Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013278.1 Kokia drynarioides strain JFW-HI SEQ_128299, 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: 66197
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:868 original size:24 final size:26
Alignment explanation
Indices: 841--888 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
831 AGAGAAATGT
841 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
865 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
889 CCCATACCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:969 original size:23 final size:22
Alignment explanation
Indices: 937--992 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
927 ACGCTAGCGC
*
937 GCTTAATGTTCAGCACTGCGTGT
1 GCTTACTGTTC-GCACTGCGTGT
*
960 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTG-TTCGCACTGCGTGT
983 GCTTACTGTT
1 GCTTACTGTT
993 TCCCACCTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 2 0.07
23 25 0.83
24 3 0.10
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.41
Consensus pattern (22 bp):
GCTTACTGTTCGCACTGCGTGT
Found at i:993 original size:23 final size:23
Alignment explanation
Indices: 949--1022 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
939 TTAATGTTCA
*
949 GCACTGCGTGTGCTTACTGTTTC
1 GCACTTCGTGTGCTTACTGTTTC
972 GCACTTCGTGTGCTTACTGTTTC
1 GCACTTCGTGTGCTTACTGTTTC
* * *
995 CCACCTCGTGTGCCTACTGATTT-
1 GCACTTCGTGTGCTTACTG-TTTC
1018 GCACT
1 GCACT
1023 ATGTGCGCCT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.11, C:0.30, G:0.22, T:0.38
Consensus pattern (23 bp):
GCACTTCGTGTGCTTACTGTTTC
Found at i:1044 original size:22 final size:22
Alignment explanation
Indices: 1006--1067 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 22
996 CACCTCGTGT
1006 GCCTACTGATTTGCACTATGTGC
1 GCCTACTGA-TTGCACTATGTGC
*
1029 GCCTACTGATTGCACTATGTGT
1 GCCTACTGATTGCACTATGTGC
*
1051 GCCTACTGGATTACACT
1 GCCTACT-GATTGCACT
1068 GTGTTTGCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 19 0.53
23 17 0.47
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (22 bp):
GCCTACTGATTGCACTATGTGC
Found at i:1080 original size:23 final size:23
Alignment explanation
Indices: 1002--1081 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
992 TTCCCACCTC
*
1002 GTGTGCCTACT-GATTTGCACTAT
1 GTGTGCCTACTGGA-TTACACTAT
* *
1025 GTGCGCCTACT-GATTGCACTAT
1 GTGTGCCTACTGGATTACACTAT
*
1047 GTGTGCCTACTGGATTACACTGT
1 GTGTGCCTACTGGATTACACTAT
* *
1070 GTTTGCTTACTG
1 GTGTGCCTACTG
1082 TTTGCCCAGC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
22 19 0.38
23 31 0.62
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.38
Consensus pattern (23 bp):
GTGTGCCTACTGGATTACACTAT
Found at i:4325 original size:20 final size:20
Alignment explanation
Indices: 4295--4340 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
4285 CAAGTGGGCG
*
4295 GGACA-TCCGGGGATGAACT
1 GGACATTCCGGGGATGAACC
4314 GGACATTCCGGGGATGAACC
1 GGACATTCCGGGGATGAACC
4334 GGACATT
1 GGACATT
4341 GGCACTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.26, C:0.22, G:0.35, T:0.17
Consensus pattern (20 bp):
GGACATTCCGGGGATGAACC
Found at i:6834 original size:22 final size:23
Alignment explanation
Indices: 6809--6857 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
6799 TTTTGAAAAG
* *
6809 TTAAAATATAATTTTAT-TATTA
1 TTAAAATAAAATTTTATAAATTA
**
6831 TTAATTTAAAATTTTATAAATTA
1 TTAAAATAAAATTTTATAAATTA
6854 TTAA
1 TTAA
6858 GGGTTGTAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAAAATAAAATTTTATAAATTA
Found at i:11442 original size:19 final size:19
Alignment explanation
Indices: 11420--11462 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
11410 TTTTAAAGGG
* *
11420 TAAATATACTTTTTATATT
1 TAAATATAATTTTAATATT
* *
11439 TAAATTTAATTTTAATGTT
1 TAAATATAATTTTAATATT
11458 TAAAT
1 TAAAT
11463 TGATTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TAAATATAATTTTAATATT
