Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010405.1 Kokia drynarioides strain JFW-HI SEQ_125288, 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: 25538
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Found at i:332 original size:182 final size:181
Alignment explanation
Indices: 15--901 Score: 1169
Period size: 182 Copynumber: 4.9 Consensus size: 181
5 GGCACTTTAG
*
15 TATCTTAATACCTCTCCTGAAGCAGGAAAACATACATCTGTTTCAATACTATCTTCTGCTTCAAC
1 TATCTAAATACCTCTCCTGAAGCAGGAAAACATACATCTGTTTCAATACTATCTTCTGCTTCAAC
* ** *
80 GATAGTAGCACCAGCACATCTGACTCCTCAGGAGCCAATATTGGTGCTACTATCGTTGAAGCAGA
66 GATAGCAGCACCAATACAT-TGACTCCTCAGGAGCCAATATTGGTGCTGCTATCGTTGAAGCAGA
* * *
145 AGATAGTATTGAAACAGATGTGTGTTTTCCTGTTTCAGGAGAGGGA-TTAAGA
130 AGATAGTATTGAAACAGATGTATGTTTTCCTGCTTCAGGAGAGAGACTTAA-A
* *
197 TAT-TAAAGTGCCTCTCCTGAAGCAGGAAAACATACATTTGTTTCAATACTATCTTCTGCTTCAA
1 TATCTAAA-TACCTCTCCTGAAGCAGGAAAACATACATCTGTTTCAATACTATCTTCTGCTTCAA
* * *
261 CGATAGCTGCATCAATACATATGACTCCTCAGGAGCCAATATTGGTGCTACTATCGTTGAAGCAG
65 CGATAGCAGCACCAATACAT-TGACTCCTCAGGAGCCAATATTGGTGCTGCTATCGTTGAAGCAG
* * *
326 AAGATAGTATTGAAACAAATGTATGTTTTCCTGCTTCAGGAGAGGGCACTTTAA
129 AAGATAGTATTGAAACAGATGTATGTTTTCCTGCTTCAGGAGAGAG-ACTTAAA
* * *
380 TATCTTAATACCTCTCCTGAAACAGGAAAACACACATCTGTTTCAATACTATCTTCTGCTTCAAC
1 TATCTAAATACCTCTCCTGAAGCAGGAAAACATACATCTGTTTCAATACTATCTTCTGCTTCAAC
* * *
445 GATAGCAGCACCAAT--ATTGGCTCCTGAGGAGTCAGATGTATTGGTGCTGCTATCGTTGAAGCA
66 GATAGCAGCACCAATACATTGACTCCTCAGGAGCCA-A--TATTGGTGCTGCTATCGTTGAAGCA
* *
508 GAAGATAGTATTGAAACAGATGTATGTTTTCATGCTTCAGGAGAGATA-TTAAGA
128 GAAGATAGTATTGAAACAGATGTATGTTTTCCTGCTTCAGGAGAGAGACTTAA-A
** *
562 TAT-TAAAGTGTCTCTCTTGAAGCAGGAAAACATACATCTGTTTCAATACTATCTTCTGCTTCAA
1 TATCTAAA-TACCTCTCCTGAAGCAGGAAAACATACATCTGTTTCAATACTATCTTCTGCTTCAA
* * * * * *
626 CGATAGCAGCACCAAT--ATTGGCTCTTGAGGAGTCAGATGTATTAGTGTTGCTATCGTTGAAGC
65 CGATAGCAGCACCAATACATTGACTCCTCAGGAGCCA-A--TATTGGTGCTGCTATCGTTGAAGC
* * * * * * *
689 AGAAAATAGTATTGAAACAGATGTATGCTTTCCTGTTTTAAGAGAGACACTTTAA
127 AGAAGATAGTATTGAAACAGATGTATGTTTTCCTGCTTCAGGAGAGAGACTTAAA
* * * **
744 TATCTTAATACCTCTCTTGAAGTAGGAAAACATACATCTGTTTCAATACTATCACCTGCTTCAAC
1 TATCTAAATACCTCTCCTGAAGCAGGAAAACATACATCTGTTTCAATACTATCTTCTGCTTCAAC
* *
809 GATAGCAGCACCAATACATCTGACTCCTCAGAAGCCAATATTGGTGCTGCTATCGTTGAAGCAGG
66 GATAGCAGCACCAATACAT-TGACTCCTCAGGAGCCAATATTGGTGCTGCTATCGTTGAAGCAGA
874 AGATAGTATTGAAACAGATGTATGTTTT
130 AGATAGTATTGAAACAGATGTATGTTTT
902 GACTCCTTCA
Statistics
Matches: 629, Mismatches: 62, Indels: 28
0.87 0.09 0.04
Matches are distributed among these distances:
180 14 0.02
181 12 0.02
182 438 0.70
183 144 0.23
184 9 0.01
185 12 0.02
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (181 bp):
TATCTAAATACCTCTCCTGAAGCAGGAAAACATACATCTGTTTCAATACTATCTTCTGCTTCAAC
GATAGCAGCACCAATACATTGACTCCTCAGGAGCCAATATTGGTGCTGCTATCGTTGAAGCAGAA
GATAGTATTGAAACAGATGTATGTTTTCCTGCTTCAGGAGAGAGACTTAAA
Found at i:682 original size:365 final size:361
