Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 1 of 126
Found at i:375 original size:11 final size:10
Alignment explanation
Indices: 358--431 Score: 53
Period size: 11 Copynumber: 7.0 Consensus size: 10
348 TAAAAAATTC
358 TAAAATAAAA
1 TAAAATAAAA
368 TGAAAATAAAA
1 T-AAAATAAAA
*
379 -ATAGATAAAA
1 TA-AAATAAAA
*
389 TTAAACTAAAA
1 -TAAAATAAAA
400 TAAAATCAAAA
1 TAAAAT-AAAA
411 TGGAAAATAAAA
1 T--AAAATAAAA
*
423 -AAAAGAAAA
1 TAAAATAAAA
432 AGAAATTACC
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
9 9 0.17
10 13 0.25
11 20 0.38
12 5 0.10
13 5 0.10
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.18
Consensus pattern (10 bp):
TAAAATAAAA
Found at i:423 original size:6 final size:5
Alignment explanation
Indices: 358--431 Score: 53
Period size: 5 Copynumber: 14.0 Consensus size: 5
348 TAAAAAATTC
* *
358 TAAAA TAAAA TGAAAA TAAAA -ATAGA TAAAA TTAAAC TAAAA TAAAA
1 TAAAA TAAAA T-AAAA TAAAA TA-AAA TAAAA -TAAAA TAAAA TAAAA
*
405 TCAAAA TGGAAAA TAAAA -AAAA GAAAA
1 T-AAAA T--AAAA TAAAA TAAAA TAAAA
432 AGAAATTACC
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
4 5 0.09
5 32 0.56
6 15 0.26
7 5 0.09
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.18
Consensus pattern (5 bp):
TAAAA
Found at i:1761 original size:43 final size:43
Alignment explanation
Indices: 1573--1792 Score: 217
Period size: 43 Copynumber: 5.1 Consensus size: 43
1563 AAGGTTTAAC
* * * * * * *
1573 AAACAAATTTAAATTAAGAAATAGCCTCTTCTATTTAGAGGCT
1 AAACAACTTTAAAATAGGAAATGGGCTCCTCTATTCAGAGGCT
* * * *
1616 AAACAACTTTAAAAT-GACAAATGAGCTCATCTATTCAGAGACT
1 AAACAACTTTAAAATAG-GAAATGGGCTCCTCTATTCAGAGGCT
* * ***
1659 AAACAACTTTAAAATAGGGAATGGACTCCTCTATTCAGAAATT
1 AAACAACTTTAAAATAGGAAATGGGCTCCTCTATTCAGAGGCT
* *
1702 AAATAACTTTAAAATAGGGAATGGGCTCCTCTATTCAGAGGCT
1 AAACAACTTTAAAATAGGAAATGGGCTCCTCTATTCAGAGGCT
* * * *
1745 AAATAACTTTAAAATAGGAAATAGGCTCTTTCTATTCAAAGGCT
1 AAACAACTTTAAAATAGGAAATGGGCTC-CTCTATTCAGAGGCT
1789 AAAC
1 AAAC
1793 TTTAAAATAA
Statistics
Matches: 147, Mismatches: 27, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
43 130 0.88
44 17 0.12
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (43 bp):
AAACAACTTTAAAATAGGAAATGGGCTCCTCTATTCAGAGGCT
Found at i:3869 original size:162 final size:160
Alignment explanation
Indices: 3592--3913 Score: 502
Period size: 162 Copynumber: 2.0 Consensus size: 160
3582 ACACAAATAA
* *
3592 TATCAACTCAGAAAGGGTATAAGTGCCATCATTTGCTTACCAAAAAATTTTGTGTCTTTTGATAT
1 TATCAACTCAGAAAGGGTATAAGTGCCATCATTTGATTACCAAAAAATTTTGTGTCTTTAGATAT
* *
3657 CACTGTTAAAGAAAGTAAACTATTTTTTACTGAACCTTATCTTCAAGAGGATACTTCATTC-GTG
66 CACTGTTAAAGAAAGTAAACTATTTTTTACTGAACCTTATCTTCAAGAGGAGACTGCATTCTG-G
*
3721 GAAGATAAGGATAAAGATTTCTTTTTGCTTG
130 GAAGATAAAGATAAAGATTTCTTTTTGCTTG
*
3752 TATCAACTTAGAAAGGGTATAAGTGCCATCATTTGATTACCAAAAAATTATATGTGTCTTTAGAT
1 TATCAACTCAGAAAGGGTATAAGTGCCATCATTTGATTACCAAAAAATT-T-TGTGTCTTTAGAT
* * * * *
3817 GTTACTGTTGAAGAAAGTAAACTATTTTTTACTGAATCTTATCTTTAAGAGGAGACTGCATTCTG
64 ATCACTGTTAAAGAAAGTAAACTATTTTTTACTGAACCTTATCTTCAAGAGGAGACTGCATTCTG
*
3882 GGAAGATAAAGATAAAGATTTCTTTTTTCTTG
129 GGAAGATAAAGATAAAGATTTCTTTTTGCTTG
3914 GTTTGCCCTC
Statistics
Matches: 147, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
160 47 0.32
161 1 0.01
162 98 0.67
163 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (160 bp):
TATCAACTCAGAAAGGGTATAAGTGCCATCATTTGATTACCAAAAAATTTTGTGTCTTTAGATAT
CACTGTTAAAGAAAGTAAACTATTTTTTACTGAACCTTATCTTCAAGAGGAGACTGCATTCTGGG
AAGATAAAGATAAAGATTTCTTTTTGCTTG
Found at i:11772 original size:33 final size:33
Alignment explanation
Indices: 11727--11799 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
11717 CTTCTCAAAC
* *
11727 TCTAGTACTTTAAACTTTTGAGGTATCACCATA
1 TCTAGTAATTTAAACTTTTGAGGTATCACCACA
* *
11760 TCTAGTAATTTAAACTTTTGGGGTATCACTACA
1 TCTAGTAATTTAAACTTTTGAGGTATCACCACA
11793 TCTAGTA
1 TCTAGTA
11800 CCAGATAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (33 bp):
TCTAGTAATTTAAACTTTTGAGGTATCACCACA
Found at i:16031 original size:6 final size:5
Alignment explanation
Indices: 15999--16103 Score: 52
Period size: 5 Copynumber: 19.4 Consensus size: 5
15989 AAAAATAGTG
* ** *
15999 AATAA AATACTA ATTAA AGATAA AATAA TAAT-A AGCAA AATAG AATGAA
1 AATAA AATA--A AATAA A-ATAA AATAA -AATAA AATAA AATAA AAT-AA
* *
16048 AATCTAA AATAA AATGAA AAT-A AATAA AATCA AATAA AAGTAA AATTA
1 AAT--AA AATAA AAT-AA AATAA AATAA AATAA AATAA AA-TAA AATAA
16096 AATCAA AA
1 AAT-AA AA
16104 CGTAAAATAG
Statistics
Matches: 76, Mismatches: 13, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
4 5 0.07
5 38 0.50
6 24 0.32
7 9 0.12
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.22
Consensus pattern (5 bp):
AATAA
Found at i:16082 original size:10 final size:10
Alignment explanation
Indices: 16052--16103 Score: 52
Period size: 11 Copynumber: 5.0 Consensus size: 10
16042 AATGAAAATC
16052 TAAAATAAAA
1 TAAAATAAAA
16062 TGAAAAT-AAA
1 T-AAAATAAAA
*
16072 TAAAATCAAA
1 TAAAATAAAA
16082 TAAAAGTAAAA
1 TAAAA-TAAAA
*
16093 TTAAATCAAAA
1 TAAAAT-AAAA
16104 CGTAAAATAG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
9 5 0.14
10 14 0.39
11 17 0.47
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (10 bp):
TAAAATAAAA
Found at i:16945 original size:3 final size:3
Alignment explanation
Indices: 16937--16970 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
16927 AGACACAATA
16937 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
16971 TGTTTGGCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17890 original size:22 final size:22
Alignment explanation
Indices: 17862--17904 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
17852 TAATCTCAAC
*
17862 AAATATACATATATTTATAATA
1 AAATATACATATAATTATAATA
17884 AAATATACATATAATTATAAT
1 AAATATACATATAATTATAAT
17905 TTCATGTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATACATATAATTATAATA
Found at i:18911 original size:16 final size:16
Alignment explanation
Indices: 18881--18913 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18871 AGGAAGACAA
18881 AAAGCAAGAAGAGAAC
1 AAAGCAAGAAGAGAAC
18897 AAAG-AAGAAGAAGAAC
1 AAAGCAAGAAG-AGAAC
18913 A
1 A
18914 TAGATAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.67, C:0.09, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAGCAAGAAGAGAAC
Found at i:21474 original size:35 final size:34
Alignment explanation
Indices: 21410--21476 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
21400 TTTATTGCTC
* * *
21410 ATATCTACTTTATTTTTTTTGTATTTATTTGTTT
1 ATATCTACTTGATTTTTTATGTATATATTTGTTT
*
21444 ATATTTACTTGATTATTTTATGTATATATTTGT
1 ATATCTACTTGATT-TTTTATGTATATATTTGT
21477 CATACATTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 12 0.43
35 16 0.57
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.66
Consensus pattern (34 bp):
ATATCTACTTGATTTTTTATGTATATATTTGTTT
Found at i:28509 original size:21 final size:20
Alignment explanation
Indices: 28485--28531 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
28475 CCTAATCCTA
* *
28485 ATTTAAAGATCGTTTATATTT
1 ATTTAAA-ATCGTTTATAATC
*
28506 ATTTAAATTCGTTTATAATC
1 ATTTAAAATCGTTTATAATC
28526 ATTTAA
1 ATTTAA
28532 GATTTATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.51
Consensus pattern (20 bp):
ATTTAAAATCGTTTATAATC
Found at i:34631 original size:5 final size:5
Alignment explanation
Indices: 34621--34645 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
34611 CAGTTGCAGG
34621 GACCA GACCA GACCA GACCA GACCA
1 GACCA GACCA GACCA GACCA GACCA
34646 AGACAGAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.20, T:0.00
Consensus pattern (5 bp):
GACCA
Found at i:35508 original size:28 final size:29
Alignment explanation
Indices: 35460--35518 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
35450 TTATTTTGTA
35460 TTATTTATATTATTTTTTTTTTTTCTTTC
1 TTATTTATATTATTTTTTTTTTTTCTTTC
*
35489 TTATTT-TATT-TTTTTGTTTTTTTGTTTC
1 TTATTTATATTATTTTT-TTTTTTTCTTTC
35517 TT
1 TT
35519 TCTTTCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 5 0.18
28 17 0.61
29 6 0.21
ACGTcount: A:0.10, C:0.05, G:0.03, T:0.81
Consensus pattern (29 bp):
TTATTTATATTATTTTTTTTTTTTCTTTC
Found at i:36710 original size:21 final size:22
Alignment explanation
Indices: 36666--36710 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
36656 GTAAAAATTT
*
36666 AATTAAATAAAAAATAACACAA
1 AATTAAATAAAAAATAACAAAA
*
36688 AATT-AATAAAAAATAAGAAAA
1 AATTAAATAAAAAATAACAAAA
36709 AA
1 AA
36711 AAATTTTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (22 bp):
AATTAAATAAAAAATAACAAAA
Found at i:48959 original size:48 final size:48
Alignment explanation
Indices: 48854--49233 Score: 406
Period size: 48 Copynumber: 7.8 Consensus size: 48
48844 AACATATAAG
* * * * *
48854 ATTTTTAAAGTTGTTGAACCTCTGCTGAAAGGA-TTTTTTCAAGATAA
1 ATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGA
* * *
48901 ATTTTTAAAGTTGTTGAGCCTCTATTTAGAGGAGCCTTTTCAAGATGA
1 ATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGA
* * *
48949 ATTTTTAAAGTTGTTTAGTCTCTACTGAAAGGAGCTTTTTCAAGAT-A
1 ATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGA
* *
48996 AATTTTAAAGTTGTTGAGCCTCTATTGAGAGGAGCCTTTTTCAAGATGA
1 ATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAG-CTTTTTCAAGATGA
* *
49045 GATTCTTTTAAAGTTATTGAGCCTCTACTGAGATGAGCTTTTTTCAAGAT-A
1 -A-T-TTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGC-TTTTTCAAGATGA
* * * * * * *
49096 AATTTTAAAATTGTTGAACCTCTATTTAGAGGAGTTTTTTCAAGATAA
1 ATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGA
* * * * *
49144 GATTCTTAAAGTTGTTGAGCCTCTACTTAGAAGAACTTTTTCAAAATGA
1 -ATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGA
* * *
49193 ATTTTTAAAGTTGTTGAGCCTCTTCTTAGATGAGCCTTTTT
1 ATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAG-CTTTTT
49234 TACATTTTCG
Statistics
Matches: 278, Mismatches: 45, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
47 69 0.25
48 120 0.43
49 45 0.16
50 2 0.01
51 2 0.01
52 40 0.14
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (48 bp):
ATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGA
Found at i:49300 original size:44 final size:44
Alignment explanation
Indices: 49151--49414 Score: 192
Period size: 44 Copynumber: 5.9 Consensus size: 44
49141 TAAGATTCTT
* **
49151 AAAGTTGTTGAGCCTCTACTTAGAAGA-ACTTTTTCAAAATGAATTTTT
1 AAAGTTGTTGAGCCTCTACTTAGAAGAGCCTTTTT--AAAT---TTTCA
* * * *
49199 AAAGTTGTTGAGCCTCTTCTTAGATGAGCCTTTTTTACATTTTCG
1 AAAGTTGTTGAGCCTCTACTTAGAAGAGCC-TTTTTAAATTTTCA
** * * *
49244 AAAGTCATTGAGCCTCTACTTAAAAGAGCCTCTTTAAATTTTTA
1 AAAGTTGTTGAGCCTCTACTTAGAAGAGCCTTTTTAAATTTTCA
* * *
49288 AAAGTTGTTGAGCCTTTACTTAGAGGAGCCTATTTAAATTTTCA
1 AAAGTTGTTGAGCCTCTACTTAGAAGAGCCTTTTTAAATTTTCA
* * * * * * *
49332 AAATTTGTTAAGCATCTGCTCAGAGGAG-CTTTGTAAATTTTCA
1 AAAGTTGTTGAGCCTCTACTTAGAAGAGCCTTTTTAAATTTTCA
* * * *
49375 AAAATATCGTTGAACCTCTATTTA-AAGGATCCTTTTTAAA
1 AAAGT-T-GTTGAGCCTCTACTTAGAA-GAGCCTTTTTAAA
49415 AAAAAATTTT
Statistics
Matches: 170, Mismatches: 40, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
43 17 0.10
44 71 0.42
45 40 0.24
46 8 0.05
48 28 0.16
49 1 0.01
50 5 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (44 bp):
AAAGTTGTTGAGCCTCTACTTAGAAGAGCCTTTTTAAATTTTCA
Found at i:49539 original size:3 final size:3
Alignment explanation
Indices: 49531--49581 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
49521 CACCATTTTG
49531 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
49579 TAT
1 TAT
49582 ATTTTTCTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:49631 original size:13 final size:12
Alignment explanation
Indices: 49583--49631 Score: 62
Period size: 12 Copynumber: 3.9 Consensus size: 12
49573 TATTATTATA
49583 TTTTTCTTTCTT
1 TTTTTCTTTCTT
*
49595 TCTTTCTTTCTTT
1 TTTTTCTTTC-TT
*
49608 TTTTTCCTTCTT
1 TTTTTCTTTCTT
49620 TTTTTCTGTTCT
1 TTTTTCT-TTCT
49632 GATCAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 17 0.55
13 14 0.45
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:49783 original size:23 final size:23
Alignment explanation
Indices: 49746--49798 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
49736 ATTTTGGGTT
* *
49746 AAAAATATGATATTTGAATCTCA
1 AAAAATTTGAGATTTGAATCTCA
49769 AAAAATTTGAGATTTGAATCTCA
1 AAAAATTTGAGATTTGAATCTCA
49792 AAAAATT
1 AAAAATT
49799 CTATAAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.34
Consensus pattern (23 bp):
AAAAATTTGAGATTTGAATCTCA
Found at i:50775 original size:21 final size:22
Alignment explanation
Indices: 50731--50775 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
50721 GTAAAAATTT
* * *
50731 AATTAAATACAAAATAATACAA
1 AATTAAATAAAAAATAAAAAAA
50753 AATT-AATAAAAAATAAAAAAA
1 AATTAAATAAAAAATAAAAAAA
50774 AA
1 AA
50776 AATTTTATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (22 bp):
AATTAAATAAAAAATAAAAAAA
Found at i:53020 original size:20 final size:20
Alignment explanation
Indices: 52995--53042 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
52985 CGACCCGACA
52995 TTATATAAAT-TA-ATTATTAT
1 TTATATAAATATATA-TA-TAT
*
53015 TTATATATATATATATATAT
1 TTATATAAATATATATATAT
53035 TTATATAA
1 TTATATAA
53043 TGATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 19 0.79
21 4 0.17
22 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATATAAATATATATATAT
Found at i:53039 original size:14 final size:14
Alignment explanation
Indices: 52995--53066 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 14
52985 CGACCCGACA
* *
52995 TTATATAAAT-TAA
1 TTATATATATATAT
*
53008 TTAT-TATTTATAT
1 TTATATATATATAT
*
53021 ATATATATATATAT
1 TTATATATATATAT
53035 TTATATA-ATGATATT
1 TTATATATAT-ATA-T
* *
53050 TTAAATATTTATAT
1 TTATATATATATAT
53064 TTA
1 TTA
53067 AAAAATAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
12 3 0.07
13 11 0.24
14 21 0.46
15 10 0.22
16 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (14 bp):
TTATATATATATAT
Found at i:53062 original size:29 final size:29
Alignment explanation
Indices: 53025--53081 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
53015 TTATATATAT
* * *
53025 ATATATATATTTATATAATGATATTTTAA
1 ATATATATATTTAAAAAATAATATTTTAA
*
53054 ATATTTATATTTAAAAAATAATATTTTA
1 ATATATATATTTAAAAAATAATATTTTA
53082 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (29 bp):
ATATATATATTTAAAAAATAATATTTTAA
Found at i:53081 original size:21 final size:22
Alignment explanation
Indices: 53053--53104 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
53043 TGATATTTTA
53053 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
53073 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
53095 AATATTTTAT
1 AATATTTTAT
53105 TAATTTCGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:53215 original size:38 final size:33
Alignment explanation
Indices: 53140--53222 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 33
53130 TTTATATAGT
53140 GTCGGGTCGGGTTGGGTTCGAGTATTAAAAAAA
1 GTCGGGTCGGGTTGGGTTCGAGTATTAAAAAAA
* *
53173 -TCGGGTAGGGTTGGGTTCGGGTATGCTAAAGCATAAA
1 GTCGGGTCGGGTTGGGTTCGAGTAT--TAAA--A-AAA
53210 GTCGGGTCGGGTT
1 GTCGGGTCGGGTT
53223 CGGGCCGAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
32 22 0.54
34 4 0.10
36 1 0.02
37 3 0.07
38 11 0.27
ACGTcount: A:0.22, C:0.11, G:0.40, T:0.28
Consensus pattern (33 bp):
GTCGGGTCGGGTTGGGTTCGAGTATTAAAAAAA
Found at i:53573 original size:2 final size:2
Alignment explanation
Indices: 53560--53607 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
53550 AAAATTAGTG
* * * *
53560 TA TA TA TG TA TA TA TA CA AA TA TA TA TA TA TA TA CA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53601 TA TA TA T
1 TA TA TA T
53608 TCCTTTTGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:55953 original size:2 final size:2
Alignment explanation
Indices: 55946--55972 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55936 TTGAATTTAG
55946 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
55973 GTTTCTGTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56134 original size:22 final size:21
Alignment explanation
Indices: 56106--56152 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
56096 TTCAATTTTA
56106 ATTAAATTAACTAATCAAATTG
1 ATTAAATTAACTAAT-AAATTG
* *
56128 ATTAAATTAATTAATTAATTG
1 ATTAAATTAACTAATAAATTG
56149 ATTA
1 ATTA
56153 TTAAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (21 bp):
ATTAAATTAACTAATAAATTG
Found at i:56527 original size:24 final size:25
Alignment explanation
Indices: 56474--56528 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
56464 ATAAAAATAA
* *
56474 AATAAAATGATTTAATTAATTCAATT
1 AATAAAATAATTTAATT-ATTAAATT
56500 --TAAAATAATTTAATT-TTAAATT
1 AATAAAATAATTTAATTATTAAATT
56522 AATAAAA
1 AATAAAA
56529 CCAAACTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 6 0.24
24 19 0.76
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
AATAAAATAATTTAATTATTAAATT
Found at i:73376 original size:281 final size:281
Alignment explanation
Indices: 72873--73439 Score: 1082
Period size: 281 Copynumber: 2.0 Consensus size: 281
72863 ACACAAAAAG
* *
72873 AAATGATGATGATTATCCAAAAAGAGTATAAACAACATCCATAATTGATCCATGACAAGATGGAA
1 AAATGATGATGATTATCCAAAAAGAGCATAAACAACATCCATAATTGATCCATGACAAGATGAAA
*
72938 CAAGATGAAACTATAAAAAAGATGAAACCCTTTCATTCATCATTAACTAGAAGTAATTCATACAA
66 CAAGATGAAACTATAAAAAAGATGAAACCCTTTCATTCATCATTAACTAAAAGTAATTCATACAA
*
73003 CATCCAACAATGTACCTTCATACACATAAATAAATTGATCATGAATATCCAAAAATAACAGAAAC
131 CATCCAACAATGTACCTTCATACACATAAATAAATTGATCATGAAAATCCAAAAATAACAGAAAC
73068 AACATTCATCATATTCATAAACAAAGAGCATAAAAAAGTTACAAAAAGTTATCATGTTAACAAAC
196 AACATTCATCATATTCATAAACAAAGAGCATAAAAAAGTTACAAAAAGTTATCATGTTAACAAAC
73133 AACATTCATATCAGTTCCTAA
261 AACATTCATATCAGTTCCTAA
73154 AAATGATGATGATTATCCAAAAAGAGCATAAACAACATCCATAATTGATCCATAGACAAGATGAA
1 AAATGATGATGATTATCCAAAAAGAGCATAAACAACATCCATAATTGATCCAT-GACAAGATGAA
73219 ACAAGATGAAACTATAAAAAAGATGAAACCCTTTCATTCATCATTAACTAAAAGTAATTCATACA
65 ACAAGATGAAACTATAAAAAAGATGAAACCCTTTCATTCATCATTAACTAAAAGTAATTCATACA
73284 ACATCCAACAATGTACCTTCATACACATAAAT-AATTGATCATGAAAATCCAAAAATAACAGAAA
130 ACATCCAACAATGTACCTTCATACACATAAATAAATTGATCATGAAAATCCAAAAATAACAGAAA
73348 CAACATTCATCATATTCATAAACAAAGAGCATAAAAAAGTTACAAAAAGTTATCATGTTAACAAA
