Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012511.1 Kokia drynarioides strain JFW-HI SEQ_127516, 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: 50105
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3073 original size:18 final size:17
Alignment explanation
Indices: 2999--3073 Score: 89
Period size: 17 Copynumber: 4.3 Consensus size: 17
2989 CAAACTCATC
2999 TTAAATTTATTTTAAGA-
1 TTAAATTTATTTTAA-AT
* *
3016 TTAAATTTGTTTAAAATT
1 TTAAATTTATTTTAAA-T
*
3034 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAT
3051 TTAAATTTATTTTCAAAT
1 TTAAATTTATTTT-AAAT
3069 TTAAA
1 TTAAA
3074 ATAATTAAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
16 1 0.02
17 27 0.55
18 21 0.43
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:4869 original size:30 final size:30
Alignment explanation
Indices: 4809--5056 Score: 271
Period size: 29 Copynumber: 8.4 Consensus size: 30
4799 GTCCTTAAAC
*
4809 CTTCCAAAAATTCCATTTTT-ACCCCCAAA
1 CTTCCAAAAATTCCATTTTTGACCCCAAAA
*
4838 CTTCCAAAAATTCCATTTTTGACCCCGAAA
1 CTTCCAAAAATTCCATTTTTGACCCCAAAA
*
4868 CTTCCAAAAA-TCTCATTTTTGACCTCAAAA
1 CTTCCAAAAATTC-CATTTTTGACCCCAAAA
* * *
4898 CTTCCAACAAGTCCATTTTT-ACCCCTAAA
1 CTTCCAAAAATTCCATTTTTGACCCCAAAA
*
4927 CTTCCAAAAA-TCATATTTTTGACCCCAAAA
1 CTTCCAAAAATTC-CATTTTTGACCCCAAAA
* *
4957 CTTCCAAAAATCCCATTTTT-ACCCCCAAA
1 CTTCCAAAAATTCCATTTTTGACCCCAAAA
* *
4986 CTTCCAAAAATCCCATTTTTG-CCCTC-GAA
1 CTTCCAAAAATTCCATTTTTGACCC-CAAAA
**
5015 CTTCC-AAAATCTCCATTTTTGACTTCAAAA
1 CTTCCAAAAAT-TCCATTTTTGACCCCAAAA
5045 C-TCTCAAAAATT
1 CTTC-CAAAAATT
5057 ACCCTCTTAC
Statistics
Matches: 189, Mismatches: 17, Indels: 25
0.82 0.07 0.11
Matches are distributed among these distances:
28 7 0.04
29 94 0.50
30 80 0.42
31 8 0.04
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.31
Consensus pattern (30 bp):
CTTCCAAAAATTCCATTTTTGACCCCAAAA
Found at i:4922 original size:59 final size:58
Alignment explanation
Indices: 4809--5034 Score: 273
Period size: 59 Copynumber: 3.8 Consensus size: 58
4799 GTCCTTAAAC
* *
4809 CTTCCAAAAAT-TCCATTTTT-ACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCGAAA
1 CTTCCAAAAATCT-CATTTTTGACCCCAAAACTTCCAAAAA-TCCATTTTT-ACCCCCAAA
* * *
4868 CTTCCAAAAATCTCATTTTTGACCTCAAAACTTCCAACAAGTCCATTTTTACCCCTAAA
1 CTTCCAAAAATCTCATTTTTGACCCCAAAACTTCCAA-AAATCCATTTTTACCCCCAAA
4927 CTTCCAAAAATCAT-ATTTTTGACCCCAAAACTTCCAAAAATCCCATTTTTACCCCCAAA
1 CTTCCAAAAATC-TCATTTTTGACCCCAAAACTTCCAAAAAT-CCATTTTTACCCCCAAA
* * *
4986 CTTCCAAAAATCCCATTTTTG-CCCTC-GAACTTCCAAAATCTCCATTTTT
1 CTTCCAAAAATCTCATTTTTGACCC-CAAAACTTCCAAAA-ATCCATTTTT
5035 GACTTCAAAA
Statistics
Matches: 149, Mismatches: 10, Indels: 17
0.85 0.06 0.10
Matches are distributed among these distances:
58 25 0.17
59 97 0.65
60 25 0.17
61 2 0.01
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (58 bp):
CTTCCAAAAATCTCATTTTTGACCCCAAAACTTCCAAAAATCCATTTTTACCCCCAAA
Found at i:5503 original size:96 final size:96
Alignment explanation
Indices: 5360--5544 Score: 237
Period size: 96 Copynumber: 1.9 Consensus size: 96
5350 AAAACTATAA
** * * * * **
5360 AATCGAGGCAATATTTTTTTATTTCGAGTTTTGAAAAATTGCGCCTTAACTTACTGGGTGCAATT
