Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010423.1 Kokia drynarioides strain JFW-HI SEQ_125309, 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, 958
Length: 1598
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.39
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1124 original size:215 final size:210
Alignment explanation
Indices: 310--1586 Score: 1120
Period size: 215 Copynumber: 6.0 Consensus size: 210
300 GTAAGCTACT
* * *** * * *
310 TTTGATCTTTGAATTAAAAACTTATTTAGGTGAGAACAATTTCTCTCTTGGTTCTGGGCCGAACT
1 TTTGGTCTTTGAATTAAAAATTTATTTAGGTGAGAATTGTTTC-CTTTTGGTTCTCGGCCAAACT
* * * * * * *
375 TTCAAAGTT-AACAAACTTTTAGGATTTCTTTTATAACTTTGGTTCCTTAAAGTATTTAAGACGA
65 TT-GAACTTGAA-AAACTTTTACGAGTTCTTTTATAA-TTTTGTTCATTAAAGTATTCAAGACGA
* * * * * * *
439 TCCATTCCTTTGACCAATTTTCTGAACTTTCCATGCTT-GGAAATCGCACCATTTGGTTTAAATA
127 TCCATTCCTTCGAGCAATTTTCTGAACATTCCATG-TTGGGAAATCACATCATTAGGTCTAAATA
503 GTTGTCATTTTGTAAACAAC
191 GTTGTCATTTTGTAAACAAC
* *
523 TTTCGGTCTTTGAATTAAAAA-TTCTTTAGGTGAGAATTGTTTCTTTCTTGGTTCTCGGCCAAAC
1 TTT-GGTCTTTGAATTAAAAATTTATTTAGGTGAGAATTGTTTCCTT-TTGGTTCTCGGCCAAAC
* * *
587 TTTAAACTTGACAAAA-TTTT-CAAGTTCTTTTATAAATTTTGTTCATTAAAGTATTCAAGACAA
64 TTTGAACTTGA-AAAACTTTTACGAGTTCTTTTAT-AATTTTGTTCATTAAAGTATTCAAGACGA
* * * * * *
650 TCCATTCCTTC-AGCAATATAT-TGTACAGTCCGTGCTTGGGAAATCACATTATTAGGTCTCAAT
127 TCCATTCCTTCGAGCAAT-TTTCTGAACATTCCATG-TTGGGAAATCACATCATTAGGTCTAAAT
* *
713 TGTTGTCATTTTGTAAACTAC
190 AGTTGTCATTTTGTAAACAAC
* * * * * *
734 TTTCGGTTTTTCAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTATTCGTTCTCAGCCAAAC
1 TTT-GGTCTTTGAATTAAAAATTTATTTAGGTGAGAATTGTTTC-CTTTTGGTTCTCGGCCAAAC
* *
799 -TTG-AC-----AAAGTTTTACGAGTACTTTTATAACTTTTGTTCATTAAAGTATTCAAGACGAT
64 TTTGAACTTGAAAAACTTTTACGAGTTCTTTTATAA-TTTTGTTCATTAAAGTATTCAAGACGAT
* * * *
857 CGATTCCTTCGAGTAATTTTCTGTACAGTCCATGCTTGGGAAATCACATCATTAGGTCTAAATAG
128 CCATTCCTTCGAGCAATTTTCTGAACATTCCATG-TTGGGAAATCACATCATTAGGTCTAAATAG
* * **
922 TTGTCATTTTTTCAACTCC
192 TTGTCATTTTGTAAACAAC
* * *
941 TTCTGGTCTTCT-AATTAAAAATTTATTTAGTTGAGAATTGTTTCGCTTTTGGTTCTCGGTCGAA
1 TT-TGGTCTT-TGAATTAAAAATTTATTTAGGTGAGAATTGTTTC-CTTTTGGTTCTCGGCCAAA
* * * *
1005 CTTCCGAACTAGAAAAACTTTTACGAGTTAC-TTTATAATTTTGATTCGTTAAACTATTCAAGAC
63 CTT-TGAACTTGAAAAACTTTTACGAGTT-CTTTTATAATTTTG-TTCATTAAAGTATTCAAGAC
* ** * * ** * *
1069 GATTCATTCCTTCGAGCAATTTTAAGAAAATTCTATGTTCTAGAAATCGCATCATTTA-GTGTAA
125 GATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGTT-GGGAAATCACATCA-TTAGGTCTAA
