Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004652.1 Hibiscus syriacus cultivar Beakdansim tig00010426_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: 38747
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:261 original size:17 final size:17
Alignment explanation
Indices: 239--271 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
229 TTTACCGAAT
239 TTTACAGAC-TTTAACAC
1 TTTACA-ACTTTTAACAC
256 TTTACAACTTTTAACA
1 TTTACAACTTTTAACA
272 TAATTCCGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.39
Consensus pattern (17 bp):
TTTACAACTTTTAACAC
Found at i:5386 original size:21 final size:21
Alignment explanation
Indices: 5362--5414 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
5352 TAATTTCCCA
5362 AATTGGCCATTT-AATATTTCG
1 AATTGGCCATTTAAAT-TTTCG
* *
5383 AATTGTCCTTTTAAATTTTCG
1 AATTGGCCATTTAAATTTTCG
5404 AATTGGCCATT
1 AATTGGCCATT
5415 CATTATAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (21 bp):
AATTGGCCATTTAAATTTTCG
Found at i:13132 original size:6 final size:6
Alignment explanation
Indices: 13116--13148 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
13106 TCAAACAGAA
*
13116 AAAAAC GAAAAC AAAAAC AAAAAC -AAAAC AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
13149 CCCAAAGCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.82, C:0.15, G:0.03, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:13133 original size:22 final size:22
Alignment explanation
Indices: 13108--13149 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
13098 CTCAGGAATC
*
13108 AAACAGAAA-AAAACGAAAACAA
1 AAACAAAAACAAAAC-AAAACAA
13130 AAACAAAAACAAAACAAAAC
1 AAACAAAAACAAAACAAAAC
13150 CCAAAGCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.79, C:0.17, G:0.05, T:0.00
Consensus pattern (22 bp):
AAACAAAAACAAAACAAAACAA
Found at i:18358 original size:6 final size:6
Alignment explanation
Indices: 18347--18373 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
18337 TCTCGTCTCG
18347 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
18374 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:18493 original size:41 final size:39
Alignment explanation
Indices: 18448--18534 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 39
18438 ATCTTTTTTT
* *
18448 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCG
1 CAACGAA-ATGGAAAATCGCAACG-CAACTATAGACTATCG
*
18489 CAACGCGAAATGGAAAATCGCAACGCGACTATAGACTATCG
1 CAA--CGAAATGGAAAATCGCAACGCAACTATAGACTATCG
*
18530 AAACG
1 CAACG
18535 CGAAATGCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
39 2 0.05
41 19 0.47
42 15 0.38
43 4 0.10
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (39 bp):
CAACGAAATGGAAAATCGCAACGCAACTATAGACTATCG
Found at i:18535 original size:41 final size:42
Alignment explanation
Indices: 18457--18541 Score: 136
Period size: 41 Copynumber: 2.0 Consensus size: 42
18447 TCAACGAATT
* *
18457 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTATAGACTATCGAAACGCGAAA
*
18499 TGGAAAATCGCAACG-CGACTATAGACTATCGAAACGCGAAA
1 TGGAAAATCGCAACGACAACTATAGACTATCGAAACGCGAAA
18540 TG
1 TG
18542 CAACGCGAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 25 0.62
42 15 0.38
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.15
Consensus pattern (42 bp):
TGGAAAATCGCAACGACAACTATAGACTATCGAAACGCGAAA
Found at i:18639 original size:101 final size:101
Alignment explanation
Indices: 18482--18671 Score: 285
Period size: 101 Copynumber: 1.9 Consensus size: 101
18472 ACAACTGTAG
*
18482 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTATAGACTATCGAAACGCGAAATGCAACG
1 ACTATCGCAACGCAAAATGGAAAATCGCAACGCGACTATAGACTATCGAAACGCGAAATGCAACG
*
18547 CGAATTTGTGAT-GATGGAGATCGCGTTGCGATCTCA
66 CGAATTTGCGATAG-TGGAGATCGCGTTGCGATCTCA
* * * *
18583 ACTATCGCAACGCAAAATGGAAAATCGCAACGCGATTTTCA-ACTATCGCAATGCGAAATGCAAC
