Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007378.1 Hibiscus syriacus cultivar Beakdansim tig00019814_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: 157030
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1444 original size:79 final size:80
Alignment explanation
Indices: 1286--1445 Score: 286
Period size: 79 Copynumber: 2.0 Consensus size: 80
1276 ATAATATGAT
* *
1286 TGGATTTTAATGATAACCCTTTTACATCAAAAAATTGTAATTGGTTACAATTAAAAAAAACATAA
1 TGGATTTTAATGATAACCCTTTTACATCAAAAAATTGAAATCGGTTACAATTAAAAAAAACATAA
1351 GAATTCACATATTTA
66 GAATTCACATATTTA
*
1366 TGGATTTTAATGATAACCCTTTTACATCAAAAAA-TGAAATCGGTTACAATTAAAAAAAACTTAA
1 TGGATTTTAATGATAACCCTTTTACATCAAAAAATTGAAATCGGTTACAATTAAAAAAAACATAA
1430 GAATTCACATATTTA
66 GAATTCACATATTTA
1445 T
1 T
1446 TTCAAAATCG
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 43 0.56
80 34 0.44
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (80 bp):
TGGATTTTAATGATAACCCTTTTACATCAAAAAATTGAAATCGGTTACAATTAAAAAAAACATAA
GAATTCACATATTTA
Found at i:5678 original size:29 final size:27
Alignment explanation
Indices: 5644--5854 Score: 188
Period size: 29 Copynumber: 7.4 Consensus size: 27
5634 GACGTTGACC
* *
5644 GGTGGTATTTTGGTAATTATTTTGAAAA
1 GGTGCTATTTTTGTAATTATTTT-AAAA
* *** *
5672 TGGTGGTATTCAGGTAATTATCTTGAAAA
1 -GGTGCTATTTTTGTAATTAT-TTTAAAA
* *
5701 GGTGTTTTTTTTGTAATTATTTTTCAAAA
1 GGTGCTATTTTTGTAATTA-TTTT-AAAA
**
5730 GGTGCTATTTTAATAATTATTTCTAAAA
1 GGTGCTATTTTTGTAATTATTT-TAAAA
5758 GGGTGCTATTTTTGTAATTATTTTTAAAA
1 -GGTGCTATTTTTGTAATTA-TTTTAAAA
* *
5787 GGTTCTATTTTAGTAATTATTTCTAAAA
1 GGTGCTATTTTTGTAATTATTT-TAAAA
*
5815 GGGTGTTATTTTTGTAATTATTTTAAAA
1 -GGTGCTATTTTTGTAATTATTTTAAAA
*
5843 GGGTGATATTTT
1 -GGTGCTATTTT
5855 CATAAAATGG
Statistics
Matches: 153, Mismatches: 21, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
27 3 0.02
28 61 0.40
29 84 0.55
30 5 0.03
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (27 bp):
GGTGCTATTTTTGTAATTATTTTAAAA
Found at i:5747 original size:57 final size:57
Alignment explanation
Indices: 5644--5859 Score: 242
Period size: 57 Copynumber: 3.8 Consensus size: 57
5634 GACGTTGACC
* * * * * * *
5644 GGTGGTATTTTGGTAATTATTTTGAAAATGGTGGTA-TTCAGGTAATTATCTT-GAAAA-
1 GGTGTTATTTTTGTAATTATTTTTAAAA-GGTGCTATTTTA-ATAATTAT-TTCTAAAAG
*
5701 GGTGTTTTTTTTGTAATTATTTTTCAAAAGGTGCTATTTTAATAATTATTTCTAAAAG
1 GGTGTTATTTTTGTAATTATTTTT-AAAAGGTGCTATTTTAATAATTATTTCTAAAAG
* * *
5759 GGTGCTATTTTTGTAATTATTTTTAAAAGGTTCTATTTTAGTAATTATTTCTAAAAG
1 GGTGTTATTTTTGTAATTATTTTTAAAAGGTGCTATTTTAATAATTATTTCTAAAAG
* *
5816 GGTGTTATTTTTGTAATTA-TTTTAAAAGGGTGATATTTTCATAA
1 GGTGTTATTTTTGTAATTATTTTTAAAA-GGTGCTATTTTAATAA
5860 AATGGTTGAT
Statistics
Matches: 137, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
56 10 0.07
57 98 0.72
58 29 0.21
ACGTcount: A:0.30, C:0.04, G:0.18, T:0.49
Consensus pattern (57 bp):
GGTGTTATTTTTGTAATTATTTTTAAAAGGTGCTATTTTAATAATTATTTCTAAAAG
Found at i:6603 original size:24 final size:24
Alignment explanation
Indices: 6569--6636 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
6559 TTTTTGACGA
*
6569 GATTTTGATATGATACTTGACTTG
1 GATTTTGATATGATACTTGACATG
* *
6593 GATTTTTATATGATACATGACATG
1 GATTTTGATATGATACTTGACATG
* *
6617 GATTCTGATATGCTACTTGA
1 GATTTTGATATGATACTTGA
6637 GCTGAATTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (24 bp):
GATTTTGATATGATACTTGACATG
Found at i:13226 original size:29 final size:28
Alignment explanation
Indices: 13184--13401 Score: 256
Period size: 29 Copynumber: 7.6 Consensus size: 28
13174 TCGTTAACCG
* * *
13184 GGTGGTATTTTGGTAATTATTTTGAAAA
1 GGTGCTATTTTTGTAATTATTTTTAAAA
* * * * *
13212 TGGTGGTATTCTGGTAATTATCTTGAAAA
1 -GGTGCTATTTTTGTAATTATTTTTAAAA
13241 TGGTGCTATTTTTGTAATTATTTTTAAAA
1 -GGTGCTATTTTTGTAATTATTTTTAAAA
* *
13270 GGTGCTATTTTAGTAATTATTTCTAAAAAA
1 GGTGCTATTTTTGTAATTATTT-T-TAAAA
*
13300 GGTACTATTTTTGTAATTATTTTTAAAA
1 GGTGCTATTTTTGTAATTATTTTTAAAA
* *
13328 GGTGCTATTTTAGTAATTATTTCTAAAA
1 GGTGCTATTTTTGTAATTATTTTTAAAA
13356 GGATGCTATTTTTGTAATTATTTTTAAAA
1 GG-TGCTATTTTTGTAATTATTTTTAAAA
*
13385 GGGTGCTATTTTCGTAA
1 -GGTGCTATTTTTGTAA
13402 AATGGTTGAT
Statistics
Matches: 167, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
28 52 0.31
29 89 0.53
30 26 0.16
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.48
Consensus pattern (28 bp):
GGTGCTATTTTTGTAATTATTTTTAAAA
Found at i:13308 original size:58 final size:58
Alignment explanation
Indices: 13184--13401 Score: 282
Period size: 58 Copynumber: 3.8 Consensus size: 58
13174 TCGTTAACCG
* * * * * * * * *
13184 GGTGGTATTTTGGTAATTATTTTGAAAATGGTGGTATTCTGGTAATTATCTT-GAAAAT
1 GGTGCTATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTAT-TTCTAAAAA
