Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, whole genome shotgun sequence
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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 14 of 129
Found at i:2290883 original size:31 final size:28
Alignment explanation
Indices: 2290845--2290904 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 28
2290835 TAAAAATAAT
*
2290845 AATAAATATTATTATTATTATTATTGAAAAA
1 AATAAATATTA-TA-T-TTATGATTGAAAAA
2290876 AATAAATATTATATTTATGATTGAAAAA
1 AATAAATATTATATTTATGATTGAAAAA
2290904 A
1 A
2290905 TTTTAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 14 0.50
29 1 0.04
30 2 0.07
31 11 0.39
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (28 bp):
AATAAATATTATATTTATGATTGAAAAA
Found at i:2290926 original size:28 final size:29
Alignment explanation
Indices: 2290888--2290943 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
2290878 TAAATATTAT
2290888 ATTTATGATTGAAAAAATTTTAATAAAAA
1 ATTTATGATTGAAAAAATTTTAATAAAAA
** *
2290917 ATTTAT-ATTGAATTAATTTTATTAAAA
1 ATTTATGATTGAAAAAATTTTAATAAAA
2290944 TTAATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (29 bp):
ATTTATGATTGAAAAAATTTTAATAAAAA
Found at i:2291150 original size:3 final size:3
Alignment explanation
Indices: 2291142--2291193 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
2291132 AATTGGTAGG
2291142 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2291190 TAA T
1 TAA T
2291194 GCTCAGTCCG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2294930 original size:30 final size:29
Alignment explanation
Indices: 2294857--2294964 Score: 119
Period size: 30 Copynumber: 3.7 Consensus size: 29
2294847 TGTCTCTTCG
*
2294857 ATTTTTAAGAATTTAG-CCTTATAGTATT
1 ATTTTTAAGAATTTAGTCCTTATAATATT
** * *
2294885 ATTTAAAAGAATTTAGTCCTTGTAATACT
1 ATTTTTAAGAATTTAGTCCTTATAATATT
**
2294914 ATTTTTAAGAAATTTAGTCCCAATAATATT
1 ATTTTTAAG-AATTTAGTCCTTATAATATT
2294944 ATTTTTTAAGGAATTTAGTCC
1 A-TTTTTAA-GAATTTAGTCC
2294965 CTATGCATTA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
28 14 0.22
29 16 0.25
30 17 0.26
31 17 0.26
32 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.45
Consensus pattern (29 bp):
ATTTTTAAGAATTTAGTCCTTATAATATT
Found at i:2294950 original size:31 final size:30
Alignment explanation
Indices: 2294907--2294965 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
2294897 TTAGTCCTTG
2294907 TAATACTATTTTTAAGAAATTTAGTCCCAA
1 TAATACTATTTTTAAGAAATTTAGTCCCAA
* *
2294937 TAATATTATTTTTTAAGGAATTTAGTCCC
1 TAATACTA-TTTTTAAGAAATTTAGTCCC
2294966 TATGCATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (30 bp):
TAATACTATTTTTAAGAAATTTAGTCCCAA
Found at i:2295141 original size:12 final size:12
Alignment explanation
Indices: 2295110--2295135 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2295100 AGCACTTAAA
2295110 TTATTCCAAGGT
1 TTATTCCAAGGT
2295122 TTATTCCAAGGT
1 TTATTCCAAGGT
2295134 TT
1 TT
2295136 CATCCAGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (12 bp):
TTATTCCAAGGT
Found at i:2302690 original size:2 final size:2
Alignment explanation
Indices: 2302683--2302708 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2302673 AAATAGAATA
2302683 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2302709 TCTTTCAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2303020 original size:12 final size:12
Alignment explanation
Indices: 2303003--2303079 Score: 52
Period size: 12 Copynumber: 6.4 Consensus size: 12
2302993 ATAAAAAAAG
*
2303003 TTTTTATCTAAT
1 TTTTTATATAAT
2303015 TTTTTATATAA-
1 TTTTTATATAAT
*
2303026 TTTTTAT-TAAA
1 TTTTTATATAAT
* *
2303037 ATTTTA-AAACAT
1 TTTTTATATA-AT
*
2303049 ATTATTTTTATAAT
1 -TT-TTTATATAAT
*
2303063 TTTTTATATTAT
1 TTTTTATATAAT
2303075 TTTTT
1 TTTTT
2303080 GATGATATTT
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
10 3 0.06
11 13 0.26
12 24 0.48
13 3 0.06
14 5 0.10
15 2 0.04
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTTTATATAAT
Found at i:2303090 original size:23 final size:22
Alignment explanation
Indices: 2303047--2303098 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
2303037 ATTTTAAAAC
*
2303047 ATATTA-TTTTTATAATTTTTT
1 ATATTATTTTTTATAATATTTT
*
2303068 ATATTATTTTTTGATGATATTTT
1 ATATTATTTTTT-ATAATATTTT
*
2303091 AAATTATT
1 ATATTATT
2303099 AAATTTATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 6 0.23
22 5 0.19
23 15 0.58
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
ATATTATTTTTTATAATATTTT
Found at i:2303560 original size:29 final size:30
Alignment explanation
Indices: 2303497--2303567 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
2303487 CAATTAACTT
* *
2303497 TAAATTATAATAAAATATTTAATGTATTATT
1 TAAATTATAA-AAAATATTTAATATATTATA
*
2303528 TAAATTTTAAAAAAT-TTTAATATGA-TATA
1 TAAATTATAAAAAATATTTAATAT-ATTATA
2303557 TAAATTATAAA
1 TAAATTATAAA
2303568 TATATTGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 20 0.57
30 6 0.17
31 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (30 bp):
TAAATTATAAAAAATATTTAATATATTATA
Found at i:2303735 original size:19 final size:19
Alignment explanation
Indices: 2303667--2303736 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
2303657 ATTAATAAAT
* *
2303667 TTATAATTTAATTATTATA
1 TTATAATTTAAATATTTTA
* *
2303686 TTAAAATTTTAAAT-TTTAA
1 TTATAA-TTTAAATATTTTA
* *
2303705 ATATTAAATTAAATATTTTA
1 TTA-TAATTTAAATATTTTA
2303725 TTATAATTTAAA
1 TTATAATTTAAA
2303737 AAATGTTAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 24 0.63
20 14 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATAATTTAAATATTTTA
Found at i:2305579 original size:25 final size:25
Alignment explanation
Indices: 2305551--2305601 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
2305541 AATATTAAAA
*
2305551 TTTTTA-ATTAT-TTTATAATCATAT
1 TTTTTATATTATATTTAT-ATAATAT
2305575 TTTTTATATTATATTTATATAATAT
1 TTTTTATATTATATTTATATAATAT
2305600 TT
1 TT
2305602 GTTGCGCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 6 0.25
25 13 0.54
26 5 0.21
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTTTATATTATATTTATATAATAT
Found at i:2306319 original size:16 final size:16
Alignment explanation
Indices: 2306295--2306328 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2306285 TATTTATTTG
* *
2306295 TATATAATAAATAATT
1 TATAAAATAAAAAATT
2306311 TATAAAATAAAAAATT
1 TATAAAATAAAAAATT
2306327 TA
1 TA
2306329 GTTTTATAAA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TATAAAATAAAAAATT
Found at i:2307131 original size:19 final size:19
Alignment explanation
Indices: 2307107--2307144 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2307097 CATATATTTA
* *
2307107 AATAATTTTAAATTTAAAT
1 AATAATATTAAACTTAAAT
2307126 AATAATATTAAACTTAAAT
1 AATAATATTAAACTTAAAT
2307145 GAATTCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAATATTAAACTTAAAT
Found at i:2308076 original size:31 final size:29
Alignment explanation
Indices: 2308011--2308101 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 29
2308001 ACCGTGTATC
* *
2308011 ATATAAAATATTATAT-TTATTAAATATTTT
1 ATATAAAA-ATTATATATTA-TAATTTTTTT
2308041 ATATAAAAATTATATATTATAATTTTTATT
1 ATATAAAAATTATATATTATAATTTTT-TT
* *
2308071 GATATAAAAA-TATAAAATATAATTTTTTT
1 -ATATAAAAATTATATATTATAATTTTTTT
2308100 AT
1 AT
2308102 TTTATTAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.04
29 15 0.28
30 28 0.52
31 9 0.17
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
ATATAAAAATTATATATTATAATTTTTTT
Found at i:2312904 original size:21 final size:20
Alignment explanation
Indices: 2312874--2312923 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2312864 GATATTTTTA
*
2312874 AATA-TTTATATTTCAAAAAT
1 AATATTTTATA-TTAAAAAAT
2312894 AATATTTTATATTAAAAAAT
1 AATATTTTATATTAAAAAAT
2312914 AATATTTTAT
1 AATATTTTAT
2312924 TAATTTCGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AATATTTTATATTAAAAAAT
Found at i:2315660 original size:21 final size:20
Alignment explanation
Indices: 2315607--2315669 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
2315597 CGATTGATTC
*
2315607 ATTTT-TAAT-TTTTTAA-A
1 ATTTTATAATATTTTAAATA
*
2315624 ATTTTATATTATTTTAATATA
1 ATTTTATAATATTTTAA-ATA
2315645 ATTTT-TAATATATTTAAATA
1 ATTTTATAATAT-TTTAAATA
2315665 GATTT
1 -ATTT
2315670 ACATAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 5 0.14
18 3 0.08
19 5 0.14
20 9 0.24
21 15 0.41
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTTATAATATTTTAAATA
Found at i:2317054 original size:37 final size:37
Alignment explanation
Indices: 2317013--2317085 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
2317003 GCATATAGAG
*
2317013 TTGTAGCTATGTCGGACCTTAGATATTTCAGAGAAAA
1 TTGTAACTATGTCGGACCTTAGATATTTCAGAGAAAA
2317050 TTGTAACTATGTCGGACCTTAGATATTTCAGAGAAA
1 TTGTAACTATGTCGGACCTTAGATATTTCAGAGAAA
2317086 TTATAGTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (37 bp):
TTGTAACTATGTCGGACCTTAGATATTTCAGAGAAAA
Found at i:2329490 original size:15 final size:16
