Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014088.1 Kokia drynarioides strain JFW-HI SEQ_129119, 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: 3016
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.39
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:438 original size:215 final size:214
Alignment explanation
Indices: 1--932 Score: 1000
Period size: 215 Copynumber: 4.4 Consensus size: 214
* * * *
1 TTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAAATTCTTTATGTGAGAATTGTTTCTT
1 TTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTATTTAGGTGAGAATTGTTTCTC
* *
66 TCTTGGTTCTCGACCGAACATT-AAACTTGACAAACTTTTACAAGTTCTTTTATAACTTTTGTGC
66 TCTTGGTTCTCGGCCGAACATTCAAACTTGACAAACTTTTA-AAGTTCTTTTATAACTTTTGTTC
* * * *
130 AC-TAAAGTATTC---A--ATAC-TTCCTTCGGGCAA-TTTTCTGTACAGTCCATGCTTG-GAAA
130 -CTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTC-GAACAGTCCATGCTCGAG-AA
186 ATCACATCATTAGGTCTAAATAG
192 ATCACATCATTAGGTCTAAATAG
* * *
209 TTGTCATTTTGTAAACAACTTTTGGTTTTTGAATTAAAAACTTATTTAGGTGAGAATTTTTTCTC
1 TTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTATTTAGGTGAGAATTGTTTCTC
* * * ***
274 TCTTGGTTCTCGGCCGAAC-TTCCGAACTTGACTAACTTTTAAGAGTTCCTTTATAACTTCAATT
66 TCTTGGTTCTCGGCCGAACATT-CAAACTTGACAAACTTTTAA-AGTTCTTTTATAACTTTTGTT
* * * *
338 CCTTAAAGTAATCAAGATGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAGATAT
129 CCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACAGTCCATGCTCGAGAAAT
** *
403 TGCATCATTTGGTCTAAATAG
194 CACATCATTAGGTCTAAATAG
* * **
424 TTGTTATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAATTTCTC
1 TTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTATTTAGGTGAGAATTGTTTCTC
* * * * * * *
489 TCTTGGTTCTGGGCTGAACGTTCGAAGTTGACAAACTTTTACGAGTTCTTTTATAACTTTGGTTC
66 TCTTGGTTCTCGGCCGAACATTCAAACTTGACAAACTTTTA-AAGTTCTTTTATAACTTTTGTTC
* * ** * *
554 CTTAAAGTATTTAAGACGATTCATTCCTTTTAGCAATTTTTTGAACATTCCATGCTTC--GAAAT
130 CTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACAGTCCATGC-TCGAGAAAT
* *
617 CATATCATTTGGTCTAAATAG
194 CACATCATTAGGTCTAAATAG
* * * * *
638 TTGTAATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAAATTCTTTATGTGAGAATTGTTTCTT
1 TTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTATTTAGGTGAGAATTGTTTCTC
* * * * * **
703 TCTTGGTTCTCAGCCAAAC-TTTAAACTTGACAAAATTTTCAAGTTCTTTTATAA-TTTT-TTTA
66 TCTTGGTTCTCGGCCGAACATTCAAACTTGACAAACTTTTAAAGTTCTTTTATAACTTTTGTTCC
* * * *
765 TTAAAGTATTCAAGACGATCCATTCCTTC-ATCAATTTATT-GTACAGTCCATGCTTGGGAAATC
131 TTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTT-TTCGAACAGTCCATGCTCGAGAAATC
* **
828 ACATTATTAGGTCTACTTTAGG
195 ACATCATTAGGTCTA-AATA-G
* * * * *
850 TTGTCATTCTGTAAACTACTTTAGGTTTTTCAATTAAAAACTTATTTAGGTGAGAATTGTTTCTC
