Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 126 of 226
Found at i:42435380 original size:11 final size:11
Alignment explanation
Indices: 42435364--42435389 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42435354 TGGAAGGAAA
42435364 AGCATTGGACT
1 AGCATTGGACT
42435375 AGCATTGGACT
1 AGCATTGGACT
42435386 AGCA
1 AGCA
42435390 CCACTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (11 bp):
AGCATTGGACT
Found at i:42442606 original size:43 final size:43
Alignment explanation
Indices: 42442320--42442592 Score: 395
Period size: 43 Copynumber: 6.3 Consensus size: 43
42442310 TTATGTAAAA
*
42442320 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACACAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
*
42442363 AAACGCCGCTACTAAAGAACATGTTCTTTAGCGGCGC-TTACCCAC
1 AAACGCCG---CTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
* *
42442408 AAATGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
*
42442451 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
* * *
42442494 AAACGCCGCTAAAGAGCATGACCTTTAGCGGCACTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
* ***
42442537 AAACGCCGCTAAAGAACTTGATCTTTAGCGGCGCTTTTGTCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
*
42442580 AAATGCCGCTAAA
1 AAACGCCGCTAAA
42442593 AGTACGGTTC
Statistics
Matches: 206, Mismatches: 20, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
42 24 0.12
43 143 0.69
45 14 0.07
46 25 0.12
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
Found at i:42443549 original size:2 final size:2
Alignment explanation
Indices: 42443544--42443568 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42443534 AATAAAAAAC
42443544 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
42443569 TGCAAAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42446343 original size:148 final size:148
Alignment explanation
Indices: 42446130--42446624 Score: 814
Period size: 148 Copynumber: 3.3 Consensus size: 148
42446120 ATGGCGCAAT
* ** * *
42446130 TTTTTTAAACTAAAATTATTTTTTTGTGGCGTTTTTTATAAAAATACCGTTATTACTCACTTTTT
1 TTTTTTAAAATAAAATTA-TTTTTTGTGGCGTTTTTTATAAAAACGCCGCTATTACTCACCTTTT
* * * *
42446195 GCGGTGTTTT-TATGTAAAACGCCGCAAAAAATTATTTCATTTGGAATAAAACGACACTGTTTTG
65 GCGGCGTTTTACAT-AAAAACGCCGCAAAAAATTATTACATTTGGAATAAAACGACACTGTTTTG
*
42446259 CTATGCTAAAAATCTCGTTA
129 CTATGCTAAAAATCTCGCTA
*
42446279 TTTTTTAAAATAAAATTATTTTTTGTGGCGTTTTTTATAAAAACGCCGCTATTTCTCACCTTTTG
1 TTTTTTAAAATAAAATTATTTTTTGTGGCGTTTTTTATAAAAACGCCGCTATTACTCACCTTTTG
42446344 CGGCGTTTTACATAAAAACGCCGCAAAAAATTATTACATTTGGAATAAAACGACACTGTTTTGCT
66 CGGCGTTTTACATAAAAACGCCGCAAAAAATTATTACATTTGGAATAAAACGACACTGTTTTGCT
42446409 ATGCTAAAAATCTCGCTA
131 ATGCTAAAAATCTCGCTA
*
42446427 TTTTTTAAAATAAAATTATTTTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTCACCTTTTG
1 TTTTTTAAAATAAAATTATTTTTTGTGGCGTTTTTTATAAAAACGCCGCTATTACTCACCTTTTG
*
42446492 CGGCGTTTTACATAAAAACGCCGCAAAAGATTATTACATTTGGAATAAAACGACACTGTTTTGCT
66 CGGCGTTTTACATAAAAACGCCGCAAAAAATTATTACATTTGGAATAAAACGACACTGTTTTGCT
42446557 ATGCTAAAAATCTCGCTA
131 ATGCTAAAAATCTCGCTA
*
42446575 TTTTTTAAAGA-AAATTTATTTTTTGTGGCGTTTTTTTATAAAAACGCCGC
1 TTTTTTAAA-ATAAAATTATTTTTTGTGGCG-TTTTTTATAAAAACGCCGC
42446625 AAAAAATTAT
Statistics
Matches: 329, Mismatches: 14, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
148 290 0.88
149 39 0.12
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (148 bp):
TTTTTTAAAATAAAATTATTTTTTGTGGCGTTTTTTATAAAAACGCCGCTATTACTCACCTTTTG
CGGCGTTTTACATAAAAACGCCGCAAAAAATTATTACATTTGGAATAAAACGACACTGTTTTGCT
ATGCTAAAAATCTCGCTA
Found at i:42447093 original size:14 final size:14
Alignment explanation
Indices: 42447074--42447137 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
42447064 ACCCTTGAAT
42447074 CCCTAAATCCTAAC
1 CCCTAAATCCTAAC
42447088 CCCTAAATCACTAA-
1 CCCTAAATC-CTAAC
* * *
42447102 CTCTTAACCCATAAC
1 CCCTAAATCC-TAAC
* *
42447117 CCCTAACTACTAAC
1 CCCTAAATCCTAAC
42447131 CCCTAAA
1 CCCTAAA
42447138 CCTTAAATCC
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
13 1 0.03
14 28 0.74
15 9 0.24
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.22
Consensus pattern (14 bp):
CCCTAAATCCTAAC
Found at i:42447390 original size:7 final size:7
Alignment explanation
Indices: 42447378--42447430 Score: 63
Period size: 7 Copynumber: 7.4 Consensus size: 7
42447368 CACTAGTTAA
42447378 CCTAAAC
1 CCTAAAC
42447385 CCTAAAC
1 CCTAAAC
*
42447392 CATAAA-
1 CCTAAAC
*
42447398 CTTAAAC
1 CCTAAAC
42447405 CCTAAAAC
1 CCT-AAAC
42447413 CCTAAAC
1 CCTAAAC
42447420 CCATAAAC
1 CC-TAAAC
42447428 CCT
1 CCT
42447431 TAATACATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
6 5 0.12
7 21 0.52
8 14 0.35
ACGTcount: A:0.45, C:0.38, G:0.00, T:0.17
Consensus pattern (7 bp):
CCTAAAC
Found at i:42447420 original size:15 final size:15
Alignment explanation
Indices: 42447381--42447430 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
42447371 TAGTTAACCT
*
42447381 AAACCCTAAACCAT-
1 AAACCCTAAACCCTA
*
42447395 AAA-CTTAAACCCTA
1 AAACCCTAAACCCTA
42447409 AAACCCTAAACCC-A
1 AAACCCTAAACCCTA
42447423 TAAACCCT
1 -AAACCCT
42447431 TAATACATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 8 0.27
14 7 0.23
15 15 0.50
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (15 bp):
AAACCCTAAACCCTA
Found at i:42447454 original size:21 final size:21
Alignment explanation
Indices: 42447380--42447509 Score: 84
Period size: 21 Copynumber: 6.0 Consensus size: 21
42447370 CTAGTTAACC
* *
42447380 TAAACCCTAAACCATAAAC-T
1 TAAACCTTAAACCATAACCTT
* * **
42447400 TAAACCCTAAAACCCTAAACCCA
1 TAAA-CCTTAAACCAT-AACCTT
42447423 TAAACCCTTAATA-CATAACCTT
1 TAAA-CCTTAA-ACCATAACCTT
** *
42447445 TAAACCTTAAACCCCAGCCTT
1 TAAACCTTAAACCATAACCTT
* *
42447466 TAAACCATAAACCATAACCTC
1 TAAACCTTAAACCATAACCTT
*
42447487 TAAACCTATAATCCATAAACCTT
1 TAAACCT-TAAACCAT-AACCTT
42447510 AAAATGGTAA
Statistics
Matches: 83, Mismatches: 20, Indels: 11
0.73 0.18 0.10
Matches are distributed among these distances:
20 5 0.06
21 42 0.51
22 18 0.22
23 17 0.20
24 1 0.01
ACGTcount: A:0.44, C:0.32, G:0.01, T:0.23
Consensus pattern (21 bp):
TAAACCTTAAACCATAACCTT
Found at i:42447793 original size:41 final size:41
Alignment explanation
Indices: 42447731--42447812 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
42447721 TAAATTATTT
*
42447731 TAAATCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
**
42447772 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
42447813 AAAATCCCCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.27, C:0.32, G:0.21, T:0.21
Consensus pattern (41 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
Found at i:42448055 original size:114 final size:114
Alignment explanation
Indices: 42447748--42448341 Score: 953
Period size: 113 Copynumber: 5.2 Consensus size: 114
42447738 CTGAGCATTA
42447748 GCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
1 GCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
* *
42447813 AAAATCCCCGAAAGCTCACAAAACGGTGTCGTTGGGCTTAGGTTTTTTT
66 TAAATCCCCGAAAGCTCAAAAAACGGTGTCGTTGGGCTTAGGTTTTTTT
* * * *
42447862 GCGGCGCTTTCCCAAAAATGCTGC-AAAGCCCTGATCATTAGCGGCGCTTTCTTAAAAACGCTGC
1 GCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
* * *
42447926 TAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTTGGCTTAGGTTTTTTT
66 TAAATCCCCGAAAGCTCAAAAAACGGTGTCGTTGGGCTTAGGTTTTTTT
* *
42447975 GCGGCGCTTTCCCAAAAACGCCGCTAAAGACTTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
1 GCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
* * *
42448040 TAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
66 TAAATCCCCGAAAGCTCAAAAAACGGTGTCGTTGGGCTTAGGTTTTTTT
* *
42448089 GCGGCGC-TTCACCAAAAACGCCGCTAAAGACCTGAGCATTCGCGGCGCTTTCTTAAAAACGCCG
1 GCGGCGCTTTC-CCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCG
* *
42448153 CTAAAT-CCCGAAAGTTCAAAAAACGGTGTCGTTTGGCTTAGGTTTTTTT
65 CTAAATCCCCGAAAGCTCAAAAAACGGTGTCGTTGGGCTTAGGTTTTTTT
*
42448202 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
1 GCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
42448267 TAAATCCCCGAAAGCTCAAAAAACGGTGTCGTTGGGCTTAGG-TTTTTT
66 TAAATCCCCGAAAGCTCAAAAAACGGTGTCGTTGGGCTTAGGTTTTTTT
***
42448315 GCGGCGCTTTCTGGAAAACGCCGCTAA
1 GCGGCGCTTTCCCAAAAACGCCGCTAA
42448342 TGCCTATTTT
Statistics
Matches: 446, Mismatches: 30, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
113 240 0.54
114 206 0.46
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (114 bp):
GCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
TAAATCCCCGAAAGCTCAAAAAACGGTGTCGTTGGGCTTAGGTTTTTTT
Found at i:42448165 original size:227 final size:226
Alignment explanation
Indices: 42447748--42448323 Score: 958
Period size: 227 Copynumber: 2.5 Consensus size: 226
42447738 CTGAGCATTA
42447748 GCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
1 GCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
* *
42447813 AAAATCCCCGAAAGCTCACAAAACGGTGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAA
66 TAAATCCCCGAAAGCTCAAAAAACGGTGTCGTTGGGCTTAGGTTTTTTTGCGGCGC-TTCCCAAA
* * * * *
42447878 AATGCTGCAAAGCCCTGATCATTAGCGGCGCTTTCTTAAAAACGCTGCTAAATCCCCGAAAGCTC
130 AACGCCGCAAAGACCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTC
*
42447943 AGAAAACGGCGTCGTTTGGCTTAGGTTTTTTT
195 AAAAAACGGCGTCGTTTGGCTTAGGTTTTTTT
* *
42447975 GCGGCGCTTTCCCAAAAACGCCGCTAAAGACTTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
1 GCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
* * *
42448040 TAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTCACCAAA
66 TAAATCCCCGAAAGCTCAAAAAACGGTGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTC-CCAAA
* *
42448105 AACGCCGCTAAAGACCTGAGCATTCGCGGCGCTTTCTTAAAAACGCCGCTAAAT-CCCGAAAGTT
130 AACGCCGC-AAAGACCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCT
*
42448169 CAAAAAACGGTGTCGTTTGGCTTAGGTTTTTTT
194 CAAAAAACGGCGTCGTTTGGCTTAGGTTTTTTT
*
42448202 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
1 GCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
42448267 TAAATCCCCGAAAGCTCAAAAAACGGTGTCGTTGGGCTTAGG-TTTTTTGCGGCGCTT
66 TAAATCCCCGAAAGCTCAAAAAACGGTGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTT
42448324 TCTGGAAAAC
Statistics
Matches: 326, Mismatches: 21, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
226 18 0.06
227 267 0.82
228 41 0.13
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (226 bp):
GCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
TAAATCCCCGAAAGCTCAAAAAACGGTGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTCCCAAAA
ACGCCGCAAAGACCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCA
AAAAACGGCGTCGTTTGGCTTAGGTTTTTTT
Found at i:42448756 original size:22 final size:22
Alignment explanation
Indices: 42448730--42448783 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
42448720 ACAAAGTTGC
42448730 AGAG-AAGAACAAGAAAAATTAG
1 AGAGAAAGAA-AAGAAAAATTAG
*
42448752 AGAGAAAGAAGAGAAAAATTAG