Alignment explanation
Indices: 2329459--2329490 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2329449 CGTTTCTATC
2329459 TTTTTTTTTCCCTTTT
1 TTTTTTTTTCCCTTTT
*
2329475 TTTTTTTTTCGCTTTT
1 TTTTTTTTTCCCTTTT
2329491 GGGGTCTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTTTTTCCCTTTT
Found at i:2332585 original size:2 final size:2
Alignment explanation
Indices: 2332578--2332610 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2332568 TTTGACCAAC
2332578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2332611 CACACACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2336712 original size:20 final size:18
Alignment explanation
Indices: 2336668--2336723 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
2336658 TTAATATAAT
2336668 ATTTAAA-TT-TTAAAAA
1 ATTTAAATTTATTAAAAA
* *
2336684 ATTTTAATTTGATTCAAAA
1 ATTTAAATTT-ATTAAAAA
2336703 ATTATAAATTTATTAAAAA
1 ATT-TAAATTTATTAAAAA
2336722 AT
1 AT
2336724 ATATTATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
19 18 0.56
20 6 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTTAAATTTATTAAAAA
Found at i:2337609 original size:21 final size:21
Alignment explanation
Indices: 2337585--2337626 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2337575 GAAATTATTT
2337585 ATTAAAA-TAATTAAATAAAAA
1 ATTAAAATTAA-TAAATAAAAA
*
2337606 ATTAAAATTAATAAATTAAAA
1 ATTAAAATTAATAAATAAAAA
2337627 TGCCACATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
ATTAAAATTAATAAATAAAAA
Found at i:2337829 original size:12 final size:12
Alignment explanation
Indices: 2337812--2337840 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2337802 ATTTATTAAT
2337812 TTAAATTTTTTA
1 TTAAATTTTTTA
2337824 TTAAA-TTTTTA
1 TTAAATTTTTTA
2337835 TTAAAT
1 TTAAAT
2337841 CAATTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTAAATTTTTTA
Found at i:2338977 original size:26 final size:24
Alignment explanation
Indices: 2338941--2338988 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 24
2338931 ATTTAAAATT
2338941 TTAACAATTTG-ACTTTTTTTAATG
1 TTAACAATTTGTA-TTTTTTTAATG
2338965 TTAACATATTTTGTATTTTTTTAA
1 TTAACA-A-TTTGTATTTTTTTAA
2338989 AACTTTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 6 0.29
25 1 0.05
26 13 0.62
27 1 0.05
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (24 bp):
TTAACAATTTGTATTTTTTTAATG
Found at i:2341251 original size:20 final size:21
Alignment explanation
Indices: 2341226--2341267 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2341216 TAGATAGTTA
* *
2341226 AAATT-AAATTTTAATCATTT
1 AAATTAAAATTTCAATAATTT
2341246 AAATTAAAATTTCAATAATTT
1 AAATTAAAATTTCAATAATTT
2341267 A
1 A
2341268 TTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATTAAAATTTCAATAATTT
Found at i:2342704 original size:7 final size:7
Alignment explanation
Indices: 2342692--2342722 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2342682 AAAAATCACG
2342692 GGCCGGT
1 GGCCGGT
2342699 GGCCGGT
1 GGCCGGT
2342706 GGCCGGT
1 GGCCGGT
2342713 GGCCGGT
1 GGCCGGT
2342720 GGC
1 GGC
2342723 TGGCGGGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.29, G:0.58, T:0.13
Consensus pattern (7 bp):
GGCCGGT
Found at i:2343244 original size:20 final size:19
Alignment explanation
Indices: 2343209--2343251 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
2343199 ATTTTATATA
* *
2343209 TATTTAATAAATAAATTTT
1 TATTAAATAAATAAATTAT
2343228 TATTAAATAATATAAATTAT
1 TATTAAATAA-ATAAATTAT
2343248 TATT
1 TATT
2343252 TTAGATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTAAATAAATAAATTAT
Found at i:2343305 original size:20 final size:19
Alignment explanation
Indices: 2343280--2343340 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 19
2343270 AAAAAAATTT
2343280 TATTTAAGAAAATATTAATA
1 TATTTAAGAAAATATTAA-A
*
2343300 TATTTATAAAAAATTATCTAAA
1 TATTTA-AGAAAA-TAT-TAAA
* *
2343322 TATATAAGAAAAAATTAAA
1 TATTTAAGAAAATATTAAA
2343341 ATAAATTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
19 4 0.12
20 8 0.24
21 10 0.29
22 9 0.26
23 3 0.09
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (19 bp):
TATTTAAGAAAATATTAAA
Found at i:2344557 original size:7 final size:7
Alignment explanation
Indices: 2344547--2344575 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2344537 ATGAATAATT
2344547 TATAAAA
1 TATAAAA
2344554 TATAAAA
1 TATAAAA
2344561 TATAAAA
1 TATAAAA
2344568 TATAAAA
1 TATAAAA
2344575 T
1 T
2344576 TATCATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TATAAAA
Found at i:2356295 original size:22 final size:23
Alignment explanation
Indices: 2356250--2356296 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
2356240 TTTATTGTAA
*
2356250 AAATAAATATTTATTCATTAATT
1 AAATAAATATTTATTAATTAATT
* *
2356273 AAAT-AATATTTTTTAATTTATT
1 AAATAAATATTTATTAATTAATT
2356295 AA
1 AA
2356297 TATTAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATAAATATTTATTAATTAATT
Found at i:2367195 original size:100 final size:102
Alignment explanation
Indices: 2367020--2367206 Score: 283
Period size: 100 Copynumber: 1.9 Consensus size: 102
2367010 CTGGAAATAA
* *
2367020 AAACATTGACCATATGACAACATATCAGGACATTCATGTTACTGCTACCCAGATGTATTGGCTGA
1 AAACATTGACCATATGACAACATATCAGGACATTCATGTCACTGCTACCAAGATGTATTGGCTGA
2367085 TAACCACCTCATATTTACTAAAGACTGAATTGGTTAT
66 TAACCACCTCATATTTACTAAAGACTGAATTGGTTAT
* *
2367122 AAACATTGATCATATGAC-A-ATATCAGGACATTCGTGTCACCT-CTACCAAGATGTATCT-GCT
1 AAACATTGACCATATGACAACATATCAGGACATTCATGTCA-CTGCTACCAAGATGTAT-TGGCT
*
2367183 GATAGCCACCTCATATTTACTAAA
64 GATAACCACCTCATATTTACTAAA
2367207 TAATGTATCA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
100 57 0.73
101 4 0.05
102 17 0.22
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (102 bp):
AAACATTGACCATATGACAACATATCAGGACATTCATGTCACTGCTACCAAGATGTATTGGCTGA
TAACCACCTCATATTTACTAAAGACTGAATTGGTTAT
Found at i:2370895 original size:11 final size:11
Alignment explanation
Indices: 2370879--2370922 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
2370869 ATACAATAAT
2370879 ATAATATAAAA
1 ATAATATAAAA
2370890 ATAATATAAATA
1 ATAATATAAA-A
*
2370902 AAAATTATAAAA
1 ATAA-TATAAAA
2370914 ATAATATAA
1 ATAATATAA
2370923 TTTAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 15 0.52
12 8 0.28
13 6 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:2370904 original size:15 final size:15
Alignment explanation
Indices: 2370873--2370917 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
2370863 AATATGATAC
2370873 AATAATATAATATAAA
1 AATAATATAA-ATAAA
2370889 AATAATATAAATAAA
1 AATAATATAAATAAA
* *
2370904 AATTATAAAAATAA
1 AATAATATAAATAA
2370918 TATAATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 17 0.63
16 10 0.37
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAATATAAATAAA
Found at i:2370914 original size:24 final size:24
Alignment explanation
Indices: 2370883--2370931 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
2370873 AATAATATAA
2370883 TATAAAAATAATATAAATAAAAAT
1 TATAAAAATAATATAAATAAAAAT
* *
2370907 TATAAAAATAATATAATTTAAAAT
1 TATAAAAATAATATAAATAAAAAT
2370931 T
1 T
2370932 TTAATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
TATAAAAATAATATAAATAAAAAT
Found at i:2370952 original size:24 final size:24
Alignment explanation
Indices: 2370925--2370981 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 24
2370915 TAATATAATT
*
2370925 TAAAATTTTAATTAAAATT-ATATA
1 TAAAATTTTAA-TAAAATTAAAATA
2370949 T-AAA-TTTAATAAAATTAAAATA
1 TAAAATTTTAATAAAATTAAAATA
2370971 TATAAATTTTA
1 TA-AAATTTTA
2370982 TATTTTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 7 0.25
22 10 0.36
23 3 0.11
24 4 0.14
25 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAAATTTTAATAAAATTAAAATA
Found at i:2370958 original size:22 final size:22
Alignment explanation
Indices: 2370931--2370979 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 22
2370921 AATTTAAAAT
2370931 TTTAATTAAAATT-ATATATAAA
1 TTTAA-TAAAATTAATATATAAA
2370953 TTTAATAAAATTAAAATATATAAA
1 TTTAATAAAATT--AATATATAAA
2370977 TTT
1 TTT
2370980 TATATTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.29
22 5 0.21
24 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAATAAAATTAATATATAAA
Found at i:2371975 original size:18 final size:17
Alignment explanation
Indices: 2371952--2371985 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2371942 TTTCATATAT
*
2371952 TTTTATTTTATATTTAAA
1 TTTTATTATAT-TTTAAA
2371970 TTTTATTATATTTTAA
1 TTTTATTATATTTTAA
2371986 TTAATTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATTATATTTTAAA
Found at i:2372114 original size:18 final size:16
Alignment explanation
Indices: 2372052--2372116 Score: 53
Period size: 18 Copynumber: 3.8 Consensus size: 16
2372042 TCATTAACTT
2372052 TTAATCAATTAAAATTAA
1 TTAATCAATT-AAA-TAA
2372070 TTTAAT-AATT-AATAAA
1 -TTAATCAATTAAAT-AA
2372086 TTAATCAAATTAAATAA
1 TTAATC-AATTAAATAA
2372103 CTTCAATCAATTAA
1 -TT-AATCAATTAA
