Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold7
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: 6555642
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 349864 characters in sequence are not A, C, G, or T
File 19 of 37
Found at i:3339233 original size:79 final size:78
Alignment explanation
Indices: 3339142--3339427 Score: 437
Period size: 79 Copynumber: 3.6 Consensus size: 78
3339132 AAATTTTCTT
* * *
3339142 AATCGGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAACCCTGGCTTTATTCCTAAAA
1 AATC-GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAA
*
3339207 TATTGATTTCTCAT
65 TATTGATTTCTCAC
* *
3339221 AATCGAGGATACTCCAACCCCGTTATTTTCGAGAGGATACTCCAACCCCGGCTTTATTTCTAAAA
1 AATCG-GGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAA
3339286 TATTGATTTCTCAC
65 TATTGATTTCTCAC
*
3339300 AATCGGGAATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAA
1 AATCGGG-ATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAA
3339365 TATTGATTTCTCAC
65 TATTGATTTCTCAC
* *** *
3339379 AATCGGGGTACTCCAACCCCGTTATTTCATCGGGGATACTCCAATCCCG
1 AATCGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG
3339428 TTATTTCTTA
Statistics
Matches: 191, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
78 40 0.21
79 151 0.79
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (78 bp):
AATCGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAT
ATTGATTTCTCAC
Found at i:3339421 original size:28 final size:28
Alignment explanation
Indices: 3339380--3339455 Score: 118
Period size: 28 Copynumber: 2.8 Consensus size: 28
3339370 ATTTCTCACA
3339380 ATCGGGG-TACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
3339407 ATCGGGGATACTCCAATCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
* *
3339435 TTAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
3339456 ATTTTATTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 7 0.16
28 37 0.84
ACGTcount: A:0.21, C:0.32, G:0.20, T:0.28
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:3339428 original size:106 final size:106
Alignment explanation
Indices: 3339301--3339501 Score: 305
Period size: 106 Copynumber: 1.9 Consensus size: 106
3339291 ATTTCTCACA
*
3339301 ATCGGGAATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAT
1 ATCGGGAATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAAT
*** *
3339366 ATTGA-TTTCTCACAATCGGGGTACTCCAACCCCGTTATTTC
66 ACCAATTTTC-CACAATCGGGATACTCCAACCCCGTTATTTC
* * **
3339407 ATCGGGGATACTCCAATCCCGTTATTTCTTAGGGGATACTCCAACCCCGATTTTATTTCTAAAAT
1 ATCGGGAATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAAT
3339472 ACCAATTTTCCACAATCGGGATACTCCAAC
66 ACCAATTTTCCACAATCGGGATACTCCAAC
3339502 TCCGATTTTA
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
106 81 0.95
107 4 0.05
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (106 bp):
ATCGGGAATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAAT
ACCAATTTTCCACAATCGGGATACTCCAACCCCGTTATTTC
Found at i:3339498 original size:50 final size:51
Alignment explanation
Indices: 3339439--3339600 Score: 169
Period size: 50 Copynumber: 3.3 Consensus size: 51
3339429 TATTTCTTAG
3339439 GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATC-
1 GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATCA
* * * * *
3339489 GGGATACTCCAACTCCGATTTTATTTCCAAAACACCAA-TTTCTCACAACCG
1 GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTC-CACAATCA
* * * *
3339540 GGGATACTCCAA-----ATTTTATTT-TCAAAATATCGATTTTCTATAATCA
1 GGGATACTCCAACCCCGATTTTATTTCT-AAAATACCAATTTTCCACAATCA
3339586 GGGATACTCCAACCC
1 GGGATACTCCAACCC
3339601 TATTATTTTC
Statistics
Matches: 93, Mismatches: 12, Indels: 15
0.77 0.10 0.12
Matches are distributed among these distances:
46 32 0.34
47 4 0.04
49 4 0.04
50 41 0.44
51 12 0.13
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.31
Consensus pattern (51 bp):
GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATCA
Found at i:3341756 original size:13 final size:12
Alignment explanation
Indices: 3341728--3341779 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
3341718 ATTTAAAAGT
3341728 TTTTATATTATT-
1 TTTTAT-TTATTA
*
3341740 TTTTATTGTTTTA
1 TTTTATT-TATTA
3341753 TTTTAGTTTATTA
1 TTTTA-TTTATTA
3341766 TTTTATTT-TTA
1 TTTTATTTATTA
3341777 TTT
1 TTT
3341780 AAATATCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
11 7 0.20
12 12 0.34
13 14 0.40
14 2 0.06
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:3342117 original size:27 final size:27
Alignment explanation
Indices: 3342087--3342142 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
3342077 ATCTTACCAG
3342087 AATCAATTTCATCGTCCATCTAAATGA
1 AATCAATTTCATCGTCCATCTAAATGA
* *
3342114 AATCAATTTTATTGTCCATCTAAATGA
1 AATCAATTTCATCGTCCATCTAAATGA
3342141 AA
1 AA
3342143 CCTAAGCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (27 bp):
AATCAATTTCATCGTCCATCTAAATGA
Found at i:3344829 original size:26 final size:24
Alignment explanation
Indices: 3344783--3344830 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
3344773 TTTATTTTAA
**
3344783 ATATTTATATTATAATTTTATAAT
1 ATATTTATATTATAAAATTATAAT
3344807 ATATTTATAAATTATAAAATTATA
1 ATATTTAT--ATTATAAAATTATA
3344831 GAAGAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
26 12 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATTTATATTATAAAATTATAAT
Found at i:3345996 original size:7 final size:7
Alignment explanation
Indices: 3345984--3346024 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
3345974 TGATAAAAGT
3345984 TATATAA
1 TATATAA
3345991 TATATAA
1 TATATAA
3345998 -ATATAA
1 TATATAA
*
3346004 AAT-TAA
1 TATATAA
*
3346010 TATATAT
1 TATATAA
3346017 TATATAA
1 TATATAA
3346024 T
1 T
3346025 TAAAAATAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 11 0.38
7 18 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TATATAA
Found at i:3346012 original size:24 final size:25
Alignment explanation
Indices: 3345976--3346031 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
3345966 TTTTTATATG
3345976 ATAAAAGTTATATA-A-TATATAAAT
1 ATAAAA-TTATATATATTATATAAAT
*
3346000 ATAAAATTAATATATATTATATAATT
1 ATAAAATT-ATATATATTATATAAAT
3346026 A-AAAAT
1 ATAAAAT
3346032 AGGCCGAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 2 0.07
24 11 0.39
25 6 0.21
26 9 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (25 bp):
ATAAAATTATATATATTATATAAAT
Found at i:3353116 original size:28 final size:26
Alignment explanation
Indices: 3353065--3353120 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
3353055 TTATTAGAAT
3353065 AATCTGTAAAACCCCTCTCATATATA
1 AATCTGTAAAACCCCTCTCATATATA
3353091 AATCTGTAAAACTCCC-CTCATATATA
1 AATCTGTAAAAC-CCCTCTCATATATA
3353117 AATC
1 AATC
3353121 GGAGAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 26 0.90
27 3 0.10
ACGTcount: A:0.39, C:0.27, G:0.04, T:0.30
Consensus pattern (26 bp):
AATCTGTAAAACCCCTCTCATATATA
Found at i:3353682 original size:154 final size:154
Alignment explanation
Indices: 3353360--3353682 Score: 373
Period size: 153 Copynumber: 2.1 Consensus size: 154
3353350 ATCCGGTAAT
* ** * *
3353360 CCTAAAGGGCTTAAAAGGATTATAGATGGGGTGAACCTATCCTAAATGTCCACCTTCGGCATAAA
1 CCTAAAGGACTTAAAAGGATTATAGATGGGGTGAACCTATCCTAAATACCCACATTCGGCACAAA
* * * ** *
3353425 AGCAGACCCGATGACAACCTAAGACTCGGTTCTAAAAAATTACAAAATTGGCCGTATAAGATACC
66 AGCAGAACCGATGACAACCTAAGACTCGATTCTAAAAAATTACAAAAATACCCGTAGAAGATACC
* * *
3353490 TTTGACGTAGAAGTGCCTAATACC
131 TTTGACATAGAAGTACCCAATACC
* *
3353514 CCT-AAGGACATAAAATGGATTATAGATGGGGTGAACCTATCCTAAATACCCATATTCGGCACAA
1 CCTAAAGGACTTAAAA-GGATTATAGATGGGGTGAACCTATCCTAAATACCCACATTCGGCACAA
* ** * * * **
3353578 AAG-TGAACTTAGTGATAACCT-AGATTCGATTCTAAAAAATTACAAAAATACCCTTAGGGGATA
65 AAGCAGAACCGA-TGACAACCTAAGACTCGATTCTAAAAAATTACAAAAATACCCGTAGAAGATA
*
3353641 CCTTTGACATAGAAGTACCCGATACC
129 CCTTTGACATAGAAGTACCCAATACC
*
3353667 CCTAAAGGATTTAAAA
1 CCTAAAGGACTTAAAA
3353683 AGGTAAAGAA
Statistics
Matches: 139, Mismatches: 27, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
153 72 0.52
154 67 0.48
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (154 bp):
CCTAAAGGACTTAAAAGGATTATAGATGGGGTGAACCTATCCTAAATACCCACATTCGGCACAAA
AGCAGAACCGATGACAACCTAAGACTCGATTCTAAAAAATTACAAAAATACCCGTAGAAGATACC
TTTGACATAGAAGTACCCAATACC
Found at i:3353985 original size:11 final size:11
Alignment explanation
Indices: 3353966--3353994 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
3353956 AGAGGATATG
3353966 AAATTTTTTT-
1 AAATTTTTTTA
3353976 AAATTTTTTTA
1 AAATTTTTTTA
3353987 AAATTTTT
1 AAATTTTT
3353995 ATACCCTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
AAATTTTTTTA
Found at i:3357128 original size:52 final size:53
Alignment explanation
Indices: 3357038--3357191 Score: 161
Period size: 52 Copynumber: 2.9 Consensus size: 53
3357028 TCGATTGTGA
* * * * *
3357038 AAAAATTGGTGTTTTTGGAAATAAAATCAGAGCTGGAGTATCCCTGATTAAAGG
1 AAAAATTGGTG-TTTTGAAAATAAAACCGGGGTTGGAGTATCCCTGATTAAAGG
* **
3357092 -AAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTAACCCTGATT-GTGG
1 AAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCTGATTAAAGG
* * * *
3357143 AAAAATTAGTGTTTT-AGCAATAAAACTGGGGTTGGAGTATCCCCGATTA
1 AAAAATTGGTGTTTTGA-AAATAAAACCGGGGTTGGAGTATCCCTGATTA
3357192 TGAGAAATCA
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
51 3 0.04
52 71 0.85
53 10 0.12
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.30
Consensus pattern (53 bp):
AAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCTGATTAAAGG
Found at i:3357255 original size:28 final size:25
Alignment explanation
Indices: 3357221--3357291 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 25
3357211 GAATAAAGTA
3357221 GGGGTTGGAGTATCCCCTCGGAAATAAC
1 GGGGTTGGAGTATCCCCT--G-AATAAC
* *
3357249 GGGGTTGGAGTATCCCGATGATTAAC
1 GGGGTTGGAGTATCCC-CTGAATAAC
3357275 GGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
3357292 GATTGTGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
26 21 0.54
27 1 0.03
28 16 0.41
29 1 0.03
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.24
Consensus pattern (25 bp):
GGGGTTGGAGTATCCCCTGAATAAC
Found at i:3358920 original size:19 final size:20
Alignment explanation
Indices: 3358875--3358927 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
3358865 AAAATGCCTG
*
3358875 AATGTATCGATACATTGTAA
1 AATGTATCGATACATTCTAA
3358895 AATGTATCGATACA-TCTAA
1 AATGTATCGATACATTCTAA
*
3358914 GATGTATCGATACA
1 AATGTATCGATACA
3358928 AAGAATAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTCTAA
Found at i:3359041 original size:19 final size:19
Alignment explanation
Indices: 3359013--3359077 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
3359003 AGCGATACAT
*
3359013 TGTATTGATACAAAACTTA
1 TGTATCGATACAAAACTTA
3359032 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
3359045 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
3359064 TGTATCGATACAAA
1 TGTATCGATACAAA
3359078 TTGCTGAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:3359046 original size:32 final size:32
Alignment explanation
Indices: 3359005--3359075 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
3358995 AGCTTCCTAG
*
3359005 CGATACATTGTATTGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
3359037 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
3359069 CGATACA
1 CGATACA
3359076 AATTGCTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:3359050 original size:13 final size:13
Alignment explanation
Indices: 3359032--3359056 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3359022 ACAAAACTTA
3359032 TGTATCGATACAT
1 TGTATCGATACAT
3359045 TGTATCGATACA
1 TGTATCGATACA
3359057 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3359854 original size:29 final size:29
Alignment explanation
Indices: 3359773--3359854 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 29
3359763 GACTAGAAAA
3359773 TGCCACCAACTTGTGTGGGCTTTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAGG
** *
3359802 TGTCCTGC-TCTT-TG-GGGAC--TGAAAGG
1 TG-CCACCAACTTGTGTGGG-CTTTGAAAGG
3359828 TGCCACCAACTTGTGTGGGCTTTGAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAA
3359855 AGAAAAAGCA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
25 3 0.08
26 12 0.30
27 6 0.15
28 6 0.15
29 10 0.25
30 3 0.08
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (29 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGG
Found at i:3359959 original size:170 final size:171
Alignment explanation
Indices: 3359529--3360414 Score: 1052
Period size: 170 Copynumber: 5.1 Consensus size: 171
3359519 AATAAAGTGT
* * * *
3359529 ATCCTGCTCTTTGAGGAGTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCGTCCTGCTC
1 ATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGTGTCCTGCTC
* *
3359593 TTTGAGGACT-GAAAGGTGCCACTAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGAA
66 TTTGAGGACTGGAAA--TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGA
** *
3359656 CTGAAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG---ATG-
128 CTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
* * * * *
3359695 -TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTAGGC-TT-AAGAGGTGTCTTGTTC
1 ATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGTGTCCTGCTC
* *
3359757 TTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACT
66 TTTGAGGACT-GGAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT
3359822 GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
130 GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
3359864 ATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTC
1 ATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGTGTCCTGCTC
* *
3359928 TTTGAGGACTGGAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTTTTTGGGGACTG
66 TTTGAGGACTGGAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
3359993 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
131 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
* * * *
3360034 ATCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCC
1 ATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAG---AGGTGTCCT
* * * * *
3360098 GCTCTTTGAGGACT-GAAGGTGCCACCAACTCGTGTGGTCTTTAAAAGAAAAGGCGTCCCGCTCT
62 GCTCTTTGAGGACTGGAA-ATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCT
* *
3360162 TTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGT
121 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
* * **
3360211 GTCCTGCTTTTTGAGGA-TTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCCT
1 ATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAG---AGGTGTCCT
* *
3360275 GCTCTTTGAGGACTGGAAAATGCTACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCT
62 GCTCTTTGAGGACTGG-AAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCT
* * * * *
3360340 TTGCGGACTGGAAA-ATGCCACCAACTTGTGGGGGCTTTTAAAAGGAAAAGGC
121 TTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAA-GAAAAAGC
3360392 ATCCTGCTCTTTGAGGACTAAAA
1 ATCCTGCTCTTTGAGGACTAAAA
3360415 AGCGGAAGGA
Statistics
Matches: 637, Mismatches: 53, Indels: 44
0.87 0.07 0.06
Matches are distributed among these distances:
163 2 0.00
164 93 0.15
165 45 0.07
166 3 0.00
168 2 0.00
169 26 0.04
170 154 0.24
171 29 0.05
173 3 0.00
174 42 0.07
176 1 0.00
177 81 0.13
178 78 0.12
179 47 0.07
180 6 0.01
181 22 0.03
182 3 0.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (171 bp):
ATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGTGTCCTGCTC
TTTGAGGACTGGAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
Found at i:3360114 original size:59 final size:59
Alignment explanation
Indices: 3359530--3360410 Score: 963
Period size: 55 Copynumber: 15.3 Consensus size: 59
3359520 ATAAAGTGTA
* * * *
3359530 TCCTGCTCTTTGAGGAGTAAAAAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
*
3359585 TCCTGCTCTTTGAGGACTGAAAGGTGCCACTAACTTGTGTGGGCTTT--AAG---AGGTG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* ** *
3359640 TCCTGCTCTTTGAGAACTGAAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGATG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* *
3359695 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTAGGC-TT--AAG---AGGTG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* * **
3359749 TCTTGTTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* * **
3359804 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGTG
*
3359865 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
*
3359920 TCCTGCTCTTTGAGGACTGGAA-ATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* * * **
3359974 TCCTGCTTTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGTG
* *
3360035 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* * * *
3360094 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTCGTGTGGTCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
*
3360153 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* *
3360212 TCCTGCTTTTTGAGGATTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
** * *
3360271 TCCTGCTCTTTGAGGACTGGAAAATGCTACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* ** * **
3360331 TCCTGCTCTTTGCGGACTGGAAAATGCCACCAACTTGTGGGGGCTTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGC-TTTAAAA-GAAAAGGTG
3360393 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
3360411 AAAAAGCGGA
Statistics
Matches: 724, Mismatches: 70, Indels: 57
0.85 0.08 0.07
Matches are distributed among these distances:
52 1 0.00
53 3 0.00
54 89 0.12
55 225 0.31
56 1 0.00
57 1 0.00
58 3 0.00
59 194 0.27
60 106 0.15
61 76 0.10
62 25 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (59 bp):
TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
Found at i:3361419 original size:13 final size:13
Alignment explanation
Indices: 3361396--3361441 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
3361386 TTTTCTCTCT
3361396 TTTTCTTTGTTTTG
1 TTTT-TTTGTTTTG
3361410 TTTTTTTGTTTTG
1 TTTTTTTGTTTTG
3361423 -TTTTTT-TTTTG
1 TTTTTTTGTTTTG
3361434 CTTTTTTT
1 -TTTTTTT
3361442 TTGAAGAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.17
12 6 0.20
13 15 0.50
14 4 0.13
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.85
Consensus pattern (13 bp):
TTTTTTTGTTTTG
Found at i:3361432 original size:11 final size:11
Alignment explanation
Indices: 3361405--3361444 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
3361395 TTTTTCTTTG
3361405 TTTTGTTTTTTT
1 TTTTG-TTTTTT
3361417 GTTTTGTTTTTT
1 -TTTTGTTTTTT
*
3361429 TTTTGCTTTTT
1 TTTTGTTTTTT
3361440 TTTTG
1 TTTTG
3361445 AAGAGAAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 15 0.58
12 6 0.23
13 5 0.19
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:3364778 original size:165 final size:165
Alignment explanation
Indices: 3364577--3365116 Score: 448
Period size: 165 Copynumber: 3.3 Consensus size: 165
3364567 TTAATAACAC
* ** * * * * * *
3364577 TATTAGATGAATTTTAAAAATTTTAAATCGAGAAAAATCCCTCTAACAACATTTATGCAATAGAA
1 TATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAACATTTATGCAATAAAA
* * * * *
3364642 AACTTAGT-TTTTCTAAAACGAGAAAATTTCAAAGAAAAAAAT-AAAAACTCATGAAAATAAATT
66 AACTTAGTATTTT-GAAAACAAAAAAATTTCAAAG--AAAAATGAAAAACCCATGAAAATAAATG
* **
3364705 AATTTTTTAAAGCTGATTTAATATGA-ATAAATAATAA
128 AATTTTTCAAAAATGATTTAATATGAGATAAATAATAA
* * * *
3364742 TATTTGATTAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAATATTTATGGAGTAAAA
1 TATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAACATTTATGCAATAAAA
* * **
3364807 AACTTCGTATTTTGAAAATAAAAAAATTTTGAAGAAAAATGAAAAACCCATGAAAATAAATGAAT
66 AACTTAGTATTTTGAAAACAAAAAAATTTCAAAGAAAAATGAAAAACCCATGAAAATAAATGAAT
* ** *
3364872 TTTTCAAAAATGATTTAATATGAGTTAAATGTTGA
131 TTTTCAAAAATGATTTAATATGAGATAAATAATAA
* * * *
3364907 TATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCCCCTCAAAAATATTT-T-CAAAGAAG
1 TATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAACATTTATGC-AATAA-
* * ** * * *
3364970 AAAACTCTA-TATTTCGAAAACAGAAAAATTT---------ATTCAAAACTCATGGAAATGAATG
64 AAAACT-TAGTATTTTGAAAACAAAAAAATTTCAAAGAAAAATGAAAAACCCATGAAAATAAATG
* * *
3365025 AATTTCTAAAAAATGATTTAATATGA-ATTAAATAATGA
128 AATTTTTCAAAAATGATTTAATATGAGA-TAAATAATAA
* * * * * *
3365063 TATTTTATGAATTTTAAAAATTTTAAATCCATG-AAAATCCTCCCAAAAAAATTT
1 TATTTGATGAATTTTAAAAA-TTAAAAACCAAGAAAAATCCCCCCAAAAACATTT
3365117 TCGAAAAAGA
Statistics
Matches: 310, Mismatches: 57, Indels: 25
0.79 0.15 0.06
Matches are distributed among these distances:
156 88 0.28
157 8 0.03
163 6 0.02
164 46 0.15
165 157 0.51
166 5 0.02
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.32
Consensus pattern (165 bp):
TATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAACATTTATGCAATAAAA
AACTTAGTATTTTGAAAACAAAAAAATTTCAAAGAAAAATGAAAAACCCATGAAAATAAATGAAT
TTTTCAAAAATGATTTAATATGAGATAAATAATAA
Found at i:3365079 original size:156 final size:156
Alignment explanation
Indices: 3364849--3365147 Score: 408
Period size: 156 Copynumber: 1.9 Consensus size: 156
3364839 AGAAAAATGA
* * * **
3364849 AAAACCCATGAAAATAAATGAATTTTTCAAAAATGATTTAATATGAGTTAAATGTTGATATTTGA
1 AAAACCCATGAAAATAAATGAATTTCTAAAAAATGATTTAATATGAATTAAATAATGATATTTGA
*
3364914 TGAATTTTAAAAATTATAAA-CCAAGAAAAATCC-CCTCAAAAATATTTTC-AAAGAAGAAAA-C
66 TGAATTTTAAAAATTATAAATCCAAG-AAAATCCTCC-CAAAAAAATTTTCGAAA-AAGAAAATC
*
3364975 TCTATATTTCGAAAACAGAAAAATTTATTC
128 TC-ATATTTCAAAAACAGAAAAATTTATTC
* * * *
3365005 AAAACTCATGGAAATGAATGAATTTCTAAAAAATGATTTAATATGAATTAAATAATGATATTTTA
1 AAAACCCATGAAAATAAATGAATTTCTAAAAAATGATTTAATATGAATTAAATAATGATATTTGA
* * *
3365070 TGAATTTTAAAAATTTTAAATCCATGAAAATCCTCCCAAAAAAATTTTCGAAAAAGAAAATTTCA
66 TGAATTTTAAAAATTATAAATCCAAGAAAATCCTCCCAAAAAAATTTTCGAAAAAGAAAATCTCA
3365135 TATTTCAAAAACA
131 TATTTCAAAAACA
3365148 CGAGGAATTT
Statistics
Matches: 125, Mismatches: 14, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
156 114 0.91
157 11 0.09
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.32
Consensus pattern (156 bp):
AAAACCCATGAAAATAAATGAATTTCTAAAAAATGATTTAATATGAATTAAATAATGATATTTGA
TGAATTTTAAAAATTATAAATCCAAGAAAATCCTCCCAAAAAAATTTTCGAAAAAGAAAATCTCA
TATTTCAAAAACAGAAAAATTTATTC
Found at i:3365194 original size:156 final size:156
Alignment explanation
Indices: 3364684--3365233 Score: 399
Period size: 156 Copynumber: 3.5 Consensus size: 156
3364674 AGAAAAAAAT
* * * * ** * * *
3364684 AAAAACTCATGAAAATAAATTAATTTTTTAAAGCTGATTTAATATGAA-TAAATAATAATATTTG
1 AAAAA-TCATAAAAATGAATGAATTTTTAAAAAATGATTTAATATGAATTAAATGATGATATTTA
* * * * **
3364748 ATTAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAATATTTAT-GGAGTAA-AAAACT
65 ATGAATTTTAAAAATTATAAACCAAGAAAAATCCCCTCAAAAAAATTT-TCAAAG-AAGAAAAC-
*
3364811 TCGTAT-TTTGAAAATA-A-AAAAATTTTGAAG-
127 TC-TATATTTCAAAA-ACAGAAAAA-TTT-AAGC
* * * * *
3364841 AAAAATGAAAAACCCATGAAAATAAATGAATTTTTCAAAAATGATTTAATATGAGTTAAATGTTG
1 AAAAAT--------CATAAAAATGAATGAATTTTTAAAAAATGATTTAATATGAATTAAATGATG
* *
3364906 ATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCCCCTCAAAAATATTTTCAAAGAAGA
58 ATATTTAATGAATTTTAAAAATTATAAACCAAGAAAAATCCCCTCAAAAAAATTTTCAAAGAAGA
* **
3364971 AAACTCTATATTTCGAAAACAGAAAAATTTATTC
123 AAACTCTATATTTCAAAAACAGAAAAATTTAAGC
* ** * * *
3365005 AAAACTCATGGAAATGAATGAATTTCTAAAAAATGATTTAATATGAATTAAATAATGATATTTTA
1 AAAAATCATAAAAATGAATGAATTTTTAAAAAATGATTTAATATGAATTAAATGATGATATTTAA
* *
3365070 TGAATTTTAAAAATTTTAAATCCATG-AAAATCCTCC-CAAAAAAATTTTCGAAA-AAGAAAA-T
66 TGAATTTTAAAAATTATAAA-CCAAGAAAAATCC-CCTCAAAAAAATTTTC-AAAGAAGAAAACT
* ** *
3365131 TTCATATTTCAAAAACACGAGGAATTTAAAGG
128 CT-ATATTTCAAAAACA-GAAAAATTT-AAGC
** * * *
3365163 AAAAAT-A-AAAAATGAATGAATTTTTTGAAAATAATTTAAT-GGTAATTAAATGATAATATTTA
1 AAAAATCATAAAAATGAATGAATTTTTAAAAAATGATTTAATATG-AATTAAATGATGATATTTA
*
3365225 AAGAATTTT
65 ATGAATTTT
3365234 GATGTTCAAA
Statistics
Matches: 323, Mismatches: 48, Indels: 45
0.78 0.12 0.11
Matches are distributed among these distances:
155 3 0.01
156 161 0.50
157 22 0.07
158 6 0.02
163 5 0.02
164 56 0.17
165 70 0.22
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.32
Consensus pattern (156 bp):
AAAAATCATAAAAATGAATGAATTTTTAAAAAATGATTTAATATGAATTAAATGATGATATTTAA
TGAATTTTAAAAATTATAAACCAAGAAAAATCCCCTCAAAAAAATTTTCAAAGAAGAAAACTCTA
TATTTCAAAAACAGAAAAATTTAAGC
Found at i:3373074 original size:167 final size:166
Alignment explanation
Indices: 3372535--3373346 Score: 984
Period size: 165 Copynumber: 4.9 Consensus size: 166
3372525 AAAATTCTTT
* * *
3372535 AAATATTATTATTTATTTCATATTGAATCAGTTTTTAAAAATTAATTCATTTTTATGAGTTTTTG
1 AAATATTATCATTTATTTCATATTAAATCAGTTTTTAAAAATTAATTCATTTTCATGAGTTTTTG
* * * *
3372600 AATTTTTTCCTTGAAA-TTT-TTTTTCCGAAATATGTTGTTTTCTACTTCGTAAATTTTTTTGAG
66 AATTTTTTCCTTGAAATTTTCTTTTTTCGAAATACGTTATTTTCTACTTCGTAAATTTTTTCGAG
3372663 GGGATTTTTCTTGGTTTTTAATTTTTAAATTTCATC
131 GGGATTTTTCTTGGTTTTTAATTTTTAAATTTCATC
* *
3372699 AAATATTATAAGTTATTTCATATTAAATCAGTTTTTAAAAATTAATTCATTTTCATGAGTTTTT-
1 AAATATTATCATTTATTTCATATTAAATCAGTTTTTAAAAATTAATTCATTTTCATGAGTTTTTG
* ** * * *
3372763 AAATTTTTCCTTGAAATTCCCTTTTTCCAAAATACGTTGTTTTCTACTTCGTAAATTTTTTCGA-
66 AATTTTTTCCTTGAAATTTTCTTTTTTCGAAATACGTTATTTTCTACTTCGTAAATTTTTTCGAG
3372827 GGGAGTTTTTCTTGGTTTTTAATTTTTAAATTTCATC
131 GGGA-TTTTTCTTGGTTTTTAATTTTTAAATTTCATC
* * * * *
3372864 AAATATTAGCATTTATTTTATGTTAAATTAGTTTTAAAAAATTAATTCATTTTCATGAGTTTTTG
1 AAATATTATCATTTATTTCATATTAAATCAGTTTTTAAAAATTAATTCATTTTCATGAGTTTTTG
3372929 AATTTTTTCCTTGAAATATTTCTTTTTTCGAAATACGTTATTTTCTACTTCGTAAATTTTTTCGA
