Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403141.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_808.0, 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: 24322
ACGTcount: A:0.22, C:0.07, G:0.08, T:0.22
Warning! 9969 characters in sequence are not A, C, G, or T
Found at i:8633 original size:171 final size:171
Alignment explanation
Indices: 8422--8758 Score: 426
Period size: 171 Copynumber: 2.0 Consensus size: 171
8412 ATTAAGGTTT
*
8422 TTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATTAATTATGAGATGATAAGACCATTTAAAG
1 TTTTAACCAAAAATGTAAAAAAATACAACTTAAAATTAATTATGAGATGATAAGACCATTTAAAG
* * * * **
8487 CATGTAATAAGGCTTTTGAAGAAATACGTGACTATAAATAGACTTT-TCTTACCAATGAATTTCT
66 CAAGCAATAAGGCTTTCGAAGAAATACGTGACTATAAATAGAATTTGT-TTACCAATGAATGCCT
*
8551 TTTTATTCATATTTCTCGAGGTAAACATTCAATTATAATCTG
130 TTTTATTCATATTTCTCGAGATAAACATTCAATTATAATCTG
* **********
8593 TTTTAACTAAAAATG-ATAAAAAATACAACTTAAAATTAATTATGAGATNNNNNNNNNNTTTAAA
1 TTTTAACCAAAAATGTA-AAAAAATACAACTTAAAATTAATTATGAGATGATAAGACCATTTAAA
* **
8657 GCAAGCAATAAGGCTTTCGAAGGAATGGGTGACTATAAATAGAATTTGTTTACCAATGAATGCCT
65 GCAAGCAATAAGGCTTTCGAAGAAATACGTGACTATAAATAGAATTTGTTTACCAATGAATGCCT
* *
8722 TTTTCTTCATGTTTCTCGAGATAAACATTCAATTATA
130 TTTTATTCATATTTCTCGAGATAAACATTCAATTATA
8759 NNNNNNNNNN
Statistics
Matches: 140, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
170 1 0.01
171 138 0.99
172 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.34
Consensus pattern (171 bp):
TTTTAACCAAAAATGTAAAAAAATACAACTTAAAATTAATTATGAGATGATAAGACCATTTAAAG
CAAGCAATAAGGCTTTCGAAGAAATACGTGACTATAAATAGAATTTGTTTACCAATGAATGCCTT
TTTATTCATATTTCTCGAGATAAACATTCAATTATAATCTG
Found at i:9263 original size:171 final size:171
Alignment explanation
Indices: 9016--9653 Score: 585
Period size: 171 Copynumber: 3.7 Consensus size: 171
9006 NNNNNNNGAG
* * * * *
9016 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGAAATAGGTGACAATAAATAGACTTT
1 ATTATAAAACCATTTAAAGCAAGCAATAAGGCTTTTGAAGAAATACGTGACTATAAATAGACTTT
* * * * * * *
9081 TCTTGTCAATGAATGCCTTTTTATTCATGTTCCCCAAGGTAGACATTTAATTATAGTCTGTTTTA
66 TCTTCTCAATGAATGACTTTTTATACATGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTTA
*
9146 ACAAAAAATGTTAAAAAATCTAACTTAAAATCAATTATTAT
131 ACAAAAAATGTTAAAAAATCTAACTTAAAATCAATTATGAT
* * * *
9187 ATTATGAAACAATTTAAAGCAAGCAATAAGGCTTTTGAAGGAATGA-GTGACTATAAATATACTT
1 ATTATAAAACCATTTAAAGCAAGCAATAAGGCTTTTGAAGAAAT-ACGTGACTATAAATAGACTT
* * *
9251 TCCTTCTCAATGAATGACTTTTT-TCACATGTTTCTCGAGGCA-AGCATTCAATTATTGTCTGTT
65 TTCTTCTCAATGAATGACTTTTTAT-ACATGTTTCTCAAGGCAGA-CATTCAATTATAGTCTGTT
*** * * *
9314 TTAGTGAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAG
128 TTAACAAAAAATGTTAAAAAATCTAACTTAAAATCAATTATGAT
