Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009530.1 Kokia drynarioides strain JFW-HI SEQ_124242, 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: 1911
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.38
Warning! 117 characters in sequence are not A, C, G, or T
Found at i:1288 original size:432 final size:427
Alignment explanation
Indices: 1--1666 Score: 1585
Period size: 432 Copynumber: 3.9 Consensus size: 427
*
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAATTTAT
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTAT
*** * ** *
66 TTACGTGAGAATTGTTTCTCTCCCAGTTCTTGGATGAACTTCCGAACTTTTCAAAAATTTACAAG
66 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAAC-TAGCAAACATTTA-AAG
* * * *
131 TTCTTTTATAACTTTGGTTCCTATTAGTATTTAAA-AAGATGCATTCCTTCA-ACCAATTTTTCG
129 TTCTTTTATAACTTTAGTTCCTA-GAGTA-TTAAAGACGATCCATTCCTT-AGACCAATTTTTCG
* * * *
194 AACATTCCATTCTCGAAAAAATTGCATCATTTGGTC-AAAATAGTTTGTCA-TATGGTAAACAAC
191 AACATTCCATGCTCG-AGAAATCGCATCATTCGGTCTAAAA-AGTTTGTCATTAT-GTAAACAAC
** * * * * **
257 TTTTGGGGTTTGAATTTAAAATTTATTTGCTTGAGAATAT-TTTCTCTCTTGGTTCTTGGATTAA
253 TTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAAT-TGTTTCTCTCTTGGTTCTTGGACGAA
* * * * *
321 CTTTCAAACTTTTCAAAAATTTACAAGTTCTTTTATTATAACTTTGGTTCTTGAGAGTATTAAAG
317 C-TTCAAACTTGTCAAAAATTTACAAGTTC--TT-TTATAACTTTGGTTCCTCAAAGTATTCAAG
* *
386 ACGATCCATTCCTTTGTGCAATTTTTCAAACATTCCATGCTCGGGAAATCG
378 ACTATCCATTCCTTTGTGCAATTTTT-AAACATTCCATGCTCGAGAAATCG
* *
437 CATCAGTTGGTCTAAATAGTTTGTCATTTTTTAAA-AACCTTTTGGTCTTTGAATTAAAAACTTA
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAA-CTTTTGGTCTTTGAATTAAAAACTTA
* * * * * **
501 TTTACATGAGGATTGTTTCTCTCTTGGTTCTTGGACGAACTTCAGAACTTGTCAAATATTTACCC
65 TTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTAG-CAAACATTTA-AA
* * ** * * * *
566 GTTCTTTTATAACTTCTA-TTTCTGAGAGCATTAAAGTTGACCCATTCGTTCGACTAAGTTTTT-
128 GTTCTTTTATAACTT-TAGTTCCT-AGAGTATTAAAGACGATCCATTCCTTAGACCAA-TTTTTC
* * * ** * * * *
629 GAGCATTCCAGGCTCGAGAAATCACATCATTCATTCT-AAATGTTTTTTTAATTTTGTAAACAAC
190 GAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAAAAG--TTTGTCATTATGTAAACAAC
*** *
693 TTTTGGTCTTTGAATTGGGAACTTATTTACGTGACAATTGTTTCTCTCTTGGTTCTTGGACGAAC
253 TTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAAC
** * * * * *
758 TTCTAAACTTGTCAAACTTTTTATC-AGTTCCTTTATAACTTCGGTTCCTTAAACTATTCAAG-G
318 TTC-AAACTTGTCAAA-AATTTA-CAAGTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGAC
* *
821 TGATCCATTCCTTTGTGCAATTTTTCAAGCATTCCATGC-CTGAGAAATGG
380 T-ATCCATTCCTTTGTGCAATTTTT-AAACATTCCATGCTC-GAGAAATCG
* * * * *
871 CATCATTTGGTCTAAATAGGTTATCATTTTCTAAACAATTTTTGGCCTTTGAATTAAAAACTTAT
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTAT
* * *
936 TTACGTGAGAATTGTTTCTCTCATGGTTTTTGGACGAACTTCCGTACTAGCAGAACATTTAATAG
66 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTAGCA-AACATTTAA-AG
* * * *
1001 CTCTTTTGTAACTTAAGTTCCTGAGAGTATTAAAGACGATTCATTCCTTAGACCAATTTTTCGAA
129 TTCTTTTATAACTTTAGTTCCT-AGAGTATTAAAGACGATCCATTCCTTAGACCAATTTTTCGAA
* * * * *
1066 CTTTCCATGCTCG-GGAATCGTATCATTCGGTCTAAAAACTTTGTCATTATGTAAACAACTTTTA
193 CATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAAAAGTTTGTCATTATGTAAACAACTTTTG
* * *
1130 GTCTTCGAATTAAAAACCTATTTACGTGAGAATTGTTTCTCT-TGTGGTTCTAGGACGAACTTAC
258 GTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT-TGGTTCTTGGACGAACTT-C
* * ** * *