1 AGAGAAAGAAAAGAAAAATTAG
*
42448774 AGAAAAAGAA
1 AGAGAAAGAA
42448784 GAACAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 24 0.83
23 5 0.17
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (22 bp):
AGAGAAAGAAAAGAAAAATTAG
Found at i:42448775 original size:11 final size:11
Alignment explanation
Indices: 42448741--42448780 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
42448731 GAGAAGAACA
42448741 AGAAAAATTAG
1 AGAAAAATTAG
* **
42448752 AGAGAAAGAAG
1 AGAAAAATTAG
42448763 AGAAAAATTAG
1 AGAAAAATTAG
42448774 AGAAAAA
1 AGAAAAA
42448781 GAAGAACAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.10
Consensus pattern (11 bp):
AGAAAAATTAG
Found at i:42448784 original size:22 final size:22
Alignment explanation
Indices: 42448741--42448785 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
42448731 GAGAAGAACA
*
42448741 AGAAAAATTAGAGAGAAAGAAG
1 AGAAAAATTAGAGAAAAAGAAG
42448763 AGAAAAATTAGAGAAAAAGAAG
1 AGAAAAATTAGAGAAAAAGAAG
42448785 A
1 A
42448786 ACAATAATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (22 bp):
AGAAAAATTAGAGAAAAAGAAG
Found at i:42451153 original size:18 final size:19
Alignment explanation
Indices: 42451132--42451174 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
42451122 AATAATAAAT
42451132 TTAAAT-TTTATATTAATA
1 TTAAATATTTATATTAATA
*
42451150 TT-AATATTTCTATTAATA
1 TTAAATATTTATATTAATA
42451168 TTAAATA
1 TTAAATA
42451175 AATATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 3 0.14
18 15 0.68
19 4 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAAATATTTATATTAATA
Found at i:42459194 original size:27 final size:27
Alignment explanation
Indices: 42459155--42459432 Score: 239
Period size: 27 Copynumber: 10.4 Consensus size: 27
42459145 GCTTGGGCCA
*
42459155 AAAATTTACTGAAATACCCTCG-AGGAAT
1 AAAA-TTACTGAAATACCCTCGAAGG-GT
*
42459183 AAAATTACTGAAATACCCTTGAAGGGT
1 AAAATTACTGAAATACCCTCGAAGGGT
*
42459210 AAAATTAC-CACAATACCCTCGAAGGGT
1 AAAATTACTGA-AATACCCTCGAAGGGT
* * * *
42459237 AAAATTACTAAAATAACTTCGAATGGT
1 AAAATTACTGAAATACCCTCGAAGGGT
*
42459264 GAAATTA-TCGAAATACCCTCGAAGGGT
1 AAAATTACT-GAAATACCCTCGAAGGGT
* * *
42459291 ---GTTA-TCAAAATACCCCCGAAGGGT
1 AAAATTACT-GAAATACCCTCGAAGGGT
* * *
42459315 AATATTACCGAAATACCCTTGAAGGGT
1 AAAATTACTGAAATACCCTCGAAGGGT
** *
42459342 AAAATTACCAAAATAACCTCGAAGGGT
1 AAAATTACTGAAATACCCTCGAAGGGT
** *
42459369 AAAATTACCAAAATACCC-CTGAAAGGT
1 AAAATTACTGAAATACCCTC-GAAGGGT
* *
42459396 AAAATTATTGAAATACCCTCGAGGGGT
1 AAAATTACTGAAATACCCTCGAAGGGT
*
42459423 AAAATGACTG
1 AAAATTACTG
42459433 TTATATCCCA
Statistics
Matches: 206, Mismatches: 34, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
24 21 0.10
26 3 0.01
27 173 0.84
28 9 0.04
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTCGAAGGGT
Found at i:42459301 original size:24 final size:24
Alignment explanation
Indices: 42459268--42459314 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
42459258 AATGGTGAAA
* *
42459268 TTATCGAAATACCCTCGAAGGGTG
1 TTATCAAAATACCCCCGAAGGGTG
42459292 TTATCAAAATACCCCCGAAGGGT
1 TTATCAAAATACCCCCGAAGGGT
42459315 AATATTACCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (24 bp):
TTATCAAAATACCCCCGAAGGGTG
Found at i:42459375 original size:105 final size:105
Alignment explanation
Indices: 42459193--42459386 Score: 282
Period size: 105 Copynumber: 1.8 Consensus size: 105
42459183 AAAATTACTG
** * *
42459193 AAATACCCTTGAAGGGTAAAATTACCACAATACCCTCGAAGGGTAAAATTACTAAAATAACTTCG
1 AAATACCCCCGAAGGGTAAAATTACCACAATACCCTCGAAGGGTAAAATTACCAAAATAACCTCG
* * * *
42459258 AATGGTGAAATTATCGAAATACCCTCGAAGGGTGTTATCA
66 AAGGGTAAAATTACCAAAATACCCTCGAAGGGTGTTATCA
* *
42459298 AAATACCCCCGAAGGGTAATATTACCGA-AATACCCTTGAAGGGTAAAATTACCAAAATAACCTC
1 AAATACCCCCGAAGGGTAAAATTACC-ACAATACCCTCGAAGGGTAAAATTACCAAAATAACCTC
42459362 GAAGGGTAAAATTACCAAAATACCC
65 GAAGGGTAAAATTACCAAAATACCC
42459387 CTGAAAGGTA
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
105 77 0.99
106 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (105 bp):
AAATACCCCCGAAGGGTAAAATTACCACAATACCCTCGAAGGGTAAAATTACCAAAATAACCTCG
AAGGGTAAAATTACCAAAATACCCTCGAAGGGTGTTATCA
Found at i:42459638 original size:25 final size:25
Alignment explanation
Indices: 42459610--42459684 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
42459600 TTACCACAAA
*
42459610 TACTATTACTGGTAGCTTTCTGCAT
1 TACTATTACTGGCAGCTTTCTGCAT
** * * *
42459635 TACTAAAATTGGCAGCTCTACTGCGT
1 TACTATTACTGGCAGCT-TTCTGCAT
42459661 TACTATTACTGGCAGCTTTACTGC
1 TACTATTACTGGCAGCTTT-CTGC
42459685 GATATTGGTG
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
25 14 0.37
26 24 0.63
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (25 bp):
TACTATTACTGGCAGCTTTCTGCAT
Found at i:42459835 original size:27 final size:27
Alignment explanation
Indices: 42459792--42459892 Score: 78
Period size: 30 Copynumber: 3.5 Consensus size: 27
42459782 TTGCATTTGT
*
42459792 ACTGATTACTGTTTTGGGCTAAGGCTCC-
1 ACTG-TTACTGTATTGGGCTAAGGC-CCA
*
42459820 ACTGTTACTGTATTGGCCTAAGGCCCA
1 ACTGTTACTGTATTGGGCTAAGGCCCA
* *
42459847 TACTCTGTTACTGTAATGGGCTATGGCCAACA
1 -A--CTGTTACTGTATTGGGCTAAGGCC--CA
*
42459879 CACTGCTACTGTAT
1 -ACTGTTACTGTAT
42459893 AAGGCTCAGG
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
26 2 0.03
27 18 0.31
28 5 0.08
30 31 0.53
32 3 0.05
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (27 bp):
ACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:42459889 original size:30 final size:30
Alignment explanation
Indices: 42459819--42459891 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
42459809 GCTAAGGCTC
* * *
42459819 CACTGTTACTGTATTGGCCTAAGGCCCATA
1 CACTGTTACTGTAATGGCCTAAGGCCAACA
* * *
42459849 CTCTGTTACTGTAATGGGCTATGGCCAACA
1 CACTGTTACTGTAATGGCCTAAGGCCAACA
*
42459879 CACTGCTACTGTA
1 CACTGTTACTGTA
42459892 TAAGGCTCAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (30 bp):
CACTGTTACTGTAATGGCCTAAGGCCAACA
Found at i:42466937 original size:27 final size:27
Alignment explanation
Indices: 42466903--42467177 Score: 311
Period size: 27 Copynumber: 10.2 Consensus size: 27
42466893 GCTTGGGTAG
*
42466903 AAAATTACCGAAATACCCTCGAGGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
**
42466930 AAAATTACTAAAATACCCTCGAAGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
*
42466957 AAAATTACCGATATACCCTCGAAGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
* * *
42466984 AAAATTATCGAAATATCCTCGAATGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
* ** **
42467011 GAAATTATTGAAATACCCTTAAAGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
* *
42467038 GAAATTACTGAAATACCCTCGAAGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
* * *
42467065 GAAATAACCGAAATACCCCCGAAGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
42467092 AAAATTACCGAAATACCC-CTGAAGGGT
1 AAAATTACCGAAATACCCTC-GAAGGGT
* * *
42467119 AAAATTACCAAAATACCAC-CAAAAGGT
1 AAAATTACCGAAATACC-CTCGAAGGGT
* * *
42467146 AAAAGTACCGAAATGCCCTTGAAGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
42467173 AAAAT
1 AAAAT
42467178 AACTGTTATA
Statistics
Matches: 211, Mismatches: 34, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
26 2 0.01
27 207 0.98
28 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (27 bp):
AAAATTACCGAAATACCCTCGAAGGGT
Found at i:42467426 original size:26 final size:26
Alignment explanation
Indices: 42467359--42467427 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 26
42467349 TTGCCACAAA
* * *
42467359 TACTGTTACTGGCAGCTTTGCTGCGT
1 TACTGTTACTGACAGCTCTACTGCGT
* **
42467385 TAGTGAAACT-AGCAGCTCTACTGCGT
1 TACTGTTACTGA-CAGCTCTACTGCGT
42467411 TACTGTTACTGACAGCT
1 TACTGTTACTGACAGCT
42467428 TTGTTGCATT
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
26 31 0.97
27 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (26 bp):
TACTGTTACTGACAGCTCTACTGCGT
Found at i:42467612 original size:27 final size:28
Alignment explanation
Indices: 42467574--42467680 Score: 90
Period size: 30 Copynumber: 3.8 Consensus size: 28
42467564 TTGTACTAAC
* *
42467574 TACTGTTTTGGGTTAAGGCCCCAC-TGT
1 TACTGTATTGGGCTAAGGCCCCACTTGT
* *
42467601 TACTGTATTGGGCTAAGTCCACACTTTGT
1 TACTGTATTGGGCTAAGGCCCCAC-TTGT
* * * *
42467630 TACTGTAATGGGCTATGGCCCACACACTGC
1 TACTGTATTGGGCTAAGGCCC-CAC-TTGT
* *
42467660 TACTGTATAGGGCTCAGGCCC
1 TACTGTATTGGGCTAAGGCCC
42467681 AGACTGATTC
Statistics
Matches: 62, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
27 20 0.32
29 20 0.32
30 22 0.35
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCCCACTTGT
Found at i:42467664 original size:30 final size:29
Alignment explanation
Indices: 42467595--42467666 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
42467585 GTTAAGGCCC
* *
42467595 CACTGTTACTGTATTGGGCTAAGTCCACA
1 CACTGTTACTGTAATGGGCTAAGCCCACA
** *
42467624 CTTTGTTACTGTAATGGGCTATGGCCCACA
1 CACTGTTACTGTAATGGGCTA-AGCCCACA
*
42467654 CACTGCTACTGTA
1 CACTGTTACTGTA
42467667 TAGGGCTCAG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (29 bp):
CACTGTTACTGTAATGGGCTAAGCCCACA
Found at i:42475252 original size:11 final size:11
Alignment explanation
Indices: 42475214--42475252 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
42475204 TGAGAATGAA
*
42475214 TGAGGAATGCT
1 TGAGGGATGCT
*
42475225 TGAGGGAAGCT
1 TGAGGGATGCT
42475236 TGAGGGATGCT
1 TGAGGGATGCT
42475247 TGAGGG
1 TGAGGG
42475253 TTGATTAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.23, C:0.08, G:0.46, T:0.23
Consensus pattern (11 bp):
TGAGGGATGCT
Found at i:42485930 original size:11 final size:11
Alignment explanation
Indices: 42485906--42485947 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
42485896 TGAGAATGAA
* *
42485906 TGAGGAATGAT
1 TGAGGGATGCT
42485917 TGAGGGATGCT
1 TGAGGGATGCT
42485928 TGAGGGATGCT
1 TGAGGGATGCT
42485939 TGAGGGATG
1 TGAGGGATG
42485948 ATTAATGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.24, C:0.05, G:0.45, T:0.26
Consensus pattern (11 bp):
TGAGGGATGCT
Found at i:42493767 original size:11 final size:13
Alignment explanation
Indices: 42493747--42493778 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
42493737 AATAAATTAA
42493747 TAAAATATCAT-T
1 TAAAATATCATAT
42493759 TAAAA-ATCATAT
1 TAAAATATCATAT
42493771 TAAAATAT
1 TAAAATAT
42493779 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:42497163 original size:13 final size:13
Alignment explanation
Indices: 42497145--42497169 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42497135 ACGGCCAGGC
42497145 ACACGGGCGTGTG
1 ACACGGGCGTGTG
42497158 ACACGGGCGTGT
1 ACACGGGCGTGT
42497170 AACCTTACTC
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:0.16, C:0.24, G:0.44, T:0.16
Consensus pattern (13 bp):
ACACGGGCGTGTG
Found at i:42499097 original size:23 final size:22
Alignment explanation
Indices: 42499067--42499153 Score: 104
Period size: 23 Copynumber: 3.9 Consensus size: 22
42499057 CGATAAGATC
42499067 TATTCTGTGATGCCTTTGTGGT
