Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015297.1 Kokia drynarioides strain JFW-HI SEQ_130342, 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: 53669
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Warning! 189 characters in sequence are not A, C, G, or T
Found at i:761 original size:6 final size:6
Alignment explanation
Indices: 744--774 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
734 TGATCAAAAT
744 TGAAAG TG-AAG TGAAAG TGAAAG TGAAAG TG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TG
775 TGATTGGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.19
Consensus pattern (6 bp):
TGAAAG
Found at i:2333 original size:19 final size:17
Alignment explanation
Indices: 2295--2335 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
2285 AATTTTTTTC
*
2295 TTAATTTTAAAATATTT
1 TTAATTTTAAAAAATTT
2312 TTAATTATTAAAAAATATT
1 TTAATT-TTAAAAAAT-TT
2331 TTAAT
1 TTAAT
2336 AGTTAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 8 0.38
19 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAATTTTAAAAAATTT
Found at i:19050 original size:3 final size:3
Alignment explanation
Indices: 19042--19066 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19032 GAGTTTATAG
19042 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
19067 AACACATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:19222 original size:16 final size:16
Alignment explanation
Indices: 19201--19243 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 16
19191 CTTTGCTTTT
19201 TTTTTAACATATTTAA
1 TTTTTAACATATTTAA
19217 TTTTT---ATA-TTAA
1 TTTTTAACATATTTAA
19229 TTTTTAACATATTTA
1 TTTTTAACATATTTA
19244 GATATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
12 9 0.39
13 3 0.13
15 3 0.13
16 8 0.35
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTTAACATATTTAA
Found at i:23341 original size:3 final size:3
Alignment explanation
Indices: 23333--23373 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
23323 ATTGAAGATC
* * *
23333 TCT TCT TCT TCT TCT TCT TTT TCA TCA TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
23374 GACTAGAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:23486 original size:170 final size:170
Alignment explanation
Indices: 23204--23516 Score: 554
Period size: 170 Copynumber: 1.8 Consensus size: 170
23194 CTGGTTCAGA
*
23204 GACTAGAAAAAATAAATAATTTGAGGTGTTATGGATCTCACTATCTTTTCAAACTCATCACATTC
1 GACTAGAAAAAATAAATAATTTGAGGTGTTATGGATCTCACTATCTTTTCAAACTCACCACATTC
* *
23269 TTCTCATTATTAGAATTGTAAAAGCTTAGAAAAATAGGACCTTTGCTTGGAATAATTGAAGATCT
66 TTCTCATTATTAGAATTGTAAAAGCTTAGAAAAATAGGACCTTTGCTTAGAATAAATGAAGATCT
23334 CTTCTTCTTCTTCTTCTTTTTCATCATCTTCTTCTTCTTC
131 CTTCTTCTTCTTCTTCTTTTTCATCATCTTCTTCTTCTTC
* *
23374 GACTAGAAAAAATAAATAATTTGAGGTGTTCTGGATTTCACTATCTTTTCAAACTCACCACATTC
1 GACTAGAAAAAATAAATAATTTGAGGTGTTATGGATCTCACTATCTTTTCAAACTCACCACATTC
