Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007456.1 Hibiscus syriacus cultivar Beakdansim tig00020433_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: 91406
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3428 original size:136 final size:138
Alignment explanation
Indices: 3098--3433 Score: 424
Period size: 137 Copynumber: 2.5 Consensus size: 138
3088 TATTTTTATT
* * *
3098 TTTAT-AAAT-AAGATATTTATTTACTTAGAAATATCAGAAAA-GGACTTCTAGGTT-TTTTAAG
1 TTTATAAAATAAAGATA-TTATTTATTTAAAAATATCAGAAAATGGACTTCTA-GTTGCTTTAAG
* *
3159 ACAGCCTATTTCTTTAATATTAAAAAATAAATAAATATTAATAAAACATTTCTCTAAAAATAAAT
64 ACAGCCTATTTCTTTAATATTAAAAAATAAAAAAATATTAATAAAACATTTATCTAAAAATAAAT
3224 TAATATATAA
129 TAATATATAA
* * *
3234 TTTATAAAA-ATAGGATATTATTTATTTAAGAATATCAGAAAAT-GACTTCTAGGTGCTTTAAGA
1 TTTATAAAATA-AAGATATTATTTATTTAAAAATATCAGAAAATGGACTTCTAGTTGCTTTAAGA
* *
3297 CATCC-ATTT-TCTTAATATTAAAAAATACAAAAAATATTAATAAAACATTTAT-TAAAAATAGA
65 CAGCCTATTTCT-TTAATATTAAAAAATA-AAAAAATATTAATAAAACATTTATCTAAAAATAAA
3359 TT-A-ATATAA
128 TTAATATATAA
* * *
3368 TTTATAAAATAAAAATATGTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGCTTTAAGA
1 TTTATAAAATAAAGATAT-TATTTATTTAAAAATATCAGAAAATGGACTTCTAGTTGCTTTAAGA
3433 C
65 C
3434 TGCTCTTTCA
Statistics
Matches: 174, Mismatches: 16, Indels: 20
0.83 0.08 0.10
Matches are distributed among these distances:
134 20 0.11
135 27 0.16
136 56 0.32
137 66 0.38
138 5 0.03
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (138 bp):
TTTATAAAATAAAGATATTATTTATTTAAAAATATCAGAAAATGGACTTCTAGTTGCTTTAAGAC
AGCCTATTTCTTTAATATTAAAAAATAAAAAAATATTAATAAAACATTTATCTAAAAATAAATTA
ATATATAA
Found at i:5056 original size:3 final size:3
Alignment explanation
Indices: 5048--5094 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
5038 AATATTTATT
*
5048 TAA TAA TAA TAA TAA TAA TAA TAA -ATT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
5093 TA
1 TA
5095 GAATGAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 1 0.03
3 38 0.95
4 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5282 original size:45 final size:45
Alignment explanation
Indices: 5215--5361 Score: 231
Period size: 45 Copynumber: 3.3 Consensus size: 45
5205 GATGGAAATG
5215 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTT
* *
5260 TTAAAAACATCATGCACTGAAGGGCTTACAGATGACGCAAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTT
* * * *
5305 TTGAAAACATCATGCAGTGAAGGGCTTGCAGATGATCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTT
*
5350 TTGAAAATATCA
1 TTGAAAACATCA
5362 AAAAGCTCCC
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 93 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (45 bp):
TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTT
Found at i:5441 original size:45 final size:44
Alignment explanation
Indices: 5385--5528 Score: 198
Period size: 45 Copynumber: 3.2 Consensus size: 44
5375 GGCTTTTATA
* * **
5385 AAAACATCATGCATTGCAGGTCTTATGGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGG-CTTACAGATGACCCGAAGGTTTTG
*
5430 AAAGCATCATGCACTGAATGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAA-GGCTTACAGATGACCCGAAGGTTTTG
*
5475 AAAACATCATGCACTGAAGGGCTTACAGATGACTCGAAGGTTTTG
1 AAAACATCATGCACTGAA-GGCTTACAGATGACCCGAAGGTTTTG
*
5520 AAAATATCA
1 AAAACATCA
5529 AAAAAAACTC
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 87 0.98
46 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (44 bp):
AAAACATCATGCACTGAAGGCTTACAGATGACCCGAAGGTTTTG
Found at i:5478 original size:122 final size:122
Alignment explanation
Indices: 5261--5483 Score: 329
Period size: 122 Copynumber: 1.8 Consensus size: 122
5251 CCAAAGGTTT
* *
5261 TAAAAACATCATGCACTGAAGGGCTTACAGATGACGCAAAGGTTTTGAAAACATCATGCAGTGAA
1 TAAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAA
* * *
5326 GGGCTTGCAGATGATCCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTA
66 GGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTA
* * * ** * *
5383 TAAAAACATCATGCATTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGAA
1 TAAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAA
*
5448 TGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
66 GGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
5484 TGCACTGAAG
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
122 88 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (122 bp):
TAAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAA
GGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTA
Found at i:5640 original size:31 final size:31
Alignment explanation
Indices: 5581--5640 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
5571 AGGTCTTATG
* *
5581 GATGACCCGAAGGTTTTGAAAGCCTCATGCA
1 GATGACCCGAAGGTTTTGAAAACATCATGCA
5612 GATGACCCGAAGGTTTTGAAAACATCATG
1 GATGACCCGAAGGTTTTGAAAACATCATG
5641 TACTGAAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (31 bp):
GATGACCCGAAGGTTTTGAAAACATCATGCA
Found at i:5741 original size:77 final size:77
Alignment explanation
Indices: 5470--5760 Score: 304
Period size: 79 Copynumber: 3.8 Consensus size: 77
5460 GACCCGAAGG
*
5470 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACTCGAAGGTTTTGAAAATATCAAAAAAA
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATC--AAAAA
*
5535 ACTCCTGAAGGCTT
64 ACTCCCGAAGGCTT
* * * * ** * *
5549 TTTAGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCCTCATGCAGA
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAA--AT-AT-CAAA
**
5614 TGA--CCCGAAGG---
62 AAACTCCCGAAGGCTT
* *
5625 TTTTGAAAACATCATGTACTGAAGGGATTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAAC
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAAC
5690 TCCCGAAGGCTT
66 TCCCGAAGGCTT
* * * * ** *
5702 TTTTGAAAACATCCTGCACTGCATGTCTTATGGATGACCCGAAGGTTTTGAAAAGATCA
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATCA
5761 TGCACTGAAG
Statistics
Matches: 170, Mismatches: 33, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
72 4 0.02
73 2 0.01
74 9 0.05
76 45 0.26
77 50 0.29
79 53 0.31
81 4 0.02
82 2 0.01
83 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (77 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAAC
TCCCGAAGGCTT
Found at i:5765 original size:45 final size:45
Alignment explanation
Indices: 5702--6095 Score: 621
Period size: 45 Copynumber: 8.8 Consensus size: 45
5692 CCGAAGGCTT
* * * * **
5702 TTTTGAAAACATCCTGCACTGCATGTCTTATGGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
5747 TTTTGAAAAGATCATGCACTGAAGGGCTTACAGATGACCAGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
5792 TTTTGAAAACATCATGCACTGAAGGGCTAACAGATGACCCAAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
5837 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
5882 TTTTGAAAATATCATGCACTGAAGGGCTTACAGATGA-CCGTAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
5926 TTTCGAAAA-ATCATGCACTAAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
5970 TTTTGAAAACATCATGCACTGAAGGGCTTATAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
6015 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
6060 TTTTGAAAACATCATGCACTGAAGGTCTTACAGATG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
6096 TGGGAAATAA
Statistics
Matches: 321, Mismatches: 26, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
43 26 0.08
44 28 0.09
45 267 0.83
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
Found at i:6007 original size:178 final size:180
Alignment explanation
Indices: 5702--6095 Score: 639
Period size: 178 Copynumber: 2.2 Consensus size: 180
5692 CCGAAGGCTT
* * * ** *
5702 TTTTGAAAACATCCTGCACTGCATGTCTTATGGATGACCCGAAGGTTTTGAAAAGATCATGCACT
1 TTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTCGAAAAGATCATGCACT
*
5767 GAAGGGCTTACAGATGACCAGAAGGTTTTGAAAACATCATGCACTGAAGGGCTAACAGATGACCC
66 AAAGGGCTTACAGATGACCAGAAGGTTTTGAAAACATCATGCACTGAAGGGCTAACAGATGACCC
5832 AAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
