Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008941.1 Kokia drynarioides strain JFW-HI SEQ_123633, 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: 54023
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3441 original size:4 final size:4
Alignment explanation
Indices: 3432--3466 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
3422 AAATGAAATA
3432 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
3467 AAACTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:5396 original size:29 final size:29
Alignment explanation
Indices: 5335--5396 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
5325 GGATACCCGG
***
5335 GGGGGCAAAATGGTAATTTTGGACTCTTA
1 GGGGGCAAAATGGTAATTTTGGAAAATTA
5364 GGGGGCAAAATGGTAATTTTGGGAAAATT-
1 GGGGGCAAAATGGTAATTTT-GGAAAATTA
5393 GGGG
1 GGGG
5397 TTAAAAATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.29, C:0.06, G:0.37, T:0.27
Consensus pattern (29 bp):
GGGGGCAAAATGGTAATTTTGGAAAATTA
Found at i:30158 original size:22 final size:22
Alignment explanation
Indices: 30109--30162 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
30099 TTACTTTGTT
*
30109 ACTATTTTACTGTTATATTGCA
1 ACTATTTTATTGTTATATTGCA
30131 ACTATTTTATTGTTATTATTTG-A
1 ACTATTTTATTGTTA-TA-TTGCA
30154 A-TATTTTAT
1 ACTATTTTAT
30163 ATTGAACTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 22 0.76
23 4 0.14
24 3 0.10
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.57
Consensus pattern (22 bp):
ACTATTTTATTGTTATATTGCA
Found at i:39707 original size:3 final size:3
Alignment explanation
Indices: 39699--39751 Score: 61
Period size: 3 Copynumber: 17.0 Consensus size: 3
39689 TTAATAACAT
* * *
39699 TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAG TAT TAA TAT TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA T-AA TAA
39746 TAA TAA
1 TAA TAA
39752 AAGAAATTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
3 38 0.88
4 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:40166 original size:20 final size:20
Alignment explanation
Indices: 40138--40179 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
40128 TCACCTTGGA
40138 TGGCCGCGCGTGATGGCAAT
1 TGGCCGCGCGTGATGGCAAT
*
40158 TGGCGGCGCGTGATGGCAAT
1 TGGCCGCGCGTGATGGCAAT
40178 TG
1 TG
40180 ATGGGCGTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.21, G:0.43, T:0.21
Consensus pattern (20 bp):
TGGCCGCGCGTGATGGCAAT
Found at i:40955 original size:29 final size:28
Alignment explanation
Indices: 40894--41020 Score: 98
Period size: 29 Copynumber: 4.4 Consensus size: 28
40884 TAGAAATTAT
* *
40894 ATTTTGACCCTCAAACTTCTCTAAAATTCC
1 ATTTTTACCCTCGAACTT-TC-AAAATTCC
* * *
40924 ATTTTTATCCT-GATCTTTTCATAAATTAC
1 ATTTTTACCCTCGAAC-TTTCA-AAATTCC
40953 ATTTTTACCCTCGAACTTTCAAAATTCC
1 ATTTTTACCCTCGAACTTTCAAAATTCC
* *
40981 ATTTTTGA-CCTCAAAACTTCCAAAAATTACC
1 ATTTTT-ACCCTC-GAACTTTC-AAAATT-CC
41012 A-TTTTACCC
1 ATTTTTACCC
41021 CCAAATGTCT
Statistics
Matches: 79, Mismatches: 10, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
28 17 0.22
29 33 0.42
30 26 0.33
31 3 0.04
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (28 bp):
ATTTTTACCCTCGAACTTTCAAAATTCC
Found at i:41015 original size:59 final size:59
Alignment explanation
Indices: 40973--41429 Score: 570
Period size: 59 Copynumber: 7.7 Consensus size: 59
40963 TCGAACTTTC
* * * *
40973 AAAATTCCATTTTTGA-CCTCAAAACTTCCAAAAATTACCATTTTACCCCCAAATGTCTA
1 AAAATTCCATTTTTTATCC-GAAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCTA
* *
41032 AAAACTT-CATTTTTTATCCGAAACCTTCCAAAATTTACCATTTTACCCCCGGATGTCTA
1 AAAA-TTCCATTTTTTATCCGAAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCTA
* *
41091 AAAACTT-CATTTTTTATCCGAAACCTTCCAAAATTTACCATTTTACCCCCGGATGTCTA