* * *
23439 TTCTCATTATTAGGATTGTAAAAGCTTGGAAAAATAGGATCTTTGCTTAGAATAAATGAAGATCT
66 TTCTCATTATTAGAATTGTAAAAGCTTAGAAAAATAGGACCTTTGCTTAGAATAAATGAAGATCT
23504 CTTCTTCTTCTTC
131 CTTCTTCTTCTTC
23517 GGCTAGAAAA
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
170 135 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.39
Consensus pattern (170 bp):
GACTAGAAAAAATAAATAATTTGAGGTGTTATGGATCTCACTATCTTTTCAAACTCACCACATTC
TTCTCATTATTAGAATTGTAAAAGCTTAGAAAAATAGGACCTTTGCTTAGAATAAATGAAGATCT
CTTCTTCTTCTTCTTCTTTTTCATCATCTTCTTCTTCTTC
Found at i:23618 original size:143 final size:143
Alignment explanation
Indices: 23360--23659 Score: 537
Period size: 143 Copynumber: 2.1 Consensus size: 143
23350 TTTTTCATCA
* *
23360 TCTTCTTCTTCTTCGACTAGAAAAAATAAATAATTTGAGGTGTTCTGGATTTCACTATCTTTTCA
1 TCTTCTTCTTCTTCGACTAGAAAAAATAAATAATTTGAGGTGTTATGGATCTCACTATCTTTTCA
* *
23425 AACTCACCACATTCTTCTCATTATTAGGATTGTAAAAGCTTGGAAAAATAGGATCTTTGCTTAGA
66 AACTCACCACATTCTTCTCATTATTAGAATTGTAAAAGCTTGGAAAAATAGGACCTTTGCTTAGA
23490 ATAAATGAAGATC
131 ATAAATGAAGATC
*
23503 TCTTCTTCTTCTTCGGCTAGAAAAAATAAATAATTTGAGGTGTTATGGATCTCACTATCTTTTCA
1 TCTTCTTCTTCTTCGACTAGAAAAAATAAATAATTTGAGGTGTTATGGATCTCACTATCTTTTCA
*
23568 AACTCACCACATTCTTCTCATTATTAGAATTGTAAAAGCTTGGGAAAATAGGACCTTTGCTTAGA
66 AACTCACCACATTCTTCTCATTATTAGAATTGTAAAAGCTTGGAAAAATAGGACCTTTGCTTAGA
*
23633 TTAAATGAAGATC
131 ATAAATGAAGATC
23646 TCTTCTTCTTCTTC
1 TCTTCTTCTTCTTC
23660 TTCTTCTTCT
Statistics
Matches: 150, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
143 150 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (143 bp):
TCTTCTTCTTCTTCGACTAGAAAAAATAAATAATTTGAGGTGTTATGGATCTCACTATCTTTTCA
AACTCACCACATTCTTCTCATTATTAGAATTGTAAAAGCTTGGAAAAATAGGACCTTTGCTTAGA
ATAAATGAAGATC
Found at i:23654 original size:3 final size:3
Alignment explanation
Indices: 23646--23680 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
23636 AATGAAGATC
23646 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
23681 ATTTGTCTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:23913 original size:17 final size:17
Alignment explanation
Indices: 23883--23924 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
23873 GAAACATTAC
* *
23883 ATATTTATATTAAAAAT
1 ATATTAATAGTAAAAAT
*
23900 ATATTAATAGTAAAAGT
1 ATATTAATAGTAAAAAT
23917 A-ATTAATA
1 ATATTAATA
23925 ATGAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (17 bp):
ATATTAATAGTAAAAAT
Found at i:24898 original size:35 final size:35
Alignment explanation
Indices: 24821--24942 Score: 88
Period size: 36 Copynumber: 3.4 Consensus size: 35
24811 AATTTTAATC
* *
24821 ATTAATTATAATAGATAATATATTATTACATAATAT
1 ATTAATAATAATA-ATAATATATTATTACAAAATAT
*
24857 AATAATAATAAT-ATAATATGATTATTACAAAA-ATT
1 ATTAATAATAATAATAATAT-ATTATTACAAAATA-T
* * * *
24892 ATTAATATATATTAACAATTAAATTATTTA-AAATTAT
1 ATTAATA-ATAATAATAA-TATATTA-TTACAAAATAT
