Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015977.1 Corchorus olitorius cultivar O-4 contig16010, 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: 117963
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:8312 original size:1 final size:1
Alignment explanation
Indices: 8306--8333 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
8296 TGAGCGTAGG
8306 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
8334 AAAAAAAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:9232 original size:44 final size:44
Alignment explanation
Indices: 9165--9377 Score: 186
Period size: 44 Copynumber: 4.9 Consensus size: 44
9155 GCTCCAACGT
* * *
9165 TGAAATATTGATAACCACACTGTGAAAATTTGATAACCTCATTA
1 TGAAATTTTGATAACCACACTATGAAAATTTGATAACCTCATTG
* * * * * * *
9209 CGAAATTTCGATAACCTCCCTGTGAAAATTTGATAACCACATGG
1 TGAAATTTTGATAACCACACTATGAAAATTTGATAACCTCATTG
* * *
9253 TGAAATTTTAATAAACACACTATGAAATTTTGATAACCTCATTG
1 TGAAATTTTGATAACCACACTATGAAAATTTGATAACCTCATTG
* * *
9297 TGAAGTTTTGATAATCTC-CTTAT-AAAATTTTGATAACCTCA---
1 TGAAATTTTGATAACCACAC-TATGAAAA-TTTGATAACCTCATTG
* * *
9338 TAAAATTTTGATAATCACACCATG-AAATTTAGATAACCTC
1 TGAAATTTTGATAACCACACTATGAAAATTT-GATAACCTC
9378 CCTATGAGAA
Statistics
Matches: 137, Mismatches: 27, Indels: 13
0.77 0.15 0.07
Matches are distributed among these distances:
40 3 0.02
41 29 0.21
42 1 0.01
43 4 0.03
44 100 0.73
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (44 bp):
TGAAATTTTGATAACCACACTATGAAAATTTGATAACCTCATTG
Found at i:9249 original size:66 final size:66
Alignment explanation
Indices: 9167--9310 Score: 164
Period size: 66 Copynumber: 2.2 Consensus size: 66
9157 TCCAACGTTG
* * * * *
9167 AAATATTGATAACCACACT-GTGAAAATTTGATAACCTCATTACGAAATTTCGATAACCTCCCTG
1 AAAT-TTGATAACCACA-TGGTGAAAATTTAATAAACACACTACGAAATTTCGATAACCTCACTG
9231 TGA
64 TGA
* * * *
9234 AAATTTGATAACCACATGGTGAAATTTTAATAAACACACTATGAAATTTTGATAACCTCATTGTG
1 AAATTTGATAACCACATGGTGAAAATTTAATAAACACACTACGAAATTTCGATAACCTCACTGTG
9299 A
66 A
**
9300 AGTTTTGATAA
1 AAATTTGATAA
9311 TCTCCTTATA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
65 1 0.02
66 60 0.92
67 4 0.06
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (66 bp):
AAATTTGATAACCACATGGTGAAAATTTAATAAACACACTACGAAATTTCGATAACCTCACTGTG
A
Found at i:9384 original size:22 final size:22
Alignment explanation
Indices: 9165--9384 Score: 126
Period size: 22 Copynumber: 10.1 Consensus size: 22
9155 GCTCCAACGT
* * * *
9165 TGAAATATTGATAACCACACTG
1 TGAAATTTTGATAACCTCCCTA
* **
9187 TGAAAATTTGATAACCTCATTA
1 TGAAATTTTGATAACCTCCCTA
* * *
9209 CGAAATTTCGATAACCTCCCTG
1 TGAAATTTTGATAACCTCCCTA
* * * *
9231 TGAAAATTTGATAACC-ACATGG
1 TGAAATTTTGATAACCTCCCT-A
* * * *
9253 TGAAATTTTAATAAACACACTA
1 TGAAATTTTGATAACCTCCCTA
** *
9275 TGAAATTTTGATAACCTCATTG
1 TGAAATTTTGATAACCTCCCTA
* * *
9297 TGAAGTTTTGATAATCTCCTTA
1 TGAAATTTTGATAACCTCCCTA
*
9319 TAAAATTTTGATAACCT--C-A
1 TGAAATTTTGATAACCTCCCTA
* * *
9338 TAAAATTTTGATAATCACACC-A
1 TGAAATTTTGATAACCTC-CCTA
*
9360 TGAAATTTAGATAACCTCCCTA
1 TGAAATTTTGATAACCTCCCTA
9382 TGA
1 TGA
9385 GAATGAAACC
Statistics
Matches: 150, Mismatches: 42, Indels: 12
0.74 0.21 0.06
Matches are distributed among these distances:
19 16 0.11
21 4 0.03
22 129 0.86
23 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCCCTA
Found at i:9588 original size:44 final size:43
Alignment explanation
Indices: 9529--9637 Score: 121
Period size: 44 Copynumber: 2.5 Consensus size: 43
9519 GAAATTCTGT
9529 TAACCTTCTTATGAAATTTTGATAACCACACTATA-AAATATCGA
1 TAACCTT-TTATGAAATTTTGATAACCACACTA-AGAAATATCGA
* * * * *
9573 TAACCTTTGTATGAAATTTTGTTAACCTCCCTAAGAAATTTTGA
1 TAACCTTT-TATGAAATTTTGATAACCACACTAAGAAATATCGA
*
9617 TAACCTTTTTATGAAAATTTG
1 TAACC-TTTTATGAAATTTTG
9638 GTTTGATTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
43 2 0.04
44 51 0.91
45 3 0.05
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (43 bp):
TAACCTTTTATGAAATTTTGATAACCACACTAAGAAATATCGA
Found at i:9632 original size:22 final size:22
Alignment explanation
Indices: 9413--9637 Score: 101
Period size: 22 Copynumber: 10.3 Consensus size: 22
9403 CTTTCTATAT
* *
9413 AATTGTGATAACCTCTCC-ATAA
1 AATTTTGATAACCT-TCCTATGA
* *
9435 AATTTTTATAACCTCCCTATGA
1 AATTTTGATAACCTTCCTATGA
*
9457 AATTTTGTTAACC-TCCT-TAGTA
1 AATTTTGATAACCTTCCTAT-G-A
* * *
9479 AATTTTAATAA----GC-A-CA
1 AATTTTGATAACCTTCCTATGA
9495 AATTTTGATAACCTTCCTCCATATGA
1 AATTTTGATAACC-T--TCC-TATGA
* * *
9521 AATTCTGTTAACCTTCTTATGA
1 AATTTTGATAACCTTCCTATGA
* *
9543 AATTTTGATAACC-ACACTATAA
1 AATTTTGATAACCTTC-CTATGA
* * **
9565 AATATCGATAACCTTTGTATGA
1 AATTTTGATAACCTTCCTATGA
* * *
9587 AATTTTGTTAACCTCCCTAAGA
1 AATTTTGATAACCTTCCTATGA
**
9609 AATTTTGATAACCTTTTTATGA
1 AATTTTGATAACCTTCCTATGA
*
9631 AAATTTG
1 AATTTTG
9638 GTTTGATTGT
Statistics
Matches: 146, Mismatches: 41, Indels: 32
0.67 0.19 0.15
Matches are distributed among these distances:
16 11 0.08
19 1 0.01
20 1 0.01
21 7 0.05
22 109 0.75
23 3 0.02
25 2 0.01
26 12 0.08
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (22 bp):
AATTTTGATAACCTTCCTATGA
Found at i:10086 original size:3 final size:3
Alignment explanation
Indices: 10078--10134 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
10068 AATTTGAGAG
* * * *
10078 TAT TAT TAT TAT TAT TAT TAT TAA TAT TACA TACT TAT TAT TAA TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT
10125 TAT TAT TAT T
1 TAT TAT TAT T
10135 CATATTTGGA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
3 41 0.89
4 5 0.11
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:12002 original size:141 final size:142
Alignment explanation
Indices: 11847--12115 Score: 387
Period size: 141 Copynumber: 1.9 Consensus size: 142
11837 GACAGAAAAA
* *
11847 CTGTATCTAATAATGACAATTATGTCGACACAAGAAACAGTAAGAGTGACAATATAAGTTGTCAT
1 CTGTACCTAATAATGACAATTATGTCGACACAAGAAACACTAAGAGTGACAATATAAGTTGTCAT
* *
11912 TATACGTAATCTTTTGTGACGAC-CTTTTTGACACTATAATTATTGATAATAGTGACAAAAGGGA
66 TATACGTAATCTTGTGTGACGACACTTTTTGAAACTATAATTATTGATAATAGTGACAAAAGGGA
11976 TCGACACAATAG
131 TCGACACAATAG
* * ** * * * *
11988 CTGTACCTATTAATGGCGGTTATGTCGACACAAGGAACCCTAATAGTGACTATATAAGTTGTCAT
1 CTGTACCTAATAATGACAATTATGTCGACACAAGAAACACTAAGAGTGACAATATAAGTTGTCAT
* * * *
12053 TATACTTACTCTTGTGTGACGACATTTTTTGAAACTATAATTATTGATAATAGTGACGAAAGG
66 TATACGTAATCTTGTGTGACGACACTTTTTGAAACTATAATTATTGATAATAGTGACAAAAGG
12116 AATGGTCATA
Statistics
Matches: 111, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
141 75 0.68
142 36 0.32
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32
Consensus pattern (142 bp):
CTGTACCTAATAATGACAATTATGTCGACACAAGAAACACTAAGAGTGACAATATAAGTTGTCAT
TATACGTAATCTTGTGTGACGACACTTTTTGAAACTATAATTATTGATAATAGTGACAAAAGGGA
TCGACACAATAG
Found at i:17457 original size:40 final size:39
Alignment explanation
Indices: 17384--17482 Score: 182
Period size: 40 Copynumber: 2.5 Consensus size: 39
17374 AGCATCGAAC
17384 TTACATTTTCTTATAAAG-TTTTTTTGACATTTTTGACA
1 TTACATTTTCTTATAAAGTTTTTTTTGACATTTTTGACA
17422 TTACATTTTCTTATAAAGTTTTTTTTGACATTTTTTGACA
1 TTACATTTTCTTATAAAGTTTTTTTTGACA-TTTTTGACA
17462 TTACATTTTCTTATAAAGTTT
1 TTACATTTTCTTATAAAGTTT
17483 AGGTGGAGAC
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
38 18 0.31
39 11 0.19
40 30 0.51
ACGTcount: A:0.26, C:0.10, G:0.07, T:0.57
Consensus pattern (39 bp):
TTACATTTTCTTATAAAGTTTTTTTTGACATTTTTGACA
