Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 177 of 207
Found at i:54530014 original size:162 final size:165
Alignment explanation
Indices: 54529629--54530016 Score: 611
Period size: 165 Copynumber: 2.4 Consensus size: 165
54529619 GGTTTGTAGA
*
54529629 GAAAATTGAGAAGAAATACGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAATCCT
1 GAAAATTGAGAAGAAATAGGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAATCCT
* *
54529694 AATTGTGCTAGGAAATGGTTTATTAGTTGGACTTTGGGAAAAAAAATAAGGGTTGTTTGAAAACC
66 AATTGTGCTAGGAAACGGTTTATTAGTTGCACTTTGGGAAAAAAAATAAGGGTTGTTTGAAAACC
* *
54529759 AACCTTTTTTGGCCGAAATTAAGGAAAAATTAAAG
131 AACCTCTTTTGGCCGAAATCAAGGAAAAATTAAAG
*
54529794 GAAAATTGATAAGAAATAGGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAATCCT
1 GAAAATTGAGAAGAAATAGGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAATCCT
* * * * **
54529859 ATTTGTGCTAGGGAGCGGTTTATTAGTTGCACTTT-GG-AAAAAAATAAGGGTTGTTTGACAATT
66 AATTGTGCTAGGAAACGGTTTATTAGTTGCACTTTGGGAAAAAAAATAAGGGTTGTTTGAAAACC
* * *
54529922 AACC-CTTTTGGCCGGAATCAATGAAAAATTAAGG
131 AACCTCTTTTGGCCGAAATCAAGGAAAAATTAAAG
*
54529956 GAAAATTGAGAAGAAATAGGGAGAATGGGGGTTTCAGTTTGGGTTAGAATCAAATAGGAAA
1 GAAAATTGAGAAGAAATAGGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAA
54530017 CTTTAAGAGA
Statistics
Matches: 206, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
162 84 0.41
163 27 0.13
164 2 0.01
165 93 0.45
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.28
Consensus pattern (165 bp):
GAAAATTGAGAAGAAATAGGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAATCCT
AATTGTGCTAGGAAACGGTTTATTAGTTGCACTTTGGGAAAAAAAATAAGGGTTGTTTGAAAACC
AACCTCTTTTGGCCGAAATCAAGGAAAAATTAAAG
Found at i:54534942 original size:6 final size:6
Alignment explanation
Indices: 54534931--54534958 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
54534921 GAAGTTTGGG
54534931 TTCACT TTCACT TTCACT TTCACT TTCA
1 TTCACT TTCACT TTCACT TTCACT TTCA
54534959 ACTTGGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (6 bp):
TTCACT
Found at i:54538610 original size:19 final size:20
Alignment explanation
Indices: 54538568--54538610 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
54538558 TCATGCTTTC
*
54538568 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
54538588 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
54538606 TATTC
1 TATTC
54538611 TACAATCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:54538856 original size:45 final size:45
Alignment explanation
Indices: 54538783--54538886 Score: 154
Period size: 45 Copynumber: 2.3 Consensus size: 45
54538773 CAGTAATCAA
* * *
54538783 TAACGGTAGCAGTAACAATATTCAACACACAAAGTGTCAAATCGG
1 TAACAGTAACAGTAACAATATTCAACACACAAAGTGCCAAATCGG
* * *
54538828 TAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGG
1 TAACAGTAACAGTAACAATATTCAACACACAAAGTGCCAAATCGG
54538873 TAACAGTAACAGTA
1 TAACAGTAACAGTA
54538887 GTCGGCATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.19
Consensus pattern (45 bp):
TAACAGTAACAGTAACAATATTCAACACACAAAGTGCCAAATCGG
Found at i:54543233 original size:3 final size:3
Alignment explanation
Indices: 54543225--54543277 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
54543215 TTGCACCATG
54543225 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54543273 TAT TA
1 TAT TA
54543278 GTCATTCACC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:54555345 original size:27 final size:27
Alignment explanation
Indices: 54555306--54555417 Score: 161
Period size: 27 Copynumber: 4.1 Consensus size: 27
54555296 AGAGGTCGAT
* * * *
54555306 AAATGACCAAAATACCCCTACAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
*
54555333 AAATGATCGAAATACCCCCGTAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
54555360 AAATGATTGAAATACCCCCGTAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
54555387 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
54555414 AAAT
1 AAAT
54555418 AACTGTTATA
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGATCGAAATACCCCCATAGGGTA
Found at i:54555446 original size:54 final size:54
Alignment explanation
Indices: 54555327--54555431 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
54555317 ATACCCCTAC
* * *
54555327 AGGGTAAAATGATCGAAATACCCCCGTAGGGTAAAATGATTGAAATACCCCCGT
1 AGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATAACTGAAATACCCCCGT
**
54555381 AGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATAACTGTTATACCCC
1 AGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATAACTGAAATACCCC
54555432 TAGGAGATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (54 bp):
AGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATAACTGAAATACCCCCGT
Found at i:54558430 original size:26 final size:26
Alignment explanation
Indices: 54558390--54558448 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
54558380 AGCTTGACAG
*
54558390 AATCATTTTAGACCAATCTAGTCCTT
1 AATCATTTTACACCAATCTAGTCCTT
54558416 AATCATTTTACACCAATCTAGTCCTT
1 AATCATTTTACACCAATCTAGTCCTT
54558442 AATCATT
1 AATCATT
54558449 AACATGTCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (26 bp):
AATCATTTTACACCAATCTAGTCCTT
Found at i:54562058 original size:21 final size:20
Alignment explanation
Indices: 54562020--54562058 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54562010 AATCAGTTTC
*
54562020 CCGAAATCCCTTATTTTTTT
1 CCGAAATCCCTTAATTTTTT
*
54562040 CCGAAATCCCTTAAATTTT
1 CCGAAATCCCTTAATTTTT
54562059 CCCCGATCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.44
Consensus pattern (20 bp):
CCGAAATCCCTTAATTTTTT
Found at i:54562064 original size:21 final size:20
Alignment explanation
Indices: 54562019--54562064 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
54562009 AAATCAGTTT
* *
54562019 CCCGAAATCCCTTATTTTTT
1 CCCGAAATCCCTTAATTTTC
*
54562039 TCCGAAATCCCTTAAATTTTC
1 CCCGAAATCCCTT-AATTTTC
54562060 CCCGA
1 CCCGA
54562065 TCGTCTGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.24, C:0.33, G:0.07, T:0.37
Consensus pattern (20 bp):
CCCGAAATCCCTTAATTTTC
Found at i:54565924 original size:50 final size:50
Alignment explanation
Indices: 54565797--54566093 Score: 283
Period size: 50 Copynumber: 5.8 Consensus size: 50
54565787 GATAATAACA
* * *** * *
54565797 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGGTGTTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * **
54565846 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
54565896 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
54565946 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * *
54565996 TACCAACGCCATGTCCCAAACATGGTCTTACATGTGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC--GG
* * *
54566051 ATACCAATGCCATGTCCTAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
54566094 TTACCCAAAT
Statistics
Matches: 206, Mismatches: 34, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
48 1 0.00
49 37 0.18
50 127 0.62
53 2 0.01
55 2 0.01
56 37 0.18
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:54567243 original size:13 final size:13
Alignment explanation
Indices: 54567207--54567243 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
54567197 AATTAATACA
54567207 TTGTTATAATTATT
1 TTGTTATAA-TATT
54567221 TT-TTAT-ATATT
1 TTGTTATAATATT
54567232 TTGTTATAATAT
1 TTGTTATAATAT
54567244 ATGCGAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 6 0.29
12 5 0.24
13 8 0.38
14 2 0.10
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (13 bp):
TTGTTATAATATT
Found at i:54567585 original size:51 final size:50
Alignment explanation
Indices: 54567509--54567699 Score: 215
Period size: 51 Copynumber: 3.8 Consensus size: 50
54567499 TGTCTGCGAA
54567509 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGTAAATAAC-GGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGG-AAA-AACTGGT
* * ***
54567560 CACGTGTGTAGTACTAAGTGCAGGCTACTATGTGAATCGGAAGGCCTTGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGAAAAAC-TGGT
* * * * * *
54567611 CACGTGTGTAGTACTATGTGTAGGCTACTACGTG-AACCGAAAAGCTTGAT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGAAAAAC-TGGT
* *
54567661 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCG
54567700 AATGATAATA
Statistics
Matches: 120, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
49 1 0.01
50 45 0.38
51 74 0.62
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (50 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGAAAAACTGGT
Found at i:54570618 original size:25 final size:25
Alignment explanation
Indices: 54570590--54570698 Score: 119
Period size: 25 Copynumber: 4.4 Consensus size: 25
54570580 CACTTAACGA
*
54570590 GAAGCTCATGTGAGTTGTATAACAG
1 GAAGCTCATGTGAGCTGTATAACAG
* *
54570615 GAAGCTCATGTGAGCCGTATAACGG
1 GAAGCTCATGTGAGCTGTATAACAG
* *
54570640 GAAGCTCATGTGAGCTCTATAACGG
1 GAAGCTCATGTGAGCTGTATAACAG
* *** * *
54570665 GAAGCTTATCCAAGTTGTATAACAA
1 GAAGCTCATGTGAGCTGTATAACAG
54570690 GAAGCTCAT
1 GAAGCTCAT
54570699 AAGAGCCATA
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 70 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (25 bp):
GAAGCTCATGTGAGCTGTATAACAG
Found at i:54570685 original size:50 final size:50
Alignment explanation
Indices: 54570584--54570698 Score: 131
Period size: 50 Copynumber: 2.3 Consensus size: 50
54570574 TACGAGCACT
* * ***
54570584 TAACGAGAAGCTCATGTGAGTTGTATAACAGGAAGCTCATGTGAGCCGTA
1 TAACGAGAAGCTCATGTGAGCTCTATAACAGGAAGCTCATCCAAGCCGTA
* * * **
54570634 TAACGGGAAGCTCATGTGAGCTCTATAACGGGAAGCTTATCCAAGTTGTA
1 TAACGAGAAGCTCATGTGAGCTCTATAACAGGAAGCTCATCCAAGCCGTA
*
54570684 TAACAAGAAGCTCAT
1 TAACGAGAAGCTCAT
54570699 AAGAGCCATA
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (50 bp):
TAACGAGAAGCTCATGTGAGCTCTATAACAGGAAGCTCATCCAAGCCGTA
Found at i:54573082 original size:18 final size:18
Alignment explanation
Indices: 54573049--54573083 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54573039 GTGAGGAGAA
* *
54573049 TGCTGATACAGGTGGTGG
1 TGCTGATAAAGATGGTGG
54573067 TGCTGATAAAGATGGTG
1 TGCTGATAAAGATGGTG
54573084 ATGGAGATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.09, G:0.40, T:0.29
Consensus pattern (18 bp):
TGCTGATAAAGATGGTGG
Found at i:54576343 original size:8 final size:8
Alignment explanation
Indices: 54576332--54576356 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54576322 ATAAATATTT
54576332 ATTTTAAA
1 ATTTTAAA
54576340 ATTTTAAA
1 ATTTTAAA
54576348 ATTTTAAA
1 ATTTTAAA
54576356 A
1 A