66 AATTTTTTCCTTGAAAT-TTTCTTTTTTCGAAATACGTTATTTTCTACTTCGTAAATTTTTTCGA
3372994 GGGGA-TTTTCTTGGTTTTT-ATTTTTAAAATTTCATC
130 GGGGATTTTTCTTGGTTTTTAATTTTT-AAATTTCATC
* *
3373030 AAATATTGTCATTTATTTCATATTAAATCAGTTTTTTAAAAATTAATTCATTTTCAAGAGTTTTT
1 AAATATTATCATTTATTTCATATTAAATCAG-TTTTTAAAAATTAATTCATTTTCATGAGTTTTT
* * * * * * *
3373095 GAAATTTTTCCTTGAAATTCCTCTTTTTTCGAAATACGATATTTTCTACTCCGTAAATTCTTCCA
65 GAATTTTTTCCTTGAAATT-TTCTTTTTTCGAAATACGTTATTTTCTACTTCGTAAATTTTTTCG
* * *
3373160 AAGGAATTTTTCTTGGTTTTTAATTTTTAAAATTCATC
129 AGGGGATTTTTCTTGGTTTTTAATTTTTAAATTTCATC
* * * *
3373198 -AA-A-CATCA-TCA----ATATTAAAACA-TTTTCAAAAAATTAATTCATTTTCATGAG-TTTT
1 AAATATTATCATTTATTTCATATTAAATCAGTTTT-TAAAAATTAATTCATTTTCATGAGTTTTT
* *
3373253 GGATTTTTT-ATTGAAATTCCCTT-TTTTTTCGAGAA-ATCGAGTT-TTTT-T-CTTCGTAAATT
65 GAATTTTTTCCTTGAAATT---TTCTTTTTTCGA-AATA-C--GTTATTTTCTACTTCGTAAATT
* **
3373312 TTTTTGAGGGGATTTTTCTTGGTTTAGAATTTTTA
123 TTTTCGAGGGGATTTTTCTTGGTTTTTAATTTTTA
3373347 TAACTCATCT
Statistics
Matches: 570, Mismatches: 60, Indels: 42
0.85 0.09 0.06
Matches are distributed among these distances:
157 8 0.01
158 62 0.11
159 28 0.05
160 14 0.02
161 2 0.00
163 15 0.03
164 67 0.12
165 138 0.24
166 68 0.12
167 135 0.24
168 27 0.05
169 6 0.01
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (166 bp):
AAATATTATCATTTATTTCATATTAAATCAGTTTTTAAAAATTAATTCATTTTCATGAGTTTTTG
AATTTTTTCCTTGAAATTTTCTTTTTTCGAAATACGTTATTTTCTACTTCGTAAATTTTTTCGAG
GGGATTTTTCTTGGTTTTTAATTTTTAAATTTCATC
Found at i:3373767 original size:17 final size:17
Alignment explanation
Indices: 3373742--3373782 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
3373732 GCAAAGTGAG
*
3373742 AAGAAAAAGAGAAAGAA
1 AAGAAAAAGAAAAAGAA
*
3373759 AAGAGAAAGAAAAAG-A
1 AAGAAAAAGAAAAAGAA
3373775 AAGAAAAA
1 AAGAAAAA
3373783 TAGTGAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAAAAGAA
Found at i:3373782 original size:10 final size:11
Alignment explanation
Indices: 3373746--3373781 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
3373736 AGTGAGAAGA
3373746 AAAAGAGAAAG
1 AAAAGAGAAAG
3373757 AAAAGAGAAAG
1 AAAAGAGAAAG
3373768 AAAA-AGAAAG
1 AAAAGAGAAAG
3373778 AAAA
1 AAAA
3373782 ATAGTGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:3373782 original size:11 final size:11
Alignment explanation
Indices: 3373742--3373782 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
3373732 GCAAAGTGAG
3373742 AAGAAAAAGAGA
1 AAGAAAAA-AGA
*
3373754 AAGAAAAGAGA
1 AAGAAAAAAGA
3373765 AAG-AAAAAGA
1 AAGAAAAAAGA
3373775 AAGAAAAA
1 AAGAAAAA
3373783 TAGTGAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 9 0.35
11 10 0.38
12 7 0.27
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAGA
Found at i:3378004 original size:52 final size:51
Alignment explanation
Indices: 3377941--3378270 Score: 178
Period size: 52 Copynumber: 6.3 Consensus size: 51
3377931 GAAATAACGA
*
3377941 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
** * ** *
3377992 GAGTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAATCG
1 G-GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATCG
* * *
3378044 GGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAATCGG
1 GG-TTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATC-G
* **** * *
3378097 GGTTGGAGTATCCCC--TCG-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CG
1 GGTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCG
* *
3378151 GGTTAGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATC-G
* * * * **
3378205 AGTTAGAGTATCCCCGATTATGAAAAATT-G-ATGTTTTAGAAATAAAGCCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTAT-TTTTGGAAATAAAATC-G
3378256 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
3378271 TCGGAAATAA
Statistics
Matches: 210, Mismatches: 41, Indels: 56
0.68 0.13 0.18
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 3 0.01
51 31 0.15
52 90 0.43
53 23 0.11
54 43 0.20
55 2 0.01
56 4 0.02
57 7 0.03
58 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
Found at i:3378192 original size:212 final size:211
Alignment explanation
Indices: 3377877--3378270 Score: 564
Period size: 212 Copynumber: 1.9 Consensus size: 211
3377867 AGAAGAAAAA
*
3377877 AAAATCGGGATTGGAGTATCCCCTCGAAAGTAACGGGGTTGGATAATCTCCGATGAAATAACGAG
1 AAAATCGGGATTGGAGTATCCCCTCGAAAGTAACGGGGTTGGATAATCCCCGATGAAATAACGAG
* * * *
3377942 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
66 GTTAGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCAGAGTTAGAGTATCCC
* * *
3378007 CGATTAAAGGAAAATTGGCGTTTT-GAAAATAAAATCGGGATTGGAGTATCCCCGATTGTGGAAA
131 CGATT-AAGAAAAATTGACGTTTTAG-AAATAAAACCGGGATTGGAGTATCCCCGATTGTGGAAA
3378071 AATTAGTGTTTTAGCGAT
194 AATTAGTGTTTTAGCGAT
* *
3378089 AAAATCGGGGTTGGAGTATCCCCTCGGAAA-TAACGGGGTTGGAGT-ATCCCCGATG-ATTAACG
1 AAAATCGGGATTGGAGTATCCCCTC-GAAAGTAACGGGGTTGGA-TAATCCCCGATGAAATAACG
*
3378151 -GGTTAGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCAGAGTTAGAGTA
64 AGGTTAGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCAGAGTTAGAGTA
* * * *
3378215 TCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAGCCGGGGTTGGAGTATCCCC
127 TCCCCGATTAAGAAAAATTGACGTTTTAGAAATAAAACCGGGATTGGAGTATCCCC
3378271 TCGGAAATAA
Statistics
Matches: 162, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
210 22 0.14
211 52 0.32
212 83 0.51
213 5 0.03
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.28
Consensus pattern (211 bp):
AAAATCGGGATTGGAGTATCCCCTCGAAAGTAACGGGGTTGGATAATCCCCGATGAAATAACGAG
GTTAGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCAGAGTTAGAGTATCCC
CGATTAAGAAAAATTGACGTTTTAGAAATAAAACCGGGATTGGAGTATCCCCGATTGTGGAAAAA
TTAGTGTTTTAGCGAT
Found at i:3378268 original size:51 final size:53
Alignment explanation
Indices: 3378150--3378270 Score: 147
Period size: 51 Copynumber: 2.3 Consensus size: 53
3378140 GATGATTAAC
* * * *
3378150 GGGTTAGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCA
1 GGGTTAGAGTATCCCCGATTATGAAGAAATTGATG-TTTTTAGAAATAAAACCA
* * *
3378204 GAGTTAGAGTATCCCCGATTATGAA-AAATTGATG-TTTTAGAAATAAAGCCG
1 GGGTTAGAGTATCCCCGATTATGAAGAAATTGATGTTTTTAGAAATAAAACCA
*
3378255 GGGTTGGAGTATCCCC
1 GGGTTAGAGTATCCCC
3378271 TCGGAAATAA
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
51 27 0.47
53 8 0.14
54 23 0.40
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (53 bp):
GGGTTAGAGTATCCCCGATTATGAAGAAATTGATGTTTTTAGAAATAAAACCA
Found at i:3378301 original size:79 final size:79
Alignment explanation
Indices: 3378210--3378393 Score: 332
Period size: 79 Copynumber: 2.3 Consensus size: 79
3378200 ATCAGAGTTA
*
3378210 GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCTCGG
1 GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGG
*
3378275 AAATAACGGGGTTG
66 AAATAACGGGATTG
*
3378289 GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAACCGGGGTTGGAGTATCCCCTCGG
1 GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGG
3378354 AAATAACGGGATTG
66 AAATAACGGGATTG
*
3378368 GAGTATCCCCGATTGTGAAAAATTGA
1 GAGTATCCCCGATTATGAAAAATTGA
3378394 GAACCTTAAC
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 101 1.00
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (79 bp):
GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGG
AAATAACGGGATTG
Found at i:3380758 original size:13 final size:13
Alignment explanation
Indices: 3380740--3380765 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3380730 ACAAAGATCC
3380740 ATGTATCGATACA
1 ATGTATCGATACA
3380753 ATGTATCGATACA
1 ATGTATCGATACA
3380766 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3380761 original size:33 final size:33
Alignment explanation
Indices: 3380719--3380785 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3380709 AAAATTTCCA
***
3380719 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
3380752 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
3380785 A
1 A
3380786 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:3380829 original size:19 final size:18
Alignment explanation
Indices: 3380805--3380872 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
3380795 CAGTAGCTAA
3380805 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
3380824 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
*
3380839 -T-TGTATCTATACAAAAC
1 TTATGTATCGATAC-AAAC
3380856 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
3380873 TTGTTGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 10 0.24
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.59
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:3380851 original size:32 final size:32
Alignment explanation
Indices: 3380808--3380870 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
3380798 TAGCTAATTA
*
3380808 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
*
3380840 TGTATCTATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
3380871 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:3380952 original size:21 final size:21
Alignment explanation
Indices: 3380928--3380984 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3380918 CATTTGTAGG
3380928 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
3380949 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
3380970 ATGTATCGATACATT
1 ATGTATCGATACATT
3380985 TGGATAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:3381802 original size:55 final size:55
Alignment explanation
Indices: 3381718--3382354 Score: 734
Period size: 55 Copynumber: 11.3 Consensus size: 55
3381708 ATAAAGTGTA
* * * * * *
3381718 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
3381773 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
3381828 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * * *
3381883 TCCTGCTCTTTGGGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAGGGG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * * **
3381938 TCCTGCTCTTCCGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTCGAAAAGAAAAAGCA
1 TCCTGCTCTT-TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* *
3382000 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* * *
3382059 TCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGATTTAAAAGAAAATGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
*
3382118 TCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
3382172 TCCTGCTCTCTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
3382227 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
3382282 TCCTGCTCTTTGAGGACTGGAAA-ATGCCATCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
3382337 TCCTGCTCTTTGGGGACT
1 TCCTGCTCTTTGAGGACT
3382355 AAAAAGCGAA
Statistics
Matches: 523, Mismatches: 39, Indels: 40
0.87 0.06 0.07
Matches are distributed among these distances:
53 2 0.00
54 25 0.05
55 299 0.57
56 44 0.08
57 4 0.01
59 100 0.19
60 26 0.05
61 6 0.01
62 11 0.02
64 6 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:3382249 original size:27 final size:27
Alignment explanation
Indices: 3382219--3382304 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
3382209 TGTGGGCTTT
3382219 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
3382246 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
3382274 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
3382301 GAAA
1 GAAA
3382305 ATGCCATCAA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.12
27 14 0.35
28 10 0.25
29 5 0.12
30 3 0.08
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:3383358 original size:17 final size:16
Alignment explanation
Indices: 3383338--3383397 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
3383328 CTTTTCTCTC
*
3383338 TTTTTCTTTGTTTTGT
1 TTTTTTTTTGTTTTGT
* *
3383354 TTTTTTATTTTTTTTCCT
1 TTTTTT-TTTGTTTT-GT
*
3383372 TTTTTTTTTCTTTTGCT
1 TTTTTTTTTGTTTTG-T
3383389 TTTTTTTTT
1 TTTTTTTTT
3383398 TGAAGAGAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 5 0.14
17 24 0.67
18 7 0.19
ACGTcount: A:0.02, C:0.08, G:0.05, T:0.85
Consensus pattern (16 bp):
TTTTTTTTTGTTTTGT
Found at i:3383376 original size:12 final size:11
Alignment explanation
Indices: 3383322--3383398 Score: 50
Period size: 11 Copynumber: 6.6 Consensus size: 11
3383312 CTAAGTAGGT
3383322 TTTTTTCTTTTC
1 TTTTTT-TTTTC
*
3383334 TCTCTTTTTCTTTG
1 T-T-TTTTT-TTTC
3383348 TTTTGTTTTTT-
1 TTTT-TTTTTTC
*
3383359 TATTTTTTTTCC
1 T-TTTTTTTTTC
3383371 TTTTTTTTTTC
1 TTTTTTTTTTC
**
3383382 TTTTGCTTTT-
1 TTTTTTTTTTC
3383392 TTTTTTT
1 TTTTTTT
3383399 GAAGAGAAGG
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
10 5 0.10
11 23 0.44
12 10 0.19
13 6 0.12
14 8 0.15
ACGTcount: A:0.01, C:0.12, G:0.04, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:3383376 original size:34 final size:35
Alignment explanation
