Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008038.1 Kokia drynarioides strain JFW-HI SEQ_122693, 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: 163781
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 279 characters in sequence are not A, C, G, or T
Found at i:1533 original size:23 final size:22
Alignment explanation
Indices: 1503--1575 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
1493 GTACTGAGCA
1503 CACA-AAGTGCTAATCAGAGAG
1 CACAGAAGTGCTAATCAGAGAG
1524 CACATGAAGTGCTAATAACAGAGAG
1 CACA-GAAGTGCTAAT--CAGAGAG
* *
1549 TACGAGACGTGCTGAA-CAGAGAG
1 CAC-AGAAGTGCT-AATCAGAGAG
1572 CACA
1 CACA
1576 CACAGTGCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
21 4 0.09
22 1 0.02
23 19 0.44
25 16 0.37
26 3 0.07
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.14
Consensus pattern (22 bp):
CACAGAAGTGCTAATCAGAGAG
Found at i:1583 original size:23 final size:22
Alignment explanation
Indices: 1498--1613 Score: 60
Period size: 23 Copynumber: 5.0 Consensus size: 22
1488 ACAAAGTACT
*
1498 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAA-CAGA
*
1521 GAGCACATGA-AGTGCTAATAACAGA
1 GAGCACA-CACAGTGC---TAACAGA
* *
1546 GAGTACGAGAC-GTGCTGAACAGA
1 GAGCAC-ACACAGTGCT-AACAGA
1569 GAGCACACACAGTGC-AATCCA-A
1 GAGCACACACAGTGCTAA--CAGA
*
1591 TAAGCACACACAGTGCTGAACAG
1 -GAGCACACACAGTGCT-AACAG
1614 TAAGCGCGCT
Statistics
Matches: 74, Mismatches: 5, Indels: 27
0.70 0.05 0.25
Matches are distributed among these distances:
21 2 0.03
22 5 0.07
23 45 0.61
24 1 0.01
25 17 0.23
26 4 0.05
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.13
Consensus pattern (22 bp):
GAGCACACACAGTGCTAACAGA
Found at i:1617 original size:23 final size:23
Alignment explanation
Indices: 1557--1618 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
1547 AGTACGAGAC
1557 GTGCTGAACAG-AGAGCACACACA
1 GTGCTGAACAGTA-AGCACACACA
*
1580 GTGC--AATCCAATAAGCACACACA
1 GTGCTGAA--CAGTAAGCACACACA
1603 GTGCTGAACAGTAAGC
1 GTGCTGAACAGTAAGC
1619 GCGCTAGCGT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
21 2 0.06
23 27 0.84
24 1 0.03
25 2 0.06
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.13
Consensus pattern (23 bp):
GTGCTGAACAGTAAGCACACACA
Found at i:7500 original size:20 final size:21
Alignment explanation
Indices: 7465--7503 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
7455 TAGTTGTTCT
*
7465 ATCAAACAGAATAATAAAAGA
1 ATCAAACAGAAAAATAAAAGA
7486 ATCAAA-AGAAAAATAAAA
1 ATCAAACAGAAAAATAAAA
7504 CATAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.72, C:0.08, G:0.08, T:0.13
Consensus pattern (21 bp):
ATCAAACAGAAAAATAAAAGA
Found at i:8516 original size:23 final size:23
Alignment explanation
Indices: 8489--8536 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
8479 ATTCGCTTTT
8489 GATTTGTTTCATAAAATTTTTGG
1 GATTTGTTTCATAAAATTTTTGG
* ** *
8512 GATTTTTTTGTTAAGATTTTTGG
1 GATTTGTTTCATAAAATTTTTGG
8535 GA
1 GA
8537 ATCTTATGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.21, T:0.54
Consensus pattern (23 bp):
GATTTGTTTCATAAAATTTTTGG
