Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399799.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_304.0, 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: 29381
ACGTcount: A:0.23, C:0.08, G:0.07, T:0.24
Warning! 11081 characters in sequence are not A, C, G, or T
Found at i:2916 original size:342 final size:326
Alignment explanation
Indices: 2275--2897 Score: 599
Period size: 343 Copynumber: 1.8 Consensus size: 326
2265 TTTAAAGCGA
* *
2275 GTAATAAGGCTTTTGAAAGAACGAGTGACTATAAATGGATTTTTCTTACCAATGAATAACGTTTT
1 GTAATAAGGCTTTTGAAAGAACGAGTGACTAGAAATGGACTTTTCTTACCAATGAATAACGTTTT
*
2340 CTTCATGTTTCTCAATGTGGACATCCAACTATAGTCTATTTTAATCAAAAATATAAAAAAATTGA
66 CTTCATGTTTCTCAATGTAGACATCCAACTATAGTCTATTTTAATCAAAAATATAAAAAAATTGA
****
2405 ACATAAAATAAATTTTGAGATAATAAAANNNNNNNNNNTGAGTAATAAGGCTTTTGAAGGAATAG
131 ACATAAAATAAATTTTGAGATAATAAAA------AAAGTGAGTAATAAGGCTTTTGAAGGAATAG
* * * * * * * *
2470 GAGACTATAGATGGTCTTTTCTTGTCAATGAATGTATTTTTCTTCACGTTTCTTGATGTAGACAT
190 GAGACTATAAATGGTCTTTTCTTGCCAATGAATGCATTTTTCTTAACATTTCTCGATATAAACAT
***
2535 TCAATTATAGTTTGTCTTAACCATAAATGTCAAAAAAATTAAACATAAAATCAATTGNNNNNNNN
255 TCAATTATAACCTGTCTTAACCATAAATGTCAAAAAAATTAAACATAAAATCAATTG--------
2600 NNAACTATTTAAAATGG
312 --AACTATTTAAAATGG
* * ** *
2617 GTAATAAGGCTTTTGAAGGAATGAGTGACTAGAAATGGACTTTTCTTACCAAT-AATTTCCTTTT
1 GTAATAAGGCTTTTGAAAGAACGAGTGACTAGAAATGGACTTTTCTTACCAATGAA-TAACGTTT
* * * * * *
2681 TCTTCATGTTTCTCAATGTAGACATTCAATTATAGTCTGTTTTCA-CTAATAATGTAAAAAAAAT
65 TCTTCATGTTTCTCAATGTAGACATCCAACTATAGTCTATTTTAATC-AAAAATAT-AAAAAAAT
* * **** *
2745 TGAACATAAAATCAATTATT-AGATTATNNNNNNNNNNAAAGTGAGTAATTAGGCTTTTGAAGGA
128 TGAACATAAAATAAATT-TTGAGATAAT------AAAAAAAGTGAGTAATAAGGCTTTTGAAGGA
* * *
2809 AT-GAGAGACTCTAAATGGAT-TTTTCTTGCCAATGAATGCCTTTTTCTTAATATTTCTCGATAT
186 ATAG-GAGACTATAAATGG-TCTTTTCTTGCCAATGAATGCATTTTTCTTAACATTTCTCGATAT
*
2872 AAACATTCAATTATAACCTGTTTTAA
249 AAACATTCAATTATAACCTGTCTTAA
2898 TCAAGGAAGT
Statistics
Matches: 229, Mismatches: 40, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
341 3 0.01
342 101 0.44
343 122 0.53
344 3 0.01
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.35
Consensus pattern (326 bp):
GTAATAAGGCTTTTGAAAGAACGAGTGACTAGAAATGGACTTTTCTTACCAATGAATAACGTTTT
CTTCATGTTTCTCAATGTAGACATCCAACTATAGTCTATTTTAATCAAAAATATAAAAAAATTGA
ACATAAAATAAATTTTGAGATAATAAAAAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACT
ATAAATGGTCTTTTCTTGCCAATGAATGCATTTTTCTTAACATTTCTCGATATAAACATTCAATT