1 AAAA-TTCCATTTTTTATCCGAAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCTA
* * * * *
41150 AAAACTCTATTTTTGATCCGAAACCTTCCAAAAATTACCATTTTATCCTCGGAA-GTCTA
1 AAAATTCCATTTTTTATCCGAAACCTTCCAAAAATTACCATTTTA-CCCCCGAATGTCTA
*
41209 AAAACTCCATTTTTTATCCTG-AACCTTCCAAAAATTACCATTTTACCCCCGAATGTCTA
1 AAAATTCCATTTTTTATCC-GAAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCTA
* * * *
41268 AAAATTCTATTTTTGATCCGAAACCTTCCAAAAATTACCATTTTATCCTCGGAA-GTCTA
1 AAAATTCCATTTTTTATCCGAAACCTTCCAAAAATTACCATTTTA-CCCCCGAATGTCTA
* *
41327 AAAACTCCATTTTTTTATCCTG-AACCTTCCAAAAATTACCATTTTACCCCCGAATGTCCA
1 AAAATTCCA-TTTTTTATCC-GAAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCTA
* * *
41387 AAAATTTCATTTTTTACCTCG-AGCCTTCCAAAAATTACCATTT
1 AAAATTCCATTTTTTATC-CGAAACCTTCCAAAAATTACCATTT
41430 CGCCCCCTAG
Statistics
Matches: 354, Mismatches: 32, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
58 8 0.02
59 284 0.80
60 61 0.17
61 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (59 bp):
AAAATTCCATTTTTTATCCGAAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCTA
Found at i:41074 original size:31 final size:31
Alignment explanation
Indices: 41039--41134 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 31
41029 CTAAAAACTT
41039 CATTTTTTATCCGAAACCTTCCAAAATTTAC
1 CATTTTTTATCCGAAACCTTCCAAAATTTAC
**** * * *
41070 CATTTTACCCCCG-GA--TGTCTAAAAACTT--
1 CATTTTTTATCCGAAACCT-TC-CAAAATTTAC
41098 CATTTTTTATCCGAAACCTTCCAAAATTTAC
1 CATTTTTTATCCGAAACCTTCCAAAATTTAC
41129 CATTTT
1 CATTTT
41135 ACCCCCGGAT
Statistics
Matches: 44, Mismatches: 14, Indels: 14
0.61 0.19 0.19
Matches are distributed among these distances:
28 10 0.23
29 9 0.20
30 9 0.20
31 16 0.36
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.39
Consensus pattern (31 bp):
CATTTTTTATCCGAAACCTTCCAAAATTTAC
Found at i:41104 original size:118 final size:119
Alignment explanation
Indices: 40973--41429 Score: 665
Period size: 118 Copynumber: 3.9 Consensus size: 119
40963 TCGAACTTTC
* * * *
40973 AAAATTCCATTTTTGA-CCTCAAAACTTCCAAAAATTACCATTTTACCCCCAAATGTCTAAAAAC
1 AAAACTCCATTTTTTATCCT-AAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCTAAAAAC
* * * * *
41037 TTC-ATTTTTTATCCGAAACCTTCCAAAATTTACCATTTTACCCCCGGATGTCTA
65 TTCTATTTTTGATCCGAAACCTTCCAAAAATTACCATTTTATCCTCGGAAGTCTA
* * * *
41091 AAAACTTCATTTTTTATCCGAAACCTTCCAAAATTTACCATTTTACCCCCGGATGTCTAAAAAC-
1 AAAACTCCATTTTTTATCCTAAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCTAAAAACT
41155 TCTATTTTTGATCCGAAACCTTCCAAAAATTACCATTTTATCCTCGGAAGTCTA
66 TCTATTTTTGATCCGAAACCTTCCAAAAATTACCATTTTATCCTCGGAAGTCTA
*
41209 AAAACTCCATTTTTTATCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCTAAAAA-T
1 AAAACTCCATTTTTTATCCTAAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCTAAAAACT
41273 TCTATTTTTGATCCGAAACCTTCCAAAAATTACCATTTTATCCTCGGAAGTCTA
66 TCTATTTTTGATCCGAAACCTTCCAAAAATTACCATTTTATCCTCGGAAGTCTA
* * *
41327 AAAACTCCATTTTTTTATCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCCAAAAAT
1 AAAACTCCA-TTTTTTATCCTAAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCTAAAAAC
* * *
41392 TTC-ATTTTTTACCTCG-AGCCTTCCAAAAATTACCATTT
65 TTCTATTTTTGATC-CGAAACCTTCCAAAAATTACCATTT
41430 CGCCCCCTAG
Statistics
Matches: 311, Mismatches: 22, Indels: 11
0.90 0.06 0.03
Matches are distributed among these distances:
117 2 0.01
118 220 0.71
119 84 0.27
120 5 0.02
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (119 bp):
AAAACTCCATTTTTTATCCTAAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCTAAAAACT
TCTATTTTTGATCCGAAACCTTCCAAAAATTACCATTTTATCCTCGGAAGTCTA
Found at i:41222 original size:177 final size:177
Alignment explanation
Indices: 40997--41429 Score: 631