Alignment explanation
Indices: 1--901 Score: 1322
Period size: 365 Copynumber: 2.5 Consensus size: 361
*
1 GAGAGGCACTTTAGTATCTTAATACCTCTCCTGAAGCAGGAAAACATACATCTGTTTCAATACTA
1 GAGAGGCACTTTAATATCTTAATACCTCTCCTGAAGCAGGAAAACATACATCTGTTTCAATACTA
* * *
66 TCTTCTGCTTCAACGATAGTAGCACCAGCACATCTGACTCCTCAGGAGCCAATATTGGTGCTACT
66 TCTTCTGCTTCAACGATAGCAGCACCA--ATATCTGACTCCTCAGGAGCCAATATTGGTGCTGCT
* * * *
131 ATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTGTGTTTTCCTGTTTCAGGAGAGGGATTAAG
129 ATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTTCATGCTTCAGGAGAGAGATTAAG
*
196 ATATTAAAGTGCCTCTCCTGAAGCAGGAAAACATACATTTGTTTCAATACTATCTTCTGCTTCAA
194 ATATTAAAGTGCCTCTCCTGAAGCAGGAAAACATACATCTGTTTCAATACTATCTTCTGCTTCAA
* * *
261 CGATAGCTGCATCAATACATATGACTCCTCAGGAGCCAATATTGGTGCTACTATCGTTGAAGCAG
259 CGATAGCAGCACCAATA-ATATGACTCCTCAGGAGCCAATATTAGTGCTACTATCGTTGAAGCAG
* * *
326 AAGATAGTATTGAAACAAATGTATGTTTTCCTGCTTCAG
323 AAAATAGTATTGAAACAAATGTATGCTTTCCTGCTTCAA
* *
365 GAGAGGGCACTTTAATATCTTAATACCTCTCCTGAAACAGGAAAACACACATCTGTTTCAATACT
1 GAGA-GGCACTTTAATATCTTAATACCTCTCCTGAAGCAGGAAAACATACATCTGTTTCAATACT
* * *
430 ATCTTCTGCTTCAACGATAGCAGCACCAATAT-TGGCTCCTGAGGAGTCAGATGTATTGGTGCTG
65 ATCTTCTGCTTCAACGATAGCAGCACCAATATCTGACTCCTCAGGAGCCA-A--TATTGGTGCTG
*
494 CTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTTCATGCTTCAGGAGAGATATTA
127 CTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTTCATGCTTCAGGAGAGAGATTA
* *
559 AGATATTAAAGTGTCTCTCTTGAAGCAGGAAAACATACATCTGTTTCAATACTATCTTCTGCTTC
192 AGATATTAAAGTGCCTCTCCTGAAGCAGGAAAACATACATCTGTTTCAATACTATCTTCTGCTTC
* * * * * *
624 AACGATAGCAGCACCAAT-AT-TGGCTCTTGAGGAGTCAGATGTATTAGTGTTGCTATCGTTGAA
257 AACGATAGCAGCACCAATAATATGACTCCTCAGGAGCCA-A--TATTAGTGCTACTATCGTTGAA
* * *
687 GCAGAAAATAGTATTGAAACAGATGTATGCTTTCCTGTTTTAA
319 GCAGAAAATAGTATTGAAACAAATGTATGCTTTCCTGCTTCAA
* * *
730 GAGAGACACTTTAATATCTTAATACCTCTCTTGAAGTAGGAAAACATACATCTGTTTCAATACTA
1 GAGAGGCACTTTAATATCTTAATACCTCTCCTGAAGCAGGAAAACATACATCTGTTTCAATACTA
** *
795 TCACCTGCTTCAACGATAGCAGCACCAATACATCTGACTCCTCAGAAGCCAATATTGGTGCTGCT
66 TCTTCTGCTTCAACGATAGCAGCACCAAT--ATCTGACTCCTCAGGAGCCAATATTGGTGCTGCT
*
860 ATCGTTGAAGCAGGAGATAGTATTGAAACAGATGTATGTTTT
129 ATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTT
902 GACTCCTTCA
Statistics
Matches: 483, Mismatches: 44, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
362 27 0.06
363 7 0.01
364 141 0.29
365 292 0.60
366 3 0.01
367 13 0.03
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (361 bp):
GAGAGGCACTTTAATATCTTAATACCTCTCCTGAAGCAGGAAAACATACATCTGTTTCAATACTA
TCTTCTGCTTCAACGATAGCAGCACCAATATCTGACTCCTCAGGAGCCAATATTGGTGCTGCTAT
CGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTTCATGCTTCAGGAGAGAGATTAAGAT
ATTAAAGTGCCTCTCCTGAAGCAGGAAAACATACATCTGTTTCAATACTATCTTCTGCTTCAACG
ATAGCAGCACCAATAATATGACTCCTCAGGAGCCAATATTAGTGCTACTATCGTTGAAGCAGAAA
ATAGTATTGAAACAAATGTATGCTTTCCTGCTTCAA
Found at i:5816 original size:14 final size:14
Alignment explanation
