Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001290.1 Kokia drynarioides strain JFW-HI SEQ_112683, 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: 113338
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 124 characters in sequence are not A, C, G, or T
Found at i:9051 original size:18 final size:18
Alignment explanation
Indices: 9007--9048 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
8997 TTATTTTTTT
*
9007 TATAT-AATTTTTAAAAA
1 TATATAAATATTTAAAAA
9024 TATATAAATATTTAAAAA
1 TATATAAATATTTAAAAA
9042 TAT-TAAA
1 TATATAAA
9049 ATAAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATATAAATATTTAAAAA
Found at i:14114 original size:51 final size:51
Alignment explanation
Indices: 14058--14160 Score: 129
Period size: 51 Copynumber: 2.0 Consensus size: 51
14048 AAACCCCATT
* * * *
14058 GGATTAA-CAAACTCCATTTCGTAATCGTAC-TTTGGATGAGAAATCGGATCC
1 GGATTAACCAAAC-CCAATTCATAATCATACGTTT-GACGAGAAATCGGATCC
*
14109 GGATTAACCAAGCCCAATTCATAATCATACGTTTGACGAGAAATCGGATCC
1 GGATTAACCAAACCCAATTCATAATCATACGTTTGACGAGAAATCGGATCC
14160 G
1 G
14161 AAAGAGTTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
51 38 0.84
52 7 0.16
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (51 bp):
GGATTAACCAAACCCAATTCATAATCATACGTTTGACGAGAAATCGGATCC
Found at i:14447 original size:20 final size:20
Alignment explanation
Indices: 14401--14448 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
14391 CGTCGGAACC
**
14401 CTAATTTTGTTGGTGTTGAAA
1 CTAA-TTTGTTGGTACTGAAA
* *
14422 CCAATTTGTTGGTACTGAGA
1 CTAATTTGTTGGTACTGAAA
14442 CTAATTT
1 CTAATTT
14449 CCATGGACAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (20 bp):
CTAATTTGTTGGTACTGAAA
Found at i:25542 original size:18 final size:19
Alignment explanation
Indices: 25521--25570 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
25511 TTAACTCGAA
25521 TTTTATAATTTTT-ATAAT
1 TTTTATAATTTTTAATAAT
25539 TTTTATAAATTTTTTAATAAT
1 TTTTAT-AA-TTTTTAATAAT
25560 TTATT-TAATTT
1 TT-TTATAATTT
25571 AAATTTCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
18 6 0.21
19 5 0.18
20 7 0.25
21 8 0.29
22 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTATAATTTTTAATAAT
Found at i:25549 original size:10 final size:9
Alignment explanation
Indices: 25521--25570 Score: 57
Period size: 9 Copynumber: 5.2 Consensus size: 9
25511 TTAACTCGAA
25521 TTTTATAAT
1 TTTTATAAT
25530 TTTTATAAT
1 TTTTATAAT
25539 TTTTATAAATT
1 TTTTAT-AA-T
25550 TTTTAATAAT
1 TTTT-ATAAT
25560 TTATT-TAAT
1 TT-TTATAAT
25569 TT
1 TT
25571 AAATTTCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
9 21 0.57
10 5 0.14
11 9 0.24
12 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Found at i:30511 original size:35 final size:35
Alignment explanation
Indices: 30469--30538 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
30459 TTTATATAGC
30469 TTTTCTTGTTTGATACATTGTCTTTTCCTTTCTTT
1 TTTTCTTGTTTGATACATTGTCTTTTCCTTTCTTT
30504 TTTTCTTGTTTGATACATTGTCTTTTCCTTTCTTT
1 TTTTCTTGTTTGATACATTGTCTTTTCCTTTCTTT
30539 CCTTTTGCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.09, C:0.17, G:0.09, T:0.66
Consensus pattern (35 bp):
TTTTCTTGTTTGATACATTGTCTTTTCCTTTCTTT
Found at i:35442 original size:30 final size:30
Alignment explanation
Indices: 35407--35466 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
35397 TACAAGTTAA
35407 AATAATTT-TGATTACAGAGACTTATTTTTT
1 AATAATTTCT-ATTACAGAGACTTATTTTTT
* * *
35437 AATAATTTCTTTTACAGAGATTTCTTTTTT
1 AATAATTTCTATTACAGAGACTTATTTTTT
35467 CAAGCTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.53
