Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397874.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1179.0, 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: 32808
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.23
Warning! 12257 characters in sequence are not A, C, G, or T
Found at i:321 original size:172 final size:172
Alignment explanation
Indices: 1--508 Score: 485
Period size: 172 Copynumber: 3.0 Consensus size: 172
* * * * * *** * *
1 TTTATAATCTCATAATTCATTTTAAGTTGAA-GTTTTTTACATT-TTTTATCAAAATAGACTATA
1 TTTATAATCTCAAAATTGATTTTCAGTTCAATATTTTTTACATTATTGGCT-AAAACAGATTATA
* ** * * *
64 ATTGAATGTCTAGCTAGAGAAACGTCAAG-GAAAAAGCATTCATTGGCAAGAAATGTCTATTTAT
65 ATTGAATGTCTAGCTCGAGAAATATGAAGAG-AAAGGCATTCATTGGCAAGAAAAGTCTATTTAT
* *
128 AGTCTA-CTATTCCTTCAAAAGCCTTATTACTCACTTTAATTGGT
129 AGTC-ACCTATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGT
********** * * *
172 TTTATAATCTCAAAANNNNNNNNNNGTTCAATTTTTTTTATATTATTGGTTAAAACAGATTATAA
1 TTTATAATCTCAAAATTGATTTTCAGTTCAATATTTTTTACATTATTGGCTAAAACAGATTATAA
* * *
237 TTGAATGTCTAGCTCGAGAAATATGAAGAGCAAGGCATTCATTGGCAAGAAAAGTCCATTTAGAG
66 TTGAATGTCTAGCTCGAGAAATATGAAGAGAAAGGCATTCATTGGCAAGAAAAGTCTATTTATAG
* *
302 TCACCTATTCCTGCAAAAGCCTTATTACTAACTTTAAATAGT
131 TCACCTATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGT
** * *
344 TTTATAATCTCGTAATTGATTTTCAGTTCAATATTTTTTACATTTTTTGCT-AAACAGATTATAA
1 TTTATAATCTCAAAATTGATTTTCAGTTCAATATTTTTTACATTATTGGCTAAAACAGATTATAA
* * * * *
408 TTGAGTGTCTATG-TCAAGAAATATGGAA-A-AAAGGCATTTATTGGGAGGAAAAGTCTATTTAT
66 TTGAATGTCTA-GCTCGAGAAATAT-GAAGAGAAAGGCATTCATTGGCAAGAAAAGTCTATTTAT
*
470 AGTCACGC-ATTCCTTCAAAAGCCTTATTACTCGCTTTAA
129 AGTCAC-CTATTCCTTCAAAAGCCTTATTACTCACTTTAA
509 NNNNNNNNNN
Statistics
Matches: 270, Mismatches: 60, Indels: 15
0.78 0.17 0.04
Matches are distributed among these distances:
170 61 0.23
171 55 0.20
172 150 0.56
173 4 0.01
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.37
Consensus pattern (172 bp):
TTTATAATCTCAAAATTGATTTTCAGTTCAATATTTTTTACATTATTGGCTAAAACAGATTATAA
TTGAATGTCTAGCTCGAGAAATATGAAGAGAAAGGCATTCATTGGCAAGAAAAGTCTATTTATAG
TCACCTATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGT
Found at i:2209 original size:171 final size:171
Alignment explanation
Indices: 1893--3368 Score: 1585
Period size: 171 Copynumber: 8.6 Consensus size: 171
1883 NNNNNNNNNN
* * *
1893 AAAAAATTCAACTTAAAATCCATTATGAGATTATAAAACAATTTAAAGCGAGTAGTAAGGCTTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
* * * * * * * *
1958 TAAGGAATGGGTGACTATAAATGGACTTTTCTTCCCAATTAATG-GTTTTTCCTACATGTTTTCC
66 GAAGGAATGGATGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTT-CTTCATG-TTTCT
* * * *
2022 T-AAGTAGGCATTCAATTATAGTCTGGTTTAACTAAAAAGGT-
129 TGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTA
* *
2063 AAAAAATTCTAACTTAAAATCAATTATGAGGTTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
1 AAAAAATTC-AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * * ** **
2128 TGAAGGAATGGACGACTATAAATAGACTTTTTTTACCAATGAATGTCTTTTTCTTCACCTTTCCC
