Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398267.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_157.0, 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: 31655
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.23
Warning! 12408 characters in sequence are not A, C, G, or T
Found at i:386 original size:170 final size:161
Alignment explanation
Indices: 182--507 Score: 347
Period size: 170 Copynumber: 2.0 Consensus size: 161
172 TGGATATCTT
* *
182 TTTCTTCACGTTTCTCGAGGTAAAAATACAATTATAATCTATTTTAATAATAA-ATATAAAAAAG
1 TTTCTTCACGTTTCTAGAGGTAAAAATACAATTATAATCTATTTTAATAA-AATATATAAAAAAA
* * *
246 TTC-AACTTCAAA-CTAATTATGAGATTATAAACTATTT-AAAGCGAATAATAAGGCTTTCGAAG
65 TTCAAAC-TAAAATC-AATTATGAGATTATAAAATATTTCAAAGCGAATAATAAAGCTTTCGAAG
*
308 GCAT-GAGTTACAATAAATGGACTTTTCTTGCCAA
128 GCATAG-GTGACAATAAATGGACTTTTCTTGCCAA
* * * * *
342 NNNNNNNNNNTTTCTTCACGTTTCTAGATGTACACATTCAATTATAATCTGTTTTAATAAAATAT
1 ----------TTTCTTCACGTTTCTAGAGGTAAAAATACAATTATAATCTATTTTAATAAAATAT
* * *
407 ATAAAAAAATTCAAACTAAAATCAATTATGAGGTTATAAAATGTTTCAAAGCGAGTAATAAAGCT
56 ATAAAAAAATTCAAACTAAAATCAATTATGAGATTATAAAATATTTCAAAGCGAATAATAAAGCT
* *
472 TTTGAAGGCATAGGTGACTATAAATGGACTTTTCTT
121 TTCGAAGGCATAGGTGACAATAAATGGACTTTTCTT
508 NNNNNNNNNN
Statistics
Matches: 135, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
169 2 0.01
170 81 0.60
171 51 0.38
172 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.34
Consensus pattern (161 bp):
TTTCTTCACGTTTCTAGAGGTAAAAATACAATTATAATCTATTTTAATAAAATATATAAAAAAAT
TCAAACTAAAATCAATTATGAGATTATAAAATATTTCAAAGCGAATAATAAAGCTTTCGAAGGCA
TAGGTGACAATAAATGGACTTTTCTTGCCAA
Found at i:1725 original size:170 final size:169
Alignment explanation
Indices: 1201--1743 Score: 455
Period size: 170 Copynumber: 3.2 Consensus size: 169
1191 NNNNNNNNNN
* * * * * *
1201 ATTAAAATCAATTATGAGATTATCAAATTATTTAAAGCGAGTAATGATGCTTTCCAAGGCATGGT
1 ATTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATGGT
* * * * * * *
1266 GACTATGAATGAACTTTTTTTGTCAATA-AATATCTTTTTCTTCACGTTTCTCGAGTTAAACATT
66 GACTATAAATGGACTTTTCTTGCCAA-AGGATATCTTTTTCTTCACGTTTCTCGAGATAGACATT
* * *
1330 TAATTATAATCTGTTTTAATAAAAATATAAAAAAAATTAA
130 CAATTATAATCAGTTTTAATAAAAATATAAAAAAAATCAA
* * * ** * *
1370 CTTAAAATTAATTATGGGGCTATAAAAACATTT-AAGCCGAGCAATAAGGCTTTCGAAGGTATGG
1 ATTAAAATCAATTATGAGATTATAAAATCATTTAAAG-CGAGTAATAAGGCTTTCGAAGGTATGG
* * * * * *
1434 ATGACTATAAATGGACTTTTCTTGCTAACGGATGTCTGTTTCTTCTCGTTTCTCGAGGTAGACAT
65 -TGACTATAAATGGACTTTTCTTGCCAAAGGATATCTTTTTCTTCACGTTTCTCGAGATAGACAT
* *************
1499 TCCATTATAATCCAG-TTTAATAAAAA-ANNNNNNNNNNNNNN
129 TCAATTATAAT-CAGTTTTAATAAAAATA-TAAAAAAAATCAA
********* * *
1540 NNNNNNNNNAATTATGAGATTATAAAATCATTTAAAGCAAGTGATAAGGCTTTCGAAGGTATGAG
1 ATTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATG-G
* * * *
1605 TGACCATAAATGGACTTTTCTTGCCAAAGGATATCTTTTTCCTCACATTGCTCGAGATAGACATT
65 TGACTATAAATGGACTTTTCTTGCCAAAGGATATCTTTTTCTTCACGTTTCTCGAGATAGACATT
**
1670 CAATTATAATCAGTTTTAATAAAAATATAAAAAATCTCAA
130 CAATTATAATCAGTTTTAATAAAAATATAAAAAAAATCAA
*
1710 ATTAAAATCAATTATGAGGTTATAAAATCATTTA
1 ATTAAAATCAATTATGAGATTATAAAATCATTTA
1744 NNNNNNNNNN
Statistics