Found at i:29065 original size:99 final size:99
Alignment explanation
Indices: 28894--29087 Score: 361
Period size: 99 Copynumber: 2.0 Consensus size: 99
28884 ATACATCTTG
28894 TCTAAAAACATTTTATCACACTAAGTAAGAACTCATGAAATATTCGAAAGATATATGAGGAAGAG
1 TCTAAAAACATTTTATCACACTAAGTAAGAACTCATGAAATATTCGAAAGATATATGAGGAAGAG
28959 TTCGTGATGATATCTGTCAATTCATCACATATTA
66 TTCGTGATGATATCTGTCAATTCATCACATATTA
* * *
28993 TCTAAAAACATTTTATCACACTAAGTAATAACTCATGAAATCTTCGAAAGATATATGGGGAAGAG
1 TCTAAAAACATTTTATCACACTAAGTAAGAACTCATGAAATATTCGAAAGATATATGAGGAAGAG
29058 TTCGTGATGATATCTGTCAATTCATCACAT
66 TTCGTGATGATATCTGTCAATTCATCACAT
29088 CCAGGCTTGA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 92 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (99 bp):
TCTAAAAACATTTTATCACACTAAGTAAGAACTCATGAAATATTCGAAAGATATATGAGGAAGAG
TTCGTGATGATATCTGTCAATTCATCACATATTA
Found at i:32935 original size:18 final size:18
Alignment explanation
Indices: 32914--32949 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
32904 TACTTAGTCC
32914 TTATTAATAA-ATAATTAA
1 TTATTAA-AAGATAATTAA
32932 TTATTAAAAGATAATTAA
1 TTATTAAAAGATAATTAA
32950 GCATAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TTATTAAAAGATAATTAA
Found at i:33261 original size:20 final size:20
Alignment explanation
Indices: 33216--33261 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
33206 TTCAAAAAAG
*
33216 TATAAAAATATAAAAATTCA
1 TATAAAAATATAAAAATTAA
*
33236 TTTAAAAATCA-AAAAATTAA
1 TATAAAAAT-ATAAAAATTAA
33256 TATAAA
1 TATAAA
33262 GTACATGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (20 bp):
TATAAAAATATAAAAATTAA
Found at i:35092 original size:178 final size:178
Alignment explanation
Indices: 34859--35314 Score: 720
Period size: 178 Copynumber: 2.6 Consensus size: 178
34849 ATGGTTGGTT
* * * * *
34859 TTATGTATGATGCTTCCTTGTCTATATAGCTTTAAAATCAAGCGATTTTATCTTATAATTCTTCT
1 TTATGTATGATG-TTACTTGTATATATGGCTTTGAAATCAAGCAATTTTATCTTATAATTCTTCT
34924 TGTATGAATGAACTACTTGCCAACCCCATGGTGTTGGTATCTTTTAATGTTTTAAC-TTTTTTTT
65 TGTATGAATGAACTACTTGCCAACCCCATGGTGTTGGTATCTTTTAATGTTTTAACTTTTTTTTT
34988 TTTTGTGCATTAAAAATATTGTTTAGCAATGATCATTTGATATATATGG
130 TTTTGTGCATTAAAAATATTGTTTAGCAATGATCATTTGATATATATGG
*
35037 TTATGTATGATGTTTACTTGTATATATGGCTTTGAAATCAAGCAATTTTATCTTATAATTTTTC-
1 TTATGTATGATG-TTACTTGTATATATGGCTTTGAAATCAAGCAATTTTATCTTATAATTCTTCT
35101 T-TATGAATGAACTACTTGCCAACCCCATGGTGTTGGTATCTTTTAATGTTTTAACTTGTTTTTT
65 TGTATGAATGAACTACTTGCCAACCCCATGGTGTTGGTATCTTTTAATGTTTTAAC-T-TTTTTT
* * *
35165 TTTTTTTTGCATTAAAAATCTTGTTTAGCAATGATCATTTGATATATGTGG
128 TTTTTTGTGCATTAAAAATATTGTTTAGCAATGATCATTTGATATATATGG
* *
35216 TTATGTATGATGTTACTTATATATATGGCTTTGAAATCAAGCAATTTTATCTTATAATTGTTCTT
1 TTATGTATGATGTTACTTGTATATATGGCTTTGAAATCAAGCAATTTTATCTTATAATTCTTCTT
* * * *
35281 GGATGAATGAACTGCTTGCTAACCCCATGTTGTT
66 GTATGAATGAACTACTTGCCAACCCCATGGTGTT
35315 ATAATATAAT
Statistics
Matches: 257, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
176 54 0.21
177 1 0.00
178 106 0.41
179 67 0.26
180 29 0.11
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (178 bp):
