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 162 of 226
Found at i:51975938 original size:3 final size:3
Alignment explanation
Indices: 51975930--51976002 Score: 112
Period size: 3 Copynumber: 24.3 Consensus size: 3
51975920 TTAGTTCTTG
51975930 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
51975978 TTA -TA TTA TATA GTA TTA TAA TTA T
1 TTA TTA TTA T-TA TTA TTA TTA TTA T
51976003 ACTTACATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 60 0.94
4 2 0.03
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:51976130 original size:16 final size:16
Alignment explanation
Indices: 51976109--51976139 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51976099 TTTTAGCTTT
51976109 TATATACATATATATG
1 TATATACATATATATG
*
51976125 TATATACATTTATAT
1 TATATACATATATAT
51976140 TTCTATTATA
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:0.06, G:0.03, T:0.48
Consensus pattern (16 bp):
TATATACATATATATG
Found at i:51976549 original size:22 final size:22
Alignment explanation
Indices: 51976524--51976566 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
51976514 ACAGCAGAAC
* *
51976524 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
51976546 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
51976567 AACGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:51976848 original size:43 final size:42
Alignment explanation
Indices: 51976656--51976950 Score: 301
Period size: 42 Copynumber: 7.0 Consensus size: 42
51976646 GCGCTTACAT
* *
51976656 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGGTTAT
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
** * * * *
51976698 AAAAATGCTCCGCTAAAGATCGTGTTCTTTAGTGGCGCTTAC
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* * **
51976740 AAATAAACGCCGCTAAAGAACATAATCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* *
51976782 AAATAAACGCCGCTAAATATCATGTTCTTTAGCGGCGCTTAGG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-G
* *
51976825 AAAAAAACGCCGCTAAAGTTCATGTTCTTTAGCGGCGCTTTTG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTAG
** * * *
51976868 AGGAAAACGCCTCTAAA-AGTAATGTTCTATAGCGGCGCTT-G
1 AAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTAG
**
51976909 TTCAAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGCTTA
1 -AAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
51976951 TTTCACAAAT
Statistics
Matches: 211, Mismatches: 36, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
41 2 0.01
42 139 0.66
43 68 0.32
44 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
Found at i:51977390 original size:12 final size:12
Alignment explanation
Indices: 51977373--51977412 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
51977363 TTTTGAACCT
*
51977373 CTGCTTCTATTG
1 CTGCTTCTATCG
*
51977385 CTGCTTCTCTCG
1 CTGCTTCTATCG
*
51977397 CTGCTTCTCTCG
1 CTGCTTCTATCG
51977409 CTGC
1 CTGC
51977413 AGCCTCTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.03, C:0.38, G:0.17, T:0.42
Consensus pattern (12 bp):
CTGCTTCTATCG
Found at i:51977423 original size:21 final size:21
Alignment explanation
Indices: 51977397--51977475 Score: 113
Period size: 21 Copynumber: 3.8 Consensus size: 21
51977387 GCTTCTCTCG
51977397 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
51977418 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* * *
51977439 CTGCTTCTCTCACTGTAGCCG
1 CTGCTTCTCTCGCTGCAGCCT
*
51977460 CTGCTTCCCTCGCTGC
1 CTGCTTCTCTCGCTGC
51977476 CGCATCNNNN
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.04, C:0.43, G:0.20, T:0.33
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:51981665 original size:9 final size:9
Alignment explanation
Indices: 51981651--51981921 Score: 184
Period size: 9 Copynumber: 32.1 Consensus size: 9
51981641 AACTTATTTA
51981651 TTATGTAAG
1 TTATGTAAG
51981660 TTATGTAAG
1 TTATGTAAG
*
51981669 TTGTGTAAG
1 TTATGTAAG
51981678 TTATGTAAG
1 TTATGTAAG
*
51981687 CTATGTAAG
1 TTATGTAAG
*
51981696 TTGTGT-A-
1 TTATGTAAG
* *
51981703 TTATGAAAC
1 TTATGTAAG
51981712 TTATGTAAG
1 TTATGTAAG
*
51981721 TTGTGT-A-
1 TTATGTAAG
*
51981728 TTATG-ATGG
1 TTATGTA-AG
51981737 TTATGTAAG
1 TTATGTAAG
*
51981746 TTGTGT-A-
1 TTATGTAAG
51981753 TTATGTAAG
1 TTATGTAAG
*
51981762 TTATGTTAG
1 TTATGTAAG
*
51981771 TTGTGT-A-
1 TTATGTAAG
* *
51981778 TTATGAAAC
1 TTATGTAAG
51981787 TTATGTAAG
1 TTATGTAAG
*
51981796 TTATGT--C
1 TTATGTAAG
51981803 TTATGTAAG
1 TTATGTAAG
* *
51981812 TGATGTAAA
1 TTATGTAAG
*
51981821 ATATGT-A-
1 TTATGTAAG
51981828 TTATGTAAG
1 TTATGTAAG
*
51981837 TTATGTCAG
1 TTATGTAAG
*
51981846 TTGTGT-A-
1 TTATGTAAG
*
51981853 TTATGTAAA
1 TTATGTAAG
51981862 TTATGT-A-
1 TTATGTAAG
51981869 TTATGTAAG
1 TTATGTAAG
*
51981878 TTATGTAAT
1 TTATGTAAG
*
51981887 TTGTGT-A-
1 TTATGTAAG
*
51981894 TTATGTAAC
1 TTATGTAAG
* *
51981903 TTATTTAAT
1 TTATGTAAG
51981912 TTATGTAAG
1 TTATGTAAG
51981921 T
1 T
51981922 GTGTATTATT
Statistics
Matches: 204, Mismatches: 38, Indels: 40
0.72 0.13 0.14
Matches are distributed among these distances:
7 44 0.22
8 15 0.07
9 144 0.71
10 1 0.00
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:51981716 original size:25 final size:25
Alignment explanation
Indices: 51981649--51981868 Score: 244
Period size: 25 Copynumber: 8.7 Consensus size: 25
51981639 ATAACTTATT
*
51981649 TATTATGTAAGTTATGTAAGTTGTG
1 TATTATGAAAGTTATGTAAGTTGTG
* *
51981674 TAAGTTATGTAAGCTATGTAAGTTGTG
1 T-A-TTATGAAAGTTATGTAAGTTGTG
*
51981701 TATTATGAAACTTATGTAAGTTGTG
1 TATTATGAAAGTTATGTAAGTTGTG
**
51981726 TATTATGATGGTTATGTAAGTTGTG
1 TATTATGAAAGTTATGTAAGTTGTG
* *
51981751 TATTATGTAAGTTATGTTAGTTGTG
1 TATTATGAAAGTTATGTAAGTTGTG
* *
51981776 TATTATGAAACTTATGTAAGTTATG
1 TATTATGAAAGTTATGTAAGTTGTG
* * * ** *
51981801 TCTTATGTAAGTGATGTAAAATATG
1 TATTATGAAAGTTATGTAAGTTGTG
* *
51981826 TATTATGTAAGTTATGTCAGTTGTG
1 TATTATGAAAGTTATGTAAGTTGTG
51981851 TATTATGTAAA-TTATGTA
1 TATTATG-AAAGTTATGTA
51981869 TTATGTAAGT
Statistics
Matches: 163, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
25 136 0.83
26 4 0.02
27 23 0.14
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.46
Consensus pattern (25 bp):
TATTATGAAAGTTATGTAAGTTGTG
Found at i:51981731 original size:16 final size:16
Alignment explanation
Indices: 51981644--51981884 Score: 143
Period size: 16 Copynumber: 14.4 Consensus size: 16
51981634 TAGGAATAAC
*
51981644 TTATTTATTATGTAAG
1 TTATGTATTATGTAAG
*
51981660 TTATGTAAGTTGTGTAAG
1 TTATGT-A-TTATGTAAG
*
51981678 TTATGTAAGCTATGTAAG
1 TTATGT-A-TTATGTAAG
* * *
51981696 TTGTGTATTATGAAAC
1 TTATGTATTATGTAAG
*
51981712 TTATGTAAGTTGTGT-A-
1 TTATGT-A-TTATGTAAG
*
51981728 TTATGATGGTTATGTAAG
1 TTATG-T-ATTATGTAAG
*
51981746 TTGTGTATTATGTAAG
1 TTATGTATTATGTAAG
*
51981762 TTATGTTAGTTGTGT-A-
1 TTATG-TA-TTATGTAAG
*
51981778 TTATGAAACTTATGTAAG
1 TTATG-TA-TTATGTAAG
*
51981796 TTATGTCTTATGTAAG
1 TTATGTATTATGTAAG
* *
51981812 TGATGTAAAATATGT-A-
1 TTATGT--ATTATGTAAG
*
51981828 TTATGTAAGTTATGTCAG
1 TTATGT-A-TTATGTAAG
* *
51981846 TTGTGTATTATGTAAA
1 TTATGTATTATGTAAG
51981862 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
51981878 TTATGTA
1 TTATGTA
51981885 ATTTGTGTAT
Statistics
Matches: 175, Mismatches: 34, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
15 2 0.01
16 102 0.58
17 14 0.08
18 57 0.33
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:51981753 original size:50 final size:50
Alignment explanation
Indices: 51981649--51981906 Score: 275
Period size: 50 Copynumber: 5.3 Consensus size: 50
51981639 ATAACTTATT
*
51981649 TATTATGTAAGTTATGTAAGTTGTGTAAGTTATGTAAGCTATGTAAGTTGTG
1 TATTATGTAAGTTATGTAAGTTGTGT-A-TTATGTAAGTTATGTAAGTTGTG
* * *
51981701 TATTATGAAACTTATGTAAGTTGTGTATTATG-ATGGTTATGTAAGTTGTG
1 TATTATGTAAGTTATGTAAGTTGTGTATTATGTA-AGTTATGTAAGTTGTG
* * * *
51981751 TATTATGTAAGTTATGTTAGTTGTGTATTATGAAACTTATGTAAGTTATG
1 TATTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTG
* * ** * *
51981801 TCTTATGTAAGTGATGTAAAATATGTATTATGTAAGTTATGTCAGTTGTG
1 TATTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTG
*
51981851 TATTATGTAA---AT-T-A----TGTATTATGTAAGTTATGTAATTTGTG
1 TATTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTG
*
51981892 TATTATGTAACTTAT
1 TATTATGTAAGTTAT
51981907 TTAATTTATG
Statistics
Matches: 178, Mismatches: 23, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
41 35 0.20
44 2 0.01
45 1 0.01
46 1 0.01
47 2 0.01
49 1 0.01
50 110 0.62
51 2 0.01
52 24 0.13
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (50 bp):
TATTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTG
Found at i:51981778 original size:75 final size:75
Alignment explanation
Indices: 51981644--51981906 Score: 312
Period size: 75 Copynumber: 3.6 Consensus size: 75
51981634 TAGGAATAAC
* *
51981644 TTATTTATTATGTAAGTTATGTAAGTTGTGTAAGTTATGTAAGCTATGTAAGTTGTGTATTATGA
1 TTATGTATTATGTAAGTTATGTAAGTTGTGT-A-TTATGTAAGTTATGTAAGTTGTGTATTATGA
51981709 AACTTATGTAAG
64 AACTTATGTAAG
* * *
51981721 TTGTGTATTATG-ATGGTTATGTAAGTTGTGTATTATGTAAGTTATGTTAGTTGTGTATTATGAA
1 TTATGTATTATGTA-AGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTGTATTATGAA
51981785 ACTTATGTAAG
65 ACTTATGTAAG
* * ** * *
51981796 TTATGTCTTATGTAAGTGATGTAAAATATGTATTATGTAAGTTATGTCAGTTGTGTATTATG---
1 TTATGTATTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTGTATTATGAAA
51981858 --TA---AA-
66 CTTATGTAAG
* *
51981862 TTATGTATTATGTAAGTTATGTAATTTGTGTATTATGTAACTTAT
1 TTATGTATTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTAT
51981907 TTAATTTATG
Statistics
Matches: 165, Mismatches: 19, Indels: 15
0.83 0.10 0.08
Matches are distributed among these distances:
66 39 0.24
67 2 0.01
70 2 0.01
75 93 0.56
76 3 0.02
77 26 0.16
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.48
Consensus pattern (75 bp):
TTATGTATTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTGTATTATGAAA
CTTATGTAAG
Found at i:51981832 original size:41 final size:40
Alignment explanation
Indices: 51981787--51981901 Score: 133
Period size: 41 Copynumber: 2.8 Consensus size: 40
51981777 ATTATGAAAC
51981787 TTATGTAAGTTATGTC-TTATGTAAGTGATGTAAAATATGTA
1 TTATGTAAGTTATGTCATTATGT-A-TGATGTAAAATATGTA
* * *
51981828 TTATGTAAGTTATGTCAGTTGTGTATTATGTAAATTATGTA
1 TTATGTAAGTTATGTCA-TTATGTATGATGTAAAATATGTA
* * *
51981869 TTATGTAAGTTATGTAATTTGTGTATTATGTAA
1 TTATGTAAGTTATGTCA-TTATGTATGATGTAA
51981902 CTTATTTAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 61 0.91
42 1 0.01
43 5 0.07
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (40 bp):
TTATGTAAGTTATGTCATTATGTATGATGTAAAATATGTA
Found at i:51981881 original size:25 final size:24
Alignment explanation
Indices: 51981752--51981942 Score: 102
Period size: 25 Copynumber: 7.6 Consensus size: 24
51981742 TAAGTTGTGT
* *
51981752 ATTATGTAAGTTATGTTAGTTGTGT-
1 ATTATGTAATTTATG-TA-TTATGTA
* *
51981777 ATTATGAAACTTATGTAAGTTATGT-
1 ATTATGTAATTTATGT-A-TTATGTA
* * * *
51981802 CTTATGTAAGTGATGTAAAATATGT-
1 ATTATGTAATTTATGT--ATTATGTA
* *
51981827 ATTATGTAAGTTATGTCAGTTGTGT-
1 ATTATGTAATTTATGT-A-TTATGTA
*
51981852 ATTATGTAAATTATGTATTATGTA
1 ATTATGTAATTTATGTATTATGTA
*
51981876 AGTTATGTAATTTGTGTATTATGTA
1 A-TTATGTAATTTATGTATTATGTA
* * *
51981901 ACTTATTTAATTTATGTAAGTGTGTA
1 A-TTATGTAATTTATGT-ATTATGTA
51981927 TTATTATGTAATTTAT
1 --ATTATGTAATTTAT
51981943 AATGTAGGAT
Statistics
Matches: 135, Mismatches: 23, Indels: 14
0.78 0.13 0.08
Matches are distributed among these distances:
23 5 0.04
24 4 0.03
25 105 0.78
26 8 0.06
27 12 0.09
