Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 13 of 187
Found at i:4708332 original size:24 final size:24
Alignment explanation
Indices: 4708300--4708354 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
4708290 TTTTTTCTCT
4708300 TATTTTCTCTCTTACCAAACACCA
1 TATTTTCTCTCTTACCAAACACCA
4708324 TATTTTCTCTCTTACCAAACACCA
1 TATTTTCTCTCTTACCAAACACCA
4708348 T-TTTTCT
1 TATTTTCT
4708355 TTTTCAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 6 0.19
24 25 0.81
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (24 bp):
TATTTTCTCTCTTACCAAACACCA
Found at i:4710216 original size:21 final size:19
Alignment explanation
Indices: 4710168--4710218 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
4710158 AATATCTCAA
4710168 CTAATTTAATAATAAAATT
1 CTAATTTAATAATAAAATT
* *
4710187 TTATTTTTAATATATAAAATT
1 CTA-ATTTAATA-ATAAAATT
4710208 CTAACTTTAAT
1 CTAA-TTTAAT
4710219 CATTTTAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.08
20 7 0.28
21 16 0.64
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (19 bp):
CTAATTTAATAATAAAATT
Found at i:4716748 original size:3 final size:3
Alignment explanation
Indices: 4716740--4716779 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
4716730 ACACAGGATA
4716740 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
4716780 ACAATTATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:4722756 original size:11 final size:10
Alignment explanation
Indices: 4722730--4722770 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
4722720 CATTCTAGGC
4722730 ATATTTTTTA
1 ATATTTTTTA
4722740 ATATTTTTTA
1 ATATTTTTTA
*
4722750 ATAATTTTTA
1 ATATTTTTTA
4722760 A-A-TTTTTA
1 ATATTTTTTA
4722768 ATA
1 ATA
4722771 AAATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 7 0.24
9 2 0.07
10 20 0.69
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
ATATTTTTTA
Found at i:4722779 original size:19 final size:18
Alignment explanation
Indices: 4722744--4722786 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
4722734 TTTTTAATAT
* *
4722744 TTTTTAATAATTTTTAAA
1 TTTTTAATAAATATTAAA
4722762 TTTTTAATAAAATATTAAA
1 TTTTTAAT-AAATATTAAA
*
4722781 ATTTTA
1 TTTTTA
4722787 CATTATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTTAATAAATATTAAA
Found at i:4722851 original size:19 final size:19
Alignment explanation
Indices: 4722806--4722851 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
4722796 TTTAAAATTT
*
4722806 AAAATATATAAAATCTAAA
1 AAAATATTTAAAATCTAAA
* *
4722825 AAAATATTTAAAATTTATA
1 AAAATATTTAAAATCTAAA
4722844 AAAATATT
1 AAAATATT
4722852 ATTTAACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATATTTAAAATCTAAA
Found at i:4724520 original size:6 final size:6
Alignment explanation
Indices: 4724509--4724535 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4724499 TGCCGAACCG
4724509 GTAACA GTAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTA
4724536 TTCGGCACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:4726919 original size:13 final size:11
Alignment explanation
Indices: 4726891--4726933 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
4726881 AGTTAAATAT
4726891 TATTTTATTAA
1 TATTTTATTAA
4726902 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
4726915 TA-TTTATTAT
1 TATTTTATTAA
4726925 TATTTTATT
1 TATTTTATT
4726934 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:4726920 original size:23 final size:23
Alignment explanation
Indices: 4726894--4726937 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4726884 TAAATATTAT
4726894 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
4726917 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
4726938 AAATGGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:4731203 original size:29 final size:31
Alignment explanation
Indices: 4731145--4731210 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
4731135 TGGACCAAAA
*
4731145 TTTTAAAATATGAAAAATAAAAAGATTAAAT
1 TTTTAAAATATGAAAAATAAAAAGACTAAAT
* *
4731176 TTTTAAAA-ATG-AAAATATATAGACTAAAT
1 TTTTAAAATATGAAAAATAAAAAGACTAAAT
*
4731205 TCTTAA
1 TTTTAA
4731211 TTTGTAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 20 0.65
30 3 0.10
31 8 0.26
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (31 bp):
TTTTAAAATATGAAAAATAAAAAGACTAAAT
Found at i:4731584 original size:7 final size:7
Alignment explanation
Indices: 4731504--4731587 Score: 82
Period size: 7 Copynumber: 11.9 Consensus size: 7
4731494 GGCATAATGA
4731504 TAATTTT
1 TAATTTT
4731511 T-ATTTT
1 TAATTTT
*
4731517 TAATATT
1 TAATTTT
*
4731524 TATTTTT
1 TAATTTT
*
4731531 TTATTTT
1 TAATTTT
4731538 T-ATCTTAT
1 TAAT-TT-T
**
4731546 TTCTTTT
1 TAATTTT
4731553 TAATTTTT
1 TAA-TTTT
4731561 TAATTTT
1 TAATTTT
4731568 TAATTTT
1 TAATTTT
4731575 TAATTTT
1 TAATTTT
4731582 TAATTT
1 TAATTT
4731588 AATTAAAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
6 8 0.12
7 44 0.69
8 11 0.17
9 1 0.02
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (7 bp):
TAATTTT
Found at i:4733262 original size:5 final size:5
Alignment explanation
Indices: 4733252--4733278 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
4733242 ACAATAAACT
4733252 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
4733279 GAAATATCAT
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:4740006 original size:21 final size:22
Alignment explanation
Indices: 4739958--4740011 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
4739948 CCTTTTGAAC
*
4739958 TATT-TTATTTATGTTCTTAAT
1 TATTATTATTTATATTCTTAAT
*
4739979 TA-TATTATTTATATT-TTATT
1 TATTATTATTTATATTCTTAAT
4739999 TATTATTAATTTA
1 TATTATT-ATTTA
4740012 GGGAATACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 7 0.25
21 16 0.57
22 5 0.18
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTATTTATATTCTTAAT
Found at i:4753060 original size:46 final size:46
Alignment explanation
Indices: 4752984--4753118 Score: 191
Period size: 46 Copynumber: 2.9 Consensus size: 46
4752974 TGCTATAACT
* * * *
4752984 CAGTATGATTTTCTTCACTGAAACATCATACCTACTTCTCACAACG
1 CAGTATGATTTTCTTTACTAAAATACCATACCTACTTCTCACAACG
* *
4753030 CAGTATGATTTTCTTTACTAAAATACCATACCTACTTTTCACAACT
1 CAGTATGATTTTCTTTACTAAAATACCATACCTACTTCTCACAACG
*
4753076 CAGTATGGTTTTCTTTACTAAAATACCATACCTACGTTC-CACA
1 CAGTATGATTTTCTTTACTAAAATACCATACCTAC-TTCTCACA
4753119 CTTTGCCATG
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
46 78 0.98
47 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (46 bp):
CAGTATGATTTTCTTTACTAAAATACCATACCTACTTCTCACAACG
Found at i:4774722 original size:24 final size:24
Alignment explanation
Indices: 4774695--4774746 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4774685 AATCAAAGTC
* *
4774695 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
4774719 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
4774743 AAAT
1 AAAT
4774747 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:4779140 original size:24 final size:24
Alignment explanation
Indices: 4779108--4779157 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
4779098 CTAATCAAAC
* * *
4779108 ATATTTTATGCTAATAAATGCTAA
1 ATATATTATACTAATAAATACTAA
*
4779132 ATATATTATACTCATAAATACTAA
1 ATATATTATACTAATAAATACTAA
4779156 AT
1 AT
4779158 CTTCTAGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (24 bp):
ATATATTATACTAATAAATACTAA
Found at i:4782252 original size:27 final size:27
Alignment explanation
Indices: 4782222--4782282 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
4782212 TATACATATA
4782222 TTAAGTATGATTAGTTTAGTTTCTTGT
1 TTAAGTATGATTAGTTTAGTTTCTTGT
4782249 TTAAGTATGATTAGTTTAGTTTCTTGT
1 TTAAGTATGATTAGTTTAGTTTCTTGT
4782276 TTAAGTA
1 TTAAGTA
4782283 AAAATGGTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.25, C:0.03, G:0.18, T:0.54
Consensus pattern (27 bp):
TTAAGTATGATTAGTTTAGTTTCTTGT
Found at i:4788255 original size:3 final size:3
Alignment explanation
Indices: 4788247--4788280 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
4788237 TTGCCCAGAT
4788247 TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
4788281 AACTCACGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:4790846 original size:3 final size:3
Alignment explanation
Indices: 4790840--4790883 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
4790830 GAATAAGACA
4790840 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
4790884 ATACTAGTAA
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:4812302 original size:2 final size:2
Alignment explanation
Indices: 4812295--4812333 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4812285 TTGTTACTTT
4812295 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
4812334 TTGTTTATTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4816979 original size:15 final size:15
Alignment explanation
Indices: 4816959--4816988 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4816949 TCCACCTATA
4816959 ATAGGCTACTATCAT
1 ATAGGCTACTATCAT
4816974 ATAGGCTACTATCAT
1 ATAGGCTACTATCAT
4816989 GTTACATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (15 bp):
ATAGGCTACTATCAT
Found at i:4828344 original size:34 final size:33
Alignment explanation
Indices: 4828303--4828371 Score: 111
Period size: 34 Copynumber: 2.1 Consensus size: 33
4828293 TCAACATTTA
*
4828303 AAAAACAAAACATTATCACAAAAGGTGAAAAACT
1 AAAAACAAAACATTATCACAAAAGGAG-AAAACT
*
4828337 AAAAACAAAACATTATCACAGAAGGAGAAAACT
1 AAAAACAAAACATTATCACAAAAGGAGAAAACT
4828370 AA
1 AA
4828372 TACTTACTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 8 0.24
34 25 0.76
ACGTcount: A:0.62, C:0.14, G:0.10, T:0.13
Consensus pattern (33 bp):
AAAAACAAAACATTATCACAAAAGGAGAAAACT
Found at i:4846003 original size:14 final size:14
Alignment explanation
Indices: 4845967--4846003 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4845957 TGCTACCATT
*
4845967 TTACTATTATGTTG
1 TTACTATTTTGTTG
4845981 TTACTATTTTGTTG
1 TTACTATTTTGTTG
