Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402463.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_554.0, 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: 20546
ACGTcount: A:0.23, C:0.07, G:0.08, T:0.22
Warning! 8084 characters in sequence are not A, C, G, or T
Found at i:632 original size:170 final size:171
Alignment explanation
Indices: 341--831 Score: 670
Period size: 171 Copynumber: 2.9 Consensus size: 171
331 NNNNNNNNNN
*
341 GTTGAATTTTTTTATATTTTTGGTTAAAACAGACTATAATTGAATGCTTGCCTTAAGAAATGTGT
1 GTTGAATTTTTTTATATTTTTGGTTAAAACAGACTATAATTGAATGCTTGCCTTAAGAAACGTGT
* * *
406 AGAAAAAGCCATTCATTGATAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAACAGCTTTATT
66 AAAAAAAGCCATTCATTGACAAGAAAAGTCCATTTATAGTCACCTATTCTTTCAACAGCTTTATT
*
471 ACTCGCTTTAAATTGTTTTAT-TTCTCATAATTG-TTTCTAA
131 ACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTT-TAA
* * * * * * * *
511 GTTGAATTTTTTTACAATTTAGCTTAAAACAGACTACAATTGAATGCTTACCTTGAGAAACATGT
1 GTTGAATTTTTTTATATTTTTGGTTAAAACAGACTATAATTGAATGCTTGCCTTAAGAAACGTGT
* * * *
576 AAAAAAAGCAATTCATAT-AGAAGAAAAGTCCATATATAGTCA-CTCGTTCTTTCAACAG-TCTT
66 AAAAAAAGCCATTCAT-TGACAAGAAAAGTCCATTTATAGTCACCT-ATTCTTTCAACAGCT-TT
* *
638 ATTACTCACTTTAAATTGTTGTATAATCTCATAATTGATTTTAA
128 ATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAA
* * *
682 GTTAAATTATTTTATATTTTTGGTTAGAAA-AGACTATAATTGAATGCTTGCCTCAAGAAACGTG
1 GTTGAATTTTTTTATATTTTTGGTTA-AAACAGACTATAATTGAATGCTTGCCTTAAGAAACGTG
* * *
746 TAAGAAAAGCCATTCATTGACAAGAAAAGTCTATTTATAGTCACCTATTCTTTCAACAGCCTTAT
65 TAAAAAAAGCCATTCATTGACAAGAAAAGTCCATTTATAGTCACCTATTCTTTCAACAGCTTTAT
811 TACTCGCTTTAAATTGTTTTA
130 TACTCGCTTTAAATTGTTTTA
832 NNNNNNNNNN
Statistics
Matches: 274, Mismatches: 38, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
169 3 0.01
170 128 0.47
171 135 0.49
172 8 0.03
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (171 bp):
GTTGAATTTTTTTATATTTTTGGTTAAAACAGACTATAATTGAATGCTTGCCTTAAGAAACGTGT
AAAAAAAGCCATTCATTGACAAGAAAAGTCCATTTATAGTCACCTATTCTTTCAACAGCTTTATT
ACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAA
Found at i:1076 original size:32 final size:32
Alignment explanation
Indices: 1039--1104 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
1029 TATAATCTCA
1039 TAATTAGTTTTAAGCTGATTTTTTTTAAATTT
1 TAATTAGTTTTAAGCTGATTTTTTTTAAATTT
*
1071 TAATTAGTTTTAAGCTGATTTTTTTTACATTT
1 TAATTAGTTTTAAGCTGATTTTTTTTAAATTT
1103 TA
1 TA
1105 GCTTAAAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.27, C:0.05, G:0.09, T:0.59
Consensus pattern (32 bp):
TAATTAGTTTTAAGCTGATTTTTTTTAAATTT
Found at i:2667 original size:21 final size:22
Alignment explanation
Indices: 2641--2687 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
2631 AAGCATGTAG
*
2641 AAAAGGCCATTCATATAGAA-A
1 AAAAGGCCATTCATATAAAACA
2662 AAAAGGCCATTCATATAAAACA
1 AAAAGGCCATTCATATAAAACA
2684 AAAA
1 AAAA
2688 TCCATTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.57, C:0.15, G:0.11, T:0.17
Consensus pattern (22 bp):
AAAAGGCCATTCATATAAAACA
Found at i:2692 original size:21 final size:21
Alignment explanation
Indices: 2641--2693 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2631 AAGCATGTAG
*
2641 AAAAGGCCATTCATATAGAAA
1 AAAAAGCCATTCATATAGAAA
*
