Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001515.1 Kokia drynarioides strain JFW-HI SEQ_113074, 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, 982
Length: 1637
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Found at i:463 original size:216 final size:216
Alignment explanation
Indices: 44--1637 Score: 2054
Period size: 216 Copynumber: 7.5 Consensus size: 216
34 ATAACTCGTA
* * *
44 AAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGT-AATAAGTTTTTCATTTAAAGACCA
1 AAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* * * *
108 AAACTTGTTTGCAGAATGACAAATTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATGTT
66 AAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTT
* * * *
173 C-AGAAAATTGCTCGAAAGAATAGATCGTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAAC
131 CGA-AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAGGGATCTAAAGTTATAAAAGAAC
* * *
237 TAGTAAAAGTTTGACAGGCTCG
195 TAGTAAAAGTTTGACAAGTTTG
* * *
259 AAACTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAGCA
1 AAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
324 AAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTT
66 AAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTT
* * * * * * * * *
389 CGAAAAATTGCTCGAAGGAATGGATCTTGTTGAAAATTTTAGGGAACTGAATTTAAAAAATAACT
131 CGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAGGGATCTAAAGTTATAAAAGAACT
* *
454 CAG-AAAAGTTTTACAATTTTG
196 -AGTAAAAGTTTGACAAGTTTG
475 AAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
1 AAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* * *
540 AAACTTGTTTGAAAAATGACAAACTATTTAGACCAAATGATGCGTTTTCTCGAGCATGGAATATT
66 AAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTT
* * * *
605 CGAAAAATTTCTAGAAGGAATGGATCGTCTTGAATACTTT-GAGGATCTAAAGTTATGACAGAAC
131 CGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAG-GGATCTAAAGTTATAAAAGAAC
669 TAGTAAAAGTTTGACAAGTTTG
195 TAGTAAAAGTTTGACAAGTTTG
* * *
691 AAAGTTCATACAAGAACAAAGAGAGAAACAATTCTCAAGTAAATAAGTTTTTAACTCAAAGACCA
1 AAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* * * * * * * * * *
756 AAACTGGTTTACAAAATGACAAGCTATTTAGAGCAAGTGACGCGATTTCCCAAGGATAGAATGTT
66 AAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTT
** ** ** * * *
821 C-AAAAATTTGCTATAAAAAATGGATATTGTTGAATACTTTAGGGAACTGAAG-T-T-AAA-AA-
131 CGAAAAA-TTGCTCGAAGGAATGGATCGTCTTGAATACTTTAGGGATCTAAAGTTATAAAAGAAC
* *
880 -A-T--AA--CT--C--G--TA
195 TAGTAAAAGTTTGACAAGTTTG
* * *
890 AAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGT-AATAAGTTTTTCATTTAAAGACCA
1 AAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* * * *
954 AAACTTGTTTGCAGAATGACAAATTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATGTT
66 AAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTT
* * * *
1019 C-AGAAAATTGCTCGAAAGAATAGATCGTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAAC
131 CGA-AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAGGGATCTAAAGTTATAAAAGAAC
* * *
1083 TAGTAAAAGTTTGACAGGCTCG
195 TAGTAAAAGTTTGACAAGTTTG
* * *
1105 AAACTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAGCA
1 AAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
1170 AAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTT
