Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007924.1 Kokia drynarioides strain JFW-HI SEQ_122569, 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: 42565
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:12786 original size:3 final size:3
Alignment explanation
Indices: 12780--12817 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
12770 TGTTTTTTTA
12780 TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
12818 TGGATCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:12804 original size:19 final size:18
Alignment explanation
Indices: 12776--12814 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
12766 ATAATGTTTT
12776 TTTATATTATTATTATTA
1 TTTATATTATTATTATTA
12794 TTTATTATTATTATTATTA
1 TTTA-TATTATTATTATTA
12813 TT
1 TT
12815 ATTTGGATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATATTATTATTATTA
Found at i:13633 original size:12 final size:13
Alignment explanation
Indices: 13610--13635 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13600 TTAAAAATCA
13610 TTTTTAATTTTTT
1 TTTTTAATTTTTT
13623 TTTTTAATTTTTT
1 TTTTTAATTTTTT
13636 AGAATTAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTAATTTTTT
Found at i:13757 original size:61 final size:61
Alignment explanation
Indices: 13620--13758 Score: 138
Period size: 61 Copynumber: 2.3 Consensus size: 61
13610 TTTTTAATTT
* * * *
13620 TTTTTTTTAATTTTTTAGAATTAAGATTAAATTGACAGATTTTGTAAAATTTGAGGGCCAA
1 TTTTTTTGAATTTTTTAGAATTAAGACTAAATTGACAGATTTTGCAAAACTTGAGGGCCAA
* ** * ** * *
13681 ATTTAATGAAGTTTTTAGAATT-AGAACTATAA-TGACATTTTTTGCAAACCTTGAGGGCTAA
1 TTTTTTTGAATTTTTTAGAATTAAG-ACTA-AATTGACAGATTTTGCAAAACTTGAGGGCCAA
13742 TTTTTTTGAATTTTTTA
1 TTTTTTTGAATTTTTTA
13759 TATTTTTATC
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
60 2 0.03
61 56 0.93
62 2 0.03
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.46
Consensus pattern (61 bp):
TTTTTTTGAATTTTTTAGAATTAAGACTAAATTGACAGATTTTGCAAAACTTGAGGGCCAA
Found at i:17628 original size:371 final size:371
Alignment explanation
Indices: 16886--17632 Score: 1390
Period size: 372 Copynumber: 2.0 Consensus size: 371
16876 ATGCCTAGAA
* *
16886 ATAAATTACAAGGACTAAATTCTAATTTTTTAAAGAGTACAGGGACTTATGCATGGTTTTTAGAA
1 ATAAATTACAAGGACTAAATTCTAATTTTTTAAAGAGTACAGAGACTTATGCATGATTTTTAGAA
* *
16951 TCTGACTGATGGTCGAATTAGTTCATTCGTCCAACAAATCTAATCGGTATGTTTGGTTCAATTAA
66 TCTGACAGATGGTCGAATTAGTTCATCCGTCCAACAAATCTAATCGGTATGTTTGGTTCAATTAA
17016 ATAGATCATTAAAATTCAAAAAATAAAAAATTTGATTCAACCAATTTTTTGCTTAGACCAATTGG
131 ATAGATCATTAAAATTCAAAAAATAAAAAATTTGATTCAACCAATTTTTTGCTTAGACCAATTGG
17081 TCTAGTGGCTTTCTTTAGACTAGTACCTTGACCAGTCGATCCGGTCCAATTCAGTTCAAACACCA
196 TCTAGTGGCTTTCTTTAGACTAGTACCTTGACCAGTCGATCCGGTCCAATTCAGTTCAAACACCA
*
17146 TTCGACGAATGACATATTTCAACCATACTTAAAGTACAATGGCAAATTTGCACATCAACCCAATA
261 TTCGACGAATGACATATTTCAACCATACTTAAAGTACAATGGCAAATTTGCACATCAACACAATA
17211 AAATAGTATAAATGTGTTTGCAAACCCTATGCAAGTTCATTTTTTT