********** * * ** *
9358 ANNNNNNNNNNATTTAATA-CGAGCAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGGCTT
1 ATTATAAAACCATTTAA-AGCAAGCAATAAGGCTTTTGAAGAAATACGTGACTATAAATAGACTT
* * * * * * *
9422 TTCTTCTAAATGAATAACTTTTTCTACACG-TT-TCAAGATGCAGACATTTAATTATAGTTTATT
65 TTCTTCTCAATGAATGACTTTTTATACATGTTTCTCAAG--GCAGACATTCAATTATAGTCTGTT
* *
9485 TTAACCAAAAATG-TAAAAAATCTCAACTAAAAATCAATTATGAGT
128 TTAACAAAAAATGTTAAAAAATCT-AACTTAAAATCAATTATGA-T
* * * *
9530 -TGATAAAACCATTTAAAGCATGTAATAAGGCTGTTGAA-AACATACGTGACTATAAATAGACTT
1 ATTATAAAACCATTTAAAGCAAGCAATAAGGCTTTTGAAGAA-ATACGTGACTATAAATAGACTT
* * * * *
9593 TTCTTAC-CAATGAATGCCTTTTTATTCATGTTTCTCGAGGTAAACATTCAATTATAGTCTG
65 TTCTT-CTCAATGAATGACTTTTTATACATGTTTCTCAAGGCAGACATTCAATTATAGTCTG
9654 NNNNNNNNNN
Statistics
Matches: 366, Mismatches: 85, Indels: 32
0.76 0.18 0.07
Matches are distributed among these distances:
169 4 0.01
170 14 0.04
171 337 0.92
172 7 0.02
173 4 0.01
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (171 bp):
ATTATAAAACCATTTAAAGCAAGCAATAAGGCTTTTGAAGAAATACGTGACTATAAATAGACTTT
TCTTCTCAATGAATGACTTTTTATACATGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTTA
ACAAAAAATGTTAAAAAATCTAACTTAAAATCAATTATGAT
Found at i:9497 original size:342 final size:331
Alignment explanation
Indices: 9027--9653 Score: 712
Period size: 342 Copynumber: 1.9 Consensus size: 331
9017 TTATAAAACC
* * *
9027 ATTTAAAGCGAGTAATAAGGCTTTTAAAGAAATAGGTGACAATAAATAGACTTTTCTTGTCAATG
1 ATTTAAAGCGAGCAATAAGGCTTTTAAAGAAATAGGTGACAATAAATAGACTTTTCTTCTAAATG
** * * * *
9092 AATGCCTTTTTATTCATGTTCCCCAAGGTAGACATTTAATTATAGTCTGTTTTAACAAAAAATGT
66 AATAACTTTTTATACACGTT-CCCAAGGCAGACATTTAATTATAGTCTATTTTAACAAAAAATG-
* * * *
9157 TAAAAAATCT-AACTTAAAATCAATTATTA-TATTATGAAACAATTTAAAGCAAGCAATAAGGCT
129 TAAAAAATCTCAACTAAAAATCAATTATGAGT-TGATAAAACAATTTAAAGCAAGCAATAAGGCT
* * *
9220 TTTGAAGGA-ATGA-GTGACTATAAATATACTTTCCTT-CTCAATGAATGACTTTTT-TCACATG
193 GTTGAA-AACAT-ACGTGACTATAAATAGACTTTCCTTAC-CAATGAATGACTTTTTAT-ACATG
* *
9281 TTTCTCGAGGCAAGCATTCAATTATTGTCTGTTTTAGTGAAAAATGTAAAAAAATTTAACTTAAA
254 TTTCTCGAGGCAAACATTCAATTATAGTCTGTTTTAGTGAAAAATGTAAAAAAATTTAACTTAAA
9346 ATCAATTATGAGA
319 ATCAATTATGAGA
* * * * *
9359 NNNNNNNNNNATTTAATA-CGAGCAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGGCTTT
1 ----------ATTTAA-AGCGAGCAATAAGGCTTTTAAAGAAATAGGTGACAATAAATAGACTTT
* * *
9423 TCTTCTAAATGAATAACTTTTTCTACACGTT-TCAAGATGCAGACATTTAATTATAGTTTATTTT
55 TCTTCTAAATGAATAACTTTTTATACACGTTCCCAAG--GCAGACATTTAATTATAGTCTATTTT
* * *
9487 AACCAAAAATGTAAAAAATCTCAACTAAAAATCAATTATGAGTTGATAAAACCATTTAAAGCATG
118 AACAAAAAATGTAAAAAATCTCAACTAAAAATCAATTATGAGTTGATAAAACAATTTAAAGCAAG
* * *
9552 TAATAAGGCTGTTGAAAACATACGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTA
183 CAATAAGGCTGTTGAAAACATACGTGACTATAAATAGACTTTCCTTACCAATGAATGACTTTTTA
* *
9617 TTCATGTTTCTCGAGGTAAACATTCAATTATAGTCTG
248 TACATGTTTCTCGAGGCAAACATTCAATTATAGTCTG
9654 NNNNNNNNNN
Statistics
Matches: 242, Mismatches: 34, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
340 4 0.02
341 12 0.05
342 222 0.92
343 4 0.02
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (331 bp):
ATTTAAAGCGAGCAATAAGGCTTTTAAAGAAATAGGTGACAATAAATAGACTTTTCTTCTAAATG
AATAACTTTTTATACACGTTCCCAAGGCAGACATTTAATTATAGTCTATTTTAACAAAAAATGTA
AAAAATCTCAACTAAAAATCAATTATGAGTTGATAAAACAATTTAAAGCAAGCAATAAGGCTGTT
GAAAACATACGTGACTATAAATAGACTTTCCTTACCAATGAATGACTTTTTATACATGTTTCTCG
AGGCAAACATTCAATTATAGTCTGTTTTAGTGAAAAATGTAAAAAAATTTAACTTAAAATCAATT
ATGAGA
Found at i:15731 original size:171 final size:171
Alignment explanation
Indices: 15412--16405 Score: 583
Period size: 171 Copynumber: 5.8 Consensus size: 171
15402 NNNNNNNNNN
* * * * * * * *
15412 ATAAGTCTTTTGAAGGAATAGGTGACTATAAATAGATTTTTCTTCTTAATGAATGACTTTTTCTA
1 ATAAGGCTTTTAAAGAAATGGGTGACTATAAATAGACTTTTCTTC-CAATGAATGCCTTTTTCTT
* * * * * * *
15477 CAT-ATTTCT-AGAAGTAAGCATTCAATCATAGTCTGTTGTAA-TGAAAAATGTAAAAAAATTCA
65 CATGTTTTCTCA-AGGCAAACATTCAATTATAGTCTGTTTTAACT-AAAAATGTTAAAAAATTCA
********** *
15539 ACTTANNNNNNNNNNTGAGATTATAAAACT-ATTTGAAGCGAGTA
128 ACTTAAAATCAATTATGAGATTATAAAA-TAATTTAAAGCGAGTA
* * *
15583 ATAAGGTTTTTAAAGAAATGGGTGACTATATATAGACTTTTCTTGCCAATGAATGCCTTTTTATT
1 ATAAGGCTTTTAAAGAAATGGGTGACTATAAATAGACTTTTCTT-CCAATGAATGCCTTTTTCTT
* * * *
15648 CATGTTTTCT-AAGGTAAATATTTAATTATAGTCTGTTTTAACTAAAAATGTTAAAAAATCCAAC
65 CATGTTTTCTCAAGGCAAACATTCAATTATAGTCTGTTTTAACTAAAAATGTTAAAAAATTCAAC
* * *
15712 GTAAAATCAATTATGAGATTATGAAATAATTTAAAGTGA-TCA
130 TTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGT-A
* * ********** * *
15754 ATAAGGCTTTTGAAGGAATGGGNNNNNNNNNNTATACTTTTCTTCTCAATGAATG-ATTTTT-TT
1 ATAAGGCTTTTAAAGAAATGGGTGACTATAAATAGACTTTTCTTC-CAATGAATGCCTTTTTCTT
* *
15817 CACT-TGTTTCTCAAGGCAAGA-ATTCAATTA-ATGTCTGTTTTAA-TGAATAATGTAAAAAAAT
65 CA-TGT-TTTCTCAAGGCAA-ACATTCAATTATA-GTCTGTTTTAACT-AAAAATGTTAAAAAAT
* ********** *
15878 TTAACTTAAAATCAATNNNNNNNNNNTAAAATAATTTAAAGCGAGCA
125 TCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTA
* * * * * ** *
15925 ATAAGGCTTTTAAAGGAATGAGAGACTATAAATGGGCTTTT-TTCTCAATGAATAACTTTTTCTA
1 ATAAGGCTTTTAAAGAAATGGGTGACTATAAATAGACTTTTCTTC-CAATGAATGCCTTTTTCTT
* * * * * *****
15989 CACG-TTT-TAAGAGGCAAGCATTTAATTATAGTTTGTTTTAACTAAAAATG-TAAAAACNNNNN
65 CATGTTTTCTCA-AGGCAAACATTCAATTATAGTCTGTTTTAACTAAAAATGTTAAAAA-ATTCA
***** * **
16051 NNNNNAAATCAATTATGAGATGATAAAACCATTTAAAGC-ATGTA
128 ACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGA-GTA
* * * *
16095 ATAAGGGTTTTGAAGAAATGCGTGACTATAAATAGACTTTTCTTGCCAATAAATGCCTTTTTCTT
