Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397894.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_120.0, 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: 3869
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.29
Warning! 714 characters in sequence are not A, C, G, or T
Found at i:389 original size:172 final size:171
Alignment explanation
Indices: 1--390 Score: 453
Period size: 172 Copynumber: 2.3 Consensus size: 171
* * * **
1 CAACTTAAAATCAATTATGAGGTTATAAAACCATTTAAAGCGAGTAATAAAGCTCTTGGAGGCTT
1 CAACTTAAAATCAATTATGAGATTATAAAACTATTTAAA-CGAGTAATAAAGCTCTTGAAGGAAT
* ** * **
66 GGGTGACTATAAATAGGATTTTCTTTCTTATGAATGGGTTTTTTTTTTACGTTTCTCGAGGCAAA
65 GGGTGACTATAAATAGGATTTTCTTGCCAATGAATGGGTTTTTTCTCCACGTTTCTCGAGGCAAA
**
131 CATTCAATTATAATATGTTTTAACCAAAAATGTATGAAAATT
130 CATTCAATTATAATATGTTTTAACCAAAAATGTAAAAAAATT
* * * *
173 CAACCTAAAATCAATTATGAGATTATAAAACTATATAGAACGAGTAATAAGGCTTTTGAAGGAAT
1 CAACTTAAAATCAATTATGAGATTATAAAACTATTTA-AACGAGTAATAAAGCTCTTGAAGGAAT
* * * *
238 GGGTGACTAT-AATTGGACTTTTCTTGCCAATGGATGGG-TTTTTCTCCATGTTTCTTGAGGCAA
65 GGGTGACTATAAATAGGA-TTTTCTTGCCAATGAATGGGTTTTTTCTCCACGTTTCTCGAGGCAA
* * * *
301 ATATTCAATTATAGTCTGTTTTAA-TAAAAAGTGTAAAAAAAATT
129 ACATTCAATTATAATATGTTTTAACCAAAAA-TGT-AAAAAAATT
* * *
345 TAACTTAAAATCAATTATGATATCATAAAACTATTTGAAACGAGTA
1 CAACTTAAAATCAATTATGAGATTATAAAACTATTT-AAACGAGTA
391 NNNNNNNNNN
Statistics
Matches: 183, Mismatches: 30, Indels: 10
0.82 0.13 0.04
Matches are distributed among these distances:
170 5 0.03
171 50 0.27
172 125 0.68
173 3 0.02
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (171 bp):
CAACTTAAAATCAATTATGAGATTATAAAACTATTTAAACGAGTAATAAAGCTCTTGAAGGAATG
GGTGACTATAAATAGGATTTTCTTGCCAATGAATGGGTTTTTTCTCCACGTTTCTCGAGGCAAAC
ATTCAATTATAATATGTTTTAACCAAAAATGTAAAAAAATT
Found at i:1139 original size:171 final size:170
Alignment explanation
Indices: 875--1645 Score: 715
Period size: 171 Copynumber: 4.5 Consensus size: 170
865 TTTCTCAAAA
875 CAAACATTCAATTATAATCTGTTTTAACCAAAAAATGTAAAAAACATTCAACTTAAAATCAATTA
1 CAAACATTCAATTATAATCTGTTTTAACC-AAAAATGTAAAAAA-ATTCAACTTAAAATCAATTA
* * * * ** ** * *
940 TGAGTTTACAAAACCATTTAAAGTGAGTAATAGGGCTTTCCAAGGTTTGGGTGACTATAAGTGGG
64 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATGGA
** * *
1005 CTTTTCTTGCCAATGAACAAGTTTTTCTTTACATTTCCTGAGG
129 CTTTTCTTGCCAATGAA-TGGTTTTTCTTCACATTTCCTAAGG
* * * *
1048 CAAACACTCAATTATAATATGTTTTAACCATAAATGTAAAAAAATTTAACTTAAAATCAATTATG
1 CAAACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATG
* * * * *
