Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001695.1 Hibiscus syriacus cultivar Beakdansim tig00003385_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: 103415
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:14294 original size:29 final size:31
Alignment explanation
Indices: 14241--14300 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
14231 AAATGTAAGG
14241 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
14272 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
14301 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:14429 original size:22 final size:19
Alignment explanation
Indices: 14380--14479 Score: 101
Period size: 22 Copynumber: 4.8 Consensus size: 19
14370 AGGGTGTCAA
14380 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA--CCTGC
14401 AGTGCATCCATGCACCTGCAC
1 AGTGCATCCATGCACCTG--C
*
14422 TAGTGCATCGATGCACCTGCAC
1 -AGTGCATCCATGCACCTG--C
*
14444 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACC-TGC
14465 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
14480 TCAAACACCG
Statistics
Matches: 73, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
19 4 0.05
20 14 0.19
21 16 0.22
22 37 0.51
23 2 0.03
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.22
Consensus pattern (19 bp):
AGTGCATCCATGCACCTGC
Found at i:14525 original size:20 final size:20
Alignment explanation
Indices: 14500--14573 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
14490 AATGCAATTA
*
14500 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
**
14520 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTGCT
14541 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
14561 GTGCATCCATGCA
1 GTGCATCGATGCA
14574 CCAAGGCTGC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 30 0.64
21 17 0.36
ACGTcount: A:0.19, C:0.28, G:0.24, T:0.28
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:14547 original size:41 final size:41
Alignment explanation
Indices: 14500--14582 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
14490 AATGCAATTA
* * *
14500 GTGCATCGATGCATCCTTCTGTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCACCAAGGCT
14541 GTGCATCGATGCATCCTGCTGTGCATCCATGCACCAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCACCAAGGCT
14582 G
1 G
14583 CAACAGCTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.19, C:0.29, G:0.25, T:0.27
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGCTGTGCATCCATGCACCAAGGCT
Found at i:17843 original size:29 final size:30
Alignment explanation
Indices: 17774--17833 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
17764 AAATTTAAGG
17774 CAAAATGATTTTTGGACTTGAATTGAATTTA
1 CAAAATG-TTTTTGGACTTGAATTGAATTTA
17805 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
17834 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:19526 original size:15 final size:15
Alignment explanation
Indices: 19494--19539 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
19484 AGCTCCAGTA
* *
19494 GTCTAGCATTTAATGT
1 GTCTA-CATTCAACGT
19510 GTCTACATTCAACGT
1 GTCTACATTCAACGT
19525 GTCTACATTCAACGT
1 GTCTACATTCAACGT
19540 ACAAACTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 23 0.82
16 5 0.18
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (15 bp):
GTCTACATTCAACGT
Found at i:23531 original size:3 final size:3
Alignment explanation
Indices: 23523--23566 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
23513 TTTGTTTTAT
*
23523 TTA TTA TTA TTA TT- TTG TT- TTA TTA TTA -TA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
23567 AATAATTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 8 0.22
3 29 0.78
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:23547 original size:16 final size:16
Alignment explanation
Indices: 23520--23566 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
23510 TCATTTGTTT
23520 TATT-TATTATTATTA
1 TATTATATTATTATTA
* * *
23535 TTTTGTTTTATTATTA
1 TATTATATTATTATTA
23551 TATTATATTATTATTA
1 TATTATATTATTATTA
23567 AATAATTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 3 0.12
16 23 0.88
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATTATATTATTATTA
Found at i:23559 original size:23 final size:23
Alignment explanation
Indices: 23513--23556 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
23503 TTTTATTTCA
23513 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTATTTATTATTATTAT
23536 TTTGTTTTA-TTATTA-TATTAT
1 TTTGTTTTATTTATTATTATTAT
23557 ATTATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.29
22 6 0.29
23 9 0.43
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (23 bp):
TTTGTTTTATTTATTATTATTAT
Found at i:25144 original size:16 final size:17
Alignment explanation
Indices: 25123--25167 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
25113 TTTTACTTTC
*
25123 ATATATTTATGATTA-T
1 ATATATTTATCATTAGT
25139 ATATATTTATCATTAGT
1 ATATATTTATCATTAGT
25156 ATTATTATTTAT
1 A-TA-TATTTAT
25168 TATTTACGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 14 0.56
17 2 0.08
18 2 0.08
19 7 0.28
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (17 bp):
ATATATTTATCATTAGT
Found at i:25580 original size:11 final size:13
Alignment explanation
Indices: 25543--25582 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
25533 TGTTTAATAA
25543 AATATA-TATATT
1 AATATATTATATT
*
25555 AATATATTATCTT
1 AATATATTATATT
25568 AA-A-ATTATATT
1 AATATATTATATT
25579 AATA
1 AATA
25583 AACTTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:27387 original size:28 final size:26
Alignment explanation
Indices: 27355--27411 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
27345 AATTCTTTCC
*
27355 TTTCAAAATTTTTATATATACTTATTAT
1 TTTCAAAATATTTATATATA--TATTAT
* *
27383 TTTCATAATATTTATATGTATATTAT
1 TTTCAAAATATTTATATATATATTAT
27409 TTT
1 TTT
27412 ATTTTCAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 9 0.35
28 17 0.65
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTCAAAATATTTATATATATATTAT
Found at i:28927 original size:8 final size:7
Alignment explanation
Indices: 28903--28944 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
28893 TTTTCATACA
28903 TGCA-TT
1 TGCATTT
28909 TGCATTT
1 TGCATTT
28916 TGCATCTT
1 TGCAT-TT
28924 TGCATTT
1 TGCATTT
* *
28931 TTCATTG
1 TGCATTT
28938 TGCATTT
1 TGCATTT
28945 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:28927 original size:15 final size:14