2372117 TTAAATTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
15 6 0.15
16 4 0.10
17 6 0.15
18 15 0.38
19 9 0.22
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAATCAATTAAATAA
Found at i:2377509 original size:24 final size:24
Alignment explanation
Indices: 2377478--2377524 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2377468 GGAAGAAGCC
2377478 GACGATGACGATGAAGCG-GAGGAT
1 GACGATGACGATGAA-CGAGAGGAT
*
2377502 GACGATGAGGATGAACGAGAGGA
1 GACGATGACGATGAACGAGAGGA
2377525 AGAGGTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.36, C:0.11, G:0.43, T:0.11
Consensus pattern (24 bp):
GACGATGACGATGAACGAGAGGAT
Found at i:2378108 original size:6 final size:6
Alignment explanation
Indices: 2378086--2378123 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
2378076 ATAATTTATG
*
2378086 TATTTA TATCT- TATTTA TATTTA TATTTA TATTTA TAT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TAT
2378124 GAATATGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (6 bp):
TATTTA
Found at i:2378129 original size:18 final size:18
Alignment explanation
Indices: 2378097--2378144 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
2378087 ATTTATATCT
* **
2378097 TATTTATATTTATATTTA
1 TATTTATATTAATATGAA
*
2378115 TATTTATATGAATATGAA
1 TATTTATATTAATATGAA
2378133 TATTATATATTA
1 TATT-TATATTA
2378145 TAATTGATGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
TATTTATATTAATATGAA
Found at i:2379520 original size:11 final size:11
Alignment explanation
Indices: 2379500--2379550 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
2379490 ATTAATAATT
2379500 TATC-TATTTA
1 TATCATATTTA
2379510 TATCATATTTA
1 TATCATATTTA
*
2379521 TATAAATATTATA
1 TAT-CATATT-TA
*
2379534 TATTATAATTTA
1 TATCAT-ATTTA
2379546 TATCA
1 TATCA
2379551 ATATGTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 4 0.12
11 9 0.26
12 13 0.38
13 8 0.24
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (11 bp):
TATCATATTTA
Found at i:2379536 original size:19 final size:19
Alignment explanation
Indices: 2379479--2379537 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
2379469 CACGTATTTA
2379479 TTATATAAAATATTA-ATAAT
1 TTATAT-AAATATTATAT-AT
* **
2379499 TTATCTATTTA-TATCATAT
1 TTATATAAATATTAT-ATAT
2379518 TTATATAAATATTATATAT
1 TTATATAAATATTATATAT
2379537 T
1 T
2379538 ATAATTTATA
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
18 2 0.07
19 18 0.60
20 10 0.33
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATATAAATATTATATAT
Found at i:2379546 original size:25 final size:23
Alignment explanation
Indices: 2379504--2379554 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
2379494 ATAATTTATC
2379504 TATTTATATCATATTTATATAAA
1 TATTTATATCATATTTATATAAA
* *
2379527 TATTATATATTATAATTTATATCAA
1 TATT-TATATCAT-ATTTATATAAA
2379552 TAT
1 TAT
2379555 GTAAAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 7 0.29
25 13 0.54
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTTATATCATATTTATATAAA
Found at i:2385085 original size:19 final size:19
Alignment explanation
Indices: 2385028--2385086 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
2385018 TCTATTTATG
2385028 TTATATAAAATATTAGTA-AT
1 TTATAT-AAATATTA-TATAT
* **
2385048 TTATGTATTTA-TATCATAT
1 TTATATAAATATTAT-ATAT
2385067 TTATATAAATATTATATAT
1 TTATATAAATATTATATAT
2385086 T
1 T
2385087 ATAATTTATG
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
17 1 0.03
18 3 0.10
19 18 0.60
20 8 0.27
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (19 bp):
TTATATAAATATTATATAT
Found at i:2385103 original size:25 final size:24
Alignment explanation
Indices: 2385021--2385099 Score: 60
Period size: 25 Copynumber: 3.4 Consensus size: 24
2385011 CAATTCATCT
* *
2385021 ATTTATGTTATATAAAATATTAGTA
1 ATTTATGTTATATTATATATTA-TA
*
2385046 ATTTATG---TATT-TATATCAT-
1 ATTTATGTTATATTATATATTATA
* *
2385065 ATTTATATAAATATTATATATTATA
1 ATTTATGT-TATATTATATATTATA
2385090 ATTTATGTTA
1 ATTTATGTTA
2385100 ATATGTAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 13
0.67 0.11 0.21
Matches are distributed among these distances:
19 6 0.15
20 1 0.02
21 5 0.12
22 3 0.07
23 4 0.10
24 8 0.20
25 14 0.34
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (24 bp):
ATTTATGTTATATTATATATTATA
Found at i:2385628 original size:164 final size:164
Alignment explanation
Indices: 2385357--2385970 Score: 1023
Period size: 164 Copynumber: 3.7 Consensus size: 164
2385347 AAAATTTCTC
* * * *
2385357 TGCATGGTGAGGCCAAAAAGTTTGCATTTTTTGGCACCAAAAGCTTGGCCACAGATGGGTTCCAT
1 TGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCACAGATGGGTTCCAT
* ** * * * *
2385422 CCCCATGGCTTGGCCAGAGAGAACAGAGTATTCAGTGATGTTAACAACCATAAAGAAGCTATAAC
66 TCCCATGGCGAGGCCAGAGCGAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGCTATAAC
2385487 GATTGAAGTGAATAGAAGCAGAAGTATCATACTT
131 GATTGAAGTGAATAGAAGCAGAAGTATCATACTT
* *
2385521 TGCATGGTGATGCCAAGAAGTTTGCCT-TTCTCAGCACCAAAAGCTTGGCCACAGATGGGTTCCA
1 TGCATGGTGAGGCCAAGAAGTTTGCCTCTT-TCGGCACCAAAAGCTTGGCCACAGATGGGTTCCA
* *
2385585 TTCCCATGGCAAGGCCAGAGCGAACTGAGTAGCCAGTGATGTTAGCAACCATAAAGAAGCTATAA
65 TTCCCATGGCGAGGCCAGAGCGAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGCTATAA
*
2385650 CGATTGAAGTGAATAGAAGCAGAAGTATCATACTC
130 CGATTGAAGTGAATAGAAGCAGAAGTATCATACTT
2385685 TGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCACAGATGGGTTCCAT
1 TGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCACAGATGGGTTCCAT
*
2385750 TCCCATGGTGAGGCCAGAGCGAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGCTATAAC
66 TCCCATGGCGAGGCCAGAGCGAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGCTATAAC
*
2385815 GATTGAAGTGAATAGAAGTAGAAGTATCATACTT
131 GATTGAAGTGAATAGAAGCAGAAGTATCATACTT
*
2385849 TGCATGGTGTGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCACAGATGGGTTCCAT
1 TGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCACAGATGGGTTCCAT
* *
2385914 TCCCATGGCGAGGCCAGTGCGAACTGACTATCCAGTGATGTTAGCAACCATAAAGAA
66 TCCCATGGCGAGGCCAGAGCGAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAA
2385971 CTGAGTATCC
Statistics
Matches: 423, Mismatches: 25, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
163 2 0.00
164 419 0.99
165 2 0.00
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (164 bp):
TGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCACAGATGGGTTCCAT
TCCCATGGCGAGGCCAGAGCGAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGCTATAAC
GATTGAAGTGAATAGAAGCAGAAGTATCATACTT
Found at i:2385951 original size:328 final size:340
Alignment explanation
Indices: 2385354--2386308 Score: 1285
Period size: 328 Copynumber: 2.8 Consensus size: 340
2385344 AAAAAAATTT
* * * *
2385354 CTCTGCATGGTGAGGCCAAAAAGTTTGCATTTTTTGGCACCAAAAGCTTGGCCACAGATGGGTTC
1 CTCTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCACAGATGGGTTC
* * * * * *
2385419 CATCCCCATGGCT-TGGCCAGAGAGAACAGAGTATTCAGTGATGTTAACAACCATAAAGAAGCTA
66 CATTCCCATGG-TGAGGCCAGAGCGAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGCTA
2385483 TAACGATTGAAGTGAATAGAAGCAGAAGTATCATACTTTGCATGGTGAT-GCCAAGAAGTTTGCC
130 TAACGATTGAAGTGAATAGAAGCAGAAGTATCATACTTTGCATGGTG-TGGCCAAGAAGTTTGCC
*
2385547 T-TTCTCAGCACCAAAAGCTTGGCCACAGATGGGTTCCATTCCCATGGCAAGGCCAGAGCGAACT
194 TCTT-TCGGCACCAAAAGCTTGGCCACAGATGGGTTCCATTCCCATGGCAAGGCCAGAGCGAACT
* * *
2385611 GAGTAGCCAGTGATGTTAGCAACCATAAAGAAGCT-A-TAACGATTGAAG-T-G-A-AT-AGAAG
258 GAGTATCCAGTGATGTTAGCAACCATAAAGAA-CTGAGTAACCAGTGAAGTTAGAACATAAGAAG
*
2385669 -C-A-GAAGT-AT-CA-TA
322 ACGATGAAGTAATACAGAA
2385682 CTCTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCACAGATGGGTTC
1 CTCTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCACAGATGGGTTC
2385747 CATTCCCATGGTGAGGCCAGAGCGAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGCTAT
66 CATTCCCATGGTGAGGCCAGAGCGAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGCTAT
*
2385812 AACGATTGAAGTGAATAGAAGTAGAAGTATCATACTTTGCATGGTGTGGCCAAGAAGTTTGCCTC
131 AACGATTGAAGTGAATAGAAGCAGAAGTATCATACTTTGCATGGTGTGGCCAAGAAGTTTGCCTC
* * *
2385877 TTTCGGCACCAAAAGCTTGGCCACAGATGGGTTCCATTCCCATGGCGAGGCCAGTGCGAACTGAC
196 TTTCGGCACCAAAAGCTTGGCCACAGATGGGTTCCATTCCCATGGCAAGGCCAGAGCGAACTGAG
* *
2385942 TATCCAGTGATGTTAGCAACCATAAAGAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGC
261 TATCCAGTGATGTTAGCAACCATAAAGAACTGAGTAACCAGTGAAGTTAG-AA-CAT-AAGAAG-
2386007 TATAACGATTGAAGTGAATAGAAGCAGAAGTTA
322 ----ACGA-TGAAGT-AAT---A-CAG-A---A
*
2386040 TCATACTTTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGTCACAGATG
1 -C-T-C--TGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCACAGATG
** * *
2386105 GGTTCCATTCCCATGACGAGGCCAGGGCGAACTGAGTAGCCAGTGATGTTAGCAACCATAAAGAA
61 GGTTCCATTCCCATGGTGAGGCCAGAGCGAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAA
*
2386170 GCTATAACGATTGAAGTGAATAGAAGCAGAAGTATCATACTTTGCATGGTGAGGCCAAGAAGTTT
126 GCTATAACGATTGAAGTGAATAGAAGCAGAAGTATCATACTTTGCATGGTGTGGCCAAGAAGTTT
* * *
