Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008621.1 Hibiscus syriacus cultivar Beakdansim tig00111584_pilon, 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: 1991651
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 11
Found at i:3351 original size:19 final size:18
Alignment explanation
Indices: 3299--3358 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
3289 TAAAGTTTGG
3299 TAAAGAAAATAGA-GGAA
1 TAAAGAAAATAGAGGGAA
3316 TAAGATGAGAGAATAGAGGGAA
1 TAA-A-GA-A-AATAGAGGGAA
3338 TTAAAGAAAATAGA-GGAA
1 -TAAAGAAAATAGAGGGAA
3356 TAA
1 TAA
3359 GTGAAATCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
17 6 0.16
18 5 0.14
19 8 0.22
20 2 0.05
21 8 0.22
22 5 0.14
23 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (18 bp):
TAAAGAAAATAGAGGGAA
Found at i:4667 original size:23 final size:23
Alignment explanation
Indices: 4623--4749 Score: 114
Period size: 23 Copynumber: 5.3 Consensus size: 23
4613 CACCACAGCT
*
4623 CATATAATTGCACACCGAAGTGCCA
1 CATATAATTG--CACCGTAGTGCCA
*
4648 CATATAATTGCACCAG-AGTGCCG
1 CATATAATTGCACC-GTAGTGCCA
* *
4671 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGTAGTGCCA
* *
4694 TATAATAATTGCACCAG-AGTGCCG
1 CAT-ATAATTGCACC-GTAGTGCCA
*
4718 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGTAGTGCCA
*
4741 TATAATAAT
1 CAT-ATAAT
4750 GTCCATAAGA
Statistics
Matches: 83, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
22 2 0.02
23 47 0.57
24 23 0.28
25 11 0.13
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGTAGTGCCA
Found at i:4707 original size:24 final size:24
Alignment explanation
Indices: 4676--4749 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
4666 TGCCGCGTAG
4676 AATTGCACCGTAGTGCCATATAAT
1 AATTGCACCGTAGTGCCATATAAT
** *
4700 AATTGCACCAG-AGTGCCGCAT-AG
1 AATTGCACC-GTAGTGCCATATAAT
4723 AATTGCACCGTAGTGCCATATAAT
1 AATTGCACCGTAGTGCCATATAAT
4747 AAT
1 AAT
4750 GTCCATAAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
22 1 0.02
23 18 0.44
24 21 0.51
25 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (24 bp):
AATTGCACCGTAGTGCCATATAAT
Found at i:4709 original size:47 final size:47
Alignment explanation
Indices: 4635--4749 Score: 196
Period size: 47 Copynumber: 2.5 Consensus size: 47
4625 TATAATTGCA
* * *
4635 CACCGAAGTGCCACAT-ATAATTGCACCAGAGTGCCGCGTAGAATTG
1 CACCGTAGTGCCATATAATAATTGCACCAGAGTGCCGCATAGAATTG
4681 CACCGTAGTGCCATATAATAATTGCACCAGAGTGCCGCATAGAATTG
1 CACCGTAGTGCCATATAATAATTGCACCAGAGTGCCGCATAGAATTG
4728 CACCGTAGTGCCATATAATAAT
1 CACCGTAGTGCCATATAATAAT
4750 GTCCATAAGA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
46 14 0.22
47 51 0.78
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (47 bp):
CACCGTAGTGCCATATAATAATTGCACCAGAGTGCCGCATAGAATTG
Found at i:10328 original size:23 final size:23
Alignment explanation
Indices: 10302--10426 Score: 117
Period size: 23 Copynumber: 5.3 Consensus size: 23
10292 CACCACATCT
*
10302 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
10325 CATATAATTGCACCGGAGTGCCT
1 CATATAATTGCACCGGAGTGCCA
* * *
10348 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
* *
10371 TATAATAATAT-CACCGGAGTGCCG
1 CAT-ATAAT-TGCACCGGAGTGCCA
* * *
10395 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
10418 TATAATAAT
1 CAT-ATAAT
10427 GTCCATAAGG
Statistics
Matches: 79, Mismatches: 19, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
22 1 0.01
23 57 0.72
24 20 0.25
25 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (23 bp):
CATATAATTGCACCGGAGTGCCA
Found at i:10393 original size:47 final size:47
Alignment explanation
Indices: 10307--10426 Score: 190
Period size: 47 Copynumber: 2.6 Consensus size: 47
10297 CATCTCATAT
* * *
10307 AATTGCACCGAAGTGCCACAT-ATAATTGCACCGGAGTGCCTCGTAG
1 AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
10353 AATTGCACCGTAGTGCCATATAATAATAT-CACCGGAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCATATAATAAT-TGCACCGGAGTGCCGCGTAG
10400 AATTGCACCGTAGTGCCATATAATAAT
1 AATTGCACCGTAGTGCCATATAATAAT
10427 GTCCATAAGG
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
46 19 0.28
47 49 0.71
48 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (47 bp):
AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
Found at i:10604 original size:103 final size:103
Alignment explanation
Indices: 10433--10650 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
10423 TAATGTCCAT
* *
10433 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
10498 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
10536 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
10601 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
10639 AAGGACCACATA
1 AAGGACCACATA
10651 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:12568 original size:25 final size:25
Alignment explanation
Indices: 12539--12588 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
12529 GATTAGGGGT
12539 ACTGAAGCATAAACATGTAGGGATA
1 ACTGAAGCATAAACATGTAGGGATA
*
12564 ACTGAAGCATAAACATGTAGTGATA
1 ACTGAAGCATAAACATGTAGGGATA
12589 TGGTGCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (25 bp):
ACTGAAGCATAAACATGTAGGGATA
Found at i:13103 original size:29 final size:28
Alignment explanation
Indices: 13061--13126 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 28
13051 AAGAGTCGAG
*
13061 GGTTCTACGTGGTCCTACGGGATATATGT
1 GGTTCTACGTGGTCCTACGGGACATA-GT
13090 GGTTCTACGTGGTCCTACGGGACATAGT
1 GGTTCTACGTGGTCCTACGGGACATAGT
*
13118 GGTCCTACG
1 GGTTCTACG
13127 GGACAAATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 10 0.29
29 25 0.71
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (28 bp):
GGTTCTACGTGGTCCTACGGGACATAGT
Found at i:14157 original size:23 final size:23
Alignment explanation
Indices: 14120--14176 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
14110 TGTCTGATAT
*
14120 GTTTTCATCTACCTTTATAATAC
1 GTTTTCTTCTACCTTTATAATAC
*
14143 GTTTTCTTCTGCCTTTATAATAC
1 GTTTTCTTCTACCTTTATAATAC
*
14166 TTTTTCTTCTA
1 GTTTTCTTCTA
14177 TCTTGACACA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.19, C:0.21, G:0.05, T:0.54
Consensus pattern (23 bp):
GTTTTCTTCTACCTTTATAATAC
Found at i:15065 original size:17 final size:17
Alignment explanation
Indices: 15045--15077 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
15035 TATGTTAGAT
15045 AATTTTTTATTATATTA
1 AATTTTTTATTATATTA
15062 AATTTTTTATTATATT
1 AATTTTTTATTATATT
15078 TATATTGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
AATTTTTTATTATATTA
Found at i:15668 original size:21 final size:20
Alignment explanation
Indices: 15643--15681 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
15633 TGATAATAAA
15643 AATAAATCAAAGAAAAAAAAC
1 AATAAATC-AAGAAAAAAAAC
*
15664 AATAAATCAATAAAAAAA
1 AATAAATCAAGAAAAAAA
15682 TAAAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.77, C:0.08, G:0.03, T:0.13
Consensus pattern (20 bp):
AATAAATCAAGAAAAAAAAC
Found at i:15686 original size:28 final size:28
Alignment explanation
Indices: 15655--15712 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
15645 TAAATCAAAG
*
15655 AAAAAAAA-CAATAAATCAATAAAAAAAT
1 AAAAAAAAGCAA-AAATAAATAAAAAAAT
* *
15683 AAAAAAAAGTAAAAATAAATAAATAAAT
1 AAAAAAAAGCAAAAATAAATAAAAAAAT
15711 AA
1 AA
15713 TAATATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.79, C:0.03, G:0.02, T:0.16
Consensus pattern (28 bp):
AAAAAAAAGCAAAAATAAATAAAAAAAT
Found at i:15702 original size:4 final size:4
Alignment explanation
Indices: 15642--15727 Score: 51
Period size: 4 Copynumber: 22.5 Consensus size: 4
15632 ATGATAATAA
* * * *
15642 AAAT AAAT CAAAG AAA- AAAA ACAAT AAAT CAAT AAAA AAAT AAA- AAA-
1 AAAT AAAT -AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT
*
15689 AAGT -AA- AAAT AAAT AAAT AAAT -AAT -AAT ATAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AA
15728 CCTAGAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
3 17 0.26
4 39 0.59
5 10 0.15
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:15714 original size:15 final size:15
Alignment explanation
Indices: 15672--15727 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
15662 ACAATAAATC
*
15672 AATAAAAAAATAA-A
1 AATAAATAAATAATA
15686 AA-AAAGTAAA-AATA
1 AATAAA-TAAATAATA
15700 AATAAATAAATAAT-
1 AATAAATAAATAATA
15714 AATATAATAAATAA
1 AATA-AATAAATAA
15728 CCTAGAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 5 0.14
14 16 0.44
15 15 0.42
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (15 bp):
AATAAATAAATAATA
Found at i:15757 original size:15 final size:15
Alignment explanation
Indices: 15731--15791 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
15721 TAAATAACCT
**
15731 AGAAAA-ATAATATC
1 AGAAAATATAATAAA
15745 AGAAAATATAATAAA
1 AGAAAATATAATAAA
15760 AGAAATATATAA-AAA
1 AGAAA-ATATAATAAA
*
15775 GAGTAAAATAAAATAAA
1 -AG-AAAATATAATAAA
15792 GGGGAAAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 6 0.15
15 14 0.36
16 13 0.33
17 6 0.15
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (15 bp):
AGAAAATATAATAAA
Found at i:16439 original size:9 final size:9
Alignment explanation
Indices: 16413--16486 Score: 55
Period size: 10 Copynumber: 7.7 Consensus size: 9
