Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011156.1 Kokia drynarioides strain JFW-HI SEQ_126130, 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: 3571
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1596 original size:827 final size:777
Alignment explanation
Indices: 1--1605 Score: 2598
Period size: 827 Copynumber: 2.0 Consensus size: 777
1 TTTTTTCCATAATCATGCTCATCTAATTTTCCAAAAAGTCAAAGGCTAAAGCAATGACTCAATTC
1 TTTTTTCCATAATCATGCTCATCTAATTTTCCAAAAAGTCAAAGGCTAAAGCAATGACTCAATTC
66 CAATCGTGAGAATTGAAAAGTACTTTATATCTTCAGATATATTTCTCAATTTTCTGCAAACTTGG
66 CAATCGTGAGAATTGAAAAGTACTTTATATCTTCAGATATATTTCTCAATTTTCTGCAAACTTGG
131 ATTGACAATCGGCCTTTCCTTTTAAAATCTTTACACTTTCAAGTTCAAAAAGGATCCGTTGGTTT
131 ATTGACAATCGGCCTTTCCTTTTAAAATCTTTACACTTTCAAGTTCAAAAAGGATCCGTTGGTTT
196 GAAGGTTGTTTCGATTTATAGTTGGGAGGAAGGATCGGCTTGCAGCACATTCGACTTCCTGTGAA
196 GAAGGTTGTTTCGATTTATAGTTGGGAGGAAGGATCGGCTTGCAGCACATTCGACTTCCTGTGAA
261 CACACTTAGCGGCGGTCCGCTAAGGGAAATTGAGATCGGATTCGATTCTCATTGAGACAATATAG
261 CACACTTAGCGGCGGTCCGCTAAGGGAAATTGAGATCGGATTCGATTCTCATTGAGACAATATAG
326 TCCGAGTCGGGTTTTTCCAGATTTTAAACTATTTTATTCTAACGGAGATAGTCGTGGTTAGTCTA
326 TCCGAGTCGGGTTTTTCCAGATTTTAAACTATTTTATTCTAACGGAGATAGTCGTGGTTAGTCTA
391 GCCAGAAAACTGAAATTCAAAAATTGATTTTGGATTTTCGATTTACCGGAGAGAAAAACAAGTTA
391 GCCAGAAAACTGAAATTCAAAAATTGATTTTGGATTTTCGATTTACCGGAGAGAAAAACAAGTTA
456 CAAGGGTTGGGCCTTGTAGATTGTAATCGGCATTTATCCGGAGTAAAATCTTATTCGATGATCGG
456 CAAGGGTTGGGCCTTGTAGATTGTAATCGGCATTTATCCGGAGTAAAATCTTATTCGATGATCGG
521 TTGGAAATGAATTAAAGCAAAGCCTGAGGCTGTTATTTAAACTGAGTTTCTTCTTAAGTTTGCTT
521 TTGGAAATGAATTAAAGCAAAGCCTGAGGCTGTTATTTAAACTGAGTTTCTTCTTAAGTTTGCTT
*
586 TCTTTAAATTCTTAGATTTAAATTTTCATTTCTTTATTTTAATTAAATTCTTTCTGTAACATCCG
586 TCTTTAAATTCTTAGATTTAAATTTTCATTTCTTTATTTTAATTAAACTCTTTCTGTAACATCCG
*
651 TGTGTTTGAACCGGATTTGGAATAGTGATAAAATAGAATAGATAATTAGAAATGTTTAGTTGAAG
651 TGTGTTTGAACCGGATTTGGAATAGTGATAAAATAGAATAGAGAATTAGAAATGTTTAGTTGAAG
716 TATGGAAGGTTAGAAAAATTTAAGGATTAAATAGTAAAGGAGAGAAAATATGGGGGACTAAA
716 TATGGAAGGTTAGAAAAATTTAAGGATTAAATAGTAAAGGAGAGAAAATATGGGGGACTAAA
************ ** * *
778 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTCCATAATCA
1 ----------------------------------------TTTTTTCCATAATCATGCT------
843 TGCTCATCTAATTTTCCAAAAAGTCAAAGGCTAAAGCAATGACTCAATTCCAATCGTGAGAATTG
20 ----CATCTAATTTTCCAAAAAGTCAAAGGCTAAAGCAATGACTCAATTCCAATCGTGAGAATTG
908 AAAAGTACTTTATATCTTCAGATATATTTCTCAATTTTCTGCAAACTTGGATTGACAATCGGCCT
81 AAAAGTACTTTATATCTTCAGATATATTTCTCAATTTTCTGCAAACTTGGATTGACAATCGGCCT
973 TTCCTTTTAAAATCTTTACACTTTCAAGTTCAAAAAGGATCCGTTGGTTTGAAGGTTGTTTCGAT
146 TTCCTTTTAAAATCTTTACACTTTCAAGTTCAAAAAGGATCCGTTGGTTTGAAGGTTGTTTCGAT
1038 TTATAGTTGGGAGGAAGGATCGGCTTGCAGCACATTCGACTTCCTGTGAACACACTTAGCGGCGG
211 TTATAGTTGGGAGGAAGGATCGGCTTGCAGCACATTCGACTTCCTGTGAACACACTTAGCGGCGG
1103 TCCGCTAAGGGAAATTGAGATCGGATTCGATTCTCATTGAGACAATATAGTCCGAGTCGGGTTTT
276 TCCGCTAAGGGAAATTGAGATCGGATTCGATTCTCATTGAGACAATATAGTCCGAGTCGGGTTTT
1168 TCCAGATTTTAAACTATTTTATTCTAACGGAGATAGTCGTGGTTAGTCTAGCCAGAAAACTGAAA
341 TCCAGATTTTAAACTATTTTATTCTAACGGAGATAGTCGTGGTTAGTCTAGCCAGAAAACTGAAA
1233 TTCAAAAATTGATTTTGGATTTTCGATTTACCGGAGAGAAAAACAAGTTACAAGGGTTGGGCCTT
406 TTCAAAAATTGATTTTGGATTTTCGATTTACCGGAGAGAAAAACAAGTTACAAGGGTTGGGCCTT
1298 GTAGATTGTAATCGGCATTTATCCGGAGTAAAATCTTATTCGATGATCGGTTGGAAATGAATTAA
471 GTAGATTGTAATCGGCATTTATCCGGAGTAAAATCTTATTCGATGATCGGTTGGAAATGAATTAA
1363 AGCAAAGCCTGAGGCTGTTATTTAAACTGAGTTTCTTCTTAAGTTTGCTTTCTTTAAATTCTTAG
536 AGCAAAGCCTGAGGCTGTTATTTAAACTGAGTTTCTTCTTAAGTTTGCTTTCTTTAAATTCTTAG
1428 ATTTAAATTTTCATTTCTTTATTTTAATTAAACTCTTTCTGTAACATCCGTGTGTTTGAACCGGA
601 ATTTAAATTTTCATTTCTTTATTTTAATTAAACTCTTTCTGTAACATCCGTGTGTTTGAACCGGA
1493 TTTGGAATAGTGATAAAATAGAATAGAGAATTAGAAATGTTTAGTTGAAGTATGGAAGGTTAGAA
666 TTTGGAATAGTGATAAAATAGAATAGAGAATTAGAAATGTTTAGTTGAAGTATGGAAGGTTAGAA
1558 AAATTTAAGGATTAAATAGTAAAGGAGAGAAAATATGGGGGACTAAA
731 AAATTTAAGGATTAAATAGTAAAGGAGAGAAAATATGGGGGACTAAA
1605 T
1 T
1606 AGCGAATTAT
Statistics
Matches: 759, Mismatches: 19, Indels: 50
0.92 0.02 0.06
Matches are distributed among these distances:
817 3 0.00
827 756 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.33
Consensus pattern (777 bp):
TTTTTTCCATAATCATGCTCATCTAATTTTCCAAAAAGTCAAAGGCTAAAGCAATGACTCAATTC
CAATCGTGAGAATTGAAAAGTACTTTATATCTTCAGATATATTTCTCAATTTTCTGCAAACTTGG
ATTGACAATCGGCCTTTCCTTTTAAAATCTTTACACTTTCAAGTTCAAAAAGGATCCGTTGGTTT