2386235 GCCTCTTTCGGCTCCAAATGCTTGGCCACAGATGGGTTCCATTCCCATGGCTAGGCCAGAGCGAA
191 GCCTCTTTCGGCACCAAAAGCTTGGCCACAGATGGGTTCCATTCCCATGGCAAGGCCAGAGCGAA
2386300 CTGAGTATC
256 CTGAGTATC
2386309 AATATTAGAA
Statistics
Matches: 555, Mismatches: 33, Indels: 43
0.88 0.05 0.07
Matches are distributed among these distances:
327 4 0.01
328 267 0.48
329 10 0.02
330 1 0.00
331 1 0.00
333 1 0.00
335 2 0.00
337 5 0.01
343 1 0.00
344 1 0.00
346 5 0.01
348 2 0.00
353 2 0.00
358 1 0.00
359 1 0.00
360 1 0.00
361 1 0.00
363 249 0.45
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.24
Consensus pattern (340 bp):
CTCTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCACAGATGGGTTC
CATTCCCATGGTGAGGCCAGAGCGAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGCTAT
AACGATTGAAGTGAATAGAAGCAGAAGTATCATACTTTGCATGGTGTGGCCAAGAAGTTTGCCTC
TTTCGGCACCAAAAGCTTGGCCACAGATGGGTTCCATTCCCATGGCAAGGCCAGAGCGAACTGAG
TATCCAGTGATGTTAGCAACCATAAAGAACTGAGTAACCAGTGAAGTTAGAACATAAGAAGACGA
TGAAGTAATACAGAA
Found at i:2385980 original size:34 final size:34
Alignment explanation
Indices: 2385934--2386004 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
2385924 AGGCCAGTGC
2385934 GAACTGACTATCCAGTGATGTTAGCAACCATAAA
1 GAACTGACTATCCAGTGATGTTAGCAACCATAAA
*
2385968 GAACTGAGTATCCAGTGATGTTAGCAACCATAAA
1 GAACTGACTATCCAGTGATGTTAGCAACCATAAA
2386002 GAA
1 GAA
2386005 GCTATAACGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (34 bp):
GAACTGACTATCCAGTGATGTTAGCAACCATAAA
Found at i:2386109 original size:199 final size:198
Alignment explanation
Indices: 2385770--2386169 Score: 728
Period size: 199 Copynumber: 2.0 Consensus size: 198
2385760 AGGCCAGAGC
*
2385770 GAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGCTATAACGATTGAAGTGAATAGAAGTA
1 GAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGCTATAACGATTGAAGTGAATAGAAGCA
*
2385835 GAAGTATCATACTTTGCATGGTGTGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCA
66 GAAGTATCATACTTTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCA
* * *
2385900 CAGATGGGTTCCATTCCCATGGCGAGGCCAGTGCGAACTGACTATCCAGTGATGTTAGCAACCAT
131 CAGATGGGTTCCATTCCCATGACGAGGCCAGGGCGAACTGACTAGCCAGTGATGTTAGCAACCAT
2385965 AAA
196 AAA
2385968 GAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGCTATAACGATTGAAGTGAATAGAAGCA
1 GAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGCTATAACGATTGAAGTGAATAGAAGCA
*
2386033 GAAGTTATCATACTTTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGTC
66 GAAG-TATCATACTTTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCC
*
2386098 ACAGATGGGTTCCATTCCCATGACGAGGCCAGGGCGAACTGAGTAGCCAGTGATGTTAGCAACCA
130 ACAGATGGGTTCCATTCCCATGACGAGGCCAGGGCGAACTGACTAGCCAGTGATGTTAGCAACCA
2386163 TAAA
195 TAAA
2386167 GAA
1 GAA
2386170 GCTATAACGA
Statistics
Matches: 194, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
198 68 0.35
199 126 0.65
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (198 bp):
GAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGCTATAACGATTGAAGTGAATAGAAGCA
GAAGTATCATACTTTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCA
CAGATGGGTTCCATTCCCATGACGAGGCCAGGGCGAACTGACTAGCCAGTGATGTTAGCAACCAT
AAA
Found at i:2386270 original size:363 final size:362
Alignment explanation
Indices: 2385606--2386308 Score: 1271
Period size: 363 Copynumber: 1.9 Consensus size: 362
2385596 AGGCCAGAGC
2385606 GAACTGAGTAGCCAGTGATGTTAGCAACCATAAAGAAGCTATAACGATTGAAGTGAATAGAAGCA
1 GAACTGAGTAGCCAGTGATGTTAGCAACCATAAAGAAGCTATAACGATTGAAGTGAATAGAAGCA
2385671 GAAGTATCATACTCTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCA
66 GAAGTATCATACTCTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCA
** *
2385736 CAGATGGGTTCCATTCCCATGGTGAGGCCAGAGCGAACTGAGTATCCAGTGATGTTAGCAACCAT
131 CAGATGGGTTCCATTCCCATGACGAGGCCAGAGCGAACTGAGTAGCCAGTGATGTTAGCAACCAT
* *
2385801 AAAGAAGCTATAACGATTGAAGTGAATAGAAGTAGAAGTATCATACTTTGCATGGTGTGGCCAAG
196 AAAGAAGCTATAACGATTGAAGTGAATAGAAGCAGAAGTATCATACTTTGCATGGTGAGGCCAAG
2385866 AAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCACAGATGGGTTCCATTCCCATGGCGAGGCCAG
261 AAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCACAGATGGGTTCCATTCCCATGGCGAGGCCAG
*
2385931 TGCGAACTGACTATCCAGTGATGTTAGCAACCATAAA
326 AGCGAACTGACTATCCAGTGATGTTAGCAACCATAAA
*
2385968 GAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGCTATAACGATTGAAGTGAATAGAAGCA
1 GAACTGAGTAGCCAGTGATGTTAGCAACCATAAAGAAGCTATAACGATTGAAGTGAATAGAAGCA
* *
2386033 GAAGTTATCATACTTTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGTC
66 GAAG-TATCATACTCTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCC
*
2386098 ACAGATGGGTTCCATTCCCATGACGAGGCCAGGGCGAACTGAGTAGCCAGTGATGTTAGCAACCA
130 ACAGATGGGTTCCATTCCCATGACGAGGCCAGAGCGAACTGAGTAGCCAGTGATGTTAGCAACCA
2386163 TAAAGAAGCTATAACGATTGAAGTGAATAGAAGCAGAAGTATCATACTTTGCATGGTGAGGCCAA
195 TAAAGAAGCTATAACGATTGAAGTGAATAGAAGCAGAAGTATCATACTTTGCATGGTGAGGCCAA
* * *
2386228 GAAGTTTGCCTCTTTCGGCTCCAAATGCTTGGCCACAGATGGGTTCCATTCCCATGGCTAGGCCA
260 GAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCACAGATGGGTTCCATTCCCATGGCGAGGCCA
*
2386293 GAGCGAACTGAGTATC
325 GAGCGAACTGACTATC
2386309 AATATTAGAA
Statistics
Matches: 326, Mismatches: 14, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
362 68 0.21
363 258 0.79
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.23
Consensus pattern (362 bp):
GAACTGAGTAGCCAGTGATGTTAGCAACCATAAAGAAGCTATAACGATTGAAGTGAATAGAAGCA
GAAGTATCATACTCTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCA
CAGATGGGTTCCATTCCCATGACGAGGCCAGAGCGAACTGAGTAGCCAGTGATGTTAGCAACCAT
AAAGAAGCTATAACGATTGAAGTGAATAGAAGCAGAAGTATCATACTTTGCATGGTGAGGCCAAG
AAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCCACAGATGGGTTCCATTCCCATGGCGAGGCCAG
AGCGAACTGACTATCCAGTGATGTTAGCAACCATAAA
Found at i:2386293 original size:164 final size:165
Alignment explanation
Indices: 2385968--2386306 Score: 608
Period size: 164 Copynumber: 2.1 Consensus size: 165
2385958 CAACCATAAA
*
2385968 GAACTGAGTATCCAGTGATGTTAGCAACCATAAAGAAGCTATAACGATTGAAGTGAATAGAAGCA
1 GAACTGAGTAGCCAGTGATGTTAGCAACCATAAAGAAGCTATAACGATTGAAGTGAATAGAAGCA
*
2386033 GAAGTTATCATACTTTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGTC
66 GAAGTTATCATACTTTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCC
*
2386098 ACAGATGGGTTCCATTCCCATGACGAGGCCAGGGC
131 ACAGATGGGTTCCATTCCCATGACGAGGCCAGAGC
2386133 GAACTGAGTAGCCAGTGATGTTAGCAACCATAAAGAAGCTATAACGATTGAAGTGAATAGAAGCA
1 GAACTGAGTAGCCAGTGATGTTAGCAACCATAAAGAAGCTATAACGATTGAAGTGAATAGAAGCA
* *
2386198 GAAG-TATCATACTTTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCTCCAAATGCTTGGCC
66 GAAGTTATCATACTTTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCC
* *
2386262 ACAGATGGGTTCCATTCCCATGGCTAGGCCAGAGC
131 ACAGATGGGTTCCATTCCCATGACGAGGCCAGAGC
2386297 GAACTGAGTA
1 GAACTGAGTA
2386307 TCAATATTAG
Statistics
Matches: 167, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
164 99 0.59
165 68 0.41
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.24
Consensus pattern (165 bp):
GAACTGAGTAGCCAGTGATGTTAGCAACCATAAAGAAGCTATAACGATTGAAGTGAATAGAAGCA
GAAGTTATCATACTTTGCATGGTGAGGCCAAGAAGTTTGCCTCTTTCGGCACCAAAAGCTTGGCC
ACAGATGGGTTCCATTCCCATGACGAGGCCAGAGC
Found at i:2386880 original size:24 final size:24
Alignment explanation
Indices: 2386848--2386893 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2386838 AGTGCCCGGG
2386848 AGTAATGGTGCACGGATTGATATA
1 AGTAATGGTGCACGGATTGATATA
*
2386872 AGTAATGGTGCACTGATTGATA
1 AGTAATGGTGCACGGATTGATA
2386894 CAGGGAGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (24 bp):
AGTAATGGTGCACGGATTGATATA
Found at i:2388000 original size:33 final size:33
Alignment explanation
Indices: 2387963--2388026 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
2387953 ATGATAGTAT
* * *
2387963 ATTTTTATATAATTTTTTATATTAATTTTAAAA
1 ATTTTTATATAACTTTTTACATTAAATTTAAAA
* *
2387996 ATTTTTGTATACCTTTTTACATTAAATTTAA
1 ATTTTTATATAACTTTTTACATTAAATTTAA
2388027 CACTATTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (33 bp):
ATTTTTATATAACTTTTTACATTAAATTTAAAA
Found at i:2391947 original size:2 final size:2
Alignment explanation
Indices: 2391942--2391980 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2391932 ATTTTTTTAC
2391942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2391981 GACACACACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2395814 original size:11 final size:11
Alignment explanation
Indices: 2395798--2395840 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
2395788 ATAATTTATG
2395798 TATTTATATTA
1 TATTTATATTA
*
2395809 TATTTATATAAA
1 TATTTATAT-TA
2395821 TATTATATATTA
1 TATT-TATATTA
2395833 TAATTTAT
1 T-ATTTAT
2395841 GTCAATAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 9 0.33
12 10 0.37
13 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTTATATTA
Found at i:2402685 original size:18 final size:19
Alignment explanation
Indices: 2402650--2402696 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
2402640 ACATAATTTT