Found at i:15732 original size:197 final size:195
Alignment explanation
Indices: 15371--15949 Score: 691
Period size: 197 Copynumber: 2.9 Consensus size: 195
15361 AAAAATCTTG
*
15371 TGTGATGACCCCTTGCTGTCAATTTGTTAGTTGACATAGTGAATTTTGT-CCTATGTTACTCGGA
1 TGTG-TGATCCCTTGCTGTCAA-TTGTTAGTTGACATAGTGAATTTT-TCCCTATGTTACTCGGA
* * *
15435 CT-TGGGTGTGAA-TATCAAATATGGGTATGTATTTAACACGAGTATCATT-AGACTTTTCAAAG
63 CTCT-GGTGT-AAGTGTCAAATATGGGTATGTATTTAATA-GAGTATCGTTGA-ACTTTTCAAAG
* * *
15497 GTTTTCCATGTAATATACATATGTCAAACACGAGTGCTTCAAGAAAAATGAAGAACCTGAGTAAC
124 GTTTTCCATGTAATATCCATATGTCAAACACAAGTGCTTCAAGAAAAATGAAGAACCTGAGCAAC
15562 ATAGCAT
189 ATAGCAT
* * **
15569 TGTGTGATCGCTTGCTGTCAATTGTTAGTTGACATAGTTAATTTTTCCCTTACCTTACTCGGACT
1 TGTGTGATCCCTTGCTGTCAATTGTTAGTTGACATAGTGAATTTTTCCC-TATGTTACTCGGACT
15634 CTGGTGTAAGTGTCAAATATGGGTATGTATTTAATGAGAGTATCGTTGAACTTTTCAAAGGTTTT
65 CTGGTGTAAGTGTCAAATATGGGTATGTATTTAAT-AGAGTATCGTTGAACTTTTCAAAGGTTTT
* * ** ** *
15699 CCATTTAATATCCATGTGTCCGACACAAGTGCTTCAAGAAAAATGAAGAGTCTGAGCAACATATC
129 CCATGTAATATCCATATGTCAAACACAAGTGCTTCAAGAAAAATGAAGAACCTGAGCAACATAGC
15764 AT
194 AT
* * *
15766 TGTGTGATCCCTAGCTGTCAATTGTTAGTTGACATAGTGAATTGTGCCCTATGTTACTCGGACTC
1 TGTGTGATCCCTTGCTGTCAATTGTTAGTTGACATAGTGAATTTTTCCCTATGTTACTCGGACTC
* * * * * *
15831 GGGTGTGAGTGTTAAATACGGGTGTGCATTTGACAT-GAGTATCGTTAGAATTTTCATTTTTCAA
66 TGGTGTAAGTGTCAAATATGGGTATGTATTT-A-ATAGAGTATCGTT-GAA----C--TTTTCAA
* **
15895 AGGTTTTCCATGTAATATCCATCTGTCAAACACTGGTGCTTCAAGAAAAATGAAG
122 AGGTTTTCCATGTAATATCCATATGTCAAACACAAGTGCTTCAAGAAAAATGAAG
15950 TGTCCGAACA
Statistics
Matches: 329, Mismatches: 37, Indels: 25
0.84 0.09 0.06
Matches are distributed among these distances:
195 1 0.00
196 76 0.23
197 186 0.57
198 9 0.03
201 1 0.00
203 56 0.17
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (195 bp):
TGTGTGATCCCTTGCTGTCAATTGTTAGTTGACATAGTGAATTTTTCCCTATGTTACTCGGACTC
TGGTGTAAGTGTCAAATATGGGTATGTATTTAATAGAGTATCGTTGAACTTTTCAAAGGTTTTCC
ATGTAATATCCATATGTCAAACACAAGTGCTTCAAGAAAAATGAAGAACCTGAGCAACATAGCAT
Found at i:25736 original size:18 final size:20
Alignment explanation
Indices: 25694--25739 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
25684 TAAAAATCTC
25694 AATAA-ATAAAAAATGTATA
1 AATAATATAAAAAATGTATA
*
25713 AA-AATATAAAATAT-TA-A
1 AATAATATAAAAAATGTATA
25730 AATAATATAA
1 AATAATATAA
25740 TATAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 3 0.12
18 11 0.46
19 10 0.42
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (20 bp):
AATAATATAAAAAATGTATA
Found at i:34649 original size:31 final size:31
Alignment explanation
Indices: 34599--34659 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
34589 GTTATTTTTG
*
34599 GGTTAATTTCATAAAAAGTTCTCAACTTTTAT
1 GGTTAATTTCAAAAAAAGTTC-CAACTTTTAT
*
34631 GGTTAATTT-AAAAAAAGTTCCGACTTTTA
1 GGTTAATTTCAAAAAAAGTTCCAACTTTTA
34660 AATTGATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 8 0.30
31 10 0.37
32 9 0.33
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (31 bp):
GGTTAATTTCAAAAAAAGTTCCAACTTTTAT
Found at i:46269 original size:30 final size:29
Alignment explanation
Indices: 46226--46311 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
46216 ATTTGACTTT
46226 TTTTTTTCCAATTTGGTATTCAAACTTGACA
1 TTTTTTT--AATTTGGTATTCAAACTTGACA
* *
46257 CTTTTTTTAATTTAGTA-CCTAAACTTGACA
1 -TTTTTTTAATTTGGTATTC-AAACTTGACA
*
46287 TTTTTTTAAGTTGGTACTT-AAACTT
1 TTTTTTTAATTTGGTA-TTCAAACTT
46312 TTTGAGGTCC
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
29 21 0.46
30 18 0.39
32 7 0.15
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.50
Consensus pattern (29 bp):
TTTTTTTAATTTGGTATTCAAACTTGACA
Found at i:46303 original size:29 final size:30
Alignment explanation
Indices: 46247--46311 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
46237 TTTGGTATTC
*