1113 AGATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAATTGGACT
66 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATGGACT
* * * * *
1178 TTTATTGCCAATGGATGGCTTTTTCTT-AAAGTTTTCTAAGA
131 TTTCTTGCCAATGAATGG-TTTTTCTTCACA-TTTCCTAAGG
* * * *
1219 CAAGCTTTCAATTATAATCTGTTTTAACTAAAAATTCATTTTAAAAAAAAAGTT-AACTTAAAAT
1 CAAACATTCAATTATAATCTGTTTTAAC-CAAAA---A-TGT--AAAAAAA-TTCAACTTAAAAT
* * * * *
1283 CAATTATGAGGTTATAAAACCATTTAAAGCGAGTAATAAGGGTTTTGAAGGCTTCGATGA-TAAT
58 CAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACT-AT
* * * * ** * *
1347 AAATGGGCTTTTCTTGTCAATGAATAGCTTTTTCTCCATGTTTCTTGAGG
122 AAATGGACTTTTCTTGCCAATGAAT-GGTTTTTCTTCACATTTCCTAAGG
* * * * * * *
1397 TAAACATTTAATTATAATATGTTTTAATCAAAAATGAAAAAAAATT-AATTTAAAATTAATTATG
1 CAAACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATG
* ** * *
1461 AGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTAAAAGGCTTGGGTGACTATAAATGGGCT
66 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATGGACT
* * * * * * * *
1526 TCTCTTACCAATG-ATCAAGATTTTCTTTACGTTTCTTGAGG
131 TTTCTTGCCAATGAAT--GGTTTTTCTTCACATTTCCTAAGG
* ** * * *
1567 CAAACATTCAATTATAATCTATTTTAATAAAAAATGTAAGAAAATTCAACCTAAAATCGATTATG
1 CAAACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATG
1632 AGATTATAAAACCA
66 AGATTATAAAACCA
1646 CATAAAACAA
Statistics
Matches: 494, Mismatches: 88, Indels: 34
0.80 0.14 0.06
Matches are distributed among these distances:
169 2 0.00
170 145 0.29
171 165 0.33
172 16 0.03
173 28 0.06
174 1 0.00
175 1 0.00
176 2 0.00
177 5 0.01
178 125 0.25
179 4 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (170 bp):
CAAACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATG
AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATGGACT
TTTCTTGCCAATGAATGGTTTTTCTTCACATTTCCTAAGG
Found at i:2036 original size:171 final size:171
Alignment explanation
Indices: 1660--2673 Score: 907
Period size: 171 Copynumber: 6.0 Consensus size: 171
1650 AAACAAGCAA
* * * * * * *
1660 TGGGTGACCATAATTGGACTTTTCTTGCCAATAAATGGGTTTTTGTTCA-AGTTTTCTAAGGTAA
1 TGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATA-TTTTCCAAGGCAA
* * * *
1724 ACATTCAATTATAATATGTTTTAACCAAAAACGTA-AAAGAATTCAATTTAAAATCAATTTTGAG
65 ACATTCAATTATAATCTGTTTTAACCAAAAAC-TATAAAAAATTCAACTTAAAATCAATTATGAG
* * *
1788 CTTATACAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGG-T
129 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCT
* * * *
1830 ATAGGTGGCTATAAATGGACCTTTCTTACCAATGAATGGCTTTTTCTTCATATTTTCCAAGGCAA
1 -TGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATATTTTCCAAGGCAA
