Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002771.1 Kokia drynarioides strain JFW-HI SEQ_115096, 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: 12388
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:77 original size:11 final size:10
Alignment explanation
Indices: 59--101 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
49 TTAATGTGTA
59 TTTA-TTATT
1 TTTATTTATT
68 TTTATGTTATT
1 TTTAT-TTATT
79 TTTATTTATT
1 TTTATTTATT
*
89 TGTTATTCATT
1 T-TTATTTATT
100 TT
1 TT
102 ATGACATTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 4 0.13
10 7 0.23
11 19 0.63
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (10 bp):
TTTATTTATT
Found at i:85 original size:17 final size:19
Alignment explanation
Indices: 52--95 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
42 TTAATATTTA
52 ATGTGTATTTATTATTT-TT
1 ATGT-TATTTATTATTTATT
71 ATGTTATTT-TTATTTATT
1 ATGTTATTTATTATTTATT
89 -TGTTATT
1 ATGTTATT
96 CATTTTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 13 0.54
18 7 0.29
19 4 0.17
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.70
Consensus pattern (19 bp):
ATGTTATTTATTATTTATT
Found at i:4447 original size:58 final size:58
Alignment explanation
Indices: 4385--4514 Score: 217
Period size: 58 Copynumber: 2.2 Consensus size: 58
4375 CTCAAGAGGC
4385 AAAATGGTAATTTTGGAA-AAGTCGGGGTCAGAAACGGGATTTCTAGACATTCGAGGGT
1 AAAATGGTAATTTTGGAAGAA-TCGGGGTCAGAAACGGGATTTCTAGACATTCGAGGGT
* *
4443 AAAATGGTACTTTTGGAAGAATCGGGGTTAGAAACGGGATTTCTAGACATTCGAGGGT
1 AAAATGGTAATTTTGGAAGAATCGGGGTCAGAAACGGGATTTCTAGACATTCGAGGGT
*
4501 AAAATGGTAGTTTT
1 AAAATGGTAATTTT
4515 TAGAAAAATC
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
58 66 0.97
59 2 0.03
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (58 bp):
AAAATGGTAATTTTGGAAGAATCGGGGTCAGAAACGGGATTTCTAGACATTCGAGGGT
Found at i:4545 original size:30 final size:30
Alignment explanation
Indices: 4511--4574 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
4501 AAAATGGTAG
4511 TTTTTAGAAAAATCGAGG-TTAAAAATGAAA
1 TTTTTAGAAAAATCG-GGATTAAAAATGAAA
* *
4541 TTTTTGGAAAAATCGGGATTAAAAATGGAA
1 TTTTTAGAAAAATCGGGATTAAAAATGAAA
4571 TTTT
1 TTTT
4575 GGAAAGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (30 bp):
TTTTTAGAAAAATCGGGATTAAAAATGAAA
Found at i:4595 original size:59 final size:59
Alignment explanation
Indices: 4530--4779 Score: 251
Period size: 59 Copynumber: 4.3 Consensus size: 59
4520 AAATCGAGGT
*
4530 TAAAAATGAAATTTTTGGAAAAATCGGGATTAAAAATGGAATTTTGGAAAGTTTAGGGG
1 TAAAAATGAAATTTTTGGAAAAATCGGGATTAAAAATAGAATTTTGGAAAGTTTAGGGG
** * * * * * *
4589 TAAAAATGTGATTTTTGAAAAAAT-TGAAGTAAAAAATGGAATTTTGGAAAGTTTGGGGG
1 TAAAAATGAAATTTTTGGAAAAATCGGGA-TTAAAAATAGAATTTTGGAAAGTTTAGGGG
* * * *
4648 TAAAAAT-ATAATTTTTTGGAAAAATTGGGGTTAAAAATAAAATTTTGGAAACTTT-GTGGG
1 TAAAAATGA-AA-TTTTTGGAAAAATCGGGATTAAAAATAGAATTTTGGAAAGTTTAG-GGG
* * *
4708 T-AAAAGGTAATTTTTGGAAAAATCGAGG-TCAAAAATAGAATTTTGGAAAGTTTA-GGG
1 TAAAAATGAAATTTTTGGAAAAATCG-GGATTAAAAATAGAATTTTGGAAAGTTTAGGGG