Indices: 3383321--3383398 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 35
3383311 CCTAAGTAGG
* * *
3383321 TTTTTTTCTTTTCTCTCTTTTTCTTTGTTTTGTTT
1 TTTTTTTTTTTTCTCTCTTTTTCTTTCTTTTGCTT
*
3383356 TTTTATTTTTTTTC-CT-TTTTTTTTTCTTTTGCTT
1 TTTT-TTTTTTTTCTCTCTTTTTCTTTCTTTTGCTT
3383390 TTTTTTTTT
1 TTTTTTTTT
3383399 GAAGAGAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 5 0.13
34 19 0.50
35 6 0.16
36 8 0.21
ACGTcount: A:0.01, C:0.12, G:0.04, T:0.83
Consensus pattern (35 bp):
TTTTTTTTTTTTCTCTCTTTTTCTTTCTTTTGCTT
Found at i:3389083 original size:17 final size:17
Alignment explanation
Indices: 3389061--3389094 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3389051 ACATCGATTC
*
3389061 TTGACTGTGGCTTCCTT
1 TTGACTGTGCCTTCCTT
*
3389078 TTGACTTTGCCTTCCTT
1 TTGACTGTGCCTTCCTT
3389095 CTTACCTCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.26, G:0.18, T:0.50
Consensus pattern (17 bp):
TTGACTGTGCCTTCCTT
Found at i:3395959 original size:28 final size:29
Alignment explanation
Indices: 3395888--3395959 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 29
3395878 AAAATCGGGA
*
3395888 TTGGAGTATCCCC--TCGAAAGTAACGGGG
1 TTGGAGTATCCCCGAT-GAAAGTAACGAGG
3395916 TTGGAGTATCCCCGATGAAA-TAACGAGG
1 TTGGAGTATCCCCGATGAAAGTAACGAGG
*
3395944 TTGGAGTATCCTCGAT
1 TTGGAGTATCCCCGAT
3395960 TGTGAAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 35 0.88
29 4 0.10
30 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (29 bp):
TTGGAGTATCCCCGATGAAAGTAACGAGG
Found at i:3396005 original size:52 final size:52
Alignment explanation
Indices: 3395942--3396323 Score: 275
Period size: 51 Copynumber: 7.3 Consensus size: 52
3395932 GAAATAACGA
* * *
3395942 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTAGAAATAAAACCGG
* ** * ** *
3395994 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGA-AAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTAGAAATAAAACCGG
* * * *
3396046 GATTGGAGTATCCCCGATTGTGGAAAAATTAGT-GTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTAGAAATAAAACCGG
* **** * *
3396098 GGTTGGAGTATCCCC--TCG-GAAATAACGGGGTTAGAGTA-TCCCCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTGTGAAA-AA-----TT-G-GTATTTTTAGA-AATAAAACCGG
* *
3396153 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAA-AAATTGGTA-TTTTTAGAAATAAAACCGG
* * * *
3396207 AGTTAGAGTATCCCCGATTATGAAAAATT-G-ATGTTTTAGAAATAAAGCCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTAT-TTTTAGAAATAAAACCGG
* * *
3396258 GGTTGGAGTATCCCTGATTATGAAAAATT-G-ATGTTTTAGAGATAAAACCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTAT-TTTTAGAAATAAAACCGG
3396309 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
3396324 TCGGAAATAA
Statistics
Matches: 259, Mismatches: 49, Indels: 45
0.73 0.14 0.13
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 3 0.01
51 83 0.32
52 82 0.32
53 25 0.10
54 26 0.10
55 18 0.07
56 6 0.02
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTAGAAATAAAACCGG
Found at i:3396161 original size:27 final size:28
Alignment explanation
Indices: 3396095--3396170 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
3396085 GCAATAAAAC
***
3396095 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
3396123 CGGGGTTAGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
3396150 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
3396171 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 24 0.57
28 18 0.43
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:3396268 original size:51 final size:51
Alignment explanation
Indices: 3395942--3396323 Score: 278
Period size: 52 Copynumber: 7.3 Consensus size: 51
3395932 GAAATAACGA
* * * *
3395942 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTAT-TTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATT-G-ATGTTTTAGAAATAAAACCGG
* * * **
3395994 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTT-GAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTGATGTTTTAG-AAATAAAACCGG
* * *
3396046 GATTGGAGTATCCCCGATTGTGGAAAAATT-AGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTGA-TGTTTTAGAAATAAAACCGG
** *** * *
3396098 GGTTGGAGTATCCCC---TCGGAAATAACGGGGTTAGA-GTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTATGAAA-AA-----TT-GATGT-T-TTAGA-AATAAAACCGG
* * * *
3396153 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAA-AAATT-G-ATGTTTTAGAAATAAAACCGG
* * *
3396207 AGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAGCCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGG
* *
3396258 GGTTGGAGTATCCCTGATTATGAAAAATTGATGTTTTAGAGATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGG
3396309 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
3396324 TCGGAAATAA
Statistics
Matches: 258, Mismatches: 47, Indels: 51
0.72 0.13 0.14
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
51 78 0.30
52 90 0.35
53 20 0.08
54 30 0.12
55 20 0.08
56 4 0.02
57 2 0.01
58 6 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGG
Found at i:3396321 original size:211 final size:212
Alignment explanation
Indices: 3395878--3396350 Score: 699
Period size: 212 Copynumber: 2.2 Consensus size: 212
3395868 AGAAGAAAAA
* *
3395878 AAAATCGGGATTGGAGTATCCCCTC-GAAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGA
1 AAAACCGGGGTTGGAGTATCCCCTCGGAAA-TAACGGGGTTGGAGTATCCCCGATGAAATAACGA
* *
3395942 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCC
65 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATCC
* * *
3396007 CCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGGGATTGGAGTATCCCCGATTGTGGAAA
130 CCGATTAAAGAAAAATTGACGTTTTGAAAATAAAACCGGGATTGGAGTATCCCCGATTATGGAAA
3396072 AATTAGTGTTTTAGCAAT
195 AATTAGTGTTTTAGCAAT
* * *
3396090 AAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTAGAGTATCCCCGATG-ATTAACGGG
1 AAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
3396154 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTTGGAAATAAAATCGGAGTTAGAGTATC
66 GTTGGAGTATCCCCGATTGTGAA-AAATTGGTA-TTTTTGGAAATAAAATCGGAGTTAGAGTATC
* * * * *
3396219 CCCGATT-ATGAAAAATTGATGTTTT-AGAAATAAAGCCGGGGTTGGAGTATCCCTGATTAT-GA
129 CCCGATTAAAGAAAAATTGACGTTTTGA-AAATAAAACCGGGATTGGAGTATCCCCGATTATGGA
3396281 AAAATT-GATGTTTTAG-AGAT
193 AAAATTAG-TGTTTTAGCA-AT
*
3396301 AAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGATTGGAGTATCCC
1 AAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCC
3396351 TGATTGTGAA
Statistics
Matches: 238, Mismatches: 17, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
210 2 0.01
211 96 0.40
212 99 0.42
213 41 0.17
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (212 bp):
AAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATCCC
CGATTAAAGAAAAATTGACGTTTTGAAAATAAAACCGGGATTGGAGTATCCCCGATTATGGAAAA
ATTAGTGTTTTAGCAAT
Found at i:3398718 original size:20 final size:20
Alignment explanation
Indices: 3398691--3398745 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
3398681 TAAAATTTCC
*
3398691 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
3398711 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
3398731 AAATGTATCGATACA
1 AAATGTATCGATACA
3398746 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:3398880 original size:21 final size:21
Alignment explanation
Indices: 3398856--3398912 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3398846 CATTTGTAGG
3398856 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
3398877 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
3398898 ATGTATCGATACATT
1 ATGTATCGATACATT
3398913 TGGATAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:3403339 original size:24 final size:24
Alignment explanation
Indices: 3403294--3403339 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
3403284 ACCCCCTACA
** *
3403294 CCACAAAACCTTACCCAAAACCGT
1 CCACAAAACCAAACACAAAACCGT
*
3403318 CCACAAAACCAAACACAGAACC
1 CCACAAAACCAAACACAAAACC
3403340 AACTTGTTCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.41, G:0.04, T:0.07
Consensus pattern (24 bp):
CCACAAAACCAAACACAAAACCGT
Found at i:3410632 original size:42 final size:42
Alignment explanation
Indices: 3410561--3411015 Score: 196
Period size: 42 Copynumber: 10.9 Consensus size: 42
3410551 ACCTCATTCC
* *
3410561 AGACTTCTTCATCTTTCGTCT-GCTCGTCGGC-CTAGAA-TCGGG
1 AGACTTCTTTATCTTTCGTCTACCT-GTCGGCTC-A-AACTCGGG
* *
3410603 AGACTTCTTTATCTTTCATCTACCTGTCGGCTCAGACTCGAGG
1 AGACTTCTTTATCTTTCGTCTACCTGTCGGCTCAAACTCG-GG
* * * *
3410646 -GACTT-TTTCATCTTTCGTTTA-CTCGTCAGCTTAAACCTAGGG
1 AGACTTCTTT-ATCTTTCGTCTACCT-GTCGGCTCAAA-CTCGGG
* * *
3410688 -GACTTCTTTATCTTTTGTCTACCCGTCGGCTCAAACTCGAG
1 AGACTTCTTTATCTTTCGTCTACCTGTCGGCTCAAACTCGGG
** * *
3410729 AGACTT-TTTCATCTTTCGTCTACCTGTTAGCTCAGACT-GAG
1 AGACTTCTTT-ATCTTTCGTCTACCTGTCGGCTCAAACTCGGG
* ** * * * *
3410770 AGACTTCCTTATCAATCATCTGCCCT-TCAGCTCAAACTTGGG
1 AGACTTCTTTATCTTTCGTCT-ACCTGTCGGCTCAAACTCGGG
* ** * * ** *** *
3410812 AGACTTCTTCA-CAATCATCTGCCCATCATTTCAGACTCGGG
1 AGACTTCTTTATCTTTCGTCTACCTGTCGGCTCAAACTCGGG
* * * * * * **
3410853 AGACTT-TTTCATCTTTCATTTGCCCGTCGGCTGAGACTCGAT
1 AGACTTCTTT-ATCTTTCGTCTACCTGTCGGCTCAAACTCGGG
* * * ** * *
3410895 AGACTTCTTCATCTTTTGTCTGCCCATCGGCTCAGACTCGAG
1 AGACTTCTTTATCTTTCGTCTACCTGTCGGCTCAAACTCGGG
* * ** * *
3410937 AGACTTCTTTATCTTTTGTCTACCCGTCAACTCAGACCCGGG
1 AGACTTCTTTATCTTTCGTCTACCTGTCGGCTCAAACTCGGG
* ** * * *
3410979 AGACTTCTTCATCAATCATCTGCCCGTCGGCTCAAAC
1 AGACTTCTTTATCTTTCGTCTACCTGTCGGCTCAAAC
3411016 CCAAGGAGAT
Statistics
Matches: 323, Mismatches: 72, Indels: 36
0.75 0.17 0.08
Matches are distributed among these distances:
40 4 0.01
41 68 0.21
42 237 0.73
43 14 0.04
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.34
Consensus pattern (42 bp):
AGACTTCTTTATCTTTCGTCTACCTGTCGGCTCAAACTCGGG
Found at i:3410963 original size:84 final size:84
Alignment explanation
Indices: 3410561--3411012 Score: 356
Period size: 84 Copynumber: 5.4 Consensus size: 84
3410551 ACCTCATTCC
* * * *
3410561 AGACTTCTTCATCTTTCGTCTGCTCGTCGGC-CTAGAATCGGGAGACTTCTTTATCTTTCATCTA
1 AGACTTCTTCATCTTTCGTCTGCCCGTCAGCTC-AGACTCGAGAGACTTCTTTATCTTTCATCTA
*
3410625 CCTGTCGGCTCAGACTCGAG
65 CCCGTCGGCTCAGACTCGAG
* * * * * * * * * **
3410645 GGACTTTTTCATCTTTCGTTTACTCGTCAGCTTAAAC-CTAGGGGACTTCTTTATCTTTTGTCTA
1 AGACTTCTTCATCTTTCGTCTGCCCGTCAGCTCAGACTCGA-GAGACTTCTTTATCTTTCATCTA
*
3410709 CCCGTCGGCTCAAACTCGAG
65 CCCGTCGGCTCAGACTCGAG
* * * * * ** *
3410729 AGACTTTTTCATCTTTCGTCTACCTGTTAGCTCAGACT-GAGAGACTTCCTTATCAATCATCTGC
1 AGACTTCTTCATCTTTCGTCTGCCCGTCAGCTCAGACTCGAGAGACTTCTTTATCTTTCATCTAC
* * * * *
3410793 CCTTCAGCTCAAACTTGGG
66 CCGTCGGCTCAGACTCGAG
** * * ** * * *
3410812 AGACTTCTTCA-CAATCATCTGCCCATCATTTCAGACTCGGGAGACTT-TTTCATCTTTCATTTG
1 AGACTTCTTCATCTTTCGTCTGCCCGTCAGCTCAGACTCGAGAGACTTCTTT-ATCTTTCATCTA
* *
3410875 CCCGTCGGCTGAGACTCGAT
65 CCCGTCGGCTCAGACTCGAG
* * * **
3410895 AGACTTCTTCATCTTTTGTCTGCCCATCGGCTCAGACTCGAGAGACTTCTTTATCTTTTGTCTAC
1 AGACTTCTTCATCTTTCGTCTGCCCGTCAGCTCAGACTCGAGAGACTTCTTTATCTTTCATCTAC
** * *
3410960 CCGTCAACTCAGACCCGGG
66 CCGTCGGCTCAGACTCGAG
** * *
3410979 AGACTTCTTCATCAATCATCTGCCCGTCGGCTCA
1 AGACTTCTTCATCTTTCGTCTGCCCGTCAGCTCA
3411013 AACCCAAGGA
Statistics
Matches: 282, Mismatches: 79, Indels: 14
0.75 0.21 0.04
Matches are distributed among these distances:
82 19 0.07
83 84 0.30
84 176 0.62
85 3 0.01
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (84 bp):
AGACTTCTTCATCTTTCGTCTGCCCGTCAGCTCAGACTCGAGAGACTTCTTTATCTTTCATCTAC
CCGTCGGCTCAGACTCGAG
Found at i:3411084 original size:86 final size:83
Alignment explanation
Indices: 3410973--3411129 Score: 206
Period size: 86 Copynumber: 1.9 Consensus size: 83
3410963 TCAACTCAGA
* *
3410973 CCCGGGAGACTTCTTCATCAATCATCTGCCCGTCGGCTCAAACCCAAGGAGATTTTTTTATCTTT
1 CCCGAGAGACTTCTTCACCAATCATCTGCCCGTC-GCTC-AACCCAAGGAGA-TTTTTTATCTTT
3411038 TGTTTGCCCGTTTATTCAGTC
63 TGTTTGCCCGTTTATTCAGTC
** ** ***
3411059 CCCGAGAGACTTCTTCACCCGTCATCTGCCCGTCGCTCAGTCTTGGGAGATTTTTTATCTTTTGT
1 CCCGAGAGACTTCTTCACCAATCATCTGCCCGTCGCTCAACCCAAGGAGATTTTTTATCTTTTGT
3411124 TTGCCC
66 TTGCCC
3411130 ATCGGCTTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
83 21 0.34
84 7 0.11
85 4 0.06
86 30 0.48
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.36
Consensus pattern (83 bp):
CCCGAGAGACTTCTTCACCAATCATCTGCCCGTCGCTCAACCCAAGGAGATTTTTTATCTTTTGT
TTGCCCGTTTATTCAGTC
Found at i:3411193 original size:42 final size:42
Alignment explanation
Indices: 3411115--3411201 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 42
3411105 GAGATTTTTT
* * * *
3411115 ATCTTTTGTTTGCCCATCGGCTTAAACCTGAGAGACTTATTC
1 ATCTTTTGTATGCCCATCGGCTCAAACCCGAAAGACTTATTC
* * * *
3411157 ATCTTTTGTATGCCCGTTGGCTCAGACCCGAAAGACTTTTTC
1 ATCTTTTGTATGCCCATCGGCTCAAACCCGAAAGACTTATTC