1 ATAAGGCTTTTAAAGAAATGGGTGACTATAAATAGACTTTTCTT-CCAATGAATGCCTTTTTCTT
* * **********
16160 CA-GGTTTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAACTAAAAANNNNNNNNNNTTCAAC
65 CATGTTTTCTCAAGGCAAACATTCAATTATAGTCTGTTTTAACTAAAAATGTTAAAAAATTCAAC
* * *
16224 TTAAAATCAATTATGAGATTATGAAATAATTTAAATCGAGCA
130 TTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTA
* *
16266 ATAAGGCTTTCGAAAG-AATGGGTGACTAGAAATAGACTTTT-TTCACCAATGAATGCCTTTTTC
1 ATAAGGCTTT-TAAAGAAATGGGTGACTATAAATAGACTTTTCTT--CCAATGAATGCCTTTTTC
* * * * * * *
16329 TTCATG-TTTCTCAAGGCAGACAATCAATTATTA-TATGTTTTAACCAAGAATGTAAAAAAATTT
63 TTCATGTTTTCTCAAGGCAAACATTCAATTA-TAGTCTGTTTTAACTAAAAATGTTAAAAAATTC
16392 AACTTAAAATCAAT
127 AACTTAAAATCAAT
16406 NNNNNNNNNN
Statistics
Matches: 611, Mismatches: 180, Indels: 64
0.71 0.21 0.07
Matches are distributed among these distances:
169 13 0.02
170 122 0.20
171 454 0.74
172 22 0.04
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.35
Consensus pattern (171 bp):
ATAAGGCTTTTAAAGAAATGGGTGACTATAAATAGACTTTTCTTCCAATGAATGCCTTTTTCTTC
ATGTTTTCTCAAGGCAAACATTCAATTATAGTCTGTTTTAACTAAAAATGTTAAAAAATTCAACT
TAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTA
Found at i:16438 original size:512 final size:491
Alignment explanation
Indices: 15554--16556 Score: 978
Period size: 512 Copynumber: 2.0 Consensus size: 491
15544 NNNNNNNNNN
* * * * * *
15554 TGAGATTATAAAACTATTTGAAGCGAGTAATAAGGTTTTTAAAGAAATGGGTGACTATATATAGA
1 TGAGATGATAAAACCATTTAAAGCGAGTAATAAGGGTTTTAAAGAAATGCGTGACTATAAATAGA
* * * *
15619 CTTTTCTTGCCAATGAATGCCTTTTTATTCATGTTTTCTAAGGTAAATATTTAATTATAGTCTGT
66 CTTTTCTTGCCAATAAATGCCTTTTTATTCAGGTTTTCTAAGGTAAACATTCAATTATAGTCTGT
15684 TTTAACTAAAAATGTTAAAAAATCCAACGTAAAATCAATTATGAGATTATGAAATAATTTAAAGT
131 TTTAACTAAAAATGTTAAAAAATCCAACGTAAAATCAATTATGAGATTATGAAATAATTTAAAGT
* * * ********** * *
15749 GATCAATAAGGCTTTTGAAGGAATGGGNNNNNNNNNNTATACTTTTCTTCTCAATGAATGATTTT
196 GAGCAATAAGGCTTTCGAAAGAATGGGTGACTAGAAATAGACTTTTCTTCCCAATGAATGATTTT
* * * ** *
15814 TTTCACTTGTTTCTCAAGGCAAGAATTCAATTAATGTCTGTTTTAATGAATAATGTAAAAAAATT
261 TTTCAC-TGTTTCTCAAGGCAAGAAATCAATTAATATATGTTTTAACCAAGAATGTAAAAAAATT
15879 TAACTTAAAATCAATNNNNNNNNNNTAAAATAATTTAAAGCGAGCAATAAGGCTTTTAAAGGAAT
325 TAACTTAAAATCAAT----------TAAAATAATTTAAAGCGAGCAATAAGGCTTTTAAAGGAAT
* * * *
15944 GAGA-GACTATAAATGGGCTTTTTTCTCAATGAATAACTTTTTCTACACGTTTTAAGAGGC-AAG
380 -AGATGACTATAAATGGACTTTTTTCTCAATGAAGAACTTTCTCTACACGTTTTAAGAGACTAA-
* *
16007 CATTTAATTATAGTTTGTTTTAACTAAAAATGTAAAAACNNNNNNNNNNAAATCAATTA
443 CATTTAATTACAGTTTGTTTTAACCAAAAATGTAAAAAC----------AAATCAATTA
*
16066 TGAGATGATAAAACCATTTAAAGC-ATGTAATAAGGGTTTTGAAGAAATGCGTGACTATAAATAG
1 TGAGATGATAAAACCATTTAAAGCGA-GTAATAAGGGTTTTAAAGAAATGCGTGACTATAAATAG