* *
4765 TTAAAATGGAATTTT
1 TAAAAATGAAATTTT
4780 AGAAAGTTAG
Statistics
Matches: 157, Mismatches: 25, Indels: 19
0.78 0.12 0.09
Matches are distributed among these distances:
57 4 0.03
58 49 0.31
59 66 0.42
60 37 0.24
61 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.33
Consensus pattern (59 bp):
TAAAAATGAAATTTTTGGAAAAATCGGGATTAAAAATAGAATTTTGGAAAGTTTAGGGG
Found at i:4770 original size:29 final size:28
Alignment explanation
Indices: 4527--4787 Score: 123
Period size: 29 Copynumber: 8.9 Consensus size: 28
4517 GAAAAATCGA
** *
4527 GGTTAAAAAT-GAAATTTTTGGAAAAATCG
1 GGTTAAAAATAG-AA-TTTTGGAAAGTTTG
*
4556 GGATTAAAAATGGAATTTTGGAAAGTTTAG
1 GG-TTAAAAATAGAATTTTGGAAAGTTT-G
* * * * **
4586 GGGTAAAAATGTGATTTTTGAAAAAATTG
1 GGTTAAAAAT-AGAATTTTGGAAAGTTTG
* * *
4615 AAGTAAAAAATGGAATTTTGGAAAGTTTGG
1 -GGTTAAAAATAGAATTTTGGAAAGTTT-G
* * * *
4645 GGGTAAAAATATAATTTTTTGGAAAAATTGG
1 GGTTAAAAATAGAA--TTTTGG-AAAGTTTG
* *
4676 GGTTAAAAATAAAATTTTGGAAACTTTG
1 GGTTAAAAATAGAATTTTGGAAAGTTTG
* * * ** *
4704 TGGGTAAAAGGTA-ATTTTTGGAAAAATCG
1 -GGTTAAAA-ATAGAATTTTGGAAAGTTTG
*
4733 AGGTCAAAAATAGAATTTTGGAAAGTTTAG
1 -GGTTAAAAATAGAATTTTGGAAAGTTT-G
* *
4763 GGTT-AAAATGGAATTTTAGAAAGTT
1 GGTTAAAAATAGAATTTTGGAAAGTT
4788 AGAGGGTAAA
Statistics
Matches: 174, Mismatches: 45, Indels: 27
0.71 0.18 0.11
Matches are distributed among these distances:
28 27 0.16
29 86 0.49
30 36 0.21
31 20 0.11
32 5 0.03
ACGTcount: A:0.42, C:0.02, G:0.24, T:0.33
Consensus pattern (28 bp):
GGTTAAAAATAGAATTTTGGAAAGTTTG
Found at i:4797 original size:28 final size:28
Alignment explanation
Indices: 4739--4799 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
4729 ATCGAGGTCA
* *
4739 AAAATAGAATTTTGGAAAGTTTAGGGTT
1 AAAATAGAATTTTAGAAAGTTTAGGGGT
*
4767 AAAATGGAATTTTAGAAAG-TTAGAGGGT
1 AAAATAGAATTTTAGAAAGTTTAG-GGGT
4795 AAAAT
1 AAAAT
4800 TTAAGTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (28 bp):
AAAATAGAATTTTAGAAAGTTTAGGGGT
Found at i:5560 original size:3 final size:3
Alignment explanation
Indices: 5491--5542 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
5481 CAAATTTCCT
** *
5491 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ACA TTAA TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
5537 TTA TTA
1 TTA TTA
5543 ATATCAGTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:8959 original size:98 final size:96
Alignment explanation
Indices: 8671--8964 Score: 295
Period size: 96 Copynumber: 3.0 Consensus size: 96
8661 GACCAGTGAA
* * *
8671 ACACCAAATCCTATCTTCCTAAAGTTGTAGTGAAGCGGATTAAAACAAGTAGCAGATCTTAATCT
1 ACACCAAATTCTATCTTCTTAAAGTTGTAGTGAAGCGGATTAAAACAAGTAGCAGATCTCAATCT
** * *
8736 CTATTGAAGTTGCAGTGGAATGGAGTGAAGCC
66 C-CCTGAAGTTGCAGTGGAATAGAGTGAAGCT
* * * * * * * * * *
8768 ACCCCAAATTCTATATCCTTAAAGTTGCAAG-G-ATCAGAGTAAAACGAGTAGCATATATCAATC
1 ACACCAAATTCTATCTTCTTAAAGTTG-TAGTGAAGCGGATTAAAACAAGTAGCAGATCTCAATC
**
8831 TCCACTGAAGTTGTTGTGGAATAGAGTGAAGCT
65 TCC-CTGAAGTTGCAGTGGAATAGAGTGAAGCT
* * * *