TTATGTATGATGTTACTTGTATATATGGCTTTGAAATCAAGCAATTTTATCTTATAATTCTTCTT
GTATGAATGAACTACTTGCCAACCCCATGGTGTTGGTATCTTTTAATGTTTTAACTTTTTTTTTT
TTTGTGCATTAAAAATATTGTTTAGCAATGATCATTTGATATATATGG
Found at i:47704 original size:20 final size:21
Alignment explanation
Indices: 47681--47719 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
47671 TAAAAAATTT
*
47681 ATAAAATTAT-TAAATATTAA
1 ATAAAATAATATAAATATTAA
47701 ATAAAATAATATAAATATT
1 ATAAAATAATATAAATATT
47720 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAAAATAATATAAATATTAA
Found at i:47725 original size:31 final size:31
Alignment explanation
Indices: 47665--47742 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 31
47655 TGTTAATATG
*
47665 ATTAAATAAAA-AATTTATAAAATTATT-AAAT
1 ATTAAATAAAATAA--TATAAAATTATTAAAAA
*
47696 ATTAAATAAAATAATATAAATATTTTTAAAAA
1 ATTAAATAAAATAATATAAA-ATTATTAAAAA
47728 ATT-AA-AAAATAATAT
1 ATTAAATAAAATAATAT
47743 GGACAATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 16 0.38
31 18 0.43
32 8 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (31 bp):
ATTAAATAAAATAATATAAAATTATTAAAAA
Found at i:53692 original size:30 final size:30
Alignment explanation
Indices: 53657--53718 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
53647 AAAGAGTACC
* *
53657 AAGTTTCA-AGACT-AATATGAACAAAAACAA
1 AAGTTT-AGAGACTAAAT-TGAAAAAAAAAAA
53687 AAGTTTAGAGACTAAATTGAAAAAAAAAAA
1 AAGTTTAGAGACTAAATTGAAAAAAAAAAA
53717 AA
1 AA
53719 TCAAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 1 0.04
30 24 0.86
31 3 0.11
ACGTcount: A:0.61, C:0.08, G:0.11, T:0.19
Consensus pattern (30 bp):
AAGTTTAGAGACTAAATTGAAAAAAAAAAA
Found at i:58077 original size:14 final size:13
Alignment explanation
Indices: 58031--58076 Score: 69
Period size: 14 Copynumber: 3.6 Consensus size: 13
58021 GATTATTTTA
58031 TTATTTTT-T-GT
1 TTATTTTTCTGGT
58042 TTATTTTTCTGGGT
1 TTATTTTTCT-GGT
58056 TTATTTTTCTGGT
1 TTATTTTTCTGGT
58069 TTATTTTT
1 TTATTTTT
58077 TTATTTTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 8 0.25
12 1 0.03
13 11 0.34
14 12 0.38
ACGTcount: A:0.09, C:0.04, G:0.13, T:0.74
Consensus pattern (13 bp):
TTATTTTTCTGGT
Found at i:61263 original size:6 final size:6
Alignment explanation
Indices: 61246--61301 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
61236 TCGTCATCAC
* * * * * *
61246 CATCTT CTTTTT CATTTT CGTCTT CTTCTT CATCTT CATTTT CATCTT
1 CATCTT CATCTT CATCTT CATCTT CATCTT CATCTT CATCTT CATCTT
61294 CATCTT CA
1 CATCTT CA
61302 ACATCATCCT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.12, C:0.29, G:0.02, T:0.57
Consensus pattern (6 bp):
CATCTT
Found at i:62521 original size:133 final size:133
Alignment explanation
Indices: 62384--62635 Score: 337
Period size: 133 Copynumber: 1.9 Consensus size: 133
62374 GCTTCACATC
* * * *
62384 TTTTTCCTTCAATTTCGGGTCGCGGCTTCTCACCTACACGAAAACATTGATATTTC-ATGACAAG
1 TTTTTCCTTCAATTTCGGGTCACGGCTTCTCACCTACACGAAAACATTGAAATCTCAAAGACAA-
* ** *
62448 AAA-ATCACTAATAAATTGACAAATTTTTCAGTTTTCACACCAATTAGCAAAAAAAAAAAAACAC
