Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398163.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1467.0, 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: 12094
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.25
Warning! 3981 characters in sequence are not A, C, G, or T
Found at i:972 original size:171 final size:171
Alignment explanation
Indices: 4--1532 Score: 1061
Period size: 171 Copynumber: 9.0 Consensus size: 171
1 ATG
* * * *
4 TTTTACATTTTTGATTAAAACAGACTATAATTGAATATCTATCTTGAGAAA-GTCAAAGAAAAAA
1 TTTTACATTTTTTATTAAAACAGACTATAATTGAATATTTATCTCGAGAAACGTGAAA-AAAAAA
*
68 GCATTCATTGACAAGAAAAA-TTCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACTCACT
65 GCATTCATTGACAA-AAAAAGTTCATTTATAGTCACCCATTCCTTTAAAAGCCATATTACTCACT
* * *
132 TCCAATGGTTTTCTAATCTCATAATTGATTTTAGGTT-AAATGT
129 TCAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAAT-T
* * * * *
175 TTTTACATTTTTTATTCAAACAGACTATAATTGAATATTTGTCTCGAGAAACATGAACAAAAGAG
1 TTTTACATTTTTTATTAAAACAGACTATAATTGAATATTTATCTCGAGAAACGTGAAAAAAAAAG
* * * * * *********
240 CACTAATTGATAAGAAAAGTCCATTTATAGTCA-CCATNNNNNNNNNNAGCCATATTACTCACTT
66 CATTCATTGACAAAAAAAGTTCATTTATAGTCACCCAT-TCCTTTAAAAGCCATATTACTCACTT
*
304 CAAATGGTTTGATAATCTCATAATTGATTTTAAGTTG-AATAT
130 CAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAAT-T
* * * * * * ** * *
346 TTTTATATTTTTTGTTAGAACAGGCTATAATCGAATGTTTGCCTCGAGAAATGTGAAGAAAAAAG
1 TTTTACATTTTTTATTAAAACAGACTATAATTGAATATTTATCTCGAGAAACGTGAAAAAAAAAG
* * * * * ********** * * *
411 CATTTATTGGA-GAAAAAAG-TCTATTTATAGCCTCTCATNNNNNNNNNNGACTTATTACTCGCT
66 CATTCATT-GACAAAAAAAGTTC-ATTTATAGTCACCCATTCCTTTAAAAGCCATATTACTCACT
* * *
474 TTAAATGGTTATATAATCTAATAATTGATTTTAAGTTG-AATT
129 TCAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAATT
* * * * * * ***
516 TTTTACATTTTTTA--AAAAGAAAC-AGTAATTAAATGTCTATCTCGAGAAACATGATGGAAAAA
1 TTTTACATTTTTTATTAAAACAGACTA-TAATTGAATATTTATCTCGAGAAACGTGAAAAAAAAA
* * * * * *
578 GTATTTATT-ATAAAGAAAAGTACATTTATAGTCACCCATTCTTTTAAAAGCC-TGAATACTCAC
65 GCATTCATTGACAAA-AAAAGTTCATTTATAGTCACCCATTCCTTTAAAAGCCAT-ATTACTCAC
* *
641 TTTAAATGGTTTTATAATCTCATACTTGATTTTAAGTT-AAATTGT
128 TTCAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAA-T-T
* * * ** * **********
686 TTTTACAATTTTCATTAAAACAGACTATAATTGAATGTTTGCCTTGAGAANNNNNNNNNNAAAAG
1 TTTTACATTTTTTATTAAAACAGACTATAATTGAATATTTATCTCGAGAAACGTGAAAAAAAAAG
* * ** * *
751 CATTCATTGGCAAGAAAAG-TCTATTTGCAGCCTCCCATTCCTTTAAAAGCCATATTACTCACTT
66 CATTCATTGACAAAAAAAGTTC-ATTTATAGTCACCCATTCCTTTAAAAGCCATATTACTCACTT
* * * *
