Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397345.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1229.0, 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: 46291
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.25
Warning! 13001 characters in sequence are not A, C, G, or T
Found at i:376 original size:172 final size:168
Alignment explanation
Indices: 11--580 Score: 597
Period size: 171 Copynumber: 3.3 Consensus size: 168
1 TTAGCCATGC
* * * *
11 CTTTAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTAATTTTAGGTTGAATT
1 CTTTCAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATT
* * * * * * * * *
76 GTTTTACATTTTTTATTTAAACCTTTTATAATTAACTGTTTTCCTTAAGAAACGTG-AAGAAAAG
66 TTTTTACATTTTTGATTAAAACATATTATAATTAA-TGTTTT-CTTGACAAACATGAAAAAAAAG
* * * *
140 CCCATTCATTGATCAGAAAAGCCCATTTATAGTTAGCCAAG
129 -CCATTTATTGATAAGAAAAGCCCATTTATAGTCACCCAAG
* * *
181 CCTTTGAAAGCCTTATCACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTATAAGTTGAAT
1 -CTTTCAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAT
* *
246 GTTTTTTACATTTTTGATTAAAACATATTAGAATTGAATGTTTGGTCTGGA-AAACATGAAAAAA
65 -TTTTTTACATTTTTGATTAAAACATATTATAATT-AATGTTT--TCTTGACAAACATGAAAAAA
* *
310 AAGCCATTTATT-AGTAAGAAAAACCCATTTATAATCACCCAAG
126 AAGCCATTTATTGA-TAAGAAAAGCCCATTTATAGTCACCCAAG
* * * *
353 TCTTTCAAAGCCTTATTACTCGCTTTAAATAGTCTTATAATCTGATAATTGATTTTAAGTTGTAT
1 -CTTTCAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAT
* * * * ** **
418 TTTTCTACTTTTTTGATTAAAATATGTTATAATTAAATGTCTACCTTGACAAACATGAAGCAAAA
65 TTTTTTACATTTTTGATTAAAACATATTATAATT-AATGT-TTTCTTGACAAACATGAAAAAAAA
* * *
483 GCCATCTATTGATATGAAAAGCCCATTTATAGTCACTCAAG
128 GCCATTTATTGATAAGAAAAGCCCATTTATAGTCACCCAAG
* * * ** *
524 CCTTCGAAAGCCATAATACTTTCTTTAAATGATTTTATAATCTCATAATTGATTTTA
1 CTTTC-AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTA
581 GGAAAGAAAA
Statistics
Matches: 334, Mismatches: 55, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
170 8 0.02
171 183 0.55
172 130 0.39
173 12 0.04
174 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (168 bp):
CTTTCAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATT
TTTTTACATTTTTGATTAAAACATATTATAATTAATGTTTTCTTGACAAACATGAAAAAAAAGCC
ATTTATTGATAAGAAAAGCCCATTTATAGTCACCCAAG
Found at i:680 original size:109 final size:109
Alignment explanation
Indices: 479--689 Score: 284
Period size: 109 Copynumber: 1.9 Consensus size: 109
469 AACATGAAGC
* *
479 AAAAGCCATCTATTGATATGAAAAGCCCATTTATAGTCACTCAAGCCTTCGAAAGCCATAATACT
1 AAAAGCCATCTATTGATAAGAAAAGCCCATTTATAGTCACTCAAGCCTTCGAAAGACATAATACT
* *
544 TTCTTTAAATGATTTTATAATCTCATAATTGATTTTAGGAAAGA
66 TACTTTAAATGATTTTACAATCTCATAATTGATTTTAGGAAAGA
* * * *
588 AAAAGCCAT-TCATTGATAAGAAAAGTCCATTTATAGTCACTCATA-CCTTTGAAAGACTTATTA
1 AAAAGCCATCT-ATTGATAAGAAAAGCCCATTTATAGTCACTCA-AGCCTTCGAAAGACATAATA
* *
651 CTTACTTTATATGGTTTTACAAT-TCCATAATTGATTTTA
64 CTTACTTTAAATGATTTTACAATCT-CATAATTGATTTTA
690 AGTTAAATCG
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
108 2 0.02
109 86 0.97
110 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (109 bp):
AAAAGCCATCTATTGATAAGAAAAGCCCATTTATAGTCACTCAAGCCTTCGAAAGACATAATACT
TACTTTAAATGATTTTACAATCTCATAATTGATTTTAGGAAAGA
Found at i:1376 original size:171 final size:170
Alignment explanation
Indices: 605--2437 Score: 1205
