Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011836.1 Kokia drynarioides strain JFW-HI SEQ_126832, 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: 501934
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 9 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:411245 original size:16 final size:16
Alignment explanation
Indices: 411208--411245 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
411198 CAAAAAGATT
411208 ACATATATTATTTTAA
1 ACATATATTATTTTAA
*
411224 AAATATATTATGTTT-A
1 ACATATATTAT-TTTAA
411240 ACATAT
1 ACATAT
411246 GCTTATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (16 bp):
ACATATATTATTTTAA
Found at i:412007 original size:16 final size:16
Alignment explanation
Indices: 411985--412021 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
411975 AGTTTAATAT
411985 AATATAAT-ATAATTA
1 AATATAATCATAATTA
412000 ATATATAATCATAATTA
1 A-ATATAATCATAATTA
412017 AATAT
1 AATAT
412022 TTTTATACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 11 0.55
17 8 0.40
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATAATCATAATTA
Found at i:415907 original size:2 final size:2
Alignment explanation
Indices: 415902--415927 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
415892 CATACACACG
415902 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
415928 CTAAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:430330 original size:19 final size:20
Alignment explanation
Indices: 430294--430341 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
430284 GTTAGTTGCA
430294 TGCATTTATTTTAATTGTCAT-
1 TGCATTT-TTTTAATTGTC-TC
*
430315 TGCATTTTTTT-CTTGTCTC
1 TGCATTTTTTTAATTGTCTC
430334 TGCATTTT
1 TGCATTTT
430342 ATTTGCTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 1 0.04
19 13 0.52
20 4 0.16
21 7 0.28
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.60
Consensus pattern (20 bp):
TGCATTTTTTTAATTGTCTC
Found at i:435296 original size:3 final size:3
Alignment explanation
Indices: 435250--435285 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
435240 CTATGCTTTA
435250 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
435286 GTTGATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:442269 original size:3 final size:3
Alignment explanation
Indices: 442223--442258 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
442213 CGATGCTTTA
442223 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
442259 GTTGATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:449279 original size:14 final size:14
Alignment explanation
Indices: 449260--449286 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
449250 TTTGTTATTT
449260 ACATATTTTGGTTA
1 ACATATTTTGGTTA
449274 ACATATTTTGGTT
1 ACATATTTTGGTT
449287 TAGGGTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (14 bp):
ACATATTTTGGTTA
Found at i:449413 original size:30 final size:31
Alignment explanation
Indices: 449344--449416 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
449334 AAATTGTTAA
* * *
449344 TTAGTGATTGTTTTGTCACTTTTTGATAACG
1 TTAGTGACTGTTTTGTCACATTTTCATAACG
*
449375 TTAGTGACTGTTTTGTCGCATTTTCA-AA-G
1 TTAGTGACTGTTTTGTCACATTTTCATAACG
449404 TTAAGTGACTGTT
1 TT-AGTGACTGTT
449417 GTGTTAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 3 0.08
30 12 0.32
31 22 0.59
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.48
Consensus pattern (31 bp):
TTAGTGACTGTTTTGTCACATTTTCATAACG
Found at i:461689 original size:19 final size:20
Alignment explanation
Indices: 461640--461689 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
461630 CGTTGAAATA
*
461640 GTACCAACATGATGGCTGGG
1 GTACCGACATGATGGCTGGG
*
461660 GTACCGACATGATGGTTGGG
1 GTACCGACATGATGGCTGGG
*
461680 TTACCG-CATG