2662 AAAAGGCCATTCATATA-AAA
1 AAAAAGCCATTCATATAGAAA
*
2682 CAAAAATCCATT
1 -AAAAAGCCATT
2694 TATAGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 3 0.10
21 26 0.90
ACGTcount: A:0.53, C:0.17, G:0.09, T:0.21
Consensus pattern (21 bp):
AAAAAGCCATTCATATAGAAA
Found at i:3557 original size:21 final size:20
Alignment explanation
Indices: 3529--3568 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3519 ACCTTAAGAA
*
3529 ACATGTAGAGAAAGCCATTC
1 ACATGTAGAAAAAGCCATTC
*
3549 ACATAGTAGAAAAATCCATT
1 ACAT-GTAGAAAAAGCCATT
3569 TATAGTCTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (20 bp):
ACATGTAGAAAAAGCCATTC
Found at i:6181 original size:172 final size:171
Alignment explanation
Indices: 5710--6906 Score: 1113
Period size: 172 Copynumber: 7.0 Consensus size: 171
5700 NNNNNNNNNN
5710 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATTG-GTGACTATAAATGGACCTTTT-TTCTCAAT
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAA-TGAGTGACTATAAATGGA-CTTTTCTTCTCAAT
* *
5773 GAATGACTTTTTCTACACGTTT-TTCAAGGTAA-ACATTCAATTATAG-TATGTTTTAATGGAAA
64 GAATGACTTTTTCTACACGTTTCTT-GAGG-AAGACATTCAATTATAGCT-TGTTTTAATGAAAA
* * *
5835 ATGTAAACAAATTTAAATTAAAATAAATTATGAGATTATAAAACAA
126 ATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAA
* *
5881 TTTAAAACGAGTAATAAGGCTTTTGAAGGAATG-GATGACTCTAAATGGACTTTTCTTCTCAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAG-TGACTATAAATGGACTTTTCTTCTCAATG
* * * * * * * * *
5945 AATGGCTTTTTATATATGTTTGTCT-AGGAA-AGCATTCAATTATAACCTGATTTAATGGAAAAT
65 AATGACTTTTTCTACACGTTTCT-TGAGGAAGA-CATTCAATTATAGCTTGTTTTAATGAAAAAT
* *
6008 GTAAAAAAATTTAACTTAAAAAT-AATTATTAGATTATAAAATAA
128 GTAAAAAAATTTAACTT-AAAATCAATTATGAGATTATAAAACAA
* * * ** * * * *
6052 TTTAAAACGAGCAATAAGACTTTTGAAGGAATTTGTGACTCTACATGTACTTTTTTTTCTCAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGAC-TTTTCTTCTCAATG
*
6117 AATGACTTTTTCTACATGTTTCTTGAGGCAAG-CATTCAATTATAGCTTGTTTTAATGAAAAATG
65 AATGACTTTTTCTACACGTTTCTTGAGG-AAGACATTCAATTATAGCTTGTTTTAATGAAAAATG
* * * ** *
6181 TAAAACAATTTAACTTAAAATCAATTTTTATTTTATAAAACCA
129 TAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAA
* * * *
6224 TTTAAAGCGAGTAATAAGGTTTTTGAAGGACTGAGTGACTATATATGGACTTTTCTTATCAATGA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGA
* * * * * * * *
6289 ATG-CATTTTCTTTTCACGTTTCTCGAGGTAGACATTTAATTATTATC-TATTTTAATTAAAAAT
66 ATGAC-TTTT-TCTACACGTTTCTTGAGGAAGACATTCAATTA-TAGCTTGTTTTAATGAAAAAT
* *
6352 AG-AAAAAAATTTAACTTAAAATCAATTATGAGCTTATAAAACCA
128 -GTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAA
* * * *
6396 TTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGAGTGATTATAAATAGACTTTTCTTGC-AAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTT-CTCAATG
* * * * * ** *
6460 AATGCCTTTTTGTTC-CAGTTTATTGAGGTAGACATTTGATTATAG-TCTGTTTTAACT-AAAAT
65 AATGACTTTTTCTACAC-GTTTCTTGAGGAAGACATTCAATTATAGCT-TGTTTTAA-TGAAAAA
* * *
6522 TGTAAAAAAAATTCAATTTAAAATCAATTATGAGATTATAAAATAA
127 TGT-AAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAA
* *
6568 TTTAAAGTG-GTAATAAGGCTTTTGAAGGAATGAGTGACTA-AAATAGG-CTTTTCCTAC-CAAT
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAAT-GGACTTTT-CTTCTCAAT
* * * * * * * *
6629 GAATGCCTTTTTCTTCACATTTCTT-ATGGTAGATATTTAATTATAGCCTGTTTT-ATCCAAAAA