28 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (24 bp):
ATTATGTAATTTATGTATTATGTA
Found at i:51982431 original size:24 final size:24
Alignment explanation
Indices: 51982402--51982483 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 24
51982392 ACTTTTAAAT
51982402 TTTATAGGTTATATTAAAACAATA
1 TTTATAGGTTATATTAAAACAATA
*
51982426 TTTATA-ATTAT-TTAGAAAACTTTTAA-A
1 TTTATAGGTTATATT--AAAAC----AATA
51982453 TTTTATAGGTTATATTAAAACAATA
1 -TTTATAGGTTATATTAAAACAATA
51982478 TTTATA
1 TTTATA
51982484 ATACTAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 20
0.68 0.03 0.29
Matches are distributed among these distances:
22 2 0.04
23 4 0.09
24 19 0.41
25 1 0.02
27 1 0.02
28 13 0.28
29 4 0.09
30 2 0.04
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (24 bp):
TTTATAGGTTATATTAAAACAATA
Found at i:51982461 original size:52 final size:51
Alignment explanation
Indices: 51982373--51982485 Score: 217
Period size: 52 Copynumber: 2.2 Consensus size: 51
51982363 ATTTAATACT
51982373 TATTTATAATTATTTAGAAACTTTTAAATTTTATAGGTTATATTAAAACAA
1 TATTTATAATTATTTAGAAACTTTTAAATTTTATAGGTTATATTAAAACAA
51982424 TATTTATAATTATTTAGAAAACTTTTAAATTTTATAGGTTATATTAAAACAA
1 TATTTATAATTATTTAG-AAACTTTTAAATTTTATAGGTTATATTAAAACAA
51982476 TATTTATAAT
1 TATTTATAAT
51982486 ACTAATATAG
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 17 0.28
52 44 0.72
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (51 bp):
TATTTATAATTATTTAGAAACTTTTAAATTTTATAGGTTATATTAAAACAA
Found at i:51982543 original size:15 final size:15
Alignment explanation
Indices: 51982523--51982555 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
51982513 AGAATTTTTT
*
51982523 ATAAATTTAATAGTA
1 ATAAATTTAATACTA
51982538 ATAAATTTAATACTA
1 ATAAATTTAATACTA
51982553 ATA
1 ATA
51982556 TAGAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
ATAAATTTAATACTA
Found at i:51990751 original size:215 final size:213
Alignment explanation
Indices: 51990206--51990916 Score: 828
Period size: 215 Copynumber: 3.3 Consensus size: 213
51990196 NNNNNNNNNN
* ** * **
51990206 AATTGTACTGGATGCCGGCCATTGACAGGCTCCAA-A---AAGATTTTTATTTACTTTTTTGGTA
1 AATTGTACTGGGTGCCGGCCATTGACAGG--CCAACACCCAATTTTTTTTTTTACTTTTTCCGTA
* * * *** *
51990267 TACTGATATCGGA-TCTGACACGAAAGAAAAGAAAAAAAAATTTTAAATTGTACTGGGTGCCAGC
64 TACTGATATCTGATTCTAACACG--A-AAAA-AAAGAATTTTTTTAAATTGTACTGGGTGCCGGC
* * * *
51990331 CATTGACAGGCCAACACCCTAATTTTTTTTTTTTACTTTTTACTTATACTGATATCTGATTCTAA
125 CATTGACAGGCCAACACCC-AA-ATTTTTTTTTTACTTTTTTCGTATACTGATATCTGATTCTGA
*
51990396 CATGAAAAAAAGGAAAAAAAAATTTTA
188 CACGAAAAAAA-GAAAAAAAAATTTTA
* * *
51990423 TAATTGTACTCGGTGCCCGGCCATTGACAAGGCCAGCACCCAAAAAAAATTATTTTTTTTACTTT
1 -AATTGTACTGGGTG-CCGGCCATTGAC-AGGCCAACACCC------AATTTTTTTTTTTACTTT
** * * * *
51990488 TTTTGTATACTGATATCTGATTCTGACACGAAAAAAATGATTTTTTTTATAATTGTACTGGATGC
57 TTCCGTATACTGATATCTGATTCTAACACGAAAAAAAAGAATTTTTTTA-AATTGTACTGGGTGC
* *
51990553 CGGCCATTGACAGGCTAGCACCCAAATTTTTTTTTTACTTTTTTCGTATACTGATATCTGATTCT
121 CGGCCATTGACAGGCCAACACCCAAATTTTTTTTTTACTTTTTTCGTATACTGATATCTGATTCT
51990618 GACACGAAAGAAAAGAAAAAAAAATTTTA
186 GACACGAAA-AAAAGAAAAAAAAATTTTA
*
51990647 AATTGTACTGGGTGCCAGCCATTGACAGGCCAACACCCAATTTTTTTTTTTACTTTTTCCGTATA
1 AATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAATTTTTTTTTTTACTTTTTCCGTATA
* *
51990712 CTGATATCTGATTCTAACATGAAAAAAAAGAATTTTTTTAAAATCGTACTGGGTGCCGGCCATTG
66 CTGATATCTGATTCTAACACGAAAAAAAAGAATTTTTTT-AAATTGTACTGGGTGCCGGCCATTG
* *
51990777 ACAAGCCAACACCCAAA-TTTTTTTTTATTTTTTTCGTATACTGATATCTGATTCTGACACGAAA
130 ACAGGCCAACACCCAAATTTTTTTTTTACTTTTTTCGTATACTGATATCTGATTCTGACACGAAA
*
51990841 AAAAGTAAAAAAAAA-ATT-
195 AAAAG-AAAAAAAAATTTTA
* *
51990859 AATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAA-ATTTTTTTTTCCTTTTTC
1 AATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAATTTTTTTTTTTACTTTTTC
51990917 TTCTTTTTCC
Statistics
Matches: 432, Mismatches: 44, Indels: 41
0.84 0.09 0.08
Matches are distributed among these distances:
211 16 0.04
212 39 0.09
213 7 0.02
214 55 0.13
215 95 0.22
216 1 0.00
218 15 0.03
219 13 0.03
220 3 0.01
221 11 0.03
222 11 0.03
223 13 0.03
224 59 0.14
225 14 0.03
226 38 0.09
227 1 0.00
228 32 0.07
229 9 0.02
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (213 bp):
AATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAATTTTTTTTTTTACTTTTTCCGTATA
CTGATATCTGATTCTAACACGAAAAAAAAGAATTTTTTTAAATTGTACTGGGTGCCGGCCATTGA
CAGGCCAACACCCAAATTTTTTTTTTACTTTTTTCGTATACTGATATCTGATTCTGACACGAAAA
AAAGAAAAAAAAATTTTA
Found at i:51990915 original size:106 final size:107
Alignment explanation
Indices: 51990206--51990915 Score: 791
Period size: 106 Copynumber: 6.5 Consensus size: 107
51990196 NNNNNNNNNN
* * *
51990206 AATTGTACTGGATGCCGGCCATTGACAGGCTCCAA-A---AAGATTTTTATTTACTTTTTTGGTA
1 AATTGTACTGGGTGCCGGCCATTGACAGG--CCAACACCCAA-ATTTTTTTTTACTTTTTTCGTA
*
51990267 TACTGATATCGGA-TCTGACACGAAAGAAAAGAAAAAAAAATTTTA
63 TACTGATATCTGATTCTGACACGAAA-AAAAGAAAAAAAAATTTTA
* * * *
51990312 AATTGTACTGGGTGCCAGCCATTGACAGGCCAACACCCTAATTTTTTTTTTTTACTTTTTACTTA
1 AATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCC-AA--ATTTTTTTTTACTTTTTTCGTA
* *
51990377 TACTGATATCTGATTCTAACATGAAAAAAAGGAAAAAAAAATTTTA
63 TACTGATATCTGATTCTGACACGAAAAAAA-GAAAAAAAAATTTTA
* *
51990423 TAATTGTACTCGGTGCCCGGCCATTGACAAGGCCAGCACCCAAAAAAAATTATTTTTTTTACTTT
1 -AATTGTACTGGGTG-CCGGCCATTGAC-AGGCCAACACCC-----AAA-T-TTTTTTTTACTTT
* ****
51990488 TTTTGTATACTGATATCTGATTCTGACACGAAAAAAATG----ATTTTTTTTA
56 TTTCGTATACTGATATCTGATTCTGACACGAAAAAAA-GAAAAAAAAATTTTA
* * *
51990537 TAATTGTACTGGATGCCGGCCATTGACAGGCTAGCACCCAAATTTTTTTTTTACTTTTTTCGTAT
1 -AATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAAA-TTTTTTTTTACTTTTTTCGTAT
51990602 ACTGATATCTGATTCTGACACGAAAGAAAAGAAAAAAAAATTTTA
64 ACTGATATCTGATTCTGACACGAAA-AAAAGAAAAAAAAATTTTA
* * *
51990647 AATTGTACTGGGTGCCAGCCATTGACAGGCCAACACCCAATTTTTTTTTTTACTTTTTCCGTATA
1 AATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAA-ATTTTTTTTTACTTTTTTCGTATA
* * * ***
51990712 CTGATATCTGATTCTAACATG--AAAAA-AAAGAATTTTTTTAA
65 CTGATATCTGATTCTGACACGAAAAAAAGAAAAAAAAATTTT-A
* * *
51990753 AATCGTACTGGGTGCCGGCCATTGACAAGCCAACACCCAAATTTTTTTTTATTTTTTTCGTATAC
1 AATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAAATTTTTTTTTACTTTTTTCGTATAC
*
51990818 TGATATCTGATTCTGACACGAAAAAAAGTAAAAAAAAA-ATT-
66 TGATATCTGATTCTGACACGAAAAAAAG-AAAAAAAAATTTTA
*
51990859 AATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAAATTTTTTTTTCCTTTTT
1 AATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAAATTTTTTTTTACTTTTT
51990916 CTTCTTTTTC
Statistics
Matches: 513, Mismatches: 63, Indels: 56
0.81 0.10 0.09
Matches are distributed among these distances:
104 4 0.01
105 50 0.10
106 168 0.33
107 15 0.03
108 2 0.00
109 84 0.16
110 39 0.08
111 25 0.05
112 24 0.05
113 23 0.04
114 30 0.06
117 1 0.00
118 48 0.09
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (107 bp):
AATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAAATTTTTTTTTACTTTTTTCGTATAC
TGATATCTGATTCTGACACGAAAAAAAGAAAAAAAAATTTTA
Found at i:51993339 original size:17 final size:18
Alignment explanation
Indices: 51993310--51993563 Score: 166
Period size: 17 Copynumber: 14.1 Consensus size: 18
51993300 ACACAATAAT
51993310 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
51993328 GATTTTTG-AAACACGAA
1 AATTTTTGAAAACACGAA
51993345 AATTTTTTGAAAACACGGAA
1 AA-TTTTTGAAAACAC-GAA
** * *
51993365 TTTTTTTGAAAACAAGGA
1 AATTTTTGAAAACACGAA
* * *
51993383 AATTTTCG-ATACATGAGA
1 AATTTTTGAAAACACGA-A
*
51993401 ATTTTTTG---ACACGAA
1 AATTTTTGAAAACACGAA
*
51993416 AAATTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
* *
51993434 AA-TTTCGAAAACATGAA
1 AATTTTTGAAAACACGAA
** * *
51993451 TTTTTTTTAAAAATACGAA
1 -AATTTTTGAAAACACGAA
** *
51993470 TTTTTTTAAAAACACGAGA
1 AATTTTTGAAAACACGA-A
*
51993489 AATTTTTTGAAAACATGAA
1 AA-TTTTTGAAAACACGAA
*
51993508 AA-TTTTGAAAACATGAA
1 AATTTTTGAAAACACGAA
51993525 AA-TTTTG-AAACACGAGA
1 AATTTTTGAAAACACGA-A
*
51993542 ATTTTTTTTGAAAACACGAA
1 A--ATTTTTGAAAACACGAA
51993562 AA
1 AA
51993564 CACGAAAATT
Statistics
Matches: 187, Mismatches: 33, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
15 7 0.04
16 12 0.06
17 52 0.28
18 52 0.28
19 33 0.18
20 23 0.12
21 8 0.04
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:51993494 original size:20 final size:20
Alignment explanation
Indices: 51993453--51993513 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
51993443 AACATGAATT
* *
51993453 TTTTTTAAAAATAC--GAAT
1 TTTTTTAAAAACACGAGAAA
51993471 TTTTTTAAAAACACGAGAAA
1 TTTTTTAAAAACACGAGAAA
* *
51993491 TTTTTTGAAAACATGA-AAA
1 TTTTTTAAAAACACGAGAAA
51993510 TTTT
1 TTTT
51993514 GAAAACATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 13 0.35
19 7 0.19
20 17 0.46
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTTTAAAAACACGAGAAA
Found at i:51993571 original size:45 final size:43
Alignment explanation
Indices: 51993514--51993607 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 43
51993504 TGAAAATTTT
* *
51993514 GAAAACATGAAAA-TTTTGAAACACGAGAATTTTTTTTGAAAACAC
1 GAAAACACGAAAATTTTTAAAACACGAGAA---TTTTTGAAAACAC
51993559 GAAAACACGAAAATTTTTTTAAAACACGAGAATTTTTGAAAACAC
1 GAAAACACGAAAA--TTTTTAAAACACGAGAATTTTTGAAAACAC
51993604 GAAA
1 GAAA
51993608 TTTTTTTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
45 29 0.66
48 15 0.34
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.27
Consensus pattern (43 bp):
GAAAACACGAAAATTTTTAAAACACGAGAATTTTTGAAAACAC
Found at i:51993583 original size:27 final size:29
Alignment explanation
Indices: 51993532--51993587 Score: 89
Period size: 27 Copynumber: 2.0 Consensus size: 29
51993522 GAAAATTTTG
*
51993532 AAACACGAGAATTTTTTTTGAAAACACGA
1 AAACACGAGAAATTTTTTTGAAAACACGA
51993561 AAACACGA-AAATTTTTTT-AAAACACGA
1 AAACACGAGAAATTTTTTTGAAAACACGA
51993588 GAATTTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 9 0.35
28 9 0.35
29 8 0.31
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (29 bp):
AAACACGAGAAATTTTTTTGAAAACACGA
Found at i:51993584 original size:19 final size:19
Alignment explanation
Indices: 51993560--51993615 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 19
51993550 TGAAAACACG
51993560 AAAACACGAAAATTTTTTT
1 AAAACACGAAAATTTTTTT
* *
51993579 AAAACACGAGAA-TTTTTG
1 AAAACACGAAAATTTTTTT
51993597 AAAACACG-AAATTTTTTT
1 AAAACACGAAAATTTTTTT
51993615 A
1 A
51993616 TTCACGAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 2 0.06
18 19 0.59
19 11 0.34
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (19 bp):
AAAACACGAAAATTTTTTT
Found at i:51993609 original size:17 final size:17
Alignment explanation
Indices: 51993310--51993612 Score: 132
Period size: 17 Copynumber: 17.4 Consensus size: 17
51993300 ACACAATAAT
51993310 AATTTTTGAAAACACGA
1 AATTTTTGAAAACACGA
51993327 AGATTTTTG-AAACACGAA
1 A-ATTTTTGAAAACACG-A
51993345 AATTTTTTGAAAACACGGA
1 AA-TTTTTGAAAACAC-GA
* *
51993364 ATTTTTTTGAAAACAAGGA
1 A-ATTTTTGAAAAC-ACGA
* * *
51993383 AATTTTCG-ATACATGA
1 AATTTTTGAAAACACGA
51993399 GAATTTTTTG---ACACGAA
1 -AA-TTTTTGAAAACACG-A
*
51993416 AAATTTTGAAAACACGA
1 AATTTTTGAAAACACGA
* * *
51993433 AAATTTCGAAAACATGA
1 AATTTTTGAAAACACGA
* * *
51993450 ATTTTTTTTAAAAATACGA
1 A--ATTTTTGAAAACACGA
* *
51993469 ATTTTTTTAAAAACACGAGA
1 A-ATTTTTGAAAACAC--GA
*
51993489 AATTTTTTGAAAACATGA
1 AA-TTTTTGAAAACACGA
* *
51993507 AAATTTTGAAAACATGA
1 AATTTTTGAAAACACGA
*
51993524 AAATTTTG-AAACACGA
1 AATTTTTGAAAACACGA
51993540 GAATTTTTTTTGAAAACAC--
