Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006775.1 Kokia drynarioides strain JFW-HI SEQ_121374, 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: 6705
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--27 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1 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
28 CATCTTGATT
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:254 original size:2 final size:2
Alignment explanation
Indices: 249--304 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
239 ACGTATGTAC
249 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
291 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
305 CTTGATTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:551 original size:16 final size:16
Alignment explanation
Indices: 513--544 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
503 TGCGGTAACA
*
513 AACGGCGATGATTGAC
1 AACGGCGATGATCGAC
529 AACGGCGATGATCGAC
1 AACGGCGATGATCGAC
545 GATGGCGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.16
Consensus pattern (16 bp):
AACGGCGATGATCGAC
Found at i:1010 original size:30 final size:30
Alignment explanation
Indices: 967--1289 Score: 302
Period size: 30 Copynumber: 10.9 Consensus size: 30
957 TGAAGGTCCT
* *
967 TAAACTTTCCCAAAATTCCATTTTAACCCC
1 TAAACTTTTCCAAAATTACATTTTAACCCC
* *
997 TAAATTTTTCCAAAATTACATTTTAACCCG
1 TAAACTTTTCCAAAATTACATTTTAACCCC
* *
1027 TAAACTTCTCTAAAATTACATTTTAACCCC
1 TAAACTTTTCCAAAATTACATTTTAACCCC
* * *
1057 TAATCTTCTCCAAAATTACA-TTTGA-CCC
1 TAAACTTTTCCAAAATTACATTTTAACCCC
* * *
1085 TAAACTTCTCTAAAATCACATTTCT-ACCCC
1 TAAACTTTTCCAAAATTACATTT-TAACCCC
* * * *
1115 TAAACTTCTCCAAAATCACATTTTGATCCC
1 TAAACTTTTCCAAAATTACATTTTAACCCC
* *
1145 TAAACTTTTCCAAAATTATATTTTTGACCCC
1 TAAACTTTTCCAAAATTACA-TTTTAACCCC
* * * *
1176 CAAACATTTCTAAAATCACA-TTTAACCCC
1 TAAACTTTTCCAAAATTACATTTTAACCCC
* *
1205 -AAACTCCTT-CAAAATCACATTTTAA-CCC
1 TAAACT-TTTCCAAAATTACATTTTAACCCC
* *
1233 TAAAC-TTTCCTAAAATTACATTTTTTACCCT
1 TAAACTTTTCC-AAAATTACA-TTTTAACCCC
*
1264 TAAACTTTTCCAAAATTACGTTTTAA
1 TAAACTTTTCCAAAATTACATTTTAA
1290 TCTCAAACTC
Statistics
Matches: 245, Mismatches: 35, Indels: 26
0.80 0.11 0.08
Matches are distributed among these distances:
27 2 0.01
28 37 0.15
29 35 0.14
30 127 0.52
31 39 0.16
32 5 0.02
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (30 bp):
TAAACTTTTCCAAAATTACATTTTAACCCC
Found at i:1130 original size:88 final size:86
Alignment explanation
Indices: 967--1271 Score: 319
Period size: 88 Copynumber: 3.4 Consensus size: 86
957 TGAAGGTCCT
* * * * * *
967 TAAACTTTCCCAAAATTCCATTTTAACCCCTAAATTTTTCCAAAATTACATTTTAACCCGTAAAC
1 TAAACTTT-CCAAAATTACATTTTGACCCCTAAA-CTTTCTAAAATCACATTTT-ACCCCTAAAC
* *
1032 TTCTCTAAAATTACATTTTAACCCC
63 TTCTCCAAAATCACATTTTAA-CCC
*
1057 TAATCTTCTCCAAAATTACA-TTTGA-CCCTAAACTTCTCTAAAATCACATTTCTACCCCTAAAC
1 TAAACTT-TCCAAAATTACATTTTGACCCCTAAACTT-TCTAAAATCACATTT-TACCCCTAAAC
*
1120 TTCTCCAAAATCACATTTTGATCCC
63 TTCTCCAAAATCACATTTT-AACCC
* * *
1145 TAAACTTTTCCAAAATTATATTTTTGACCCCCAAACATTTCTAAAATCACATTTAACCCC-AAAC
1 TAAAC-TTTCCAAAATTACA-TTTTGACCCCTAAAC-TTTCTAAAATCACATTTTACCCCTAAAC
* *
1209 TCCTTCAAAATCACATTTTAACCC
63 TTCTCCAAAATCACATTTTAACCC
* *
1233 TAAACTTTCCTAAAATTACATTTTTTACCCTTAAACTTT
1 TAAACTTTCC-AAAATTACA-TTTTGACCCCTAAACTTT
1272 TCCAAAATTA
Statistics
