Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 13 of 120
Found at i:3640121 original size:18 final size:19
Alignment explanation
Indices: 3640082--3640122 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3640072 AAAAAGAAAA
*
3640082 AAAATTAAAAATAATTTTT
1 AAAATTAAAAATAATTTAT
*
3640101 AAAATTCAAAAT-ATTTAT
1 AAAATTAAAAATAATTTAT
3640119 AAAA
1 AAAA
3640123 AATTATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTAAAAATAATTTAT
Found at i:3640123 original size:19 final size:19
Alignment explanation
Indices: 3640081--3640137 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
3640071 CAAAAAGAAA
3640081 AAAAATTAAAAATAATTTT
1 AAAAATTAAAAATAATTTT
* *
3640100 TAAAATTCAAAAT-ATTTAT
1 AAAAATTAAAAATAATTT-T
*
3640119 AAAAAATTATAAAAAAATT
1 -AAAAATTA-AAAATAATT
3640138 AAATATTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 4 0.14
19 12 0.41
20 6 0.21
21 4 0.14
22 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTAAAAATAATTTT
Found at i:3643704 original size:5 final size:5
Alignment explanation
Indices: 3643688--3643719 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
3643678 TAAGGTTTGA
3643688 ATAAT A-AAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
3643720 TTAAGGTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:3654137 original size:3 final size:3
Alignment explanation
Indices: 3654129--3654154 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3654119 GGTTCATCCT
3654129 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3654155 TGCAGAGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3654194 original size:22 final size:23
Alignment explanation
Indices: 3654169--3654215 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
3654159 GAGGCCCCTC
3654169 AATAATTAACAT-TTTTTAC-TTA
1 AATAATT-ACATATTTTTACATTA
*
3654191 AATAATTAGATATTTTTACATTA
1 AATAATTACATATTTTTACATTA
3654214 AA
1 AA
3654216 ATTATTATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 14 0.64
23 5 0.23
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (23 bp):
AATAATTACATATTTTTACATTA
Found at i:3661071 original size:25 final size:25
Alignment explanation
Indices: 3661040--3661089 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3661030 TGTTGATGGA
3661040 TCTTGGTATGTGAAAGAAATCTATC
1 TCTTGGTATGTGAAAGAAATCTATC
3661065 TCTTGGTATGTGAAAGAAATCTATC
1 TCTTGGTATGTGAAAGAAATCTATC
3661090 ATCTGGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (25 bp):
TCTTGGTATGTGAAAGAAATCTATC
Found at i:3665265 original size:17 final size:17
Alignment explanation
Indices: 3665237--3665279 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
3665227 AATGCCTTAT
3665237 GATGATATTTCTATAAGA
1 GATGA-ATTTCTATAAGA
3665255 GATGAATTTCTATAAGA
1 GATGAATTTCTATAAGA
3665272 GATGAATT
1 GATGAATT
3665280 CCCTGATGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.37
Consensus pattern (17 bp):
GATGAATTTCTATAAGA
Found at i:3666706 original size:18 final size:17
Alignment explanation
Indices: 3666683--3666724 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
3666673 TATTATTATT
3666683 TTTTATTTATCTATCTTA
1 TTTTATTTATCTAT-TTA
*
3666701 TTTTATTTATTTATTTA
1 TTTTATTTATCTATTTA
3666718 -TTTATTT
1 TTTTATTT
3666725 TTGTCTAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.30
17 3 0.13
18 13 0.57
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATTTATCTATTTA
Found at i:3666709 original size:4 final size:4
Alignment explanation
Indices: 3666678--3666724 Score: 60
Period size: 4 Copynumber: 11.5 Consensus size: 4
3666668 ATTATTATTA
*
3666678 TTAT TT-T TTAT TTAT CTAT CTTATT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT -TTA-T TTAT TTAT TTAT TTAT TTAT TT
3666725 TTGTCTAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 3 0.08
4 29 0.76
5 5 0.13
6 1 0.03
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:3667747 original size:100 final size:102
Alignment explanation
Indices: 3667474--3667869 Score: 315
Period size: 103 Copynumber: 3.9 Consensus size: 102
3667464 AAAAGAAAAA
* * *
3667474 ACAAAAAAATAGAAATAAATAAATTCGGAGTGTGTTAGACTAAGTAATCGGGGTGGAGTGCTTGG
1 ACAAAAAAA-AAAAATAAATAAATTCGGAGTGTGTTAGACTGAGTAATCGGAGTGGAGTGCTTGG
* * * *
3667539 TTGTCATTTCACTTCATGTCAAAAGGGCTAAAACATTCT
65 TTGTCATTTCACTTCACGTAAAAAGGGCTAAAACA-CCG
* * * * * * * *
3667578 ACAAAAAAAAAGAAGAAAAAAATT-GAGAGTATGTTGGGCTGAGTAACTAGGA-TAGAGTGCTTG
1 ACAAAAAAAAAAAATAAATAAATTCG-GAGTGTGTTAGACTGAGTAA-TCGGAGTGGAGTGCTTG
* * * * *
3667641 GGTGTCATTTCATTTCGCGTAAAAACGTG-T-TAAC-CCG
64 GTTGTCATTTCACTTCACGTAAAAA-GGGCTAAAACACCG
*
3667678 A-AAAAAAGAAAAAATAAATAAATTCGGAGTGTGTTAGACTGAGTAATCGGAGTGGAGTGTTTGG
1 ACAAAAAA-AAAAAATAAATAAATTCGGAGTGTGTTAGACTGAGTAATCGGAGTGGAGTGCTTGG
* * * *
3667742 TTGTCATTTCACTTCACGTCAAAAGGGCTAACACATTCT
65 TTGTCATTTCACTTCACGTAAAAAGGGCTAAAACA-CCG
* * * ** * * * *
3667781 ACAAAAAAAGAGAAGAAA-AAATT-GAGAGCATGTTGGGCTGAGTAA-CGGGGATGGAGTACTTG
1 ACAAAAAAAAAAAATAAATAAATTCG-GAGTGTGTTAGACTGAGTAATCGGAG-TGGAGTGCTTG
* * *
3667843 GGTGTCATTTCATTTCACGTCAAAAGG
64 GTTGTCATTTCACTTCACGTAAAAAGG
3667870 TCCAATGTAT
Statistics
Matches: 229, Mismatches: 50, Indels: 28
0.75 0.16 0.09
Matches are distributed among these distances:
99 12 0.05
100 63 0.28
101 8 0.03
102 59 0.26
103 67 0.29
104 20 0.09
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.26
Consensus pattern (102 bp):
ACAAAAAAAAAAAATAAATAAATTCGGAGTGTGTTAGACTGAGTAATCGGAGTGGAGTGCTTGGT
TGTCATTTCACTTCACGTAAAAAGGGCTAAAACACCG
Found at i:3667836 original size:102 final size:102
Alignment explanation
Indices: 3667516--3667869 Score: 373
Period size: 100 Copynumber: 3.5 Consensus size: 102
3667506 TGTTAGACTA
* * *
3667516 AGTAATCGGGGTGGAGTGCTTGGTTGTCATTTCACTTCATGTCAAAAGGGCTAAAACATTCTACA
1 AGTAATCGGGGTGGAGTGCTTGGGTGTCATTTCACTTCACGTCAAAAGGGCTAACACATTCTACA
3667581 AAAAAAAAGAAGAAAAAAATTGAGAGTATGTTGGGCTG
66 AAAAAAAAGAAG-AAAAAATTGAGAGTATGTTGGGCTG
* * * * * * * * *
3667619 AGTAA-CTAGGATAGAGTGCTTGGGTGTCATTTCATTTCGCGTAAAAACGTGTTAAC-C---CGA
1 AGTAATC-GGGGTGGAGTGCTTGGGTGTCATTTCACTTCACGTCAAAA-GGGCTAACACATTCTA
* * * * *
3667679 -AAAAAAGAAAAAATAAATAAATTCG-GAGTGTGTTAGACTG
64 CAAAAAA-AAAGAAGAAA-AAATT-GAGAGTATGTTGGGCTG
* * *
3667719 AGTAATCGGAGTGGAGTGTTTGGTTGTCATTTCACTTCACGTCAAAAGGGCTAACACATTCTACA
1 AGTAATCGGGGTGGAGTGCTTGGGTGTCATTTCACTTCACGTCAAAAGGGCTAACACATTCTACA
* *
3667784 AAAAAAGAGAAGAAAAAATTGAGAGCATGTTGGGCTG
66 AAAAAAAAGAAGAAAAAATTGAGAGTATGTTGGGCTG
* *
3667821 AGTAA-CGGGGATGGAGTACTTGGGTGTCATTTCATTTCACGTCAAAAGG
1 AGTAATCGGGG-TGGAGTGCTTGGGTGTCATTTCACTTCACGTCAAAAGG
3667870 TCCAATGTAT
Statistics
Matches: 197, Mismatches: 41, Indels: 27
0.74 0.15 0.10
Matches are distributed among these distances:
99 15 0.08
100 61 0.31
101 7 0.04
102 56 0.28
103 47 0.24
104 11 0.06
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (102 bp):
AGTAATCGGGGTGGAGTGCTTGGGTGTCATTTCACTTCACGTCAAAAGGGCTAACACATTCTACA
AAAAAAAAGAAGAAAAAATTGAGAGTATGTTGGGCTG
Found at i:3667852 original size:202 final size:203
Alignment explanation
Indices: 3667486--3667867 Score: 640
Period size: 203 Copynumber: 1.9 Consensus size: 203
3667476 AAAAAAATAG
*
3667486 AAATAAATAAATTCGGAGTGTGTTAGACTAAGTAATCGGGGTGGAGTGCTTGGTTGTCATTTCAC
1 AAATAAATAAATTCGGAGTGTGTTAGACTAAGTAATCGGAGTGGAGTGCTTGGTTGTCATTTCAC
* *
3667551 TTCATGTCAAAAGGGCTAAAACATTCTACAAAAAAAAAGAAGAAAAAAATTGAGAGTATGTTGGG
66 TTCACGTCAAAAGGGCTAAAACATTCTACAAAAAAAAAGAAGAAAAAAATTGAGAGCATGTTGGG
* * *
3667616 CTGAGTAACTAGGATAGAGTGCTTGGGTGTCATTTCATTTCGCGTAAAAACGTGTTAACCCGAAA
131 CTGAGTAACGAGGATAGAGTACTTGGGTGTCATTTCATTTCACGTAAAAACGTGTTAACCCGAAA
3667681 AAAAGAAA
196 AAAAGAAA
* *
3667689 AAATAAATAAATTCGGAGTGTGTTAGACTGAGTAATCGGAGTGGAGTGTTTGGTTGTCATTTCAC
1 AAATAAATAAATTCGGAGTGTGTTAGACTAAGTAATCGGAGTGGAGTGCTTGGTTGTCATTTCAC
* *
3667754 TTCACGTCAAAAGGGCTAACACATTCTACAAAAAAAGAGAAG-AAAAAATTGAGAGCATGTTGGG
66 TTCACGTCAAAAGGGCTAAAACATTCTACAAAAAAAAAGAAGAAAAAAATTGAGAGCATGTTGGG
* * *
3667818 CTGAGTAACGGGGATGGAGTACTTGGGTGTCATTTCATTTCACGTCAAAA
131 CTGAGTAACGAGGATAGAGTACTTGGGTGTCATTTCATTTCACGTAAAAA
3667868 GGTCCAATGT
Statistics
Matches: 166, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
202 65 0.39
203 101 0.61
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (203 bp):
AAATAAATAAATTCGGAGTGTGTTAGACTAAGTAATCGGAGTGGAGTGCTTGGTTGTCATTTCAC
TTCACGTCAAAAGGGCTAAAACATTCTACAAAAAAAAAGAAGAAAAAAATTGAGAGCATGTTGGG
CTGAGTAACGAGGATAGAGTACTTGGGTGTCATTTCATTTCACGTAAAAACGTGTTAACCCGAAA
AAAAGAAA
Found at i:3668462 original size:19 final size:19
Alignment explanation
Indices: 3668440--3668484 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3668430 TTATATTAGG
3668440 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
3668459 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
3668478 ATTTAAT
1 ATTTAAT
3668485 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:3669305 original size:20 final size:22
Alignment explanation
Indices: 3669282--3669340 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
3669272 TTCGGCTTCC
3669282 CTATTTTC-TAT-TTTTTAATT
1 CTATTTTCTTATATTTTTAATT
*
3669302 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTATATTTTTAATT
* *
3669324 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTATATTTTT
3669341 TTTCCTCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 8 0.23
21 16 0.46
22 11 0.31
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (22 bp):
CTATTTTCTTATATTTTTAATT
Found at i:3669330 original size:21 final size:22
Alignment explanation
Indices: 3669293--3669340 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
3669283 TATTTTCTAT
*
3669293 TTTTTAATTCTATTTTCTTTTA
1 TTTTTAATTCTAGTTTCTTTTA
3669315 TTTTTAATTCT-GTTTCTTTTA
1 TTTTTAATTCTAGTTTCTTTTA
3669336 TTTTT
1 TTTTT
3669341 TTTCCTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTTTAATTCTAGTTTCTTTTA
Found at i:3669341 original size:22 final size:23
Alignment explanation
Indices: 3669290--3669341 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
3669280 CCCTATTTTC
*
3669290 TATTTTTTAATTCTATTTTCTTT
1 TATTTTTTAATTCTAGTTTCTTT
3669313 TA-TTTTTAATTCT-GTTTCTTT
1 TATTTTTTAATTCTAGTTTCTTT
3669334 TATTTTTT
1 TATTTTTT
3669342 TTCCTCAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 9 0.33
22 16 0.59
23 2 0.07
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (23 bp):
TATTTTTTAATTCTAGTTTCTTT
Found at i:3674422 original size:78 final size:78
Alignment explanation
Indices: 3674327--3674483 Score: 296
Period size: 78 Copynumber: 2.0 Consensus size: 78
3674317 TACCAAACTG
*
3674327 TAATTTTCCTTACCCACGTCAGAACTTGCTGGACGTTGAACCACTTCGATTTTATCTTCTAAATC
1 TAATTTTCCTTACCCACGTCAGAACTTGCTGGACGTTGAACCACTTCGATTTCATCTTCTAAATC
3674392 TTCCAAAGACAGT
66 TTCCAAAGACAGT
*
3674405 TAATTTTCCTTACCCACGTCAGAACTTGTTGGACGTTGAACCACTTCGATTTCATCTTCTAAATC
1 TAATTTTCCTTACCCACGTCAGAACTTGCTGGACGTTGAACCACTTCGATTTCATCTTCTAAATC
3674470 TTCCAAAGACAGT
66 TTCCAAAGACAGT
3674483 T
1 T
3674484 TCACCATATC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (78 bp):
TAATTTTCCTTACCCACGTCAGAACTTGCTGGACGTTGAACCACTTCGATTTCATCTTCTAAATC
TTCCAAAGACAGT
Found at i:3687771 original size:21 final size:22
Alignment explanation
Indices: 3687745--3687788 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3687735 TTAACTTTAC
3687745 ATCTAAAAAATT-ATAAAAAAA
1 ATCTAAAAAATTGATAAAAAAA
* *
3687766 ATCTAAAGAATTGTTAAAAAAA
1 ATCTAAAAAATTGATAAAAAAA
3687788 A
1 A
3687789 CTTAAAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (22 bp):
ATCTAAAAAATTGATAAAAAAA
Found at i:3687786 original size:22 final size:21
Alignment explanation
Indices: 3687745--3687796 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
3687735 TTAACTTTAC
*
3687745 ATCTAAAAAATTATAAAAAAA
1 ATCTAAAGAATTATAAAAAAA
*
3687766 ATCTAAAGAATTGTTAAAAAAA
1 ATCTAAAGAATT-ATAAAAAAA
3687788 A-CTTAAAGA
1 ATC-TAAAGA
3687797 TATAAACAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (21 bp):
ATCTAAAGAATTATAAAAAAA
Found at i:3688059 original size:12 final size:12
Alignment explanation
Indices: 3688042--3688070 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3688032 AAATAGGTTA