Alignment explanation
Indices: 28903--28944 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
28893 TTTTCATACA
28903 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
28916 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
28931 TTCATTGTGCATTT
1 TGCATTTTGCATTT
28945 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:29020 original size:12 final size:12
Alignment explanation
Indices: 29003--29030 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28993 ACATTCACAT
29003 ATTTACATTTGC
1 ATTTACATTTGC
29015 ATTTACATTTGC
1 ATTTACATTTGC
29027 ATTT
1 ATTT
29031 TTAACGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:31004 original size:14 final size:14
Alignment explanation
Indices: 30985--31068 Score: 62
Period size: 15 Copynumber: 5.6 Consensus size: 14
30975 TCCAACAAAG
*
30985 AAAGAAGAAGGAAA
1 AAAGAAAAAGGAAA
*
30999 AAAGAATAAA-AAAA
1 AAAGAA-AAAGGAAA
31013 AAAGAAAAAGGAAAAA
1 AAAGAAAAAGG--AAA
**
31029 AAAGGAAAAACAAAAA
1 AAA-GAAAAA-GGAAA
*
31045 AAACAAAAAGGAAAA
1 AAAGAAAAAGG-AAA
31060 AAAGAAAAA
1 AAAGAAAAA
31069 AAAGGAAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
13 3 0.06
14 15 0.28
15 18 0.33
16 12 0.22
17 6 0.11
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.01
Consensus pattern (14 bp):
AAAGAAAAAGGAAA
Found at i:31026 original size:7 final size:7
Alignment explanation
Indices: 30985--31069 Score: 55
Period size: 7 Copynumber: 11.4 Consensus size: 7
30975 TCCAACAAAG
*
30985 AAAGAAG
1 AAAGAAA
*
30992 AAGGAAA
1 AAAGAAA
30999 AAAGAATA
1 AAAGAA-A
31007 AAA-AAA
1 AAAGAAA
31013 AAAGAAA
1 AAAGAAA
*
31020 AAGGAAAAA
1 AA--AGAAA
31029 AAAGGAAA
1 AAA-GAAA
*
31037 AACAAAAA
1 AA-AGAAA
*
31045 AAACAAA
1 AAAGAAA
*
31052 AAGGAAAA
1 AAAG-AAA
31060 AAAGAAA
1 AAAGAAA
31067 AAA
1 AAA
31070 AAGGAAAATT
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
6 4 0.07
7 30 0.49
8 20 0.33
9 7 0.11
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.01
Consensus pattern (7 bp):
AAAGAAA
Found at i:31044 original size:32 final size:30
Alignment explanation
Indices: 30996--31071 Score: 109
Period size: 32 Copynumber: 2.5 Consensus size: 30
30986 AAGAAGAAGG
* *
30996 AAAAAAGAATAAAAAAAAAAGAAAAAGGAA
1 AAAAAAGAAAAAAAAAAAAACAAAAAGGAA
31026 AAAAAAGGAAAAACAAAAAAAACAAAAAGG-A
1 AAAAAA-GAAAAA-AAAAAAAACAAAAAGGAA
31057 AAAAAAGAAAAAAAA
1 AAAAAAGAAAAAAAA
31072 GGAAAATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
29 3 0.07
30 12 0.29
31 12 0.29
32 15 0.36
ACGTcount: A:0.84, C:0.03, G:0.12, T:0.01
Consensus pattern (30 bp):
AAAAAAGAAAAAAAAAAAAACAAAAAGGAA
Found at i:31076 original size:10 final size:10
Alignment explanation
Indices: 30992--31077 Score: 74
Period size: 10 Copynumber: 8.8 Consensus size: 10
30982 AAGAAAGAAG
30992 AAGGAAAAAA
1 AAGGAAAAAA
*
31002 GAA-TAAAAAA
1 -AAGGAAAAAA
*
31012 AA--AAGAAA
1 AAGGAAAAAA
31020 AAGGAAAAAA
1 AAGGAAAAAA
31030 AAGGAAAAACA
1 AAGGAAAAA-A
**
31041 AAAAAAACAAA
1 AAGGAAA-AAA
31052 AAGG-AAAAA
1 AAGGAAAAAA
31061 AA-GAAAAAA
1 AAGGAAAAAA
31070 AAGGAAAA
1 AAGGAAAA
31078 TTAAATCAAG
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
8 8 0.13
9 14 0.23
10 27 0.44
11 11 0.18
12 2 0.03
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.01
Consensus pattern (10 bp):
AAGGAAAAAA
Found at i:31077 original size:16 final size:15
Alignment explanation
Indices: 30981--31068 Score: 88
Period size: 16 Copynumber: 5.6 Consensus size: 15
30971 CTCATCCAAC
30981 AAAGAAAGAAGAAGGAAA
1 AAAGAAA-AAGAA--AAA
*
30999 AAAGAATAA-AAAAA
1 AAAGAAAAAGAAAAA
31013 AAAGAAAAAGGAAAAA
1 AAAGAAAAA-GAAAAA
*
31029 AAAGGAAAAACAAAAA
1 AAA-GAAAAAGAAAAA
* *
31045 AAACAAAAAGGAAAA
1 AAAGAAAAAGAAAAA
31060 AAAGAAAAA
1 AAAGAAAAA
31069 AAAGGAAAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
14 11 0.18
15 17 0.28
16 18 0.30
17 8 0.13
18 6 0.10
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.01
Consensus pattern (15 bp):
AAAGAAAAAGAAAAA
Found at i:34952 original size:22 final size:22
Alignment explanation
Indices: 34924--34978 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
34914 ATCTACATTC
34924 TTCAAAGATGATAAATTATCTT
1 TTCAAAGATGATAAATTATCTT
* * *
34946 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAAATTATCTT
*
34968 TTCGAAGATGA
1 TTCAAAGATGA
34979 AAGCTTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAAATTATCTT
Found at i:35913 original size:76 final size:76
Alignment explanation
Indices: 35656--35900 Score: 418
Period size: 76 Copynumber: 3.2 Consensus size: 76
35646 CTATTTCCCA
*
35656 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
35721 AGCCTTAGGGT
66 AGCCTTAGGGT
35732 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
35797 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
35808 CATCTATAAGTCCTACAGTACATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * *
35873 AACCTTCGAGT
66 AGCCTTAGGGT
* *
35884 CAGCTGTAAGCCCTACA
1 CATCTGTAAGTCCTACA
35901 ATGCGGAATG
Statistics
Matches: 160, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 160 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.33
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:36186 original size:113 final size:113
Alignment explanation
Indices: 35932--36457 Score: 714
Period size: 113 Copynumber: 4.7 Consensus size: 113
35922 CATTTCCAGA
* * * *
35932 AGAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAATAAGTTCATAATTAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGT
* * * * * *
35997 TCAAACTTTTCGCTTAAATTCATTATTCAATGGATCAGCATTTCCAGGT
66 TCAACCTTTT-GCTTTAATTCATCACTCGATGGATCAGCATTGCCAGGT
* *
36046 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATTAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGT
** * * *
36111 TCAACCTTTTGCTCGAATTCATCACTCGGTGGATCAACAGTGCCAGGT
66 TCAACCTTTTGCTTTAATTCATCACTCGATGGATCAGCATTGCCAGGT
* *
36159 AGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTTT
1 AGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGT
* * * * *
36224 TTAACCTTTTGTTTTAATTCATCACTCGATGGATTATCATTGCCAGTT
66 TCAACCTTTTGCTTTAATTCATCACTCGATGGATCAGCATTGCCAGGT
*
36272 AGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGT
1 AGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGT
* * * * *
36337 TCAACATTTCGCTTTAATTCATCACTCGATGGATTAGCTTTTCCAGAG-
66 TCAACCTTTTGCTTTAATTCATCACTCGATGGATCAGCATTGCCAG-GT