815 TAAATGGTTTTATAATCTAATAATTAATTTTAATTTGAAATT
130 CAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAATT
* **
857 TTTTACATTTTTTATTAAAACAGACTATGATTGAATATTTATCAGGAGAAACGT-AAAAAAAAGA
1 TTTTACATTTTTTATTAAAACAGACTATAATTGAATATTTATCTCGAGAAACGTGAAAAAAAA-A
* * * *
921 GCATTCATTGACAAAAAAAGTTCATTTATAGTCACCCACTCCTTCAAAAGCCTTATTACTCGCTT
65 GCATTCATTGACAAAAAAAGTTCATTTATAGTCACCCATTCCTTTAAAAGCCATATTACTCACTT
* * * * *
986 CCAATGGTTTTCTAATCTTATAATTGATTTTAGGTTGAATTT
130 CAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAATT
* * * * * * * *
1028 TTTTACATTATTTAGTCAAACAAACTATAATTGAATATTTA-CCCTAAGAAATGTGAAGAAAAAA
1 TTTTACATTTTTTATTAAAACAGACTATAATTGAATATTTATCTC-GAGAAACGTGAAAAAAAAA
* * * * *
1092 GCATTCACTGACAAGAAAAGTCCATTT-TAGTCACCCTTTCCTTCAAAAGCCATATTACTCACTT
65 GCATTCATTGACAAAAAAAGTTCATTTATAGTCACCCATTCCTTTAAAAGCCATATTACTCACTT
* *
1156 CAAATGGTTTTATACTCTCATAATTAATTTTAAGTTGAATATT
130 CAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAA-ATT
* * ********** * ** *
1199 TTTTACATTTTTCATTAAAACAGGCNNNNNNNNNNTGTTTGCCTCGAGAAATGT-AAAGAAAAAA
1 TTTTACATTTTTTATTAAAACAGACTATAATTGAATATTTATCTCGAGAAACGTGAAA-AAAAAA
* * * * * * * * * *
1263 GCATTTATTGGCAAAAAAAG-TCTATTTATAGACTCTCATTTCTTCAAAAGCCTTATTACCCTCT
65 GCATTCATTGACAAAAAAAGTTC-ATTTATAGTCACCCATTCCTTTAAAAGCCATATTACTCACT
* * ******
1327 TTAAATGGTTTTATAATCTAATAATTGATTTTAAGTTNNNNNN
129 TCAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAATT
**** * * * * * * * *
1370 NNNNATA-TTTTTATTAAAACAAACAATAATTGAATGTCTATCTCGAGAAACATGACAGAAAAAG
1 TTTTACATTTTTTATTAAAACAGACTATAATTGAATATTTATCTCGAGAAACGTGAAAAAAAAAG
* * * * * * *
1434 TATTCATT-ATAAAAAAAAGTCCATTTGTAGTCACTCATT-CTTTCAAAAGCCTTACTACTCACT
66 CATTCATTGA-CAAAAAAAGTTCATTTATAGTCACCCATTCCTTT-AAAAGCCATATTACTCACT
* *
1497 TTAAATGGTTTTATAATCTCATACTTGATTTTAAGT
129 TCAAATGGTTTTATAATCTCATAATTGATTTTAAGT
1533 NNNNNNNNNN
Statistics
Matches: 1052, Mismatches: 271, Indels: 71
0.75 0.19 0.05
Matches are distributed among these distances:
166 1 0.00
167 4 0.00
168 105 0.10
169 5 0.00
170 220 0.21
171 522 0.50
172 188 0.18
173 7 0.01
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.36
Consensus pattern (171 bp):
TTTTACATTTTTTATTAAAACAGACTATAATTGAATATTTATCTCGAGAAACGTGAAAAAAAAAG
CATTCATTGACAAAAAAAGTTCATTTATAGTCACCCATTCCTTTAAAAGCCATATTACTCACTTC
AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAATT
Found at i:2977 original size:172 final size:172
Alignment explanation
Indices: 2770--3097 Score: 478
Period size: 172 Copynumber: 1.9 Consensus size: 172
2760 ATTTTCTTAT
2770 ATTTTTATTAAAACAAACAATAATTGAATGTCTATCTCAAGAAACATGACGAAAAAAGTATTCAT