16403 GGGGCCTGCA
16413 AAAAT-AAT
1 AAAATAAAT
16421 AAAATAAAAT
1 AAAAT-AAAT
16431 AAAATAAAT
1 AAAATAAAT
16440 AATAAT-AAT
1 AA-AATAAAT
16449 AATAAT-AAT
1 AA-AATAAAT
16458 AATAAATAAAT
1 -A-AAATAAAT
16469 ATATAATATAAT
1 A-A-AATA-AAT
16481 AAAATA
1 AAAATA
16487 TTTTTGTAGA
Statistics
Matches: 58, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
8 5 0.09
9 18 0.31
10 22 0.38
11 9 0.16
12 4 0.07
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAAATAAAT
Found at i:16445 original size:3 final size:3
Alignment explanation
Indices: 16415--16486 Score: 73
Period size: 3 Copynumber: 24.3 Consensus size: 3
16405 GGCCTGCAAA
16415 AAT AAT AA- AAT AA- AAT AA- AAT AAAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
16458 AAT AAAT AAAT ATAT AAT -AT AAT AA- AAT A
1 AAT -AAT -AAT A-AT AAT AAT AAT AAT AAT A
16487 TTTTTGTAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
2 10 0.16
3 38 0.62
4 13 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:18517 original size:32 final size:32
Alignment explanation
Indices: 18476--18539 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
18466 TCATCACATT
* * *
18476 ATTATTTATGTACATGTCATATATGTCACGTC
1 ATTACTTATGTACATATCATATATATCACGTC
*
18508 ATTACTTATGTACATATGATATATATCACGTC
1 ATTACTTATGTACATATCATATATATCACGTC
18540 TTTCATGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (32 bp):
ATTACTTATGTACATATCATATATATCACGTC
Found at i:18590 original size:32 final size:32
Alignment explanation
Indices: 18549--18656 Score: 101
Period size: 32 Copynumber: 3.3 Consensus size: 32
18539 CTTTCATGTC
18549 ATCATTTATGCATAAATAGTATATGTCACGTT
1 ATCATTTATGCATAAATAGTATATGTCACGTT
* ** * *
18581 ATCATTTATGCACATGTATTAT-TGTCACATT
1 ATCATTTATGCATAAATAGTATATGTCACGTT
* * *
18612 ATAATTTATGTACATAAATGTAGTATATGTCATGTC
1 ATCATTTATG--CATAAA--TAGTATATGTCACGTT
18648 ATCATTTAT
1 ATCATTTAT
18657 ATACATATGG
Statistics
Matches: 57, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
31 17 0.30
32 18 0.32
33 3 0.05
35 5 0.09
36 14 0.25
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (32 bp):
ATCATTTATGCATAAATAGTATATGTCACGTT
Found at i:18844 original size:20 final size:20
Alignment explanation
Indices: 18819--18856 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18809 GCCCCAACCC
18819 CTGTTATAATTTATAAATCT
1 CTGTTATAATTTATAAATCT
*
18839 CTGTTATGATTTATAAAT
1 CTGTTATAATTTATAAAT
18857 TTAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (20 bp):
CTGTTATAATTTATAAATCT
Found at i:24771 original size:17 final size:18
Alignment explanation
Indices: 24749--24787 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
24739 TCAGATGAAC
24749 AGTTTT-TTGTTAAAAAT
1 AGTTTTGTTGTTAAAAAT
* *
24766 AGTTTTGTTTTTCAAAAT
1 AGTTTTGTTGTTAAAAAT
24784 AGTT
1 AGTT
24788 CTCTTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.54
Consensus pattern (18 bp):
AGTTTTGTTGTTAAAAAT
Found at i:26153 original size:29 final size:29
Alignment explanation
Indices: 26105--26160 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
26095 GATGAAATAT
* *
26105 AAAAGCTACAAAATTTCAAAACTAAAGCC
1 AAAAGCTACAAAACTCCAAAACTAAAGCC
*
26134 AAAAGCTACAAAACTCCAAAAGTAAAG
1 AAAAGCTACAAAACTCCAAAACTAAAG
26161 TGAACAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.57, C:0.20, G:0.09, T:0.14
Consensus pattern (29 bp):
AAAAGCTACAAAACTCCAAAACTAAAGCC
Found at i:27165 original size:13 final size:13
Alignment explanation
Indices: 27147--27171 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27137 AGTTAAACAA
27147 TCTACATATGCAG
1 TCTACATATGCAG
27160 TCTACATATGCA
1 TCTACATATGCA
27172 CATCTGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (13 bp):
TCTACATATGCAG
Found at i:29359 original size:12 final size:12
Alignment explanation
Indices: 29342--29382 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
29332 TGCTTAAATG
29342 AAATAGAATCAT
1 AAATAGAATCAT
29354 AAATAGAATCAT
1 AAATAGAATCAT
*
29366 AAATAAAATCAT
1 AAATAGAATCAT
29378 AAATA
1 AAATA
29383 ACATAAGGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.24
Consensus pattern (12 bp):
AAATAGAATCAT
Found at i:29449 original size:2 final size:2
Alignment explanation
Indices: 29442--29491 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
29432 AAAATATGAA
29442 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
29484 AT AT AT AT
1 AT AT AT AT
29492 GGGACTAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31293 original size:160 final size:161
Alignment explanation
Indices: 30870--31293 Score: 399
Period size: 160 Copynumber: 2.6 Consensus size: 161
30860 GCATATATTT
* * *
30870 TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTGATCAGACGAGTTCTTC-CATTATGAACC
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT-ATTAGAAGAGTTCTTCTCATTATGAA-C
** * *
30934 CTTCCATTAGAAATGTTGATCCACATCCTGT-TGTGATGGATTTGAACAAAGTGTTGATGCTGAT
64 CTTCCATTAGAAATGAAGATCCACTTCCT-TCTGTGATGGATTTGAACAAAATGTTGATGCTGAT
* * *
30998 ATACCTCATTTTGTGGTAGAATTGAGCAAAATGGT
128 ATA-CTCATTTTGTGATAGAATTGAGCAAAAAGGG
* * * * *
31033 TGAATAAGTTCTTCTCATTATGAACTTTTTC-TCTTATTCAAAAAAGTTC-T-T-ATTATGAACC
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATT-AGAAGAGTTCTTCTCATTATGAACC
* * * * *
31094 ATTCCATTGGAAAT-AACGATCCACCTT-ATTCTATGATGGATTTGATCAAAATGTTGATGGTGA
65 -TTCCATTAGAAATGAA-GATCCA-CTTCCTTCTGTGATGGATTTGAACAAAATGTTGATGCTGA
31157 TATA-TC-TTTCTGTGATAGAATCT-AG-AAAAAGGG
127 TATACTCATTT-TGTGATAGAAT-TGAGCAAAAAGGG
* *
31190 TGAACAAG-TCTTTCTCATTATGAACTTCTTCTTCCTCTTAGGATGAGTTCTTCTCATTATGAA-
1 TGAACAAGTTC-TTCTCATTATGAACTTCTTCTTCCTATTA-GAAGAGTTCTTCTCATTATGAAC
* * * *
31253 TTCTCCATTTGAAATGCAGATCCATTTCCTTCTGTGATGGA
64 CT-TCCATTAGAAATGAAGATCCACTTCCTTCTGTGATGGA
31294 ATAGAATATG
Statistics
Matches: 211, Mismatches: 33, Indels: 37
0.75 0.12 0.13
Matches are distributed among these distances:
156 2 0.01
157 36 0.17
158 25 0.12
159 8 0.04
160 88 0.42
161 14 0.07
162 9 0.04
163 29 0.14
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (161 bp):
TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTAGAAGAGTTCTTCTCATTATGAACCT
TCCATTAGAAATGAAGATCCACTTCCTTCTGTGATGGATTTGAACAAAATGTTGATGCTGATATA
CTCATTTTGTGATAGAATTGAGCAAAAAGGG
Found at i:33507 original size:24 final size:24
Alignment explanation
Indices: 33479--33537 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
33469 TAAACTGAGT
33479 GTATCGATACCTCTATATAAAGGG
1 GTATCGATACCTCTATATAAAGGG
* *
33503 GTATCAATACCTCTGTATAAAGGG
1 GTATCGATACCTCTATATAAAGGG
*
33527 GTATCGGTACC
1 GTATCGATACC
33538 CTGTAGGGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (24 bp):
GTATCGATACCTCTATATAAAGGG
Found at i:39113 original size:20 final size:21
Alignment explanation
Indices: 39074--39113 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
39064 GAAACTTTAA
* *
39074 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
39095 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
39114 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:42098 original size:32 final size:31
Alignment explanation
Indices: 42056--42182 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
42046 AGAGTCGAGG
42056 GTTTACCTATGTTCTATGGAACATATGGACA
1 GTTTACCTATGTTCTATGGAACATATGGACA
* *
42087 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTATGGA-ACATATGGACA
* *
42119 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTATGGAACATATGGACA
* * * * *
42150 -TTTACCTAGGTTCTTTGGGACCTATAGACA
1 GTTTACCTATGTTCTATGGAACATATGGACA
42180 GTT
1 GTT
42183 GCCGAGGTTC
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
30 23 0.29
31 29 0.37
32 27 0.34
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTATGGAACATATGGACA
Found at i:47286 original size:32 final size:31
Alignment explanation
Indices: 47244--47371 Score: 134
Period size: 31 Copynumber: 4.1 Consensus size: 31
47234 AGAGTCGAGG
47244 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
47275 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* * *
47307 GTATACCTATGTTCTAAGGAACATATAGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* ** * *
47338 GTTTACCTAGGTTCTTTGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
47369 GTT
1 GTT
47372 ATCGGGGTCT
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 52 0.65
32 28 0.35
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:47354 original size:63 final size:62
Alignment explanation
Indices: 47247--47370 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 62
47237 GTCGAGGGTT
* * *
47247 TACCTATGTTCTACGGAACATATGGACAGTTTTACCTATGTCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTAAGGAACATATAGACAGTTTTACCTAGGTCTTT-GAGACATATGGACAGTA
* *
47310 TACCTATGTTCTAAGGAACATATAGACAG-TTTACCTAGGTTCTTTGGGACCTATGGACAGT
1 TACCTATGTTCTAAGGAACATATAGACAGTTTTACCTAGG-TCTTTGAGACATATGGACAGT
47371 TATCGGGGTC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
62 23 0.42
63 32 0.58
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (62 bp):
TACCTATGTTCTAAGGAACATATAGACAGTTTTACCTAGGTCTTTGAGACATATGGACAGTA
Found at i:50448 original size:1 final size:1
Alignment explanation
Indices: 50444--50522 Score: 95
Period size: 1 Copynumber: 79.0 Consensus size: 1
50434 TCCATTTTCG
