Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010496.1 Kokia drynarioides strain JFW-HI SEQ_125406, 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: 2215
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.27
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1131 original size:431 final size:431
Alignment explanation
Indices: 322--2209 Score: 1922
Period size: 431 Copynumber: 4.4 Consensus size: 431
312 NNNNNNNNNN
* * * *
322 GTTCGTAAGTTCGTCCGAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTCATTTAAA
1 GTTCG-AAGTTCGTCCAAGAACTAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
* * * * * *
387 GACCAAAATTTGTTTACAACATCACAAACTATTTAGACCAAAAGACGCGATTT-TCGGAGCATGA
65 GACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTC-GAGCATGG
** * * *
451 AATGTTCAAAAAATGGCTCAAAGGAATGGAT-AGTCTTGAATACTTTGAGGAACCAAAGTTATAA
129 AATGTTTGAAAAATTGCACAAAGGAATGGATCA-TCTTGAATACTTTAAGGAACCAAAGTTATAA
* * * * * * * ** *
515 AAGAACTCGTAAAAGTTCGACTAGTTCGTAAGTTCGTCCTAGAACCACCAGAGAAACAATTCACA
193 AAGAACTTGTAAAAGTTTGACAAGTTTGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCA
* * * * * * *
580 TGTAAATAGGTTTTTAATTCGAAGACTAAAAGTTGTTTACATAATGACAAAGTTTTTAGA-CAGA
258 TGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCA-A
* * *
644 ATGATACGA-TTCTCGAGCATGGAAA-GTTCGAAAAATTGGTCGAAGGAATGGATCGTCTTGAGT
322 ATGATGCGATTTCCCGAGCAT-GAAATGTTCGAAAAATTGGTCGAAGGAATGGATCGTCTTGAAT
* ** * * *
707 ACTCTCAGGAACTTAAGGTACAAAAGAGCTATTAAATGTTCTG-CAA
386 ACTATCAGGAACCGAAGTTATAAAAGAACTATTAAATGTT-TGACAA
* * * *
753 GTACGCAAGTTCGTCCAAAAAGTATGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
1 GTTCG-AAGTTCGTCCAAGAACTAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
* * * *
818 GACCAAAAATTGTTTAGAAAATGATAACCTATTTAGACCAAATGATGTC-ATTTCTCGAGCATGG
65 GACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATG-CGATTTCTCGAGCATGG
* * * * * * *
882 AATGCTTGAAAAATTGCACAAAGGAATGGGTCACCTTTAGTAGTTTAAGGAACCGAAGTTATAAA
129 AATGTTTGAAAAATTGCACAAAGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAA
* *
947 GGAAC-TGATAAAAAGTTTGACAAGTTT-AGAAGTTCATCCAAGAACCAAGAGAGAAACAATTGT
194 AGAACTTG-T-AAAAGTTTGACAAGTTTGA-AAGTTCATCCAAGAACCAAGAGAGAAACAATTCT
* * *
1010 CATGTAAAT-A-TTTTTAATTCACAGACGAAAAGTTGATTACAAAATGAAAAACTATTTAGACCA
256 CATGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCA
* * * *
1073 AACGATGCGATTTCCCAAGCGT-AGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAA
321 AATGATGCGATTTCCCGAGCATGA-AATGTTCGAAAAATTGGTCGAAGGAATGGATCGTCTTGAA
* * * *
1137 TACTATAAGGAACTGAAGTTATAAAAGAACTCA-TAAAAGCTTGACAA
385 TACTATCAGGAACCGAAGTTATAAAAGAACT-ATTAAATGTTTGACAA
* * * * *
1184 GTTCGAAAGTTCAG-CCAGGAA-TAAAGAGAGAAACAGTTTTGACGTAATTAAGTTTTTAATTCA
1 GTTCG-AAGTTC-GTCCAAGAACT-AAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA
* *
1247 AAGAGCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATAATGCGATTT-TCCGAGCAT
63 AAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCT-CGAGCAT
* * ** * ** *
1311 TGAATGTTTGAAAAACTGGTCGAAGG-ATAGGATCGGCTTGAATAATTTAAGGAACCGAAA-TTA
127 GGAATGTTTGAAAAATTGCACAAAGGAAT-GGATCATCTTGAATACTTTAAGGAACC-AAAGTTA
* * * * *
1374 TAAAAGAACTTGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAAAACCAAGAGAGAAAAAATTG
190 TAAAAGAACTTGTAAAAGTTTGACAAGTTTGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTC
* * * * * *
1439 TCACGTATATAAGTTTTCAATTCAAAGACCAAAAGTCGTTTACAAAATTAAAAAAC-ATTTAGAA
255 TCATGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAA-TGAAAAACTATTTAGAC
** * * * * *
1503 TGAATGATGCGATTTCCCGAGCATGTAATGCTT-GAAAAATTAGTCGAAGGAATGGGTCATCTTT
319 CAAATGATGCGATTTCCCGAGCATGAAATG-TTCGAAAAATTGGTCGAAGGAATGGATCGTCTTG
* * ** *
1567 AATACTCTCAGAAACCGAAGTTATAAAAGAACTGGTAAATATTTGACAA
383 AATACTATCAGGAACCGAAGTTATAAAAGAACTATTAAATGTTTGACAA
* * *
1616 GTTCTGAAGTTCGTCCAAGAACCAAGAGAGAAACAATCCTCATGTAAATAAGTTTTTAATTCAAA