1 -AA---TTTTTGAAAACACGA
51993559 -------GAAAACACGAA
1 AATTTTTGAAAACACG-A
*
51993570 AATTTTTTTAAAACACGA
1 AA-TTTTTGAAAACACGA
51993588 GAATTTTTGAAAACACGA
1 -AATTTTTGAAAACACGA
51993606 AATTTTT
1 AATTTTT
51993613 TTATTCACGA
Statistics
Matches: 225, Mismatches: 26, Indels: 70
0.70 0.08 0.22
Matches are distributed among these distances:
8 8 0.04
15 5 0.02
16 16 0.07
17 63 0.28
18 63 0.28
19 43 0.19
20 21 0.09
21 6 0.03
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (17 bp):
AATTTTTGAAAACACGA
Found at i:51993622 original size:35 final size:36
Alignment explanation
Indices: 51993559--51993648 Score: 121
Period size: 34 Copynumber: 2.5 Consensus size: 36
51993549 TTGAAAACAC
51993559 GAAAACACGAAAATTTTTTTAAAACACGAGAATTTTT
1 GAAAACACG-AAATTTTTTTAAAACACGAGAATTTTT
**
51993596 GAAAACACGAAATTTTTTT-ATTCACGAGAATTTTT
1 GAAAACACGAAATTTTTTTAAAACACGAGAATTTTT
* *
51993631 G-AAACAGGGAATTTTTTT
1 GAAAACACGAAATTTTTTT
51993649 TAAGAAGTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
34 15 0.31
35 15 0.31
36 10 0.20
37 9 0.18
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (36 bp):
GAAAACACGAAATTTTTTTAAAACACGAGAATTTTT
Found at i:51993627 original size:18 final size:18
Alignment explanation
Indices: 51993561--51993648 Score: 83
Period size: 17 Copynumber: 5.0 Consensus size: 18
51993551 GAAAACACGA
*
51993561 AAACACGAAAATTTTTTT
1 AAACACGAGAATTTTTTT
**
51993579 AAAACACGAGAATTTTTGA
1 -AAACACGAGAATTTTTTT
51993598 AAACACGA-AATTTTTTT
1 AAACACGAGAATTTTTTT
** *
51993615 ATTCACGAGAA-TTTTTG
1 AAACACGAGAATTTTTTT
*
51993632 AAACA-GGGAATTTTTTT
1 AAACACGAGAATTTTTTT
51993649 TAAGAAGTAC
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
16 4 0.07
17 26 0.47
18 10 0.18
19 15 0.27
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (18 bp):
AAACACGAGAATTTTTTT
Found at i:51994348 original size:16 final size:17
Alignment explanation
Indices: 51994317--51994349 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
51994307 TTGCTGTTTG
51994317 CTATTTTTTTAGGGGCTA
1 CTATTTTTTTA-GGGCTA
51994335 CTATTTTTTT-GGGCT
1 CTATTTTTTTAGGGCT
51994350 GCTGGGCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
18 10 0.67
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (17 bp):
CTATTTTTTTAGGGCTA
Found at i:51994356 original size:24 final size:26
Alignment explanation
Indices: 51994329--51994384 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
51994319 ATTTTTTTAG
51994329 GGGCTAC-TATTTT-TTTGGGCTGCT
1 GGGCTACGTATTTTATTTGGGCTGCT
* *
51994353 GGGCTGCTGTTTTTTATTTGGGCTGCT
1 GGGCTAC-GTATTTTATTTGGGCTGCT
51994380 GGGCT
1 GGGCT
51994385 GATGCGGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 6 0.22
26 5 0.19
27 16 0.59
ACGTcount: A:0.05, C:0.16, G:0.34, T:0.45
Consensus pattern (26 bp):
GGGCTACGTATTTTATTTGGGCTGCT
Found at i:51994486 original size:11 final size:11
Alignment explanation
Indices: 51994439--51994527 Score: 85
Period size: 11 Copynumber: 8.1 Consensus size: 11
51994429 TGATGGTATG
51994439 TTTTTCTTT-T
1 TTTTTCTTTCT
51994449 TCTTTT-TTTCT
1 T-TTTTCTTTCT
* * *
51994460 ATTTTATTTCCC
1 TTTTTCTTT-CT
*
51994472 TTTTTCCTTC-
1 TTTTTCTTTCT
51994482 TTTTTCTTTCT
1 TTTTTCTTTCT
*
51994493 TTTTTCTTCCTT
1 TTTTTCTTTC-T
51994505 TTTTTCTTTCT
1 TTTTTCTTTCT
51994516 TTTTTCTTTCT
1 TTTTTCTTTCT
51994527 T
1 T
51994528 CTTCGGGTCA
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
10 17 0.26
11 31 0.48
12 17 0.26
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:51994493 original size:4 final size:4
Alignment explanation
Indices: 51994484--51994527 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
51994474 TTTCCTTCTT
* *
51994484 TTTC TTTC TTT- TTTC TTCC TTTT TTTC TTTC TTT- TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
51994528 CTTCGGGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
3 6 0.18
4 28 0.82
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:51994512 original size:23 final size:24
Alignment explanation
Indices: 51994475--51994530 Score: 96
Period size: 23 Copynumber: 2.4 Consensus size: 24
51994465 ATTTCCCTTT
51994475 TTCCTTCTTTTTCTTTCTTTTTTC
1 TTCCTTCTTTTTCTTTCTTTTTTC
51994499 TTCCTT-TTTTTCTTTCTTTTTTC
1 TTCCTTCTTTTTCTTTCTTTTTTC
*
51994522 TTTCTTCTT
1 TTCCTTCTT
51994531 CGGGTCACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 22 0.73
24 8 0.27
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (24 bp):
TTCCTTCTTTTTCTTTCTTTTTTC
Found at i:51994528 original size:27 final size:26
Alignment explanation
Indices: 51994439--51994524 Score: 92
Period size: 23 Copynumber: 3.3 Consensus size: 26
51994429 TGATGGTATG
51994439 TTTTTCTTTTT-CTTTTTTTCTATT-T
1 TTTTTCTTTTTCCTTTTTTTCT-TTCT
*
51994464 TATTTCCCTTTTTCCTTCTTTTTCTTTCT
1 T-TTT-TCTTTTTCCTT-TTTTTCTTTCT
51994493 TTTTTC---TTCCTTTTTTTCTTTCT
1 TTTTTCTTTTTCCTTTTTTTCTTTCT
51994516 TTTTTCTTT
1 TTTTTCTTT
51994525 CTTCTTCGGG
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
23 17 0.33
24 6 0.12
25 1 0.02
26 3 0.06
27 7 0.14
28 8 0.16
29 9 0.18
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTTCTTTTTCCTTTTTTTCTTTCT
Found at i:51994649 original size:21 final size:21
Alignment explanation
Indices: 51994611--51994672 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
51994601 GCCTCCCTTC
*
51994611 TCTTCCTCTCTCTCTCTTTTCTT
1 TCTT-CTCT-TCTTTCTTTTCTT
51994634 TCTTCTCTTCTTTCTTTTCTT
1 TCTTCTCTTCTTTCTTTTCTT
*
51994655 TCTTCTCTTCCTTCTTTT
1 TCTTCTCTTCTTTCTTTT
51994673 TGGCTGCTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 29 0.78
22 4 0.11
23 4 0.11
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (21 bp):
TCTTCTCTTCTTTCTTTTCTT
Found at i:51994668 original size:4 final size:5
Alignment explanation
Indices: 51994607--51994669 Score: 52
Period size: 4 Copynumber: 14.0 Consensus size: 5
51994597 GCGCGCCTCC
*
51994607 CTTCT CTTC- C-TCT CTCTCT CTTTT CTT-T CTTCT CTTCT -TTCT -TT-T
1 CTTCT CTTCT CTTCT CT-TCT CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT
51994652 CTT-T CTTCT CTTC- CTTCT
1 CTTCT CTTCT CTTCT CTTCT
51994670 TTTTGGCTGC
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
3 3 0.06
4 22 0.44
5 20 0.40
6 5 0.10
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (5 bp):
CTTCT
Found at i:51995184 original size:30 final size:31
Alignment explanation
Indices: 51995148--51995235 Score: 94
Period size: 31 Copynumber: 2.9 Consensus size: 31
51995138 GTTAAAGGGA
*
51995148 AATTTTAAGAAAATTTAAGGGCCGAAATGT-
1 AATTTTAAGAAAATTTAAGGGCCAAAATGTG
* *
51995178 AATTTT-AGAAAATTT-TGGGTCAAAATGTG
1 AATTTTAAGAAAATTTAAGGGCCAAAATGTG
* *
51995207 AATTTTAAAAAAAATTT-AGGGTCAAAATG
1 AATTTT-AAGAAAATTTAAGGGCCAAAATG
51995236 GAAATTTCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
28 10 0.20
29 15 0.30
30 6 0.12
31 19 0.38
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (31 bp):
AATTTTAAGAAAATTTAAGGGCCAAAATGTG
Found at i:51995229 original size:31 final size:30
Alignment explanation
Indices: 51995148--51995248 Score: 100
Period size: 29 Copynumber: 3.4 Consensus size: 30
51995138 GTTAAAGGGA
* * *
51995148 AATTTTAAGAAAATTTAAGGGCCGAAATGT-
1 AATTTTAAAAAAATTT-AGGGTCAAAATGTG
* *
51995178 AATTTT-AGAAAATTTTGGGTCAAAATGTG
1 AATTTTAAAAAAATTTAGGGTCAAAATGTG
51995207 AATTTTAAAAAAAATTTAGGGTCAAAATG-G
1 AATTTT-AAAAAAATTTAGGGTCAAAATGTG
* *
51995237 AAATTTCAAAAA
1 AATTTTAAAAAA
51995249 GTATAGGGGT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
28 10 0.16
29 20 0.33
30 12 0.20
31 19 0.31
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.32
Consensus pattern (30 bp):
AATTTTAAAAAAATTTAGGGTCAAAATGTG
Found at i:51995915 original size:75 final size:73
Alignment explanation
Indices: 51995615--51996473 Score: 1062
Period size: 75 Copynumber: 11.4 Consensus size: 73
51995605 TCTCAGATTG
** * * * * * *
51995615 TGAGTTGACCTTTGAAAAATAGATATTGAAAGTACCTCAGCGTAACCCGAGGCTCAACGCACCTC
1 TGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTC
*
51995680 TCGCATTA
66 TCGCAATA
* * * * **
51995688 TGAGTTAATTTTTTTTGAAAAACGGAAATTTAAAAGAAATACCCCGGCATGTGACCTAAGGCTCA
1 TGAGTTGA---TTTTTGAAAAACAGAAATTT---A-AAATACCTCAGC--GTGACCCGAGGCTCA
*
51995753 ACTCACCTCTTGCAATA
57 ACTCACCTCTCGCAATA
* * * * * * *
51995770 TGAGTTGGTTTTTGTGAAAACCAAAAATTGAAAAATACCTC-GACATGACTCGATGCTCAACTCA
1 TGAGTT-GATTTT-TGAAAAACAGAAATT-TAAAATACCTCAG-CGTGACCCGAGGCTCAACTCA
*
51995834 CATCTCGCAATA
62 CCTCTCGCAATA
*
51995846 TGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGACTCAACTCACC
1 TGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACC
51995911 TCTCGCAATA
64 TCTCGCAATA
*
51995921 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCT
1 TGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCG-TGACCCGAGGCTCAACTCACCT
51995985 CTCGCAATA
65 CTCGCAATA
* *
51995994 TGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGTGACCCGAGGTTCAATTCACC
1 TGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACC
51996059 TCTCGCAATA
64 TCTCGCAATA
*
51996069 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCT
1 TGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCG-TGACCCGAGGCTCAACTCACCT
51996133 CTCGCAATA
65 CTCGCAATA
51996142 TGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACC
1 TGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACC
51996207 TCTCGCAATA
64 TCTCGCAATA
*
51996217 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCT
1 TGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCG-TGACCCGAGGCTCAACTCACCT
* * *
51996281 CTCGTATTG
65 CTCGCAATA
* *
51996290 TGAGTTGATTTTTGAAAAA-AAAAATTTAAAAGAAATACCTCGGCGTGACCCGAGGCTCAACTCA
1 TGAGTTGATTTTTGAAAAACAGAAATTT---A-AAATACCTCAGCGTGACCCGAGGCTCAACTCA
51996354 CCTCTCGCAATA
62 CCTCTCGCAATA
*
51996366 TGAGTTGATTTTTTTGAAAAACAGCAATTTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCAC
1 TGAGTTGA--TTTTTGAAAAACAGAAATTT-AAAATACCTCAGCGTGACCCGAGGCTCAACTCAC
* *
51996431 CTCTCGTATTA
63 CTCTCGCAATA
* *
51996442 TGAGTTGATTTTTGAAAAACAAAAATTGAAAA
1 TGAGTTGATTTTTGAAAAACAGAAATTTAAAA
51996474 ATATAATTCT
Statistics
Matches: 687, Mismatches: 66, Indels: 66
0.84 0.08 0.08
Matches are distributed among these distances:
72 7 0.01
73 206 0.30
74 34 0.05
75 210 0.31
76 141 0.21
77 4 0.01
78 20 0.03
79 8 0.01
80 13 0.02
81 12 0.02
82 32 0.05
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (73 bp):
TGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTC
TCGCAATA
Found at i:51995997 original size:148 final size:149
Alignment explanation
Indices: 51995615--51996473 Score: 1144
Period size: 148 Copynumber: 5.7 Consensus size: 149
51995605 TCTCAGATTG
** * * * * *
51995615 TGAGTTGACCTTTGAAAAATAGATATTGAAAGTACCTCAGCG-TAACCCGAGGCTCAACGCACCT
1 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGATGACCCGAGGCTCAACTCACCT
* * * * * * *
51995679 CTCGCATTATGAGTTAATTTTTTTTGAAAAACGGAAATTTAAAAGAAATACCCCGGCATGTGACC
66 CTCGCAATATGAGTTGA---TTTTTGAAAAACAGAAATTT---A-AAATACCTCAGCGTGCGACC
** *
51995744 TAAGGCTCAACTCACCTCTTGCAATA
124 CGAGGCTCAACTCACCTCTCGCAATA
* * * * *
51995770 TGAGTTGGTTTTTGTGAAAACCAAAAATTGAAAAATACCTC-GAC-ATGACTCGATGCTCAACTC
1 TGAGTT-GATTTT-TGAAAAACAGAAATTG-AAAATACCTCAG-CGATGACCCGAGGCTCAACTC
*
51995833 ACATCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGA
62 ACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGA
*
51995898 GACTCAACTCACCTCTCGCAATA
127 GGCTCAACTCACCTCTCGCAATA
51995921 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCT
1 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGATGACCCGAGGCTCAACTCACCT
* *
