Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000008.1 Hibiscus syriacus cultivar Beakdansim tig00000014_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: 92861
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:3526 original size:18 final size:18
Alignment explanation
Indices: 3493--3527 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3483 AGGGGGAGTA
*
3493 ATTTCAAACTTGATTTTG
1 ATTTCAAAATTGATTTTG
*
3511 ATTTCAAAATTTATTTT
1 ATTTCAAAATTGATTTT
3528 TAAAGAATCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (18 bp):
ATTTCAAAATTGATTTTG
Found at i:3857 original size:20 final size:20
Alignment explanation
Indices: 3828--3865 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3818 TTTCAAAGGG
3828 ATGCAACGATGCACCAATCC
1 ATGCAACGATGCACCAATCC
*
3848 ATGCATCGATGCACCAAT
1 ATGCAACGATGCACCAAT
3866 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCAACGATGCACCAATCC
Found at i:3953 original size:65 final size:63
Alignment explanation
Indices: 3828--4030 Score: 198
Period size: 65 Copynumber: 3.1 Consensus size: 63
3818 TTTCAAAGGG
* * ** ** *
3828 ATGCAACGATGCACCAATCCATGCATCGATGCAC-CAATGAATAAATTG-AACATCAAATGCAGT
1 ATGCATCGAGGCA-CAATCCATGCATCGATGCACTC-A-GGCTATTTTGAAACATCGAATGCA-T
3891 TT
62 TT
**
3893 ATGCATCGAGGCACTCTCCATGCATCGATGCACTCAGG-T-TTTAATGAAAACATCGAATGCATT
1 ATGCATCGAGGCACAATCCATGCATCGATGCACTCAGGCTATTT--TG-AAACATCGAATGCATT
3956 T
63 T
* *
3957 GATGCATCGATGCACAATCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCACTTC
1 -ATGCATCGAGGCACAATCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCA-TTT
4022 ATGCATCGA
1 ATGCATCGA
4031 TTTACTCTTA
Statistics
Matches: 117, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
63 3 0.03
64 45 0.38
65 63 0.54
66 1 0.01
67 3 0.03
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (63 bp):
ATGCATCGAGGCACAATCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTT
Found at i:4050 original size:19 final size:19
Alignment explanation
Indices: 4034--4073 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
4024 GCATCGATTT
4034 ACTCTTAGTGCACCGATGC
1 ACTCTTAGTGCACCGATGC
4053 ACTCTTAGTGCACCGATGC
1 ACTCTTAGTGCACCGATGC
4072 AC
1 AC
4074 CTTGTGTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.25
Consensus pattern (19 bp):
ACTCTTAGTGCACCGATGC
Found at i:10995 original size:2 final size:2
Alignment explanation
Indices: 10990--11014 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10980 TCACTTTTTA
10990 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11015 ATAAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11485 original size:5 final size:5
Alignment explanation
Indices: 11475--11500 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
11465 CCGTACACTC
11475 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
11501 AAAAATTCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:13006 original size:31 final size:31
Alignment explanation
Indices: 12968--13059 Score: 148
Period size: 31 Copynumber: 3.0 Consensus size: 31
12958 CAGTTACGTC
* *
12968 GGGGACCATATTGCAAATGGAGTAAATGTTG
1 GGGGACCATATTGTAAATGGACTAAATGTTG
*
12999 GGGGACCATATTGTAAATAGACTAAATGTTG
1 GGGGACCATATTGTAAATGGACTAAATGTTG
*
13030 GGGGACCATATTGTAAATGAACTAAATGTT
1 GGGGACCATATTGTAAATGGACTAAATGTT
13060 AGGAGACTGT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (31 bp):
GGGGACCATATTGTAAATGGACTAAATGTTG
Found at i:17895 original size:42 final size:42
Alignment explanation
Indices: 17709--17898 Score: 186
Period size: 42 Copynumber: 4.5 Consensus size: 42
17699 TCGAGATCTA
* * * *
17709 CAAAA-GTTCAGATCTTTAGCGGCGTTTTTGGAACAAAAGCTG
1 CAAAAGGTT-AGATCTATAGCGGCATTTTTGGAACAAACGCCG
* * * *
17751 CAAAAGGTCGAGATCTATAGTGGCATTTTTGGGGGA-AAACGACG
1 CAAAAGGT-TAGATCTATAGCGGCATTTTT--GGAACAAACGCCG
* *
17795 CAAAAGGTTGAGATCTATAGCGGCGTTTTTGGAACAAATGCCG
1 CAAAAGGTT-AGATCTATAGCGGCATTTTTGGAACAAACGCCG