GAAGGTTGTTTCGATTTATAGTTGGGAGGAAGGATCGGCTTGCAGCACATTCGACTTCCTGTGAA
CACACTTAGCGGCGGTCCGCTAAGGGAAATTGAGATCGGATTCGATTCTCATTGAGACAATATAG
TCCGAGTCGGGTTTTTCCAGATTTTAAACTATTTTATTCTAACGGAGATAGTCGTGGTTAGTCTA
GCCAGAAAACTGAAATTCAAAAATTGATTTTGGATTTTCGATTTACCGGAGAGAAAAACAAGTTA
CAAGGGTTGGGCCTTGTAGATTGTAATCGGCATTTATCCGGAGTAAAATCTTATTCGATGATCGG
TTGGAAATGAATTAAAGCAAAGCCTGAGGCTGTTATTTAAACTGAGTTTCTTCTTAAGTTTGCTT
TCTTTAAATTCTTAGATTTAAATTTTCATTTCTTTATTTTAATTAAACTCTTTCTGTAACATCCG
TGTGTTTGAACCGGATTTGGAATAGTGATAAAATAGAATAGAGAATTAGAAATGTTTAGTTGAAG
TATGGAAGGTTAGAAAAATTTAAGGATTAAATAGTAAAGGAGAGAAAATATGGGGGACTAAA
Found at i:3093 original size:23 final size:23
Alignment explanation
Indices: 3063--3109 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
3053 CGCTAGCACA
3063 CTTACTATTTCACACTTCGTGTG
1 CTTACTATTTCACACTTCGTGTG
*
3086 CTTACTATTTCGCACTTCGTGTG
1 CTTACTATTTCACACTTCGTGTG
3109 C
1 C
3110 CTATTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.15, C:0.28, G:0.15, T:0.43
Consensus pattern (23 bp):
CTTACTATTTCACACTTCGTGTG
Found at i:3151 original size:43 final size:44
Alignment explanation
Indices: 3104--3195 Score: 107
Period size: 43 Copynumber: 2.1 Consensus size: 44
3094 TTCGCACTTC
* *
3104 GTGTGCCTA-TTGATTTGCGCTATGTGCGCCTACT-GATTGCACT
1 GTGTGCCTACTGGA-TTGCACTATGTGCGCCTACTGGATTGCACT
* * * *
3147 GTGTGCTTACTGGATTGCACTGTGTGTGTCTACTGGATTGCACT
1 GTGTGCCTACTGGATTGCACTATGTGCGCCTACTGGATTGCACT
3191 GTGTG
1 GTGTG
3196 TGCTTACTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
43 24 0.59
44 17 0.41
ACGTcount: A:0.13, C:0.20, G:0.29, T:0.38
Consensus pattern (44 bp):
GTGTGCCTACTGGATTGCACTATGTGCGCCTACTGGATTGCACT
Found at i:3203 original size:23 final size:23
Alignment explanation
Indices: 3134--3204 Score: 105
Period size: 23 Copynumber: 3.2 Consensus size: 23
3124 TATGTGCGCC
3134 TACT-GATTGCAC--TGTGTGCT
1 TACTGGATTGCACTGTGTGTGCT
3154 TACTGGATTGCACTGTGTGTG-T
1 TACTGGATTGCACTGTGTGTGCT
3176 CTACTGGATTGCACTGTGTGTGCT
1 -TACTGGATTGCACTGTGTGTGCT
3200 TACTG
1 TACTG
3205 TTTCCCCAGC
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.09
21 8 0.17
22 1 0.02
23 32 0.70
24 1 0.02
ACGTcount: A:0.14, C:0.18, G:0.28, T:0.39
Consensus pattern (23 bp):
TACTGGATTGCACTGTGTGTGCT
Done.