* * *
1133 ATAATTGCCATTATGTAAACAAC
188 ATAGTTGTCATTTTGTAAACAAC
* * * * *
1156 TTTTGGTCTCTGAATTAAAAAACTTT-TTTAGGTGAGAATAGTTTCTCTCTTGTTTCTAGGCCAA
1 -TTTGGTCTTTGAATT-AAAAA-TTTATTTAGGTGAGAATTGTTTC-CTTTTGGTTCTCGGCCAA
* * * ** * * *
1220 ACTTCTGAAGTTGACAAACTTTTACGTGTTC-TTTATAACTTCAGTTCCTTACAGTAATCAAGAC
62 ACTT-TGAACTTGAAAAACTTTTACGAGTTCTTTTATAA-TTTTGTTCATTAAAGTATTCAAGAC
* * * * * *
1284 AAACCATTCCTTCGAGCAATTTTCTGAACATTCCAAGCTCAGGG-AATCTCATCATTTGGTCTAA
125 GATCCATTCCTTCGAGCAATTTTCTGAACATTCCATG-T-TGGGAAATCACATCATTAGGTCTAA
* *
1348 ATAGTTATCGTTTTGTAAACAAC
188 ATAGTTGTCATTTTGTAAACAAC
* * * * *
1371 TTTTGGTCTTTGAATTAAAAAATTATTTATGTGAGAATTGTTTCTTTCTTAGTTCTCGGCCGAAC
1 -TTTGGTCTTTGAATTAAAAATTTATTTAGGTGAGAATTGTTTCCTT-TTGGTTCTCGGCCAAAC
* * * *
1436 TTTAAACTTGACAAACATTTACGAGTTCTTTTATAACTTTTGTTCATTAACGTATTCAAGACGAT
64 TTTGAACTTGAAAAACTTTTACGAGTTCTTTTATAA-TTTTGTTCATTAAAGTATTCAAGACGAT
* * * * * * *
1501 CAATTCCTTCGAGCAATTTTCTGTACAGTCCATGCCTGGAAAATCACAACATTATGTC-AAATAG
128 CCATTCCTTCGAGCAATTTTCTGAACATTCCATG-TTGGGAAATCACATCATTAGGTCTAAATAG
*
1565 TTGTCATTTTGTAAACAGC
192 TTGTCATTTTGTAAACAAC
1584 TTT
1 TTT
1587 TATTTTTTGA
Statistics
Matches: 862, Mismatches: 162, Indels: 81
0.78 0.15 0.07
Matches are distributed among these distances:
204 3 0.00
205 6 0.01
206 49 0.06
207 113 0.13
208 3 0.00
209 1 0.00
210 21 0.02
211 104 0.12
212 51 0.06
213 93 0.11
214 136 0.16
215 208 0.24
216 71 0.08
217 3 0.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (210 bp):
TTTGGTCTTTGAATTAAAAATTTATTTAGGTGAGAATTGTTTCCTTTTGGTTCTCGGCCAAACTT
TGAACTTGAAAAACTTTTACGAGTTCTTTTATAATTTTGTTCATTAAAGTATTCAAGACGATCCA
TTCCTTCGAGCAATTTTCTGAACATTCCATGTTGGGAAATCACATCATTAGGTCTAAATAGTTGT
CATTTTGTAAACAAC
Found at i:1339 original size:430 final size:421
Alignment explanation
Indices: 307--1587 Score: 1285
Period size: 430 Copynumber: 3.0 Consensus size: 421
297 NNNGTAAGCT
* * * * *
307 ACTTTTGATCTTTGAATTAAAAACTTATTTAGGTGAGAACAATTTCTCTCTTGGTTCTGGGCCGA
1 ACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAGTTTCTCTCTT-GTTCTAGGCCAA
* * * * *
372 ACTTTCAAAGTTAACAAACTTTTAGGAT-TTCTTTTATAACTTTGGTTCCTTAAAGTATTTAAGA
65 AC-TTCTAAGTTGACAAACTTTTACG-TGTTCTTTTATAACTTTAGTTCCTTAAAGTATTCAAGA
* * * * * * *
436 CGATCCATTCCTTTGACCAATTTTCTGAACTTTCCATGCTTGGAAATCGCACCATTTGGTTTAAA
128 CGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTTGGGAATCACATCATTTGGTCTAAA
* *
501 TAGTTGTCATTTTGTAAACAACTTTCGGTCTTTGAATTAAAAATTCTTTAGGTGAGAATTGTTTC
