Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002962.1 Kokia drynarioides strain JFW-HI SEQ_115433, 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: 6172
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1569 original size:17 final size:17
Alignment explanation
Indices: 1542--1653 Score: 100
Period size: 17 Copynumber: 6.2 Consensus size: 17
1532 ATTTGAACTT
1542 AATTTTGAATTGT-TTTTA
1 AATTTT-AATT-TATTTTA
1560 AATTTTAATTTATTTTA
1 AATTTTAATTTATTTTA
* *
1577 AGTTTAAATTTATTTTA
1 AATTTTAATTTATTTTA
* *
1594 AATTTAAACTTATTTTGA
1 AATTTTAATTTATTTT-A
*
1612 GTAAGTTTAAATTTATTTTAA
1 --AA-TTTTAATTTATTTT-A
*
1633 AATTTAAATTTATTTTA
1 AATTTTAATTTATTTTA
1650 AATT
1 AATT
1654 AAAATTTAAT
Statistics
Matches: 83, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
16 1 0.01
17 43 0.52
18 21 0.25
19 2 0.02
20 2 0.02
21 14 0.17
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (17 bp):
AATTTTAATTTATTTTA
Found at i:1582 original size:6 final size:6
Alignment explanation
Indices: 1556--1662 Score: 53
Period size: 6 Copynumber: 17.8 Consensus size: 6
1546 TTGAATTGTT
* * * *
1556 TTTAAA TTTTAA TTT-AT TTTAAG TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
1602 CTT-AT TTTGAGTAA GTTTAAA TTT-AT TTTAAAA TTTAAA TTT-AT TTTAAA
1 TTTAAA TTT-A--AA -TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
*
1652 TTAAAA TTTAA
1 TTTAAA TTTAA
1663 TTAAAAGTAT
Statistics
Matches: 75, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
5 19 0.25
6 45 0.60
7 6 0.08
9 2 0.03
10 3 0.04
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:1626 original size:38 final size:39
Alignment explanation
Indices: 1575--1648 Score: 132
Period size: 38 Copynumber: 1.9 Consensus size: 39
1565 TAATTTATTT
1575 TAAGTTTAAATTTATTTT-AAATTTAAACTTATTTTGAG
1 TAAGTTTAAATTTATTTTAAAATTTAAACTTATTTTGAG
*
1613 TAAGTTTAAATTTATTTTAAAATTTAAATTTATTTT
1 TAAGTTTAAATTTATTTTAAAATTTAAACTTATTTT
1649 AAATTAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 18 0.53
39 16 0.47
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.55
Consensus pattern (39 bp):
TAAGTTTAAATTTATTTTAAAATTTAAACTTATTTTGAG
Found at i:1658 original size:17 final size:17
Alignment explanation
Indices: 1555--1661 Score: 133
Period size: 17 Copynumber: 6.0 Consensus size: 17
1545 TTTGAATTGT
*
1555 TTTTAAATTTTAATTTA
1 TTTTAAATTTAAATTTA
*
1572 TTTTAAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
*
1589 TTTTAAATTTAAACTTA
1 TTTTAAATTTAAATTTA
1606 TTTTGAGTAAGTTTAAATTTA
1 TTTT-A--AA-TTTAAATTTA
1627 TTTTAAAATTTAAATTTA
1 TTTT-AAATTTAAATTTA
*
1645 TTTTAAATTAAAATTTA
1 TTTTAAATTTAAATTTA
1662 ATTAAAAGTA
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
17 46 0.58
18 15 0.19
19 2 0.03
20 2 0.03
21 14 0.18
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:2357 original size:10 final size:10
Alignment explanation
Indices: 2326--2385 Score: 68
Period size: 10 Copynumber: 5.9 Consensus size: 10
2316 CATTTTCGGT
*
2326 TATTAAAAATA
1 TATTAATAA-A
2337 TATTAAATAAA
1 TATT-AATAAA
2348 TATTAATAAA
1 TATTAATAAA
*
2358 TAATAAT-AA
1 TATTAATAAA
*
2367 CATTAATAAA
1 TATTAATAAA
2377 TATTAATAA
1 TATTAATAA
2386 TAAGAAGAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
9 7 0.17
10 22 0.52
11 9 0.21
12 4 0.10
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (10 bp):
TATTAATAAA
Found at i:2371 original size:19 final size:19
Alignment explanation
Indices: 2349--2385 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2339 TTAAATAAAT
2349 ATTAATAAATAATAATAAC
1 ATTAATAAATAATAATAAC
*
2368 ATTAATAAATATTAATAA
1 ATTAATAAATAATAATAA
2386 TAAGAAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTAATAAATAATAATAAC
Found at i:3137 original size:30 final size:30
Alignment explanation
Indices: 3091--3165 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