1 TATTCTGTGATGCCTTTGTGGT
*
42499089 GTATTCTGTGATGCCTTTGTGACT
1 -TATTCTGTGATGCCTTTGTG-GT
*
42499113 TATTCTATGATGCCTTTGTGG-
1 TATTCTGTGATGCCTTTGTGGT
* *
42499134 CATATCTGTGATGCTTTTGT
1 TAT-TCTGTGATGCCTTTGT
42499154 AGCATATTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
21 2 0.04
22 14 0.25
23 39 0.70
24 1 0.02
ACGTcount: A:0.13, C:0.15, G:0.24, T:0.48
Consensus pattern (22 bp):
TATTCTGTGATGCCTTTGTGGT
Found at i:42504593 original size:84 final size:82
Alignment explanation
Indices: 42504403--42504602 Score: 258
Period size: 83 Copynumber: 2.4 Consensus size: 82
42504393 AAGTTGGATG
* * * *
42504403 GCTTTAAGGTTGAATTGAAAATAAGAGAGTCGATTAACTTGAAATTTTTACCCTTTAAAGAGGAA
1 GCTTTAAGGTTG-ATTGAAACTAAGAGAGTCAATTAAATGGAAATTTTTACCCTTTAAAGAGGAA
* *
42504468 CTGAAGTTATAATTTAGA
65 CTCAAGTTACAATTTAGA
* * * *
42504486 GTTTTAAGGTTGCATTGAAACTAAAAGAGTCAATTAAATGGAAATTTAATTATCCTTTAATGAGG
1 GCTTTAAGGTTG-ATTGAAACTAAGAGAGTCAATTAAATGGAAATTT--TTACCCTTTAAAGAGG
42504551 AACTCAAGTTACAA-TTAGA
63 AACTCAAGTTACAATTTAGA
42504570 GCTTTAAGGTTGATTTGAAACTAAGAGAGTCAA
1 GCTTTAAGGTTGA-TTGAAACTAAGAGAGTCAA
42504603 ATTGAAAATT
Statistics
Matches: 101, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
83 41 0.41
84 34 0.34
85 26 0.26
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (82 bp):
GCTTTAAGGTTGATTGAAACTAAGAGAGTCAATTAAATGGAAATTTTTACCCTTTAAAGAGGAAC
TCAAGTTACAATTTAGA
Found at i:42504773 original size:82 final size:83
Alignment explanation
Indices: 42504671--42504845 Score: 237
Period size: 82 Copynumber: 2.1 Consensus size: 83
42504661 CTTAAAGAGT
*
42504671 GAAGTTAGAATTTAGAGCTTTAAGGTGGAATTGAAACTAAAAGAGTCAATTA-AGTTGAAAATTT
1 GAAGTTAGAACTTAGAGCTTTAAGGTGGAATTGAAACTAAAAGAGTCAATTACA-TTGAAAATTT
*
42504735 TA-CCTTTAATGAGGAACC
65 TATCCTATAATGAGGAACC
* * * * * *
42504753 GAAGTTAGAACTTAGAGCTTTAAGGTTGAATTGAAACTTAAAGATTGAATTACATTTAAAGTTTT
1 GAAGTTAGAACTTAGAGCTTTAAGGTGGAATTGAAACTAAAAGAGTCAATTACATTGAAAATTTT
*
42504818 ATCCTATAATGAGGAACT
66 ATCCTATAATGAGGAACC
*
42504836 GAAGCTAGAA
1 GAAGTTAGAA
42504846 TGAAGTTTCA
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
82 57 0.70
83 24 0.30
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (83 bp):
GAAGTTAGAACTTAGAGCTTTAAGGTGGAATTGAAACTAAAAGAGTCAATTACATTGAAAATTTT
ATCCTATAATGAGGAACC
Found at i:42504960 original size:115 final size:115
Alignment explanation
Indices: 42504755--42504961 Score: 274
Period size: 115 Copynumber: 1.8 Consensus size: 115
42504745 GAGGAACCGA
* * * * *
42504755 AGTTAGAACTTAGAGCTTTAAGGTTGAATTGAAACTTAAAGATTGAATTACATTTAAAGTTTTAT
1 AGTTAGAACTTAGAGCTTTAAGGTTGAATTGAAACTTAAAAATTGAATTACAATGAAAATTTTAA
**
42504820 CCTATAATGAGGAACTGAAGCTAGAATGAAGTTTCAAAAAAAAAAAAAAG
66 CCTATAACAAGGAACTGAAGCTAGAATGAAGTTTCAAAAAAAAAAAAAAG
* * *
42504870 AGTTAGAATTTGGAGCTTTAATGTTGAATTGAAACTTAAAAACTTG-ATTGA-AATGAAAATTTT
1 AGTTAGAACTTAGAGCTTTAAGGTTGAATTGAAACTTAAAAA-TTGAATT-ACAATGAAAATTTT
* *
42504933 AACCTTTAACAAGGAACTGAAGTTAGAAT
64 AACCTATAACAAGGAACTGAAGCTAGAAT
42504962 TTTTGAGGTT
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
115 74 0.95
116 4 0.05
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.31
Consensus pattern (115 bp):
AGTTAGAACTTAGAGCTTTAAGGTTGAATTGAAACTTAAAAATTGAATTACAATGAAAATTTTAA
CCTATAACAAGGAACTGAAGCTAGAATGAAGTTTCAAAAAAAAAAAAAAG
Found at i:42506604 original size:16 final size:16
Alignment explanation
Indices: 42506571--42506617 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
42506561 TGTTAATAAG
42506571 ATAATTAAATATAAAATT
1 ATAA-TAAATA-AAAATT
*
42506589 TTAATAAATAAAAATT
1 ATAATAAATAAAAATT
42506605 ATAA-AACATAAAA
1 ATAATAA-ATAAAA
42506618 TTGAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 2 0.08
16 15 0.58
17 6 0.23
18 3 0.12
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAATAAATAAAAATT
Found at i:42515742 original size:26 final size:26
Alignment explanation
Indices: 42515702--42515751 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
42515692 ACATATTTTC
42515702 TTAAAATTTTACTAG-GGATAAAATTG
1 TTAAAATTTTACTAGAGG-TAAAATTG
*
42515728 TTAAAATTTTGCTAGAGGTAAAAT
1 TTAAAATTTTACTAGAGGTAAAAT
42515752 AGGGATGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (26 bp):
TTAAAATTTTACTAGAGGTAAAATTG
Found at i:42517710 original size:33 final size:33
Alignment explanation
Indices: 42517667--42517796 Score: 111
Period size: 33 Copynumber: 3.9 Consensus size: 33
42517657 CATGCCATCT
*
42517667 ACAGAGAAAGTTTGTTGGGACAGTAAACACAAA
1 ACAGAGAAAGTCTGTTGGGACAGTAAACACAAA
* * * *
42517700 ACAGAAAAAGTTCTCTAGGG-TAGTAAACACAAA
1 ACAGAGAAAG-TCTGTTGGGACAGTAAACACAAA
* * * * * *
42517733 ATAGAGAAAGCCCGTTGGAAC-GATAAATATAAA
1 ACAGAGAAAGTCTGTTGGGACAG-TAAACACAAA
* *
42517766 ACAGAGATAGTCTGTTGGGACAATAAACACA
1 ACAGAGAAAGTCTGTTGGGACAGTAAACACA
42517797 GAGATAGTCT
Statistics
Matches: 70, Mismatches: 23, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
32 5 0.07
33 59 0.84
34 6 0.09
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.18
Consensus pattern (33 bp):
ACAGAGAAAGTCTGTTGGGACAGTAAACACAAA
Found at i:42517832 original size:27 final size:28
Alignment explanation
Indices: 42517761--42517819 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
42517751 AACGATAAAT
*
42517761 ATAAA-ACAGAGATAGTCTGTTGGGACA
1 ATAAACACAGAGATAGTCTGTCGGGACA
42517788 ATAAACACAGAGATAGTCTGTCGGGACA
1 ATAAACACAGAGATAGTCTGTCGGGACA
42517816 ATAA
1 ATAA
42517820 CACGGGGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 5 0.17
28 25 0.83
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (28 bp):
ATAAACACAGAGATAGTCTGTCGGGACA
Found at i:42519724 original size:58 final size:58
Alignment explanation
Indices: 42519628--42519807 Score: 242
Period size: 57 Copynumber: 3.1 Consensus size: 58
42519618 ATAGAAAAGG
* *
42519628 TGAAAATGGATAAATGAAAATTTATTTGGAAATGATTATGGTTTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAATGAAAA--CATTTGGAAATGATTATGGTTTTTCTCCAAAATGAAAA
* * *
42519688 TGAAAACGGAGAAATGAAAACATTTGAAAATGATTAT--TATTTCTTCCAAAATGAAAA
1 TGAAAATGGAGAAATGAAAACATTTGGAAATGATTATGGTTTTTC-TCCAAAATGAAAA
*
42519745 TGAAAATGGAGAAATGAAAACATTTGGAAATGAATT-TGG-TTTTCTCCAAAATAAAAA
1 TGAAAATGGAGAAATGAAAACATTTGGAAATG-ATTATGGTTTTTCTCCAAAATGAAAA
42519802 TGAAAA
1 TGAAAA
42519808 AGACTTGAAA
Statistics
Matches: 107, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
56 5 0.05
57 62 0.58
58 22 0.21
60 18 0.17
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (58 bp):
TGAAAATGGAGAAATGAAAACATTTGGAAATGATTATGGTTTTTCTCCAAAATGAAAA
Found at i:42526586 original size:27 final size:27
Alignment explanation
Indices: 42526555--42526677 Score: 192
Period size: 27 Copynumber: 4.6 Consensus size: 27
42526545 AATATGACTG
*
42526555 AAATACACTCGAAGGGTAAAATGACCA
1 AAATACCCTCGAAGGGTAAAATGACCA
* **
42526582 AAATACCCTCGAAGGGTAAAATAATTA
1 AAATACCCTCGAAGGGTAAAATGACCA
*
42526609 AAATACCCTCGAAGGGTAAAATGACCG
1 AAATACCCTCGAAGGGTAAAATGACCA
*
42526636 AAATACCCTCGACGGGTAAAATGACCA
1 AAATACCCTCGAAGGGTAAAATGACCA
42526663 AAATACCCTCGAAGG
1 AAATACCCTCGAAGG
42526678 ACCCTCGAAG
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 85 1.00
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (27 bp):
AAATACCCTCGAAGGGTAAAATGACCA
Found at i:42526718 original size:65 final size:65
Alignment explanation
Indices: 42526613--42526742 Score: 215
Period size: 65 Copynumber: 2.0 Consensus size: 65
42526603 TAATTAAAAT
* * *
42526613 ACCCTCGAAGGGTAAAATGACCGAAATACCCTCGACGGGTAAAATGACCAAAATACCCTCGAAGG
1 ACCCTCGAAGGGTAAAATGACCGAAATACCCTCAAAGGGTAAAATGACCAAAAGACCCTCGAAGG
* *
42526678 ACCCTCGAAGGGTAAAATGATCGAAATACCTTCAAAGGGTAAAATGACCAAAAGACCCTCGAAGG
1 ACCCTCGAAGGGTAAAATGACCGAAATACCCTCAAAGGGTAAAATGACCAAAAGACCCTCGAAGG
42526743 GTAAAATGAC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (65 bp):
ACCCTCGAAGGGTAAAATGACCGAAATACCCTCAAAGGGTAAAATGACCAAAAGACCCTCGAAGG
Found at i:42526745 original size:92 final size:92
Alignment explanation
Indices: 42526586--42526816 Score: 266
Period size: 92 Copynumber: 2.5 Consensus size: 92
42526576 TGACCAAAAT
* * * * *
42526586 ACCCTCGAAGGGTAAAATAATTAAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGACGG
1 ACCCTCGAAGGGTAAAATAATCAAAATACCCTCAAAGGGTAAAATGACCAAAAGACCCTCGAAGG
42526651 GTAAAATGACCAAAATACCCTCGAAGG
66 GTAAAATGACCAAAATACCCTCGAAGG
* * *
42526678 ACCCTCGAAGGGTAAAATGATCGAAATACCTTCAAAGGGTAAAATGACCAAAAGACCCTCGAAGG
1 ACCCTCGAAGGGTAAAATAATCAAAATACCCTCAAAGGGTAAAATGACCAAAAGACCCTCGAAGG
**
42526743 GTAAAATGACTGAAATACCC-CTGAAAGG
66 GTAAAATGACCAAAATACCCTC-G-AAGG
* * * * * * * *
42526771 AAACCTCTAATGATAAAATGACCAAAATACCCCCGAAGGGTAAAAT
1 -ACCCTCGAAGGGTAAAATAATCAAAATACCCTCAAAGGGTAAAAT
42526817 AATTGTTATA
Statistics
Matches: 117, Mismatches: 19, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
91 1 0.01
92 76 0.65
93 4 0.03
94 36 0.31
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (92 bp):
ACCCTCGAAGGGTAAAATAATCAAAATACCCTCAAAGGGTAAAATGACCAAAAGACCCTCGAAGG
GTAAAATGACCAAAATACCCTCGAAGG
Found at i:42526762 original size:27 final size:27
Alignment explanation
Indices: 42526678--42526762 Score: 109
Period size: 27 Copynumber: 3.1 Consensus size: 27
42526668 CCCTCGAAGG
42526678 ACCCTCGAAGGGTAAAATGA-TCGAAAT
1 ACCCTCGAAGGGTAAAATGACT-GAAAT
* * ** *
42526705 ACCTTCAAAGGGTAAAATGACCAAAAG
1 ACCCTCGAAGGGTAAAATGACTGAAAT
42526732 ACCCTCGAAGGGTAAAATGACTGAAAT
1 ACCCTCGAAGGGTAAAATGACTGAAAT
42526759 ACCC
1 ACCC
42526763 CTGAAAGGAA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.16
Consensus pattern (27 bp):
ACCCTCGAAGGGTAAAATGACTGAAAT
Found at i:42527023 original size:26 final size:26
Alignment explanation
Indices: 42526994--42527070 Score: 109
Period size: 26 Copynumber: 3.0 Consensus size: 26
42526984 TTGCCACATA
*
42526994 TACTGTTACTAGCAGCTTTGCTGCGT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* *
42527020 TACTGTTACTGGCAGCGTTGCTGCAT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* *
42527046 CACTATTACTGGCAGCTTTGCTGCG
1 TACTGTTACTGGCAGCTTTGCTGCG
42527071 ATATTGGTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.35
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGCTGCGT
Found at i:42527215 original size:28 final size:28
Alignment explanation
Indices: 42527175--42527234 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
42527165 TACTGCATTG
* * *
42527175 CACTGTTACTGTATTGGGCTAAGGCCCA
1 CACTATTACTGTAATGGACTAAGGCCCA
42527203 CACTATTACTGTAATGGACTAAGGCCCA
1 CACTATTACTGTAATGGACTAAGGCCCA
42527231 CACT
1 CACT
42527235 GTACTGCTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (28 bp):
CACTATTACTGTAATGGACTAAGGCCCA
Found at i:42534085 original size:13 final size:13
Alignment explanation
Indices: 42534067--42534096 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
42534057 TCCAGCAACT
42534067 ATGAATTTATTTC
1 ATGAATTTATTTC
*
42534080 ATGAATTTATTTG
1 ATGAATTTATTTC
42534093 ATGA
1 ATGA
42534097 TGATCCAAGC
