Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000749.1 Hibiscus syriacus cultivar Beakdansim tig00001442_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: 112390
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4052 original size:18 final size:19
Alignment explanation
Indices: 4031--4068 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
4021 AACATGTACT
4031 ACATTTTAATCACCA-AAG
1 ACATTTTAATCACCACAAG
*
4049 ACATTTTAATGACCACAAG
1 ACATTTTAATCACCACAAG
4068 A
1 A
4069 AAACTAGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26
Consensus pattern (19 bp):
ACATTTTAATCACCACAAG
Found at i:8954 original size:24 final size:24
Alignment explanation
Indices: 8927--8998 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
8917 AAACGGAGAT
*
8927 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
8951 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
*
8975 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
8999 GTAATGTATC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:8998 original size:12 final size:12
Alignment explanation
Indices: 8929--8998 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
8919 ACGGAGATAT
* *
8929 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
8941 CATAATTCAGAT
1 CAGAATTCAGAA
*
8953 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
8965 CAGAATCCAGAT
1 CAGAATTCAGAA
*
8977 CAGAAATCAGAA
1 CAGAATTCAGAA
8989 CAGAATTCAG
1 CAGAATTCAG
8999 GTAATGTATC
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:9009 original size:48 final size:47
Alignment explanation
Indices: 8927--9035 Score: 121
Period size: 48 Copynumber: 2.3 Consensus size: 47
8917 AAACGGAGAT
* * * *
8927 ATCAGAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCCA
* *
8974 GATCAGAAATCAGAACAGAATTCAGGTAATG-TATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGATAA-GATATCAGAACAGAATCCA
*
9022 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
9036 TAAAATATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.02
48 50 0.96
49 1 0.02
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCCA
Found at i:9033 original size:24 final size:25
Alignment explanation
Indices: 8927--9035 Score: 93
Period size: 24 Copynumber: 4.5 Consensus size: 25
8917 AAACGGAGAT
* *
8927 ATCAGAAATCAAAACATAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
8951 ATCAGATATCATAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
8975 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
8999 GTAATG-TATCAGAACAGAATTCAAG
1 ATCA-GAAATCAGAACAGAATTCAAG
*
9024 -TCGGAAATCAGA
1 ATCAGAAATCAGA
9036 TAAAATATTT
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
23 3 0.04
24 61 0.88
25 5 0.07
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:12274 original size:2 final size:2
Alignment explanation
Indices: 12267--12330 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
12257 AATAATTATC
12267 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
12309 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
12331 CCATTACGCA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12672 original size:17 final size:18
Alignment explanation
Indices: 12641--12674 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12631 CTATATAATT
*
12641 TAATTGAAATTATTTAAA
1 TAATTGAAATAATTTAAA
12659 TAATT-AAATAATTTAA
1 TAATTGAAATAATTTAA
12675 TCAATAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TAATTGAAATAATTTAAA
Found at i:16582 original size:138 final size:137
Alignment explanation
Indices: 16279--16602 Score: 327
Period size: 138 Copynumber: 2.4 Consensus size: 137
16269 CTCAGTTACT
* *
16279 AGTCCAAGTCTTTGTCTTCTTGATG-A-CAGGTTTGGCATCCTTCATTTTAAAGGCACTGATCGT
1 AGTCCAAGTCTTTGTC-TCTTGATGAATCAGATTTGGCATCCTTCATTTTAAAGGCACTGATCAT
* * * *
16342 CTTTCCCTTAGCATCTTCATACGTAGGAACCGGAGGATTTTTCACATGCCGCTCTCCAAATTCCC
