Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398833.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2115.1, 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: 4007
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.33
Warning! 334 characters in sequence are not A, C, G, or T
Found at i:298 original size:171 final size:169
Alignment explanation
Indices: 168--3403 Score: 2678
Period size: 171 Copynumber: 18.9 Consensus size: 169
158 NNNNNNNNNN
* * *
168 ATTATAAAACCATTTAAAGTGAGTAATAAGCCTTTTGGAGGAATGAGAGACTATAATGGACTTTT
1 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAATGGACTTTT
* * * ** *
233 CTTACCAATGAATGCATTTTTCTTTACGTGTCTCAAGTTAGACATTCAATTATTGTCAGTTTTAA
66 CTTACCAATGAATGC-TTTTTCTTCACGTTTCTTAAGTTAGACATTCAATTATAATCTGTTTTAA
* * *
298 CCAAAAATGTAAAAAAATTAAACTTAAACTCAATTATGAA
130 CCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
* * * * *
338 ATTACAAAACTAATTAAAGCGAGTAATAAGGCTTCTGAAGAAAT-AG-GTATCTATAAATGGACT
1 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAG-A-CTAT-AATGGACT
* * * ********* **
401 TTCCTTACCAATAAATAGCTTTTTCTTCATGTTT-TTNNNNNNNNNNATTCAATTATAGCCTGTT
63 TTTCTTACCAATGAAT-GCTTTTTCTTCACGTTTCTT-AAGTTAGACATTCAATTATAATCTGTT
** *
465 TTAATAAAAAATGTAAAAAAAATTCAACTTCAAATCAATTATGAG
126 TTAACCAAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGAG
* * ** *
510 ATTA-CAAACCTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGCTATTATAATGGACTTT
1 ATTATAAAACC-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAATGGACTTT
* * * * * * * * * * *
574 TCCTACTAATGAATACTTTTTTCTTCATGTTTGTTGAGGTT-GATATTCATTTATAGTCTATTCT
65 TCTTACCAATGAATGC-TTTTTCTTCACGTTTCTT-AAGTTAGACATTCAATTATAATCTGTTTT
*
638 AAACAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
128 AACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
* * * * * * *
680 ATTACAAAACCATTTAAAGCGAGTAACAAAGCTTTTGAAGGAACGAGTGACAATAAATAGACTTT
1 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTAT-AATGGACTTT
** * ** * *
745 TCTTGGCAATAAATGTCTTTTTCTTCATATTTCTTAA-TGTAGATATTCAATTATAATCTATTTT
65 TCTTACCAATGAATG-CTTTTTCTTCACGTTTCTTAAGT-TAGACATTCAATTATAATCTGTTTT
* * * * *
809 AATCAAAGAA-GTAATAAACATTGAACTTATAATCAATTTTGAG
128 AACCAAA-AATGTAA-AAAAATTCAACTTAAAATCAATTATGAG
** * * *
852 ATTATAAAACCATTTAAAATGAGTAATAA-GCTTTTTGAAGGAATGGGAAACTATAATAGACTTT
1 ATTATAAAACCATTTAAAGCGAGTAATAAGGC-TTTTGAAGGAATGAGAGACTATAATGGACTTT
* * * * * * *
916 TCTTACCAATGAATACGTTTTCATCACGTTTCTTGAGTTAAACATTCAATTATTATCTGCTTTAA
65 TCTTACCAATGAATGCTTTTTCTTCACGTTTCTTAAGTTAGACATTCAATTATAATCTGTTTTAA
* * *
981 CCAAAAATATAAAAAAATTCAACTTAAACTCAATTATGAA
130 CCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
* * * * *