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:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:42534258 original size:50 final size:50
Alignment explanation
Indices: 42534183--42534368 Score: 252
Period size: 50 Copynumber: 3.7 Consensus size: 50
42534173 ATTTGGGTAA
42534183 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCAGTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCAGTGGCACCGAGATG
* * * *
42534233 AGAGGTCTCATGTAAGACCATGTCTGGGACATGAC-GTTGGCAGCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCAG-TGGCACCGAGATG
*
42534283 AGAGGTCCC-TCGTAAGACCATGTCTGGGACATGGCA-TGGGCACCGACATG
1 AGAGGTCCCAT-GTAAGACCATGTCTGGGACATGGCAGT-GGCACCGAGATG
**
42534333 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
42534369 TTTGACATGT
Statistics
Matches: 119, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
49 3 0.03
50 86 0.72
51 29 0.24
52 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.31, T:0.19
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCAGTGGCACCGAGATG
Found at i:42536651 original size:81 final size:81
Alignment explanation
Indices: 42536515--42536768 Score: 391
Period size: 81 Copynumber: 3.1 Consensus size: 81
42536505 GCCGTAATGG
** * *
42536515 GGGTAAAATGATCGAAATACCCTTAAAGGGTAAAATGATTGAAATACGCTCGAAGGGTAAAATGA
1 GGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGA
42536580 CTGAAATACCCTCGAA
66 CTGAAATACCCTCGAA
* **
42536596 TGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGACCAAAATACCCTCGAAGGGTAAAATGA
1 GGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGA
**
42536661 CCAAAATACCCTCGAA
66 CTGAAATACCCTCGAA
* *
42536677 GGGTAAAATGATCGAAATACCCTCGAAGGATAAAATGACTGAAATACCCTCGAATGGTAAAATGA
1 GGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGA
**
42536742 CTGAAATACCCTTAAA
66 CTGAAATACCCTCGAA
42536758 GGGTAAAATGA
1 GGGTAAAATGA
42536769 CGTTATAGCC
Statistics
Matches: 155, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 155 1.00
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (81 bp):
GGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGA
CTGAAATACCCTCGAA
Found at i:42536769 original size:27 final size:27
Alignment explanation
Indices: 42536515--42536769 Score: 345
Period size: 27 Copynumber: 9.4 Consensus size: 27
42536505 GCCGTAATGG
**
42536515 GGGTAAAATGA-TCGAAATACCCTTAAA
1 GGGTAAAATGACT-GAAATACCCTCGAA
* *
42536542 GGGTAAAATGATTGAAATACGCTCGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
42536569 GGGTAAAATGACTGAAATACCCTCGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
*
42536596 TGGTAAAATGA-TCGAAATACCCTCGAA
1 GGGTAAAATGACT-GAAATACCCTCGAA
**
42536623 GGGTAAAATGACCAAAATACCCTCGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
**
42536650 GGGTAAAATGACCAAAATACCCTCGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
42536677 GGGTAAAATGA-TCGAAATACCCTCGAA
1 GGGTAAAATGACT-GAAATACCCTCGAA
*
42536704 GGATAAAATGACTGAAATACCCTCGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
* **
42536731 TGGTAAAATGACTGAAATACCCTTAAA
1 GGGTAAAATGACTGAAATACCCTCGAA
42536758 GGGTAAAATGAC
1 GGGTAAAATGAC
42536770 GTTATAGCCC
Statistics
Matches: 206, Mismatches: 17, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
26 1 0.00
27 203 0.99
28 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (27 bp):
GGGTAAAATGACTGAAATACCCTCGAA
Found at i:42537071 original size:28 final size:28
Alignment explanation
Indices: 42537031--42537126 Score: 140
Period size: 28 Copynumber: 3.4 Consensus size: 28
42537021 TACTGCATTG
*
42537031 CACTGTTACTGTATTAGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
42537059 CACTGTTACTGTATTGGGCTAAGGCCCACA
1 CACTGTTACTGTATTGGGCTAAGG-CC-CA
* *
42537089 CACTATTACTGTAATGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
42537117 CACTG-TACTG
1 CACTGTTACTG
42537127 CTACTGAATA
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
27 5 0.08
28 29 0.47
29 4 0.06
30 24 0.39
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (28 bp):
CACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:42537098 original size:30 final size:30
Alignment explanation
Indices: 42537031--42537119 Score: 137
Period size: 30 Copynumber: 3.0 Consensus size: 30
42537021 TACTGCATTG
*
42537031 CACTGTTACTGTATTAGGCTAAGG-CC-CA
1 CACTGTTACTGTATTGGGCTAAGGCCCACA
42537059 CACTGTTACTGTATTGGGCTAAGGCCCACA
1 CACTGTTACTGTATTGGGCTAAGGCCCACA
* *
42537089 CACTATTACTGTAATGGGCTAAGGCCCACA
1 CACTGTTACTGTATTGGGCTAAGGCCCACA
42537119 C
1 C
42537120 TGTACTGCTA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
28 23 0.41
29 2 0.04
30 31 0.55
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (30 bp):
CACTGTTACTGTATTGGGCTAAGGCCCACA
Found at i:42537475 original size:30 final size:32
Alignment explanation
Indices: 42537401--42537463 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
42537391 GGTTTTTCCT
42537401 TGAATATTTTAAACTGCTAGATTAGGAGATGA
1 TGAATATTTTAAACTGCTAGATTAGGAGATGA
42537433 TGAATATTTTAAACTGCTAGATTAGGAGATG
1 TGAATATTTTAAACTGCTAGATTAGGAGATG
42537464 TCGAATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (32 bp):
TGAATATTTTAAACTGCTAGATTAGGAGATGA
Found at i:42542138 original size:16 final size:15
Alignment explanation
Indices: 42542117--42542151 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
42542107 ACTTTGATAT
42542117 AAAACTTAATAAATCC
1 AAAACTTAATAAAT-C
42542133 AAAACTTAATAAATC
1 AAAACTTAATAAATC
42542148 AAAA
1 AAAA
42542152 TCTGTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAACTTAATAAATC
Found at i:42551146 original size:15 final size:15
Alignment explanation
Indices: 42551123--42551152 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42551113 GATTTCTTGT
*
42551123 TTTTTATTTATTTAC
1 TTTTCATTTATTTAC
42551138 TTTTCATTTATTTAC
1 TTTTCATTTATTTAC
42551153 CTATCTATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCATTTATTTAC
Found at i:42559439 original size:18 final size:18
Alignment explanation
Indices: 42559416--42559462 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
42559406 AAGATGGGAG
42559416 TGATGACAATGAGGAAGA
1 TGATGACAATGAGGAAGA
** *
42559434 TGATGAGGAGGAGGAAGA
1 TGATGACAATGAGGAAGA
42559452 T-AT-ACAATGAG
1 TGATGACAATGAG
42559463 ACTCTAAAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
16 5 0.22
17 2 0.09
18 16 0.70
ACGTcount: A:0.43, C:0.04, G:0.36, T:0.17
Consensus pattern (18 bp):
TGATGACAATGAGGAAGA
Found at i:42560913 original size:26 final size:26
Alignment explanation
Indices: 42560882--42560938 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
42560872 TCTCATCTCT
42560882 ATTTTA-CCCTAAACAAAATTTTGATA
1 ATTTTACCCCT-AACAAAATTTTGATA
**
42560908 ATTTTACCCCTAGTAAAATTTTGATA
1 ATTTTACCCCTAACAAAATTTTGATA
42560934 ATTTT
1 ATTTT
42560939 GCCTCTGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 24 0.86
27 4 0.14
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (26 bp):
ATTTTACCCCTAACAAAATTTTGATA
Found at i:42560949 original size:26 final size:26
Alignment explanation
Indices: 42560896--42560957 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
42560886 TACCCTAAAC
42560896 AAAATTTTGATAATTTTACCCCTAGT
1 AAAATTTTGATAATTTTACCCCTAGT
* * *
42560922 AAAATTTTGATAATTTTGCCTCTGGT
1 AAAATTTTGATAATTTTACCCCTAGT
42560948 AAAATTTTGA
1 AAAATTTTGA
42560958 CGATCTTGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (26 bp):
AAAATTTTGATAATTTTACCCCTAGT
Found at i:42560966 original size:26 final size:26
Alignment explanation
Indices: 42560920--42560980 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
42560910 TTTACCCCTA
* *
42560920 GTAAAATTTTGATAATTTTGC-CTCTG
1 GTAAAATTTTGACAATCTTGCTCT-TG
*
42560946 GTAAAATTTTGACGATCTTGCTCTTG
1 GTAAAATTTTGACAATCTTGCTCTTG
*
42560972 TTAAAATTT
1 GTAAAATTT
42560981 CAAGAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 28 0.93
27 2 0.07
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (26 bp):
GTAAAATTTTGACAATCTTGCTCTTG
Found at i:42566033 original size:50 final size:49
Alignment explanation
Indices: 42565920--42566059 Score: 217
Period size: 50 Copynumber: 2.8 Consensus size: 49
42565910 CCGGTTCACA
*
42565920 TAGTAGCCTGCAGATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCA-T-TCCGATACACG
* * *
42565971 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACC-ATCATTCCGATACACG
42566021 TAGTAGCCTGCACATAGTACTACACATGTGACCATCATT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCATT
42566060 TTCACTTTCA
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
49 6 0.07
50 41 0.49
51 32 0.39
52 4 0.05
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATCATTCCGATACACG
Found at i:42569576 original size:59 final size:59
Alignment explanation
Indices: 42569507--42570075 Score: 883
Period size: 59 Copynumber: 9.6 Consensus size: 59
42569497 GGCAGATCAA
*
42569507 CTTTCCTTTCAATGATTTGCCACAAAGGCATCCTTTTCATTTAGTACCCGCCACAGAGG
1 CTTTCCTTTCAATGATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAGAGG
* **
42569566 CTTTCCTTTCAATGATTTGCCACAAAGGCATCCTTTTCATTCAGTACTAACCACAGAGG
1 CTTTCCTTTCAATGATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAGAGG
* * *
42569625 CTTTCCTTTCAATGATTTGCCATAAAGGCATCCTTTTCATTTAGTACTCACCACAAAGG
1 CTTTCCTTTCAATGATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAGAGG
*
42569684 CTTTCCTTTCAGA-GATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAGAGA
1 CTTTCCTTTCA-ATGATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAGAGG
* **
42569743 CTTTCCTTTCAATGATTTGCCACAAAGGCATCCTTTTCATTCAGTACTAACCACAGAGG
1 CTTTCCTTTCAATGATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAGAGG
* *
42569802 CTTTCCTTTCAATGATTTGCCATAAAGGCATCCTTTTCATTTAGTACTCGCCACAAAGG
1 CTTTCCTTTCAATGATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAGAGG
* *
42569861 CTTTCCTTTCAGA-GATTTGCCACAAAGGCTTCCTTTTCATTTAGTACTCGCCACAGAGA
1 CTTTCCTTTCA-ATGATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAGAGG
* * * *
42569920 CTTTCCTTTCAATGATTTTCCATAAAGGCATCCTTTTCATTTAGTACTCACCACAAAGG
1 CTTTCCTTTCAATGATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAGAGG
*
42569979 CTTTCCTTTCAGA-GATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAAAGG
1 CTTTCCTTTCA-ATGATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAGAGG
** *
42570038 CTTTCCTTTCAAAAATTTTCCACAAAGGCATCCTTTTC
1 CTTTCCTTTCAATGATTTGCCACAAAGGCATCCTTTTC
42570076 TGGTGTTTTA
Statistics
Matches: 468, Mismatches: 36, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
58 3 0.01
59 462 0.99
60 3 0.01
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (59 bp):
CTTTCCTTTCAATGATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAGAGG
Found at i:42569803 original size:177 final size:177
Alignment explanation
Indices: 42569507--42570075 Score: 989
Period size: 177 Copynumber: 3.2 Consensus size: 177
42569497 GGCAGATCAA
* *
42569507 CTTTCCTTTCA-ATGATTTGCCACAAAGGCATCCTTTTCATTTAGTACCCGCCACAGAGGCTTTC
1 CTTTCCTTTCAGA-GATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAGAGACTTTC
42569571 CTTTCAATGATTTGCCACAAAGGCATCCTTTTCATTCAGTACTAACCACAGAGGCTTTCCTTTCA