54576357 AAAATTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTTAAA
Found at i:54588514 original size:24 final size:24
Alignment explanation
Indices: 54588482--54588532 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
54588472 ATTGTTTGGT
*
54588482 TTGATTTGGTTTAATTGAATTAAA
1 TTGAATTGGTTTAATTGAATTAAA
54588506 TTGAATTGGTTTAATTGAATTAAA
1 TTGAATTGGTTTAATTGAATTAAA
54588530 TTG
1 TTG
54588533 TACGAGGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (24 bp):
TTGAATTGGTTTAATTGAATTAAA
Found at i:54595725 original size:16 final size:16
Alignment explanation
Indices: 54595686--54595725 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
54595676 AGTTAATATG
54595686 GTTAAAAAAATAAAAT
1 GTTAAAAAAATAAAAT
* *
54595702 TTTAAAAAAATTAAAT
1 GTTAAAAAAATAAAAT
54595718 GTTGAAAA
1 GTT-AAAA
54595726 CTTTCATCGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (16 bp):
GTTAAAAAAATAAAAT
Found at i:54596062 original size:14 final size:13
Alignment explanation
Indices: 54596045--54596086 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
54596035 TAAAATCTTC
54596045 ATATTAAAATTAAA
1 ATATTAAAA-TAAA
54596059 ATATATAAAA-AAA
1 ATAT-TAAAATAAA
*
54596072 ACATTAAAATAAA
1 ATATTAAAATAAA
54596085 AT
1 AT
54596087 TTTGGTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 5 0.21
13 10 0.42
14 4 0.17
15 5 0.21
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
ATATTAAAATAAA
Found at i:54598757 original size:23 final size:22
Alignment explanation
Indices: 54598731--54598775 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
54598721 AAATTAAATC
54598731 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-AAATCATATCT
* *
54598754 TCTAAGATTGCATATCATATCT
1 TCTAAGATTACAAATCATATCT
54598776 AAGATTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATCT
Found at i:54598778 original size:19 final size:19
Alignment explanation
Indices: 54598754--54598790 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
54598744 AATCATATCT
54598754 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54598773 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
54598791 TGAAGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:54598798 original size:17 final size:19
Alignment explanation
Indices: 54598757--54598798 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
54598747 CATATCTTCT
*
54598757 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCG
54598776 AAGATTGCATATCAT-T-G
1 AAGATTGCATATCATATCG
54598793 AAGATT
1 AAGATT
54598799 ATGTTTCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 1 0.05
19 15 0.68
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (19 bp):
AAGATTGCATATCATATCG
Found at i:54602497 original size:19 final size:19
Alignment explanation
Indices: 54602461--54602499 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
54602451 TTCCGTCTCG
*
54602461 TTTTATTTTATAGCAAATT
1 TTTTATTTTATAGAAAATT
* *
54602480 TTTTATTTTTTTGAAAATT
1 TTTTATTTTATAGAAAATT
54602499 T
1 T
54602500 AACTAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTATTTTATAGAAAATT
Found at i:54602591 original size:22 final size:21
Alignment explanation
Indices: 54602566--54602613 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
54602556 TATATTTCTG
*
54602566 TTTAACAATTTTTTAAAAAAAT
1 TTTAA-AATTTTTTAAAAAAAA
**
54602588 TTTAAGGTTTTTTAAAAAAAA
1 TTTAAAATTTTTTAAAAAAAA
54602609 TTTAA
1 TTTAA
54602614 GAATGATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (21 bp):
TTTAAAATTTTTTAAAAAAAA
Found at i:54602600 original size:21 final size:21
Alignment explanation
Indices: 54602574--54602614 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
54602564 TGTTTAACAA
*
54602574 TTTTTTAAAAAAATTTTAAGG
1 TTTTTTAAAAAAAATTTAAGG
54602595 TTTTTTAAAAAAAATTTAAG
1 TTTTTTAAAAAAAATTTAAG
54602615 AATGATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (21 bp):
TTTTTTAAAAAAAATTTAAGG
Found at i:54612989 original size:51 final size:51
Alignment explanation
Indices: 54612893--54612989 Score: 122
Period size: 51 Copynumber: 1.9 Consensus size: 51
54612883 CAGTATATAA
* * **
54612893 CGTAAGACCATAGATGAAAGATGCTATATCAGCCTGATATGAGGTACGTAG
1 CGTAAGACCATAGATGAAAGATGCTATAGCAGCATGATACAAGGTACGTAG
* * * *
54612944 CGTAAGACCATGGATGAAAGATGTTATGGCAGCATGGTACAAGGTA
1 CGTAAGACCATAGATGAAAGATGCTATAGCAGCATGATACAAGGTA
54612990 AAAGGTATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 38 1.00
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (51 bp):
CGTAAGACCATAGATGAAAGATGCTATAGCAGCATGATACAAGGTACGTAG
Found at i:54613006 original size:58 final size:58
Alignment explanation
Indices: 54612941--54613090 Score: 192
Period size: 58 Copynumber: 2.6 Consensus size: 58
54612931 ATGAGGTACG
* *
54612941 TAGCGTAAGACCATGGATGAAAGATGTTATGGCAGCATGGTACAAGGTAAAAGGTATA
1 TAGCGTAAGACCATGGATGAAAGATGCTATGGCAGCACGGTACAAGGTAAAAGGTATA
* ** * *
54612999 TAGCGTAAGACCATGGAAGAAAGACACTATGGCGGCACGGTACAAGGTATAAGGTATA
1 TAGCGTAAGACCATGGATGAAAGATGCTATGGCAGCACGGTACAAGGTAAAAGGTATA
** ** *
54613057 CGGTATAAGACCATAGATGAAAGATGCTATGGCA
1 TAGCGTAAGACCATGGATGAAAGATGCTATGGCA
54613091 ACCAGGCATG
Statistics
Matches: 76, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
58 76 1.00
ACGTcount: A:0.38, C:0.13, G:0.29, T:0.20
Consensus pattern (58 bp):
TAGCGTAAGACCATGGATGAAAGATGCTATGGCAGCACGGTACAAGGTAAAAGGTATA
Found at i:54613179 original size:32 final size:32
Alignment explanation
Indices: 54613142--54613203 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
54613132 GCATCCACAG
54613142 AGATAAGCCTGCTGAGACAGTAAACACAGAAT
1 AGATAAGCCTGCTGAGACAGTAAACACAGAAT
* *
54613174 AGATAAGTCTGCTGGGACAGTAAACACAGA
1 AGATAAGCCTGCTGAGACAGTAAACACAGA
54613204 TGAATTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (32 bp):
AGATAAGCCTGCTGAGACAGTAAACACAGAAT
Found at i:54627302 original size:12 final size:11
Alignment explanation
Indices: 54627283--54627312 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
54627273 CTGTGTGTTC
54627283 TTTATTTTTAT
1 TTTATTTTTAT
54627294 TTCTATTTTTAT
1 TT-TATTTTTAT
54627306 TTTATTT
1 TTTATTT
54627313 GCGATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:54629229 original size:11 final size:10
Alignment explanation
Indices: 54629208--54629264 Score: 52
Period size: 9 Copynumber: 6.1 Consensus size: 10
54629198 AATAGAAGTT
54629208 TTTAAAATTA
1 TTTAAAATTA
54629218 TTTAACAATTA
1 TTTAA-AATTA
54629229 --TAAAATTA
1 TTTAAAATTA
*
54629237 -AT-AAATTA
1 TTTAAAATTA
*
54629245 TTAAAAATTA
1 TTTAAAATTA
54629255 -TTAAAATTA
1 TTTAAAATTA
54629264 T
1 T
54629265 ATTTATTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
8 11 0.28
9 12 0.31
10 11 0.28
11 5 0.13
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTAAAATTA
Found at i:54629234 original size:19 final size:17
Alignment explanation
Indices: 54629210--54629265 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 17
54629200 TAGAAGTTTT
54629210 TAAAATTATTTAACAATTA
1 TAAAATTA-TTAA-AATTA
*
54629229 TAAAATTAAT-AAATTA
1 TAAAATTATTAAAATTA
54629245 TTAAAAATTATTAAAATTA
1 -T-AAAATTATTAAAATTA
54629264 TA
1 TA
54629266 TTTATTTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 5 0.16
17 3 0.09
18 10 0.31
19 14 0.44
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATTATTAAAATTA
Found at i:54629245 original size:27 final size:27
Alignment explanation
Indices: 54629212--54629263 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
54629202 GAAGTTTTTA
*
54629212 AAATTATTTAACAATTA-TAAAATTAAT
1 AAATTA-TTAAAAATTATTAAAATTAAT
54629239 AAATTATTAAAAATTATTAAAATTA
1 AAATTATTAAAAATTATTAAAATTA
54629264 TATTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (27 bp):
AAATTATTAAAAATTATTAAAATTAAT
Found at i:54629260 original size:9 final size:9
Alignment explanation
Indices: 54629209--54629264 Score: 62
Period size: 8 Copynumber: 6.1 Consensus size: 9
54629199 ATAGAAGTTT
54629209 TTAAAATTA
1 TTAAAATTA
54629218 TTTAACAATTA
1 -TTAA-AATTA
54629229 -TAAAATTA
1 TTAAAATTA
*
54629237 AT-AAATTA
1 TTAAAATTA
54629245 TTAAAAATTA
1 TT-AAAATTA
54629255 TTAAAATTA
1 TTAAAATTA
54629264 T
1 T
54629265 ATTTATTTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
8 12 0.29
9 12 0.29
10 12 0.29
11 5 0.12
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (9 bp):
TTAAAATTA
Found at i:54645671 original size:14 final size:13
Alignment explanation
Indices: 54645644--54645683 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
54645634 CCCTCCTTTC
*
54645644 TTTCTTTCTTTTT
1 TTTCTTTGTTTTT
*
54645657 TTTTTTTGGTTTTT
1 TTTCTTT-GTTTTT
54645671 TTTCTTTGTTTTT
1 TTTCTTTGTTTTT
54645684 GTTGCAGCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (13 bp):
TTTCTTTGTTTTT
Found at i:54646667 original size:14 final size:15
Alignment explanation
Indices: 54646648--54646679 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
54646638 ATATTAAAAG
54646648 ATAATAATATT-ATT
1 ATAATAATATTAATT
54646662 ATAATAATATTAATT
1 ATAATAATATTAATT
54646677 ATA
1 ATA
54646680 TTTTAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAATAATATTAATT
Found at i:54650024 original size:91 final size:89
Alignment explanation
Indices: 54649853--54650025 Score: 213
Period size: 91 Copynumber: 1.9 Consensus size: 89
54649843 AAAAAAGAAG
* * * * * *
54649853 AAAAACAAAGTAATTAAGCTCCTCTTTTTTTTCACTCAATTGAGCACTTGAACTTTTAAAATGCA
1 AAAAAAAAAGCAATTAAACTCCTCTTTTTTTTCACTCAATTGAGCACTTAAACTTTCAAAATACA
* *
54649918 TCAAAAATGCTCTCAAACTTCTTC
66 CCAAAAATGCCCTCAAACTTCTTC
* * *
54649942 AAAAAAAAAGCAATTAAACTCCTGCTATTTTTTTCACTTAATTGGGTACTTAAACTTTCAAAATA
1 AAAAAAAAAGCAATTAAACTCCT-CT-TTTTTTTCACTCAATTGAGCACTTAAACTTTCAAAATA
54650007 CACCAAAAA-GACCCTCAAA
64 CACCAAAAATG-CCCTCAAA
54650026 ATTTTTAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
89 20 0.29
90 3 0.04
91 47 0.67
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.32
Consensus pattern (89 bp):
AAAAAAAAAGCAATTAAACTCCTCTTTTTTTTCACTCAATTGAGCACTTAAACTTTCAAAATACA
CCAAAAATGCCCTCAAACTTCTTC
Found at i:54650408 original size:19 final size:18
Alignment explanation
Indices: 54650386--54650495 Score: 62
Period size: 19 Copynumber: 5.8 Consensus size: 18
54650376 AAATTTGTAT
54650386 TTTTTTACATTTTGTATAA
1 TTTTTTACATTTT-TATAA
* *
54650405 TTTTCTTACGACTTTATAAAA
1 TTTT-TTAC-A-TTTTTATAA
* *
54650426 TTTTATA-ATTTTT-TTA
1 TTTTTTACATTTTTATAA
* *
54650442 TATTTCTATATATTTTATAA
1 T-TTTTTACAT-TTTTATAA
54650462 TTTTTTACGATTTTTATACA
1 TTTTTTAC-ATTTTTATA-A
* *
54650482 ATTTTTATATTTTT
1 TTTTTTACATTTTT
