Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403269.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_943.0, 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: 16277
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.25
Warning! 5451 characters in sequence are not A, C, G, or T
Found at i:2533 original size:171 final size:170
Alignment explanation
Indices: 2095--2723 Score: 495
Period size: 171 Copynumber: 3.7 Consensus size: 170
2085 NNNNNNNNNT
* * * * * * * * *
2095 TATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTTTACGTTTCTTTAGG-CAGACACTCAA
1 TATAAATAGACTTTTCTTGCCAATGGATATC-TTTTCTTCATGATTCTTGAGGTAAG-CATTTAA
* * * * *
2159 TTATTATCTGTTTCATTAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTA-TAAA
64 TTATAATATGTTTTAATAAAAAATATAAAAAAATTTAACTTAAAATCAATTATGAGA-TAGTAAA
* * * * * ** ***
2223 GCAATTGAAAGCAAGTAATAAGACTTCCGAA-AGCATGGGTGAC
128 ACCATTTAAAGCGAGTAACAAGACTTTGGAAGA-CATGACAGAC
* ********** * * *
2266 TATAAATGGNNNNNNNNNNCCAATGGATATCTTTTCTTCATG-TT-TTCCGAGGAAAACATTCAA
1 TATAAATAGACTTTTCTTGCCAATGGATATCTTTTCTTCATGATTCTT--GAGGTAAGCATTTAA
* * * * *
2329 TTATAATTTGTTTTAGTAAAAAATGTAAAAAAATTTAACTTCAAATTAATTATGAGATTA-TAAA
64 TTATAATATGTTTTAATAAAAAATATAAAAAAATTTAACTTAAAATCAATTATGAGA-TAGTAAA
* * * *
2393 ACCATTTAAAGCGATTAACAAGGCTTTGGAAGATATGAGAGAC
128 ACCATTTAAAGCGAGTAACAAGACTTTGGAAGACATGACAGAC
*
2436 TATAAATAGACTTTTCTTGCCAATGAATATCGTTTTCTTCATGATTCTTGAGGTAAGCATTTAAT
1 TATAAATAGACTTTTCTTGCCAATGGATATC-TTTTCTTCATGATTCTTGAGGTAAGCATTTAAT
* *
2501 TATAAAATATTTTAATAAAAAATATAAAAAAATTTAA-TCTAAAATCAATTATGAGATAGTAAAA
65 TATAATATGTTTTAATAAAAAATATAAAAAAATTTAACT-TAAAATCAATTATGAGATAGTAAAA
* * * * * *
2565 CTATTTAAAGCGAGTAATAAGACTTTTGAAGGCATGACTGAG
129 CCATTTAAAGCGAGTAACAAGACTTTGGAAGACATGACAGAC
* * * *
2607 TATAAATGGACTTTTCTTGCCAATGGATATCTTTTTATTTAT-ATTTCCTGAGGT-AGACATTTA
1 TATAAATAGACTTTTCTTGCCAATGGATATC-TTTTCTTCATGA-TTCTTGAGGTAAG-CATTTA
* * * * *
2670 ATTATTATCTGTTTCAACAAAAAATAT-AAAAAATTCAACTTAAAATCAATTATG
63 ATTATAATATGTTTTAATAAAAAATATAAAAAAATTTAACTTAAAATCAATTATG
2724 NNNNNNNNNN
Statistics
Matches: 364, Mismatches: 82, Indels: 25
0.77 0.17 0.05
Matches are distributed among these distances:
168 2 0.01
169 2 0.01
170 152 0.42
171 204 0.56
172 2 0.01
173 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.35
Consensus pattern (170 bp):
TATAAATAGACTTTTCTTGCCAATGGATATCTTTTCTTCATGATTCTTGAGGTAAGCATTTAATT
ATAATATGTTTTAATAAAAAATATAAAAAAATTTAACTTAAAATCAATTATGAGATAGTAAAACC
ATTTAAAGCGAGTAACAAGACTTTGGAAGACATGACAGAC
Found at i:4608 original size:172 final size:170
Alignment explanation
Indices: 4297--4835 Score: 642
Period size: 172 Copynumber: 3.1 Consensus size: 170
4287 NNNNNNNNNN
* * * * *
4297 ATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTCAAAGGCATAAGTGCCTATTAATAG
1 ATGAGATTATAAAA-TATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATGG
** *
4362 ACTTTTCATACCAATGGATATC-TTTTCTTCATGTTTCTTGAGGTAAACATTCAATTATAATCTA
65 ACTTTT-ATTGCAATGGATATCTTTTTCTTCATGTTTCTTGAGGTAAACATTCAATTATAATCTG
*
4426 TTTCAATAAAAAAATATAAAAAAATTTAACTTAAAATCAATT
129 TTTAAATAAAAAAATATAAAAAAATTTAACTTAAAATCAATT
* * * *