* * * * *
50444 TTTTTTCTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTCTTTTTTTTCTTTTTTTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
50509 TTTTCTTTCTTTTT
1 TTTTTTTTTTTTTT
50523 CTTTATTCAA
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:50449 original size:8 final size:7
Alignment explanation
Indices: 50438--50551 Score: 89
Period size: 7 Copynumber: 16.6 Consensus size: 7
50428 TTTTTTTCCA
50438 TTTTCGTT
1 TTTTC-TT
50446 TTTTCTT
1 TTTTCTT
50453 TTTT-TT
1 TTTTCTT
50459 TTTT-TT
1 TTTTCTT
*
50465 TCTT-TT
1 TTTTCTT
50471 TTTT-TT
1 TTTTCTT
50477 TTTT-TT
1 TTTTCTT
50483 TTTTCTT
1 TTTTCTT
50490 TTTT-TT
1 TTTTCTT
50496 CTTTT-TT
1 -TTTTCTT
50503 TTTTCTT
1 TTTTCTT
*
50510 TTTCTTTCT
1 TTT-TCT-T
50519 TTTTCTT
1 TTTTCTT
* **
50526 TATTCAA
1 TTTTCTT
50533 TTTTCTT
1 TTTTCTT
50540 TCTTTCTT
1 T-TTTCTT
50548 TTTT
1 TTTT
50552 TTTCTTATTA
Statistics
Matches: 90, Mismatches: 10, Indels: 13
0.80 0.09 0.12
Matches are distributed among these distances:
6 34 0.38
7 36 0.40
8 16 0.18
9 4 0.04
ACGTcount: A:0.03, C:0.11, G:0.01, T:0.85
Consensus pattern (7 bp):
TTTTCTT
Found at i:50457 original size:10 final size:10
Alignment explanation
Indices: 50444--50567 Score: 107
Period size: 10 Copynumber: 12.8 Consensus size: 10
50434 TCCATTTTCG
50444 TTTTTTCTTT
1 TTTTTTCTTT
50454 TTTTTT-TTT
1 TTTTTTCTTT
*
50463 TTTCTT-TTT
1 TTTTTTCTTT
50472 TTTTTT-TTT
1 TTTTTTCTTT
50481 TTTTTTC-TT
1 TTTTTTCTTT
50490 TTTTTTCTTTT
1 TTTTTTC-TTT
50501 TTTTTTCTTT
1 TTTTTTCTTT
*
50511 TTCTTTCTTT
1 TTTTTTCTTT
* * *
50521 TTCTTTATTC
1 TTTTTTCTTT
**
50531 AATTTTC--T
1 TTTTTTCTTT
*
50539 TTCTTTCTTT
1 TTTTTTCTTT
50549 TTTTTTCTTAT
1 TTTTTTCTT-T
*
50560 TATTTTCT
1 TTTTTTCT
50568 ATCATTCTCC
Statistics
Matches: 93, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
8 4 0.04
9 34 0.37
10 38 0.41
11 17 0.18
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:50457 original size:16 final size:16
Alignment explanation
Indices: 50438--50552 Score: 96
Period size: 16 Copynumber: 7.2 Consensus size: 16
50428 TTTTTTTCCA
*
50438 TTTTCGTTTTTTCTTT
1 TTTTCTTTTTTTCTTT
*
50454 TTTTTTTTTTTTC-TT
1 TTTTCTTTTTTTCTTT
50469 TTTT-TTTTTTT-TTT
1 TTTTCTTTTTTTCTTT
50483 TTTTCTTTTTTTTCTTT
1 TTTTC-TTTTTTTCTTT
*
50500 TTTTTTTCTTTTTCTTT
1 TTTTCTT-TTTTTCTTT
* **
50517 CTTTT-TCTTTATTC-AA
1 -TTTTCT-TTTTTTCTTT
*
50533 TTTTCTTTCTTTCTTT
1 TTTTCTTTTTTTCTTT
50549 TTTT
1 TTTT
50553 TTCTTATTAT
Statistics
Matches: 80, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
14 13 0.16
15 15 0.19
16 25 0.31
17 22 0.28
18 5 0.06
ACGTcount: A:0.03, C:0.11, G:0.01, T:0.85
Consensus pattern (16 bp):
TTTTCTTTTTTTCTTT
Found at i:50462 original size:21 final size:20
Alignment explanation
Indices: 50444--50552 Score: 125
Period size: 18 Copynumber: 5.3 Consensus size: 20
50434 TCCATTTTCG
50444 TTTTTTCTTTTTTTT-TTTT
1 TTTTTTCTTTTTTTTCTTTT
*
50463 TTTCTT-TTTTTTTT-TTTT
1 TTTTTTCTTTTTTTTCTTTT
50481 TTTTTTCTTTTTTTTCTTTT
1 TTTTTTCTTTTTTTTCTTTT
50501 TTTTTTCTTTTTCTTTCTTTT
1 TTTTTTCTTTTT-TTTCTTTT
*
50522 TCTTTATTCAATTTTCTTTCTTTCT
1 T-TTT-TTC--TTTTTTTTCTTT-T
50547 TTTTTT
1 TTTTTT
50553 TTCTTATTAT
Statistics
Matches: 79, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
18 17 0.22
19 13 0.16
20 16 0.20
21 9 0.11
22 3 0.04
23 5 0.06
24 10 0.13
25 6 0.08
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (20 bp):
TTTTTTCTTTTTTTTCTTTT
Found at i:50464 original size:30 final size:30
Alignment explanation
Indices: 50428--50554 Score: 110
Period size: 30 Copynumber: 4.1 Consensus size: 30
50418 CCTCATTTAA
*
50428 TTTTTTTCCATTTTCGTTTTTTCTTTTTTT
1 TTTTTTTCCATTTTCTTTTTTTCTTTTTTT
* * * *
50458 TTTTTTTTCTTTTTTTTTTTTTTTTTTTTCT
1 TTTTTTTCCATTTTCTTTTTTTCTTTTTT-T
** *
50489 TTTTTTTCTTTTTTTTTTCTTTTTCTTTCTTTT
1 TTTTTTTC-CATTTTCTT-TTTTTCTTT-TTTT
* * *
50522 TCTTTATTCAATTTTCTTTCTTTCTTTTTTT
1 T-TTTTTTCCATTTTCTTTTTTTCTTTTTTT
50553 TT
1 TT
50555 CTTATTATTT
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
30 25 0.32
31 13 0.16
32 16 0.20
33 16 0.20
34 9 0.11
ACGTcount: A:0.03, C:0.12, G:0.01, T:0.84
Consensus pattern (30 bp):
TTTTTTTCCATTTTCTTTTTTTCTTTTTTT
Found at i:50565 original size:14 final size:13
Alignment explanation
Indices: 50444--50557 Score: 108
Period size: 14 Copynumber: 8.7 Consensus size: 13
50434 TCCATTTTCG
50444 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
*
50457 TTTTTT-TTTCTT
1 TTTTTTCTTTTTT
50469 TTTTTT-TTTTTT
1 TTTTTTCTTTTTT
50481 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
50494 TTCTTTT-TTTTTT
1 TT-TTTTCTTTTTT
*
50507 CTTTTTCTTTCTTT
1 TTTTTTCTTT-TTT
* * **
50521 TTCTTTATTCAATT
1 TTTTTTCTT-TTTT
*
50535 TTCTTTCTTTCTTT
1 TTTTTTCTTT-TTT
50549 TTTTTTCTT
1 TTTTTTCTT
50558 ATTATTTTCT
Statistics
Matches: 83, Mismatches: 12, Indels: 11
0.78 0.11 0.10
Matches are distributed among these distances:
12 26 0.31
13 24 0.29
14 33 0.40
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:53973 original size:23 final size:23
Alignment explanation
Indices: 53947--53991 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
53937 CACCACAGCT
*
53947 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* * *
53970 CGTAGAATTGTACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
53992 ATATAATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:63586 original size:13 final size:13
Alignment explanation
Indices: 63568--63593 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63558 AAGGGGGAGA
63568 AAGTGTGTGTTTT
1 AAGTGTGTGTTTT
63581 AAGTGTGTGTTTT
1 AAGTGTGTGTTTT
63594 TAAAATGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
AAGTGTGTGTTTT
Found at i:70296 original size:23 final size:23
Alignment explanation
Indices: 70270--70314 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
70260 CACCACAGCT
*
70270 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* * *
70293 CGTAGAATTGTACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
70315 ATATAATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:75675 original size:23 final size:23
Alignment explanation
Indices: 75649--75693 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
75639 CACCACAGCT
*
75649 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
75672 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
75694 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:75891 original size:129 final size:129
Alignment explanation
Indices: 75672--75926 Score: 492
Period size: 129 Copynumber: 2.0 Consensus size: 129
75662 CGAAGTGCCC
75672 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
*
75737 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTCCCGAAGAACCG
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTCCCAAAGAACCG
75801 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
*
75866 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTCCCAAAGAA
75927 TATACATATG
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 124 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (129 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTCCCAAAGAACCG
Found at i:76486 original size:17 final size:19
Alignment explanation
Indices: 76449--76486 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
76439 ATTTCATATC
*
76449 AATTCTTATACCATCACAT
1 AATTCTTATAACATCACAT
76468 AATTCTT-TAACAT-ACAT
1 AATTCTTATAACATCACAT
76485 AA
1 AA
76487 CATATCATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 5 0.28
19 7 0.39
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (19 bp):
AATTCTTATAACATCACAT
Found at i:77492 original size:21 final size:21
Alignment explanation
Indices: 77462--77506 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
77452 ATTTTGTCGT
* *
77462 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
77483 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
77504 TTG
1 TTG
77507 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:85131 original size:23 final size:23
Alignment explanation
Indices: 85105--85149 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
85095 CACCACAGCT
*
85105 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
85128 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
85150 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:86910 original size:21 final size:21
Alignment explanation
Indices: 86886--86930 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
86876 TGTTGTTCGT
* *
86886 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
86907 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
86928 TTG
1 TTG
86931 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:90055 original size:23 final size:23
Alignment explanation
Indices: 90029--90073 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
90019 CACCACAGCT
*
90029 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
90052 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
90074 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:90294 original size:149 final size:149
Alignment explanation
Indices: 90041--90355 Score: 544
Period size: 149 Copynumber: 2.1 Consensus size: 149
90031 TATAATTGCA
*
90041 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