3411199 ATC
1 ATC
3411202 CATCATATGC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (42 bp):
ATCTTTTGTATGCCCATCGGCTCAAACCCGAAAGACTTATTC
Found at i:3413567 original size:166 final size:166
Alignment explanation
Indices: 3413366--3414200 Score: 969
Period size: 166 Copynumber: 5.0 Consensus size: 166
3413356 AAATTCTTTG
3413366 AATATTATCATTTATTTCATATTAAAT-TAGTTTTCAAAAATTAATTCATTTTCATGAGTTTTTG
1 AATATTATCATTTATTTCATATTAAATCT-GTTTTCAAAAATTAATTCATTTTCATGAGTTTTTG
3413430 AATTTTTCCTTGAAATTCTCTTTTTTTCGAAATATGTTATTTTCTACTTCGTAAATTTTTTCGAG
65 AATTTTTCCTTGAAATTCTCTTTTTTTCGAAATATGTTATTTTCTACTTCGTAAATTTTTTCGAG
*
3413495 GAGATTTTTCTTGGTTTTTAATTTTTAAATTTCATCA
130 GAGATTTTTCTTAGTTTTTAATTTTTAAATTTCATCA
*
3413532 AATATTATCATTTATTTCATATTAAATCTGTTTTCAAAAATTAATTTATTTTCATGAGTTTTTGA
1 AATATTATCATTTATTTCATATTAAATCTGTTTTCAAAAATTAATTCATTTTCATGAGTTTTTGA
* ** *
3413597 ATTTTTCCTTTGAAATT-TTTCTTTTTTCGAAATACATTATTTTCTACTTCGTAAATTTTTTTGA
66 ATTTTTCC-TTGAAATTCTCT-TTTTTTCGAAATATGTTATTTTCTACTTCGTAAATTTTTTCGA
* *
3413661 GGAGATTTTTCTTAGTTTTTAATTTTTACATTTCATAA
129 GGAGATTTTTCTTAGTTTTTAATTTTTAAATTTCATCA
* * *
3413699 AATATTATAATTTATTTTATATTAAAT-TAGTTTTCAAAAATTAATTCATTTTCATGAGTTTTTA
1 AATATTATCATTTATTTCATATTAAATCT-GTTTTCAAAAATTAATTCATTTTCATGAGTTTTTG
* * ** *
3413763 AATTTTTCCTTGAAATTCTC-CTTTTTCGAAATACGTCGTTTTCTACTTCGTAAATTTTTT-TAG
65 AATTTTTCCTTGAAATTCTCTTTTTTTCGAAATATGTTATTTTCTACTTCGTAAATTTTTTCGAG
* * *
3413826 GGGATTTTTC-TCGATTTTTAATTTTTAAATTTCATAA
130 GAGATTTTTCTTAG-TTTTTAATTTTTAAATTTCATCA
* * * * *
3413863 AATGTTATCATTTATTTTATATTAAATCAGTTTTCAAAAATTAATTTATTTTCATGAGTTTTTAA
1 AATATTATCATTTATTTCATATTAAATCTGTTTTCAAAAATTAATTCATTTTCATGAGTTTTTGA
* * * * * * * *
3413928 ATTTTTTCTTCAAAATTC-CTTTTTTTCTAAAATATAG-TCTTTT-TGCTTCATAAATTCTTCCG
66 ATTTTTCCTT-GAAATTCTCTTTTTTTC-GAAATAT-GTTATTTTCTACTTCGTAAATTTTTTCG
* * * *
3413990 AGGGGATTTTTCTCAGTTCTCAATTTTTAAAATTT-ATCA
128 AGGAGATTTTTCTTAGTTTTTAATTTTT-AAATTTCATCA
* * ** * *
3414029 AAAATCATCATTTGA-TTCATATTAAATCAATTTTGAAAAATTAATTCATTTTCATGAGTTTTAG
1 AATATTATCATTT-ATTTCATATTAAATCTGTTTTCAAAAATTAATTCATTTTCATGAGTTTTTG
* ** * * * *
3414093 ATTTTTTTGTTGAAATTCTCTTTTTTTCAAGAAAAAT-AT-TTTTCTTCTCCGTAAATTTTTTCG
65 AATTTTTCCTTGAAATTCTCTTTTTTTC--GAAATATGTTATTTTCTACTTCGTAAATTTTTTC-
** ** *
3414156 GAGG-GATTTTTCTTAGTTTAGAATTTTTAAAACTCATCT
127 GAGGAGATTTTTCTTAGTTTTTAATTTTTAAATTTCATCA
3414195 AATATT
1 AATATT
3414201 GTTATCTAAC
Statistics
Matches: 577, Mismatches: 71, Indels: 42
0.84 0.10 0.06
Matches are distributed among these distances:
163 2 0.00
164 103 0.18
165 75 0.13
166 227 0.39
167 170 0.29
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (166 bp):
AATATTATCATTTATTTCATATTAAATCTGTTTTCAAAAATTAATTCATTTTCATGAGTTTTTGA
ATTTTTCCTTGAAATTCTCTTTTTTTCGAAATATGTTATTTTCTACTTCGTAAATTTTTTCGAGG
AGATTTTTCTTAGTTTTTAATTTTTAAATTTCATCA
Found at i:3414594 original size:13 final size:13
Alignment explanation
Indices: 3414576--3414622 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 13
3414566 CTAGCAAAGT
3414576 GAGAAAAAAAAAA
1 GAGAAAAAAAAAA
*
3414589 GAG--AAAGAAAA
1 GAGAAAAAAAAAA
3414600 GAGAAAAAAAAAGGA
1 GAGAAAAAAAAA--A
3414615 GAGAAAAA
1 GAGAAAAA
3414623 TAGTGAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 10 0.36
13 9 0.32
15 9 0.32
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
GAGAAAAAAAAAA
Found at i:3418334 original size:27 final size:26
Alignment explanation
Indices: 3418310--3418379 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 26
3418300 GTTTAAAAGC
3418310 AAGGTTGGAGTATCCCT-TCGAAAAAA
1 AAGGTTGGAGTATCCCTCTC-AAAAAA
**
3418336 TGGAGTTGGAGTAT-CCTCTCAAAAAAA
1 AAG-GTTGGAGTATCCCTCTC-AAAAAA
3418363 TAAGGTTGGAGTATCCC
1 -AAGGTTGGAGTATCCC
3418380 CAATAAATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 4 0.11
27 28 0.80
28 3 0.09
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (26 bp):
AAGGTTGGAGTATCCCTCTCAAAAAA
Found at i:3420921 original size:20 final size:21
Alignment explanation
Indices: 3420898--3420943 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3420888 GGCATGTATC
* *
3420898 ATACATTCATTTA-TGTATTG
1 ATACATTCACTAATTGTATTG
3420918 ATACATTCACTAATTGTATTG
1 ATACATTCACTAATTGTATTG
3420939 ATACA
1 ATACA
3420944 AATCGTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (21 bp):
ATACATTCACTAATTGTATTG
Found at i:3421005 original size:21 final size:21
Alignment explanation
Indices: 3420981--3421025 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3420971 ATTGGGACCT
*
3420981 TGTATTGATACA-TTTAAGAAA
1 TGTATCGATACATTTTAA-AAA
*
3421002 TGTATCGATATATTTTAAAAA
1 TGTATCGATACATTTTAAAAA
3421023 TGT
1 TGT
3421026 GACTTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTTTAAAAA
Found at i:3425305 original size:21 final size:20
Alignment explanation
Indices: 3425281--3425354 Score: 85
Period size: 21 Copynumber: 3.6 Consensus size: 20
3425271 TTCTACAACT
3425281 TGTATCGATACAATTAGTAAA
1 TGTATCGATAC-ATTAGTAAA
* * *
3425302 TGTATTGATACATAAGTGAA
1 TGTATCGATACATTAGTAAA
**
3425322 TGTATCGATACATGTCTTAAA
1 TGTATCGATACAT-TAGTAAA
3425343 TGTATCGATACA
1 TGTATCGATACA
3425355 AGACCATGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 19 0.43
21 25 0.57
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATTAGTAAA
Found at i:3425435 original size:20 final size:20
Alignment explanation
Indices: 3425412--3425469 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
3425402 ATACATAAGT
3425412 AAATGTATCGATACATTTCC
1 AAATGTATCGATACATTTCC
* *
3425432 AAATGTATTGATACAATTTGC
1 AAATGTATCGATAC-ATTTCC
**
3425453 -TTTGTATCGATACATTT
1 AAATGTATCGATACATTT
3425470 AGGGTTGTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
19 4 0.12
20 23 0.72
21 5 0.16
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (20 bp):
AAATGTATCGATACATTTCC
Found at i:3426104 original size:64 final size:65
Alignment explanation
Indices: 3426003--3426252 Score: 265
Period size: 64 Copynumber: 3.9 Consensus size: 65
3425993 TTCAGCCATT
* * * * *
3426003 CTAAAGCCCACACCAGTCAGTGGCAACCTTTC-TAAAGCCCACACAAGTCGGTGGTAACCCTTCC
1 CTAAAGCCCACACAAGTCAGTGGCAACCCTTCTTAAAACCCACACAAGTTGGTGGCAACCCTTCC
* ** * * * *
3426067 CTAAAGCCTACACAAGTTGGTGGCAACCCTTC-TAAAGCCCACAGATGTTGGTGGCAACCCTTCT
1 CTAAAGCCCACACAAGTCAGTGGCAACCCTTCTTAAAACCCACACAAGTTGGTGGCAACCCTTCC
* * ** * * *
3426131 CTAAAGCCTACACAAGTCGGTGGCAATACTTCTTTAAAACCTACACCAGTTAGTGGCAACCC-T-
1 CTAAAGCCCACACAAGTCAGTGGCAACCCTTC-TTAAAACCCACACAAGTTGGTGGCAACCCTTC
3426194 C
65 C
* *
3426195 TTAAAGCCCACACAAGTCAGTGGCAACCCTTCTTAAAAACCCACACAAGTTAGTGGCA
1 CTAAAGCCCACACAAGTCAGTGGCAACCCTTCTT-AAAACCCACACAAGTTGGTGGCA
3426253 TCTCCTTCTA
Statistics
Matches: 156, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
63 2 0.01
64 131 0.84
65 1 0.01
66 22 0.14
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.21
Consensus pattern (65 bp):
CTAAAGCCCACACAAGTCAGTGGCAACCCTTCTTAAAACCCACACAAGTTGGTGGCAACCCTTCC
Found at i:3426240 original size:33 final size:32
Alignment explanation
Indices: 3426004--3426261 Score: 243
Period size: 33 Copynumber: 8.0 Consensus size: 32
3425994 TCAGCCATTC
* *
3426004 TAAAGCCCACACCAGTCAGTGGCAACCTTTC-
1 TAAAGCCCACACAAGTCAGTGGCAACCCTTCT
* * *
3426035 TAAAGCCCACACAAGTCGGTGGTAACCCTTCCC
1 TAAAGCCCACACAAGTCAGTGGCAACCCTT-CT
* **
3426068 TAAAGCCTACACAAGTTGGTGGCAACCCTTC-
1 TAAAGCCCACACAAGTCAGTGGCAACCCTTCT
* * **
3426099 TAAAGCCCACAGATGTTGGTGGCAACCCTTCT
1 TAAAGCCCACACAAGTCAGTGGCAACCCTTCT
* * **
3426131 CTAAAGCCTACACAAGTCGGTGGCAATACTTCTT
1 -TAAAGCCCACACAAGTCAGTGGCAACCCTTC-T
* * * *
3426165 TAAAACCTACACCAGTTAGTGGCAACCC-TCT
1 TAAAGCCCACACAAGTCAGTGGCAACCCTTCT
3426196 TAAAGCCCACACAAGTCAGTGGCAACCCTTCT
1 TAAAGCCCACACAAGTCAGTGGCAACCCTTCT
* * *
3426228 TAAAAACCCACACAAGTTAGTGGCATCTCCTTCT
1 T-AAAGCCCACACAAGTCAGTGGCAAC-CCTTCT
3426262 AAGCCTAATG
Statistics
Matches: 190, Mismatches: 29, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
31 79 0.42
32 8 0.04
33 96 0.51
34 7 0.04
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.22
Consensus pattern (32 bp):
TAAAGCCCACACAAGTCAGTGGCAACCCTTCT
Found at i:3426252 original size:97 final size:96
Alignment explanation
Indices: 3426001--3426244 Score: 303
Period size: 97 Copynumber: 2.5 Consensus size: 96
3425991 CCTTCAGCCA
* * * *
3426001 TTCTAAAGCCCACACCAGTCAGTGGCAACCTTTC-TAAAGCCCACACAAGTCGGTGGTAACCCTT
1 TTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCTTAAAGCCCACACAAGTCGGTGGCAACACTT
* *
3426065 CCCTAAAGCCTACACAAGTTGGTGGCAACCC
66 CCCTAAAACCTACACAAGTTAGTGGCAACCC
* * ** * *
3426096 TTCTAAAGCCCACAGATGTTGGTGGCAACCCTTCTCTAAAGCCTACACAAGTCGGTGGCAATACT
1 TTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCT-TAAAGCCCACACAAGTCGGTGGCAACACT
** *
3426161 TCTTTAAAACCTACACCAGTTAGTGGCAACCC
65 TCCCTAAAACCTACACAAGTTAGTGGCAACCC
*
3426193 -TCTTAAAGCCCACACAAGTCAGTGGCAACCCTTCTTAAAAACCCACACAAGT
1 TTC-TAAAGCCCACACAAGTCAGTGGCAACCCTTCTT-AAAGCCCACACAAGT
3426245 TAGTGGCATC
Statistics
Matches: 124, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
95 28 0.23
96 3 0.02
97 93 0.75
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.22
Consensus pattern (96 bp):
TTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCTTAAAGCCCACACAAGTCGGTGGCAACACTT
CCCTAAAACCTACACAAGTTAGTGGCAACCC
Found at i:3426393 original size:52 final size:52
Alignment explanation
Indices: 3426325--3426524 Score: 229
Period size: 52 Copynumber: 3.8 Consensus size: 52
3426315 TTTTCTAAAC
* *
3426325 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTTCTCATCTTTGAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTTCTCATTTTTAAGT
** * * * * * * * *
3426377 CTGATATCGCTAGCCTTGAAGCAGCATATTGGTACCTTTATCTCCTTTTTAAGC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGG--CATTTTTCTCATTTTTAAGT
* * * *
3426431 CCAATGTCACTGGCCTTGAATCAACACATTAGCATTTTTATCATTTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTTCTCATTTTTAAGT
*
3426483 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTTCTC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTTCTC
3426525 TTCCTTATTA
Statistics
Matches: 115, Mismatches: 31, Indels: 4
0.77 0.21 0.03
Matches are distributed among these distances:
52 78 0.68
54 37 0.32
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (52 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTTCTCATTTTTAAGT
Found at i:3426444 original size:106 final size:107
Alignment explanation
Indices: 3426315--3426514 Score: 276
Period size: 106 Copynumber: 1.9 Consensus size: 107
3426305 CAAACCATTT
* * * * * **
3426315 TTTTCTAAACCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTTCTCATCTTTGAGTCTG
1 TTTTCTAAACCCAATGTCACTGGCCTTGAATCAACACATTAGCATTTTTATCATCTTTAAGTCCA
*
3426380 ATATCGCTAGCCTTGAAGCAGCATATTGGTACCTTTATCTCC
66 ATATCGCTAGCCTTGAAGCAGCACATTGGTACCTTTATCTCC
* *
3426422 TTTT-TAAGCCCAATGTCACTGGCCTTGAATCAACACATTAGCATTTTTATCATTTTTAAGTCCA
1 TTTTCTAAACCCAATGTCACTGGCCTTGAATCAACACATTAGCATTTTTATCATCTTTAAGTCCA
* * *
3426486 ATGTCGCTGGCCTTGAATCAGCACATTGG
66 ATATCGCTAGCCTTGAAGCAGCACATTGG
3426515 CACTTTTCTC
Statistics
Matches: 80, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
106 76 0.95
107 4 0.05
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (107 bp):
TTTTCTAAACCCAATGTCACTGGCCTTGAATCAACACATTAGCATTTTTATCATCTTTAAGTCCA
ATATCGCTAGCCTTGAAGCAGCACATTGGTACCTTTATCTCC
Found at i:3433890 original size:29 final size:29
Alignment explanation
Indices: 3433854--3433977 Score: 144
Period size: 29 Copynumber: 4.2 Consensus size: 29
3433844 TTCTTCAAAG
*
3433854 TCTGTGGTACCATTTTTAAAGTTCACAAC
1 TCTGTGGTACCATTTTTAAAGTCCACAAC
*
3433883 TCTGTGGTACCATTTTTAAAGTTCACAAC
1 TCTGTGGTACCATTTTTAAAGTCCACAAC
* *
3433912 TCTGTGGTACCCTTTTTTTTTAAGTCCACAAC
1 TCTGTGGTA-CC--ATTTTTAAAGTCCACAAC
** *
3433944 TCCATGGTACC-TTTTT-ATGTCCACAAC
1 TCTGTGGTACCATTTTTAAAGTCCACAAC
3433971 TCTGTGG
1 TCTGTGG
3433978 CACGTTTTTC
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
27 15 0.18
28 5 0.06
29 38 0.45
30 2 0.02
31 2 0.02
32 22 0.26
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (29 bp):
TCTGTGGTACCATTTTTAAAGTCCACAAC
Found at i:3433985 original size:27 final size:27
Alignment explanation
Indices: 3433928--3434195 Score: 97
Period size: 27 Copynumber: 9.2 Consensus size: 27
3433918 GTACCCTTTT
*
3433928 TTTTTAAGTCCACAACTCCATGGTACC
1 TTTTTAAGTCCACAACTCCATGGCACC
* ** *
3433955 TTTTTATGTCCACAACTCTGTGGCACGTTT
1 TTTTTAAGTCCACAACTCCATGGCAC---C
** *
3433985 TTCTTCTCAAAGTCCATGACT-CAGTGGCATCG
1 TT-TT-T--AAGTCCACAACTCCA-TGGCA-CC
* **
3434017 CTTTTAAGTCCACAACTCTGTGGCACC
1 TTTTTAAGTCCACAACTCCATGGCACC
*
3434044 TTTTTCTTTCAAAGTCCACAACTCCATGGCATC
1 ---TT-TTT--AAGTCCACAACTCCATGGCACC
** * * * *
3434077 TCTTTTAAAACTATAACTCTATAGCACC
