Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009508.1 Kokia drynarioides strain JFW-HI SEQ_124219, 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: 6256
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Found at i:1329 original size:218 final size:208
Alignment explanation
Indices: 940--1827 Score: 909
Period size: 218 Copynumber: 4.2 Consensus size: 208
930 CAAAACAACA
* * * * ** * *
940 CAGTCATCTTTCCGATGAGATACTGAGAAGAAAACCGAATTAAAATCATGCTCGATATGAGCAAA
1 CAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGATGTGAACAAA
* * * *
1005 ACTTCGAACCATAGCTTCCTGATGAGATACTGAGAAGCGTGTCGAAGTAATAAGACGGTTGGTTT
66 TCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCG-GTCGAAGTAATAAAACGGTTAG---
* * * *
1070 CCTGGCCATCTTTCTGATGAGGTATGGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGA
127 -CT--CCA-C--TCAGATGAGATACGGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGA
** *
1135 GAAGTAAATTGAAACAAATGACG
186 GAAGCGAATTGAAACAAACGACG
* * * * *
1158 CAGTCATCTTCCCGATGAAATACCGAGAAGAAGACCGAATTAAACCCATTCTCGATGTGAACAAA
1 CAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGATGTGAACAAA
* * * *
1223 TCTTCGAACCATAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAGACGGTTGGTTT
66 TCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCG-GTCGAAGTAATAAAACGGTTAG---
* *
1288 CCTGGCCAACTTTCAGATGAGATACAGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGA
127 -CT--CC-AC--TCAGATGAGATACGGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGA
* * **
1353 GAAGCGGATTGAAACAAGCGATA
186 GAAGCGAATTGAAACAAACGACG
* * * * *
1376 CAGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAACCAAACCCA--CGC-ATGATGAATAA
1 CAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGATG-TGAACAA
* * * * * *
1438 ACCTTCGAACCCCAGCTTCTTGATAAGATATTGAGAAGCAGGTCGAAGTAATAAAACAGTTAGCT
65 ATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGC-GGTCGAAGTAATAAAACGGTTAGCT
* *
1503 --AC-CTGATGAGATACGGAGAAGTTG-ATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGA
129 CCACTCAGATGAGATACGGAGAAG-TGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGA
1564 ATTGAAACAAACGACG
193 ATTGAAACAAACGACG
* * ** *
1580 CAGTCATCTTCCCAATGAGATACTGAGAAGAAGACCAAATCAAACTCGCGCTCGATGT-AAGTAA
1 CAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGATGTGAA-CAA
* * *
1644 ATCTTCGAA-CACAGCTTCCTGATGAGACACTGAGAAGTAGGTCGAAGCAATAAAACGGTTAGCT
65 ATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAG-CGGTCGAAGTAATAAAACGGTTAGCT
* * * *
1708 TC-CT-A-ATGAGATACTGAGAAGTGAATCATATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
129 CCACTCAGATGAGATACGGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
*
1770 TTGAAACAAACGATG
194 TTGAAACAAACGACG
* *
1785 CAGTCATCTTCCCGATGAGATACTGAGAAGAAGGCCAAGTCAA
1 CAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAA
1828 TGAAACCAAA
Statistics
Matches: 583, Mismatches: 74, Indels: 39
0.84 0.11 0.06
Matches are distributed among these distances:
204 108 0.19
205 156 0.27
206 15 0.03
207 5 0.01
212 2 0.00
215 3 0.01
216 59 0.10
217 1 0.00
218 233 0.40
219 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (208 bp):
CAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGATGTGAACAAA
TCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCGGTCGAAGTAATAAAACGGTTAGCTCC
ACTCAGATGAGATACGGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATT
GAAACAAACGACG
Found at i:1757 original size:205 final size:204
Alignment explanation
Indices: 1304--1827 Score: 748
Period size: 205 Copynumber: 2.6 Consensus size: 204
1294 CAACTTTCAG
* * *
1304 ATGAGATACAGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACA
1 ATGAGATACAGAGAAGTGAATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACA
* * * *
1369 AGCGATACAGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAACCAAACCCACGCATGATGA
66 AACGATGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGGCCAAATCAAACCCACGCATGATGA
* * * * *
1434 ATAAACCTTCGAACCCCAGCTTCTTGATAAGATATTGAGAAGCAGGTCGAAGTAATAAAACAGTT
131 ATAAACCTTCGAACCACAGCTTCCTGATAAGACACTGAGAAGCAGGTCGAAGCAATAAAACAGTT
*
1499 AGCTACCTG
196 AGCTACCTA
*
1508 ATGAGATACGGAGAAGTTG-ATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAAC
1 ATGAGATACAGAGAAG-TGAATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAAC
* * * * *
1572 AAACGACGCAGTCATCTTCCCAATGAGATACTGAGAAGAAGACCAAATCAAACTCGCGC-TCGAT
65 AAACGATGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGGCCAAATCAAACCCACGCAT-GAT
* * *
1636 GTAAGTAAATCTTCGAA-CACAGCTTCCTGATGAGACACTGAGAAGTAGGTCGAAGCAATAAAAC