51995985 CTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGTGACCCGAGGTT
66 CTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCT
*
51996050 CAATTCACCTCTCGCAATA
131 CAACTCACCTCTCGCAATA
51996069 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCT
1 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGATGACCCGAGGCTCAACTCACCT
51996133 CTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCT
66 CTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCT
51996198 CAACTCACCTCTCGCAATA
131 CAACTCACCTCTCGCAATA
51996217 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCT
1 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGATGACCCGAGGCTCAACTCACCT
* * * * *
51996281 CTCGTATTGTGAGTTGATTTTTGAAAAA-AAAAATTTAAAAGAAATACCTCGGCGT--GACCCGA
66 CTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTT---A-AAATACCTCAGCGTGCGACCCGA
51996343 GGCTCAACTCACCTCTCGCAATA
127 GGCTCAACTCACCTCTCGCAATA
* *
51996366 TGAGTTGATTTTTTTGAAAAACAGCAATTTAAAAATACCTCAGCG-TGACCCGAGGCTCAACTCA
1 TGAGTTGA--TTTTTGAAAAACAG-AAATTGAAAATACCTCAGCGATGACCCGAGGCTCAACTCA
* * * *
51996430 CCTCTCGTATTATGAGTTGATTTTTGAAAAACAAAAATTGAAAA
63 CCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAA
51996474 ATATAATTCT
Statistics
Matches: 642, Mismatches: 46, Indels: 38
0.88 0.06 0.05
Matches are distributed among these distances:
147 7 0.01
148 344 0.54
149 56 0.09
150 7 0.01
151 71 0.11
152 66 0.10
153 8 0.01
155 25 0.04
156 3 0.00
157 13 0.02
158 42 0.07
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGATGACCCGAGGCTCAACTCACCT
CTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCT
CAACTCACCTCTCGCAATA
Found at i:51996010 original size:73 final size:74
Alignment explanation
Indices: 51995615--51996473 Score: 1049
Period size: 73 Copynumber: 11.4 Consensus size: 74
51995605 TCTCAGATTG
** * * * * *
51995615 TGAGTTGACCTTTGAAAAATAGATATTGAAAGTACCTCAGCG-TAACCCGAGGCTCAACGCACCT
1 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGATGACCCGAGGCTCAACTCACCT
*
51995679 CTCGCATTA
66 CTCGCAATA
* * * * * **
51995688 TGAGTTAATTTTTTTTGAAAAACGGAAATTTAAAAGAAATACCCCGGC-ATGTGACCTAAGGCTC
1 TGAGTTGA---TTTTTGAAAAACAGAAA-TT--GA-AAATACCTCAGCGA--TGACCCGAGGCTC
*
51995752 AACTCACCTCTTGCAATA
57 AACTCACCTCTCGCAATA
* * * * *
51995770 TGAGTTGGTTTTTGTGAAAACCAAAAATTGAAAAATACCTC-GAC-ATGACTCGATGCTCAACTC
1 TGAGTT-GATTTT-TGAAAAACAGAAATTG-AAAATACCTCAG-CGATGACCCGAGGCTCAACTC
*
51995833 ACATCTCGCAATA
62 ACCTCTCGCAATA
* *
51995846 TGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCG-TGCGACCCGAGACTCAACTCAC
1 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGAT--GACCCGAGGCTCAACTCAC
51995910 CTCTCGCAATA
64 CTCTCGCAATA
51995921 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCT
1 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGATGACCCGAGGCTCAACTCACCT
51995985 CTCGCAATA
66 CTCGCAATA
* * * *
51995994 TGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGTGACCCGAGGTTCAATTCACC
1 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCG-ATGACCCGAGGCTCAACTCACC
51996059 TCTCGCAATA
65 TCTCGCAATA
51996069 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCT
1 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGATGACCCGAGGCTCAACTCACCT
51996133 CTCGCAATA
66 CTCGCAATA
*
51996142 TGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCG-TGCGACCCGAGGCTCAACTCAC
1 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGAT--GACCCGAGGCTCAACTCAC
51996206 CTCTCGCAATA
64 CTCTCGCAATA
51996217 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCT
1 TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGATGACCCGAGGCTCAACTCACCT
* * *
51996281 CTCGTATTG
66 CTCGCAATA
* * *
51996290 TGAGTTGATTTTTGAAAAA-AAAAATTTAAAAGAAATACCTCGGCG-TGACCCGAGGCTCAACTC
1 TGAGTTGATTTTTGAAAAACAGAAA-TT--GA-AAATACCTCAGCGATGACCCGAGGCTCAACTC
51996353 ACCTCTCGCAATA
62 ACCTCTCGCAATA
* *
51996366 TGAGTTGATTTTTTTGAAAAACAGCAATTTAAAAATACCTCAGCG-TGACCCGAGGCTCAACTCA
1 TGAGTTGA--TTTTTGAAAAACAG-AAATTGAAAATACCTCAGCGATGACCCGAGGCTCAACTCA
* *
51996430 CCTCTCGTATTA
63 CCTCTCGCAATA
*
51996442 TGAGTTGATTTTTGAAAAACAAAAATTGAAAA
1 TGAGTTGATTTTTGAAAAACAGAAATTGAAAA
51996474 ATATAATTCT
Statistics
Matches: 686, Mismatches: 66, Indels: 68
0.84 0.08 0.08
Matches are distributed among these distances:
72 4 0.01
73 212 0.31
74 32 0.05
75 210 0.31
76 138 0.20
77 6 0.01
78 21 0.03
79 5 0.01
80 17 0.02
81 10 0.01
82 31 0.05
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (74 bp):
TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGATGACCCGAGGCTCAACTCACCT
CTCGCAATA
Found at i:51997378 original size:28 final size:28
Alignment explanation
Indices: 51997338--51997407 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
51997328 TTCATCTTGA
* *
51997338 TTTTTCTTCTTTTTTTTACTTTTTTGCT
1 TTTTTGTTCTTTTTTTTACTTTTTTACT
* ** *
51997366 TTTTTGTTTTTTTTTTTGTTTTTTTATT
1 TTTTTGTTCTTTTTTTTACTTTTTTACT
*
51997394 TTTTTGTTGTTTTT
1 TTTTTGTTCTTTTT
51997408 CTCTCTCTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.03, C:0.06, G:0.07, T:0.84
Consensus pattern (28 bp):
TTTTTGTTCTTTTTTTTACTTTTTTACT
Found at i:51997395 original size:19 final size:19
Alignment explanation
Indices: 51997357--51997407 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
51997347 TTTTTTTTAC
51997357 TTTTTTGCTTTTTTGTTTTT
1 TTTTTTG-TTTTTTGTTTTT
51997377 TTTTTTGTTTTTT-TATTTT
1 TTTTTTGTTTTTTGT-TTTT
*
51997396 TTTGTTGTTTTT
1 TTTTTTGTTTTT
51997408 CTCTCTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 1 0.03
19 21 0.72
20 7 0.24
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.86
Consensus pattern (19 bp):
TTTTTTGTTTTTTGTTTTT
Found at i:51997407 original size:12 final size:12
Alignment explanation
Indices: 51997365--51997395 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
51997355 ACTTTTTTGC
51997365 TTTTTTGTTTTT
1 TTTTTTGTTTTT
51997377 TTTTTTGTTTTT
1 TTTTTTGTTTTT
51997389 TTATTTT
1 TT-TTTT
51997396 TTTGTTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.03, C:0.00, G:0.06, T:0.90
Consensus pattern (12 bp):
TTTTTTGTTTTT
Found at i:52001837 original size:16 final size:16
Alignment explanation
Indices: 52001816--52001883 Score: 61
Period size: 16 Copynumber: 4.4 Consensus size: 16
52001806 TTTTCTTCTT
*
52001816 TTTTTTACTTTTTTGC
1 TTTTTTATTTTTTTGC
* *
52001832 TTTTTTGTTTTTTTTGT
1 TTTTTT-ATTTTTTTGC
52001849 TTTTTTATTTTTTTG-
1 TTTTTTATTTTTTTGC
* *
52001864 TTGTTT-TTTTTCT-C
1 TTTTTTATTTTTTTGC
52001878 TTTTTT
1 TTTTTT
52001884 TTAGGCATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
14 11 0.26
15 5 0.12
16 14 0.33
17 13 0.30
ACGTcount: A:0.03, C:0.06, G:0.07, T:0.84
Consensus pattern (16 bp):
TTTTTTATTTTTTTGC
Found at i:52001837 original size:17 final size:16
Alignment explanation
Indices: 52001815--52001871 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 16
52001805 TTTTTCTTCT
*
52001815 TTTTTTTACTTTTTTG
1 TTTTTTTATTTTTTTG
52001831 CTTTTTTGT-TTTTTTTG
1 -TTTTTT-TATTTTTTTG
52001848 TTTTTTTATTTTTTTG
1 TTTTTTTATTTTTTTG
52001864 TTGTTTTT
1 TT-TTTTT
52001872 TTTCTCTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
15 1 0.03
16 16 0.44
17 18 0.50
18 1 0.03
ACGTcount: A:0.04, C:0.04, G:0.09, T:0.84
Consensus pattern (16 bp):
TTTTTTTATTTTTTTG
Found at i:52001842 original size:25 final size:25
Alignment explanation
Indices: 52001814--52001872 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
52001804 ATTTTTCTTC
*
52001814 TTTTTTTTACTTTTTTGCTTTTTTG
1 TTTTTTTTACTTTTTTACTTTTTTG
** *
52001839 TTTTTTTTGTTTTTTTATTTTTTTG
1 TTTTTTTTACTTTTTTACTTTTTTG
52001864 TTGTTTTTT
1 TT-TTTTTT
52001873 TTCTCTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 23 0.79
26 6 0.21
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.85
Consensus pattern (25 bp):
TTTTTTTTACTTTTTTACTTTTTTG
Found at i:52001870 original size:9 final size:8
Alignment explanation
Indices: 52001824--52001871 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
52001814 TTTTTTTTAC
*
52001824 TTTTTTGC
1 TTTTTTGT
52001832 TTTTTTGTT
1 TTTTTTG-T
52001841 TTTTTTGT
1 TTTTTTGT
*
52001849 TTTTTTAT
1 TTTTTTGT
52001857 TTTTTTGT
1 TTTTTTGT
52001865 TGTTTTT
1 T-TTTTT
52001872 TTTCTCTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
8 23 0.66
9 12 0.34
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.85
Consensus pattern (8 bp):
TTTTTTGT
Found at i:52007642 original size:17 final size:18
Alignment explanation
Indices: 52007613--52008044 Score: 154
Period size: 18 Copynumber: 23.1 Consensus size: 18
52007603 ACACAATAAT
52007613 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
52007631 GATTTTTG-AAACACGAA
1 AATTTTTGAAAACACGAA
52007648 AATTTTTTGAAAACACGGAA
1 AA-TTTTTGAAAACAC-GAA
** * *
52007668 TTTTTTTGAAAACAAGGA
1 AATTTTTGAAAACACGAA
* * *
52007686 AATTTTCG-ATACATGAGA
1 AATTTTTGAAAACACGA-A
*
52007704 ATTTTTTG---ACACGAA
1 AATTTTTGAAAACACGAA
*
52007719 AAATTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
* *
52007737 AA-TTTCGAAAACA-TAA
1 AATTTTTGAAAACACGAA
** * *
52007753 TTTTTTTTAAAAACATGAA
1 -AATTTTTGAAAACACGAA
** *
52007772 TTTTTTTTAAAAAAACACGAGA
1 -AATTTTT--GAAAACACGA-A
* *
52007794 ATTTTTTGAAAACACCAAAACATGA
1 AATTTTTGAAAACA-C----GA--A
52007819 AATTTTTGAAAACACGGGAA
1 AATTTTTGAAAACAC--GAA
**
52007839 CTTTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
52007857 AATTTTTG-AAACATGAGA
1 AATTTTTGAAAACACGA-A
* *
52007875 ATTTTTTG---ACACTAA
1 AATTTTTGAAAACACGAA
*
52007890 AAATTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
* *
52007908 AA-TTTCGAAAACATG-A
1 AATTTTTGAAAACACGAA
* * *
52007924 ATTTTTTAAAAATACGAA
1 AATTTTTGAAAACACGAA
** *
52007942 TTTTTTTAAAAACACGAGA
1 AATTTTTGAAAACACGA-A
*
52007961 AATTTTTTGAAAACATGAAA
1 AA-TTTTTGAAAACACG-AA
*
52007981 ACATGAAAATTTTGAAAACATGAA
1 A-AT-----TTTTGAAAACACGAA
52008005 AATTTTTG-AAACACGAGA
1 AATTTTTGAAAACACGA-A
*
52008023 ATTTTTTTTGAAAACACGAA
1 A--ATTTTTGAAAACACGAA
52008043 AA
1 AA
52008045 CACGAAAATT
Statistics
Matches: 317, Mismatches: 59, Indels: 76
0.70 0.13 0.17
Matches are distributed among these distances:
15 14 0.04
16 13 0.04
17 59 0.19
18 93 0.29
19 35 0.11
20 41 0.13
21 25 0.08
22 2 0.01
23 2 0.01
24 5 0.02
25 28 0.09
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:52007655 original size:19 final size:18
Alignment explanation
Indices: 52007597--52007741 Score: 95
Period size: 18 Copynumber: 8.0 Consensus size: 18
52007587 ACACGAGAAC
52007597 TTTGAAACAC-AATAATAATT
1 TTTGAAACACGAA-AAT--TT
*
52007617 TTTGAAAACACGAAGA-TT
1 TTTG-AAACACGAAAATTT
52007635 TTTGAAACACGAAAATTT
1 TTTGAAACACGAAAATTT
* *
52007653 TTTGAAAACACGGAATTTT
1 TTTG-AAACACGAAAATTT
* *
52007672 TTTGAAAACAAGGAAA-TT
1 TTTG-AAACACGAAAATTT
* * * *
52007690 TTCGATACATGAGAATTT
1 TTTGAAACACGAAAATTT
*
52007708 TTTG--ACACGAAAA-AT
1 TTTGAAACACGAAAATTT
52007723 TTTGAAAACACGAAAATTT
1 TTTG-AAACACGAAAATTT
52007742 CGAAAACATA
Statistics
Matches: 100, Mismatches: 16, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
15 5 0.05
16 7 0.07
17 17 0.17
18 31 0.31
19 27 0.27
20 4 0.04
21 7 0.07
22 2 0.02
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (18 bp):
TTTGAAACACGAAAATTT
Found at i:52007775 original size:19 final size:18
Alignment explanation
Indices: 52007744--52007784 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 18
52007734 GAAAATTTCG
52007744 AAAACATAATTTTTTTTA
1 AAAACATAATTTTTTTTA
52007762 AAAACATGAATTTTTTTTA
1 AAAACAT-AATTTTTTTTA
52007781 AAAA
1 AAAA
52007785 AACACGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (18 bp):