65 CTTTCCCTCAACATCTTCACACGTAGGAACCGGAGGATTTTTCACATGCCGCACTCCAAATTCCC
16407 TAGTTCCA
130 TAGTTCCA
** * * * * * * *
16415 AAACGAAGTCTTTTTCCTCTTGATAAATCAGATCTGACATCCTTCATTTTAAAGTCACTGATTAT
1 AGTCCAAGTCTTTGT-CTCTTGATGAATCAGATTTGGCATCCTTCATTTTAAAGGCACTGATCAT
* * * ** *
16480 CTTTTCCTCAACATGTTCACCCGTAGGAATTGGAGGATTTTTCACATTTTCCG-ACT-CAAAGTT
65 CTTTCCCTCAACATCTTCACACGTAGGAACCGGAGGATTTTTCACA--TGCCGCACTCCAAA-TT
*
16543 CCC-GGTTCCA
127 CCCTAGTTCCA
* *
16553 AGTCCAAGTCCTTGTCTGCTAGATGAATCA-AGTTTGGCATCCTTCATTTT
1 AGTCCAAGTCTTTGTCT-CTTGATGAATCAGA-TTTGGCATCCTTCATTTT
16603 GGAGTAAATG
Statistics
Matches: 149, Mismatches: 31, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
136 18 0.12
137 5 0.03
138 115 0.77
139 7 0.05
140 4 0.03
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (137 bp):
AGTCCAAGTCTTTGTCTCTTGATGAATCAGATTTGGCATCCTTCATTTTAAAGGCACTGATCATC
TTTCCCTCAACATCTTCACACGTAGGAACCGGAGGATTTTTCACATGCCGCACTCCAAATTCCCT
AGTTCCA
Found at i:16729 original size:17 final size:17
Alignment explanation
Indices: 16707--16740 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16697 AGGGAAGTGG
*
16707 TTAATCAGCTGTTATAA
1 TTAATCAGCTGATATAA
16724 TTAATCAGCTGATATAA
1 TTAATCAGCTGATATAA
16741 ATGAGCTGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
TTAATCAGCTGATATAA
Found at i:23780 original size:2 final size:2
Alignment explanation
Indices: 23773--23808 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
23763 AATGAGATGA
23773 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
23809 GCTTGAGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24294 original size:21 final size:21
Alignment explanation
Indices: 24218--24316 Score: 102
Period size: 21 Copynumber: 5.0 Consensus size: 21
24208 AGTCGAGGGT
* *
24218 TACAGTGGTCCTACAGGAC-A
1 TACAGTGGTCCTTCGGGACAA
* *
24238 T--AGTGGTCTTTCGAGACAA
1 TACAGTGGTCCTTCGGGACAA
24257 TACAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTTCGGGACAA
*
24278 TACAGTGGTCCTACGGG---A
1 TACAGTGGTCCTTCGGGACAA
*
24296 TATAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTTCGGGACAA
24317 ATTTTAGTGC
Statistics
Matches: 64, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
18 28 0.44
19 2 0.03
20 1 0.02
21 33 0.52
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (21 bp):
TACAGTGGTCCTTCGGGACAA
Found at i:25411 original size:21 final size:21
Alignment explanation
Indices: 25378--25418 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25368 TGTAACTAAA
*
25378 GTTGTTAAGAATTGGTTAAGT
1 GTTGTTAAGAATTAGTTAAGT
**
25399 GTTGTTACTAATTAGTTAAG
1 GTTGTTAAGAATTAGTTAAG
25419 GGAAGTTGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.44
Consensus pattern (21 bp):
GTTGTTAAGAATTAGTTAAGT
Found at i:25448 original size:17 final size:17
Alignment explanation
Indices: 25426--25459 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25416 AAGGGAAGTT
* *
25426 GTTAATTGGTTGTTATA
1 GTTAATTAGTTGATATA
25443 GTTAATTAGTTGATATA
1 GTTAATTAGTTGATATA
25460 AATGAGCTGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (17 bp):
GTTAATTAGTTGATATA
Found at i:26497 original size:144 final size:147
Alignment explanation
Indices: 26260--26577 Score: 321
Period size: 144 Copynumber: 2.2 Consensus size: 147
26250 CAACCTCTAT
* * * * *
26260 TTTGAAGTTAATGAATG-CCTTCCCTTAGCATGTTCACAGATAGAAACTGGAGGATTTTTAACAT
1 TTTGAAGTCACTGAATGTCTTTCCCTTAGCATGTTCACACATAGAAACTAGAGGATTTTTAACAT
* * *
26324 GCCACTCTTCGAAATTTCCGATTGCAAGTCTG-AG-TC-TGTTC-CCGA-GTCCTCGTGATGAAT
66 GCCACTCTTCGAAATTCCCGATTGCAAGTC-GAAGTTCAAGATCACC-ATGTCCTCGTGATGAAT
26384 CAGGTTTGACATCCTTCAA
129 CAGGTTTGACATCCTTCAA
* * *
26403 TTTGAAGTCACTGAATGTCTTTCCCTTGGCATGTTCATACATA-AGAACTAGAGGATTTTTCGA-
1 TTTGAAGTCACTGAATGTCTTTCCCTTAGCATGTTCACACATAGA-AACTAGAGGATTTTT-AAC
* * * *
26466 ATGCCATTCTTCGAAGTTCCCGGTT-CGAAGTCGAAGTTCAAGATCAAGTCCATGTCCTCTTGAT