4468 ATGAGATTGTTAAAATATTTAAAGCGAGTAATAAGCCTTTTGAATGCATAGGTGACTATAAATGG
1 ATGAGATT-ATAAAATATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATGG
*
4533 ACTTTTTTTGCAAGTGGATATCTTTTTCTTCATGTTTCTTGAGGTAAACATTCAATTATAATCTG
65 ACTTTTATTGCAA-TGGATATCTTTTTCTTCATGTTTCTTGAGGTAAACATTCAATTATAATCTG
* * *
4598 TTTAAATAAAAAACATA-AAAAAAATTCAACCTAAAATCAAAT
129 TTTAAATAAAAAA-ATATAAAAAAATTTAACTTAAAATCAATT
* * * *
4640 ATGAGATTATAAAGTCATTTAAAGCAAGTAATAAGGCTTCCGAAGGCAT-GTGTGACTAAAAATG
1 ATGAGATTATAAAAT-ATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATAG-GTGACTATAAATG
* * * * * *
4704 AACTTTTCTTGCCAATGGGTATCTTTTTCTTTGCAT-TTCCCT-AGGTAAAAATTCAATTATAAT
64 GACTTTTATTG-CAATGGATATCTTTTTC-TT-CATGTTTCTTGAGGTAAACATTCAATTATAAT
* ** *
4767 CTGTTTTAAT-AAAAGGTGTAAAAAAA-TTAACTTAAAATCAATT
126 CTGTTTAAATAAAAAAATATAAAAAAATTTAACTTAAAATCAATT
*
4810 ATGAGATTATAAAAACATTTAAAGCG
1 ATGAGATTAT-AAAATATTTAAAGCG
4836 NNNNNNNNNN
Statistics
Matches: 316, Mismatches: 41, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
170 38 0.12
171 84 0.27
172 179 0.57
173 12 0.04
174 3 0.01
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (170 bp):
ATGAGATTATAAAATATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATGGA
CTTTTATTGCAATGGATATCTTTTTCTTCATGTTTCTTGAGGTAAACATTCAATTATAATCTGTT
TAAATAAAAAAATATAAAAAAATTTAACTTAAAATCAATT
Found at i:7639 original size:171 final size:171
Alignment explanation
Indices: 7109--7649 Score: 525
Period size: 171 Copynumber: 3.2 Consensus size: 171
7099 NNNNNNNNNN
* * * * *
7109 TAATTGATTTTAAGTTTAATTTTTTTATATTTTTGGTTAAAATAGATAATAACTGAATGTTTACC
1 TAATTGATTTTAAGTTAAATTTTTTTACATTTTTGGTTAAAACAGATAATAATTGAATGTCTACC
* * *
7174 TCAGGAAATGTGAAGAAAAGGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATACCTT
66 TCAGAAAACGTGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATACCTT
* * *
7239 CGGAAGCTTTATTACTTGCTTTAAATGGTTTTATAATCTCA
131 CGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCA
********* * ** * *
7280 TAATTGNNNNNNNNNNT-AA-TTTTTTATATTTTTTATTAAAACAGATTATAATTAAATGTCTAC
1 TAATTG-ATTTTAAGTTAAATTTTTTTACATTTTTGGTTAAAACAGATAATAATTGAATGTCTAC
* * * * * *
7343 CACA-AGAAACATGAA-AAAACA-ATATCCATTGACAAGAAAAATCCATTTATGGTCTCTCATAC
65 CTCAGA-AAACGTGAAGAAAA-AGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATAC
* * *
7405 CTTTGAAAGGCTTATTACTCGCTTTAAATGGTTTCATAATCTCA
128 CTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCA
********** *
7449 TAANNNNNNNNNNGTTAAATTTTTTTACATATTTGGTTAAAACAGATAATAATTGAATGTCTACC
1 TAATTGATTTTAAGTTAAATTTTTTTACATTTTTGGTTAAAACAGATAATAATTGAATGTCTACC
* * * * *
7514 TTAGAAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTTCATTTATTGTCACCCATGCCTT
66 TCAGAAAACGTGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATACCTT
* * **
7579 CAAAAGCCTTATTAATCGCTTTAAATATTTTTATAATCTCA
131 CGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCA
*
7620 TAATTGATTTTAGGTTAAATTTTTTTACAT
1 TAATTGATTTTAAGTTAAATTTTTTTACAT
7650 NNNNNNNNNN
Statistics
Matches: 293, Mismatches: 69, Indels: 16
0.78 0.18 0.04
Matches are distributed among these distances:
168 8 0.03
169 84 0.29
170 96 0.33
171 104 0.35
