Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003955.1 Hibiscus syriacus cultivar Beakdansim tig00008553_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: 90191
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3779 original size:16 final size:16
Alignment explanation
Indices: 3758--3790 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3748 TGACCAGATA
3758 TGACATTTACCTAACT
1 TGACATTTACCTAACT
*
3774 TGACATTTACCTGACT
1 TGACATTTACCTAACT
3790 T
1 T
3791 ATATTATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.39
Consensus pattern (16 bp):
TGACATTTACCTAACT
Found at i:4472 original size:12 final size:12
Alignment explanation
Indices: 4455--4480 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4445 TTATGCTGAA
4455 TTGCATTTCATG
1 TTGCATTTCATG
4467 TTGCATTTCATG
1 TTGCATTTCATG
4479 TT
1 TT
4481 AGATAGTTAA
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:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (12 bp):
TTGCATTTCATG
Found at i:4707 original size:29 final size:29
Alignment explanation
Indices: 4674--4758 Score: 161
Period size: 29 Copynumber: 2.9 Consensus size: 29
4664 TCCCAACACA
4674 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
4703 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
*
4732 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
4759 ACCCTCGCTC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.12, C:0.38, G:0.31, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Found at i:4834 original size:23 final size:23
Alignment explanation
Indices: 4776--4835 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
4766 CTCGGCTTCC
* *
4776 CTCGGATTCCCTCGCATAGCTTG
1 CTCGGATGCCCTCGCATAGCTCG
*
4799 CTCGGTTGCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
* *
4822 TTCGGATGGCCTCG
1 CTCGGATGCCCTCG
4836 AATGCCTAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.10, C:0.35, G:0.27, T:0.28
Consensus pattern (23 bp):
CTCGGATGCCCTCGCATAGCTCG
Found at i:4916 original size:29 final size:29
Alignment explanation
Indices: 4879--4936 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
4869 GCAATCTCTT
* *
4879 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGACGACCTA
* *
4908 GTAGGTCGCCCGGAAGGCATGACGACCTA
1 GTAGCTCGCCCGGAAGACATGACGACCTA
4937 CGGCCAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGACGACCTA
Found at i:5633 original size:12 final size:11
Alignment explanation
Indices: 5606--5743 Score: 61
Period size: 12 Copynumber: 12.5 Consensus size: 11
5596 CTTCAAAGAG
*
5606 ATTTTATATTTC
1 ATTTTATA-TTA
5618 ATTTTATATTA
1 ATTTTATATTA
* *
5629 TATTTGATTTTA
1 -ATTTTATATTA
5641 ATTTTAATATTA
1 ATTTT-ATATTA
* *
5653 ATTTTTAAATAA
1 A-TTTTATATTA
**
5665 ATTAAATATTA
1 ATTTTATATTA
* *
5676 ATTTTTAAATAA
1 A-TTTTATATTA
**
5688 ATTAAATATTA
1 ATTTTATATTA
5699 A-TTT-T-TTA
1 ATTTTATATTA
*
5707 ATATTATATT-
1 ATTTTATATTA
**
5717 A-TAGATATTA
1 ATTTTATATTA
5727 ATTTTAATATTA
1 ATTTT-ATATTA
5739 ATTTT
1 ATTTT
5744 TTAAATAAAT
Statistics
Matches: 89, Mismatches: 27, Indels: 20
0.65 0.20 0.15
Matches are distributed among these distances:
8 4 0.04
9 8 0.09
10 4 0.04
11 23 0.26
12 46 0.52
13 4 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (11 bp):
ATTTTATATTA
Found at i:5672 original size:23 final size:23
Alignment explanation
Indices: 5646--5709 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
5636 TTTTAATTTT
5646 AATATTAATTTTTAAATAAATTA
1 AATATTAATTTTTAAATAAATTA
5669 AATATTAATTTTTAAATAAATTA
1 AATATTAATTTTTAAATAAATTA
*
5692 AATATTAATTTTTTAATA
1 AATATTAATTTTTAAATA
5710 TTATATTATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATTAATTTTTAAATAAATTA
Found at i:5738 original size:40 final size:37
Alignment explanation
Indices: 5692--5776 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 37
5682 AAATAAATTA
*
5692 AATATTAATTTTTTAATATTATATTATAGATATTAA-TTTT
1 AATATTAATTTTTTAA-A-TAAATTA-A-ATATTAATTTTT
5732 AATATTAATTTTTTAAATAAATTAAATATTAATTTTTT
1 AATATTAATTTTTTAAATAAATTAAATATTAA-TTTTT
5770 AATATTA
1 AATATTA
5777 TATTATAGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
36 7 0.17
37 1 0.02
38 17 0.40
39 1 0.02
40 16 0.38
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (37 bp):
AATATTAATTTTTTAAATAAATTAAATATTAATTTTT
Found at i:5748 original size:64 final size:64
Alignment explanation
Indices: 5669--5797 Score: 242
Period size: 64 Copynumber: 2.0 Consensus size: 64
5659 AAATAAATTA
5669 AATATTAATTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA-TTAATTTT
1 AATATTAATTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATATTTAATTTT
5732 AATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATATTTAATTTT
1 AATATTAA-TTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATATTTAATTTT
5797 A
1 A
5798 TAGCATATAA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
63 8 0.12
64 47 0.73
65 9 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (64 bp):
AATATTAATTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATATTTAATTTT
Found at i:6115 original size:21 final size:22
Alignment explanation
Indices: 6091--6140 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
6081 AATATTTTCT
*
6091 AAAAATAT-CATATA-ATTATAA
1 AAAAATATGAATATATATT-TAA
6112 AAAAATTATGAATATATATTTAA
1 AAAAA-TATGAATATATATTTAA
6135 AAAAAT
1 AAAAAT
6141 TAAAAGTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.20
22 4 0.16
23 13 0.52
24 3 0.12
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAAATATGAATATATATTTAA
Found at i:6362 original size:31 final size:31
Alignment explanation
Indices: 6304--6363 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
6294 TAGTTGTATG
* ** *
6304 AATTATTTAAATTTCATTATTGTAAAACTAA
1 AATTATTTAAATCTCAGCATTGCAAAACTAA
6335 AATTATTTAAATCTCAGCATTGCAAAACT
1 AATTATTTAAATCTCAGCATTGCAAAACT
6364 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGCATTGCAAAACTAA
Found at i:6740 original size:8 final size:8
Alignment explanation
Indices: 6719--7622 Score: 174
Period size: 8 Copynumber: 110.6 Consensus size: 8
6709 TAATTTGATA
*
6719 TATATAAT
1 TATATATT
*
6727 TCTATATT
1 TATATATT
6735 TATATACTT
1 TATATA-TT
6744 TA-ATACTT
1 TATATA-TT
6752 TATAT-TGT
1 TATATAT-T
*
6760 ATATTTATAT
1 -TATATAT-T
6770 TATATAGTT
1 TATATA-TT
*
6779 TA-ATACT
1 TATATATT
6786 T-TATA-T
1 TATATATT
6792 TATATA-T
1 TATATATT
6799 T-TATA-T
1 TATATATT
6805 T-TATATT
1 TATATATT
6812 TATATACTT
1 TATATA-TT
*
6821 TA-ATACT
1 TATATATT
6828 T-TATA-T
1 TATATATT
*
6834 GATATACTT
1 TATATA-TT
6843 TA-ATATT
1 TATATATT
6850 T-TATATT
1 TATATATT
6857 TA-ATACTT
1 TATATA-TT
6865 ATATTATAGTT
1 -TA-TATA-TT
*
6876 TA-ATACT
1 TATATATT
*
6883 T-TATA-G
1 TATATATT
6889 TATATACTT
1 TATATA-TT
6898 TAATATATAT
1 T-ATATAT-T
*
6908 ATATATATA
1 -TATATATT
*
6917 TATATAACT
1 TATAT-ATT
*
6926 TATACTTTGT
1 TATA-TAT-T
6936 AGTATATACTT
1 --TATATA-TT
6947 TA-ATAATT
1 TATAT-ATT
*
6955 TA-ATACT
1 TATATATT
6962 TATA-ACTT
1 TATATA-TT
6970 ATATATATAT
1 -TATATAT-T
*
6980 ATATATACT
1 -TATATATT
6989 TATATATTT
1 TATATA-TT
6998 TATATATAT
1 TATATAT-T
7007 T-TAATACTT
1 TAT-ATA-TT
* *
7016 TACATTATA
1 TATA-TATT
*
7025 TACTAAACTT
1 TA-TATA-TT
*
7035 TATATATA
1 TATATATT
*
7043 TATATACT
1 TATATATT
*
7051 TATA-CTT
1 TATATATT
* *
7058 TATATGTA
1 TATATATT
7066 TATATACTT
1 TATATA-TT
7075 T-TATA-T
1 TATATATT
7081 TATATAGTT
1 TATATA-TT
*
7090 TATATACT
1 TATATATT
*
7098 TATA-CTT
1 TATATATT
* *
7105 TATATGTG
1 TATATATT
7113 TATATACTT
1 TATATA-TT
*
7122 T-TATA-C
1 TATATATT
7128 TATATAGTT
1 TATATA-TT
*