65 CTTTCAATGATTTGCCACAAAGGCATCCTTTTCATTCAGTACTAACCACAGAGGCTTTCCTTTCA
*
42569636 ATGATTTGCCATAAAGGCATCCTTTTCATTTAGTACTCACCACAAAGG
130 ATGATTTGCCATAAAGGCATCCTTTTCATTTAGTACTCGCCACAAAGG
42569684 CTTTCCTTTCAGAGATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAGAGACTTTCC
1 CTTTCCTTTCAGAGATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAGAGACTTTCC
42569749 TTTCAATGATTTGCCACAAAGGCATCCTTTTCATTCAGTACTAACCACAGAGGCTTTCCTTTCAA
66 TTTCAATGATTTGCCACAAAGGCATCCTTTTCATTCAGTACTAACCACAGAGGCTTTCCTTTCAA
42569814 TGATTTGCCATAAAGGCATCCTTTTCATTTAGTACTCGCCACAAAGG
131 TGATTTGCCATAAAGGCATCCTTTTCATTTAGTACTCGCCACAAAGG
*
42569861 CTTTCCTTTCAGAGATTTGCCACAAAGGCTTCCTTTTCATTTAGTACTCGCCACAGAGACTTTCC
1 CTTTCCTTTCAGAGATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAGAGACTTTCC
* * * * *
42569926 TTTCAATGATTTTCCATAAAGGCATCCTTTTCATTTAGTACTCACCACAAAGGCTTTCCTTTCAG
66 TTTCAATGATTTGCCACAAAGGCATCCTTTTCATTCAGTACTAACCACAGAGGCTTTCCTTTCA-
*
42569991 A-GATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAAAGG
130 ATGATTTGCCATAAAGGCATCCTTTTCATTTAGTACTCGCCACAAAGG
* * *
42570038 CTTTCCTTTCAAAAATTTTCCACAAAGGCATCCTTTTC
1 CTTTCCTTTCAGAGATTTGCCACAAAGGCATCCTTTTC
42570076 TGGTGTTTTA
Statistics
Matches: 376, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
177 374 0.99
178 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (177 bp):
CTTTCCTTTCAGAGATTTGCCACAAAGGCATCCTTTTCATTTAGTACTCGCCACAGAGACTTTCC
TTTCAATGATTTGCCACAAAGGCATCCTTTTCATTCAGTACTAACCACAGAGGCTTTCCTTTCAA
TGATTTGCCATAAAGGCATCCTTTTCATTTAGTACTCGCCACAAAGG
Found at i:42573478 original size:12 final size:12
Alignment explanation
Indices: 42573461--42573486 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42573451 TTTCCACTCG
42573461 ATCTTGATCTAA
1 ATCTTGATCTAA
42573473 ATCTTGATCTAA
1 ATCTTGATCTAA
42573485 AT
1 AT
42573487 TAATAATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (12 bp):
ATCTTGATCTAA
Found at i:42574105 original size:21 final size:21
Alignment explanation
Indices: 42574065--42574103 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42574055 TTATGTTTTC
*
42574065 TTTATTTTATTAACCTTTTAT
1 TTTATTGTATTAACCTTTTAT
42574086 TTTATTGTATT-ACCTTTT
1 TTTATTGTATTAACCTTTT
42574104 TAATTAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.21, C:0.10, G:0.03, T:0.67
Consensus pattern (21 bp):
TTTATTGTATTAACCTTTTAT
Found at i:42575005 original size:23 final size:23
Alignment explanation
Indices: 42574975--42575026 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
42574965 TATAGGAGTT
* *
42574975 CTGTAATATCCCGAAAATTACTA
1 CTGTAATACCCCGAAAATTAATA
42574998 CTGTAATACCCCGAAAATTAATA
1 CTGTAATACCCCGAAAATTAATA
*
42575021 CAGTAA
1 CTGTAA
42575027 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (23 bp):
CTGTAATACCCCGAAAATTAATA
Found at i:42580449 original size:31 final size:31
Alignment explanation
Indices: 42580414--42580479 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
42580404 ATGGATTTAA
42580414 ATGGAAATTATGTCATAATCTATTATAGTGG
1 ATGGAAATTATGTCATAATCTATTATAGTGG
42580445 ATGGAAATTATGTCATAATCTATTATAGTGG
1 ATGGAAATTATGTCATAATCTATTATAGTGG
42580476 ATGG
1 ATGG
42580480 TTAGATTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (31 bp):
ATGGAAATTATGTCATAATCTATTATAGTGG
Found at i:42590579 original size:25 final size:26
Alignment explanation
Indices: 42590513--42590581 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
42590503 AGTATATGTT
42590513 TATTTAGCAGGCTTTGAGTCGATGAC
1 TATTTAGCAGGCTTTGAGTCGATGAC
* * *
42590539 TATTTAGTAGGTTTTGAGTCGAT-TC
1 TATTTAGCAGGCTTTGAGTCGATGAC
42590564 T-TATTAGCAGGCTTTGAG
1 TAT-TTAGCAGGCTTTGAG
42590582 CCAGTAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 1 0.03
25 15 0.41
26 21 0.57
ACGTcount: A:0.22, C:0.12, G:0.26, T:0.41
Consensus pattern (26 bp):
TATTTAGCAGGCTTTGAGTCGATGAC
Found at i:42591758 original size:22 final size:21
Alignment explanation
Indices: 42591727--42591768 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42591717 GTTTGAGCAC
42591727 ACGGGCGTGTAAGGGTAGCCAT
1 ACGGGCGTGT-AGGGTAGCCAT
* *
42591749 ACGGGTGTGTGGGGTAGCCA
1 ACGGGCGTGTAGGGTAGCCA
42591769 CACGACCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.19, C:0.17, G:0.45, T:0.19
Consensus pattern (21 bp):
ACGGGCGTGTAGGGTAGCCAT
Found at i:42592291 original size:10 final size:10
Alignment explanation
Indices: 42592267--42592304 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
42592257 AATGAGTAAT
42592267 CATTTTA-AA
1 CATTTTATAA
42592276 -ATTTTATAA
1 CATTTTATAA
42592285 CATTTTATAA
1 CATTTTATAA
*
42592295 CATTTAATAA
1 CATTTTATAA
42592305 TTTATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 6 0.23
9 2 0.08
10 18 0.69
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (10 bp):
CATTTTATAA
Found at i:42592859 original size:17 final size:17
Alignment explanation
Indices: 42592839--42592872 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42592829 ATTATAGTTT
42592839 TTTAAAATTTTATTATA
1 TTTAAAATTTTATTATA
* *
42592856 TTTAATATTTTTTTATA
1 TTTAAAATTTTATTATA
42592873 GGTTTCATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTAAAATTTTATTATA
Found at i:42593040 original size:33 final size:31
Alignment explanation
Indices: 42592983--42593063 Score: 94
Period size: 33 Copynumber: 2.6 Consensus size: 31
42592973 TATAATCCCT
*
42592983 AAAAATCAATTAAG-CCTTCTTAAAATAATTTTA
1 AAAAATCAATTAAGCCCTTCGTAAAATAA---TA
* *
42593016 AAAAATCAATTAAGCCCTT-GTAAAATGATG
1 AAAAATCAATTAAGCCCTTCGTAAAATAATA
42593046 AAAAATCAATTAAGCCCT
1 AAAAATCAATTAAGCCCT
42593064 ACATGTCAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
30 19 0.43
33 21 0.48
34 4 0.09
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (31 bp):
AAAAATCAATTAAGCCCTTCGTAAAATAATA
Found at i:42594633 original size:2 final size:2
Alignment explanation
Indices: 42594628--42594679 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
42594618 AATTTTAACT
*
42594628 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42594670 TA TA TA -A TA T
1 TA TA TA TA TA T
42594680 TATGATTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:42606809 original size:25 final size:26
Alignment explanation
Indices: 42606759--42606811 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
42606749 TTTAATATAT
* *
42606759 TTTTAAAATACTTTTTTTATTTTTTA
1 TTTTAAAATACTTTTTTTAGTGTTTA
42606785 TTTTAAAATA-TATTTTTT-GTGTTTA
1 TTTTAAAATACT-TTTTTTAGTGTTTA
42606810 TT
1 TT
42606812 AAAAAAATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (26 bp):
TTTTAAAATACTTTTTTTAGTGTTTA
Found at i:42614516 original size:14 final size:14
Alignment explanation
Indices: 42614497--42614523 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42614487 TCATTCAACT
42614497 TGCCCATTTGACTG
1 TGCCCATTTGACTG
42614511 TGCCCATTTGACT
1 TGCCCATTTGACT
42614524 ATGGATGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.30, G:0.19, T:0.37
Consensus pattern (14 bp):
TGCCCATTTGACTG
Found at i:42618069 original size:42 final size:42
Alignment explanation
Indices: 42618010--42618160 Score: 248
Period size: 42 Copynumber: 3.6 Consensus size: 42
42618000 ACGGCCTAGC
* * *
42618010 ACACGGCCTGGGACACGGGCATGTGAGGCCATTTTGAAGGTT
1 ACACGGCCTGGCACACGGGCGTGTGAGGCCATTTCGAAGGTT
*
42618052 ACACGGCCTGGCACACGGACGTGTGAGGCCATTTCGAAGGTT
1 ACACGGCCTGGCACACGGGCGTGTGAGGCCATTTCGAAGGTT
*
42618094 ACACGGCCTGGCACACAGGCGTGTGAGGCCATTTCGAAGGTT
1 ACACGGCCTGGCACACGGGCGTGTGAGGCCATTTCGAAGGTT
*
42618136 ACACAGCCTGGCACACGGGCGTGTG
1 ACACGGCCTGGCACACGGGCGTGTG
42618161 GCTTGGCCGT
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 101 1.00
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.19
Consensus pattern (42 bp):
ACACGGCCTGGCACACGGGCGTGTGAGGCCATTTCGAAGGTT
Found at i:42639315 original size:26 final size:27
Alignment explanation
Indices: 42639285--42639424 Score: 133
Period size: 27 Copynumber: 5.3 Consensus size: 27
42639275 AGAGGTCAAT
* *
42639285 AAATGATCGAATTA-CCCTAGAGGGTA
1 AAATGACCGAATTACCCCTACAGGGTA
* * *
42639311 AAATGACCAAATTACCCCCACAAGGTA
1 AAATGACCGAATTACCCCTACAGGGTA
* *
42639338 AAATGATCGAATCACCCCT-CAGGGTA
1 AAATGACCGAATTACCCCTACAGGGTA
* *
42639364 AAATGACTGAATTA-CCCTCATAGGGTA
1 AAATGACCGAATTACCCCT-ACAGGGTA
* * * *
42639391 AAATGACCAAAATACCCCCATAGGGTA
1 AAATGACCGAATTACCCCTACAGGGTA
42639418 AAATGAC
1 AAATGAC
42639425 TGTTATACCC
Statistics
Matches: 92, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
25 4 0.04
26 29 0.32
27 56 0.61
28 3 0.03
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (27 bp):
AAATGACCGAATTACCCCTACAGGGTA
Found at i:42639342 original size:27 final size:27
Alignment explanation
Indices: 42639305--42639424 Score: 134
Period size: 27 Copynumber: 4.5 Consensus size: 27
42639295 ATTACCCTAG
42639305 AGGGTAAAATGACCAAATTACCCCCAC
1 AGGGTAAAATGACCAAATTACCCCCAC
* * * * *
42639332 AAGGTAAAATGATCGAATCA-CCCCTC
1 AGGGTAAAATGACCAAATTACCCCCAC
** * *
42639358 AGGGTAAAATGACTGAATTACCCTCAT
1 AGGGTAAAATGACCAAATTACCCCCAC
* *
42639385 AGGGTAAAATGACCAAAATACCCCCAT
1 AGGGTAAAATGACCAAATTACCCCCAC
42639412 AGGGTAAAATGAC
1 AGGGTAAAATGAC
42639425 TGTTATACCC
Statistics
Matches: 76, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
26 21 0.28
27 55 0.72
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.18
Consensus pattern (27 bp):
AGGGTAAAATGACCAAATTACCCCCAC
Found at i:42639348 original size:53 final size:54
Alignment explanation
Indices: 42639285--42639424 Score: 158
Period size: 53 Copynumber: 2.6 Consensus size: 54
42639275 AGAGGTCAAT
*
42639285 AAATGATCGAATTA-CCCTAGAGGGTAAAATGACCAAATTACCCCCACAAGGTA
1 AAATGATCGAATTACCCCTACAGGGTAAAATGACCAAATTACCCCCACAAGGTA
* ** * * *
42639338 AAATGATCGAATCACCCCT-CAGGGTAAAATGACTGAATTACCCTCATAGGGTA
1 AAATGATCGAATTACCCCTACAGGGTAAAATGACCAAATTACCCCCACAAGGTA
* * * * *
42639391 AAATGACCAAAATACCCCCATAGGGTAAAATGAC
1 AAATGATCGAATTACCCCTACAGGGTAAAATGAC
42639425 TGTTATACCC
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
53 55 0.76
54 17 0.24
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (54 bp):
AAATGATCGAATTACCCCTACAGGGTAAAATGACCAAATTACCCCCACAAGGTA
Found at i:42639432 original size:27 final size:27
Alignment explanation
Indices: 42639358--42639435 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
42639348 ATCACCCCTC
*
42639358 AGGGTAAAATGACTG-AATTACCCTCAT
1 AGGGTAAAATGACTGTAA-TACCCCCAT
***
42639385 AGGGTAAAATGACCAAAATACCCCCAT
1 AGGGTAAAATGACTGTAATACCCCCAT
*
42639412 AGGGTAAAATGACTGTTATACCCC
1 AGGGTAAAATGACTGTAATACCCC
42639436 TAGGAGATGA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 41 0.95
28 2 0.05
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (27 bp):
AGGGTAAAATGACTGTAATACCCCCAT
Found at i:42639839 original size:28 final size:28
Alignment explanation
Indices: 42639808--42639877 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
42639798 AGGCTAAGAT
*
42639808 CCACATTGTTATTATATTGGGCTAAAGC