131 AAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
* * *
5882 TTTTGAAAATATCATGCACTGAAGGGCTTACAGATGA-CCGTAGGTTTCGAAAA-ATCATGCACT
1 TTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTCGAAAAGATCATGCACT
* * *
5945 AAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTATAGATGACCC
66 AAAGGGCTTACAGATGACCAGAAGGTTTTGAAAACATCATGCACTGAAGGGCTAACAGATGACCC
* *
6010 GAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
131 AAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
6060 TTTTGAAAACATCATGCACTGAAGGTCTTACAGATG
1 TTTTGAAAACATCATGCACTGAAGGTCTTACAGATG
6096 TGGGAAATAA
Statistics
Matches: 197, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
178 153 0.78
179 14 0.07
180 30 0.15
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (180 bp):
TTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTCGAAAAGATCATGCACT
AAAGGGCTTACAGATGACCAGAAGGTTTTGAAAACATCATGCACTGAAGGGCTAACAGATGACCC
AAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
Found at i:6765 original size:22 final size:23
Alignment explanation
Indices: 6737--6793 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
6727 GGACTTGCTT
*
6737 TCATCTTTGAAAAGA-GAATCTA
1 TCATCTTTGAAAAGATAAATCTA
*
6759 TCATCTTTGAAGAGATAAATCTA
1 TCATCTTTGAAAAGATAAATCTA
*
6782 TTATCTTTGAAA
1 TCATCTTTGAAA
6794 GATGTAGATG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 14 0.47
23 16 0.53
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (23 bp):
TCATCTTTGAAAAGATAAATCTA
Found at i:6787 original size:23 final size:22
Alignment explanation
Indices: 6737--6796 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
6727 GGACTTGCTT
*
6737 TCATCTTTGAAAAGA-GAATCTA
1 TCATCTTTG-AAAGATAAATCTA
6759 TCATCTTTGAAGAGATAAATCTA
1 TCATCTTTGAA-AGATAAATCTA
*
6782 TTATCTTTGAAAGAT
1 TCATCTTTGAAAGAT
6797 GTAGATGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 2 0.06
22 16 0.47
23 16 0.47
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (22 bp):
TCATCTTTGAAAGATAAATCTA
Found at i:10535 original size:32 final size:32
Alignment explanation
Indices: 10499--10560 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
10489 GAAGAAATGA
* * *
10499 TTGTTATGCTCATCTTGTAGAGATACTTCTCG
1 TTGTTATGATCATCTCGTAGAGATAATTCTCG
10531 TTGTTATGATCATCTCGTAGAGATAATTCT
1 TTGTTATGATCATCTCGTAGAGATAATTCT
10561 TGTTTCCAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.44
Consensus pattern (32 bp):
TTGTTATGATCATCTCGTAGAGATAATTCTCG
Found at i:11028 original size:8 final size:8
Alignment explanation
Indices: 11015--11069 Score: 65
Period size: 8 Copynumber: 6.8 Consensus size: 8
11005 CTTAATTCAA
*
11015 TTTTTTAT
1 TTTTTTCT
11023 TTTTTTCCT
1 TTTTTT-CT
*
11032 TTTTTCCT
1 TTTTTTCT
*
11040 TTTTTCCT
1 TTTTTTCT
*
11048 TTTTTTCC
1 TTTTTTCT
11056 TTTTTTCT
1 TTTTTTCT
11064 TTTTTT
1 TTTTTT
11070 TTCTTTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
8 35 0.85
9 6 0.15
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTCT
Found at i:11042 original size:17 final size:17
Alignment explanation
Indices: 11023--11075 Score: 81
Period size: 17 Copynumber: 3.2 Consensus size: 17
11013 AATTTTTTAT
11023 TTTTTTCC-TTTTTTCC
1 TTTTTTCCTTTTTTTCC
11039 TTTTTTCCTTTTTTTCC
1 TTTTTTCCTTTTTTTCC
* *
11056 TTTTTTCTTTTTTTTTC
1 TTTTTTCCTTTTTTTCC
11073 TTT
1 TTT
11076 ATTTTTCCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
16 8 0.24
17 26 0.76
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTCCTTTTTTTCC
Found at i:16289 original size:28 final size:26
Alignment explanation
Indices: 16250--16305 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
16240 ATAAAACATT
*
16250 AATAATATATATATATAAA-TTATGAA
1 AATAATATATATATAAAAAGTT-TGAA
16276 AATAATAAGTATATATAAAAAGTTTGAA
1 AATAAT-A-TATATATAAAAAGTTTGAA
16304 AA
1 AA
16306 GAAAGAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 6 0.23
27 1 0.04
28 17 0.65
29 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (26 bp):
AATAATATATATATAAAAAGTTTGAA
Found at i:16992 original size:137 final size:133
Alignment explanation
Indices: 16824--17134 Score: 405
Period size: 135 Copynumber: 2.3 Consensus size: 133
16814 ATATTTTTAT
*
16824 AAATAAGATATTTATTTACTT-AGAAATATCAGAAAAAGACTTATAGGTACTTTAAGACA-TCCC
1 AAATAAGATATTTATTTATTTAAG-AATATCAGAAAAAGACTTATA-GTACTTTAAGACAGT--C
*
16887 A-TTTCTTTAATATTAAAAAATAAATAAATATTAATAAAACATTTCTCTAAAAATAAATTAATAT
62 ATTTTC-TTAATATTAAAAAATAAATAAATATTAATAAAACATTTAT-TAAAAATAAATT-A-AT
16951 ATAATTTATAA
123 ATAATTTATAA
* * * *
16962 AAATAGGATA-TTATTTATTTAAGAATATCAGAAAATGACTTCTAGTGCTTTAAGACAGTCATTT
1 AAATAAGATATTTATTTATTTAAGAATATCAGAAAAAGACTTATAGTACTTTAAGACAGTCATTT
* *
17026 TCTTAATATTAAAAAATACATAAATATTAATAAAACATTTATTAAAAATAGATTAATATAATTTA
66 TCTTAATATTAAAAAATAAATAAATATTAATAAAACATTTATTAAAAATAAATTAATATAATTTA
17091 TAA
131 TAA
* * * *
17094 AAGTAAAATATTTATTTATATAAAAATATCAGAAAATAGAC
1 AAATAAGATATTTATTTATTTAAGAATATCAGAAAA-AGAC
17135 ATCAGTTGCT
Statistics
Matches: 154, Mismatches: 14, Indels: 14
0.85 0.08 0.08
Matches are distributed among these distances:
132 20 0.13
133 24 0.16
134 14 0.09
135 40 0.26
136 16 0.10
137 29 0.19
138 11 0.07
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.36
Consensus pattern (133 bp):
AAATAAGATATTTATTTATTTAAGAATATCAGAAAAAGACTTATAGTACTTTAAGACAGTCATTT
TCTTAATATTAAAAAATAAATAAATATTAATAAAACATTTATTAAAAATAAATTAATATAATTTA
TAA
Found at i:17049 original size:135 final size:132
Alignment explanation
Indices: 16824--17186 Score: 419
Period size: 133 Copynumber: 2.7 Consensus size: 132
16814 ATATTTTTAT
* * * *
16824 AAATAAGATATTTATTTACTT-AGAAATATCAGAAAAAGACTTATAGGTACTTTAAGACA-TCCC
1 AAATAAGATATTTATTTATTTAAG-AATATCAGAAAATGACTTCTA-GTGCTTTAAGACAGT--C
*
16887 ATTTCTTTAATATTAAAAAATAAATAAATATTAATAAAACATTTCTCTAAAAATAAATTAATATA
62 ATTTC-TTAATATTAAAAAATAAATAAATATTAATAAAACATTTAT-TAAAAATAAATT-A-ATA
16952 TAATTTATAA
123 TAATTTATAA
*
16962 AAATAGGATA-TTATTTATTTAAGAATATCAGAAAATGACTTCTAGTGCTTTAAGACAGTCATTT
1 AAATAAGATATTTATTTATTTAAGAATATCAGAAAATGACTTCTAGTGCTTTAAGACAGTCA-TT
* *
17026 TCTTAATATTAAAAAATACATAAATATTAATAAAACATTTATTAAAAATAGATTAATATAATTTA
65 TCTTAATATTAAAAAATAAATAAATATTAATAAAACATTTATTAAAAATAAATTAATATAATTTA
17091 TAA
130 TAA
* * * * * * ** *
17094 AAGTAAAATATTTATTTATATAAAAATATCAGAAAATAGACATC-AGTTGCTCTAAGATTGTCCT
1 AAATAAGATATTTATTTATTTAAGAATATCAGAAAAT-GACTTCTAG-TGCTTTAAGACAGTCAT
* * *
17158 TTCTTAATATTGAAAAGTAAATAGATATT
64 TTCTTAATATTAAAAAATAAATAAATATT
17187 TAAAATATGA
Statistics
Matches: 197, Mismatches: 22, Indels: 17
0.83 0.09 0.07
Matches are distributed among these distances:
132 20 0.10
133 53 0.27
134 28 0.14
135 40 0.20
136 16 0.08
137 29 0.15
138 11 0.06
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.37
Consensus pattern (132 bp):
AAATAAGATATTTATTTATTTAAGAATATCAGAAAATGACTTCTAGTGCTTTAAGACAGTCATTT
CTTAATATTAAAAAATAAATAAATATTAATAAAACATTTATTAAAAATAAATTAATATAATTTAT
AA
Found at i:18795 original size:3 final size:3
Alignment explanation
Indices: 18787--18827 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
18777 AATATTTATT
18787 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
18828 GAATGAACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:19452 original size:21 final size:20
Alignment explanation
Indices: 19419--19457 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
19409 TATCAAGGTA
*
19419 TTTATTGAAGCCATGAAATCT
1 TTTATCGAAGCCAT-AAATCT
*
19440 TTTATCGATGCCATAAAT
1 TTTATCGAAGCCATAAAT
19458 TCCTATAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (20 bp):
TTTATCGAAGCCATAAATCT
Found at i:27628 original size:35 final size:35
Alignment explanation
Indices: 27561--27631 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
27551 TATCTTTGAG
* ** *
27561 AATGCTAAATAAATTGAAATTTGAGTGAATTTAAA
1 AATGCTAAACAAATTGAAAAATGAATGAATTTAAA
*
27596 AATGCTAAACAAATTGAAAAATGAATGTATTTAAA
1 AATGCTAAACAAATTGAAAAATGAATGAATTTAAA
27631 A
1 A