7137 TATATACT
1 TATATATT
*
7145 TATATACT
1 TATATATT
7153 T-TATA-T
1 TATATATT
*
7159 TATATACAT
1 TATATA-TT
*
7168 TA-ATACT
1 TATATATT
7175 T-TATA-T
1 TATATATT
7181 TATATACTT
1 TATATA-TT
*
7190 TATA-GTT
1 TATATATT
7197 TATATA--
1 TATATATT
*
7203 TATATACT
1 TATATATT
*
7211 TATA-GTT
1 TATATATT
*
7218 TATATATA
1 TATATATT
*
7226 TACTAAAACTT
1 TA-T-ATA-TT
7237 TATATATAT
1 TATATAT-T
7246 ATATATATAT
1 -TATATAT-T
*
7256 ATATATATA
1 -TATATATT
7265 TATATACTT
1 TATATA-TT
*
7274 TATA-GTT
1 TATATATT
7281 TATATA--
1 TATATATT
*
7287 TATATACT
1 TATATATT
7295 TATATACTT
1 TATATA-TT
*
7304 TATATTATA
1 TATA-TATT
*
7313 TACTAAAACTT
1 TA-T-ATA-TT
7324 TATAGT-TT
1 TATA-TATT
7332 ATATATATACT
1 -TATATAT--T
*
7343 TATATA-C
1 TATATATT
7350 T-TATATT
1 TATATATT
*
7357 TA-ATACT
1 TATATATT
7364 TATATATAT
1 TATATAT-T
*
7373 TATATACT
1 TATATATT
*
7381 TATATACT
1 TATATATT
7389 T-TATA-T
1 TATATATT
**
7395 TATATGCT
1 TATATATT
7403 TATATACTT
1 TATATA-TT
* *
7412 TA-GTCTT
1 TATATATT
7419 TATA-A-T
1 TATATATT
7425 TATACT-TT
1 TATA-TATT
*
7433 T-TATATG
1 TATATATT
*
7440 TATATAATA
1 TATAT-ATT
7449 TACTTATACTT
1 TA--TATA-TT
7460 TATAGTA-T
1 TATA-TATT
*
7468 TATATATG
1 TATATATT
7476 TATATACTT
1 TATATA-TT
*
7485 TATATACT
1 TATATATT
7493 TATATACTT
1 TATATA-TT
7502 TATA-ATT
1 TATATATT
* *
7509 AGACTATATA
1 -TA-TATATT
7519 TATATATAT
1 TATATAT-T
* *
7528 AATATACT
1 TATATATT
*
7536 TATA-CTT
1 TATATATT
7543 TATAT-TAT
1 TATATAT-T
*
7551 TATATATG
1 TATATATT
7559 TATATATGCT
1 TATATAT--T
*
7569 T-TATATG
1 TATATATT
*
7576 TATATATA
1 TATATATT
* *
7584 TAGTTTATA
1 TA-TATATT
*
7593 TATATATA
1 TATATATT
7601 TATATATT
1 TATATATT
7609 TATATACTT
1 TATATA-TT
7618 TATAT
1 TATAT
7623 TTAAACTATA
Statistics
Matches: 672, Mismatches: 103, Indels: 241
0.66 0.10 0.24
Matches are distributed among these distances:
6 45 0.07
7 135 0.20
8 225 0.33
9 168 0.25
10 72 0.11
11 22 0.03
12 5 0.01
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (8 bp):
TATATATT
Found at i:6756 original size:35 final size:35
Alignment explanation
Indices: 6716--7498 Score: 240
Period size: 35 Copynumber: 22.1 Consensus size: 35
6706 TTATAATTTG
6716 ATATATATAATTCTATATTTATATACTTTAATACTTT
1 ATATATAT-ATT-TATATTTATATACTTTAATACTTT
* *
6753 ATATTGTATATTTATA-TTATATAGTTTAATACTTTATATT
1 ATA-TATATATTTATATTTATATACTTTAATAC----T-TT
6793 ATATATTTATATTTATATTTATATACTTTAATACTTT
1 ATATA--TATATTTATATTTATATACTTTAATACTTT
6830 ATATGATATACTTTAATATTT-TATA-TTTAATAC-TT
1 ATAT-ATATA-TTT-ATATTTATATACTTTAATACTTT
* * *
6865 ATAT-TATAGTTTAATACTT-TATAGTAT-ATACTTT
1 ATATATATA-TTT-ATATTTATATACTTTAATACTTT
* *
6899 AATATATATATATATATATATATAAC-TT-ATACTTT
1 -ATATATATATTTATATTTATAT-ACTTTAATACTTT
*
6934 GTAGTATATACTTTAATAATTTA-ATAC-TT-ATAACTTAT
1 ATA-TATATA-TTT-AT-ATTTATATACTTTAAT-ACTT-T
* * * *
6972 ATATATATATATATACTTATATA-TTTTATA-TAT
1 ATATATATATTTATATTTATATACTTTAATACTTT
* *
7005 ATTTA-ATACTTTACA-TTATATAC--TAA-ACTTT
1 ATATATATA-TTTATATTTATATACTTTAATACTTT
* *
7036 ATATATATA--TATA-CT-TATACTTT-ATA-TGT
1 ATATATATATTTATATTTATATACTTTAATACTTT
*
7065 ATATATACT-TTTATA-TTATATAGTTTATATAC-TT
1 ATATATA-TATTTATATTTATATACTTTA-ATACTTT
* * *
7099 ATACT-T-TA--TATGTGTATATACTTTTATAC--T
1 ATA-TATATATTTATATTTATATACTTTAATACTTT
* *
7129 ATATAGT-T-TATATACTTATATACTTT-ATA-TTAT
1 ATATA-TATATTTATATTTATATACTTTAATACTT-T
* *
7162 ATACATTAATACTTTATA-TTATATACTTT-ATAGTTT
1 ATATA-T-ATA-TTTATATTTATATACTTTAATACTTT
*
7198 ATATATATATACTTATAGTTTATATA-TATACTAAAACTTT
1 ATATATATAT--TTATA-TTTATATACT-T--TAATACTTT
* *
7238 ATATATATATATATATATATATATA-TATATATACTTT
1 ATATATATAT-T-TATATTTATATACTTTA-ATACTTT
* *
7275 ATAGTTTATATATATATACTTATATACTTT-ATA--TT
1 ATA---TATATATTTATATTTATATACTTTAATACTTT
*
7310 ATATACTAAAACTTTATAGTTTATATA---T-ATAC-TT
1 ATATA-T-ATA-TTTATA-TTTATATACTTTAATACTTT
*
7344 ATATACTTATATTTAATACTTATATA-TATTATATAC-TT
1 ATATA--TATATTT-ATATTTATATACT-TTA-ATACTTT
* *
7382 ATATACTTTATATTATATGCTTATATACTTTAGT-CTTT
1 ATATA-TATAT-TTATAT--TTATATACTTTAATACTTT
* * *
7420 ATAATTATACTTTTTATATGTATATA--AT-ATACTTAT
1 AT-A-TATA-TATTTATATTTATATACTTTAATACTT-T
* *
7456 ACTTTATAGTATTATATATGTATATACTTTATATAC-TT
1 A-TATATA-TATT-TATATTTATATACTTTA-ATACTTT
7494 ATATA
1 ATATA
7499 CTTTATAATT
Statistics
Matches: 576, Mismatches: 72, Indels: 196
0.68 0.09 0.23
Matches are distributed among these distances:
28 5 0.01
29 15 0.03
30 8 0.01
31 25 0.04
32 45 0.08
33 52 0.09
34 41 0.07
35 82 0.14
36 77 0.13
37 78 0.14
38 50 0.09
39 33 0.06
40 40 0.07
41 10 0.02
42 15 0.03
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (35 bp):
ATATATATATTTATATTTATATACTTTAATACTTT
Found at i:6768 original size:13 final size:12
Alignment explanation
Indices: 6750--7399 Score: 127
Period size: 14 Copynumber: 48.6 Consensus size: 12
6740 ACTTTAATAC
6750 TTTATATTGTATA
1 TTTATATT-TATA
6763 TTTATATTATATA
1 TTTATATT-TATA
6776 GTTTAATACTTTATA
1 -TTT-ATA-TTTATA
6791 TTATATATTTATA
1 TT-TATATTTATA
6804 TTTATATTTATATA
1 TTTATA-TT-TATA
6818 CTTTAATACTTTATA
1 -TTT-ATA-TTTATA
*
6833 TGATATACTTTAATA
1 T-TTATA-TTT-ATA
6848 TTTTATATTTAATA
1 -TTTATATTT-ATA
*
6862 CTTATA-TTATA
1 TTTATATTTATA
6873 GTTTAATACTTTATA
1 -TTT-ATA-TTTATA
*
6888 GTATATACTTTA-A
1 -TTTATA-TTTATA
* *
6901 TATATATATATA
1 TTTATATTTATA
* *
6913 TATATATATA-A
1 TTTATATTTATA
* *
6924 CTTATACTTTGTA
1 TTTATA-TTTATA
*
6937 GTATATACTTTAATAA
1 -TTTATA-TTT-AT-A
*
6953 TTTAATACTTATAA
1 TTT-ATATTTAT-A
*
6967 CTTATATATATATA
1 -TT-TATATTTATA
*
6981 TATATACTTATATA
1 TTTATA-TT-TATA
*
6995 TTT-TATATATA
1 TTTATATTTATA
*
7006 TTTAATACTTTACA
1 TTT-ATA-TTTATA
* *
7020 -TTATATACTAAA
1 TTTATAT-TTATA
7032 CTTTATA--TATA
1 -TTTATATTTATA
* *
7043 TATATACTTATA
1 TTTATATTTATA
*
7055 CTTTATATGTATA
1 -TTTATATTTATA
*
7068 TATACT-TTTATA
1 TTTA-TATTTATA
7080 TTATATAGTTTATA
1 TT-TATA-TTTATA
7094 TACTTATACTTTATA
1 T--TTATA-TTTATA
* * *
7109 TGTGTATATACT-
1 TTTATATTTA-TA
*
7121 TTTATACTATATA
1 TTTATA-TTTATA
7134 GTTTATATACTTATATA
1 --TT-TATA-TT-TATA
7151 CTTTATATTATATACA
1 -TTTATATT-TAT--A
*
7167 TTAATACTTTATA
1 TTTATA-TTTATA
7180 TTATATACTTTATA
1 TT-TATA-TTTATA
7194 GTTTATATATATATA
1 -TTTATAT-T-TATA
*
7209 CTTATAGTTTATA
1 TTTATA-TTTATA
* * * *
7222 TATATACTAAAA
1 TTTATATTTATA
*
7234 CTTTATATATATA
1 -TTTATATTTATA
* *
7247 TATATATATATA
1 TTTATATTTATA
* *
7259 TATATATATATA
1 TTTATATTTATA
7271 CTTTATAGTTTATA
1 -TTTATA-TTTATA
7285 TATATATACTTATATA
1 T-T-TATA-TT-TATA
7301 CTTTATATTATATA
1 -TTTATATT-TATA
* * *
7315 CTAAAACTTTATA
1 TTTATA-TTTATA
*
7328 GTTTATATATATA
1 -TTTATATTTATA
*
7341 CTTATATACTTATA
1 -TT-TATATTTATA
*
7355 TTTAATACTTATA
1 TTT-ATATTTATA
7368 --TATATTATATA
1 TTTATATT-TATA
7379 CTTATATACTTTATA
1 -TT-TATA-TTTATA
7394 -TTATAT
1 TTTATAT
7400 GCTTATATAC
Statistics
Matches: 493, Mismatches: 71, Indels: 148
0.69 0.10 0.21
Matches are distributed among these distances:
10 9 0.02
11 28 0.06
12 91 0.18
13 111 0.23
14 123 0.25
15 94 0.19
16 32 0.06
17 5 0.01
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (12 bp):
TTTATATTTATA
Found at i:6839 original size:64 final size:64
Alignment explanation
Indices: 6763--7490 Score: 371
Period size: 64 Copynumber: 11.1 Consensus size: 64
6753 ATATTGTATA
6763 TTTATATTATATAGTTTAATACTTTATAT-TATATATTTATA-TTTATATTTATATACTTTAATA
1 TTTATA-TATATA-TTTAATACTTTATATATATATATTTATACTTTATATTTATATACTTTAATA
6826 C
64 C
* * *
6827 TTTATATGATATACTTTAATATTTTATATTTA-ATACTTATA--TTATAGTTTA-ATACTTT-AT
1 TTTATAT-ATATA-TTTAATACTTTATATATATATATTTATACTTTATA-TTTATATACTTTAAT
*
6887 AG
63 AC
* * * * * * *
6889 TATATACTTTA-ATATATATA-TATATATATATATAACTTATACTTTGTA-GTATATACTTTAAT