54650496 TACAAATTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
16 2 0.03
17 9 0.13
18 3 0.04
19 26 0.37
20 18 0.26
21 9 0.13
22 3 0.04
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTTTTACATTTTTATAA
Found at i:54650433 original size:29 final size:27
Alignment explanation
Indices: 54650400--54650498 Score: 85
Period size: 29 Copynumber: 3.5 Consensus size: 27
54650390 TTACATTTTG
54650400 TATAATTTTCTTACGACTTTATAAAATTT
1 TATAATTTT-TTACGA-TTTATAAAATTT
* * *
54650429 TATAATTTTTTTA-TATTTCTATATATTT
1 TATAA-TTTTTTACGATTTATA-AAATTT
*
54650457 TATAATTTTTTACGATTTTTATACAATTT
1 TATAATTTTTTACGA--TTTATAAAATTT
54650486 T-TATATTTTTTAC
1 TATA-ATTTTTTAC
54650499 AAATTTTATA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
27 12 0.21
28 14 0.25
29 22 0.39
30 9 0.16
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (27 bp):
TATAATTTTTTACGATTTATAAAATTT
Found at i:54650478 original size:57 final size:56
Alignment explanation
Indices: 54650400--54650523 Score: 144
Period size: 57 Copynumber: 2.2 Consensus size: 56
54650390 TTACATTTTG
* *
54650400 TATAATTTTCTTACGACTTTATAAAA-TTTTATAATTTTTT-TATATTTCTATATATTT
1 TATAATTTT-TTACGACTTTATAAAATTTTTAT-ATTTTTTACAAATTT-TATATATTT
* * *
54650457 TATAATTTTTTACGATTTTTATACAATTTTTATATTTTTTACAAATTTTATATTTTT
1 TATAATTTTTTACGA-CTTTATAAAATTTTTATATTTTTTACAAATTTTATATATTT
*
54650514 TCTAATTTTT
1 TATAATTTTT
54650524 AATAAATTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
56 6 0.10
57 41 0.71
58 11 0.19
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (56 bp):
TATAATTTTTTACGACTTTATAAAATTTTTATATTTTTTACAAATTTTATATATTT
Found at i:54650490 original size:47 final size:46
Alignment explanation
Indices: 54650436--54650541 Score: 117
Period size: 47 Copynumber: 2.2 Consensus size: 46
54650426 TTTTATAATT
* * *
54650436 TTTTTATATTTCTATATATTTTATAATTTTTTAC-GATTTTT-ATACAA
1 TTTTTATATTTCTACAAATTTTAT-ATTTTTT-CTAATTTTTAATA-AA
*
54650483 TTTTTATATTTTTTACAAATTTTATATTTTTTCTAATTTTTAATAAA
1 TTTTTATA-TTTCTACAAATTTTATATTTTTTCTAATTTTTAATAAA
54650530 TTTTTAATATTT
1 TTTTT-ATATTT
54650542 TATTTTTTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
46 1 0.02
47 31 0.61
48 19 0.37
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (46 bp):
TTTTTATATTTCTACAAATTTTATATTTTTTCTAATTTTTAATAAA
Found at i:54650512 original size:37 final size:38
Alignment explanation
Indices: 54650471--54650550 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 38
54650461 ATTTTTTACG
*
54650471 ATTTTTATAC-AATTTTT-AT-ATTTTTTACAAATTTTAT
1 ATTTTTAT-CTAATTTTTAATAAATTTTTA-AAATTTTAT
*
54650508 ATTTTT-TCTAATTTTTAATAAATTTTTAATATTTTAT
1 ATTTTTATCTAATTTTTAATAAATTTTTAAAATTTTAT
54650545 -TTTTTA
1 ATTTTTA
54650551 ATTAAAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
35 1 0.03
36 13 0.35
37 16 0.43
38 7 0.19
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (38 bp):
ATTTTTATCTAATTTTTAATAAATTTTTAAAATTTTAT
Found at i:54650513 original size:18 final size:18
Alignment explanation
Indices: 54650471--54650514 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
54650461 ATTTTTTACG
*
54650471 ATTTTTATACAATTTTTAT
1 ATTTTT-TACAAATTTTAT
54650490 ATTTTTTACAAATTTTAT
1 ATTTTTTACAAATTTTAT
54650508 ATTTTTT
1 ATTTTTT
54650515 CTAATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTTTACAAATTTTAT
Found at i:54650523 original size:18 final size:18
Alignment explanation
Indices: 54650426--54650524 Score: 69
Period size: 18 Copynumber: 5.3 Consensus size: 18
54650416 CTTTATAAAA
54650426 TTTTATAATTTTTT-TATAT
1 TTTTAT-ATTTTTTCTA-AT
* * *
54650445 TTCTATATATTTTATAATT
1 TTTTATATTTTTTCTAA-T
*
54650464 TTTTACGATTTTTATAC-AAT
1 TTTTA-TATTTTT-T-CTAAT
*
54650484 TTTTATATTTTTTAC-AAA
1 TTTTATATTTTTT-CTAAT
54650502 TTTTATATTTTTTCTAAT
1 TTTTATATTTTTTCTAAT
54650520 TTTTA
1 TTTTA
54650525 ATAAATTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
17 1 0.02
18 32 0.49
19 18 0.28
20 11 0.17
21 3 0.05
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (18 bp):
TTTTATATTTTTTCTAAT
Found at i:54650704 original size:88 final size:89
Alignment explanation
Indices: 54650612--54650792 Score: 222
Period size: 88 Copynumber: 2.0 Consensus size: 89
54650602 AATTTTTAAT
** * *
54650612 AAAAGCAGGGGTTTAATTGCTTTTTTTAAAAAAGTTTGAGGG-TCTTTTTGATGCATTTTGAAAG
1 AAAAGCAGGGAATTAATTGCTTTTTTTAAAAAAGTTTGAGGGCT-TTTTTGATACATTTTAAAAG
*
54650676 TTCAAGTACCCAATTGAGTAC-AAA
65 TTCAAGTACCCAAATGAGTACGAAA
* ** * * * *
54650700 AAAAGTAGGGAATTAATTTTTTTTTTTGAAAAGGTTTGAGGGCTTTTTTTATATATTTTAAAAGT
1 AAAAGCAGGGAATTAATTGCTTTTTTTAAAAAAGTTTGAGGGCTTTTTTGATACATTTTAAAAGT
*
54650765 TCAAGTACCCAAATGAGTGCGAAA
66 TCAAGTACCCAAATGAGTACGAAA
54650789 AAAA
1 AAAA
54650793 AGTAAAACTT
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
88 70 0.90
89 8 0.10
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.37
Consensus pattern (89 bp):
AAAAGCAGGGAATTAATTGCTTTTTTTAAAAAAGTTTGAGGGCTTTTTTGATACATTTTAAAAGT
TCAAGTACCCAAATGAGTACGAAA
Found at i:54650813 original size:88 final size:86
Alignment explanation
Indices: 54650624--54650820 Score: 209
Period size: 88 Copynumber: 2.2 Consensus size: 86
54650614 AAGCAGGGGT
* * *
54650624 TTAATTGCTTTTTTTAAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAA
1 TTAATTAC-TTTTTTAAAAAAGTTTGAGGGTCTTTTTGATACATTTTAAAAGTTCAAGTACCCAA
* *
54650689 TTGAGTACAAAAAAAGTAGGGAA
65 ATGAGTACAAAAAAAGTA-GAAA
** * * * *
54650712 TTAATTTTTTTTTTTGAAAAGGTTTGAGGG-CTTTTTTTATATATTTTAAAAGTTCAAGTACCCA
1 TTAA-TTACTTTTTTAAAAAAGTTTGAGGGTC-TTTTTGATACATTTTAAAAGTTCAAGTACCCA
*
54650776 AATGAGTGCGAAAAAAAAGTA-AAA
64 AATGAGTAC--AAAAAAAGTAGAAA
54650800 CTTAATTACTTTTTTAAAAAA
1 -TTAATTACTTTTTTAAAAAA
54650821 AAAATTGAGG
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
87 1 0.01
88 72 0.81
89 6 0.07
90 10 0.11
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (86 bp):
TTAATTACTTTTTTAAAAAAGTTTGAGGGTCTTTTTGATACATTTTAAAAGTTCAAGTACCCAAA
TGAGTACAAAAAAAGTAGAAA
Found at i:54654691 original size:41 final size:40
Alignment explanation
Indices: 54654639--54654718 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 40
54654629 CATTTTAACG
* *
54654639 CATATCGATGCCACTGTCCTAGACAAGGTCTTATACGAAT
1 CATATCGATGCCAATGTCCCAGACAAGGTCTTATACGAAT
*
54654679 CATATACGATGCCAATGTCCCAGACATGGTCTTATACGAA
1 CATAT-CGATGCCAATGTCCCAGACAAGGTCTTATACGAA
54654719 ATCACACCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 5 0.14
41 31 0.86
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (40 bp):
CATATCGATGCCAATGTCCCAGACAAGGTCTTATACGAAT
Found at i:54654908 original size:30 final size:30
Alignment explanation
Indices: 54654868--54655151 Score: 334
Period size: 30 Copynumber: 9.3 Consensus size: 30
54654858 ATATATGTAA
* *
54654868 ACATATACAAATCATTTCGGCAATATATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* *
54654898 ACATGTACAAATCAATTCGGCAATGTATCT
1 ACATATACAAATCAATTCGGCAATGTATAT
* *
54654928 CCATATAAAAATCAATTCGGCAATGTATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
**
54654958 ACATATACAAATCAATTCGATAATGTATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* *
54654988 CCATATACAAATCAATTCGGCTATGTATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* *
54655018 CCATATACAAATCAATTCGGCAATATATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* * *
54655048 ATCCATATACAAATCAATTCGACAATATATGTAA
1 A--CATATACAAATCAATTCGGCAATGTA--TAT
* * *
54655082 ACATATACAAATCATTTCGACAATGCATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* * *
54655112 ACATGTACAAATCATTTCGGCAATGTATAAA
1 ACATATACAAATCAATTCGGCAATGTAT-AT
54655143 ACATATACA
1 ACATATACA
54655152 TTTGAATTCA
Statistics
Matches: 219, Mismatches: 30, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
30 159 0.73
31 9 0.04
32 48 0.22
34 3 0.01
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (30 bp):
ACATATACAAATCAATTCGGCAATGTATAT
Found at i:54659941 original size:30 final size:30
Alignment explanation
Indices: 54659907--54659969 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
54659897 ACTTATTTTA
54659907 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
54659937 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
54659967 TTG
1 TTG
54659970 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:54666132 original size:38 final size:38
Alignment explanation
Indices: 54666081--54666158 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
54666071 ATGGGATTGA
54666081 TTTGAAAATTGGAGGTATCTTCATTTTTTCTCTTCTCT
1 TTTGAAAATTGGAGGTATCTTCATTTTTTCTCTTCTCT
54666119 TTTGAAAATTGGAGGTATCTTCATTTTTTCTCTTCTCT
1 TTTGAAAATTGGAGGTATCTTCATTTTTTCTCTTCTCT
54666157 TT
1 TT
54666159 CTCTTTCTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.18, C:0.15, G:0.13, T:0.54
Consensus pattern (38 bp):
TTTGAAAATTGGAGGTATCTTCATTTTTTCTCTTCTCT
Found at i:54669544 original size:12 final size:12
Alignment explanation
Indices: 54669524--54669553 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
54669514 AATATTGTTT
*
54669524 TAATGAATTTAA
1 TAATTAATTTAA
54669536 TAATTAATTTAA
1 TAATTAATTTAA
54669548 TAATTA
1 TAATTA
54669554 TCTAGATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (12 bp):
TAATTAATTTAA
Found at i:54669638 original size:31 final size:30
Alignment explanation
Indices: 54669538--54669639 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 30
54669528 GAATTTAATA
* *
54669538 ATTAATTTAATAATTATCTAGATAGT-TTTT
1 ATTAATTTAAT-ATTATATAGATAATATTTT
* * **
54669568 GATTAATTTAATATGA-ATACGA-GATATTAA
1 -ATTAATTTAATATTATATA-GATAATATTTT
54669598 ATTTAATTTAATATTTATATAGATAATATTTT
1 A-TTAATTTAATA-TTATATAGATAATATTTT
54669630 ATTAATTTAA
1 ATTAATTTAA
54669640 AATTGATGTG
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
29 4 0.07
30 18 0.33
31 24 0.44
32 9 0.16
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (30 bp):
ATTAATTTAATATTATATAGATAATATTTT
Found at i:54670210 original size:42 final size:42
Alignment explanation
Indices: 54670158--54670240 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
54670148 AAACAAAAGC
* * *
54670158 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACAAAT
1 GCCGCTAAAGAACATATTCTTTAGCGGCGCTTTTATACAAAT
* *
54670200 GCCGCTAAAGAACATATTTTTTAGTGGCGCTTTTATACAAA
1 GCCGCTAAAGAACATATTCTTTAGCGGCGCTTTTATACAAA
54670241 AATGCCACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (42 bp):
GCCGCTAAAGAACATATTCTTTAGCGGCGCTTTTATACAAAT
Found at i:54674411 original size:9 final size:9
Alignment explanation