Matches: 274, Mismatches: 91, Indels: 17
0.72 0.24 0.04
Matches are distributed among these distances:
168 3 0.01
169 51 0.19
170 213 0.78
171 7 0.03
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.34
Consensus pattern (169 bp):
ATTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATGGT
GACTATAAATGGACTTTTCTTGCCAAAGGATATCTTTTTCTTCACGTTTCTCGAGATAGACATTC
AATTATAATCAGTTTTAATAAAAATATAAAAAAAATCAA
Found at i:3193 original size:171 final size:161
Alignment explanation
Indices: 2999--3309 Score: 333
Period size: 171 Copynumber: 1.9 Consensus size: 161
2989 NNNNNNNNNA
* *
2999 CTTTCGAAGGCATAAGGGACTATAAATGGACTTTTCTT-ATCAATGGATAT-CTTTTTCTT-CAT
1 CTTTCGAAGGCATAAGGGACTATAAATGGACTTCTCTTGAT-AATGGATATAATTTTTCTTACA-
** * * *
3061 GTTTTTTGAGGTGGACATTTAATTATAATCTATTTTTATAAAAATTATAAAAAAATTCAACTTAA
64 -TTTTTTGAGGCAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAAATTCAACTTAA
3126 AATCAATTATGAGGTTATAANNNNNNNNNNGGCGAGTAATAAGG
128 AATCAATTATGAGGTTATAA----------GGCGAGTAATAAGG
* * * *
3170 CTTTCGAAGGTAT-GGGTGACTATAAATGGACTTCTCTTGGTAATGGATATAATTTTTTTTACAT
1 CTTTCGAAGGCATAAGG-GACTATAAATGGACTTCTCTTGATAATGGATATAATTTTTCTTACAT
* * * *
3234 TTTTTGAGGCAGACGTTCAATTATAATCTATTTTAATAAAAAATCTAAACAAGTTCAACTTAAAA
65 TTTTTGAGGCAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAAATTCAACTTAAAA
3299 TCAATTATGAG
130 TCAATTATGAG
3310 ATTAAAAAAC
Statistics
Matches: 121, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
170 2 0.02
171 109 0.90
172 8 0.07
173 2 0.02
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.37
Consensus pattern (161 bp):
CTTTCGAAGGCATAAGGGACTATAAATGGACTTCTCTTGATAATGGATATAATTTTTCTTACATT
TTTTGAGGCAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAAATTCAACTTAAAAT
CAATTATGAGGTTATAAGGCGAGTAATAAGG
Found at i:6058 original size:171 final size:171
Alignment explanation
Indices: 5101--6118 Score: 702
Period size: 171 Copynumber: 6.0 Consensus size: 171
5091 NNNNNNNNNN
* * * * * *
5101 ATAATTGAATATCTGACTCAAGAAACGCGAAGAAAAAGATATCCATTGGCAAGAAAGGTTC-ATT
1 ATAATTGAATGTCTGCCTCAAGAAATGTGAAGAAAAAGATATCCATTGACAAGAAAAG-TCAATT
* * *
5165 TATAGTCACCCATGTCTTCGAGAA-CCTTATTACTCGCTTTAAATACTTTTTTAACCTCATAATT
65 TATAGTCACCCATGCCTTCGA-AAGCCTTATTACTCGCTTTAAATAGTTTTTTAATCTCATAATT
*
5229 -AGTTTAAAGTTAAA-TTTTTTATATTTTTTTATTAAAATAGATT
129 GA-TTTTAAGTTAAACTTTTTTATA-TTTTTTATTAAAATAGATT
*********** * * * *
5272 ATAATTGAANNNNNNNNNNGAGGAATGTGAAGAAAAAGATATCCATT-AGCAAGAATATTCCATT
1 ATAATTGAATGTCTGCCTCAAGAAATGTGAAGAAAAAGATATCCATTGA-CAAGAAAAGTCAATT
* * * *
5336 TATAGTCACCTATGCCATCGAAAGCCTTATGACTCGCTTTAATTAGTTTTTTAATCTCATAATTG
65 TATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTTTAATCTCATAATTG
* * *
5401 ATTTTAAGTTGAACTTGTTTATATTTTTTATTAAAACAGATT
130 ATTTTAAGTTAAACTTTTTTATATTTTTTATTAAAATAGATT
* * * * * * *
5443 ATAATTGAACGTAC-GCCTTAAAAAATATTAA-AAAAATGATA-CTCATTGACAAAAAAAGTCTA
1 ATAATTGAATGT-CTGCCTCAAGAAATGTGAAGAAAAA-GATATC-CATTGACAAGAAAAGTCAA
* * * * ********** *
5505 TTCATAGTCACCCATGCCTCCGAAAGCATCATTACTCGCTTTAANNNNNNNNNNAATCTCGTAAT
63 TTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTTTAATCTCATAAT
* * * *
5570 TGGTTTTAAGGTAAA-TTGTTTTATAATTTGTATTAAAATAGATT
