Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011599.1 Kokia drynarioides strain JFW-HI SEQ_126589, 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: 7603
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:344 original size:17 final size:16
Alignment explanation
Indices: 317--384 Score: 50
Period size: 17 Copynumber: 4.1 Consensus size: 16
307 AAATCTTTAT
*
317 TTTAAATTTATTCTAAG
1 TTTAAA-TTATTCTAAA
*
334 TTTAGAATTATTTTAAA
1 TTTA-AATTATTCTAAA
*
351 TTTAAATT-TAT-TAAG
1 TTTAAATTAT-TCTAAA
*
366 TTTAAATTTATTTTAAA
1 TTTAAA-TTATTCTAAA
383 TT
1 TT
385 CAATTTTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 10 0.24
16 8 0.19
17 22 0.52
18 2 0.05
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (16 bp):
TTTAAATTATTCTAAA
Found at i:377 original size:32 final size:34
Alignment explanation
Indices: 317--384 Score: 106
Period size: 32 Copynumber: 2.1 Consensus size: 34
307 AAATCTTTAT
317 TTTAAATTTATTCTAAGTTTAGAATTATTTTAAA
1 TTTAAATTTATTCTAAGTTTAGAATTATTTTAAA
351 TTTAAATTTA-T-TAAGTTTA-AATTTATTTTAAA
1 TTTAAATTTATTCTAAGTTTAGAA-TTATTTTAAA
383 TT
1 TT
385 CAATTTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 2 0.06
32 20 0.61
33 1 0.03
34 10 0.30
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (34 bp):
TTTAAATTTATTCTAAGTTTAGAATTATTTTAAA
Found at i:1189 original size:3 final size:3
Alignment explanation
Indices: 1171--1232 Score: 63
Period size: 3 Copynumber: 20.7 Consensus size: 3
1161 GCATTAAATG
* * *
1171 AAT ATT AAT AAAT AAT AAT ATT ATT AAT -AT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
1216 ATT AAT AAT AGT AAT AA
1 AAT AAT AAT AAT AAT AA
1233 CAACAAAAAG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:1200 original size:9 final size:9
Alignment explanation
Indices: 1171--1232 Score: 76
Period size: 9 Copynumber: 7.2 Consensus size: 9
1161 GCATTAAATG
1171 AATATTAAT
1 AATATTAAT
1180 AA-A-TAAT
1 AATATTAAT
*
1187 AATATTATT
1 AATATTAAT
1196 AATA-TAAT
1 AATATTAAT
*
1204 AATAATAAT
1 AATATTAAT
1213 AATATTAAT
1 AATATTAAT
*
1222 AATAGTAAT
1 AATATTAAT
1231 AA
1 AA
1233 CAACAAAAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
7 6 0.13
8 9 0.20
9 31 0.67
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (9 bp):
AATATTAAT
Found at i:1206 original size:20 final size:19
Alignment explanation
Indices: 1173--1210 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1163 ATTAAATGAA
1173 TATTAATAAATAATAATAT
1 TATTAATAAATAATAATAT
1192 TATTAATATAATAATAATA
1 TATTAATA-AATAATAATA
1211 ATAATATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATTAATAAATAATAATAT
Found at i:2371 original size:29 final size:29
Alignment explanation
Indices: 2317--2846 Score: 241
Period size: 29 Copynumber: 17.9 Consensus size: 29
2307 CAAAATTTTG
*
2317 ATTTTAACCCCTAAACTTTTCC-AAAATTCC
1 ATTTTTACCCC-AAA-TTTTCCAAAAATTCC
* * *
2347 ATTTTTGA-CCCAAACTTTCTAAAAATTATC
1 ATTTTT-ACCCCAAATTTTCCAAAAATT-CC
* *
2377 A-TTTTACCCCTCAA-CTTCCAAAAATTCC
1 ATTTTTACCCC-AAATTTTCCAAAAATTCC
* ** *
2405 ATTTTTAACCTCGATTTTTTTCCAAAAGTTACC
1 ATTTTT-ACC-CCA-AATTTTCCAAAAATT-CC
*
2438 A-TTTTACCCCTAAA-TTTCTAAAAATTCC