326 AAATAGTATAAATGTGTTTGCAAACCCTATGCAAGTTCATTTTTTT
*
17257 ATAAATTACAAGGACTAAATTCTAATTTTTTAAAGAGTACAGAGACTTATGCGTGATTTTTAGAA
1 ATAAATTACAAGGACTAAATTCTAATTTTTTAAAGAGTACAGAGACTTATGCATGATTTTTAGAA
*
17322 TCTGACCAG-TGGTCGAATTAGTTCATCCGTCCAACAAATCTAATCGGTCTGTTTGGTTCAATTA
66 TCTGA-CAGATGGTCGAATTAGTTCATCCGTCCAACAAATCTAATCGGTATGTTTGGTTCAATTA
17386 AATAGATCATTAAAAATTCAAAAAATAAAAAATTTGATTCAACCAATTTTTTGCTTAGACCAATT
130 AATAGATCATT-AAAATTCAAAAAATAAAAAATTTGATTCAACCAATTTTTTGCTTAGACCAATT
17451 GGTCTAGTGGCTTTCTTTAGACTAGTACCTTGACCAGTCGATCCGGTCCAATTCAGTTCAAACAC
194 GGTCTAGTGGCTTTCTTTAGACTAGTACCTTGACCAGTCGATCCGGTCCAATTCAGTTCAAACAC
*
17516 CATTCGACGAATGACATATTTCAACCTTACTTAAAGTACAATGGCAAATTTGCACATCAACACAA
259 CATTCGACGAATGACATATTTCAACCATACTTAAAGTACAATGGCAAATTTGCACATCAACACAA
17581 TAAAATAGTATAAATGTGTTTGCAAACCCTATGCAAGTTCA-TTTTTT
324 TAAAATAGTATAAATGTGTTTGCAAACCCTATGCAAGTTCATTTTTTT
17628 ATAAA
1 ATAAA
17633 GGGAAGAATG
Statistics
Matches: 366, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
371 142 0.39
372 224 0.61
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (371 bp):
ATAAATTACAAGGACTAAATTCTAATTTTTTAAAGAGTACAGAGACTTATGCATGATTTTTAGAA
TCTGACAGATGGTCGAATTAGTTCATCCGTCCAACAAATCTAATCGGTATGTTTGGTTCAATTAA
ATAGATCATTAAAATTCAAAAAATAAAAAATTTGATTCAACCAATTTTTTGCTTAGACCAATTGG
TCTAGTGGCTTTCTTTAGACTAGTACCTTGACCAGTCGATCCGGTCCAATTCAGTTCAAACACCA
TTCGACGAATGACATATTTCAACCATACTTAAAGTACAATGGCAAATTTGCACATCAACACAATA
AAATAGTATAAATGTGTTTGCAAACCCTATGCAAGTTCATTTTTTT
Found at i:33795 original size:15 final size:17
Alignment explanation
Indices: 33770--33802 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
33760 GTTATTATCA
33770 TTAATTTTAAT-TTTTT
1 TTAATTTTAATGTTTTT
33786 TTAA-TTTAATGTTTTT
1 TTAATTTTAATGTTTTT
33802 T
1 T
33803 GTTTGACCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
TTAATTTTAATGTTTTT
Found at i:41162 original size:10 final size:10
Alignment explanation
Indices: 41135--41200 Score: 55
Period size: 10 Copynumber: 6.7 Consensus size: 10
41125 TAGAATTTTT
41135 TTAT-AAAAA
1 TTATAAAAAA
*
41144 TCATCAAAAAA
1 TTAT-AAAAAA
41155 TTATAAAAAA
1 TTATAAAAAA
* ***
41165 TTGTAAACCT
1 TTATAAAAAA
41175 TTATAAAAAA
1 TTATAAAAAA
*
41185 -TATAAAAGA
1 TTATAAAAAA
41194 TTATAAA
1 TTATAAA
41201 TTGCATAAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
9 11 0.26
10 24 0.56
11 8 0.19
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:41427 original size:19 final size:20
Alignment explanation
Indices: 41375--41427 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
41365 TTAGTACGAT
*
41375 AATTTTTATAACTTTTTTTAC
1 AATTTTTATAA-TTTCTTTAC
*
41396 AACTTTTAT-ATTTCTTTAC
1 AATTTTTATAATTTCTTTAC
41415 -ATTTTTATAATTT
1 AATTTTTATAATTT
41428 TCTTACGACT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 7 0.25
19 12 0.43
20 1 0.04
21 8 0.29
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.62
Consensus pattern (20 bp):
AATTTTTATAATTTCTTTAC
