Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009911.1 Kokia drynarioides strain JFW-HI SEQ_124651, 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: 73094
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:1527 original size:16 final size:16
Alignment explanation
Indices: 1494--1527 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1484 ATTCATTTCC
*
1494 AATTTTTTATACTCAT
1 AATTTTTTATACTAAT
*
1510 AATTTTTTATATTAAT
1 AATTTTTTATACTAAT
1526 AA
1 AA
1528 ACAATGAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTTTTTATACTAAT
Found at i:9348 original size:18 final size:17
Alignment explanation
Indices: 9322--9372 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
9312 TATATTTTAG
*
9322 ATATTTTATATTATTGA
1 ATATATTATATTATTGA
*
9339 ATTATATTATCATT-TTTA
1 A-TATATTAT-ATTATTGA
9357 ATATA-TATATTATTGA
1 ATATATTATATTATTGA
9373 GTTTGGATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 3 0.11
16 6 0.21
17 5 0.18
18 11 0.39
19 3 0.11
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (17 bp):
ATATATTATATTATTGA
Found at i:9695 original size:30 final size:31
Alignment explanation
Indices: 9660--9729 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
9650 GTTTTTATAC
*
9660 TTTAATTTGATTAATTTTAGTCAT-TGTA-TT
1 TTTAATTTGATCAATTTTAGTC-TGTGTACTT
*
9690 TTTAATTTGGTCAATTTTAGTCTGTGTACTT
1 TTTAATTTGATCAATTTTAGTCTGTGTACTT
9721 TTTGAATTT
1 TTT-AATTT
9730 TAAAGTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 1 0.03
30 24 0.69
31 5 0.14
32 5 0.14
ACGTcount: A:0.23, C:0.06, G:0.13, T:0.59
Consensus pattern (31 bp):
TTTAATTTGATCAATTTTAGTCTGTGTACTT
Found at i:11793 original size:30 final size:29
Alignment explanation
Indices: 11728--11796 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
11718 AGTATATTTC
* *
11728 TTTATAATTTCTAAAAGATTAAATGAAAT
1 TTTATCATTTCTAAAAGATCAAATGAAAT
* * *
11757 TATTATCATTTTTAAGAGATCAAAGTGTAAT
1 T-TTATCATTTCTAAAAGATCAAA-TGAAAT
11788 TTTATCATT
1 TTTATCATT
11797 GATAATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 1 0.03
30 26 0.79
31 6 0.18
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.45
Consensus pattern (29 bp):
TTTATCATTTCTAAAAGATCAAATGAAAT
Found at i:17637 original size:23 final size:23
Alignment explanation
Indices: 17610--17653 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
17600 TTTCCAATAA
17610 AAGAAAAA-GAGAAGAAGGAGAAG
1 AAGAAAAAGGAGAAG-AGGAGAAG
17633 AAGAAAAAGGAGAAGAGGAGA
1 AAGAAAAAGGAGAAGAGGAGA
17654 GGAATGTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGGAGAAGAGGAGAAG
Found at i:17642 original size:15 final size:15
Alignment explanation
Indices: 17619--17648 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17609 AAAGAAAAAG
*
17619 AGAAGAAGGAGAAGA
1 AGAAAAAGGAGAAGA
17634 AGAAAAAGGAGAAGA
1 AGAAAAAGGAGAAGA
17649 GGAGAGGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (15 bp):
AGAAAAAGGAGAAGA
Found at i:19391 original size:29 final size:30
Alignment explanation
Indices: 19359--19416 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
19349 TTGAGTGTAT
19359 AATTACACA-AAATTAAAATCAATGTATCA
1 AATTACACATAAATTAAAATCAATGTATCA
* *
19388 AATTACACATTAAATTAAAGTTAATGTAT
1 AATTACACA-TAAATTAAAATCAATGTAT
19417 TTTGATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.36
31 16 0.64
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (30 bp):
AATTACACATAAATTAAAATCAATGTATCA
Found at i:22268 original size:14 final size:15
Alignment explanation
Indices: 22249--22277 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22239 TCACCATATT
22249 TAAATG-ATTTTGTA
1 TAAATGTATTTTGTA
22263 TAAATGTATTTTGTA
1 TAAATGTATTTTGTA
22278 ATAGTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (15 bp):
TAAATGTATTTTGTA
Found at i:23505 original size:8 final size:8
Alignment explanation
Indices: 23494--23520 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
23484 ACAATTCACT
23494 AATTTTAA
1 AATTTTAA
23502 AATTTTAA
1 AATTTTAA
23510 AATTTTAA
1 AATTTTAA
23518 AAT
1 AAT
23521 ATCTCCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:30836 original size:2 final size:2
Alignment explanation
Indices: 30819--30850 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