65 AAAGATCACTAATAAATTAACAAAAATTTCAATTTTCACA-CAATTAGCAAAAAAAAAAAAACAC
62512 ATTTT
129 ATTTT
* * * * * *
62517 TTTTTCCTTCTATTTCGGTTCACTGCTTCTCGCCTACATGAAAACATTGAAATCTCAAAGATAAA
1 TTTTTCCTTCAATTTCGGGTCACGGCTTCTCACCTACACGAAAACATTGAAATCTCAAAGACAAA
*
62582 AAGATCACTAATAAATTAACAAAAATTTCAATTTTCACACAATTAGCAGAAAAA
66 AAGATCACTAATAAATTAACAAAAATTTCAATTTTCACACAATTAGCAAAAAAA
62636 CAACAACAAT
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
133 65 0.64
134 37 0.36
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (133 bp):
TTTTTCCTTCAATTTCGGGTCACGGCTTCTCACCTACACGAAAACATTGAAATCTCAAAGACAAA
AAGATCACTAATAAATTAACAAAAATTTCAATTTTCACACAATTAGCAAAAAAAAAAAAACACAT
TTT
Found at i:69713 original size:2 final size:2
Alignment explanation
Indices: 69706--69736 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
69696 AGTGCTTGTA
69706 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 A
69737 CTTACAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:74597 original size:14 final size:15
Alignment explanation
Indices: 74572--74600 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
74562 ATTATTCCAT
74572 TTTAATAATTATTTA
1 TTTAATAATTATTTA
74587 TTTAA-AATTATTTA
1 TTTAATAATTATTTA
74601 ACATATTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAATAATTATTTA
Found at i:76354 original size:19 final size:20
Alignment explanation
Indices: 76309--76355 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
76299 TTTTATTGAT
*
76309 TTTTTTTCATTATAAATATC
1 TTTTTTTCATTATAAATATA
*
76329 TTATTTT-ATT-TCAAATATA
1 TTTTTTTCATTAT-AAATATA
76348 TTTTTTTC
1 TTTTTTTC
76356 CTTCTAGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.05
19 15 0.68
20 6 0.27
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTTTCATTATAAATATA
Found at i:87557 original size:7 final size:7
Alignment explanation
Indices: 87545--87573 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
87535 AGAGAGGGTC
87545 TCAGCAG
1 TCAGCAG
87552 TCAGCAG
1 TCAGCAG
87559 TCAGCAG
1 TCAGCAG
87566 TCAGCAG
1 TCAGCAG
87573 T
1 T
87574 GAGAAGACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (7 bp):
TCAGCAG
Found at i:91780 original size:8 final size:8
Alignment explanation
Indices: 91763--91796 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
91753 TTTATAATAG
*
91763 TAATAATA
1 TAATATTA
91771 TAATATTA
1 TAATATTA
91779 TAATATTA
1 TAATATTA
91787 TAATATTA
1 TAATATTA
91795 TA
1 TA
91797 CTACTAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TAATATTA
Found at i:94169 original size:10 final size:10
Alignment explanation
Indices: 94146--94204 Score: 56
Period size: 10 Copynumber: 6.3 Consensus size: 10
94136 TTTTTTTTAT
94146 ATTTTT-ATA
1 ATTTTTAATA
*
94155 CTTTTTAATA
1 ATTTTTAATA
*
94165 ATTTTAAATA
1 ATTTTTAATA
94175 ATTTTTAAT-
1 ATTTTTAATA
94184 -TTTTT--TA
1 ATTTTTAATA
94191 ATTTTTAAATA
1 ATTTTT-AATA
94202 ATT
1 ATT
94205 AATCCACGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
6 1 0.03
8 10 0.25
9 5 0.12
10 19 0.47
11 5 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:95155 original size:8 final size:8