*
90105 TTCCTTAAGAATCATATACATATTCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACACATGTT
* *
90170 CCACAGAATATATATATATC
130 CCAAAGAATATACATATATC
90190 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
*
90255 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTTTCAAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTCTCTCAAGACTTCACACATGTT
*
90319 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATATC
90339 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
90356 CCCTCGACTC
Statistics
Matches: 158, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
148 1 0.01
149 156 0.99
150 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:100498 original size:18 final size:18
Alignment explanation
Indices: 100462--100501 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
100452 TTTCTTTTTT
**
100462 AAATATCATAAAATTGTA
1 AAATATCATAAAAGAGTA
100480 AAATATCATAAAAGAGTA
1 AAATATCATAAAAGAGTA
100498 AAAT
1 AAAT
100502 TTTTCCCAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (18 bp):
AAATATCATAAAAGAGTA
Found at i:100594 original size:30 final size:31
Alignment explanation
Indices: 100543--100603 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
100533 TAATTTCCTC
100543 ATTTCTTGAAAAATGTAATTATGTTCAATTA
1 ATTTCTTGAAAAATGTAATTATGTTCAATTA
*
100574 ATTTCTTGAAAAAT-TAATTATGTTTAATTA
1 ATTTCTTGAAAAATGTAATTATGTTCAATTA
100604 CTTTTTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (31 bp):
ATTTCTTGAAAAATGTAATTATGTTCAATTA
Found at i:107074 original size:151 final size:151
Alignment explanation
Indices: 106800--107102 Score: 606
Period size: 151 Copynumber: 2.0 Consensus size: 151
106790 AGAGGGGAAA
106800 CCCTATCTTATAAAGAGAAGAGCATGATGGGGCCCTGCTAATTGGGTTGAGTAGCCTTTCCAAGG
1 CCCTATCTTATAAAGAGAAGAGCATGATGGGGCCCTGCTAATTGGGTTGAGTAGCCTTTCCAAGG
106865 AGTCTCATAGCCAATCTCCATCACTAAGGGAGAGCTTTTGACTAGCCTAGCTTTTACAAAAGAAC
66 AGTCTCATAGCCAATCTCCATCACTAAGGGAGAGCTTTTGACTAGCCTAGCTTTTACAAAAGAAC
106930 CCCATTCAATAAGCTAAAAGT
131 CCCATTCAATAAGCTAAAAGT
106951 CCCTATCTTATAAAGAGAAGAGCATGATGGGGCCCTGCTAATTGGGTTGAGTAGCCTTTCCAAGG
1 CCCTATCTTATAAAGAGAAGAGCATGATGGGGCCCTGCTAATTGGGTTGAGTAGCCTTTCCAAGG
107016 AGTCTCATAGCCAATCTCCATCACTAAGGGAGAGCTTTTGACTAGCCTAGCTTTTACAAAAGAAC
66 AGTCTCATAGCCAATCTCCATCACTAAGGGAGAGCTTTTGACTAGCCTAGCTTTTACAAAAGAAC
107081 CCCATTCAATAAGCTAAAAGT
131 CCCATTCAATAAGCTAAAAGT
107102 C
1 C
107103 GAGCTTTGAG
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
151 152 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (151 bp):
CCCTATCTTATAAAGAGAAGAGCATGATGGGGCCCTGCTAATTGGGTTGAGTAGCCTTTCCAAGG
AGTCTCATAGCCAATCTCCATCACTAAGGGAGAGCTTTTGACTAGCCTAGCTTTTACAAAAGAAC
CCCATTCAATAAGCTAAAAGT
Found at i:108258 original size:11 final size:11
Alignment explanation
Indices: 108242--108267 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
108232 TATATATAAT
108242 TTTTTTTTTTA
1 TTTTTTTTTTA
108253 TTTTTTTTTTA
1 TTTTTTTTTTA
108264 TTTT
1 TTTT
108268 CAATAATAGA
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:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:119449 original size:21 final size:21
Alignment explanation
Indices: 119425--119500 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
119415 TTGACTGTTA
* *
119425 ATTAATGTGATATTTTATTTT
1 ATTAATGTGATAATTTATTAT
*
119446 ATTAATGTAATAATTTATTAT
1 ATTAATGTGATAATTTATTAT
* * *
119467 ATTATTGTGATAATTCATGAT
1 ATTAATGTGATAATTTATTAT
* *
119488 AATGATGTGATAA
1 ATTAATGTGATAA
119501 ATCATGTGTG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.37, C:0.01, G:0.12, T:0.50
Consensus pattern (21 bp):
ATTAATGTGATAATTTATTAT
Found at i:119703 original size:20 final size:22
Alignment explanation
Indices: 119663--119709 Score: 71
Period size: 20 Copynumber: 2.2 Consensus size: 22
119653 ATTAAGACAT
119663 TATTAAAATATTTTAATAAAAA
1 TATTAAAATATTTTAATAAAAA
*
119685 TATTAAAATA-TTT-ATAAAAG
1 TATTAAAATATTTTAATAAAAA
119705 TATTA
1 TATTA
119710 TAAAAGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 11 0.46
21 3 0.12
22 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAATATTTTAATAAAAA
Found at i:119713 original size:22 final size:24
Alignment explanation
Indices: 119661--119714 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
119651 GTATTAAGAC
119661 ATTATTAAAATATTTTAATAAAAAT
1 ATTA-TAAAATATTTTAATAAAAAT
*
119686 A-T-TAAAATA-TTT-ATAAAAGT
1 ATTATAAAATATTTTAATAAAAAT
119706 ATTATAAAA
1 ATTATAAAA
119715 GTTAACTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 8 0.31
21 4 0.15
22 12 0.46
24 1 0.04
25 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
ATTATAAAATATTTTAATAAAAAT
Found at i:122047 original size:23 final size:20
Alignment explanation
Indices: 121994--122072 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
121984 TCGAAATGGA
121994 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTACATG
*
122014 GTGCATCGATGCACTAGTGGCA-G
1 GTGCATGGATGCACTA----CATG
* *
122037 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTACA-TG
*
122058 GTTCATGGATGCACT
1 GTGCATGGATGCACT
122073 TTGACACCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
19 2 0.04
20 15 0.31
21 15 0.31
23 15 0.31
24 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (20 bp):
GTGCATGGATGCACTACATG
Found at i:122320 original size:21 final size:21
Alignment explanation
Indices: 122296--122335 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
122286 ATGTTTAATG
122296 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
122317 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
122336 CCAATTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:122434 original size:103 final size:106
Alignment explanation
Indices: 122272--122482 Score: 374
Period size: 103 Copynumber: 2.0 Consensus size: 106
122262 TTGGAAAAAC
* *
122272 TCCCCCTTAATAAAATGTTTAATGAAAAAGATATCAATTGTTAACAAAATGATATCAATTGTTAC
1 TCCCCCTTAATAAAATGTTTAATGAAAAAGAAACCAATTGTTAACAAAATGATATCAATTGTTAC
122337 CAATTGTTTGAAAATATATGAAAATGTTAAGCTCCCCCTTT
66 CAATTGTTTGAAAATATATGAAAATGTTAAGCTCCCCCTTT
122378 TCCCCC-TAATAAAATGTTTAAT-AAAAA-AAACCAATTGTTAACAAAATGATATCAATTGTTAC
1 TCCCCCTTAATAAAATGTTTAATGAAAAAGAAACCAATTGTTAACAAAATGATATCAATTGTTAC
*
122440 CAATTGTTTGAAAATATATGAAAATGTTAAGCTCCCCTTTT
66 CAATTGTTTGAAAATATATGAAAATGTTAAGCTCCCCCTTT
122481 TC
1 TC
122483 ATTAAGAAAT
Statistics
Matches: 102, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
103 75 0.74
104 5 0.05
105 16 0.16
106 6 0.06
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (106 bp):
TCCCCCTTAATAAAATGTTTAATGAAAAAGAAACCAATTGTTAACAAAATGATATCAATTGTTAC
CAATTGTTTGAAAATATATGAAAATGTTAAGCTCCCCCTTT
Found at i:125220 original size:23 final size:23
Alignment explanation
Indices: 125194--125262 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
125184 CACCACAGCT
*
125194 CATATAATTTCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
125217 CATATAACTGCACCGGAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
125240 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
125263 TATAATACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:125457 original size:103 final size:103
Alignment explanation
Indices: 125278--125495 Score: 436
Period size: 103 Copynumber: 2.1 Consensus size: 103
125268 TACTATCCAT
125278 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
125343 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
125381 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
125446 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
125484 AAGGACCACATA
1 AAGGACCACATA
125496 GACCCTCGAC
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:129218 original size:31 final size:31
Alignment explanation
Indices: 129180--129273 Score: 163
Period size: 31 Copynumber: 3.0 Consensus size: 31
129170 CCCGAAGGAC
*
129180 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
129211 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
129242 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
129273 C
1 C
129274 CCTCGACCCT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 60 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:130063 original size:64 final size:64
Alignment explanation
Indices: 129925--130086 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 64
129915 TCTTTCAATG
* * *
129925 AAAGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGGTGTTGTATTATTA
1 AAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTA
*** * * * *
129989 CTGGTATGCATCGATGCACTACTTATGCATCGATGCATCAATTGCATTCGATGTTTTTATT-TTA
1 AAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATG-TTGTATTATTA
*
130053 AAAG-AGTGCATCGATGCACTACCAATGCATCGAT
1 AAAGTA-TGCATCGATGCACTACTAATGCATCGAT
130087 ACACCTTCAA
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
63 1 0.01
64 75 0.91
65 6 0.07
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
AAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTA
Found at i:133650 original size:31 final size:31
Alignment explanation
Indices: 133604--133759 Score: 269
Period size: 31 Copynumber: 5.0 Consensus size: 31
133594 CCCGAAAGAC
*
133604 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