2402650 TATATAAAATATAACAAAAA
1 TATAT-AAATATAACAAAAA
* *
2402670 TATATAAAT-TATCAAATA
1 TATATAAATATAACAAAAA
*
2402688 TATTTAAAT
1 TATATAAAT
2402697 GTTTATCGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 4 0.17
20 5 0.21
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
TATATAAATATAACAAAAA
Found at i:2405811 original size:31 final size:31
Alignment explanation
Indices: 2405760--2405834 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
2405750 TGTACTGTAC
*
2405760 TCATATTAAAAATTATATATTCAT-ATTATAT-T
1 TCATA-TAAAAATTAAATATT-ATAATT-TATGT
*
2405792 TCATATAAAATTTAAATATTATAATTTATGT
1 TCATATAAAAATTAAATATTATAATTTATGT
*
2405823 TAATATAAAAAT
1 TCATATAAAAAT
2405835 ATATAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 5 0.14
31 27 0.73
32 5 0.14
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (31 bp):
TCATATAAAAATTAAATATTATAATTTATGT
Found at i:2405844 original size:25 final size:26
Alignment explanation
Indices: 2405805--2405869 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
2405795 TATAAAATTT
2405805 AAATATTATAATTTATGTTA-ATATAA
1 AAATA-TATAATTTATGTTATATATAA
* * *
2405831 AAATATATAATTTATTTTATTTTATTA
1 AAATATATAATTTATGTTA-TATATAA
2405858 AAATATATAATT
1 AAATATATAATT
2405870 ATTAATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 13 0.38
26 5 0.15
27 16 0.47
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
AAATATATAATTTATGTTATATATAA
Found at i:2405885 original size:27 final size:27
Alignment explanation
Indices: 2405805--2405886 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
2405795 TATAAAATTT
2405805 AAATATTATAATTTATGTTAATA-TA--A
1 AAATA-TATAATTTAT-TTAATATTATTA
* *
2405831 AAATATATAATTTATTTTATTTTATTA
1 AAATATATAATTTATTTAATATTATTA
2405858 AAATATATAA-TTATTAATAATATT-TTA
1 AAATATATAATTTATT--TAATATTATTA
2405885 AA
1 AA
2405887 TCATATTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
24 4 0.09
25 12 0.26
26 10 0.21
27 16 0.34
28 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (27 bp):
AAATATATAATTTATTTAATATTATTA
Found at i:2411787 original size:15 final size:16
Alignment explanation
Indices: 2411767--2411799 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2411757 GGGTTTAAGG
2411767 TTTTAAATTTTTG-TT
1 TTTTAAATTTTTGATT
*
2411782 TTTTAAGTTTTTGATT
1 TTTTAAATTTTTGATT
2411798 TT
1 TT
2411800 AGGGTTTGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (16 bp):
TTTTAAATTTTTGATT
Found at i:2412394 original size:13 final size:12
Alignment explanation
Indices: 2412370--2412395 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2412360 AAATAATATT
2412370 AAAAATTTAAAA
1 AAAAATTTAAAA
2412382 AAAAATTTAAAA
1 AAAAATTTAAAA
2412394 AA
1 AA
2412396 TAAAAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAATTTAAAA
Found at i:2413521 original size:21 final size:21
Alignment explanation
Indices: 2413491--2413531 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2413481 CTGTAAGGGG
2413491 TGGCTACAAGTATGATTGGTC
1 TGGCTACAAGTATGATTGGTC
*
2413512 TGGCTGCAAGTATGATTGGT
1 TGGCTACAAGTATGATTGGT
2413532 GCTAGTGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.34
Consensus pattern (21 bp):
TGGCTACAAGTATGATTGGTC
Found at i:2415944 original size:27 final size:27
Alignment explanation
Indices: 2415914--2415965 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2415904 TGGAGAAGAT
*
2415914 GAAGAT-AGAGATGGTGAAGGAGATGGA
1 GAAGATGAGA-ATGGAGAAGGAGATGGA
*
2415941 GAAGATGAGAATGGAGATGGAGATG
1 GAAGATGAGAATGGAGAAGGAGATG
2415966 AAGCATAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.44, T:0.15
Consensus pattern (27 bp):
GAAGATGAGAATGGAGAAGGAGATGGA
Found at i:2425743 original size:2 final size:2
Alignment explanation
Indices: 2425736--2425762 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2425726 TATAAAGAAC
2425736 TA 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 TA T
2425763 CTAAGAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2430842 original size:2 final size:2
Alignment explanation
Indices: 2430835--2430864 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2430825 ATGGTGAGCA
2430835 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2430865 TCATGTTTGT
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2441147 original size:20 final size:21
Alignment explanation
Indices: 2441107--2441149 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
2441097 ATTTATAAAT
*
2441107 ATAAATCTCACATAAAATTTTA
1 ATAAATATCACAT-AAATTTTA
2441129 ATAAATATCACAT-AATTTTA
1 ATAAATATCACATAAATTTTA
2441149 A
1 A
2441150 ATTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
22 12 0.60
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAAATATCACATAAATTTTA
Found at i:2441183 original size:14 final size:16
Alignment explanation
Indices: 2441152--2441183 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
2441142 AATTTTAAAT
2441152 TATTATTAATTAATTA
1 TATTATTAATTAATTA
2441168 TATTA-TAA-TAATTA
1 TATTATTAATTAATTA
2441182 TA
1 TA
2441184 AATGAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTATTAATTAATTA
Found at i:2447318 original size:75 final size:74
Alignment explanation
Indices: 2447077--2447354 Score: 243
Period size: 75 Copynumber: 3.7 Consensus size: 74
2447067 AAAACGGGCA
* * ** * * * *
2447077 TTGCCTTCATGGGCTAATAATGAGAGAGAGGATGATGATGAGAGTGTTGATGAGGAATTGGAGGT
1 TTGCCTTCATGGGC---TAATGGGAGAGTGGGGGATGATGAGAGAGCTGATGAAGAATTGGAGGC
* *
2447142 TAATGAAGAGGAG
63 TAATGAA-AAGAT
* * * ** * * * *
2447155 TTGCTTTCATGGGATCATGGGAGAAAGGTGGATGATGAGAGAGCCGTTGAAGAATTGAAGGCTAA
1 TTGCCTTCATGGGCTAATGGGAGAGTGGGGGATGATGAGAGAGCTGATGAAGAATTGGAGGCTAA
2447220 TGAAAAGGAGT
66 TGAAAA-GA-T
* *
2447231 TT-TCTTCATGGGCTAATGGGAGAGTGGGGGATGATGAGAGAGCTGATGAAGAAGTGGAGGCTAA
1 TTGCCTTCATGGGCTAATGGGAGAGTGGGGGATGATGAGAGAGCTGATGAAGAATTGGAGGCTAA
2447295 TGAAACAGAT
66 TGAAA-AGAT
* * * * * *
2447305 TTGCCTTCGTGGGCTAATGGTAGGGTGAGGGATAATAAGAGAGCTGATGA
1 TTGCCTTCATGGGCTAATGGGAGAGTGGGGGATGATGAGAGAGCTGATGA
2447355 GGAACTTGAT
Statistics
Matches: 162, Mismatches: 34, Indels: 11
0.78 0.16 0.05
Matches are distributed among these distances:
74 4 0.02
75 143 0.88
76 3 0.02
78 12 0.07
ACGTcount: A:0.31, C:0.08, G:0.37, T:0.24
Consensus pattern (74 bp):
TTGCCTTCATGGGCTAATGGGAGAGTGGGGGATGATGAGAGAGCTGATGAAGAATTGGAGGCTAA
TGAAAAGAT
Found at i:2455357 original size:19 final size:19
Alignment explanation
Indices: 2455301--2455358 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 19
2455291 AAAAATATAT
*
2455301 ATTTTTTAATTTTATTAAA
1 ATTTTTAAATTTTATTAAA
*
2455320 TTTATTTATAATTTTTATTAAA
1 ATT-TTTA-AA-TTTTATTAAA
*
2455342 ATTTTTAAATTATATTA
1 ATTTTTAAATTTTATTA
2455359 TTTTTTATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 9 0.28
20 5 0.16
21 6 0.19
22 12 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTTAAATTTTATTAAA
Found at i:2455360 original size:22 final size:22
Alignment explanation
Indices: 2455310--2455352 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2455300 TATTTTTTAA
*
2455310 TTTTATTAAATTTATTTATAAT
1 TTTTATTAAAATTATTTATAAT
2455332 TTTTATTAAAATT-TTTA-AAT
1 TTTTATTAAAATTATTTATAAT
2455352 T
1 T
2455353 ATATTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 4 0.20
22 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTATTAAAATTATTTATAAT
Found at i:2455374 original size:36 final size:36
Alignment explanation
Indices: 2455332--2455400 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
2455322 TATTTATAAT
*
2455332 TTTTATTAAAATTTTTAAATTATATTATTTTTTATC
1 TTTTATTAAAATTTTTAAATTATATTATATTTTATC
* * **
2455368 TTTTATTTATATTTTTTTATTATATTATATTTT
1 TTTTATTAAAATTTTTAAATTATATTATATTTT
2455401 GTTTGAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (36 bp):
TTTTATTAAAATTTTTAAATTATATTATATTTTATC
Found at i:2455395 original size:18 final size:20
Alignment explanation
Indices: 2455350--2455400 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 20
2455340 AAATTTTTAA
2455350 ATTATATTAT-TTTTTATCT
1 ATTATATTATATTTTTATCT
*
2455369 TTTAT-TTATATTTTT-T-T
1 ATTATATTATATTTTTATCT
2455386 ATTATATTATATTTT
1 ATTATATTATATTTT
2455401 GTTTGAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 5 0.18
18 14 0.50
19 9 0.32
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
ATTATATTATATTTTTATCT
Found at i:2456803 original size:23 final size:24
Alignment explanation
Indices: 2456754--2456803 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
2456744 TTTTTATTAG
*
2456754 ATAAAAAGGTTTAAAATTTTTTCAA
1 ATAAAAA-GTTTAAAATTATTTCAA
2456779 ATAAAAA-TTTAATAATTATTT-AA
1 ATAAAAAGTTTAA-AATTATTTCAA
2456802 AT
1 AT
2456804 TTTTAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 9 0.39
24 7 0.30
25 7 0.30
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (24 bp):
ATAAAAAGTTTAAAATTATTTCAA
Found at i:2456832 original size:29 final size:30
Alignment explanation
Indices: 2456799--2456856 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
