Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012593.1 Kokia drynarioides strain JFW-HI SEQ_127602, 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: 45501
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:695 original size:26 final size:26
Alignment explanation
Indices: 659--713 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
649 CATTACCAAC
659 ACACTTGAAATATGCTTTCCTAGGTG
1 ACACTTGAAATATGCTTTCCTAGGTG
685 ACACTTGAAATATGCTTTCCTAGGTG
1 ACACTTGAAATATGCTTTCCTAGGTG
711 ACA
1 ACA
714 ATGAAACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (26 bp):
ACACTTGAAATATGCTTTCCTAGGTG
Found at i:5299 original size:3 final size:3
Alignment explanation
Indices: 5291--5349 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
5281 GTATTGGGGT
*
5291 AGA AGA AGA AGA AGAA AGA A-A AGA AGA AGA AAA AGA AG- AGA AGGA
1 AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA
*
5336 AGA AAA AGA AGA AG
1 AGA AGA AGA AGA AG
5350 CAAATGTTAC
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 4 0.08
3 38 0.79
4 6 0.12
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5317 original size:21 final size:23
Alignment explanation
Indices: 5291--5349 Score: 77
Period size: 21 Copynumber: 2.6 Consensus size: 23
5281 GTATTGGGGT
5291 AGAAGAAGAAGAAGAA-AGAA-A
1 AGAAGAAGAAGAAGAAGAGAAGA
*
5312 AGAAGAAGAAAAAGAAGAGAAGGA
1 AGAAGAAGAAGAAGAAGAGAA-GA
*
5336 AGAAAAAGAAGAAG
1 AGAAGAAGAAGAAG
5350 CAAATGTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.47
22 4 0.12
24 13 0.41
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (23 bp):
AGAAGAAGAAGAAGAAGAGAAGA
Found at i:5346 original size:18 final size:17
Alignment explanation
Indices: 5294--5347 Score: 81
Period size: 18 Copynumber: 3.1 Consensus size: 17
5284 TTGGGGTAGA
*
5294 AGAAGAAGAAGAAAGAAA
1 AGAAGAAGAA-AAAGAAG
5312 AGAAGAAGAAAAAGAAG
1 AGAAGAAGAAAAAGAAG
5329 AGAAGGAAGAAAAAGAAG
1 AGAA-GAAGAAAAAGAAG
5347 A
1 A
5348 AGCAAATGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
17 10 0.29
18 24 0.71
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
AGAAGAAGAAAAAGAAG
Found at i:6359 original size:22 final size:22
Alignment explanation
Indices: 6320--6361 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6310 GATACATATA
*
6320 TATATATATATATGTATGTTAT
1 TATATATATAAATGTATGTTAT
6342 TATATA-ATAAATGCTATGTT
1 TATATATATAAATG-TATGTT
6362 GGTTAAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (22 bp):
TATATATATAAATGTATGTTAT
Found at i:12185 original size:14 final size:14
Alignment explanation
Indices: 12166--12202 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
12156 TTGGTACTTT
12166 TGCCTTTTGTCGTA
1 TGCCTTTTGTCGTA
12180 TGCCTTTTGTCGTA
1 TGCCTTTTGTCGTA
12194 TGCCTTTTG
1 TGCCTTTTG
12203 GTCTTTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TGCCTTTTGTCGTA
Found at i:25080 original size:81 final size:81
Alignment explanation
Indices: 24945--25386 Score: 568
Period size: 81 Copynumber: 5.5 Consensus size: 81
24935 AGGCAAAGCT
*
24945 ACCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAG-CTATCCAATATTTTACCCTAACTA
1 ACCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAGTC-ATCCAATCTTTTACCCTAACTA
* * *
25009 GAGGGAAAATTGAAGAC
65 AAGGGCAGATTGAAGAC
* * * *
25026 ACCATCCAATCTCTTACCCTGACCATGGTGCATATTGAAGTCATCCAATCTTTTACCATAACCAA
1 ACCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAGTCATCCAATCTTTTACCCTAACTAA
*
25091 AAGGCAGATTGAAGAC
66 AGGGCAGATTGAAGAC
* * * * *
25107 ACCATCCAATCTTTTACCCCGACCATGAGGCAGATTGAAGTCATCCAATCTTTTACCCTTACTAG
1 ACCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAGTCATCCAATCTTTTACCCTAACTAA
* *
25172 AGGGTAGATTGAAAAC
66 AGGGCAGATTGAAGAC
* * * * *
25188 ACCATCCAATCTCTTACCCCGACCATGGGGTAGATTAAAGTCATCCAATATTTTACCCTAACAAA
1 ACCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAGTCATCCAATCTTTTACCCTAACTAA
25253 AGGGCAGATTGAAGAC
66 AGGGCAGATTGAAGAC
* * * * *
25269 ACCATCCAATCTCCTACCTTGACCATGGGGTAGATTGAAGCCATCCAATC-TTTACCGTAACTAA
1 ACCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAGTCATCCAATCTTTTACCCTAACTAA