Period size: 177 Copynumber: 2.4 Consensus size: 177
40987 GACCTCAAAA
*
40997 CTTCCAAAAATTACCATTTTACCCCCAAATGTCTAAAAACTTCATTTTTTATCCGAAACCTTCCA
1 CTTCCAAAAATTACCATTTTACCCCCGAATGTCTAAAAACTTCATTTTTTATCCG-AACCTTCCA
* * * *
41062 AAATTTACCATTTTACCCCCGGATGTCTAAAAACTTC-ATTTTTTATCCGAAACCTTCCAAAATT
65 AAAATTACCATTTTACCCCCGAATGTCTAAAAA-TTCTATTTTTGATCCGAAACCTTCCAAAAAT
* *
41126 TACCATTTTACCCCCGGATGTCTAAAAACTCTA-TTTTTGATCC-GAAAC
129 TACCATTTTACCCCCGGAAGTCTAAAAACTCCATTTTTTGATCCTG-AAC
* * *
41174 CTTCCAAAAATTACCATTTTATCCTCGGAA-GTCTAAAAACTCCATTTTTTATCCTGAACCTTCC
1 CTTCCAAAAATTACCATTTTA-CCCCCGAATGTCTAAAAACTTCATTTTTTATCC-GAACCTTCC
41238 AAAAATTACCATTTTACCCCCGAATGTCTAAAAATTCTATTTTTGATCCGAAACCTTCCAAAAAT
64 AAAAATTACCATTTTACCCCCGAATGTCTAAAAATTCTATTTTTGATCCGAAACCTTCCAAAAAT
* * *
41303 TACCATTTTATCCTCGGAAGTCTAAAAACTCCATTTTTTTATCCTGAAC
129 TACCATTTTACCCCCGGAAGTCTAAAAACTCCATTTTTTGATCCTGAAC
* * * *
41352 CTTCCAAAAATTACCATTTTACCCCCGAATGTCCAAAAATTTCATTTTTTACCTCGAGCCTTCCA
1 CTTCCAAAAATTACCATTTTACCCCCGAATGTCTAAAAACTTCATTTTTTATC-CGAACCTTCCA
41417 AAAATTACCATTT
65 AAAATTACCATTT
41430 CGCCCCCTAG
Statistics
Matches: 229, Mismatches: 20, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
176 3 0.01
177 144 0.63
178 80 0.35
179 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (177 bp):
CTTCCAAAAATTACCATTTTACCCCCGAATGTCTAAAAACTTCATTTTTTATCCGAACCTTCCAA
AAATTACCATTTTACCCCCGAATGTCTAAAAATTCTATTTTTGATCCGAAACCTTCCAAAAATTA
CCATTTTACCCCCGGAAGTCTAAAAACTCCATTTTTTGATCCTGAAC
Found at i:41386 original size:29 final size:29
Alignment explanation
Indices: 41235--41392 Score: 85
Period size: 29 Copynumber: 5.3 Consensus size: 29
41225 TCCTGAACCT
41235 TCCAAAAATTACCATTTTACCCCCGAATG
1 TCCAAAAATTACCATTTTACCCCCGAATG
* * ****
41264 TCTAAAAATT-CTATTTTTGATCCGAAACCT-
1 TCCAAAAATTACCATTTTACCCCCG-AA--TG
* *
41294 TCCAAAAATTACCATTTTATCCTCGGAA-G
1 TCCAAAAATTACCATTTTA-CCCCCGAATG
* * * *
41323 TCTAAAAACT-CCATTTTTTTA-TCCTGAACCT-
1 TCCAAAAATTACCA---TTTTACCCCCGAA--TG
41354 TCCAAAAATTACCATTTTACCCCCGAATG
1 TCCAAAAATTACCATTTTACCCCCGAATG
41383 TCCAAAAATT
1 TCCAAAAATT
41393 TCATTTTTTA
Statistics
Matches: 93, Mismatches: 21, Indels: 30
0.65 0.15 0.21
Matches are distributed among these distances:
28 13 0.14
29 38 0.41
30 14 0.15
31 22 0.24
32 6 0.06
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCCCGAATG
Found at i:45632 original size:30 final size:31
Alignment explanation
Indices: 45598--45664 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
45588 GTTACATTTA
*
45598 ACAAAACAATCACTCAACTT-T-GAAAATGTG
1 ACAAAACAATCACTAAACTTATCGAAAA-GTG
* *
45628 ACAAAACAGTCACTAAAGTTATCGAAAAGTG
1 ACAAAACAATCACTAAACTTATCGAAAAGTG
45659 ACAAAA
1 ACAAAA
45665 TAGTCCTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 17 0.53
31 10 0.31
32 5 0.16
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.19
Consensus pattern (31 bp):
ACAAAACAATCACTAAACTTATCGAAAAGTG
Found at i:46484 original size:30 final size:31
Alignment explanation
Indices: 46425--46491 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
46415 TAGAGGATTG
* * *
46425 TTTTGTCACTTTTTGATAACTTTAGTGACTA
1 TTTTGTCACATTTTCATAACTTAAGTGACTA
* *
46456 TTTTGTCACATTTTCA-AAGTTAAGTGACTG
1 TTTTGTCACATTTTCATAACTTAAGTGACTA
46486 TTTTGT
1 TTTTGT
46492 TAAATGTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.51
Consensus pattern (31 bp):
TTTTGTCACATTTTCATAACTTAAGTGACTA
Found at i:49430 original size:11 final size:11
Alignment explanation
Indices: 49416--49442 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
49406 TTTTACATTA
49416 TTTTTCTTTTT
1 TTTTTCTTTTT
49427 TTTTTCTTTTT
1 TTTTTCTTTTT
49438 TTTTT
1 TTTTT
49443 TTCTTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTCTTTTT
Done.