Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002467.1 Kokia drynarioides strain JFW-HI SEQ_114602, 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: 9421
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:1656 original size:22 final size:22
Alignment explanation
Indices: 1628--1669 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1618 TAAAGGTTTA
1628 TTTATTTATTTTATTTTATTTG
1 TTTATTTATTTTATTTTATTTG
*
1650 TTTATTTGTTTTATTTTATT
1 TTTATTTATTTTATTTTATT
1670 CTATTGGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.79
Consensus pattern (22 bp):
TTTATTTATTTTATTTTATTTG
Found at i:2230 original size:123 final size:122
Alignment explanation
Indices: 1997--2518 Score: 378
Period size: 123 Copynumber: 4.3 Consensus size: 122
1987 AACAAACTGT
* * * * *
1997 TTTGACCCACTTCTCCGTACCTCACCAGGAAGATAGTATTTGAAGT-TCCATTCATATTTGAGCT
1 TTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGGATTTGAAGTCT-CATTCGTA-TTGAGCT
* * * *
2061 TCACCTCATTATTTTGGTAC-ACTTTTCTGTATCTCACCAAGAAGATGACCACTTTATTGC
64 TCGCTTCATTA-TTTGGT-CTACTTCTCTGTATCTCATCAAGAAGATGACCACTTTATTGC
* * * *
2121 TTTGACCCACTTCTTTATATCTCATCAAGAAGATAGGGTTTGAAGTCTCATTCGTATTGAGCTTC
1 TTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGGATTTGAAGTCTCATTCGTATTGAGCTTC
* * * * *
2186 GCTTCATTGATTTGGTCTACTTCTCTGTGTCTTATCAAGAAGATGATCGAC-TCATTGT
66 GCTTCATT-ATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGA-CCACTTTATTGC
* * * * * * * *
2244 TTTAATCCACTTCTCTGTATCTTATTAGGAAGAT-GAATTTG--GTC-AACTTCTTA-GGAAG--
1 TTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGGATTTGAAGTCTCA-TTCGTATTG-AGCT
* * * * *
2302 ACG----A--ATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGATCGCTTTATTAC
64 TCGCTTCATTATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCACTTTATTGC
* ** * * * *
2355 TTTGACCCACTTCACTGTATCTTGTCAGGATGATGGGGTTTGAAGTCTCATTTGTATTGAGCTTC
1 TTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGGATTTGAAGTCTCATTCGTATTGAGCTTC
* * * * * * * *
2420 GCTTAATTGATTTGGTCTACTTCTCTGTATCTTATCAGGAAGATGATCGCCTCATT-A
66 GCTTCATT-ATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCACTTTATTGC
* * * *
2477 TTTCAATCCACTTCTCTATATCTCATCAGGAAGA-CGGATTTG
1 TTT-GACCCACTTCTCTGTATCTCATCAGGAAGATAGGATTTG
2519 GTTCACTTCT
Statistics
Matches: 308, Mismatches: 68, Indels: 46
0.73 0.16 0.11
Matches are distributed among these distances:
110 1 0.00
111 66 0.21
112 5 0.02
114 10 0.03
115 2 0.01
116 2 0.01
118 2 0.01
119 2 0.01
120 11 0.04
122 15 0.05
123 142 0.46
124 49 0.16
125 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (122 bp):
TTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGGATTTGAAGTCTCATTCGTATTGAGCTTC
GCTTCATTATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCACTTTATTGC
Found at i:2302 original size:26 final size:26
Alignment explanation
Indices: 2268--2320 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
2258 CTGTATCTTA
*
2268 TTAGGAAGATGAATTTGGTCAACTTC
1 TTAGGAAGACGAATTTGGTCAACTTC
*
2294 TTAGGAAGACGAATTTGGTCCACTTC
1 TTAGGAAGACGAATTTGGTCAACTTC
2320 T
1 T
2321 CTGTATCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (26 bp):
TTAGGAAGACGAATTTGGTCAACTTC
Found at i:2510 original size:234 final size:234
Alignment explanation
Indices: 2073--2528 Score: 662
Period size: 234 Copynumber: 1.9 Consensus size: 234
2063 ACCTCATTAT
* * **
2073 TTTGGTACACTTTTCTGTATCTCACCAAGAAGATGACCACTTTATTGCTTTGACCCACTTCTTTA
1 TTTGGTACACTTCTCTGTATCTCACCAAGAAGATGACCACTTTATTACTTTGACCCACTTCACTA
*
2138 TATCTCATCAAGAAGATAGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTC
66 TATCTCATCAAGAAGATAGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTAATTGATTTGGTC
* * * * *
2203 TACTTCTCTGTGTCTTATCAAGAAGATGATCGACTCATTGTTTTAATCCACTTCTCTGTATCTTA
131 TACTTCTCTGTATCTTATCAAGAAGATGATCGACTCATTATTTCAATCCACTTCTCTATATCTCA
* *
2268 TTAGGAAGATGAATTTGG-TCAACTTCTTAGGAAGACGAA
196 TCAGGAAGACGAATTTGGTTC-ACTTCTTAGGAAGACGAA
* * * * *
2307 TTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGATCGCTTTATTACTTTGACCCACTTCACTG
1 TTTGGTACACTTCTCTGTATCTCACCAAGAAGATGACCACTTTATTACTTTGACCCACTTCACTA
** * * * *
2372 TATCTTGTCAGGATGATGGGGTTTGAAGTCTCATTTGTATTGAGCTTCGCTTAATTGATTTGGTC
66 TATCTCATCAAGAAGATAGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTAATTGATTTGGTC
* *
2437 TACTTCTCTGTATCTTATCAGGAAGATGATCGCCTCATTATTTCAATCCACTTCTCTATATCTCA
131 TACTTCTCTGTATCTTATCAAGAAGATGATCGACTCATTATTTCAATCCACTTCTCTATATCTCA
*
2502 TCAGGAAGACGGATTTGGTTCACTTCT
196 TCAGGAAGACGAATTTGGTTCACTTCT
2529 CTGCATCTCG
Statistics
Matches: 195, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
234 193 0.99
235 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.39
Consensus pattern (234 bp):
TTTGGTACACTTCTCTGTATCTCACCAAGAAGATGACCACTTTATTACTTTGACCCACTTCACTA
TATCTCATCAAGAAGATAGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTAATTGATTTGGTC
TACTTCTCTGTATCTTATCAAGAAGATGATCGACTCATTATTTCAATCCACTTCTCTATATCTCA
TCAGGAAGACGAATTTGGTTCACTTCTTAGGAAGACGAA
Found at i:2632 original size:39 final size:39
Alignment explanation
Indices: 2575--2838 Score: 296
Period size: 39 Copynumber: 6.8 Consensus size: 39
2565 CGAATGACTA
*
2575 CAATCTGCCCTATGATCGGGGTAAGAGATTGGATGGCTG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTG
* * * * **
2614 CAGTCTGCCCCATGATC-GGGTAAAAGATCGGGTGATTG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTG
* * * * *
2652 CAATCTGCCTCATTATCGGGGTAAAAGATTGGATTGCTA