** * * *
17838 CAAAATATCATATCTATAGCGACATTTTTGGAACAAACGCCG
1 CAAAAGGTTAGATCTATAGCGGCATTTTTGGAACAAACGCCG
17880 CAAAAGGTTAGATCTATAG
1 CAAAAGGTTAGATCTATAG
17899 TGGGGGTTTT
Statistics
Matches: 117, Mismatches: 25, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
42 52 0.44
43 31 0.26
44 31 0.26
45 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (42 bp):
CAAAAGGTTAGATCTATAGCGGCATTTTTGGAACAAACGCCG
Found at i:21626 original size:82 final size:81
Alignment explanation
Indices: 21448--21626 Score: 205
Period size: 82 Copynumber: 2.2 Consensus size: 81
21438 AAATCATCAT
* * * * *
21448 TAAAGTACTACTATGTTACTGTGTTGGTTGAAAAAAGCACTATAGATGGACCCTATTACGGCGTT
1 TAAAGTACTACTCTGTTACGGCGTTGGTTGAAAAAAGCACTATAGATGAACCCTATTACGGCATT
* *
21513 TGTATAAAAACGCTGC
66 TGTATAAAAACGCCGA
* * * * * * *
21529 TAAAATACTATTCTGTTGCGGCGTTTGTTGAAAAATGTCACTATAGATGAACCCTATTGCGGTAT
1 TAAAGTACTACTCTGTTACGGCGTTGGTTGAAAAAAG-CACTATAGATGAACCCTATTACGGCAT
* *
21594 TTGTTTAAAAATGCCGA
65 TTGTATAAAAACGCCGA
21611 TAAAGTACTACTCTGT
1 TAAAGTACTACTCTGT
21627 CGTGGTGTTT
Statistics
Matches: 79, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
81 29 0.37
82 50 0.63
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (81 bp):
TAAAGTACTACTCTGTTACGGCGTTGGTTGAAAAAAGCACTATAGATGAACCCTATTACGGCATT
TGTATAAAAACGCCGA
Found at i:26736 original size:23 final size:22
Alignment explanation
Indices: 26702--26764 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
26692 CACCACAGCT
*
26702 CGTATAAATGCACCGAATTGCCA
1 CGTAGAAATGCACCGAATT-CCA
* * *
26725 CGTAGAATTGCACCGTAGTTCCG
1 CGTAGAAATGCACCG-AATTCCA
26748 CGTAGAAATGCACCGAA
1 CGTAGAAATGCACCGAA
26765 GTGTCATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 1 0.03
23 29 0.88
24 3 0.09
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (22 bp):
CGTAGAAATGCACCGAATTCCA
Found at i:27164 original size:14 final size:14
Alignment explanation
Indices: 27145--27185 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
27135 TTTTTTCTTT
*
27145 CATATATCTCATGA
1 CATATATCACATGA
27159 CATATATCACATGA
1 CATATATCACATGA
27173 CATATATCACATG
1 CATATATCACATG
27186 GCTCTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (14 bp):
CATATATCACATGA
Found at i:29405 original size:21 final size:21
Alignment explanation
Indices: 29379--29432 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
29369 CTCTACTTGT
* *
29379 AGTATCGATACCCTAGGGTTA
1 AGTATCGATACCCCAGGGTCA
29400 AGTATCGATACCCCAGGGTCA
1 AGTATCGATACCCCAGGGTCA
*
29421 AGTATCAATACC
1 AGTATCGATACC
29433 ACTTATGAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
AGTATCGATACCCCAGGGTCA
Found at i:30012 original size:13 final size:14
Alignment explanation
Indices: 29970--30018 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
29960 GAAGGCTTGG
*
29970 AGAAGAAAAGAAGA
1 AGAATAAAAGAAGA
* *
29984 AGAA-AAAGGAATA
1 AGAATAAAAGAAGA
29997 AGAATAAAAGAA-A
1 AGAATAAAAGAAGA
30010 AGAATAAAA
1 AGAATAAAA
30019 TATGGGAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 21 0.68
14 10 0.32
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.06
Consensus pattern (14 bp):
AGAATAAAAGAAGA
Found at i:31586 original size:44 final size:44
Alignment explanation
Indices: 31484--31568 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 44
31474 ATGCACATGA
*
31484 AGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATC
1 AGTGTATCGATGCACTCC-TTAAAATAAAAACATCGAATGGCATC
*
31529 AGTGTATCGATGCACCTCC-TAAAATACAAACATCGAATGG
1 AGTGTATCGATGCA-CTCCTTAAAATAAAAACATCGAATGG
31569 GATTTATGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
44 19 0.51
45 14 0.38
46 4 0.11
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (44 bp):
AGTGTATCGATGCACTCCTTAAAATAAAAACATCGAATGGCATC
Found at i:32205 original size:18 final size:18
Alignment explanation
Indices: 32182--32254 Score: 110
Period size: 18 Copynumber: 3.9 Consensus size: 18
32172 AGGGATTATC