1 TTTATA-TATATATTTA-ATACTTTATATATATAT-ATTTATACTTTATATTTATATACTTTAAT
*
6951 AA
63 AC
* *
6953 TTTA-ATACT-TA--T-A-AC-TTATATATATATATATATACTTATATATTTTATATATATTTAA
1 TTTATATA-TATATTTAATACTTTATATATATATATTTATACTT-TATA-TTTATATA-CTTTAA
7011 TAC
62 TAC
* * *
7014 TTTACAT-TATATACTAA-ACTTTATATATATATATACTTATACTTTATATGTATATATACTTTT
1 TTTATATATATAT-TTAATACTTTATATATATATAT--TTATACTTTATAT-T-TATATACTTTA
7077 ATA-
61 ATAC
* * *
7080 TTATATAGTTTATATACTT-ATACTTTATATGTGTATATACTTTTATACTATATAGTTTATATAC
1 TT-TATA---TATATATTTAATACTTTATA--TATATATA--TTTATACTTTATA-TTTATATAC
7144 -TTATATAC
57 TTTA-ATAC
* * *
7152 TTTATATTATATACATTAATACTTTATAT-TATATACTTTATAGTTTATATATATATAC-TT-AT
1 TTTATA-TATATA-TTTAATACTTTATATATATATA-TTTATACTTTATATTTATATACTTTAAT
*
7214 AG
63 AC
* * * *
7216 TTTATATATATA-CTAAAACTTTATATATATATATATATATA-TATATATATATATACTTT-ATA
1 TTTATATATATATTTAATACTTTATATATATATAT-T-TATACTTTATATTTATATACTTTAATA
*
7278 G
64 C
* * *
7279 TTTATATATATATACTTATATACTTTATAT-TATATACTAAAACTTTATAGTTTATATA---T-A
1 TTTATATATATAT--TTA-ATACTTTATATATATATATTTATACTTTATA-TTTATATACTTTAA
7339 TAC
62 TAC
*
7342 -TTATATACTTATATTTAATACTTATATATATTATATACTTATATACTTTATA-TTATATGC-TT
1 TTTATATA--TATATTTAATACTT-TATATA-TATATA-TT-TATACTTTATATTTATATACTTT
7404 ATATAC
60 A-ATAC
* * *
7410 TTTAGTCTTTATAATT-ATACTTTTTATATGTATATAATATACTTATACTTTATAGTATTATATA
1 TTTA-TATATATATTTAATAC--TTTATA--TATAT-ATAT--TTATACTTTATA-T-TTATATA
*
7474 -TGTATATAC
56 CTTTA-ATAC
7483 TTTATATA
1 TTTATATA
7491 CTTATATACT
Statistics
Matches: 528, Mismatches: 58, Indels: 148
0.72 0.08 0.20
Matches are distributed among these distances:
57 8 0.02
58 15 0.03
59 1 0.00
60 18 0.03
61 39 0.07
62 58 0.11
63 56 0.11
64 76 0.14
65 12 0.02
66 52 0.10
67 39 0.07
68 33 0.06
69 18 0.03
70 32 0.06
71 29 0.05
72 23 0.04
73 18 0.03
74 1 0.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (64 bp):
TTTATATATATATTTAATACTTTATATATATATATTTATACTTTATATTTATATACTTTAATAC
Found at i:6976 original size:2 final size:2
Alignment explanation
Indices: 6969--7614 Score: 128
Period size: 2 Copynumber: 318.0 Consensus size: 2
6959 ACTTATAACT
* *
6969 TA TA TA TA TA TA TA TA TA CT- TA TA TA T- TT TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
7010 -A TA CTT TA CA T- TA TA TA CTA AA CTT TA TA TA TA TA TA TA CT-
1 TA TA -TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA -TA
* * * *
7051 TA TA CTT TA TA TG TA TA TA TA CT- TT TA TA T- TA TA TA GTT TA
1 TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA
* * * *
7092 TA TA CT- TA TA CTT TA TA TG TG TA TA TA CT- TT TA TA CTA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA
* * *
7134 GTT TA TA TA CT- TA TA TA CTT TA TA T- TA TA TA CA T- TA -A TA
1 -TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * *
7173 CTT TA TA T- TA TA TA CTT TA TA GTT TA TA TA TA TA TA CT- TA TA
1 -TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA -TA TA TA
* * *
7215 GTT TA TA TA TA TA CTA -A AA CTT TA TA TA TA TA TA TA TA TA TA
1 -TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* *
7257 TA TA TA TA TA TA TA CTT TA TA GTT TA TA TA TA TA TA CT- TA TA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA -TA TA TA
* * * *
7299 TA CTT TA TA T- TA TA TA CTA -A AA CTT TA TA GTT TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA
*
7341 CT- TA TA TA CT- TA TA TT TA -A TA CT- TA TA TA TA T- TA TA TA
1 -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * *
7379 CT- TA TA TA CTT TA TA T- TA TA TGC T- TA TA TA CTT TA GTC TT TA
1 -TA TA TA TA -TA TA TA TA TA TA T-A TA TA TA TA -TA TA -TA TA TA
* * * *
7421 TA -A T- TA TA CTT TT TA TA TG TA TA TA -A TA TA CT- TA TA CTT
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * *
7460 TA TA GTA T- TA TA TA TG TA TA TA CTT TA TA TA CT- TA TA TA CTT
1 TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA -TA
* *
7502 TA TA -A T- TA GA CTA TA TA TA TA TA TA TA -A TA TA CT- TA TA CTT
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * * *
7543 TA TA T- TA T- TA TA TA TG TA TA TA TGC TT TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
* *
7584 TA GTT TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7615 CTTTATATTT
Statistics
Matches: 468, Mismatches: 88, Indels: 176
0.64 0.12 0.24
Matches are distributed among these distances:
1 39 0.08
2 378 0.81
3 51 0.11
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7093 original size:7 final size:6
Alignment explanation
Indices: 7039--7399 Score: 75
Period size: 7 Copynumber: 53.8 Consensus size: 6
7029 AAACTTTATA
* * * *
7039 TATATA TATACT TATACTT TATATG TATATA TACT-TT TATATT ATATAGTT
1 TATATT TATATT TATA-TT TATATT TATATT TA-TATT TATATT -TATA-TT
* * * *
7090 TATATACT TATACTT TATATG TGTATA TACT-TT TATACTA TATAGTTT
1 TATAT--T TATA-TT TATATT TATATT TA-TATT TATA-TT TATA--TT
*
7138 ATATACTT ATATACTT TATATT ATATACATT AATACTT TATATT ATATACTT
1 -TATA-TT -TATA-TT TATATT -TAT--ATT TATA-TT TATATT -TATA-TT
* * * * * *
7190 TATAGTT TATATAT ATATACT TATAGTT TATATA TATACT AAAACTT TATATA
1 TATA-TT TATAT-T -TATATT TATA-TT TATATT TATATT TATA-TT TATATT
* * * *
7243 TATATA TATATA TATATA TATATA TATACTT TATAGTT TATATAT ATATACTT
1 TATATT TATATT TATATT TATATT TATA-TT TATA-TT TATAT-T -TATA-TT
* * * *
7296 ATATACTT TATATT ATATACT AAAACTT TATAGTT TATATA TATACTT
1 -TATA-TT TATATT -TATATT TATA-TT TATA-TT TATATT TATA-TT
* *
7344 ATATACT TATATT TAATACT TATA-- TATATT ATATACTT ATATACTT
1 -TATATT TATATT T-ATATT TATATT TATATT -TATA-TT -TATA-TT
7390 TATA-T TATAT
1 TATATT TATAT
7400 GCTTATATAC
Statistics
Matches: 275, Mismatches: 43, Indels: 74
0.70 0.11 0.19
Matches are distributed among these distances:
4 4 0.01
5 7 0.03
6 96 0.35
7 106 0.39
8 53 0.19
9 9 0.03
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.52
Consensus pattern (6 bp):
TATATT
Found at i:7427 original size:22 final size:22
Alignment explanation
Indices: 6729--7613 Score: 431
Period size: 22 Copynumber: 40.9 Consensus size: 22
6719 TATATAATTC
*
6729 TATATTTATATACTTTAATACTT-
1 TATACTTATATACTTT-ATA-TTA
*
6752 TATA-TTGTATA-TTTATATTA
1 TATACTTATATACTTTATATTA
*
6772 TATAGTT-TAATACTTTATATTA
1 TATACTTAT-ATACTTTATATTA
6794 TATA-TT-TATA-TTTATATTTA
1 TATACTTATATACTTTATA-TTA
*
6814 TATACTT-TAATACTTTATATGA
1 TATACTTAT-ATACTTTATATTA
*
6836 TATACTT-TAATATTTTATATT-
1 TATACTTAT-ATACTTTATATTA
*
6857 TAATACTTATATTATAGTTTAATACTT-
1 T-ATAC-T-TA-TATACTTT-ATA-TTA
*
6884 TATA-GTATATACTTTA-A-TA
1 TATACTTATATACTTTATATTA
*
6903 TATA--TATATA-TATATA-TA
1 TATACTTATATACTTTATATTA
* *
6921 TA-ACTTAT--ACTTTGTAGTA
1 TATACTTATATACTTTATATTA
*
6940 TATACTT-TAATAATTTAATACTTA
1 TATACTTAT-ATACTTT-ATA-TTA
*
6964 TA-ACTTATATA-TATATA-TA
1 TATACTTATATACTTTATATTA
6983 TATACTTATATA-TTT-TA-TA
1 TATACTTATATACTTTATATTA
* *
7002 TATATTTA-ATACTTTACATTA
1 TATACTTATATACTTTATATTA
7023 TATAC-TA-A-ACTTTATA-TA
1 TATACTTATATACTTTATATTA
7041 TATA-TATACTTATACTTTATATGTATA
1 TATACT-TA--TATACTTTATA--T-TA
*
7068 TATACTTTTATA-TTATATAGTTTA
1 TATACTTATATACTT-TATA--TTA
7092 TATAC-T-TATACTTTATATGTGTA
1 TATACTTATATACTTTATA--T-TA
* *
7115 TATACTTTTATACTATATAGTTTA
1 TATACTTATATACTTTATA--TTA
7139 TATACTTATATACTTTATATTA
1 TATACTTATATACTTTATATTA
7161 TATACATTA-ATACTTTATATTA
1 TATAC-TTATATACTTTATATTA
*
7183 TATACTT-TATAGTTTATATATA
1 TATACTTATATACTTTATAT-TA
*
7205 TATAC-T-TATAGTTTATA-TA
1 TATACTTATATACTTTATATTA
*
7224 TATAC-TA-AAACTTTATATATA
1 TATACTTATATACTTTATAT-TA
*
7245 TATA-TATATATA-TATATATATA
1 TATACT-TATATACTTTATAT-TA
*
