Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold826
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: 341534
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 2
Found at i:215763 original size:158 final size:159
Alignment explanation
Indices: 215569--215905 Score: 430
Period size: 158 Copynumber: 2.1 Consensus size: 159
215559 GGGGTTGGAA
* * * * * *
215569 TATCCCCGAGATGAAAAAAATTTAAT-ATTTTCAAAGTAAGAAGGGGGTTGGAGTATCCTCTCGA
1 TATCCCCGAGATG--AAAATTTTGATGCTTTTAAAAGTAAAAACGGGGTTGGAGTATCCTCTCGA
* **
215633 AAATGATGGGGTTGGAGTATCCCCAATGGTGAAAAATT-GATATTTTGAAA-AAAAACGGGGTTG
64 AAATGATGAGGTTGGAGTATCCCCAATGGTGAAAAATTCGATATTTTGAAAGAAAAACAAGGTTG
* *
215696 GAGTA-TCTCCTTGAAAATAATGGGGTTGAAG
129 GAGTATTC-CCTCGAAAATAATGGGATTGAAG
*
215727 TATCCCCGATGGTGAAAATTTTGATGCTTTTAAAAGTAAAAACGGGGTTGGAGTATCCTCTCGAA
1 TATCCCCGA-GATGAAAATTTTGATGCTTTTAAAAGTAAAAACGGGGTTGGAGTATCCTCTCGAA
* * * *
215792 AATGATGAGGTTGGAGTATTCTCGATGGTTAAAAATTCGATATTTTGAAAGTAAAAACAAGGTTG
65 AATGATGAGGTTGGAGTATCCCCAATGGTGAAAAATTCGATATTTTGAAAG-AAAAACAAGGTTG
* *
215857 GAGTATTCCCTCGAAAATGATGGGATTGGAG
129 GAGTATTCCCTCGAAAATAATGGGATTGAAG
*
215888 TATCTCCGAGATGAAAAT
1 TATCCCCGAGATGAAAAT
215906 CGATATTTGT
Statistics
Matches: 153, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
157 9 0.06
158 76 0.50
159 15 0.10
160 8 0.05
161 43 0.28
162 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (159 bp):
TATCCCCGAGATGAAAATTTTGATGCTTTTAAAAGTAAAAACGGGGTTGGAGTATCCTCTCGAAA
ATGATGAGGTTGGAGTATCCCCAATGGTGAAAAATTCGATATTTTGAAAGAAAAACAAGGTTGGA
GTATTCCCTCGAAAATAATGGGATTGAAG
Found at i:215870 original size:80 final size:79
Alignment explanation
Indices: 215559--215918 Score: 383
Period size: 81 Copynumber: 4.5 Consensus size: 79
215549 GGTGAAAATC
* * * * * *
215559 GGGGTTGGAATATCCCCGA-GATGAAAAAAATTTAATATTTTCAAAGTAAGAAGGGGGTTGGAGT
1 GGGGTTGGAGTATCCCCGATGGTG--AAAAA-TTGATATTTTGAAAGTAAAAACGGGGTTGGAGT
215623 ATCCTCTCGAAAATGAT
63 ATCCTCTCGAAAATGAT
*
215640 GGGGTTGGAGTATCCCCAATGGTGAAAAATTGATATTTTGAAA--AAAAACGGGGTTGGAGTAT-
1 GGGGTTGGAGTATCCCCGATGGTGAAAAATTGATATTTTGAAAGTAAAAACGGGGTTGGAGTATC
* *
215702 CTCCTTGAAAATAAT
66 CT-CTCGAAAATGAT
* * * *
215717 GGGGTTGAAGTATCCCCGATGGTGAAAATTTTGATGCTTTTAAAAGTAAAAACGGGGTTGGAGTA
1 GGGGTTGGAGTATCCCCGATGGTGAAAA-ATTGAT-ATTTTGAAAGTAAAAACGGGGTTGGAGTA
215782 TCCTCTCGAAAATGAT
64 TCCTCTCGAAAATGAT
* * * * **
215798 GAGGTTGGAGTATTCTCGATGGTTAAAAATTCGATATTTTGAAAGTAAAAACAAGGTTGGAGTAT
1 GGGGTTGGAGTATCCCCGATGGTGAAAAATT-GATATTTTGAAAGTAAAAACGGGGTTGGAGTA-
215863 TCC-CTCGAAAATGAT
64 TCCTCTCGAAAATGAT
* * * *
215878 GGGATTGGAGTATCTCCGA-GATG-AAAATCGATATTTGTGAA
1 GGGGTTGGAGTATCCCCGATGGTGAAAAATTGATATTT-TGAA
215919 GGAAAAATTT
Statistics
Matches: 235, Mismatches: 34, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
76 2 0.01
77 60 0.26
78 14 0.06
79 21 0.09
80 58 0.25
81 75 0.32
82 5 0.02
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCCGATGGTGAAAAATTGATATTTTGAAAGTAAAAACGGGGTTGGAGTATC
CTCTCGAAAATGAT
Found at i:218299 original size:32 final size:31
Alignment explanation
Indices: 218263--218339 Score: 109
Period size: 32 Copynumber: 2.5 Consensus size: 31
218253 AATACATTGA
*
218263 AGAATGTATCGATGCATTTGGGTCAAAAACCC
1 AGAATGTATCGATACATTTGGGTC-AAAACCC
* * *
218295 AGAATGTATCAATATATTTGGGTCAAAACTC
1 AGAATGTATCGATACATTTGGGTCAAAACCC
218326 AGAATGTATCGATA
1 AGAATGTATCGATA
218340 TAATGAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 19 0.47
32 21 0.52
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (31 bp):
AGAATGTATCGATACATTTGGGTCAAAACCC
Found at i:218329 original size:31 final size:32
Alignment explanation
Indices: 218263--218341 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 32
218253 AATACATTGA
**
218263 AGAATGTATCGATGCATTTGGGTCAAAAACCC
1 AGAATGTATCGATATATTTGGGTCAAAAACCC
* *
218295 AGAATGTATCAATATATTTGGGTC-AAAACTC
1 AGAATGTATCGATATATTTGGGTCAAAAACCC
218326 AGAATGTATCGATATA
1 AGAATGTATCGATATA
218342 ATGAAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 21 0.50
32 21 0.50
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (32 bp):
AGAATGTATCGATATATTTGGGTCAAAAACCC