*
4845995 TTATTATTT
1 TTACTATTT
4846004 GGATATTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.11, T:0.65
Consensus pattern (14 bp):
TTACTATTTTGTTG
Found at i:4846244 original size:12 final size:12
Alignment explanation
Indices: 4846214--4846246 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4846204 TATATATTTT
4846214 AAAATT-ATATA
1 AAAATTAATATA
4846225 AAAA-TAATATA
1 AAAATTAATATA
4846236 AAAATTAATAT
1 AAAATTAATAT
4846247 GGGTGAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:4851344 original size:25 final size:25
Alignment explanation
Indices: 4851310--4851360 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
4851300 TACTCTGTGA
4851310 GTAAGGCTTGATAGACATAGGAAGG
1 GTAAGGCTTGATAGACATAGGAAGG
4851335 GTAAGGCTTGATAGACATAGGAAGG
1 GTAAGGCTTGATAGACATAGGAAGG
4851360 G
1 G
4851361 ATTTCCAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.37, T:0.20
Consensus pattern (25 bp):
GTAAGGCTTGATAGACATAGGAAGG
Found at i:4851875 original size:15 final size:15
Alignment explanation
Indices: 4851855--4851885 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4851845 AAAAGACTTT
4851855 TTCCTTCTATTATTA
1 TTCCTTCTATTATTA
4851870 TTCCTTCTATTATTA
1 TTCCTTCTATTATTA
4851885 T
1 T
4851886 AATAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (15 bp):
TTCCTTCTATTATTA
Found at i:4853729 original size:19 final size:20
Alignment explanation
Indices: 4853705--4853752 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
4853695 ATTAATAAGC
*
4853705 AATACATAT-TTTATTATTA
1 AATACACATGTTTATTATTA
4853724 AATACACATGTTTATTATT-
1 AATACACATGTTTATTATTA
*
4853743 ATTACACATG
1 AATACACATG
4853753 AATTTACCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (20 bp):
AATACACATGTTTATTATTA
Found at i:4854953 original size:26 final size:25
Alignment explanation
Indices: 4854897--4854945 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
4854887 ATATCAAACC
4854897 TAAATACCAAATTGAGAAAAAAAAT
1 TAAATACCAAATTGAGAAAAAAAAT
*
4854922 TAAATACTAAATT-AGAAAAAAAAT
1 TAAATACCAAATTGAGAAAAAAAAT
4854946 ATCAAATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.22
Consensus pattern (25 bp):
TAAATACCAAATTGAGAAAAAAAAT
Found at i:4855596 original size:25 final size:26
Alignment explanation
Indices: 4855546--4855596 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
4855536 TATAACTTTT
* *
4855546 TTATTTACTAAAATATTATAAAAAAA
1 TTATTTACCAAAATAATATAAAAAAA
4855572 TTATTTACCAAAA-AATATAAAAAAA
1 TTATTTACCAAAATAATATAAAAAAA
4855597 CAAAAAGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (26 bp):
TTATTTACCAAAATAATATAAAAAAA
Found at i:4855665 original size:11 final size:11
Alignment explanation
Indices: 4855649--4855681 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
4855639 GGCCAACCAC
4855649 ATTGATAATTT
1 ATTGATAATTT
*
4855660 ATTGATAATAT
1 ATTGATAATTT
4855671 ATTGATAATTT
1 ATTGATAATTT
4855682 CCAAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (11 bp):
ATTGATAATTT
Found at i:4862841 original size:16 final size:17
Alignment explanation
Indices: 4862785--4862840 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 17
4862775 AAATATTTAT
4862785 TTTATTTTATGTAAATA
1 TTTATTTTATGTAAATA
* * *
4862802 TTT-GTTTATTTATAT-
1 TTTATTTTATGTAAATA
4862817 TTTATTTTATGTAAATA
1 TTTATTTTATGTAAATA
4862834 TTTATTT
1 TTTATTT
4862841 AATTGAATTC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 3 0.10
16 18 0.58
17 10 0.32
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (17 bp):
TTTATTTTATGTAAATA
Found at i:4865009 original size:20 final size:20
Alignment explanation
Indices: 4864983--4865031 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 20
4864973 AACAATGAAT
4864983 CTGTTCATCAAGAGATAAGA
1 CTGTTCATCAAGAGATAAGA
* *
4865003 TTGTTCA--AA-AGATACGA
1 CTGTTCATCAAGAGATAAGA
4865020 CTGTTCATCAAG
1 CTGTTCATCAAG
4865032 TGACAGAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 6
0.72 0.09 0.19
Matches are distributed among these distances:
17 13 0.57
18 2 0.09
19 2 0.09
20 6 0.26
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (20 bp):
CTGTTCATCAAGAGATAAGA
Found at i:4869217 original size:30 final size:30
Alignment explanation
Indices: 4869161--4869218 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
4869151 AAATTATAAA
*
4869161 ATTTTTAAAAGGTTAAAATATAATTTTATT
1 ATTTTTAAAAGGTTAAAAAATAATTTTATT
*
4869191 ATTTTT-AAAGGATTAAATAAATATTTTT
1 ATTTTTAAAAGG-TTAAA-AAATAATTTT
4869219 CCATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 11 0.46
31 8 0.33
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (30 bp):
ATTTTTAAAAGGTTAAAAAATAATTTTATT
Found at i:4869416 original size:11 final size:11
Alignment explanation
Indices: 4869402--4869427 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4869392 ATAAAAAAAC
4869402 AAAAAACCAAA
1 AAAAAACCAAA
4869413 AAAAAACCAAA
1 AAAAAACCAAA
4869424 AAAA
1 AAAA
4869428 GCTGTACCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAACCAAA
Found at i:4869729 original size:3 final size:3
Alignment explanation
Indices: 4869721--4869762 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
4869711 ATAGTTTTAG
4869721 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4869763 CTGTTGTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4870622 original size:18 final size:18
Alignment explanation
Indices: 4870599--4870636 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4870589 GGTTGGTGGT
4870599 GAAGAAGAAGGTGCTGGC
1 GAAGAAGAAGGTGCTGGC
*
4870617 GAAGAAGAAGGTGGTGGC
1 GAAGAAGAAGGTGCTGGC
4870635 GA
1 GA
4870637 TCATTGGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.08, G:0.47, T:0.11
Consensus pattern (18 bp):
GAAGAAGAAGGTGCTGGC
Found at i:4876215 original size:36 final size:36
Alignment explanation
Indices: 4876159--4876314 Score: 147
Period size: 38 Copynumber: 4.1 Consensus size: 36
4876149 TTTTTTTCCT
*
4876159 TCCTTCCCTCTTC-TTCTTC-TTTTTTTTTCTCTTC
1 TCCTTTCCTCTTCTTTCTTCTTTTTTTTTTCTCTTC
* *
4876193 TCCTTTCCTTTTCTTTCATTCTTTTTCTTTCTTTTTTCTTC
1 TCCTTTCCTCTTCTTTC-TTC--TTT-TTT-TTTTCTCTTC
*
4876234 TCCTTTCCTCTTCTTCTTCTTCATTTTTTTTTCTCTTC
1 TCCTTTCCTCTTC-T-TTCTTCTTTTTTTTTTCTCTTC
* *
4876272 TCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTT-TCCTC
1 TCCTTTCCTCTTCTTT-CTTCTTTTT-TTT-TTCTCTTC
4876310 TCCTT
1 TCCTT
4876315 CTTTCCCTTC
Statistics
Matches: 101, Mismatches: 9, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
34 11 0.11
35 3 0.03
36 5 0.05
37 9 0.09
38 33 0.33
39 7 0.07
40 5 0.05
41 21 0.21
42 4 0.04
43 3 0.03
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (36 bp):
TCCTTTCCTCTTCTTTCTTCTTTTTTTTTTCTCTTC
Found at i:4876257 original size:46 final size:42
Alignment explanation
Indices: 4876169--4876305 Score: 185
Period size: 38 Copynumber: 3.4 Consensus size: 42
4876159 TCCTTCCCTC
* *
4876169 TTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCA
1 TTCTTTTTCTTTCTTTTTCTCTTCTCCTTTCCTTTTCTTTCA
*
4876211 TTCTTTTTCTTTCTTTTT-TCTTCTCCTTTCCTCTTC-TTC-
1 TTCTTTTTCTTTCTTTTTCTCTTCTCCTTTCCTTTTCTTTCA
** *
4876250 TTCTTCAT-TTT-TTTTTCTCTTCTCCTTTCCTTTTCTTTCC
1 TTCTTTTTCTTTCTTTTTCTCTTCTCCTTTCCTTTTCTTTCA
4876290 TTCTTTTTCTTTCTTT
1 TTCTTTTTCTTTCTTT
4876306 CCTCTCCTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
37 5 0.06
38 20 0.24
39 9 0.11
40 9 0.11
41 20 0.24
42 19 0.23
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.70
Consensus pattern (42 bp):
TTCTTTTTCTTTCTTTTTCTCTTCTCCTTTCCTTTTCTTTCA
Found at i:4876280 original size:5 final size:5
Alignment explanation
Indices: 4876272--4876365 Score: 80
Period size: 5 Copynumber: 20.6 Consensus size: 5
4876262 TTTTCTCTTC
* * * *
4876272 TCCTT TCCTT TTCTT TCC-T TCTTT TTCTT T-CTT TCCTC TCC-T T-CTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
*
4876318 TCCCT TCCTT TCCTT TCCTT TCCTT T-CTT T-CTT T-CTT T-CTT T-CTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
4876363 TCC
1 TCC
4876366 CTCTCATTCT
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
3 1 0.01
4 30 0.40
5 44 0.59
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (5 bp):
TCCTT
Found at i:4876289 original size:10 final size:9
Alignment explanation
Indices: 4876274--4876365 Score: 74
Period size: 8 Copynumber: 10.7 Consensus size: 9
4876264 TTCTCTTCTC
4876274 CTTTCCTTTT
1 CTTTCC-TTT
4876284 CTTTCC-TT
1 CTTTCCTTT
4876292 C-TT--TTT
1 CTTTCCTTT
4876298 CTTT-CTTT
1 CTTTCCTTT
*
4876306 CCTCTCC-TT
1 -CTTTCCTTT
*
4876315 CTTTCCCTTC
1 CTTT-CCTTT
4876325 CTTTCCTTT
1 CTTTCCTTT
4876334 CCTTTCCTTT
1 -CTTTCCTTT
4876344 CTTT-CTTT
1 CTTTCCTTT
4876352 CTTT-CTTT
1 CTTTCCTTT
4876360 CTTTCC
1 CTTTCC
4876366 CTCTCATTCT
Statistics
Matches: 69, Mismatches: 4, Indels: 19
0.75 0.04 0.21
Matches are distributed among these distances:
6 3 0.04
7 4 0.06
8 25 0.36
9 16 0.23
10 21 0.30
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (9 bp):
CTTTCCTTT
Found at i:4876319 original size:79 final size:77
Alignment explanation
Indices: 4876155--4876324 Score: 261
Period size: 79 Copynumber: 2.2 Consensus size: 77
4876145 TTTCTTTTTT
*
4876155 TCCTTCCTTCCC-TCTTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCATTCTTTTT
1 TCCTTCTTTCCCTTCTTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCATTCTTTTT
**
4876219 CTTTCTTTTTTC
66 CTTTCTTTCCTC
* * *
4876231 TTCTCCTTTCCTCTTCTTCTTCTTCATTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTT
1 TCCTTCTTTCC-CTTCTTCTTCTTC-TTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCATTCTTT
4876296 TTCTTTCTTTCCTC
64 TTCTTTCTTTCCTC
4876310 TCCTTCTTTCCCTTC
1 TCCTTCTTTCCCTTC
4876325 CTTTCCTTTC
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
76 8 0.10
77 1 0.01
78 15 0.18
79 59 0.71
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (77 bp):
TCCTTCTTTCCCTTCTTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCATTCTTTTT
CTTTCTTTCCTC
Found at i:4876335 original size:15 final size:14
