Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 87 of 135
Found at i:33380067 original size:29 final size:29
Alignment explanation
Indices: 33380025--33380108 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 29
33380015 AATAAAAATC
33380025 ATAAAAGT-TATAAAAAATATAAAAATTTA
1 ATAAAA-TATATAAAAAATATAAAAATTTA
* *
33380054 ATAAAATATATAAAAAATGAT-AGAATTTT
1 ATAAAATATATAAAAAAT-ATAAAAATTTA
33380083 ATAAAA-ATCATAAAAAAATTATAAAA
1 ATAAAATAT-AT-AAAAAA-TATAAAA
33380109 TATGTCAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
28 3 0.07
29 30 0.65
30 10 0.22
31 3 0.07
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (29 bp):
ATAAAATATATAAAAAATATAAAAATTTA
Found at i:33380108 original size:9 final size:9
Alignment explanation
Indices: 33380016--33380108 Score: 53
Period size: 9 Copynumber: 9.7 Consensus size: 9
33380006 ACATTAAAAA
*
33380016 ATAAAAATC
1 ATAAAAATT
*
33380025 ATAAAAGTT
1 ATAAAAATT
*
33380034 ATAAAAAAT
1 ATAAAAATT
33380043 ATAAAAATT
1 ATAAAAATT
33380052 -TAATAAAATAT
1 AT-A-AAAAT-T
*
33380063 ATAAAAAATG
1 AT-AAAAATT
**
33380073 ATAGAATTTT
1 ATA-AAAATT
33380083 ATAAAAATCAT
1 ATAAAAAT--T
*
33380094 AAAAAAATT
1 ATAAAAATT
33380103 ATAAAA
1 ATAAAA
33380109 TATGTCAAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 14
0.70 0.14 0.15
Matches are distributed among these distances:
8 1 0.02
9 33 0.52
10 13 0.20
11 14 0.22
12 3 0.05
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (9 bp):
ATAAAAATT
Found at i:33380390 original size:27 final size:27
Alignment explanation
Indices: 33380352--33380418 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
33380342 CCTATCAGGT
* *
33380352 AGGCGCCAATGAAGGTGTCTCATAGAG
1 AGGCGCCAATGAAGGAGCCTCATAGAG
*
33380379 AGGCGCCAATGAAGGAGCCTTATAGAG
1 AGGCGCCAATGAAGGAGCCTCATAGAG
33380406 AGGCGCCAATGAA
1 AGGCGCCAATGAA
33380419 ATTTATGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.33, C:0.19, G:0.33, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGAGCCTCATAGAG
Found at i:33380871 original size:3 final size:3
Alignment explanation
Indices: 33380865--33380905 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
33380855 TAGAGAAAGG
* *
33380865 AGA AGA AG- AGA AGG AGA AGG AGA AGA AG- AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
33380906 AGAAAGAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:33380886 original size:20 final size:20
Alignment explanation
Indices: 33380861--33380903 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
33380851 AAAATAGAGA
*
33380861 AAGGAGAAGAAGAGAAGGAG
1 AAGGAGAAGAAGAGAAGAAG
33380881 AAGGAGAAGAAGAGAAGAAG
1 AAGGAGAAGAAGAGAAGAAG
33380901 AAG
1 AAG
33380904 AAAGAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (20 bp):
AAGGAGAAGAAGAGAAGAAG
Found at i:33380912 original size:14 final size:15
Alignment explanation
Indices: 33380858--33380913 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 15
33380848 AAAAAAATAG
33380858 AGAAAGGAGAAGAAG-
1 AGAAA-GAGAAGAAGA
* *
33380873 AGAAGGAGAAGGAGA
1 AGAAAGAGAAGAAGA
33380888 AG-AAGAGAAGAAGA
1 AGAAAGAGAAGAAGA
33380902 AGAAAGA-AAGAA
1 AGAAAGAGAAGAA
33380914 AGAAAGAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 25 0.71
15 10 0.29
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (15 bp):
AGAAAGAGAAGAAGA
Found at i:33381123 original size:15 final size:15
Alignment explanation
Indices: 33381082--33381123 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
33381072 GTTAACTCAT
*
33381082 TTAATTTTTATATAA
1 TTAACTTTTATATAA
33381097 TGTAACTTTTATATAA
1 T-TAACTTTTATATAA
*
33381113 TTAAGTTTTAT
1 TTAACTTTTAT
33381124 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (15 bp):
TTAACTTTTATATAA
Found at i:33384780 original size:22 final size:23
Alignment explanation
Indices: 33384755--33384808 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
33384745 ATACCTTATT
*
33384755 TTTTTCTTCT-TTTCCTTCCTTC
1 TTTTTCTTCTGCTTCCTTCCTTC
33384777 -TTTTCTTCTGCTTCCTTCCTTC
1 TTTTTCTTCTGCTTCCTTCCTTC
33384799 TTATTTCTTC
1 TT-TTTCTTC
33384809 CGTTTCTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 9 0.32
22 11 0.39
23 1 0.04
24 7 0.25
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTTCTTCTGCTTCCTTCCTTC
Found at i:33384780 original size:24 final size:22
Alignment explanation
Indices: 33384748--33384808 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
33384738 AACCAAAATA
*
33384748 CCTTATTTTTTTCTTCTTTTCCTT
1 CCTTCTTTTTTTCTTC--TTCCTT
* *
33384772 CCTTCTTTTCTTCTGCTTCCTT
1 CCTTCTTTTTTTCTTCTTCCTT
*
33384794 CCTTC-TTATTTCTTC
1 CCTTCTTTTTTTCTTC
33384809 CGTTTCTCTA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 7 0.23
22 11 0.35
24 13 0.42
ACGTcount: A:0.03, C:0.31, G:0.02, T:0.64
Consensus pattern (22 bp):
CCTTCTTTTTTTCTTCTTCCTT
Found at i:33387094 original size:36 final size:36
Alignment explanation
Indices: 33387016--33387096 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 36
33387006 ACGAGGTTTA
* *
33387016 GGATTGAATTGTAGAATAAGAAAATATGTGTTTGAG
1 GGATTAAATTGTAGAATAAGAAAATATGTGTTTAAG
* *
33387052 GAATTAAATTGTAGAAT-AGTAAAATTTG-GATTTAAG
1 GGATTAAATTGTAGAATAAG-AAAATATGTG-TTTAAG
33387088 GGATTAAAT
1 GGATTAAAT
33387097 CGTAAAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
35 3 0.08
36 35 0.92
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (36 bp):
GGATTAAATTGTAGAATAAGAAAATATGTGTTTAAG
Found at i:33391601 original size:18 final size:17
Alignment explanation
Indices: 33391571--33391604 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
33391561 TCTCTTATAG
*
33391571 TTTGATTTTATTTTAAT
1 TTTGATTTAATTTTAAT
33391588 TTTGAATTTAATTTTAA
1 TTTG-ATTTAATTTTAA
33391605 GAATTAGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTGATTTAATTTTAAT
Found at i:33403254 original size:9 final size:9
Alignment explanation
Indices: 33403240--33403284 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
33403230 AAACCTCTAA
33403240 GCCTCCGCC
1 GCCTCCGCC
33403249 GCCTCCGCC
1 GCCTCCGCC
*
33403258 GCCACCGCC
1 GCCTCCGCC
* * *
33403267 TCCGCCACC
1 GCCTCCGCC
33403276 GCCTCCGCC
1 GCCTCCGCC
33403285 TCCGCTTCCG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.04, C:0.67, G:0.20, T:0.09
Consensus pattern (9 bp):
GCCTCCGCC
Found at i:33403265 original size:6 final size:6
Alignment explanation
Indices: 33403241--33403305 Score: 76
Period size: 6 Copynumber: 10.8 Consensus size: 6
33403231 AACCTCTAAG
* * * * *
33403241 CCTCCG CCGCCT CCGCCG CCACCG CCTCCG CCACCG CCTCCG CCTCCG
1 CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG
*
33403289 CTTCCG CCTCCG CCTCC
1 CCTCCG CCTCCG CCTCC
33403306 ACCACTGCCA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.03, C:0.66, G:0.17, T:0.14
Consensus pattern (6 bp):
CCTCCG
Found at i:33403277 original size:18 final size:18
Alignment explanation
Indices: 33403256--33403315 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
33403246 GCCGCCTCCG
33403256 CCGCCACCGCCTCCGCCA
1 CCGCCACCGCCTCCGCCA
* **
33403274 CCGCCTCCGCCTCCGCTT
1 CCGCCACCGCCTCCGCCA
* *
33403292 CCGCCTCCGCCTCCACCA
1 CCGCCACCGCCTCCGCCA
*
33403310 CTGCCA
1 CCGCCA
33403316 TCATTTGCTC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.08, C:0.63, G:0.15, T:0.13
Consensus pattern (18 bp):
CCGCCACCGCCTCCGCCA
Found at i:33407161 original size:12 final size:12
Alignment explanation
Indices: 33407146--33407181 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
33407136 TGTTGATATG
33407146 GATGATAGTTAT
1 GATGATAGTTAT
33407158 GATGA-AGATTAT
1 GATGATAG-TTAT
33407170 GATGATAGTTAT
1 GATGATAGTTAT
33407182 AACTACTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.09
12 18 0.82
13 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (12 bp):
GATGATAGTTAT
Found at i:33407910 original size:113 final size:114
Alignment explanation
Indices: 33407698--33407926 Score: 451
Period size: 113 Copynumber: 2.0 Consensus size: 114
33407688 ACTAAGTATA
33407698 AAAATATGACTTGAGAATTAATTTAAGATTTTTAAATTATTATTTAATTAATTATAATTAAATAA
1 AAAATATGACTTGAGAATTAATTTAAGATTTTTAAATTATTATTTAATTAATTATAATTAAATAA
33407763 TTGATGTTTAAAAATAAAATTAAATTAATTAGTCAATTTGAATTTGTTG
66 TTGATGTTTAAAAATAAAATTAAATTAATTAGTCAATTTGAATTTGTTG
33407812 AAAATATGACTTG-GAATTAATTTAAGATTTTTAAATTATTATTTAATTAATTATAATTAAATAA
1 AAAATATGACTTGAGAATTAATTTAAGATTTTTAAATTATTATTTAATTAATTATAATTAAATAA
33407876 TTGATGTTTAAAAATAAAATTAAATTAATTAGTCAATTTGAATTTGTTG
66 TTGATGTTTAAAAATAAAATTAAATTAATTAGTCAATTTGAATTTGTTG
33407925 AA
1 AA
33407927 TATGTAAATT
Statistics
Matches: 115, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
113 102 0.89
114 13 0.11
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (114 bp):
AAAATATGACTTGAGAATTAATTTAAGATTTTTAAATTATTATTTAATTAATTATAATTAAATAA
TTGATGTTTAAAAATAAAATTAAATTAATTAGTCAATTTGAATTTGTTG
Found at i:33409359 original size:17 final size:17
Alignment explanation
Indices: 33409337--33409373 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
33409327 ATGATTAATA
33409337 TAATTTTTAACATTTTT
1 TAATTTTTAACATTTTT
*
33409354 TAATTTTTAATATTTTT
1 TAATTTTTAACATTTTT
33409371 TAA
1 TAA
33409374 ATTATTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TAATTTTTAACATTTTT
Found at i:33412531 original size:43 final size:43
Alignment explanation
Indices: 33412444--33412653 Score: 217
Period size: 43 Copynumber: 4.9 Consensus size: 43
33412434 AGCTCGTACA
* ** * *** *
33412444 ATGCCAACATCCCAGACATGGTCTTACATGTATTTACAAATCG
1 ATGCCAACGTCCCAGATGTGGTCTTACACGTAAACACAAGTCG
33412487 ATGCC-ACTGTCCCAGATAG-GGTCTTACACGTAAACACAAGTCG
1 ATGCCAAC-GTCCCAGAT-GTGGTCTTACACGTAAACACAAGTCG
* * * *
33412530 ATGCCAACATCCAAGATGTGGTCTTACACGTAAACATAAGTAG
1 ATGCCAACGTCCCAGATGTGGTCTTACACGTAAACACAAGTCG
** * * *
33412573 ATGTTAATGTCCCAGATGTGGTCTTACACGTAAACATAAGTCC
1 ATGCCAACGTCCCAGATGTGGTCTTACACGTAAACACAAGTCG
* *
33412616 ATGCCAACGTTCCAGACGTGGTCTTACACGTAAACACA
1 ATGCCAACGTCCCAGATGTGGTCTTACACGTAAACACA
33412654 TATTGAAAAT
Statistics
