Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002430.1 Kokia drynarioides strain JFW-HI SEQ_114537, 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: 3795
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Found at i:320 original size:62 final size:61
Alignment explanation
Indices: 168--357 Score: 193
Period size: 62 Copynumber: 3.0 Consensus size: 61
158 TCGTAAAAAG
* * *
168 TTTGACAAGTTC-AAATGTTCGTCCAAGAACCAAGAGAGAAACAACTCTTACATAGAAAAAGTT
1 TTTGACAAGTTCGAAA-GTTCGTCCAAGAACCAAGAGAGAAACAA-TCTCACGTA-AATAAGTT
** * * * * *
231 TTTGGTAGGCTCGAAAGTTCGTCCAAGAACTAAGAGAGAAGCAATACTCACGTTAATAAGTT
1 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAAT-CTCACGTAAATAAGTT
* * ** *
293 TTTGACAAGTTCGGAAGTTCGTCCAAGATCCAAGAGAGATCCAATTCTCATGTAAATAAGTT
1 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAA-TCTCACGTAAATAAGTT
355 TTT
1 TTT
358 ATTTCAATGA
Statistics
Matches: 103, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
62 60 0.58
63 40 0.39
64 3 0.03
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (61 bp):
TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATCTCACGTAAATAAGTT
Found at i:594 original size:62 final size:62
Alignment explanation
Indices: 509--694 Score: 300
Period size: 62 Copynumber: 3.0 Consensus size: 62
499 ATCGTAAAAG
*
509 TTTGAAAAGTTCGGATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
1 TTTGAAAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
* * *
571 TTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGACACAATTCTCACGTAAATAAGTT
1 TTTGAAAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
* * * *
633 TTTGATAAGTTCCGAAGTTTGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTT
1 TTTGAAAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
695 ATTAATTAAC
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 114 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (62 bp):
TTTGAAAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
Found at i:668 original size:340 final size:341
Alignment explanation
Indices: 1--913 Score: 1149
Period size: 340 Copynumber: 2.7 Consensus size: 341
* *
1 ACGTAAATAAGTTTTTAATTCAAAGACCAAAA-TAT-TTTTCAAAATGACAAATTATTTAGACCA
1 ACGTAAATAAGTTTTTAATTCAAAGACCAAAACT-TGTTTACAAAATGACAAAATATTTAGACCA
* * * *
64 AATGATTCGATTTCTCGAGCAAGGAATGTTTGGAAAATA--GCTCGAAGGAATGGATCGTCATGA
65 AATGATGCGATTTCTCGAGCATGGAATGCTT-GAAAATATTGCTCAAAGGAATGGATCGTCATGA
* * *
127 TTACCTTGAGGAACCGAAGTTATAAAAGAAATCGTAAAAAGTTTGACAAGTTCAAATGTTCGTCC
129 ATACTTTAAGGAACCGAAGTTATAAAAGAAATCGT-AAAAGTTTGACAAGTTCAAATGTTCGTCC
* * * * ** *
192 AAGAACCAAGAGAGAAACAACTCTTACATAGAAAAAGTTTTTGGTAGGCTCGAAAGTTCGTCCAA
193 AAGAACCAAGAGAGAAACAATTCTCACGTA-AATAAGTTTTTGACAAGCTCGAAAGTTCGTCCAA
* * * *
257 GAACTAAGAGAGAAGCAATACTCACGTTAATAAGTTTTTGACAAGTTCGGAAGTTCGTCCAAGAT
257 GAACCAAGAGAGAAGCAATACTCACGTAAATAAGTTTTTGACAAGTTCCGAAGTTCGTCCAAGAA
**
322 CCAAGAGAGATCCAATTCTC
322 CCAAGAGAGAAACAATTCTC
* * * * *
342 ATGTAAATAAGTTTTTATTTCAATGACCAAAACTTGTTTACAAAAGGACAAAATATTTAAACCAA
1 ACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAAATATTTAGACCAA
* * * * * * *