1 ACTATCGCAACGCAAAATGGAAAATCGCAACGCGACTAT-AGACTATCGAAACGCGAAATGCAAC
*
18647 GTGAATTTGCGATAGTGGAGATCGC
65 GCGAATTTGCGATAGTGGAGATCGC
18672 AATGCGAATT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
101 78 0.98
102 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.21
Consensus pattern (101 bp):
ACTATCGCAACGCAAAATGGAAAATCGCAACGCGACTATAGACTATCGAAACGCGAAATGCAACG
CGAATTTGCGATAGTGGAGATCGCGTTGCGATCTCA
Found at i:18646 original size:21 final size:21
Alignment explanation
Indices: 18581--18646 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
18571 GTTGCGATCT
*
18581 CAACTATCGCAACGCAAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
18602 GAA-AATCGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
18622 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
18643 CAAC
1 CAAC
18647 GTGAATTTGC
Statistics
Matches: 32, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:19170 original size:42 final size:41
Alignment explanation
Indices: 19089--19215 Score: 106
Period size: 42 Copynumber: 3.1 Consensus size: 41
19079 TTTTCGTCTG
* *
19089 ATATATTATAT-A-GTTT-ACAAATG-TTTTTGAAATACATAT
1 ATATATTATATAATGTTTGA-AAA-GCTTTTTGAAACATATAT
* * *
19128 A-ATA-TATATAGT-TTTGAAAATGGTTTTTGGAAATATATAT
1 ATATATTATATAATGTTTGAAAA-GCTTTTT-GAAACATATAT
*
19168 ATATATTATATAATGTTTGGAAAGCTTTTTGAAACATATAT
1 ATATATTATATAATGTTTGAAAAGCTTTTTGAAACATATAT
19209 AATATAT
1 -ATATAT
19216 GGTTTTTGAA
Statistics
Matches: 73, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
37 5 0.07
38 11 0.15
39 7 0.10
40 11 0.15
41 13 0.18
42 19 0.26
43 7 0.10
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.45
Consensus pattern (41 bp):
ATATATTATATAATGTTTGAAAAGCTTTTTGAAACATATAT
Found at i:19172 original size:39 final size:36
Alignment explanation
Indices: 19089--19415 Score: 164
Period size: 37 Copynumber: 8.5 Consensus size: 36
19079 TTTTCGTCTG
** ** *
19089 ATATAT-TATATAGTTTACAAATGTTTTTGAAATAC
1 ATATATATATATAGTTTTGAAAACTTTTTGAAATAT
*
19124 ATATAATATATATAGTTTTGAAAATGGTTTTTGGAAATATAT
1 ATAT-ATATATATAGTTTTGAAAA--CTTTTT-G-AA-ATAT
* * *
19166 ATATATATTATATAATGTTTGGAAAGCTTTTTGAAACAT
1 ATATATA-TATAT-A-GTTTTGAAAACTTTTTGAAATAT
* * *
19205 ATATA-ATATATGGTTTTTGAAAACATTTTAAAATTAT
1 ATATATATATATAG-TTTTGAAAACTTTTTGAAA-TAT
*
19242 ATATATAATATATAGTTTTTGAAAAAAACATTTCTGAATATATATATAT
1 ATATAT-ATATATAG-TTTTG---AAAAC-TTT-T---T-GA-A-ATAT
* *
19291 ATATATATATATAGTTTTGAAATCATTTTTAAAATAT
1 ATATATATATATAGTTTTGAAAAC-TTTTTGAAATAT
*
19328 TTATATAATATATAGTTTT-AAAACATTTTTGAAA-ACT
1 ATATAT-ATATATAGTTTTGAAAAC-TTTTTGAAATA-T
* ** * *
19365 ATATA-ATATATAATTTAAAAAACATTTTGTAA-AT
1 ATATATATATATAGTTTTGAAAACTTTTTGAAATAT
19399 ATATA-ATATATAGTTTT
1 ATATATATATATAGTTTT
19416 TTTAATATTT
Statistics
Matches: 235, Mismatches: 29, Indels: 57
0.73 0.09 0.18
Matches are distributed among these distances:
34 16 0.07
35 23 0.10
36 23 0.10
37 52 0.22
38 14 0.06
39 28 0.12
40 4 0.02
41 6 0.03
42 22 0.09
43 4 0.02
44 17 0.07
47 6 0.03
48 9 0.04
49 10 0.04
50 1 0.00
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (36 bp):
ATATATATATATAGTTTTGAAAACTTTTTGAAATAT
Found at i:19284 original size:2 final size:2
Alignment explanation
Indices: 19279--19303 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19269 ACATTTCTGA
19279 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
19304 GTTTTGAAAT
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:19357 original size:37 final size:33
Alignment explanation
Indices: 19289--19450 Score: 137
Period size: 35 Copynumber: 4.6 Consensus size: 33
19279 ATATATATAT
*
19289 ATATATATATATATAGTTTTGAAATCATTTTTAAAA
1 ATATATA-ATATATAGTTTT-AAAACATTTTT-AAA
19325 TATTTATATAATATATAGTTTTAAAACATTTTTGAAA
1 -A--TATATAATATATAGTTTTAAAACATTTTT-AAA
* *
19362 ACTATATAATATATAATTTAAAAAACATTTTGT-AA