3688042 AATCCTACTCAT
1 AATCCTACTCAT
3688054 AATCCTACTCAT
1 AATCCTACTCAT
3688066 AATCC
1 AATCC
3688071 CTTCCAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (12 bp):
AATCCTACTCAT
Found at i:3709681 original size:38 final size:38
Alignment explanation
Indices: 3709637--3709715 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
3709627 ACGAGTTTTT
* * *
3709637 TTTACACGTGTCAGGAAAGCTCGCCTAGCTGAACACGC
1 TTTACACGTATCAGAAAAGCTCGCCTAACTGAACACGC
* *
3709675 TTTACACGTATCAGAAAAGCTCGCCTAACTGGACGCGC
1 TTTACACGTATCAGAAAAGCTCGCCTAACTGAACACGC
3709713 TTT
1 TTT
3709716 CCCTTTAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (38 bp):
TTTACACGTATCAGAAAAGCTCGCCTAACTGAACACGC
Found at i:3713013 original size:9 final size:9
Alignment explanation
Indices: 3712999--3713023 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3712989 CTTGAGTTTG
3712999 AATCGCACT
1 AATCGCACT
3713008 AATCGCACT
1 AATCGCACT
3713017 AATCGCA
1 AATCGCA
3713024 TTGCTATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.32, G:0.12, T:0.20
Consensus pattern (9 bp):
AATCGCACT
Found at i:3717310 original size:2 final size:2
Alignment explanation
Indices: 3717303--3717327 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3717293 AAAATAAAAG
3717303 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3717328 TAGTATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3719053 original size:4 final size:4
Alignment explanation
Indices: 3719044--3719072 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
3719034 CCAACATTTT
3719044 CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA C
3719073 GTTTCTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:3720183 original size:22 final size:22
Alignment explanation
Indices: 3720167--3720264 Score: 97
Period size: 22 Copynumber: 4.2 Consensus size: 22
3720157 GAAATAGTAG
3720167 CAAAATAACAGCAAAATGACTA
1 CAAAATAACAGCAAAATGACTA
* *
3720189 CAAAATAACATCAAAATGACAACAAA
1 CAAAATAACAGCAAAATG---AC-TA
*
3720215 CAACAATAAACAGCAAAATGACAA
1 CAA-AAT-AACAGCAAAATGACTA
* *
3720239 CAAAATAACATCAAAATGACAA
1 CAAAATAACAGCAAAATGACTA
3720261 CAAA
1 CAAA
3720265 CAACAATAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
22 36 0.55
23 3 0.05
24 5 0.08
25 4 0.06
26 4 0.06
27 3 0.05
28 11 0.17
ACGTcount: A:0.63, C:0.19, G:0.06, T:0.11
Consensus pattern (22 bp):
CAAAATAACAGCAAAATGACTA
Found at i:3720232 original size:50 final size:50
Alignment explanation
Indices: 3720173--3720282 Score: 202
Period size: 50 Copynumber: 2.2 Consensus size: 50
3720163 GTAGCAAAAT
*
3720173 AACAGCAAAATGACTACAAAATAACATCAAAATGACAACAAACAACAATA
1 AACAGCAAAATGACAACAAAATAACATCAAAATGACAACAAACAACAATA
3720223 AACAGCAAAATGACAACAAAATAACATCAAAATGACAACAAACAACAATA
1 AACAGCAAAATGACAACAAAATAACATCAAAATGACAACAAACAACAATA
*
3720273 AACAACAAAA
1 AACAGCAAAA
3720283 AATAGCAGTG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.65, C:0.20, G:0.05, T:0.10
Consensus pattern (50 bp):
AACAGCAAAATGACAACAAAATAACATCAAAATGACAACAAACAACAATA
Found at i:3720264 original size:11 final size:11
Alignment explanation
Indices: 3720167--3720264 Score: 73
Period size: 11 Copynumber: 9.4 Consensus size: 11
3720157 GAAATAGTAG
* *
3720167 CAAAATAACAG
1 CAAAATGACAA
*
3720178 CAAAATGACTA
1 CAAAATGACAA
* *
3720189 CAAAATAACAT
1 CAAAATGACAA
3720200 CAAAATGACAA
1 CAAAATGACAA
3720211 C--AA--ACAA
1 CAAAATGACAA
*
3720218 CAATAA--ACAG
1 CAA-AATGACAA
3720228 CAAAATGACAA
1 CAAAATGACAA
* *
3720239 CAAAATAACAT
1 CAAAATGACAA
3720250 CAAAATGACAA
1 CAAAATGACAA
3720261 CAAA
1 CAAA
3720265 CAACAATAAA
Statistics
Matches: 68, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
7 5 0.07
9 4 0.06
10 8 0.12
11 51 0.75
ACGTcount: A:0.63, C:0.19, G:0.06, T:0.11
Consensus pattern (11 bp):
CAAAATGACAA
Found at i:3721696 original size:58 final size:59
Alignment explanation
Indices: 3721627--3721781 Score: 183
Period size: 58 Copynumber: 2.6 Consensus size: 59
3721617 AATTTTAATG
* *
3721627 ATTATTATTAAATATAATTTAATAAAAATATTA-ATTAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATA-TAATTTAATAATATTTTTAACATA
* * *
3721685 ATTATTATTAAATACAATTTAAT-AAAATAATATATGATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAATATTTTTAACATA
* *
3721743 ATTATTATTAAAATATCAA-TTAGTAAAAATTATAATATA
1 ATTATTATT-AAATAT-AATTTAATAAAAATAAT-ATATA
3721782 TAATATTAGA
Statistics
Matches: 82, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
57 19 0.23
58 41 0.50
59 9 0.11
60 9 0.11
61 4 0.05
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAATATTTTTAACATA
Found at i:3721775 original size:25 final size:24
Alignment explanation
Indices: 3721746--3721796 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
3721736 TAATATAATT
*
3721746 ATTATTAAAATATCA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
3721771 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
3721795 AT
1 AT
3721797 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:3732470 original size:17 final size:15
Alignment explanation
Indices: 3732448--3732486 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3732438 GTTTGGATTA
*
3732448 TTATTTTATTTTTTACT
1 TTATTTTA-TATTTA-T
3732465 TTATTTTATATTTAT
1 TTATTTTATATTTAT
3732480 TTATTTT
1 TTATTTT
3732487 TAGTTATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 5 0.24
17 8 0.38
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
TTATTTTATATTTAT
Found at i:3732910 original size:19 final size:18
Alignment explanation
Indices: 3732873--3732911 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3732863 ATATGTATAA
* *
3732873 TATAAAAAATGTTATAAT
1 TATAAAAAATATTACAAT
3732891 TATAAAAAATTATTACAAT
1 TATAAAAAA-TATTACAAT
3732910 TA
1 TA
3732912 ATCTTGTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
TATAAAAAATATTACAAT
Found at i:3735646 original size:57 final size:55
Alignment explanation
Indices: 3735575--3735682 Score: 126
Period size: 57 Copynumber: 1.9 Consensus size: 55
3735565 TTGATATATG
* * *
3735575 AACTTAACATTTTTTACTAATTTGATACCTAAATTTTTTTTTGATCCAATTTGTTCA
1 AACTTAACACTTTTTACTAAGTTGATA-CTAAA-GTTTTTTTGATCCAATTTGTTCA
* ** * *
3735632 AACTTGACACTTTTTTGTAAGTTGGTACTTAAGTTTTTTTGATCCAATTTG
1 AACTTAACACTTTTTACTAAGTTGATACTAAAGTTTTTTTGATCCAATTTG
3735683 GTACTTGAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
55 18 0.42
56 4 0.09
57 21 0.49
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.50
Consensus pattern (55 bp):
AACTTAACACTTTTTACTAAGTTGATACTAAAGTTTTTTTGATCCAATTTGTTCA
Found at i:3735725 original size:56 final size:55
Alignment explanation
Indices: 3735592--3735726 Score: 139
Period size: 56 Copynumber: 2.4 Consensus size: 55
3735582 CATTTTTTAC
* *
3735592 TAATTTGATACCTAAATTTTTTTTTGATCCAATTTGTTCAAACTTGACACTTTTTTG
1 TAATTTGGTACCT-AA-TTTTTTTTGATCCAATTTGTTCAAACTTGACACTTTTCTG
* * * ** *
3735649 TAAGTTGGTACTTAAGTTTTTTTGATCCAATTTGGTACTTGAACTTGACTC-TTTCT-
1 TAATTTGGTACCTAATTTTTTTTGATCCAATTT-GT--TCAAACTTGACACTTTTCTG
3735705 TAATTTGGTACCTAATTTTTTT
1 TAATTTGGTACCTAATTTTTTT
3735727 ATATTAATTC
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
55 17 0.27
56 23 0.36
57 14 0.22
58 10 0.16
ACGTcount: A:0.24, C:0.13, G:0.12, T:0.51
Consensus pattern (55 bp):
TAATTTGGTACCTAATTTTTTTTGATCCAATTTGTTCAAACTTGACACTTTTCTG
Found at i:3735976 original size:60 final size:58
Alignment explanation
Indices: 3735885--3736056 Score: 184
Period size: 58 Copynumber: 2.9 Consensus size: 58
3735875 ATTAAATCTA
* * **
3735885 AAAAAGAAACTTTGGTACCAAATTAAGAAAAAATACCAAGTTCAAGTATCAAATTGAGTCT
1 AAAAA-AAACTTAGGTACCAAATTAAAAAAAAATGTCAAGTTCAAGTATCAAATTG-G-CT
* * * * *
3735946 CAAAAAAGCTTAGGTACAAAATTAAAAAAAAGTGTCAAGTTC-AGATATCAAATTGGGT
1 AAAAAAAACTTAGGTACCAAATTAAAAAAAAATGTCAAGTTCAAG-TATCAAATTGGCT
* ** *
3736004 AAAAAAAATTTAAATACCAAATTAAAAAAAAATGTCAAGTTCAGGTATCAAAT
1 AAAAAAAACTTAGGTACCAAATTAAAAAAAAATGTCAAGTTCAAGTATCAAAT
3736057 GTTATATTAA
Statistics
Matches: 92, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
58 44 0.48
59 4 0.04
60 40 0.43
61 4 0.04
ACGTcount: A:0.52, C:0.11, G:0.13, T:0.24
Consensus pattern (58 bp):
AAAAAAAACTTAGGTACCAAATTAAAAAAAAATGTCAAGTTCAAGTATCAAATTGGCT
Found at i:3741524 original size:23 final size:23
Alignment explanation
Indices: 3741481--3741525 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3741471 AAAAAAATTC
**
3741481 AACTCGATTCGTTTAACTCAAAT
1 AACTCGATTCGAATAACTCAAAT
*
3741504 AACTCGATTCGAATAATTCAAA
1 AACTCGATTCGAATAACTCAAA
3741526 ATTCGAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCAAAT
Found at i:3743035 original size:18 final size:18
Alignment explanation
Indices: 3743012--3743058 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
3743002 TATAGTTGGT
*
3743012 ATCGATACCACAAGAAAA
1 ATCGATACCAAAAGAAAA
*
3743030 ATCGATACCAAAATAAAA
1 ATCGATACCAAAAGAAAA
3743048 ATCGATACCAA
1 ATCGATACCAA
3743059 CCTAGCATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.55, C:0.21, G:0.09, T:0.15
Consensus pattern (18 bp):
ATCGATACCAAAAGAAAA
Found at i:3743737 original size:2 final size:2
Alignment explanation
Indices: 3743730--3743759 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3743720 TTATAATATC
3743730 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3743760 TATATATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3747715 original size:7 final size:7
Alignment explanation
Indices: 3747658--3747746 Score: 66
Period size: 7 Copynumber: 13.6 Consensus size: 7
3747648 TCGAAAAAAA
3747658 GTCAACG
1 GTCAACG
*
3747665 GTCAA-A
1 GTCAACG
* *
3747671 GTTAATG
1 GTCAACG
3747678 GTCAACG
1 GTCAACG
*
3747685 ATCAACG
1 GTCAACG
3747692 GTCAACAG
1 GTCAAC-G
3747700 GT---CG
1 GTCAACG
*
3747704 ATCAACG
1 GTCAACG
3747711 GTCAACG
1 GTCAACG
*
3747718 GTTAACG
1 GTCAACG
3747725 GTC-A--
1 GTCAACG
3747729 GTCAACG
1 GTCAACG
3747736 GTCAACG
1 GTCAACG
3747743 GTCA
1 GTCA
3747747 GTCGATGGTC
Statistics
Matches: 63, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
4 5 0.08
5 2 0.03
6 5 0.08
7 48 0.76
8 3 0.05
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:3747733 original size:25 final size:25
Alignment explanation
Indices: 3747678--3747746 Score: 95
Period size: 25 Copynumber: 2.7 Consensus size: 25
3747668 AAAGTTAATG
*
3747678 GTCAACGATCAACGGTCAACAGGTC
1 GTCAACGGTCAACGGTCAACAGGTC
*
3747703 GATCAACGGTCAACGGTTAAC-GGTC
1 G-TCAACGGTCAACGGTCAACAGGTC
3747728 AGTCAACGGTCAACGGTCA
1 -GTCAACGGTCAACGGTCA
3747747 GTCGATGGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
25 21 0.54
26 18 0.46
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (25 bp):
GTCAACGGTCAACGGTCAACAGGTC
Found at i:3747734 original size:18 final size:18
Alignment explanation
Indices: 3747711--3747760 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
3747701 TCGATCAACG
*
3747711 GTCAACGGTTAACGGTCA
1 GTCAACGGTCAACGGTCA
3747729 GTCAACGGTCAACGGTCA
1 GTCAACGGTCAACGGTCA
* *
3747747 GTCGATGGTCAACG
1 GTCAACGGTCAACG
3747761 ATTAACGGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (18 bp):
GTCAACGGTCAACGGTCA
Found at i:3747757 original size:25 final size:26
Alignment explanation
Indices: 3747677--3747803 Score: 89
Period size: 25 Copynumber: 4.8 Consensus size: 26
3747667 CAAAGTTAAT
* * *
3747677 GGTCAACGATCAACGGTCA-ACAGGTC
1 GGTCAACGGTCAACGGTCAGTC-GATC
* * * *
3747703 GATCAACGGTCAACGGTTA-ACGGTC
1 GGTCAACGGTCAACGGTCAGTCGATC
*
3747728 AGTCAACGGTCAACGGTCAGTCGAT-
1 GGTCAACGGTCAACGGTCAGTCGATC
* *
3747753 GGTCAACGATTAACGGTCAGTCAACGATC
1 GGTCAACGGTCAACGGTCAGT---CGATC
* *
3747782 GATCAACGGTCAACGATCAGTC
1 GGTCAACGGTCAACGGTCAGTC
3747804 AAACTTAAAT
Statistics
Matches: 81, Mismatches: 15, Indels: 10
0.76 0.14 0.09
Matches are distributed among these distances:
25 38 0.47
26 22 0.27
28 4 0.05
29 17 0.21
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (26 bp):
GGTCAACGGTCAACGGTCAGTCGATC
Found at i:3747805 original size:18 final size:18
Alignment explanation
Indices: 3747711--3747805 Score: 72
Period size: 18 Copynumber: 5.3 Consensus size: 18
3747701 TCGATCAACG
* *
3747711 GTCAACGGTTAACGGTCA
