Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014302.1 Kokia drynarioides strain JFW-HI SEQ_129338, 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, 962
Length: 1604
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Found at i:684 original size:216 final size:215
Alignment explanation
Indices: 5--1604 Score: 1438
Period size: 216 Copynumber: 7.4 Consensus size: 215
1 CCTA
* * ** * * * * *
5 TCCTTCGACCAGTTTTTCAAACATTCAATGCCCGAAAAATCGCATTATTTGATCTAAATAGTTTG
1 TCCTTTGACCAATTTTTTGAACATTCCATGCTCGAGAAAT-GCATCATTTGGTCTAAATAGTTTG
* ** * * *
70 TCATTTCGTAAACAACTTTTACTCTTTGAATTAAAAACTTATTTACGTGAGAACTGCTTCCCTCT
65 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
* * * ***
135 TTGTTCTTGG-CTGAACTTTCGAACTTGTCAAGC-TTTTATGAGTTCTTTTATAACTTCAATTCC
130 TGGTTCTTGGAC-GAACTTTCGAACTTGTCAAACATTTAAT-AGTTCTTTTATAACTTTGGTTCC
*
198 TTAAAGTATTCAAGACGATCCAT
193 TGAAAGTATTCAAGACGATCCAT
* * ** * * * * * * *
221 TCCTTCGAGCAATTTTCCGAACATTCTACGCTTGGGAAATCGCAACGTTTGGTCTAAATAGTTTT
1 TCCTTTGACCAATTTTTTGAACATTCCATGCTCGAGAAAT-GCATCATTTGGTCTAAATAGTTTG
* * * * *
286 TCATTTTGTAATCAACTTTTCGTCTTTTAATTAAAAA--TATTTACATGACAATTGTTTCTCTCT
65 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
* * * *
349 TGGTTCTTGGACGAAC-TTCTAAACTTGTCAAACTTTTTATCAGTTCTTTTATAACTTCGGTTCC
130 TGGTTCTTGGACGAACTTTC-GAACTTGTCAAACATTTAAT-AGTTCTTTTATAACTTTGGTTCC
* * * **
413 TTAAACTATTAAAGGTGATCCAT
193 TGAAAGTATTCAAGACGATCCAT
** * *
436 TCCTTTGTGCAA-TTTTTCAATCATTCCATGCTCGAGAAATGACATCATTTGGTCTAAATAGGTT
1 TCCTTTGACCAATTTTTTGAA-CATTCCATGCTCGAGAAATG-CATCATTTGGTCTAAATAGTTT
* * * *
500 ATCATTTTCTAAACAATTTTTGGTCTTCGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC
64 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC
* * * * * * * **
565 ATGGTTTTTGGACGAACTTTCGTACTTG-CGGAACATTTAATAGCTCTTTTGTATCTTAAGTTCC
129 TTGGTTCTTGGACGAACTTTCGAACTTGTC-AAACATTTAATAGTTCTTTTATAACTTTGGTTCC
* *
629 TGAGAGTACTCAAGACGATCCAT
193 TGAAAGTATTCAAGACGATCCAT
* * ** * *
652 TCCTTTGACCAATTTTTTGAACTTTCCATGCTCG-GGAAT-CTTATCATTCAGTCTAAAAACTTT
1 TCCTTTGACCAATTTTTTGAACATTCCATGCTCGAGAAATGC--ATCATTTGGTCTAAATAGTTT
* * * *
715 GTCATTATGTAAACAACTTTTAGTCTTCGAATTAAAAACCTATTTACGTGAGAATTGTTTCTCT-
64 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC
* * * * * **
779 TGTGGTTCTAGGACGAACTTACGAACTAGTCGAACTTTTACGAGTTCTTTTATAACTTTGGTTCC
129 T-TGGTTCTTGGACGAACTTTCGAACTTGTCAAACATTTAATAGTTCTTTTATAACTTTGGTTCC
* *