Alignment explanation
Indices: 95142--95166 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
95132 AATTGAACTT
95142 AAATTTTA
1 AAATTTTA
95150 AAATTTTA
1 AAATTTTA
95158 AAATTTTA
1 AAATTTTA
95166 A
1 A
95167 GGATTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AAATTTTA
Found at i:96159 original size:27 final size:26
Alignment explanation
Indices: 96104--96165 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
96094 CAATTTAAAT
* *
96104 TTAATTTTAAACCAAATATTTGAGTA
1 TTAATTTTAAACCAAATAATTGAGCA
*
96130 TTAATTCTTAAATCAAATAAATTGA-CA
1 TTAATT-TTAAACCAAAT-AATTGAGCA
*
96157 TTAAATTTA
1 TTAATTTTA
96166 TGAAACTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 9 0.30
27 16 0.53
28 5 0.17
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (26 bp):
TTAATTTTAAACCAAATAATTGAGCA
Found at i:99926 original size:10 final size:10
Alignment explanation
Indices: 99913--100001 Score: 51
Period size: 10 Copynumber: 9.1 Consensus size: 10
99903 GCATTTAATT
99913 AAATTTTTAA
1 AAATTTTTAA
*
99923 AAATTTTAAA
1 AAATTTTTAA
99933 AAATATTTT-A
1 AAAT-TTTTAA
* *
99943 TAATTTTTAT
1 AAATTTTTAA
**
99953 ACCTTTTTAA
1 AAATTTTTAA
*
99963 TAATTTTT--
1 AAATTTTTAA
*
99971 -AATTTCTAA
1 AAATTTTTAA
*
99980 AATATTTATAA
1 AA-ATTTTTAA
*
99991 AATTTTTTAA
1 AAATTTTTAA
100001 A
1 A
100002 CCACGTGTAT
Statistics
Matches: 58, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
7 6 0.10
9 4 0.07
10 36 0.62
11 12 0.21
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (10 bp):
AAATTTTTAA
Found at i:103699 original size:20 final size:21
Alignment explanation
Indices: 103655--103699 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 21
103645 ATCGAAATTT
*
103655 TTAATTTTAATATATATTTAA
1 TTAATTTTAATATATATTAAA
*
103676 --AATTTTTATAT-TATTAAA
1 TTAATTTTAATATATATTAAA
103694 TTAATT
1 TTAATT
103700 ATTGTCCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 5
0.74 0.07 0.19
Matches are distributed among these distances:
18 6 0.30
19 10 0.50
20 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAATTTTAATATATATTAAA
Found at i:106164 original size:164 final size:164
Alignment explanation
Indices: 105887--106208 Score: 511
Period size: 164 Copynumber: 2.0 Consensus size: 164
105877 TTTAGGACTA
* ** * * * *
105887 AAATCTTGTGGTTTTTGATGTAGTATGATGCAGAGGAAGTAAAACTTGATTGCTTGTTGTCTTCC
1 AAATCATGTGGTTTTAAATGTACTATGATGCAGAGGAAGTAAAAATTGATTGCTTATTGTCTGCC
*
105952 AATAAATAACATTTAAATTTGCTATGTTCTTGTTGGTTGAGAATCTTCTGTTTTGATTCTGATCG
66 AATAAATAACATTTAAATTTGCTATGATCTTGTTGGTTGAGAATCTTCTGTTTTGATTCTGATCG
106017 AGGTCATGGTCATTTTTATCAAGATAGTAACACT
131 AGGTCATGGTCATTTTTATCAAGATAGTAACACT
* *
106051 AAATCATGTGGTTTTAAATGTACTAT-AGTGCTGAGGAAGTAAAAATTGGTTGCTTATTGTCTGC
1 AAATCATGTGGTTTTAAATGTACTATGA-TGCAGAGGAAGTAAAAATTGATTGCTTATTGTCTGC
* *
106115 CAATAGATAACATTTAAATTTGCTATGATCTTGTTGGTTGAGAATCTTCTGTTTTGATTCTGGTC
65 CAATAAATAACATTTAAATTTGCTATGATCTTGTTGGTTGAGAATCTTCTGTTTTGATTCTGATC
*
106180 GAGGTCATGGTCATTTTTATCAATATAGT
130 GAGGTCATGGTCATTTTTATCAAGATAGT
106209 TAAATTCTTT
Statistics
