Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006877.1 Kokia drynarioides strain JFW-HI SEQ_121478, 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: 17082
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Found at i:503 original size:216 final size:215
Alignment explanation
Indices: 115--2232 Score: 2097
Period size: 216 Copynumber: 9.9 Consensus size: 215
105 AAGGAACTAG
* ** * * * **
115 GAGAGAAACAATTCACATGTAAATATGTTTTTAATTCAAAGACAAAAAGCAGTTTACAAAATGAC
1 GAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGTTTACAAAATGAC
* * * * * * * * *
180 AAACTGTTTGGACCAAATGATGCTATTTCTCAAGCATGAAAGGTTCGAAAAATTTCTAGAAGGAA
66 AAATTATTTGGACCAAATGATGCGATTTCTCGAGAATGGAATGTTCGAAAAATTGCTCGAAGGAA
* * * * *
245 TGGATGGTCTTGAATACTTTAAGGAACCTAAGTGAAAAAAGAACTCGTAAAAGTTTGACAAGTTC
131 T-GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGACAAGTTC
**
310 GGAAGTTCGGTTAAGAACCAA
195 GGAAGTTCGGCCAAGAACCAA
* * ** * * *
331 TAGAGAAATAATTCTCATGTAAATAATTTTTTAATCCAAAGACCAAAAATTGTTTACAAAATAAC
1 GAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGTTTACAAAATGAC
* * ** * * *
396 AGATTATTTGGACCAAATGATGCAATTTCTCGAGAATCAAATATTCAAAAAATTGCTCCAAGGAA
66 AAATTATTTGGACCAAATGATGCGATTTCTCGAGAATGGAATGTTCGAAAAATTGCTCGAAGGAA
* * * * *
461 TGAATGGTCTAGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGAAAAAGTTTGAAAACTTC
131 TG-ATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGACAAGTTC
** *
526 AAAAGTACGGCCAAGAACCAA
195 GGAAGTTCGGCCAAGAACCAA
** *
547 GAGAGAAACAATTCTCACATAAATAAGTTTTTAATTTAAAGACCAAAAGTTTTTTAC-AAATGGA
1 GAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGTTTACAAAAT-GA
* * * ** * *
611 CAAACTATTTGGACCAAATGGTGCGATTTCCCGAGGCTAGAATGCTT-GAAAAATTGCTTGAAAG
65 CAAATTATTTGGACCAAATGATGCGATTTCTCGAGAATGGAATG-TTCGAAAAATTGCTCG-AAG
* * * * * *
675 G-ATCAATCATCTTGAATACTTTAAAGAACTGGAGTTATAAAAGAACTCGAAAAAGTTTGTCAAG
128 GAAT-GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGACAAG
*
739 TTCGGAAGTTCGGCAAAGAACCAA
192 TTCGGAAGTTCGGCCAAGAACCAA
* * *
763 GAGCG-AACAATTGTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTCTTTACAAAATGAC
1 GAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGTTTACAAAATGAC
* ** * *
827 AGATTATTTGGACCAAGGGATGCGATTTCCCGAGAATGTAATGTTCGAAAAATTGCTCGAAGGAA
66 AAATTATTTGGACCAAATGATGCGATTTCTCGAGAATGGAATGTTCGAAAAATTGCTCGAAGGAA
* * * * *
892 TCGATCATCTTTAATACTTTAAGGGAA-CGAAGTTATACAAGAACTC-AAAAAGTTTTAAAAGTT
131 T-GATCGTCTTGAATACTTTAA-GGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGACAAGTT
* *
955 CAGAAGTTCGGCCAAGAACTAA
194 CGGAAGTTCGGCCAAGAACCAA
* * * * * * * *
977 GAGAGAAACCATTCTCACGTAAATAATTTTTTAATTCAAATACCGAAAGTTTTTTAC-TAATGGA
1 GAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGTTTACAAAAT-GA
* * * * *
1041 CAAAGTATTTGGACCAAATGATGTGATTTTTCGAGCATGGAATGTTTGAAAAATTGCTCGAAGGA
65 CAAATTATTTGGACCAAATGATGCGATTTCTCGAGAATGGAATGTTCGAAAAATTGCTCGAAGGA
* * * *
1106 ATCGATCCTCTTGAAAACTTTAAGGAACCGAAGTTTTAAAAAAACTCGAAAAAGTTTGACAAGTT
130 AT-GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGACAAGTT
**
1171 CGGAAGTTCACCCAAGAACCAA
194 CGGAAGTTCGGCCAAGAACCAA
* *
1193 GAGAGAAACAATTCTCACATAAATTAGTTTTTAATCCAAAGACTAAAAGTTGTTTACAAAATGAC
1 GAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGTTTACAAAATGAC
* *
1258 AAATTATTTGGACCAAATGATGCGATTTCTTGAGAATGAAATGTTCGAAAAATTGCT--------
66 AAATTATTTGGACCAAATGATGCGATTTCTCGAGAATGGAATGTTCGAAAAATTGCTCGAAGGAA
* * * * * * **
1315 TGA-AG----G---A----AAGGAACCGAAGTTGTGAAAGAACTCAAAAAATTTTGAAATTTTCG
131 TGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGACAAGTTCG
* * *
1368 AAAGTTTGACCAAGAACCAA
196 GAAGTTCGGCCAAGAACCAA
* * *
1388 GAGAGAAATAATTCTCACATAAATAAGTTTTTAATCCAATGACAAAAAGTTGTTTACAAAATGAC
1 GAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGTTTACAAAATGAC
** * * * * * ** **
1453 TGATTATTTTGGACCAAAGGCTGTGATTTCTCGATAATGGAATTTTCGAAAAATTATTCGAAATA
66 AAATTA-TTTGGACCAAATGATGCGATTTCTCGAGAATGGAATGTTCGAAAAATTGCTCGAAGGA
* * * * *
1518 ATGGATCGTCTTAAATACTTTAAGGAACCGAAGTTATAAAAGGACTCGAGAAAGTTTAAAAAGTT
130 AT-GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGACAAGTT
* * * *
1583 TGAAAGTTCAGCCAAGAACAAA
194 CGGAAGTTCGGCCAAGAACCAA
* * * * * * *
1605 GAGAGAAACAATTCTTACATAAATAAGCTTTTATTTCAAAGATCAAAAGTTTTTTACAAAAGGAC
1 GAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGTTTACAAAATGAC
* * * * * * ** * * *
1670 AAACTGTTTGGACCAAATGGTGTGATTTCCCTAGGCTGGAATGTTTGGAAAATTGC-CCAGAGGA
66 AAATTATTTGGACCAAATGATGCGATTTCTCGAGAATGGAATGTTCGAAAAATTGCTCGA-AGGA
* * *
1734 ATCGATCGTCTTAAATACTTTAAGGAACCGAAATTATAAAAGAACTCAAAAAAGTTTGACAAGTT
130 AT-GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGACAAGTT
* *
1799 CGGAAGTTTGGCCAAGAACGAA
194 CGGAAGTTCGGCCAAGAACCAA
* *
1821 GAGA-AAA-AATTCTCAAATAAATAAGTTTTTAATCCAAAGACC--AA---CTTTACAAAATGAC
1 GAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGTTTACAAAATGAC
*
1879 --ATTATTTGGACCATAA-GATGCGATTTCCCGAGAATGGAATGTTCGAAAAATTGCTCGAAGGA
66 AAATTATTTGGACCA-AATGATGCGATTTCTCGAGAATGGAATGTTCGAAAAATTGCTCGAAGGA
