Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001953.1 Hibiscus syriacus cultivar Beakdansim tig00003953_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: 86567
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:834 original size:55 final size:55
Alignment explanation
Indices: 775--1388 Score: 751
Period size: 55 Copynumber: 11.2 Consensus size: 55
765 CTCGATTGCA
* * *
775 GAAGATTATTCAAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGATTGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * *
830 GAAGATTGTTTGAGTCTTATACTCTCTGAAGAAATAGGGAGTAGACACGATTGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
** * ***
885 GAAGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACAATTACA
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
*
940 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGTCAC-ATTTGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGTT
* * *
995 GAAGATTGTTCGAGTCCTATACTCTCTGAAGAAATAGGGAGCA-AAACGATTGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* *
1049 GAAGATTGTTTGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * *
1104 GAAGATTGTTCGAGTCTTATACTCTCAGAAGAAATAGGGAGTAGACAC-ATTTGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGTT
* * **
1159 AAAGATTATTCGAGTCTTATACTCTCTGAAGGAATAAAGAGCAGACACGATTTGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGTT
* *
1215 GAAGATTATTCGAGTCTTATACTCTCTGAA-AGAATAGGGAGCTGACACGTTTGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGA-AATAGGGAGCAGACACGATTGTT
* * * * * * *
1270 GAAG---A-TCGAATCCTAAACTCTCTTAAGGAATAGGGAGCGGACACGTTTGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * * * *
1321 GAAGATTTGTTCAAGTCCTATACTCTCTGAA-AGAATAGGGAGCGGACACGTTTGTT
1 GAAGA-TTATTCGAGTCTTATACTCTCTGAAGA-AATAGGGAGCAGACACGATTGTT
1377 GAAGATCTATTC
1 GAAGAT-TATTC
1389 TATACTCCCT
Statistics
Matches: 490, Mismatches: 55, Indels: 27
0.86 0.10 0.05
Matches are distributed among these distances:
51 43 0.09
52 1 0.00
54 50 0.10
55 297 0.61
56 99 0.20
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (55 bp):
GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
Found at i:1108 original size:219 final size:220
Alignment explanation
Indices: 775--1369 Score: 810
Period size: 219 Copynumber: 2.7 Consensus size: 220
765 CTCGATTGCA
* * *
775 GAAGATTATTCAAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGATTGTTGAAGATTGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCA-ACACGATTGTTGAAGATTGTT
* *
840 TGAGTCTTATACTCTCTGAAGAAATAGGGAGTAGACACGATTGTTGAAGATTGCTCGAGTCTTAT
65 TGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTAT
905 ACTCTCTGAAGAAATAGGGAGCAGACACAATT-ACAGAAGATTATTCGAGTCTTATACTCTCTGA
130 ACTCTCTGAAGAAATAGGGAGCAGACACAATTGACA-AAGATTATTCGAGTCTTATACTCTCTGA
** *
969 AGAAATAGGGAGCAGTCAC-ATTTGTT
194 AGAAATAAAGAGCAGACACGATTTGTT
* * *
995 GAAGATTGTTCGAGTCCTATACTCTCTGAAGAAATAGGGAGCAAAACGATTGTTGAAGATTGTTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAACACGATTGTTGAAGATTGTTT
1060 GAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATA
66 GAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATA
* * * **
1125 CTCTCAGAAGAAATAGGGAGTAGACACATTTGTTAAAGATTATTCGAGTCTTATACTCTCTGAAG
131 CTCTCTGAAGAAATAGGGAGCAGACACAATTGACAAAGATTATTCGAGTCTTATACTCTCTGAAG
*
1190 GAATAAAGAGCAGACACGATTTGTT
196 AAATAAAGAGCAGACACGATTTGTT
* *
1215 GAAGATTATTCGAGTCTTATACTCTCTGAA-AGAATAGGGAGCTGACACGTTTGTTGAAGA----
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGA-AATAGGGAGC-AACACGATTGTTGAAGATTGT
* * * * * * * * * *
1275 TCGAATCCTAAACTCTCTTAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTTGTTCAAGTCCT
64 TTGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGA-TTGTTCGAGTCTT
*
1340 ATACTCTCTGAA-AGAATAGGGAGCGGACAC
128 ATACTCTCTGAAGA-AATAGGGAGCAGACAC
1370 GTTTGTTGAA
Statistics
Matches: 334, Mismatches: 35, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
217 44 0.13
218 36 0.11
219 156 0.47
220 84 0.25
221 14 0.04
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (220 bp):
GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAACACGATTGTTGAAGATTGTTT
GAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATA
CTCTCTGAAGAAATAGGGAGCAGACACAATTGACAAAGATTATTCGAGTCTTATACTCTCTGAAG
AAATAAAGAGCAGACACGATTTGTT
Found at i:1655 original size:3 final size:3
Alignment explanation
Indices: 1647--1700 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
1637 TTAAAATATA
*
1647 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAA TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1693 TAT TAT TA
1 TAT TAT TA
1701 CTAATAATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:3720 original size:20 final size:20
Alignment explanation
Indices: 3695--3826 Score: 97
Period size: 20 Copynumber: 6.5 Consensus size: 20
3685 TGGGAAAATT
3695 GCAATGCGATACTGACTATC
1 GCAATGCGATACTGACTATC
* *
3715 GCAATGTGATACTTACTATC
1 GCAATGCGATACTGACTATC
* *
3735 GCAATGCGATAAT-ACAAAATC
1 GCAATGCGATACTGAC--TATC
* * *
3756 GCAACGAGATACTGACTTTC
1 GCAATGCGATACTGACTATC
* * *
3776 GCAACGCGATTCTGACTTTC
1 GCAATGCGATACTGACTATC
* * *
3796 GTAACGCGATAAT-ACATAATC
1 GCAATGCGATACTGAC-T-ATC
3817 GCAATGCGAT
1 GCAATGCGAT
3827 TTTCAAAGCG
Statistics
Matches: 89, Mismatches: 18, Indels: 9
0.77 0.16 0.08
Matches are distributed among these distances:
19 4 0.04
20 60 0.67
21 23 0.26
22 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (20 bp):
GCAATGCGATACTGACTATC
Found at i:3754 original size:61 final size:61
Alignment explanation
Indices: 3689--3826 Score: 168
Period size: 61 Copynumber: 2.3 Consensus size: 61
3679 GCGAATTGGG
* * * * *
3689 AAAATTGCAATGCGATACTGACTATCGCAATGTGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * * *
3750 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGTAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
3811 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
3827 TTTCAAAGCG
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:4022 original size:22 final size:22
Alignment explanation
Indices: 3994--4037 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3984 CACTCTCTCA
3994 CCCATCTCCGACAAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
* *
4016 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
4038 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:4354 original size:20 final size:20
Alignment explanation
Indices: 4302--4358 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
4292 GATTCTCTCA
**
4302 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCATTTTCGCG
*
4322 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCG
**
4342 TTGCGATTTTCATTTTC
1 TTGCGATAGTCATTTTC
4359 AGAAACTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.44
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:4549 original size:25 final size:24
Alignment explanation
Indices: 4495--4549 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
4485 TGTTTATTAT
* *
4495 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
4519 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
4545 TGTTT
1 TGTTT
4550 ATTGTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:5696 original size:18 final size:18
Alignment explanation
Indices: 5675--5719 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5665 TCCACTTCGG
*
5675 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
5693 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
5711 GAGCCATCA
1 GAGCCATCA
5720 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:6245 original size:19 final size:20
