Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003406.1 Kokia drynarioides strain JFW-HI SEQ_116155, 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: 19745
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Found at i:764 original size:17 final size:17
Alignment explanation
Indices: 744--782 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
734 TATTTATTTT
744 ATAAATATAAATAAT-AA
1 ATAAATA-AAATAATAAA
761 ATAAATAAAATAATAAA
1 ATAAATAAAATAATAAA
778 ATAAA
1 ATAAA
783 ACTTGTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAATAAAATAATAAA
Found at i:1700 original size:11 final size:11
Alignment explanation
Indices: 1684--1709 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1674 TAATGTCCTA
1684 AATCAGTACCT
1 AATCAGTACCT
1695 AATCAGTACCT
1 AATCAGTACCT
1706 AATC
1 AATC
1710 TCGTATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.27, G:0.08, T:0.27
Consensus pattern (11 bp):
AATCAGTACCT
Found at i:2125 original size:29 final size:29
Alignment explanation
Indices: 2092--2176 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 29
2082 AAATTTAAAA
*
2092 TAGGGTCAAAT-TAGAATTTTTGGAAAGTT
1 TAGGGTCAAATCCA-AATTTTTGGAAAGTT
*
2121 TAGGGGTCAAATCCAAATTTTTGAAAAGTT
1 TA-GGGTCAAATCCAAATTTTTGGAAAGTT
*
2151 TGGGGGTCAAATCCAAATTTTTGGAA
1 T-AGGGTCAAATCCAAATTTTTGGAA
2177 GTTCAAGAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 2 0.04
30 46 0.94
31 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (29 bp):
TAGGGTCAAATCCAAATTTTTGGAAAGTT
Found at i:2128 original size:30 final size:30
Alignment explanation
Indices: 2106--2176 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
2096 GTCAAATTAG
2106 AATTTTTGGAAAGTTTAGGGGTCAAATCCA
1 AATTTTTGGAAAGTTTAGGGGTCAAATCCA
* *
2136 AATTTTTGAAAAGTTTGGGGGTCAAATCCA
1 AATTTTTGGAAAGTTTAGGGGTCAAATCCA
2166 AATTTTTGGAA
1 AATTTTTGGAA
2177 GTTCAAGAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (30 bp):
AATTTTTGGAAAGTTTAGGGGTCAAATCCA
Found at i:4231 original size:42 final size:41
Alignment explanation
Indices: 4133--4265 Score: 116
Period size: 40 Copynumber: 3.3 Consensus size: 41
4123 ATAGCTTTAG
* *
4133 GGGTAAAAGTTTGGAT-TG-CTTCAATTTGCCC-CATGG-TA
1 GGGTAAAAGATTGGATGTGTCTTCAATCTGCCCTC-TGGTTA
* **
4171 GGGGTAAGAGATCAGATGGTGTCTTCAATCTGCCCTCTGGTTA
1 -GGGTAAAAGATTGGAT-GTGTCTTCAATCTGCCCTCTGGTTA
* * *
4214 GGGTAAAAGATTGGATG-GTCTTCAA-CGTACTCTCTGATTA
1 GGGTAAAAGATTGGATGTGTCTTCAATC-TGCCCTCTGGTTA
4254 GGGTAAAAGATT
1 GGGTAAAAGATT
4266 CGGGGTTGTA
Statistics
Matches: 77, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
39 13 0.17
40 30 0.39
41 3 0.04
42 28 0.36
43 3 0.04
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.32
Consensus pattern (41 bp):
GGGTAAAAGATTGGATGTGTCTTCAATCTGCCCTCTGGTTA
Found at i:4385 original size:50 final size:50
Alignment explanation
Indices: 4321--4464 Score: 225
Period size: 50 Copynumber: 2.9 Consensus size: 50
4311 CAGGAGTATA
* * * *
4321 AGATTCGCCCTTGCGACTTCGATCTGCCCCTCTACAGCTTTAGGTGAATG
1 AGATTCGCCATTGCGGCTTCAATCTGCTCCTCTACAGCTTTAGGTGAATG
*
4371 AGATTCGCCATTGCGGCTTCAATCTGCTCCTCTACAGCTTTAGGTGTATG
1 AGATTCGCCATTGCGGCTTCAATCTGCTCCTCTACAGCTTTAGGTGAATG
* *
4421 AGATTTGCCATTGCGGCTTCAATCTGTTCCTCTACAGCTTTAGG
1 AGATTCGCCATTGCGGCTTCAATCTGCTCCTCTACAGCTTTAGG
4465 GGTAGAGGAT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 87 1.00
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.33
Consensus pattern (50 bp):
AGATTCGCCATTGCGGCTTCAATCTGCTCCTCTACAGCTTTAGGTGAATG