ATAACCTGTCTTAACCATAAATGTCAAAAAAATTAAACATAAAATCAATTGAACTATTTAAAATG
G
Found at i:3006 original size:171 final size:172
Alignment explanation
Indices: 2253--3143 Score: 460
Period size: 171 Copynumber: 5.2 Consensus size: 172
2243 NNNNNNNNNN
* * * * *
2253 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAACGAGTGACTATAAATGGATTTT
1 ATTATAAAACCATTTAAAGTGAGCAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTT
** * * * * ** * * ** *
2318 TCTTACCAATGAATAACGTTTTCTTCATGTTTCTCAATGTGGACATCCAACTATAGTCTATTTTA
66 TCTTACCAATGAATGCCTTTTTCTTAATATTTCTCAATATAAACATTCAATTATAACCTGTTTTA
* * *
2383 A-TCAAAAATAT-AAAAAAATTGAACATAAAATAAATT-TTGAG
131 ACT-AAGAATGTAAAAAAAATTGAACATAAAATCAATTATT-AG
* ********** * * * *
2424 ATAATAAAANNNNNNNNNNTGAGTAATAAGGCTTTTGAAGGAAT-AGGAGACTATAGATGGTCTT
1 ATTATAAAACCATTTAAAGTGAGCAATAAGGCTTTTGAAGGAATGA-GTGACTATAAATGGACTT
** ** * ** ** * * *** *
2488 TTCTTGTCAATGAATGTATTTTTCTTCACGTTTCTTGATGTAGACATTCAATTATAGTTTGTCTT
65 TTCTTACCAATGAATGCCTTTTTCTTAATATTTCTCAATATAAACATTCAATTATAACCTGTTTT
* * * ****
2553 AACCATA-AATGTCAAAAAAATTAAACATAAAATCAATT-GNNN
130 AACTA-AGAATGTAAAAAAAATTGAACATAAAATCAATTATTAG
******* * * * * *
2595 NNNNNNNAACTATTTAAAATGGGTAATAAGGCTTTTGAAGGAATGAGTGACTAGAAATGGACTTT
1 ATTATAAAACCATTTAAAGTGAGCAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTT
* * * * * **
2660 TCTTACCAAT-AATTTCCTTTTTCTTCATGTTTCTCAATGTAGACATTCAATTATAGTCTGTTTT
66 TCTTACCAATGAA-TGCCTTTTTCTTAATATTTCTCAATATAAACATTCAATTATAACCTGTTTT
* *
2724 CACTAATAATGTAAAAAAAATTGAACATAAAATCAATTATTAG
130 AACTAAGAATGTAAAAAAAATTGAACATAAAATCAATTATTAG
********** * * * * *
2767 ATTATNNNNNNNNNNAAAGTGAGTAATTAGGCTTTTGAAGGAATGAGAGACTCTAAATGGATTTT
1 ATTATAAAACCATTTAAAGTGAGCAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTT
* *
2832 TCTTGCCAATGAATGCCTTTTTCTTAATATTTCTCGATATAAACATTCAATTATAACCTGTTTTA
66 TCTTACCAATGAATGCCTTTTTCTTAATATTTCTCAATATAAACATTCAATTATAACCTGTTTTA
* *
2897 A-TCAAGGAA-GT-AAAAAAATTGAACTTAAAATGAATT-TTAAG
131 ACT-AA-GAATGTAAAAAAAATTGAACATAAAATCAATTATT-AG
* * * *
2938 ATTATAAAACCATTTAAAGTGAGCAATAAGGCTTTCGAAGGAATGAGTCATTATAAATAGACTTT
1 ATTATAAAACCATTTAAAGTGAGCAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTT
* *** * * * * ** * * * ** *
3003 TCTTACAAATGAATTTATTTTTTTTCATGTTTCTAAAGGTAGATATTCATTTATAGTCTATTTTA
66 TCTTACCAATGAATGCCTTTTTCTTAATATTTCTCAATATAAACATTCAATTATAACCTGTTTTA
* * * * *
3068 ATTAA-AATAT-AAAAAAA-TCAACTTAAAATCAATTATAAG