1 T-TTTTAAGTCCACAACTCCATGGCACC
* *
3434105 ATTTTCTTTTAAGTCCACAACTTCGTGGCACC
1 ----T-TTTTAAGTCCACAACTCCATGGCACC
* * **
3434137 TTTTTAAGTCTATAACTCTGTGGCACC
1 TTTTTAAGTCCACAACTCCATGGCACC
* * *
3434164 CTTTTAAGTCCATAACTCTATGGCACC
1 TTTTTAAGTCCACAACTCCATGGCACC
3434191 TTTTT
1 TTTTT
3434196 CTTTAAAGTC
Statistics
Matches: 176, Mismatches: 44, Indels: 42
0.67 0.17 0.16
Matches are distributed among these distances:
27 73 0.41
28 31 0.18
30 8 0.05
31 8 0.05
32 22 0.12
33 19 0.11
34 14 0.08
35 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (27 bp):
TTTTTAAGTCCACAACTCCATGGCACC
Found at i:3434163 original size:59 final size:59
Alignment explanation
Indices: 3433867--3434318 Score: 271
Period size: 61 Copynumber: 7.5 Consensus size: 59
3433857 GTGGTACCAT
* * * *
3433867 TTTTAAAGTTCACAAC-TCTGTGGTACCATTTTTAAAGTTCACAACTCTGTGGTACCCTTTTT-
1 TTTT-AAGTCCACAACTTC-GTGGCACC-TTTTT-AAGTCCACAACTCTGTGGCA-CCTTTTTC
* * * * *
3433929 TTTTAAGTCCACAACTCCATGGTACCTTTTTATGTCCACAACTCTGTGGCACGTTTTTC
1 TTTTAAGTCCACAACTTCGTGGCACCTTTTTAAGTCCACAACTCTGTGGCACCTTTTTC
* **
3433988 TTCTCAAAGTCCATGAC-TCAGTGGCATCGC-TTTTAAGTCCACAACTCTGTGGCACCTTTTTC
1 TT-T-TAAGTCCACAACTTC-GTGGCA-C-CTTTTTAAGTCCACAACTCTGTGGCACCTTTTTC
* * * * ** * * * * *
3434050 TTTCAAAGTCCACAACTCCATGGCATCTCTTTTAAAACTATAACTCTATAGCACCATTTTC
1 TTT-TAAGTCCACAACTTCGTGGCACCT-TTTTAAGTCCACAACTCTGTGGCACCTTTTTC
* *
3434111 TTTTAAGTCCACAACTTCGTGGCACCTTTTTAAGTCTATAACTCTGTGGCACC-----C
1 TTTTAAGTCCACAACTTCGTGGCACCTTTTTAAGTCCACAACTCTGTGGCACCTTTTTC
* * * ** * *
3434165 TTTTAAGTCCATAAC-TCTATGGCACCTTTTTCTTTAAAGTCCATAACTCCATAGCACCTGTTTC
1 TTTTAAGTCCACAACTTC-GTGGCACC---TT-TTT-AAGTCCACAACTCTGTGGCACCTTTTTC
* * * * * * *
3434229 TTTTAAAGTCTACAATTTCGTGGCATCTCTTTAAGTCTACAACTCCGTGGCATCTTTTTC
1 TTTT-AAGTCCACAACTTCGTGGCACCTTTTTAAGTCCACAACTCTGTGGCACCTTTTTC
* *
3434289 TTCTAAGTCTACAAC-TCTGTGGCA-CTTTTT
1 TTTTAAGTCCACAACTTC-GTGGCACCTTTTT
3434319 CCTTTTAAAG
Statistics
Matches: 310, Mismatches: 56, Indels: 52
0.74 0.13 0.12
Matches are distributed among these distances:
53 2 0.01
54 22 0.07
57 2 0.01
58 16 0.05
59 76 0.25
60 52 0.17
61 78 0.25
62 40 0.13
63 1 0.00
64 5 0.02
65 14 0.05
66 2 0.01
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.38
Consensus pattern (59 bp):
TTTTAAGTCCACAACTTCGTGGCACCTTTTTAAGTCCACAACTCTGTGGCACCTTTTTC
Found at i:3434273 original size:92 final size:93
Alignment explanation
Indices: 3434017--3434397 Score: 345
Period size: 92 Copynumber: 4.2 Consensus size: 93
3434007 AGTGGCATCG
* * * **
3434017 CTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTCAAAGTCCACAACTCCATGGCATCTCTTT
1 CTTTAAAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAAGTCCACAACTCTGTGGCATCTCTTT
** * * *
3434082 TAAAACTATAACTCTATAGCACCATTTT
66 TAAGTCTACAACTCTATGGCACCTTTTT
* * * * *
3434110 CTTTTAAGTCCACAACTTCGTGGCACC----T-TTTT-AAGTCTATAACTCTGTGGCA-CCCTTT
1 CTTTAAAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAAGTCCACAACTCTGTGGCATCTCTTT
* *
3434168 TAAGTCCATAACTCTATGGCACCTTTTT
66 TAAGTCTACAACTCTATGGCACCTTTTT
* * * * * *
3434196 CTTTAAAGTCCATAACTCCATAGCACCTGTTTCTTTTAAAGTCTACAA-TTTCGTGGCATCTC-T
1 CTTTAAAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAAGTCCACAACTCT-GTGGCATCTCTT
** *
3434259 TTAAGTCTACAACTCCGTGGCATCTTTTT
65 TTAAGTCTACAACTCTATGGCACCTTTTT
* * * *
3434288 CTTCT-AAGTCTACAACTCTGTGGCA-CTTTTTCCTTTTAAAGTCCACAACTCTGTGGTAAC-CT
1 CTT-TAAAGTCCACAACTCCGTGGCACCTTTTT-CTTTTAAAGTCCACAACTCTGTGGCATCTCT
*
3434350 TTTAAGTCTACAACTCTGTGGCACCTTTTT
64 TTTAAGTCTACAACTCTATGGCACCTTTTT
* *
3434380 CTTTTAAAGCCCATAACT
1 C-TTTAAAGTCCACAACT
3434398 TCATGGCATC
Statistics
Matches: 233, Mismatches: 41, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
86 50 0.21
87 16 0.07
88 3 0.01
89 1 0.00
90 1 0.00
91 12 0.05
92 109 0.47
93 41 0.18
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (93 bp):
CTTTAAAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAAGTCCACAACTCTGTGGCATCTCTTT
TAAGTCTACAACTCTATGGCACCTTTTT
Found at i:3434379 original size:27 final size:27
Alignment explanation
Indices: 3434111--3434379 Score: 121
Period size: 27 Copynumber: 9.1 Consensus size: 27
3434101 CACCATTTTC
*
3434111 TTTTAAGTCCACAACT-TCGTGGCACCT
1 TTTTAAGTCTACAACTCT-GTGGCACCT
* *
3434138 TTTTAAGTCTATAACTCTGTGGCACCC
1 TTTTAAGTCTACAACTCTGTGGCACCT
* * *
3434165 TTTTAAGTCCATAACTCTATGGCACCTTTT
1 TTTTAAGTCTACAACTCTGTGGCACC---T
* * ** *
3434195 TCTTTAAAGTCCATAACTCCATAGCACCTGTTT
1 T-TTT-AAGTCTACAACTCTGTGGCACC----T
* *
3434228 CTTTTAAAGTCTACAA-TTTCGTGGCATCT
1 -TTTT-AAGTCTACAACTCT-GTGGCACCT
* * *
3434257 CTTTAAGTCTACAACTCCGTGGCATCTTTT
1 TTTTAAGTCTACAACTCTGTGGCA-C--CT
3434287 TCTTCTAAGTCTACAACTCTGTGGCACTTTTTCCT
1 T-TT-TAAGTCTACAACTCTGTGGCA------CCT
* * *
3434322 TTTAAAGTCCACAACTCTGTGGTAACC-
1 TTTTAAGTCTACAACTCTGTGG-CACCT
3434349 TTTTAAGTCTACAACTCTGTGGCACCT
1 TTTTAAGTCTACAACTCTGTGGCACCT
3434376 TTTT
1 TTTT
3434380 CTTTTAAAGC
Statistics
Matches: 190, Mismatches: 30, Indels: 44
0.72 0.11 0.17
Matches are distributed among these distances:
26 3 0.02
27 86 0.45
28 7 0.04
29 1 0.01
30 2 0.01
31 5 0.03
32 41 0.22
33 37 0.19
34 4 0.02
35 2 0.01
37 2 0.01
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.39
Consensus pattern (27 bp):
TTTTAAGTCTACAACTCTGTGGCACCT
Found at i:3434424 original size:61 final size:61
Alignment explanation
Indices: 3434287--3434435 Score: 178
Period size: 60 Copynumber: 2.5 Consensus size: 61
3434277 GGCATCTTTT
* * * *
3434287 TCTTCTAAGTCTACAACTCTGTGGCACTTTTTCCTTTTAAAGTCCACAACTCTGTGGTAAC
1 TCTTTTAAGTCTACAACTCTGTGGCACTTTTTCCTTTTAAAGCCCACAACTCTATGGCAAC
* *
3434348 -CTTTTAAGTCTACAACTCTGTGGCACCTTTTT-CTTTTAAAGCCCATAACT-TCATGGCATC
1 TCTTTTAAGTCTACAACTCTGTGGCA-CTTTTTCCTTTTAAAGCCCACAACTCT-ATGGCAAC
* **
3434408 TCTTTTAAGTCCACAACTCCATGGCACT
1 TCTTTTAAGTCTACAACTCTGTGGCACT
3434436 CCTTTTTTTC
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
59 1 0.01
60 47 0.62
61 28 0.37
ACGTcount: A:0.23, C:0.28, G:0.12, T:0.37
Consensus pattern (61 bp):
TCTTTTAAGTCTACAACTCTGTGGCACTTTTTCCTTTTAAAGCCCACAACTCTATGGCAAC
Found at i:3434546 original size:31 final size:31
Alignment explanation
Indices: 3434498--3435004 Score: 471
Period size: 31 Copynumber: 16.0 Consensus size: 31
3434488 CATGGAATCT
* *
3434498 CTTTTAAAAGTCCACACAGGTCGGTGGCAACC
1 CTTTT-AAAGCCCACACAAGTCGGTGGCAACC
*
3434530 GTTTTAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTAAAGCCCACACAAGTCGGTGGCAACC
* * * *
3434561 CTTTTAAAGCCTAAACAAGTAGATGGCAA-C
1 CTTTTAAAGCCCACACAAGTCGGTGGCAACC
*
3434591 CTTTCTAAAGCCCACACAAGT-GGGGGCAACC
1 CTTT-TAAAGCCCACACAAGTCGGTGGCAACC
** **
3434622 CTTTTAAAGCTAACACAAGTCAATGGCAACTC
1 CTTTTAAAGCCCACACAAGTCGGTGGCAAC-C
* *
3434654 TTTTCTAAAGCCCACACAAGTCGGTAGCAACC
1 CTTT-TAAAGCCCACACAAGTCGGTGGCAACC
* * ** *
3434686 CTTATAAAGCCTACACAAGTTAGTGGAAACC
1 CTTTTAAAGCCCACACAAGTCGGTGGCAACC
* *
3434717 CTTCTCTAAAGCCCACATAAGTCGGTAGCAACC
1 CTT-T-TAAAGCCCACACAAGTCGGTGGCAACC
* * * **
3434750 TTTCTCTAAA-ACCATACAAGTCAATGGCAACC
1 CTT-T-TAAAGCCCACACAAGTCGGTGGCAACC
** * *
3434782 CTTCCAAAGCCCACACAAGTCGGTAGTAACC
1 CTTTTAAAGCCCACACAAGTCGGTGGCAACC
* *
3434813 CTTCTAAAGCCCACACAAGTCGGTGACAACC
1 CTTTTAAAGCCCACACAAGTCGGTGGCAACC
** * *
3434844 CTTCTTTAAAGTACACACAAGTCGATGGCAATC
1 C-T-TTTAAAGCCCACACAAGTCGGTGGCAACC
* *
3434877 CTTCTCTAAAGCCCACACCAGTCGGTGGTAACC
1 CTT-T-TAAAGCCCACACAAGTCGGTGGCAACC
* *
3434910 CTTCTAAAGCCCACACAAGTTGGTGGCAACC
1 CTTTTAAAGCCCACACAAGTCGGTGGCAACC
*
3434941 CTTCTAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTAAAGCCCACACAAGTCGGTGGCAACC
** *
3434972 CTTCTCTAAAGTTCACACAAGTCGATGGCAACC
1 CTT-T-TAAAGCCCACACAAGTCGGTGGCAACC
3435005 TTTCTCAAAA
Statistics
Matches: 383, Mismatches: 78, Indels: 27
0.78 0.16 0.06
Matches are distributed among these distances:
30 28 0.07
31 200 0.52
32 32 0.08
33 123 0.32
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (31 bp):
CTTTTAAAGCCCACACAAGTCGGTGGCAACC
Found at i:3434694 original size:64 final size:63
Alignment explanation
Indices: 3434504--3435034 Score: 466
Period size: 64 Copynumber: 8.4 Consensus size: 63
3434494 ATCTCTTTTA
* * * * *
3434504 AAAGTCCACACAGGTCGGTGGCAACCGTTT-TAAAGCCCACACAAGTCGGTGGCAACCCTTTT
1 AAAGCCCACACAAGTCAGTGGCAACCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
* * * *
3434566 AAAGCCTAAACAAGT-AGATGGCAACC-TTTCTAAAGCCCACACAAGT-GGGGGCAACCCTTTT
1 AAAGCCCACACAAGTCAG-TGGCAACCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
** * * *
3434627 AAAGCTAACACAAGTCAATGGCAACTCTTTTCTAAAGCCCACACAAGTCGGTAGCAACCCTTAT
1 AAAGCCCACACAAGTCAGTGGCAAC-CTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
* * * * * * *
3434691 AAAGCCTACACAAGTTAGTGGAAACCCTTCTCTAAAGCCCACATAAGTCGGTAGCAACCTTTCTC
1 AAAGCCCACACAAGTCAGTGGCAA-CCTTTTCTAAAGCCCACACAAGTCGGTGGCAACC-CT-TC
3434756 T
63 T
* * * * * * *
3434757 AAA-ACCATACAAGTCAATGGCAACC-CTTCCAAAGCCCACACAAGTCGGTAGTAACCCTTCT
1 AAAGCCCACACAAGTCAGTGGCAACCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
* * ** * *
3434818 AAAGCCCACACAAGTCGGTGACAACCCTTCTT-TAAAGTACACACAAGTCGATGGCAATCCTTCT
1 AAAGCCCACACAAGTCAGTGGCAA-CCTT-TTCTAAAGCCCACACAAGTCGGTGGCAA-CCCT-T
3434882 CT
62 CT
* * * * *
3434884 AAAGCCCACACCAGTCGGTGGTAACC-CTTCTAAAGCCCACACAAGTTGGTGGCAACCCTTCT
1 AAAGCCCACACAAGTCAGTGGCAACCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
* * ** * *
3434946 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGTTCACACAAGTCGATGGCAACCTTTCT
1 AAAGCCCACACAAGTCAGTGGCAA-CCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
* * *
3435010 CAAAAACTCACACAAGTTAGTGGCA
1 --AAAGCCCACACAAGTCAGTGGCA
3435035 TCTCCTTCTA
Statistics
Matches: 380, Mismatches: 69, Indels: 36
0.78 0.14 0.07
Matches are distributed among these distances:
61 43 0.11
62 78 0.21
63 55 0.14
64 133 0.35
65 23 0.06
66 48 0.13
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (63 bp):
AAAGCCCACACAAGTCAGTGGCAACCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
Found at i:3435282 original size:52 final size:53
Alignment explanation
Indices: 3435034--3435299 Score: 180
Period size: 52 Copynumber: 4.9 Consensus size: 53
3435024 AGTTAGTGGC
* * * * * *
3435034 ATCTCCTTCTAAGCCTATTGTCATTGGCCTTGAATCAACACATTAGCA-CTTGT
1 ATCTCTTTTTAAGCCCAATGTCACTGGCCTTGAATCAACACATTGGCACCTT-T
* * * * * *
3435087 CATACCATCTCTTTCTAAGCCTAATGTCACTAGCCTTGAATCAGCATATTGGTA-CTCT
1 -AT--C-TCT-TTT-TAAGCCCAATGTCACTGGCCTTGAATCAACACATTGGCACCTTT
* * * * * ** * *
3435145 -TCTCATCTTTGAGTCCGATATCGTTGGCTTTGAATCAACATATTGGCACCTTT
1 ATCTC-TTTTTAAGCCCAATGTCACTGGCCTTGAATCAACACATTGGCACCTTT
*
3435198 ATCTCCTTTTTAAGCCCAATGTCACTAGCCTTGAATCAACACATTGGCACCTTT
1 ATCT-CTTTTTAAGCCCAATGTCACTGGCCTTGAATCAACACATTGGCACCTTT
* ** * *
3435252 ATCT-TTTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTAGCAC
1 ATCTCTTTTTAAGCCCAATGTCACTGGCCTTGAATCAACACATTGGCAC
3435300 TCTTCTCTTC
Statistics
Matches: 164, Mismatches: 39, Indels: 20
0.74 0.17 0.09
Matches are distributed among these distances:
52 66 0.40
53 7 0.04
54 49 0.30
55 1 0.01
56 2 0.01
57 2 0.01
58 3 0.02
59 34 0.21
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (53 bp):
ATCTCTTTTTAAGCCCAATGTCACTGGCCTTGAATCAACACATTGGCACCTTT
Found at i:3435287 original size:106 final size:105
Alignment explanation
Indices: 3435093--3435287 Score: 239
Period size: 106 Copynumber: 1.8 Consensus size: 105
3435083 TTGTCATACC
* * * * * *
3435093 ATCTCTTTCTAAGCCTAATGTCACTAGCCTTGAATCAGCATATTGGTACTCTTCTCATCTTTGAG
1 ATCTCTTTCTAAGCCCAATGTCACTAGCCTTGAATCAACACATTGGCACTCTTATCATCTTTAAG
* * *
3435158 TCCGATATCGTTGGCTTTGAATCAACATATTGGCACCTTT
66 TCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTT
* * *
3435198 ATCTCCTTTTTAAGCCCAATGTCACTAGCCTTGAATCAACACATTGGCAC-CTTTATCTTTTTTA
1 ATCT-CTTTCTAAGCCCAATGTCACTAGCCTTGAATCAACACATTGGCACTC-TTATCATCTTTA
* *
3435262 AGTCCAATGTTGCTGGCCTTGAATCA
64 AGTCCAATATCGCTGGCCTTGAATCA
3435288 GCACATTAGC
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
105 5 0.07
106 69 0.93
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (105 bp):
ATCTCTTTCTAAGCCCAATGTCACTAGCCTTGAATCAACACATTGGCACTCTTATCATCTTTAAG
TCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTT
Found at i:3435972 original size:21 final size:20
Alignment explanation
Indices: 3435948--3435998 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3435938 TTCAATAATT
* *
3435948 TGTATCGGTACAATTAGTGAA
1 TGTATCGATAC-ATAAGTGAA
*
3435969 TGTATTGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
*
3435989 TGTATTGATA
1 TGTATCGATA
3435999 AATGTCTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:3436102 original size:111 final size:112
Alignment explanation
Indices: 3435987--3436204 Score: 341
Period size: 111 Copynumber: 2.0 Consensus size: 112
