Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 44 of 141
Found at i:13260323 original size:14 final size:14
Alignment explanation
Indices: 13260278--13260327 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
13260268 TGTCTAAATC
13260278 AATGTGAATATTAT
1 AATGTGAATATTAT
* *
13260292 AATGTCTAA-A-T-C
1 AATGT-GAATATTAT
13260304 AATGTGAATATTAT
1 AATGTGAATATTAT
13260318 AATGTGAATA
1 AATGTGAATA
13260328 CCAAATTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
11 2 0.07
12 6 0.21
13 2 0.07
14 16 0.57
15 2 0.07
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (14 bp):
AATGTGAATATTAT
Found at i:13261547 original size:17 final size:18
Alignment explanation
Indices: 13261525--13261569 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
13261515 TGAAATAAAT
13261525 AATAAAGAGAACA-AAGA
1 AATAAAGAGAACAGAAGA
*
13261542 AATAAAGA-AATAGAAGA
1 AATAAAGAGAACAGAAGA
13261559 AATAAA-AGAAC
1 AATAAAGAGAAC
13261570 TCTAACTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.71, C:0.04, G:0.16, T:0.09
Consensus pattern (18 bp):
AATAAAGAGAACAGAAGA
Found at i:13261558 original size:9 final size:8
Alignment explanation
Indices: 13261516--13261564 Score: 55
Period size: 9 Copynumber: 6.0 Consensus size: 8
13261506 ATTATGTTAT
13261516 GAAATAAA
1 GAAATAAA
*
13261524 -TAATAAA
1 GAAATAAA
*
13261531 GAGAACAAA
1 GA-AATAAA
13261540 GAAATAAA
1 GAAATAAA
13261548 GAAATAGAA
1 GAAATA-AA
13261557 GAAATAAA
1 GAAATAAA
13261565 AGAACTCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
7 6 0.18
8 13 0.38
9 15 0.44
ACGTcount: A:0.71, C:0.02, G:0.14, T:0.12
Consensus pattern (8 bp):
GAAATAAA
Found at i:13268598 original size:26 final size:26
Alignment explanation
Indices: 13268538--13268599 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
13268528 TACCCTCAAC
* * *
13268538 AAAATTTTGATGATTTTATCCTTTGT
1 AAAATTTTGACGATTTTACCCTTGGT
*
13268564 AAACA-TTTGACGATTTTGCCCTTGGT
1 AAA-ATTTTGACGATTTTACCCTTGGT
13268590 AAAATTTTGA
1 AAAATTTTGA
13268600 GAAAAATATG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 1 0.03
26 28 0.93
27 1 0.03
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (26 bp):
AAAATTTTGACGATTTTACCCTTGGT
Found at i:13274916 original size:24 final size:24
Alignment explanation
Indices: 13274864--13274925 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
13274854 TATTCTTTAG
13274864 AATTTTTAAAAA-ATATATTATAT
1 AATTTTTAAAAATATATATTATAT
* * *
13274887 ATTTTTTAAAAATATA-ATTTTTTT
1 AATTTTTAAAAATATATA-TTATAT
*
13274911 AATTTTTATAAATAT
1 AATTTTTAAAAATAT
13274926 TTTGAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 12 0.38
24 20 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
AATTTTTAAAAATATATATTATAT
Found at i:13274942 original size:19 final size:20
Alignment explanation
Indices: 13274902--13274948 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
13274892 TTAAAAATAT
*
13274902 AATT-TTTTTAATTTTTATA
1 AATTATTTTGAATTTTTATA
13274921 AA-TATTTTGAATTTTTGA-A
1 AATTATTTTGAATTTTT-ATA
13274940 AATTATTTT
1 AATTATTTT
13274949 CAAATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 16 0.67
20 7 0.29
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
AATTATTTTGAATTTTTATA
Found at i:13275457 original size:51 final size:51
Alignment explanation
Indices: 13275397--13275503 Score: 205
Period size: 51 Copynumber: 2.1 Consensus size: 51
13275387 CATTGTTTAA
*
13275397 TTCAACCATGACCAAACATGATATTAATTCATAATATATCTTAAAACTGTT
1 TTCATCCATGACCAAACATGATATTAATTCATAATATATCTTAAAACTGTT
13275448 TTCATCCATGACCAAACATGATATTAATTCATAATATATCTTAAAACTGTT
1 TTCATCCATGACCAAACATGATATTAATTCATAATATATCTTAAAACTGTT
13275499 TTCAT
1 TTCAT
13275504 AGTGTTGCTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (51 bp):
TTCATCCATGACCAAACATGATATTAATTCATAATATATCTTAAAACTGTT
Found at i:13276102 original size:44 final size:44
Alignment explanation
Indices: 13276037--13276122 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
13276027 ATATTGCTAT
*
13276037 ATTAGCTCTTTTGGAGCTTTCAACTAATTTTGTACTACCAAACA
1 ATTAGCTCTTTTAGAGCTTTCAACTAATTTTGTACTACCAAACA
* *
13276081 ATTAGCTCTTTTAGAGGTTTCAATTAATTTTGTACTACCAAA
1 ATTAGCTCTTTTAGAGCTTTCAACTAATTTTGTACTACCAAA
13276123 TATTGCATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (44 bp):
ATTAGCTCTTTTAGAGCTTTCAACTAATTTTGTACTACCAAACA
Found at i:13276818 original size:3 final size:3
Alignment explanation
Indices: 13276810--13276853 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
13276800 ATTTAAAACA
13276810 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
13276854 CAGACCTCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:13279684 original size:11 final size:11
Alignment explanation
Indices: 13279663--13279692 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
13279653 AATAATATTT
13279663 TTATATTTTTAA
1 TTAT-TTTTTAA
13279675 TTATTTTTTAA
1 TTATTTTTTAA
13279686 TTATTTT
1 TTATTTT
13279693 GGAAATTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTTTTTAA
Found at i:13279746 original size:21 final size:22
Alignment explanation
Indices: 13279715--13279766 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
13279705 TAATTTGTAT
13279715 ATTTTTA-TAA-TATTTT-TAGA
1 ATTTTTATTAATTATTTTATA-A
13279735 ATTTTTATTAATTATTTTATAA
1 ATTTTTATTAATTATTTTATAA
*
13279757 ATTTTAATTA
1 ATTTTTATTA
13279767 TTTTAAAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 7 0.25
21 3 0.11
22 16 0.57
23 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
ATTTTTATTAATTATTTTATAA
Found at i:13279760 original size:9 final size:10
Alignment explanation
Indices: 13279654--13279771 Score: 51
Period size: 9 Copynumber: 12.1 Consensus size: 10
13279644 GTATCGTTTA
13279654 ATAATATTTT
1 ATAATATTTT
13279664 -T-ATATTTT
1 ATAATATTTT
13279672 -TAATTATTTT
1 ATAA-TATTTT
*
13279682 TTAATTATTTT
1 ATAA-TATTTT
13279693 GGA-AAT-TGTTT
1 --ATAATAT-TTT
*
13279704 ATAAT-TTGT
1 ATAATATTTT
13279713 AT-AT-TTTT
1 ATAATATTTT
13279721 ATAATATTTTT
1 ATAATA-TTTT
*
13279732 AGAAT-TTTT
1 ATAATATTTT
13279741 ATTAATTATTTT
1 A-TAA-TATTTT
13279753 ATAA-ATTTT
1 ATAATATTTT
*
13279762 A-ATTATTTT
1 ATAATATTTT
13279771 A
1 A
13279772 AAGATTTAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 29
0.72 0.05 0.24
Matches are distributed among these distances:
8 16 0.18
9 26 0.30
10 13 0.15
11 26 0.30
12 7 0.08
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (10 bp):
ATAATATTTT
Found at i:13292155 original size:22 final size:25
Alignment explanation
Indices: 13292130--13292183 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
13292120 TTATGAATTC
13292130 AATTTAAAAG-ATA-TAAT-ACAAT
1 AATTTAAAAGCATATTAATAACAAT
*
13292152 AATTT-CAAGCATATTTAATAACAAT
1 AATTTAAAAGCATA-TTAATAACAAT
13292177 AATTTAA
1 AATTTAA
13292184 GTTTTTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
24 4 0.16
25 10 0.40
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (25 bp):
AATTTAAAAGCATATTAATAACAAT
Found at i:13319634 original size:86 final size:86
Alignment explanation
Indices: 13319487--13319657 Score: 243
Period size: 86 Copynumber: 2.0 Consensus size: 86
13319477 TCACGATAGA
* ** * ** * *
13319487 TTGCGGCTTGGTTTGATAGTAGATCGGATTACTCATTGCTGAGGTGTTACTGTCTATTCAGAATA
1 TTGCGGCTTGGTTCGATAGTAGATCAAATTACTCATTGCTAAGGCATTACTATCTACTCAGAATA
13319552 AAGATTCGGTAATTTCGAAAG
66 AAGATTCGGTAATTTCGAAAG
* **
13319573 TTGCGGCTTGGTTCGATAGTAGATCAAATTACTCGTTGCTAAGGCATTGTTATCTACTCAGAATA
1 TTGCGGCTTGGTTCGATAGTAGATCAAATTACTCATTGCTAAGGCATTACTATCTACTCAGAATA
13319638 AAGATTCGGTAATTTCGAAA
66 AAGATTCGGTAATTTCGAAA
13319658 CCTTTATTTC
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 74 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.35
Consensus pattern (86 bp):
TTGCGGCTTGGTTCGATAGTAGATCAAATTACTCATTGCTAAGGCATTACTATCTACTCAGAATA
AAGATTCGGTAATTTCGAAAG
Found at i:13322363 original size:22 final size:23
Alignment explanation
Indices: 13322335--13322389 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
13322325 GTGGCTTGAC
**
13322335 CACATTATTGGTAG-TTTATATG
1 CACATTATTGGTAGCACTATATG
*
13322357 CACATTATTGGTAGCACTATCTG
1 CACATTATTGGTAGCACTATATG
13322380 CACATTATTG
1 CACATTATTG
13322390 TCAGCTTGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (23 bp):
CACATTATTGGTAGCACTATATG
Found at i:13323141 original size:17 final size:17
Alignment explanation
Indices: 13323121--13323159 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
13323111 TCGACCTTCC
13323121 TTTAAGGAAGACCCAAT
1 TTTAAGGAAGACCCAAT
13323138 TTTAAGGAAGACCCAAT
1 TTTAAGGAAGACCCAAT
13323155 TTTAA
1 TTTAA
13323160 CATCTTCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (17 bp):
TTTAAGGAAGACCCAAT
Found at i:13331753 original size:29 final size:28
Alignment explanation
Indices: 13331687--13331755 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
13331677 GTAAACTAAG
13331687 CAAAAGAAAATAAAAACCAAAAATAAAC
1 CAAAAGAAAATAAAAACCAAAAATAAAC
* *
13331715 CAAACTGAAAATAAGAAA-CAAACATGCAAA-
1 CAAA-AGAAAATAA-AAACCAAAAAT--AAAC
13331745 CAAAAGAAAAT
1 CAAAAGAAAAT
13331756 GTACTTGAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 4 0.12
29 20 0.59
30 7 0.21
31 3 0.09
ACGTcount: A:0.70, C:0.14, G:0.07, T:0.09
Consensus pattern (28 bp):
CAAAAGAAAATAAAAACCAAAAATAAAC
Found at i:13335427 original size:35 final size:35
Alignment explanation
Indices: 13335388--13335460 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
13335378 AAAAGTAAGA
13335388 GTAGAAGAAAATGGATTG-CAACGTAAAAGAAAAAG
1 GTAGAAGAAAATGGA-TGACAACGTAAAAGAAAAAG
13335423 GTAGAAGAAAATGGATGACAACGTAAAAGAAAAAG
1 GTAGAAGAAAATGGATGACAACGTAAAAGAAAAAG
13335458 GTA
1 GTA
13335461 AGTAATTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 2 0.05
35 35 0.95
ACGTcount: A:0.55, C:0.05, G:0.26, T:0.14
Consensus pattern (35 bp):
GTAGAAGAAAATGGATGACAACGTAAAAGAAAAAG
Found at i:13338996 original size:20 final size:21
Alignment explanation
Indices: 13338970--13339016 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
13338960 CCTGCTTGTG
13338970 CAATTTGTTTC-TTTTCAATT
1 CAATTTGTTTCTTTTTCAATT