131 ACTAAGAATGTAAAAAAAATTGAACATAAAATCAATTATTAG
* ** * *
3107 GTTATAAAACCGCTTAAAGCGAGAAATAAGGCTTTTG
1 ATTATAAAACCATTTAAAGTGAGCAATAAGGCTTTTG
3144 NNNNNNNNNN
Statistics
Matches: 544, Mismatches: 161, Indels: 32
0.74 0.22 0.04
Matches are distributed among these distances:
169 50 0.09
170 15 0.03
171 347 0.64
172 128 0.24
173 4 0.01
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (172 bp):
ATTATAAAACCATTTAAAGTGAGCAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTT
TCTTACCAATGAATGCCTTTTTCTTAATATTTCTCAATATAAACATTCAATTATAACCTGTTTTA
ACTAAGAATGTAAAAAAAATTGAACATAAAATCAATTATTAG
Found at i:4290 original size:169 final size:169
Alignment explanation
Indices: 4066--4379 Score: 429
Period size: 169 Copynumber: 1.9 Consensus size: 169
4056 ATTTAAAAAA
* *
4066 AATTAAACTTAAAATCAATTTTGAGATAATAAAACCGTTTAAAGAGAGTAATAAGGCTTTTC-AA
1 AATTAAACTTAAAATCAATTTTGAGATAATAAAACCATTTAAAGAGAGCAATAAGGC-TTTCGAA
* * *
4130 GGAA-TGAGAGACTATAAATAGATTTTTCATACC-AATGAATATC-TTTTTCTTCACGTTTCTTG
65 GAAATTG-GAGACTATAAATAGACTTTTC-TACCAAATGAAT-TCATTTTTCTTCACATTTCTTG
**
4192 ATTTAGACATTCAATTATAATCTATTTAGTTAAAAAAGTAAAC
127 AGGTAGACATTCAATTATAATCTATTTAGTTAAAAAAGTAAAC
* * * * *
4235 AATTGAACTTAAAATTAATTTTGAGATTATAAAGCCATTTAAAGTGAGCAATAAGGCTTTCGAAG
1 AATTAAACTTAAAATCAATTTTGAGATAATAAAACCATTTAAAGAGAGCAATAAGGCTTTCGAAG
* * *
4300 AAATTGGTGACTATAAATAGACTTTTCTTCCAAATGAATTCATTTTTCTTCACATTTCTTTAGGT
66 AAATTGGAGACTATAAATAGACTTTTCTACCAAATGAATTCATTTTTCTTCACATTTCTTGAGGT
4365 AGACATTCAATTATA
131 AGACATTCAATTATA
4380 GTTTATTTTA
Statistics
Matches: 126, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
168 9 0.07
169 115 0.91
170 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (169 bp):
AATTAAACTTAAAATCAATTTTGAGATAATAAAACCATTTAAAGAGAGCAATAAGGCTTTCGAAG
AAATTGGAGACTATAAATAGACTTTTCTACCAAATGAATTCATTTTTCTTCACATTTCTTGAGGT
AGACATTCAATTATAATCTATTTAGTTAAAAAAGTAAAC
Found at i:7025 original size:18 final size:19
Alignment explanation
Indices: 7002--7037 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
6992 GAAAGACGTG
7002 TAAAAAAAGT-TATTTATT
1 TAAAAAAAGTCTATTTATT
7020 TAAAAAAAGTCTATTTAT
1 TAAAAAAAGTCTATTTAT
7038 AGTCTCTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (19 bp):
TAAAAAAAGTCTATTTATT
Found at i:7092 original size:168 final size:169
Alignment explanation
Indices: 6733--7287 Score: 611
Period size: 168 Copynumber: 3.3 Consensus size: 169
6723 TATTACTCAT
* * * * **
