Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006577.1 Kokia drynarioides strain JFW-HI SEQ_121163, 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: 4748
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Found at i:1203 original size:216 final size:216
Alignment explanation
Indices: 788--4498 Score: 3837
Period size: 216 Copynumber: 17.2 Consensus size: 216
778 GCTCGCATCA
** * * * *
788 ACAAGTTCAAAAGTTTGTCCAAGAACCAAGAGAGAAACAATTTTCACATAAAAAAAGTTTTTAAA
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGT-AAAAAAGTTTTTAAT
* * * * **
853 TCAAAGACCAAAAATTGTTTACAAAATGACAAACTTTTTAGACCAACTGATCGTGACTTCCAAAG
65 TCAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGAT-GCGATTTCCTGAG
* ** ** * ** * *
918 CATGAAATGTTCGGAAAATAAGTCGAAGGAATGGATCACCTTAAATACTCTTAGGAAACGAAGTT
129 CATGGAATGTTTAGAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACCGAAGTT
* * *
983 ATAAAATAACTTGTAAATGGTTG
194 ATAAAAGAACTAGTAAATGTTTG
* ** * *
1006 ACAAGTTCGGAAGTTCGTACAAGAACCAAGAGAGTGACAATTCTCATGTAAATAAGTTTTTAATT
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATT
* * * * *
1071 CAAAGGCCAAAAGTTGTTTACAAATTGACAGACTTTTTAGACCAAATTATGCGATTTCCTAAGCA
66 CAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGCA
* * * * * **
1136 TAGAATGTTTAGAAAATTTGTCGAAGGAATAGATCATCTTGAATACTCTTAGGAACAAAAGTTAT
131 TGGAATGTTTAGAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACCGAAGTTAT
* * *
1201 AAAAGAACTCGTAACTGTTAG
196 AAAAGAACTAGTAAATGTTTG
* * * * * *
1222 ACAAGTTCGGAAGTTCATCCACGAACCAAGAGAAAAATAATTCTCATGTAAATAAGTTTTTAATT
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATT
* * * * * * *
1287 TAAAGA-AAAAAGGTTGTTTACAAAAGGACAAACTATTTAAACCAAATGATGCAATTTCC-CAGC
66 CAAAGACCAAAA-GTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGC
* * * * ** * * *
1350 AAGGAATGTTCAAAAAATTGCTCAAACTAATGGATCTTCTTGAATACT-TTAAGGAACGGAAGCT
130 ATGGAATGTTTAGAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTT-AGGAACCGAAGTT
* **
1414 ATAAAAGAACTTGTAAAACTTTG
194 ATAAAAGAACTAGTAAATGTTTG
* * * * * * * * * * ** *
1437 ACTAGGTCGTATGTTCATCCAAGAACCAAGAGAGAAATAATTCTCATGTCAATATGTACTTAGTT
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATT
* * * *
1502 CAGAG-CACAAAAGTTATTTACAAAATTACAAACTTTTTAGACCAAATGATGCGATTTTCCAG-G
66 CAAAGAC-CAAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGA-TTTCCTGAG
* ** * * *
1565 CATGGAAAGTTT-GAAAAATTGGTTGAAGGAATGGATTGCCTTGAATACTCTCAGGAACCGAAGT
129 CATGGAATGTTTAG-AAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACCGAAGT
1629 TATAAAAGAACTAGTAAATGTTTG
193 TATAAAAGAACTAGTAAATGTTTG
* * *
1653 ACGAGTTCGGAAGTTCGTCCAAGAACCAATAGAGAAACAATTGTCACGTAAAAAAGTTTTTAATT
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATT
* * * * * *
1718 CAAAGACCAAAGGTTATATATAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCT-AGCA
66 CAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGCA
* * * * * * * * *
1782 TGGAATGTTCAAAAAATTGCTAAAATGAATGCATCGTCTTTAATACT-TTCATGAATCGAAGTTA
131 TGGAATGTTTAGAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTT-AGGAACCGAAGTTA
* *
1846 TAAAAGAACTCGTAAATGTTTA
195 TAAAAGAACTAGTAAATGTTTG
* * * * **
1868 ACCAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCTCATAAAAAA-AATTTAATT
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATT
* * * * * *
1932 CAAAGACCAAAAAGTTGTTTACAAGATGACAAAC-TATTATACCAAATGATGTGATTTCCCGATC