128 TGATTTTAAGTTAAACTT-TTTTATATTTTTTATTAAAATAGATT
* * ** ** * * ** *
5614 ATAATTGAATGTCTACTTTGAGAAACATAAAGAAAAAGATATCGATTGGTAAGAAAAGTCCATTT
1 ATAATTGAATGTCTGCCTCAAGAAATGTGAAGAAAAAGATATCCATTGACAAGAAAAGTCAATTT
* * **********
5679 ATAGTC-CCTTATGCCTTCGAAAGTCNNNNNNNNNNCTTTAAATAGTTTTTTAATCTCATAATT-
66 ATAGTCACC-CATGCCTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTTTAATCTCATAATTG
* * * * *
5742 AGTTTTAAGTTACACTTTTTTATATTTTTTTATTGAAACAAATA
130 A-TTTTAAGTTAAACTTTTTTATA-TTTTTTATTAAAATAGATT
* *
5786 ATAATTGAATGT-TCACCTCAAGAAATGTCAAGAAAAAGATATCCATT-AGCAAGAAAAGTCAAT
1 ATAATTGAATGTCT-GCCTCAAGAAATGTGAAGAAAAAGATATCCATTGA-CAAGAAAAGTCAAT
* *************** * * *
5849 TTATAGCCACCCATGCCNNNNNNNNNNNNNNNACTCGCTTTAAAT-GATTTTATAACCTTATAAT
64 TTATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATAG-TTTTTTAATCTCATAAT
* * * *
5913 TGATTTTAATTTAAATTTTTTTCTATTTTTTATTAAAATAAATT
128 TGATTTTAAGTTAAACTTTTTTATATTTTTTATTAAAATAGATT
* * *
5957 ATAATTGAATGTTTGCCTCAAGAAATGTGAAGAAAACGATATCCATTGACAAAAAAAGTCAATTT
1 ATAATTGAATGTCTGCCTCAAGAAATGTGAAGAAAAAGATATCCATTGACAAGAAAAGTCAATTT
* *
6022 AAAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAA-CGCTTTTTTAATCTCATAATT-
66 ATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATAG-TTTTTTAATCTCATAATTG
* *
6085 AGTTTCAAGTTGAACTTTTTTATA-TTTTTATTAA
130 A-TTTTAAGTTAAACTTTTTTATATTTTTTATTAA
6119 NNNNNNNNNN
Statistics
Matches: 635, Mismatches: 186, Indels: 53
0.73 0.21 0.06
Matches are distributed among these distances:
170 26 0.04
171 465 0.73
172 141 0.22
173 3 0.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.36
Consensus pattern (171 bp):
ATAATTGAATGTCTGCCTCAAGAAATGTGAAGAAAAAGATATCCATTGACAAGAAAAGTCAATTT
ATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTTTAATCTCATAATTGA
TTTTAAGTTAAACTTTTTTATATTTTTTATTAAAATAGATT
Found at i:10853 original size:168 final size:160
Alignment explanation
Indices: 10645--10954 Score: 385
Period size: 168 Copynumber: 1.9 Consensus size: 160
10635 NNNNNNNNNN
* *
10645 GAGTAATAAGGCTTTCGAAGGCATGGGTGACAATAAATGGA--TTTCTCTGATCAATGGATATCA
1 GAGTAATAACGCTTTCGAAGGCATGGATGACAATAAATGGACTTTTCT-TG-TCAATGGATATCA
* * *
10708 TTTTCTTTACGTTTTTTGAGGTAGACATTCAATTAAAATCTATTTAAAT-AAAA-TAAAAAAAAT
64 TTTTCTTCACGTTTTTCGAGGTAAACATTCAATTAAAATCTATTTAAATAAAAATTAAAAAAAAT
10771 TCAAATTAAAATCANNNNNNNNNNTATAAAATCATTTAAAGC
129 TCAAATTAAAATCA----------TATAAAATCATTTAAAGC
* *
10813 GAGTAATAACGCTTTCTAAGGCATGGATGACTATAAATGGACTTTTCTTGTCAATGGATATCATT
1 GAGTAATAACGCTTTCGAAGGCATGGATGACAATAAATGGACTTTTCTTGTCAATGGATATCATT
* * * *
10878 TTCTTCACGTTTTTCGAGGTAAACATTCAATTATAATCTTTTTTAATAAAAATTAAAAAAAATTG
66 TTCTTCACGTTTTTCGAGGTAAACATTCAATTAAAATCTATTTAAATAAAAATTAAAAAAAATTC
10943 AAATTAAAATCA
131 AAATTAAAATCA
10955 ATTATGAGGT
Statistics
Matches: 127, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
168 93 0.73
169 6 0.05
170 28 0.22
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (160 bp):
GAGTAATAACGCTTTCGAAGGCATGGATGACAATAAATGGACTTTTCTTGTCAATGGATATCATT
TTCTTCACGTTTTTCGAGGTAAACATTCAATTAAAATCTATTTAAATAAAAATTAAAAAAAATTC
AAATTAAAATCATATAAAATCATTTAAAGC
Found at i:12302 original size:170 final size:155
Alignment explanation