64 ATGCCACTCTTCGAAATTCCCGATTGC-AAGTCGAAGTTCAAGATC-A--CCATGTCCTCGTGAT
* * *
26530 GAATTAGGTTTGATATCCTTCAT
125 GAATCAGGTTTGACATCCTTCAA
* *
26553 TTTGAAGCCACTGATTGTCTTTCCC
1 TTTGAAGTCACTGAATGTCTTTCCC
26578 AAACTTTGAT
Statistics
Matches: 143, Mismatches: 20, Indels: 17
0.79 0.11 0.09
Matches are distributed among these distances:
143 18 0.13
144 63 0.44
145 3 0.02
146 3 0.02
149 1 0.01
150 55 0.38
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (147 bp):
TTTGAAGTCACTGAATGTCTTTCCCTTAGCATGTTCACACATAGAAACTAGAGGATTTTTAACAT
GCCACTCTTCGAAATTCCCGATTGCAAGTCGAAGTTCAAGATCACCATGTCCTCGTGATGAATCA
GGTTTGACATCCTTCAA
Found at i:28820 original size:17 final size:17
Alignment explanation
Indices: 28798--28831 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28788 GATTTTGTGC
28798 CTTGTAGAACTCGAGGT
1 CTTGTAGAACTCGAGGT
28815 CTTGTAGAACTCGAGGT
1 CTTGTAGAACTCGAGGT
28832 AGTCTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (17 bp):
CTTGTAGAACTCGAGGT
Found at i:29232 original size:38 final size:38
Alignment explanation
Indices: 29190--29274 Score: 143
Period size: 38 Copynumber: 2.2 Consensus size: 38
29180 TTCGCACCTA
* *
29190 TGAATGATTCAGTGCTGACTGATTCAGTAAAACAGTGT
1 TGAATGATTCAGTGCTGACTGATTCAGCAAAACAGTGC
*
29228 TGAATGATTCAGTGCTGATTGATTCAGCAAAACAGTGC
1 TGAATGATTCAGTGCTGACTGATTCAGCAAAACAGTGC
29266 TGAATGATT
1 TGAATGATT
29275 TAGCACAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (38 bp):
TGAATGATTCAGTGCTGACTGATTCAGCAAAACAGTGC
Found at i:29677 original size:40 final size:40
Alignment explanation
Indices: 29620--29698 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
29610 ATATTTCCGG
*
29620 TAAAATGCCCAACAATAACAAAACCGATAGAAAAAATAAC
1 TAAAATGCCCAACAATAACAAAACCGATAAAAAAAATAAC
* * *
29660 TAAAATGTCCAATAATAACAAAACCGGTAAAAAAAATAA
1 TAAAATGCCCAACAATAACAAAACCGATAAAAAAAATAA
29699 TGTTTCAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.61, C:0.16, G:0.08, T:0.15
Consensus pattern (40 bp):
TAAAATGCCCAACAATAACAAAACCGATAAAAAAAATAAC
Found at i:31566 original size:2 final size:2
Alignment explanation
Indices: 31559--31589 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
31549 TACCGAAATA
31559 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31590 TTTTAATGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:32251 original size:21 final size:21
Alignment explanation
Indices: 32222--32262 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
32212 CATCGTCTGC
*
32222 CGCCACTCGATCTCCTTCGAA
1 CGCCACTCGATCTCCCTCGAA
* *
32243 CGCCGCTCGTTCTCCCTCGA
1 CGCCACTCGATCTCCCTCGA
32263 CTGGAACGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.46, G:0.17, T:0.24
Consensus pattern (21 bp):
CGCCACTCGATCTCCCTCGAA
Found at i:34506 original size:14 final size:14
Alignment explanation
Indices: 34487--34518 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
34477 AAATATCATT
34487 TATTTTTTGTTAAA
1 TATTTTTTGTTAAA
34501 TA-TTTTTGTTAAA
1 TATTTTTTGTTAAA
34514 -ATTTT
1 TATTTT
34519 ATTTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.06
13 14 0.82
14 2 0.12
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (14 bp):
TATTTTTTGTTAAA
Found at i:35303 original size:41 final size:41
Alignment explanation
Indices: 35258--35351 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 41
35248 GTTACACGTG
*
35258 GGGTATAGTGCGCGCCCTGCTCCGCGCTATACACCACGTAA
1 GGGTATAGCGCGCGCCCTGCTCCGCGCTATACACCACGTAA
* * * *
35299 GGGTATAGCGCGCGCCCTGCTTCTCGCTATACGCCACGTAG
1 GGGTATAGCGCGCGCCCTGCTCCGCGCTATACACCACGTAA
35340 GGGTATAGCGCG
1 GGGTATAGCGCG
35352 GATCAGGGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.17, C:0.32, G:0.31, T:0.20
Consensus pattern (41 bp):
GGGTATAGCGCGCGCCCTGCTCCGCGCTATACACCACGTAA
Found at i:38279 original size:26 final size:24
Alignment explanation
Indices: 38250--38321 Score: 60
Period size: 26 Copynumber: 3.0 Consensus size: 24