1 ATTTTTATTAAAACAAACAATAATTGAATGTCTATCTCAAGAAACATGACGAAAAAAGTATTCAT
* * *
2835 TATAAAGAAAACTCCATTTATAGTCACCCATTCTTTCAAAAGA-CTTCTTACTCACTTTAAATGG
66 TATAAAGAAAACTCCATTTATAGTCACCCATTCCTTCAAAA-ACCTTATTACTCACTCTAAATGG
*
2899 TTTTCTAACCACATACTTGATTTTAAGTTCAATTGTTTTTACA
130 TTTTATAACCACATACTTGATTTTAAGTTCAATTGTTTTTACA
* **********
2942 ATTTTTATTAAAACAAACAATAATTGAATGTCTATCTCGAGAAACATGNNNNNNNNNNTATTCAT
1 ATTTTTATTAAAACAAACAATAATTGAATGTCTATCTCAAGAAACATGACGAAAAAAGTATTCAT
*
3007 TATAAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAACCTTATTACTCACTCTAAATGGT
66 TATAAAGAAAACTCCATTTATAGTCACCCATTCCTTCAAAAACCTTATTACTCACTCTAAATGGT
* *
3072 TTTATAATCTCATACTTGATTTTAAG
131 TTTATAACCACATACTTGATTTTAAG
3098 NNNNNNNNNN
Statistics
Matches: 137, Mismatches: 18, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
171 1 0.01
172 136 0.99
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.36
Consensus pattern (172 bp):
ATTTTTATTAAAACAAACAATAATTGAATGTCTATCTCAAGAAACATGACGAAAAAAGTATTCAT
TATAAAGAAAACTCCATTTATAGTCACCCATTCCTTCAAAAACCTTATTACTCACTCTAAATGGT
TTTATAACCACATACTTGATTTTAAGTTCAATTGTTTTTACA
Found at i:5318 original size:171 final size:171
Alignment explanation
Indices: 4313--5490 Score: 465
Period size: 171 Copynumber: 6.9 Consensus size: 171
4303 NNNNNNNNNN
* * * * * * * * *
4313 ATCTCATAATTGATTTTAGGTTGAATTTTTTTGCATTTATTATTCAAACAAACTCTAATTCAATA
1 ATCTCATAATCGATTTTAAGTTAAATTTTTTTACATTTTTTATTAAAACAGACTATAATTGAATA
* * * * ** * *
4378 TTTGTCTCGAGAAACT-TGAA-GAAAAAAGCATTCACTGGTAAGAAAAGTCCATTTATAGTCA-C
66 TCTATCTCGAGAAA-TGT-AATGAAAAAAACATTCATTGACAAGAAAAATCCATTTATAGCCACC
***********
4440 CATTTCCTTCAAAAGCCATATTACTNNNNNNNNNNGGTTTTATA
129 CA-TTCCTTCAAAAGCCATATTACTCACTTCAAATAGTTTTATA
* * * * * *
4484 ATCTCATAATTGATTTTAAGTTGAATATTTTCT-CATTTTATGTTAAAACAGGCTATAATTGAAT
1 ATCTCATAATCGATTTTAAGTTAAAT-TTTTTTACATTTTTTATTAAAACAGACTATAATTGAAT
* * * * * ********** * *
4548 GTCT-CCTCAAGAAATGTGAA-GAAAAAAGCATTCATTGGCAAGAAANNNNNNNNNNTAGCCTCT
65 ATCTATCTCGAGAAATGT-AATGAAAAAAACATTCATTGACAAGAAAAATCCATTTATAGCCACC
* * * * *
4611 TATTCCTTCAAAAACCTTATTACTCGCTTTAAAT-GCTTTTATA
129 CATTCCTTCAAAAGCCATATTACTCACTTCAAATAG-TTTTATA
* * * ** * *
4654 ATCTAATAATTGATTTTCAGTTGGATTGTTTTACA-TTTTTATTAAAACA-AATAATAATTGAAT
1 ATCTCATAATCGATTTTAAGTTAAATTTTTTTACATTTTTTATTAAAACAGACT-ATAATTGAAT
* * * * * * * ****
4717 GTCTAACTCGAGAAACGTGAAGGAAAAAGTAC--TCATT-ATAAAGAAAAGTCCATTTATANNNN
65 ATCTATCTCGAGAAATGT-AATGAAAAA-AACATTCATTGA-CAAGAAAAATCCATTTATAGCCA
****** * * *
4779 NNNNNNCCTTCAAAAGCCTTATTACTCATTTTAAAT-GATTTTATA