Matches: 144, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
163 1 0.01
164 143 0.99
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.41
Consensus pattern (164 bp):
AAATCATGTGGTTTTAAATGTACTATGATGCAGAGGAAGTAAAAATTGATTGCTTATTGTCTGCC
AATAAATAACATTTAAATTTGCTATGATCTTGTTGGTTGAGAATCTTCTGTTTTGATTCTGATCG
AGGTCATGGTCATTTTTATCAAGATAGTAACACT
Found at i:121392 original size:30 final size:30
Alignment explanation
Indices: 121334--121445 Score: 121
Period size: 30 Copynumber: 4.0 Consensus size: 30
121324 GAGCTGGATT
* *
121334 TGGAATTGGAACT-GGACTCAAATTGGAAC
1 TGGAACTGGAACTGGGATTCAAATTGGAAC
*
121363 TGGAACTGGAATTGGGATTCAAA-T----C
1 TGGAACTGGAACTGGGATTCAAATTGGAAC
* *
121388 -GGAACTGGAAATGGGATTCATATTGGAAC
1 TGGAACTGGAACTGGGATTCAAATTGGAAC
*
121417 TGGAACTGGGACTGGGATTCAAATTGGAA
1 TGGAACTGGAACTGGGATTCAAATTGGAA
121446 TGTGCATCCC
Statistics
Matches: 68, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
24 20 0.29
25 2 0.03
29 13 0.19
30 33 0.49
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.25
Consensus pattern (30 bp):
TGGAACTGGAACTGGGATTCAAATTGGAAC
Found at i:121445 original size:24 final size:24
Alignment explanation
Indices: 121363--121427 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
121353 AAATTGGAAC
*
121363 TGGAACTGGAATTGGGATTCAAAT
1 TGGAACTGGAAATGGGATTCAAAT
* *
121387 CGGAACTGGAAATGGGATTCATAT
1 TGGAACTGGAAATGGGATTCAAAT
*
121411 TGGAACTGGAACTGGGA
1 TGGAACTGGAAATGGGA
121428 CTGGGATTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.25
Consensus pattern (24 bp):
TGGAACTGGAAATGGGATTCAAAT
Found at i:127014 original size:2 final size:2
Alignment explanation
Indices: 127002--127035 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
126992 GATCCGGAGC
127002 AT AT A- 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
127036 ATGACAGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:127054 original size:6 final size:6
Alignment explanation
Indices: 127045--127080 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
127035 AATGACAGTT
127045 GGAAAA GGAAAA GGAAAA GGAAAA GGAAAA GGAAAA
1 GGAAAA GGAAAA GGAAAA GGAAAA GGAAAA GGAAAA
127081 CCTGGGCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (6 bp):
GGAAAA
Found at i:131876 original size:21 final size:21
Alignment explanation
Indices: 131852--131894 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
131842 ATGATCTCTC
131852 TTTCTTTGTTTCTTTATTTTT
1 TTTCTTTGTTTCTTTATTTTT
131873 TTTCTTTGTTTCTTTATTTTT
1 TTTCTTTGTTTCTTTATTTTT
131894 T
1 T
131895 AGCCATTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.05, C:0.09, G:0.05, T:0.81
Consensus pattern (21 bp):
TTTCTTTGTTTCTTTATTTTT
Found at i:132018 original size:39 final size:39
Alignment explanation
Indices: 131964--132039 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
131954 ATATGGCCAG
* * *
131964 ACTATGACCTTGAATCTCTACCTTCCTCCAAGAAATCAT
1 ACTATGACCTTGAATCTCTAACATCCCCCAAGAAATCAT
132003 ACTATGACCTTGAATCTCTAACATCCCCCAAGAAATC
1 ACTATGACCTTGAATCTCTAACATCCCCCAAGAAATC
132040 TTTATTTGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.33, C:0.32, G:0.08, T:0.28