65 TGAAGGAATGGATGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTT
* * * * * *
2193 GAGCTGGACTTTCAATTATAATATGTTTTAAAC-AATAATGTA
130 GAGGTAGACATTCAATTATAGTCTGTTTT-AACTAAAAATGTA
* * * * * **
2235 AAACAAATTAAACCTAAAATTAATTTTGAGACTATAAAACCATTTAAAATGAGTAATAAGGCTTT
1 AAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * * *
2300 TAAAGAAATAGGA-GATTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTTCTTTATGTTTC
65 TGAAGGAAT-GGATGACTATAAATAGACTTTTCTTGCCAATGAATGC-CTTTTTCTTCATGTTTC
* * * * *
2364 TCGAGGTAAACATTCAATTATAGTCTGTTTTAACCAAAATTCTA
128 TTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTA
* * *
2408 AAACAATTTAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
* * * * * *
2473 GAAGGAATGGGTGACTATAAATAGACTTTTTTTGCTAGTAAATGCCTTTTTCTTCATGTTTCTGG
66 GAAGGAATGGATGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTG
* * * * *
2538 AGATAGACTTTTAATTGTAGTCTGTTTTAACTAAAAAT-TC
131 AGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTA
* *
2578 AAAAAA-TCTGACTTAAAATCAATTATGAGATTATAATACCATTTAAAGCGAGTAATAAGGCTTT
1 AAAAAATTC-AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
** * * * *** *
2642 TGAAGGAATGGGCGGCTATAAATAAACTTTTTTTAAGAGTGAATGCCTTTTTCTTCATGTTT-TT
65 TGAAGGAATGGATGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTT
* * *
2706 CGAGATAGACATTCAATTATAGTATGTTTTAACTAAAAATGAA
130 -GAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTA
* * * * * *
2749 AAAAAAATCAACTTAAAATTAAATATGAGATTATAAAACTATTTAAAGCGAGTTATAAGACTTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
* * * * * *
2814 GAAGAAATAGATGACTATAAATAGA-TGTTTCTTGTCAATGAATGCCTTTTTGTTCAAGTTTTTT
66 GAAGGAATGGATGACTATAAATAGACT-TTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTT
* * *
2878 GATGTAGACATTCAATTATAGTCTATTTGAA-TCAAAAATGTA
130 GAGGTAGACATTCAATTATAGTCTGTTTTAACT-AAAAATGTA
* * * *
2920 AACAAATTCAACTTAAAATCAATTATGAGATCATAAAACAATTTAAAGCTAGTAATAAGGCTTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
* * * * *
2985 GAAGGAATGGGTGACTATAAAAAGATTTTTCTT-CCAAATGAATGACTTTTTCTGCATGTTTCTT
66 GAAGGAATGGATGACTATAAATAGACTTTTCTTGCC-AATGAATGCCTTTTTCTTCATGTTTCTT
*
3049 GAGGTAGGCATTCAATTATAGTCTGTTTTAACTAAAAATGTA
130 GAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTA
* **
3091 AAAAAATTCAACTTAAAATCAATTATGATATT-TCAAAATAATTTAAAGCGAGTAATAAGGCTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTAT-AAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * * * * **
3155 TAAAGAAATTAGA-GACTATAAATGGACTTTTCTTGCCAATGGATGCTTTTTTCTTCACATTTCT
65 TGAAGGAA-TGGATGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCT
* * * * * *
3219 TGTGGTAAATATTCAATTATAGTCTATTTTAACCAAAAATATA
129 TGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTA
* * * * * *
3262 AAAAAATTTAACTTAAAATCAATTATAAGATTATAAAATCATTTTAAGCAAGAAATAAGGCTTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
* *
3327 GAAGAAATAGGA-GACTATAAATGGACTTTTCTTGCCAATGAA
66 GAAGGAAT-GGATGACTATAAATAGACTTTTCTTGCCAATGAA
3369 NNNNNNNNNN
Statistics
Matches: 1097, Mismatches: 184, Indels: 49