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTG
* * *
2691 CAATTTGTCCCATGATCGGGGTAAGAGATTGGATGGTTG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTG
* * * * *
2730 CAAACTGCCCCATGGTTGAGGTAAGAGATTGGATGGCTA
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTG
* * *
2769 CAATTTACCCCATGATCTGGGTAAGAGATTGGATGGCTG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTG
* *
2808 CAATCTGCCCCATGGTCGAGGTAAGAGATTG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTG
2839 CATGATGATG
Statistics
Matches: 179, Mismatches: 45, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
38 30 0.17
39 149 0.83
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (39 bp):
CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTG
Found at i:3139 original size:49 final size:48
Alignment explanation
Indices: 3082--3373 Score: 153
Period size: 49 Copynumber: 5.9 Consensus size: 48
3072 ATGTTCTTAA
*
3082 GGTACCAGGTTCACCATTGCAGCCTCAACCTTTCCCTTCAAATCTTTAT
1 GGTACC-GGTTCACCGTTGCAGCCTCAACCTTTCCCTTCAAATCTTTAT
* * * * *
3131 GGTACCAGGTTCGCCGTTGCAACCTCAACCTTTCCCATCACAT-TTCAT
1 GGTACC-GGTTCACCGTTGCAGCCTCAACCTTTCCCTTCAAATCTTTAT
* * * ** * *
3179 GGTACCGGATTCGCCGTTGCAGCTTCAATCC-TTCCCATCATGTTTTCTAA
1 GGTACCGG-TTCACCGTTGCAGCCTCAA-CCTTTCCCTTCAAATCTT-TAT
* * * * ** *
3229 AGTATCGAGTTTATCCTTATG--GCCTCAACCTTTCCCTTCATGTCTTCAT
1 GGTACCG-GTTCA-CCGT-TGCAGCCTCAACCTTTCCCTTCAAATCTTTAT
* ** * ** *
3278 GGTACCGGGTTCACCATTGTGGCCTCAGCCTTT-CCTATCTCATCTTTTAA
1 GGTACC-GGTTCACCGTTGCAGCCTCAACCTTTCCCT-TCAAATC-TTTAT
*** **
3328 GGTACCGGGTTTGTCGTTGTGGCCTCAACCTTTCCCTTCAAATCTT
1 GGTACC-GGTTCACCGTTGCAGCCTCAACCTTTCCCTTCAAATCTT
3374 CATGTTTTCT
Statistics
Matches: 190, Mismatches: 39, Indels: 28
0.74 0.15 0.11
Matches are distributed among these distances:
47 4 0.02
48 43 0.23
49 70 0.37
50 64 0.34
51 7 0.04
52 2 0.01
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (48 bp):
GGTACCGGTTCACCGTTGCAGCCTCAACCTTTCCCTTCAAATCTTTAT
Found at i:3198 original size:48 final size:49
Alignment explanation
Indices: 3082--3218 Score: 172
Period size: 49 Copynumber: 2.8 Consensus size: 49
3072 ATGTTCTTAA
* * * *
3082 GGTACCAGGTTCACCATTGCAGCCTCAACCTTTCCCTTCAAATCTTTAT
1 GGTACCAGGTTCGCCGTTGCAGCCTCAACCTTTCCCATCAAATCTTCAT
* *
3131 GGTACCAGGTTCGCCGTTGCAACCTCAACCTTTCCCATCACAT-TTCAT
1 GGTACCAGGTTCGCCGTTGCAGCCTCAACCTTTCCCATCAAATCTTCAT
*
3179 GGTACC-GGATTCGCCGTTGCAGCTTCAATCC-TTCCCATCA
1 GGTACCAGG-TTCGCCGTTGCAGCCTCAA-CCTTTCCCATCA
3219 TGTTTTCTAA
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
47 2 0.03
48 36 0.46
49 40 0.51
ACGTcount: A:0.20, C:0.34, G:0.15, T:0.30
Consensus pattern (49 bp):
GGTACCAGGTTCGCCGTTGCAGCCTCAACCTTTCCCATCAAATCTTCAT
Found at i:3373 original size:50 final size:50
