Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008953.1 Hibiscus syriacus cultivar Beakdansim tig00112281_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: 2822058
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 15
Found at i:999611 original size:20 final size:20
Alignment explanation
Indices: 999586--999779 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
999576 GATTTTCCAT
* *
999586 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
999606 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
999626 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
999646 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
999666 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
999686 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
999706 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
999726 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
999747 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
999767 AATCGCAACGCGA
1 AATCGCAACGCGA
999780 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:999631 original size:40 final size:39
Alignment explanation
Indices: 999582--999779 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
999572 TTGCGATTTT
* ** *
999582 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
999620 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
999661 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
999701 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
999740 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
999780 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:999669 original size:60 final size:60
Alignment explanation
Indices: 999586--999778 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
999576 GATTTTCCAT
* ** * *
999586 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
999646 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
999706 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
999767 AATCGCAACGCG
1 AATCGCAACGCG
999779 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:1000197 original size:33 final size:33
Alignment explanation
Indices: 1000158--1000228 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1000148 TTCACTTAGA
*
1000158 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1000191 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1000224 TTTCA
1 TTTCA
1000229 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1000368 original size:14 final size:14
Alignment explanation
Indices: 1000349--1000403 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1000339 AGAATGACTG
1000349 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
1000363 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
1000382 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1000396 TCGCAACG
1 TCGCAACG
1000404 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1000386 original size:33 final size:33
Alignment explanation
Indices: 1000349--1000419 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1000339 AGAATGACTG
**
1000349 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1000382 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1000415 TCGCA
1 TCGCA
1000420 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:1000437 original size:19 final size:19
Alignment explanation
Indices: 1000415--1000517 Score: 100
Period size: 19 Copynumber: 5.9 Consensus size: 19
1000405 GAAACCAAAA
* *
1000415 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATC
1000434 TCGCGTTGCGA--TTC-TC
1 TCGCGTTGCGATTTTCATC
*
1000450 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATC
*
1000467 TCGCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATC
1000486 TCGCGTTGCGA--TTC-TC
1 TCGCGTTGCGATTTTCATC
1000502 T--CGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
1000518 TTCAACCAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
14 16 0.23
16 11 0.16
17 8 0.11
19 35 0.50
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATC
Found at i:1000498 original size:52 final size:52
Alignment explanation
Indices: 1000415--1000520 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
1000405 GAAACCAAAA
* *
1000415 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
*
1000467 TCGCGTTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1000519 TC
1 TC
1000521 AACCAAAAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1002778 original size:12 final size:12
Alignment explanation
Indices: 1002761--1002785 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1002751 TCTTCGGGGA
1002761 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1002773 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1002785 C
1 C
1002786 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1002994 original size:24 final size:24
Alignment explanation
Indices: 1002960--1003006 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1002950 CTGAAACATC
1002960 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1002984 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1003007 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1003717 original size:20 final size:20
Alignment explanation
Indices: 1003689--1004057 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1003679 AAATTTCAGT
* * * *
1003689 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1003709 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1003729 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1003749 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1003769 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1003789 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1003809 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1003829 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1003849 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1003869 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1003889 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1003909 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1003929 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1003949 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1003969 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1003989 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1004009 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1004029 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1004049 GTTGCGATT
1 GTTGCGATT
1004058 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1006630 original size:11 final size:11
Alignment explanation
Indices: 1006614--1006639 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1006604 TTTTTGTCCG
1006614 ATTACATATAT
1 ATTACATATAT
1006625 ATTACATATAT
1 ATTACATATAT
1006636 ATTA
1 ATTA
1006640 TTATTTTATT
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTACATATAT
Found at i:1007743 original size:19 final size:19
Alignment explanation
Indices: 1007719--1007759 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1007709 AACATTGTTT
1007719 TGTGTATATATATAGTGTG
1 TGTGTATATATATAGTGTG
1007738 TGTGTATATATATAGTGTG
1 TGTGTATATATATAGTGTG
1007757 TGT
1 TGT
1007760 TTTTTTACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (19 bp):
TGTGTATATATATAGTGTG
Found at i:1007979 original size:3 final size:3
Alignment explanation
Indices: 1007971--1008041 Score: 133
Period size: 3 Copynumber: 23.7 Consensus size: 3
1007961 TTTTTAGCCA
1007971 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1008019 TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
1008042 AATATATATT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1008053 original size:11 final size:11
Alignment explanation
Indices: 1008037--1008061 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1008027 TTATTATTAT
1008037 TATTAAATATA
1 TATTAAATATA
1008048 TATTAAATATA
1 TATTAAATATA
1008059 TAT
1 TAT
1008062 ATAATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TATTAAATATA
Found at i:1011651 original size:8 final size:7
Alignment explanation
Indices: 1011627--1011668 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
1011617 TTTTCATACA
1011627 TGCA-TT
1 TGCATTT
1011633 TGCATTT
1 TGCATTT
1011640 TGCATCTT
1 TGCAT-TT
1011648 TGCATTT
1 TGCATTT
* *
1011655 TTCATTG
1 TGCATTT
1011662 TGCATTT
1 TGCATTT
1011669 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:1011651 original size:15 final size:14
Alignment explanation
Indices: 1011627--1011668 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
1011617 TTTTCATACA
1011627 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
1011640 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
1011655 TTCATTGTGCATTT
1 TGCATTTTGCATTT
1011669 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:1011759 original size:27 final size:26
Alignment explanation
Indices: 1011728--1011787 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
1011718 CATTCACATA
*
1011728 TTTACATTTGAATTTGCATTTGCATTT
1 TTTACATTTGAATTTACATTTGCA-TT
* * *
1011755 TTTACGTTTGTATTTACATTTTCATT
1 TTTACATTTGAATTTACATTTGCATT
1011781 TTTACAT
1 TTTACAT
1011788 AATTACATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (26 bp):
TTTACATTTGAATTTACATTTGCATT
Found at i:1013766 original size:17 final size:16
Alignment explanation
Indices: 1013742--1013812 Score: 70
Period size: 19 Copynumber: 4.1 Consensus size: 16
1013732 TCAAGCAAAG
1013742 AAAGGAAAAAAGAAAA
1 AAAGGAAAAAAGAAAA
1013758 AAGAGGAAAAAAGAAAAAA
1 AA-AGGAAAAAAG--AAAA
1013777 AAAGGAAAGAAATAGAAAA
1 AAAGG-AA-AAA-AGAAAA
**
1013796 AAACAAAAAAAGAAAA
1 AAAGGAAAAAAGAAAA
1013812 A
1 A
1013813 GAAACAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
16 9 0.19
17 13 0.28
18 5 0.11
19 15 0.32
20 3 0.06
21 2 0.04
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.01
Consensus pattern (16 bp):
AAAGGAAAAAAGAAAA
Found at i:1013768 original size:10 final size:9
Alignment explanation
Indices: 1013747--1013812 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 9
1013737 CAAAGAAAGG
1013747 AAAAA-AGA
1 AAAAAGAGA
1013755 AAAAAGAGGA
1 AAAAAGA-GA
1013765 AAAAAGA-A
1 AAAAAGAGA
*
1013773 AAAAAAAGGA
1 AAAAAGA-GA
*
1013783 AAGAAATAGA
1 AA-AAAGAGA
*
1013793 AAAAA-ACA
1 AAAAAGAGA
1013801 AAAAA-AGA
1 AAAAAGAGA
1013809 AAAA
1 AAAA
1013813 GAAACAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
8 25 0.51
9 4 0.08
10 16 0.33
11 4 0.08
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (9 bp):
AAAAAGAGA
Found at i:1013770 original size:29 final size:26
Alignment explanation
Indices: 1013738--1013812 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 26
1013728 AAAATCAAGC
1013738 AAAGAAAGGAAAAAAGAAAAAAGAGGAAA
1 AAAGAAA--AAAAAAGAAAAAAGA-GAAA
*
1013767 AAAGAAAAAAAAAGGAAAGAAATAGAAA
1 AAAGAAAAAAAAA-GAAA-AAAGAGAAA
*
1013795 AAA-ACAAAAAAAGAAAAA
1 AAAGAAAAAAAAAGAAAAA
1013813 GAAACAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
25 2 0.05
26 4 0.10
27 14 0.33
28 11 0.26
29 11 0.26
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.01
Consensus pattern (26 bp):
AAAGAAAAAAAAAGAAAAAAGAGAAA
Found at i:1013798 original size:22 final size:21
Alignment explanation
Indices: 1013738--1013821 Score: 71
Period size: 22 Copynumber: 3.9 Consensus size: 21
1013728 AAAATCAAGC
*
1013738 AAAG-AAAGGAAAAAAGAAAAA
1 AAAGAAAAAGAAAAAA-AAAAA
* **
1013759 AGAGGAAAAAAGAAAAAAAAAGG
1 A-AAG-AAAAAGAAAAAAAAAAA
*
1013782 AAAGAAATAGAAAAAAACAAAA
1 AAAGAAAAAGAAAAAAA-AAAA
*
1013804 AAAGAAAAAGAAACAAAA
1 AAAGAAAAAGAAAAAAAA
1013822 TTAAATCAAG
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