1021 ATTACAAAACTATTTAAAGCGAGTAATAAGGCTTCTGAAGGAAT-ATGTA-TCTATAAACGGACT
1 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA-G-AGACTAT-AATGGACT
* * ** * *
1084 TTTCTTACAAAT-AATAGCTTTTTCTTCACGGTTT-TTGAGACAGACATTCAATTATAGTATGTT
63 TTTCTTACCAATGAAT-GCTTTTTCTTCAC-GTTTCTTAAGTTAGACATTCAATTATAATCTGTT
* *
1147 TTAACCAAAAATTTTAAAAAAAAATTCAACTTGAAATCAATTATGAG
126 TTAACCAAAAA-TGT--AAAAAAATTCAACTTAAAATCAATTATGAG
* * * ** *
1194 ATTACAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGCTACTATAATAGACTTTT
1 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAATGGACTTTT
* * * * *
1259 -TCTACCAATGATTGCTTTTTTCTTCA-GATTTGC-TAAGGTAGACATTCATTTATAGTCTGTTA
66 CT-TACCAATGAATGC-TTTTTCTTCACG-TTT-CTTAAGTTAGACATTCAATTATAATCTGTTT
**
1321 TAAATAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
127 TAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
* * * * * *
1364 ATTATAAAACCATTTAAAGCAAATAACAAAGCTTTTGAAGGAATGAGTGA-TAATAAATAGACTT
1 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACT-AT-AATGGACTT
* * * * *
1428 TTATTGCCAATGAATGTCTTTTTCTTCACATTTCTT-ATTGTAGACATTCAATTATAATCTGATT
64 TTCTTACCAATGAATG-CTTTTTCTTCACGTTTCTTAAGT-TAGACATTCAATTATAATCTGTTT
* * * *
1492 TAACCAAAAAAGTAAAAAACATTGAACTTAAAATCAATTTTGTG
127 TAACCAAAAATGTAAAAAA-ATTCAACTTAAAATCAATTATGAG
* * * *
1536 ATTATAAAATCATTTAAAGTGAGTAATAAGCCTTTT-AGAGGAATGGGAGACTATAATGGACTTT
1 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGA-AGGAATGAGAGACTATAATGGACTTT
* * * * * *
1600 TCTTACTAATGGATACATTTTTCTTCACGTTTCTCAAGTTAGACATTCAATTATTATCCGTTTTA
65 TCTTACCAATGAATGC-TTTTTCTTCACGTTTCTTAAGTTAGACATTCAATTATAATCTGTTTTA
* *
1665 ACTAAAAATGTAAAAAAATTCAACTTAAACTCAATTATGAG
129 ACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
* * * * * * *
1706 ATT-TCAAAACTATTTAAATCGAGTAATAAGGCTTCTAAAGGAAT-AGATATCTGTAAATGAACT
1 ATTAT-AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGA-CTAT-AATGGACT
* * * * * ** * * * *
1769 TTTTTTATCAATAAATAGCTTTTTCTTCATGTTTTTTAAGACAAAGAATCAATTAT-AGCTTGTT
63 TTTCTTACCAATGAAT-GCTTTTTCTTCACGTTTCTTAAGTTAGACATTCAATTATAATC-TGTT
* * *
1833 TTAACCAAAAATGTAAAAAAAAATT-AACTTACAATCAATTGTAAG
126 TTAACCAAAAATGT--AAAAAAATTCAACTTAAAATCAATTATGAG
* * * * ** *
1878 ATTACAAAACCATTTAAAGCGAGTAATAAGGTTTTTGAAGAAATGGGCTACTATAATAGACTTTT
1 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAATGGACTTTT
* * ** * * * * *
1943 CCTACCAATGAATGCTTTTTTCTTCATGTTTCTCGAGGTAGACATTTATTTATAGTCTGTTATAA
66 CTTACCAATGAATGC-TTTTTCTTCACGTTTCTTAAGTTAGACATTCAATTATAATCTGTTTTAA
* *
2008 ACAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAG
130 CCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
* * * * * * * *
2048 ATTATAAAACTATTTAAAGCAAATAACAAAGCTTTTGAAGGAATGAGTGACAATAAATAGACTTT