195 CAACATTCATCATATTCATAAACAAAGAGCATAAAAAAGTTACAAAAAGTTATCATGTTAACAAA
73413 CAACATTCATATCAGTTCCTAA
260 CAACATTCATATCAGTTCCTAA
73435 AAATG
1 AAATG
73440 TTGCTGGACT
Statistics
Matches: 281, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
281 175 0.62
282 106 0.38
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.25
Consensus pattern (281 bp):
AAATGATGATGATTATCCAAAAAGAGCATAAACAACATCCATAATTGATCCATGACAAGATGAAA
CAAGATGAAACTATAAAAAAGATGAAACCCTTTCATTCATCATTAACTAAAAGTAATTCATACAA
CATCCAACAATGTACCTTCATACACATAAATAAATTGATCATGAAAATCCAAAAATAACAGAAAC
AACATTCATCATATTCATAAACAAAGAGCATAAAAAAGTTACAAAAAGTTATCATGTTAACAAAC
AACATTCATATCAGTTCCTAA
Found at i:80118 original size:23 final size:24
Alignment explanation
Indices: 80066--80118 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
80056 GCTTTTTTTT
* *
80066 TCTCATACCAAAAATGCAACTAGC
1 TCTCATACAAAAAATGCAACTACC
*
80090 TTTCATA-AAAAAATGCAACTACC
1 TCTCATACAAAAAATGCAACTACC
80113 TCTCAT
1 TCTCAT
80119 GGATCATCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (24 bp):
TCTCATACAAAAAATGCAACTACC
Found at i:82528 original size:2 final size:2
Alignment explanation
Indices: 82521--82561 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
82511 TTGTCATCCA
*
82521 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AA 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
82562 TTGTTCTAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:82977 original size:21 final size:20
Alignment explanation
Indices: 82951--82992 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
82941 AGGTTAATGT
82951 GTTCTTTTATCTCTTTTTTTG
1 GTTCTTTT-TCTCTTTTTTTG
* *
82972 GTTCTTTTTTTTTTTTTTTG
1 GTTCTTTTTCTCTTTTTTTG
82992 G
1 G
82993 GGGGGGGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.02, C:0.10, G:0.12, T:0.76
Consensus pattern (20 bp):
GTTCTTTTTCTCTTTTTTTG
Found at i:98626 original size:18 final size:20
Alignment explanation
Indices: 98603--98645 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
98593 AACTTTAAAA
98603 TTAATA-GTGAATAT-TTTT
1 TTAATATGTGAATATCTTTT
*
98621 TTAATATTTGAATATCTTTT
1 TTAATATGTGAATATCTTTT
98641 TTAAT
1 TTAAT
98646 TAAAATAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 7 0.32
20 9 0.41
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (20 bp):
TTAATATGTGAATATCTTTT
Found at i:100658 original size:21 final size:22
Alignment explanation
Indices: 100616--100663 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
100606 TCCGAAATTA
100616 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
100638 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
100659 ATAAA
1 ATAAA
100664 TGTTTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:107704 original size:18 final size:18
Alignment explanation
Indices: 107681--107717 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
107671 ATCTGTGGCA
107681 AACATCACATGCTTATTT
1 AACATCACATGCTTATTT
107699 AACATCACATGCTTATTT
1 AACATCACATGCTTATTT
107717 A
1 A
107718 TGTATGTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (18 bp):
AACATCACATGCTTATTT
Found at i:117899 original size:17 final size:16
Alignment explanation
Indices: 117879--117929 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
117869 TAATTATACT
117879 TTTAAAAATTATATAAA
1 TTTAAAAATTA-ATAAA
* *
117896 TTTAAAAA-AAATAAT
1 TTTAAAAATTAATAAA
117911 TTTAATAAATTAATAAA
1 TTTAA-AAATTAATAAA
117928 TT
1 TT
117930 ATCTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 9 0.32
16 4 0.14
17 15 0.54
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAAAAATTAATAAA
Found at i:125249 original size:17 final size:18
Alignment explanation
Indices: 125224--125264 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
125214 ATCTTTGGAT
125224 AAATATTAATAA-AAAA-A
1 AAATATTAA-AAGAAAAGA
*
125241 AAATTTTAAAAGAAAAGA
1 AAATATTAAAAGAAAAGA
125259 AAATAT
1 AAATAT
125265 ATATAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 12 0.60
18 6 0.30
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATATTAAAAGAAAAGA
Found at i:129444 original size:6 final size:6
Alignment explanation
Indices: 129435--129487 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
129425 ATATATGTAT
* * *
129435 AGAGAA AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAA AGAGAA
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG
129483 AGAGA
1 AGAGA
129488 TTTTCTTAGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (6 bp):
AGAGAG
Found at i:129446 original size:8 final size:8
Alignment explanation
Indices: 129435--129487 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
129425 ATATATGTAT
129435 AGAGAAAG
1 AGAGAAAG
129443 AGAGAGAGAG
1 AGAGA-A-AG
*
129453 AGAGAGAG
1 AGAGAAAG
*
129461 AGAGAGAG
1 AGAGAAAG
129469 AGAGAGAA-
1 AGAGA-AAG
129477 AGAGAAAG
1 AGAGAAAG
129485 AGA
1 AGA
129488 TTTTCTTAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
7 2 0.05
8 28 0.72
9 2 0.05
10 7 0.18
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (8 bp):
AGAGAAAG
Found at i:138537 original size:47 final size:48
Alignment explanation
Indices: 138451--138545 Score: 156
Period size: 49 Copynumber: 2.0 Consensus size: 48
138441 AATCACATAC
138451 CAGTAAAAAATTATTAAAAAAAAAGAAGGAAGAAGAACTGAATCAAGTA
1 CAGTAAAAAATTATTAAAAAAAAAG-AGGAAGAAGAACTGAATCAAGTA
* *
138500 CAGTAAATAATTATTAAAAAAAAAG-GGAAGAATAACTGAATCAAGT
1 CAGTAAAAAATTATTAAAAAAAAAGAGGAAGAAGAACTGAATCAAGT
138546 GAGTTTAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 20 0.45
49 24 0.55
ACGTcount: A:0.59, C:0.06, G:0.16, T:0.19
Consensus pattern (48 bp):
CAGTAAAAAATTATTAAAAAAAAAGAGGAAGAAGAACTGAATCAAGTA
Found at i:142973 original size:20 final size:20
Alignment explanation
Indices: 142933--142971 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
142923 TCCACTCTCT
142933 TATAAATTTTAGAAATTTTA
1 TATAAATTTTAGAAATTTTA
142953 TATAACATTTTAGAAATTT
1 TATAA-ATTTTAGAAATTT
142972 ATTTATGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (20 bp):
TATAAATTTTAGAAATTTTA
Found at i:144444 original size:2 final size:2
Alignment explanation
Indices: 144437--144468 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
144427 CTCTATGAAC
144437 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
144469 TATGGAATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:148849 original size:27 final size:28
Alignment explanation
Indices: 148788--148849 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
148778 TATTTAGGTG
148788 TAAAATAAAAAATAAAAAATAATTTAAA
1 TAAAATAAAAAATAAAAAATAATTTAAA
* * * *
148816 CATAATAAAAAAT-AAAATTTATTTAAA
1 TAAAATAAAAAATAAAAAATAATTTAAA
148843 TAAAATA
1 TAAAATA
148850 TTGAAATTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (28 bp):
TAAAATAAAAAATAAAAAATAATTTAAA
Found at i:149634 original size:12 final size:12
Alignment explanation
Indices: 149617--149642 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
149607 AGTTGAATTA
149617 TTATTATTATTG
1 TTATTATTATTG
149629 TTATTATTATTG
1 TTATTATTATTG
149641 TT
1 TT
149643 TTTGTGCTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTATTATTATTG
Found at i:158088 original size:2 final size:2
Alignment explanation
Indices: 158083--158112 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
158073 TGTATGTGTG
158083 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
158113 ATACGAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:171343 original size:8 final size:8
Alignment explanation
Indices: 171330--171356 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
171320 CCTCGCTTCT
171330 TATTTATC
1 TATTTATC
171338 TATTTATC
1 TATTTATC
171346 TATTTATC
1 TATTTATC
171354 TAT
1 TAT
171357 CTTGTCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (8 bp):
TATTTATC
Found at i:172650 original size:8 final size:8
Alignment explanation
Indices: 172637--172666 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
172627 CACACGTACG
172637 TATATTTA
1 TATATTTA
172645 TATATTTA
1 TATATTTA
172653 TATATTTA
1 TATATTTA
172661 TATATT
1 TATATT
172667 AGCTTTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATATTTA
Found at i:175203 original size:16 final size:16
Alignment explanation
Indices: 175178--175208 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
175168 GATCATTGAG
175178 AGCATACTATCAAACA
1 AGCATACTATCAAACA
*
175194 AGCATCCTATCAAAC
1 AGCATACTATCAAAC
175209 TGAACCCTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.29, G:0.06, T:0.19
Consensus pattern (16 bp):
AGCATACTATCAAACA
Found at i:186846 original size:2 final size:2
Alignment explanation
Indices: 186839--186871 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
186829 TTACATGTTT
186839 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
186872 TCAGATGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:187462 original size:45 final size:47
Alignment explanation
Indices: 187398--187486 Score: 137
Period size: 45 Copynumber: 1.9 Consensus size: 47
187388 TTCAGCTATA
*
187398 TATTGAAACTATAACCACAAA-AAGTATA-TATTTTTGTATTTTATT
1 TATTGAAACCATAACCACAAATAAGTATATTATTTTTGTATTTTATT
* *