6733 TTTAAATGGTTTTATAATCTCAAAATTGA-TTTAGAGTTGACTTCCTTTACATTTCACATTAAAA
1 TTTAAATGGTTTTATAATCTCATAATTGATTTTA-AGTAGAATT-TTTTACATTTTTCATTAAAA
********** * * *
6797 CAAACTATAATTGAATGCCNNNNNNNNNNAACATGTAGAAAAACCCATTTATTTGAAAGAAAAGT
64 CAAACTATAATTGAATGCCTGCCTCGGAAAACATATAAAAAAATCCATTTATTTGAAAGAAAAGT
* * **
6862 CCATTTGTATTCTCTCATTCCTTCAAAAATCCTATTACTCAT
129 CCATTTGTAGTCTCTCATTCCTTC-AAAATCCTATTAGTCGC
** * **
6904 TTTAAATACTTTTTTAATCTCATAATTGATTTTAAGTAGAATTTTTTACATTTTTTGTTAAAACA
1 TTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTAGAATTTTTTACATTTTTCATTAAAACA
* * *
6969 AACTATAATTGAAT-CCATGCCTC-GAAAGACGTGTAAAAAAAGT-TATTTATTT-AAA-AAAAG
66 AACTATAATTGAATGCC-TGCCTCGGAAA-ACATATAAAAAAA-TCCATTTATTTGAAAGAAAAG
* * *
7029 TCTATTTATAGTCTCTCATTCCTTCAAAAGCCTTATTAGTCGC
128 TCCATTTGTAGTCTCTCATTCCTTCAAAATCC-TATTAGTCGC
*
7072 TTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTACATTTTTCATTAAAACA
1 TTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTAGAATTTTTTACATTTTTCATTAAAACA
* * * *
7137 GACTATAATTGAATGCCTGCCTCGGGAAACATATAGAAAAATCCATTTATTTGAAAGACAAGTCC
66 AACTATAATTGAATGCCTGCCTCGGAAAACATATAAAAAAATCCATTTATTTGAAAGAAAAGTCC
*
7202 ATTTGTAGTCTCTCATTCCTTCAAAATCCTACTAGTCGC
131 ATTTGTAGTCTCTCATTCCTTCAAAATCCTATTAGTCGC
* *
7241 TTTAACTGGTTTTATAATCTCTTAATTGATTTTAAG-ATGAATTTTTT
1 TTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTA-GAATTTTTT
7288 TNNNNNNNNN
Statistics
Matches: 322, Mismatches: 51, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
167 7 0.02
168 130 0.40
169 66 0.20
170 83 0.26
171 32 0.10
172 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.40
Consensus pattern (169 bp):
TTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTAGAATTTTTTACATTTTTCATTAAAACA
AACTATAATTGAATGCCTGCCTCGGAAAACATATAAAAAAATCCATTTATTTGAAAGAAAAGTCC
ATTTGTAGTCTCTCATTCCTTCAAAATCCTATTAGTCGC
Found at i:8577 original size:173 final size:168
Alignment explanation
Indices: 8105--8657 Score: 639
Period size: 170 Copynumber: 3.2 Consensus size: 168
8095 NNNNNNAATG
* *
8105 GTTTTATAATCTCATAATTGATTTTAAGTTCAATTATTTTTACTTTTTTATTAAAAAAGATTATA
1 GTTTTATAATCTCATAATTGAATTTAAGTTCAATTATTTTTACTTTTTTATTAAAACAGATTATA
* * *
8170 ATTGAATGTCTGCATTAAGAAACATAAAGAAAAAGACAATCACAGGCAAGAAAAGTCCATTTATA
66 ATTGAATGTCTGCATCAAGAAACAT-AAGAAAAAGACATTCATAGG-AAGAAAAGTCCATTTATA
*
8235 GTCACCCATTTCTTCAAAAGCCTTATTACTCACTTTAAAT
129 GTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAAT
* * * * * *
8275 GGTTTATTAATCTCATAATTGAATTTAAGTTGAA-T-TTTTTACATTTCTCATTAAAACATACTA
