Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 146 of 199
Found at i:42946167 original size:27 final size:27
Alignment explanation
Indices: 42946137--42946314 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
42946127 ATATTGAGCC
* *
42946137 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
42946164 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
42946191 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
42946219 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
42946246 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
42946273 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
42946300 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42946315 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:42946249 original size:55 final size:54
Alignment explanation
Indices: 42946137--42946314 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
42946127 ATATTGAGCC
* * * * *
42946137 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
42946191 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
42946246 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
42946300 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42946315 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:42966592 original size:12 final size:12
Alignment explanation
Indices: 42966570--42966603 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
42966560 TGTAGTTTCA
42966570 AAAAAATAATTCG
1 AAAAAA-AATTCG
*
42966583 AAAAAAAATTTG
1 AAAAAAAATTCG
42966595 AAAAAAAAT
1 AAAAAAAAT
42966604 GTATACGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:42968798 original size:17 final size:16
Alignment explanation
Indices: 42968776--42968807 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
42968766 GAAGAAAAAC
42968776 AAAAAAGATGAGTGATA
1 AAAAAAGA-GAGTGATA
42968793 AAAAAAGAGAGTGAT
1 AAAAAAGAGAGTGAT
42968808 TCCAAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.25, T:0.16
Consensus pattern (16 bp):
AAAAAAGAGAGTGATA
Found at i:42972976 original size:12 final size:12
Alignment explanation
Indices: 42972954--42972987 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
42972944 GTAGTTTCAA
42972954 AAAAAATAATTCG
1 AAAAAA-AATTCG
*
42972967 AAAAAAAATTTG
1 AAAAAAAATTCG
42972979 AAAAAAAAT
1 AAAAAAAAT
42972988 GTATACGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:42989057 original size:21 final size:21
Alignment explanation
Indices: 42989027--42989068 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
42989017 TCTTGTTCAA
42989027 TCTCAATCTCGTTTTTCTTTT
1 TCTCAATCTCGTTTTTCTTTT
* *
42989048 TCTCACTCTCTTTTTTCTTTT
1 TCTCAATCTCGTTTTTCTTTT
42989069 CCTTGAGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.07, C:0.26, G:0.02, T:0.64
Consensus pattern (21 bp):
TCTCAATCTCGTTTTTCTTTT
Found at i:43009223 original size:27 final size:27
Alignment explanation
Indices: 43009193--43009370 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
43009183 ATATTGAGCC
* *
43009193 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
43009220 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
43009247 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
43009275 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
43009302 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
43009329 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
43009356 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43009371 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:43009305 original size:55 final size:54
Alignment explanation
Indices: 43009193--43009370 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
43009183 ATATTGAGCC
* * * * *
43009193 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
43009247 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
43009302 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
43009356 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43009371 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:43012609 original size:23 final size:22
Alignment explanation
Indices: 43012574--43012618 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
43012564 ATTCATGTTT
*
43012574 AAGACAAAATAAAATTGGACAAC
1 AAGACAAAAT-AAATTCGACAAC
* *
43012597 AAGACATATTAAATTCGACAAC
1 AAGACAAAATAAATTCGACAAC
43012619 CACACTAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.56, C:0.16, G:0.11, T:0.18
Consensus pattern (22 bp):
AAGACAAAATAAATTCGACAAC
Found at i:43015718 original size:40 final size:40
Alignment explanation
Indices: 43015688--43015857 Score: 207
Period size: 40 Copynumber: 4.3 Consensus size: 40
43015678 GGACTAAGAT
* *
43015688 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * *
43015728 CCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* ** *
43015768 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
43015808 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
43015847 CCGAAGGCATT
1 CCGAAGGCATT
43015858 TGAACGAGGA
Statistics
Matches: 116, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
39 33 0.28
40 83 0.72
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:43015784 original size:80 final size:79
Alignment explanation
Indices: 43015635--43015857 Score: 241
Period size: 80 Copynumber: 2.8 Consensus size: 79
43015625 TTGAATGCTG
* * * * * * * * *
43015635 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAAACCGGGCTAAG-TCCCGAAGGCATT
*
43015699 TGTGCGAGATACTAAA
64 CGTGCGAGATACTAAA
* * *
43015715 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* **
43015780 GTGCGAGTTGTTAAA
65 GTGCGAGATACTAAA
* * *
43015795 TCCGGGTTACGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
43015858 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
79 35 0.29
80 82 0.68
81 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATACTAAA
Found at i:43015877 original size:79 final size:80
Alignment explanation
Indices: 43015710--43015892 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
43015700 GTGCGAGATA
* * *
43015710 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
43015775 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
43015790 TTAAATCCGGGTTACGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
43015854 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
43015869 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
43015893 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:43019888 original size:30 final size:29
Alignment explanation
Indices: 43019828--43019888 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
43019818 GTAATTTGGG
* *
43019828 CTAAATTGTAAAAATAATAAATTGAGGGA
1 CTAAAATGTAAAAATAATAAATTCAGGGA
*
43019857 CTAAAATGT-AAAATAAATGAAATTCATGGA
1 CTAAAATGTAAAAAT-AAT-AAATTCAGGGA
43019887 CT
1 CT
43019889 TTTATGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.19
29 11 0.41
30 11 0.41
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.28
Consensus pattern (29 bp):
CTAAAATGTAAAAATAATAAATTCAGGGA
Found at i:43020474 original size:41 final size:41
Alignment explanation
Indices: 43020411--43020553 Score: 187
Period size: 41 Copynumber: 3.5 Consensus size: 41
43020401 TCGGGTTCTG
* * *
43020411 TGCCTAGCAGGCTTTATACCGGTGAATTATATCAGGCTTTA
1 TGCCTAGCAGGCTTTATGCCGGTGTATCATATCAGGCTTTA
* * *
43020452 TACCTAGCAGGCTATATGCCGGTGTACCATATCAGGCTTTA
1 TGCCTAGCAGGCTTTATGCCGGTGTATCATATCAGGCTTTA
** * *
43020493 TGCCTAGCAGGCTTCGTGCCGGTGTATCATATCTGGCTTTG
1 TGCCTAGCAGGCTTTATGCCGGTGTATCATATCAGGCTTTA
*
43020534 TGCCTAGAAGGCTTTATGCC
1 TGCCTAGCAGGCTTTATGCC
43020554 TATGTGGTAT
Statistics
Matches: 86, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 86 1.00
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.32
Consensus pattern (41 bp):
TGCCTAGCAGGCTTTATGCCGGTGTATCATATCAGGCTTTA
Found at i:43030734 original size:20 final size:20
Alignment explanation
Indices: 43030709--43030747 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
43030699 TACTTTCTTC
43030709 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
43030729 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
43030748 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:43036655 original size:40 final size:40
Alignment explanation
Indices: 43036610--43036707 Score: 124
Period size: 40 Copynumber: 2.5 Consensus size: 40
43036600 GCGTTTGGAT
*
43036610 AAAAAACACCGCTAAAAATCAAGCATCAGCGGCACTTTCC
1 AAAAAACGCCGCTAAAAATCAAGCATCAGCGGCACTTTCC
* * * * **
43036650 AAAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTTT
1 AAAAAACGCCGCTAAAAATCAAGCATCAGCGGCACTTTCC
*
43036690 GAAAAACGCCGCTAAAAA
1 AAAAAACGCCGCTAAAAA
43036708 CGAGCATTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCAAGCATCAGCGGCACTTTCC
Found at i:43036746 original size:39 final size:39
Alignment explanation
Indices: 43036651--43036748 Score: 117
Period size: 40 Copynumber: 2.5 Consensus size: 39
43036641 GCACTTTCCA
* * *
43036651 AAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTTTG
1 AAAAACGCCGCTAAA-AACGAGCATTAACGACGCTTTTTG
43036691 AAAAACGCCGCTAAAAACGAGCATTAACGACG-TTTCTTAG
1 AAAAACGCCGCTAAAAACGAGCATTAACGACGCTTT-TT-G
* *
43036731 AAAAGCGCCGCAAAAAAC
1 AAAAACGCCGCTAAAAAC
43036749 CTAAGCCCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
38 3 0.06
39 16 0.31
40 32 0.63
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.17
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAACGAGCATTAACGACGCTTTTTG
Found at i:43036841 original size:41 final size:39
Alignment explanation
Indices: 43036796--43036893 Score: 124
Period size: 39 Copynumber: 2.5 Consensus size: 39
43036786 TTTAGCCGCA
*
43036796 TTTTTGAAAAAGCGCCGCTAATGCTCAGAGCTTTAGCGACG
1 TTTTTGAAAAAGCGCCGCTAATGCTC-G-GCATTAGCGACG
* * * *
43036837 TTTTTGGAAAAGCGTCGCTAATGCTCGGGATTAGCGGCG
1 TTTTTGAAAAAGCGCCGCTAATGCTCGGCATTAGCGACG
*
43036876 TTTTTAAAAAAGCGCCGC
1 TTTTTGAAAAAGCGCCGC
43036894 AAAAACATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 24 0.49
40 1 0.02
41 24 0.49
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (39 bp):
TTTTTGAAAAAGCGCCGCTAATGCTCGGCATTAGCGACG
Found at i:43036887 original size:39 final size:41
Alignment explanation
Indices: 43036787--43036893 Score: 128
Period size: 41 Copynumber: 2.7 Consensus size: 41
43036777 TTTCGGGGCT
* * *
43036787 TTAGCCGCATTTTTGAAAAAGCGCCGCTAATGCTCAGAGCT
1 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAGCA
* * * *
43036828 TTAGCGACGTTTTTGGAAAAGCGTCGCTAATGCTC-G-GGA
1 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAGCA
*