1 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTAT-AATGGACTTT
* * * *
2113 CCTTACCAATGAATACCTTTTTCTTCACATTTCTTAA-TGTAGACATTCAATTATAATCTATTTT
65 TCTTACCAATGAAT-GCTTTTTCTTCACGTTTCTTAAGT-TAGACATTCAATTATAATCTGTTTT
* *
2177 AACCAAAGAA-GTAAAAAACATTGAACTTAAAATCAATTTTGAG
128 AACCAAA-AATGTAAAAAA-ATTCAACTTAAAATCAATTATGAG
* * * * *
2220 ATTATAAAATCATTTAAAGTGAGTAATAAGTCTTTTGGAGGAATGGGAGACTATAATGGACTTTT
1 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAATGGACTTTT
* * * *
2285 CTTACCAATGAATGTGTTTTTCTTCACGTTTCTCAAGTTAGACATTCAATTATTATCTATTTTAA
66 CTTACCAATGAATG-CTTTTTCTTCACGTTTCTTAAGTTAGACATTCAATTATAATCTGTTTTAA
* *
2350 CTAAAAATGTAAAAAAATTCAACTTAAACTCAATTATGAG
130 CCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
* *
2390 ATTACAAAACCATTTAAAGCGAGTAATAAGGCTTATGAAGGAAT-AG-GTATCTATAAATGGACT
1 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAG-A-CTAT-AATGGACT
* * * * * * ** * * **
2453 TTTTTTATCAATAAATAGCTTTTTCTTCACTTTTTTTGAGACAGATATTAAATTATAGCCTGTTT
63 TTTCTTACCAATGAAT-GCTTTTTCTTCACGTTTCTTAAGTTAGACATTCAATTATAATCTGTTT
* * *
2518 TAACTAAAAAGGTAAAAAAAATTTAACTTAAAATCAATTATGAG
127 TAACCAAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGAG
* * * * * * *
2562 ATTA-CAAACCTTTTAAAGTGAGTAATAAGGGTTTTGAAGGAATGGGTGACTTTAATGGACTTTT
1 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAATGGACTTTT
* * * ** * * * * * * *
2626 CCTACCAATGAATGATTTTTTCTTCATGTTTCTCGAGGTAAAAACTCATTTATAGTCTGTTATAA
66 CTTACCAATGAATG-CTTTTTCTTCACGTTTCTTAAGTTAGACATTCAATTATAATCTGTTTTAA
** *
2691 ATAAAAATGTAAACAAAATT-AACCTTCAAATCAATTATGAG
130 CCAAAAATGTAAA-AAAATTCAA-CTTAAAATCAATTATGAG
* * * *
2732 ATTAGAAAACCATTTAAAGCGAGTAATAA-GCTTTTTTG-AGAAATGGGTGACTATAAT-GAGCT
1 ATTATAAAACCATTTAAAGCGAGTAATAAGGC--TTTTGAAGGAATGAGAGACTATAATGGA-CT
* * * ** * * *
2794 TTTCTTACTAATGAAAGCATTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATTATCTATTT
63 TTTCTTACCAATGAATGC-TTTTTCTTCACGTTTCTTAAGTTAGACATTCAATTATAATCTGTTT
** * *
2859 TAATTAAAAATGTAAAAAAAAAT-AACTTAAACTCAATTATGAG
127 TAACCAAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGAG
* * * * * *
2902 ATTCTAAAACTATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATAAGTGACTATAAATGGGCTTT
1 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTAT-AATGGACTTT
* * * ** * * *
2967 T-TTTCTCAATGAATGGCTTTTTCTACATGTTTCCCAAGGTA-AGCATTCAATTATAGTTTGTTT
65 TCTTAC-CAATGAAT-GCTTTTTCTTCACGTTTCTTAAGTTAGA-CATTCAATTATAATCTGTTT
* * * * *
3030 TAACGAAAAATAT-AAGAAATTGAACTTAAAATCAATTGTGAG
127 TAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
* * * *
3072 ATGT-TAAAACCAATTAAAGCGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGA-TT
1 AT-TATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTAT-AATGGACTT