407 ATTATGCGATTTCCCGATCATGGAATG-GTCAAAATATTGCTCAAAGGAATGGATCCTCCTGAAT
66 ATGATGCGATTTCTCGAGCATGGAATGCTTGAAAATATTGCTCAAAGGAATGGATCGTCATGAAT
* * * * **
471 AGTTTCAGGAACCGAAGTTATAAGAGAAATCGTAAAAGTTTGAAAAGTTCGGATGTTCGTCCAAG
131 ACTTTAAGGAACCGAAGTTATAAAAGAAATCGTAAAAGTTTGACAAGTTCAAATGTTCGTCCAAG
* * *
536 AACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAGTTTGGAAGTTCGTCCAAGAAC
196 AACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAGCTCGAAAGTTCGTCCAAGAAC
* * *
601 CAAGAGAGACA-CAATTCTCACGTAAATAAGTTTTTGATAAGTTCCGAAGTTTGTCCAAGAACCA
261 CAAGAGAGA-AGCAATACTCACGTAAATAAGTTTTTGACAAGTTCCGAAGTTCGTCCAAGAACCA
665 AGAGAGAAACAATTCTC
325 AGAGAGAAACAATTCTC
* * * * * *
682 ACGTAACTAAGTTATTAATT-AACAGTCCAAAACTTGTTTACAAATTGACAAACTATTTTGACCA
1 ACGTAAATAAGTTTTTAATTCAA-AGACCAAAACTTGTTTACAAAATGACAAAATATTTAGACCA
* * * * *
746 GATGGTGTGATTTCTCGAGCATGGAATGCTTGGAAAT-TTGCTCAAAGGAATGGATCGTCTTGAA
65 AATGATGCGATTTCTCGAGCATGGAATGCTTGAAAATATTGCTCAAAGGAATGGATCGTCATGAA
* * * * *
810 TACTTTAAGGAACCTAAGTTATAAAAGAACTCGTGAAAGTTTGACAAGTTCAAAAGTTCATCCAA
130 TACTTTAAGGAACCGAAGTTATAAAAGAAATCGTAAAAGTTTGACAAGTTCAAATGTTCGTCCAA
*
875 GAACCGAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
195 GAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
914 AATTCAAACA
Statistics
Matches: 487, Mismatches: 78, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
339 2 0.00
340 296 0.61
341 90 0.18
342 99 0.20
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (341 bp):
ACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAAATATTTAGACCAA
ATGATGCGATTTCTCGAGCATGGAATGCTTGAAAATATTGCTCAAAGGAATGGATCGTCATGAAT
ACTTTAAGGAACCGAAGTTATAAAAGAAATCGTAAAAGTTTGACAAGTTCAAATGTTCGTCCAAG
AACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAGCTCGAAAGTTCGTCCAAGAAC
CAAGAGAGAAGCAATACTCACGTAAATAAGTTTTTGACAAGTTCCGAAGTTCGTCCAAGAACCAA
GAGAGAAACAATTCTC
Found at i:1030 original size:216 final size:216
Alignment explanation
Indices: 633--3312 Score: 1580
Period size: 216 Copynumber: 12.3 Consensus size: 216
623 TAAATAAGTT
* ** * * *
633 TTTGATAAGTTCCGAAGTTTGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTTATT
1 TTTGACAAGTTCAAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * * * * *
698 AATT--AACAGTCCAAAACTTGTTTACAAATTGACAAACTATTTTGACCAGATGGTGTGATTTCT
66 AATTCAAACA--CCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCA
* * *
761 CGAGCATGGAATGCTT-GGAAATTTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCT
129 CGAGCATGGAATG-TTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCG
*
825 AAGTTATAAAAGAACTCGTGAAAG
193 AAGTTATAAAAGAACTCGTAAAAG
* *
849 TTTGACAAGTTCAAAAGTTCATCCAAGAACCGAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
1 TTTGACAAGTTCAAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * *
914 AATTCAAACACCAAAACTTGTTTACAAACTGACAAACTATTTATACCAAATTATGCGATTTCACG
66 AATTCAAACACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCACG
* * * * * *
979 AGCATGGAATGTTCCAAAAATTGC-CTAAAGGAATAGATCATCTTAAATACTTTCAGGAACCGAG
131 AGCATGGAATGTTCGAAAAATTGCTC-AAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAA
* *
1043 GTTATGAAAGAAATCGTAAAAG
195 GTTATAAAAGAACTCGTAAAAG