*
13338990 TAATTTGTTTCTTTTTCAATT
1 CAATTTGTTTCTTTTTCAATT
13339011 CAATTT
1 CAATTT
13339017 TGTTCTCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.21, C:0.13, G:0.04, T:0.62
Consensus pattern (21 bp):
CAATTTGTTTCTTTTTCAATT
Found at i:13339022 original size:21 final size:21
Alignment explanation
Indices: 13338970--13339023 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
13338960 CCTGCTTGTG
13338970 CAATTTGTT-TCTTTTCAATT
1 CAATTTGTTCTCTTTTCAATT
*
13338990 TAATTTGTT-TCTTTTTCAATT
1 CAATTTGTTCTC-TTTTCAATT
13339011 CAATTTTGTTCTC
1 CAA-TTTGTTCTC
13339024 CTTCTAGCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 10 0.34
21 11 0.38
22 6 0.21
23 2 0.07
ACGTcount: A:0.19, C:0.15, G:0.06, T:0.61
Consensus pattern (21 bp):
CAATTTGTTCTCTTTTCAATT
Found at i:13340190 original size:14 final size:14
Alignment explanation
Indices: 13340171--13340199 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13340161 ATTAATGTCA
13340171 TAATTTATTTAAAT
1 TAATTTATTTAAAT
13340185 TAATTTATTTAAAT
1 TAATTTATTTAAAT
13340199 T
1 T
13340200 TTGGTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTTATTTAAAT
Found at i:13341187 original size:29 final size:29
Alignment explanation
Indices: 13341154--13341209 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
13341144 TTTGGGACAT
* * *
13341154 GATCAATTTAATCTCTTTACTATTAAATG
1 GATCAATTTAACCCCTATACTATTAAATG
13341183 GATCAATTTAACCCCTATACTATTAAA
1 GATCAATTTAACCCCTATACTATTAAA
13341210 AATAATCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (29 bp):
GATCAATTTAACCCCTATACTATTAAATG
Found at i:13342906 original size:17 final size:17
Alignment explanation
Indices: 13342851--13342920 Score: 51
Period size: 17 Copynumber: 4.2 Consensus size: 17
13342841 TTTTTAATAT
*
13342851 TTTCCCTCCAAAATTTTA
1 TTTCCCT-CAAACTTTTA
13342869 -TTCCCTC---CTATTTA
1 TTTCCCTCAAACT-TTTA
13342883 TTTTCCCTCAAACTTTTA
1 -TTTCCCTCAAACTTTTA
*
13342901 TTTCCC-AAAACTTTTTA
1 TTTCCCTCAAAC-TTTTA
13342918 TTT
1 TTT
13342921 TTCCCCTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
13 1 0.02
14 4 0.09
16 12 0.28
17 20 0.47
18 4 0.09
19 2 0.05
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTCCCTCAAACTTTTA
Found at i:13352379 original size:9 final size:9
Alignment explanation
Indices: 13352339--13352402 Score: 58
Period size: 9 Copynumber: 6.9 Consensus size: 9
13352329 CGTTTTTAAA
*
13352339 AAAAATATT
1 AAAAATAAT
*
13352348 AATAA-AAT
1 AAAAATAAT
13352356 AACAAGATAAT
1 AA-AA-ATAAT
*
13352367 AAAAATCAT
1 AAAAATAAT
13352376 AAAAATAAT
1 AAAAATAAT
*
13352385 AATAATAAT
1 AAAAATAAT
13352394 AATAAATAA
1 AA-AAATAA
13352403 AAATTAAAGC
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
8 4 0.09
9 27 0.61
10 8 0.18
11 5 0.11
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (9 bp):
AAAAATAAT
Found at i:13354002 original size:26 final size:24
Alignment explanation
Indices: 13353954--13354002 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
13353944 ATTAGTTTAT
*
13353954 TAATATTTTAATTTGATTTTTAAA
1 TAATATTTTAATTTGATTATTAAA
*
13353978 TAATATTTTATTATTTTATTATTAA
1 TAATATTTTA--ATTTGATTATTAA
13354003 TTTATTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
26 11 0.52
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TAATATTTTAATTTGATTATTAAA
Found at i:13373577 original size:46 final size:46
Alignment explanation
Indices: 13373523--13373987 Score: 738
Period size: 46 Copynumber: 10.1 Consensus size: 46
13373513 CTTGTTCCTA
* * *
13373523 ATCAGATAAGTATAGCTAAGGCTACCAGTTATCACTTTGTCACTTG
1 ATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACTTG
*
13373569 ATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTGTCACTTG
1 ATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACTTG
* *
13373615 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTG
1 ATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACTTG
* *
13373661 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTG
1 ATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACTTG
* * *
13373707 ATCAGATAAGTGCAGCTAACGCTAACACTTATCACTTTGTCACCTG
1 ATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACTTG
*
13373753 ATCAGATAAGTATAGCT-AGAGCTAACACTTATCACTTTGTCACTTG
1 ATCAGATAAGTGTAGCTAAG-GCTAACACTTATCACTTTGTCACTTG
13373799 ATCAGATAAGTGTAGCT-AGAGCTAACACTTATCACTTTGTCACTTG
1 ATCAGATAAGTGTAGCTAAG-GCTAACACTTATCACTTTGTCACTTG
* * *
13373845 ATAAGATAAGTGTAGCTAATGCTAACACTTATCACTTTGTCACATG
1 ATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACTTG
*
13373891 ATCAGATAAGTGTAGCTAATGCTAACACTTATCACTTTGTCACTTG
1 ATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACTTG
*
13373937 ATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCAC-TG
1 ATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACTTG
13373982 ATCAGA
1 ATCAGA
13373988 ACTACTCAAA
Statistics
Matches: 399, Mismatches: 18, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
45 9 0.02
46 389 0.97
47 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (46 bp):
ATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACTTG
Found at i:13377891 original size:49 final size:48
Alignment explanation
Indices: 13377835--13378005 Score: 213
Period size: 49 Copynumber: 3.5 Consensus size: 48
13377825 GTTTTCACAT
* * *
13377835 TGCCATAGTCCAACTATGATCTTACATGTAATCACATATCACATACTGA
1 TGCCATAGCCCAGCTATGGTCTTACATG-AATCACATATCACATACTGA
*
13377884 TGCCATAGCCCAGCTATGGTCTTATACA-GAATCACATATCACTTACTGA
1 TGCCATAGCCCAGCTATGGTC-T-TACATGAATCACATATCACATACTGA
* *
13377933 TGCCATAGCCCAGCTATGGTTTTACATAGAATCACATAT--CATAATGA
1 TGCCATAGCCCAGCTATGGTCTTACAT-GAATCACATATCACATACTGA
* *
13377980 TGCCATATCCCAGATATGGTCTTACA
1 TGCCATAGCCCAGCTATGGTCTTACA
13378006 CGGAGATCAC
Statistics
Matches: 108, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
47 33 0.31
48 1 0.01
49 68 0.63
50 2 0.02
51 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (48 bp):
TGCCATAGCCCAGCTATGGTCTTACATGAATCACATATCACATACTGA
Found at i:13379359 original size:46 final size:46
Alignment explanation
Indices: 13379285--13379675 Score: 605
Period size: 46 Copynumber: 8.6 Consensus size: 46
13379275 TACGTATGAT
* *
13379285 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
*
13379329 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
* *
13379375 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
* *
13379421 CACTTATCACTTTGTCACTTGATTAGATAAGT-TAGCTAATGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
*
13379466 CACTTATCAATTTGTCACTTGATCAGATAAGTGTAGCT-AGAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAG-GCTAA
* *
13379512 CACTTATCACTTTGTCATTTTATCAGATAAGTGTAGCT-AGAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAG-GCTAA
* *
13379558 CACTTATCACTTTGTCACTTGATCAGATAACTGTAGCTAATGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
*
13379604 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
13379650 CACTTATCACTTTGTCAC-TGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
13379676 AGTACTCAAA
Statistics
Matches: 324, Mismatches: 18, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
44 10 0.03
45 55 0.17
46 258 0.80
47 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
Found at i:13379610 original size:183 final size:183
Alignment explanation
Indices: 13379285--13379675 Score: 619
Period size: 183 Copynumber: 2.1 Consensus size: 183
13379275 TACGTATGAT
* * *
13379285 CACTTATC-ACTTGTCCCTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCAATTTGTCACTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACTT
* *
13379349 GATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTA
66 GATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACTTGATCAGATAACTGTAGCTA
* * *
13379414 AAGCTATCACTTATCACTTTGTCACTTGATTAGATAAGT-TAGCTAATGCTAA
131 AAGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAA
*
13379466 CACTTATCAATTTGTCACTTGATCAGATAAGTGTAGCT-AGAGCTAACACTTATCACTTTGTCAT
1 CACTTATCAATTTGTCAC-TGATCAGATAAGTGTAGCTAAG-GCTAACACTTATCACTTTGTCAC
*
13379530 TTTATCAGATAAGTGTAGCT-AGAGCTAACACTTATCACTTTGTCACTTGATCAGATAACTGTAG
64 TTGATCAGATAAGTGTAGCTAAG-GCTAACACTTATCACTTTGTCACTTGATCAGATAACTGTAG
*
13379594 CTAATGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAA
128 CTAAAGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAA
*
13379650 CACTTATCACTTTGTCACTGATCAGA
1 CACTTATCAATTTGTCACTGATCAGA
13379676 AGTACTCAAA
Statistics
Matches: 193, Mismatches: 12, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
181 8 0.04
182 11 0.06
183 145 0.75
184 29 0.15
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (183 bp):
CACTTATCAATTTGTCACTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACTT
GATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACTTGATCAGATAACTGTAGCTA
AAGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAA
Found at i:13386985 original size:17 final size:16
Alignment explanation
Indices: 13386956--13386989 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
13386946 AAATATTATG
13386956 AAATAACAACAAACAA
1 AAATAACAACAAACAA
*
13386972 AAATAAACATCAAACAA
1 AAAT-AACAACAAACAA
13386989 A
1 A
13386990 CGCCATCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.74, C:0.18, G:0.00, T:0.09
Consensus pattern (16 bp):
AAATAACAACAAACAA
Found at i:13402678 original size:51 final size:51
Alignment explanation
Indices: 13402564--13402826 Score: 377
Period size: 51 Copynumber: 5.2 Consensus size: 51
13402554 CTTACGTATG
* * *
13402564 ATCACTTATCACTTGTCCCTGATCAGATAATTGTAGCT-AAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* *
13402614 ATCACTTGCCACTTGTCACTGATCAGAT-AGTTGTAGCTAAAGCTACAACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAG-TGTAGCTAAAGCTACCACTT
13402665 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* * * *
13402716 ATCACTTGTCACTTGCCACTAATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* * * * *
13402767 ATCACTTGCCATTTGTCATTGATCAGATAAGTGTAGCTGAAGCTACTACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
13402818 ATCACTTGT
1 ATCACTTGT
13402827 TACTGATCAG
Statistics
Matches: 191, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