Found at i:18693 original size:142 final size:142
Alignment explanation
Indices: 18437--18731 Score: 511
Period size: 142 Copynumber: 2.1 Consensus size: 142
18427 TTATTGAAAA
**
18437 ATAATTGTGACGAAGATATTTTAGTCACAATTGCATCTATACCCGCCAAAATTGTTTAGGCGCCA
1 ATAATTGTGACGAAGATATTTTAGTCACAATTAAATCTATACCCGCCAAAATTGTTTAGGCGCCA
18502 ATTTGGGAAAGCTATTAGTGACAATTGTATAGTGACAAAGTATTTGTCGTCACTACTAACATATC
66 ATTTGGGAAAGCTATTAGTGACAATTGTATAGTGACAAAGTATTTGTCGTCACTACTAACATATC
18567 ATTAGTGACAAT
131 ATTAGTGACAAT
*
18579 ATAATTGTGACGAAGATATTTTCA-TCACAATTAAATCTATTCCCGCCAAAATTGTTTAGGCGCC
1 ATAATTGTGACGAAGATATTTT-AGTCACAATTAAATCTATACCCGCCAAAATTGTTTAGGCGCC
* * *
18643 AATTTGGGAATGCTATTAGTGACAATTGTATAGTGACAACGTATTTGTCGTCACTATTAACATAT
65 AATTTGGGAAAGCTATTAGTGACAATTGTATAGTGACAAAGTATTTGTCGTCACTACTAACATAT
18708 CATTAGTGACAAT
130 CATTAGTGACAAT
*
18721 ATACTTGTGAC
1 ATAATTGTGAC
18732 TGACACTTAC
Statistics
Matches: 145, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
142 144 0.99
143 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (142 bp):
ATAATTGTGACGAAGATATTTTAGTCACAATTAAATCTATACCCGCCAAAATTGTTTAGGCGCCA
ATTTGGGAAAGCTATTAGTGACAATTGTATAGTGACAAAGTATTTGTCGTCACTACTAACATATC
ATTAGTGACAAT
Found at i:23287 original size:16 final size:17
Alignment explanation
Indices: 23260--23291 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
23250 ATCAATCCAA
23260 AAATCATCACAATTTTT
1 AAATCATCACAATTTTT
23277 AAATC-TCACAATTTT
1 AAATCATCACAATTTT
23292 ATTAAAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATCATCACAATTTTT
Found at i:25330 original size:22 final size:23
Alignment explanation
Indices: 25305--25350 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
25295 ACTCGCGAGC
*
25305 TACTCGGGTTCGACTCG-AGAAA
1 TACTCGAGTTCGACTCGAAGAAA
*
25327 TACTCGAGTTCGGCTCGAAGAAA
1 TACTCGAGTTCGACTCGAAGAAA
25350 T
1 T
25351 CGAGCTCGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (23 bp):
TACTCGAGTTCGACTCGAAGAAA
Found at i:25955 original size:11 final size:11
Alignment explanation
Indices: 25941--25965 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25931 TATCTTCATC
25941 TTTTCTTTTTT
1 TTTTCTTTTTT
25952 TTTTCTTTTTT
1 TTTTCTTTTTT
25963 TTT
1 TTT
25966 CTGGGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:28739 original size:72 final size:72
Alignment explanation
Indices: 28646--28967 Score: 491
Period size: 72 Copynumber: 4.5 Consensus size: 72
28636 GTCGGTGCCA
* * * * * * *
28646 TGCTTGGTCGAGGTCAGCTCTCCACCACCTGCCAACCGGTCTCACTGGACCCTTAAGAGGGTTCT
1 TGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCAGCCGGTATCTCTGGACCCTTAAGAGGGCTCT
*
28711 ACATCCG
66 TCATCCG
* **
28718 TGCTTGGTCAAGGCCGGCTCTCCACCGCCTGCCAGCTAGTATCTCTGGACCCTTAAGAGGGCTCT
1 TGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCAGCCGGTATCTCTGGACCCTTAAGAGGGCTCT
28783 TCATCCG
66 TCATCCG
* *
28790 TGCTTGGTCAAGGTCGGCTTTCCACCGCCTGCCAGCCGGTATCTTTGGACCCTTAAGAGGGCTCT
1 TGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCAGCCGGTATCTCTGGACCCTTAAGAGGGCTCT
28855 TCATCCG
66 TCATCCG
* * *
28862 TGCTTGGTCAAGCTCGGCTCTCCACTGCCTGCCAGCCGGTATCTCTGAACCCTTAAGAGGGCTCT
1 TGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCAGCCGGTATCTCTGGACCCTTAAGAGGGCTCT
28927 TCATCCG
66 TCATCCG
*
28934 TGCTTGGTCAAGGTCGGCTCTCCACCACCTGCCA
1 TGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCA
28968 ACCGAGACCG
Statistics
Matches: 226, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 226 1.00
ACGTcount: A:0.16, C:0.34, G:0.25, T:0.25
Consensus pattern (72 bp):
TGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCAGCCGGTATCTCTGGACCCTTAAGAGGGCTCT
TCATCCG
Found at i:29986 original size:27 final size:27
Alignment explanation
Indices: 29952--30050 Score: 119
Period size: 27 Copynumber: 3.7 Consensus size: 27
29942 GGTCACCTAG
29952 GGGGCATTTTAGTCATTTGCACGTCCA
1 GGGGCATTTTAGTCATTTGCACGTCCA
* *
29979 GGGACATTTTAGTCATTTGCACATCCA
1 GGGGCATTTTAGTCATTTGCACGTCCA
* * * *
30006 GGGGTATTTTGGTCATTTTCATGAT-CA
1 GGGGCATTTTAGTCATTTGCACG-TCCA
*
30033 GGGGCATTTTGGTCATTT
1 GGGGCATTTTAGTCATTT
30051 TAGGTTCACT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 61 0.98
28 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (27 bp):
GGGGCATTTTAGTCATTTGCACGTCCA
Found at i:33831 original size:9 final size:9
Alignment explanation
Indices: 33817--33848 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
33807 TTGGGTTTGA
33817 ATGTTCTTC
1 ATGTTCTTC
33826 ATGTTCTTC
1 ATGTTCTTC
33835 ATTGTTCTTC
1 A-TGTTCTTC
33845 ATGT
1 ATGT
33849 GTTCTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.56
Consensus pattern (9 bp):
ATGTTCTTC
Found at i:33842 original size:10 final size:10
Alignment explanation
Indices: 33818--33854 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
33808 TGGGTTTGAA
33818 TGTTCTTCA-
1 TGTTCTTCAT
33827 TGTTCTTCAT
1 TGTTCTTCAT
33837 TGTTCTTCAT
1 TGTTCTTCAT
33847 GTGTTCTT
1 -TGTTCTT
33855 GAAATAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.35
10 10 0.38
11 7 0.27
ACGTcount: A:0.08, C:0.19, G:0.14, T:0.59
Consensus pattern (10 bp):
TGTTCTTCAT
Found at i:34116 original size:29 final size:30
Alignment explanation
Indices: 34058--34120 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
34048 ACCTAAAAAA
34058 GTACTAAATTGAACCATTAATAAAACGTTTG
1 GTACTAAATTGAACCA-TAATAAAACGTTTG
* * *
34089 GTACTAAATTGGACGA-AATAAAAGGTTTG
1 GTACTAAATTGAACCATAATAAAACGTTTG
34118 GTA
1 GTA
34121 TTAAGTGGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.52
31 14 0.48
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (30 bp):
GTACTAAATTGAACCATAATAAAACGTTTG
Found at i:41237 original size:12 final size:11
Alignment explanation
Indices: 41218--41255 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
41208 CATAAAAATA
41218 AAAAAATGAAG
1 AAAAAATGAAG
41229 AAAAGAATGAATG
1 AAAA-AATGAA-G
41242 AAAAAATGAA-
1 AAAAAATGAAG
41252 AAAA
1 AAAA
41256 TGAAAAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.16
11 4 0.16
12 12 0.48
13 5 0.20
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.11
Consensus pattern (11 bp):
AAAAAATGAAG
Found at i:41251 original size:8 final size:8
Alignment explanation
Indices: 41211--41275 Score: 73
Period size: 8 Copynumber: 8.4 Consensus size: 8
41201 ATTTTCCCAT
*
41211 AAAAATAA
1 AAAAATGA
41219 AAAAATGA
1 AAAAATGA
41227 AGAAAA-GA
1 A-AAAATGA
**
41235 ATGAATGA
1 AAAAATGA
41243 AAAAATGA
1 AAAAATGA
41251 AAAAATG-
1 AAAAATGA
41258 AAAAATG-
1 AAAAATGA
41265 AAAAATGA
1 AAAAATGA
41273 AAA
1 AAA
41276 TAAAGGCACT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
7 16 0.33
8 29 0.59
9 4 0.08
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (8 bp):
AAAAATGA
Found at i:41682 original size:14 final size:14
Alignment explanation
Indices: 41658--41696 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
41648 CTCCATCAAG
*
41658 AAATTAAAAAAAT-
1 AAATAAAAAAAATC
*
41671 TAATAAAAAAAATC
1 AAATAAAAAAAATC
41685 AAATAAAAAAAA
1 AAATAAAAAAAA
41697 AAAAAGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (14 bp):
AAATAAAAAAAATC
Found at i:43655 original size:163 final size:163
Alignment explanation
Indices: 43362--43832 Score: 464
Period size: 163 Copynumber: 2.8 Consensus size: 163
43352 TCCATATCGG
* * * * *
43362 TAAAACCTCCGGGTACCATTTAATTTCATCAAGTCTTTTTCATGAAAGATTCATATTTAAGTTTG
1 TAAAACCTCCGGGTATCATTTCATTTCATCAAG--TTTTTCATCAAAAATTC--A--T--GTTTA