2456789 AATAATTATT
*
2456799 TAAATTTTTAATATTTTATTACAA-TCAAC
1 TAAATTATTAATATTTTATTACAACTCAAC
* *
2456828 TAAATTATTAATTTTTTATTTCAACTCAA
1 TAAATTATTAATATTTTATTACAACTCAA
2456857 TTCAATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (30 bp):
TAAATTATTAATATTTTATTACAACTCAAC
Found at i:2464251 original size:147 final size:148
Alignment explanation
Indices: 2463983--2464278 Score: 522
Period size: 147 Copynumber: 2.0 Consensus size: 148
2463973 ATGTCTACTC
* *
2463983 CAAATTTAGTTTTTAAGCATCAAAACCAAGATATTATAAACAGATCTACGTTAACTTTCCCAAGT
1 CAAATTTAGTTTTTAAGCATCAAAACCAAGATATTATAAACAGATCTAAGTTAACTTCCCCAAGT
*
2464048 TTATATGCATATTAGAACATACACTTTTCAACTATGAACTCAATGCAGTCACCTTGTTGGATAAA
66 TTATATGCATATTAGAACATACACTTTTCAACTATGAACTCAATGCAGTCACCTTGTTGCATAAA
2464113 TAAAGCTTCTTCACAATT
131 TAAAGCTTCTTCACAATT
* **
2464131 CAAATTTAGTTTTTAAGCATC-AAACCAAGATATTATTAATGGATCTAAGTTAACTTCCCCAAGT
1 CAAATTTAGTTTTTAAGCATCAAAACCAAGATATTATAAACAGATCTAAGTTAACTTCCCCAAGT
*
2464195 TTATATGCATATTAGAACATACCCTTTTCAACTATGAACTCAATGCAGTCACCTTGTTGCATAAA
66 TTATATGCATATTAGAACATACACTTTTCAACTATGAACTCAATGCAGTCACCTTGTTGCATAAA
2464260 TAAAGCTTCTTCACAATT
131 TAAAGCTTCTTCACAATT
2464278 C
1 C
2464279 TCACAATCCT
Statistics
Matches: 141, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
147 120 0.85
148 21 0.15
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (148 bp):
CAAATTTAGTTTTTAAGCATCAAAACCAAGATATTATAAACAGATCTAAGTTAACTTCCCCAAGT
TTATATGCATATTAGAACATACACTTTTCAACTATGAACTCAATGCAGTCACCTTGTTGCATAAA
TAAAGCTTCTTCACAATT
Found at i:2465496 original size:20 final size:20
Alignment explanation
Indices: 2465459--2465497 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2465449 TTATGTGTTT
*
2465459 AATAAATAAATTTTTTATTA
1 AATAAATAAATTTATTATTA
2465479 AATAATATAAA-TTATTATT
1 AATAA-ATAAATTTATTATT
2465498 TTAAATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATAAATAAATTTATTATTA
Found at i:2465511 original size:22 final size:24
Alignment explanation
Indices: 2465476--2465523 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
2465466 AAATTTTTTA
2465476 TTAAATAATATAAATT-AT-TATT
1 TTAAATAATATAAATTAATATATT
2465498 TTAAATTAAT-TAAATTAATATATT
1 TTAAA-TAATATAAATTAATATATT
2465522 TT
1 TT
2465524 TATTGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 11 0.48
23 6 0.26
24 6 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TTAAATAATATAAATTAATATATT
Found at i:2471246 original size:33 final size:33
Alignment explanation
Indices: 2471204--2471267 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
2471194 TATCCTCATC
2471204 AAGGCTTTCCAAATCTCTTCCAGGCAGTATAAA
1 AAGGCTTTCCAAATCTCTTCCAGGCAGTATAAA
2471237 AAGGCTTTCCAAATCTCTTCCAGGCAGTATA
1 AAGGCTTTCCAAATCTCTTCCAGGCAGTATA
2471268 TTGGAAAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (33 bp):
AAGGCTTTCCAAATCTCTTCCAGGCAGTATAAA
Found at i:2480604 original size:83 final size:83
Alignment explanation
Indices: 2480475--2480629 Score: 256
Period size: 83 Copynumber: 1.9 Consensus size: 83
2480465 ATTACTGAAA
* * *
2480475 ATTTACATCTTATGAGTGTGTATATTTAAATGTTTAAGTGGACTTTAGGTGGACTAAAGGAGATT
1 ATTTACATCTTATAAGTGTATATATTTAAATGTTTAAGTGGACTTTAGGTAGACTAAAGGAGATT
*
2480540 GATATGGGATTACTAGAG
66 GAGATGGGATTACTAGAG
* *
2480558 ATTTACATCTTATAAGTGTATATGTTTAAATGTTTAGGTGGACTTTAGGTAGACTAAAGGAGATT
1 ATTTACATCTTATAAGTGTATATATTTAAATGTTTAAGTGGACTTTAGGTAGACTAAAGGAGATT
2480623 GAGATGG
66 GAGATGG
2480630 TCCACATAGA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 66 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (83 bp):
ATTTACATCTTATAAGTGTATATATTTAAATGTTTAAGTGGACTTTAGGTAGACTAAAGGAGATT
GAGATGGGATTACTAGAG
Found at i:2482661 original size:23 final size:23
Alignment explanation
Indices: 2482634--2482683 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
2482624 ACTACTAGAG
*
2482634 ATTTACATCTTAT-AAGTGTATAT
1 ATTTACACCTTATGAA-TGTATAT
2482657 ATTTACACCTTATGAATGTATAT
1 ATTTACACCTTATGAATGTATAT
2482680 ATTT
1 ATTT
2482684 GAATGTTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (23 bp):
ATTTACACCTTATGAATGTATAT
Found at i:2490095 original size:62 final size:61
Alignment explanation
Indices: 2490021--2490203 Score: 237
Period size: 62 Copynumber: 2.9 Consensus size: 61
2490011 ACTTAAAGCG
**
2490021 TTTTTATCCAAAAATATCTTAAATAATTTTCAATAATTTTTTTTAAAA-AATTATTTAAGGTAT
1 TTTTTAT-CAAAAATATCTTAAATAATTTT-AAT-ATTTTTTTTAAAAGAATTATTTAAAATAT
* *
2490084 TTTTGT-TCAAAAATACCTTAAATAATTTTTAATATTTTTTTAAAAAGAATTATTTAAAATAT
1 TTTT-TATCAAAAATATCTTAAATAA-TTTTAATATTTTTTTTAAAAGAATTATTTAAAATAT
*
2490146 TTTTTATCAAAAATATCTTAAATAATCTTTAATA-TTTTTTTAAAATGGATTATTTAAA
1 TTTTTATCAAAAATATCTTAAATAAT-TTTAATATTTTTTTTAAAA-GAATTATTTAAA
2490204 GCGTTTTGTC
Statistics
Matches: 107, Mismatches: 7, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
61 24 0.22
62 73 0.68
63 9 0.08
64 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.49
Consensus pattern (61 bp):
TTTTTATCAAAAATATCTTAAATAATTTTAATATTTTTTTTAAAAGAATTATTTAAAATAT
Found at i:2490231 original size:61 final size:62
Alignment explanation
Indices: 2490001--2490231 Score: 186
Period size: 62 Copynumber: 3.8 Consensus size: 62
2489991 TTAAAAAATA
* * * *
2490001 TAAAAAG-ATTACTTAAAGCGTTTT-TATCCAAAAATATCTTAAATAAT-TTTCAATAATTTTTT
1 TAAAAAGAATTATTTAAAACATTTTGTA-CCAAAAACATCTTAAATAATCTTT-AAT-ATTTTTT
* *** * * * *
2490063 TTAAAA-AATTATTTAAGGTATTTTTGT-TCAAAAATACCTTAAATAATTTTTAATATTTTTT
1 TAAAAAGAATTATTTAAAACA-TTTTGTACCAAAAACATCTTAAATAATCTTTAATATTTTTT
* * * *
2490124 TAAAAAGAATTATTTAAAATATTTTTTATCAAAAATATCTTAAATAATCTTTAATATTTTTT
1 TAAAAAGAATTATTTAAAACATTTTGTACCAAAAACATCTTAAATAATCTTTAATATTTTTT
* * * * * *
2490186 TAAAATGGATTATTTAAAGCGTTTTGT-CCAAAAACGTTTTAAATAA
1 TAAAAAGAATTATTTAAAACATTTTGTACCAAAAACATCTTAAATAA
2490232 GTCAAATAAA
Statistics
Matches: 140, Mismatches: 23, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
61 32 0.23
62 100 0.71
63 7 0.05
64 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (62 bp):
TAAAAAGAATTATTTAAAACATTTTGTACCAAAAACATCTTAAATAATCTTTAATATTTTTT
Found at i:2496223 original size:30 final size:34
Alignment explanation
Indices: 2496166--2496229 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
2496156 TTTATTTAAC
*
2496166 TTTTATTTATAGAATATTAAACCAAT-AAAGTTTT
1 TTTTATTTATAAAATATTAAA-CAATAAAAGTTTT
2496200 TTTTATTT-TAAAATATT-AA-AATAAAAGTTT
1 TTTTATTTATAAAATATTAAACAATAAAAGTTT
2496230 GATAGATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 3 0.11
31 7 0.25
32 2 0.07
33 8 0.29
34 8 0.29
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (34 bp):
TTTTATTTATAAAATATTAAACAATAAAAGTTTT
Found at i:2499566 original size:50 final size:50
Alignment explanation
Indices: 2499506--2499605 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 50
2499496 GAGGTTTTTT
* *
2499506 TAATACAGCTAAATGTCCATATAATATTAACTGAACACAGAACAGTGGGG
1 TAATAAAGCTAAATGTCAATATAATATTAACTGAACACAGAACAGTGGGG
* *
2499556 TAATAAAGCTAAATGTCAATATAATATTACCTGAACATAGAACAGTGGGG
1 TAATAAAGCTAAATGTCAATATAATATTAACTGAACACAGAACAGTGGGG
2499606 AAAACTGTGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (50 bp):
TAATAAAGCTAAATGTCAATATAATATTAACTGAACACAGAACAGTGGGG
Found at i:2501057 original size:50 final size:49
Alignment explanation
Indices: 2500976--2501078 Score: 161
Period size: 50 Copynumber: 2.1 Consensus size: 49
2500966 CATAAAAGAT
* *
2500976 AAAATCTTTTGTCTCGGACCCAGGTGGTCACCAATATTTAAATTGTACGA
1 AAAATCTTTTGTCTCGGACCCAGATGATCACCAATATTTAAATTGTAC-A
* *
2501026 AAACTCTTTTGTCTCGGTCCCAGATGATCACCAATATTTAAATTGTACA
1 AAAATCTTTTGTCTCGGACCCAGATGATCACCAATATTTAAATTGTACA
2501075 AAAA
1 AAAA
2501079 GTCATCAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 4 0.08
50 44 0.92
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (49 bp):
AAAATCTTTTGTCTCGGACCCAGATGATCACCAATATTTAAATTGTACA
Found at i:2513002 original size:22 final size:22
Alignment explanation
Indices: 2512955--2513049 Score: 88
Period size: 22 Copynumber: 4.3 Consensus size: 22
2512945 AAAAATTAAT
*
2512955 ATTTATTAAATGAATTTAA-AA
1 ATTTATTAAATGAATTCAATAA
2512976 TATTTATTAAATGAATTCAATAA
1 -ATTTATTAAATGAATTCAATAA
* **
2512999 ATTTAATGAAGAT-AATT-TTTAA
1 ATTT-ATTAA-ATGAATTCAATAA
*
2513021 ATTTTATTAAATAAATTCAATAA
1 A-TTTATTAAATGAATTCAATAA
2513044 ATTTAT
1 ATTTAT
2513050 ATGAAAAATA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
21 2 0.03
22 39 0.65
23 17 0.28
24 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
ATTTATTAAATGAATTCAATAA
Found at i:2513058 original size:22 final size:23
Alignment explanation
Indices: 2512989--2513058 Score: 58
Period size: 23 Copynumber: 3.1 Consensus size: 23
2512979 TTATTAAATG
2512989 AATTCAATAAATTTA-ATGAAGA
1 AATTCAATAAATTTATATGAAGA
** * *
2513011 TAATT-TTTAAATTT-TATTAAATA
1 -AATTCAATAAATTTATA-TGAAGA
2513034 AATTCAATAAATTTATATGAA-A
1 AATTCAATAAATTTATATGAAGA
2513056 AAT
1 AAT
2513059 AAAATTTAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
22 16 0.44