172 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.37
Consensus pattern (171 bp):
TAATTGATTTTAAGTTAAATTTTTTTACATTTTTGGTTAAAACAGATAATAATTGAATGTCTACC
TCAGAAAACGTGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATACCTT
CGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCA
Found at i:8793 original size:170 final size:169
Alignment explanation
Indices: 7907--9739 Score: 1077
Period size: 171 Copynumber: 10.7 Consensus size: 169
7897 NNNNNNNNNN
*
7907 TAATCTCATAATTGATTTTA-AGTTGAATTTTTTTACATATTTGGTTAAAACAAATAATAATTGA
1 TAATCTCATAATTGATTTTAGA-TTGAATTTTTTTACATTTTTGGTT--AACAAATAATAATTGA
* * * *
7971 ATGTTTACCTTAGGAAACGTGAAAAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATTA-TCA
63 ATGTCTACCTCAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTA-TAGTCA
*
8035 CCCATACCTTCAAAAGCCTTATTAATCGCTTTAAAT-GTTTTTA
127 CCCATGCCTTCAAAAGCCTTATTAATCGCTTTAAATAG-TTTTA
* * * *
8078 TAATCTCATAATTGATTTTAGGTTCAATTTTTTTACATTTTTTGTTGAAACAGAA-AATAATTCA
1 TAATCTCATAATTGATTTTAGATTGAATTTTTTTACATTTTTGGTT--AACA-AATAATAATTGA
** * * * * * *
8142 ATGTCTGGCTCAACAAATGTGAAGAAAAAGATTTTCATTGGCAAGAAAAATCCATTTATAGTGAC
63 ATGTCTACCTCAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCAC
* * *
8207 CCAAGCCTTTC-AAAGCCTTATCACTCGCTTTAAAT-GATTTTA
128 CCATGCC-TTCAAAAGCCTTATTAATCGCTTTAAATAG-TTTTA
* * ** * * *
8249 TAATCACATAATTGATTTTAGGTTGAATTTTTTTACATTTTTTATTAAAACACATTATAATTAAA
1 TAATCTCATAATTGATTTTAGATTGAATTTTTTTACATTTTTGGTT--AACAAATAATAATTGAA
* * *** * * *
8314 TGTTTACCTCAAGAAACGTGAAGAGAAAGATATCCATTAATAAGAAAAGTCTATTTACAGTCTCC
64 TGTCTACCTCAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACC
* **
8379 CATGCCTTCGAAAGCCTTGCTAATCGCTTTAAATAGTTTTA
129 CATGCCTTCAAAAGCCTTATTAATCGCTTTAAATAGTTTTA
********** ** * * *
8420 TAATCTCATAATNNNNNNNNNNTTGAATTTTTTTGTATTTTTAGTTAAAATAGATAATAACTGAA
1 TAATCTCATAATTGATTTTAGATTGAATTTTTTTACATTTTTGGTTAACA-A-ATAATAATTGAA
* * * * * * * * ** *
8485 TGTCTGCCTTAGGAAACTTGAAGAAAAA-A-ATTCATTGGCAACAAAAATTCAGCTATTGTCACC
64 TGTCTACCTCAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACC
* * * *
8548 CATGCTTTCAAAAGCCTTATTAGTCACTTTAAATATTTTTA
129 CATGCCTTCAAAAGCCTTATTAATCGCTTTAAATAGTTTTA
********* *
8589 TAATCTCATAANNNNNNNNNNG-TTAAATTTTTTTACATTTTTGGTTGAACAAATAATAATTGAA
1 TAATCTCATAA-TTGATTTTAGATTGAATTTTTTTACATTTTTGGTT-AACAAATAATAATTGAA
* * * * *
8653 TGTCTACCTCAAGAAACGTAAACAAAAAGATATCCATTGGCAAGAAAAGTCCATGTATAATCAGC
64 TGTCTACCTCAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACC
* * *
8718 CATGCCTTAAAAAGCCTTATTATTCGCTTTGAATAGTTTTA
129 CATGCCTTCAAAAGCCTTATTAATCGCTTTAAATAGTTTTA
* * *
8759 CT-ATCTCATAATTGATTTTAGATTGAACTTTTTTACATTTTT-ATTAA-AATAGTTTATAATT-
1 -TAATCTCATAATTGATTTTAGATTGAATTTTTTTACATTTTTGGTTAACAA-A--TAATAATTG
* ** * *
8820 ACATGCCTACCTCAAGAATTGTGAAGAAAATGATATCCATCGGCAAGAAAAGTCCATTTATAGTC
62 A-ATGTCTACCTCAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTC
* *************************** *
8885 TCNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTTAAATTGTTTTA
126 ACCCATGCCTTCAAAAGCCTTATTAATCGCTTTAAATAGTTTTA
* * *** * *
8929 TAATCTTATAATTAATTTTA-AGTTGAATTTTTTTTACATTTTTTACTAAAAAATATTATAACTG