* * * * * * * *
43427 AAATCC-TTGTTCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAGA
58 AAATCCGTGGTT-AAGGTTTCAATTTAAAGTTTGCATTGATAAGACCTCCAGGCACAAATTCAGA
*
43491 AACCTCCGGGTA-TCAATTCTGATAAGTCCTCCGGGCAATCAGA
122 AACCTCCGGGTACT-AATTCTGATAAGCCCTCCGGGC-ATCAGA
*
43534 -AAAACCTTCGGGTATCATTTCATTTCATCAAGTTTTTCATCAAAAATTCATGTTTAAAATCCGT
1 TAAAACCTCCGGGTATCATTTCATTTCATCAAGTTTTTCATCAAAAATTCATGTTTAAAATCCGT
* * *
43598 GGTTAAGGTTTCAATTTAAAGTTTGCATTGATGAGACCTCCAGGCACGATTTCAGAAACCTCCGG
66 GGTTAAGGTTTCAATTTAAAGTTTGCATTGATAAGACCTCCAGGCACAAATTCAGAAACCTCCGG
* **
43663 GTACTAATTCTGATTAGCCCTCCGGGCATTTGA
131 GTACTAATTCTGATAAGCCCTCCGGGCATCAGA
* *
43696 TAAAACCTCCGGGTATCATTTCATTTTATCGAGTTTTTCATCAAAAATTCATGTTTAAGTTTAAA
1 TAAAACCTCCGGGTATCATTTCATTTCATCAAGTTTTTCATCAAAAATTCA----T--GTTTAAA
* * * * * * * * *
43761 ATCCTTGGTCAAGGTCTCGATTTAAAGCTTGTACTTG-TAAGTCCTCCGGGCACAAATTCAGAAG
60 ATCCGTGGTTAAGGTTTCAATTTAAAGTTTGCA-TTGATAAGACCTCCAGGCACAAATTCAGAAA
43825 CCTCCGGG
124 CCTCCGGG
43833 CATTTGATGA
Statistics
Matches: 253, Mismatches: 36, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
162 4 0.02
163 131 0.52
164 5 0.02
165 1 0.00
167 2 0.01
169 78 0.31
170 3 0.01
171 29 0.11
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (163 bp):
TAAAACCTCCGGGTATCATTTCATTTCATCAAGTTTTTCATCAAAAATTCATGTTTAAAATCCGT
GGTTAAGGTTTCAATTTAAAGTTTGCATTGATAAGACCTCCAGGCACAAATTCAGAAACCTCCGG
GTACTAATTCTGATAAGCCCTCCGGGCATCAGA
Found at i:43950 original size:38 final size:38
Alignment explanation
Indices: 43889--44145 Score: 297
Period size: 38 Copynumber: 6.8 Consensus size: 38
43879 TACTTTGTCA
* * *
43889 ATTTCGATCCTGGTTTAGAATCATTGCTTTATCAGGTT
1 ATTTCGATCCTGGTTTAGGATCATTGCTTTATTAGTTT
* *
43927 ATTTTGATCCTGGTTTATGATCATTGCTTTATTAGTTT
1 ATTTCGATCCTGGTTTAGGATCATTGCTTTATTAGTTT
* *
43965 ATTTCGATCCTAGTTTAGGATCATTGCTTAATTAGTTT
1 ATTTCGATCCTGGTTTAGGATCATTGCTTTATTAGTTT
* * * *
44003 ATTTCGATCCTAGTTTAGGATCATTTC-CT-TT-CTTT
1 ATTTCGATCCTGGTTTAGGATCATTGCTTTATTAGTTT
44038 A-TTCGATCCTGGTTTAGGATCATTGCTTTATTAGTTT
1 ATTTCGATCCTGGTTTAGGATCATTGCTTTATTAGTTT
* * * * *
44075 ATTTCGATCCTAGTTTAGGGTCATTTCCTTTGTTACTTT
1 ATTTCGATCCTGGTTTAGGATCA-TTGCTTTATTAGTTT
** * *
44114 ATTTTAATCCTGGTTTATGATTATTGCTTTAT
1 ATTTCGATCCTGGTTTAGGATCATTGCTTTAT
44146 CTTAATCCTG
Statistics
Matches: 184, Mismatches: 30, Indels: 10
0.82 0.13 0.04
Matches are distributed among these distances:
34 23 0.12
35 5 0.03
36 4 0.02
37 4 0.02
38 119 0.65
39 29 0.16
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (38 bp):
ATTTCGATCCTGGTTTAGGATCATTGCTTTATTAGTTT
Found at i:44071 original size:72 final size:74
Alignment explanation
Indices: 43889--44145 Score: 311
Period size: 72 Copynumber: 3.4 Consensus size: 74
43879 TACTTTGTCA
* * * * * * *
43889 ATTTCGATCCTGGTTTAGAATCATTGCTTTATCAGGTTATTTTGATCCTGGTTTATGATCATTGC
1 ATTTCGATCCTGGTTTAGGATCATTGCTTTATTAGTTTATTTCGATCCTAGTTTAGGATCATTTC
* *
43954 TTTATTAGTTT
66 -CT-TTACTTT
* *
43965 ATTTCGATCCTAGTTTAGGATCATTGCTTAATTAGTTTATTTCGATCCTAGTTTAGGATCATTTC
1 ATTTCGATCCTGGTTTAGGATCATTGCTTTATTAGTTTATTTCGATCCTAGTTTAGGATCATTTC
44030 CTTT-CTTT
66 CTTTACTTT
*
44038 A-TTCGATCCTGGTTTAGGATCATTGCTTTATTAGTTTATTTCGATCCTAGTTTAGGGTCATTTC
1 ATTTCGATCCTGGTTTAGGATCATTGCTTTATTAGTTTATTTCGATCCTAGTTTAGGATCATTTC
44102 CTTTGTTACTTT
66 C--T-TTACTTT
** * *
44114 ATTTTAATCCTGGTTTATGATTATTGCTTTAT
1 ATTTCGATCCTGGTTTAGGATCATTGCTTTAT
44146 CTTAATCCTG
Statistics
Matches: 158, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
72 61 0.39
73 4 0.03
74 3 0.02
75 3 0.02
76 61 0.39
77 26 0.16
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (74 bp):
ATTTCGATCCTGGTTTAGGATCATTGCTTTATTAGTTTATTTCGATCCTAGTTTAGGATCATTTC
CTTTACTTT
Found at i:44144 original size:30 final size:30
Alignment explanation
Indices: 44110--44401 Score: 363
Period size: 30 Copynumber: 10.1 Consensus size: 30
44100 TCCTTTGTTA
* *
44110 CTTTATTTTAATCCTGGTTTATGATTATTG
1 CTTTATTTTAATCCTGGTTTAGGATCATTG
* *
44140 CTTTATCTTAATCCTGGTTTAGGATTATTG
1 CTTTATTTTAATCCTGGTTTAGGATCATTG
* * *
44170 CTTCATTTTAATCATGATTTAGGATCATTG
1 CTTTATTTTAATCCTGGTTTAGGATCATTG
*
44200 C-TT-TTTTAATCCTGGTTAAGGATCATTG
1 CTTTATTTTAATCCTGGTTTAGGATCATTG
* * *
44228 CTTCATTTTAATCTTGATTTAGGATCATTG
1 CTTTATTTTAATCCTGGTTTAGGATCATTG
44258 C--T-TTTTAATCCTGGTTTAGGATCATTG
1 CTTTATTTTAATCCTGGTTTAGGATCATTG
*
44285 CTTTATTTTAATCCTGATTTAGGATCATTG
1 CTTTATTTTAATCCTGGTTTAGGATCATTG
* *
44315 C--T-TTTTAATCCTGATTTAAGATCATTG
1 CTTTATTTTAATCCTGGTTTAGGATCATTG
44342 C--T-TTTTAATCCTGGTTTAGGATCATTG
1 CTTTATTTTAATCCTGGTTTAGGATCATTG
**
44369 CTTTATTTTAATCCTGGTTTAAAATCATTG
1 CTTTATTTTAATCCTGGTTTAGGATCATTG
44399 CTT
1 CTT
44402 CATCAATTAA
Statistics
Matches: 230, Mismatches: 24, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
27 74 0.32
28 24 0.10
29 4 0.02
30 128 0.56
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.50
Consensus pattern (30 bp):
CTTTATTTTAATCCTGGTTTAGGATCATTG
Found at i:44293 original size:57 final size:58
Alignment explanation
Indices: 44110--44401 Score: 387
Period size: 57 Copynumber: 5.1 Consensus size: 58
44100 TCCTTTGTTA
* * * *
44110 CTTTATTTTAATCCTGGTTTATGATTATTGCTTTATCTTAATCCTGGTTTAGGATTATTG
1 CTTTATTTTAATCCTGATTTAGGATCATTGCTTT-T-TTAATCCTGGTTTAGGATCATTG
* * *
44170 CTTCATTTTAATCATGATTTAGGATCATTGCTTTTTTAATCCTGGTTAAGGATCATTG
1 CTTTATTTTAATCCTGATTTAGGATCATTGCTTTTTTAATCCTGGTTTAGGATCATTG
* *
44228 CTTCATTTTAATCTTGATTTAGGATCATTGC-TTTTTAATCCTGGTTTAGGATCATTG
1 CTTTATTTTAATCCTGATTTAGGATCATTGCTTTTTTAATCCTGGTTTAGGATCATTG
* *
44285 CTTTATTTTAATCCTGATTTAGGATCATTGC-TTTTTAATCCTGATTTAAGATCATTG
1 CTTTATTTTAATCCTGATTTAGGATCATTGCTTTTTTAATCCTGGTTTAGGATCATTG
* **
44342 C--T-TTTTAATCCTGGTTTAGGATCATTGCTTTATTTTAATCCTGGTTTAAAATCATTG
1 CTTTATTTTAATCCTGATTTAGGATCATTGC-TT-TTTTAATCCTGGTTTAGGATCATTG
44399 CTT
1 CTT
44402 CATCAATTAA
Statistics
Matches: 211, Mismatches: 16, Indels: 11
0.89 0.07 0.05
Matches are distributed among these distances:
54 25 0.12
55 1 0.00
56 1 0.00
57 103 0.49
58 51 0.24
59 1 0.00
60 29 0.14
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.50
Consensus pattern (58 bp):
CTTTATTTTAATCCTGATTTAGGATCATTGCTTTTTTAATCCTGGTTTAGGATCATTG
Found at i:44343 original size:84 final size:85
Alignment explanation
Indices: 44110--44401 Score: 392
Period size: 84 Copynumber: 3.4 Consensus size: 85
44100 TCCTTTGTTA
* * * *
44110 CTTTATTTTAATCCTGGTTTATGATTATTGCTTTATCTTAATCCTGGTTTAGGATTATTGCTTCA
1 CTTTATTTTAATCCTGGTTTAGGATCATTGCTTT-T-TTAATCCTGATTTAGGATCATTGC-T--
* *
44175 TTTTAATCATGATTTAGGATCATTG
61 TTTTAATCCTGGTTTAGGATCATTG
* *
44200 C-TT-TTTTAATCCTGGTTAAGGATCATTGCTTCATTTTAATCTTGATTTAGGATCATTGCTTTT
1 CTTTATTTTAATCCTGGTTTAGGATCATTGCTT--TTTTAATCCTGATTTAGGATCATTGCTTTT
44263 TAATCCTGGTTTAGGATCATTG
64 TAATCCTGGTTTAGGATCATTG
* *
44285 CTTTATTTTAATCCTGATTTAGGATCATTGC-TTTTTAATCCTGATTTAAGATCATTGCTTTTTA
1 CTTTATTTTAATCCTGGTTTAGGATCATTGCTTTTTTAATCCTGATTTAGGATCATTGCTTTTTA
44349 ATCCTGGTTTAGGATCATTG
66 ATCCTGGTTTAGGATCATTG
**
44369 CTTTATTTTAATCCTGGTTTAAAATCATTGCTT
1 CTTTATTTTAATCCTGGTTTAGGATCATTGCTT
44402 CATCAATTAA
Statistics
Matches: 182, Mismatches: 15, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
84 78 0.43
85 25 0.14
86 3 0.02
87 25 0.14
88 46 0.25
89 3 0.02
90 2 0.01
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.50
Consensus pattern (85 bp):
CTTTATTTTAATCCTGGTTTAGGATCATTGCTTTTTTAATCCTGATTTAGGATCATTGCTTTTTA