8864 ACACCAAATTCTACCTTCTTGAAGTTGTAGTGAAGCGGATTAAAACTACAGTAACGGATCTCAAT
1 ACACCAAATTCTATCTTCTTAAAGTTGTAGTGAAGCGGATTAAAAC-A-AGTAGCAGATCTCAAT
* * *
8929 CTCCCTAAAATTGCAGTGGAATAGAGTGAAGTT
64 CTCCCTGAAGTTGCAGTGGAATAGAGTGAAGCT
8962 ACA
1 ACA
8965 TCACTAAATC
Statistics
Matches: 153, Mismatches: 38, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
95 2 0.01
96 73 0.48
97 33 0.22
98 29 0.19
99 16 0.10
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (96 bp):
ACACCAAATTCTATCTTCTTAAAGTTGTAGTGAAGCGGATTAAAACAAGTAGCAGATCTCAATCT
CCCTGAAGTTGCAGTGGAATAGAGTGAAGCT
Found at i:9099 original size:48 final size:48
Alignment explanation
Indices: 8970--9161 Score: 232
Period size: 48 Copynumber: 4.1 Consensus size: 48
8960 TTACATCACT
* * *
8970 AAATCTTATAC-CCTAAATCTAGAGGGGCAGATTGAAGCTACCAAATC
1 AAATCTTATACACCTAAATCCAGAGGGGCAGATTAAAGCTACCACATC
*
9017 AAATCTTAT--A-CTAAATCCAAAGGGGCAGATTAAAGCTACCACATC
1 AAATCTTATACACCTAAATCCAGAGGGGCAGATTAAAGCTACCACATC
* * * *
9062 AAATCTTATACACTTAAATCCAGAGTGGCATATTAAAGCCACCACATC
1 AAATCTTATACACCTAAATCCAGAGGGGCAGATTAAAGCTACCACATC
* * * *
9110 CAATCTTATACCCCTAAATCCA-AGGGGCAGATTGAAGCTACCATATC
1 AAATCTTATACACCTAAATCCAGAGGGGCAGATTAAAGCTACCACATC
*
9157 CAATC
1 AAATC
9162 CAAAGGGGTA
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
45 40 0.32
47 35 0.28
48 49 0.40
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23
Consensus pattern (48 bp):
AAATCTTATACACCTAAATCCAGAGGGGCAGATTAAAGCTACCACATC
Found at i:9191 original size:33 final size:32
Alignment explanation
Indices: 9126--9193 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
9116 TATACCCCTA
*
9126 AATCCAAGGGGCAGATTGAAGCTACCATATCC
1 AATCCAAGGGGCAGATTGAAGCTACCACATCC
* **
9158 AATCCAAAGGGGTAGATTGAAGCTACTGCATCC
1 AATCC-AAGGGGCAGATTGAAGCTACCACATCC
9191 AAT
1 AAT
9194 ATTATACGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 5 0.16
33 26 0.84
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (32 bp):
AATCCAAGGGGCAGATTGAAGCTACCACATCC
Found at i:9247 original size:48 final size:47
Alignment explanation
Indices: 9195--9351 Score: 122
Period size: 48 Copynumber: 3.3 Consensus size: 47
9185 GCATCCAATA
* *
9195 TTATACGCCTAAATTTAGAGGGACAGATTGAAGCCACCATATCTAATC
1 TTATAC-CCTAAATTAAGAGGGACAGATTGAAGCCACCAAATCTAATC
* ** * * * *
9243 TTATACCTATAAATCCAGAGGGATAGATTAAAGCTACCACATCCT-ATC
1 TTATACC-CTAAATTAAGAGGGACAGATTGAAGCCACCAAAT-CTAATC
* * * *
9291 TTATTCCCTTAAATCTAAAAGGG-CAAATTGAAGCCACCAAATCAAATC
1 TTATACCC-TAAAT-TAAGAGGGACAGATTGAAGCCACCAAATCTAATC
9339 TT-TACCACTAAAT
1 TTATACC-CTAAAT
9352 CCAAAGAGGT
Statistics
Matches: 84, Mismatches: 19, Indels: 13
0.72 0.16 0.11
Matches are distributed among these distances:
47 10 0.12
48 67 0.80
49 7 0.08
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.27
Consensus pattern (47 bp):
TTATACCCTAAATTAAGAGGGACAGATTGAAGCCACCAAATCTAATC
Found at i:9258 original size:128 final size:129
Alignment explanation
Indices: 9030--9286 Score: 311
Period size: 128 Copynumber: 2.0 Consensus size: 129