21 14 0.29
22 21 0.43
23 4 0.08
24 10 0.20
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.01
Consensus pattern (21 bp):
AAAGAAAAAGAAAAAAAAAAA
Found at i:1013821 original size:10 final size:10
Alignment explanation
Indices: 1013754--1013821 Score: 55
Period size: 10 Copynumber: 6.4 Consensus size: 10
1013744 AGGAAAAAAG
**
1013754 AAAAAAGAGG
1 AAAAAAGAAA
1013764 AAAAAAGAAA
1 AAAAAAGAAA
1013774 AAAAAAGGAAA
1 AAAAAA-GAAA
* *
1013785 GAAATAGAAA
1 AAAAAAGAAA
*
1013795 AAAACAAAAAA
1 AAAA-AAGAAA
1013806 AGAAAAAGAAA
1 A-AAAAAGAAA
1013817 CAAAA
1 -AAAA
1013822 TTAAATCAAG
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
10 21 0.46
11 21 0.46
12 4 0.09
ACGTcount: A:0.81, C:0.03, G:0.15, T:0.01
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:1016150 original size:83 final size:83
Alignment explanation
Indices: 1016049--1016313 Score: 460
Period size: 83 Copynumber: 3.2 Consensus size: 83
1016039 AATGGAACAA
1016049 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1016114 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
1016132 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
*
1016197 AATCATTGAATTTAGAAG
66 AATCATTGAATTTGGAAG
* * * *
1016215 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGG-TTGGACAGAAC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAAAAC
1016279 CAATCATTGAATTTGGAAG
65 CAATCATTGAATTTGGAAG
*
1016298 ATGAATTTGCTCATAG
1 ATGAATGTGCTCATAG
1016314 TAGAAATAAG
Statistics
Matches: 174, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
82 4 0.02
83 170 0.98
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (83 bp):
ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
AATCATTGAATTTGGAAG
Found at i:1018606 original size:40 final size:40
Alignment explanation
Indices: 1018551--1018630 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
1018541 TGAGCAGAGT
1018551 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
1 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
* *
1018591 CCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATC
1 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
1018631 TAAGCTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (40 bp):
CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
Found at i:1018995 original size:22 final size:22
Alignment explanation
Indices: 1018966--1019020 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1018956 GTCTACACTC
*
1018966 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
1018988 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
1019010 TTCAAAGATGA
1 TTCAAAGATGA
1019021 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:1019871 original size:116 final size:115
Alignment explanation
Indices: 1019428--1020438 Score: 1531
Period size: 116 Copynumber: 8.9 Consensus size: 115
1019418 GATTCAAATC
** * *
1019428 CATCATTCAATGGATCAACATTTCC-GGAAGAGTTCATAATGAGAAGAA--CTCATCTGAAGAAA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCTCATCTGAAGAAG
* *
1019490 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG-TTCAAAT
66 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
** * * *
1019539 C--CATAACGATGGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAA--CTCATCTGAACA
1 CATCAT-TTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCTCATCTGAAGA
* * *
1019599 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG-TTCAAATC
64 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT-GAATT
* * * * *
1019651 CATCACTTGATAGATCAGCTTTTCCAGAGAAGA-TTCATAATGAGAAGAA--CTCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCTCATCTGAAGAA
1019713 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-TCTTTTGCTTGAATT
65 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACT-TTTTGCTTGAATT
* *
1019764 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATTTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAA
1019829 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
65 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
*
1019880 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAA
*
1019945 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATT
65 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
1019996 CATCATTTGATGGATCAACATTGCCAGGAAG-GTTCATAATGAGAAGAA--CTCATCTGAAGAAG
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCTCATCTGAAGAAG
1020058 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-TCTTTTGCTTGAATT
66 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACT-TTTTGCTTGAATT
*
1020108 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAA
*
1020173 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATT
65 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
1020224 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAA
*
1020289 GGAAGAAGAAGTTCATAAT--GAAGAACTTGTTCAACTTTTTGTTTGAATT
65 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
1020338 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAA
* *
1020403 GGAAGAAGAAGTTTATAATAAGAAGAACTTGTTCAA
65 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1020439 TAATTCTATC
Statistics
Matches: 844, Mismatches: 34, Indels: 39
0.92 0.04 0.04
Matches are distributed among these distances:
109 3 0.00
110 16 0.02
111 76 0.09
112 100 0.12
113 149 0.18
114 117 0.14
115 19 0.02
116 362 0.43
117 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (115 bp):
CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCTCATCTGAAGAAG
GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
Found at i:1020082 original size:344 final size:342
Alignment explanation
Indices: 1019428--1020439 Score: 1614
Period size: 344 Copynumber: 3.0 Consensus size: 342
1019418 GATTCAAATC
** * *
1019428 CATCATTCAATGGATCAACATTTCC-GGAAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
* * * **
1019489 AGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATC--CATAACGATGGA
66 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTGAATTCATCAT-TTGATGGA
* * * *
1019552 TCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTGAACAAGGAAGAAGAAGTTC
130 TCAACATTGCCAG-GAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
* ** * * * * * *
1019614 ATAATGAGAAGAACTTGTTCAACCTTTTGTTCAAATCCATCACTTGATAGATCAGCTTTTCCAGA
194 ATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-
*
1019679 GAAGATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
258 GAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
1019744 TTCAATCTTTTGCTTGAATT
323 TTCAATCTTTTGCTTGAATT
*
1019764 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATTTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1019829 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTTGATGGA
66 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG-TTGAATTCATCATTTGATGGA
1019894 TCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
130 TCAACATTGCCAGG-AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
1019959 ATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGG
194 ATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGG
1020024 AAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
259 AAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1020089 TCAATCTTTTGCTTGAATT
324 TCAATCTTTTGCTTGAATT
1020108 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1020173 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGA
66 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG-TTGAATTCATCATTTGATGGA
1020238 TCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
130 TCAACATTGCCAGG-AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
1020303 ATAAT--GAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGG
194 ATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGG
* *
1020366 AAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAAGTTTATAATAAGAAGAAC
259 AAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
1020431 TTGTTCAAT
320 TTGTTCAAT
1020440 AATTCTATCA
Statistics
Matches: 632, Mismatches: 29, Indels: 20
0.93 0.04 0.03
Matches are distributed among these distances:
336 22 0.03
337 22 0.03
339 1 0.00
340 53 0.08
341 7 0.01
342 97 0.15
343 20 0.03
344 282 0.45
345 81 0.13
346 47 0.07
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (342 bp):
CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTGAATTCATCATTTGATGGAT
CAACATTGCCAGGAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAA
GGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AATCTTTTGCTTGAATT
Found at i:1020134 original size:228 final size:230
Alignment explanation
Indices: 1019428--1020438 Score: 1547
Period size: 228 Copynumber: 4.4 Consensus size: 230
1019418 GATTCAAATC
** * *
1019428 CATCATTCAATGGATCAACATTTCC-GGAAGAGTTCATAATGAGAAGAA--CTCATCTGAAGAAA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCTCATCTGAAGAAG
** * **
1019490 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCAT-A-ACGATGGAT
66 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGAT
* * *
1019553 CAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAA-C-TCATCTGAACAAGGAAGAAGAAGTTCA
131 CAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGAAGTTCA
* * *
1019615 TAATGAGAAGAACTTGTTCAACCTTTTG-TTCAAATC
195 TAATGAGAAGAACTTGTTCAACTTTTTGCTT-GAATT
* * * * *
1019651 CATCACTTGATAGATCAGCTTTTCCAGAGAAGA-TTCATAATGAGAAGAA--CTCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCTCATCTGAAGAA
*
1019713 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-TCTTTTGCTTGAATTCATCATTTGATGG
65 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACT-TTTTGTTTGAATTCATCATTTGATGG
* *
1019777 ATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATTTGAAGAAGGAAGAAGAAGTT
129 ATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGGAAGAAGAAGTT
1019842 CATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
193 CATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
*
1019880 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAA
1019945 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGA
65 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGA
1020010 TCAACATTGCCAGGAAG-GTTCATAATGAGAAGAA-C-TCATCTGAAGAAGGAAGAAGAAGTTCA
130 TCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGAAGTTCA
1020072 TAATGAGAAGAACTTGTTCAA-TCTTTTGCTTGAATT
195 TAATGAGAAGAACTTGTTCAACT-TTTTGCTTGAATT
*
1020108 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAA
1020173 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGA
65 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGA
1020238 TCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
130 TCAACATTGCCAGGAAGAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGGAAGAAGAAGTTC
*
1020303 ATAAT--GAAGAACTTGTTCAACTTTTTGTTTGAATT
194 ATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
1020338 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAA
* *
1020403 GGAAGAAGAAGTTTATAATAAGAAGAACTTGTTCAA
65 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1020439 TAATTCTATC
Statistics
Matches: 732, Mismatches: 35, Indels: 35
0.91 0.04 0.04
Matches are distributed among these distances:
223 20 0.03
224 77 0.11
225 8 0.01
226 35 0.05
227 1 0.00
228 212 0.29
229 111 0.15
230 126 0.17
231 20 0.03
232 121 0.17
233 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (230 bp):
CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCTCATCTGAAGAAG
GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGAT
CAACATTGCCAGGAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
Found at i:1020764 original size:3 final size:3
Alignment explanation
Indices: 1020756--1020849 Score: 172
