Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005329.1 Kokia drynarioides strain JFW-HI SEQ_119280, 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: 51223
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--35 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36 GCACAAATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5974 original size:19 final size:21
Alignment explanation
Indices: 5952--5990 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5942 AAATTTTCAT
5952 TCAA-TTTTA-ATGTTAAAAA
1 TCAATTTTTATATGTTAAAAA
5971 TCAATTTTTATATGTTAAAA
1 TCAATTTTTATATGTTAAAA
5991 TTGCATTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 9 0.50
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (21 bp):
TCAATTTTTATATGTTAAAAA
Found at i:18467 original size:3 final size:3
Alignment explanation
Indices: 18452--18486 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
18442 GACATGTCTC
*
18452 TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
18487 CAAGCTTGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:19520 original size:14 final size:14
Alignment explanation
Indices: 19501--19527 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19491 TTTGTGTGTG
19501 TGTATATATATATA
1 TGTATATATATATA
19515 TGTATATATATAT
1 TGTATATATATAT
19528 GTATGTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TGTATATATATATA
Found at i:19532 original size:4 final size:4
Alignment explanation
Indices: 19513--19565 Score: 88
Period size: 4 Copynumber: 13.2 Consensus size: 4
19503 TATATATATA
* *
19513 TATG TATA TATA TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
19561 TATG T
1 TATG T
19566 GTTGGGTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:20808 original size:2 final size:2
Alignment explanation
Indices: 20803--20838 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20793 TCCTGTTCCA
20803 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
20839 TCGGCAACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28263 original size:30 final size:28
Alignment explanation
Indices: 28216--28302 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 28
28206 TTTTGGAATT
*
28216 AAATTTTAAGAGTTTAATTAAAATTTTCA
1 AAATTCTAAG-GTTTAATTAAAATTTTCA
* *
28245 AAGATTCTAATTGTTTAATGAAAACTTTTCA
1 AA-ATTCTAA-GGTTTAATTAAAA-TTTTCA
* *
28276 AAATTTTGAGGTTATAATTAAAATTTT
1 AAATTCTAAGGTT-TAATTAAAATTTT
28303 TGAAAAATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
29 9 0.19
30 30 0.64
31 8 0.17
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (28 bp):
AAATTCTAAGGTTTAATTAAAATTTTCA
Found at i:28310 original size:31 final size:31
Alignment explanation
Indices: 28260--28333 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
28250 TCTAATTGTT
* * * * *
28260 TAATGAAAACTTTT-CAAAATTTTGAGGTTA
1 TAATGAAAATTTTTGAAAAATTTTAAAGTAA
*
28290 TAATTAAAATTTTTGAAAAATTTTAAAGTAA
1 TAATGAAAATTTTTGAAAAATTTTAAAGTAA
28321 TAATGAAAATTTT
1 TAATGAAAATTTT
28334 CCAAAATTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 12 0.33
31 24 0.67
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (31 bp):
TAATGAAAATTTTTGAAAAATTTTAAAGTAA
Found at i:28342 original size:30 final size:30
Alignment explanation
Indices: 28260--28342 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
28250 TCTAATTGTT
* * *
28260 TAATGAAAACTTTTCAAAATTTTGAGGTTA
1 TAATGAAAACTTTTCAAAATTTTAAAGTAA
* * *
28290 TAATTAAAATTTTTGAAAAATTTTAAAGTAA
1 TAATGAAAACTTTT-CAAAATTTTAAAGTAA
28321 TAATGAAAA-TTTTCCAAAATTT
1 TAATGAAAACTTTT-CAAAATTT
28343 GGAGGGGCGC
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
30 23 0.53
31 20 0.47
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (30 bp):
TAATGAAAACTTTTCAAAATTTTAAAGTAA
Found at i:30344 original size:30 final size:29
Alignment explanation
Indices: 30297--30411 Score: 124
Period size: 30 Copynumber: 3.8 Consensus size: 29
30287 CATTTTCCTC
*
30297 CCAAAGTTTTCAAAAATTCAAATTTGACCC
1 CCAAA-TTTTCAAAAATTCAAATTTGACCA
* * *
30327 CCTAATTTTCTAAAAATTCAAGTTTCACCA
1 CCAAATTTTC-AAAAATTCAAATTTGACCA
*
30357 CCAAATTTTCCAAAAATTCAAATTTGA-AA
1 CCAAATTTT-CAAAAATTCAAATTTGACCA
*
30386 TCTAAATTTTTCAAAAATTCAAATTT
1 -CCAAA-TTTTCAAAAATTCAAATTT
30412 AATCCTTAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
29 6 0.08
30 61 0.85
31 5 0.07