1 GTACCGACATG
461690 TGTTGCGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (20 bp):
GTACCGACATGATGGCTGGG
Found at i:470258 original size:24 final size:25
Alignment explanation
Indices: 470207--470256 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
470197 AAATCAATCC
470207 ACAAGGGAAAATTTTTTGAAGCAAA
1 ACAAGGGAAAATTTTTTGAAGCAAA
470232 ACAAGGGAAAATTTTTTGAAGCAAA
1 ACAAGGGAAAATTTTTTGAAGCAAA
470257 CACCTTCTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (25 bp):
ACAAGGGAAAATTTTTTGAAGCAAA
Found at i:479186 original size:64 final size:65
Alignment explanation
Indices: 479080--479208 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 65
479070 TCGATCCAAA
479080 TATTGTGGATTACAGAATGGAAAAACCCATTAAGGTTGCTGTAACTTGTTAACAAAGCTAGAAGG
1 TATTGTGGATTACAGAATGGAAAAACCCATTAAGGTTGCTGTAACTTGTTAACAAAGCTAGAAGG
479145 TATT-TGGATTACAGAATGGAAAAACCCATTAAGGTTGCTGTAACTTGTTAACAAAGCTAGAAGG
1 TATTGTGGATTACAGAATGGAAAAACCCATTAAGGTTGCTGTAACTTGTTAACAAAGCTAGAAGG
479209 ATATCTCAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
64 60 0.94
65 4 0.06
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.28
Consensus pattern (65 bp):
TATTGTGGATTACAGAATGGAAAAACCCATTAAGGTTGCTGTAACTTGTTAACAAAGCTAGAAGG
Found at i:481885 original size:149 final size:149
Alignment explanation
Indices: 481694--481993 Score: 487
Period size: 147 Copynumber: 2.0 Consensus size: 149
481684 AAAAACGTAG
* *
481694 AGGGCTATAAATTATCAAATTTTAGTAGAGGGACTAAACATGCAAAAAAAACATAAAATAGGGAC
1 AGGGCTATAAATGATCAAATTATAGTAGAGGGACTAAACATGC-AAAAAAA-ATAAAATAGGGAC
*
481759 CTCTAAAATTAGACCTATTGATAGTAAAAAAAGATGATAATTCCT-AA-AAGTACGCTCCCCAAC
64 CTCTAAAATTAGACCTATTGATAGTAAAAAAAGATGATAATTCCTAAAGAAGTACGCTCCCCAAA
*
481822 TAGTAGAATATGGCCATGGTT
129 TAGTAGAATATAGCCATGGTT
481843 AGGGCTATAAATGATCAAATTATAGTAGAGGGACTAAACATGCAAAAAAAATAAAATAGGGACCT
1 AGGGCTATAAATGATCAAATTATAGTAGAGGGACTAAACATGCAAAAAAAATAAAATAGGGACCT
* * * *
481908 CTAAAATTAGACCTATTGATAGTCAAAAAAGATGATAATTCTTAAAAGAAGTATGCTGCCCAAAT
66 CTAAAATTAGACCTATTGATAGTAAAAAAAGATGATAATTCCT-AAAGAAGTACGCTCCCCAAAT
481973 AGTAGAATATAGCCATGGTT
130 AGTAGAATATAGCCATGGTT
481993 A
1 A
481994 AAACTAATAA
Statistics
Matches: 140, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
147 56 0.40
148 7 0.05
149 43 0.31
150 34 0.24
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (149 bp):
AGGGCTATAAATGATCAAATTATAGTAGAGGGACTAAACATGCAAAAAAAATAAAATAGGGACCT
CTAAAATTAGACCTATTGATAGTAAAAAAAGATGATAATTCCTAAAGAAGTACGCTCCCCAAATA
GTAGAATATAGCCATGGTT
Found at i:485250 original size:30 final size:28
Alignment explanation
Indices: 485174--485251 Score: 102
Period size: 28 Copynumber: 2.7 Consensus size: 28
485164 GTTGAAAATT
*
485174 AAAATAATATAATATTTTTATATTTAAA
1 AAAATAATATAATAATTTTATATTTAAA
* *
485202 AAAATTATATAATTATTTTATATTTCAAA
1 AAAATAATATAATAATTTTATATTT-AAA
*
485231 AAAATAATTTTAATAATTTTA
1 AAAATAA-TATAATAATTTTA
485252 AAATTATTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 22 0.52
29 9 0.21
30 11 0.26
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (28 bp):
AAAATAATATAATAATTTTATATTTAAA
Found at i:489228 original size:10 final size:10
Alignment explanation
Indices: 489213--489248 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
489203 GTTAATCTAA
489213 AAATAAAATG
1 AAATAAAATG
489223 AAATAAAAT-
1 AAATAAAATG
*
489232 AAATAAAGTG
1 AAATAAAATG
489242 AAATAAA
1 AAATAAA
489249 TCTTGTTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (10 bp):
AAATAAAATG
Found at i:497467 original size:16 final size:14
Alignment explanation
Indices: 497448--497490 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 14
497438 TTTTAATGAA
497448 TTTATTATTATTTAGT
1 TTTATT-TTATTTA-T
497464 TTTATTTTATTTTAT
1 TTTATTTTA-TTTAT