844 TCAAAGTATTCAAGACTATCCAT
193 TGAAAGTATTCAAGACGATCCAT
* *
867 TCCTTTGATCC-ATTTTCTGAACATTCCATGCTCTGA-AAGTCGCATC-TTTCGGTCTAAATAGT
1 TCCTTTGA-CCAATTTTTTGAACATTCCATGCTC-GAGAAAT-GCATCATTT-GGTCTAAATAGT
* * * *
929 TTGTGATTTTGTAAACAAATTTTGGTCTTTAAATTAAAAACTTATTTACGTGAGAATTGTCTCTC
62 TTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTC
* * * * * ** *
994 TCTTGGTTCTCGGACGAACTTACAAACTAGTCAAACTTTTACGAGTTCTTTTACAACTTTGGTTC
127 TCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACATTTAATAGTTCTTTTATAACTTTGGTTC
* * *
1059 CTTAAAGTATTCAGGACTATCCAT
192 CTGAAAGTATTCAAGACGATCCAT
* * * **
1083 TCATTTTAGCC-ACTTTCCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTT
1 TCCTTTGA-CCAATTTTTTGAACATTCCATGCTCGAGAAAT-GCATCATTTGGTCTAAATAGTTT
*
1147 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTAATTTACGTGAGAATTGTTTCTCTC
64 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC
*** * * * * *
1212 CCAGTTCTTGGATGAACTTCCGAACTTTTCAAAAATTCACA-AGTTCTTTTATAACTTTGGTTCC
129 TTGGTTCTTGGACGAACTTTCGAACTTGTCAAACATTTA-ATAGTTCTTTTATAACTTTGGTTCC
* * * *
1276 TGATAGTATTTAAGAAGATGCAT
193 TGAAAGTATTCAAGACGATCCAT
** * * * *
1299 TCCTTCAACCAATTTTTCGAACATTCCATTCTC-AGAAAATTGCATCATTTTGTCAAAATAGTTT
1 TCCTTTGACCAATTTTTTGAACATTCCATGCTCGAG-AAA-TGCATCATTTGGTCTAAATAGTTT
* * * * * * * *
1363 GTCATATGGTAAACAACTTTTGGTGTTTAAATTTAAAATTTATTTGCATGAGAATAT-TTTCTCT
64 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAAT-TGTTTCTCT
* ** * * * *
1427 CTTGGTTCTTGTATTAACTTTCAAACTTTTAAAAAATTTACA-AGTTCTTTTATTATAACTTTGG
128 CTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACATTTA-ATAGTTC--TT-TTATAACTTTGG
* * * *
1491 TTCTTGAGAGCATTAAAGACGATCCAT
189 TTCCTGAAAGTATTCAAGACGATCCAT
* ** * *
1518 TCATTTGTGCAA-TTTTTCAAGCATTCCATGCTCGAGAAATGACATCATTTGGTCTAAATAGGTT
1 TCCTTTGACCAATTTTTTGAA-CATTCCATGCTCGAGAAATG-CATCATTTGGTCTAAATAGTTT
* * *
1582 ATCATTTTCTAAACAATTTTTGG
64 GTCATTTTGTAAACAACTTTTGG
Statistics
Matches: 1139, Mismatches: 211, Indels: 65
0.80 0.15 0.05
Matches are distributed among these distances:
213 4 0.00
214 51 0.04
215 303 0.27
216 610 0.54
217 64 0.06
218 14 0.01
219 91 0.08
220 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (215 bp):
TCCTTTGACCAATTTTTTGAACATTCCATGCTCGAGAAATGCATCATTTGGTCTAAATAGTTTGT
CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT
GGTTCTTGGACGAACTTTCGAACTTGTCAAACATTTAATAGTTCTTTTATAACTTTGGTTCCTGA
AAGTATTCAAGACGATCCAT