1 GTCAACGGTCAACGATCA
*
3747729 GTCAACGGTCAACGGTCA
1 GTCAACGGTCAACGATCA
* * *
3747747 GTCGATGGTCAACGATTAACG
1 GTCAACGGTCAACGA-T--CA
3747768 GTC-A--GTCAACGATC-
1 GTCAACGGTCAACGATCA
3747782 GATCAACGGTCAACGATCA
1 G-TCAACGGTCAACGATCA
3747801 GTCAA
1 GTCAA
3747806 ACTTAAATTA
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
14 1 0.02
15 3 0.05
16 1 0.02
17 1 0.02
18 51 0.80
19 2 0.03
20 1 0.02
21 4 0.06
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (18 bp):
GTCAACGGTCAACGATCA
Found at i:3747853 original size:17 final size:16
Alignment explanation
Indices: 3747822--3747859 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
3747812 ATTAGTTTAG
*
3747822 GGTTTGGTTTGGGCTT
1 GGTTTAGTTTGGGCTT
3747838 GGTTTAGTTATGGGCTT
1 GGTTTAGTT-TGGGCTT
3747855 GGTTT
1 GGTTT
3747860 GATTTGGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.05, C:0.05, G:0.39, T:0.50
Consensus pattern (16 bp):
GGTTTAGTTTGGGCTT
Found at i:3756652 original size:29 final size:29
Alignment explanation
Indices: 3756547--3756643 Score: 140
Period size: 29 Copynumber: 3.3 Consensus size: 29
3756537 GGATTGTGTA
*
3756547 ATCATGTCTGCATCTGTAACTGTCTCTGT
1 ATCATGTCTGCATCTGTAACTGTATCTGT
* * *
3756576 ATCATTTTTGCATCTGTAACTATATCTGT
1 ATCATGTCTGCATCTGTAACTGTATCTGT
* *
3756605 ATCATGTCCGCATCTGTAACTGTATCTAT
1 ATCATGTCTGCATCTGTAACTGTATCTGT
3756634 ATCATGTCTG
1 ATCATGTCTG
3756644 TATTAGTAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (29 bp):
ATCATGTCTGCATCTGTAACTGTATCTGT
Found at i:3761526 original size:22 final size:23
Alignment explanation
Indices: 3761501--3761550 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
3761491 ATGAACAGAT
*
3761501 CACTTAATGGTT-TCAAGATTCC
1 CACTTAATCGTTATCAAGATTCC
* *
3761523 CACTCAATCGTTATCAATATTCC
1 CACTTAATCGTTATCAAGATTCC
3761546 C-CTTA
1 CACTTA
3761551 TCCATCATGC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (23 bp):
CACTTAATCGTTATCAAGATTCC
Found at i:3765931 original size:11 final size:11
Alignment explanation
Indices: 3765915--3765977 Score: 67
Period size: 11 Copynumber: 5.8 Consensus size: 11
3765905 TTATAATAAT
3765915 ATTAAATTTAA
1 ATTAAATTTAA
3765926 ATTAAA-TTAA
1 ATTAAATTTAA
*
3765936 ATTGAATTTAA
1 ATTAAATTTAA
*
3765947 AATAAATTTAAA
1 ATTAAATTT-AA
*
3765959 ATTAAA-ATAA
1 ATTAAATTTAA
*
3765969 ATTTAATTT
1 ATTAAATTT
3765978 TCAAATGATT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 16 0.38
11 19 0.45
12 7 0.17
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:3765932 original size:5 final size:5
Alignment explanation
Indices: 3765915--3765976 Score: 52
Period size: 5 Copynumber: 11.6 Consensus size: 5
3765905 TTATAATAAT
* *
3765915 ATTAA ATTTAA ATTAA ATTAA ATTGAA TTTAA AATAA ATTTAAA ATTAA
1 ATTAA A-TTAA ATTAA ATTAA ATT-AA ATTAA ATTAA A-TT-AA ATTAA
* *
3765964 AATAA ATTTA ATT
1 ATTAA ATTAA ATT
3765977 TTCAAATGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
5 31 0.67
6 12 0.26
7 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (5 bp):
ATTAA
Found at i:3765951 original size:38 final size:38
Alignment explanation
Indices: 3765899--3765976 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
3765889 ACTTTTCTTT
* * *
3765899 TTGAATTTATAAT-AATATTAAATTTAAATTAAATTAAA
1 TTGAATTTAAAATAAAT-TTAAAATTAAAATAAATTAAA
*
3765937 TTGAATTTAAAATAAATTTAAAATTAAAATAAATTTAA
1 TTGAATTTAAAATAAATTTAAAATTAAAATAAATTAAA
3765975 TT
1 TT
3765977 TTCAAATGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 32 0.91
39 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (38 bp):
TTGAATTTAAAATAAATTTAAAATTAAAATAAATTAAA
Found at i:3765963 original size:17 final size:17
Alignment explanation
Indices: 3765917--3765974 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
3765907 ATAATAATAT
*
3765917 TAAATTT-AAATTAAAT
1 TAAATTTAAAATTAAAA
* *
3765933 TAAA-TTGAATTTAAAA
1 TAAATTTAAAATTAAAA
3765949 TAAATTTAAAATTAAAA
1 TAAATTTAAAATTAAAA
3765966 TAAATTTAA
1 TAAATTTAA
3765975 TTTTCAAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 2 0.06
16 15 0.42
17 19 0.53
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAATTTAAAATTAAAA
Found at i:3765983 original size:17 final size:16
Alignment explanation
Indices: 3765917--3765977 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 16
3765907 ATAATAATAT
* *
3765917 TAAATTTAAATTAAAT
1 TAAATTTAATTTAAAA
*
3765933 TAAATTGAATTTAAAA
1 TAAATTTAATTTAAAA
*
3765949 TAAATTTAAAATTAAAA
1 TAAATTT-AATTTAAAA
3765966 TAAATTTAATTT
1 TAAATTTAATTT
3765978 TCAAATGATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
16 23 0.61
17 15 0.39
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
TAAATTTAATTTAAAA
Found at i:3769220 original size:30 final size:31
Alignment explanation
Indices: 3769186--3769257 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
3769176 ATTACATTTA
* *
3769186 ACAAAACAGTCACTCAACTT-T-GAAAATGTG
1 ACAAAACAGTCACTAAAATTATCGAAAA-GTG
3769216 ACAAAACAGTCACTAAAATTATCGAAAAGTG
1 ACAAAACAGTCACTAAAATTATCGAAAAGTG
3769247 ACAAAACAGTC
1 ACAAAACAGTC
3769258 TTATTGGCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 18 0.47
31 15 0.39
32 5 0.13
ACGTcount: A:0.49, C:0.19, G:0.12, T:0.19
Consensus pattern (31 bp):
ACAAAACAGTCACTAAAATTATCGAAAAGTG
Found at i:3770090 original size:31 final size:30
Alignment explanation
Indices: 3770047--3770118 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 30
3770037 GTAAGTAGAG
* * *
3770047 GACTGTTTTGTCACTTTTTGATAACTTTAGT
1 GACTGTTTTGTCACATTTTCA-AACTTGAGT
* *
3770078 GACTATTTTGTCACATTTTCAAAGTTGAGT
1 GACTGTTTTGTCACATTTTCAAACTTGAGT
3770108 GACTGTTTTGT
1 GACTGTTTTGT
3770119 TAAATGTAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 17 0.49
31 18 0.51
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (30 bp):
GACTGTTTTGTCACATTTTCAAACTTGAGT
Found at i:3770111 original size:30 final size:31
Alignment explanation
Indices: 3770038--3770118 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 31
3770028 AAATGAATAG
* * *
3770038 TAAGTAGAG-GACTGTTTTGTCACTTTTTGA
1 TAAGTTGAGTGACTGTTTTGTCACATTTTCA
* * *
3770068 TAACTTTAGTGACTATTTTGTCACATTTTCA
1 TAAGTTGAGTGACTGTTTTGTCACATTTTCA
3770099 -AAGTTGAGTGACTGTTTTGT
1 TAAGTTGAGTGACTGTTTTGT
3770119 TAAATGTAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
30 23 0.56
31 18 0.44
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.46
Consensus pattern (31 bp):
TAAGTTGAGTGACTGTTTTGTCACATTTTCA
Found at i:3775121 original size:78 final size:77
Alignment explanation
Indices: 3774992--3775310 Score: 377
Period size: 78 Copynumber: 4.1 Consensus size: 77
3774982 CTTTATTGCT
* * * * * * *
3774992 TCGAATGACTACAATCTGCCCCATGATCAGGGTAAGAGATTGGTTGATGGTGATCTACACCAAGC
1 TCGAATGGCTACAATCTACCCCAGGCTCAAGGTAAGAGATTGGCTGATGGTGATCTGC-CCAAGC
3775057 TCGGGGTAAAAGA
65 TCGGGGTAAAAGA
* *
3775070 TCGAATGGCTACAATCTGCCCCAAGCTCAAGGTAAGAGATTGGCTGATGGTGATCTGTCCCAAGC
1 TCGAATGGCTACAATCTACCCCAGGCTCAAGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGC
3775135 TCGGGGTAAAAGA
65 TCGGGGTAAAAGA
* * * * **
3775148 TTGGATGGCTGCAATCTACCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
1 TCGAATGGCTACAATCTACCCCAGGCTCAAGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGC
3775213 TCGGGGTAAAAGA
65 TCGGGGTAAAAGA
* * * * * * * * *
3775226 TCGAATGGCTGCAATCTACCCTAGGGTCGAGGTAAGAGATTAGTTAATGATGATCTGCCTTAAGC
1 TCGAATGGCTACAATCTACCCCAGGCTCAAGGTAAGAGATTGGCTGATGGTGATCTGCC-CAAGC
*
3775291 TCAGGGTAAAAGA
65 TCGGGGTAAAAGA
3775304 TCGAATG
1 TCGAATG
3775311 ATGGTGATCT
Statistics
Matches: 214, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
77 2 0.01
78 211 0.99
79 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (77 bp):
TCGAATGGCTACAATCTACCCCAGGCTCAAGGTAAGAGATTGGCTGATGGTGATCTGCCCAAGCT
CGGGGTAAAAGA
Found at i:3775291 original size:156 final size:156
Alignment explanation
Indices: 3775021--3775304 Score: 417
Period size: 156 Copynumber: 1.8 Consensus size: 156
3775011 CCCATGATCA
*
3775021 GGGTAAGAGATTGGTTGATGGTGATCTACACCAAGCTCGGGGTAAAAGATCGAATGGCTACAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTACACCAAGCTCGGGGTAAAAGATCGAATGGCTACAATC
* * * * *
3775086 TGCCCCAAGCTCAAGGTAAGAGATTGGCTGATGGTGATCTGTCCCAAGCTCGGGGTAAAAGATTG
66 TACCCCAAGCTCAAGGTAAGAGATTAGCTAATGATGATCTGTCCCAAGCTCAGGGTAAAAGATTG
3775151 GATGGCTGCAATCTACCCTAGGCTCG
131 GATGGCTGCAATCTACCCTAGGCTCG
* * *
3775177 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTGCAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTACACCAAGCTCGGGGTAAAAGATCGAATGGCTACAATC
* * * * * *
3775242 TACCCTAGGGTCGAGGTAAGAGATTAGTTAATGATGATCTG-CCTTAAGCTCAGGGTAAAAGAT
66 TACCCCAAGCTCAAGGTAAGAGATTAGCTAATGATGATCTGTCC-CAAGCTCAGGGTAAAAGAT
3775305 CGAATGATGG
Statistics
Matches: 112, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
155 2 0.02
156 110 0.98
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (156 bp):
GGGTAAGAGATTGGCTGATGGTGATCTACACCAAGCTCGGGGTAAAAGATCGAATGGCTACAATC
TACCCCAAGCTCAAGGTAAGAGATTAGCTAATGATGATCTGTCCCAAGCTCAGGGTAAAAGATTG
GATGGCTGCAATCTACCCTAGGCTCG
Found at i:3775596 original size:39 final size:39
Alignment explanation
Indices: 3775005--3775594 Score: 307
Period size: 39 Copynumber: 15.1 Consensus size: 39
3774995 AATGACTACA
* * * * *
3775005 ATCTGCCCCATGATCAGGGTAAGAGATTGG-TTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGAT-GTG
* * * * * ***
3775044 ATCTACACCAAGCTCGGGGTAAAAGATCGAATGGCTACA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGATGTG
** * *
3775083 ATCTGCCCCAAGCTCAAGGTAAGAGATTGGCT-GATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGAT-GTG
* * **
3775122 ATCTGTCCCAAGCTCGGGGTAAAAGATTGGATGGCTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGATGTG
* * * * *
3775161 ATCTACCCTAGGCTCGGGGTAAGAGATTGGCT-GATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGAT-GTG
* * * **
3775200 ATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGATGTG
* * * * * * * **
3775239 ATCTACCCTAGGGTCGAGGTAAGAGATTAG-TTAATGATG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGATG-TG
** * * *
3775278 ATCTGCCTTAAGCTCAGGGTAAAAGATCGAAT-GATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGAT-GTG
* * * * * * * * **
3775317 ATCTACCTCAAGCTCAGGGTTAAAGATCGAATAGCTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGATGTG
* *
3775356 ATCTGCCCCAAGCTCGGGGTAAGAGATTGG-TTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGAT-GTG
* * * * ** *
3775395 ATATGCCCCAAGCTCGGAGTAAAAAAATGGATGCCTGTA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGATGTG
* *
3775434 ATCTGCCCCAACCTCGGGGTAAAAGATTGGCT-GATGATG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGATG-TG
* * * **
3775473 ATTTGTCCCAAGCTCGGGGTAAAAGATCGGAT-GACTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGA-TGTG
* * * *
3775512 ATCTGCCTCAAGCTCGAGGTAAAAGATTGGCT-TATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGAT-GTG
* * * * * *
3775551 ACCTGTCCTAGGCTCGGGGTAAAAGATCGGATGGCTGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGATGTG
3775590 ATCTG
1 ATCTG
3775595 TCTCATAATC
Statistics
Matches: 397, Mismatches: 139, Indels: 30
0.70 0.25 0.05
Matches are distributed among these distances:
38 13 0.03
39 368 0.93
40 16 0.04
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGATGTG
Found at i:3776081 original size:148 final size:147
Alignment explanation
Indices: 3775872--3776250 Score: 377
Period size: 148 Copynumber: 2.6 Consensus size: 147
3775862 GTCTTTATGA
* * *
3775872 CCTCAACCTTTTCCTTCA-ACTCTTCATGGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCA
1 CCTCAACCTTTCCCTTCATA-TC-TCATGGTACCGGATTCACCATTGCGACCTCAACCTTT-CCA
* * * *
3775936 TCACAGC-TTCATGGTACCAGATTCGCCGTCGCGGCCTCAATCCTTCCT-ATCACATCTTTTAAG
63 TCACAGCTTTCAAGGTACCAGATTCACCGTCACAGCCTCAA-CCTTCCTCATCACATCTTTTAAG
* * *
3775999 GTATCGGGTTCACCATTGCGG
127 GTACCGGATTCACCATTACGG
* * *
3776020 CCTCAACCTTTCCCTTCATATCTCATGGTATCGGATTCGCCATTGCGACCTCAATCTTTTCCATC
1 CCTCAACCTTTCCCTTCATATCTCATGGTACCGGATTCACCATTGCGACCTCAA-CCTTTCCATC
* * * * * *
3776085 ACATCTTTTAAGGTACCAGGTTCACCGTTACAGCCTCAACCTTTCTCATCACTTCTTTTAAGGTA