* * * * *
1895 ACACTCAATTATAATCTTTTTTAA-TAAAAACTATAAAAATATTTAACTTAAAATCAATTATAAG
65 ACATTCAATTATAATCTGTTTTAACCAAAAACTATAAAAA-ATTCAACTTAAAATCAATTATGAG
* * * *
1959 ATTATAAAACCATTTGAAGCGAGTAATAAAGATTTCAAAGGCT
129 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCT
** * * * ***
2002 TAAGTGACTAGAAATGCACTTTTCTTGGCAATGAATTGG-TTTTTCTTCATATTTTTTGAGGCAA
1 TGGGTGACTATAAATGGACTTTTCTTGCCAATGAA-TGGCTTTTTCTTCATATTTTCCAAGGCAA
* * * *
2066 ACATTCAATTATAATCTGTTTTAACCAAAAA-TGTTAAAAAACTCAACTTAAAATTAATTTTGAG
65 ACATTCAATTATAATCTGTTTTAACCAAAAACT-ATAAAAAATTCAACTTAAAATCAATTATGAG
* * * * * *
2130 GTTATAAAGA-TATTTAAAACGAGTAATAAGGCTTTTGAAGACA
129 ATTATAAA-ACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCT
* * * * * * * *
2173 TGGGTGACTAT-AATAGGACTTTTTTTACTAATGAATGCCTTTTTCATCATGTTTTCTAAGGCAG
1 TGGGTGACTATAAAT-GGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATATTTTCCAAGGCAA
* * *
2237 ACATTCAATTATAATCTGCTTTAA--AAAAA-TGTAAAAAATTTC-ACTGAAAATCAATTATGAG
65 ACATTCAATTATAATCTGTTTTAACCAAAAACTATAAAAAA-TTCAACTTAAAATCAATTATGAG
* * ** * *
2298 ATT-TAAAATCATTTAAAGCAAGTACCAAGGCTTTCGAAAGCA
129 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCT
* ** ** * * *
2340 TGTGTGACTATAAATAAACTTTTCTTGTTAATGAATGGTTTTTTCTTCACA-TTTCACAAGGTAG
1 TGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATATTTTC-CAAGGCA-
* * * *
2404 AA-AGTT-TATTATAATCTTTTTTAACCAAAAATCTA-AACAAATTCAACCTAAAATCAATTATG
64 AACA-TTCAATTATAATCTGTTTTAACCAAAAA-CTATAAAAAATTCAACTTAAAATCAATTATG
* * * *
2466 AGAATATAAAACCATTTAAAGTGAGTAACAAGGCTTTCGAATG-T
127 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCT
* * * * * * * * *
2510 ATGGGTAACTATAAATGGGCTTTTCTAGCCAATAAATGGTTTTTTGTTCATGTTTCCCAAAGCAA
1 -TGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATATTTTCCAAGGCAA
* * * *
2575 ACATTCAATTATAATCTATTTTAA-CAAAAAATGTAAACAAATTCAACCTAAAATCAATTATGA-
65 ACATTCAATTATAATCTGTTTTAACCAAAAACTATAAA-AAATTCAACTTAAAATCAATTATGAG
* *
2638 AGTTATAAAACAATTTAAAGTGAGTAATAAGGCTTT
129 A-TTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
2674 TAAAGGTTTG
Statistics
Matches: 678, Mismatches: 136, Indels: 58
0.78 0.16 0.07
Matches are distributed among these distances:
166 5 0.01
167 86 0.13
168 31 0.05
169 19 0.03
170 52 0.08
171 465 0.69
172 20 0.03
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.36
Consensus pattern (171 bp):
TGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATATTTTCCAAGGCAAA
CATTCAATTATAATCTGTTTTAACCAAAAACTATAAAAAATTCAACTTAAAATCAATTATGAGAT
TATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCT
Found at i:2476 original size:509 final size:504
Alignment explanation
Indices: 847--2676 Score: 1699
Period size: 509 Copynumber: 3.6 Consensus size: 504
837 GGTAACAACA
* * *** * *
847 AATGGGTTTTTCTTCATGTTTCTCAAAACAAACATTCAATTATAATCTGTTTTAACCAAAAAATG
1 AATGGCTTTTTCTTCATATTTC-CAAGGTAAACATT-TATTATAATCTGTTTTAACC-AAAAATC
* * * *
912 TAAAAAACATTCAACTTAAAATCAATTATGAGTTTACAAAACCATTTAAAGTGAGTAATAGGGCT
63 TAAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT
* * * * *
977 TTCCAAGGTTTGGGTGACTATAAGTGGGCTTTTCTTGCCAATGAACAAGTTTTTCTTTACATTTC
128 TTCAAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCCAATGAATAAGTTTTTCTTCACATTTC
* * * * * * *
1042 CTGAGGCAAACACTCAATTATAATATGTTTTAACCATAAATGTAAAAAAATTTAACTTAAAATCA
193 CTGAGGCAAACATTCAATTATAATCTATTTTAACAAAAAATGT-AAAAAATTCAACCTAAAATCA
* **
1107 ATTATGAGATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGA-ATGGGTGACTATAA
257 ATTATGAGATTATAAAA-CATTTAAAACGAGTAATAAGGCTTTT-AA-GACATGGGTGACTATAA
* * * *
1171 TTGGACTTTTATTGCCAATGGATGGCTTTTTCTTAAAGTTTTCTAAGACAAGCTTTCAATTATAA
319 TTGGACTTTTATTGCCAATGAATGGCTTTTTCTTCAAGTTTTCTAAGGCAA-CATTCAATTATAA
* * *
1236 TCTGTTTTAACTAAAAATTCATTTTAAAAAAAAAGTTAACTTAAAATCAATTATGAGGTTATAAA
383 TCTGTTTT-A--AAAAA---A-TGT---AAAAAA-TTCACTTAAAATCAATTATGAGATTATAAA
* *
1301 ACCATTTAAAGCGAGTAATAAGGGTTTTGAAGGC-T-TCGATGA-TAATAAATGGGCTTTTCTTG
437 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGT-G-TGACT-ATAAATGGACTTTTCTTG
1363 TCAATG
499 TCAATG
* * * ** * * *
1369 AATAGCTTTTTCTCCATGTTTCTTGAGGTAAACATTTAATTATAATATGTTTTAATCAAAAAT-G
1 AATGGCTTTTTCTTCATATTTC-CAAGGTAAACATTT-ATTATAATCTGTTTTAACCAAAAATCT
* * * *
1433 AAAAAAAATT-AATTTAAAATTAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTT
64 AAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT
* * * * * *
1497 TAAAAGGCTTGGGTGACTATAAATGGGCTTCTCTTACCAATG-ATCAAGATTTTCTTTACGTTTC
129 TCAAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCCAATGAAT-AAGTTTTTCTTCACATTTC
* * *
1561 TTGAGGCAAACATTCAATTATAATCTATTTTAATAAAAAATGTAAGAAAATTCAACCTAAAATCG
193 CTGAGGCAAACATTCAATTATAATCTATTTTAACAAAAAATGTAA-AAAATTCAACCTAAAATCA
* *
1626 ATTATGAGATTATAAAAC------CAC-A-TAA-AA--C----AAG-CAATGGGTGACCATAATT
257 ATTATGAGATTATAAAACATTTAAAACGAGTAATAAGGCTTTTAAGAC-ATGGGTGACTATAATT
* * * * * *
1675 GGACTTTTCTTGCCAATAAATGGGTTTTTGTTCAAGTTTTCTAAGGTAAACATTCAATTATAATA
321 GGACTTTTATTGCCAATGAATGGCTTTTTCTTCAAGTTTTCTAAGG-CAACATTCAATTATAATC
* * * * *
1740 TGTTTTAACCAAAAACGTAAAAGAATTCAATTTAAAATCAATTTTGAGCTTATACAACCATTTAA
385 TGTTTTAA--AAAAATGTAAAA-AATTC-ACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* * * **