* *
25333 TGGGCAGATTGAACAC
66 AGGGCAGATTGAAGAC
* * *
25349 ACCGT-CTATCTCTTACCC-GACCATGGGGTAGATTGAAG
1 ACCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAG
25387 ACCACTTGAT
Statistics
Matches: 315, Mismatches: 45, Indels: 5
0.86 0.12 0.01
Matches are distributed among these distances:
78 20 0.06
79 10 0.03
80 30 0.10
81 254 0.81
82 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (81 bp):
ACCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAGTCATCCAATCTTTTACCCTAACTAA
AGGGCAGATTGAAGAC
Found at i:26281 original size:41 final size:41
Alignment explanation
Indices: 26215--26616 Score: 437
Period size: 41 Copynumber: 9.8 Consensus size: 41
26205 TTACACAAAT
*
26215 GCCGCAAAAGGT-AGAGCAATAGCGGCGCTTATGGGAAAGC
1 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGC
* * * *
26255 GTCGCTAAAGGTCAGAGCAGTTGCGGCGCTTATGGGAAAGA
1 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGC
* ** * * *
26296 GCCGCTAAAGGTTAGAGCAATAGCGGTACTTTTTGAAAAGC
1 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGC
* * * * * * *
26337 ACTGCTAAAGGTTAGAGCAATAGCGGCACTTTTTGAAAAGC
1 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGC
* ** *
26378 GTCGCTAAAGGTCAGAGCAATAGCGATGCTTATGGGCAAGC
1 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGC
*
26419 GCCGCTAAAGGTCAGTGCAATAGCGGCGCTTATGGGAAAGC
1 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGC
* * *
26460 GCCGCTAAAGGTTAGAGCAATAGCGGAGCTTATGGGCAAGC
1 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGC
* * * * * * *
26501 ACCGCTAAAGATCAAAGCTATAGCGGTGCTTAAGGGCAAGC
1 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGC
* * **
26542 GCCGCTAAAGGTTAGAGCAATAGCGACGCTTATGTAAAAGC
1 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGC
* * *
26583 GCCGCTAAAAGTCAAAGCAGTAGCGGCGCTTATG
1 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATG
26617 AAAGGTCAAA
Statistics
Matches: 300, Mismatches: 61, Indels: 1
0.83 0.17 0.00
Matches are distributed among these distances:
40 10 0.03
41 290 0.97
ACGTcount: A:0.31, C:0.20, G:0.31, T:0.19
Consensus pattern (41 bp):
GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGC
Found at i:26663 original size:28 final size:28
Alignment explanation
Indices: 26632--26689 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
26622 TCAAAGCAAT
26632 AGTGATGCTTTTGGGAAAGCACCGCTAA
1 AGTGATGCTTTTGGGAAAGCACCGCTAA
26660 AGTGATGCTTTTGGGAAAGCACCGCTAA
1 AGTGATGCTTTTGGGAAAGCACCGCTAA
26688 AG
1 AG
26690 GTCAGAGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (28 bp):
AGTGATGCTTTTGGGAAAGCACCGCTAA
Found at i:27083 original size:21 final size:22
Alignment explanation
Indices: 27058--27104 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
27048 TGAATGTTTC
*
27058 AAAATTC-AAATTTAAACTAAA
1 AAAATTCAAAATTTAAACGAAA
*
27079 AAAA-TCAAAATTTAAAGGAAA
1 AAAATTCAAAATTTAAACGAAA
27100 AAAAT
1 AAAAT
27105 GGTCGTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.23
Consensus pattern (22 bp):
AAAATTCAAAATTTAAACGAAA
Found at i:30985 original size:27 final size:27
Alignment explanation
Indices: 30947--31000 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
30937 TACATTGCCC
30947 ATGCTTTACTGTGCATAAGGTGTTTTT
1 ATGCTTTACTGTGCATAAGGTGTTTTT
* *
30974 ATGCTTTACTGTGTATAAGTTGTTTTT
1 ATGCTTTACTGTGCATAAGGTGTTTTT
31001 CATCAAGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.09, G:0.20, T:0.52
Consensus pattern (27 bp):
ATGCTTTACTGTGCATAAGGTGTTTTT
Found at i:32201 original size:42 final size:42
Alignment explanation
Indices: 32154--32411 Score: 329
Period size: 42 Copynumber: 6.1 Consensus size: 42
32144 TGTTAGTGGT
* * *
32154 GTTTGTGGGAAAAACGCCGCT-AAGACCATGTTCATCAGCGGC
1 GTTTGT-GGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
* *
32196 GTTTGTGGAAAAGTGCCACTAAAGACCATGTTCTTTAGCGGC
1 GTTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
* * *
32238 GTTTATGGTATAAGCGCCGCTAAAGAACATGTTCTTTAGCGGC
1 GTTTGTGG-AAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
* **