13242 GGTGCTATTTTTGTAATTATTTTTAAAA-GGTGCTATTTTAGTAATTATTTCTAAAAAA
1 GGTGCTATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTATTTCT-AAAAA
*
13300 GGTACTATTTTTGTAATTATTTTTAAAA-GGTGCTATTTTAGTAATTATTTCT-AAAA
1 GGTGCTATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTATTTCTAAAAA
*
13356 GGATGCTATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTCGTAA
1 GG-TGCTATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTAGTAA
13402 AATGGTTGAT
Statistics
Matches: 145, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
56 8 0.06
57 42 0.29
58 95 0.66
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.48
Consensus pattern (58 bp):
GGTGCTATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTATTTCTAAAAA
Found at i:13335 original size:86 final size:86
Alignment explanation
Indices: 13184--13401 Score: 267
Period size: 86 Copynumber: 2.5 Consensus size: 86
13174 TCGTTAACCG
* * * * * * *
13184 GGTGGTATTTTGGTAATTATTTTGAAAATGGTGGTATTCTGGTAATTATCTTGAAAATGGTGCTA
1 GGTGCTATTTTAGTAATTATTTTAAAAAAGGTGCTATTTTCGTAATTATCTTGAAAATGGTGCTA
* *
13249 TTTTTGTAATTATTTTTAAAA
66 TTTTAGTAATTATTTCTAAAA
* * * *
13270 GGTGCTATTTTAGTAATTATTTCTAAAAAAGGTACTATTTTTGTAATTATTTTTAAAA-GGTGCT
1 GGTGCTATTTTAGTAATTATTT-TAAAAAAGGTGCTATTTTCGTAATTATCTTGAAAATGGTGCT
13334 ATTTTAGTAATTATTTCTAAAA
65 ATTTTAGTAATTATTTCTAAAA
* * *
13356 GGATGCTATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTCGTAA
1 GG-TGCTATTTTAGTAATTATTTTAAAAAAGGTGCTATTTTCGTAA
13402 AATGGTTGAT
Statistics
Matches: 113, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
86 67 0.59
87 46 0.41
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.48
Consensus pattern (86 bp):
GGTGCTATTTTAGTAATTATTTTAAAAAAGGTGCTATTTTCGTAATTATCTTGAAAATGGTGCTA
TTTTAGTAATTATTTCTAAAA
Found at i:14140 original size:24 final size:24
Alignment explanation
Indices: 14113--14185 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
14103 ATTTTTTACG
14113 GGATTTTGATATGATACTTGACCT
1 GGATTTTGATATGATACTTGACCT
* * *
14137 GGATTTTTATATGATACATGACAT
1 GGATTTTGATATGATACTTGACCT
* * *
14161 AGATTCTGATCA-GCTACTTGACCT
1 GGATTTTGAT-ATGATACTTGACCT
14185 G
1 G
14186 AATTATGTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
24 37 0.97
25 1 0.03
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.38
Consensus pattern (24 bp):
GGATTTTGATATGATACTTGACCT
Found at i:14208 original size:2 final size:2
Alignment explanation
Indices: 14201--14225 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14191 TGTTTTAATT
14201 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
14226 CCATTATGAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20865 original size:56 final size:58
Alignment explanation
Indices: 20707--20917 Score: 243
Period size: 56 Copynumber: 3.7 Consensus size: 58
20697 TCGTTAACCA
* * * * * * * *
20707 GGTGGTATTTTGGTAATTATTTTGAAAATGGTGGTATTCT-GATAATTATCTT-GAAAAT
1 GGTGATATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTAG-TAATTAT-TTCTAAAAG
*
20765 GGTGATATTTTCGTAATTATTTTTAAAA-GGTGCTATTTTAGTAATTATTTCTAAAAG
1 GGTGATATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTATTTCTAAAAG
* *
20822 GGTGTTATTTTTGTAATTA-TTTTAAAA-GGTGTTATTTTAGTAATTATTTCTAAAAG
1 GGTGATATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTATTTCTAAAAG
* * *
20878 GATGCTATTTTTATAATTATTTTTAAAAGGGTGCTATTTT
1 GGTGATATTTTTGTAATTATTTTTAAAAGGGTGCTATTTT
20918 TCGTAAAATG
Statistics
Matches: 135, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
56 54 0.40
57 45 0.33
58 36 0.27
ACGTcount: A:0.30, C:0.04, G:0.18, T:0.49
Consensus pattern (58 bp):
GGTGATATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTATTTCTAAAAG
Found at i:20918 original size:29 final size:29
Alignment explanation
Indices: 20720--20918 Score: 192
Period size: 29 Copynumber: 7.0 Consensus size: 29
20710 GGTATTTTGG
* * * * *
20720 TAATTATTTTGAAAATGGTGGTATTCTGA
1 TAATTATTTTTAAAAGGGTGCTATTTTTA
* * * * **
20749 TAATTATCTTGAAAATGGTGATATTTTCG
1 TAATTATTTTTAAAAGGGTGCTATTTTTA
20778 TAATTATTTTTAAAA-GGTGCTA-TTTTA
1 TAATTATTTTTAAAAGGGTGCTATTTTTA
* * *
20805 GTAATTATTTCTAAAAGGGTGTTATTTTTG
1 -TAATTATTTTTAAAAGGGTGCTATTTTTA
*
20835 TAATTA-TTTTAAAA-GGTGTTA-TTTTA
1 TAATTATTTTTAAAAGGGTGCTATTTTTA
* *
20861 GTAATTATTTCTAAAAGGATGCTATTTTTA
1 -TAATTATTTTTAAAAGGGTGCTATTTTTA
20891 TAATTATTTTTAAAAGGGTGCTATTTTT
1 TAATTATTTTTAAAAGGGTGCTATTTTT
20919 CGTAAAATGG
Statistics
Matches: 143, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
26 4 0.03
27 16 0.11
28 34 0.24
29 80 0.56
30 9 0.06
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (29 bp):
TAATTATTTTTAAAAGGGTGCTATTTTTA
Found at i:21661 original size:24 final size:24