133635 CAGTCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
133666 CAGTCCATATGTCCTGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
133697 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
133728 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
133759 C
1 C
133760 CCTCGACCCT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:134549 original size:64 final size:64
Alignment explanation
Indices: 134411--134572 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 64
134401 TCTTTCAATG
* * *
134411 AAAGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTA
1 AAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATACATTCGATGTTGTATTATTA
*** * * * *
134475 CTGGTATGCATCGATGCACTACTTATGCATCGATGCATGAATTACATTCGATGTTTTTATT-TTA
1 AAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATACATTCGATG-TTGTATTATTA
*
134539 AAAG-AGTGCATCGATGCACTACCAATGCATCGAT
1 AAAGTA-TGCATCGATGCACTACTAATGCATCGAT
134573 ACACCTTCAA
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
63 1 0.01
64 75 0.91
65 6 0.07
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (64 bp):
AAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATACATTCGATGTTGTATTATTA
Found at i:138036 original size:23 final size:23
Alignment explanation
Indices: 138010--138054 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
138000 CACCACAGCT
*
138010 CATATAATTGCACCGAAGTGCCA
1 CATATAATTACACCGAAGTGCCA
*
138033 CATATAATTACACCGGAGTGCC
1 CATATAATTACACCGAAGTGCC
138055 GTGTAGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (23 bp):
CATATAATTACACCGAAGTGCCA
Found at i:138273 original size:103 final size:103
Alignment explanation
Indices: 138094--138311 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
138084 TACTGTCCAT
*
138094 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATAAATATACTAGGGATCAAGTATGTGTCTCACCA
138159 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
138197 AAGGACCACATATCATTCCTTAAGAATCATATAAATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATAAATATACTAGGGATCAAGTATGTGTCTCACCA
* *
138262 GACTTCACACATGTTTCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
138300 AAGGACCACATA
1 AAGGACCACATA
138312 GACCCTCAAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATAAATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:139842 original size:3 final size:3
Alignment explanation
Indices: 139836--139953 Score: 155
Period size: 3 Copynumber: 38.7 Consensus size: 3
139826 TCATTTAAAT
** *
139836 TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
139884 TTA TTA TAA TTA TTA TTA TTA TTA TCA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* *
139930 TCA ATA TTA TATA TTA TTA TTA TT
1 TTA TTA TTA T-TA TTA TTA TTA TT
139954 TAATAAATAA
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
3 93 0.94
4 6 0.06
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:140139 original size:30 final size:27
Alignment explanation
Indices: 140071--140134 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
140061 CCTAGCCACC
* *
140071 CCCAGCCGCCTCTGATGCTTCCAGAAT
1 CCCAGCCGCCTCTGATACTTCAAGAAT
140098 CCCAGCCGCCTCTGATACTTCAAGAAT
1 CCCAGCCGCCTCTGATACTTCAAGAAT
140125 CCCAGCCGCC
1 CCCAGCCGCC
140135 GCCTCACTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.20, C:0.44, G:0.17, T:0.19
Consensus pattern (27 bp):
CCCAGCCGCCTCTGATACTTCAAGAAT
Found at i:140397 original size:15 final size:16
Alignment explanation
Indices: 140372--140408 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
140362 GAGAACGACA
140372 AGAAA-AAAAAAACAG
1 AGAAAGAAAAAAACAG
140387 A-AAAGAAAAAAACAG
1 AGAAAGAAAAAAACAG
140402 AGAAAGA
1 AGAAAGA
140409 GAACACAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.15
15 12 0.60
16 5 0.25
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAAAAACAG
Found at i:140411 original size:18 final size:18
Alignment explanation
Indices: 140371--140411 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
140361 AGAGAACGAC
140371 AAGA-AAAAAAAAACAGA
1 AAGAGAAAAAAAAACAGA
* *
140388 AA-AGAAAAAAACAGAGA
1 AAGAGAAAAAAAAACAGA
140405 AAGAGAA
1 AAGAGAA
140412 CACAGCAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 15 0.75
18 4 0.20
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (18 bp):
AAGAGAAAAAAAAACAGA
Found at i:142197 original size:20 final size:21
Alignment explanation
Indices: 142174--142225 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
142164 AGAAATTAAA
142174 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
142194 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
142216 -ATT-ATTTATT
1 AATTCATTTATT
142226 ATTTATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:146955 original size:16 final size:18
Alignment explanation
Indices: 146920--146963 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 18
146910 CTCATCCAGC
146920 AAAGAAAGAAGAAGAAGAA
1 AAAGAAA-AAGAAGAAGAA
146939 AAAGAAAAA-AA-AAGAA
1 AAAGAAAAAGAAGAAGAA
146955 AAAGGAAAA
1 AAA-GAAAA
146964 TCGAATAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.33
17 7 0.29
18 2 0.08
19 7 0.29
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAGAAGAAGAA
Found at i:149354 original size:84 final size:84
Alignment explanation
Indices: 149213--149603 Score: 687
Period size: 84 Copynumber: 4.7 Consensus size: 84
149203 TGGAACAAAT
* *
149213 ATAATGTGCTCAATAGCATCTTTTGGAAATGTTCTTTGAGTTATCTGATCTGGTTGGACA-AGAC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA-AC
*
149277 CAATCATTGAATTTGGAAGA
65 TAATCATTGAATTTGGAAGA
149297 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACT
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACT
149362 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
149381 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACT
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACT
149446 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
*
149465 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACA-AGAC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA-AC
149529 TAATCATTGAATTTGGAAGA
65 TAATCATTGAATTTGGAAGA
* * *
149549 ATAATGTGTTCAATAGCATCTTTTGGAAATGTTCTTTGAGTTATCTGATCTGGTT
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
149604 CGGTAGGAAT
Statistics
Matches: 298, Mismatches: 7, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
83 1 0.00
84 296 0.99
85 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (84 bp):
ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACT
AATCATTGAATTTGGAAGA
Found at i:152236 original size:22 final size:22
Alignment explanation
Indices: 152207--152261 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
152197 ATCTACACTC
*
152207 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
152229 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
152251 TTCAAAGATGA
1 TTCAAAGATGA
152262 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:152915 original size:118 final size:114
Alignment explanation
Indices: 152682--153421 Score: 943
Period size: 118 Copynumber: 6.4 Consensus size: 114
152672 ATATGATGGA
* * *
152682 TCAA-CTTTTCGCTTGAATTCATCA-TTCGAT-GATTCAGTATTTCC--AGTTCGAGTTCATAAT
1 TCAACCTTTT-GCTTGAATTCATCACTT-GATGGATT-A-TTTTTCCAGAGGTAGAGTTCATAAT
*
152742 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
62 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
*
152795 TCAA-CTTTTCGCTTGAATTCATCA-TTCGAT-GATTCAGTATTTCCAGAGGTAGAGTTCATAAT
1 TCAACCTTTT-GCTTGAATTCATCACTT-GATGGATT-A-TTTTTCCAGAGGTAGAGTTCATAAT
152857 GAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
62 GAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* * * * * **
152913 TCAACCTTTTACTTGAATCCATCATTTGCTGGATCAGCCTTTCC--AGGTAGAGTTCATAATGAG
1 TCAACCTTTTGCTTGAATTCATCACTTGATGGATTA-TTTTTCCAGAGGTAGAGTTCATAATGAG
*
152976 AAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
65 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* *
153026 TCAACCTTTTTGTTTGAATTCATCACTTGATGGATTATTGTTGCCAGAGGTAGAGTTCATAATGA
1 TCAACC-TTTTGCTTGAATTCATCACTTGATGGATTATT-TTTCCAGAGGTAGAGTTCATAATGA
*
153091 GAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
64 GAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
** * * * *
153145 TCAACCTTTTGCTCAAATCCATCACTTGATGAATCAACTTTTCCAGA-G-A-AGTTCATAATGAG
1 TCAACCTTTTGCTTGAATTCATCACTTGATGGAT-TATTTTTCCAGAGGTAGAGTTCATAATGAG
153207 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
65 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
*
153257 TCAACCTTTT-TTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGGTAGAGTTCATAATGA
1 TCAACCTTTTGCT-TGAATTCATCACTTGATGGATTATTTTT-CCAGAGGTAGAGTTCATAATGA
153321 GAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
64 GAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
153375 TCAACCTTTTG-TCTGAATTCATCACTTGATGGATTATTTTTGCCAGA
1 TCAACCTTTTGCT-TGAATTCATCACTTGATGGATTATTTTT-CCAGA
153422 TGGATTATTT
Statistics
Matches: 565, Mismatches: 37, Indels: 45
0.87 0.06 0.07
Matches are distributed among these distances:
111 6 0.01
112 75 0.13
113 95 0.17
114 30 0.05
115 58 0.10
116 49 0.09
117 3 0.01
118 189 0.33
119 60 0.11
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