Alignment explanation
Indices: 4876298--4876367 Score: 63
Period size: 14 Copynumber: 4.9 Consensus size: 14
4876288 CCTTCTTTTT
4876298 CTTTCTTT-CCTCTC
1 CTTTCTTTCCCT-TC
4876312 C-TTCTTTCCCTTC
1 CTTTCTTTCCCTTC
*
4876325 CTTTCCTTTCCTTTC
1 CTTT-CTTTCCCTTC
* *
4876340 CTTTCTTTCTTTCTTT
1 CTTTCTTTC--CCTTC
4876356 CTTTCTTTCCCT
1 CTTTCTTTCCCT
4876368 CTCATTCTCC
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
13 9 0.20
14 13 0.28
15 13 0.28
16 11 0.24
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (14 bp):
CTTTCTTTCCCTTC
Found at i:4880016 original size:24 final size:23
Alignment explanation
Indices: 4879975--4880022 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
4879965 TATGTTATCT
4879975 GTACTTTTATTTTTAAAAATTTA
1 GTACTTTTATTTTTAAAAATTTA
4879998 GTACTTTTATTTTTAAAAATTTA
1 GTACTTTTATTTTTAAAAATTTA
4880021 GT
1 GT
4880023 CTAATTGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.56
Consensus pattern (23 bp):
GTACTTTTATTTTTAAAAATTTA
Found at i:4880112 original size:17 final size:17
Alignment explanation
Indices: 4880090--4880123 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4880080 CCAAAAATAA
*
4880090 AAGTAAGTAGATTAAAT
1 AAGTAAATAGATTAAAT
4880107 AAGTAAATAGATTAAAT
1 AAGTAAATAGATTAAAT
4880124 TTAAGGGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (17 bp):
AAGTAAATAGATTAAAT
Found at i:4880599 original size:34 final size:35
Alignment explanation
Indices: 4880545--4880611 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
4880535 CAAACAACAG
* *
4880545 AAAATATTTTCTAGTAAATCATTTCACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTCACAGAAAAGT
* *
4880580 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTCACAGAAAA
4880612 CATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTCACAGAAAAGT
Found at i:4880603 original size:14 final size:14
Alignment explanation
Indices: 4880580--4880619 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
4880570 ACAGAAAAGT
*
4880580 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
4880594 AAATCATTTTACGG
1 AAAACATTTTACAG
4880608 AAAACATTTTAC
1 AAAACATTTTAC
4880620 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:4888606 original size:4 final size:4
Alignment explanation
Indices: 4888597--4888623 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4888587 TTATAGAGTT
4888597 TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTT
4888624 TTGTGTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (4 bp):
TTTG
Found at i:4894312 original size:28 final size:29
Alignment explanation
Indices: 4894280--4894341 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 29
4894270 TGCCTTTGCA
4894280 TTAGTTTTTGTCAAGAGATGTTAAGAAG-
1 TTAGTTTTTGTCAAGAGATGTTAAGAAGC
4894308 TTAGTTTTTGTCAAGAGATGTTAAGAAGC
1 TTAGTTTTTGTCAAGAGATGTTAAGAAGC
4894337 TTAGT
1 TTAGT
4894342 AATAGTTGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 28 0.85
29 5 0.15
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (29 bp):
TTAGTTTTTGTCAAGAGATGTTAAGAAGC
Found at i:4914673 original size:26 final size:26
Alignment explanation
Indices: 4914637--4914688 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
4914627 GTAAATAGAT
4914637 CAACTAGGATTTAATTTCATTTATTA
1 CAACTAGGATTTAATTTCATTTATTA
*
4914663 CAACTTGGATTTAATTTCATTTATTA
1 CAACTAGGATTTAATTTCATTTATTA
4914689 ACAAGTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48
Consensus pattern (26 bp):
CAACTAGGATTTAATTTCATTTATTA
Found at i:4915691 original size:150 final size:150
Alignment explanation
Indices: 4915128--4915984 Score: 1227
Period size: 150 Copynumber: 5.7 Consensus size: 150
4915118 CACATTTTGT
* *
4915128 AATCATAAATTCCCAAGATTTTGAAATTCATGTTTTTCTATACATTTCAAATACATAATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATAATCAAAGT
* * * * *
4915193 TCAACCTTAACTAATTTGTC-TTTTCATAGCTCATAGTTAATATAACAAATAAAAAATCCAAATT
66 TCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAATT
* * *
4915257 CAGCTTTTCATAGCTTACAA
131 CAGCTTCTCATACCTTATAA
* * **
4915277 AATCATAAATTCTTAAGATTTTGAAATTTATGTTTTTCTTAATACATTTCAAATACATAATCAGC
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTT-TT-ATACATTTCAAATACATAATCAAA
* * * *
4915342 GTTCAACCTTAACTAATTTGGCCTTTTCATAGCTCAAAATTAATAAAAGAAATGAAAAATCCAAA
64 GTTCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAA
* *
4915407 TTCAGCTTTTCATAGCTTATAA
129 TTCAGCTTCTCATACCTTATAA
* * *
4915429 AATCATAAATTCCTAAGATTTTGAAATTCTTGTTTTCTTATACATTTCAAATACATGATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATAATCAAAGT
* *
4915494 TCAACCTTAACCAATTTGGCTTTTTCA-AGCTCAAAATCAATATAACAAATGAAATATCCAAATT
66 TCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAATT
* *
4915558 AAACTTCTCATACCTTATAA
131 CAGCTTCTCATACCTTATAA
* *
4915578 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTAATATATTTCAAATACATAGTCAAAG
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTT-ATACATTTCAAATACATAATCAAAG
* * * *
4915643 TTCAACCTTGAGTAATTTGGCTTTTTCA-AGCTCAAAATCAATATAACAAGTGAAATATCCAAAT
65 TTCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAAT
*
4915707 TTAGCTTCTCATACCTTATAA
130 TCAGCTTCTCATACCTTATAA
* *
4915728 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTTAATATATTTCAAATACATAGTCAAA
1 AATCATAAATTCCTAAGATTTTGAAATTCATG-TTTTTTT-ATACATTTCAAATACATAATCAAA
* *
4915793 GTTCAACCTCAACTAATTTGGCTTTTTCA-AGCTCAAAATCAATATAACAAATGAAAAATCTAAA
64 GTTCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAA
*
4915857 TTTAGCTTCTCATACCTTATAA
129 TTCAGCTTCTCATACCTTATAA
* * * * *
4915879 AATCCTAAATTCCTAAGATTTTGACATTCATGTTTTCTTATACAATTCAAATACAGAATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATAATCAAAGT
*
4915944 TCAACCTTAACTAAATTTGGCTTTTTCAGAGCTCAAAATCA
66 TCAACCTTAACT-AATTTGGCTTTTTCATAGCTCAAAATCA
4915985 TAAATCTCAA
Statistics
Matches: 646, Mismatches: 55, Indels: 12
0.91 0.08 0.02
Matches are distributed among these distances:
149 153 0.24
150 203 0.31
151 199 0.31
152 91 0.14
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (150 bp):
AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATAATCAAAGT
TCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAATT
CAGCTTCTCATACCTTATAA
Found at i:4915779 original size:301 final size:299
Alignment explanation
Indices: 4915128--4915988 Score: 1235
Period size: 301 Copynumber: 2.9 Consensus size: 299
4915118 CACATTTTGT
* *
4915128 AATCATAAATTCCCAAGATTTTGAAATTCATGTTTTTCTATACATTTCAAATACATAATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACAT-ATCAAAGT
* * * * *
4915193 TCAACCTTAACTAATTTGTC-TTTTCATAGCTCATAGTTAATATAACAAATAAAAAATCCAAATT
65 TCAACCTTAACTAATTTGGCTTTTTCA-AGCTCAAAATCAATATAACAAATGAAAAATCCAAATT
* * * * * *
4915257 CAGCTTTTCATAGCTTACAAAATCATAAATTCTTAAGATTTTGAAATTTATGTTTTTCTTAATAC
129 AAGCTTCTCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTTT-TTAATAC
** * * *
4915322 ATTTCAAATACATAATCAGCGTTCAACCTTAACTAATTTGGCCTTTTCATAGCTCAAAATTAATA
193 ATTTCAAATACATAATCAAAGTTCAACCTTAACTAATTTGGCTTTTTCAGAGCTCAAAATCAATA
* * *
4915387 AAAGAAATGAAAAATCCAAATTCAGCTTTTCATAGCTTATAA
258 AAACAAATGAAAAATCCAAATTCAGCTTCTCATACCTTATAA
* *
4915429 AATCATAAATTCCTAAGATTTTGAAATTCTTGTTTTCTTATACATTTCAAATACATGATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACAT-ATCAAAGT
* *
4915494 TCAACCTTAACCAATTTGGCTTTTTCAAGCTCAAAATCAATATAACAAATGAAATATCCAAATTA
65 TCAACCTTAACTAATTTGGCTTTTTCAAGCTCAAAATCAATATAACAAATGAAAAATCCAAATTA
* *
4915559 AACTTCTCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTAATATAT
130 AGCTTCTCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTAATACAT
* * * *
4915624 TTCAAATACATAGTCAAAGTTCAACCTTGAGTAATTTGGCTTTTTCA-AGCTCAAAATCAATATA
195 TTCAAATACATAATCAAAGTTCAACCTTAACTAATTTGGCTTTTTCAGAGCTCAAAATCAATAAA
* * *
4915688 ACAAGTGAAATATCCAAATTTAGCTTCTCATACCTTATAA
260 ACAAATGAAAAATCCAAATTCAGCTTCTCATACCTTATAA
*
4915728 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTTAATATATTTCAAATACATAGTCAAA
1 AATCATAAATTCCTAAGATTTTGAAATTCATG-TTTTTTT-ATACATTTCAAATACATA-TCAAA
* *
4915793 GTTCAACCTCAACTAATTTGGCTTTTTCAAGCTCAAAATCAATATAACAAATGAAAAATCTAAAT
63 GTTCAACCTTAACTAATTTGGCTTTTTCAAGCTCAAAATCAATATAACAAATGAAAAATCCAAAT
* * * *
4915858 TTAGCTTCTCATACCTTATAAAATCCTAAATTCCTAAGATTTTGACATTCATGTTTTCTT-ATAC
128 TAAGCTTCTCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTAATAC
* *
4915922 AATTCAAATACAGAATCAAAGTTCAACCTTAACTAAATTTGGCTTTTTCAGAGCTCAAAATC-AT
193 ATTTCAAATACATAATCAAAGTTCAACCTTAACT-AATTTGGCTTTTTCAGAGCTCAAAATCAAT
4915986 AAA
257 AAA
4915989 TCTCAAAATT
Statistics
Matches: 501, Mismatches: 53, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
299 80 0.16
300 88 0.18
301 316 0.63
302 17 0.03
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (299 bp):
AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATATCAAAGTT
CAACCTTAACTAATTTGGCTTTTTCAAGCTCAAAATCAATATAACAAATGAAAAATCCAAATTAA
GCTTCTCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTAATACATT
TCAAATACATAATCAAAGTTCAACCTTAACTAATTTGGCTTTTTCAGAGCTCAAAATCAATAAAA
CAAATGAAAAATCCAAATTCAGCTTCTCATACCTTATAA
Found at i:4916022 original size:109 final size:107
Alignment explanation
Indices: 4915885--4916089 Score: 286
Period size: 109 Copynumber: 1.9 Consensus size: 107
4915875 ATAAAATCCT
* * *
4915885 AAATTCCTAAGATTTTGACATTCATGTTTTCTTATACAATTC-AAATACAGAATCAAAGTTCAAC
1 AAATTCCTAAGATTTCGAAATTCATGTTTTCTAATACAATTCAAAATACAGAATCAAAGTTCAAC
4915949 CTTAACTAAATTTGGCTTTTTCAGAGCTCAAAATCATAAATCTCA
66 CTTAAC-AAATTT-GC-TTTTCAGAGCTCAAAATCATAAATCTCA
* ** * * *
4915994 AAATTCCTAAGCTTTCGAAATTTGTGTTTTCTAATACATTTCAAAATTCATAATCAAAGTTCAAC
1 AAATTCCTAAGATTTCGAAATTCATGTTTTCTAATACAATTCAAAATACAGAATCAAAGTTCAAC
*
4916059 CTTAACAAATTTGCTTTTCATAGCTCAAAAT
66 CTTAACAAATTTGCTTTTCAGAGCTCAAAAT
4916090 TAATATAACA
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 16 0.19
108 2 0.02
109 41 0.48
110 26 0.31
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (107 bp):
AAATTCCTAAGATTTCGAAATTCATGTTTTCTAATACAATTCAAAATACAGAATCAAAGTTCAAC
