Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007739.1 Kokia drynarioides strain JFW-HI SEQ_122372, 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, 846
Length: 1410
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Found at i:438 original size:216 final size:216
Alignment explanation
Indices: 1--1257 Score: 1004
Period size: 216 Copynumber: 5.9 Consensus size: 216
* *
1 CATCATTTGGTCTAAATAGTTT-ACGATTTTGTAAACAAGTTTTGGTCTTTGAA--ATAAA---A
1 CATCATTTGGTCTAAATAGTTTGTC-ATTTTGTAAACAAATTTTGGTCTTTGAATTATAAACTTA
60 ACTTACATGAGAATTGTTTCTCTCTTGGTTC-TGCACGAACTT-CGAAAC-ATGTCAAACTTTTA
65 A-TTACATGAGAATTGTTTCTCTCTTGGTTCTTGCACGAACTTCCG-AACTA-GTCAAACTTTTA
* * * *
122 CGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATCCAAG-CTGATCCATTCTTCGAAGCAA-TAT
127 CGAGTTCTTTTATAACTTCGATTCCTTAAAATATTCAAGAC-GATCCATTCTTCG-AGCAATTTT
** **
185 TCTGAACATACCATATTC-AGGAAATCG
190 TCTGAACATTTCATGCTCGA-GAAATCG
* * * * * *
212 CATAATTTGGTCTAAATATTTTGTTATTTGGTAAACAAAATTTGGCCTTTGAATTATAAACTTAA
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAATTTTGGTCTTTGAATTATAAACTTAA
* * * * * *
277 TTACGTTAGAATTGTTTCTCTCTTGGTTCTTGTACGAGCTCCCGAACTAGTAAAACTTTTACGAG
66 TTACATGAGAATTGTTTCTCTCTTGGTTCTTGCACGAACTTCCGAACTAGTCAAACTTTTACGAG
* * * * * *
342 TTCCTTCACAACTTCTATTCCTTAAAATATTCAAGACAATCCATTCCTTTGAGCAATTTTTC-GA
131 TTCTTTTATAACTTCGATTCCTTAAAATATTCAAGACGATCCATT-CTTCGAGCAATTTTTCTGA
**
406 ACATTTCATGCTCGAGAAATTT
195 ACATTTCATGCTCGAGAAATCG
** * * * * *
428 CATCATTTGGTCTAAATAGTTTACCATTTTGTAAATAAGTTTTGGTCTTTGAAATAGAAACTTAC
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAATTTTGGTCTTTGAATTATAAACTTAA
* * ** *
493 TTACGTCAGAATTGTTTCTCTCTTGGTTC-TGCACGAACTTCAAAAC-ATGTCAAACTTTTACAA
66 TTACATGAGAATTGTTTCTCTCTTGGTTCTTGCACGAACTTCCGAACTA-GTCAAACTTTTACGA
* * *
556 GTTCTTTTATAACCTT-GATT--TTGAAAAGTATTGAAGACAATCCATTCCTTCGAG-AAATTTT
130 GTTCTTTTATAA-CTTCGATTCCTT-AAAA-TATTCAAGACGATCCATT-CTTCGAGCAATTTTT
**
617 CTGAACATACCATGCTCTG-GAAATCG
191 CTGAACATTTCATGCTC-GAGAAATCG
* * * ** * *
643 CATCATTTTGTTTAAATAGTTTGTCATTTTGT-AACAAGTTTTAAT-TTTCAATTAAAAACTT-A
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAATTTTGGTCTTTGAATTATAAACTTAA
* * * * * * * * *
705 TTCACATGAGAATTGTTTCTCTCTTGATTCTTAG-ATGTACTTCTGCATTTGTGAAACTTTTACA
66 TT-ACATGAGAATTGTTTCTCTCTTGGTTCTT-GCACGAACTTCCGAACTAGTCAAACTTTTACG
* * * * * *
769 AGATGTTTTAAAACTTCTG-TTCCTTAAAGTTTTCAA-AGCGATCCATTCCTTCGAGAAATTTTT
