Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013692.1 Kokia drynarioides strain JFW-HI SEQ_128720, 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: 21865
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:1027 original size:30 final size:28
Alignment explanation
Indices: 970--1204 Score: 165
Period size: 30 Copynumber: 8.0 Consensus size: 28
960 AGGGTCCCTA
*
970 AACTGTCCAAAAATTTCATTTTTACCCCTG
1 AACT-TCCAAAAATTCCATTTTTACCCC-G
* *
1000 AACTTCCAAAAA-ACATATTTTTAACCCCG
1 AACTTCCAAAAATTC-CATTTTT-ACCCCG
* * **
1029 AAATTTCTAAAAATTCCATTTTTACCACTA
1 -AACTTCCAAAAATTCCATTTTTACC-CCG
1059 AACTTCCAAAAA-TCCTATTTTTGACCCCG
1 AACTTCCAAAAATTCC-ATTTTT-ACCCCG
*
1088 AAACTTTCAAAAATTCCATTTTTACCCCCCG
1 -AACTTCCAAAAATTCCATTTTTA--CCCCG
* *
1119 AACTTCCAAAAA-TCTCATTTTGACCCCCA
1 AACTTCCAAAAATTC-CATTTTTA-CCCCG
* *
1148 AACTACCAAAAA-TCTCATTTTTGACCCCAA
1 AACTTCCAAAAATTC-CATTTTT-ACCCC-G
*
1178 AACTTTCAAAAATTACCA-TTTTACCCC
1 AACTTCCAAAAATT-CCATTTTTACCCC
1205 CGGATGACCA
Statistics
Matches: 168, Mismatches: 21, Indels: 33
0.76 0.09 0.15
Matches are distributed among these distances:
28 3 0.02
29 72 0.43
30 80 0.48
31 12 0.07
32 1 0.01
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTTACCCCG
Found at i:1140 original size:59 final size:59
Alignment explanation
Indices: 977--1190 Score: 231
Period size: 59 Copynumber: 3.6 Consensus size: 59
967 CTAAACTGTC
* * *
977 CAAAAATTTCATTTTTACCCCTGAACTTCCAAAAAACAT-ATTTTTAACCCCGAAA-TTT
1 CAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATC-TCATTTTTGACCCCGAAACTTT
* *
1035 CTAAAAATTCCATTTTTACCACTAAACTTCCAAAAATC-CTATTTTTGACCCCGAAACTTT
1 C-AAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCTC-ATTTTTGACCCCGAAACTTT
* * **
1095 CAAAAATTCCATTTTTACCCCCCGAACTTCCAAAAATCTCA-TTTTGACCCCCAAACTAC
1 CAAAAATTCCATTTTTA-CCCCTGAACTTCCAAAAATCTCATTTTTGACCCCGAAACTTT
** *
1154 CAAAAA-TCTCATTTTTGACCCCAAAACTTTCAAAAAT
1 CAAAAATTC-CATTTTT-ACCCCTGAACTTCCAAAAAT
1191 TACCATTTTA
Statistics
Matches: 134, Mismatches: 14, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
58 3 0.02
59 107 0.80
60 23 0.17
61 1 0.01
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (59 bp):
CAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCTCATTTTTGACCCCGAAACTTT
Found at i:1204 original size:59 final size:58
Alignment explanation
Indices: 1134--1262 Score: 154
Period size: 59 Copynumber: 2.2 Consensus size: 58
1124 CCAAAAATCT
*
1134 CATTTTGACCCCCAAACT-ACCAAAAA-TCTCATTTTTGACCCCAAAACTTTCAAAAATTAC
1 CATTTT-ACCCCCAAA-TGACCAAAAACTC-CATTTTCGACCCCAAAACTTTC-AAAATTAC
** * *
1194 CATTTTACCCCCGGATGACCAAAAACTCCATTTTCGACCTCGAAACTTTCAAAATTAC
1 CATTTTACCCCCAAATGACCAAAAACTCCATTTTCGACCCCAAAACTTTCAAAATTAC
*
1252 CTTTTTACCCC
1 CATTTTACCCC
1263 TATATGTTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
58 19 0.31
59 34 0.56
60 8 0.13
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.29
Consensus pattern (58 bp):
CATTTTACCCCCAAATGACCAAAAACTCCATTTTCGACCCCAAAACTTTCAAAATTAC
Found at i:1247 original size:89 final size:89
Alignment explanation
Indices: 1058--1247 Score: 237
Period size: 89 Copynumber: 2.1 Consensus size: 89
1048 TTTTACCACT
*
1058 AAACTTCCAAAAATCCTATTTTTGACCCCGAAACTTTCAAAAATTCCATTTTTACCCCCCGAACT