Alignment explanation
Indices: 6191--6257 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
6181 TAGTTTACTT
* *
6191 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
6211 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
6231 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
6250 TCGCAACG
1 TCGCAACG
6258 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:6293 original size:25 final size:25
Alignment explanation
Indices: 6261--6312 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
6251 CGCAACGACA
*
6261 AAATCGCAATGCGAAATGAAATCGC
1 AAATCGCAACGCGAAATGAAATCGC
6286 AAATCGCAACGCGAAATGAAATCGC
1 AAATCGCAACGCGAAATGAAATCGC
6311 AA
1 AA
6313 TGCGATTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.13
Consensus pattern (25 bp):
AAATCGCAACGCGAAATGAAATCGC
Found at i:6348 original size:14 final size:14
Alignment explanation
Indices: 6329--6386 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
6319 TTGTGTTTCG
6329 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
6343 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
6359 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
6375 CGTTGCGATTTT
1 CGTTGCGATTTT
6387 CATTTCCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:6367 original size:32 final size:33
Alignment explanation
Indices: 6324--6434 Score: 163
Period size: 32 Copynumber: 3.4 Consensus size: 33
6314 GCGATTTGTG
*
6324 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
6356 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
* *
6389 TTTC-CATTGCAATTTTGTCGTTGCAATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
* *
6421 TTTCACGTTGCGAT
1 TTTCGCATTGCGAT
6435 AGTCATTTTC
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
32 56 0.78
33 16 0.22
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.48
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:6368 original size:18 final size:18
Alignment explanation
Indices: 6345--6403 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
6335 GATTTTGTCG
6345 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
*
6363 TTGCGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
6377 TTGCGATTTTCATTTC-CA
1 TTGCGA-TTTCATTTCGCA
*
6395 TTGCAATTT
1 TTGCGATTT
6404 TGTCGTTGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 4 0.12
17 6 0.18
18 14 0.42
ACGTcount: A:0.15, C:0.19, G:0.17, T:0.49
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Found at i:6910 original size:41 final size:41
Alignment explanation
Indices: 6814--6901 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
6804 GACTCACCTG
* * *
6814 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTA
* *
6856 TCCTCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
6897 TCATC
1 TCATC
6902 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
Found at i:8333 original size:14 final size:14
Alignment explanation
Indices: 8314--8349 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
8304 ATTGTTTAAT
8314 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
8328 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
8342 TGATTTGT
1 TGATTTGT
8350 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:8510 original size:19 final size:19
Alignment explanation
Indices: 8486--8553 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
8476 ATCGCAACGA
8486 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
8505 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
8524 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
8538 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
8554 TTTTTCGTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:9165 original size:12 final size:12
Alignment explanation
Indices: 9146--9179 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
9136 CTCTCCGGCG
9146 ACATCCGTTCCT
1 ACATCCGTTCCT
*
9158 ATATCCGTTCCT
1 ACATCCGTTCCT
9170 ACATCC-TTCC
1 ACATCCGTTCC
9180 CCATCTGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:9972 original size:12 final size:12
Alignment explanation
Indices: 9955--9979 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9945 ATATAATCCT
9955 GAAGAAGAAAAA
1 GAAGAAGAAAAA
9967 GAAGAAGAAAAA
1 GAAGAAGAAAAA
9979 G
1 G
9980 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:12286 original size:19 final size:19
Alignment explanation
Indices: 12264--12396 Score: 98
Period size: 19 Copynumber: 7.8 Consensus size: 19
12254 GGAAATTACT
12264 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
12283 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
12297 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
12316 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
12330 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
12349 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
12363 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
12382 ATCGCAACGCGAAAT
1 ATCGCAATGCGAAAT
12397 TAAATTCGCG
Statistics
Matches: 86, Mismatches: 13, Indels: 30
0.67 0.10 0.23
Matches are distributed among these distances:
14 27 0.31
15 3 0.03
16 6 0.07
17 6 0.07
18 3 0.03
19 41 0.48
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:12306 original size:33 final size:33
Alignment explanation
Indices: 12264--12390 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
12254 GGAAATTACT
12264 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
12297 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
12329 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
12363 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
12391 CGAAATTAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:12371 original size:66 final size:66
Alignment explanation
Indices: 12265--12391 Score: 245
Period size: 66 Copynumber: 1.9 Consensus size: 66
12255 GAAATTACTA
12265 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
12330 T
66 T
*
12331 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGC
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGC
12392 GAAATTAAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
T
Found at i:12405 original size:19 final size:19
Alignment explanation
Indices: 12244--12396 Score: 84
Period size: 19 Copynumber: 8.8 Consensus size: 19
12234 CCTAATGTCT
* **
12244 ATCGCAACGCGGAAATTACT
1 ATCGCAACGC-GAAATGAAA
*
12264 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
12283 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
12297 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
12316 ATCGCAACGC----T-AAT
1 ATCGCAACGCGAAATGAAA
* *
12330 TTCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
**
12349 ATCGCAA--CG--A-GGGA
1 ATCGCAACGCGAAATGAAA
*
12363 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
12382 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
12397 TAAATTCGCG
Statistics
Matches: 101, Mismatches: 17, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
14 29 0.29
15 3 0.03
16 4 0.04
17 4 0.04
18 3 0.03
19 49 0.49
20 9 0.09
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:12422 original size:14 final size:14
Alignment explanation
Indices: 12405--12457 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
12395 ATTAAATTCG
12405 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
12419 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
12438 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
12452 CGTTGC
1 CGTTGC
12458 AATTTTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 16 0.50