3081 CCCAAACTAT
*
3091 CCAAAAATCATA-TTTTGACACTCGAACTTA
1 CCAAAAATTATATTTTTGAC-CTCGAACTTA
* * *
3121 CC-AAAATTCTATTTTTGACCTCGAATTTT
1 CCAAAAATTATATTTTTGACCTCGAACTTA
3150 CCAAAAATTATATTTT
1 CCAAAAATTATATTTT
3166 AACCCTAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
29 17 0.45
30 21 0.55
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (30 bp):
CCAAAAATTATATTTTTGACCTCGAACTTA
Found at i:3163 original size:59 final size:58
Alignment explanation
Indices: 3090--3383 Score: 290
Period size: 59 Copynumber: 5.0 Consensus size: 58
3080 TCCCAAACTA
* * * * * *
3090 TCCAAAAATCATATTTTGACACTCGAACTTACCAAAATTCTATTTTTGACCTCGAATTT
1 TCCAAAAATTACATTTT-ACCCTCAAACTTTCCAAAATTCCATTTTTGACCTCGAATTT
* * * * *
3149 TCCAAAAATTATATTTTAACCCT-AAACTTTCAAAAATTCCA-TTTTAACCCCAAATTT
1 TCCAAAAATTACATTTT-ACCCTCAAACTTTCCAAAATTCCATTTTTGACCTCGAATTT
* ** *
3206 TCCAAAAATTACATTTTTACCCTTAAACTTTCCAAAATTCCATTTTTGACCTTTATTTT
1 TCCAAAAATTACA-TTTTACCCTCAAACTTTCCAAAATTCCATTTTTGACCTCGAATTT
* * ** *
3265 TCCAAAAATTACATTTTACCCTCAAAATTTCCAAAAATTCAAAATTTGACC-CCAATTTT
1 TCCAAAAATTACATTTTACCCTCAAACTTTCC-AAAATTCCATTTTTGACCTCGAA-TTT
* * *
3324 TCCAAAAATTACCATTTTACCCTCGAAC-TTCCAAAAATTCTATTTTTGACCTCGATTTT
1 TCCAAAAATTA-CATTTTACCCTCAAACTTTCC-AAAATTCCATTTTTGACCTCGAATTT
3383 T
1 T
3384 ATTTTCAAAA
Statistics
Matches: 196, Mismatches: 32, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
57 30 0.15
58 53 0.27
59 97 0.49
60 16 0.08
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (58 bp):
TCCAAAAATTACATTTTACCCTCAAACTTTCCAAAATTCCATTTTTGACCTCGAATTT
Found at i:3179 original size:29 final size:28
Alignment explanation
Indices: 3147--3362 Score: 168
Period size: 29 Copynumber: 7.4 Consensus size: 28
3137 GACCTCGAAT
*
3147 TTTCCAAAAATTATATTTTAACCCTAAAC
1 TTTCCAAAAATTACATTTT-ACCCTAAAC
* * *
3176 TTT-CAAAAATTCCATTTTAACCCCAAAT
1 TTTCCAAAAATTACATTTT-ACCCTAAAC
3204 TTTCCAAAAATTACATTTTTACCCTTAAAC
1 TTTCCAAAAATTACA-TTTTACCC-TAAAC
* * * **
3234 TTTCC-AAAATTCCATTTTTGACCTTTATT
1 TTTCCAAAAATTACA-TTTT-ACCCTAAAC
*
3263 TTTCCAAAAATTACATTTTACCCTCAAAA
1 TTTCCAAAAATTACATTTTACCCT-AAAC
* * * **
3292 TTTCCAAAAATTCAAAATTTGACCCCAATT
1 TTTCCAAAAATT--ACATTTTACCCTAAAC
*
3322 TTTCCAAAAATTACCATTTTACCCTCGAAC
1 TTTCCAAAAATTA-CATTTTACCCT-AAAC
3352 -TTCCAAAAATT
1 TTTCCAAAAATT
3363 CTATTTTTGA
Statistics
Matches: 149, Mismatches: 28, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
28 29 0.19
29 73 0.49
30 38 0.26
31 9 0.06
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.38
Consensus pattern (28 bp):
TTTCCAAAAATTACATTTTACCCTAAAC
Found at i:3370 original size:29 final size:29
Alignment explanation
Indices: 3083--3370 Score: 139
Period size: 29 Copynumber: 9.8 Consensus size: 29
3073 CTAGAGGTCC
* *
3083 CAAACTATCCAAAAA-TCATATTTTGACACT
1 CAAACT-TCCAAAAATTC-TATTTTTACCCT
*
3113 CGAACTTACC-AAAATTCTATTTTTGA-CCT
1 CAAACTT-CCAAAAATTCTATTTTT-ACCCT
** * *
3142 CGAATTTTCCAAAAATTATATTTTAACCCT
1 C-AAACTTCCAAAAATTCTATTTTTACCCT
* * *
3172 -AAACTTTCAAAAATTCCATTTTAACCC-
1 CAAACTTCCAAAAATTCTATTTTTACCCT
*
3199 CAAATTTTCCAAAAATTAC-ATTTTTACCCT
1 CAAA-CTTCCAAAAATT-CTATTTTTACCCT
* * *
3229 TAAACTTTCC-AAAATTCCATTTTTGACCTT
1 CAAAC-TTCCAAAAATTCTATTTTT-ACCCT
* ***
3259 TATTTTTCCAAAAATTAC-A-TTTTACCCT
1 CAAACTTCCAAAAATT-CTATTTTTACCCT
* * * *
3287 CAAAATTTCCAAAAATTCAAAATTTGACCC-
1 C-AAACTTCCAAAAATTC-TATTTTTACCCT
** *
3317 CAATTTTTCCAAAAATTACCA-TTTTACCCT
1 CAA-ACTTCCAAAAATT-CTATTTTTACCCT
*
3347 CGAACTTCCAAAAATTCTATTTTT
1 CAAACTTCCAAAAATTCTATTTTT
3371 GACCTCGATT
Statistics
Matches: 201, Mismatches: 34, Indels: 47
0.71 0.12 0.17
Matches are distributed among these distances:
28 33 0.16
29 93 0.46
30 66 0.33
31 9 0.04
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.38
Consensus pattern (29 bp):
CAAACTTCCAAAAATTCTATTTTTACCCT
Done.