* * * * * ** *
3135 TTCCTTACTAATGAATGCTTGTTTCCTCATGTTTCTTAGGATAGACATTCAATTATGGTCTATTT
64 TT-CTTACCAATGAATGCTT-TTTCTTCACGTTTCTTAAGTTAGACATTCAATTATAATCTGTTT
* * * *
3200 TAACTAAAAATATAAAAAAAATT-AACTTAAAATTAATTATAAG
127 TAACCAAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGAG
* * * * * * * * * *
3243 AATATAAAACTATTTAAACCAAGTAATAAGGCTTTTGAAGGAATGGGTGGCAATAAATAGATTTT
1 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTAT-AATGGACTTT
* * * * * ** ** * * *
3308 TCTTGCCAATGATTTCCTTTTTCTCCACATTTCTCGACATAGATATTTAATTATAATCTATTTTA
65 TCTTACCAATGA-ATGCTTTTTCTTCACGTTTCTTAAGTTAGACATTCAATTATAATCTGTTTTA
* * **
3373 ATCAAAAAAGTAAAAAATATTGGACTTAAAA
129 ACCAAAAATGTAAAAAA-ATTCAACTTAAAA
3404 NNNNNNNNNN
Statistics
Matches: 2478, Mismatches: 481, Indels: 212
0.78 0.15 0.07
Matches are distributed among these distances:
168 2 0.00
169 113 0.05
170 761 0.31
171 1050 0.42
172 418 0.17
173 134 0.05
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (169 bp):
ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAATGGACTTTT
CTTACCAATGAATGCTTTTTCTTCACGTTTCTTAAGTTAGACATTCAATTATAATCTGTTTTAAC
CAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
Found at i:1314 original size:684 final size:680
Alignment explanation
Indices: 7--3289 Score: 4060
Period size: 684 Copynumber: 4.8 Consensus size: 680
1 GATACT
* *
7 ATTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGAGTGACAATAAATAGATTTTTCTTGCCAATG
1 ATTTAAAGCGAGTAACAAAGCTTTTGAAGGAATGAGTGACAATAAATAGACTTTTCTTGCCAATG
********** * * *
72 AATGCCTTTTTNNNNNNNNNNCTCAATGTAAACATTCAATTATAATCTTTTTTAACCAAAGAAGT
66 AATGCCTTTTTCTTCACATTTCTTAATGTAGACATTCAATTATAATCTATTTTAACCAAAGAAGT
**********
137 AAAAAACATTGAACTTAAAATNNNNNNNNNNATTATAAAACCATTTAAAGTGAGTAATAAGCCTT
131 AAAAAACATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGCCTT
* * * *
202 TTGGAGGAATGAGAGACTATAATGGACTTTTCTTACCAATGAATGCATTTTTCTTTACGTGTCTC
196 TTGAAGGAATGGGAGACTATAATGGACTTTTCTTACCAATGAATGC-TTTTTCTTCACGTTTCTC
* * *
267 AAGTTAGACATTCAATTATTGTCAGTTTTAACCAAAAATGTAAAAAAATTAAACTTAAACTCAAT
260 AAGTTAGACATTCAATTATTATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAACTCAAT
* * *
332 TATGAAATTACAAAACTAATTAAAGCGAGTAATAAGGCTTCTGAAGAAATAGGTATCTATAAATG
325 TATGAGATTACAAAACTATTTAAAGCGAGTAATAAGGCTTCTGAAGGAATAGGTATCTATAAATG
* ********* *
397 GACTTTCCTTACCAATAAATAGCTTTTTCTTCATGTTTTTNNNNNNNNNNATTCAATTATAGCCT
390 GACTTTTCTTA-CAATAAATAGCTTTTTCTTCATGTTTTT-GAGACAGACATTCAATTATAGTCT
* *
462 GTTTTAA-TAAAAAATGTAAAAAAAATTCAACTTCAAATCAATTATGAGATTACAAACCTATTTA
453 GTTTTAACT-AAAAATGTAAAAAAAATT-AACTTAAAATCAATTATGAGATTACAAAACTATTTA
* * * *
526 AAGCGAGTAATAAGGCTTTTGAAGGAATGGGCTATTATAATGGACTTTTCCTACTAATGAATACT