Indices: 12098--12412 Score: 357
Period size: 170 Copynumber: 1.9 Consensus size: 155
12088 TTTCGAAGGC
* **
12098 ATGGGTGACAATAAATGGACTTCTCTGATCAATGGATATCATTATT-TTTACGTTTCTTGAGGCA
1 ATGGGTGACAATAAATGGACTTCTCTGATCAATGGATATCATT-TTCTTCACGTTTCACGAGGCA
* *
12162 GACATTCAATTAAAATCTATTTTAATAAAAAAATAAAAACAATTCAAATTAAAATCAATTATGTG
65 AACATTCAATTAAAATCTATTTTAAT-AAAAAATAAAAA-AATTCAAATTAAAATCAATTATGAG
12227 GTTATAAAATCATTTAAAGCGAGTAATA
128 GTTATAAAATCATTTAAAGCGAGTAATA
*
12255 ANNNNNNNNNNNNNNTGGGTGACTATAAATGGACTT-TCTTG-TCAATGGATATCATTTTCTTCA
1 A--------------TGGGTGACAATAAATGGACTTCTC-TGATCAATGGATATCATTTTCTTCA
* * * *
12318 CGTTTCACGAGGCAAACATTCAATTATAATCTATTTTAATGAAAATTAAAAAAATTGAAATTAAA
51 CGTTTCACGAGGCAAACATTCAATTAAAATCTATTTTAATAAAAAATAAAAAAATTCAAATTAAA
12383 ATCAATTATGAGGTTATAAAATCATTTAAA
116 ATCAATTATGAGGTTATAAAATCATTTAAA
12413 NNNNNNNNNN
Statistics
Matches: 132, Mismatches: 10, Indels: 21
0.81 0.06 0.13
Matches are distributed among these distances:
157 1 0.01
168 41 0.31
169 12 0.09
170 56 0.42
171 22 0.17
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.34
Consensus pattern (155 bp):
ATGGGTGACAATAAATGGACTTCTCTGATCAATGGATATCATTTTCTTCACGTTTCACGAGGCAA
ACATTCAATTAAAATCTATTTTAATAAAAAATAAAAAAATTCAAATTAAAATCAATTATGAGGTT
ATAAAATCATTTAAAGCGAGTAATA
Found at i:13162 original size:16 final size:17
Alignment explanation
Indices: 13141--13174 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
13131 TGTAACTTCA
13141 TAATTGATTT-TAATTT
1 TAATTGATTTATAATTT
*
13157 TAATTGTTTTATAATTT
1 TAATTGATTTATAATTT
13174 T
1 T
13175 TAATAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TAATTGATTTATAATTT
Found at i:14542 original size:170 final size:171
Alignment explanation
Indices: 14361--14771 Score: 430
Period size: 171 Copynumber: 2.4 Consensus size: 171
14351 NNNNNNNNNN
* * * *
14361 TGATATTATAACCTCATAATTGATTTTAATTTGAATATTTTTAGA-TTTTTATGAAAACAGATTA
1 TGATTTTATAACCTCATAATTGATTTTAATTTAAATATTTTTAAATTTTTTATTAAAACAGATTA
* * * * * *
14425 TAATTGAATGTCTACCTCGAGAAATGTGAGGAGAA-AGATATTCATTGGTAAGAAAAGTCCTTTT
66 TAATTGAATGTCTACCTCGAGAAACGTGA-AAAAATAGATATCCATTGGCAAGAAAAGTCCATTT
*
14489 ATGGTCACCCATGCCTTCCAAAGCCTTATTACTTGCTTTAAA
130 ATGGTCACCCATGCCTTCCAAAGCCTTATTACTCGCTTTAAA
********** *
14531 TGATTTTATAACCTCATAATTGATTTTAATTNNNNNNNNNNTATATTTTTTATTAAAACAGATTA
1 TGATTTTATAACCTCATAATTGATTTTAATTTAAATATTTTTAAATTTTTTATTAAAACAGATTA
*
14596 TAATTGAATGTCTGCCTCGAGAAACGTGAAAAAATAGATATCCATTGGCAAGAAAAGTCCATTTA
66 TAATTGAATGTCTACCTCGAGAAACGTGAAAAAATAGATATCCATTGGCAAGAAAAGTCCATTTA
********** * * *
14661 TNNNNNNNNNNGCTTTCGAAAGCCTTATTACTCGTTTTAAA
131 TGGTCACCCATGCCTTCCAAAGCCTTATTACTCGCTTTAAA
* * * * *
14702 TGAATTTATAATCTCATAATTGAATTTAATTTAAATTTTTTTAAATTTTTTATTAAACCAGATTA
1 TGATTTTATAACCTCATAATTGATTTTAATTTAAATATTTTTAAATTTTTTATTAAAACAGATTA
14767 TAATT
66 TAATT
14772 NNNNNNNNNN
Statistics
Matches: 190, Mismatches: 49, Indels: 3
0.79 0.20 0.01
Matches are distributed among these distances:
170 36 0.19
171 154 0.81
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.38
Consensus pattern (171 bp):
TGATTTTATAACCTCATAATTGATTTTAATTTAAATATTTTTAAATTTTTTATTAAAACAGATTA