43036867 TTAGCGGCGTTTTTAAAAAAGCGCCGC
1 TTAGCGGCGTTTTTGAAAAAGCGCCGC
43036894 AAAAACATTT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
39 24 0.44
40 1 0.02
41 30 0.55
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.27
Consensus pattern (41 bp):
TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAGCA
Found at i:43037245 original size:14 final size:14
Alignment explanation
Indices: 43037228--43037264 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
43037218 GGGTTTAATA
*
43037228 TATATGTTTTAGGG
1 TATATGGTTTAGGG
43037242 TATATGGTTTAGGG
1 TATATGGTTTAGGG
43037256 TATATGGTT
1 TATATGGTT
43037265 AATTTAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.49
Consensus pattern (14 bp):
TATATGGTTTAGGG
Found at i:43037345 original size:14 final size:15
Alignment explanation
Indices: 43037312--43037345 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
43037302 TAAGGTTTAT
43037312 AGATTATGGAATTAG
1 AGATTATGGAATTAG
43037327 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
*
43037341 GGATT
1 AGATT
43037346 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:43037556 original size:21 final size:21
Alignment explanation
Indices: 43037510--43037584 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 21
43037500 TAGGGGTTGG
* *
43037510 GGTTTGGGGGTTAGTAATTAAG-
1 GGTTT-GGGGTTAGGAGTT-AGT
*
43037532 GGTTTGGGGTTAGGGGTTAGT
1 GGTTTGGGGTTAGGAGTTAGT
* * *
43037553 GGTTAGAGGTTAAGAGTTAGT
1 GGTTTGGGGTTAGGAGTTAGT
* *
43037574 GATTTAGGGTT
1 GGTTTGGGGTT
43037585 TAGAAATTCG
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 2 0.05
21 34 0.83
22 5 0.12
ACGTcount: A:0.20, C:0.00, G:0.43, T:0.37
Consensus pattern (21 bp):
GGTTTGGGGTTAGGAGTTAGT
Found at i:43037563 original size:28 final size:29
Alignment explanation
Indices: 43037497--43037563 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 29
43037487 AATGTATAGG
* *
43037497 AGTTAG-GGGTTGGGGTTTGGGGGTTAGT
1 AGTTAGAGGTTTGGGGTTTAGGGGTTAGT
*
43037525 AATTA-AGGGTTTGGGG-TTAGGGGTTAGT
1 AGTTAGA-GGTTTGGGGTTTAGGGGTTAGT
*
43037553 GGTTAGAGGTT
1 AGTTAGAGGTT
43037564 AAGAGTTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
28 22 0.71
29 9 0.29
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.36
Consensus pattern (29 bp):
AGTTAGAGGTTTGGGGTTTAGGGGTTAGT
Found at i:43037720 original size:7 final size:7
Alignment explanation
Indices: 43037681--43037716 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
43037671 TAAAAGAGGA
43037681 GTTAGGG
1 GTTAGGG
*
43037688 GTTAGAG
1 GTTAGGG
43037695 GTTAGGG
1 GTTAGGG
43037702 GTTAGGG
1 GTTAGGG
43037709 GTTTAGGG
1 G-TTAGGG
43037717 TTTATGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.17, C:0.00, G:0.53, T:0.31
Consensus pattern (7 bp):
GTTAGGG
Found at i:43038443 original size:148 final size:147
Alignment explanation
Indices: 43038274--43038539 Score: 453
Period size: 148 Copynumber: 1.8 Consensus size: 147
43038264 GCGGCGTTTT
* *
43038274 GGTAAGCAATAGCGGCGTTTTATAAAAAAAATGCCACAAAAAATAATTTTACTTT-AAAAAAATA
1 GGTAAGCAATAGCGACGTTTTATAAAAAAAATACCACAAAAAATAATTTT-CTTTAAAAAAAATA
*
43038338 GCGCCATTTTATATAGCAAAACAGTGTCGTTTTAATCCAAATGAAATAATTTTTGCGGCGTTTTT
65 GCGCCATTTTATATAACAAAACAGTGTCGTTTTAATCCAAATGAAATAATTTTTGCGGCGTTTTT
43038403 ATGAAATACGCTGCAAAA
130 ATGAAATACGCTGCAAAA
* *
43038421 GGTAAGCAATAGCGACATTTTTATAAAAAAAATACCACAAAAAATAATTTTTTTTAAAAAAAATA
1 GGTAAGCAATAGCGAC-GTTTTATAAAAAAAATACCACAAAAAATAATTTTCTTTAAAAAAAATA
*
43038486 GCGCCATTTTATATAACAAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTT
65 GCGCCATTTTATATAACAAAACAGTGTCGTTTTAATCCAAATGAAATAATTTTT
43038540 TGTGGGCATT
Statistics
Matches: 111, Mismatches: 6, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
147 18 0.16
148 93 0.84
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (147 bp):
GGTAAGCAATAGCGACGTTTTATAAAAAAAATACCACAAAAAATAATTTTCTTTAAAAAAAATAG
CGCCATTTTATATAACAAAACAGTGTCGTTTTAATCCAAATGAAATAATTTTTGCGGCGTTTTTA
TGAAATACGCTGCAAAA
Found at i:43039301 original size:6 final size:6
Alignment explanation
Indices: 43039290--43039341 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
43039280 TGTGGTTTGA
43039290 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
43039338 TTTT
1 TTTT
43039342 TTGAGGGGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:43040740 original size:18 final size:18
Alignment explanation
Indices: 43040717--43040752 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
43040707 TATTTTTCAT
*
43040717 TTGCTTCAATTTCTATGC
1 TTGCTTCAATTTCCATGC
43040735 TTGCTTCAATTTCCATGC
1 TTGCTTCAATTTCCATGC
43040753 CTTACAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.25, G:0.11, T:0.47
Consensus pattern (18 bp):
TTGCTTCAATTTCCATGC
Found at i:43041726 original size:43 final size:43
Alignment explanation
Indices: 43041593--43041726 Score: 166
Period size: 43 Copynumber: 3.1 Consensus size: 43
43041583 AAAGTCATGT
* *
43041593 TTTTAGCGGCGTTTGT-GAAAAAGCGTCGCTAAAGGTCAT-TC
1 TTTTAGTGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCATGAC
* * * *
43041634 TTTATAGTGGCGTTTGTGGTAGAAGCGCCGCAAAAGGTCATGA-
1 TTT-TAGTGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCATGAC
*
43041677 TCTTTAGTGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCATGAC
1 T-TTTAGTGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCATGAC
43041721 TTTTAG
1 TTTTAG
43041727 CGGCATTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
41 3 0.04
42 12 0.15
43 60 0.77
44 3 0.04
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (43 bp):
TTTTAGTGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCATGAC
Found at i:43041760 original size:85 final size:84
Alignment explanation
Indices: 43041581--43041776 Score: 220
Period size: 85 Copynumber: 2.3 Consensus size: 84
43041571 TAATTTTTTT
* * * *
43041581 TAAAAGTCATGTTTTTAGCGGCGTTTGTGAAAAAGCGTCGCTAAAGGTCATTCTTTATAGTGGCG
1 TAAAAGTCATGTCTTTAGCGGCGTTTGTGAAAAAGCGTCGCTAAAGGTCATACTTTATAGCGGCA
*
43041646 TTTGTGGTAGAAGCGCCGC
66 TTTGTGATAGAAGCGCCGC
* *
43041665 -AAAAGGTCATGATCTTTAGTGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCATGACTTT-TAGC
1 TAAAA-GTCATG-TCTTTAGCGGCGTTTGT-GAAAAAGCGTCGCTAAAGGTCAT-ACTTTATAGC
* *
43041728 GGCATTT-TTATA-ATAGCGCTGC
62 GGCATTTGTGATAGA-AGCGCCGC
*
43041750 TAAAAGTCATGGCCTTTAGCGGCGTTT
1 TAAAAGTCAT-GTCTTTAGCGGCGTTT
43041777 ATTTCTAAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
83 4 0.04
84 7 0.07
85 43 0.46
86 36 0.38
87 4 0.04
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (84 bp):
TAAAAGTCATGTCTTTAGCGGCGTTTGTGAAAAAGCGTCGCTAAAGGTCATACTTTATAGCGGCA
TTTGTGATAGAAGCGCCGC
Found at i:43042967 original size:90 final size:90
Alignment explanation
Indices: 43042814--43042994 Score: 317
Period size: 90 Copynumber: 2.0 Consensus size: 90
43042804 AAAACCACAA
* * * *
43042814 ACATATTGGTTAAAATTATTAACATAATTGCATGCTTTACTGTGCATTTGAGCTTGAATTCCATC
1 ACATATTGGTCAAAATTATTAACATAATTGCATGCATTACTGTACATTTGAGCTTGAATTCCATA
43042879 TATTAACTCCCATTATACCTATTAT
66 TATTAACTCCCATTATACCTATTAT
43042904 ACATATTGGTCAAAATTATTAACATAATTGCATGCATTACTGTACATTTGAGCTTGAATTCCATA
1 ACATATTGGTCAAAATTATTAACATAATTGCATGCATTACTGTACATTTGAGCTTGAATTCCATA
*
43042969 TATTAACTCCCATTATACCTGTTAT
66 TATTAACTCCCATTATACCTATTAT
43042994 A
1 A
43042995 GCTTAAATTT
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.40
Consensus pattern (90 bp):
ACATATTGGTCAAAATTATTAACATAATTGCATGCATTACTGTACATTTGAGCTTGAATTCCATA
TATTAACTCCCATTATACCTATTAT
Found at i:43043246 original size:16 final size:16
Alignment explanation
Indices: 43043222--43043289 Score: 84
Period size: 16 Copynumber: 4.2 Consensus size: 16
43043212 TGGTTCACTA
*
43043222 TAATGAAATAGAGCTG
1 TAATTAAATAGAGCTG
*
43043238 TAATTAAATAGAGTTG
1 TAATTAAATAGAGCTG
* *
43043254 TAATTGAATAGAGTTG
1 TAATTAAATAGAGCTG
43043270 TAATGT-AATAGAGCTG
1 TAAT-TAAATAGAGCTG
43043286 TAAT
1 TAAT
43043290 CAGTAATCCA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
16 46 0.98
17 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (16 bp):
TAATTAAATAGAGCTG
Found at i:43043545 original size:58 final size:58
Alignment explanation
Indices: 43043466--43043589 Score: 178
Period size: 58 Copynumber: 2.1 Consensus size: 58
43043456 TTTTAATAAG
* *
43043466 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACCATATT-TTAACATA
1 ATTATTATTAAAAATAATTTAAT-AAAATAATAAATAATTTAACAAAATTCTTAACATA
* * * *
43043524 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATA
1 ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
43043582 ATTATTAT
1 ATTATTAT
43043590 ATGAATTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 22 0.37
58 37 0.63
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
Found at i:43049054 original size:3 final size:3
Alignment explanation
Indices: 43049046--43049073 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
43049036 TAATATTACC
43049046 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
43049074 GCTTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:43061887 original size:88 final size:86
Alignment explanation
Indices: 43061751--43061995 Score: 264
Period size: 85 Copynumber: 2.8 Consensus size: 86
43061741 TGAAGCCGAT
* * *
43061751 AATCCTATCTCCCTGAAATTGTAATGGAGCGGATTA-AAGTA-ATGGATCTCATCTCCCTGAAGT
1 AATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTACAACTACA--GATCTCATCTCCCTGAAGT
* *
43061814 TGCAGTGGAGCAGACAGA-AGAAACC
64 TGTAGT-GA-AAG-CAGATAGAAACC
* * *
43061839 AATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTACAACTACAGATCTTATCTCTCTAAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTACAACTACAGATCTCATCTCCCTGAAGTTG
* * *
43061904 TAGT-AAAGCAGATCGCATCC
66 TAGTGAAAGCAGATAGAAACC
* * ** * *
43061924 AGTCTTATCTCCCTGAAGTTGCTGTGGAGCGGATTACAACCACAGACCTCATCTCCCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTACAACTACAGATCTCATCTCCCTGAAGTTG
43061989 TAGTGAA
66 TAGTGAA
43061996 GCGGATCGAA
Statistics
Matches: 133, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
84 4 0.03
85 66 0.50
86 3 0.02
88 55 0.41
89 4 0.03
90 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27
Consensus pattern (86 bp):
AATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTACAACTACAGATCTCATCTCCCTGAAGTTG
TAGTGAAAGCAGATAGAAACC
Found at i:43061892 original size:44 final size:44
Alignment explanation
Indices: 43061756--43062001 Score: 164
Period size: 44 Copynumber: 5.7 Consensus size: 44
43061746 CCGATAATCC
* * * *
43061756 TATCTCCCTGAAATTGTAATGGAGCGGATTA-AAGTA-ATGGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTACAACTACA--GATCT
