Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014707.1 Kokia drynarioides strain JFW-HI SEQ_129746, 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: 49144
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 96 characters in sequence are not A, C, G, or T
Found at i:27459 original size:14 final size:14
Alignment explanation
Indices: 27442--27484 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
27432 TCAAAAGTAC
27442 TTTTCAAAATCATT
1 TTTTCAAAATCATT
*
27456 TTTTCAAAA-CACT
1 TTTTCAAAATCATT
* *
27469 TTTTAAAAATAATT
1 TTTTCAAAATCATT
27483 TT
1 TT
27485 AAAAAACAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTTCAAAATCATT
Found at i:27472 original size:27 final size:27
Alignment explanation
Indices: 27428--27484 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
27418 TTAAACTAAA
* * *
27428 TTTTTCAAAAGTACTTTTCAAAATCAT
1 TTTTTCAAAAGCACTTTTAAAAATAAT
27455 TTTTTCAAAA-CACTTTTTAAAAATAAT
1 TTTTTCAAAAGCAC-TTTTAAAAATAAT
27482 TTT
1 TTT
27485 AAAAAACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (27 bp):
TTTTTCAAAAGCACTTTTAAAAATAAT
Found at i:30294 original size:20 final size:20
Alignment explanation
Indices: 30271--30310 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
30261 TGATCAAATT
30271 ATAAATTTACTA-ATAATTTA
1 ATAAATTT-CTATATAATTTA
*
30291 ATAACTTTCTATATAATTTA
1 ATAAATTTCTATATAATTTA
30311 CCCTTACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAAATTTCTATATAATTTA
Found at i:32031 original size:18 final size:20
Alignment explanation
Indices: 31986--32025 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
31976 CAAATACCTG
31986 AGAAA-GATTAAAATAAAAA
1 AGAAATGATTAAAATAAAAA
32005 AGAAATGATTAAAATAAAAA
1 AGAAATGATTAAAATAAAAA
32025 A
1 A
32026 AATGATATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (20 bp):
AGAAATGATTAAAATAAAAA
Found at i:32188 original size:17 final size:17
Alignment explanation
Indices: 32166--32199 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
32156 AAATTCTATT
32166 AGTACGACTCATAATCA
1 AGTACGACTCATAATCA
32183 AGTACGACTCATAATCA
1 AGTACGACTCATAATCA
32200 TGTAGTCGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (17 bp):
AGTACGACTCATAATCA
Found at i:33582 original size:16 final size:16
Alignment explanation
Indices: 33561--33594 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
33551 GTAATTAAGG
33561 ATAAAATA-TTAATCAA
1 ATAAAATACTT-ATCAA
33577 ATAAAATACTTATCAA
1 ATAAAATACTTATCAA
33593 AT
1 AT
33595 TCCCCCTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAAAATACTTATCAA
Found at i:34239 original size:22 final size:22
Alignment explanation
Indices: 34189--34241 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
34179 GTACGAATAG
*
34189 TTTTC-TCTTTTTTTTTGTTGT
1 TTTTCTTCTTTTTTTTTATTGT
*
34210 TCTT-TTCTTTTTTCTTTATT-T
1 TTTTCTTCTTTTTT-TTTATTGT
34231 TTTTCTTCTTT
1 TTTTCTTCTTT
34242 ATCCGAACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (22 bp):
TTTTCTTCTTTTTTTTTATTGT
Found at i:46484 original size:12 final size:11
Alignment explanation
Indices: 46452--46486 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
46442 CATTTATCTT
*
46452 TAATTTTTTAT
1 TAATTTTTTAA
46463 TAATTTTTTAA
1 TAATTTTTTAA
46474 TAATTTATTTAA
1 TAATTT-TTTAA
46486 T
1 T
46487 TGATCCATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TAATTTTTTAA
Found at i:47515 original size:73 final size:73
Alignment explanation
Indices: 47428--47587 Score: 248
Period size: 73 Copynumber: 2.2 Consensus size: 73
47418 AATTTATCAT
* * *
47428 TTGTTGACATATATTTGATACAATGTCTAAAACGATATTGATATCGACCGATTTAATATTCAATC
1 TTGTTGATATATATTTGATACAATGTCTAAAACGATATTGATATAGACCGATTTAAGATTCAATC
***
47493 TGTAACAC
66 CACAACAC
* *
47501 TTGTTGATATATATTTGATACAATGTTTAAAACGATATTGATATAGATCGATTTAAGATTCAATC
1 TTGTTGATATATATTTGATACAATGTCTAAAACGATATTGATATAGACCGATTTAAGATTCAATC
47566 CACAACAC
66 CACAACAC
47574 TTGTTGATATATAT
1 TTGTTGATATATAT
47588 AATAAAATAT
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 79 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (73 bp):
TTGTTGATATATATTTGATACAATGTCTAAAACGATATTGATATAGACCGATTTAAGATTCAATC
CACAACAC
Done.