Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012014.1 Kokia drynarioides strain JFW-HI SEQ_127012, 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: 31722
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:1132 original size:25 final size:25
Alignment explanation
Indices: 1104--1160 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
1094 TTTCGATTTA
1104 TTTTTTTAACAGATTTAATAAATAT
1 TTTTTTTAACAGATTTAATAAATAT
1129 TTTTTTTAACAGATTTAATAAATAT
1 TTTTTTTAACAGATTTAATAAATAT
1154 TTTTTTT
1 TTTTTTT
1161 CTTTCAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (25 bp):
TTTTTTTAACAGATTTAATAAATAT
Found at i:5214 original size:27 final size:27
Alignment explanation
Indices: 5176--5230 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
5166 TCTTCACACT
5176 TACGTAAGTAATTTCATCAAGTCTATC
1 TACGTAAGTAATTTCATCAAGTCTATC
5203 TACGTAAGTAATTTCATCAAGTCTATC
1 TACGTAAGTAATTTCATCAAGTCTATC
5230 T
1 T
5231 CAATATAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (27 bp):
TACGTAAGTAATTTCATCAAGTCTATC
Found at i:5496 original size:87 final size:87
Alignment explanation
Indices: 5311--5482 Score: 204
Period size: 87 Copynumber: 2.0 Consensus size: 87
5301 TTAAGTTCAA
* ** * *
5311 TGAATTCATCAAGTCTGTCTCAATAGGACCATTAAAACTCTGGGATATGAATTCATTATGAGTAA
1 TGAATTCATCAAGTCTCTCTCAATAGGACCACCAAAACTCTGGGATATGAACTCATTAAGAGTAA
* *
5376 TAAACTCAACCTCTCATGTCGG
66 TAAACTCAACCTATCATGTCAG
* * *
5398 TGAATTCATCAAGTCTCTCTCAATAGGACTACCCAAA-TCTTGGGATATGAACTCATTAAGAGTG
1 TGAATTCATCAAGTCTCTCTCAATAGGACCACCAAAACTC-TGGGATATGAACTCATTAAGAGTA
*
5462 A-GAACTCAACCTTATGCATGT
65 ATAAACTCAACC-TAT-CATGT
5483 ACATTGATCA
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
86 11 0.15
87 56 0.78
88 5 0.07
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (87 bp):
TGAATTCATCAAGTCTCTCTCAATAGGACCACCAAAACTCTGGGATATGAACTCATTAAGAGTAA
TAAACTCAACCTATCATGTCAG
Found at i:7654 original size:45 final size:46
Alignment explanation
Indices: 7585--7673 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 46
7575 CCATAAATAG
* * * *
7585 AAAAAGATTTTTCTCAACTAAAAATATTTTAAAAATATT-TTTTAC
1 AAAAAAATTTTCCACAACTAAAAATATTATAAAAATATTATTTTAC
* *
7630 AAAAAAATTTTCCACAACTGAAAATATTATGAAAATATTATTTT
1 AAAAAAATTTTCCACAACTAAAAATATTATAAAAATATTATTTT
7674 GTATTACCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 33 0.89
46 4 0.11
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.39
Consensus pattern (46 bp):
AAAAAAATTTTCCACAACTAAAAATATTATAAAAATATTATTTTAC
Found at i:7960 original size:82 final size:82
Alignment explanation
Indices: 7823--7983 Score: 322
Period size: 82 Copynumber: 2.0 Consensus size: 82
7813 TATTCTCTTT
7823 CATTATCTCCTCTGTTCCTCTACCTTTCCTAGCTTTTTTCTCTAATCAACAAAGCCCCTTGATTC
1 CATTATCTCCTCTGTTCCTCTACCTTTCCTAGCTTTTTTCTCTAATCAACAAAGCCCCTTGATTC
7888 AACATTAGATGGCATTG
66 AACATTAGATGGCATTG
7905 CATTATCTCCTCTGTTCCTCTACCTTTCCTAGCTTTTTTCTCTAATCAACAAAGCCCCTTGATTC
1 CATTATCTCCTCTGTTCCTCTACCTTTCCTAGCTTTTTTCTCTAATCAACAAAGCCCCTTGATTC
7970 AACATTAGATGGCA
66 AACATTAGATGGCA
7984 CTGGAGATAT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.22, C:0.30, G:0.09, T:0.39
Consensus pattern (82 bp):
CATTATCTCCTCTGTTCCTCTACCTTTCCTAGCTTTTTTCTCTAATCAACAAAGCCCCTTGATTC
AACATTAGATGGCATTG
Found at i:15430 original size:29 final size:29
Alignment explanation
Indices: 15403--15462 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
15393 TTTGAAATTT
*
15403 AATTATTATAATTTT-ATTTTTAAGAATTT
1 AATTATTATAATTTTAAATTTTAA-AATTT
* * *
15432 AATTTTTTTATTTTTAAATTTTAAAATTT
1 AATTATTATAATTTTAAATTTTAAAATTT
15461 AA
1 AA