Found at i:222477 original size:2 final size:2
Alignment explanation
Indices: 222470--222501 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
222460 TTGTGTTATG
*
222470 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
222502 CTAATACTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:235530 original size:25 final size:24
Alignment explanation
Indices: 235520--235583 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 24
235510 AGGAAGAGAG
235520 AAAAAA-AAAGGAAAAAGGAAGAA
1 AAAAAAGAAAGGAAAAAGGAAGAA
235543 AAAAAAGAAA-G--AAA-GAA-AA
1 AAAAAAGAAAGGAAAAAGGAAGAA
235562 AAAGAAAGAAA-GAAAGAAGGAA
1 AAA-AAAGAAAGGAAA-AAGGAA
235584 TAAGAAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
19 5 0.14
20 11 0.31
21 3 0.09
22 1 0.03
23 9 0.26
24 6 0.17
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (24 bp):
AAAAAAGAAAGGAAAAAGGAAGAA
Found at i:235546 original size:12 final size:12
Alignment explanation
Indices: 235519--235613 Score: 65
Period size: 11 Copynumber: 8.0 Consensus size: 12
235509 GAGGAAGAGA
*
235519 GAAAAAAA-AAG
1 GAAAAAAAGAAA
235530 GAAAAAGGAAGAAA
1 GAAAAA--AAGAAA
*
235544 AAAAAGAAAGAAA
1 GAAAA-AAAGAAA
235557 GAAAAAAAGAAA
1 GAAAAAAAGAAA
*
235569 GAAAGAAAG-AA
1 GAAAAAAAGAAA
* *
235580 G-GAATAAGAAA
1 GAAAAAAAGAAA
*
235591 -AGAAAAAGAAA
1 GAAAAAAAGAAA
235602 -AAAAAAGAGAAA
1 GAAAAAA-AGAAA
235614 ATAGGGTGGC
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
10 4 0.06
11 25 0.37
12 20 0.29
13 12 0.18
14 6 0.09
15 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (12 bp):
GAAAAAAAGAAA
Found at i:235549 original size:13 final size:14
Alignment explanation
Indices: 235530--235613 Score: 66
Period size: 16 Copynumber: 5.7 Consensus size: 14
235520 AAAAAAAAAG
*
235530 GAAAAAGGAAGAAA
1 GAAAAAGAAAGAAA
235544 -AAAAAGAAAGAAA
1 GAAAAAGAAAGAAA
235557 GAAAAAAAGAAAGAAA
1 G--AAAAAGAAAGAAA
235573 GAAAGAAGGAATAAGAAAA
1 GAAA-AA-G-A-AAG-AAA
235592 GAAAAAGAAA-AAA
1 GAAAAAGAAAGAAA
*
235605 -AAAGAGAAA
1 GAAAAAGAAA
235614 ATAGGGTGGC
Statistics
Matches: 60, Mismatches: 2, Indels: 18
0.75 0.03 0.22
Matches are distributed among these distances:
12 8 0.13
13 15 0.25
14 3 0.05
15 4 0.07
16 16 0.27
17 2 0.03
18 5 0.08
19 7 0.12
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.01
Consensus pattern (14 bp):
GAAAAAGAAAGAAA
Found at i:235553 original size:4 final size:4
Alignment explanation
Indices: 235546--235579 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
235536 GGAAGAAAAA
*
235546 AAAG AAAG AAAG AAAA AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
235580 GGAATAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:235614 original size:12 final size:11
Alignment explanation
Indices: 235520--235614 Score: 66
Period size: 12 Copynumber: 8.3 Consensus size: 11
235510 AGGAAGAGAG
*
235520 AAAAAAAAAGG
1 AAAAAAAAAGA
**
235531 AAAAAGGAAGAA
1 AAAAAAAAAG-A
235543 AAAAAAGAAAGA
1 AAAAAA-AAAGA
235555 AAGAAAAAAAGA
1 AA-AAAAAAAGA
*
235567 AAGAAAGAAAG-
1 AA-AAAAAAAGA
** *
235578 AAGGAATAAGA
1 AAAAAAAAAGA
*
235589 AAAGAAAAAGA
1 AAAAAAAAAGA
235600 AAAAAAAAGAGA
1 AAAAAAAA-AGA
235612 AAA
1 AAA
235615 TAGGGTGGCT
Statistics
Matches: 66, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
10 4 0.06
11 26 0.39
12 29 0.44
13 7 0.11
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:236870 original size:110 final size:108
Alignment explanation
Indices: 236423--236870 Score: 379
Period size: 110 Copynumber: 4.1 Consensus size: 108
236413 AAAGTAGCGT
* ** ** * ** *
236423 TTGAGCACCAAAGGATTGGCCTCGAAATAAATCATTGTCTAGGGTAATAAAGTGGTGTATGAATG
1 TTGAGCACCAAAGGATTGGCCTTGAAATAGGTCATTGTCTAAAGTCATAAAGTGACGTACGAATG
* * * ** *
236488 CCTTTTATATAAGATAACTCATTTTTTTGCATAAATTAGGTT-TA
66 CCCTTTATATAGGATAATTCA--TTTTTGCATAAATTATATTAGA
* * *
236532 TTCGAGCA-CTAAGAGATTGGCCCTGAAATA-GTCATTGTCTAGAGTCATAAAGTGACGTACGAA
1 TT-GAGCACCAAAG-GATTGGCCTTGAAATAGGTCATTGTCTAAAGTCATAAAGTGACGTACGAA
** * *
236595 TGTTCTTTATATAGGATAACTT-ATTTTTGCATTAATTAT-GTAGA
64 TGCCCTTTATATAGGATAA-TTCATTTTTGCATAAATTATATTAGA
* * * * * *
236639 TTAAGGCACTAAGGGATTGGCCTTGAAATAGGTCATTGTCTAAAG-CTATAAAATGGCGTATGAA