TCAACCTTTTGCTTGAATTCATCACTTGATGGATTATTTTTCCAGAGGTAGAGTTCATAATGAGA
AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
Found at i:153425 original size:18 final size:18
Alignment explanation
Indices: 153402--153439 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
153392 TTCATCACTT
153402 GATGGATTATTTTTGCCA
1 GATGGATTATTTTTGCCA
153420 GATGGATTATTTTTGCCA
1 GATGGATTATTTTTGCCA
153438 GA
1 GA
153440 GAAGTCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.42
Consensus pattern (18 bp):
GATGGATTATTTTTGCCA
Found at i:153469 original size:248 final size:240
Alignment explanation
Indices: 152963--153854 Score: 1306
Period size: 248 Copynumber: 3.8 Consensus size: 240
152953 TTCCAGGTAG
*
152963 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* *
153028 AACCTTTTTGTTTGAATTCATCACTTGATGGATTATTGTTGCCAGAGGTAGAGTTCATAATGAGA
66 AACCTTTTT-TCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGGTAGAGTTCATAATGAGA
*
153093 AGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG-C
130 AGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTC
* * *
153157 TCAAATCCATCACTTGAT-GA--A----T--CA-ACTTTTCCAGAGA
195 T-GAATTCATCACTTGATGGATTATTTTTGCCAGAATTTTCCAGAGA
153194 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
153259 AACCTTTTTTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGGTAGAGTTCATAATGAGAA
66 AACCTTTTTTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGGTAGAGTTCATAATGAGAA
153324 GAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCT
131 GAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCT
153389 GAATTCATCACTTGATGGATTATTTTTGCCAGATGGATTATTTTTGCCAGAGA
196 GAATTCATCACTTGATGGATTATTTTTGCC--A--GA--A-TTTT-CCAGAGA
* *
153442 AGTCCATAATGAGAAGAACTCATCTGAAGAAGGAAGAACAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
153507 AACCTTTTTTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGGTAGAGTTCATAATGAGAA
66 AACCTTTTTTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGGTAGAGTTCATAATGAGAA
153572 GAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCT
131 GAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCT
153637 GAATTCATCACTTGATGGATTATTTTTGCCAGAA------A-AG-
196 GAATTCATCACTTGATGGATTATTTTTGCCAGAATTTTCCAGAGA
* *
153674 -GTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * **
153738 AACC-TTTTGCTCAAATCCATCACTTGATGG---GCTTTT-CCAGA-G-A-AGTTCATAATGAGA
66 AACCTTTTTTCT-GAATTCATCACTTGATGGATTATTTTTGCCAGAGGTAGAGTTCATAATGAGA
* *
153795 AGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACTTTTTG
130 AGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
153855 CATAATTCTA
Statistics
Matches: 621, Mismatches: 20, Indels: 50
0.90 0.03 0.07
Matches are distributed among these distances:
221 53 0.09
222 1 0.00
224 18 0.03
225 1 0.00
226 1 0.00
227 5 0.01
228 4 0.01
230 135 0.22
231 157 0.25
233 3 0.00
234 1 0.00
237 1 0.00
239 1 0.00
241 1 0.00
242 1 0.00
244 3 0.00
246 1 0.00
247 4 0.01
248 230 0.37
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.30
Consensus pattern (240 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTTTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGGTAGAGTTCATAATGAGAA
GAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCT
GAATTCATCACTTGATGGATTATTTTTGCCAGAATTTTCCAGAGA
Found at i:153476 original size:130 final size:132
Alignment explanation
Indices: 153284--153669 Score: 581
Period size: 118 Copynumber: 3.0 Consensus size: 132
153274 TTCATCACTT
153284 GATGGATTATTTTTGCCAGAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGA
1 GATGGATTATTTTTGCCAGA-G-A-AGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGGAAGA
153349 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTT
62 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTT
153414 TTGCCA
127 TTGCCA
* *
153420 GATGGATTATTTTTGCCAGAGAAGTCCATAATGAGAAGAA-C-TCATCTGAAGAAGGAAGAACAA
1 GATGGATTATTTTTGCCAGAGAAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGAA
*
153483 GTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCACTTGATGGATTATTTTTGC
66 GTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGC
153548 CA
131 CA
153550 GA-GG--------T-----AG-AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGA
1 GATGGATTATTTTTGCCAGAGAAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGGAAGAAGA
153600 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTG
65 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTG
153665 CCA
130 CCA
153668 GA
1 GA
153670 AAAGGTTCAT
Statistics
Matches: 241, Mismatches: 6, Indels: 24
0.89 0.02 0.09
Matches are distributed among these distances:
115 17 0.07
116 2 0.01
117 1 0.00
118 89 0.37
121 1 0.00
129 2 0.01
130 89 0.37
131 1 0.00
133 17 0.07
134 1 0.00
135 1 0.00
136 20 0.08
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.32
Consensus pattern (132 bp):
GATGGATTATTTTTGCCAGAGAAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGAA
GTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGC
CA
Found at i:153603 original size:118 final size:112
Alignment explanation
Indices: 153420--153853 Score: 646
Period size: 118 Copynumber: 3.9 Consensus size: 112
153410 ATTTTTGCCA
* *
153420 GATGGATTATTTTTGCCAGAGAAGTCCATAATGAGAAGAACTCATCTGAAGAAGGAAGAACAAGT
1 GATGGATTATTTTTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
153485 TCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCACTT
66 TCATAATAAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCACTT
153532 GATGGATTATTTTTGCCAGAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGA
1 GATGGATTATTTTTGCCAGA-G-A-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGA
* *
153597 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTT
60 AGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCACTT
* *
153650 GATGGATTATTTTTGCCAGAAAAGGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1 GATGGATTATTTTTGCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* * *
153715 TTCATAATAAGAAGAATTTGTTCAACC-TTTTGCTCAAATCCATCACTT
65 TTCATAATAAGAAGAATTTGTTCAACCTTTTTTCT-GAATTCATCACTT
**
153763 GATGG---GCTTTT-CCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 GATGGATTATTTTTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
153824 TCATAATAAGAAGAATTTGTTCAA-CTTTTT
66 TCATAATAAGAAGAATTTGTTCAACCTTTTT
153854 GCATAATTCT
Statistics
Matches: 299, Mismatches: 14, Indels: 22
0.89 0.04 0.07
Matches are distributed among these distances:
107 1 0.00
108 69 0.23
109 7 0.02
110 4 0.01
112 25 0.08
113 66 0.22
114 2 0.01
115 18 0.06
116 17 0.06
117 1 0.00
118 89 0.30
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (112 bp):
GATGGATTATTTTTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATAAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCACTT
Found at i:154503 original size:3 final size:3
Alignment explanation
Indices: 154497--154605 Score: 150
Period size: 3 Copynumber: 36.7 Consensus size: 3
154487 TCATTTAAAT
**
154497 TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
154544 TTA TTA TTA TTA TTA TTA TCA TTA TTA -TA TTA TTA TTA TTA TCA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
154591 TTA TATA TTA TTA TT
1 TTA T-TA TTA TTA TT
154606 TAATAAATAA
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
2 4 0.04
3 86 0.92
4 3 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:154542 original size:35 final size:35
Alignment explanation
Indices: 154501--154605 Score: 149
Period size: 35 Copynumber: 3.0 Consensus size: 35
154491 TTAAATTTAT
154501 TATTATTATTATTAAAATTATTATTATTATTATTA
1 TATTATTATTATTAAAATTATTATTATTATTATTA
** *
154536 TATTATTATTATTATTATTATTATTATCATTATTA
1 TATTATTATTATTAAAATTATTATTATTATTATTA
*
154571 TATTATTATTATTATCAA-TATTATATATTATTATT
1 TATTATTATTATTA-AAATTATTAT-TATTATTATT
154606 TAATAAATAA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
35 52 0.84
36 10 0.16
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (35 bp):
TATTATTATTATTAAAATTATTATTATTATTATTA
Found at i:154791 original size:30 final size:27
Alignment explanation
Indices: 154723--154786 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
154713 CCTAGCCACC
* *
154723 CCCAGCCGCCTCTGATGCTTCCAGAAT
1 CCCAGCCGCCTCTGATACTTCAAGAAT
154750 CCCAGCCGCCTCTGATACTTCAAGAAT
1 CCCAGCCGCCTCTGATACTTCAAGAAT
154777 CCCAGCCGCC
1 CCCAGCCGCC
154787 GCCTCACTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.20, C:0.44, G:0.17, T:0.19
Consensus pattern (27 bp):
CCCAGCCGCCTCTGATACTTCAAGAAT
Found at i:155050 original size:15 final size:16
Alignment explanation
Indices: 155025--155061 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
155015 GAGAACGACA
155025 AGAAA-AAAAAAACAG
1 AGAAAGAAAAAAACAG
155040 A-AAAGAAAAAAACAG
1 AGAAAGAAAAAAACAG
155055 AGAAAGA
1 AGAAAGA
155062 GAACACAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.15
15 12 0.60
16 5 0.25
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAAAAACAG
Found at i:155064 original size:18 final size:18
Alignment explanation
Indices: 155024--155064 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
155014 AGAGAACGAC
155024 AAGA-AAAAAAAAACAGA
1 AAGAGAAAAAAAAACAGA
* *
155041 AA-AGAAAAAAACAGAGA