129 AGTTCTTTTATAACTTC-GATTCCTTAAAATATTCAAGA-CGATCCATT-CTTCGAGCAATTTTT
* * * *
832 C-AAAC-TTTCCTTACTCTG-TAAATCG
191 CTGAACATTT-CATGCTC-GAGAAATCG
* * * * * * * *
857 CATCGTTTGGTTTAAATAGTTTCTCAGTTTGTAAACAAGTTTTAGTCTTTGAATTACAAACTTAT
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAATTTTGGTCTTTGAATTATAAACTTAA
* * * * * * * * *
922 TTACCTAAGAATTGTCTCTCTCTTGGTTCATGGATGAACTTCCGCACTTGTCAAACTTTTATGAG
66 TTACATGAGAATTGTTTCTCTCTTGGTTCTTGCACGAACTTCCGAACTAGTCAAACTTTTACGAG
** ** ** * * * * * * *
987 TTCTTCGACGACTTCGGGTACTTAAAATTTTTAGGACGATCCATTCTTTCGA-AAAATTTTCAGA
131 TTCTTTTATAACTTCGATTCCTTAAAATATTCAAGACGATCCATTC-TTCGAGCAATTTTTCTGA
*
1051 ACATTTGATGCTCGAGAAATCG
195 ACATTTCATGCTCGAGAAATCG
* * *
1073 CATCATTTGGTCTAAA-ATTTTGTCATTTTTTAAA-AAACTTTTGGTTTTTGAATTATAAACTTA
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAA-TTTTGGTCTTTGAATTATAAACTTA
* * * * *
1136 TTTAC-TGATAA-T-TTT-TCTCTTAGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGA
65 ATTACATGAGAATTGTTTCTCTCTTGGTTCTTGCACGAACTTCCGAACTAGTCAAACTTTTACGA
* *
1197 GTTCTTTTATAGCTTCGATTCCTTAAAGTATTCAAG-CTGATCCATTCTTTCGAGCAATTTT
130 GTTCTTTTATAACTTCGATTCCTTAAAATATTCAAGAC-GATCCATTC-TTCGAGCAATTTT
1258 AAAACTTCGG
Statistics
Matches: 837, Mismatches: 166, Indels: 85
0.77 0.15 0.08
Matches are distributed among these distances:
210 1 0.00
211 124 0.15
212 9 0.01
213 50 0.06
214 127 0.15
215 211 0.25
216 296 0.35
217 19 0.02
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (216 bp):
CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAATTTTGGTCTTTGAATTATAAACTTAA
TTACATGAGAATTGTTTCTCTCTTGGTTCTTGCACGAACTTCCGAACTAGTCAAACTTTTACGAG
TTCTTTTATAACTTCGATTCCTTAAAATATTCAAGACGATCCATTCTTCGAGCAATTTTTCTGAA
CATTTCATGCTCGAGAAATCG
Found at i:920 original size:429 final size:429
Alignment explanation
Indices: 1--991 Score: 1078
Period size: 429 Copynumber: 2.3 Consensus size: 429
*
1 CATCATTTGGTCTAAATAGTTTACGATTTTGTAAACAAGTTTTGGTCTTTGAAATAAAA---ACT
1 CATCATTTGGTCTAAATAGTTTACCATTTTGTAAACAAGTTTTGGTCTTTGAAATAAAACTTACT
* *
63 TACATGAGAATTGTTTCTCTCTTGGTTCTGCACGAACTTCGAAACATGTCAAACTTTTACGAGTT
66 TACATAAGAATTGTTTCTCTCTTGGTTCTGCACGAACTTCAAAACATGTCAAACTTTTACGAGTT
* * *
128 CTTTTATAACTTCGGTTCCTTAAAGTATCCAAGCTGATCCATTCTTCGAAGCAATATTCTGAACA
131 CTTTTATAACTTCGATT-CTTAAAGTATCCAAGCTAATCCATTCTTCGAAGAAATATTCTGAACA
* * * **
193 TACCATATTCAGGAAATCGCATAATTTGGTCTAAATATTTTGTTATTTGGTAAACAAAATTTGGC