CTTAACAAATTTGCTTTTCAGAGCTCAAAATCATAAATCTCA
Found at i:4920749 original size:21 final size:21
Alignment explanation
Indices: 4920683--4920750 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
4920673 CAATGAAGCA
* * *
4920683 CATAAGTGCTACACAGAAACC
1 CATAAGAGCTAAACGGAAACC
* * * * *
4920704 CGTAAGGGTTAAACGGAAGCT
1 CATAAGAGCTAAACGGAAACC
4920725 CATAAGAGCTAAACGGAAACC
1 CATAAGAGCTAAACGGAAACC
4920746 CATAA
1 CATAA
4920751 AGGTTAATTT
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.15
Consensus pattern (21 bp):
CATAAGAGCTAAACGGAAACC
Found at i:4920765 original size:42 final size:42
Alignment explanation
Indices: 4920676--4920854 Score: 133
Period size: 42 Copynumber: 4.3 Consensus size: 42
4920666 AATGCTGCAA
* * * * *
4920676 TGAAGCACATAAGTGCTACACAGAAACCCGTAAGGGTTAAAC
1 TGAAGCTCATAAGAGCTAAACAGAAACCCATAAAGGTTAAAC
* * **
4920718 GGAAGCTCATAAGAGCTAAACGGAAACCCATAAAGGTTAATT
1 TGAAGCTCATAAGAGCTAAACAGAAACCCATAAAGGTTAAAC
* * ** * * *
4920760 TGAAGCTCAAAATAGCTAAATTGAAACCCATTAGGGTAAAAC
1 TGAAGCTCATAAGAGCTAAACAGAAACCCATAAAGGTTAAAC
* * * * * * * *
4920802 TAAAGCTCAAAATAGTTGAACTGAAACCCAGAAGGGTTAAAC
1 TGAAGCTCATAAGAGCTAAACAGAAACCCATAAAGGTTAAAC
*
4920844 TGAAACTCATA
1 TGAAGCTCATA
4920855 TGAGTTGACT
Statistics
Matches: 108, Mismatches: 29, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 108 1.00
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.20
Consensus pattern (42 bp):
TGAAGCTCATAAGAGCTAAACAGAAACCCATAAAGGTTAAAC
Found at i:4920861 original size:42 final size:41
Alignment explanation
Indices: 4920762--4920867 Score: 99
Period size: 42 Copynumber: 2.5 Consensus size: 41
4920752 GGTTAATTTG
** * **
4920762 AAGCTCAAAATAGCTAAATTGAAACCCATTAGGGTAAAACTA
1 AAGCTCAAAATAG-TTGACTGAAACCCAGAAGGGTAAAACTA
*
4920804 AAGCTCAAAATAGTTGAACTGAAACCCAGAAGGGTTAAACTGA
1 AAGCTCAAAATAGTTG-ACTGAAACCCAGAAGGGTAAAACT-A
*
4920847 AA-CTC-ATATGAGTTGACTGAA
1 AAGCTCAAAAT-AGTTGACTGAA
4920868 GCTCACAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
41 10 0.19
42 41 0.76
43 3 0.06
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.22
Consensus pattern (41 bp):
AAGCTCAAAATAGTTGACTGAAACCCAGAAGGGTAAAACTA
Found at i:4932417 original size:16 final size:16
Alignment explanation
Indices: 4932383--4932417 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4932373 AATTTTCATG
*
4932383 TATTTTTATAATATCT
1 TATTTTTATAAAATCT
*
4932399 TATTTTTATAAAATTT
1 TATTTTTATAAAATCT
4932415 TAT
1 TAT
4932418 AATATATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTTTATAAAATCT
Found at i:4936131 original size:6 final size:6
Alignment explanation
Indices: 4936099--4936149 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
4936089 AGGGGTTACG
* * * * *
4936099 GGTTCG GGTT-T GGGTCT GGTACT GGTTCA GGTTCT GGTTCT GGTTAT
1 GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT
4936146 GGTT
1 GGTT
4936150 ATGGGAGTGG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
5 3 0.08
6 33 0.92
ACGTcount: A:0.06, C:0.12, G:0.39, T:0.43
Consensus pattern (6 bp):
GGTTCT
Found at i:4936231 original size:18 final size:18
Alignment explanation
Indices: 4936181--4936232 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
4936171 GTGGTGGATA
* *
4936181 TGGTGCTGGAAGTGGAAC
1 TGGTGGTGGAAGTGGTAC
* ** *
4936199 CGGTGGTGGTGGTGGTTC
1 TGGTGGTGGAAGTGGTAC
4936217 TGGTGGTGGAAGTGGT
1 TGGTGGTGGAAGTGGT
4936233 GGTGGTGGTT
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.12, C:0.08, G:0.52, T:0.29
Consensus pattern (18 bp):
TGGTGGTGGAAGTGGTAC
Found at i:4936729 original size:24 final size:24
Alignment explanation
Indices: 4936697--4936744 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
4936687 TTAATTGAAA
4936697 CAATTAATTCTGACGGTGTATAAT
1 CAATTAATTCTGACGGTGTATAAT
4936721 CAATTAATTCTGACGGTGTATAAT
1 CAATTAATTCTGACGGTGTATAAT
4936745 GTGATGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (24 bp):
CAATTAATTCTGACGGTGTATAAT
Found at i:4938560 original size:16 final size:16
Alignment explanation
Indices: 4938521--4938561 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
4938511 TTTGGGTCGA
4938521 ATCATTTTAAGTTTTG
1 ATCATTTTAAGTTTTG
*
4938537 ATCGTTTTAAGTTTGTG
1 ATCATTTTAAGTTT-TG
4938554 -TCATTTTA
1 ATCATTTTA
4938562 GGTTATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (16 bp):
ATCATTTTAAGTTTTG
Found at i:4958336 original size:21 final size:20
Alignment explanation
Indices: 4958298--4958336 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
4958288 TCAATCAGCA
*
4958298 AAATGGGATGAGGTAAAAAC
1 AAATGGGATGAGGAAAAAAC
*
4958318 AAATGAGGATGATGAAAAA
1 AAATG-GGATGAGGAAAAA
4958337 TGCATCAACG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.54, C:0.03, G:0.28, T:0.15
Consensus pattern (20 bp):
AAATGGGATGAGGAAAAAAC
Found at i:4962986 original size:17 final size:18
Alignment explanation
Indices: 4962964--4962997 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
4962954 AATCCATACA
4962964 AACTCAATCATT-TCATC
1 AACTCAATCATTATCATC
4962981 AACTCAATCATTATCAT
1 AACTCAATCATTATCAT
4962998 TTCTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.38, C:0.26, G:0.00, T:0.35
Consensus pattern (18 bp):
AACTCAATCATTATCATC
Found at i:4973288 original size:23 final size:23
Alignment explanation
Indices: 4973240--4973289 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
4973230 TATTTATATC
* * *
4973240 ATATAAGAATTAAACATATAATA
1 ATATAAGAAATAAAAATATAAAA
4973263 ATATAA-AAATAAAAATATTAAAA
1 ATATAAGAAATAAAAATA-TAAAA
4973286 ATAT
1 ATAT
4973290 TTACTCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
ATATAAGAAATAAAAATATAAAA
Found at i:4976308 original size:17 final size:17
Alignment explanation
Indices: 4976282--4976322 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4976272 AAAACCAAAT
*
4976282 CAGTTTATTAGAAATAA
1 CAGTTCATTAGAAATAA
*
4976299 CAGTTCATTAGACATAA
1 CAGTTCATTAGAAATAA
*
4976316 CAATTCA
1 CAGTTCA
4976323 CACACACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (17 bp):
CAGTTCATTAGAAATAA
Found at i:4982001 original size:42 final size:42
Alignment explanation
Indices: 4981893--4982099 Score: 315
Period size: 42 Copynumber: 4.9 Consensus size: 42
4981883 GTTTACAAAC
4981893 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG-AA
* * * *
4981936 AAAAACGACTCTAAAGACCATGTTTTTTAGCGGCGCTTAGGA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* * * *
4981978 AAAAACACCGCTAAAAACAATGTTCTTTAGCGGTGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
4982020 AAAAACGCCGCTAAAGACCATGTACTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
4982062 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT
4982100 TTATACAAAA
Statistics
Matches: 145, Mismatches: 19, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
42 108 0.74
43 37 0.26
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:4982445 original size:21 final size:21
Alignment explanation
Indices: 4982418--4982467 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
4982408 TTTTGGCCTG
* *
4982418 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
4982439 TTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
4982460 CTCTGCTT
1 CTCTGCTT
4982468 TAAGTTGTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.02, C:0.42, G:0.18, T:0.38
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:4985000 original size:18 final size:17
Alignment explanation
Indices: 4984967--4985005 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
4984957 TTTTATAAAT
4984967 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
4984985 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
4985002 TGTG
1 TGTG
4985006 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:4985258 original size:23 final size:23
Alignment explanation
Indices: 4985231--4985306 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
4985221 AGTGTTATTG
*
4985231 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
4985254 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
4985277 AACAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
4985300 ATTAGTG
1 ATCAGTG
4985307 TTGCACTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:4990681 original size:7 final size:7
Alignment explanation
Indices: 4990671--4990716 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
4990661 TGATATATTT
4990671 TTATGTA
1 TTATGTA
4990678 TTATGTAA
1 TTATGT-A
4990686 GTTATGTAA
1 -TTATGT-A
4990695 GTTATGTA
1 -TTATGTA
4990703 TTATGTA
1 TTATGTA
4990710 TTATGTA
1 TTATGTA
4990717 AGTACTGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 20 0.54
8 2 0.05
9 15 0.41
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.52
Consensus pattern (7 bp):
TTATGTA
Found at i:4990692 original size:9 final size:9
Alignment explanation
Indices: 4990678--4991633 Score: 943
Period size: 9 Copynumber: 107.2 Consensus size: 9
4990668 TTTTTATGTA
4990678 TTATGTAAG
1 TTATGTAAG
4990687 TTATGTAAG
1 TTATGTAAG
4990696 TTATGT-A-
1 TTATGTAAG
4990703 TTATGT-A-
1 TTATGTAAG
4990710 TTATGTAAG
1 TTATGTAAG
4990719 -TACTGTAAG
1 TTA-TGTAAG
*
4990728 TAATGTAAG
1 TTATGTAAG
4990737 TTATGTAAG
1 TTATGTAAG
* * *
4990746 -AAAGTTA-
1 TTATGTAAG
4990753 TTATGTAAG
1 TTATGTAAG
*
4990762 TTGTGTATA-
1 TTATGTA-AG
*
4990771 ATAT-TAA-
1 TTATGTAAG
*
4990778 TTATGTGAG
1 TTATGTAAG
**
4990787 TCGTGT-A-
1 TTATGTAAG
*
4990794 TAATGTAAG
1 TTATGTAAG
*
4990803 TTAAG-AAGG
1 TTATGTAA-G
4990812 TTATGT-A-
1 TTATGTAAG
*
4990819 TAATGTAAG
1 TTATGTAAG
4990828 TTATGTAAG
1 TTATGTAAG
* * *
4990837 TAATTTAAT
1 TTATGTAAG
4990846 TTATGTAAG
1 TTATGTAAG
4990855 TTATGTAAG
1 TTATGTAAG
* *
4990864 TTATTTAAT
1 TTATGTAAG
*
4990873 TTATGCAAG
1 TTATGTAAG
4990882 TTATGTAAG
1 TTATGTAAG
4990891 TTATGTAAG
1 TTATGTAAG
*
4990900 TTATTTAAG
1 TTATGTAAG
* *
4990909 TTATTTAAT
1 TTATGTAAG
4990918 TTATGTAAG
1 TTATGTAAG
* **
4990927 TTATTTATT
1 TTATGTAAG
4990936 TTATGTAAG
1 TTATGTAAG