*
16130 ACTTTTCTTGCCAATAAATGCCTTTTTCTTCAGG-TTTCTCAAGGTAAACATTCAATTATAGTCT
65 ACTTTTCTTGCCAATAAATGCCTTTTTATTCAGGTTTTCT-AAGGTAAACATTCAATTATAGTCT
********** * *
16194 GTTTTAACTAAAAANNNNNNNNNNTTCAACTTAAAATCAATTATGAGATTATGAAATAATTTAAA
129 GTTTTAACTAAAAATGTTAAAAAATCCAACGTAAAATCAATTATGAGATTATGAAATAATTTAAA
16259 -TCGAGCAATAAGGCTTTCGAAAGAATGGGTGACTAGAAATAGACTTTT-TTCACCAATGAATGC
194 GT-GAGCAATAAGGCTTTCGAAAGAATGGGTGACTAGAAATAGACTTTTCTTC-CCAATGAATG-
* *
16322 CTTTTTCTTCA-TGTTTCTCAAGGC-AGACAATCAATTATTATATGTTTTAACCAAGAATGTAAA
256 ATTTTT-TTCACTGTTTCTCAAGGCAAGA-AATCAATTAATATATGTTTTAACCAAGAATGTAAA
******** * *
16385 AAAATTTAACTTAAAATCAATNNNNNNNNNNNNNNNNNNTTTAAAGTGAGCAATAAGGCTTTTGA
319 AAAATTTAACTTAAAATCAAT----------TAAAATAATTTAAAGCGAGCAATAAGGCTTTTAA
* * * **
16450 AGGAATAGATGACTGTAAATGGACTTTTTTCTGAATGAAGAACTTTCTCTATACGTTTTTCGAGA
374 AGGAATAGATGACTATAAATGGACTTTTTTCTCAATGAAGAACTTTCTCTACACGTTTTAAGAGA
16515 CTAACATTTAATTACAGTTTGTTTTAACCAAAAATGTAAAAA
439 CTAACATTTAATTACAGTTTGTTTTAACCAAAAATGTAAAAA
16557 AATTCAACTT
Statistics
Matches: 414, Mismatches: 68, Indels: 18
0.83 0.14 0.04
Matches are distributed among these distances:
511 16 0.04
512 387 0.93
513 7 0.02
514 4 0.01
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.34
Consensus pattern (491 bp):
TGAGATGATAAAACCATTTAAAGCGAGTAATAAGGGTTTTAAAGAAATGCGTGACTATAAATAGA
CTTTTCTTGCCAATAAATGCCTTTTTATTCAGGTTTTCTAAGGTAAACATTCAATTATAGTCTGT
TTTAACTAAAAATGTTAAAAAATCCAACGTAAAATCAATTATGAGATTATGAAATAATTTAAAGT
GAGCAATAAGGCTTTCGAAAGAATGGGTGACTAGAAATAGACTTTTCTTCCCAATGAATGATTTT
TTTCACTGTTTCTCAAGGCAAGAAATCAATTAATATATGTTTTAACCAAGAATGTAAAAAAATTT
AACTTAAAATCAATTAAAATAATTTAAAGCGAGCAATAAGGCTTTTAAAGGAATAGATGACTATA
AATGGACTTTTTTCTCAATGAAGAACTTTCTCTACACGTTTTAAGAGACTAACATTTAATTACAG
TTTGTTTTAACCAAAAATGTAAAAACAAATCAATTA
Found at i:18707 original size:170 final size:171
Alignment explanation
Indices: 18410--18775 Score: 406
Period size: 170 Copynumber: 2.1 Consensus size: 171
18400 NNNNNNNNTA
* * * * * ** * *
18410 AGAAGAAAAATCTATTTATAGTCACTCATTCCTTTAAAAGCCTTATTAATCGTTTTACATTGTTT
1 AGAAGAAAAGTCCATTTATAGTCACCCATTCATTCAAAAGCCTTATTAATCACTTTAAATGGTTT
* * *
18475 TATAATCTCATAATTGATTTTAAGTAGAATGTTTTTATATTTTCGGTTAAAACAGACTATAATTG
66 TATAATATCAAAATTGATTTTAAGTAGAATGTTTTTATATTTTCGATTAAAACAGACTATAATTG
* *
18540 AATGTCTACCT-GAAGAAACATG-AAGAAAAA-TACATTTATTTG
131 AATGTCCACCTCG-AGAAACATGTAA-AAAAAGT-CATTCA-TTG
* * *
18582 -TAAGAAAAGTCCA-TTATAGTCACCCATTCATTCGAAAGCCTTATTACTCACTTTAAATGGTTT
1 AGAAGAAAAGTCCATTTATAGTCACCCATTCATTCAAAAGCCTTATTAATCACTTTAAATGGTTT
* * * *
18645 TTTAATATCAAAATTGATTTTAAGCT-GAAT-TGTTTTATATTTGT-TATTAAACCATACTATAA
66 TATAATATCAAAATTGATTTTAAG-TAGAATGT-TTTTATATTT-TCGATTAAAACAGACTATAA