23 18 0.50
24 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.41
Consensus pattern (23 bp):
AATTCAATAAATTTATATGAAGA
Found at i:2513339 original size:19 final size:18
Alignment explanation
Indices: 2513317--2513355 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
2513307 TTATAAAATA
*
2513317 ATATTAAAATTTATTTTTT
1 ATATTAAAAGTT-TTTTTT
*
2513336 ATATTAATAGTTTTTTTT
1 ATATTAAAAGTTTTTTTT
2513354 AT
1 AT
2513356 GTTTTTAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
ATATTAAAAGTTTTTTTT
Found at i:2521831 original size:1 final size:1
Alignment explanation
Indices: 2521825--2521849 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2521815 TTCTTCATAG
2521825 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
2521850 AAGACTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2523853 original size:20 final size:21
Alignment explanation
Indices: 2523818--2523856 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2523808 ATTGATAAAT
2523818 ATTAAAATTTTAATTTTAATA
1 ATTAAAATTTTAATTTTAATA
*
2523839 ATTAAAA-TTTGATTTTAA
1 ATTAAAATTTTAATTTTAA
2523857 CAGTTACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
ATTAAAATTTTAATTTTAATA
Found at i:2531608 original size:28 final size:28
Alignment explanation
Indices: 2531561--2531616 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2531551 AAGCAGGACG
* *
2531561 ATGGAAGTGATAAAATGTATCAAATATA
1 ATGGAAGTGACAAAACGTATCAAATATA
*
2531589 ATGGAAGTGACAAAGCGTATCAAATATA
1 ATGGAAGTGACAAAACGTATCAAATATA
2531617 TTATGTGATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.25
Consensus pattern (28 bp):
ATGGAAGTGACAAAACGTATCAAATATA
Found at i:2534875 original size:66 final size:66
Alignment explanation
Indices: 2534768--2534964 Score: 245
Period size: 66 Copynumber: 3.0 Consensus size: 66
2534758 CCCAAGAATC
* * *
2534768 TGCTATTTGGATACCAGCACTCCGCTGCATTGCTTCAGATGGTCTAACATTGTTAC-GGTTTGGT
1 TGCTATTTGGATACCAGCACTCCGCTGCAATGCTTCAGATGGTCGAACATTGTT-CTGGTTTGGA
*
2534832 TT
65 TG
* * *
2534834 TGCTATTTGGATACCAGTA-TCCCGCTTCAATGCTTCCGATGGTCGAACATTGTTCTGGTTTGGA
1 TGCTATTTGGATACCAGCACT-CCGCTGCAATGCTTCAGATGGTCGAACATTGTTCTGGTTTGGA
2534898 TG
65 TG
* * * * * *
2534900 TGCTATTTGGATACCAGCACTCCACCGCATTGCTTCGGATAGTCTAACATTGTTCTGGTTTGGAT
1 TGCTATTTGGATACCAGCACTCCGCTGCAATGCTTCAGATGGTCGAACATTGTTCTGGTTTGGAT
2534965 TAGGCCTAGG
Statistics
Matches: 113, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
65 2 0.02
66 110 0.97
67 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.37
Consensus pattern (66 bp):
TGCTATTTGGATACCAGCACTCCGCTGCAATGCTTCAGATGGTCGAACATTGTTCTGGTTTGGAT
G
Found at i:2535630 original size:2 final size:2
Alignment explanation
Indices: 2535625--2535655 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2535615 ATATTAGAAT
*
2535625 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2535656 GAAGATGGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:2535851 original size:2 final size:2
Alignment explanation
Indices: 2535844--2535881 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2535834 CTTATCCTAA
* *
2535844 AT AT AT AT AT AT AT AT AT AT AT -T TT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2535882 AGTAGGAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2536328 original size:81 final size:80
Alignment explanation
Indices: 2536125--2536371 Score: 354
Period size: 81 Copynumber: 3.0 Consensus size: 80
2536115 CTTAAGAATT
2536125 TAATTTTAATCTAAAAGTAAAAAAAAAAAATGTAACTCTTA-AGCTAATACAAATAAATTCTTAC
1 TAATTTTAATCTAAAAGT-AAAAAAAAAAATGTAACTCTTACA-CTAATACAAATAAATTCTTAC
2536189 TCATATATATATATATATA
64 TC--ATATATATATATATA
* * * *
2536208 TTTAATTTTAATCTAAAAGT-TAAAACAAAATATAACTCTTACACTAACACAAATAAATTCTTAC
1 --TAATTTTAATCTAAAAGTAAAAAAAAAAATGTAACTCTTACACTAATACAAATAAATTCTTAC
2536272 TCATATATATATATATA
64 TCATATATATATATATA
* * *
2536289 TAATTTTGATCTAAAAGTACAAAAAGAAAATGTAACTCTTACACTAATACAAATAAATTCTTATT
1 TAATTTTAATCTAAAAGTA-AAAAAAAAAATGTAACTCTTACACTAATACAAATAAATTCTTACT
2536354 CATATATATATATATA
65 CATATATATATATATA
2536370 TA
1 TA
2536372 TGTTGACGTT
Statistics
Matches: 149, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
79 17 0.11
81 73 0.49
83 40 0.27
84 1 0.01
85 18 0.12
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.36
Consensus pattern (80 bp):
TAATTTTAATCTAAAAGTAAAAAAAAAAATGTAACTCTTACACTAATACAAATAAATTCTTACTC
ATATATATATATATA
Found at i:2538585 original size:16 final size:16
Alignment explanation
Indices: 2538564--2538603 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
2538554 AACCACCTAT
2538564 TTTTTATTTTTTTCAC
1 TTTTTATTTTTTTCAC
* *
2538580 TTTTTATTTTTTTTAT
1 TTTTTATTTTTTTCAC
2538596 TTTTTATT
1 TTTTTATT
2538604 AGTAAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTATTTTTTTCAC
Found at i:2540350 original size:19 final size:18
Alignment explanation
Indices: 2540316--2540351 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2540306 TTTTTTTGGG
*
2540316 TAAAAAAAATATAACTTA
1 TAAAAAAAATAAAACTTA
2540334 TAAAAAAAATACAAACTT
1 TAAAAAAAATA-AAACTT
2540352 TTAATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAAAAAAATAAAACTTA
Found at i:2540494 original size:3 final size:3
Alignment explanation
Indices: 2540488--2540525 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2540478 TTTTTTGTGG
2540488 ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2540526 TGTATGGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2540510 original size:17 final size:17
Alignment explanation
Indices: 2540488--2540521 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2540478 TTTTTTGTGG
2540488 ATTATTATTATTATTAT
1 ATTATTATTATTATTAT
2540505 ATTATTATTATTATTAT
1 ATTATTATTATTATTAT
2540522 TATTTGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTATTATTATTATTAT
Found at i:2544426 original size:31 final size:32
Alignment explanation
Indices: 2544368--2544433 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
2544358 TAAAAAATGG
** *
2544368 AAATAAAATAGAAATAAAAACTTAAAATAATA
1 AAATAAAATAGAAATAAAAACAAAAAATAAAA
* *
2544400 AAATAAAAT-GAAATGAAATCAAAAAATAAAA
1 AAATAAAATAGAAATAAAAACAAAAAATAAAA
2544431 AAA
1 AAA
2544434 AATAAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 20 0.69
32 9 0.31
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (32 bp):
AAATAAAATAGAAATAAAAACAAAAAATAAAA
Found at i:2544446 original size:11 final size:10
Alignment explanation
Indices: 2544420--2544445 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2544410 AAATGAAATC
2544420 AAAAAATAAA
1 AAAAAATAAA
2544430 AAAAAATAAA
1 AAAAAATAAA
2544440 AAAAAA
1 AAAAAA
2544446 AACTTGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:2550111 original size:2 final size:2
Alignment explanation
Indices: 2550104--2550139 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2550094 AGCCTTCCTC
2550104 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2550140 GTAGGAATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2553071 original size:18 final size:18
Alignment explanation
Indices: 2553050--2553129 Score: 58
Period size: 18 Copynumber: 4.4 Consensus size: 18
2553040 ATAGTTAAAG
2553050 ATAAAA-AAATATAAAAAT
1 ATAAAATAAA-ATAAAAAT
*
2553068 ATAAAATAAAATGAAAAT
1 ATAAAATAAAATAAAAAT
* * *
2553086 AAAATAGACAAAAT-GAAAT
1 ATAA-A-ATAAAATAAAAAT
*
2553105 A-AAAATAAAATCAAAAT
1 ATAAAATAAAATAAAAAT
*
2553122 AAAAAATA
1 ATAAAATA
2553130 TAACGAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
16 6 0.12
17 6 0.12
18 24 0.47
19 9 0.18
20 6 0.12
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.19
Consensus pattern (18 bp):
ATAAAATAAAATAAAAAT
Found at i:2553078 original size:5 final size:5
Alignment explanation
Indices: 2553055--2553125 Score: 56
Period size: 5 Copynumber: 13.8 Consensus size: 5
2553045 TAAAGATAAA
* * * *
2553055 AAAAT ATAAA- AATAT AAAAT AAAAT GAAAAT AAAAT -AGAC AAAAT GAAAT
1 AAAAT A-AAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT
2553105 AAAAAT AAAAT CAAAAT AAAA
1 -AAAAT AAAAT -AAAAT AAAA
2553126 AATATAACGA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
4 4 0.08
5 31 0.60
6 17 0.33
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:2553084 original size:11 final size:11
Alignment explanation
Indices: 2553070--2553125 Score: 58
Period size: 11 Copynumber: 4.8 Consensus size: 11
2553060 ATAAAAATAT
2553070 AAAATAAAATG
1 AAAATAAAATG
2553081 AAAATAAAATAG
1 AAAATAAAAT-G
* *
2553093 ACAAAATGAAATA
1 --AAAATAAAATG
*
2553106 AAAATAAAATC
1 AAAATAAAATG
2553117 AAAATAAAA
1 AAAATAAAA
2553126 AATATAACGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
11 28 0.74
12 1 0.03
14 9 0.24
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (11 bp):
AAAATAAAATG
Found at i:2553112 original size:6 final size:6
Alignment explanation
Indices: 2553055--2553126 Score: 51
Period size: 6 Copynumber: 11.8 Consensus size: 6
2553045 TAAAGATAAA
* * *
2553055 AAAATAT AAAAAT ATAAAAT -AAAAT GAAAAT AAAATAG ACAAAAT -GAAAT
