Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015350.1 Kokia drynarioides strain JFW-HI SEQ_130397, 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: 324464
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 268 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:286789 original size:56 final size:56
Alignment explanation
Indices: 286727--286841 Score: 203
Period size: 56 Copynumber: 2.1 Consensus size: 56
286717 CATAAATTAA
* *
286727 ATAAAAAACTTAACAAATAGTATAAATATATAATTATTGAAGATAATAAATTGTGC
1 ATAAAAAACTTAACAAATAGTATAAATATATAATTACTGAAGATAATAAATTGTAC
*
286783 ATAAAAAACTTAATAAATAGTATAAATATATAATTACTGAAGATAATAAATTGTAC
1 ATAAAAAACTTAACAAATAGTATAAATATATAATTACTGAAGATAATAAATTGTAC
286839 ATA
1 ATA
286842 TTAAAATAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (56 bp):
ATAAAAAACTTAACAAATAGTATAAATATATAATTACTGAAGATAATAAATTGTAC
Found at i:288276 original size:20 final size:20
Alignment explanation
Indices: 288240--288277 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
288230 ATGTGGCATA
288240 AATTTAGTCATTATATTTTT
1 AATTTAGTCATTATATTTTT
*
288260 AATTATAGTTATT-TATTT
1 AATT-TAGTCATTATATTT
288278 AATTAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (20 bp):
AATTTAGTCATTATATTTTT
Found at i:289675 original size:23 final size:23
Alignment explanation
Indices: 289643--289689 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
289633 TGCACCGGTA
289643 TATTAAAAAAAATGTAATTTCCT
1 TATTAAAAAAAATGTAATTTCCT
* **
289666 TATTAGAAAATGTGTAATTTCCT
1 TATTAAAAAAAATGTAATTTCCT
289689 T
1 T
289690 TACTTGTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (23 bp):
TATTAAAAAAAATGTAATTTCCT
Found at i:291183 original size:14 final size:15
Alignment explanation
Indices: 291159--291188 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
291149 GCATCTTTTC
291159 TTTCTCTTTTTCTTT
1 TTTCTCTTTTTCTTT
291174 TTTC-CTTTTTCTTT
1 TTTCTCTTTTTCTTT
291188 T
1 T
291189 CTTTCCCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTCTCTTTTTCTTT
Found at i:293348 original size:15 final size:16
Alignment explanation
Indices: 293323--293352 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
293313 TAACTATTAA
293323 TTAATAATAAAATATC
1 TTAATAATAAAATATC
293339 TTAA-AATAAAATAT
1 TTAATAATAAAATAT
293353 TAAAAAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAATAATAAAATATC
Found at i:300093 original size:18 final size:20
Alignment explanation
Indices: 300067--300104 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
300057 AAATAATACA
300067 TTAAATT-AA-AAATAACTC
1 TTAAATTAAAGAAATAACTC
*
300085 TTAATTTAAAGAAATAACTC
1 TTAAATTAAAGAAATAACTC
300105 AATAGATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TTAAATTAAAGAAATAACTC
Found at i:314380 original size:59 final size:60
Alignment explanation
Indices: 314309--314463 Score: 213
Period size: 59 Copynumber: 2.6 Consensus size: 60
314299 GAACTTCTCT
*
314309 AAAATTATATTTTGACCCTCAAACTTCTCCAAAATTTCATTTTAACCC-CAAAATTTTCC
1 AAAATTACATTTTGACCCTCAAACTTCTCCAAAATTTCATTTTAACCCTCAAAATTTTCC
* * * * * *
314368 AAAATTACATTTTAACCCTCAAACTTCTCTAAAATTTCATTTTGACCCTTAAACTTTTCT
1 AAAATTACATTTTGACCCTCAAACTTCTCCAAAATTTCATTTTAACCCTCAAAATTTTCC
* * *
314428 AACATTTCATTTTGACCCTCAAACTTTTCCAAAATT
1 AAAATTACATTTTGACCCTCAAACTTCTCCAAAATT
314464 ACGTTTTGAC
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
59 44 0.53
60 39 0.47
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (60 bp):
AAAATTACATTTTGACCCTCAAACTTCTCCAAAATTTCATTTTAACCCTCAAAATTTTCC
Found at i:314422 original size:89 final size:90
Alignment explanation
Indices: 314271--314475 Score: 263
Period size: 89 Copynumber: 2.3 Consensus size: 90
314261 ATTGTTTGGT
* * **