3435977 TACATAAGTG
* * *
3435987 AATGTATTGATAAATGTCTCAAATGTATCGATACAAGACCATGTCAAGGAAAATTTTGCATT-TT
1 AATGTATCGATAAATGTCTCAAATATATCGATACAAGACCATGTCAAGGAAAATTTTGCATTCTG
3436051 GTCGAAAAATTATATCGATACA-AAGAAAATTGTATCGATACATTTCC
66 GTCGAAAAATTATATCGATACATAAGAAAA-TGTATCGATACATTTCC
* * *
3436098 AATGTATCGATAAATGTCTCAAATATATTGATACAGGACCATGTCAAGGCAAATTTTGCATTCTG
1 AATGTATCGATAAATGTCTCAAATATATCGATACAAGACCATGTCAAGGAAAATTTTGCATTCTG
* *
3436163 GTCGAAAAATTATATCGATACATAAGTAAATGTATTGATACA
66 GTCGAAAAATTATATCGATACATAAGAAAATGTATCGATACA
3436205 ATTTGCTTTG
Statistics
Matches: 97, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
111 57 0.59
112 34 0.35
113 6 0.06
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (112 bp):
AATGTATCGATAAATGTCTCAAATATATCGATACAAGACCATGTCAAGGAAAATTTTGCATTCTG
GTCGAAAAATTATATCGATACATAAGAAAATGTATCGATACATTTCC
Found at i:3442733 original size:21 final size:21
Alignment explanation
Indices: 3442688--3442734 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3442678 TCAATTTCAA
* *
3442688 CAGGAAACAAGAGCCAACATT
1 CAGGAAACAAGAGACAACATC
3442709 CAGGAAACAAG-GACAAGCATC
1 CAGGAAACAAGAGACAA-CATC
3442730 CAGGA
1 CAGGA
3442735 TTTAGGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.47, C:0.23, G:0.23, T:0.06
Consensus pattern (21 bp):
CAGGAAACAAGAGACAACATC
Found at i:3447760 original size:1 final size:1
Alignment explanation
Indices: 3447754--3447792 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
3447744 TAGCAATTGT
* * *
3447754 AAAAAAAAAAGAAAAAAAGAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3447793 GTGAAGATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.92, C:0.03, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:3447778 original size:18 final size:18
Alignment explanation
Indices: 3447755--3447789 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3447745 AGCAATTGTA
*
3447755 AAAAAAAAAGAAAAAAAG
1 AAAAAAAAACAAAAAAAG
3447773 AAAAAAAAACAAAAAAA
1 AAAAAAAAACAAAAAAA
3447790 AAAGTGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.91, C:0.03, G:0.06, T:0.00
Consensus pattern (18 bp):
AAAAAAAAACAAAAAAAG
Found at i:3447778 original size:19 final size:19
Alignment explanation
Indices: 3447754--3447790 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3447744 TAGCAATTGT
3447754 AAAAAAAAA-AGAAAAAAAG
1 AAAAAAAAACA-AAAAAAAG
3447773 AAAAAAAAACAAAAAAAA
1 AAAAAAAAACAAAAAAAA
3447791 AAGTGAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.92, C:0.03, G:0.05, T:0.00
Consensus pattern (19 bp):
AAAAAAAAACAAAAAAAAG
Found at i:3447780 original size:21 final size:21
Alignment explanation
Indices: 3447754--3447793 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3447744 TAGCAATTGT
*
3447754 AAAAAAAA-AAGAAAAAAAGA
1 AAAAAAAACAAAAAAAAAAGA
3447774 AAAAAAAACAAAAAAAAAAG
1 AAAAAAAACAAAAAAAAAAG
3447794 TGAAGATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (21 bp):
AAAAAAAACAAAAAAAAAAGA
Found at i:3451601 original size:52 final size:52
Alignment explanation
Indices: 3451519--3451640 Score: 217
Period size: 52 Copynumber: 2.3 Consensus size: 52
3451509 TGAAAAGTTA
* *
3451519 CCTGCATGTATCGATACATTTAATAGTGTATTGATACATCTGGGCAAATTTG
1 CCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTG
*
3451571 CCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTG
1 CCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTG
3451623 CCTGCATGTATCGATACA
1 CCTGCATGTATCGATACA
3451641 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTG
Found at i:3452715 original size:49 final size:49
Alignment explanation
Indices: 3452573--3453070 Score: 567
Period size: 49 Copynumber: 10.5 Consensus size: 49
3452563 GTGATAAAGA
* * * *
3452573 TGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G---AAGG
* * * *
3452627 ATGTCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGG
1 -TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
*
3452677 TGCCAATATGCTGATTAAAGGCCAGCGATATTGGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * *
3452720 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
*
3452769 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
*
3452818 TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * *
3452861 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
3452910 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * *
3452953 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
3453002 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
*
3453045 TGCCAATGTGCTGATTCAAGGCCAGC
1 TGCCAATATGCTGATTCAAGGCCAGC
3453071 TACATTGGGC
Statistics
Matches: 385, Mismatches: 40, Indels: 48
0.81 0.08 0.10
Matches are distributed among these distances:
43 144 0.37
45 3 0.01
47 3 0.01
49 194 0.50
50 4 0.01
53 1 0.00
55 36 0.09
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
Found at i:3452749 original size:92 final size:91
Alignment explanation
Indices: 3452621--3453088 Score: 485
Period size: 92 Copynumber: 5.1 Consensus size: 91
3452611 AAAGATGAGA
* * * *
3452621 AAAAGGATGTCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGGTGCCAATAT
1 AAAAGG-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA--AAGGTGCCAATAT
* *
3452686 GCTGATTAAAGGCCAGCGATATTGGACTT
63 GCTGATTCAAGGCCAGCGACATTGGACTT
* * * *
3452715 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA--AAGGTGCCAATATG
*
3452779 CTGATTCAAGGCCAGCGATATTGGACTT
64 CTGATTCAAGGCCAGCGACATTGGACTT
*
3452807 AAAGGTGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTT----AAAGGTGCCAAT
1 -AA----AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAAGGTGCCAAT
* *
3452868 GTGCTGATTCAAGGCCAGCTACATTGGACTT
61 ATGCTGATTCAAGGCCAGCGACATTGGACTT
3452899 AAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----AAAGGTGCCAAT
1 AAA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAAGGTGCCAAT
* *
3452960 GTGCTGATTCAAGGCCAGCTACATTGGACTT
61 ATGCTGATTCAAGGCCAGCGACATTGGACTT
3452991 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----AAAGGTGCCAAT
1 --A-A--AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAAGGTGCCAAT
* * *
3453052 GTGCTGATTCAAGGCCAGCTACATTGGGCTT
61 ATGCTGATTCAAGGCCAGCGACATTGGACTT
*
3453083 AGAAGG
1 AAAAGG
3453089 GTTGCCACCG
Statistics
Matches: 343, Mismatches: 15, Indels: 39
0.86 0.04 0.10
Matches are distributed among these distances:
87 5 0.01
88 1 0.00
89 1 0.00
90 1 0.00
91 3 0.01
92 280 0.82
93 6 0.02
94 3 0.01
95 2 0.01
96 1 0.00
97 1 0.00
98 39 0.11
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (91 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAAGGTGCCAATATGCT
GATTCAAGGCCAGCGACATTGGACTT
Found at i:3452827 original size:141 final size:141
Alignment explanation
Indices: 3452626--3453088 Score: 626
Period size: 141 Copynumber: 3.3 Consensus size: 141
3452616 TGAGAAAAAG
* * * *
3452626 GATGTCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGGTGCCAATATGCTGA
1 GATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGAAGGTGCCAATATGCTGA
* *
3452691 TTAAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
66 TTCAAGGCCAGCAATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
3452756 TTAAAGATGAA
131 TTAAAGATGAA
*
3452767 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATATGCTGA
1 GATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGAAGGTGCCAATATGCTGA
3452832 TTCAAGGCCAGCAATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
66 TTCAAGGCCAGCAATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
3452897 TTAAAGATGAA
131 TTAAAGATGAA
* *
3452908 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A----AAGGTGCCAATGTGCTGA
1 GATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGAAGGTGCCAATATGCTGA
* * * * *
3452967 TTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATA
66 TTCAAGGCCAGCAATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACA
3453032 TTGGACTT-AA-A-G--
125 TTGGACTTAAAGATGAA
* * *
3453044 G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGGCTTAGAAGG
1 GATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA-AAGG
3453089 GTTGCCACCG
Statistics
Matches: 294, Mismatches: 17, Indels: 23
0.88 0.05 0.07
Matches are distributed among these distances:
135 73 0.25
136 1 0.00
138 2 0.01
139 3 0.01
140 2 0.01
141 213 0.72
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (141 bp):
GATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGAAGGTGCCAATATGCTGA
TTCAAGGCCAGCAATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
TTAAAGATGAA
Found at i:3453127 original size:33 final size:33
Alignment explanation
Indices: 3453083--3453318 Score: 304
Period size: 33 Copynumber: 7.2 Consensus size: 33
3453073 CATTGGGCTT
3453083 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* * * *
3453116 AGAATGGTTGCCACCAACCTATGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
3453149 AGAAGGGTTGCCACCGACCTGTGTGGGCTTTAAA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-AG
* *
3453183 AGAA-GGTTGCCATCGACTTGTGTGGGATTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
3453214 A-AAGATGGTTGCCACCGACTTGTGTGGGCTTTGG
1 AGAAG--GGTTGCCACCGACTTGTGTGGGCTTTAG
3453248 AAGAA-GGTTGCCACCGACTTGTGTGGGCTTTAG
1 -AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
3453281 -GAAGGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
3453312 GGAAGGG
1 AGAAGGG
3453319 AGAAAGATGC
Statistics
Matches: 179, Mismatches: 15, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
30 2 0.01
31 5 0.03
32 32 0.18
33 131 0.73
34 6 0.03
35 1 0.01
36 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.35, T:0.27
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:3453371 original size:35 final size:34
Alignment explanation
Indices: 3453321--3453684 Score: 435
Period size: 34 Copynumber: 10.8 Consensus size: 34
3453311 GGGAAGGGAG
* *
3453321 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAA-GGAA
*
3453355 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
3453390 AAAGGTGCTACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
3453424 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAA
*
3453460 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
3453495 AAA-GTGCCACGGAGTGGTGGGCTTTGAGAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGAA
* *
3453528 AAAGGTTGCCACAGAATTGTGGGCTTTAAAA-G--
1 AAAGG-TGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
3453560 ---GGTGCCATGGAGTTGTGGAC-TTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
3453590 CAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAA-GGAA
*
3453624 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGAA
3453659 AAAGGTGCCACGGAGTTGTGGGCTTT
1 AAAGGTGCCACGGAGTTGTGGGCTTT
3453685 GAAGAAAAGG
Statistics
Matches: 292, Mismatches: 21, Indels: 34
0.84 0.06 0.10
Matches are distributed among these distances:
27 6 0.02
28 15 0.05
29 2 0.01
33 52 0.18
34 95 0.33
35 77 0.26
36 23 0.08
37 22 0.08
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (34 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
Found at i:3453625 original size:96 final size:96
Alignment explanation
Indices: 3453459--3453718 Score: 244
Period size: 96 Copynumber: 2.7 Consensus size: 96
3453449 TGAAAAGGGA
* * *
3453459 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGGCTTTGAGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGACTTTGAAA
3453524 AGAAAAAG-GTTGCCACAGAATTGTGGGCTTT
66 AGAAAAAGAG-TGCCACAGAATTGTGGGCTTT
* * * * *
3453555 AAAAGGGTGCCATGGAGTTGTGGAC-TTAAAAGGAACAAGGTGCCACGGAGTTGTGGAC-TT-AA
1 AAAAGAGTGCCACGGAGTTGTGGACTTTAAAAAGAA-AAAGTGCCACGGAGTGGTGGACTTTGAA
* *
3453617 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
65 AA--GAAAAAGAGTGCCACAGAATTGTGGGCTTT
* * * * *
3453651 AAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT--GAAGAAAAGGATGCCACTGAGTCGTGGAC
1 -AAAAG----A-GTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAG-TGCCACGGAGTGGTGGAC
3453714 TTTGA
59 TTTGA
3453719 GACAAAATGC
Statistics
Matches: 133, Mismatches: 17, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
94 3 0.02
95 11 0.08
96 67 0.50
97 6 0.05
100 4 0.03
101 20 0.15
102 19 0.14
103 3 0.02
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (96 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGACTTTGAAA
AGAAAAAGAGTGCCACAGAATTGTGGGCTTT
Found at i:3453744 original size:164 final size:162
Alignment explanation
Indices: 3453417--3453777 Score: 462
Period size: 164 Copynumber: 2.2 Consensus size: 162
3453407 GTGGGCTTTA
*
3453417 AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGG
1 AAAAG-AAAAGGTGCCACGGAGTTGTGGAC-TTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGG
* *
3453482 GCTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGGCTTTGAGAAGAAAAAGGTTGCCACAGAATTG