64 GAATGACTTTTTCTACACGTTTCTTGA-GGAAGACATTCAATTATAGCTTGTTTTAAT-GAAAAA
*
6692 TGTAAAAAAATTTAACTTAAAATCAATTATAAGATTATAAAACAA
127 TGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAA
* * * * * *
6737 TTTAAAGCGAGTAATAAGTCTTTTGAAGTAATGGGTGAGTACAAATAGG-CTTTTCTTACT-GAT
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAAT-GGACTTTTCTT-CTCAAT
* * * * * *
6800 GAATG-CATTTTTCTTCATC-TTTCTCGAGGTAA-ACATTCAATTCTATC-AGTTTGAACT-AAA
64 GAATGAC-TTTTTCTACA-CGTTTCTTGAGG-AAGACATTCAATTATAGCTTGTTTTAA-TGAAA
* * *
6860 AATATAAAAAAATTGAACTTAAAATCAATTATGAGATTATGAAACAA
125 AATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAA
6907 NNNNNNNNNN
Statistics
Matches: 868, Mismatches: 115, Indels: 87
0.81 0.11 0.08
Matches are distributed among these distances:
168 1 0.00
169 48 0.06
170 159 0.18
171 324 0.37
172 328 0.38
173 8 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (171 bp):
TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGA
ATGACTTTTTCTACACGTTTCTTGAGGAAGACATTCAATTATAGCTTGTTTTAATGAAAAATGTA
AAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAA
Found at i:6462 original size:343 final size:340
Alignment explanation
Indices: 5710--6906 Score: 1227
Period size: 343 Copynumber: 3.5 Consensus size: 340
5700 NNNNNNNNNN
*
5710 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATGGACCTTTT-TTCTCAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAA-TGGTGACTATAAATAGA-CTTTTCTTCTCAATG
* * *
5774 AATGACTTTTTCTACACGTTT-TTCAAGGTAAACATTCAATTATAGTATGTTTTAA-TGGAAAAT
64 AATGACTTTTTCTACATGTTTCTT-GAGGTAAACATTCAATTATAGTATGTTTTAACT-AAAAAT
* * * *
5837 GTAAACAAATTTAAATTAAAATAAATTATGAGATTATAAAACAATTTAAAACGAGTAATAAGGCT
127 GTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCT
* * * *
5902 TTTGAAGGAATG-GATGACTCTAAATGGACTTTTCTTCTCAATGAATGGCTTTTTATAT-ATGTT
192 TTTGAAGGAATGAG-TGACTATAAATGGACTTTTCTTATCAATGAAT-GCTTTTT-TTTCACGTT
* * * * **
5965 TGTCTAGG-AAAGCATTCAATTATAACCTGA-TTTAATGGAAAATGTAAAAAAATTTAACTTAAA
254 TCTCTAGGTAGA-CATTTAATTATTACCT-ATTTTAATCAAAAATGTAAAAAAATTTAACTT-AA
* *
6028 AAT-AATTATTAGATTATAAAATAA
316 AATCAATTATAAGATTATAAAACAA
* * * * * * *
6052 TTTAAAACGAGCAATAAGACTTTTGAAGGAATTTGTGACTCTACAT-GTACTTTTTTTTCTCAAT
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAA-TGGTGACTATAAATAG-AC-TTTTCTTCTCAAT
* *
6116 GAATGACTTTTTCTACATGTTTCTTGAGGCAAGCATTCAATTATAGCT-TGTTTTAA-TGAAAAA
63 GAATGACTTTTTCTACATGTTTCTTGAGGTAAACATTCAATTATAG-TATGTTTTAACT-AAAAA
* * * ** * *
6179 TGTAAAACAATTTAACTTAAAATCAATTTTTATTTTATAAAACCATTTAAAGCGAGTAATAAGGT
126 TGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGC
* *
6244 TTTTGAAGGACTGAGTGACTATATATGGACTTTTCTTATCAATGAATGCATTTTCTTTTCACGTT
191 TTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTATCAATGAATGC-TTTT-TTTTCACGTT
* * *
6309 TCTCGAGGTAGACATTTAATTATTATCTATTTTAATTAAAAATAG-AAAAAAATTTAACTTAAAA
254 TCTCTAGGTAGACATTTAATTATTACCTATTTTAATCAAAAAT-GTAAAAAAATTTAACTTAAAA
* * *
6373 TCAATTATGAGCTTATAAAACCA
318 TCAATTATAAGATTATAAAACAA
* * *
6396 TTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGAGTGATTATAAATAGACTTTTCTTGC-AAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG-GTGACTATAAATAGACTTTTCTT-CTCAATG
* * * * * ** * *
6460 AATGCCTTTTTGTTCCA-GTTTATTGAGGTAGACATTTGATTATAGTCTGTTTTAACTAAAATTG