1 GTTTTA-TAATCTCATAATTGAATTTAAGTTCAATTATTTTTAC-TTTTTTATTAAAACAGATTA
* * * ** **
8338 TAATTGAATGCCTGCCTCAAGAAACCTATAGAAAAACCCATTTTTTTA-GAAGAAAAGTCCATTT
64 TAATTGAATGTCTGCATCAAGAAACATA-AGAAAAAGACA--TTCATAGGAAGAAAAGTCCATTT
* * *
8402 ATATTCTCCCATTCCTTCAAAAGCCTAATTACTCACTTTAAAT
126 ATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAAT
*
8445 AGTTTTATAATCTCATAATT-AATTTTAAGTTCAATTTATTTTTACTTTTTTGGTTAAAACAGAT
1 -GTTTTATAATCTCATAATTGAA-TTTAAGTTCAA-TTATTTTTACTTTTTT-ATTAAAACAGAT
* * * * * * *
8509 TACAATTGAATATCTACGTCAAGAAACGTGAAGAAAAAGGCATTCATAGGTAAGAAAAGTCTATT
62 TATAATTGAATGTCTGCATCAAGAAACAT-AAGAAAAAGACATTCATAGG-AAGAAAAGTCCATT
* * *
8574 TATAGTCACCCATTCCTTCATAAGCTTTATTACTAACTTTAAAT
125 TATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAAT
*
8618 GATTTTATAATCTCATAATTGAATTTAAGTTGAATT-TTTT
1 G-TTTTATAATCTCATAATTGAATTTAAGTTCAATTATTTT
8658 ACATTTCTCA
Statistics
Matches: 320, Mismatches: 47, Indels: 31
0.80 0.12 0.08
Matches are distributed among these distances:
169 10 0.03
170 130 0.41
171 39 0.12
172 11 0.03
173 127 0.40
174 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (168 bp):
GTTTTATAATCTCATAATTGAATTTAAGTTCAATTATTTTTACTTTTTTATTAAAACAGATTATA
ATTGAATGTCTGCATCAAGAAACATAAGAAAAAGACATTCATAGGAAGAAAAGTCCATTTATAGT
CACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAAT
Found at i:10203 original size:171 final size:171
Alignment explanation
Indices: 9283--10717 Score: 1328
Period size: 171 Copynumber: 8.4 Consensus size: 171
9273 GTCCACATTG
** * * * *
9283 AGAAACATGAAGAAAAAGATATTCA-CTGACAAG-AAAGTCTATTTATAGTCTCCTATTACTTCA
1 AGAAACATGAAGAAAAAGGCATTCATTTGA-AAGAAAAGTCTATTTATAGTCACCCATTCCTTCA
* * * *
9346 AAAGCCTTATTACTCGCTTTAAATAGTTTTATAGTCTCATAGTTGATTTTATGTTTAATTTTTTT
65 AAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTT
* *
9411 ATATTATTGGT--AAACAGATTATAATTGAATGTCTACATCA
130 ACATTTTTGGTAAAAACAGATTATAATTGAATGTCTACATCA
* *** * * * ***
9451 TGAAACATGAAGAAAAAAATATT-TTTTGATGAGAAAAGTTTATTTATAGTCACATTTTCCTTCA
1 AGAAACATGAAGAAAAAGGCATTCATTTGA-AAGAAAAGTCTATTTATAGTCACCCATTCCTTCA
* ** * * ** *
9515 AAAGCCTTATTACCCATTTTAAAT-GATTTTATTATCTCAAAATTGATTTTATTTTGAATTTTTT
65 AAAGCCTTATTACTCGCTTTAAATAG-TTTTATAATCTCATAATTGATTTTAAGTTCAA--TTTT
* * * * * *
9579 TTTATATTTTTAGTTAAGACA-AGCTATAATTGAATGTCTATC-TCG
127 TTTACATTTTTGGTAAAAACAGA-TTATAATTGAATGTCTA-CATCA
** * * * * * ** * * *
9624 AGAAATGTTAAGAAAAAAGTATTCA-CTGACAAGAAAAGTCTATTAACGGTCTCTCATTCCTTTA