Alignment explanation
Indices: 3103--3373 Score: 162
Period size: 50 Copynumber: 5.5 Consensus size: 50
3093 CACCATTGCA
* **
3103 GCCTCAACCTTTCCCTTCAAATC-TTTATGGTACCAGGTTCGCCGTTGCA
1 GCCTCAACCTTTCCCTTCAAATCTTTTATGGTACCGGGTTCGCCGTTGTG
* * * * * **
3152 ACCTCAACCTTTCCCATCACA--TTTCATGGTACCGGATTCGCCGTTGCA
1 GCCTCAACCTTTCCCTTCAAATCTTTTATGGTACCGGGTTCGCCGTTGTG
* * ** ** * * ** *
3200 GCTTCAATCC-TTCCCATCATGT-TTTCTAAAGTATCGAGTTTATCC-TTATG
1 GCCTCAA-CCTTTCCCTTCAAATCTTT-TATGGTACCG-GGTTCGCCGTTGTG
** * * *
3250 GCCTCAACCTTTCCCTTCATGTC-TTCATGGTACCGGGTTCACCATTGTG
1 GCCTCAACCTTTCCCTTCAAATCTTTTATGGTACCGGGTTCGCCGTTGTG
* ** * * *
3299 GCCTCAGCCTTT-CCTATCTCATCTTTTAAGGTACCGGGTTTGTCGTTGTG
1 GCCTCAACCTTTCCCT-TCAAATCTTTTATGGTACCGGGTTCGCCGTTGTG
3349 GCCTCAACCTTTCCCTTCAAATCTT
1 GCCTCAACCTTTCCCTTCAAATCTT
3374 CATGTTTTCT
Statistics
Matches: 168, Mismatches: 43, Indels: 21
0.72 0.19 0.09
Matches are distributed among these distances:
48 45 0.27
49 50 0.30
50 65 0.39
51 8 0.05
ACGTcount: A:0.18, C:0.31, G:0.15, T:0.36
Consensus pattern (50 bp):
GCCTCAACCTTTCCCTTCAAATCTTTTATGGTACCGGGTTCGCCGTTGTG
Found at i:4344 original size:13 final size:13
Alignment explanation
Indices: 4309--4356 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
4299 CACCTCGACC
4309 TCTCTTTTTCTTTT
1 TCTCTTTTT-TTTT
**
4323 TC-CCCTTTTTTT
1 TCTCTTTTTTTTT
4335 T-TCTTTTTTTTT
1 TCTCTTTTTTTTT
4347 TCTCTTTTTT
1 TCTCTTTTTT
4357 ATTCTTGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
12 14 0.50
13 12 0.43
14 2 0.07
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TCTCTTTTTTTTT
Found at i:4354 original size:20 final size:20
Alignment explanation
Indices: 4331--4391 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 20
4321 TTTCCCCTTT
4331 TTTTTTCTTTT-TTTTTTCTC
1 TTTTTTCTTTTCTTTTTT-TC
* *
4351 TTTTTTATTCTTGTTTTTATTC
1 TTTTTTCTT-TTCTTTTT-TTC
4373 TTTTATTCTTTTCTTTTTT
1 TTTT-TTCTTTTCTTTTTT
4392 ATTTATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 8 0.24
21 3 0.09
22 18 0.53
23 5 0.15
ACGTcount: A:0.05, C:0.11, G:0.02, T:0.82
Consensus pattern (20 bp):
TTTTTTCTTTTCTTTTTTTC
Found at i:4367 original size:13 final size:12
Alignment explanation
Indices: 4328--4391 Score: 71
Period size: 12 Copynumber: 5.4 Consensus size: 12
4318 CTTTTTCCCC
4328 TTTTTTT-TTCT
1 TTTTTTTATTCT
4339 TTTTTTT-TTCT
1 TTTTTTTATTCT
*
4350 CTTTTTTATTCT
1 TTTTTTTATTCT
*
4362 TGTTTTTATTCT
1 TTTTTTTATTCT
4374 TTTATTCTT-TTCT
1 TTT-TT-TTATTCT
4387 TTTTT
1 TTTTT
4392 ATTTATTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
11 17 0.37
12 18 0.39
13 9 0.20
14 2 0.04
ACGTcount: A:0.05, C:0.11, G:0.02, T:0.83
Consensus pattern (12 bp):
TTTTTTTATTCT
Done.