27632 GTAGATAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.31
Consensus pattern (35 bp):
AATGCTAAACAAATTGAAAAATGAATGAATTTAAA
Found at i:28394 original size:14 final size:14
Alignment explanation
Indices: 28365--28434 Score: 85
Period size: 14 Copynumber: 5.1 Consensus size: 14
28355 CGTTCGTGAA
28365 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
28381 CGTTCATTTATGTT
1 CGTTCATTTATGTT
*
28395 CATTCATTTA---T
1 CGTTCATTTATGTT
28406 -GTTCATTTATGTT
1 CGTTCATTTATGTT
28419 CGTTCATTTATGTT
1 CGTTCATTTATGTT
28433 CG
1 CG
28435 AACATAGGGC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
10 8 0.17
11 1 0.02
13 1 0.02
14 30 0.62
15 3 0.06
16 5 0.10
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.54
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:28411 original size:24 final size:24
Alignment explanation
Indices: 28382--28433 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
28372 TTATATGTTC
28382 GTTCATTTATGTTCATTCATTTAT
1 GTTCATTTATGTTCATTCATTTAT
*
28406 GTTCATTTATGTTCGTTCATTTAT
1 GTTCATTTATGTTCATTCATTTAT
28430 GTTC
1 GTTC
28434 GAACATAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.17, C:0.13, G:0.12, T:0.58
Consensus pattern (24 bp):
GTTCATTTATGTTCATTCATTTAT
Found at i:28759 original size:20 final size:19
Alignment explanation
Indices: 28727--28767 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
28717 TTATATTCGT
*
28727 TTATTTTCGTTCGTTTGTG
1 TTATTTTCGTTCGTTTATG
28746 TTATTTTACGTTCGTTTATG
1 TTATTTT-CGTTCGTTTATG
28766 TT
1 TT
28768 CGTTTATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.10, C:0.10, G:0.17, T:0.63
Consensus pattern (19 bp):
TTATTTTCGTTCGTTTATG
Found at i:28773 original size:20 final size:20
Alignment explanation
Indices: 28734--28773 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28724 CGTTTATTTT
* *
28734 CGTTCGTTTGTGTTATTTTA
1 CGTTCGTTTATGTTAGTTTA
*
28754 CGTTCGTTTATGTTCGTTTA
1 CGTTCGTTTATGTTAGTTTA
28774 TCATTTAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.57
Consensus pattern (20 bp):
CGTTCGTTTATGTTAGTTTA
Found at i:30028 original size:23 final size:23
Alignment explanation
Indices: 29993--30065 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
29983 ATACTTTACA
* *
29993 ATATAAGCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
30016 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
30039 ATATTAAA-GCTACCTATTACATC
1 ATA-TAAACGCTACCTATTACATT
30062 ATAT
1 ATAT
30066 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
22 1 0.02
23 41 0.89
24 4 0.09
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:30066 original size:23 final size:24
Alignment explanation
Indices: 30002--30066 Score: 107
Period size: 23 Copynumber: 2.8 Consensus size: 24
29992 AATATAAGCA
30002 CTACCTATTACATTATA-TAAACG
1 CTACCTATTACATTATATTAAACG
30025 CTACCTATTACATTATATTAAA-G
1 CTACCTATTACATTATATTAAACG
*
30048 CTACCTATTACATCATATT
1 CTACCTATTACATTATATT
30067 TTTACCTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
23 36 0.90
24 4 0.10
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (24 bp):
CTACCTATTACATTATATTAAACG
Found at i:30516 original size:23 final size:23
Alignment explanation
Indices: 30481--30553 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
30471 ATACTTTACA
*
30481 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
30504 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
30527 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
30550 ATAT
1 ATAT
30554 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:31006 original size:23 final size:23
Alignment explanation
Indices: 30971--31043 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
30961 ATACTTTACA
*
30971 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
30994 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
31017 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
31040 ATAT
1 ATAT
31044 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:31049 original size:490 final size:490
Alignment explanation
Indices: 29592--31761 Score: 4084
Period size: 490 Copynumber: 4.4 Consensus size: 490
29582 TTATAATATG
*
29592 TTGAAAGTGTCTATACTTTTTTATAAAAAAGATCGATAC-TTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCTATAC-TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
29656 TTCAA--TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
65 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
29719 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATA
*
29784 TTAACCAAATATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
195 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
* *
29849 TACCGTAACGTAAAAAATAAATCATTAGAAGCCTATAATTACTAAATTAATATTTTAAAACTCAC
260 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
*
29914 TCAAAAGATAACCTTAAATGAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATG
325 TCAAAAGATAACCTTAAATGAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
*
29979 ATAAATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATT
390 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATA-T
*
30044 AA-AGCTACCTATTACATCATATTTTTACCTATTATA
454 AAGCGCTACCTATTACATCATATTTTTACCTATTATA
* * **
30080 TTGAAAGTGTATATAATTTTTATAAAAATAATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
30145 TCAATTTTTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
30210 TAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
30275 TAACCAAAGATAATAATAAATATGT-A-ATATATGTTTATTGTTTTTAATTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
30338 ACCGTAACGTAAAAAATAAATCATTAGACGTCTATAATTACTAAATTAATATCTTAAAACTCACT
261 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
30403 CAAAAGATAACCTTAAATGAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
326 CAAAAGATAACCTTAAATGAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
*
30468 TATATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
391 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
30533 GCGCTACCTATTACATCATATTTTTACCTATTATA
456 GCGCTACCTATTACATCATATTTTTACCTATTATA
*
30568 TTGAAAGTGTCTATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
30633 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
30698 TAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
30763 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
30828 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
261 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
*
30893 CAAAAGATAACCTTAAATGAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGA
326 CAAAAGATAACCTTAAATGAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
30958 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
391 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
31023 GCGCTACCTATTACATCATATTTTTACCTATTATA
456 GCGCTACCTATTACATCATATTTTTACCTATTATA
31058 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
31123 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
31188 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
31253 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
31318 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAACCTCACT
261 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
31383 CAAAAGATAACCTTAAATGAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
326 CAAAAGATAACCTTAAATGAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
*
31448 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATCATATAA
391 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
31513 GCGCTACCTATTACATCATATTTTTACCTATTATA
456 GCGCTACCTATTACATCATATTTTTACCTATTATA
31548 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
31613 TCAA-TTTTTTTAAAAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
31677 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
31742 TAACCAAAGATAATAATAAA
196 TAACCAAAGATAATAATAAA
31762 ACTCACTCAA
Statistics
Matches: 1650, Mismatches: 26, Indels: 11