Alignment explanation
Indices: 21634--21702 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
21624 ATTTTTTACG
*
21634 GGATTTTGATATGATACTTGACCT
1 GGATTTTGATATGATACTTGACAT
* *
21658 GGATTTTTATATGATACATGACAT
1 GGATTTTGATATGATACTTGACAT
* *
21682 GGATTCTGATA-GCTACTTGAC
1 GGATTTTGATATGATACTTGAC
21703 TTGAATTATG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 8 0.21
24 30 0.79
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (24 bp):
GGATTTTGATATGATACTTGACAT
Found at i:22912 original size:24 final size:26
Alignment explanation
Indices: 22865--22912 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
22855 CAATAGTTCT
22865 CATACTATTTATATAAGATTTTTATC
1 CATACTATTTATATAAGATTTTTATC
*
22891 CATATTATTT-TAT-AGATTTTTA
1 CATACTATTTATATAAGATTTTTA
22913 ATCATGTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 3 0.14
26 9 0.43
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.54
Consensus pattern (26 bp):
CATACTATTTATATAAGATTTTTATC
Found at i:28305 original size:29 final size:29
Alignment explanation
Indices: 28263--28479 Score: 233
Period size: 29 Copynumber: 7.6 Consensus size: 29
28253 TCGTTAACCG
* * *
28263 GGTGGTATTTTGGTAATTATTTTGAAAAT
1 GGTGCTATTTTAGTAATTATTTTTAAAAT
* * * * * *
28292 GGTGGTATTCTGGTAATTATCTTGAAGAT
1 GGTGCTATTTTAGTAATTATTTTTAAAAT
28321 GGTGCTATTTTCA-TAATTATTTTTAAAA-
1 GGTGCTATTTT-AGTAATTATTTTTAAAAT
* * *
28349 GGTGCTATTTTAGTAATTATTTCTAGAAG
1 GGTGCTATTTTAGTAATTATTTTTAAAAT
*
28378 GGTGCTATTTTCGTAATTATTTTTAAAA-
1 GGTGCTATTTTAGTAATTATTTTTAAAAT
* * *
28406 GGTGTTATTTTAGTAATTATTTCTAAAAA
1 GGTGCTATTTTAGTAATTATTTTTAAAAT
* *
28435 GATGCTATTTTTGTAATTATTTTTAAAAT
1 GGTGCTATTTTAGTAATTATTTTTAAAAT
*
28464 GGTGCTATTTTCGTAA
1 GGTGCTATTTTAGTAA
28480 AATGATTGAT
Statistics
Matches: 160, Mismatches: 24, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
27 1 0.01
28 49 0.31
29 110 0.69
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.48
Consensus pattern (29 bp):
GGTGCTATTTTAGTAATTATTTTTAAAAT
Found at i:28385 original size:57 final size:58
Alignment explanation
Indices: 28262--28479 Score: 264
Period size: 57 Copynumber: 3.8 Consensus size: 58
28252 ATCGTTAACC
* * * * * * *
28262 GGGTGGTATTTTGGTAATTATTTTGAAAATGGTGGTATTCTGGTAATTA--TCTTGAA
1 GGGTGCTATTTTCGTAATTATTTTTAAAATGGTGCTATTTTAGTAATTATTTCTAGAA
*
28318 GATGGTGCTATTTTCATAATTATTTTTAAAA-GGTGCTATTTTAGTAATTATTTCTAGAA
1 G--GGTGCTATTTTCGTAATTATTTTTAAAATGGTGCTATTTTAGTAATTATTTCTAGAA
* *
28377 GGGTGCTATTTTCGTAATTATTTTTAAAA-GGTGTTATTTTAGTAATTATTTCTAAAA
1 GGGTGCTATTTTCGTAATTATTTTTAAAATGGTGCTATTTTAGTAATTATTTCTAGAA
* * * *
28434 AGATGCTATTTTTGTAATTATTTTTAAAATGGTGCTATTTTCGTAA
1 GGGTGCTATTTTCGTAATTATTTTTAAAATGGTGCTATTTTAGTAA
28480 AATGATTGAT
Statistics
Matches: 141, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
56 1 0.01
57 95 0.67
58 38 0.27
59 7 0.05
ACGTcount: A:0.28, C:0.06, G:0.18, T:0.48
Consensus pattern (58 bp):
GGGTGCTATTTTCGTAATTATTTTTAAAATGGTGCTATTTTAGTAATTATTTCTAGAA
Found at i:28435 original size:86 final size:85
Alignment explanation
Indices: 28263--28479 Score: 249
Period size: 86 Copynumber: 2.5 Consensus size: 85
28253 TCGTTAACCG
* * * * * *
28263 GGTGGTATTTTGGTAATTATTTTGAAAATGGTGGTATTCTGGTAATTATCTTGAAGATGGTGCTA
1 GGTGCTATTTTAGTAATTATTTT-AAAATGGTGCTATTTTCGTAATTATCTTGAAGAAGGTGCTA
*
28328 TTTTCATAATTATTTTTAAAA
65 TTTTCATAATTATTTTAAAAA
* * * * *
28349 GGTGCTATTTTAGTAATTATTTCTAGAAGGGTGCTATTTTCGTAATTATTTTTAA-AAGGTGTTA
1 GGTGCTATTTTAGTAATTATTT-TAAAATGGTGCTATTTTCGTAATTATCTTGAAGAAGGTGCTA
28413 TTTT-AGTAATTATTTCTAAAAA
65 TTTTCA-TAATTATTT-TAAAAA
* *
28435 GATGCTATTTTTGTAATTATTTTTAAAATGGTGCTATTTTCGTAA
1 GGTGCTATTTTAGTAATTA-TTTTAAAATGGTGCTATTTTCGTAA
28480 AATGATTGAT
Statistics
Matches: 111, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
84 1 0.01
85 20 0.18
86 86 0.77
87 4 0.04
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.48
Consensus pattern (85 bp):
GGTGCTATTTTAGTAATTATTTTAAAATGGTGCTATTTTCGTAATTATCTTGAAGAAGGTGCTAT
TTTCATAATTATTTTAAAAA
Found at i:28529 original size:10 final size:10
Alignment explanation
Indices: 28516--28545 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
28506 TTTGACCATA
28516 ACTTTGACCG
1 ACTTTGACCG
28526 ACTTTGACCG
1 ACTTTGACCG
28536 ACTTTGACCG
1 ACTTTGACCG
28546 GCTATTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (10 bp):
ACTTTGACCG
Found at i:29227 original size:24 final size:24
Alignment explanation
Indices: 29200--29272 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
29190 ATTTCTTACG
29200 GGATTTTGATATGATACTTGACCT
1 GGATTTTGATATGATACTTGACCT
* * *
29224 GGATTTTTATATGATACATGACAT
1 GGATTTTGATATGATACTTGACCT
* * *