* *
24929 ATTTATGATAATAA
1 ATTAATAATAATAA
24943 AATTTAATTA
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
34 8 0.12
35 18 0.26
36 20 0.29
37 16 0.24
38 6 0.09
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (35 bp):
ATTAATAATAATAATAATATATTATTACAAAATAT
Found at i:24982 original size:36 final size:35
Alignment explanation
Indices: 24908--24982 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 35
24898 ATATATTAAC
* * *
24908 AATTAAATTATTTAAAATTATATTTATGATAATAA
1 AATTAAATTATTTAAAATTATATGTATAAAAATAA
*
24943 AATTTAATTATTTATTAAATTAT-TGTATAAAAATAA
1 AATTAAATTATTTA--AAATTATATGTATAAAAATAA
24979 AATT
1 AATT
24983 GTTGACACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 13 0.38
36 14 0.41
37 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (35 bp):
AATTAAATTATTTAAAATTATATGTATAAAAATAA
Found at i:36369 original size:27 final size:25
Alignment explanation
Indices: 36339--36395 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
36329 TCAAATAACA
*
36339 TAAAAACTTTAAATTTTACACAAAAAT
1 TAAAAACATT-AATTTTACA-AAAAAT
**
36366 TAAAAACATTAATTTTTGAAAAAAT
1 TAAAAACATTAATTTTACAAAAAAT
36391 TAAAA
1 TAAAA
36396 TGATTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 11 0.41
26 7 0.26
27 9 0.33
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (25 bp):
TAAAAACATTAATTTTACAAAAAAT
Found at i:49437 original size:367 final size:367
Alignment explanation
Indices: 48670--49412 Score: 964
Period size: 367 Copynumber: 2.0 Consensus size: 367
48660 CAGCTATTTC
*
48670 CTCTGGTAAAAATTTGACATTCTCACTGAAAAAGCAGGGTCACACAGGGAAGGGGGTTGATTAAG
1 CTCTCGTAAAAATTTGACATTCTCACTGAAAAAGCAGGGTCACACAGGGAAGGGGGTTGATTAAG
48735 AAAAGGTTGTAAATAAAACCGAAATATTAACAAGTATAACATATGAACAAATTTCAAAGTCTTAA
66 AAAAGGTTGTAAATAAAACCGAAATATTAACAAGTATAACATATGAACAAATTTCAAAGTCTTAA
48800 ACTACATTATTCCCAGACATCAATAACCCAACAACAATTGTGACAGGAAGTTCCCTTCAAATCAG
131 ACTACATTATTCCCAGACATCAATAACCCAACAACAATTGTGACAGGAAGTTCCCTTCAAATCAG
*
48865 AAAACTTCTTTTGTCAACCCTGCTGGACCAGCAACACTAGCATCAAAGCGATGGCATGATGCTTT
196 AAAACTTCTTTTGTCAACCCTGCTGGACCAGCAACACAAGCATCAAAGCGATGGCATGATGCTTT
********
48930 ACAATAGAAAACTGCTTTCATTAATCAAGGACATATGCTTCCATGTTTTCCCCGTAANNNNNNNN
261 ACAATAGAAAACTGCTTTCATTAATCAAGGACATATGCTTCCATGTTTTCCCCGTAAGCATCACA
******************************************
48995 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
326 AGTATCATCAATTAACAAAAAAATGAAAACTTTACCTTTACT
*
49037 CTCTGGTAAAAATTTGACATTCTCACTGAAAAAGCAGGGTCACACAGGGAAGGGGGTTGATTAAG
1 CTCTCGTAAAAATTTGACATTCTCACTGAAAAAGCAGGGTCACACAGGGAAGGGGGTTGATTAAG
*
49102 AAAAGGTTGTAAATAAAACTGAAATATTAACAAGTATAACATATGAACAAATTTCAAAGTCTTAA
66 AAAAGGTTGTAAATAAAACCGAAATATTAACAAGTATAACATATGAACAAATTTCAAAGTCTTAA
*
49167 ACTACATTATTCCCAGACATCAATAACCCAACCACAATTGTGACAGGAAGTTCCCTTCAAATCAG
131 ACTACATTATTCCCAGACATCAATAACCCAACAACAATTGTGACAGGAAGTTCCCTTCAAATCAG