0.98 0.02 0.01
Matches are distributed among these distances:
487 23 0.01
488 517 0.31
489 146 0.09
490 964 0.58
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.42
Consensus pattern (490 bp):
TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
CAAAAGATAACCTTAAATGAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
GCGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:31496 original size:23 final size:23
Alignment explanation
Indices: 31461--31533 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
31451 ATACTTTACA
* *
31461 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATC
*
31484 ATATAAACGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATC
31507 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATC
31530 ATAT
1 ATAT
31534 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.33
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATC
Found at i:34581 original size:183 final size:183
Alignment explanation
Indices: 34271--34844 Score: 956
Period size: 183 Copynumber: 3.1 Consensus size: 183
34261 TACTTAAAAT
*
34271 TACCGACACAATATTAAAACGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
34336 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATTTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
*
34401 CGACACTTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
34454 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
34519 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
* *
34584 CGACGCTTTTTTAAATGGTATCGATACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
** *
34637 TTTCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* *
34702 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTTTTTTCAA
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATG---TGTAAA
*
34767 --TCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCATTCTGGACATAAAG
128 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
**
34821 TACAAACACAATATTAAAAAGTGT
1 TACCGACACAATATTAAAAAGTGT
34845 GAAAACTTTG
Statistics
Matches: 366, Mismatches: 21, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
182 3 0.01
183 288 0.79
184 71 0.19
186 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (183 bp):
TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
Found at i:36059 original size:9 final size:9
Alignment explanation
Indices: 36045--36122 Score: 84
Period size: 9 Copynumber: 8.7 Consensus size: 9
36035 ACTTGTTTGG
36045 ATCATCATC
1 ATCATCATC
36054 ATCATCATC
1 ATCATCATC
36063 ATCATCATC
1 ATCATCATC
*
36072 TTCATCATC
1 ATCATCATC
* *
36081 TTCATCGTC
1 ATCATCATC
* *
36090 AGCTTCATC
1 ATCATCATC
*
36099 GTCATCATC
1 ATCATCATC
*
36108 ATCGTCATC
1 ATCATCATC
*
36117 TTCATC
1 ATCATC
36123 GTCAGCTTCA
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 56 1.00
ACGTcount: A:0.24, C:0.33, G:0.05, T:0.37
Consensus pattern (9 bp):
ATCATCATC
Found at i:36098 original size:36 final size:36
Alignment explanation
Indices: 36058--36139 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 36
36048 ATCATCATCA
*
36058 TCATCATCATCATCTTCATCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
* *
36094 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
*
36130 TCATCTTCAT
1 TCATCATCAT
36140 TGGCCGCTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.39
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGTCAGCT
Found at i:36123 original size:12 final size:12
Alignment explanation
Indices: 36046--36139 Score: 98
Period size: 12 Copynumber: 7.8 Consensus size: 12
36036 CTTGTTTGGA
* *
36046 TCATCATCATCA
1 TCATCGTCATCT
* *
36058 TCATCATCATCA
1 TCATCGTCATCT
* *
36070 TCTTCATCATCT
1 TCATCGTCATCT
*
36082 TCATCGTCAGCT
1 TCATCGTCATCT
*
36094 TCATCGTCATCA
1 TCATCGTCATCT
36106 TCATCGTCATCT
1 TCATCGTCATCT
*
36118 TCATCGTCAGCT
1 TCATCGTCATCT
*
36130 TCATCTTCAT
1 TCATCGTCAT
36140 TGGCCGCTTG
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 71 1.00
ACGTcount: A:0.22, C:0.33, G:0.06, T:0.38
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:36139 original size:6 final size:6
Alignment explanation
Indices: 36045--36122 Score: 84
Period size: 6 Copynumber: 13.0 Consensus size: 6
36035 ACTTGTTTGG
* * * *
36045 ATCATC ATCATC ATCATC ATCATC ATCTTC ATCATC TTCATC GTCAGC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* * * *
36093 TTCATC GTCATC ATCATC GTCATC TTCATC
1 ATCATC ATCATC ATCATC ATCATC ATCATC
36123 GTCAGCTTCA
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.24, C:0.33, G:0.05, T:0.37
Consensus pattern (6 bp):
ATCATC
Found at i:36148 original size:18 final size:18
Alignment explanation
Indices: 36076--36139 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
36066 ATCATCTTCA
*
36076 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGGCAGCT
* ** * *
36094 TCATCGTCATCATCATCG
1 TCATCTTCATCGGCAGCT
*
36112 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGGCAGCT
36130 TCATCTTCAT
1 TCATCTTCAT
36140 TGGCCGCTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCGGCAGCT
Found at i:37946 original size:200 final size:200
Alignment explanation
Indices: 37603--38957 Score: 2102
Period size: 200 Copynumber: 6.9 Consensus size: 200
37593 TTTAAATTAG
* * * *
37603 TATCGACA-AAACATTAAACAGTGTCGATACA-TATTATATACCA-ATTCTCTCATAAAACCGGT
1 TATCGACACAAAC-TAAAAAAGTGTCGACACATTATT-TAGA-CATATTCTCTCATAAAACCGGT
* *
37665 ATACTTGTACCGGTTAGATTGAAAATTTACATATTACATTGTACTTTTGGTTTTCGATGTTTTTG
63 ATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTG
*
37730 GGATCGACACTTTCTATATATGGATCGACACTTTATGGTTGCACCATGTTTTCCATTCATTCTGG
128 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTTCCATTCATTCTGG
37795 ACCAAAAA
193 ACCAAAAA
* * * *
37803 TATCGACACAAACTAAAAAAGTGTCGACAAATTATTTAGATATATTCTCTTATAAAACCAGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
37868 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
37933 TCGACACTTTCTATATATGGATCGACACTTTATGGTTGCACCATGTTTTCCATTCATTCAGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTTCCATTCATTCTGGACC
37998 AAAAA
196 AAAAA
* *
38003 TATCGACACAAACTAAAAAAGTGTCGACAAATTATTTAGACATATTCTCTCATAAAATCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
38068 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
38133 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTATGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTTCCATTCATTCTGGACC
38198 AAAAA
196 AAAAA
*
38203 TATCGACACAAACTAAAAAAGTATCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
38268 TTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
38333 TCGACACTTTTTATATATGGATTGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTTCCATTCATTCTGGACC
38398 AAAAA
196 AAAAA
38403 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
38468 CTTGTACCGGTTATATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* * * * **
38533 TCGACAC----T-T-TATGG-TTGCACCCTGT-T--TT---CCA----TT-CATTC--T-GGACC
131 TCGACACTTTTTATATATGGATCG-ACACTTTATGGTTGCACCATGTTTTCCATTCATTCTGGAC
*
38577 AAAAATA
195 CAAAA-A
* *
38584 TCGA-C-ACA-AAC-TAAAAAAGTGTCGACATATTATTTAGACATATTCTCTCATAAAACCGGTA
1 T--ATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
* *
38645 TACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTAGTTTTCGATATTTTTGG
64 TACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGG
38710 GATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCA-CATGTTTTCCATTCATTCTGGA
129 GATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTTCCATTCATTCTGGA
38774 CCAAAAA
194 CCAAAAA
38781 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
38846 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGAAGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* * *
38911 TCGATACTTTTTATATATGGTTCGACACTTTATGGTTGCACCCTGTT
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTT
38958 GGCCATATTG
Statistics
Matches: 1067, Mismatches: 55, Indels: 66
0.90 0.05 0.06