Matches: 138, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
42 3 0.02
43 133 0.96
44 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGATGTGGTCTTACACGTAAACACAAGTCG
Found at i:33412589 original size:86 final size:86
Alignment explanation
Indices: 33412494--33412651 Score: 248
Period size: 86 Copynumber: 1.8 Consensus size: 86
33412484 TCGATGCCAC
* *
33412494 TGTCCCAGATAG-GGTCTTACACGTAAACACAAGTCGATGCCAAC-ATCCAAGATGTGGTCTTAC
1 TGTCCCAGAT-GTGGTCTTACACGTAAACACAAGTCCATGCCAACGATCC-AGACGTGGTCTTAC
33412557 ACGTAAACATAAGTAGATGTTAA
64 ACGTAAACATAAGTAGATGTTAA
* *
33412580 TGTCCCAGATGTGGTCTTACACGTAAACATAAGTCCATGCCAACGTTCCAGACGTGGTCTTACAC
1 TGTCCCAGATGTGGTCTTACACGTAAACACAAGTCCATGCCAACGATCCAGACGTGGTCTTACAC
33412645 GTAAACA
66 GTAAACA
33412652 CATATTGAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
85 1 0.02
86 62 0.94
87 3 0.05
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (86 bp):
TGTCCCAGATGTGGTCTTACACGTAAACACAAGTCCATGCCAACGATCCAGACGTGGTCTTACAC
GTAAACATAAGTAGATGTTAA
Found at i:33418046 original size:18 final size:18
Alignment explanation
Indices: 33418023--33418060 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
33418013 TTACCAATGC
33418023 TCTTGGTGTGGGTTTAAG
1 TCTTGGTGTGGGTTTAAG
33418041 TCTTGGTGTGGGTTTAAG
1 TCTTGGTGTGGGTTTAAG
33418059 TC
1 TC
33418061 CAATCTCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.08, G:0.37, T:0.45
Consensus pattern (18 bp):
TCTTGGTGTGGGTTTAAG
Found at i:33420661 original size:43 final size:43
Alignment explanation
Indices: 33420599--33420786 Score: 261
Period size: 43 Copynumber: 4.3 Consensus size: 43
33420589 ATGACCTTTA
*
33420599 ACAAACGCCGCTAAAGACCACGACCTTTAGCGGCGATTTTTTC
1 ACAAACGCCGCTAATGACCACGACCTTTAGCGGCGATTTTTTC
* * **
33420642 ACAAACGCCGCTAATGACCAGGACCTTTAGCGGCGCTTTTGCC
1 ACAAACGCCGCTAATGACCACGACCTTTAGCGGCGATTTTTTC
*
33420685 ACAAACGCCGCTAAAGACC-CTGACCTTTAGCGGCGATTTTTTCC
1 ACAAACGCCGCTAATGACCAC-GACCTTTAGCGGCGATTTTTT-C
* * *
33420729 ACAAACGCCGCTAATGACAACGACCTTTAGCGGCGCTTTTTTA
1 ACAAACGCCGCTAATGACCACGACCTTTAGCGGCGATTTTTTC
*
33420772 AAAAACGCCGCTAAT
1 ACAAACGCCGCTAAT
33420787 TTTGGCAGAT
Statistics
Matches: 127, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
43 88 0.69
44 38 0.30
45 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (43 bp):
ACAAACGCCGCTAATGACCACGACCTTTAGCGGCGATTTTTTC
Found at i:33420766 original size:87 final size:86
Alignment explanation
Indices: 33420599--33420768 Score: 297
Period size: 86 Copynumber: 2.0 Consensus size: 86
33420589 ATGACCTTTA
* *
33420599 ACAAACGCCGCTAAAGACCACGACCTTTAGCGGCGATTTTTTCACAAACGCCGCTAATGACCAGG
1 ACAAACGCCGCTAAAGACCACGACCTTTAGCGGCGATTTTTTCACAAACGCCGCTAATGACAACG
33420664 ACCTTTAGCGGCGCTTTTGCC
66 ACCTTTAGCGGCGCTTTTGCC
33420685 ACAAACGCCGCTAAAGACC-CTGACCTTTAGCGGCGATTTTTTCCACAAACGCCGCTAATGACAA
1 ACAAACGCCGCTAAAGACCAC-GACCTTTAGCGGCGATTTTTT-CACAAACGCCGCTAATGACAA
33420749 CGACCTTTAGCGGCGCTTTT
64 CGACCTTTAGCGGCGCTTTT
33420769 TTAAAAAACG
Statistics
Matches: 80, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
85 1 0.01
86 40 0.50
87 39 0.49
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (86 bp):
ACAAACGCCGCTAAAGACCACGACCTTTAGCGGCGATTTTTTCACAAACGCCGCTAATGACAACG
ACCTTTAGCGGCGCTTTTGCC
Found at i:33420778 original size:87 final size:86
Alignment explanation
Indices: 33420595--33420785 Score: 303
Period size: 87 Copynumber: 2.2 Consensus size: 86
33420585 GACCATGACC
33420595 TTTAACAAACGCCGCTAAAGACCACGACCTTTAGCGGCGATTTTTTCACAAACGCCGCTAATGAC
1 TTTAACAAACGCCGCTAAAGACCACGACCTTTAGCGGCGATTTTTTCACAAACGCCGCTAATGAC
* *
33420660 CAGGACCTTTAGCGGCGCTTT
66 AACGACCTTTAGCGGCGCTTT
***
33420681 TGCCACAAACGCCGCTAAAGACC-CTGACCTTTAGCGGCGATTTTTTCCACAAACGCCGCTAATG
1 TTTAACAAACGCCGCTAAAGACCAC-GACCTTTAGCGGCGATTTTTT-CACAAACGCCGCTAATG
33420745 ACAACGACCTTTAGCGGCGCTTT
64 ACAACGACCTTTAGCGGCGCTTT
*
33420768 TTTAAAAAACGCCGCTAA
1 TTTAACAAACGCCGCTAA
33420786 TTTTGGCAGA
Statistics
Matches: 94, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
85 1 0.01
86 41 0.44
87 52 0.55
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.24
Consensus pattern (86 bp):
TTTAACAAACGCCGCTAAAGACCACGACCTTTAGCGGCGATTTTTTCACAAACGCCGCTAATGAC
AACGACCTTTAGCGGCGCTTT
Found at i:33424513 original size:16 final size:16
Alignment explanation
Indices: 33424494--33424525 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
33424484 TATTTATTTC
33424494 TTAATTGTATCTTTTA
1 TTAATTGTATCTTTTA
33424510 TTAATTGTATCTTTTA
1 TTAATTGTATCTTTTA
33424526 ATTACTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (16 bp):
TTAATTGTATCTTTTA
Found at i:33424929 original size:2 final size:2
Alignment explanation
Indices: 33424924--33424950 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33424914 TAAAGTTATC
33424924 TA 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 TA T
33424951 CTATTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33425548 original size:41 final size:41
Alignment explanation
Indices: 33425486--33425798 Score: 405
Period size: 41 Copynumber: 7.6 Consensus size: 41
33425476 TTAACAAATA
* *
33425486 TTCTACAAAAACGCCGCTAAAGGCCCGAGCATTAGTGGCGC
1 TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
* * *
33425527 TTTTTCAAAAACGCAGCTAAAGGCCCAAGCATTAGCGGCGC
1 TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
*
33425568 TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGTCG-
1 TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
* * *
33425608 TTGCTTCAAAAACGCCGCTAAAGGCCCCAGCAGTAGCAGCG-
1 TT-CTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
* * ** *
33425649 TTTTTGAAGAAGTGCCGCTAAAGGCCAGAGCATTAGCGGCGC
1 TTCTTCAA-AAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
* *
33425691 TGCTTAAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
1 TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
* *
33425732 TTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGTGGCGC
1 TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
* * *
33425773 TTCTTAAAAAACGCCACTACAGGCCC
1 TTCTTCAAAAACGCCGCTAAAGGCCC
33425799 CAAAAACTCA
Statistics
Matches: 234, Mismatches: 35, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
40 6 0.03
41 223 0.95
42 5 0.02
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.19
Consensus pattern (41 bp):
TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
Found at i:33427595 original size:40 final size:40
Alignment explanation
Indices: 33427550--33427677 Score: 133
Period size: 40 Copynumber: 3.3 Consensus size: 40
33427540 TTTATTAAAA
33427550 TATAAAAAAATAAATACCTTCAAAATACTATTAATTGTTT
1 TATAAAAAAATAAATACCTTCAAAATACTATTAATTGTTT
* * * * ****
33427590 TATAAAAAAAT-AATA-TTTTATTAAT--T-TTTATTAAAA
1 TATAAAAAAATAAATACCTTCA-AAATACTATTAATTGTTT
33427626 TAT-AAAAAATAAATACCTTCAAAATACTATTAATTGTTT
1 TATAAAAAAATAAATACCTTCAAAATACTATTAATTGTTT
33427665 TATAAAAAAATAA
1 TATAAAAAAATAA
33427678 TATTTTATTA
Statistics
Matches: 65, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
35 7 0.11
36 15 0.23
37 4 0.06
38 4 0.06
39 15 0.23
40 20 0.31
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (40 bp):
TATAAAAAAATAAATACCTTCAAAATACTATTAATTGTTT
Found at i:33427601 original size:36 final size:37
Alignment explanation
Indices: 33427556--33427676 Score: 88
Period size: 37 Copynumber: 3.3 Consensus size: 37
33427546 AAAATATAAA
33427556 AAAATAAATACCTTCAAAATACTATTAATTGTTTTAT
1 AAAATAAATACCTTCAAAATACTATTAATTGTTTTAT
** * * ** ** * *
33427593 AAAA-AAATAATATTTTATTAATTTTTATTAA--AATATAA
1 AAAATAAAT-A-CCTTCA--AAATACTATTAATTGTTTTAT
33427631 AAAATAAATACCTTCAAAATACTATTAATTGTTTTAT
1 AAAATAAATACCTTCAAAATACTATTAATTGTTTTAT
33427668 AAAA-AAATA
1 AAAATAAATA
33427677 ATATTTTATT
Statistics
Matches: 57, Mismatches: 20, Indels: 15
0.62 0.22 0.16
Matches are distributed among these distances:
35 9 0.16
36 9 0.16
37 15 0.26
38 11 0.19
39 4 0.07
40 9 0.16
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.40
Consensus pattern (37 bp):
AAAATAAATACCTTCAAAATACTATTAATTGTTTTAT
Found at i:33427695 original size:76 final size:76
Alignment explanation
Indices: 33427540--33427693 Score: 301
Period size: 75 Copynumber: 2.0 Consensus size: 76
33427530 TTTTTCTAAA
33427540 TTTATTAAAATATAAAAAAATAAATACCTTCAAAATACTATTAATTGTTTTATAAAAAAATAATA
1 TTTATTAAAATATAAAAAAATAAATACCTTCAAAATACTATTAATTGTTTTATAAAAAAATAATA
33427605 TTTTATTAATT
66 TTTTATTAATT
33427616 TTTATTAAAATAT-AAAAAATAAATACCTTCAAAATACTATTAATTGTTTTATAAAAAAATAATA
1 TTTATTAAAATATAAAAAAATAAATACCTTCAAAATACTATTAATTGTTTTATAAAAAAATAATA
33427680 TTTTATTAATT
66 TTTTATTAATT
33427691 TTT
1 TTT
33427694 TAACCAAGTT
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
75 65 0.83
76 13 0.17
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (76 bp):
TTTATTAAAATATAAAAAAATAAATACCTTCAAAATACTATTAATTGTTTTATAAAAAAATAATA
TTTTATTAATT
Found at i:33429825 original size:37 final size:37
Alignment explanation
Indices: 33429719--33430102 Score: 362
Period size: 37 Copynumber: 10.2 Consensus size: 37
33429709 AAAAATGGAA
* * * *
33429719 TACTGAATATACTGAATGTGCTCAAAAGAGAAATGTC
1 TACTGATTATACTGAATGTGCTCAAACGAGCAATATC
* *
33429756 TACTAATTATACTGAAAGTTGCTCAAACGAGCAATATCC
1 TACTGATTATACTGAATG-TGCTCAAACGAGCAATAT-C
* * *
33429795 T-CTGATTATACTGAATGGGCTCAAATGAGCAATGTC
1 TACTGATTATACTGAATGTGCTCAAACGAGCAATATC
* * * *
33429831 TAATGCTTATATTGAATGTACTCAAACGAGCAATATC
1 TACTGATTATACTGAATGTGCTCAAACGAGCAATATC
* *
33429868 TACTG-TATCTACTGAATGTGCTCGAAA-GAGCAATGTC
1 TACTGAT-TATACTGAATGTGCTC-AAACGAGCAATATC
* *
33429905 TACTGATTATACTGAAAGTTGTTCAAACGAGCAATATC
1 TACTGATTATACTGAATG-TGCTCAAACGAGCAATATC
* * *
33429943 CACTAATTATACTGAATGGGCTCAAACGAGCAATATC
1 TACTGATTATACTGAATGTGCTCAAACGAGCAATATC
* * * * *
33429980 TACTGAATATACTAAACGTGCTCAAAAGAGCAATGTC
1 TACTGATTATACTGAATGTGCTCAAACGAGCAATATC
* * *
33430017 TACTGATTATACTGAAAGTTGCTCAAACAAGCGATATC
1 TACTGATTATACTGAATG-TGCTCAAACGAGCAATATC
* * *
33430055 CACTGATTATAC-GAAATTCATGCTCAAACGAGCATTATC