1 CCACATTGTTACTATATTGGGCTAAAGC
*
42639836 CCACATTGTTACTATATTGGGCTAAGGC
1 CCACATTGTTACTATATTGGGCTAAAGC
*
42639864 CCACACTG-TACTAT
1 CCACATTGTTACTAT
42639878 TACTGAATAG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 6 0.15
28 33 0.85
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (28 bp):
CCACATTGTTACTATATTGGGCTAAAGC
Found at i:42649381 original size:19 final size:20
Alignment explanation
Indices: 42649349--42649386 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
42649339 CAATTAATTG
42649349 ATTTATTATCATTA-ATTTC
1 ATTTATTATCATTATATTTC
* *
42649368 ATTTATTGTTATTATATTT
1 ATTTATTATCATTATATTT
42649387 AATAGTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
ATTTATTATCATTATATTTC
Found at i:42649448 original size:17 final size:18
Alignment explanation
Indices: 42649426--42649461 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42649416 AACTTAATTT
*
42649426 TTATATAA-ATTCTTTTA
1 TTATATAATATTATTTTA
42649443 TTATATAATATTATTTTA
1 TTATATAATATTATTTTA
42649461 T
1 T
42649462 GTATTCATTA
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:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATAATATTATTTTA
Found at i:42653980 original size:27 final size:27
Alignment explanation
Indices: 42653933--42653989 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
42653923 CTTCAGATTC
42653933 AATCAATAAAAAAATAGAAAT-AAAAA
1 AATCAATAAAAAAATAGAAATGAAAAA
42653959 AATCAATCAAAAAAAT-GAAAATGAAAAA
1 AATCAAT-AAAAAAATAG-AAATGAAAAA
42653987 AAT
1 AAT
42653990 GAAAAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 8 0.29
27 12 0.43
28 8 0.29
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (27 bp):
AATCAATAAAAAAATAGAAATGAAAAA
Found at i:42654957 original size:15 final size:16
Alignment explanation
Indices: 42654937--42654973 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
42654927 CTTTGAGTCA
42654937 AAAAAATGAAAAATT-
1 AAAAAATGAAAAATTG
42654952 AAAAAATGAAAAATTG
1 AAAAAATGAAAAATTG
42654968 AAAAAA
1 AAAAAA
42654974 GTAAAAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (16 bp):
AAAAAATGAAAAATTG
Found at i:42656372 original size:44 final size:44
Alignment explanation
Indices: 42656324--42656548 Score: 133
Period size: 44 Copynumber: 5.2 Consensus size: 44
42656314 TGATACAAGC
* *
42656324 CTTGCCTCCCTCGATTGCAGTGGAGCGGGTTAAAGATGGTAGAT
1 CTTGCCTCCCTCGATTGCAGTGGAGCGGGTTAAAGATAGAAGAT
* * * * * * *
42656368 CTTGCCTTCCT-GCATTGACAGCGAAGCAGATTGAAA-ACA-AAG-C
1 CTTGCCTCCCTCG-ATTG-CAGTGGAGCGGGTT-AAAGATAGAAGAT
* *
42656411 CTTGCCTCCCTCGGTTGCAGTGGAGCGGGTTAAAGATAGCAGAT
1 CTTGCCTCCCTCGATTGCAGTGGAGCGGGTTAAAGATAGAAGAT
* * * * * * * *
42656455 CTTACCTTCCTAC-ATTGACAGTGAAGCAGATCGAAA-ACA-AAG-C
1 CTTGCCTCCCT-CGATTG-CAGTGGAGCGGGT-TAAAGATAGAAGAT
* * * *
42656498 CTTGCCTTCCTCGGTTGTAGTGGAGCGGGTTAAAGATAGCAGAT
1 CTTGCCTCCCTCGATTGCAGTGGAGCGGGTTAAAGATAGAAGAT
42656542 CTTGCCT
1 CTTGCCT
42656549 TCCTGCATTG
Statistics
Matches: 129, Mismatches: 38, Indels: 28
0.66 0.19 0.14
Matches are distributed among these distances:
41 6 0.05
42 24 0.19
43 31 0.24
44 38 0.29
45 24 0.19
46 6 0.05
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (44 bp):
CTTGCCTCCCTCGATTGCAGTGGAGCGGGTTAAAGATAGAAGAT
Found at i:42656417 original size:43 final size:42
Alignment explanation
Indices: 42656368--42656509 Score: 117
Period size: 43 Copynumber: 3.3 Consensus size: 42
42656358 GATGGTAGAT
*
42656368 CTTGCCTTCCTGCATTGACAGCGAAGCAGATTGAAAACAAAGC
1 CTTGCCTTCCT-CATTGACAGTGAAGCAGATTGAAAACAAAGC
* * * * * * * *
42656411 CTTGCCTCCCTCGGTTG-CAGTGGAGCGGGTT-AAAGATAGCAGAT
1 CTTGCCTTCCTC-ATTGACAGTGAAGCAGATTGAAA-ACA-AAG-C
* *
42656455 CTTACCTTCCTACATTGACAGTGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCT-CATTGACAGTGAAGCAGATTGAAAACAAAGC
42656498 CTTGCCTTCCTC
1 CTTGCCTTCCTC
42656510 GGTTGTAGTG
Statistics
Matches: 72, Mismatches: 20, Indels: 15
0.67 0.19 0.14
Matches are distributed among these distances:
41 3 0.04
42 14 0.19
43 25 0.35
44 14 0.19
45 13 0.18
46 3 0.04
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (42 bp):
CTTGCCTTCCTCATTGACAGTGAAGCAGATTGAAAACAAAGC
Found at i:42656438 original size:87 final size:86
Alignment explanation
Indices: 42656237--42656664 Score: 599
Period size: 87 Copynumber: 4.9 Consensus size: 86
42656227 ATCACCAGCG
* * *
42656237 TTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAAA-ATAGCAGATCTTGCCTTCCTGTATTGACAG
1 TTGCCTCCCTCGGTTGCAGTGGAGCGGGTT-AAAGATAGCAGATCTTGCCTTCCTGCATTGACAG
* *
42656301 CGAAGCAAATCGATGATACAAGCC
65 CGAAGCAGATCGA--AAACAAGCC
* * *
42656325 TTGCCTCCCTCGATTGCAGTGGAGCGGGTTAAAGATGGTAGATCTTGCCTTCCTGCATTGACAGC
1 TTGCCTCCCTCGGTTGCAGTGGAGCGGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGC
*
42656390 GAAGCAGATTGAAAACAAAGCC
66 GAAGCAGATCGAAAAC-AAGCC
* * *
42656412 TTGCCTCCCTCGGTTGCAGTGGAGCGGGTTAAAGATAGCAGATCTTACCTTCCTACATTGACAGT
1 TTGCCTCCCTCGGTTGCAGTGGAGCGGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGC
42656477 GAAGCAGATCGAAAACAAAGCC
66 GAAGCAGATCGAAAAC-AAGCC
* *
42656499 TTGCCTTCCTCGGTTGTAGTGGAGCGGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGC
1 TTGCCTCCCTCGGTTGCAGTGGAGCGGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGC
*
42656564 GAAGCAGATCGAAGATACTAGCC
66 GAAGCAGATCGAA-A-ACAAGCC
* * * *
42656587 TTTCCTCCCTTGGTTGCAGTGGAGCAGGTTAAAGATAGCAGAT-TTGGCCTTCCTGCATCGACAG
1 TTGCCTCCCTCGGTTGCAGTGGAGCGGGTTAAAGATAGCAGATCTT-GCCTTCCTGCATTGACAG
42656651 CGAAGCAGATCGAA
65 CGAAGCAGATCGAA
42656665 GATACCAGTC
Statistics
Matches: 307, Mismatches: 28, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
86 3 0.01
87 163 0.53
88 139 0.45
89 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (86 bp):
TTGCCTCCCTCGGTTGCAGTGGAGCGGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGC
GAAGCAGATCGAAAACAAGCC
Found at i:42656596 original size:175 final size:173
Alignment explanation
Indices: 42656237--42656664 Score: 610
Period size: 175 Copynumber: 2.5 Consensus size: 173
42656227 ATCACCAGCG
* *
42656237 TTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAAA-ATAGCAGATCTTGCCTTCCTGTATTGACAG
1 TTGCCTCCCTCGGTTGCAGTGGAGCAGGTT-AAAGATAGCAGATCTTGCCTTCCTGCATTGACAG
* * * *
42656301 CGAAGCAAATCGATGATACAAGCCTTGCCTCCCTCGATTGCAGTGGAGCGGGTTAAAGATGGTAG
65 CGAAGCAGATCGA--AAACAAGCCTTGCCTCCCTCGATTGCAGTGGAGCGGGTTAAAGATAGCAG
*
42656366 ATCTTGCCTTCCTGCATTGACAGCGAAGCAGATTGAAAACAAAGCC
128 ATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCC
* * * *
42656412 TTGCCTCCCTCGGTTGCAGTGGAGCGGGTTAAAGATAGCAGATCTTACCTTCCTACATTGACAGT
1 TTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGC
* * *
42656477 GAAGCAGATCGAAAACAAAGCCTTGCCTTCCTCGGTTGTAGTGGAGCGGGTTAAAGATAGCAGAT
66 GAAGCAGATCGAAAAC-AAGCCTTGCCTCCCTCGATTGCAGTGGAGCGGGTTAAAGATAGCAGAT
*
42656542 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGATAC-TAGCC
130 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAA-A-ACAAAGCC
* * *
42656587 TTTCCTCCCTTGGTTGCAGTGGAGCAGGTTAAAGATAGCAGAT-TTGGCCTTCCTGCATCGACAG
1 TTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTT-GCCTTCCTGCATTGACAG
42656651 CGAAGCAGATCGAA
65 CGAAGCAGATCGAA
42656665 GATACCAGTC
Statistics
Matches: 226, Mismatches: 22, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
173 3 0.01
174 82 0.36
175 139 0.62
176 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (173 bp):
TTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGC
GAAGCAGATCGAAAACAAGCCTTGCCTCCCTCGATTGCAGTGGAGCGGGTTAAAGATAGCAGATC
TTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCC
Found at i:42656667 original size:45 final size:44
Alignment explanation
Indices: 42656530--42656668 Score: 124
Period size: 45 Copynumber: 3.1 Consensus size: 44
42656520 GAGCGGGTTA
42656530 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCG
1 AAGATAGCAGAT-TTGCCTTCCTGCATTGACAGCGAAGCAGATCG
* * * * * * **
42656575 AAGATA-CTAGCCTTT-CCTCCCTTG-GTTG-CAGTGGAGCAGGTTA
1 AAGATAGC-AG-ATTTGCCTTCC-TGCATTGACAGCGAAGCAGATCG
*
42656618 AAGATAGCAGATTTGGCCTTCCTGCATCGACAGCGAAGCAGATCG
1 AAGATAGCAGATTT-GCCTTCCTGCATTGACAGCGAAGCAGATCG
42656663 AAGATA
1 AAGATA
42656669 CCAGTCCTAT
Statistics
Matches: 69, Mismatches: 17, Indels: 16
0.68 0.17 0.16
Matches are distributed among these distances:
42 3 0.04
43 20 0.29
44 17 0.25
45 28 0.41
46 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (44 bp):
AAGATAGCAGATTTGCCTTCCTGCATTGACAGCGAAGCAGATCG
Found at i:42657075 original size:44 final size:44
Alignment explanation
Indices: 42656895--42657077 Score: 106
Period size: 44 Copynumber: 4.2 Consensus size: 44
42656885 TGGTGAATTC
* * * *
42656895 TATCTCCTTGGGCAGCAATGGAATAGATTGAAGATTTTAGATCT
1 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATAT
** * ** * ** *
42656939 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTT
1 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATAT
* * * * * * *
42656983 TACCTCCCTGTG-ATTACAGCGGACTACATTGAAG---CCAG-TAATT
1 TATCTCCCTGGGCA--GCAGTGGAATAGATTGAAGATTTCAGAT-A-T
42657026 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATAT
1 -TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATAT
42657071 TATCTCC
1 TATCTCC
42657078 TTAAGCAGTA
Statistics
Matches: 98, Mismatches: 31, Indels: 20
0.66 0.21 0.13
Matches are distributed among these distances:
41 1 0.01
42 3 0.03
43 17 0.17
44 58 0.59
45 14 0.14
46 4 0.04
47 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (44 bp):
TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATAT
Found at i:42657355 original size:44 final size:44
Alignment explanation
Indices: 42657307--42657633 Score: 116
Period size: 44 Copynumber: 7.4 Consensus size: 44
42657297 CCTGGTTGGC
*
42657307 AGTGGAATAGATTGAAGATTATAGATCTTATCTCCCTAATCAGT
1 AGTGGAGTAGATTGAAGATTATAGATCTTATCTCCCTAATCAGT
* * * * * * ** *
42657351 AGTGGAGCAGATCGAAGATGATGGATTTTACCT-CCTTGT-GGTT
1 AGTGGAGTAGATTGAAGATTATAGATCTTATCTCCCTAATCAG-T
* * ** ** ** *
42657394 ACAATGGAGTACATTGAAG-CCAGTA-AT-TCTATCTCCCTGGTTGGC
1 --AGTGGAGTAGATTGAAGATTA-TAGATCT-TATCTCCCTAATCAGT
* *
42657439 AGTGGAATAGATTGAAGATTATAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATTATAGATCTTATCTCCCTAATCAGT
* *** * * * *
42657483 AGTGGAGCAGATTGAAGATGGCAGATTTTACCTCCCT--GCGGTT
1 AGTGGAGTAGATTGAAGATTATAGATCTTATCTCCCTAATCAG-T
* * * ** *
42657526 ACAGTGGAGTACATTGAAG-TCAATA-AT-TCTATCTCTCTAGGCAGC
1 --AGTGGAGTAGATTGAAGAT-TATAGATCT-TATCTCCCTAATCAGT
* * * * *
42657571 AGTGGAATAGATTGAAGATTACAAATCTAATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATTATAGATCTTATCTCCCTAATCAGT
* *
42657615 AGTGGAGCAAATTGAAGAT
1 AGTGGAGTAGATTGAAGAT
42657634 GGCGGATTTT
Statistics
Matches: 204, Mismatches: 59, Indels: 40
0.67 0.19 0.13
Matches are distributed among these distances:
42 4 0.02
43 41 0.20
44 117 0.57
45 37 0.18
46 5 0.02
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (44 bp):
AGTGGAGTAGATTGAAGATTATAGATCTTATCTCCCTAATCAGT
Found at i:42657736 original size:132 final size:132
Alignment explanation
