Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014596.1 Kokia drynarioides strain JFW-HI SEQ_129635, 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: 39270
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:2909 original size:96 final size:96
Alignment explanation
Indices: 2735--2926 Score: 255
Period size: 96 Copynumber: 2.0 Consensus size: 96
2725 ATTTTGGGAA
* *
2735 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCTCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAGATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
2800 GAATCGAAGAT-AAAGAAACATTGCCTCGATT
66 GAATCGAAGATAAAAG-AACATTACCTCGATT
* * * **
2831 AAGGGTATTCGATTATTTCGATTTGAAGAAATATTGCACCTAGTAAGTTAAGGCACAA-ATTTTT
1 AAGGATATTCGATTATCTCGATTTGAAGAAAGATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
2895 GAAACTCGAA-ATAAAAGAATATTACCTCGATT
66 G-AA-TCGAAGATAAAAGAACATTACCTCGATT
2927 TTAAAGTCTT
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
95 5 0.06
96 70 0.83
97 9 0.11
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAGATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAAGAACATTACCTCGATT
Found at i:3264 original size:58 final size:59
Alignment explanation
Indices: 3185--3360 Score: 155
Period size: 59 Copynumber: 3.0 Consensus size: 59
3175 ATTTTGGATT
* *
3185 TTCGAGGG-CAAAATGGTAATTTTGGGAAA-ATTCAGGGTTAAAAAGGGAATTTTTAGACA-
1 TTCGAGGGTAAAAATGG-AATTTT-GGAAAGATTCAGGGTCAAAAAGGGAATTTTTAGA-AG
* * * ** * *
3244 TTCGGGGGTAAAAA-GGAATTTTTGAAAGTTTTTGGGTCAAAAATGGAATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTGGAAAGATTCAGGGTCAAAAAGGGAATTTTTAGAAG
* ** * *
3302 TTCGAGGGTAAAAATGGAATTTTTGG-AAGTTTTGGGGTCAAAAATGGAATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAA-TTTTGGAAAGATTCAGGGTCAAAAAGGGAATTTTTAGAAG
3361 NNNNNNNNNN
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
57 5 0.05
58 41 0.41
59 45 0.45
60 9 0.09
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (59 bp):
TTCGAGGGTAAAAATGGAATTTTGGAAAGATTCAGGGTCAAAAAGGGAATTTTTAGAAG
Found at i:3294 original size:30 final size:29
Alignment explanation
Indices: 3249--3360 Score: 154
Period size: 30 Copynumber: 3.8 Consensus size: 29
3239 AGACATTCGG
* *
3249 GGGTAAAAA-GGAATTTTTGAAAGTTTTT
1 GGGTAAAAATGGAATTTTTGGAAGTTTTA
**
3277 GGGTCAAAAATGGAATTTTTGGAAGTTCGA
1 GGGT-AAAAATGGAATTTTTGGAAGTTTTA
*
3307 GGGTAAAAATGGAATTTTTGGAAGTTTTG
1 GGGTAAAAATGGAATTTTTGGAAGTTTTA
3336 GGGTCAAAAATGGAATTTTTGGAAG
1 GGGT-AAAAATGGAATTTTTGGAAG
3361 NNNNNNNNNN
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
28 4 0.05
29 31 0.42
30 39 0.53
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTTA
Found at i:3344 original size:59 final size:58
Alignment explanation
Indices: 3219--3360 Score: 205
Period size: 59 Copynumber: 2.4 Consensus size: 58
3209 GGAAAATTCA
* * * * *
3219 GGGTTAAAAAGGGAATTTTTAGACA-TTCGGGGGTAAAAAGGAATTTTTGAAAGTTTTT
1 GGGTCAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAAGGAATTTTTGAAAGTTTTG
*
3277 GGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTG
1 GGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAA-GGAATTTTTGAAAGTTTTG
3336 GGGTCAAAAATGGAATTTTTGGAAG
1 GGGTCAAAAATGGAATTTTTGGAAG
3361 NNNNNNNNNN
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
57 1 0.01
58 33 0.43
59 42 0.55
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.33
Consensus pattern (58 bp):
GGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAAGGAATTTTTGAAAGTTTTG
Found at i:3464 original size:30 final size:30
Alignment explanation
Indices: 3411--3569 Score: 177
Period size: 29 Copynumber: 5.4 Consensus size: 30
3401 NNNNNNNNNN