1 ATTTTTACCCC-AAATTTTCCAAAAATTCC
* * * *
2466 ATTTTTGACCCTAATTTTTTTCAAAAAATTAC
1 ATTTTT-ACCCCAA--ATTTTCCAAAAATTCC
* * *
2498 AATTTTACCCCTGAA-CTTCCAAAAATTCC
1 ATTTTTACCCC-AAATTTTCCAAAAATTCC
** *
2527 ATTTTTAACCTTAATTTTTCCAAAAATTACC
1 ATTTTT-ACCCCAAATTTTCCAAAAATT-CC
* *
2558 A-TTTTACCCTCGAATTTT-CGAAAATTCC
1 ATTTTTACCC-CAAATTTTCCAAAAATTCC
* ** * *
2586 ATTTTTGATCTTAATTTTTCCAAAAAGTACC
1 ATTTTT-ACCCCAAATTTTCCAAAAA-TTCC
* *
2617 A-TTTTACCCTCGAA-TTTCTAAAAATTCC
1 ATTTTTACCC-CAAATTTTCCAAAAATTCC
* **
2645 ATTTTTAACCCTTATTTTCCAAAAATTACC
1 ATTTTTACCCCAAATTTTCCAAAAATT-CC
* *
2675 A-TTTTACCCTCAAA-CTTCAAAAAATTCC
1 ATTTTTACCC-CAAATTTTCCAAAAATTCC
*
2703 ATTTTTGA-CCCTAATTTTCCAAAAATTACC
1 ATTTTT-ACCCCAAATTTTCCAAAAATT-CC
* * *
2733 -GTTTTACCCTCGAA-CTTCCAAAAATTCC
1 ATTTTTACCC-CAAATTTTCCAAAAATTCC
* * *
2761 ATTTTTGACCTCGAATTTTCCAAAAATTAC
1 ATTTTT-ACCCCAAATTTTCCAAAAATTCC
* * *
2791 A-TTTTACCCACGAA-TGTCTAAAAATTCC
1 ATTTTTACCC-CAAATTTTCCAAAAATTCC
* * * *
2819 AGTTTTGACCCCTAACTTTCCCAAAATT
1 A-TTTTTACCCCAAATTTTCCAAAAATT
2847 ACCAATTTAC
Statistics
Matches: 373, Mismatches: 83, Indels: 88
0.69 0.15 0.16
Matches are distributed among these distances:
28 43 0.12
29 180 0.48
30 98 0.26
31 17 0.05
32 32 0.09
33 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.39
Consensus pattern (29 bp):
ATTTTTACCCCAAATTTTCCAAAAATTCC
Found at i:2698 original size:58 final size:58
Alignment explanation
Indices: 2335--2863 Score: 525
Period size: 58 Copynumber: 9.0 Consensus size: 58
2325 CCCTAAACTT
** * * *
2335 TTCC-AAAATTCCATTTTTGACCCAAACTTTCTAAAAATTATCATTTTACCCCTC-AAC
1 TTCCAAAAATTCCATTTTTGACCCTTATTTTCCAAAAATTACCATTTTA-CCCTCGAAC
* * * * *
2392 TTCCAAAAATTCCATTTTTAACCTCGATTTTTTTCCAAAAGTTACCATTTTACCC-CTAAAT
1 TTCCAAAAATTCCATTTTTGACC-C--TTATTTTCCAAAAATTACCATTTTACCCTC-GAAC
* * * *
2453 TTCTAAAAATTCCATTTTTGACCCTAATTTTTTTCAAAAAATTACAATTTTACCC-CTGAAC
1 TTCCAAAAATTCCATTTTTGACCC---TTATTTTCCAAAAATTACCATTTTACCCTC-GAAC
* *
2514 TTCCAAAAATTCCATTTTT-AACCTTAATTTTTCCAAAAATTACCATTTTACCCTCGAAT
1 TTCCAAAAATTCCATTTTTGACCCTT-A-TTTTCCAAAAATTACCATTTTACCCTCGAAC
* * * * *
2573 TTTCGAAAATTCCATTTTTGA-TCTTAATTTTTCCAAAAAGTACCATTTTACCCTCGAAT
1 TTCCAAAAATTCCATTTTTGACCCTT-A-TTTTCCAAAAATTACCATTTTACCCTCGAAC
* * *
2632 TTCTAAAAATTCCATTTTTAACCCTTATTTTCCAAAAATTACCATTTTACCCTCAAAC
1 TTCCAAAAATTCCATTTTTGACCCTTATTTTCCAAAAATTACCATTTTACCCTCGAAC
* * *
2690 TTCAAAAAATTCCATTTTTGACCCTAATTTTCCAAAAATTACCGTTTTACCCTCGAAC
1 TTCCAAAAATTCCATTTTTGACCCTTATTTTCCAAAAATTACCATTTTACCCTCGAAC
** *
2748 TTCCAAAAATTCCATTTTTGACCTCGAATTTTCCAAAAATTA-CATTTTACCCACGAA-
1 TTCCAAAAATTCCATTTTTGACC-CTTATTTTCCAAAAATTACCATTTTACCCTCGAAC
* * * * * *
2805 TGTCTAAAAATTCCAGTTTTGACCCCTAACTTTCCCAAAATTACCAATTTACCCATCGA
1 T-TCCAAAAATTCCATTTTTGA-CCCTTATTTTCCAAAAATTACCATTTTACCC-TCGA
2864 GTGACCAAAA
Statistics
Matches: 404, Mismatches: 51, Indels: 31
0.83 0.10 0.06
Matches are distributed among these distances:
57 7 0.02
58 166 0.41
59 127 0.31
60 15 0.04
61 89 0.22
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (58 bp):
TTCCAAAAATTCCATTTTTGACCCTTATTTTCCAAAAATTACCATTTTACCCTCGAAC
Done.