Found at i:5391 original size:10 final size:9
Alignment explanation
Indices: 5378--5402 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5368 ACCTTTTTTG
5378 TTTTTTTAT
1 TTTTTTTAT
5387 TTTTTTTAT
1 TTTTTTTAT
5396 TTTTTTT
1 TTTTTTT
5403 GGGTTTAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:16225 original size:30 final size:30
Alignment explanation
Indices: 16179--16413 Score: 233
Period size: 30 Copynumber: 8.1 Consensus size: 30
16169 AAATAAAACC
*
16179 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAG
* * * *
16209 AGGTTAAATTTCAATTTTTAGAAAGTTT-G
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAG
* *
16238 GCGGTCAAATCTAAATTTTTGGAAAGTTTA-
1 G-GGTCAAATTTGAATTTTTGGAAAGTTTAG
*
16268 ---TCTAA----AA-TTTTGGAAAGTTTAG
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAG
* *
16290 GGGTCAAATTTGATTTTTTGGGAAA-TTTAA
1 GGGTCAAATTTGAATTTTT-GGAAAGTTTAG
*
16320 GGGTCAAATTTGAATTTTTAGAAAGTTTAG
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAG
* * *
16350 GGGTCAAATCTAAATTTTTGGAAA-TTTTG
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAG
16379 GAGGTCAAATTTGAATTTTTGGAAAGTTTAG
1 G-GGTCAAATTTGAATTTTTGGAAAGTTTAG
16410 GGGT
1 GGGT
16414 TAAAATGTAA
Statistics
Matches: 166, Mismatches: 24, Indels: 30
0.75 0.11 0.14
Matches are distributed among these distances:
21 14 0.08
22 2 0.01
25 4 0.02
26 4 0.02
29 10 0.06
30 122 0.73
31 10 0.06
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (30 bp):
GGGTCAAATTTGAATTTTTGGAAAGTTTAG
Found at i:16270 original size:21 final size:21
Alignment explanation
Indices: 16246--16288 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
16236 TGGCGGTCAA
*
16246 ATCTAAATTTTTGGAAAGTTT
1 ATCTAAAATTTTGGAAAGTTT
16267 ATCTAAAATTTTGGAAAGTTT
1 ATCTAAAATTTTGGAAAGTTT
16288 A
1 A
16289 GGGGTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (21 bp):
ATCTAAAATTTTGGAAAGTTT
Found at i:17600 original size:17 final size:18
Alignment explanation
Indices: 17569--17615 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
17559 ATTTGGTTTG
* *
17569 TATTTGTTTAATTTT-AT
1 TATTTATTTATTTTTCAT
17586 TATTTATTTATTTTTCAT
1 TATTTATTTATTTTTCAT
*
17604 T-TGTATTTATTT
1 TATTTATTTATTT
17616 ACATTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 23 0.88
18 3 0.12
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72
Consensus pattern (18 bp):
TATTTATTTATTTTTCAT
Found at i:17763 original size:13 final size:13
Alignment explanation
Indices: 17745--17779 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
17735 TTATAAAATG
*
17745 ATAAATAAATAAA
1 ATAAATAAACAAA
*
17758 ATAAATATACAAA
1 ATAAATAAACAAA
17771 ATAAATAAA
1 ATAAATAAA
17780 ATTGAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (13 bp):
ATAAATAAACAAA
Found at i:19655 original size:2 final size:2
Alignment explanation
Indices: 19648--19710 Score: 108
Period size: 2 Copynumber: 31.5 Consensus size: 2
19638 CACATACCAT
* *
19648 TC TC TC TC TC TT TC TA TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19690 TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC T
19711 ATATATATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.02, C:0.46, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:19715 original size:2 final size:2
Alignment explanation
Indices: 19710--19745 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19700 TCTCTCTCTC
19710 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.