193 TAGTTGTCATTTTGTAAACAACTTT-GGTCTTTGAATTAAAAATTATTTAGTTGAGAATTGTTTC
* *
566 TTTCTTGGTTCTCGGCCAAACTTTAAACTTGACAAAA-TTTT-CAAGTTCTTTTATAAATTTTGT
257 TTTCTTGGTTCTCGGCCGAACTTTAAACTTGA-AAAACTTTTACGAGTTCTTTTAT-AATTTTGT
* * * * * * *
629 TCATTAAAGTATTCAAGACAATCCATTCCTTC-AGCAATATATTGTACAGTCCGTGCTTGGGAAA
320 TCATTAAACTATTCAAGACGATTCATTCCTTCGAGCAAT-T-TTGAAAAGTCCATGCTTGAGAAA
* * ** * * *
693 TCACATTATTAGGTCTCAATTGTTGTCATTTTGTAAACT
383 TCACATCATTAGGTCTAAATAATTGCCATTATGTAAACA
* * * * *
732 ACTTTCGGTTTTTCAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTATTCGTTCTCA-GCCA
1 ACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAGTTTCTCTCTT-GTTCT-AGGCCA
* * * * *
796 AA---C----TTGACAAAGTTTTACGAGTACTTTTATAACTTTTGTTCATTAAAGTATTCAAGAC
64 AACTTCTAAGTTGACAAACTTTTACGTGTTCTTTTATAACTTTAGTTCCTTAAAGTATTCAAGAC
* * * * *
854 GATCGATTCCTTCGAGTAATTTTCTGTACAGTCCATGCTTGGGAAATCACATCATTAGGTCTAAA
129 GATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTTGGG-AATCACATCATTTGGTCTAAA
* * **
919 TAGTTGTCATTTTTTCAACTCCTTCTGGTCTTCT-AATTAAAAATTTATTTAGTTGAGAATTGTT
193 TAGTTGTCATTTTGTAAACAACTT-TGGTCTT-TGAATTAAAAA-TTATTTAGTTGAGAATTGTT
* * ** *
983 TCGCTT-TTGGTTCTCGGTCGAACTTCCGAACTAGAAAAACTTTTACGAGTTAC-TTTATAATTT
255 TC-TTTCTTGGTTCTCGGCCGAACTT-TAAACTTGAAAAACTTTTACGAGTT-CTTTTATAATTT
* * * *
1046 TGATTCGTTAAACTATTCAAGACGATTCATTCCTTCGAGCAATTTTAAGAAAATTCTATG-TTCT
317 TG-TTCATTAAACTATTCAAGACGATTCATTCCTTCGAGCAATTTT--GAAAAGTCCATGCTT-G
* *
1110 AGAAATCGCATCATTTA-GTGTAAATAATTGCCATTATGTAAACA
378 AGAAATCACATCA-TTAGGTCTAAATAATTGCCATTATGTAAACA
* *
1154 ACTTTTGGTCTCTGAATTAAAAAACTTTTTTAGGTGAGAATAGTTTCTCTCTTGTTTCTAGGCCA
1 ACTTTTGGTCTTTGAATT-AAAAACTTATTTAGGTGAGAATAGTTTCTCTCTTG-TTCTAGGCCA
* * *
1219 AACTTCTGAAGTTGACAAACTTTTACGTGTTC-TTTATAACTTCAGTTCCTTACAGTAATCAAGA
64 AACTTCT-AAGTTGACAAACTTTTACGTGTTCTTTTATAACTTTAGTTCCTTAAAGTATTCAAGA
* * * * *
1283 CAAACCATTCCTTCGAGCAATTTTCTGAACATTCCAAGCTCAGGGAATCTCATCATTTGGTCTAA
128 CGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCT-TGGGAATCACATCATTTGGTCTAA
* *
1348 ATAGTTATCGTTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATTATTTA-TGTGAGAATTGT
192 ATAGTTGTCATTTTGTAAACAAC-TTTGGTCTTTGAATT-AAAAATTATTTAGT-TGAGAATTGT
* * *
1412 TTCTTTCTTAGTTCTCGGCCGAACTTTAAACTTGACAAACATTTACGAGTTCTTTTATAACTTTT
254 TTCTTTCTTGGTTCTCGGCCGAACTTTAAACTTGAAAAACTTTTACGAGTTCTTTTATAA-TTTT
* * *
1477 GTTCATT-AACGTATTCAAGACGA-TCAATTCCTTCGAGCAATTTTCTGTACAGTCCATGCCTG-
318 GTTCATTAAAC-TATTCAAGACGATTC-ATTCCTTCGAGCAA-TTT-TGAAAAGTCCATGCTTGA