3411 TTTGGAAG-TTCGAGGGT-AAAAATGGAATT
1 TTTGGAAGTTTCG-GGGTCAAAAATGGAATT
*
3440 TTTGGAAGTTTTGGGGTCAAAAATGGAATT
1 TTTGGAAGTTTCGGGGTCAAAAATGGAATT
3470 TTTGGAAG-TTCGAGGGT-AAAAATGGAATT
1 TTTGGAAGTTTCG-GGGTCAAAAATGGAATT
* * * * *
3499 TTTAGAAATTTTGAGGTCAAAAATGAAATT
1 TTTGGAAGTTTCGGGGTCAAAAATGGAATT
*
3529 TTTGGAAG-TTCAGGGG-CAAAAATGTAATT
1 TTTGGAAGTTTC-GGGGTCAAAAATGGAATT
3558 TTTGGATAGTTT
1 TTTGGA-AGTTT
3570 AGGGACCTCC
Statistics
Matches: 110, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
29 56 0.51
30 52 0.47
31 2 0.02
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (30 bp):
TTTGGAAGTTTCGGGGTCAAAAATGGAATT
Found at i:3511 original size:59 final size:59
Alignment explanation
Indices: 3411--3560 Score: 230
Period size: 59 Copynumber: 2.5 Consensus size: 59
3401 NNNNNNNNNN
* * * *
3411 TTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATT
1 TTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTTGAGGTCAAAAATGAAATT
3470 TTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTTGAGGTCAAAAATGAAATT
1 TTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTTGAGGTCAAAAATGAAATT
* *
3529 TTTGGAAGTTC-AGGGGCAAAAATGTAATTTTT
1 TTTGGAAGTTCGA-GGGTAAAAATGGAATTTTT
3561 GGATAGTTTA
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
58 1 0.01
59 83 0.99
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (59 bp):
TTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTTGAGGTCAAAAATGAAATT
Found at i:4596 original size:3 final size:3
Alignment explanation
Indices: 4578--4612 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
4568 ATTAAAATAG
*
4578 TTA TTG TTA TTTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA T
4613 ACTTATGAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5318 original size:6 final size:6
Alignment explanation
Indices: 5307--5357 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
5297 TCAAATTTGA
**
5307 TTAAAT TTAAAT TTAAA- GCAAAT TTAAAT TTAAGA- -TAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT
5353 TTAAA
1 TTAAA
5358 AAAGAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 1 0.03
5 6 0.16
6 29 0.78
7 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:5331 original size:17 final size:18
Alignment explanation
Indices: 5309--5357 Score: 75
Period size: 17 Copynumber: 2.8 Consensus size: 18
5299 AAATTTGATT
5309 AAATTTAAATTTAAAG-C
1 AAATTTAAATTTAAAGAC
*
5326 AAATTTAAATTT-AAGAT
1 AAATTTAAATTTAAAGAC
5343 AAATTTAAATTTAAA
1 AAATTTAAATTTAAA
5358 AAAGAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 3 0.10
17 24 0.83
18 2 0.07
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (18 bp):
AAATTTAAATTTAAAGAC
Found at i:6210 original size:115 final size:114
Alignment explanation
Indices: 6009--6219 Score: 343
Period size: 115 Copynumber: 1.8 Consensus size: 114
5999 AATTTGATCC
* **
6009 ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGCCCTACTTCTCAGTATCTCATC
1 ACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCAACCTACTTCTCAGTATCTCATC
6074 AGGAAGCTGGGATTCGAAGATTTGCTCACATTGAGTCCTGAGTTGGTAT
66 AGGAAGCTGGGATTCGAAGATTTGCTCACATTGAGTCCTGAGTTGGTAT
* * *
6123 ACTTCTCTGTATCTCATCAAGAAGCTAACCATTTTATTTCTTCAACCTGCTTCTCAGTATCTCAT
1 ACTTCTCAGTATCTCATCAAGAAGCTAACC-TTTTATTGCTTCAACCTACTTCTCAGTATCTCAT
6188 CAGGAAGCT-GGAGTTCGAAGATTTGCTCACAT
65 CAGGAAGCTGGGA-TTCGAAGATTTGCTCACAT
6220 CAAGTGTGAA
Statistics
Matches: 89, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
114 31 0.35
115 58 0.65
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (114 bp):
ACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCAACCTACTTCTCAGTATCTCATC
AGGAAGCTGGGATTCGAAGATTTGCTCACATTGAGTCCTGAGTTGGTAT