0.82 0.14 0.04
Matches are distributed among these distances:
169 2 0.00
170 167 0.15
171 676 0.62
172 198 0.18
173 54 0.05
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (171 bp):
AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
GAAGGAATGGATGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTG
AGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTA
Found at i:6981 original size:31 final size:31
Alignment explanation
Indices: 6938--7004 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
6928 TAAATGGACT
*
6938 TTTCTTGCAAATAAATACCTTTTTCTTCATG
1 TTTCTTGCAAATAAATACCTTTTTCTGCATG
* *
6969 TTTCTTGTAAATAAATGCCTTTTTCTGCATG
1 TTTCTTGCAAATAAATACCTTTTTCTGCATG
7000 TTTCT
1 TTTCT
7005 CAAAGTAGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.51
Consensus pattern (31 bp):
TTTCTTGCAAATAAATACCTTTTTCTGCATG
Found at i:9254 original size:171 final size:161
Alignment explanation
Indices: 8936--9264 Score: 345
Period size: 171 Copynumber: 2.0 Consensus size: 161
8926 NNNNNNNAAA
* *
8936 TCAA-TTATGAGATTATAAAATCATTTAAAGCGACTAATAAGGCTTTTAAAGAAATAGGAGACTA
1 TCAACTTATGAAATTATAAAACCATTTAAAGCGACTAATAAGGCTTTTAAAGAAATAGGAGACTA
* * * * * * *
9000 TAAACGAACATTTCTTCCCAATGAATGCTTTTTTCTTTACATTTCTCAAGCTAGACATTTAGTTA
66 TAAACGAACATTTCTTCCCAATAAATGCCTTTTTCTTCACATTTCTCAAGCTAAACACTGAATTA
*
9065 TAGTCTGTTTTAACCAAAAATATAAAAAACT
131 TAATCTGTTTTAACCAAAAATATAAAAAACT
* * * *
9096 TCAACTTANNNNNNNNNNTGAAATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAG
1 TCAACTTA----------TGAAATTATAAAACCATTTAAAGCGACTAATAAGGCTTTTAAAGAAA
* * * ** * *
9161 TATGTGACTATAAATGAAGTTTTCTTCTCAATAAATGCCTTTTTCTTCACATTTCTCAAGGTAAA
56 TAGGAGACTATAAACGAACATTTCTTCCCAATAAATGCCTTTTTCTTCACATTTCTCAAGCTAAA
* * *
9226 CACTGAATTATAATCTTTTTTGACCAAAAATGTAAAAAA
121 CACTGAATTATAATCTGTTTTAACCAAAAATATAAAAAA
9265 AAATTGAGCT
Statistics
Matches: 134, Mismatches: 24, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
160 4 0.03
161 3 0.02
171 127 0.95
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.34
Consensus pattern (161 bp):
TCAACTTATGAAATTATAAAACCATTTAAAGCGACTAATAAGGCTTTTAAAGAAATAGGAGACTA
TAAACGAACATTTCTTCCCAATAAATGCCTTTTTCTTCACATTTCTCAAGCTAAACACTGAATTA
TAATCTGTTTTAACCAAAAATATAAAAAACT
Found at i:12165 original size:172 final size:173
Alignment explanation
Indices: 11805--12130 Score: 426
Period size: 172 Copynumber: 1.9 Consensus size: 173
11795 TTTTTGAAGG
* * * *
11805 TAGACACTCAATTATAATCTATTTTGACCAAAAATATAAAAAAAAATTGAACTTAAAATCAATTA
1 TAGACACTCAATTATAATCTATTTTAACCAAAAATAGAAAAAAAAATTAAACCTAAAATCAATTA
** * * * * * *
11870 CGAGATTATTAAACCATTTAAAGCCAGTAATAAGGCTTTTGCAGGATTGGGTGACTCTAAATGGA
66 CGAGATTACAAAACCAATTAAAGCCAGTAATAAGGCTTTTGAAGGATAGGATGACTATAAATGAA
*
11935 CTTTTCTTGCCAATGAATGCCTTTTTCTTAACATTTCCCGAGC
131 CATTTCTTGCCAATGAATGCCTTTTTCTTAACATTTCCCGAGC
* * * * * *
11978 TAGACATTCAATTATATTCTATTTTAACCAATACT-GCAAAAAAAATTAAACCTAAACTCAATTT
1 TAGACACTCAATTATAATCTATTTTAACCAAAAATAGAAAAAAAAATTAAACCTAAAATCAA-TT
*
12042 A-GAGATTACAAAACCAATTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAT-ACTATAAATG