187443 TATTGAAACCATAGCCACAAATAAGTATATTTTTTTTGTATTTT
1 TATTGAAACCATAACCACAAATAAGTATATTATTTTTGTATTTT
187487 TTTCAACCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 19 0.49
46 7 0.18
47 13 0.33
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (47 bp):
TATTGAAACCATAACCACAAATAAGTATATTATTTTTGTATTTTATT
Found at i:192211 original size:52 final size:52
Alignment explanation
Indices: 192124--192280 Score: 210
Period size: 52 Copynumber: 3.0 Consensus size: 52
192114 TGGACAAGAA
* *
192124 GACTTGCAA-ATGAAGAATTCCAAGA-GAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGA-GAAGAATTCTAAGAGGAAAG-GGATTCTTAATAGGCAAGTTT
*
192176 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
* ** * *
192228 GACTTACGGGAGAAGAATTCTAAGAGGAGAGGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
192280 G
1 G
192281 TATGGTTATA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 88 0.94
53 6 0.06
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
Found at i:193653 original size:3 final size:3
Alignment explanation
Indices: 193647--193685 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
193637 TTATTTTTAT
* *
193647 TAG TAG TAG TAG TAG TAG TAG TAA TAA TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
193686 AGGTGCTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.33
Consensus pattern (3 bp):
TAG
Found at i:195782 original size:2 final size:2
Alignment explanation
Indices: 195775--195803 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
195765 TTTTATTTTG
195775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
195804 GACTTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:198081 original size:19 final size:18
Alignment explanation
Indices: 198059--198096 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
198049 TTAATTTATA
198059 TTTATATTAAAAATAATAT
1 TTTATATTAAAAA-AATAT
*
198078 TTTATATTTAAAAAATAT
1 TTTATATTAAAAAAATAT
198096 T
1 T
198097 CTATTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATATTAAAAAAATAT
Found at i:201655 original size:315 final size:315
Alignment explanation
Indices: 200640--201881 Score: 2135
Period size: 315 Copynumber: 4.0 Consensus size: 315
200630 AATGCTTGGG
*
200640 ATATGTTTTCTCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTAAGAATGTAATTGAGAA
1 ATATGTTTTCTCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTACGAATGTAATTGAGAA
200705 TTTGAATTAACATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAATTTAA
66 TTTGAATTAACATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAATTTAA
200770 TTAAAATATAATCTAATTTTATTTTTTAAATTTCTTTTAAAAAAATTAAATTACTCGTATTCAAA
131 TTAAAATATAATCTAATTTTATTTTTTAAATTTCTTTTAAAAAAATTAAATTACTCGTATTCAAA
200835 CATAGTCAATTAATTAGATTAATTTGTAAAAATAAATTTAATTTTTATATTTAATAAAAATTTAA
196 CATAGTCAATTAATTAGATTAATTTGTAAAAATAAATTTAATTTTTATATTTAATAAAAATTTAA
200900 TTATTTATATTCAAATTTAAATTTAAAATATTTTATTAATTAAAATAATTAAAAT
261 TTATTTATATTCAAATTTAAATTTAAAATATTTTATTAATTAAAATAATTAAAAT
200955 ATATGTTTTCTCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTACGAATGTAATTGAGAA
1 ATATGTTTTCTCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTACGAATGTAATTGAGAA
201020 TTTGAATTAACATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAATTTAA
66 TTTGAATTAACATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAATTTAA
201085 TTAAAATATAATCTAATTTTATTTTTTAAATTTCTTTTAAAAAAATTAAATTACTCGTATTCAAA
131 TTAAAATATAATCTAATTTTATTTTTTAAATTTCTTTTAAAAAAATTAAATTACTCGTATTCAAA
201150 CATAGTCAATTAATTAGATTAATTTGT-AAAATAAATTTAA-TTTTATATTTAATAAAAATTTAA
196 CATAGTCAATTAATTAGATTAATTTGTAAAAATAAATTTAATTTTTATATTTAATAAAAATTTAA
201213 TTATTTATATTCAAATTTAAATTTAAAATATTTTATTAATTAAAATAATTAAAAT
261 TTATTTATATTCAAATTTAAATTTAAAATATTTTATTAATTAAAATAATTAAAAT
*
201268 ATATGTTTTCTCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTACAAATGTAATTGAGAA
1 ATATGTTTTCTCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTACGAATGTAATTGAGAA
*
201333 TTTGAATTAATATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAATTTAA
66 TTTGAATTAACATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAATTTAA
201398 TTAAAATATAATCTAATTTTATTTTTTAAATTTCTTTTAAAAAAATTAAATTACTCGTATTCAAA
131 TTAAAATATAATCTAATTTTATTTTTTAAATTTCTTTTAAAAAAATTAAATTACTCGTATTCAAA
201463 CATAGTCAATTAATTAGATTAATTTGTAAAAATAAATTTAATTTTTATATTTAATAAAAATTTAA
196 CATAGTCAATTAATTAGATTAATTTGTAAAAATAAATTTAATTTTTATATTTAATAAAAATTTAA
201528 TTATTTATATTCAAATTTAAATTTAAAATATTTTATTAATTAAAATAATTAAAAT
261 TTATTTATATTCAAATTTAAATTTAAAATATTTTATTAATTAAAATAATTAAAAT
201583 ATATGTTTTCTCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTACGAATGTAATTGAGAA
1 ATATGTTTTCTCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTACGAATGTAATTGAGAA
*
201648 TTTGAATTAATATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAA--T--
66 TTTGAATTAACATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAATTTAA
* *
201709 TT---A-AT--T-T-A----ATTTTTTAAA-TTCTTTTTAAAAAAATCAAATTACTCGGA-TC--
131 TTAAAATATAATCTAATTTTATTTTTTAAATTTC-TTTTAAAAAAATTAAATTACTCGTATTCAA
* * *
201758 -CA-A-AC-A-T-ATTCGATTAATTTGTAAAAATAAATTTAATTTTTATATTTAATAAAAAATTA
195 ACATAGTCAATTAATTAGATTAATTTGTAAAAATAAATTTAATTTTTATATTTAATAAAAATTTA
*
201817 ATTATTTATATTCAAATTTAAATTCAAATTTTAAATATTTTATTAATTAAAATAATTAAAAT
260 ATTATTTATATTCAAA--T---TT-AAATTTAAAATATTTTATTAATTAAAATAATTAAAAT
201879 ATA
1 ATA
201882 AAAATTTAAT
Statistics
Matches: 908, Mismatches: 10, Indels: 37
0.95 0.01 0.04
Matches are distributed among these distances:
290 66 0.07
291 1 0.00
292 2 0.00
293 1 0.00
294 1 0.00
295 4 0.00
296 39 0.04
298 5 0.01
299 33 0.04
303 1 0.00
304 1 0.00
305 1 0.00
307 2 0.00
308 1 0.00
311 2 0.00
313 299 0.33
314 26 0.03
315 423 0.47
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (315 bp):
ATATGTTTTCTCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTACGAATGTAATTGAGAA
TTTGAATTAACATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAATTTAA
TTAAAATATAATCTAATTTTATTTTTTAAATTTCTTTTAAAAAAATTAAATTACTCGTATTCAAA
CATAGTCAATTAATTAGATTAATTTGTAAAAATAAATTTAATTTTTATATTTAATAAAAATTTAA
TTATTTATATTCAAATTTAAATTTAAAATATTTTATTAATTAAAATAATTAAAAT
Found at i:201716 original size:19 final size:19
Alignment explanation
Indices: 201692--201728 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
201682 TTGGATTTTA
201692 AATTTAATATTTAAAATTT
1 AATTTAATATTTAAAATTT
* *
201711 AATTTAATTTTTTAAATT
1 AATTTAATATTTAAAATT
201729 CTTTTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTTAATATTTAAAATTT
Found at i:201869 original size:628 final size:618
Alignment explanation
Indices: 200640--201881 Score: 2095
Period size: 628 Copynumber: 2.0 Consensus size: 618
200630 AATGCTTGGG
200640 ATATGTTTTCTCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTAAGAATGTAATTGAGAA
1 ATATGTTTTCTCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTAAGAATGTAATTGAGAA
200705 TTTGAATTAACATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAATTTAA
66 TTTGAATTAACATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAATTTAA
200770 TTAAAATATAATCTAATTTTATTTTTTAAATTTCTTTTAAAAAAATTAAATTACTCGTATTCAAA
131 TTAAAATATAATCTAATTTTATTTTTTAAATTTCTTTTAAAAAAATTAAATTACTCGTATTCAAA
200835 CATAGTCAATTAATTAGATTAATTTGTAAAAATAAATTTAATTTTTATATTTAATAAAAATTTAA
196 CATAGTCAATTAATTAGATTAATTTGTAAAAATAAATTTAATTTTTATATTTAATAAAAATTTAA
200900 TTATTTATATTCAAATTTAAATTTAAAATATTTTATTAATTAAAATAATTAAAATATATGTTTTC
261 TTATTTATATTCAAATTTAAATTTAAAATATTTTATTAATTAAAATAATTAAAATATATGTTTTC
200965 TCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTACGAATGTAATTGAGAATTTGAATTAA
326 TCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTACGAATGTAATTGAGAATTTGAATTAA
201030 CATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAATTTAATTAAAATATA
391 CATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAA-TT-ATT--AATAT-
* * *
201095 ATCTAATTTTATTTTTTAAATTTCTTTTAAAAAAATTAAATTACTCGTATTCAAACATAGTCAAT
451 ATCTAA---TATTTTTTAAATTTCTTTTAAAAAAATCAAATTACTCGGATTC--ACATAGACAAT
*
201160 TAATTAGATTAATTTGTAAAATAAATTTAATTTTATATTTAATAAAAATTTAATTATTTATATTC
511 TAATTAGATTAATTTGTAAAATAAATTTAATTTTATATTTAATAAAAATTTAATTATTTAAATTC
201225 AAATTTAAATTTAAAATATTTTATTAATTAAAATAATTAAAAT
576 AAATTTAAATTTAAAATATTTTATTAATTAAAATAATTAAAAT
201268 ATATGTTTTCTCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTACA-AATGTAATTGAGA
1 ATATGTTTTCTCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTA-AGAATGTAATTGAGA
*
201332 ATTTGAATTAATATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAATTTA
65 ATTTGAATTAACATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAATTTA
201397 ATTAAAATATAATCTAATTTTATTTTTTAAATTTCTTTTAAAAAAATTAAATTACTCGTATTCAA
130 ATTAAAATATAATCTAATTTTATTTTTTAAATTTCTTTTAAAAAAATTAAATTACTCGTATTCAA
201462 ACATAGTCAATTAATTAGATTAATTTGTAAAAATAAATTTAATTTTTATATTTAATAAAAATTTA
195 ACATAGTCAATTAATTAGATTAATTTGTAAAAATAAATTTAATTTTTATATTTAATAAAAATTTA
201527 ATTATTTATATTCAAATTTAAATTTAAAATATTTTATTAATTAAAATAATTAAAATATATGTTTT
260 ATTATTTATATTCAAATTTAAATTTAAAATATTTTATTAATTAAAATAATTAAAATATATGTTTT
201592 CTCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTACGAATGTAATTGAGAATTTGAATTA
325 CTCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTACGAATGTAATTGAGAATTTGAATTA