Matches are distributed among these distances:
179 120 0.11
180 8 0.01
181 6 0.01
182 1 0.00
183 7 0.01
184 3 0.00
185 10 0.01
186 3 0.00
188 4 0.00
190 2 0.00
191 2 0.00
193 4 0.00
194 12 0.01
195 7 0.01
196 2 0.00
197 6 0.01
198 8 0.01
199 152 0.14
200 702 0.66
201 8 0.01
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (200 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTTCCATTCATTCTGGACC
AAAAA
Found at i:38574 original size:179 final size:179
Alignment explanation
Indices: 38351--38920 Score: 800
Period size: 179 Copynumber: 3.1 Consensus size: 179
38341 TTTTATATAT
*
38351 GGATTGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAAC
38416 TAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
66 TAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
*
38481 TATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTG
131 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTG
38530 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAAC
*
38595 TAAAAAAGTGTCGACATATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
66 TAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
* *
38660 GATTGAAAAATTACATATTACATTATACTTTTAGTTTTCGATATTTTTG
131 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTG
* * * *****
38709 GGATCGACACTTTTTAT-ATATGGATCGACACTTTATGGTTGCACATGTTTTCCATTCATTCTGG
1 GGATCGACAC--TTTATGGT-T-G--C-ACCCTGT-T--TT-C-CA----TT-CATTC-TGGACC
*
38773 ACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA
48 A-AAAA--TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA
*
38838 CCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGAAGT
110 CCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGT
38903 TTTTG
175 TTTTG
*
38908 GGATCGATACTTT
1 GGATCGACACTTT
38921 TTATATATGG
Statistics
Matches: 351, Mismatches: 19, Indels: 24
0.89 0.05 0.06
Matches are distributed among these distances:
179 184 0.52
180 1 0.00
181 6 0.02
182 1 0.00
184 1 0.00
185 5 0.01
186 1 0.00
188 2 0.01
189 1 0.00
190 2 0.01
194 2 0.01
195 5 0.01
196 2 0.01
197 6 0.02
199 132 0.38
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (179 bp):
GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAAC
TAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTG
Found at i:38871 original size:199 final size:199
Alignment explanation
Indices: 38530--38951 Score: 774
Period size: 199 Copynumber: 2.1 Consensus size: 199
38520 GATGTTTTTG
*
38530 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGTTGCA-CATGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAAC
*
38595 TAAAAAAGTGTCGACATATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
65 TAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
38660 GATTGAAAAATTACATATTACATTATACTTTTAGTTTTCGATA-TTTTTGGGATCGACACTTTTT
130 GATTGAAAAATTACATATTACATTATACTTTTAGTTTTCGA-AGTTTTTGGGATCGACACTTTTT
38724 ATATAT
194 ATATAT
38730 GGATCGACACTTTATGGTTGCACATGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
1 GGATCGACACTTTATGGTTGCACATGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
38795 AAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAG
66 AAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAG
* *
38860 ATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGAAGTTTTTGGGATCGATACTTTTTAT
131 ATTGAAAAATTACATATTACATTATACTTTTAGTTTTCGAAGTTTTTGGGATCGACACTTTTTAT
38925 ATAT
196 ATAT
*
38929 GGTTCGACACTTTATGGTTGCAC
1 GGATCGACACTTTATGGTTGCAC
38952 CCTGTTGGCC
Statistics
Matches: 216, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
198 1 0.00
199 193 0.89
200 22 0.10
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (199 bp):
GGATCGACACTTTATGGTTGCACATGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
AAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAG
ATTGAAAAATTACATATTACATTATACTTTTAGTTTTCGAAGTTTTTGGGATCGACACTTTTTAT
ATAT
Found at i:39087 original size:18 final size:18
Alignment explanation
Indices: 39064--39124 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
39054 TCTAATTCAT
*
39064 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
39082 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
39101 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
39120 AATTA
1 AATTA
39125 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:39100 original size:19 final size:19
Alignment explanation
Indices: 39076--39124 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
39066 TTATATTCAC
39076 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
39095 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
39114 ATACAAAATTA
1 ATACAAAATTA
39125 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:40951 original size:33 final size:33
Alignment explanation
Indices: 40905--40970 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
40895 CATCTTAATA
*
40905 TCACCCCTTAACACCACAACTTATTTCACCACT
1 TCACCCCTCAACACCACAACTTATTTCACCACT
* * *
40938 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCACAACTTATTTCACCACT
40971 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.26, C:0.45, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCACAACTTATTTCACCACT
Found at i:41029 original size:21 final size:21
Alignment explanation
Indices: 41004--41068 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
40994 CCCCTTATGC
* *
41004 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
41025 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
41046 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
41067 CT
1 CT
41069 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:43130 original size:24 final size:24
Alignment explanation
Indices: 43093--43145 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
43083 CCGTTCTATC
43093 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
43117 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
43141 TATTT
1 TATTT
43146 AATCAATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:43321 original size:20 final size:20
Alignment explanation
Indices: 43289--43345 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
43279 ATCCGGTATC
*
43289 ATTT-TACCAGTTTTATCAT
1 ATTTATACCTGTTTTATCAT
43308 -TTTGATACCTGTTTTATCAT
1 ATTT-ATACCTGTTTTATCAT
* *
43328 ATTTTTACCTGTTATATC
1 ATTTATACCTGTTTTATC
43346 GTTGTGGATC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.54
Consensus pattern (20 bp):
ATTTATACCTGTTTTATCAT
Found at i:43516 original size:20 final size:19
Alignment explanation
Indices: 43471--43516 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
43461 TCCGGTAACA
43471 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
43490 TTCTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
43511 TTTTAC
1 TTTTAC
43517 ATGGTATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:43561 original size:181 final size:182
Alignment explanation
Indices: 43257--43729 Score: 657
Period size: 181 Copynumber: 2.6 Consensus size: 182
43247 CGTACTTACG
* * * *
43257 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCAGTTTTATCATTTTGATACCTGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACATTTTACCGGTTTTATCATTTTCATACCGGTTT
* * *
43322 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAA
*
43387 AGG-CGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTTGATCCTTATA-T
131 AGGAC-CTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
43438 AAAGTATCAACACTTTCAATATATCCGGTAACATTTTACCGGTTTTATCATTTTCTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACATTTTACCGGTTTTATCATTTTCATACCGGTTT
* * * *
43503 TATCATATTTTTACATGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAA
* *
43568 AGGACTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGACCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * ** *
43620 AAAGTA-CTGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCA-TTTCAATACTGGT
1 AAAGTATC-GACACTTTCAATATATCCGGTAACATTTTACCGGTTTTATCATTTTC-ATACCGGT
* * * *