30809 GGATGCCAGC
30819 CA CA C- CA CA C- CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
30851 TAATATGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.53, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:36465 original size:27 final size:27
Alignment explanation
Indices: 36413--36466 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
36403 CAATTTTGAC
**
36413 ATAATTATAAAATTTAAAAATATTTTT
1 ATAATTATAAAAAATAAAAATATTTTT
*
36440 ATAATT-TAAAAAATAAATAATTTTTTT
1 ATAATTATAAAAAATAAA-AATATTTTT
36467 GGAATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATAATTATAAAAAATAAAAATATTTTT
Found at i:36497 original size:20 final size:20
Alignment explanation
Indices: 36458--36505 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
36448 AAAAATAAAT
36458 AATTTTTTTGGAATTTTTTAA
1 AATTTTTTTGGAA-TTTTTAA
*
36479 GATTTTTTTGAGAA-TTTTAA
1 AATTTTTTTG-GAATTTTTAA
36499 AATTTTT
1 AATTTTT
36506 AAAATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 12 0.50
21 9 0.38
22 3 0.12
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.60
Consensus pattern (20 bp):
AATTTTTTTGGAATTTTTAA
Found at i:36935 original size:16 final size:17
Alignment explanation
Indices: 36904--36936 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
36894 AGCACAATTT
36904 TAGGTAAACTTTTTTTC
1 TAGGTAAACTTTTTTTC
36921 TAGGTAAACTTTTTTT
1 TAGGTAAACTTTTTTT
36937 ACAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (17 bp):
TAGGTAAACTTTTTTTC
Found at i:38363 original size:34 final size:34
Alignment explanation
Indices: 38318--38388 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
38308 CAAGTAAGTA
38318 TTAGTTTTCACCTTTTGTGATAATGTGTTGTT-T
1 TTAGTTTTCACCTTTTGTGATAATGTGTTGTTAT
*
38351 TTAGTTTTTCACCTTTTGTGATAATGTTTTGTTAT
1 TTAG-TTTTCACCTTTTGTGATAATGTGTTGTTAT
38386 TTA
1 TTA
38389 AATGTTGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 4 0.11
34 27 0.77
35 4 0.11
ACGTcount: A:0.17, C:0.08, G:0.15, T:0.59
Consensus pattern (34 bp):
TTAGTTTTCACCTTTTGTGATAATGTGTTGTTAT
Found at i:61620 original size:20 final size:21
Alignment explanation
Indices: 61583--61627 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
61573 TAAAATGATA
*
61583 AAAATTTATAAATATATAA-T
1 AAAATTTAAAAATATATAATT
61603 AAAATTTAAAAA-ATTATAATT
1 AAAATTTAAAAATA-TATAATT
61624 AAAA
1 AAAA
61628 ATAGTTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 16 0.73
21 5 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATTTAAAAATATATAATT
Found at i:65604 original size:25 final size:26
Alignment explanation
Indices: 65560--65610 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
65550 TTAAAAAAGC
* * *
65560 ATATATTTTAAAAAATATATCTTTAA
1 ATATATTTAAAAAAACATATATTTAA
65586 ATATA-TTAAAAAAACATATATTTAA
1 ATATATTTAAAAAAACATATATTTAA
65611 TTCAATTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (26 bp):
ATATATTTAAAAAAACATATATTTAA
Found at i:72153 original size:15 final size:15
Alignment explanation
Indices: 72154--72183 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
72144 TATTAATCGA
72154 ATTAATCGAATTAAT
1 ATTAATCGAATTAAT
72169 ATTAATCGAATTAAT
1 ATTAATCGAATTAAT
72184 CGAATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (15 bp):
ATTAATCGAATTAAT
Found at i:72159 original size:9 final size:9
Alignment explanation
Indices: 72133--72190 Score: 74
Period size: 9 Copynumber: 7.1 Consensus size: 9
72123 TGATTAACCG
72133 AATCGAATT
1 AATCGAATT
72142 AAT---ATT
1 AATCGAATT
72148 AATCGAATT
1 AATCGAATT
72157 AATCGAATT
1 AATCGAATT
72166 AAT---ATT
1 AATCGAATT
72172 AATCGAATT
1 AATCGAATT
72181 AATCGAATT
1 AATCGAATT
72190 A
1 A
72191 TATAATTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
6 12 0.28
9 31 0.72
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (9 bp):
AATCGAATT
Found at i:72165 original size:24 final size:24
Alignment explanation
Indices: 72133--72190 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
72123 TGATTAACCG
72133 AATCGAATTAATATTAATCGAATT
1 AATCGAATTAATATTAATCGAATT
72157 AATCGAATTAATATTAATCGAATT
1 AATCGAATTAATATTAATCGAATT
72181 AATCGAATTA
1 AATCGAATTA
72191 TATAATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (24 bp):
AATCGAATTAATATTAATCGAATT
Done.