*
201657 ATATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAA-T-TT-A-AT-T-T
390 ACATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAATTATTAATATATCT
*
201716 -A-ATTTTTTAAA-TTCTTTTTAAAAAAATCAAATTACTCGGA-TC-CA-A-AC-A-T-ATTCGA
455 AATATTTTTTAAATTTC-TTTTAAAAAAATCAAATTACTCGGATTCACATAGACAATTAATTAGA
* *
201771 TTAATTTGTAAAAATAAATTTAATTTTTATATTTAATAAAAAATTAATTATTTATATTCAAATTT
519 TTAATTTGT-AAAATAAATTTAA-TTTTATATTTAATAAAAATTTAATTATTTAAATTCAAA--T
*
201836 AAATTCAAATTTTAAATATTTTATTAATTAAAATAATTAAAAT
580 ---TT-AAATTTAAAATATTTTATTAATTAAAATAATTAAAAT
201879 ATA
1 ATA
201882 AAAATTTAAT
Statistics
Matches: 596, Mismatches: 8, Indels: 37
0.93 0.01 0.06
Matches are distributed among these distances:
603 14 0.02
604 14 0.02
605 38 0.06
606 1 0.00
607 2 0.00
608 2 0.00
610 2 0.00
611 44 0.07
612 33 0.06
616 1 0.00
617 1 0.00
618 1 0.00
620 2 0.00
621 1 0.00
624 2 0.00
626 1 0.00
628 436 0.73
629 1 0.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (618 bp):
ATATGTTTTCTCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTAAGAATGTAATTGAGAA
TTTGAATTAACATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAATTTAA
TTAAAATATAATCTAATTTTATTTTTTAAATTTCTTTTAAAAAAATTAAATTACTCGTATTCAAA
CATAGTCAATTAATTAGATTAATTTGTAAAAATAAATTTAATTTTTATATTTAATAAAAATTTAA
TTATTTATATTCAAATTTAAATTTAAAATATTTTATTAATTAAAATAATTAAAATATATGTTTTC
TCCATGGTTCTAGATTGTCGGCTGATAGAATATAGTTTACGAATGTAATTGAGAATTTGAATTAA
CATAATATTAAATTTAAGTTTGATTTGGATTTTAAATTTAATATTTAAAATTATTAATATATCTA
ATATTTTTTAAATTTCTTTTAAAAAAATCAAATTACTCGGATTCACATAGACAATTAATTAGATT
AATTTGTAAAATAAATTTAATTTTATATTTAATAAAAATTTAATTATTTAAATTCAAATTTAAAT
TTAAAATATTTTATTAATTAAAATAATTAAAAT
Found at i:201911 original size:21 final size:22
Alignment explanation
Indices: 201881--201940 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
201871 ATTAAAATAT
201881 AAAA-ATTTAATTTAATTTAT-
1 AAAATATTTAATTTAATTTATA
* * *
201901 AAATTATTTAAATTAA-ATATA
1 AAAATATTTAATTTAATTTATA
201922 AAAATATTTAAATTTAATT
1 AAAATATTT-AATTTAATT
201941 CAATCAATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 6 0.20
21 18 0.60
22 6 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAATATTTAATTTAATTTATA
Found at i:201967 original size:32 final size:30
Alignment explanation
Indices: 201919--201989 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
201909 TAAATTAAAT
* * *
201919 ATAAAAATATTTAAATTTAATTCAATCAATAA
1 ATAAAATTATTCAAATTAAATTCAAT-AAT-A
* *
201951 ATTAAATTATTCAAATTAAATTCGATAATA
1 ATAAAATTATTCAAATTAAATTCAATAATA
201981 ATAAAATTA
1 ATAAAATTA
201990 AAAGTAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 9 0.27
31 3 0.09
32 21 0.64
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (30 bp):
ATAAAATTATTCAAATTAAATTCAATAATA
Found at i:217669 original size:13 final size:13
Alignment explanation
Indices: 217651--217676 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
217641 TTCCTCATTG
217651 TTTTTTTCAAAAT
1 TTTTTTTCAAAAT
217664 TTTTTTTCAAAAT
1 TTTTTTTCAAAAT
217677 CATGTGAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTTTCAAAAT
Found at i:218066 original size:3 final size:3
Alignment explanation
Indices: 218052--218086 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
218042 CATTAGAAGT
* *
218052 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA CTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
218087 TGTATGCTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:218466 original size:2 final size:2
Alignment explanation
Indices: 218459--218488 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
218449 GATATTGGAA
*
218459 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
218489 GTTTTCTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:238554 original size:103 final size:103
Alignment explanation
Indices: 238375--238582 Score: 346
Period size: 103 Copynumber: 2.0 Consensus size: 103
238365 AATGGAGTTT
* *
238375 ATAATTAAATGTCTATAGCAATGAAGACATGAATAAGAAATTCCACCTATATAAACATAGAAGTG
1 ATAATTAAATGTCTATAGCAATGAAAACATGAATAAGAAATTCCACCGATATAAACATAGAAGTG
* *
238440 GTGTCGCTTCAATAAGAAAATTAAAAACTTTCTTGTAA
66 GTATCACTTCAATAAGAAAATTAAAAACTTTCTTGTAA
*
238478 ATAATTAAATGTTTATAGCAATGAAAACATGAATAAGAAACTT-CACCGATATAAACATAGAAGT
1 ATAATTAAATGTCTATAGCAATGAAAACATGAATAAGAAA-TTCCACCGATATAAACATAGAAGT
*
238542 GGTATCACTTCAATAAGAAAATTGAAAACTTTCTTGTAA
65 GGTATCACTTCAATAAGAAAATTAAAAACTTTCTTGTAA
238581 AT
1 AT
238583 GTTTATGAAT
Statistics
Matches: 98, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 96 0.98
104 2 0.02
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (103 bp):
ATAATTAAATGTCTATAGCAATGAAAACATGAATAAGAAATTCCACCGATATAAACATAGAAGTG
GTATCACTTCAATAAGAAAATTAAAAACTTTCTTGTAA
Found at i:245317 original size:11 final size:10
Alignment explanation
Indices: 245290--245320 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
245280 TTAATCATCG
245290 ATTATTATAA
1 ATTATTATAA
245300 ATTATTATAA
1 ATTATTATAA
245310 ATTTATTATAA
1 A-TTATTATAA
245321 TATATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTATTATAA
Found at i:245678 original size:24 final size:24
Alignment explanation
Indices: 245651--245696 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
245641 AAATAATCAT
*
245651 AATAAATGTATTAAA-AACAATGAA
1 AATAAATG-ATAAAAGAACAATGAA
*
245675 AATATATGATAAAAGAACAATG
1 AATAAATGATAAAAGAACAATG
245697 CCAGCTTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.61, C:0.04, G:0.11, T:0.24
Consensus pattern (24 bp):
AATAAATGATAAAAGAACAATGAA
Found at i:254414 original size:64 final size:64
Alignment explanation
Indices: 254313--254495 Score: 366
Period size: 64 Copynumber: 2.9 Consensus size: 64
254303 GCAGAGATAC
254313 TGAGAGTGAGAGTGAGAGAGATTTGGTTGGACTTGGATAACAGATAAGAAAGAGATGCTGAGAG
1 TGAGAGTGAGAGTGAGAGAGATTTGGTTGGACTTGGATAACAGATAAGAAAGAGATGCTGAGAG
254377 TGAGAGTGAGAGTGAGAGAGATTTGGTTGGACTTGGATAACAGATAAGAAAGAGATGCTGAGAG
1 TGAGAGTGAGAGTGAGAGAGATTTGGTTGGACTTGGATAACAGATAAGAAAGAGATGCTGAGAG
254441 TGAGAGTGAGAGTGAGAGAGATTTGGTTGGACTTGGATAACAGATAAGAAAGAGA
1 TGAGAGTGAGAGTGAGAGAGATTTGGTTGGACTTGGATAACAGATAAGAAAGAGA
254496 AGGTAAAATT
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 119 1.00
ACGTcount: A:0.37, C:0.04, G:0.37, T:0.22
Consensus pattern (64 bp):
TGAGAGTGAGAGTGAGAGAGATTTGGTTGGACTTGGATAACAGATAAGAAAGAGATGCTGAGAG
Found at i:256942 original size:13 final size:14
Alignment explanation
Indices: 256924--256952 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
256914 TTTAGGATAA
256924 AAAAAAGAAGA-AG
1 AAAAAAGAAGAGAG
256937 AAAAAAGAAGAGAG
1 AAAAAAGAAGAGAG
256951 AA
1 AA
256953 GCCCCACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAGAGAG
Found at i:258051 original size:16 final size:16
Alignment explanation
Indices: 258020--258049 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
258010 GGATTAGTTG
258020 TTTTTATTGTACTTTC
1 TTTTTATTGTACTTTC
258036 TTTTTA-TGTACTTT
1 TTTTTATTGTACTTT
258050 TCAATGATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (16 bp):
TTTTTATTGTACTTTC
Found at i:258286 original size:16 final size:14
Alignment explanation
Indices: 258262--258301 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
258252 ATTTAAAAAA
258262 TAATAATAATAAAT
1 TAATAATAATAAAT
*
258276 TATATATATAATAATT
1 TA-ATA-ATAATAAAT
258292 TAATAATAAT
1 TAATAATAAT
258302 TTATAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 7 0.30
15 6 0.26
16 10 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATAATAATAAAT
Found at i:263374 original size:18 final size:21
Alignment explanation
Indices: 263352--263407 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
263342 ATCATATCAC
263352 TTTTATTTT-TTAT-ATCATA
1 TTTTATTTTATTATAATCATA
263371 -TTTATGTTTATTATCGAATCATA
1 TTTTAT-TTTATTAT--AATCATA
263394 TTTTATTTTATTAT
1 TTTTATTTTATTAT
263408 TTGTATTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 5 0.16
19 3 0.10
20 4 0.13
23 14 0.45
24 5 0.16
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTATTTTATTATAATCATA
Found at i:266127 original size:31 final size:31
Alignment explanation
Indices: 266059--266129 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
266049 TATAAATTAT
* * **
266059 AATATATATTTTTTATATAATATATGATATG
1 AATATATAATTTTAATATAATATATGATACA
* *
266090 ATTATATAATTTTAATATATTATATGATACA
1 AATATATAATTTTAATATAATATATGATACA
266121 AATATATAA
1 AATATATAA
266130 ATCGATAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (31 bp):
AATATATAATTTTAATATAATATATGATACA
Found at i:267166 original size:31 final size:31
Alignment explanation
Indices: 267109--267201 Score: 95
Period size: 30 Copynumber: 3.0 Consensus size: 31
267099 TTTAATAAAA
* *
267109 TAAAA-AAATTATATTTTAT-ATTTTTATAT
1 TAAAATAAATTATAATATATAATTTTTATAT
*
267138 TAACATAAATTATAATATATAATTTTTATA-
1 TAAAATAAATTATAATATATAATTTTTATAT
*
267168 TAAAATATAA-TATAAATATATAAATTTTAATAT
1 TAAAATA-AATTAT-AATATAT-AATTTTTATAT
267201 T
1 T
267202 TTACACAACA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
29 4 0.08
30 21 0.40
31 18 0.34
32 9 0.17
33 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (31 bp):