*
18707 TTGAATGTCCACCTCGAGAAACGTGTAAAAAAAGTCATTCATTG
128 TTGAATGTCCACCTCGAGAAACATGTAAAAAAAGTCATTCATTG
*
18751 AGAAGAAAAGTCTATTTATAGTCAC
1 AGAAGAAAAGTCCATTTATAGTCAC
18776 NNNNNNNNNN
Statistics
Matches: 162, Mismatches: 24, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
169 4 0.02
170 132 0.81
171 26 0.16
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (171 bp):
AGAAGAAAAGTCCATTTATAGTCACCCATTCATTCAAAAGCCTTATTAATCACTTTAAATGGTTT
TATAATATCAAAATTGATTTTAAGTAGAATGTTTTTATATTTTCGATTAAAACAGACTATAATTG
AATGTCCACCTCGAGAAACATGTAAAAAAAGTCATTCATTG
Found at i:19384 original size:169 final size:167
Alignment explanation
Indices: 18878--19410 Score: 584
Period size: 169 Copynumber: 3.1 Consensus size: 167
18868 NNNNNNNNAT
* * * **
18878 AAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAACGGACTTTTCTTTT
1 AAAAATATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAACAGACTTTTCTTCA
* *
18943 AATGAATGTTTTTTTCTTCACGTTTCTTGAGGTATA-CATTCAATTATAGTCTATTTTAACTAAA
66 AATGAATG-CTTTTTCTTCACGTTTCTTGAGGTA-AGCATTCAATTATAGTCTATTTTAATTAAA
19007 AATGTAAAAAAATT-TCACTTAAAATCAATTATGAGATTA
129 AATGTAAAAAAATTCT-ACTTAAAATCAATTATGAGATTA
* * * * *********
19046 GAAAATAATTTAATGCGAGCAATAAGGCTTTTGAAGGAATAGGTGACTANNNNNNNNNNTTTCTT
1 AAAAAT-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTA-TAACAGACTTTTCTT
* * * * * * *
19111 CTCAATGAATAACTTTTTCTACACGTTTTTTGAGGCAAGCATTTAATTATAGTCTATTTTAATCA
64 C-AAATGAAT-GCTTTTTCTTCACGTTTCTTGAGGTAAGCATTCAATTATAGTCTATTTTAATTA
* * * *
19176 AAAATTTAAAAGAATTCAACTTAAAATCAATTTTGAGATTA
127 AAAATGTAAAAAAATTCTACTTAAAATCAATTATGAGATTA
* * * *
19217 AAAAACTATTTAAAGTGAGTAATAAAGCTTTCGAAGGAATGGGTGACTATAATAGACTTTTCTTG
1 AAAAA-TATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAACAGACTTTTCTT-
* * * * *
19282 CAAATGAATGCATTTTCTTCACATTTCTCGAGGTAGGCATTCAATTATAGTCTGTTTTAATTAAA
64 CAAATGAATGCTTTTTCTTCACGTTTCTTGAGGTAAGCATTCAATTATAGTCTATTTTAATTAAA
19347 AATGTAAAAAAATTCTACTTAAAATCAATTATGAGATTA
129 AATGTAAAAAAATTCTACTTAAAATCAATTATGAGATTA
* *
19386 TAAAAAAATTTAAAGCGATTAATAA
1 -AAAAATATTTAAAGCGAGTAATAA
19411 NNNNNNNNNN
Statistics
Matches: 292, Mismatches: 64, Indels: 17
0.78 0.17 0.05
Matches are distributed among these distances:
168 4 0.01
169 134 0.46
170 25 0.09
171 128 0.44
172 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.36
Consensus pattern (167 bp):
AAAAATATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAACAGACTTTTCTTCA
AATGAATGCTTTTTCTTCACGTTTCTTGAGGTAAGCATTCAATTATAGTCTATTTTAATTAAAAA
TGTAAAAAAATTCTACTTAAAATCAATTATGAGATTA
Found at i:19437 original size:169 final size:171
Alignment explanation
Indices: 18878--19537 Score: 487
Period size: 169 Copynumber: 3.9 Consensus size: 171
18868 NNNNNNNNAT
* * * * * * **