16 3 0.09
17 3 0.09
19 10 0.31
ACGTcount: A:0.08, C:0.26, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:12443 original size:19 final size:19
Alignment explanation
Indices: 12419--12479 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
12409 GCGATTCTCT
12419 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
12438 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
12452 CGTTGCAATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
12471 CATTGCGAT
1 CGTTGCGAT
12480 AGTACTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
14 9 0.28
16 3 0.09
17 3 0.09
19 17 0.53
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:12443 original size:33 final size:33
Alignment explanation
Indices: 12401--12479 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
12391 CGAAATTAAA
*
12401 TTCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTCTCTCGTTGCAATTTTCAT
12434 TTCGCGTTGCGATTCTCTCGTTGCAATTTTCAT
1 TTCGCGTTGCGATTCTCTCGTTGCAATTTTCAT
*
12467 TTCGCATTGCGAT
1 TTCGCGTTGCGAT
12480 AGTACTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (33 bp):
TTCGCGTTGCGATTCTCTCGTTGCAATTTTCAT
Found at i:12604 original size:14 final size:14
Alignment explanation
Indices: 12585--12621 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
12575 CATCAATTAA
12585 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
12599 ACAAATCACCTTTT
1 ACAAATCAACTTTT
12613 ACAAATCAA
1 ACAAATCAA
12622 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:14036 original size:42 final size:41
Alignment explanation
Indices: 13977--14179 Score: 140
Period size: 42 Copynumber: 4.8 Consensus size: 41
13967 GTGAATCGGG
* *
13977 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGAAAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGAAAGTGGC
* * *
14019 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGAAAGTGGC
* * * * * * *
14061 CACTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGAAAGTGGC
* * * *
14103 CTCTTGAACGGTGAGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGAAAGTGGC
* * * * *
14145 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGA
14180 CAGGCGAGTC
Statistics
Matches: 122, Mismatches: 31, Indels: 16
0.72 0.18 0.09
Matches are distributed among these distances:
41 9 0.07
42 102 0.84
43 11 0.09
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGAAAGTGGC
Found at i:14043 original size:21 final size:21
Alignment explanation
Indices: 13977--14043 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
13967 GTGAATCGGG
*
13977 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
13997 CCTCTTCAACGATGAAAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
14019 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
14040 CTCT
1 CTCT
14044 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:14127 original size:21 final size:21
Alignment explanation
Indices: 13977--14127 Score: 51
Period size: 21 Copynumber: 7.2 Consensus size: 21
13967 GTGAATCGGG
* *
13977 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGAGAGGGGA
* * * * *
13997 CCTCTTCAACGATGAAAGTGGC
1 -CTCTTGAACGGTGAGAGGGGA
*
14019 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGAGAGGGGA
* * *
14040 CTCTCG-A-GGAATGATAGGGGC
1 CTCTTGAACGG--TGAGAGGGGA
* * * *
14061 CACTTCAACGAT-AGGAGTGGA
1 CTCTTGAACGGTGA-GAGGGGA
* * * *
14082 CTCTTG-AGGGATGACAGTGGC
1 CTCTTGAACGG-TGAGAGGGGA
14103 CTCTTGAACGGTGAGAGGGGA
1 CTCTTGAACGGTGAGAGGGGA
14124 CTCT
1 CTCT
14128 CGAGGAATGA
Statistics
Matches: 87, Mismatches: 34, Indels: 18
0.63 0.24 0.13
Matches are distributed among these distances:
19 2 0.02
20 4 0.05
21 73 0.84
22 7 0.08
23 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGAGAGGGGA
Found at i:14139 original size:84 final size:84
Alignment explanation
Indices: 14007--14182 Score: 325
Period size: 84 Copynumber: 2.1 Consensus size: 84
13997 CCTCTTCAAC
* *
14007 GATGAAAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCACTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGAGAGGGGACTCTCGAGGAATGATAGGGGCCACTTCAACGA
14072 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
*
14091 GATGACAGTGGCCTCTTGAACGGTGAGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGAGAGGGGACTCTCGAGGAATGATAGGGGCCACTTCAACGA
14156 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
14175 GATGACAG
1 GATGACAG
14183 GCGAGTCGGG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.25, C:0.17, G:0.38, T:0.20
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGAGAGGGGACTCTCGAGGAATGATAGGGGCCACTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:14576 original size:91 final size:90
Alignment explanation
Indices: 14401--14585 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
14391 ATTTCAAACT
* *
14401 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAAACAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
14466 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
14494 TTCAAACAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAAACAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
14558 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
14585 T
1 T
14586 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.48
93 18 0.21
95 27 0.31
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAAACAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:16311 original size:20 final size:19
Alignment explanation
Indices: 16266--16406 Score: 86
Period size: 19 Copynumber: 7.8 Consensus size: 19
16256 TCTTTTGGTT
*
16266 GAAATGAAAATTGCAACGA
1 GAAATGAAAATCGCAACGA
* *
16285 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
16306 GAAATGACTATCGTAACGA
1 GAAATGAAAATCGCAACGA
*
16325 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
16339 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
16358 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
16372 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
16391 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
16407 TGCGATTTTG
Statistics
Matches: 94, Mismatches: 16, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
14 18 0.19
16 4 0.04
17 4 0.04
19 39 0.41
20 27 0.29
21 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:16348 original size:33 final size:33
Alignment explanation
Indices: 16291--16389 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
16281 ACGAGATAAT
*
16291 GAGAATCGCAACGCGGAAATGACTATCGTAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
16325 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
16358 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
16390 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 46 0.77
34 14 0.23
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:16383 original size:19 final size:19
Alignment explanation
Indices: 16361--16411 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
16351 GCGACGAGAG
16361 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
16380 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
16399 AATCGCAATGCGA
1 AATCGCAACGCGA
16412 TTTTGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:16434 original size:19 final size:19
Alignment explanation
Indices: 16407--16450 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
16397 AAAATCGCAA
**
16407 TGCGATTTTGGTTTCGCG-
1 TGCGATTTTTATTTCGCGT
16425 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
16444 TGCGATT
1 TGCGATT
16451 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:17006 original size:20 final size:20
Alignment explanation