TAATTGAATGTCTACCTCGAGAAACGTGAAAAAATAGATATCCATTGGCAAGAAAAGTCCATTTA
TGGTCACCCATGCCTTCCAAAGCCTTATTACTCGCTTTAAA
Found at i:15738 original size:171 final size:170
Alignment explanation
Indices: 15376--15766 Score: 487
Period size: 171 Copynumber: 2.3 Consensus size: 170
15366 NNNNNNNNNN
* * * *
15376 CCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTTATAAATGATTTTAATTTTAAT
1 CCTTCAAAAGCCTTATTACTCGCTTTAAATAATTTTATAACCTCATAATTGATTTTAATTTTAAT
* ** * *
15441 TTTTTTATATTTTTTATTAAAAAAGATTATAATTGAACTTTACCTTGAGAAACATGAAGAAAAAG
66 TTTTTAATAAGTTTTATTAAAAAAGATTATAATTGAACTTTACCTTAAGAAACAAGAAGAAAAAG
**********
15506 ATATCCATTGGCAAGANNNNNNNNNNTATAGTCACCCATG
131 ATATCCATTGGCAAGATAAGTCCATTTATAGTCACCCATG
* *
15546 CCTTCAAATGCCTTATTACTCGCTTTAAATAAGTTTATAACCTCATAATTGATTTTAATTTTAAT
1 CCTTCAAAAGCCTTATTACTCGCTTTAAATAATTTTATAACCTCATAATTGATTTTAATTTTAAT
* ** * * * *
15611 TTTTTAATAAGTTTTGTTAAAATGGATTGTAATTGAATGTTTGCCTTAAGAAACAAGAAGAAAAT
66 TTTTTAATAAGTTTTATTAAAAAAGATTATAATTGAA-CTTTACCTTAAGAAACAAGAAGAAAAA
* *
15676 GATATCCATTGGTAAGATAAGTCCATTTATAGTCACTCATG
130 GATATCCATTGGCAAGATAAGTCCATTTATAGTCACCCATG
15717 CCTT-AGAAAGCCTTATTACTCGCTTTAAATAATTTTATAACCTCATAATT
1 CCTTCA-AAAGCCTTATTACTCGCTTTAAATAATTTTATAACCTCATAATT
15767 NNNNNNNNNN
Statistics
Matches: 187, Mismatches: 32, Indels: 3
0.84 0.14 0.01
Matches are distributed among these distances:
170 90 0.48
171 97 0.52
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.39
Consensus pattern (170 bp):
CCTTCAAAAGCCTTATTACTCGCTTTAAATAATTTTATAACCTCATAATTGATTTTAATTTTAAT
TTTTTAATAAGTTTTATTAAAAAAGATTATAATTGAACTTTACCTTAAGAAACAAGAAGAAAAAG
ATATCCATTGGCAAGATAAGTCCATTTATAGTCACCCATG
Found at i:20323 original size:171 final size:171
Alignment explanation
Indices: 20066--20436 Score: 471
Period size: 171 Copynumber: 2.2 Consensus size: 171
20056 NNNNNNNNNN
* * *
20066 TTTTTTATTAAAACAGATTATAATTGAATGTTTACCTCGAGAAACGTGAAGAAATAGATATCCAT
1 TTTTTTATTAAAACAGATTATAATTGAATGTCTACCTCAAGAAACGAGAAGAAATAGATATCCAT
* * * * * *
20131 TGGCAAGAAAGGTCCATTTATAGTCATCCATGCTTTCGAAAGCCTTATTACTC-GCATGAAATGA
66 TAGAAAGAAAAGTCAATTTATAGACATCCATGCCTTCGAAAGCCTTATTACTCGGC-TGAAAT-A
* *
20195 -ATTTATAATCTCAT-AATTGAATTTAATTTAAATTTTTTTATA
129 TATTTATAACCTCATAAATT-AATTTAAGTTAAATTTTTTTATA
* * * * * *
20237 TATTTTT-TTAAACCAGATTATAATTGAATGTCTACCTTAAGAAGCGAGAAGAAATGGATATTCG
1 T-TTTTTATTAAAACAGATTATAATTGAATGTCTACCTCAAGAAACGAGAAGAAATAGATATCCA
* *
20301 TTAGAAAGAAAAGTCAATTTATAGACATGCATGCCTTCGAAAGCCTTATTACTCGGCTTAAATAT
65 TTAGAAAGAAAAGTCAATTTATAGACATCCATGCCTTCGAAAGCCTTATTACTCGGCTGAAATAT
* * * *
20366 TTTTATAGCCTTATAAATTATTTTAAGTTAAATTTTTTTATA
130 ATTTATAACCTCATAAATTAATTTAAGTTAAATTTTTTTATA
20408 TTTTTTATTAAAACAGATTATAATTGAAT
1 TTTTTTATTAAAACAGATTATAATTGAAT
20437 NNNNNNNNNN
Statistics
Matches: 171, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
170 6 0.04
171 154 0.90
172 11 0.06
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.39
Consensus pattern (171 bp):
TTTTTTATTAAAACAGATTATAATTGAATGTCTACCTCAAGAAACGAGAAGAAATAGATATCCAT
TAGAAAGAAAAGTCAATTTATAGACATCCATGCCTTCGAAAGCCTTATTACTCGGCTGAAATATA
TTTATAACCTCATAAATTAATTTAAGTTAAATTTTTTTATA
Found at i:23038 original size:170 final size:171