Period size: 171 Copynumber: 10.8 Consensus size: 170
595 ATTCATTGAT
* * ** * *
605 AAGAAAAGTCCATTTATAGTCACTCATACCTTTGAAAGACTTATTACTTACTTTATATGGTTTTA
1 AAGAAAAGTCCATTTATAGTCACCCAAACCTTCAAAAGCCTTATTACTTACTTTAAATGGTTTTA
* * * ** * ** * *
670 CAAT-TCCATAATTGATTTTAAGTTAAATCGTTTTACTTTTTTAATTAAAATATATTATAATTGA
66 TAATCT-CATAATTGATTTTAGGTTGAATTTTTTTACATTTTTGGTTAAAACAGATTATAATTGA
* * * * * * *
734 ATGTCTACTTTAAGAAACATGTAGCAAAAGAT-ATCCA-TTG-
130 ATGTTTGCCTCAGGAAACATGAAG-AAAA-ATAATTCATTTGC
* * * *
774 ATATGAAAGGTCCATTTATAGTCTCTCAAACCTTCGAAAGCCTTATTACTTACTTTAAATGGTTT
1 A-A-GAAAAGTCCATTTATAGTCACCCAAACCTTCAAAAGCCTTATTACTTACTTTAAATGGTTT
* *
839 TATAATCTCATAATTGATTTTAAGTTGAATTGTTTTTACATTTTTGGTTAAAATAGATTATAATT
64 TATAATCTCATAATTGATTTTAGGTTGAATT-TTTTTACATTTTTGGTTAAAACAGATTATAATT
* * * * *
904 GAATATTTGCCTTAGGAAACTTGAAGAAAAATCCATTCATTGGC
128 GAATGTTTGCCTCAGGAAACATGAAGAAAAAT-AATTCATTTGC
** * * *
948 AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTAGTTACTTTAATTAGTTTTA
1 AAGAAAAGTCCATTTATAGTCACCCAAACCTTCAAAAGCCTTATTACTTACTTTAAATGGTTTTA
* * * *
1013 TAATCTCATAATTGATTTTAGGTTAAATTTTCTTACATTTTTTGTTAAAAAAGATTATAATT-AA
66 TAATCTCATAATTGATTTTAGGTTGAATTTTTTTACATTTTTGGTTAAAACAGATTATAATTGAA
* * * *
1077 GTGTCTACCTCAAGAAACATGTAGAAAAATAATTCA-TTGAC
131 -TGTTTGCCTCAGGAAACATGAAGAAAAATAATTCATTTG-C
* * ** * *
1118 AAGAAAAGTCCATTTATAGTCTCTCATGCCTTCAAAAGCCTTATTACTCACTTGAAATGGTTTTA
1 AAGAAAAGTCCATTTATAGTCACCCAAACCTTCAAAAGCCTTATTACTTACTTTAAATGGTTTTA
* * * *
1183 TAATCTCATAATTGATTTTAGGTTGCATTTTTTTACATATTTAGTTAAAACAGATTATACTTGAA
66 TAATCTCATAATTGATTTTAGGTTGAATTTTTTTACATTTTTGGTTAAAACAGATTATAATTGAA
* * * * * * *
1248 TGTTTGCCGCGGGAAACATAAAGAAAAGCTTATTTATTTGT
131 TGTTTGCCTCAGGAAACATGAAGAAAA-ATAATTCATTTGC
* * ** * **
1289 AGGAAAATTCCATTTATAGTCACCCAAACCTTTGAAAGCCTTATTACTTGCTTTATGTGGTTTTA
1 AAGAAAAGTCCATTTATAGTCACCCAAACCTTCAAAAGCCTTATTACTTACTTTAAATGGTTTTA
* * * * *
1354 TAATC-CAATAGTTAATTTTAGGTTGAATTTTTTTATATTTTTGGTTAAAACAGATTATAGTTGG
66 TAATCTC-ATAATTGATTTTAGGTTGAATTTTTTTACATTTTTGGTTAAAACAGATTATAATTGA
* * * * * * *
1418 CTGTGTGCCTTAAGAAACGTGAAGAGAAAACT-ATTTA-ATGAC
130 ATGTTTGCCTCAGGAAACATGAAGA-AAAA-TAATTCATTTG-C
* ** * *** * * **
1460 AAGAAGAGTATATTTATAGTCACTCGTGCCTTCGAAAA-CCTTATCACATGTTTTAAATGGTTTT
1 AAGAAAAGTCCATTTATAGTCACCCAAACCTTC-AAAAGCCTTATTACTTACTTTAAATGGTTTT
* ********** * * * *
1524 ATAATCTCATAACTGNNNNNNNNNNGAATTGTTTTACATTTTTAGTTAAAACATATTATAATTAA
65 ATAATCTCATAATTGATTTTAGGTTGAATTTTTTTACATTTTTGGTTAAAACAGATTATAATTGA
* ** *
1589 ATGTTTGCCTCAAGAAACATGAAGAAAAACCCATTCATTAGC
130 ATGTTTGCCTCAGGAAACATGAAGAAAAA-TAATTCATTTGC
* * * * ************
1631 AAGAAAAGCCCATTTATTGTCACCCAAGCTTTCAAAAGCCTTATTACTCGNNNNNNNNNNTTTTA
1 AAGAAAAGTCCATTTATAGTCACCCAAACCTTCAAAAGCCTTATTACTTACTTTAAATGGTTTTA
* * ** * *
1696 TAAACTCATAATTGATTTGAACTTG-ATGTTTTTTACATTTCTAGTTAAAACAGATTATAATTGA
66 TAATCTCATAATTGATTTTAGGTTGAAT-TTTTTTACATTTTTGGTTAAAACAGATTATAATTGA
* * *
1760 GTGTTTAG-CTTAGGAAACATGAAGGAAAAGCT-ATTCA-TTGAC
130 ATGTTT-GCCTCAGGAAACATGAA-GAAAA-ATAATTCATTTG-C
* * * ** * * * *
1802 AAGAAAAGTCCAATTAGAGTCACTCATTCTTTCAAAAGCCTTACTACTCACTTCT-ATTGGTTTT
1 AAGAAAAGTCCATTTATAGTCACCCAAACCTTCAAAAGCCTTATTACTTACTT-TAAATGGTTTT
** * * * *
1866 GGAATCTTATAATTGATTTTAAGTTGAATGCTTTTTACATTTCTT-GTTCAAACCA-ATTATAAT
65 ATAATCTCATAATTGATTTTAGGTTGAAT-TTTTTTACATTT-TTGGTT-AAAACAGATTATAAT
* ** *