Indices: 16981--17033 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
16971 GCGCTATGTA
16981 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
*
17001 AATCGCGTTACGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
17021 TATCTCGTTGCGA
1 AATCGCGTTGCGA
17034 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:17067 original size:20 final size:20
Alignment explanation
Indices: 17042--17095 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
17032 GATTTTGTAT
17042 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
17062 TATCGCATTACGATAGTCAG
1 TATCGCATTGCGATAGTAAG
17082 TATCGCATTGCGAT
1 TATCGCATTGCGAT
17096 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:17080 original size:61 final size:61
Alignment explanation
Indices: 16982--17098 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
16972 CGCTATGTAA
* * * * *
16982 ATCGCGTTGCGAAAGTCAGAATCGCGTTACGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
17043 ATCGCATTGCGATAGTAAGTATCGCATTACGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTT
17099 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:17114 original size:61 final size:61
Alignment explanation
Indices: 16982--17116 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
16972 CGCTATGTAA
* * * * * ** *
16982 ATCGCGTTGCGAAAGTCAGAATCGCGTTACGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
17043 ATCGCATTGCGATAGTAAGTATCGCATTACGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
17105 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
17117 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:17227 original size:21 final size:21
Alignment explanation
Indices: 17166--17219 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
17156 ACTGTAGACC
17166 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTCCAACT
17187 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTCCAACT
17208 ATCGCAACGCGA
1 ATCGCAACGCGA
17220 AATGCAACGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTCCAACT
Found at i:19576 original size:2 final size:2
Alignment explanation
Indices: 19569--19593 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19559 GATATGACCC
19569 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
19594 CGGGTCGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21491 original size:19 final size:19
Alignment explanation
Indices: 21467--21511 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
21457 ATTTCAGTTT
*
21467 AGAAACGTTGTTTTATTTA
1 AGAAACGCTGTTTTATTTA
21486 AGAAACGCTGTTTTATTTA
1 AGAAACGCTGTTTTATTTA
21505 AGAAACG
1 AGAAACG
21512 AGTTGAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (19 bp):
AGAAACGCTGTTTTATTTA
Found at i:21598 original size:13 final size:13
Alignment explanation
Indices: 21580--21605 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21570 ATTTCATTTG
21580 CAAGCATTAGGAT
1 CAAGCATTAGGAT
21593 CAAGCATTAGGAT
1 CAAGCATTAGGAT
21606 TTGAATTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
CAAGCATTAGGAT
Found at i:33345 original size:18 final size:18
Alignment explanation
Indices: 33308--33348 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
33298 AGAACATCAC
* * *
33308 GAGGAACAAGCACGAGCA
1 GAGGAACAAGAACAACCA
33326 GAGGAACAAGAACAACCA
1 GAGGAACAAGAACAACCA
33344 GAGGA
1 GAGGA
33349 TCAAATGCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.20, G:0.32, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGAACAACCA
Found at i:35376 original size:40 final size:40
Alignment explanation
Indices: 35316--35539 Score: 148
Period size: 40 Copynumber: 5.5 Consensus size: 40
35306 CCATCGATTG
* *
35316 TGACTTTGCATCCTTCAGAGGAAGGAGTAAGATCGTCACA
1 TGACTTAGCATCCTTTAGAGGAAGGAGTAAGATCGTCACA
* *
35356 TGACTTAGCATCCTTTAGAGGAATGAGTAAGATCGTCCCCA
1 TGACTTAGCATCCTTTAGAGGAAGGAGTAAGATCGT-CACA
* * * * ** ***
35397 -GAATCAGCATCCTTCAGAAAGAGAAGCGAATCACCCATCGTTTGA
1 TGACTTAGCATCCTTTAG--AG-GAAG-GAGT-A-AGATCGTCACA
* ** *
35442 -GACTTAACATCCTTTAGAAAAAGAAGTAAGATCGTCACA
1 TGACTTAGCATCCTTTAGAGGAAGGAGTAAGATCGTCACA
* ** *
35481 TGACTTAGCACCCTTTAGAGGAATAAGTAAGATCGTCCCA
1 TGACTTAGCATCCTTTAGAGGAAGGAGTAAGATCGTCACA
* *
35521 AGA-TTCATCATCCTTTAGA
1 TGACTT-AGCATCCTTTAGA
35540 AAGAAGAGTA
Statistics
Matches: 139, Mismatches: 36, Indels: 18
0.72 0.19 0.09
Matches are distributed among these distances:
39 8 0.06
40 94 0.68
41 5 0.04
42 5 0.04
43 4 0.03
44 3 0.02
45 15 0.11
46 5 0.04
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (40 bp):
TGACTTAGCATCCTTTAGAGGAAGGAGTAAGATCGTCACA
Found at i:35410 original size:125 final size:125
Alignment explanation
Indices: 35188--35535 Score: 385
Period size: 125 Copynumber: 2.8 Consensus size: 125
35178 ACCCCACCGG
* * * * * *
35188 TTGTGACTTAGCATCCTTAATAGGTAGTAGTAAGATTGTCTCACGACTTAGCATCCTTTAGAGGA
1 TTGTGACTTAGCATCCTTAAGAGGAAGAAGTAAGATCGTCACATGACTTAGCATCCTTTAGAGGA
* * * ** * * * *
35253 ATAAGAAAAATCTTGTCGAGATTCAGTATCCTTCAAAAAACAGAA-C-AGATTATCCATCGA
66 ATAAGTAAGATCGTCCCAAGATTCAGCATCCTTC-AAAAACAGAAGCGA-ATCACCCATCGA
* * *
35313 TTGTGACTTTGCATCCTTCAGAGGAAGGAGTAAGATCGTCACATGACTTAGCATCCTTTAGAGGA
1 TTGTGACTTAGCATCCTTAAGAGGAAGAAGTAAGATCGTCACATGACTTAGCATCCTTTAGAGGA
* * * * * *
35378 ATGAGTAAGATCGTCCCCAGAATCAGCATCCTTCAGAAAGAGAAGCGAATCACCCATCGT
66 ATAAGTAAGATCGTCCCAAGATTCAGCATCCTTCAAAAACAGAAGCGAATCACCCATCGA
* * * ** *
35438 TTGAGACTTAACATCCTTTAGAAAAAGAAGTAAGATCGTCACATGACTTAGCACCCTTTAGAGGA
1 TTGTGACTTAGCATCCTTAAGAGGAAGAAGTAAGATCGTCACATGACTTAGCATCCTTTAGAGGA
*
35503 ATAAGTAAGATCGTCCCAAGATTCATCATCCTT
66 ATAAGTAAGATCGTCCCAAGATTCAGCATCCTT
35536 TAGAAAGAAG
Statistics
Matches: 187, Mismatches: 34, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
124 8 0.04
125 178 0.95
126 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (125 bp):
TTGTGACTTAGCATCCTTAAGAGGAAGAAGTAAGATCGTCACATGACTTAGCATCCTTTAGAGGA
ATAAGTAAGATCGTCCCAAGATTCAGCATCCTTCAAAAACAGAAGCGAATCACCCATCGA
Found at i:35958 original size:15 final size:15
Alignment explanation
Indices: 35938--35970 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
35928 TTATATGTTA
35938 TATGACAT-TTTTTAT
1 TATGACATATTTTT-T
35953 TATGACATATTTTTT
1 TATGACATATTTTTT
35968 TAT
1 TAT
35971 TATTATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (15 bp):
TATGACATATTTTTT
Found at i:36024 original size:31 final size:33
Alignment explanation
Indices: 35986--36083 Score: 94
Period size: 31 Copynumber: 2.9 Consensus size: 33
35976 TTATATATTA
* *
35986 AAAATATATATTGTAGT-ATA-TATATTATTTT
1 AAAATATATATTATAATAATAGTATATTATTTT
36017 AAAATATATA-TATAATAATAGGTATATTATTTT
1 AAAATATATATTATAATAATA-GTATATTATTTT
* *
36050 AATATATATATATTATTTAAAAATATTATATTAT
1 AA-A-ATATATATTA--TAATAATAGTATATTAT
36084 AGATATATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
30 4 0.07
31 13 0.24
33 13 0.24
34 1 0.02
35 7 0.13
36 2 0.04
37 8 0.15
38 7 0.13
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (33 bp):
AAAATATATATTATAATAATAGTATATTATTTT
Found at i:36138 original size:13 final size:12
Alignment explanation
Indices: 36109--36144 Score: 63
Period size: 13 Copynumber: 2.9 Consensus size: 12
36099 AATATCTCAG
36109 TATATATTATTA
1 TATATATTATTA
36121 TATATATTATTAA
1 TATATATTATT-A
36134 TATATATTATT
1 TATATATTATT
36145 TTTAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATATATTATTA
Found at i:38211 original size:55 final size:55
Alignment explanation
Indices: 38127--38268 Score: 194
Period size: 55 Copynumber: 2.6 Consensus size: 55
38117 ACATTCAAGT
* * * ** *