1 TAATCTCATAATTGATTTTAGA-TTGAA-TTTTTTTACATTTTTGGTTAACAAATA--ATAATTG
* * * * * *
8993 AATGTTTTCTTCGAGAAACATGAAG-AAAAGATATCCATTGGCAAGAAAAGTCTATTTATAGTCA
62 AATGTCTACCTCAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCA
*************** * * * * *
9057 CCCNNNNNNNNNNNNNNNTTATTACTTGCTTTCAATGGCTTTA
127 CCCATGCCTTCAAAAGCCTTATTAATCGCTTTAAATAGTTTTA
* * *
9100 TAATCTCATAATTGATTTTA-AGTTGAATTTTTTTACATTTTTCGATGAAACAGATAATAATTGA
1 TAATCTCATAATTGATTTTAGA-TTGAATTTTTTTACATTTTT-GGT-TAACAAATAATAATTGA
* * * * * *
9164 GTGTC-AGCCTCAAGAAACATAAAGAAAAAGATATCCATTGGCAAGAAGAGTCCGTTTATAATCA
63 ATGTCTA-CCTCAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCA
* * * *
9228 GCCATGCCTTCAAAAGCCTTATTACTCGCATTGAATAGTTTTA
127 CCCATGCCTTCAAAAGCCTTATTAATCGCTTTAAATAGTTTTA
* * * ** * * * **
9271 CAATCTCATAATTGATTTTA-AGTTGAATTGTTTTATATTTTTTAATAAAACAGATTATAATTTC
1 TAATCTCATAATTGATTTTAGA-TTGAATTTTTTTACA-TTTTTGGT-TAACAAATAATAATTGA
* * * * * *
9335 ATGTTTTCCTCAGGAAACATGAAG-AAAAGATATCCATTGACAAGAAAAGTCCATTTATAGACAC
63 ATGTCTACCTCAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCAC
* ** *********
9399 CCATGCTTTTGAAAGCCTTATTACA-CGCTTTAANNNNNNNNN
128 CCATGCCTTCAAAAGCCTTATTA-ATCGCTTTAAATAGTTTTA
* * * * * *
9441 NAATCTCATAATTGATTTTA-AGTT-AATTTTTTTATACCTTTT-ATTAAAACAGATTATAATTG
1 TAATCTCATAATTGATTTTAGA-TTGAATTTTTTTACA-TTTTTGGTT--AACAAATAATAATTG
* * * * ** *
9503 AATGTTTACCT-ATGGAAATGTGAAGAAAAAGATACCCATTGGCAAGAAAAGTTTATTTTTAGTC
62 AATGTCTACCTCA-AGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTC
* * * * *
9567 ACCCATGCCTTCGAAAGCCTTATTATTTGCTTTAAATGGCTTTA
126 ACCCATGCCTTCAAAAGCCTTATTAATCGCTTTAAATAGTTTTA
* * * * * * *
9611 TAATCTCATATTTGATTTTAGGTTGAATTTTTTTTATATTTTTTGTTTAAACAGATTATAATTCA
1 TAATCTCATAATTGATTTTAGATTGAA-TTTTTTTACA-TTTTTGGTT-AACAAATAATAATTGA
* * * **
9676 ATGTTTACCTCGAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTTTATTTATAGTCA
63 ATGTCTACCTCAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCA
9740 NNNNNNNNNN
Statistics
Matches: 1291, Mismatches: 327, Indels: 87
0.76 0.19 0.05
Matches are distributed among these distances:
167 2 0.00
168 39 0.03
169 145 0.11
170 405 0.31
171 565 0.44
172 130 0.10
173 5 0.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.36
Consensus pattern (169 bp):
TAATCTCATAATTGATTTTAGATTGAATTTTTTTACATTTTTGGTTAACAAATAATAATTGAATG
TCTACCTCAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCA
TGCCTTCAAAAGCCTTATTAATCGCTTTAAATAGTTTTA
Found at i:11213 original size:170 final size:169
Alignment explanation
Indices: 10902--11246 Score: 453
Period size: 170 Copynumber: 2.0 Consensus size: 169
10892 NNNNNNNNNN
* ** *
10902 ATCTCATAATTGATTTTAGGTTGAATTTTTTTACATTTTTATTAAAACAGATTACACTTGAATGT
1 ATCTCATAATTCATTTTAAATTGAATTTTTTTACATTTTTATTAAAACAGATTACAATTGAATGT
* * * * *
10967 TTACCTCGAGAGAAGTGAAGAAAAGATATTCATTGGCAAGAAAAGTCCATTTATAATCACCCTTA
66 CTACATCGAGAGAAATGAAGAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAATCACCCATA
* **
11032 CCTTTGAAAGCCTTATTACTCACTTTAAATGTTTTTATA
131 CCTTCGAAAGCCTTATTACTCACTTTAAATGGCTTTATA
* * *
11071 ATCTCATAGTTCATTTTAAATT-AATTTTTTTATTC-TTTTTATTAAGACAGATTATAATTGAAT