1929 TGAATGTTTGCCTTAGGAAACATGAAGAAAAACCCATTCATTGGC
127 TGAATGTTTGCCTCAGGAAACATGAAGAAAAA-TAATTCATTTGC
* * * * * * ** *
1974 AGGAAAAGCCCATTGATAGTCACCCAAGCTTTCGAAAGCCTTATTACTCGCCTTAAATGGTTTTA
1 AAGAAAAGTCCATTTATAGTCACCCAAACCTTCAAAAGCCTTATTACTTACTTTAAATGGTTTTA
* * * * * *
2039 TAGTCTCGTAAATGATTTTAAGTTGAATTTTTTTATATTTTTAGTTAAAACAGATTATAATTGAA
66 TAATCTCATAATTGATTTTAGGTTGAATTTTTTTACATTTTTGGTTAAAACAGATTATAATTGAA
* ** * *
2104 TGTCTGCCTTGGGAAACATGAAGAAAAAGCT-ATTCATTGGA
131 TGTTTGCCTCAGGAAACATGAAGAAAAA--TAATTCATTTGC
* * ** **
2145 AAGAAAAGCCCATTTATAGT----C--ACC--C--AAGCCTTATTTCTCGCTTTAAATAATTTTA
1 AAGAAAAGTCCATTTATAGTCACCCAAACCTTCAAAAGCCTTATTACTTACTTTAAATGGTTTTA
** * ** * ** *
2200 TAATCTCATAATTGATTTTAAATT-ATATTTTTCTAC-TTTTTTATTAAAATATTTTATAATTAA
66 TAATCTCATAATTGATTTTAGGTTGA-ATTTTTTTACATTTTTGGTTAAAACAGATTATAATTGA
* * ** * * *** *
2263 ATGTCTACCTTGGGAAACGTGAAGCCAAAGCCATTTA-TTG-
130 ATGTTTGCCTCAGGAAACATGAAG-AAAAATAATTCATTTGC
* * * * ** **
2303 ATATGAAAAGTTCATTTATAGTTACTCAAA-CTTCCGAAAGCCTTATTACTCGCTTTAAACAGTT
1 A-A-GAAAAGTCCATTTATAGTCACCCAAACCTT-CAAAAGCCTTATTACTTACTTTAAATGGTT
* * *
2367 TAATAATCTCATAATTGATTTTAAGTT-AAGTTTTTTTACATTTTTGGTTAAAATAGATTATAAT
63 TTATAATCTCATAATTGATTTTAGGTTGAA-TTTTTTTACATTTTTGGTTAAAACAGATTATAAT
2431 TGAATGT
127 TGAATGT
2438 CTACGTAGCA
Statistics
Matches: 1318, Mismatches: 289, Indels: 112
0.77 0.17 0.07
Matches are distributed among these distances:
158 1 0.00
159 3 0.00
160 64 0.05
161 57 0.04
163 1 0.00
164 1 0.00
165 2 0.00
166 1 0.00
167 1 0.00
168 1 0.00
169 4 0.00
170 224 0.17
171 668 0.51
172 278 0.21
173 11 0.01
174 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (170 bp):
AAGAAAAGTCCATTTATAGTCACCCAAACCTTCAAAAGCCTTATTACTTACTTTAAATGGTTTTA
TAATCTCATAATTGATTTTAGGTTGAATTTTTTTACATTTTTGGTTAAAACAGATTATAATTGAA
TGTTTGCCTCAGGAAACATGAAGAAAAATAATTCATTTGC
Found at i:1627 original size:513 final size:513
Alignment explanation
Indices: 584--2435 Score: 1335
Period size: 513 Copynumber: 3.6 Consensus size: 513
574 GATTTTAGGA
* * ** *
584 AAGAAAAAGCCATTCATTGATAAGAAAAGTCCATTTATAGTCACTCATACCTTTGAAAGACTTAT
1 AAGAAAAA-CCATTCATTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCAAAAGCCTTAT
* * * * *
649 TACTTACTTTATATGGTTTTACAATTCCATAATTGATTTTAAGTTAAATCGTTTTACTTTTTTAA
65 TACTCACTTGAAATGGTTTTACAATTCCATAATTGATTTTAAGTTAAATCGTTTTACATATTTAA
* * *** ** *
714 TTAAAATATATTATAATTGAATGTCTACTTTAAGAAACATGTAGCAAAAGATATCCATTGATATG
130 TTAAAACAGATTATAATTGAATGTCTACCGCAAGAAACATAAAGCAAAAGATATCCATTGATAGG
* * *
779 AAAGGTCCATTTATAGTCTCTCAAACCTTCGAAAGCCTTATTACTTACTTTAAATGGTTTTATAA
195 AAAAGTCCATTTATAGTCACCCAAACCTTCGAAAGCCTTATTACTTACTTTAAATGGTTTTATAA
* *
844 TCTCATAATTGATTTTAAGTTGAATTGTTTTTACATTTTTGGTTAAAATAGATTATAATTGAATA
260 TCTCATAATTAATTTTAAGTTGAATTGTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATA
* * * * * *
909 TTTGCCTTAGGAAACTTGAAGAAAAATCCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCA
325 TGTGCCTTAAGAAACGTGAAGAAAAATCCATTCAATGACAAGAAAAGTACATTTATAGTCACCCA
* * ** * *
974 TTCCTTCAAAAGCCTTATTAGTTACTTTAATTAGTTTTATAATCTCATAATTGATTTTAGGTTAA
390 TGCCTTCAAAAGCCTTATCACATACTTTAAATAGTTTTATAATCTCATAACTGATTTTAGGTTAA
* *
1039 ATTTTCTTACATTTTTTGTTAAAAAAGATTATAATTAAGTGTCTACCTCAAGAAACATG
455 ATTTTCTTACATTTTTAGTTAAAAAAGATTATAATTAAATGTCTACCTCAAGAAACATG
* ** *
1098 TAGAAAAATAATTCATTGACAAGAAAAGTCCATTTATAGTCTCTCATGCCTTCAAAAGCCTTATT
1 AAGAAAAACCATTCATTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCAAAAGCCTTATT
* * ** ** *
1163 ACTCACTTGAAATGGTTTTATAA-TCTCATAATTGATTTTAGGTTGCATTTTTTTACATATTTAG
66 ACTCACTTGAAATGGTTTTACAATTC-CATAATTGATTTTAAGTTAAATCGTTTTACATATTTAA
* * * ** * **
1227 TTAAAACAGATTATACTTGAATGTTTGCCGCGGGAAACATAAAG-AAAAGCTTATTTATTTG-TA
130 TTAAAACAGATTATAATTGAATGTCTACCGCAAGAAACATAAAGCAAAAG-ATATCCA-TTGATA
* * * **
1290 GGAAAATTCCATTTATAGTCACCCAAACCTTTGAAAGCCTTATTACTTGCTTTATGTGGTTTTAT
193 GGAAAAGTCCATTTATAGTCACCCAAACCTTCGAAAGCCTTATTACTTACTTTAAATGGTTTTAT
* * * * *
1355 AATC-CAATAGTTAATTTTAGGTTGAATT-TTTTTATATTTTTGGTTAAAACAGATTATAGTTGG
258 AATCTC-ATAATTAATTTTAAGTTGAATTGTTTTTACATTTTTGGTTAAAACAGATTATAATTGA
* * * * * *
1418 CTGTGTGCCTTAAGAAACGTGAAGAGAAAA-CTATTTAATGACAAGAAGAGTATATTTATAGTCA
322 ATATGTGCCTTAAGAAACGTGAAGA-AAAATCCATTCAATGACAAGAAAAGTACATTTATAGTCA
* * ** * *******
1482 CTCGTGCCTTCGAAAA-CCTTATCACATGTTTTAAATGGTTTTATAATCTCATAACTGNNNNNNN
386 CCCATGCCTTC-AAAAGCCTTATCACATACTTTAAATAGTTTTATAATCTCATAACTGATTTTAG
**** * * * *
1546 NNNGAATTGTT-TTACATTTTTAGTTAAAACATATTATAATTAAATGTTTGCCTCAAGAAACATG
450 GTTAAATT-TTCTTACATTTTTAGTTAAAAAAGATTATAATTAAATGTCTACCTCAAGAAACATG
* * * * *
1610 AAGAAAAACCCATTCATT-AGCAAGAAAAGCCCATTTATTGTCACCCAAGCTTTCAAAAGCCTTA
1 AAGAAAAA-CCATTCATTGA-CAAGAAAAGTCCATTTATAGTCACTCATGCCTTCAAAAGCCTTA
*********** * * * * *
1674 TTACTCGNNNNNNNNNNTTTTATAA-ACTCATAATTGATTTGAACTT-GAT-GTTTTTTACAT-T
64 TTACTCACTTGAAATGGTTTTACAATTC-CATAATTGATTTTAAGTTAAATCG--TTTTACATAT
* * * * ** * * * * *
1735 TCTAGTTAAAACAGATTATAATTGAGTGTTTAGCTTAGGAAACATGAAGGAAAAGCTATTCATTG
126 T-TAATTAAAACAGATTATAATTGAATGTCTACCGCAAGAAACATAAAGCAAAAGATATCCATTG
* * * * * ** * * * * *
1800 ACAAGAAAAGTCCAATTAGAGTCACTCATTCTTTCAAAAGCCTTACTACTCACTTCT-ATTGGTT
190 ATAGGAAAAGTCCATTTATAGTCACCCAAACCTTCGAAAGCCTTATTACTTACTT-TAAATGGTT
** * * *
1864 TTGGAATCTTATAATTGATTTTAAGTTGAA-TGCTTTTTACATTTCTT-GTTCAAACCA-ATTAT
254 TTATAATCTCATAATTAATTTTAAGTTGAATTG-TTTTTACATTT-TTGGTT-AAAACAGATTAT
* * * * * * * * ** *
1926 AATTGAATGTTTGCCTTAGGAAACATGAAGAAAAACCCATTCATTGGCAGGAAAAGCCCATTGAT
316 AATTGAATATGTGCCTTAAGAAACGTGAAGAAAAATCCATTCAATGACAAGAAAAGTACATTTAT
* * * * * * * * * *
1991 AGTCACCCAAGCTTTCGAAAGCCTTATTAC-TCGCCTTAAATGGTTTTATAGTCTCGTAAATGAT
381 AGTCACCCATGCCTTCAAAAGCCTTATCACAT-ACTTTAAATAGTTTTATAATCTCATAACTGAT
* * * * * * * ***
2055 TTTAAGTTGAATTTTTTTATATTTTTAGTTAAAACAGATTATAATTGAATGTCTGCCTTGGGAAA
445 TTTAGGTTAAATTTTCTTACATTTTTAGTTAAAAAAGATTATAATTAAATGTCTACCTCAAGAAA
2120 CATG
510 CATG
* *
2124 AAGAAAAAGCTATTCATTGGA-AAGAAAAGCCCATTTATAG----TCA--CC--C--AAGCCTTA
1 AAGAAAAA-CCATTCATT-GACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCAAAAGCCTTA
* * * ** * * * * *
2178 TTTCTCGCTTTAAATAATTTTATAA-TCTCATAATTGATTTTAAATTATAT-TTTTCTAC-TTTT
64 TTACTCACTTGAAATGGTTTTACAATTC-CATAATTGATTTTAAGTTAAATCGTTT-TACATATT
* * ** * **** * * * ** **
2240 TTATTAAAATATTTTATAATTAAATGTCTACCTTGGGAAACGTGAAGCCAAAGCCATTTATTGAT
127 TAATTAAAACAGATTATAATTGAATGTCTACCGCAAGAAACATAAAGCAAAAGATATCCATTGAT
* * * * ** ** *
2305 ATGAAAAGTTCATTTATAGTTACTCAAA-CTTCCGAAAGCCTTATTACTCGCTTTAAACAGTTTA
192 AGGAAAAGTCCATTTATAGTCACCCAAACCTT-CGAAAGCCTTATTACTTACTTTAAATGGTTTT
* *
2369 ATAATCTCATAATTGATTTTAAGTT-AAGTT-TTTTTACATTTTTGGTTAAAATAGATTATAATT
256 ATAATCTCATAATTAATTTTAAGTTGAA-TTGTTTTTACATTTTTGGTTAAAACAGATTATAATT