1 TTGA-GCACCAAAGGATTGGCCTTGAAATAGGTCATTGTCTAAAGTC-ATAAAGTGACGTACGAA
* * * *
236703 TGCCCTTTATGTAGGATAATTCAATTAATTGCATTAATTACA-TAGA
64 TGCCCTTTATATAGGATAATTC-ATT-TTTGCATAAATTATATTAGA
* * * *
236749 TTCGGGTACCAAAGGATTGGTCTTGAAATAGGTCATTGTCTAAAGTCATAAAGTGACGTACGAAC
1 TT-GAGCACCAAAGGATTGGCCTTGAAATAGGTCATTGTCTAAAGTCATAAAGTGACGTACGAAT
* * * *
236814 GCCCTTTACATAGGATAATTCATTTTTCACATAAAGTATATTATA
65 GCCCTTTATATAGGATAATTCATTTTT-GCATAAATTATATTAGA
236859 CTTGAGCACCAA
1 -TTGAGCACCAA
236871 TAGATTAGCT
Statistics
Matches: 270, Mismatches: 52, Indels: 33
0.76 0.15 0.09
Matches are distributed among these distances:
106 2 0.01
107 38 0.14
108 47 0.17
109 63 0.23
110 117 0.43
111 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (108 bp):
TTGAGCACCAAAGGATTGGCCTTGAAATAGGTCATTGTCTAAAGTCATAAAGTGACGTACGAATG
CCCTTTATATAGGATAATTCATTTTTGCATAAATTATATTAGA
Found at i:236887 original size:110 final size:106
Alignment explanation
Indices: 236423--236930 Score: 320
Period size: 110 Copynumber: 4.7 Consensus size: 106
236413 AAAGTAGCGT
* ** ** * ** * *
236423 TTGAGCACCAAAGGATTGGCCTCGAAATAAATCATTGTCTAGGGTAATAAAGTGGTGTATGAATG
1 TTGAGCACCAAA-GATTGGCCTTGAAATAGGTCATTGTCTAAAGTCATAAAGTGACGTACGAACG
* * * * * *
236488 CCTTTTATATAAGATAACTCATTTTTTTGCATAAAT-TAGGTT-TA
65 CCCTTTACATAGGATAATTCA--TTTTTGCATTAATATA--TTAGA
* * * *
236532 TTCGAGCACTAAGAGATTGGCCCTGAAATA-GTCATTGTCTAGAGTCATAAAGTGACGTACGAAT
1 TT-GAGCACCAA-AGATTGGCCTTGAAATAGGTCATTGTCTAAAGTCATAAAGTGACGTACGAAC
** *
236596 GTTCTTTATATAGGATAACTT-ATTTTTGCATTAAT-TATGTAGA
64 GCCCTTTACATAGGATAA-TTCATTTTTGCATTAATATAT-TAGA
* * * * * *
236639 TTAAGGCACTAAGGGATTGGCCTTGAAATAGGTCATTGTCTAAAG-CTATAAAATGGCGTATGAA
1 TTGA-GCACCAA-AGATTGGCCTTGAAATAGGTCATTGTCTAAAGTC-ATAAAGTGACGTACGAA
* ** * *
236703 TGCCCTTTATGTAGGATAATTCAATTAATTGCATTAAT-TACATAGA
63 CGCCCTTTACATAGGATAATTC-ATT-TTTGCATTAATATA-TTAGA
* * *
236749 TTCGGGTACCAAAGGATTGGTCTTGAAATAGGTCATTGTCTAAAGTCATAAAGTGACGTACGAAC
1 TT-GAGCACCAAA-GATTGGCCTTGAAATAGGTCATTGTCTAAAGTCATAAAGTGACGTACGAAC
* * *
236814 GCCCTTTACATAGGATAATTCATTTTTCACATAAAGTATATTATA
64 GCCCTTTACATAGGATAATTCATTTTT-GCATTAA-TATATTAGA
* * * *
236859 CTTGAGCACCAATAGATTAG-CTTCGAAATAGG-C-TTATCT--AGTCGTAAAGGTGACGTACAA
1 -TTGAGCACCAA-AGATTGGCCTT-GAAATAGGTCATTGTCTAAAGTCATAAA-GTGACGTACGA
236919 ACGCCTCTTTAC
62 ACGCC-CTTTAC
236931 TTAGAAAGAG
Statistics
Matches: 325, Mismatches: 51, Indels: 47
0.77 0.12 0.11
Matches are distributed among these distances:
105 1 0.00
106 10 0.03
107 58 0.18
108 56 0.17
109 60 0.18
110 133 0.41
111 7 0.02
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (106 bp):
TTGAGCACCAAAGATTGGCCTTGAAATAGGTCATTGTCTAAAGTCATAAAGTGACGTACGAACGC
CCTTTACATAGGATAATTCATTTTTGCATTAATATATTAGA
Found at i:241629 original size:52 final size:52
Alignment explanation
Indices: 241549--241679 Score: 199
Period size: 52 Copynumber: 2.5 Consensus size: 52
241539 CCCGAAATAT
* * * * *
241549 GAAAATTTGTCTGCATGTATTGATACATTTTATAGTGTTTCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTAG
*
241601 GCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTAG
1 GAAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTAG
*
241653 GAAAATTTGCTTGCATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
241680 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.38
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTAG
Found at i:241692 original size:52 final size:52
Alignment explanation
Indices: 241549--241699 Score: 169
Period size: 52 Copynumber: 2.9 Consensus size: 52
241539 CCCGAAATAT
* * *** * *
241549 GAAAATTTGTCTGCATGTATTGATACATTTTATAGTGTTTCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATAAGATAGTGTATCGATACATCTAG
* *** *
241601 GCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTAG
1 GAAAATTTGCCTGCATGTATCGATACATAAGATAGTGTATCGATACATCTAG
*
241653 GAAAATTTGCTTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACATAAGAT-AGTGTATCGATACA
241700 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATAAGATAGTGTATCGATACATCTAG
Found at i:241706 original size:13 final size:13
Alignment explanation