1 AATCGAGGCAATATTTCCTTATTCCGAGTTCTGAAAAATTGCACCTTAACTTACTAGGTGCAACC
*
5425 TTTCTTCAAATCGAAATAATCGAATACCCTT
66 TTTCGTCAAATCGAAATAATCGAATACCCTT
* *
5456 AATCGAGGCAATGTTTCCTTATCTCCGA-TTCTGAAAATTTGCACCTTAACTTACTAGGTGCAAC
1 AATCGAGGCAATATTTCCTTAT-TCCGAGTTCTGAAAAATTGCACCTTAACTTACTAGGTGCAAC
**
5520 CTTTCGTCAAATCGGGATAATCGAA
65 CTTTCGTCAAATCGAAATAATCGAA
5545 CATCCTTTTC
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
96 71 0.95
97 4 0.05
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (96 bp):
AATCGAGGCAATATTTCCTTATTCCGAGTTCTGAAAAATTGCACCTTAACTTACTAGGTGCAACC
TTTCGTCAAATCGAAATAATCGAATACCCTT
Found at i:7266 original size:97 final size:98
Alignment explanation
Indices: 7089--7277 Score: 231
Period size: 97 Copynumber: 1.9 Consensus size: 98
7079 GATACATTTC
*** * * **
7089 AGTATCGATATCAAAATGACATTCTGTTTTCCAAAGTATTTATCAAGTATCGATACAGTGTTGAT
1 AGTATCGATATCAAAATGACATTCTAACTTCCAAAGTATTTATCAAGTATCGATACAATATCAAT
* * *
7154 ACTTTTTGTTGGGTATCAATA-AATTTTTTTTA
66 ACCTTATATTGGGTATCAATAGAATTTTTTTTA
7186 AGTATCGATA-CAAAATTGACATTCTAACTTCCAAA-TGATTTATCAAGTATCGATACAATATCA
1 AGTATCGATATCAAAA-TGACATTCTAACTTCCAAAGT-ATTTATCAAGTATCGATACAATATCA
* *
7249 ATACCTTATATTTGGTATCGATAGAATTT
64 ATACCTTATATTGGGTATCAATAGAATTT
7278 CTTTGGTATC
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
96 6 0.08
97 66 0.86
98 5 0.06
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (98 bp):
AGTATCGATATCAAAATGACATTCTAACTTCCAAAGTATTTATCAAGTATCGATACAATATCAAT
ACCTTATATTGGGTATCAATAGAATTTTTTTTA
Found at i:9049 original size:29 final size:29
Alignment explanation
Indices: 9016--9073 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
9006 ATATAAATCG
9016 ATAAAACTCGTAATTTCCATAAAATACAA
1 ATAAAACTCGTAATTTCCATAAAATACAA
9045 ATAAAACTCGTAATTTCCATAAAATACAA
1 ATAAAACTCGTAATTTCCATAAAATACAA
9074 TTTATTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (29 bp):
ATAAAACTCGTAATTTCCATAAAATACAA
Found at i:16668 original size:30 final size:30
Alignment explanation
Indices: 16606--16665 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
16596 CTAAACATTT
16606 TCACTTTTCCCCAAAAACTTTTACTTCTTC
1 TCACTTTTCCCCAAAAACTTTTACTTCTTC
* *
16636 TCAC-TTTCCCCCAAAACTTTTTC-TCTTC
1 TCACTTTTCCCCAAAAACTTTTACTTCTTC
16664 TC
1 TC
16666 TCATCCCTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 7 0.25
29 17 0.61
30 4 0.14
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (30 bp):
TCACTTTTCCCCAAAAACTTTTACTTCTTC
Found at i:19329 original size:31 final size:31
Alignment explanation
Indices: 19294--19371 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
19284 CCAAAAGGAC
*
19294 TGTTTTGTCATGTTTTGATAACTTTAGTGAT
1 TGTTTTGTCACGTTTTGATAACTTTAGTGAT
19325 TGTTTTGTCACGTTTTGATAACTTTAGTGAT
1 TGTTTTGTCACGTTTTGATAACTTTAGTGAT
*
19356 TGTTTTGTCACATTTT
1 TGTTTTGTCACGTTTT
19372 CAAAGTTGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (31 bp):
TGTTTTGTCACGTTTTGATAACTTTAGTGAT
Found at i:19390 original size:30 final size:31
Alignment explanation
Indices: 19291--19391 Score: 132
Period size: 31 Copynumber: 3.3 Consensus size: 31
19281 AAGCCAAAAG
*
19291 GACTGTTTTGTCATGTTTTGATAACTTTAGT
1 GACTGTTTTGTCACGTTTTGATAACTTTAGT
*
19322 GATTGTTTTGTCACGTTTTGATAACTTTAGT