* * * *
36385 AAAGTTCATAATGAGAAGAACTTATCTGAAGCA-GAAGAAGAAGTTCATAATGAGAAGAGCTTGT
1 AGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGT
36449 TCAACCTTT
66 TCAACCTTT
36458 GTATGACTCT
Statistics
Matches: 371, Mismatches: 40, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
112 36 0.10
113 263 0.71
114 72 0.19
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (113 bp):
AGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGT
TCAACCTTTTGCTTTAATTCATCACTCGATGGATCAGCATTGCCAGGT
Found at i:36659 original size:123 final size:123
Alignment explanation
Indices: 36374--36702 Score: 422
Period size: 122 Copynumber: 2.7 Consensus size: 123
36364 GATGGATTAG
*
36374 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGCAGAAGA-AGAAGTTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAGA-AAGTTCATAATGA
* * *
36438 GAAGAGCTTGTTCAACC-TTTGTATGACTCTATCACAGAAAGAGATAGATCAACACCAA
65 GAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAGAAAGAGATAGATCAACACCAA
*
36496 CTTTTCCAGAGAAAGTTCATAATGAGAAAAACTTATCTGAAGAAGAAGAGAAAGTTCATAATGAG
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAGAAAGTTCATAATGAG
* * * *
36561 AAGAACTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATATATCATCATC-A
66 AAGAACTTGTTCAACCTTTTGCATAACTCTATCACAGAAAGAGATAGATCAACACCAA
* * * *
36618 GTATTTCTAGA-AGGAGTTCATAATGAGAAGAACTCATCTGAAGAAG-A-AG-AAGTTCATAA-G
1 CT-TTTCCAGAGA-AAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAGAAAGTTCATAATG
* * *
36678 AAGGAGAATTTGTTCAACTTTTTGC
64 -AGAAGAACTTGTTCAACCTTTTGC
36703 TAGATTACAT
Statistics
Matches: 185, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
119 1 0.01
120 31 0.17
121 2 0.01
122 80 0.43
123 71 0.38
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (123 bp):
CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAGAAAGTTCATAATGAG
AAGAACTTGTTCAACCTTTTGCATAACTCTATCACAGAAAGAGATAGATCAACACCAA
Found at i:36966 original size:10 final size:11
Alignment explanation
Indices: 36949--36978 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
36939 TTATTTTGTT
36949 TTATTATTATA
1 TTATTATTATA
36960 TTA-TATTATA
1 TTATTATTATA
36970 TTATTATTA
1 TTATTATTA
36979 AATAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTATTATTATA
Found at i:36990 original size:18 final size:21
Alignment explanation
Indices: 36949--36990 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
36939 TTATTTTGTT
*
36949 TTATTATTATATTATATTATA
1 TTATTATTATAATATATTATA
36970 TTATTATTA-AATA-ATTA-A
1 TTATTATTATAATATATTATA
36988 TTA
1 TTA
36991 ATTTTAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 4 0.20
19 4 0.20
20 3 0.15
21 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTATTATAATATATTATA
Found at i:38573 original size:29 final size:31
Alignment explanation
Indices: 38540--38608 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 31
38530 TTAGTATTAT
* *
38540 TATTTATTATGTC-AATATATATAT-AATAA
1 TATTTATTAAGTCTAATAAATATATAAATAA
*
38569 TATTTATCTAAGTCTTATAAATATATAAATAA
1 TATTTAT-TAAGTCTAATAAATATATAAATAA
38601 TATTTATT
1 TATTTATT
38609 TAATTTATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.21
30 5 0.15
31 10 0.29
32 12 0.35
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (31 bp):
TATTTATTAAGTCTAATAAATATATAAATAA
Found at i:38932 original size:11 final size:13
Alignment explanation
Indices: 38895--38934 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
38885 TGTTTAATAA
38895 AATATA-TATATT
1 AATATATTATATT
*
38907 AATATATTATCTT
1 AATATATTATATT
38920 AA-A-ATTATATT
1 AATATATTATATT
38931 AATA
1 AATA
38935 AACTTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:39333 original size:17 final size:17
Alignment explanation
Indices: 39311--39347 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
39301 CAGTGACCAA
39311 AGTAAAACATAAATGAT
1 AGTAAAACATAAATGAT
39328 AGTAAAACATAAATGAT
1 AGTAAAACATAAATGAT
39345 AGT
1 AGT
39348 TGGGATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.24
Consensus pattern (17 bp):
AGTAAAACATAAATGAT
Found at i:41913 original size:26 final size:26
Alignment explanation
Indices: 41877--41937 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
41867 TTGGTAGGAT
41877 TCGAACTTGGCCACCACTTGTGATGG
1 TCGAACTTGGCCACCACTTGTGATGG
41903 TCGAACTTGGCCACCACTTGTGATGG
1 TCGAACTTGGCCACCACTTGTGATGG
*
41929 TAGAACTTG
1 TCGAACTTG
41938 ACTTTACAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (26 bp):
TCGAACTTGGCCACCACTTGTGATGG
Found at i:48100 original size:20 final size:20
Alignment explanation
Indices: 48077--48114 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48067 TAAGTAAATT
48077 TTTAATATTTGTATTAAAAA
1 TTTAATATTTGTATTAAAAA
* *
48097 TTTAGTATTTTTATTAAA
1 TTTAATATTTGTATTAAA
48115 GTTTAACTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTAATATTTGTATTAAAAA
Found at i:48579 original size:16 final size:16
Alignment explanation
Indices: 48558--48589 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
48548 ACAATAAATT
48558 ATTCAATCACTTTTAC
1 ATTCAATCACTTTTAC
48574 ATTCAATCACTTTTAC
1 ATTCAATCACTTTTAC
48590 TCATTTATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTCAATCACTTTTAC
Found at i:50325 original size:29 final size:29
Alignment explanation
Indices: 50283--50341 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
50273 CACACCTAAA
50283 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
50312 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
50341 T
1 T
50342 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:54989 original size:29 final size:29
Alignment explanation
Indices: 54955--55013 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
54945 CCTAAATTAA
54955 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
*
54984 TTTGATGTCATTGTTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
55013 T
1 T
55014 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:61676 original size:17 final size:17
Alignment explanation
Indices: 61654--61694 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
61644 TATAATAAAC
61654 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
61671 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
*
61688 ATATGAT
1 TTATGAT
61695 TACTTTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (17 bp):
TTATGATAATTAAATTA
Found at i:61722 original size:51 final size:52
Alignment explanation