4990945 TTATGTAAG
1 TTATGTAAG
* *
4990954 TTATTTAAT
1 TTATGTAAG
*
4990963 TTATGTAGG
1 TTATGTAAG
4990972 TTATGTAAG
1 TTATGTAAG
*
4990981 TTATGTAGG
1 TTATGTAAG
* *
4990990 TTATTTAAT
1 TTATGTAAG
* *
4990999 TTGTGTAGG
1 TTATGTAAG
4991008 TTATGTAAG
1 TTATGTAAG
4991017 TTATGTAAG
1 TTATGTAAG
* *
4991026 TTATTTAAT
1 TTATGTAAG
4991035 TTATGTAAG
1 TTATGTAAG
*
4991044 TTACGTAAG
1 TTATGTAAG
* *
4991053 TTATTTAAT
1 TTATGTAAG
*
4991062 TTATGTAGG
1 TTATGTAAG
4991071 TTATGTAAG
1 TTATGTAAG
4991080 TTATGTAAG
1 TTATGTAAG
* *
4991089 TTATTTAAT
1 TTATGTAAG
*
4991098 TTATGTAGG
1 TTATGTAAG
4991107 TTATGTAAG
1 TTATGTAAG
* * *
4991116 TCCATGGAAT
1 T-TATGTAAG
4991126 TTATGTAAG
1 TTATGTAAG
4991135 TTATGTAAG
1 TTATGTAAG
4991144 TTATGTAAG
1 TTATGTAAG
* *
4991153 TTATTTAAT
1 TTATGTAAG
4991162 TTATGTAAG
1 TTATGTAAG
4991171 TTATGTAAG
1 TTATGTAAG
* *
4991180 TTATTTAAT
1 TTATGTAAG
*
4991189 TTATGTTAG
1 TTATGTAAG
4991198 TTATGTAAG
1 TTATGTAAG
* *
4991207 TTATTTAAT
1 TTATGTAAG
*
4991216 TTATGTAGG
1 TTATGTAAG
4991225 TTATGTAAG
1 TTATGTAAG
4991234 TTATGTAAG
1 TTATGTAAG
* *
4991243 TTATTTAAT
1 TTATGTAAG
4991252 TTATGTAAG
1 TTATGTAAG
* *
4991261 TTATTTAAT
1 TTATGTAAG
4991270 TTATGTAAG
1 TTATGTAAG
4991279 TTATGTAAG
1 TTATGTAAG
4991288 TTATGTAAG
1 TTATGTAAG
* *
4991297 TTATTTAAT
1 TTATGTAAG
* *
4991306 TTGTGTAGG
1 TTATGTAAG
4991315 TTATGTAAG
1 TTATGTAAG
4991324 TTATGTAAG
1 TTATGTAAG
* *
4991333 TTATTTAAT
1 TTATGTAAG
4991342 TTATGTAAG
1 TTATGTAAG
*
4991351 TTACGTAAG
1 TTATGTAAG
* **
4991360 TTATTTACT
1 TTATGTAAG
*
4991369 TTATGTAGG
1 TTATGTAAG
4991378 TTATGTAAG
1 TTATGTAAG
4991387 TTATGTAAG
1 TTATGTAAG
* *
4991396 TTATTTAAT
1 TTATGTAAG
*
4991405 TTATGTAGG
1 TTATGTAAG
4991414 TTATGTAAG
1 TTATGTAAG
* * * *
4991423 TCCACGGAAT
1 T-TATGTAAG
4991433 TTATGTAAG
1 TTATGTAAG
4991442 TTATGTAAG
1 TTATGTAAG
4991451 TTATGTAAG
1 TTATGTAAG
* *
4991460 TTATTTAAT
1 TTATGTAAG
4991469 TTATGTAAG
1 TTATGTAAG
4991478 TTATGTAAG
1 TTATGTAAG
* *
4991487 TTATTTAAT
1 TTATGTAAG
*
4991496 TTATGTTAG
1 TTATGTAAG
4991505 TTATGTAAG
1 TTATGTAAG
* *
4991514 TTATTTAAT
1 TTATGTAAG
*
4991523 TTATGTAGG
1 TTATGTAAG
4991532 TTATGTAAG
1 TTATGTAAG
4991541 TTATGTAAG
1 TTATGTAAG
* *
4991550 TTATTTAAT
1 TTATGTAAG
*
4991559 TTATGCAAG
1 TTATGTAAG
4991568 TTTATGTAAG
1 -TTATGTAAG
4991578 TTATGTAAG
1 TTATGTAAG
* *
4991587 TTATTTAAT
1 TTATGTAAG
4991596 TTATGTAAG
1 TTATGTAAG
4991605 TTATGTAAG
1 TTATGTAAG
* *
4991614 TTATTTAAT
1 TTATGTAAG
*
4991623 TTATGTCAG
1 TTATGTAAG
4991632 TT
1 TT
4991634 TCTATATATG
Statistics
Matches: 755, Mismatches: 174, Indels: 36
0.78 0.18 0.04
Matches are distributed among these distances:
7 26 0.03
8 21 0.03
9 687 0.91
10 21 0.03
ACGTcount: A:0.32, C:0.01, G:0.18, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:4991758 original size:8 final size:7
Alignment explanation
Indices: 4991740--4991785 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
4991730 ATAATATAAG
4991740 TTATGTA
1 TTATGTA
4991747 TTATGTTA
1 TTATG-TA
4991755 TTATGTA
1 TTATGTA
4991762 TTATGTA
1 TTATGTA
*
4991769 --ATTTA
1 TTATGTA
4991774 TTATGTTA
1 TTATG-TA
4991782 TTAT
1 TTAT
4991786 ATATACGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 4 0.12
7 16 0.48
8 13 0.39
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (7 bp):
TTATGTA
Found at i:4991758 original size:27 final size:26
Alignment explanation
Indices: 4991727--4991800 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 26
4991717 GTTATGCAAG
4991727 ATTATAATATAAGTTATGTATTATGTT
1 ATTAT-ATATAAGTTATGTATTATGTT
* * * *
4991754 ATTATGTATTATGTAATTTATTATGTT
1 ATTATATA-TAAGTTATGTATTATGTT
*
4991781 ATTATATATACGTTATGTAT
1 ATTATATATAAGTTATGTAT
4991801 GCTGTAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
26 11 0.29
27 27 0.71
ACGTcount: A:0.34, C:0.01, G:0.11, T:0.54
Consensus pattern (26 bp):
ATTATATATAAGTTATGTATTATGTT
Found at i:4991760 original size:15 final size:15
Alignment explanation
Indices: 4991740--4991785 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
4991730 ATAATATAAG
4991740 TTATGTATTATGTTA
1 TTATGTATTATGTTA
4991755 TTATGTATTATG-TA
1 TTATGTATTATGTTA
*
4991769 --ATTTATTATGTTA
1 TTATGTATTATGTTA
4991782 TTAT
1 TTAT
4991786 ATATACGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
14 2 0.07
15 14 0.52
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (15 bp):
TTATGTATTATGTTA
Found at i:4992013 original size:61 final size:61
Alignment explanation
Indices: 4991922--4992069 Score: 176
Period size: 61 Copynumber: 2.4 Consensus size: 61
4991912 AAAAAATAAT
* * * *
4991922 AATTATTTACAAAACGTGTAAAATTGATACTTA-TAAA-TTTTATTAATAATAAATCTAGAAC
1 AATTATTTACAAAACTTATAAATTTAATAC-TACTAAATTTTTA-TAATAATAAATCTAGAAC
* * * *
4991983 ACATT-TTTAGAAAACTTATAAATTTAATACTACTAAATTTTTATACTAATAAATTTAGAAT
1 A-ATTATTTACAAAACTTATAAATTTAATACTACTAAATTTTTATAATAATAAATCTAGAAC
4992044 AATTATTTACAAAACTTATAAATTTA
1 AATTATTTACAAAACTTATAAATTTA
4992070 GAAAACTTAT
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
60 5 0.07
61 61 0.82
62 8 0.11
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (61 bp):
AATTATTTACAAAACTTATAAATTTAATACTACTAAATTTTTATAATAATAAATCTAGAAC
Found at i:4992021 original size:15 final size:15
Alignment explanation
Indices: 4992000--4992039 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
4991990 TAGAAAACTT
4992000 ATAAATTTAATACTA
1 ATAAATTTAATACTA
* *
4992015 CTAAATTTTTATACTA
1 ATAAA-TTTAATACTA
4992031 ATAAATTTA
1 ATAAATTTA
4992040 GAATAATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAAATTTAATACTA
Found at i:4992074 original size:17 final size:17
Alignment explanation
Indices: 4992048--4992080 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4992038 TAGAATAATT
4992048 ATTTACAAAACTTATAA
1 ATTTACAAAACTTATAA
*
4992065 ATTTAGAAAACTTATA
1 ATTTACAAAACTTATA
4992081 TAGAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (17 bp):
ATTTACAAAACTTATAA
Found at i:4993783 original size:39 final size:39
Alignment explanation
Indices: 4993729--4993806 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
4993719 GAGATGAAGA
4993729 AAGGATGAGGGGAAATCGAAGAAAGACTTAGGGATTTGG
1 AAGGATGAGGGGAAATCGAAGAAAGACTTAGGGATTTGG
*
4993768 AAGGATGAGGGGAAATCGCAGAAAGACTTAGGGATTTGG
1 AAGGATGAGGGGAAATCGAAGAAAGACTTAGGGATTTGG
4993807 CTGAAAAGGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.37, C:0.06, G:0.38, T:0.18
Consensus pattern (39 bp):
AAGGATGAGGGGAAATCGAAGAAAGACTTAGGGATTTGG
Found at i:4996020 original size:115 final size:113
Alignment explanation
Indices: 4995802--4996026 Score: 260
Period size: 115 Copynumber: 2.0 Consensus size: 113
4995792 GCCACGAACT
* * * ** *
4995802 CTAATCTATCTCAAGACCAAACAGTGCGTTTTGGTTAAGATGTTGGCGGCGCTTTTTGTAATACG
1 CTAATATACCTCAAAACCAAACAGTGCGTTTTGGTTAAGATGTTGGCGGCGCTTCATATAATACG
* * *
4995867 CCGCTAATACTGTTCTTTAGCGGCGTTTTCTCGTAAACGCCACTAATA
66 CCACTAATACTGTTCTTTAGCGGCGTTTTCTAGAAAACGCCACTAATA
* *
4995915 CTAATATACCTCAAAACCAAAC-GCTGCGTTTTGGTTAAGGTATTTTTGCGGCGCTTACATATAA
1 CTAATATACCTCAAAACCAAACAG-TGCGTTTTGGTTAA-G-ATGTTGGCGGCGCTT-CATATAA
*
4995979 -ACGCCACTAATGA-TGTTCTTTTA-CGGCGTTTTTTAGAAAACGCCACTA
62 TACGCCACTAAT-ACTGTTC-TTTAGCGGCGTTTTCTAGAAAACGCCACTA
4996027 GGTGTTCAGG
Statistics
Matches: 94, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
112 1 0.01
113 33 0.35
114 1 0.01
115 50 0.53
116 9 0.10
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (113 bp):
CTAATATACCTCAAAACCAAACAGTGCGTTTTGGTTAAGATGTTGGCGGCGCTTCATATAATACG
CCACTAATACTGTTCTTTAGCGGCGTTTTCTAGAAAACGCCACTAATA
Found at i:4999946 original size:6 final size:6
Alignment explanation
Indices: 4999935--4999969 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
4999925 AAATTATTGG
4999935 AAATAA AAATAA AAATAA AAATAA AAATAA AAATA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATA
4999970 CCAAATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:5000352 original size:11 final size:11
Alignment explanation
Indices: 5000332--5000365 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5000322 TTTTATATAA
5000332 AAAT-TAACTT
1 AAATCTAACTT
5000342 AAATCTAACTT
1 AAATCTAACTT
*
5000353 AAATCAAACTT
1 AAATCTAACTT
5000364 AA
1 AA
5000366 TATTATCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATCTAACTT
Found at i:5002308 original size:189 final size:193
Alignment explanation
Indices: 5001845--5002423 Score: 603
Period size: 189 Copynumber: 2.9 Consensus size: 193
5001835 GCTAATGTAA
* *** * * *
5001845 AAATCTGGATCGAAAACTTGGGCTATAAAGTCGTATATTAGTTGCTCGAAAACTCTGATTTAGTG
1 AAATCCGGATCGAAAACTCATGTTATAAAGTCGTATAGTAGTTGCTCGAAAACTCCGATTTAGTG
*** * * *
5001910 AAAGGAAAAGAAATTTCTCTGGTGATCGATCATACATCGTTTTGAAGCTAGTTTTCTTAATCCGG
66 AAAGGAAAAGAAATTTCTCCACTGATCGATCATACATCGTTTTAAAGCAAG-GTT-TT-AT----
* * * * *
5001975 GGAAGACGATTGAAAGATGTTAATGGTAACATCTTGTATAAGCATCTTTAGTTGTTTGTTTAGCT
124 TGAAGACGA-CGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGATTGTATAGCT
5002040 ATGAAC
188 ATGAAC
** * * *
5002046 AAATCCGGATCGAAAACTTGTGTTATAAAGTCGTATATTAGTTGCTCGAAAAGTCTGATTTAGTG
1 AAATCCGGATCGAAAACTCATGTTATAAAGTCGTATAGTAGTTGCTCGAAAACTCCGATTTAGTG
* * **
5002111 AAAGGAAAAGAAATTTCTCCACTGATCGATCATGCATCGTTTTAAATCAAGGTTTT-TT-AATCC
66 AAAGGAAAAGAAATTTCTCCACTGATCGATCATACATCGTTTTAAAGCAAGGTTTTATTGAAGAC
* *
5002174 G-GGAAAGATGCTAATGGTAACATCTTGTATAAGGATCTTTAGTT-ATTGTATAGCTAT-ATAC
131 GACGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGATTGTATAGCTATGA-AC
* ** * *
5002235 AATTCCGGATCGAAAACTCATGTTATAAAGTTTTATAGTAGTTGCTTGAAAACTCCGATTTATTT
1 AAATCCGGATCGAAAACTCATGTTATAAAGTCGTATAGTAGTTGCTCGAAAACTCCGATTTA-GT
* ** * * *
5002300 G-TAGGAAAAGAAATTTCTCCGGTGATCTATCTTACATCGTTTTAAAGCAAGTTTTTAATTCGGG
65 GAAAGGAAAAGAAATTTCTCCACTGATCGATCATACATCGTTTTAAAGCAAGGTTTT-ATT----
*
5002364 GAAGACGACCGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGTTTGTAT
125 GAAGACGA-CGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGATTGTAT
5002424 CGGTGTTGAA
Statistics
Matches: 323, Mismatches: 43, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
188 1 0.00
189 113 0.35
190 42 0.13
191 2 0.01
192 4 0.01
196 4 0.01
197 1 0.00
198 41 0.13
199 8 0.02
200 2 0.01
201 105 0.33
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (193 bp):
AAATCCGGATCGAAAACTCATGTTATAAAGTCGTATAGTAGTTGCTCGAAAACTCCGATTTAGTG
AAAGGAAAAGAAATTTCTCCACTGATCGATCATACATCGTTTTAAAGCAAGGTTTTATTGAAGAC
GACGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGATTGTATAGCTATGAAC
Found at i:5003353 original size:17 final size:18
Alignment explanation
Indices: 5003307--5003355 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
5003297 AGAATTGATT
*
5003307 AATTTTTTAAAATTTAGA
1 AATTTATTAAAATTTAGA
**
5003325 AATTTAAAAAAATTT-GA
1 AATTTATTAAAATTTAGA
5003342 AATTTATTAAAATT
1 AATTTATTAAAATT
5003356 ATTAAAAGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (18 bp):
AATTTATTAAAATTTAGA
Found at i:5004522 original size:23 final size:23
Alignment explanation
Indices: 5004495--5004542 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
5004485 ATTGAATGGA
*
5004495 ATTTTGTTAGGCAGTACGGTACT
1 ATTTTGTTAGGCAGTACAGTACT
5004518 ATTTTGTTAGGCAGTACAGTACT
1 ATTTTGTTAGGCAGTACAGTACT
5004541 AT
1 AT
5004543 ATAAATTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (23 bp):
ATTTTGTTAGGCAGTACAGTACT
Found at i:5011930 original size:10 final size:10
Alignment explanation
Indices: 5011915--5011949 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
5011905 TGTAATTCAC
5011915 AAAAAAAAAT
1 AAAAAAAAAT
5011925 --AAAAAAAT
1 AAAAAAAAAT
5011933 AAAAAAAAAT
1 AAAAAAAAAT
5011943 AAAAAAA
1 AAAAAAA
5011950 CCAAACTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.35
10 15 0.65
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:5011938 original size:18 final size:18
Alignment explanation
Indices: 5011915--5011949 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5011905 TGTAATTCAC
5011915 AAAAAAAAATAAAAAAAT
1 AAAAAAAAATAAAAAAAT
5011933 AAAAAAAAATAAAAAAA
1 AAAAAAAAATAAAAAAA
5011950 CCAAACTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (18 bp):
AAAAAAAAATAAAAAAAT
Found at i:5014801 original size:12 final size:13
Alignment explanation
Indices: 5014778--5014812 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
5014768 CCTCAACAAT
5014778 AAAAAGACAAAAA
1 AAAAAGACAAAAA
*
5014791 AAAAAGAAAAAAA
1 AAAAAGACAAAAA
5014804 AAAAAGACA
1 AAAAAGACA
5014813 GAAGACCCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.86, C:0.06, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAGACAAAAA
Found at i:5017732 original size:7 final size:7
Alignment explanation
Indices: 5017720--5017753 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
5017710 TAAAATGCAC
5017720 ATTTATT
1 ATTTATT
5017727 ATTTATT
1 ATTTATT
5017734 ATTTATT
1 ATTTATT
5017741 ATTTATT
1 ATTTATT
5017748 ATTTAT
1 ATTTAT
5017754 AAATATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTTATT
Found at i:5023055 original size:2 final size:2
Alignment explanation
Indices: 5023048--5023091 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5023038 CATGTTAATG
5023048 AT AT AT AT AT AT 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 AT AT AT AT AT AT
5023090 AT
1 AT
5023092 GTTCCATTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5025489 original size:30 final size:32
Alignment explanation
Indices: 5025437--5025504 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
5025427 TTTTTTAGTT
* *
5025437 AAATTTGATCATTTACTTTTT-AAAAAGAGTC
1 AAATTTGATCATTCAATTTTTAAAAAAGAGTC
*
5025468 AAATTTGATCA-TCAATTTTTAAAAAAGAGTT
1 AAATTTGATCATTCAATTTTTAAAAAAGAGTC
5025499 AAATTT
1 AAATTT
5025505 TTAACATCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (32 bp):
AAATTTGATCATTCAATTTTTAAAAAAGAGTC
Found at i:5027571 original size:38 final size:37
Alignment explanation
Indices: 5027516--5027628 Score: 131
Period size: 38 Copynumber: 3.3 Consensus size: 37
5027506 TCCTTTTTGT
5027516 AAATTTAAAAACAAATCGGAAAAGGAAAATAACTCTA
1 AAATTTAAAAACAAATCGGAAAAGGAAAATAACTCTA
5027553 AAATATTAAAAACAAATC------GGAAAAT---T-T-
1 AAAT-TTAAAAACAAATCGGAAAAGGAAAATAACTCTA
5027580 AAATTTAAAAACAAATCGGAAAAGGAAAATAACTCTA
1 AAATTTAAAAACAAATCGGAAAAGGAAAATAACTCTA
5027617 AAATATTAAAAA
1 AAAT-TTAAAAA
5027629 AAAACTAATA
Statistics
Matches: 63, Mismatches: 0, Indels: 25
0.72 0.00 0.28
Matches are distributed among these distances:
26 13 0.21
27 4 0.06
28 1 0.02
29 1 0.02
32 14 0.22
35 1 0.02
36 1 0.02
37 8 0.13
38 20 0.32
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.21
Consensus pattern (37 bp):
AAATTTAAAAACAAATCGGAAAAGGAAAATAACTCTA
Found at i:5027609 original size:26 final size:27
Alignment explanation
Indices: 5027552--5027610 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
5027542 AAATAACTCT
**
5027552 AAAATATTAAAAACAAATCGGAAAATT
1 AAAATATTAAAAACAAATCGGAAAAGG
*
5027579 TAAAT-TTAAAAACAAATCGGAAAAGG
1 AAAATATTAAAAACAAATCGGAAAAGG
5027605 AAAATA
1 AAAATA
5027611 ACTCTAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (27 bp):
AAAATATTAAAAACAAATCGGAAAAGG
Found at i:5028774 original size:45 final size:45
Alignment explanation
Indices: 5028709--5028866 Score: 210
Period size: 45 Copynumber: 3.5 Consensus size: 45
5028699 CACCATCTTT
* *
5028709 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
1 GATCTGCTATCTTTGATCTACTTCGCCACCAGTATGGGAAGACAA
* * * * ***
5028754 GATCTACTATCTTTGATCTACTTC-ACGCCAATACATGAAGACAA
1 GATCTGCTATCTTTGATCTACTTCGCCACCAGTATGGGAAGACAA
* *
5028798 GATCTGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAA
1 GATCTGCTATCTTTGATCTACTTCGCCACCAGTATGGGAAGACAA
5028843 GATCTGCTATCTTTGATCTACTTC
1 GATCTGCTATCTTTGATCTACTTC
5028867 ACGCCAATAC
Statistics
Matches: 92, Mismatches: 20, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
44 35 0.38
45 57 0.62
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (45 bp):
GATCTGCTATCTTTGATCTACTTCGCCACCAGTATGGGAAGACAA
Found at i:5028816 original size:44 final size:45
Alignment explanation
Indices: 5028709--5028889 Score: 195
Period size: 45 Copynumber: 4.1 Consensus size: 45
5028699 CACCATCTTT
* * * * **
5028709 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
1 GATCTGCTATCTTTGATCTACTTCGACACCAATACAGGAAGACAA
* * *
5028754 GATCTACTATCTTTGATCTACTTC-ACGCCAATACATGAAGACAA
1 GATCTGCTATCTTTGATCTACTTCGACACCAATACAGGAAGACAA
* * * * **
5028798 GATCTGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAA
1 GATCTGCTATCTTTGATCTACTTCGACACCAATACAGGAAGACAA
* *
5028843 GATCTGCTATCTTTGATCTACTTC-ACGCCAATACATGAAGACAA
1 GATCTGCTATCTTTGATCTACTTCGACACCAATACAGGAAGACAA
5028887 GAT
1 GAT
5028890 NNNNNNNNNN
Statistics
Matches: 109, Mismatches: 26, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
44 52 0.48
45 57 0.52
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (45 bp):
GATCTGCTATCTTTGATCTACTTCGACACCAATACAGGAAGACAA
Found at i:5028860 original size:89 final size:89
Alignment explanation
Indices: 5028709--5028889 Score: 344
Period size: 89 Copynumber: 2.0 Consensus size: 89
5028699 CACCATCTTT
5028709 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTA
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTA
5028774 CTTCACGCCAATACATGAAGACAA
66 CTTCACGCCAATACATGAAGACAA
* *
5028798 GATCTGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTA
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTA
5028863 CTTCACGCCAATACATGAAGACAA
66 CTTCACGCCAATACATGAAGACAA
5028887 GAT
1 GAT
5028890 NNNNNNNNNN
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (89 bp):
GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTA
CTTCACGCCAATACATGAAGACAA
Found at i:5029098 original size:47 final size:44
Alignment explanation
Indices: 5028990--5029504 Score: 273
Period size: 45 Copynumber: 11.5 Consensus size: 44
5028980 NNNNNNNNNN
* * * *
5028990 TGCTTTCTTGGATCTACTTCGCCACCAGTA-ATGAGAAAGACAAGACC
1 TGCTTTCTTGGATCTACTTC-ACGCCAATACAT--G-AAGACAAGATC
* * *
5029037 TACTATCTTTGATCTACTTCACGCCAATACATGAAGACAAAGATC
1 TGCTTTCTTGGATCTACTTCACGCCAATACATGAAGAC-AAGATC
* * * *** *
5029082 TGCTTTTCTTGGGATCTACTTCGCCACCAGTATGGGAAGATAAGATC
1 TGC-TTTCTT-GGATCTACTTC-ACGCCAATACATGAAGACAAGATC
* * *
5029129 TGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATT
1 TGCTTTCTTGGATCTACTTCACGCCAATACATGAAGACAAGATC
* * * ***
5029173 TGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATC
1 TGCTTTCTTGGATCTACTTC-ACGCCAATACATGAAGACAAGATC
** * * * *** * *
5029218 TGCTTTCTTCAATCTACTCCACCACCAGTATGGGGAGACAATATC
1 TGCTTTCTTGGATCTACTTCA-CGCCAATACATGAAGACAAGATC
* * * *
5029263 T-ATTGTGTTTGATCTACTTCACGCCGATACATGAAGACAAGATC
1 TGCTT-TCTTGGATCTACTTCACGCCAATACATGAAGACAAGATC
** * * * * * * ***
5029307 TATTTTTTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATC
1 TGCTTTCTTGGATCTACTTC-ACGCCAATACATGAAGACAAGATC
* * * *
5029352 TGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATC
1 TGCTTTCTTGGATCTACTTCACGCCAATACATGAAGACAAGATC
* * ** *
5029396 TGTTTTCTTTGATCTACTT--CGCCACCAGTATGGAAAGACAAGATC
1 TGCTTTCTTGGATCTACTTCACGCCAATA-CAT-G-AAGACAAGATC
* * * * * * *
5029441 TGGTATCTTTGATCTACTTCACGCTAGTACATGAAGATATGATC
1 TGCTTTCTTGGATCTACTTCACGCCAATACATGAAGACAAGATC
* *
5029485 TGTTTTCTTCGATCTACTTC
1 TGCTTTCTTGGATCTACTTC
5029505 GCCACCAGTA
Statistics
Matches: 360, Mismatches: 93, Indels: 33
0.74 0.19 0.07
Matches are distributed among these distances:
42 6 0.02
43 2 0.01
44 132 0.37
45 148 0.41
46 18 0.05
47 43 0.12
48 11 0.03
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (44 bp):
TGCTTTCTTGGATCTACTTCACGCCAATACATGAAGACAAGATC
Found at i:5029220 original size:89 final size:90
Alignment explanation
Indices: 5028990--5029235 Score: 377
Period size: 89 Copynumber: 2.7 Consensus size: 90
5028980 NNNNNNNNNN
* * *
5028990 TGCTTTCTTGGATCTACTTCGCCACCAGTAATGAGAAAGACAAGACCTACTATCTTTGATCTACT
1 TGCTTTCTTGGATCTACTTCGCCACCAGT-ATG-GGAAGACAAGATCTGCTATCTTTGATCTACT