1 TACTGATTATACTG-AA-T-GTGCTCAAACGAGCAATATC
* *
33430094 CAATGATTA
1 TACTGATTA
33430103 CGTGAAATAA
Statistics
Matches: 281, Mismatches: 54, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
36 3 0.01
37 163 0.58
38 89 0.32
39 26 0.09
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (37 bp):
TACTGATTATACTGAATGTGCTCAAACGAGCAATATC
Found at i:33429931 original size:112 final size:111
Alignment explanation
Indices: 33429726--33430066 Score: 368
Period size: 112 Copynumber: 3.0 Consensus size: 111
33429716 GAATACTGAA
* * *
33429726 TATACTGAATGTG-CTCAAAAGAGAAATGTCTACT-AATTATACTGAAAGTTGCTCAAACGAGCA
1 TATACTGAATG-GACTCAAACGAGCAATATCTACTGAA-TATACTGAAAG-TGCTCAAA-GAGCA
* * * * * * **
33429789 ATATCCT-CTGATTATACTGAATG-GGCTCAAATGAGCAATGTCTAATGCT
62 ATGT-CTACTGATTATACTGAAAGTTGCTCAAACGAGCAATATCCAATAAT
* * * * *
33429838 TATATTGAATGTACTCAAACGAGCAATATCTACTGTATCTACTGAATGTGCTCGAAAGAGCAATG
1 TATACTGAATGGACTCAAACGAGCAATATCTACTGAATATACTGAAAGTGCTC-AAAGAGCAATG
* *
33429903 TCTACTGATTATACTGAAAGTTGTTCAAACGAGCAATATCCACTAAT
65 TCTACTGATTATACTGAAAGTTGCTCAAACGAGCAATATCCAATAAT
*
33429950 TATACTGAATGGGCTCAAACGAGCAATATCTACTGAATATACT-AAACGTGCTCAAAAGAGCAAT
1 TATACTGAATGGACTCAAACGAGCAATATCTACTGAATATACTGAAA-GTGCTC-AAAGAGCAAT
* * * *
33430014 GTCTACTGATTATACTGAAAGTTGCTCAAACAAGCGATATCCACTGAT
64 GTCTACTGATTATACTGAAAGTTGCTCAAACGAGCAATATCCAATAAT
33430062 TATAC
1 TATAC
33430067 GAAATTCATG
Statistics
Matches: 194, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
110 2 0.01
111 30 0.15
112 161 0.83
113 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (111 bp):
TATACTGAATGGACTCAAACGAGCAATATCTACTGAATATACTGAAAGTGCTCAAAGAGCAATGT
CTACTGATTATACTGAAAGTTGCTCAAACGAGCAATATCCAATAAT
Found at i:33430004 original size:149 final size:147
Alignment explanation
Indices: 33429719--33430095 Score: 450
Period size: 149 Copynumber: 2.5 Consensus size: 147
33429709 AAAAATGGAA
* *
33429719 TACTGAATATACTGAATGTGCTCAAAAGAGAAATGTCTACTAATTATACTGAAAGTTGCTCAAAC
1 TACTG-ATATACTGAATGTGCTC-AAAGAGCAATGTCTACTGATTATACTGAAAGTTGCTCAAAC
* * * * ** * * *
33429784 GAGCAATATCCTCTGATTATACTGAATGGGCTCAAATGAGCAATGTCTAATGCTTATATTGAATG
64 GAGCAATATCCACTAATTATACTGAATGGGCTCAAACGAGCAATATCTAATGAATATACTAAACG
*
33429849 TACTCAAACGAGCAATATC
129 TACTCAAAAGAGCAATATC
* *
33429868 TACTGTATCTACTGAATGTGCTCGAAAGAGCAATGTCTACTGATTATACTGAAAGTTGTTCAAAC
1 TACTG-ATATACTGAATGTGCTC-AAAGAGCAATGTCTACTGATTATACTGAAAGTTGCTCAAAC
*
33429933 GAGCAATATCCACTAATTATACTGAATGGGCTCAAACGAGCAATATCTACTGAATATACTAAACG
64 GAGCAATATCCACTAATTATACTGAATGGGCTCAAACGAGCAATATCTAATGAATATACTAAACG
* *
33429998 TGCTCAAAAGAGCAATGTC
129 TACTCAAAAGAGCAATATC
* * * * * *
33430017 TACTGATTATACTGAAAGTTGCTCAAACAAGCGATATCCACTGATTATAC-GAAATTCATGCTCA
1 TACTGA-TATACTGAATG-TGCTCAAA-GAGCAATGTCTACTGATTATACTGAAAGT--TGCTCA
*
33430081 AACGAGCATTATCCA
61 AACGAGCAATATCCA
33430096 ATGATTACGT
Statistics
Matches: 195, Mismatches: 28, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
148 1 0.01
149 152 0.78
150 23 0.12
151 19 0.10
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (147 bp):
TACTGATATACTGAATGTGCTCAAAGAGCAATGTCTACTGATTATACTGAAAGTTGCTCAAACGA
GCAATATCCACTAATTATACTGAATGGGCTCAAACGAGCAATATCTAATGAATATACTAAACGTA
CTCAAAAGAGCAATATC
Found at i:33435012 original size:15 final size:14
Alignment explanation
Indices: 33434992--33435039 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
33434982 TTTTAAAATA
33434992 TTTTTAAAATACTTT
1 TTTTTAAAATA-TTT
** *
33435007 TTTTTAATTTTTTT
1 TTTTTAAAATATTT
33435021 ATTTTTAAAATATTT
1 -TTTTTAAAATATTT
33435036 TTTT
1 TTTT
33435040 AATGTTTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTAAAATATTT
Found at i:33435024 original size:30 final size:28
Alignment explanation
Indices: 33434990--33435047 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
33434980 AATTTTAAAA
*
33434990 TATTTTTAAAATACTTTTTTTTAATTTTTT
1 TATTTTTAAAATA--TTTTTTTAATGTTTT
33435020 TATTTTTAAAATATTTTTTTAATGTTTT
1 TATTTTTAAAATATTTTTTTAATGTTTT
33435048 ATTAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 14 0.52
30 13 0.48
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (28 bp):
TATTTTTAAAATATTTTTTTAATGTTTT
Found at i:33439025 original size:29 final size:29
Alignment explanation
Indices: 33438993--33439051 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
33438983 ATAAAATAAA
*
33438993 ATCCTAAAATTAGATAATCCTTA-ATAATT
1 ATCCTAAAATTA-ATAATCCTAACATAATT
* *
33439022 ATCCTAATATTAATTATCCTAACATAATT
1 ATCCTAAAATTAATAATCCTAACATAATT
33439051 A
1 A
33439052 AAATAGAGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (29 bp):
ATCCTAAAATTAATAATCCTAACATAATT
Found at i:33445406 original size:14 final size:15
Alignment explanation
Indices: 33445387--33445415 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
33445377 ATTTAAGTTT
33445387 AAAAAATC-TTTTAA
1 AAAAAATCATTTTAA
33445401 AAAAAATCATTTTAA
1 AAAAAATCATTTTAA
33445416 TAGCCTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAAATCATTTTAA
Found at i:33452615 original size:174 final size:175
Alignment explanation
Indices: 33452297--33452617 Score: 414
Period size: 174 Copynumber: 1.8 Consensus size: 175
33452287 AATCCTAATA
* * *
33452297 TCTAAACCAACTCAGAGAATATCAAACTAAACAAGTGCACTACTAGCAAGTTAAATTTCACCTTT
1 TCTAAACCAACTCAAAGAATATCAAACTAAACAAGTGCACTAATAGCAAATTAAATTTCACCTTT
* * * * * *
33452362 CCAGCATTTCTCAAGCATCTAAATAAACTAATTAAGAGATTCAAATCTCACAACCAATTTTCCTA
66 CCAGCATTTCTCAAGCAGCCAAATAAACTAATTAAGAGATCCAAATCTCACAACCAATCTTACAA
* *
33452427 GACCTAATGCTAAAATGAGATTCACAGAAAACAAATTTCTTAGCC
131 AACCTAAAGCTAAAATGAGATTCACAGAAAACAAATTTCTTAGCC
* * * ** *
33452472 TCTAAACCAACTCAAAGAA-ATCAAAGTAAAC-AGCTTCATTAATAGCAAATTGCATTTCACTTT
1 TCTAAACCAACTCAAAGAATATCAAACTAAACAAG-TGCACTAATAGCAAATTAAATTTCACCTT
* * * *
33452535 TCCATCATTTCTCAAGCAGCCAAATAAACTGATTAAAGAGATCCTAATCTCACTACCAA-CTTAC
65 TCCAGCATTTCTCAAGCAGCCAAATAAACTAATT-AAGAGATCCAAATCTCACAACCAATCTTAC
33452599 AAAACCTAAAGCTAAAATG
129 AAAACCTAAAGCTAAAATG
33452618 TAATTTTTTT
Statistics
Matches: 123, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
173 2 0.02
174 82 0.67
175 39 0.32
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (175 bp):
TCTAAACCAACTCAAAGAATATCAAACTAAACAAGTGCACTAATAGCAAATTAAATTTCACCTTT
CCAGCATTTCTCAAGCAGCCAAATAAACTAATTAAGAGATCCAAATCTCACAACCAATCTTACAA
AACCTAAAGCTAAAATGAGATTCACAGAAAACAAATTTCTTAGCC
Found at i:33461166 original size:61 final size:61
Alignment explanation
Indices: 33461101--33461227 Score: 166
Period size: 61 Copynumber: 2.1 Consensus size: 61
33461091 ATCCTAAATA
* ** *
33461101 TAAAATATTCAACAAAATTAGCCTTCAATGTTTACAA-AATTTGTCATTTTAGTTCGAATTC
1 TAAAAAATTCAACAAAATTAGCCTTCAAAATTTACAATAATTT-TCAATTTAGTTCGAATTC
** * *
33461162 TAAAAAATTCAGTAAATTTAGCCTTCAAAATTTACAATAATTTTCAATTTAGTTCTAATTC
1 TAAAAAATTCAACAAAATTAGCCTTCAAAATTTACAATAATTTTCAATTTAGTTCGAATTC
33461223 TAAAA
1 TAAAA
33461228 CAATAAATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
61 52 0.91
62 5 0.09
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.39
Consensus pattern (61 bp):
TAAAAAATTCAACAAAATTAGCCTTCAAAATTTACAATAATTTTCAATTTAGTTCGAATTC
Found at i:33461239 original size:61 final size:61
Alignment explanation
Indices: 33461118--33461240 Score: 160
Period size: 61 Copynumber: 2.0 Consensus size: 61
33461108 TTCAACAAAA
** * * *
33461118 TTAGCCTTCAATGTTTACAAAATTTGTCATTTTAGTTCGAATTCTAAAAAATTCAGTAAAT
1 TTAGCCTTCAAAATTTACAAAATTTGTCAATTTAGTTCGAATTCTAAAAAATTAAATAAAT
*
33461179 TTAGCCTTCAAAATTTACAATAATTT-TCAATTTAGTTCTAATTCTAAAACAA-TAAATAAAT
1 TTAGCCTTCAAAATTTACAA-AATTTGTCAATTTAGTTCGAATTCTAAAA-AATTAAATAAAT
33461240 T
1 T
33461241 ATTTTTGACC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
61 47 0.87
62 7 0.13
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.41
Consensus pattern (61 bp):
TTAGCCTTCAAAATTTACAAAATTTGTCAATTTAGTTCGAATTCTAAAAAATTAAATAAAT
Found at i:33462418 original size:33 final size:33
Alignment explanation
Indices: 33462309--33462403 Score: 82
Period size: 36 Copynumber: 2.8 Consensus size: 33
33462299 GTCTCAAAAA
* * * * *
33462309 ATAATAGCAAAATTAACAATAAAATAAGAATTAT
1 ATAATAGCAAAA-TGACAATAAAATAATAGTAAC
* *
33462343 ATAATATTCAAACAATAACAATAAAATAATAGTAAC
1 ATAATA-GC-AA-AATGACAATAAAATAATAGTAAC
*
33462379 ATAATAGTAAAATGACAATAAAATA
1 ATAATAGCAAAATGACAATAAAATA
33462404 GTGAGAAATG
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
33 14 0.28
34 8 0.16
35 1 0.02
36 25 0.50
37 2 0.04
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (33 bp):
ATAATAGCAAAATGACAATAAAATAATAGTAAC
Found at i:33464336 original size:16 final size:15
Alignment explanation
Indices: 33464308--33464337 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
33464298 AAATATACAT
33464308 ATTAAAATAATTATA
1 ATTAAAATAATTATA
33464323 ATTAAAATTAATTAT
1 ATTAAAA-TAATTAT
33464338 TATCATACGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTAAAATAATTATA
Found at i:33468969 original size:294 final size:294
Alignment explanation
Indices: 33468440--33468999 Score: 1057
Period size: 294 Copynumber: 1.9 Consensus size: 294
33468430 GATTATTTAA
*
33468440 GGTAACATTAAAATAATAAAGTTAACAAAAATTGACTAAATAATAAAAAATGCTAAAAAAGGGAT
1 GGTAACATTAAAATAATAAAGTTAACAAAAATTGACTAAATAATAAAAAATGCTAAAAAAGGCAT
*
33468505 TAAATCGAAATGAAATAAAACATATAGGGTCAATCCGAAATAAAGGAAAACGAAAAGGATCCAAT
66 TAAATCGAAATGAAATAAAACATATAGGGCCAATCCGAAATAAAGGAAAACGAAAAGGATCCAAT
* *
33468570 TGCGGCGCGCGTAAAAAGGGAAGGACCGAAACAGAAAATAAACCCAAAGTTCTAAAACGCAGCGC
131 TGCGACGCGCGTAAAAAGGGAAGGACCGAAACAAAAAATAAACCCAAAGTTCTAAAACGCAGCGC
33468635 CTCAATGGACTAAAATGAAACAAAAGTAAAATCTTAGGGCTAAATCAAAATAAAACAAAACAACA
196 CTCAATGGACTAAAATGAAACAAAAGTAAAATCTTAGGGCTAAATCAAAATAAAACAAAACAACA
33468700 AAATAATAAAGATGATGATAATAATAATAATAAT
261 AAATAATAAAGATGATGATAATAATAATAATAAT
*
33468734 GGTAACATTAAAATAATAAAGTTAACAAAAATTGACTAAATAATAAAAGATGCTAAAAAAGGCAT
1 GGTAACATTAAAATAATAAAGTTAACAAAAATTGACTAAATAATAAAAAATGCTAAAAAAGGCAT
*