Alignment explanation
Indices: 22392--23582 Score: 835
Period size: 171 Copynumber: 7.0 Consensus size: 171
22382 NNNNNNTTTG
* *
22392 AATTGTTTTTATATTTTTTATTAAAATAGATTATAATTGAATGTCTACATAGAGAAACGTGAAGA
1 AATT-TTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCTAGAGAAACGTGAAGA
* * ** * * * * * *
22457 AAAAGATATCAACT-GCGAAGAAAAGTTCATTTATTTTAACTCATACCTTCGAAAGCATTATTAT
65 AAAAGATATCAATTGGC-AAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTAC
* * *****
22521 TCGCTTTAAAT-AGTTTTTTAATCTCATAATT-AGTTTTANNNNN
129 TCGCTTTAAATGA-TTTTATAACCTCATAATTGA-TTTTAAGTTA
***** * * * * *
22564 NNNNNTTTTATATTTATTGTTAAAACATATTATAATTGTATGTTTACCTCA-AGAAACGTGAAGA
1 AATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCT-AGAGAAACGTGAAGA
* * * * * * **********
22628 AAAAAATATCCATTAGTATGAAAAGTCTATTTATAGTCACCCATGCCTTCNNNNNNNNNNTTACT
65 AAAAGATATCAATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACT
* * *
22693 CGCGTTAAATGATTTTATAACCTTATAATTGATTTTAATTTGA
130 CGCTTTAAATGATTTTATAACCTCATAATTGATTTTAAGTT-A
** * * * ********
22736 GTTTTTTTTATATTTTTTATTAAAATAGATTATAATTGAATGTTTTCCTCA-AGAAANNNNNNNN
1 AATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCT-AGAGAAACGTGAAGA
******* * * * * *
22800 NNNNNNNATCCATTGGTAAGAAAAGTGCATTTATAGTCACCCATGCCTTCAAAAGCTTTATCACT
65 AAAAGATATCAATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACT
* *
22865 CGCTTTAAATGATTTTATAACCTTATAATTGATTTT-AG-TG
130 CGCTTTAAATGATTTTATAACCTCATAATTGATTTTAAGTTA
* * *
22905 AATTGTTTTTATATTTTTTATTAAAACAGATTATAATTAAATGTCTACATAGAGAAACATGAAGA
1 AATT-TTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCTAGAGAAACGTGAAGA
* ** * * * *
22970 AAAAGATATCAACTGGCAAGAAAAGTCCATTTATTTTAACTCATTCCTTCGAAAGCCTTATTACT
65 AAAAGATATCAATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACT
* *********
23035 CGCTTTAAATGCTNNNNNNNNNNT-ATAATT-AGTTTTAAGTTA
130 CGCTTTAAATGAT-TTTATAACCTCATAATTGA-TTTTAAGTTA
* * * * * *
23077 AACTTTTTTATATTCTTT-TTAAAACATATTATAATTTAATGTCTACTTTGAGAAACGTGAAG-A
1 AATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCTAGAGAAACGTGAAGAA
* * * *
23140 AAATATATTAATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCATTCAAAAGCCTTATTACTN
66 AAAGATATCAATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTC
**************
23205 NNNNNNNNNNNNNNTATAACCTCATAATTGATTTTAAGTTA
131 GCTTTAAATGATTTTATAACCTCATAATTGATTTTAAGTTA
* * * * * *
23246 AATTTTTTTATAATTTTTATAAAAACATATTATAATTAAATGTCTACCCAGAGAAACGTGAGGAA
1 AATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCTAGAGAAACGTGAAGAA
* * ** * ** * *
23311 AAAGATATCCATTGGCAAGAAAAGTTCATTTATAGTCACATATGCGTTTGAAAGTCTTATTAATC
66 AAAGATATCAATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTC
* * *
23376 GCTTTAAATGGTTTTTTAATCTCATAATTTG-TTTTAAGTTA
131 GCTTTAAATGATTTTATAACCTCATAA-TTGATTTTAAGTTA
* * * * *
23417 AACTTTTTTATATTTTCTATTTAAACAGATTATAATTGAGTGTTTACCTCA-AGAAACGTGAAGA
1 AATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCT-AGAGAAACGTGAAGA
* * * * *
23481 GAAAGATAT-ACATTAGCAAGAAAAGTCCATTTATAGCCACCCATGTCATCAAAAGCCTTATTAC
65 AAAAGATATCA-ATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTAC
*
23545 TCGCTTTAAATGATTTTATAACCCCATAATTGATTTTA