1 A-TATATAATATATAGTTT-TAAAACATTTT-TAAA
** *
19397 ATATATAATATATAGTTTTTTTAATATTTTTTAAA
1 ATATATAATATATAG-TTTTAAAACA-TTTTTAAA
* *
19432 ATATATATTATATAATTTT
1 ATATATAATATATAGTTTT
19451 TTAAAAATAT
Statistics
Matches: 106, Mismatches: 12, Indels: 17
0.79 0.09 0.13
Matches are distributed among these distances:
34 21 0.20
35 41 0.39
36 11 0.10
37 15 0.14
38 12 0.11
39 6 0.06
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (33 bp):
ATATATAATATATAGTTTTAAAACATTTTTAAA
Found at i:19369 original size:86 final size:82
Alignment explanation
Indices: 19203--19378 Score: 200
Period size: 86 Copynumber: 2.1 Consensus size: 82
19193 TTTTTGAAAC
*
19203 ATATATAATATATGGTTTTTGAAAACATTTTAAAATTATATATATAATATATAGTTTTTGAAAAA
1 ATATATAATATATAGTTTTTGAAAACATTTTAAAATTATATATATAATATATAGTTTTT---AAA
19268 AACATTTCTGAATATATATAT
63 AACATTTCTGAATATA-ATAT
* *
19289 ATATATATATATATAG-TTTTGAAATCATTTTTAAAA-TATTTATATAATATATAG-TTTT-AAA
1 ATATATA-ATATATAGTTTTTGAAAACA-TTTTAAAATTATATATATAATATATAGTTTTTAAAA
* *
19350 ACATTTTTGAAAACT-ATAT
64 ACATTTCTGAATA-TAATAT
19369 AATATATAAT
1 -ATATATAAT
19379 TTAAAAAACA
Statistics
Matches: 81, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
80 6 0.07
81 21 0.26
82 1 0.01
85 4 0.05
86 34 0.42
87 15 0.19
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (82 bp):
ATATATAATATATAGTTTTTGAAAACATTTTAAAATTATATATATAATATATAGTTTTTAAAAAC
ATTTCTGAATATAATAT
Found at i:19444 original size:35 final size:37
Alignment explanation
Indices: 19343--19480 Score: 110
Period size: 35 Copynumber: 3.8 Consensus size: 37
19333 TAATATATAG
* *
19343 TTTTAAAACAT-TTTTGA-AAACTATATAATATATAA--
1 TTTTAAAA-ATATTTTTATAAA-TATATATTATATAATT
* * * * *
19378 TTTAAAAAACA-TTTTGTAAATATATAATATATAGTT
1 TTTTAAAAATATTTTTATAAATATATATTATATAATT
* *
19414 TTTTTAATAT-TTTTTA-AAATATATATTATATAATT
1 TTTTAAAAATATTTTTATAAATATATATTATATAATT
*
19449 TTTTAAAAATATTTTTATATATAATATATTAT
1 TTTTAAAAATATTTTTATAAAT-ATATATTAT
19481 TATTATTTCT
Statistics
Matches: 80, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
34 17 0.21
35 35 0.44
36 16 0.20
37 3 0.04
38 9 0.11
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (37 bp):
TTTTAAAAATATTTTTATAAATATATATTATATAATT
Found at i:19447 original size:26 final size:27
Alignment explanation
Indices: 19418--19475 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
19408 ATAGTTTTTT
*
19418 TAATATTTTTTAAAATATATAT-TATA
1 TAATATTTTTAAAAATATATATATATA
* *
19444 TAAT-TTTTTAAAAATATTTTTATATA
1 TAATATTTTTAAAAATATATATATATA
19470 TAATAT
1 TAATAT
19476 ATTATTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 14 0.52
26 12 0.44
27 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TAATATTTTTAAAAATATATATATATA
Found at i:19454 original size:24 final size:24
Alignment explanation
Indices: 19422--19469 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
19412 TTTTTTTAAT
19422 ATTTTTT-AAAATATATATTATATA
1 ATTTTTTAAAAATAT-TATTATATA
*
19446 ATTTTTTAAAAATATTTTTATATA
1 ATTTTTTAAAAATATTATTATATA
19470 TAATATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTTTTAAAAATATTATTATATA
Found at i:20744 original size:18 final size:18
Alignment explanation
Indices: 20687--20846 Score: 64
Period size: 18 Copynumber: 8.7 Consensus size: 18
20677 TTAAAAAATA
* *
20687 TTTTTTTCTTTT-TTTAT
1 TTTTTTTATTTTATTTCT
20704 TTTCTTTTA-TTTA-TTCGT
1 TTT-TTTTATTTTATTTC-T
*
20722 ATTTTTTATTTTATTTCT
1 TTTTTTTATTTTATTTCT
* *
20740 TTTTTATGTACTATATTT-T
1 TTTTT-T-TATTTTATTTCT
**
20759 TTTTCTTT-TTCAACTTT-T
1 TTTT-TTTATTTTA-TTTCT
* *
20777 TATTTTTATTTTTTTTCT
1 TTTTTTTATTTTATTTCT
*
20795 TATTTTTCATTTT-TTTCTT
1 T-TTTTTTATTTTATTTC-T
*
20814 TTGATTTGTTATTTTTTTTCT
1 TT--TTT-TTATTTTATTTCT
*
20835 TTTATTTATTTT
1 TTTTTTTATTTT
20847 TGATTTATTA
Statistics
Matches: 109, Mismatches: 17, Indels: 33
0.69 0.11 0.21
Matches are distributed among these distances:
17 21 0.19
18 40 0.37
19 23 0.21
20 12 0.11
21 9 0.08
22 4 0.04
ACGTcount: A:0.12, C:0.07, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTTTTATTTTATTTCT
Found at i:20782 original size:6 final size:6
Alignment explanation
Indices: 20773--20870 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
20763 CTTTTTCAAC
*
20773 TTTTTA TTTTTA TTTTT- TTTCTTA TTTTTCA TTTTTT TCTTTTGA TTTGTTA
1 TTTTTA TTTTTA TTTTTA TTT-TTA TTTTT-A TTTTTA T-TTTT-A TTT-TTA
* *
20825 TTTTT- TTTCTT- TTATTTA TTTTTGA TTTATTA TTATTA TTATTA TT
1 TTTTTA TTT-TTA TT-TTTA TTTTT-A TTT-TTA TTTTTA TTTTTA TT
20871 AGTATTATTA
Statistics
Matches: 78, Mismatches: 3, Indels: 22
0.76 0.03 0.21
Matches are distributed among these distances:
5 6 0.08
6 38 0.49
7 29 0.37
8 5 0.06
ACGTcount: A:0.15, C:0.04, G:0.03, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:20791 original size:9 final size:9
Alignment explanation
Indices: 20779--20847 Score: 50
Period size: 9 Copynumber: 7.2 Consensus size: 9
20769 CAACTTTTTA
20779 TTTTTATTT
1 TTTTTATTT
*
20788 TTTTTCTTAT
1 TTTTTATT-T
*
20798 TTTTCATTT
1 TTTTTATTT
20807 TTTTCT-TTT
1 TTTT-TATTT
20816 GATTTGTTATTT
1 --TTT-TTATTT
*
20828 TTTTTCTTT
1 TTTTTATTT
*
20837 TATTTATTT
1 TTTTTATTT
20846 TT
1 TT
20848 GATTTATTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 28 0.61
10 10 0.22
11 4 0.09
12 4 0.09
ACGTcount: A:0.10, C:0.06, G:0.03, T:0.81
Consensus pattern (9 bp):
TTTTTATTT
Found at i:20801 original size:40 final size:40
Alignment explanation
Indices: 20758--20847 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 40
20748 TACTATATTT
*
20758 TTTTTC-TTTTTCAACTTTTTATTT-TTATTTTTTTTCTTA
1 TTTTTCATTTTT-AACTTTTGATTTGTTATTTTTTTTCTTA
**
20797 TTTTTCATTTTTTTCTTTTGATTTGTTATTTTTTTTCTT-
1 TTTTTCATTTTTAACTTTTGATTTGTTATTTTTTTTCTTA
20836 TTATTT-ATTTTT
1 TT-TTTCATTTTT
20848 GATTTATTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
39 23 0.51
40 22 0.49
ACGTcount: A:0.11, C:0.08, G:0.02, T:0.79
Consensus pattern (40 bp):
TTTTTCATTTTTAACTTTTGATTTGTTATTTTTTTTCTTA
Found at i:20809 original size:21 final size:20
Alignment explanation
Indices: 20773--20841 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
20763 CTTTTTCAAC
20773 TTTTTATTT-TTA-TTTTTT
1 TTTTTATTTGTTATTTTTTT
*
20791 TTCTTATTT-TTCATTTTTTT
1 TTTTTATTTGTT-ATTTTTTT
*
20811 CTTTTGATTTGTTATTTTTTT
1 -TTTTTATTTGTTATTTTTTT
20832 TCTTTTATTT
1 T-TTTTATTT
20842 ATTTTTGATT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 10 0.24
19 1 0.02
20 7 0.17
21 22 0.52
22 2 0.05
ACGTcount: A:0.10, C:0.06, G:0.03, T:0.81
Consensus pattern (20 bp):
TTTTTATTTGTTATTTTTTT
Found at i:20809 original size:32 final size:31
Alignment explanation
Indices: 20685--20852 Score: 98
Period size: 32 Copynumber: 5.4 Consensus size: 31
20675 CTTTAAAAAA
* *
20685 TATTTTT-TTCTTTTTTTA-TTTTCTTTTATT
1 TATTTTTATTTTTTTTTTATTTTTCATTT-TT
**
20715 TATTCGTATTTTTTATTTTA--TTTC-TTTTT
1 TATTTTTATTTTTT-TTTTATTTTTCATTTTT
** * * *
20744 TATGTACTATATTTTTTTTCTTTTTCAACTTTT
1 TAT-TTTTATTTTTTTTTTATTTTTC-ATTTTT
20777 TATTTTTATTTTTTTTCTTATTTTTCATTTTT
1 TATTTTTATTTTTTTT-TTATTTTTCATTTTT
* * *
20809 T-TCTTTTGATTTGTTATTT-TTTTTCTTTTATT
1 TAT-TTTT-ATTTTTTTTTTATTTTTCATTT-TT
20841 TATTTTTGATTT
1 TATTTTT-ATTT
20853 ATTATTATTA
Statistics
Matches: 110, Mismatches: 16, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
29 9 0.08
30 16 0.15
31 23 0.21
32 39 0.35
33 23 0.21
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (31 bp):
TATTTTTATTTTTTTTTTATTTTTCATTTTT
Found at i:20859 original size:3 final size:3
Alignment explanation
Indices: 20851--20885 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
20841 TATTTTTGAT
*
20851 TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20886 TTCTTATCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:20860 original size:17 final size:17
