Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001800.1 Kokia drynarioides strain JFW-HI SEQ_113535, 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: 35393
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Warning! 118 characters in sequence are not A, C, G, or T
Found at i:468 original size:6 final size:6
Alignment explanation
Indices: 441--509 Score: 76
Period size: 6 Copynumber: 12.0 Consensus size: 6
431 TTTTGGACTT
*
441 TTTAAT TTTGAAA -TTAAA -TTAAA TTTAAA TTTAAGA -TT-AA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA
487 TTTAAA TTTAAA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
510 ATAAATTAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
4 1 0.02
5 16 0.29
6 36 0.64
7 3 0.05
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:470 original size:11 final size:11
Alignment explanation
Indices: 451--516 Score: 82
Period size: 11 Copynumber: 5.9 Consensus size: 11
441 TTTAATTTTG
451 AAATTAAA-TT
1 AAATTAAATTT
461 AAATTTAAATTT
1 AAA-TTAAATTT
473 AAGATT-AATTT
1 AA-ATTAAATTT
484 AAATTTAAATTT
1 AAA-TTAAATTT
496 AAATTAAATTT
1 AAATTAAATTT
*
507 AAAATAAATT
1 AAATTAAATT
517 AAAAAGGGCC
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
10 4 0.08
11 31 0.62
12 14 0.28
13 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:474 original size:17 final size:17
Alignment explanation
Indices: 454--516 Score: 85
Period size: 17 Copynumber: 3.7 Consensus size: 17
444 AATTTTGAAA
454 TTAAATTAAATTTAAAT
1 TTAAATTAAATTTAAAT
471 TTAAGATT-AATTTAAAT
1 TTAA-ATTAAATTTAAAT
488 TTAAATTTAAA-TTAAAT
1 TTAAA-TTAAATTTAAAT
*
505 TTAAAATAAATT
1 TTAAATTAAATT
517 AAAAAGGGCC
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
16 5 0.12
17 31 0.76
18 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
TTAAATTAAATTTAAAT
Found at i:506 original size:23 final size:23
Alignment explanation
Indices: 441--509 Score: 97
Period size: 23 Copynumber: 3.0 Consensus size: 23
431 TTTTGGACTT
*
441 TTTAATTTTGAAATTAAA-TTAAA
1 TTTAAATTT-AAATTAAATTTAAA
464 TTTAAATTTAAGATT-AATTTAAA
1 TTTAAATTTAA-ATTAAATTTAAA
487 TTTAAATTTAAATTAAATTTAAA
1 TTTAAATTTAAATTAAATTTAAA
510 ATAAATTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
22 7 0.17
23 35 0.83
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (23 bp):
TTTAAATTTAAATTAAATTTAAA
Found at i:4208 original size:21 final size:22
Alignment explanation
Indices: 4184--4231 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
4174 TTTTAATTAG
*
4184 ATATTATT-TATTATTAAATTT
1 ATATTATTATATTAATAAATTT
**
4205 ATA-TATTATATTAATATTTTT
1 ATATTATTATATTAATAAATTT
4226 ATATTA
1 ATATTA
4232 CATATGTGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 4 0.18
21 16 0.73
22 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTATTATATTAATAAATTT
Found at i:4236 original size:21 final size:18
Alignment explanation
Indices: 4195--4231 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
4185 TATTATTTAT
4195 TATTAAATTTATATATTA
1 TATTAAATTTATATATTA
*
4213 TATTAATATTTTTATATTA
1 TATTAA-ATTTATATATTA
4232 CATATGTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTAAATTTATATATTA
Found at i:17088 original size:24 final size:23
Alignment explanation
Indices: 17020--17089 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 23
17010 TTCGTTTAAC
* * *
17020 TTAATCGAACATGTCCACAAACA
1 TTAATTGAACATGTTCACGAACA
* *
17043 TTAAATGAACATATTC-CTGAACA
1 TTAATTGAACATGTTCAC-GAACA
17066 TATAATTGAACATGTTCACGAACA
1 T-TAATTGAACATGTTCACGAACA
17090 GTGTTAATGA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
22 1 0.03
23 17 0.46
24 18 0.49
25 1 0.03
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (23 bp):
TTAATTGAACATGTTCACGAACA
Found at i:22530 original size:40 final size:40
Alignment explanation
Indices: 22486--22566 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
22476 AGTATTATGG
22486 TTCATTTACAGTTACTTAACATAGATTTAATACCTGAATC
1 TTCATTTACAGTTACTTAACATAGATTTAATACCTGAATC
22526 TTCATTTACAGTTACTTAACATAGATTTAATACCTGAATC
1 TTCATTTACAGTTACTTAACATAGATTTAATACCTGAATC
22566 T
1 T
22567 ACACTGCACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (40 bp):
TTCATTTACAGTTACTTAACATAGATTTAATACCTGAATC
Found at i:23205 original size:33 final size:33
Alignment explanation
Indices: 23159--23225 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
23149 ATCTTTATGT
* **
23159 CTTAAATTGAAAATGATTTTTA-TATAGGGGGAG
1 CTTAAATTCAAAATGACATTTATTA-AGGGGGAG
23192 CTTAAATTCAAAATGACATTTATTAAGGGGGAG
1 CTTAAATTCAAAATGACATTTATTAAGGGGGAG
23225 C
1 C
23226 AAGTATTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.33
Consensus pattern (33 bp):
CTTAAATTCAAAATGACATTTATTAAGGGGGAG