* ** * * * *
1065 TTTGACGAGTTCGGATGTTCGTCCAAGAGCCAAGAGAGAAACAGTTCTTACGTAAATAAGTTTTT
1 TTTGACAAGTTCAAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * * *
1130 AATTCGAAA-ACCAAAACATGTTTACAAAATGACAAACTTTTTAGACCATACT-ATGCGATTTTA
66 AATTC-AAACACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCA-AATGATGCGATTTCA
* * * * * * *
1193 TGAGCACGGAGTGTTCGAAAAATT-CTCAAAGGAATGGATCGTCTTAAATACTGTAAGGCATCGA
129 CGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGA
* *
1257 AGTTATAAAAGATCTCATAAAAG
194 AGTTATAAAAGAACTCGTAAAAG
* * * *
1280 TTTGAGAAGTTCAAAAGTTCATCCAGGAACCAAGAGAAAAACAATTCTCACGTAAATAAGTTTTT
1 TTTGACAAGTTCAAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * * * * * *
1345 AATTGAAAGACCAAATCCTGTTTACATAATGACAAACTATTCAGACCAAATGATGCGAATTC-CT
66 AATTCAAACACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCAC-
* * * * * *
1409 GAGCATGGAAATCTTCGAAAAACTGCCCGAAGGAATGGATCGCCTTGAATACTTTAAGGAATCGA
130 GAGCATGG-AATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGA
*
1474 AGTTATAAAACAACTCGTAAAAG
194 AGTTATAAAAGAACTCGTAAAAG
* ** * ** * * * * *
1497 TTT-A-AATTGATCGGAAGTTCGTCTAAGAAAAAATAAAGAAACAGTTCTCATGTAAATATGTTT
1 TTTGACAA--GTTCAAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTT
* *
1560 TTAATTCAAAGACCAAAA-TAT-TTTTCAAAATGACAAACTATTTAGACCAAATGATGCGATTTC
64 TTAATTCAAACACCAAAACT-TGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTC
* * * * * * * * * *
1623 TCGAGCAAGGAATGTTCGGAAAATAGCTCGAAGGAATAGATTGTCATGAATACCTTCAGGAACCG
128 ACGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCG
*
1688 AAGTTATAAAAGAAATCGTAAAAAG
193 AAGTTATAAAAGAACTCGT-AAAAG
* **
1713 TTTGACAAGTTCAAATGTTCGTCCAAGAACC-A-AGAGTTAC-A---T-A---AAATAAGTTTTT
1 TTTGACAAGTTCAAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * * * * * * * * * * * * *
1768 GA--CAAGC-TCGAAAGTT-TGTCCAAGAACTAAGAGAGAAGCAATACT-CACGTAAAT-AAG-T
66 AATTCAAACACCAAAACTTGTTTACAA-AA-T--GACA-AA-CTAT-TTAGAC-CAAATGATGCG
* * * * ** * ** * *
1826 TTTTGACAAG-TTCGGAA-GTTCGTCCAAGTT-C-C-AAGAGAGATCCAATTC-TCACGTAAATA
123 ATTTCACGAGCAT-GGAATGTTCG-AAAAATTGCTCAAAG-GA-AT-GGA-TCGT--CTTGAAT-
* * * **
1885 AGTTTTTAATTCAGCAACCAAAACTTGTT-TACAAA-AAGAC--AAACTAG
179 A--CTTT-A---AGGAACC-GAA---GTTATA-AAAGAACTCGTAAA--AG
* * **** * * *** * * *
1932 TTAGATCAAATTGTGTGATTTC-T-C--GAGCGTGGA-ATGTTCAAAAAATTGCTCAAAG-GAAT
1 TTTGA-CAAGTT-CAAAAGTTCGTCCAAGAACCAAGAGA-G---AAACAATT-CTC-ACGTAAAT
* * * * * * * * *
1991 -GGATCCTCCTGAATAATTTCAGGA-ACC-GAAGTT-ATAAAAGAAATCGTA-AAA--GTTT-GA
58 AAG-T--T--T--TTAA-TTCA-AACACCAAAACTTGTTTACA-AAAT-G-ACAAACTATTTAGA
* ** * * * *** **
2048 --AAA-G-TACGGATGTT--CGTCCAAGAACCAAGAGAGAAACAATT-CTCACGTAAATAAGTTT
111 CCAAATGATGC-GAT-TTCACGAGCATGGA--ATGTTCGAAA-AATTGCTCA---AAGGAA----
* * ** * *
2106 TTGA-CAAGT-TTGGAATTTCGTCCAA-GAACC-AAG--AGAGAAACAATTCTCACGTAAATAAG
164 TGGATC--GTCTT-GAA-TAC-TTTAAGGAACCGAAGTTATA-AAAGAA--CT--CGT-AA-AAG
* ** * * * *
2165 TTTTCGATAAGTTCGGAAGTTAGTCCAAGAACCAAGAGAGAAACAATTCTCATGTAACTAAGTTA
1 -TTT-GACAAGTTCAAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTT
* ** * * * ** * *
2230 TTAATT-ATAGTCCAAAACTTGTTTACAAAATGACAAACTATTTTGACCAGATGGTTAGTTTTCT
