTCATCCTCATC
* *
43368 CATCTCTTCCTCCTCATC
1 CATCTATTCATCCTCATC
43386 ATTGTCATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.44, G:0.00, T:0.39
Consensus pattern (18 bp):
CATCTATTCATCCTCATC
Found at i:44535 original size:21 final size:21
Alignment explanation
Indices: 44511--44554 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
44501 GTGACAGTTT
44511 TACCAAAACAAGTCTTACTTC
1 TACCAAAACAAGTCTTACTTC
* * *
44532 TACCGATACAAGTTTTACTTC
1 TACCAAAACAAGTCTTACTTC
44553 TA
1 TA
44555 TCGATTCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (21 bp):
TACCAAAACAAGTCTTACTTC
Found at i:44559 original size:21 final size:21
Alignment explanation
Indices: 44518--44559 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
44508 TTTTACCAAA
44518 ACAAGTCTTACTTCTACCGAT
1 ACAAGTCTTACTTCTACCGAT
* *
44539 ACAAGTTTTACTTCTATCGAT
1 ACAAGTCTTACTTCTACCGAT
44560 TCCAAAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.38
Consensus pattern (21 bp):
ACAAGTCTTACTTCTACCGAT
Found at i:46155 original size:13 final size:12
Alignment explanation
Indices: 46119--46157 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
46109 AAATGATGAA
46119 AATTTCTATTTT
1 AATTTCTATTTT
46131 AATTTCTATTTT
1 AATTTCTATTTT
46143 AATTTCTTATTTT
1 AATTTC-TATTTT
46156 AA
1 AA
46158 CTTATATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (12 bp):
AATTTCTATTTT
Found at i:50697 original size:53 final size:55
Alignment explanation
Indices: 50606--50717 Score: 129
Period size: 53 Copynumber: 2.1 Consensus size: 55
50596 TTGATAACTC
* * * * * *
50606 ATGATGACACAGTCATCGGACCCTTAATCCGTAATAGGA-TTCGTATAAGTCACG
1 ATGATGACAAAGTCATCAGACCCTTAACCCATAATAGGATTTCATATAACTCACG
* * *
50660 ATGAT-ACAAAGTCATCAGACCTTTAACCCATAGTAGGATTTCATATAACTCAGG
1 ATGATGACAAAGTCATCAGACCCTTAACCCATAATAGGATTTCATATAACTCACG
50714 ATGA
1 ATGA
50718 CACAGAGTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
53 27 0.56
54 21 0.44
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (55 bp):
ATGATGACAAAGTCATCAGACCCTTAACCCATAATAGGATTTCATATAACTCACG
Found at i:65441 original size:21 final size:22
Alignment explanation
Indices: 65417--65457 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
65407 TGCTCTTACT
*
65417 TTCTC-ACGAGTTTATTTTATG
1 TTCTCTACAAGTTTATTTTATG
*
65438 TTCTCTACAAGTTTCTTTTA
1 TTCTCTACAAGTTTATTTTA
65458 ACCTTCTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.54
Consensus pattern (22 bp):
TTCTCTACAAGTTTATTTTATG
Found at i:67435 original size:33 final size:33
Alignment explanation
Indices: 67349--67426 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
67339 TTATTTATTA
* *
67349 TTGCATGTTCATATTAGTTTAACTGCATTGTAG
1 TTGCATTTTCATATTAGTTTAACTACATTGTAG
67382 TTGCATTTTCATATTAGTTTAACTACATTGTAG
1 TTGCATTTTCATATTAGTTTAACTACATTGTAG
67415 TTGCATTTTCAT
1 TTGCATTTTCAT
67427 TCTTGTTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.49
Consensus pattern (33 bp):
TTGCATTTTCATATTAGTTTAACTACATTGTAG
Found at i:69862 original size:16 final size:15
Alignment explanation
Indices: 69829--69866 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
69819 CCTAATTTAA
69829 ATTTTATTAGTTTTT
1 ATTTTATTAGTTTTT
69844 ATTTTATTA-TTCATTT
1 ATTTTATTAGTT--TTT
69860 ATTTTAT
1 ATTTTAT
69867 CAATTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 9 0.43
16 10 0.48
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (15 bp):
ATTTTATTAGTTTTT
Found at i:73672 original size:21 final size:21
Alignment explanation
Indices: 73648--73687 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
73638 TCCCACTCCA
73648 TCTCACCTCC-TTATTTCTCTT
1 TCTC-CCTCCATTATTTCTCTT
*
73669 TCTCTCTCCATTATTTCTC
1 TCTCCCTCCATTATTTCTC
73688 CATTTTTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.10, C:0.38, G:0.00, T:0.53
Consensus pattern (21 bp):