497479 TTTATTGTTATT
1 TTTATT-TTATT
497491 GTTCAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:497473 original size:5 final size:5
Alignment explanation
Indices: 497448--497509 Score: 54
Period size: 5 Copynumber: 11.4 Consensus size: 5
497438 TTTTAATGAA
497448 TTTAT TATTA- TTTAGT TTTAT TTTAT TTTAT TTTAT TGTTAT TGTTCAAT
1 TTTAT T-TTAT TTTA-T TTTAT TTTAT TTTAT TTTAT T-TTAT T-TT--AT
*
497498 TTTGT TTTAT TT
1 TTTAT TTTAT TT
497510 CTTGTTTTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
4 3 0.06
5 26 0.53
6 15 0.31
7 2 0.04
8 3 0.06
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:499269 original size:24 final size:21
Alignment explanation
Indices: 499221--499273 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
499211 ACTTGCTGTT
*
499221 GAGGAGGAAGTAAATGTTGGC
1 GAGGAGGAAGTAAATGTTGAC
499242 GAGGAGGAAGTAAATGTTGAC
1 GAGGAGGAAGTAAATGTTGAC
*
499263 AAGGAGGAAGT
1 GAGGAGGAAGT
499274 CCTTGTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.04, G:0.42, T:0.17
Consensus pattern (21 bp):
GAGGAGGAAGTAAATGTTGAC
Found at i:499593 original size:15 final size:15
Alignment explanation
Indices: 499573--499636 Score: 74
Period size: 15 Copynumber: 4.0 Consensus size: 15
499563 GTGCTTTTGT
499573 AAATAGTGGTGTTGA
1 AAATAGTGGTGTTGA
*
499588 AAATAGTGGTTTTGA
1 AAATAGTGGTGTTGA
499603 AAATTTTTAGTGGTGTTGA
1 AAA----TAGTGGTGTTGA
*
499622 AAATAGTGGTTTTGA
1 AAATAGTGGTGTTGA
499637 GACCACAGCT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
15 28 0.67
19 14 0.33
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (15 bp):
AAATAGTGGTGTTGA
Found at i:501066 original size:24 final size:24
Alignment explanation
Indices: 501030--501104 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
501020 GTATACTGGT
*
501030 TAACCATTTTGGGCTCATAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
*
501054 TAACCATTCTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
* *
501078 TAATCA-TCTTGGGCTCATGAGAGC
1 TAACCATTC-TGGGCTCATAAGAGC
501102 TAA
1 TAA
501105 TGTTTCTACA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 2 0.04
24 43 0.96
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (24 bp):
TAACCATTCTGGGCTCATAAGAGC
Found at i:501261 original size:23 final size:23
Alignment explanation
Indices: 501219--501273 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
501209 TCCGCATAGA
501219 GCCTTTGT-G-ACATTCTGTTTG
1 GCCTTTGTGGCACATTCTGTTTG
501240 GCCTTTGTGGCACATT-TAGTTTG
1 GCCTTTGTGGCACATTCT-GTTTG
501263 GCCTTTGTGGC
1 GCCTTTGTGGC
501274 GTATTCTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 8 0.26
22 2 0.06
23 21 0.68
ACGTcount: A:0.09, C:0.20, G:0.27, T:0.44
Consensus pattern (23 bp):
GCCTTTGTGGCACATTCTGTTTG
Found at i:501285 original size:23 final size:23
Alignment explanation
Indices: 501219--501286 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
501209 TCCGCATAGA
*
501219 GCCTTTGT-G-ACATTCTGTTTG
1 GCCTTTGTGGCACATTCTATTTG
501240 GCCTTTGTGGCACATT-TAGTTTG
1 GCCTTTGTGGCACATTCTA-TTTG
**
501263 GCCTTTGTGGCGTATTCTATTTG
1 GCCTTTGTGGCACATTCTATTTG
501286 G
1 G
501287 TTTATATGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 8 0.20
22 2 0.05
23 28 0.70
24 2 0.05
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.46
Consensus pattern (23 bp):
GCCTTTGTGGCACATTCTATTTG
Found at i:501906 original size:20 final size:21
Alignment explanation
Indices: 501870--501920 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
501860 ATTGGTATGG
*
501870 TTTATATTAAGTGTAAATA-GA
1 TTTA-ATTAAGTGTAAAAATGA
501891 TTTAATTAAGAT-TAAAAATGA
1 TTTAATTAAG-TGTAAAAATGA
501912 -TTAATTAAG
1 TTTAATTAAG
501921 GCTTAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (21 bp):
TTTAATTAAGTGTAAAAATGA
Done.