195 TACCATACTCAGGAAATCGCATAATTTGGTCTAAATAGTTTGTCATTTGGTAAACAAAATTTGAA
* * * * *
258 CTTTGAATTATAAACTTAATTACGTTAGAATTGTTTCTCTCTTGGTTCTTGTACGAGCTCCCGAA
260 CTTTCAATTAAAAACTTAATTACATGAGAATTGTTTCTCTCTTGATTCTTGTACGAGCTCCCGAA
* * *
323 CTAGTAAAACTTTTACGAGTTCCTTCACAACTTCTATTCCTTAAAATATTCAAGACAATCCATTC
325 CTAGTAAAACTTTTACAAGATCCTTCAAAACTTCTATTCCTTAAAATATTCAAGACAATCCATTC
* * * * **
388 CTTTGAGCAATTTTTCGAACATTTCATGCTCGAGAAATTT
390 CTTCGAGAAATTTTTCAAACATTTCATACTCGAGAAATCG
*
428 CATCATTTGGTCTAAATAGTTTACCATTTTGTAAATAAGTTTTGGTCTTTGAAATAGAAACTTAC
1 CATCATTTGGTCTAAATAGTTTACCATTTTGTAAACAAGTTTTGGTCTTTGAAATA-AAACTTAC
* * *
493 TTACGTCAGAATTGTTTCTCTCTTGGTTCTGCACGAACTTCAAAACATGTCAAACTTTTACAAGT
65 TTACATAAGAATTGTTTCTCTCTTGGTTCTGCACGAACTTCAAAACATGTCAAACTTTTACGAGT
** *
558 TCTTTTATAACCTT-GATT-TTGAAAAGTATTGAAGAC-AATCCATTCCTTCG-AGAAATTTTCT
130 TCTTTTATAA-CTTCGATTCTT--AAAGTATCCAAG-CTAATCCATT-CTTCGAAGAAATATTCT
* * * * * * *
619 GAACATACCATGCTCTGGAAATCGCATCATTTTGTTTAAATAGTTTGTCATTTTGT-AAC-AAGT
190 GAACATACCATACTCAGGAAATCGCATAATTTGGTCTAAATAGTTTGTCATTTGGTAAACAAAAT
* * *
682 TTTAATTTTCAATTAAAAACTT-ATTCACATGAGAATTGTTTCTCTCTTGATTCTTAG-ATGTA-
255 TTGAACTTTCAATTAAAAACTTAATT-ACATGAGAATTGTTTCTCTCTTGATTCTT-GTACG-AG
* * * * * * ** * * * *
744 CTTCTGCATTTGTGAAACTTTTACAAGATGTTTTAAAACTTCTGTTCCTTAAAGTTTTCAA-AGC
317 CTCCCGAACTAGTAAAACTTTTACAAGATCCTTCAAAACTTCTATTCCTTAAAATATTCAAGA-C
* * *
808 GATCCATTCCTTCGAGAAATTTTTCAAAC-TTTCCTTACTCTG-TAAATCG
381 AATCCATTCCTTCGAGAAATTTTTCAAACATTT-CATACTC-GAGAAATCG
* * * * *
857 CATCGTTTGGTTTAAATAGTTT-CTCAGTTTGTAAACAAGTTTTAGTCTTTGAATTACAAACTTA
1 CATCATTTGGTCTAAATAGTTTAC-CATTTTGTAAACAAGTTTTGGTCTTTGAAATA-AAACTTA
* * * * * *** * *
921 TTTACCTAAGAATTGTCTCTCTCTTGGTTCATGGATGAACTTCCGCACTTGTCAAACTTTTATGA
64 CTTACATAAGAATTGTTTCTCTCTTGGTTC-TGCACGAACTTCAAAACATGTCAAACTTTTACGA
986 GTTCTT
128 GTTCTT
992 CGACGACTTC
Statistics
Matches: 472, Mismatches: 75, Indels: 31
0.82 0.13 0.05
Matches are distributed among these distances:
427 54 0.11
428 11 0.02
429 211 0.45
430 38 0.08
431 149 0.32
432 9 0.02
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (429 bp):
CATCATTTGGTCTAAATAGTTTACCATTTTGTAAACAAGTTTTGGTCTTTGAAATAAAACTTACT
TACATAAGAATTGTTTCTCTCTTGGTTCTGCACGAACTTCAAAACATGTCAAACTTTTACGAGTT
CTTTTATAACTTCGATTCTTAAAGTATCCAAGCTAATCCATTCTTCGAAGAAATATTCTGAACAT
ACCATACTCAGGAAATCGCATAATTTGGTCTAAATAGTTTGTCATTTGGTAAACAAAATTTGAAC