7267 TATACTT-TATAGTTTATATATA
1 TATACTTATATACTTTATAT-TA
7289 TATACTTATATACTTTATATTA
1 TATACTTATATACTTTATATTA
*
7311 TATAC-TA-AAACTTTATAGTT-
1 TATACTTATATACTTTATA-TTA
7331 TATA--TATATACTTATATACTTA
1 TATACTTATATACTT-TATA-TTA
7353 TAT--TTA-ATACTTATATATATTA
1 TATACTTATATAC-T-T-TATATTA
7375 TATACTTATATACTTTATATTA
1 TATACTTATATACTTTATATTA
* *
7397 TATGCTTATATACTTTAGTCTT-
1 TATACTTATATACTTTA-TATTA
* *
7419 TATAATTATACT-TTTTATATGTA
1 TATACTTATA-TACTTTATAT-TA
7442 TATA---ATATAC-TTATACTTTA
1 TATACTTATATACTTTATA--TTA
7462 TAGTA-TTATATA-TGTATATACTTTA
1 TA-TACTTATATACT-T-TATA--TTA
*
7487 TATACTTATATACTTTATAAT-
1 TATACTTATATACTTTATATTA
* * *
7508 TAGACTATATATA-TATATATAA
1 TATACT-TATATACTTTATATTA
7530 TATAC-T-TATACTTTATATTA
1 TATACTTATATACTTTATATTA
* *
7550 TTATATATGTATATATGCTTTATA-TG
1 -TATA-CT-TATATA--CTTTATATTA
*
7576 TATA--TATATAGTTTATA-TA
1 TATACTTATATACTTTATATTA
7595 TATA-TATATATA-TTTATAT
1 TATACT-TATATACTTTATAT
7614 ACTTTATATT
Statistics
Matches: 706, Mismatches: 58, Indels: 198
0.73 0.06 0.21
Matches are distributed among these distances:
17 5 0.01
18 25 0.04
19 86 0.12
20 77 0.11
21 104 0.15
22 201 0.28
23 77 0.11
24 47 0.07
25 57 0.08
26 9 0.01
27 17 0.02
28 1 0.00
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (22 bp):
TATACTTATATACTTTATATTA
Found at i:7530 original size:83 final size:81
Alignment explanation
Indices: 7375--7574 Score: 257
Period size: 83 Copynumber: 2.4 Consensus size: 81
7365 ATATATATTA
* * * *
7375 TATAC-TTATATACTT-TATAT-TATATGC-TTATATACTTTAGTCTTTATAATTATACTTTTTA
1 TATACTTTATATA-TTATATATGTATATACTTTATATACTTTAGTCTTTATAATTAGACTATATA
*
7436 TATGTATATAATATACT
65 TATATATATAATATACT
7453 TATACTTTATAGTATTATATATGTATATACTTTATATACTTATA-TACTTTATAATTAGACTATA
1 TATACTTTATA-TATTATATATGTATATACTTTATATACTT-TAGT-CTTTATAATTAGACTATA
7517 TATATATATATAATATACT
63 TATATATATATAATATACT
7536 TATACTTTATATTATTATATATGTATATATGCTTTATAT
1 TATACTTTATA-TATTATATATGTATATA--CTTTATAT
7575 GTATATATAT
Statistics
Matches: 107, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
78 5 0.05
79 7 0.07
80 7 0.07
81 6 0.06
82 11 0.10
83 63 0.59
85 8 0.07
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (81 bp):
TATACTTTATATATTATATATGTATATACTTTATATACTTTAGTCTTTATAATTAGACTATATAT
ATATATATAATATACT
Found at i:7634 original size:22 final size:21
Alignment explanation
Indices: 7609--7662 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
7599 TATATATATT
*
7609 TATATACTTTATATT-TAAAC
1 TATATAATTTATATTATAAAC
7629 TATATAATTTATATTAATAAAC
1 TATATAATTTATATT-ATAAAC
*
7651 TATATAGTTTAT
1 TATATAATTTAT
7663 GATGTAAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 14 0.47
22 16 0.53
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.50
Consensus pattern (21 bp):
TATATAATTTATATTATAAAC
Found at i:7638 original size:29 final size:29
Alignment explanation
Indices: 7570--7642 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
7560 ATATATGCTT
* * * *
7570 TATATGTATATATATAGTTTATATATATA
1 TATATATATTTATATACTTTATATATAAA
*
7599 TATATATATTTATATACTTTATATTTAAA
1 TATATATATTTATATACTTTATATATAAA
7628 CTATATA-ATTTATAT
1 -TATATATATTTATAT
7643 TAATAAACTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 32 0.84
30 6 0.16
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (29 bp):
TATATATATTTATATACTTTATATATAAA
Found at i:8455 original size:13 final size:13
Alignment explanation
Indices: 8435--8469 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
8425 AGTTCTAGGG
8435 AGCCTTGTGGTGT
1 AGCCTTGTGGTGT
*
8448 ATCCTTGTGGTGT
1 AGCCTTGTGGTGT
8461 AGCCTTGTG
1 AGCCTTGTG
8470 CATGGGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.09, C:0.17, G:0.34, T:0.40
Consensus pattern (13 bp):
AGCCTTGTGGTGT
Found at i:16058 original size:17 final size:17
Alignment explanation
Indices: 16038--16074 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
16028 AATCGGATCG
*
16038 GGTCGGTTATCGGGTCA
1 GGTCGGTTATCGAGTCA
16055 GGTCGGTTATCGAGTCA
1 GGTCGGTTATCGAGTCA
16072 GGT
1 GGT
16075 AAATTTTCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.14, C:0.16, G:0.41, T:0.30
Consensus pattern (17 bp):
GGTCGGTTATCGAGTCA
Found at i:16181 original size:32 final size:31
Alignment explanation
Indices: 16135--16208 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 31
16125 ACATCAGATA
16135 GGTTGATTTTTGGGTCGAGTCAATATCAAATC
1 GGTTGA-TTTTGGGTCGAGTCAATATCAAATC
*
16167 GGTTAGATTTTGGGTCGAGTCAATATCAAATT
1 GGTT-GATTTTGGGTCGAGTCAATATCAAATC
16199 GGTTGATTTT
1 GGTTGATTTT
16209 CGGTTTAGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
31 6 0.15
32 32 0.80
33 2 0.05
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (31 bp):
GGTTGATTTTGGGTCGAGTCAATATCAAATC
Found at i:21233 original size:67 final size:67
Alignment explanation
Indices: 21157--21291 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
21147 CAAATTGGCT
21157 AACACTTAATTTAGTCTTAAAAAATCAGTTTAATTTTGAGTCATATTCAACTGAGAAAAGGATCC
1 AACACTTAATTTAGTCTTAAAAAATCAGTTTAATTTTGAGTCATATTCAACTGAGAAAAGGATCC
21222 CG
66 CG
21224 AACACTTAATTTAGTCTTAAAAAATCAGTTTAATTTTGAGTCATATTCAACTGAGAAAAGGATCC
1 AACACTTAATTTAGTCTTAAAAAATCAGTTTAATTTTGAGTCATATTCAACTGAGAAAAGGATCC
21289 CG
66 CG
21291 A
1 A
21292 GACAAAATAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (67 bp):
AACACTTAATTTAGTCTTAAAAAATCAGTTTAATTTTGAGTCATATTCAACTGAGAAAAGGATCC
CG
Found at i:23127 original size:3 final size:3
Alignment explanation
Indices: 23121--23167 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
23111 TATCATTATT
*
23121 ATA ATA ATA ATA ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
23168 TATTATTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:24605 original size:28 final size:27
Alignment explanation
Indices: 24531--24606 Score: 64
Period size: 29 Copynumber: 2.7 Consensus size: 27
24521 GTTCTAATTG
** *
24531 TATTTTTATTATTGTT-TATTTATGTTT
1 TATTTTTATTATT-TTATATTTAAATAT
* *
24558 TAATTTTACTTGTTTATATATTTAAATAT
1 TATTTTTA-TTATTT-TATATTTAAATAT
24587 TATTTTTATTATTATTATAT
1 TATTTTTATTATT-TTATAT
24607 AGTCATATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
27 8 0.21
28 14 0.37
29 16 0.42
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (27 bp):
TATTTTTATTATTTTATATTTAAATAT
Found at i:29550 original size:29 final size:29
Alignment explanation
Indices: 29486--29543 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
29476 CAATAGACTG
29486 AAATAAATACAACATACAAATTAGAAACC
1 AAATAAATACAACATACAAATTAGAAACC
*
29515 AAATAAATACAAGATACAAATTAGAAACC
1 AAATAAATACAACATACAAATTAGAAACC
29544 GATTAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.17
Consensus pattern (29 bp):
AAATAAATACAACATACAAATTAGAAACC
Found at i:40387 original size:12 final size:11
Alignment explanation
Indices: 40370--40410 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
40360 TATTATGCTT
*
40370 AAAAAAATGAGG
1 AAAAAAA-GAAG
40382 AAAAAAAGAAG
1 AAAAAAAGAAG
*
40393 AAAAAAAAAAG
1 AAAAAAAGAAG
40404 AAAAAAA
1 AAAAAAA
40411 AAGGGTCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 20 0.74
12 7 0.26
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:40399 original size:14 final size:13
Alignment explanation
Indices: 40382--40412 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
40372 AAAAATGAGG
40382 AAAAAAAGAAGAAA
1 AAAAAAAGAA-AAA
40396 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
40409 AAAA
1 AAAA
40413 GGGTCAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAA
Found at i:40804 original size:19 final size:17
Alignment explanation