TCTCCCTCCATTATTTCTCTT
Found at i:85694 original size:22 final size:22
Alignment explanation
Indices: 85669--85710 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
85659 CTGCTTGCTT
* *
85669 TGTCGCGACATAGGTCCTAGTG
1 TGTCACGACATAGATCCTAGTG
*
85691 TGTCACGACATTGATCCTAG
1 TGTCACGACATAGATCCTAG
85711 ATGTCAATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (22 bp):
TGTCACGACATAGATCCTAGTG
Found at i:90666 original size:12 final size:12
Alignment explanation
Indices: 90649--90701 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
90639 CAGGTTCTGT
90649 TTCTTCCTTCTC
1 TTCTTCCTTCTC
90661 TTCTTCCTTTCCTTC
1 TTCTTCC-TT-C-TC
* *
90676 TTCTTCTTTTTC
1 TTCTTCCTTCTC
*
90688 TTCATCCTTCTC
1 TTCTTCCTTCTC
90700 TT
1 TT
90702 GATCACCTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
12 20 0.61
13 2 0.06
14 3 0.09
15 8 0.24
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCTTCCTTCTC
Found at i:96672 original size:15 final size:15
Alignment explanation
Indices: 96649--96688 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
96639 GCTATTGTTG
*
96649 TAACTCCCTTACTTA
1 TAACCCCCTTACTTA
96664 TAACCCCCTTACTTA
1 TAACCCCCTTACTTA
96679 TAACCCCCTT
1 TAACCCCCTT
96689 TATTTGAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.25, C:0.40, G:0.00, T:0.35
Consensus pattern (15 bp):
TAACCCCCTTACTTA
Found at i:110972 original size:11 final size:12
Alignment explanation
Indices: 110954--110984 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
110944 AAGTTAAAAA
110954 TATATTTTAATT
1 TATATTTTAATT
110966 T-TATTTTAATT
1 TATATTTTAATT
110977 TATATTTT
1 TATATTTT
110985 TATAGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TATATTTTAATT
Found at i:114999 original size:18 final size:18
Alignment explanation
Indices: 114968--115003 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
114958 TTGTTTAAAG
114968 CATCTATTCATCCTCATC
1 CATCTATTCATCCTCATC
* *
114986 CATCTCTTCCTCCTCATC
1 CATCTATTCATCCTCATC
115004 ATTGTTGTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.44, G:0.00, T:0.39
Consensus pattern (18 bp):
CATCTATTCATCCTCATC
Found at i:116150 original size:21 final size:21
Alignment explanation
Indices: 116126--116173 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
116116 CAAGTGACAG
116126 TTCTACC-ACAACAAGTCTTAC
1 TTCTACCGA-AACAAGTCTTAC
* *
116147 TTCTACCGATACAAGTTTTAC
1 TTCTACCGAAACAAGTCTTAC
116168 TTCTAC
1 TTCTAC
116174 TGATACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (21 bp):
TTCTACCGAAACAAGTCTTAC
Found at i:116178 original size:21 final size:21
Alignment explanation
Indices: 116136--116179 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
116126 TTCTACCACA
116136 ACAAGTCTTACTTCTACCGAT
1 ACAAGTCTTACTTCTACCGAT
* *
116157 ACAAGTTTTACTTCTACTGAT
1 ACAAGTCTTACTTCTACCGAT
116178 AC
1 AC
116180 CAAAAACTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (21 bp):
ACAAGTCTTACTTCTACCGAT
Found at i:133094 original size:15 final size:15
Alignment explanation
Indices: 133069--133110 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
133059 GATAACCAAC
*
133069 AAAAGGAGAAGGAAG
1 AAAAAGAGAAGGAAG
*
133084 AAGAAGAGAAGGAAG
1 AAAAAGAGAAGGAAG
133099 AAAAAGAAGAAG
1 AAAAAG-AGAAG
133111 AGAATGAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (15 bp):
AAAAAGAGAAGGAAG
Found at i:142624 original size:30 final size:30
Alignment explanation
Indices: 142588--142651 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
142578 TACGAGAGTG
142588 TCTTTTAATGTTAGATCATTTTGATTCTTA
1 TCTTTTAATGTTAGATCATTTTGATTCTTA
142618 TCTTTTAATGTTAGATCATTTTGATTCTTA
1 TCTTTTAATGTTAGATCATTTTGATTCTTA
142648 -CTTT
1 TCTTT
142652 ATATTACTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.58
Consensus pattern (30 bp):
TCTTTTAATGTTAGATCATTTTGATTCTTA