33468799 TAAATCGAAATGAAATAAAACATATAGGGCCAATTCGAAATAAAGGAAAACGAAAAGGATCCAAT
66 TAAATCGAAATGAAATAAAACATATAGGGCCAATCCGAAATAAAGGAAAACGAAAAGGATCCAAT
33468864 TGCGACGCGCGTAAAAAGGGAAGGACCGAAACAAAAAATAAACCCAAAGTTCTAAAACGCAGCGC
131 TGCGACGCGCGTAAAAAGGGAAGGACCGAAACAAAAAATAAACCCAAAGTTCTAAAACGCAGCGC
*
33468929 CTCAATGGACTAAAATGAAACAAAAGTAAAATCTTAGGGCTAAATCAAAATAAAAGAAAACAACA
196 CTCAATGGACTAAAATGAAACAAAAGTAAAATCTTAGGGCTAAATCAAAATAAAACAAAACAACA
33468994 AAATAA
261 AAATAA
33469000 GACCAAATTG
Statistics
Matches: 259, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
294 259 1.00
ACGTcount: A:0.54, C:0.13, G:0.16, T:0.17
Consensus pattern (294 bp):
GGTAACATTAAAATAATAAAGTTAACAAAAATTGACTAAATAATAAAAAATGCTAAAAAAGGCAT
TAAATCGAAATGAAATAAAACATATAGGGCCAATCCGAAATAAAGGAAAACGAAAAGGATCCAAT
TGCGACGCGCGTAAAAAGGGAAGGACCGAAACAAAAAATAAACCCAAAGTTCTAAAACGCAGCGC
CTCAATGGACTAAAATGAAACAAAAGTAAAATCTTAGGGCTAAATCAAAATAAAACAAAACAACA
AAATAATAAAGATGATGATAATAATAATAATAAT
Found at i:33469736 original size:17 final size:17
Alignment explanation
Indices: 33469716--33469748 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
33469706 GGCGCGGCAT
33469716 CAGAACGGTGGCGGCGA
1 CAGAACGGTGGCGGCGA
*
33469733 CAGAATGGTGGCGGCG
1 CAGAACGGTGGCGGCG
33469749 CCGGGCTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.48, T:0.09
Consensus pattern (17 bp):
CAGAACGGTGGCGGCGA
Found at i:33470689 original size:24 final size:24
Alignment explanation
Indices: 33470662--33470708 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
33470652 AAATCAATTA
33470662 TATGCAAAAC-AATTTTAGAAATAC
1 TATGCAAAACAAATTTTA-AAATAC
* *
33470686 TATGTATAACAAATTTTAAAATA
1 TATGCAAAACAAATTTTAAAATA
33470709 AATAAAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (24 bp):
TATGCAAAACAAATTTTAAAATAC
Found at i:33478065 original size:17 final size:18
Alignment explanation
Indices: 33478043--33478082 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
33478033 TGTAATCATC
33478043 ATAATT-TTTATTAAAT-T
1 ATAATTATTT-TTAAATAT
33478060 ATAATTATTTTTAAATAT
1 ATAATTATTTTTAAATAT
33478078 ATAAT
1 ATAAT
33478083 CATCACACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATAATTATTTTTAAATAT
Found at i:33478218 original size:87 final size:89
Alignment explanation
Indices: 33478121--33478295 Score: 221
Period size: 87 Copynumber: 2.0 Consensus size: 89
33478111 TTTAAATAAA
* * * * * * * * *
33478121 AATTTTAAATGTTAATTTAGTAATA-AGATTAAAAATATAGGGTATTTTTGTTGGTTCAAAT-CT
1 AATTTTAAATGTCAACTTAGTAATATA-ATGAAAAATAAAGAGTATTCTCGTCGATTCAAATACT
33478184 TTTCTAAACTCAT-ATTTTATAATT
65 TTTCTAAACTCATGATTTTATAATT
*
33478208 AATTTTAAATGTCAACTTAGTAATATAATGAAAAATAAAGAGTATTCTCGTCGATTCAAATATTT
1 AATTTTAAATGTCAACTTAGTAATATAATGAAAAATAAAGAGTATTCTCGTCGATTCAAATACTT
*
33478273 TTTTAAACTCATGATTTTATAAT
66 TTCTAAACTCATGATTTTATAAT
33478296 ATATATTATA
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
87 50 0.68
88 14 0.19
89 10 0.14
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (89 bp):
AATTTTAAATGTCAACTTAGTAATATAATGAAAAATAAAGAGTATTCTCGTCGATTCAAATACTT
TTCTAAACTCATGATTTTATAATT
Found at i:33478863 original size:43 final size:43
Alignment explanation
Indices: 33478815--33478999 Score: 264
Period size: 43 Copynumber: 4.3 Consensus size: 43
33478805 TTATTTTTAA
**
33478815 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGC-TTTCTCCAC
1 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTTC-CCAC
*
33478858 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTTCCCAC
* * *
33478901 AAACGTCGCGAAAGATCATGTTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTTCCCAC
* * **
33478944 AAACGCTGCTAAAGACCTTGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTTCCCAC
33478987 AAACGCCGCTAAA
1 AAACGCCGCTAAA
33479000 NNNNNNNNNN
Statistics
Matches: 126, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
43 123 0.98
44 3 0.02
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTTCCCAC
Found at i:33480548 original size:21 final size:21
Alignment explanation
Indices: 33480519--33480564 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
33480509 CTAGCCCCTA
* *
33480519 AACCCCTAACCCTTAAATCCC
1 AACCACTAAACCTTAAATCCC
33480540 AACCACTAAACCTTAAATCCC
1 AACCACTAAACCTTAAATCCC
33480561 AACC
1 AACC
33480565 CATAATCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.43, G:0.00, T:0.17
Consensus pattern (21 bp):
AACCACTAAACCTTAAATCCC
Found at i:33480577 original size:21 final size:20
Alignment explanation
Indices: 33480519--33480579 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
33480509 CTAGCCCCTA
*
33480519 AACCCCTAACCCTTAAATCCC
1 AACCCATAACCC-TAAATCCC
*
33480540 AA-CCACTAAACCTTAAATCCC
1 AACCCA-T-AACCCTAAATCCC
33480561 AACCCATAATCCCTAAATC
1 AACCCATAA-CCCTAAATC
33480580 TATACCCCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
20 4 0.12
21 22 0.67
22 7 0.21
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCATAACCCTAAATCCC
Found at i:33480818 original size:22 final size:22
Alignment explanation
Indices: 33480793--33480857 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
33480783 CTTAACCCCA
33480793 TAACCTCTAACCCTTAAACCAT
1 TAACCTCTAACCCTTAAACCAT
* *
33480815 TAACCCCTAACCCCTAAACC-T
1 TAACCTCTAACCCTTAAACCAT
** *
33480836 TAAATTCCAACCCTTAAACCAT
1 TAACCTCTAACCCTTAAACCAT
33480858 AATCCATAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 16 0.46
22 19 0.54
ACGTcount: A:0.37, C:0.38, G:0.00, T:0.25
Consensus pattern (22 bp):
TAACCTCTAACCCTTAAACCAT
Found at i:33481355 original size:41 final size:41
Alignment explanation
Indices: 33481114--33481357 Score: 335
Period size: 41 Copynumber: 5.9 Consensus size: 41
33481104 TAGTATTTTA
* **
33481114 CATTAGCGGCGCTTTTGCAAAAACGCCGCTAAAGAATAGAG
1 CATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAG
* *
33481155 CATTAGCGGCGCTTTTCCAAAAAACGCCGCTAAAGGCAAGAG
1 CATTAGCGGCGCTTTTCC-AAAAACGCCGCTAAAGACCAGAG
* * ** * * * *
33481197 CATTAGCGACCCTTTTTTAAAAATGCCACTAAAGGCAAGAG
1 CATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAG
33481238 CATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAG
1 CATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAG
* *
33481279 CATTAGCGGCGCTTTTACAAAAAGGCCGCTAAAGACCAGAG
1 CATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAG
*
33481320 CATTAGCGGCGCTTTTCCAAAAATGCCGCTAAAGACCA
1 CATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCA
33481358 CGAAAGGTCC
Statistics
Matches: 180, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
41 146 0.81
42 34 0.19
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (41 bp):
CATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAG
Found at i:33481475 original size:55 final size:56
Alignment explanation
Indices: 33481398--33481503 Score: 160
Period size: 55 Copynumber: 1.9 Consensus size: 56
33481388 TAAGTTTTTT
*
33481398 GTGGCGTTTTTCAAAAAACGCCGCTAATGCT-CATTTTTAGCGGCGTTTTTCTTTA
1 GTGGCGATTTTCAAAAAACGCCGCTAATGCTCCATTTTTAGCGGCGTTTTTCTTTA
* * * *
33481453 GTGGCGATTTTCATAGAGCGCCGCTAATGTTCCATTTTTAGCGGCGTTTTT
1 GTGGCGATTTTCAAAAAACGCCGCTAATGCTCCATTTTTAGCGGCGTTTTT
33481504 TTGTCCAAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
55 26 0.58
56 19 0.42
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.40
Consensus pattern (56 bp):
GTGGCGATTTTCAAAAAACGCCGCTAATGCTCCATTTTTAGCGGCGTTTTTCTTTA
Found at i:33483741 original size:13 final size:13
Alignment explanation
Indices: 33483694--33483746 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
33483684 AGTTTGACAA
33483694 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
33483707 TGCTGTGGAAAAT
1 TGCTTTTGAAAAG
*
33483720 TGTTTTTGAGAAA-
1 TGCTTTTGA-AAAG
33483733 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
33483746 T
1 T
33483747 TTGGTTTAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
12 3 0.10
13 25 0.81
14 3 0.10
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:33484519 original size:19 final size:19
Alignment explanation
Indices: 33484480--33484519 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
33484470 ATTCATGCAA
* *
33484480 AATTCATGTACGTTGATTG
1 AATTCATGTACGTCGAATG
*
33484499 AATTCATGTGCGTCGAATG
1 AATTCATGTACGTCGAATG
33484518 AA
1 AA
33484520 GAAGAACACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (19 bp):
AATTCATGTACGTCGAATG
Found at i:33489513 original size:31 final size:31
Alignment explanation
Indices: 33489470--33489539 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
33489460 TTACAAAATG
*
33489470 GTCACTGAACTATTCGAAAA-TTTTCATTTAA
1 GTCATTGAACTATT-GAAAAGTTTTCATTTAA
* * *
33489501 GTTATTGAACTATTTAAAAGTTTTTATTTAA
1 GTCATTGAACTATTGAAAAGTTTTCATTTAA
33489532 GTCATTGA
1 GTCATTGA
33489540 GTTGCTAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.44
Consensus pattern (31 bp):
GTCATTGAACTATTGAAAAGTTTTCATTTAA
Found at i:33489595 original size:13 final size:13
Alignment explanation
Indices: 33489577--33489603 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
33489567 AGTCTGGCTA
33489577 GTTAGCTCTAAAT
1 GTTAGCTCTAAAT
33489590 GTTAGCTCTAAAT
1 GTTAGCTCTAAAT
33489603 G
1 G
33489604 ACGATTCGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (13 bp):
GTTAGCTCTAAAT
Found at i:33492604 original size:7 final size:7
Alignment explanation
Indices: 33492594--33492667 Score: 78
Period size: 7 Copynumber: 10.7 Consensus size: 7
33492584 CAGGTTTAAT
*
33492594 GTTTATG
1 GTTTAGG
33492601 GTTTAGG
1 GTTTAGG
*
33492608 GTTTAGA
1 GTTTAGG
*
33492615 GTTTATG
1 GTTTAGG
*
33492622 GTTTACG
1 GTTTAGG
*
33492629 ATTTAGG
1 GTTTAGG
*
33492636 GTTTAAG
1 GTTTAGG
33492643 G-TTAGG
1 GTTTAGG
*
33492649 GTTTAGA
1 GTTTAGG
33492656 GTTTAGG
1 GTTTAGG
33492663 GTTTA
1 GTTTA
33492668 ATTTAAGATT
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
6 5 0.09
7 49 0.91
ACGTcount: A:0.20, C:0.01, G:0.32, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:33492612 original size:21 final size:21
Alignment explanation
Indices: 33492586--33492667 Score: 96