TTTCAATTAAAAACTTAATTACATGAGAATTGTTTCTCTCTTGATTCTTGTACGAGCTCCCGAAC
TAGTAAAACTTTTACAAGATCCTTCAAAACTTCTATTCCTTAAAATATTCAAGACAATCCATTCC
TTCGAGAAATTTTTCAAACATTTCATACTCGAGAAATCG
Found at i:1097 original size:429 final size:427
Alignment explanation
Indices: 1--1257 Score: 1052
Period size: 429 Copynumber: 2.9 Consensus size: 427
* * *
1 CATCATTTGGTCTAAATAGTTTACGATTTTGTAAACAAGTTTTGGTCTTTGAAATA-AAA---AC
1 CATCATTTGGTCTAAATAGTTTACCAGTTTGTAAACAAGTTTTAGTCTTTGAAATACAAACTTAC
* * * * *
62 TTACATGAGAATTGTTTCTCTCTTGGTTCTGCACGAACTTCGAAACATGTCAAACTTTTACGAGT
66 TTACCTAAGAATTGTCTCTCTCTTGGTTCTGCACGAACTTCAAAACATGTCAAACTTTTACAAGT
** * * ** * * *
127 TCTTTTATAA-CTTCGGTTCCTT--AAAGTATCCAAG-CTGATCCATT-CTTCGAAGCAATATTC
131 TCTTCGACAACCTT--GAT-CTTGAAAAGTATTGAAGAC-AATCCATTCCTTCGAA-AAATTTTC
* ** * * * * *
187 TGAACATACCATATTCAGGAAATCGCATAATTTGGTCTAAATATTTTGTTATTTGGTAAACAAA-
191 AGAACATACCATGCTCTGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-AAAC
* *** * * * *
251 ATTTGGCCTTTGAATTATAAACTTAATT-ACGTTAGAATTGTTTCTCTCTTGGTTCTT-GTACGA
255 TTTTGAATTTTCAATTAAAAACTT-ATTCAC-TGAGAA-T-TTT-TCTCTTAGTTCTTAG-ACGA
* * * * * * * * * * *
314 GCTCCCGAACTAGTAAAACTTTTACGAGTTCCTTCACAACTTCTATTCCTTAAAATATTCAAGAC
314 ACTTCCGAACTTGTCAAACTTTTACAAGATCTTTTAAAACTTCGATTCCTTAAAGTATTCAAG-C
* * * * * * * **
379 -AATCCATTCCTTTGAGCAATTTTTCGAACATTT-CATGCTC-GAGAAATTT
378 TGATCCATTCCTTCGAGAAATTTTTCAAAC-TTTCCTTACTCTG-TAAATCG
* * * *
428 CATCATTTGGTCTAAATAGTTTACCATTTTGTAAATAAGTTTTGGTCTTTGAAATAGAAACTTAC
1 CATCATTTGGTCTAAATAGTTTACCAGTTTGTAAACAAGTTTTAGTCTTTGAAATACAAACTTAC
* * *
493 TTACGTCAGAATTGTTTCTCTCTTGGTTCTGCACGAACTTCAAAACATGTCAAACTTTTACAAGT
66 TTACCTAAGAATTGTCTCTCTCTTGGTTCTGCACGAACTTCAAAACATGTCAAACTTTTACAAGT
** * * * *
558 TCTTTTATAACCTTGATTTTGAAAAGTATTGAAGACAATCCATTCCTTCGAGAAATTTTCTGAAC
131 TCTTCGACAACCTTGATCTTGAAAAGTATTGAAGACAATCCATTCCTTCGAAAAATTTTCAGAAC
* * * *
623 ATACCATGCTCTGGAAATCGCATCATTTTGTTTAAATAGTTTGTCATTTTGT-AACAAGTTTT-A
196 ATACCATGCTCTGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAACTTTTGA
* * * * *
686 ATTTTCAATTAAAAACTTATTCACATGAGAATTGTTTCTCTCTTGATTCTTAGATGTACTTCTGC
261 ATTTTCAATTAAAAACTTATTCAC-TGAGAATT-TTTCTCT-TAG-TTCTTAGACGAACTTCCGA
* * * *
751 ATTTGTGAAACTTTTACAAGATGTTTTAAAACTTCTG-TTCCTTAAAGTTTTCAAAGC-GATCCA
322 ACTTGTCAAACTTTTACAAGATCTTTTAAAACTTC-GATTCCTTAAAGTATTC-AAGCTGATCCA
814 TTCCTTCGAGAAATTTTTCAAACTTTCCTTACTCTGTAAATCG