Period size: 3 Copynumber: 31.7 Consensus size: 3
1020746 TTTTTATCCA
1020756 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1020803 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1020850 AATATATATT
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 86 0.98
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1020861 original size:11 final size:11
Alignment explanation
Indices: 1020845--1020874 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1020835 TTATTATTAT
1020845 TATTAAATATA
1 TATTAAATATA
1020856 TATTAAATATA
1 TATTAAATATA
1020867 TA-TAAATA
1 TATTAAATA
1020875 ATTAATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAAATATA
Found at i:1023870 original size:17 final size:17
Alignment explanation
Indices: 1023850--1023882 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1023840 CTCACTAACC
*
1023850 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
1023867 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
1023883 GTCGTTTGCA
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:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:1024518 original size:18 final size:19
Alignment explanation
Indices: 1024497--1024541 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1024487 ATTTAGACAT
1024497 TTTGCATTTT-TTATTTTC
1 TTTGCATTTTGTTATTTTC
1024515 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
1024534 TTTGCATT
1 TTTGCATT
1024542 CACATTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.69
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Found at i:1028221 original size:164 final size:168
Alignment explanation
Indices: 1027950--1028658 Score: 719
Period size: 164 Copynumber: 4.3 Consensus size: 168
1027940 TTTTTAAAAG
*
1027950 ATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGAC
1 ATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGAC
* * *
1028015 TACGCTCAGCTCCAA-GGCATATCATTTACAGCATAGCTTAAGTCGAGGAGGGCTATCTG-C-C-
66 TACGCTCAGCTCCAACGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACA
* *
1028076 AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGC
131 AAAGACCCTCGAGTTCGACTACACTCAGCTTCGAGGGC
* * * *
1028114 ATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTTGAC
1 ATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGAC
* * * * * *
1028179 TACGCTCAGCTCCCA-GGCATATCATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAAC
66 TACGCTCAGCTCCAACGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-AC
* * * * * * *
1028243 AAAAGACCTTTGAGTTCAACTACGCTCAGC-TCAACGGT
130 AAAAGACCCTCGAGTTCGACTACACTCAGCTTCGAGGGC
* * * * **
1028281 ACATCATTTGCAGCATAGCTTAAGTCGATG-AGGGCTATCT-T--CCAAAGACCCCCGAGTTCGA
1 ATATCATTTGCAGCATAACTTAAGTCTA-GAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGA
* * * * * * * * *
1028342 TTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAC
65 CTACGCTCAGCTCCAACGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAC
* * * * * *
1028407 TAAAGACCTTCGAGTTTGACTACGCTCAGCTCCCA-GGC
130 AAAAGACCCTCGAGTTCGACTACACTCAGCTTCGAGGGC
* * * * * *
1028445 ATATCATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGA
1 ATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGA
* * * * * * *
1028510 CTACGCTCAGCT-TAACGACACATCATTTGCAGCATAGCTTAAGTCGAGGAGGGTTATATG-C-C
65 CTACGCTCAGCTCCAACGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAC
*
1028572 -AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
130 AAAAGACCCTCGAGTTCGACTACACTCAGCTTCGAGGGC
* * * * *
1028610 ACATTATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAA
1 ATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACCAAA
1028659 TTTTCAACTC
Statistics
Matches: 439, Mismatches: 93, Indels: 26
0.79 0.17 0.05
Matches are distributed among these distances:
163 1 0.00
164 233 0.53
165 80 0.18
166 2 0.00
167 73 0.17
168 50 0.11
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.26
Consensus pattern (168 bp):
ATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGAC
TACGCTCAGCTCCAACGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACA
AAAGACCCTCGAGTTCGACTACACTCAGCTTCGAGGGC
Found at i:1028248 original size:84 final size:83
Alignment explanation
Indices: 1027950--1028654 Score: 687
Period size: 84 Copynumber: 8.5 Consensus size: 83
1027940 TTTTTAAAAG
*
1027950 ATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGAC
1 ATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTCA-CAAAGACCTTCGAGTTCGAC
1028015 TACGCTCAGCTCCAA-GGC
65 TACGCTCAGCTCCAAGGGC
* * * * * ** *
1028033 ATATCATTTACAGCATAGCTTAAGTCGAGGAGGGCTATCTG-C-CAAAGACCCCCGAGTTCGATT
1 ATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACAAAGACCTTCGAGTTCGACT
* * *
1028096 ACACTCAGCTTCGAGGGC
66 ACGCTCAGCTCCAAGGGC
* * * *
1028114 ATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTTGAC
1 ATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTCA-CAAAGACCTTCGAGTTCGAC
*
1028179 TACGCTCAGCTCCCA-GGC
65 TACGCTCAGCTCCAAGGGC
* * * * * *
1028197 ATATCATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCAA
1 ATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTC-AC-AAAGACCTTCGAGTTCGA
* *
1028262 CTACGCTCAGCT-CAACGGT
64 CTACGCTCAGCTCCAAGGGC
* * * * ** *
1028281 ACATCATTTGCAGCATAGCTTAAGTCGATG-AGGGCTATCT-TC-CAAAGACCCCCGAGTTCGAT
1 ATATCATTTGCAGCATAACTTAAGTCTA-GAAGGGTTATCTGTCACAAAGACCTTCGAGTTCGAC
* * *
1028343 TACACTCAGCTTCGAGGGC
65 TACGCTCAGCTCCAAGGGC
* * * *
1028362 ATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACTAAAGACCTTCGAGTTTGAC
1 ATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTCAC-AAAGACCTTCGAGTTCGAC
*
1028427 TACGCTCAGCTCCCA-GGC
65 TACGCTCAGCTCCAAGGGC
* * * * *
1028445 ATATCATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGA
1 ATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTC-AC-AAAGACCTTCGAGTTCGA
* * *
1028510 CTACGCTCAGCT-TAACGAC
64 CTACGCTCAGCTCCAAGGGC
* * * * * * *
1028529 ACATCATTTGCAGCATAGCTTAAGTCGAGGAGGGTTATATG-C-CAAAGACCCTCGAGTTCGATT
1 ATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACAAAGACCTTCGAGTTCGACT
* * *
1028592 ACACTCAGCTTCGAGGGC
66 ACGCTCAGCTCCAAGGGC
* * * * *
1028610 ACATTATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAC
1 ATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTCAC
1028655 CAAATTTTCA
Statistics
Matches: 501, Mismatches: 103, Indels: 36
0.78 0.16 0.06
Matches are distributed among these distances:
80 80 0.16
81 111 0.22
82 5 0.01
83 123 0.25
84 181 0.36
85 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.26
Consensus pattern (83 bp):
ATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGGC
Found at i:1028387 original size:248 final size:248
Alignment explanation
Indices: 1027950--1028658 Score: 1206
Period size: 248 Copynumber: 2.9 Consensus size: 248
1027940 TTTTTAAAAG
* * * * * * *
1027950 ATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGA
1 ATATCATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGA
* *
1028014 CTACGCTCAGCTCCAA-GGCATATCATTTACAGCATAGCTTAAGTCGAGGAGGGCTATCTGCCAA
66 CTACGCTCAGCT-CAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGGAGGGCTATCTGCCAA
1028078 AGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAG
130 AGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAG
1028143 AAGGGTTATCTGTCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCCAGGC
195 AAGGGTTATCTGTCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCCAGGC
*
1028197 ATATCATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCAA
1 ATATCATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGA
* * *
1028262 CTACGCTCAGCTCAACGGTACATCATTTGCAGCATAGCTTAAGTCGATGAGGGCTATCTTCCAAA
66 CTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGGAGGGCTATCTGCCAAA
1028327 GACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGA
131 GACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGA
*
1028392 AGGGTTATCTGTCACTAAAGACCTTCGAGTTTGACTACGCTCAGCTCCCAGGC
196 AGGGTTATCTGTCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCCAGGC
1028445 ATATCATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGA
1 ATATCATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGA
* * * *
1028510 CTACGCTCAGCTTAACGACACATCATTTGCAGCATAGCTTAAGTCGAGGAGGGTTATATGCCAAA
66 CTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGGAGGGCTATCTGCCAAA
* * *
1028575 GACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATTATTTACAGCATAACTCAAGGCTAGA
131 GACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGA
1028640 AGGGTTATCTGTCACCAAA
196 AGGGTTATCTGTCACCAAA
1028659 TTTTCAACTC
Statistics
Matches: 434, Mismatches: 26, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
247 41 0.09
248 393 0.91
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.26
Consensus pattern (248 bp):
ATATCATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGA
CTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGGAGGGCTATCTGCCAAA
GACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGA
AGGGTTATCTGTCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCCAGGC
Found at i:1029788 original size:4 final size:4
Alignment explanation
Indices: 1029779--1029835 Score: 78
Period size: 4 Copynumber: 13.8 Consensus size: 4
1029769 TTTAATCCTT
* *
1029779 TTTA TTTA TTTA TTTA TTTA TTATA TATA TATA TATTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA T-TTA TTTA TTTA TTTA
1029829 TTTA TTT
1 TTTA TTT
1029836 TTAATTTTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
4 43 0.88
5 6 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:1029849 original size:34 final size:37
Alignment explanation
Indices: 1029777--1029860 Score: 113
Period size: 38 Copynumber: 2.4 Consensus size: 37
1029767 ATTTTAATCC
1029777 TTTTTATTTATTTATTTATTTATTATATATATATATA
1 TTTTTATTTATTTATTTATTTATTATATATATATATA
*
1029814 TTATTTATTTATTTATTTATTT-TTA-AT-TTTA-ATA
1 TT-TTTATTTATTTATTTATTTATTATATATATATATA
*
1029848 TTTTTCTTTATTT
1 TTTTTATTTATTT
1029861 CTTTTAACAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
33 10 0.23
34 5 0.11
35 3 0.07
36 2 0.05
37 5 0.11
38 19 0.43
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.71
Consensus pattern (37 bp):
TTTTTATTTATTTATTTATTTATTATATATATATATA
Found at i:1030026 original size:32 final size:33
Alignment explanation
Indices: 1029977--1030040 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
1029967 TTCTCAATTT
* **
1029977 ATTTATTTATTTATTTTT-TCTTTCTTTTTTTG
1 ATTTATTTATCTATTTTTATCTAACTTTTTTTG
1030009 ATTTATTTAATCT-TTTTTATCTAACTTTTTTT
1 ATTTATTT-ATCTATTTTTATCTAACTTTTTTT
1030041 ACCTTTTAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (33 bp):
ATTTATTTATCTATTTTTATCTAACTTTTTTTG
Found at i:1030829 original size:209 final size:209
Alignment explanation
Indices: 1030440--1030959 Score: 611
Period size: 209 Copynumber: 2.4 Consensus size: 209
1030430 ATTTTATGAA
* * * *
1030440 AAATACAAATTTAAGAATTAAATTGAACAAATATAAAATTACATATTAAAATTTAAATAAAGTAA
1 AAATATAAATTTAAGGATTAAATTGAACAAATATAAAATTACAAATTAAAATTTAAATAAA-TTA
* *
1030505 ACAACACACATTGATGAGGGATCAAATTGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAA
65 A-AA-A-ACA--GA-AAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAA
* **
1030570 AAAAGTACTAAATTATACCCATTTAAAAAATTATGGGTCAATTAAAAAATATAAAT-A-AA-TAA
124 AAAAGGACTAAATTATACCCATTTAAAAAATTATGGACCAATTAAAAAATATAAATAACAACTAA
* * **
1030632 TAAGTATGAGTCAATTTCAGATGC
189 CAA-TA-G-GTCAAATGAAGATGC
* * *
1030656 AAATAT-AATTTGGAGGATTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTA
1 AAATATAAATTT-AAGGATTAAATTGAACAAATATAAAATTACAAATTAAAATTTAAATAAATTA
* *
1030720 AAAAACAGAAAGGGATCAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATA-TAAAAAGG