* * * * ** *
43061800 CATCTCCCTGAAGTTGCAGTGGAGCAGA-CAGAAGAAACCA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTACAA-CTA-CAGATCT
*
43061844 TATCTCCCTGAAGTTGCAATGGAGCGGATTACAACTACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTACAACTACAGATCT
* * * ** * ** *
43061888 TATCTCTCTAAAGTTGTAGTAAAGCAGATCGC-A-TCCAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTACAACTACAGATCT
* * *
43061929 TATCTCCCTGAAGTTGCTGTGGAGCGGATTACAACCACAGACCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTACAACTACAGATCT
* * *
43061973 CATCTCCCTGAAGTTGTAGTGAAGCGGAT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGAT
43062002 CGAAACACCG
Statistics
Matches: 150, Mismatches: 43, Indels: 18
0.71 0.20 0.09
Matches are distributed among these distances:
41 26 0.17
42 5 0.03
43 7 0.05
44 107 0.71
45 4 0.03
47 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTACAACTACAGATCT
Found at i:43063322 original size:3 final size:3
Alignment explanation
Indices: 43063314--43063387 Score: 121
Period size: 3 Copynumber: 24.3 Consensus size: 3
43063304 TAATATTTCC
*
43063314 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATA ATT ATT ATT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
*
43063360 ATT ATT ATT ATT ATC ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
43063388 GCTTTTTTAT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
3 63 0.95
4 3 0.05
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:43071073 original size:24 final size:25
Alignment explanation
Indices: 43071046--43071099 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
43071036 ACATGTTTAT
*
43071046 TTTTTAAAAT-TTTTAAATAATATA
1 TTTTTAAAATATTTTAAAAAATATA
*
43071070 TTTTT-ATATATTTTAAAAAATATA
1 TTTTTAAAATATTTTAAAAAATATA
*
43071094 TATTTA
1 TTTTTA
43071100 CTAATTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTTAAAATATTTTAAAAAATATA
Found at i:43086470 original size:27 final size:27
Alignment explanation
Indices: 43086437--43086752 Score: 497
Period size: 27 Copynumber: 11.6 Consensus size: 27
43086427 TAAATTGTGC
43086437 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
43086464 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
43086491 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
43086519 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
43086546 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
43086573 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
43086601 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
43086628 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* *
43086656 AGCACTAAGTGTGCGAGTTGACTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
43086683 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * *
43086711 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
43086738 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43086753 GACTTAATAT
Statistics
Matches: 272, Mismatches: 13, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
27 170 0.62
28 102 0.38
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:43086524 original size:55 final size:55
Alignment explanation
Indices: 43086437--43086752 Score: 519
Period size: 55 Copynumber: 5.8 Consensus size: 55
43086427 TAAATTGTGC
*
43086437 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* *
43086491 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
43086546 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
43086601 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
43086656 AGCACTAAGTGTGCGAGTTGACTACGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * * *
43086711 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCG
43086753 GACTTAATAT
Statistics
Matches: 250, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
54 42 0.17
55 208 0.83
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:43086574 original size:82 final size:82
Alignment explanation
Indices: 43086437--43086752 Score: 535
Period size: 82 Copynumber: 3.8 Consensus size: 82
43086427 TAAATTGTGC
43086437 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTG
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTG
43086502 TGCGAGTTTGACTATGT
66 TGCGAGTTTGACTATGT
43086519 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTG
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTG
43086584 TGCGAGTTTGACTATGT
66 TGCGAGTTTGACTATGT
*
43086601 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGA-ATTGACTATGTAGCACTAAGT
*
43086666 GTGCGAG-TTGACTACGT
65 GTGCGAGTTTGACTATGT
* * * * * *
43086683 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGT
1 AGCACTAAGTGTGCGA-ATTGACTATGTAGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGT
43086748 GTGCG
65 GTGCG
43086753 GACTTAATAT
Statistics
Matches: 224, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
82 172 0.77
83 52 0.23
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (82 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTG
TGCGAGTTTGACTATGT
Found at i:43092199 original size:6 final size:6
Alignment explanation
Indices: 43092136--43092205 Score: 63
Period size: 6 Copynumber: 11.5 Consensus size: 6
43092126 GTTTTATTTG
* * *
43092136 TTTTAT TTTTAAT TTTCT-T TTTTAT GTTTAT GTTTAT TTCTAT TTTTAGT
1 TTTTAT TTTT-AT TTT-TAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T
*
43092186 TGTT-T TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTT
43092206 ATTGTAATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
5 5 0.09
6 38 0.72
7 9 0.17
8 1 0.02
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:43092725 original size:187 final size:187
Alignment explanation
Indices: 43092405--43092772 Score: 592
Period size: 187 Copynumber: 2.0 Consensus size: 187
43092395 GGTAGTTTCA
* * *
43092405 GTTTCCTCCCTCTCGTATGATATTATGTTTATACTGTGATTATATTTGTTTGCACATTGAGGACA
1 GTTTCCTCCCTCTCATATGATATTATGTTTATACTATGATTATATTTGTTTGCACATTAAGGACA
* * **
43092470 ATGTAGATCTTAAGTGTGGGGAGGTTATTTATATATTTACTAGAAAATCTTTGAACTATGTCTTG
66 ATGTACATCTTAAGTGTGGGGAGGTTATTTATATAATTACTAGAAAATCCCTGAACTATGTCTTG
*
43092535 TATTTAAGTAATTTTCTCATACTTCAATTAGAATTAATTTTTGACGATTTGAAATGT
131 TATTTAAGTAATTTTCTCATACTTCAATTAGAATGAATTTTTGACGATTTGAAATGT
* * * *
43092592 GTTTTCTCCCTCTCATATGATATTCTGTTTATATTATGATTATATTTGTTTGTACATTAAGGACA
1 GTTTCCTCCCTCTCATATGATATTATGTTTATACTATGATTATATTTGTTTGCACATTAAGGACA
* *
43092657 ATGTACATCTTAAGTGTGGGGAGGTTATTTATATAATTATTAGAAAATCCCTGAATTATGTCTTG
66 ATGTACATCTTAAGTGTGGGGAGGTTATTTATATAATTACTAGAAAATCCCTGAACTATGTCTTG
* *
43092722 TATTTAATTAATTTTCTCATACTTCTATTAGAATGAATTTTTGACGATTTG
131 TATTTAAGTAATTTTCTCATACTTCAATTAGAATGAATTTTTGACGATTTG
43092773 GAATTTTTGT
Statistics
Matches: 165, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
187 165 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (187 bp):
GTTTCCTCCCTCTCATATGATATTATGTTTATACTATGATTATATTTGTTTGCACATTAAGGACA
ATGTACATCTTAAGTGTGGGGAGGTTATTTATATAATTACTAGAAAATCCCTGAACTATGTCTTG
TATTTAAGTAATTTTCTCATACTTCAATTAGAATGAATTTTTGACGATTTGAAATGT
Found at i:43102389 original size:21 final size:22
Alignment explanation
Indices: 43102354--43102415 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
43102344 AATATAAAAA
*
43102354 AATATAT-AATAAAATAG-ATGT
1 AATATATAAAT-AAATAGAATAT
*
43102375 AATATATAAATAAATTGAATAT
1 AATATATAAATAAATAGAATAT
*
43102397 AATAT-TAAATATATA-AATA
1 AATATATAAATAAATAGAATA
43102416 AATTAAACCA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 4 0.11
21 20 0.57
22 11 0.31
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (22 bp):
AATATATAAATAAATAGAATAT
Found at i:43102420 original size:17 final size:17
Alignment explanation
Indices: 43102375--43102422 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 17
43102365 AAATAGATGT
43102375 AATATATAAATAAATT-
1 AATATATAAATAAATTA
*
43102391 GA-ATAT-AAT--ATTA
1 AATATATAAATAAATTA
43102404 AATATATAAATAAATTA
1 AATATATAAATAAATTA
43102421 AA
1 AA
43102423 CCAAAAGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 9
0.69 0.06 0.25
Matches are distributed among these distances:
12 3 0.12
13 1 0.04
14 7 0.28
15 7 0.28
16 1 0.04
17 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AATATATAAATAAATTA
Found at i:43104321 original size:25 final size:25
Alignment explanation
Indices: 43104266--43104358 Score: 96
Period size: 25 Copynumber: 3.7 Consensus size: 25
43104256 TACAGATTTT
* * *
43104266 AGCTCCTATGAGCTTACCGATACTC
1 AGCTCGTATGAGCTTACCGTTATTC
*
43104291 AGCTCGTATAAGCTTACCGTTATTC
1 AGCTCGTATGAGCTTACCGTTATTC
* * *
43104316 AGCTCGGAGGAGCTTACCATTATTC
1 AGCTCGTATGAGCTTACCGTTATTC
* * *
43104341 AACTCGGAGGAGCTTACC
1 AGCTCGTATGAGCTTACC
43104359 ATTTACTGCT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGTTATTC
Found at i:43104359 original size:25 final size:25
Alignment explanation
Indices: 43104301--43104361 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
43104291 AGCTCGTATA
* *
43104301 AGCTTACCGTTATTCAGCTCGGAGG
1 AGCTTACCATTATTCAACTCGGAGG
43104326 AGCTTACCATTATTCAACTCGGAGG
1 AGCTTACCATTATTCAACTCGGAGG
43104351 AGCTTACCATT
1 AGCTTACCATT
43104362 TACTGCTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (25 bp):
AGCTTACCATTATTCAACTCGGAGG
Found at i:43107021 original size:9 final size:9
Alignment explanation
Indices: 43106953--43107022 Score: 52
Period size: 9 Copynumber: 7.2 Consensus size: 9
43106943 AATTTTCTTC
43106953 TTTTCTTTCT
1 TTTTCTTT-T
43106963 TTTTCGTTTT
1 TTTTC-TTTT
**
43106973 TTTTCAGTT
1 TTTTCTTTT
43106982 TTTTCAGTTTT
1 TTTTC--TTTT
*
43106993 TTTTATTTT
1 TTTTCTTTT
43107002 TATTT-TATTT
1 T-TTTCT-TTT
43107012 TTTTCTTTT
1 TTTTCTTTT
43107021 TT
1 TT
43107023 CATTTGTTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
9 21 0.43
10 19 0.39
11 9 0.18
ACGTcount: A:0.07, C:0.09, G:0.04, T:0.80
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:43107021 original size:20 final size:21
Alignment explanation
Indices: 43106989--43107027 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
43106979 GTTTTTTCAG
43106989 TTTTTTTTATTTTT-ATTTTA
1 TTTTTTTTATTTTTCATTTTA
43107009 TTTTTTTCT-TTTTTCATTT
1 TTTTTTT-TATTTTTCATTT
43107028 GTTCTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (21 bp):
TTTTTTTTATTTTTCATTTTA
Found at i:43109862 original size:17 final size:18
Alignment explanation
Indices: 43109833--43109867 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
43109823 ATACTCAAAT
*
43109833 TTTTTTTATTTCATATAC
1 TTTTTTTATTTCAAATAC
43109851 TTTTTTTA-TTCAAATAC
1 TTTTTTTATTTCAAATAC