64 TTAATTCAAACACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCA
* * * * *
2294 CGAGCATGGAAATGTTTGGAAATTTGCTCAAAGGAATGGATCGTCTTGAAAACTTTAAGGAACCT
129 CGAGCATGG-AATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCG
*
2359 AAGTTATAAAAGAACTCGTGAAAG
193 AAGTTATAAAAGAACTCGTAAAAG
* *
2383 TTTGACAAGTTCAAAAGTTCATCCAAGAACCGAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
1 TTTGACAAGTTCAAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * * *
2448 AATTCAAACACCAAAACTTGTTTACAAACTGACAAACTATTTATACCAAATTATGCGATTTCCCG
66 AATTCAAACACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCACG
* * * * *
2513 AGCATGGAATGTTCAAAAAATTGCCCGAAGGAATAGATCGTCTTGAATACTTTCAGGAACCGAAG
131 AGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAG
* * *
2578 TTATGAAAGAAATCATAAAAG
196 TTATAAAAGAACTCGTAAAAG
* ** * * * *
2599 TTTGACGAGTTCGGATGTTCGTCCAAGAGCCAAGAGAGAAACAGTTCTTACGTAAATAAGTTTTT
1 TTTGACAAGTTCAAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * ** * * ** *
2664 AATTCGAAA-AGCAAAACATGTTTATGAAATGACAAACTTTTTAGACCATACAATGCGATTTTAC
66 AATTC-AAACACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCAC
* * * * * **
2728 GAGCAAGGAGTGATCGAAAAATT-CTCGAAGGAATGGATCGTCTTGAATACTGTAAGGCGCCGAA
130 GAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAA
*
2792 GTTATAAAAGATCTCGTAAAAG
195 GTTATAAAAGAACTCGTAAAAG
* * * * * * *
2814 TTTGAGAAGTTCAGAAGTTCATCCAGGAACCAAGAGAAAAACAATTATCACATAAATAAGTTTTT
1 TTTGACAAGTTCAAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * * * * * *
2879 AATTGAAAGACCAAATCCTGTTTACAAAATGACAAACTAGTCAGACCAAATGATGCGATTTCTCG
66 AATTCAAACACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCACG
* * * * * **
2944 AGCATGGAAATCTTCGAAAAACTGCCCGAAGGAATGGATCGCCTTGAATACTTTAAGGAATTGAA
131 AGCATGG-AATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAA
*
3009 GTTATAAAACAACTCGTAAAAG
195 GTTATAAAAGAACTCGTAAAAG
* * * * * *
3031 TTT-AAAATGTTCGAAAGTTCGTCTAAGAACAAAAAGAGAAACAGTTCTCACGTAAATAAGTTTT
1 TTTGACAA-GTTCAAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
* * *
3095 TAATTCAAAGACCAAAA-TAT-TTTTCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCC
65 TAATTCAAACACCAAAACT-TGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCA
* * * * * * *
3158 CGAGGAAGGAATGTTCGAAAAATAGCTCGAAGGAATGGATCGTCATGAATACCTTCAGGAACCGA
129 CGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGA
*
3223 AGTTATAAAAGAAATCGTAAAATG
194 AGTTATAAAAGAACTCGTAAAA-G
* * * * *
3247 TTTGACAAGTTCACATGGTCGTCCAAGAACCAAGAGAGAAACAATTCTTACATAAAATAAGTTTT
1 TTTGACAAGTTCAAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGT-AAATAAGTTTT
3312 T
65 T
3313 GACAAGCTCG
Statistics
Matches: 1865, Mismatches: 444, Indels: 309
0.71 0.17 0.12
Matches are distributed among these distances:
203 10 0.01
204 6 0.00
205 4 0.00
206 15 0.01
207 11 0.01
208 17 0.01
209 9 0.00
210 11 0.01
211 1 0.00
213 2 0.00
214 13 0.01
215 448 0.24
216 730 0.39
217 327 0.18
218 12 0.01
219 10 0.01
220 14 0.01
221 12 0.01
222 9 0.00
223 9 0.00
224 12 0.01
225 10 0.01
226 14 0.01
227 13 0.01
228 6 0.00
229 1 0.00
230 16 0.01
231 19 0.01
232 16 0.01