32182 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
32200 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
32219 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
32238 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
32255 AATATTCAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
18 31 0.63
19 4 0.08
20 14 0.29
ACGTcount: A:0.19, C:0.22, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:32230 original size:38 final size:38
Alignment explanation
Indices: 32179--32255 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
32169 TCGAGGGATT
*
32179 ATCAGTGGTCCTTCGGGACATAGTGGTTCTTCGGAACA
1 ATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACA
*
32217 ATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACA
1 ATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACA
32255 A
1 A
32256 ATATTCAGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (38 bp):
ATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACA
Found at i:34633 original size:35 final size:35
Alignment explanation
Indices: 34587--34657 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
34577 AAAAGTATTC
34587 ATGGGCATTGAGCAAATCACAATTTACATTAGTAA
1 ATGGGCATTGAGCAAATCACAATTTACATTAGTAA
*
34622 ATGGGCATTGAGCAAATCACAATTTACATTTGTAA
1 ATGGGCATTGAGCAAATCACAATTTACATTAGTAA
34657 A
1 A
34658 AGTGTAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (35 bp):
ATGGGCATTGAGCAAATCACAATTTACATTAGTAA
Found at i:35496 original size:171 final size:171
Alignment explanation
Indices: 35205--35545 Score: 592
Period size: 171 Copynumber: 2.0 Consensus size: 171
35195 AAATGTCAGC
* *
35205 AATAACAAAATCGATAAGAAAAATAATTAAAATGTCAAATAATAACAAAATCAGTATAAATAATA
1 AATAACAAAATCGATAAGAAAAATAATTAAAACGTCAAATAATAACAAAATCAATATAAATAATA
35270 ATATTTTCGATAATTTTTACCAATTTTATTATTTAAATAATTAAAAAACTAATAACACTTTTTTT
66 ATATTTTCGATAATTTTTACCAATTTTATTATTTAAATAATTAAAAAACTAATAACACTTTTTTT
* *
35335 AATCGTATAATAAGATTGCCGCTCGTTATTATTTCCCCATA
131 AATCGTATAATAAGACTGACGCTCGTTATTATTTCCCCATA
* * *
35376 AATAACAAAATTGATAAGAAAAATAATTAAAACGTCAAATAATAATAAAATTAATATAAATAATA
1 AATAACAAAATCGATAAGAAAAATAATTAAAACGTCAAATAATAACAAAATCAATATAAATAATA
* * *
35441 ATATTTTTGATAATTTTTACTAATTTTATTATTTAAATAATTAAAAAATTAATAACACTTTTTTT
66 ATATTTTCGATAATTTTTACCAATTTTATTATTTAAATAATTAAAAAACTAATAACACTTTTTTT
35506 AATCGTATAATAAGACTGACGCTCGTTATTATTTCCCCAT
131 AATCGTATAATAAGACTGACGCTCGTTATTATTTCCCCAT
35546 CTCAAGCCCT
Statistics
Matches: 160, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
171 160 1.00
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.38
Consensus pattern (171 bp):
AATAACAAAATCGATAAGAAAAATAATTAAAACGTCAAATAATAACAAAATCAATATAAATAATA
ATATTTTCGATAATTTTTACCAATTTTATTATTTAAATAATTAAAAAACTAATAACACTTTTTTT
AATCGTATAATAAGACTGACGCTCGTTATTATTTCCCCATA
Found at i:37444 original size:2 final size:2
Alignment explanation
Indices: 37437--37470 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
37427 AAAGGCCTAT
37437 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
37471 TGTACCTGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40161 original size:20 final size:20
Alignment explanation
Indices: 40136--40179 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
40126 TAAAAGACAC
40136 TATAGTTTGGATATTTATTT
1 TATAGTTTGGATATTTATTT
40156 TATAGTTTGGATATTTATTT
1 TATAGTTTGGATATTTATTT
40176 TATA
1 TATA
40180 TTTAACCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (20 bp):
TATAGTTTGGATATTTATTT
Found at i:48801 original size:30 final size:30
Alignment explanation
Indices: 48713--48804 Score: 123
Period size: 30 Copynumber: 3.1 Consensus size: 30
48703 AAATAAAACG
*
48713 CTCTCACCCCGTAAACATTCACACAACAATC
1 CTCTCAACCCGTAAACA-TCACACAACAATC
*
48744 CTCTCAA-CCGAAAACATCACACAACAATC
1 CTCTCAACCCGTAAACATCACACAACAATC
* * *
48773 CTCTCAACCCGTAAATATCACCCGACAATC
1 CTCTCAACCCGTAAACATCACACAACAATC
48803 CT
1 CT
48805 TTTATCTTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
