Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011740.1 Kokia drynarioides strain JFW-HI SEQ_126734, 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: 10863
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:261 original size:22 final size:24
Alignment explanation
Indices: 236--299 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
226 TTTCTTGAGC
236 GATAT-GAT-ATGGAAGACTTGGT
1 GATATCGATAATGGAAGACTTGGT
**
258 GATATCTTTAATGGAAGACTTGGT
1 GATATCGATAATGGAAGACTTGGT
* **
282 GATTTCTTTAATGGAAGA
1 GATATCGATAATGGAAGA
300 GCTTACGTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 5 0.14
23 1 0.03
24 31 0.84
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (24 bp):
GATATCGATAATGGAAGACTTGGT
Found at i:272 original size:24 final size:24
Alignment explanation
Indices: 244--299 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
234 GCGATATGAT
244 ATGGAAGACTTGGTGATATCTTTA
1 ATGGAAGACTTGGTGATATCTTTA
*
268 ATGGAAGACTTGGTGATTTCTTTA
1 ATGGAAGACTTGGTGATATCTTTA
292 ATGGAAGA
1 ATGGAAGA
300 GCTTACGTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (24 bp):
ATGGAAGACTTGGTGATATCTTTA
Found at i:1190 original size:43 final size:43
Alignment explanation
Indices: 1123--1215 Score: 141
Period size: 43 Copynumber: 2.2 Consensus size: 43
1113 ATAGCTTGAA
*
1123 ACACGGTCTAGGACATGGCCATGTAAGGGTATTTCGTGTATGC
1 ACACGGTCTAGGACATGACCATGTAAGGGTATTTCGTGTATGC
* * * *
1166 TCACGGTCTAGGGCATGACTATGTAAGGGTATTTTGTGTATGC
1 ACACGGTCTAGGACATGACCATGTAAGGGTATTTCGTGTATGC
1209 ACACGGT
1 ACACGGT
1216 TTGGCACAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (43 bp):
ACACGGTCTAGGACATGACCATGTAAGGGTATTTCGTGTATGC
Found at i:1673 original size:15 final size:15
Alignment explanation
Indices: 1653--1683 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1643 TGTGAAGAGT
1653 ATTAATCTAAACTAA
1 ATTAATCTAAACTAA
*
1668 ATTAATCTAAATTAA
1 ATTAATCTAAACTAA
1683 A
1 A
1684 ATTGAAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTAATCTAAACTAA
Found at i:3562 original size:826 final size:776
Alignment explanation
Indices: 1971--3574 Score: 2260
Period size: 826 Copynumber: 2.0 Consensus size: 776
1961 AATAATCTCG
1971 TGTACATATATGTATGCCAATTCAACTAACTAATTAACATTCATAAGCAAGTAAAGGATCAAGTG
1 TGTACATATATGTATGCCAATTCAACTAACTAATTAACATTCATAAGCAAGTAAAGGATCAAGTG
2036 AAGTAACAAAATATATCTATATTGAAACAATTTAATCACAAAAATCCTGCAAGTTATGCAAAGCT
66 AAGTAACAAAATATATCTATATTGAAACAATTTAATCACAAAAATCCTGCAAGTTATGCAAAGCT
* *
2101 AATGTATTGTTTAATACCGTCGCTAAATCTAACCTTCAGCTCCCTTAAAAGATTAAACATGCACA
131 AATATATTGTTTAATACCGTCGCTAAATCTAACCTTCAACTCCCTTAAAAGATTAAACATGCACA
2166 AATTAAATAGTGTGTCCATTAATCACAATTTCAATCCACTTAAATGATTAATTCAAAATTTATAT
196 AATTAAATAGTGTGTCCATTAATCACAATTTCAATCCACTTAAATGATTAATTCAAAATTTATAT
2231 CACAAGGATAATGCAATTATAACTTAGGCATTATAGTATTTAATTAAACAAAATATTCAGGGCCT