49 1 0.01
50 32 0.17
51 156 0.82
52 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:13414582 original size:3 final size:3
Alignment explanation
Indices: 13414574--13414600 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
13414564 CTATGGGATG
13414574 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
13414601 AGGATCCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:13416197 original size:16 final size:15
Alignment explanation
Indices: 13416172--13416205 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
13416162 AAAGTTGATA
*
13416172 ATAATTAATATATATT
1 ATAATAAATATA-ATT
13416188 ATAATAAATATAATT
1 ATAATAAATATAATT
13416203 ATA
1 ATA
13416206 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:13423754 original size:20 final size:20
Alignment explanation
Indices: 13423729--13423780 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
13423719 GGAAAAGTTT
13423729 TTTTTACATATATT-AATAAA
1 TTTTTACATATATTAAAT-AA
* *
13423749 TTTTT--ATATTTTAAATTA
1 TTTTTACATATATTAAATAA
13423767 TTTTTACATATATT
1 TTTTTACATATATT
13423781 GCAATGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 12 0.46
19 3 0.12
20 11 0.42
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTACATATATTAAATAA
Found at i:13424657 original size:43 final size:43
Alignment explanation
Indices: 13424588--13424803 Score: 240
Period size: 43 Copynumber: 5.0 Consensus size: 43
13424578 AGCGCCACTG
* * *
13424588 AAGACC-CTGACCTTTAACGACACTTTTTCCACAATCACCGCTA
1 AAGACCAC-GACCTTTAGCGACGCTTTTTCCACAAACACCGCTA
* * *
13424631 AA-ACCAACGATCTTTAGCGATGCTTTTT-CACAAATACCGCTA
1 AAGACC-ACGACCTTTAGCGACGCTTTTTCCACAAACACCGCTA
* * *
13424673 AAGACCACGACATTTAGCGACGCTTTTTACACAAACGCCGCTA
1 AAGACCACGACCTTTAGCGACGCTTTTTCCACAAACACCGCTA
* * * *
13424716 AAGACCACAACCTTTAACGGCGCTTTTCCCACAAACACCGCTA
1 AAGACCACGACCTTTAGCGACGCTTTTTCCACAAACACCGCTA
** * *
13424759 AAGACCACGACCTTTAGCGGTGCTTTTTCCAAAAACGCCGCTA
1 AAGACCACGACCTTTAGCGACGCTTTTTCCACAAACACCGCTA
13424802 AA
1 AA
13424804 AACATAATCT
Statistics
Matches: 145, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
42 36 0.25
43 108 0.74
44 1 0.01
ACGTcount: A:0.32, C:0.31, G:0.13, T:0.23
Consensus pattern (43 bp):
AAGACCACGACCTTTAGCGACGCTTTTTCCACAAACACCGCTA
Found at i:13424677 original size:85 final size:86
Alignment explanation
Indices: 13424588--13424774 Score: 218
Period size: 85 Copynumber: 2.2 Consensus size: 86
13424578 AGCGCCACTG
* * * * *
13424588 AAGACC-CTGACCTTTAACGACACTTTTTCCACAATCACCGCTAAA-ACCAACGATCTTTAGCGA
1 AAGACCAC-GACCTTTAACGACACTTTTTACACAAACACCGCTAAAGACC-ACAACCTTTAACGA
* * *
13424651 TGCTTTT-TCACAAATACCGCTA
64 CGCTTTTCCCACAAACACCGCTA
* * * * *
13424673 AAGACCACGACATTTAGCGACGCTTTTTACACAAACGCCGCTAAAGACCACAACCTTTAACGGCG
1 AAGACCACGACCTTTAACGACACTTTTTACACAAACACCGCTAAAGACCACAACCTTTAACGACG
13424738 CTTTTCCCACAAACACCGCTA
66 CTTTTCCCACAAACACCGCTA
13424759 AAGACCACGACCTTTA
1 AAGACCACGACCTTTA
13424775 GCGGTGCTTT
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
85 53 0.62
86 32 0.38
ACGTcount: A:0.33, C:0.32, G:0.12, T:0.23
Consensus pattern (86 bp):
AAGACCACGACCTTTAACGACACTTTTTACACAAACACCGCTAAAGACCACAACCTTTAACGACG
CTTTTCCCACAAACACCGCTA
Found at i:13428426 original size:27 final size:27
Alignment explanation
Indices: 13428396--13428452 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
13428386 AAGCATTCTT
13428396 TTTTCTTGTTTACATTCCCTTAATTAA
1 TTTTCTTGTTTACATTCCCTTAATTAA
13428423 TTTTCTTGTTTACATTCCCTTAATTAA
1 TTTTCTTGTTTACATTCCCTTAATTAA
13428450 TTT
1 TTT
13428453 CAACATGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.21, C:0.18, G:0.04, T:0.58
Consensus pattern (27 bp):
TTTTCTTGTTTACATTCCCTTAATTAA
Found at i:13428609 original size:61 final size:61
Alignment explanation
Indices: 13428539--13428659 Score: 233
Period size: 61 Copynumber: 2.0 Consensus size: 61
13428529 TCGAGATCAA
13428539 TTTTTATGTCTAAACTCGACTCTTGAAAAGGATTACTAAAAATTTTCATATTTGAATTTAT
1 TTTTTATGTCTAAACTCGACTCTTGAAAAGGATTACTAAAAATTTTCATATTTGAATTTAT
*
13428600 TTTTTATGTCTAAAGTCGACTCTTGAAAAGGATTACTAAAAATTTTCATATTTGAATTTA
1 TTTTTATGTCTAAACTCGACTCTTGAAAAGGATTACTAAAAATTTTCATATTTGAATTTA
13428660 AATAGAAAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (61 bp):
TTTTTATGTCTAAACTCGACTCTTGAAAAGGATTACTAAAAATTTTCATATTTGAATTTAT
Found at i:13429760 original size:41 final size:41
Alignment explanation
Indices: 13429703--13429980 Score: 434
Period size: 41 Copynumber: 6.8 Consensus size: 41
13429693 AAATGTTTTT
* * *
13429703 GCGGCGATTTTTCAAAAACGCCACT-AAAGCCTCGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAAGCCT-GAGCATTA
*
13429744 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTA
*
13429785 GCGGCGCTTTCTCAAAAACACCGCTAAAAGCCTGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTA
13429826 GCGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTA
13429867 GCGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTA
* *
13429908 GCGGCGCTTTCTCAAAAATGCCGCT-AAAGCTCTGAGTATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAAGC-CTGAGCATTA
* * *
13429949 GTGGTGCTTTTTCAAAAACGCCGCTAAAAGCC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAAGCC
13429981 CCAAAAGGTT
Statistics
Matches: 223, Mismatches: 11, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
40 5 0.02
41 206 0.92
42 12 0.05
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTA
Found at i:13431937 original size:22 final size:21
Alignment explanation
Indices: 13431907--13431950 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
13431897 AATTATAAAT
* *
13431907 AATTAAAAGTTATTTCTCTTA
1 AATTAAAAGTTATGTCACTTA
13431928 AATTCAAAAGTTATGTCACTTA
1 AATT-AAAAGTTATGTCACTTA
13431950 A
1 A
13431951 TTATTAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (21 bp):
AATTAAAAGTTATGTCACTTA
Found at i:13434780 original size:14 final size:14
Alignment explanation
Indices: 13434761--13434789 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13434751 ACACATAGCC
13434761 ATAATAGTGTCACT
1 ATAATAGTGTCACT
13434775 ATAATAGTGTCACT
1 ATAATAGTGTCACT
13434789 A
1 A
13434790 GATATTGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (14 bp):
ATAATAGTGTCACT
Found at i:13440475 original size:22 final size:22
Alignment explanation
Indices: 13440443--13440489 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
13440433 ACAAATCCTA
13440443 TCTCAAATTCCTTCCAAAATCC
1 TCTCAAATTCCTTCCAAAATCC
* * *
13440465 TCTCAATTTCCTTCTAAAATTC
1 TCTCAAATTCCTTCCAAAATCC
13440487 TCT
1 TCT
13440490 TAAACTCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.32, G:0.00, T:0.40
Consensus pattern (22 bp):
TCTCAAATTCCTTCCAAAATCC
Found at i:13440521 original size:52 final size:52
Alignment explanation
Indices: 13440443--13440541 Score: 162
Period size: 52 Copynumber: 1.9 Consensus size: 52
13440433 ACAAATCCTA
* * *
13440443 TCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCTAAAATTCTCTTAAAC
1 TCTCAAATTCCTTCCAAAATCCTCTCAATTTCATTCCAAAAATCTCTTAAAC
*
13440495 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCATTCCAAAAATCTCT
1 TCTCAAATTCCTTCCAAAATCCTCTCAATTTCATTCCAAAAATCTCT
13440542 CAAATCCATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.30, C:0.31, G:0.00, T:0.38
Consensus pattern (52 bp):
TCTCAAATTCCTTCCAAAATCCTCTCAATTTCATTCCAAAAATCTCTTAAAC
Found at i:13440522 original size:22 final size:22
Alignment explanation
Indices: 13440494--13440544 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
13440484 TTCTCTTAAA
*
13440494 CTCTCAATTTCCTTCC-AAAAT
1 CTCTCAATTTCATTCCAAAAAT
13440515 CCTCTCAATTTCATTCCAAAAAT
1 -CTCTCAATTTCATTCCAAAAAT
13440538 CTCTCAA
1 CTCTCAA
13440545 ATCCATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.35
Consensus pattern (22 bp):
CTCTCAATTTCATTCCAAAAAT
Found at i:13440611 original size:10 final size:10
Alignment explanation
Indices: 13440578--13440643 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
13440568 CCTCAATTTC
13440578 ATTTTTTTAA
1 ATTTTTTTAA
** *
13440588 ATAATTTCAA
1 ATTTTTTTAA
*
13440598 ATTTTTTTAT
1 ATTTTTTTAA
13440608 ATTTTTTTAAA
1 ATTTTTTT-AA
**
13440619 ATAATTTTAA
1 ATTTTTTTAA
*
13440629 ATTTTTTTAT
1 ATTTTTTTAA
13440639 ATTTT
1 ATTTT
13440644 CATCAATGGC
Statistics
Matches: 42, Mismatches: 13, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
10 35 0.83
11 7 0.17
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTTTAA
Found at i:13440621 original size:31 final size:30
Alignment explanation
Indices: 13440578--13440643 Score: 114
Period size: 31 Copynumber: 2.2 Consensus size: 30
13440568 CCTCAATTTC
13440578 ATTTTTTTAAATAATTTCAAATTTTTTTAT
1 ATTTTTTTAAATAATTTCAAATTTTTTTAT
*
13440608 ATTTTTTTAAAATAATTTTAAATTTTTTTAT
1 ATTTTTTT-AAATAATTTCAAATTTTTTTAT
13440639 ATTTT
1 ATTTT
13440644 CATCAATGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 8 0.24
31 26 0.76
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (30 bp):
ATTTTTTTAAATAATTTCAAATTTTTTTAT
Found at i:13445719 original size:123 final size:123
Alignment explanation
Indices: 13445499--13445788 Score: 492
Period size: 123 Copynumber: 2.3 Consensus size: 123
13445489 CAAAATCGCG
13445499 TCCACGAGGGCGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGAC
1 TCCACGAGGGCGCGATTTTATACTATTTGCTCAGAAACGTC-AAAAAAATTATTTCTTACATGAC
* *
13445564 CAACTGTAGCGAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAATTAGCA
65 CAACTGTAGCGAAATCGCGTCCACGAGGGCACGATTGCACAATGTCTTCTCAATTAGCA
* *
13445623 TCCACGAGGGCACGATTTTATAGTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGACC
1 TCCACGAGGGCGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGACC
*
13445688 AACTGTAGCGAAATCGCGTCCACGAGGGCACGATTGCACAATGTCTTCTCAGTTAGCA
66 AACTGTAGCGAAATCGCGTCCACGAGGGCACGATTGCACAATGTCTTCTCAATTAGCA
* *
13445746 TCCTCGAGGGCGCGATTTTATATTATTTGAC-CAGAAACGTCAA
1 TCCACGAGGGCGCGATTTTATACTATTTG-CTCAGAAACGTCAA
13445789 CTCGAAATAA
Statistics
Matches: 157, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
123 117 0.75
124 40 0.25
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (123 bp):
TCCACGAGGGCGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGACC
AACTGTAGCGAAATCGCGTCCACGAGGGCACGATTGCACAATGTCTTCTCAATTAGCA
Found at i:13451139 original size:26 final size:27
Alignment explanation
Indices: 13451110--13451162 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
13451100 TTTGCTTTTC
*
13451110 TATTTCCCA-AAATAAACTTCTCAATA
1 TATTTCCAATAAATAAACTTCTCAATA
*
13451136 TATTTCCAATTAAATAATCTTCTCAAT
1 TATTTCCAA-TAAATAAACTTCTCAAT
13451163 CCAATTCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
28 15 0.65
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.40
Consensus pattern (27 bp):
TATTTCCAATAAATAAACTTCTCAATA
Found at i:13451174 original size:28 final size:28
Alignment explanation
Indices: 13451119--13451174 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
13451109 CTATTTCCCA
* *
13451119 AAATAAACTTCTCAATATATTTCCAATT
1 AAATAAACTTCTCAATACAATTCCAATT
* * *
13451147 AAATAATCTTCTCAATCCAATTCTAATT
1 AAATAAACTTCTCAATACAATTCCAATT
13451175 TTGTTAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (28 bp):
AAATAAACTTCTCAATACAATTCCAATT
Found at i:13455479 original size:38 final size:39
Alignment explanation
Indices: 13455392--13455479 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 39
13455382 CTGGATTTAA
* * *
13455392 GGAGTGACACCATGAAAAATGGTTATCTACTAGCTTTAC
1 GGAGCGACACCATGAAAAATGGTTATCTACTAGATCTAC
* * * * *
13455431 GAAACAACACCATG-GAAATGGTTATCTACTAGATCTAT
1 GGAGCGACACCATGAAAAATGGTTATCTACTAGATCTAC
13455469 GGAGCGACACC
1 GGAGCGACACC
13455480 TCTAAAGAGG
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
38 28 0.74
39 10 0.26
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (39 bp):
GGAGCGACACCATGAAAAATGGTTATCTACTAGATCTAC
Found at i:13457112 original size:30 final size:30
Alignment explanation
Indices: 13457077--13457145 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
13457067 ATACCGCCGT
13457077 AAAGGC-TC-ACATATCACAGAGAATAGCCAC
1 AAAGGCTTCTACATATCA-A-AGAATAGCCAC
*
13457107 AAAGGCTTCTACTTATCAAAGAATAGCCAC
1 AAAGGCTTCTACATATCAAAGAATAGCCAC
*
13457137 AAATGCTTC
1 AAAGGCTTC
13457146 CAAATTTCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 25 0.71
31 3 0.09
32 7 0.20
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.20
Consensus pattern (30 bp):
AAAGGCTTCTACATATCAAAGAATAGCCAC
Found at i:13468780 original size:25 final size:26
Alignment explanation
Indices: 13468682--13468782 Score: 114
Period size: 26 Copynumber: 3.9 Consensus size: 26
13468672 AGCAATGTCA
** * *
13468682 CAGCAAAGCTGCCCTTAATAGTATCA
1 CAGCAAAGCTGCCAGTAACAGTATCG
* *
13468708 CAGCAAAGCTGCTAGTAATAGTATCG
1 CAGCAAAGCTGCCAGTAACAGTATCG
* *
13468734 CAGCAAAGCTGCCAATATCAGTATCG
1 CAGCAAAGCTGCCAGTAACAGTATCG
*
13468760 CAGTAAA-CTGCCAGTAACAGTAT
1 CAGCAAAGCTGCCAGTAACAGTAT
13468783 ACTTCCTCCA
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
25 14 0.22
26 50 0.78
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.22
Consensus pattern (26 bp):
CAGCAAAGCTGCCAGTAACAGTATCG
Found at i:13476305 original size:26 final size:26
Alignment explanation
Indices: 13476268--13476344 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 26
13476258 AACACACCAA
* * * *
13476268 TATCGCAGCAAAGCTGCCCGTTATAG
1 TATCGCAACAAAGCTGCCAGTAACAG
* * *
13476294 TATCGTAACAAAACTACCAGTAACAG
1 TATCGCAACAAAGCTGCCAGTAACAG
* *
13476320 TATCGCAGCAAAGCTGCCAATAACA
1 TATCGCAACAAAGCTGCCAGTAACA
13476345 ATATACTTCC
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (26 bp):
TATCGCAACAAAGCTGCCAGTAACAG
Found at i:13480321 original size:23 final size:23
Alignment explanation
Indices: 13480295--13480338 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
13480285 TGCCATCATT
*
13480295 TACTTTGTTGTTTTTCATTTTTA
1 TACTTTGTCGTTTTTCATTTTTA
13480318 TACTTTGTCGTTTTTCATTTT
1 TACTTTGTCGTTTTTCATTTT
13480339 GTGTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.68
Consensus pattern (23 bp):
TACTTTGTCGTTTTTCATTTTTA
Found at i:13480876 original size:25 final size:24
Alignment explanation
Indices: 13480847--13480910 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
13480837 ATAATTGATG
*
13480847 AATATTTTATATTTAAAATTTATTC
1 AATATTTTATATTTAAAATTTA-TA
* *
13480872 AATATTATT-TATTTGATATTTATA
1 AATATT-TTATATTTAAAATTTATA
13480896 AATATTTATATATTT
1 AATATTT-TATATTT
13480911 TTTAATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 1 0.03
24 8 0.24
25 22 0.67
26 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
AATATTTTATATTTAAAATTTATA
Found at i:13480885 original size:32 final size:31
Alignment explanation
Indices: 13480849--13480928 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 31
13480839 AATTGATGAA
13480849 TATTTTATATTTAAAATTTATTCA-ATATTATT
1 TATTTTATATTTAAAA--TATTCATATATTATT
* * *
13480881 TATTTGATATTTATAAATATTTATATATTTTT
1 TATTTTATATTTA-AAATATTCATATATTATT
* *
13480913 TAATTTATTTTTAAAA
1 TATTTTATATTTAAAA
13480929 AATAATATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
31 8 0.20
32 29 0.73
33 3 0.08
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (31 bp):
TATTTTATATTTAAAATATTCATATATTATT
Found at i:13485643 original size:24 final size:24
Alignment explanation
Indices: 13485603--13485706 Score: 111
Period size: 24 Copynumber: 4.2 Consensus size: 24
13485593 GGACACACCA
*
13485603 CAGCTCGT-ATGAGCTTCCTGATTT
1 CAGCTC-TCATGAGCTTCCCGATTT
*
13485627 CAGGTCTCATGAGCTTCCCGATTT
1 CAGCTCTCATGAGCTTCCCGATTT
* *
13485651 CAGCTCTTATGAGCTTCCCAATATT
1 CAGCTCTCATGAGCTTCCCGAT-TT
* * *
13485676 TAGCTCGCATGAGCTTCCCGTTATT
1 CAGCTCTCATGAGCTTCCCGAT-TT
13485701 CAGCTC
1 CAGCTC
13485707 GGAGGAACTT
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
23 1 0.01
24 39 0.58
25 27 0.40
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (24 bp):
CAGCTCTCATGAGCTTCCCGATTT
Found at i:13485662 original size:48 final size:50
Alignment explanation
Indices: 13485603--13485707 Score: 133
Period size: 49 Copynumber: 2.1 Consensus size: 50
13485593 GGACACACCA
** * *
13485603 CAGCTCGTATGAGCTTCCTGAT-TTCAGGTCTCATGAGCTTCCCGAT-TT
1 CAGCTCGTATGAGCTTCCCAATATTCAGCTCGCATGAGCTTCCCGATATT
* * *
13485651 CAGCTCTTATGAGCTTCCCAATATTTAGCTCGCATGAGCTTCCCGTTATT
1 CAGCTCGTATGAGCTTCCCAATATTCAGCTCGCATGAGCTTCCCGATATT
13485701 CAGCTCG
1 CAGCTCG
13485708 GAGGAACTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 19 0.40
49 20 0.43
50 8 0.17
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.34
Consensus pattern (50 bp):
CAGCTCGTATGAGCTTCCCAATATTCAGCTCGCATGAGCTTCCCGATATT
Found at i:13485700 original size:25 final size:26
Alignment explanation
Indices: 13485603--13485722 Score: 99
Period size: 25 Copynumber: 4.8 Consensus size: 26
13485593 GGACACACCA
* *
13485603 CAGCTCGTATGAGCTT-CC-TGATTT
1 CAGCTCGCATGAGCTTCCCGTTATTT
* *
13485627 CAGGTCTCATGAGCTTCCCG--ATTT
1 CAGCTCGCATGAGCTTCCCGTTATTT
** **
13485651 CAGCTCTTATGAGCTTCCCAATATTT
1 CAGCTCGCATGAGCTTCCCGTTATTT
13485677 -AGCTCGCATGAGCTTCCCGTTA-TT
1 CAGCTCGCATGAGCTTCCCGTTATTT
* * *
13485701 CAGCTCGGAGGAACTTCCCGTT
1 CAGCTCGCATGAGCTTCCCGTT
13485723 TATAACTCGT
Statistics
Matches: 78, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
24 36 0.46
25 38 0.49
26 4 0.05
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.33
Consensus pattern (26 bp):
CAGCTCGCATGAGCTTCCCGTTATTT
Found at i:13489266 original size:12 final size:12
Alignment explanation
Indices: 13489249--13489286 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
13489239 AGCCACATGC
*
13489249 CCGTGTGCCAGG
1 CCGTGTGCTAGG
13489261 CCGTGTGCTAGG
1 CCGTGTGCTAGG
13489273 CCGTGTGCTAGG
1 CCGTGTGCTAGG
13489285 CC
1 CC
13489287 ATGTAACTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.08, C:0.32, G:0.39, T:0.21
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:13493288 original size:14 final size:15
Alignment explanation
Indices: 13493271--13493299 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13493261 TGACAATGTG
13493271 ATTATG-TGAATGAT
1 ATTATGATGAATGAT
13493285 ATTATGATGAATGAT
1 ATTATGATGAATGAT
13493300 TGTGTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (15 bp):
ATTATGATGAATGAT
Found at i:13499705 original size:25 final size:25
Alignment explanation
Indices: 13499677--13499724 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
13499667 TATAGTCTAT
* *
13499677 CTATAGTAGTCTTAGTATATACTAC
1 CTATAGCAGTCTTAGGATATACTAC
*
13499702 CTATAGCAGTTTTAGGATATACT
1 CTATAGCAGTCTTAGGATATACT
13499725 GTCAAAGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (25 bp):
CTATAGCAGTCTTAGGATATACTAC
Found at i:13504358 original size:23 final size:23
Alignment explanation
Indices: 13504330--13504427 Score: 106
Period size: 23 Copynumber: 4.3 Consensus size: 23
13504320 GTGTTATTGA
* *
13504330 TCAGTGGTAACTTTGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
* * *
13504353 TTAGTGGTAGCTACGACTACATT
1 TCAGTGGTAGCTTCGGCTACATT
* * *
13504376 ACAATGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
* *
13504399 TCAGTGGTAGCTTTGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
13504422 TCAGTG
1 TCAGTG
13504428 TGGCACTTAT
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:13504678 original size:23 final size:25
Alignment explanation
Indices: 13504632--13504679 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
13504622 GAAATAGCTA
* *
13504632 AGAAATGTTTGATTAGTTATATGAG
1 AGAAATGTTTAATTAGTTAAATGAG
13504657 AGAAATG-TTAATT-GTTAAATGAG
1 AGAAATGTTTAATTAGTTAAATGAG
13504680 TATTTATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 5 0.24
25 7 0.33
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.38
Consensus pattern (25 bp):
AGAAATGTTTAATTAGTTAAATGAG
Found at i:13511469 original size:5 final size:5
Alignment explanation
Indices: 13511459--13511485 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
13511449 CTAATATCCC
13511459 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
13511486 TCTTATCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:13511882 original size:28 final size:27
Alignment explanation
Indices: 13511851--13511940 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 27