1 ATCTCATAATTCATTTTAAATTGAATTTTTTTA--CATTTTTATTAAAACAGATTACAATTGAAT
* * *
11134 GTCTACATTGGGA-AATATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCTATTTATAATCACC
64 GTCTACATCGAGAGAA-ATGAAG-AAAAGATATCCATTGGCAAGAAAAGTCCATTTATAATCACC
* *
11198 CATGCCTTCGAAAGCCTTATTACTTACTTTAAATGGCTTTATA
127 CATACCTTCGAAAGCCTTATTACTCACTTTAAATGGCTTTATA
11241 ATCTCA
1 ATCTCA
11247 NNNNNNNNNN
Statistics
Matches: 152, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
168 12 0.08
169 57 0.38
170 83 0.55
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (169 bp):
ATCTCATAATTCATTTTAAATTGAATTTTTTTACATTTTTATTAAAACAGATTACAATTGAATGT
CTACATCGAGAGAAATGAAGAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAATCACCCATA
CCTTCGAAAGCCTTATTACTCACTTTAAATGGCTTTATA
Found at i:11719 original size:171 final size:169
Alignment explanation
Indices: 11378--11721 Score: 415
Period size: 169 Copynumber: 2.0 Consensus size: 169
11368 NNNNNNNNNN
* * *
11378 TTACTCGCTTTAAATGTTTTTATAATCTTATAATTGATTTTAAGTTAAATTTTTCTAAATATTTT
1 TTACTCGCTTTAAAAGTTTTTATAATCTAATAATAGATTTTAAGTTAAATTTTTCTAAATATTTT
* ** *
11443 ATCGAAACAGATTATAATTGAATGTTACCTTGAGAAAAGTGAAGAAAAGATATCCATTGGCAAGA
66 ATCGAAACAGATTACAATTGAATGTTACCTCAAGAAAAGTGAAGAAAAGATATCCATTGGCAAAA
* * ** *
11508 AAAGTCCATTTATAGTTTTCATTGCCTTCGAAATCCTTA
131 AAAGTCCATTTACAATTACCATTGCCTTCGAAAGCCTTA
* * * *
11547 TTACTCGCTTTAAAAGTTTTTATAATCTAATAATAGATTTTTAGTTGAATTGTTT-TATATTTTT
1 TTACTCGCTTTAAAAGTTTTTATAATCTAATAATAGATTTTAAGTTAAATT-TTTCTAAATATTT
* * * ** *
11611 TAT-TAAACTATATTACAATTTAATGTCTACCTCAAGAAGCGTGAAGAAAAAGATATCCATTGGT
65 TATCGAAAC-AGATTACAATTGAATGT-TACCTCAAGAAAAGTGAAG-AAAAGATATCCATTGGC
*
11675 AAAAAAAGTTCATTTACAATTACCATT-CCGTTCGAAAGCCTTA
127 AAAAAAAGTCCATTTACAATTACCATTGCC-TTCGAAAGCCTTA
11718 TTAC
1 TTAC
11722 ATATCTACCT
Statistics
Matches: 147, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
168 4 0.03
169 70 0.48
170 20 0.14
171 53 0.36
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (169 bp):
TTACTCGCTTTAAAAGTTTTTATAATCTAATAATAGATTTTAAGTTAAATTTTTCTAAATATTTT
ATCGAAACAGATTACAATTGAATGTTACCTCAAGAAAAGTGAAGAAAAGATATCCATTGGCAAAA
AAAGTCCATTTACAATTACCATTGCCTTCGAAAGCCTTA
Found at i:11862 original size:145 final size:147
Alignment explanation
Indices: 11584--11866 Score: 349
Period size: 145 Copynumber: 1.9 Consensus size: 147
11574 TAATAATAGA
* ** * * *
11584 TTTTTAGTTGAATTGTTTTATATTTTTTATTAAACTATATTACAATTTAATGTCTACCTCAAGAA
1 TTTTAAGTTGAATTGTTTTATATTTTTTATTAAAAAAGATTACAATTGAATATCTACCTCAAGAA
* * * *
11649 GCGTGAAGAAAAAGATATCCATTGGTAAAAAAAGTTCATTTACAATTACCATTCCGTTCGAAAGC
66 ACGTGAAGAAAAAGATATCCATTGGCAAAAAAAGTTCATTTACAATGACCATGCCGTTCGAAAGC
11714 CTTATTACATATCTACC
131 CTTATTACATATCTACC
* * * *
11731 TTTTAAGTT-AATT-TTTTATATTTTTTATTAAAAAAGATTATAATTGCATATCTATCTTAAGAA
1 TTTTAAGTTGAATTGTTTTATATTTTTTATTAAAAAAGATTACAATTGAATATCTACCTCAAGAA
** * * *
11794 ACGTGAAGAAAAAGATATTTATTGGCAAGAAAAA-TTCATTTATAGTGACCAATGCCTTTC-AAA
66 ACGTGAAGAAAAAGATATCCATTGGCAA-AAAAAGTTCATTTACAATGACC-ATGCCGTTCGAAA
11857 GCCTTATTAC
129 GCCTTATTAC
11867 TCGCTTTAAA
Statistics
Matches: 115, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
145 91 0.79
146 16 0.14
147 8 0.07