Matches: 184, Mismatches: 21, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
87 10 0.05
88 94 0.51
89 29 0.16
90 26 0.14
91 23 0.12
92 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.01, T:0.36
Consensus pattern (86 bp):
TAAACTTTCCAAAATTACATTTTGACCCCTAAACTTTCTAAAATCACATTTTACCCCTAAACTTC
TCCAAAATCACATTTTAACCC
Found at i:1234 original size:118 final size:115
Alignment explanation
Indices: 977--1289 Score: 335
Period size: 118 Copynumber: 2.6 Consensus size: 115
967 TAAACTTTCC
* * * *
977 CAAAATTC-CATTTTAACCCCTAAATTTTTCCAAAATTACATTTTAACCCGTAAACTTCTCTAAA
1 CAAAA-TCACATTTTAA-CCCTAAA-CTTTCCAAAATTACATTTTATCCCGTAAACTTTTCCAAA
* * * * * *
1041 ATTACATTTTAACCCCTAATCTTCTCCAAAATTACATTTGACCCTAAACTTCT
63 ATTACATTTTAACCCCCAAACTTCTCCAAAATCACATTTAACCCCAAACTCCT
* *
1094 CTAAAATCACATTTCTACCCCTAAACTTCTCCAAAATCACATTTTGATCCC-TAAACTTTTCCAA
1 C-AAAATCACATTT-TAACCCTAAACTT-TCCAAAATTACATTTT-ATCCCGTAAACTTTTCCAA
* * *
1158 AATTATATTTTTGACCCCCAAACATT-TCTAAAATCACATTTAACCCCAAACTCCTT
62 AATTACA-TTTTAACCCCCAAAC-TTCTCCAAAATCACATTTAACCCCAAACTCC-T
* *
1214 CAAAATCACATTTTAACCCTAAACTTTCCTAAAATTACATTTTTTACCCTTAAACTTTTCCAAAA
1 CAAAATCACATTTTAACCCTAAACTTTCC-AAAATTACATTTTAT-CCCGTAAACTTTTCCAAAA
*
1279 TTACGTTTTAA
64 TTACATTTTAA
1290 TCTCAAACTC
Statistics
Matches: 164, Mismatches: 21, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
117 9 0.05
118 80 0.49
119 71 0.43
120 4 0.02
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (115 bp):
CAAAATCACATTTTAACCCTAAACTTTCCAAAATTACATTTTATCCCGTAAACTTTTCCAAAATT
ACATTTTAACCCCCAAACTTCTCCAAAATCACATTTAACCCCAAACTCCT
Found at i:2681 original size:60 final size:60
Alignment explanation
Indices: 2615--2739 Score: 241
Period size: 60 Copynumber: 2.1 Consensus size: 60
2605 AAGGTATTAG
2615 ACACCAAGCCAAACCTGAACAAAGTAGACTCGCAAATTGCAACAAAACTTAAACCAGAGT
1 ACACCAAGCCAAACCTGAACAAAGTAGACTCGCAAATTGCAACAAAACTTAAACCAGAGT
2675 ACACCAAGCCAAACCTGAACAAAGTAGACTCGCAAATTGCAACAAAACTTAAACCAGAGT
1 ACACCAAGCCAAACCTGAACAAAGTAGACTCGCAAATTGCAACAAAACTTAAACCAGAGT
*
2735 CCACC
1 ACACC
2740 TATCAAAACA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.46, C:0.29, G:0.13, T:0.13
Consensus pattern (60 bp):
ACACCAAGCCAAACCTGAACAAAGTAGACTCGCAAATTGCAACAAAACTTAAACCAGAGT
Found at i:5672 original size:17 final size:17
Alignment explanation
Indices: 5647--5746 Score: 110
Period size: 17 Copynumber: 5.9 Consensus size: 17
5637 AAATTTTAAT
*
5647 TTTTAAATTTTAATTTA
1 TTTTAAATTTAAATTTA
* *
5664 TTGTAAATTTGAATTTA
1 TTTTAAATTTAAATTTA
* *
5681 TTTTAAATTTAAACTCA
1 TTTTAAATTTAAATTTA
* * *
5698 TTTTGAGTTTGAATTTA
1 TTTTAAATTTAAATTTA
*
5715 CTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
*
5732 TTTTAAATTGAAATT
1 TTTTAAATTTAAATT
5747 AATTAAAAAG
Statistics
Matches: 66, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 66 1.00
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:5690 original size:34 final size:34
Alignment explanation
Indices: 5647--5740 Score: 125
Period size: 34 Copynumber: 2.8 Consensus size: 34
5637 AAATTTTAAT
* *
5647 TTTTAAATTTTAATTTATTGTAAATTTGAATTTA
1 TTTTAAATTTAAATTTATTTTAAATTTGAATTTA
* * * *
5681 TTTTAAATTTAAACTCATTTTGAGTTTGAATTTA
1 TTTTAAATTTAAATTTATTTTAAATTTGAATTTA
*
5715 CTTTAAATTTAAATTTATTTTAAATT
1 TTTTAAATTTAAATTTATTTTAAATT
5741 GAAATTAATT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.56
Consensus pattern (34 bp):
TTTTAAATTTAAATTTATTTTAAATTTGAATTTA
Done.