ATCCTGGTTTAGGATCATTG
Found at i:45010 original size:27 final size:26
Alignment explanation
Indices: 44912--45002 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 26
44902 AGGGACTTAG
44912 GGGGCATTTTAGTCATTTGCAAGTCCA
1 GGGGCATTTTAGTCATTTGCAA-TCCA
*
44939 GGGACATTTTAGTCATTTGCACATCCA
1 GGGGCATTTTAGTCATTTGCA-ATCCA
*
44966 GGGGCATTTTGGTCATTTGCATTAT-CA
1 GGGGCATTTTAGTCATTTGCA--ATCCA
44993 GGGGCATTTT
1 GGGGCATTTT
45003 GGCCATTTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
27 55 0.95
28 3 0.05
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (26 bp):
GGGGCATTTTAGTCATTTGCAATCCA
Found at i:46255 original size:24 final size:23
Alignment explanation
Indices: 46211--46271 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
46201 GCTTTAAAAA
** *
46211 AAACGATAAATAGGTATAGAGAT
1 AAACGATAAATAAATACAGAGAT
46234 AAACTGATAAATAAATACAGAGAAT
1 AAAC-GATAAATAAATACAGAG-AT
46259 AATA-GATAAATAA
1 AA-ACGATAAATAA
46272 GAGAATAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 4 0.12
24 23 0.72
25 4 0.12
26 1 0.03
ACGTcount: A:0.59, C:0.05, G:0.15, T:0.21
Consensus pattern (23 bp):
AAACGATAAATAAATACAGAGAT
Found at i:46276 original size:19 final size:20
Alignment explanation
Indices: 46244--46289 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
46234 AAACTGATAA
*
46244 ATAAATACAGAGAATAATAG
1 ATAAATACAGAGAATAACAG
46264 ATAAATA-AGAGAATAACAG
1 ATAAATACAGAGAATAACAG
46283 ATAAATA
1 ATAAATA
46290 TGTAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.63, C:0.04, G:0.13, T:0.20
Consensus pattern (20 bp):
ATAAATACAGAGAATAACAG
Found at i:46327 original size:18 final size:17
Alignment explanation
Indices: 46294--46329 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
46284 TAAATATGTA
46294 AATAAAAAAGGGATAAT
1 AATAAAAAAGGGATAAT
*
46311 AATAAATAAATGGATAAT
1 AATAAA-AAAGGGATAAT
46329 A
1 A
46330 GCTAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.22
Consensus pattern (17 bp):
AATAAAAAAGGGATAAT
Found at i:46342 original size:23 final size:22
Alignment explanation
Indices: 46315--46431 Score: 86
Period size: 23 Copynumber: 5.3 Consensus size: 22
46305 GATAATAATA
*
46315 AATAAATGGATAATAGCTAAATT
1 AATAAATAGATAATAG-TAAATT
*
46338 AATAAAAAGATAAATAGT--A--
1 AATAAATAGAT-AATAGTAAATT
46357 AATAAATAGATAATAGTTAAATT
1 AATAAATAGATAATAG-TAAATT
46380 AATAAATA-A-AA-AGATAAATAGT
1 AATAAATAGATAATAG-TAAAT--T
*
46402 AAATAAATAAATAATAGTTAAATT
1 -AATAAATAGATAATAG-TAAATT
46426 AATAAA
1 AATAAA
46432 AAAAATCTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 24
0.73 0.05 0.23
Matches are distributed among these distances:
18 5 0.06
19 11 0.14
20 7 0.09
21 4 0.05
22 2 0.03
23 32 0.42
24 7 0.09
25 2 0.03
26 7 0.09
ACGTcount: A:0.62, C:0.01, G:0.09, T:0.28
Consensus pattern (22 bp):
AATAAATAGATAATAGTAAATT
Found at i:46362 original size:27 final size:27
Alignment explanation
Indices: 46355--46415 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
46345 AGATAAATAG
* *
46355 TAAATAAATAGAT-AATAGTTAAATTAA
1 TAAATAAAAAGATAAATAG-TAAATAAA
46382 TAAATAAAAAGATAAATAGTAAATAAA
1 TAAATAAAAAGATAAATAGTAAATAAA
46409 TAAATAA
1 TAAATAA
46416 TAGTTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (27 bp):
TAAATAAAAAGATAAATAGTAAATAAA
Found at i:46383 original size:19 final size:18
Alignment explanation
Indices: 46305--46414 Score: 61
Period size: 19 Copynumber: 6.0 Consensus size: 18
46295 ATAAAAAAGG
* *
46305 GATAATAATAAATAAATG
1 GATAATAGTAAATAAATA
*
46323 GATAATAGCTAAATTAATAAAAA
1 GATAATAG-T--A--AATAAATA
46346 GATAAATAGTAAATAAATA
1 GAT-AATAGTAAATAAATA
*
46365 GATAATAGTTAAATTAATA
1 GATAATAG-TAAATAAATA
*
46384 AATAA-A--AAGATAAATA
1 GATAATAGTAA-ATAAATA
46400 G-TAA-A-TAAATAAATA
1 GATAATAGTAAATAAATA
46415 ATAGTTAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
15 13 0.17
16 8 0.11
18 13 0.17
19 24 0.32
21 2 0.03
23 10 0.13
24 5 0.07
ACGTcount: A:0.63, C:0.01, G:0.09, T:0.27
Consensus pattern (18 bp):
GATAATAGTAAATAAATA
Found at i:46388 original size:46 final size:46
Alignment explanation
Indices: 46308--46436 Score: 187
Period size: 46 Copynumber: 2.9 Consensus size: 46
46298 AAAAAGGGAT
* * *
46308 AATAATAAATAAATGGATAATAGCTAAA-T--T-AATAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAGATA
46350 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAGATA
*
46396 AATAGTAAATAAATAAATAATAGTTAAATTAATAAA-AAAAA
1 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAA
46437 TCTTTTTGGT
Statistics
Matches: 79, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
42 25 0.32
43 1 0.01
45 6 0.08
46 47 0.59
ACGTcount: A:0.64, C:0.01, G:0.08, T:0.27
Consensus pattern (46 bp):
AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAGATA
Found at i:46415 original size:19 final size:20
Alignment explanation
Indices: 46338--46415 Score: 65
Period size: 19 Copynumber: 4.0 Consensus size: 20
46328 TAGCTAAATT
46338 AATAAA-AAGATAAATAG-TA
1 AATAAATAA-ATAAATAGATA
* *
46357 AATAAATAGAT-AATAGTTA
1 AATAAATAAATAAATAGATA
* *
46376 AATTAATAAATAAAAAGATA
1 AATAAATAAATAAATAGATA
* *
46396 AAT-AGTAAATAAATAAATA
1 AATAAATAAATAAATAGATA
46415 A
1 A
46416 TAGTTAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.10
19 33 0.69
20 10 0.21
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.26
Consensus pattern (20 bp):
AATAAATAAATAAATAGATA
Found at i:46429 original size:19 final size:18
Alignment explanation
Indices: 46306--46431 Score: 59
Period size: 19 Copynumber: 7.1 Consensus size: 18
46296 TAAAAAAGGG
* **
46306 ATAATAATAAATAAATGG
1 ATAATAGTAAATAAATAA
*
46324 ATAATAGCTAAATTAATAA
1 ATAATAG-TAAATAAATAA
* *
46343 A-AAGA-TAAAT-AGTAA
1 ATAATAGTAAATAAATAA
**
46358 ATAAATAG-ATAATAGTTAA
1 AT-AATAGTA-AATAAATAA
*
46377 AT--TAATAAATAAA-AA
1 ATAATAGTAAATAAATAA
46392 GATAAATAGTAAATAAATAA
1 -AT-AATAGTAAATAAATAA
*
46412 ATAATAGTTAAATTAATAA
1 ATAATAG-TAAATAAATAA
46431 A
1 A
46432 AAAAATCTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 25
0.68 0.12 0.21
Matches are distributed among these distances:
15 7 0.09
16 13 0.16
17 5 0.06
18 17 0.21
19 37 0.46
20 2 0.02
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.29
Consensus pattern (18 bp):
ATAATAGTAAATAAATAA
Found at i:47966 original size:54 final size:54
Alignment explanation
Indices: 47868--48257 Score: 498
Period size: 54 Copynumber: 7.2 Consensus size: 54
47858 GCGAAAACCT
* * * *
47868 TTCTTGGAATGATCGCACTGGATCCATTTGAAAATCAACTCTGATCATCAAAAAC
1 TTCTTGGAATGACCGCACTGGAT-CATCTGAAGATCAACTCTGATCATTAAAAAC
* * * * *
47923 GTCTTGGAATGACTGCACTGTATCAAT-TGAAGATCAACTCTGATCATTGAAAAT
1 TTCTTGGAATGACCGCACTGGATC-ATCTGAAGATCAACTCTGATCATTAAAAAC
* * * * *
47977 TTTTTGGAAAGACCGCACTAGATCATCTG-GGATCAACTCTGATCTTTAAAAAC
1 TTCTTGGAATGACCGCACTGGATCATCTGAAGATCAACTCTGATCATTAAAAAC
48030 TTCTTGGAATGACCGCACTGGATCATCTG-AGAATCAACTCTGATCATTAAAAAC
1 TTCTTGGAATGACCGCACTGGATCATCTGAAG-ATCAACTCTGATCATTAAAAAC
* * *
48084 TTCTTGTAAGGACCGCACTGGATCATCTGGAGATCAACTCTGATCATTAAAAAC
1 TTCTTGGAATGACCGCACTGGATCATCTGAAGATCAACTCTGATCATTAAAAAC
* * ** *
48138 GTCTTCGAATGACCGCACTGGATCATCTGTGGATCAACTCTGATCATTGAAAAC
1 TTCTTGGAATGACCGCACTGGATCATCTGAAGATCAACTCTGATCATTAAAAAC
* * * *
48192 TTCTTGGAATGACCGCACTGGATCATCTTAGGATCAACTCTGACCATTGAAAAC
1 TTCTTGGAATGACCGCACTGGATCATCTGAAGATCAACTCTGATCATTAAAAAC
48246 TTCTTGGAATGA
1 TTCTTGGAATGA
48258 GATCAACTCT
Statistics
