Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012207.1 Kokia drynarioides strain JFW-HI SEQ_127208, 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: 40492
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1148 original size:30 final size:30
Alignment explanation
Indices: 1098--1204 Score: 135
Period size: 30 Copynumber: 3.6 Consensus size: 30
1088 AAGGACGATC
* *
1098 GCACACG-GCTTGAAACACGGTCGTGTGTG
1 GCACACGAGCTAGACACACGGTCGTGTGTG
*
1127 GCACACGAGCTAGACACACGGTCGTATGTG
1 GCACACGAGCTAGACACACGGTCGTGTGTG
** **
1157 ATACACGAGCTAGACACACGACCGTGTGTG
1 GCACACGAGCTAGACACACGGTCGTGTGTG
*
1187 GCACATGAGCTAGACACA
1 GCACACGAGCTAGACACA
1205 TGAGCGTATG
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
29 7 0.11
30 59 0.89
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (30 bp):
GCACACGAGCTAGACACACGGTCGTGTGTG
Found at i:1443 original size:6 final size:6
Alignment explanation
Indices: 1390--1446 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
1380 TAAAGCTTAT
* * * *
1390 TTTTTA TTATTT- TTTTAA TATTTAA TTTTTA TTTTCA TTTTCA TTTTTA
1 TTTTTA TT-TTTA TTTTTA T-TTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1439 TTTTTA TT
1 TTTTTA TT
1447 ATGCACCGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
5 2 0.05
6 33 0.75
7 9 0.20
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTTA
Found at i:5209 original size:14 final size:14
Alignment explanation
Indices: 5190--5244 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
5180 CAAAGTTTTT
*
5190 AGTTTTCAAATTTA
1 AGTTTTAAAATTTA
*
5204 AGTTTTAAAATTCA
1 AGTTTTAAAATTTA
*
5218 AATTTTAAAATTTA
1 AGTTTTAAAATTTA
*
5232 AGTTTTCAAATTT
1 AGTTTTAAAATTT
5245 TAATTACATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (14 bp):
AGTTTTAAAATTTA
Found at i:5249 original size:28 final size:28
Alignment explanation
Indices: 5186--5249 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
5176 TCTCCAAAGT
* *
5186 TTTTAGTTTTCAAATTTAAGTTTTAAAA
1 TTTTAATTTTAAAATTTAAGTTTTAAAA
** *
5214 TTCAAATTTTAAAATTTAAGTTTTCAAA
1 TTTTAATTTTAAAATTTAAGTTTTAAAA
5242 TTTTAATT
1 TTTTAATT
5250 ACATTATTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (28 bp):
TTTTAATTTTAAAATTTAAGTTTTAAAA
Found at i:8590 original size:22 final size:22
Alignment explanation
Indices: 8562--8636 Score: 132
Period size: 22 Copynumber: 3.4 Consensus size: 22
8552 AAATGAGCAG
*
8562 TGAGATTTTTTGACGTGAACAA
1 TGAGATTCTTTGACGTGAACAA
*
8584 TGAGATTCTTTGACATGAACAA
1 TGAGATTCTTTGACGTGAACAA
8606 TGAGATTCTTTGACGTGAACAA
1 TGAGATTCTTTGACGTGAACAA
8628 TGAGATTCT
1 TGAGATTCT
8637 CTGGTAATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (22 bp):
TGAGATTCTTTGACGTGAACAA
Found at i:8932 original size:14 final size:14
Alignment explanation
Indices: 8913--8967 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
8903 CAAAGTTTTT
*
8913 AGTTTTCAAATTTA
1 AGTTTTAAAATTTA
*
8927 AGTTTTAAAATTCA
1 AGTTTTAAAATTTA
*
8941 AATTTTAAAATTTA
