Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013934.1 Kokia drynarioides strain JFW-HI SEQ_128964, 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: 3634
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Found at i:1146 original size:13 final size:13
Alignment explanation
Indices: 1130--1156 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1120 AATTGAGAAA
1130 AAAGAAAGAAAAG
1 AAAGAAAGAAAAG
1143 AAAGAAAGAAAAG
1 AAAGAAAGAAAAG
1156 A
1 A
1157 GAAAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAAG
Found at i:1148 original size:20 final size:19
Alignment explanation
Indices: 1125--1194 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
1115 CAAAAAATTG
1125 AGAAAAAAGAAAGAAAAGAA
1 AGAAAAAAGAAAGAAAA-AA
*
1145 AGAAAGAAA-AGAGAAAAAA
1 AGAAA-AAAGAAAGAAAAAA
* * *
1164 ATAAAAAAAAAAGGAAAAA
1 AGAAAAAAGAAAGAAAAAA
*
1183 AGGAAAAAGAAA
1 AGAAAAAAGAAA
1195 AGGAGAGGTC
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
18 3 0.07
19 23 0.56
20 12 0.29
21 3 0.07
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (19 bp):
AGAAAAAAGAAAGAAAAAA
Found at i:1195 original size:20 final size:20
Alignment explanation
Indices: 1128--1198 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
1118 AAAATTGAGA
*
1128 AAAAAGAAAGAAAAGAAAGAAAG
1 AAAAGGAAA-AAAAG-AA-AAAG
* *
1151 AAAAGAGAAAAAAATAAAAAA
1 AAAAG-GAAAAAAAGAAAAAG
*
1172 AAAAGGAAAAAAGGAAAAAG
1 AAAAGGAAAAAAAGAAAAAG
1192 AAAAGGA
1 AAAAGGA
1199 GAGGTCGAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
20 19 0.46
21 8 0.20
22 2 0.05
23 8 0.20
24 4 0.10
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (20 bp):
AAAAGGAAAAAAAGAAAAAG
Found at i:1692 original size:111 final size:111
Alignment explanation
Indices: 1498--1700 Score: 309
Period size: 111 Copynumber: 1.8 Consensus size: 111
1488 TTGATCAATG
*
1498 TTTAATTTTCTCATTCATGCAATCTTTGCCTCCAATAAAATTAAATTTTATCCACCTCACAATCC
1 TTTAATTTTCTCATTCATGCAAGCTTTGCCTCCAATAAAATTAAATTTTATCCACCTCACAATCC
1563 CGTTCAAACATTTTTGCATAGAAATGATGGTTAGTGGACTAATATT
66 CGTTCAAACATTTTTGCATAGAAATGATGGTTAGTGGACTAATATT
* * * * * *
1609 TTTAATTTTTTCATTCATGCAAGCTTTGCCTTCAATCAAATTCAATTTTATCCACTTTACAA-CC
1 TTTAATTTTCTCATTCATGCAAGCTTTGCCTCCAATAAAATTAAATTTTATCCACCTCACAATCC
* *
1673 CTGTTCAAGCATTTTTGCATTGAAATGA
66 C-GTTCAAACATTTTTGCATAGAAATGA
1701 CGATTAATGG
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
110 3 0.04
111 79 0.96
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.40
Consensus pattern (111 bp):
TTTAATTTTCTCATTCATGCAAGCTTTGCCTCCAATAAAATTAAATTTTATCCACCTCACAATCC
CGTTCAAACATTTTTGCATAGAAATGATGGTTAGTGGACTAATATT
Found at i:3439 original size:28 final size:28
Alignment explanation
Indices: 3398--3453 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3388 CCAAATTTTA
* *
3398 CCCCTAAATTTTCCAAAAAATTAAATTT
1 CCCCAAAACTTTCCAAAAAATTAAATTT
* *
3426 CCCCAAAACTTTCCAAAAATTTGAATTT
1 CCCCAAAACTTTCCAAAAAATTAAATTT
3454 GACCCTCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.41, C:0.23, G:0.02, T:0.34
Consensus pattern (28 bp):
CCCCAAAACTTTCCAAAAAATTAAATTT
Found at i:3513 original size:88 final size:89
Alignment explanation
Indices: 3343--3547 Score: 238
Period size: 88 Copynumber: 2.3 Consensus size: 89
3333 TTTGACTCTC
* * * **
3343 AAACTTTTCAAAAATTCGAATTTGACCCTTAAATTTTCCAAAAATCCAAATTTTACCCCTAAATT
1 AAACTTTTCAAAAATTTGAATTTGACCCTCAAATTTTCCAAAAATCCAAAGTCAACCCCTAAATT
*
3408 TTCCAAAAAATTAAATTTCCCCA-
66 TTCCAAAAAATTAAATTTCACCAT
* *
3431 AAACTTTCCAAAAATTTGAATTTGACCCTCAAACTTTT-TAAAAATTCC-AAGTCAACCCCTAAA
1 AAACTTTTCAAAAATTTGAATTTGACCCTCAAA-TTTTCCAAAAA-TCCAAAGTCAACCCCTAAA
* * *
3494 TTTT-CTAAAAATTCCAATTTGACCAT
64 TTTTCCAAAAAATT-AAATTTCACCAT
* *
3520 TAACTTTTCAAAAATTTAAATTTGACCC
1 AAACTTTTCAAAAATTTGAATTTGACCC
3548 GATTTTAATG
Statistics
Matches: 99, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
87 8 0.08
88 59 0.60
89 32 0.32
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.35
Consensus pattern (89 bp):
AAACTTTTCAAAAATTTGAATTTGACCCTCAAATTTTCCAAAAATCCAAAGTCAACCCCTAAATT
TTCCAAAAAATTAAATTTCACCAT
Found at i:3541 original size:29 final size:29
Alignment explanation
Indices: 3344--3547 Score: 142
Period size: 30 Copynumber: 6.9 Consensus size: 29
3334 TTGACTCTCA
*
3344 AACTTTTCAAAAATTCGAATTTGACCCTT
1 AACTTTTCAAAAATTCAAATTTGACCCTT
* * * *
3373 AAATTTTCCAAAAATCCAAATTTTACCCCT
1 AACTTTT-CAAAAATTCAAATTTGACCCTT
* * **
3403 AAATTTTCCAAAAAATT-AAATTT-CCCCAA
1 AACTTTT-C-AAAAATTCAAATTTGACCCTT
* ** *
3432 AACTTTCCAAAAATTTGAATTTGACCCTCA
1 AACTTTTCAAAAATTCAAATTTGACCCT-T
* * * ** *
3462 AACTTTTTAAAAATTCCAAGTCAACCCCT
1 AACTTTTCAAAAATTCAAATTTGACCCTT
* * *
3491 AAATTTTCTAAAAATTCCAATTTGACCATT
1 AACTTTTC-AAAAATTCAAATTTGACCCTT
*
3521 AACTTTTCAAAAATTTAAATTTGACCC
1 AACTTTTCAAAAATTCAAATTTGACCC
3548 GATTTTAATG
Statistics
Matches: 135, Mismatches: 34, Indels: 12
0.75 0.19 0.07
Matches are distributed among these distances:
27 7 0.05
28 6 0.04
29 39 0.29
30 77 0.57
31 6 0.04
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.35
Consensus pattern (29 bp):
AACTTTTCAAAAATTCAAATTTGACCCTT
Done.