38127 GATTCATAAAGAGGGACGTCCGATGAATGAAGAAATTTGAACTTGATTGAAGAAC
1 GATTCATGAAGAAGGACATCCGATGAATGAAGAAAACTGAAATTGATTGAAGAAC
*
38182 GATTCATGAAGATGGACATCCGATGAATGAAGAAAACTGAAATTGATTGAAGAAC
1 GATTCATGAAGAAGGACATCCGATGAATGAAGAAAACTGAAATTGATTGAAGAAC
* * *
38237 GATCCATGAAGAAAGACATTCGATGAATGAAG
1 GATTCATGAAGAAGGACATCCGATGAATGAAG
38269 TTTGAAGTTG
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 77 1.00
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.22
Consensus pattern (55 bp):
GATTCATGAAGAAGGACATCCGATGAATGAAGAAAACTGAAATTGATTGAAGAAC
Found at i:38649 original size:13 final size:13
Alignment explanation
Indices: 38631--38655 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38621 TTTGCACTTG
38631 CATTTAGCATTTA
1 CATTTAGCATTTA
38644 CATTTAGCATTT
1 CATTTAGCATTT
38656 GCATCGTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (13 bp):
CATTTAGCATTTA
Found at i:43968 original size:55 final size:55
Alignment explanation
Indices: 43898--44671 Score: 1018
Period size: 55 Copynumber: 14.1 Consensus size: 55
43888 CCCGATTGCA
* * *
43898 GAAGATTATTCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* *
43953 GAAGATTGTTTGAGTCTTATACTCTCTGAAGAAATAGGGAGTAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * ***
44008 GAAGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACAATTACA
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * *
44063 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGTCACGTTTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* *
44118 GAAGATTGTTCGAGTCCTATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* ** * **
44173 GAAGATTGTTCGAGTCTTATACTCTTTGAAGGGATAGGGAGCAGACGCGATTGCA
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * *
44228 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAAGAAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * * *
44283 GAAGATTGTTTGAGTCTTATACTCTCTGAAAAAATAAGGAGCAAACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* *
44338 GAAGATTGTTTGAGTCTTATACTCTCTGAATAAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * *
44393 GAAGATTGTTCGAGTCTTATACTCTCAGAAGAAATAGGGAGTAGACACGTTTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * * **
44448 AAAGATTATTCGAGTCTTATACTCTCTGAAGGAATAAAGAGCAGACACGATTTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGTT
* * * *
44504 GAAGATTATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCTGACACGTTTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * * * * *
44559 GAAGA----TCGAATCCTAAACTCTCTGAAGGAATAGGGAGCATACACGTTTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * * *
44610 GAAGATTTGTTCAAGTCCTATACTCTCTGAA-AGAATAGGGAGCGGACACGTTTGTT
1 GAAGA-TTGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGAGCAGACACGATTGTT
44666 GAAGAT
1 GAAGAT
44672 CTAGTTCTAT
Statistics
Matches: 633, Mismatches: 79, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
51 46 0.07
55 493 0.78
56 94 0.15
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
Found at i:44961 original size:3 final size:3
Alignment explanation
Indices: 44943--44999 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
44933 TAAAAATATA
*
44943 TAT TA- TAT TGAT TAT TAT TAT TAT TAT TA- TAT TAA TA- TAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44986 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
45000 CTAATAATTT
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
2 6 0.12
3 40 0.82
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:48935 original size:2 final size:2
Alignment explanation
Indices: 48928--48980 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
48918 GATATGACCC
48928 AT AT AT AT 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 AT AT AT AT
48970 AT AT AT AT AT A
1 AT AT AT AT AT A
48981 CGGGTCGTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50887 original size:19 final size:19
Alignment explanation
Indices: 50865--50901 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
50855 TTAGAAATGT
50865 TGTTTTATTTAAGAAACGC
1 TGTTTTATTTAAGAAACGC
50884 TGTTTTATTTAAGAAACG
1 TGTTTTATTTAAGAAACG
50902 AGTTGAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.43
Consensus pattern (19 bp):
TGTTTTATTTAAGAAACGC
Found at i:50988 original size:13 final size:13
Alignment explanation
Indices: 50970--50995 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50960 ATTTCATTTG
50970 CAAGCATTAGGAT
1 CAAGCATTAGGAT
50983 CAAGCATTAGGAT
1 CAAGCATTAGGAT
50996 TTGAATTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
CAAGCATTAGGAT
Found at i:62546 original size:18 final size:17
Alignment explanation
Indices: 62519--62554 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
62509 AATTATATTT
62519 ATTTTGATTCACGTTTA
1 ATTTTGATTCACGTTTA
62536 ATTTCTGATTCACGTTTA
1 ATTT-TGATTCACGTTTA
62554 A
1 A
62555 ATCTTTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.50
Consensus pattern (17 bp):
ATTTTGATTCACGTTTA
Found at i:66254 original size:11 final size:11
Alignment explanation
Indices: 66238--66263 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
66228 TTAAGAGAAA
66238 AAATAATAAAT
1 AAATAATAAAT
66249 AAATAATAAAT
1 AAATAATAAAT
66260 AAAT
1 AAAT
66264 TAAAGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:67463 original size:13 final size:13
Alignment explanation
Indices: 67445--67498 Score: 60
Period size: 12 Copynumber: 4.3 Consensus size: 13
67435 TGAGGCCTGC
67445 AAAATAATTAATA
1 AAAATAATTAATA
67458 AAAAT-ATTAATA
1 AAAATAATTAATA
67470 ATAAATAA-TAATA
1 A-AAATAATTAATA
* *
67483 AATATAAAT-ATA
1 AAAATAATTAATA
67495 AAAA
1 AAAA
67499 ATTATATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
12 19 0.53
13 16 0.44
14 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATAATTAATA
Found at i:67478 original size:22 final size:23
Alignment explanation
Indices: 67447--67496 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
67437 AGGCCTGCAA
* *
67447 AATAATTAATAA-AAATATTAAT
1 AATAAATAATAATAAATATAAAT
67469 AATAAATAATAATAAATATAAAT
1 AATAAATAATAATAAATATAAAT
67492 -ATAAA
1 AATAAA
67497 AAATTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AATAAATAATAATAAATATAAAT
Found at i:67504 original size:16 final size:16
Alignment explanation
Indices: 67477--67532 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
67467 ATAATAAATA
*
67477 ATAATAAATATA-AAT
1 ATAAAAAATATATAAT
*
67492 ATAAAAAATTATATATTT
1 ATAAAAAA-TATATA-AT
*
67510 ATTAAAAACTATATAAT
1 A-TAAAAAATATATAAT
67527 ATAAAA
1 ATAAAA
67533 TTTTTAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
15 7 0.21
16 9 0.27
17 3 0.09
18 8 0.24
19 6 0.18
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAAAAAATATATAAT
Found at i:67505 original size:18 final size:18
Alignment explanation
Indices: 67484--67532 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
67474 ATAATAATAA
*
67484 ATATAAATATAAAAAATT
1 ATATAAATATAAAAAACT
** *
67502 ATATATTTATTAAAAACT
1 ATATAAATATAAAAAACT
67520 ATAT-AATATAAAA
1 ATATAAATATAAAA
67533 TTTTTAAAAC
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
ATATAAATATAAAAAACT
Found at i:67530 original size:41 final size:39
Alignment explanation
Indices: 67483--67565 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
67473 AATAATAATA
*
67483 AATAT-AAATATAAAAAATTATATATTTATTAAAAACTATAT
1 AATATAAAATATAAAAAACTAT-T-TTT-TTAAAAACTATAT
* **
67524 AATATAAAATTTTTAAAACTATTTTTTTAAAAACTATAT
1 AATATAAAATATAAAAAACTATTTTTTTAAAAACTATAT
67563 AAT
1 AAT
67566 TTTCAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
39 16 0.43
40 3 0.08
41 6 0.16