* * * * *
1539 GAAAATCACAACATTATGTC-AAATAGTTGTCATTTTGTAAACA
379 G-AAATCACATCATTAGGTCTAAATAATTGCCATTATGTAAACA
*
1582 GCTTTT
1 ACTTTT
1588 ATTTTTTGAA
Statistics
Matches: 696, Mismatches: 117, Indels: 83
0.78 0.13 0.09
Matches are distributed among these distances:
417 81 0.12
418 52 0.07
419 43 0.06
420 21 0.03
421 43 0.06
422 60 0.09
423 44 0.06
425 54 0.08
426 1 0.00
428 35 0.05
429 81 0.12
430 152 0.22
431 29 0.04
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (421 bp):
ACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAGTTTCTCTCTTGTTCTAGGCCAAA
CTTCTAAGTTGACAAACTTTTACGTGTTCTTTTATAACTTTAGTTCCTTAAAGTATTCAAGACGA
TCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTTGGGAATCACATCATTTGGTCTAAATAG
TTGTCATTTTGTAAACAACTTTGGTCTTTGAATTAAAAATTATTTAGTTGAGAATTGTTTCTTTC
TTGGTTCTCGGCCGAACTTTAAACTTGAAAAACTTTTACGAGTTCTTTTATAATTTTGTTCATTA
AACTATTCAAGACGATTCATTCCTTCGAGCAATTTTGAAAAGTCCATGCTTGAGAAATCACATCA
TTAGGTCTAAATAATTGCCATTATGTAAACA
Found at i:1547 original size:644 final size:631
Alignment explanation
Indices: 387--1574 Score: 1520
Period size: 644 Copynumber: 1.9 Consensus size: 631
377 CAAAGTTAAC
* * * * * *
387 AAACTTTTAGGATTTCTTTTATAACTTTGGTTCCTTAAAGTATTTAAGACGATCCATTCCTTTGA
1 AAACTTTTACGATTACTTTTATAACTTTGATTCCTTAAACTATTCAAGACGATCCATTCCTTCGA
** ** * * * * * *
452 CCAATTTTCTGAACTTTCCATGCTTGGAAATCGCACCATTTGGTTTAAATAGTTGTCATTTTGTA
66 CCAATTTTAAGAAAATTCCATGCTTAGAAATCGCACCATTTAGTGTAAATAATTGCCATTATGTA
* * * *
517 AACAACTTTCGGTCTTTGAATTAAAAATTCTTTAGGTGAGAATTGTTTCTTTCTTGGTTCTCGGC
131 AACAACTTTCGGTCTCTGAATTAAAAATTCTTTAGGTGAGAATAGTTTCTCTCTTGGTTCTAGGC
** *
582 CAAACTTTAAACTTGACAAAATTTTCAAGTTCTTTTATAAATTTTGTTCATTAAAGTATTCAAGA
196 CAAACTTTAAACTTGACAAAATTTTCAAGTTCTTTTATAAATTCAGTTCATTAAAGTAATCAAGA
* * ** * * *
647 CAATCCATTCCTTCAGCAATATATTGTACAGTCCGTGCTTGGGAAATCACATTATTAGGTCTCAA
261 CAAACCATTCCTTCAGCAATATATTGAACAGTCCAAGCTAGGGAAATCACATCATTAGGTCTAAA
* * * * *
712 TTGTTGTCATTTTGTAAACTACTTTCGGTTTTTCAATTAAAAACTTATTTAGGTGAGAATTGTTT
326 TAGTTATCATTTTGTAAACAACTTTCGGTCTTTCAATTAAAAAATTATTTAGGTGAGAATTGTTT
* **
777 CTCTATTCGTTCTCAGCCAAACTTGACAAAGTTTTACGAGTACTTTTATAACTTTTGTTCATTAA
391 CTCTATTAGTTCTCAGCCAAACTTGACAAACATTTACGAGTACTTTTATAACTTTTGTTCATTAA
* * * * *
842 AGTATTCAAGACGATCGATTCCTTCGAGTAATTTTCTGTACAGTCCATGCTTGGGAAATCACATC
456 AGTATTCAAGACGATCAATTCCTTCGAGCAATTTTCTGTACAGTCCATGCCTGGAAAATCACAAC
907 ATTAGGTCTAAATAGTTGTCATTTTTTCAACTCCTTCTGGTCTTCTAATTAAAAATTTATTTAGT