2432 GAAT
320 GAAT
2436 GTCTACGTAG
Statistics
Matches: 1050, Mismatches: 253, Indels: 82
0.76 0.18 0.06
Matches are distributed among these distances:
501 6 0.01
502 32 0.03
503 119 0.11
504 46 0.04
505 2 0.00
506 1 0.00
508 1 0.00
510 2 0.00
512 194 0.18
513 431 0.41
514 208 0.20
515 7 0.01
516 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (513 bp):
AAGAAAAACCATTCATTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCAAAAGCCTTATT
ACTCACTTGAAATGGTTTTACAATTCCATAATTGATTTTAAGTTAAATCGTTTTACATATTTAAT
TAAAACAGATTATAATTGAATGTCTACCGCAAGAAACATAAAGCAAAAGATATCCATTGATAGGA
AAAGTCCATTTATAGTCACCCAAACCTTCGAAAGCCTTATTACTTACTTTAAATGGTTTTATAAT
CTCATAATTAATTTTAAGTTGAATTGTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATAT
GTGCCTTAAGAAACGTGAAGAAAAATCCATTCAATGACAAGAAAAGTACATTTATAGTCACCCAT
GCCTTCAAAAGCCTTATCACATACTTTAAATAGTTTTATAATCTCATAACTGATTTTAGGTTAAA
TTTTCTTACATTTTTAGTTAAAAAAGATTATAATTAAATGTCTACCTCAAGAAACATG
Found at i:6474 original size:170 final size:168
Alignment explanation
Indices: 5893--7129 Score: 652
Period size: 170 Copynumber: 7.3 Consensus size: 168
5883 NNNNNTTATA
* * * * ** *
5893 AGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGATTGGGTGATTATAAATGGACT
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTAAGTGACTATAAATGGACT
* * * ** * * * * ** *
5958 TATCTTGCCAATGAATGATTTTTTTCTTCACATTTCCCGAGATAGACATTCAATTATAATCTGTT
66 TTTCTTACTAATGAATG--GCTTTTCTT-TCGTTTCTCAAGGCAGACATTCAATTATAATATGTT
* ********* *
6023 TTAACCAAAAATGCAAAA-ATATNNNNNNNNNNATCAATTATG
128 TTAACCAAAAATGTAAAACAT-T-CAACTTAAAATCAATTAAG
* * * ** * * *
6065 AGAGTGTAAAACCATATAAAGTAAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATAGACT
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTAAGTGACTATAAATGGACT
* * * * * * * * *
6130 TTTATTGCCAATGAATGGCTTTTTCTTCACGTTTTTCAAGGTAAACACTCAATTATAATCTGTTT
66 TTTCTTACTAATGAATGGC-TTTTCTT-TCGTTTCTCAAGGCAGACATTCAATTATAATATGTTT
* * * * **
6195 TAACTAAAAATATAAGAAAATTCAACCTAAAATCAATTTTG
129 TAACCAAAAATGTAA-AACATTCAACTTAAAATCAATTAAG
********** * * * *** *
6236 AGATTANNNNNNNNNNTAAAGTGAGTAATAAAGCTTTTGAAGAAATAGGTGACTATAAATGGACT
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTAAGTGACTATAAATGGACT
* *
6301 TTTCTCACTAATGAATGGCCTTTTCTTTGCGTTTCCCAAGGCAGACATTCAATTATAATATGTTT
66 TTTCTTACTAATGAATGG-CTTTTCTTT-CGTTTCTCAAGGCAGACATTCAATTATAATATGTTT
*
6366 GAACCAAAAATGTAAAACATTCAACTTAAAATCAATTAAG
129 TAACCAAAAATGTAAAACATTCAACTTAAAATCAATTAAG
* * * * *
6406 AGATTATAAAACCATTTAAAGCGAGTACTAAGGCTTCCGAAGGCTTAAGTAACTCTAAATGAACT
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTAAGTGACTATAAATGGACT
* * * * * * * *
6471 TTTCATA-TCAAT-AGATGGCTTTTGCTTCACGTTTCTTAAAGTAGACATTCAATTACAACATAT
66 TTTCTTACT-AATGA-ATGGCTTTT-CTT-TCGTTTCTCAAGGCAGACATTCAATTATAATATGT
* * * ** * * *
6534 TTGAA-TAACAAAAGTAGCACAATACAACTTAAAATTAATTATG
127 TTTAACCAA-AAATGTAAAAC-ATTCAACTTAAAATCAATTAAG
* * * * * ** *
6577 AGAATAT-AAACCATTTAAAGTGAGCAATAAAGCTTTCGAAGTCTTGGGTGACTATAAATGGGCT
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTAAGTGACTATAAATGGACT
* * ** * * * * *
6641 TTTCTTGCCAATGAAAAGCTTTT-TTTCATGTTTCCCAAAGG-AAATATTCAATTGTAATTTGTT
66 TTTCTTACTAATGAATGGCTTTTCTTTC--GTTTCTC-AAGGCAGACATTCAATTATAATATGTT
* * ***
6704 TTAACC-AAAATGTAAAAAAATTCAATTTAAAATCAATTNNN
128 TTAACCAAAAATGT-AAAACATTCAACTTAAAATCAATTAAG