Found at i:23319 original size:12 final size:12
Alignment explanation
Indices: 23302--23326 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23292 TCTGTCCAGA
23302 TGGTATCGATAC
1 TGGTATCGATAC
23314 TGGTATCGATAC
1 TGGTATCGATAC
23326 T
1 T
23327 TTCCATAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (12 bp):
TGGTATCGATAC
Found at i:23376 original size:22 final size:22
Alignment explanation
Indices: 23335--23381 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
23325 CTTTCCATAA
23335 GGTATCGATAATTTGCTCC-AC
1 GGTATCGATAATTTGCTCCAAC
* *
23356 GGTATCGATAGTTTTGGTCCAAC
1 GGTATCGATA-ATTTGCTCCAAC
23379 GGT
1 GGT
23382 CACTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 7 0.32
23 5 0.23
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (22 bp):
GGTATCGATAATTTGCTCCAAC
Found at i:25423 original size:19 final size:19
Alignment explanation
Indices: 25399--25442 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
25389 GAACTTGAAG
25399 AGAAAGTAAGCAAAATGCA
1 AGAAAGTAAGCAAAATGCA
25418 AGAAAGTAAGCAAAATGCA
1 AGAAAGTAAGCAAAATGCA
25437 AGAAAG
1 AGAAAG
25443 CATTAATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.59, C:0.09, G:0.23, T:0.09
Consensus pattern (19 bp):
AGAAAGTAAGCAAAATGCA
Found at i:28389 original size:27 final size:28
Alignment explanation
Indices: 28357--28410 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
28347 CAATTTTAAT
*
28357 AGTATTTTGTAAGTTTC-TTTTAAAAAA
1 AGTATTTTATAAGTTTCATTTTAAAAAA
28384 AGTATTTTATAAGTTTCATTTTAAAAA
1 AGTATTTTATAAGTTTCATTTTAAAAA
28411 TGATACTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (28 bp):
AGTATTTTATAAGTTTCATTTTAAAAAA
Found at i:28535 original size:15 final size:19
Alignment explanation
Indices: 28496--28542 Score: 64
Period size: 17 Copynumber: 2.6 Consensus size: 19
28486 TTTAAATTCT
28496 TAAAATAATTATTATTTTA
1 TAAAATAATTATTATTTTA
28515 TAAAATAA-TATT-TTTT-
1 TAAAATAATTATTATTTTA
28531 TAAATATAATTA
1 TAAA-ATAATTA
28543 AATATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.15
17 8 0.31
18 6 0.23
19 8 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAAATAATTATTATTTTA
Found at i:28576 original size:28 final size:29
Alignment explanation
Indices: 28528--28586 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
28518 AATAATATTT
* *
28528 TTTTAAATATAATTAAATATTT-TTAATA
1 TTTTAAAAATAATTAAATATTTCTAAATA
*
28556 TTTTAAAAATAA-TATACTATTTCTAAATA
1 TTTTAAAAATAATTA-AATATTTCTAAATA
28585 TT
1 TT
28587 ATTTTAAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.08
28 17 0.65
29 7 0.27
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (29 bp):
TTTTAAAAATAATTAAATATTTCTAAATA
Found at i:29388 original size:16 final size:16
Alignment explanation
Indices: 29364--29428 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
29354 ATCGTTTAAA
*
29364 AAATTATAAAGATATT
1 AAATAATAAAGATATT
29380 AAATAAT-AA-A-ATT
1 AAATAATAAAGATATT
29393 ---T-ATAAAGATATT
1 AAATAATAAAGATATT
*
29405 AAATAATAAAAATATT
1 AAATAATAAAGATATT
29421 ATAATAAT
1 A-AATAAT
29429 TGTAATAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 15
0.70 0.04 0.27
Matches are distributed among these distances:
9 2 0.05
10 3 0.08
11 1 0.03
12 3 0.08
13 3 0.08
14 1 0.03
15 3 0.08
16 17 0.44
17 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
AAATAATAAAGATATT
Found at i:29390 original size:25 final size:25
Alignment explanation
Indices: 29362--29417 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
29352 TAATCGTTTA
29362 AAAAATTATAAAGATATTAAATAAT
1 AAAAATTATAAAGATATTAAATAAT
*
29387 AAAATTTATAAAGATATTAAATAAT
1 AAAAATTATAAAGATATTAAATAAT
29412 AAAAAT
1 AAAAAT
29418 ATTATAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (25 bp):
AAAAATTATAAAGATATTAAATAAT
Found at i:29748 original size:22 final size:22
Alignment explanation
Indices: 29720--29765 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
29710 ATGTGTGACT
29720 TGAATTCAAACTGTACTAATCG
1 TGAATTCAAACTGTACTAATCG
29742 TGAATTCAAACTGTACTAATCG
1 TGAATTCAAACTGTACTAATCG
29764 TG
1 TG
29766 TTTGTTATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (22 bp):
TGAATTCAAACTGTACTAATCG
Found at i:32968 original size:27 final size:28
Alignment explanation
Indices: 32938--33003 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
32928 TAATTATTAA
32938 TTTATAAAATAAAATA-TA-TTTTAATAT
1 TTTA-AAAATAAAATACTATTTTTAATAT
* **
32965 TTTAAAAACAATCTACTATTTTTAATAT
1 TTTAAAAATAAAATACTATTTTTAATAT
32993 TTTAAAAATAA
1 TTTAAAAATAA
33004 TCTTGTTATG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 8 0.24
27 6 0.18
28 19 0.58
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (28 bp):
TTTAAAAATAAAATACTATTTTTAATAT
Done.