385 TTCCTTCGAGAAATTTTTCAAACTTTCCTTACTCTGTAAATCG
* * *
857 CATCGTTTGGTTTAAATAGTTT-CTCAGTTTGTAAACAAGTTTTAGTCTTTGAATTACAAACTTA
1 CATCATTTGGTCTAAATAGTTTAC-CAGTTTGTAAACAAGTTTTAGTCTTTGAAATACAAACTTA
* * * *** * **
921 TTTACCTAAGAATTGTCTCTCTCTTGGTTCATGGATGAACTTCCGCACTTGTCAAACTTTTATGA
65 CTTACCTAAGAATTGTCTCTCTCTTGGTTC-TGCACGAACTTCAAAACATGTCAAACTTTTACAA
* * * * * * *
986 GTTCTTCGACGA-CTTCGGGTACTT-AAAA-TTTTTAGGACGATCCATTCTTTCGAAAAATTTTC
129 GTTCTTCGACAACCTT--GAT-CTTGAAAAGTATTGAAGACAATCCATTCCTTCGAAAAATTTTC
*** * *
1048 AGAACATTTGATGCTC-GAGAAATCGCATCATTTGGTCTAAA-ATTTTGTCATTTTTTAAAAAAC
191 AGAACATACCATGCTCTG-GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAC
** * * * * *
1111 TTTTGGTTTTTGAATTATAAACTTATTTACTGATAATTTTTCTCTTAGTTCTTGGACGAACTTCC
255 TTTTGAATTTTCAATTAAAAACTTATTCACTGAGAATTTTTCTCTTAGTTCTTAGACGAACTTCC
* * * *
1176 GAACTTGTCAAACTTTTACGAGTTCTTTTATAGCTTCGATTCCTTAAAGTATTCAAGCTGATCCA
320 GAACTTGTCAAACTTTTACAAGATCTTTTAAAACTTCGATTCCTTAAAGTATTCAAGCTGATCCA
* *
1241 TTCTTTCGAGCAATTTT
385 TTCCTTCGAGAAATTTT
1258 AAAACTTCGG
Statistics
Matches: 678, Mismatches: 123, Indels: 58
0.79 0.14 0.07
Matches are distributed among these distances:
426 5 0.01
427 137 0.20
428 17 0.03
429 215 0.32
430 122 0.18
431 170 0.25
432 12 0.02
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (427 bp):
CATCATTTGGTCTAAATAGTTTACCAGTTTGTAAACAAGTTTTAGTCTTTGAAATACAAACTTAC
TTACCTAAGAATTGTCTCTCTCTTGGTTCTGCACGAACTTCAAAACATGTCAAACTTTTACAAGT
TCTTCGACAACCTTGATCTTGAAAAGTATTGAAGACAATCCATTCCTTCGAAAAATTTTCAGAAC
ATACCATGCTCTGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAACTTTTGA
ATTTTCAATTAAAAACTTATTCACTGAGAATTTTTCTCTTAGTTCTTAGACGAACTTCCGAACTT
GTCAAACTTTTACAAGATCTTTTAAAACTTCGATTCCTTAAAGTATTCAAGCTGATCCATTCCTT
CGAGAAATTTTTCAAACTTTCCTTACTCTGTAAATCG
Found at i:1309 original size:53 final size:53
Alignment explanation
Indices: 1209--1310 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
1199 TCTTTTATAG
* * *
1209 CTTCGATTCCTTAAAGTATTCAAGCTGATCCATTCTTTCGAGCAATTTTAAAA
1 CTTCGATTCCTTAAAGTATTCAAGCTGATCCACTCCTTCGAGAAATTTTAAAA
* * *
1262 CTTCGGTTCCTTAAAGTTTTCAAGAC-GATCCACTCCTTCGGGAAATTTT
1 CTTCGATTCCTTAAAGTATTCAAG-CTGATCCACTCCTTCGAGAAATTTT
1311 TCGAACATTC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 41 0.98
54 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (53 bp):
CTTCGATTCCTTAAAGTATTCAAGCTGATCCACTCCTTCGAGAAATTTTAAAA
Done.