Consensus pattern (30 bp):
AATAATTTCTATTACAGAGACTTATTTTTT
Found at i:37579 original size:6 final size:6
Alignment explanation
Indices: 37568--37636 Score: 63
Period size: 6 Copynumber: 11.5 Consensus size: 6
37558 AATGATTAAG
* *
37568 TTAAAT TTAAAT TTAAAT TT--A- TTAACAG TTAAAT TTAAATT TATAAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAA-AT TTAAAT TTAAA-T T-TAAAT
*
37616 ATAAAT TTAAAT TTAAAT TTA
1 TTAAAT TTAAAT TTAAAT TTA
37637 TTAACAGTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
6 39 0.75
7 6 0.12
8 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (6 bp):
TTAAAT
Found at i:37599 original size:22 final size:22
Alignment explanation
Indices: 37574--37648 Score: 89
Period size: 22 Copynumber: 3.2 Consensus size: 22
37564 TAAGTTAAAT
37574 TTAAATTTAAATTTATTAACAG
1 TTAAATTTAAATTTATTAACAG
*
37596 TTAAATTTAAATTTATAAAAATAA-AT
1 TTAAATTTAAATTTAT-----TAACAG
37622 TTAAATTTAAATTTATTAACAG
1 TTAAATTTAAATTTATTAACAG
37644 TTAAA
1 TTAAA
37649 CACAGTAAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
21 3 0.07
22 22 0.49
26 17 0.38
27 3 0.07
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (22 bp):
TTAAATTTAAATTTATTAACAG
Found at i:41942 original size:15 final size:17
Alignment explanation
Indices: 41918--41954 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
41908 TTTTCACATT
41918 TTTTAATTTTA-TAT-A
1 TTTTAATTTTATTATAA
*
41933 TTTTAGTTTTATTATAA
1 TTTTAATTTTATTATAA
41950 TTTTA
1 TTTTA
41955 TAATTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 3 0.16
17 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTAATTTTATTATAA
Found at i:42527 original size:17 final size:17
Alignment explanation
Indices: 42496--42548 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
42486 CCCTTTTTGA
*
42496 ATTAAAATATAATTTTT
1 ATTAAAATATTATTTTT
***
42513 ATTATTTTATTATTTTT
1 ATTAAAATATTATTTTT
42530 ATTAAAATATTATTTTT
1 ATTAAAATATTATTTTT
42547 AT
1 AT
42549 ATGTGATATC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTAAAATATTATTTTT
Found at i:57017 original size:50 final size:52
Alignment explanation
Indices: 56943--57046 Score: 149
Period size: 50 Copynumber: 2.0 Consensus size: 52
56933 ATCGTATAGG
*
56943 AGTAAATAGGGTCAAAGTTGTC-TTTTTACTTTATGA-TTTTTATTCAATAT
1 AGTAAATAGGGTCAAAGTTATCTTTTTTACTTTATGATTTTTTATTCAATAT
* * *
56993 AGTAAATAGGGTCAAAGTTATCTTTTTTTGCTTTGTTATTTTTTATTCAATAT
1 AGTAAATAGGGTCAAAGTTATC-TTTTTTACTTTATGATTTTTTATTCAATAT
57046 A
1 A
57047 TCCAATTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
50 21 0.45
52 11 0.23
53 15 0.32
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (52 bp):
AGTAAATAGGGTCAAAGTTATCTTTTTTACTTTATGATTTTTTATTCAATAT
Found at i:90814 original size:6 final size:6
Alignment explanation
Indices: 90803--90849 Score: 78
Period size: 6 Copynumber: 8.0 Consensus size: 6
90793 TTCCTTCACG
*
90803 TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC TTT-CC TTTCTC TTTCCC
1 TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC
90850 GTTGTTTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (6 bp):
TTTCCC
Found at i:90816 original size:18 final size:17
Alignment explanation
Indices: 90803--90849 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
90793 TTCCTTCACG
90803 TTTCCCTTTCCCTTTCCC
1 TTTCCCTTTCCC-TTCCC
*
90821 TTTCCCTTTCCCTTTCC
1 TTTCCCTTTCCCTTCCC
*
90838 TTTCTCTTTCCC
1 TTTCCCTTTCCC
90850 GTTGTTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTCCCTTTCCCTTCCC
Found at i:106259 original size:15 final size:15
Alignment explanation
Indices: 106239--106270 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