Indices: 42656890--42657695 Score: 1114
Period size: 132 Copynumber: 6.1 Consensus size: 132
42656880 GAAGATGGTG
* *** * *
42656890 AATTCTATCTCCTTGGGCAGCAATGGAATAGATTGAAGATTTTAGATCTTATCTCCCTAAGCAGT
1 AATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTATAGATCTTATCTCCCTAAGCAGT
* * *
42656955 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGATTACAGCGGACTACATTGAAGCCA
66 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
42657020 GT
131 GT
*** * *
42657022 AATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATT-TCAGATATTATCTCCTTAAGCAG
1 AATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTAT-AGATCTTATCTCCCTAAGCAG
* * * * ** *
42657086 TAGTGGAGCAGACCGAAAATGGCAGATTTTATCTCCCTGTGATTACAACGGAGTACATTGAATCC
65 TAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
42657151 AGT
130 AGT
*
42657154 AATTCTATCTCCCTGGTTGGCAGTGGAATAGATTAAAGATTATAGATCTTATCTCCCTAAGCAGT
1 AATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTATAGATCTTATCTCCCTAAGCAGT
* * **
42657219 AGTAGAACAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
66 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
42657284 GT
131 GT
* *
42657286 AATTCTATATCCCTGGTTGGCAGTGGAATAGATTGAAGATTATAGATCTTATCTCCCTAATCAGT
1 AATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTATAGATCTTATCTCCCTAAGCAGT
*** * *
42657351 AGTGGAGCAGATCGAAGATGATGGATTTTACCTCCTTGTGGTTACAATGGAGTACATTGAAGCCA
66 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
42657416 GT
131 GT
42657418 AATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTATAGATCTTATCTCCCTAAGCAGT
1 AATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTATAGATCTTATCTCCCTAAGCAGT
* * *
42657483 AGTGGAGCAGATTGAAGATGGCAGATTTTACCTCCCTGCGGTTACAGTGGAGTACATTGAAGTCA
66 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
*
42657548 AT
131 GT
* ** * * *
42657550 AATTCTATCTCTCTAGG-CAGCAGTGGAATAGATTGAAGATTACAAATCTAATCTCCCTAAGCAG
1 AATTCTATCTCCCT-GGTTGGCAGTGGAATAGATTGAAGATTATAGATCTTATCTCCCTAAGCAG
* * * * * *
42657614 TAGTGGAGCAAATTGAAGATGGCGGATTTTACCTCCCTGAGGTTACGGTGGAGTACATTAAAGCC
65 TAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
*
42657679 ACT
130 AGT
42657682 AA-TCTTATCTCCCT
1 AATTC-TATCTCCCT
42657696 AAAGTTGCAG
Statistics
Matches: 610, Mismatches: 60, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
131 3 0.00
132 604 0.99
133 3 0.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (132 bp):
AATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTATAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
GT
Found at i:42658140 original size:14 final size:14
Alignment explanation
Indices: 42658119--42658158 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
42658109 CCCAAATCGG
42658119 AAATAAATAAAA-A
1 AAATAAATAAAATA
42658132 AATATAAATAAAATA
1 AA-ATAAATAAAATA
42658147 AAATAAAATAAA
1 AAAT-AAATAAA
42658159 TAATCCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.08
14 12 0.50
15 10 0.42
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAAATAAAATA
Found at i:42658145 original size:19 final size:19
Alignment explanation
Indices: 42658119--42658161 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
42658109 CCCAAATCGG
42658119 AAAT-AAATAAAA-AAATAT
1 AAATAAAATAAAATAAA-AT
42658137 AAATAAAATAAAATAAAAT
1 AAATAAAATAAAATAAAAT
42658156 AAATAA
1 AAATAA
42658162 TCCATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.17
19 16 0.70
20 3 0.13
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (19 bp):
AAATAAAATAAAATAAAAT
Found at i:42658147 original size:5 final size:5
Alignment explanation
Indices: 42658119--42658158 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
42658109 CCCAAATCGG
42658119 AAAT- AAAT- AAA-A AAATA TAAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA -AAATA AAATA AAATA AAATA AA
42658159 TAATCCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
4 10 0.30
5 18 0.55
6 5 0.15
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:42659348 original size:17 final size:18
Alignment explanation
Indices: 42659326--42659361 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42659316 AACTTAATTT
*
42659326 TTATATAA-ATTTTTTTA
1 TTATATAATATTCTTTTA
42659343 TTATATAATATTCTTTTA
1 TTATATAATATTCTTTTA
42659361 T
1 T
42659362 GTATTCATTA
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:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATATAATATTCTTTTA
Found at i:42659768 original size:9 final size:9
Alignment explanation
Indices: 42659754--42659780 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
42659744 TTTACTTCAT
42659754 TTTTTTTAA
1 TTTTTTTAA
42659763 TTTTTTTAA
1 TTTTTTTAA
42659772 TTTTTTTAA
1 TTTTTTTAA
42659781 ATCTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:42659774 original size:19 final size:21
Alignment explanation
Indices: 42659743--42659792 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
42659733 TCCACTTTTA
* *
42659743 TTTTACTTCATTTTTTTTAAT-
1 TTTTA-TTAATTTTTTTAAATC
42659764 TTTT-TTAATTTTTTTAAATC
1 TTTTATTAATTTTTTTAAATC
42659784 TTTTATTAA
1 TTTTATTAA
42659793 AATTTATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 13 0.52
20 4 0.16
21 8 0.32
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTATTAATTTTTTTAAATC
Found at i:42659787 original size:18 final size:18
Alignment explanation
Indices: 42659754--42659788 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42659744 TTTACTTCAT
* *
42659754 TTTTTTTAATTTTTTTAA
1 TTTTTTTAAATCTTTTAA
42659772 TTTTTTTAAATCTTTTA
1 TTTTTTTAAATCTTTTA
42659789 TTAAAATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTTAAATCTTTTAA
Found at i:42662167 original size:25 final size:25
Alignment explanation
Indices: 42662129--42662187 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
42662119 ACATAAATGG
* *
42662129 GAAGCTCTTTTGAGCCATATAACGA
1 GAAGCTCATGTGAGCCATATAACGA
* * * *
42662154 GAAGCTCATGTGAGTCATGTAATGG
1 GAAGCTCATGTGAGCCATATAACGA
42662179 GAAGCTCAT
1 GAAGCTCAT
42662188 AAGAACCGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (25 bp):
GAAGCTCATGTGAGCCATATAACGA
Found at i:42673572 original size:6 final size:6
Alignment explanation
Indices: 42673561--42673589 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
42673551 TAGGTTTCCA
42673561 AAATGG AAATGG AAATGG AAATGG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATG
42673590 ATTCATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:42678260 original size:31 final size:31
Alignment explanation
Indices: 42678195--42678341 Score: 122
Period size: 31 Copynumber: 4.8 Consensus size: 31
42678185 TAAGGTATCC
* *
42678195 AACACC-AGTACATAGTACCTAATA-AGTTATA
1 AACACCGA-TACATAGTACCTGATACA-ATATA
* *
42678226 AACACCGACACATAGTACCTGATACAATACA
1 AACACCGATACATAGTACCTGATACAATATA
* * *
42678257 AACACCGAAACAAAGTACCAGAT--AATATA
1 AACACCGATACATAGTACCTGATACAATATA
** * * *
42678286 GTCACTGGTACATAGTACCTGATATAATATA
1 AACACCGATACATAGTACCTGATACAATATA
* *
42678317 ATCACCGATACATAGTACATGATAC
1 AACACCGATACATAGTACCTGATAC
42678342 TTTAAAACCC
Statistics
Matches: 92, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
29 21 0.23
31 69 0.75
32 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.22
Consensus pattern (31 bp):
AACACCGATACATAGTACCTGATACAATATA
Found at i:42680998 original size:116 final size:116
Alignment explanation
Indices: 42680789--42681021 Score: 403
Period size: 116 Copynumber: 2.0 Consensus size: 116
42680779 GCCAAGAAAG
*
42680789 TCAAAGCTAAGGTCTTTGGGATACCACAAGTGGGAAAGAAGAGAACCAAGAAGCCTAAATACTTA
1 TCAAAGCTAAGGTCTTTGGGATACCACAAGTGGGAAAGAAGAGAACCAAGAAGCCTAAATACCTA
*
42680854 TCTAAGTCCAAATGCTTTTGCTACAGTAAGAAAGGGCACTTCAAGGTGAAT
66 TCTAAGTCCAAATGCTTTTGCTACAGTAAGAAAGGACACTTCAAGGTGAAT
* * **
42680905 TCAAGGCTAAGGTCTTTGGGCTACCACAAGTGGGAAAGAAGAGAATGAAGAAGCCTAAATACCTA
1 TCAAAGCTAAGGTCTTTGGGATACCACAAGTGGGAAAGAAGAGAACCAAGAAGCCTAAATACCTA
*
42680970 TCTAAGTCCAAATGCTTTTTCTACAGTAAGAAAGGACACTTCAAGGTGAAT
66 TCTAAGTCCAAATGCTTTTGCTACAGTAAGAAAGGACACTTCAAGGTGAAT
42681021 T
1 T
42681022 GCTAAGAGTG
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 110 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (116 bp):
TCAAAGCTAAGGTCTTTGGGATACCACAAGTGGGAAAGAAGAGAACCAAGAAGCCTAAATACCTA
TCTAAGTCCAAATGCTTTTGCTACAGTAAGAAAGGACACTTCAAGGTGAAT
Found at i:42684631 original size:16 final size:16
Alignment explanation
Indices: 42684590--42684640 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
42684580 GTAATTATTT
* *
42684590 TTTTATTTATATATATG
1 TTTT-TTTATATACATA
42684607 TTGTTTTTATATACATA
1 TT-TTTTTATATACATA
*
42684624 TTTTTTTATATTCATA
1 TTTTTTTATATACATA
42684640 T
1 T
42684641 ATATACACGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.47
17 14 0.47
18 2 0.07
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (16 bp):
TTTTTTTATATACATA
Found at i:42693841 original size:50 final size:50
Alignment explanation
Indices: 42693773--42693871 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
42693763 GCATTACAGT
* * *
42693773 GGAGCAGATTGAAACCACGACGGTGAATCTTACTTCCCTGGCATTGTAGC
1 GGAGCAGATTGAAACCACGACGGCGAATCTTACTTCCCCGACATTGTAGC
* **
42693823 GGAGCAGATTGAAGCCACGACGGCGAATCTTGTTTCCCCGACATTGTAG
1 GGAGCAGATTGAAACCACGACGGCGAATCTTACTTCCCCGACATTGTAG
42693872 ATGGCAAATC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.23
Consensus pattern (50 bp):
GGAGCAGATTGAAACCACGACGGCGAATCTTACTTCCCCGACATTGTAGC
Found at i:42698632 original size:27 final size:27
Alignment explanation
Indices: 42698457--42698634 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
42698447 ACCCTAACAG
* *
42698457 GGGTATTACGGTAATTTTACCCATCGA
1 GGGTATTTCGATAATTTTACCCATCGA
* * * * *
42698484 GGATATTTTGGTAATTTTACCTATCAA
1 GGGTATTTCGATAATTTTACCCATCGA
* * *
42698511 GGGTATTT-TAGTAATTTTACCTATCAA
1 GGGTATTTCGA-TAATTTTACCCATCGA
* * * *
42698538 GGGTATTTCAATAATTTTACTCATTGG
1 GGGTATTTCGATAATTTTACCCATCGA
*
42698565 GGGTATTTCGATAATTTTACCCATTG-
1 GGGTATTTCGATAATTTTACCCATCGA
* *
42698591 GGGTATTTTGCTAATTTTACCCATCGA
1 GGGTATTTCGATAATTTTACCCATCGA
*
42698618 GGGTGTTTCGATAATTT
1 GGGTATTTCGATAATTT
42698635 GCCCACGAAT
Statistics
Matches: 126, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
26 23 0.18
27 102 0.81
28 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.42
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACCCATCGA
Found at i:42708385 original size:26 final size:26
Alignment explanation
Indices: 42708356--42708438 Score: 105
Period size: 26 Copynumber: 3.2 Consensus size: 26
42708346 GAGTTCATTA
42708356 TATACAATTCATATAACCATTCAAGC
1 TATACAATTCATATAACCATTCAAGC
* *
42708382 TATAGAAATCATATAACCATTCAAGC
1 TATACAATTCATATAACCATTCAAGC
* * *
42708408 TATACAAGTT-ATATATCTATTCAAGT
1 TATACAA-TTCATATAACCATTCAAGC
42708434 TATAC
1 TATAC
42708439 CAGTTAATTC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
26 48 0.98
27 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.34
Consensus pattern (26 bp):
TATACAATTCATATAACCATTCAAGC