66 AAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTT
* * * * * * * * *
1235 CGAAAAATTGCTCGAAGGAATGGATCTTGTTGAAAATTTTAGGGAACTGATGTTAAAAAATAACT
131 CGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAGGGATCTAAAGTTATAAAAGAACT
* *
1300 CAG-AAAAGTTTTACAATTTTG
196 -AGTAAAAGTTTGACAAGTTTG
*
1321 AAAGTTAATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
1 AAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
*
1386 AAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGC-ATTTTCTCGAGCATGGAATAT
66 AAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGA-TTTCTCGAGCATGGAATGT
* * * *
1450 TCGAAAAATTTCTAGAAGGAATGGATCGTCTTGAATACTTT-GAGGATCTAAAGTTATGACAGAA
130 TCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAG-GGATCTAAAGTTATAAAAGAA
1514 CTAGTAAAAGTTTGACAAGTTTG
194 CTAGTAAAAGTTTGACAAGTTTG
* *
1537 AAAGTTCATACAAGAACAAAGAGAGAAACAATTCTCAAGTAAATAAGTTTTTAATTCAAAGACCA
1 AAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* *
1602 AAACTGGTTTACAAAATGACAAACTATTTAGACCAA
66 AAACTTGTTTGCAAAATGACAAACTATTTAGACCAA
Statistics
Matches: 1190, Mismatches: 158, Indels: 61
0.84 0.11 0.04
Matches are distributed among these distances:
198 110 0.09
199 43 0.04
200 1 0.00
201 4 0.00
202 2 0.00
203 1 0.00
204 1 0.00
205 2 0.00
207 4 0.00
209 2 0.00
210 1 0.00
211 1 0.00
212 2 0.00
213 3 0.00
214 1 0.00
215 91 0.08
216 914 0.77
217 7 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Consensus pattern (216 bp):
AAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
AAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTT
CGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAGGGATCTAAAGTTATAAAAGAACT
AGTAAAAGTTTGACAAGTTTG
Found at i:895 original size:432 final size:431
Alignment explanation
Indices: 44--1637 Score: 2330
Period size: 432 Copynumber: 3.7 Consensus size: 431
34 ATAACTCGTA
* * *
44 AAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAATAAGTTTTTCATTTAAAGACCAA
1 AAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAATAAGTTTTTAATTCAAAGACCAA
* * *
109 AACTTGTTTGCAGAATGACAAATTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATGTTC
66 AACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATATTC
*
174 AGAAAATTGCTCGAAAGAATAGATCGTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAACTA
131 AGAAAATTGCTAGAAAGAATAGATCGTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAACTA
* * * *
239 GTAAAAGTTTGACAGGCTCGAAACTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATA
196 GTAAAAGTTTGACAAGCTCGAAACTTCATACAAGAACAAAGAGAGAAACAATTCTCAAGTAAATA
* * *
304 AGTTTTTAATTCAAAGAGCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGA
261 AGTTTTTAATTCAAAGACCAAAACTGGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
369 TTTCTCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCTTGTTGAAAATTTTAGGGA
326 TTTCTCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCTTGTTGAAAATTTTAGGGA
*
434 ACTGAATTTAAAAAATAACTCAGAAAAGTTTTACAATTTTG
391 ACTGAAGTTAAAAAATAACTCAGAAAAGTTTTACAATTTTG
475 AAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
1 AAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGT-AATAAGTTTTTAATTCAAAGACCA
* * * *
540 AAACTTGTTTGAAAAATGACAAACTATTTAGACCAAATGATGCGTTTTCTCGAGCATGGAATATT
65 AAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATATT
* * * * * * *
605 C-GAAAAATTTCTAGAAGGAATGGATCGTCTTGAATACTTTGAGGATCTAAAGTTATGACAGAAC
130 CAG-AAAATTGCTAGAAAGAATAGATCGTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAAC
* * *
669 TAGTAAAAGTTTGACAAGTTTGAAAGTTCATACAAGAACAAAGAGAGAAACAATTCTCAAGTAAA
194 TAGTAAAAGTTTGACAAGCTCGAAACTTCATACAAGAACAAAGAGAGAAACAATTCTCAAGTAAA
* * * * *
734 TAAGTTTTTAACTCAAAGACCAAAACTGGTTTACAAAATGACAAGCTATTTAGAGCAAGTGACGC
259 TAAGTTTTTAATTCAAAGACCAAAACTGGTTTACAAAATGACAAACTATTTAGACCAAATGATGC
* * * * ** ** * * *
799 GATTTCCCAAGGATAGAATGTTC-AAAAATTTGCTATAAAAAATGGATATTGTTGAATACTTTAG
324 GATTTCTCGAGCATGGAATGTTCGAAAAA-TTGCTCGAAGGAATGGATCTTGTTGAAAATTTTAG
863 GGAACTGAAGTTAAAAAATAACTC------G---T---A-----
388 GGAACTGAAGTTAAAAAATAACTCAGAAAAGTTTTACAATTTTG
* * *
890 AAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAATAAGTTTTTCATTTAAAGACCAA
1 AAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAATAAGTTTTTAATTCAAAGACCAA
* * *
955 AACTTGTTTGCAGAATGACAAATTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATGTTC
66 AACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATATTC
*
1020 AGAAAATTGCTCGAAAGAATAGATCGTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAACTA
131 AGAAAATTGCTAGAAAGAATAGATCGTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAACTA
* * * *
1085 GTAAAAGTTTGACAGGCTCGAAACTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATA
196 GTAAAAGTTTGACAAGCTCGAAACTTCATACAAGAACAAAGAGAGAAACAATTCTCAAGTAAATA
* * *
1150 AGTTTTTAATTCAAAGAGCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGA
261 AGTTTTTAATTCAAAGACCAAAACTGGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
1215 TTTCTCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCTTGTTGAAAATTTTAGGGA
326 TTTCTCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCTTGTTGAAAATTTTAGGGA
*
1280 ACTGATGTTAAAAAATAACTCAGAAAAGTTTTACAATTTTG
391 ACTGAAGTTAAAAAATAACTCAGAAAAGTTTTACAATTTTG
*
1321 AAAGTTAATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
1 AAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGT-AATAAGTTTTTAATTCAAAGACCA
* *
1386 AAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGC-ATTTTCTCGAGCATGGAATAT
65 AAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGA-TTCCCCGAGCATGGAATAT
* * * * * * *
1450 TC-GAAAAATTTCTAGAAGGAATGGATCGTCTTGAATACTTTGAGGATCTAAAGTTATGACAGAA
129 TCAG-AAAATTGCTAGAAAGAATAGATCGTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAA
* * *
1514 CTAGTAAAAGTTTGACAAGTTTGAAAGTTCATACAAGAACAAAGAGAGAAACAATTCTCAAGTAA
193 CTAGTAAAAGTTTGACAAGCTCGAAACTTCATACAAGAACAAAGAGAGAAACAATTCTCAAGTAA
1579 ATAAGTTTTTAATTCAAAGACCAAAACTGGTTTACAAAATGACAAACTATTTAGACCAA
258 ATAAGTTTTTAATTCAAAGACCAAAACTGGTTTACAAAATGACAAACTATTTAGACCAA
Statistics
Matches: 1021, Mismatches: 117, Indels: 49
0.86 0.10 0.04
Matches are distributed among these distances:
414 319 0.31
415 45 0.04
420 2 0.00
423 2 0.00
426 2 0.00
431 85 0.08
432 566 0.55
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Consensus pattern (431 bp):
AAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAATAAGTTTTTAATTCAAAGACCAA
AACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATATTC
AGAAAATTGCTAGAAAGAATAGATCGTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAACTA
GTAAAAGTTTGACAAGCTCGAAACTTCATACAAGAACAAAGAGAGAAACAATTCTCAAGTAAATA
AGTTTTTAATTCAAAGACCAAAACTGGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
TTTCTCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCTTGTTGAAAATTTTAGGGA
ACTGAAGTTAAAAAATAACTCAGAAAAGTTTTACAATTTTG
Found at i:1206 original size:630 final size:631
Alignment explanation
Indices: 263--1637 Score: 1794
Period size: 630 Copynumber: 2.2 Consensus size: 631
253 GGCTCGAAAC
*
263 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAGCAAAAC
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
* *
328 TTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCGAA
66 TTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATGTTCGAA
* * * * * * ** * *
393 AAATTGCTCGAAGGAATGGATCTTGTTGAAAATTTTAGGGAACTGAATTTAAAAAATAACTCAGA
131 AAATTGCTCGAAAGAATAGATCGTCTTGAAAACTTTAAGGAACCAAAGTTAAAAAAGAACTCAGA
* ** * *
458 AAAGTTTTACAATTTTGAAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGT
196 AAAGTTTGACAAGCTCGAAACTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGT
*
523 TTTTAATTCAAAGACCAAAACTTGTTTGAAAAATGACAAACTATTTAGACCAAATGATGCGTTTT
261 TTTTAATTCAAAGACCAAAACTTGTTTGAAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * *
588 CTCGAGCATGGAATATTCGAAAAATTTCTAGAAGGAATGGATCGTCTTGAATACTTTGA-GGATC
326 CTCGAGCATGGAATATTCGAAAAATTGCTAGAAGGAATGGATCGTCTTGAA-AATTTGAGGGAAC
** * *
652 TAAAGTTATGACAGAACT-AGTAAAAGTTTGACAAGTTTGAAAGTTCATACAAGAACAAAGAGAG
390 TAAAGTTAAAAAAGAACTCAG-AAAAGTTTGACAAGTTTGAAAGTTAATACAAGAACAAAGAGAG
*
716 AAACAATTCTCAAGTAAATAAGTTTTTAACTCAAAGACCAAAACTGGTTTACAAAATGACAAGCT
454 AAACAATTCTCAAGTAAATAAGTTTTTAACTCAAAGACCAAAACTGGTTTACAAAATGACAAACT
781 ATTTAGAGCAAGTGACGCGATTTCCCAAGGATAGAATGTTCAAAAATTTGCTATAAAAAATGGAT
519 ATTTAGAGCAAGTGACGCGATTTCCCAAGGATAGAATGTTCAAAAATTTGCTATAAAAAATGGAT
846 ATTGTTGAATACTTTAGGGAACTGAAGTTAAAAAATAACTCGTAAAAG
584 ATTGTTGAATACTTTAGGGAACTGAAGTTAAAAAATAACTCGTAAAAG
* *
894 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGT-AATAAGTTTTTCATTTAAAGACCAAAAC
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
* *
958 TTGTTTGCAGAATGACAAATTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATGTTC-AG
66 TTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATGTTCGA-
* * *
1022 AAAATTGCTCGAAAGAATAGATCGTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAACT-AG
130 AAAATTGCTCGAAAGAATAGATCGTCTTGAAAACTTTAAGGAACCAAAGTTAAAAAAGAACTCAG
* *
1086 TAAAAGTTTGACAGGCTCGAAACTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAA
195 -AAAAGTTTGACAAGCTCGAAACTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAA
* *
1151 GTTTTTAATTCAAAGAGCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGAT
259 GTTTTTAATTCAAAGACCAAAACTTGTTTGAAAAATGACAAACTATTTAGACCAAATGATGCGAT
* * * * *
1216 TTCTCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCTTGTTGAAAATTTTAGGGAA
324 TTCTCGAGCATGGAATATTCGAAAAATTGCTAGAAGGAATGGATCGTCTTGAAAATTTGAGGGAA
* * * * * *
1281 CTGATGTTAAAAAATAACTCAGAAAAGTTTTACAATTTTGAAAGTTAATCCAAGAACAAAGAGAG
389 CTAAAGTTAAAAAAGAACTCAGAAAAGTTTGACAAGTTTGAAAGTTAATACAAGAACAAAGAGAG
* * * *
1346 AAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACT
454 AAACAATTCTCAAGTAAATAAGTTTTTAACTCAAAGACCAAAACTGGTTTACAAAATGACAAACT
* * * * * * * * * **