Found at i:41433 original size:19 final size:20
Alignment explanation
Indices: 41375--41433 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 20
41365 TTAGTACGAT
*
41375 AATTTTTATAACTTTTTTTAC
1 AATTTTTATAA-TTTTCTTAC
*
41396 AACTTTTAT-A-TTTCTTTAC
1 AATTTTTATAATTTTC-TTAC
41415 -ATTTTTATAATTTTCTTAC
1 AATTTTTATAATTTTCTTAC
41434 GACTTTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 10 0.31
19 9 0.28
20 5 0.16
21 8 0.25
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (20 bp):
AATTTTTATAATTTTCTTAC
Found at i:41576 original size:10 final size:10
Alignment explanation
Indices: 41483--41577 Score: 54
Period size: 10 Copynumber: 9.6 Consensus size: 10
41473 GTTTTATGAT
41483 TTTTTAA-AGA
1 TTTTTAATA-A
41493 TTTTT-ATAA
1 TTTTTAATAA
**
41502 TTTTTTTCTAA
1 -TTTTTAATAA
41513 TTTTTAATAA
1 TTTTTAATAA
**
41523 AATTTAA-ATA
1 TTTTTAATA-A
* *
41533 GTTTTAATAG
1 TTTTTAATAA
*
41543 TTTTTATTAA
1 TTTTTAATAA
**
41553 AATTTAATAA
1 TTTTTAATAA
41563 -TTTTAATAA
1 TTTTTAATAA
41572 TTTTTA
1 TTTTTA
41578 TTTTTTTAAT
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
9 11 0.17
10 49 0.77
11 4 0.06
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:41578 original size:29 final size:30
Alignment explanation
Indices: 41510--41579 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 30
41500 AATTTTTTTC
* *
41510 TAATTTTTAATAAAATTTAAATAGTTTTAA
1 TAATTTTTATTAAAATTTAAATAATTTTAA
*
41540 TAGTTTTTATTAAAATTT-AATAATTTTAA
1 TAATTTTTATTAAAATTTAAATAATTTTAA
41569 TAATTTTTATT
1 TAATTTTTATT
41580 TTTTTAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 20 0.56
30 16 0.44
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (30 bp):
TAATTTTTATTAAAATTTAAATAATTTTAA
Found at i:41857 original size:89 final size:87
Alignment explanation
Indices: 41685--41868 Score: 192
Period size: 89 Copynumber: 2.1 Consensus size: 87
41675 TAATTTAGTA
* * * * *
41685 AAAAAATAAAGTAGGGGTTTAATTACTTTTTTGAAAAGTTTAAGGGTTTTTTTTATGCATTTTGA
1 AAAAAA-AAAGTAGGGGCTTAATTACTTTTTTGAAAAGTTTAAGAGTATTTTTGATACATTTTGA
* *
41750 AAGTTCAAGTATCAAATTGAGTG
65 AAGTTCAAATATCAAATTGAATG
* * * *
41773 TAAAAAAAATGTA-GGGCTTAATTGCTTTTTTCGAAAAATTTTGAGAGTATTTTTGATACATTTT
1 -AAAAAAAAAGTAGGGGCTTAATTACTTTTTT-G-AAAAGTTTAAGAGTATTTTTGATACATTTT
**
41837 GGTAGTTCAAATACTC-AATTGAATG
63 GAAAGTTCAAATA-TCAAATTGAATG
41862 AAAAAAA
1 AAAAAAA
41869 TAAAAACTTA
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
87 16 0.20
88 13 0.16
89 48 0.61
90 2 0.03
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (87 bp):
AAAAAAAAAGTAGGGGCTTAATTACTTTTTTGAAAAGTTTAAGAGTATTTTTGATACATTTTGAA
AGTTCAAATATCAAATTGAATG
Found at i:42231 original size:3 final size:3
Alignment explanation
Indices: 42223--42260 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
42213 AAGAAAGTAG
42223 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
42261 GTATGATGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.