46247 AAACTTGACACTTTTTTTAATTTAGTACCT
1 AAACTTGACACTTTTTTTAAGTTAGTACCT
* *
46277 AAACTTGACA-TTTTTTTAAGTTGGTACTT
1 AAACTTGACACTTTTTTTAAGTTAGTACCT
46306 AAACTT
1 AAACTT
46312 TTTGAGGTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (30 bp):
AAACTTGACACTTTTTTTAAGTTAGTACCT
Found at i:46597 original size:31 final size:32
Alignment explanation
Indices: 46542--46613 Score: 119
Period size: 31 Copynumber: 2.3 Consensus size: 32
46532 AAAAGCTTAG
46542 GTACCAAATTAGGAAAAAAATGTCAAATTCAA
1 GTACCAAATTAGGAAAAAAATGTCAAATTCAA
*
46574 GTACCAAATTAGG-AAAAAGTGTCAAATTCAA
1 GTACCAAATTAGGAAAAAAATGTCAAATTCAA
*
46605 GTATCAAAT
1 GTACCAAAT
46614 GTTATATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 25 0.66
32 13 0.34
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (32 bp):
GTACCAAATTAGGAAAAAAATGTCAAATTCAA
Found at i:47694 original size:3 final size:3
Alignment explanation
Indices: 47686--47714 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
47676 AGTTTATCCC
47686 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
47715 CTTTTCGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:51337 original size:13 final size:13
Alignment explanation
Indices: 51319--51343 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51309 AAAATTGATT
51319 TCTTTTTTTTTTC
1 TCTTTTTTTTTTC
51332 TCTTTTTTTTTT
1 TCTTTTTTTTTT
51344 TTTAATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TCTTTTTTTTTTC
Found at i:65510 original size:23 final size:23
Alignment explanation
Indices: 65433--65582 Score: 148
Period size: 23 Copynumber: 6.4 Consensus size: 23
65423 ACGGAACAAA
* *
65433 CAGAGAGTAC-CAAAGTACTAA-
1 CAGAGAGCACACAAAGTGCTAAT
*
65454 CAGAGAGCACA-TAAGTGCTGGGCAA-
1 CAGAGAGCACACAAAGTGCT----AAT
*
65479 CAGAGAGCACACACAGTGCTAAAT
1 CAGAGAGCACACAAAGTGCT-AAT
*
65503 -AGAGAGCACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT
65525 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
65548 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
65571 AACAGAGAGCAC
1 --CAGAGAGCAC
65583 GAGACGTGCT
Statistics
Matches: 109, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
21 15 0.14
22 3 0.03
23 62 0.57
25 23 0.21
26 6 0.06
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:65552 original size:69 final size:66
Alignment explanation
Indices: 65434--65569 Score: 184
Period size: 69 Copynumber: 2.0 Consensus size: 66
65424 CGGAACAAAC
* *
65434 AGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAGTGCT
1 AGAGAGCACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACACAGTGCT
65499 AAAT
63 AAAT
65503 AGAGAGCACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACACAGTGC
1 AGAGAGCAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACACAGTGC
65567 TAA
62 TAA
65570 TAACAGAGAG
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
68 2 0.03
69 30 0.49
70 11 0.18
71 11 0.18
72 7 0.11
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.12
Consensus pattern (66 bp):
AGAGAGCACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGCACACACAGTGCTAAA
T
Found at i:65596 original size:23 final size:23
Alignment explanation
Indices: 65451--65603 Score: 125
Period size: 23 Copynumber: 6.5 Consensus size: 23
65441 ACCAAAGTAC
*
65451 TAACAGAGAGCACATA-AGTGCT
1 TAACAGAGAGCACACACAGTGCT
*
65473 GGGCAACAGAGAGCACACACAGTGCT
1 ---TAACAGAGAGCACACACAGTGCT
* * * *
65499 AAATAGAGAGCACACAAAGTAC-
1 TAACAGAGAGCACACACAGTGCT
*
65521 TAATCAGAGAGCACACAAAGTGC-
1 TAA-CAGAGAGCACACACAGTGCT
65544 TAATCAGAGAGCACACACAGTGCT
1 TAA-CAGAGAGCACACACAGTGCT
*
65568 AATAACAGAGAGCACGAGAC-GTGCT
1 --TAACAGAGAGCAC-ACACAGTGCT
*
65593 TAACAAAGAGC
1 TAACAGAGAGC
65604 GCGCTAGTGT
Statistics
Matches: 110, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
22 2 0.02
23 67 0.61
25 29 0.26
26 12 0.11
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
TAACAGAGAGCACACACAGTGCT
Done.