65 ACGAGATTACAAAACCAATTAAAGCCAGTAATAAGGCTTTTGAAGG-ATAGGATGACTATAAATG
12105 AACATTTCTTGCCAATGAATG-CTTTT
129 AACATTTCTTGCCAATGAATGCCTTTT
12131 NNNNNNNNNN
Statistics
Matches: 131, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
171 5 0.04
172 88 0.67
173 38 0.29
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.32
Consensus pattern (173 bp):
TAGACACTCAATTATAATCTATTTTAACCAAAAATAGAAAAAAAAATTAAACCTAAAATCAATTA
CGAGATTACAAAACCAATTAAAGCCAGTAATAAGGCTTTTGAAGGATAGGATGACTATAAATGAA
CATTTCTTGCCAATGAATGCCTTTTTCTTAACATTTCCCGAGC
Found at i:13521 original size:171 final size:173
Alignment explanation
Indices: 13134--13534 Score: 492
Period size: 171 Copynumber: 2.3 Consensus size: 173
13124 CATTGACAAG
* * *
13134 AAATGTCTATTTATAGTCTCCTATTTCTTCAAAAGCCTTATTACTCCCTTTAAATAG-TTTAATA
1 AAATGTCTATTTATAGTCTCCTATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAATA
* * *
13198 ATCTCAAAATTGATTTTAAGTTCAATTGTTTTTACATTATTGGTTAAAAAAGATTATAATTTAAT
66 ATCTCAAAATTGATTTTAAGTTCAATTGTTTTTACATTATTGGTTAAAAAAGACTATAACTGAAT
* *
13263 GCCTACCCTAAGAAACATGAAGAAAAAGGCATTCATTGGCAAA
131 GCCTACCCTAAGAAACATGAAGAAAAAAGCATTCATCGGCAAA
* * * * * **
13306 AAAAGTCTATTTATACTAATGC-ATTCCTTCAAAAGCCATATTACTCGTTTTAAATGGTTTTAA-
1 AAATGTCTATTTATAGT-CTCCTATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAAT
* * *
13369 AATCTCATAATTGATTTTAAGTTGCAGTT-TTTTATACATT-TT-GTTAAAATAGACTATAACTG
65 AATCTCAAAATTGATTTTAAGTT-CAATTGTTTT-TACATTATTGGTTAAAAAAGACTATAACTG
* * * * *
13431 AATGTCTA-CCTCAAGAAACGTGAAGAAAAAATCATTTATCGGTAAA
128 AATGCCTACCCT-AAGAAACATGAAGAAAAAAGCATTCATCGGCAAA
* *
13477 AAATGTCCATTTATAGTCTCCTAATCCTTCAAAAGCCTTATTACTCACTTTAAATGGT
1 AAATGTCTATTTATAGTCTCCTATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGT
13535 NNNNNNNNNN
Statistics
Matches: 192, Mismatches: 31, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
170 5 0.03
171 97 0.51
172 73 0.38
173 17 0.09
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (173 bp):
AAATGTCTATTTATAGTCTCCTATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAATA
ATCTCAAAATTGATTTTAAGTTCAATTGTTTTTACATTATTGGTTAAAAAAGACTATAACTGAAT
GCCTACCCTAAGAAACATGAAGAAAAAAGCATTCATCGGCAAA
Found at i:20794 original size:171 final size:169
Alignment explanation
Indices: 20123--20867 Score: 575
Period size: 171 Copynumber: 4.4 Consensus size: 169
20113 NNNNNNNNNC
* ** *
20123 TACTCGCTTTAAATTATTTTATAATCTAATAATTGATTTTAAGTTGAA--TTTTTAGGGTTTTTA
1 TACTCGCTTTAAATTATTTTATAATCTAATAATT-AATTTAAGTTGAATTTTTTTA-CATTTTTG
* *
20186 GTTAAAATAGACTATACTTGAATGTCTACCTTAAGAAACGTGAAGAAAAAGAAATTCATTGGCAA
64 GTTAAAACAGACTATAATTGAATGTCTACCTTAAGAAACGTGAAGAAAAAGAAATTCATTGGCAA
*
20251 GAAAAGCC-TATTATAGTCACCCATTTCTTCAAAAGCCTTAT
129 GAAAAGCCAT-TTATAGTCACCCATTCCTTCAAAAGCCTTAT
* ********** *
20292 TACTCACTTNNNNNNNNNNTATAATCTCATAATTAATTGTAAGTTGAATTTTTTTACATTTGTT-
1 TACTCGCTTTAAATTATTTTATAATCTAATAATTAATT-TAAGTTGAATTTTTTTACATTT-TTG
* * * * * * * *
20356 GTTAAAACAAACTATAATTAAATATCTACTTTGAGAAATGTGAAGAAAAACATATTCATTGGCAA