1 AAGAGAAAAAAAAACAGA
155058 AAGAGAA
1 AAGAGAA
155065 CACAGCAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 15 0.75
18 4 0.20
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (18 bp):
AAGAGAAAAAAAAACAGA
Found at i:159167 original size:3 final size:3
Alignment explanation
Indices: 159159--159206 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
159149 GATAAGAGAA
159159 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
159207 GATAGGAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:164937 original size:2 final size:2
Alignment explanation
Indices: 164927--164969 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
164917 AAAGGAAAAA
164927 AT AT A- 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
164968 AT
1 AT
164970 CAAAGAATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:165469 original size:18 final size:17
Alignment explanation
Indices: 165446--165488 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
165436 ATATATATAC
165446 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
165464 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
165481 ATAA-AATA
1 ATAATAATA
165489 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:165496 original size:58 final size:55
Alignment explanation
Indices: 165378--165496 Score: 123
Period size: 56 Copynumber: 2.1 Consensus size: 55
165368 TATTAAAGAA
* * * ** *
165378 ATATATATATATATAATAATAAAATATAGTAAAAAAATGAAAATAATTTAATATAT
1 ATATATATATACATAATAATAAAACATAATAAAAAAAT-AAAATAATAAAATATAC
*
165434 ATATATATATACATAATAATAATAACATGAATAATAAAAAT-AAATGAATAAAATATCC
1 ATATATATATACATAATAATAA-AACAT-AATAA-AAAAATAAAAT-AATAAAATATAC
165492 ATATA
1 ATATA
165497 ATAAATAAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
56 21 0.40
57 8 0.15
58 17 0.33
59 6 0.12
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (55 bp):
ATATATATATACATAATAATAAAACATAATAAAAAAATAAAATAATAAAATATAC
Found at i:165900 original size:37 final size:37
Alignment explanation
Indices: 165850--165954 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
165840 GTGCTTGTGG
* * * *
165850 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
165887 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
165924 ATCTTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
165955 GACGAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:166686 original size:105 final size:105
Alignment explanation
Indices: 166497--167021 Score: 835
Period size: 105 Copynumber: 5.0 Consensus size: 105
166487 GCATTGTTCC
* *
166497 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-TGA-AA-TT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
166557 CAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
166597 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
166662 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
166702 GAGTCCAATATCCTTCGTTGTGAAGTTGAAACTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
166767 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
166807 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGATAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
166872 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
166912 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAA
* ** * * *
166977 CCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
167018 GAGT
1 GAGT
167022 GTCACGATAT
Statistics
Matches: 394, Mismatches: 25, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
100 37 0.09
101 1 0.00
102 2 0.01
103 2 0.01
104 2 0.01
105 302 0.77
106 48 0.12
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:167268 original size:36 final size:36
Alignment explanation
Indices: 167221--167296 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
167211 TGTTTGGAGA
* * *
167221 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
167257 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
167293 GAAA
1 GAAA
167297 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:167471 original size:39 final size:39
Alignment explanation
Indices: 167417--167491 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
167407 TCAATGTTTA
* *
167417 TGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCTC-AGGAGAGAAAAAATTTTC
* *
167456 TGTTTCGAGGGAAACTATCTCAGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATT
167492 AATTTCAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATTTTC
Found at i:167530 original size:105 final size:104
Alignment explanation
Indices: 167196--167514 Score: 509
Period size: 105 Copynumber: 3.1 Consensus size: 104
167186 TTCGTTAAAT
* ** *
167196 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
167258 AAACTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
167297 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* * *
167362 AAACTATCTCAAAAGAGAAAAAAAATCATTTCAATGGAAA
66 AAACTATCTCAAGAGAG-AAAAAATTCATTTCAAGGGAAA
167402 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
167467 AAACTATCTCAGGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
167506 TGTTTTCAA
1 TGTTTTCAA
167515 GAGAAACTGT
Statistics
Matches: 200, Mismatches: 14, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
101 46 0.23
103 3 0.01
104 52 0.26
105 99 0.50
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:167670 original size:36 final size:36
Alignment explanation
Indices: 167630--167743 Score: 113
Period size: 36 Copynumber: 3.2 Consensus size: 36
167620 CTTTCGAGTG
* * *
167630 AAAACGGTCTCAAGCGAGACAAATCTTGTTTTAAGA
1 AAAACAGTCTTAAGTGAGACAAATCTTGTTTTAAGA
* * * * * **
167666 AAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGA
1 AAAACAGTCTTAAGTGAGACAAATCTTGTTTTAAGA
*
167702 AAAACAGTCTTAAGTGAGACAAAGT-ATGTTTTAAGA
1 AAAACAGTCTTAAGTGAGACAAA-TCTTGTTTTAAGA
167738 AAAACA
1 AAAACA
167744 AATTTGAGTG
Statistics
Matches: 59, Mismatches: 18, Indels: 2
0.75 0.23 0.03
Matches are distributed among these distances:
36 58 0.98
37 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (36 bp):
AAAACAGTCTTAAGTGAGACAAATCTTGTTTTAAGA
Found at i:167733 original size:72 final size:74
Alignment explanation
Indices: 167585--167759 Score: 207
Period size: 72 Copynumber: 2.4 Consensus size: 74
167575 TAAAATCTTC
** * *
167585 TTAA-AAAAACAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGA
*
167649 CAAATCTTGTT
64 CAAATCATGTT
* *
167660 TTAAGAAAAACAATCTTGAGTGAAATAAAT-CTTCTTTCGAG-AAAAACAGTCTTAAGTGAGACA
1 TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACA
167723 AAGT-ATGTT
66 AA-TCATGTT
*
167732 TTAAGAAAAACAAAT-TTGAGTGAGATAA
1 TTAAGAAAAAC-AATCTTGAGTGAAATAA
167760 TCATCTGCAT
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
72 47 0.53
73 15 0.17
75 8 0.09
76 19 0.21
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (74 bp):
TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACA
AATCATGTT
Found at i:169349 original size:183 final size:182
Alignment explanation
Indices: 168895--169430 Score: 921
Period size: 183 Copynumber: 2.9 Consensus size: 182
168885 ATCAGGTTTA
*
168895 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* * **
168960 GCCAAGTGTCCGAGCAATGTCAT-GATATGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
169024 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAAGGGACAAATC
* * * *
169077 ACTAAAGGATTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAGCACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* *
169142 GACAAGTGTCCAAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
169207 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGTGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA-AGGGACAAATC
*
169260 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCAAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
169325 GCCAAGTGTTCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
169390 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
169431 CGGATTTAAT
Statistics
Matches: 332, Mismatches: 20, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
182 158 0.48
183 174 0.52
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (182 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAAGGGACAAATC
Found at i:173451 original size:47 final size:50
Alignment explanation
Indices: 173373--173466 Score: 117
Period size: 47 Copynumber: 1.9 Consensus size: 50
173363 ATATTAAAGA
*
173373 AATATATATAATAATAATAAAATATAGTAAAA-AA-ATGAA-AATAATTT
1 AATATATATAATAATAATAAAATATAATAAAATAACATGAATAATAATTT
*
173420 AATATATAT-AT-ATATATATACATATAATAAAATAACATGAATAATAA
1 AATATATATAATAATA-ATA-AAATATAATAAAATAACATGAATAATAA
173467 AAATAAATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
45 3 0.08
46 5 0.12
47 20 0.50
48 2 0.05
49 5 0.12
50 5 0.12
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (50 bp):
AATATATATAATAATAATAAAATATAATAAAATAACATGAATAATAATTT
Found at i:173465 original size:17 final size:17
Alignment explanation
Indices: 173443--173480 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
173433 ATATATACAT
173443 ATAAT-AAAATAACATGA
1 ATAATAAAAATAA-ATGA
173460 ATAATAAAAATAAATGA
1 ATAATAAAAATAAATGA
173477 ATAA
1 ATAA
173481 ATTATCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (17 bp):
