Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009939.1 Kokia drynarioides strain JFW-HI SEQ_124681, 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: 31706
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:684 original size:41 final size:40
Alignment explanation
Indices: 639--745 Score: 101
Period size: 39 Copynumber: 2.6 Consensus size: 40
629 ACGTCGTTAT
** * *
639 TGCTTAATTTTTAGCGGTCTTTTTCCCATAAACGCTGCTAA
1 TGCTTAATTTTTAGCGAACGTTTT-CCATAAACGCTACTAA
* * * *
680 TGCTTTTTATTTATAGC-AACGTTTTCCATAAACGTTACTAT
1 TGC--TTAATTTTTAGCGAACGTTTTCCATAAACGCTACTAA
721 TGCTTAATTTTTAGCG-ACGTTTTCC
1 TGCTTAATTTTTAGCGAACGTTTTCC
746 CGTAAATGCC
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
39 19 0.36
41 19 0.36
42 5 0.09
43 10 0.19
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.45
Consensus pattern (40 bp):
TGCTTAATTTTTAGCGAACGTTTTCCATAAACGCTACTAA
Found at i:2494 original size:41 final size:41
Alignment explanation
Indices: 2449--2528 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
2439 TTAATAAAAA
* * *
2449 CCGCTAATGCTTTGACCTTTAGTGACGTTTTCTCATAAACG
1 CCGCTAATGCTCTGACCTTTAATGACATTTTCTCATAAACG
*
2490 CCGCTAATGCTCTGACCTTTAATGATATTTTCTCATAAA
1 CCGCTAATGCTCTGACCTTTAATGACATTTTCTCATAAA
2529 TGTTGATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.38
Consensus pattern (41 bp):
CCGCTAATGCTCTGACCTTTAATGACATTTTCTCATAAACG
Found at i:4725 original size:23 final size:23
Alignment explanation
Indices: 4682--4734 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
4672 AAAATTGAAT
* * *
4682 TTCGAGTTAATCGAATCGAGTTA
1 TTCGAGTAAATCAAATCGAGTAA
4705 TTCGAGTAAACTCAAAT-GAGTAA
1 TTCGAGTAAA-TCAAATCGAGTAA
4728 TTCGAGT
1 TTCGAGT
4735 TTTGAGTTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (23 bp):
TTCGAGTAAATCAAATCGAGTAA
Found at i:7617 original size:22 final size:21
Alignment explanation
Indices: 7591--7635 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
7581 AGAAAATAAA
7591 AATTTAAAAATTAATTGTTTAT
1 AATTTAAAAATTAATT-TTTAT
* *
7613 AATTTATAATTTAATTTTTAT
1 AATTTAAAAATTAATTTTTAT
7634 AA
1 AA
7636 ATATTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
AATTTAAAAATTAATTTTTAT
Found at i:7645 original size:18 final size:18
Alignment explanation
Indices: 7622--7674 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
7612 TAATTTATAA
7622 TTTAATTTTT-ATAAATAT
1 TTTAATTTTTAAT-AATAT
*
7640 TTTAATTTTTAATATTAT
1 TTTAATTTTTAATAATAT
*
7658 TTTGAATTTTTAGTAAT
1 TTT-AATTTTTAATAAT
7675 TTTATAGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 17 0.57
19 13 0.43
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTAATTTTTAATAATAT
Found at i:14677 original size:15 final size:15
Alignment explanation
Indices: 14659--14690 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
14649 TCGTATTAGT
*
14659 AATTAATTTTAATTA
1 AATTAATTTTAAATA
14674 AATTAATTTTAAATA
1 AATTAATTTTAAATA
14689 AA
1 AA
14691 AAAATAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTAATTTTAAATA
Found at i:17780 original size:23 final size:23
Alignment explanation
Indices: 17752--17916 Score: 107
Period size: 23 Copynumber: 7.3 Consensus size: 23
17742 ACACTAGCGC
17752 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
17775 GATCTCTGTTTAGCA-TGTTTGGT
1 GCTCTCTGTTTAGCACTGTGT-GT
*
17798 GCTCTCTGTTATTAGCACT-TCGCGT
1 GCTCTCTG-T-TTAGCACTGT-GTGT
* *
17823 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
17846 G--CTC-----AGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
17862 ACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
17885 GCTCTCTGTTGCCTAGCACT-TATGT
1 GCTCTCTGTT---TAGCACTGTGTGT
17910 GCTCTCT
1 GCTCTCT
17917 ATTCAGTACT
Statistics
Matches: 114, Mismatches: 12, Indels: 30
0.73 0.08 0.19
Matches are distributed among these distances:
16 11 0.10
18 3 0.03
21 3 0.03
22 4 0.04
23 55 0.48
24 2 0.02
25 28 0.25
26 8 0.07
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:17848 original size:48 final size:46
Alignment explanation
Indices: 17752--17849 Score: 110
Period size: 48 Copynumber: 2.1 Consensus size: 46
17742 ACACTAGCGC
* * *
17752 GCTCTCTGTTTAGCACTGTGTGTGATCTCTGTTTAGCATGTTTGGT
1 GCTCTCTGTTTAGCACTGTGCGTGATCTCTGATTAGCATCTTTGGT
*
17798 GCTCTCTGTTATTAGCACT-TCGCGTGCTCTCTGATTAGCA-CTTTGTGT
1 GCTCTCTG-T-TTAGCACTGT-GCGTGATCTCTGATTAGCATCTTTG-GT
17846 GCTC
1 GCTC
17850 AGTACTTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
46 8 0.18
47 6 0.14
48 30 0.68
ACGTcount: A:0.11, C:0.22, G:0.23, T:0.43
Consensus pattern (46 bp):
GCTCTCTGTTTAGCACTGTGCGTGATCTCTGATTAGCATCTTTGGT
Found at i:31612 original size:21 final size:19
Alignment explanation
Indices: 31587--31629 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
31577 TTTAATTTTT
*
31587 TAATATTTAAAAATATTAAAA
1 TAATA-TTAAAAA-ATAAAAA
31608 TAATATTAAAAAATAAAAA
1 TAATATTAAAAAATAAAAA
31627 TAA
1 TAA
31630 CTAAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 7 0.33
21 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATATTAAAAAATAAAAA
Found at i:31614 original size:11 final size:10
Alignment explanation
Indices: 31588--31622 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
31578 TTAATTTTTT
*
31588 AATATTTAAA
1 AATATTAAAA
31598 AATATTAAAA
1 AATATTAAAA
31608 TAATATTAAAA
1 -AATATTAAAA
31619 AATA
1 AATA
31623 AAAATAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AATATTAAAA
Done.