AAAACATAATTTTTTTTA
Found at i:52007814 original size:27 final size:25
Alignment explanation
Indices: 52007783--52007833 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
52007773 TTTTTTTAAA
52007783 AAAACACGAGAATTTTTTGAAAACACC
1 AAAACACGA-AA-TTTTTGAAAACACC
*
52007810 AAAACATGAAATTTTTGAAAACAC
1 AAAACACGAAATTTTTGAAAACAC
52007834 GGGAACTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.57
26 2 0.09
27 8 0.35
ACGTcount: A:0.51, C:0.16, G:0.10, T:0.24
Consensus pattern (25 bp):
AAAACACGAAATTTTTGAAAACACC
Found at i:52007848 original size:171 final size:167
Alignment explanation
Indices: 52007651--52008000 Score: 533
Period size: 171 Copynumber: 2.1 Consensus size: 167
52007641 ACACGAAAAT
* * *
52007651 TTTTTGAAAACACGGAATTTTTTTGAAAACAAGGAAATTTTCGATACATGAGAATTTTTTGACAC
1 TTTTTGAAAACACGGAACTTTTTTGAAAACAAGAAAATTTTCGAAACATGAGAATTTTTTGACAC
*
52007716 GAAAAATTTTGAAAACACGAAAATTTCGAAAACAT-AATTTTTTTTAAAAACATGAATTTTTTTT
66 GAAAAATTTTGAAAACACGAAAATTTCGAAAACATGAA--TTTTTTAAAAACACGAA-TTTTTTT
52007780 AAAAAAACACGAG-AATTTTTTGAAAACACCAAAACATGAAA
128 --AAAAACACGAGAAATTTTTTGAAAACACCAAAACATGAAA
* *
52007821 TTTTTGAAAACACGGGAACTTTTTTGAAAACACGAAAATTTTTGAAACATGAGAATTTTTTGACA
1 TTTTTGAAAACAC-GGAACTTTTTTGAAAACAAGAAAATTTTCGAAACATGAGAATTTTTTGACA
* *
52007886 CTAAAAATTTTGAAAACACGAAAATTTCGAAAACATGAATTTTTTAAAAATACGAATTTTTTTAA
65 CGAAAAATTTTGAAAACACGAAAATTTCGAAAACATGAATTTTTTAAAAACACGAATTTTTTTAA
**
52007951 AAACACGAGAAATTTTTTGAAAACATGAAAACATGAAA
130 AAACACGAGAAATTTTTTGAAAACACCAAAACATGAAA
*
52007989 ATTTTGAAAACA
1 TTTTTGAAAACA
52008001 TGAAAATTTT
Statistics
Matches: 166, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
167 11 0.07
168 37 0.22
169 7 0.04
170 28 0.17
171 81 0.49
172 2 0.01
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (167 bp):
TTTTTGAAAACACGGAACTTTTTTGAAAACAAGAAAATTTTCGAAACATGAGAATTTTTTGACAC
GAAAAATTTTGAAAACACGAAAATTTCGAAAACATGAATTTTTTAAAAACACGAATTTTTTTAAA
AACACGAGAAATTTTTTGAAAACACCAAAACATGAAA
Found at i:52007869 original size:37 final size:36
Alignment explanation
Indices: 52007810--52008129 Score: 131
Period size: 36 Copynumber: 9.0 Consensus size: 36
52007800 TGAAAACACC
* *
52007810 AAAACATGAAATTTTTGAAAACACGGGAACTTTTTTG
1 AAAACACGAAATTTTTGAAAACACGAGAA-TTTTTTG
*
52007847 AAAACACGAAAATTTTTG-AAACATGAGAATTTTTTG
1 AAAACACG-AAATTTTTGAAAACACGAGAATTTTTTG
* * * *
52007883 ---ACACTAAAAATTTTGAAAACACGA-AA-ATTTCG
1 AAAACAC-GAAATTTTTGAAAACACGAGAATTTTTTG
* * * * * *
52007915 AAAACATGAATTTTTTAAAAATACGA-ATTTTTTTA
1 AAAACACGAAATTTTTGAAAACACGAGAATTTTTTG
* **
52007950 AAAACACGAGAAATTTTTTGAAAACATGAAAACATGAAAATTTTG
1 AAAACAC--GAAA-TTTTTGAAAACACG-----A-GAATTTTTTG
*
52007995 AAAACATGAAAATTTTTG-AAACACGAGAATTTTTTTTG
1 AAAACACG-AAATTTTTGAAAACACGAGAA--TTTTTTG
* *
52008033 AAAACAC---------GAAAACACGAAAATTTTTTT
1 AAAACACGAAATTTTTGAAAACACGAGAATTTTTTG
*
52008060 AAAACACGAGAATTTTTGAAAACACGA-AATTTTTTT
1 AAAACACGA-AATTTTTGAAAACACGAGAATTTTTTG
* ** *
52008096 TATTCACGAGAATTGTTG-AAACACG-GAATTTTTT
1 AAAACACGA-AATTTTTGAAAACACGAGAATTTTTT
52008130 TAAGAAGTAC
Statistics
Matches: 213, Mismatches: 38, Indels: 66
0.67 0.12 0.21
Matches are distributed among these distances:
27 13 0.06
28 1 0.00
29 10 0.05
32 4 0.02
33 14 0.07
34 22 0.10
35 27 0.13
36 33 0.15
37 30 0.14
38 31 0.15
42 6 0.03
43 8 0.04
44 3 0.01
45 11 0.05
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (36 bp):
AAAACACGAAATTTTTGAAAACACGAGAATTTTTTG
Found at i:52007981 original size:8 final size:8
Alignment explanation
Indices: 52007968--52008006 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
52007958 AGAAATTTTT
52007968 TGAAAACA
1 TGAAAACA
52007976 TGAAAACA
1 TGAAAACA
**
52007984 TGAAAATTT
1 TGAAAA-CA
52007993 TGAAAACA
1 TGAAAACA
52008001 TGAAAA
1 TGAAAA
52008007 TTTTTGAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 20 0.77
9 6 0.23
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.21
Consensus pattern (8 bp):
TGAAAACA
Found at i:52008011 original size:63 final size:63
Alignment explanation
Indices: 52007913--52008095 Score: 192
Period size: 63 Copynumber: 2.9 Consensus size: 63
52007903 ACGAAAATTT
* * * * ** *
52007913 CGAAAACATG-AATTTTTTAAAAATACGAATTTTTTTAAAAACACGAGAAATTTTTTGAAAACA
1 CGAAAACACGAAAATTTTTGAAAACACGAAAATTTTT-AAAACACGAGAATTTTTTTGAAAACA
* * * *
52007976 TGAAAACATGAAAA-TTTTGAAAACATGAAAATTTTTGAAACACGAGAATTTTTTTTGAAAACA
1 CGAAAACACGAAAATTTTTGAAAACACGAAAATTTTTAAAACACGAGAA-TTTTTTTGAAAACA
* *
52008039 CGAAAACACGAAAATTTTTTTAAAACACGAGAATTTTTGAAAACACGA-AATTTTTTT
1 CGAAAACACGAAAA-TTTTTGAAAACACGAAAATTTTT-AAAACACGAGAATTTTTTT
52008096 TATTCACGAG
Statistics
Matches: 100, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
62 11 0.11
63 51 0.51
64 9 0.09
65 21 0.21
66 8 0.08
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (63 bp):
CGAAAACACGAAAATTTTTGAAAACACGAAAATTTTTAAAACACGAGAATTTTTTTGAAAACA
Found at i:52008052 original size:46 final size:44
Alignment explanation
Indices: 52007994--52008088 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 44
52007984 TGAAAATTTT
* *
52007994 GAAAACATGAAAA-TTTTTGAAACACGAGAATTTTTTTTGAAAACAC
1 GAAAACACGAAAATTTTTTAAAACACGAGAA---TTTTTGAAAACAC
52008040 GAAAACACGAAAATTTTTTTAAAACACGAGAATTTTTGAAAACAC
1 GAAAACACGAAAA-TTTTTTAAAACACGAGAATTTTTGAAAACAC
52008085 GAAA
1 GAAA
52008089 TTTTTTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
45 17 0.38
46 12 0.27
48 16 0.36
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (44 bp):
GAAAACACGAAAATTTTTTAAAACACGAGAATTTTTGAAAACAC
Found at i:52008064 original size:27 final size:29
Alignment explanation
Indices: 52008013--52008068 Score: 89
Period size: 27 Copynumber: 2.0 Consensus size: 29
52008003 AAAATTTTTG
*
52008013 AAACACGAGAATTTTTTTTGAAAACACGA
1 AAACACGAGAAATTTTTTTGAAAACACGA
52008042 AAACACGA-AAATTTTTTT-AAAACACGA
1 AAACACGAGAAATTTTTTTGAAAACACGA
52008069 GAATTTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 9 0.35
28 9 0.35
29 8 0.31
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (29 bp):
AAACACGAGAAATTTTTTTGAAAACACGA
Found at i:52008081 original size:18 final size:18
Alignment explanation
Indices: 52008040--52008128 Score: 76
Period size: 18 Copynumber: 5.0 Consensus size: 18
52008030 TTGAAAACAC
*
52008040 GAAAACACGAAAATTTTTT
1 GAAAACACGAGAA-TTTTT
*
52008059 TAAAACACGAGAATTTTT
1 GAAAACACGAGAATTTTT
52008077 GAAAACACGA-AATTTTTT
1 GAAAACACGAGAA-TTTTT
** ** *
52008095 TTATTCACGAGAATTGTT
1 GAAAACACGAGAATTTTT
52008113 G-AAACACG-GAATTTTT
1 GAAAACACGAGAATTTTT
52008129 TTAAGAAGTA
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
16 7 0.12
17 7 0.12
18 29 0.52
19 13 0.23
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (18 bp):
GAAAACACGAGAATTTTT
Found at i:52008848 original size:18 final size:16
Alignment explanation
Indices: 52008827--52008864 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
52008817 TTTTGCTGTT
52008827 TGCTATTTTTTTAGGGGC
1 TGCTATTTTTTT--GGGC
52008845 TGCTATTTTTTTGGGC
1 TGCTATTTTTTTGGGC
52008861 TGCT
1 TGCT
52008865 GGGCTGCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
18 12 0.60
ACGTcount: A:0.08, C:0.13, G:0.26, T:0.53
Consensus pattern (16 bp):
TGCTATTTTTTTGGGC
Found at i:52008868 original size:24 final size:26
Alignment explanation
Indices: 52008841--52008897 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
52008831 ATTTTTTTAG
52008841 GGGCTGC-TATTTT-TTTGGGCTGCT
1 GGGCTGCGTATTTTATTTGGGCTGCT
*
52008865 GGGCTGCTGTTTTTTATTTGGGCTGCT
1 GGGCTGC-GTATTTTATTTGGGCTGCT
52008892 GGGCTG
1 GGGCTG
52008898 ATGCGGGTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 7 0.24
26 5 0.17
27 17 0.59
ACGTcount: A:0.04, C:0.16, G:0.37, T:0.44
Consensus pattern (26 bp):
GGGCTGCGTATTTTATTTGGGCTGCT
Found at i:52009005 original size:20 final size:19
Alignment explanation
Indices: 52008982--52009024 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
52008972 TTTTATTTCC
*
52008982 CTTTTTCCTTCTTTTTCTTT
1 CTTTTTCCTTCCTTTT-TTT
*
52009002 CTTTTTTCTTCCTTTTTTT
1 CTTTTTCCTTCCTTTTTTT
52009021 CTTT
1 CTTT
52009025 CTTCTTCGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (19 bp):
CTTTTTCCTTCCTTTTTTT
Found at i:52009029 original size:19 final size:20
Alignment explanation
Indices: 52008989--52009031 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
52008979 TCCCTTTTTC
* *
52008989 CTTCTTTTTCTTTCTTTTTT
1 CTTCCTTTTCTTTCTTTCTT
52009009 CTTCCTTTT-TTTCTTTCTT
1 CTTCCTTTTCTTTCTTTCTT
52009028 CTTC
1 CTTC
52009032 GGGTCACCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (20 bp):
CTTCCTTTTCTTTCTTTCTT
Found at i:52009142 original size:21 final size:21
Alignment explanation
Indices: 52009111--52009173 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 21
52009101 GCCTCCCTTC
52009111 TCTTCCTCTCTCTCTCTTTTTCTT
1 TCTT-CTCT-TCTCTC-TTTTCTT
*
52009135 TCTTCTCTTCTTTCTTTTCTT
1 TCTTCTCTTCTCTCTTTTCTT
52009156 TCTTCTCTTC-CTTCTTTT
1 TCTTCTCTTCTC-TCTTTT
52009174 TGGCCGCTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
21 23 0.64
22 5 0.14
23 4 0.11
24 4 0.11
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (21 bp):
TCTTCTCTTCTCTCTTTTCTT
Found at i:52009147 original size:12 final size:12
Alignment explanation
Indices: 52009130--52009171 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
52009120 CTCTCTCTTT
52009130 TTCTTTCTTCTC
1 TTCTTTCTTCTC
52009142 TTCTTTC-T-T-
1 TTCTTTCTTCTC
52009151 TTCTTTCTTCTC
1 TTCTTTCTTCTC
*
52009163 TTCCTTCTT
1 TTCTTTCTT
52009172 TTTGGCCGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 7 0.27
10 2 0.08
11 2 0.08
12 15 0.58
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (12 bp):
TTCTTTCTTCTC
Found at i:52009686 original size:30 final size:30
Alignment explanation
Indices: 52009650--52009737 Score: 90
Period size: 29 Copynumber: 2.9 Consensus size: 30
52009640 GTTAAAGGGC
*
52009650 AATTTTAAGAAAATTTAAGGGCCGAAATGT-
1 AATTTTAAGAAAATTT-AGGGCCAAAATGTG
* *
52009680 AATTTT-AGAAAATTTTGGGTCAAAATGTG
1 AATTTTAAGAAAATTTAGGGCCAAAATGTG
* * *
52009709 AATTTTAAAAAAAGTTTGGGGTCAAAATG
1 AATTTTAAGAAAA-TTTAGGGCCAAAATG
52009738 GAAATTTCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
28 10 0.20
29 15 0.30
30 11 0.22
31 14 0.28
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (30 bp):
AATTTTAAGAAAATTTAGGGCCAAAATGTG
Found at i:52009750 original size:30 final size:30
Alignment explanation
Indices: 52009674--52009760 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
52009664 TTAAGGGCCG
* * *
52009674 AAATGT-AATTTTAGAAAA-TTTTGGGTCA
1 AAATGTGAAATTTAAAAAAGTTTGGGGTCA
*
52009702 AAATGTGAATTTTAAAAAAAGTTTGGGGTCA
1 AAATGTGAAATTT-AAAAAAGTTTGGGGTCA
*
52009733 AAATG-GAAATTTCAAAAAGTATTGGGGT
1 AAATGTGAAATTTAAAAAAGT-TTGGGGT
52009761 TAAACTGTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
28 6 0.12
29 13 0.25
30 18 0.35
31 14 0.27
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.33
Consensus pattern (30 bp):
AAATGTGAAATTTAAAAAAGTTTGGGGTCA
Found at i:52010112 original size:23 final size:23
Alignment explanation
Indices: 52010086--52010135 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
52010076 CAAAATAGAA
*
52010086 AAAAACAATGGA-AAAGAAAAAAT
1 AAAAACAAAGGAGAAA-AAAAAAT
* *
52010109 AAAAATAAAGGAGTAAAAAAAAT
1 AAAAACAAAGGAGAAAAAAAAAT
52010132 AAAA
1 AAAA
52010136 TAAAAAACAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (23 bp):
AAAAACAAAGGAGAAAAAAAAAT
Found at i:52010260 original size:19 final size:19
Alignment explanation