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (29 bp):
CCAAATTTTCAAAAATTCAAATTTGACCA
Found at i:30427 original size:30 final size:30
Alignment explanation
Indices: 30295--30439 Score: 115
Period size: 30 Copynumber: 4.8 Consensus size: 30
30285 ATCATTTTCC
*
30295 TCCC-AAAGTTTTCAAAAATTCAAATTTGAC
1 TCCCTAAA-TTTTCAAAAATTCAAATTTGAA
* * *
30325 CCCCT-AATTTTCTAAAAATTCAAGTTT-CA
1 TCCCTAAATTTTC-AAAAATTCAAATTTGAA
*
30354 -CCACCAAATTTTCCAAAAATTCAAATTTGAAA
1 TCC-CTAAATTTT-CAAAAATTCAAATTTG-AA
30386 T--CTAAATTTTTCAAAAATTCAAATTT-AA
1 TCCCTAAA-TTTTCAAAAATTCAAATTTGAA
* *
30414 TCCTTAAAGTTTTCAAAAATTAAAAT
1 TCCCTAAA-TTTTCAAAAATTCAAAT
30440 CTAACCACGT
Statistics
Matches: 93, Mismatches: 11, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
28 5 0.05
29 6 0.06
30 76 0.82
31 5 0.05
32 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.36
Consensus pattern (30 bp):
TCCCTAAATTTTCAAAAATTCAAATTTGAA
Found at i:30431 original size:60 final size:60
Alignment explanation
Indices: 30297--30439 Score: 150
Period size: 60 Copynumber: 2.4 Consensus size: 60
30287 CATTTTCCTC
** * *
30297 CCAAAGTTTTCAAAAATTCAAATTTGACCCCCTAATTTTCTAAAAATTCAAGTTTCACCA
1 CCAAAGTTTTCAAAAATTCAAATTTGACAACCTAATTTTCTAAAAATTCAAATTTAACCA
*
30357 CCAAA-TTTTCCAAAAATTCAAATTTGA-AATCTAAATTTT-TCAAAAATTCAAATTTAATCC-
1 CCAAAGTTTT-CAAAAATTCAAATTTGACAACCT-AATTTTCT-AAAAATTCAAATTTAA-CCA
** *
30417 TTAAAGTTTTCAAAAATTAAAAT
1 CCAAAGTTTTCAAAAATTCAAAT
30440 CTAACCACGT
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
59 7 0.10
60 57 0.81
61 6 0.09
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (60 bp):
CCAAAGTTTTCAAAAATTCAAATTTGACAACCTAATTTTCTAAAAATTCAAATTTAACCA
Found at i:31338 original size:22 final size:22
Alignment explanation
Indices: 31313--31356 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
31303 TATATAGCTC
* *
31313 GAACCTAAAGTGTTAATTAAAA
1 GAACATAAAGTGTTAATAAAAA
*
31335 GAACATAATGTGTTAATAAAAA
1 GAACATAAAGTGTTAATAAAAA
31357 TTAAGAAGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.27
Consensus pattern (22 bp):
GAACATAAAGTGTTAATAAAAA
Found at i:32872 original size:6 final size:6
Alignment explanation
Indices: 32861--32885 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
32851 AAGGTTATCG
32861 TCACCA TCACCA TCACCA TCACCA T
1 TCACCA TCACCA TCACCA TCACCA T
32886 GATTATTGTC
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:0.32, C:0.48, G:0.00, T:0.20
Consensus pattern (6 bp):
TCACCA
Found at i:33857 original size:49 final size:49
Alignment explanation
Indices: 33780--33894 Score: 221
Period size: 49 Copynumber: 2.3 Consensus size: 49
33770 CATTAAATCG
*
33780 TGTAGAAGGACTAAATAGTAAATAGGTATTAAATTGTTAGCTTACTTGC
1 TGTACAAGGACTAAATAGTAAATAGGTATTAAATTGTTAGCTTACTTGC
33829 TGTACAAGGACTAAATAGTAAATAGGTATTAAATTGTTAGCTTACTTGC
1 TGTACAAGGACTAAATAGTAAATAGGTATTAAATTGTTAGCTTACTTGC
33878 TGTACAAGGACTAAATA
1 TGTACAAGGACTAAATA
33895 AGATAAGGAG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (49 bp):
TGTACAAGGACTAAATAGTAAATAGGTATTAAATTGTTAGCTTACTTGC
Found at i:35265 original size:3 final size:3
Alignment explanation
Indices: 35257--35281 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35247 AATGAATGTG
35257 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
35282 ACAACAAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:35473 original size:2 final size:2
Alignment explanation
Indices: 35466--35494 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35456 ATTCCCTCAC
35466 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35495 CAATTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42594 original size:2 final size:2
Alignment explanation
Indices: 42587--42613 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42577 ATGGACAATA
42587 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
42614 AAAAAGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43229 original size:19 final size:20
Alignment explanation
Indices: 43190--43229 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
43180 GGGATTTATC
*
43190 TATTTTAAATTATATAAAGT
1 TATTTTAAATTATAGAAAGT
*
43210 TATTTTAAA-TGTAGAAAGT
1 TATTTTAAATTATAGAAAGT
43229 T
1 T
43230 TTAAATTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (20 bp):
TATTTTAAATTATAGAAAGT
Done.