1 AGTTTTAAAATTTA
*
8955 AGTTTTCAAATTT
1 AGTTTTAAAATTT
8968 TAATTACATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (14 bp):
AGTTTTAAAATTTA
Found at i:8972 original size:28 final size:28
Alignment explanation
Indices: 8909--8972 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
8899 TCTTCAAAGT
* *
8909 TTTTAGTTTTCAAATTTAAGTTTTAAAA
1 TTTTAATTTTAAAATTTAAGTTTTAAAA
** *
8937 TTCAAATTTTAAAATTTAAGTTTTCAAA
1 TTTTAATTTTAAAATTTAAGTTTTAAAA
8965 TTTTAATT
1 TTTTAATT
8973 ACATTATTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (28 bp):
TTTTAATTTTAAAATTTAAGTTTTAAAA
Found at i:9483 original size:186 final size:186
Alignment explanation
Indices: 9169--9544 Score: 743
Period size: 186 Copynumber: 2.0 Consensus size: 186
9159 CAGCGGTCAA
9169 ATTTTAATCACCTCTCTTTCCTGGGACCCATTACCTGTTGCATGGTTCACACTGACTTCTTTGGT
1 ATTTTAATCACCTCTCTTTCCTGGGACCCATTACCTGTTGCATGGTTCACACTGACTTCTTTGGT
9234 TTTTCCCTTAAAAGAAAAACTATGGAGAATCAAAATTGTTTTTCTTTTATGATTTATTGATTCTT
66 TTTTCCCTTAAAAGAAAAACTATGGAGAATCAAAATTGTTTTTCTTTTATGATTTATTGATTCTT
*
9299 GTGAATGGATATTATAAAATTTTCATAGCATGCCATGCATATATTAGAAGCATGTC
131 GTGAATGAATATTATAAAATTTTCATAGCATGCCATGCATATATTAGAAGCATGTC
9355 ATTTTAATCACCTCTCTTTCCTGGGACCCATTACCTGTTGCATGGTTCACACTGACTTCTTTGGT
1 ATTTTAATCACCTCTCTTTCCTGGGACCCATTACCTGTTGCATGGTTCACACTGACTTCTTTGGT
9420 TTTTCCCTTAAAAGAAAAACTATGGAGAATCAAAATTGTTTTTCTTTTATGATTTATTGATTCTT
66 TTTTCCCTTAAAAGAAAAACTATGGAGAATCAAAATTGTTTTTCTTTTATGATTTATTGATTCTT
9485 GTGAATGAATATTATAAAATTTTCATAGCATGCCATGCATATATTAGAAGCATGTC
131 GTGAATGAATATTATAAAATTTTCATAGCATGCCATGCATATATTAGAAGCATGTC
9541 ATTT
1 ATTT
9545 AGATTAGGTA
Statistics
Matches: 189, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
186 189 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (186 bp):
ATTTTAATCACCTCTCTTTCCTGGGACCCATTACCTGTTGCATGGTTCACACTGACTTCTTTGGT
TTTTCCCTTAAAAGAAAAACTATGGAGAATCAAAATTGTTTTTCTTTTATGATTTATTGATTCTT
GTGAATGAATATTATAAAATTTTCATAGCATGCCATGCATATATTAGAAGCATGTC
Found at i:11467 original size:19 final size:19
Alignment explanation
Indices: 11426--11480 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
11416 TTATTCTATC
* *
11426 TATATATA-TTTCAATTATT
1 TATATATATTTTTAA-TATG
11445 TATATATATTTTTAATATG
1 TATATATATTTTTAATATG
11464 TATATTATATTTTTAAT
1 TATA-TATATTTTTAAT
11481 CTCTCTCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TATATATATTTTTAATATG
Found at i:19443 original size:27 final size:27
Alignment explanation
Indices: 19404--19505 Score: 143
Period size: 27 Copynumber: 3.8 Consensus size: 27
19394 GAGGAGTAAA
19404 CTGATTCTGGCTCGAAAGAGCGTTATT
1 CTGATTCTGGCTCGAAAGAGCGTTATT
* *
19431 TTGATTCTGGCTCGAAAGAGAGTTATT
1 CTGATTCTGGCTCGAAAGAGCGTTATT
* *
19458 CTGATTTTGGCTCGATAGAGCGTTATT
1 CTGATTCTGGCTCGAAAGAGCGTTATT
*
19485 CTGATTCTAGGCT-GTAAGAGC
1 CTGATTCT-GGCTCGAAAGAGC
19506 TAACTATTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
27 61 0.94
28 4 0.06
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (27 bp):