1805 AGCGAGTAATAAGGCTTTTGAAGGTATAG-GTGGCTATAAATGGACCTTTCTTACCAATG
446 AGCGAGTAATAAGGCTTTTGAAGGCAT-GTGTGACTATAAATGGACTTTTCTTGTCAATG
* ** * *
1864 AATGGCTTTTTCTTCATATTTTCCAAGGCAAACACTCAATTATAATCTTTTTTAA-TAAAAA-CT
1 AATGGCTTTTTCTTCATA-TTTCCAAGGTAAACA-TTTATTATAATCTGTTTTAACCAAAAATCT
* * * * * *
1927 ATAAAAATATTTAACTTAAAATCAATTATAAGATTATAAAACCATTTGAAGCGAGTAATAAAGAT
64 A-AAAAACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT
** * ** * ** * *
1992 TTCAAAGGCTTAAGTGACTAGAAATGCACTTTTCTTGGCAATGAATTGGTTTTTCTTCATATTTT
128 TTCAAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCCAATGAATAAGTTTTTCTTCACATTTC
* * * * * *
2057 TTGAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAATGTTAAAAAACTCAACTTAAAATTA
193 CTGAGGCAAACATTCAATTATAATCTATTTTAACAAAAAATG-TAAAAAATTCAACCTAAAATCA
* * *
2122 ATTTTGAGGTTATAAAGATATTTAAAACGAGTAATAAGGCTTTTGAAGACATGGGTGACTATAAT
257 ATTATGAGATTATAAA-ACATTTAAAACGAGTAATAAGGCTTTT-AAGACATGGGTGACTATAAT
* * * * * * *
2187 AGGACTTTTTTTACTAATGAATGCCTTTTTCATCATGTTTTCTAAGGCAGACATTCAATTATAAT
320 TGGACTTTTATTGCCAATGAATGGCTTTTTCTTCAAGTTTTCTAAGGCA-ACATTCAATTATAAT
* * *
2252 CTGCTTTAAAAAAATGTAAAAAATTTCACTGAAAATCAATTATGAGATT-TAAAATCATTTAAAG
384 CTGTTTTAAAAAAATGTAAAAAA-TTCACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* ** * * ** *
2316 CAAGTACCAAGGCTTTCGAAAGCATGTGTGACTATAAATAAACTTTTCTTGTTAATG
448 CGAGTAATAAGGCTTTTGAAGGCATGTGTGACTATAAATGGACTTTTCTTGTCAATG
* * *
2373 AATGGTTTTTTCTTCACATTTCACAAGGTAGAA-AGTTTATTATAATCTTTTTTAACCAAAAATC
1 AATGGCTTTTTCTTCATATTTC-CAAGGTA-AACA-TTTATTATAATCTGTTTTAACCAAAAATC
* * * * *
2437 TAAACAA-ATTCAACCTAAAATCAATTATGAGAATATAAAACCATTTAAAGTGAGTAACAAGGCT
63 TAAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT
* * * * * * * **
2501 TTCGAATG-TATGGGTAACTATAAATGGGCTTTTCTAGCCAATAAAT-GGTTTTTTGTTCATGTT
128 TTCAAAGGCT-TGGGTGACTATAAATGGGCTTTTCTTGCCAATGAATAAG-TTTTTCTTCACATT
** *
2564 TCCCAAAGCAAACATTCAATTATAATCTATTTTAACAAAAAATGTAAACAAATTCAACCTAAAAT
191 TCCTGAGGCAAACATTCAATTATAATCTATTTTAACAAAAAATGTAAA-AAATTCAACCTAAAAT
**
2629 CAATTATGA-AGTTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTAA
255 CAATTATGAGA-TTATAAAAC-ATTTAAAACGAGTAATAAGGCTTTTAA
2677 AGGTTTGGGC
Statistics
Matches: 1063, Mismatches: 194, Indels: 116
0.77 0.14 0.08
Matches are distributed among these distances:
494 12 0.01
495 125 0.12
496 168 0.16
497 7 0.01
498 1 0.00
499 1 0.00
501 6 0.01
502 75 0.07
503 4 0.00
504 1 0.00
505 3 0.00
506 2 0.00
507 1 0.00
508 16 0.02
509 279 0.26
510 34 0.03
511 18 0.02
512 1 0.00