127 CCCATTCCTTCAAAAGCCATATTACTCACTTCAAATAG-TTTTATA
* * * * * *
4824 ATCTCATACTTGATTTTAAGTTCAATTTTTTTTACATTTCTGATTAAAACATACTATAATTGAAT
1 ATCTCATAATCGATTTTAAGTT-AAATTTTTTTACATTTTTTATTAAAACAGACTATAATTGAAT
* ****** * * *** * * **
4889 GT-TNNNNNNNNNNAG-CATG-AA-GAAAAAAGCATTCATTGGTTAGAAAAGTCTATTTGCAGCC
65 ATCT----ATCTCGAGAAATGTAATGAAAAAAACATTCATTGACAAGAAAAATCCATTTATAGCC
* * * * * *
4950 TCCCTTTTCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATA
126 ACCCATTCCTTCAAAAGCCATATTACTCACTTCAAATAGTTTTATA
* ********** * *
4996 ATCTAANNNNNNNNNNTAAGCTGAAA-TTTTTTAGATTTTTTATTAAAACAGACTATAATTGAAT
1 ATCTCATAATCGATTTTAAG-TTAAATTTTTTTACATTTTTTATTAAAACAGACTATAATTGAAT
* * *
5060 ATCTATCTCGAGAAATGTAATGAAAAGAGCATTCATTGACAAGAAAAGTCCATTTATAGCCACCC
65 ATCTATCTCGAGAAATGTAATGAAAAAAACATTCATTGACAAGAAAAATCCATTTATAGCCACCC
********** * * *
5125 ATTCCTNNNNNNNNNNTATTACTCACTTCCAATGGTTTTCTA
130 ATTCCTTCAAAAGCCATATTACTCACTTCAAATAGTTTTATA
* * * *
5167 ATCTCCTAATTGATTTTAGGTTAAATTTTTTTACATTTTTTATTTAAACAGACTATAATTGAATA
1 ATCTCATAATCGATTTTAAGTTAAATTTTTTTACATTTTTTATTAAAACAGACTATAATTGAATA
* * * ** *
5232 TTTATCTTGAGAAATGTGAA-GAAAAAAACATTCATTGACTAGAAAAATCCATTTATAGTTACTC
66 TCTATCTCGAGAAATGT-AATGAAAAAAACATTCATTGACAAGAAAAATCCATTTATAGCCACCC
* *
5296 TTTCCTTCAAAAGCCATATTACTCACTTTAAATAGTTTTATA
130 ATTCCTTCAAAAGCCATATTACTCACTTCAAATAGTTTTATA
* * * * * * *
5338 ATCTCATAATCGATTTTAAGTTGAATATTGTTACATTTTTTGTTAAAAAAGGCTATAATTGAATG
1 ATCTCATAATCGATTTTAAGTTAAATTTTTTTACATTTTTTATTAAAACAGACTATAATTGAATA
* ** * ** * * * **
5403 TTTGCCTC-ATGAAATGTGGA-GAAAAAAGTATTCA-TAAGCAAGAAAAGTCTATTTATAGCCTT
66 TCTATCTCGA-GAAATGT-AATGAAAAAAACATTCATTGA-CAAGAAAAATCCATTTATAGCCAC
* *
5465 TCATTCCTTCAAAAGCCTTATTACTC
128 CCATTCCTTCAAAAGCCATATTACTC
5491 GCNNNNNNNN
Statistics
Matches: 742, Mismatches: 235, Indels: 60
0.72 0.23 0.06
Matches are distributed among these distances:
168 3 0.00
169 35 0.05
170 181 0.24
171 415 0.56
172 100 0.13
173 4 0.01
174 2 0.00
175 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.36
Consensus pattern (171 bp):
ATCTCATAATCGATTTTAAGTTAAATTTTTTTACATTTTTTATTAAAACAGACTATAATTGAATA
TCTATCTCGAGAAATGTAATGAAAAAAACATTCATTGACAAGAAAAATCCATTTATAGCCACCCA
TTCCTTCAAAAGCCATATTACTCACTTCAAATAGTTTTATA
Found at i:9180 original size:171 final size:161
Alignment explanation
Indices: 9028--9636 Score: 359
Period size: 171 Copynumber: 3.6 Consensus size: 161
9018 NNNNNNNNNN
*
9028 TCACCCATTCCTTCAAAAGCCTTATTACTCAC-TTCAAATCGTTTTATAATCTAATAATTGATTT
1 TCACCCATTCCTTCAAAAGCCTTATTACTCACTTTC-AATCGTTTTATAACCTAATAATTGATTT
* *