38240 AAAATCCAAC
38250 AAATTTAACAAAATAAAGTAAGTATT
1 AAATTTAACAAAATAAAGTAA--ATT
* *
38276 AAATGATAA-ATAATAAA--AAATT
1 AAAT-TTAACAAAATAAAGTAAATT
*
38298 ACAATTAAACAAAATAAAGTAAAT
1 A-AATTTAACAAAATAAAGTAAAT
38322 ACAAATATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 2 0.06
25 4 0.11
26 11 0.31
27 3 0.08
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (24 bp):
AAATTTAACAAAATAAAGTAAATT
Found at i:40428 original size:96 final size:96
Alignment explanation
Indices: 40317--40504 Score: 349
Period size: 96 Copynumber: 2.0 Consensus size: 96
40307 TAATTCTTAA
*
40317 TCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAATTAAAACGT
1 TCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTAAATTAAAACGT
**
40382 TAAAATGTTATTGTATCAGCAAAGTGTCGAG
66 TAAAATGTTACCGTATCAGCAAAGTGTCGAG
40413 TCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTAAATTAAAACGT
1 TCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTAAATTAAAACGT
40478 TAAAATGTTACCGTATCAGCAAAGTGT
66 TAAAATGTTACCGTATCAGCAAAGTGT
40505 AGAGATATAT
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 89 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.35
Consensus pattern (96 bp):
TCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTAAATTAAAACGT
TAAAATGTTACCGTATCAGCAAAGTGTCGAG
Found at i:40592 original size:17 final size:18
Alignment explanation
Indices: 40572--40612 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
40562 GAATTATATT
40572 AGTAAAATA-TTAAATAA
1 AGTAAAATATTTAAATAA
40589 AGTAAAATATTTAAATAA
1 AGTAAAATATTTAAATAA
*
40607 ATTAAA
1 AGTAAA
40613 TACATAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (18 bp):
AGTAAAATATTTAAATAA
Found at i:43181 original size:101 final size:103
Alignment explanation
Indices: 43004--43214 Score: 263
Period size: 101 Copynumber: 2.1 Consensus size: 103
42994 TTTGTCACCT
* *
43004 TTGAGATTGTTTATCTCAAAACAAAGTTTCGTCTCGCTTGAGACAGTTTCCCTTGAAGCCCAAAT
1 TTGAGATTGTTTATCCCAAAACAAAGTTTCGTCTCGCTTGAGACAGTTTCCCTTGAAACCCAAAT
43069 TTCAAACTTGTTTCACTTGAAACAAAA-TTGATCTCAC
66 TTCAAACTTGTTTCACTTGAAACAAAATTTGATCTCAC
* **
43106 TTGAGATTGTTT-TCCCAAAA-ATTAA-TTT-GTCTCGCTTGAGATAGTTTTCCCTTGAAATGCA
1 TTGAGATTGTTTATCCCAAAACA--AAGTTTCGTCTCGCTTGAGACAG-TTTCCCTTGAAACCCA
* * *
43167 AATTTTGAAA-TTGTTTCCCTTGAAACAAAATTTTATCTCAC
63 AA-TTTCAAACTTGTTTCACTTGAAACAAAATTTGATCTCAC
*
43208 CTGAGAT
1 TTGAGAT
43215 AGCTTCTCTA
Statistics
Matches: 95, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
100 16 0.17
101 44 0.46
102 35 0.37
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (103 bp):
TTGAGATTGTTTATCCCAAAACAAAGTTTCGTCTCGCTTGAGACAGTTTCCCTTGAAACCCAAAT
TTCAAACTTGTTTCACTTGAAACAAAATTTGATCTCAC
Found at i:44886 original size:20 final size:20
Alignment explanation
Indices: 44863--44902 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
44853 AAAAATGGAA
44863 TCAAAAGGTAAAATAATTTT
1 TCAAAAGGTAAAATAATTTT
44883 TCAAAAGGTAAAATAATTTT
1 TCAAAAGGTAAAATAATTTT
44903 ACTCCATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (20 bp):
TCAAAAGGTAAAATAATTTT
Found at i:47153 original size:9 final size:9
Alignment explanation
Indices: 47139--47168 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
47129 TATTTTCTTC
47139 TTATTTTAT
1 TTATTTTAT
47148 TTATTTTAT
1 TTATTTTAT
47157 TTATTTTAT
1 TTATTTTAT
47166 TTA
1 TTA
47169 CTGTCTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTATTTTAT
Found at i:47177 original size:18 final size:18
Alignment explanation
Indices: 47139--47177 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
47129 TATTTTCTTC
* *
47139 TTATTTTATTTATTTTAT
1 TTATTTTATTTACTGTAT
*
47157 TTATTTTATTTACTGTCT
1 TTATTTTATTTACTGTAT
47175 TTA
1 TTA
47178 CCATTTCTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (18 bp):
TTATTTTATTTACTGTAT
Found at i:47842 original size:21 final size:21
Alignment explanation