129 TCGCTTTAAATGATTTTATAACCTCATAATTGATTTTA
23583 NNNNNNNNNN
Statistics
Matches: 764, Mismatches: 236, Indels: 39
0.74 0.23 0.04
Matches are distributed among these distances:
168 3 0.00
169 90 0.12
170 195 0.26
171 341 0.45
172 135 0.18
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.38
Consensus pattern (171 bp):
AATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCTAGAGAAACGTGAAGAA
AAAGATATCAATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTC
GCTTTAAATGATTTTATAACCTCATAATTGATTTTAAGTTA
Found at i:23420 original size:340 final size:326
Alignment explanation
Indices: 22879--23545 Score: 693
Period size: 340 Copynumber: 2.0 Consensus size: 326
22869 TTAAATGATT
* * * *
22879 TTATAACCTTATAATTGATTTTAGTGAATTGTTTTTATATTTTTTATTAAAACAGATTATAATTA
1 TTATAACCTCATAATTGATTTTAGTAAATTGTTTTTATAATTTTTATAAAAACAGATTATAATTA
* **
22944 AATGTCTACATAGAGAAACATGAAGAAAAAGATATCAACTGGCAAGAAAAGTCCATTTATTTTAA
66 AATGTCTACACAGAGAAACATGAAGAAAAAGATATCAACTGGCAAGAAAAGTCCATTTATAGTAA
* * **********
23009 CTCATTCCTTCGAAAGCCTTATTACTCGCTTTAAATGCTNNNNNNNNNNTATAATTAGTTTTAAG
131 CTCATGCCTTCGAAAGCCTTATTAATCGCTTTAAATGCTATTTTTAATCTATAATTAGTTTTAAG
* * * **
23074 TTAAACTTTTTTATATTCTT-T-TTAAAACATATTATAATTTAATGTCTACTTTGAGAAACGTGA
196 TTAAACTTTTTTATATT-TTCTATTAAAACAGATTATAATTGAATGTCTACCTCAAGAAACGTGA
* * *
23137 AGA-AAATATATTA-ATTGGCAAGAAAAGTCCATTTATAGTCACCCATG-CATTCAAAAGCCTTA
260 AGAGAAAGATA-TACATTAGCAAGAAAAGTCCATTTATAGCCACCCATGTCA-TCAAAAGCCTTA
23199 TTAC
323 TTAC
23203 TNNNNNNNNNNNNNNNTATAACCTCATAATTGATTTTAAGTTAAATT-TTTTTATAATTTTTATA
1 T---------------TATAACCTCATAATTGATTTT-AG-TAAATTGTTTTTATAATTTTTATA
* * * * * *
23267 AAAACATATTATAATTAAATGTCTACCCAGAGAAACGTGAGGAAAAAGATATCCATTGGCAAGAA
49 AAAACAGATTATAATTAAATGTCTACACAGAGAAACATGAAGAAAAAGATATCAACTGGCAAGAA
* * * * * *
23332 AAGTTCATTTATAGTCACAT-ATGCGTTTGAAAGTCTTATTAATCGCTTTAAATGGT-TTTTTAA
114 AAGTCCATTTATAGTAAC-TCATGCCTTCGAAAGCCTTATTAATCGCTTTAAATGCTATTTTTAA
* * *
23395 TCTCATAATTTGTTTTAAGTTAAACTTTTTTATATTTTCTATTTAAACAGATTATAATTGAGTGT
178 TCT-ATAATTAGTTTTAAGTTAAACTTTTTTATATTTTCTATTAAAACAGATTATAATTGAATGT
*
23460 TTACCTCAAGAAACGTGAAGAGAAAGATATACATTAGCAAGAAAAGTCCATTTATAGCCACCCAT
242 CTACCTCAAGAAACGTGAAGAGAAAGATATACATTAGCAAGAAAAGTCCATTTATAGCCACCCAT
23525 GTCATCAAAAGCCTTATTAC
307 GTCATCAAAAGCCTTATTAC
23545 T
1 T
23546 CGCTTTAAAT
Statistics
Matches: 277, Mismatches: 42, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
324 1 0.00
339 23 0.08
340 151 0.55
341 45 0.16
342 55 0.20
343 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.37
Consensus pattern (326 bp):
TTATAACCTCATAATTGATTTTAGTAAATTGTTTTTATAATTTTTATAAAAACAGATTATAATTA
AATGTCTACACAGAGAAACATGAAGAAAAAGATATCAACTGGCAAGAAAAGTCCATTTATAGTAA
CTCATGCCTTCGAAAGCCTTATTAATCGCTTTAAATGCTATTTTTAATCTATAATTAGTTTTAAG
TTAAACTTTTTTATATTTTCTATTAAAACAGATTATAATTGAATGTCTACCTCAAGAAACGTGAA
GAGAAAGATATACATTAGCAAGAAAAGTCCATTTATAGCCACCCATGTCATCAAAAGCCTTATTA
C
Found at i:26463 original size:171 final size:170
Alignment explanation
Indices: 26036--26501 Score: 454
Period size: 171 Copynumber: 2.7 Consensus size: 170
26026 NNNNNNNNNN
* * * *
26036 TCATAATTGATTTTAATTTGAATTTTTTTAT-TTTTCTATTAAAACAAAATATAATTGAATGTCT