1194 GAACTGGTCAAACTTTTTACGAGTTCTTTTATAACTTTGGTTCCTCAAAGTACTCAAGACTATCC
321 AAACTTGTCAAA-AATTTACAAGTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGACTATCC
* * * * * *
1259 ATTCATTTGAGCCATTTTCTGAACATTCCACGCTCCAGAAATCG
385 ATTCCTTTGTGCAATTTT-TAAACATTCCATGCTCGAGAAATCG
* * * * * * * *
1303 CACCTTTTGGTTTAAATAGTTTGTGATTTTGTAAACAAATTTTGGTCTTTAAAATAAAAACTTAA
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTAT
* * * * * *
1368 TTACGTGAGAATTGTTTCTCTCTTGGTTCTCGGACGAACTTCGGGACTATTCAAACTTTTACGAG
66 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTA-GCAAACATTTA-AAG
* * * * * *
1433 TTCTTTTACAACTTT-GATTCCATAAAGTATTCAAGACTATCCATTCATTTGAGCC-ATTTTTCG
129 TTCTTTTATAACTTTAG-TTCC-TAGAGTATTAAAGACGATCCATTCCTTAGA-CCAATTTTTCG
* * *
1496 AACACTCCATGCTCGAGAAATCGCATCACTT-GGTCTAAATAGTTTGTCATTTTGTAAACAACTC
191 AACATTCCATGCTCGAGAAATCGCATCA-TTCGGTCTAAAAAGTTTGTCATTATGTAAACAACT-
* * *** *
1560 TTT-GTCTTTTAA-TAAAAA---ACTTACGTGAGAATTGTTTCTCTCCCAGTTCTTGGATGAACT
254 TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACT
* * *
1620 TCCGAACTTTTCAAAAATTTACAAGTTCTTTCATAACTTTGGTTCCT
319 T-CAAACTTGTCAAAAATTTACAAGTTCTTTTATAACTTTGGTTCCT
1667 AATATTATTT
Statistics
Matches: 1011, Mismatches: 181, Indels: 84
0.79 0.14 0.07
Matches are distributed among these distances:
428 28 0.03
429 47 0.05
431 3 0.00
432 330 0.33
433 79 0.08
434 238 0.24
435 33 0.03
436 234 0.23
437 18 0.02
438 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (427 bp):
CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTAT
TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTAGCAAACATTTAAAGTT
CTTTTATAACTTTAGTTCCTAGAGTATTAAAGACGATCCATTCCTTAGACCAATTTTTCGAACAT
TCCATGCTCGAGAAATCGCATCATTCGGTCTAAAAAGTTTGTCATTATGTAAACAACTTTTGGTC
TTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCAAACT
TGTCAAAAATTTACAAGTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGACTATCCATTCCT
TTGTGCAATTTTTAAACATTCCATGCTCGAGAAATCG
Found at i:1582 original size:216 final size:216
Alignment explanation
Indices: 1--1666 Score: 1575
Period size: 217 Copynumber: 7.7 Consensus size: 216
*
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAATTTAT
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTAT
*** * *
66 TTACGTGAGAATTGTTTCTCTCCCAGTTCTTGGATGAACTTCCGAACTTTTCAAAAATTTACAAG
66 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTTTCAAACATTTACAAG
* ** * * *
131 TTCTTTTATAACTTTGGTTCCT-ATTAGTATTTAAA-AAGATGCATTCC-TTCAACCAATTTTTC
131 TTCTTTTATAACTTTGGTTCCTGA-AAGTA-TTAAAGACTATCCATTCCTTTGAGCC-ATTTTTC
* * *
193 GAACATTCCATTCTCGAAAAAATTG
193 GAACATTCCATGCTCG-AGAAATCG
* * * ** * *
218 CATCATTTGGTCAAAATAGTTTGTCATATGGTAAACAACTTTTGGGGTTTGAATTTAAAATTTAT
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTAT
* * ** * * *
283 TTGCTTGAGAATAT-TTTCTCTCTTGGTTCTTGGATTAACTTTCAAACTTTTCAAAAATTTACAA
66 TTACGTGAGAAT-TGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTTTCAAACATTTACAA
* * * * *
347 GTTCTTTTATTATAACTTTGGTTCTTGAGAGTATTAAAGACGATCCATTCCTTTGTGCAATTTTT
130 GTTC--TT-TTATAACTTTGGTTCCTGAAAGTATTAAAGACTATCCATTCCTTTGAGCCATTTTT
* *
412 CAAACATTCCATGCTCGGGAAATCG
192 CGAACATTCCATGCTCGAGAAATCG
* *
437 CATCAGTTGGTCTAAATAGTTTGTCATTTTTTAAA-AACCTTTTGGTCTTTGAATTAAAAACTTA
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAA-CTTTTGGTCTTTGAATTAAAAACTTA
* * * * * **
501 TTTACATGAGGATTGTTTCTCTCTTGGTTCTTGGACGAACTTCAGAACTTGTCAAATATTTACCC