Matches: 294, Mismatches: 37, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
53 49 0.17
54 222 0.76
55 23 0.08
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (54 bp):
TTCTTGGAATGACCGCACTGGATCATCTGAAGATCAACTCTGATCATTAAAAAC
Found at i:48262 original size:35 final size:35
Alignment explanation
Indices: 48223--48807 Score: 745
Period size: 35 Copynumber: 16.8 Consensus size: 35
48213 ATCATCTTAG
* ** * *
48223 GATCAACTCTGACCATTGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
48258 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
*
48293 GATCAACTCTGATCATCGAAAACTTCTTGAAA-GAA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACG-A
* * *
48328 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
* *
48363 GATAAACTCTGATTAT-AAAAATCTTCTTGAAACGA
1 GATCAACTCTGATCATCAAAAA-CTTCTTGAAACGA
*
48398 GATCAACTCTGATCATCGAAAACTTCTTGAAA-GAA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACG-A
* * *
48433 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
* *
48468 GATAAACTCTGATTAT-AAAAATCTTCTTGAAACGA
1 GATCAACTCTGATCATCAAAAA-CTTCTTGAAACGA
* * *
48503 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
* * *
48538 GATAAACTCTGATCATAAAAAACTACTTGAAACGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
*
48573 GATCAACTCTGAT-A-AAAAAATCTTCTTGAAACGA
1 GATCAACTCTGATCATCAAAAA-CTTCTTGAAACGA
* * *
48607 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
* * *
48642 GATAAACTCTGATCATAAAAAACTACTTGAAACGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
*
48677 GATCAACTCTGAT-A-AAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
*
48710 GATCAACTCTGATCATAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCAT-CAAAAACTTCTTGAAACGA
* *
48746 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
*
48781 GATCAACTCTGATCATAAAAAACTTCT
1 GATCAACTCTGATCATCAAAAACTTCT
48808 CTGATCATGA
Statistics
Matches: 486, Mismatches: 50, Indels: 28
0.86 0.09 0.05
Matches are distributed among these distances:
33 37 0.08
34 38 0.08
35 362 0.74
36 49 0.10
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.26
Consensus pattern (35 bp):
GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
Found at i:48352 original size:105 final size:103
Alignment explanation
Indices: 48223--49096 Score: 1077
Period size: 105 Copynumber: 8.5 Consensus size: 103
48213 ATCATCTTAG
* * * * *
48223 GATCAACTCTGACCATTGAAAACTTCTTGGAATGAGATCAACTCTGATCATCAAAAACTTCTTGA
1 GATCAACTCTGATCA-AGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGA
48288 AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGAA
65 AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAG-A
* * *
48328 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATAAACTCTGATTATAAAAATCTTCTTGA
1 GATCAACTCTGATCAA-GAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGA
48393 AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGAA
65 AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAG-A
* * *
48433 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATAAACTCTGATTATAAAAATCTTCTTGA
1 GATCAACTCTGATCAA-GAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGA
*
48498 AACGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
65 AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAA-GA
* * * *
48538 GATAAACTCTGATCATAAAAAACTACTTGAAACGAGATCAACTCTGAT-A-AAAAAATCTTCTTG
1 GATCAACTCTGATCA-AGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAA-CTTCTTG
*
48601 AAACGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
64 AAACGAGATCAACTCTGATCATCGAAAACTTCTTGAAA-GA
* * * *
48642 GATAAACTCTGATCATAAAAAACTACTTGAAACGAGATCAACTCTGAT-A-AAAAAACTTCTTGA
1 GATCAACTCTGATCA-AGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGA
**
48705 AACGAGATCAACTCTGATCATAAAAAAACTTCTTGAAACGA
65 AACGAGATCAACTCTGATCAT-CGAAAACTTCTTGAAA-GA
*
48746 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTC-T--
1 GATCAACTCTGATCA-AGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGA
* **
48808 --C-TGATC-A---TGA--A-AAAAAACTTCTTGAAATGA
65 AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAA-GA
* *
48838 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGATATCAACTCTGATCATAAAAAACTTTTTGA
1 GATCAACTCTGATCAA-GAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGA
* * *
48903 AAGGAGATCAACTTTGATCATCGAAAACTTCTTAAAATGA
65 AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAA-GA
* **
48943 GATCAACTCTGATCCTAA-AAAACTTCTTGAAATGAGATCAACTCTGATCATCGAAAACTTCTTG
1 GATCAACTCTGAT-C-AAGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTG
* *
49007 AAAGGAGATCAACTCTGATCAT--AAAACTTCTTGAAACAA
64 AAACGAGATCAACTCTGATCATCGAAAACTTCTTGAAA-GA
* *
49046 GATCAACTCTGATCATAGAAAGCTTCTTGAAATGAGATCAACTCTGATCAT
1 GATCAACTCTGATCA-AGAAAACTTCTTGAAAGGAGATCAACTCTGATCAT
49097 CGAAAACCTC
Statistics
Matches: 700, Mismatches: 44, Indels: 52
0.88 0.06 0.07
Matches are distributed among these distances:
92 75 0.11
93 1 0.00
94 1 0.00
96 3 0.00
98 4 0.01
99 2 0.00
100 4 0.01
101 2 0.00
102 5 0.01
103 92 0.13
104 164 0.23
105 332 0.47
106 13 0.02
107 2 0.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (103 bp):
GATCAACTCTGATCAAGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGAA
ACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGA
Found at i:48833 original size:92 final size:90
Alignment explanation
Indices: 48716--48897 Score: 319
Period size: 92 Copynumber: 2.0 Consensus size: 90
48706 ACGAGATCAA
*
48716 CTCTGATCATAAAAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
1 CTCTGATCATAAAAAAACTTCTTGAAACGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
48781 GATCAACTCTGATCATAAAAAACTT
66 GATCAACTCTGATCATAAAAAACTT
*
48806 CTCTGATCATGAAAAAAAACTTCTTGAAATGAGATCAACTCTGATCAACGAAAACTTCTTGAAAG
1 CTCTGATCAT--AAAAAAACTTCTTGAAACGAGATCAACTCTGATCAACGAAAACTTCTTGAAAG
*
48871 GATATCAACTCTGATCATAAAAAACTT
64 GAGATCAACTCTGATCATAAAAAACTT
48898 TTTGAAAGGA
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
90 10 0.11
92 77 0.89
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (90 bp):
CTCTGATCATAAAAAAACTTCTTGAAACGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
GATCAACTCTGATCATAAAAAACTT
Found at i:48837 original size:20 final size:22
Alignment explanation
Indices: 48797--48837 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
48787 CTCTGATCAT
*
48797 AAAAAACTTCTCTGATCATGAA
1 AAAAAACTTCTCTGATAATGAA
48819 AAAAAACTTCT-TGA-AATGA
1 AAAAAACTTCTCTGATAATGA
48838 GATCAACTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 3 0.17
22 11 0.61
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.27
Consensus pattern (22 bp):
AAAAAACTTCTCTGATAATGAA
Found at i:49096 original size:35 final size:35
Alignment explanation
Indices: 48821--49108 Score: 393
Period size: 35 Copynumber: 8.3 Consensus size: 35
48811 ATCATGAAAA
48821 AAAACTTCTTGAAATGAGATCAACTCTGATCA-ACG
1 AAAACTTCTTGAAATGAGATCAACTCTGATCATA-G
* * *
48856 AAAACTTCTTGAAAGGATATCAACTCTGATCATAA
1 AAAACTTCTTGAAATGAGATCAACTCTGATCATAG
* * * *
48891 AAAACTTTTTGAAAGGAGATCAACTTTGATCATCG
1 AAAACTTCTTGAAATGAGATCAACTCTGATCATAG
* * *
48926 AAAACTTCTTAAAATGAGATCAACTCTGATCCTAA
1 AAAACTTCTTGAAATGAGATCAACTCTGATCATAG
*
48961 AAAACTTCTTGAAATGAGATCAACTCTGATCATCG
1 AAAACTTCTTGAAATGAGATCAACTCTGATCATAG
*
48996 AAAACTTCTTGAAAGGAGATCAACTCTGATCAT--
1 AAAACTTCTTGAAATGAGATCAACTCTGATCATAG
**
49029 AAAACTTCTTGAAACAAGATCAACTCTGATCATAG
1 AAAACTTCTTGAAATGAGATCAACTCTGATCATAG