129 G-AA-TAAACCTTCGAACCACAGCTTCCTGATAAGACACTGAGAAGCAGGTCGAAGCAATAAAAC
* *
1700 GGTTAGCTTCCTA
192 AGTTAGCTACCTA
* *
1713 ATGAGATACTGAGAAGTGAATCATATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACA
1 ATGAGATACAGAGAAGTGAATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACA
*
1778 AACGATGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGGCCAAGTCAA
66 AACGATGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGGCCAAATCAA
1828 TGAAACCAAA
Statistics
Matches: 285, Mismatches: 30, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
203 1 0.00
204 113 0.40
205 160 0.56
206 11 0.04
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.21
Consensus pattern (204 bp):
ATGAGATACAGAGAAGTGAATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACA
AACGATGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGGCCAAATCAAACCCACGCATGATGA
ATAAACCTTCGAACCACAGCTTCCTGATAAGACACTGAGAAGCAGGTCGAAGCAATAAAACAGTT
AGCTACCTA
Found at i:4073 original size:88 final size:89
Alignment explanation
Indices: 3917--4420 Score: 522
Period size: 88 Copynumber: 5.7 Consensus size: 89
3907 GAAGGTCCCT
* * * * ** * *
3917 AAACTTTCAAAAATTCCATTTTTGACCTTGAAACTTCCAAAAATTTCGTTTTTAACTCCAAAACT
1 AAACTTCCAAAAATCCCATTTTT-ACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
3982 TCCAAAAATCCCATTTTTGACCCCA
65 TCCAAAAATCCCATTTTTGACCCCA
* * * *
4007 AAACTTCCAAAAATTCCA-TTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAATTT
1 AAACTTCCAAAAATCCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTT
4071 CCAAAAATCCCATTTTTGACCCCA
66 CCAAAAATCCCATTTTTGACCCCA
* * * * * *
4095 AAACTTCAAAAAAATCCCATTTTTAACCTAGAAACTTCCAAAAATTCCGTTTTT-ACCCTC-GAA
1 AAACTTC-CAAAAATCCCATTTTTACCCT-CAAACTTCCAAAAATCCCATTTTTAACCC-CAAAA
* *
4158 CTTCCAAAAATCCCATTTTTAACCCCG
63 CTTCCAAAAATCCCATTTTTGACCCCA
* * * *
4185 AAACTT-CAAAAATCCCA-TTTTAACCTCAAAACCTCCAAAAATTCCATTTTTAACCTCAAAACT
1 AAACTTCCAAAAATCCCATTTTTACCCTC-AAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
*
4248 TCCAAAAAATCCCA-TTTT-ACCCCC
65 TCC-AAAAATCCCATTTTTGACCCCA
* * *
4272 AAACTTCCAAAAATCCCA-TTTTACCCTTAAACTTCCAAAAATCCCATTTTT-ACCCCCAAATTT
1 AAACTTCCAAAAATCCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTT
* * *
4335 CCAAAAATCCCATTTTTTACCTCG
66 CCAAAAATCCCATTTTTGACCCCA
** * * * * ***
4359 AAACTTTTAAAAATTCTATTTTTACCCCCAAACTTTCAAATCCCCCATTTTTTAACCCCAAA
1 AAACTTCCAAAAATCCCATTTTTACCCTCAAACTTCCAAAAATCCCA-TTTTTAACCCCAAA
4421 TTTTCCTAAA
Statistics
Matches: 352, Mismatches: 48, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
85 10 0.03
86 15 0.04
87 81 0.23
88 129 0.37
89 28 0.08
90 68 0.19
91 21 0.06
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.31
Consensus pattern (89 bp):
AAACTTCCAAAAATCCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTT
CCAAAAATCCCATTTTTGACCCCA
Found at i:4076 original size:29 final size:29
Alignment explanation
Indices: 3917--4398 Score: 472
Period size: 30 Copynumber: 16.4 Consensus size: 29
3907 GAAGGTCCCT
* * ***
3917 AAACTTTCAAAAATTCCATTTTTGACCTTG
1 AAACTTCCAAAAATCCCATTTTT-ACCCCA
** * *
3947 AAACTTCCAAAAATTTCGTTTTTAACTCCA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCA
3977 AAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCA
*
4007 AAACTTCCAAAAATTCCA-TTTTACCCTC-
1 AAACTTCCAAAAATCCCATTTTTACCC-CA
*
4035 GAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCA
*
4065 AAATTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCA
* * *
4095 AAACTTCAAAAAAATCCCATTTTTAACCTA
1 AAACTTC-CAAAAATCCCATTTTTACCCCA
* *
4125 GAAACTTCCAAAAATTCCGTTTTTACCCTC-
1 -AAACTTCCAAAAATCCCATTTTTACCC-CA
* *
4155 GAACTTCCAAAAATCCCATTTTTAACCCCG
1 AAACTTCCAAAAATCCCATTTTT-ACCCCA
* *
4185 AAACTT-CAAAAATCCCATTTTAACCTCA
1 AAACTTCCAAAAATCCCATTTTTACCCCA
* * *
4213 AAACCTCCAAAAATTCCATTTTTAACCTCA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCA
*
4243 AAACTTCCAAAAAATCCCA-TTTTACCCCC
1 AAACTTCC-AAAAATCCCATTTTTACCCCA
**
4272 AAACTTCCAAAAATCCCA-TTTTACCCTT
1 AAACTTCCAAAAATCCCATTTTTACCCCA
*
4300 AAACTTCCAAAAATCCCATTTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTACCCCA
* * *
4329 AAATTTCCAAAAATCCCATTTTTTACCTCG
1 AAACTTCCAAAAATCCCA-TTTTTACCCCA
** * * *
4359 AAACTTTTAAAAATTCTATTTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTACCCCA
*
4388 AAACTTTCAAA
1 AAACTTCCAAA
4399 TCCCCCATTT
Statistics
Matches: 382, Mismatches: 56, Indels: 29
0.82 0.12 0.06
Matches are distributed among these distances:
28 65 0.17
29 116 0.30
30 170 0.45
31 31 0.08
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.31
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTACCCCA
Done.