43683 TTTGTCATAGTTTTACCTGTTATAGCGTTTTGGATCGACACATTTTT
64 TTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
43730 AATTTGGATC
Statistics
Matches: 258, Mismatches: 30, Indels: 7
0.87 0.10 0.02
Matches are distributed among these distances:
181 167 0.65
182 91 0.35
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACATTTTACCGGTTTTATCATTTTCATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAA
AGGACCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:44161 original size:14 final size:15
Alignment explanation
Indices: 44142--44170 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
44132 AATATGGTGA
44142 TTTTAAAAT-TTATT
1 TTTTAAAATATTATT
44156 TTTTAAAATATTATT
1 TTTTAAAATATTATT
44171 ATTATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAAAATATTATT
Found at i:44711 original size:3 final size:3
Alignment explanation
Indices: 44703--44755 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
44693 ATTAAGTCTA
44703 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
44751 ATG AT
1 ATG AT
44756 AGAGTATGGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:45838 original size:3 final size:3
Alignment explanation
Indices: 45832--45883 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
45822 GATATTTTTG
45832 TAA TAA TAA TAA TAA TAA TAA TAA 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
45880 TAA T
1 TAA T
45884 TTATCTTATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:46793 original size:35 final size:35
Alignment explanation
Indices: 46698--46795 Score: 124
Period size: 35 Copynumber: 2.8 Consensus size: 35
46688 GCAACACAAT
* *
46698 CATCAATTACATTCTAAACCCTAAAATCCAAAATA
1 CATCAATTACATTCTAAACCCCAAATTCCAAAATA
**
46733 CATCAATTACATTCTAAACATCAAATTCCAAAATA
1 CATCAATTACATTCTAAACCCCAAATTCCAAAATA
* * **
46768 CTTCAATTACATGCCCAACCCCAAATTC
1 CATCAATTACATTCTAAACCCCAAATTC
46796 ATATTCCATT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.44, C:0.29, G:0.01, T:0.27
Consensus pattern (35 bp):
CATCAATTACATTCTAAACCCCAAATTCCAAAATA
Found at i:47209 original size:148 final size:143
Alignment explanation
Indices: 46946--47237 Score: 476
Period size: 148 Copynumber: 2.0 Consensus size: 143
46936 ACATAAATAC
46946 TCAATTCAGTTTATAAAATAGATGACTCGAAATTTTTTTGAGTTTATAAAATTTAAATCAAGTCG
1 TCAATTCAGTTTATAAAATAGATGACTCGAAATTTTTTTGAGTTTATAAAATTTAAATCAAGTCG
* * * *
47011 AATTGAATTGAATTTTCCAGTTTATGTTTAAATTTAATTATAAATATTTATCATATTATAATATT
66 AATTGAATTGAATTTTCCAGTTTATATTTAAATTTAATTATAAATATTTATAACACTATAATATT
47076 ATTTGATTCTAAT
131 ATTTGATTCTAAT
*
47089 TCAATTCAGTTTATAAAATAGTTGACTCGAAATTTTTCCGATTTGAGTTTATAAAATTTAAATCA
1 TCAATTCAGTTTATAAAATAGATGACTCGAAA-TTTT----TTTGAGTTTATAAAATTTAAATCA
* *
47154 AGTCGAATTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAACACTATA
61 AGTCGAATTGAATTGAATTTTCCAGTTTATATTTAAATTTAATTATAAATATTTATAACACTATA
47219 ATATTATTTGATTCTAAT
126 ATATTATTTGATTCTAAT
47237 T
1 T
47238 TAAATAGTTT
Statistics
Matches: 137, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
143 31 0.23
144 4 0.03
148 102 0.74
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (143 bp):
TCAATTCAGTTTATAAAATAGATGACTCGAAATTTTTTTGAGTTTATAAAATTTAAATCAAGTCG
AATTGAATTGAATTTTCCAGTTTATATTTAAATTTAATTATAAATATTTATAACACTATAATATT
ATTTGATTCTAAT
Found at i:47799 original size:35 final size:36
Alignment explanation
Indices: 47741--47810 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 36
47731 GTTGGGCATG
*
47741 TAATTGAAGTATTTTTGGAATTTGAGGTTTAGAATA
1 TAATTGAAATATTTTTGGAATTTGAGGTTTAGAATA
*
47777 TAATTGAAATA-TTTTGGAATTTGGGGTTTAGAAT
1 TAATTGAAATATTTTTGGAATTTGAGGTTTAGAAT
47811 GTAACTGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 22 0.69
36 10 0.31
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (36 bp):
TAATTGAAATATTTTTGGAATTTGAGGTTTAGAATA
Found at i:48258 original size:18 final size:20
Alignment explanation
Indices: 48204--48279 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
48194 TAAAATTTAT
* *
48204 ATTAAATTATTTATTTATAAT
1 ATTATATTATTTATTT-TAAA
* **
48225 ATTAT-GTAAATATTTTAAA
1 ATTATATTATTTATTTTAAA
48244 A-TAT-TTATTTATTTTTTAAA
1 ATTATATTATTTA--TTTTAAA
48264 ATTATATTATTTATTT
1 ATTATATTATTTATTT
48280 ATTTAAAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
18 7 0.16
19 4 0.09
20 18 0.42
21 7 0.16
22 7 0.16
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (20 bp):
ATTATATTATTTATTTTAAA
Found at i:48271 original size:19 final size:19
Alignment explanation
Indices: 48237--48299 Score: 56
Period size: 22 Copynumber: 3.1 Consensus size: 19
48227 TATGTAAATA
*
48237 TTTTAAAATATTTATTTATT
1 TTTTAAAATATATA-TTATT
48257 TTTTAAAATTATATTATTTATT
1 TTTTAAAA-TATA-TA-TTATT
*
48279 TATTTAAAATA-ATGTTATT
1 T-TTTAAAATATATATTATT
48298 TT
1 TT
48300 AAATTATCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 1 0.03
19 6 0.16
20 9 0.24
21 4 0.11
22 11 0.29
23 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTAAAATATATATTATT
Found at i:48297 original size:26 final size:22
Alignment explanation
Indices: 48237--48298 Score: 83
Period size: 23 Copynumber: 2.9 Consensus size: 22
48227 TATGTAAATA
48237 TTTTAAAA-TAT-TTATTTATT
1 TTTTAAAATTATATTATTTATT
48257 TTTTAAAATTATATTATTTATT
1 TTTTAAAATTATATTATTTATT
* *
48279 TATTTAAAATAATGTTATTT
1 T-TTTAAAATTATATTATTT
48299 TAAATTATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 8 0.22
21 3 0.08
22 10 0.27
23 16 0.43
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTAAAATTATATTATTTATT
Found at i:48312 original size:59 final size:62
Alignment explanation
Indices: 48194--48328 Score: 154
Period size: 59 Copynumber: 2.2 Consensus size: 62
48184 TATGTATTTA
* * *
48194 TAAAATTTATATTAAATTATTTATTTATAATATTATGTAAATATTTTAAAATATTTATTTATTTT
1 TAAAA-TTATATTAAATTATTTATTTATAATATAATGT--ATATTTTAAAATATCTATTTA-GTT
48259 T
62 T
* *
48260 TAAAATTATATT-ATTTATTTATTTA-AA-ATAATGT-TATTTTAAATTATCTATTTAGTTT
1 TAAAATTATATTAAATTATTTATTTATAATATAATGTATATTTTAAAATATCTATTTAGTTT
48318 T-AAATTATATT
1 TAAAATTATATT
48329 GTACGAAACC
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
57 10 0.16
58 4 0.06
59 18 0.28
62 6 0.09
63 2 0.03
64 12 0.19
65 7 0.11
66 5 0.08
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (62 bp):
TAAAATTATATTAAATTATTTATTTATAATATAATGTATATTTTAAAATATCTATTTAGTTT
Found at i:51667 original size:14 final size:14
Alignment explanation
Indices: 51647--51712 Score: 78
Period size: 14 Copynumber: 4.7 Consensus size: 14
51637 TCATATAATC
51647 AGATTTAGGGTTTA
1 AGATTTAGGGTTTA
*
51661 TGATTTAGGGTTTA
1 AGATTTAGGGTTTA
* *
51675 AGGTTTAGAGTTTA
1 AGATTTAGGGTTTA
*
51689 AGATTTATGGTTTA
1 AGATTTAGGGTTTA
* *
51703 GGTTTTAGGG
1 AGATTTAGGG
51713 CTTAGGGTTA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.45
Consensus pattern (14 bp):
AGATTTAGGGTTTA
Found at i:51674 original size:7 final size:7
Alignment explanation
Indices: 51650--51721 Score: 63
Period size: 7 Copynumber: 10.3 Consensus size: 7
51640 TATAATCAGA
51650 TTTAGGG
1 TTTAGGG
* *
51657 TTTATGA
1 TTTAGGG
51664 TTTAGGG
1 TTTAGGG
*
51671 TTTAAGG
1 TTTAGGG
*
51678 TTTAGAG
1 TTTAGGG
* *
51685 TTTAAGA
1 TTTAGGG
*
51692 TTTATGG
1 TTTAGGG
*
51699 TTTAGGT
1 TTTAGGG
51706 TTTAGGG
1 TTTAGGG
*
51713 CTTAGGG
1 TTTAGGG
51720 TT
1 TT
51722 AATTACAAAT
Statistics
Matches: 48, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:51881 original size:14 final size:14
Alignment explanation
Indices: 51862--51891 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
51852 TATAATTATC
*
51862 AATAATGTATTTTT
1 AATAATGTAATTTT
51876 AATAATGTAATTTT
1 AATAATGTAATTTT
51890 AA
1 AA
51892 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:52372 original size:35 final size:35
Alignment explanation
Indices: 52325--52400 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
52315 AACACAATCA
* *
52325 TCAATTATATTCTAAACC-CTAAATTCCAAAATGCT
1 TCAATTAGATTCTAAACCTC-AAATTCCAAAATACT
*
52360 TCAATTAGATTCTAAACCTCAAATTCTAAAATACT