64 AATGACTTTTT-CTACATGTTTCTTGAGGTAAACATTCAATTATAGTATGTTTTAACTAAAAATG
* * * *
6524 TAAAAAAAATTCAATTTAAAATCAATTATGAGATTATAAAATAATTTAAAGTG-GTAATAAGGCT
128 T-AAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCT
* * * *
6588 TTTGAAGGAATGAGTGACTA-AAATAGG-CTTTTCCTACCAATGAATGCCTTTTTCTTCACATTT
192 TTTGAAGGAATGAGTGACTATAAAT-GGACTTTTCTTATCAATGAATG-CTTTTTTTTCACGTTT
* *
6651 CT-TATGGTAGATATTTAATTA-TAGCCTGTTTT-ATCCAAAAATGTAAAAAAATTTAACTTAAA
255 CTCTA-GGTAGACATTTAATTATTA-CCTATTTTAAT-CAAAAATGTAAAAAAATTTAACTTAAA
6713 ATCAATTATAAGATTATAAAACAA
317 ATCAATTATAAGATTATAAAACAA
* * * * * *
6737 TTTAAAGCGAGTAATAAGTCTTTTGAAGTAATGGGTGAGTACAAATAGGCTTTTCTTACT-GATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGTGACTATAAATAGACTTTTCTT-CTCAATG
* * * * *
6801 AATG-CATTTTTCTTCATCTTTCTCGAGGTAAACATTCAATTCTA-TCA-GTTTGAACTAAAAAT
64 AATGAC-TTTTTCTACATGTTTCTTGAGGTAAACATTCAATTATAGT-ATGTTTTAACTAAAAAT
* * *
6863 ATAAAAAAATTGAACTTAAAATCAATTATGAGATTATGAAACAA
127 GTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAA
6907 NNNNNNNNNN
Statistics
Matches: 714, Mismatches: 110, Indels: 65
0.80 0.12 0.07
Matches are distributed among these distances:
339 38 0.05
340 25 0.04
341 161 0.23
342 73 0.10
343 258 0.36
344 155 0.22
345 4 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (340 bp):
TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGTGACTATAAATAGACTTTTCTTCTCAATGAA
TGACTTTTTCTACATGTTTCTTGAGGTAAACATTCAATTATAGTATGTTTTAACTAAAAATGTAA
AAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTG
AAGGAATGAGTGACTATAAATGGACTTTTCTTATCAATGAATGCTTTTTTTTCACGTTTCTCTAG
GTAGACATTTAATTATTACCTATTTTAATCAAAAATGTAAAAAAATTTAACTTAAAATCAATTAT
AAGATTATAAAACAA
Found at i:12017 original size:170 final size:170
Alignment explanation
Indices: 11624--12019 Score: 384
Period size: 170 Copynumber: 2.3 Consensus size: 170
11614 NNNNNNNNNN
* * ** * *
11624 AAGGCTTTTGAAGGAATGGATGACTACAAATAGACTTTTCTTGTCAATGAATACAATTTTCTTCT
1 AAGGCTTTTGAAGGAATGGGTGACTATAAAT-GACTTTTCTTAACAATGAATGCAATTTTCTTCA
* * * * *
11689 TATTTCTTGAAGTAGATATTCAATTATAGAATGTTTTAACCAAAAATGTAAAAAAAAATTGAACT
65 TATTTCTTCAAGTAGACATTCAATTATA-AATCTTTTAACCAAAAATGT-AAAAAAAATTCAACA
* * *
11754 TAAAATCAATTATGAGTTTACGAAATAATTTAAAGCGAGTAAT
128 TAAAATCAATTATGAGATTACAAAACAATTTAAAGCGAGTAAT
* * ********** ***
11797 CAGGCTTTTGAAGGAATGGGTGACTATAAATAANNNNNNNNNNCCAATGAATGTGTTTTTCTTCA
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGA-CTTTTCTTAACAATGAATGCAATTTTCTTCA
* * * *
11862 TGTTTC-TCAAGGTAGACATTCAATTAT-TATCTATTTAATCAAAAATGT-AAAAAAATTCTACA
65 TATTTCTTCAA-GTAGACATTCAATTATAAATCT-TTTAACCAAAAATGTAAAAAAAATTCAACA
*
11924 TAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAAT
128 TAAAATCAATTATGAGATTACAAAACAATTTAAAGCGAGTAAT
* *
11967 AAGGCTGTTCAAGGAATGGGTGACTATAAATGGACTTTTCTTAACAATGAATG
1 AAGGCTTTTGAAGGAATGGGTGACTATAAAT-GACTTTTCTTAACAATGAATG
12020 ACTTTTTCGA
Statistics
Matches: 173, Mismatches: 46, Indels: 11
0.75 0.20 0.05
Matches are distributed among these distances:
170 87 0.50
171 4 0.02
172 18 0.10
173 64 0.37
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.33
Consensus pattern (170 bp):
AAGGCTTTTGAAGGAATGGGTGACTATAAATGACTTTTCTTAACAATGAATGCAATTTTCTTCAT
ATTTCTTCAAGTAGACATTCAATTATAAATCTTTTAACCAAAAATGTAAAAAAAATTCAACATAA