1411 ATTTAGACCAAATGATGC-ATTTTCTCGAGCATGGAATATTCGAAAAATTT-CTAGAAGGAATGG
519 ATTTAGAGCAAGTGACGCGA-TTTCCCAAGGATAGAATGTTC-AAAAATTTGCTATAAAAAATGG
** * * * * *
1474 ATCGTCTTGAATACTTT-GAGGATCTAAAGTTATGACAGAACTAGTAAAAGTTTGACAAGTTTGA
582 ATATTGTTGAATACTTTAG-GGAACTGAAGTTA--A-A-AA--A-T--AA--CT--C--G--TAA
1538 AAG
629 AAG
* * *
1541 TTCATACAAGAACAAAGAGAGAAACAATTCTCAAGTAAATAAGTTTTTAATTCAAAGACCAAAAC
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
* *
1606 TGGTTTACAAAATGACAAACTATTTAGACCAA
66 TTGTTTGCAAAATGACAAACTATTTAGACCAA
Statistics
Matches: 639, Mismatches: 80, Indels: 33
0.85 0.11 0.04
Matches are distributed among these distances:
629 10 0.02
630 480 0.75
631 46 0.07
632 1 0.00
633 1 0.00
634 2 0.00
636 1 0.00
637 1 0.00
639 2 0.00
641 1 0.00
643 1 0.00
645 1 0.00
647 38 0.06
648 54 0.08
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (631 bp):
TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
TTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATGTTCGAA
AAATTGCTCGAAAGAATAGATCGTCTTGAAAACTTTAAGGAACCAAAGTTAAAAAAGAACTCAGA
AAAGTTTGACAAGCTCGAAACTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGT
TTTTAATTCAAAGACCAAAACTTGTTTGAAAAATGACAAACTATTTAGACCAAATGATGCGATTT
CTCGAGCATGGAATATTCGAAAAATTGCTAGAAGGAATGGATCGTCTTGAAAATTTGAGGGAACT
AAAGTTAAAAAAGAACTCAGAAAAGTTTGACAAGTTTGAAAGTTAATACAAGAACAAAGAGAGAA
ACAATTCTCAAGTAAATAAGTTTTTAACTCAAAGACCAAAACTGGTTTACAAAATGACAAACTAT
TTAGAGCAAGTGACGCGATTTCCCAAGGATAGAATGTTCAAAAATTTGCTATAAAAAATGGATAT
TGTTGAATACTTTAGGGAACTGAAGTTAAAAAATAACTCGTAAAAG
Found at i:1632 original size:846 final size:846
Alignment explanation
Indices: 1--1633 Score: 3205
Period size: 846 Copynumber: 1.9 Consensus size: 846
1 TTGTTGAATACTTTAGGGAACTGAAGTTAAAAAATAACTCGTAAAAGTTCGTCCAAGAACAAAGA
1 TTGTTGAATACTTTAGGGAACTGAAGTTAAAAAATAACTCGTAAAAGTTCGTCCAAGAACAAAGA
66 GAGAAACAATTCTCACGTAATAAGTTTTTCATTTAAAGACCAAAACTTGTTTGCAGAATGACAAA
66 GAGAAACAATTCTCACGTAATAAGTTTTTCATTTAAAGACCAAAACTTGTTTGCAGAATGACAAA
131 TTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATGTTCAGAAAATTGCTCGAAAGAATAG
131 TTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATGTTCAGAAAATTGCTCGAAAGAATAG
196 ATCGTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAGGCTCGAA
196 ATCGTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAGGCTCGAA
261 ACTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAGCAAA
261 ACTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAGCAAA
326 ACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCG
326 ACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCG
391 AAAAATTGCTCGAAGGAATGGATCTTGTTGAAAATTTTAGGGAACTGAATTTAAAAAATAACTCA
391 AAAAATTGCTCGAAGGAATGGATCTTGTTGAAAATTTTAGGGAACTGAATTTAAAAAATAACTCA
*
456 GAAAAGTTTTACAATTTTGAAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAA
456 GAAAAGTTTTACAATTTTGAAAGTTAATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAA
*
521 GTTTTTAATTCAAAGACCAAAACTTGTTTGAAAAATGACAAACTATTTAGACCAAATGATGCGTT
521 GTTTTTAATTCAAAGACCAAAACTTGTTTGAAAAATGACAAACTATTTAGACCAAATGATGCATT
586 TTCTCGAGCATGGAATATTCGAAAAATTTCTAGAAGGAATGGATCGTCTTGAATACTTTGAGGAT
586 TTCTCGAGCATGGAATATTCGAAAAATTTCTAGAAGGAATGGATCGTCTTGAATACTTTGAGGAT
651 CTAAAGTTATGACAGAACTAGTAAAAGTTTGACAAGTTTGAAAGTTCATACAAGAACAAAGAGAG
