Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001408.1 Kokia drynarioides strain JFW-HI SEQ_112899, 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: 42649
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:71 original size:3 final size:3
Alignment explanation
Indices: 63--125 Score: 99
Period size: 3 Copynumber: 20.3 Consensus size: 3
53 TTTTATTTAT
*
63 ATA ATA ATA ATA ATA ATA ATAA ATA TTA TATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA -ATA ATA ATA ATA ATA ATA
110 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
126 ATATTATATT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
3 51 0.91
4 5 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:5332 original size:14 final size:14
Alignment explanation
Indices: 5313--5339 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5303 CAAAACTCAT
5313 AAAAATAATATAAA
1 AAAAATAATATAAA
5327 AAAAATAATATAA
1 AAAAATAATATAA
5340 TTAATCATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAAATAATATAAA
Found at i:6116 original size:3 final size:3
Alignment explanation
Indices: 6108--6139 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
6098 TTTTATTTAT
6108 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6140 TTATATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:23641 original size:13 final size:13
Alignment explanation
Indices: 23625--23657 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
23615 ATTAAGCTTT
23625 TCCAGCAAGCCTA
1 TCCAGCAAGCCTA
23638 TCCAGCAAGCCTA
1 TCCAGCAAGCCTA
23651 TCCAGCA
1 TCCAGCA
23658 TCTGATCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.30, C:0.39, G:0.15, T:0.15
Consensus pattern (13 bp):
TCCAGCAAGCCTA
Found at i:27534 original size:27 final size:27
Alignment explanation
Indices: 27504--27602 Score: 126
Period size: 27 Copynumber: 3.7 Consensus size: 27
27494 CACCAAAATA
* *
27504 ACTGGCGAACCTTAGCTCGCCAAACAC
1 ACTGACGAACCCTAGCTCGCCAAACAC
** *
27531 ACTGGTGAACCCGAGCTCGCCAAACAC
1 ACTGACGAACCCTAGCTCGCCAAACAC
* *
27558 ACTGACGAACCCTAGCTTGCCAAACAA
1 ACTGACGAACCCTAGCTCGCCAAACAC
*
27585 ACTGACAAACCCTAGCTC
1 ACTGACGAACCCTAGCTC
27603 ACCATACAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.32, C:0.36, G:0.17, T:0.14
Consensus pattern (27 bp):
ACTGACGAACCCTAGCTCGCCAAACAC
Found at i:27611 original size:27 final size:27
Alignment explanation
Indices: 27511--27623 Score: 111
Period size: 27 Copynumber: 4.2 Consensus size: 27
27501 ATAACTGGCG
* * ***
27511 AACCTTAGCTCGCCAAACACACTGGTG
1 AACCCTAGCTCGCCAAACAAACTGACA
* * *
27538 AACCCGAGCTCGCCAAACACACTGACG
1 AACCCTAGCTCGCCAAACAAACTGACA
*
27565 AACCCTAGCTTGCCAAACAAACTGACA
1 AACCCTAGCTCGCCAAACAAACTGACA
* *
27592 AACCCTAGCTCACCATACAAACT-AGCA
1 AACCCTAGCTCGCCAAACAAACTGA-CA
27619 AACCC
1 AACCC
27624 CCAGTTCATT
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
26 1 0.01
27 73 0.99
ACGTcount: A:0.36, C:0.37, G:0.13, T:0.13
Consensus pattern (27 bp):
AACCCTAGCTCGCCAAACAAACTGACA
Found at i:28240 original size:26 final size:26
Alignment explanation
Indices: 28211--28286 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 26
28201 GATAGAATTG
* *
28211 TCATAATTTCATCGGGGGTAAAATCA
1 TCATAATTTTATCAGGGGTAAAATCA
* *
28237 TCATAATTTTACCAAGGGTAAAATCA
1 TCATAATTTTATCAGGGGTAAAATCA
*
28263 TCATAATTTTATCAGGAGTAAAAT
1 TCATAATTTTATCAGGGGTAAAAT
28287 TGGGATGAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (26 bp):
TCATAATTTTATCAGGGGTAAAATCA
Found at i:41200 original size:24 final size:24
Alignment explanation
Indices: 41159--41204 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41149 AATTACATGA
*
41159 ATAATAAATATAAAAAACAAATAT
1 ATAATAAATAAAAAAAACAAATAT
41183 ATAA-AAATAAAAATAAACAAAT
1 ATAATAAATAAAAA-AAACAAAT
41205 TATGCAGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (24 bp):
ATAATAAATAAAAAAAACAAATAT