49232 AAAACTTCTTTTGTCAACCCTGCTGGACCAGCAACACAAGCATCAAAGCGATGGCATGATGCTTT
196 AAAACTTCTTTTGTCAACCCTGCTGGACCAGCAACACAAGCATCAAAGCGATGGCATGATGCTTT
49297 ACAATAGAAAACTGCTTTCATTAATCAAGGACATATGCTTCCATGTTTTCCCCGTAATATGCATC
261 ACAATAGAAAACTGCTTTCATTAATCAAGGACATATGCTTCCATGTTTTCCCCGT-A-A-GCATC
49362 ACAAGTATCATCAATTAACAAAAAAATGAAAACTTTACCTTTACT
323 ACAAGTATCATCAATTAACAAAAAAATGAAAACTTTACCTTTACT
49407 CTCTCG
1 CTCTCG
49413 ATGAATTAGT
Statistics
Matches: 319, Mismatches: 54, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
367 312 0.98
368 1 0.00
369 1 0.00
370 5 0.02
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.24
Consensus pattern (367 bp):
CTCTCGTAAAAATTTGACATTCTCACTGAAAAAGCAGGGTCACACAGGGAAGGGGGTTGATTAAG
AAAAGGTTGTAAATAAAACCGAAATATTAACAAGTATAACATATGAACAAATTTCAAAGTCTTAA
ACTACATTATTCCCAGACATCAATAACCCAACAACAATTGTGACAGGAAGTTCCCTTCAAATCAG
AAAACTTCTTTTGTCAACCCTGCTGGACCAGCAACACAAGCATCAAAGCGATGGCATGATGCTTT
ACAATAGAAAACTGCTTTCATTAATCAAGGACATATGCTTCCATGTTTTCCCCGTAAGCATCACA
AGTATCATCAATTAACAAAAAAATGAAAACTTTACCTTTACT
Found at i:49708 original size:89 final size:89
Alignment explanation
Indices: 49558--49822 Score: 410
Period size: 89 Copynumber: 3.0 Consensus size: 89
49548 TATTTTCCTT
* * *
49558 GAGAAAGGAAATACAATGTCATACTATA-TAAATCCGCTAATAAGGTCAAGATCCAATAAGAATT
1 GAGAAATGAAATACAATGTCATACTATATTCAATCCGCTAATAAGGTCAACATCCAATAAGAATT
49622 AACTTTAATAGTTTACATGTAACC
66 AACTTTAATAGTTTACATGTAACC
*
49646 GAGAAATGAAATACAATGTCATACTATATTCAATCCGTTAATAAGGTCAACATCCAATAAGAATT
1 GAGAAATGAAATACAATGTCATACTATATTCAATCCGCTAATAAGGTCAACATCCAATAAGAATT
49711 AACTTTAATAGTTTACATGTAACC
66 AACTTTAATAGTTTACATGTAACC
* * * * *
49735 GAGAAATGAAATACAATGTCCTAGTATATTCAATCTGCTAATAAGGTC-ACATCCGATAATAATT
1 GAGAAATGAAATACAATGTCATACTATATTCAATCCGCTAATAAGGTCAACATCCAATAAGAATT
*
49799 AACTGTAAT-GTTTTACATGTAACC
66 AACTTTAATAG-TTTACATGTAACC
49823 AGACATATGC
Statistics
Matches: 164, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
87 1 0.01
88 62 0.38
89 101 0.62
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (89 bp):
GAGAAATGAAATACAATGTCATACTATATTCAATCCGCTAATAAGGTCAACATCCAATAAGAATT
AACTTTAATAGTTTACATGTAACC
Found at i:52934 original size:50 final size:50
Alignment explanation
Indices: 52859--52998 Score: 253
Period size: 50 Copynumber: 2.8 Consensus size: 50
52849 AACTGGTCAG
* * *
52859 AATAAACACACAGAAAATAAGTACAATCTCTGCAAATAGACGAGTCCTTT
1 AATAAACATATAGAAAATAAGTACAATCCCTGCAAATAGACGAGTCCTTT
52909 AATAAACATATAGAAAATAAGTACAATCCCTGCAAATAGACGAGTCCTTT
1 AATAAACATATAGAAAATAAGTACAATCCCTGCAAATAGACGAGTCCTTT
52959 AATAAACATATAGAAAATAAGTACAATCCCTGCAAATAGA
1 AATAAACATATAGAAAATAAGTACAATCCCTGCAAATAGA
52999 TGTGGTATAT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 87 1.00
ACGTcount: A:0.49, C:0.18, G:0.11, T:0.22
Consensus pattern (50 bp):
AATAAACATATAGAAAATAAGTACAATCCCTGCAAATAGACGAGTCCTTT
Done.