513 76 0.07
514 1 0.00
518 4 0.00
519 168 0.16
520 9 0.01
521 6 0.01
522 45 0.04
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (504 bp):
AATGGCTTTTTCTTCATATTTCCAAGGTAAACATTTATTATAATCTGTTTTAACCAAAAATCTAA
AAAACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTC
AAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCCAATGAATAAGTTTTTCTTCACATTTCCTG
AGGCAAACATTCAATTATAATCTATTTTAACAAAAAATGTAAAAAATTCAACCTAAAATCAATTA
TGAGATTATAAAACATTTAAAACGAGTAATAAGGCTTTTAAGACATGGGTGACTATAATTGGACT
TTTATTGCCAATGAATGGCTTTTTCTTCAAGTTTTCTAAGGCAACATTCAATTATAATCTGTTTT
AAAAAAATGTAAAAAATTCACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
AAGGCTTTTGAAGGCATGTGTGACTATAAATGGACTTTTCTTGTCAATG
Found at i:2485 original size:338 final size:335
Alignment explanation
Indices: 847--2657 Score: 1198
Period size: 342 Copynumber: 5.3 Consensus size: 335
837 GGTAACAACA
* ** *
847 AATGGGTTTTTCTTCATG-TTTCTCAAAACAAACATTCAATTATAATCTGTTTTAACCAAAAAAT
1 AATGGCTTTTTCTTCATGTTTTC-CAAGGCAAACATTCAATTATAATCTATTTT-A--AAAAAAT
* * * ** * ** *
911 GTAAAAAACATTCAACTTAAAATCAATTATGAGTTTACAAAACCATTTAAAGTGAGTAATAGGGC
62 GTAAAAAA-TTTC-AC-TAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAACAAAGA
* ** ** * * *** * *** *
976 TTTCCAAGGTTTGGGTGACTATAAGTGGGCTTTTCTTGCCAATGAACAAGTTTTTCTTTACATTT
124 TTTCAAAGGCATAAGTGACTAGAAATAAACTTTTCTTGGCAATGAATTGGTTTTTCTTCACATTT
* * * * * *
1041 C-CTGAGGCAAACACTCAATTATAATATGTTTTAACCATAAATGTAAAAAAATTTAACTTAAAAT
189 CAC-AAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAATCT-AAAAAATTCAACTTAAAAT
* * * * *
1105 CAATTATGAGATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATA
252 CAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA-GTATGGGTGACTATA
* *
1170 ATTGGACTTTTATTGCCAATG
316 AATGGACTTTT-TTACCAATG
* * * * * * * *
1191 GATGGCTTTTTCTTAAAGTTTTCTAAGACAAGCTTTCAATTATAATCTGTTTTAACTAAAAATTC
1 AATGGCTTTTTCTTCATGTTTTCCAAGGCAAACATTCAATTATAATCTATTTT-A--AAAAA---
* * * * * *
1256 ATTTTAAAAAAAAAGTTAACTTAAAATCAATTATGAGGTTATAAAACCATTTAAAGCGAGTAATA
60 A-TGT---AAAAAATTTCAC-TAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAACA
* * ** ** * *** * * * *
1321 AGGGTTTTGAAGGC-TTCGATGA-TAATAAATGGGCTTTTCTTGTCAATGAATAGCTTTTTCTCC
120 AAGATTTCAAAGGCATAAG-TGACT-AGAAATAAACTTTTCTTGGCAATGAATTGGTTTTTCTTC
** *** * * * * ** *
1384 ATGTTTCTTGAGGTAAACATTTAATTATAATATGTTTTAATCAAAAATGAAAAAAAATT-AATTT
183 ACATTTCACAAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAAT-CTAAAAAATTCAACTT
* * * **
1448 AAAATTAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTAAAAGGCT-TGGGTG