29248 GGATTCTGATAAGCTACTTGACCT
1 GGATTTTGATATGATACTTGACCT
29272 G
1 G
29273 AATTATGTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (24 bp):
GGATTTTGATATGATACTTGACCT
Found at i:30632 original size:15 final size:15
Alignment explanation
Indices: 30612--30647 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
30602 TTACTGAACC
30612 CATGCTTGGTAATGA
1 CATGCTTGGTAATGA
*
30627 CATGCTTGGTATTGA
1 CATGCTTGGTAATGA
30642 CATGCT
1 CATGCT
30648 CCTCAACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (15 bp):
CATGCTTGGTAATGA
Found at i:41215 original size:10 final size:10
Alignment explanation
Indices: 41202--41270 Score: 68
Period size: 10 Copynumber: 6.7 Consensus size: 10
41192 CGACCCGACC
*
41202 CGTTGACCAA
1 CGTTGACCAG
41212 CGTTGACC-G
1 CGTTGACCAG
*
41221 CGTTGACCTG
1 CGTTGACCAG
41231 CGTTGACCAG
1 CGTTGACCAG
*
41241 AACTTTGACCAG
1 --CGTTGACCAG
*
41253 CGTTGACCGG
1 CGTTGACCAG
41263 CCGTTGAC
1 -CGTTGAC
41271 TTTTTATGGG
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
9 8 0.16
10 26 0.52
11 7 0.14
12 9 0.18
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (10 bp):
CGTTGACCAG
Found at i:41226 original size:19 final size:19
Alignment explanation
Indices: 41198--41261 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
41188 GACCCGACCC
*
41198 GACC-CGTTGACCAACGTT
1 GACCGCGTTGACCAGCGTT
*
41216 GACCGCGTTGACCTGCGTT
1 GACCGCGTTGACCAGCGTT
*
41235 GACCAGAACTTTGACCAGCGTT
1 GACC-G--CGTTGACCAGCGTT
41257 GACCG
1 GACCG
41262 GCCGTTGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
18 4 0.11
19 16 0.42
20 1 0.03
21 1 0.03
22 16 0.42
ACGTcount: A:0.20, C:0.31, G:0.27, T:0.22
Consensus pattern (19 bp):
GACCGCGTTGACCAGCGTT
Found at i:43582 original size:24 final size:24
Alignment explanation
Indices: 43555--43604 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
43545 GTTTTTTTTT
*
43555 ATTTCTGATATGAATTTTGTTCTG
1 ATTTCTGATATGAATTATGTTCTG
*
43579 ATTTCTGATCTGAATTATGTTCTG
1 ATTTCTGATATGAATTATGTTCTG
43603 AT
1 AT
43605 ATATGTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.10, G:0.16, T:0.52
Consensus pattern (24 bp):
ATTTCTGATATGAATTATGTTCTG
Found at i:43602 original size:12 final size:12
Alignment explanation
Indices: 43565--43633 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
43555 ATTTCTGATA
*
43565 TGAATTTTGTTC
1 TGAATTATGTTC
* * *
43577 TGATTTCTGATC
1 TGAATTATGTTC
43589 TGAATTATGTTC
1 TGAATTATGTTC
*
43601 TG-ATATATGTTT
1 TGAAT-TATGTTC
* *
43613 TGAATTCTGTTT
1 TGAATTATGTTC
*
43625 TGATTTATG
1 TGAATTATG
43634 ACATCTCTGT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.91
13 2 0.04
ACGTcount: A:0.20, C:0.07, G:0.17, T:0.55
Consensus pattern (12 bp):
TGAATTATGTTC
Found at i:43616 original size:24 final size:24
Alignment explanation
Indices: 43555--43634 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
43545 GTTTTTTTTT
* * *
43555 ATTTCTGATATGAATTTTGTTCTG
1 ATTTATGATCTGAATTATGTTCTG
*
43579 ATTTCTGATCTGAATTATGTTCTG
1 ATTTATGATCTGAATTATGTTCTG
* * * * *
43603 ATATATGTTTTGAATTCTGTTTTG
1 ATTTATGATCTGAATTATGTTCTG
43627 ATTTATGA
1 ATTTATGA
43635 CATCTCTGTT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.54
Consensus pattern (24 bp):
ATTTATGATCTGAATTATGTTCTG
Found at i:45139 original size:2 final size:2
Alignment explanation
Indices: 45132--45156 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45122 TTTTTAAAAC
45132 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
45157 CCCCCATCCC
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:45344 original size:12 final size:12
Alignment explanation
Indices: 45319--45388 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
45309 ACGAAGATAT
* *
45319 CAGAAATCAAAA
1 CAGAATTCAGAA
45331 CAGAATTCAGAA
1 CAGAATTCAGAA
45343 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
45355 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
45367 CAGAAATCATAA
1 CAGAATTCAGAA
45379 CAGAATTCAG
1 CAGAATTCAG
45389 GTCATTTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:45388 original size:48 final size:48
Alignment explanation
Indices: 45317--45408 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
45307 AAACGAAGAT
45317 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
* ** **
45365 ATCAGAAATCATAACAGAATTCAGGTCATTTATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAAT
45409 TCAAGTCGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
Found at i:45421 original size:48 final size:48
Alignment explanation
Indices: 45317--45423 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 48
45307 AAACGAAGAT
*
45317 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCAAG
* ** **