18878 AAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT-AACGGACTTTTCTT-
1 AAAACAATTTAAAGCGAGTAATAAAGCTTTCGAAGCAATGGGTCACTATAAATAGACTTTTCTTC
* ** ** * *
18941 TTAATGAATGTTTTTTTCTTCAC-GTTTCTTGAGGTATA-CATTCAATTATAGTCTATTTTAA-C
66 TAAATGAATG-CATTTTCTTCACAGTTTCTAAAGGCA-AGCATTCAATTATAGTCTGTTTTAATC
*
19003 TAAAAATGTAAAAAAATTTC-ACTTAAAATCAATTATGAGATTAG
129 -AAAAATGTAAAAAAA-TTCAACTTAAAATCAATTATGAGATTAA
* * * * * * * * **********
19047 AAAATAATTTAATGCGAGCAATAAGGCTTTTGAAGGAATAGGTGACTANNNNNNNNNNTTTCTTC
1 AAAACAATTTAAAGCGAGTAATAAAGCTTTCGAAGCAATGGGTCACTATAAATAGACTTTTCTTC
* * * * * ** * *
19112 TCAATGAATAACTTTTTCTACAC-GTTTTTTGAGGCAAGCATTTAATTATAGTCTATTTTAATCA
66 TAAATGAAT-GCATTTTCTTCACAGTTTCTAAAGGCAAGCATTCAATTATAGTCTGTTTTAATCA
* * *
19176 AAAATTTAAAAGAATTCAACTTAAAATCAATTTTGAGATTAA
130 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAA
* * * *
19218 AAAACTATTTAAAGTGAGTAATAAAGCTTTCGAAGGAATGGGTGACTAT-AATAGACTTTTCTTG
1 AAAACAATTTAAAGCGAGTAATAAAGCTTTCGAAGCAATGGGTCACTATAAATAGACTTTTCTT-
** * * *
19282 C-AAATGAATGCATTTTCTTCACA-TTTCTCGAGGTAGGCATTCAATTATAGTCTGTTTTAATTA
65 CTAAATGAATGCATTTTCTTCACAGTTTCTAAAGGCAAGCATTCAATTATAGTCTGTTTTAATCA
*
19345 AAAATGTAAAAAAATTCTACTTAAAATCAATTATGAGATTATA
130 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTA-A
* ********** *
19388 AAAA-AATTTAAAGCGATTAATAANNNNNNNNNNGCAATGGTTCACTATAAATAGACTTTTCTTC
1 AAAACAATTTAAAGCGAGTAATAAAGCTTTCGAAGCAATGGGTCACTATAAATAGACTTTTCTTC
* * * * * *
19452 TTAATGAATGCCTTTTTTTTACATGTTTCTAAAGGCAAGCATTCAATTATAGTCTGTTGTAATGA
66 TAAATGAATGCATTTTCTTCACA-GTTTCTAAAGGCAAGCATTCAATTATAGTCTGTTTTAATCA
* *
19517 AAAGTGTAAAAAAAATCAACT
130 AAAATGTAAAAAAATTCAACT
19538 NNNNNNNNNN
Statistics
Matches: 391, Mismatches: 87, Indels: 23
0.78 0.17 0.05
Matches are distributed among these distances:
169 151 0.39
170 60 0.15
171 127 0.32
172 53 0.14
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.36
Consensus pattern (171 bp):
AAAACAATTTAAAGCGAGTAATAAAGCTTTCGAAGCAATGGGTCACTATAAATAGACTTTTCTTC
TAAATGAATGCATTTTCTTCACAGTTTCTAAAGGCAAGCATTCAATTATAGTCTGTTTTAATCAA
AAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAA
Found at i:20277 original size:22 final size:22
Alignment explanation
Indices: 20249--20304 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
20239 TATGGTCTGT
20249 TTTAACCAAAAATGTAAAAAAA
1 TTTAACCAAAAATGTAAAAAAA
20271 TTTAACCAAAAATGTAAAAAAA
1 TTTAACCAAAAATGTAAAAAAA
* *
20293 TTCAACCTAAAA
1 TTTAACCAAAAA
20305 CCAATTATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.61, C:0.12, G:0.04, T:0.23
Consensus pattern (22 bp):
TTTAACCAAAAATGTAAAAAAA
Found at i:21893 original size:171 final size:171
Alignment explanation
Indices: 21245--22089 Score: 634