AATCAATTATGAGATTACAAAACAATTTAAAGCGAGTAAT
Found at i:14272 original size:172 final size:162
Alignment explanation
Indices: 13935--14423 Score: 452
Period size: 172 Copynumber: 2.9 Consensus size: 162
13925 NNNNNNNNNN
*
13935 TTTTGAAGGAATTTGTGACTCTACATGGACTTTTTTTCTCAATGAATGGCTTTTTTACATGTTTC
1 TTTTGAAGGAATTTGTGACTCTACATGGACTTTTTTTCTCAATGAATGACTTTTTTACATGTTTC
* * *
14000 TTGAGGTAAGAATTCAATTATAGTTTGTTTTAACT-AAAAATGTAAAA-AACTTTAACTTAAAAT
66 TTGAGGTAGGCATTCAATTATAGTCTGTTTTAA-TGAAAAATGTAAAACAA-TTTAACTTAAAAT
* ** *
14063 TAATTATT-AGATTATAAANNNNNNNNNNGCGAGTAATAAGGC
129 CAATT-TTGAGATTATAAA--------AAGCAAGTAATAAGGC
*
14105 TTTTGAAGGAATTTGCGACTCTACATGGACTTTTTTTTCTCAATGAATGACTTTTTCTACATGTT
1 TTTTGAAGGAATTTGTGACTCTACATGGAC-TTTTTTTCTCAATGAATGACTTTTT-TACATGTT
*
14170 TCTTGAGG-AGGGCATTCAATTATAGCCTGTTTTAATGAAAAATGTAAAACAATTTAACTTAAAA
64 TCTTGAGGTA-GGCATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAACAATTTAACTTAAAA
* **
14234 TCAATTTTGAGTTTATANNNNNNNNNNAAGCAAGTAATAAGGC
128 TCAATTTTGAGATTATA--------AAAAGCAAGTAATAAGGC
* ** * * * * *
14277 TTTTGAAGGACTGAGTGACTATATATGGACTTTTCTTGTCAATGAATGTATTTTTTTCACA--TT
1 TTTTGAAGGAATTTGTGACTCTACATGGACTTTTTTTCTCAATGAATG-ACTTTTTT-ACATGTT
* * * * *
14340 TCTCGAGGTAGACATTCAATTATTA-TCTATTTTCATGAAAAATATAAAACAATTTAACTTAAAA
64 TCTTGAGGTAGGCATTCAATTA-TAGTCTGTTTTAATGAAAAATGTAAAACAATTTAACTTAAAA
* *
14404 TCAATTATGAGCTTATAAAA
128 TCAATTTTGAGATTATAAAA
14424 CCGTTTAAAG
Statistics
Matches: 269, Mismatches: 32, Indels: 44
0.78 0.09 0.13
Matches are distributed among these distances:
162 1 0.00
170 99 0.37
171 48 0.18
172 119 0.44
173 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.38
Consensus pattern (162 bp):
TTTTGAAGGAATTTGTGACTCTACATGGACTTTTTTTCTCAATGAATGACTTTTTTACATGTTTC
TTGAGGTAGGCATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAACAATTTAACTTAAAATCA
ATTTTGAGATTATAAAAAGCAAGTAATAAGGC
Found at i:14437 original size:170 final size:171
Alignment explanation
Indices: 13935--14461 Score: 435
Period size: 170 Copynumber: 3.1 Consensus size: 171
13925 NNNNNNNNNN
** * * *
13935 TTTTGAAGGAATTTGTGACTCTACATGGACTTTTT-TTCTCAATGAATGGCTTTTT-TACATGTT
1 TTTTGAAGGAATGAGCGACTATACATGGACTTTTTCTTCTCAATGAATGACTTTTTCTACA-GTT
* * ** * *
13998 TCTTGAGGTAAGA-ATTCAATTATAGTTTGTTTTAACT-AAAAATGTAAAA-AACTTTAACTTAA
65 TCTCGAGG-AGGACATTCAATTATAGCCTATTTTAA-TGAAAAATATAAAACAA-TTTAACTTAA
* * * ********** *
14060 AATTAATTATTAGATTATAAANNNNNNNNNNGCGAGTAATAAGGC
127 AATCAATTATGAGCTTATAAAACCGTTTAAAGCAAGTAATAAGGC
** * *
14105 TTTTGAAGGAATTTGCGACTCTACATGGACTTTTTTTTCTCAATGAATGACTTTTTCTACATGTT
1 TTTTGAAGGAATGAGCGACTATACATGGACTTTTTCTTCTCAATGAATGACTTTTTCTACA-GTT
* * * *
14170 TCTTGAGGAGGGCATTCAATTATAGCCTGTTTTAATGAAAAATGTAAAACAATTTAACTTAAAAT
65 TCTCGAGGAGGACATTCAATTATAGCCTATTTTAATGAAAAATATAAAACAATTTAACTTAAAAT
* * **********
14235 CAATTTTGAGTTTATANNNNNNNNNNAAGCAAGTAATAAGGC
130 CAATTATGAGCTTATAAAACCGTTTAAAGCAAGTAATAAGGC
* * * * *
14277 TTTTGAAGGACTGAGTGACTATATATGGAC-TTTTCTTGTCAATGAATGTA-TTTTTTTCACA-T
1 TTTTGAAGGAATGAGCGACTATACATGGACTTTTTCTTCTCAATGAATG-ACTTTTTCT-ACAGT
* *
14339 TTCTCGAGGTA-GACATTCAATTATTA-TCTATTTTCATGAAAAATATAAAACAATTTAACTTAA
64 TTCTCGAGG-AGGACATTCAATTA-TAGCCTATTTTAATGAAAAATATAAAACAATTTAACTTAA