******* * * * * * *
6745 NNNNNNNAAAAGCATTTAAAGTGAGTAATAAGACTTTTGAAGGCTT-GGATGACTATAAATGGGC
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTAAG-TGACTATAAATGGAC
* * * * * *
6809 TTTTCTTGCTGATGAATGAGTTTTTC-TTCATGTTTCTCATGGCAAACATTAAATTATAATATGT
65 TTTTCTTACTAATGAATG-GCTTTTCTTTC--GTTTCTCAAGGCAGACATTCAATTATAATATGT
* * * *
6873 TTTCACTAAAAATGTAAAAAAATTCAACCTAAAATCAATTATA-
127 TTTAACCAAAAATGT-AAAACATTCAACTTAAAATCAATTA-AG
** * * * *
6916 AGATTATAAAAATATTTAAAGCGAATAATAAGG-TTTCGAAGGCATGAA-TTACTATAAATGTAC
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGC-TTAAGTGACTATAAATGGAC
* * *
6979 TTTTCTTA-TCATTGAATGGCTTTGT-TTTCATGTTTCTCAAGGTAGACA-GCTAATTATAATAT
65 TTTTCTTACT-AATGAATGGCTTT-TCTTTC--GTTTCTCAAGGCAGACATTC-AATTATAATAT
* * * * *
7041 GTTTTAACCGAAAATATCAAACAATTCAACCTAAAATCAATTATG
125 GTTTTAACCAAAAATGTAAAAC-ATTCAACTTAAAATCAATTAAG
* * * *
7086 AGATTATAAAATCATATAATGCGAGTAATAAGGCTTTTGAAGGC
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGC
7130 ATGGGTCACT
Statistics
Matches: 810, Mismatches: 221, Indels: 69
0.74 0.20 0.06
Matches are distributed among these distances:
167 1 0.00
168 25 0.03
169 107 0.13
170 346 0.43
171 256 0.32
172 73 0.09
173 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.33
Consensus pattern (168 bp):
AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTAAGTGACTATAAATGGACT
TTTCTTACTAATGAATGGCTTTTCTTTCGTTTCTCAAGGCAGACATTCAATTATAATATGTTTTA
ACCAAAAATGTAAAACATTCAACTTAAAATCAATTAAG
Found at i:6811 original size:169 final size:161
Alignment explanation
Indices: 6588--6913 Score: 347
Period size: 169 Copynumber: 2.0 Consensus size: 161
6578 GAATATAAAC
* *
6588 CATTTAAAGTGAGCAATAAAGCTTTCGAAGTCTTGGGTGACTATAAATGGGCTTTTCTTGCCAAT
1 CATTTAAAGTGAGCAATAAAGCTTTCGAAGGCTTGGATGACTATAAATGGGCTTTTCTTGCCAAT
* * * * *
6653 GAA-AAGCTTTTT-TTCATGTTTCCCAAAGG-AAATATTCAATTGTAATTTGTTTTAAC-CAAAA
66 GAATAAG-TTTTTCTTCATGTTTCCC-AAGGCAAACATTAAATTATAATATGTTTTAACTAAAAA
**
6714 TGTAAAAAAATTCAATTTAAAATCAATTNNNNNNNNNNAAAAG
129 TGTAAAAAAATTCAACCTAAAATCAATT----------AAAAG
* * **
6757 CATTTAAAGTGAGTAAT-AAGACTTTTGAAGGCTTGGATGACTATAAATGGGCTTTTCTTGCTGA
1 CATTTAAAGTGAGCAATAAAG-CTTTCGAAGGCTTGGATGACTATAAATGGGCTTTTCTTGCCAA
* * * *
6821 TGAATGAGTTTTTCTTCATGTTTCTCATGGCAAACATTAAATTATAATATGTTTTCACTAAAAAT
65 TGAATAAGTTTTTCTTCATGTTTCCCAAGGCAAACATTAAATTATAATATGTTTTAACTAAAAAT
6886 GTAAAAAAATTCAACCTAAAATCAATTA
130 GTAAAAAAATTCAACCTAAAATCAATTA
6914 TAAGATTATA
Statistics
Matches: 135, Mismatches: 17, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
161 1 0.01
168 3 0.02
169 66 0.49
170 35 0.26
171 30 0.22
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (161 bp):
CATTTAAAGTGAGCAATAAAGCTTTCGAAGGCTTGGATGACTATAAATGGGCTTTTCTTGCCAAT
GAATAAGTTTTTCTTCATGTTTCCCAAGGCAAACATTAAATTATAATATGTTTTAACTAAAAATG
TAAAAAAATTCAACCTAAAATCAATTAAAAG
Found at i:13100 original size:29 final size:29
Alignment explanation
Indices: 13058--13114 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
13048 TAGATAAACA
*
13058 GTCACACAAGTATCCCTTTTGAAAATATT
1 GTCACACAAATATCCCTTTTGAAAATATT
*
13087 GTCACACAAATATCCTTTTTGAAAATAT
1 GTCACACAAATATCCCTTTTGAAAATAT
13115 AGTCTTANNN
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (29 bp):
GTCACACAAATATCCCTTTTGAAAATATT
Found at i:27590 original size:17 final size:17
Alignment explanation