106229 TCGTTGTCGT
106239 TGCTGGTACTGGTGA
1 TGCTGGTACTGGTGA
*
106254 TGCTGGTGCTGGTGA
1 TGCTGGTACTGGTGA
106269 TG
1 TG
106271 GCGACGGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.44, T:0.34
Consensus pattern (15 bp):
TGCTGGTACTGGTGA
Found at i:106481 original size:27 final size:27
Alignment explanation
Indices: 106451--106507 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
106441 GCTACCGATG
*
106451 GTGATGGTGTCGTTGTAGCTGCTAATT
1 GTGATGGTGTCGTTGTAGCCGCTAATT
*
106478 GTGATGGTGTCGTTGTAGCCGCTGATT
1 GTGATGGTGTCGTTGTAGCCGCTAATT
106505 GTG
1 GTG
106508 TTGGAGCTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.12, C:0.12, G:0.37, T:0.39
Consensus pattern (27 bp):
GTGATGGTGTCGTTGTAGCCGCTAATT
Found at i:106545 original size:18 final size:18
Alignment explanation
Indices: 106489--106546 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
106479 TGATGGTGTC
* *
106489 GTTGTAGCCGCTGATTGT
1 GTTGTAGCTGATGATTGT
* **
106507 GTTGGAGCTGGCG-TTGCT
1 GTTGTAGCTGATGATTG-T
106525 GTTGTAGCTGATGATTGT
1 GTTGTAGCTGATGATTGT
106543 GTTG
1 GTTG
106547 GTACTAGTGC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
17 3 0.10
18 25 0.81
19 3 0.10
ACGTcount: A:0.10, C:0.12, G:0.38, T:0.40
Consensus pattern (18 bp):
GTTGTAGCTGATGATTGT
Found at i:106734 original size:33 final size:37
Alignment explanation
Indices: 106627--106793 Score: 111
Period size: 39 Copynumber: 4.6 Consensus size: 37
106617 TGACGACGAC
*
106627 GATAATAGTGTCGTTATAGCCGCTG-AT-TG-T-GAT
1 GATAATAGTGTCGTTGTAGCCGCTGCATATGATGGAT
* * * * *
106660 GATGATTGTGTTGGTGCT-GCTGCTGCATATGATGGCGAT
1 GATAATAGTGTCGTTG-TAGCCGCTGCATATGAT-G-GAT
106699 GATAATAGTGTCGTTGTAGCCGCTG-AT-TG-T-GAT
1 GATAATAGTGTCGTTGTAGCCGCTGCATATGATGGAT
* * * * *
106732 GATGATTGTGTTGGTGCT-GCTGCTGCATATGATGGCGAT
1 GATAATAGTGTCGTTG-TAGCCGCTGCATATGAT-G-GAT
106771 GATAATAGTGTCGTTGTAGCCGC
1 GATAATAGTGTCGTTGTAGCCGC
106794 CGGTTGTGCT
Statistics
Matches: 97, Mismatches: 21, Indels: 26
0.67 0.15 0.18
Matches are distributed among these distances:
33 38 0.39
34 6 0.06
35 4 0.04
36 3 0.03
37 2 0.02
38 4 0.04
39 40 0.41
ACGTcount: A:0.19, C:0.13, G:0.32, T:0.35
Consensus pattern (37 bp):
GATAATAGTGTCGTTGTAGCCGCTGCATATGATGGAT
Found at i:106801 original size:72 final size:72
Alignment explanation
Indices: 106590--106793 Score: 347
Period size: 72 Copynumber: 2.8 Consensus size: 72
106580 TTGCAGCTGC
* * * * *
106590 TGATTGTGTTGGTGCTGCTGCAG-ATGATGACGACGACGATAATAGTGTCGTTATAGCCGCTGAT
1 TGATTGTGTTGGTGCTGCTGCTGCAT-ATGATGGCGATGATAATAGTGTCGTTGTAGCCGCTGAT
106654 TGTGATGA
65 TGTGATGA
106662 TGATTGTGTTGGTGCTGCTGCTGCATATGATGGCGATGATAATAGTGTCGTTGTAGCCGCTGATT
1 TGATTGTGTTGGTGCTGCTGCTGCATATGATGGCGATGATAATAGTGTCGTTGTAGCCGCTGATT
106727 GTGATGA
66 GTGATGA
106734 TGATTGTGTTGGTGCTGCTGCTGCATATGATGGCGATGATAATAGTGTCGTTGTAGCCGC
1 TGATTGTGTTGGTGCTGCTGCTGCATATGATGGCGATGATAATAGTGTCGTTGTAGCCGC
106794 CGGTTGTGCT
Statistics
Matches: 126, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
72 124 0.98
73 2 0.02
ACGTcount: A:0.19, C:0.14, G:0.33, T:0.34
Consensus pattern (72 bp):
TGATTGTGTTGGTGCTGCTGCTGCATATGATGGCGATGATAATAGTGTCGTTGTAGCCGCTGATT
GTGATGA
Found at i:112635 original size:18 final size:17
Alignment explanation
Indices: 112612--112652 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
112602 TTCTTAATTT
112612 TTAAATTAATAATTAAAA
1 TTAAATTAATAA-TAAAA
*
112630 TTAAATTAATAATATAA
1 TTAAATTAATAATAAAA
112647 TTAAAT
1 TTAAAT
112653 AAATTTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAATTAATAATAAAA
Done.