14402 AATCAATTATGAGCTTATAAAACCGTTTAAAGCAAGTAATAAGGC
127 AATCAATTATGAGCTTATAAAACCGTTTAAAGCAAGTAATAAGGC
14447 TTTTGAAGGAATGAG
1 TTTTGAAGGAATGAG
14462 NNNNNNNNNN
Statistics
Matches: 305, Mismatches: 43, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
170 134 0.44
171 47 0.15
172 122 0.40
173 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.37
Consensus pattern (171 bp):
TTTTGAAGGAATGAGCGACTATACATGGACTTTTTCTTCTCAATGAATGACTTTTTCTACAGTTT
CTCGAGGAGGACATTCAATTATAGCCTATTTTAATGAAAAATATAAAACAATTTAACTTAAAATC
AATTATGAGCTTATAAAACCGTTTAAAGCAAGTAATAAGGC
Found at i:15187 original size:171 final size:170
Alignment explanation
Indices: 15059--15470 Score: 425
Period size: 171 Copynumber: 2.4 Consensus size: 170
15049 NNNNNNNNNN
* * *
15059 CCAAAAATGTAAAAAAATTAAACTTAAAATCAATTATAAGT-TTATGAAATAATTTAAAGCGAGT
1 CCAAAAATGTAAAAAAATTAAACTTAAAACCAATTATAA-TATTATAAAACAATTTAAAGCGAGT
* * * *
15123 AATCAGGCTTTTGAAGGAATTGGTGACTATAAATAAACTTTTCTTGCCAATGAATGTGTTTTTCT
65 AATAAGGCTGTTGAAGGAATAGGTGACAATAAATAAACTTTTCTTGCCAATGAATGT-TTTTTCT
** **********
15188 TCACATTTCTCAAGGTNNNNNNNNNNTTATTATCTGTTTTAA
129 TCATGTTTCTCAAGGTAGATATTCAATTATTATCTGTTTTAA
* * *
15230 TCAAAAATGTAAAAAAATTCAACTTAAAACCAATTATGATATTATAAAACAATTTAAAGCGAGTA
1 CCAAAAATGTAAAAAAATTAAACTTAAAACCAATTATAATATTATAAAACAATTTAAAGCGAGTA
*
15295 ATAAGGCTGTTGAAGGAATAGGTGACAATAAATGAACTTTTCTTGCCAATGAATGCTTTTTTCTT
66 ATAAGGCTGTTGAAGGAATAGGTGACAATAAATAAACTTTTCTTGCCAATGAATG-TTTTTTCTT
* **
15360 CATGTTTCTTTAA-GTAGACGTTCAATTA-TAGTCTGTTTTAA
130 CATGTTTC-TCAAGGTAGATATTCAATTATTA-TCTGTTTTAA
* * * * * ** * ** *
15401 CTAGAAATGTAAACAAATTCAACGTAAAATAAATTATGACCTTATAAAATAATTTAAAGCGAGTA
1 CCAAAAATGTAAAAAAATTAAACTTAAAACCAATTATAATATTATAAAACAATTTAAAGCGAGTA
15466 ATAAG
66 ATAAG
15471 ACNNNNNNNN
Statistics
Matches: 203, Mismatches: 34, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
170 3 0.01
171 196 0.97
172 4 0.02
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.34
Consensus pattern (170 bp):
CCAAAAATGTAAAAAAATTAAACTTAAAACCAATTATAATATTATAAAACAATTTAAAGCGAGTA
ATAAGGCTGTTGAAGGAATAGGTGACAATAAATAAACTTTTCTTGCCAATGAATGTTTTTTCTTC
ATGTTTCTCAAGGTAGATATTCAATTATTATCTGTTTTAA
Found at i:17495 original size:171 final size:170
Alignment explanation
Indices: 17254--17906 Score: 659
Period size: 171 Copynumber: 3.8 Consensus size: 170
17244 TTCACGTTTT
* * * * ** * * *
17254 TCAAGGTAAACATTCAATTATACTCTATTTTAACCAAAAACATGAAAAAATTCAACTTAAAATTA
1 TCAAGGTAGATATTCAATTATAGTCTATTTTAACTAAAAATGTAAAAAAATTTAACTTAAAATCA
*
17319 ATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGTCTTTT-AATAGAATGGGTAACTATAA
66 ATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAG-CTTTTGAA-AGAATGGATAACTATAA
*
17383 ATGGACTTTTTTTCTATATGAATGGCTTTTTCTACACATTTG
129 ATGGACTTTTTTTCTATATGAATGGCTTTTTCTACACATTTC
* *
17425 TCAAGGTAGATATTCAATTATAGTCTATTTTAACTAAAAATGTAAAAAAATTTAACATAAACTCA
1 TCAAGGTAGATATTCAATTATAGTCTATTTTAACTAAAAATGTAAAAAAATTTAACTTAAAATCA
* *
17490 ATTATGAG-TTCATAAAACAATTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGGATGACTATAA
66 ATTATGAGATT-ATAAAACAATTTAAAGCGAGTAAT-AAGCTTTTGAAAGAATGGATAACTATAA
* *
17554 ATGGA-TTTTTCTTCTATATGAATGGCTTTCTCTACATATTTC
129 ATGGACTTTTT-TTCTATATGAATGGCTTTTTCTACACATTTC
* * * ********** *