Indices: 54674394--54674782 Score: 208
Period size: 9 Copynumber: 44.4 Consensus size: 9
54674384 TATGTATTAA
*
54674394 GTAAATTAT
1 GTAAGTTAT
54674403 GTAAGTTAT
1 GTAAGTTAT
*
54674412 GTACGTGTA-
1 GTAAGT-TAT
*
54674421 -TAAGTTAA
1 GTAAGTTAT
54674429 GTAAGTTAT
1 GTAAGTTAT
*
54674438 GT-A-TTAA
1 GTAAGTTAT
54674445 GTAAGTTAT
1 GTAAGTTAT
54674454 GTAAGTTAT
1 GTAAGTTAT
* *
54674463 GAAAGTAAT
1 GTAAGTTAT
* *
54674472 GTATGTAAT
1 GTAAGTTAT
54674481 GTAAG-T-T
1 GTAAGTTAT
54674488 GTAAGTTAT
1 GTAAGTTAT
*
54674497 -TATGTATTAT
1 GTAAG--TTAT
54674507 GTAAGTTAT
1 GTAAGTTAT
54674516 GTAAGTTAT
1 GTAAGTTAT
54674525 GTAAGTTAAAT
1 GTAAGTT--AT
54674536 GT-A-TTAT
1 GTAAGTTAT
54674543 GTAAG-T-T
1 GTAAGTTAT
54674550 GTAAGTTAAAT
1 GTAAGTT--AT
54674561 GT-A-TTAT
1 GTAAGTTAT
54674568 GTAAGTTAT
1 GTAAGTTAT
*
54674577 -TATGTATTAT
1 GTAAG--TTAT
54674587 GTAAG-T-T
1 GTAAGTTAT
54674594 GTAAGTTAAAT
1 GTAAGTT--AT
54674605 GT-A-TTAT
1 GTAAGTTAT
54674612 GTAAG-T-T
1 GTAAGTTAT
54674619 GTAAGTTAAGT
1 GTAAGTT-A-T
54674630 GT-A-TTAT
1 GTAAGTTAT
54674637 GTAAG-T-T
1 GTAAGTTAT
54674644 GTAAGTTAT
1 GTAAGTTAT
*
54674653 -TATGTATTAT
1 GTAAG--TTAT
54674663 GTAAG-T-T
1 GTAAGTTAT
54674670 GTAAGTTAT
1 GTAAGTTAT
*
54674679 -TATGTATTAT
1 GTAAG--TTAT
54674689 GTAAGTTAT
1 GTAAGTTAT
54674698 GTAAGTTAAAT
1 GTAAGTT--AT
54674709 GT-A-TTAT
1 GTAAGTTAT
*
54674716 GTAGGTTAT
1 GTAAGTTAT
*
54674725 GTAAGTTGT
1 GTAAGTTAT
**
54674734 GTAAGAGAT
1 GTAAGTTAT
*
54674743 TTAAGTTAT
1 GTAAGTTAT
*
54674752 GTAGGTTAT
1 GTAAGTTAT
* *
54674761 TTAGGTTAT
1 GTAAGTTAT
*
54674770 GTAAGTTTT
1 GTAAGTTAT
54674779 GTAA
1 GTAA
54674783 TGTGCAAGTG
Statistics
Matches: 296, Mismatches: 35, Indels: 98
0.69 0.08 0.23
Matches are distributed among these distances:
7 62 0.21
8 34 0.11
9 148 0.50
10 23 0.08
11 29 0.10
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:54674413 original size:25 final size:25
Alignment explanation
Indices: 54674383--54674736 Score: 168
Period size: 25 Copynumber: 14.3 Consensus size: 25
54674373 TGATATATAT
*
54674383 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
*
54674408 TTATGTACGTGT-A-TAAGTTAAGTAAG
1 TTATGTA--T-TAAGTAAGTTATGTAAG
54674434 TTATGTATTAAGTAAGTTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
54674459 TTATG-A--AAGTAA-TGTATGTAA-
1 TTATGTATTAAGTAAGT-TATGTAAG
* *
54674480 TGTAAGT-TGTAAGTTA-TTATGT-A-
1 T-TATGTAT-TAAGTAAGTTATGTAAG
*
54674503 TTATGTAAGTTATGTAAGTTATGTAAG
1 TTATGT-A-TTAAGTAAGTTATGTAAG
*
54674530 TTAAATGTATTATGTAAG-T-TGTAAG
1 TT--ATGTATTAAGTAAGTTATGTAAG
*
54674555 TTAAATGTATTATGTAAG---T-T-A-
1 TT--ATGTATTAAGTAAGTTATGTAAG
*
54674576 TTATGTATTATGTAAG-T-TGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
*
54674599 TTAAATGTATTATGTAAG-T-TGTAAG
1 TT--ATGTATTAAGTAAGTTATGTAAG
*
54674624 TTAAGTGTATTATGTAAG-T-TGTAAG
1 TT-A-TGTATTAAGTAAGTTATGTAAG
*
54674649 TTATTATGTATTATGTAAG-T-TGTAAG
1 ---TTATGTATTAAGTAAGTTATGTAAG
*
54674675 TTATTATGTATTATGTAAGTTATGTAAG
1 ---TTATGTATTAAGTAAGTTATGTAAG
* *
54674703 TTAAATGTATTATGTAGGTTATGTAAG
1 TT--ATGTATTAAGTAAGTTATGTAAG
*
54674730 TTGTGTA
1 TTATGTA
54674737 AGAGATTTAA
Statistics
Matches: 286, Mismatches: 10, Indels: 66
0.79 0.03 0.18
Matches are distributed among these distances:
19 14 0.05
20 1 0.00
21 5 0.02
22 22 0.08
23 6 0.02
24 16 0.06
25 110 0.38
26 59 0.21
27 39 0.14
28 10 0.03
29 4 0.01
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.45
Consensus pattern (25 bp):
TTATGTATTAAGTAAGTTATGTAAG
Found at i:54674542 original size:18 final size:18
Alignment explanation
Indices: 54674487--54674593 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
54674477 TAATGTAAGT
*
54674487 TGTAAGTTATTATGTATTA
1 TGTAAGTTA-AATGTATTA
54674506 TGTAAGTT--ATGTAAGTTA
1 TGTAAGTTAAATGT-A-TTA
54674524 TGTAAGTTAAATGTATTATGTAA
1 TGTAAGTTAAATG---TAT-T-A
54674547 GTTGTAAGTTAAATGTATTA
1 --TGTAAGTTAAATGTATTA
*
54674567 TGTAAGTTATTATGTATTA
1 TGTAAGTTA-AATGTATTA
54674586 TGTAAGTT
1 TGTAAGTT
54674594 GTAAGTTAAA
Statistics
Matches: 75, Mismatches: 1, Indels: 24
0.75 0.01 0.24
Matches are distributed among these distances:
16 4 0.05
17 1 0.01
18 20 0.27
19 24 0.32
20 4 0.05
21 2 0.03
22 5 0.07
23 2 0.03
25 13 0.17
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.48
Consensus pattern (18 bp):
TGTAAGTTAAATGTATTA
Found at i:54674603 original size:69 final size:69
Alignment explanation
Indices: 54674501--54674724 Score: 295
Period size: 76 Copynumber: 3.0 Consensus size: 69
54674491 AGTTATTATG
54674501 TATTATGTAAGTTATGTAAGTTATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTATT
1 TATTATGT-A-TTATGTAAG-T-TGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTATT
54674566 ATGTAAGT
62 ATGTAAGT
*
54674574 TATTATGTATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAGTGTATTATGT
1 TATTATGTATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATG---TAT-T
54674639 AAGTTGTAAGT
62 -A--TGTAAGT
*
54674650 TATTATGTATTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTATGTAAGTTAAATGTATTA
1 TATTATGTATTATGTAAGTTGTAAGTTA-AATGTATTATGTAAG-T-TGTAAGTTAAATGTATTA
*
54674715 TGTAGGT
63 TGTAAGT
54674722 TAT
1 TAT
54674725 GTAAGTTGTG
Statistics
Matches: 137, Mismatches: 4, Indels: 21
0.85 0.02 0.13
Matches are distributed among these distances:
69 37 0.27
70 1 0.01
71 9 0.07
72 13 0.09
73 9 0.07
74 2 0.01
75 1 0.01
76 38 0.28
77 14 0.10
78 1 0.01
79 12 0.09
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (69 bp):
TATTATGTATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTATTATGT
AAGT
Found at i:54674725 original size:69 final size:70
Alignment explanation
Indices: 54674398--54674727 Score: 256
Period size: 69 Copynumber: 4.6 Consensus size: 70
54674388 TATTAAGTAA
* * * *
54674398 ATTATGTAAGTTATGTACGTGTATAA-G--TTAAGTAAGTTATGTATTAAGTAAGTTATGTAAGT
1 ATTATGTAAGTTATGTAAGT-TA-AATGTATTATGTAGGTTATGTATTATGTAAGTTATGTAAGT
*
54674460 TATGAAAGT
64 TA--AATGT
* * *
54674469 A--ATGTATGTAATGTAAGTTGTAA-GTTATTATGTA--TTATGTAAGTTATGTAAGTTATGTAA
1 ATTATGTAAGTTATGTAAGTT-AAATG-TATTATGTAGGTTATGT-A-TTATGTAAGTTATGTAA
54674529 GTTAAATGT
62 GTTAAATGT
*
54674538 ATTATGTAAG-T-TGTAAGTTAAATGTATTATGTAAGTTATTATGTATTATGTAAG-T-TGTAAG
1 ATTATGTAAGTTATGTAAGTTAAATGTATTATGT-AG--GTTATGTATTATGTAAGTTATGTAAG
54674599 TTAAATGT
63 TTAAATGT
* * * *
54674607 ATTATGTAAG-T-TGTAAGTTAAGTGTATTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTT
1 ATTATGTAAGTTATGTAAGTTAAATGTATTATGT-AGGT-TATG-TATTATGTA--A-GTTA--T
*
54674670 GTAAGTTATTATGT
58 GTAAGTTA-AATGT
54674684 ATTATGTAAGTTATGTAAGTTAAATGTATTATGTAGGTTATGTA
1 ATTATGTAAGTTATGTAAGTTAAATGTATTATGTAGGTTATGTA
54674728 AGTTGTGTAA
Statistics
Matches: 215, Mismatches: 18, Indels: 47
0.77 0.06 0.17
Matches are distributed among these distances:
67 1 0.00
68 17 0.08
69 92 0.43
70 2 0.01
71 43 0.20
72 2 0.01
73 6 0.03
76 11 0.05
77 17 0.08
78 4 0.02
79 20 0.09
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.45
Consensus pattern (70 bp):
ATTATGTAAGTTATGTAAGTTAAATGTATTATGTAGGTTATGTATTATGTAAGTTATGTAAGTTA
AATGT
Found at i:54674731 original size:62 final size:61
Alignment explanation
Indices: 54674434--54674733 Score: 227
Period size: 62 Copynumber: 4.9 Consensus size: 61
54674424 GTTAAGTAAG
* * *
54674434 TTATGTATTAAGTAAGTTATGTAAGTTATGAAAGTA--ATGTATGTAATGTAAGTTGTAAGTTA
1 TTATGTATTATGTAAGTTATGTAAGTTA--AATGTATTATGTA-GTTATGTAAGTTGTAAGTTA
54674496 TTATGTATTATGTAAGTTATGTAAGTT--ATGTAAGTTAAATGTA-TTATGTAAGTTGTAAGTTA
1 TTATGTATTATGTAAGTTATGTAAGTTAAATGT-A-TT--ATGTAGTTATGTAAGTTGTAAGTTA
* * * * *
54674558 -AATGTATTATGTAAGTTAT-TATG-TATTATGTAAGT-TGTAAGTTAAATGT-ATTATGTAAGT
1 TTATGTATTATGTAAGTTATGTAAGTTA-AATGT-ATTATGT-AGTT--ATGTAAGT-TGTAAGT
54674618 T-
60 TA
* * * *
54674619 GTAAGT-TAAGTGT-A-TTATGTAAGTTGTAA-GTTATTATGTA-TTATGTAAGTTGTAAGTTA
1 TTATGTATTA-TGTAAGTTATGTAAGTT-AAATG-TATTATGTAGTTATGTAAGTTGTAAGTTA
54674678 TTATGTATTATGTAAGTTATGTAAGTTAAATGTATTATGTAGGTTATGTAAGTTGT
1 TTATGTATTATGTAAGTTATGTAAGTTAAATGTATTATGTA-GTTATGTAAGTTGT
54674734 GTAAGAGATT
Statistics
Matches: 190, Mismatches: 19, Indels: 58
0.71 0.07 0.22
Matches are distributed among these distances:
58 18 0.09
59 12 0.06
60 25 0.13
61 43 0.23
62 87 0.46
64 5 0.03
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (61 bp):
TTATGTATTATGTAAGTTATGTAAGTTAAATGTATTATGTAGTTATGTAAGTTGTAAGTTA
Found at i:54677336 original size:83 final size:83
Alignment explanation
Indices: 54677239--54677397 Score: 257
Period size: 83 Copynumber: 1.9 Consensus size: 83
54677229 CAAATTTTAA
* * * *
54677239 TTCATGAAATGGCTCCGTTTTATTCAATTTTCCAAATATTTTTTGCGGCGTTTTTGTA-AAAAAC
1 TTCACGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTATTTGCGGCGTTTGT-TACAAAAAC
54677303 GCCACTAAATTAATTTCAT
65 GCCACTAAATTAATTTCAT
*
54677322 TTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTGTTACAAAAACG
1 TTCACGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTATTTGCGGCGTTTGTTACAAAAACG
54677387 CCACTAAATTA
66 CCACTAAATTA
54677398 TTTATATTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
82 2 0.03
83 68 0.97
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.40
Consensus pattern (83 bp):
TTCACGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTATTTGCGGCGTTTGTTACAAAAACG
CCACTAAATTAATTTCAT
Found at i:54678171 original size:39 final size:40
Alignment explanation
Indices: 54678106--54678182 Score: 113
Period size: 39 Copynumber: 1.9 Consensus size: 40
54678096 ACCCATAACC
*
54678106 CCTAAATCCCCCTTAACCCTTAAAGCATAAA-CCCTAAACT
1 CCTAAATCCCCCTTAACCCCTAAAGCA-AAACCCCTAAACT
*
54678146 CCTAAATCTCCC-TAACCCCTAAAGCAAAACCCCTAAA
1 CCTAAATCCCCCTTAACCCCTAAAGCAAAACCCCTAAA
54678183 AAATTTATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 3 0.09
39 20 0.59
40 11 0.32
ACGTcount: A:0.39, C:0.39, G:0.03, T:0.19
Consensus pattern (40 bp):
CCTAAATCCCCCTTAACCCCTAAAGCAAAACCCCTAAACT
Found at i:54678358 original size:15 final size:16
Alignment explanation
Indices: 54678333--54678364 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
54678323 TTAAATAATA
54678333 TAAACTATATTAAATT
1 TAAACTATATTAAATT
54678349 TAAA-TATATTAAATT
1 TAAACTATATTAAATT
54678364 T
1 T
54678365 CTTATTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAACTATATTAAATT
Found at i:54678455 original size:7 final size:7
Alignment explanation
Indices: 54678445--54678507 Score: 54
Period size: 8 Copynumber: 8.4 Consensus size: 7
54678435 CTTTACCGTT
*
54678445 TAAACTC
1 TAAACCC
54678452 TAAACCC
1 TAAACCC
*
54678459 CAAATCCC