65 AAAAACAGAAAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGG
* *
1030784 ACTAAATTATACCCATTTAAAAAGTTATGGACCAGTTACAAAAATATAAATAACAACTAACAATA
130 ACTAAATTATACCCATTTAAAAAATTATGGACCAATTA-AAAAATATAAATAACAACTAACAATA
1030849 GGTCAAATGAAGATGC
194 GGTCAAATGAAGATGC
* * * * *
1030865 AAATATAAATTTAAGGACTAAATTGAAGACATATAAAAGTGA-AAGACTTAAAATTAAAATAAAT
1 AAATATAAATTTAAGGATTAAATTGAACAAATATAAAA-TTACAA-A-TTAAAATTTAAATAAAT
* * *
1030929 TAAAAAACACAAAAGGATGAAATCGAAATAA
63 TAAAAAACAGAAAGGGATCAAATCGAAATAA
1030960 ATGCAAAATA
Statistics
Matches: 264, Mismatches: 31, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
208 40 0.15
209 97 0.37
210 12 0.05
211 47 0.18
212 8 0.03
213 1 0.00
214 2 0.01
215 8 0.03
216 49 0.19
ACGTcount: A:0.53, C:0.08, G:0.12, T:0.28
Consensus pattern (209 bp):
AAATATAAATTTAAGGATTAAATTGAACAAATATAAAATTACAAATTAAAATTTAAATAAATTAA
AAAACAGAAAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGGA
CTAAATTATACCCATTTAAAAAATTATGGACCAATTAAAAAATATAAATAACAACTAACAATAGG
TCAAATGAAGATGC
Found at i:1031071 original size:15 final size:14
Alignment explanation
Indices: 1031053--1031170 Score: 64
Period size: 13 Copynumber: 7.9 Consensus size: 14
1031043 TATAAGTTCA
1031053 TATATAAACTATATTT
1 TATATAAACTATA--T
1031069 ATATTATAAACTATATAAT
1 -TA-TATAAAC--TAT-AT
*
1031088 TATTATGAACTATA-
1 TA-TATAAACTATAT
* *
1031102 TATATAAATTATGTT
1 TATATAAACTAT-AT
*
1031117 TATATGAACTATA-
1 TATATAAACTATAT
1031130 TATATAAACTATA-
1 TATATAAACTATAT
*
1031143 TATGTAAACTATA-
1 TATATAAACTATAT
1031156 TAGGTATAAACTATA
1 TA--TATAAACTATA
1031171 AAAAGTATAT
Statistics
Matches: 83, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
13 34 0.41
14 2 0.02
15 21 0.25
16 3 0.04
17 2 0.02
18 16 0.19
19 1 0.01
20 3 0.04
21 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (14 bp):
TATATAAACTATAT
Found at i:1031085 original size:20 final size:19
Alignment explanation
Indices: 1031055--1031106 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
1031045 TAAGTTCATA
*
1031055 TATAAACTATATTTA-TAT
1 TATAAACTATATATATTAT
1031073 TATAAACTATATA-ATTAT
1 TATAAACTATATATATTAT
*
1031091 TATGAACTATATATAT
1 TATAAACTATATATAT
1031107 AAATTATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 1 0.03
18 27 0.90
19 2 0.07
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (19 bp):
TATAAACTATATATATTAT
Found at i:1031112 original size:20 final size:20
Alignment explanation
Indices: 1031059--1031114 Score: 66
Period size: 18 Copynumber: 3.0 Consensus size: 20
1031049 TTCATATATA
*
1031059 AACTATAT-T-TATATTATA
1 AACTATATATATATATTATG
1031077 AACTATATA-AT-TATTATG
1 AACTATATATATATATTATG
*
1031095 AACTATATATATAAATTATG
1 AACTATATATATATATTATG
1031115 TTTATATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 23 0.72
19 3 0.09
20 6 0.19
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (20 bp):
AACTATATATATATATTATG
Found at i:1031133 original size:13 final size:13
Alignment explanation
Indices: 1031068--1031170 Score: 82
Period size: 13 Copynumber: 7.3 Consensus size: 13
1031058 AAACTATATT
1031068 TATAT-TATAAAC
1 TATATATATAAAC
1031080 TATATAATTATTATGAAC
1 TATAT-A-TA-TA--AAC
*
1031098 TATATATATAAAT
1 TATATATATAAAC
* *
1031111 TATGTTTATATGAAC
1 TA--TATATATAAAC
1031126 TATATATATAAAC
1 TATATATATAAAC
*
1031139 TATATATGTAAAC
1 TATATATATAAAC
1031152 TATATAGGTATAAAC
1 TATATA--TATAAAC
1031167 TATA
1 TATA
1031171 AAAAGTATAT
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
12 5 0.07
13 31 0.42
15 24 0.33
16 4 0.05
17 1 0.01
18 8 0.11
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:1031194 original size:25 final size:25
Alignment explanation
Indices: 1031160--1031221 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
1031150 ACTATATAGG
1031160 TATAAACTATAAAAAGTATATACTT
1 TATAAACTATAAAAAGTATATACTT
1031185 TATAAACTATAAAAAGTATATACTT
1 TATAAACTATAAAAAGTATATACTT
1031210 TATAAACTATAA
1 TATAAACTATAA
1031222 TTTATATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.35
Consensus pattern (25 bp):
TATAAACTATAAAAAGTATATACTT
Found at i:1031722 original size:20 final size:20
Alignment explanation
Indices: 1031668--1031724 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
1031658 TAAATAATTT
*
1031668 TATATAATATGTATGTATAAAC
1 TATATAA-AT-TATATATAAAC
* *
1031690 CATGTATAA-TATATATAAAC
1 TATATA-AATTATATATAAAC
1031710 TATATAAATTATATA
1 TATATAAATTATATA
1031725 GTTTACATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
19 2 0.07
20 20 0.71
22 5 0.18
23 1 0.04
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (20 bp):
TATATAAATTATATATAAAC
Found at i:1031751 original size:24 final size:24
Alignment explanation
Indices: 1031720--1031766 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1031710 TATATAAATT
1031720 ATATAGTTTACAT-ATGAACTATAC
1 ATATAGTTTA-ATAATGAACTATAC
*
1031744 ATATAGTTTATTAATGAACTATA
1 ATATAGTTTAATAATGAACTATA
1031767 TAAACTAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (24 bp):
ATATAGTTTAATAATGAACTATAC
Found at i:1031796 original size:13 final size:13
Alignment explanation
Indices: 1031775--1032087 Score: 103
Period size: 13 Copynumber: 23.8 Consensus size: 13
1031765 TATAAACTAG
* *
1031775 TATACACTACATA
1 TATAAACTATATA
1031788 TATAAACTATATA
1 TATAAACTATATA
1031801 TATAAACTATATA
1 TATAAACTATATA
* * *
1031814 TACTATATAGTTTACA
1 TA-TA-A-ACTATATA
*
1031830 TATGAACTATATA
1 TATAAACTATATA
*
1031843 TAAAAACTATATA
1 TATAAACTATATA
*
1031856 TATAAACTGTATA
1 TATAAACTATATA
* *
1031869 AACTATAA-TTTATA
1 TA-TA-AACTATATA
1031883 TATAAACTATATA
1 TATAAACTATATA
** *
1031896 CTAT-AGTTGATATT
1 -TATAAACT-ATATA
*
1031910 TATATACTATATA
1 TATAAACTATATA
1031923 -AT--A-TATATA
1 TATAAACTATATA
* * * *
1031932 GTTTACATTATTACA
1 -TATAAACTA-TATA
*
1031947 TATGAACTATATA
1 TATAAACTATATA
1031960 TATAAACTATATA
1 TATAAACTATATA
* * *
1031973 AACTATA-TAGTTTA
1 TA-TAAACTA-TATA
*
1031987 CCTATGAACTATATA
1 --TATAAACTATATA
***
1032002 TATAGTTTAT-TA
1 TATAAACTATATA
*
1032014 -ATGAACTATATA
1 TATAAACTATATA
* **
1032026 AACT-ATTTATATA
1 TA-TAAACTATATA
*
1032039 GTATATACTATATA
1 -TATAAACTATATA
1032053 -A-AAACTATATA
1 TATAAACTATATA
*
1032064 TATATA-TATATAA
1 TATAAACTATAT-A
1032077 TATAAACTATA
1 TATAAACTATA
1032088 ATTTATATAT
Statistics
Matches: 215, Mismatches: 56, Indels: 57
0.66 0.17 0.17
Matches are distributed among these distances:
9 6 0.03
10 1 0.00
11 15 0.07
12 15 0.07
13 112 0.52
14 44 0.20
15 12 0.06
16 10 0.05
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.41
Consensus pattern (13 bp):
TATAAACTATATA
Found at i:1031971 original size:22 final size:21
Alignment explanation
Indices: 1031944--1032005 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
1031934 TTACATTATT
1031944 ACATATGAACTATATATATAA
1 ACATATGAACTATATATATAA
* *
1031965 ACTATATAAACTATATAGT-T-T
1 AC-ATATGAACTATATA-TATAA
*
1031986 ACCTATGAACTATATATATA
1 ACATATGAACTATATATATA
1032006 GTTTATTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 1 0.03
20 13 0.39
21 4 0.12
22 14 0.42
23 1 0.03
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (21 bp):
ACATATGAACTATATATATAA
Found at i:1032003 original size:24 final size:24
Alignment explanation
Indices: 1031976--1032025 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1031966 CTATATAAAC
1031976 TATATAGTTTACCT-ATGAACTATA
1 TATATAGTTTA-CTAATGAACTATA
*
1032000 TATATAGTTTATTAATGAACTATA
1 TATATAGTTTACTAATGAACTATA
1032024 TA
1 TA
1032026 AACTATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (24 bp):
TATATAGTTTACTAATGAACTATA
Found at i:1032034 original size:24 final size:24
Alignment explanation
Indices: 1031990--1032035 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1031980 TAGTTTACCT
*
1031990 ATGAACTATATATATAGTTTATTA
1 ATGAACTATATAAATAGTTTATTA
1032014 ATGAACTATATAAACTA-TTTAT
1 ATGAACTATATAAA-TAGTTTAT
1032036 ATAGTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (24 bp):
ATGAACTATATAAATAGTTTATTA
Found at i:1032049 original size:27 final size:26
Alignment explanation
Indices: 1031850--1032107 Score: 98
Period size: 27 Copynumber: 9.7 Consensus size: 26
1031840 ATATAAAAAC
* *
1031850 TATATATATAAACTGTATAAACTATAAT
1 TATATATATATACTATATAAACTAT--T
*
1031878 T-TATATATAAACTATAT--ACTATAGT
1 TATATATATATACTATATAAACTAT--T
* *
1031903 TGATATTTATATACTATATAATA-TATA
1 T-ATATATATATACTATATAA-ACTATT
* * *
1031930 TAGTTTACATTATTAC-ATATGAACTA--
1 TA-TATATA-TA-TACTATATAAACTATT
*
1031956 TATATATA-A-ACTATATAAACTATA
1 TATATATATATACTATATAAACTATT
* *
1031980 TAGTTTACCTATGA-ACTATATATA-TAGTT
1 TA-TATA--TAT-ATACTATATAAACTA-TT
1032009 TAT-TA-ATGA-ACTATATAAACTATT
1 TATATATAT-ATACTATATAAACTATT
*
1032033 TATATAGTATATACTATATAAAAACTATA
1 TATATA-TATATACTATAT--AAACTATT
1032062 TATATATATATA-TAATATAAACTATAAT
1 TATATATATATACT-ATATAAACTAT--T
*
1032090 T-TATATATAAACTATATA
1 TATATATATATACTATATA
1032108 GTTTACATAT
Statistics
Matches: 182, Mismatches: 19, Indels: 59
0.70 0.07 0.23
Matches are distributed among these distances:
21 2 0.01
22 9 0.05
23 1 0.01
24 20 0.11
25 19 0.10
26 11 0.06
27 62 0.34
28 25 0.14
29 32 0.18
30 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (26 bp):
TATATATATATACTATATAAACTATT
Found at i:1032088 original size:35 final size:37
Alignment explanation
Indices: 1032017--1032107 Score: 89
Period size: 37 Copynumber: 2.5 Consensus size: 37
1032007 TTTATTAATG
* * *
1032017 AACTATATAAACTATTTATATAGTATATACTATATAAA
1 AACTATATAAACTATATATATAATATAAAC-ATATAAA
* *
1032055 AACTATATATA-TATATATATAATATAAAC-TATAATT
1 AACTATATAAACTATATATATAATATAAACATATAA-A
*
1032091 TA-TATATAAACTATATA
1 AACTATATAAACTATATA
1032108 GTTTACATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
35 12 0.27
36 7 0.16
37 15 0.34
38 10 0.23
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.41
Consensus pattern (37 bp):
AACTATATAAACTATATATATAATATAAACATATAAA
Found at i:1032105 original size:25 final size:26
Alignment explanation
Indices: 1032021--1032098 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 26
1032011 TTAATGAACT
*
1032021 ATATAAACTATTTATATAGTATATACTA
1 ATATAAACTATATATATA-TATATA-TA
*
1032049 TATAAAAACTATATATATATATATATA
1 -ATATAAACTATATATATATATATATA
*
1032076 ATATAAACTATA-ATTTATATATA
1 ATATAAACTATATATATATATATA
1032099 AACTATATAG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.22
26 11 0.24
27 2 0.04
28 6 0.13
29 16 0.36
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (26 bp):
ATATAAACTATATATATATATATATA
Found at i:1032112 original size:20 final size:19
Alignment explanation
Indices: 1032066--1032128 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 19
1032056 ACTATATATA
*
1032066 TATATATATA-ATATAAAC
1 TATATATTTACATATAAAC
*
1032084 TATA-ATTTATATATAAAC
1 TATATATTTACATATAAAC
* *
1032102 TATATAGTTTACATATGAAT
1 TATATA-TTTACATATAAAC
1032122 TATATAT
1 TATATAT
1032129 ACAAAATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
17 4 0.11
18 16 0.42
19 2 0.05
20 16 0.42
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (19 bp):
TATATATTTACATATAAAC
Found at i:1032574 original size:15 final size:16
Alignment explanation
Indices: 1032554--1032585 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1032544 TTTTGAATAT
1032554 ATTTATAAA-ATAAAA
1 ATTTATAAATATAAAA
1032569 ATTTATAAATATAAAA
1 ATTTATAAATATAAAA
1032585 A
1 A
1032586 ATATATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATTTATAAATATAAAA
Found at i:1036632 original size:32 final size:34
Alignment explanation
Indices: 1036596--1036678 Score: 143
Period size: 34 Copynumber: 2.5 Consensus size: 34
1036586 CCCGAACCCG
*