17596 TTAGGGTAGATATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAANNNNNNNNNNAACTCA
1 TCAAGGTAGATATTCAATTATAGTCTATTTTAACTAAAAATGTAAAAAAATTTAACTTAAAATCA
* * * *
17661 ATTATGAGGTTATAAAATAATTTAAAGCGAGTCATAAGGCTTTTGAAGGAATGGATAACTATAAA
66 ATTATGAGATTATAAAACAATTTAAAGCGAGTAATAA-GCTTTTGAAAGAATGGATAACTATAAA
* * *********
17726 TAGACTTTTCTTCTATATGAATGGCTTTTTCTNNNNNNNNN
130 TGGACTTTTTTTCTATATGAATGGCTTTTTCTACACATTTC
* * * * ** *
17767 NCTAGGTA-ATTATTTAATTGTAGTCTATTTTAAGAAAAAATGAAAAAAAAAATTTAACTTAAAA
1 TCAAGGTAGA-TATTCAATTATAGTCTATTTTAACTAAAAATG--TAAAAAAATTTAACTTAAAA
* * * *
17831 TCAATTATGACATTATAAAACAATTT-AAGCAAGTAATAAGACTTTTGAAAGAATGGGTGACTAT
63 TCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAG-CTTTTGAAAGAATGGATAACTAT
*
17895 AAATGAACTTTT
127 AAATGGACTTTT
17907 CTTGTCAATG
Statistics
Matches: 395, Mismatches: 76, Indels: 21
0.80 0.15 0.04
Matches are distributed among these distances:
170 10 0.03
171 302 0.76
172 52 0.13
173 31 0.08
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.35
Consensus pattern (170 bp):
TCAAGGTAGATATTCAATTATAGTCTATTTTAACTAAAAATGTAAAAAAATTTAACTTAAAATCA
ATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGCTTTTGAAAGAATGGATAACTATAAAT
GGACTTTTTTTCTATATGAATGGCTTTTTCTACACATTTC
Found at i:17956 original size:172 final size:162
Alignment explanation
Indices: 17778--18094 Score: 307
Period size: 172 Copynumber: 1.9 Consensus size: 162
17768 CTAGGTAATT
* * * *
17778 ATTTAATT-GTAGTCTATTTTAAGAAAAAATGAAAAAAAAAATTTAACTTAAAATCAATTATGAC
1 ATTTAATTAGTA-TCTAGTTTAACAAAAAATG--AAAAAAAATTCAACTAAAAATCAATTATGAC
* * *
17842 ATTATAAAACAATTT-AAGCAAGTAATAAGACTTTTGAAAGAATGGGTGACTATAAATGAA-CTT
63 ATTATAAAACAATTTAAAGCAAGTAATAAGACTTTTGAAAGAATGAGAGACTATAAATAAATCTT
17905 TTCTTGTCAATGAATGTNNNNNNNNNNACGTTGCTCGATATAGAC
128 TTCTTGTCAATGAATGT----------ACGTTGCTCGATATAGAC
* * * * * * *
17950 ATTTAATTATTATCTGGTTTAACTAAAAATGTAAAACAATTCAACTAAAAATTAATTATGAGATT
1 ATTTAATTAGTATCTAGTTTAACAAAAAATGAAAAAAAATTCAACTAAAAATCAATTATGACATT
* * ** * * *
18015 ATAAAATAATTTAAAGCAAGTAATAGGGTTTTTTAAAGAATTAGAGACTATAAATAAATCTTTTT
66 ATAAAACAATTTAAAGCAAGTAATAAGACTTTTGAAAGAATGAGAGACTATAAATAAATCTTTTC
18080 TTGTCAATGAATGTA
131 TTGTCAATGAATGTA
18095 NNNNNNNNNN
Statistics
Matches: 121, Mismatches: 21, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
162 1 0.01
170 39 0.32
171 37 0.31
172 42 0.35
173 2 0.02
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.34
Consensus pattern (162 bp):
ATTTAATTAGTATCTAGTTTAACAAAAAATGAAAAAAAATTCAACTAAAAATCAATTATGACATT
ATAAAACAATTTAAAGCAAGTAATAAGACTTTTGAAAGAATGAGAGACTATAAATAAATCTTTTC
TTGTCAATGAATGTACGTTGCTCGATATAGAC
Found at i:19220 original size:171 final size:171
Alignment explanation
Indices: 18814--19350 Score: 533
Period size: 171 Copynumber: 3.2 Consensus size: 171
18804 NNNNNNNNCA
** * * * * *
18814 AAAATATGCAAAAATTCAACTTAAAATCAATTATAAGATTATAAAACAATTTTAAGCGAGTAATA
1 AAAATATAAAAAAATTCAACTTAAAACCAATTATGAGATTATAAAACAACTTAAAGCCAGTAATA
* * * *
18879 AGTCT-TTTAATAGAATGGGTGACTATAAATGGACTTTTCTTCCATATGAATGGCTTTTTCTACA
66 AGGCTATTGAA-GGAATGGGTGACTATAAATGGACTTTTCTTCTATATGAATGGCTTTTTCTACA
**********
18943 TGTTTCTTNNNNNNNNNNTTCAATTGTAGTCTATTTTAAGCT
130 TGTTTCTTGAAGTAGGCATTCAATTGTAGTCTATTTTAAGCT
* ** * *