Alignment explanation
Indices: 20812--20861 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
20802 CATTTTTTTC
* *
20812 TTTTGATTTGTTATTTT
1 TTTTGATTTATTATTAT
**
20829 TTTTCTTTTA-T-TTAT
1 TTTTGATTTATTATTAT
20844 TTTTGATTTATTATTAT
1 TTTTGATTTATTATTAT
20861 T
1 T
20862 ATTATTATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
15 11 0.44
16 2 0.08
17 12 0.48
ACGTcount: A:0.16, C:0.02, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTGATTTATTATTAT
Found at i:21815 original size:24 final size:24
Alignment explanation
Indices: 21783--21836 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
21773 CGTTCGGTAA
* *
21783 TATGTTCGTTTATGTTTGTTCATT
1 TATGTTCGTTTATATTCGTTCATT
21807 TATGTTCGTTTATATTCGTTCATT
1 TATGTTCGTTTATATTCGTTCATT
21831 TATGTT
1 TATGTT
21837 TAGCTCAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.15, C:0.09, G:0.15, T:0.61
Consensus pattern (24 bp):
TATGTTCGTTTATATTCGTTCATT
Found at i:22043 original size:23 final size:23
Alignment explanation
Indices: 22013--22107 Score: 82
Period size: 23 Copynumber: 3.9 Consensus size: 23
22003 TTTTCATTTA
22013 TGTTCGTTTATGTTCATTTATTG
1 TGTTCGTTTATGTTCATTTATTG
** *
22036 TGTTCGTTTACATTCGTTTATTG
1 TGTTCGTTTATGTTCATTTATTG
* *
22059 TGTTCGCTTACATCCGTTCATTTATGTT
1 TGTTCG-TT-TAT--GTTCATTTAT-TG
* *
22087 TGTTCATCTATGTTCATTTAT
1 TGTTCGTTTATGTTCATTTAT
22108 CATTTAAATG
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
23 26 0.46
24 12 0.21
25 1 0.02
26 2 0.04
27 9 0.16
28 6 0.11
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (23 bp):
TGTTCGTTTATGTTCATTTATTG
Found at i:22169 original size:16 final size:16
Alignment explanation
Indices: 22148--22178 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22138 ATTCCTTAAC
22148 GAACGAACACGAACAA
1 GAACGAACACGAACAA
*
22164 GAACGAACATGAACA
1 GAACGAACACGAACA
22179 TACCCCCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.23, G:0.19, T:0.03
Consensus pattern (16 bp):
GAACGAACACGAACAA
Found at i:24720 original size:22 final size:22
Alignment explanation
Indices: 24669--24727 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
24659 ACGCGATTCT
24669 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * * *
24691 AAAT-TCGCGTTGCGATTTTTC
1 GACTATCGCATTGCGATTTTCC
*
24712 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
24728 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:24759 original size:20 final size:20
Alignment explanation
Indices: 24713--24807 Score: 70
Period size: 20 Copynumber: 4.8 Consensus size: 20
24703 CGATTTTTCG
*
24713 ACTATCGCAATGCGAATATGTA
1 ACTATCGCAATGCGAGTA--TA
24735 A--ATCGCAATGCGAGTATA
1 ACTATCGCAATGCGAGTATA
* * * *
24753 ACTATCGCAACGCGATTCTG
1 ACTATCGCAATGCGAGTATA
* * *
24773 ACTGTCGCAACGCGATGT-TG
1 ACTATCGCAATGCGA-GTATA
24793 ACTATCGCAATGCGA
1 ACTATCGCAATGCGA
24808 TTTTCAAAGC
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
18 3 0.05
20 56 0.92
21 1 0.02
22 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (20 bp):
ACTATCGCAATGCGAGTATA
Found at i:24808 original size:20 final size:21
Alignment explanation
Indices: 24736--24808 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 21
24726 GAATATGTAA
* *
24736 ATCGCAATGCGA-GTATAACT
1 ATCGCAACGCGATGTATGACT
*
24756 ATCGCAACGCGAT-TCTGACT
1 ATCGCAACGCGATGTATGACT
*
24776 GTCGCAACGCGATGT-TGACT
1 ATCGCAACGCGATGTATGACT
*
24796 ATCGCAATGCGAT
1 ATCGCAACGCGAT
24809 TTTCAAAGCG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 44 0.98
21 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (21 bp):
ATCGCAACGCGATGTATGACT
Found at i:26252 original size:24 final size:24
Alignment explanation
Indices: 26225--26293 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
26215 CACCATAGCT
26225 CATATAATTGCACCGAAGTGCCCA