261 CACAAGGATAATGCAATTATAACTTAGGCATTATAGTATTTAATTAAACAAAATATTCAGGGCCT
*
2296 ATAAAATTATAAACATGATTCATAAATAATCAAGCAATCAACACAATCAACCTAACACTGAAAGA
326 ATAAAATTATAAACATGATTCATAAATAATCAAGCAATCAACACAATCAACCTAACACTAAAAGA
2361 AAATTAAGTCATTTTTATTAAATAAACAATAACATTCATAATAACAATCAAGAAACTAAAAGAGA
391 AAATTAAGTCATTTTTATTAAATAAACAATAACATTCATAATAACAATCAAGAAACTAAAAGAGA
*
2426 GAAAAAGAATAGGATTAAATCCGACAATTTCTCAAAAATTATTGTCACATTCTTCGTCATTCTCG
456 GAAAAAGAATAGGATTAAATCCGACAATTTCTCAAAAACTATTGTCACATTCTTCGTCATTCTCG
2491 CTCGATTCTTCCCAGACTGAGGCCTCTGATGAACAATTAACAAAGCTATTTCAAGGCTGGAAACC
521 CTCGATTCTTCCCAGACTGAGGCCTCTGATGAACAATTAACAAAGCTATTTCAAGGCTGGAAACC
2556 ACTCTTTCCCAAGAGGGAAAATTGACAAGGGAATGGAAGGGGAAAATGAAAGAGAAAATAGAAAG
586 ACTCTTTCCCAAGAGGGAAAATTGACAAGGGAATGGAAGGGGAAAATGAAAGAGAAAATAGAAAG
*
2621 CAAAGGAGAGAAAAGAAGAGAGAATGGAGTGAATTTGTATGTTGAAATGAGAGTTGTGAGGGGGG
651 CAAAGGAGAGAAAAGAAGAGACAATGGAGTGAATTTGTATGTTGAAATGAGAGTTGTGAGGGGGG
2686 TTTTATAGGTGAGAGTTGAGGTTTATATTTAGTAAATAAATATCAACCACTCAACTCCNNNNNNN
716 TTTTATAGGTGAGAGTTGAGGTTTATATTTAGTAAATAAATATCAACCACTCAACTCC-------
***
2751 NNNNNNNNNNNNNNNNNNNNNN
774 -------------------TCT
********************* *** * *
2773 NNNNNNNNNNNNNNNNNNNNNTCTTGT-ACATATATGTATGCCAATTCAACTAA-CTAATTAACA
1 TGTACATATATGTATGCCAATTCAACTAAC-TA-AT-TA--AC-ATTC-A-TAAGC-AAGTAA-A
** *
2836 TTCATAAGCAAGTAAAGGATCAAGTGAAGTAACAAAATATATTTATATTGAAACAATTTAATCAC
56 -GGAT---CAAGT------------GAAGTAACAAAATATATCTATATTGAAACAATTTAATCAC
2901 AAAAATCCTGCAAGTTATGCAAAGCTAATATATTGTTTAATACCGTCGCTAAATCTAACCTTCAA
105 AAAAATCCTGCAAGTTATGCAAAGCTAATATATTGTTTAATACCGTCGCTAAATCTAACCTTCAA
2966 CTCCCTTAAAAGATTAAACATGCACAAATTAAATAGTGTGTCCATTAATCACAATTTCAATCCAC
170 CTCCCTTAAAAGATTAAACATGCACAAATTAAATAGTGTGTCCATTAATCACAATTTCAATCCAC
3031 TTAAATGATTAATTCAAAATTTATATCACAAGGATAATGCAATTATAACTTAGGCATTATAGTAT
235 TTAAATGATTAATTCAAAATTTATATCACAAGGATAATGCAATTATAACTTAGGCATTATAGTAT
3096 TTAATTAAACAAAATATTCAGGGCCTATAACAA-TATAAACATGATTCATAAATAATCAAGCAAT
300 TTAATTAAACAAAATATTCAGGGCCTATAA-AATTATAAACATGATTCATAAATAATCAAGCAAT
3160 CAACACAATCAACCTAACACTAAAAGAAAATTAAGTCATTTTTATTAAATAAACAATAACATTCA
364 CAACACAATCAACCTAACACTAAAAGAAAATTAAGTCATTTTTATTAAATAAACAATAACATTCA
* * * *
3225 TAATAACATTCAAGAAACTAAAAGAGAGAAAAATAATATGATTAAATCCGATAATTTCTCAAAAA
429 TAATAACAATCAAGAAACTAAAAGAGAGAAAAAGAATAGGATTAAATCCGACAATTTCTCAAAAA
* *
3290 CTGTTGTCACATTCTTCGTCGTTCTCGCTCGATTCTTCCCAGACTGAGGCCTCTGATGAACAATT
494 CTATTGTCACATTCTTCGTCATTCTCGCTCGATTCTTCCCAGACTGAGGCCTCTGATGAACAATT
* *
3355 AACAAAGTTATTTCAAGGCTGGAAACCACTCTTTCCCAAGAGGGAAATTTGACAAGGGAATGGAA
559 AACAAAGCTATTTCAAGGCTGGAAACCACTCTTTCCCAAGAGGGAAAATTGACAAGGGAATGGAA
* *
3420 GGGGAAAATGAAAGAGAAACTAGAAAGCAAATGAGAGAAAAGAAGAGACAATGGAGTGAATTTGT