1 AGAAACATGAAGAAAAAGGCATTCATTTGA-AAGAAAAGTCTATTTATAGTCACCCATTCCTTCA
* * * * * *
9688 AAAGCCTCATTACTTGCTTGAAATGGTTTTATATTCTCATAATTGATTTGAAGTTCAATTATTTT
65 AAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTCAATT-TTTT
** * * *
9753 TATTTTTTTGATTAAAACAGATTATAATTGATTGTCTACATCA
129 TACATTTTTGGTAAAAACAGATTATAATTGAATGTCTACATCA
* * * * * * **
9796 AGAAACGTGAAGAAAAAGGCATTCCTTGGTAAGAAAAGTCCATTTCTAGTCACGTATTCCTTCAA
1 AGAAACATGAAGAAAAAGGCATTCATTTGAAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAA
* * * *
9861 AAGCCTTATTACTTGCTTTAAATCGTTTTATAATCTCATAATTGATTTTAAATTGAA-TTTTTTA
66 AAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTA
* * * * * **
9925 CAATTTTTGTTAAAAA-ATACTATAATTGAATGGCTACCTTG
131 C-ATTTTTGGTAAAAACAGATTATAATTGAATGTCTACATCA
* * ** * * * * * *
9966 GGAAACATGTAGAAAAACCCATTTATTTGGACGAAAAGTCTATTTATAGTCTCTCATTCTTTCAA
1 AGAAACATGAAGAAAAAGGCATTCATTTGAAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAA
* * * * * *
10031 AAGCCTTATTAGTCGCTCTAAATAGTTTTATAATATCATAATTGACTTTAAGTTGAATTATTTTA
66 AAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTA
* *
10096 CATTTTTGGTAAAAACAGAATATAATTGAATGTCTACCTCA
131 CATTTTTGGTAAAAACAGATTATAATTGAATGTCTACATCA
* * *
10137 AGAATCATGAAGAAAAATGAATTCATTTGAAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAA
1 AGAAACATGAAGAAAAAGGCATTCATTTGAAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAA
* * * * *
10202 AAGCCTTATTGCTCACTTTGAATGGTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTA
66 AAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTA
* *
10267 C---TTT-G-ACTAAATAGATTATAATTGAATGTCTACATCA
131 CATTTTTGGTA-AAAACAGATTATAATTGAATGTCTACATCA
* * * * * * *
10304 AGAAACATGAAGAAAGAGGCATTCATTGGCAAA-AAAAATCTATTTATAGTCTCTCATTCTTTGA
1 AGAAACATGAAGAAAAAGGCATTCATTTG-AAAGAAAAGTCTATTTATAGTCACCCATTCCTTCA
* * * *
10368 AAAGCCTTATTACTCACTTTAAATGGTTTTATTATCTCAAAATTGATTTTAAGTTCAATTTTTTT
65 AAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTCAA--TTTTT
* * * *
10433 TTACATTTTAAGTTAAAATC-GATTATAATTGAATGTCTACGTCA
128 TTACATTTT-TGGTAAAAACAGATTATAATTGAATGTCTACATCA
* * * * *
10477 TGAAAGATGAAGAAAAAGGCATTCATTAGGAAGAAAAGTCCATTTATAGTCA-CCATT-CTTCAA
1 AGAAACATGAAGAAAAAGGCATTCATTTGAAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAA
* * *
10540 AAGTCATATTACTAGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTCAATTATTTTT
66 AAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTCAATT-TTTTT
* * *