1 CATATAATTGCACCGAAGTGCCCA
*
26249 CATATAATTGCACCGAAGTG-CCG
1 CATATAATTGCACCGAAGTGCCCA
* *
26272 CGTATAATTGCACCGTAGTGCC
1 CATATAATTGCACCGAAGTGCC
26294 ATATAATACT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 20 0.49
24 21 0.51
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (24 bp):
CATATAATTGCACCGAAGTGCCCA
Found at i:26281 original size:23 final size:23
Alignment explanation
Indices: 26225--26294 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
26215 CACCATAGCT
26225 CATATAATTGCACCGAAGTGCCCA
1 CATATAATTGCACCGAAGTG-CCA
*
26249 CATATAATTGCACCGAAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
26272 CGTATAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
26295 TATAATACTG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 22 0.52
24 20 0.48
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:26482 original size:103 final size:103
Alignment explanation
Indices: 26310--26527 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
26300 TACTGTCCAT
* *
26310 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
26375 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
* * * *
26413 AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAATGATCAGGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
26478 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
26516 AAGGACCACATA
1 AAGGACCACATA
26528 GACCCTCGAC
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATATTCCAAAGAATACATATATGTCCCG
Found at i:28406 original size:20 final size:20
Alignment explanation
Indices: 28322--28408 Score: 106
Period size: 20 Copynumber: 4.5 Consensus size: 20
28312 ATAATCGCAA
*
28322 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
*
28341 TGTGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
28360 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
28380 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
28400 TGCGATTTT
1 TGCGATTTT
28409 AAGTTTCAGA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
19 24 0.41
20 35 0.59
ACGTcount: A:0.11, C:0.15, G:0.23, T:0.51
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:30161 original size:18 final size:18
Alignment explanation
Indices: 30138--30187 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
30128 TTTACTCGTA
30138 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
30156 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
*
30174 ATTTTACTTAGATT
1 ATTTCACTTAGATT
30188 GCTTAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:30376 original size:20 final size:20
Alignment explanation
Indices: 30337--30384 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
30327 TAGTTTACTT
*
30337 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATAACTA
* **
30357 TTGCAACGCGAATTTAACTA
1 TCGCAACGCGAAAATAACTA
30377 TCGCAACG
1 TCGCAACG
30385 AAAGAATCGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAAAATAACTA
Found at i:30450 original size:18 final size:19
Alignment explanation
Indices: 30408--30454 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
30398 GCGATTCTCT
30408 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
30428 CGTTGCGATAGTCA-TTCG
1 CGTTGCGATAGTCATTTCG
*
30446 TGTTGCGAT
1 CGTTGCGAT
30455 TTTAAGTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
20 14 0.54
ACGTcount: A:0.15, C:0.19, G:0.28, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:32512 original size:36 final size:30
Alignment explanation
Indices: 32432--32497 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
32422 ATAAGAGTTG
*
32432 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTATT
32462 ATTTGTTTAATTGATGTGTAAATAATTATT
1 ATTTGTTTAATTGATGTGTAAATAATTATT
32492 ATTTGT
1 ATTTGT
32498 GCTTGTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTATT
Found at i:32672 original size:20 final size:20