1 TCATAATTGACTTTAAGTTGAATTTTTTTATATTTT-TATTAAAACAAATTATAATTGAAAGTCT
* ** **
26100 GCCTCAAAAAACATGAAGAAAATGATATCCATTGGCAAGAGAAGTCCATTTATTTTCACCCATGG
65 GCCTCAAAAAACAAGAAGAAAATGATATCCATTGGCAAGAGAAGTCCATTTATAGTCACCCATAC
** * *
26165 ATTCGAAAGCCTTATAACTCGTTTTAAATGATTTTGTAATC
130 ATTCGAAAGCCTTATAACTCGCCTTAAATGATTTTATAACC
* * * * *
26206 TCATAATTGACTTTAAGTTGAACTTTTTTACATTTTTTATTAAAACATATTACAATTGAACGTCT
1 TCATAATTGACTTTAAGTTGAATTTTTTTATA-TTTTTATTAAAACAAATTATAATTGAAAGTCT
* * * * *
26271 GTCTCAAAAAATACA-AAGAAAATGATATCCATCGGCAAGAGAAGTACATTTACAGTCACCCATA
65 GCCTCAAAAAACA-AGAAGAAAATGATATCCATTGGCAAGAGAAGTCCATTTATAGTCACCCATA
* * *
26335 CCTTCGAAAGCCTTATTATTCGCCTTAAAT-ATTTTTATAACC
129 CATTCGAAAGCCTTATAACTCGCCTTAAATGA-TTTTATAACC
********** * *
26377 TCATAATNNNNNNNNNNTTGAATTTTTTTATAATTTTTATTAAAACAGATTATAATTAAAAGTCT
1 TCATAATTGACTTTAAGTTGAATTTTTTTAT-ATTTTTATTAAAACAAATTATAATTGAAAGTCT
* * * * * *
26442 ACCTCGAGAAACAAGAAGAAAACGATATCTATTGG-AAGGAAAAGTCCATTTATAGTCACC
65 GCCTCAAAAAACAAGAAGAAAATGATATCCATTGGCAA-GAGAAGTCCATTTATAGTCACC
26502 TATGCCNNNN
Statistics
Matches: 237, Mismatches: 52, Indels: 13
0.78 0.17 0.04
Matches are distributed among these distances:
170 31 0.13
171 201 0.85
172 5 0.02
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.35
Consensus pattern (170 bp):
TCATAATTGACTTTAAGTTGAATTTTTTTATATTTTTATTAAAACAAATTATAATTGAAAGTCTG
CCTCAAAAAACAAGAAGAAAATGATATCCATTGGCAAGAGAAGTCCATTTATAGTCACCCATACA
TTCGAAAGCCTTATAACTCGCCTTAAATGATTTTATAACC
Found at i:27719 original size:170 final size:170
Alignment explanation
Indices: 27315--27742 Score: 421
Period size: 170 Copynumber: 2.5 Consensus size: 170
27305 NNNNNNNNTA
* * * *
27315 CCTTCAAAAGCCTTATTACTCACTTTAAATGATTTTATAACCTCATAATTGACTTTAATTTGAA-
1 CCTTCAAAAGCCTTATTACTCGCTTAAAAGGATTTTATAACCTCATAATTGATTTTAATTTGAAT
* * *
27379 TTTTTTATATTTTTATGAAAACAGACTATAATTCAATGTCTACCTTGAGAAACATGAAGAAAAAG
66 TTTTTTATATTTTTATTAAAACAGACTATAATTCAATGTCTACCTTCACAAACATGAAGAAAAAG
27444 ATATTCATTGGCAAAAAAAGTCCATTTATAGTCATCCATG
131 ATATTCATTGGCAAAAAAAGTCCATTTATAGTCATCCATG
* ************ * * ** *
27484 CCTTCGAAAGCCTTATTACTCGCNNNNNNNNNNNNTATAATCTCATAATTGCTTGAAAGTTGAAT
1 CCTTCAAAAGCCTTATTACTCGCTTAAAAGGATTTTATAACCTCATAATTGATTTTAATTTGAAT
* * * *
27549 TTTTTTATATTTTTATTAACACAGGCTATAGTTGAATGTCTACC-TCATCAAACATGAAGAAAAA
66 TTTTTTATATTTTTATTAAAACAGACTATAATTCAATGTCTACCTTCA-CAAACATGAAGAAAAA
********** *
27613 GATATTCATTGGCANNNNNNNNNNATTTATAGTCATTCACT-
130 GATATTCATTGGCAAAAAAAGTCCATTTATAGTCATCCA-TG
* *
27654 CCTTCAAAAACCTTATTACTCGCTTAAAAGGATTTTATAACCTCATCATTGATTTTAATTTGAAT
1 CCTTCAAAAGCCTTATTACTCGCTTAAAAGGATTTTATAACCTCATAATTGATTTTAATTTGAAT
*
27719 TTTTTTAAAATTTTTATTAAAACA
66 TTTTTT-ATATTTTTATTAAAACA
27743 AATTAGAATT
Statistics
Matches: 195, Mismatches: 60, Indels: 6
0.75 0.23 0.02
Matches are distributed among these distances:
169 46 0.24
170 133 0.68
171 16 0.08
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.37
Consensus pattern (170 bp):
CCTTCAAAAGCCTTATTACTCGCTTAAAAGGATTTTATAACCTCATAATTGATTTTAATTTGAAT
TTTTTTATATTTTTATTAAAACAGACTATAATTCAATGTCTACCTTCACAAACATGAAGAAAAAG
ATATTCATTGGCAAAAAAAGTCCATTTATAGTCATCCATG
Done.