15463 GCATAAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
AATTATTATAATTTTAAATTTTAAAATTT
Found at i:22099 original size:18 final size:18
Alignment explanation
Indices: 22078--22120 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
22068 CAAAAATACC
*
22078 AAATTTTTTTAAAATTCA
1 AAATTTTTATAAAATTCA
*
22096 AAATATTTATAAAATTCA
1 AAATTTTTATAAAATTCA
22114 AAATTTT
1 AAATTTT
22121 ATATTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATTTTTATAAAATTCA
Found at i:23824 original size:23 final size:22
Alignment explanation
Indices: 23794--23870 Score: 100
Period size: 23 Copynumber: 3.4 Consensus size: 22
23784 GCTGGGGAAA
23794 CAGTAGGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
*
23816 CCAGTAGGCATACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * *
23839 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
23862 CAGTAGGCA
1 CAGTAGGCA
23871 TACAAGGTGC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.32
23 32 0.68
ACGTcount: A:0.35, C:0.26, G:0.25, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:23888 original size:23 final size:22
Alignment explanation
Indices: 23791--23912 Score: 95
Period size: 23 Copynumber: 5.4 Consensus size: 22
23781 AGTGCTGGGG
23791 AAACAGTAGGCACACACAGTGC
1 AAACAGTAGGCACACACAGTGC
* *
23813 AATCCAGTAGGCATACACAGTGC
1 AA-ACAGTAGGCACACACAGTGC
* * * *
23836 AATCAGTAGGCGCACATAGCGC
1 AAACAGTAGGCACACACAGTGC
*
23858 AAATCAGTAGGCATACA-AGGTGC
1 AAA-CAGTAGGCACACACA-GTGC
* *
23881 GAAACAGTAAGCACATGA-AGTGC
1 -AAACAGTAGGCACA-CACAGTGC
23904 GAAACAGTA
1 -AAACAGTA
23913 AGCGCGCTAG
Statistics
Matches: 81, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
22 20 0.25
23 56 0.69
24 5 0.06
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.14
Consensus pattern (22 bp):
AAACAGTAGGCACACACAGTGC
Found at i:26105 original size:23 final size:22
Alignment explanation
Indices: 26078--26173 Score: 63
Period size: 23 Copynumber: 4.2 Consensus size: 22
26068 CGTGCTGGGC
*
26078 AACAGTAGACACGCAAAGTGCTA
1 AACAG-AGACACACAAAGTGCTA
* *
26101 AACAGA-AGCACACACAGTGCTG
1 AACAGAGA-CACACAAAGTGCTA
* *
26123 AATAGAGGGCACACACAA-TGCTA
1 AACAGA-GACACACA-AAGTGCTA
*
26146 AACAGAGGACACGA-AACGTGCTA
1 AACAGA-GACAC-ACAAAGTGCTA
26169 AACAG
1 AACAG
26174 TAGGCGTGCT
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
21 1 0.02
22 18 0.32
23 36 0.63
24 2 0.04
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (22 bp):
AACAGAGACACACAAAGTGCTA
Found at i:27270 original size:18 final size:18
Alignment explanation
Indices: 27224--27270 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
27214 TATAAATCAA
*
27224 AACTCTTGTACTACTTAC
1 AACTCTTGTAGTACTTAC
27242 AACTCTTGTAGTACTTAC
1 AACTCTTGTAGTACTTAC
*
27260 AATTCTTGTAG
1 AACTCTTGTAG
27271 ATAATCCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (18 bp):
AACTCTTGTAGTACTTAC
Found at i:30065 original size:72 final size:72
Alignment explanation
Indices: 29976--30141 Score: 260
Period size: 72 Copynumber: 2.3 Consensus size: 72
29966 AAATCAAATT
* *
29976 TAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAAAATATAAATTCAATATCCAAAAA
1 TAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAAAACACAAATTCAATATCCAAAAA
*
30041 CCAAGCA
66 CCAAACA
* * * *
30048 TAATCAACTATTGATAAAACTATATTACACATAAATAAGTAGAACACAATTTCAATATCCAAAAA
1 TAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAAAACACAAATTCAATATCCAAAAA
30113 CCAAACA
66 CCAAACA
*
30120 TAAACAATTATTGATAAAACTA
1 TAAACAACTATTGATAAAACTA
30142 GTTTATCATT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 85 1.00
ACGTcount: A:0.55, C:0.16, G:0.04, T:0.25