64 GTTAAAACAGACTATAATTGAATGTCTACCTTAAGAAACGTGAAGAAAAAGAAATTCATTGGCAA
* * **********
20421 GAAAAATCCATTTATAGTCACCTATNNNNNNNNNNGCCTTAT
129 G-AAAAGCCATTTATAGTCACCCATTCCTTCAAAAGCCTTAT
* * ** * * * * ** *
20463 TACTCACTTTAAGTGGTTTTATAATCTCATATTTTATTTCAAGTTGAAATTTTTTATGTCTTTGG
1 TACTCGCTTTAAATTATTTTATAATCTAATAATTAATTT-AAGTTGAATTTTTTTACATTTTTGG
* * * * * * * ** *
20528 CTAAAACAGACTATTATTGAATGTCTACTTTGAGAAACATGAATAACAAGCCATTCATTAGCAAG
65 TTAAAACAGACTATAATTGAATGTCTACCTTAAGAAACGTGAAGAAAAAGAAATTCATTGGCAAG
********** *
20593 AAAAGTCCATTTATNNNNNNNNNNTCCTTCAAAAGCCATAT
130 AAAAG-CCATTTATAGTCACCCATTCCTTCAAAAGCCTTAT
* *
20634 TACTCGCTTTAAATTATTTTATGATGTAAT-ATTCAATCTTAAGTTGAATTTTTTTACATTTTTG
1 TACTCGCTTTAAATTATTTTATAATCTAATAATT-AAT-TTAAGTTGAATTTTTTTACATTTTTG
* * *
20698 GTTAAAACTGACTATAATTGAATGTTTACCTTAAGAAACGTGAAGAAAAAAAAATTCATTGGCAA
64 GTTAAAACAGACTATAATTGAATGTCTACCTTAAGAAACGTGAAGAAAAAGAAATTCATTGGCAA
* * *
20763 GAAAAGCCTTTTTATAGTCACCCATTCCTTCAAAAGACTTTT
129 GAAAAGCC-ATTTATAGTCACCCATTCCTTCAAAAGCCTTAT
* * * * *
20805 TATTCGCTTTAAA-TAGTTTTATAATCTCATAATTGATTGTAAGTTAAATTTTTTTATATTTTT
1 TACTCGCTTTAAATTA-TTTTATAATCTAATAATTAATT-TAAGTTGAATTTTTTTACATTTTT
20868 NNNNNNNNNN
Statistics
Matches: 426, Mismatches: 135, Indels: 28
0.72 0.23 0.05
Matches are distributed among these distances:
168 3 0.01
169 31 0.07
170 73 0.17
171 313 0.73
172 6 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.38
Consensus pattern (169 bp):
TACTCGCTTTAAATTATTTTATAATCTAATAATTAATTTAAGTTGAATTTTTTTACATTTTTGGT
TAAAACAGACTATAATTGAATGTCTACCTTAAGAAACGTGAAGAAAAAGAAATTCATTGGCAAGA
AAAGCCATTTATAGTCACCCATTCCTTCAAAAGCCTTAT
Found at i:22599 original size:172 final size:162
Alignment explanation
Indices: 22304--22636 Score: 348
Period size: 172 Copynumber: 2.0 Consensus size: 162
22294 ATATTTTTGG
* * * *
22304 TTAAAATAGACTATAATTGAATGTCTACTTTAAGAAACGTGAAGAAAAAGGCATTCATTTGTAAA
1 TTAAAATAGACTATAATTGAATGTCTACCTTAAGAAACGTGAAGAAAAAAGCATTCATTGGCAAA
* ** * * *
22369 AAAAGTCCATTTATAGTCACCCATTCTTTCAAAAACCTTATTACTCGCTCCGAATGGTTTTATAA
66 AAAAGTCCATTTATAGTAACCCATTCCATCAAAAACCTCATTACTCACTCCAAATGGTTTTATAA
*
22434 TCTCATAAT-TGATTTTAAGTTGAATGTTTTTT
131 TCTCAAAATAT-ATTTTAAGTTGAATGTTTTTT
* *
22466 NNNNNNNNNNTTAAAATAGACTATAATTGAATG-CTAGCCTTGAGAAACGT-AATGAAAAAAGTA
1 ----------TTAAAATAGACTATAATTGAATGTCTA-CCTTAAGAAACGTGAA-GAAAAAAGCA
* * ** **
22529 TTCATTGGCAAGAAAAGTCCTTTTATAGTAACCCATTCCATCAAAAGTCTCATTACTCACTTTAA
54 TTCATTGGCAAAAAAAGTCCATTTATAGTAACCCATTCCATCAAAAACCTCATTACTCACTCCAA
*
22594 ATGGTTTTATAATCTCAAAATATATTTTAGGTTGAATGTTTTT
119 ATGGTTTTATAATCTCAAAATATATTTTAAGTTGAATGTTTTT
22637 ACATTTTTCA
Statistics
Matches: 138, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
171 5 0.04
172 132 0.96
173 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.36
Consensus pattern (162 bp):
TTAAAATAGACTATAATTGAATGTCTACCTTAAGAAACGTGAAGAAAAAAGCATTCATTGGCAAA
AAAAGTCCATTTATAGTAACCCATTCCATCAAAAACCTCATTACTCACTCCAAATGGTTTTATAA
TCTCAAAATATATTTTAAGTTGAATGTTTTTT
Found at i:23685 original size:171 final size:170
Alignment explanation