521 ATTAGGTC-AAATAGTTGTCATTTTTTCAACTCCTTCTGGTCTTCTAATTAAAAATTTATTTAGT
972 TGAGAATTGTTTCGCTTTTGGTTCTCGGTCGAACTTCCGAACTAGAA
585 TGAGAATTGTTTCGCTTTTGGTTCTCGGTCGAACTTCCGAACTAGAA
* * *
1019 AAACTTTTACGAGTTAC-TTTATAATTTTGATTCGTTAAACTATTCAAGACGATTCATTCCTTCG
1 AAACTTTTACGA-TTACTTTTATAACTTTGATTCCTTAAACTATTCAAGACGATCCATTCCTTCG
* * * *
1083 AGCAATTTTAAGAAAATTCTATGTTCTAGAAATCGCATCATTTAGTGTAAATAATTGCCATTATG
65 ACCAATTTTAAGAAAATTCCATGCT-TAGAAATCGCACCATTTAGTGTAAATAATTGCCATTATG
* * *
1148 TAAACAACTTTTGGTCTCTGAATTAAAAAACTTTTTTAGGTGAGAATAGTTTCTCTCTTGTTTCT
129 TAAACAACTTTCGGTCTCTGAATT-AAAAA-TTCTTTAGGTGAGAATAGTTTCTCTCTTGGTTCT
* * * ** * * *
1213 AGGCCAAACTTCTGAAGTTGACAAACTTTTACGTGTTC-TTTATAACTTCAGTTCCTTACAGTAA
192 AGGCCAAACTT-TAAACTTGACAAAATTTT-CAAGTTCTTTTATAAATTCAGTTCATTAAAGTAA
* * *
1277 TCAAGACAAACCATTCCTTCGAGCAAT-TTTCTGAACATTCCAAGCTCAGGG-AATCTCATCATT
255 TCAAGACAAACCATTCCTTC-AGCAATATAT-TGAACAGTCCAAGCT-AGGGAAATCACATCATT
* * * * *
1340 TGGTCTAAATAGTTATCGTTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATTATTTATGTGA
317 AGGTCTAAATAGTTATCATTTTGTAAACAACTTTCGGTCTTTCAATTAAAAAATTATTTAGGTGA
* * * *
1405 GAATTGTTTCTTTCTTAGTTCTCGGCCGAACTTTAAACTTGACAAACATTTACGAGTTCTTTTAT
382 GAATTGTTTCTCTATTAGTTCTCAG-C---C---AAACTTGACAAACATTTACGAGTACTTTTAT
*
1470 AACTTTTGTTCATTAACGTATTCAAGACGATCAATTCCTTCGAGCAATTTTCTGTACAGTCCATG
440 AACTTTTGTTCATTAAAGTATTCAAGACGATCAATTCCTTCGAGCAATTTTCTGTACAGTCCATG
*
1535 CCTGGAAAATCACAACATTATGTCAAATAGTTGTCATTTT
505 CCTGGAAAATCACAACATTAGGTCAAATAGTTGTCATTTT
1575 GTAAACAGCT
Statistics
Matches: 465, Mismatches: 75, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
632 69 0.15
633 57 0.12
634 5 0.01
635 40 0.09
636 56 0.12
637 107 0.23
638 4 0.01
641 1 0.00
643 16 0.03
644 110 0.24
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (631 bp):
AAACTTTTACGATTACTTTTATAACTTTGATTCCTTAAACTATTCAAGACGATCCATTCCTTCGA
CCAATTTTAAGAAAATTCCATGCTTAGAAATCGCACCATTTAGTGTAAATAATTGCCATTATGTA
AACAACTTTCGGTCTCTGAATTAAAAATTCTTTAGGTGAGAATAGTTTCTCTCTTGGTTCTAGGC
CAAACTTTAAACTTGACAAAATTTTCAAGTTCTTTTATAAATTCAGTTCATTAAAGTAATCAAGA
CAAACCATTCCTTCAGCAATATATTGAACAGTCCAAGCTAGGGAAATCACATCATTAGGTCTAAA
TAGTTATCATTTTGTAAACAACTTTCGGTCTTTCAATTAAAAAATTATTTAGGTGAGAATTGTTT
CTCTATTAGTTCTCAGCCAAACTTGACAAACATTTACGAGTACTTTTATAACTTTTGTTCATTAA
AGTATTCAAGACGATCAATTCCTTCGAGCAATTTTCTGTACAGTCCATGCCTGGAAAATCACAAC
ATTAGGTCAAATAGTTGTCATTTTTTCAACTCCTTCTGGTCTTCTAATTAAAAATTTATTTAGTT
GAGAATTGTTTCGCTTTTGGTTCTCGGTCGAACTTCCGAACTAGAA
Done.