516 AAGCGAGTAATAAGGCTTTTGAAGGAATGGGCTACTATAATAGACTTTTCCTACCAATGAATGCT
* * * * * *
591 TTTTTCTTCATGTTTGTTGAGGTTGATATTCATTTATAGTCTATTCTAAACAAAAATGTAAAAAA
581 TTTTTCTTCATGTTTCTCGAGGTAGACATTCATTTATAGTCTGTTATAAACAAAAATGTAAAAAA
*
656 ATTCAACTTAAAATCAATTATGAGATTACAAAACC
646 ATTCAACTTAAAATCAATTATGAGATTATAAAACC
* * *
691 ATTTAAAGCGAGTAACAAAGCTTTTGAAGGAACGAGTGACAATAAATAGACTTTTCTTGGCAATA
1 ATTTAAAGCGAGTAACAAAGCTTTTGAAGGAATGAGTGACAATAAATAGACTTTTCTTGCCAATG
* * * *
756 AATGTCTTTTTCTTCATATTTCTTAATGTAGATATTCAATTATAATCTATTTTAATCAAAGAAGT
66 AATGCCTTTTTCTTCACATTTCTTAATGTAGACATTCAATTATAATCTATTTTAACCAAAGAAGT
* * * *
821 AATAAACATTGAACTTATAATCAATTTTGAGATTATAAAACCATTTAAAATGAGTAATAAGCTTT
131 AAAAAACATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGCCTT
* * * * * **
886 TTGAAGGAATGGGAAACTATAATAGACTTTTCTTACCAATGAATACGTTTTCATCACGTTTCTTG
196 TTGAAGGAATGGGAGACTATAATGGACTTTTCTTACCAATGAATGCTTTTTCTTCACGTTTCTCA
* * *
951 AGTTAAACATTCAATTATTATCTGCTTTAACCAAAAATATAAAAAAATTCAACTTAAACTCAATT
261 AGTTAGACATTCAATTATTATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAACTCAATT
* * *
1016 ATGAAATTACAAAACTATTTAAAGCGAGTAATAAGGCTTCTGAAGGAATATGTATCTATAAACGG
326 ATGAGATTACAAAACTATTTAAAGCGAGTAATAAGGCTTCTGAAGGAATAGGTATCTATAAATGG
* *
1081 ACTTTTCTTACAA-ATAATAGCTTTTTCTTCACGGTTTTTGAGACAGACATTCAATTATAGTATG
391 ACTTTTCTTACAATA-AATAGCTTTTTCTTCA-TGTTTTTGAGACAGACATTCAATTATAGTCTG
* * *
1145 TTTTAACCAAAAATTTTAAAAAAAAATTCAACTTGAAATCAATTATGAGATTACAAAACTATTTA
454 TTTTAACTAAAAA-TGT-AAAAAAAATT-AACTTAAAATCAATTATGAGATTACAAAACTATTTA
* *
1210 AAGCGAGTAATAAGGCTTTTGAAGGAATGGGCTACTATAATAGACTTTTTCTACCAATGATTGCT
516 AAGCGAGTAATAAGGCTTTTGAAGGAATGGGCTACTATAATAGACTTTTCCTACCAATGAATGCT
* *
1275 TTTTTCTTCA-GATTTGCT-AAGGTAGACATTCATTTATAGTCTGTTATAAATAAAAATGTAAAA
581 TTTTTCTTCATG-TTT-CTCGAGGTAGACATTCATTTATAGTCTGTTATAAACAAAAATGTAAAA
1338 AAATTCAACTTAAAATCAATTATGAGATTATAAAACC
644 AAATTCAACTTAAAATCAATTATGAGATTATAAAACC
* * * *
1375 ATTTAAAGCAAATAACAAAGCTTTTGAAGGAATGAGTGATAATAAATAGACTTTTATTGCCAATG
1 ATTTAAAGCGAGTAACAAAGCTTTTGAAGGAATGAGTGACAATAAATAGACTTTTCTTGCCAATG
* * *
1440 AATGTCTTTTTCTTCACATTTCTTATTGTAGACATTCAATTATAATCTGA-TTTAACCAAAAAAG
66 AATGCCTTTTTCTTCACATTTCTTAATGTAGACATTCAATTATAATCT-ATTTTAACCAAAGAAG
* *
1504 TAAAAAACATTGAACTTAAAATCAATTTTGTGATTATAAAATCATTTAAAGTGAGTAATAAGCCT
130 TAAAAAACATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGCCT
* * *
1569 TTT-AGAGGAATGGGAGACTATAATGGACTTTTCTTACTAATGGATACATTTTTCTTCACGTTTC
195 TTTGA-AGGAATGGGAGACTATAATGGACTTTTCTTACCAATGAATGC-TTTTTCTTCACGTTTC
* *
1633 TCAAGTTAGACATTCAATTATTATCCGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAACTCA
258 TCAAGTTAGACATTCAATTATTATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAACTCA
* * * * *
1698 ATTATGAGATTTCAAAACTATTTAAATCGAGTAATAAGGCTTCTAAAGGAATAGATATCTGTAAA
323 ATTATGAGATTACAAAACTATTTAAAGCGAGTAATAAGGCTTCTGAAGGAATAGGTATCTATAAA
* * * * * *
1763 TGAACTTTTTTTATCAATAAATAGCTTTTTCTTCATGTTTTTTAAGACAAAGAATCAATTATAG-
388 TGGACTTTTCTTA-CAATAAATAGCTTTTTCTTCATG-TTTTTGAGACAGACATTCAATTATAGT
* * * * *
1827 CTTGTTTTAACCAAAAATGTAAAAAAAAATTAACTTACAATCAATTGTAAGATTACAAAACCATT
451 C-TGTTTTAACTAAAAATGT-AAAAAAAATTAACTTAAAATCAATTATGAGATTACAAAACTATT
* *
1892 TAAAGCGAGTAATAAGGTTTTTGAAGAAATGGGCTACTATAATAGACTTTTCCTACCAATGAATG
514 TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGCTACTATAATAGACTTTTCCTACCAATGAATG
*
1957 CTTTTTTCTTCATGTTTCTCGAGGTAGACATTTATTTATAGTCTGTTATAAACAAAAATGTAAAA
579 CTTTTTTCTTCATGTTTCTCGAGGTAGACATTCATTTATAGTCTGTTATAAACAAAAATGTAAAA
* *
2022 AAATTTAACTTAAAATCAATTATGAGATTATAAAACT
644 AAATTCAACTTAAAATCAATTATGAGATTATAAAACC
* * * *
2059 ATTTAAAGCAAATAACAAAGCTTTTGAAGGAATGAGTGACAATAAATAGACTTTCCTTACCAATG
1 ATTTAAAGCGAGTAACAAAGCTTTTGAAGGAATGAGTGACAATAAATAGACTTTTCTTGCCAATG
*
2124 AATACCTTTTTCTTCACATTTCTTAATGTAGACATTCAATTATAATCTATTTTAACCAAAGAAGT
66 AATGCCTTTTTCTTCACATTTCTTAATGTAGACATTCAATTATAATCTATTTTAACCAAAGAAGT
* *
2189 AAAAAACATTGAACTTAAAATCAATTTTGAGATTATAAAATCATTTAAAGTGAGTAATAAGTCTT
131 AAAAAACATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGCCTT
* *
2254 TTGGAGGAATGGGAGACTATAATGGACTTTTCTTACCAATGAATGTGTTTTTCTTCACGTTTCTC
196 TTGAAGGAATGGGAGACTATAATGGACTTTTCTTACCAATGAATG-CTTTTTCTTCACGTTTCTC
* *
2319 AAGTTAGACATTCAATTATTATCTATTTTAACTAAAAATGTAAAAAAATTCAACTTAAACTCAAT
260 AAGTTAGACATTCAATTATTATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAACTCAAT
* *
2384 TATGAGATTACAAAACCATTTAAAGCGAGTAATAAGGCTTATGAAGGAATAGGTATCTATAAATG
325 TATGAGATTACAAAACTATTTAAAGCGAGTAATAAGGCTTCTGAAGGAATAGGTATCTATAAATG
* * * * *
2449 GACTTTTTTTATCAATAAATAGCTTTTTCTTCACTTTTTTTGAGACAGATATTAAATTATAGCCT
390 GACTTTTCTTA-CAATAAATAGCTTTTTCTTCA-TGTTTTTGAGACAGACATTCAATTATAGTCT
* *
2514 GTTTTAACTAAAAAGGTAAAAAAAATTTAACTTAAAATCAATTATGAGATTACAAACCT-TTTAA
453 GTTTTAACTAAAAATGTAAAAAAAA-TTAACTTAAAATCAATTATGAGATTACAAAACTATTTAA
* * * * *
2578 AGTGAGTAATAAGGGTTTTGAAGGAATGGG-TGACTTTAATGGACTTTTCCTACCAATGAATGAT
517 AGCGAGTAATAAGGCTTTTGAAGGAATGGGCT-ACTATAATAGACTTTTCCTACCAATGAATGCT
* * * *
2642 TTTTTCTTCATGTTTCTCGAGGTAAAAACTCATTTATAGTCTGTTATAAATAAAAATGTAAACAA
581 TTTTTCTTCATGTTTCTCGAGGTAGACATTCATTTATAGTCTGTTATAAACAAAAATGTAAA-AA
* *
2707 AATT-AACCTTCAAATCAATTATGAGATTAGAAAACC
645 AATTCAA-CTTAAAATCAATTATGAGATTATAAAACC
* * * * * *
2743 ATTTAAAGCGAGTAA-TAAGCTTTTTTG-AGAAATGGGTGACTAT-AAT-GAGCTTTTCTTACTA
1 ATTTAAAGCGAGTAACAAAGC--TTTTGAAGGAATGAGTGACAATAAATAGA-CTTTTCTTGCCA