Indices: 47808--47866 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 21
47798 TTTTTTTTAA
*
47808 TTTTAGAAAAATAAGGTTTTT
1 TTTTAGAAAAATAAGATTTTT
* * *
47829 TTTTATAAATAT-A-ATATTT
1 TTTTAGAAAAATAAGATTTTT
*
47848 TTTTA-AAAAATAAAATTTT
1 TTTTAGAAAAATAAGATTTT
47867 CAATTACTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 5 0.17
19 10 0.33
20 5 0.17
21 10 0.33
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
TTTTAGAAAAATAAGATTTTT
Found at i:47860 original size:18 final size:19
Alignment explanation
Indices: 47826--47866 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
47816 AAATAAGGTT
* *
47826 TTTTTTTATAAATATAATA
1 TTTTTTTATAAAAATAAAA
47845 TTTTTTTA-AAAAATAAAA
1 TTTTTTTATAAAAATAAAA
47863 TTTT
1 TTTT
47867 CAATTACTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTTTTATAAAAATAAAA
Found at i:56275 original size:21 final size:21
Alignment explanation
Indices: 56251--56290 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
56241 TTTTTGTTCA
56251 ACCGAAAATGTTAATTTTCTT
1 ACCGAAAATGTTAATTTTCTT
*
56272 ACCGAAAATGTTATTTTTC
1 ACCGAAAATGTTAATTTTC
56291 ATGTAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (21 bp):
ACCGAAAATGTTAATTTTCTT
Found at i:59149 original size:6 final size:6
Alignment explanation
Indices: 59138--59711 Score: 1070
Period size: 6 Copynumber: 96.0 Consensus size: 6
59128 TAACTTAACC
59138 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
59186 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
59234 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
59282 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
59330 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
59378 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA C--ATATA
59428 CATATA CATATA C--ATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
59474 CATATA CATATA CATATA CATATA CATATA CATATA CATATA C--ATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
59520 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
59568 CATATA CATATA CATATA CATATA CATATA CATACATA CATATA C--ATA
1 CATATA CATATA CATATA CATATA CATATA CAT--ATA CATATA CATATA
59616 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
59664 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
59712 TTAGTTTATT
Statistics
Matches: 558, Mismatches: 0, Indels: 20
0.97 0.00 0.03
Matches are distributed among these distances:
4 12 0.02
6 534 0.96
8 12 0.02
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
CATATA
Found at i:60668 original size:16 final size:17
Alignment explanation
Indices: 60641--60672 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
60631 ATCCTTTTGT
60641 TAAATCGTCAACAATTA
1 TAAATCGTCAACAATTA
60658 TAAAT-GTCAACAATT
1 TAAATCGTCAACAATT
60673 TGTATTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (17 bp):
TAAATCGTCAACAATTA
Found at i:60943 original size:31 final size:31
Alignment explanation
Indices: 60905--60968 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
60895 TCATTGTCAC
60905 CGCTATAATCATCAATATCTAATATATTAAT
1 CGCTATAATCATCAATATCTAATATATTAAT
* *
60936 CGCTATAATTATCAATATCTGATATATTAAT
1 CGCTATAATCATCAATATCTAATATATTAAT
60967 CG
1 CG
60969 AGGTTATGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (31 bp):
CGCTATAATCATCAATATCTAATATATTAAT
Found at i:67466 original size:24 final size:24
Alignment explanation
Indices: 67438--67492 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
67428 GAATATTTTA
* * *
67438 TCTGATTTCCGATTTGAATTCTGT
1 TCTGATTTCCGATCTGAAATATGT
* *
67462 TCTGATATCTGATCTGAAATATGT
1 TCTGATTTCCGATCTGAAATATGT
67486 TCTGATT
1 TCTGATT
67493 CCTAACCTGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.47
Consensus pattern (24 bp):
TCTGATTTCCGATCTGAAATATGT
Found at i:70718 original size:20 final size:20
Alignment explanation