624 GGGGAAAATGAAAGAGAAAATAGAAAGCAAAGGAGAGAAAAGAAGAGACAATGGAGTGAATTTGT
* *
3485 GTGTTGAAATGAGAGTTGTGAGTGGGGTTTTATAGGTGAGAGTTGAGGTTTATATTTAGTAAATA
689 ATGTTGAAATGAGAGTTGTGAGGGGGGTTTTATAGGTGAGAGTTGAGGTTTATATTTAGTAAATA
*
3550 AATATCAACCACTCAACTCCCCT
754 AATATCAACCACTCAACTCCTCT
3573 TG
1 TG
3575 GCCGGCCATG
Statistics
Matches: 724, Mismatches: 51, Indels: 56
0.87 0.06 0.07
Matches are distributed among these distances:
801 2 0.00
802 5 0.01
803 2 0.00
804 2 0.00
806 1 0.00
807 4 0.01
808 2 0.00
809 8 0.01
810 1 0.00
811 2 0.00
814 5 0.01
826 688 0.95
827 2 0.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.27
Consensus pattern (776 bp):
TGTACATATATGTATGCCAATTCAACTAACTAATTAACATTCATAAGCAAGTAAAGGATCAAGTG
AAGTAACAAAATATATCTATATTGAAACAATTTAATCACAAAAATCCTGCAAGTTATGCAAAGCT
AATATATTGTTTAATACCGTCGCTAAATCTAACCTTCAACTCCCTTAAAAGATTAAACATGCACA
AATTAAATAGTGTGTCCATTAATCACAATTTCAATCCACTTAAATGATTAATTCAAAATTTATAT
CACAAGGATAATGCAATTATAACTTAGGCATTATAGTATTTAATTAAACAAAATATTCAGGGCCT
ATAAAATTATAAACATGATTCATAAATAATCAAGCAATCAACACAATCAACCTAACACTAAAAGA
AAATTAAGTCATTTTTATTAAATAAACAATAACATTCATAATAACAATCAAGAAACTAAAAGAGA
GAAAAAGAATAGGATTAAATCCGACAATTTCTCAAAAACTATTGTCACATTCTTCGTCATTCTCG
CTCGATTCTTCCCAGACTGAGGCCTCTGATGAACAATTAACAAAGCTATTTCAAGGCTGGAAACC
ACTCTTTCCCAAGAGGGAAAATTGACAAGGGAATGGAAGGGGAAAATGAAAGAGAAAATAGAAAG
CAAAGGAGAGAAAAGAAGAGACAATGGAGTGAATTTGTATGTTGAAATGAGAGTTGTGAGGGGGG
TTTTATAGGTGAGAGTTGAGGTTTATATTTAGTAAATAAATATCAACCACTCAACTCCTCT
Found at i:5177 original size:23 final size:21
Alignment explanation
Indices: 5151--5196 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
5141 AATCAATAAA
5151 TAAATAAACA-ATAATACAACAAT
1 TAAATAAA-ATATAATA-AA-AAT
5174 TAAATAAAATATAATAAAAAT
1 TAAATAAAATATAATAAAAAT
5195 TA
1 TA
5197 TGATAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 5 0.23
22 3 0.14
23 14 0.64
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAATAAAATATAATAAAAAT
Found at i:5409 original size:26 final size:25
Alignment explanation
Indices: 5358--5408 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
5348 ATAAAAGTAC
*
5358 TAAAAAATGAACAAAATAAAATAAAA
1 TAAAAAAT-AACAAAACAAAATAAAA
*
5384 TAAAAAATAACAGAACAAAATAAAA
1 TAAAAAATAACAAAACAAAATAAAA
5409 ACAAACAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (25 bp):
TAAAAAATAACAAAACAAAATAAAA
Found at i:6738 original size:18 final size:17
Alignment explanation
Indices: 6715--6761 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
6705 GGTATTGGGC
**
6715 TATTTGTAATTGTTTTT
1 TATTTGTAATTGTAATT
6732 ATATTTGTAATGTGTAATT
1 -TATTTGTAAT-TGTAATT
6751 TATTTGTAATT
1 TATTTGTAATT
6762 TGGACTAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 1 0.04
18 20 0.77
19 5 0.19
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.62
Consensus pattern (17 bp):
TATTTGTAATTGTAATT
Done.