10605 AC-TATTTTGGTTAAAACATATTATAATTGAATGTCTACATCT
130 ACAT-TTTTGGTAAAAACAGATTATAATTGAATGTCTACATCA
** ** * *
10647 AGAAATGTGAAGAAAAAGGCATTCATAGGTAAGAAAATTCTATTTATAGTCACCCATTCCTTCAA
1 AGAAACATGAAGAAAAAGGCATTCATTTGAAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAA
10712 AAGCCT
66 AAGCCT
10718 NNNNNNNNNN
Statistics
Matches: 1024, Mismatches: 209, Indels: 64
0.79 0.16 0.05
Matches are distributed among these distances:
166 1 0.00
167 132 0.13
168 33 0.03
169 90 0.09
170 211 0.21
171 225 0.22
172 151 0.15
173 176 0.17
174 4 0.00
175 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (171 bp):
AGAAACATGAAGAAAAAGGCATTCATTTGAAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAA
AAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTA
CATTTTTGGTAAAAACAGATTATAATTGAATGTCTACATCA
Found at i:12399 original size:171 final size:163
Alignment explanation
Indices: 12153--12472 Score: 328
Period size: 171 Copynumber: 1.9 Consensus size: 163
12143 NNNATCTCAA
* * * *
12153 AATTGATTTTATGTTCAGTTTTTTTTATATATTTTTGGTCAAAACAAACTATAATTGAATGTCCA
1 AATTGATTTTAAGTTCAATTATTTTTATATATTTTCGGTCAAAACAAACTATAATTGAATGTCCA
* * * * *
12218 CCATGAGAAACGTGAAGAAAAAA-ACATTCATTGATAAGAAATGTCCATTTATAGTC-TCTCATT
66 CCA-GAGAAACATAAAGAAAAAAGA-ATTCATTGATAAGAAAAGTCCATTTATAGCCACCT-ATT
12281 CCTTCAAAAG-CTTATTACTCACTTTAAATGGTTTT
128 CCTTCAAAAGACTTATTACTCACTTTAAATGGTTTT
* * * *
12316 NNNNNNNNNNAATTGATTTTAAGTTCAATTATTTTTA-CT-TTTTCGGTTAAAATAAATTATAAT
1 ----------AATTGATTTTAAGTTCAATTATTTTTATATATTTTCGGTCAAAACAAACTATAAT
* *
12379 TGAATGTCTACACC-GAGAAACATAAAGAAAAAAGAATTCATTGGTAAGAAAAGTCTATTTATAG
56 TGAATGTC--CACCAGAGAAACATAAAGAAAAAAGAATTCATTGATAAGAAAAGTCCATTTATAG
12443 CCACCTATTCCTTCAAAAGACTTATTACTC
119 CCACCTATTCCTTCAAAAGACTTATTACTC
12473 NNNNNNNNNN
Statistics
Matches: 127, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
171 85 0.67
172 14 0.11
173 28 0.22
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.37
Consensus pattern (163 bp):
AATTGATTTTAAGTTCAATTATTTTTATATATTTTCGGTCAAAACAAACTATAATTGAATGTCCA
CCAGAGAAACATAAAGAAAAAAGAATTCATTGATAAGAAAAGTCCATTTATAGCCACCTATTCCT
TCAAAAGACTTATTACTCACTTTAAATGGTTTT
Found at i:12849 original size:169 final size:157
Alignment explanation
Indices: 12674--12998 Score: 332
Period size: 169 Copynumber: 2.0 Consensus size: 157
12664 CTCATAATTA
*
12674 ATTTTAAGTAT-AATTTTTTACATTTTTCATTAAAACATACT-ATAATTGAATGTTTCCCTCAAG
1 ATTTTAAGT-TGAATTTTTTACATTTTTCATTAAAACAGA-TAATAATTGAATGTTTCCCTCAAG