Found at i:151607 original size:22 final size:20
Alignment explanation
Indices: 151570--151614 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
151560 TCAGTCACTT
*
151570 GAAAAAAATGAGAAAAAGAA
1 GAAAAAAAAGAGAAAAAGAA
151590 GAAAAAAAAGAAGAAAAAAGAA
1 GAAAAAAAAG-AG-AAAAAGAA
151612 GAA
1 GAA
151615 GAATAAAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
21 2 0.09
22 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (20 bp):
GAAAAAAAAGAGAAAAAGAA
Found at i:151622 original size:13 final size:12
Alignment explanation
Indices: 151580--151622 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
151570 GAAAAAAATG
151580 AGAAAAAGAAGA
1 AGAAAAAGAAGA
*
151592 AAAAAAAGAAG-
1 AGAAAAAGAAGA
151603 A-AAAAAGAAGA
1 AGAAAAAGAAGA
151614 AGAATAAAG
1 AGAA-AAAG
151623 TGCTAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 9 0.33
11 2 0.07
12 12 0.44
13 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (12 bp):
AGAAAAAGAAGA
Found at i:160859 original size:47 final size:47
Alignment explanation
Indices: 160790--160881 Score: 175
Period size: 47 Copynumber: 2.0 Consensus size: 47
160780 CATTGAATGT
*
160790 GGCTCACCCAATCACTATCGAAAATAAGGTATATAATGCTCGCATGG
1 GGCTCACCCAATCACTATCGAAAATAAGGTATATAATGCCCGCATGG
160837 GGCTCACCCAATCACTATCGAAAATAAGGTATATAATGCCCGCAT
1 GGCTCACCCAATCACTATCGAAAATAAGGTATATAATGCCCGCAT
160882 CTAGCCATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (47 bp):
GGCTCACCCAATCACTATCGAAAATAAGGTATATAATGCCCGCATGG
Found at i:164323 original size:7 final size:7
Alignment explanation
Indices: 164311--164338 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
164301 AAATCCAATT
164311 GTGTTGA
1 GTGTTGA
164318 GTGTTGA
1 GTGTTGA
164325 GTGTTGA
1 GTGTTGA
164332 GTGTTGA
1 GTGTTGA
164339 ATATTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
GTGTTGA
Found at i:169570 original size:22 final size:22
Alignment explanation
Indices: 169542--169583 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
169532 AGAAAGACGG
*
169542 AATGAAATAACTAAGCCTAAGA
1 AATGAAATAACTAAACCTAAGA
*
169564 AATGAAATGACTAAACCTAA
1 AATGAAATAACTAAACCTAA
169584 TTACAAAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.14, G:0.12, T:0.19
Consensus pattern (22 bp):
AATGAAATAACTAAACCTAAGA
Found at i:172103 original size:17 final size:17
Alignment explanation
Indices: 172081--172114 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
172071 ATAGGGAAAA
*
172081 TAATCTTAGAAGATTTG
1 TAATCTAAGAAGATTTG
*
172098 TAATCTAATAAGATTTG
1 TAATCTAAGAAGATTTG
172115 ATTTTGTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (17 bp):
TAATCTAAGAAGATTTG
Found at i:172715 original size:21 final size:21
Alignment explanation
Indices: 172691--172739 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
172681 GGTTACATAG
172691 CCGTGTGGCTC-TCCCACATGC
1 CCGTGTGGC-CATCCCACATGC
172712 CCGTGTGGCCATCCCACATGC
1 CCGTGTGGCCATCCCACATGC
*
172733 CCATGTG
1 CCGTGTG
172740 TCCAACCTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.12, C:0.41, G:0.24, T:0.22
Consensus pattern (21 bp):
CCGTGTGGCCATCCCACATGC
Found at i:176708 original size:19 final size:18
Alignment explanation
Indices: 176667--176713 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
176657 AATTTTTTTT
176667 ATTTTTCTTCTCTCTTCTC
1 ATTTTTCTT-TCTCTTCTC
*
176686 -TTTTTCTTTCTTTATCTC
1 ATTTTTCTTTCTCT-TCTC
*
176704 ATTTTCCTTT
1 ATTTTTCTTT
176714 TCATGTGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 4 0.17
18 12 0.50
19 8 0.33
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTTCTTTCTCTTCTC
Found at i:204687 original size:30 final size:31
Alignment explanation
Indices: 204651--204717 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
204641 AATTCTAACT
*
204651 TGTTTGAAAT-GATTAAAACATATTTGAAAA
1 TGTTTGAAATCAATTAAAACATATTTGAAAA