43109868 AATTGAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTTTATTTCAAATAC
Found at i:43111705 original size:32 final size:32
Alignment explanation
Indices: 43111637--43111793 Score: 208
Period size: 32 Copynumber: 4.9 Consensus size: 32
43111627 ACAAAATAAT
* * *
43111637 GGTAACATGATTGGCAC-AAGCCATCAATAAC
1 GGTAATATGATCGGCACAAAGCCATCAGTAAC
*
43111668 GGTAATATGATCGACACAAAGCCATCAGTAAC
1 GGTAATATGATCGGCACAAAGCCATCAGTAAC
* *
43111700 TGTAATATGATCGGTACAAAGCCATCAGTAAC
1 GGTAATATGATCGGCACAAAGCCATCAGTAAC
* * *
43111732 GGTAATACGATTGGCACAAAGCCATCAGTAAT
1 GGTAATATGATCGGCACAAAGCCATCAGTAAC
* *
43111764 AGTAATATGATCGGTACAAAGCCATCAGTA
1 GGTAATATGATCGGCACAAAGCCATCAGTA
43111794 GCATCGCAGC
Statistics
Matches: 109, Mismatches: 16, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
31 14 0.13
32 95 0.87
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (32 bp):
GGTAATATGATCGGCACAAAGCCATCAGTAAC
Found at i:43112005 original size:24 final size:24
Alignment explanation
Indices: 43111969--43112022 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
43111959 GCTCAGAATT
43111969 AGTCATACAAATCACAAACAAATC
1 AGTCATACAAATCACAAACAAATC
* * *
43111993 AGTCATACCAATCATAGACAAATC
1 AGTCATACAAATCACAAACAAATC
43112017 AGTCAT
1 AGTCAT
43112023 TTACATGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.20
Consensus pattern (24 bp):
AGTCATACAAATCACAAACAAATC
Found at i:43112321 original size:81 final size:81
Alignment explanation
Indices: 43112068--43112324 Score: 232
Period size: 81 Copynumber: 3.2 Consensus size: 81
43112058 GGACAAAATA
* * * * * *
43112068 GTCA-TTTACCCTACAGGGGCATTACGGTCATTTTACCTTACAGGGGCATTACGATCATTTTACC
1 GTCATTTTACCCTATAGGGGCATCACAGTCATTTTACCTTATAGGGGTATTTCGATCATTTTACC
* * * *
43112132 TTACAGGGGCATTATG
66 ATATAGGGGTATTTTG
* * * ** *
43112148 ATTATTTTACCCTATAGGGGTATCACAGTCATTTTACCCTT-TAAAGGTATTTCGACCATTTTAC
1 GTCATTTTACCCTATAGGGGCATCACAGTCATTTTA-CCTTATAGGGGTATTTCGATCATTTTAC
**
43112212 CAT-TCAGGGGTATTTCA
65 CATAT-AGGGGTATTTTG
* * * *** *
43112229 GTCTTTTTACCCTTTGGGGGCATTTTAGTCATTTTACCTTATAGGGGTATTTCGGTCATTTTACC
1 GTCATTTTACCCTATAGGGGCATCACAGTCATTTTACCTTATAGGGGTATTTCGATCATTTTACC
*
43112294 CTATAGGGGTATTTTG
66 ATATAGGGGTATTTTG
*
43112310 GTCATTCTACCCTAT
1 GTCATTTTACCCTAT
43112325 CAAGGTATTT
Statistics
Matches: 135, Mismatches: 37, Indels: 9
0.75 0.20 0.05
Matches are distributed among these distances:
80 6 0.04
81 124 0.92
82 5 0.04
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (81 bp):
GTCATTTTACCCTATAGGGGCATCACAGTCATTTTACCTTATAGGGGTATTTCGATCATTTTACC
ATATAGGGGTATTTTG
Found at i:43112324 original size:27 final size:27
Alignment explanation
Indices: 43112067--43112324 Score: 175
Period size: 27 Copynumber: 9.6 Consensus size: 27
43112057 GGGACAAAAT
* * *
43112067 AGTCA-TTTACCCTACAGGGGCATTAC
1 AGTCATTTTACCCTATAGGGGTATTTC
* * * * *
43112093 GGTCATTTTACCTTACAGGGGCATTAC
1 AGTCATTTTACCCTATAGGGGTATTTC
* * * *
43112120 -GATCATTTTACCTTACAGGGGCATTATG
1 AG-TCATTTTACCCTATAGGGGTATT-TC
* **
43112148 A-TTATTTTACCCTATAGGGGTATCAC
1 AGTCATTTTACCCTATAGGGGTATTTC
* **
43112174 AGTCATTTTACCCTTTAAAGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTC
* *
43112201 -GACCATTTTACCAT-TCAGGGGTATTTC
1 AG-TCATTTTACCCTAT-AGGGGTATTTC
* * * * *
43112228 AGTCTTTTTACCCTTTGGGGGCATTTT
1 AGTCATTTTACCCTATAGGGGTATTTC
*
43112255 AGTCATTTTACCTTATAGGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTC
* *
43112282 GGTCATTTTACCCTATAGGGGTATTTT
1 AGTCATTTTACCCTATAGGGGTATTTC
* *
43112309 GGTCATTCTACCCTAT
1 AGTCATTTTACCCTAT
43112325 CAAGGTATTT
Statistics
Matches: 186, Mismatches: 37, Indels: 17
0.77 0.15 0.07
Matches are distributed among these distances:
26 8 0.04
27 176 0.95
28 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (27 bp):
AGTCATTTTACCCTATAGGGGTATTTC
Found at i:43112331 original size:27 final size:27
Alignment explanation
Indices: 43112256--43112339 Score: 98
Period size: 27 Copynumber: 3.1 Consensus size: 27
43112246 GGGCATTTTA
* * *
43112256 GTCATTTTACCTTATAGGGGTATTTCG
1 GTCATTCTACCCTATAGAGGTATTTCG
* * *
43112283 GTCATTTTACCCTATAGGGGTATTTTG
1 GTCATTCTACCCTATAGAGGTATTTCG
43112310 GTCATTCTACCCTATCA-AGGTATTTCG
1 GTCATTCTACCCTAT-AGAGGTATTTCG
43112337 GTC
1 GTC
43112340 CAGATATCGA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 50 0.98
28 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (27 bp):
GTCATTCTACCCTATAGAGGTATTTCG
Found at i:43112332 original size:54 final size:54
Alignment explanation
Indices: 43112220--43112339 Score: 143
Period size: 54 Copynumber: 2.2 Consensus size: 54
43112210 ACCATTCAGG
* * * * * * *
43112220 GGTATTTCAGTCTTTTTACCCTTTGGGGGCATTTTAGTCATTTTACCTTATAGG
1 GGTATTTCGGTCATTTTACCCTATAGGGGCATTTTAGTCATTCTACCCTATAGA
* *
43112274 GGTATTTCGGTCATTTTACCCTATAGGGGTATTTTGGTCATTCTACCCTATCA-A
1 GGTATTTCGGTCATTTTACCCTATAGGGGCATTTTAGTCATTCTACCCTAT-AGA
43112328 GGTATTTCGGTC
1 GGTATTTCGGTC
43112340 CAGATATCGA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 55 0.98
55 1 0.02
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.43
Consensus pattern (54 bp):
GGTATTTCGGTCATTTTACCCTATAGGGGCATTTTAGTCATTCTACCCTATAGA
Found at i:43116104 original size:27 final size:27
Alignment explanation
Indices: 43116045--43116116 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
43116035 TCCAAACTAA
43116045 TATAAAATGACTGTTATGCCTCCACGT
1 TATAAAATGACTGTTATGCCTCCACGT
** * *
43116072 GGTAAAATGGCTGTTATGCC-CCTATGT
1 TATAAAATGACTGTTATGCCTCC-ACGT
43116099 TATAAAATGACTG-TATGC
1 TATAAAATGACTGTTATGC
43116117 TTTATGTTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
26 7 0.19
27 30 0.81
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (27 bp):
TATAAAATGACTGTTATGCCTCCACGT
Found at i:43122160 original size:12 final size:12
Alignment explanation
Indices: 43122140--43122173 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
43122130 GTAATAAGGT
43122140 GGAGAGATTTTA
1 GGAGAGATTTTA
*
43122152 GGAGGGATTTTA
1 GGAGAGATTTTA
43122164 GGAGTAGATT
1 GGAG-AGATT
43122174 ATGGGATTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.29, C:0.00, G:0.38, T:0.32
Consensus pattern (12 bp):
GGAGAGATTTTA
Found at i:43122701 original size:27 final size:27
Alignment explanation
Indices: 43122642--43122703 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
43122632 CCCAAACTGA
* *
43122642 TATAAAGTGATTATTATGCCCCCACGT
1 TATAAAATGACTATTATGCCCCCACGT
** * *
43122669 GGTAAAATGACTATTATGCCCCTATGT
1 TATAAAATGACTATTATGCCCCCACGT
43122696 TATAAAAT
1 TATAAAAT
43122704 AATTGTATGC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (27 bp):
TATAAAATGACTATTATGCCCCCACGT
Found at i:43124099 original size:25 final size:25
Alignment explanation
Indices: 43124057--43124121 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 25
43124047 GCAACGGATT
*
43124057 CATGTTAGGGG-TGTGACAACACGAG
1 CATGTGAGGGGTTG-GACAACACGAG
* *
43124082 CATGTGAGGGGTTGG---ACATGGG
1 CATGTGAGGGGTTGGACAACACGAG
43124104 CATGTGAGGGGTTGGACA
1 CATGTGAGGGGTTGGACA
43124122 CAGGCATGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
22 20 0.61
25 11 0.33
26 2 0.06
ACGTcount: A:0.23, C:0.12, G:0.43, T:0.22
Consensus pattern (25 bp):
CATGTGAGGGGTTGGACAACACGAG
Found at i:43124109 original size:22 final size:22
Alignment explanation
Indices: 43124081--43124131 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
43124071 GACAACACGA
**
43124081 GCATGTGAGGGGTTGGACATGG
1 GCATGTGAGGGGTTGGACACAG
43124103 GCATGTGAGGGGTTGGACACAG
1 GCATGTGAGGGGTTGGACACAG
43124125 GCATGTG
1 GCATGTG
43124132 GAAACTGGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.12, G:0.47, T:0.22
Consensus pattern (22 bp):
GCATGTGAGGGGTTGGACACAG
Found at i:43128312 original size:21 final size:21
Alignment explanation
Indices: 43128286--43128342 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
43128276 AGCTAAGAAC
43128286 TGATAGGTAAATTTTCTTGCA
1 TGATAGGTAAATTTTCTTGCA
*
43128307 TGATAGGTAAATCTTCTTGCA
1 TGATAGGTAAATTTTCTTGCA
43128328 TGATAGGTAAATTTT
1 TGATAGGTAAATTTT
43128343 AACCATTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (21 bp):
TGATAGGTAAATTTTCTTGCA
Found at i:43128645 original size:8 final size:8
Alignment explanation
Indices: 43128632--43128656 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
43128622 AAATGTTGAT
43128632 AATTTTGG
1 AATTTTGG
43128640 AATTTTGG
1 AATTTTGG
43128648 AATTTTGG
1 AATTTTGG
43128656 A
1 A
43128657 TTTAGGAACT
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:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (8 bp):
AATTTTGG
Found at i:43128664 original size:15 final size:16
Alignment explanation
Indices: 43128632--43128664 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
43128622 AAATGTTGAT
*
43128632 AATTTTGGAATTTTGG
1 AATTTTGGAATTTAGG
43128648 AATTTTGG-ATTTAGG
1 AATTTTGGAATTTAGG
43128663 AA
1 AA
43128665 CTAAATTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
AATTTTGGAATTTAGG
Found at i:43138946 original size:357 final size:358
Alignment explanation
Indices: 43138284--43138999 Score: 1281
Period size: 357 Copynumber: 2.0 Consensus size: 358
43138274 TTGCAATCAC
* * * *
43138284 TGACACTGGAAAGTGTAGTGACAGTTTGAGCCAAGAAGCATTACAACAGAAGTTGAGTGAGGATT
1 TGACACTGGAAAGTGCAGTGACAGTGTGAGCCAACAAGCATTACAACAGAAGTTGAGTGAGGAAT
43138349 AGAGGAACTTAGTCCACTTGTTCTTAATAGTGCCGTATTGCCATCATCGAAAGGTGAGGTTAGTA
66 AGAGGAACTTAGTCCACTTGTTCTTAATAGTGCCGTATTGCCATCATCGAAAGGTGAGGTTAGTA
*
43138414 TGCATGTTTAAGTCTCAGATTAAATAGAGGAGTGATGCTGGGTAAGATATACATTGAACTTTATT
131 TGCATGTTTAAGTCTCAGATTAAACAGAGGAGTGATGCTGGGTAAGATATACATTGAACTTTATT
* *
43138479 GCTTCGGCAATCACCTATCCTTTTTATACCTTGTGAGCACTTTGTATTCTACTGAAGATTCATGT
196 GCTTCGACAATCACCTATCCTTTTTATACCTTGTGAGCACTTAGTATTCTACTGAAGATTCATGT
*
43138544 TGGGGATCTCATTTTATCATTATCATATTTTATTTTATATTTTTCAAGTTATTGCATTGACAACT
261 TGGGGATCTCAGTTTATCATTATCATATTTTATTTTATATTTTTCAAGTTATTGCATTGACAACT
43138609 ATTCTCACAATTTATCTTGTTTCCATCTAGTTG
326 ATTCTCACAATTTATCTTGTTTCCATCTAGTTG
43138642 TGACACTGGAAAGTGCAGTGACAGTGTGAGCCAACAAGCATTACAACAGAAGTTGAGTGAGGAAT
1 TGACACTGGAAAGTGCAGTGACAGTGTGAGCCAACAAGCATTACAACAGAAGTTGAGTGAGGAAT
* * * * *
43138707 AGAGGAATTTA-TCCACTTGTTTTTAATAGTGTCGTATTTCCATCATCGGAAGGTGAGGTTAGTA
66 AGAGGAACTTAGTCCACTTGTTCTTAATAGTGCCGTATTGCCATCATCGAAAGGTGAGGTTAGTA
43138771 TGCATGTTTAAGTCTCAGATTAAACAGAGGAGTGATGCTGGGTAAGATATACATTGAACTTTATT
131 TGCATGTTTAAGTCTCAGATTAAACAGAGGAGTGATGCTGGGTAAGATATACATTGAACTTTATT
* *
43138836 GCTTCGACAATCACCTATCCTTTTTATACCTTGTGAGCACTTAGTATTTTACTGAAGATTTATGT
196 GCTTCGACAATCACCTATCCTTTTTATACCTTGTGAGCACTTAGTATTCTACTGAAGATTCATGT