Alignment explanation
Indices: 32647--32891 Score: 262
Period size: 20 Copynumber: 12.8 Consensus size: 20
32637 GCGATTTTCT
*
32647 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
32667 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
32687 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
32707 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
32727 TGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
**
32747 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
32767 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
32781 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
32801 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
32821 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* *
32835 CGTTGCGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
32855 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
32875 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
32892 GAATGTGTAA
Statistics
Matches: 188, Mismatches: 25, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
14 20 0.11
16 2 0.01
18 2 0.01
19 2 0.01
20 162 0.86
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:32673 original size:34 final size:36
Alignment explanation
Indices: 32606--32891 Score: 169
Period size: 40 Copynumber: 7.7 Consensus size: 36
32596 AATCTGCATC
* * *
32606 ATATTCGCGTTGCGATAGTCTAATACACTTTGCGAT
1 ATATTCGCGTTGCGATAGTCAAATTCACGTTGCGAT
* *
32642 -T-TTCTCGTTGCGATAGTCAAATTCCCGTTGCGAT
1 ATATTCGCGTTGCGATAGTCAAATTCACGTTGCGAT
*
32676 AATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 -AT---ATTCGCGTTGCGATAGTCAAATTCACGTTGCGAT
* * *
32716 AGTTAAATTCGTGTTGCGATAGTCATATTCGCGTTGCGAT
1 A--T--ATTCGCGTTGCGATAGTCAAATTCACGTTGCGAT
* *
32756 AGTCATTTTCGCATTGCGAT--T---A-TCCCGTTGCGAT
1 A-T-A--TTCGCGTTGCGATAGTCAAATTCACGTTGCGAT
** * *
32790 AGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGAT
1 A-T---ATTCGCGTTGCGATAGTCAAATTCACGTTGCGAT
* *
32830 -TA-TCCCGTTGCGATATTCAAATTCACGTTGCGATAGT
1 ATATTCGCGTTGCGATAGTCAAATTCACGTTGCG--A-T
32867 CATATTCGCGTTGCGATAGTCAAAT
1 -ATATTCGCGTTGCGATAGTCAAAT
32892 GAATGTGTAA
Statistics
Matches: 199, Mismatches: 27, Indels: 44
0.74 0.10 0.16
Matches are distributed among these distances:
34 78 0.39
35 3 0.02
36 4 0.02
37 1 0.01
38 3 0.02
39 4 0.02
40 105 0.53
41 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (36 bp):
ATATTCGCGTTGCGATAGTCAAATTCACGTTGCGAT
Found at i:32810 original size:54 final size:54
Alignment explanation
Indices: 32664--32883 Score: 287
Period size: 54 Copynumber: 4.0 Consensus size: 54
32654 ATAGTCAAAT
* * *
32664 TCCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAA
1 TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCATTGCG--A-TT--A
** * *
32723 TTCGTGTTGCGATAGTCATATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
1 -TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCATTGCGATTA
*
32778 TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
1 TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCATTGCGATTA
* * *
32832 TCCCGTTGCGATATTCAAATTCACGTTGCGATAGTCATATTCGCGTTGCGAT
1 TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCATTGCGAT
32884 AGTCAAATGA
Statistics
Matches: 146, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
54 99 0.68
55 1 0.01
57 2 0.01
58 1 0.01
60 43 0.29
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (54 bp):
TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCATTGCGATTA
Found at i:32859 original size:74 final size:73
Alignment explanation
Indices: 32687--32888 Score: 228
Period size: 74 Copynumber: 2.7 Consensus size: 73
32677 ATCAAATTCG
* * * * *
32687 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGTGTTGCGATAGTCATATTCGCGTTG
1 CGTTGCGATATTCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCATTG
32752 CGATAGTC