1 GTTC-GAAGTTCGTCCAAGAACTAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
* *
1681 GACCAATAGGTT-TTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGG
65 GACCAA-AAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGG
* * *
1745 AATGTTTGAAAAATTGCACAAAGGAATGGATCATCTTTAATACTGTCAA-GAAACAAAGTTATAG
129 AATGTTTGAAAAATTGCACAAAGGAATGGATCATCTTGAATACT-TTAAGGAACCAAAG-T-TA-
** * *
1809 TAAAAGAACTTGTAAATTTTTGAAAAGTTTGAAAGTTAATCCAAGAACCAAGAGAGAAA-ATATT
190 TAAAAGAACTTGTAAAAGTTTGACAAGTTTGAAAGTTCATCCAAGAACCAAGAGAGAAACA-ATT
* * * * * * *
1873 CTCATGCAAATAA-ATTTTATATTCAAACACCAAAAGTTGTTTACCATATGACAAACTATTTTGA
254 CTCATGTAAATAAGTTTTTA-ATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGA
* * * * ** * * *
1937 CCAAATGATGCAAATTT-TCGAGAATGAAATGTTCGAAAAATTGGTTGAAATAATGCATCTTTTT
318 CCAAATGATGC-GATTTCCCGAGCATGAAATGTTCGAAAAATTGGTCGAAGGAATGGATCGTCTT
* ** * * *
2001 AAATACTATTTGGAACCAAAGTTATAAAAGCACT-TGTAAATTTTTGA-AA
382 GAATACTATCAGGAACCGAAGTTATAAAAGAACTAT-TAAATGTTTGACAA
* * **
2050 GTTCGGAAGTTCATACAAGAACTGGGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
1 GTTC-GAAGTTCGTCCAAGAACTAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
* * *
2115 GACCAAAAGTTGTTTAAAAAATGACAAACTATTTAGACCAAATGATGCCATTTCTCGAGCAAGGA
65 GACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGA
* * * * *
2180 ATGTTCGGAAAATGGCTCAAATGAATGGAT
130 ATGTTTGAAAAATTGCACAAAGGAATGGAT
2210 AGTCTT
Statistics
Matches: 1201, Mismatches: 212, Indels: 85
0.80 0.14 0.06
Matches are distributed among these distances:
429 1 0.00
430 115 0.10
431 403 0.34
432 328 0.27
433 24 0.02
434 154 0.13
435 172 0.14
436 4 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (431 bp):
GTTCGAAGTTCGTCCAAGAACTAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG
ACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAA
TGTTTGAAAAATTGCACAAAGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAG
AACTTGTAAAAGTTTGACAAGTTTGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCATGT
AAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATGA
TGCGATTTCCCGAGCATGAAATGTTCGAAAAATTGGTCGAAGGAATGGATCGTCTTGAATACTAT
CAGGAACCGAAGTTATAAAAGAACTATTAAATGTTTGACAA
Found at i:1289 original size:216 final size:215
Alignment explanation
Indices: 322--2215 Score: 1727
Period size: 216 Copynumber: 8.8 Consensus size: 215
312 NNNNNNNNNN
* * * *
322 GTTCGTAAGTTC-GTCCGAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTCATTTAA
1 GTTCGAAAGTTCAG-CCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA
* * * * * * *
386 AGACCAAAATTTGTTTACAACATCACAAACTATTTAGACCAAAAGACGCGATTTTCGGAGCATGA
65 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATG-
* * * * * *
451 AATGTTCAAAAAATGGCTCAAAGGAATGGATAGTCTTGAATACTTTGAGGAACCAAAGTTATAAA
129 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * *
516 AGAACTCGTAAAAGTTCGACTA
194 AGAACTTGTAAAAGTTTGACAA
* * ** * * * *
538 GTTCGTAAGTTC-GTCCTAGAACCACCAGAGAAACAATTCACATGTAAATAGGTTTTTAATTCGA
1 GTTCGAAAGTTCAG-CCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA
* * * * * *
602 AGACTAAAAGTTGTTTACATAATGACAAAGTTTTTAGA-CAGAATGATACGA-TTCTCGAGCATG
65 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCA-AATGATGCGATTTCCCGAGCAT-
* * * * * ** * *
665 GAAAGTTCGAAAAATTGGTCGAAGGAATGGATCGTCTTGAGTACTCTCAGGAACTTAAGGTACAA
128 GAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAA
* *
730 AAGAGCTAT-TAAATGTTCTG-CAA
193 AAGAACT-TGTAAAAGTT-TGACAA
* * * ** *
753 GTACGCAAGTTC-GTCCAAAAAGTATGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA
1 GTTCGAAAGTTCAG-CCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA
* * * * *
817 AGACCAAAAATTGTTTAGAAAATGATAACCTATTTAGACCAAATGATGTC-ATTTCTCGAGCATG
65 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATG-CGATTTCCCGAGCAT-
* * * ** * * *
881 GAATGCTT-GAAAAATTGCACAAAGGAATGGGTCACCTTTAGTAGTTTAAGGAACCGAAGTTATA