65 ACAGCTTTCAAGGTACCAGATTCACCGTCACAGCCTCAACCTTCCTCATCACATCTTTTAAGGTA
* *
3776150 CCGGATTCGCCGTTACGG
130 CCGGATTCACCATTACGG
* * * * * * * * *
3776168 CCTCAACCTTTCCATTCATATCTCCGTGATACCGGGTTTACCGTTACGGCCTCAACATTTCCCAT
1 CCTCAACCTTTCCCTTCATATCT-CATGGTACCGGATTCACCATTGCGACCTCAACCTTT-CCAT
* * *
3776233 CACATCTTTTAAGATACC
64 CACAGCTTTCAAGGTACC
3776251 GAGTTTACCG
Statistics
Matches: 192, Mismatches: 33, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
147 43 0.22
148 105 0.55
149 44 0.23
ACGTcount: A:0.20, C:0.33, G:0.15, T:0.32
Consensus pattern (147 bp):
CCTCAACCTTTCCCTTCATATCTCATGGTACCGGATTCACCATTGCGACCTCAACCTTTCCATCA
CAGCTTTCAAGGTACCAGATTCACCGTCACAGCCTCAACCTTCCTCATCACATCTTTTAAGGTAC
CGGATTCACCATTACGG
Found at i:3776088 original size:98 final size:99
Alignment explanation
Indices: 3775899--3776136 Score: 318
Period size: 98 Copynumber: 2.4 Consensus size: 99
3775889 AACTCTTCAT
*
3775899 GGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCATCACAGCTTCATGGTACCAGATTCGCCG
1 GGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCATCACAGCTTCATGGTACCAGATTCGCCA
*
3775964 TCGCGGCCTCAATCCTTCCTATCACATCTTTTAA
66 TCGCGACCTCAATCCTTCCTATCACATCTTTTAA
* * * * * *
3775998 GGTATCGGGTTCACCATTGCGGCCTCAACCTTTCCCTTCATATC-TCATGGTATCGGATTCGCCA
1 GGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCATCACAGCTTCATGGTACCAGATTCGCCA
* *
3776062 TTGCGACCTCAATCTTTTCC-ATCACATCTTTTAA
66 TCGCGACCTCAATC-CTTCCTATCACATCTTTTAA
* * * * *
3776096 GGTACCAGGTTCACCGTTACAGCCTCAACCTTTCTCATCAC
1 GGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCATCAC
3776137 TTCTTTTAAG
Statistics
Matches: 120, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
98 76 0.63
99 44 0.37
ACGTcount: A:0.20, C:0.34, G:0.16, T:0.31
Consensus pattern (99 bp):
GGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCATCACAGCTTCATGGTACCAGATTCGCCA
TCGCGACCTCAATCCTTCCTATCACATCTTTTAA
Found at i:3776178 original size:50 final size:50
Alignment explanation
Indices: 3775899--3776277 Score: 247
Period size: 50 Copynumber: 7.6 Consensus size: 50
3775889 AACTCTTCAT
* * * * *
3775899 GGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCATCACAGC-TTCAT
1 GGTACCGGATTCACCATTGCGGCCTCAACCTTTCTCATCACATCTTTTAA
* * * * *
3775948 GGTACCAGATTCGCCGTCGCGGCCTCAATCCTTCCT-ATCACATCTTTTAA
1 GGTACCGGATTCACCATTGCGGCCTCAA-CCTTTCTCATCACATCTTTTAA
* * * * * * *
3775998 GGTATCGGGTTCACCATTGCGGCCTCAACCTTTCCCTTCATATC--TCAT
1 GGTACCGGATTCACCATTGCGGCCTCAACCTTTCTCATCACATCTTTTAA
* * * *
3776046 GGTATCGGATTCGCCATTGCGACCTCAATCTTT-TCCATCACATCTTTTAA
1 GGTACCGGATTCACCATTGCGGCCTCAACCTTTCT-CATCACATCTTTTAA
* * * *
3776096 GGTACCAGG-TTCACCGTTACAGCCTCAACCTTTCTCATCACTTCTTTTAA
1 GGTACC-GGATTCACCATTGCGGCCTCAACCTTTCTCATCACATCTTTTAA
* * * * **
3776146 GGTACCGGATTCGCCGTTACGGCCTCAACCTTTC-CATTCATATCTCCGT--
1 GGTACCGGATTCACCATTGCGGCCTCAACCTTTCTCA-TCACATCT-TTTAA
* * * * * * *
3776195 GATACCGGGTTTACCGTTACGGCCTCAACATTTCCCATCACATCTTTTAA
1 GGTACCGGATTCACCATTGCGGCCTCAACCTTTCTCATCACATCTTTTAA
* * * *
3776245 GATACC-GAGTTTACCGTTGCGACCTCAATCCTT
1 GGTACCGGA-TTCACCATTGCGGCCTCAA-CCTT
3776278 CCCTTCAACT
Statistics
Matches: 257, Mismatches: 57, Indels: 30
0.75 0.17 0.09
Matches are distributed among these distances:
48 39 0.15
49 76 0.30
50 135 0.53
51 7 0.03
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (50 bp):
GGTACCGGATTCACCATTGCGGCCTCAACCTTTCTCATCACATCTTTTAA
Found at i:3776262 original size:99 final size:100
Alignment explanation
Indices: 3776098--3776277 Score: 238
Period size: 99 Copynumber: 1.8 Consensus size: 100
3776088 TCTTTTAAGG
* * * * *
3776098 TACCAGGTTCACCGTTACAGCCTCAACCTTTCTCATCACTTCTTTTAAGGTACCGGATTCGCCGT
1 TACCAGGTTCACCGTTACAGCCTCAACATTTCCCATCACATCTTTTAAGATACCGGATTCACCGT
*
3776163 TACGGCCTCAA-CCTTTCCATTCATATCTCCGTGA
66 TACGACCTCAATCCTTTCCATTCATATCTCCGTGA
* * * *
3776197 TACCGGGTTTACCGTTACGGCCTCAACATTTCCCATCACATCTTTTAAGATACC-GAGTTTACCG
1 TACCAGGTTCACCGTTACAGCCTCAACATTTCCCATCACATCTTTTAAGATACCGGA-TTCACCG
*
3776261 TTGCGACCTCAATCCTT
65 TTACGACCTCAATCCTT
3776278 CCCTTCAACT
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
98 2 0.03
99 62 0.91
100 4 0.06
ACGTcount: A:0.21, C:0.32, G:0.14, T:0.32
Consensus pattern (100 bp):
TACCAGGTTCACCGTTACAGCCTCAACATTTCCCATCACATCTTTTAAGATACCGGATTCACCGT
TACGACCTCAATCCTTTCCATTCATATCTCCGTGA
Found at i:3777318 original size:1 final size:1
Alignment explanation
Indices: 3777314--3777367 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
3777304 CTATTTTCTA
* ** * * *
3777314 TTTTTTTTTTTTTTTTTTTCTTTTTTACTTTTTTTTTTCTTTTCTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3777368 ATTTATTTAT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.02, C:0.09, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:3777329 original size:19 final size:18
Alignment explanation
Indices: 3777298--3777382 Score: 73
Period size: 20 Copynumber: 4.5 Consensus size: 18
3777288 CTTTTTCCCG
*
3777298 TTTTTTCTATTTTCTATTTT
1 TTTTTTCT-TTTT-TTTTTT
*
3777318 TTTTTT-TTTTTTTTTCT
1 TTTTTTCTTTTTTTTTTT
*
3777335 TTTTTACTTTTTTTTTTCT
1 TTTTTTCTTTTTTTTTT-T
*
3777354 TTTCTTTCTTTTTTATTTAT
1 TTT-TTTCTTTTTT-TTTTT
*
3777374 TTATTTCTT
1 TTTTTTCTT
3777383 CATTGAATCC
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
17 9 0.17
18 13 0.24
19 11 0.20
20 18 0.33
21 3 0.06
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTCTTTTTTTTTTT
Found at i:3777329 original size:28 final size:28
Alignment explanation
Indices: 3777298--3777382 Score: 102
Period size: 28 Copynumber: 3.0 Consensus size: 28
3777288 CTTTTTCCCG
*
3777298 TTTTTTCTATTTTCTA-TTTTTTTTTTTTT
1 TTTTTTCT-TTTT-TACTTTTTTTTTTCTT
3777327 TTTTTTCTTTTTTACTTTTTTTTTTCTT
1 TTTTTTCTTTTTTACTTTTTTTTTTCTT
* *
3777355 TTCTTTCTTTTTTA-TTTATTTATTTCTT
1 TTTTTTCTTTTTTACTTT-TTTTTTTCTT
3777383 CATTGAATCC
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
27 5 0.10
28 38 0.75
29 8 0.16
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (28 bp):
TTTTTTCTTTTTTACTTTTTTTTTTCTT
Found at i:3792852 original size:19 final size:19
Alignment explanation
Indices: 3792814--3792853 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3792804 ATATGTATAA
* * *
3792814 TATAAAAAGATGTTATAAT
1 TATAAAAAAATATTACAAT
3792833 TATAAAAAAATATTACAAT
1 TATAAAAAAATATTACAAT
3792852 TA
1 TA
3792854 ATCTTGTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (19 bp):
TATAAAAAAATATTACAAT
Found at i:3823647 original size:26 final size:24
Alignment explanation
Indices: 3823614--3823663 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
3823604 AAACCCACAT
*
3823614 CATAAATATATCACAAATTAATAATA
1 CATAAATAAATCA-AAATT-ATAATA
*
3823640 CATAAATAAATTAAAATTATAATA
1 CATAAATAAATCAAAATTATAATA
3823664 TATCAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 5 0.23
26 11 0.50
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (24 bp):
CATAAATAAATCAAAATTATAATA
Found at i:3823698 original size:42 final size:42
Alignment explanation
Indices: 3823618--3823698 Score: 96
Period size: 42 Copynumber: 1.9 Consensus size: 42
3823608 CCACATCATA
**
3823618 AATATATCACAAATTAATAATACATAAATAAATTAAAATTAT
1 AATATATCACAAATTAATAATACATAAATAAAACAAAATTAT
3823660 AATATATCA-AAATCTAAATAA-A-ATAAAATAAAACAAAAT
1 AATATATCACAAAT-T-AATAATACAT-AAATAAAACAAAAT
3823699 CGACCAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
41 6 0.18
42 23 0.68
43 5 0.15
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.28
Consensus pattern (42 bp):
AATATATCACAAATTAATAATACATAAATAAAACAAAATTAT
Found at i:3824604 original size:20 final size:20
Alignment explanation
Indices: 3824579--3824616 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3824569 CAAAAACAAA
*
3824579 ATTCAAAATATTTTTAAAGG
1 ATTCAAAATATTTATAAAGG
3824599 ATTCAAAATATTTATAAA
1 ATTCAAAATATTTATAAA
3824617 AAAATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
ATTCAAAATATTTATAAAGG
Found at i:3845064 original size:20 final size:22
Alignment explanation
Indices: 3845030--3845070 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
3845020 AACAAATGAC
3845030 TTTAAAATTATTAAAATTATTT
1 TTTAAAATTATTAAAATTATTT
3845052 TTTAAAA-TA-TAAAATTATT
1 TTTAAAATTATTAAAATTATT
3845071 AAAATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAAAATTATTAAAATTATTT
Found at i:3846344 original size:27 final size:27
Alignment explanation
Indices: 3846275--3846344 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
3846265 TGATTTATTT
*
3846275 AATAATTTTAATAATTTTATATTTAAA
1 AATAATTTTAATAATTATATATTTAAA
** *
3846302 AAT-ATTAAAAAAAATTATAT-TTTAAAA
1 AATAATT-TTAATAATTATATATTT-AAA
3846329 AATAATTTTAATAATT
1 AATAATTTTAATAATT
3846345 TTAAAATCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
26 6 0.18
27 24 0.73
28 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AATAATTTTAATAATTATATATTTAAA
Found at i:3854091 original size:22 final size:23
Alignment explanation
Indices: 3854041--3854089 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
3854031 ACTCTTATTG
*
3854041 AAAAATTAATGATTAAATTTAAT
1 AAAAATAAATGATTAAATTTAAT
*
3854064 TAAAATAAAT-ATT-AATTTAAT
1 AAAAATAAATGATTAAATTTAAT
3854085 AAAAA
1 AAAAA
3854090 ATGTAAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 12 0.52
22 3 0.13
23 8 0.35
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
AAAAATAAATGATTAAATTTAAT
Found at i:3854794 original size:23 final size:23
Alignment explanation
Indices: 3854768--3854844 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
3854758 CTAAAATAGA
*
3854768 ACCAAAAACAGTACCAAAACTGC
1 ACCAAAAACAGTACCAAATCTGC
* * ** **
3854791 ACCAAAAAAAGCATTAAATCAAC
1 ACCAAAAACAGTACCAAATCTGC
*
3854814 ACCAAAAACAGTACCAAATTTGC
1 ACCAAAAACAGTACCAAATCTGC
3854837 ACCAAAAA
1 ACCAAAAA
3854845 AAACTTGTAA
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.56, C:0.26, G:0.06, T:0.12
Consensus pattern (23 bp):
ACCAAAAACAGTACCAAATCTGC
Found at i:3857388 original size:692 final size:692
Alignment explanation
Indices: 3856062--3857447 Score: 2596
Period size: 692 Copynumber: 2.0 Consensus size: 692
3856052 ACACATCTTG
* * * *
3856062 ACGCAACTTTTTGGTCACATTCAAATGAAAGCTCTTTTCGGCCACATCATAAAATCGTTTCCTAC
1 ACGCAACTTTTTGGTCACATTCAAATGAAAGCTCATGTCAGCCACATCATAAAATCATTTCCTAC
3856127 GAATTCCCGACCTTTTTATGTACTTAATTCCATTTCGTATCTTACCAATAACATCATCAGCAAGT
66 GAATTCCCGACCTTTTTATGTACTTAATTCCATTTCGTATCTTACCAATAACATCATCAGCAAGT
*
3856192 TCCAAACCGGCTTTAACTATAAGATTCAATATATGTGCACAACATCTAACTTGAAAAAAAGTACC
131 TCCAAACCGGCTTTAACTATAAGATTCAATATATATGCACAACATCTAACTTGAAAAAAAGTACC
3856257 ATCACACAAAAGAGCTCGATTCGCACGAAAACGGTTTTTAAGACAAGAAACCATAACATCATTAT
196 ATCACACAAAAGAGCTCGATTCGCACGAAAACGGTTTTTAAGACAAGAAACCATAACATCATTAT
*
3856322 AAGAAGCATTATCCAAAGTGATACTAAAAATTTTCTTGTCTATACCCCACTGAGATAAACATAAA
261 AAGAAGCATTATCCAAAGTGATACTAAAAATTTTCTTGTCTATACCCCACTGAGAAAAACATAAA
*
3856387 ACAAGCTCATCCGCTATGTTCAAACCATCATACGGAGGAGATAAATCTCTAAACCTTATGATTCT
326 ACAAGCTCATCCGCTATGTTCAAACCATCATACGGAGAAGATAAATCTCTAAACCTTATGATTCT
3856452 CTTTTGTAACTTCCAGTCTTTGTCAACCCAATGAGCAGTAATACAAATGTATTCATCATTAGTAT
391 CTTTTGTAACTTCCAGTCTTTGTCAACCCAATGAGCAGTAATACAAATGTATTCATCATTAGTAT
*
3856517 GCTCAGAGTTTCAATTATCAAAAGTTAGACAAATTAAACCAGGTGCTTTAGCCAACTCTTCTTTA
456 GCTCAGAGTTCCAATTATCAAAAGTTAGACAAATTAAACCAGGTGCTTTAGCCAACTCTTCTTTA
* *
3856582 ACATGGTCTCTCTCTTTTGTATAGTACATTAGGACATCCCTTGAAGTTGTATGTCTACTTATATT
521 ACATGGTCTCTCTCTTTTGCATAGTACATTAGGACATCCCTTGAAGCTGTATGTCTACTTATATT
3856647 CTTAAAATTAGGACTAGCAATGCTCATCATGTATCTAAATCCTGGTTCTTCAACTGTCCTAAATG
586 CTTAAAATTAGGACTAGCAATGCTCATCATGTATCTAAATCCTGGTTCTTCAACTGTCCTAAATG
3856712 AATGTTTTCCACACACAAGAAAAGTAGAAATAGCTCGACAAC
651 AATGTTTTCCACACACAAGAAAAGTAGAAATAGCTCGACAAC
3856754 ACGCAACTTTTTGGTCACATTCAAATGAAAGCTCATGTCAGCCACATCATAAAAT-ATTTGCCTA
1 ACGCAACTTTTTGGTCACATTCAAATGAAAGCTCATGTCAGCCACATCATAAAATCATTT-CCTA
*
3856818 CGAATTCCTGACCTTTTTATGTACTTAATTCCATTTCGTATCTTACCAATAACATCATCAGCAAG
65 CGAATTCCCGACCTTTTTATGTACTTAATTCCATTTCGTATCTTACCAATAACATCATCAGCAAG
3856883 TTCCAAACCGGCTTTAACTATAAGATTCAATATATATGCACAACATCTAACTTGAAAAAAAGTAC
