Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009699.1 Kokia drynarioides strain JFW-HI SEQ_124418, 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: 14927
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Found at i:1306 original size:120 final size:121
Alignment explanation
Indices: 1097--1631 Score: 559
Period size: 120 Copynumber: 4.5 Consensus size: 121
1087 ATAGCTTTAG
* * * * * *
1097 GGGTAAAAGATTGGATTGT-TTCAATCT-GCCCCATG-GTCGTGGTAAGAGATCGAATGGTCTTC
1 GGGTAAAAGATTGGATGGTCTTCAATCTATCCCTATGATTAG-GGTAAGAGATCGGATGGTCTTC
* * * * *
1159 AATCTACCCTCTGGTTAAGGCAAAAGATTTAATGGTCTTCTATCTGCCCTCTGATTA
65 AATCTGCCCTCTGATTAGGGTAAAAGATTTAATGGTCTTCAATCTGCCCTCTGATTA
* * **
1216 GGGTAAAAGATTGGATGGTCTTCCATCTATCAC-ATGGCT-GGGATAAGAGATCGGATGGTCTTC
1 GGGTAAAAGATTGGATGGTCTTCAATCTATCCCTATGATTAGGG-TAAGAGATCGGATGGTCTTC
* * * * * *
1279 AATCTGCCTTTTGATTAGGGTAAAAGATTTGATGGTCTTCAATTTTCCCTCTAATTA
65 AATCTGCCCTCTGATTAGGGTAAAAGATTTAATGGTCTTCAATCTGCCCTCTGATTA
* * * * * * *
1336 GGATGAAAGATTTGATGGTGTTCAATCT-TCCCTTTGATTAGGGGTAA-AGTTTGGATGGTCTTC
1 GGGTAAAAGATTGGATGGTCTTCAATCTATCCCTATGATTA-GGGTAAGAGATCGGATGGTCTTC
* * * * * *
1399 AATATGTCCTTTGATTAGGGTAAAAAATTTGATGGTCTTCAATCTGTCCTCTGATTA
65 AATCTGCCCTCTGATTAGGGTAAAAGATTTAATGGTCTTCAATCTGCCCTCTGATTA
* * * * **
1456 GGGTAAAAGATTTGATGGTCTTCAATCTA-CCCTTTGATTAGGGTAAAACATTTGATGGTCTTCA
1 GGGTAAAAGATTGGATGGTCTTCAATCTATCCCTATGATTAGGGTAAGAGATCGGATGGTCTTCA
1520 ATCTGCCCTCTGATTAGGGTAAAAGA-TTAGATGGTCTTCAATCTGCCCTCTGATTA
66 ATCTGCCCTCTGATTAGGGTAAAAGATTTA-ATGGTCTTCAATCTGCCCTCTGATTA
* * * * *
1576 GGGCAAAAGATTGGATGTTCTTCAATCTA-CCCTTTGATTAGGGTAAAAGATTGGAT
1 GGGTAAAAGATTGGATGGTCTTCAATCTATCCCTATGATTAGGGTAAGAGATCGGAT
1632 AGTTGTAACT
Statistics
Matches: 353, Mismatches: 53, Indels: 19
0.83 0.12 0.04
Matches are distributed among these distances:
119 31 0.09
120 313 0.89
121 6 0.02
122 3 0.01
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (121 bp):
GGGTAAAAGATTGGATGGTCTTCAATCTATCCCTATGATTAGGGTAAGAGATCGGATGGTCTTCA
ATCTGCCCTCTGATTAGGGTAAAAGATTTAATGGTCTTCAATCTGCCCTCTGATTA
Found at i:1631 original size:40 final size:40
Alignment explanation
Indices: 1150--1627 Score: 532
Period size: 40 Copynumber: 11.9 Consensus size: 40
1140 AAGAGATCGA
* * * * *
1150 ATGGTCTTCAATCTACCCTCTGGTTAAGGCAAAAGATTTA
1 ATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTTG
* *
1190 ATGGTCTTCTATCTGCCCTCTGATTAGGGTAAAAGATTGG
1 ATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTTG
* * * * ** * **
1230 ATGGTCTTCCATCTATCAC-ATGGCT-GGGATAAGAGATCGG
1 ATGGTCTTCAATCT-GCCCTCTGATTAGGG-TAAAAGATTTG
* *
1270 ATGGTCTTCAATCTGCCTTTTGATTAGGGTAAAAGATTTG
1 ATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTTG
* * * * *
1310 ATGGTCTTCAATTTTCCCTCTAATTAGGATGAAAGATTTG
1 ATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTTG
* * *
1350 ATGGTGTTCAATCTTCCCTTTGATTAGGGGT-AAAG-TTTGG
1 ATGGTCTTCAATCTGCCCTCTGATTA-GGGTAAAAGATTT-G
* * * *
1390 ATGGTCTTCAATATGTCCTTTGATTAGGGTAAAAAATTTG
1 ATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTTG
*
1430 ATGGTCTTCAATCTGTCCTCTGATTAGGGTAAAAGATTTG
1 ATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTTG
* * *
1470 ATGGTCTTCAATCTACCCTTTGATTAGGGTAAAACATTTG
1 ATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTTG
*
1510 ATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTAG
1 ATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTTG
* *