Indices: 241688--241712 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
241678 CAAAGATCAG
241688 TGTATCGATACAA
1 TGTATCGATACAA
241701 TGTATCGATACA
1 TGTATCGATACA
241713 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:245619 original size:20 final size:20
Alignment explanation
Indices: 245572--245646 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
245562 AAAAAGACAT
*
245572 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
245591 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
245612 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
245632 AATGTATCGATACAT
1 AATGTATCGATACAT
245647 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:245640 original size:40 final size:39
Alignment explanation
Indices: 245569--245646 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
245559 GGTAAAAAGA
* *
245569 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
245608 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
245647 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:252676 original size:76 final size:75
Alignment explanation
Indices: 252562--252756 Score: 207
Period size: 76 Copynumber: 2.6 Consensus size: 75
252552 TTTATTTATG
** *
252562 TTAATGGGAAATTTTAGCAAACACATATT-CT-ATGTCATGTTCTTCTATTTCAACTTATT-ATT
1 TTAATGGGAAATTGCAG-AAA-ACATATTCCTCA--TCATGATCTTCTATTTCAACTTATTGA-T
*
252624 AGTTTGTTTCAGCTA
61 AGTTTATTTCAGCTA
* * * * *
252639 TTGATGGGAAATTGCAGAATCATATATTCCTCATCATGATCTTCTATTTCAGCTTGTTGATAGTT
1 TTAATGGGAAATTGCAGAA-AACATATTCCTCATCATGATCTTCTATTTCAACTTATTGATAGTT
**
252704 TATTTTGGCTA
65 TATTTCAGCTA
*
252715 TTAATGGGAAATTGCAGAAAACATATTCCTTATCATGATCTT
1 TTAATGGGAAATTGCAGAAAACATATTCCTCATCATGATCTT
252757 TTACTTTAGC
Statistics
Matches: 99, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
75 20 0.20
76 61 0.62
77 17 0.17
78 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (75 bp):
TTAATGGGAAATTGCAGAAAACATATTCCTCATCATGATCTTCTATTTCAACTTATTGATAGTTT
ATTTCAGCTA
Found at i:252779 original size:75 final size:76
Alignment explanation
Indices: 252635--252784 Score: 198
Period size: 75 Copynumber: 2.0 Consensus size: 76
252625 GTTTGTTTCA
* * * *
252635 GCTATTGATGGGAAATTGCAGAATCATATATTCCTCATCATGATCTTCTATTTCAGCTTGTTGAT
1 GCTATTAATGGGAAATTGCAGAATAACATATTCCTCATCATGATCTTCTATTTCAGCTTGTTGAC
252700 AGTTTATTTTG
66 AGTTTATTTTG
* *
252711 GCTATTAATGGGAAATTGCAGAA-AACATATTCCTTATCATGATCTTTTACTTT-AGCTTGTT-A
1 GCTATTAATGGGAAATTGCAGAATAACATATTCCTCATCATGATCTTCTA-TTTCAGCTTGTTGA
*
252773 GCAGTTTGTTTT
65 -CAGTTTATTTT
252785 AGCCATTGAT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
74 1 0.02
75 39 0.60
76 25 0.38
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (76 bp):
GCTATTAATGGGAAATTGCAGAATAACATATTCCTCATCATGATCTTCTATTTCAGCTTGTTGAC
AGTTTATTTTG
Found at i:253292 original size:41 final size:41
Alignment explanation
Indices: 253247--253332 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
253237 AAATGTTACA
*
253247 CAACCCTTT-TTCATTTATTGACTTATTGGTTTTGTC-CTGGT
1 CAACCCTTTATTC-TTTATTGACTTATAGGTTTTGTCTC-GGT
* *
253288 CAACCTTTTATTCTTTGTTGACTTATAGGTTTTGTCTCGGT
1 CAACCCTTTATTCTTTATTGACTTATAGGTTTTGTCTCGGT
253329 CAAC
1 CAAC
253333 ATTTTTTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
41 36 0.90
42 4 0.10
ACGTcount: A:0.16, C:0.20, G:0.15, T:0.49
Consensus pattern (41 bp):
CAACCCTTTATTCTTTATTGACTTATAGGTTTTGTCTCGGT
Found at i:254670 original size:6 final size:6
Alignment explanation
Indices: 254659--254711 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
254649 TGATTAATAA
* * *
254659 TTTTAT TTTTAT TTTTAT TTTTAT TTTGAAA TTTTAA TTTTA- TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT-TAT TTTTAT TTTTAT TTTTAT
254707 TTTTA
1 TTTTA
254712 ACTAGTTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
5 5 0.12
6 33 0.79
7 4 0.10
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (6 bp):
TTTTAT
Found at i:273955 original size:142 final size:142
Alignment explanation
Indices: 273699--273984 Score: 572
Period size: 142 Copynumber: 2.0 Consensus size: 142
273689 GAACTATCAT
273699 ATAAAGAGGACACCTTAATTCTCCCTAGGTTAACAGAATACCTGCATGCCAGATTGCTGCATTTG