Indices: 5791--5826 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5781 GACAGAAAGA
5791 GGGAGGGAGGAGGG
1 GGGAGGGAGGAGGG
* *
5805 GGTAGGGGGGAGGG
1 GGGAGGGAGGAGGG
5819 GGGAGGGA
1 GGGAGGGA
5827 AGCGACTATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.78, T:0.03
Consensus pattern (14 bp):
GGGAGGGAGGAGGG
Found at i:7665 original size:19 final size:19
Alignment explanation
Indices: 7641--7677 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
7631 GCAAGATAGT
*
7641 TAAGTAGAGCATCAATAAA
1 TAAGTAAAGCATCAATAAA
7660 TAAGTAAAGCATCAATAA
1 TAAGTAAAGCATCAATAA
7678 TTAAAACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.22
Consensus pattern (19 bp):
TAAGTAAAGCATCAATAAA
Found at i:17115 original size:20 final size:20
Alignment explanation
Indices: 17066--17128 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 20
17056 TTTAAATTTT
*
17066 TAATAAATAAAAATATAAAA
1 TAATTAATAAAAATATAAAA
* *
17086 TAA-TAGTAAAAGATAT-ATA
1 TAATTAATAAAA-ATATAAAA
*
17105 TAATTAAT--AAATATTAAA
1 TAATTAATAAAAATATAAAA
17123 TAATTA
1 TAATTA
17129 TCATTTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
17 4 0.11
18 10 0.29
19 11 0.31
20 10 0.29
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
TAATTAATAAAAATATAAAA
Found at i:21325 original size:22 final size:23
Alignment explanation
Indices: 21300--21360 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 23
21290 ATCATTACTT
* *
21300 TAATACTTCTTTAC-ATTTGATA
1 TAATACTTCATAACAATTTGATA
*
21322 TAATATTTCATAACAAATTTGATA
1 TAATACTTCATAAC-AATTTGATA
*
21346 TAATATTTCATAACA
1 TAATACTTCATAACA
21361 CAATGATAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.32
23 1 0.03
24 22 0.65
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.44
Consensus pattern (23 bp):
TAATACTTCATAACAATTTGATA
Found at i:21342 original size:24 final size:24
Alignment explanation
Indices: 21314--21360 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
21304 ACTTCTTTAC
21314 ATTTGATATAATATTTCATAACAA
1 ATTTGATATAATATTTCATAACAA
21338 ATTTGATATAATATTTCATAACA
1 ATTTGATATAATATTTCATAACA
21361 CAATGATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (24 bp):
ATTTGATATAATATTTCATAACAA
Found at i:21409 original size:16 final size:16
Alignment explanation
Indices: 21388--21418 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21378 CACAATTATA
*
21388 TAAATATTAGTAAAAT
1 TAAATAGTAGTAAAAT
21404 TAAATAGTAGTAAAA
1 TAAATAGTAGTAAAA
21419 CTATCAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (16 bp):
TAAATAGTAGTAAAAT
Found at i:21776 original size:22 final size:21
Alignment explanation
Indices: 21728--21777 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
21718 TTCCACATTA
*
21728 TTTTT-TTTAAATATATATAT
1 TTTTTATTTAAATATATAAAT
* *
21748 ATATTATTTAAATATTATAAAT
1 TTTTTATTTAAATA-TATAAAT
21770 TTTTTATT
1 TTTTTATT
21778 GAAAATGTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 3 0.13
21 8 0.35
22 12 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTATTTAAATATATAAAT
Done.