1 AAAA-AT AAAAAT A-AAAAT AAAAAT AAAAAT AAAA-AT A-AAAAT AAAAAT
*
2553105 AAAAAT -AAAAT CAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAA
2553127 ATATAACGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
5 14 0.26
6 24 0.45
7 12 0.23
8 3 0.06
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:2553562 original size:17 final size:17
Alignment explanation
Indices: 2553542--2553574 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2553532 TTTTTTTACT
2553542 TTTTATTTA-TTTTATTA
1 TTTTA-TTAGTTTTATTA
2553559 TTTTATTAGTTTTATT
1 TTTTATTAGTTTTATT
2553575 GGGATGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTATTAGTTTTATTA
Found at i:2554561 original size:35 final size:34
Alignment explanation
Indices: 2554500--2554572 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 34
2554490 ATTTTTTGGT
* ** *
2554500 TTTTCTTTAGTATTTTTTATTTATTTTATTTAGTA
1 TTTTCCTTAGTATTTTTTATAGATTTT-TTTAGCA
2554535 TTTTCCTTAGTATTTTTCT-TAGATTTTTTTAGCA
1 TTTTCCTTAGTATTTTT-TATAGATTTTTTTAGCA
2554569 TTTT
1 TTTT
2554573 TTTCCATGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 10 0.30
35 22 0.67
36 1 0.03
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.68
Consensus pattern (34 bp):
TTTTCCTTAGTATTTTTTATAGATTTTTTTAGCA
Found at i:2554562 original size:11 final size:12
Alignment explanation
Indices: 2554499--2554573 Score: 61
Period size: 12 Copynumber: 6.4 Consensus size: 12
2554489 CATTTTTTGG
2554499 TTTTTCTTTAGTA
1 TTTTTC-TTAGTA
*
2554512 -TTTT-TTATTTA
1 TTTTTCTTA-GTA
2554523 TTTTAT-TTAGTA
1 TTTT-TCTTAGTA
*
2554535 TTTTCCTTAGTA
1 TTTTTCTTAGTA
2554547 TTTTTCTTAG-A
1 TTTTTCTTAGTA
*
2554558 TTTTT-TTAGCA
1 TTTTTCTTAGTA
2554569 TTTTT
1 TTTTT
2554574 TTCCATGATT
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
10 7 0.13
11 14 0.26
12 28 0.53
13 4 0.08
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.69
Consensus pattern (12 bp):
TTTTTCTTAGTA
Found at i:2554574 original size:11 final size:11
Alignment explanation
Indices: 2554491--2554575 Score: 68
Period size: 11 Copynumber: 7.5 Consensus size: 11
2554481 AACCGAGCCA
*
2554491 TTTTTTGGT-T
1 TTTTTTAGTAT
2554501 TTTCTTTAGTA-
1 TTT-TTTAGTAT
*
2554512 TTTTTTATTTAT
1 TTTTTTA-GTAT
2554524 TTTATTTAGTAT
1 TTT-TTTAGTAT
*
2554536 TTTCCTTAGTAT
1 TTT-TTTAGTAT
2554548 TTTTCTTAG-AT
1 TTTT-TTAGTAT
*
2554559 TTTTTTAGCAT
1 TTTTTTAGTAT
2554570 TTTTTT
1 TTTTTT
2554576 CCATGATTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
10 11 0.18
11 24 0.39
12 23 0.37
13 4 0.06
ACGTcount: A:0.15, C:0.06, G:0.08, T:0.71
Consensus pattern (11 bp):
TTTTTTAGTAT
Found at i:2555150 original size:55 final size:55
Alignment explanation
Indices: 2554998--2555223 Score: 210
Period size: 55 Copynumber: 4.1 Consensus size: 55
2554988 AAAAATAAAT
2554998 AAAGAGAAAATATTTCTAAATTGAACCAAATGGTGAAAAATTTAGAAATCAAACAAA
1 AAAGAGAAAATATTTCTAAATTG-ACCAAATGGTGAAAAATTTAGAAAT-AAACAAA
* * * * ** *
2555055 AAAAAGAGAGA-ATTTCTAAATAGGCCTAAATGGTGAAAAATTTAGAAAT-TTCGAA
1 AAAGAGA-AAATATTTCTAAATTGACC-AAATGGTGAAAAATTTAGAAATAAACAAA
* * *
2555110 AAGGAGAAAATATTTCTAAATTGACCAAAATGGTGGAAAATTTAGAAATCCAACTAAA
1 AAAGAGAAAATATTTCTAAATTGACC-AAATGGTGAAAAATTTAGAAAT-AAAC-AAA
* * * * *
2555168 AAAGAG-AGA-ATTTCTAAATAGGCATAAATGGTGAAAAATTTAGAAATTAA-AAA
1 AAAGAGAAAATATTTCTAAATTGAC-CAAATGGTGAAAAATTTAGAAATAAACAAA
2555221 AAA
1 AAA
2555224 TATTTTTAAT
Statistics
Matches: 138, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
53 6 0.04
54 2 0.01
55 44 0.32
56 35 0.25
57 42 0.30
58 9 0.07
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.24
Consensus pattern (55 bp):
AAAGAGAAAATATTTCTAAATTGACCAAATGGTGAAAAATTTAGAAATAAACAAA
Found at i:2555197 original size:56 final size:54
Alignment explanation
Indices: 2555025--2555223 Score: 215
Period size: 55 Copynumber: 3.6 Consensus size: 54
2555015 AAATTGAACC
*
2555025 AAATGGTGAAAAATTTAGAAATCAAACAAAAAAAAGAGAGAATTTCTAAATAGGCCT
1 AAATGGTGAAAAATTTAGAAATC-AAC--AAAAAAGAGAGAATTTCTAAATAGGCAT
** * * * * *
2555082 AAATGGTGAAAAATTTAGAAAT-TTCGAAAAGGAGAAAATATTTCTAAATTGACCA-
1 AAATGGTGAAAAATTTAGAAATCAACAAAAAAGAG-AGA-ATTTCTAAATAG-GCAT
*
2555137 AAATGGTGGAAAATTTAGAAATCCAACTAAAAAAGAGAGAATTTCTAAATAGGCAT
1 AAATGGTGAAAAATTTAGAAAT-CAAC-AAAAAAGAGAGAATTTCTAAATAGGCAT
*
2555193 AAATGGTGAAAAATTTAGAAATTAA-AAAAAA
1 AAATGGTGAAAAATTTAGAAATCAACAAAAAA
2555224 TATTTTTAAT
Statistics
Matches: 117, Mismatches: 18, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
53 13 0.11
54 2 0.02
55 37 0.32
56 33 0.28
57 25 0.21
58 7 0.06
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.24
Consensus pattern (54 bp):
AAATGGTGAAAAATTTAGAAATCAACAAAAAAGAGAGAATTTCTAAATAGGCAT
Found at i:2555208 original size:111 final size:112
Alignment explanation
Indices: 2555001--2555215 Score: 371
Period size: 111 Copynumber: 1.9 Consensus size: 112
2554991 AATAAATAAA
2555001 GAGAAAATATTTCTAAATTGAACCAAATGGTGAAAAATTTAGAAATCAAACAAAAAAAAGAGAGA
1 GAGAAAATATTTCTAAATTGAACCAAATGGTGAAAAATTTAGAAATCAAACAAAAAAAAGAGAGA
*
2555066 ATTTCTAAATAGGCCTAAATGGTGAAAAATTTAGAAATTTCGAAAAG
66 ATTTCTAAATAGGCATAAATGGTGAAAAATTTAGAAATTTCGAAAAG
* * *
2555113 GAGAAAATATTTCTAAATTG-ACCAAAATGGTGGAAAATTTAGAAATCCAAC-TAAAAAAGAGAG
1 GAGAAAATATTTCTAAATTGAACC-AAATGGTGAAAAATTTAGAAATCAAACAAAAAAAAGAGAG
2555176 AATTTCTAAATAGGCATAAATGGTGAAAAATTTAGAAATT
65 AATTTCTAAATAGGCATAAATGGTGAAAAATTTAGAAATT
2555216 AAAAAAAATA
Statistics
Matches: 98, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
111 53 0.54
112 45 0.46
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.25
Consensus pattern (112 bp):
GAGAAAATATTTCTAAATTGAACCAAATGGTGAAAAATTTAGAAATCAAACAAAAAAAAGAGAGA
ATTTCTAAATAGGCATAAATGGTGAAAAATTTAGAAATTTCGAAAAG
Found at i:2559253 original size:11 final size:11
Alignment explanation
Indices: 2559234--2559278 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
2559224 AAAAATTAAA
2559234 GAAAA-AAAAT
1 GAAAAGAAAAT
2559244 GAAAAGAAAAT
1 GAAAAGAAAAT
2559255 G-AAAG--AAT
1 GAAAAGAAAAT
*
2559263 GAAAAAAAAAT
1 GAAAAGAAAAT
2559274 GAAAA
1 GAAAA
2559279 TGAGAGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
8 4 0.13
9 3 0.10
10 9 0.30
11 14 0.47
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (11 bp):
GAAAAGAAAAT
Found at i:2559265 original size:19 final size:19
Alignment explanation
Indices: 2559241--2559277 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2559231 AAAGAAAAAA
*
2559241 AATGAAAAGAAAATGAAAG
1 AATGAAAAAAAAATGAAAG
2559260 AATGAAAAAAAAATGAAA
1 AATGAAAAAAAAATGAAA
2559278 ATGAGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (19 bp):
AATGAAAAAAAAATGAAAG
Found at i:2559267 original size:25 final size:25
Alignment explanation
Indices: 2559225--2559294 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
2559215 GAAAGAGATA
* *
2559225 AAAATTAAAGAAAAAAAATGAAAA-G
1 AAAATGAAAGAAAAAAAA-AAAAATG
**
2559250 AAAATGAAAGAATGAAAAAAAAATG
1 AAAATGAAAGAAAAAAAAAAAAATG
* *
2559275 AAAATGAGAGAAAAAGAAAA
1 AAAATGAAAGAAAAAAAAAA
2559295 CTCGAATTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
24 4 0.11
25 32 0.89
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (25 bp):
AAAATGAAAGAAAAAAAAAAAAATG
Found at i:2560166 original size:23 final size:23
Alignment explanation
Indices: 2560140--2560183 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2560130 GAAACCTATG
*
2560140 AATGGTGATCAAG-TAATGAAAAT
1 AATGATGATC-AGTTAATGAAAAT
2560163 AATGATGATCAGTTAATGAAA
1 AATGATGATCAGTTAATGAAA
2560184 CTTGTTCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (23 bp):
AATGATGATCAGTTAATGAAAAT
Found at i:2560592 original size:21 final size:21
Alignment explanation
Indices: 2560511--2560606 Score: 70
Period size: 22 Copynumber: 4.5 Consensus size: 21
2560501 TCTCTTGATA
*
2560511 AGAATTTTTGAGTTCTCAAATG
1 AGAATCTTTGAGTT-TCAAATG
* *
2560533 AGAGTCTTTGAAGTTTGAATATG
1 AGAATCTTTG-AGTTTCAA-ATG
* * **
2560556 A-AGTCTTGGA-ACTCAAATG
1 AGAATCTTTGAGTTTCAAATG
*
2560575 AGAATCTTTGAGTTTCAAATA
1 AGAATCTTTGAGTTTCAAATG
*
2560596 AGAATATTTGA
1 AGAATCTTTGA
2560607 AGTGTGAAAC
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
19 4 0.07
20 10 0.18
21 17 0.30
22 18 0.32
23 8 0.14
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.36
Consensus pattern (21 bp):
AGAATCTTTGAGTTTCAAATG
Found at i:2560677 original size:42 final size:44
Alignment explanation
Indices: 2560631--2560732 Score: 129
Period size: 44 Copynumber: 2.4 Consensus size: 44
2560621 AAGTTTGTCA
* * *
2560631 GATGTGAATCTTCGAA-TTAGAATG-AAAAGTTTTAAAC-TTTTG
1 GATGTGAATCTTCAAAGTTAGAACGAAAAAG-CTTAAACTTTTTG
*
2560673 GATGTGAATCTTCAAAGTTCGAACGAAAAAGCTTAAACTTTTTG
1 GATGTGAATCTTCAAAGTTAGAACGAAAAAGCTTAAACTTTTTG
*
2560717 GATGTGAATCTCCAAA
1 GATGTGAATCTTCAAA
2560733 ATTCAAATGA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
42 15 0.29
43 12 0.23
44 25 0.48
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (44 bp):
GATGTGAATCTTCAAAGTTAGAACGAAAAAGCTTAAACTTTTTG
Done.