1 TTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTATTTAGGTGAGAATTGTTTCTC
* *
915 TTTTGGTTCTCGGTCGAA
66 TCTTGGTTCTCGGCCGAA
933 NNNNNNNNNN
Statistics
Matches: 608, Mismatches: 96, Indels: 36
0.82 0.13 0.05
Matches are distributed among these distances:
207 2 0.00
208 79 0.13
209 60 0.10
210 48 0.08
211 5 0.01
212 84 0.14
213 16 0.03
214 97 0.16
215 207 0.34
216 10 0.02
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (214 bp):
TTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTATTTAGGTGAGAATTGTTTCTC
TCTTGGTTCTCGGCCGAACATTCAAACTTGACAAACTTTTAAAGTTCTTTTATAACTTTTGTTCC
TTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACAGTCCATGCTCGAGAAATCA
CATCATTAGGTCTAAATAG
Found at i:1708 original size:214 final size:212
Alignment explanation
Indices: 983--1828 Score: 896
Period size: 214 Copynumber: 4.0 Consensus size: 212
973 NNNNNNNNNN
* * * * * *
983 TTTGTAAACAACTTTTGGTCTTTAAATTAAAAAATTCTTTATGTGAGAATTGTTTCTTTCTTGGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAGTTTCTCTCTTGGT
* * ** * * * **
1048 TCTCAGCCAAACTTTAAACCTGACAAAATTTT-CGAGTTCTTTTATAA-TTT-TTTTATTAAAGT
66 TCTCGGCCGAACTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTTGATTCCTTAAAGT
* * * * * *
1110 ATTCAAGACGATCCATTCCTTC-ATCAATTTATTGTACAGTCCATGCTTGGGAAATCACATTATT
131 ATTCAAGACGATCCATTCCTTCGAGCAATTT-TTGAACATTCCATGCTT-AGAAATCTCATCATT
* *
1174 AGGTCTAAATTGTTGTCAT
194 TGGTCTAAATAGTTGTCAT
* * * * * * *
1193 TCTGTAAACTACTTTAGGTTTTTCAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTTTTGGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAGTTTCTCTCTTGGT
* *
1258 TCTCGGTCGAACTTTCGAACTTGA-AACACTTTTACGAGGTCTTTTATAACTTTGATTCCTTAAA
66 TCTCGGCCGAAC-TTCGAACTTGACAA-ACTTTTACGAGTTCTTTTATAACTTTGATTCCTTAAA
* * * * * * * *
1322 CTATACAAGATGATCCCTTCGTTCGAGCAATTTTAAGAGCATTCCATGCTCTAGAAATCGCATCA
129 GTATTCAAGACGATCCATTCCTTCGAGCAATTTT-TGAACATTCCATGCT-TAGAAATCTCATCA
* * * *
1387 ATTAGTCTGAATAGTTGGCAT
192 TTTGGTCTAAATAGTTGTCAT
* * * * * * * *
1408 TATGTATACAACATTTGGTCATTGAATTAAAAACTTATTTAGGTTAGAATAGCTTATCTATTGGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAGTTTCTCTCTTGGT
* * * * * * **
1473 TCTAGGTCGAA-TATCCGAAGTTGACAAACTTTTACGACTTCTTTTACAACTTCGGCTCCTTAAA
66 TCTCGGCCGAACT-T-CGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTTGATTCCTTAAA
* * * *
1537 GTATCCAAGACAAACCATTCCTTCGAGCAATTTTCTGAACATTCCAAGCTTAGAAATCTCATCAT
129 GTATTCAAGACGATCCATTCCTTCGAGCAATTTT-TGAACATTCCATGCTTAGAAATCTCATCAT
1602 TTGGTCTAAATAGTTGTCAT
193 TTGGTCTAAATAGTTGTCAT
*
1622 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAATTTCTCTCTTGGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAGTTTCTCTCTTGGT
* *
1687 TCTGGGCCGAACTGTCGAAGTTGACAAACTTTTACGAGTTCTTTTATAACTTTGATTCCTTAAAG
66 TCTCGGCCGAACT-TCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTTGATTCCTTAAAG
* * * *
1752 TATTTAAGACGAGCCATTCCTTCGAGGAATTTTTCGAACATTCCATGCTTGGAAATCGT-ATCAT
130 TATTCAAGACGATCCATTCCTTCGAGCAATTTTT-GAACATTCCATGCTTAGAAATC-TCATCAT
1816 TTGGTCTAAATAG
193 TTGGTCTAAATAG
1829 NNNNNNNNNN
Statistics
Matches: 521, Mismatches: 101, Indels: 24
0.81 0.16 0.04
Matches are distributed among these distances:
210 66 0.13
211 13 0.02
212 14 0.03
213 5 0.01
214 234 0.45
215 186 0.36
216 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (212 bp):
TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAGTTTCTCTCTTGGT
TCTCGGCCGAACTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTTGATTCCTTAAAGT
ATTCAAGACGATCCATTCCTTCGAGCAATTTTTGAACATTCCATGCTTAGAAATCTCATCATTTG
GTCTAAATAGTTGTCAT
Found at i:2281 original size:210 final size:214
Alignment explanation
Indices: 1879--2438 Score: 573
Period size: 210 Copynumber: 2.6 Consensus size: 214
1869 NNNNNNNNNN
* * * * *
1879 ACAAACTTTTACGAGTTC-TTTTATAACTT-TGGTTCCTTAAAGTATTTAAGACGATCCATTCCT
1 ACAAAATTTTACGAGATCTTTTTA-AAATTCT-GTTCATTAAAGTATTCAAGACGATCCATTCC-
* ** *
1942 TTTAGCAATTTTTTGAACATTCCATGCTT-GGAAATCGTATCATTTGGTCTAAATAGTTGTCATT
63 TTCAGCAATTTTTTGAACATTCCATGCTTGGGAAATCACATCATTAGGTCTAAATAGTTGTCATT
* * * * * * *
2006 TTGTAAACAACTTTTGGTCTTTGAATTAAAAAATTCTTTATGTGAGAATTGTTTCTTTCTTGGTT
128 CTGTAAACAACTTTTGGTCTTTCAATTAAAAAATTATTAAGGTGAGAATTGTTTCTCTATTGGTT
* *
2071 CTCAGCCAAACTT-TAAACTTG
193 CACAGCCAAACTTCCAAACTTG
* *
2092 ACAAAATTTT-CTAGTTCTTTTTAAAATT-T-TTCATTAAAGTATTCAAGACGATCCATTCCTTC
1 ACAAAATTTTACGAGATCTTTTTAAAATTCTGTTCATTAAAGTATTCAAGACGATCCATTCCTTC
* * * * *
2154 AGCAATTTATTGTACAGTCCATGCTTGGGAAATCACATTATTAGGTCTAAATTGTTGTCATTCTG
66 AGCAATTTTTTGAACATTCCATGCTTGGGAAATCACATCATTAGGTCTAAATAGTTGTCATTCTG
* * *
2219 TAAACTACTTTTGGT-TTATCATTTAAAAACTTATTAAGGTGAGAATTGTTTCTCTATTGGTTCA
131 TAAACAACTTTTGGTCTT-TCAATTAAAAAATTATTAAGGTGAGAATTGTTTCTCTATTGGTTCA
*** *
2283 CAGTTGAACTTCCGAACTTG
195 CAGCCAAACTTCCAAACTTG
* * * * * * *
2303 ACAAACTTTTACGAGATCTTTTTTAACTTCTGTTCCTTATAGAATTCAAGACGATACATTCCTTC
1 ACAAAATTTTACGAGATCTTTTTAAAATTCTGTTCATTAAAGTATTCAAGACGATCCATTCCTTC
* * * * * *
2368 GACCAATTTTTTAAACATTCCATGCTCGGGAAATCGCATCACTT-GTTCTTAATAGATTGTCAAT
66 -AGCAATTTTTTGAACATTCCATGCTTGGGAAATCACATCA-TTAGGTCTAAATAG-TTGTC-AT
2432 T-TGTAAA
127 TCTGTAAA
2439 AAAAAGTTAT
Statistics
Matches: 286, Mismatches: 50, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
209 27 0.09
210 119 0.42
211 15 0.05
212 25 0.09
213 15 0.05
214 29 0.10
215 40 0.14
216 13 0.05
217 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (214 bp):
ACAAAATTTTACGAGATCTTTTTAAAATTCTGTTCATTAAAGTATTCAAGACGATCCATTCCTTC
AGCAATTTTTTGAACATTCCATGCTTGGGAAATCACATCATTAGGTCTAAATAGTTGTCATTCTG
TAAACAACTTTTGGTCTTTCAATTAAAAAATTATTAAGGTGAGAATTGTTTCTCTATTGGTTCAC
AGCCAAACTTCCAAACTTG