Indices: 40762--40810 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
40752 TATTTTCTCT
40762 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTG
*
40778 AGATTCAATTTATTTTCG
1 AAATTCAATTTATTTT-G
*
40796 AAAATTCAACTTATT
1 -AAATTCAATTTATT
40811 CTTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.41
17 3 0.11
18 1 0.04
19 12 0.44
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTATTTTG
Found at i:41303 original size:114 final size:114
Alignment explanation
Indices: 41103--41328 Score: 346
Period size: 114 Copynumber: 2.0 Consensus size: 114
41093 AAGTGCTACG
*
41103 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGATC
** * * * *
41168 CGATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATT
66 CGATTCAGTAAGAACCACAAAACCAATCATTGGAATTGAAAGATGAATT
*
41217 TGCTCATAGTAGAAATAA-AATGACCCAATAGCATCTTCTGGAAGTTTTCTTTGAGTCATCTGAT
1 TGCTCATAGTAGAAATAAGAA-GACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGAT
* *
41281 CTGGTTCAGTAAGAACCACAAAACCAATCATTGGAATTGAAAGATGAA
65 CCGATTCAGTAAGAACCACAAAACCAATCATTGGAATTGAAAGATGAA
41329 CTGCATGATC
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
113 2 0.02
114 99 0.98
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGATC
CGATTCAGTAAGAACCACAAAACCAATCATTGGAATTGAAAGATGAATT
Found at i:42259 original size:113 final size:113
Alignment explanation
Indices: 42061--42433 Score: 640
Period size: 113 Copynumber: 3.3 Consensus size: 113
42051 AGTTCATAAT
*
42061 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTTTTCAACTTTTTGCTCAAATCCATCACTTG
1 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCACTTG
*
42126 ATGGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTG
66 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
*
42174 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAATTTTTGCTCAAATCCATCACTTG
1 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCACTTG
*
42239 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
66 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* * * * *
42287 AAGAATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATCCATCACTTG
1 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCACTTG
42352 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
66 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
*
42400 AAGAAGAAAG-AGAAAGTTCATAATGAGAAGAACT
1 AAGAAGGAAGAAG-AAGTTCATAATGAGAAGAACT
42434 CATCTGAAGA
Statistics
Matches: 245, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
112 2 0.01
113 243 0.99
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (113 bp):
AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCACTTG
ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
Found at i:42423 original size:40 final size:40
Alignment explanation
Indices: 42368--42471 Score: 183
Period size: 40 Copynumber: 2.6 Consensus size: 40
42358 CAACTTTTCC
42368 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
*
42408 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
42448 AGA-AGAAGTTCATAATGAGAAGAA
1 AGAGA-AAGTTCATAATGAGAAGAA
42472 TTTGTTCAAC
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
39 1 0.02
40 61 0.98
ACGTcount: A:0.50, C:0.09, G:0.24, T:0.17
Consensus pattern (40 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
Found at i:42443 original size:153 final size:153
Alignment explanation
Indices: 42255--42584 Score: 590
Period size: 153 Copynumber: 2.2 Consensus size: 153
42245 CAGCTTTTCC
*
42255 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
* *
42320 TTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATG
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATG
42385 AGAAGAACTCATCTGAAGAAGAA
131 AGAAGAACTCATCTGAAGAAGAA
42408 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
* *
42473 TTGTTCAACTTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATG
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATG
*
42538 AGAAGAACTCATCTGAAGAAGGA
131 AGAAGAACTCATCTGAAGAAGAA
42561 AGA-AGAAGTTCATAATGAGAAGAA
1 AGAGA-AAGTTCATAATGAGAAGAA
42585 TTTGTTCAAC
Statistics
Matches: 170, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
152 1 0.01
153 169 0.99
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (153 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATG
AGAAGAACTCATCTGAAGAAGAA
Found at i:42531 original size:113 final size:113
Alignment explanation
Indices: 42408--42810 Score: 754
Period size: 113 Copynumber: 3.6 Consensus size: 113
42398 TGAAGAAGAA
42408 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
* * * *
42473 TTGTTCAACTTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCC
66 TTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCC
42521 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
42586 TTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCC
66 TTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCC
42634 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
42699 TTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCC
66 TTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCC
42747 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGAAAGTTCATAATGAGAAGAA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-AAGTTCATAATGAGAAGAA
42811 CTCATCTGAA
Statistics
Matches: 285, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
112 2 0.01
113 283 0.99
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (113 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
TTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCC
Found at i:42616 original size:266 final size:265
Alignment explanation
Indices: 42147--42965 Score: 1064
Period size: 266 Copynumber: 3.1 Consensus size: 265
42137 TTTCCAGAGA
*
42147 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA-TTGTT
*
42212 CAAATTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAG
65 CAACTTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAG
*
42277 AACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAAT
130 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAAT
*
42342 CCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
195 CCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
42407 AAG-AG
260 AAGAAG
42412 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 -AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA-TTGT
42477 TCAACTTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA
64 TCAACTTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA
42542 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAA
129 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAA
42607 TCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
194 TCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
42672 GAAGAAG
259 GAAGAAG
* ** * ****** *** * * * * * *
42679 AAGTTCATAATGAGAAGAATTTGT-TCAA-CCTTTTGTTTAAATCCATCACT----TG-ATGGAT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT-AATGAGAAGAATTGTT
* ** * * * * * * *****
42737 CAAC-TTTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAGAAAGTTCAT
65 CAACTTTTTGC--TCAAA-TCCATCACT-TGATGGA-TCAGCT----TTTCCAGAGAAAGTTCAT
* *
42800 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTT
121 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
* * *
42865 TGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATC
186 TGTTTAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATC
42930 TGAAGAAGGAAGAAG
251 TGAAGAAGGAAGAAG
*
42945 AAGTTCATAATGAGATGAACT
1 AAGTTCATAATGAGAAGAACT
42966 TGTTCAACCT
Statistics