9020 TCTTATACTA
* * *
9030 AATCCAAAGGGGCAGATTAAAGCTACCACATCAAATCTTATACACTTAAATCCAGAGTGGCATAT
1 AATCCAAAGGGGCAGATTAAAGCTACCACATCAAATATTATACACCTAAATCCAGAGTGGCAGAT
* * * *
9095 TAAAGCCACCACATCCAATCTTATACCCCTAAATCCA-AGGGGCAGATTGAAGCTACCATATCC
66 TAAAGCCACCACATCCAATCTTATACCCATAAATCCAGAGGGACAGATTAAAGCTACCACATCC
* * ** * * **
9158 AATCCAAAGGGGTAGATTGAAGCTACTGCATCCAATATTATACGCCTAAATTTAGAG-GGACAGA
1 AATCCAAAGGGGCAGATTAAAGCTACCACATCAAATATTATACACCTAAATCCAGAGTGG-CAGA
* * * * *
9222 TTGAAGCCACCATATCTAATCTTATACCTATAAATCCAGAGGGATAGATTAAAGCTACCACATCC
65 TTAAAGCCACCACATCCAATCTTATACCCATAAATCCAGAGGGACAGATTAAAGCTACCACATCC
9287 TATCTTATTC
Statistics
Matches: 107, Mismatches: 20, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
127 2 0.02
128 83 0.78
129 22 0.21
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (129 bp):
AATCCAAAGGGGCAGATTAAAGCTACCACATCAAATATTATACACCTAAATCCAGAGTGGCAGAT
TAAAGCCACCACATCCAATCTTATACCCATAAATCCAGAGGGACAGATTAAAGCTACCACATCC
Found at i:9576 original size:101 final size:99
Alignment explanation
Indices: 9372--9553 Score: 224
Period size: 101 Copynumber: 1.8 Consensus size: 99
9362 AGATTGAAAT
* * *
9372 TACAA-AACCAAATCTCATACCCCTGAAGTTGTAGTGTGTAGGATTAAAGTTACAAAACCAAATC
1 TACAATAA-CAAATCTCATACCCCTGAAGCTGTAGTGGGTAGAATTAAAGTTACAAAACCAAATC
*
9436 TTTATCTCCCTAAAGTTACAATAGAGCAAGATGAAGC
65 TTAATCTCCCTAAAGTT--AATAGAGCAAGATGAAGC
* * * * *
9473 TACAATATCAAATCTTATACCCTTGAAGCTGTAGTGGGTCGAATTAAAGTTACAATAA-CGAATC
1 TACAATAACAAATCTCATACCCCTGAAGCTGTAGTGGGTAGAATTAAAGTTACAA-AACCAAATC
*
9537 TTAATCTCCTTAAAGTT
65 TTAATCTCCCTAAAGTT
9554 GTAGTGGAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
101 66 0.96
102 3 0.04
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (99 bp):
TACAATAACAAATCTCATACCCCTGAAGCTGTAGTGGGTAGAATTAAAGTTACAAAACCAAATCT
TAATCTCCCTAAAGTTAATAGAGCAAGATGAAGC
Found at i:9607 original size:14 final size:14
Alignment explanation
Indices: 9588--9617 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
9578 ATAACAAAAT
9588 TTATCTCTTTGAAG
1 TTATCTCTTTGAAG
9602 TTATCTCTTTGAAG
1 TTATCTCTTTGAAG
9616 TT
1 TT
9618 TTCATGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (14 bp):
TTATCTCTTTGAAG
Found at i:9947 original size:7 final size:7
Alignment explanation
Indices: 9935--9959 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9925 TAAACTACTC
9935 AAACCCA
1 AAACCCA
9942 AAACCCA
1 AAACCCA
9949 AAACCCA
1 AAACCCA
9956 AAAC
1 AAAC
9960 AATTTACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (7 bp):
AAACCCA
Found at i:11584 original size:19 final size:18
Alignment explanation
Indices: 11549--11590 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
11539 TTTATGACAT
11549 TTTAATTTTTGCCATTTTA
1 TTTAATTTTTGCCA-TTTA
*
11568 TTTAATTATTTG-TATTTA
1 TTTAATT-TTTGCCATTTA
11586 TTTAA
1 TTTAA
11591 CCACTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 9 0.43
19 8 0.38
20 4 0.19
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (18 bp):
TTTAATTTTTGCCATTTA
Done.