45365 ATCAGAAATCATAACAGAATTCAGGTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAA-TCAAG
*
45414 -TCGGAAATCA
1 ATCAGAAATCA
45424 GATAAAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 47 0.92
49 4 0.08
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCAAG
Found at i:45423 original size:24 final size:25
Alignment explanation
Indices: 45317--45425 Score: 100
Period size: 24 Copynumber: 4.5 Consensus size: 25
45307 AAACGAAGAT
*
45317 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
45341 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
45365 ATCAGAAATCATAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
45389 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
45414 -TCGGAAATCAGA
1 ATCAGAAATCAGA
45426 TAAAATATTT
Statistics
Matches: 67, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
23 2 0.03
24 61 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.19
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:46565 original size:18 final size:18
Alignment explanation
Indices: 46544--46584 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
46534 TTTTCCTTCC
* *
46544 ATTCGATCTTATTATTTA
1 ATTCAATCTTATCATTTA
46562 ATTCAATCTTATCATTTA
1 ATTCAATCTTATCATTTA
*
46580 CTTCA
1 ATTCA
46585 GTCCTTTCGA
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:0.29, C:0.17, G:0.02, T:0.51
Consensus pattern (18 bp):
ATTCAATCTTATCATTTA
Found at i:47787 original size:15 final size:15
Alignment explanation
Indices: 47767--47830 Score: 96
Period size: 15 Copynumber: 4.3 Consensus size: 15
47757 TGGTCAACGT
47767 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
47782 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
47797 GGGTCAACGGGTCAAC
1 GGGTCAAC-GGTCAAC
*
47813 GGGTC--GGGTCAAC
1 GGGTCAACGGTCAAC
47826 GGGTC
1 GGGTC
47831 GGGTCGGGTC
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
13 12 0.26
15 23 0.49
16 12 0.26
ACGTcount: A:0.22, C:0.25, G:0.39, T:0.14
Consensus pattern (15 bp):
GGGTCAACGGTCAAC
Found at i:47788 original size:8 final size:8
Alignment explanation
Indices: 47748--47830 Score: 95
Period size: 8 Copynumber: 10.5 Consensus size: 8
47738 TCAAAGTTTT
47748 GGTCAACAG
1 GGTCAAC-G
47757 TGGTCAACGTG
1 -GGTCAAC--G
47768 GGTCAAC-
1 GGTCAACG
47775 GGTCAACG
1 GGTCAACG
47783 GGTCAAC-
1 GGTCAACG
47790 GGTCAACG
1 GGTCAACG
47798 GGTCAACG
1 GGTCAACG
47806 GGTCAACG
1 GGTCAACG
47814 GGT---CG
1 GGTCAACG
47819 GGTCAACG
1 GGTCAACG
47827 GGTC
1 GGTC
47831 GGGTCGGGTC
Statistics
Matches: 66, Mismatches: 1, Indels: 14
0.81 0.01 0.17
Matches are distributed among these distances:
5 5 0.08
7 14 0.21
8 32 0.48
10 14 0.21
11 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.37, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:47835 original size:18 final size:18
Alignment explanation
Indices: 47796--47852 Score: 78
Period size: 18 Copynumber: 3.0 Consensus size: 18
47786 CAACGGTCAA
47796 CGGGTCAACGGGTCAACGGGT
1 CGGGTCAACGGGT---CGGGT
47817 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
*
47835 CGGGTCAACTGGTCGGGT
1 CGGGTCAACGGGTCGGGT
47853 AAACGGGTCG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
18 22 0.63
21 13 0.37
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.18
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:47839 original size:31 final size:31
Alignment explanation
Indices: 47804--47865 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
47794 AACGGGTCAA
*
47804 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
*
47835 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
47866 TATGACCGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
Found at i:47852 original size:13 final size:13
Alignment explanation
Indices: 47775--47835 Score: 68
Period size: 13 Copynumber: 4.3 Consensus size: 13
47765 GTGGGTCAAC
*
47775 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
47790 GGTCAACGGGTCAACG
1 GGTCAACGGGT---CG
47806 GGTCAACGGGTCG
1 GGTCAACGGGTCG
47819 GGTCAACGGGTCG
1 GGTCAACGGGTCG
47832 GGTC
1 GGTC
47836 GGGTCAACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
13 19 0.45
15 11 0.26
16 11 0.26
18 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.41, T:0.15
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:47861 original size:13 final size:13
Alignment explanation
Indices: 47830--47865 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
47820 GTCAACGGGT
*
47830 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
*
47843 CTGGTCGGGTAAA
1 CGGGTCGGGTAAA
47856 CGGGTCGGGT
1 CGGGTCGGGT
47866 TATGACCGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:50033 original size:23 final size:23
Alignment explanation