1550 ATGGTCTTCAATCTGCCCTCTGATTAGGGCAAAAGATTGG
1 ATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTTG
* * *
1590 ATGTTCTTCAATCTACCCTTTGATTAGGGTAAAAGATT
1 ATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATT
1628 GGATAGTTGT
Statistics
Matches: 371, Mismatches: 59, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
39 11 0.03
40 349 0.94
41 11 0.03
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (40 bp):
ATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTTG
Found at i:2047 original size:119 final size:119
Alignment explanation
Indices: 1813--2041 Score: 298
Period size: 119 Copynumber: 1.9 Consensus size: 119
1803 TACCAAGAAG
* * * *
1813 ATGAGATTTGAAGTCTCACTCGCATTGAGTTTCGCTTTATTGTTTTAGTCCACTTTTCTGTATCT
1 ATGAGATTTGAAGTCTCACTCGCATTGAGCTTCGCTTCATTGTTTGAGTCCACTTCTCTGTATCT
* ** * * * * *
1878 CATTAGGAAGATGACTTCGTTGTTTGATCCACTTCTCTGTATCTCATTAGGAAA
66 CATCAGGAAGATGACTTCGGAGTCTCATCCACTCCACTGTAACTCATTAGGAAA
*
1932 ATGAGATTTGAAGTCTCACTCGCATTGAGCTTCGCTTCATTGTTTGGGTCCACTTCTCTGTATCT
1 ATGAGATTTGAAGTCTCACTCGCATTGAGCTTCGCTTCATTGTTTGAGTCCACTTCTCTGTATCT
*
1997 CATCAGGAAGATGGGA-TTTGGAGTCTCACTCCACTCCACTGTAAC
66 CATCAGGAAGAT--GACTTCGGAGTCTCA-TCCACTCCACTGTAAC
2042 CTTAGGGACG
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
119 71 0.76
120 7 0.08
121 15 0.16
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (119 bp):
ATGAGATTTGAAGTCTCACTCGCATTGAGCTTCGCTTCATTGTTTGAGTCCACTTCTCTGTATCT
CATCAGGAAGATGACTTCGGAGTCTCATCCACTCCACTGTAACTCATTAGGAAA
Found at i:2128 original size:49 final size:50
Alignment explanation
Indices: 2071--2174 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 50
2061 TTGTTGTTTT
* *
2071 AATCTGCTTCACTGT-AACTTT-GAG--GTAGAAGATTCGTCGTTGCGGCTTC
1 AATCTGCTTCACT-TCAACTTTAGAGACGT--AAGATTCGCCGTTGCAGCTTC
*
2120 AATCTGCTTCACTTCAACTTTAGAGACGTAAGATTCGCCTTTGCAGCTTC
1 AATCTGCTTCACTTCAACTTTAGAGACGTAAGATTCGCCGTTGCAGCTTC
2170 AATCT
1 AATCT
2175 ACTTTTCCTC
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
48 1 0.02
49 19 0.40
50 26 0.54
52 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (50 bp):
AATCTGCTTCACTTCAACTTTAGAGACGTAAGATTCGCCGTTGCAGCTTC
Found at i:2296 original size:49 final size:49
Alignment explanation
Indices: 2217--2425 Score: 151
Period size: 49 Copynumber: 4.3 Consensus size: 49
2207 CATTGCGACC
* * * * **
2217 TCAATCTTTT-CCTTCACATCTTTAGAGTACAAGGTTCGTCGTTGCGGCT
1 TCAA-CTTTTCCCTTCATATCTCTAGGGTACAAGATTCACCGTTGCGGCT
* * ***
2266 TCAACTTTTCCCTTCATAACTCTAGGGTACAAGATTCACCATCATGGCT
1 TCAACTTTTCCCTTCATATCTCTAGGGTACAAGATTCACCGTTGCGGCT
* ** * *
2315 TCAA-TCTTTCCCATCACGTC-CTTAAGGTACAAGGTTCACCGTTGCGGCT
1 TCAACT-TTTCCCTTCATATCTC-TAGGGTACAAGATTCACCGTTGCGGCT
* * **
2364 TCAACCTTTCTCTT-ATATCTCTAGGGTATC-AGATTTGCCGTTGCGGCT
1 TCAACTTTTCCCTTCATATCTCTAGGGTA-CAAGATTCACCGTTGCGGCT
2412 TCAA-TCTTTCCCTT
1 TCAACT-TTTCCCTT
2426 TAAACCTATA
Statistics
Matches: 121, Mismatches: 32, Indels: 15
0.72 0.19 0.09
Matches are distributed among these distances:
48 42 0.35
49 79 0.65
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (49 bp):
TCAACTTTTCCCTTCATATCTCTAGGGTACAAGATTCACCGTTGCGGCT
Found at i:2421 original size:97 final size:98
Alignment explanation
Indices: 2217--2423 Score: 240
Period size: 98 Copynumber: 2.1 Consensus size: 98
2207 CATTGCGACC
* * * ** *
2217 TCAATCTTTTCCTTCACATCTTTAGAGTACAAGGTTCGTCGTTGCGGCTTCAACTTTTCCCTTCA
1 TCAATCTTTCCCATCACATCTTAAGAGTACAAGGTTCACCGTTGCGGCTTCAACCTTTCCCTTCA