TAAAATAAATTATAATATATAATTTTTATAT
Found at i:274230 original size:3 final size:3
Alignment explanation
Indices: 274224--274253 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
274214 TTTAATTTTA
274224 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
274254 TAAAAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:275635 original size:18 final size:18
Alignment explanation
Indices: 275592--275638 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
275582 AAAAAATTTT
275592 TTAA-TAATAAATAAAAA
1 TTAAGTAATAAATAAAAA
* *
275609 TTGATTAATAAATTAAAAA
1 TTAAGTAATAAA-TAAAAA
275628 -TAAGTAATAAA
1 TTAAGTAATAAA
275639 AATATGAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 3 0.12
18 16 0.64
19 6 0.24
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (18 bp):
TTAAGTAATAAATAAAAA
Found at i:276181 original size:192 final size:193
Alignment explanation
Indices: 275894--276279 Score: 641
Period size: 192 Copynumber: 2.0 Consensus size: 193
275884 GCATGGCATG
* * *
275894 CATGACATGATTTCTTATGAAAAGTAAATTTAGACCTCCAAAAATGAGATTCTAAAAGTATTCCG
1 CATGACAT-ATTTCTTACGAAAAATAAATTGAGACCTCCAAAAATGAGATTCTAAAAGTATTCCG
*
275959 AGTAGAGATGCTTTAAGAAATCTTTAGGTGAGAAAAAATTCTTTTAATGTTACCAACGTACTGGA
65 AGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAAAATTCTTTTAATGTTACCAACGTACTGGA
**
276024 ACATTTTAAAAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATATTTTTTTTAA
130 ACATTTTAAAAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTTAA
*
276088 CATGACAT-TTTCTTACGAAAAATAAATTCGAG-CCTCCAAAGATGAGATTCTAAAAGTATTCCG
1 CATGACATATTTCTTACGAAAAATAAATT-GAGACCTCCAAAAATGAGATTCTAAAAGTATTCCG
* * *
276151 AGTAGATATGCTTTAAGAAATCTCTAGGTGAGAAATAGTTCTTTTAATGTTACCAACGTACTGGA
65 AGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAAAATTCTTTTAATGTTACCAACGTACTGGA
*
276216 ACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTTAA
130 ACATTTTAAAAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTTAA
276280 TAAATAAAAA
Statistics
Matches: 180, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
192 170 0.94
193 2 0.01
194 8 0.04
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.37
Consensus pattern (193 bp):
CATGACATATTTCTTACGAAAAATAAATTGAGACCTCCAAAAATGAGATTCTAAAAGTATTCCGA
GTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAAAATTCTTTTAATGTTACCAACGTACTGGAA
CATTTTAAAAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTTAA
Found at i:276748 original size:11 final size:12
Alignment explanation
Indices: 276731--276776 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
276721 CAATTTTAGT
*
276731 AAAAAAAAAAAC
1 AAAAAAAAAAGC
*
276743 AAAAAAATAAATC
1 AAAAAAA-AAAGC
276756 AAAAATAAAAAGC
1 AAAAA-AAAAAGC
276769 AAAAAAAA
1 AAAAAAAA
276777 TTCACACATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 10 0.33
13 18 0.60
14 2 0.07
ACGTcount: A:0.85, C:0.07, G:0.02, T:0.07
Consensus pattern (12 bp):
AAAAAAAAAAGC
Found at i:287959 original size:48 final size:47
Alignment explanation
Indices: 287833--288393 Score: 747
Period size: 45 Copynumber: 12.0 Consensus size: 47
287823 AATTTGAAAA
* * *
287833 CAAGATAAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAACCTTTT
1 CAAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGG-AGCTTTT
*
287881 CAAGA-GA-ATTTTAAAGTCGTTGAGCCTCTGCTGAGAGGAGCTTTT
1 CAAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT
*
287926 CCAAGATGAGATTTTAAAGTCGTTGAGCCTCTGCTGAGAGGAGCTTTT
1 -CAAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT
*
287974 TAAGA-GA-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT
1 CAAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT
**
288019 CAAGA-GA-ATTTTAAAGTCATTGAGCCTCTGCTGAGAGGAGCTTTT
1 CAAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT
* * *
288064 CTAAAAAGAGAATTTTAAAGTCGTTGAGCCTCTGCTGAGAGGAGCTTTT
1 C-AAGATGAG-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT
288113 CTAAGAT-AGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT
1 C-AAGATGAG-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTT
* *
288162 CAAGATGAGATTTTAAAGTCGTTGAGCCTCTGCTGATAGGAGCTTTT
1 CAAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT
* *
288209 CTAAGATGAGATTTTAAAGTTGTTGAGCCTCTGTTGAGATGAGCTTTTT
1 C-AAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTT
*
288258 CAAGA-GA-ATTTTAAAGTTGTTGAGCCTCTGCTGAGATGAGCCTTTT
1 CAAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTT
288304 C---ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTT
1 CAAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTT
* *
288349 C---ATTAGATTTTAAAGTTGTTGAGCTTCTGCTGAGAGGAGCCTTTT
1 CAAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTT
288394 AAACTTTCAA
Statistics
Matches: 476, Mismatches: 23, Indels: 31
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.00
44 2 0.00
45 167 0.35
46 77 0.16
47 17 0.04
48 158 0.33
49 54 0.11
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (47 bp):
CAAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT
Found at i:288000 original size:45 final size:45
Alignment explanation
Indices: 287841--288395 Score: 727
Period size: 48 Copynumber: 11.9 Consensus size: 45
287831 AACAAGATAA
* *
287841 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAACCTTTTCAAGAG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGG-AGCTTTTTAAGAG
* *
287887 AATTTTAAAGTCGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT-TAAGA-G
*
287934 AGATTTTAAAGTCGTTGAGCCTCTGCTGAGAGGAGCTTTTTAAGAG
1 A-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTAAGAG
*
287980 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGAG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTAAGAG
**
288025 AATTTTAAAGTCATTGAGCCTCTGCTGAGAGGAGCTTTTCTAAAAAGAG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT-T---AAGAG
*
288074 AATTTTAAAGTCGTTGAGCCTCTGCTGAGAGGAGCTTTTCTAAGATAG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT-TAAG--AG
288122 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT-AAGA-G
* *
288169 AGATTTTAAAGTCGTTGAGCCTCTGCTGATAGGAGCTTTTCTAAGATG
1 A-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT-TAAGA-G
* *
288217 AGATTTTAAAGTTGTTGAGCCTCTGTTGAGATGAGCTTTTTCAAGAG
1 A-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT-AAGAG
* * *
288264 AATTTTAAAGTTGTTGAGCCTCTGCTGAGATGAGCCTTTTCATGAG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTAAGAG
* **
288310 -ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTCATTAG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTAAGAG
* *
288355 -ATTTTAAAGTTGTTGAGCTTCTGCTGAGAGGAGCCTTTTAA
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTAA
288396 ACTTTCAAAA
Statistics
Matches: 469, Mismatches: 25, Indels: 32
0.89 0.05 0.06
Matches are distributed among these distances:
44 5 0.01
45 160 0.34
46 78 0.17
47 17 0.04
48 163 0.35
49 46 0.10
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (45 bp):
AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTAAGAG
Found at i:296105 original size:2 final size:2
Alignment explanation
Indices: 296098--296147 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
296088 AACAAATGGT
296098 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
296140 AG GG AG AG
1 AG AG AG AG
296148 GGAGGGAGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:308412 original size:12 final size:12
Alignment explanation
Indices: 308395--308433 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
308385 TTCAATCAAA
308395 TTTAAATTAAAT
1 TTTAAATTAAAT
308407 TTTAAATAATAAAT
1 TTTAAAT--TAAAT
*
308421 TTAAAATTAAAT
1 TTTAAATTAAAT
308433 T
1 T
308434 CAACCTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 13 0.54
14 11 0.46
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TTTAAATTAAAT
Found at i:309972 original size:29 final size:29
Alignment explanation
Indices: 309940--309997 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
309930 TAATAATTTA
309940 TATAT-TTATATTATATTTTATATAAAAAT
1 TATATGTTATATTATATTTTA-ATAAAAAT
* *
309969 TATATGTTATGTTTTATTTTAATAAAAAT
1 TATATGTTATATTATATTTTAATAAAAAT
309998 ATAAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
TATATGTTATATTATATTTTAATAAAAAT
Found at i:313161 original size:19 final size:19
Alignment explanation
Indices: 313123--313166 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
313113 AACTGTGGGA
*
313123 AAAACAGAGACACAGAGAG
1 AAAACAGAGACAAAGAGAG
*
313142 AAAACAGAGAGAAAGTGAGAG
1 AAAACAGAGACAAA--GAGAG
313163 AAAA
1 AAAA
313167 TCATTTGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
21 9 0.43
ACGTcount: A:0.61, C:0.09, G:0.27, T:0.02
Consensus pattern (19 bp):
AAAACAGAGACAAAGAGAG
Found at i:326513 original size:45 final size:45
Alignment explanation
Indices: 326413--326815 Score: 720
Period size: 45 Copynumber: 8.9 Consensus size: 45
326403 AACAAGATGA
326413 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTCAAGAG
326459 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGAG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGAG
*