Period size: 21 Copynumber: 4.0 Consensus size: 21
33492576 GTAGTTTACA
33492586 GGTTTA-ATGTTTATGGTTTAG
1 GGTTTAGA-GTTTATGGTTTAG
*
33492607 GGTTTAGAGTTTATGGTTTAC
1 GGTTTAGAGTTTATGGTTTAG
* * *
33492628 GATTTAGGGTTTAAGG-TTAG
1 GGTTTAGAGTTTATGGTTTAG
*
33492648 GGTTTAGAGTTTAGGGTTTA
1 GGTTTAGAGTTTATGGTTTA
33492668 ATTTAAGATT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
20 16 0.31
21 34 0.67
22 1 0.02
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.46
Consensus pattern (21 bp):
GGTTTAGAGTTTATGGTTTAG
Found at i:33492930 original size:27 final size:25
Alignment explanation
Indices: 33492884--33492938 Score: 60
Period size: 27 Copynumber: 2.1 Consensus size: 25
33492874 CATCATTTTT
33492884 TATTTATATATTGCATATATACATAAA
1 TATTTATATATTGCATATATA-A-AAA
33492911 TATTTATATTTATT-CA-ATATAAAAA
1 TATTTATA--TATTGCATATATAAAAA
33492936 TAT
1 TAT
33492939 AAAAATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
25 6 0.23
26 1 0.04
27 13 0.50
28 2 0.08
29 4 0.15
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (25 bp):
TATTTATATATTGCATATATAAAAA
Found at i:33492939 original size:8 final size:8
Alignment explanation
Indices: 33492926--33492955 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
33492916 ATATTTATTC
33492926 AATATAAA
1 AATATAAA
33492934 AATATAAA
1 AATATAAA
33492942 AATATAAA
1 AATATAAA
33492950 AATATA
1 AATATA
33492956 TTGATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
AATATAAA
Found at i:33493283 original size:148 final size:150
Alignment explanation
Indices: 33492986--33493619 Score: 550
Period size: 148 Copynumber: 4.3 Consensus size: 150
33492976 TTTTTCTAAA
* * * * *
33492986 TTTCCATGTTCTTAGTGGCGTTTTATGCCAAAACGCCA-CAAAA-TTGTCCTAATTATGAGGGAA
1 TTTCCATGTACTTAGTGGCGTTTTATACCAAAACGCCAGAAAAATTTGTCATAATTATGTGGGAA
* * * * *
33493049 ACGACTGT-GTTTC-ACGGTTATTTAGTGGCAC-ATACGTATTAACGCCGCAGACA--GGTTAAT
66 ACGAC-GTCATTTCTACGGTTATTTAGTGGCGCTA-ATGTATAAACGCCGC-GA-ATGGGTTCAT
* * * *
33493109 TTAATCCTGGAAAACGACGACATT
127 TTAGTCATGGAAAACGTCGTCATT
* *
33493133 TTTCTATGTACTTAGTGGCGTTTTATGCCAAAACGCCAGAAAAATTT-TCATAATTATGTGGGAA
1 TTTCCATGTACTTAGTGGCGTTTTATACCAAAACGCCAGAAAAATTTGTCATAATTATGTGGGAA
* * *
33493197 ACGACGTCATTTCTGCGGTTATTTAGTGGCGCACAAT-TATAAACTCCGCGAATGGGTTCATTTA
66 ACGACGTCATTTCTACGGTTATTTAGTGGCGC-TAATGTATAAACGCCGCGAATGGGTTCATTTA
* *
33493261 GTCAT-GAATACGTCGTCGTT
130 GTCATGGAAAACGTCGTCATT
* * * * * * *
33493281 TTTCTATGTTCTTAGTGGCGTTTTATACCAAAACACC--AAAAATTTGTCCTAATTGTTTTGGAA
1 TTTCCATGTACTTAGTGGCGTTTTATACCAAAACGCCAGAAAAATTTGTCATAATTATGTGGGAA
* ** * * ** *
33493344 ACGACTTCATTTCTACAATTAATTTAGTGGCGCTTATGTATAAACGCCGC-AAAGTTCTTCGTTT
66 ACGACGTCATTTCTACGGTT-ATTTAGTGGCGCTAATGTATAAACGCCGCGAATG-GGTTCATTT
*
33493408 AGTCATGGAATACGTCGTCATT
129 AGTCATGGAAAACGTCGTCATT
* * * * *
33493430 TTTCCAGGTTA-GTAGTGGCGTTTTATACCAAAACGCCAG--AAATTTGTCATAACTGTTTGGGA
1 TTTCCATG-TACTTAGTGGCGTTTTATACCAAAACGCCAGAAAAATTTGTCATAATTATGTGGGA
** * * * ** *
33493492 AACGAAATCGTTT-T-CGGGGTTATTTAGTGGCGCTTATGTATAAACGCCGCTAATTTGTTCGTT
65 AACGACGTCATTTCTAC--GGTTATTTAGTGGCGCTAATGTATAAACGCCGCGAATGGGTTCATT
* *
33493555 TAGTCATGGAAAACGTCATCGTT
128 TAGTCATGGAAAACGTCGTCATT
* *
33493578 TTTCAATGTTA-TGAGTGGCGTTTTATACCAAAACGCCAGAAA
1 TTTCCATG-TACTTAGTGGCGTTTTATACCAAAACGCCAGAAA
33493620 TAAGACTATT
Statistics
Matches: 406, Mismatches: 60, Indels: 39
0.80 0.12 0.08
Matches are distributed among these distances:
146 8 0.02
147 74 0.18
148 202 0.50
149 118 0.29
150 3 0.01
151 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (150 bp):
TTTCCATGTACTTAGTGGCGTTTTATACCAAAACGCCAGAAAAATTTGTCATAATTATGTGGGAA
ACGACGTCATTTCTACGGTTATTTAGTGGCGCTAATGTATAAACGCCGCGAATGGGTTCATTTAG
TCATGGAAAACGTCGTCATT
Found at i:33494158 original size:14 final size:14
Alignment explanation
Indices: 33494141--33494175 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
33494131 GTAGTGTTGA
*
33494141 GTTATTCGGATTTT
1 GTTATTCGAATTTT
33494155 GTTATTCGAATTTT
1 GTTATTCGAATTTT
33494169 GTTATTC
1 GTTATTC
33494176 AGGTTTCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.09, G:0.17, T:0.57
Consensus pattern (14 bp):
GTTATTCGAATTTT
Found at i:33495218 original size:9 final size:9
Alignment explanation
Indices: 33495202--33495267 Score: 77
Period size: 9 Copynumber: 7.8 Consensus size: 9
33495192 CATAATAAAC
33495202 AACTTACAT
1 AACTTACAT
*
33495211 AGCTTACAT
1 AACTTACAT
33495220 AA--TACAT
1 AACTTACAT
33495227 AACTTACAT
1 AACTTACAT
*
33495236 AACTTATAT
1 AACTTACAT
33495245 AA--TACAT
1 AACTTACAT
33495252 AACTTACAT
1 AACTTACAT
*
33495261 AATTTAC
1 AACTTAC
33495268 CTAATACATA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
7 13 0.27
9 35 0.73
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (9 bp):
AACTTACAT
Found at i:33495225 original size:16 final size:16
Alignment explanation
Indices: 33495191--33495263 Score: 60
Period size: 16 Copynumber: 4.4 Consensus size: 16
33495181 TGTTTTTCTG
* *
33495191 ACATAATAAACAACTT
1 ACATAATACATAACTT
*
33495207 ACATAGCTTACATAA--T
1 ACATA--ATACATAACTT
33495223 ACATAACTTACATAACTT
1 ACATAA--TACATAACTT
*
33495241 ATATAATACATAACTT
1 ACATAATACATAACTT
33495257 ACATAAT
1 ACATAAT
33495264 TTACCTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
16 34 0.76
18 11 0.24
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.32
Consensus pattern (16 bp):
ACATAATACATAACTT
Found at i:33495230 original size:25 final size:25
Alignment explanation
Indices: 33495191--33495278 Score: 122
Period size: 25 Copynumber: 3.5 Consensus size: 25
33495181 TGTTTTTCTG
* * *
33495191 ACATAATAAACAACTTACATAGCTT
1 ACATAATACATAACTTACATAACTT
33495216 ACATAATACATAACTTACATAACTT
1 ACATAATACATAACTTACATAACTT
* *
33495241 ATATAATACATAACTTACATAATTT
1 ACATAATACATAACTTACATAACTT
*
33495266 ACCTAATACATAA
1 ACATAATACATAA
33495279 ATATATATCA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.32
Consensus pattern (25 bp):
ACATAATACATAACTTACATAACTT
Found at i:33495531 original size:39 final size:39
Alignment explanation
Indices: 33495477--33495557 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
33495467 AAGCCAAGAG
33495477 AACATGATTCTTTGCCCGTGTAAGAAGTGTGTCAACATA
1 AACATGATTCTTTGCCCGTGTAAGAAGTGTGTCAACATA
*
33495516 AACATGATTCTTTGCCCGTGTAAGATGTGTGTCAACATA
1 AACATGATTCTTTGCCCGTGTAAGAAGTGTGTCAACATA
33495555 AAC
1 AAC
33495558 TGACATTATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (39 bp):
AACATGATTCTTTGCCCGTGTAAGAAGTGTGTCAACATA
Found at i:33501181 original size:43 final size:43
Alignment explanation
Indices: 33501130--33501374 Score: 334
Period size: 43 Copynumber: 5.7 Consensus size: 43
33501120 TATAAAAAAA
*
33501130 CGCCGCTAAAAGTCATGTTCTATAGCGGCGTTTGTGGGAGAAG
1 CGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAG
* *
33501173 CACCGCTAAAAGTCATGATCTATAACGGCGTTTGTGGGAGAAG
1 CGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAG
*
33501216 CGCTGCT-AAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAG
1 CGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAG
* *** *
33501258 CGCCGCTAAAAGTCATGACCTATAGCGGCGTTTGTTAAAAAAG
1 CGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAG
* * *
33501301 TGCCGCTAAAAGTCATGACCTATAGCGGCATTTGTGGGAGAAG
1 CGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAG
*
33501344 CGCCGCT-AAAGATCATGA-CATTTAGCGGCGT
1 CGCCGCTAAAAG-TCATGATC-TATAGCGGCGT
33501375 GTATTTCTAA
Statistics
Matches: 178, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
42 45 0.25
43 133 0.75
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (43 bp):
CGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAG
Found at i:33501257 original size:85 final size:86
Alignment explanation
Indices: 33501114--33501362 Score: 342
Period size: 85 Copynumber: 2.9 Consensus size: 86
33501104 TAAAATTAGT
* * * *
33501114 GGCGTTTAT-AAAAAAACGCCGCTAAAAGTCATGTTCTATAGCGGCGTTTGTGGGAGAAGCACCG
1 GGCGTTTGTGAAAAAAGCGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCGCCG
*
33501178 CTAAAAGTCATGATCTATAAC
66 CTAAAAGTCATGACCTATAAC
** * *
33501199 GGCGTTTGTGGGAGAAGCGCTGCT-AAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCGCCG
1 GGCGTTTGTGAAAAAAGCGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCGCCG
*
33501263 CTAAAAGTCATGACCTATAGC
66 CTAAAAGTCATGACCTATAAC
* * * *
33501284 GGCGTTTGTTAAAAAAGTGCCGCTAAAAGTCATGACCTATAGCGGCATTTGTGGGAGAAGCGCCG
1 GGCGTTTGTGAAAAAAGCGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCGCCG
33501349 CT-AAAGATCATGAC
66 CTAAAAG-TCATGAC
33501363 ATTTAGCGGC
Statistics
Matches: 143, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
85 87 0.61
86 56 0.39
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (86 bp):
GGCGTTTGTGAAAAAAGCGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCGCCG
CTAAAAGTCATGACCTATAAC
Found at i:33509817 original size:25 final size:25
Alignment explanation
Indices: 33509789--33509910 Score: 79
Period size: 25 Copynumber: 4.9 Consensus size: 25
33509779 TCCGAGATAT
*
33509789 ATAACGGGAAGCTCATGTGAGCTAA
1 ATAACGGGAAGCTCATGCGAGCTAA
* **
33509814 ATAATGGGAAGCTCATGCGAGCTGT
1 ATAACGGGAAGCTCATGCGAGCTAA
* ** ** *
33509839 ATATCGAAAAGCTCATAAGAGTTGAA
1 ATAACGGGAAGCTCATGCGAGCT-AA
* *
33509865 ATCAA---AAAGTTCATGCGAGCTAA
1 AT-AACGGGAAGCTCATGCGAGCTAA
* *
33509888 ATATCGGGAAGCTCATGAGAGCT
1 ATAACGGGAAGCTCATGCGAGCT
33509911 GTGGTGTGTC
Statistics
Matches: 70, Mismatches: 22, Indels: 10
0.69 0.22 0.10
Matches are distributed among these distances:
22 1 0.01
23 4 0.06
24 12 0.17
25 50 0.71
26 2 0.03
27 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (25 bp):
ATAACGGGAAGCTCATGCGAGCTAA
Found at i:33514943 original size:43 final size:43
Alignment explanation
Indices: 33514876--33515299 Score: 614
Period size: 43 Copynumber: 9.9 Consensus size: 43
33514866 TTTTAGAAAT
* * * * *
33514876 AAACACCGCTATAGGCCATAACCTTTAGCGACACTTTACCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* *