42 12 0.32
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (39 bp):
AATATAAAATATAAAAAACTATTTTTTTAAAAACTATAT
Found at i:67628 original size:26 final size:26
Alignment explanation
Indices: 67578--67667 Score: 137
Period size: 26 Copynumber: 3.4 Consensus size: 26
67568 TCAAAAAAAT
*
67578 GTTTTTAAAAATTATATATTATATATAA
1 GTTTTCAAAAATTATATA-T-TATATAA
67606 GTTTTCAAAAATTATATATTATATAA
1 GTTTTCAAAAATTATATATTATATAA
*
67632 GTTTTCAAAAACTATATATTATATAA
1 GTTTTCAAAAATTATATATTATATAA
67658 GTTTT-AAAAA
1 GTTTTCAAAAA
67668 CGTTTTCAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
25 5 0.08
26 37 0.62
27 1 0.02
28 17 0.28
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (26 bp):
GTTTTCAAAAATTATATATTATATAA
Found at i:67676 original size:37 final size:36
Alignment explanation
Indices: 67632--67767 Score: 175
Period size: 37 Copynumber: 3.7 Consensus size: 36
67622 TATTATATAA
*
67632 GTTTTCAAAAACTATATATTATATAAGTTTTAAAAAC
1 GTTTT-AAAAACTATATATTATATAAGTTTTAAAAAT
* *
67669 GTTTTCAAAAACTATATATTACATAAGTTTTCAAAAT
1 GTTTT-AAAAACTATATATTATATAAGTTTTAAAAAT
*
67706 GATTTTAAAAACTATATATTATATATA-TTTTCTAAAAT
1 G-TTTTAAAAACTATATATTATATA-AGTTTT-AAAAAT
*
67744 GTTTTAAAAATTATATATTATATA
1 GTTTTAAAAACTATATATTATATA
67768 CGTATTTTCA
Statistics
Matches: 90, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
37 79 0.88
38 11 0.12
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
GTTTTAAAAACTATATATTATATAAGTTTTAAAAAT
Found at i:68440 original size:33 final size:32
Alignment explanation
Indices: 68355--68478 Score: 153
Period size: 33 Copynumber: 3.8 Consensus size: 32
68345 ATAGTCGAAC
* *
68355 TCAAAGG-TCTTTGTGTTTCAAGAGGAACATTT
1 TCAAAGGTTTTTTGTGTTTCAAGA-GAACAGTT
*
68387 TCAAAGGTTTTTTTTATGTTTCAAGAGACACAGTT
1 TCAAAGG--TTTTTTGTGTTTCAAGAGA-ACAGTT
68422 TCAAAGGTTTTTTGTGTTTCAAGAGAA-ACGATT
1 TCAAAGGTTTTTTGTGTTTCAAGAGAACA-G-TT
68455 TCAAAGGTTTTTTGTGTTTCAAGA
1 TCAAAGGTTTTTTGTGTTTCAAGA
68479 TAATGTGTCT
Statistics
Matches: 82, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
31 1 0.01
32 9 0.11
33 44 0.54
34 2 0.02
35 26 0.32
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.41
Consensus pattern (32 bp):
TCAAAGGTTTTTTGTGTTTCAAGAGAACAGTT
Found at i:68603 original size:17 final size:17
Alignment explanation
Indices: 68583--68635 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
68573 TGTTTCAAGG
68583 GAAACTGTCTCAAGAGA
1 GAAACTGTCTCAAGAGA
* *
68600 GAAAATTTGTTTC-A-AGA
1 G-AAA-CTGTCTCAAGAGA
68617 GAAACTGTCTCAAGAGA
1 GAAACTGTCTCAAGAGA
68634 GA
1 GA
68636 TAAAACTTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 5 0.18
16 4 0.14
17 10 0.36
18 4 0.14
19 5 0.18
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.23
Consensus pattern (17 bp):
GAAACTGTCTCAAGAGA
Found at i:68616 original size:19 final size:19
Alignment explanation
Indices: 68559--68618 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
68549 AATGTCTCAA
*
68559 AAGAGATAAAACTTTGTTTC
1 AAGAGAGAAAA-TTTGTTTC
* *
68579 AAG-G-G-AAA-CTGTCTC
1 AAGAGAGAAAATTTGTTTC
68594 AAGAGAGAAAATTTGTTTC
1 AAGAGAGAAAATTTGTTTC
68613 AAGAGA
1 AAGAGA
68619 AACTGTCTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 9
0.69 0.11 0.20
Matches are distributed among these distances:
15 8 0.26
16 1 0.03
17 4 0.13
18 3 0.10
19 12 0.39
20 3 0.10
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.27
Consensus pattern (19 bp):
AAGAGAGAAAATTTGTTTC
Found at i:68754 original size:36 final size:36
Alignment explanation
Indices: 68707--68966 Score: 338
Period size: 36 Copynumber: 7.4 Consensus size: 36
68697 ATTCAAAGAT
68707 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
68743 TTTGTTTCAAGGGAAACTGTCTCAAGAGTGAAAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
68779 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
** * *
68815 CTTTGTTTCAAAAGAAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
68852 TTTGTTTCAAGGAAAACAGAT-TC---AGAG----AT
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
*
68881 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACCAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
68917 TTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
68953 TTTGTTTCAAGGGA
1 TTTGTTTCAAGGGA
68967 GACAAAATTT
Statistics
Matches: 195, Mismatches: 19, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
28 1 0.01
29 20 0.10
32 4 0.02
33 3 0.02
36 133 0.68
37 34 0.17
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:68788 original size:174 final size:172
Alignment explanation
Indices: 68504--68963 Score: 665
Period size: 174 Copynumber: 2.6 Consensus size: 172
68494 GAGGCAAACT
* * * * * *
68504 TTTGTTTCAA-GAGAAACACATTCAAATG-TTGGTGTTTCAAGAGAAAATGTCTCAAAAGAGATA
1 TTTGTTTCAAGGA-AAACAGATTCAAA-GATT-TTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
*
68567 AAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAATTTGTTTCAAGAGAAACTGTCTCAAGA
63 AAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAAAAAATTTGTTTCAAGAGAAACTGTCTCAAGA
* **
68632 GAGATAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGGTGAAA
127 GAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
* *
68678 TTTGTTT-AATGTAAAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
1 TTTGTTTCAA-GGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
68742 ATTTGTTTCAAGGGAAACTGTCTCAAGAGTGAAAAAATTTGTTTCAAGAGAAACTGTCTCAAGAG
65 ATTTGTTTCAAGGGAAACTGTCTCAAGA--GAAAAAATTTGTTTCAAGAGAAACTGTCTCAAGAG
* *
68807 AGACAAAACTTTGTTTCAAAAGAAACTGTCTCAAGGGAGACGAAA
128 AGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
* *
68852 TTTGTTTCAAGGAAAACAGATTCAGAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACCAAA
1 TTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
68917 TTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAATTTGTTTCAAG
66 TTTGTTTCAAGGGAAACTGTCTCAAG--AGAAAAAATTTGTTTCAAG
68964 GGAGACAAAA
Statistics
Matches: 260, Mismatches: 18, Indels: 16
0.88 0.06 0.05
Matches are distributed among these distances:
172 27 0.10
173 33 0.13
174 196 0.75
175 3 0.01
176 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (172 bp):
TTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
TTTGTTTCAAGGGAAACTGTCTCAAGAGAAAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
Found at i:68820 original size:138 final size:133
Alignment explanation
Indices: 68571--69040 Score: 437
Period size: 138 Copynumber: 3.5 Consensus size: 133
68561 GAGATAAAAC
*
68571 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
* * * * * ***
68636 TAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGGTGAAATTTGTTT-AATGTAAAACATATT
66 -AAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA-G-AAAACATATT
68700 CAAAGA
128 CAAAGA
68706 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAG
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAG--AAAATTTGTTTCAAGGGAAACTGTCTCAAGAG
* * *
68771 TGAAAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAAGAAAC-TG
63 AGAAAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGA-AAACATA
68835 TCTCAAGGGAGACGAAA
126 T-TC-A---A-A-G--A
* * *
68852 TTTGTTTCAAGGAAAACAGAT-TC---AGAG--ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAG
** * * ** *
68911 ACCAAATTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAATTTGTTTCAAG---GGAGA--CA
65 AAAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAAAACATATTCA
68971 AA-A
130 AAGA
* * *
68974 TTTGTTTCAAGAGAAACTGTCTCAATAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCATGAGA
1 TTTGTTTCAAGGGAAACTGTCTC-A-AGAGAGAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
69039 GA
64 GA
69041 CTAAACTTTG
Statistics
Matches: 279, Mismatches: 31, Indels: 55
0.76 0.08 0.15
Matches are distributed among these distances:
121 1 0.00
122 19 0.07
126 1 0.00
127 4 0.01
129 31 0.11
130 1 0.00
131 1 0.00
136 30 0.11
137 46 0.16
138 114 0.41
139 3 0.01
142 5 0.02
143 1 0.00
144 1 0.00
145 19 0.07
146 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (133 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
AAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAAAACATATTCAA
AGA
Found at i:68969 original size:21 final size:21
Alignment explanation
Indices: 68945--69023 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
68935 GTCTCAAGAA
68945 AGACAAAATTTGTTTCAAGGG
1 AGACAAAATTTGTTTCAAGGG
68966 AGACAAAATTTGTTTCAA--G
1 AGACAAAATTTGTTTCAAGGG
* * **
68985 AG---AAA-CTGTCTCAATAG
1 AGACAAAATTTGTTTCAAGGG
69002 AGACAAAATTTGTTTCAAGGG
1 AGACAAAATTTGTTTCAAGGG
69023 A
1 A
69024 AACTGTCTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
15 7 0.15
16 3 0.07
17 3 0.07
19 3 0.07
20 3 0.07
21 27 0.59
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (21 bp):
AGACAAAATTTGTTTCAAGGG
Found at i:68990 original size:57 final size:57
Alignment explanation
Indices: 68902--69023 Score: 199
Period size: 57 Copynumber: 2.1 Consensus size: 57
68892 GGAAACTGTC
* * *
68902 TCAAGAGAGACCAAATTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAATTTGTT
* *
68959 TCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAATAGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAATTTGTT
69016 TCAAGGGA
1 TCAAGGGA
69024 AACTGTCTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.26
Consensus pattern (57 bp):
TCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAATTTGTT
Found at i:69012 original size:36 final size:36
Alignment explanation
Indices: 68965--69053 Score: 135
Period size: 36 Copynumber: 2.4 Consensus size: 36
68955 TGTTTCAAGG
68965 GAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAT-A
1 GAGACAAAATTTGTTTCAAGAGAAACTGTCTC-ATGA
*
69001 GAGACAAAATTTGTTTCAAGGGAAACTGTCTCATGA
1 GAGACAAAATTTGTTTCAAGAGAAACTGTCTCATGA
*
69037 GAGACTAAACTTTGTTT
1 GAGAC-AAAATTTGTTT
69054 TGAGTAAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
35 2 0.04
36 37 0.76
37 10 0.20
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (36 bp):
GAGACAAAATTTGTTTCAAGAGAAACTGTCTCATGA
Found at i:69707 original size:53 final size:54
Alignment explanation
Indices: 69608--69761 Score: 168
Period size: 55 Copynumber: 2.8 Consensus size: 54
69598 CTTCGTCATG
* * * * *
69608 AAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGTAT-TGT
1 AAGTTG-GCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAA-TATCAGA
* * *
69663 ATGTT-GCTTTGAGTTGGATATCCTTCTTCATGAAGTTGAAATCCAATATCGAGA
1 AAGTTGGCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATATC-AGA
* * *
69717 AAGTTGGTTTTGAGTTGGATATCCTCCGTCGTGGAGTTGAAATCC
1 AAGTTGGCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCC
69762 TATTTCAAAA
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
52 3 0.04
53 36 0.44
54 5 0.06
55 38 0.46
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (54 bp):
AAGTTGGCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATATCAGA
Found at i:69741 original size:55 final size:53
Alignment explanation
Indices: 69618--69761 Score: 164
Period size: 53 Copynumber: 2.7 Consensus size: 53
69608 AAGTTGAGCC
* * * * *
69618 TTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGTATTGTATGTTGCT
1 TTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGTATAGAAAGTTGCT
* * *
69671 TTGAGTTGGATATCCTTCTTCATGAAGTTGAAATCCAA-TATCGAGAAAGTTGGTT
1 TTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGTAT--AGAAAGTT-GCT
* *
69726 TTGAGTTGGATATCCTCCGTCGTGGAGTTGAAATCC
1 TTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCC
69762 TATTTCAAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
52 3 0.04
53 34 0.45
54 5 0.07
55 34 0.45
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (53 bp):
TTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGTATAGAAAGTTGCT
Found at i:75381 original size:3 final size:3
Alignment explanation
Indices: 75367--75413 Score: 67
Period size: 3 Copynumber: 14.7 Consensus size: 3
75357 AGGCCTGCAA
75367 AAT AATT AAT AAT AAT AAAT AAAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AA-T AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA
75414 ATATAAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 32 0.76
4 10 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:75388 original size:17 final size:16
Alignment explanation
Indices: 75366--75416 Score: 72
Period size: 14 Copynumber: 3.3 Consensus size: 16
75356 GAGGCCTGCA
75366 AAATAATTAATAATAAT
1 AAATAA-TAATAATAAT
75383 AAAT-A-AATAATAAT
1 AAATAATAATAATAAT
75397 -AATAATAATAATAAT
1 AAATAATAATAATAAT
75412 AAATA
1 AAATA
75417 TAAAAAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.10
14 10 0.32
15 9 0.29
16 5 0.16
17 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATAATAATAATAAT
Found at i:75419 original size:9 final size:10
Alignment explanation
Indices: 75367--75416 Score: 68
Period size: 10 Copynumber: 5.1 Consensus size: 10
75357 AGGCCTGCAA
*
75367 AATAATTAAT
1 AATAATAAAT
75377 AATAATAAAT
1 AATAATAAAT
75387 AAATAAT-AAT
1 -AATAATAAAT
75397 AATAAT-AAT
1 AATAATAAAT
75406 AATAATAAAT
1 AATAATAAAT
75416 A
1 A
75417 TAAAAAAGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
9 15 0.41
10 16 0.43
11 6 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AATAATAAAT
Found at i:75489 original size:42 final size:41
Alignment explanation
Indices: 75426--75622 Score: 129
Period size: 40 Copynumber: 4.7 Consensus size: 41
75416 ATAAAAAAGT
*
75426 ATATATTTTTTAAAAACTATATA--ATATA-AATTTTTTAAAA
1 ATAT-TTTTTTAAAAACTATATATTATATATAA-ATTTTAAAA
75466 ATATTTTTTTTAAAAACTATATATTATATATAAATTTTAAAA
1 ATA-TTTTTTTAAAAACTATATATTATATATAAATTTTAAAA
* * * * *
75508 ACTA-TTTTTAAAAAACTATATAAGTTTCAAAAAACGTTAATTTTTAAA
1 A-TATTTTTTTAAAAACTATAT-A--TT--ATATA--TAAATTTTAAAA
* * * *
75556 A-A-TGTTTTAAAAATTATATATTATATATAAGTTTTCAAA
1 ATATTTTTTTAAAAACTATATATTATATATAAATTTTAAAA
* * *
75595 A-ATGTTTTCAAAAATTATATATTATATA
1 ATATTTTTTTAAAAACTATATATTATATA
75623 AGTTTTCAAA
Statistics
Matches: 127, Mismatches: 17, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
39 11 0.09
40 43 0.34
41 20 0.16
42 15 0.12
43 6 0.05
44 2 0.02
45 1 0.01
46 18 0.14
48 11 0.09
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.46
Consensus pattern (41 bp):
ATATTTTTTTAAAAACTATATATTATATATAAATTTTAAAA
Found at i:75623 original size:38 final size:37
Alignment explanation
Indices: 75548--75848 Score: 269
Period size: 37 Copynumber: 8.3 Consensus size: 37
75538 AAAACGTTAA
*
75548 TTTTTAAAAATGTTTTAAAAATTATATATTATATATAAG
1 TTTTCAAAAATGTTTTAAAAATTATATA-T-TATATAAG
75587 TTTTCAAAAATGTTTTCAAAAATTATATATTATATAAG
1 TTTTCAAAAATGTTTT-AAAAATTATATATTATATAAG
*
75625 TTTTC-----------AAAAACTATATATTATATAAG
1 TTTTCAAAAATGTTTTAAAAATTATATATTATATAAG
* * * *
75651 TTTT-AAAAACGTTTTCAAAAACTATATATTACATAAA
1 TTTTCAAAAATGTTTT-AAAAATTATATATTATATAAG
75688 TTTTC-AAAATGATTTTAAAAATTATATATTATAT-A-
1 TTTTCAAAAATG-TTTTAAAAATTATATATTATATAAG
** * *
75723 TTTTTTAAAATGTTTTAAAAACTATATATTATGT-AG
1 TTTTCAAAAATGTTTTAAAAATTATATATTATATAAG
75759 TTTTCAAAAATGTTTTAAAAATTATATATTATATACA-
1 TTTTCAAAAATGTTTTAAAAATTATATATTATATA-AG
*
75796 TTTTCAAAATAT-TTTTAGAAATATATATATATTATATATG