1 GACTGTTTTGTCACGTTTTGATAACTTTAGT
* * * * *
19353 GATTGTTTTGTCACATTTTCA-AAGTTGAGT
1 GACTGTTTTGTCACGTTTTGATAACTTTAGT
19383 GACTGTTTT
1 GACTGTTTT
19392 ATTAAATGTA
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 15 0.24
31 48 0.76
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.50
Consensus pattern (31 bp):
GACTGTTTTGTCACGTTTTGATAACTTTAGT
Found at i:21184 original size:14 final size:14
Alignment explanation
Indices: 21165--21191 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21155 CACAAAAACG
21165 GAAATGAAAATAAA
1 GAAATGAAAATAAA
21179 GAAATGAAAATAA
1 GAAATGAAAATAA
21192 CTAAAAGCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
GAAATGAAAATAAA
Found at i:22253 original size:10 final size:10
Alignment explanation
Indices: 22238--22268 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
22228 TGACACATTG
22238 TATTGTTCCC
1 TATTGTTCCC
22248 TATTGTTCCC
1 TATTGTTCCC
22258 TATTGTTCCC
1 TATTGTTCCC
22268 T
1 T
22269 TTTTAGTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.10, C:0.29, G:0.10, T:0.52
Consensus pattern (10 bp):
TATTGTTCCC
Found at i:28637 original size:14 final size:14
Alignment explanation
Indices: 28618--28644 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28608 CACAAAAACG
28618 GAAATGAAAATAAA
1 GAAATGAAAATAAA
28632 GAAATGAAAATAA
1 GAAATGAAAATAA
28645 CTAAGAGCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
GAAATGAAAATAAA
Found at i:33526 original size:18 final size:18
Alignment explanation
Indices: 33505--33549 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
33495 GGTTGATAAC
*
33505 GAAGAGGGAGTTGAAAAT
1 GAAGAGGGAGCTGAAAAT
33523 GAAGAGGGAGCTGAAAAT
1 GAAGAGGGAGCTGAAAAT
33541 GAAGAGGGA
1 GAAGAGGGA
33550 TCTAAAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.42, T:0.11
Consensus pattern (18 bp):
GAAGAGGGAGCTGAAAAT
Found at i:38089 original size:33 final size:28
Alignment explanation
Indices: 38023--38078 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
38013 GTTGAAACAC
* *
38023 CTTATTCTAATTAAAATAAAATAGATGA
1 CTTATTCTAATTAAAATAAAATAAAAGA
38051 CTTATTCTAATTAAAATAAAATAAAAGA
1 CTTATTCTAATTAAAATAAAATAAAAGA
38079 ATTCTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (28 bp):
CTTATTCTAATTAAAATAAAATAAAAGA
Found at i:42431 original size:175 final size:175
Alignment explanation
Indices: 42149--42471 Score: 540
Period size: 175 Copynumber: 1.8 Consensus size: 175
42139 GCCTACTCAT
* *
42149 GTATGACAAAAAGATGCATAGTGCTAATTCCAAGCTTTAGAAAATATCTATGAAAACAGAGATGG
1 GTATGAAAAAAAGATGCATAGTGCTAATTCCAAGCTTTAGAAAATAACTATGAAAACAGAGATGG
42214 ACTCTATGTATTCCAACTCAGTGTGAGAACTTCTAAACTTACCGAAAGGGATAAAACCCATAGAG
66 ACTCTATGTATTCCAACTCAGTGTGAGAACTTCTAAACTTACCGAAAGGGATAAAACCCATAGAG
42279 TGTAACTGGATATACAAATGCCTAGCAGGAAGAAGTCCCATTCAC
131 TGTAACTGGATATACAAATGCCTAGCAGGAAGAAGTCCCATTCAC
* * *
42324 GTATGAAAAAAAGATGCATAGTTCTAATTCCAAGCTTTGGGAAATAACTATGAAAACTA-AGATG
1 GTATGAAAAAAAGATGCATAGTGCTAATTCCAAGCTTTAGAAAATAACTATGAAAAC-AGAGATG
* * *
42388 GACTCTATGTATTCCAACTCAGTGTGAGAACTTGTAGACTTACCGAAAGGGATAAAACCCATAGG
65 GACTCTATGTATTCCAACTCAGTGTGAGAACTTCTAAACTTACCGAAAGGGATAAAACCCATAGA
* *
42453 GTGTAAGTGGATCTACAAA
130 GTGTAACTGGATATACAAA