1036596 AAAATATTTTATATA-AATTAATAT-AAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
1036628 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
1036662 AAAATATTATATATATA
1 AAAATATTATATATATA
1036679 TAATCGGGGC
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
32 14 0.29
33 9 0.19
34 25 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:1036679 original size:18 final size:18
Alignment explanation
Indices: 1036605--1036681 Score: 63
Period size: 18 Copynumber: 4.4 Consensus size: 18
1036595 GAAAATATTT
* *
1036605 TATATAAATTAATATAAA
1 TATATAAAATATTATAAA
*
1036623 AATATAAAATATTAT--A
1 TATATAAAATATTATAAA
1036639 TATATAATTAATA-TA-AAA
1 TATATAA--AATATTATAAA
* *
1036657 AATATAAAATATTATATA
1 TATATAAAATATTATAAA
1036675 TATATAA
1 TATATAA
1036682 TCGGGGCGGG
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
16 11 0.24
17 4 0.09
18 31 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TATATAAAATATTATAAA
Found at i:1038846 original size:22 final size:22
Alignment explanation
Indices: 1038812--1038853 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1038802 ATAATTATTT
1038812 AAAAAATTAAATA-AAAATACC
1 AAAAAATTAAATACAAAATACC
*
1038833 AAAAATATTTAATACAAAATA
1 AAAAA-ATTAAATACAAAATA
1038854 TTTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 7 0.39
23 6 0.33
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAAAATTAAATACAAAATACC
Found at i:1044549 original size:30 final size:29
Alignment explanation
Indices: 1044479--1044560 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 29
1044469 TTAATTCTGG
* *
1044479 TTTAGACCCTTAAATTTATATTTTTGATAT
1 TTTAGACCTTTACATTT-TATTTTTGATAT
* *
1044509 TTTAGACCTTTAACCTTTTATTTTTGCTAT
1 TTTAGACCTTT-ACATTTTATTTTTGATAT
*
1044539 TTGT-GTCCTTTACATTTTATTT
1 TT-TAGACCTTTACATTTTATTT
1044561 ATTTATTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 10 0.23
30 29 0.66
31 5 0.11
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.57
Consensus pattern (29 bp):
TTTAGACCTTTACATTTTATTTTTGATAT
Found at i:1045826 original size:16 final size:16
Alignment explanation
Indices: 1045805--1045848 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
1045795 ACTTTGTTTC
1045805 CCCTTTCATTTTTGTT
1 CCCTTTCATTTTTGTT
1045821 CCCTTTCATTTTTGTT
1 CCCTTTCATTTTTGTT
*
1045837 CTCTTTCATTTT
1 CCCTTTCATTTT
1045849 ATTTTCATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.07, C:0.25, G:0.05, T:0.64
Consensus pattern (16 bp):
CCCTTTCATTTTTGTT
Found at i:1047510 original size:2 final size:2
Alignment explanation
Indices: 1047503--1047558 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1047493 TCATTTATCC
1047503 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
1047545 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1047559 CCCTTGTTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1047772 original size:30 final size:30
Alignment explanation
Indices: 1047737--1047805 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 30
1047727 ATCAGAACAA
1047737 AAAGAGAAAAGTAGAAAAA-A-AAGA-AAAAAC
1 AAAGAGAAAA-TA-AAAAAGAGAA-ACAAAAAC
1047767 AAAGAGAAAATAAAAAAGAGAAACAAAAAC
1 AAAGAGAAAATAAAAAAGAGAAACAAAAAC
1047797 AAAG-GAAAA
1 AAAGAGAAAA
1047806 AGCGAAGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
28 5 0.14
29 9 0.25
30 22 0.61
ACGTcount: A:0.77, C:0.04, G:0.16, T:0.03
Consensus pattern (30 bp):
AAAGAGAAAATAAAAAAGAGAAACAAAAAC
Found at i:1047776 original size:13 final size:14
Alignment explanation
Indices: 1047735--1047789 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 14
1047725 CAATCAGAAC
1047735 AAAAAGAGAAAAGTAGA
1 AAAAAGAGAAAA-T--A
*
1047752 AAAAAAAGAAAA-A
1 AAAAAGAGAAAATA
*
1047765 ACAAAGAGAAAATA
1 AAAAAGAGAAAATA
1047779 AAAAAGAGAAA
1 AAAAAGAGAAA
1047790 CAAAAACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
13 11 0.33
14 11 0.33
17 11 0.33
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (14 bp):
AAAAAGAGAAAATA
Found at i:1047795 original size:14 final size:13
Alignment explanation
Indices: 1047751--1047795 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1047741 AGAAAAGTAG
1047751 AAAAAAA-AGAAA
1 AAAAAAAGAGAAA
*
1047763 AAACAAAGAGAAA
1 AAAAAAAGAGAAA
1047776 ATAAAAAAGAGAAA
1 A-AAAAAAGAGAAA
*
1047790 CAAAAA
1 AAAAAA
1047796 CAAAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 6 0.21
13 11 0.39
14 11 0.39
ACGTcount: A:0.82, C:0.04, G:0.11, T:0.02
Consensus pattern (13 bp):
AAAAAAAGAGAAA
Found at i:1049780 original size:65 final size:65
Alignment explanation
Indices: 1049659--1049782 Score: 169
Period size: 65 Copynumber: 1.9 Consensus size: 65
1049649 AAACAATATT
* * * *
1049659 CAAGATTAGATTTCAACTTCACAACGAAGGATATCTAACCTAATGCTAATTCGGTGAAATTTATA
1 CAAGATTAGATTTCAACTTCACAACGAAAGATATCAAACCTAAAGCCAATTCGGTGAAATTTATA
* * *
1049724 CAAGATTGGATTTCACCTTCACAACGAAAGATATCAAA-CTCAAAGCCAATTTGGTGAAA
1 CAAGATTAGATTTCAACTTCACAACGAAAGATATCAAACCT-AAAGCCAATTCGGTGAAA
1049783 CAATACTTGG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
64 2 0.04
65 49 0.96
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (65 bp):
CAAGATTAGATTTCAACTTCACAACGAAAGATATCAAACCTAAAGCCAATTCGGTGAAATTTATA
Found at i:1049817 original size:60 final size:62
Alignment explanation
Indices: 1049667--1049818 Score: 166
Period size: 65 Copynumber: 2.4 Consensus size: 62
1049657 TTCAAGATTA
* * * **
1049667 GATTTCAACTTCACAACGAAGGATATCTAACCTAATGCTAATTCGGTGAAATTTATACAAGATTG
1 GATTTCAACTTCACAACGAAGGATATCAAACCTAAAGCCAATTCGGTGAAATCAATAC---ATTG
* * *
1049732 GATTTCACCTTCACAACGAAAGATATCAAA-CTCAAAGCCAATTTGGTGAAA-CAATAC-TTG
1 GATTTCAACTTCACAACGAAGGATATCAAACCT-AAAGCCAATTCGGTGAAATCAATACATTG
*
1049792 GATTTCAACTTCACGACGAAGGATATC
1 GATTTCAACTTCACAACGAAGGATATC
1049819 CACTTCAAAG
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
60 27 0.36
64 6 0.08
65 42 0.56
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (62 bp):
GATTTCAACTTCACAACGAAGGATATCAAACCTAAAGCCAATTCGGTGAAATCAATACATTG
Found at i:1050391 original size:85 final size:85
Alignment explanation
Indices: 1050065--1050374 Score: 494
Period size: 85 Copynumber: 3.6 Consensus size: 85
1050055 TACAACATAG
* * *
1050065 CTCAAGGCGAGAAGGGCTATCTGTCAATAAAGACATTCGAGTTCGATTACATTCAGCTCAAAGGC
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGC
*
1050130 ATATCAAATTCACAATATAA
66 ATATCAAATTCACAGTATAA
* * *
1050150 CTCAAGGTGAGAAGGGTTATCTGTCAACAAAGACTTTTGAGTTCGATTACATTCAGCTCAAAGGC
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGC
*
1050215 ATATCAAATTCACAGCATAA
66 ATATCAAATTCACAGTATAA
* * *
1050235 CTCAAGGCGAGAAGGGTTATCTGTCAATAAAGACCTCCGAGTTCGATTACATTCAGCTCAGAGGC
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGC
*
1050300 ATATCAAATTTACAGTATAA
66 ATATCAAATTCACAGTATAA
* *
1050320 CTCAAGGCGAGAAGGGTTATCTGTCAACAAATACCTTCGAGTTCGATTCCATTCA
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCA
1050375 ACTCGATGAC
Statistics
Matches: 206, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 206 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (85 bp):
CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGC
ATATCAAATTCACAGTATAA
Found at i:1052236 original size:30 final size:30
Alignment explanation
Indices: 1052202--1052263 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1052192 TTAATTTCGG
1052202 TTTAGAACC-TTAAA-TTTCTATTTTTGATAT
1 TTTAG-ACCTTTAAACTTT-TATTTTTGATAT
* *
1052232 TTTAGTCCTTTAAACTTTTATTTTTGCTAT
1 TTTAGACCTTTAAACTTTTATTTTTGATAT
1052262 TT
1 TT
1052264 GTGTCCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 2 0.07
30 23 0.82
31 3 0.11
ACGTcount: A:0.24, C:0.11, G:0.06, T:0.58
Consensus pattern (30 bp):
TTTAGACCTTTAAACTTTTATTTTTGATAT
Found at i:1052270 original size:30 final size:29
Alignment explanation
Indices: 1052211--1052283 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 29
1052201 GTTTAGAACC
1052211 TTAAATTTCTATTTTTGATATTTTAGTCCT
1 TTAAATTT-TATTTTTGATATTTTAGTCCT
*
1052241 TTAAACTTTTATTTTTGCTATTTGT-GTCCT
1 TTAAA-TTTTATTTTTGATATTT-TAGTCCT
*
1052271 TTACATTTTATTT
1 TTAAATTTTATTT
1052284 ATTTATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
29 8 0.21
30 27 0.69
31 4 0.10
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.62
Consensus pattern (29 bp):
TTAAATTTTATTTTTGATATTTTAGTCCT
Found at i:1052293 original size:20 final size:18
Alignment explanation
Indices: 1052270--1052333 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 18
1052260 ATTTGTGTCC
1052270 TTTACATTTTATTTATTTAT
1 TTTA-ATTTT-TTTATTTAT
*
1052290 TTTATATATTTTTATTTTTAT
1 TTTA-AT-TTTTT-TATTTAT
* *
1052311 TTTAATATTTTTATTTCT
1 TTTAATTTTTTTATTTAT
1052329 TTTAA
1 TTTAA
1052334 AATCATTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 10 0.27
19 4 0.11
20 10 0.27
21 13 0.35
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTAATTTTTTTATTTAT
Found at i:1053574 original size:3 final size:3
Alignment explanation
Indices: 1053560--1053654 Score: 64
Period size: 3 Copynumber: 30.7 Consensus size: 3
1053550 TTTCATCTTT
* * * ** *
1053560 TTA TTT TTA TTA TTA TTA CTCA TTA TTA TCTA ATA TTA GAA TTA TTT
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* * * * *
1053607 TTA TCA TTA CTC TCA TTA GTA TATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
1053653 TT
1 TT
1053655 TCTTAATAAT
Statistics
Matches: 67, Mismatches: 22, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
3 60 0.90
4 7 0.10
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1053645 original size:40 final size:41
Alignment explanation
Indices: 1053560--1053637 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
1053550 TTTCATCTTT
* * * *
1053560 TTATTTTTATTATTATTACTCATTATTATCTAATATTAGAA
1 TTATTTTTATCATTACTACTCATTAGTATATAATATTAGAA
*
1053601 TTATTTTTATCATTACT-CTCATTAGTATATATTATTA
1 TTATTTTTATCATTACTACTCATTAGTATATAATATTA
1053638 TTATTATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.56
Consensus pattern (41 bp):
TTATTTTTATCATTACTACTCATTAGTATATAATATTAGAA
Found at i:1055055 original size:139 final size:138
Alignment explanation
Indices: 1054730--1055068 Score: 351
Period size: 139 Copynumber: 2.4 Consensus size: 138
1054720 TATTGTATCA
* * * * ** * * ***
1054730 AATAATTAAAATGGGACCTCGGGTATAAATATGAGGACTAAATAAAAAATTCTCCTAAATTAGGG
1 AATAATTGAAATAGAACCTAGGG-ATAAATGCGAGGACCAAATAAAAAATTCACCTAAATTAAAA
* * *
1054795 GACTAGAGTGAAATTAAACCTAAGGTGAATGCACTAATATTAACACTGATCAATTTTAATCAAAT
65 GACTAAAGTGAAATTAAACCTAAGGTGAAGGCACTAATATTAACACTGATCAATTTTAACCAAAT
* *
1054860 ATTGGATCG
130 AATAGATCG
* ** * * * *
1054869 AATAATTG-AATTGAAAGTTTGAGTATAAATGCAAGGACCAAATAAAAAATTCACATAAATTAAA
1 AATAATTGAAATAG-AACCTAG-GGATAAATGCGAGGACCAAATAAAAAATTCACCTAAATTAAA
* * * *
1054933 AGACTAAAGTGAAATTAAACCTAAGCTTG-AGGCTCTAATGTTAACCAC-GATCGATTTTAACCA
64 AGACTAAAGTGAAATTAAACCTAAG-GTGAAGGCACTAATATTAA-CACTGATCAATTTTAACCA
*
1054996 ATTAATAGATCG
127 AATAATAGATCG
*
1055008 AATAATTGAAATAGAACCTAGGGATAAATGCGAGGACCAAATAAAAAATTTACCTAAATTA
1 AATAATTGAAATAGAACCTAGGGATAAATGCGAGGACCAAATAAAAAATTCACCTAAATTA
1055069 GAAGTTTATG
Statistics
Matches: 161, Mismatches: 34, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
138 40 0.25
139 111 0.69
140 10 0.06
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (138 bp):
AATAATTGAAATAGAACCTAGGGATAAATGCGAGGACCAAATAAAAAATTCACCTAAATTAAAAG
ACTAAAGTGAAATTAAACCTAAGGTGAAGGCACTAATATTAACACTGATCAATTTTAACCAAATA
ATAGATCG
Found at i:1056035 original size:8 final size:8
Alignment explanation
Indices: 1056024--1056055 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
1056014 TTTATTATTA
1056024 TTCTTTTT
1 TTCTTTTT
1056032 TTC-TTTT
1 TTCTTTTT
1056039 TTCTTTTT
1 TTCTTTTT