13511841 TGACAATGCA
*
13511851 CCACTGTTTTAATAATTTTACAGTCCTG
1 CCACTGTTTTAA-AATTTTACAGTTCTG
* * *
13511879 CCACTGCTTTTCAAATTTTACAATTTTG
1 CCACTG-TTTTAAAATTTTACAGTTCTG
*
13511907 CCACTAGTTTTCCAAATTTTTACAGTTCTG
1 CCACT-GTTTT--AAAATTTTACAGTTCTG
13511937 CCAC
1 CCAC
13511941 CTTTTTCCCA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
28 27 0.54
29 6 0.12
30 17 0.34
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (27 bp):
CCACTGTTTTAAAATTTTACAGTTCTG
Found at i:13511956 original size:30 final size:28
Alignment explanation
Indices: 13511864--13511969 Score: 83
Period size: 29 Copynumber: 3.7 Consensus size: 28
13511854 CTGTTTTAAT
*
13511864 AATTTTACAGTCCTGCCA-CTGCTTTT-CA
1 AATTTTACAGTTCTGCCACCT--TTTTCCA
* *
13511892 AATTTTACAATTTTGCCA-CTAGTTTTCCA
1 AATTTTACAGTTCTGCCACCT--TTTTCCA
13511921 AATTTTTACAGTTCTGCCACCTTTTTCCCA
1 AA-TTTTACAGTTCTGCCACCTTTTT-CCA
* * *
13511951 TATTTTATAGTTTTGCCAC
1 AATTTTACAGTTCTGCCAC
13511970 TGATTTTTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
28 21 0.33
29 23 0.36
30 18 0.28
31 2 0.03
ACGTcount: A:0.23, C:0.25, G:0.08, T:0.44
Consensus pattern (28 bp):
AATTTTACAGTTCTGCCACCTTTTTCCA
Found at i:13513047 original size:13 final size:13
Alignment explanation
Indices: 13513016--13513040 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13513006 CTTAGGATGC
13513016 ATGTTATTTATTA
1 ATGTTATTTATTA
13513029 ATGTTATTTATT
1 ATGTTATTTATT
13513041 TTCGTTAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
ATGTTATTTATTA
Found at i:13514606 original size:64 final size:64
Alignment explanation
Indices: 13514505--13514632 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
13514495 TTGAACGCTG
13514505 TCGTTTTGTGATGGATTGTGATGCTTGCACTTAATTGCTGGATTAACCCCTCAGTTTTGAAATA
1 TCGTTTTGTGATGGATTGTGATGCTTGCACTTAATTGCTGGATTAACCCCTCAGTTTTGAAATA
*
13514569 TCGTTTTGTGATGGATTGTGATGCTTGCGCTTAATTGCTGGATTAACCCCTCAGTTTTGAAATA
1 TCGTTTTGTGATGGATTGTGATGCTTGCACTTAATTGCTGGATTAACCCCTCAGTTTTGAAATA
13514633 GACTTCAATT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.41
Consensus pattern (64 bp):
TCGTTTTGTGATGGATTGTGATGCTTGCACTTAATTGCTGGATTAACCCCTCAGTTTTGAAATA
Found at i:13520123 original size:14 final size:14
Alignment explanation
Indices: 13520095--13520139 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
13520085 AATCAATGTC
*
13520095 AAAATGAAAATGAAA
1 AAAAAGAAAA-GAAA
* *
13520110 AAAGAGAGAAGAAA
1 AAAAAGAAAAGAAA
13520124 AAAAAGAAAAGAAA
1 AAAAAGAAAAGAAA
13520138 AA
1 AA
13520140 GAAAAGGAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAAAGAAAAGAAA
Found at i:13520986 original size:6 final size:6
Alignment explanation
Indices: 13520977--13521012 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
13520967 AAAAAGGTGA
13520977 AAAATG AAAAATG AAAATG AAAAATG AAAATG AAAA
1 AAAATG -AAAATG AAAATG -AAAATG AAAATG AAAA
13521013 AGTAAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 16 0.57
7 12 0.43
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:13520986 original size:7 final size:7
Alignment explanation
Indices: 13520974--13521022 Score: 68
Period size: 7 Copynumber: 7.3 Consensus size: 7
13520964 AAAAAAAAGG
13520974 TGAAAAA
1 TGAAAAA
13520981 TGAAAAA
1 TGAAAAA
13520988 TG-AAAA
1 TGAAAAA
13520994 TGAAAAA
1 TGAAAAA
13521001 TG-AAAA
1 TGAAAAA
13521007 TGAAAAA
1 TGAAAAA
13521014 -GTAAAAA
1 TG-AAAAA
13521021 TG
1 TG
13521023 GAGAGGCTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
6 13 0.34
7 24 0.63
8 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.16, T:0.16
Consensus pattern (7 bp):
TGAAAAA
Found at i:13520997 original size:20 final size:19
Alignment explanation
Indices: 13520974--13521022 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
13520964 AAAAAAAAGG
13520974 TGAAAAATGAAAAATGAAAA
1 TGAAAAATG-AAAATGAAAA
13520994 TGAAAAATGAAAATGAAAA
1 TGAAAAATGAAAATGAAAA
*
13521013 AGTAAAAATG
1 TG-AAAAATG
13521023 GAGAGGCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.67, C:0.00, G:0.16, T:0.16
Consensus pattern (19 bp):
TGAAAAATGAAAATGAAAA
Found at i:13521019 original size:13 final size:13
Alignment explanation
Indices: 13520977--13521013 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
13520967 AAAAAGGTGA
13520977 AAAATGAAAAATG
1 AAAATGAAAAATG
13520990 AAAATGAAAAATG
1 AAAATGAAAAATG
13521003 AAAATGAAAAA
1 AAAATGAAAAA
13521014 GTAAAAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:13522341 original size:87 final size:87
Alignment explanation
Indices: 13522195--13523029 Score: 867
Period size: 88 Copynumber: 9.5 Consensus size: 87
13522185 CAGATCAGTG
* *
13522195 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAAAGCAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
** *
13522260 TCGGTTGCAGTAGAGCGGGTTA
66 TCGGTTGCAGCGGAGCAGGTTA
* * * * *
13522282 AAGATAACAGATCTTGCCTTCTTGTATTGACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* * * *
13522347 TCAGTTGTAGTGGAGCAAGTTA
66 TCGGTTGCAGCGGAGCAGGTTA
* *
13522369 AAGATAGTAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
*
13522434 TCGGTTGCAGCGGAGCTGGTTA
66 TCGGTTGCAGCGGAGCAGGTTA
* * * * * *
13522456 AAGATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGACCCTAA-TCTTACCTC
1 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCTC
* * *
13522520 CATAGGTTACAGTGGAGCAGGTTA
64 CATCGGTTGCAGCGGAGCAGGTTA
* * * * *
13522544 AAGATAGCAGATATTGCCTTCCTGCATAGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCT-C
1 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAAACA-AAGCCTTGCCTCC
* *
13522608 ATTGGGTTGTAGCGGAGCAGGTTA
65 A-TCGGTTGCAGCGGAGCAGGTTA
* * * * * *
13522632 AAAATAGCACATCTTG-CTTCCTGCACCGACAGCGAAGCAAATCGAAGACACCAGCCTTGCCT-C
1 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAAACA-AAGCCTTGCCTCC
* *
13522695 ATTGGGTTGAAGCGGAGCAGGTTA
65 A-TCGGTTGCAGCGGAGCAGGTTA
* * * *
13522719 AAAATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATC-AAAGACACCAA-CCTTGTCT
1 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAA-ACA--AAGCCTTGCCT
* * *
13522782 CCCTAGGTTGTAGCGGAGCAGGTTA
63 CCATCGGTTGCAGCGGAGCAGGTTA
* * * * *
13522807 AAAATAGCAGATCTTGCCTTCATGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAAACA-AAGCCTTGCCTCC
* * *
13522872 CT-GTGTTGCAGCAGAGAAGGTTA
65 ATCG-GTTGCAGCGGAGCAGGTTA
* * * *
13522895 AAAATAGCAGATCTTGCCTTCCTACA-CTGACAGCGAAGCAGATCGAAGACACGAGCCTTGCCTC
1 AAGATAGCAGATCTTGCCTTCCTGCATC-GACAGCGAAGCAGATCGAAAACA-AAGCCTTGCCTC
* ** * * * *
13522959 CCTCGGTCACAGTGTAGCAAGTTG
64 CATCGGTTGCAGCGGAGCAGGTTA
* * *
13522983 AAGATAGTAGATCTTGCCTTCCTGCATCAACAGTGAAGCAGATCGAA
1 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAA
13523030 GATTACAAGT
Statistics
Matches: 646, Mismatches: 87, Indels: 29
0.85 0.11 0.04
Matches are distributed among these distances:
86 1 0.00
87 286 0.44
88 349 0.54
89 10 0.02
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.22
Consensus pattern (87 bp):
AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
TCGGTTGCAGCGGAGCAGGTTA
Found at i:13522728 original size:263 final size:261
Alignment explanation
Indices: 13522195--13523031 Score: 966
Period size: 263 Copynumber: 3.2 Consensus size: 261
13522185 CAGATCAGTG
* * * *
13522195 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAA-AGCAAAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCGAAGACCCAA-CCTTGCCTCC
* * * * * * *
13522259 ATCGGTTGCAGTAGAGCGGGTTAAAGATAACAGATCTTGCCTTCTTGTATTGACAGCGAAGCAGA
65 ATAGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCATGCATAGACAGCGAAGCAGA
* * * * * * * *
13522324 TCAAAAACA-AAGCCTTGCCTCCATCAGTTGTAGTGGAGCAAGTTAAAGATAGTAGATCTTGCCT
130 TCGAAGACACCAGCCTTGCCT-CATGAGTTGTAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCT
* * * *
13522388 TCCTGCATTGACAGCGAAGCAGATCGAAAACA-AAGCCTTGCCTCCATCGGTTGCAGCGGAGCTG
194 TCCTGCACTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT-CATCGGTTGAAGCGGAGCAG
13522452 GTTA
258 GTTA
* * *
13522456 AAGATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGACCCTAATCTTACCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCGAAGACCC-AACCTTGCCTCC
* * * *
13522521 ATAGGTTACAGTGGAGCAGGTTAAAGATAGCAGATATTGCCTTCCTGCATAGACAGCGAAGTAGA
65 ATAGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCATGCATAGACAGCGAAGCAGA
* *
13522586 TCGAAGACACCAGCCTTGCCTCATTGGGTTGTAGCGGAGCAGGTTAAAAATAGCACATCTTG-CT
130 TCGAAGACACCAGCCTTGCCTCA-TGAGTTGTAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCT
* * * *
13522650 TCCTGCACCGACAGCGAAGCAAATCGAAGACACCAGCCTTGCCTCATTGGGTTGAAGCGGAGCAG
194 TCCTGCACTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCTCA-TCGGTTGAAGCGGAGCAG
13522715 GTTA
258 GTTA
* * ** * *
13522719 AAAATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCAAAGACACCAACCTTGTCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCGAAGAC-CCAACCTTGCCTCC
* * * * **
13522784 CTAGGTTGTAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCATGCACCGACAGCGAAGCAGA
65 ATAGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCATGCATAGACAGCGAAGCAGA
* * * * *
13522849 TCGAAGACACCAGCCTTGCCTCCCTGTGTTGCAGCAGAGAAGGTTAAAAATAGCAGATCTTGCCT
130 TCGAAGACACCAGCCTTGCCT-CATGAGTTGTAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCT
* * * * * *
13522914 TCCTACACTGACAGCGAAGCAGATCGAAGACACGAGCCTTGCCTCCCTCGG-TCACAGTGTAGCA
194 TCCTGCACTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT-CATCGGTTGA-AGCGGAGCA
* *
13522978 AGTTG
257 GGTTA
* *
13522983 AAGATAGTAGATCTTGCCTTCCTGCATCA-ACAGTGAAGCAGATCGAAGA
1 AAGATAGCAGATCTTGCCTTCCTGCAT-AGACAGCGAAGCAGATCGAAGA
13523032 TTACAAGTCC
Statistics
Matches: 486, Mismatches: 78, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
261 44 0.09
262 106 0.22
263 236 0.49
264 99 0.20
265 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (261 bp):
AAGATAGCAGATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCGAAGACCCAACCTTGCCTCCA
TAGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCATGCATAGACAGCGAAGCAGAT
CGAAGACACCAGCCTTGCCTCATGAGTTGTAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTC
CTGCACTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCTCATCGGTTGAAGCGGAGCAGGTT
A
Found at i:13523031 original size:45 final size:42
Alignment explanation
Indices: 13522898--13523032 Score: 103
Period size: 44 Copynumber: 3.0 Consensus size: 42
13522888 AAGGTTAAAA
* *
13522898 ATAGCAGATCTTGCCTTCCTACACTGACAGCGAAGCAGATCGAAG
1 ATAG-AGATCTTGCCTTCCT-CA-TCACAGTGAAGCAGATCGAAG
* * * * * *
13522943 ACACGAG-CCTTGCCTCCCTCGGTCACAGTGTAGCA-AGTTGAAG
1 ATA-GAGATCTTGCCTTCCTC-ATCACAGTGAAGCAGA-TCGAAG
13522986 ATAGTAGATCTTGCCTTCCTGCATCAACAGTGAAGCAGATCGAAG
1 ATAG-AGATCTTGCCTTCCT-CATC-ACAGTGAAGCAGATCGAAG
13523031 AT
1 AT
13523033 TACAAGTCCT
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
42 2 0.03
43 20 0.29
44 22 0.32
45 22 0.32
46 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (42 bp):
ATAGAGATCTTGCCTTCCTCATCACAGTGAAGCAGATCGAAG
Found at i:13523469 original size:100 final size:100
Alignment explanation
Indices: 13523314--13523564 Score: 385
Period size: 100 Copynumber: 2.5 Consensus size: 100
13523304 TCCCAAGAGG
* * *
13523314 TGTAGTGGAACATATTAAAGCCACATCGATGAATCTTGCTTCCCCGACATTGCAATTAAAAAGAT
1 TGTAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACATTGCAATTAAAAAGAT
* *
13523379 TAAAGCTACAACAGTGAATCTTACTCCCCAGGCGA
66 TAAAGCTACAACAGCGAATCTTACTCCCCAGGCAA
* * *
13523414 TGTAGTGGAACAGATTAAAGCCATATCGGTGAATCTTCCTTCCCTGATATTGCAATTAAAAAGAT
1 TGTAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACATTGCAATTAAAAAGAT
* *
13523479 TAAAGCTACGACAGCGAATCTTACTCCTCAGGCAA
66 TAAAGCTACAACAGCGAATCTTACTCCCCAGGCAA
* **
13523514 TGCAGTGGAACAGATTAAAGCCACATTTGTGAATCTTGCTTCCCTGACATT
1 TGTAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACATT
13523565 TATAACGGCG
Statistics
Matches: 135, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 135 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (100 bp):
TGTAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACATTGCAATTAAAAAGAT
TAAAGCTACAACAGCGAATCTTACTCCCCAGGCAA
Found at i:13523548 original size:50 final size:49
Alignment explanation
Indices: 13523317--13523550 Score: 148
Period size: 50 Copynumber: 4.7 Consensus size: 49
13523307 CAAGAGGTGT
* * * * *
13523317 AGTGGAACATATTAAAGCCACATC-GATGAATCTTGCTTCCCCGACATTGC
1 AGTGGAACAGATTAAAGCCACATCAG-TGAATCTTAC-TCCCAGGCAATGC
* ** * * * * *
13523367 AATTAAAAAGATTAAAGCTACAACAGTGAATCTTACTCCCCAGGCGATGT
1 AGTGGAACAGATTAAAGCCACATCAGTGAATCTTACT-CCCAGGCAATGC
* * * * ** *
13523417 AGTGGAACAGATTAAAGCCATATCGGTGAATCTTCCTTCCCTGATATTGC
1 AGTGGAACAGATTAAAGCCACATCAGTGAATCTTAC-TCCCAGGCAATGC
* ** * * *
13523467 AATTAAAAAGATTAAAGCTACGA-CAGCGAATCTTACTCCTCAGGCAATGC
1 AGTGGAACAGATTAAAGCCAC-ATCAGTGAATCTTACTCC-CAGGCAATGC
**
13523517 AGTGGAACAGATTAAAGCCACATTTGTGAATCTT
1 AGTGGAACAGATTAAAGCCACATCAGTGAATCTT
13523551 GCTTCCCTGA
Statistics
Matches: 129, Mismatches: 49, Indels: 12
0.68 0.26 0.06
Matches are distributed among these distances:
49 5 0.04
50 121 0.94
51 3 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (49 bp):
AGTGGAACAGATTAAAGCCACATCAGTGAATCTTACTCCCAGGCAATGC
Found at i:13523626 original size:80 final size:80
Alignment explanation
Indices: 13523492--13523644 Score: 234
Period size: 80 Copynumber: 1.9 Consensus size: 80
13523482 AGCTACGACA
* * **
13523492 GCGAATCTTACTCCTCAGGCAATGCAGTGGAACAGATTAAAGCCACATTTGTGAATCTTGCTTCC
1 GCGAATCTTACTCCCCAGGCAATGCAATGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCC
*
13523557 CTGACATTTATAACG
66 CCGACATTTATAACG
** *
13523572 GCGAATCTTACTCCCCAGGCGGTGCAATGGAATAGATTAAAGCCACATCAGTGAATCTTGCTTCC
1 GCGAATCTTACTCCCCAGGCAATGCAATGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCC
13523637 CCGACATT
66 CCGACATT
13523645 GCAATTTAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (80 bp):
GCGAATCTTACTCCCCAGGCAATGCAATGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCC
CCGACATTTATAACG
Found at i:13523731 original size:181 final size:180
Alignment explanation
Indices: 13523394--13523745 Score: 440
Period size: 181 Copynumber: 1.9 Consensus size: 180
13523384 CTACAACAGT
* * * * *
13523394 GAATCTTACTCCCCAGGCGATGTAGTGGAACAGATTAAAGCCATATCGGTGAATCTTCCTTCCCT
1 GAATCTTACTCCCCAGGCGATGCAATGGAACAGATTAAAGCCACATCAGTGAATCTTCCTTCCCC
* * * *
13523459 GATATTGCAATTAAAAAGATTAAAGCTACGACAGCGAATCTTACTCCTCAGGCAATGCAGTGGAA
66 GACATTGCAATTAAAAAAATAAAAGCTACAACAGCGAATCTTACTCCTCAGGCAATGCAGTGGAA
* *** *
13523524 CAGATTAAAGCCACATTTGTGAATCTTGCTTC-CCTGACATTTATAACGGC
131 CAAATTAAAGCCACAACGGCGAATCTTGCTTCTCC-GACATTTATAACGGC
* * *
13523574 GAATCTTACTCCCCAGGCGGTGCAATGGAATAGATTAAAGCCACATCAGTGAATCTTGCTTCCCC
1 GAATCTTACTCCCCAGGCGATGCAATGGAACAGATTAAAGCCACATCAGTGAATCTTCCTTCCCC
* ** * **
13523639 GACATTGCAATTTAAAAAAATAAAAGCTATAATGGCGAATCTTA-T-TTCATTGGCGGTGCAGTG
66 GACATTGCAA-TTAAAAAAATAAAAGCTACAACAGCGAATCTTACTCCTCA--GGCAATGCAGTG
13523702 GAACAAATTAAAGCCACAACGGCGAATCTTGCTTCTCCGACATT
128 GAACAAATTAAAGCCACAACGGCGAATCTTGCTTCTCCGACATT
13523746 GCAGTTAAAA
Statistics
Matches: 145, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
179 3 0.02
180 67 0.46
181 73 0.50
182 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (180 bp):
GAATCTTACTCCCCAGGCGATGCAATGGAACAGATTAAAGCCACATCAGTGAATCTTCCTTCCCC
GACATTGCAATTAAAAAAATAAAAGCTACAACAGCGAATCTTACTCCTCAGGCAATGCAGTGGAA
CAAATTAAAGCCACAACGGCGAATCTTGCTTCTCCGACATTTATAACGGC
Found at i:13523762 original size:50 final size:50
Alignment explanation
Indices: 13523605--13523764 Score: 117
Period size: 50 Copynumber: 3.2 Consensus size: 50
13523595 GCAATGGAAT
* * * * *
13523605 AGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAATTTAAAA
1 AGATTAAAGCCACAACGGCGAATCTTGCTTCTCCGACATTGC-AGTTAAAA
* * * * * ** * * ** * *
13523656 AAATAAAAGCTATAATGGCGAATCTTATTTCAT-TGGCGGTGCAGTGGAACA
1 AGATTAAAGCCACAACGGCGAATCTTGCTTC-TCCGACATTGCAGT-TAAAA
13523707 A-ATTAAAGCCACAACGGCGAATCTTGCTTCTCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGCGAATCTTGCTTCTCCGACATTGCAGTTAAAA
13523756 AGATTAAAG
1 AGATTAAAG
13523765 TTACGAGTTA
Statistics
Matches: 75, Mismatches: 30, Indels: 9
0.66 0.26 0.08
Matches are distributed among these distances:
49 5 0.07
50 40 0.53
51 30 0.40
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (50 bp):
AGATTAAAGCCACAACGGCGAATCTTGCTTCTCCGACATTGCAGTTAAAA
Found at i:13525490 original size:14 final size:15
Alignment explanation
Indices: 13525463--13525491 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13525453 GTTTTCAAAC
13525463 TTTTTTTAGTAAAAT
1 TTTTTTTAGTAAAAT
13525478 TTTTTTTAG-AAAAT
1 TTTTTTTAGTAAAAT
13525492 AATACACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (15 bp):
TTTTTTTAGTAAAAT
Found at i:13530274 original size:21 final size:21
Alignment explanation
Indices: 13530213--13530282 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
13530203 TAAATAGAAT
*
13530213 AAATAAAAT-A-AAAATAAGAA
1 AAATAAAATAATAAAATAA-TA
* **
13530233 AAATAAATTAATAAAGGAATA
1 AAATAAAATAATAAAATAATA
13530254 AAATAAAATAATAAAATAAT-
1 AAATAAAATAATAAAATAATA
13530274 AAATAAAAT
1 AAATAAAAT
13530283 GGGGAAAATG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 17 0.41
21 19 0.46
22 5 0.12
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (21 bp):
AAATAAAATAATAAAATAATA
Found at i:13530770 original size:12 final size:13
Alignment explanation
Indices: 13530745--13530777 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
13530735 TCAGACATGC
13530745 CCGTGTGTCCAGG
1 CCGTGTGTCCAGG
13530758 CCGTGTG-CCAGG
1 CCGTGTGTCCAGG
*
13530770 CCATGTGT
1 CCGTGTGT
13530778 GATCTCCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.30, G:0.36, T:0.24
Consensus pattern (13 bp):
CCGTGTGTCCAGG
Found at i:13536963 original size:41 final size:40
Alignment explanation
Indices: 13536918--13537016 Score: 135
Period size: 41 Copynumber: 2.4 Consensus size: 40
13536908 TTCAGAACAC
* *
13536918 CGGCATTAAGCCTGCTAGACGTAAAGTTTGAAATATTTCA
1 CGGCATTAAGCCTACTAGACGTAAAGTCTGAAATATTTCA
* *
13536958 TCGGCATTAAGCCTACTAGACGTACAGTCTGAATTATTTCA
1 -CGGCATTAAGCCTACTAGACGTAAAGTCTGAAATATTTCA
*
13536999 CTGGCATTAAGTCTACTA
1 C-GGCATTAAGCCTACTA
13537017 AGCACAGAGC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
40 1 0.02
41 51 0.98
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (40 bp):
CGGCATTAAGCCTACTAGACGTAAAGTCTGAAATATTTCA
Found at i:13538654 original size:15 final size:16
Alignment explanation
Indices: 13538623--13538655 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
13538613 ACGAAAATTT
*
13538623 CACATAATCAAATTCA
1 CACATAATCAAACTCA
13538639 CACATAAT-AAACTCA
1 CACATAATCAAACTCA
13538654 CA
1 CA
13538656 AAATAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (16 bp):
CACATAATCAAACTCA
Found at i:13539293 original size:33 final size:32
Alignment explanation
Indices: 13539256--13539324 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
13539246 CTTATTTTGA
*
13539256 AATTCAAATTAATCCTTTTAAAATCCTAATTAG
1 AATTCAAATTAATACTTTTAAAATCCTAA-TAG
* * *
13539289 AATTCAAATTACTACTTTTTAAATTCTAATAG
1 AATTCAAATTAATACTTTTAAAATCCTAATAG
13539321 AATT
1 AATT
13539325 TATCTTTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 7 0.22
33 25 0.78
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (32 bp):
AATTCAAATTAATACTTTTAAAATCCTAATAG
Found at i:13539849 original size:29 final size:29
Alignment explanation
Indices: 13539733--13539842 Score: 125
Period size: 29 Copynumber: 3.8 Consensus size: 29
13539723 TTCACTGATC
*
13539733 TGCCACTGTTTTTCCAGATTTTACAATTT
1 TGCCACTGGTTTTCCAGATTTTACAATTT
* * *
13539762 TGCAACTGGTTTTCAAAATTTTA-AAGTTT
1 TGCCACTGGTTTTCCAGATTTTACAA-TTT
* *
13539791 TGCCACT-ATATTTCCATATTTTACAATTT
1 TGCCACTGGT-TTTCCAGATTTTACAATTT
*
13539820 TACCACTGGTTTTCCAGATTTTA
1 TGCCACTGGTTTTCCAGATTTTA
13539843 TAGTTTTTCT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
28 3 0.05
29 60 0.91
30 3 0.05
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.46
Consensus pattern (29 bp):
TGCCACTGGTTTTCCAGATTTTACAATTT
Found at i:13539857 original size:58 final size:58
Alignment explanation
Indices: 13539733--13539849 Score: 162