247 AAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA-G-TATGGGTG
* *
1512 ACTATAAATGGGCTTCTCTTACCAATG
310 ACTATAAATGGACTT-TTTTACCAATG
* * * * **
1539 -ATCAAG-ATTTTCTTTACG-TTTCTTGAGGCAAACATTCAATTATAATCTATTTTAATAAAAAA
1 AAT--GGCTTTTTCTTCATGTTTTC-CAAGGCAAACATTCAATTATAATCTATTTT-A-AAAAAA
* * *
1601 TGTAAGAAAA-TTCAACCTAAAATCGATTATGAGATTATAAAACC----ACA-TAA--AAC-AAG
61 TGTAA-AAAATTTC-A-CTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAACAAAG
* * * * ** * * * *
1657 ----CAATGG-----GTGACCATAATTGGACTTTTCTTGCCAATAAATGGGTTTTTGTTCA-AGT
123 ATTTCAAAGGCATAAGTGACTAGAAATAAACTTTTCTTGGCAATGAATTGGTTTTTCTTCACA--
* * * *
1712 TTTC-TAAGGTAAACATTCAATTATAATATGTTTTAACCAAAAA-CGTAAAAGAATTCAATTTAA
186 TTTCACAAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAATC-TAAAA-AATTCAACTTAA
* * * *
1775 AATCAATTTTGAGCTTATACAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGGCT
249 AATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA-GTATGGGTGACT
*
1840 ATAAATGGACCTTTCTTACCAATG
313 ATAAATGGA-CTTTTTTACCAATG
* * * *
1864 AATGGCTTTTTCTTCATATTTTCCAAGGCAAACACTCAATTATAATCTTTTTTAATAAAAACTAT
1 AATGGCTTTTTCTTCATGTTTTCCAAGGCAAACATTCAATTATAATCTATTTTAA-AAAAA-TGT
* * * * *
1929 AAAAATATTTAACTTAAAATCAATTATAAGATTATAAAACCATTTGAAGCGAGTAATAAAGATTT
64 AAAAA-ATTTCAC-TAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAACAAAGATTT
* ** * ***
1994 CAAAGGCTTAAGTGACTAGAAATGCACTTTTCTTGGCAATGAATTGGTTTTTCTTCATATTTTTT
127 CAAAGGCATAAGTGACTAGAAATAAACTTTTCTTGGCAATGAATTGGTTTTTCTTCACATTTCAC
* * * *
2059 GAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAATGTTAAAAAACTCAACTTAAAATTAAT
192 AAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAAT-CTAAAAAATTCAACTTAAAATCAAT
* * * *
2124 TTTGAGGTTATAAAGA-TATTTAAAACGAGTAATAAGGCTTTTGAAGACATGGGTGACTAT-AAT
256 TTTGAGATTATAAA-ACCATTTAAAGCGAGTAATAAGGCTTTTGAAG-TATGGGTGACTATAAAT
*
2187 AGGACTTTTTTTACTAATG
319 -GGAC-TTTTTTACCAATG
* * * * **
2206 AATGCCTTTTTCATCATGTTTTCTAAGGCAGACATTCAATTATAATCTGCTTTAAAAAAATGTAA
1 AATGGCTTTTTCTTCATGTTTTCCAAGGCAAACATTCAATTATAATCTATTTTAAAAAAATGTAA
* * * *
2271 AAAATTTCACTGAAAATCAATTATGAGATT-TAAAATCATTTAAAGCAAGTACCAAGGCTTTCGA
66 AAAATTTCACT-AAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAACAAAGATTTC-A
** * **
2335 AA-GCATGTGTGACTATAAATAAACTTTTCTTGTTAATGAA-TGGTTTTTTCTTCACATTTCACA
129 AAGGCATAAGTGACTAGAAATAAACTTTTCTTGGCAATGAATTGG-TTTTTCTTCACATTTCACA
* * * *
2398 AGGTAGAA-AGTT-TATTATAATCTTTTTTAACCAAAAATCTAAACAAATTCAACCTAAAATCAA
193 AGGCA-AACA-TTCAATTATAATCTGTTTTAACCAAAAATCTAAA-AAATTCAACTTAAAATCAA
* * * * * *