Found at i:13100 original size:15 final size:15
Alignment explanation
Indices: 13063--13101 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
13053 TTATGTGTGC
*
13063 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
13078 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
13092 TTAATTCTTG
1 TTAATTCTTG
13102 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:16953 original size:25 final size:23
Alignment explanation
Indices: 16910--16955 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
16900 CCAGTTAGGG
16910 AATTATTGTTTAGATTTAATTCA
1 AATTATTGTTTAGATTTAATTCA
*
16933 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
16956 TGGATCCAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCA
Found at i:17372 original size:15 final size:15
Alignment explanation
Indices: 17335--17373 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
17325 TTATGTGTGC
*
17335 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
17350 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
17364 TTAATTCTTG
1 TTAATTCTTG
17374 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:24527 original size:45 final size:45
Alignment explanation
Indices: 24463--24553 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
24453 TTGATGGCAT
*
24463 ACCATCTCCGAAAGCCGAAAGGGTACTTTTGAGTTC-AGTGGAGGC
1 ACCATCTCCGAAAGCCGAAAAGGTACTTTTGAGTTCAAG-GGAGGC
*
24508 ACCATCTCCGGAAGCCGAAAAGGTACTTTTGAGTTCAAGGGAGGC
1 ACCATCTCCGAAAGCCGAAAAGGTACTTTTGAGTTCAAGGGAGGC
24553 A
1 A
24554 GAATCTCTAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 41 0.95
46 2 0.05
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.21
Consensus pattern (45 bp):
ACCATCTCCGAAAGCCGAAAAGGTACTTTTGAGTTCAAGGGAGGC
Found at i:26124 original size:45 final size:44
Alignment explanation
Indices: 25982--26107 Score: 209
Period size: 44 Copynumber: 2.8 Consensus size: 44
25972 TTGATGGCGT
25982 ACCATCTCCGGAAGCCGAAAGGGTACTTTTGAGTTCAGCGGAGGC
1 ACCATCTCCGGAAG-CGAAAGGGTACTTTTGAGTTCAGCGGAGGC
*
26027 ACCATCTCCGGACA-CCAAAGGGTACTTTTGAGTTCAGCGGAGGC
1 ACCATCTCCGGA-AGCGAAAGGGTACTTTTGAGTTCAGCGGAGGC
26071 ACCATCTCCGGAAGCTGAAAGGGTACTTTTGAGTTCA
1 ACCATCTCCGGAAGC-GAAAGGGTACTTTTGAGTTCA
26108 AGGGAGACAG
Statistics
Matches: 76, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
43 1 0.01
44 42 0.55
45 32 0.42
46 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (44 bp):
ACCATCTCCGGAAGCGAAAGGGTACTTTTGAGTTCAGCGGAGGC
Found at i:34614 original size:16 final size:17
Alignment explanation
Indices: 34593--34625 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
34583 TTTAAAGTGA
34593 GTATTTA-ATATTTTTT
1 GTATTTACATATTTTTT
34609 GTATTTACATATTTTTT
1 GTATTTACATATTTTTT
34626 AATCTCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (17 bp):
GTATTTACATATTTTTT
Found at i:35210 original size:24 final size:24
Alignment explanation
Indices: 35165--35210 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
35155 AGTTAAACTT
*
35165 TGTTTATTTGTTTCAATTAAACAC
1 TGTTTATTTGTTTCAATCAAACAC
* *
35189 TGTTTATTTGTTTGAGTCAAAC
1 TGTTTATTTGTTTCAATCAAAC
35211 TCTTATTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (24 bp):
TGTTTATTTGTTTCAATCAAACAC
Found at i:37153 original size:24 final size:24
Alignment explanation
Indices: 37126--37177 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
37116 CTTTGACTTG
37126 AACTTTGTTTAATTGTTTCAATTA
1 AACTTTGTTTAATTGTTTCAATTA
*
37150 AACTTTGTTTATTTGTTTCAATTA
1 AACTTTGTTTAATTGTTTCAATTA
37174 AACT
1 AACT
37178 ATTTATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.54
Consensus pattern (24 bp):
AACTTTGTTTAATTGTTTCAATTA
Done.