Indices: 52010236--52010272 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
52010226 GCTGAGATTG
*
52010236 TAAAAAATAAAATAAAAAA
1 TAAAAAATAAAAGAAAAAA
52010255 TAAAAAATAAAAGAAAAA
1 TAAAAAATAAAAGAAAAA
52010273 GGTGCAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.14
Consensus pattern (19 bp):
TAAAAAATAAAAGAAAAAA
Found at i:52011352 original size:14 final size:14
Alignment explanation
Indices: 52011333--52011366 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
52011323 TTTTGGGCCT
52011333 GTTTTTGGGTTTGG
1 GTTTTTGGGTTTGG
52011347 GTTTTTGGGTTTGG
1 GTTTTTGGGTTTGG
52011361 GTTTTT
1 GTTTTT
52011367 TATTTCTTAT
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:0.00, C:0.00, G:0.38, T:0.62
Consensus pattern (14 bp):
GTTTTTGGGTTTGG
Found at i:52011559 original size:16 final size:18
Alignment explanation
Indices: 52011520--52011561 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
52011510 TTCCTAACGT
52011520 GAGTTGTTCTCAATATAA
1 GAGTTGTTCTCAATATAA
52011538 -AGGTTGTTC-CAA-ATAA
1 GA-GTTGTTCTCAATATAA
52011554 GAGTTGTT
1 GAGTTGTT
52011562 TTGTTGTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 10 0.45
17 5 0.23
18 7 0.32
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (18 bp):
GAGTTGTTCTCAATATAA
Found at i:52014669 original size:92 final size:88
Alignment explanation
Indices: 52014498--52014759 Score: 206
Period size: 92 Copynumber: 2.9 Consensus size: 88
52014488 GTCTTTAAAT
* * * * * ** *
52014498 TTTTTCAAAAAAGGTAATTAAGTTTATGTTTTTTTTTTCACTTAATTGGGTACTTGAATTTTCAA
1 TTTTTCAAAAAAAGCAATTAAGTTTATCTTTTTTTTTCCACTCAATTGGGTACTTGAAGCTGCAA
52014563 AATGCATAAAAAAGGACTTCAAA
66 AATGCATAAAAAAGGACTTCAAA
52014586 TTTTTCAAAAAAAGCAATTAAGCTTTTACTCTCTTTTTTTTCCCACTCAATTGGGTACTTG-AGC
1 TTTTTCAAAAAAAGCAATTAAG--TTTA-TCT-TTTTTTTT-CCACTCAATTGGGTACTTGAAGC
** * *
52014650 TGCAAAATGCATGCAAAAGGCCGTCAAA
61 TGCAAAATGCATAAAAAAGGACTTCAAA
*** * * ** * * *
52014678 CTTTAAAAAAAAAAAACCAATTACGCTCCAGC-TTTTATTCCCACTCAATTGGGTACTTGAA-CT
1 -TTT--TTCAAAAAAAGCAATTAAG-TTTATCTTTTTTTTTCCACTCAATTGGGTACTTGAAGCT
*
52014741 ATCAAAATGCATAAAAAAG
62 -GCAAAATGCATAAAAAAG
52014760 CCTCTCAAAC
Statistics
Matches: 138, Mismatches: 26, Indels: 17
0.76 0.14 0.09
Matches are distributed among these distances:
88 20 0.14
90 25 0.18
91 24 0.17
92 32 0.23
93 21 0.15
94 2 0.01
95 14 0.10
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (88 bp):
TTTTTCAAAAAAAGCAATTAAGTTTATCTTTTTTTTTCCACTCAATTGGGTACTTGAAGCTGCAA
AATGCATAAAAAAGGACTTCAAA
Found at i:52014735 original size:90 final size:91
Alignment explanation
Indices: 52014620--52014796 Score: 250
Period size: 91 Copynumber: 2.0 Consensus size: 91
52014610 TTTACTCTCT
* * * * * *
52014620 TTTTTTTCCCACTCAATTGGGTACTTGAGCT-GCAAAATGCATGCAAAAGGCC-GTCAAACTTTA
1 TTTTATTCCCACTCAATTGGGTACTTGAACTAGCAAAATGCAT-AAAAAAGCCTCTCAAACTTAA
* *
52014683 AAAAAAAAAAACCAATTACGCTCCAGC
65 AAAAAAAAAAAACAATTAAGCTCCAGC
*
52014710 TTTTATTCCCACTCAATTGGGTACTTGAACTATCAAAATGCATAAAAAAGCCTCTCAAACTTAAA
1 TTTTATTCCCACTCAATTGGGTACTTGAACTAGCAAAATGCATAAAAAAGCCTCTCAAACTTAAA
52014775 AAAAAAAAAAACAATTAAGCTC
66 AAAAAAAAAAACAATTAAGCTC
52014797 TTGTTCTTGT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
90 36 0.47
91 40 0.53
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.26
Consensus pattern (91 bp):
TTTTATTCCCACTCAATTGGGTACTTGAACTAGCAAAATGCATAAAAAAGCCTCTCAAACTTAAA
AAAAAAAAAAACAATTAAGCTCCAGC
Found at i:52014974 original size:9 final size:9
Alignment explanation
Indices: 52014962--52015078 Score: 67
Period size: 9 Copynumber: 12.4 Consensus size: 9
52014952 ACATGTGGTA
*
52014962 AAAAATGAT
1 AAAAATAAT
52014971 AAAAA-AAT
1 AAAAATAAT
52014979 AAAAATCAAT
1 AAAAAT-AAT
* *
52014989 AAAATTTAT
1 AAAAATAAT
52014998 AAAAATAATT
1 AAAAATAA-T
**
52015008 AAATTTTAAT
1 AAA-AATAAT
*
52015018 AAAAATATTT
1 AAAAATA-AT
* *
52015028 AAAATTGATT
1 AAAAAT-AAT
52015038 AAAAATAGAAT
1 AAAAAT--AAT
*
52015049 AAAACT-AT
1 AAAAATAAT
52015057 AAAAATAAT
1 AAAAATAAT
*
52015066 AAAAATTAT
1 AAAAATAAT
52015075 AAAA
1 AAAA
52015079 TATATAGAAC
Statistics
Matches: 84, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
8 14 0.17
9 29 0.35
10 29 0.35
11 12 0.14
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.29
Consensus pattern (9 bp):
AAAAATAAT
Found at i:52014999 original size:19 final size:18
Alignment explanation
Indices: 52014977--52015078 Score: 89
Period size: 19 Copynumber: 5.3 Consensus size: 18
52014967 TGATAAAAAA
52014977 ATAAAAATCAATAAAATTT
1 ATAAAAAT-AATAAAATTT
*
52014996 ATAAAAATAATTAAATTTT
1 ATAAAAATAA-TAAAATTT
* *
52015015 AATAAAAATATTTAAAATTG
1 -ATAAAAATA-ATAAAATTT
*
52015035 ATTAAAAATAGAATAAAA-CT
1 A-TAAAAAT--AATAAAATTT
*
52015055 ATAAAAATAATAAAAATT
1 ATAAAAATAATAAAATTT
52015073 ATAAAA
1 ATAAAA
52015079 TATATAGAAC
Statistics
Matches: 68, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
17 7 0.10
18 9 0.13
19 23 0.34
20 23 0.34
21 5 0.07
22 1 0.01
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (18 bp):
ATAAAAATAATAAAATTT
Found at i:52015019 original size:20 final size:20
Alignment explanation
Indices: 52014976--52015072 Score: 85
Period size: 20 Copynumber: 5.0 Consensus size: 20
52014966 ATGATAAAAA
52014976 AATAAAAATCAA-TAAAATTT
1 AATAAAAAT-AATTAAAATTT
*
52014996 -ATAAAAATAATTAAATTTT
1 AATAAAAATAATTAAAATTT
* *
52015015 AATAAAAATATTTAAAATTG
1 AATAAAAATAATTAAAATTT
* * *
52015035 ATTAAAAATAGAATAAAA-CT
1 AATAAAAATA-ATTAAAATTT
*
52015055 -ATAAAAATAATAAAAATT
1 AATAAAAATAATTAAAATT
52015073 ATAAAATATA
Statistics
Matches: 60, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
18 7 0.12
19 23 0.38
20 25 0.42
21 5 0.08
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
AATAAAAATAATTAAAATTT
Found at i:52015020 original size:39 final size:38
Alignment explanation
Indices: 52014976--52015078 Score: 102
Period size: 39 Copynumber: 2.7 Consensus size: 38
52014966 ATGATAAAAA
* **
52014976 AATAAAAATCAATAAAATTTATAAAAATA-ATTAAATTTT
1 AATAAAAAT-AATAAAATTTATAAAAATAGAATAAA-ACT
* *
52015015 AATAAAAATATTTAAAATTGATTAAAAATAGAATAAAACT
1 AATAAAAATA-ATAAAATTTA-TAAAAATAGAATAAAACT
*
52015055 -ATAAAAATAATAAAAATTATAAAA
1 AATAAAAATAATAAAATTTATAAAA
52015079 TATATAGAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
37 5 0.09
38 8 0.15
39 26 0.49
40 9 0.17
41 5 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (38 bp):
AATAAAAATAATAAAATTTATAAAAATAGAATAAAACT
Found at i:52015068 original size:17 final size:17
Alignment explanation
Indices: 52014962--52015126 Score: 84
Period size: 17 Copynumber: 9.0 Consensus size: 17
52014952 ACATGTGGTA
* **
52014962 AAAAATGATAAAAAAAT
1 AAAAATAATAAAATTAT
52014979 AAAAATCAATAAAATTTAT
1 AAAAAT-AATAAAA-TTAT
*
52014998 AAAAATAATTAAATTTTAAT
1 AAAAATAA-TAAA-ATT-AT
*
52015018 AAAAATATTTAAAATTGATT
1 AAAAATA-ATAAAATT-A-T
*
52015038 AAAAATAGAATAAAACTAT
1 AAAAAT--AATAAAATTAT
52015057 AAAAATAATAAAAATTAT
1 AAAAATAAT-AAAATTAT
* * *
52015075 -AAAATATATAGAACTGT
1 AAAAATA-ATAAAATTAT
52015092 -AAAATATATAAAAATGTA-
1 AAAAATA-AT-AAAAT-TAT
*
52015110 AAAAATTATAAAATTAT
1 AAAAATAATAAAATTAT
52015127 TCCCGCAAAA
Statistics
Matches: 116, Mismatches: 17, Indels: 30
0.71 0.10 0.18
Matches are distributed among these distances:
16 2 0.02
17 34 0.29
18 22 0.19
19 30 0.26
20 21 0.18
21 6 0.05
22 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (17 bp):
AAAAATAATAAAATTAT
Found at i:52015209 original size:19 final size:19
Alignment explanation
Indices: 52015163--52015214 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
52015153 AAGCAGTAAG
52015163 AAAATTATAAAAAATATAAA
1 AAAATTAT-AAAAATATAAA
* **
52015183 GAAA-TATAAATTTATAAA
1 AAAATTATAAAAATATAAA
52015201 AAAATTATAAAAAT
1 AAAATTATAAAAAT
52015215 TATCATACCA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
18 12 0.48
19 10 0.40
20 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATTATAAAAATATAAA
Found at i:52015214 original size:9 final size:9
Alignment explanation
Indices: 52015049--52015217 Score: 55
Period size: 9 Copynumber: 17.9 Consensus size: 9
52015039 AAAATAGAAT
*
52015049 AAAACTATA
1 AAAATTATA
*
52015058 AAAATAATA
1 AAAATTATA
52015067 AAAATTAT-
1 AAAATTATA
52015075 AAAA-TATA
1 AAAATTATA
* * *
52015083 TAGAACTGT-
1 -AAAATTATA
52015092 AAAATATATA
1 AAAAT-TATA
52015102 AAAATGTA-A
1 AAAAT-TATA
52015111 AAAATTAT-
1 AAAATTATA
52015119 AAAATTATTCCCGCA
1 AAAATTA-T-----A
52015134 AAAATTATA
1 AAAATTATA
*
52015143 AAATTTTATA
1 AAA-ATTATA
* *
52015153 AAGCAGTA-A
1 AA-AATTATA
52015162 GAAAATTATA
1 -AAAATTATA
*
52015172 AAAAATATA
1 AAAATTATA
*
52015181 AAGAAATAT-
1 AA-AATTATA
*
52015190 AAATTTATAAA
1 AAAATTAT--A
52015201 AAAATTATA
1 AAAATTATA
52015210 AAAATTAT
1 AAAATTAT
52015218 CATACCAAAA
Statistics
Matches: 120, Mismatches: 19, Indels: 42
0.66 0.10 0.23
Matches are distributed among these distances:
7 3 0.03
8 20 0.17
9 55 0.46
10 27 0.22
11 7 0.06
14 1 0.01
15 7 0.06
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:52015444 original size:21 final size:20
Alignment explanation
Indices: 52015418--52015460 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
52015408 TTTATAAAAG
52015418 TTTACAATCTTTATAAATTTT
1 TTTACAATCTTTAT-AATTTT
*
52015439 TTTACAATTTTTATAATTTT
1 TTTACAATCTTTATAATTTT
52015459 TT
1 TT
52015461 ACTAATAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTACAATCTTTATAATTTT
Found at i:52015460 original size:19 final size:19
Alignment explanation
Indices: 52015388--52015462 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
52015378 TTTTGGTACA
* **
52015388 TTTTATATTTTTTTATGAT
1 TTTTATAATTTTTTACAAT
***
52015407 TTTTATAAAAGTTTACAAT
1 TTTTATAATTTTTTACAAT
*
52015426 CTTTATAAATTTTTTTACAAT
1 TTTTAT-AA-TTTTTTACAAT
52015447 TTTTATAATTTTTTAC
1 TTTTATAATTTTTTAC
52015463 TAATAAGAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 26 0.60
20 4 0.09
21 13 0.30
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:52018201 original size:33 final size:33
Alignment explanation
Indices: 52018164--52018229 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
52018154 AGTAAGAAAA
52018164 ATCTCATCAAGTACCATTTACTTGTGGGCTCAT
1 ATCTCATCAAGTACCATTTACTTGTGGGCTCAT
52018197 ATCTCATCAAGTACCATTTACTTGTGGGCTCAT
1 ATCTCATCAAGTACCATTTACTTGTGGGCTCAT
52018230 CTTTTATGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (33 bp):
ATCTCATCAAGTACCATTTACTTGTGGGCTCAT
Found at i:52019437 original size:20 final size:21
Alignment explanation
Indices: 52019406--52019444 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
52019396 ACTTTCACAA
52019406 TGACTGTGGGTCAAGTTAATT
1 TGACTGTGGGTCAAGTTAATT
*
52019427 TGACT-TGGGTCAATTTAA
1 TGACTGTGGGTCAAGTTAA
52019445 AATTCAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (21 bp):
TGACTGTGGGTCAAGTTAATT
Found at i:52019759 original size:92 final size:96
Alignment explanation
Indices: 52019630--52019855 Score: 223
Period size: 96 Copynumber: 2.4 Consensus size: 96
52019620 TTTTTTTTTT
* * * * * * *
52019630 CACTCAATTGAG-GCTTGAGCT-GCAAAATGCATGAAAAAGGCTTTTAAACTT-A-AA-AAAAAA
1 CACTCAATTGAGTACTTGAACTACCAAAATGCATAAAAAAGACCTTCAAACTTAAGAAGAAAAAA
* * *
52019690 A-AA-ACCCAATTAAACTCCAGCTTTTATTCT
66 AGAAGAACCAATTAAACTCCAGATTTT-TTCG
* * *
52019720 CACTCAATTGGGTACTTGAACTACCAAAATACATAAAAAAGACCTTCAAATTTAAGAAGAAAAAA
1 CACTCAATTGAGTACTTGAACTACCAAAATGCATAAAAAAGACCTTCAAACTTAAGAAGAAAAAA
* * * *
52019785 AGAAGAAGCAATTAAGCTCTATATTTTTTCG
66 AGAAGAACCAATTAAACTCCAGATTTTTTCG
* *
52019816 CACTCAATTGAGTACTTGAACTGCTAAAATGCATAAAAAA
1 CACTCAATTGAGTACTTGAACTACCAAAATGCATAAAAAA