* *
49064 AAAGCTTCTTGAAATGAGATCAACTCTGATCATCG
1 AAAACTTCTTGAAATGAGATCAACTCTGATCATAG
*
49099 AAAACCTCTT
1 AAAACTTCTT
49109 ATGAAAGACC
Statistics
Matches: 222, Mismatches: 28, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
33 31 0.14
35 190 0.86
36 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (35 bp):
AAAACTTCTTGAAATGAGATCAACTCTGATCATAG
Found at i:49185 original size:54 final size:54
Alignment explanation
Indices: 49098--49297 Score: 249
Period size: 54 Copynumber: 3.7 Consensus size: 54
49088 TCTGATCATC
* * ** * * *
49098 GAAAACCTCTTATGAAAGACCGCACAAGGTCATCTGAAGATCAACTTAAATTTCT
1 GAAAACTTC-TATGAAAGACCACACTGGGTCATCTTAAGATCAATTTAGATTTCT
* * *
49153 GAAAACTTATATGAAAGACCACACTGGATCATCTTAAGAT-ATGTTTAGATTTCT
1 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCA-ATTTAGATTTCT
* *
49207 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTATTTAGATCTCT
1 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAATTTAGATTTCT
* *
49261 GAAAACTTCTATGAAAGACCATACTGGGTCATTTTAA
1 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
49298 ACACATGTAC
Statistics
Matches: 126, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 118 0.94
55 7 0.06
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (54 bp):
GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAATTTAGATTTCT
Found at i:49238 original size:108 final size:109
Alignment explanation
Indices: 49098--49297 Score: 276
Period size: 108 Copynumber: 1.8 Consensus size: 109
49088 TCTGATCATC
* *
49098 GAAAACCTCTTATGAAAGACCGCACAAGGTCATCTGAAGATCAACTTAAATTTCTGAAAACTTAT
1 GAAAACCTCTTATGAAAGACCACACAAGGTCATCTGAAGATCAACTTAAATCTCTGAAAACTTAT
49163 ATGAAAGACCACACTGGATCATCTTAAGATATGTTTAGATTTCT
66 ATGAAAGACCACACTGGATCATCTTAAGATATGTTTAGATTTCT
* ** * * * * *
49207 GAAAACTTC-TATGAAAGACCACACTGGGTCATCTTAAGATCTATTTAGATCTCTGAAAACTTCT
1 GAAAACCTCTTATGAAAGACCACACAAGGTCATCTGAAGATCAACTTAAATCTCTGAAAACTTAT
* * *
49271 ATGAAAGACCATACTGGGTCATTTTAA
66 ATGAAAGACCACACTGGATCATCTTAA
49298 ACACATGTAC
Statistics
Matches: 78, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
108 70 0.90
109 8 0.10
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (109 bp):
GAAAACCTCTTATGAAAGACCACACAAGGTCATCTGAAGATCAACTTAAATCTCTGAAAACTTAT
ATGAAAGACCACACTGGATCATCTTAAGATATGTTTAGATTTCT
Found at i:50661 original size:21 final size:21
Alignment explanation
Indices: 50637--50692 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
50627 ATTTCCTCCG
*
50637 TCTTTTGCTTTTTCAA-CTTTT
1 TCTTTT-CTTTTTCAATCATTT
50658 TCTTTTCTTTTTCAATCATTT
1 TCTTTTCTTTTTCAATCATTT
50679 TCTTCTT-TTTTTCA
1 TCTT-TTCTTTTTCA
50693 TTTTGTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 9 0.28
21 21 0.66
22 2 0.06
ACGTcount: A:0.11, C:0.20, G:0.02, T:0.68
Consensus pattern (21 bp):
TCTTTTCTTTTTCAATCATTT
Found at i:50669 original size:20 final size:20
Alignment explanation
Indices: 50637--50704 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
50627 ATTTCCTCCG
50637 TCTTTTGCTTTTTCAACTTTT
1 TCTTTT-CTTTTTCAACTTTT
*
50658 TCTTTTCTTTTTCAATCATTT
1 TCTTTTCTTTTTCAA-CTTTT
50679 TCTTCTT-TTTTTC-A-TTTT
1 TCTT-TTCTTTTTCAACTTTT
50697 GTCTTTTC
1 -TCTTTTC
50705 CTCCCCATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
18 5 0.12
19 4 0.10
20 10 0.24
21 20 0.49
22 2 0.05
ACGTcount: A:0.09, C:0.19, G:0.03, T:0.69
Consensus pattern (20 bp):
TCTTTTCTTTTTCAACTTTT
Found at i:53789 original size:8 final size:8
Alignment explanation
Indices: 53750--53940 Score: 60
Period size: 8 Copynumber: 24.5 Consensus size: 8
53740 AAATAATAAT
53750 AATA-ATA
1 AATAGATA
53757 AA-AGATA
1 AATAGATA
*
53764 AATAGGTA
1 AATAGATA
* *
53772 TAGAGATA
1 AATAGATA
*
53780 AATTGATA
1 AATAGATA
53788 AATAGATA
1 AATAGATA
* *
53796 CAGAGA-A
1 AATAGATA
53803 TAATAGATA
1 -AATAGATA
*
53812 AATAGGTA
1 AATAGATA
* *
53820 AGTA-AAA
1 AATAGATA
**
53827 AAGGGATAA
1 AATAGAT-A
*
53836 TAATAAATA
1 -AATAGATA
*
53845 AATGGAT-
1 AATAGATA
*
53852 AATAGCTA
1 AATAGATA
53860 AATTA-ATA
1 AA-TAGATA
*
53868 AAAAGATA
1 AATAGATA
53876 AATAG-TA
1 AATAGATA
*
53883 AATAAATA
1 AATAGATA
*
53891 GATA-ATA
1 AATAGATA
** *
53898 GTTTA-ATT
1 -AATAGATA
*
53906 AATAAATA
1 AATAGATA
*
53914 AAAAGATA
1 AATAGATA
53922 AATAG-TA
1 AATAGATA
*
53929 AATAAATA
1 AATAGATA
53937 AATA
1 AATA
53941 ATAGTTAAAT
Statistics
Matches: 128, Mismatches: 42, Indels: 27
0.65 0.21 0.14
Matches are distributed among these distances:
6 1 0.01
7 33 0.26
8 85 0.66
9 5 0.04
10 4 0.03
ACGTcount: A:0.60, C:0.01, G:0.13, T:0.26
Consensus pattern (8 bp):
AATAGATA
Found at i:53791 original size:24 final size:24
Alignment explanation
Indices: 53753--53819 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
53743 TAATAATAAT
* *
53753 AATAAAAGATAAATAGGTATAGAG
1 AATAATAGATAAATAGGTACAGAG
* *
53777 -ATAAATTGATAAATAGATACAGAG
1 AAT-AATAGATAAATAGGTACAGAG
53801 AATAATAGATAAATAGGTA
1 AATAATAGATAAATAGGTA
53820 AGTAAAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
23 2 0.06
24 31 0.89
25 2 0.06
ACGTcount: A:0.57, C:0.01, G:0.18, T:0.24
Consensus pattern (24 bp):
AATAATAGATAAATAGGTACAGAG
Found at i:53888 original size:19 final size:18
Alignment explanation
Indices: 53864--53899 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
53854 TAGCTAAATT
53864 AATAAAAAGATAAATAGTA
1 AATAAAAAGAT-AATAGTA
*
53883 AATAAATAGATAATAGT
1 AATAAAAAGATAATAGT
53900 TTAATTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (18 bp):
AATAAAAAGATAATAGTA
Found at i:53895 original size:27 final size:27
Alignment explanation
Indices: 53881--53941 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
53871 AGATAAATAG
* * *
53881 TAAATAAATAGAT-AATAGTTTAATTAA
1 TAAATAAAAAGATAAATAG-TAAATAAA
53908 TAAATAAAAAGATAAATAGTAAATAAA
1 TAAATAAAAAGATAAATAGTAAATAAA
53935 TAAATAA
1 TAAATAA
53942 TAGTTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (27 bp):
TAAATAAAAAGATAAATAGTAAATAAA
Found at i:53895 original size:42 final size:42
Alignment explanation
Indices: 53834--53959 Score: 171
Period size: 46 Copynumber: 2.9 Consensus size: 42
53824 AAAAAGGGAT
* * *
53834 AATAATAAATAAATGGATAATAGCTAAATTAATAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAAATTAATAAAAAGATA
*
53876 AATAGTAAATAAATAGATAATAGTTTAATTAATAAATAAAAAGATA
1 AATAGTAAATAAATAGATAATAG-TT-A--AATTAATAAAAAGATA
*
53922 AATAGTAAATAAATAAATAATAGTTAAATTAATAAAAA
1 AATAGTAAATAAATAGATAATAGTTAAATTAATAAAAA
53960 AAATCTTTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
42 32 0.43
43 1 0.01
44 2 0.03
45 2 0.03
46 37 0.50
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.29
Consensus pattern (42 bp):
AATAGTAAATAAATAGATAATAGTTAAATTAATAAAAAGATA
Found at i:53914 original size:46 final size:46
Alignment explanation
Indices: 53864--53962 Score: 173
Period size: 46 Copynumber: 2.2 Consensus size: 46
53854 TAGCTAAATT
* *
53864 AATAAAAAGATAAATAGTAAATAAATAGATAATAGTTTAATTAATA
1 AATAAAAAGATAAATAGTAAATAAATAAATAATAGTTAAATTAATA
53910 AATAAAAAGATAAATAGTAAATAAATAAATAATAGTTAAATTAATA
1 AATAAAAAGATAAATAGTAAATAAATAAATAATAGTTAAATTAATA
53956 AA-AAAAA
1 AATAAAAA
53963 TCTTTTTGGT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 5 0.10
46 46 0.90
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (46 bp):
AATAAAAAGATAAATAGTAAATAAATAAATAATAGTTAAATTAATA
Found at i:53941 original size:19 final size:19
Alignment explanation
Indices: 53908--53957 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