130 TTCCAAACCGGCTTTAACTATAAGATTCAATATATATGCACAACATCTAACTTGAAAAAAAGTAC
3856948 CATCACACAAAAGAGCTCGATTCGCACGAAAACGGTTTTTAAGACAAGAAACCATAACATCATTA
195 CATCACACAAAAGAGCTCGATTCGCACGAAAACGGTTTTTAAGACAAGAAACCATAACATCATTA
3857013 TAAGAAGCATTATCCAAAGTGATACTAAAAATTTTCTTGTCTATACCCCACTGAGAAAAACATAA
260 TAAGAAGCATTATCCAAAGTGATACTAAAAATTTTCTTGTCTATACCCCACTGAGAAAAACATAA
3857078 AACAAGCTCATCCGCTATGTTCAAACCATCATACGGAGAAGATAAATCTCTAAACCTTATGATTC
325 AACAAGCTCATCCGCTATGTTCAAACCATCATACGGAGAAGATAAATCTCTAAACCTTATGATTC
*
3857143 TCTTTTGTAACTTCCAGTCTTTGTCAACCCAATGAGCAGTAATGCAAATGTATTCATCATTAGTA
390 TCTTTTGTAACTTCCAGTCTTTGTCAACCCAATGAGCAGTAATACAAATGTATTCATCATTAGTA
* *
3857208 TGCTCAGAGTTCCAATTATCAAAAGTTAGGCTAATTAAACCAGGTGCTTTAGCCAACTCTTCTTT
455 TGCTCAGAGTTCCAATTATCAAAAGTTAGACAAATTAAACCAGGTGCTTTAGCCAACTCTTCTTT
*
3857273 AACATGGTCTCTCTCTTTTGCATAGTACATTAGGACATCCCTTGCAGCTGTATGTCTACTTATAT
520 AACATGGTCTCTCTCTTTTGCATAGTACATTAGGACATCCCTTGAAGCTGTATGTCTACTTATAT
3857338 TCTTAAAATTAGGACTAGCAATGCTCATCATGTATCTAAAT-CTCGGTTCTTCAACTGTCCTAAA
585 TCTTAAAATTAGGACTAGCAATGCTCATCATGTATCTAAATCCT-GGTTCTTCAACTGTCCTAAA
*
3857402 TGAATGTTTTCCATACACAAGAAAAGTAGAAATAGCTCGACAAC
649 TGAATGTTTTCCACACACAAGAAAAGTAGAAATAGCTCGACAAC
3857446 AC
1 AC
3857448 TCATCAGCAT
Statistics
Matches: 676, Mismatches: 16, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
691 5 0.01
692 671 0.99
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.31
Consensus pattern (692 bp):
ACGCAACTTTTTGGTCACATTCAAATGAAAGCTCATGTCAGCCACATCATAAAATCATTTCCTAC
GAATTCCCGACCTTTTTATGTACTTAATTCCATTTCGTATCTTACCAATAACATCATCAGCAAGT
TCCAAACCGGCTTTAACTATAAGATTCAATATATATGCACAACATCTAACTTGAAAAAAAGTACC
ATCACACAAAAGAGCTCGATTCGCACGAAAACGGTTTTTAAGACAAGAAACCATAACATCATTAT
AAGAAGCATTATCCAAAGTGATACTAAAAATTTTCTTGTCTATACCCCACTGAGAAAAACATAAA
ACAAGCTCATCCGCTATGTTCAAACCATCATACGGAGAAGATAAATCTCTAAACCTTATGATTCT
CTTTTGTAACTTCCAGTCTTTGTCAACCCAATGAGCAGTAATACAAATGTATTCATCATTAGTAT
GCTCAGAGTTCCAATTATCAAAAGTTAGACAAATTAAACCAGGTGCTTTAGCCAACTCTTCTTTA
ACATGGTCTCTCTCTTTTGCATAGTACATTAGGACATCCCTTGAAGCTGTATGTCTACTTATATT
CTTAAAATTAGGACTAGCAATGCTCATCATGTATCTAAATCCTGGTTCTTCAACTGTCCTAAATG
AATGTTTTCCACACACAAGAAAAGTAGAAATAGCTCGACAAC
Found at i:3859085 original size:20 final size:20
Alignment explanation
Indices: 3859057--3859095 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3859047 GCTGCGATTT
*
3859057 GCAACTGATGGAAGGACTTA
1 GCAACTGATGGAAGCACTTA
*
3859077 GCAATTGATGGAAGCACTT
1 GCAACTGATGGAAGCACTT
3859096 TGGTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.23
Consensus pattern (20 bp):
GCAACTGATGGAAGCACTTA
Found at i:3861607 original size:6 final size:6
Alignment explanation
Indices: 3861596--3861621 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3861586 TTTGAATCTA
3861596 TTCAAT TTCAAT TTCAAT TTCAAT TT
1 TTCAAT TTCAAT TTCAAT TTCAAT TT
3861622 AAACCAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (6 bp):
TTCAAT
Found at i:3864492 original size:18 final size:18
Alignment explanation
Indices: 3864461--3864495 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3864451 TGACCAGACG
*
3864461 TTGACCGACCGTTGACCA
1 TTGACCGACAGTTGACCA
*
3864479 TTGACTGACAGTTGACC
1 TTGACCGACAGTTGACC
3864496 GGCCATTGGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (18 bp):
TTGACCGACAGTTGACCA
Found at i:3864533 original size:7 final size:7
Alignment explanation
Indices: 3864520--3864567 Score: 62
Period size: 7 Copynumber: 6.9 Consensus size: 7
3864510 GACTGTGGAC
3864520 CGTTGAT
1 CGTTGAT
*
3864527 AGTTGAT
1 CGTTGAT
3864534 CGTTGAT
1 CGTTGAT
*
3864541 CGTTGAC
1 CGTTGAT
3864548 CGTTGA-
1 CGTTGAT
3864554 CTGTTGAT
1 C-GTTGAT
3864562 CGTTGA
1 CGTTGA
3864568 CTTTTTTCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 1 0.03
7 34 0.94
8 1 0.03
ACGTcount: A:0.17, C:0.15, G:0.29, T:0.40
Consensus pattern (7 bp):
CGTTGAT
Found at i:3864544 original size:21 final size:21
Alignment explanation
Indices: 3864508--3864568 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
3864498 CCATTGGCCA
* * *
3864508 TTGACTGTGGACCGTTGATAG
1 TTGACTGTTGATCGTTGACAG
*
3864529 TTGA-TCGTTGATCGTTGACCG
1 TTGACT-GTTGATCGTTGACAG
3864550 TTGACTGTTGATCGTTGAC
1 TTGACTGTTGATCGTTGAC
3864569 TTTTTTCGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.16, C:0.16, G:0.30, T:0.38
Consensus pattern (21 bp):
TTGACTGTTGATCGTTGACAG
Found at i:3864568 original size:14 final size:15
Alignment explanation
Indices: 3864508--3864569 Score: 60
Period size: 14 Copynumber: 4.4 Consensus size: 15
3864498 CCATTGGCCA
*
3864508 TTGACT-GTGGACCG
1 TTGACTAGTTGACCG
*
3864522 TTGA-TAGTTGATCG
1 TTGACTAGTTGACCG
*
3864536 TTGA-TCGTTGACCG
1 TTGACTAGTTGACCG
*
3864550 TTGACT-GTTGATCG
1 TTGACTAGTTGACCG
3864564 TTGACT
1 TTGACT
3864570 TTTTTCGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 1 0.02
14 39 0.95
15 1 0.02
ACGTcount: A:0.16, C:0.16, G:0.29, T:0.39
Consensus pattern (15 bp):
TTGACTAGTTGACCG
Found at i:3870571 original size:20 final size:21
Alignment explanation
Indices: 3870545--3870598 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
3870535 AAATTAAGAT
3870545 TTTAAATTAATTTT-TAAA-C
1 TTTAAATTAATTTTATAAATC
*
3870564 TTTAAAAT-ATTTTAATAAATC
1 TTTAAATTAATTTT-ATAAATC
3870585 TTTAAATTAATTTT
1 TTTAAATTAATTTT
3870599 CGATATCCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 5 0.17
19 7 0.24
20 4 0.14
21 8 0.28
22 5 0.17
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAAATTAATTTTATAAATC
Found at i:3874826 original size:9 final size:9
Alignment explanation
Indices: 3874812--3874850 Score: 60
Period size: 9 Copynumber: 4.1 Consensus size: 9
3874802 ACAAATGATT
3874812 TTAAAATTA
1 TTAAAATTA
3874821 TTAAAATTA
1 TTAAAATTA
3874830 TTAAAATTA
1 TTAAAATTA
3874839 TTTTAAAATTA
1 --TTAAAATTA
3874850 T
1 T
3874851 AATCATTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 19 0.68
11 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TTAAAATTA
Found at i:3874835 original size:18 final size:19
Alignment explanation
Indices: 3874812--3874850 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
3874802 ACAAATGATT
3874812 TTAAAATTA-TTAAAATTA
1 TTAAAATTATTTAAAATTA
3874830 TTAAAATTATTTTAAAATTA
1 TTAAAATTA-TTTAAAATTA
3874850 T
1 T
3874851 AATCATTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAAAATTATTTAAAATTA
Found at i:3875973 original size:9 final size:9
Alignment explanation
Indices: 3875947--3875985 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
3875937 CATGATGATT
3875947 ATAATTTTAA
1 ATAATTTT-A
3875957 AGTAATTTTA
1 A-TAATTTTA
3875967 ATAATTTTA
1 ATAATTTTA
*
3875976 ATAAATTTA
1 ATAATTTTA
3875985 A
1 A
3875986 AATCATTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 17 0.63
10 3 0.11
11 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (9 bp):
ATAATTTTA
Found at i:3876628 original size:16 final size:16
Alignment explanation
Indices: 3876607--3876661 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
3876597 GTTTGGTTCA
3876607 TTGTAATTGAATAGAG
1 TTGTAATTGAATAGAG
3876623 TTGTAATAT-AATAGAG
1 TTGTAAT-TGAATAGAG
* * *
3876639 CTGTAATGGAATAGGG
1 TTGTAATTGAATAGAG
3876655 TTGTAAT
1 TTGTAAT
3876662 CAATAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 32 0.97
17 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.36
Consensus pattern (16 bp):
TTGTAATTGAATAGAG
Found at i:3876899 original size:52 final size:52
Alignment explanation
Indices: 3876843--3876982 Score: 131
Period size: 52 Copynumber: 2.6 Consensus size: 52
3876833 TTTTAATAAG
* *
3876843 ATTATTATTAAATTATATTTAATAATAAATAACTTAATCATATT-TTAACATA
1 ATTATTATTAAA-TATATTTAATAATAAATAACTTAATAACATTCTTAACATA
* * *
3876895 ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAACATTCTTAATATA
1 ATTATTATTAAATA-TATTTAAT--AAT-A-A-ATAACTTAATAACATTCTTAACATA
*
3876953 ATTATTATTAAAATATGAATTAATAA-AAAT
1 ATTATTATT-AAATAT-ATTTAATAATAAAT
3876983 CATAATATAT
Statistics
Matches: 72, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
51 2 0.03
52 19 0.26
53 2 0.03
54 4 0.06
55 2 0.03
56 1 0.01
57 15 0.21
58 16 0.22
59 11 0.15
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (52 bp):
ATTATTATTAAATATATTTAATAATAAATAACTTAATAACATTCTTAACATA
Found at i:3882199 original size:20 final size:19
Alignment explanation
Indices: 3882183--3882218 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3882173 ATTAAAATAA
3882183 ATTT-TAAAAATTTAAAAT
1 ATTTATAAAAATTTAAAAT
3882201 ATTTATAAAAATTTAAAA
1 ATTTATAAAAATTTAAAA
3882219 AAAAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTATAAAAATTTAAAAT
Found at i:3882220 original size:9 final size:9
Alignment explanation
Indices: 3882181--3882220 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
3882171 TAATTAAAAT
*
3882181 AAATTTTAA
1 AAATTTAAA
3882190 AAATTTAAA
1 AAATTTAAA
*
3882199 ATATTTATAA
1 AAATTTA-AA
3882209 AAATTTAAA
1 AAATTTAAA
3882218 AAA
1 AAA
3882221 AAATTATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AAATTTAAA
Found at i:3884310 original size:29 final size:30
Alignment explanation
Indices: 3884261--3884369 Score: 131
Period size: 29 Copynumber: 3.8 Consensus size: 30
3884251 TTTTGAGGAA
*
3884261 TTTGGGGTTAAAATTG-AAATTTTTGGATGT
1 TTTGGGG-TAAAATGGTAAATTTTTGGATGT
*
3884291 TTTGGGG-CAAATGGTAAA-TTTTGGATGT
1 TTTGGGGTAAAATGGTAAATTTTTGGATGT
3884319 TTTGGGGTAAAATGGT-AATTTTTGGATG-
1 TTTGGGGTAAAATGGTAAATTTTTGGATGT
*
3884347 TTCGAGGGTAAAATGGT-AATTTT
1 TTTG-GGGTAAAATGGTAAATTTT
3884370 CAAATATTCG
Statistics
Matches: 71, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
28 27 0.38
29 37 0.52
30 7 0.10
ACGTcount: A:0.27, C:0.02, G:0.29, T:0.42
Consensus pattern (30 bp):
TTTGGGGTAAAATGGTAAATTTTTGGATGT
Found at i:3884368 original size:57 final size:58
Alignment explanation
Indices: 3884261--3884369 Score: 143
Period size: 57 Copynumber: 1.9 Consensus size: 58
3884251 TTTTGAGGAA
* * *
3884261 TTTGGGGTTAAAATTGAAATTTTTGGATGTTTTGGGGCAAATGGTAAATTTTGGATGT
1 TTTGGGGTTAAAATGGAAATTTTTGGATGTTTCGGGGAAAATGGTAAATTTTGGATGT
*
3884319 TTTGGGG-TAAAATGGTAATTTTTGGATG-TTCGAGGGTAAAATGGT-AATTTT
1 TTTGGGGTTAAAATGGAAATTTTTGGATGTTTCG-GGG-AAAATGGTAAATTTT
3884370 CAAATATTCG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
56 3 0.07
57 28 0.62
58 14 0.31
ACGTcount: A:0.27, C:0.02, G:0.29, T:0.42
Consensus pattern (58 bp):
TTTGGGGTTAAAATGGAAATTTTTGGATGTTTCGGGGAAAATGGTAAATTTTGGATGT
Found at i:3884379 original size:29 final size:29
Alignment explanation
Indices: 3884323--3884398 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
3884313 GGATGTTTTG
*** *
3884323 GGGTAAAATGGTAATTTTTGGATGTTCGA
1 GGGTAAAATGGTAATTTTCAAATATTCGA
3884352 GGGTAAAATGGTAATTTTCAAATATTCGA
1 GGGTAAAATGGTAATTTTCAAATATTCGA
**
3884381 GGGTAAAATCATAATTTT
1 GGGTAAAATGGTAATTTT
3884399 GGAGAAGTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTCAAATATTCGA
Found at i:3884413 original size:29 final size:28
Alignment explanation
Indices: 3884381--3884449 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 28
3884371 AAATATTCGA
*
3884381 GGGTAAAATCATAATTTTGGAGAAGTTTG
1 GGGTAAAAT-AGAATTTTGGAGAAGTTTG
* *
3884410 GGGTCAAAATGGGATTTTGGAGAAGTTTG
1 GGGT-AAAATAGAATTTTGGAGAAGTTTG
3884439 GGAGTTAAAAT
1 GG-G-TAAAAT
3884450 GTAACCTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 22 0.65
30 11 0.32
31 1 0.03
ACGTcount: A:0.33, C:0.03, G:0.32, T:0.32
Consensus pattern (28 bp):
GGGTAAAATAGAATTTTGGAGAAGTTTG
Found at i:3884554 original size:88 final size:89
Alignment explanation
Indices: 3884432--3884635 Score: 243
Period size: 88 Copynumber: 2.3 Consensus size: 89
3884422 GATTTTGGAG
* **
3884432 AAGTTT-GGGAGTTAAAATGTAACCTTGAAGAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGT
1 AAGTTTAGGG-GTTAAAATGTGATTTTGAAGAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGT
*
3884496 TAGAGAGTC-AATGTGATCTTGAAA
65 TAGAGAGTCAAATGTAATCTTGAAA
* * *
3884520 AAGTTTAGGGGTTAAAATGTGATTTTGGAA-AAGTTTAGGGGTTAAAATGTGATTTTGGAAAAGT
1 AAGTTTAGGGGTTAAAATGTGATTTT-GAAGAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGT
** * *
3884584 TTTAGGGTCAAAATGTAATTTTGAAA