Indices: 49988--50045 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
49978 ACGAAGATAT
* *
49988 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATC-ATACAGAATCCAGAA
* *
50012 CAGATATCATACAGAATCCAGAT
1 CAGAAATCATACAGAATCCAGAA
50035 CAGAAATCATA
1 CAGAAATCATA
50046 ACATTCAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.52, C:0.19, G:0.12, T:0.17
Consensus pattern (23 bp):
CAGAAATCATACAGAATCCAGAA
Found at i:51199 original size:18 final size:18
Alignment explanation
Indices: 51178--51218 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
51168 TTTTCCTTCC
* *
51178 ATTCGATCTTATTATTTA
1 ATTCAATCTTATCATTTA
51196 ATTCAATCTTATCATTTA
1 ATTCAATCTTATCATTTA
*
51214 CTTCA
1 ATTCA
51219 GTCCTTTCGA
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:0.29, C:0.17, G:0.02, T:0.51
Consensus pattern (18 bp):
ATTCAATCTTATCATTTA
Found at i:52432 original size:8 final size:8
Alignment explanation
Indices: 52392--52475 Score: 79
Period size: 8 Copynumber: 10.5 Consensus size: 8
52382 TCAAAGTTTT
52392 GGTCAACAG
1 GGTCAAC-G
52401 TGGTCAACGTG
1 -GGTCAAC--G
52412 GGTCAAC-
1 GGTCAACG
52419 GGTCAACG
1 GGTCAACG
52427 GGTCAAAC-
1 GGTC-AACG
52435 GGTCAACG
1 GGTCAACG
52443 GGTCAACG
1 GGTCAACG
52451 GGTCAAC-
1 GGTCAACG
*
52458 GGT--TCG
1 GGTCAACG
52464 GGTCAACG
1 GGTCAACG
52472 GGTC
1 GGTC
52476 GGGTCGGGTC
Statistics
Matches: 64, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
5 1 0.02
6 3 0.05
7 13 0.20
8 29 0.45
9 3 0.05
10 14 0.22
11 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:52467 original size:13 final size:13
Alignment explanation
Indices: 52435--52480 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
52425 CGGGTCAAAC
52435 GGTCAACGGGTCAACG
1 GGTCAACGGGT---CG
*
52451 GGTCAACGGTTCG
1 GGTCAACGGGTCG
52464 GGTCAACGGGTCG
1 GGTCAACGGGTCG
52477 GGTC
1 GGTC
52481 GGGTCAACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 18 0.64
16 10 0.36
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:52484 original size:18 final size:18
Alignment explanation
Indices: 52441--52497 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
52431 AAACGGTCAA
*
52441 CGGGTCAACGGGTCAACGGTT
1 CGGGTCAACGGGT---CGGGT
52462 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
*
52480 CGGGTCAACTGGTCGGGT
1 CGGGTCAACGGGTCGGGT
52498 AAACGGGTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 21 0.62
21 13 0.38
ACGTcount: A:0.14, C:0.23, G:0.44, T:0.19
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:52487 original size:31 final size:31
Alignment explanation
Indices: 52449--52510 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
52439 AACGGGTCAA
*
52449 CGGGTCAAC-GGTTCGGGTCAACGGGTCGGGT
1 CGGGTCAACTGG-TCGGGTAAACGGGTCGGGT
52480 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
52511 TATGACCGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.15, C:0.21, G:0.45, T:0.19
Consensus pattern (31 bp):
CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
Found at i:52493 original size:13 final size:13
Alignment explanation
Indices: 52475--52510 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
52465 GTCAACGGGT
*
52475 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
*
52488 CTGGTCGGGTAAA
1 CGGGTCGGGTAAA
52501 CGGGTCGGGT
1 CGGGTCGGGT
52511 TATGACCGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:59723 original size:29 final size:29
Alignment explanation
Indices: 59690--59794 Score: 183
Period size: 29 Copynumber: 3.6 Consensus size: 29
59680 AACCCGACCC
59690 GGTGACATTTTGGGAATTATTTTGAAAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
59719 GGTGACATTTTGGGAATTATTTTGAAAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
**
59748 AATGACATTTTGGGAATTATTTTGAAAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
*
59777 TGTGACATTTTGGGAATT
1 GGTGACATTTTGGGAATT
59795 TTCGAATGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 72 1.00
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.39
Consensus pattern (29 bp):
GGTGACATTTTGGGAATTATTTTGAAAAA
Found at i:81699 original size:28 final size:28
Alignment explanation
Indices: 81649--81809 Score: 193
Period size: 28 Copynumber: 5.7 Consensus size: 28
81639 GTCCACATTC
*
81649 AAAAATT-CCAAAATGTCACCTTTTTCA
1 AAAAATTCCCAGAATGTCACCTTTTTCA
81676 AAATAATTCCCAGAATGTCA-CTTTTTCA
1 AAA-AATTCCCAGAATGTCACCTTTTTCA
*
81704 AAATAATTCCCAGAATATCACCTTTTTCA
1 AAA-AATTCCCAGAATGTCACCTTTTTCA
* * *
81733 CAAAATTCCCATAATGACACCTTTTTCA
1 AAAAATTCCCAGAATGTCACCTTTTTCA
*
81761 CAAAAATT-CCAAAATGTCACCTTTTTCA
1 -AAAAATTCCCAGAATGTCACCTTTTTCA
**
81789 CAAAAATTCTTAGAATGTCAC
1 -AAAAATTCCCAGAATGTCAC
81810 TAGGTCGGGT
Statistics