65 TTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTTTCAAACATTTACAA
* * * * * * * * *
566 GTTCTTTTATAACTTCT-ATTTCTGAGAGCATTAAAG-TTGACCCATTCGTTCGA-CTAAGTTTT
130 GTTCTTTTATAACTT-TGGTTCCTGAAAGTATTAAAGACT-ATCCATTCCTTTGAGC-CA-TTTT
* * *
628 T-GAGCATTCCAGGCTCGAGAAATCA
191 TCGAACATTCCATGCTCGAGAAATCG
*** * * ***
653 CATCATTCATTCTAAAT-GTTTTTTTAATTTTGTAAACAACTTTTGGTCTTTGAATTGGGAACTT
1 CATCATTTGGTCTAAATAG--TTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTT
* ** * *
717 ATTTACGTGACAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTAAACTTGTCAAACTTTTTAT
64 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTTTCAAAC-ATTTA-
* * * * * * * *
782 C-AGTTCCTTTATAACTTCGGTTCCTTAAACTATTCAAG-GTGATCCATTCCTTTGTGCAATTTT
127 CAAGTTCTTTTATAACTTTGGTTCCTGAAAGTATTAAAGACT-ATCCATTCCTTTGAGCCATTTT
*
845 TC-AAGCATTCCATGC-CTGAGAAATGG
191 TCGAA-CATTCCATGCTC-GAGAAATCG
* * * * *
871 CATCATTTGGTCTAAATAGGTTATCATTTTCTAAACAATTTTTGGCCTTTGAATTAAAAACTTAT
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTAT
* * * **
936 TTACGTGAGAATTGTTTCTCTCATGGTTTTTGGACGAACTTCCGTAC-TAGCAGAACATTTA-AT
66 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTTTCA-AACATTTACA-
* * ** * * * *
999 AGCTCTTTTGTAACTTAAGTTCCTGAGAGTATTAAAGACGATTCATTCCTTAGA-CCAATTTTTC
129 AGTTCTTTTATAACTTTGGTTCCTGAAAGTATTAAAGACTATCCATTCCTTTGAGCC-ATTTTTC
* *
1063 GAACTTTCCATGCTCG-GGAATCG
193 GAACATTCCATGCTCGAGAAATCG
* * * * * * * *
1086 TATCATTCGGTCTAAAAACTTTGTCATTATGTAAACAACTTTTAGTCTTCGAATTAAAAACCTAT
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTAT
* * ** * *
1151 TTACGTGAGAATTGTTTCTCT-TGTGGTTCTAGGACGAACTTACGAACTGGTCAAACTTTTTACG
66 TTACGTGAGAATTGTTTCTCTCT-TGGTTCTTGGACGAACTTCCGAACTTTTCAAAC-ATTTACA
* * * *
1215 AGTTCTTTTATAACTTTGGTTCCTCAAAGTACTCAAGACTATCCATTCATTTGAGCCA-TTTTCT
129 AGTTCTTTTATAACTTTGGTTCCTGAAAGTATTAAAGACTATCCATTCCTTTGAGCCATTTTTC-
* *
1279 GAACATTCCACGCTCCAGAAATCG
193 GAACATTCCATGCTCGAGAAATCG
* * * * * * * *
1303 CACCTTTTGGTTTAAATAGTTTGTGATTTTGTAAACAAATTTTGGTCTTTAAAATAAAAACTTAA
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTAT
* * * * * *
1368 TTACGTGAGAATTGTTTCTCTCTTGGTTCTCGGACGAACTTCGGGACTATTCAAACTTTTACGAG
66 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTTTCAAACATTTACAAG
* * * *
1433 TTCTTTTACAACTTTGATTCCAT-AAAGTATTCAAGACTATCCATTCATTTGAGCCATTTTTCGA
131 TTCTTTTATAACTTTGGTTCC-TGAAAGTATTAAAGACTATCCATTCCTTTGAGCCATTTTTCGA
*
1497 ACACTCCATGCTCGAGAAATCG
195 ACATTCCATGCTCGAGAAATCG
* *
1519 CATCACTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTCTTT-GTCTTTTAA-TAAAAA---A
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACT-TTTGGTCTTTGAATTAAAAACTTA
* *** * *
1579 CTTACGTGAGAATTGTTTCTCTCCCAGTTCTTGGATGAACTTCCGAACTTTTCAAAAATTTACAA
65 TTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTTTCAAACATTTACAA
*
1644 GTTCTTTCATAACTTTGGTTCCT
130 GTTCTTTTATAACTTTGGTTCCT
1667 AATATTATTT
Statistics
Matches: 1180, Mismatches: 227, Indels: 90
0.79 0.15 0.06
Matches are distributed among these distances:
211 1 0.00
212 73 0.06
215 115 0.10
216 316 0.27
217 417 0.35
218 81 0.07
219 122 0.10
220 51 0.04
221 4 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (216 bp):
CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTAT
TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTTTCAAACATTTACAAG
TTCTTTTATAACTTTGGTTCCTGAAAGTATTAAAGACTATCCATTCCTTTGAGCCATTTTTCGAA
CATTCCATGCTCGAGAAATCG
Done.