9092 TAAGTTAAAATTTTTTACCTTT-TTGATTAAAACAGACTATAATTGNNNNNNNNNNTCAAGAAAC
65 TAAGTTAAAATTTTTTACATTTATT-ACTAAAACAGACTATAATTG----------TCAAGAAAC
9156 ATGAAGAAAAGAGCATTAATTGACAAAAAAAGTCCATTTATAG
119 ATGAAGAAAAGAGCATTAATTGACAAAAAAAGTCCATTTATAG
* * * * *
9199 TCAGCCATTCCTTCAAAAGCCTTATTACTCGCTTTCAATGGTTTTCTAACCTCATAATTGATTTT
1 TCACCCATTCCTTCAAAAGCCTTATTACTCACTTTCAATCGTTTTATAACCTAATAATTGATTTT
* * * * *
9264 AGGTTGAATTTTTTTACATTTATTACTCAAACAGACTATAATTGAATATTTGTCTCGAGAAACAT
66 AAGTTAAAATTTTTTACATTTATTACTAAAACAGAC--T-A-T--A-A-TTG--TCAAGAAACAT
* * * * *
9329 GAAGAAAAAAGTATTCACTGACAAGAAAAGTCCATTTATAG
121 GAAGAAAAGAGCATTAATTGACAAAAAAAGTCCATTTATAG
* * * **********
9370 TCACCC-TTGCCTTCAAAACCCATATTACTCAC-TTCAAATGGTTNNNNNNNNNNATAATTGATT
1 TCACCCATT-CCTTCAAAAGCCTTATTACTCACTTTC-AATCGTTTTATAACCTAATAATTGATT
* * * * * *
9433 TTAAGTTGAATATTTTCT-CATTT-TTCATTAAAACGGGCTATAATTGAATGTTTTCTCGAGAAA
64 TTAAGTT-AAAATTTTTTACATTTATT-ACTAAAACAGACTATAA-T---TG-----TCAAGAAA
** * * * * *
9496 TGTGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAG
118 CATGAAGAAAAGAGCATTAATTGACAAAAAAAGTCCATTTATAG
* * * * * * * *
9540 CCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTAATAATTTATTTT
1 TCACCCATTCCTTCAAAAGCCTTATTACTCACTTTCAATCGTTTTATAACCTAATAATTGATTTT
* * *
9605 AAGTTGAATTTTTTTACATTT-TTATTAAAACA
66 AAGTTAAAATTTTTTACATTTATTACTAAAACA
9637 AATAATAATT
Statistics
Matches: 342, Mismatches: 73, Indels: 48
0.74 0.16 0.10
Matches are distributed among these distances:
164 3 0.01
165 1 0.00
167 3 0.01
168 1 0.00
169 15 0.04
170 107 0.31
171 193 0.56
172 11 0.03
173 1 0.00
174 1 0.00
175 1 0.00
177 1 0.00
178 1 0.00
179 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.37
Consensus pattern (161 bp):
TCACCCATTCCTTCAAAAGCCTTATTACTCACTTTCAATCGTTTTATAACCTAATAATTGATTTT
AAGTTAAAATTTTTTACATTTATTACTAAAACAGACTATAATTGTCAAGAAACATGAAGAAAAGA
GCATTAATTGACAAAAAAAGTCCATTTATAG
Found at i:9568 original size:170 final size:161
Alignment explanation
Indices: 9423--9878 Score: 142
Period size: 170 Copynumber: 2.7 Consensus size: 161
9413 NNNNNNNNNN
* * * *
9423 ATAATTGATTTTAAGTTGAATATTTTCT-CATTT-TTCATTAAAACGGGCTATAATTGAATGTTT
1 ATAATTGATTTTAAGTTGAAT-TTTTCTACATTTATT-ACTAAAACAGACTATAATTGAATATTT
** * * * *
9486 -TCTCGAGAAATGTGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAGCCTCTCATT-
64 GTCTCGAGAAACATGAAGAAAAAAGCATTCACTGACAAGAAAAGTCCATTTATAGCCAC-CATTG
* * * * *
9549 CCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCT
128 CCTTCAAAACCCATATTACTCACTTCAAA-TG-------GT-T
* * * * * *
9592 AATAATTTATTTTAAGTTGAATTTTTTTACATTT-TTATTAAAACA-AATAATAATTGAATGTCT