Found at i:41495 original size:60 final size:60
Alignment explanation
Indices: 41400--41556 Score: 153
Period size: 60 Copynumber: 2.6 Consensus size: 60
41390 GACCAAATTC
* * **
41400 CAATTTTGGAGAAGTTTGAGGGTCAAATCCAAATTTTTGGCAA-AATTT-GGGGTCAAAACTTA
1 CAATTTTGGA-AAGTTTGAGGGTTAAAACTTAATTTTTGG-AAGAATTTAGGGGTCAAAA--TA
* *
41462 -ATTTTTGGAAAGTTTGAGGGTTAAAACTTAA-TTTTGGAAGAGTTTAGGGGTCAAAATA
1 CAATTTTGGAAAGTTTGAGGGTTAAAACTTAATTTTTGGAAGAATTTAGGGGTCAAAATA
* *
41520 CAATTTTGAAAAAGTTTAAGGGTTAAAA-TATAATTTT
1 CAATTTTG-GAAAGTTTGAGGGTTAAAACT-TAATTTT
41557 AAAAAGTTTA
Statistics
Matches: 80, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
58 4 0.05
59 17 0.21
60 48 0.60
61 11 0.14
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (60 bp):
CAATTTTGGAAAGTTTGAGGGTTAAAACTTAATTTTTGGAAGAATTTAGGGGTCAAAATA
Found at i:41497 original size:29 final size:29
Alignment explanation
Indices: 41372--41590 Score: 139
Period size: 30 Copynumber: 7.4 Consensus size: 29
41362 CAAAAAATGA
* *
41372 AATTTTGGAAAGTTTG-GGGACCAAAT-T
1 AATTTTGGAAAGTTTGAGGGTCAAAATAT
41399 CCAATTTTGGAGAAGTTTGAGGGTC-AAATCCA-
1 --AATTTTGGA-AAGTTTGAGGGTCAAAAT--AT
*
41431 AATTTTTGGCAAAATTTG-GGGTCAAAACT-T
1 AA-TTTTGG-AAAGTTTGAGGGTCAAAA-TAT
*
41461 AATTTTTGGAAAGTTTGAGGGTTAAAACT-T
1 AA-TTTTGGAAAGTTTGAGGGTCAAAA-TAT
*
41491 AATTTTGGAAGAGTTT-AGGGGTCAAAATAC
1 AATTTTGGAA-AGTTTGA-GGGTCAAAATAT
* * *
41521 AATTTTGAAAAAGTTTAAGGGTTAAAATAT
1 AATTTTG-GAAAGTTTGAGGGTCAAAATAT
** * * *
41551 AATTTTAAAAAGTTTAAGGGTTAAAATGT
1 AATTTTGGAAAGTTTGAGGGTCAAAATAT
*
41580 AATTTTTGAAA
1 AATTTTGGAAA
41591 AAAAAGGGTT
Statistics
Matches: 161, Mismatches: 13, Indels: 32
0.78 0.06 0.16
Matches are distributed among these distances:
29 56 0.35
30 81 0.50
31 22 0.14
32 2 0.01
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.35
Consensus pattern (29 bp):
AATTTTGGAAAGTTTGAGGGTCAAAATAT
Found at i:41548 original size:30 final size:30
Alignment explanation
Indices: 41470--41592 Score: 151
Period size: 30 Copynumber: 4.1 Consensus size: 30
41460 TAATTTTTGG
* *
41470 AAAGTTTGAGGGTTAAAACT-TAATTTTGGA
1 AAAGTTTAAGGGTTAAAA-TATAATTTTGAA
* * * *
41500 AGAGTTTAGGGGTCAAAATACAATTTTGAA
1 AAAGTTTAAGGGTTAAAATATAATTTTGAA
41530 AAAGTTTAAGGGTTAAAATATAATTTT-AA
1 AAAGTTTAAGGGTTAAAATATAATTTTGAA
*
41559 AAAGTTTAAGGGTTAAAATGTAATTTTTGAA
1 AAAGTTTAAGGGTTAAAATATAA-TTTTGAA
41590 AAA
1 AAA
41593 AAAGGGTTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
29 25 0.32
30 49 0.62
31 5 0.06
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.35
Consensus pattern (30 bp):
AAAGTTTAAGGGTTAAAATATAATTTTGAA
Found at i:41587 original size:60 final size:61
Alignment explanation
Indices: 41449--41592 Score: 163
Period size: 60 Copynumber: 2.4 Consensus size: 61
41439 GCAAAATTTG
* * * * *
41449 GGGTCAAAACT-TAATTTTTG-GAAAGTTTGAGGGTTAAAACTTAATTTTGGAAGAGTTTAG
1 GGGTCAAAA-TATAATTTTTGAAAAAGTTTAAGGGTTAAAACTTAATTTTGAAAAAGTTTAA
*
41509 GGGTCAAAATACAA-TTTTGAAAAAGTTTAAGGGTTAAAA-TATAATTTT-AAAAAGTTTAA
1 GGGTCAAAATATAATTTTTGAAAAAGTTTAAGGGTTAAAACT-TAATTTTGAAAAAGTTTAA
* *
41568 GGGTTAAAATGTAATTTTTGAAAAA
1 GGGTCAAAATATAATTTTTGAAAAA
41593 AAAGGGTTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
59 26 0.37
60 45 0.63
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.35
Consensus pattern (61 bp):
GGGTCAAAATATAATTTTTGAAAAAGTTTAAGGGTTAAAACTTAATTTTGAAAAAGTTTAA
Found at i:42281 original size:16 final size:16
Alignment explanation
Indices: 42262--42300 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
42252 TTAAAATCTA
42262 TTTTTTATTTTGTTGT
1 TTTTTTATTTTGTTGT
* * *
42278 TTTTATCTTTTTTTGT
1 TTTTTTATTTTGTTGT
42294 TTTTTTA
1 TTTTTTA
42301 AAAACTCGAG
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.08, C:0.03, G:0.08, T:0.82
Consensus pattern (16 bp):
TTTTTTATTTTGTTGT
Done.