*
43138901 TGGGGATCTCAGTTTATCATTATCATATTTTATTTTATTTTTTTCAAGTTATTGCATTGACAACT
261 TGGGGATCTCAGTTTATCATTATCATATTTTATTTTATATTTTTCAAGTTATTGCATTGACAACT
43138966 ATTCTCACAATTTATCTTGTTTCCATCTAGTTG
326 ATTCTCACAATTTATCTTGTTTCCATCTAGTTG
43138999 T
1 T
43139000 TGCACCGACA
Statistics
Matches: 342, Mismatches: 16, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
357 271 0.79
358 71 0.21
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.37
Consensus pattern (358 bp):
TGACACTGGAAAGTGCAGTGACAGTGTGAGCCAACAAGCATTACAACAGAAGTTGAGTGAGGAAT
AGAGGAACTTAGTCCACTTGTTCTTAATAGTGCCGTATTGCCATCATCGAAAGGTGAGGTTAGTA
TGCATGTTTAAGTCTCAGATTAAACAGAGGAGTGATGCTGGGTAAGATATACATTGAACTTTATT
GCTTCGACAATCACCTATCCTTTTTATACCTTGTGAGCACTTAGTATTCTACTGAAGATTCATGT
TGGGGATCTCAGTTTATCATTATCATATTTTATTTTATATTTTTCAAGTTATTGCATTGACAACT
ATTCTCACAATTTATCTTGTTTCCATCTAGTTG
Found at i:43143980 original size:22 final size:22
Alignment explanation
Indices: 43143939--43143981 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
43143929 CATCCATTTG
*
43143939 AAGGAGGCACACACTCGTGTGA
1 AAGGAGGCACAAACTCGTGTGA
43143961 AAGGAGGCACAAAGCT-GTGTG
1 AAGGAGGCACAAA-CTCGTGTG
43143982 GCTAAGGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.33, C:0.19, G:0.35, T:0.14
Consensus pattern (22 bp):
AAGGAGGCACAAACTCGTGTGA
Found at i:43148033 original size:22 final size:22
Alignment explanation
Indices: 43148008--43148053 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
43147998 GGTAGCGAAA
* * *
43148008 TGCGAAGCAGTAGGCACCGTAG
1 TGCGAAGCAATAAGCACCATAG
*
43148030 TGCGAATCAATAAGCACCATAG
1 TGCGAAGCAATAAGCACCATAG
43148052 TG
1 TG
43148054 AAAACCCCGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (22 bp):
TGCGAAGCAATAAGCACCATAG
Found at i:43159564 original size:5 final size:5
Alignment explanation
Indices: 43159554--43159596 Score: 59
Period size: 5 Copynumber: 8.4 Consensus size: 5
43159544 TGACTCATTT
* *
43159554 TTTTA TTTTA TGTTA CTTTA TTTTA TTTTA TTTTA TCTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TT
43159597 GGGTTGTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:43173202 original size:20 final size:20
Alignment explanation
Indices: 43173177--43173225 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
43173167 TGAGTTATTT
*
43173177 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAATAAAC
*
43173197 AAGTAAG-AGAGTAAATAAAG
1 AAGTAAGCA-AGTAAATAAAC
43173217 AAG-AAGCAA
1 AAGTAAGCAA
43173226 AGACCATGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.59, C:0.06, G:0.22, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAATAAAC
Found at i:43190106 original size:26 final size:26
Alignment explanation
Indices: 43190077--43190137 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 26
43190067 AATTTACCAA
43190077 GGGTAAAATCATCAAAATTTTACTAG-
1 GGGTAAAATCATCAAAATTTTAC-AGT
*
43190103 GGGTAAAATCGTCAAAATTTTACAGT
1 GGGTAAAATCATCAAAATTTTACAGT
43190129 GGGTAAAAT
1 GGGTAAAAT
43190138 AGGTATGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
25 2 0.06
26 31 0.94
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.30
Consensus pattern (26 bp):
GGGTAAAATCATCAAAATTTTACAGT
Found at i:43194504 original size:39 final size:40
Alignment explanation
Indices: 43194300--43194522 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
43194290 TTGAATGCTG
* * * * * *
43194300 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
43194340 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
43194380 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
43194420 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
43194460 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
43194499 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
43194523 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 35 0.22
40 118 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:43194542 original size:79 final size:80
Alignment explanation
Indices: 43194375--43194557 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
43194365 GTGCGAGATA
* * *
43194375 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
43194440 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
43194455 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
43194519 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
43194534 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
43194558 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:43199732 original size:13 final size:13
Alignment explanation
Indices: 43199716--43199745 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
43199706 TTAATATAAC
*
43199716 ATATATAACTTAT
1 ATATATAAATTAT
43199729 ATATATAAATTAT
1 ATATATAAATTAT
43199742 ATAT
1 ATAT
43199746 CTCTTGACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATATAAATTAT
Found at i:43207482 original size:68 final size:68
Alignment explanation
Indices: 43207374--43207511 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
43207364 GGTAAGGGTG
43207374 GTATGTGTCATTTGTGGCATGTTTTAGTATGGAAACTAGTTAGTTGCTAAATGGTTAAATATGCA
1 GTATGTGTCATTTGTGGCATGTTTTAGTATGGAAACTAGTTAGTTGCTAAATGGTTAAATATGCA
43207439 TAT
66 TAT
43207442 GTATGTGTCATTTGTGGCATGTTTTAGTATGGAAACTAGTTAGTTGCTAAATGGTTAAATATGCA
1 GTATGTGTCATTTGTGGCATGTTTTAGTATGGAAACTAGTTAGTTGCTAAATGGTTAAATATGCA
43207507 TAT
66 TAT
43207510 GT
1 GT
43207512 TCAGGTATGT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (68 bp):
GTATGTGTCATTTGTGGCATGTTTTAGTATGGAAACTAGTTAGTTGCTAAATGGTTAAATATGCA
TAT
Found at i:43210482 original size:12 final size:13
Alignment explanation
Indices: 43210458--43210486 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
43210448 GGGCTATAAC
43210458 TATTGCATTTATT
1 TATTGCATTTATT
43210471 TATTGC-TTTATT
1 TATTGCATTTATT
43210483 TATT
1 TATT
43210487 CATCTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:43215102 original size:50 final size:50
Alignment explanation
Indices: 43215035--43215166 Score: 149
Period size: 50 Copynumber: 2.6 Consensus size: 50
43215025 TTTTGAGGTT
* * *
43215035 ATGAGAGCTCTCACGTAATACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGCTCTCACGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
* * * *
43215085 ATGAGAGGTCCTC-CGTAAGACCTTGTCTGGGACATGGCATGGGCACTGAT
1 ATGAGAGCT-CTCACGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
* * * *
43215135 ATGAGAACTCCCATGTAAGACCATATCTGGGA
1 ATGAGAGCTCTCACGTAAGACCATGTCTGGGA
43215167 TATGACATTG
Statistics
Matches: 67, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
49 2 0.03
50 62 0.93
51 3 0.04
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.23
Consensus pattern (50 bp):
ATGAGAGCTCTCACGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
Found at i:43215432 original size:20 final size:19
Alignment explanation
Indices: 43215407--43215454 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
43215397 TGAGTTATTT
43215407 AAGTAAGTATGTAACTAAAG
1 AAGTAAGTAT-TAACTAAAG
* *
43215427 AAGTAAGAGATTAAGTAAAG
1 AAGTAAG-TATTAACTAAAG
43215447 AAG-AAGTA
1 AAGTAAGTA
43215455 AAGATCATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.04
19 3 0.12
20 18 0.75
21 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.23, T:0.21
Consensus pattern (19 bp):
AAGTAAGTATTAACTAAAG
Found at i:43222640 original size:56 final size:50
Alignment explanation
Indices: 43222578--43222761 Score: 170
Period size: 50 Copynumber: 3.6 Consensus size: 50
43222568 GAGACCCTAT
* *
43222578 GTAAGACCATGTCTGGGACATGGCATTGACATTATTGAGGTTATGAGAGGTCTCAC
1 GTAAGACCATGTCTGGGACATGGCATTGAC---ATCGA-G--ATGAGAGGTCCCAC
* * * *
43222634 GTAAGACCATGTTTGGGACATGCCATTGGCATCGAGATGAGAGGTCCCCC
1 GTAAGACCATGTCTGGGACATGGCATTGACATCGAGATGAGAGGTCCCAC
* * * * ** *
43222684 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGACATCGAGATGAGAGGTCCCAC
* * *
43222734 GTAAGACCATATCTGGGATATGGAATTG
1 GTAAGACCATGTCTGGGACATGGCATTG
43222762 GCAGTACAGG
Statistics
Matches: 109, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
50 77 0.71
52 1 0.01
53 4 0.04
56 27 0.25
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTGACATCGAGATGAGAGGTCCCAC
Found at i:43222812 original size:49 final size:49
Alignment explanation
Indices: 43222634--43222813 Score: 166
Period size: 50 Copynumber: 3.6 Consensus size: 49
43222624 GAGGTCTCAC
* * * * ** **
43222634 GTAAGACCATGTTTGGGACATGCCATTGGCATCGAGATGAGAGGTCCCCC
1 GTAAGACCATGTCTGGGACATGGCATTGGCA-CGACAGGAGAACTCCCAT
* * *
43222684 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCA-CGACAGGAGAACTCCCAT
* * *
43222734 GTAAGACCATATCTGGGATATGGAATTGGCA-GTACAGGA-AACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACG-ACAGGAGAAC-TCCCAT
* *
43222783 GTAAGACCATGTCTGGTACATGGCTTTGGCA
1 GTAAGACCATGTCTGGGACATGGCATTGGCA
43222814 TGTTATTATC
Statistics
Matches: 108, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
48 4 0.04
49 36 0.33
50 68 0.63
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.23
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACGACAGGAGAACTCCCAT
Found at i:43223863 original size:30 final size:30
Alignment explanation
Indices: 43223822--43223885 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
43223812 TTGTTTACTT
43223822 ACTTGCGTATTTAAATAACTCATGATTATA
1 ACTTGCGTATTTAAATAACTCATGATTATA
*
43223852 ACTTGCTTATTTAAATAACTCATGATTATA
1 ACTTGCGTATTTAAATAACTCATGATTATA
43223882 ACTT
1 ACTT
43223886 CTCCTCCCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (30 bp):
ACTTGCGTATTTAAATAACTCATGATTATA
Found at i:43224189 original size:50 final size:50
Alignment explanation
Indices: 43224114--43224306 Score: 190
Period size: 50 Copynumber: 3.7 Consensus size: 50
43224104 TTTCCTGTAC
* * **
43224114 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACATCTCATATCGG
* * ** * *
43224164 TGCCCATGCCATGTCCAAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACATCTCATATCGG
* * **
43224214 TGCCAACGCCATGTCCTAGACATGGTGTTACATGGGACATCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACATCTCAT-A--TC---GG
43224270 TGCCAATGCCATGT-CTCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCT-AGACATGGTCTTACATGGGA
43224307 TCTCATCCCC
Statistics
Matches: 115, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
50 79 0.69
53 2 0.02
55 2 0.02
56 32 0.28
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACATCTCATATCGG
Found at i:43226839 original size:23 final size:22
Alignment explanation
Indices: 43226807--43226853 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
43226797 ACTTAGGAAA
*