Indices: 70661--70718 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 20
70651 TTTAAATTGA
70661 TTTTTAAATT--TT-TAAATT
1 TTTTTAAATTCATTATAAA-T
70679 TTTTTAAATTCATTAT-AAT
1 TTTTTAAATTCATTATAAAT
** *
70698 TTTTTATTTTCATTCTAAAT
1 TTTTTAAATTCATTATAAAT
70718 T
1 T
70719 GATTTACAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 10 0.30
19 14 0.42
20 8 0.24
21 1 0.03
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTAAATTCATTATAAAT
Found at i:77067 original size:11 final size:11
Alignment explanation
Indices: 77051--77120 Score: 70
Period size: 11 Copynumber: 6.3 Consensus size: 11
77041 AATTACTTAC
77051 TGTTTATTTGT
1 TGTTTATTTGT
77062 TGTTTATTTGCT
1 TGTTTATTTG-T
*
77074 AT-TTTAGTTGT
1 -TGTTTATTTGT
77085 TGTTTATTTGT
1 TGTTTATTTGT
* *
77096 TATTTATTTGC
1 TGTTTATTTGT
* *
77107 TATTTAGTTGT
1 TGTTTATTTGT
77118 TGT
1 TGT
77121 GAATTCAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
10 1 0.02
11 39 0.80
12 8 0.16
13 1 0.02
ACGTcount: A:0.13, C:0.03, G:0.17, T:0.67
Consensus pattern (11 bp):
TGTTTATTTGT
Found at i:77079 original size:23 final size:22
Alignment explanation
Indices: 77053--77105 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 22
77043 TTACTTACTG
77053 TTTATTTGTTGTTTATTTGCTA
1 TTTATTTGTTGTTTATTTGCTA
* *
77075 TTTTAGTTGTTGTTTATTTGTTA
1 -TTTATTTGTTGTTTATTTGCTA
77098 TTTATTTG
1 TTTATTTG
77106 CTATTTAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.13, C:0.02, G:0.15, T:0.70
Consensus pattern (22 bp):
TTTATTTGTTGTTTATTTGCTA
Found at i:77094 original size:34 final size:33
Alignment explanation
Indices: 77051--77120 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 33
77041 AATTACTTAC
*
77051 TGTTTATTTGTTGTTTATTTGCTATTTTAGTTGT
1 TGTTTATTTGTTATTTATTTGCTA-TTTAGTTGT
77085 TGTTTATTTGTTATTTATTTGCTATTTAGTTGT
1 TGTTTATTTGTTATTTATTTGCTATTTAGTTGT
77118 TGT
1 TGT
77121 GAATTCAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 12 0.34
34 23 0.66
ACGTcount: A:0.13, C:0.03, G:0.17, T:0.67
Consensus pattern (33 bp):
TGTTTATTTGTTATTTATTTGCTATTTAGTTGT
Found at i:77286 original size:11 final size:11
Alignment explanation
Indices: 77249--77300 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
77239 TTATTGGATG
77249 TTTAGTTGTTA
1 TTTAGTTGTTA
* *
77260 TTTTAGTTGATG
1 -TTTAGTTGTTA
*
77272 TTTATTTGTTA
1 TTTAGTTGTTA
* *
77283 TTTATTTGCTA
1 TTTAGTTGTTA
77294 TTTAGTT
1 TTTAGTT
77301 ATTGTGAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
11 24 0.73
12 9 0.27
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.65
Consensus pattern (11 bp):
TTTAGTTGTTA
Found at i:77361 original size:74 final size:74
Alignment explanation
Indices: 77268--77427 Score: 275
Period size: 74 Copynumber: 2.2 Consensus size: 74
77258 TATTTTAGTT
* *
77268 GATGTTTATTTGTTATTTATTTGCTATTTAGTTATTGTGAATTCAATATTATTGGATATTATGTC
1 GATGTTTAGTTGTCATTTATTTGCTATTTAGTTATTGTGAATTCAATATTATTGGATATTATGTC
77333 TGTTTATTG
66 TGTTTATTG
* * *
77342 GATGTTTAGTTGTCGTTTATTTGCTATTTAGTTGTTGTGAATTCAATATTATTGGATATTATGTT
1 GATGTTTAGTTGTCATTTATTTGCTATTTAGTTATTGTGAATTCAATATTATTGGATATTATGTC
77407 TGTTTATTG
66 TGTTTATTG
77416 GATGTTTAGTTG
1 GATGTTTAGTTG
77428 CTATTTTGGT
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 81 1.00
ACGTcount: A:0.21, C:0.04, G:0.19, T:0.56
Consensus pattern (74 bp):
GATGTTTAGTTGTCATTTATTTGCTATTTAGTTATTGTGAATTCAATATTATTGGATATTATGTC
TGTTTATTG
Found at i:77362 original size:22 final size:23
Alignment explanation
Indices: 77316--77376 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
77306 GAATTCAATA
77316 TTATTGGATA-TTA--TGTCTGT
1 TTATTGGATATTTAGTTGTCTGT
*
77336 TTATTGGATGTTTAGTTGTC-GT
1 TTATTGGATATTTAGTTGTCTGT
* *
77358 TTATTTGCTATTTAGTTGT
1 TTATTGGATATTTAGTTGT
77377 TGTGAATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 9 0.26
21 3 0.09
22 18 0.53
23 4 0.12
ACGTcount: A:0.16, C:0.05, G:0.21, T:0.57
Consensus pattern (23 bp):