65 TAGAGAGTC-AAATGTAATCTTGAAA
* *
3884610 AAGTTTAGGGGTCAAAATATGATTTT
1 AAGTTTAGGGGTTAAAATGTGATTTT
3884636 CAAAGAAAAT
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
88 56 0.57
89 6 0.06
90 37 0.37
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.34
Consensus pattern (89 bp):
AAGTTTAGGGGTTAAAATGTGATTTTGAAGAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTT
AGAGAGTCAAATGTAATCTTGAAA
Found at i:3884624 original size:118 final size:117
Alignment explanation
Indices: 3884403--3884614 Score: 311
Period size: 118 Copynumber: 1.8 Consensus size: 117
3884393 AATTTTGGAG
*
3884403 AAGTTTGGGGTCAAAATGGGATTTTGGAGAAGTTTGGGAGTTAAAATGTAACCTTGAAGAAGTTT
1 AAGTTTGGGGTCAAAATGGGATTTTGGAAAAGTTTGGGAGTTAAAATGTAACCTTGAAGAAGTTT
*
3884468 AAGGGTCAAAATGTAATTTTGGAAAAGTTAGAGAGTCAATGTGATCTTGAAA
66 AAGGGTCAAAATGTAATTTTGAAAAAGTTAGAGAGTCAATGTGATCTTGAAA
* * * **
3884520 AAGTTTAGGGGTTAAAATGTGATTTTGGAAAAGTTTAGGG-GTTAAAATGTGATTTTGGAA-AAG
1 AAGTTT-GGGGTCAAAATGGGATTTTGGAAAAGTTT-GGGAGTTAAAATGTAACCTT-GAAGAAG
*
3884583 TTTTAGGGTCAAAATGTAATTTTGAAAAAGTT
63 TTTAAGGGTCAAAATGTAATTTTGAAAAAGTT
3884615 TAGGGGTCAA
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
117 6 0.07
118 72 0.86
119 6 0.07
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (117 bp):
AAGTTTGGGGTCAAAATGGGATTTTGGAAAAGTTTGGGAGTTAAAATGTAACCTTGAAGAAGTTT
AAGGGTCAAAATGTAATTTTGAAAAAGTTAGAGAGTCAATGTGATCTTGAAA
Found at i:3884635 original size:30 final size:30
Alignment explanation
Indices: 3884394--3884635 Score: 246
Period size: 30 Copynumber: 8.2 Consensus size: 30
3884384 TAAAATCATA
* *
3884394 ATTTTGGAGAAGTTT-GGGGTCAAAATGGG
1 ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
* * *
3884423 ATTTTGGAGAAGTTT-GGGAGTTAAAATGTA
1 ATTTTGGAAAAGTTTAGGG-GTCAAAATGTG
** * *
3884453 ACCTT-GAAGAAGTTTAAGGGTCAAAATGTA
1 ATTTTGGAA-AAGTTTAGGGGTCAAAATGTG
*
3884483 ATTTTGGAAAAG-TTAGAGAGTC--AATGTG
1 ATTTTGGAAAAGTTTAG-GGGTCAAAATGTG
* * *
3884511 ATCTTGAAAAAGTTTAGGGGTTAAAATGTG
1 ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
*
3884541 ATTTTGGAAAAGTTTAGGGGTTAAAATGTG
1 ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
*
3884571 ATTTTGGAAAAGTTTTA-GGGTCAAAATGTA
1 ATTTTGGAAAAG-TTTAGGGGTCAAAATGTG
* *
3884601 ATTTTGAAAAAGTTTAGGGGTCAAAATATG
1 ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
3884631 ATTTT
1 ATTTT
3884636 CAAAGAAAAT
Statistics
Matches: 179, Mismatches: 24, Indels: 19
0.81 0.11 0.09
Matches are distributed among these distances:
28 18 0.10
29 31 0.17
30 121 0.68
31 9 0.05
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.34
Consensus pattern (30 bp):
ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
Found at i:3886828 original size:28 final size:27
Alignment explanation
Indices: 3886797--3887226 Score: 150
Period size: 30 Copynumber: 14.7 Consensus size: 27
3886787 ATCGGGGTCG
*
3886797 AAAATGGGATTTTAGGAAATTCGAGAGT
1 AAAATGGGATTTT-GGAAATTCGAGGGT
*
3886825 AAAATGGTAATTTTGGTGAAATT--AGGGTT
1 AAAATGG-GATTTT-G-GAAATTCGAGGG-T
*
3886854 AAAAATGGGATTTTGGAAAGTTCGGGGGT
1 -AAAATGGGATTTTGGAAA-TTCGAGGGT
*
3886883 AAAATGGTAATTTTTGGTAAAATT--AGGGTT
1 AAAATGG-GA-TTTTGG--AAATTCGAGGG-T
**
3886913 AAAAATGGGATTTTGGAAAGTTTAAGGGT
1 -AAAATGGGATTTTGGAAA-TTCGAGGGT
*
3886942 AAAATGGTAATTTTTGGTGAAA-TC-AGGGTT
1 AAAATGG-GA-TTTT-G-GAAATTCGAGGG-T
*
3886972 AAAAATGGGATTTTTGAAAGTTCGAGGGT
1 -AAAATGGGATTTTGGAAA-TTCGAGGGT
* *
3887001 AAAATGGTAATATTTGGTGAAAATCG-GGGTT
1 AAAATGG-GAT-TTT-G-GAAATTCGAGGG-T
*
3887032 AAAAATTGGATTTTGGAAAGTTCGAGGGT
1 -AAAATGGGATTTTGGAAA-TTCGAGGGT
*
3887061 AAAATGGTAATTTTTGGTGAAATT-G-GGGTT
1 AAAATGG-GA-TTTT-G-GAAATTCGAGGG-T
* *
3887091 AAAAATGGGATTTAGGAAAGTTTG-GAGGT
1 -AAAATGGGATTTTGGAAA-TTCGAG-GGT
*
3887120 -AAA-GGAGTAATTTTTGGTGAAA-TCGAGGTT
1 AAAATGG-G--A-TTTT-G-GAAATTCGAGGGT
*
3887150 AAAATGAGATTTTGGAAAGTTCGAGGGT
1 AAAATGGGATTTTGGAAA-TTCGAGGGT
* * *
3887178 TAAATGGTAATTTTTGGTTAAA-TCGAGGTT
1 AAAATGG-GA-TTTTGG--AAATTCGAGGGT
*
3887208 AAAAATGGAATTTTGGAAA
1 -AAAATGGGATTTTGGAAA
3887227 GTTTGGGGTC
Statistics
Matches: 312, Mismatches: 32, Indels: 117
0.68 0.07 0.25
Matches are distributed among these distances:
26 6 0.02
27 23 0.07
28 65 0.21
29 62 0.20
30 82 0.26
31 45 0.14
32 29 0.09
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.33
Consensus pattern (27 bp):
AAAATGGGATTTTGGAAATTCGAGGGT
Found at i:3886829 original size:58 final size:59
Alignment explanation
Indices: 3886760--3887229 Score: 628
Period size: 59 Copynumber: 8.0 Consensus size: 59
3886750 TTTGACTTCT
**
3886760 GAGGGTAAAAAT-GTAATTTTTGGTGAAATCGGGGTCGAAAATGGGATTTTAGGAAA-TTC
1 GAGGGT-AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTT-GGAAAGTTC
* **
3886819 GAGAGTAAAATGGTAA-TTTTGGTGAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTC
1 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTC
* * ** *
3886877 GGGGGTAAAATGGTAATTTTTGGTAAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTT
1 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTC
* * *
3886936 AAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTTGAAAGTTC
1 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTC
* *
3886995 GAGGGTAAAATGGTAATATTTGGTGAAAATCGGGGTTAAAAATTGGATTTTGGAAAGTTC
1 GAGGGTAAAATGGTAATTTTTGGTG-AAATCGGGGTTAAAAATGGGATTTTGGAAAGTTC
* * *
3887055 GAGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGGATTTAGGAAAGTTT
1 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTC
* * *
3887114 G-GAGGT-AAAGGAGTAATTTTTGGTGAAATCGAGGTT-AAAATGAGATTTTGGAAAGTTC
1 GAG-GGTAAAATG-GTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTC
* * * *
3887172 GAGGGTTAAATGGTAATTTTTGGTTAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
1 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTT
3887230 TGGGGTCAAA
Statistics
Matches: 367, Mismatches: 35, Indels: 18
0.87 0.08 0.04
Matches are distributed among these distances:
57 5 0.01
58 102 0.28
59 205 0.56
60 55 0.15
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (59 bp):
GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTC
Found at i:3886945 original size:117 final size:118
Alignment explanation
Indices: 3886762--3887234 Score: 625
Period size: 117 Copynumber: 4.0 Consensus size: 118
3886752 TGACTTCTGA
* ** *
3886762 GGGTAAAAAT-GTAATTTTTGGTGAAATCGGGGTCGAAAATGGGATTTTAGGAAA-TTCGAGAGT
1 GGGT-AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGGATTTT-GGAAAGTTCGAGGGT
3886825 AAAATGGTAA-TTTTGGTGAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTCGG
64 AAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTCGG
** **
3886879 GGGTAAAATGGTAATTTTTGGTAAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTTAAGGGTAA
1 GGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTAA
* * *
3886944 AATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTTGAAAGTTCGA
66 AATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTCGG
* *
3886997 GGGTAAAATGGTAATATTTGGTGAAAATCGGGGTTAAAAATTGGATTTTGGAAAGTTCGAGGGTA
1 GGGTAAAATGGTAATTTTTGGT-AAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTA
* * *
3887062 AAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGGATTTAGGAAAGTTTGG
65 AAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTCGG
* * * * * *
3887116 AGGT-AAAGGAGTAATTTTTGGTGAAATCGAGGTT-AAAATGAGATTTTGGAAAGTTCGAGGGTT
1 GGGTAAAATG-GTAATTTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTA
* * * *
3887179 AAATGGTAATTTTTGGTTAAA-TCGAGGTTAAAAATGGAATTTTGGAAAGTTTGG
65 AAATGGTAATTTTTGGTGAAATTAG-GGTTAAAAATGGGATTTTGGAAAGTTCGG
3887233 GG
1 GG
3887235 TCAAAACATA
Statistics
Matches: 314, Mismatches: 36, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
116 12 0.04
117 127 0.40
118 76 0.24
119 99 0.32
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.33
Consensus pattern (118 bp):
GGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTAA
AATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTCGG
Found at i:3888308 original size:15 final size:16
Alignment explanation
Indices: 3888284--3888319 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
3888274 TTTCCTTTTT
*
3888284 TATTATTTATTA-TAA
1 TATTAATTATTATTAA
3888299 TATTAATTATTATTAA
1 TATTAATTATTATTAA
3888315 TATTA
1 TATTA
3888320 TGAACAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTAATTATTATTAA
Found at i:3890076 original size:85 final size:85
Alignment explanation
Indices: 3889933--3890090 Score: 228
Period size: 85 Copynumber: 1.9 Consensus size: 85
3889923 CTATTGGTCT
* * **
3889933 ACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGTTTTAATCCACTTCTCTGTATCTCAT
1 ACTTCTCTGCATCTCATCAAGAAGATGACCACTTCATTGTTCGAATCCACTTCTCTGTATCTCAT
*
3889998 CAGGAAGACGGATTTGATTC
66 CAAGAAGACGGATTTGATTC
* * *
3890018 ACTTCTCTGCATCTCGTCAAGAAGATGACCACTTTATTGCTTCGACT-CACTTCTCTGTATCTCA
1 ACTTCTCTGCATCTCATCAAGAAGATGACCACTTCATTG-TTCGAATCCACTTCTCTGTATCTCA
3890082 TCAAGAAGA
65 TCAAGAAGA
3890091 TGGGGTTTGG
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
85 60 0.94
86 4 0.06
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (85 bp):
ACTTCTCTGCATCTCATCAAGAAGATGACCACTTCATTGTTCGAATCCACTTCTCTGTATCTCAT
CAAGAAGACGGATTTGATTC
Found at i:3890323 original size:39 final size:38
Alignment explanation
Indices: 3890280--3890391 Score: 143
Period size: 39 Copynumber: 2.9 Consensus size: 38
3890270 GATAATTGCA
*
3890280 ATCTGCCCCATGATTGAGGTAAGAGATTGGATGGCTGTG
1 ATCTGCCCCATGATCG-GGTAAGAGATTGGATGGCTGTG
* * *
3890319 ATCTGCCCCATGGTCGGGGTAAGAGATCGGGTGGCTGTG
1 ATCTGCCCCATGATC-GGGTAAGAGATTGGATGGCTGTG
* *
3890358 ATCTGTCCCATGATCGGGATAAAAGATTGGATGG
1 ATCTGCCCCATGATCGGG-TAAGAGATTGGATGG
3890392 TGGTAATCTA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
38 3 0.05
39 58 0.94
40 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.26
Consensus pattern (38 bp):
ATCTGCCCCATGATCGGGTAAGAGATTGGATGGCTGTG
Found at i:3890478 original size:78 final size:77
Alignment explanation
Indices: 3890332--3890854 Score: 358
Period size: 78 Copynumber: 6.7 Consensus size: 77
3890322 TGCCCCATGG
* * * * *
3890332 TCGGGGTAAGAGATCGGGTGGCT-GTGATCTGTCC-CATGATCGG-GATAAAAGATTGGATGG-T
1 TCGGGGTAAGAGATTGGCT-GATGGTGATCTG-CCTCATGATCGGAG-TAAAAGATCGAATGGCT
* *
3890393 GGTAATCTACCTCTATC
63 --CAATCTACCTCTAGC
* * * * *
3890410 GCGGGGAAAGAGATTGGCCGACGGTGATCTACC-CTATGATCGGAGTAAAAGATCGAATGGCTAC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCTC-ATGATCGGAGTAAAAGATCGAATGGCT-C
*
3890474 AATCTACCTCAAGC
64 AATCTACCTCTAGC
* * * * *
3890488 TCGAGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGACTGCA
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCTCATGATCGGAGTAAAAGATCGAATGGCT-CA
3890553 ATCT-CCT-TAGGC
65 ATCTACCTCTA-GC
**
3890565 TCGGGGTAAGAGATTAACTGATGGTGATCTGCCTCATGATC-GAGGTAAAAGATCGAATGGCTCA
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCTCATGATCGGA-GTAAAAGATCGAATGGCTCA
*
3890629 ATCTACCAC-AGGC
65 ATCTACCTCTA-GC
** * * * * * * *
3890642 TTAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGTTGCA
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCTCATGATCGGAGTAAAAGATCGAATGGCT-CA
* *
3890707 ATCTGTCC-CAAGC
65 ATCT-ACCTCTAGC
* * * * *
3890720 TCGGGGTAAAAAATTGGCTGATGGTGATCTG-CTCCAAGCTC-GAGGTAAAAGATC-AGATGGTT
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCT-CATGATCGGA-GTAAAAGATCGA-ATGGCT
* ** * *
3890782 GAAATCTGTC-CAAGGT
63 -CAATCTACCTCTA-GC
* *
3890798 TCGGGGTAAGAGATTGGCTGATGGTGATCTG-CTCCATAATCAGG-GTAAGAGATCGAA
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCT-CATGATC-GGAGTAAAAGATCGAA
3890855 ATCTTCAATT
Statistics
Matches: 361, Mismatches: 64, Indels: 40
0.78 0.14 0.09
Matches are distributed among these distances:
76 8 0.02
77 123 0.34
78 222 0.61
79 7 0.02
80 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (77 bp):
TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCTCATGATCGGAGTAAAAGATCGAATGGCTCAA
TCTACCTCTAGC
Found at i:3890523 original size:39 final size:39
Alignment explanation
Indices: 3890475--3890829 Score: 212
Period size: 39 Copynumber: 9.2 Consensus size: 39
3890465 AATGGCTACA
* * *
3890475 ATCTACCTCAAGCTCGAGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCTCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
* * ** **
3890514 ATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGACT-GCA
1 ATCTGCCTCAAGCTCGGGGTAAAAGATTGGCTGA-TGGTG
* * * **
3890553 ATCT-CCTTAGGCTCGGGGTAAGAGATTAACTGATGGTG
1 ATCTGCCTCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
* * * *
3890591 ATCTGCCTCATGATCGAGGTAAAAGA-T--C-GAATGGCTCA
1 ATCTGCCTCAAGCTCGGGGTAAAAGATTGGCTG-ATGG-T-G
* * * ** *
3890629 ATCTACCACAGGCTTAGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCTCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
* * * * **
3890668 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGTTGCA
1 ATCTGCCTCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
*
3890707 ATCTGTCC-CAAGCTCGGGGTAAAAAATTGGCTGATGGTG
1 ATCTG-CCTCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
* *
3890746 ATCTG-CTCCAAGCTCGAGGTAAAAGA-T--CAGATGGTTG
1 ATCTGCCT-CAAGCTCGGGGTAAAAGATTGGCTGATGG-TG
* * *
3890783 AAATCTGTC-CAAGGTTCGGGGTAAGAGATTGGCTGATGGTG
1 --ATCTGCCTCAA-GCTCGGGGTAAAAGATTGGCTGATGGTG
3890824 ATCTGC
1 ATCTGC
3890830 TCCATAATCA
Statistics
Matches: 239, Mismatches: 56, Indels: 42
0.71 0.17 0.12
Matches are distributed among these distances:
35 1 0.00
36 11 0.05
37 5 0.02
38 52 0.22
39 150 0.63
40 6 0.03
41 7 0.03
42 7 0.03
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.25
Consensus pattern (39 bp):
ATCTGCCTCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
Found at i:3890594 original size:77 final size:76
Alignment explanation
Indices: 3890411--3890829 Score: 414
Period size: 78 Copynumber: 5.4 Consensus size: 76
3890401 ACCTCTATCG
* * * * * * * *
3890411 CGGGGAAAGAGATTGGCCGACGGTGATCTACC-CTATGATCGGAGTAAAAGATCGAATGGCTACA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCTC-AAGCTCGGGGTAAAAGATCGAATGGCTGCA
*
3890475 ATCTACCTCAAGCT
65 ATCT-CC-CAGGCT
* * *
3890489 CGAGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGACTGCAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCGAATGGCTGCAA
*
3890554 TCTCCTTAGGCT
66 TCTCC-CAGGCT
** * * *
3890566 CGGGGTAAGAGATTAACTGATGGTGATCTGCCTCATGATCGAGGTAAAAGATCGAATGGCT-CAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCGAATGGCTGCAA
3890630 TCTACCACAGGCT
66 TCT-CC-CAGGCT
** * * * *
3890643 TAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGTTGCAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCGAATGGCTGCAA
*
3890708 TCTGTCCCAAGCT
66 TC--TCCCAGGCT
* * * * *
3890721 CGGGGTAAAAAATTGGCTGATGGTGATCTG-CTCCAAGCTCGAGGTAAAAGATC-AGATGGTTGA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCT-CAAGCTCGGGGTAAAAGATCGA-ATGGCTGC
* *
3890784 AATCTGTCCAAGGTT
64 AATC--TCCCAGGCT
3890799 CGGGGTAAGAGATTGGCTGATGGTGATCTGC
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGC
3890830 TCCATAATCA
Statistics
Matches: 286, Mismatches: 47, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
76 6 0.02
77 119 0.42
78 157 0.55
79 3 0.01
80 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (76 bp):
CGGGGTAAGAGATTGGCTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCGAATGGCTGCAA
TCTCCCAGGCT
Found at i:3890981 original size:22 final size:22
Alignment explanation
Indices: 3890953--3891005 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
3890943 ATTTGATGTC
3890953 GAAACTTCATCTTGCTCTTACT
1 GAAACTTCATCTTGCTCTTACT
3890975 GAAACTTCATCTTGCTCTTACT
1 GAAACTTCATCTTGCTCTTACT
*
3890997 GCAACTTCA
1 GAAACTTCA
3891006 GAGATATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.09, T:0.38
Consensus pattern (22 bp):
GAAACTTCATCTTGCTCTTACT
Found at i:3891319 original size:99 final size:98
Alignment explanation
Indices: 3891189--3891851 Score: 652
Period size: 99 Copynumber: 6.7 Consensus size: 98
3891179 CAACTTTTCA
* * * *
3891189 CTTCATATCTTCATGGTATCGGGTTCACCGTTGCGGCCTTAACTTTTCCCATCACATCTTCTAAG
1 CTTCATCTCTTCATGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAG
*
3891254 GTATCGGATTCGCCGTCGCGACCTCAATCCTTCC
66 GTACCGGATTCGCCGTCGCGACCTCAA-CCTTCC
* * * ** * *
3891288 CTTCATCTCTTAATGGTATCGGGTTCGCCGTTACGGCCTCAACATTTTTCATCACATCTTTTTAG
1 CTTCATCTCTTCATGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAG
* * ** *
3891353 GTACCGGGTTCACCGTTACGACCTCAACTTTTCC
66 GTACCGGATTCGCCGTCGCGACCTCAAC-CTTCC
* * * *
3891387 CTTCATATCTTAATGGT-TCTGAGTTTGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAA
1 CTTCATCTCTTCATGGTATC-GGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAA
* * *
3891451 GGTACCAGATTCGTCGTCGCGATCTCAATCCTTCC
65 GGTACCGGATTCGCCGTCGCGACCTCAA-CCTTCC
* * * * * ** * * *
3891486 TTTTATCTCTTCCTGGTACCGAGTTTACCGTTACGGTCTCAACTTTTCCCATCACATCTTCTTAA
1 CTTCATCTCTTCATGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTC-TAA
* * * *
3891551 -GTACCGGATTCACCGTTGCGGCCTCAACTTTTCC
65 GGTACCGGATTCGCCGTCGCGACCTCAAC-CTTCC
* * * * *
3891585 CTTCGTATCTTCGTGGTATCGGGTTCACCGTTGCGGCCTTAACCTTTCCCATCACATCTTCTAAG
1 CTTCATCTCTTCATGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAG
* * *
3891650 GTACCGGATTCGTCGTCGCGACCTCAATTCTTCT
66 GTACCGGATTCGCCGTCGCGACCTCAA-CCTTCC
* * * * * *
3891684 CTTTATCTCTTCATGGTA-CTGAGTTCGCCGTTGCGGCCACAACCTTTCCTATCGCATCTTCTTA
1 CTTCATCTCTTCATGGTATC-GGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAA
* * * *
3891748 GGTACCGGGTTCGTCGTTGCGGCCTCAACCTTTCC
65 GGTACCGGATTCGCCGTCGCGACCTCAACC-TTCC
* * * *
3891783 CTTTACATCT-TT-ATGGTACCGGGTTCGTCGTTGCGGCCTCAACCTTTCCCATTACATCTTCTT
1 C-TT-CATCTCTTCATGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTA
3891846 AGGTAC
64 AGGTAC
3891852 TAGGTTAGCC
Statistics
Matches: 459, Mismatches: 92, Indels: 26
0.80 0.16 0.05
Matches are distributed among these distances:
98 9 0.02
99 436 0.95
100 10 0.02
101 4 0.01
ACGTcount: A:0.16, C:0.31, G:0.17, T:0.35
Consensus pattern (98 bp):
CTTCATCTCTTCATGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAG
GTACCGGATTCGCCGTCGCGACCTCAACCTTCC
Found at i:3891519 original size:198 final size:197
Alignment explanation
Indices: 3891169--3891851 Score: 884
Period size: 198 Copynumber: 3.5 Consensus size: 197
3891159 TAGGTTAGCT
* * * *
3891169 GTTGTGGCCTCAACTTTTCACTTCATATCTTCATGGTATCGGGTTCACCGTTGCGGCCTTAACTT
1 GTTGCGGCCTCAACTTTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTGCGGCCTCAACCT
* * * *
3891234 TTCCCATCACATCTTCTAAGGTATCGGATTCGCCGTCGCGACCTCAATCCTTCCCTTCATCTCTT
66 TTCCCATCACATCTTCTAAGGTACCGGATTCGTCGTCGCGACCTCAATCCTTCCTTTTATCTCTT
* * * * *
3891299 AATGGTATCGGGTTCGCCGTTACGGCCTCAACATTTTTCATCACATCTTTTTAGGTACCGGGTTC
131 CATGGTACCGAGTTCGCCGTTACGGCCTCAAC-TTTTCCATCACATCTTCTTAGGTACCGGGTTC
3891364 ACC
195 ACC
* * * * **
3891367 GTTACGACCTCAACTTTTCCCTTCATATCTTAATGGT-TCTGAGTTTGCCGTTGCGGCCTCAACC
1 GTTGCGGCCTCAACTTTTCCCTTCATATCTTCATGGTATC-GGGTTCACCGTTGCGGCCTCAACC
* *
3891431 TTTCCCATCACATCTTCTAAGGTACCAGATTCGTCGTCGCGATCTCAATCCTTCCTTTTATCTCT
65 TTTCCCATCACATCTTCTAAGGTACCGGATTCGTCGTCGCGACCTCAATCCTTCCTTTTATCTCT
* ** * * *
3891496 TCCTGGTACCGAGTTTACCGTTACGGTCTCAACTTTTCCCATCACATCTTCTTAAGTACCGGATT
130 TCATGGTACCGAGTTCGCCGTTACGGCCTCAACTTTT-CCATCACATCTTCTTAGGTACCGGGTT
3891561 CACC
194 CACC
* * *
3891565 GTTGCGGCCTCAACTTTTCCCTTCGTATCTTCGTGGTATCGGGTTCACCGTTGCGGCCTTAACCT
1 GTTGCGGCCTCAACTTTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTGCGGCCTCAACCT
*
3891630 TTCCCATCACATCTTCTAAGGTACCGGATTCGTCGTCGCGACCTCAATTCTT-CTCTTTATCTCT
66 TTCCCATCACATCTTCTAAGGTACCGGATTCGTCGTCGCGACCTCAATCCTTCCT-TTTATCTCT
* * * * *
3891694 TCATGGTACTGAGTTCGCCGTTGCGGCCACAACCTTTCCTATCGCATCTTCTTAGGTACCGGGTT
130 TCATGGTACCGAGTTCGCCGTTACGGCCTCAACTTTTCC-ATCACATCTTCTTAGGTACCGGGTT
**
3891759 CGTC
194 CACC
* * * * * **
3891763 GTTGCGGCCTCAACCTTTCCCTTTACATCTTTATGGTACCGGGTTCGTCGTTGCGGCCTCAACCT
1 GTTGCGGCCTCAACTTTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTGCGGCCTCAACCT
* *
3891828 TTCCCATTACATCTTCTTAGGTAC
66 TTCCCATCACATCTTCTAAGGTAC
3891852 TAGGTTAGCC
Statistics
Matches: 416, Mismatches: 64, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
197 10 0.02
198 404 0.97
199 2 0.00
ACGTcount: A:0.16, C:0.31, G:0.17, T:0.35
Consensus pattern (197 bp):
GTTGCGGCCTCAACTTTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTGCGGCCTCAACCT
TTCCCATCACATCTTCTAAGGTACCGGATTCGTCGTCGCGACCTCAATCCTTCCTTTTATCTCTT
CATGGTACCGAGTTCGCCGTTACGGCCTCAACTTTTCCATCACATCTTCTTAGGTACCGGGTTCA
CC
Found at i:3891708 original size:297 final size:297
Alignment explanation
Indices: 3891176--3891892 Score: 784
Period size: 297 Copynumber: 2.4 Consensus size: 297
3891166 GCTGTTGTGG
* * * * * *
3891176 CCTCAACTTTTCACTTCATATCTTCATGGTATCGGGTTCACCGTTGCGGCCTTAACTTTTCCCAT
1 CCTCAACCTTTCCCTTTACATCTTCATGGTACCGGGTTCACCGTTGCGGCCTCAACTTTTCCCAT
* * * * * *
3891241 CACATCTTC-TAAGGTATCGGATTCGCCGTCGCGACCTCAA-TCCTTCCCTTCATCTCTTAATGG
66 CACATCTTCTTAA-GTACCGGATTCACCGTTGCGGCCTCAACT-TTTCCCTTCATATCTTAATGG
* ** * * *
3891304 TATCGGGTTCGCCGTTACGGCCTCAACATTTTTCATCACATCTTTTTAGGTACCGGGTTCACCGT
129 TATCGGGTTCACCGTTACGGCCTCAACATTTCCCATCACATCTTCTAAGGTACCGGATTCACCGT
* * * *
3891369 TACGACCTCAACTTTTCCCTTCATATCTTAATGGTTCTGAGTTTGCCGTTGCGGCCTCAACCTTT
194 CACGACCTCAACTTTTCCCTTCATATCTTAATGGTACTGAGTTCGCCGTTGCGGCCACAACCTTT
3891434 CCCATCACATCTTCTAAGGTACCAGATTCGTCGTCGCGA
259 CCCATCACATCTTCTAAGGTACCAGATTCGTCGTCGCGA
* * * * * * *
3891473 TCTCAATCC-TTCCTTTTATC-TCTTCCTGGTACCGAGTTTACCGTTACGGTCTCAACTTTTCCC
1 CCTCAA-CCTTTCCCTTTA-CATCTTCATGGTACCGGGTTCACCGTTGCGGCCTCAACTTTTCCC
* **
3891536 ATCACATCTTCTTAAGTACCGGATTCACCGTTGCGGCCTCAACTTTTCCCTTCGTATCTTCGTGG
64 ATCACATCTTCTTAAGTACCGGATTCACCGTTGCGGCCTCAACTTTTCCCTTCATATCTTAATGG
* * * **
3891601 TATCGGGTTCACCGTTGCGGCCTTAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCGTCGT
129 TATCGGGTTCACCGTTACGGCCTCAACATTTCCCATCACATCTTCTAAGGTACCGGATTCACCGT
* * * * *
3891666 CGCGACCTCAA-TTCTTCTCTTTATCTCTTCATGGTACTGAGTTCGCCGTTGCGGCCACAACCTT
194 CACGACCTCAACTT-TTCCCTTCATATCTTAATGGTACTGAGTTCGCCGTTGCGGCCACAACCTT
* * * * * * *
3891730 TCCTATCGCATCTTCTTAGGTACCGGGTTCGTCGTTGCGG
258 TCCCATCACATCTTCTAAGGTACCAGATTCGTCGTCGCGA
* ** *
3891770 CCTCAACCTTTCCCTTTACATCTTTATGGTACCGGGTTCGTCGTTGCGGCCTCAACCTTTCCCAT
1 CCTCAACCTTTCCCTTTACATCTTCATGGTACCGGGTTCACCGTTGCGGCCTCAACTTTTCCCAT
* * * * *
3891835 TACATCTTCTTAGGTACTAGG-TT-AGCCGTTACGGCCTCAACCTTTT-CCTTCAGATCTT
66 CACATCTTCTTAAGTAC-CGGATTCA-CCGTTGCGGCCTCAA-CTTTTCCCTTCATATCTT
3891893 TTAAGGTACC
Statistics
Matches: 344, Mismatches: 66, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
296 6 0.02
297 326 0.95
298 12 0.03
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.35
Consensus pattern (297 bp):
CCTCAACCTTTCCCTTTACATCTTCATGGTACCGGGTTCACCGTTGCGGCCTCAACTTTTCCCAT
CACATCTTCTTAAGTACCGGATTCACCGTTGCGGCCTCAACTTTTCCCTTCATATCTTAATGGTA
TCGGGTTCACCGTTACGGCCTCAACATTTCCCATCACATCTTCTAAGGTACCGGATTCACCGTCA
CGACCTCAACTTTTCCCTTCATATCTTAATGGTACTGAGTTCGCCGTTGCGGCCACAACCTTTCC
CATCACATCTTCTAAGGTACCAGATTCGTCGTCGCGA
Found at i:3891892 original size:50 final size:49
Alignment explanation
Indices: 3891169--3891909 Score: 414
Period size: 50 Copynumber: 15.0 Consensus size: 49
3891159 TAGGTTAGCT
* * * * * * *
3891169 GTTGTGGCCTCAACTTTTCACTTCATATC-TTCATGGTATCGGGTTCACC
1 GTTGCGGCCTCAACCTTTCCCTTCACATCTTTTA-GGTACCGGGTTCGCC
* * * * * *
3891218 GTTGCGGCCTTAACTTTTCCCATCACATCTTCTAAGGTATCGGATTCGCC
1 GTTGCGGCCTCAACCTTTCCCTTCACATCTT-TTAGGTACCGGGTTCGCC
* * * *
3891268 GTCGCGACCTCAATCC-TTCCCTT--CATCTCTTAATGGTATCGGGTTCGCC
1 GTTGCGGCCTCAA-CCTTTCCCTTCACATCT-TTTA-GGTACCGGGTTCGCC
* * ** * *
3891317 GTTACGGCCTCAACATTTTTCATCACATCTTTTTAGGTACCGGGTTCACC
1 GTTGCGGCCTCAACCTTTCCCTTCACATC-TTTTAGGTACCGGGTTCGCC
* * * * * * * * *
3891367 GTTACGACCTCAACTTTTCCCTTCATATC-TTAATGGTTCTGAGTTTGCC
1 GTTGCGGCCTCAACCTTTCCCTTCACATCTTTTA-GGTACCGGGTTCGCC
* * * * *
3891416 GTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCAGATTCGTC
1 GTTGCGGCCTCAACCTTTCCCTTCACATCTT-TTAGGTACCGGGTTCGCC
* ** * * * * **
3891466 GTCGCGATCTCAATCC-TTCCTTTTATC-TCTTCCT-GGTACCGAGTTTACC
1 GTTGCGGCCTCAA-CCTTTCCCTTCA-CATCTT-TTAGGTACCGGGTTCGCC
* * * * * * *
3891515 GTTACGGTCTCAACTTTTCCCATCACATCTTCTTAAGTACCGGATTCACC