233 23 0.01
234 19 0.01
235 5 0.00
236 2 0.00
237 14 0.01
238 7 0.00
239 4 0.00
240 12 0.01
241 2 0.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (216 bp):
TTTGACAAGTTCAAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
AATTCAAACACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCACG
AGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAG
TTATAAAAGAACTCGTAAAAG
Found at i:1832 original size:62 final size:62
Alignment explanation
Indices: 1756--1891 Score: 191
Period size: 62 Copynumber: 2.2 Consensus size: 62
1746 GAGTTACATA
* * *
1756 AAATAAGTTTTTGACAAGCTCGAAAGTTTGTCCAAGAACTAAGAGAGAAGCAATACTCACGT
1 AAATAAGTTTTTGACAAGCTCGAAAGTTCGTCCAAGAACCAAGAGAGAACCAATACTCACGT
* * ** * *
1818 AAATAAGTTTTTGACAAGTTCGGAAGTTCGTCCAAGTTCCAAGAGAGATCCAATTCTCACGT
1 AAATAAGTTTTTGACAAGCTCGAAAGTTCGTCCAAGAACCAAGAGAGAACCAATACTCACGT
1880 AAATAAGTTTTT
1 AAATAAGTTTTT
1892 AATTCAGCAA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (62 bp):
AAATAAGTTTTTGACAAGCTCGAAAGTTCGTCCAAGAACCAAGAGAGAACCAATACTCACGT
Found at i:2128 original size:62 final size:62
Alignment explanation
Indices: 2049--2228 Score: 279
Period size: 62 Copynumber: 2.9 Consensus size: 62
2039 AAAGTTTGAA
* * *
2049 AAGTACGGATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGAC
1 AAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTCGAC
* * *
2111 AAGTTTGGAATTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTCGAT
1 AAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTCGAC
* * *
2173 AAGTTCGGAAGTTAGTCCAAGAACCAAGAGAGAAACAATTCTCATGTAACTAAGTT
1 AAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
2229 ATTAATTATA
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 107 1.00
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (62 bp):
AAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTCGAC
Found at i:2193 original size:340 final size:339
Alignment explanation
Indices: 1533--2447 Score: 1108
Period size: 340 Copynumber: 2.7 Consensus size: 339
1523 GAAAAAATAA
* * *
1533 AGAAACAGTTCTCATGTAAATATGTTTTTAATTCAAAGACCAAAA-TAT-TTTTCAAAATGACAA
1 AGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGACCAAAACT-TGTTTACAAAATGACAA
* * * *
1596 ACTATTTAGACCAAA-TGATGCGATTTCTCGAGCAAGGAATGTTCGGAAAATAGCTCGAAGGAAT
65 ACTATTTAGACCAAATTG-TGTGATTTCTCGAGCATGGAATGTTCGGAAAATTGCTCAAAGGAAT
* * **
1660 AGATTGTCATGAATACCTTCAGGAACCGAAGTTATAAAAGAAATCGTAAAAAGTTTGACAAGTTC
129 GGATCGTCATGAATAATTTCAGGAACCGAAGTTATAAAAGAAATCGT-AAAAGTTTGACAAGTTC
**
1725 AAATGTTCGTCCAAGAACCA-AGAGTTAC-A---T-A---AAATAAGTTTTTGACAAGCTCGAAA
193 AAATGTTCGTCCAAGAACCAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAGCTCGAAA
* * *
1781 GTTTGTCCAAGAACTAAGAGAGAAGCAATACTCACGTAAATAAGTTTTTGACAAGTTCGGAAGTT
258 GTTTGTCCAAGAACCAAGAGAGAAACAATACTCACGTAAATAAGTTTTCGACAAGTTCGGAAGTT
* **
1846 CGTCCAAGTTCCAAGAG
323 AGTCCAAGAACCAAGAG
** * * *
1863 AGATCCAATTCTCACGTAAATAAGTTTTTAATTCAGCA-ACCAAAACTTGTTTACAAAAAGACAA
1 AGAAACAATTCTCATGTAAATAAGTTTTTAATTCA-AAGACCAAAACTTGTTTACAAAATGACAA
* * * **
1927 ACTAGTTAGATCAAATTGTGTGATTTCTCGAGCGTGGAATGTTCAAAAAATTGCTCAAAGGAATG
65 ACTATTTAGACCAAATTGTGTGATTTCTCGAGCATGGAATGTTCGGAAAATTGCTCAAAGGAATG