5029055 TCACGCCAATACATGAAGACAAAGATC
64 TCACGCCAATACATGAAGACAAAGATC
*
5029082 TGCTTTTCTTGGGATCTACTTCGCCACCAGTATGGGAAGATAAGATCTGCTATCTTTGATCTACT
1 TGC-TTTCTT-GGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACT
*
5029147 TCACGCCAATACATGAAGAC-AAGATT
64 TCACGCCAATACATGAAGACAAAGATC
* **
5029173 TGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTTTCTTCAATCTACT
1 TGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACT
5029236 CCACCACCAG
Statistics
Matches: 143, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
89 50 0.35
90 6 0.04
91 8 0.06
92 50 0.35
93 9 0.06
94 20 0.14
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (90 bp):
TGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTC
ACGCCAATACATGAAGACAAAGATC
Found at i:5029299 original size:89 final size:89
Alignment explanation
Indices: 5029161--5029548 Score: 474
Period size: 89 Copynumber: 4.4 Consensus size: 89
5029151 GCCAATACAT
* * * * * * *** *
5029161 GAAGACAAGATTTGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTTTCT
1 GAAGACAAGATCTGGTATCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGTTTTCT
* * *
5029226 TCAATCTACTCCACCACCAGTATGG
65 TCGATCTACTTCGCCACCAGTATGG
* * ** * * * *
5029251 GGAGACAATATCTATTGTGTTTGATCTACTTCACGCC-GATACATGAAGACAAGATCTATTTTTT
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTGTTTTCT
*
5029315 TCGATCTGCTTCGCCACCAGTATGG
65 TCGATCTACTTCGCCACCAGTATGG
5029340 GAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
*
5029405 TGATCTACTTCGCCACCAGTATGG
66 CGATCTACTTCGCCACCAGTATGG
* * * *
5029429 AAAGACAAGATCTGGTATCTTTGATCTACTTCACGCTAGTACATGAAGATATGATCTGTTTTCTT
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
5029494 CGATCTACTTCGCCACCAGTATGG
66 CGATCTACTTCGCCACCAGTATGG
* * *
5029518 GAAGACAAGATCT-GTATATTCGATCCACTTC
1 GAAGACAAGATCTGGTATCTTTGATCTACTTC
5029549 GCTACCAATA
Statistics
Matches: 257, Mismatches: 39, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
88 16 0.06
89 216 0.84
90 25 0.10
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (89 bp):
GAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
CGATCTACTTCGCCACCAGTATGG
Found at i:5029458 original size:223 final size:226
Alignment explanation
Indices: 5029044--5029458 Score: 665
Period size: 223 Copynumber: 1.8 Consensus size: 226
5029034 ACCTACTATC
* *
5029044 TTTGATCTACTTCACGCCAATACATGAAGACAAAGATCTGCTTTTCTTGGGATCTACTTCGCCAC
1 TTTGATCTACTTCACGCCAATACATGAAGACAAAGATCTGATTTTCTTGCGATCTACTTCGCCAC
* *
5029109 CAGTATGGGAAGATAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATTT
66 CAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCT
* *
5029174 GCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTTTCTTCAATCTACTCCA
131 GCTTTCTTGGATCTACTTCGCCACCAGTATGGAAAGACAAGATCTGCTATCTTCAATCTACTCCA
5029239 CCACCAGTATGGGGAGACAATATCTATTGTG
196 CCACCAGTATGGGGAGACAATATCTATTGTG
* * *
5029270 TTTGATCTACTTCACGCCGATACATGAAGAC-AAGATCT-ATTTT-TTTCGATCTGCTTCGCCAC
1 TTTGATCTACTTCACGCCAATACATGAAGACAAAGATCTGATTTTCTTGCGATCTACTTCGCCAC
* *
5029332 CAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
66 CAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCT
* * * **
5029397 GTTTTCTTTGATCTACTTCGCCACCAGTATGGAAAGACAAGATCTGGTATCTTTGATCTACT
131 GCTTTCTTGGATCTACTTCGCCACCAGTATGGAAAGACAAGATCTGCTATCTTCAATCTACT
5029459 TCACGCTAGT
Statistics
Matches: 173, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
223 132 0.76
224 4 0.02
225 7 0.04
226 30 0.17
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (226 bp):
TTTGATCTACTTCACGCCAATACATGAAGACAAAGATCTGATTTTCTTGCGATCTACTTCGCCAC
CAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCT
GCTTTCTTGGATCTACTTCGCCACCAGTATGGAAAGACAAGATCTGCTATCTTCAATCTACTCCA
CCACCAGTATGGGGAGACAATATCTATTGTG
Found at i:5029531 original size:134 final size:133
Alignment explanation
Indices: 5028995--5029576 Score: 451
Period size: 134 Copynumber: 4.3 Consensus size: 133
5028985 NNNNNTGCTT
* * *
5028995 TCTTGGATCTACTTCGCCACCAGTAATGAGAAAGACAAGACCTACTATCTTTGATCTACTTC-AC
1 TCTTTGATCTACTTCGCCACCA-T-ATG-G-AAGACAAGATCTGCTATCTTTGATCTACTTCGAC
* * * * *
5029059 GCCAATACATGAAGACAAAGATCTGCTTTTCTTGGGATCTACTTCGCCACCAGTATGGGAAGATA
62 ACCAGTACAGGAAGAC-AAGATCTG-TTTTCTT-CGATCTACTTCGCCACCAGTATGGGAAGACA
*
5029124 AGATCTGCTA
124 AGATCTGTTA
** * * * * *
5029134 TCTTTGATCTACTTCACGCCAATACAT-GAAGACAAGATTTGCTTTCTTGGATCTACTTCGCCAC
1 TCTTTGATCTACTT--CGCCACCATATGGAAGACAAGATCTGCTATCTTTGATCTACTTCGACAC
** * * * * * *
5029198 CAGTATGGGAAGACAAGATCTGCTTTCTTCAATCTACTCCACCACCAGTATGGGGAGACAATATC
64 CAGTACAGGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATC
* *
5029263 TATTG
129 TGTTA
* * * * * * * *
5029268 TGTTTGATCTACTTCACGCCGA-TACAT-GAAGACAAGATCT-ATTTTTTTCGATCTGCTTCGCC
1 TCTTTGATCTACTT--CGCC-ACCATATGGAAGACAAGATCTGCTATCTTT-GATCTACTTCGAC
** * * * * * ***
5029330 ACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGA
62 ACCAGTACAGGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGA
*
5029394 TCTGTTT
127 TCTGTTA
* *
5029401 TCTTTGATCTACTTCGCCACCAGTATGGAAAGACAAGATCTGGTATCTTTGATCTACTTC-ACGC
1 TCTTTGATCTACTTCGCCACCA-TATGG-AAGACAAGATCTGCTATCTTTGATCTACTTCGACAC
* * * *
5029465 TAGTACATGAAGATATGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATC
64 CAGTACAGGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATC
5029530 TG-TA
129 TGTTA
* * * * *
5029534 TATTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGC
1 TCTTTGATCTACTTCGCCACC-ATAT-GGAAGACAAGATCTGC
5029577 CACTTTTCAA
Statistics
Matches: 354, Mismatches: 76, Indels: 32
0.77 0.16 0.07
Matches are distributed among these distances:
130 1 0.00
131 5 0.01
132 2 0.01
133 105 0.30
134 161 0.45
135 12 0.03
136 34 0.10
137 13 0.04
139 15 0.04
141 6 0.02
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (133 bp):
TCTTTGATCTACTTCGCCACCATATGGAAGACAAGATCTGCTATCTTTGATCTACTTCGACACCA
GTACAGGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG
TTA
Found at i:5029566 original size:89 final size:89
Alignment explanation
Indices: 5029094--5029575 Score: 448
Period size: 89 Copynumber: 5.4 Consensus size: 89
5029084 CTTTTCTTGG
* ** * * * * * * *
5029094 GATCTACTTCGCCACCAGTATGGGAAGATAAGATCTGCTATCTTTGATCTACTTC-ACGCCAATA
1 GATCTACTTC-ACACCAGTACAGGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTA
*** * * * *
5029158 CATGAAGACAAGATTTGCTTTCTTG
65 TGGGAAGACAAGATCTGGTATCTTT
* ** * * * *
5029183 GATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTTTCTTCAATCTACTCCACCACCAGTA
1 GATCTACTTC-ACACCAGTACAGGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTA
* * ** * *
5029248 TGGGGAGACAATATCTATTGTGTTT
65 TGGGAAGACAAGATCTGGTATCTTT
* * * * *
5029273 GATCTACTTCACGCC-GATACATGAAGACAAGATCTATTTTTTTCGATCTGCTTCGCCACCAGTA
1 GATCTACTTCACACCAG-TACAGGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTA
5029337 TGGGAAGACAAGATCTGGTATCTTT
65 TGGGAAGACAAGATCTGGTATCTTT
* * *
5029362 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTTGATCTACTTCGCCACCAGTAT
1 GATCTACTTCACACCAGTACAGGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTAT
*
5029427 GGAAAGACAAGATCTGGTATCTTT
66 GGGAAGACAAGATCTGGTATCTTT
* * * * *
5029451 GATCTACTTCACGCTAGTACATGAAGATATGATCTGTTTTCTTCGATCTACTTCGCCACCAGTAT
1 GATCTACTTCACACCAGTACAGGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTAT
* *
5029516 GGGAAGACAAGATCT-GTATATTC
66 GGGAAGACAAGATCTGGTATCTTT
* * * * *
5029539 GATCCACTTCGCTACCAATATAGGAAGACAGGATCTG
1 GATCTACTTCAC-ACCAGTACAGGAAGACAAGATCTG
5029576 CCACTTTTCA
Statistics
Matches: 331, Mismatches: 58, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
88 17 0.05
89 283 0.85
90 31 0.09
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (89 bp):
GATCTACTTCACACCAGTACAGGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTAT
GGGAAGACAAGATCTGGTATCTTT
Found at i:5035281 original size:13 final size:13
Alignment explanation
Indices: 5035263--5035294 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5035253 TTTCCAGCAA
5035263 TTATGAATTTATT
1 TTATGAATTTATT
5035276 TTATGAATTTATT
1 TTATGAATTTATT
*
5035289 TGATGA
1 TTATGA
5035295 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:5035502 original size:50 final size:50
Alignment explanation
Indices: 5035399--5035588 Score: 245
Period size: 50 Copynumber: 3.7 Consensus size: 50
5035389 AGAGATCCTA
* * *
5035399 TGTAAGACAATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCCC
1 TGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--GAGAGGTCCCC
*
5035455 TGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAGGTCCCC
* * * *
5035505 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGATGTCCCC
1 TGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAGGTCCCC
*
5035555 TATAAGACCATGTCTGGGACATGGCATGGGCACC
1 TGTAAGACCATGTCTGGGACATGGCATGGGCACC
5035589 AACATGAGAA
Statistics
Matches: 122, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
50 86 0.70
52 1 0.01
53 3 0.02
55 2 0.02
56 30 0.25
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAGGTCCCC
Found at i:5035577 original size:100 final size:103
Alignment explanation
Indices: 5035389--5035588 Score: 289
Period size: 100 Copynumber: 1.9 Consensus size: 103
5035379 ATTTGGGTAA
*
5035389 AGAGATCCTATGTAAGACAATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACAATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
*
5035454 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * * * *
5035495 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGATGTCCCCTA
1 AGAGATCCCATGTAAGACAATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
5035557 TAAGACCATGTCTGGGACATGGCATGGGCACC
66 TAAGACCATGTCTGGGACATGGCATGGGCACC
5035589 AACATGAGAA
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
100 45 0.52
101 2 0.02
105 2 0.02
106 38 0.44
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACAATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:5051002 original size:16 final size:15