* * ** *
1941 ATGGATCATCTTGAATACTTTAAGAAACCGAAGTTATAATGGAACTCGAAAAAGTTTGAAAAGTT
130 AT-GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGACAAGTT
** *
2006 TAGAAGTTCAGCCAAGAACCAA
194 CGGAAGTTCGGCCAAGAACCAA
* * * * * * * *
2028 TAGAGAAATC-AGTCTCACGTAAATAAGTTTTTAATTCAAAGACTAAAAGTTTTTTTCAAAAGGA
1 GAGAGAAA-CAATTCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGTTTACAAAATGA
* * * * *
2092 CAAACTATGTGGACCAAATGATGCAATTTCTCGAGCATGGAATGTTC-AGAAAATTGCTCAAAGG
65 CAAATTATTTGGACCAAATGATGCGATTTCTCGAGAATGGAATGTTCGA-AAAATTGCTCGAAGG
* *
2156 AATCGATTC-TCTTGAATACTTTAAGGAACCGAAGTTTTGAAAGAACTC-AAAAATGTTTGACAA
129 AAT-GA-TCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAA-GTTTGACAA
2219 GTTCGGAAGTTCGG
191 GTTCGGAAGTTCGG
2233 TGATAGCATT
Statistics
Matches: 1555, Mismatches: 294, Indels: 106
0.80 0.15 0.05
Matches are distributed among these distances:
195 119 0.08
196 42 0.03
199 1 0.00
202 1 0.00
204 1 0.00
205 2 0.00
206 1 0.00
207 124 0.08
208 8 0.01
209 41 0.03
211 2 0.00
212 2 0.00
213 1 0.00
214 90 0.06
215 287 0.18
216 713 0.46
217 120 0.08
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.28
Consensus pattern (215 bp):
GAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGTTTACAAAATGAC
AAATTATTTGGACCAAATGATGCGATTTCTCGAGAATGGAATGTTCGAAAAATTGCTCGAAGGAA
TGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGACAAGTTCG
GAAGTTCGGCCAAGAACCAA
Found at i:1309 original size:431 final size:429
Alignment explanation
Indices: 115--2232 Score: 2128
Period size: 423 Copynumber: 5.0 Consensus size: 429
105 AAGGAACTAG
* ** * * **
115 GAGAGAAACAATTCACATGTAAATATGTTTTTAATTCAAAGACAAAAAGCAGTTTACAAAATGAC
1 GAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAC
* * * * * * *
180 AAACTGTTTGGACCAAATGATGCT-ATTTCTCAAGCATGAAAGGTTCGAAAAATTTCTAGAAGGA
66 AAACTATTTGGACCAAATGATG-TGATTTCTCGAGCATGGAATGTTTGAAAAATTGCTCGAAGGA
** * * * *
244 ATGGATGGTCTTGAATACTTTAAGGAACCTAAGTGAAAAAAGAACTCGTAAAAGTTTGACAAGTT
130 ATGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGACAAGTT
* ** * * ** *
309 CGGAAGTTCGGTTAAGAACCAATAGAGAAATAATTCTCATGTAAATAATTTTTTAATCCAAAGAC
195 CGGAAGTTCAGCCAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGAC
* * * * * * *
374 CAAAAATTGTTTACAAAATAACAGATTATTTGGACCAAATGATGCAATTTCTCGAGAATCAAATA
260 TAAAAGTTGTTTACAAAATGACAAATTATTTGGACCAAATGATGCGATTTCTCGAGAATGAAATG
* * * *
439 TTCAAAAAATTGCTCCAAGGAAT-GAATGGTCTAGAATACTTTAAGGAATCGAAGTTATAAAAGA