* * * * **
1992 GATCCTCCTGAATAATTTCAGGAACCGAAGTTATAAAAGAAATCGTAAAAGTTTGAAAAGTACGG
130 GATCGTCATGAATAATTTCAGGAACCGAAGTTATAAAAGAAATCGTAAAAGTTTGACAAGTTCAA
* * *
2057 ATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAGTTTGGAA-
195 ATGTTCGTCCAAGAACC-AGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAGCTCGAAAG
* *
2121 TTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTCGATAAGTTCGGAAGTT
259 TTT-GTCCAAGAACCAAGAGAGAAACAATACTCACGTAAATAAGTTTTCGACAAGTTCGGAAGTT
2186 AGTCCAAGAACCAAGAG
323 AGTCCAAGAACCAAGAG
* * * *
2203 AGAAACAATTCTCATGTAACTAAGTTATTAATT-ATAGTCCAAAACTTGTTTACAAAATGACAAA
1 AGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAA
* * * * * *
2267 CTATTTTGACCAGATGGT-TAGTTTTCTCGAGCATGGAAATGTTTGGAAATTTGCTCAAAGGAAT
66 CTATTTAGACCAAATTGTGT-GATTTCTCGAGCATGG-AATGTTCGGAAAATTGCTCAAAGGAAT
* * * * *
2331 GGATCGTCTTGAA-AACTTTAAGGAACCTAAGTTATAAAAGAACTCGTGAAAGTTTGACAAGTTC
129 GGATCGTCATGAATAA-TTTCAGGAACCGAAGTTATAAAAGAAATCGTAAAAGTTTGACAAGTTC
* *
2395 AAAAGTTCATCCAAGAACCGAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
193 AAATGTTCGTCCAAGAACC-AGAGAGAAACAATTCTCACGTAAATAAGTTTTT
2448 AATTCAAACA
Statistics
Matches: 494, Mismatches: 72, Indels: 28
0.83 0.12 0.05
Matches are distributed among these distances:
330 70 0.14
331 109 0.22
332 8 0.02
333 1 0.00
336 1 0.00
337 1 0.00
338 2 0.00
339 58 0.12
340 244 0.49
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (339 bp):
AGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAA
CTATTTAGACCAAATTGTGTGATTTCTCGAGCATGGAATGTTCGGAAAATTGCTCAAAGGAATGG
ATCGTCATGAATAATTTCAGGAACCGAAGTTATAAAAGAAATCGTAAAAGTTTGACAAGTTCAAA
TGTTCGTCCAAGAACCAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAGCTCGAAAGTT
TGTCCAAGAACCAAGAGAGAAACAATACTCACGTAAATAAGTTTTCGACAAGTTCGGAAGTTAGT
CCAAGAACCAAGAG
Found at i:3389 original size:62 final size:62
Alignment explanation
Indices: 3247--3436 Score: 254
Period size: 62 Copynumber: 3.0 Consensus size: 62
3237 TCGTAAAATG
* * * * *
3247 TTTGACAAGTTCACATGGTCGTCCAAGAACCAAGAGAGAAACAATTCTTACATAAAATAAGTT
1 TTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGT-AAATAAGTT
* * * * *
3310 TTTGACAAGCTCGGAAGTTCGTCCAAGAACTAAGAGAGAAGCAATACTCACGTAAATAAGTT
1 TTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
* * *
3372 TTTGACAAGTTCAGAAGTTCGTCCAAGATCCAAGAGAGAACCAATTCTCACGTAGATAAGTT
1 TTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
3434 TTT
1 TTT
3437 AATTGAGCAA
Statistics
Matches: 110, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
62 67 0.61
63 43 0.39
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (62 bp):
TTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
Found at i:3673 original size:62 final size:62
Alignment explanation
Indices: 3605--3773 Score: 250
Period size: 62 Copynumber: 2.7 Consensus size: 62
3595 GGTTCGGATG
3605 TTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAGTTTCG-AAA
1 TTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAG-TTCGTAAA
* * * * * * *
3667 TTCGTCCAAGAACCGAGAGAGAAACAGTTTTCACGTAAATATGTTTTTGATAAGTTCGTTAG
1 TTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAGTTCGTAAA
*
3729 TTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTT
1 TTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
3774 ATTAATTAAC
Statistics
Matches: 94, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
61 4 0.04
62 90 0.96
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (62 bp):
TTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAGTTCGTAAA
Found at i:3793 original size:340 final size:341
Alignment explanation
Indices: 3045--3795 Score: 1009
Period size: 340 Copynumber: 2.2 Consensus size: 341
3035 AAATGTTCGA
* * * *
3045 AAGTTCGTCTAAGAACAAAAAGAGAAACAGTTCTCACGTAAATAAGTTTTTAATTCAA-AGACCA
1 AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGT-AATAAGTTTTTAATTCAACAGACCA
* * *
3109 AAA-TATTTTTCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGGAAGGAATGTT
65 AAACT-TTTTACAAAAGGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCAAGGAATGTT
* * *
3173 CGAAAAATAGCTCGAAGGAATGGATCGTCATGAATACCTTCAGGAACCGAAGTTATAAAAGAAAT
129 CAAAAAATAGCTCAAAGGAATGGATCCTCATGAATACCTTCAGGAACCGAAGTTATAAAAGAAAT
*
3238 CGTAAAATGTTTGACAAGTTCACATGGTCGTCCAAGAACCAAGAGAGAAACAATTCTTACATAAA
194 CGTAAAATGTTTGACAAGTTCACATGGTCGTCCAAGAACCAAGAGAGAAACAATTCTCACATAAA
* * *
3303 ATAAGTTTTTGACAAGCTCGGAAGTTCGTCCAAGAACTAAGAGAGAAGCAATACTCACGTAAATA
259 ATAAGTTTTTGACAAGCTCGGAAATTCGTCCAAGAACCAAGAGAGAAACAATACTCACGTAAATA
3368 AGTTTTTGACAAGTTCAG
324 AGTTTTTGACAAGTTCAG
* * * *
3386 AAGTTCGTCCAAGATCCAAGAGAGAACCAATTCTCACGTAGATAAGTTTTTAATTGAGCA-ACCA
1 AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTA-ATAAGTTTTTAATTCAACAGACCA
* *
3450 AAACTTGTTTACAAAAGGACAAACTATTTAGACCAAATTATGCGATTTCCCGAGCATGGAATGTT
65 AAACTT-TTTACAAAAGGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCAAGGAATGTT
* * * *
3515 CAAAAAATTA-CTCAAATGAATGGATCCTCCTGAATACTTTCAGGAATCGAAGTTATAAAAGAAA
129 CAAAAAA-TAGCTCAAAGGAATGGATCCTCATGAATACCTTCAGGAACCGAAGTTATAAAAGAAA
** * *
3579 TCGTAAAA-GTTTGA-AAGGTTCGGATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGT-
193 TCGTAAAATGTTTGACAA-GTTCACATGGTCGTCCAAGAACCAAGAGAGAAACAATTCTCACATA
* * * **
3641 AAATAAGTTTTTGACAAGTTTC-GAAATTCGTCCAAGAACCGAGAGAGAAACAGTTTTCACGTAA
257 AAATAAGTTTTTGACAAG-CTCGGAAATTCGTCCAAGAACCAAGAGAGAAACAATACTCACGTAA
* *
3705 ATATGTTTTTGATAAGTTC-G
321 ATAAGTTTTTGACAAGTTCAG
* * *
3725 TTAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTTATTAATT-AACAGTCC
1 -AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAA-TAAGTTTTTAATTCAACAGACC
3789 AAAACTT
64 AAAACTT
Statistics
Matches: 359, Mismatches: 41, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
339 5 0.01
340 131 0.36
341 104 0.29
342 117 0.33
343 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.26
Consensus pattern (341 bp):
AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAATAAGTTTTTAATTCAACAGACCAA
AACTTTTTACAAAAGGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCAAGGAATGTTCA
AAAAATAGCTCAAAGGAATGGATCCTCATGAATACCTTCAGGAACCGAAGTTATAAAAGAAATCG
TAAAATGTTTGACAAGTTCACATGGTCGTCCAAGAACCAAGAGAGAAACAATTCTCACATAAAAT
AAGTTTTTGACAAGCTCGGAAATTCGTCCAAGAACCAAGAGAGAAACAATACTCACGTAAATAAG
TTTTTGACAAGTTCAG
Done.