651 CTAAAGTTATGACAGAACTAGTAAAAGTTTGACAAGTTTGAAAGTTCATACAAGAACAAAGAGAG
*
716 AAACAATTCTCAAGTAAATAAGTTTTTAACTCAAAGACCAAAACTGGTTTACAAAATGACAAGCT
716 AAACAATTCTCAAGTAAATAAGTTTTTAACTCAAAGACCAAAACTGGTTTACAAAATGACAAACT
781 ATTTAGAGCAAGTGACGCGATTTCCCAAGGATAGAATGTTCAAAAATTTGCTATAAAAAATGGAT
781 ATTTAGAGCAAGTGACGCGATTTCCCAAGGATAGAATGTTCAAAAATTTGCTATAAAAAATGGAT
846 A
846 A
847 TTGTTGAATACTTTAGGGAACTGAAGTTAAAAAATAACTCGTAAAAGTTCGTCCAAGAACAAAGA
1 TTGTTGAATACTTTAGGGAACTGAAGTTAAAAAATAACTCGTAAAAGTTCGTCCAAGAACAAAGA
912 GAGAAACAATTCTCACGTAATAAGTTTTTCATTTAAAGACCAAAACTTGTTTGCAGAATGACAAA
66 GAGAAACAATTCTCACGTAATAAGTTTTTCATTTAAAGACCAAAACTTGTTTGCAGAATGACAAA
977 TTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATGTTCAGAAAATTGCTCGAAAGAATAG
131 TTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATGTTCAGAAAATTGCTCGAAAGAATAG
1042 ATCGTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAGGCTCGAA
196 ATCGTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAGGCTCGAA
1107 ACTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAGCAAA
261 ACTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAGCAAA
1172 ACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCG
326 ACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCG
1237 AAAAATTGCTCGAAGGAATGGATCTTGTTGAAAATTTTAGGGAACTG-ATGTTAAAAAATAACTC
391 AAAAATTGCTCGAAGGAATGGATCTTGTTGAAAATTTTAGGGAACTGAAT-TTAAAAAATAACTC
1301 AGAAAAGTTTTACAATTTTGAAAGTTAATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATA
455 AGAAAAGTTTTACAATTTTGAAAGTTAATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATA
*
1366 AGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCAT
520 AGTTTTTAATTCAAAGACCAAAACTTGTTTGAAAAATGACAAACTATTTAGACCAAATGATGCAT
1431 TTTCTCGAGCATGGAATATTCGAAAAATTTCTAGAAGGAATGGATCGTCTTGAATACTTTGAGGA
585 TTTCTCGAGCATGGAATATTCGAAAAATTTCTAGAAGGAATGGATCGTCTTGAATACTTTGAGGA
1496 TCTAAAGTTATGACAGAACTAGTAAAAGTTTGACAAGTTTGAAAGTTCATACAAGAACAAAGAGA
650 TCTAAAGTTATGACAGAACTAGTAAAAGTTTGACAAGTTTGAAAGTTCATACAAGAACAAAGAGA
*
1561 GAAACAATTCTCAAGTAAATAAGTTTTTAATTCAAAGACCAAAACTGGTTTACAAAATGACAAAC
715 GAAACAATTCTCAAGTAAATAAGTTTTTAACTCAAAGACCAAAACTGGTTTACAAAATGACAAAC
1626 TATTTAGA
780 TATTTAGA
1634 CCAA
Statistics
Matches: 781, Mismatches: 5, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
845 2 0.00
846 779 1.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (846 bp):
TTGTTGAATACTTTAGGGAACTGAAGTTAAAAAATAACTCGTAAAAGTTCGTCCAAGAACAAAGA
GAGAAACAATTCTCACGTAATAAGTTTTTCATTTAAAGACCAAAACTTGTTTGCAGAATGACAAA
TTATTTAGACCAAATGATGCGATTCCCCGAGCATGGAATGTTCAGAAAATTGCTCGAAAGAATAG
ATCGTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAGGCTCGAA
ACTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAGCAAA
ACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCG
AAAAATTGCTCGAAGGAATGGATCTTGTTGAAAATTTTAGGGAACTGAATTTAAAAAATAACTCA
GAAAAGTTTTACAATTTTGAAAGTTAATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAA
GTTTTTAATTCAAAGACCAAAACTTGTTTGAAAAATGACAAACTATTTAGACCAAATGATGCATT
TTCTCGAGCATGGAATATTCGAAAAATTTCTAGAAGGAATGGATCGTCTTGAATACTTTGAGGAT
CTAAAGTTATGACAGAACTAGTAAAAGTTTGACAAGTTTGAAAGTTCATACAAGAACAAAGAGAG
AAACAATTCTCAAGTAAATAAGTTTTTAACTCAAAGACCAAAACTGGTTTACAAAATGACAAACT
ATTTAGAGCAAGTGACGCGATTTCCCAAGGATAGAATGTTCAAAAATTTGCTATAAAAAATGGAT
A
Done.