Found at i:1323 original size:432 final size:429
Alignment explanation
Indices: 5--1604 Score: 1545
Period size: 431 Copynumber: 3.7 Consensus size: 429
1 CCTA
* * * * * * *
5 TCCTTCGACCAGTTTTTCAAACATTCAATGCCCGAAAAATCGCATTATTTGATCTAAATAGTTTG
1 TCCTTCAACCAATTTTTCGAACATTCCATGCTCG-AAAATCGCATCATTTGGTCTAAATAGTTTG
* ** * * *
70 TCATTTCGTAAACAACTTTTACTCTTTGAATTAAAAACTTATTTACGTGAGAACTG-CTTCCCTC
65 TCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTATTTACGTGAGAATTGTC-TCTCTC
* * * * * * *
134 TTTGTTCTTGG-CTGAACTTTCGAACTTGTCAAGCTTTTATGAGTTCTTTTATAACTTCAATTCC
129 TTGGTTCTTGGAC-GAACTTTCAAACTTGTCAAACATTTACGAGTTCTTTTATAACTTTAGTTCC
* * * * * *
198 TTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCTACGCTTGGGAAATCG
193 TTAAAGTATTCAAGACGATCCATTCATTTGAGCAATTTTCCGAACATTCCATGCTCGAGAAATCG
* * * * * *
263 CAACGTTTGGTCTAAATAGTTTTTCATTTTGTAATCAACTTTTCGTCTTTTAATTAAAAA-TATT
258 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTATT
* * * ** *
327 TACATGACAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTAAACTTGTCAAACTTTTTATCAG
323 TACGTGAGAATTGTTTCTCTCCTGGTTCTTGGACGAACTTCCGAACTTGTCAAA-ATTTTA-CAG
* * * **
392 TTCTTTTATAACTTCGGTTCCTTAAACTATTAAAGGTGATCCAT
386 TTCTTTTATAACTTTGGTTCCTCAAAGTATTAAAGAAGATCCAT
**** *
436 TCCTTTGTGCAATTTTTC-AATCATTCCATGCTCGAGAAAT-GACATCATTTGGTCTAAATAGGT
1 TCCTTCAACCAATTTTTCGAA-CATTCCATGCTCGA-AAATCG-CATCATTTGGTCTAAATAGTT
* * * ** *
499 TATCATTTTCTAAACAATTTTTGGTCTTCGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCT
63 TGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTATTTACGTGAGAATTGTCTCTCT
* * ** * ** * * * *
564 CATGGTTTTTGGACGAACTTTCGTACTTG-CGGAACATTTAATAGCTCTTTTGTATCTTAAGTTC
128 CTTGGTTCTTGGACGAACTTTCAAACTTGTC-AAACATTTACGAGTTCTTTTATAACTTTAGTTC
* * * * * ** * *
628 CTGAGAGTACTCAAGACGATCCATTCCTTTGACCAATTTTTTGAACTTTCCATGCTCG-GGAATC
192 CTTAAAGTATTCAAGACGATCCATTCATTTGAGCAATTTTCCGAACATTCCATGCTCGAGAAATC
** ** * * * * *
692 TTATCATTCAGTCTAAAAACTTTGTCATTATGTAAACAACTTTTAGTCTTCGAATTAAAAACCTA
257 GCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAA-CTA
** * * * * *
757 TTTACGTGAGAATTGTTTCTCTTGTGGTTCTAGGACGAACTTACGAACTAGTCGAACTTTTACGA
321 TTTACGTGAGAATTGTTTCTCTCCTGGTTCTTGGACGAACTTCCGAACTTGTCAAAATTTTAC-A
* **
822 GTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGACTATCCAT
385 GTTCTTTTATAACTTTGGTTCCTCAAAGTATTAAAGAAGATCCAT
* * *
867 TCCTTTGATCC-A-TTTTCTGAACATTCCATGCTCTGAAAGTCGCATC-TTTCGGTCTAAATAGT