326504 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTAAGAG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGAG
326549 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGAG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGAG
326594 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGATG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGA-G
326640 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGATG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGA-G
326686 AGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGA-
1 A-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTCAAGAG
*
326732 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCATGAG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGAG
326777 -ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTT
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTT
326816 TTTAAACTTT
Statistics
Matches: 349, Mismatches: 3, Indels: 11
0.96 0.01 0.03
Matches are distributed among these distances:
44 41 0.12
45 181 0.52
46 84 0.24
47 34 0.10
48 9 0.03
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (45 bp):
AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGAG
Found at i:326568 original size:136 final size:137
Alignment explanation
Indices: 326406--326816 Score: 740
Period size: 136 Copynumber: 3.0 Consensus size: 137
326396 ATTTGAAAAC
326406 AAGATGAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAATTTTAAAGTT
1 AAGATG-AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAATTTTAAAGTT
326471 GTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGG
65 GTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGG
326536 AGCTTTTT
130 AGCTTTTT
326544 AAGA-GAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTCAAGAGAATTTTAAAGTTG
1 AAGATGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAATTTTAAAGTTG
326607 TTGAGCCTCTGCTGAGAGGAGCTTTTCAAGATGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGG
66 TTGAGCCTCTGCTGAGAGGAGCTTTTCAAGA-GAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGG
*
326672 AGCTTTTC
130 AGCTTTTT
326680 AAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGA-AATTTTAAAGTT
1 AAGATGA-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAATTTTAAAGTT
*
326744 GTTGAGCCTCTGCTGAGAGGAGCTTTTCATGAG-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGG
65 GTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGG
326808 AGCCTTTTT
130 AG-CTTTTT
326817 TTAAACTTTC
Statistics
Matches: 265, Mismatches: 3, Indels: 11
0.95 0.01 0.04
Matches are distributed among these distances:
135 54 0.20
136 112 0.42
137 9 0.03
138 81 0.31
139 9 0.03
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (137 bp):
AAGATGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAATTTTAAAGTTG
TTGAGCCTCTGCTGAGAGGAGCTTTTCAAGAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGA
GCTTTTT
Found at i:344209 original size:19 final size:19
Alignment explanation
Indices: 344167--344211 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
344157 AAATTGATTT
344167 TTATTATAAAATTATCATC
1 TTATTATAAAATTATCATC
* *
344186 GTATTAT-AATTTATCTATC
1 TTATTATAAAATTATC-ATC
344205 TTATTAT
1 TTATTAT
344212 CTAATGATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (19 bp):
TTATTATAAAATTATCATC
Found at i:348154 original size:29 final size:29
Alignment explanation
Indices: 348122--348179 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
348112 TAATAATTTA
*
348122 TATAT-TTATATTATATTTTATATAAAAAT
1 TATATGTTATATTATATTTT-GATAAAAAT
* *
348151 TATATGTTATGTTTTATTTTGATAAAAAT
1 TATATGTTATATTATATTTTGATAAAAAT
348180 ATAAAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (29 bp):
TATATGTTATATTATATTTTGATAAAAAT
Found at i:351345 original size:19 final size:19
Alignment explanation
Indices: 351307--351350 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
351297 AACTGTGGGA
*
351307 AAAACAGAGACACAGAGAG
1 AAAACAGAGACAAAGAGAG
*
351326 AAAACAGAGAGAAAGTGAGAG
1 AAAACAGAGACAAA--GAGAG
351347 AAAA
1 AAAA
351351 TCATTTGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
21 9 0.43
ACGTcount: A:0.61, C:0.09, G:0.27, T:0.02
Consensus pattern (19 bp):
AAAACAGAGACAAAGAGAG
Found at i:374994 original size:2 final size:2
Alignment explanation
Indices: 374987--375016 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
374977 AGTCTTTCTA
374987 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
375017 GTGTGTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:384359 original size:17 final size:18
Alignment explanation
Indices: 384337--384375 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
384327 AAAGTTTTAT
*
384337 AATTTTT-AATATCA-AA
1 AATTTTTAAAAATCATAA
384353 AATTTTTAAAAATCATAA
1 AATTTTTAAAAATCATAA
384371 AATTT
1 AATTT
384376 AATTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 6 0.30
18 7 0.35
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTTTAAAAATCATAA
Found at i:387233 original size:23 final size:25
Alignment explanation
Indices: 387205--387257 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
387195 AATTATTATT
* *
387205 TATTTAATTAA-ATTAAATA-AATA
1 TATTTAATAAATATTAAATATAAAA
387228 TATTT-ATAAATATTAAATATAAAA
1 TATTTAATAAATATTAAATATAAAA
387252 TATTTA
1 TATTTA
387258 TGTTCAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 4 0.16
23 13 0.52
24 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TATTTAATAAATATTAAATATAAAA
Found at i:387332 original size:12 final size:12
Alignment explanation
Indices: 387308--387357 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
387298 TCGTTAGTAA
387308 ATATTAAATAAAT
1 ATATT-AATAAAT
*
387321 ATATTCATAAAT
1 ATATTAATAAAT
*
387333 ATATAAATAAAT
1 ATATTAATAAAT
*
387345 ATATTTATAAAT
1 ATATTAATAAAT
387357 A
1 A
387358 ATCAACAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 27 0.84
13 5 0.16
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATTAATAAAT
Found at i:387342 original size:24 final size:23
Alignment explanation
Indices: 387305--387357 Score: 88
Period size: 24 Copynumber: 2.3 Consensus size: 23
387295 AGTTCGTTAG
387305 TAAATATTAAATAAATATATTCA
1 TAAATATTAAATAAATATATTCA
*
387328 TAAATATATAAATAAATATATTTA
1 TAAATAT-TAAATAAATATATTCA
387352 TAAATA
1 TAAATA
387358 ATCAACAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAATATTAAATAAATATATTCA
Found at i:392795 original size:9 final size:9
Alignment explanation
Indices: 392772--392806 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
392762 TATAAAATAT
*
392772 AATTTTTTA
1 AATTTATTA
*
392781 ATTTTATTA
1 AATTTATTA
392790 AATTTATTA
1 AATTTATTA
392799 AATTTATT
1 AATTTATT
392807 TAAAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
AATTTATTA
Found at i:392809 original size:19 final size:19
Alignment explanation
Indices: 392772--392815 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
392762 TATAAAATAT
* *
392772 AATTTTTTAATTTTATT-A
1 AATTTATTAAATTTATTAA
392790 AATTTATTAAATTTATTTAA
1 AATTTATTAAATTTA-TTAA
392810 AATTTA
1 AATTTA
392816 AAATTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 13 0.59
19 2 0.09
20 7 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTATTAAATTTATTAA
Found at i:392842 original size:15 final size:16
Alignment explanation
Indices: 392818--392853 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
392808 AAAATTTAAA
392818 ATTATATTATTTATAT
1 ATTATATTATTTATAT
392834 ATTAT-TTATTTATAT
1 ATTATATTATTTATAT
*
392849 TTTAT
1 ATTAT
392854 CAAATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTATATTATTTATAT
Found at i:393219 original size:14 final size:14
Alignment explanation
Indices: 393202--393244 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
393192 TATCATATCT
393202 AATAATTTAAAATA
1 AATAATTTAAAATA
*
393216 AATAATTATAAATTA
1 AATAATT-TAAAATA
*
393231 TAT-ATTTAAAATA
1 AATAATTTAAAATA
393244 A
1 A
393245 TTTTAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 6 0.25
14 10 0.42
15 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATAATTTAAAATA
Found at i:395376 original size:21 final size:23
Alignment explanation
Indices: 395352--395394 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
395342 ATTTTATCTC
*
395352 AAATTAAA-TTTGAAT-TAAAAA
1 AAATAAAATTTTGAATATAAAAA
395373 AAATAAAATTTTGAATATAAAA
1 AAATAAAATTTTGAATATAAAA
395395 TTTTAAGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 7 0.37
23 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (23 bp):
AAATAAAATTTTGAATATAAAAA
Found at i:395866 original size:16 final size:15
Alignment explanation
Indices: 395845--395876 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
395835 TATACAAGAT
395845 AAAAATAAAAAATTTA
1 AAAAAT-AAAAATTTA
395861 AAAAATAAAAATTTA
1 AAAAATAAAAATTTA
395876 A
1 A
395877 TTTTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAAATAAAAATTTA
Found at i:396302 original size:24 final size:24
Alignment explanation
Indices: 396261--396307 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
396251 TAATAATTTA
* *
396261 AAATATGATACAATAATATAATAT
1 AAATATGATACAAAAATAAAATAT
*
396285 AAATATGATATAAAAATAAAATA
1 AAATATGATACAAAAATAAAATA