Indices: 23409--23787 Score: 444
Period size: 171 Copynumber: 2.2 Consensus size: 170
23399 TTTTCTATAC
* * *
23409 GTTTTTCAAGGC-AAGCATTCAATTATAGTCTGTTGTAATGAAAAATATAAAACATTCAACTTAA
1 GTTTCTCAAGGCTAA-CATTCAATTATAGTCTGTTTTAAAGAAAAATATAAAACATTCAACTTAA
* * * * * * *
23473 AATATATTTTGAGATTATAAAATCATTTAAAGTGAGTAATAAGGGTTTTGATGAAATGGGTGACT
65 AATATATTATGAGATTATAAAACCATTCAAAGCGAGTAATAAGGCTTTTGAAGAAATAGGTGACT
* *
23538 ATAAAACG-ACTTTCTTGCCAATAAAT-GCTTGTTTCATTAT
130 ATAAAACGAACTTTCTTGCCAATAAATACCTT-TTTCATCAT
* *
23578 GTTTCTCAAGGCTAACACTCAATTATAGTCTGTTTTAAAGAAAAATATAAAAAATATTCAACTTA
1 GTTTCTCAAGGCTAACATTCAATTATAGTCTGTTTTAAAGAAAAATAT--AAAACATTCAACTTA
* *
23643 AAAT-TAATTATGAGATTATAAAACCATTCAGAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGA
64 AAATAT-ATTATGAGATTATAAAACCATTCAAAGCGAGTAATAAGGCTTTTGAAGAAATAGGTGA
* ** * * *
23707 CTATCAATGGAATTTTCTTGCCAATGAATACCTTTTTCCTCAT
128 CTATAAAACGAACTTTCTTGCCAATAAATACCTTTTTCATCAT
* * *
23750 GTTTCTTAAAG-TAGACATTCAATTATAGTCTATTTTAA
1 GTTTCTCAAGGCTA-ACATTCAATTATAGTCTGTTTTAA
23788 CNNNNNNNNN
Statistics
Matches: 177, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
169 41 0.23
170 3 0.02
171 76 0.43
172 54 0.31
173 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (170 bp):
GTTTCTCAAGGCTAACATTCAATTATAGTCTGTTTTAAAGAAAAATATAAAACATTCAACTTAAA
ATATATTATGAGATTATAAAACCATTCAAAGCGAGTAATAAGGCTTTTGAAGAAATAGGTGACTA
TAAAACGAACTTTCTTGCCAATAAATACCTTTTTCATCAT
Found at i:24116 original size:171 final size:171
Alignment explanation
Indices: 23816--24285 Score: 488
Period size: 171 Copynumber: 2.7 Consensus size: 171
23806 NNNNNNNNNN
**
23816 AGCGAG-AAATAAGGCTTTTGAAGGAAT-TGATGACTATAAA-AGGACTTTTCTTGCCAATGAAT
1 AGCGAGTAAA-AAGGCTTTTGAAGGAATGTG-TGACTATAAATA-GACTTTTCTTAACAATGAAT
* * ** * * * *
23878 G-TTTGTCTCTTTATGTTTCTCAAGGCTGACA-A-TCAATTATAGTCTGCTGTAACAAAAAATAT
63 GCTTT-TTTCTTTACGTTTCTTGAGG-T-ACACATTCAATTATAGTCTGTTTTAACCAAAAATGT
* ** **
23940 AAAAAAATTTAATTTAAAATCAATTATGAGATTAT-AAAGCTATTCAA
125 AAAAAAATTGAACCTAAAAAAAATTATGAGATTATAAAAG-TATTCAA
* * *
23987 AGCGAGTAAAAAGGCTTTTGAAGAAATGTGTGACTATAAATAGACTTTTTTTATCAATGAATGCT
1 AGCGAGTAAAAAGGCTTTTGAAGGAATGTGTGACTATAAATAGACTTTTCTTAACAATGAATGCT
* * *
24052 TTTTTCTTCACATTTCTTGAGGTACACATTCAATTATAGTCTGTTTTAACCAATAATGTAAAAAA
66 TTTTTCTTTACGTTTCTTGAGGTACACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAA
* *
24117 ATTGAACCTAAAAAAAATTTTGAGATTATAAAAGTATTTAA
131 ATTGAACCTAAAAAAAATTATGAGATTATAAAAGTATTCAA
* * ** *** * * *
24158 AACGAGTAATAAGGCTTTTGTTGGAATAG-AACACTATAAATGGACATTTCTTAACAATGGATGC
1 AGCGAGTAAAAAGGCTTTTGAAGGAAT-GTGTGACTATAAATAGACTTTTCTTAACAATGAATGC
* * *
24222 TTTTTTCTTTAGGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAA
65 TTTTTTCTTTACGTTTCTTGAGGTACACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAA
24286 CANNNNNNNN
Statistics
Matches: 250, Mismatches: 41, Indels: 16
0.81 0.13 0.05
Matches are distributed among these distances:
169 3 0.01
170 2 0.01
171 231 0.92
172 14 0.06
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (171 bp):