Consensus pattern (39 bp):
ACTATGACCTTGAATCTCTAACATCCCCCAAGAAATCAT
Found at i:133372 original size:26 final size:26
Alignment explanation
Indices: 133336--133396 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
133326 TCACTAGGTT
133336 TTTTTAGCATGCTCCAGAAACCCTAA
1 TTTTTAGCATGCTCCAGAAACCCTAA
133362 TTTTTAGCATGCTCCAGAAACCCTAA
1 TTTTTAGCATGCTCCAGAAACCCTAA
133388 TTTTTAGCA
1 TTTTTAGCA
133397 GTTCATAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (26 bp):
TTTTTAGCATGCTCCAGAAACCCTAA
Found at i:136817 original size:31 final size:31
Alignment explanation
Indices: 136782--136852 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
136772 AAATTTGAAT
136782 CAAGCTTCTAGCCTCAAATTCAAGTCAAACA
1 CAAGCTTCTAGCCTCAAATTCAAGTCAAACA
*
136813 CAAGCTTCTAGCCTCGAATTCAAGTCAAACA
1 CAAGCTTCTAGCCTCAAATTCAAGTCAAACA
136844 CAAGCTTCT
1 CAAGCTTCT
136853 TACAGCTTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.35, C:0.30, G:0.11, T:0.24
Consensus pattern (31 bp):
CAAGCTTCTAGCCTCAAATTCAAGTCAAACA
Found at i:141200 original size:19 final size:18
Alignment explanation
Indices: 141161--141201 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
141151 TAACAGTATA
*
141161 AAATAATATCTTTTAGGT
1 AAATAATATCTTTTAGCT
*
141179 AAATAATATTTTTTAAGCT
1 AAATAATATCTTTT-AGCT
141198 AAAT
1 AAAT
141202 TATGTCACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (18 bp):
AAATAATATCTTTTAGCT
Found at i:147400 original size:122 final size:122
Alignment explanation
Indices: 147222--147466 Score: 481
Period size: 122 Copynumber: 2.0 Consensus size: 122
147212 ACGTCAATTT
147222 ATCGTTGCATCGTTAAAGACAATTAACGGCTCAATGGCTAAAATGTTACAACACGATGACGTAAG
1 ATCGTTGCATCGTTAAAGACAATTAACGGCTCAATGGCTAAAATGTTACAACACGATGACGTAAG
147287 TGATTGAAACGTAATATTTTAAACATAATTAACTAAAATGTAACACGAAATAAACAA
66 TGATTGAAACGTAATATTTTAAACATAATTAACTAAAATGTAACACGAAATAAACAA
*
147344 ATCGTTGCATCGTTAAAGACAATTAACGGCTCAATGGCTAAAATGTTACAACACGATGATGTAAG
1 ATCGTTGCATCGTTAAAGACAATTAACGGCTCAATGGCTAAAATGTTACAACACGATGACGTAAG
147409 TGATTGAAACGTAATATTTTAAACATAATTAACTAAAATGTAACACGAAATAAACAA
66 TGATTGAAACGTAATATTTTAAACATAATTAACTAAAATGTAACACGAAATAAACAA
147466 A
1 A
147467 ATTAACCATG
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
122 122 1.00
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (122 bp):
ATCGTTGCATCGTTAAAGACAATTAACGGCTCAATGGCTAAAATGTTACAACACGATGACGTAAG
TGATTGAAACGTAATATTTTAAACATAATTAACTAAAATGTAACACGAAATAAACAA
Found at i:155181 original size:88 final size:87
Alignment explanation
Indices: 155079--155238 Score: 214
Period size: 88 Copynumber: 1.8 Consensus size: 87
155069 GTTGTCTTTA
* * * * *
155079 AGAATGTATTTTATAACTACATTTAATA-TTCGATGGTATAATTTATTTACTTTTTGGATTAAAA
1 AGAATGTATCTTATAACTACACTCAATACTTAG-TGGTACAATTTATTTACTTTTTGGA-TAAAA
*
155143 TTTGACTACTTATACTAATATATC
64 ATTGACTACTTATACTAATATATC
* **
155167 AGAATGTATCTTATAATTGTACTCAATACTTAGTGGTACAATTTATTTACTTTTTGGATAAAAAT
1 AGAATGTATCTTATAACTACACTCAATACTTAGTGGTACAATTTATTTACTTTTTGGATAAAAAT
155232 TGACTAC
66 TGACTAC