128 GAATG-TTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATA
*
945 AAGGAAC-TGATAAAAAGTTTGACAA
192 AAAGAACTTG-T-AAAAGTTTGACAA
* * * * *
970 GTT-TAGAAGTTCATCCAAGAACCAAGAGAGAAACAATTGTCATGTAAAT-A-TTTTTAATTCAC
1 GTTCGA-AAGTTCAGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA
* * * * * *
1032 AGACGAAAAGTTGATTACAAAATGAAAAACTATTTAGACCAAACGATGCGATTTCCCAAGCGTAG
65 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCAT-G
* *
1097 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTATAAGGAACTGAAGTTATAAA
129 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAA
** *
1162 AGAACTCATAAAAGCTTGACAA
194 AGAACTTGTAAAAGTTTGACAA
* ** * * * *
1184 GTTCGAAAGTTCAGCCAGGAATAAAGAGAGAAACAGTTTTGACGTAATTAAGTTTTTAATTCAAA
1 GTTCGAAAGTTCAGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
* * *
1249 GAGCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATAATGCGATTTTCCGAGCATTGA
66 GACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCA-TGA
* * * * * *
1314 ATGTTTGAAAAACTGGTCGAAGG-ATAGGATCGGCTTGAATAATTTAAGGAACCGAAATTATAAA
130 ATGTTCGAAAAATTGCTCGAAGGAAT-GGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAA
1378 AGAACTTGTAAAAGTTTGACAA
194 AGAACTTGTAAAAGTTTGACAA
* * * * * * *
1400 GTTCGGAAGTTCATCCAAAAACCAAGAGAGAAAAAATTGTCACGTATATAAGTTTTCAATTCAAA
1 GTTCGAAAGTTCAGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
* * * ***
1465 GACCAAAAGTCGTTTACAAAATTAAAAAAC-ATTTAGAATGAATGATGCGATTTCCCGAGCATGT
66 GACCAAAAGTTGTTTACAAAA-TGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATG-
* * * * * *
1529 AATGCTT-GAAAAATTAG-TCGAAGGAATGGGTCATCTTTAATACTCTCAGAAACCGAAGTTATA
129 AATG-TTCGAAAAATT-GCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATA
*
1592 AAAGAACTGGTAAATA-TTTGACAA
192 AAAGAACTTGTAAA-AGTTTGACAA
* *
1616 GTTCTG-AAGTTC-GTCCAAGAACCAAGAGAGAAACAATCCTCATGTAAATAAGTTTTTAATTCA
1 GTTC-GAAAGTTCAG-CCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA
*
1679 AAGACCAATAGGTT-TTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCAT
64 AAGACCAA-AAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCAT
* * * * * * * *
1743 GGAATGTTTGAAAAATTGCACAAAGGAATGGATCATCTTTAATACTGTCAA-GAAACAAAGTTAT
128 -GAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACT-TTAAGGAACCGAAG-T-T
** *
1807 AGTAAAAGAACTTGTAAATTTTTGAAAA
189 A-TAAAAGAACTTGTAAAAGTTTGACAA
* * * * * *
1835 GTTTGAAAGTTAATCCAAGAACCAAGAGAGAAA-ATATTCTCATGCAAATAA-ATTTTATATTCA
1 GTTCGAAAGTTCAGCCAAGAACCAAGAGAGAAACA-ATTCTCACGTAAATAAGTTTTTA-ATTCA
* * * * * * *
1898 AACACCAAAAGTTGTTTACCATATGACAAACTATTTTGACCAAATGATGCAAATTT-TCGAGAAT
64 AAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGC-GATTTCCCGAGCAT
* * ** * * * * * *
1962 GAAATGTTCGAAAAATTGGTTGAAATAATGCATCTTTTTAAATACTATT-TGGAACCAAAGTTAT
128 G-AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACT-TTAAGGAACCGAAGTTAT
* **
2026 AAAAGCACTTGTAAATTTTTGA-AA
191 AAAAGAACTTGTAAAAGTTTGACAA
* ** ***
2050 GTTCGGAAGTTCATACAAGAACTGGGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
1 GTTCGAAAGTTCAGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
* * * *
2115 GACCAAAAGTTGTTTAAAAAATGACAAACTATTTAGACCAAATGATGCCATTTCTCGAGCAAGGA
66 GACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGC-ATGA
* * * * *
2180 ATGTTCGGAAAATGGCTCAAATGAATGGATAGTCTT
130 ATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTT
Statistics
Matches: 1361, Mismatches: 265, Indels: 105
0.79 0.15 0.06
Matches are distributed among these distances:
214 57 0.04
215 423 0.31
216 636 0.47
217 70 0.05
218 15 0.01
219 156 0.11
220 4 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (215 bp):
GTTCGAAAGTTCAGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
GACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGAA
TGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAG
AACTTGTAAAAGTTTGACAA
Done.