Found at i:42713266 original size:60 final size:59
Alignment explanation
Indices: 42713159--42713274 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 59
42713149 ATTGAATGTT
* * *
42713159 ATGTGACAATATAGGGTATAAATATGAAAATATGAATGGTTATAGGTATGGAAATGCAA
1 ATGTGACAATATAGGGTATAAATATGAAAATATGAATGGATAAAGGTATGAAAATGCAA
* * *
42713218 ATGTGACCAATTATAGGGTAT-GATATGCAAATGTGAAT-GATACAAGGTATGAAAATG
1 ATGTGA-CAA-TATAGGGTATAAATATGAAAATATGAATGGATA-AAGGTATGAAAATG
42713275 TAAAATGTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
59 9 0.19
60 29 0.60
61 10 0.21
ACGTcount: A:0.42, C:0.05, G:0.24, T:0.28
Consensus pattern (59 bp):
ATGTGACAATATAGGGTATAAATATGAAAATATGAATGGATAAAGGTATGAAAATGCAA
Found at i:42713826 original size:21 final size:21
Alignment explanation
Indices: 42713802--42713842 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42713792 TCTATGTCGC
42713802 GACACAACC-AAAGGATGTTGA
1 GACAC-ACCTAAAGGATGTTGA
*
42713823 GACACACCTAGAGGATGTTG
1 GACACACCTAAAGGATGTTG
42713843 TGGCACAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.17
Consensus pattern (21 bp):
GACACACCTAAAGGATGTTGA
Found at i:42724351 original size:50 final size:50
Alignment explanation
Indices: 42724223--42724469 Score: 192
Period size: 50 Copynumber: 4.8 Consensus size: 50
42724213 ATTTGGGTAA
* * * *
42724223 AGAGATCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCATTGAGCTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCA---AG---ATG
* *
42724279 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
** * * * * *
42724329 AGAGGTCCCCCGTAAGACCATGTCCGGGGCATGGCATGGGCACCAATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
** * * **
42724379 AGAACTCCCATGTAAGACCATATCTGGGATATGGCGTTGGCAGTATA-A-G
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCA-AGATG
* ** * * *
42724428 AAACATCCCATGTAATACCATGTCTGGGACATTGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
42724470 TGTTATTATC
Statistics
Matches: 155, Mismatches: 35, Indels: 9
0.78 0.18 0.05
Matches are distributed among these distances:
49 35 0.23
50 78 0.50
51 1 0.01
53 2 0.01
56 39 0.25
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
Found at i:42731893 original size:50 final size:50
Alignment explanation
Indices: 42731782--42732028 Score: 192
Period size: 50 Copynumber: 4.8 Consensus size: 50
42731772 ATTTGGGTAA
* * * * *
42731782 AGAGATCCAATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGGTTATG
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCA-C--CGA---CATG
* * *
42731838 AGAGGTCCCATGTAAGACCATATTTGGGACATGGCTTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGACATG
** * * * * **
42731888 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGAACCAATTTG
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGACATG
** * *
42731938 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAGG
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCG-ACATG
* ** * *
42731987 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCA
42732029 TGTTATTATC
Statistics
Matches: 155, Mismatches: 35, Indels: 9
0.78 0.18 0.05
Matches are distributed among these distances:
49 38 0.25
50 77 0.50
53 2 0.01
55 1 0.01
56 37 0.24
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGACATG
Found at i:42731952 original size:100 final size:103
Alignment explanation
Indices: 42731793--42731979 Score: 254
Period size: 100 Copynumber: 1.8 Consensus size: 103
42731783 GAGATCCAAT
* * * **
42731793 GTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGGTTATGAGAGGTCCCATGTAAGACCA
1 GTAAGACCATGTCTGGGACATGGCATGGGAACCA-T-A-GTTATGAGAACTCCCATGTAAGACCA
* *
42731858 TATTTGGGACATGGCTTTGGCACCGAGATGAGAGGTCCCCC
63 TATCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCCC
42731899 GTAAGACCATGTCTGGGACATGGCATGGGAACCA-A-TT-TGAGAACTCCCATGTAAGACCATAT
1 GTAAGACCATGTCTGGGACATGGCATGGGAACCATAGTTATGAGAACTCCCATGTAAGACCATAT
*
42731961 CTGGGATATGGCATTGGCA
66 CTGGGACATGGCATTGGCA
42731980 GTACAGGAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
100 39 0.53
101 2 0.03
103 1 0.01
106 31 0.42
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (103 bp):
GTAAGACCATGTCTGGGACATGGCATGGGAACCATAGTTATGAGAACTCCCATGTAAGACCATAT
CTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCCC
Found at i:42742571 original size:31 final size:31
Alignment explanation
Indices: 42742533--42742626 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
42742523 TGATATAAAT
*
42742533 ATGAAAATATGAATGATTACAAGGTATGGAA
1 ATGAAAATGTGAATGATTACAAGGTATGGAA
*** * * *
42742564 ATGAAAATGTGACCAATTATAGGGTAT-GAT
1 ATGAAAATGTGAATGATTACAAGGTATGGAA
*
42742594 ATGAAAATGTGAATGA-TACAAGGTATGAAA
1 ATGAAAATGTGAATGATTACAAGGTATGGAA
42742624 ATG
1 ATG
42742627 TAATATGTAA
Statistics
Matches: 48, Mismatches: 14, Indels: 3
0.74 0.22 0.05
Matches are distributed among these distances:
29 8 0.17
30 19 0.40
31 21 0.44
ACGTcount: A:0.46, C:0.04, G:0.23, T:0.27
Consensus pattern (31 bp):
ATGAAAATGTGAATGATTACAAGGTATGGAA
Found at i:42745871 original size:93 final size:93
Alignment explanation
Indices: 42745711--42745899 Score: 297
Period size: 93 Copynumber: 2.0 Consensus size: 93
42745701 TGATGACTAA
* * *
42745711 GTTTTCTCTCACTTTTGTGACTTCTTTGTTTTGTCACTTCACTTTTTACTCTTTTTTTAGTGCTT
1 GTTTTCTCTCACTTTTGTGACTTCTTTGTTTTGTCACTTCACCTTTTACTCTTTTCTTAGTGATT
* *
42745776 TTGTTTCTATTCGATACTTTTTCTACTC
66 TTGTTTCTATTCGATACTCTTTCCACTC
* *
42745804 GTTTTCTCTCACTTTTGTGACTTTTTTGTTTTGTCACTTGACCTTTTACTCTTTTCTTAGTGATT
1 GTTTTCTCTCACTTTTGTGACTTCTTTGTTTTGTCACTTCACCTTTTACTCTTTTCTTAGTGATT
* *
42745869 TTGTTTTTGTTCGATACTCTTTCCACTC
66 TTGTTTCTATTCGATACTCTTTCCACTC
42745897 GTT
1 GTT
42745900 CTTACTTTTA
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 87 1.00
ACGTcount: A:0.11, C:0.20, G:0.11, T:0.58
Consensus pattern (93 bp):
GTTTTCTCTCACTTTTGTGACTTCTTTGTTTTGTCACTTCACCTTTTACTCTTTTCTTAGTGATT
TTGTTTCTATTCGATACTCTTTCCACTC
Found at i:42750021 original size:20 final size:22
Alignment explanation
Indices: 42749982--42750021 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42749972 AATTAATTCG
*
42749982 TATATTACGATAAACCATAAGA
1 TATATTACGATAAACAATAAGA
42750004 TATATTA-GATAAA-AATAA
1 TATATTACGATAAACAATAA
42750022 ACAACAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 6 0.35
22 7 0.41
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (22 bp):
TATATTACGATAAACAATAAGA
Found at i:42761457 original size:50 final size:54
Alignment explanation
Indices: 42761356--42761488 Score: 177
Period size: 50 Copynumber: 2.5 Consensus size: 54
42761346 TGAGACCCCA
42761356 TGTAAGACCATGTCTGGGACATGGCATTGGTATTATTGAGGTTATGAGAGGTCTCAC
1 TGTAAGACCATGTCTGGGACATGGCATTGGTATTA-TGAGG-TATGAGAGGTC-CAC
* *
42761413 -GTAAGACCATGTCTGGGACATGGCGTTGGTA-TA-GA-G-ATGAGAGGTCCCC
1 TGTAAGACCATGTCTGGGACATGGCATTGGTATTATGAGGTATGAGAGGTCCAC
*
42761462 TGTATGACCATGTCTGGGACATGGCAT
1 TGTAAGACCATGTCTGGGACATGGCAT
42761489 GGGCACCGAT
Statistics
Matches: 71, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
49 2 0.03
50 34 0.48
52 1 0.01
53 2 0.03
55 2 0.03
56 30 0.42
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.28
Consensus pattern (54 bp):
TGTAAGACCATGTCTGGGACATGGCATTGGTATTATGAGGTATGAGAGGTCCAC
Found at i:42761503 original size:50 final size:50
Alignment explanation
Indices: 42761357--42761538 Score: 132
Period size: 50 Copynumber: 3.5 Consensus size: 50
42761347 GAGACCCCAT
* * *
42761357 GTAAGACCATGTCTGGGACATGGCATTGGTATTATTGAGGTTATGAGAGGTCTCAC
1 GTAAGACCATGTCTGGGACATGGCATGGGCA-CA--GA---TATGAGAGGTCTCAC
* * * * * *
42761413 GTAAGACCATGTCTGGGACATGGCGTTGGTATAGAGATGAGAGGTC-CCC
1 GTAAGACCATGTCTGGGACATGGCATGGGCACAGATATGAGAGGTCTCAC
* * ** *
42761462 TGTATGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCTCAT
1 -GTAAGACCATGTCTGGGACATGGCATGGGCACAGATATGAGAGGTCTCAC
* * * *
42761513 GTAAGATCATATCTGGAATATGGCAT
1 GTAAGACCATGTCTGGGACATGGCAT
42761539 TTGCAGTACA
Statistics
Matches: 105, Mismatches: 19, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
49 2 0.02
50 68 0.65
51 1 0.01
53 2 0.02
55 2 0.02
56 30 0.29
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCACAGATATGAGAGGTCTCAC
Found at i:42761817 original size:20 final size:20
Alignment explanation
Indices: 42761792--42761830 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
42761782 TGAGTTATTT
42761792 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
42761812 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
42761831 GAAAAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:42772966 original size:24 final size:25
Alignment explanation
Indices: 42772927--42772989 Score: 101
Period size: 24 Copynumber: 2.5 Consensus size: 25
42772917 TAATCTGGTT
42772927 AATGCTATGGCAAGACTGATGAATAA
1 AATGCTA-GGCAAGACTGATGAATAA
42772953 AATGCTA-GCAAGACTGATGAATAA
1 AATGCTAGGCAAGACTGATGAATAA
42772977 AATGCTATGGCAA
1 AATGCTA-GGCAA
42772990 ATTGAAAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
24 24 0.69
26 11 0.31
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (25 bp):
AATGCTAGGCAAGACTGATGAATAA
Found at i:42777818 original size:15 final size:16
Alignment explanation
Indices: 42777798--42777830 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42777788 AAACATTATG
42777798 ATAATTATGG-TAATT
1 ATAATTATGGTTAATT
*
42777813 ATAATTTTGGTTAATT
1 ATAATTATGGTTAATT
42777829 AT
1 AT
42777831 TATGATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (16 bp):
ATAATTATGGTTAATT
Found at i:42784389 original size:14 final size:14
Alignment explanation
Indices: 42784370--42784396 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42784360 TTGTTGTCGA
42784370 TTTTCCCTCTTCTC
1 TTTTCCCTCTTCTC
42784384 TTTTCCCTCTTCT
1 TTTTCCCTCTTCT
42784397 TTACTTTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTCCCTCTTCTC
Found at i:42785318 original size:27 final size:27
Alignment explanation
Indices: 42785274--42785538 Score: 302
Period size: 27 Copynumber: 9.8 Consensus size: 27
42785264 TGCGATTCAT
*
42785274 GGTAAAATTAAC-AAAATACCCCCGAAG
1 GGTAAAATT-ACTGAAATACCCCCGAAG
* * * *
42785301 GGTAAAATGACTGGAATACGCTCGAAG
1 GGTAAAATTACTGAAATACCCCCGAAG
* * *
42785328 GGTAAAATTATTGAAATAACCTCGAAG
1 GGTAAAATTACTGAAATACCCCCGAAG
**
42785355 GGTAAAATTA-TCGAAATACCCTTGAAG
1 GGTAAAATTACT-GAAATACCCCCGAAG
* *
42785382 GGTAAAATTACTGAAATACCCTCGAGG
1 GGTAAAATTACTGAAATACCCCCGAAG
42785409 GGTAAAATTACTGAAATACCCCCGAAG
1 GGTAAAATTACTGAAATACCCCCGAAG
* *
42785436 GGTAAAATTACCGAAATACCACCGAAG
1 GGTAAAATTACTGAAATACCCCCGAAG
* *
42785463 GATAAAATTACCGAAATACCCCCGAAG
1 GGTAAAATTACTGAAATACCCCCGAAG
*
42785490 GGTAAAATAAGC-GAAATACCCCCGAAG
1 GGTAAAATTA-CTGAAATACCCCCGAAG
* **
42785517 GGTAAAATAACTGTTATACCCC
1 GGTAAAATTACTGAAATACCCC
42785539 TAGGAGTTGA
Statistics
Matches: 209, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
26 4 0.02
27 203 0.97
28 2 0.01
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (27 bp):
GGTAAAATTACTGAAATACCCCCGAAG
Done.