43226807 TTCTTATTTTTATTTTTTGTTTT
1 TTCTTA-TTTTATTTTTAGTTTT
* *
43226830 TTCTTCTTTTCTTTTTAGTTTT
1 TTCTTATTTTATTTTTAGTTTT
43226852 TT
1 TT
43226854 AATTATTAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.06, C:0.09, G:0.04, T:0.81
Consensus pattern (22 bp):
TTCTTATTTTATTTTTAGTTTT
Found at i:43228847 original size:18 final size:17
Alignment explanation
Indices: 43228803--43228850 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
43228793 GGTTTATTGA
*
43228803 TTTAGTTCATTTGTTTAT
1 TTTAGTT-ATTTATTTAT
**
43228821 TTTTCTTATTTATATTAT
1 TTTAGTTATTTAT-TTAT
43228839 TTTAGTTATTTA
1 TTTAGTTATTTA
43228851 GTTTTCTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.21, C:0.04, G:0.06, T:0.69
Consensus pattern (17 bp):
TTTAGTTATTTATTTAT
Found at i:43228907 original size:3 final size:3
Alignment explanation
Indices: 43228899--43228979 Score: 162
Period size: 3 Copynumber: 27.0 Consensus size: 3
43228889 ATAGGGATTA
43228899 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
43228947 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
43228980 TAGACTTATT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ACT
Found at i:43230330 original size:45 final size:45
Alignment explanation
Indices: 43230281--43230499 Score: 287
Period size: 45 Copynumber: 4.9 Consensus size: 45
43230271 ATACCAGAAA
*
43230281 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACTATTCTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* * *
43230326 CGAGTAAGACCATGACTAAAAGACGTTATGGAATCACAATTCTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* * *
43230371 CAAGTAAGAACATGACTGAAAGACGTTATGGCATCACGATCCTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* * *
43230416 CGAGTATGACCATGACTGAATGACGTTATGGCATCACGATTTTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* * ***
43230461 CGGGTAAGACCAT-AGCTAAAAGACACAATGGCATCACGA
1 CGAGTAAGACCATGA-CTGAAAGACGTTATGGCATCACGA
43230500 ATAAAAGGAA
Statistics
Matches: 151, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
44 1 0.01
45 150 0.99
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (45 bp):
CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
Found at i:43230536 original size:135 final size:135
Alignment explanation
Indices: 43230281--43230538 Score: 304
Period size: 135 Copynumber: 1.9 Consensus size: 135
43230271 ATACCAGAAA
*
43230281 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACTATTCTATCGAGTAAGACCATGACTAAA
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGAGTAAGACCATGACTAAA
*** *** * **
43230346 AGACGTTATGGAATCACAATTCTATCAAGTAAGAACATGACTGAAAGACGTTATGGCATCACGAT
66 AGACACAATGGAATCACAATAAAAGCAAGTAAGAACATGACTGAAAGACACTATGGCATCACGAT
43230411 CCTAT
131 CCTAT
* * * *
43230416 CGAGTATGACCATGACTGAATGACGTTATGGCATCACGATTTTATCGGGTAAGACCAT-AGCTAA
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGAGTAAGACCATGA-CTAA
* * * ** *
43230480 AAGACACAATGGCATCACGAATAAAAGGAA-TAAGACCATGGGTGAAATACACTATGGCA
65 AAGACACAATGGAATCAC-AATAAAAGCAAGTAAGAACATGACTGAAAGACACTATGGCA
43230539 ACTCGACAGA
Statistics
Matches: 101, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
134 1 0.01
135 94 0.93
136 6 0.06
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.23
Consensus pattern (135 bp):
CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGAGTAAGACCATGACTAAA
AGACACAATGGAATCACAATAAAAGCAAGTAAGAACATGACTGAAAGACACTATGGCATCACGAT
CCTAT
Found at i:43230537 original size:45 final size:47
Alignment explanation
Indices: 43230465--43230584 Score: 127
Period size: 45 Copynumber: 2.6 Consensus size: 47
43230455 TTTTATCGGG
* * * *
43230465 TAAGACCATAGCTAAAAGACACAATGGCATCACGA-ATAAAA-GGAA
1 TAAGACCATGGCTGAAAGACACAATGGCAACACGACAGAAAACGGAA
* * * * *
43230510 TAAGACCATGGGTGAAATACACTATGGCAACTCGACAGAAAACTGAA
1 TAAGACCATGGCTGAAAGACACAATGGCAACACGACAGAAAACGGAA
* *
43230557 TAAGACCATGGTTGAAAGACACCATGGC
1 TAAGACCATGGCTGAAAGACACAATGGC
43230585 GCACTCCGAC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
45 28 0.46
46 5 0.08
47 28 0.46
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (47 bp):
TAAGACCATGGCTGAAAGACACAATGGCAACACGACAGAAAACGGAA
Found at i:43237472 original size:49 final size:47
Alignment explanation
Indices: 43237412--43237868 Score: 639
Period size: 47 Copynumber: 9.6 Consensus size: 47
43237402 GATAATTGTG
* *
43237412 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
43237459 ATGTGAAAGTGTATATACATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATAT--ATGTGATAAGGCCTAATGGCCGATGTGATGA
*
43237508 ATGTGAAAGTGTATATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG----TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
43237559 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
43237606 ATGTGAAAGTGTATATATATGTGATAAGGGCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
43237655 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
43237702 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * *
43237749 ATGTGAAAGTGTATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAG-GCCTAATGGCCGATGTGATGA
* * * * * *
43237796 ATGTGAAAGTGTATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAG-GCCTAATGGCCGATGTGATGA
*
43237843 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
43237869 TCCCGAAGGG
Statistics
Matches: 383, Mismatches: 17, Indels: 19
0.91 0.04 0.05
Matches are distributed among these distances:
46 2 0.01
47 245 0.64
48 2 0.01
49 88 0.23
51 41 0.11
53 5 0.01
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:43246251 original size:4 final size:4
Alignment explanation
Indices: 43246242--43246268 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
43246232 AAGTTTTATT
43246242 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
43246269 TACTTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:43255880 original size:31 final size:31
Alignment explanation
Indices: 43255821--43255916 Score: 183
Period size: 31 Copynumber: 3.1 Consensus size: 31
43255811 GGCAAATTAC
43255821 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
43255853 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
43255884 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
43255915 AA
1 AA
43255917 ATTATCTAAG
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 44 0.69
32 20 0.31
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:43258951 original size:55 final size:54
Alignment explanation
Indices: 43258890--43259065 Score: 203
Period size: 55 Copynumber: 3.2 Consensus size: 54
43258880 GAGATTGGCG
* *
43258890 CTAAGTGTGCGGGTTTAAATTGTGCAGCACTAAGTGTGC-AATTGAATATGTAGCA
1 CTAAGTGTGCGAGTTT-AATTGTG-AGCACTAAGTGTGCGAGTTGAATATGTAGCA
* *
43258945 CTAAGTGTGCGAGTTTGACTATGT-AGCACTAAGTGTGCGAGTTGACTATGTAGCA
1 CTAAGTGTGCGAGTTT-AAT-TGTGAGCACTAAGTGTGCGAGTTGAATATGTAGCA
* * * * *
43259000 CTAAGTGTGCGAGTATGATTATGTAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAATTGTG-AGCACTAAGTGTGCGAGTTGAATATGTAGCA
*
43259055 CTGAGTGTGCG
1 CTAAGTGTGCG
43259066 GACTTAATAA
Statistics
Matches: 105, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
53 2 0.02
54 15 0.14
55 85 0.81
56 3 0.03
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (54 bp):
CTAAGTGTGCGAGTTTAATTGTGAGCACTAAGTGTGCGAGTTGAATATGTAGCA
Found at i:43258997 original size:27 final size:27
Alignment explanation
Indices: 43258915--43259065 Score: 223
Period size: 28 Copynumber: 5.6 Consensus size: 27
43258905 TAAATTGTGC
* *
43258915 AGCACTAAGTGTGC-AATTGAATATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
43258941 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
43258969 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
43258996 AGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGT-TGACTATGT
* *
43259024 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
43259051 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43259066 GACTTAATAA
Statistics
Matches: 117, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
26 14 0.12
27 51 0.44
28 52 0.44
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:43266945 original size:27 final size:27
Alignment explanation
Indices: 43266907--43267058 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
43266897 TAAATTGTGC
* *
43266907 AGCACTAAGTGTGCGAATTGAATATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
43266934 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
43266962 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
43266989 AGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGT-TGACTATGT
* *
43267017 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
43267044 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43267059 GACTTAATAA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:43266964 original size:28 final size:28
Alignment explanation
Indices: 43266879--43267058 Score: 224
Period size: 27 Copynumber: 6.5 Consensus size: 28
43266869 CATGAGATTG
* *
43266879 GCACTAAGTGTGCGGGTTTAAAT-TGTGCA
1 GCACTAAGTGTGCGAGTTTGAATATGT--A
*
43266908 GCACTAAGTGTGCGA-ATTGAATATGTA
1 GCACTAAGTGTGCGAGTTTGAATATGTA
*
43266935 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAGTTTGAATATGTA
*
43266963 GCACTAAGTGTGCGAG-TTGACTATGTA
1 GCACTAAGTGTGCGAGTTTGAATATGTA
* *
43266990 GCACTAAGTGTGCGAGTATGATTATGTA
1 GCACTAAGTGTGCGAGTTTGAATATGTA
* *
43267018 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGAATATGTA
*
43267045 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
43267059 GACTTAATAA
Statistics
Matches: 138, Mismatches: 10, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
27 65 0.47
28 56 0.41
29 17 0.12
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGAATATGTA
Found at i:43266975 original size:55 final size:55
Alignment explanation
Indices: 43266879--43267058 Score: 245
Period size: 55 Copynumber: 3.3 Consensus size: 55
43266869 CATGAGATTG
* * *
43266879 GCACTAAGTGTGCGGGTTTAAAT-TGTGCAGCACTAAGTGTGCGAATTGAATATGTA
1 GCACTAAGTGTGCGAGTTTGAATATGT--AGCACTAAGTGTGCGAGTTGAATATGTA
* *
43266935 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGTA
1 GCACTAAGTGTGCGAGTTTGAATATGTAGCACTAAGTGTGCGAGTTGAATATGTA
* * * *
43266990 GCACTAAGTGTGCGAGTATGATTATGTAGCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGAATATGTAGCACTAAGTGTGCGAGTTGAATATGTA
*
43267045 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
43267059 GACTTAATAA
Statistics
Matches: 113, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
55 90 0.80
56 20 0.18
57 3 0.03
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (55 bp):