33514919 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCATTACCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* *
33514962 AAACGCTGCTATAGGCCATGACCTTTAGCGGCGCCTTTCCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* *
33515005 AAACGCCGCTATAGGCCATGACCTTTAGCGGTGCTTTTCTCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
33515048 AAACCCCGCTATAGGCCACGACCTTTAGCGGCGCTTTTCCTAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* *
33515091 AAACGCCGCTATAGGCCACGACCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* *
33515134 AAACGCCGCTATAGGCCATGACCTTTAGCGGTGCTTTTCTCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
33515177 AAACCCCGCTATAGGCCACGACCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* *
33515220 AAACGCCGCTATAGGCCATGACCTTTAGCGGTGCTTTTCTCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
33515263 AAACCCCGCTATAGGCCACGACCTTTAGCGGCACTTT
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTT
33515300 GTAATTTGTT
Statistics
Matches: 343, Mismatches: 38, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 343 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:33517842 original size:16 final size:16
Alignment explanation
Indices: 33517805--33517844 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
33517795 ATTTACCCTA
* *
33517805 GCGACGGCAGAGGAGT
1 GCGACGGTAGAGGACT
33517821 GCGACGGTAGAGGACT
1 GCGACGGTAGAGGACT
*
33517837 GTGACGGT
1 GCGACGGT
33517845 CGACGAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.47, T:0.12
Consensus pattern (16 bp):
GCGACGGTAGAGGACT
Found at i:33522914 original size:21 final size:22
Alignment explanation
Indices: 33522870--33522923 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
33522860 ACAAAAGTTA
* *
33522870 AATAACAATAAACATATGATTT
1 AATAAAAATAAACATATAATTT
*
33522892 AATAAAAATAAA-ATCTAATTT
1 AATAAAAATAAACATATAATTT
*
33522913 AATACAAATAA
1 AATAAAAATAA
33522924 TTATTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (22 bp):
AATAAAAATAAACATATAATTT
Found at i:33531365 original size:90 final size:89
Alignment explanation
Indices: 33531172--33531380 Score: 249
Period size: 90 Copynumber: 2.3 Consensus size: 89
33531162 ACTACTATTC
** * * *
33531172 AAAATGTTTGTATTATTTTTGTATCCGTAAATCAAATTTAGTTTGTATTATTTGGTGGTCGAATT
1 AAAATGTTTGTATTA-TTTTGTATATGTAAATAAAAATTAGTCTGTATTATTTGGTGGTCGAATT
* *
33531237 TTATATTTTTGTATATCAAGTTTCT
65 ATATATTTTCGTATATCAAGTTTCT
* * *
33531262 AAAATATTTGTATTAATTTTGTATATGTAAATAAAAATTAGTCTGTGTTATTTGTTGGTCGAATT
1 AAAATGTTTGTATT-ATTTTGTATATGTAAATAAAAATTAGTCTGTATTATTTGGTGGTCGAATT
* *
33531327 ATATATTTTCGTATATTAATTTTCT
65 ATATATTTTCGTATATCAAGTTTCT
** *
33531352 AGGATGTTCGTATT-TTCTTGTATATGTAA
1 AAAATGTTTGTATTATT-TTGTATATGTAA
33531381 TTTTTGTTGG
Statistics
Matches: 101, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
88 2 0.02
89 12 0.12
90 86 0.85
91 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (89 bp):
AAAATGTTTGTATTATTTTGTATATGTAAATAAAAATTAGTCTGTATTATTTGGTGGTCGAATTA
TATATTTTCGTATATCAAGTTTCT
Found at i:33531841 original size:42 final size:42
Alignment explanation
Indices: 33531785--33531871 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
33531775 GTGTGAGAAC
33531785 AATCCGGAGAGTGCTGAGTGTTGAAGCTCAAGGTCGTCGCCA
1 AATCCGGAGAGTGCTGAGTGTTGAAGCTCAAGGTCGTCGCCA
* *
33531827 AATCCGGAGTGTGCTGAGTGTTGAGGCTCAAGGTCGTCGCCA
1 AATCCGGAGAGTGCTGAGTGTTGAAGCTCAAGGTCGTCGCCA
33531869 AAT
1 AAT
33531872 ATGTCTTCGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (42 bp):
AATCCGGAGAGTGCTGAGTGTTGAAGCTCAAGGTCGTCGCCA
Found at i:33533070 original size:15 final size:15
Alignment explanation
Indices: 33533059--33533090 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
33533049 ATCTATACTT
*
33533059 TAATTGGTTATAATC
1 TAATTGGCTATAATC
33533074 TAATTGGCTATAATC
1 TAATTGGCTATAATC
33533089 TA
1 TA
33533091 TTCTATTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.44
Consensus pattern (15 bp):
TAATTGGCTATAATC
Found at i:33533212 original size:19 final size:19
Alignment explanation
Indices: 33533169--33533206 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
33533159 AATTCAATTA
*
33533169 AATT-TTAATTTAAACTTT
1 AATTATTAAGTTAAACTTT
33533187 AATTATTAAGTTAAACTTT
1 AATTATTAAGTTAAACTTT
33533206 A
1 A
33533207 TGTATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (19 bp):
AATTATTAAGTTAAACTTT
Found at i:33533346 original size:165 final size:168
Alignment explanation
Indices: 33533089--33533422 Score: 539
Period size: 165 Copynumber: 2.0 Consensus size: 168
33533079 GGCTATAATC
* * * * *
33533089 TATTCTATTGAAATGTATTAAATTATTTTTTATTTAATCTTGAAATTGTTTTTTTAAATTAAAAT
1 TATTCAATTGAAACGTATTAAATTATTTTTTATTTAACCTTGAAATTGATTTTGTAAATTAAAAT
* * *
33533154 TAAAAAATTCAATTAAATTTTAATTTAAACTTTAATTATTAAGTTAAACTTTATGTATTTAAT-T
66 TAAAAAATCCAATTAAATTTTAATTTAAACTTTAATTATCAAGTTAAACTTAATGTATTTAATAT
33533218 TTTAT-TTTTAATTGAAATTATCTATACTTTAATTGGT
131 TTTATGTTTTAATTGAAATTATCTATACTTTAATTGGT
*
33533255 TATTCAATTGAAACGTATTAAATTATTTTTTATTTAACCTTTAAATTGATTTTGT-AATTAAAAT
1 TATTCAATTGAAACGTATTAAATTATTTTTTATTTAACCTTGAAATTGATTTTGTAAATTAAAAT
** *
33533319 TAAGGAATCCAATTAATTTTTAATTTAAACTTTAATTATCAAGTTAAACTTAATGTATTTAATAT
66 TAAAAAATCCAATTAAATTTTAATTTAAACTTTAATTATCAAGTTAAACTTAATGTATTTAATAT
33533384 TTTATGTTTTAATTGAAATTATCTATACTTTAATTGGT
131 TTTATGTTTTAATTGAAATTATCTATACTTTAATTGGT
33533422 T
1 T
33533423 TATTAGTTGG
Statistics
Matches: 154, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
165 66 0.43
166 55 0.36
167 33 0.21
ACGTcount: A:0.37, C:0.05, G:0.06, T:0.51
Consensus pattern (168 bp):
TATTCAATTGAAACGTATTAAATTATTTTTTATTTAACCTTGAAATTGATTTTGTAAATTAAAAT
TAAAAAATCCAATTAAATTTTAATTTAAACTTTAATTATCAAGTTAAACTTAATGTATTTAATAT
TTTATGTTTTAATTGAAATTATCTATACTTTAATTGGT
Found at i:33537130 original size:15 final size:15
Alignment explanation
Indices: 33537095--33537133 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
33537085 TCACTATCGA
* *
33537095 ACCCTTTATTATCGG
1 ACCCTTCATTATCAG
*
33537110 AACCTTCATTATCAG
1 ACCCTTCATTATCAG
33537125 ACCCTTCAT
1 ACCCTTCAT
33537134 CACCATCTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.31, G:0.08, T:0.36
Consensus pattern (15 bp):
ACCCTTCATTATCAG
Found at i:33537983 original size:108 final size:110
Alignment explanation
Indices: 33537869--33538065 Score: 249
Period size: 108 Copynumber: 1.8 Consensus size: 110
33537859 AGTTGATGTC
* * * *
33537869 GGCCATCTAGCT-CCCCCAATCCAAAAT-TTTTTTATCTAATAAAGTGAGTGTCGACCATTACTG
1 GGCCATCTAG-TACCCCCAA-CCAAAATATTATTTATCTAATAAAGCGAGTGCCGACCATCACTG
*
33537932 TGCTAGCA-C-AAAAAAATTATTTTTTTAATCTGAAAAGCTGATGCT
64 TGCCAGCACCTAAAAAAATTATTTTTTTAATCTGAAAAGCTGATGCT
* * * * * *
33537977 GGCCATCTAGTACTCCCAACCCAAATATTATTTATCTGATAAAGCGGGTGCCGGCCATCAGTGTG
1 GGCCATCTAGTACCCCCAACCAAAATATTATTTATCTAATAAAGCGAGTGCCGACCATCACTGTG
33538042 CCAGCACCTAAAAAAATTATTTTT
66 CCAGCACCTAAAAAAATTATTTTT
33538066 AAAAAATTAT
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
107 7 0.09
108 51 0.69
109 1 0.01
110 15 0.20
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (110 bp):
GGCCATCTAGTACCCCCAACCAAAATATTATTTATCTAATAAAGCGAGTGCCGACCATCACTGTG
CCAGCACCTAAAAAAATTATTTTTTTAATCTGAAAAGCTGATGCT
Found at i:33542177 original size:29 final size:30
Alignment explanation
Indices: 33542124--33542180 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
33542114 GAATTGAATT
*
33542124 AAATCAAAATTTCATATATAAAATTACATA
1 AAATCAAAATTCCATATATAAAATTACATA
* *
33542154 AAATCAAAA-TCCATGTATACAATTACA
1 AAATCAAAATTCCATATATAAAATTACA
33542181 CATTAGACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (30 bp):
AAATCAAAATTCCATATATAAAATTACATA
Found at i:33555090 original size:45 final size:45
Alignment explanation
Indices: 33554994--33555100 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
33554984 TTGTAACAAG
* *
33554994 CTTTTTGCTGCTGTTTTTGTAGAGTAAATGCGGCATATGTGTGCA
1 CTTTTTGTTGCTGTTTTTGTAGAGTAAATGCGGCATATGTGCGCA
* *
33555039 CTTTTTGTTGCTGTTTTTGTCGAGTGAATGTC-GCATATGTGCGCA
1 CTTTTTGTTGCTGTTTTTGTAGAGTAAATG-CGGCATATGTGCGCA
*
33555084 -TATTTTGTTGTTGTTTT
1 CT-TTTTGTTGCTGTTTT
33555101 CGGATGAGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
44 1 0.02
45 53 0.96
46 1 0.02
ACGTcount: A:0.14, C:0.12, G:0.25, T:0.49
Consensus pattern (45 bp):
CTTTTTGTTGCTGTTTTTGTAGAGTAAATGCGGCATATGTGCGCA
Found at i:33557967 original size:20 final size:17
Alignment explanation
Indices: 33557888--33558119 Score: 119
Period size: 20 Copynumber: 13.1 Consensus size: 17
33557878 TAATATTGTT
*
33557888 TTAATAGTTTAATATTAAA
1 TTAATA-TTAAATATT-AA
33557907 TTAA-ATTAAATACTTATA
1 TTAATATTAAATA-TTA-A
* **
33557925 TTAATAGTATTTTATTAA
1 TTAATATTA-AATATTAA
33557943 TTTAATATTAAAGTGATTAA
1 -TTAATATTAAA-T-ATTAA
33557963 CTTAATATTAAAT-TTAA
1 -TTAATATTAAATATTAA
* *
33557980 TCTAATATT-TATATTGA
1 T-TAATATTAAATATTAA
33557997 -TAATCATT--ATATTAA
1 TTAAT-ATTAAATATTAA
33558012 TTTAATATTAAAGTGATTAA
1 -TTAATATTAAA-T-ATTAA
33558032 CTTAATATTAAAT-TTAA
1 -TTAATATTAAATATTAA
* *
33558049 TCTAATATT-TATATTGA
1 T-TAATATTAAATATTAA
33558066 -TAATCATT--ATATTAA
1 TTAAT-ATTAAATATTAA
33558081 TTTAATATTAAAGTGATTAA
1 -TTAATATTAAA-T-ATTAA
33558101 CTTAATATTAAAT-TTAA
1 -TTAATATTAAATATTAA
33558118 TT
1 TT
33558120 TAATGTGTCG
Statistics
Matches: 172, Mismatches: 16, Indels: 53
0.71 0.07 0.22
Matches are distributed among these distances:
15 20 0.12
16 20 0.12
17 47 0.27
18 11 0.06
19 24 0.14
20 50 0.29
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.48
Consensus pattern (17 bp):
TTAATATTAAATATTAA
Found at i:33558025 original size:69 final size:69
Alignment explanation
Indices: 33557896--33558123 Score: 379
Period size: 69 Copynumber: 3.3 Consensus size: 69
33557886 TTTTAATAGT
* * * * *
33557896 TTAATATTAAATTAAAT-TAAATACTTATATTAATAGT-ATTTTATTAATTTAATATTAAAGTGA
1 TTAATATTAAATTTAATCT-AATATTTATATTGATAATCATTATATTAATTTAATATTAAAGTGA
33557959 TTAAC
65 TTAAC
33557964 TTAATATTAAATTTAATCTAATATTTATATTGATAATCATTATATTAATTTAATATTAAAGTGAT