AGCGAGTAAAAAGGCTTTTGAAGGAATGTGTGACTATAAATAGACTTTTCTTAACAATGAATGCT
TTTTTCTTTACGTTTCTTGAGGTACACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAA
ATTGAACCTAAAAAAAATTATGAGATTATAAAAGTATTCAA
Found at i:26624 original size:171 final size:171
Alignment explanation
Indices: 26277--26639 Score: 413
Period size: 171 Copynumber: 2.1 Consensus size: 171
26267 NNNNNNNNNN
* * * * *
26277 ATAAGGTTTTTGAAGGAATTGGTGACTCTAAATGGACTTTTCTTGCCAATGAATATGTTTTTCTT
1 ATAAGGCTTTTGAAGGAATGGGTGACTATAAAAGGACTTTTCTTGCCAATGAATATCTTTTTCTT
*** * * * *
26342 CACATTTCTCAAGGTAGGTATTTAATTATAGTTTGTTTTAACAAAAAATGTAAAAAAATTGAACT
66 CACATTTCTCAAGGTAAACATTCAATTATAGTCTATTTTAACAAAAAATATAAAAAAATTGAACT
* * ********** *
26407 TACAATCAATTATGAGATTATAAAANNNNNNNNNNCGAGTA
131 TAAAATCAATTATGAAATTATAAAACAATTGAAAGCGAGCA
*
26448 ATAAGGCTTTTGAAGGAATGGGTGACTATAAAAAGG-CTTTTCTTGCCAATGAATTTCTTTTTCT
1 ATAAGGCTTTTGAAGGAATGGGTGACTAT-AAAAGGACTTTTCTTGCCAATGAATATCTTTTTCT
** * * * *
26512 TCATGTTTCTTAAGGTAAACATTCAATTATAGTCTATTTTAACTAAAAATATAAGAAAATTTAAC
65 TCACATTTCTCAAGGTAAACATTCAATTATAGTCTATTTTAACAAAAAATATAAAAAAATTGAAC
26577 TTAAAATCAATTATGAAATTATAAAACAATTGAAAGCGAGCA
130 TTAAAATCAATTATGAAATTATAAAACAATTGAAAGCGAGCA
*
26619 ATAAGGCTTTTGAAGAAATGG
1 ATAAGGCTTTTGAAGGAATGG
26640 AAAAATATAA
Statistics
Matches: 158, Mismatches: 33, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
171 153 0.97
172 5 0.03
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.35
Consensus pattern (171 bp):
ATAAGGCTTTTGAAGGAATGGGTGACTATAAAAGGACTTTTCTTGCCAATGAATATCTTTTTCTT
CACATTTCTCAAGGTAAACATTCAATTATAGTCTATTTTAACAAAAAATATAAAAAAATTGAACT
TAAAATCAATTATGAAATTATAAAACAATTGAAAGCGAGCA
Found at i:28335 original size:170 final size:172
Alignment explanation
Indices: 27952--28341 Score: 398
Period size: 170 Copynumber: 2.3 Consensus size: 172
27942 AAAGTCCTTT
* * ** **
27952 TATAGTCACTCATTCCTTAAAAAACCTTATTACTCTTTTTAAATTATTTTATAATATAATAATTG
1 TATAGTCACACATTCCTTAAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATATAATAATTG
* * * **
28017 ATTTTAAGTTGATTTTTTTTTGCAATTTTACTTAAAAACAGACTATAATTGATTGTCTACCTTGA
66 ATTTTAAGTTGATTTTTTTTT-CAATTTTACTTAAAAACAGACAATAATTGAATGTCTACATCAA
* *
28082 GAAACGTGAAGAAAAAAGCATACACTGGCAAAAAATATCCATT
130 GAAACGTGAAGAAAAAAGCATACACTGACAAAAAATATCCATC
* * * *
28125 TATAGTCTCATATT-CTCTCAAAAGCCTTTTTACT-GCTTTAAATGGTTTTATAATATCAA-AAT
1 TATAGTCACACATTCCT-TAAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATAT-AATAAT
* * *
28187 TGATTTTAGGTTTATTTTTTTTAT-ATTTTTACTT-AAAACAGACAATAATTGAATGTCTACATC
64 TGATTTTAAGTTGATTTTTTTT-TCAATTTTACTTAAAAACAGACAATAATTGAATGTCTACATC
* * * * ** * **
28250 AAGGAATGTGAAGAAAAAGGCATTA-ATTGATTAAAAATGTTTA-C
128 AAGAAACGTGAAGAAAAAAGCA-TACACTGACAAAAAATATCCATC
* * *
28294 TATATTCACCCATTCCTTTAAAAGCCTTATTACTCGCTTTAAATGGTT
1 TATAGTCACACATTCCTTAAAAAGCCTTATTACTCGCTTTAAATGGTT
28342 NNNNNNNNNN
Statistics
Matches: 176, Mismatches: 35, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
169 25 0.14
170 69 0.39
171 11 0.06
172 43 0.24
173 28 0.16