Indices: 61664--61761 Score: 171
Period size: 51 Copynumber: 1.9 Consensus size: 52
61654 TTATGATAAT
* *
61664 TAAATTATTATGATAATTAAATTAATATGATTAC-TTTTTGAAATTTTATCA
1 TAAATTATTATGATAATCAAAATAATATGATTACTTTTTTGAAATTTTATCA
61715 TAAATTATTATGATAATCAAAATAATATGATTACTTTTTTGAAATTT
1 TAAATTATTATGATAATCAAAATAATATGATTACTTTTTTGAAATTT
61762 AGTTTTATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 32 0.73
52 12 0.27
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (52 bp):
TAAATTATTATGATAATCAAAATAATATGATTACTTTTTTGAAATTTTATCA
Found at i:62447 original size:23 final size:23
Alignment explanation
Indices: 62417--62496 Score: 88
Period size: 23 Copynumber: 3.3 Consensus size: 23
62407 CAGCAACCGA
62417 CAAGCATCAATGTACCAATTCAG
1 CAAGCATCAATGTACCAATTCAG
62440 CAAGCATCATCAATGTACCAATTCAG
1 CAAG---CATCAATGTACCAATTCAG
** * * *
62466 CAAGCATCGTTGCATCGATTCAG
1 CAAGCATCAATGTACCAATTCAG
62489 CAAGCATC
1 CAAGCATC
62497 CTACATTAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
23 26 0.53
26 23 0.47
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.23
Consensus pattern (23 bp):
CAAGCATCAATGTACCAATTCAG
Found at i:62455 original size:26 final size:26
Alignment explanation
Indices: 62421--62473 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
62411 AACCGACAAG
62421 CATCAATGTACCAATTCAGCAAGCAT
1 CATCAATGTACCAATTCAGCAAGCAT
62447 CATCAATGTACCAATTCAGCAAGCAT
1 CATCAATGTACCAATTCAGCAAGCAT
62473 C
1 C
62474 GTTGCATCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.23
Consensus pattern (26 bp):
CATCAATGTACCAATTCAGCAAGCAT
Found at i:62623 original size:16 final size:16
Alignment explanation
Indices: 62602--62636 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
62592 TATCAAGTAG
*
62602 AAACAAGCAATATCAA
1 AAACAAGCAATAACAA
62618 AAACAAGCAATAACAA
1 AAACAAGCAATAACAA
62634 AAA
1 AAA
62637 GGAAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.69, C:0.17, G:0.06, T:0.09
Consensus pattern (16 bp):
AAACAAGCAATAACAA
Found at i:64858 original size:31 final size:30
Alignment explanation
Indices: 64781--64863 Score: 121
Period size: 30 Copynumber: 2.7 Consensus size: 30
64771 TAATATAGTT
* *
64781 TATATATACTATATTTTATATACTAATGAAC
1 TATATATA-TATAGTTTATATACTAAAGAAC
64812 TATATATATATAGTTTATATACTAAAGAAC
1 TATATATATATAGTTTATATACTAAAGAAC
*
64842 TATATAATGTATAGTTTATATA
1 TATAT-ATATATAGTTTATATA
64864 TACCATATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
30 25 0.52
31 23 0.48
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (30 bp):
TATATATATATAGTTTATATACTAAAGAAC
Found at i:64973 original size:2 final size:2
Alignment explanation
Indices: 64961--65026 Score: 53
Period size: 2 Copynumber: 31.0 Consensus size: 2
64951 ATATGTAAAT
*
64961 TA TA CTA TA TA TA TA TA GTT TA TA TA TA TA -A TA TA GTA TA TA
1 TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA
* *
65003 AA TA TA AA CTA TA GTA TA TA TA TA
1 TA TA TA TA -TA TA -TA TA TA TA TA
65027 GGTCATATGT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
1 1 0.02
2 43 0.83
3 8 0.15
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:64977 original size:31 final size:31
Alignment explanation
Indices: 64941--65008 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
64931 TTAGGATTTT
*
64941 TATATAGTTCATATGTA-AATTATACTATATA
1 TATATAGTTCATATATATAA-TATACTATATA
* *
64972 TATATAGTTTATATATATAATATAGTATATA
1 TATATAGTTCATATATATAATATACTATATA
*
65003 AATATA
1 TATATA
65009 AACTATAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (31 bp):
TATATAGTTCATATATATAATATACTATATA
Found at i:64996 original size:18 final size:18
Alignment explanation
Indices: 64961--65026 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
64951 ATATGTAAAT
64961 TATACTATATAT-ATATAG
1 TATA-TATATATAATATAG
*
64979 TTTATATATATAATATAG
1 TATATATATATAATATAG
*
64997 TATATAAATATAAACTATAG
1 TATATATATAT-AA-TATAG
65017 TATATATATA
1 TATATATATA
65027 GGTCATATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
17 7 0.17
18 18 0.44
19 2 0.05
20 14 0.34
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (18 bp):
TATATATATATAATATAG
Found at i:65007 original size:20 final size:20
Alignment explanation
Indices: 64966--65022 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
64956 TAAATTATAC
*
64966 TATATATATATAGT-T-TATA
1 TATATA-ATATAGTATATAAA
64985 TATATAATATAGTATATAAA
1 TATATAATATAGTATATAAA
65005 TATA-AACTATAGTATATA
1 TATATAA-TATAGTATATA
65023 TATAGGTCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 7 0.21
19 9 0.26
20 18 0.53
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (20 bp):
TATATAATATAGTATATAAA
Found at i:65077 original size:50 final size:49
Alignment explanation
Indices: 64966--65107 Score: 182
Period size: 50 Copynumber: 2.9 Consensus size: 49
64956 TAAATTATAC
* * * *
64966 TATATATATATAGTTTATATATATA--ATATAGTATATAAATATAAACTA
1 TATATATATATAGGTCATATGTAAACTATATAGTATAT-AATATAAACTA
*
65014 TAGTATATATATAGGTCATATGTAAACTATATAGTATATAATATCAACTA
1 TA-TATATATATAGGTCATATGTAAACTATATAGTATATAATATAAACTA
*
65064 GTATATATATATAGGTCATATGTAAACTATATAGTTTAT-ATATA
1 -TATATATATATAGGTCATATGTAAACTATATAGTATATAATATA
65108 GTTCATATGT
Statistics
Matches: 83, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
48 2 0.02
49 23 0.28
50 45 0.54
51 13 0.16
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (49 bp):
TATATATATATAGGTCATATGTAAACTATATAGTATATAATATAAACTA
Found at i:65107 original size:31 final size:29
Alignment explanation
Indices: 65069--65133 Score: 103
Period size: 31 Copynumber: 2.2 Consensus size: 29
65059 AACTAGTATA
65069 TATATATAGGTCATATGTAAACTATATAGTT
1 TATATATAGGTCATATGTAAAC--TATAGTT
*
65100 TATATATAGTTCATATGTAAACTATAGTT
1 TATATATAGGTCATATGTAAACTATAGTT
65129 TATAT
1 TATAT
65134 GTAAATATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 12 0.36
31 21 0.64
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (29 bp):
TATATATAGGTCATATGTAAACTATAGTT
Found at i:65127 original size:18 final size:18
Alignment explanation
Indices: 65104--65218 Score: 97
Period size: 18 Copynumber: 5.9 Consensus size: 18
65094 ATAGTTTATA
*
65104 TATAGTTCATATGTAAAC
1 TATAGTTTATATGTAAAC
65122 TATAGTTTATATGTAAATATTAAC
1 TATAGTTTATATG----TA--AAC
*
65146 TATAGTTTATATGTAACC
1 TATAGTTTATATGTAAAC
*
65164 TATAG-TTAGTATATAAAC
1 TATAGTTTA-TATGTAAAC
65182 TATATAGTTTATATGTAAAC
1 --TATAGTTTATATGTAAAC