Matches: 497, Mismatches: 45, Indels: 22
0.88 0.08 0.04
Matches are distributed among these distances:
258 5 0.01
259 7 0.01
260 6 0.01
261 9 0.02
262 5 0.01
264 7 0.01
265 5 0.01
266 451 0.91
267 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (265 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTGTTC
AACTTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGA
ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATC
CATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAG
Found at i:42760 original size:379 final size:379
Alignment explanation
Indices: 42061--43091 Score: 1884
Period size: 379 Copynumber: 2.7 Consensus size: 379
42051 AGTTCATAAT
42061 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTT-TTCAACTTTTTGCTCAAATCCATCACTT
1 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAA-TTTGTTCAACTTTTTGCTCAAATCCATCACTT
* *
42125 GATGGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
65 GATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
** * * *
42190 TTCATAATGAGAAGAACTTGTTCAAATTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCC
130 TTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCC
*
42255 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAAT
195 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
42320 TTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATG
260 TTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATG
42385 AGAAGAACTCATCTGAAGAAGAAAGAGAAAGTTCATAATGAGAAGAACTCATCTG
325 AGAAGAACTCATCTGAAGAAGAAAGAGAAAGTTCATAATGAGAAGAACTCATCTG
42440 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTG
1 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTG
42505 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
66 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
42570 TCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCCA
131 TCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCCA
42635 GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATT
196 GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATT
42700 TGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGA
261 TGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGA
*
42765 GAAGAACTCATCTGAAGAAGGAAGAGAAAGTTCATAATGAGAAGAACTCATCTG
326 GAAGAACTCATCTGAAGAAGAAAGAGAAAGTTCATAATGAGAAGAACTCATCTG
*
42819 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCACTTG
1 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTG
42884 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
66 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* *
42949 TCATAATGAGATGAACTTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTACA
131 TCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCCA
* * **
43014 GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAAAAGAGCT
196 GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATT
*
43079 TATTCAACCTTTT
261 TGTTCAACCTTTT
43092 AAACGACTCT
Statistics
Matches: 632, Mismatches: 19, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
378 3 0.00
379 629 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (379 bp):
AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTG
ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCCA
GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATT
TGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGA
GAAGAACTCATCTGAAGAAGAAAGAGAAAGTTCATAATGAGAAGAACTCATCTG
Found at i:42802 original size:40 final size:40
Alignment explanation
Indices: 42747--42852 Score: 196
Period size: 40 Copynumber: 2.6 Consensus size: 40
42737 CAACTTTTCC
42747 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
42787 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
42827 AGA-AGAAGTTCATAATGAGAAGAACT
1 AGAGA-AAGTTCATAATGAGAAGAACT
42853 TGTTCAACTT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
39 1 0.02
40 64 0.98
ACGTcount: A:0.48, C:0.09, G:0.25, T:0.18
Consensus pattern (40 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
Found at i:42822 original size:153 final size:153
Alignment explanation
Indices: 42634--42965 Score: 594
Period size: 153 Copynumber: 2.2 Consensus size: 153
42624 CAACTTTTCC
*
42634 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* *
42699 TTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATG
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATG
42764 AGAAGAACTCATCTGAAGAAGGA
131 AGAAGAACTCATCTGAAGAAGGA
42787 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* *
42852 TTGTTCAACTTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATG
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATG
42917 AGAAGAACTCATCTGAAGAAGGA
131 AGAAGAACTCATCTGAAGAAGGA
*
42940 AGA-AGAAGTTCATAATGAGATGAACT
1 AGAGA-AAGTTCATAATGAGAAGAACT
42966 TGTTCAACCT
Statistics
Matches: 172, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
152 1 0.01
153 171 0.99
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (153 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATG
AGAAGAACTCATCTGAAGAAGGA
Found at i:42916 original size:113 final size:113
Alignment explanation
Indices: 42787--43091 Score: 520
Period size: 113 Copynumber: 2.7 Consensus size: 113
42777 TGAAGAAGGA
42787 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* * *
42852 TTGTTCAACTTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCC
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTAC
*
42900 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGATGAAC
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* *
42965 TTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTAC
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTAC
* * *
43013 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAAAAGAGC
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
*
43078 TTATTCAACCTTTT
66 TTGTTCAACCTTTT
43092 AAACGACTCT
Statistics
Matches: 181, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
113 181 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (113 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTAC
Found at i:42995 original size:266 final size:266
Alignment explanation
Indices: 42255--43075 Score: 1027
Period size: 266 Copynumber: 3.1 Consensus size: 266
42245 CAGCTTTTCC
* *
42255 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* *
42320 TTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATG
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATG
* ** * ******
42385 AGAAGAACTCATCTGAAGAAGAAAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
131 AGAAGAACTCATCTGAAGAAGGAAGAAG-AAGTTCATAATGAGAAGAACTTGT-TCAA-CCTTTT
*** * * * * * * * ** * * * * *
42449 GAAGAAGTTCAT-AATGAGAAGAATTTGTTCAACTTTT--TGCTCAAA-TCCATCACT-TGATGG
193 GTTTAAATCCATCACT----TG-A-TGGATCAACTTTTACAG-AGAAAGTTCAT-AATGAGAAGA
* *****
42509 A-TCAGCT----TTTCC
250 ACTCATCTGAAGAAGAA
*
42521 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* *
42586 TTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATG
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATG
*
42651 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTT
131 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTT
*
42716 TAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
196 TAAATCCATCACTTGATGGATCAACTTTTACAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
42781 GAAGGA
261 GAAGAA
42787 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* *
42852 TTGTTCAACTTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATG
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATG
*
42917 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGATGAACTTGTTCAACCTTTTGTT
131 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTT
42982 TAAATCCATCACTTGATGGATCAACTTTTACAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
196 TAAATCCATCACTTGATGGATCAACTTTTACAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
43047 GAAGAA
261 GAAGAA
*
43053 AGA-AGAAGTTCATAATGAAAAGA
1 AGAGA-AAGTTCATAATGAGAAGA
43076 GCTTATTCAA
Statistics
Matches: 498, Mismatches: 45, Indels: 24
0.88 0.08 0.04
Matches are distributed among these distances:
259 11 0.02
260 6 0.01
261 10 0.02
262 5 0.01
264 7 0.01
265 6 0.01
266 451 0.91
267 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (266 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATG
AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTT
TAAATCCATCACTTGATGGATCAACTTTTACAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGAA
Found at i:43389 original size:30 final size:30
Alignment explanation
Indices: 43318--43399 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 30
43308 TTTTCATTTA
* *
43318 AATATTATTTAT-ATTATCATTATTATTAT
1 AATATTATTAATAATTATTATTATTATTAT
* *
43347 AATAATAATAATAATTATTATTATTATTAT
1 AATATTATTAATAATTATTATTATTATTAT
** *
43377 TTTATTATTAATAAATATTATTA
1 AATATTATTAATAATTATTATTA
43400 CATGCCCAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 9 0.21
30 34 0.79
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (30 bp):
AATATTATTAATAATTATTATTATTATTAT
Found at i:43399 original size:3 final size:3
Alignment explanation
Indices: 43320--43386 Score: 57
Period size: 3 Copynumber: 22.7 Consensus size: 3
43310 TTCATTTAAA
* * * * * *
43320 TAT TAT T-T ATAT TAT CAT TAT TAT TAT AAT AAT AAT AAT AAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
43365 TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
43387 ATAAATATTA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 3 0.05
3 53 0.93
4 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:44800 original size:28 final size:27
Alignment explanation
Indices: 44726--44801 Score: 64
Period size: 29 Copynumber: 2.7 Consensus size: 27
44716 GTTCTAATTG
** *
44726 TATTTTTATTATTGTT-TATTTATGTTT
1 TATTTTTATTATT-TTATATTTAAATAT
* *
44753 TAATTTTACTTGTTTATATATTTAAATAT
1 TATTTTTA-TTATTT-TATATTTAAATAT
44782 TATTTTTATTATTATTATAT
1 TATTTTTATTATT-TTATAT
44802 AGTCATATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
27 8 0.21
28 14 0.37
29 16 0.42
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (27 bp):
TATTTTTATTATTTTATATTTAAATAT
Found at i:46053 original size:16 final size:16
Alignment explanation
Indices: 46012--46053 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
46002 ACAGAGCCTC
*
46012 TGAATCATTAAGCATT
1 TGAATCATTCAGCATT
46028 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
46044 TGAATCATTC
1 TGAATCATTC
46054 TAAAGTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:46172 original size:2 final size:2
Alignment explanation
Indices: 46165--46197 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
46155 TGAGTTAGTG
46165 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
46198 CTTTTTCCTG
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:47909 original size:2 final size:2
Alignment explanation
Indices: 47904--47943 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
47894 ACACACACAA
47904 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
47944 TTCAAATAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62373 original size:46 final size:46
Alignment explanation
Indices: 62323--62419 Score: 142
Period size: 46 Copynumber: 2.1 Consensus size: 46
62313 AAATGCAACA
* *
62323 TAGAAATGTCCCGAATGACTACATAGTATTATCCCGAA-GAACCACG
1 TAGAAATGTCCCGAATGACCACATAGAATTATCCCGAATG-ACCACG
* *
62369 TAGAAATGTGCCGAATGACCACATAGAATTATCCCGAATGACCGCG
1 TAGAAATGTCCCGAATGACCACATAGAATTATCCCGAATGACCACG
62415 TAGAA
1 TAGAA
62420 CCCTCGACTC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (46 bp):
TAGAAATGTCCCGAATGACCACATAGAATTATCCCGAATGACCACG
Found at i:62419 original size:23 final size:23
Alignment explanation
Indices: 62320--62411 Score: 96
Period size: 23 Copynumber: 4.0 Consensus size: 23
62310 CCGAAATGCA
* * *
62320 ACATAGAAATGTCCCGAATGACT
1 ACATAGAATTATCCCGAATGACC
*
62343 ACATAGTATTATCCCGAA-GAACC
1 ACATAGAATTATCCCGAATG-ACC
* * * *
62366 ACGTAGAAATGTGCCGAATGACC
1 ACATAGAATTATCCCGAATGACC
62389 ACATAGAATTATCCCGAATGACC
1 ACATAGAATTATCCCGAATGACC
62412 GCGTAGAACC
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
22 1 0.02
23 52 0.96
24 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (23 bp):
ACATAGAATTATCCCGAATGACC
Found at i:65858 original size:20 final size:20
Alignment explanation
Indices: 65833--65897 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
65823 TCGGCACTTA
65833 GTGCATTTTGTAGCACTTCG
1 GTGCATTTTGTAGCACTTCG
65853 GTGCATTTTGTAGCACTTCG
1 GTGCATTTTGTAGCACTTCG
*
65873 GTGCATTATG--GCACTTCG
1 GTGCATTTTGTAGCACTTCG
65891 GTGCATT
1 GTGCATT
65898 GTAGGAATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
18 15 0.34
20 29 0.66
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.38
Consensus pattern (20 bp):
GTGCATTTTGTAGCACTTCG
Found at i:68199 original size:17 final size:15
Alignment explanation
Indices: 68177--68218 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
68167 ATGAAATGGA
68177 TTATTTTATTACTATAT
1 TTATTTTATTA-TA-AT
*
68194 TTATTTTAATATAAT
1 TTATTTTATTATAAT
68209 TT-TTTTATTA
1 TTATTTTATTA
68219 ATATTTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 4 0.17
16 2 0.09
17 10 0.43
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTTTATTATAAT
Found at i:77789 original size:18 final size:19
Alignment explanation
Indices: 77748--77790 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
77738 TTGGTTCACA
* *
77748 GAATATAAGATTACCGGTGG
1 GAATAAAAGATTACCAGT-G
77768 GAATAAAAGATTACCAGT-
1 GAATAAAAGATTACCAGTG
77786 GAATA
1 GAATA
77791 GGATTATTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
20 16 0.76
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.23
Consensus pattern (19 bp):
GAATAAAAGATTACCAGTG
Found at i:77958 original size:15 final size:15
Alignment explanation
Indices: 77940--77971 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
77930 AAATTCTAAA
77940 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
77955 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
77970 TA
1 TA
77972 CATTTGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:79618 original size:22 final size:22
Alignment explanation
Indices: 79566--79618 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
79556 AAATTTCTTT
*
79566 TCAAAAACCAAACAAACCCAGCA
1 TCAAAAA-CAAAAAAACCCAGCA
**
79589 TCTGAAACAAAAAAACCCAG-A
1 TCAAAAACAAAAAAACCCAGCA
79610 TACAAAAAC
1 T-CAAAAAC
79619 CTCATAAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 2 0.08
22 17 0.71
23 5 0.21
ACGTcount: A:0.58, C:0.28, G:0.06, T:0.08
Consensus pattern (22 bp):
TCAAAAACAAAAAAACCCAGCA
Found at i:79755 original size:16 final size:16
Alignment explanation
Indices: 79736--79767 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
79726 GAGACATCAC
79736 GAAAGGGAGAGGAGAA
1 GAAAGGGAGAGGAGAA
79752 GAAAGGGAGAGGAGAA
1 GAAAGGGAGAGGAGAA
79768 AAATCTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (16 bp):
GAAAGGGAGAGGAGAA
Found at i:79844 original size:16 final size:16
Alignment explanation
Indices: 79823--79855 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