52019856 AGATCATTTG
Statistics
Matches: 108, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
90 11 0.10
91 7 0.06
92 23 0.21
93 1 0.01
94 2 0.02
95 7 0.06
96 41 0.38
97 16 0.15
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.26
Consensus pattern (96 bp):
CACTCAATTGAGTACTTGAACTACCAAAATGCATAAAAAAGACCTTCAAACTTAAGAAGAAAAAA
AGAAGAACCAATTAAACTCCAGATTTTTTCG
Found at i:52020021 original size:20 final size:20
Alignment explanation
Indices: 52019973--52020041 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
52019963 AAATGATAAA
*
52019973 AATAAAAATCAA-TAAAGTTT
1 AATAAAAAT-AATTAAAATTT
* *
52019993 -ATAAGAATAATTAAATTTT
1 AATAAAAATAATTAAAATTT
52020012 AATAAAAAT-ATTAAAAATTT
1 AATAAAAATAATT-AAAATTT
*
52020032 ATTAAAAATA
1 AATAAAAATA
52020042 GAATAAAACT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.05
19 17 0.43
20 21 0.52
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (20 bp):
AATAAAAATAATTAAAATTT
Found at i:52020108 original size:18 final size:18
Alignment explanation
Indices: 52020062--52020119 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
52020052 ATAAAAATCG
52020062 TAAAAAGTGT-AAAATATA
1 TAAAAA-TGTAAAAATATA
* *
52020080 T-AGACTGTAAAAATATA
1 TAAAAATGTAAAAATATA
52020097 TAAAAATGTAAAAGA-ATA
1 TAAAAATGTAAAA-ATATA
52020115 TAAAA
1 TAAAA
52020120 TTATTCCCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 3 0.09
17 11 0.33
18 18 0.55
19 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.26
Consensus pattern (18 bp):
TAAAAATGTAAAAATATA
Found at i:52020109 original size:17 final size:17
Alignment explanation
Indices: 52020062--52020119 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
52020052 ATAAAAATCG
52020062 TAAAAAGTGTAAAATATA
1 TAAAAA-TGTAAAATATA
* *
52020080 T-AGACTGTAAAAATATA
1 TAAAAATGT-AAAATATA
*
52020097 TAAAAATGTAAAAGAATA
1 TAAAAATGTAAAA-TATA
52020115 TAAAA
1 TAAAA
52020120 TTATTCCCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 3 0.09
17 15 0.47
18 14 0.44
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.26
Consensus pattern (17 bp):
TAAAAATGTAAAATATA
Found at i:52022788 original size:95 final size:95
Alignment explanation
Indices: 52022664--52022952 Score: 294
Period size: 95 Copynumber: 3.1 Consensus size: 95
52022654 TAAATAAGGG
* * * * * *
52022664 ATTAGAGTTTAGGGTTTCTTAATTAAATTAATTATAAATTTTT-CAAAATTAGATTAGGGTTTCG
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAG
* * * *
52022728 TGTTTATAGTATTTAAATAAAAATTAATTAA
66 TGTTTA-AGTTTTTAAAAAAAAATCAAATAA
* * * *
52022759 ATTAGGGTTTAGGGCTACTTGAGTAAATTAA-T-TAAATTTTTAAAAAAATCATATTAGGG-TAA
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTT-AAAAAATTAGATTAGGGTTTA
**
52022821 G-G-----GTTTTTAAGGAAAAATCAAATAA
65 GTGTTTAAGTTTTTAAAAAAAAATCAAATAA
*
52022846 ATTAGGG-TTAAGGTTACTTGAGTAAATTAATTATAAAATTTTTAAAAAATTAGATTAGGGTTTA
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT-AAATTTTTAAAAAATTAGATTAGGGTTTA
*
52022910 GTGTTTAAGGTTTTTAAAGAAAAAATCAAATAC
65 GTGTTTAA-GTTTTTAAA-AAAAAATCAAATAA
52022943 ATTAGGGTTT
1 ATTAGGGTTT
52022953 TGGATTTAGG
Statistics
Matches: 156, Mismatches: 23, Indels: 27
0.76 0.11 0.13
Matches are distributed among these distances:
86 21 0.13
87 26 0.17
88 16 0.10
89 11 0.07
90 1 0.01
93 10 0.06
94 3 0.02
95 39 0.25
96 8 0.05
97 19 0.12
98 2 0.01
ACGTcount: A:0.40, C:0.03, G:0.16, T:0.40
Consensus pattern (95 bp):
ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAG
TGTTTAAGTTTTTAAAAAAAAATCAAATAA
Found at i:52022940 original size:97 final size:96
Alignment explanation
Indices: 52022687--52022951 Score: 279
Period size: 87 Copynumber: 2.9 Consensus size: 96
52022677 GTTTCTTAAT
* * * *
52022687 TAAATTAATTATAAATTTTT-CAAAATTAGATTAGGGTTTCGTGTTTATA-GTATTTAAA-TAAA
1 TAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAGTGTTTA-AGGTTTTTAAAGAAAA
* * *
52022749 AATTAATTAAATTAGGGTTTAGGGCTACTTGAG
65 AATCAAATAAATTAGGG-TTAAGGCTACTTGAG
* * * *
52022782 TAAATTAA-T-TAAATTTTTAAAAAAATCATATTAGGG--TA------AGGGTTTTT-AAGGAAA
1 TAAATTAATTATAAATTTTT-AAAAAATTAGATTAGGGTTTAGTGTTTAAGGTTTTTAAAGAAAA
*
52022836 AATCAAATAAATTAGGGTTAAGGTTACTTGAG
65 AATCAAATAAATTAGGGTTAAGGCTACTTGAG
52022868 TAAATTAATTATAAAATTTTTAAAAAATTAGATTAGGGTTTAGTGTTTAAGGTTTTTAAAGAAAA
1 TAAATTAATTAT-AAATTTTTAAAAAATTAGATTAGGGTTTAGTGTTTAAGGTTTTTAAAGAAAA
*
52022933 AATCAAATACATTAGGGTT
65 AATCAAATAAATTAGGGTT
52022952 TTGGATTTAG
Statistics
Matches: 138, Mismatches: 16, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
86 23 0.17
87 25 0.18
88 16 0.12
89 8 0.06
90 2 0.01
93 10 0.07
94 1 0.01
95 21 0.15
96 8 0.06
97 24 0.17
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (96 bp):
TAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAGTGTTTAAGGTTTTTAAAGAAAAA
ATCAAATAAATTAGGGTTAAGGCTACTTGAG
Found at i:52023223 original size:125 final size:126
Alignment explanation
Indices: 52022999--52023410 Score: 675
Period size: 125 Copynumber: 3.3 Consensus size: 126
52022989 TTAAAAAAAT
* * * * *
52022999 TCCCACGTGGAAGCGCTTTTGCTACAGTAGCTACTAAAAAAATAGTTTCGAGAAGACGTTTCTGA
1 TCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTGA
* *
52023064 GCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAACAAAAGTACTGAAAGAAGC
66 GCAAATAGTGTCAAAAACGCTTTAAGCAGAATGCTTTGTCAGCAAAAGTACTGAAAGAAGC
52023125 TCCCACGTGGACGCGCTTTTGCTACAGTA-CTCCTGAAAAAATAATTTCGAGTAGACGTTTCTGA
1 TCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTGA
*
52023189 GCAAATAGCGTCAAAAACGCTTTAAGCAGAATGCTTTGTCAGCAAAAGTACTGAAAGAAGC
66 GCAAATAGTGTCAAAAACGCTTTAAGCAGAATGCTTTGTCAGCAAAAGTACTGAAAGAAGC
* * * *
52023250 TCCCACGTGGATGCGTTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGTAGACGTTTCTAA
1 TCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTGA
* * *
52023315 GCAAATAGTGTCAAAAACGCTTTAAACA-CATGCTTTGTCAGCAAAAGTACTGAAAGAAAC
66 GCAAATAGTGTCAAAAACGCTTTAAGCAGAATGCTTTGTCAGCAAAAGTACTGAAAGAAGC
52023375 TCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTG
1 TCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTG
52023411 TTTGGCCTAA
Statistics
Matches: 267, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
125 180 0.67
126 87 0.33
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (126 bp):
TCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTGA
GCAAATAGTGTCAAAAACGCTTTAAGCAGAATGCTTTGTCAGCAAAAGTACTGAAAGAAGC
Found at i:52023657 original size:15 final size:15
Alignment explanation
Indices: 52023637--52023670 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
52023627 GACAGAATTT
52023637 CGTAAAAGAATTAGG
1 CGTAAAAGAATTAGG
52023652 CGTAAAAGAATTAGG
1 CGTAAAAGAATTAGG
52023667 CGTA
1 CGTA
52023671 TCAGTTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (15 bp):
CGTAAAAGAATTAGG
Found at i:52027920 original size:116 final size:117
Alignment explanation
Indices: 52027711--52027920 Score: 300
Period size: 116 Copynumber: 1.8 Consensus size: 117
52027701 ACTTTTTATT
* *
52027711 ATTTATATTTTTTAAAATAAAATAATATAGAAATATTCAGAATATTGACTTATTTAAAAGAAAAT
1 ATTTATATTTTTTAAAATAAAATAATATAGAAATATTCAAAATATTGACTTACTTAAAAGAAAAT
**
52027776 CTACTTTATTAAAAATATTAAAGTAAATTACAATTACTTTATTCAAAACAAC
66 CTACTTTATTAAAAATAGAAAAGTAAATTACAATTACTTTATTCAAAACAAC
* * **
52027828 ATTT-TATTTTATT-AAATGAAATAATATAGAAATATTCAAAATATTGCCTTACTTAAAAGAATT
1 ATTTATATTTT-TTAAAATAAAATAATATAGAAATATTCAAAATATTGACTTACTTAAAAGAAAA
*
52027891 TCTA-TTATATTAAAAATGGAAAAGTAAATT
65 TCTACTT-TATTAAAAATAGAAAAGTAAATT
52027921 TCTATTTTAT
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
115 2 0.02
116 74 0.90
117 6 0.07
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.39
Consensus pattern (117 bp):
ATTTATATTTTTTAAAATAAAATAATATAGAAATATTCAAAATATTGACTTACTTAAAAGAAAAT
CTACTTTATTAAAAATAGAAAAGTAAATTACAATTACTTTATTCAAAACAAC
Found at i:52028545 original size:29 final size:30
Alignment explanation
Indices: 52028496--52028573 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
52028486 TCGATTGAAG
* * *
52028496 TGCTGGGCCGAGTGACTGTATCAGTGCTGT
1 TGCTGGGCCGAGTGATTGTATCAGCGATGT
* *
52028526 TGCTGGGCC-TGTGATTGTATGAGCGATGT
1 TGCTGGGCCGAGTGATTGTATCAGCGATGT
*
52028555 TGATGGGCCGAGTGATTGT
1 TGCTGGGCCGAGTGATTGT
52028574 GTGTGCACTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 23 0.57
30 17 0.43
ACGTcount: A:0.14, C:0.15, G:0.38, T:0.32
Consensus pattern (30 bp):
TGCTGGGCCGAGTGATTGTATCAGCGATGT
Found at i:52036638 original size:56 final size:56
Alignment explanation
Indices: 52036535--52036668 Score: 177
Period size: 56 Copynumber: 2.4 Consensus size: 56
52036525 ATATCAGGGG
* *
52036535 CTAACTTGGACTAAAAAAATTCATACCCCAATTTGTGAACAATTACCAATTTCAAGGA
1 CTAACTTGGAC-AAAAAAATTCA-ACCCCAATGTGTGAACAATTACCAAGTTCAAGGA
*
52036593 CTAACTTGGACAAAAAAATTCAACCCTAATGTG-GAAACAATTACCAAGTTCAAGGA
1 CTAACTTGGACAAAAAAATTCAACCCCAATGTGTG-AACAATTACCAAGTTCAAGGA
*
52036649 CTAA-TTTG--AAAAAAATTCAA
1 CTAACTTGGACAAAAAAATTCAA
52036669 ACTTTCATAT
Statistics
Matches: 71, Mismatches: 4, Indels: 7
0.87 0.05 0.09
Matches are distributed among these distances:
53 12 0.17
55 4 0.06
56 33 0.46
57 11 0.15
58 11 0.15
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.25
Consensus pattern (56 bp):
CTAACTTGGACAAAAAAATTCAACCCCAATGTGTGAACAATTACCAAGTTCAAGGA
Found at i:52037324 original size:16 final size:16
Alignment explanation
Indices: 52037305--52037340 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
52037295 TTTAAACATT
52037305 AAATAATTTCAACTCA
1 AAATAATTTCAACTCA
*
52037321 AAATAATTTGAACTCA
1 AAATAATTTCAACTCA
52037337 AAAT
1 AAAT
52037341 GCATAATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.31
Consensus pattern (16 bp):
AAATAATTTCAACTCA
Found at i:52038328 original size:20 final size:20
Alignment explanation
Indices: 52038303--52038342 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
52038293 TATTATTTCA
52038303 ATAAAATAT-TTAAATTATAT
1 ATAAAATATATT-AATTATAT
52038323 ATAAAATATATTAATTATAT
1 ATAAAATATATTAATTATAT
52038343 TTTATTAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAAAATATATTAATTATAT
Found at i:52038982 original size:18 final size:17
Alignment explanation
Indices: 52038957--52038990 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
52038947 AGATTTTTGA
52038957 TAATTTCACTATTTAAT
1 TAATTTCACTATTTAAT
*
52038974 TAATATTCACTTTTTAA
1 TAAT-TTCACTATTTAA
52038991 CATTTAAATA
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:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTTCACTATTTAAT
Found at i:52040237 original size:18 final size:18
Alignment explanation
Indices: 52040200--52040240 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
52040190 TAAAAATAAC
*
52040200 TTTTTAGTATTTTTCTAT
1 TTTTTAGTATTTTTCAAT
52040218 TTTTTA-TATTTTTCAAAT
1 TTTTTAGTATTTTTC-AAT
52040236 TTTTT
1 TTTTT
52040241 CCATGCCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTTAGTATTTTTCAAT
Found at i:52040238 original size:17 final size:18
Alignment explanation
Indices: 52040200--52040239 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
52040190 TAAAAATAAC
* *
52040200 TTTTTAGTATTTTTCTAT
1 TTTTTAGTATTTTTCAAA
52040218 TTTTTA-TATTTTTCAAA
1 TTTTTAGTATTTTTCAAA
52040235 TTTTT
1 TTTTT
52040240 TCCATGCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTTAGTATTTTTCAAA
Found at i:52043595 original size:18 final size:18
Alignment explanation
Indices: 52043552--52043595 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
52043542 TGCTCGGGGA
52043552 ATTTTTTATTTTTATTTT
1 ATTTTTTATTTTTATTTT
*
52043570 ATTATTTTA-TTTTGTTTT