18985 AAAATATAAAAAAATTTAGTTTAAAACCAATTATGAGATTATAAAACAACTTATAGCGAGTAATA
1 AAAATATAAAAAAATTCAACTTAAAACCAATTATGAGATTATAAAACAACTTAAAGCCAGTAATA
* * *
19050 AGGCTATTGAAGGAATAGGTGACTATAAATAGACTTTTCTTCTATATGAATAGCTTTTTCTACAT
66 AGGCTATTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTATATGAATGGCTTTTTCTACAT
* *
19115 GTTTCTTGAGGTAGGCATTCAATTGTAGCCTATTTTAAGCT
131 GTTTCTTGAAGTAGGCATTCAATTGTAGTCTATTTTAAGCT
* * **********
19156 AAAATGTAAAACAATTCAACTTAAAACCAATTATGAGATTATNNNNNNNNNNAAAGCCAGTAATA
1 AAAATATAAAAAAATTCAACTTAAAACCAATTATGAGATTATAAAACAACTTAAAGCCAGTAATA
* * * * * *
19221 AGGCTGTTGAAGGAATGGGTGACCATAAATGGACTATTCTTGTA-ATGAATGGC-TTTTCTATAC
66 AGGCTATTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTATATGAATGGCTTTTTCTACAT
* * * *
19284 GTTTCTTGAAGTAGGTATTCAATTATAGTCTGTTTTAA-CAA
131 GTTTCTTGAAGTAGGCATTCAATTGTAGTCTATTTTAAGC-T
* *
19325 AAAATATAAAAAACTTTAACTTAAAA
1 AAAATATAAAAAAATTCAACTTAAAA
19351 TCANNNNNNN
Statistics
Matches: 300, Mismatches: 64, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
168 1 0.00
169 63 0.21
170 8 0.03
171 224 0.75
172 4 0.01
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.34
Consensus pattern (171 bp):
AAAATATAAAAAAATTCAACTTAAAACCAATTATGAGATTATAAAACAACTTAAAGCCAGTAATA
AGGCTATTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTATATGAATGGCTTTTTCTACAT
GTTTCTTGAAGTAGGCATTCAATTGTAGTCTATTTTAAGCT
Found at i:19899 original size:171 final size:171
Alignment explanation
Indices: 19458--19941 Score: 564
Period size: 171 Copynumber: 2.8 Consensus size: 171
19448 NNNNNNTTGA
* * * * **
19458 TTTTAAGTTAAAGTTTTTTATATTTTTTG-TTAAAACAGACTATAATTGAACACCTA-CTTCAAG
1 TTTTAAGTTAAATTTTTTTATA-TTTTAGCTTAAAATAGACTACAATTGAATGCCTACCTT-AAG
* * * * *
19521 AAACATATAG-AAAAGCCATTCAT-TACAAGAATAGTCCATTTATAGTCACTCATTCCTTCAACA
64 AAACATGTAGAAAAAGCCATTCATATAGAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
* * ********** *
19584 GCCTTATTACTGGCTTTAANNNNNNNNNNAATCTCATAATTGG
129 GCCTTATTACTCGCTATAAGTTGTTTTATAATCTCATAATTGC
* * * *
19627 TTTTAAGTTGAATTTTTTTTACATTTTAGCTTAAAATAGGCTACAATTGAATGCCTACCTCAAGA
1 TTTTAAGTT-AAATTTTTTTATATTTTAGCTTAAAATAGACTACAATTGAATGCCTACCTTAAGA
* * *
19692 AACGTGTAGAAAAAGCTATTCATATAGAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAATAG
65 AACATGTAGAAAAAGCCATTCATATAGAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAG
19757 CCTTATTACTCGCTATAAGTTGTTTTATAATCTCATAATTGC
130 CCTTATTACTCGCTATAAGTTGTTTTATAATCTCATAATTGC
* *
19799 TTTTAAGCTAAATTTTTTTATATTTTAGCTTAAAATAGACTACAATTGAATGCCTACCTTGAGAA
1 TTTTAAGTTAAATTTTTTTATATTTTAGCTTAAAATAGACTACAATTGAATGCCTACCTTAAGAA
* * *
19864 ACATGTAGAAAAAGCCATTCATATGGAAAAAAAGTCCATTTATAGTCACCCATT-CTATTAAAAG
66 ACATGTAGAAAAAGCCATTCATATAGAAGAAAAGTCCATTTATAGTCACCCATTCCT-TCAAAAG
*
19928 ACTTATTACTCGCT
130 CCTTATTACTCGCT
19942 TTAAANNNNN
Statistics
Matches: 266, Mismatches: 43, Indels: 10
0.83 0.13 0.03
Matches are distributed among these distances:
169 14 0.05
170 45 0.17
171 133 0.50
172 74 0.28
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.36
Consensus pattern (171 bp):
TTTTAAGTTAAATTTTTTTATATTTTAGCTTAAAATAGACTACAATTGAATGCCTACCTTAAGAA
ACATGTAGAAAAAGCCATTCATATAGAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGC
CTTATTACTCGCTATAAGTTGTTTTATAATCTCATAATTGC
Done.