Consensus pattern (72 bp):
TAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAAAACACAAATTCAATATCCAAAAA
CCAAACA
Found at i:31279 original size:23 final size:22
Alignment explanation
Indices: 31228--31405 Score: 149
Period size: 23 Copynumber: 7.6 Consensus size: 22
31218 TATACGGAAC
*
31228 AAACAGAGAGCACATAAGTGCT
1 AAACAGAGAGCACACAAGTGCT
31250 GAGAAACAGAGAGCACACATAGTGCT
1 ---AAACAGAGAGCACACA-AGTGCT
* *
31276 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACAC-AAGTGCT
* *
31299 AATCAGAGAGAACACAAAGTGCT
1 AAACAGAGAGCACAC-AAGTGCT
* *
31322 AATCAGAGAGCACACACAATGCT
1 AAACAGAGAGCACACA-AGTGCT
* * *
31345 AATAATAGAGAGCACGAGACGTGCT
1 -A-AACAGAGAGCAC-ACAAGTGCT
*
31370 AAACATAGAGCACACACAGTGCT
1 AAACAGAGAGCACACA-AGTGCT
*
31393 AATCAGAGAGCAC
1 AAACAGAGAGCAC
31406 GCTAGTGTTC
Statistics
Matches: 127, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
22 3 0.02
23 84 0.66
24 3 0.02
25 29 0.23
26 8 0.06
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (22 bp):
AAACAGAGAGCACACAAGTGCT
Found at i:31309 original size:48 final size:47
Alignment explanation
Indices: 31257--31402 Score: 161
Period size: 48 Copynumber: 3.1 Consensus size: 47
31247 GCTGAGAAAC
* *
31257 AGAGAGCACACATAGTGCTAAACAGAGAGTACACAAAGTACTAATCAG
1 AGAGAGCACACA-AGTGCTAAACAGAGAGCACACAAAGTGCTAATCAG
* * * *
31305 AGAGAACACA-AAGTGCTAATCAGAGAGCACACACAA-TGCTAATAAT
1 AGAGAGCACACAAGTGCTAAACAGAGAGCACACA-AAGTGCTAATCAG
* * * *
31351 AGAGAGCACGAGACGTGCTAAACATAGAGCACACACAGTGCTAATCAG
1 AGAGAGCAC-ACAAGTGCTAAACAGAGAGCACACAAAGTGCTAATCAG
31399 AGAG
1 AGAG
31403 CACGCTAGTG
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
46 35 0.43
47 5 0.06
48 41 0.51
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.14
Consensus pattern (47 bp):
AGAGAGCACACAAGTGCTAAACAGAGAGCACACAAAGTGCTAATCAG
Found at i:31320 original size:46 final size:46
Alignment explanation
Indices: 31228--31402 Score: 165
Period size: 46 Copynumber: 3.7 Consensus size: 46
31218 TATACGGAAC
* * * *
31228 AAACAGAGAGCACA-TAAGTGCTGAGAAACAGAGAGCACACATAGTGCT
1 AAACAGAGAGCACACAAAGTGCT---AATCAGAGAGAACACAAAGTGCT
* *
31276 AAACAGAGAGTACACAAAGTACTAATCAGAGAGAACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCTAATCAGAGAGAACACAAAGTGCT
* * * * *
31322 AATCAGAGAGCACACACAA-TGCTAATAATAGAGAGCACGAGACGTGCT
1 AAACAGAGAGCACACA-AAGTGCTAATCAGAGAGAACAC-A-AAGTGCT
* *
31370 AAACATAGAGCACACACAGTGCTAATCAGAGAG
1 AAACAGAGAGCACACAAAGTGCTAATCAGAGAG
31403 CACGCTAGTG
Statistics
Matches: 104, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
46 49 0.47
47 4 0.04
48 45 0.43
49 6 0.06
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (46 bp):
AAACAGAGAGCACACAAAGTGCTAATCAGAGAGAACACAAAGTGCT
Found at i:31403 original size:46 final size:45
Alignment explanation
Indices: 31228--31406 Score: 157
Period size: 48 Copynumber: 3.8 Consensus size: 45
31218 TATACGGAAC
* *
31228 AAACAGAGAGCACATA-AGTGCTGAGAAACAGAGAGCAC-ACATAGTGCT
1 AAACAGAGAGCACACACAGTGCT---AATCAGAGAGCACGA-A-AGTGCT
* * *
31276 AAACAGAGAGTACACAAAGTACTAATCAGAGAGAACAC-AAAGTGCT
1 AAACAGAGAGCACACACAGTGCTAATCAGAGAG--CACGAAAGTGCT
* * * *
31322 AATCAGAGAGCACACACAATGCTAATAATAGAGAGCACGAGACGTGCT
1 AAACAGAGAGCACACACAGTGCTAAT--CAGAGAGCACGA-AAGTGCT
*
31370 AAACATAGAGCACACACAGTGCTAATCAGAGAGCACG
1 AAACAGAGAGCACACACAGTGCTAATCAGAGAGCACG
31407 CTAGTGTTCC
Statistics
Matches: 109, Mismatches: 15, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
46 49 0.45
47 2 0.02
48 53 0.49
49 5 0.05
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (45 bp):
AAACAGAGAGCACACACAGTGCTAATCAGAGAGCACGAAAGTGCT
Done.