Indices: 27552--27594 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
27542 TTCTTAGTAA
*
27552 CTTTAATTTA-TGTTAG
1 CTTTAATTTAGTGCTAG
27568 --TTAATTTAGTGCTAG
1 CTTTAATTTAGTGCTAG
27583 CTTTAATTTAGT
1 CTTTAATTTAGT
27595 TTTAATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 8 0.35
15 5 0.22
17 10 0.43
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.53
Consensus pattern (17 bp):
CTTTAATTTAGTGCTAG
Found at i:31624 original size:132 final size:132
Alignment explanation
Indices: 31387--31647 Score: 441
Period size: 132 Copynumber: 2.0 Consensus size: 132
31377 TCGCCTTCGA
* * *
31387 AAATTTAACGAGTAGATCCCATCATCGGGGTAATCGTTTGACATGATAAAAATGACATTTTCATG
1 AAATTTAACGAGTAGATCCCATCATCAGGATAATCGTTTGACACGATAAAAATGACATTTTCATG
** * *
31452 AATGCAAATCCTAATTTGAGTGAAAGCTTTTTATTGAAGATATTTCTCCGAACCCTCTCATCGTC
66 AATGCAAATCCTAATCCGAGTGAAAGCTTTTTATTGAAGATATTTCTCCAAACCCTCCCATCGTC
31517 GC
131 GC
* *
31519 AAATTTAACGAGTAGATCCTATCATCAGGATAATCGTTTGACACGATAAAAATGACATTTTTATG
1 AAATTTAACGAGTAGATCCCATCATCAGGATAATCGTTTGACACGATAAAAATGACATTTTCATG
31584 AATGCAAATCCTAATCCGAGTGAAAGCTTTTTATTGAAGATATTTCTCCAAACCCTCCCATCGT
66 AATGCAAATCCTAATCCGAGTGAAAGCTTTTTATTGAAGATATTTCTCCAAACCCTCCCATCGT
31648 ACTGGTGGGA
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 120 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (132 bp):
AAATTTAACGAGTAGATCCCATCATCAGGATAATCGTTTGACACGATAAAAATGACATTTTCATG
AATGCAAATCCTAATCCGAGTGAAAGCTTTTTATTGAAGATATTTCTCCAAACCCTCCCATCGTC
GC
Found at i:32056 original size:19 final size:19
Alignment explanation
Indices: 32034--32081 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
32024 TTTTATTTCT
*
32034 TTTATTTTTAT-AATTATTG
1 TTTATTTTTATGAATT-TTA
* *
32053 TTTATTTATATGTATTTTA
1 TTTATTTTTATGAATTTTA
32072 TTTATTTTTA
1 TTTATTTTTA
32082 CAAGTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTATTTTTATGAATTTTA
Found at i:33093 original size:33 final size:32
Alignment explanation
Indices: 33029--33096 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
33019 AACCCTCCTT
*
33029 TCTCTCTTTCTTCTTCCCGGCGGCGCGCTTCTC
1 TCTCTCTTTCTTCTTCCCGGC-GCGCACTTCTC
*
33062 TCTCTCTTTACTTCTTCGCCGGC-CTCACTTCTC
1 TCTCTCTTT-CTTCTTC-CCGGCGCGCACTTCTC
33095 TC
1 TC
33097 CTCCCTTCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 19 0.61
34 7 0.23
35 5 0.16
ACGTcount: A:0.03, C:0.43, G:0.13, T:0.41
Consensus pattern (32 bp):
TCTCTCTTTCTTCTTCCCGGCGCGCACTTCTC
Found at i:33209 original size:33 final size:34
Alignment explanation
Indices: 33160--33226 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 34
33150 CCTTCCTTCC
*
33160 CTCTCTTTCTTCCTGG-CGGTG-CACTTCTCTCT
1 CTCTCTTTCTTCCTGGCCGGCGTCACTTCTCTCT
33192 CTCTCTTTCCTTCCTGGCCGGCGTCACTTCTCTCT
1 CTCTCTTT-CTTCCTGGCCGGCGTCACTTCTCTCT
33227 TTCCTTCCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 8 0.26
33 8 0.26
34 4 0.13
35 11 0.35
ACGTcount: A:0.03, C:0.40, G:0.15, T:0.42
Consensus pattern (34 bp):
CTCTCTTTCTTCCTGGCCGGCGTCACTTCTCTCT
Found at i:33221 original size:129 final size:130
Alignment explanation
Indices: 33058--33299 Score: 387
Period size: 129 Copynumber: 1.9 Consensus size: 130
33048 GCGGCGCGCT
*
33058 TCTCTCTCTCTTTACTTCTTCGCCGGCCTCACTTCTCTCCTCCCTTCCTTCACTTTCTCTCCTTT
1 TCTCTCTCTCTTTACTTCCTCGCCGGCCTCACTTCTCTCCTCCCTTCCTTCACTTTCTCTCCTTT
*
33123 TCTTCTTATCTTTCTTAGCCGCCAGC-GCCTTCCTTCCCTCTCTTTCTTCCTGGCGGTGCACTTC