1 AAACTTCCAAAAATCCTATTTTTGACCCCAAAACTTTCAAAAATTCCATTTTTACCCCCCGAACT
*
1123 TCCAAAAATCTCATTTTGACCCCC
66 ACCAAAAATCTCATTTTGACCCCC
* *
1147 AAACTACCAAAAAT-CTCATTTTTGACCCCAAAACTTTCAAAAATTACCA-TTTTA-CCCCCGGA
1 AAACTTCCAAAAATCCT-ATTTTTGACCCCAAAACTTTCAAAAATT-CCATTTTTACCCCCCGAA
* *
1209 -TGACCAAAAA-CTCCATTTTCGACCTCG
64 CT-ACCAAAAATCT-CATTTT-GACCCCC
*
1236 AAACTTTCAAAA
1 AAACTTCCAAAA
1248 TTACCTTTTT
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
87 3 0.03
88 22 0.25
89 60 0.68
90 3 0.03
ACGTcount: A:0.36, C:0.31, G:0.05, T:0.28
Consensus pattern (89 bp):
AAACTTCCAAAAATCCTATTTTTGACCCCAAAACTTTCAAAAATTCCATTTTTACCCCCCGAACT
ACCAAAAATCTCATTTTGACCCCC
Found at i:2967 original size:26 final size:25
Alignment explanation
Indices: 2938--2986 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2928 TTTATAAAAT
2938 TTGGGCTAGTGGGGGGTATTTGGGTA
1 TTGGGCTAGT-GGGGGTATTTGGGTA
* *
2964 TTGGGCTTGTGGGTGTATTTGGG
1 TTGGGCTAGTGGGGGTATTTGGG
2987 CTTGTTTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.08, C:0.04, G:0.49, T:0.39
Consensus pattern (25 bp):
TTGGGCTAGTGGGGGTATTTGGGTA
Found at i:3683 original size:24 final size:24
Alignment explanation
Indices: 3654--3705 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
3644 AAATATCTTT
3654 AAAATAATCAAAATTTAAAT-AGAA
1 AAAATAAT-AAAATTTAAATAAGAA
* * *
3678 AAAATAGTAAATTTTAATTAAGAA
1 AAAATAATAAAATTTAAATAAGAA
3702 AAAA
1 AAAA
3706 ATATGAGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (24 bp):
AAAATAATAAAATTTAAATAAGAA
Found at i:12531 original size:19 final size:19
Alignment explanation
Indices: 12496--12544 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
12486 AGAAATAGTG
* *
12496 AAACAATGAAAACCAATTA
1 AAACAAAGAAAACCAATGA
* *
12515 AAATAAAGAAAATCAATGA
1 AAACAAAGAAAACCAATGA
12534 AAACAAAGAAA
1 AAACAAAGAAA
12545 TCCCAATTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.69, C:0.10, G:0.08, T:0.12
Consensus pattern (19 bp):
AAACAAAGAAAACCAATGA
Found at i:14871 original size:21 final size:21
Alignment explanation
Indices: 14845--14905 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
14835 ATACTTGATA
*
14845 AAAGGTATCGATACTTTTTGT
1 AAAGGTGTCGATACTTTTTGT
* *
14866 AAAGGTGTTGATGCTTTTTGT
1 AAAGGTGTCGATACTTTTTGT
*
14887 AAAGGTGTCAATACTTTTT
1 AAAGGTGTCGATACTTTTT
14906 ATGTTTGTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.44
Consensus pattern (21 bp):
AAAGGTGTCGATACTTTTTGT
Found at i:15172 original size:23 final size:22
Alignment explanation
Indices: 15129--15174 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
15119 ATTATGTTCA
*
15129 ACTTTAACTTTTATTTAAAAAC
1 ACTTTAACTTTTATATAAAAAC
* *
15151 ACTTTAATTTGTTATATCAAAAC
1 ACTTTAACTT-TTATATAAAAAC
15174 A
1 A
15175 TATTATCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.43
Consensus pattern (22 bp):
ACTTTAACTTTTATATAAAAAC
Found at i:18407 original size:21 final size:22
Alignment explanation
Indices: 18372--18412 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18362 CTACCTAAGA
*
18372 TTCATAAAGTCCTC-TCAACAC
1 TTCATAAAGTACTCTTCAACAC
*
18393 TTCATAAGGTACTCTTCAAC
1 TTCATAAAGTACTCTTCAAC
18413 CACATATCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (22 bp):
TTCATAAAGTACTCTTCAACAC
Done.