325 TTCGAAAAATTGCTCCAAGGAATCG-AT-CTCTTGAATACTTTAAGGAACCGAAGTTAT-AAAGA
* * *
503 ACTCGAAAAAGTTTGAAAACTTCAAAAGTACGGCCAAGAACCAA
387 ACTC-AAAAAGTTTGAAAAGTTCAGAAGTTCGGCCAAGAACCAA
* *
547 GAGAGAAACAATTCTCACATAAATAAGTTTTTAATTTAAAGACCAAAAGTTTTTTAC-AAATGGA
1 GAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAT-GA
* * * * * *
611 CAAACTATTTGGACCAAATGGTGCGATTTCCCGAGGC-TAGAATGCTTGAAAAATTGCTTGAAAG
65 CAAACTATTTGGACCAAATGATGTGATTTCTCGA-GCATGGAATGTTTGAAAAATTGCTCG-AAG
** * * * *
675 G-ATCAATCATCTTGAATACTTTAAAGAACTGGAGTTATAAAAGAACTCGAAAAAGTTTGTCAAG
128 GAATGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGACAAG
* * * *
739 TTCGGAAGTTCGGCAAAGAACCAAGAGCG-AACAATTGTCACATAAATAAGTTTTTAATCCAAAG
193 TTCGGAAGTTCAGCCAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAG
* * * ** * *
803 ACCAAAAGTTCTTTACAAAATGACAGATTATTTGGACCAAGGGATGCGATTTCCCGAGAATGTAA
258 ACTAAAAGTTGTTTACAAAATGACAAATTATTTGGACCAAATGATGCGATTTCTCGAGAATGAAA
* *
868 TGTTCGAAAAATTGCTCGAAGGAATCGATCATCTTTAATACTTTAAGGGAA-CGAAGTTATACAA
323 TGTTCGAAAAATTGCTCCAAGGAATCGATC-TCTTGAATACTTTAA-GGAACCGAAGTTATA-AA
* *
932 GAACTCAAAAAGTTTTAAAAGTTCAGAAGTTCGGCCAAGAACTAA
385 GAACTCAAAAAGTTTGAAAAGTTCAGAAGTTCGGCCAAGAACCAA
* * * * * * *
977 GAGAGAAACCATTCTCACGTAAATAATTTTTTAATTCAAATACCGAAAGTTTTTTAC-TAATGGA
1 GAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAT-GA
* *
1041 CAAAGTATTTGGACCAAATGATGTGATTTTTCGAGCATGGAATGTTTGAAAAATTGCTCGAAGGA
65 CAAACTATTTGGACCAAATGATGTGATTTCTCGAGCATGGAATGTTTGAAAAATTGCTCGAAGGA
* * * * *
1106 ATCGATCCTCTTGAAAACTTTAAGGAACCGAAGTTTTAAAAAAACTCGAAAAAGTTTGACAAGTT
130 ATGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGACAAGTT
* *
1171 CGGAAGTTCACCCAAGAACCAAGAGAGAAACAATTCTCACATAAATTAGTTTTTAATCCAAAGAC
195 CGGAAGTTCAGCCAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGAC
*
1236 TAAAAGTTGTTTACAAAATGACAAATTATTTGGACCAAATGATGCGATTTCTTGAGAATGAAATG
260 TAAAAGTTGTTTACAAAATGACAAATTATTTGGACCAAATGATGCGATTTCTCGAGAATGAAATG
* *
1301 TTCGAAAAATTGCT----TGAA--G-------G---A----AAGGAACCGAAGTTGTGAAAGAAC
325 TTCGAAAAATTGCTCCAAGGAATCGATCTCTTGAATACTTTAAGGAACCGAAGTTAT-AAAGAAC
* ** * *
1346 TCAAAAAATTTTGAAATTTTC-GAAAGTTTGACCAAGAACCAA
389 TC-AAAAAGTTTGAAAAGTTCAG-AAGTTCGGCCAAGAACCAA
* * * *
1388 GAGAGAAATAATTCTCACATAAATAAGTTTTTAATCCAATGACAAAAAGTTGTTTACAAAATGAC
1 GAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAC
** * * * ** ** **
1453 TGATTATTTTGGACCAAAGGCTGTGATTTCTCGATAATGGAAT-TTTCGAAAAATTATTCGAAAT
66 AAACTA-TTTGGACCAAATGATGTGATTTCTCGAGCATGGAATGTTT-GAAAAATTGCTCGAAGG