*
2282 TAACTCTAGGGTACAAGATTCACCATCATGGCT
66 TAACTCTAGGGTACAAGATTCACCATCACGGCT
* *
2315 TCAATCTTTCCCATCACGTCCTTAAG-GTACAAGGTTCACCGTTGCGGCTTCAACCTTTCTCTT-
1 TCAATCTTTCCCATCACAT-CTTAAGAGTACAAGGTTCACCGTTGCGGCTTCAACCTTTCCCTTC
* ** * **
2378 ATATCTCTAGGGTATC-AGATTTGCCGTTGCGGCT
65 ATAACTCTAGGGTA-CAAGATTCACCATCACGGCT
2412 TCAATCTTTCCC
1 TCAATCTTTCCC
2424 TTTAAACCTA
Statistics
Matches: 92, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
97 37 0.40
98 50 0.54
99 5 0.05
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (98 bp):
TCAATCTTTCCCATCACATCTTAAGAGTACAAGGTTCACCGTTGCGGCTTCAACCTTTCCCTTCA
TAACTCTAGGGTACAAGATTCACCATCACGGCT
Found at i:3327 original size:8 final size:8
Alignment explanation
Indices: 3310--3361 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
3300 TCGACCTCTC
3310 TTTTTCTT
1 TTTTTCTT
3318 CTTTTT-TT
1 -TTTTTCTT
*
3326 CTTTTCTT
1 TTTTTCTT
*
3334 TTTCTCTT
1 TTTTTCTT
*
3342 TTTCTCTT
1 TTTTTCTT
*
3350 TTTTCCTT
1 TTTTTCTT
3358 TTTT
1 TTTT
3362 GTTTTTTGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
7 4 0.11
8 28 0.76
9 5 0.14
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:3332 original size:16 final size:16
Alignment explanation
Indices: 3311--3368 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 16
3301 CGACCTCTCT
3311 TTTTCTTCTTTTTTTC
1 TTTTCTTCTTTTTTTC
* *
3327 TTTTCTT-TTTCTCT-
1 TTTTCTTCTTTTTTTC
*
3341 TTTTC-TCTTTTTTCC
1 TTTTCTTCTTTTTTTC
*
3356 TTTT-TTGTTTTTT
1 TTTTCTTCTTTTTT
3369 GTTTTTATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
13 1 0.03
14 9 0.27
15 16 0.48
16 7 0.21
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTCTTCTTTTTTTC
Found at i:3352 original size:22 final size:22
Alignment explanation
Indices: 3308--3351 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
3298 CCTCGACCTC
*
3308 TCTTTTTCTTCTTTTTTTCTTT
1 TCTTTTTCTTCTTTTTCTCTTT
3330 TCTTTTTC-TCTTTTTCTCTTT
1 TCTTTTTCTTCTTTTTCTCTTT
3351 T
1 T
3352 TTCCTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (22 bp):
TCTTTTTCTTCTTTTTCTCTTT
Found at i:3382 original size:38 final size:38
Alignment explanation
Indices: 3306--3382 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
3296 CACCTCGACC
* *
3306 TCTCTTTTTCTTCTTTTTTTCTTTTCTTTTTCTCTTTT
1 TCTCTTTTTCTCCTTTTTTTCTTTTCTTTTTATCTTTT
* * *
3344 TCTCTTTTT-TCCTTTTTTGTTTTTTGTTTTTATTTTTT
1 TCTCTTTTTCTCCTTTTTT-TCTTTTCTTTTTATCTTTT
3382 T
1 T
3383 GGTGAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
37 8 0.24
38 25 0.76
ACGTcount: A:0.01, C:0.16, G:0.03, T:0.81
Consensus pattern (38 bp):
TCTCTTTTTCTCCTTTTTTTCTTTTCTTTTTATCTTTT
Found at i:4254 original size:20 final size:20
Alignment explanation
Indices: 4219--4256 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4209 CTGGAACTAT
*
4219 GGTATCGATACCTTTCCAAA
1 GGTATCGATAACTTTCCAAA
*
4239 GGTATCGATAATTTTCCA
1 GGTATCGATAACTTTCCA
4257 CAATTATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (20 bp):
GGTATCGATAACTTTCCAAA
Found at i:7993 original size:22 final size:23
Alignment explanation
Indices: 7968--8020 Score: 90
Period size: 22 Copynumber: 2.3 Consensus size: 23
7958 GAGCTCCGAG
7968 GTGCTAAACGGAGAGCACAAA-C
1 GTGCTAAACGGAGAGCACAAACC
*
7990 GTGCTAATCGGAGAGCACAAACC
1 GTGCTAAACGGAGAGCACAAACC
8013 GTGCTAAA
1 GTGCTAAA
8021 TGAATGGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.13
Consensus pattern (23 bp):
GTGCTAAACGGAGAGCACAAACC
Done.