* * * * * *
12737 AGACGTGTAG-AAAAGCCATTTATTTAGAAGAAAAGTCTATTTATAGTGTCTCATTCCTTTAAAA
64 AAACGTATAGAAAAAGCCATTTATTT-GAAAAAAAGTCTATTTATAATCTCTCATTCCTTCAAAA
* *
12801 GCCTTATTAGTCACTTTAAATGATTTTANNNNNNNNNNNNTG
128 GCCTTATCACTCACTTTAAATGATTTTA------------TG
** * *
12843 ATTTTAAGTTGAATTTTTTACATTTTTTGTTAAAACAGATAATAATTGAATGTTTGCCTCGAGAA
1 ATTTTAAGTTGAATTTTTTACATTTTTCATTAAAACAGATAATAATTGAATGTTTCCCTCAAGAA
* * * *
12908 ACGTATAGAAAAATCTATTTATTTGAAAAAAAGTTTGTTTATAATCTCTCATTCCTTCAAAAGCC
66 ACGTATAGAAAAAGCCATTTATTTGAAAAAAAGTCTATTTATAATCTCTCATTCCTTCAAAAGCC
*
12973 TTATCACTCGCTTTAAATGATTTTAT
131 TTATCACTCACTTTAAATGATTTTAT
12999 AATCTCANNN
Statistics
Matches: 135, Mismatches: 18, Indels: 18
0.79 0.11 0.11
Matches are distributed among these distances:
157 1 0.01
168 2 0.01
169 119 0.88
170 13 0.10
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.40
Consensus pattern (157 bp):
ATTTTAAGTTGAATTTTTTACATTTTTCATTAAAACAGATAATAATTGAATGTTTCCCTCAAGAA
ACGTATAGAAAAAGCCATTTATTTGAAAAAAAGTCTATTTATAATCTCTCATTCCTTCAAAAGCC
TTATCACTCACTTTAAATGATTTTATG
Found at i:17944 original size:169 final size:169
Alignment explanation
Indices: 17647--17959 Score: 423
Period size: 169 Copynumber: 1.9 Consensus size: 169
17637 NNNNTTTCCA
* * *
17647 TTAAAACAGACTATAATTGAATGCCCGCCTTGGGAAACATGTAGAAAATCCAATTATTTGAAAGA
1 TTAAAACAAACTATAATTGAATGCCCGCCTCGGGAAACATGTAGAAAAACCAATTATTTGAAAGA
* * * *
17712 AAAGTTCATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTAGTCACTTTAAATAGCTTTATAAT
66 AAAGTCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCACTTTAAACAGCTTTATAAC
17777 CTCATAATTAATTTTAAGTTGACTTGTTTGAAATTTTTG
131 CTCATAATTAATTTTAAGTTGACTTGTTTGAAATTTTTG
* * * *
17816 TTAAAACAAACTGTAATTGATTGCCTGCCTCGGGAAACGTGTA-AAGAAACC-ATATATTTGAAA
1 TTAAAACAAACTATAATTGAATGCCCGCCTCGGGAAACATGTAGAA-AAACCAAT-TATTTGAAA
* * * * * *
17879 GAAAAGTCCATTTATAGTCTCTCATTTCTTCAAAAGCCTTATTTCTCGCTTTAAACGGTTTTATA
64 GAAAAGTCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCACTTTAAACAGCTTTATA
* *
17944 ACCTTATAATTGATTT
129 ACCTCATAATTAATTT
17960 NNNNNNNNNN
Statistics
Matches: 123, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
168 4 0.03
169 119 0.97
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (169 bp):
TTAAAACAAACTATAATTGAATGCCCGCCTCGGGAAACATGTAGAAAAACCAATTATTTGAAAGA
AAAGTCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCACTTTAAACAGCTTTATAAC
CTCATAATTAATTTTAAGTTGACTTGTTTGAAATTTTTG
Done.