Alignment explanation
Indices: 5050983--5051028 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
5050973 TTATGTTATT
5050983 TTTATATATTATATAA
1 TTTATATA-TATATAA
*
5050999 TTTATAGTATATAAAA
1 TTTATA-TATATATAA
*
5051015 TTTAAATATATATA
1 TTTATATATATATA
5051029 CAAAAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 7 0.27
16 17 0.65
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TTTATATATATATAA
Found at i:5054107 original size:16 final size:17
Alignment explanation
Indices: 5054079--5054113 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5054069 ATTTATAATA
5054079 AAATTATTTAAAAAATT
1 AAATTATTTAAAAAATT
*
5054096 AAATTA-TTAAAATATT
1 AAATTATTTAAAAAATT
5054112 AA
1 AA
5054114 TCACATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATTATTTAAAAAATT
Found at i:5059610 original size:33 final size:32
Alignment explanation
Indices: 5059568--5059723 Score: 106
Period size: 33 Copynumber: 4.6 Consensus size: 32
5059558 AATAACAAGG
5059568 GGTTGCTAAGTGCTGATTCCCCGACTCTTTGGT
1 GGTTGCTAAGTGCTGATTCCCC-ACTCTTTGGT
*
5059601 GGTTGCTAAGTGCTGATTCCACCATATCTTTGAATGT
1 GGTTGCTAAGTGCTGATTCC-CCA-CTCTTTG---GT
* **
5059638 GAAAGGGGCTGCTAAGTGCTGATT--CC-CTC-AAGG-
1 ------GGTTGCTAAGTGCTGATTCCCCACTCTTTGGT
*
5059671 GGTAGCTAAGTGCTGATTCCCCGACTCTTTGGT
1 GGTTGCTAAGTGCTGATTCCCC-ACTCTTTGGT
*
5059704 GGTTGTTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
5059724 ACCATATCCT
Statistics
Matches: 95, Mismatches: 11, Indels: 34
0.68 0.08 0.24
Matches are distributed among these distances:
27 16 0.17
29 2 0.02
31 3 0.03
32 2 0.02
33 39 0.41
34 9 0.09
37 3 0.03
38 2 0.02
40 2 0.02
43 17 0.18
ACGTcount: A:0.18, C:0.21, G:0.28, T:0.33
Consensus pattern (32 bp):
GGTTGCTAAGTGCTGATTCCCCACTCTTTGGT
Found at i:5059678 original size:27 final size:27
Alignment explanation
Indices: 5059640--5059691 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
5059630 TTGAATGTGA
5059640 AAGGGGCTGCTAAGTGCTGATTCCCTC
1 AAGGGGCTGCTAAGTGCTGATTCCCTC
5059667 AAGGGG-TAGCTAAGTGCTGATTCCC
1 AAGGGGCT-GCTAAGTGCTGATTCCC
5059692 CGACTCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (27 bp):
AAGGGGCTGCTAAGTGCTGATTCCCTC
Found at i:5059686 original size:103 final size:103
Alignment explanation
Indices: 5059563--5059767 Score: 374
Period size: 103 Copynumber: 2.0 Consensus size: 103
5059553 TATTGAATAA
*
5059563 CAAGGGGTTGCTAAGTGCTGATTCCCCGACTCTTTGGTGGTTGCTAAGTGCTGATTCCACCATAT
1 CAAGGGGTAGCTAAGTGCTGATTCCCCGACTCTTTGGTGGTTGCTAAGTGCTGATTCCACCATAT
*
5059628 CTTTGAATGTGAAAGGGGCTGCTAAGTGCTGATTCCCT
66 CCTTGAATGTGAAAGGGGCTGCTAAGTGCTGATTCCCT
*
5059666 CAAGGGGTAGCTAAGTGCTGATTCCCCGACTCTTTGGTGGTTGTTAAGTGCTGATTCCACCATAT
1 CAAGGGGTAGCTAAGTGCTGATTCCCCGACTCTTTGGTGGTTGCTAAGTGCTGATTCCACCATAT
*
5059731 CCTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCC
66 CCTTGAATGTGAAAGGGGCTGCTAAGTGCTGATTCCC
5059768 CGAATCACTG
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (103 bp):
CAAGGGGTAGCTAAGTGCTGATTCCCCGACTCTTTGGTGGTTGCTAAGTGCTGATTCCACCATAT
CCTTGAATGTGAAAGGGGCTGCTAAGTGCTGATTCCCT
Found at i:5059765 original size:43 final size:42
Alignment explanation
Indices: 5059704--5059843 Score: 140
Period size: 33 Copynumber: 3.5 Consensus size: 42
5059694 ACTCTTTGGT
*
5059704 GGTTGTTAAGTGCTGATTCCACCATATCCTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCATATCCTTGAATGT-AAAGG
5059747 GGTTGCTAAGTGCTGATTCC-CCGA-ATCAC-TG---GT-----
1 GGTTGCTAAGTGCTGATTCCACC-ATATC-CTTGAATGTAAAGG
*
5059780 GGTTGCTATGTGCTGATTCCACCATATCCTTGAATGTAAAAGGG
1 GGTTGCTAAGTGCTGATTCCACCATATCCTTGAATGT-AAA-GG
5059824 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
5059844 CCGAATCACT
Statistics
Matches: 79, Mismatches: 3, Indels: 29
0.71 0.03 0.26
Matches are distributed among these distances:
33 21 0.27
34 7 0.09
37 2 0.03
39 2 0.03
42 7 0.09
43 21 0.27
44 19 0.24
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.32
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCATATCCTTGAATGTAAAGG
Found at i:5059860 original size:77 final size:76
Alignment explanation
Indices: 5059667--5059879 Score: 345
Period size: 76 Copynumber: 2.8 Consensus size: 76
5059657 TGATTCCCTC
* * ** *
5059667 AAGGGGTAGCTAAGTGCTGATTCCCCGACTCTTTGGTGGTTGTTAAGTGCTGATTCCACCATATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCATATC
*
5059732 CTTGAATGTGA
66 CTTGAATGTAA
*
5059743 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTATGTGCTGATTCCACCATATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCATATC
5059808 CTTGAATGTAA
66 CTTGAATGTAA
*
5059819 AAGGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCACC
1 AA-GGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACC
5059880 GATAACGGTT
Statistics
Matches: 127, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
76 71 0.56
77 56 0.44
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.31
Consensus pattern (76 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCATATC
CTTGAATGTAA
Found at i:5063043 original size:33 final size:34
Alignment explanation
Indices: 5062997--5063131 Score: 114
Period size: 33 Copynumber: 3.7 Consensus size: 34
5062987 ATAACCGTTA
*
5062997 TCGGTGGATTCAGCACTTAGCAACCACCAGTGAT
1 TCGGTGGAATCAGCACTTAGCAACCACCAGTGAT
*
5063031 TCGG-GGAATCAGCACTTAGCAACCCCTTTTTACATCCAATGAT
1 TCGGTGGAATCAGCACTTAGCAA---C------CA-CCAGTGAT
*
5063074 AT-GGTGGAATCAGTACTTAGCAACCACCAGTGAT
1 -TCGGTGGAATCAGCACTTAGCAACCACCAGTGAT
*
5063108 TCGG-GGAATCAGCATTTAGCAACC
1 TCGGTGGAATCAGCACTTAGCAACC
5063132 CCTTTCACAT
Statistics
Matches: 82, Mismatches: 6, Indels: 27
0.71 0.05 0.23
Matches are distributed among these distances:
33 36 0.44
34 13 0.16
35 2 0.02
36 1 0.01
41 1 0.01
42 2 0.02
43 9 0.11
44 18 0.22
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (34 bp):
TCGGTGGAATCAGCACTTAGCAACCACCAGTGAT
Found at i:5063127 original size:77 final size:77
Alignment explanation
Indices: 5062999--5063211 Score: 320
Period size: 76 Copynumber: 2.8 Consensus size: 77
5062989 AACCGTTATC
* *
5062999 GGTGGATTCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTTTAC
1 GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCAC
*
5063064 ATCCAATGATAT
66 ATCCAAGGATAT
* *
5063076 GGTGGAATCAGTACTTAGCAACCACCAGTGATTCGGGGAATCAGCATTTAGCAACCCC-TTTCAC
1 GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCAC
*
5063140 ATTCAAGGATAT
66 ATCCAAGGATAT
* ** * *
5063152 GGTGGAATCAACACTTAGCAACCACCAAAGAGTCGGGGAATCAGCACTTAGCTACCCCTT
1 GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTT
5063212 GAGGGAATCA
Statistics
Matches: 122, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
76 66 0.54
77 56 0.46
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (77 bp):
GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCAC
ATCCAAGGATAT
Found at i:5063217 original size:27 final size:27
Alignment explanation
Indices: 5063187--5063238 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
5063177 CAAAGAGTCG
*
5063187 GGGAATCAGCACTTAGCTACCCCTTGA
1 GGGAATCAGCACTTAGCAACCCCTTGA
5063214 GGGAATCAGCACTTAGCAACCCCTT
1 GGGAATCAGCACTTAGCAACCCCTT
5063239 TAACATTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (27 bp):
GGGAATCAGCACTTAGCAACCCCTTGA
Found at i:5065026 original size:29 final size:30
Alignment explanation
Indices: 5064972--5065031 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
5064962 GACCTGAACT
**
5064972 TTAAAATATAAAAAGTAAAATTTTAAATTC
1 TTAAAATATAAAAAGTAAAAAATTAAATTC
5065002 TTAAAA-ATAAAAA-TATAAAAATTAAATTC
1 TTAAAATATAAAAAGTA-AAAAATTAAATTC
5065031 T
1 T
5065032 AAATTCTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 19 0.70
30 6 0.22
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (30 bp):
TTAAAATATAAAAAGTAAAAAATTAAATTC
Found at i:5069556 original size:2 final size:2
Alignment explanation
Indices: 5069511--5069546 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5069501 AATACCTTGA
*
5069511 AT AT AA 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 AT AT AT
5069547 GTCAATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5072077 original size:15 final size:12
Alignment explanation
Indices: 5072048--5072073 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5072038 TGTAAATGTC
5072048 AATTTTATTATA
1 AATTTTATTATA
5072060 AATTTTATTATA
1 AATTTTATTATA
5072072 AA
1 AA
5072074 AAATATATTT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AATTTTATTATA
Found at i:5079948 original size:31 final size:31
Alignment explanation
Indices: 5079895--5079953 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
5079885 ATTCAAGTTA
* * *
5079895 GGTCTTGAACTTGATAATTATTCCCACACTG
1 GGTCTTGAACTAGACAACTATTCCCACACTG
*
5079926 GGTCTTGAACTAGACAACTATTCTCACA
1 GGTCTTGAACTAGACAACTATTCCCACA
5079954 TTAGAGCTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (31 bp):
GGTCTTGAACTAGACAACTATTCCCACACTG
Found at i:5083469 original size:3 final size:3
Alignment explanation
Indices: 5083461--5083489 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5083451 TCCTTCTTTC
5083461 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
5083490 AGCCTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:5084468 original size:18 final size:17
Alignment explanation
Indices: 5084445--5084479 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5084435 GGCTTGGTTG
5084445 CCTCAGGATCATCTATCT
1 CCTCAGGATCATC-ATCT
*
5084463 CCTCAGGCTCATCATCT
1 CCTCAGGATCATCATCT
5084480 AACCATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.20, C:0.37, G:0.11, T:0.31
Consensus pattern (17 bp):
CCTCAGGATCATCATCT
Found at i:5087605 original size:12 final size:12
Alignment explanation
Indices: 5087588--5087622 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
5087578 TTATATTTAT
5087588 TTAATGTTAATG
1 TTAATGTTAATG
5087600 TTAATGTTAATG
1 TTAATGTTAATG
5087612 TTAATGTTAAT
1 TTAATGTTAAT
5087623 ATAATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (12 bp):
TTAATGTTAATG
Done.