1 ATAAAGAGGACACCTTAATTCTCCCTAGGTTAACAGAATACCTGCATGCCAGATTGCTGCATTTG
273764 TATTGAGAAGATAAAGGAAAAAGAGAGGAAAATTTTCATTTATATTAGTAAACACAATGACTCCC
66 TATTGAGAAGATAAAGGAAAAAGAGAGGAAAATTTTCATTTATATTAGTAAACACAATGACTCCC
273829 AGCATCCGGAAA
131 AGCATCCGGAAA
273841 ATAAAGAGGACACCTTAATTCTCCCTAGGTTAACAGAATACCTGCATGCCAGATTGCTGCATTTG
1 ATAAAGAGGACACCTTAATTCTCCCTAGGTTAACAGAATACCTGCATGCCAGATTGCTGCATTTG
273906 TATTGAGAAGATAAAGGAAAAAGAGAGGAAAATTTTCATTTATATTAGTAAACACAATGACTCCC
66 TATTGAGAAGATAAAGGAAAAAGAGAGGAAAATTTTCATTTATATTAGTAAACACAATGACTCCC
273971 AGCATCCGGAAA
131 AGCATCCGGAAA
273983 AT
1 AT
273985 TAGGTCAGAA
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 144 1.00
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (142 bp):
ATAAAGAGGACACCTTAATTCTCCCTAGGTTAACAGAATACCTGCATGCCAGATTGCTGCATTTG
TATTGAGAAGATAAAGGAAAAAGAGAGGAAAATTTTCATTTATATTAGTAAACACAATGACTCCC
AGCATCCGGAAA
Found at i:276186 original size:2 final size:2
Alignment explanation
Indices: 276181--276210 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
276171 TTTTTTTTTG
*
276181 CA CA CA CA CA CA CA CA CC CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
276211 TATATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.53, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:280198 original size:25 final size:27
Alignment explanation
Indices: 280170--280223 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 27
280160 TTGCGCATGC
* *
280170 TTGATACTTTAATT-GTAGC-ATTATT
1 TTGAGACTTAAATTAGTAGCTATTATT
*
280195 TTGAGACTTAAATTAGTAGCTTTTATT
1 TTGAGACTTAAATTAGTAGCTATTATT
280222 TT
1 TT
280224 ATTAGCACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 12 0.50
26 5 0.21
27 7 0.29
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (27 bp):
TTGAGACTTAAATTAGTAGCTATTATT
Found at i:283487 original size:2 final size:2
Alignment explanation
Indices: 283482--283520 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
283472 AAAAATACTC
*
283482 CT CT CT CT CT CT CT CT CT CT CT CT CT CT GT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
283521 CCGCCAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.03, T:0.49
Consensus pattern (2 bp):
CT
Found at i:283772 original size:2 final size:2
Alignment explanation
Indices: 283767--283809 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
283757 GAGAGAAAGA
* *
283767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
283809 A
1 A
283810 AGCGAGAGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:286103 original size:20 final size:19
Alignment explanation
Indices: 286078--286182 Score: 96
Period size: 20 Copynumber: 5.7 Consensus size: 19
286068 CTGCCAGTTT
*
286078 TATGTATCGATACAATTGTA
1 TATGTATCGATACAA-TGAA
286098 TATGTATCGATACAATGAA
1 TATGTATCGATACAATGAA
*
286117 CATGTATCGAT---AT-AA
1 TATGTATCGATACAATGAA
*
286132 -A-GTATCGATACAAAGAA
1 TATGTATCGATACAATGAA
* *
286149 TGATGTATCGATACATCTGGA
1 T-ATGTATCGATACA-ATGAA
286170 TATGTATCGATAC
1 TATGTATCGATAC
286183 TTTCAAGGGT
Statistics
Matches: 71, Mismatches: 6, Indels: 16
0.76 0.06 0.17
Matches are distributed among these distances:
13 8 0.11
14 1 0.01
15 2 0.03
16 3 0.04
17 2 0.03
19 14 0.20
20 38 0.54
21 3 0.04
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.32
Consensus pattern (19 bp):
TATGTATCGATACAATGAA
Found at i:286143 original size:52 final size:53
Alignment explanation
Indices: 286081--286181 Score: 134
Period size: 52 Copynumber: 1.9 Consensus size: 53
286071 CCAGTTTTAT
* *
286081 GTATCGATACAATTGTAT-ATGTATCGATACA-ATGAACATGTATCGATATAAA
1 GTATCGATACAA-AGAATGATGTATCGATACATATGAACATGTATCGATATAAA
* * *
286133 GTATCGATACAAAGAATGATGTATCGATACATCTGGATATGTATCGATA
1 GTATCGATACAAAGAATGATGTATCGATACATATGAACATGTATCGATA
286182 CTTTCAAGGG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
51 3 0.07
52 25 0.60
53 14 0.33
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.32
Consensus pattern (53 bp):
GTATCGATACAAAGAATGATGTATCGATACATATGAACATGTATCGATATAAA
Found at i:286861 original size:18 final size:19
Alignment explanation
Indices: 286823--286861 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