66 TCTTCTTATCTTTCTTAGCCGCCAGCGGCCTTCCTTCCCTCTCCTTCTTCCTGGCGGTGCACTTC
* * * * * * *
33187 TCTCTCTCTCTTTCCTTCCTGGCCGGCGTCACTTCTCTCTTTCCTTCCTTCAGTTTCTTTCCTTT
1 TCTCTCTCTCTTTACTTCCTCGCCGGCCTCACTTCTCTCCTCCCTTCCTTCACTTTCTCTCCTTT
*
33252 TCTTCTTCTCTTTCTTAGCCGCCAGCGGCCTTCCTTCCCTCTCCTTCT
66 TCTTCTTATCTTTCTTAGCCGCCAGCGGCCTTCCTTCCCTCTCCTTCT
33300 CTTCTTTTCT
Statistics
Matches: 102, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
129 82 0.80
130 20 0.20
ACGTcount: A:0.05, C:0.41, G:0.10, T:0.45
Consensus pattern (130 bp):
TCTCTCTCTCTTTACTTCCTCGCCGGCCTCACTTCTCTCCTCCCTTCCTTCACTTTCTCTCCTTT
TCTTCTTATCTTTCTTAGCCGCCAGCGGCCTTCCTTCCCTCTCCTTCTTCCTGGCGGTGCACTTC
Found at i:33235 original size:33 final size:33
Alignment explanation
Indices: 33160--33237 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
33150 CCTTCCTTCC
* *
33160 CTCT-CTTTCTTCCTGGCGGTGCACTTCTCTCT
1 CTCTCCTTCCTTCCTGGCGGCGCACTTCTCTCT
*
33192 CTCTCTTTCCTTCCTGGCCGGCGTCACTTCTCTCT
1 CTCTCCTTCCTTCCTGG-CGGCG-CACTTCTCTCT
33227 -T-TCCTTCCTTC
1 CTCTCCTTCCTTC
33238 AGTTTCTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
32 4 0.10
33 19 0.49
34 5 0.13
35 11 0.28
ACGTcount: A:0.03, C:0.41, G:0.13, T:0.44
Consensus pattern (33 bp):
CTCTCCTTCCTTCCTGGCGGCGCACTTCTCTCT
Found at i:33297 original size:65 final size:64
Alignment explanation
Indices: 33096--33311 Score: 160
Period size: 65 Copynumber: 3.3 Consensus size: 64
33086 TCACTTCTCT
* *
33096 CCTC-CCTTCCTTCACTTTCTCTCCTTTTCTTCTTATCTTTCTTAGCCGCCAGC-GCCTTCCTTC
1 CCTCTCCTTCCTTC-CTTTCTTTCCTTTTCTTCTTCTCTTTCTTAGCCGCCAGCGGCCTTCCTTC
* ** * * * * *
33159 CCTCT-CTTTCTTCCTGGCGGTGCACTTCTC-TCTCTCTCTTTCCTT--CCTGGCCGGCGTCACT
1 CCTCTCCTTCCTTCCTTTC-TTTC-CTTTTCTTCT-TCTCTTT-CTTAGCC--GCCAGCGGC-CT
33220 T-C-TC
59 TCCTTC
* * *
33224 TCTTTCCTTCCTTCAGTTTCTTTCCTTTTCTTCTTCTCTTTCTTAGCCGCCAGCGGCCTTCCTTC
1 CCTCTCCTTCCTTC-CTTTCTTTCCTTTTCTTCTTCTCTTTCTTAGCCGCCAGCGGCCTTCCTTC
*
33289 CCTCTCCTTCTCTTCTTTTCTTT
1 CCTCTCCTTC-CTTCCTTTCTTT
33312 TTCTTCCTCC
Statistics
Matches: 112, Mismatches: 24, Indels: 32
0.67 0.14 0.19
Matches are distributed among these distances:
62 3 0.03
63 20 0.18
64 22 0.20
65 42 0.38
66 20 0.18
67 5 0.04
ACGTcount: A:0.04, C:0.40, G:0.09, T:0.46
Consensus pattern (64 bp):
CCTCTCCTTCCTTCCTTTCTTTCCTTTTCTTCTTCTCTTTCTTAGCCGCCAGCGGCCTTCCTTC
Found at i:36163 original size:17 final size:16
Alignment explanation
Indices: 36142--36224 Score: 68
Period size: 17 Copynumber: 5.2 Consensus size: 16
36132 CCACTACCAA
36142 GAAGAAAAGAGAAAGG
1 GAAGAAAAGAGAAAGG
*
36158 AGAAGAAAGAAAGAAA-G
1 -GAAGAAA-AGAGAAAGG
*
36175 GAAGGAAGGAGAGAAAGG
1 GAA-GAA-AAGAGAAAGG
*
36193 G-AGAAAGGAG-AA-G
1 GAAGAAAAGAGAAAGG
36206 GAAGAAAA-AGAAAGG
1 GAAGAAAAGAGAAAGG
36221 GAAG
1 GAAG
36225 GTTCAGCTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
13 4 0.08
14 9 0.17
15 8 0.15
16 6 0.11
17 18 0.34
18 8 0.15
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (16 bp):
GAAGAAAAGAGAAAGG
Found at i:36174 original size:18 final size:17
Alignment explanation
Indices: 36141--36176 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
36131 CCCACTACCA
*
36141 AGAAGAAAAGAGAAAGG
1 AGAAGAAAAAAGAAAGG
36158 AGAAGAAAGAAAGAAAGG
1 AGAAGAAA-AAAGAAAGG
36176 A
1 A
36177 AGGAAGGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
AGAAGAAAAAAGAAAGG
Done.