32281 ATTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGTAGC
1 GTTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
* * * *
32323 GTTTATGAGATAAGCGTCGCTAAAGACCATGTTCTTTAACGGC
1 GTTTGTG-GAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
* *
32366 ATTTGTGGAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGC
1 GTTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
32408 GTTT
1 GTTT
32412 ATCAGATAAA
Statistics
Matches: 183, Mismatches: 30, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
41 11 0.06
42 101 0.55
43 71 0.39
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (42 bp):
GTTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
Found at i:32270 original size:43 final size:42
Alignment explanation
Indices: 32161--32450 Score: 323
Period size: 43 Copynumber: 6.9 Consensus size: 42
32151 GGTGTTTGTG
* * * *
32161 GGAAAAACGCCGCT-AAGACCATGTTCATCAGCGGCGTTTGT
1 GGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTAT
* *
32202 GGAAAAGTGCCACTAAAGACCATGTTCTTTAGCGGCGTTTAT
1 GGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTAT
* * * *
32244 GGTATAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCATTTGT
1 GG-AAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTAT
**
32287 GGAAAAGCGCCGCTAAAGACCATGTTCTTTAGTAGCGTTTAT
1 GGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTAT
* * * * *
32329 GAGATAAGCGTCGCTAAAGACCATGTTCTTTAACGGCATTTGT
1 G-GAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTAT
*
32372 GGAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTAT
1 GGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTAT
* * * * *
32414 CAGATAAA-TGCTGCTAAAGATCATGTTCTATAGCGGC
1 -GGA-AAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
32451 TTTTTTCCTC
Statistics
Matches: 208, Mismatches: 36, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
41 11 0.05
42 96 0.46
43 98 0.47
44 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (42 bp):
GGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTAT
Found at i:32325 original size:85 final size:84
Alignment explanation
Indices: 32168--32450 Score: 379
Period size: 85 Copynumber: 3.3 Consensus size: 84
32158 GTGGGAAAAA
* * * * *
32168 CGCCGCT-AAGACCATGTTCATCAGCGGCGTTTGTGGAAAAGTGCCACTAAAGACCATGTTCTTT
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCATTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTTT
32232 AGCGGCGTTTATGGTATAAG
66 AGCGGCGTTTATGG-ATAAG
*
32252 CGCCGCTAAAGAACATGTTCTTTAGCGGCATTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTTT
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCATTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTTT
**
32317 AGTAGCGTTTATGAGATAAG
66 AGCGGCGTTTATG-GATAAG
* * *
32337 CGTCGCTAAAGACCATGTTCTTTAACGGCATTTGTGGAAAAGCGCCGCTAAAGAACATGTTCTTT
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCATTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTTT
* *
32402 AGCGGCGTTTATCAGATAAA
66 AGCGGCGTTTAT-GGATAAG
* * * *
32422 TGCTGCTAAAGATCATGTTCTATAGCGGC
1 CGCCGCTAAAGACCATGTTCTTTAGCGGC
32451 TTTTTTCCTC
Statistics
Matches: 174, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
84 7 0.04
85 166 0.95
86 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.28
Consensus pattern (84 bp):
CGCCGCTAAAGACCATGTTCTTTAGCGGCATTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTTT
AGCGGCGTTTATGGATAAG
Found at i:43669 original size:13 final size:14
Alignment explanation
Indices: 43640--43669 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43630 TTCAATACAT
43640 TGACATTTAACCTC
1 TGACATTTAACCTC
43654 TGACATTTAA-CTC
1 TGACATTTAACCTC
43667 TGA
1 TGA
43670 TTGTGTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:45410 original size:3 final size:3
Alignment explanation
Indices: 45402--45471 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
45392 AGGAAATAAT
45402 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
45450 TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
45472 GTTAGTGGAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Done.