1 TAAA-CCC
54678467 TAAACTCC
1 TAAAC-CC
*
54678475 TAAACCA
1 TAAACCC
54678482 TAAACCCC
1 TAAA-CCC
54678490 TAAATCCC
1 TAAA-CCC
*
54678498 TAAATCC
1 TAAACCC
54678505 TAA
1 TAA
54678508 CTCTTAAATC
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
7 20 0.43
8 26 0.57
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:54678490 original size:23 final size:23
Alignment explanation
Indices: 54678445--54678501 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
54678435 CTTTACCGTT
* *
54678445 TAAACT-CTAAACCCCAAATCCC
1 TAAACTCCTAAACCACAAACCCC
*
54678467 TAAACTCCTAAACCATAAACCCC
1 TAAACTCCTAAACCACAAACCCC
54678490 TAAA-TCCCTAAA
1 TAAACT-CCTAAA
54678502 TCCTAACTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.23
23 23 0.77
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (23 bp):
TAAACTCCTAAACCACAAACCCC
Found at i:54678506 original size:15 final size:16
Alignment explanation
Indices: 54678451--54678507 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 16
54678441 CGTTTAAACT
*
54678451 CTAAAC-CCCAAATCC
1 CTAAACTCCTAAATCC
54678466 CTAAACTCCTAAA-CC
1 CTAAACTCCTAAATCC
* *
54678481 ATAAACCCCTAAATCC
1 CTAAACTCCTAAATCC
54678497 CTAAA-TCCTAA
1 CTAAACTCCTAA
54678508 CTCTTAAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 24 0.69
16 11 0.31
ACGTcount: A:0.42, C:0.39, G:0.00, T:0.19
Consensus pattern (16 bp):
CTAAACTCCTAAATCC
Found at i:54679090 original size:114 final size:111
Alignment explanation
Indices: 54678797--54679240 Score: 434
Period size: 114 Copynumber: 3.9 Consensus size: 111
54678787 TTTAAATCCC
* * * * *
54678797 TGAGCATTACCGGCGCTTTTTAAAAAACGCCGCTAAAACCCCTAAAGCTAAGAAAACGACGTCGT
1 TGAGCATTAGCGGCGCTTTAT-AAAAACGCCGCTAAATCCCCGAAAGCTCAG-AAACGACGTCGT
* * * * * *
54678862 TGGGCTTAGGTTTTTAGTGGCGCTTTTACAAAAAACGCCTCTAAAAACC
64 TGCGCTTAGGTTTTTAGCGGCGC-TTTCCCAAAAACGCCGCTAAAAACA
* * * * *
54678911 TGAGCATTAGCGGCGCTTTATATAAAGCGCCACTAAATCCCTGAAAGCTGGC-GAGACGACATCG
1 TGAGCATTAGCGGCGCTTTATA-AAAACGCCGCTAAATCCCCGAAAGCT--CAGAAACGACGTCG
* * *
54678975 TTGCGC-TAGATTTTTTTGCGGCGCTTTCCCAGAAACGCCGCTAAAAGACA
63 TTGCGCTTAG-GTTTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAAA-ACA
*
54679025 TGAGCATTAGCGGCGCTTTCATAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGT
1 TGAGCATTAGCGGCGCTTT-ATAAAAACGCCGCTAAATCCCCGAAAGCTCAG-AAACGACGTCGT
* * *
54679090 TG-GCCTTAGGTTTTTAGTGGCGC-TTCCTTAAAAACGCCGCTAAAAACT
64 TGCG-CTTAGGTTTTTAGCGGCGCTTTCC-CAAAAACGCCGCTAAAAACA
* * *
54679138 TGAGCATTAGCGGCGC-TTACTTAAAAACGCCGCTAAATCACC-AAATGCTCTTGAAACGGCGTC
1 TGAGCATTAGCGGCGCTTTA--TAAAAACGCCGCTAAATCCCCGAAA-GCTC-AGAAACGACGTC
* * *
54679201 GTTGCGC-TAGGTTTTTTGCGGCGCTTTTCCGAAAACGCCG
62 GTTGCGCTTAGGTTTTTAGCGGCGCTTTCCCAAAAACGCCG
54679241 GTAATGTTTA
Statistics
Matches: 275, Mismatches: 38, Indels: 36
0.79 0.11 0.10
Matches are distributed among these distances:
111 1 0.00
112 30 0.11
113 88 0.32
114 149 0.54
115 7 0.03
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (111 bp):
TGAGCATTAGCGGCGCTTTATAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAACGACGTCGTTG
CGCTTAGGTTTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAAAACA
Found at i:54681556 original size:26 final size:23
Alignment explanation
Indices: 54681525--54681577 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 23
54681515 ATAAAGTACA
54681525 AAATATTAAAA-TTATGAATAATAGTT
1 AAATA-TAAAATTTAT-AA-AAT-GTT
54681551 AAATATAAAATTTATAAAATGTT
1 AAATATAAAATTTATAAAATGTT
54681574 AAAT
1 AAAT
54681578 GTATTTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.27
24 3 0.12
25 7 0.27
26 9 0.35
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.38
Consensus pattern (23 bp):
AAATATAAAATTTATAAAATGTT
Found at i:54686056 original size:7 final size:7
Alignment explanation
Indices: 54686044--54686068 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54686034 ATTATTGTTC
54686044 AGTGCTA
1 AGTGCTA
54686051 AGTGCTA
1 AGTGCTA
54686058 AGTGCTA
1 AGTGCTA
54686065 AGTG
1 AGTG
54686069 GACTATTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.28
Consensus pattern (7 bp):
AGTGCTA
Found at i:54688637 original size:41 final size:41
Alignment explanation
Indices: 54688586--54688744 Score: 194
Period size: 41 Copynumber: 3.9 Consensus size: 41
54688576 TTTAAACAGA
* * * *
54688586 TTCACTGGCACTTCA-CCTGATAGGCTTATAGTTTAATTCAG
1 TTCACCGGCACTT-AGCCTGCTAGGCTTATAGTCTGATTCAG
* *
54688627 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGTCTGATTCAG
* * * *
54688668 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCCGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGTCTGATTCAG
* *
54688709 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGA
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGTCTGA
54688745 ATAATTTCAC
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
40 1 0.01
41 103 0.99
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAGTCTGATTCAG
Found at i:54688754 original size:41 final size:40
Alignment explanation
Indices: 54688627--54688759 Score: 167
Period size: 41 Copynumber: 3.2 Consensus size: 40
54688617 TTTAATTCAG
* * * * *
54688627 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGATT-AA
*
54688668 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCCGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGATT-AA
*
54688709 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGAATAA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGATTAA
*
54688749 TTTCACTGGCA
1 -TTCACCGGCA
54688760 ATAAATCCGA
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 2 0.02
41 80 0.98
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.29
Consensus pattern (40 bp):
TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGATTAA
Found at i:54702209 original size:9 final size:9
Alignment explanation
Indices: 54702197--54702255 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
54702187 AAATTTAAAA
54702197 AATATTTTT
1 AATATTTTT
54702206 AATATTTTT
1 AATATTTTT
* *
54702215 AACACTTTT
1 AATATTTTT
54702224 AA-ATTTTT
1 AATATTTTT
*
54702232 AAATAAATTTT
1 -AAT-ATTTTT
54702243 -ATATTTTT
1 AATATTTTT
54702251 -ATATT
1 AATATT
54702256 AAAAAATTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
8 15 0.36
9 22 0.52
11 5 0.12
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (9 bp):
AATATTTTT
Found at i:54704827 original size:12 final size:12
Alignment explanation
Indices: 54704810--54704835 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54704800 GGGTTCATTT
54704810 AACCAAAAAAGA
1 AACCAAAAAAGA
54704822 AACCAAAAAAGA
1 AACCAAAAAAGA
54704834 AA
1 AA
54704836 TTGTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.15, G:0.08, T:0.00
Consensus pattern (12 bp):
AACCAAAAAAGA
Found at i:54709307 original size:17 final size:16
Alignment explanation
Indices: 54709282--54709332 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
54709272 ACATATTGCA
54709282 AAAATTTATAAAAAAAT
1 AAAA-TTATAAAAAAAT
*
54709299 AAAAGTTATAAAAATTAT
1 AAAA-TTATAAAAA-AAT
*
54709317 TAAATTATAAAAAAAT
1 AAAATTATAAAAAAAT
54709333 TATAAAAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 2 0.07
17 22 0.76
18 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
AAAATTATAAAAAAAT
Found at i:54709330 original size:19 final size:20
Alignment explanation
Indices: 54709308--54709390 Score: 62
Period size: 20 Copynumber: 4.2 Consensus size: 20
54709298 TAAAAGTTAT
* *
54709308 AAAAATTAT-TAAATTATAA
1 AAAAATTATAAAAATCATAA
54709327 AAAAATTATAAAAATCATAA
1 AAAAATTATAAAAATCATAA
* * * *
54709347 AAATATAAAAAAAAAT-TTATA
1 AAAAAT-TATAAAAATCATA-A
**
54709368 AAATTTTATAAAAATCATAA
1 AAAAATTATAAAAATCATAA
54709388 AAA
1 AAA
54709391 TAGATATAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
19 9 0.18
20 26 0.52
21 15 0.30
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAATTATAAAAATCATAA
Found at i:54709335 original size:28 final size:28
Alignment explanation
Indices: 54709299--54709359 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
54709289 ATAAAAAAAT
* * * *
54709299 AAAAGTTATAAAAATTATTAAATTATAA
1 AAAAATTATAAAAATCATAAAAATATAA
54709327 AAAAATTATAAAAATCATAAAAATATAA
1 AAAAATTATAAAAATCATAAAAATATAA
54709355 AAAAA
1 AAAAA
54709360 AATTTATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (28 bp):
AAAAATTATAAAAATCATAAAAATATAA
Found at i:54709361 original size:30 final size:31
Alignment explanation
Indices: 54709293--54709390 Score: 103
Period size: 30 Copynumber: 3.2 Consensus size: 31
54709283 AAATTTATAA
*
54709293 AAAAATAAAAGTTATAAAAATTAT-TAAAT-T
1 AAAAA-AAAAGTTATAAAAATTATAAAAATAT
* *
54709323 ATAAAAAAA-TTATAAAAATCATAAAAATAT
1 AAAAAAAAAGTTATAAAAATTATAAAAATAT
* *
54709353 AAAAAAAAATTTATAAAATTTTATAAAAATCAT
1 AAAAAAAAAGTTATAAAA-ATTATAAAAAT-AT
54709386 AAAAA
1 AAAAA
54709391 TAGATATAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
28 12 0.21
29 8 0.14
30 13 0.23
31 8 0.14
32 9 0.16
33 7 0.12
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (31 bp):
AAAAAAAAAGTTATAAAAATTATAAAAATAT
Found at i:54709647 original size:27 final size:29
Alignment explanation
Indices: 54709614--54709679 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
54709604 TTTACATTTT
54709614 TTTATAATTTTCT-TATGATTT-TATAAAA
1 TTTATAATTTTCTCTAT-ATTTATATAAAA
*
54709642 -TTATAATTTTTTTCTATATTTATATAAAA
1 TTTATAA-TTTTCTCTATATTTATATAAAA
54709671 TTTATAATT
1 TTTATAATT
54709680 ACAAATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
27 6 0.18
28 9 0.27
29 12 0.36
30 6 0.18
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTATAATTTTCTCTATATTTATATAAAA
Found at i:54709668 original size:29 final size:31
Alignment explanation
Indices: 54709621--54709679 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
54709611 TTTTTTATAA
54709621 TTTTCTTATGATTTTATAAAA-TTATAATTT
1 TTTTCTTATGATTTTATAAAATTTATAATTT
54709651 TTTTC-TAT-ATTTATATAAAATTTATAATT
1 TTTTCTTATGATTT-TATAAAATTTATAATT
54709680 ACAAATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 4 0.15
29 10 0.37
30 13 0.48
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (31 bp):
TTTTCTTATGATTTTATAAAATTTATAATTT
Found at i:54709702 original size:19 final size:18
Alignment explanation
Indices: 54709678--54709716 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
54709668 AAATTTATAA
54709678 TTACAAATTTTATAA-AATT
1 TTAC-AATTTT-TAATAATT
54709697 TTACAATTTTTAATAATT
1 TTACAATTTTTAATAATT
54709715 TT
1 TT
54709717 TAATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 12 0.63