29 20 0.37
30 28 0.52
31 6 0.11
ACGTcount: A:0.37, C:0.40, G:0.04, T:0.18
Consensus pattern (30 bp):
CTCTCAACCCGTAAACATCACACAACAATC
Found at i:52557 original size:3 final size:3
Alignment explanation
Indices: 52549--52578 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
52539 CCTCACTTTA
*
52549 ATC ATC ATC ATC ATC ATC ACC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
52579 GTCGTCGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (3 bp):
ATC
Found at i:52589 original size:12 final size:12
Alignment explanation
Indices: 52574--52599 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52564 ATCACCATCA
52574 TCATCGTCGTCG
1 TCATCGTCGTCG
52586 TCATCGTCGTCG
1 TCATCGTCGTCG
52598 TC
1 TC
52600 GTCAGGACCA
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:0.08, C:0.35, G:0.23, T:0.35
Consensus pattern (12 bp):
TCATCGTCGTCG
Found at i:52589 original size:15 final size:15
Alignment explanation
Indices: 52571--52603 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
52561 ATCATCACCA
52571 TCATCATCGTCGTCG
1 TCATCATCGTCGTCG
*
52586 TCATCGTCGTCGTCG
1 TCATCATCGTCGTCG
52601 TCA
1 TCA
52604 GGACCATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.33, G:0.21, T:0.33
Consensus pattern (15 bp):
TCATCATCGTCGTCG
Found at i:54671 original size:33 final size:29
Alignment explanation
Indices: 54600--54671 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 29
54590 GCAAAAAAAT
* * *
54600 TAATTAAATAAAATACTAAATATTTTAAA
1 TAATAAAATAAAATACTAAAAATATTAAA
*
54629 TAATTAAATAAAATACTAACAAAATATTAAA
1 TAATAAAATAAAATACT-A-AAAATATTAAA
54660 TAGAATAAAATA
1 T--AATAAAATA
54672 TACCTTATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 17 0.47
30 1 0.03
31 10 0.28
33 8 0.22
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (29 bp):
TAATAAAATAAAATACTAAAAATATTAAA
Found at i:57995 original size:15 final size:14
Alignment explanation
Indices: 57975--58018 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
57965 TATGCTGAGA
57975 TTATTATGCAGGGAT
1 TTATTA-GCAGGGAT
57990 TTATTAGCAGGGAT
1 TTATTAGCAGGGAT
*
58004 TTATTAGCAAGGAT
1 TTATTAGCAGGGAT
58018 T
1 T
58019 ACTTACCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 22 0.79
15 6 0.21
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.39
Consensus pattern (14 bp):
TTATTAGCAGGGAT
Found at i:63295 original size:17 final size:17
Alignment explanation
Indices: 63273--63311 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
63263 TGAATCAAAT
*
63273 TAATTAGATATTATTTA
1 TAATTAGATACTATTTA
63290 TAATTAGATACTATTTA
1 TAATTAGATACTATTTA
63307 -AATTA
1 TAATTA
63312 ATTTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (17 bp):
TAATTAGATACTATTTA
Found at i:65663 original size:16 final size:16
Alignment explanation
Indices: 65644--65696 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
65634 CACCAAAATA
65644 TTATGAATCCAAATTT
1 TTATGAATCCAAATTT
*** *
65660 TTATTCCCTCCAAAATT
1 TTA-TGAATCCAAATTT
65677 TTATGAATCCAAATTT
1 TTATGAATCCAAATTT
65693 TTAT
1 TTAT
65697 TTAATTAGTT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 16 0.57
17 12 0.43
ACGTcount: A:0.34, C:0.17, G:0.04, T:0.45
Consensus pattern (16 bp):
TTATGAATCCAAATTT
Found at i:65736 original size:15 final size:16
Alignment explanation
Indices: 65718--65753 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
65708 ATGTACCAAA
65718 AATTAATAATAA-TAC
1 AATTAATAATAATTAC
65733 AATTAA-AATAATTAC
1 AATTAATAATAATTAC
65748 -ATTAAT
1 AATTAAT
65754 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTAATAATAATTAC
Found at i:66957 original size:31 final size:31
Alignment explanation
Indices: 66907--66977 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
66897 AAAATGATTT
* *
66907 TTTGTGACGTAACATGTGGACCCATCACAAA
1 TTTGTGACATAACAGGTGGACCCATCACAAA
* * * *
66938 TTTGTGACATAATAGGTGGATCTATCAGAAA
1 TTTGTGACATAACAGGTGGACCCATCACAAA