1 TCAATTAGATTCTAAACCTCAAATTCCAAAATACT
*
52395 TTAATT
1 TCAATT
52401 GCATGCTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 35 0.97
36 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.03, T:0.37
Consensus pattern (35 bp):
TCAATTAGATTCTAAACCTCAAATTCCAAAATACT
Found at i:52418 original size:35 final size:35
Alignment explanation
Indices: 52325--52420 Score: 95
Period size: 35 Copynumber: 2.7 Consensus size: 35
52315 AACACAATCA
* * * *
52325 TCAATTATATTCTAAACCCTAAATTCCAAAATGCT
1 TCAATTAGATGCTAAACCCCAAATTCCAAAATACT
* * *
52360 TCAATTAGATTCTAAACCTCAAATTCTAAAATACT
1 TCAATTAGATGCTAAACCCCAAATTCCAAAATACT
* *
52395 TTAATT-GCATGCTCAACCCCAAATTC
1 TCAATTAG-ATGCTAAACCCCAAATTC
52421 ATAATCCATT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
34 1 0.02
35 50 0.98
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (35 bp):
TCAATTAGATGCTAAACCCCAAATTCCAAAATACT
Found at i:53414 original size:35 final size:35
Alignment explanation
Indices: 53375--53451 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
53365 GTTGGGCATG
*
53375 TAATTGAAGTATTTTGGAATTCAAGATTTAGAATA
1 TAATTGAAGTATTTTAGAATTCAAGATTTAGAATA
* * * * *
53410 TAATTGAAGTATTTTATAATTTAGGGTTTAGAATG
1 TAATTGAAGTATTTTAGAATTCAAGATTTAGAATA
53445 TAATTGA
1 TAATTGA
53452 TGACGGTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.01, G:0.18, T:0.43
Consensus pattern (35 bp):
TAATTGAAGTATTTTAGAATTCAAGATTTAGAATA
Found at i:57750 original size:24 final size:23
Alignment explanation
Indices: 57708--57784 Score: 109
Period size: 24 Copynumber: 3.2 Consensus size: 23
57698 GGTAATTTAA
*
57708 AAATAATATTATTTCAAATAAAT
1 AAATAATATTATTTTAAATAAAT
57731 AAATAATATTTATTTTAAATAAAT
1 AAATAATA-TTATTTTAAATAAAT
*
57755 AAATAATATGATTTTAATAATAAAT
1 AAATAATATTATTTT-A-AATAAAT
57780 AAATA
1 AAATA
57785 TTTACAATGT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
23 14 0.29
24 23 0.47
25 12 0.24
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (23 bp):
AAATAATATTATTTTAAATAAAT
Found at i:59792 original size:31 final size:31
Alignment explanation
Indices: 59687--59798 Score: 93
Period size: 31 Copynumber: 3.5 Consensus size: 31
59677 TTAGGTCCAT
* *
59687 AAGGAATTACCAGTCGGTGTTGAACCTATTC
1 AAGGAATTACCAGTCGATGTTGAACCTATAC
** * *
59718 AAGGAATTACCA-TCAGCA-ACTGAACCTGCAAGAGAT
1 AAGGAATTACCAGTC-G-ATGTTGAACCT-----ATAC
59754 AAGGAATTACCAGTCGATGTTGAACCTATAC
1 AAGGAATTACCAGTCGATGTTGAACCTATAC
59785 AAGGAATTACCAGT
1 AAGGAATTACCAGT
59799 AGCGACTGAA
Statistics
Matches: 62, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
30 2 0.03
31 36 0.58
35 1 0.02
36 21 0.34
37 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.23
Consensus pattern (31 bp):
AAGGAATTACCAGTCGATGTTGAACCTATAC
Found at i:59793 original size:67 final size:67
Alignment explanation
Indices: 59685--59818 Score: 216
Period size: 67 Copynumber: 2.0 Consensus size: 67
59675 CCTTAGGTCC
* *
59685 ATAAGGAATTACCAGTCGGTGTTGAACCTATTCAAGGAATTACCA-TCAGCAACTGAACCTGCAA
1 ATAAGGAATTACCAGTCGATGTTGAACCTATACAAGGAATTACCAGT-AGCAACTGAACCTGCAA
59749 GAG
65 GAG
* *
59752 ATAAGGAATTACCAGTCGATGTTGAACCTATACAAGGAATTACCAGTAGCGACTGAACCTTCAAG
1 ATAAGGAATTACCAGTCGATGTTGAACCTATACAAGGAATTACCAGTAGCAACTGAACCTGCAAG
59817 AG
66 AG
59819 TCTTCATTCC
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 61 0.98
68 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (67 bp):
ATAAGGAATTACCAGTCGATGTTGAACCTATACAAGGAATTACCAGTAGCAACTGAACCTGCAAG
AG
Found at i:60872 original size:8 final size:8
Alignment explanation
Indices: 60859--60884 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
60849 TTCATAGTAC
60859 TTTGCTCA
1 TTTGCTCA
60867 TTTGCTCA
1 TTTGCTCA
60875 TTTGCTCA
1 TTTGCTCA
60883 TT
1 TT
60885 AGAGGTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.23, G:0.12, T:0.54
Consensus pattern (8 bp):
TTTGCTCA
Found at i:61556 original size:22 final size:22
Alignment explanation
Indices: 61509--61563 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
61499 ACTTTTTCGG
* *
61509 TCAAAGTCAACGGTCAGAACGG
1 TCAAAGTCAACAGTCAGAACGA
*
61531 TCAAAGTCAACAGT-ATGATCGA
1 TCAAAGTCAACAGTCA-GAACGA
*
61553 TCAAATTCAAC
1 TCAAAGTCAAC
61564 GATTTGATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (22 bp):
TCAAAGTCAACAGTCAGAACGA
Found at i:63677 original size:42 final size:42
Alignment explanation
Indices: 63618--63701 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
63608 TTTGAAATTA
63618 CTCCCCCTTACGTTAACACTAACACTTCTCCCATTTATCATT
1 CTCCCCCTTACGTTAACACTAACACTTCTCCCATTTATCATT
*
63660 CTCCCCCTTACTTTAACACTAACACTTCTCCCATTTATCATT
1 CTCCCCCTTACGTTAACACTAACACTTCTCCCATTTATCATT
63702 TTTAACTTCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.38, G:0.01, T:0.37
Consensus pattern (42 bp):
CTCCCCCTTACGTTAACACTAACACTTCTCCCATTTATCATT
Found at i:65807 original size:20 final size:20
Alignment explanation
Indices: 65770--65808 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
65760 AGATTGAGTG
* * *
65770 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
65790 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
65809 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:73512 original size:34 final size:34
Alignment explanation
Indices: 73473--73546 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
73463 TTTTTAAGCC
* *
73473 TATAAAAGATATATT-AA-GTAATTAAATATATTT
1 TATAAAAGATATATTGAAGGT-ATAAAATATATTG
*
73506 TGAT-AAATATATATTGAAGGTATAAAATATATTG
1 T-ATAAAAGATATATTGAAGGTATAAAATATATTG
73540 TATAAAA
1 TATAAAA
73547 TTAAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
33 13 0.38
34 19 0.56
35 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.39
Consensus pattern (34 bp):
TATAAAAGATATATTGAAGGTATAAAATATATTG
Found at i:78680 original size:20 final size:21
Alignment explanation
Indices: 78657--78704 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
78647 CTTCAATATT
*
78657 GATACCAAACC-TTGGGTATC
1 GATACCAAACCTTTAGGTATC
*
78677 GATACC-CACCTTTAGGTATC
1 GATACCAAACCTTTAGGTATC
78697 GATACCAA
1 GATACCAA
78705 CGGAATGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (21 bp):
GATACCAAACCTTTAGGTATC
Found at i:80968 original size:21 final size:21
Alignment explanation
Indices: 80938--80988 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
80928 TTATCGATAT
* *
80938 TTAATATTATTATTTTTATCA
1 TTAATATTATTAATATTATCA
*
80959 TTAATTTTATTAATATTATCAA
1 TTAATATTATTAATATTATC-A
*
80981 TTTATATT
1 TTAATATT
80989 TAATTTCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
TTAATATTATTAATATTATCA
Found at i:82058 original size:23 final size:22
Alignment explanation
Indices: 81996--82147 Score: 116
Period size: 21 Copynumber: 7.0 Consensus size: 22
81986 AAGGTTCTAC
*
81996 GTGGTCATTCGGGAC-ATATAT
1 GTGGTCCTTCGGGACAATATAT
* * *
82017 GTGATCCTTTGGAAC-ATATAT
1 GTGGTCCTTCGGGACAATATAT
*
82038 GCGGTCCTTCGGGAC-ATATAT
1 GTGGTCCTTCGGGACAATATAT
* **
82059 TTGGT-CTTTTGGAC-ATATAT
1 GTGGTCCTTCGGGACAATATAT
* *
82079 GTGGTCCTTAGGGATAATTATAT
1 GTGGTCCTTCGGGACAA-TATAT
* * *
82102 GTGGTCTTTCGGGACAATTCTAC
1 GTGGTCCTTCGGGACAA-TATAT
*
82125 GTGGTCCTTTGGGACATATATAT
1 GTGGTCCTTCGGGACA-ATATAT
82148 AGTCTTTAGA
Statistics
Matches: 102, Mismatches: 25, Indels: 6
0.77 0.19 0.05
Matches are distributed among these distances:
20 17 0.17
21 43 0.42
22 1 0.01
23 40 0.39
24 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (22 bp):
GTGGTCCTTCGGGACAATATAT
Found at i:82070 original size:42 final size:41
Alignment explanation
Indices: 81998--82110 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 41
81988 GGTTCTACGT
* * *
81998 GGTCATTCGGGACATATATGTGATCCTTTGGAACATATATGC
1 GGTCCTTCGGGACATATATGTGGTCTTTTGG-ACATATATGC
* *
82040 GGTCCTTCGGGACATATATTTGGTCTTTTGGACATATATGT
1 GGTCCTTCGGGACATATATGTGGTCTTTTGGACATATATGC
* *
82081 GGTCCTTAGGGATAATTATATGTGGTCTTT
1 GGTCCTTCGGGA-CA-TATATGTGGTCTTT
82111 CGGGACAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