155239 CGAAACCAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
87 13 0.21
88 46 0.74
89 3 0.05
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (87 bp):
AGAATGTATCTTATAACTACACTCAATACTTAGTGGTACAATTTATTTACTTTTTGGATAAAAAT
TGACTACTTATACTAATATATC
Found at i:157327 original size:29 final size:28
Alignment explanation
Indices: 157251--157598 Score: 239
Period size: 29 Copynumber: 11.8 Consensus size: 28
157241 CCCCTAATTT
* *
157251 TTTCAAAAATTTACATTTTAACCCTAAAAC
1 TTTCCAAAA-TTACATTTTAACCC-CAAAC
* *
157281 TTTTCAAAGATTATATTTTAAACCCCAAAC
1 TTTCCAAA-ATTACATTTT-AACCCCAAAC
**
157311 TTTCCAAAATTACATTTTAACAACAAAC
1 TTTCCAAAATTACATTTTAACCCCAAAC
* **
157339 TTTTCTAAAATTACATTTTAACAACAAAC
1 -TTTCCAAAATTACATTTTAACCCCAAAC
**
157368 TTTTCCAAAATTACATTTTAACAACAAAC
1 -TTTCCAAAATTACATTTTAACCCCAAAC
* ** * *
157397 TTTTCTAAAATTATGTTTTGACCTCTAAACC
1 -TTTCCAAAATTACATTTTAACC-CCAAA-C
* *
157428 TTTCCAAAATTACATTTTGAGCCCTAAAC
1 TTTCCAAAATTACATTTT-AACCCCAAAC
*
157457 TTCTACAAAATTACATTTTAACCCCTAAAC
1 TT-TCCAAAATTACATTTTAACCCC-AAAC
* * * * * *
157487 CTTCTCGAAATCACA-TTTGACCCAAAAA
1 TTTC-CAAAATTACATTTTAACCCCAAAC
* * * *
157515 TTCTCCAAAATCACATTTTGACCCTAAGC
1 TT-TCCAAAATTACATTTTAACCCCAAAC
* *
157544 TTTCCTAAGATTACATTTTTACCCTCCAAAC
1 TTTCC-AAAATTACA-TTTTAACC-CCAAAC
*
157575 TTTTCCAAAATTACATTTTGACCC
1 -TTTCCAAAATTACATTTTAACCC
157599 GTATTCTCCA
Statistics
Matches: 257, Mismatches: 46, Indels: 31
0.77 0.14 0.09
Matches are distributed among these distances:
28 24 0.09
29 119 0.46
30 88 0.34
31 21 0.08
32 5 0.02
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.36
Consensus pattern (28 bp):
TTTCCAAAATTACATTTTAACCCCAAAC
Found at i:157618 original size:27 final size:27
Alignment explanation
Indices: 157578--157630 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
157568 TCCAAACTTT
157578 TCCAAAATTACA-TTTTGACCCGTATTC
1 TCCAAAATTACATTTTTGACCC-TATTC
157605 TCCAAAACTT-CATTTTTGACCCTATT
1 TCCAAAA-TTACATTTTTGACCCTATT
157631 TTTTTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (27 bp):
TCCAAAATTACATTTTTGACCCTATTC
Found at i:160266 original size:22 final size:22
Alignment explanation
Indices: 160235--160289 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
160225 TACAAGGTCG
160235 ATGTCGCGACACCCTGGTGCCT
1 ATGTCGCGACACCCTGGTGCCT
* *
160257 ATGTCACGACACCTTGGTGCCT
1 ATGTCGCGACACCCTGGTGCCT
*
160279 GTGTCGCGACA
1 ATGTCGCGACA
160290 TCGAAGGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.16, C:0.33, G:0.27, T:0.24
Consensus pattern (22 bp):
ATGTCGCGACACCCTGGTGCCT
Found at i:161109 original size:30 final size:30
Alignment explanation
Indices: 161073--161137 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
161063 CAACTTAATA
* *
161073 AACAAATGTCTCTAAAATAGTAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
161103 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
161133 AACAA
1 AACAA
161138 TAAAATAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.57, C:0.15, G:0.05, T:0.23
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Done.