* * * * * *
1517 AATGGATCGTCTTAAATACTTTAAGGAACCGAAGTTATAAAAGGACTCGAGAAAGTTTAAAAAGT
129 AATGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGACAAGT
* * * * * * *
1582 TTGAAAGTTCAGCCAAGAACAAAGAGAGAAACAATTCTTACATAAATAAGCTTTTATTTCAAAGA
194 TCGGAAGTTCAGCCAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGA
* * * * * * * * ** *
1647 -TCAAAAGTTTTTTACAAAAGGACAAACTGTTTGGACCAAATGGTGTGATTTCCCTAGGCTGGAA
259 CT-AAAAGTTGTTTACAAAATGACAAATTATTTGGACCAAATGATGCGATTTCTCGAGAATGAAA
* * * *
1711 TGTTTGGAAAATTGC-CCAGAGGAATCGATCGTCTTAAATACTTTAAGGAACCGAAATTATAAAA
323 TGTTCGAAAAATTGCTCCA-AGGAATCGATC-TCTTGAATACTTTAAGGAACCGAAGTTAT-AAA
* * * *
1775 GAACTCAAAAAAGTTTGACAAGTTCGGAAGTTTGGCCAAGAACGAA
385 GAACTC-AAAAAGTTTGAAAAGTTCAGAAGTTCGGCCAAGAACCAA
* * *
1821 GAGA-AAA-AATTCTCAAATAAATAAGTTTTTAATCCAAAGACC--AA---CTTTACAAAATGAC
1 GAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAC
* * * * *
1879 --ATTATTTGGACCATAA-GATGCGATTTCCCGAGAATGGAATGTTCGAAAAATTGCTCGAAGGA
66 AAACTATTTGGACCA-AATGATGTGATTTCTCGAGCATGGAATGTTTGAAAAATTGCTCGAAGGA
* ** *
1941 ATGGATCATCTTGAATACTTTAAGAAACCGAAGTTATAATGGAACTCGAAAAAGTTTGAAAAGTT
130 ATGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGACAAGTT
** * * * *
2006 TAGAAGTTCAGCCAAGAACCAATAGAGAAATC-AGTCTCACGTAAATAAGTTTTTAATTCAAAGA
195 CGGAAGTTCAGCCAAGAACCAAGAGAGAAA-CAATTCTCACATAAATAAGTTTTTAATCCAAAGA
* * * * * * * *
2070 CTAAAAGTTTTTTTCAAAAGGACAAACTATGTGGACCAAATGATGCAATTTCTCGAGCATGGAAT
259 CTAAAAGTTGTTTACAAAATGACAAATTATTTGGACCAAATGATGCGATTTCTCGAGAATGAAAT
* *
2135 GTTC-AGAAAATTGCTCAAAGGAATCGATTCTCTTGAATACTTTAAGGAACCGAAGTTTTGAAAG
324 GTTCGA-AAAATTGCTCCAAGGAATCGA-TCTCTTGAATACTTTAAGGAACCGAAGTTAT-AAAG
* *
2199 AACTCAAAAATGTTTGACAAGTTCGGAAGTTCGG
386 AACTCAAAAA-GTTTGAAAAGTTCAGAAGTTCGG
2233 TGATAGCATT
Statistics
Matches: 1411, Mismatches: 225, Indels: 109
0.81 0.13 0.06
Matches are distributed among these distances:
409 4 0.00
410 19 0.01
411 88 0.06
412 221 0.16
414 1 0.00
416 3 0.00
418 1 0.00
422 5 0.00
423 283 0.20
424 14 0.01
425 1 0.00
426 13 0.01
427 3 0.00
429 9 0.01
430 220 0.16
431 282 0.20
432 178 0.13
433 65 0.05
434 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.28
Consensus pattern (429 bp):
GAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAC
AAACTATTTGGACCAAATGATGTGATTTCTCGAGCATGGAATGTTTGAAAAATTGCTCGAAGGAA
TGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGACAAGTTC
GGAAGTTCAGCCAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACT
AAAAGTTGTTTACAAAATGACAAATTATTTGGACCAAATGATGCGATTTCTCGAGAATGAAATGT
TCGAAAAATTGCTCCAAGGAATCGATCTCTTGAATACTTTAAGGAACCGAAGTTATAAAGAACTC
AAAAAGTTTGAAAAGTTCAGAAGTTCGGCCAAGAACCAA
Found at i:1461 original size:195 final size:196
Alignment explanation
Indices: 1127--1507 Score: 534
Period size: 195 Copynumber: 1.9 Consensus size: 196
1117 TGAAAACTTT
* * *
1127 AAGGAACCGAAGTTTTAAAAAAACTCGAAAAAGTTTGACAAGTTCGGAAGTTCACCCAAGAACCA
1 AAGGAACCGAAGTTGTAAAAAAACTCAAAAAAGTTTGACAAGTTCGAAAGTTCACCCAAGAACCA
* *
1192 AGAGAGAAACAATTCTCACATAAATTAGTTTTTAATCCAAAGACTAAAAGTTGTTTACAAAATGA
66 AGAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACAAAAAGTTGTTTACAAAATGA
* *
1257 CAAATTA-TTTGGACCAAATGATGCGATTTCTTGAGAATGAAATGTTCGAAAAATTGCTTGAAGG
131 CAAATTATTTTGGACCAAAGGATGCGATTTCTCGAGAATGAAATGTTCGAAAAATTGCTTGAAGG
1321 A
196 A
* * * * *
1322 AAGGAACCGAAGTTGTGAAAGAACTCAAAAAATTTTGA-AATTTTCGAAAGTTTGA-CCAAGAAC
1 AAGGAACCGAAGTTGTAAAAAAACTCAAAAAAGTTTGACAA-GTTCGAAAG-TTCACCCAAGAAC
* *
1385 CAAGAGAGAAATAATTCTCACATAAATAAGTTTTTAATCCAATGACAAAAAGTTGTTTACAAAAT
64 CAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACAAAAAGTTGTTTACAAAAT
** * * * * *
1450 GACTGATTATTTTGGACCAAAGGCTGTGATTTCTCGATAATGGAATTTTCGAAAAATT
129 GACAAATTATTTTGGACCAAAGGATGCGATTTCTCGAGAATGAAATGTTCGAAAAATT
1508 ATTCGAAATA
Statistics
Matches: 162, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
194 2 0.01
195 116 0.72
196 44 0.27
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (196 bp):
AAGGAACCGAAGTTGTAAAAAAACTCAAAAAAGTTTGACAAGTTCGAAAGTTCACCCAAGAACCA
AGAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACAAAAAGTTGTTTACAAAATGA
CAAATTATTTTGGACCAAAGGATGCGATTTCTCGAGAATGAAATGTTCGAAAAATTGCTTGAAGG
A
Found at i:2819 original size:24 final size:24
Alignment explanation
Indices: 2792--2837 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2782 TCTCTTATTA
*
2792 ATTTGCTCTAACATTTTATATTTC
1 ATTTGCACTAACATTTTATATTTC
*
2816 ATTTGCACTGACATTTTATATT
1 ATTTGCACTAACATTTTATATT
2838 CTTAACCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (24 bp):
ATTTGCACTAACATTTTATATTTC
Found at i:4221 original size:31 final size:31
Alignment explanation
Indices: 4183--4241 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
4173 TAGGCAAGGA
4183 AGTTACAGTCAACAGCAGCAGAATTATAGGG
1 AGTTACAGTCAACAGCAGCAGAATTATAGGG
4214 AGTTACAGTCAACAGCAGCAGAATTATA
1 AGTTACAGTCAACAGCAGCAGAATTATA
4242 ATCATCCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (31 bp):
AGTTACAGTCAACAGCAGCAGAATTATAGGG
Done.