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (172 bp):
TATAGTCACACATTCCTTAAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATATAATAATTG
ATTTTAAGTTGATTTTTTTTTCAATTTTACTTAAAAACAGACAATAATTGAATGTCTACATCAAG
AAACGTGAAGAAAAAAGCATACACTGACAAAAAATATCCATC
Found at i:29026 original size:170 final size:161
Alignment explanation
Indices: 28892--29205 Score: 247
Period size: 170 Copynumber: 1.9 Consensus size: 161
28882 NNNNNNNNNN
* * * * * *
28892 AGTTGATTTTTTTTATATTTTTGGTTAAAACAGATTATAATTGAATGTCTACTTTGAGAAACATG
1 AGTTGATTTTTTTTACATTTTTAGTCAAAACAGATTATAATTGAATATCTACCTCGAGAAACATG
* * * * *
28957 AAGAGAAAGGCATTTATT-GGAAGAAAAGTCCATTTATAGTCACCCATTCCATCAAAAGCCTTGT
66 AACAAAAAGGCATTCATTGGGAAGAAAAGTCCATTTATAGTAACCCATTCCATCAAAAGCCTTAT
*
29021 TACTCACTTTGAATAGTTTTATAATCTCATA
131 TACTCACTTTAAATAGTTTTATAATCTCATA
* * * * * * *
29052 A-TTGATTNNNNNNNNNNTTTTTTTATATTTTTAGTTAAAATAGACTGTAATTGAATGTCAACCT
1 AGTTGA-T----------TTTTTTTACATTTTTAGTCAAAACAGATTATAATTGAATATCTACCT
* * * * * * * **
29116 CGAGAAACATAAAGAAACAA-GTATTCATTGGCAAGAGAAGTCCTTTTATAGTCACCCATTCTTT
55 CGAGAAACATGAACAAA-AAGGCATTCATTGGGAAGAAAAGTCCATTTATAGTAACCCATTCCAT
29180 CAAAAGCCTTATTACTCACTTTAAAT
119 CAAAAGCCTTATTACTCACTTTAAAT
29206 GNNNNNNNNN
Statistics
Matches: 123, Mismatches: 18, Indels: 15
0.79 0.12 0.10
Matches are distributed among these distances:
159 4 0.03
160 2 0.02
170 62 0.50
171 55 0.45
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.37
Consensus pattern (161 bp):
AGTTGATTTTTTTTACATTTTTAGTCAAAACAGATTATAATTGAATATCTACCTCGAGAAACATG
AACAAAAAGGCATTCATTGGGAAGAAAAGTCCATTTATAGTAACCCATTCCATCAAAAGCCTTAT
TACTCACTTTAAATAGTTTTATAATCTCATA
Found at i:30800 original size:172 final size:171
Alignment explanation
Indices: 30515--30840 Score: 408
Period size: 172 Copynumber: 1.9 Consensus size: 171
30505 NNNNNNNNNN
* * *
30515 AATCTCATAATTGATTTTAAGTTAAATTTTTTTACTTTTTTGGTTAAAATAGACTATAATTGAGT
1 AATCTCATAATTGACTTTAAGTTAAATTTTTTTACTTTTTTGGTTAAAACAGACTATAATTGAAT
* * * * * *
30580 GCCTACTTTAAGAAATACGAGGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTTACTC
66 GCCTACCTCAAGAAACACAAGGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCC
* * * *
30645 ATTGCTTTAAAAGCCTTATTACTCGCTCTGAATGGTTTTAT
131 ATTCCATCAAAACCCTTATTACTCGCTCTGAATGGTTTTAT
*
30686 AATCTCATAATTGACTTTAAGTTGAATTGTTTTGATA-TTTTTT-GTTAAAACAGACTATAATTG
1 AATCTCATAATTGACTTTAAGTTAAATT-TTTT--TACTTTTTTGGTTAAAACAGACTATAATTG
* * * * *
30749 AATG-TTAACCTCGAGAAACATAATGAAACAA-GCATTCATTGGCAAGAAAAGTCCTTTTATAGT
63 AATGCCT-ACCTCAAGAAACACAAGGAAA-AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGT
30812 CACCCATTCCATCAAAACCCTTATTACTC
126 CACCCATTCCATCAAAACCCTTATTACTC
30841 ACTTTAAANN
Statistics
Matches: 131, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
171 27 0.21
172 94 0.72
173 8 0.06
174 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (171 bp):
AATCTCATAATTGACTTTAAGTTAAATTTTTTTACTTTTTTGGTTAAAACAGACTATAATTGAAT
GCCTACCTCAAGAAACACAAGGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCC
ATTCCATCAAAACCCTTATTACTCGCTCTGAATGGTTTTAT
Done.