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (147 bp):
TTTTAAGTTGAATTGTTTTATATTTTTTATTAAAAAAGATTACAATTGAATATCTACCTCAAGAA
ACGTGAAGAAAAAGATATCCATTGGCAAAAAAAGTTCATTTACAATGACCATGCCGTTCGAAAGC
CTTATTACATATCTACC
Found at i:13009 original size:172 final size:168
Alignment explanation
Indices: 12579--13186 Score: 752
Period size: 172 Copynumber: 3.6 Consensus size: 168
12569 NNNNNNNNNN
** *
12579 ATATTTTTTATTAAAACAGATTATAATTGAATGTTTTTCTCGAGAAACATGAAGAAAAGATATCC
1 ATATTTTTTATTAAAACAGATTATAATTGAATGTTTACCTCGAGAAACATAAAGAAAAGATATCC
* * * *
12644 ATTGGCAAGAAAAATCCATTCATAGTCACCCATTCCTTCGAAATCCTTATTACTCACTTTAAATG
66 ATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAGT-CTTATTACTCACTTTAAATG
* *
12709 TTTTTATAATCTCATAATTGATTTTAAATTAATTTTTTTT
130 TTTTTATAATCTCA-AATTGATTTTAAGTTAAATTTTTTT
* * * * * * * *
12749 ACACTTTTTATTAAAACAGATTATAATTTAATGTCTACCTTGAGAAATACAATGAAAAAGATATC
1 ATATTTTTTATTAAAACAGATTATAATTGAATGTTTACCTCGAGAAACATAAAG-AAAAGATATC
* *
12814 CATTGGCAAGAAAAGTCTATTTATAGTCACCCATGCCTTCGCAAGTCTTATTACTTACTTTAAAT
65 CATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCG-AAGTCTTATTACTCACTTTAAAT
* *
12879 CG-CTTTATAATCTCAAATTTGATTTTAGGTTAAAATTTTTTT
129 -GTTTTTATAATCTCAAA-TTGATTTTAAGTT-AAATTTTTTT
* * * *
12921 ATATTTTTTGTTTAAACAGATTATAGTTGAATGTTTGCCTCGAGAAACATAAAGAAAAAGATATC
1 ATATTTTTTATTAAAACAGATTATAATTGAATGTTTACCTCGAGAAACATAAAG-AAAAGATATC
** * * *
12986 CATTGGCAAGAAAAGTATATTTATATTCACACATGCCTTCGAAAGGCTTATTACTCACTTTAAAT
65 CATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCG-AAGTCTTATTACTCACTTTAAAT
*
13051 GTTTTTATAATCTCCTAATTGATTTTAAGTTAAATTTTTTT
129 GTTTTTATAATCT-CAAATTGATTTTAAGTTAAATTTTTTT
* * * * * * * *
13092 ATATTTTTTATTGAAACAAACTATAATTGAATGTTTACTTCAAGAAATATCAAGAATAGATATCC
1 ATATTTTTTATTAAAACAGATTATAATTGAATGTTTACCTCGAGAAACATAAAGAAAAGATATCC
13157 ATT-GCTAAGAAAAGTCCATTTATAGTCACC
66 ATTGGC-AAGAAAAGTCCATTTATAGTCACC
13187 NNNNNNNNNN
Statistics
Matches: 373, Mismatches: 57, Indels: 16
0.84 0.13 0.04
Matches are distributed among these distances:
169 2 0.01
170 78 0.21
171 143 0.38
172 147 0.39
173 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (168 bp):
ATATTTTTTATTAAAACAGATTATAATTGAATGTTTACCTCGAGAAACATAAAGAAAAGATATCC
ATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAGTCTTATTACTCACTTTAAATGT
TTTTATAATCTCAAATTGATTTTAAGTTAAATTTTTTT
Found at i:13535 original size:171 final size:169
Alignment explanation
Indices: 13358--14250 Score: 738
Period size: 170 Copynumber: 5.3 Consensus size: 169
13348 NNNNNNNNNN
13358 CGCTTTAAAT-AGTTTTACAATCTCATAATTGATTTTAAGTTGAATTTTTTTACACTTTTTATTA
1 CGCTTTAAATGA-TTTTACAATCTCATAATTGATTTTAAGTTGAATTTTTTTACA-TTTTTATTA
* * * * *
13422 AAACAGATTATAATTTAATATCTACCTCAAGATACGAGATGAAAAGAATATCCATTGATAAAAAA
64 AAACAGATTATAATTGAATGTCTACCTCAAGAAACGAGAAGAAAAG-ATATCCATTGATAAGAAA
* * *
13487 AGTCCATTTACAGTCA-CCATTGCGTTCGAAAGCCTTATTACT
128 AGTCCATTTATAGTCACCCA-TGCCTTCAAAAGCCTTATTACT
********** *
13529 CGCTTTAAATGATTTNNNNNNNNNNTAATTGATTTTAAGTT-AACTTTTTTTATATTTTTATTAA
1 CGCTTTAAATGATTTTACAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTACATTTTTATTAA
* ** *