Period size: 171 Copynumber: 4.9 Consensus size: 171
21235 TAAAACGATT
* * * *
21245 AATAAGGCTTTTAAAGGAATGGGTGACTATAAATAGATTTTTTTTCTTAATGAATGGCTTTTTCT
1 AATAAGGCTTTTAAAGGAATGGGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTTTTCT
* ********** *
21310 ACATCTTTCTAGAGGCAAGCATNNNNNNNNNNTCTGTTTTAAT-GAAAAATGTAAAAGAA-TTAA
66 ACATGTTTCTAGAGGCAAGCATTCAATTATAGTCTGTTTTAATAG-AAAATGTAAAAAAATTTAA
* *
21373 TTTAAAATCAATTATAAGATTATAAAACCATTTAAAGCGAGC
130 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGC
********** * * *
21415 AATAAGGCNNNNNNNNNNATGGGTGACTATAAATAGACTTTTCTTGTCAATGAATGCCTTTTTAT
1 AATAAGGCTTTTAAAGGAATGGGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTTTTCT
** * * * * * *
21480 TTATGTTTCCTA-AGG-TAGACATTTAATTATAGTCTGTTTTAACTA-AAACTATTAAAAAATCT
66 ACATGTTT-CTAGAGGCAAG-CATTCAATTATAGTCTGTTTTAA-TAGAAAATGTAAAAAAATTT
* * * * * *
21542 AACTTAAAAGCAATTATGATATTATGAAACAATTTAAAACAAGC
128 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGC
* * * *
21586 AATAAGGCTTTTGAAGGAATGAGTGACTATAAATATACTTTTCTTCTCAAAGAATGACGTTTTTC
1 AATAAGGCTTTTAAAGGAATGGGTGACTATAAATAGACTTTTCTTCTCAATGAATGAC-TTTTTC
* * * * *********
21651 -ACACGTTTCTCGAGACAAGCATTCAATTATTGTCTGTTTTAAT-GAAAAATGTAANNNNNNNNN
65 TACATGTTTCTAGAGGCAAGCATTCAATTATAGTCTGTTTTAATAG-AAAATGTAAAAAAATTTA
* * * *
21714 NCTTAAAATCCATTATGAGATTATAAAACAATTTAATGCGAGC
129 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGC
* * *
21757 AATAAGGCTTTTAAAGGAATGGGTGACTATAACTAGACTTTTCTTCTCGATGAATGTCTTTTTCT
1 AATAAGGCTTTTAAAGGAATGGGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTTTTCT
*
21822 GCATGTTTCTAGAGGCAAGCATTCAATTATAGTCTGTTTTAATAGAAAATGTAAAAAAATTTAAC
66 ACATGTTTCTAGAGGCAAGCATTCAATTATAGTCTGTTTTAATAGAAAATGTAAAAAAATTTAAC
************* * *
21887 TTAAAATCNNNNNNNNNNNNNTAAAACCATTTAAAGTGAGT
131 TTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGC
* * * *
21928 AATAAAGTTTTTGAAGGAATGGGTGACTATAAATAAACTTTTCTTAC-CAATGAAT-ACTTTTTT
1 AATAAGGCTTTTAAAGGAATGGGTGACTATAAATAGACTTTTCTT-CTCAATGAATGAC-TTTTT
* * * * * *
21991 CTTCAGGTTTCTCA-AAG-TAGACATTCAATTATAGTCTGTTTTAAGCA-AAAATGTAAAATAAT
64 CTACATGTTTCT-AGAGGCAAG-CATTCAATTATAGTCTGTTTTAA-TAGAAAATGTAAAAAAAT
* *
22053 TCAACTTAAAATCAATTTTGAGATTATAAAACCATTT
126 TTAACTTAAAATCAATTATGAGATTATAAAACCATTT
22090 NNNNNNNNNN
Statistics
Matches: 505, Mismatches: 153, Indels: 33
0.73 0.22 0.05
Matches are distributed among these distances:
169 2 0.00
170 92 0.18
171 400 0.79
172 11 0.02
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.34
Consensus pattern (171 bp):
AATAAGGCTTTTAAAGGAATGGGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTTTTCT
ACATGTTTCTAGAGGCAAGCATTCAATTATAGTCTGTTTTAATAGAAAATGTAAAAAAATTTAAC
TTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGC
Done.