314271 AATTTTCTAAAATTGCATTTTGAA-CCTTGAACTTCTCTAAAATTATATTTTGACCCTCAAACTT
1 AATTTTCCAAAATTACATTTT-AACCCTCAAACTTCTCTAAAATTATATTTTGACCCTCAAACTT
314335 CTCCAAAATTTCATTTTAACCC-CAA
65 CTCCAAAATTTCATTTTAACCCTCAA
*
314360 AATTTTCCAAAATTACATTTTAACCCTCAAACTTCTCTAAAATT-TCATTTTGACCCTTAAACTT
1 AATTTTCCAAAATTACATTTTAACCCTCAAACTTCTCTAAAATTAT-ATTTTGACCCTCAAACTT
* * * *
314424 TTCTAACATTTCATTTTGACCCTCAA
65 CTCCAAAATTTCATTTTAACCCTCAA
* * *
314450 ACTTTTCCAAAATTACGTTTTGACCC
1 AATTTTCCAAAATTACATTTTAACCC
314476 CGCATCCTCC
Statistics
Matches: 101, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
88 3 0.03
89 72 0.71
90 26 0.26
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (90 bp):
AATTTTCCAAAATTACATTTTAACCCTCAAACTTCTCTAAAATTATATTTTGACCCTCAAACTTC
TCCAAAATTTCATTTTAACCCTCAA
Found at i:314473 original size:30 final size:30
Alignment explanation
Indices: 314273--314475 Score: 219
Period size: 30 Copynumber: 6.8 Consensus size: 30
314263 TGTTTGGTAA
* * **
314273 TTTTCTAAAATTGCATTTTGAACCTTGAAC
1 TTTTCTAAAATTACATTTTGACCCTCAAAC
* *
314303 TTCTCTAAAATTATATTTTGACCCTCAAAC
1 TTTTCTAAAATTACATTTTGACCCTCAAAC
* * * * *
314333 TTCTCCAAAATTTCATTTTAACCC-CAAAA
1 TTTTCTAAAATTACATTTTGACCCTCAAAC
* *
314362 TTTTCCAAAATTACATTTTAACCCTCAAAC
1 TTTTCTAAAATTACATTTTGACCCTCAAAC
* * *
314392 TTCTCTAAAATTTCATTTTGACCCTTAAAC
1 TTTTCTAAAATTACATTTTGACCCTCAAAC
* *
314422 TTTTCTAACATTTCATTTTGACCCTCAAAC
1 TTTTCTAAAATTACATTTTGACCCTCAAAC
* *
314452 TTTTCCAAAATTACGTTTTGACCC
1 TTTTCTAAAATTACATTTTGACCC
314476 CGCATCCTCC
Statistics
Matches: 146, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
29 26 0.18
30 120 0.82
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (30 bp):
TTTTCTAAAATTACATTTTGACCCTCAAAC
Found at i:315560 original size:6 final size:6
Alignment explanation
Indices: 315549--315573 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
315539 TGAGATTAAA
315549 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
315574 TGGAACAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:315692 original size:7 final size:7
Alignment explanation
Indices: 315661--315694 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
315651 CAATTCCAGC
315661 CTCC-CA
1 CTCCTCA
*
315667 CTCCCCA
1 CTCCTCA
315674 CTCCTCA
1 CTCCTCA
315681 CTCCTCA
1 CTCCTCA
315688 CTCCTCA
1 CTCCTCA
315695 TTTCCCCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 4 0.15
7 22 0.85
ACGTcount: A:0.15, C:0.62, G:0.00, T:0.24
Consensus pattern (7 bp):
CTCCTCA
Found at i:316830 original size:23 final size:23
Alignment explanation
Indices: 316804--316854 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
316794 GAAGCTATCA
*
316804 ACAAAATCAAATCTTTAAGATTT
1 ACAAAATCAAATCTTTAAGAATT
*
316827 ACAAAATCAAATCTTTTAGAATT
1 ACAAAATCAAATCTTTAAGAATT
316850 ACAAA
1 ACAAA
316855 TCCTCTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (23 bp):
ACAAAATCAAATCTTTAAGAATT
Found at i:318429 original size:2 final size:2
Alignment explanation
Indices: 318422--318462 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
318412 TAAGCAGAGA
*
318422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
318463 CAGGTGGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:320993 original size:28 final size:28
Alignment explanation
Indices: 320937--320993 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
320927 ACTATAGAGT
* *
320937 AAAAATCAAGGCATTGATCTTAAAGAAG
1 AAAAATCAAAGCATTGATCTTAAACAAG
320965 AAAAATCAAAGCATTGAT-TTCAAACAAG
1 AAAAATCAAAGCATTGATCTT-AAACAAG
320993 A
1 A
320994 GGTGTCAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 24 0.92
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.21
Consensus pattern (28 bp):
AAAAATCAAAGCATTGATCTTAAACAAG
Done.