19 4 0.21
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (18 bp):
TTACAATTTTTAATAATT
Found at i:54709714 original size:10 final size:10
Alignment explanation
Indices: 54709701--54709766 Score: 57
Period size: 10 Copynumber: 6.8 Consensus size: 10
54709691 AAAATTTTAC
54709701 AATTTTTAAT
1 AATTTTTAAT
54709711 AATTTTTAAT
1 AATTTTTAAT
54709721 -ATTTTT-AT
1 AATTTTTAAT
* *
54709729 ATTCTTTTATT
1 AAT-TTTTAAT
**
54709740 AAAATTTAAT
1 AATTTTTAAT
54709750 AATTTTT-AT
1 AATTTTTAAT
*
54709759 AACTTTTA
1 AATTTTTA
54709767 TTGATTTTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
8 2 0.05
9 15 0.35
10 24 0.56
11 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:54714220 original size:9 final size:9
Alignment explanation
Indices: 54714203--54714239 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
54714193 TGAGTTTTCA
54714203 AATTCGAAT
1 AATTCGAAT
*
54714212 AACTCGAAT
1 AATTCGAAT
*
54714221 AATTCAAAT
1 AATTCGAAT
54714230 AATTCGAAT
1 AATTCGAAT
54714239 A
1 A
54714240 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:54714486 original size:30 final size:31
Alignment explanation
Indices: 54714452--54714511 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
54714442 AAACCTTTTA
*
54714452 TTTTCTCCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAACTTTTACTCCCTTCCCAC
*
54714482 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
54714512 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:54715176 original size:5 final size:5
Alignment explanation
Indices: 54715166--54715191 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
54715156 GAACAAATAT
54715166 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
54715192 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:54718321 original size:41 final size:41
Alignment explanation
Indices: 54718272--54718410 Score: 208
Period size: 41 Copynumber: 3.4 Consensus size: 41
54718262 ATATGATTGA
* *
54718272 CACTAAGTGTGCGAAATTAAATAATGATGTTGAATAACGAG
1 CACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGAG
*
54718313 CACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACAAG
1 CACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGAG
* * *
54718354 CACTAAGTGTGCGAAACCAAGTAATTATGTT-AATAACGGG
1 CACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGAG
*
54718394 CACTAAGTGTGCAAAAC
1 CACTAAGTGTGCGAAAC
54718411 GGAGATCAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 23 0.26
41 67 0.74
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (41 bp):
CACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGAG
Found at i:54722421 original size:264 final size:265
Alignment explanation
Indices: 54721940--54722448 Score: 885
Period size: 264 Copynumber: 1.9 Consensus size: 265
54721930 TTCTCCCACT
*
54721940 CAATATTTTAAAAAAAAAATATGCAAGGTTTTTTATCCTAGATTTCAAGAATGATGATACAACAG
1 CAATATTTT-AAAAAAAAATATGCAAGGTTTTTTATCCTAAATTTCAAGAATGATGATACAACAG
* * * *
54722005 TCCTAGTGGCATTCTTACCTAATTTACATGTCATGCTTTCAGTATATGCATGACATGTTATGAAA
65 TCCTAGTAGCATTCTTACCTAATCTACATGACATGCTTTCAGTATATGCATGACATGCTATGAAA
54722070 ATTTTATAATATTCACATTCATTCAGAAGAAGAATCAATCAACCATAAAAACAAACAATTTTGAT
130 ATTTTATAATATTCACATTCATTCAGAAGAAGAATCAATCAACCATAAAAACAAACAATTTTGAT
*
54722135 TCTCCACAATTTTTCGTTTAAGGGAAAAACCAAAGAAGTGAATGTGAACATTTCAGGGACCTTCT
195 TCTCCACAATTTTTCGTTTAAGGAAAAAACCAAAGAAGTGAATGTGAACATTTCAGGGACCTTCT
54722200 CTTACA
260 CTTACA
*
54722206 CAATATTTT-AAAAAAAATATGCAAGGTTTTTTATCCTAAATTTCAAGAATGATGATACAATAGT
1 CAATATTTTAAAAAAAAATATGCAAGGTTTTTTATCCTAAATTTCAAGAATGATGATACAACAGT
* * *
54722270 CCTAGTAGCATTCTTACCTAATCTATATGACATGCTTTCAGTATATGCATGACATGCTATGATAG
66 CCTAGTAGCATTCTTACCTAATCTACATGACATGCTTTCAGTATATGCATGACATGCTATGAAAA
* *
54722335 TTTTATAATATTCACATTCATTTAGAAGAAGAATCAATCAACCATAAAAACTAACAATTTTGATT
131 TTTTATAATATTCACATTCATTCAGAAGAAGAATCAATCAACCATAAAAACAAACAATTTTGATT
*
54722400 CTCCACAATTTTTCGTTTAAGGAAAAAACCGAAGAAGTGAATGTGAACA
196 CTCCACAATTTTTCGTTTAAGGAAAAAACCAAAGAAGTGAATGTGAACA
54722449 GTGCACCAGG
Statistics
Matches: 230, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
264 221 0.96
266 9 0.04
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (265 bp):
CAATATTTTAAAAAAAAATATGCAAGGTTTTTTATCCTAAATTTCAAGAATGATGATACAACAGT
CCTAGTAGCATTCTTACCTAATCTACATGACATGCTTTCAGTATATGCATGACATGCTATGAAAA
TTTTATAATATTCACATTCATTCAGAAGAAGAATCAATCAACCATAAAAACAAACAATTTTGATT
CTCCACAATTTTTCGTTTAAGGAAAAAACCAAAGAAGTGAATGTGAACATTTCAGGGACCTTCTC
TTACA
Found at i:54725253 original size:23 final size:23
Alignment explanation
Indices: 54725223--54725270 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
54725213 TATCATCTGT
* *
54725223 TTTATGATATGAGATTAGTCTTA
1 TTTATGATATGAGATCACTCTTA
54725246 TTTATGATATGAGATCACTCTTA
1 TTTATGATATGAGATCACTCTTA
54725269 TT
1 TT
54725271 GGATTAGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (23 bp):
TTTATGATATGAGATCACTCTTA
Found at i:54733113 original size:19 final size:20
Alignment explanation
Indices: 54733089--54733139 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
54733079 CCAATCATAT
54733089 GTATCGATACCTT-TGTAAA
1 GTATCGATACCTTGTGTAAA
**
54733108 GTATCGATACCTTGGTGTAGG
1 GTATCGATACCTT-GTGTAAA
54733129 GTATCGATACC
1 GTATCGATACC
54733140 AAATTGGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.46
21 15 0.54
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
GTATCGATACCTTGTGTAAA
Found at i:54735566 original size:23 final size:23
Alignment explanation
Indices: 54735540--54735607 Score: 118
Period size: 23 Copynumber: 3.0 Consensus size: 23
54735530 TGTTATTGAT
54735540 CAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATAA
**
54735563 CAGTGGTAGCTTCGGCTACATTT
1 CAGTGGTAGCTTCGGCTACATAA
54735586 CAGTGGTAGCTTCGGCTACATA
1 CAGTGGTAGCTTCGGCTACATA
54735608 TTAGTGTTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (23 bp):
CAGTGGTAGCTTCGGCTACATAA
Found at i:54736209 original size:24 final size:27
Alignment explanation
Indices: 54736163--54736212 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 27
54736153 ATAAAAATTA
54736163 ACCAAAATATTATAACTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTATTT
54736190 ACCAAAATA-T-T-ACTTTTTTTATT
1 ACCAAAATATTATAACTTTTTTTATT
54736213 ATTTACGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 12 0.52
25 1 0.04
26 1 0.04
27 9 0.39
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (27 bp):
ACCAAAATATTATAACTTTTTTTATTT
Found at i:54736327 original size:27 final size:27
Alignment explanation
Indices: 54736297--54736348 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
54736287 GGTCAATCAC
54736297 ATTGGCGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAAAGGTGCCAAAGAG
* *
54736324 ATTGGTGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAAAGGTGCCAAAG
54736349 TGATGGACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.33, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAGAG
Found at i:54736454 original size:19 final size:19
Alignment explanation
Indices: 54736427--54736496 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
54736417 TCAACTCATT
*
54736427 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
54736446 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
54736464 -TTTACATTTAATAACTCTA
1 TTTTA-ATTTAATAACTCTA
54736483 TTTTAATTTAATAA
1 TTTTAATTTAATAA
54736497 ACTATTAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
17 4 0.09
18 12 0.27
19 25 0.56
20 4 0.09
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:54736477 original size:37 final size:37
Alignment explanation
Indices: 54736432--54736502 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
54736422 TCATTTTTTT
54736432 ATTTAATAACTCTATTTTAATTTAATAAACTATTTAC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTTAC
54736469 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
54736503 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTTAC
Found at i:54736749 original size:19 final size:19
Alignment explanation
Indices: 54736722--54736793 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
54736712 TCAACTCATT
*
54736722 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
**
54736741 TTTTAATTTAATAA-AATA
1 TTTTAATTTAATAACTCTA
* *
54736759 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
54736778 TTTTAATTTAATAACT
1 TTTTAATTTAATAACT
54736794 ATTAAGTAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
18 14 0.33
19 29 0.67
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:54736953 original size:293 final size:295
Alignment explanation
Indices: 54736359--54737060 Score: 1302
Period size: 293 Copynumber: 2.4 Consensus size: 295
54736349 TGATGGACTA
54736359 AAATGTGGCTAATTGCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAACTC
1 AAATGTGGCTAATTGCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAACTC
54736424 ATTTTTTTATTTAATAACTCTATTTTAATTTAATAAACTATT-TACATTTAATAACTCTATTTTA
66 ATTTTTTTATTTAATAACTCTATTTTAATTTAATAAACTATTCT-CATTTAATAACTCTATTTTA
54736488 ATTTAATAAACTATTAAGTAATACTTAATTTTTTTAAAATTAAAATAGAGTTATTAAATGAGAGA
130 ATTTAATAAACTATTAAGTAATACTTAATTTTTTTAAAATTAAAATAGAGTTATTAAATGAGAGA
* * *
54736553 ATTCTAATTAAGTGACCATTTGCAGTTTTGAGGACTTGACATGCAAATTTACCATTTTGAATTTT
195 ATTCTAATTAAGTGACCATTTGCAGTTTTAAGGACGTGACATGCAAATTTACCATTTTAAATTTT
54736618 GAAAGTGAATTGCTGCTGCTGTGCGCACTAAAATTG
260 GAAAGTGAATTGCTGCTGCTGTGCGCACTAAAATTG
* *
54736654 AAATGTGGCTAATTTCCTTCTAATCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAACTC
1 AAATGTGGCTAATTGCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAACTC
*
54736719 ATTTTTTTATTTAATAACTCTATTTTAATTTAATAAAATATTCTCATTTAATAACTCTATTTTAA
66 ATTTTTTTATTTAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATTTTAA
54736784 TTTAAT-AACTATTAAGTAATACTTAATTTTTTT-AAATTAAAATAGAGTTATTAAATGAGAGAA
131 TTTAATAAACTATTAAGTAATACTTAATTTTTTTAAAATTAAAATAGAGTTATTAAATGAGAGAA
54736847 TTCTAATTAAGTGACCATTTGCAGTTTTAAGGACGTGACATGCAAATTTACCATTTTAAATTTTG
196 TTCTAATTAAGTGACCATTTGCAGTTTTAAGGACGTGACATGCAAATTTACCATTTTAAATTTTG
54736912 AAAGTGAATTGCTGCTGCTGTGCGCACTAAAATTG
261 AAAGTGAATTGCTGCTGCTGTGCGCACTAAAATTG
*
54736947 AAATGTGACTAATTGCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAACTC
1 AAATGTGGCTAATTGCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAACTC
*
54737012 ATTTTTTTATTTAATAACTCTATTTTAATTTAAGAAACTATTCTCATTT
66 ATTTTTTTATTTAATAACTCTATTTTAATTTAATAAACTATTCTCATTT
54737061 TTTTATTTAA
Statistics