396308 AAAAATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
AAATATGATACAAAAATAAAATAT
Found at i:396443 original size:32 final size:31
Alignment explanation
Indices: 396389--396454 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 31
396379 TATTGCATTA
*
396389 ATATAAATTTTGTATAAAATATTATATAAAT
1 ATATAAATTTTATATAAAATATTATATAAAT
**
396420 ATATAAATTTTAATATATTATATTATATAAAT
1 ATATAAATTTT-ATATAAAATATTATATAAAT
396452 ATA
1 ATA
396455 CGAATGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 11 0.35
32 20 0.65
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (31 bp):
ATATAAATTTTATATAAAATATTATATAAAT
Found at i:400315 original size:40 final size:40
Alignment explanation
Indices: 400260--400338 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
400250 TTGTCACACA
*
400260 TTGTAATCCTTAGTTCAATGTCGTTAATCAGAAAGTGTTT
1 TTGTAATCCTTAGTTCAATGTAGTTAATCAGAAAGTGTTT
* * *
400300 TTGTATTCCTTAGTTCAATGTAGTTGATCATAAAGTGTT
1 TTGTAATCCTTAGTTCAATGTAGTTAATCAGAAAGTGTT
400339 CATTTCATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (40 bp):
TTGTAATCCTTAGTTCAATGTAGTTAATCAGAAAGTGTTT
Found at i:401914 original size:13 final size:14
Alignment explanation
Indices: 401896--401933 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
401886 TAATGATTAA
401896 ATAAATTAAAATCG
1 ATAAATTAAAATCG
*
401910 A-AAATCAAAATCG
1 ATAAATTAAAATCG
401923 ATAAATTAAAA
1 ATAAATTAAAA
401934 ATTTTCGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.63, C:0.08, G:0.05, T:0.24
Consensus pattern (14 bp):
ATAAATTAAAATCG
Found at i:404311 original size:29 final size:29
Alignment explanation
Indices: 404278--404334 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
404268 AAAAAATAAT
* * *
404278 AAAAGTTATTGTAATTGTGATTGAAAAAC
1 AAAAGTTATTATAAGTGTGATTAAAAAAC
404307 AAAAGTTATTATAAGTGTGATTAAAAAA
1 AAAAGTTATTATAAGTGTGATTAAAAAA
404335 AATTCAACGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (29 bp):
AAAAGTTATTATAAGTGTGATTAAAAAAC
Found at i:405040 original size:21 final size:21
Alignment explanation
Indices: 404996--405041 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
404986 TAAAAAAATT
*
404996 AAAAAAGAAAAAAAAGGAGGA
1 AAAAAAGAAAAAAAAGGAGAA
*
405017 AAAAAAGAAAGGAAAA-GAGAA
1 AAAAAAGAAA-AAAAAGGAGAA
405038 AAAA
1 AAAA
405042 TAACCTGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
AAAAAAGAAAAAAAAGGAGAA
Found at i:410421 original size:17 final size:18
Alignment explanation
Indices: 410399--410435 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
410389 GAAATGCGAA
410399 TTTGTCACTT-TATTTTT
1 TTTGTCACTTCTATTTTT
*
410416 TTTGTCACTTCTCTTTTT
1 TTTGTCACTTCTATTTTT
410434 TT
1 TT
410436 CATTAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.08, C:0.16, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTGTCACTTCTATTTTT
Found at i:411127 original size:2 final size:2
Alignment explanation
Indices: 411114--411144 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
411104 ATTAGAATAC
*
411114 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
411145 ATAAAGAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:412774 original size:23 final size:24
Alignment explanation
Indices: 412739--412783 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
412729 TTTTACCAGA
* *
412739 TTTTATTTCTTTAATCTATATATT
1 TTTTATATCTTTAATCCATATATT
*
412763 TTTTATAT-TTTACTCCATATA
1 TTTTATATCTTTAATCCATATA
412784 ATGTAGAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTATATCTTTAATCCATATATT
Found at i:415226 original size:21 final size:21
Alignment explanation
Indices: 415182--415227 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
415172 TCGTTAACTT
* * *
415182 TTTTATTAAAAAATTTACATA
1 TTTTATTAAAAAATTAAAAAA
*
415203 TTTTATTTAAAAATTAAAAAA
1 TTTTATTAAAAAATTAAAAAA
415224 TTTT
1 TTTT
415228 GTATATATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTATTAAAAAATTAAAAAA
Found at i:424434 original size:35 final size:33
Alignment explanation
Indices: 424393--424459 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
424383 TTTTTATATT
* * *
424393 TTAAAATTATTTTTATTGATAATTTTATAAAAAAA
1 TTAAAATTAATTTT-TT-AAAATTATATAAAAAAA
424428 TTAAAATTAATTTTTTAAAATTATATAAAAAA
1 TTAAAATTAATTTTTTAAAATTATATAAAAAA
424460 TAATAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 14 0.48
34 2 0.07
35 13 0.45
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (33 bp):
TTAAAATTAATTTTTTAAAATTATATAAAAAAA
Found at i:441268 original size:18 final size:18
Alignment explanation
Indices: 441225--441268 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
441215 AAATTTGAAT
441225 TAAT-ATATAAATATATA
1 TAATAATATAAATATATA
*
441242 T-TTATATATAAATATATA
1 TAATA-ATATAAATATATA
441260 TAATAATAT
1 TAATAATAT
441269 TTTAATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
16 1 0.05
17 1 0.05
18 18 0.82
19 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATAATATAAATATATA
Found at i:443667 original size:20 final size:21
Alignment explanation
Indices: 443628--443668 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
443618 ATATATTATT
443628 TTAATATAAATTTTAATATAA
1 TTAATATAAATTTTAATATAA
443649 TTAA-ATAAA-TTTAAGTATAA
1 TTAATATAAATTTTAA-TATAA
443669 AATAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TTAATATAAATTTTAATATAA
Found at i:451710 original size:2 final size:2
Alignment explanation
Indices: 451703--451730 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
451693 GTTGAGCAGC
451703 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
451731 TTTGTCTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:454600 original size:24 final size:24
Alignment explanation
Indices: 454573--454627 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
454563 TTTATATAAA
454573 ATATTTTTTATTATTTATTTAA-TT
1 ATATTTTTTA-TATTTATTTAATTT
*
454597 ATATATGTTTATATTTATTTAATTT
1 ATAT-TTTTTATATTTATTTAATTT
454622 ATATTT
1 ATATTT
454628 ATATTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
ATATTTTTTATATTTATTTAATTT
Found at i:454624 original size:15 final size:16
Alignment explanation
Indices: 454604--454634 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
454594 ATTATATATG
454604 TTTATATTTAT-TTAA
1 TTTATATTTATATTAA
454619 TTTATATTTATATTAA
1 TTTATATTTATATTAA
454635 ATAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATATTTATATTAA
Found at i:461033 original size:23 final size:23
Alignment explanation
Indices: 461007--461050 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
460997 TTCAATTAAA
*
461007 ATTTATGAATTTGTTAAATTTTT
1 ATTTATAAATTTGTTAAATTTTT
* *
461030 ATTTATAAATTTTTTAGATTT
1 ATTTATAAATTTGTTAAATTT
461051 ACAAATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (23 bp):
ATTTATAAATTTGTTAAATTTTT
Found at i:463949 original size:20 final size:20
Alignment explanation
Indices: 463924--463962 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
463914 TTTATTTTAA
*
463924 AATTCGTTTATATTTATTTG
1 AATTCGTTTATATTCATTTG
463944 AATTCGTTTATATTCATTT
1 AATTCGTTTATATTCATTT
463963 AAAATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.59
Consensus pattern (20 bp):
AATTCGTTTATATTCATTTG
Found at i:463999 original size:15 final size:14
Alignment explanation
Indices: 463961--464005 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
463951 TTATATTCAT
*
463961 TTAAAATTTATTTT
1 TTAAAATTTATTTA
463975 TTAAAATTTATTTGA
1 TTAAAATTTATTT-A
*
463990 TTATAATTTATTTA
1 TTAAAATTTATTTA
464004 TT
1 TT
464006 GTTCATGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TTAAAATTTATTTA
Found at i:465427 original size:204 final size:204
Alignment explanation
Indices: 465077--465488 Score: 824
Period size: 204 Copynumber: 2.0 Consensus size: 204
465067 TGAGACAATT
465077 CTTTGAACCATTGGGGGCAAATAGTCAAAAGCAACTCAGGATAATCTAATATATTCTCAGCTCAA
1 CTTTGAACCATTGGGGGCAAATAGTCAAAAGCAACTCAGGATAATCTAATATATTCTCAGCTCAA
465142 AGGCTGCAAATCCACTCTAGCCATTCAACTATGTTCATTTTTCACAAAATTCATCAGATAATGTA
66 AGGCTGCAAATCCACTCTAGCCATTCAACTATGTTCATTTTTCACAAAATTCATCAGATAATGTA
465207 ACCATCCATCCATTAAGTGCAAACAAAAAATGATCGATGATGAAAAGAACTCATTTCTCTAAATT
131 ACCATCCATCCATTAAGTGCAAACAAAAAATGATCGATGATGAAAAGAACTCATTTCTCTAAATT
465272 CGGGTTTAA
196 CGGGTTTAA
465281 CTTTGAACCATTGGGGGCAAATAGTCAAAAGCAACTCAGGATAATCTAATATATTCTCAGCTCAA
1 CTTTGAACCATTGGGGGCAAATAGTCAAAAGCAACTCAGGATAATCTAATATATTCTCAGCTCAA
465346 AGGCTGCAAATCCACTCTAGCCATTCAACTATGTTCATTTTTCACAAAATTCATCAGATAATGTA
66 AGGCTGCAAATCCACTCTAGCCATTCAACTATGTTCATTTTTCACAAAATTCATCAGATAATGTA
465411 ACCATCCATCCATTAAGTGCAAACAAAAAATGATCGATGATGAAAAGAACTCATTTCTCTAAATT
131 ACCATCCATCCATTAAGTGCAAACAAAAAATGATCGATGATGAAAAGAACTCATTTCTCTAAATT
465476 CGGGTTTAA
196 CGGGTTTAA
465485 CTTT
1 CTTT
465489 ATCTCAATCC
Statistics
Matches: 208, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
204 208 1.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.29
Consensus pattern (204 bp):
CTTTGAACCATTGGGGGCAAATAGTCAAAAGCAACTCAGGATAATCTAATATATTCTCAGCTCAA
AGGCTGCAAATCCACTCTAGCCATTCAACTATGTTCATTTTTCACAAAATTCATCAGATAATGTA
ACCATCCATCCATTAAGTGCAAACAAAAAATGATCGATGATGAAAAGAACTCATTTCTCTAAATT
CGGGTTTAA
Done.