286813 TTTCATAATA
*
286823 GTCAAGTTATAATGTGTTT
1 GTCAAGTTAGAATGTGTTT
*
286842 GTCATGTTAGAATG-GTTT
1 GTCAAGTTAGAATGTGTTT
286860 GT
1 GT
286862 AACATGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.23, C:0.05, G:0.26, T:0.46
Consensus pattern (19 bp):
GTCAAGTTAGAATGTGTTT
Found at i:287482 original size:24 final size:24
Alignment explanation
Indices: 287443--287491 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
287433 AACTAGTTGT
* *
287443 TGCTTATGCTAGAAAATGTGCTAG
1 TGCTTATGCTAGAAAAGGTACTAG
287467 TGCTTATGCT-GTAAAAGGTACTAG
1 TGCTTATGCTAG-AAAAGGTACTAG
287491 T
1 T
287492 ACTAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (24 bp):
TGCTTATGCTAGAAAAGGTACTAG
Found at i:288286 original size:19 final size:20
Alignment explanation
Indices: 288249--288286 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
288239 TCTTGTAGCT
288249 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
288269 ATGTATCGATAC-ATTCAT
1 ATGTATCGATACAATTCAT
288287 TTGAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:288429 original size:20 final size:20
Alignment explanation
Indices: 288404--288460 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
288394 TGCAAATTTT
* *
288404 ATGTATCAATACAATTGTCC
1 ATGTATCGATACAATTGTAC
*
288424 ATGTATCGATACAA-TGAAC
1 ATGTATCGATACAATTGTAC
288443 ATGTATCGATAC-ATTGTA
1 ATGTATCGATACAATTGTA
288461 TGGATACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 1 0.03
19 18 0.56
20 13 0.41
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATTGTAC
Found at i:289530 original size:22 final size:21
Alignment explanation
Indices: 289495--289544 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
289485 TTTGTTGATG
*
289495 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
289515 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
289536 AATTTGAAG
1 ATTTTGAAG
289545 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:289541 original size:21 final size:22
Alignment explanation
Indices: 289502--289544 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
289492 ATGATTTTGA
* *
289502 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
289524 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
289545 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:295145 original size:13 final size:13
Alignment explanation
Indices: 295127--295156 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
295117 ATAATTCATC
*
295127 ATGTATCGATACA
1 ATGTATCAATACA
295140 ATGTATCAATACA
1 ATGTATCAATACA
295153 ATGT
1 ATGT
295157 GCCATGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:295250 original size:19 final size:20
Alignment explanation
Indices: 295206--295251 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
295196 TAGTTTTATG
* * *
295206 TATCGATACAATTATCCATG
1 TATCGATACAATGATACATA
295226 TATCGATACAATGA-ACATA
1 TATCGATACAATGATACATA
295245 TATCGAT
1 TATCGAT
295252 GTATTGTATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (20 bp):
TATCGATACAATGATACATA
Found at i:295812 original size:16 final size:16
Alignment explanation
Indices: 295781--295823 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
295771 AACTAATCCG
*
295781 AACCCGAAAATGACTCA
1 AACCC-AAAATAACTCA
*
295798 AACCCAAAATAACTCG
1 AACCCAAAATAACTCA
*
295814 AATCCAAAAT
1 AACCCAAAAT
295824 GATCCGAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.51, C:0.28, G:0.07, T:0.14
Consensus pattern (16 bp):
AACCCAAAATAACTCA
Found at i:300572 original size:18 final size:18
Alignment explanation
Indices: 300522--300572 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
300512 AAACAAAATT
* *
300522 TAATTAGTTATATAATATG
1 TAATTA-TTATTTAATATA
*
300541 TGATTA-TATGTTAATATA
1 TAATTATTAT-TTAATATA
300559 TAATTATTATTTAA
1 TAATTATTATTTAA
300573 AAATAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
17 3 0.12
18 15 0.58
19 8 0.31
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (18 bp):
TAATTATTATTTAATATA
Found at i:301437 original size:54 final size:53
Alignment explanation
Indices: 301377--301482 Score: 122