13593 AACAGATTATAATTGAATGTCTACTTCAAGAAACCTGAAGGAAAAGATATCCATTGACAAGAAAA
65 AACAGATTATAATTGAATGTCTACCTCAAGAAACGAGAA-GAAAAGATATCCATTGATAAGAAAA
* * * * *
13658 GTCAATTTATAGTCACCCATACCTTCAGAAGTCTTATTATT
129 GTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACT
* * *
13699 CGCTTTAAATGGTTTTACAATCTCATAATTGATCTTAAGTTGAATTTTTGTACATTTTTATTAAA
1 CGCTTTAAATGATTTTACAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTATTAAA
* * ** * * *
13764 ACAAATTATAATTGAATGTTTACCTTGAGAAAAGTGAAGAAAAGATATCCATTGGTAAGAAAAGT
66 ACAGATTATAATTGAATGTCTACCTCAAGAAACGAGAAGAAAAGATATCCATTGATAAGAAAAGT
* * * *
13829 CTATTTATAGTCACCCATGCTTTTAAAAGCCTTATTAGT
131 CCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACT
* * * * ********** * * *
13868 CACTTTAATTGTTTTTATAATCTCATAATTNNNNNNNNNNTAAATTTTTTTACATTTTTGGTTGA
1 CGCTTTAAATGATTTTACAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTT-ATTAA
* *
13933 AACAGATAATAATTGAATGTC-AGCCT-----TA-G-G-A-AAAAGATATCCATTGATAAGAAAA
65 AACAGATTATAATTGAATGTCTA-CCTCAAGAAACGAGAAGAAAAGATATCCATTGATAAGAAAA
* ** * **
13988 GTCCATTTATAATCAGTCATGTCTTTGAAAGCCTTATTACT
129 GTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACT
* * * ** *
14029 CGCTTTGAAT-AGTTTTGCAATCTCATAATAGATTTTAAACTGAATTTTTTTATATTTTTTATTA
1 CGCTTTAAATGA-TTTTACAATCTCATAATTGATTTTAAGTTGAATTTTTTTACA-TTTTTATTA
* * * * *** **
14093 AAACAAATTATAATTTACTATCTACCTTTGGAAAC-ATGAAGAAGAAGATATCCATTGGCAAGAA
64 AAACAGATTATAATTGAATGTCTACCTCAAGAAACGA-GAAGAA-AAGATATCCATTGATAAGAA
* * * * ** * *
14157 AAATCCACTTATAATTATTCATACCTTCAAAAGCCTTATTACA
127 AAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACT
* *
14200 CGTTTTAAATGATTTTATAATCTCATAATTGATTTTAAGTT-AATTTTTTTA
1 CGCTTTAAATGATTTTACAATCTCATAATTGATTTTAAGTTGAATTTTTTTA
14251 TATTNNNNNN
Statistics
Matches: 566, Mismatches: 134, Indels: 45
0.76 0.18 0.06
Matches are distributed among these distances:
161 112 0.20
162 7 0.01
163 1 0.00
164 1 0.00
165 1 0.00
166 1 0.00
168 1 0.00
169 102 0.18
170 205 0.36
171 133 0.23
172 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.39
Consensus pattern (169 bp):
CGCTTTAAATGATTTTACAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTATTAAA
ACAGATTATAATTGAATGTCTACCTCAAGAAACGAGAAGAAAAGATATCCATTGATAAGAAAAGT
CCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACT
Found at i:14052 original size:330 final size:321
Alignment explanation
Indices: 13634--14229 Score: 682
Period size: 330 Copynumber: 1.8 Consensus size: 321
13624 AACCTGAAGG
* * *
13634 AAAAGATATCCATTGACAAGAAAAGTCAATTTATAGTCACCCATACCTTCAGAAGTCTTATTATT
1 AAAAGATATCCATTGACAAGAAAAGTCAATTTATAATCACCCATACCTTCAGAAGCCTTATTACT
* * **
13699 CGCTTTAAATGGTTTTACAATCTCATAATTGATCTTAAGTTGAATTTTTGTACA-TTTTTATTAA
66 CGCTTTAAATAGTTTTACAATCTCATAATAGATCTTAAACTGAATTTTTGTACATTTTTTATTAA
* * *
13763 AACAAATTATAATTGAATGTTTACC-TTGAGAAA-AGTGAAGAA-AAGATATCCATTGGTAAGAA
131 AACAAATTATAATTGAATATCTACCTTTG-GAAACA-TGAAGAAGAAGATATCCATTGGCAAGAA
* * * * * * * * *
13825 AAGTCTATTTATAGTCACCCATGCTTTTAAAAGCCTTATTAGTCAC-TTTAATTGTTTTTATAAT
194 AAATCCACTTATAATCACCCATACCTTCAAAAGCCTTATTA--CACGTTTAAATGATTTTATAAT
13889 CTCATAATTNNNNNNNNNNTAAATTTTTTTACATTTTTGGTTGAAACAGATAATAATTGAATGTC