*
66969 TTTATGACA
1 TTTGTGACA
66978 GGTCCACAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (31 bp):
TTTGTGACATAACAGGTGGACCCATCACAAA
Found at i:67743 original size:31 final size:31
Alignment explanation
Indices: 67687--67748 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
67677 TTTATTTCCG
*
67687 ACGGAATGATTATTCCATCACAAATTAAATT
1 ACGGAATCATTATTCCATCACAAATTAAATT
* * *
67718 ACGGAATCATTGTTCCGTCATAAATTAAATT
1 ACGGAATCATTATTCCATCACAAATTAAATT
67749 GATATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (31 bp):
ACGGAATCATTATTCCATCACAAATTAAATT
Found at i:68465 original size:23 final size:25
Alignment explanation
Indices: 68421--68466 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
68411 ATATATATAT
* *
68421 ATATATTATTTATTTTATAAATAAG
1 ATATATTATTTATCTTAGAAATAAG
68446 ATAT-TTATTTA-CTTAGAAATA
1 ATATATTATTTATCTTAGAAATA
68467 TAAGAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 7 0.37
25 4 0.21
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (25 bp):
ATATATTATTTATCTTAGAAATAAG
Found at i:68838 original size:8 final size:8
Alignment explanation
Indices: 68827--68863 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
68817 AAATAATAAT
68827 TAAATATA
1 TAAATATA
68835 TAAATATA
1 TAAATATA
68843 TAAA-AT-
1 TAAATATA
68849 TAAA-ATA
1 TAAATATA
68856 TAAATATA
1 TAAATATA
68864 AATAAACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.22
7 6 0.22
8 15 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
TAAATATA
Found at i:68838 original size:21 final size:20
Alignment explanation
Indices: 68809--68865 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
68799 ACTACATAAT
68809 AATA-ATAAAAATAATAATTA
1 AATATATAAAAATAA-AATTA
68829 AATATATAAATATATAAAATTA
1 AATATATAAA-A-ATAAAATTA
*
68851 AA-ATATAAATATAAA
1 AATATATAAAAATAAA
68866 TAAACAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 5 0.15
20 4 0.12
21 12 0.36
22 8 0.24
23 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATATATAAAAATAAAATTA
Found at i:68886 original size:17 final size:16
Alignment explanation
Indices: 68836--68887 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
68826 TTAAATATAT
*
68836 AAATATATAAAATTAA
1 AAATAAATAAAATTAA
68852 AATATAAATATAAA-TAA
1 AA-ATAAATA-AAATTAA
68869 ACAATAAATAAAATTAA
1 A-AATAAATAAAATTAA
68886 AA
1 AA
68888 CTATAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 6 0.19
17 21 0.68
18 4 0.13
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAAATAAAATTAA
Found at i:70376 original size:3 final size:3
Alignment explanation
Indices: 70368--70442 Score: 107
Period size: 3 Copynumber: 25.0 Consensus size: 3
70358 AATTATTTAT
* *
70368 TAA TAA TAA T-A TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
70415 TAA TGTA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA
70443 AAGCAAACTG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
2 2 0.03
3 60 0.94
4 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:70655 original size:20 final size:20
Alignment explanation
Indices: 70630--70701 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 20
70620 ACATCATGCT
70630 CTGAAGGGCTTACAGATGAC
1 CTGAAGGGCTTACAGATGAC
** *
70650 CTGAAGGTTTTAAAAACATCAT-AC
1 CTGAAGGGCTT----ACA-GATGAC
70674 ACTGAAGGGCTTACAGATGAC
1 -CTGAAGGGCTTACAGATGAC
70695 CTGAAGG
1 CTGAAGG
70702 TTTTGAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
20 18 0.46
21 5 0.13
24 5 0.13
25 11 0.28
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (20 bp):
CTGAAGGGCTTACAGATGAC
Found at i:70681 original size:45 final size:45
Alignment explanation
Indices: 70571--70962 Score: 676
Period size: 45 Copynumber: 8.7 Consensus size: 45
70561 GAAAATATCA
* *
70571 AAAACATCATGCACTGAAGGGATTACAGATGACCTGAAGGTTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTG
* * *
70617 AAAACATCATGCTCTGAAGGGCTTACAGATGACCTGAAGGTTTTA
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