Matches: 117, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
27 3 0.03
28 79 0.68
29 35 0.30
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAAATTCCCAGAATGTCACCTTTTTCA
Found at i:81741 original size:56 final size:55
Alignment explanation
Indices: 81648--81810 Score: 202
Period size: 57 Copynumber: 2.9 Consensus size: 55
81638 AGTCCACATT
* *
81648 CAAAAATTCCAAAATGTCACCTTTTTCAAAATAATTCCCAGAATGTCACTTTTTCA
1 CAAAAATTCCAAAATATCACCTTTTTCACAA-AATTCCCAGAATGTCACTTTTTCA
* * *
81704 -AAATAATTCCCAGAATATCACCTTTTTCACAAAATTCCCATAATGACACCTTTTTCA
1 CAAA-AATT-CCAAAATATCACCTTTTTCACAAAATTCCCAGAATGTCA-CTTTTTCA
* **
81761 CAAAAATTCCAAAATGTCACCTTTTTCACAAAAATTCTTAGAATGTCACT
1 CAAAAATTCCAAAATATCACCTTTTTCAC-AAAATTCCCAGAATGTCACT
81811 AGGTCGGGTG
Statistics
Matches: 91, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
55 3 0.03
56 39 0.43
57 46 0.51
58 3 0.03
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (55 bp):
CAAAAATTCCAAAATATCACCTTTTTCACAAAATTCCCAGAATGTCACTTTTTCA
Found at i:81859 original size:9 final size:9
Alignment explanation
Indices: 81822--81872 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
81812 GGTCGGGTGG
*
81822 GGTCAGACC
1 GGTCAAACC
81831 GGTC-AACC
1 GGTCAAACC
*
81839 GGTTCGAACC
1 GG-TCAAACC
81849 GGTCAAACC
1 GGTCAAACC
*
81858 GGTACAGACC
1 GGT-CAAACC
81868 GGTCA
1 GGTCA
81873 TAACATCACC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
8 5 0.14
9 17 0.47
10 14 0.39
ACGTcount: A:0.25, C:0.31, G:0.29, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:81868 original size:19 final size:19
Alignment explanation
Indices: 81825--81872 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
81815 CGGGTGGGGT
*
81825 CAGACCGGTC-AACCGGTT
1 CAGACCGGTCAAACCGGTA
81843 C-GAACCGGTCAAACCGGTA
1 CAG-ACCGGTCAAACCGGTA
81862 CAGACCGGTCA
1 CAGACCGGTCA
81873 TAACATCACC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.04
18 8 0.31
19 16 0.62
20 1 0.04
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.12
Consensus pattern (19 bp):
CAGACCGGTCAAACCGGTA
Found at i:85901 original size:20 final size:20
Alignment explanation
Indices: 85876--85915 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
85866 AGCCATTATC
85876 CAGTAATGCAAAGTATGTAA
1 CAGTAATGCAAAGTATGTAA
85896 CAGTAATGCAAAGTATGTAA
1 CAGTAATGCAAAGTATGTAA
85916 TAGAATAAAT
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:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (20 bp):
CAGTAATGCAAAGTATGTAA
Found at i:89134 original size:28 final size:28
Alignment explanation
Indices: 89076--89312 Score: 232
Period size: 28 Copynumber: 8.4 Consensus size: 28
89066 CACATTCGAA
* *
89076 AATTCCCAAAATGTGAACTTTTTCAAAAT
1 AATTCCCAGAATGT-CACTTTTTCAAAAT
* *
89105 AATTCCCATAATGTCATTTTTTCAAAAT
1 AATTCCCAGAATGTCACTTTTTCAAAAT
*
89133 AATTCCCA-AATTTTCA-TTTTTCAAAAT
1 AATTCCCAGAA-TGTCACTTTTTCAAAAT
*
89160 AATCCCCAGAATGTCACTTTTTCAAAAT
1 AATTCCCAGAATGTCACTTTTTCAAAAT
* * *
89188 AATTCCTAGAATATCACTTTTTCACAAT
1 AATTCCCAGAATGTCACTTTTTCAAAAT
* *
89216 AATTCCTAGAATGTCACATTTTCACAAA-
1 AATTCCCAGAATGTCACTTTTTCA-AAAT
* * * *
89244 ATTTCCTAGAATGTCACATTTTGCACAA-
1 AATTCCCAGAATGTCAC-TTTTTCAAAAT
* *
89272 AATTCCTAGAATGTTACCTTTTTCACAAA-
1 AATTCCCAGAATGTCA-CTTTTTCA-AAAT
89301 AATTCCCAGAAT
1 AATTCCCAGAAT
89313 ATCAATGGGT
Statistics
Matches: 179, Mismatches: 22, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
27 24 0.13
28 121 0.68
29 34 0.19
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.37
Consensus pattern (28 bp):
AATTCCCAGAATGTCACTTTTTCAAAAT
Found at i:100999 original size:64 final size:65
Alignment explanation
Indices: 100929--101069 Score: 176
Period size: 64 Copynumber: 2.2 Consensus size: 65
100919 TGGAACACTT
** * * * *
100929 AGTGCATCGATGCATTAAGTGTGCATCGATGCATGAAATACATTCGATGTTTTGAAT-AAGCCTA
1 AGTGCATCGATGCAGGAAGTGTGCATCGATGCATAAAATACAATCGATGTTTTCAATAAAACCTA
** * * *
100993 AGTGCATCGATGCAGGGTGTGTGCATCGATGCATAAAATGCAATCGATGTTTTCATTAAAACCTG
1 AGTGCATCGATGCAGGAAGTGTGCATCGATGCATAAAATACAATCGATGTTTTCAATAAAACCTA
101058 AGTGCATCGATG
1 AGTGCATCGATG
101070 TATAAATTAC
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
64 48 0.74
65 17 0.26
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (65 bp):
AGTGCATCGATGCAGGAAGTGTGCATCGATGCATAAAATACAATCGATGTTTTCAATAAAACCTA
Found at i:101125 original size:20 final size:20
Alignment explanation
Indices: 101100--101137 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
101090 CAATTTATTC
101100 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
101120 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
101138 TCCTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:103798 original size:24 final size:24