1 TCC-TTCAACCAATTTTTC-GAACATTCCATGCTC-GAAAATCGCATCATTT-GGTCTAAATAGT
* *
929 TTGTGATTTTGTAAACAAATTTTGGTCTTTAAATTAAAAACTTATTTACGTGAGAATTGTCTCTC
62 TTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTATTTACGTGAGAATTGTCTCTC
* * * * * *
994 TCTTGGTTCTCGGACGAACTTACAAACTAGTCAAACTTTTACGAGTTCTTTTACAACTTTGGTTC
127 TCTTGGTTCTTGGACGAACTTTCAAACTTGTCAAACATTTACGAGTTCTTTTATAACTTTAGTTC
* * * * *
1059 CTTAAAGTATTCAGGACTATCCATTCATTTTAGCCACTTTCCGAACATTCCATGCTCGAGAAATC
192 CTTAAAGTATTCAAGACGATCCATTCATTTGAGCAATTTTCCGAACATTCCATGCTCGAGAAATC
1124 GCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTAA
257 GCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACT-A
** * * * *
1189 TTTACGTGAGAATTGTTTCTCTCCCAGTTCTTGGATGAACTTCCGAACTTTTCAAAAATTCACAA
321 TTTACGTGAGAATTGTTTCTCTCCTGGTTCTTGGACGAACTTCCGAACTTGTCAAAATTTTAC-A
* * * *
1254 GTTCTTTTATAACTTTGGTTCCTGATAGTATTTAAGAAGATGCAT
385 GTTCTTTTATAACTTTGGTTCCTCAAAGTATTAAAGAAGATCCAT
* * * *
1299 TCCTTCAACCAATTTTTCGAACATTCCATTCTCAGAAAATTGCATCATTTTGTCAAAATAGTTTG
1 TCCTTCAACCAATTTTTCGAACATTCCATGCTC-GAAAATCGCATCATTTGGTCTAAATAGTTTG
* * * * * * * *
1364 TCATATGGTAAACAACTTTTGGTGTTTAAATTTAAAATTTATTTGCATGAGAATAT-TTTCTCTC
65 TCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTATTTACGTGAGAAT-TGTCTCTCTC
* ** * * * * *
1428 TTGGTTCTTGTATTAACTTTCAAACTTTTAAAAAATTTACAAGTTCTTTTATTATAACTTTGGTT
129 TTGGTTCTTGGACGAACTTTCAAACTTGTCAAACATTTACGAGTTC--TT-TTATAACTTTAGTT
* * * * *
1493 -CTTGAGAGCATTAAAGACGATCCATTCATTTGTGCAATTTTTC-AAGCATTCCATGCTCGAGAA
191 CCTT-AAAGTATTCAAGACGATCCATTCATTTGAGCAATTTTCCGAA-CATTCCATGCTCGAGAA
* * * *
1556 AT-GACATCATTTGGTCTAAATAGGTTATCATTTTCTAAACAATTTTTGG
254 ATCG-CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGG
Statistics
Matches: 948, Mismatches: 193, Indels: 52
0.79 0.16 0.04
Matches are distributed among these distances:
430 66 0.07
431 428 0.45
432 335 0.35
433 9 0.01
434 8 0.01
435 102 0.11
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (429 bp):
TCCTTCAACCAATTTTTCGAACATTCCATGCTCGAAAATCGCATCATTTGGTCTAAATAGTTTGT
CATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTATTTACGTGAGAATTGTCTCTCTCTT
GGTTCTTGGACGAACTTTCAAACTTGTCAAACATTTACGAGTTCTTTTATAACTTTAGTTCCTTA
AAGTATTCAAGACGATCCATTCATTTGAGCAATTTTCCGAACATTCCATGCTCGAGAAATCGCAT
CATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTATTTAC
GTGAGAATTGTTTCTCTCCTGGTTCTTGGACGAACTTCCGAACTTGTCAAAATTTTACAGTTCTT
TTATAACTTTGGTTCCTCAAAGTATTAAAGAAGATCCAT
Done.