1 TTAATATTAAATTTAATCTAATATTTATATTGATAATCATTATATTAATTTAATATTAAAGTGAT
33558029 TAAC
66 TAAC
33558033 TTAATATTAAATTTAATCTAATATTTATATTGATAATCATTATATTAATTTAATATTAAAGTGAT
1 TTAATATTAAATTTAATCTAATATTTATATTGATAATCATTATATTAATTTAATATTAAAGTGAT
33558098 TAAC
66 TAAC
*
33558102 TTAATATTAAATTTAATTTAAT
1 TTAATATTAAATTTAATCTAAT
33558124 GTGTCGAAAC
Statistics
Matches: 152, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
68 31 0.20
69 121 0.80
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (69 bp):
TTAATATTAAATTTAATCTAATATTTATATTGATAATCATTATATTAATTTAATATTAAAGTGAT
TAAC
Found at i:33562296 original size:5 final size:5
Alignment explanation
Indices: 33562286--33562314 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
33562276 TTTAATAACA
33562286 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
33562315 AAATGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:33563099 original size:21 final size:21
Alignment explanation
Indices: 33563075--33563122 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
33563065 TGTGTCCCCG
*
33563075 TCACACAGCCGTGTGCCTCTT
1 TCACACAGCCGTGTACCTCTT
* *
33563096 TCACACGGGCGTGTACCTCTT
1 TCACACAGCCGTGTACCTCTT
*
33563117 CCACAC
1 TCACAC
33563123 GGCTATGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.40, G:0.19, T:0.25
Consensus pattern (21 bp):
TCACACAGCCGTGTACCTCTT
Found at i:33563123 original size:21 final size:21
Alignment explanation
Indices: 33563084--33563124 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
33563074 GTCACACAGC
* *
33563084 CGTGTGCCTCTTTCACACGGG
1 CGTGTACCTCTTCCACACGGG
33563105 CGTGTACCTCTTCCACACGG
1 CGTGTACCTCTTCCACACGG
33563125 CTATGTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.37, G:0.24, T:0.27
Consensus pattern (21 bp):
CGTGTACCTCTTCCACACGGG
Found at i:33565963 original size:5 final size:5
Alignment explanation
Indices: 33565953--33565980 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
33565943 TTTAATGAAA
33565953 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
33565981 GAAATGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:33566091 original size:29 final size:30
Alignment explanation
Indices: 33566035--33566091 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
33566025 CTCACATTCC
* *
33566035 TTTTTTCTCTCCCTCTTTTCCATGTCAATT
1 TTTTTTCTCTCCCTCTTTCCCATATCAATT
33566065 TTTTTTCTCT-CCT-TTTCCCGATATCAA
1 TTTTTTCTCTCCCTCTTTCCC-ATATCAA
33566092 GCTTTTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.21
29 9 0.38
30 10 0.42
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (30 bp):
TTTTTTCTCTCCCTCTTTCCCATATCAATT
Found at i:33569495 original size:101 final size:102
Alignment explanation
Indices: 33569309--33569512 Score: 401
Period size: 101 Copynumber: 2.0 Consensus size: 102
33569299 GGTCTCAGGT
33569309 TCGAGTCCATGTGTGCAAGGTAGGAGATGGTTTATTTTTGGTTTCAATTCTGAAAATTCTGATAG
1 TCGAGTCCATGTGTGCAAGGTAGGAGATGGTTTATTTTTGGTTTCAATTCTGAAAATTCTGATAG
33569374 GATAAATATTAGTTAAAAATATTTTTAATGAAATTTA
66 GATAAATATTAGTTAAAAATATTTTTAATGAAATTTA
33569411 TCGAGTCCAT-TGTGCAAGGTAGGAGATGGTTTATTTTTGGTTTCAATTCTGAAAATTCTGATAG
1 TCGAGTCCATGTGTGCAAGGTAGGAGATGGTTTATTTTTGGTTTCAATTCTGAAAATTCTGATAG
33569475 GATAAATATTAGTTAAAAATATTTTTAATGAAATTTA
66 GATAAATATTAGTTAAAAATATTTTTAATGAAATTTA
33569512 T
1 T
33569513 TTTATTTTAT
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
101 92 0.90
102 10 0.10
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (102 bp):
TCGAGTCCATGTGTGCAAGGTAGGAGATGGTTTATTTTTGGTTTCAATTCTGAAAATTCTGATAG
GATAAATATTAGTTAAAAATATTTTTAATGAAATTTA
Found at i:33569644 original size:28 final size:29
Alignment explanation
Indices: 33569589--33569644 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
33569579 CTCACATTCC
* *
33569589 TTTTTTCTCTCCCTCTTTTCCATGTCAAT
1 TTTTTTCTCTCCCTCTTTCCCATATCAAT
33569618 TTTTTTCTCT-CCT-TTTCCCGATATCAA
1 TTTTTTCTCTCCCTCTTTCCC-ATATCAA
33569645 GCTTTTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 9 0.38
29 10 0.42
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (29 bp):
TTTTTTCTCTCCCTCTTTCCCATATCAAT
Found at i:33569650 original size:29 final size:29
Alignment explanation
Indices: 33569588--33569655 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
33569578 TCTCACATTC
* *
33569588 CTTTTTTCTCTCCCTCTTTTCCATGTCAA
1 CTTTTTTCTCTCCCTCTTTCCCATATCAA
*
33569617 TTTTTTTCTCT-CCT-TTTCCCGATATCAA
1 CTTTTTTCTCTCCCTCTTTCCC-ATATCAA
33569645 GCTTTTGTTCT
1 -CTTTT-TTCT
33569656 AGTCACTTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 5 0.16
28 9 0.28
29 14 0.44
30 4 0.12
ACGTcount: A:0.10, C:0.29, G:0.06, T:0.54
Consensus pattern (29 bp):
CTTTTTTCTCTCCCTCTTTCCCATATCAA
Found at i:33571726 original size:18 final size:18
Alignment explanation
Indices: 33571703--33571739 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
33571693 ACATACTAGA
33571703 GTGTTTTGAAAATGATTT
1 GTGTTTTGAAAATGATTT
*
33571721 GTGTTTTGAAAATGTTTT
1 GTGTTTTGAAAATGATTT
33571739 G
1 G
33571740 CGAAAATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (18 bp):
GTGTTTTGAAAATGATTT
Found at i:33572140 original size:39 final size:39
Alignment explanation
Indices: 33572085--33572171 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 39
33572075 TCAAAATCTA
* *
33572085 AAATAATTTGAAAATGGGTGAG-GATTGTTGGAGCATTTTC
1 AAAT-ATTTGAAAATGGG-GAGAGATTGTTGGAACATTTAC
*
33572125 AAATATTTGAAAATGGGGGGAGATTGTTGGAACATTTAC
1 AAATATTTGAAAATGGGGAGAGATTGTTGGAACATTTAC
33572164 AAATATTT
1 AAATATTT
33572172 ATAGTGTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 2 0.05
39 37 0.86
40 4 0.09
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (39 bp):
AAATATTTGAAAATGGGGAGAGATTGTTGGAACATTTAC
Found at i:33575785 original size:68 final size:68
Alignment explanation
Indices: 33575705--33575853 Score: 181
Period size: 68 Copynumber: 2.2 Consensus size: 68
33575695 TAAGGTTTTG
* * * * * **
33575705 CAGACCGTGTGAGAATAAGCAGCTCGTGTGGCTGGACCATGTGAGGCACACGGCCATGTGGAAAG
1 CAGACCGTGTGAGAATAAACAACCCATGTGGCTAGACCATGTGAGGCACACGGCCACATGGAAAG
33575770 GTT
66 GTT
* * * * *
33575773 CAGACCGTGTGAGAATAAACAACCCATGTGGCTAGATCGTGTGAGGCACATGGCCGCATGGAAAT
1 CAGACCGTGTGAGAATAAACAACCCATGTGGCTAGACCATGTGAGGCACACGGCCACATGGAAAG
33575838 GTT
66 GTT
*
33575841 CAAACCGTGTGAG
1 CAGACCGTGTGAG
33575854 TGGCCCATGT
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.28, C:0.21, G:0.32, T:0.19
Consensus pattern (68 bp):
CAGACCGTGTGAGAATAAACAACCCATGTGGCTAGACCATGTGAGGCACACGGCCACATGGAAAG
GTT
Found at i:33582467 original size:14 final size:15
Alignment explanation
Indices: 33582443--33582471 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
33582433 TTATGCATGT
33582443 TATGATTTGATATGA
1 TATGATTTGATATGA
33582458 TATG-TTTGATATGA
1 TATGATTTGATATGA
33582472 CCTAGCATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (15 bp):
TATGATTTGATATGA
Found at i:33583542 original size:21 final size:21
Alignment explanation
Indices: 33583516--33583558 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
33583506 TTCTTGATAT
33583516 GTTAGTGAAGGGAAATAAGAG
1 GTTAGTGAAGGGAAATAAGAG
33583537 GTTAGTGAAGGGAAATAAGAG
1 GTTAGTGAAGGGAAATAAGAG
33583558 G
1 G
33583559 AAGTGATAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.40, T:0.19
Consensus pattern (21 bp):
GTTAGTGAAGGGAAATAAGAG
Found at i:33583570 original size:20 final size:21
Alignment explanation
Indices: 33583519--33583572 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
33583509 TTGATATGTT
*
33583519 AGTGAAGGGAAATAAGAGGTT
1 AGTGAAGGGAAATAAGAGGTA
33583540 AGTGAAGGGAAATAAGAGG-A
1 AGTGAAGGGAAATAAGAGGTA
33583560 AGTGATA-GGAAAT
1 AGTGA-AGGGAAAT
33583573 GTTGTAGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (21 bp):
AGTGAAGGGAAATAAGAGGTA
Found at i:33586589 original size:11 final size:11
Alignment explanation
Indices: 33586573--33586601 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
33586563 TACTGCATAC
33586573 AATAATTACTT
1 AATAATTACTT
33586584 AATAATTACTT
1 AATAATTACTT
33586595 AATAATT
1 AATAATT
33586602 TCGAAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (11 bp):
AATAATTACTT
Found at i:33586738 original size:22 final size:22
Alignment explanation
Indices: 33586702--33586760 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
33586692 TAACTACAAA
* *
33586702 AATTAAATAACAATAAACATA-T
1 AATTTAATAAAAATAAA-ATACT
*
33586724 CATTTAATAAAAAT-AAATACT
1 AATTTAATAAAAATAAAATACT
33586745 AATTTAATAAAAATAA
1 AATTTAATAAAAATAA
33586761 TTATTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 3 0.10
21 16 0.52
22 12 0.39
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.31
Consensus pattern (22 bp):
AATTTAATAAAAATAAAATACT
Found at i:33593421 original size:30 final size:30
Alignment explanation
Indices: 33593376--33593433 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
33593366 CACGGGCTGG
* *
33593376 CACATGGGCGTGTGGCTAGCCCGTGTGGCT
1 CACACGGGCGTGTGGCCAGCCCGTGTGGCT
*
33593406 CACACGGGTGTGTGGCCAGCCCGTGTGG
1 CACACGGGCGTGTGGCCAGCCCGTGTGG
33593434 AAATTTTCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.10, C:0.28, G:0.41, T:0.21
Consensus pattern (30 bp):
CACACGGGCGTGTGGCCAGCCCGTGTGGCT
Found at i:33595367 original size:19 final size:19
Alignment explanation
Indices: 33595338--33595377 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
33595328 ATCAAAATTT
33595338 TTAATATATTAATAGTAAAA
1 TTAATATATTAA-AGTAAAA
*
33595358 TTAA-ATATTAAATTAAAA
1 TTAATATATTAAAGTAAAA
33595376 TT
1 TT
33595378 TATTAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TTAATATATTAAAGTAAAA
Found at i:33598690 original size:13 final size:14
Alignment explanation
Indices: 33598659--33598692 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
33598649 TTGTTTTACT
33598659 AAAAATAATTTTCG
1 AAAAATAATTTTCG
33598673 AAAAATAATTTTCG
1 AAAAATAATTTTCG
33598687 AAAAAT
1 AAAAAT
33598693 GACTTACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (14 bp):