* * ** ** * * **
2804 ATGAAAGCATTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATTATCTATTTTAATTAAA-A
63 ATGAATGCCTTTTTCTTCACATTTCTTAATGTAGACATTCAATTATAATCTATTTTAACCAAAGA
* * * * * * **
2868 ATGTAAAAAAAAAT-AACTTAAACTCAATTATGAGATTCTAAAACTATTTAAAGCAAGTAATAAG
128 A-GTAAAAAACATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAG
* ** * * * * *
2932 GCTTTTGAAGGAATAAGTGACTATAAATGGGCTTTT-TTTCTCAATGAATGGCTTTTTCTACATG
192 CCTTTTGAAGGAATGGGAGACTAT-AATGGACTTTTCTTAC-CAATGAAT-GCTTTTTCTTCACG
* * * * * * *
2996 TTTCCCAAGGTA-AGCATTCAATTA-TAGTTTGTTTTAACGAAAAATAT-AAGAAATTGAACTTA
254 TTTCTCAAGTTAGA-CATTCAATTATTA-TCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTA
* * * * * * * *
3058 AAATCAATTGTGAGATGT-TAAAACCAATTAAAGCGAGTAATAAAGCTTTTGAAGGAATGGGTGA
317 AACTCAATTATGAGAT-TACAAAACTATTTAAAGCGAGTAATAAGGCTTCTGAAGGAATAGGT-A
* * *
3122 -CTATAAATGGA-TTTTCCTTACTAATGAAT-GCTTGTTTCCTCATGTTTCTT-AGGATAGACAT
380 TCTATAAATGGACTTTT-CTTAC-AATAAATAGCTT-TTTCTTCATGTTT-TTGA-GACAGACAT
* * * * * * *
3183 TCAATTATGGTCTATTTTAACTAAAAATATAAAAAAAATTAACTTAAAATTAATTATAAGAATAT
440 TCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAAATTAACTTAAAATCAATTATGAGATTAC
* *
3248 AAAACTATTTAAACCAAGTAATAAGGCTTTTGAAGGAATGGG
505 AAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGG
3290 TGGCAATAAA
Statistics
Matches: 2282, Mismatches: 275, Indels: 86
0.86 0.10 0.03
Matches are distributed among these distances:
681 43 0.02
682 282 0.12
683 428 0.19
684 1308 0.57
685 164 0.07
686 56 0.02
687 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (680 bp):
ATTTAAAGCGAGTAACAAAGCTTTTGAAGGAATGAGTGACAATAAATAGACTTTTCTTGCCAATG
AATGCCTTTTTCTTCACATTTCTTAATGTAGACATTCAATTATAATCTATTTTAACCAAAGAAGT
AAAAAACATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGCCTT
TTGAAGGAATGGGAGACTATAATGGACTTTTCTTACCAATGAATGCTTTTTCTTCACGTTTCTCA
AGTTAGACATTCAATTATTATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAACTCAATT
ATGAGATTACAAAACTATTTAAAGCGAGTAATAAGGCTTCTGAAGGAATAGGTATCTATAAATGG
ACTTTTCTTACAATAAATAGCTTTTTCTTCATGTTTTTGAGACAGACATTCAATTATAGTCTGTT
TTAACTAAAAATGTAAAAAAAATTAACTTAAAATCAATTATGAGATTACAAAACTATTTAAAGCG
AGTAATAAGGCTTTTGAAGGAATGGGCTACTATAATAGACTTTTCCTACCAATGAATGCTTTTTT
CTTCATGTTTCTCGAGGTAGACATTCATTTATAGTCTGTTATAAACAAAAATGTAAAAAAATTCA
ACTTAAAATCAATTATGAGATTATAAAACC
Found at i:2466 original size:21 final size:20
Alignment explanation
Indices: 2437--2476 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2427 AAGGAATAGG
* *
2437 TATCTATAAATGGACTTTTTT
1 TATCAATAAATAG-CTTTTTT
2458 TATCAATAAATAGCTTTTT
1 TATCAATAAATAGCTTTTT
2477 CTTCACTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (20 bp):
TATCAATAAATAGCTTTTTT
Done.