1 TTTTCAAAA-ATGTTTTA-AAA-AT-TATATATTATATAAG
75836 TATTTTCAAAAAT
1 --TTTTCAAAAAT
75849 CATTTGCCAA
Statistics
Matches: 221, Mismatches: 15, Indels: 50
0.77 0.05 0.17
Matches are distributed among these distances:
26 24 0.11
35 25 0.11
36 37 0.17
37 58 0.26
38 23 0.10
39 18 0.08
40 25 0.11
41 2 0.01
42 9 0.04
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTTCAAAAATGTTTTAAAAATTATATATTATATAAG
Found at i:75646 original size:24 final size:26
Alignment explanation
Indices: 75598--75660 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
75588 TTTCAAAAAT
*
75598 GTTTTCAAAAATTATATATTATATAA
1 GTTTTCAAAAACTATATATTATATAA
75624 GTTTTCAAAAACTATATATTATATAA
1 GTTTTCAAAAACTATATATTATATAA
75650 GTTTT-AAAAAC
1 GTTTTCAAAAAC
75661 GTTTTCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 6 0.17
26 30 0.83
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (26 bp):
GTTTTCAAAAACTATATATTATATAA
Found at i:75677 original size:63 final size:66
Alignment explanation
Indices: 75559--75696 Score: 203
Period size: 63 Copynumber: 2.2 Consensus size: 66
75549 TTTTAAAAAT
* * * *
75559 GTTTT-AAAAATTATATATTATATATAAGTTTTCAAAAATGTTTTCAAAAATTATATATTATATA
1 GTTTTCAAAAACTATATATTATATATAAGTTTTCAAAAACGTTTTCAAAAACTATATATTACATA
75623 A
66 A
75624 GTTTTCAAAAACTATATA-T-TATATAAGTTTT-AAAAACGTTTTCAAAAACTATATATTACATA
1 GTTTTCAAAAACTATATATTATATATAAGTTTTCAAAAACGTTTTCAAAAACTATATATTACATA
75686 A
66 A
*
75687 ATTTTCAAAA
1 GTTTTCAAAA
75697 TGATTTTAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
63 38 0.57
64 12 0.18
65 6 0.09
66 11 0.16
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (66 bp):
GTTTTCAAAAACTATATATTATATATAAGTTTTCAAAAACGTTTTCAAAAACTATATATTACATA
A
Found at i:79095 original size:31 final size:32
Alignment explanation
Indices: 79057--79125 Score: 131
Period size: 31 Copynumber: 2.2 Consensus size: 32
79047 ACACTATTCG
79057 AACAGTTCAGTTTGGTTTGAACAATA-AGAAA
1 AACAGTTCAGTTTGGTTTGAACAATACAGAAA
79088 AACAGTTCAGTTTGGTTTGAACAATACAGAAA
1 AACAGTTCAGTTTGGTTTGAACAATACAGAAA
79120 AACAGT
1 AACAGT
79126 CCAGAAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 26 0.70
32 11 0.30
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (32 bp):
AACAGTTCAGTTTGGTTTGAACAATACAGAAA
Found at i:79994 original size:11 final size:12
Alignment explanation
Indices: 79965--79994 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
79955 TGAATTAGTA
79965 GGCATGACTTGC
1 GGCATGACTTGC
79977 GGCATGACTTGC
1 GGCATGACTTGC
79989 -GCATGA
1 GGCATGA
79995 GTCTATTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.23
Consensus pattern (12 bp):
GGCATGACTTGC
Found at i:80156 original size:45 final size:44
Alignment explanation
Indices: 80100--80205 Score: 169
Period size: 45 Copynumber: 2.4 Consensus size: 44
80090 CAGAATTATC
80100 TTTA-TTTTAGGATTTAATTCAAACAATTTTTAGAAATTATATTT
1 TTTATTTTTAGGATTTAATTCAAACAATTTTTAGAAATTAT-TTT
*
80144 TTTATTTTTAGGATTTAATTCAAACAATTTTTAGGAATTATTTT
1 TTTATTTTTAGGATTTAATTCAAACAATTTTTAGAAATTATTTT
*
80188 TGTATTTTATAGGATTTA
1 TTTATTTT-TAGGATTTA
80206 TCTTTATCAT
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
44 14 0.24
45 44 0.76
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (44 bp):
TTTATTTTTAGGATTTAATTCAAACAATTTTTAGAAATTATTTT
Found at i:80173 original size:23 final size:23
Alignment explanation
Indices: 80104--80179 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
80094 ATTATCTTTA
80104 TTTTAGGATTTAATTCAAACAAT
1 TTTTAGGATTTAATTCAAACAAT
* * ****
80127 TTTTAGAAATTATATT--TTTTAT
1 TTTTAGGATTTA-ATTCAAACAAT
80149 TTTTAGGATTTAATTCAAACAAT
1 TTTTAGGATTTAATTCAAACAAT
80172 TTTTAGGA
1 TTTTAGGA
80180 ATTATTTTTG
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
21 3 0.08
22 12 0.32
23 20 0.53
24 3 0.08
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (23 bp):
TTTTAGGATTTAATTCAAACAAT
Found at i:80222 original size:22 final size:21
Alignment explanation
Indices: 80170--80222 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
80160 AATTCAAACA
* *
80170 ATTTTTAGGAATTATTTTTGT
1 ATTTTTAGGAATTATCTTTAT
*
80191 ATTTTATAGGATTTATCTTTAT
1 ATTTT-TAGGAATTATCTTTAT
80213 CATTTTTAGG
1 -ATTTTTAGG
80223 GCTTTTAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.19
22 17 0.63
23 5 0.19
ACGTcount: A:0.25, C:0.04, G:0.13, T:0.58
Consensus pattern (21 bp):
ATTTTTAGGAATTATCTTTAT
Found at i:80358 original size:20 final size:21
Alignment explanation
Indices: 80328--80377 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
80318 TTTTATAAAA
80328 TTTTTACTTTTCTTTTTCAAG
1 TTTTTACTTTTCTTTTTCAAG
* *
80349 TTTTTA-TTTTTTTTTTCTAG
1 TTTTTACTTTTCTTTTTCAAG
*
80369 TTTTCACTT
1 TTTTTACTT
80378 ATTTTTCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.12, C:0.12, G:0.04, T:0.72
Consensus pattern (21 bp):
TTTTTACTTTTCTTTTTCAAG
Found at i:80382 original size:20 final size:20
Alignment explanation
Indices: 80340--80383 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
80330 TTTACTTTTC
* * *
80340 TTTTTCAAGTTTTTATTTTT
1 TTTTTCAAGTTTTCACTTAT
*
80360 TTTTTCTAGTTTTCACTTAT
1 TTTTTCAAGTTTTCACTTAT
80380 TTTT
1 TTTT
80384 CTTTTAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.73
Consensus pattern (20 bp):
TTTTTCAAGTTTTCACTTAT
Found at i:82233 original size:28 final size:29
Alignment explanation
Indices: 82202--82256 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
82192 ATTCAGGTTG
82202 CTTTCAGG-TCAGGTT-AAATTCGGTTCGA
1 CTTTC-GGATCAGGTTAAAATTCGGTTCGA
**
82230 CTTTCGGATTGGGTTAAAATTCGGTTC
1 CTTTCGGATCAGGTTAAAATTCGGTTC
82257 AGGTTTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.09
28 10 0.43
29 11 0.48
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.38
Consensus pattern (29 bp):
CTTTCGGATCAGGTTAAAATTCGGTTCGA
Found at i:82283 original size:16 final size:16
Alignment explanation
Indices: 82249--82367 Score: 87
Period size: 16 Copynumber: 7.4 Consensus size: 16
82239 TGGGTTAAAA
**
82249 TTCGGTTCAGGTTTCT
1 TTCGGTTCAGGTTAAT
* *
82265 TTCTGTTCTGGTTAAT
1 TTCGGTTCAGGTTAAT
* **
82281 TTCGATTCAGGTTGCT
1 TTCGGTTCAGGTTAAT
82297 TTCGGTTCAGGTTAAGT
1 TTCGGTTCAGGTTAA-T
* * *
82314 TT-GGTTCGGGCTACT
1 TTCGGTTCAGGTTAAT
** *
82329 TTTAGTTCGGGTTAAT
1 TTCGGTTCAGGTTAAT
* *
82345 TTCGGTTCTGGTTGAT
1 TTCGGTTCAGGTTAAT
82361 TTCGGTT
1 TTCGGTT
82368 TTGCTAAATT
Statistics
Matches: 79, Mismatches: 22, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
15 3 0.04
16 73 0.92
17 3 0.04
ACGTcount: A:0.11, C:0.14, G:0.27, T:0.48
Consensus pattern (16 bp):
TTCGGTTCAGGTTAAT
Found at i:82299 original size:32 final size:32
Alignment explanation
Indices: 82249--82363 Score: 108
Period size: 32 Copynumber: 3.6 Consensus size: 32
82239 TGGGTTAAAA
* *
82249 TTCGGTTCAGGTTTCTTTCTGTTCTGGTTAAT
1 TTCGGTTCAGGTTGCTTTCTGTTCAGGTTAAT
* *
82281 TTCGATTCAGGTTGCTTTCGGTTCAGGTTAAGT
1 TTCGGTTCAGGTTGCTTTCTGTTCAGGTTAA-T
* * * *
82314 TT-GGTTCGGGCTACTTT-TAGTTCGGGTTAAT
1 TTCGGTTCAGGTTGCTTTCT-GTTCAGGTTAAT
* *
82345 TTCGGTTCTGGTTGATTTC
1 TTCGGTTCAGGTTGCTTTC
82364 GGTTTTGCTA
Statistics
Matches: 65, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
31 3 0.05
32 59 0.91
33 3 0.05
ACGTcount: A:0.11, C:0.15, G:0.26, T:0.48
Consensus pattern (32 bp):
TTCGGTTCAGGTTGCTTTCTGTTCAGGTTAAT
Found at i:85828 original size:3 final size:3
Alignment explanation
Indices: 85820--85848 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
85810 CTTTCCAATG
85820 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
85849 ATAATAATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Done.