Found at i:2799 original size:394 final size:393
Alignment explanation
Indices: 2033--2802 Score: 885
Period size: 411 Copynumber: 1.9 Consensus size: 393
2023 TCTTTGAATT
* *
2033 AAAAAATTCTTTATGTGAGAATTGTTTCTTTCTTGGTTCTCAGCCAAACTTTAAACTTGACAAAA
1 AAAAAATTATTTATGTGAGAATTGTTTCTTTCTTGGTTCTCAGCCAAACTTCAAACTTGACAAAA
*
2098 TTTTCTAGTTCTTTTTAAAATTTTTCATTAAAGTATTCAAGACGATCCATTCCTTCAGCAATTTA
66 TTTTCGAGTTCTTTTTAAAATTTTTCATTAAAGTATTCAAGACGATCCATTCCTTCAGCAATTTA
*** * * * *
2163 TTGTACAGTCCATGCTTGGGAAATCACATTATTAGGTCTAAATTGTTGTCATTCTGTAAACTACT
131 CCATACAGTCCATGCATGGGAAATCACATCATTAGATCTAAATAGTTGTCATTCTGTAAACTACT
*
2228 TTTGGTTTATCATTTAAAAACTTATTAAGGTGAGAATTGTTTCTCTATTGGTTCACAGTTGAACT
196 TTTGGTTTATCAATTAAAAACTTATTAAGGTGAGAATTGTTTCTCTATTGGTTCACAG-TG-A--
* * *
2293 TCCGAACTTGACAAACTTTTACGAGATCTTTTTTAACTTCTGTTCCTTATAGAATTCAAGACGAT
257 T----AC-TG--AAACTTTTACGAGATCTTTTATAACTTCTGTTCCTTAAACAATTCAAGACGAT
*
2358 ACATTCCTTCGACCAATTTTTTAAACATTCCATGCTCGGGAAATCGCATCACTTGTTCTTAATAG
315 ACATTCCTTCGACCAA-TTTTTAAACATTCCATGCTCGCGAAATCGCATCACTTGTTCTTAATAG
2423 ATTGTCAATTTGTAA
379 ATTGTCAATTTGTAA
* ** *** *
2438 AAAAAAGTTATTTATGTTAGAATTGTTTCTTTCTTTTTTCTCAGTTGAACTTCCGAACTTGAC-A
1 AAAAAA-TTATTTATGTGAGAATTGTTTCTTTCTTGGTTCTCAGCCAAACTT-CAAACTTGACAA
** * *
2502 AATTTTAACGAGTTCTTTTATAACTTTTGTTCATTAAAGTATTCAGGACGATCCATTCTTTCGAG
64 AATTTT--CGAGTTCTTTT-TAAAATTT-TTCATTAAAGTATTCAAGACGATCCATTCCTTC-AG
* * * *
2567 CAATTTCCCATACAGTCCATGCATGGGAGATCACATCATTAGATCTAAATAGTTGTCATTTTTTA
124 CAATTTACCATACAGTCCATGCATGGGAAATCACATCATTAGATCTAAATAGTTGTCATTCTGTA
* * * * *
2632 AACTACTTTTGGTCTT-TGAATTAAAAACTTATTTAGGTTAGAATTGTTTCTCTTTTGGTTCTC-
189 AACTACTTTTGGT-TTATCAATTAAAAACTTATTAAGGTGAGAATTGTTTCTCTATTGGTTCACA
* * * * *
2695 G-G-T-C-G-AACTTTTACTAGTTCTTTTATAACTT-TGATTCCTTAAACTATTCAAGATGATCC
253 GTGATACTGAAACTTTTACGAGATCTTTTATAACTTCTG-TTCCTTAAACAATTCAAGACGATAC
* *
2754 CTTCCTTCGAGCAA-TTTTAAGAGCATTCCATGCTCGCGAAATCGCATCA
317 ATTCCTTCGACCAATTTTTAA-A-CATTCCATGCTCGCGAAATCGCATCA
2803 TTTTGTCTGA
Statistics
Matches: 312, Mismatches: 42, Indels: 33
0.81 0.11 0.09
Matches are distributed among these distances:
392 6 0.02
393 3 0.01
394 80 0.26
397 1 0.00
399 1 0.00
404 1 0.00
405 6 0.02
406 45 0.14
407 8 0.03
408 11 0.04
409 6 0.02
410 32 0.10
411 110 0.35
412 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (393 bp):
AAAAAATTATTTATGTGAGAATTGTTTCTTTCTTGGTTCTCAGCCAAACTTCAAACTTGACAAAA
TTTTCGAGTTCTTTTTAAAATTTTTCATTAAAGTATTCAAGACGATCCATTCCTTCAGCAATTTA
CCATACAGTCCATGCATGGGAAATCACATCATTAGATCTAAATAGTTGTCATTCTGTAAACTACT
TTTGGTTTATCAATTAAAAACTTATTAAGGTGAGAATTGTTTCTCTATTGGTTCACAGTGATACT
GAAACTTTTACGAGATCTTTTATAACTTCTGTTCCTTAAACAATTCAAGACGATACATTCCTTCG
ACCAATTTTTAAACATTCCATGCTCGCGAAATCGCATCACTTGTTCTTAATAGATTGTCAATTTG
TAA
Done.