TTATTGGATATTTAGTTGTCTGT
Found at i:77410 original size:171 final size:174
Alignment explanation
Indices: 77051--77524 Score: 675
Period size: 171 Copynumber: 2.7 Consensus size: 174
77041 AATTACTTAC
* * * *
77051 TGTTTATTTGTTGTTTATTTGCTATTTTAGTTGTTGTTTATTTGTTATTTATTTGCTATTTAGTT
1 TGTTTATTGGATGTTTAGTTGCTATTTTAGTTGATGTTTATTTGTTATTTATTTGCTATTTAGTT
* * *
77116 GTTGTGAATTCAATATTATTAGATATTATGTCTGTTTATTGGATCTTTAATTGCTATTGTAGTTG
66 GTTGTGAATTCAATATTATTGGATATTATGTCTGTTTATTGGATGTTT-A--G----T-T-GTCG
*
77181 TTTATTTGTTATTTAGTTACTGTGAATTCAATTCAATATTATTGGATATTATGTT
122 TTTATTTGCTATTTAGTTACTGTG-A-TCAATTCAATATTATTGGATATTATGTT
*
77236 TGTTTATTGGATGTTTAGTTGTTATTTTAGTTGATGTTTATTTGTTATTTATTTGCTATTTAGTT
1 TGTTTATTGGATGTTTAGTTGCTATTTTAGTTGATGTTTATTTGTTATTTATTTGCTATTTAGTT
*
77301 ATTGTGAATTCAATATTATTGGATATTATGTCTGTTTATTGGATGTTTAGTTGTCGTTTATTTGC
66 GTTGTGAATTCAATATTATTGGATATTATGTCTGTTTATTGGATGTTTAGTTGTCGTTTATTTGC
* *
77366 TATTTAGTT-GT-TG-TGAATTCAATATTATTGGATATTATGTT
131 TATTTAGTTACTGTGATCAATTCAATATTATTGGATATTATGTT
* * * *
77407 TGTTTATTGGATGTTTAGTTGCTATTTTGGTTGCTATTTATTTGTTATTTATTTTCTATTTAGTT
1 TGTTTATTGGATGTTTAGTTGCTATTTTAGTTGATGTTTATTTGTTATTTATTTGCTATTTAGTT
*
77472 GTTGTGAATTCAATATTATTGGATATTATGTTTGTTTATTGGATGTTTAGTTG
66 GTTGTGAATTCAATATTATTGGATATTATGTCTGTTTATTGGATGTTTAGTTG
77525 CTATGTTAGA
Statistics
Matches: 270, Mismatches: 19, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
171 138 0.51
174 2 0.01
175 1 0.00
176 20 0.07
177 1 0.00
178 1 0.00
182 1 0.00
184 1 0.00
185 105 0.39
ACGTcount: A:0.21, C:0.04, G:0.18, T:0.58
Consensus pattern (174 bp):
TGTTTATTGGATGTTTAGTTGCTATTTTAGTTGATGTTTATTTGTTATTTATTTGCTATTTAGTT
GTTGTGAATTCAATATTATTGGATATTATGTCTGTTTATTGGATGTTTAGTTGTCGTTTATTTGC
TATTTAGTTACTGTGATCAATTCAATATTATTGGATATTATGTT
Found at i:81162 original size:29 final size:29
Alignment explanation
Indices: 81120--81182 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
81110 AGCTTCAATA
* *
81120 TGTGTTGATGGATGTTA-ACTGCCATTTTT
1 TGTGTTGATAGATGTTACA-TGCCATCTTT
*
81149 TGTGTTGATAGATGTTACATGTCATCTTT
1 TGTGTTGATAGATGTTACATGCCATCTTT
81178 TGTGT
1 TGTGT
81183 CATTTTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.17, C:0.10, G:0.24, T:0.49
Consensus pattern (29 bp):
TGTGTTGATAGATGTTACATGCCATCTTT
Found at i:81199 original size:41 final size:41
Alignment explanation
Indices: 81142--81233 Score: 141
Period size: 41 Copynumber: 2.2 Consensus size: 41
81132 TGTTAACTGC
* * *
81142 CATTTTTTGTGTTGATAGATGTTACA-TGTCATCTTTTGTGT
1 CATTTTTTGTGTTGATAAATG-TAAAGTGTCATCTTTAGTGT
81183 CATTTTTTGTGTTGATAAATGTAAAGTGTCATCTTTAGTGT
1 CATTTTTTGTGTTGATAAATGTAAAGTGTCATCTTTAGTGT
81224 CATTTTTTGT
1 CATTTTTTGT
81234 ATATGGCATA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 3 0.06
41 44 0.94
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (41 bp):
CATTTTTTGTGTTGATAAATGTAAAGTGTCATCTTTAGTGT
Found at i:81679 original size:35 final size:35
Alignment explanation
Indices: 81624--81735 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 35
81614 TCTAAACCTT
* *
81624 AAATTGAAGTATTTTAGAATTTGAGGTTTAGAATG
1 AAATTAAATTATTTTAGAATTTGAGGTTTAGAATG
* *
81659 TAATTAAATTATTTTAGAATTT-AGGGTTTAGAATA
1 AAATTAAATTATTTTAGAATTTGA-GGTTTAGAATG
* * * *
81694 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTAAATTATTTTAGAATTTGAGGTTTAGAATG
81729 AAATTAA
1 AAATTAA
81736 GGAATGTTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 1 0.02
35 63 0.98
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.41
Consensus pattern (35 bp):
AAATTAAATTATTTTAGAATTTGAGGTTTAGAATG
Found at i:88305 original size:24 final size:24
Alignment explanation
Indices: 88273--88321 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
88263 AGCTGCCTTC
**
88273 ATTGGTTGCTGTACTATTATCAAT
1 ATTGGTTGCTCCACTATTATCAAT
*
88297 ATTGGTTGCTCCAGTATTATCAAT
1 ATTGGTTGCTCCACTATTATCAAT