* *
204681 TGTTTG-ACTCAATTGAAACATATTTGAAAA
1 TGTTTGAAATCAATTAAAACATATTTGAAAA
204711 TGTTTGA
1 TGTTTGA
204718 CTCAATTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 2 0.06
30 30 0.94
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.39
Consensus pattern (31 bp):
TGTTTGAAATCAATTAAAACATATTTGAAAA
Found at i:204718 original size:30 final size:30
Alignment explanation
Indices: 204666--204729 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
204656 GAAATGATTA
204666 AAACATATTTGAAAATGTTTGACTCAATTG
1 AAACATATTTGAAAATGTTTGACTCAATTG
204696 AAACATATTTGAAAATGTTTGACTCAATTG
1 AAACATATTTGAAAATGTTTGACTCAATTG
204726 AAAC
1 AAAC
204730 CATTTCAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (30 bp):
AAACATATTTGAAAATGTTTGACTCAATTG
Found at i:205106 original size:25 final size:23
Alignment explanation
Indices: 205054--205099 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
205044 ACCTTATGAG
205054 AACACCTTTTTTAATTAGTCATA
1 AACACCTTTTTTAATTAGTCATA
205077 AACACCTTTTTTAATTAGTCATA
1 AACACCTTTTTTAATTAGTCATA
205100 TATACACGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.43
Consensus pattern (23 bp):
AACACCTTTTTTAATTAGTCATA
Found at i:213913 original size:48 final size:48
Alignment explanation
Indices: 213813--214035 Score: 212
Period size: 49 Copynumber: 4.6 Consensus size: 48
213803 GGGTAGTCAA
* * * * * *
213813 GTCACTTTACTACCTTCTATAAGCTTCCCCTCATGCATTTGGGAGCAAG
1 GTCACTTTATTACTTTCCATAAGCCTCCCC-CATGCATCTAGGAGCAAG
* * *
213862 GTCACTTTATTACTTTCCATAAGTCTCCCCCATGCGTCTGGGAGCAAG
1 GTCACTTTATTACTTTCCATAAGCCTCCCCCATGCATCTAGGAGCAAG
* * * * *
213910 GTCACTTTATTACCTTCCGTAAGCCTCCCCCCATGCGTCCAGGAGCAGG
1 GTCACTTTATTACTTTCCATAAGCCT-CCCCCATGCATCTAGGAGCAAG
* * * * *
213959 GTCATTTTCTTACTTTCCGTAAGCCTCAACCCATGCATCTAGGAGCAGG
1 GTCACTTTATTACTTTCCATAAGCCTC-CCCCATGCATCTAGGAGCAAG
* * * *
214008 GTCATTTTCTTACTTACCATAAACCTCC
1 GTCACTTTATTACTTTCCATAAGCCTCC
214036 TTAACGCATA
Statistics
Matches: 149, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
48 40 0.27
49 109 0.73
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.31
Consensus pattern (48 bp):
GTCACTTTATTACTTTCCATAAGCCTCCCCCATGCATCTAGGAGCAAG
Found at i:215597 original size:21 final size:22
Alignment explanation
Indices: 215572--215621 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
215562 TTGTTGATAT
*
215572 TTTTTAGATCAA-AATTTTAAA
1 TTTTTACATCAATAATTTTAAA
* *
215593 TTTTTACCTCAATTATTTTAAA
1 TTTTTACATCAATAATTTTAAA
215615 TATTTTA
1 T-TTTTA
215622 ATTAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.42
22 9 0.38
23 5 0.21
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTTTACATCAATAATTTTAAA
Found at i:215628 original size:22 final size:22
Alignment explanation
Indices: 215572--215629 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
215562 TTGTTGATAT
* *
215572 TTTTTAGATCAA-AATTTTAAA
1 TTTTTACATCAATTATTTTAAA
*
215593 TTTTTACCTCAATTATTTTAAA
1 TTTTTACATCAATTATTTTAAA
*
215615 TATTTTA-ATTAATTA
1 T-TTTTACATCAATTA
215630 AATTTTATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 10 0.33
22 15 0.50
23 5 0.17
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTTACATCAATTATTTTAAA
Found at i:217903 original size:37 final size:37
Alignment explanation
Indices: 217852--217953 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
217842 GTTCTTGGAT
* * *
217852 CACCGACACAAAGCCTACTAGGCACATAGCCCGAATA
1 CACCGACACAAAGCCTACTAGGCACAAAGCCCAAAAA
* *
217889 CACCGACACGAAGCCTACTAGGCACAAAGCCTAAAAA
1 CACCGACACAAAGCCTACTAGGCACAAAGCCCAAAAA
* *
217926 CACCGGCATAAAGCCTACTAGGCACAAA
1 CACCGACACAAAGCCTACTAGGCACAAA
217954 ACCTGAATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.40, C:0.33, G:0.17, T:0.10
Consensus pattern (37 bp):
CACCGACACAAAGCCTACTAGGCACAAAGCCCAAAAA
Done.