Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011666.1 Kokia drynarioides strain JFW-HI SEQ_126658, 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: 13931
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:499 original size:29 final size:29
Alignment explanation
Indices: 467--724 Score: 224
Period size: 29 Copynumber: 8.8 Consensus size: 29
457 TAAACTATAA
**
467 AAAAATTATATTTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTTACCCTCGAACTTCC
* * *
496 AAAAATTCCATTTTCGA-CCTCGAAATTTTC
1 AAAAATTCCATTTT-TACCCTCG-AACTTCC
*
526 AAAAATTCCATTTTTATCCCT-AAACTTCC
1 AAAAATTCCATTTTTA-CCCTCGAACTTCC
* *
555 AAAAATTCCATTTTTGACCC-CAAAACTTCT
1 AAAAATTCCATTTTT-ACCCTC-GAACTTCC
*
585 AAAAATTCCATTTTTACCC-CTAAACTTCC
1 AAAAATTCCATTTTTACCCTC-GAACTTCC
614 AAAAATTCCATTTTTGA-CCTCGAAACTTCC
1 AAAAATTCCATTTTT-ACCCTCG-AACTTCC
* * * *
644 AAAAATTCTATTTTTACCCCCGAACCTCT
1 AAAAATTCCATTTTTACCCTCGAACTTCC
* *
673 AAAAATTCCA-TTTTAACCTCGAATTCTCC
1 AAAAATTCCATTTTTACCCTCGAACT-TCC
* *
702 TAAAATTACCA-TTTTGCCCTCGA
1 AAAAATT-CCATTTTTACCCTCGA
725 GAATCCAAAA
Statistics
Matches: 190, Mismatches: 26, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
28 11 0.06
29 93 0.49
30 83 0.44
31 3 0.02
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCTCGAACTTCC
Found at i:559 original size:59 final size:59
Alignment explanation
Indices: 467--695 Score: 275
Period size: 59 Copynumber: 3.9 Consensus size: 59
457 TAAACTATAA
** * * *
467 AAAAATTATATTTTTA-CCCTCGAACTTCCAAAAATTCCATTTTCGACCTCGAAATTTTC
1 AAAAATTCCATTTTTACCCCT-AAACTTCCAAAAATTCCATTTTTGACCTCGAAAATTTC
* * *
526 AAAAATTCCATTTTTATCCCTAAACTTCCAAAAATTCCATTTTTGACC-CCAAAACTTC
1 AAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCGAAAATTTC
* *
584 TAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCC
1 -AAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCGAAAATTTC
* ** * * *
644 AAAAATTCTATTTTTACCCCCGAACCTCTAAAAATTCCA-TTTTAACCTCGAA
1 AAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCGAA
696 TTCTCCTAAA
Statistics
Matches: 149, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
58 19 0.13
59 120 0.81
60 10 0.07
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (59 bp):
AAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCGAAAATTTC
Found at i:2329 original size:166 final size:166
Alignment explanation
Indices: 2055--2389 Score: 607
Period size: 166 Copynumber: 2.0 Consensus size: 166
2045 TGAAGTTGAG
*
2055 TAAGGAAATGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATATTTATTTCAGATGACTTT
1 TAAGGAAAAGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATATTTATTTCAGATGACTTT
* * *
2120 GAGGATCTTATGACTCTGTTGTGTTCTTCTTTTAGGAAATCTTTCAGCATTTTTATGTAATCATT
66 GAGGATCTTATGACTCTGTTCTGTTCTTCTTTTAGGAAATCTTTCAGCATCTTCATGTAATCATT
*
2185 GCGATTGTTTAGTTGTCTTCCCTAATTTCTTTTAAT
131 GCGATTGTCTAGTTGTCTTCCCTAATTTCTTTTAAT
* *
2221 TAAGGAAAAGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATCTTTATTTCAGATGATTTT
1 TAAGGAAAAGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATATTTATTTCAGATGACTTT
2286 GAGGATCTTATGACTCTGTTCTGTTCTTCTTTTAGGAAATCTTTCAGCATCTTCATGTAATCATT
66 GAGGATCTTATGACTCTGTTCTGTTCTTCTTTTAGGAAATCTTTCAGCATCTTCATGTAATCATT
2351 GCGATTGTCTAGTTGTCTTCCCTAATTTCTTTTAAT
131 GCGATTGTCTAGTTGTCTTCCCTAATTTCTTTTAAT
2387 TAA
1 TAA
2390 TGTTAATTTT
Statistics
Matches: 162, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
166 162 1.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.44
Consensus pattern (166 bp):
TAAGGAAAAGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATATTTATTTCAGATGACTTT
GAGGATCTTATGACTCTGTTCTGTTCTTCTTTTAGGAAATCTTTCAGCATCTTCATGTAATCATT
GCGATTGTCTAGTTGTCTTCCCTAATTTCTTTTAAT
Found at i:8406 original size:20 final size:20
Alignment explanation
Indices: 8381--8448 Score: 86
Period size: 20 Copynumber: 3.4 Consensus size: 20
8371 TATAAATCTT
8381 AATTTTTTATAAA-TATTTTG
1 AATTTTTTA-AAATTATTTTG
*
8401 AA-TTTTAAAAATTATTTTG
1 AATTTTTTAAAATTATTTTG
*
8420 AATTTTTGAAAATTATTTTG
1 AATTTTTTAAAATTATTTTG
8440 AATTATTTT
1 AATT-TTTT
8449 GTAATTTTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 3 0.07
19 14 0.33
20 22 0.52
21 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
AATTTTTTAAAATTATTTTG
Found at i:11091 original size:19 final size:19
Alignment explanation
Indices: 11046--11097 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
11036 ACTGGCATGT
* *
11046 AAGTGCATATTAGCGCACA
1 AAGTGCATCTTAGCACACA
* * *
11065 GAGAGCATCTTGGCACACA
1 AAGTGCATCTTAGCACACA
*
11084 AAGTGCATCCTAGC
1 AAGTGCATCTTAGC
11098 GCATAAGCGC
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (19 bp):
AAGTGCATCTTAGCACACA
Found at i:11763 original size:3 final size:3
Alignment explanation
Indices: 11755--11802 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
11745 ACAGTGGTGA
11755 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
11803 TAGTAGTTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12452 original size:31 final size:31
Alignment explanation
Indices: 12414--12485 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
12404 TTCTGCCATA
12414 GTTTATCATTTGAGCAAGGTTAGTGTTGATG
1 GTTTATCATTTGAGCAAGGTTAGTGTTGATG
*
12445 GTTTATCATTTGGGCAAGGTTAGTGTTGATG
1 GTTTATCATTTGAGCAAGGTTAGTGTTGATG
12476 GTTTATCATT
1 GTTTATCATT
12486 CAGGCAAAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.21, C:0.07, G:0.28, T:0.44
Consensus pattern (31 bp):
GTTTATCATTTGAGCAAGGTTAGTGTTGATG
Found at i:12492 original size:31 final size:30
Alignment explanation
Indices: 12414--12498 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 30
12404 TTCTGCCATA
*
12414 GTTTATCATTTGAGCAAGGTTAGTGTTGATG
1 GTTTATCATTAG-GCAAGGTTAGTGTTGATG
*
12445 GTTTATCATTTGGGCAAGGTTAGTGTTGATG
1 GTTTATCA-TTAGGCAAGGTTAGTGTTGATG
12476 GTTTATCATTCAGGCAAAGGTTA
1 GTTTATCATT-AGGC-AAGGTTA
12499 AGAGTTTAGG
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
30 2 0.04
31 37 0.76
32 10 0.20
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (30 bp):
GTTTATCATTAGGCAAGGTTAGTGTTGATG
Done.