* *
70662 AAAACATCATACACTGAAGGGCTTACAGATGACCTGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
* *
70707 AAAATATCATGCACTGAAGGGCTTACAGATGGCCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
70752 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
*
70797 AAAACATCATGCACTGAAGGGCTTACAGACGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
70842 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
*
70887 AAAACATCATGTACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
70932 AAAACATCATGCACTGAAGGGCTTACAGATG
1 AAAACATCATGCACTGAAGGGCTTACAGATG
70963 TGGGAAATAG
Statistics
Matches: 330, Mismatches: 16, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
45 292 0.88
46 38 0.12
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (45 bp):
AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
Found at i:71672 original size:22 final size:22
Alignment explanation
Indices: 71617--71673 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
71607 AATAAAGCTT
*
71617 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
71639 TCATCTTTGAAGATAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
71661 TCATCTTTGAAGA
1 TCATCTTTGAAGA
71674 ATGTAGATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:72130 original size:54 final size:54
Alignment explanation
Indices: 72039--72176 Score: 154
Period size: 54 Copynumber: 2.6 Consensus size: 54
72029 TCACTGGTTC
* * * * *
72039 GTAAAACATGTGACAATATATTAATCCTTTCTCGTGGCTTCTGCCC-GAAT-TTT
1 GTAAAGCATTTGACAACACATTCATCCTTTCTCGTGGCTTCTGCCCAG-ATGTTT
* * * * *
72092 CGTAAAGCTTTTGATAACACATTCATCCTTTGTTGTGGCTTCTGGCCAGATGTTT
1 -GTAAAGCATTTGACAACACATTCATCCTTTCTCGTGGCTTCTGCCCAGATGTTT
72147 GTAAAGCATTTGACAACACATTCATCCTTT
1 GTAAAGCATTTGACAACACATTCATCCTTT
72177 TCTGTGATTT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
54 66 0.94
55 4 0.06
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (54 bp):
GTAAAGCATTTGACAACACATTCATCCTTTCTCGTGGCTTCTGCCCAGATGTTT
Found at i:73988 original size:712 final size:712
Alignment explanation
Indices: 72589--74009 Score: 2441
Period size: 711 Copynumber: 2.0 Consensus size: 712
72579 TAACATAAGT
*
72589 TGAGCCTCTTTATTCAATGTCATCAAGTAAGCGAAAATTGTTGTGAAAAACATCTTCGTAGCCCC
1 TGAGCCTCTTTATTCAATGTCATCAAGTAAGCGAAAACTGTTGTGAAAAACATCTTCGTAGCCCC
* *
72654 AATAGTATGATTGAAACTAACTGCAATGAATCTTAAAGAAATATGTCCAATCATCACCGAAACAC
66 AACAGTATGATTGAAACTAACTACAATGAATCTTAAAGAAATATGTCCAATCATCACCGAAACAC
* *
72719 AGAATACAAAATTCAAAGCTGAGATTTTGAGGAACTGAACCGTGGATCGAATAGTCTGCCTGGGG
131 AGAATACAAAATTCAAAGCCGAGATTTTGAGGAACTGAACCGTGGATCAAATAGTCTGCCTGGGG
* * *
72784 ACCATTTTTATCCATGCAACCATGGTGTATCTTAACAAAGAACATGCTGTCATGTGGCACATGGT
196 ACCATCTTTATCCATGCAACCATGATGTATCTTAACAAAGAACATGCTGTCATGTGACACATGGT
72849 TAAGAATATTGGGTATTTGAAACCATATTTACTGAGTAAATATTTGTTCAACACCAGGACCCTGA
261 TAAGAATATTGGGTATTTGAAACCATATTTACTGAGTAAATATTTGTTCAACACCAGGACCCTGA
* *
72914 TGTAACTGCTTGATGAACGAAGCAATTATGTATAGTCAGTTCCACTATCACTGTTTCACCATTTT
326 TGTAACTGCTTGATGAACGAAACAATTATGTATAATCAGTTCCACTATCACTGTTTCACCATTTT
* *
72979 CATTCTTCATTCCTTTCTTTTTATTGGAAATATTTGCTCAAAACAATGATATTTAACACATAATG
391 CATTCTTCATTCCTTTCTTCTTATTGGAAATATTTGCTCAAAACAATGACATTTAACACATAATG
* * *
73044 ACGTGGGCCTTCAGCATGCCCTAGCATTTACTGATATGAACGTTCTTAATACATCAACATTCCTG
456 ACGTGGGCCTTCAGCATGCCCCAACATTTACTGATATGAACGTTCTTAATACATCAACATTCATG
* *
73109 ATTCTGATTGAAATGAGGTTTCAGTATGTCCTAGCATTTGCTTATTGTTGATGTGAGCTTTTAAA
521 ATTCTGATTGAAATGAGCTTTCAGTATGTCCCAGCATTTGCTTATTGTTGATGTGAGCTTTTAAA
*
73174 ATGCCTCAACATTTTTTCATACTGATGTGAACCTTCAAAATGCCCACATGGATCTGTCTGAAATA
586 ATGCCTCAACAGTTTTTCATACTGATGTGAACCTTCAAAATGCCCACATGGATCTGTCTGAAATA
*
73239 ACTATTAAAATTCCCCAACATTTGTTGATATAGATTTTAAAAATGTGTTCAACATTACTAGC
651 ACTATTAAAATTCCCCAACATTTGTTGATACAGATTTTAAAAATGTGTTCAACATTACTAGC
* *
73301 TGAGCCTCTTTATTCAATGTCATCAAGTAAGCGAAAACTGTTGTGAAAAACAT-TTTGTAGCCCT