Period size: 58 Copynumber: 2.0 Consensus size: 58
13539723 TTCACTGATC
* * *
13539733 TGCCACTGTTTTTCCAGATTTTACAATTTTGCAACTGGTTTTCAAAATTTTAAAGTTT
1 TGCCACTATATTTCCAGATTTTACAATTTTACAACTGGTTTTCAAAATTTTAAAGTTT
* * * * *
13539791 TGCCACTATATTTCCATATTTTACAATTTTACCACTGGTTTTCCAGATTTTATAGTTT
1 TGCCACTATATTTCCAGATTTTACAATTTTACAACTGGTTTTCAAAATTTTAAAGTTT
13539849 T
1 T
13539850 TCTACTATTC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (58 bp):
TGCCACTATATTTCCAGATTTTACAATTTTACAACTGGTTTTCAAAATTTTAAAGTTT
Found at i:13541959 original size:10 final size:9
Alignment explanation
Indices: 13541895--13541964 Score: 51
Period size: 9 Copynumber: 8.0 Consensus size: 9
13541885 CAATACATTC
13541895 AAAATATATA
1 AAAATAT-TA
*
13541905 AAAAT-CTA
1 AAAATATTA
13541913 AAAA-A-TA
1 AAAATATTA
*
13541920 TAAAT-TTA
1 AAAATATTA
*
13541928 TAAAT-TTA
1 AAAATATTA
13541936 TAAAATTATTA
1 -AAAA-TATTA
13541947 AAAATATTA
1 AAAATATTA
13541956 AAAATATTA
1 AAAATATTA
13541965 TTTGTCACTA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
7 5 0.10
8 16 0.31
9 17 0.33
10 10 0.20
11 3 0.06
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAATATTA
Found at i:13542081 original size:26 final size:26
Alignment explanation
Indices: 13542052--13542116 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 26
13542042 TAGACATGCT
13542052 TTTTAGTAAATTTAT-ATATTTTTAAA
1 TTTTA-TAAATTTATAATATTTTTAAA
*
13542078 TTTTCATAAA-TTATAATATTTTTATA
1 TTTT-ATAAATTTATAATATTTTTAAA
13542104 TTATTATTAAATT
1 TT-TTA-TAAATT
13542117 AAAATACAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
25 4 0.12
26 21 0.64
27 7 0.21
28 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTTATAAATTTATAATATTTTTAAA
Found at i:13544759 original size:19 final size:22
Alignment explanation
Indices: 13544719--13544771 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 22
13544709 ATTTCAATGT
13544719 AATTTTTATTAATTATTTTTAA
1 AATTTTTATTAATTATTTTTAA
13544741 AATTTTTA-T-ATTA-TTTTAA
1 AATTTTTATTAATTATTTTTAA
* *
13544760 AATATATATTAA
1 AATTTTTATTAA
13544772 AAAAAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 12 0.44
20 5 0.19
21 2 0.07
22 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AATTTTTATTAATTATTTTTAA
Found at i:13546362 original size:17 final size:19
Alignment explanation
Indices: 13546340--13546374 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
13546330 TATGAAATTA
13546340 AAATAATT-TT-ATATATC
1 AAATAATTATTCATATATC
13546357 AAATAATTATTCATATAT
1 AAATAATTATTCATATAT
13546375 ATATATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATAATTATTCATATATC
Found at i:13551815 original size:9 final size:8
Alignment explanation
Indices: 13551792--13551824 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
13551782 TTAATTAATT
13551792 TTTAAAAA
1 TTTAAAAA
13551800 TTTAAAAA
1 TTTAAAAA
13551808 TTTAAAAA
1 TTTAAAAA
13551816 TATTAAAAA
1 T-TTAAAAA
13551825 GTATAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TTTAAAAA
Found at i:13559289 original size:44 final size:44
Alignment explanation
Indices: 13559231--13559314 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
13559221 AAGATCTATT
* *
13559231 ACTTTAATCCGCTCCACTGCAA-CTTCAGGGAAATAGGATTATCG
1 ACTTCAATCCGCTCCACTGCAACCTT-AGGGAAATAAGATTATCG
* * *
13559275 ACTTCAATCTGCTCCATTGCAACCTTAGGGAGATAAGATT
1 ACTTCAATCCGCTCCACTGCAACCTTAGGGAAATAAGATT
13559315 TGCTTCTTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 31 0.91
45 3 0.09
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (44 bp):
ACTTCAATCCGCTCCACTGCAACCTTAGGGAAATAAGATTATCG
Found at i:13559354 original size:44 final size:44
Alignment explanation
Indices: 13559244--13559401 Score: 126
Period size: 44 Copynumber: 3.6 Consensus size: 44
13559234 TTAATCCGCT
* * * * *
13559244 CCACTGCAACTTCAGGGAAATAGGATTATCG-ACT-TCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATT-T-GTTCTCTCAGTCTGCC
*
13559288 CCATTGCAACCTT-AGGGAGATAAGATTTGCTTCT-TCAGTCTGCC
1 CCACTGCAA-CTTCAGGGAGATAAGATTTG-TTCTCTCAGTCTGCC
** * * * * *
13559332 CCACTGTGACTTCAGGGGGATAAGACTTGTTTTCTCAGTCTTCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTTCTCTCAGTCTGCC
*
13559376 CCACTGCAACTTCAGAGAGATAAGAT
1 CCACTGCAACTTCAGGGAGATAAGAT
13559402 CCTTTTAATC
Statistics
Matches: 90, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
42 1 0.01
43 7 0.08
44 79 0.88
45 3 0.03
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGATTTGTTCTCTCAGTCTGCC
Found at i:13559700 original size:88 final size:88
Alignment explanation
Indices: 13559575--13560101 Score: 429
Period size: 88 Copynumber: 6.0 Consensus size: 88
13559565 AGGAGTTGTA
* **
13559575 ATCTTCGATCTACTTCACTGTC-GATGCAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACT
1 ATCTTCGATCTGCTTCGTTGTCAG-TGCAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACT
13559639 GCAACCGAGGGAGGCAAGGCTGGT
65 GCAACCGAGGGAGGCAAGGCTGGT
* * * *
13559663 ATCTTCGATCTGCTTTGTTGTCAGTGCAGGAAGGCAAGATCTACTATCTTCGACGTACTCCACTG
1 ATCTTCGATCTGCTTCGTTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTG
* *
13559728 CAACTGAGGGAGACAAGGCTGGT
66 CAACCGAGGGAGGCAAGGCTGGT
* * * * * * * **
13559751 ATCTTCGATCTGCTTCGCTGTTAGTGCAGAAAGGCAAGATCTGCTATCTTCGATCTGCTTCGTTG
1 ATCTTCGATCTGCTTCGTTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTG
* * ** * *
13559816 TCGA-TGTAGAAAGGCAAGATCTGCT
66 -CAACCG-AGGGAGGCAAG-GCTGGT
* * * ** ** * * * * * ** * *
13559841 ATCTTCAACCTGCTCCACTG-CA-ACCGAGGGAGGCAAG-GCTGGTATCTTCGATCTGTTTCGCT
1 ATCTTCGATCTGCTTCGTTGTCAGTGC-AGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACT
** * * *
13559903 GTC-AGTGCAGGAAGGCAAGATCTGTT
65 G-CAACCG-AGGGAGGCAAG-GCTGGT
*
13559929 ATCTTCGATCTGCTTCGTTGTC-GATGCAGGAAGGCAAGATCTACTATCTTCAACCTACTCCACT
1 ATCTTCGATCTGCTTCGTTGTCAG-TGCAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACT
* *
13559993 GTAACCGAGGGAGGCAAAGCTGGT
65 GCAACCGAGGGAGGCAAGGCTGGT
* * * * * *
13560017 ACCTTCGATCTGCTTCATTGTCAATGCAGGAAGGCAAGACCTGCTATCTTTAACCTGCTCCAACT
1 ATCTTCGATCTGCTTCGTTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCTACTCC-ACT
13560082 GCAACCGAGGGAGGCAAGGC
65 GCAACCGAGGGAGGCAAGGC
13560102 GTTGTTTTCG
Statistics
Matches: 351, Mismatches: 75, Indels: 25
0.78 0.17 0.06
Matches are distributed among these distances:
87 1 0.00
88 248 0.71
89 62 0.18
90 40 0.11
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (88 bp):
ATCTTCGATCTGCTTCGTTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTG
CAACCGAGGGAGGCAAGGCTGGT
Found at i:13560099 original size:133 final size:133
Alignment explanation
Indices: 13559662--13560066 Score: 614
Period size: 133 Copynumber: 3.0 Consensus size: 133
13559652 GCAAGGCTGG
* * *
13559662 TATCTTCGATCTGCTTTGTTGTC-AGTGCAGGAAGGCAAGATCTACTATCTTCGACGTACTCCAC
1 TATCTTCGATCTGCTTCGTTGTCGA-TGCAGGAAGGCAAGATCTACTATCTTCAACCTACTCCAC
* * * *
13559726 TGCAACTGAGGGAGACAAGGCTGGTATCTTCGATCTGCTTCGCTGTTAGTGCAGAAAGGCAAGAT
65 TGCAACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGAT
13559791 CTGC
130 CTGC
* * * *
13559795 TATCTTCGATCTGCTTCGTTGTCGATGTAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
1 TATCTTCGATCTGCTTCGTTGTCGATGCAGGAAGGCAAGATCTACTATCTTCAACCTACTCCACT
*
13559860 GCAACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGTTTCGCTGTCAGTGCAGGAAGGCAAGATC
66 GCAACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATC
*
13559925 TGT
131 TGC
13559928 TATCTTCGATCTGCTTCGTTGTCGATGCAGGAAGGCAAGATCTACTATCTTCAACCTACTCCACT
1 TATCTTCGATCTGCTTCGTTGTCGATGCAGGAAGGCAAGATCTACTATCTTCAACCTACTCCACT
* * * ** * *
13559993 GTAACCGAGGGAGGCAAAGCTGGTACCTTCGATCTGCTTCATTGTCAATGCAGGAAGGCAAGACC
66 GCAACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATC
13560058 TGC
131 TGC
13560061 TATCTT
1 TATCTT
13560067 TAACCTGCTC
Statistics
Matches: 245, Mismatches: 26, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
133 244 1.00
134 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (133 bp):
TATCTTCGATCTGCTTCGTTGTCGATGCAGGAAGGCAAGATCTACTATCTTCAACCTACTCCACT
GCAACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATC
TGC
Found at i:13560115 original size:221 final size:221
Alignment explanation
Indices: 13559577--13560101 Score: 646
Period size: 221 Copynumber: 2.4 Consensus size: 221
13559567 GAGTTGTAAT
* * *
13559577 CTTCGATCTACTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTGCA
1 CTTCGATCTGCTTCATTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCA
*
13559642 ACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTTGTTGTCAGTGCAGGAAGGCAAGATCTAC
66 ACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTTGCTGTCAGTGCAGGAAGGCAAGATCTAC
* ** * * * * *
13559707 TATCTTCGACGTACTCCACTGCAACTGAGGGAGACAAGGCTGGTATCTTCGATCTGCTTCGCTGT
131 TATCTTCGACGTACTCCACTGCAACTGAGGAAGACAAGGCTACTATCTTCAACCTACTCCACTGT
* ** * *
13559772 TAGTGCAGAAAGGCAAGATCTGCTAT
196 AACCGCAGAAAGGCAAGAGCTGCTAC
* * *
13559798 CTTCGATCTGCTTCGTTGTCGATGTAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCA
1 CTTCGATCTGCTTCATTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCA
*
13559863 ACCGAGGGAGGCAAGGCTGGTATCTTCGATCTG-TTTCGCTGTCAGTGCAGGAAGGCAAGATCTG
66 ACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTT-GCTGTCAGTGCAGGAAGGCAAGATCTA
* * * ** * * *
13559927 TTATCTTCGATC-TGCTTCGTTGTCGA-TGCAGGAAGGCAAGATCTACTATCTTCAACCTACTCC
130 CTATCTTCGA-CGTACTCCACTG-CAACTG-AGGAAGACAAG-GCTACTATCTTCAACCTACTCC
** *
13559990 ACTGTAACCG-AGGGAGGCAA-AGCTGGTAC
191 ACTGTAACCGCAGAAAGGCAAGAGCTGCTAC
* * *
13560019 CTTCGATCTGCTTCATTGTCAATGCAGGAAGGCAAGACCTGCTATCTTTAACCTGCTCCAACTGC
1 CTTCGATCTGCTTCATTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCC-ACTGC
13560084 AACCGAGGGAGGCAAGGC
65 AACCGAGGGAGGCAAGGC
13560102 GTTGTTTTCG
Statistics
Matches: 260, Mismatches: 38, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
220 3 0.01
221 193 0.74
222 43 0.17
223 21 0.08
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (221 bp):
CTTCGATCTGCTTCATTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCA
ACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTTGCTGTCAGTGCAGGAAGGCAAGATCTAC