* *
65202 TATAGTTCATATATAAA
1 TATAGTTTATATGTAAA
65219 TATCAACCAT
Statistics
Matches: 80, Mismatches: 7, Indels: 20
0.75 0.07 0.19
Matches are distributed among these distances:
17 3 0.04
18 41 0.51
20 15 0.19
21 3 0.04
22 2 0.03
24 16 0.20
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.43
Consensus pattern (18 bp):
TATAGTTTATATGTAAAC
Found at i:65197 original size:38 final size:37
Alignment explanation
Indices: 65146--65218 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 37
65136 AAATATTAAC
*
65146 TATAGTTTATATGTAACCTATAGTTAGTATATAAACTA
1 TATAGTTTATATGTAAACTATAGTTA-TATATAAACTA
65184 TATAGTTTATATGTAAACTATAGTTCATATATAAA
1 TATAGTTTATATGTAAACTATAGTT-ATATATAAA
65219 TATCAACCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
38 32 0.97
39 1 0.03
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (37 bp):
TATAGTTTATATGTAAACTATAGTTATATATAAACTA
Found at i:65288 original size:18 final size:17
Alignment explanation
Indices: 65243--65288 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
65233 TATATATATT
65243 TATATATATAGTTCATA
1 TATATATATAGTTCATA
* *
65260 TGTAAACTATAGTTCATA
1 TATATA-TATAGTTCATA
65278 TATATAGTATA
1 TATATA-TATA
65289 TAAATATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (17 bp):
TATATATATAGTTCATA
Found at i:65299 original size:33 final size:32
Alignment explanation
Indices: 65262--65328 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
65252 AGTTCATATG
*
65262 TAAACTAT-AGTTCATATATATAGTATATAAATA
1 TAAACTATGA-TTCATATAAATAGTATA-AAATA
*
65295 TAAACTATGATTTATATAAATAGTATAAAATA
1 TAAACTATGATTCATATAAATAGTATAAAATA
65327 TA
1 TA
65329 GTATATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 7 0.23
33 23 0.74
34 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (32 bp):
TAAACTATGATTCATATAAATAGTATAAAATA
Found at i:65343 original size:20 final size:20
Alignment explanation
Indices: 65279--65348 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 20
65269 TAGTTCATAT
65279 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
* *
65299 CTATGATTTATATAAATAGTATAAA
1 ATAT-A-GTATAT-AA-A-TATAAA
65324 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
65344 TTATA
1 ATATA
65349 ATATGTAGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 7 0.17
23 7 0.17
24 2 0.05
25 9 0.22
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:65448 original size:17 final size:17
Alignment explanation
Indices: 65413--65463 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
65403 TATAAACTAT
65413 ATAATTTATACAATATAC
1 ATAATTTATA-AATATAC
* *
65431 ATTATTTATAAGTATAC
1 ATAATTTATAAATATAC
*
65448 ATAATATATAAATATA
1 ATAATTTATAAATATA
65464 AATTGTATAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 19 0.68
18 9 0.32
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (17 bp):
ATAATTTATAAATATAC
Found at i:65581 original size:27 final size:28
Alignment explanation
Indices: 65536--65596 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
65526 ATGTATAAAC
* **
65536 TATATAGTATTATAGTTTATACATGGTA
1 TATATAGTATTATACTTTATACATAATA
65564 TATATAGT-TTATACTTTATACATAATA
1 TATATAGTATTATACTTTATACATAATA
65591 TATATA
1 TATATA
65597 TATATAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (28 bp):
TATATAGTATTATACTTTATACATAATA
Found at i:65596 original size:20 final size:20
Alignment explanation
Indices: 65573--65661 Score: 73
Period size: 20 Copynumber: 4.6 Consensus size: 20
65563 ATATATAGTT
*
65573 TATACTTTATACATAATATA
1 TATACTTTATATATAATATA
65593 TATA---TATATA-AACTATA
1 TATACTTTATATATAA-TATA
* *
65610 TAGT-TTTTATATATAATACA
1 TA-TACTTTATATATAATATA
65630 TATACTTTATATATAA-ACTA
1 TATACTTTATATATAATA-TA
*
65650 TATAGTTTATAT
1 TATACTTTATAT
65662 TCTATATATA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
16 2 0.04
17 11 0.20
18 1 0.02
19 2 0.04
20 38 0.68
21 2 0.04
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (20 bp):
TATACTTTATATATAATATA
Found at i:65623 original size:22 final size:22
Alignment explanation
Indices: 65595--65657 Score: 87
Period size: 20 Copynumber: 3.0 Consensus size: 22
65585 ATAATATATA
65595 TATATATAAACTATATAGTTTT
1 TATATATAAACTATATAGTTTT
*
65617 TATATATAATAC-ATATA--CTT
1 TATATATAA-ACTATATAGTTTT
65637 TATATATAAACTATATAGTTT
1 TATATATAAACTATATAGTTT
65658 ATATTCTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
19 2 0.06
20 16 0.46
22 15 0.43
23 2 0.06
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (22 bp):
TATATATAAACTATATAGTTTT
Found at i:65641 original size:42 final size:42
Alignment explanation
Indices: 65564--65669 Score: 135
Period size: 42 Copynumber: 2.5 Consensus size: 42
65554 ATACATGGTA
*
65564 TATATAGTTTATACTTTATACATAATATATATATATATAAAC
1 TATATAGTTTATACTATATACATAATATATATATATATAAAC
* *
65606 TATATAGTTTTTA-TATATA-ATACATATACTTTATATATAAAC
1 TATATAGTTTATACTATATACATA-ATATA-TATATATATAAAC
65648 TATATAGTTTATATTCTATATA
1 TATATAGTTTATA--CTATATA
65670 TAGTTGTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 3 0.05
41 10 0.18
42 36 0.65
45 6 0.11
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (42 bp):
TATATAGTTTATACTATATACATAATATATATATATATAAAC
Found at i:66099 original size:216 final size:214
Alignment explanation
Indices: 65695--66299 Score: 1006
Period size: 216 Copynumber: 2.8 Consensus size: 214
65685 TTTTCTCTCA
* * * *
65695 ACTTACTACTTATTTTTATTTATTAATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACAT
1 ACTTATTACTTATTTCTATTT-TTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
*
65760 TTTTGTATTAATTTCAATCTCAAAATTTAAAATTATTTCGATTTGATCCCT--T---T-TGTGTT
65 TTTTGTATTAATTTCAA-CTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
*
65819 GTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
129 GTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
65884 TTGCATATGAAATTGACCCAT
194 TTGCATATGAAATTGACCCAT
65905 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
1 ACTTATTACTTATTTCTATTTTT-AATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
*
65970 TTTTATATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
65 TTTTGTATTAATTTCAAC-TCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
* *
66035 ATTTAATTTATTTAAATTTTTATTTGTAATTTCATAGTTGTTCAATTTAGTCCTCCAAATTTTAT
129 GTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
*
66100 TTGCATATGAAATTGATCCAT
194 TTGCATATGAAATTGACCCAT
* *
66121 ACTTATTACTTAATTCTATTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTATTT
1 ACTTATTACTTATTTCTA-TTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
66186 TTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
65 TTTTGTATTAATTTCAA-CTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
66251 GTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
129 GTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
66300 ATTCTTAAAT
Statistics
Matches: 370, Mismatches: 15, Indels: 14
0.93 0.04 0.04
Matches are distributed among these distances:
209 3 0.01
210 105 0.28
212 1 0.00
215 1 0.00
216 254 0.69
217 6 0.02
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (214 bp):
ACTTATTACTTATTTCTATTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTT
TTTGTATTAATTTCAACTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGT
TTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTT
GCATATGAAATTGACCCAT
Found at i:67973 original size:23 final size:23
Alignment explanation
Indices: 67934--68019 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
67924 GAAACTGACG
67934 CATAGAATT-TGCACCGAAGTG-CCA
1 CATAGAATTGT-C-CCGAAG-GACCA
* *
67958 CATA-AATTTGTCCCGACGGACCG
1 CATAGAA-TTGTCCCGAAGGACCA
*
67981 CGTAGAATTGTCCCGAAGGACCA
1 CATAGAATTGTCCCGAAGGACCA
68004 CATAGAATTGTCCCGA
1 CATAGAATTGTCCCGA
68020 GGGTCCGCGT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
22 1 0.02
23 41 0.79
24 9 0.17
25 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (23 bp):
CATAGAATTGTCCCGAAGGACCA
Found at i:68178 original size:57 final size:57
Alignment explanation
Indices: 68108--68216 Score: 146
Period size: 57 Copynumber: 1.9 Consensus size: 57
68098 ATATAAGTGC
* ** * *
68108 TCACATAACATTATTGAAATTGTCATTTATTCACGTAGAACATATACGCATAATATT
1 TCACATAACATTATTCAAATTAACATTTATTCACATAAAACATATACGCATAATATT
* * *
68165 TCACATAGCATTATTCAAATTAACGTTTATTCACATAAAAGATATACGCATA
1 TCACATAACATTATTCAAATTAACATTTATTCACATAAAACATATACGCATA
68217 GCAATGAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 44 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (57 bp):
TCACATAACATTATTCAAATTAACATTTATTCACATAAAACATATACGCATAATATT
Found at i:69608 original size:110 final size:110
Alignment explanation
Indices: 69413--69626 Score: 347
Period size: 110 Copynumber: 1.9 Consensus size: 110
69403 TTAATCCTAA
* * * * * *
69413 ACAAAAATTTCCAACTCAATCCTTGAATATTTTAGTTTATCAAAATCAAACCACTAAAATTTGAA
1 ACAAAAATTTCCAAATCAATCCTTGAACATTTCAATTAATCAAAATCAAACCACTAAAATTTAAA
* *
69478 TTCTTATACTTTAGTCACTGACCTGATGTTTGGGATATTACAATT
66 TTCTTACACTTTAGTAACTGACCTGATGTTTGGGATATTACAATT
*
69523 ACAAAAATTTCCAAATCAATCCTTGAACATTTCAATTAATCAAAATCAAACCACTAAATTTTAAA
1 ACAAAAATTTCCAAATCAATCCTTGAACATTTCAATTAATCAAAATCAAACCACTAAAATTTAAA
69588 TTCTTACACTTTAGTAACTGACCTGATGTTTGGGATATT
66 TTCTTACACTTTAGTAACTGACCTGATGTTTGGGATATT
69627 GCACACCAGC
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
110 95 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (110 bp):
ACAAAAATTTCCAAATCAATCCTTGAACATTTCAATTAATCAAAATCAAACCACTAAAATTTAAA
TTCTTACACTTTAGTAACTGACCTGATGTTTGGGATATTACAATT
Found at i:75544 original size:15 final size:14
Alignment explanation
Indices: 75512--75545 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
75502 AAAAGCTCCC
75512 ATTTAGAAAAATAT
1 ATTTAGAAAAATAT
*
75526 ATTTTGAAAAATAT
1 ATTTAGAAAAATAT
75540 AATTTA
1 -ATTTA
75546 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (14 bp):
ATTTAGAAAAATAT
Found at i:77005 original size:21 final size:21
Alignment explanation
Indices: 76966--77006 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
76956 ATTATGAATA
* *
76966 AAAAAGATATAAAATTAAATG
1 AAAAAGAAATAAAACTAAATG
*
76987 AAAAAGAAATAATACTAAAT
1 AAAAAGAAATAAAACTAAAT
77007 TATCAAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.22
Consensus pattern (21 bp):
AAAAAGAAATAAAACTAAATG
Found at i:77574 original size:2 final size:2
Alignment explanation
Indices: 77567--77600 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
77557 TTATCTAACC
77567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
77601 TCTTTCATAT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78042 original size:148 final size:154
Alignment explanation
Indices: 77850--78213 Score: 363
Period size: 157 Copynumber: 2.4 Consensus size: 154
77840 GTTACATAGG
* * * * *
77850 TATTCTAATGTGGTATATGAGCATGTGGTTC-AATTTGGTAAAAAAAAAGAA-TTAAAATAAATC
1 TATTCTACTATGGTTTAGGAGCATGTGATTCAAATTTGGT-AAAAAAAAGAACTTAAAATAAATC
* * *
77913 ACAAATTGAAGGAATAAGGAGATTATGA-AAA-AAAAGAACTAAATTG-AAAAT-AAA-A-TGTT
65 ACAAATTGAA-AAAT-AGAAAATTATGATAAATAAAAGAACTAAA-TGAAAAATAAAATATTGTT
77972 ATCAAAAGAGG-ATTGAAAGTACACA-A
127 ATCAAAAGAGGAATTGAAAGTACACATA
* * ** * **
77998 TATTCTACTATGGTTTAGGAGCATGTGACTCAAATTTGATAAAAAAGCGAACTAAAAATAAATGG
1 TATTCTACTATGGTTTAGGAGCATGTGATTCAAATTTGGTAAAAAAAAGAACTTAAAATAAATCA
** ** *
78063 TGAATTGAAAAATAGAAAATTATGATAAATTGAAGGACTAAATGAAAAATAAAAAAATATTGTTA
66 CAAATTGAAAAATAGAAAATTATGATAAATAAAAGAACTAAATGAAAAAT---AAAATATTGTTA
78128 TCAAAAGAGGAATTGAAAGTACACATA
128 TCAAAAGAGGAATTGAAAGTACACATA
* * * *
78155 TATTATACTATGGTTTAGGAGCTTAT-AGTTCAAATTTGGTAAAAAAATGAACTTAAAAT
1 TATTCTACTATGGTTTAGGAGCATGTGA-TTCAAATTTGGTAAAAAAAAGAACTTAAAAT
78214 GAAAAAGGAA
Statistics
Matches: 174, Mismatches: 28, Indels: 19
0.79 0.13 0.09
Matches are distributed among these distances:
147 10 0.06
148 42 0.24
149 38 0.22
153 3 0.02
154 1 0.01
155 15 0.09
156 15 0.09
157 50 0.29
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.28
Consensus pattern (154 bp):
TATTCTACTATGGTTTAGGAGCATGTGATTCAAATTTGGTAAAAAAAAGAACTTAAAATAAATCA
CAAATTGAAAAATAGAAAATTATGATAAATAAAAGAACTAAATGAAAAATAAAATATTGTTATCA
AAAGAGGAATTGAAAGTACACATA
Found at i:79500 original size:20 final size:20
Alignment explanation
Indices: 79475--79524 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
79465 TTTTGATCCC
79475 GTATCGATACC-ACCCAATG-A
1 GTATCGATACCAACCC--TGTA
79495 GTATCGATACCAACCCTGTA
1 GTATCGATACCAACCCTGTA
79515 GTATCGATAC
1 GTATCGATAC
79525 TCCTTGTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.07
20 22 0.79
21 4 0.14
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (20 bp):
GTATCGATACCAACCCTGTA
Found at i:80596 original size:5 final size:5
Alignment explanation
Indices: 80588--81199 Score: 279
Period size: 5 Copynumber: 120.8 Consensus size: 5