1 TGAGCCTCTTTATTCAATGTCATCAAGTAAGCGAAAACTGTTGTGAAAAACATCTTCGTAGCCCC
*
73365 AACAGTATGATTGAAACTAACTACAATGAATCTTAAAGAAATATGTCCAATCATCACCGAAACAT
66 AACAGTATGATTGAAACTAACTACAATGAATCTTAAAGAAATATGTCCAATCATCACCGAAACAC
73430 AGAATACAAAATTCAAAGCCGAGATTTTGAGGAACTGAACCGTGGATCAAATAGTCTGCCTGGGG
131 AGAATACAAAATTCAAAGCCGAGATTTTGAGGAACTGAACCGTGGATCAAATAGTCTGCCTGGGG
* *
73495 ACCATCTTTATCCATGCAACCGTGATGTATCTTAACAAAGAACATGTTGTCATGTGACACATGGT
196 ACCATCTTTATCCATGCAACCATGATGTATCTTAACAAAGAACATGCTGTCATGTGACACATGGT
*
73560 TAAGAATATTGGGTATTTGAAACCATATTTGCTGAGTAAATATTTGTTCAACACCAGGACCCTGA
261 TAAGAATATTGGGTATTTGAAACCATATTTACTGAGTAAATATTTGTTCAACACCAGGACCCTGA
* * *
73625 TGTAACTGCTTGATGAACGAAACAATTATTTATAATCAGTTCCACTGTCATTGTTTCACCATTTT
326 TGTAACTGCTTGATGAACGAAACAATTATGTATAATCAGTTCCACTATCACTGTTTCACCATTTT
* *
73690 CATTCTTCATTCCTTTCTGTCTTATTGGAAATATTTGCTCAAAGCAATGACCTTTAACACATAAT
391 CATTCTTCATTCCTTTCT-TCTTATTGGAAATATTTGCTCAAAACAATGACATTTAACACATAAT
* * * * * *
73755 TATGTGGGCCTTCAGCATGCCCCAACATTTACTGATATGAATGTTCTTAATGCGTCAACATTTAT
455 GACGTGGGCCTTCAGCATGCCCCAACATTTACTGATATGAACGTTCTTAATACATCAACATTCAT
* *
73820 GATTCTGATTGAAATGAGCTTTTAGTATGTCCCAGCATTTGCTTCTTGTTGATGTGAGCTTTTAA
520 GATTCTGATTGAAATGAGCTTTCAGTATGTCCCAGCATTTGCTTATTGTTGATGTGAGCTTTTAA
* *
73885 AATTCCTCAAC-GTTTTTCATATTGATGTGAACCTTCAAAATGCCCCACATGGATCTGTCTGAAA
585 AATGCCTCAACAGTTTTTCATACTGATGTGAACCTTCAAAATG-CCCACATGGATCTGTCTGAAA
*
73949 TAACTATTAAAATTCCTCAACATTTGTTGATACAGATTTTAAAAATGTGTTCAACATTACT
649 TAACTATTAAAATTCCCCAACATTTGTTGATACAGATTTTAAAAATGTGTTCAACATTACT
74010 TCTTGCTGAG
Statistics
Matches: 666, Mismatches: 41, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
711 365 0.55
712 301 0.45
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (712 bp):
TGAGCCTCTTTATTCAATGTCATCAAGTAAGCGAAAACTGTTGTGAAAAACATCTTCGTAGCCCC
AACAGTATGATTGAAACTAACTACAATGAATCTTAAAGAAATATGTCCAATCATCACCGAAACAC
AGAATACAAAATTCAAAGCCGAGATTTTGAGGAACTGAACCGTGGATCAAATAGTCTGCCTGGGG
ACCATCTTTATCCATGCAACCATGATGTATCTTAACAAAGAACATGCTGTCATGTGACACATGGT
TAAGAATATTGGGTATTTGAAACCATATTTACTGAGTAAATATTTGTTCAACACCAGGACCCTGA
TGTAACTGCTTGATGAACGAAACAATTATGTATAATCAGTTCCACTATCACTGTTTCACCATTTT
CATTCTTCATTCCTTTCTTCTTATTGGAAATATTTGCTCAAAACAATGACATTTAACACATAATG
ACGTGGGCCTTCAGCATGCCCCAACATTTACTGATATGAACGTTCTTAATACATCAACATTCATG
ATTCTGATTGAAATGAGCTTTCAGTATGTCCCAGCATTTGCTTATTGTTGATGTGAGCTTTTAAA
ATGCCTCAACAGTTTTTCATACTGATGTGAACCTTCAAAATGCCCACATGGATCTGTCTGAAATA
ACTATTAAAATTCCCCAACATTTGTTGATACAGATTTTAAAAATGTGTTCAACATTACTAGC
Found at i:79841 original size:6 final size:6
Alignment explanation
Indices: 79820--79867 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
79810 ACAAACGTAA
* * *
79820 AAATGC AAAGATGC AAATGC AAATAC AAATGC AAATAC AAATGT AAAT
1 AAATGC -AA-ATGC AAATGC AAATGC AAATGC AAATGC AAATGC AAAT
79868 AAGTGAATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
6 27 0.77
7 4 0.11
8 4 0.11
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (6 bp):
AAATGC
Found at i:79850 original size:12 final size:12
Alignment explanation
Indices: 79833--79868 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
79823 TGCAAAGATG
79833 CAAATGCAAATA
1 CAAATGCAAATA
79845 CAAATGCAAATA
1 CAAATGCAAATA
*
79857 CAAATGTAAATA
1 CAAATGCAAATA
79869 AGTGAATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.58, C:0.14, G:0.08, T:0.19
Consensus pattern (12 bp):
CAAATGCAAATA
Found at i:83067 original size:21 final size:22
Alignment explanation
Indices: 83026--83080 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
83016 TAATAATAAT
83026 AACAATAATAATTAAATATATA
1 AACAATAATAATTAAATATATA
83048 AACATATAA-AATTAAAATATAAATA
1 AACA-ATAATAATT-AAATAT--ATA
83073 AACAATAA
1 AACAATAA
83081 ATAAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.28
23 10 0.34
24 4 0.14
25 7 0.24
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.27
Consensus pattern (22 bp):
AACAATAATAATTAAATATATA