66 CAAAGACC-AAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGC
* * * *
1996 ATGGAATGTTT-GACAAATTGGTCAAAGGAATGGATCGTCTTGACTACTATCAAGAACCGAAGTT
130 ATGGAATGTTTAGA-AAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACCGAAGTT
*
2060 ATTAAAGAACTAGTAAATGTTTG
194 ATAAAAGAACTAGTAAATGTTTG
* * * * * *
2083 ACAAGTTCAGAACTTCATCAAAGAACCAAGAGAGGAATAATTCTCACGTAAAAAAGTTTTTAATT
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATT
* * * * *
2148 CAAAGACCAAAAGTTATTTACAAAATGACGAACTATTTT-GACCAAATGATGTGATTTCCCGATC
66 CAAAGACCAAAAGTTGTTTACAAAATGACAAACT-TTTTAGACCAAATGATGCGATTTCCTGAGC
* * * * * *
2212 ATGGAAT-CTTCGAAAAATTGGTCAAAGGAATGTATCGTCTTTAATACTCTCAGGAACCAAAGTT
130 ATGGAATGTTTAG-AAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACCGAAGTT
*
2276 ATAAAAGAACTCGTAAATGTTT-
194 ATAAAAGAACTAGTAAATGTTTG
** * * *
2298 ATCAAGTTCTTAAGTTCGTCCAAGAACCAAGAGAGAAAAAATTCTCTCGTAAAAAAGTTTTTAAC
1 A-CAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAAT
* * * * *
2363 TCAAATACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGAGATTTCCTGATC
65 TCAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGC
* * * *
2428 ATGGAATG-TTAGAAAAATTGGTCAAAGGAATGGATCGTCTTGACTACTATCAAGAACCGAAGTT
130 ATGGAATGTTTAG-AAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACCGAAGTT
*
2492 ATAAAAGAACTAGTAAATGATTG
194 ATAAAAGAACTAGTAAATGTTTG
* * * ** *
2515 ACAACTTCAGAAGTTCGTCCAAGAACTAAGAGAGAAGGAATTCTAACGTAAAAAAGTTTTTAATT
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATT
* * * * * *
2580 CAAAGACCAAAAGTTATTTACAAAATGACTAACTATTTT-GATCAAATGAAGCGATTT-CTCAAT
66 CAAAGACCAAAAGTTGTTTACAAAATGACAAACT-TTTTAGACCAAATGATGCGATTTCCT-GAG
* * *
2643 CATGGAATCTTCAGAAAATGGGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACCGAAGTT
129 CATGGAATGTTTAGAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACCGAAGTT
* *
2708 ATAAAAGAACTTGTAAATGTTTA
194 ATAAAAGAACTAGTAAATGTTTG
* * * * *
2731 ACCAGTTTGGAATTTTGTCCAAGAACCAAGAGAGAAACAATTCTCTCGTAAAAAAGTTTTTAATT
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATT
* * * *
2796 CAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCCCGATCA
66 CAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGCA
* * * * * * *
2861 TTGAATG-TTCGAAAAATTGGTAAAAGAAATGGATCATCTTGAATACTATCAGGAACCGAAGTTA
131 TGGAATGTTTAG-AAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACCGAAGTTA
2925 TAAAAGAACTAGTAAATGTTTG
195 TAAAAGAACTAGTAAATGTTTG
* * * *
2947 ACAAGTTCGAAACTTCATCCAAGAACCAAGAGAGAAAGAATTCTCACGTAAAAAAGTTTTTAATT
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATT
* * ** *
3012 CAAAGACCAAAAGTTATTTACAAAATGATAAACTATTTT-GACCAAATGATGTAATTTCCTGATC
66 CAAAGACCAAAAGTTGTTTACAAAATGACAAACT-TTTTAGACCAAATGATGCGATTTCCTGAGC
* * * *
3076 ATGG-A-GTCTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTCTCAGGAACCAAAGT
130 ATGGAATGT-TTAG-AAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACCGAAGT
*
3139 TATAAAAGAACTTGTAGAA-GTTTG
193 TATAAAAGAACTAGTA-AATGTTTG
* * * * * * * * *
3163 ACTAGTTTGTATGTTTGTCCATGAACCAAGAGGGAAACAATTCTCAC-AAAAATAAGTATTTAAT
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAA-AAGTTTTTAAT
** * * * * * * * *
3227 TCAAAGGTCAAGAGTTGTTTACTAAATGACAAACTATTAAGATCAAATGATGCGATTTCTTGGGT
65 TCAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGC
* * * * *
3292 ATGGAAT-TTTTGAAAAATTGGTCGAAGGAAAGGACCGTCTTTAATACTCTTAGGAACCGAAGTT
130 ATGGAATGTTTAG-AAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACCGAAGTT
* *
3356 ATAAAAGAACTCGTAAACGTTTG
194 ATAAAAGAACTAGTAAATGTTTG
* * * * *** * *
3379 ACGAGTTCGAAAGTTTGTCCAATAACCATTTGAGAAACAATTCTCAAGTAAAAAAGTTTTTCATT
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATT
* * * * *
3444 CAAAGATCAAATGTTGTTTACAAAATGACAAACTATTTAGACCAAATGGTGCGATTT-CTCAGCA
66 CAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGCA
** * * * * *
3508 TTCAATG-ATCGAAAAATTGCTCAAAGGAATGAATTGTCTTGAATACT-TTAAGGAACCGAAGTT
131 TGGAATGTTTAG-AAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTT-AGGAACCGAAGTT
*
3571 ATAAAAGAACTTGTAAAAT-TTTG
194 ATAAAAGAACTAGT-AAATGTTTG
* * * * * * * * * *
3594 ACTAGTTTGTATGTTCGTCCAAGAACTAAGAGGGAAGCAATTCTCGCATAAAAAAGTGTTTAATT
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATT
* * * *
3659 CAAAG-CATAAAAGTTTTTTTTACAAAATGACAAACTATTTT-GACCAAATGATGTGATTTCCCG
66 CAAAGAC-CAAAAG--TTGTTTACAAAATGACAAACT-TTTTAGACCAAATGATGCGATTTCCTG
* * ** * * * * *
3722 ATCAT-GAACTG-TTCGACAAATTGGTTGAAGGAATGGATCATCTTGACTACTATTAGTAATCGA
127 AGCATGGAA-TGTTTAGA-AAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACCGA
*
3785 AGTTATCAAAGAACTAGTAAATGTTTG
190 AGTTATAAAAGAACTAGTAAATGTTTG
* * *
3812 ACAAGTTTGAAACTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAG-TTTTAATT
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATT
* * * * ** *
3876 CAAAGACCAAAATTTTTTTACAAAATGACAAACGTTTTAGACCAAATGATGTGATTTCCCAAGTA
66 CAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGCA
* * * * *
3941 TGGAATGTTCAAAAAATTGGTCAAAGGAATGGATCATCTTGACTACTATCT-GGAACCGAAGTTA
131 TGGAATGTTTAGAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCT-TAGGAACCGAAGTTA
*
4005 TAAAAGAACTAGGAAATGTTTG
195 TAAAAGAACTAGTAAATGTTTG
* * * * *
4027 ACAAGTTCGGTACTTCTTCCAAGAACCGAGAGAGAAGCAATTCTCACGT-AAAAAGTTTTTAATT
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATT
* * * * **
4091 CAAAGACTAAATGTTGTTTATAAAATGACAAACTTTTTAGACCAAATGATGTGATTTCCCAAGCA
66 CAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGCA
* *
4156 TGGAATG-TTCGAAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTTAGAAACC-AAGGTT
131 TGGAATGTTTAG-AAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACCGAA-GTT
4219 ATAAAAGAACTCA-TAAATGTTTG
194 ATAAAAGAACT-AGTAAATGTTTG
* * * *
4242 ACAAGTTCGGAAGTTTGTCTAAGAACCAAGAGAGAACCAATTCTCACGTAAAAAAGTTTTTAAAT
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATT
* * * * * *
4307 CAAAGACCAAAATTTTTTTACAACATGACAAACTTTTTAGACCAAGTGATGCGATTTTC-GAGAA
66 CAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGCA
* * ** * * ** *
4371 TGAAATGTTTGGAAAATAAGTCGAAGGAATGGATCGTCTTAAATACTCGCAGGAACTGAAGTTAT
131 TGGAATGTTTAGAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACCGAAGTTAT
*
4436 AAAAGAACTTGTAAATGTTTG
196 AAAAGAACTAGTAAATGTTTG
*
4457 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAAGAATT
1 ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATT
4499 TGATACGATC
Statistics
Matches: 2919, Mismatches: 507, Indels: 137
0.82 0.14 0.04
Matches are distributed among these distances:
214 58 0.02
215 1035 0.35
216 1527 0.52
217 142 0.05
218 155 0.05
219 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (216 bp):
ACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATT
CAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGCA
TGGAATGTTTAGAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACCGAAGTTAT
AAAAGAACTAGTAAATGTTTG
Done.