80578 ACATGACATT
* * * * * * * * *
80588 ATAAC ATAAC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC CTAGC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * * * * * * * * * *
80638 ATAGC ATAGC CTAGC CTAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * * * * * * *
80688 ATAGC ATAGC ATATC ATAGC ATAGC ATAGC ATAAC ATAGC ATAGC ATAGC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * * * * * * *
80738 ATAGC ATAGC ATAGC ATAGC ATAAC ATAGC ATAGC ATAGC ATAGC ATAGC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * * * * *
80788 ATAGC ATAGC ATAGC ATAAC ATAAC ATACC ATAAC ATGAC ATGAC ATGAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * * * * * * * *
80838 ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * * * * * * * *
80888 ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * * * * * * * *
80938 ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * * * * * * * *
80988 ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * * * * * * *
81038 ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
81088 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAAC ATAAC ATAAAC ATAAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC AT-AAC ATAAC AT-AAC AT-AAC
* *
81141 ATAAA ATAAAC ATAAA ATAAAC ATAAC ATAAAC ATAAC ATAAAC ATAAC
1 ATAAC AT-AAC ATAAC AT-AAC ATAAC AT-AAC ATAAC AT-AAC ATAAC
81190 ATAAAC ATAA
1 AT-AAC ATAA
81200 TATCATATCA
Statistics
Matches: 580, Mismatches: 20, Indels: 14
0.94 0.03 0.02
Matches are distributed among these distances:
5 541 0.93
6 39 0.07
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (5 bp):
ATAAC
Found at i:80615 original size:15 final size:15
Alignment explanation
Indices: 80592--80820 Score: 368
Period size: 15 Copynumber: 15.3 Consensus size: 15
80582 GACATTATAA
*
80592 CATAACATAGCATAG
1 CATAGCATAGCATAG
80607 CATAGCATAGCATAG
1 CATAGCATAGCATAG
*
80622 CATAGCATAGCCTAG
1 CATAGCATAGCATAG
*
80637 CATAGCATAGCCTAG
1 CATAGCATAGCATAG
*
80652 CCTAGCATAGCATAG
1 CATAGCATAGCATAG
80667 CATAGCATAGCATAG
1 CATAGCATAGCATAG
80682 CATAGCATAGCATAG
1 CATAGCATAGCATAG
*
80697 CATATCATAGCATAG
1 CATAGCATAGCATAG
*
80712 CATAGCATAACATAG
1 CATAGCATAGCATAG
80727 CATAGCATAGCATAG
1 CATAGCATAGCATAG
80742 CATAGCATAGCATAG
1 CATAGCATAGCATAG
*
80757 CATAACATAGCATAG
1 CATAGCATAGCATAG
80772 CATAGCATAGCATAG
1 CATAGCATAGCATAG
80787 CATAGCATAGCATAG
1 CATAGCATAGCATAG
* * *
80802 CATAACATAACATAC
1 CATAGCATAGCATAG
80817 CATA
1 CATA
80821 ACATGACATG
Statistics
Matches: 200, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 200 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.21
Consensus pattern (15 bp):
CATAGCATAGCATAG
Found at i:80821 original size:15 final size:15
Alignment explanation
Indices: 80797--81191 Score: 322
Period size: 15 Copynumber: 25.9 Consensus size: 15
80787 CATAGCATAG
* *
80797 CATAGCATAACATAA
1 CATAACATAACATGA
*
80812 CATACCATAACATGA
1 CATAACATAACATGA
* *
80827 CATGACATGACATGA
1 CATAACATAACATGA
* *
80842 CATGACATGACATGA
1 CATAACATAACATGA
* *
80857 CATGACATGACATGA
1 CATAACATAACATGA
* *
80872 CATGACATGACATGA
1 CATAACATAACATGA
* *
80887 CATGACATGACATGA
1 CATAACATAACATGA
* *
80902 CATGACATGACATGA
1 CATAACATAACATGA
* *
80917 CATGACATGACATGA
1 CATAACATAACATGA
* *
80932 CATGACATGACATGA
1 CATAACATAACATGA
* *
80947 CATGACATGACATGA
1 CATAACATAACATGA
* *
80962 CATGACATGACATGA
1 CATAACATAACATGA
* *
80977 CATGACATGACATGA
1 CATAACATAACATGA
* *
80992 CATGACATGACATGA
1 CATAACATAACATGA
* *
81007 CATGACATGACATGA
1 CATAACATAACATGA
* *
81022 CATGACATGACATGA
1 CATAACATAACATGA
* *
81037 CATGACATGACATGA
1 CATAACATAACATGA
* *
81052 CATGACATGACATGA
1 CATAACATAACATGA
* *
81067 CATGACATGACATGA
1 CATAACATAACATGA
*
81082 CATAACATAACATAA
1 CATAACATAACATGA
*
81097 CATAACATAACATAA
1 CATAACATAACATGA
*
81112 CATAACATAAACATAA
1 CATAACAT-AACATGA
*
81128 CATAAACATAAACATAA
1 CAT-AACAT-AACATGA
* * *
81145 AATAAACATAAAATAAA
1 CAT-AACATAACAT-GA
*
81162 CATAACATAAACATAA
1 CATAACAT-AACATGA
81178 CATAAACATAACAT
1 CAT-AACATAACAT
81192 AAACATAATA
Statistics
Matches: 363, Mismatches: 12, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
15 300 0.83
16 29 0.08
17 34 0.09
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.20
Consensus pattern (15 bp):
CATAACATAACATGA
Found at i:80824 original size:10 final size:10
Alignment explanation
Indices: 80592--80820 Score: 368
Period size: 10 Copynumber: 22.9 Consensus size: 10
80582 GACATTATAA
*
80592 CATAACATAG
1 CATAGCATAG
80602 CATAGCATAG
1 CATAGCATAG
80612 CATAGCATAG
1 CATAGCATAG
80622 CATAGCATAG
1 CATAGCATAG
*
80632 CCTAGCATAG
1 CATAGCATAG
*
80642 CATAGCCTAG
1 CATAGCATAG
*
80652 CCTAGCATAG
1 CATAGCATAG
80662 CATAGCATAG
1 CATAGCATAG
80672 CATAGCATAG
1 CATAGCATAG
80682 CATAGCATAG
1 CATAGCATAG
*
80692 CATAGCATAT
1 CATAGCATAG
80702 CATAGCATAG
1 CATAGCATAG
*
80712 CATAGCATAA
1 CATAGCATAG
80722 CATAGCATAG
1 CATAGCATAG
80732 CATAGCATAG
1 CATAGCATAG
80742 CATAGCATAG
1 CATAGCATAG
*
80752 CATAGCATAA
1 CATAGCATAG
80762 CATAGCATAG
1 CATAGCATAG
80772 CATAGCATAG
1 CATAGCATAG
80782 CATAGCATAG
1 CATAGCATAG
80792 CATAGCATAG
1 CATAGCATAG
* *
80802 CATAACATAA
1 CATAGCATAG
*
80812 CATACCATA
1 CATAGCATA
80821 ACATGACATG
Statistics
Matches: 203, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 203 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.21
Consensus pattern (10 bp):
CATAGCATAG
Found at i:80834 original size:10 final size:10
Alignment explanation
Indices: 80821--81119 Score: 535
Period size: 10 Copynumber: 29.9 Consensus size: 10
80811 ACATACCATA
80821 ACATGACATG
1 ACATGACATG
80831 ACATGACATG
1 ACATGACATG
80841 ACATGACATG
1 ACATGACATG
80851 ACATGACATG
1 ACATGACATG
80861 ACATGACATG
1 ACATGACATG
80871 ACATGACATG
1 ACATGACATG
80881 ACATGACATG
1 ACATGACATG
80891 ACATGACATG
1 ACATGACATG
80901 ACATGACATG
1 ACATGACATG
80911 ACATGACATG
1 ACATGACATG
80921 ACATGACATG
1 ACATGACATG
80931 ACATGACATG
1 ACATGACATG
80941 ACATGACATG
1 ACATGACATG
80951 ACATGACATG
1 ACATGACATG
80961 ACATGACATG
1 ACATGACATG
80971 ACATGACATG
1 ACATGACATG
80981 ACATGACATG
1 ACATGACATG
80991 ACATGACATG
1 ACATGACATG
81001 ACATGACATG
1 ACATGACATG
81011 ACATGACATG
1 ACATGACATG
81021 ACATGACATG
1 ACATGACATG
81031 ACATGACATG
1 ACATGACATG
81041 ACATGACATG
1 ACATGACATG
81051 ACATGACATG
1 ACATGACATG
81061 ACATGACATG
1 ACATGACATG
81071 ACATGACATG
1 ACATGACATG