CTGATTCTGGCTCGAAAGAGCGTTATT
Found at i:19527 original size:24 final size:24
Alignment explanation
Indices: 19488--19645 Score: 205
Period size: 24 Copynumber: 6.6 Consensus size: 24
19478 CGTTATTCTG
19488 ATTCTAGGCT-GTAAGAGCTAACT
1 ATTCTAGGCTCGTAAGAGCTAACT
*
19511 ATTTTAGGCTCGTAAGAGCTAACT
1 ATTCTAGGCTCGTAAGAGCTAACT
* *
19535 ATTCTGGGCTCATAAGAGCTAA-T
1 ATTCTAGGCTCGTAAGAGCTAACT
19558 CATTCTAGGCTCGTAAGAGCTAACT
1 -ATTCTAGGCTCGTAAGAGCTAACT
*
19583 ATTCTAGGTTCGTAAGAGCTAA-T
1 ATTCTAGGCTCGTAAGAGCTAACT
* * *
19606 CATTCTGGGCTCATAAGAGCTAACC
1 -ATTCTAGGCTCGTAAGAGCTAACT
*
19631 ATTCTATGCTCGTAA
1 ATTCTAGGCTCGTAA
19646 TGAGTTAAAA
Statistics
Matches: 116, Mismatches: 14, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
23 11 0.09
24 104 0.90
25 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (24 bp):
ATTCTAGGCTCGTAAGAGCTAACT
Found at i:19580 original size:72 final size:72
Alignment explanation
Indices: 19488--19645 Score: 257
Period size: 72 Copynumber: 2.2 Consensus size: 72
19478 CGTTATTCTG
*
19488 ATTCTAGGCT-GTAAGAGCTAACTATTTTAGGCTCGTAAGAGCTAA-CTATTCTGGGCTCATAAG
1 ATTCTAGGCTCGTAAGAGCTAACTATTCTAGGCTCGTAAGAGCTAATC-ATTCTGGGCTCATAAG
*
19551 AGCTAATC
65 AGCTAACC
*
19559 ATTCTAGGCTCGTAAGAGCTAACTATTCTAGGTTCGTAAGAGCTAATCATTCTGGGCTCATAAGA
1 ATTCTAGGCTCGTAAGAGCTAACTATTCTAGGCTCGTAAGAGCTAATCATTCTGGGCTCATAAGA
19624 GCTAACC
66 GCTAACC
*
19631 ATTCTATGCTCGTAA
1 ATTCTAGGCTCGTAA
19646 TGAGTTAAAA
Statistics
Matches: 81, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
71 10 0.12
72 70 0.86
73 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (72 bp):
ATTCTAGGCTCGTAAGAGCTAACTATTCTAGGCTCGTAAGAGCTAATCATTCTGGGCTCATAAGA
GCTAACC
Found at i:20633 original size:10 final size:10
Alignment explanation
Indices: 20620--20664 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
20610 AAAAAATCAC
20620 AAAAAGAAAG
1 AAAAAGAAAG
20630 AAAAAGAAAG
1 AAAAAGAAAG
*
20640 AAGAAGACAAG
1 AAAAAGA-AAG
*
20651 ACAAAAAAAAG
1 A-AAAAGAAAG
20662 AAA
1 AAA
20665 TACATTGCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 18 0.60
11 8 0.27
12 4 0.13
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:27529 original size:21 final size:21
Alignment explanation
Indices: 27486--27533 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
27476 CCTATGACGG
* * *
27486 TTCTACCGATACAAGTGAAGC
1 TTCTACCGAAACAAATCAAGC
*
27507 TTCTACCGAAACAAATCATGC
1 TTCTACCGAAACAAATCAAGC
27528 TTCTAC
1 TTCTAC
27534 AAGTACTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (21 bp):
TTCTACCGAAACAAATCAAGC
Found at i:28350 original size:52 final size:52
Alignment explanation
Indices: 28274--28826 Score: 779
Period size: 52 Copynumber: 10.6 Consensus size: 52
28264 GTTTCATTTA
* ** *
28274 ATACTCACGATGTACACATAGTCATCGGACCTCGTAATATATAAAGGAATCAT
1 ATACTCACGATG-ACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
28327 ATACTCACGATGACACATAGTCATC-GATCCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGA-CCTCATAATCCATAAAGGATTCAT