1056047 TTCTTTTT
1 TTCTTTTT
1056055 T
1 T
1056056 CCCTTTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTCTTTTT
Found at i:1056044 original size:15 final size:15
Alignment explanation
Indices: 1056024--1056056 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1056014 TTTATTATTA
1056024 TTCTTTTTTTCTTTT
1 TTCTTTTTTTCTTTT
1056039 TTCTTTTTTTCTTTT
1 TTCTTTTTTTCTTTT
1056054 TTC
1 TTC
1056057 CCTTTTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTCTTTTTTTCTTTT
Found at i:1056062 original size:15 final size:15
Alignment explanation
Indices: 1056029--1056063 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1056019 TATTATTCTT
**
1056029 TTTTTCTTTTTTCTT
1 TTTTTCTTTTTTCCC
1056044 TTTTTCTTTTTTCCC
1 TTTTTCTTTTTTCCC
1056059 TTTTT
1 TTTTT
1056064 ACTGGTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTCTTTTTTCCC
Found at i:1056392 original size:37 final size:36
Alignment explanation
Indices: 1056323--1056399 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 36
1056313 ATTTTGAAGT
* * *
1056323 TTTTATTTCAAGGGAAACTATGTCGAGAGAGATGAAA
1 TTTTATTTCAAGGGAAACGATCTCAAGAGAGAT-AAA
* * *
1056360 TTTTGTTTTAAGGGAAACGATCTCAAGTGAGATAAA
1 TTTTATTTCAAGGGAAACGATCTCAAGAGAGATAAA
1056396 TTTT
1 TTTT
1056400 TTGTTTCAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 7 0.21
37 27 0.79
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (36 bp):
TTTTATTTCAAGGGAAACGATCTCAAGAGAGATAAA
Found at i:1056476 original size:103 final size:104
Alignment explanation
Indices: 1056328--1056598 Score: 330
Period size: 103 Copynumber: 2.6 Consensus size: 104
1056318 GAAGTTTTTA
** * * * *
1056328 TTTCAAGGGAAACTATGTCGAGAGAGATGAAAT-TTTGTTTTAAGGGAAACGATCTCAAGTGAGA
1 TTTCAAGGGAAACTATCCCAAGAGAGAT-CAATCTTTGTTTCAAGGGAAACAATCTCAAGTGAGA
1056392 TAAATTTTTTGTTTCAAATGAAGCAATCTCAAAATTTGTG
65 TAAATTTTTTGTTTCAAATGAAGCAATCTCAAAATTTGTG
* * * *
1056432 TTTGAAGGGAAACTGTCCCAAGTGAGA-CAATCTTTGTTTCAAGGGAAACAATCTCAAGTAAGAT
1 TTTCAAGGGAAACTATCCCAAGAGAGATCAATCTTTGTTTCAAGGGAAACAATCTCAAGTGAGAT
* * * * **
1056496 AATTTTTTTGTTTCGACTGAAGTAATCTCAATGTTTGTG
66 AAATTTTTTGTTTCAAATGAAGCAATCTCAAAATTTGTG
* * * * *
1056535 TTTCAAGGGAAACTATCTCAAGAGAGATGAATTTTTGTTTCAATGGAAACAATTTCAAGTGAGA
1 TTTCAAGGGAAACTATCCCAAGAGAGATCAATCTTTGTTTCAAGGGAAACAATCTCAAGTGAGA
1056599 AGAAATTTGT
Statistics
Matches: 140, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
102 3 0.02
103 85 0.61
104 52 0.37
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (104 bp):
TTTCAAGGGAAACTATCCCAAGAGAGATCAATCTTTGTTTCAAGGGAAACAATCTCAAGTGAGAT
AAATTTTTTGTTTCAAATGAAGCAATCTCAAAATTTGTG
Found at i:1056486 original size:65 final size:66
Alignment explanation
Indices: 1056357--1056488 Score: 162
Period size: 67 Copynumber: 2.0 Consensus size: 66
1056347 GAGAGAGATG
* * * * *
1056357 AAATTTTGTTTTAAGGGAAACGATCTCAAGTGAGATAAATTTTTTGTTTCAAATGAAGCAATCTC
1 AAATTTTGTTTGAAGGGAAACGATCCCAAGTGAGATAAATTCTTTGTTTCAAAGGAAACAATCTC
1056422 A
66 A
* *
1056423 AAATTTGTGTTTGAAGGGAAACTG-TCCCAAGTGAGA-CAA-TCTTTGTTTCAAGGGAAACAATC
1 AAATTT-TGTTTGAAGGGAAAC-GATCCCAAGTGAGATAAATTCTTTGTTTCAAAGGAAACAATC
1056485 TCA
64 TCA
1056488 A
1 A
1056489 GTAAGATAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
65 23 0.40
66 8 0.14
67 25 0.44
68 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (66 bp):
AAATTTTGTTTGAAGGGAAACGATCCCAAGTGAGATAAATTCTTTGTTTCAAAGGAAACAATCTC
A
Found at i:1056490 original size:36 final size:35
Alignment explanation
Indices: 1056322--1056634 Score: 139
Period size: 36 Copynumber: 8.9 Consensus size: 35
1056312 GATTTTGAAG
* * * *
1056322 TTTTTATTTCAAGGGAAACTATGTCGAGAGAGATGAAA
1 TTTTTGTTTCAAGGGAAACAATCTC-A-AGTGA-GAAA
* *
1056360 -TTTTGTTTTAAGGGAAACGATCTCAAGTGAGATAAA
1 TTTTTGTTTCAAGGGAAACAATCTCAAGTGAG--AAA
** *
1056396 TTTTTTGTTTCAAATGAAGCAATCTC-----A-AAA
1 -TTTTTGTTTCAAGGGAAACAATCTCAAGTGAGAAA
* * ** *
1056426 TTTGTGTTTGAAGGGAAACTGTCCCAAGTGAGACAA
1 TTTTTGTTTCAAGGGAAACAATCTCAAGTGAGA-AA
* *
1056462 TCTTTGTTTCAAGGGAAACAATCTCAAGTAAGATAA
1 TTTTTGTTTCAAGGGAAACAATCTCAAGTGAGA-AA
* ** **
1056498 TTTTTTTGTTTCGACTGAAGTAATCTCAA-T--G---
1 --TTTTTGTTTCAAGGGAAACAATCTCAAGTGAGAAA
* * *
1056529 TTTGTGTTTCAAGGGAAACTATCTCAAGAGAGATGAA
1 TTTTTGTTTCAAGGGAAACAATCTCAAGTGAGA--AA
* *
1056566 TTTTTGTTTCAATGGAAACAATTTCAAGTGAGAAGA
1 TTTTTGTTTCAAGGGAAACAATCTCAAGTGAGAA-A
** * **
1056602 AATTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TTTTTGTTTCAAGGGAAACAATCTCAAGTGAGA
1056635 TTAGATTTCC
Statistics
Matches: 201, Mismatches: 52, Indels: 46
0.67 0.17 0.15
Matches are distributed among these distances:
29 37 0.18
30 3 0.01
32 1 0.00
33 1 0.00
34 2 0.01
35 7 0.03
36 61 0.30
37 49 0.24
38 40 0.20
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (35 bp):
TTTTTGTTTCAAGGGAAACAATCTCAAGTGAGAAA
Found at i:1056807 original size:142 final size:137
Alignment explanation
Indices: 1056528--1056873 Score: 426
Period size: 142 Copynumber: 2.5 Consensus size: 137
1056518 TAATCTCAAT
* * * * *
1056528 GTTTGTGTTTCAAGGGAAACTATCTCAAGAGAGATGAATTTTTGTTTCAATGGAAACAATTTCAA
1 GTTTGTGTTTCAAGGGAAATTGTCTCAAGTGAGATGAA-ATTTGTTTCAATGGAAACAATCTCAA
* * * * * *
1056593 GTGAGAAGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATTAGATTTCCTTTGAGTGAAATG
65 GTGAGAAGAAATTAGTTTCAAGAAAAACAATATCAAATGAGATAAGATTTCCTTTAAGTGAAATG
1056658 ATCTTAAA
130 ATCTTAAA
**
1056666 GTTTGTGTTTCAAGGGAAATTGTCTCAAGTGAGATGAAATTTGTTTTTA-GGAAAACAATCTCAA
1 GTTTGTGTTTCAAGGGAAATTGTCTCAAGTGAGATGAAATTTGTTTCAATGG-AAACAATCTCAA
*
1056730 GTGAGACA-AAATTAGTTTCAAGAAAAAAAAAACAATATCAAATGAGATAAGATTTCGTTTAAGT
65 GTGAGA-AGAAATTAGTTTCAAG-----AAAAACAATATCAAATGAGATAAGATTTCCTTTAAGT
1056794 GAAATGATCTTAAA
124 GAAATGATCTTAAA
* * * *
1056808 GTTTGTGTTTCAAGGGAAATTGTCTCAAGTGAGACGAAATTTTCATTTCGAGGGAAACAATCTCA
1 GTTTGTGTTTCAAGGGAAATTGTCTCAAGTGAGATGAAA-TTT-GTTTCAATGGAAACAATCTCA
1056873 A
64 A
1056874 AGTTTGAAAA
Statistics
Matches: 180, Mismatches: 18, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
136 2 0.01
137 37 0.21
138 36 0.20
142 84 0.47
143 3 0.02
144 16 0.09
145 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (137 bp):
GTTTGTGTTTCAAGGGAAATTGTCTCAAGTGAGATGAAATTTGTTTCAATGGAAACAATCTCAAG
TGAGAAGAAATTAGTTTCAAGAAAAACAATATCAAATGAGATAAGATTTCCTTTAAGTGAAATGA
TCTTAAA
Found at i:1061935 original size:24 final size:24
Alignment explanation
Indices: 1061882--1061935 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1061872 AATATTGATG
1061882 CGTCCAGCTGTGGTTTTGGTGCAT
1 CGTCCAGCTGTGGTTTTGGTGCAT
* *
1061906 CATCCAGCTGTGGTTTTGGTGCGT
1 CGTCCAGCTGTGGTTTTGGTGCAT
1061930 CGTCCA
1 CGTCCA
1061936 CTACGTGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.09, C:0.24, G:0.31, T:0.35
Consensus pattern (24 bp):
CGTCCAGCTGTGGTTTTGGTGCAT
Found at i:1063262 original size:21 final size:22
Alignment explanation
Indices: 1063236--1063277 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1063226 ACTATGGAGA
1063236 AAATGA-AG-GAAAAAGATAAAT
1 AAATGAGAGAGAAAAAG-TAAAT
1063257 AAATGAGAGAGAAAAAGTAAA
1 AAATGAGAGAGAAAAAGTAAA
1063278 AGTTAAGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (22 bp):
AAATGAGAGAGAAAAAGTAAAT
Found at i:1063300 original size:20 final size:20
Alignment explanation
Indices: 1063275--1063318 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1063265 GAGAAAAAGT
1063275 AAAAGTTAAGAACGAAAGAG
1 AAAAGTTAAGAACGAAAGAG
*
1063295 AAAAGTTAAGAATGAAAGAG
1 AAAAGTTAAGAACGAAAGAG
1063315 AAAA
1 AAAA
1063319 AGAAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.64, C:0.02, G:0.23, T:0.11
Consensus pattern (20 bp):
AAAAGTTAAGAACGAAAGAG
Found at i:1065602 original size:100 final size:100
Alignment explanation
Indices: 1065429--1065624 Score: 392
Period size: 100 Copynumber: 2.0 Consensus size: 100
1065419 CTCAAATGGT
1065429 GATGTCCAATAAGGAGGAACTACAATGGGTATCGATATCAATCGTCGTTTCAACTCAGTGAATGC
1 GATGTCCAATAAGGAGGAACTACAATGGGTATCGATATCAATCGTCGTTTCAACTCAGTGAATGC
1065494 GCCAAGGCATAACTCGTCAAACACAAAGGGAAATG
66 GCCAAGGCATAACTCGTCAAACACAAAGGGAAATG
1065529 GATGTCCAATAAGGAGGAACTACAATGGGTATCGATATCAATCGTCGTTTCAACTCAGTGAATGC
1 GATGTCCAATAAGGAGGAACTACAATGGGTATCGATATCAATCGTCGTTTCAACTCAGTGAATGC
1065594 GCCAAGGCATAACTCGTCAAACACAAAGGGA
66 GCCAAGGCATAACTCGTCAAACACAAAGGGA
1065625 TGGTTTTGTT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (100 bp):
GATGTCCAATAAGGAGGAACTACAATGGGTATCGATATCAATCGTCGTTTCAACTCAGTGAATGC
GCCAAGGCATAACTCGTCAAACACAAAGGGAAATG
Found at i:1069488 original size:48 final size:48
Alignment explanation
Indices: 1069432--1069530 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
1069422 GATATATACA
1069432 ATGTCACAGAAATGAAAATGTGTATGCTGGTGGATATGGATTGATGGT
1 ATGTCACAGAAATGAAAATGTGTATGCTGGTGGATATGGATTGATGGT
1069480 ATGTCACAGAAATGAAAATGTGTATGCTGGTGGATATGGATTGATGGT
1 ATGTCACAGAAATGAAAATGTGTATGCTGGTGGATATGGATTGATGGT
1069528 ATG
1 ATG
1069531 ATGGTGTAGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.31
Consensus pattern (48 bp):
ATGTCACAGAAATGAAAATGTGTATGCTGGTGGATATGGATTGATGGT
Found at i:1074967 original size:13 final size:13
Alignment explanation
Indices: 1074923--1074969 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1074913 CTTTTCTTCG
*
1074923 ATATTGAAAAGTAA
1 ATATTTAAAA-TAA
1074937 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
1074949 TTTATTTAAAATAA
1 -ATATTTAAAATAA
1074963 ATATTTA
1 ATATTTA
1074970 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:1076316 original size:2 final size:2
Alignment explanation
Indices: 1076311--1076337 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1076301 ATTATTTATG
1076311 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1076338 TAATAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1076346 original size:3 final size:3
Alignment explanation
Indices: 1076338--1076437 Score: 128
Period size: 3 Copynumber: 33.0 Consensus size: 3
1076328 ATATATATAT
* *
1076338 TAA TAA TAA TAAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
1076384 TAA TAT TTA TAG TAA TAA TAA TAA TAA TAA TAA TTA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1076432 TAA TAA
1 TAA TAA
1076438 ATAAATCAAA
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
3 79 0.96
4 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1076379 original size:27 final size:27
Alignment explanation
Indices: 1076338--1076437 Score: 164
Period size: 27 Copynumber: 3.7 Consensus size: 27
1076328 ATATATATAT
1076338 TAATAATAATAAATAATAATAATATTTA
1 TAATAATAAT-AATAATAATAATATTTA
1076366 TAATAATAATAATAATAATAATATTTA
1 TAATAATAATAATAATAATAATATTTA
* *
1076393 TAGTAATAATAATAATAATAATAATTA
1 TAATAATAATAATAATAATAATATTTA
*
1076420 TAGTAATAATAATAATAA
1 TAATAATAATAATAATAA
1076438 ATAAATCAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 60 0.86
28 10 0.14
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
TAATAATAATAATAATAATAATATTTA
Found at i:1076809 original size:89 final size:90
Alignment explanation
Indices: 1076709--1076895 Score: 234
Period size: 92 Copynumber: 2.1 Consensus size: 90
1076699 ATGAACTTCC
* * *
1076709 TCTTCTTCAGAT-GAGTTCTTCTAATTATGAACT-TTCTCTGTAAAAGTTGATCCATCGAGTGAT
1 TCTTCTTCAGATAGAGTTCTTCTAATTATGAACTCTTC-CTGGAAAAGTTAATCCATCAAGTGAT
* * * *
1076772 GGATTTGAGCAAGAGGTTGAACAAAT
65 GAATTTAAACAAAAGGTTGAACAAAT
* * * *
1076798 TCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTGGCAATGTTAATCCATCAATTGA
1 TCTTCTTCAGAT-A-GAGTTCTTCTAATTATGAACTCTTCCTGGAAAAGTTAATCCATCAAGTGA
1076863 TGAATTTAAACAAAAGGTTGAACAAAT
64 TGAATTTAAACAAAAGGTTGAACAAAT
1076890 TCTTCT
1 TCTTCT
1076896 CATTATGAAC
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
89 12 0.14