* *
81081 ACATAACATA
1 ACATGACATG
* *
81091 ACATAACATA
1 ACATGACATG
* *
81101 ACATAACATA
1 ACATGACATG
*
81111 ACATAACAT
1 ACATGACAT
81120 AAACATAACA
Statistics
Matches: 287, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
10 287 1.00
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (10 bp):
ACATGACATG
Found at i:81126 original size:11 final size:11
Alignment explanation
Indices: 81076--81199 Score: 168
Period size: 11 Copynumber: 11.5 Consensus size: 11
81066 ACATGACATG
*
81076 ACATGACAT-A
1 ACATAACATAA
81086 ACATAACAT-A
1 ACATAACATAA
81096 ACATAACAT-A
1 ACATAACATAA
81106 ACATAACAT-A
1 ACATAACATAA
81116 ACATAAACAT-A
1 ACAT-AACATAA
81127 ACATAAACATAA
1 ACAT-AACATAA
*
81139 ACATAAAATAA
1 ACATAACATAA
*
81150 ACATAAAATAA
1 ACATAACATAA
81161 ACATAACATAA
1 ACATAACATAA
81172 ACATAACATAA
1 ACATAACATAA
81183 ACATAACATAA
1 ACATAACATAA
81194 ACATAA
1 ACATAA
81200 TATCATATCA
Statistics
Matches: 109, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
10 33 0.30
11 71 0.65
12 5 0.05
ACGTcount: A:0.64, C:0.17, G:0.01, T:0.19
Consensus pattern (11 bp):
ACATAACATAA
Found at i:81207 original size:5 final size:5
Alignment explanation
Indices: 81199--81276 Score: 147
Period size: 5 Copynumber: 15.6 Consensus size: 5
81189 CATAAACATA
*
81199 ATATC ATATC ATATC ATATC ATATA ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
81249 ATATC ATATC ATATC ATATC ATATC ATA
1 ATATC ATATC ATATC ATATC ATATC ATA
81277 CAATATAGTA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 71 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATC
Found at i:81331 original size:5 final size:5
Alignment explanation
Indices: 81281--81329 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
81271 ATCATACAAT
* * *
81281 ATAGT ATAGT ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGT ATAG
1 ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAG
81330 TACAGAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (5 bp):
ATAGC
Found at i:83273 original size:3 final size:3
Alignment explanation
Indices: 83265--83290 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
83255 ACTTCCTCAA
83265 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
83291 AACTGTCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:86350 original size:72 final size:73
Alignment explanation
Indices: 86229--86375 Score: 278
Period size: 72 Copynumber: 2.0 Consensus size: 73
86219 AGCGGCGTTA
*
86229 ATGAAAACTTTTATTTATTATATTGGATTTGATGTTGCTTGTTATGGATATATAGATTGATGTTA
1 ATGAAAACTTTTATTTATTATATTGGATTTGATGTTGCTTGTTATGGATATAGAGATTGATGTTA
86294 TTGATGTC
66 TTGATGTC
86302 ATGAAAACTTTTATTTATTATATT-GATTTGATGTTGCTTGTTATGGATATAGAGATTGATGTTA
1 ATGAAAACTTTTATTTATTATATTGGATTTGATGTTGCTTGTTATGGATATAGAGATTGATGTTA
86366 TTGATGTC
66 TTGATGTC
86374 AT
1 AT
86376 AAGAGGTGGA
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
72 49 0.67
73 24 0.33
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.49
Consensus pattern (73 bp):
ATGAAAACTTTTATTTATTATATTGGATTTGATGTTGCTTGTTATGGATATAGAGATTGATGTTA
TTGATGTC
Found at i:86524 original size:44 final size:43
Alignment explanation
Indices: 86476--86605 Score: 134
Period size: 44 Copynumber: 3.0 Consensus size: 43
86466 TTTCTAACAA
* *
86476 AAAAATGCCGCTATATACCATACATTTTGCGGCGTTTGTATTCT
1 AAAAATGCCGCTATATACCATAC-TTTAGCGGCGTTTGTATCCT
* * * ** *
86520 AAAAATGCCGCTATAAACCAGACCTTCAGCGATGTTTTTATCCT
1 AAAAATGCCGCTATATACCATA-CTTTAGCGGCGTTTGTATCCT
* * *
86564 CAAAACGCCGTTATATACCATATCTTTAGCGGCGTTTGTATC
1 AAAAATGCCGCTATATACCATA-CTTTAGCGGCGTTTGTATC
86606 AAAAAAACTC
Statistics
Matches: 67, Mismatches: 18, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
44 66 0.99
45 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (43 bp):
AAAAATGCCGCTATATACCATACTTTAGCGGCGTTTGTATCCT
Found at i:86936 original size:43 final size:43
Alignment explanation
Indices: 86804--86925 Score: 172
Period size: 43 Copynumber: 2.8 Consensus size: 43
86794 TTTTTGGGGG
86804 AAACACCGCTAAATCTTAACACCTATTGCGACGTTTATAAGAC
1 AAACACCGCTAAATCTTAACACCTATTGCGACGTTTATAAGAC
* * * *
86847 AAACACCACTAAACCTTAACACCTATTGTGACGTTTATAATAC
1 AAACACCGCTAAATCTTAACACCTATTGCGACGTTTATAAGAC
* * * *
86890 AAACACCGCTAAATATCAACACCTATTACGGCGTTT
1 AAACACCGCTAAATCTTAACACCTATTGCGACGTTT
86926 GTTGAACAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.26
Consensus pattern (43 bp):
AAACACCGCTAAATCTTAACACCTATTGCGACGTTTATAAGAC
Found at i:88047 original size:16 final size:15
Alignment explanation
Indices: 88015--88056 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
88005 TAATAGACTT
88015 GTCTGTTTTCT-ACA
1 GTCTGTTTTCTAACA
88029 GTCTGTTTTCTACACA
1 GTCTGTTTTCTA-ACA
*
88045 GTCTATTTTCTA
1 GTCTGTTTTCTA
88057 TATGGTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.44
16 14 0.56
ACGTcount: A:0.17, C:0.21, G:0.12, T:0.50
Consensus pattern (15 bp):
GTCTGTTTTCTAACA
Found at i:98695 original size:42 final size:41
Alignment explanation
Indices: 98624--98713 Score: 94
Period size: 42 Copynumber: 2.2 Consensus size: 41
98614 AGCTCAAATG
*
98624 CGCAATAGAGTGTAATGTAGCGACATTTATACCAT-AAACGC
1 CGCAATAAAGTGTAATGTAGCGACATTTATA-CATAAAACGC
* * *
98665 CGCAATAAAGTGGTAAAT-TAGCGGCGTTTATATATAAAACGC
1 CGCAATAAAGT-GT-AATGTAGCGACATTTATACATAAAACGC
*
98707 TGCAATA
1 CGCAATA
98714 TGGTAGTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
41 12 0.29
42 26 0.63
43 3 0.07
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (41 bp):
CGCAATAAAGTGTAATGTAGCGACATTTATACATAAAACGC
Found at i:100546 original size:44 final size:44
Alignment explanation
Indices: 100479--100634 Score: 145
Period size: 44 Copynumber: 3.6 Consensus size: 44
100469 TATACCAATA
*
100479 TTTAGCGG-GTTTGTATCCAAAAAATGCCGCTATATACAAGACC
1 TTTAGCGGCGTTTGTATCCAAAAAACGCCGCTATATACAAGACC
* ** * *
100522 TTTAGCGGCGTTTGTATCCTAAAAACGTTGCTATATACTATACC
1 TTTAGCGGCGTTTGTATCCAAAAAACGCCGCTATATACAAGACC
* * * * * * * **
100566 TATCGCGACATTTGTATCTTAAAAAACGCCGCTAAATACCAGAAT
1 TTTAGCGGCGTTTGTATC-CAAAAAACGCCGCTATATACAAGACC
*
100611 TTTAGCGGCGTTTGCAT-CAAAAAA
1 TTTAGCGGCGTTTGTATCCAAAAAA
100635 TGCCACTAAA
Statistics
Matches: 86, Mismatches: 25, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
43 14 0.16
44 43 0.50
45 29 0.34
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (44 bp):
TTTAGCGGCGTTTGTATCCAAAAAACGCCGCTATATACAAGACC
Done.