53898 GTTTAATTAA
53908 TAAATAAA-AAGATAAATAG-
1 TAAATAAATAA-AT-AATAGT
53927 TAAATAAATAAATAATAGT
1 TAAATAAATAAATAATAGT
*
53946 TAAATTAATAAA
1 TAAATAAATAAA
53958 AAAAATCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.18
19 21 0.75
20 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (19 bp):
TAAATAAATAAATAATAGT
Found at i:60008 original size:13 final size:15
Alignment explanation
Indices: 59983--60014 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
59973 GAGAACACAA
59983 CTTTACAATC-TTTT
1 CTTTACAATCTTTTT
59997 CTTTAC-ATCTTTTT
1 CTTTACAATCTTTTT
60011 CTTT
1 CTTT
60015 TCTTCTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (15 bp):
CTTTACAATCTTTTT
Found at i:63781 original size:56 final size:55
Alignment explanation
Indices: 63695--63800 Score: 126
Period size: 56 Copynumber: 1.9 Consensus size: 55
63685 CAAAGCATAG
* * *
63695 AGATCAATAAATAAACCAAACATATGAATTAAGTTACTAAGGATTCACTTAAAACAT
1 AGATCAATAAATAAACCAAACATATAAATT-AGCTACTAAAGATTCA-TTAAAACAT
* *
63752 AGATCAAT-AATAATCCAATTCA-ATAAATTAGCTACTAAAGATTCATTAA
1 AGATCAATAAATAAACCAA-ACATATAAATTAGCTACTAAAGATTCATTAA
63801 CATAACCGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
54 4 0.09
55 14 0.33
56 15 0.35
57 10 0.23
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28
Consensus pattern (55 bp):
AGATCAATAAATAAACCAAACATATAAATTAGCTACTAAAGATTCATTAAAACAT
Found at i:70676 original size:15 final size:16
Alignment explanation
Indices: 70658--70691 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
70648 TGAAAGAATG
70658 CAATTAAAC-AGAAAA
1 CAATTAAACTAGAAAA
*
70673 CAATTATACTAGAAAA
1 CAATTAAACTAGAAAA
70689 CAA
1 CAA
70692 AGCAAAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.62, C:0.15, G:0.06, T:0.18
Consensus pattern (16 bp):
CAATTAAACTAGAAAA
Found at i:77301 original size:49 final size:49
Alignment explanation
Indices: 77171--77309 Score: 167
Period size: 49 Copynumber: 2.8 Consensus size: 49
77161 TTTTTTTTTC
77171 AAAAACGCAAAACCTAA--TTTTTTTTATCAAAAACGGAAAACAAAAAAAT
1 AAAAACGCAAAA-C-AATTTTTTTTTTATCAAAAACGGAAAACAAAAAAAT
** *
77220 AAAAACGCAAAACAATTTTTTTTTTAGAAAAAACGGAAAAC-AAAAATT
1 AAAAACGCAAAACAATTTTTTTTTTATCAAAAACGGAAAACAAAAAAAT
* * *
77268 AAAAGACGGAAAAGAATTTTTTTTTTTTCAAAAACGGGAAAA
1 AAAA-ACGCAAAACAATTTTTTTTTTATCAAAAAC-GGAAAA
77310 ATGGATTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
47 2 0.03
48 11 0.14
49 59 0.76
50 6 0.08
ACGTcount: A:0.54, C:0.11, G:0.10, T:0.25
Consensus pattern (49 bp):
AAAAACGCAAAACAATTTTTTTTTTATCAAAAACGGAAAACAAAAAAAT
Found at i:77629 original size:15 final size:16
Alignment explanation
Indices: 77605--77644 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
77595 AGAGGTTGAA
*
77605 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
77620 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
77636 AGAAAACAA
1 AGAAAACAA
77645 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:80608 original size:22 final size:22
Alignment explanation
Indices: 80578--80623 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
80568 CTCTTCCCTC
*
80578 TCTTCTCTT-TCTTTTCTTTTCT
1 TCTTCTCTTCT-TTTTCTTGTCT
*
80600 TCTTTTCTTCTTTTTCTTGTCT
1 TCTTCTCTTCTTTTTCTTGTCT
80622 TC
1 TC
80624 CTATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (22 bp):
TCTTCTCTTCTTTTTCTTGTCT
Found at i:81175 original size:17 final size:17
Alignment explanation
Indices: 81149--81182 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
81139 CATTAAAAAG
81149 AAAAGCTTTTATATTTTA
1 AAAAGCTTTTAT-TTTTA
81167 AAAAG-TTTTATTTTTA
1 AAAAGCTTTTATTTTTA
81183 TTTTTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (17 bp):
AAAAGCTTTTATTTTTA
Found at i:81198 original size:22 final size:22
Alignment explanation
Indices: 81155--81198 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
81145 AAAGAAAAGC
81155 TTTTATATTTTAAAAAGTTTTAT
1 TTTTATATTTTAAAAAG-TTTAT
*
81178 TTTTATTTTTTATAAAA-TTTA
1 TTTTATATTTTA-AAAAGTTTA
81199 AATGGAGCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTATATTTTAAAAAGTTTAT
Found at i:85321 original size:18 final size:17
Alignment explanation
Indices: 85278--85322 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
85268 GAAATCACGG
*
85278 AATAAGAAATAAAGAGA
1 AATAAGAAATAAAGAAA
*
85295 CATAAAGAAATAAAGAAA
1 AAT-AAGAAATAAAGAAA
85313 AATAGAGAAA
1 AATA-AGAAA
85323 AGAAGAAGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.71, C:0.02, G:0.16, T:0.11
Consensus pattern (17 bp):
AATAAGAAATAAAGAAA
Found at i:93014 original size:21 final size:21
Alignment explanation
Indices: 92989--93071 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
92979 TATCTTAGAT
92989 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
93010 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
**
93031 ATAAATAATGA-ATTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
*
93053 ATAAATAATTTATATTTAA
1 AT-AATAATATAT-TTTAA
93072 TTACTAAACG
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
21 18 0.36
22 22 0.44
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:93022 original size:25 final size:25
Alignment explanation
Indices: 92991--93039 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
92981 TCTTAGATAT
*
92991 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
93016 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
93040 GAATTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:104522 original size:2 final size:2
Alignment explanation
Indices: 104515--104562 Score: 51
Period size: 2 Copynumber: 23.0 Consensus size: 2
104505 TTCTTTTATT
* * *
104515 TA TA TA TA TA TA TA TA TA TA CA TA TC TA TA CTA TC TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA
104559 TA TA
1 TA TA
104563 AAAGTACGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
2 34 0.89
3 4 0.11
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:105697 original size:503 final size:502
Alignment explanation
Indices: 104698--105707 Score: 1574
Period size: 503 Copynumber: 2.0 Consensus size: 502
104688 CATCCTCATT
* * *
104698 AATT-AGGATTCAACGTGGCCAATAGGAATGCTCCACATCATCTGTAATATCTAATTTCGCCCAA
1 AATTGAGGATCCAACGTGGCCAACAGGAATGCTACACATCATCTGTAATATCTAATTTCGCCCAA
* * * *
104762 AACATTCTACAAGTTGGTTTAGGAGAAGATCAATTCTGTTCATAAATTTCAAGGGTAAAATCGTC
66 AACATTCTACAAGTCGGTTTAGGAGAAGATCAATTCTGTCCATAAATTTCAAGAGAAAAATCGTC
* * *
104827 CACCGGAACGGCAGAATTAGGTCTTGAGGTGAACATAAAAGTTGTAGATCTTGGAATCCTCTTTC
131 CACCGAAACGGCAGAATTAGGTCTTGAGGTAAACATAAAAGTTGTAGACCTTGGAATCCTCTTTC
* * * * ** *
104892 CAACGGTACATCATTTGTATTTTTCTGAGTTCTGGATCAAAAGTTATGAATTTTCTTCCAGAACT
196 CAACGGTACATCACTTGCATTTTTCTAAGCTCTAAATCAAAAGTTATGAATTTTCTTCCAAAACT
* * *
104957 GCTATTGTGAAATCCTCCTTTAAATATGATTTAACAATGCTGCATCAGGACTGAATCATTACTGC
261 ACTATTGTGAAATCCTCCTTTAAATATGATTTAACAATGCTGCATCAAGACTGAATCAATACTGC
* *
105022 ATTATAATTACTGATTGGACTTGGACTCCTTCTTTGGGCTCCCATATTAACGAGTTGGGTCTAAG
326 ATCATAATTACTAATTGGACTTGGACTCCTTCTTTGGGCTCCCATATTAACGAGTTGGGTCTAAG
* *
105087 AATATCAGATTTAGCCTTCAGGACATCTAGCTTGGCAATTTGGGCTTCATAGACTCAAACTGGCC
391 AATATCAGATTTAGCCTTAAGGACATCTAGCTTGGCAATTTGGGCTTCATAGACTCAAACGGGCC
*
105152 TAATGGGCCTACTAGGCCGAAATGAGACAAAATCAGTAGTTTCTCCA
456 TAATGAGCCTACTAGGCCGAAATGAGACAAAATCAGTAGTTTCTCCA
*
105199 AATTGAGGATCCAACGTGGCCAACAGGAATGCTACACATCATCTGTAGTATCTGAATTTCGCCCA