AAAAATAATTTTCG
Found at i:33603813 original size:42 final size:42
Alignment explanation
Indices: 33603743--33603830 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
33603733 GCACAGAAAG
* *
33603743 AGGACATGAGCACATGCCCAAGTCGTGTGTGTCACACGGGTA
1 AGGACATGAGCACATGCCCAAGTCGTGTGAGTCACACGGGAA
* * *
33603785 AGGACATGAGCATATGTCC-AGGCTGTGTGAGTCACACGGGAA
1 AGGACATGAGCACATGCCCAAGTC-GTGTGAGTCACACGGGAA
33603827 AGGA
1 AGGA
33603831 TATGGCCGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 3 0.08
42 37 0.93
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.18
Consensus pattern (42 bp):
AGGACATGAGCACATGCCCAAGTCGTGTGAGTCACACGGGAA
Found at i:33609965 original size:35 final size:35
Alignment explanation
Indices: 33609881--33609955 Score: 134
Period size: 35 Copynumber: 2.1 Consensus size: 35
33609871 ATTATGGCTG
33609881 AATCTAGGAGTGTTACGAAAAAGGTTTTTGAAATC
1 AATCTAGGAGTGTTACGAAAAAGGTTTTTGAAATC
33609916 AATCTAGGAGTGTTACGAAAAATGG-TTTTGAAATC
1 AATCTAGGAGTGTTACGAAAAA-GGTTTTTGAAATC
33609951 AATCT
1 AATCT
33609956 TATTATGTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 37 0.95
36 2 0.05
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.32
Consensus pattern (35 bp):
AATCTAGGAGTGTTACGAAAAAGGTTTTTGAAATC
Found at i:33614514 original size:20 final size:20
Alignment explanation
Indices: 33614489--33614551 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
33614479 AGTCCAAACA
*
33614489 GGGCACAGATGTGCATCCAG
1 GGGCACAGATGTGCATACAG
* * * * * *
33614509 GGGCACCGAAGAGCAAAAAA
1 GGGCACAGATGTGCATACAG
*
33614529 GGGCACAGATGTGCATTCAG
1 GGGCACAGATGTGCATACAG
33614549 GGG
1 GGG
33614552 TACCGAAGTA
Statistics
Matches: 29, Mismatches: 14, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.37, T:0.11
Consensus pattern (20 bp):
GGGCACAGATGTGCATACAG
Found at i:33614581 original size:40 final size:39
Alignment explanation
Indices: 33614466--33614708 Score: 220
Period size: 40 Copynumber: 6.1 Consensus size: 39
33614456 GAATGTGTGA
* * *
33614466 TTAGGGGTACTGAAGTCCAAACAGGGCACAGATGTGCAT
1 TTAGGGGTACCGAAGTACAAACAGGGCACATATGTGCAT
** * * *
33614505 CCAGGGGCACCGAAG-AGCAAAAAAGGGCACAGATGTGCAT
1 TTAGGGGTACCGAAGTA-C-AAACAGGGCACATATGTGCAT
* * *
33614545 TCAGGGGTACCGAAGTACAAATAGGGACATATATGTGCAT
1 TTAGGGGTACCGAAGTACAAACAGGG-CACATATGTGCAT
* * *
33614585 TTTGGGGTACCAAACTACAAACAGGGGCA-AGTATGTGCAT
1 TTAGGGGTACCGAAGTACAAACA-GGGCACA-TATGTGCAT
* * *
33614625 TTAAGGGTACCAAAGTACAAACAGGGGCACGTATGTGCAT
1 TTAGGGGTACCGAAGTACAAACA-GGGCACATATGTGCAT
* * * *
33614665 TTAAGGGTACCGAAATACAAACAAAGGCACGTATGTGCAT
1 TTAGGGGTACCGAAGTACAAAC-AGGGCACATATGTGCAT
33614705 TTAG
1 TTAG
33614709 TAACATTTTC
Statistics
Matches: 172, Mismatches: 24, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
39 20 0.12
40 147 0.85
41 5 0.03
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (39 bp):
TTAGGGGTACCGAAGTACAAACAGGGCACATATGTGCAT
Found at i:33615218 original size:20 final size:19
Alignment explanation
Indices: 33615182--33615237 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
33615172 TAGCAAAAAA
*
33615182 CAAATAGAACAGGACAGAG
1 CAAATAGAACAGAACAGAG
* *
33615201 CAAAGTAGAACATAACAGAA
1 CAAA-TAGAACAGAACAGAG
*
33615221 CAGAATAGAGCAGAACA
1 CA-AATAGAACAGAACA
33615238 AAACTAAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.13
20 24 0.80
21 2 0.07
ACGTcount: A:0.55, C:0.16, G:0.21, T:0.07
Consensus pattern (19 bp):
CAAATAGAACAGAACAGAG
Found at i:33627080 original size:17 final size:16
Alignment explanation
Indices: 33627036--33627082 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
33627026 TTTTGTCTGC
*
33627036 TAAAATTATTAATTAAG
1 TAAAATTATT-TTTAAG
33627053 TAAAATTATTTTTAAAG
1 TAAAATTATTTTT-AAG
33627070 TAAAATTATTTTT
1 TAAAATTATTTTT
33627083 TGTGGCGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 2 0.07
17 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (16 bp):
TAAAATTATTTTTAAG
Found at i:33627593 original size:41 final size:41
Alignment explanation
Indices: 33627536--33627622 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
33627526 TTATATGGAT
*
33627536 AAAATTTTTATATGGATAAGCCCGTATAACAAAGTCGGCCC
1 AAAATTTTTATATGGATAAGCCCGTATAACAAAGTCAGCCC
* *
33627577 AAAATTTTTATATGGATATGCCCGTATAACAAAGTCAGTCC
1 AAAATTTTTATATGGATAAGCCCGTATAACAAAGTCAGCCC
33627618 AAAAT
1 AAAAT
33627623 CGTAGAACTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (41 bp):
AAAATTTTTATATGGATAAGCCCGTATAACAAAGTCAGCCC
Found at i:33628113 original size:41 final size:41
Alignment explanation
Indices: 33628007--33628200 Score: 184
Period size: 41 Copynumber: 5.0 Consensus size: 41
33627997 TAAATTATTT
* * * *
33628007 TAAATCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCTGC
1 TAAAGCCCTGAGCATTAGCAGCGCTTTCTCTAAAACGCCGC
*
33628048 TAAAG-CC---GCATTAGCGGCGCTTTCTCTAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCAGCGCTTTCTCTAAAACGCCGC
* *
33628085 TAAAGCCCTGACCATTAGCAGCGCTTTCTCAAAAACG-C-C
1 TAAAGCCCTGAGCATTAGCAGCGCTTTCTCTAAAACGCCGC
*
33628124 T-------TGAGCATTAGCAGCGCTTTCT-TAAAAACGCCGT
1 TAAAGCCCTGAGCATTAGCAGCGCTTTCTCT-AAAACGCCGC
*
33628158 TAAAGCCCTGAGCATTAGCAGCGCTTTCT-TAAAAACGTCGC
1 TAAAGCCCTGAGCATTAGCAGCGCTTTCTCT-AAAACGCCGC
33628199 TA
1 TA
33628201 GTTGGGCTTA
Statistics
Matches: 128, Mismatches: 11, Indels: 28
0.77 0.07 0.17
Matches are distributed among these distances:
32 26 0.20
33 1 0.01
34 1 0.01
37 33 0.26
38 2 0.02
39 2 0.02
40 3 0.02
41 60 0.47
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (41 bp):
TAAAGCCCTGAGCATTAGCAGCGCTTTCTCTAAAACGCCGC
Found at i:33628162 original size:73 final size:76
Alignment explanation
Indices: 33628006--33628200 Score: 254
Period size: 73 Copynumber: 2.6 Consensus size: 76
33627996 TTAAATTATT
* * * *
33628006 TTAAATCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCTGCTAAAGCCGCATTAGCGGCGCTTT
1 TTAAAGCCCTGAGCATTAGCAGCGCTTTCTCAAAAACGC-GCT-AAGCAGCATTAGCAGCGCTTT
33628071 CTCTAAAACGCCG
64 CTCTAAAACGCCG
* * *
33628084 CTAAAGCCCTGACCATTAGCAGCGCTTTCTCAAAAACGC-CT-TG-AGCATTAGCAGCGCTTTCT
1 TTAAAGCCCTGAGCATTAGCAGCGCTTTCTCAAAAACGCGCTAAGCAGCATTAGCAGCGCTTTCT
33628146 -TAAAAACGCCG
66 CT-AAAACGCCG
*
33628157 TTAAAGCCCTGAGCATTAGCAGCGCTTTCTTAAAAACGTCGCTA
1 TTAAAGCCCTGAGCATTAGCAGCGCTTTCTCAAAAACG-CGCTA
33628201 GTTGGGCTTA
Statistics
Matches: 103, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
72 1 0.01
73 61 0.59
74 2 0.02
75 2 0.02
76 2 0.02
78 35 0.34
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.25
Consensus pattern (76 bp):
TTAAAGCCCTGAGCATTAGCAGCGCTTTCTCAAAAACGCGCTAAGCAGCATTAGCAGCGCTTTCT
CTAAAACGCCG
Found at i:33628715 original size:3 final size:3
Alignment explanation
Indices: 33628707--33628748 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
33628697 ATATGCATAT
33628707 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
33628749 TCAAGCCAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:33633118 original size:5 final size:5
Alignment explanation
Indices: 33633108--33633133 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
33633098 GAGATGGAAT
33633108 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
33633134 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:33633133 original size:26 final size:26
Alignment explanation
Indices: 33633082--33633133 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
33633072 TGAAGTTTTC
* *
33633082 TCGAATCGAGTCAAATGAGATGGAAT
1 TCGAATCGAATCAAATGAGATCGAAT
*
33633108 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCAAAT-GAGATCGAAT
33633134 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCAAATGAGATCGAAT
Found at i:33633502 original size:16 final size:16
Alignment explanation
Indices: 33633481--33633511 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33633471 NNGGAAAATA
*
33633481 AAAAGTTTTGGGGAAT
1 AAAAGTTTTAGGGAAT
33633497 AAAAGTTTTAGGGAA
1 AAAAGTTTTAGGGAA
33633512 AGTAAATAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (16 bp):
AAAAGTTTTAGGGAAT
Found at i:33633858 original size:9 final size:9
Alignment explanation
Indices: 33633844--33633880 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
33633834 TATAGTTTGA
33633844 TATTCGAAT
1 TATTCGAAT
33633853 TATTCGAAT
1 TATTCGAAT
*
33633862 TATTCGAGT
1 TATTCGAAT
33633871 TATTCGAAT
1 TATTCGAAT
33633880 T
1 T
33633881 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:33633957 original size:14 final size:14
Alignment explanation
Indices: 33633938--33633973 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
33633928 TTGATTTGAA
33633938 TAACTCGATCCGTT
1 TAACTCGATCCGTT
*
33633952 TAACTCGATTCGTT
1 TAACTCGATCCGTT
33633966 TAACTCGA
1 TAACTCGA
33633974 AATTCGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (14 bp):
TAACTCGATCCGTT
Found at i:33639804 original size:24 final size:26
Alignment explanation
Indices: 33639761--33639810 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
33639751 AAAAAAAATT
*
33639761 AATAGTATTTAAAAAATTTAATTTTA
1 AATAGTATTTAAAAAATTTAAATTTA
*
33639787 AATAG-ATTT-AAAATTTTAAATTTA
1 AATAGTATTTAAAAAATTTAAATTTA
33639811 GAAACAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 4 0.18
26 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
AATAGTATTTAAAAAATTTAAATTTA
Found at i:33640019 original size:15 final size:15
Alignment explanation
Indices: 33639999--33640028 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33639989 ATGTTATGGC
33639999 CAGATCATGAAGTGT
1 CAGATCATGAAGTGT
33640014 CAGATCATGAAGTGT
1 CAGATCATGAAGTGT
33640029 TATGTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (15 bp):
CAGATCATGAAGTGT
Found at i:33643770 original size:4 final size:4
Alignment explanation
Indices: 33643718--33643751 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
33643708 ATAATATATC
33643718 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
33643752 AATATAGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Done.