64 GCTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGGCTTT-AGAAGAAAAAGGATGCCACAGAATCG
* ** *
3453547 TGGGCTTTAAAAGGGTGCCATGGAGTTGTGGACTT
128 TGGACTTTAAAAGAATGCCATGGAGTCGTGGACTT
3453582 AAAAGGAACAAGGTGCCACGGAGTTGTGGACTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGG
1 AAAA-GAA-AAGGTGCCACGGAGTTGTGGACTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGG
* * *
3453646 GCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-GAAG-AAAAGGATGCCACTGAGTCG
64 GCTTTAAAAAGAAAAA-GTGCCACGGAGTGGTGGGCTTTAGAAGAAAAAGGATGCCACAGAATCG
3453709 TGGACTTTGAGACAA-AATGCCACT-GAGTCGTGGACTT
128 TGGACTTT-A-A-AAGAATGCCA-TGGAGTCGTGGACTT
** * *
3453746 TGAAGAAAAGGATGCCACTGAGTCGTGGACTT
1 AAAAGAAAAGG-TGCCACGGAGTTGTGGACTT
3453778 TGAGAAGAGA
Statistics
Matches: 174, Mismatches: 14, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
162 27 0.16
163 26 0.15
164 67 0.39
165 32 0.18
166 22 0.13
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (162 bp):
AAAAGAAAAGGTGCCACGGAGTTGTGGACTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
TTTAAAAAGAAAAAGTGCCACGGAGTGGTGGGCTTTAGAAGAAAAAGGATGCCACAGAATCGTGG
ACTTTAAAAGAATGCCATGGAGTCGTGGACTT
Found at i:3453747 original size:62 final size:63
Alignment explanation
Indices: 3453664--3453811 Score: 237
Period size: 62 Copynumber: 2.4 Consensus size: 63
3453654 AAGAAAAAGG
* * *
3453664 TGCCACGGAGTTGTGGGCTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGA-AGAGAA
*
3453726 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGAAGAGAA
3453789 TGCCACTGAGTCGTGGACTTTGA
1 TGCCACTGAGTCGTGGACTTTGA
3453812 GAAGAGATTT
Statistics
Matches: 80, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
61 1 0.01
62 55 0.69
63 24 0.30
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (63 bp):
TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGAAGAGAA
Found at i:3453820 original size:31 final size:30
Alignment explanation
Indices: 3453658--3453819 Score: 209
Period size: 32 Copynumber: 5.2 Consensus size: 30
3453648 TTTAAAAAGA
* * * *
3453658 AAAAGGTGCCACGGAGTTGTGGGCTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTG-AG
3453689 AAAAGGATGCCACTGAGTCGTGGACTTTGAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTGAG
3453720 ACAAA-ATGCCACTGAGTCGTGGACTTTGAAG
1 A-AAAGATGCCACTGAGTCGTGGACTTTG-AG
3453751 AAAAGGATGCCACTGAGTCGTGGACTTTGAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTGAG
*
3453782 AAGAGATTGCCACTGAGTCGTGGACTTTGAG
1 AAAAGA-TGCCACTGAGTCGTGGACTTTGAG
*
3453813 AAGAGAT
1 AAAAGAT
3453820 TTAAAGAATT
Statistics
Matches: 120, Mismatches: 5, Indels: 13
0.87 0.04 0.09
Matches are distributed among these distances:
30 29 0.24
31 45 0.38
32 46 0.38
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.23
Consensus pattern (30 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAG
Found at i:3455133 original size:18 final size:20
Alignment explanation
Indices: 3455112--3455155 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
3455102 TTTGTTTGTT
*
3455112 TTTTGACTTT-T-TTTTTAC
1 TTTTGACTTTGTGTGTTTAC
3455130 TTTTG--TTTGTGTGTTTAC
1 TTTTGACTTTGTGTGTTTAC
3455148 TTTTGACT
1 TTTTGACT
3455156 GTTCCGGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
16 3 0.14
17 1 0.05
18 16 0.76
20 1 0.05
ACGTcount: A:0.09, C:0.09, G:0.14, T:0.68
Consensus pattern (20 bp):
TTTTGACTTTGTGTGTTTAC
Found at i:3458266 original size:16 final size:15
Alignment explanation
Indices: 3458245--3458275 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
3458235 TCGATACATC
3458245 ACTGTTCATCACTGTT
1 ACTGTTCAT-ACTGTT
3458261 ACTGTTCATACTGTT
1 ACTGTTCATACTGTT
3458276 CACATATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (15 bp):
ACTGTTCATACTGTT
Found at i:3458345 original size:13 final size:13
Alignment explanation
Indices: 3458327--3458366 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
3458317 TAACTATTCA
* *
3458327 TGTATCAATACAT
1 TGTATCGATACAC
3458340 TGTATCGATACAC
1 TGTATCGATACAC
3458353 TGTATCGATACAC
1 TGTATCGATACAC
3458366 T
1 T
3458367 ATAAATTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:3458815 original size:34 final size:35
Alignment explanation
Indices: 3458752--3458818 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
3458742 CTAAGTGATT
3458752 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
3458788 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
3458819 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:3463210 original size:52 final size:52
Alignment explanation
Indices: 3463141--3463260 Score: 222
Period size: 52 Copynumber: 2.3 Consensus size: 52
3463131 ATGAAAATTT
*
3463141 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
*
3463193 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
3463245 TGCATGTATCGATACA
1 TGCATGTATCGATACA
3463261 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Found at i:3463273 original size:52 final size:51
Alignment explanation
Indices: 3463141--3463280 Score: 210
Period size: 52 Copynumber: 2.7 Consensus size: 51
3463131 ATGAAAATTT
3463141 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGCC
* *
3463193 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGCC
*
3463245 TGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TGCATGTATCGATACATTA-AT-AGTGTATCGATACA
3463281 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 79 0.98
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGCC
Found at i:3463287 original size:13 final size:13
Alignment explanation
Indices: 3463269--3463293 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3463259 CAAAGATCAG
3463269 TGTATCGATACAA
1 TGTATCGATACAA
3463282 TGTATCGATACA
1 TGTATCGATACA
3463294 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3465730 original size:21 final size:21
Alignment explanation
Indices: 3465706--3465748 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3465696 TAGGTGGAAG
*
3465706 ATTCGACGTATGTGGGGACGA
1 ATTCGACGTATGTAGGGACGA
3465727 ATTCGACGTATGTAGGGACGA
1 ATTCGACGTATGTAGGGACGA
3465748 A
1 A
3465749 AATGGTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (21 bp):
ATTCGACGTATGTAGGGACGA
Found at i:3465973 original size:13 final size:13
Alignment explanation
Indices: 3465955--3465982 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3465945 TACATAAAAT
3465955 ATTGTATCGATAC
1 ATTGTATCGATAC
3465968 ATTGTATCGATAC
1 ATTGTATCGATAC
3465981 AT
1 AT
3465983 AAATTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
ATTGTATCGATAC
Found at i:3465997 original size:32 final size:33
Alignment explanation
Indices: 3465936--3466000 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
3465926 TTTCAACGAT
3465936 TTGTATCGATACATAAAATATTGTATCGATACA
1 TTGTATCGATACATAAAATATTGTATCGATACA
*
3465969 TTGTATCGATACAT-AAATTTTGTATCGATACA
1 TTGTATCGATACATAAAATATTGTATCGATACA
3466001 ATTTAAGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATAAAATATTGTATCGATACA
Found at i:3466061 original size:13 final size:13
Alignment explanation
Indices: 3466043--3466067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3466033 ATTACTCAAA
3466043 TGTATCGATACAT
1 TGTATCGATACAT
3466056 TGTATCGATACA
1 TGTATCGATACA
3466068 CTGATCTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3466118 original size:52 final size:52
Alignment explanation
Indices: 3466078--3466204 Score: 236
Period size: 52 Copynumber: 2.4 Consensus size: 52
3466068 CTGATCTTTA
*
3466078 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATG
*
3466130 TATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATG
3466182 TATCGATACATGCAGGCAAATTT
1 TATCGATACATGCAGGCAAATTT
3466205 TCATATTTCG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (52 bp):
TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATG
Found at i:3475836 original size:20 final size:20
Alignment explanation
Indices: 3475813--3475885 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3475803 ACAATTCAAA
3475813 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3475833 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3475854 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3475874 GTATCGATACAT
1 GTATCGATACAT
3475886 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3475857 original size:21 final size:21
Alignment explanation
Indices: 3475831--3475906 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3475821 ACATGTTGCA
3475831 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
3475852 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
3475872 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
3475893 ATGTATCGATACAT
1 ATGTATCGATACAT
3475907 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:3475864 original size:41 final size:41
Alignment explanation
Indices: 3475813--3475906 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
3475803 ACAATTCAAA
*
3475813 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3475854 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3475895 GTATCGATACAT
1 GTATCGATACAT
3475907 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:3475963 original size:13 final size:13
Alignment explanation
Indices: 3475945--3475970 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3475935 TACAGCAAGT
3475945 ATGTATCGATACA
1 ATGTATCGATACA
3475958 ATGTATCGATACA
1 ATGTATCGATACA
3475971 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3480052 original size:15 final size:15
Alignment explanation
Indices: 3480032--3480062 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3480022 TAAAAATGTC
*
3480032 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3480047 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3480062 C
1 C
3480063 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3482155 original size:20 final size:21
Alignment explanation
Indices: 3482077--3482154 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
3482067 ATGTCCAAAA
*
3482077 TGTATCGATACATGTTTTTG-
1 TGTATCGATACATCTTTTTGT
** *
3482097 TGTATCGATACATCTGGAAATTCT
1 TGTATCGATACATCT---TTTTGT
3482121 ATGTATCGATACAT-TTTTTGT
1 -TGTATCGATACATCTTTTTGT
3482142 TGTATCGATACAT
1 TGTATCGATACAT
3482155 TGTATCGATA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 27 0.59
21 3 0.07
23 2 0.04
24 1 0.02
25 13 0.28
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATCTTTTTGT
Found at i:3482159 original size:13 final size:13
Alignment explanation
Indices: 3482141--3482179 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3482131 ACATTTTTTG
3482141 TTGTATCGATACA
1 TTGTATCGATACA
3482154 TTGTATCGATACA
1 TTGTATCGATACA
*
3482167 CTGTATCGATACA
1 TTGTATCGATACA
3482180 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3484645 original size:20 final size:20
Alignment explanation
Indices: 3484622--3484694 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3484612 ACAATTCAAA
3484622 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3484642 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3484663 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3484683 GTATCGATACAT
1 GTATCGATACAT
3484695 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3484666 original size:21 final size:21
Alignment explanation
Indices: 3484640--3484715 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3484630 ACATGTTGCA
3484640 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
3484661 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
3484681 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
3484702 ATGTATCGATACAT
1 ATGTATCGATACAT
3484716 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:3484673 original size:41 final size:41
Alignment explanation
Indices: 3484622--3484715 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
3484612 ACAATTCAAA
*
3484622 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3484663 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3484704 GTATCGATACAT
1 GTATCGATACAT
3484716 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:3484772 original size:13 final size:13
Alignment explanation
Indices: 3484754--3484779 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3484744 TACAGCAAGT
3484754 ATGTATCGATACA
1 ATGTATCGATACA
3484767 ATGTATCGATACA
1 ATGTATCGATACA
3484780 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3488705 original size:13 final size:13
Alignment explanation
Indices: 3488687--3488713 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3488677 ACAAAAAAAT
3488687 ATGTATCGATACA
1 ATGTATCGATACA
3488700 ATGTATCGATACA
1 ATGTATCGATACA
3488713 A
1 A
3488714 CACTTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Done.