92 68 0.82
93 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (90 bp):
TCTTCTTCAGATAGAGTTCTTCTAATTATGAACTCTTCCTGGAAAAGTTAATCCATCAAGTGATG
AATTTAAACAAAAGGTTGAACAAAT
Found at i:1077115 original size:113 final size:112
Alignment explanation
Indices: 1076799--1077126 Score: 391
Period size: 107 Copynumber: 2.9 Consensus size: 112
1076789 TGAACAAATT
* * * * *
1076799 CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTC-CTGGCAATGTTAATCCATCAATTGA
1 CTTCTTCAGAT---GAGTTCTTCT-ATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGA
* *
1076863 TGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTC
61 TGGATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTC
* * *
1076915 CTTCTTCAGATGA--T-TTC-ATTATG-ACCTTCTCTGGAAAAGCTGATCCATCAAGTGATGAAT
1 CTTCTTCAGATGAGTTCTTCTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGAT
* *
1076975 TCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTC
66 TTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTT-TTCTTC
*
1077022 CTTCTTCAGATGAGTTCTTCTTATTATGAAATTTCTCTGGAAAAGCTGATCCATCAAATGATGGA
1 CTTCTTCAGATGAGTTCTTC-TATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGA
* * **
1077087 TTTGAGCAAACGGTTGAACAAGCTCTTCTCATTATGAACT
65 TTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACT
1077127 CTTCCAGAAA
Statistics
Matches: 184, Mismatches: 19, Indels: 20
0.83 0.09 0.09
Matches are distributed among these distances:
106 6 0.03
107 80 0.43
108 6 0.03
109 1 0.01
110 6 0.03
111 1 0.01
112 6 0.03
113 66 0.36
114 1 0.01
116 11 0.06
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (112 bp):
CTTCTTCAGATGAGTTCTTCTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGAT
TTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTC
Found at i:1077155 original size:72 final size:73
Alignment explanation
Indices: 1077061--1077203 Score: 207
Period size: 72 Copynumber: 2.0 Consensus size: 73
1077051 AATTTCTCTG
* ** * **
1077061 GAAAAGCTGATCCATCAAATGATGGATTTGAGCAAACGGTTGAACAAGCTCTTCTCATTATGAAC
1 GAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGCTCTTCTCATTATGAAC
1077126 -TCTTCCA
66 TTCTTCCA
* *
1077133 GAAATGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
1 GAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGCTCTTCTCATTATGAAC
1077198 TTCTTC
66 TTCTTC
1077204 TTCCTTCTTC
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
72 57 0.92
73 5 0.08
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (73 bp):
GAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGCTCTTCTCATTATGAAC
TTCTTCCA
Found at i:1077158 original size:185 final size:186
Alignment explanation
Indices: 1076930--1077316 Score: 580
Period size: 185 Copynumber: 2.1 Consensus size: 186
1076920 TCAGATGATT
* ** * ** *
1076930 TCATTATGACCTTC-TCTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACA
1 TCATTATGAACTTCTTCCAGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACA
* *
1076994 AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAATTTCTC
66 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAATTTCTC
* * * * * *
1077059 TGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAACGGTTGAACAAGCTCTTC
131 TGGAAAAGATAATCCATCAAATAATAGATTTGAGCAAAAGGTTGAACAAACTCTTC
*
1077115 TCATTATGAAC-TCTTCCAGAAATGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACA
1 TCATTATGAACTTCTTCCAGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACA
* *
1077179 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
66 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAATTTCTC
* *
1077244 TGGAAAAGATAATCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAATTCTTC
131 TGGAAAAGATAATCCATCAAATAATAGATTTGAGCAAAAGGTTGAACAAACTCTTC
1077300 TCATTATGAACTTCTTC
1 TCATTATGAACTTCTTC
1077317 TTCCTTCTTC
Statistics
Matches: 180, Mismatches: 20, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
184 2 0.01
185 173 0.96
186 5 0.03
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (186 bp):
TCATTATGAACTTCTTCCAGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACA
AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAATTTCTC
TGGAAAAGATAATCCATCAAATAATAGATTTGAGCAAAAGGTTGAACAAACTCTTC
Found at i:1077235 original size:112 final size:112
Alignment explanation
Indices: 1077110--1077593 Score: 641
Period size: 113 Copynumber: 4.3 Consensus size: 112
1077100 TTGAACAAGC
*
1077110 TCTTCTCATTATGAACTCTTCCAGAAATGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTG
1 TCTTCTCATTATGAACTCTTCCAGAAATGCTGATCCATCAAATGATGAATTCAAGCAAAAAGTTG
*
1077175 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
66 AACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
* * * * * * ** *
1077222 TCTTCTCATTATGAACT-TTCTCTGGAAAAGATAATCCATCAAGTAAT-AGATTTGAGCAAAAGG
1 TCTTCTCATTATGAACTCTTC-C-AGAAATGCTGATCCATCAAATGATGA-ATTCAAGCAAAAAG
1077285 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
63 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
* * *** *
1077335 TCTTCTCATTATGAACTCTTCCAGAAATGCTGATCCATCAAGTGATGGATTTGGGCAAAAGGTTG
1 TCTTCTCATTATGAACTCTTCCAGAAATGCTGATCCATCAAATGATGAATTCAAGCAAAAAGTTG
* *
1077400 AATAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGT
66 AACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
* * * * *
1077447 TCTTCTCATTATGAACT-TTCTCTGGTAATGCTGATTCATCGAATGATGAATTCAAGCGAAAAGT
1 TCTTCTCATTATGAACTCTTC-C-AGAAATGCTGATCCATCAAATGATGAATTCAAGCAAAAAGT
* ** *
1077511 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTATTTCTTCATATGAGT
64 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
*
1077560 TCTTCTCATTATGAACTCTTCCAGAAATGTTGAT
1 TCTTCTCATTATGAACTCTTCCAGAAATGCTGAT
1077594 ATATTTCATG
Statistics
Matches: 325, Mismatches: 39, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
111 6 0.02
112 126 0.39
113 187 0.58
114 6 0.02
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
TCTTCTCATTATGAACTCTTCCAGAAATGCTGATCCATCAAATGATGAATTCAAGCAAAAAGTTG
AACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
Found at i:1077415 original size:225 final size:225
Alignment explanation
Indices: 1077110--1077593 Score: 713
Period size: 225 Copynumber: 2.2 Consensus size: 225
1077100 TTGAACAAGC
1077110 TCTTCTCATTATGAACTCTTCCAGAAATGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTG
1 TCTTCTCATTATGAACTCTTCCAGAAATGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTG
* *
1077175 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
66 AACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTT
**
1077240 TCTCTGGAAAAGATAATCCATC-AAGTAAT-AGATTTGAGC-AAAAGGTTGAACAAATTCTTCTC
131 TCTCTGGAAAAGATAATCCATCGAA-TAATGA-ATTCAAGCGAAAA-GTTGAACAAATTCTTCTC
*
1077302 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
193 ATTATGAACTTCTTCTTACTTCTTCAGATGAGT
* * **** *
1077335 TCTTCTCATTATGAACTCTTCCAGAAATGCTGATCCATCAAGTGATGGATTTGGGCAAAAGGTTG
1 TCTTCTCATTATGAACTCTTCCAGAAATGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTG
*
1077400 AATAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTT
66 AACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTT
* * * * * * *
1077465 TCTCTGGTAATGCTGATTCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATT
131 TCTCTGGAAAAGATAATCCATCGAATAATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTCATT
* *
1077530 ATGAACTTCTTCTTATTTCTTCATATGAGT
196 ATGAACTTCTTCTTACTTCTTCAGATGAGT
*
1077560 TCTTCTCATTATGAACTCTTCCAGAAATGTTGAT
1 TCTTCTCATTATGAACTCTTCCAGAAATGCTGAT
1077594 ATATTTCATG
Statistics
Matches: 233, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
225 226 0.97
226 7 0.03
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (225 bp):
TCTTCTCATTATGAACTCTTCCAGAAATGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTG
AACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTT
TCTCTGGAAAAGATAATCCATCGAATAATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTCATT
ATGAACTTCTTCTTACTTCTTCAGATGAGT
Found at i:1078532 original size:81 final size:83
Alignment explanation
Indices: 1078337--1078637 Score: 552
Period size: 83 Copynumber: 3.7 Consensus size: 83
1078327 GGTTCCTACT
1078337 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAAT
1078402 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
* *
1078420 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGAACACATTCCTC-T-CAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAAT
* *
1078483 TCAATGATTGGTTTTACC
66 TCAATGATTGGTTCTGCC
1078501 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAAT
1078566 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
1078584 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTC
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTC
1078638 ATTTGTTCCA
Statistics
Matches: 208, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
81 76 0.37
82 2 0.01
83 130 0.62
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.24
Consensus pattern (83 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAAT
TCAATGATTGGTTCTGCC
Found at i:1078608 original size:164 final size:164
Alignment explanation
Indices: 1078337--1078637 Score: 584
Period size: 164 Copynumber: 1.8 Consensus size: 164
1078327 GGTTCCTACT
1078337 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAAT
1078402 TCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGAA
66 TCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGAA
1078467 CACATTCCTCTCAAATTCAATGATTGGTTTTACC
131 CACATTCCTCTCAAATTCAATGATTGGTTTTACC
1078501 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAAT
* *
1078566 TCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
66 TCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGAA
1078631 CACATTC
131 CACATTC
1078638 ATTTGTTCCA
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
164 135 1.00
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.24
Consensus pattern (164 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAAT
TCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGAA
CACATTCCTCTCAAATTCAATGATTGGTTTTACC
Found at i:1079796 original size:10 final size:9
Alignment explanation
Indices: 1079780--1079840 Score: 70
Period size: 9 Copynumber: 6.8 Consensus size: 9
1079770 TTGACCCCTC
*
1079780 CTTTTTCTT
1 CTTTTTTTT
*
1079789 CTTTTTTCT
1 CTTTTTTTT
1079798 CTTTTCTTTT
1 CTTTT-TTTT
1079808 -TTTTTTTT
1 CTTTTTTTT
*
1079816 TTTTTTTTT
1 CTTTTTTTT
*
1079825 TTTTTTTTT
1 CTTTTTTTT
1079834 CTTTTTT
1 CTTTTTT
1079841 CTTCAAGCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
8 4 0.09
9 39 0.85
10 3 0.07
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:1079802 original size:7 final size:6
Alignment explanation
Indices: 1079791--1079839 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 6
1079781 TTTTTCTTCT
1079791 TTTTTC TCTTTTC TTTTT- TTTTT- TTTTT- TTTTT- TTTTT- TTTTTC
1 TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
1079835 TTTTT
1 TTTTT
1079840 TCTTCAAGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
5 25 0.61
6 10 0.24
7 6 0.15
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (6 bp):
TTTTTC
Found at i:1079808 original size:1 final size:1
Alignment explanation
Indices: 1079799--1079840 Score: 66
Period size: 1 Copynumber: 42.0 Consensus size: 1
1079789 CTTTTTTCTC
* *
1079799 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1079841 CTTCAAGCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:1079840 original size:7 final size:7
Alignment explanation
Indices: 1079782--1079843 Score: 78
Period size: 6 Copynumber: 9.3 Consensus size: 7
1079772 GACCCCTCCT
1079782 TTTTCTTC
1 TTTT-TTC
1079790 TTTTTTC
1 TTTTTTC
*
1079797 TCTTTTC
1 TTTTTTC
1079804 TTTTTT-