Matches: 395, Mismatches: 11, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
293 236 0.60
294 27 0.07
295 131 0.33
296 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.45
Consensus pattern (295 bp):
AAATGTGGCTAATTGCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAACTC
ATTTTTTTATTTAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATTTTAA
TTTAATAAACTATTAAGTAATACTTAATTTTTTTAAAATTAAAATAGAGTTATTAAATGAGAGAA
TTCTAATTAAGTGACCATTTGCAGTTTTAAGGACGTGACATGCAAATTTACCATTTTAAATTTTG
AAAGTGAATTGCTGCTGCTGTGCGCACTAAAATTG
Found at i:54737030 original size:20 final size:20
Alignment explanation
Indices: 54737007--54737074 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 20
54736997 ATTCCCCTTC
54737007 AACTCATTTTTTTATTTAAT
1 AACTCATTTTTTTATTTAAT
***
54737027 AACTCTATTTTAATTTAAGAAACT
1 AACTC-ATTTT--TTTATTTAA-T
*
54737051 ATTCTCATTTTTTTATTTAAT
1 A-ACTCATTTTTTTATTTAAT
54737072 AAC
1 AAC
54737075 AGTTTTGTTG
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
20 6 0.17
21 7 0.20
22 6 0.17
23 6 0.17
24 7 0.20
25 3 0.09
ACGTcount: A:0.34, C:0.12, G:0.01, T:0.53
Consensus pattern (20 bp):
AACTCATTTTTTTATTTAAT
Found at i:54741279 original size:46 final size:46
Alignment explanation
Indices: 54741229--54741318 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
54741219 GGTAACACAC
* *
54741229 ATATGACAAGGTCA-TTGGAAAAAGCAGTTGGATGAATTGCTTTCGT
1 ATATGACAAGGTCATTTGG-AAAAGCAGTTAGACGAATTGCTTTCGT
*
54741275 ATATGATAAGGTCATTTGGAAAAGCAGTTAGACGAATTGCTTTC
1 ATATGACAAGGTCATTTGGAAAAGCAGTTAGACGAATTGCTTTC
54741319 ATAAAGAGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 36 0.90
47 4 0.10
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.31
Consensus pattern (46 bp):
ATATGACAAGGTCATTTGGAAAAGCAGTTAGACGAATTGCTTTCGT
Found at i:54743600 original size:25 final size:23
Alignment explanation
Indices: 54743559--54743652 Score: 64
Period size: 25 Copynumber: 3.9 Consensus size: 23
54743549 AAGCAAAAAA
* *
54743559 CGGTAAGCTCCTCCGAGCTAGATAT
1 CGGTAAGCTCATACGAGCT-GA-AT
*
54743584 CGGTAAGCTCATACGAGTTGTGAAT
1 CGGTAAGCTCATACGAG--CTGAAT
* *
54743609 CGGTAAGTTC-TGATGAGCTGAAAT
1 CGGTAAGCTCAT-ACGAGCTG-AAT
* *
54743633 TGGAAAGCTCATACGAGCTG
1 CGGTAAGCTCATACGAGCTG
54743653 TGGTGTGTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
23 2 0.04
24 18 0.33
25 31 0.57
26 2 0.04
27 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (23 bp):
CGGTAAGCTCATACGAGCTGAAT
Found at i:54748618 original size:31 final size:30
Alignment explanation
Indices: 54748574--54748687 Score: 104
Period size: 31 Copynumber: 3.7 Consensus size: 30
54748564 TTAATATGAG
* * *
54748574 ATATTTAATTTAATTTAATATTTGTCTAAAT
1 ATATTTTA-TTAATTTAATATTTATCTAGAT
* * *
54748605 AGTATTTTATTAATTTAATATTAATAT-GAG
1 A-TATTTTATTAATTTAATATTTATCTAGAT
**
54748635 ATATTAAATTTAATTTAATATTTATCTAGAT
1 ATATTTTA-TTAATTTAATATTTATCTAGAT
*
54748666 AATATTTTATTATTTTAATATT
1 -ATATTTTATTAATTTAATATT
54748688 AATGTGATTA
Statistics
Matches: 65, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
29 5 0.08
30 18 0.28
31 30 0.46
32 12 0.18
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (30 bp):
ATATTTTATTAATTTAATATTTATCTAGAT
Found at i:54748632 original size:61 final size:61
Alignment explanation
Indices: 54748561--54748690 Score: 215
Period size: 61 Copynumber: 2.1 Consensus size: 61
54748551 ATTTATCTAG
* * *
54748561 ATATTAATATGAGATATTTAATTTAATTTAATATTTGTCTAAATAGTATTTTATTAATTTA
1 ATATTAATATGAGATATTAAATTTAATTTAATATTTATCTAAATAATATTTTATTAATTTA
* *
54748622 ATATTAATATGAGATATTAAATTTAATTTAATATTTATCTAGATAATATTTTATTATTTTA
1 ATATTAATATGAGATATTAAATTTAATTTAATATTTATCTAAATAATATTTTATTAATTTA
54748683 ATATTAAT
1 ATATTAAT
54748691 GTGATTAATT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (61 bp):
ATATTAATATGAGATATTAAATTTAATTTAATATTTATCTAAATAATATTTTATTAATTTA
Found at i:54753147 original size:16 final size:17
Alignment explanation
Indices: 54753113--54753147 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
54753103 TTTGTCTTTG
*
54753113 AATTTTTGGTGAGATTA
1 AATTTTTGGTGAGACTA
54753130 AATTTTTGGTG-GACTA
1 AATTTTTGGTGAGACTA
54753146 AA
1 AA
54753148 ATGTGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.31, C:0.03, G:0.23, T:0.43
Consensus pattern (17 bp):
AATTTTTGGTGAGACTA
Found at i:54754493 original size:41 final size:41
Alignment explanation
Indices: 54754411--54754495 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 41
54754401 CTCATTGCCA
* ***** *
54754411 GTGAAATAATTCAGACTCTATGTCTAGCAGTTTGGATGCCG
1 GTGAAACAATTCAGACTCTATGTCTAGCAGGCCAAAAGCCG
54754452 GTGAAACAATTCAGACTCTATGTCTAGCAGGCCAAAAGCCG
1 GTGAAACAATTCAGACTCTATGTCTAGCAGGCCAAAAGCCG
54754493 GTG
1 GTG
54754496 TACTGAATCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (41 bp):
GTGAAACAATTCAGACTCTATGTCTAGCAGGCCAAAAGCCG
Found at i:54763944 original size:20 final size:20
Alignment explanation
Indices: 54763903--54763947 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
54763893 GGAAAGTATA
* *
54763903 ATATATATACGTACATATAT
1 ATATATATAAGTACATAAAT
54763923 ATATATATAAGTTA-ATAAAT
1 ATATATATAAG-TACATAAAT
54763943 ATATA
1 ATATA
54763948 GATCATAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (20 bp):
ATATATATAAGTACATAAAT
Found at i:54763971 original size:46 final size:46
Alignment explanation
Indices: 54763923--54764073 Score: 146
Period size: 50 Copynumber: 3.2 Consensus size: 46
54763913 GTACATATAT
*
54763923 ATATATATAAGTTAATAAATATATAGATCATAAAGATAATGATTAT
1 ATATATATAAGTTAATAAATATATAGATCATAAAGATAATGATTAC
* * * *
54763969 ATATATATAGAAATT-ATAAAATATGTATAGA-AAGTATA-ATATATAGACGTAC
1 ATATATAT--AAGTTAAT-AAATA--TATAGATCA-TAAAGATA-AT-GA-TTAC
*
54764021 ATATATATAAGTTAATAAATATATAGATCACAAAGATAATGATTAC
1 ATATATATAAGTTAATAAATATATAGATCATAAAGATAATGATTAC
54764067 ATATATA
1 ATATATA
54764074 AACTTAAAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 24
0.71 0.09 0.21
Matches are distributed among these distances:
46 18 0.22
47 4 0.05
48 19 0.23
49 8 0.10
50 20 0.24
51 4 0.05
52 10 0.12
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.34
Consensus pattern (46 bp):
ATATATATAAGTTAATAAATATATAGATCATAAAGATAATGATTAC
Found at i:54763972 original size:104 final size:98
Alignment explanation
Indices: 54763863--54764071 Score: 319
Period size: 104 Copynumber: 2.1 Consensus size: 98
54763853 ATAAAGAAAA
* *
54763863 ATATATAGATAGAAATTATAAAATATGTATGGAAAGTATAATATATATACGTACATATATATATA
1 ATATATAGATAGAAATTATAAAATATGTATAGAAAGTATAATATATAGACGTAC------ATATA
*
54763928 TATAAGTTAATAAATATATAGATCATAAAGATAATGATT
60 TATAAGTTAATAAATATATAGATCACAAAGATAATGATT
*
54763967 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATAGACGTACATATATATAAG
1 ATATATAGATAGAAATTATAAAATATGTATAGAAAGTATAATATATAGACGTACATATATATAAG
54764032 TTAATAAATATATAGATCACAAAGATAATGATT
66 TTAATAAATATATAGATCACAAAGATAATGATT
*
54764065 ACATATA
1 ATATATA
54764072 TAAACTTAAA
Statistics
Matches: 100, Mismatches: 5, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
98 49 0.49
104 51 0.51
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.34
Consensus pattern (98 bp):
ATATATAGATAGAAATTATAAAATATGTATAGAAAGTATAATATATAGACGTACATATATATAAG
TTAATAAATATATAGATCACAAAGATAATGATT
Found at i:54763997 original size:20 final size:20
Alignment explanation
Indices: 54763969--54764013 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
54763959 TAATGATTAT
*
54763969 ATATATATAGAAATTATAAA
1 ATATATATAGAAAGTATAAA
* *
54763989 ATATGTATAGAAAGTATAAT
1 ATATATATAGAAAGTATAAA
54764009 ATATA
1 ATATA
54764014 GACGTACATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:54764027 original size:52 final size:52
Alignment explanation
Indices: 54763865--54764029 Score: 151
Period size: 52 Copynumber: 3.2 Consensus size: 52
54763855 AAAGAAAAAT
* * *
54763865 ATATAGATAGAAATTATAAAATATGTATGGAAAGTATAATATATATACGTAC
1 ATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATAGACGTAC
* * * * * * * *
54763917 ATATATATATATATAAGTTAATAA-ATATATAGATCA-TA-AAGATA-ATGA-TTAT
1 ATATATATAGAAATTA--TAA-AATATGTATAGA-AAGTATAATATATA-GACGTAC
54763969 ATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATAGACGTAC
1 ATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATAGACGTAC
54764021 ATATATATA
1 ATATATATA
54764030 AGTTAATAAA
Statistics
Matches: 84, Mismatches: 19, Indels: 20
0.68 0.15 0.16
Matches are distributed among these distances:
49 3 0.04
50 13 0.15
51 7 0.08
52 40 0.48
53 6 0.07
54 12 0.14
55 3 0.04
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.35
Consensus pattern (52 bp):
ATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATAGACGTAC
Found at i:54764060 original size:52 final size:48
Alignment explanation
Indices: 54763918--54764073 Score: 146
Period size: 46 Copynumber: 3.2 Consensus size: 48
54763908 TATACGTACA
* *
54763918 TATATATATATATAAGTTAATAAATATATAGATCATAAAGATAATGAT
1 TATACATATATATAAGTTAATAAATATATAGATCACAAAGATAATGAT
* * * *
54763966 TATATATATATAGAAATT-ATAAA-ATAT-GTAT-AGAAAGTATAAT-AT
1 TATACATATATATAAGTTAATAAATATATAG-ATCACAAAG-ATAATGAT
54764011 ATAGACGTACATATATATAAGTTAATAAATATATAGATCACAAAGATAATGA-
1 -T--A--TACATATATATAAGTTAATAAATATATAGATCACAAAGATAATGAT
54764063 T-TACATATATA
1 TATACATATATA
54764074 AACTTAAAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
45 8 0.09
46 22 0.25
47 5 0.06
48 17 0.19
50 13 0.15
51 6 0.07
52 11 0.12
53 7 0.08
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (48 bp):
TATACATATATATAAGTTAATAAATATATAGATCACAAAGATAATGAT
Found at i:54765426 original size:44 final size:44
Alignment explanation
Indices: 54765363--54765647 Score: 326
Period size: 44 Copynumber: 6.4 Consensus size: 44
54765353 TATGAGCAGG
* * *
54765363 CAAGATCTGCTACCTTTGATCTATTTCATGCC-GATACATGAAGA
1 CAAGATCTGCTATCTTTGATCTACTTCACGCCAG-TACATGAAGA
*
54765407 CAAGATCTGCTTTCTTTGATCTACTTCACGCCAGTACATGAAGA
1 CAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGA
* * *
54765451 CAAGATCCGCTATATTTGATCTACTTCACGCCAGTACATAAAGA
1 CAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGA
* * * *
54765495 CAAGATCTGCTTTTTTTGATCTACCTCACGCCAATACATGAAGA
1 CAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGA
* * *
54765539 CAAGATCTGCTTTCTTCGATTCTACTTTGC-CACCAGT--ATGGAAAGA
1 CAAGATCTGCTATCTTTGA-TCTAC-TT-CACGCCAGTACAT-G-AAGA
* * * *
54765585 CAAGATCTGCTATCTTCGATCTAATTCATGCCAATACATGAAGA
1 CAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGA
54765629 CAAGATCTGCTATCTTTGA
1 CAAGATCTGCTATCTTTGA