42472 AGGAAAAGAA
Statistics
Matches: 137, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
175 136 0.99
176 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.25
Consensus pattern (175 bp):
GTATGAAAAAAAGATGCATAGTGCTAATTCCAAGCTTTAGAAAATAACTATGAAAACAGAGATGG
ACTCTATGTATTCCAACTCAGTGTGAGAACTTCTAAACTTACCGAAAGGGATAAAACCCATAGAG
TGTAACTGGATATACAAATGCCTAGCAGGAAGAAGTCCCATTCAC
Found at i:44660 original size:2 final size:2
Alignment explanation
Indices: 44653--44677 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44643 ATTCAACTTT
44653 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
44678 TATTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47091 original size:40 final size:39
Alignment explanation
Indices: 47047--47137 Score: 94
Period size: 40 Copynumber: 2.3 Consensus size: 39
47037 GCTTGGATCT
*
47047 ATTTTAACTTGTCTGAAAAACATTTTGAAGTG-TTAAAATG
1 ATTTTAACTTGT-TG-AAAACATTTTGAAGTGTTTAAAATC
* * * **
47087 ATTTTGACTTGGTTGAAATCGTTTTGACTTGTTTAAAATC
1 ATTTTAACTT-GTTGAAAACATTTTGAAGTGTTTAAAATC
47127 ATTTTAACTTG
1 ATTTTAACTTG
47138 ATTTTAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
39 13 0.31
40 27 0.64
41 2 0.05
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (39 bp):
ATTTTAACTTGTTGAAAACATTTTGAAGTGTTTAAAATC
Found at i:47111 original size:20 final size:20
Alignment explanation
Indices: 47078--47137 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
47068 ATTTTGAAGT
*
47078 GTTAAAATGATTTTGACTTG
1 GTTAAAATCATTTTGACTTG
* *
47098 GTTGAAATCGTTTTGACTTG
1 GTTAAAATCATTTTGACTTG
* *
47118 TTTAAAATCATTTTAACTTG
1 GTTAAAATCATTTTGACTTG
47138 ATTTTAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (20 bp):
GTTAAAATCATTTTGACTTG
Found at i:49153 original size:20 final size:20
Alignment explanation
Indices: 49128--49167 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
49118 TAATATTACC
49128 AAAAATATTTATTATTATTA
1 AAAAATATTTATTATTATTA
49148 AAAAATATTTATTATTATTA
1 AAAAATATTTATTATTATTA
49168 TTAATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAAATATTTATTATTATTA
Found at i:49609 original size:14 final size:14
Alignment explanation
Indices: 49592--49618 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49582 ATTTGTTTCT
49592 TCTCACTAAATGCG
1 TCTCACTAAATGCG
49606 TCTCACTAAATGC
1 TCTCACTAAATGC
49619 TTGTCCATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.30
Consensus pattern (14 bp):
TCTCACTAAATGCG
Found at i:49915 original size:17 final size:17
Alignment explanation
Indices: 49889--49984 Score: 77
Period size: 17 Copynumber: 5.6 Consensus size: 17
49879 CTTTTCAATT
* *
49889 AATTTTAATTTACAGTA
1 AATTTAAATTTAAAGTA
49906 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAAGTA
** * *
49923 AATTTAAACTCAAAAATG
1 AATTTAAA-TTTAAAGTA
*
49941 AATTTAAATTTAGAA-CA
1 AATTTAAATTTA-AAGTA
* *
49958 AATTCAAACTTAAAGTA
1 AATTTAAATTTAAAGTA
*
49975 AATTAAAATT
1 AATTTAAATT
49985 AAAAATTGGA
Statistics
Matches: 61, Mismatches: 15, Indels: 6
0.74 0.18 0.07
Matches are distributed among these distances:
16 2 0.03
17 44 0.72
18 15 0.25
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.36
Consensus pattern (17 bp):
AATTTAAATTTAAAGTA
Done.