2461 TTATGAGAATATAAAACCATTTAAAGTGAGTAACAAGGCTTTCGAATGTATGGGTAACTATAAAT
255 TTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA-GTATGGGTGACTATAAAT
* * *
2526 GGGCTTTTCTAGCCAATA
319 GGACTTTTTTA-CCAATG
* * * *
2544 AATGGTTTTTTGTTCATGTTTCCCAAAGCAAACATTCAATTATAATCTATTTTAACAAAAAATGT
1 AATGGCTTTTTCTTCATGTTTTCCAAGGCAAACATTCAATTATAATCTATTTT-A-AAAAAATGT
*
2609 AAACAAA-TTCAACCTAAAATCAATTATGA-AGTTATAAAACAATTTAAAG
64 AAA-AAATTTC-A-CTAAAATCAATTATGAGA-TTATAAAACCATTTAAAG
2658 TGAGTAATAA
Statistics
Matches: 1185, Mismatches: 204, Indels: 158
0.77 0.13 0.10
Matches are distributed among these distances:
323 5 0.00
324 87 0.07
325 150 0.13
326 11 0.01
329 4 0.00
330 1 0.00
332 2 0.00
333 5 0.00
334 2 0.00
336 1 0.00
337 21 0.02
338 212 0.18
339 35 0.03
340 27 0.02
341 63 0.05
342 216 0.18
343 9 0.01
344 49 0.04
345 4 0.00
347 13 0.01
348 123 0.10
349 137 0.12
350 2 0.00
351 6 0.01
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (335 bp):
AATGGCTTTTTCTTCATGTTTTCCAAGGCAAACATTCAATTATAATCTATTTTAAAAAAATGTAA
AAAATTTCACTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAACAAAGATTTCAAA
GGCATAAGTGACTAGAAATAAACTTTTCTTGGCAATGAATTGGTTTTTCTTCACATTTCACAAGG
CAAACATTCAATTATAATCTGTTTTAACCAAAAATCTAAAAAATTCAACTTAAAATCAATTTTGA
GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGTATGGGTGACTATAAATGGACTTT
TTTACCAATG
Found at i:2732 original size:151 final size:150
Alignment explanation
Indices: 2541--2836 Score: 396
Period size: 151 Copynumber: 2.0 Consensus size: 150
2531 TTTCTAGCCA
* *
2541 ATAAATGGTTTTTTGTTCATGTTTCCCAAAGCAAACATTCAATTATAATCTATTTTAACAAAAAA
1 ATAAATGGTTTTTTGTTCACGTCTCCCAAAGCAAACATTCAATTATAATCTATTTTAACAAAAAA
* * *
2606 TGTAAACAAATTCAACCTAAAATCAATTATGAAG-TTATAAAACAATTTAAAGTGAGTAATAAGG
66 AGTAAAAAAATTCAACCTAAAATCAATTAT-AAGATTATAAAACAATTTAAAGCGAGTAATAAGG
* *
2670 CTTTTAAAGGTTTGGGCGAAC
130 CTTTCAAAGGCTTGGGCGAAC
* * * * * * * *
2691 ATAAATGGGTTTTTTTTTCACGTCTCTCAAGGTAAATATTCAATTATAGTCTGTTTTAATAAAAA
1 ATAAAT-GGTTTTTTGTTCACGTCTCCCAAAGCAAACATTCAATTATAATCTATTTTAACAAAAA
** * *
2756 AAGTAAAAAAATTCAATTTAAAATCAATTATAAGATTATAAAGCCATTTAAAGCGAGTAATAAGG
65 AAGTAAAAAAATTCAACCTAAAATCAATTATAAGATTATAAAACAATTTAAAGCGAGTAATAAGG
2821 CTTTCAAAGGCTTGGG
130 CTTTCAAAGGCTTGGG
2837 TGACTATATA
Statistics
Matches: 125, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
150 9 0.07
151 116 0.93
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (150 bp):
ATAAATGGTTTTTTGTTCACGTCTCCCAAAGCAAACATTCAATTATAATCTATTTTAACAAAAAA
AGTAAAAAAATTCAACCTAAAATCAATTATAAGATTATAAAACAATTTAAAGCGAGTAATAAGGC
TTTCAAAGGCTTGGGCGAAC
Done.