Found at i:83111 original size:28 final size:28
Alignment explanation
Indices: 83053--83114 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
83043 ATATAAACAT
*
83053 ATAAAATTAAAATATAAATAAACAATAA
1 ATAAAATTAAAATATAAATAAAAAATAA
*
83081 ATAAAATTAAAACTAT-AGTACAAAAAT-A
1 ATAAAATTAAAA-TATAAATA-AAAAATAA
83109 ATAAAA
1 ATAAAA
83115 CTTGTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 22 0.73
29 8 0.27
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (28 bp):
ATAAAATTAAAATATAAATAAAAAATAA
Found at i:84598 original size:3 final size:3
Alignment explanation
Indices: 84590--84690 Score: 114
Period size: 3 Copynumber: 32.0 Consensus size: 3
84580 AATTATTTAT
* *
84590 TAA TAA TAA T-A TAA TAA TAT TTA TAA TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
*
84635 TAA TAA TAA TAA TGTA TAA TAA TAA TAA TAAA TAAA TAAA TAAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA T-AA T-AA T-AA T-AA TAA
84682 TAA TAA TAA
1 TAA TAA TAA
84691 AAGCAAATTG
Statistics
Matches: 88, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
2 2 0.02
3 66 0.75
4 20 0.23
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:84628 original size:25 final size:25
Alignment explanation
Indices: 84590--84690 Score: 130
Period size: 25 Copynumber: 3.9 Consensus size: 25
84580 AATTATTTAT
* *
84590 TAATAATAATATAATAATATTTATAA
1 TAATAATAA-ATAATAATAATAATAA
84616 TAATAATAAATAATAATAATAATAA
1 TAATAATAAATAATAATAATAATAA
**
84641 TAATAATGTATAATAATAATAATAAA
1 TAATAATAAATAATAATAATAAT-AA
84667 TAAATAAATAAATAATAATAATAA
1 T-AAT-AATAAATAATAATAATAA
84691 AAGCAAATTG
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
25 35 0.53
26 12 0.18
27 3 0.05
28 16 0.24
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (25 bp):
TAATAATAAATAATAATAATAATAA
Found at i:84691 original size:25 final size:22
Alignment explanation
Indices: 84590--84690 Score: 123
Period size: 22 Copynumber: 4.4 Consensus size: 22
84580 AATTATTTAT
* *
84590 TAATAATAATATAATAATATTTA
1 TAATAATAATA-AATAATAATAA
84613 TAATAATAATAAATAATAATAA
1 TAATAATAATAAATAATAATAA
*
84635 TAATAATAAT-AATGTATAATAA
1 TAATAATAATAAAT-AATAATAA
84657 TAATAATAAATAAATAAATAAATAA
1 TAATAAT-AATAAAT-AAT-AATAA
84682 TAATAATAA
1 TAATAATAA
84691 AAGCAAATTG
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
21 3 0.04
22 33 0.48
23 14 0.20
24 7 0.10
25 12 0.17
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (22 bp):
TAATAATAATAAATAATAATAA
Found at i:86419 original size:3 final size:3
Alignment explanation
Indices: 86413--86469 Score: 71
Period size: 3 Copynumber: 18.0 Consensus size: 3
86403 ATTTGGTTTT
86413 TTA TTA TTTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTAA
1 TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TT-A
86462 TT- TTA TTA
1 TTA TTA TTA
86470 CAGGCCCAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.04
3 35 0.70
4 13 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:88022 original size:117 final size:118
Alignment explanation
Indices: 87895--88111 Score: 271
Period size: 116 Copynumber: 1.8 Consensus size: 118
87885 TGTTTTAATA
* * * * *
87895 TTTTTCAATATTAA-G-AAAGGGCAGTCTTAAAACAACTGGATGTCCATTTTCTAATATTTTTAA
1 TTTTTCAATATCAAGGAAAAGAGC-GTCTTAAAAC-ACTAGAAGTCC-TTTTCTAATATTTCTAA
87958 ATAAATAAATATCATATTTATAAAT-TATAT-ATTAATTGTTTTAATTATTTATTT
63 ATAAATAAATATCATATTTATAAATATATATAATTAATTGTTTTAATTATTTATTT
* ** * *
88012 TTTTTTAATATCAAGGAAAAGAGCGTCTTAAGGCACTAGAAGTTCTTTTCTGATATTTCTAAATA
1 TTTTTCAATATCAAGGAAAAGAGCGTCTTAAAACACTAGAAGTCCTTTTCTAATATTTCTAAATA
**
88077 AATAAATATTTTATTTATAAATATATATAATTAAT
66 AATAAATATCATATTTATAAATATATATAATTAAT
88112 ATATATTTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
116 38 0.45
117 25 0.30
118 15 0.18
119 6 0.07
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (118 bp):
TTTTTCAATATCAAGGAAAAGAGCGTCTTAAAACACTAGAAGTCCTTTTCTAATATTTCTAAATA
AATAAATATCATATTTATAAATATATATAATTAATTGTTTTAATTATTTATTT
Done.