54765648 CCTATTCCGC
Statistics
Matches: 207, Mismatches: 25, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
43 1 0.00
44 163 0.79
45 12 0.06
46 30 0.14
47 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (44 bp):
CAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGA
Found at i:54765749 original size:88 final size:88
Alignment explanation
Indices: 54765619--54766471 Score: 1229
Period size: 88 Copynumber: 9.7 Consensus size: 88
54765609 TTCATGCCAA
* * ** ** *
54765619 TACATGAAGACAAGATCTGCTATCTTTGACCTATTCCGCTACGACCCAGGGAGGCAAGGCTGGTA
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTGGTA
* *
54765684 TCTTCAATCTACTTCACTGTCGG
66 TCTTCGATCTGCTTCACTGTCGG
54765707 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTGGTA
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTGGTA
* * * *
54765772 CCTTTGATCTGCGTCACTATCGG
66 TCTTCGATCTGCTTCACTGTCGG
* * *
54765795 TATAGGAAAGCAAGATCTGCTATCTTCAACCTGCTCTACTACGACCCAGGGAGGCAAGGCTGGTA
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTGGTA
* * * *
54765860 TCTTTGATCTGCTTCATTTTCAG
66 TCTTCGATCTGCTTCACTGTCGG
54765883 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTGGTA
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTGGTA
* * * *
54765948 CCTTCGATTTGCTTCACTATTGG
66 TCTTCGATCTGCTTCACTGTCGG
*
54765971 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGTAAGGCTGGTA
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTGGTA
*
54766036 TCTTCGATCTGCTTCATTGTCGG
66 TCTTCGATCTGCTTCACTGTCGG
* *
54766059 TACAAGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTAGTA
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTGGTA
*
54766124 TCTTCGATCTGCTTCACTATCGG
66 TCTTCGATCTGCTTCACTGTCGG
*
54766147 TACAGGAAGGCAATATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTGGTA
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTGGTA
54766212 TCTTCGATCTGCTTCACTGTCGG
66 TCTTCGATCTGCTTCACTGTCGG
* * * * *
54766235 TATAGAAAGGCAAGATCTGTTATCTTCAACCTGCTCCACTACGACCCAGAGAGACAAGGCTGGTA
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTGGTA
* * *
54766300 TCTTCGATCTGCTTCGCTGTTGA
66 TCTTCGATCTGCTTCACTGTCGG
* * *
54766323 TGCAGGAAGGCAAGGTCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAAGCAAGGCTGGTA
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTGGTA
* *
54766388 TCTTCGATCTGCTTCGCTGTCGA
66 TCTTCGATCTGCTTCACTGTCGG
** ** * ** * * *
54766411 CGCAGGAAGGCAAGATCTATTATTTTCAAATTGCTCCACTGCAAACCAGGGAGGCAAGGCT
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCT
54766472 TTATGCTTTC
Statistics
Matches: 690, Mismatches: 75, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 690 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (88 bp):
TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTGGTA
TCTTCGATCTGCTTCACTGTCGG
Found at i:54772799 original size:102 final size:103
Alignment explanation
Indices: 54772683--54772895 Score: 374
Period size: 104 Copynumber: 2.1 Consensus size: 103
54772673 ATAAAGAAAA
* *
54772683 ATATATATATAGAAATTATAAAATATGTATGGAAAGTATAAT-ATATAGACATACATGTATATAT
1 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATAATATAGACATACATATATATAT
54772747 AAGTTAATAAATATATAGATCATAAAGATAATGATTAC
66 AAGTTAATAAATATATAGATCATAAAGATAATGATTAC
* *
54772785 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATACATATATACGTACATATATATA
1 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATA-ATATAGACATACATATATATA
54772850 TAAGTTAATAAATATATAGATCATAAAGATAATGATTAC
65 TAAGTTAATAAATATATAGATCATAAAGATAATGATTAC
54772889 ATATATA
1 ATATATA
54772896 AACTTAACAA
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
102 41 0.39
104 64 0.61
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (103 bp):
ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATAATATAGACATACATATATATAT
AAGTTAATAAATATATAGATCATAAAGATAATGATTAC
Found at i:54772815 original size:20 final size:20
Alignment explanation
Indices: 54772787--54772835 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
54772777 ATGATTACAT
*
54772787 ATATATATAGAAATTATAAA
1 ATATATATAGAAAGTATAAA
*
54772807 ATATGTATAGAAAGTATAATA
1 ATATATATAGAAAGTATAA-A
54772828 CATATATA
1 -ATATATA
54772836 CGTACATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.71
21 1 0.04
22 6 0.25
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:54772863 original size:54 final size:53
Alignment explanation
Indices: 54772685--54772866 Score: 155
Period size: 54 Copynumber: 3.5 Consensus size: 53
54772675 AAAGAAAAAT
* * *
54772685 ATATATATAGAAATTATAAAATATGTATGGAAAGTATAAT-ATATAGACATAC
1 ATATATATATAAATTATAAAATATGTATAGAAAGTATAATAATATATACATAC
* * * *
54772737 ATGTATATATAAGTTAATAAATATATAG-ATCATAAAG-ATAAT--GAT-TACAT--
1 ATATATATATAAATT-ATAAA-ATAT-GTAT-AGAAAGTATAATAATATATACATAC
* *
54772787 ATATATATAGAAATTATAAAATATGTATAGAAAGTATAATACATATATACGTAC
1 ATATATATATAAATTATAAAATATGTATAGAAAGTATAATA-ATATATACATAC
*
54772841 ATATATATATAAGTTAATAAATATAT
1 ATATATATATAAATT-ATAAA-ATAT
54772867 AGATCATAAA
Statistics
Matches: 101, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
47 6 0.06
48 11 0.11
49 5 0.05
50 12 0.12
51 2 0.02
52 20 0.20
53 7 0.07
54 24 0.24
55 10 0.10
56 4 0.04
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (53 bp):
ATATATATATAAATTATAAAATATGTATAGAAAGTATAATAATATATACATAC
Found at i:54773690 original size:15 final size:15
Alignment explanation
Indices: 54773656--54773695 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
54773646 TTATTTATTT
*
54773656 TAGTAAA-ATAAAAA
1 TAGTAAACAAAAAAA
54773670 TA-TAAACAAAAAAA
1 TAGTAAACAAAAAAA
54773684 TAGTAAACAAAA
1 TAGTAAACAAAA
54773696 GTAAGCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 10 0.43
15 9 0.39
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.17
Consensus pattern (15 bp):
TAGTAAACAAAAAAA
Found at i:54776623 original size:55 final size:55
Alignment explanation
Indices: 54776562--54776672 Score: 170
Period size: 55 Copynumber: 2.0 Consensus size: 55
54776552 TTGTCTTAAT
* *
54776562 TGTTGGAATACTGCTTCTTTTAAA-TATATTTTTTATATGTTTAAATCGATTGTTA
1 TGTTGGAATACTGCTTCTTTTAAATTA-ATTGTTTATATGTTTAAATCGACTGTTA
* *
54776617 TGTTGGAATACTGCTTCTTTTGAATTAATTGTTTATATGTTTAAATTGACTGTTA
1 TGTTGGAATACTGCTTCTTTTAAATTAATTGTTTATATGTTTAAATCGACTGTTA
54776672 T
1 T
54776673 AGCACTTCTA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
55 49 0.96
56 2 0.04
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.52
Consensus pattern (55 bp):
TGTTGGAATACTGCTTCTTTTAAATTAATTGTTTATATGTTTAAATCGACTGTTA
Found at i:54777941 original size:25 final size:22
Alignment explanation
Indices: 54777898--54777943 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
54777888 GATGTTTAGA
*
54777898 ATTTTACTCAAATAATAACTTT
1 ATTTTACTCAAAAAATAACTTT
54777920 ATTTTACATCAATAAAATTAACTT
1 ATTTTAC-TCAA-AAAA-TAACTT
54777944 AACTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 3 0.15
25 6 0.30
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTTACTCAAAAAATAACTTT
Found at i:54782902 original size:20 final size:20
Alignment explanation
Indices: 54782846--54782914 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
54782836 AGACAGATCC
54782846 TATTGAATTAATCAATTTTAT
1 TATTGAATTAATCAATTTT-T
* ** * *
54782867 GATT-TCTTATTTAATTTTT
1 TATTGAATTAATCAATTTTT
54782886 TATTGAATTAATCAATTTTT
1 TATTGAATTAATCAATTTTT
*
54782906 TAGTGAATT
1 TATTGAATT
54782915 TTTTTATTTA
Statistics
Matches: 36, Mismatches: 11, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
19 4 0.11
20 29 0.81
21 3 0.08
ACGTcount: A:0.32, C:0.04, G:0.07, T:0.57
Consensus pattern (20 bp):
TATTGAATTAATCAATTTTT
Found at i:54785925 original size:22 final size:23
Alignment explanation
Indices: 54785867--54785911 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
54785857 ATGCAATCTT
*
54785867 ATATATGA-TATGTAATCTTAGA
1 ATATATGATTCTGTAATCTTAGA
54785889 ATATATGATTCTGTAATCTTAGA
1 ATATATGATTCTGTAATCTTAGA
54785912 GATTTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (23 bp):
ATATATGATTCTGTAATCTTAGA
Found at i:54786977 original size:19 final size:19
Alignment explanation
Indices: 54786933--54786978 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
54786923 TATTAATCCA
*
54786933 AAATTCATGTTTAATTTTG
1 AAATTCTTGTTTAATTTTG
54786952 AAATTCTTGTTTAATTTTG
1 AAATTCTTGTTTAATTTTG
54786971 AAATTCTT
1 AAATTCTT
54786979 CCTTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (19 bp):
AAATTCTTGTTTAATTTTG
Found at i:54792291 original size:125 final size:125
Alignment explanation
Indices: 54791926--54792346 Score: 598
Period size: 125 Copynumber: 3.4 Consensus size: 125
54791916 ACGTGGACGC
** * *
54791926 GAAGAATTTGTGAAATTGCGCCCTCCTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
1 GAAGAATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
* *
54791991 TTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTACGA
66 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGA
* * * *
54792051 GAAGAATTTGTTAAATCACGTCCACACG-GG-CGCACTTTTGCTACAGTAGGTCCT-GAAAAAAT
1 GAAGAATTTGTGAAATCACG-CC-CACGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAAT
* * * * *
54792113 TATTTCGAGTTGACGTTTTTGAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATT-TGA
64 AATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCT-TTATGA
* * *
54792175 GAAGAATTTCTGAAATCACGCCCTCGTGGATGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
1 GAAGAATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
54792240 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGA
66 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGA
** *
54792300 GAAGAATTTGTGAAATTGCGCTCACGTGGACGCGCTTTTGCTACAGT
1 GAAGAATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGT
54792347 AGCATGTTTG
Statistics
Matches: 256, Mismatches: 33, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
122 3 0.01
123 4 0.02
124 100 0.39
125 143 0.56
126 4 0.02
127 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (125 bp):
GAAGAATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGA
Found at i:54794649 original size:18 final size:18
Alignment explanation
Indices: 54794626--54794665 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
54794616 GACTCGGAAA
54794626 AGGATACATATAAGAGTT
1 AGGATACATATAAGAGTT
*
54794644 AGGATACATATAAGGGTT
1 AGGATACATATAAGAGTT
54794662 AGGA
1 AGGA
54794666 AACGCACCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.28, T:0.25
Consensus pattern (18 bp):
AGGATACATATAAGAGTT
Done.