41 20 0.33
42 28 0.46
43 13 0.21
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.39
Consensus pattern (41 bp):
GGTCCTTCGGGACATATATGTGGTCTTTTGGACATATATGC
Found at i:82211 original size:25 final size:25
Alignment explanation
Indices: 82161--82211 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
82151 CTTTAGAACG
* *
82161 TTCTATGTGGCACTTCAGTGCGTAT
1 TTCTATGCGGCACTTCAGTGCATAT
82186 TTCTATGCGGCACTTC-GATGCATAT
1 TTCTATGCGGCACTTCAG-TGCATAT
82211 T
1 T
82212 ATACGAACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.39
Consensus pattern (25 bp):
TTCTATGCGGCACTTCAGTGCATAT
Found at i:84281 original size:24 final size:25
Alignment explanation
Indices: 84193--84283 Score: 98
Period size: 25 Copynumber: 3.7 Consensus size: 25
84183 TTTTTAAAAC
**
84193 TTCATCAAACATTTTTTGAAATTCT
1 TTCATCAAACATTTTTCAAAATTCT
* *
84218 TTCATTAAACATTATTCAAAATTCT
1 TTCATCAAACATTTTTCAAAATTCT
* *
84243 TTTATAAAACA-TTTTCAAAACTTC-
1 TTCATCAAACATTTTTCAAAA-TTCT
84267 TTCATCAAAC-TTTTTCA
1 TTCATCAAACATTTTTCA
84284 CCTTTTGAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
24 22 0.40
25 33 0.60
ACGTcount: A:0.36, C:0.18, G:0.01, T:0.45
Consensus pattern (25 bp):
TTCATCAAACATTTTTCAAAATTCT
Found at i:84642 original size:30 final size:30
Alignment explanation
Indices: 84606--84697 Score: 112
Period size: 30 Copynumber: 3.1 Consensus size: 30
84596 GTCGAGGCTA
* * * *
84606 AACACCAAATAGTACATAGATTTGGCCACC
1 AACACCAAGTAATACATGGACTTGGCCACC
* *
84636 AACACCAAGTAATACAGGGACTTGGCCATC
1 AACACCAAGTAATACATGGACTTGGCCACC
* *
84666 AACACCAAGTATTATATGGACTTGGCCACC
1 AACACCAAGTAATACATGGACTTGGCCACC
84696 AA
1 AA
84698 TGTTAAATAG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (30 bp):
AACACCAAGTAATACATGGACTTGGCCACC
Found at i:87363 original size:11 final size:12
Alignment explanation
Indices: 87338--87368 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
87328 TTAGCATCTC
87338 GTTATTTTTTGG
1 GTTATTTTTTGG
87350 GTTATTTTTTGG
1 GTTATTTTTTGG
*
87362 TTTATTT
1 GTTATTT
87369 ATTTATTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.19, T:0.71
Consensus pattern (12 bp):
GTTATTTTTTGG
Found at i:89656 original size:78 final size:78
Alignment explanation
Indices: 89522--89764 Score: 261
Period size: 78 Copynumber: 3.0 Consensus size: 78
89512 TAAGCTAAAT
* *
89522 TAAGAGAAAACAGAAAAGTCAATACAGAAAACAGGATTACTAGGGGCGAAAATAGGGTTAGGGGT
1 TAAGAGAAAACAGAAAAGCCAATACAGAAAACAGGATTACTAAGGGCGAAAATAGGGTTAGGGGT
89587 GAACTTAAACTAA
66 GAACTTAAACTAA
* * * *
89600 TAAGCGAAAACAGAAAAGCCAATACAGAAAACAGGGTTACTAAGGGCGATAATAGGGTTAGTGGT
1 TAAGAGAAAACAGAAAAGCCAATACAGAAAACAGGATTACTAAGGGCGAAAATAGGGTTAGGGGT
89665 GAACTTAAACTACTTAAACTCA
66 GAACTT-AA--AC-T--A---A
* ** * * * *
89687 TAAGAGAAAATAGAAAAGAAAATACAAAAAACAGGGTTACTAGGGGCAAAAATAGGGTTAGGGGG
1 TAAGAGAAAACAGAAAAGCCAATACAGAAAACAGGATTACTAAGGGCGAAAATAGGGTTA-GGGG
* *
89752 AGAACATAAACTA
65 TGAACTTAAACTA
89765 CTTAAATTCA
Statistics
Matches: 138, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
78 65 0.47
79 2 0.01
81 2 0.01
82 2 0.01
84 2 0.01
85 2 0.01
87 55 0.40
88 8 0.06
ACGTcount: A:0.48, C:0.11, G:0.24, T:0.17
Consensus pattern (78 bp):
TAAGAGAAAACAGAAAAGCCAATACAGAAAACAGGATTACTAAGGGCGAAAATAGGGTTAGGGGT
GAACTTAAACTAA
Found at i:89690 original size:87 final size:88
Alignment explanation
Indices: 89589--89787 Score: 258
Period size: 87 Copynumber: 2.3 Consensus size: 88
89579 TTAGGGGTGA
* * ** * * *
89589 ACTTAAACTAATAAGCGAAAACAGAAAAGCCAATACAGAAAACAGGGTTACTAAGGGCGATAATA
1 ACTTAAACTCATAAGAGAAAACAGAAAAGAAAATACAAAAAACAGGGTTACTAAGGGCAAAAATA
* * *
89654 GGGTTA-GTGGTGAACTTAAACT
66 GGGTTAGGGGGAGAACATAAACT
* *
89676 ACTTAAACTCATAAGAGAAAATAGAAAAGAAAATACAAAAAACAGGGTTACTAGGGGCAAAAATA
1 ACTTAAACTCATAAGAGAAAACAGAAAAGAAAATACAAAAAACAGGGTTACTAAGGGCAAAAATA
89741 GGGTTAGGGGGAGAACATAAACT
66 GGGTTAGGGGGAGAACATAAACT
*
89764 ACTTAAATTCATAAGA-AAATACAG
1 ACTTAAACTCATAAGAGAAA-ACAG
89788 GGTTACTAGG
Statistics
Matches: 96, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
87 65 0.68
88 31 0.32
ACGTcount: A:0.49, C:0.12, G:0.21, T:0.19
Consensus pattern (88 bp):
ACTTAAACTCATAAGAGAAAACAGAAAAGAAAATACAAAAAACAGGGTTACTAAGGGCAAAAATA
GGGTTAGGGGGAGAACATAAACT
Found at i:89865 original size:54 final size:56
Alignment explanation
Indices: 89784--89930 Score: 183
Period size: 55 Copynumber: 2.7 Consensus size: 56
89774 ATAAGAAAAT
* * *
89784 ACAGGGTTACTAGGGGTAAGAATGTGAACTTAAATTTAATA-GGGTTAGGGTGAAA
1 ACAGGGTTAATAGGGGTAAGAAGGTGAACTTAAACTTAATAGGGGTTAGGGTGAAA
* * * *
89839 ATAGGGTTATTA-GGGTAAGAAGGTGAACTTAAACTTATTAGGGGTTGGGGTGAAA
1 ACAGGGTTAATAGGGGTAAGAAGGTGAACTTAAACTTAATAGGGGTTAGGGTGAAA
* * *
89894 ACAAGGTTAATAGGGGTTAG-GGGTGAACTTAAACTTA
1 ACAGGGTTAATAGGGGTAAGAAGGTGAACTTAAACTTA
89931 CTAAGTGTTA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
54 25 0.32
55 48 0.61
56 6 0.08
ACGTcount: A:0.35, C:0.05, G:0.32, T:0.28
Consensus pattern (56 bp):
ACAGGGTTAATAGGGGTAAGAAGGTGAACTTAAACTTAATAGGGGTTAGGGTGAAA
Found at i:89876 original size:28 final size:28
Alignment explanation
Indices: 89797--89881 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 28
89787 GGGTTACTAG
* * *
89797 GGGTAAGAATGTGAACTTAAATTTAATA
1 GGGTAAGAAGGTGAACTTAAACTTATTA
* ** ***
89825 GGGTTAG--GGTGAAAATAGGGTTATTA
1 GGGTAAGAAGGTGAACTTAAACTTATTA
89851 GGGTAAGAAGGTGAACTTAAACTTATTA
1 GGGTAAGAAGGTGAACTTAAACTTATTA
89879 GGG
1 GGG
89882 GTTGGGGTGA
Statistics
Matches: 41, Mismatches: 14, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
26 18 0.44
28 23 0.56
ACGTcount: A:0.36, C:0.04, G:0.31, T:0.29
Consensus pattern (28 bp):
GGGTAAGAAGGTGAACTTAAACTTATTA
Found at i:89949 original size:36 final size:35
Alignment explanation
Indices: 89906--89981 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 35
89896 AAGGTTAATA
* *
89906 GGGGTTAGGGGTGAACTTAAACTTACTAAGTGTTAG
1 GGGGTTAGGGGTGAACTTAAACTTACAAAGGGTT-G
*
89942 GGGGTTAGGGGTGAATTTAAACTTACAAAGGGTTG
1 GGGGTTAGGGGTGAACTTAAACTTACAAAGGGTTG
89977 GGGGT
1 GGGGT
89982 GAATTAAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 6 0.16
36 31 0.84
ACGTcount: A:0.26, C:0.07, G:0.38, T:0.29
Consensus pattern (35 bp):
GGGGTTAGGGGTGAACTTAAACTTACAAAGGGTTG
Found at i:90081 original size:52 final size:52
Alignment explanation
Indices: 90019--90118 Score: 173
Period size: 52 Copynumber: 1.9 Consensus size: 52
90009 TTACCAAAGG
*
90019 CTTACCAAGGGTGAAAATATAGTAATAGAGTTGGAAGTAAATTTGAATTTAT
1 CTTACCAAGGGTGAAAATAGAGTAATAGAGTTGGAAGTAAATTTGAATTTAT
* *
90071 CTTACTAAGGGTGAAAATAGAGTAATAGAGTTGGAGGTAAATTTGAAT
1 CTTACCAAGGGTGAAAATAGAGTAATAGAGTTGGAAGTAAATTTGAAT
90119 ATATAAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (52 bp):
CTTACCAAGGGTGAAAATAGAGTAATAGAGTTGGAAGTAAATTTGAATTTAT
Found at i:90865 original size:23 final size:23
Alignment explanation
Indices: 90835--90909 Score: 80
Period size: 29 Copynumber: 3.0 Consensus size: 23
90825 TTATTTTCTC
*
90835 TAAATATATACTAATTTTAAATT
1 TAAATATATAGTAATTTTAAATT
90858 TAAATATATAGTAAATTTAATTCTAAATT
1 TAAATATATAGT-AA--T--TT-TAAATT
90887 TAAATATAT-GTAATTTTAAATT
1 TAAATATATAGTAATTTTAAATT
90909 T
1 T
90910 TTAAAATATG
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
22 7 0.16
23 13 0.29
24 2 0.04
25 1 0.02
26 1 0.02
27 2 0.04
28 4 0.09
29 15 0.33
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (23 bp):
TAAATATATAGTAATTTTAAATT
Found at i:90879 original size:29 final size:28
Alignment explanation
Indices: 90846--90910 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 28
90836 AAATATATAC
90846 TAATTTTAAATTTAAATATATAGTAAATT
1 TAATTTTAAATTTAAATATAT-GTAAATT
* *
90875 TAATTCTAAATTTAAATATATGTAATTT
1 TAATTTTAAATTTAAATATATGTAAATT
90903 TAAATTTT
1 T-AATTTT
90911 TAAAATATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 7 0.22
29 25 0.78
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (28 bp):
TAATTTTAAATTTAAATATATGTAAATT
Done.