GCACTAAGTGTGCGAGTTTGAATATGTAGCACTAAGTGTGCGAGTTGAATATGTA
Found at i:43269261 original size:21 final size:21
Alignment explanation
Indices: 43269257--43269356 Score: 80
Period size: 22 Copynumber: 4.7 Consensus size: 21
43269247 GCTTTTTTGC
43269257 TTTTTGCTTTTTTTTTTTGCGC-
1 TTTTTGCTTTT--TTTTTGCGCT
* *
43269279 TTTTTACTCTCTTTTTTGCGCT
1 TTTTTGCT-TTTTTTTTGCGCT
*
43269301 TTTTACT-CTTTTTTTTTACGCT
1 TTTT--TGCTTTTTTTTTGCGCT
**
43269323 TTTTTGCTTTTTTTTTG-TTT
1 TTTTTGCTTTTTTTTTGCGCT
*
43269343 TTTTTGCTATTTTT
1 TTTTTGCTTTTTTT
43269357 ACTGTTTTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
20 15 0.23
21 19 0.29
22 26 0.40
23 4 0.06
24 1 0.02
ACGTcount: A:0.04, C:0.14, G:0.09, T:0.73
Consensus pattern (21 bp):
TTTTTGCTTTTTTTTTGCGCT
Found at i:43269280 original size:15 final size:15
Alignment explanation
Indices: 43269235--43269283 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
43269225 GGTAGGCAAC
43269235 TTTTTTTTTTGCGCT
1 TTTTTTTTTTGCGCT
43269250 TTTTTGCTTTTT--GCT
1 TTTTT--TTTTTGCGCT
43269265 TTTTTTTTTTGCGCT
1 TTTTTTTTTTGCGCT
43269280 TTTT
1 TTTT
43269284 ACTCTCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 5 0.17
15 20 0.67
17 5 0.17
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.76
Consensus pattern (15 bp):
TTTTTTTTTTGCGCT
Found at i:43269364 original size:20 final size:19
Alignment explanation
Indices: 43269312--43269373 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
43269302 TTTACTCTTT
*
43269312 TTTTTTAC-GCTTTTTTGC
1 TTTTTTACTGTTTTTTTGC
**
43269330 TTTTTTTTTGTTTTTTTTGC
1 TTTTTTACTG-TTTTTTTGC
43269350 TATTTTTACTGTTTTTTTGC
1 T-TTTTTACTGTTTTTTTGC
43269370 TTTT
1 TTTT
43269374 ATTTAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 6 0.17
19 4 0.11
20 19 0.53
21 7 0.19
ACGTcount: A:0.05, C:0.10, G:0.10, T:0.76
Consensus pattern (19 bp):
TTTTTTACTGTTTTTTTGC
Found at i:43269980 original size:32 final size:32
Alignment explanation
Indices: 43269913--43270008 Score: 169
Period size: 31 Copynumber: 3.1 Consensus size: 32
43269903 GGCAAATTAC
*
43269913 AAGAGTAATTGAATCCTAATAAAAA-TCTTTC
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
43269944 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
43269976 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
43270007 AA
1 AA
43270009 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 38 0.60
32 25 0.40
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:43271175 original size:20 final size:19
Alignment explanation
Indices: 43271150--43271212 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 19
43271140 TAAATATCTT
43271150 TAATATTATTAATAATTTGA
1 TAATATTATTAATAATTT-A
*
43271170 TAATA-T-TTAAT-ATATAA
1 TAATATTATTAATAAT-TTA
* *
43271187 TGATATTATTTATAATTTA
1 TAATATTATTAATAATTTA
43271206 T-ATATTA
1 TAATATTA
43271213 ATTTTTATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 7 0.20
18 13 0.37
19 8 0.23
20 7 0.20
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (19 bp):
TAATATTATTAATAATTTA
Found at i:43272805 original size:10 final size:10
Alignment explanation
Indices: 43272790--43272814 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
43272780 TTTATAGTTC
43272790 ATTTTGATTA
1 ATTTTGATTA
43272800 ATTTTGATTA
1 ATTTTGATTA
43272810 ATTTT
1 ATTTT
43272815 TACTATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (10 bp):
ATTTTGATTA
Found at i:43281146 original size:226 final size:226
Alignment explanation
Indices: 43280752--43281432 Score: 1328
Period size: 226 Copynumber: 3.0 Consensus size: 226
43280742 TAAAATAGGG
43280752 TCATACGACCATGTGGCTAGGCCA-GTTAAAGCAAGGTTACATGGTCATGTTGCCAAGTCCTATA
1 TCATACGACCATGTGGCTAGGCCATG-TAAAGCAAGGTTACATGGTCATGTTGCCAAGTCCTATA
*
43280816 ACAAACTGTGGTCGTGTGGACTTAAATGTAAAATCCTACAAAAATTCGCACGGCCATATCGCCAA
65 ACAAACTGTGGTCGTGTGGACTTAAATGTAAAATCCTACAAACATTCGCACGGCCATATCGCCAA
43280881 GCCATGTGAGAGACTGTAATCAAGTTTAACCCAAACCACTATTATAATACAGAGCACATGGACAT
130 GCCATGTGAGAGACTGTAATCAAGTTTAACCCAAACCACTATTATAATACAGAGCACATGGACAT
43280946 GTCACTTGCCTGTGTGTGAGAAAATATGCCTT
195 GTCACTTGCCTGTGTGTGAGAAAATATGCCTT
43280978 TCATACGACCATGTGGCTAGGCCATGTAAAGCAAGGTTACATGGTCATGTTGCCAAGTCCTATAA
1 TCATACGACCATGTGGCTAGGCCATGTAAAGCAAGGTTACATGGTCATGTTGCCAAGTCCTATAA
43281043 CAAACTGTGGTCGTGTGGACTTAAATGTAAAATCCTACAAACATTCGCACGGCCATATCGCCAAG
66 CAAACTGTGGTCGTGTGGACTTAAATGTAAAATCCTACAAACATTCGCACGGCCATATCGCCAAG
43281108 CCATGTGAGAGACTGTAATCAAGTTTAACCCAAACCACTATTATAATACAGAGCACATGGACATG
131 CCATGTGAGAGACTGTAATCAAGTTTAACCCAAACCACTATTATAATACAGAGCACATGGACATG
43281173 TCACTTGCCTGTGTGTGAGAAAATATGCCTT
196 TCACTTGCCTGTGTGTGAGAAAATATGCCTT
*
43281204 TCATACGACTATGTGGCTAGGCCATGTAAAGCAAGGTTACATGGTCATGTTGCCAAGTCCTATAA
1 TCATACGACCATGTGGCTAGGCCATGTAAAGCAAGGTTACATGGTCATGTTGCCAAGTCCTATAA
43281269 CAAACTGTGGTCGTGTGGACTTAAATGTAAAATCCTACAAACATTCGCACGGCCATATCGCCAAG
66 CAAACTGTGGTCGTGTGGACTTAAATGTAAAATCCTACAAACATTCGCACGGCCATATCGCCAAG
43281334 CCATGTGAGAGACTGTAATCAAGTTTAACCCAAACCACTATTATAATACAGAGCACATGGACATG
131 CCATGTGAGAGACTGTAATCAAGTTTAACCCAAACCACTATTATAATACAGAGCACATGGACATG
43281399 TCACTTGCCTGTGTGTGAGAAAATATGCCTT
196 TCACTTGCCTGTGTGTGAGAAAATATGCCTT
43281430 TCA
1 TCA
43281433 AATCAAGTCA
Statistics
Matches: 452, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
226 451 1.00
227 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (226 bp):
TCATACGACCATGTGGCTAGGCCATGTAAAGCAAGGTTACATGGTCATGTTGCCAAGTCCTATAA
CAAACTGTGGTCGTGTGGACTTAAATGTAAAATCCTACAAACATTCGCACGGCCATATCGCCAAG
CCATGTGAGAGACTGTAATCAAGTTTAACCCAAACCACTATTATAATACAGAGCACATGGACATG
TCACTTGCCTGTGTGTGAGAAAATATGCCTT
Found at i:43290318 original size:7 final size:6
Alignment explanation
Indices: 43290279--43290348 Score: 76
Period size: 6 Copynumber: 12.0 Consensus size: 6
43290269 GACCCCTTCT
* *
43290279 ATTAAA A-T-AA A-TAAA ACTAAT ATTAAA ATTAAA GATTAAA GATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA -ATTAAA -ATTAAA
43290326 A-TAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA
43290349 GACAAAGATA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
4 4 0.07
5 9 0.16
6 31 0.54
7 13 0.23
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (6 bp):
ATTAAA
Found at i:43290363 original size:6 final size:7
Alignment explanation
Indices: 43290300--43290367 Score: 71
Period size: 6 Copynumber: 10.9 Consensus size: 7
43290290 TAAAACTAAT
43290300 ATTAAA-
1 ATTAAAG
43290306 ATTAAAG
1 ATTAAAG
43290313 ATTAAAG
1 ATTAAAG
43290320 ATTAAA-
1 ATTAAAG
43290326 A-TAAA-
1 ATTAAAG
43290331 ATTAAA-
1 ATTAAAG
43290337 ATTAAA-
1 ATTAAAG
43290343 ATTAAAG
1 ATTAAAG
*
43290350 A-CAAAG
1 ATTAAAG
43290356 A-TAAAG
1 ATTAAAG
43290362 ATTAAA
1 ATTAAA
43290368 ATGAGAAATA
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
5 5 0.09
6 33 0.59
7 18 0.32
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.26
Consensus pattern (7 bp):
ATTAAAG
Found at i:43290369 original size:37 final size:37
Alignment explanation
Indices: 43290287--43290357 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
43290277 CTATTAAAAT
* * *
43290287 AAATAAAACTAATATTAAAATTAAAGATTAAAGATTA
1 AAATAAAATTAAAATTAAAATTAAAGATCAAAGATTA
43290324 AAATAAAATTAAAATTAAAATTAAAGA-CAAAGAT
1 AAATAAAATTAAAATTAAAATTAAAGATCAAAGAT
43290358 AAAGATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 6 0.19
37 25 0.81
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.27
Consensus pattern (37 bp):
AAATAAAATTAAAATTAAAATTAAAGATCAAAGATTA
Found at i:43299626 original size:339 final size:341
Alignment explanation
Indices: 43298968--43299628 Score: 874
Period size: 339 Copynumber: 1.9 Consensus size: 341
43298958 GGATGATTAG
* *
43298968 GTAACATTTAACGTCTTTAAGTCTATGTAGTTTCTTGACACAATAGATGATTGCTCTGCAGTGTC
1 GTAACATTTAACGTCTTTAAGTCTATGGAGTTTCCTGACACAATAGATGATTGCTCTGCAGTGTC
* * *
43299033 CAATTTAGAGGATTTAATAGTGGAGAAGGAACTAAACTATGTTGAGGACCCACTGGAAAGAATTT
66 CAATTTAGAGGAATTAATAATGGAAAAGGAACTAAACTATGTTGAGGACCCACTGGAAAGAATTT
** * *
43299098 TGACATTGGATCCTCCAAATGATGAAGAGGAGGATGAATACTTAGCTTTGCTAGAAGCTAATCAA
131 TGACATCAGACCCTCCAAATGATGAAGAGGAGGATGAATACTTAGCTTTGCTAGAAGATAATCAA
* * * *
43299163 AGGGGATTTAATCCACAATCCTGTTTTGAATCTTTGGAGTTAGAAAAGATGGACTATTCTCAACC
196 AGCGGATTTAATCCACAATCCCGTTTTGAATCTTTGGAGTTAGAAAAGAGGGACTATCCTCAACC
* * * *
43299228 AAAAGCATCGATCAAAGAGCCATCTAAATTAGAACTCAAGGTATTACCTTCTCATTTAAAATGCG
261 AAAAGCATCAATCAAAGAGCCAACTAAATTAGAACTCAAAGTATTACCCTCTCATTTAAAATGCG
43299293 TATTCAGGACGACCAA
326 TATTCAGGACGACCAA
* * * * * *
43299309 GTAACATTTAATGTTTTTAAGTC-ATGCGA-TTTCCTGACACAATTGATTATTGTTCTGTAGTGT
1 GTAACATTTAACGTCTTTAAGTCTATG-GAGTTTCCTGACACAATAGATGATTGCTCTGCAGTGT
* * *
43299372 CTAATTTAGAGGAATTAATAATGGAAAAGGAACTCAACTATGTTGAGGACCCA-TTGAACA-AAT
65 CCAATTTAGAGGAATTAATAATGGAAAAGGAACTAAACTATGTTGAGGACCCACTGGAA-AGAAT
*
43299435 TTTGACATCAGACCCTCCGAATGATGAAGAGGAGGATGAATACTTAGCTTTGCTAGAAGATAATC
129 TTTGACATCAGACCCTCCAAATGATGAAGAGGAGGATGAATACTTAGCTTTGCTAGAAGATAATC
* * *
43299500 AAAGCGGATTTAATCTACAATCCCGTTTTGAATCTTTGGAGTTA-AAGAATAGGGATTATGCCT-
194 AAAGCGGATTTAATCCACAATCCCGTTTTGAATCTTTGGAGTTAGAA-AAGAGGGACTAT-CCTC
* * * *
43299563 AACCAAAAG-AGTCAATCGAGGAG-CAACATAAATTAGAATTGAAAGTACTT-CCCTCAT-ATTT
257 AACCAAAAGCA-TCAATCAAAGAGCCAAC-TAAATTAGAACTCAAAGTA-TTACCCTC-TCATTT
43299624 AAAAT
318 AAAAT
43299629 ATGTTTATTT
Statistics
Matches: 278, Mismatches: 34, Indels: 18
0.84 0.10 0.05
Matches are distributed among these distances:
338 6 0.02
339 164 0.59
340 86 0.31
341 22 0.08
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (341 bp):
GTAACATTTAACGTCTTTAAGTCTATGGAGTTTCCTGACACAATAGATGATTGCTCTGCAGTGTC
CAATTTAGAGGAATTAATAATGGAAAAGGAACTAAACTATGTTGAGGACCCACTGGAAAGAATTT
TGACATCAGACCCTCCAAATGATGAAGAGGAGGATGAATACTTAGCTTTGCTAGAAGATAATCAA
AGCGGATTTAATCCACAATCCCGTTTTGAATCTTTGGAGTTAGAAAAGAGGGACTATCCTCAACC
AAAAGCATCAATCAAAGAGCCAACTAAATTAGAACTCAAAGTATTACCCTCTCATTTAAAATGCG
TATTCAGGACGACCAA
Found at i:43303406 original size:8 final size:8
Alignment explanation
Indices: 43303393--43303430 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
43303383 AATTTTAATT
43303393 TTATTTAA
1 TTATTTAA
43303401 TTATTTAA
1 TTATTTAA
43303409 TT-TTTAAA
1 TTATTT-AA
43303417 GTTATTTAA
1 -TTATTTAA
43303426 TTATT
1 TTATT
43303431 AATGTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 3 0.11
8 17 0.63
9 4 0.15
10 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (8 bp):
TTATTTAA
Found at i:43303449 original size:24 final size:25
Alignment explanation
Indices: 43303397--43303449 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