257 CTCATAATT----------TAAATTTTTTTACATTTTTGGTTGAAACAGATAATAATTGAATGTC
13954 AGCCTTAGGA
312 AGCCTTAGGA
* * ** ** *
13964 AAAAGATATCCATTGATAAGAAAAGTCCATTTATAATCAGTCATGTCTT-TGAAAGCCTTATTAC
1 AAAAGATATCCATTGACAAGAAAAGTCAATTTATAATCACCCATACCTTCAG-AAGCCTTATTAC
* * * * *
14028 TCGCTTTGAATAGTTTTGCAATCTCATAATAGATTTTAAACTGAATTTTTTTATATTTTTTATTA
65 TCGCTTTAAATAGTTTTACAATCTCATAATAGATCTTAAACTGAATTTTTGTACATTTTTTATTA
* *
14093 AAACAAATTATAATTTACTATCTACCTTTGGAAACATGAAGAAGAAGATATCCATTGGCAAGAAA
130 AAACAAATTATAATTGAATATCTACCTTTGGAAACATGAAGAAGAAGATATCCATTGGCAAGAAA
* **
14158 AATCCACTTATAATTATTCATACCTTCAAAAGCCTTATTACACGTTTTAAATGATTTTATAATCT
195 AATCCACTTATAATCACCCATACCTTCAAAAGCCTTATTACACG-TTTAAATGATTTTATAATCT
14223 CATAATT
259 CATAATT
14230 GATTTTAAGT
Statistics
Matches: 223, Mismatches: 36, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
329 1 0.00
330 101 0.45
331 42 0.19
332 79 0.35
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.38
Consensus pattern (321 bp):
AAAAGATATCCATTGACAAGAAAAGTCAATTTATAATCACCCATACCTTCAGAAGCCTTATTACT
CGCTTTAAATAGTTTTACAATCTCATAATAGATCTTAAACTGAATTTTTGTACATTTTTTATTAA
AACAAATTATAATTGAATATCTACCTTTGGAAACATGAAGAAGAAGATATCCATTGGCAAGAAAA
ATCCACTTATAATCACCCATACCTTCAAAAGCCTTATTACACGTTTAAATGATTTTATAATCTCA
TAATTTAAATTTTTTTACATTTTTGGTTGAAACAGATAATAATTGAATGTCAGCCTTAGGA
Found at i:15384 original size:170 final size:171
Alignment explanation
Indices: 15208--15687 Score: 511
Period size: 170 Copynumber: 2.8 Consensus size: 171
15198 NNNNNNNNNN
* *
15208 ACTATAAATGGACTTTTCTTACCAATGGATATC-TTTTCTTCATGTTTCTCGAGGAAAACATTCA
1 ACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCAAGGAAAACATTCA
* * * * **********
15272 ATTATACTTTGTTTTAGTGAAAAATATAAAAAAATTCAACTTANNNNNNNNNNTGAGATTATAAA
66 ATTATAATTTGTTTTAATAAAAAATATAAAAAAATTCAACCTAAAATCAAATATGAGATTATAAA
* * *
15337 ACCATTTAAAGCGATTAACAAGGCTTTGGAAGGCAT-GTGAG
131 ACCATTTAAAGCGAGTAACAAGGCTTTGAAAGGCATAG-GAC
* * ** *
15378 ACTATAAATGGACTTTTCTTGCC-ATGGATATCTTTTTCTTCATGTTTCTTAAGGTAGGCATTTA
1 ACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCAAGGAAAACATTCA
* *
15442 ATTATAATTTTTTTTAATAAAAAATATAAAAAAATTCTACCTAAAATCAAATATGAGATTATAAA
66 ATTATAATTTGTTTTAATAAAAAATATAAAAAAATTCAACCTAAAATCAAATATGAGATTATAAA
* * * *
15507 ACTATTTAAAGCGGGTAATAAGGCTTTGAAAGGCATAGGTC
131 ACCATTTAAAGCGAGTAACAAGGCTTTGAAAGGCATAGGAC
* * * * * * *
15548 ACTATAAATGGATTTTTGTTGCCAATGGATATCTTTTTCTTCACGTTTCTCAAGGTAGATATGCA
1 ACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCAAGGAAAACATTCA
* * * * * *
15613 ATTATGATCTT-TTTTAATAAAATATATAAAAAAAATT-AACTTGAAATGAATTATGAGATTATA
66 ATTATAAT-TTGTTTTAATAAAAAATAT-AAAAAAATTCAACCTAAAATCAAATATGAGATTATA
15676 AAACCATTTAAA
129 AAACCATTTAAA
15688 NNNNNNNNNN
Statistics
Matches: 259, Mismatches: 46, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
169 9 0.03
170 149 0.58
171 90 0.35
172 11 0.04
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.36
Consensus pattern (171 bp):
ACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCAAGGAAAACATTCA
ATTATAATTTGTTTTAATAAAAAATATAAAAAAATTCAACCTAAAATCAAATATGAGATTATAAA
ACCATTTAAAGCGAGTAACAAGGCTTTGAAAGGCATAGGAC
Done.