1 AATTGAGGATCCAACGTGGCCAACAGGAATGCTACACATCATCTGTAATATCT-AATTTCGCCCA
* * *
105264 AAACATTCTCCAAGTCGGTTTAGGAGAAGATCAATTTTGTCCATAACTTTCAAGAGAAAAATCGT
65 AAACATTCTACAAGTCGGTTTAGGAGAAGATCAATTCTGTCCATAAATTTCAAGAGAAAAATCGT
* * * * *
105329 TCACTGAAACGGTAGAATTAGGTCTTGAGGTAAACATAAAAGTTGTATACCTTGGAATTCTCTTT
130 CCACCGAAACGGCAGAATTAGGTCTTGAGGTAAACATAAAAGTTGTAGACCTTGGAATCCTCTTT
* *
105394 CCAACGGTACCTTACTTGCATTTTTCTAAGCTCTAAATCAAAAGTTATGAATTTTCTTCCAAAAC
195 CCAACGGTACATCACTTGCATTTTTCTAAGCTCTAAATCAAAAGTTATGAATTTTCTTCCAAAAC
* * *
105459 TACTCTTGTGAAGTCCTCCTTTGAATA-GAATTTAACAATGCTGCATCAAGACTGAATCAATACT
260 TACTATTGTGAAATCCTCCTTTAAATATG-ATTTAACAATGCTGCATCAAGACTGAATCAATACT
*
105523 GCATCATAATTACTAATTGGACTTGGACTCCTTCTTTGGGCTTCCATATTAACGAGTTGGGTCTA
324 GCATCATAATTACTAATTGGACTTGGACTCCTTCTTTGGGCTCCCATATTAACGAGTTGGGTCTA
** * * *
105588 AGAATATCAGATTTAGGTTTAAGGACATCTAGCTTGGCAATTTGGGTTTCATGGGCTCAAACGGG
389 AGAATATCAGATTTAGCCTTAAGGACATCTAGCTTGGCAATTTGGGCTTCATAGACTCAAACGGG
*
105653 CTTAATGAGCCTACTAGGCCGAAATGAGACAAAATCAGTAGTTTCTCCA
454 CCTAATGAGCCTACTAGGCCGAAATGAGACAAAATCAGTAGTTTCTCCA
105702 AATTGA
1 AATTGA
105708 TCCAAATGGA
Statistics
Matches: 460, Mismatches: 46, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
501 4 0.01
502 45 0.10
503 411 0.89
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (502 bp):
AATTGAGGATCCAACGTGGCCAACAGGAATGCTACACATCATCTGTAATATCTAATTTCGCCCAA
AACATTCTACAAGTCGGTTTAGGAGAAGATCAATTCTGTCCATAAATTTCAAGAGAAAAATCGTC
CACCGAAACGGCAGAATTAGGTCTTGAGGTAAACATAAAAGTTGTAGACCTTGGAATCCTCTTTC
CAACGGTACATCACTTGCATTTTTCTAAGCTCTAAATCAAAAGTTATGAATTTTCTTCCAAAACT
ACTATTGTGAAATCCTCCTTTAAATATGATTTAACAATGCTGCATCAAGACTGAATCAATACTGC
ATCATAATTACTAATTGGACTTGGACTCCTTCTTTGGGCTCCCATATTAACGAGTTGGGTCTAAG
AATATCAGATTTAGCCTTAAGGACATCTAGCTTGGCAATTTGGGCTTCATAGACTCAAACGGGCC
TAATGAGCCTACTAGGCCGAAATGAGACAAAATCAGTAGTTTCTCCA
Found at i:108009 original size:352 final size:352
Alignment explanation
Indices: 107365--108055 Score: 1346
Period size: 352 Copynumber: 2.0 Consensus size: 352
107355 GTCAACCTCT
*
107365 AATGTTAATGAAAATGTTAGAGTTGATGAGAGATCGACTTATGAAGAGGGAGTTACTCCTGCCAT
1 AATGTTAATGAAAATGTCAGAGTTGATGAGAGATCGACTTATGAAGAGGGAGTTACTCCTGCCAT
107430 GTTGACAAAAGCGATAATGGAACTCATTTCACAAGTGCAGAAAACACAAATGAATACTGATAAAA
66 GTTGACAAAAGCGATAATGGAACTCATTTCACAAGTGCAGAAAACACAAATGAATACTGATAAAA
* *
107495 ATGCAGAACAGGTGAGTTTGCTTGTGCAATTACAAAATGTAATGATAGAACAGAATGGACAAAAT
131 ATGCAGAACAAGTGAGTTTGCTTGTGCAATTACAAAATGCAATGATAGAACAGAATGGACAAAAT
107560 CATGCAATCTTAACTAATGCAATTAATAATTTGTCTAAACATGTTATATCTATGACTGCTTTGAA
196 CATGCAATCTTAACTAATGCAATTAATAATTTGTCTAAACATGTTATATCTATGACTGCTTTGAA
107625 TGCTGGTACTATACCAGAAGGTCTTAGAGTGTCTAATTCAGTTAGTGGAAGTTCACAAAATAATG
261 TGCTGGTACTATACCAGAAGGTCTTAGAGTGTCTAATTCAGTTAGTGGAAGTTCACAAAATAATG
107690 TGACTAGGATAAGTCACATGTAATGTG
326 TGACTAGGATAAGTCACATGTAATGTG
107717 AATGTTAATGAAAATGTCAGAGTTGATGAGAGATCGACTTATGAAGAGGGAGTTACTCCTGCCAT
1 AATGTTAATGAAAATGTCAGAGTTGATGAGAGATCGACTTATGAAGAGGGAGTTACTCCTGCCAT
107782 GTTGACAAAAGCGATAATGGAACTCATTTCACAAGTGCAGAAAACACAAATGAATACTGATAAAA
66 GTTGACAAAAGCGATAATGGAACTCATTTCACAAGTGCAGAAAACACAAATGAATACTGATAAAA
*
107847 ATGCAGAACAAGTGAGTTTGCTTGTGCAATTACAAAATGCAATGATAGAACAGAATGGGCAAAAT
131 ATGCAGAACAAGTGAGTTTGCTTGTGCAATTACAAAATGCAATGATAGAACAGAATGGACAAAAT
107912 CATGCAATCTTAACTAATGCAATTAATAATTTGTCTAAACATGTTATATCTATGACTGCTTTGAA
196 CATGCAATCTTAACTAATGCAATTAATAATTTGTCTAAACATGTTATATCTATGACTGCTTTGAA
107977 TGCTGGTACTATACCAGAAGGTCTTAGAGTGTCTAATTCAGTTAGTGGAAGTTCACAAAATAATG
261 TGCTGGTACTATACCAGAAGGTCTTAGAGTGTCTAATTCAGTTAGTGGAAGTTCACAAAATAATG
108042 TGACTAGGATAAGT
326 TGACTAGGATAAGT
108056 AATGTTAGAC
Statistics
Matches: 335, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
352 335 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (352 bp):
AATGTTAATGAAAATGTCAGAGTTGATGAGAGATCGACTTATGAAGAGGGAGTTACTCCTGCCAT
GTTGACAAAAGCGATAATGGAACTCATTTCACAAGTGCAGAAAACACAAATGAATACTGATAAAA
ATGCAGAACAAGTGAGTTTGCTTGTGCAATTACAAAATGCAATGATAGAACAGAATGGACAAAAT
CATGCAATCTTAACTAATGCAATTAATAATTTGTCTAAACATGTTATATCTATGACTGCTTTGAA
TGCTGGTACTATACCAGAAGGTCTTAGAGTGTCTAATTCAGTTAGTGGAAGTTCACAAAATAATG
TGACTAGGATAAGTCACATGTAATGTG
Found at i:109316 original size:1 final size:1
Alignment explanation
Indices: 109310--109403 Score: 107
Period size: 1 Copynumber: 94.0 Consensus size: 1
109300 CAGAATCTGG
* * * * * *
109310 AAAAAAAAAACAAAAAAAAACAAAAAAAACAAAAAAAAAACAAAAAAAAAACAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
109375 AAAAAACAAAAAAAACAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
109404 GATAAAAGAT
Statistics
Matches: 75, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 75 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:109326 original size:9 final size:9
Alignment explanation
Indices: 109312--109403 Score: 121
Period size: 9 Copynumber: 9.4 Consensus size: 9
109302 GAATCTGGAA
109312 AAAAAAAAC
1 AAAAAAAAC
109321 AAAAAAAAAC
1 -AAAAAAAAC
109331 AAAAAAAAC
1 AAAAAAAAC
109340 AAAAAAAAAAC
1 --AAAAAAAAC
109351 AAAAAAAAAAC
1 --AAAAAAAAC
109362 AAAAAAAAC
1 AAAAAAAAC
109371 AAAAAAAAAAC
1 --AAAAAAAAC
109382 AAAAAAAAC
1 AAAAAAAAC
109391 AAAAAAAAC
1 AAAAAAAAC
109400 AAAA
1 AAAA
109404 GATAAAAGAT
Statistics
Matches: 78, Mismatches: 0, Indels: 9
0.90 0.00 0.10
Matches are distributed among these distances:
9 40 0.51
10 9 0.12
11 29 0.37
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:109326 original size:11 final size:11
Alignment explanation
Indices: 109310--109398 Score: 129
Period size: 11 Copynumber: 8.7 Consensus size: 11
109300 CAGAATCTGG
109310 AAAAAAAAAAC
1 AAAAAAAAAAC
109321 -AAAAAAAAAC
1 AAAAAAAAAAC
109331 --AAAAAAAAC
1 AAAAAAAAAAC
109340 AAAAAAAAAAC
1 AAAAAAAAAAC
109351 AAAAAAAAAAC
1 AAAAAAAAAAC
109362 --AAAAAAAAC
1 AAAAAAAAAAC
109371 AAAAAAAAAAC
1 AAAAAAAAAAC
109382 --AAAAAAAAC
1 AAAAAAAAAAC
109391 AAAAAAAA
1 AAAAAAAA
109399 CAAAAGATAA
Statistics
Matches: 72, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
9 27 0.38
10 10 0.14
11 35 0.49
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:109336 original size:20 final size:20
Alignment explanation
Indices: 109311--109403 Score: 131
Period size: 20 Copynumber: 4.7 Consensus size: 20
109301 AGAATCTGGA
109311 AAAAAAAAACAAAAAAAAAC
1 AAAAAAAAACAAAAAAAAAC
109331 -AAAAAAAACAAAAAAAAAAC
1 AAAAAAAAAC-AAAAAAAAAC
109351 AAAAAAAAA-ACAAAAAAAAC
1 AAAAAAAAACA-AAAAAAAAC
109371 AAAAAAAAA-ACAAAAAAAAC
1 AAAAAAAAACA-AAAAAAAAC
109391 -AAAAAAAACAAAA
1 AAAAAAAAACAAAA
109404 GATAAAAGAT
Statistics
Matches: 69, Mismatches: 0, Indels: 9
0.88 0.00 0.12
Matches are distributed among these distances:
19 21 0.30
20 40 0.58
21 8 0.12
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (20 bp):
AAAAAAAAACAAAAAAAAAC
Found at i:109348 original size:31 final size:30
Alignment explanation
Indices: 109310--109403 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 30
109300 CAGAATCTGG
109310 AAAAAAAAAACAAAAAAAAACAAAAAAAAC
1 AAAAAAAAAACAAAAAAAAACAAAAAAAAC
109340 AAAAAAAAAACAAAAAAAAAACAAAAAAAAC
1 AAAAAAAAAAC-AAAAAAAAACAAAAAAAAC
109371 AAAAAAAAAAC-AAAAAAAACAAAAAAAAC
1 AAAAAAAAAACAAAAAAAAACAAAAAAAAC
109400 AAAA
1 AAAA
109404 GATAAAAGAT
Statistics
Matches: 63, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
29 22 0.35
30 11 0.17
31 30 0.48
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (30 bp):
AAAAAAAAAACAAAAAAAAACAAAAAAAAC
Done.