Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011159.1 Kokia drynarioides strain JFW-HI SEQ_126133, 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: 7786
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:278 original size:20 final size:20
Alignment explanation
Indices: 255--292 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
245 GAATTTTTAT
*
255 AATGTTTTTTTTATTTTCAA
1 AATGTTTTTTATATTTTCAA
275 AATGTTTTTTATATTTTC
1 AATGTTTTTTATATTTTC
293 GAATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (20 bp):
AATGTTTTTTATATTTTCAA
Found at i:1453 original size:30 final size:30
Alignment explanation
Indices: 1419--1490 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
1409 TTGTAATTTC
*
1419 ATTTTTATTTTAAATTTCCTGTAGATTTTA
1 ATTTTTATTTTAAATTTCCTGTAGATTATA
* * *
1449 ATTTTAATTTCAAATTTCCTGTATATTATA
1 ATTTTTATTTTAAATTTCCTGTAGATTATA
*
1479 ATTATTTTTTTT
1 ATT-TTTATTTT
1491 TTGAAAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 29 0.85
31 5 0.15
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (30 bp):
ATTTTTATTTTAAATTTCCTGTAGATTATA
Found at i:2423 original size:60 final size:60
Alignment explanation
Indices: 2297--2448 Score: 168
Period size: 59 Copynumber: 2.5 Consensus size: 60
2287 TGTATGGCTA
*
2297 ACAAAAAAAATTGATTTTTTACCAGATAAAAAAGAAAGTGTCGGTCGTGCAATGACCAAC
1 ACAAAAAAAATTGATTTTTTACCAGATAAAAAAGAAAGTGTCGGCCGTGCAATGACCAAC
* ** * * *
2357 AC-AAAAAAATTGATTTTTTACCAAATAAAAAAG-GGGTGTTGGCCATTGC-AT-AGTCAAC
1 ACAAAAAAAATTGATTTTTTACCAGATAAAAAAGAAAGTGTCGGCC-GTGCAATGA-CCAAC
*
2415 ACAAAAAAAAATTAATTTTTTTACCAGATAAAAA
1 AC-AAAAAAAATTGA-TTTTTTACCAGATAAAAA
2449 TGGCCGACAC
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
57 1 0.01
58 15 0.19
59 33 0.42
60 12 0.15
61 17 0.22
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (60 bp):
ACAAAAAAAATTGATTTTTTACCAGATAAAAAAGAAAGTGTCGGCCGTGCAATGACCAAC
Found at i:2686 original size:61 final size:61
Alignment explanation
Indices: 2565--2800 Score: 246
Period size: 61 Copynumber: 3.9 Consensus size: 61
2555 GTGTTGGCCA
* * * *
2565 TTATCTGAATAAAAAATCAAA-TTTTTGGGTGTTAACCATGCCAT-GACGACA-CCATTTTT
1 TTATCTG-ATAAAAAATCAAATTTTTTTGGTGTTGACCATGCAATGGCCGACACCCATTTTT
* * * * *
2624 TTGTCAGATAAAAAATTTAAATTTTTTTGGTGTTGGCCATGCAATTGCCGACACCCATTTTT
1 TTATCTGATAAAAAA-TCAAATTTTTTTGGTGTTGACCATGCAATGGCCGACACCCATTTTT
* * ** **
2686 TTATCTGGTAAAAAATTCAAATTTTTTT-ATGTTGACCATGCAATGGTTGACACCCCCTTTT
1 TTATCTGATAAAAAA-TCAAATTTTTTTGGTGTTGACCATGCAATGGCCGACACCCATTTTT
* * * *
2747 TTATCTGGTAAAAAATCAATTTTTTTTTGTGTTGGCCATGCAATGGCCGACACC
1 TTATCTGATAAAAAATCAAATTTTTTTGGTGTTGACCATGCAATGGCCGACACC
2801 AACTTTCCCT
Statistics
Matches: 148, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
58 8 0.05
59 9 0.06
60 30 0.20
61 69 0.47
62 32 0.22
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (61 bp):
TTATCTGATAAAAAATCAAATTTTTTTGGTGTTGACCATGCAATGGCCGACACCCATTTTT
Found at i:3554 original size:13 final size:13
Alignment explanation
Indices: 3524--3560 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3514 ATTATCGACA
3524 AATTAAAAAT-AT
1 AATTAAAAATAAT
3536 -ATTAAAAATAAT
1 AATTAAAAATAAT
*
3548 AATTAAAATTAAT
1 AATTAAAAATAAT
3561 TTTAAGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 9 0.41
12 2 0.09
13 11 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATTAAAAATAAT
Found at i:6690 original size:10 final size:11
Alignment explanation
Indices: 6652--6692 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
6642 TTGAAGTTGA
6652 AATTT-AAATT
1 AATTTAAAATT
6662 ACATTTAAAATT
1 A-ATTTAAAATT
*
6674 AATTTAACATT
1 AATTTAAAATT
6685 -ATTTAAAA
1 AATTTAAAA
6693 AAAAAGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 8 0.30
11 13 0.48
12 6 0.22
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:6792 original size:85 final size:84
Alignment explanation
Indices: 6684--6896 Score: 338
Period size: 85 Copynumber: 2.5 Consensus size: 84
6674 AATTTAACAT
* * *
6684 TATTTAAAAAAAAAGATTATTATTATATTTCAATTTATATCAAATAATGTGTTGATTTGATAATA
1 TATTTAAATAAAAAGATTATTATTATATTTCAATTT-TATCAAATAATATGTTGATTTGACAATA
6749 CATTATTTATCAAATTTTAA
65 CATTATTTATCAAATTTTAA
* *
6769 TATTTAAATAAAAAGATTATTATTATATTGCAATTTTTATCAAATAATATTTTGATTTGACAATA
1 TATTTAAATAAAAAGATTATTATTATATTTCAA-TTTTATCAAATAATATGTTGATTTGACAATA
6834 CATTATTTATCAAATTTTAA
65 CATTATTTATCAAATTTTAA
* *
6854 TATTTAAATTAAAA-ATTATTATTATATTTTAATTTTATCAAAT
1 TATTTAAATAAAAAGATTATTATTATATTTCAATTTTATCAAAT
6897 TTTAAATTTA
Statistics
Matches: 119, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
83 11 0.09
84 16 0.13
85 89 0.75
86 3 0.03
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (84 bp):
TATTTAAATAAAAAGATTATTATTATATTTCAATTTTATCAAATAATATGTTGATTTGACAATAC
ATTATTTATCAAATTTTAA
Found at i:6891 original size:16 final size:16
Alignment explanation
Indices: 6867--6910 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
6857 TTAAATTAAA
*
6867 AATTATTATTATATTTT
1 AATT-TTATTAAATTTT
*
6884 AATTTTATCAAATTTT
1 AATTTTATTAAATTTT
*
6900 AAATTTATTAA
1 AATTTTATTAA
6911 CCAAAATAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTTTATTAAATTTT
Done.