Period size: 53 Copynumber: 2.0 Consensus size: 53
301367 AAATCTAAAC
* * ** *
301377 CTAAAATTACTCGAACCCAATTTAACTTGAATGTTAAACCCAATTAACTTGAAT
1 CTAAAATGACCCGAACCCAA-TTAACCCGAACGTTAAACCCAATTAACTTGAAT
* * * *
301431 CTAAAATGGCCCGAACCCGATTAACCCGAGCGTTAAACCCAATTGACTTGAA
1 CTAAAATGACCCGAACCCAATTAACCCGAACGTTAAACCCAATTAACTTGAA
301483 CCCGAAATGA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
53 27 0.63
54 16 0.37
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (53 bp):
CTAAAATGACCCGAACCCAATTAACCCGAACGTTAAACCCAATTAACTTGAAT
Found at i:301548 original size:32 final size:32
Alignment explanation
Indices: 301474--301557 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
301464 TAAACCCAAT
* *
301474 TGACTTGAACCCGAAATGACCTGAATCCGAAA
1 TGACCTGAACCCGAAATGACCAGAATCCGAAA
** * **
301506 CAACCCGAACCCGAAATGACCAGAATTTGAAA
1 TGACCTGAACCCGAAATGACCAGAATCCGAAA
*
301538 TGACCTGAACCCAAAATGAC
1 TGACCTGAACCCGAAATGAC
301558 TTGAACCAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.40, C:0.27, G:0.17, T:0.15
Consensus pattern (32 bp):
TGACCTGAACCCGAAATGACCAGAATCCGAAA
Found at i:301569 original size:16 final size:16
Alignment explanation
Indices: 301535--301605 Score: 88
Period size: 16 Copynumber: 4.4 Consensus size: 16
301525 CCAGAATTTG
*
301535 AAATGACCTGAACCCA
1 AAATGACTTGAACCCA
*
301551 AAATGACTTGAACCAA
1 AAATGACTTGAACCCA
* ***
301567 AAATGACTCGAATTTA
1 AAATGACTTGAACCCA
301583 AAATGACTTGAACCCA
1 AAATGACTTGAACCCA
301599 AAATGAC
1 AAATGAC
301606 CCGAACCGAA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.20
Consensus pattern (16 bp):
AAATGACTTGAACCCA
Found at i:301571 original size:32 final size:32
Alignment explanation
Indices: 301535--301618 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
301525 CCAGAATTTG
301535 AAATGACCTGAACCCAAAATGACTTGAACCAA
1 AAATGACCTGAACCCAAAATGACTTGAACCAA
*** *
301567 AAATGA-CTCGAATTTAAAATGACTTGAACCCA
1 AAATGACCT-GAACCCAAAATGACTTGAACCAA
* *
301599 AAATGACCCGAACCGAAAAT
1 AAATGACCTGAACCCAAAAT
301619 AACCGAAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
31 2 0.05
32 39 0.93
33 1 0.02
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (32 bp):
AAATGACCTGAACCCAAAATGACTTGAACCAA
Found at i:301611 original size:16 final size:16
Alignment explanation
Indices: 301474--301618 Score: 85
Period size: 16 Copynumber: 9.1 Consensus size: 16
301464 TAAACCCAAT
* *
301474 TGACTTGAACCCGAAA
1 TGACCTGAACCCAAAA
* *
301490 TGACCTGAATCCGAAA
1 TGACCTGAACCCAAAA
** * *
301506 CAACCCGAACCCGAAA
1 TGACCTGAACCCAAAA
* ****
301522 TGACCAGAATTTGAAA
1 TGACCTGAACCCAAAA
301538 TGACCTGAACCCAAAA
1 TGACCTGAACCCAAAA
* *
301554 TGACTTGAACCAAAAA
1 TGACCTGAACCCAAAA
***
301570 TGA-CTCGAATTTAAAA
1 TGACCT-GAACCCAAAA
*
301586 TGACTTGAACCCAAAA
1 TGACCTGAACCCAAAA
* *
301602 TGACCCGAACCGAAAA
1 TGACCTGAACCCAAAA
301618 T
1 T
301619 AACCGAAAAT
Statistics
Matches: 97, Mismatches: 30, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
15 1 0.01
16 95 0.98
17 1 0.01
ACGTcount: A:0.43, C:0.25, G:0.15, T:0.17
Consensus pattern (16 bp):
TGACCTGAACCCAAAA
Found at i:301612 original size:48 final size:48
Alignment explanation
Indices: 301487--301618 Score: 149
Period size: 48 Copynumber: 2.8 Consensus size: 48
301477 CTTGAACCCG
* * ** ** *
301487 AAATGACCTGAATCCGAAACAACCCGAACCCGAAATGACCAGAATTTG
1 AAATGACCTGAACCCAAAATGACCCGAACCAAAAATGACCAGAATTTA
**
301535 AAATGACCTGAACCCAAAATGACTTGAACCAAAAATGACTC-GAATTTA
1 AAATGACCTGAACCCAAAATGACCCGAACCAAAAATGAC-CAGAATTTA
* *
301583 AAATGACTTGAACCCAAAATGACCCGAACCGAAAAT
1 AAATGACCTGAACCCAAAATGACCCGAACCAAAAAT
301619 AACCGAAAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
48 69 0.99
49 1 0.01
ACGTcount: A:0.45, C:0.24, G:0.14, T:0.17
Consensus pattern (48 bp):
AAATGACCTGAACCCAAAATGACCCGAACCAAAAATGACCAGAATTTA
Found at i:307624 original size:36 final size:36
Alignment explanation
Indices: 307579--307651 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
307569 AGTACTTACT
307579 TTTTGCTTATAATTCATTAAACTCATAATAGAAAAC
1 TTTTGCTTATAATTCATTAAACTCATAATAGAAAAC
307615 TTTTGCTTATAATTCATTAAACTCATAATAGAAAAC
1 TTTTGCTTATAATTCATTAAACTCATAATAGAAAAC