43303387 TTAATTTTAT
*
43303397 TTAATTATTTAATTTTTAAAGTTAT
1 TTAATTATTTAATTTTTAAAGTTAA
*
43303422 TTAATTA-TTAATGTTTTATA-TTAA
1 TTAATTATTTAAT-TTTTAAAGTTAA
43303446 TTAA
1 TTAA
43303450 ATTTTTGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
TTAATTATTTAATTTTTAAAGTTAA
Found at i:43303452 original size:25 final size:25
Alignment explanation
Indices: 43303393--43303452 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
43303383 AATTTTAATT
*
43303393 TTATTTAATTATTTAATTTTTAAAG
1 TTATTAAATTATTTAATTTTTAAAG
* *
43303418 TTATTTAATTA-TTAATGTTTTATA-
1 TTATTAAATTATTTAAT-TTTTAAAG
43303442 TTAATTAAATT
1 TT-ATTAAATT
43303453 TTTGTGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (25 bp):
TTATTAAATTATTTAATTTTTAAAG
Found at i:43304332 original size:3 final size:3
Alignment explanation
Indices: 43304324--43304354 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
43304314 GAGGATCCTA
43304324 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
43304355 TCCCACAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:43310185 original size:51 final size:52
Alignment explanation
Indices: 43310072--43310196 Score: 175
Period size: 51 Copynumber: 2.4 Consensus size: 52
43310062 TGACTCAAAT
*
43310072 GTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCACAAGT
1 GTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCACAAGG
* * *
43310124 GTAGTGCTATGTGAAGGCCACTTTGTGAAG-AAGGTAGCTTTGG-CTACAAGG
1 GTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTC-ACAAGG
43310175 GTGGTACTATGTGCAA-GCCACT
1 GTGGTACTATGTG-AAGGCCACT
43310197 GGGTATCTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
50 1 0.02
51 34 0.52
52 30 0.46
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.28
Consensus pattern (52 bp):
GTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCACAAGG
Found at i:43312709 original size:30 final size:30
Alignment explanation
Indices: 43312675--43312750 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
43312665 TGGTTGACCC
* * *
43312675 ATCCCTTTTCATAATTCGATAACTAAAGTT
1 ATCCCTTTTCATAATTCGACAACCAAAGCT
*
43312705 ATCCCTTTTCATAGTTCGACAACCAAAGCT
1 ATCCCTTTTCATAATTCGACAACCAAAGCT
43312735 ATCCCTTTTCATAATT
1 ATCCCTTTTCATAATT
43312751 TGATGGTGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGACAACCAAAGCT
Found at i:43312891 original size:120 final size:119
Alignment explanation
Indices: 43312663--43312924 Score: 314
Period size: 120 Copynumber: 2.2 Consensus size: 119
43312653 GTAATAATAT
* *
43312663 GATGGTTGAC-CCATCCCTTTTCATAATTCGATAACTAAAGTTATCCCTTTTCATAGTTCGACAA
1 GATGGTTGTCACCATCCCTTTTCATAATTCGATAACTAAAGCTATCCCTTTTCATAGTTCGACAA
** * * *
43312727 CCAAAGCTATCCCTTTTCATAATTTGATGGTGGTCACCTTCCCTTTTCATTGTTC
66 CCAAAGCTATCCCTTTTCATAATTCAATAGTGG-CACCATCCCTTTTCATAGTTC
* * * * * *
43312782 GATGGTTGTCACCATGCCTTTTTATAATTTGATAGCTGAAGCTATCCC-TTTCTATAGTTCGATA
1 GATGGTTGTCACCATCCCTTTTCATAATTCGATAACTAAAGCTATCCCTTTTC-ATAGTTCGACA
* * *
43312846 GCCGAAGCTATCCCTTTTCATAGTTCAATAGTCGG-AGCCATCCCTTTTCATAGTTC
65 ACCAAAGCTATCCCTTTTCATAATTCAATAGT-GGCA-CCATCCCTTTTCATAGTTC
*
43312902 GATGGTCGTCACCATCCCTTTTC
1 GATGGTTGTCACCATCCCTTTTC
43312925 TTTGTTGATG
Statistics
Matches: 120, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 14 0.12
120 104 0.87
121 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (119 bp):
GATGGTTGTCACCATCCCTTTTCATAATTCGATAACTAAAGCTATCCCTTTTCATAGTTCGACAA
CCAAAGCTATCCCTTTTCATAATTCAATAGTGGCACCATCCCTTTTCATAGTTC
Found at i:43312942 original size:29 final size:30
Alignment explanation
Indices: 43312735--43312956 Score: 150
Period size: 30 Copynumber: 7.4 Consensus size: 30
43312725 AACCAAAGCT
* * *
43312735 ATCCCTTTTCATAATTTGATGGTGGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* * *
43312765 TTCCCTTTTCATTGTTCGATGGTTGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* * * * * * *
43312795 ATGCCTTTTTATAATTTGATAG-C-TGAAGCT
1 ATCCCTTTTCATAGTTCGATGGTCGT-CA-CC
* * * *
43312825 ATCCC-TTTCTATAGTTCGATAGCCG-AAGCT
1 ATCCCTTTTC-ATAGTTCGATGGTCGTCA-CC
* * *
43312855 ATCCCTTTTCATAGTTCAATAGTCG-GAGCC
1 ATCCCTTTTCATAGTTCGATGGTCGTCA-CC
43312885 ATCCCTTTTCATAGTTCGATGGTCGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* *
43312915 ATCCCTTTTCTTTGTT-GATGGTCGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
*
43312944 ATCCCTTTGCATA
1 ATCCCTTTTCATA
43312957 ATCTATAGCC
Statistics
Matches: 154, Mismatches: 31, Indels: 15
0.77 0.16 0.08
Matches are distributed among these distances:
28 1 0.01
29 27 0.18
30 120 0.78
31 6 0.04
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (30 bp):
ATCCCTTTTCATAGTTCGATGGTCGTCACC
Found at i:43318877 original size:7 final size:6
Alignment explanation
Indices: 43318827--43318953 Score: 53
Period size: 6 Copynumber: 20.3 Consensus size: 6
43318817 AAGTTGTAAT
* * * * **
43318827 AAAATA AAAA-A AGAAGA AAAAGA AAAGGC AAGTGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
* * * * *
43318874 AAAA-A AGAGAATGA AAATGAGA AAAAGA AAAAG- AGAAGT GAGAGA AAACGA
1 AAAAGA A-A-AA-GA AAA--AGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
*
43318925 AAACGA AAAAGA GAAAATTGA AAAAGA AA
1 AAAAGA AAAAGA -AAAA--GA AAAAGA AA
43318954 TTGAGATTGA
Statistics
Matches: 92, Mismatches: 18, Indels: 22
0.70 0.14 0.17
Matches are distributed among these distances:
5 10 0.11
6 60 0.65
7 7 0.08
8 10 0.11
9 5 0.05
ACGTcount: A:0.71, C:0.02, G:0.21, T:0.06
Consensus pattern (6 bp):
AAAAGA
Found at i:43318879 original size:27 final size:26
Alignment explanation
Indices: 43318834--43318953 Score: 77
Period size: 27 Copynumber: 4.3 Consensus size: 26
43318824 AATAAAATAA
*
43318834 AAAAAGAAGAAA-AAGAAAAG-GCAAGTG
1 AAAAAGAA-AAAGAAAAAAAGAG-AA-TG
43318861 AAAAAGAAAAAGAAAAAAAGAGAATG
1 AAAAAGAAAAAGAAAAAAAGAGAATG
43318887 AAAATGAGAAAAAG--AAAAAGAGAAGTGAG
1 AAAA--AGAAAAAGAAAAAAAGAGAA-T--G
* * *
43318916 AGAAAACGAAAACGAAAAAGAGAAAATTG
1 A-AAAA-GAAAAAGAAAAAAAGAGAA-TG
43318945 AAAAAGAAA
1 AAAAAGAAA
43318954 TTGAGATTGA
Statistics
Matches: 77, Mismatches: 5, Indels: 22
0.74 0.05 0.21
Matches are distributed among these distances:
26 19 0.25
27 22 0.29
28 14 0.18
29 10 0.13
30 3 0.04
31 9 0.12
ACGTcount: A:0.70, C:0.03, G:0.23, T:0.05
Consensus pattern (26 bp):
AAAAAGAAAAAGAAAAAAAGAGAATG
Found at i:43318880 original size:14 final size:14
Alignment explanation
Indices: 43318861--43318910 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
43318851 AAGGCAAGTG
43318861 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
* *
43318875 AAAAAGAGAATGAA
1 AAAAAGAAAAAGAA
**
43318889 AATGAGAAAAAGAA
1 AAAAAGAAAAAGAA
*
43318903 AAAGAGAA
1 AAAAAGAA
43318911 GTGAGAGAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (14 bp):
AAAAAGAAAAAGAA
Found at i:43318906 original size:26 final size:25
Alignment explanation
Indices: 43318840--43318953 Score: 90
Period size: 29 Copynumber: 4.2 Consensus size: 25
43318830 ATAAAAAAAG
43318840 AAGAAAAAG-AAAAG-GCAAGTGAAA
1 AAGAAAAAGAAAAAGAG-AAGTGAAA
43318864 AAGAAAAAGAAAAAAAGAGAA-TGAAA
1 AAGAAAAAG--AAAAAGAGAAGTGAAA
43318890 ATGAGAAAAAGAAAAAGAGAAGTGAGAGAA
1 A--AGAAAAAGAAAAAGAGAAGT--GA-AA
* *
43318920 AACGAAAACGAAAAAGAGAAAATTGAAA
1 AA-GAAAAAGAAAAAGAG--AAGTGAAA
43318948 AAGAAA
1 AAGAAA
43318954 TTGAGATTGA
Statistics
Matches: 75, Mismatches: 2, Indels: 23
0.75 0.02 0.23
Matches are distributed among these distances:
24 9 0.12
26 16 0.21
27 12 0.16
28 14 0.19
29 18 0.24
30 3 0.04
31 3 0.04
ACGTcount: A:0.69, C:0.03, G:0.23, T:0.05
Consensus pattern (25 bp):
AAGAAAAAGAAAAAGAGAAGTGAAA
Found at i:43318959 original size:21 final size:20
Alignment explanation
Indices: 43318860--43318959 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
43318850 AAAGGCAAGT
* *
43318860 GAAAAAGAAAAAGAAAAAAA
1 GAAAAAGAAAATGAGAAAAA
* *
43318880 GAGAATGAAAATGAGAAAAA
1 GAAAAAGAAAATGAGAAAAA
*
43318900 GAAAAAGAGAAGTGAGAGAAAA
1 GAAAAAGA-AAATGAGA-AAAA
* * *
43318922 CGAAAACGAAAAAGAGAAAATT
1 -GAAAAAGAAAATGAGAAAA-A
*
43318944 GAAAAAGAAATTGAGA
1 GAAAAAGAAAATGAGA
43318960 TTGAGAAAGG
Statistics
Matches: 62, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
20 22 0.35
21 23 0.37
22 10 0.16
23 7 0.11
ACGTcount: A:0.68, C:0.02, G:0.23, T:0.07
Consensus pattern (20 bp):
GAAAAAGAAAATGAGAAAAA
Found at i:43323010 original size:40 final size:40
Alignment explanation
Indices: 43322955--43323181 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
43322945 GAATGATATT
* *
43322955 CGGGCTAAGTCCCGAAGGCAATTATGCTAGTGATTTTATC
1 CGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATC
* * * * *
43322995 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATACC
1 CGGGCTAAGACCCGAAGGCAATTGTGCTAG-TGATTTTATC
*
43323035 CGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATC
1 CGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATC
*
43323075 CGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATC
1 CGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATC
* * *
43323115 CGGGCTAAGA-CCGAAGGCATTTGTGCGAGTTGA-TATATC
1 CGGGCTAAGACCCGAAGGCAATTGTGCTAG-TGATTTTATC
* *
43323154 CGAGCTAAGACCCGAAGGCATTTGTGCT
1 CGGGCTAAGACCCGAAGGCAATTGTGCT
43323182 TGTGGTTATA
Statistics
Matches: 164, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
39 33 0.20
40 129 0.79
41 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
CGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATC
Found at i:43323179 original size:119 final size:120
Alignment explanation
Indices: 43322955--43323181 Score: 375
Period size: 119 Copynumber: 1.9 Consensus size: 120
43322945 GAATGATATT
*
43322955 CGGGCTAAGTCCCGAAGGCAATTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTGT
1 CGGGCTAAGACCCGAAGGCAATTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTGT
* * *
43323020 GCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATC
66 GCGAGTTGATATACCCGAGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATC
* *
43323075 CGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGA-CCGAAGGCATTTGT
1 CGGGCTAAGACCCGAAGGCAATTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTGT
* *
43323139 GCGAGTTGATATATCCGAGCTAAGACCCGAAGGCATTTGTGCT
66 GCGAGTTGATATACCCGAGCTAAGACCCGAAGGCAATTGTGCT
43323182 TGTGGTTATA
Statistics
Matches: 99, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
119 52 0.53
120 47 0.47
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (120 bp):
CGGGCTAAGACCCGAAGGCAATTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTGT
GCGAGTTGATATACCCGAGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATC
Done.