88321 A
1 A
88322 AGCAGGATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (24 bp):
ATTGGTTGCTCCACTATTATCAAT
Found at i:90054 original size:14 final size:15
Alignment explanation
Indices: 90031--90061 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
90021 TTTTTTTTAA
90031 AAATATTTTAATTTT
1 AAATATTTTAATTTT
90046 AAATA-TTTAATTTT
1 AAATATTTTAATTTT
90060 AA
1 AA
90062 GATAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATATTTTAATTTT
Found at i:96317 original size:19 final size:19
Alignment explanation
Indices: 96280--96317 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
96270 TCACAATTAG
*
96280 GTATCTAATTTTTTATGGT
1 GTATCTAATCTTTTATGGT
96299 GTATCTAACTCTTTT-TGGT
1 GTATCTAA-TCTTTTATGGT
96318 ATAGTTGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.55
Consensus pattern (19 bp):
GTATCTAATCTTTTATGGT
Found at i:97929 original size:5 final size:5
Alignment explanation
Indices: 97919--97944 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
97909 TGACTTAGAA
97919 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
97945 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:103098 original size:23 final size:23
Alignment explanation
Indices: 103071--103168 Score: 169
Period size: 23 Copynumber: 4.3 Consensus size: 23
103061 CTTTTACAAG
*
103071 CCGTCTAAATCTTATACGGTGTT
1 CCGTCTAAGTCTTATACGGTGTT
103094 CCGTCTAAGTCTTATACGGTGTT
1 CCGTCTAAGTCTTATACGGTGTT
*
103117 TCGTCTAAGTCTTATACGGTGTT
1 CCGTCTAAGTCTTATACGGTGTT
*
103140 CCGTCTAAGTCTTATATGGTGTT
1 CCGTCTAAGTCTTATACGGTGTT
103163 CCGTCT
1 CCGTCT
103169 TTATTCCAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.41
Consensus pattern (23 bp):
CCGTCTAAGTCTTATACGGTGTT
Found at i:106801 original size:16 final size:16
Alignment explanation
Indices: 106782--106878 Score: 59
Period size: 16 Copynumber: 5.9 Consensus size: 16
106772 AACCATAACT
106782 GAAATTAACCCGAACC
1 GAAATTAACCCGAACC
** * *
106798 GAAAGCAACCCCAACT
1 GAAATTAACCCGAACC
* * *
106814 GAATTTTAACTCGATCC
1 GAA-ATTAACCCGAACC
* *
106831 GAAAATAACCCGAACT
1 GAAATTAACCCGAACC
* *
106847 GAATTTAACCCGACCCC
1 GAAATTAACCCGA-ACC
**
106864 GAAAGCAACCCGAAC
1 GAAATTAACCCGAAC
106879 AAATTGAAAT
Statistics
Matches: 55, Mismatches: 24, Indels: 4
0.66 0.29 0.05
Matches are distributed among these distances:
16 35 0.64
17 20 0.36
ACGTcount: A:0.40, C:0.32, G:0.13, T:0.14
Consensus pattern (16 bp):
GAAATTAACCCGAACC
Found at i:106875 original size:33 final size:32
Alignment explanation
Indices: 106778--106878 Score: 121
Period size: 33 Copynumber: 3.1 Consensus size: 32
106768 AATCAACCAT
* *
106778 AACTGAAATTAACCCGAACCGAAAGCAACCCC
1 AACTGAATTTAACCCGAACCGAAAGCAACCCG
* * **
106810 AACTGAATTTTAACTCGATCCGAAAATAACCCG
1 AACTGAA-TTTAACCCGAACCGAAAGCAACCCG
*
106843 AACTGAATTTAACCCGACCCCGAAAGCAACCCG
1 AACTGAATTTAACCCGA-ACCGAAAGCAACCCG
106876 AAC
1 AAC
106879 AAATTGAAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
32 16 0.28
33 41 0.72
ACGTcount: A:0.41, C:0.32, G:0.13, T:0.15
Consensus pattern (32 bp):
AACTGAATTTAACCCGAACCGAAAGCAACCCG
Found at i:112190 original size:57 final size:57
Alignment explanation
Indices: 112105--112246 Score: 200
Period size: 57 Copynumber: 2.5 Consensus size: 57
112095 TACTTTATTG
112105 AGTCCCTTGACTATTAAGAGTT--AAAATGATCCCCGACTATAGAAATTGCTTTCTTT
1 AGTCCCTTGACTA-TAAGAGTTACAAAATGATCCCCGACTATAGAAATTGCTTTCTTT
* *
112161 AGTCCCTTGACTATAAGAGTTACAAAATGATCCTCGACTATAGAAATTGTTTTCTTT
1 AGTCCCTTGACTATAAGAGTTACAAAATGATCCCCGACTATAGAAATTGCTTTCTTT
** *
112218 AGT-CCTCAACTATCAAAAGTTACAAAATG
1 AGTCCCTTGACTAT-AAGAGTTACAAAATG
112247 GTCACCCAAC
Statistics
Matches: 78, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
55 8 0.10
56 21 0.27
57 49 0.63
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (57 bp):
AGTCCCTTGACTATAAGAGTTACAAAATGATCCCCGACTATAGAAATTGCTTTCTTT
Done.