307651 T
1 T
307652 ATCTAGCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (36 bp):
TTTTGCTTATAATTCATTAAACTCATAATAGAAAAC
Found at i:309238 original size:21 final size:21
Alignment explanation
Indices: 309212--309253 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
309202 TAAGCACCTG
*
309212 GGTGCACAATTGAGGCTTACA
1 GGTGCACAAGTGAGGCTTACA
*
309233 GGTGCATAAGTGAGGCTTACA
1 GGTGCACAAGTGAGGCTTACA
309254 CCTTAATGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.24
Consensus pattern (21 bp):
GGTGCACAAGTGAGGCTTACA
Found at i:315445 original size:52 final size:52
Alignment explanation
Indices: 315364--315484 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
315354 TGAAAAGTTA
*
315364 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
315416 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
315468 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
315485 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:315497 original size:52 final size:51
Alignment explanation
Indices: 315364--315504 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
315354 TGAAAAGTTA
315364 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
315416 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
315468 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
315505 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:315511 original size:13 final size:13
Alignment explanation
Indices: 315493--315517 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
315483 CAAAGATCAG
315493 TGTATCGATACAA
1 TGTATCGATACAA
315506 TGTATCGATACA
1 TGTATCGATACA
315518 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:315605 original size:13 final size:13
Alignment explanation
Indices: 315587--315611 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
315577 AAAAAAAATA
315587 TGTATCGATACAT
1 TGTATCGATACAT
315600 TGTATCGATACA
1 TGTATCGATACA
315612 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:317559 original size:21 final size:22
Alignment explanation
Indices: 317535--317578 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
317525 TTTTTGCATG
*
317535 AAAATTTTATTTTAATT-CTTT
1 AAAATTTTATTTCAATTCCTTT
317556 AAAATTTTATTTCAATTCCTTT
1 AAAATTTTATTTCAATTCCTTT
317578 A
1 A
317579 TCACTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (22 bp):
AAAATTTTATTTCAATTCCTTT
Found at i:323623 original size:18 final size:17
Alignment explanation
Indices: 323591--323627 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
323581 TTATAATTAG
*
323591 TAGATAATTTTATTTAT
1 TAGATAATATTATTTAT
323608 TAGATGAATATTATTTAT
1 TAGAT-AATATTATTTAT
323626 TA
1 TA
323628 AAATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (17 bp):
TAGATAATATTATTTAT
Found at i:326051 original size:119 final size:119
Alignment explanation
Indices: 325837--326061 Score: 353
Period size: 119 Copynumber: 1.9 Consensus size: 119
325827 AGTTAGTATG
* * * * * *
325837 AAAAGAGGTGGTAAGTCAAATTGATATAAGAGCTGATTCTTGAATTAAGGAGAGAGATTTGTTTT
1 AAAAGAGATGGTAAGTCAAATTGATATAAGAGCTAATTATTGAATCAAGGAGAGAGATTTATTTG
*
325902 GTGAGAAAATAAGTTCTTTAAAGTTTTCTATAGCTATTGCTTAAGAAGCATATA
66 GTGAGAAAATAAGTTCTTTAAAGTTCTCTATAGCTATTGCTTAAGAAGCATATA
* *
325956 AAAAGAGATGGCT-AGTCAAATTGATATAAGAGTTAATTATTGGATCAAGGAGAGAGATTTATTT
1 AAAAGAGATGG-TAAGTCAAATTGATATAAGAGCTAATTATTGAATCAAGGAGAGAGATTTATTT
326020 GGTGAGAAAATAAGTTCTTTAAAGTTCTCTATAGCTATTGCT
65 GGTGAGAAAATAAGTTCTTTAAAGTTCTCTATAGCTATTGCT
326062 CAAAGAGTAA
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
119 95 0.99
120 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (119 bp):
AAAAGAGATGGTAAGTCAAATTGATATAAGAGCTAATTATTGAATCAAGGAGAGAGATTTATTTG
GTGAGAAAATAAGTTCTTTAAAGTTCTCTATAGCTATTGCTTAAGAAGCATATA
Found at i:336850 original size:16 final size:17
Alignment explanation
Indices: 336829--336863 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
336819 ATAGATAAAT
*
336829 TTACTCTT-TTTTTTTA
1 TTACTCTTATTTTTCTA
336845 TTACTCTTATTTTTCTA
1 TTACTCTTATTTTTCTA
336862 TT
1 TT
336864 TTATATTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (17 bp):
TTACTCTTATTTTTCTA
Done.