79813 AGCCATTAAC
79823 ACACTGGAACAAAAGA
1 ACACTGGAACAAAAGA
*
79839 ACACTGGAATAAAAGA
1 ACACTGGAACAAAAGA
79855 A
1 A
79856 TACCAAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.15, G:0.18, T:0.09
Consensus pattern (16 bp):
ACACTGGAACAAAAGA
Found at i:80490 original size:23 final size:23
Alignment explanation
Indices: 80464--80507 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
80454 AAACTTGTAA
80464 GGGGTAAGGATCGAGGGTTTGGC
1 GGGGTAAGGATCGAGGGTTTGGC
80487 GGGGTAAGGATCGAGGGTTTG
1 GGGGTAAGGATCGAGGGTTTG
80508 CCATCCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.18, C:0.07, G:0.52, T:0.23
Consensus pattern (23 bp):
GGGGTAAGGATCGAGGGTTTGGC
Found at i:82940 original size:15 final size:15
Alignment explanation
Indices: 82900--82989 Score: 87
Period size: 15 Copynumber: 6.0 Consensus size: 15
82890 CAAATTAAAG
*
82900 CAAAGAG-AAA-AAG
1 CAAAGAGAAAAGAAA
*
82913 CAAAGAAAGAAAGAAA
1 CAAAGAGA-AAAGAAA
*
82929 CAAAGAGAAAAGAAG
1 CAAAGAGAAAAGAAA
*
82944 CAAAGAGAAGAAAAAA
1 CAAAGAGAA-AAGAAA
82960 CAAAGAGAAAA-AAA
1 CAAAGAGAAAAGAAA
*
82974 GCAAAGAAAAAAGAAA
1 -CAAAGAGAAAAGAAA
82990 AAGAACTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
13 6 0.09
14 3 0.05
15 30 0.47
16 25 0.39
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (15 bp):
CAAAGAGAAAAGAAA
Found at i:82948 original size:31 final size:30
Alignment explanation
Indices: 82900--82989 Score: 132
Period size: 31 Copynumber: 3.0 Consensus size: 30
82890 CAAATTAAAG
82900 CAAAGAG-AAAAAGCAAAGAAAGAAAGAAA
1 CAAAGAGAAAAAAGCAAAGAAAGAAAGAAA
82929 CAAAGAGAAAAGAAGCAAAGAGAAGAAA-AAA
1 CAAAGAGAAAA-AAGCAAAGA-AAGAAAGAAA
82960 CAAAGAGAAAAAAAGCAAAGAAA-AAAGAAA
1 CAAAGAG-AAAAAAGCAAAGAAAGAAAGAAA
82990 AAGAACTAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 9
0.86 0.00 0.14
Matches are distributed among these distances:
29 10 0.18
30 8 0.14
31 28 0.50
32 10 0.18
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (30 bp):
CAAAGAGAAAAAAGCAAAGAAAGAAAGAAA
Found at i:82970 original size:11 final size:10
Alignment explanation
Indices: 82918--83011 Score: 53
Period size: 10 Copynumber: 8.8 Consensus size: 10
82908 AAAAGCAAAG
82918 AAAGAAAGAAA
1 AAAGAAA-AAA
*
82929 CAAAGAGAAAA
1 -AAAGAAAAAA
* * *
82940 GAAGCAAAGA
1 AAAGAAAAAA
*
82950 GAAGAAAAAA
1 AAAGAAAAAA
*
82960 CAAAGAGAAAA
1 -AAAGAAAAAA
82971 AAAGCAAAGAAA
1 AAAG-AAA-AAA
*
82983 AAAGAAAAAG
1 AAAGAAAAAA
**
82993 AACTAAAAAA
1 AAAGAAAAAA
83003 GAAAGAAAA
1 -AAAGAAAA
83012 GAAGACAAGA
Statistics
Matches: 62, Mismatches: 16, Indels: 9
0.71 0.18 0.10
Matches are distributed among these distances:
10 27 0.44
11 22 0.35
12 13 0.21
ACGTcount: A:0.76, C:0.05, G:0.18, T:0.01
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:83002 original size:31 final size:30
Alignment explanation
Indices: 82907--83016 Score: 109
Period size: 31 Copynumber: 3.6 Consensus size: 30
82897 AAGCAAAGAG
*
82907 AAAAAGCAAAGAAAGAAAGAAACAAAGAGAA
1 AAAAAGCAAAGAAA-AAAGAAAAAAAGAGAA
* *
82938 AAGAAGCAAAGAGAAGAAA-AAACAAAGAGAA
1 AAAAAGCAAAGA-AA-AAAGAAAAAAAGAGAA
* **
82969 AAAAAGCAAAGAAAAAAGAAAAAGA-ACTA
1 AAAAAGCAAAGAAAAAAGAAAAAAAGAGAA
82998 AAAAAG-AAAGAAAAGAAGA
1 AAAAAGCAAAGAAAA-AAGA
83017 CAAGAAACAT
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.11
29 15 0.21
30 7 0.10
31 34 0.49
32 6 0.09
ACGTcount: A:0.75, C:0.05, G:0.19, T:0.01
Consensus pattern (30 bp):
AAAAAGCAAAGAAAAAAGAAAAAAAGAGAA
Found at i:83023 original size:13 final size:11
Alignment explanation
Indices: 82914--83023 Score: 68
Period size: 11 Copynumber: 10.0 Consensus size: 11
82904 GAGAAAAAGC
82914 AAAGAAAGAAA
1 AAAGAAAGAAA
* *
82925 GAAACAAAGAGA
1 -AAAGAAAGAAA
*
82937 AAAG-AAGCAA
1 AAAGAAAGAAA
*
82947 AGAG-AAGAAA
1 AAAGAAAGAAA
* *
82957 AAACAAAGAGA
1 AAAGAAAGAAA
82968 AAA-AAAGCAAA
1 AAAGAAAG-AAA
82979 GAAA-AAAG-AA
1 -AAAGAAAGAAA
**
82989 AAAGAACTAAA
1 AAAGAAAGAAA
83000 AAAGAAAGAAA
1 AAAGAAAGAAA
83011 AGAAGACAAGAAA
1 A-AAGA-AAGAAA
83024 CATATACAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 13
0.73 0.14 0.12
Matches are distributed among these distances:
9 3 0.04
10 22 0.29
11 25 0.33
12 20 0.26
13 6 0.08
ACGTcount: A:0.75, C:0.05, G:0.19, T:0.01
Consensus pattern (11 bp):
AAAGAAAGAAA
Found at i:85980 original size:66 final size:66
Alignment explanation
Indices: 85900--86079 Score: 234
Period size: 67 Copynumber: 2.7 Consensus size: 66
85890 CAAAACTGAT
* * *
85900 AAACTTTAAGATTGTTTCACTCGAAACAAATTTTGTCTCTCTTGAGACAGTTTATCTTTAAACGT
1 AAACTTTGAGATTGTTTCACTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTATCTTTAAACAT
85965 C
66 C
* * *
85966 AAACTTTGAGATTGTTTCTCTTGAAACAACTTTTTGTCTCTCTTAAGACAGTTTATCTTTAAACA
1 AAACTTTGAGATTGTTTCACTTGAAACAA-ATTTTGTCTCTCTTGAGACAGTTTATCTTTAAACA
*
86031 TT
65 TC
* * * * * *
86033 AAACATTGTGATTATTTCCCTTGAAACATATTTTGTCTCACTTGAGA
1 AAACTTTGAGATTGTTTCACTTGAAACAAATTTTGTCTCTCTTGAGA
86080 TTGTTTCTTT
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
66 41 0.42
67 57 0.58
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (66 bp):
AAACTTTGAGATTGTTTCACTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTATCTTTAAACAT
C
Found at i:86322 original size:138 final size:138
Alignment explanation
Indices: 86099--86643 Score: 591
Period size: 138 Copynumber: 4.0 Consensus size: 138
86089 TTGAAACAAA
* * * * * * * * * *
86099 TTATCCCTAAAGATGACCAACCATCCTCATCACGTAAGAATCGTGTAATCCATCGACCAGATCTC
1 TTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTTTCATCTACCAACCAGATCTC
* * * *
86164 CTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTTCTCATCACGTAGAAACTGTATT
66 CTCATCACGTAGGAGTCGTGTCAACCTTAGATAACCAGCCGTCCTCATCACGTAGAAACTGTGTT
86229 ATCACCAT
131 ATCACCAT
* * ** ** *
86237 TTATCCCTAAAGATAGCTAGTTGTTTTCATCACGTAGGAACCGTTTCATCTACCAACCAGTTCTC
1 TTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTTTCATCTACCAACCAGATCTC
*
86302 CTCATCACGTAGGAGTCGTGTCAACCTTAGATAACCAGCCATCCTCATCACGTAGAAA-TCGTGT
66 CTCATCACGTAGGAGTCGTGTCAACCTTAGATAACCAGCCGTCCTCATCACGTAGAAACT-GTGT
86366 TATCACCAT
130 TATCACCAT
* *
86375 TTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTT-ATCCACCAACCAGATAT
1 TTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGT-TTCATCTACCAACCAGATCT
* ** * ** * *
86439 CCTCATCACGTATGAGTCACGTCAATCTTAGATAACCAGTTTGTCCTCATCACGTAGGAACCGTG
65 CCTCATCACGTAGGAGTCGTGTCAACCTTAGATAACCAG-CCGTCCTCATCACGTAGAAACTGTG
86504 TTATCTA-CA-
129 TTATC-ACCAT
* **
86513 TTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTCTCATCTACTGACCAGATC-C
1 TTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTTTCATCTACCAACCAGATCTC
* ** ** * * * * *
86577 TCTCATCACGTAGG-CT-GCCTCAACCTTAGATAGTCAGACTTTCTCATCACGTAGGAACCGTGT
66 -CTCATCACGTAGGAGTCGTGTCAACCTTAGATAACCAGCCGTCCTCATCACGTAGAAACTGTGT
86640 TATC
130 TATC
86644 TCTAAATTTA
Statistics
Matches: 344, Mismatches: 56, Indels: 17
0.82 0.13 0.04
Matches are distributed among these distances:
135 26 0.08
136 16 0.05
137 4 0.01
138 269 0.78
139 28 0.08
140 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (138 bp):
TTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTTTCATCTACCAACCAGATCTC
CTCATCACGTAGGAGTCGTGTCAACCTTAGATAACCAGCCGTCCTCATCACGTAGAAACTGTGTT
ATCACCAT
Found at i:86834 original size:3 final size:3
Alignment explanation
Indices: 86828--86874 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
86818 TCTGGGTCTT
86828 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
86875 ACAATTAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Done.