66 CGATAGTC
** * * * * * *
32760 ATTTTCGCAT-TGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCAT
1 CGTTGCG-ATATTCAAAT-TCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCAT
32824 TGCGATTA-TCC
64 TGCGA-TAGT-C
*
32835 CGTTGCGATATTCAAATTCACGTTGCGATAGTCATATTCGCGTTGCGATAGTCA
1 CGTTGCGATATTCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCA
32889 AATGAATGTG
Statistics
Matches: 104, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
73 7 0.07
74 86 0.83
75 11 0.11
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (73 bp):
CGTTGCGATATTCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCATTG
CGATAGTC
Found at i:33086 original size:17 final size:17
Alignment explanation
Indices: 33064--33097 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
33054 AAGCCGGTTG
33064 TGATTGAGATTTTGATT
1 TGATTGAGATTTTGATT
*
33081 TGATTGCGATTTTGATT
1 TGATTGAGATTTTGATT
33098 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.03, G:0.24, T:0.53
Consensus pattern (17 bp):
TGATTGAGATTTTGATT
Found at i:35380 original size:23 final size:24
Alignment explanation
Indices: 35347--35399 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
35337 CTGAAACATC
35347 ATCAAAATCCGAG-TA-TGACCAAG
1 ATCAAAATCCG-GTTATTGACCAAG
*
35370 ATCAAAGTCCGGTTATTGACCAAG
1 ATCAAAATCCGGTTATTGACCAAG
35394 ATCAAA
1 ATCAAA
35400 TTTCGATACC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 1 0.04
23 12 0.44
24 14 0.52
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.21
Consensus pattern (24 bp):
ATCAAAATCCGGTTATTGACCAAG
Found at i:36303 original size:22 final size:20
Alignment explanation
Indices: 36220--36349 Score: 136
Period size: 20 Copynumber: 6.3 Consensus size: 20
36210 AAATTCAGTG
* *
36220 TTGCGACAGTCAAAATCGCG
1 TTGCGATAGTCAAAATCGCA
36240 TTGCGATAGTCAAAATCGCA
1 TTGCGATAGTCAAAATCGCA
* * *
36260 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAAAATCGCA
36280 TTGCGATAGTCGGAAAATCGCA
1 TTGCGATAGTC--AAAATCGCA
36302 TTGCGATAGTCGAAAAATCGCA
1 TTGCGATAGTC--AAAATCGCA
* * *
36324 ATGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAAAATCGCA
36344 TTGCGA
1 TTGCGA
36350 ATCTGGAAAC
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.01
20 53 0.57
21 1 0.01
22 38 0.41
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (20 bp):
TTGCGATAGTCAAAATCGCA
Found at i:37145 original size:27 final size:27
Alignment explanation
Indices: 37082--37146 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 27
37072 GGTCTACCAG
*
37082 ACCTGGCCCAAAAATTATAAACCTTCC
1 ACCTGGCCCCAAAATTATAAACCTTCC
*
37109 ACCT-GACCCAAAA-TATAATACCTTCC
1 ACCTGGCCCCAAAATTATAA-ACCTTCC
*
37135 ACTTGGCCCCAA
1 ACCTGGCCCCAA
37147 CCCGACTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 5 0.16
26 17 0.53
27 10 0.31
ACGTcount: A:0.35, C:0.35, G:0.08, T:0.22
Consensus pattern (27 bp):
ACCTGGCCCCAAAATTATAAACCTTCC
Found at i:37206 original size:43 final size:42
Alignment explanation
Indices: 37141--37225 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 42
37131 TTCCACTTGG
* * *
37141 CCCCAACCCGACTTGATCTTTTGAGATAAGATTCGAACCCGA
1 CCCCAACCCAACTTGATCTTTTGAGATAAAATTCAAACCCGA
37183 CCCCGAACCCAACTTGATCTTTTGAGATAAAATTCAAACCCGA
1 CCCC-AACCCAACTTGATCTTTTGAGATAAAATTCAAACCCGA
37226 TCCGACCCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 4 0.10
43 35 0.90
ACGTcount: A:0.32, C:0.31, G:0.14, T:0.24
Consensus pattern (42 bp):
CCCCAACCCAACTTGATCTTTTGAGATAAAATTCAAACCCGA
Found at i:38473 original size:13 final size:13
Alignment explanation
Indices: 38451--38492 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
38441 GTCACAACCC
* *
38451 GACCCCACCCATT
1 GACCCGACCCGTT
38464 GACCCGACCCGTT
1 GACCCGACCCGTT
38477 GACCCGACCCGTT
1 GACCCGACCCGTT
38490 GAC
1 GAC
38493 TGTTGACTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Done.