1 -ATAATTGATTTTAAGTTGAATTTTTCTACATTTATTACTAAAACAGACT-ATAATTGAATATTT
* * * * * **
9655 ATCTCGAGAAACATGAAGGAAAAAA-TATTCA-TTATAAAGAAAAGTCCTTTTATAGTTACCCAT
64 GTCTCGAGAAACATGAA-GAAAAAAGCATTCACTGA-CAAGAAAAGTCCATTTATAGCCA-CCAT
********** * *
9718 T-CCTTCANNNNNNNNNNTACTCACTTTAAATAGTTTTAT
126 TGCCTTCAAAACCCATATTACTCACTTCAAAT-G--GT-T
* * *
9757 AATCTCATACTTAATTTTAAGTAT-AATTTTTTTACATTT-TTCATTAAAACAGACTATAATTGA
1 -A--T-A-A-TTGATTTTAAGT-TGAATTTTTCTACATTTATT-ACTAAAACAGACTATAATTGA
* * * * *
9820 AAATTTATCTCGAGAAACATGAAGAAAAGAGCATTCATTGATAAGAAAAGTCCATTTAT
58 ATATTTGTCTCGAGAAACATGAAGAAAAAAGCATTCACTGACAAGAAAAGTCCATTTAT
9879 NNNNNNNNNN
Statistics
Matches: 228, Mismatches: 41, Indels: 33
0.75 0.14 0.11
Matches are distributed among these distances:
165 5 0.02
167 1 0.00
168 2 0.01
169 29 0.13
170 120 0.53
171 67 0.29
172 4 0.02
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.38
Consensus pattern (161 bp):
ATAATTGATTTTAAGTTGAATTTTTCTACATTTATTACTAAAACAGACTATAATTGAATATTTGT
CTCGAGAAACATGAAGAAAAAAGCATTCACTGACAAGAAAAGTCCATTTATAGCCACCATTGCCT
TCAAAACCCATATTACTCACTTCAAATGGTT
Found at i:9845 original size:341 final size:337
Alignment explanation
Indices: 8583--9878 Score: 1087
Period size: 341 Copynumber: 3.8 Consensus size: 337
8573 NNNNNNNNNN
* * * *
8583 AGTTGAATGTTTTTACATTTTTATTAAAGCA-AATAATAATTGAATGTCTATCTCAAGAAATATG
1 AGTTGAATTTTTTTACATTTTTATTAAAACAGAAT-ATAATTGAATATCTATCTCAAGAAACATG
* ** *
8647 AAGGAAAAAGTATTCATTATAAAGAAAAGT-CTATTTATAGTCATACATTCCTTCAAAAGCC-TA
65 AA-GAAAAAATATTCATTA-AAAGAAAAGTCCT-TTTATAGTCACCCATTCCTTCAAAAACCATA
* * *
8710 TTACTCACTTTAAATGGTTTTATAATCTCATACTTGATTTTAAGTT-CATTTTTTTACATTTTTC
127 TTACTCACTTCAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTC
********** * * ** * * *
8774 ATTAAAACNNNNNNNNNNTGAATGTTTGCCTTGAGAGGCATGAAAAAAAAAGCATTCACTGGCAA
192 ATTAAAACAGACTATAATTGAATGTTT-TCTCGAGAAACATGAAGAAAAAAGCATTCATTGACAA
* * * *
8839 GAAAAGTCTATTTACAGCCCCCCATTCCTTTAAAAGCCTTATTACTCACTTTAAATGGTTTTATA
256 GAAAAGTCCATTTATAG-CCCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATA
**********
8904 ATCTNNNNNNNNNNTTTA
320 ATCTAATAATTGATTTTA
* * *
8922 AGTTGAATTTTTTTTACATTTTTAATTAAAACAGACTATAATTGAAAATTTATCTCAAGAAACAT
1 AGTTGAA-TTTTTTTACATTTTT-ATTAAAACAGAATATAATTGAATATCTATCTCAAGAAACAT
** * * ********** * *
8987 GAAGAAAAGAGCATTCATTGACAAGAAAAATNNNNNNNNNNTCACCCATTCCTTCAAAAGCCTTA
64 GAAGAAAA-AATATTCATT-AAAAGAAAAGTCCTTTTATAGTCACCCATTCCTTCAAAAACCATA
* * * * *
9052 TTACTCACTTCAAATCGTTTTATAATCTAATAATTGATTTTAAGTTAAAATTTTTTACCTTTTTG
127 TTACTCACTTCAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTC
********* * * *
9117 ATTAAAACAGACTATAATTGNNNNNNNNNNTCAAGAAACATGAAGAAAAGAGCATTAATTGACAA
192 ATTAAAACAGACTATAATTG-AATGTTTTCTCGAGAAACATGAAGAAAAAAGCATTCATTGACAA
* ** * *
9182 AAAAAGTCCATTTATAGTCAGCCATTCCTTCAAAAGCCTTATTACTCGCTTTCAATGGTTTTCTA
256 GAAAAGTCCATTTATAG-CCCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATA
* *
9247 ACCTCATAATTGATTTTA
320 ATCTAATAATTGATTTTA
* * * * * * *
9265 GGTTGAATTTTTTTACATTTATTACTCAAACAGACTATAATTGAATATTTGTCTCGAGAAACATG
1 AGTTGAATTTTTTTACATTT-TTATTAAAACAGAATATAATTGAATATCTATCTCAAGAAACATG
* * * *
9330 AAGAAAAAAGTATTCACTGACAAGAAAAGTCCATTTATAGTCACCC-TTGCCTTCAAAACCCATA
65 AAGAAAAAA-TATTCA-TTAAAAGAAAAGTCCTTTTATAGTCACCCATT-CCTTCAAAAACCATA
********** * *
9394 TTACTCACTTCAAATGGTTNNNNNNNNNNATAATTGATTTTAAGTTGAATATTTTCT-CATTTTT
127 TTACTCACTTCAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAAT-TTTTTTACATTTTT
* * ** *
9458 CATTAAAACGGGCTATAATTGAATGTTTTCTCGAGAAATGTGAAGAAAAAAGCATTCATTGGCAA
191 CATTAAAACAGACTATAATTGAATGTTTTCTCGAGAAACATGAAGAAAAAAGCATTCATTGACAA
* * *
9523 GAAAAGTCTATTTATAGCCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATA
256 GAAAAGTCCATTTATAGCC-CCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATA
*
9588 ATCTAATAATTTATTTTA
320 ATCTAATAATTGATTTTA
* *
9606 AGTTGAATTTTTTTACATTTTTATTAAAACA-AATAATAATTGAATGTCTATCTCGAGAAACATG
1 AGTTGAATTTTTTTACATTTTTATTAAAACAGAAT-ATAATTGAATATCTATCTCAAGAAACATG
* **********
9670 AAGGAAAAAATATTCATTATAAAGAAAAGTCCTTTTATAGTTACCCATTCCTTCANNNNNNNNNN
65 AA-GAAAAAATATTCATTA-AAAGAAAAGTCCTTTTATAGTCACCCATTCCTTCAAAAACCATAT
* * * *
9735 TACTCACTTTAAATAGTTTTATAATCTCATACTTAATTTTAAG-TATAATTTTTTTACATTTTTC
128 TACTCACTTCAAATGGTTTTATAATCTCATAATTGATTTTAAGTTA-AATTTTTTTACATTTTTC
** * *
9799 ATTAAAACAGACTATAATTGAAAATTTATCTCGAGAAACATGAAGAAAAGAGCATTCATTGATAA
192 ATTAAAACAGACTATAATTGAATGTTT-TCTCGAGAAACATGAAGAAAAAAGCATTCATTGACAA
9864 GAAAAGTCCATTTAT
256 GAAAAGTCCATTTAT
9879 NNNNNNNNNN
Statistics
Matches: 744, Mismatches: 191, Indels: 42
0.76 0.20 0.04
Matches are distributed among these distances:
339 17 0.02
340 155 0.21
341 247 0.33
342 199 0.27
343 126 0.17
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.36
Consensus pattern (337 bp):
AGTTGAATTTTTTTACATTTTTATTAAAACAGAATATAATTGAATATCTATCTCAAGAAACATGA
AGAAAAAATATTCATTAAAAGAAAAGTCCTTTTATAGTCACCCATTCCTTCAAAAACCATATTAC
TCACTTCAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTCATTA
AAACAGACTATAATTGAATGTTTTCTCGAGAAACATGAAGAAAAAAGCATTCATTGACAAGAAAA
GTCCATTTATAGCCCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTAA
TAATTGATTTTA
Done.