TATCTTCGACGTACTCCACTGCAACTGAGGAAGACAAGGCTACTATCTTCAACCTACTCCACTGT
AACCGCAGAAAGGCAAGAGCTGCTAC
Found at i:13562317 original size:24 final size:26
Alignment explanation
Indices: 13562280--13562337 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
13562270 TTGACTTTAA
13562280 TTGATTTCTCTTTTTTG-CTTTTGACT
1 TTGATTT-TCTTTTTTGTCTTTTGACT
* *
13562306 TTGA-TTT-TTTTTTGTTTTTTGATT
1 TTGATTTTCTTTTTTGTCTTTTGACT
13562330 TTGATTTT
1 TTGATTTT
13562338 AATTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 7 0.25
24 12 0.43
25 5 0.18
26 4 0.14
ACGTcount: A:0.09, C:0.07, G:0.12, T:0.72
Consensus pattern (26 bp):
TTGATTTTCTTTTTTGTCTTTTGACT
Found at i:13562343 original size:30 final size:30
Alignment explanation
Indices: 13562267--13562355 Score: 115
Period size: 30 Copynumber: 3.0 Consensus size: 30
13562257 TCATATCTTT
** * *
13562267 ATTTTGACTTTAATTGATTTCTCTTTTTTG
1 ATTTTGACTTTAATTTTTTTTTGTTTTTTG
* *
13562297 CTTTTGACTTTGATTTTTTTTTGTTTTTTG
1 ATTTTGACTTTAATTTTTTTTTGTTTTTTG
*
13562327 ATTTTGATTTTAATTTTTTTTTGTTTTTT
1 ATTTTGACTTTAATTTTTTTTTGTTTTTT
13562356 TTATTTTTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.12, C:0.06, G:0.10, T:0.72
Consensus pattern (30 bp):
ATTTTGACTTTAATTTTTTTTTGTTTTTTG
Found at i:13562347 original size:24 final size:24
Alignment explanation
Indices: 13562298--13562349 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
13562288 TCTTTTTTGC
*
13562298 TTTTGACTTTGATTTTTTTTTGTT
1 TTTTGACTTTGATTTTATTTTGTT
* *
13562322 TTTTGATTTTGATTTTAATTT-TT
1 TTTTGACTTTGATTTTATTTTGTT
13562345 TTTTG
1 TTTTG
13562350 TTTTTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.12, C:0.02, G:0.12, T:0.75
Consensus pattern (24 bp):
TTTTGACTTTGATTTTATTTTGTT
Found at i:13562357 original size:20 final size:21
Alignment explanation
Indices: 13562305--13562365 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 21
13562295 TGCTTTTGAC
*
13562305 TTTGA-TTT-TTTT-TTGTTT
1 TTTGATTTTATTTTATTTTTT
13562323 TTTGATTTTGATTTTAATTTTTT
1 TTTGATTTT-ATTTT-ATTTTTT
13562346 TTTG-TTTT-TTTTATTTTTT
1 TTTGATTTTATTTTATTTTTT
13562365 T
1 T
13562366 ATCTGAACCC
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
18 5 0.14
19 11 0.30
20 4 0.11
21 4 0.11
22 4 0.11
23 9 0.24
ACGTcount: A:0.10, C:0.00, G:0.08, T:0.82
Consensus pattern (21 bp):
TTTGATTTTATTTTATTTTTT
Found at i:13569278 original size:23 final size:21
Alignment explanation
Indices: 13569211--13569284 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
13569201 CCTGATCAGT
* * *
13569211 ATATGACACA-TAAGTGCCTA
1 ATATGACACACGAGGTGCCTG
*
13569231 AAATGACACACGAGGTGCCTG
1 ATATGACACACGAGGTGCCTG
*
13569252 ATATGACACACGAGGTTCCTG
1 ATATGACACACGAGGTGCCTG
13569273 AAATATGACACA
1 --ATATGACACA
13569285 TAAAGTGTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.20
21 26 0.58
23 10 0.22
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (21 bp):
ATATGACACACGAGGTGCCTG
Found at i:13569296 original size:23 final size:23
Alignment explanation
Indices: 13569269--13569343 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
13569259 ACACGAGGTT
* *
13569269 CCTGAAATATGACACATAAAGTG
1 CCTGATATACGACACATAAAGTG
*
13569292 TCTGATATACGACACATAAAGTG
1 CCTGATATACGACACATAAAGTG
13569315 CCTGATATACGACACATAAAGTG
1 CCTGATATACGACACATAAAGTG
13569338 CCTGAT
1 CCTGAT
13569344 CAGCACAGCT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (23 bp):
CCTGATATACGACACATAAAGTG
Found at i:13569299 original size:21 final size:22
Alignment explanation
Indices: 13569210--13569343 Score: 112
Period size: 23 Copynumber: 6.0 Consensus size: 22
13569200 ACCTGATCAG
*
13569210 TATATGACACAT-AAGTGCCTAA
1 TATA-GACACATAAAGTGCCTGA
* ** *
13569232 AAT-GACACACGAGGTGCCTGA
1 TATAGACACATAAAGTGCCTGA
** * *
13569253 TAT-GACACACGAGGTTCCTGA
1 TATAGACACATAAAGTGCCTGA
* *
13569274 AATATGACACATAAAGTGTCTGA
1 TATA-GACACATAAAGTGCCTGA
13569297 TATACGACACATAAAGTGCCTGA
1 TATA-GACACATAAAGTGCCTGA
13569320 TATACGACACATAAAGTGCCTGA
1 TATA-GACACATAAAGTGCCTGA
13569343 T
1 T
13569344 CAGCACAGCT
Statistics
Matches: 94, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
20 6 0.06
21 29 0.31
22 2 0.02
23 57 0.61
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.23
Consensus pattern (22 bp):
TATAGACACATAAAGTGCCTGA
Found at i:13569929 original size:16 final size:16
Alignment explanation
Indices: 13569908--13569941 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13569898 AACCCTAGTT
*
13569908 TTTCCCTTTTCATTTC
1 TTTCCCCTTTCATTTC
*
13569924 TTTCCCCTTTCCTTTC
1 TTTCCCCTTTCATTTC
13569940 TT
1 TT
13569942 CTTTTTTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTCCCCTTTCATTTC
Found at i:13570226 original size:19 final size:18
Alignment explanation
Indices: 13570199--13570243 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
13570189 AACAAAAAAG
13570199 TTTGGAAATTGAATAATGA
1 TTTGGAAA-TGAATAATGA
* *
13570218 TTTGTAAATGAATAATGT
1 TTTGGAAATGAATAATGA
13570236 TTTGGAAA
1 TTTGGAAA
13570244 CGAACGACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (18 bp):
TTTGGAAATGAATAATGA
Found at i:13578076 original size:15 final size:16
Alignment explanation
Indices: 13578049--13578079 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
13578039 ATTTTATTTT
13578049 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
13578065 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
13578080 GTTTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:13578138 original size:15 final size:15
Alignment explanation
Indices: 13578120--13578177 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
13578110 AATATATATT
13578120 AATATTTTAATAATA
1 AATATTTTAATAATA
*
13578135 AATATATATTAAAATTATA
1 AATAT-T-TT--AATAATA
*
13578154 AATATATTAATAATA
1 AATATTTTAATAATA
*
13578169 AATGTTTTA
1 AATATTTTA
13578178 TGGTATAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 18 0.53
16 1 0.03
17 4 0.12
19 11 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:13578146 original size:17 final size:17
Alignment explanation
Indices: 13578121--13578171 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
13578111 ATATATATTA
*
13578121 ATATTTTAATAATAAAT
1 ATATATTAATAATAAAT
13578138 ATATATTAA-AATTATAA-
1 ATATATTAATAA-TA-AAT
13578155 ATATATTAATAATAAAT
1 ATATATTAATAATAAAT
13578172 GTTTTATGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
16 4 0.14
17 21 0.72
18 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATATTAATAATAAAT
Found at i:13591565 original size:23 final size:24
Alignment explanation
Indices: 13591546--13591592 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
13591536 TAAATTTTAT
13591546 ATTATTTAGTGATAATA-TTTAGG
1 ATTATTTAGTGATAATATTTTAGG
13591569 ATTATTTAGTGATAATA-TTTAGG
1 ATTATTTAGTGATAATATTTTAGG
13591592 A
1 A
13591593 AAAATCTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (24 bp):
ATTATTTAGTGATAATATTTTAGG
Found at i:13591566 original size:13 final size:13
Alignment explanation
Indices: 13591548--13591590 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
13591538 AATTTTATAT
13591548 TATTTAGTGATAA
1 TATTTAGTGATAA
13591561 TATTTAG-GAT--
1 TATTTAGTGATAA
13591571 TATTTAGTGATAA
1 TATTTAGTGATAA
13591584 TATTTAG
1 TATTTAG
13591591 GAAAAATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 7 0.26
11 3 0.11
12 3 0.11
13 14 0.52
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:13591820 original size:21 final size:21
Alignment explanation
Indices: 13591794--13591835 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
13591784 TTAATTAGTT
13591794 TCCTATGCCCTTCCCCTTTCC
1 TCCTATGCCCTTCCCCTTTCC
13591815 TCCTATGCCCTTCCCCTTTCC
1 TCCTATGCCCTTCCCCTTTCC
13591836 ATCTTCCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.05, C:0.52, G:0.05, T:0.38
Consensus pattern (21 bp):
TCCTATGCCCTTCCCCTTTCC
Found at i:13604248 original size:15 final size:15
Alignment explanation
Indices: 13604216--13604259 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
13604206 TGCATTAGTT
* * *
13604216 TTTTTGATTTAATCG
1 TTTTTGCTTTATTTG
13604231 TTTTTGCTTTATTTG
1 TTTTTGCTTTATTTG
13604246 TTTTT-CTTTATTTG
1 TTTTTGCTTTATTTG
13604260 ATTGGGATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.11, C:0.07, G:0.11, T:0.70
Consensus pattern (15 bp):
TTTTTGCTTTATTTG
Found at i:13606173 original size:23 final size:23
Alignment explanation
Indices: 13606147--13606203 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
13606137 TCATAACTGT
13606147 TGTCTTTTCATTTTTTTTATATA
1 TGTCTTTTCATTTTTTTTATATA
** * *
13606170 TGTCTTTTCGCTTTTTTTATTTT
1 TGTCTTTTCATTTTTTTTATATA
*
13606193 TGTCTGTTCAT
1 TGTCTTTTCAT
13606204 GCATTGAGAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.11, C:0.12, G:0.09, T:0.68
Consensus pattern (23 bp):
TGTCTTTTCATTTTTTTTATATA
Found at i:13606563 original size:3 final size:3
Alignment explanation
Indices: 13606555--13606591 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
13606545 TTCTCAATTT
*
13606555 ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
13606592 ATGCCATAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:13610632 original size:34 final size:34
Alignment explanation
Indices: 13610576--13610643 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
13610566 TACAGCTCGT
* ***
13610576 GTGAGCATACCATTTTGTAGCTCATGA-GAGCATA
1 GTGAGCATACCAATTCACAGCTCAT-ATGAGCATA
13610610 GTGAGCATACCAATTCACAGCTCATATGAGCATA
1 GTGAGCATACCAATTCACAGCTCATATGAGCATA
13610644 CATGTACAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 1 0.03
34 28 0.97
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (34 bp):
GTGAGCATACCAATTCACAGCTCATATGAGCATA
Found at i:13611769 original size:20 final size:20
Alignment explanation
Indices: 13611736--13611773 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13611726 GCCATATGGT
13611736 TTGGCTTGTGTTATGGTAAC
1 TTGGCTTGTGTTATGGTAAC
13611756 TTGG-TTGTGATTATGGTA
1 TTGGCTTGTG-TTATGGTA
13611774 TTTTGAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.16, C:0.05, G:0.32, T:0.47
Consensus pattern (20 bp):
TTGGCTTGTGTTATGGTAAC
Done.