1 TTTTTTC
1079810 TTTTTT-
1 TTTTTTC
1079816 TTTTTT-
1 TTTTTTC
1079822 TTTTTT-
1 TTTTTTC
1079828 TTTTTTC
1 TTTTTTC
1079835 TTTTTTC
1 TTTTTTC
1079842 TT
1 TT
1079844 CAAGCATAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
6 24 0.47
7 23 0.45
8 4 0.08
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:1091119 original size:13 final size:13
Alignment explanation
Indices: 1091082--1091121 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
1091072 TCGATATTGA
1091082 AAAATAAATA-TT
1 AAAATAAATATTT
*
1091094 AAAATAATTTATTT
1 AAAATAA-ATATTT
1091108 AAAATAAATATTT
1 AAAATAAATATTT
1091121 A
1 A
1091122 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:1092490 original size:3 final size:3
Alignment explanation
Indices: 1092482--1092574 Score: 116
Period size: 3 Copynumber: 31.3 Consensus size: 3
1092472 ATATATATAT
* * * *
1092482 ATA ATA ATA ATA ATA ATA AT- ATA TTT ATA ATA ATA ATA ATA ATA TTT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
1092529 ATA GTA ATA ATA ATA ATA ATA ATA ATT ATA GTA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1092575 ATAAATCAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
2 2 0.03
3 73 0.97
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:1096771 original size:60 final size:60
Alignment explanation
Indices: 1096703--1096829 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
1096693 ATATATCCAT
* * * **
1096703 AAACTATGACCCTCATT-TCAAATTAGTCTTTGAACTTTTAAACATTTTAATTTTATCCCA
1 AAACTATGAACCTCATTCT-AAATTAGTCATTAAACTTTTAAACATTCCAATTTTATCCCA
* * *
1096763 AAACTATGAATCTCATTCTAAATTAGTCATTAAACTTTTGAACATTCCAATTTTATCCCC
1 AAACTATGAACCTCATTCTAAATTAGTCATTAAACTTTTAAACATTCCAATTTTATCCCA
1096823 AAACTAT
1 AAACTAT
1096830 TAATATCAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 57 0.98
61 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.39
Consensus pattern (60 bp):
AAACTATGAACCTCATTCTAAATTAGTCATTAAACTTTTAAACATTCCAATTTTATCCCA
Found at i:1097518 original size:28 final size:29
Alignment explanation
Indices: 1097474--1097536 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
1097464 GCAAAGTTAG
*
1097474 AAAATTTATTTTGAGGTATC-AATTT-TA
1 AAAATTTATTTTAAGGTATCAAATTTATA
* *
1097501 AAGAATTTTTTTTAAGGTGTCAAATTTATA
1 AA-AATTTATTTTAAGGTATCAAATTTATA
1097531 AAAATT
1 AAAATT
1097537 ACTTTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 2 0.07
28 15 0.50
29 9 0.30
30 4 0.13
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (29 bp):
AAAATTTATTTTAAGGTATCAAATTTATA
Found at i:1097925 original size:50 final size:49
Alignment explanation
Indices: 1097754--1097989 Score: 210
Period size: 51 Copynumber: 4.7 Consensus size: 49
1097744 TAACTCACTT
* * * *
1097754 TAAAAAAATGTAATATTTAACACATACT-TACACCGGTGTAAGTGAATAAAAA
1 TAAAAAAGTGTAACACTTAACACATACTATACA---ATGTAAGTGAAT-AAAA
* * ** *
1097806 TAAACAAGTGTAGCACTTAACACATACTTATACCGGTGTAAGTGAATTAAA
1 TAAAAAAGTGTAACACTTAACACATAC-TATA-CAATGTAAGTGAATAAAA
* *
1097857 CAAAAAAGTGTATA-ACTTAACACATACTATATCAATATAAGTGAATAAAA
1 TAAAAAAGTGTA-ACACTTAACACATACTATA-CAATGTAAGTGAATAAAA
*
1097907 TAAAAAAGTGTAACACTTAACACATACT-TACAATGGTGTAAGTAAATAAAA
1 TAAAAAAGTGTAACACTTAACACATACTATACAA---TGTAAGTGAATAAAA
* * *
1097958 TAAAAAAATGTAGCACTTAACACACACT-TACA
1 TAAAAAAGTGTAACACTTAACACATACTATACA
1097990 CTGGTATATG
Statistics
Matches: 155, Mismatches: 21, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
48 3 0.02
49 3 0.02
50 43 0.28
51 68 0.44
52 34 0.22
53 1 0.01
54 2 0.01
55 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (49 bp):
TAAAAAAGTGTAACACTTAACACATACTATACAATGTAAGTGAATAAAA
Found at i:1097932 original size:101 final size:102
Alignment explanation
Indices: 1097792--1097981 Score: 274
Period size: 101 Copynumber: 1.9 Consensus size: 102
1097782 TACACCGGTG
* * * * * *
1097792 TAAGTGAATAAAAATAAACAAGTGTAGCACTTAACACATACTTATACCGGTGTAAGTGAATTAAA
1 TAAGTGAATAAAAATAAAAAAGTGTAACACTTAACACATACTTACAACGGTGTAAGTAAATAAAA
* *
1097857 CAAAAAAGTGTATAACTTAACACATACTATATCAATA
66 CAAAAAAATGTAGAACTTAACACATACTATATCAATA
*
1097894 TAAGTGAAT-AAAATAAAAAAGTGTAACACTTAACACATACTTACAATGGTGTAAGTAAATAAAA
1 TAAGTGAATAAAAATAAAAAAGTGTAACACTTAACACATACTTACAACGGTGTAAGTAAATAAAA
* *
1097958 TAAAAAAATGTAGCACTTAACACA
66 CAAAAAAATGTAGAACTTAACACA
1097982 CACTTACACT
Statistics
Matches: 77, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
101 68 0.88
102 9 0.12
ACGTcount: A:0.51, C:0.13, G:0.12, T:0.25
Consensus pattern (102 bp):
TAAGTGAATAAAAATAAAAAAGTGTAACACTTAACACATACTTACAACGGTGTAAGTAAATAAAA
CAAAAAAATGTAGAACTTAACACATACTATATCAATA
Found at i:1098734 original size:57 final size:57
Alignment explanation
Indices: 1098646--1098757 Score: 215
Period size: 57 Copynumber: 2.0 Consensus size: 57
1098636 ATGAGCATCA
1098646 TTCAAAAAGCATCCCTACATCTAATGGTGGAAAAATAATACACCATATCGATATCTT
1 TTCAAAAAGCATCCCTACATCTAATGGTGGAAAAATAATACACCATATCGATATCTT
*
1098703 TTCAAAAAGCATCCCTACATCTAATGGTGGAAAAATAGTACACCATATCGATATC
1 TTCAAAAAGCATCCCTACATCTAATGGTGGAAAAATAATACACCATATCGATATC
1098758 AAAGATGTAG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (57 bp):
TTCAAAAAGCATCCCTACATCTAATGGTGGAAAAATAATACACCATATCGATATCTT
Found at i:1098828 original size:37 final size:37
Alignment explanation
Indices: 1098780--1098856 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
1098770 AACCATTACA
*
1098780 CAAGGTAAGACTCATACACACAAACAACCATTCTCAT
1 CAAGATAAGACTCATACACACAAACAACCATTCTCAT
1098817 CAAGATAAGACTCATACACACAAACAACCATTCTCAT
1 CAAGATAAGACTCATACACACAAACAACCATTCTCAT
1098854 CAA
1 CAA
1098857 ATAGCTGGTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.45, C:0.30, G:0.06, T:0.18
Consensus pattern (37 bp):
CAAGATAAGACTCATACACACAAACAACCATTCTCAT
Found at i:1101545 original size:18 final size:18
Alignment explanation
Indices: 1101524--1101705 Score: 67
Period size: 18 Copynumber: 10.1 Consensus size: 18
1101514 TGAATACAAT
1101524 AAATAAAAAATAAAAATA
1 AAATAAAAAATAAAAATA
*
1101542 AAATGAAAAAA-AAGAATA
1 AAAT-AAAAAATAAAAATA
* *
1101560 ATAAT-AATAATAATAATA
1 A-AATAAAAAATAAAAATA
* * * *
1101578 ATAATAATATATACATATA
1 A-AATAAAAAATAAAAATA
*
1101597 AACA-AATAAATAAAAATA
1 AA-ATAAAAAATAAAAATA
* * *
1101615 AGA-AGAAAATACAAAT-
1 AAATAAAAAATAAAAATA
*
1101631 AGATAAATAAATAAAACA-A
1 AAATAAA-AAATAAAA-ATA
*
1101650 ATATAAAGAAGAT-AAAA-A
1 AAATAAA-AA-ATAAAAATA
* *
1101668 AAAT-AAAGATGAAGAATA
1 AAATAAAAAAT-AAAAATA
*
1101686 AAAAAATAAAATAAAAATA
1 AAATAA-AAAATAAAAATA
1101705 A
1 A
1101706 GTAAAATAGA
Statistics
Matches: 123, Mismatches: 26, Indels: 29
0.69 0.15 0.16
Matches are distributed among these distances:
15 2 0.02
16 4 0.03
17 22 0.18
18 51 0.41
19 38 0.31
20 6 0.05
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.19
Consensus pattern (18 bp):
AAATAAAAAATAAAAATA
Found at i:1101551 original size:7 final size:6
Alignment explanation
Indices: 1101502--1101705 Score: 60
Period size: 6 Copynumber: 32.5 Consensus size: 6
1101492 ATAAAAAGGG
* *
1101502 TAAAGA TAAAAA TGAATACAA TAAATA -AAAAA TAAAAA T-AAAA TGAAAAA
1 TAAAAA TAAAAA T-AA-A-AA TAAAAA TAAAAA TAAAAA TAAAAA T-AAAAA
* * * * * * *
1101552 -AAAGAA TAATAA TAATAA TAATAA TAATAA TAATATA TACATA TAAACAA
1 TAAA-AA TAAAAA TAAAAA TAAAAA TAAAAA TAA-AAA TAAAAA TAAA-AA
* * * *
1101602 -ATAAA TAAAAA TAAGAA -GAAAA TACAAA TAGATAAA TAAATAA -AACAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA-A-AAA TAAA-AA TAA-AAA
* * * * * *
1101651 TATAAA GAAGATAA AAAAAA TAAAGA TGAAGAA TAAAAA AATAAAA TAAAAA
1 TAAAAA TAA-A-AA TAAAAA TAAAAA T-AAAAA TAAAAA TA-AAAA TAAAAA
1101703 TAA
1 TAA
1101706 GTAAAATAGA
Statistics
Matches: 149, Mismatches: 28, Indels: 42
0.68 0.13 0.19
Matches are distributed among these distances:
5 17 0.11
6 88 0.59
7 29 0.19
8 12 0.08
9 3 0.02
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:1101562 original size:3 final size:3
Alignment explanation
Indices: 1101556--1101586 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1101546 GAAAAAAAAG
1101556 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1101587 TATACATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1101667 original size:21 final size:21
Alignment explanation
Indices: 1101614--1101689 Score: 54
Period size: 21 Copynumber: 3.6 Consensus size: 21
1101604 AAATAAAAAT
*
1101614 AAGAAGA-AAATACAAATAGATA
1 AAGAAGATAAAAACAAAT--ATA
*
1101636 AATAA-AT-AAAACAAATATA
1 AAGAAGATAAAAACAAATATA
1101655 AAGAAGATAAAAA-AAATA-A
1 AAGAAGATAAAAACAAATATA
1101674 AGATGAAGAATAAAAA
1 A-A-GAAG-ATAAAAA
1101690 AATAAAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
19 9 0.20
20 8 0.18
21 17 0.38
22 11 0.24
ACGTcount: A:0.72, C:0.03, G:0.11, T:0.14
Consensus pattern (21 bp):
AAGAAGATAAAAACAAATATA
Found at i:1101690 original size:21 final size:19
Alignment explanation
Indices: 1101640--1101696 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 19
1101630 TAGATAAATA
1101640 AATAAAACAAATATAAAGAAG
1 AATAAAA-AAATA-AAAGAAG
1101661 -ATAAAAAAAATAAAGATGAAG
1 AAT-AAAAAAATAAA-A-GAAG
1101682 AATAAAAAAATAAAA
1 AATAAAAAAATAAAA
1101697 TAAAAATAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
19 2 0.06
20 9 0.28
21 19 0.59
22 2 0.06
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (19 bp):
AATAAAAAAATAAAAGAAG
Found at i:1101723 original size:3 final size:3
Alignment explanation
Indices: 1101690--1101747 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
1101680 AGAATAAAAA
* *
1101690 AAT AA- AAT AAA AAT AAGT AA- AAT -AG AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1101733 AAT ACT AAT AAT AAT
1 AAT AAT AAT AAT AAT
1101748 GAAAACAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 5 0.11
3 37 0.82
4 3 0.07
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:1101979 original size:8 final size:8
Alignment explanation
Indices: 1101956--1102029 Score: 55
Period size: 8 Copynumber: 9.4 Consensus size: 8
1101946 AATAGTCGGG
1101956 AAATATAA
1 AAATATAA
*
1101964 TAATA-AA
1 AAATATAA
*
1101971 AGATA-AA
1 AAATATAA
1101978 AAATATAA
1 AAATATAA
1101986 AAATATAA
1 AAATATAA
* *
1101994 AAATAGAT
1 AAATATAA
*
1102002 ATATATATA
1 AAATATA-A
*
1102011 TAATA-AA
1 AAATATAA
1102018 CAAATATAA
1 -AAATATAA
1102027 AAA
1 AAA
1102030 ATATGATAAT
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
7 12 0.24
8 33 0.66
9 5 0.10
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (8 bp):
AAATATAA
Found at i:1101981 original size:22 final size:23
Alignment explanation
Indices: 1101956--1102040 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 23
1101946 AATAGTCGGG
*
1101956 AAATATAATAATA-AAAGATAAA
1 AAATATAATAATACAAAAATAAA
* *
1101978 AAATATAAAAATATAAAAATAGATA
1 AAATATAATAATACAAAAATA-A-A
*
1102003 TATATATATAATAA-ACAAATATAAA
1 -A-A-ATATAATAATACAAAAATAAA
*
1102028 AAATATGATAATA
1 AAATATAATAATA
1102041 ATTAATAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
22 20 0.40
23 8 0.16
24 2 0.04
25 2 0.04
26 2 0.04
27 8 0.16
28 8 0.16
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (23 bp):
AAATATAATAATACAAAAATAAA
Found at i:1102818 original size:14 final size:13
Alignment explanation
Indices: 1102801--1102867 Score: 57
Period size: 14 Copynumber: 5.1 Consensus size: 13
1102791 AAATGAATTG
1102801 AAAAAAAT--AAA
1 AAAAAAATAAAAA
*
1102812 TAAAAAATAAAACA
1 AAAAAAATAAAA-A
* * *
1102826 AAATAAGTCAAAGA
1 AAAAAAAT-AAAAA
1102840 AAAAAAATAAAAA
1 AAAAAAATAAAAA
1102853 AAAAGAAATAAAAA
1 AAAA-AAATAAAAA
1102867 A
1 A
1102868 TATTCAAAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
11 7 0.16
13 10 0.23
14 23 0.53
15 3 0.07
ACGTcount: A:0.82, C:0.03, G:0.04, T:0.10
Consensus pattern (13 bp):
AAAAAAATAAAAA
Done.