* * *
28379 ATACTCACGATGACACATAGTCATC-GATTCACATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGA-CCTCATAATCCATAAAGGATTCAT
* * *
28431 ATACTCATGATGACACATAGTCATCGGACCTCTTAATCCATAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
*
28483 ATACTCACGATGACACATAGTCATCGGTCCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
* *
28535 ATACTCACGATGACACATAATCATC-GATCCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGA-CCTCATAATCCATAAAGGATTCAT
* * *
28587 ATACTCATGATAACACATAGTCATCGGACCTCATAATCCGTAAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCAT-AAAGGATTCAT
* * *
28640 ATACTCACGATGACATATAGTCATCGGTCCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
* * *
28692 ATACTCACGATGACACATAGTCATTGGACCTCATAATCCGTAAAGGTTTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
* * * * *
28744 ATACTCACAATGACACATAGTCATAGGACCCCATAGTCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
* *
28796 ATACTCATGATGACACATAGTCATCAGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
28827 TTTTCTTTTA
Statistics
Matches: 454, Mismatches: 41, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
51 3 0.01
52 387 0.85
53 64 0.14
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
Found at i:29329 original size:20 final size:22
Alignment explanation
Indices: 29282--29329 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
29272 GATTTATATT
*
29282 GTTTATAAATAGGTTTAATAAA
1 GTTTAAAAATAGGTTTAATAAA
* *
29304 GGTTAAAAATA-G-TTAATTAA
1 GTTTAAAAATAGGTTTAATAAA
29324 GTTTAA
1 GTTTAA
29330 TGGTGAAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 12 0.55
21 1 0.05
22 9 0.41
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.40
Consensus pattern (22 bp):
GTTTAAAAATAGGTTTAATAAA
Found at i:33150 original size:13 final size:13
Alignment explanation
Indices: 33132--33165 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
33122 TTACTAGTAA
*
33132 GAAATTTCGGGAC
1 GAAATTTCGGAAC
33145 GAAATTTCGGAAC
1 GAAATTTCGGAAC
33158 GAAATTTC
1 GAAATTTC
33166 CCTAAAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (13 bp):
GAAATTTCGGAAC
Found at i:37329 original size:18 final size:18
Alignment explanation
Indices: 37288--37339 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
37278 ATATATTCAG
37288 TATTTTTCTATCTA--TA-
1 TATTTTTCTAT-TATTTAT
*
37304 TATATTTCTATTATTTAT
1 TATTTTTCTATTATTTAT
37322 TATTTTTCTATTATTTAT
1 TATTTTTCTATTATTTAT
37340 ATATATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 2 0.06
16 10 0.32
17 2 0.06
18 17 0.55
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTTTCTATTATTTAT
Found at i:37344 original size:2 final size:2
Alignment explanation
Indices: 37337--37361 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37327 TTCTATTATT
37337 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
37362 TACTTTGCCA
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
Done.