1 GTTGCGGCCTCAACCTTTCCCTTCACATCTT-TTAGGTACCGGGTTCGCC
* ** * * *
3891565 GTTGCGGCCTCAACTTTTCCCTTCGTATCTTCGT-GGTATCGGGTTCACC
1 GTTGCGGCCTCAACCTTTCCCTTCACATCTT-TTAGGTACCGGGTTCGCC
* * * * *
3891614 GTTGCGGCCTTAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCGTC
1 GTTGCGGCCTCAACCTTTCCCTTCACATCTT-TTAGGTACCGGGTTCGCC
* * * * * * * *
3891664 GTCGCGACCTCAA-TTCTTCTCTT--TATCTCTTCATGGTACTGAGTTCGCC
1 GTTGCGGCCTCAACCT-TTCCCTTCACATCT-TTTA-GGTACCGGGTTCGCC
* * *
3891713 GTTGCGGCCACAACCTTT-CCTATCGCATCTTCTTAGGTACCGGGTTCGTC
1 GTTGCGGCCTCAACCTTTCCCT-TCACATCTT-TTAGGTACCGGGTTCGCC
* *
3891763 GTTGCGGCCTCAACCTTTCCCTTTACATC-TTTATGGTACCGGGTTCGTC
1 GTTGCGGCCTCAACCTTTCCCTTCACATCTTTTA-GGTACCGGGTTCGCC
** *
3891812 GTTGCGGCCTCAACCTTTCCCATT-ACATCTTCTTAGGTACTAGGTTAGCC
1 GTTGCGGCCTCAACCTTTCCC-TTCACATCTT-TTAGGTACCGGGTTCGCC
* * * *
3891862 GTTACGGCCTCAACCTTTTCCTTCAGATCTTTTAAGGTACCGGATTCG
1 GTTGCGGCCTCAACCTTTCCCTTCACATCTTTT-AGGTACCGGGTTCG
3891910 TCGTCAAGGT
Statistics
Matches: 529, Mismatches: 130, Indels: 65
0.73 0.18 0.09
Matches are distributed among these distances:
48 25 0.05
49 229 0.43
50 246 0.47
51 28 0.05
52 1 0.00
ACGTcount: A:0.17, C:0.30, G:0.18, T:0.35
Consensus pattern (49 bp):
GTTGCGGCCTCAACCTTTCCCTTCACATCTTTTAGGTACCGGGTTCGCC
Found at i:3891893 original size:99 final size:98
Alignment explanation
Indices: 3891148--3891892 Score: 597
Period size: 99 Copynumber: 7.5 Consensus size: 98
3891138 CCTATTGCAT
* * * * * *
3891148 TTCTAAGGTGCTAGGTTAGCTGTTGTGGCCTCAACTTTTCACTTCATATCTTCATGGTATCGGGT
1 TTCTAAGGTACCAGGTTAGCCGTTGCGACCTCAACTTTTC-CTTCATATCTTCATGGTACCGGGT
* * *
3891213 TCACCGTTGCGGCCTTAACTTTTCCCATCACATC
65 TCGCCGTTGCGGCCTCAACCTTTCCCATCACATC
* * * * * * * *
3891247 TTCTAAGGTATC-GGATTCGCCGTCGCGACCTCAATCCTTCCCTTCATCTCTTAATGGTATCGGG
1 TTCTAAGGTACCAGG-TTAGCCGTTGCGACCTCAA-CTTTTCCTTCATATCTTCATGGTACCGGG
* * **
3891311 TTCGCCGTTACGGCCTCAACATTTTTCATCACATC
64 TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATC
* * * * * * * *
3891346 TTTTTAGGTACCGGGTTCA-CCGTTACGACCTCAACTTTTCCCTTCATATCTTAATGGTTCTGAG
1 TTCTAAGGTACCAGGTT-AGCCGTTGCGACCTCAACTTTT-CCTTCATATCTTCATGGTACCGGG
*
3891410 TTTGCCGTTGCGGCCTCAACCTTTCCCATCACATC
64 TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATC
* * * * * * * * * *
3891445 TTCTAAGGTACCAGATTCGTCGTCGCGATCTCAA-TCCTTCCTTTTATCTCTTCCTGGTACCGAG
1 TTCTAAGGTACCAGGTTAGCCGTTGCGACCTCAACT-TTTCC-TTCATATCTTCATGGTACCGGG
** * * *
3891509 TTTACCGTTACGGTCTCAACTTTTCCCATCACATC
64 TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATC
* * * *
3891544 TTCTTAA-GTACC-GGATTCA-CCGTTGCGGCCTCAACTTTTCCCTTCGTATCTTCGTGGTATCG
1 TTC-TAAGGTACCAGG-TT-AGCCGTTGCGACCTCAACTTTT-CCTTCATATCTTCATGGTACCG
* *
3891606 GGTTCACCGTTGCGGCCTTAACCTTTCCCATCACATC
62 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATC
* * * * * * *
3891643 TTCTAAGGTACC-GGATTCGTCGTCGCGACCTCAA-TTCTTCTCTTTATCTCTTCATGGTACTGA
1 TTCTAAGGTACCAGG-TTAGCCGTTGCGACCTCAACTT-TTC-CTTCATATCTTCATGGTACCGG
* * *
3891706 GTTCGCCGTTGCGGCCACAACCTTTCCTATCGCATC
63 GTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATC
* * * * * * * * *
3891742 TTCTTAGGTACCGGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTTACATCTTTATGGTACCGGGT
1 TTCTAAGGTACCAGGTTAGCCGTTGCGACCTCAA-CTTTTCCTTCATATCTTCATGGTACCGGGT
* *
3891807 TCGTCGTTGCGGCCTCAACCTTTCCCATTACATC
65 TCGCCGTTGCGGCCTCAACCTTTCCCATCACATC
* * * * *
3891841 TTCTTAGGTACTAGGTTAGCCGTTACGGCCTCAACCTTTTCCTTCAGATCTT
1 TTCTAAGGTACCAGGTTAGCCGTTGCGACCTCAA-CTTTTCCTTCATATCTT
3891893 TTAAGGTACC
Statistics
Matches: 514, Mismatches: 112, Indels: 40
0.77 0.17 0.06
Matches are distributed among these distances:
98 15 0.03
99 481 0.94
100 16 0.03
101 2 0.00
ACGTcount: A:0.17, C:0.30, G:0.18, T:0.36
Consensus pattern (98 bp):
TTCTAAGGTACCAGGTTAGCCGTTGCGACCTCAACTTTTCCTTCATATCTTCATGGTACCGGGTT
CGCCGTTGCGGCCTCAACCTTTCCCATCACATC
Found at i:3892860 original size:6 final size:6
Alignment explanation
Indices: 3892846--3892917 Score: 65
Period size: 6 Copynumber: 11.7 Consensus size: 6
3892836 CAACCTCTCC
* * *
3892846 TTTTAT TTTTC- TTTTAT TTTTCTT TTTTCT TTTTTT CTTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT -TTTTCT TTTTCT
* *
3892895 TCTTCT TCTTCT TCTTTCT TTTT
1 TTTTCT TTTTCT T-TTTCT TTTT
3892918 TTATTTATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
5 4 0.07
6 35 0.64
7 16 0.29
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:3892861 original size:11 final size:10
Alignment explanation
Indices: 3892845--3892919 Score: 62
Period size: 11 Copynumber: 6.8 Consensus size: 10
3892835 TCAACCTCTC
3892845 CTTTTATTTTT
1 CTTTT-TTTTT
3892856 CTTTTATTTTT
1 CTTTT-TTTTT
3892867 CTTTTTTCTTT
1 CTTTTTT-TTT
*
3892878 -TTTTCTTTT
1 CTTTTTTTTT
3892887 CTTTTTCTTCTT
1 CTTTTT-TT-TT
3892899 CTTCTTCTTCTTT
1 CTT-TT-TT-TTT
3892912 CTTTTTTT
1 CTTTTTTT
3892920 ATTTATTTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
9 3 0.05
10 12 0.22
11 23 0.42
12 7 0.13
13 8 0.15
14 2 0.04
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:3892872 original size:12 final size:12
Alignment explanation
Indices: 3892846--3892917 Score: 65
Period size: 13 Copynumber: 5.8 Consensus size: 12
3892836 CAACCTCTCC
*
3892846 TTTTATTTTTC-
1 TTTTCTTTTTCT
*
3892857 TTTTATTTTTCTT
1 TTTTCTTTTTC-T
*
3892870 TTTTCTTTTTTT
1 TTTTCTTTTTCT
3892882 CTTTTCTTTTTCT
1 -TTTTCTTTTTCT
* *
3892895 TCTTCTTCTTCT
1 TTTTCTTTTTCT
3892907 TCTTTCTTTTT
1 T-TTTCTTTTT
3892918 TTATTTATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
11 11 0.22
12 12 0.24
13 27 0.54
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:3892885 original size:26 final size:29
Alignment explanation
Indices: 3892851--3892916 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 29
3892841 TCTCCTTTTA
3892851 TTTTTCTTTTATTTTTCTT-TT-TTCTT-
1 TTTTTCTTTTATTTTTCTTCTTCTTCTTC
*
3892877 TTTTTCTTTTCTTTTTCTTCTTCTTCTTC
1 TTTTTCTTTTATTTTTCTTCTTCTTCTTC
3892906 TTCTTTCTTTT
1 TT-TTTCTTTT
3892917 TTTATTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
26 18 0.51
27 2 0.06
28 5 0.14
29 2 0.06
30 8 0.23
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (29 bp):
TTTTTCTTTTATTTTTCTTCTTCTTCTTC
Found at i:3892916 original size:38 final size:37
Alignment explanation
Indices: 3892845--3892928 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
3892835 TCAACCTCTC
* *
3892845 CTTTTATTTTTCTTTTATTTTTCTTTTTTCTTTTTTT
1 CTTTTATTTTTCTTTTATTCTTCTTCTTTCTTTTTTT
* *
3892882 CTTTTCTTTTTCTTCTTCTTCTTCTTCTTTCTTTTTTT
1 CTTTTATTTTTCTT-TTATTCTTCTTCTTTCTTTTTTT
*
3892920 -ATTTATTTT
1 CTTTTATTTT
3892929 CTTCATCGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
37 20 0.50
38 20 0.50
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (37 bp):
CTTTTATTTTTCTTTTATTCTTCTTCTTTCTTTTTTT
Found at i:3895731 original size:20 final size:20
Alignment explanation
Indices: 3895706--3895744 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3895696 TTTCTTATGA
3895706 CTAGTTCTCTATTTGGCAAC
1 CTAGTTCTCTATTTGGCAAC
3895726 CTAGTTCTCTATTTGGCAA
1 CTAGTTCTCTATTTGGCAA
3895745 TAAAACATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (20 bp):
CTAGTTCTCTATTTGGCAAC
Found at i:3898687 original size:29 final size:29
Alignment explanation
Indices: 3898655--3898773 Score: 136
Period size: 29 Copynumber: 4.1 Consensus size: 29
3898645 AATTTGGGGT
* *
3898655 CAAAATTGAAATTTTTGGATATTCGAGGG
1 CAAAATGGTAATTTTTGGATATTCGAGGG
* *
3898684 CAAAATGGTAATTTTTGGATATT-TAGGAA
1 CAAAATGGTAATTTTTGGATATTCGAGG-G
*
3898713 CAAAATGGTAATTTTTGGATGTTC-AGGGG
1 CAAAATGGTAATTTTTGGATATTCGA-GGG
*
3898742 TAAAATGGTAA-TTTTGGATATTCGAGAGG
1 CAAAATGGTAATTTTTGGATATTCGAG-GG
3898771 CAA
1 CAA
3898774 GATCATAATT
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
28 15 0.20
29 59 0.78
30 2 0.03
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (29 bp):
CAAAATGGTAATTTTTGGATATTCGAGGG
Found at i:3898717 original size:58 final size:57
Alignment explanation
Indices: 3898655--3898763 Score: 157
Period size: 58 Copynumber: 1.9 Consensus size: 57
3898645 AATTTGGGGT
*
3898655 CAAAATTGAAATTTTTGGATATTC-GAGGGCAAAATGGTAATTTTTGGATATTTAGGAA
1 CAAAATGGAAATTTTTGGATATTCAG-GGGCAAAATGGTAA-TTTTGGATATTTAGGAA
* * *
3898713 CAAAATGGTAATTTTTGGATGTTCAGGGGTAAAATGGTAATTTTGGATATT
1 CAAAATGGAAATTTTTGGATATTCAGGGGCAAAATGGTAATTTTGGATATT
3898764 CGAGAGGCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
57 11 0.24
58 34 0.74
59 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.38
Consensus pattern (57 bp):
CAAAATGGAAATTTTTGGATATTCAGGGGCAAAATGGTAATTTTGGATATTTAGGAA
Found at i:3898813 original size:29 final size:29
Alignment explanation
Indices: 3898781--3899022 Score: 181
Period size: 30 Copynumber: 8.2 Consensus size: 29
3898771 CAAGATCATA
* *
3898781 ATTTTGGAGAAGTTTGGGGTCAAAATGAG
1 ATTTTAGAAAAGTTTGGGGTCAAAATGAG
*
3898810 ATTTTAGAAAAGCTTGGGGGTCAAAATGTA-
1 ATTTTAGAAAAG-TTTGGGGTCAAAATG-AG
** *
3898840 AACTTGGAAAAGTTTGAGGGTCAAAATGTA-
1 ATTTTAGAAAAGTTTG-GGGTCAAAATG-AG
* * * *
3898870 ATTTCAAAAAAGTTTGGGAGTTAAAATGTG
1 ATTTTAGAAAAGTTTGGG-GTCAAAATGAG
* * * *
3898900 ATTTTGGAAAA-TTATAAGGGTTAAAAT-ATA
1 ATTTTAGAAAAGTT-T-GGGGTCAAAATGA-G
* *
3898930 ATTTTAGAAAAGTTTGGGGTGAAAATGTG
1 ATTTTAGAAAAGTTTGGGGTCAAAATGAG
3898959 ATTTTAGAAAAGTTTAGGGGTC-AAATGTA-
1 ATTTTAGAAAAGTTT-GGGGTCAAAATG-AG
* *
3898988 ATTTTAGAAAAGTTCGAGGGTCAAAATGTG
1 ATTTTAGAAAAGTTTG-GGGTCAAAATGAG
3899018 ATTTT
1 ATTTT
3899023 TAAAGAAAAT
Statistics
Matches: 169, Mismatches: 29, Indels: 29
0.74 0.13 0.13
Matches are distributed among these distances:
28 1 0.01
29 65 0.38
30 98 0.58
31 5 0.03
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.33
Consensus pattern (29 bp):
ATTTTAGAAAAGTTTGGGGTCAAAATGAG
Found at i:3898881 original size:60 final size:59
Alignment explanation
Indices: 3898781--3899022 Score: 260
Period size: 60 Copynumber: 4.1 Consensus size: 59
3898771 CAAGATCATA
* *
3898781 ATTTTGGAGAAGTTTG-GGGTCAAAATG-AGATTTTAGAAAAGCTTGGGGGTCAAAATGTA
1 ATTTTGGAAAAGTTTGAGGGTCAAAATGTA-ATTTTAGAAAAG-TTGGGGGTCAAAATGTG
** * * * *
3898840 AACTTGGAAAAGTTTGAGGGTCAAAATGTAATTTCAAAAAAGTTTGGGAGTTAAAATGTG
1 ATTTTGGAAAAGTTTGAGGGTCAAAATGTAATTTTAGAAAAG-TTGGGGGTCAAAATGTG
* * * * *
3898900 ATTTTGGAAAA-TTATAAGGGTTAAAATATAATTTTAGAAAAGTTTGGGGTGAAAATGTG
1 ATTTTGGAAAAGTT-TGAGGGTCAAAATGTAATTTTAGAAAAGTTGGGGGTCAAAATGTG
* *
3898959 ATTTTAGAAAAGTTT-AGGGGTC-AAATGTAATTTTAGAAAAGTTCGAGGGTCAAAATGTG
1 ATTTTGGAAAAGTTTGA-GGGTCAAAATGTAATTTTAGAAAAGTT-GGGGGTCAAAATGTG
3899018 ATTTT
1 ATTTT
3899023 TAAAGAAAAT
Statistics
Matches: 152, Mismatches: 25, Indels: 12
0.80 0.13 0.06
Matches are distributed among these distances:
58 21 0.14
59 61 0.40
60 69 0.45
61 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.33
Consensus pattern (59 bp):
ATTTTGGAAAAGTTTGAGGGTCAAAATGTAATTTTAGAAAAGTTGGGGGTCAAAATGTG
Found at i:3899036 original size:59 final size:58
Alignment explanation
Indices: 3898857--3899037 Score: 163
Period size: 59 Copynumber: 3.1 Consensus size: 58
3898847 AAAAGTTTGA
* * * * **
3898857 GGGTCAAAATGTAATTTCAAAAAAGTTTGGGAGTTAAAATGTGATTTTGGAAA-ATTATAAG
1 GGGTC-AAATGTAATTTTAGAAAAGTTTGGG-GTCAAAATGTGATTTT-TAAAGAAAAT-AG
* * * *
3898918 GGTTAAAATATAATTTTAGAAAAGTTTGGGGTGAAAATGTGA-TTTT--AGAAAAGTTTAG
1 GGGTCAAATGTAATTTTAGAAAAGTTTGGGGTCAAAATGTGATTTTTAAAGAAAA---TAG
*
3898976 GGGTCAAATGTAATTTTAGAAAAGTTCGAGGGTCAAAATGTGATTTTTAAAGAAAATAG
1 GGGTCAAATGTAATTTTAGAAAAGTTTG-GGGTCAAAATGTGATTTTTAAAGAAAATAG
3899035 GGG
1 GGG
3899038 CTTAATTCGT
Statistics
Matches: 98, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
55 1 0.01
56 2 0.02
58 29 0.30
59 31 0.32
60 26 0.27
61 3 0.03
62 6 0.06
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.33
Consensus pattern (58 bp):
GGGTCAAATGTAATTTTAGAAAAGTTTGGGGTCAAAATGTGATTTTTAAAGAAAATAG
Found at i:3899636 original size:4 final size:4
Alignment explanation
Indices: 3899627--3899654 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3899617 AAAAGGTAAA
3899627 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
3899655 TAAAATGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Done.