1 ATT-TTTTATTTTTATTTT
52043588 ATCTTTTT
1 AT-TTTTT
52043596 GTGTGAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (18 bp):
ATTTTTTATTTTTATTTT
Found at i:52044191 original size:22 final size:23
Alignment explanation
Indices: 52044165--52044207 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
52044155 CCTGATCAAT
52044165 ATACGACACAT-AAGTGCCTGGA
1 ATACGACACATAAAGTGCCTGGA
52044187 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
52044208 ATCGGCAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGGA
Found at i:52044362 original size:18 final size:18
Alignment explanation
Indices: 52044327--52044382 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
52044317 TTTCATACTA
52044327 AATTTAATATCACTATTC
1 AATTTAATATCACTATTC
*
52044345 AATTTCAATTTCAC-ATTC
1 AATTT-AATATCACTATTC
* *
52044363 AA-TCAATAT-ACAATTC
1 AATTTAATATCACTATTC
52044379 AATT
1 AATT
52044383 ATACATACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 2 0.06
16 10 0.31
17 2 0.06
18 11 0.34
19 7 0.22
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTTAATATCACTATTC
Found at i:52044893 original size:3 final size:3
Alignment explanation
Indices: 52044880--52044951 Score: 51
Period size: 3 Copynumber: 24.3 Consensus size: 3
52044870 ATTTTATTTC
* * * *
52044880 ATA AT- ATA ATA ATA TTA ATA ATA ATA TTT A-A ATA GAAA ACT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A-TA ATA
* *
52044924 ATA ATA ATA ATA ATT ATA AAA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
52044952 ATTAATAACA
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
2 4 0.08
3 46 0.88
4 2 0.04
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:52048389 original size:33 final size:33
Alignment explanation
Indices: 52048325--52048389 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
52048315 TGTAAAAATG
*
52048325 TAGAAAATAAAAATGATTTTTCAGAAATAAAAA
1 TAGAAAATAAAAATGATTTTTCAAAAATAAAAA
*
52048358 TAGATAATGAAAAAT-ATTTTT-AAAAACTAAAA
1 TAGAAAAT-AAAAATGATTTTTCAAAAA-TAAAA
52048390 CGAGTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 4 0.14
33 18 0.64
34 6 0.21
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.29
Consensus pattern (33 bp):
TAGAAAATAAAAATGATTTTTCAAAAATAAAAA
Found at i:52048700 original size:21 final size:22
Alignment explanation
Indices: 52048674--52048719 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
52048664 TACTTACTTA
*
52048674 AAAAATACTATATTTTT-TTAC
1 AAAAATAATATATTTTTATTAC
*
52048695 AAAAATAATATGTTTTTATTAC
1 AAAAATAATATATTTTTATTAC
52048717 AAA
1 AAA
52048720 GGATAAACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAAATAATATATTTTTATTAC
Found at i:52049008 original size:11 final size:11
Alignment explanation
Indices: 52048974--52049008 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
52048964 ATGTAATTGA
*
52048974 TCTTTTTCTTT
1 TCTTTTTTTTT
52048985 TCTTTTTCTTTT
1 TCTTTTT-TTTT
52048997 TCTTTTTTTTT
1 TCTTTTTTTTT
52049008 T
1 T
52049009 TGTAGCTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:52049008 original size:17 final size:17
Alignment explanation
Indices: 52048974--52049007 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
52048964 ATGTAATTGA
52048974 TCTTTTTCTTTTCTTTT
1 TCTTTTTCTTTTCTTTT
52048991 TCTTTTTCTTTT-TTTT
1 TCTTTTTCTTTTCTTTT
52049007 T
1 T
52049008 TTGTAGCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TCTTTTTCTTTTCTTTT
Found at i:52049009 original size:6 final size:6
Alignment explanation
Indices: 52048974--52049008 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
52048964 ATGTAATTGA
52048974 TCTTTT TC-TTT TCTTTT TCTTTT TCTTTT T-TTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT T
52049009 TGTAGCTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TCTTTT
Found at i:52057229 original size:18 final size:18
Alignment explanation
Indices: 52057198--52057244 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
52057188 TTAAAAATAA
*
52057198 AAATAATTTTTAAATATTT-
1 AAAT-ATTTATAAAT-TTTC
52057217 AAATATTTATAAATTTTC
1 AAATATTTATAAATTTTC
52057235 AAAT-TTTATA
1 AAATATTTATA
52057245 CTTTTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 9 0.35
18 13 0.50
19 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATATTTATAAATTTTC
Found at i:52057244 original size:17 final size:17
Alignment explanation
Indices: 52057202--52057244 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
52057192 AAATAAAAAT
52057202 AATTTT-TAAATATTTA
1 AATTTTATAAATATTTA
52057218 AATATTTATAAAT-TTTCA
1 AAT-TTTATAAATATTT-A
52057236 AATTTTATA
1 AATTTTATA
52057245 CTTTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 3 0.12
17 12 0.50
18 9 0.38
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTTATAAATATTTA
Found at i:52058127 original size:21 final size:23
Alignment explanation
Indices: 52058102--52058148 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
52058092 CAATTGAAAA
52058102 TTAATTAA-AAAT-TAAATAA-AT
1 TTAATTAATAAATAT-AATAATAT
52058123 TTAATTAATAAATATAATAATAT
1 TTAATTAATAAATATAATAATAT
52058146 TTA
1 TTA
52058149 CTAACAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 8 0.35
22 9 0.39
23 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAATTAATAAATATAATAATAT
Found at i:52060482 original size:22 final size:23
Alignment explanation
Indices: 52060443--52060490 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
52060433 TACTTACTTA
* *
52060443 AAAAATACTATTTATTTT-TTTAC
1 AAAAATAATATGTATTTTATTT-C
52060466 AAAAATAATATGT-TTTTATTTC
1 AAAAATAATATGTATTTTATTTC
52060488 AAA
1 AAA
52060491 GGGTAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (23 bp):
AAAAATAATATGTATTTTATTTC
Found at i:52060867 original size:16 final size:17
Alignment explanation
Indices: 52060846--52060879 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
52060836 TATATCTTGA
*
52060846 ATTTTTGG-ATGTTTTC
1 ATTTTTGGTATATTTTC
52060862 ATTTTTGGTATATTTTC
1 ATTTTTGGTATATTTTC
52060879 A
1 A
52060880 ATCAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.62
Consensus pattern (17 bp):
ATTTTTGGTATATTTTC
Found at i:52061942 original size:3 final size:3
Alignment explanation
Indices: 52061936--52061987 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
52061926 TCCTCAAAAT
*
52061936 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
52061984 ATA A
1 ATA A
52061988 AATCTTTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:52062070 original size:20 final size:20
Alignment explanation
Indices: 52062025--52062073 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
52062015 ATACGTGATT
52062025 TTTTTTACTTTTTTTGAAAA
1 TTTTTTACTTTTTTTGAAAA
*
52062045 TGTTTTA-TTTTTTAT-AATAA
1 TTTTTTACTTTTTT-TGAA-AA
52062065 TTTTTTACT
1 TTTTTTACT
52062074 CATCATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 8 0.33
20 15 0.62
21 1 0.04
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTTTTACTTTTTTTGAAAA
Found at i:52066425 original size:105 final size:105
Alignment explanation
Indices: 52066290--52066518 Score: 316
Period size: 105 Copynumber: 2.2 Consensus size: 105
52066280 GCCATTAACT
52066290 AATGTATTATACGTGACAACATTAGGCTCAATGCCTTGCTTTATCATTGCGTCAACAATATCCT-
1 AATGTATTATACGTGACAACATTAGGCTCAATGCCTTGCTTTATCATTGCGTCAACAATAT-CTA
* * * *
52066354 CTGCTTCAGAGACCATACCTTCCTTGCAATGCGCATCAACC
65 CAGCTTCAGAAACCATACCTTCCTTGCAAAGAGCATCAACC
* * * * *
52066395 AATGTATTGTACGTGACAACATTAGGCTCAATGCCTTGCTTTCTCATTGTGTCAACGATCTCTAC
1 AATGTATTATACGTGACAACATTAGGCTCAATGCCTTGCTTTATCATTGCGTCAACAATATCTAC
* * * *
52066460 AGCTTTAGAAATCGTTCCTTCCTTGCAAAGAGCATCAACC
66 AGCTTCAGAAACCATACCTTCCTTGCAAAGAGCATCAACC
*
52066500 AATGTATTATACATGACAA
1 AATGTATTATACGTGACAA
52066519 TATCAAGTGA
Statistics
Matches: 108, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
104 2 0.02
105 106 0.98
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (105 bp):
AATGTATTATACGTGACAACATTAGGCTCAATGCCTTGCTTTATCATTGCGTCAACAATATCTAC
AGCTTCAGAAACCATACCTTCCTTGCAAAGAGCATCAACC
Found at i:52067634 original size:6 final size:6
Alignment explanation
Indices: 52067623--52067648 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
52067613 ATAAAATTTA
52067623 TTAAAT TTAAAT TTAAAT TTAAAT TT
1 TTAAAT TTAAAT TTAAAT TTAAAT TT
52067649 TTAGACTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:52068283 original size:18 final size:17
Alignment explanation
Indices: 52068215--52068399 Score: 144
Period size: 17 Copynumber: 10.6 Consensus size: 17
52068205 CGTGATCTGA
* **
52068215 TTGAAACATGAATTTTT
1 TTGAAACACGAAAATTT
* *
52068232 TTAAAACACGAGAA-TT
1 TTGAAACACGAAAATTT
* *
52068248 TTGAAGCACAAAAATTT
1 TTGAAACACGAAAATTT
52068265 TTGAAACACGAAAATTTT
1 TTGAAACACGAAAA-TTT
* *
52068283 TTAAAATAC-AGAAATTT
1 TTGAAACACGA-AAATTT
* *
52068300 GTGAAACACGAGAATTTT
1 TTGAAACACGA-AAATTT
*
52068318 TTGAAAACATGAAAA--T
1 TTG-AAACACGAAAATTT
52068334 TTGAAACACGAGAAATTTTT
1 TTGAAACACGA-AAA--TTT
*
52068354 TTGAAACACGAGAATTT
1 TTGAAACACGAAAATTT
*
52068371 TTGAAAACATGAAAATTT
1 TTG-AAACACGAAAATTT
52068389 TTGAAACACGA
1 TTGAAACACGA
52068400 TCCTTTTTTT
Statistics
Matches: 132, Mismatches: 25, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
15 7 0.05
16 19 0.14
17 46 0.35
18 39 0.30
19 9 0.07
20 12 0.09
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (17 bp):
TTGAAACACGAAAATTT
Found at i:52068298 original size:35 final size:35
Alignment explanation
Indices: 52068259--52068390 Score: 142
Period size: 35 Copynumber: 3.7 Consensus size: 35
52068249 TGAAGCACAA
52068259 AAATTTTTGAAACACGAAAATTTTTTAAAATACA-G
1 AAATTTTTGAAACACGAAAATTTTTTAAAA-ACACG
* * * *
52068294 AAATTTGTGAAACACGAGAATTTTTTGAAAACATG
1 AAATTTTTGAAACACGAAAATTTTTTAAAAACACG
* **
52068329 AAA-ATTTGAAACACGAGAAATTTTTTTGAAACACG
1 AAATTTTTGAAACACGA-AAATTTTTTAAAAACACG
*
52068364 AGAATTTTTGAAAACATGAAAATTTTT
1 A-AATTTTTG-AAACACGAAAATTTTT
52068391 GAAACACGAT
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
34 14 0.17
35 46 0.57
36 2 0.02
37 12 0.15
38 7 0.09
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.33
Consensus pattern (35 bp):
AAATTTTTGAAACACGAAAATTTTTTAAAAACACG
Found at i:52068391 original size:35 final size:35
Alignment explanation
Indices: 52068215--52068399 Score: 125
Period size: 35 Copynumber: 5.3 Consensus size: 35
52068205 CGTGATCTGA
* * * *
52068215 TTGAAACATGA-ATTTTTTTAAAACACGAGAA-TT
1 TTGAAACACGAGAATTTTTGAAAACACGAAAATTT
* * *
52068248 TTGAAGCACAAAAATTTTTG-AAACACGAAAATTTT
1 TTGAAACACGAGAATTTTTGAAAACACGAAAA-TTT
* * * *
52068283 TTAAAATAC-AGAAATTTGTG-AAACACGAGAATTTT
1 TTGAAACACGAG-AATTTTTGAAAACACGA-AAATTT
**
52068318 TTGAAA-AC-ATGAAAATTTG-AAACACGAGAAATTTTT
1 TTGAAACACGA-GAATTTTTGAAAACACGA-AAA--TTT
*
52068354 TTGAAACACGAGAATTTTTGAAAACATGAAAATTT
1 TTGAAACACGAGAATTTTTGAAAACACGAAAATTT
52068389 TTGAAACACGA
1 TTGAAACACGA
52068400 TCCTTTTTTT
Statistics
Matches: 121, Mismatches: 20, Indels: 20
0.75 0.12 0.12
Matches are distributed among these distances:
33 18 0.15
34 26 0.21
35 46 0.38
36 11 0.09
37 12 0.10
38 8 0.07
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (35 bp):
TTGAAACACGAGAATTTTTGAAAACACGAAAATTT
Found at i:52068703 original size:16 final size:15
Alignment explanation
Indices: 52068677--52068710 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
52068667 TTATTTATTG
52068677 AAATTAATTAAATTA
1 AAATTAATTAAATTA
52068692 AAATTGAATTAAATTA
1 AAATT-AATTAAATTA
52068708 AAA
1 AAA
52068711 ATATAAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
AAATTAATTAAATTA
Done.