ATAATAAAAATAAATGA
Found at i:173926 original size:37 final size:37
Alignment explanation
Indices: 173844--173945 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 37
173834 GTGCTTGTTG
* * * * * *
173844 ATCCTATCTTTAGGAATTTAAATCTTAGTATAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* * *
173881 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
173918 ATCCTATTTTTAGAAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
173946 TAGGACGAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:174441 original size:17 final size:17
Alignment explanation
Indices: 174419--174453 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
174409 TTATTATTTC
174419 ATTGTTATAAAAAATAA
1 ATTGTTATAAAAAATAA
174436 ATTGTTATAAAAAATAA
1 ATTGTTATAAAAAATAA
174453 A
1 A
174454 AGAAACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
ATTGTTATAAAAAATAA
Found at i:177863 original size:2 final size:2
Alignment explanation
Indices: 177856--177898 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
177846 CTCTATCACT
177856 TA TA TA 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 TA TA TA
177898 T
1 T
177899 GTGTGTGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:178514 original size:2 final size:2
Alignment explanation
Indices: 178492--178532 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
178482 ATTTGTACTC
178492 AT AT A- AT AT A- AT AT A- 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
178531 AT
1 AT
178533 TAGGTACATG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:180284 original size:2 final size:2
Alignment explanation
Indices: 180279--180320 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
180269 CAATTATGTA
180279 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT CAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
180321 TAAAAATGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:180713 original size:15 final size:15
Alignment explanation
Indices: 180689--180718 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
180679 TTTAATTAAC
180689 AAATAATATCAATAT
1 AAATAATATCAATAT
*
180704 AAATAGTATCAATAT
1 AAATAATATCAATAT
180719 TATTATTACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (15 bp):
AAATAATATCAATAT
Found at i:181868 original size:8 final size:8
Alignment explanation
Indices: 181848--181876 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
181838 TAATGTGTTT
181848 ATTTTATA
1 ATTTTATA
181856 A-TTTATA
1 ATTTTATA
181863 ATTTTATA
1 ATTTTATA
181871 ATTTTA
1 ATTTTA
181877 ATTAATACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTTTATA
Found at i:181868 original size:15 final size:14
Alignment explanation
Indices: 181848--181879 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
181838 TAATGTGTTT
181848 ATTTTATAATTTATA
1 ATTTTATAATTT-TA
181863 ATTTTATAATTTTA
1 ATTTTATAATTTTA
181877 ATT
1 ATT
181880 AATACATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTTATAATTTTA
Found at i:182336 original size:43 final size:43
Alignment explanation
Indices: 182287--182391 Score: 133
Period size: 43 Copynumber: 2.5 Consensus size: 43
182277 ACAATTCAAT
*
182287 TAATATTTTAAAATAATTAAAATAATA-AATTTATAATTATTTA
1 TAATATTTT-AAATAATTAAAATAATATAATTTATAATAATTTA
* * * *
182330 TAATATTTTAAGTGATTAAAATGATATAGTTTATAATAATTTA
1 TAATATTTTAAATAATTAAAATAATATAATTTATAATAATTTA
*
182373 TTATATTTT-AATAATTAAA
1 TAATATTTTAAATAATTAAA
182392 GGATATATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 22 0.42
43 31 0.58
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.48
Consensus pattern (43 bp):
TAATATTTTAAATAATTAAAATAATATAATTTATAATAATTTA
Found at i:185849 original size:44 final size:45
Alignment explanation
Indices: 185799--185883 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 45
185789 CTATGTGTAC
185799 TATCGACACTAAATATGAAACCATGGAATTCATAA-GAATTACCA
1 TATCGACACTAAATATGAAACCATGGAATTCATAATGAATTACCA
** * * *
185843 TATCGACACTATGTGTGCAACCATGGAATTTATAATGAATT
1 TATCGACACTAAATATGAAACCATGGAATTCATAATGAATT
185884 TGTGAATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 30 0.86
45 5 0.14
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (45 bp):
TATCGACACTAAATATGAAACCATGGAATTCATAATGAATTACCA
Found at i:185892 original size:53 final size:54
Alignment explanation
Indices: 185834--185954 Score: 181
Period size: 54 Copynumber: 2.3 Consensus size: 54
185824 GAATTCATAA
* * *
185834 GAATTACCATATCGACACTATGTGTGC-AACCATGGAATTTATAATGAATTTGT
1 GAATTACCATATCGACACTATGTGTGCAAACCATAGAATTAATAACGAATTTGT
* *
185887 GAATTATCATATCGACACTATGTGTGCAAACCATAGAATTAATAACGAGTTTGT
1 GAATTACCATATCGACACTATGTGTGCAAACCATAGAATTAATAACGAATTTGT
*
185941 GAATTACCACATCG
1 GAATTACCATATCG
185955 GTACTTAGGT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
53 26 0.43
54 34 0.57
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (54 bp):
GAATTACCATATCGACACTATGTGTGCAAACCATAGAATTAATAACGAATTTGT
Found at i:189412 original size:18 final size:18
Alignment explanation
Indices: 189383--189448 Score: 96
Period size: 18 Copynumber: 3.7 Consensus size: 18
189373 AGAAAATTCT
*
189383 CGAAGGATCACTATGTCC
1 CGAAGGACCACTATGTCC
*
189401 CGAATGACCACTATGTCC
1 CGAAGGACCACTATGTCC
*
189419 CGAAGGACCACTATGTCT
1 CGAAGGACCACTATGTCC
*
189437 CGAAGTACCACT
1 CGAAGGACCACT
189449 CCTTAAGAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (18 bp):
CGAAGGACCACTATGTCC
Found at i:192329 original size:21 final size:21
Alignment explanation
Indices: 192300--192341 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
192290 TTGGTGTATT
*
192300 CAAATTCAAGAGAGAAGCATG
1 CAAAGTCAAGAGAGAAGCATG
*
192321 CAAAGTCAAGAGAGGAGCATG
1 CAAAGTCAAGAGAGAAGCATG
192342 ATGCTCATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.14, G:0.29, T:0.12
Consensus pattern (21 bp):
CAAAGTCAAGAGAGAAGCATG
Found at i:196262 original size:53 final size:53
Alignment explanation
Indices: 196205--196320 Score: 207
Period size: 53 Copynumber: 2.2 Consensus size: 53
196195 CTATGTGTAC
*
196205 TATCGACACTATGTGTGCAACCAT-GAATTTCATAATGAGTTTGTGAATTACCA
1 TATCGGCACTATGTGTGCAACCATGGAA-TTCATAATGAGTTTGTGAATTACCA
196258 TATCGGCACTATGTGTGCAACCATGGAATTCATAATGAGTTTGTGAATTACCA
1 TATCGGCACTATGTGTGCAACCATGGAATTCATAATGAGTTTGTGAATTACCA
196311 TATCGGCACT
1 TATCGGCACT
196321 TAGGTGCAAC
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
53 58 0.95
54 3 0.05
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (53 bp):
TATCGGCACTATGTGTGCAACCATGGAATTCATAATGAGTTTGTGAATTACCA
Found at i:196547 original size:3 final size:3
Alignment explanation
Indices: 196539--196575 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
196529 ATTTCACCTC
196539 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
196576 GTATGTCTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:201213 original size:3 final size:3
Alignment explanation
Indices: 201205--201254 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
201195 AGGGATTTTA
* *
201205 AAG AAG AAG ATG AAG AGAG ATG AAG ACA- AA- AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG A-AG AAG AAG A-AG AAG AAG AAG AAG AAG AAG
201250 AAG AA
1 AAG AA
201255 AAGGTGAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 3 0.08
3 33 0.82
4 4 0.10
ACGTcount: A:0.64, C:0.02, G:0.30, T:0.04
Consensus pattern (3 bp):
AAG
Found at i:204365 original size:20 final size:20
Alignment explanation
Indices: 204340--204379 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
204330 TATTGGAATA
*
204340 TGCATTCTGGAATATACATT
1 TGCATTCTAGAATATACATT
*
204360 TGCATTCTAGAATATGCATT
1 TGCATTCTAGAATATACATT
204380 GTTAACGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
TGCATTCTAGAATATACATT
Found at i:206067 original size:35 final size:35
Alignment explanation
Indices: 206011--206124 Score: 158
Period size: 35 Copynumber: 3.3 Consensus size: 35
206001 TCGTCTATAG
* * *
206011 TAGAAC-GAAGGGAGGCGTCGCACTTTCGATTCAAG
1 TAGAACGGAA-GGAAGCATCGCACTTTCGATTCAAC
* *
206046 AAGAACGGAAGGAAGCATCGCACTTTCGATTCAAT
1 TAGAACGGAAGGAAGCATCGCACTTTCGATTCAAC
*
206081 TAGAAAGGAAGGAAGCATCGCACTTTCGATTCAAC
1 TAGAACGGAAGGAAGCATCGCACTTTCGATTCAAC
206116 TAGAACGGA
1 TAGAACGGA
206125 TGATTTACTA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
35 67 0.96
36 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (35 bp):
TAGAACGGAAGGAAGCATCGCACTTTCGATTCAAC
Found at i:206259 original size:20 final size:20
Alignment explanation
Indices: 206234--206273 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
206224 TATTGAAATA
*
206234 TGCATTCTGGAATATACATT
1 TGCATTCTAGAATATACATT
*
206254 TGCATTCTAGAATATGCATT
1 TGCATTCTAGAATATACATT
206274 GTTAACGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
TGCATTCTAGAATATACATT
Found at i:207384 original size:14 final size:14
Alignment explanation
Indices: 207365--207401 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
207355 GTAAGTATAA
207365 TTTAGGGTTTAAAG
1 TTTAGGGTTTAAAG
*
207379 TTTAGGGTTTAAGG
1 TTTAGGGTTTAAAG
*
207393 TTTAAGGTT
1 TTTAGGGTT
207402 CATTGTAATG
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:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (14 bp):
TTTAGGGTTTAAAG
Done.