Alignment explanation
Indices: 103777--103833 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
103767 TCATGATGTC
103777 TCGATGCACATACAAAGAGATGCA
1 TCGATGCACATACAAAGAGATGCA
* * *
103801 TCGATGTACATACAAAGGGTTGCA
1 TCGATGCACATACAAAGAGATGCA
103825 TCGATGCAC
1 TCGATGCAC
103834 TGTTCAGTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (24 bp):
TCGATGCACATACAAAGAGATGCA
Found at i:108848 original size:64 final size:65
Alignment explanation
Indices: 108776--108955 Score: 202
Period size: 64 Copynumber: 2.8 Consensus size: 65
108766 TGGAACACTT
* * * *
108776 AGTGCATCGGTGCATTAAGTGTGCATCAATGCATAAAATGCATTTGATGTTTTGAAT-AAGCCTA
1 AGTGCATCGGTGCATGAAGTGTGCATCAATGCATAAAATGCATTCGATGTTTTCAATAAAACCTA
** * * *
108840 AGTGCATCGAGT-CATGGTGTGTGCATCGATGCATAAAATGCAATCGATGTTTTCATTAAAACCT
1 AGTGCATCG-GTGCATGAAGTGTGCATCAATGCATAAAATGCATTCGATGTTTTCAATAAAACCT
*
108904 G
65 A
* ** * *
108905 AGTGCATCGATGCATGAAGAATGCATCAATGCATAAACTACATTCGATGTT
1 AGTGCATCGGTGCATGAAGTGTGCATCAATGCATAAAATGCATTCGATGTT
108956 CAATTTATTC
Statistics
Matches: 94, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
64 47 0.50
65 47 0.50
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (65 bp):
AGTGCATCGGTGCATGAAGTGTGCATCAATGCATAAAATGCATTCGATGTTTTCAATAAAACCTA
Found at i:110172 original size:13 final size:13
Alignment explanation
Indices: 110154--110180 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
110144 CGCGTCATTT
110154 ACGATCAATACTA
1 ACGATCAATACTA
110167 ACGATCAATACTA
1 ACGATCAATACTA
110180 A
1 A
110181 GATATTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.22
Consensus pattern (13 bp):
ACGATCAATACTA
Found at i:112724 original size:13 final size:13
Alignment explanation
Indices: 112706--112743 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
112696 CGACCCGACT
112706 GACCCGTTGACCC
1 GACCCGTTGACCC
*
112719 GACCCGTGGACCC
1 GACCCGTTGACCC
*
112732 AACCCGTTGACC
1 GACCCGTTGACC
112744 GGGTGCTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (13 bp):
GACCCGTTGACCC
Found at i:119912 original size:17 final size:18
Alignment explanation
Indices: 119877--119915 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
119867 GACCGGTTTC
119877 GACCCGACACGACCCGTT
1 GACCCGACACGACCCGTT
*
119895 GACCCGACCCGA-CCGTT
1 GACCCGACACGACCCGTT
119912 GACC
1 GACC
119916 GTAGATCGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.21, C:0.46, G:0.23, T:0.10
Consensus pattern (18 bp):
GACCCGACACGACCCGTT
Found at i:120008 original size:28 final size:29
Alignment explanation
Indices: 119923--120019 Score: 142
Period size: 29 Copynumber: 3.4 Consensus size: 29
119913 ACCGTAGATC
*
119923 GGGTGCTATTTTGGGAATTAATTCGAAAT
1 GGGTGCTATTTTGGGAATTAATTCGAAAA
119952 GGGTGCTATTTTGGGAATTAATTCGAAAA
1 GGGTGCTATTTTGGGAATTAATTCGAAAA
* * **
119981 GGGTGCTA-TTTGGTAATTATTTTAAAAA
1 GGGTGCTATTTTGGGAATTAATTCGAAAA
120009 GGGTGCTATTT
1 GGGTGCTATTT
120020 CTGTAAAATG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
28 24 0.39
29 38 0.61
ACGTcount: A:0.28, C:0.06, G:0.27, T:0.39
Consensus pattern (29 bp):
GGGTGCTATTTTGGGAATTAATTCGAAAA
Found at i:121311 original size:21 final size:21
Alignment explanation
Indices: 121285--121324 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
121275 TTTGTATATA
121285 TCTGTATTATTAATATTTTGT
1 TCTGTATTATTAATATTTTGT
121306 TCTGTATTATTAATATTTT
1 TCTGTATTATTAATATTTT
121325 AAGCTGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (21 bp):
TCTGTATTATTAATATTTTGT
Found at i:121331 original size:21 final size:21
Alignment explanation
Indices: 121286--121336 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
121276 TTGTATATAT
***
121286 CTGTATTATTAATATTTTGTT
1 CTGTATTATTAATATTTTAAG
121307 CTGTATTATTAATATTTTAAG
1 CTGTATTATTAATATTTTAAG
121328 CTGTATTAT
1 CTGTATTAT
121337 ATCTAATGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.57
Consensus pattern (21 bp):
CTGTATTATTAATATTTTAAG
Found at i:124458 original size:29 final size:29
Alignment explanation
Indices: 124413--124595 Score: 171
Period size: 29 Copynumber: 6.3 Consensus size: 29
124403 ACCCTACCCG
124413 GTGATATTTTGGGAATTATTTTGAAAAAT
1 GTGATATTTTGGGAATTATTTTGAAAAAT
* *
124442 GTGATATTTTGGAAATTATTTTGAAAAAA
1 GTGATATTTTGGGAATTATTTTGAAAAAT
* *
124471 GTGACAATTTGGG-ATT-TTTT-AAAAAT
1 GTGATATTTTGGGAATTATTTTGAAAAAT
* * * *
124497 AGTGACATTCTGGTAATTA-TTTGTAAAAT
1 -GTGATATTTTGGGAATTATTTTGAAAAAT
* *
124526 GATGCTATTTTGGGAATTA-TTTGTAAAAT
1 G-TGATATTTTGGGAATTATTTTGAAAAAT
* *
124555 GGTGATATTTTGGTAATTATTTT-ACATAAAG
1 -GTGATATTTTGGGAATTATTTTGA-A-AAAT
124586 GTGATATTTT
1 GTGATATTTT
124596 TGTAATTTTC
Statistics
Matches: 127, Mismatches: 18, Indels: 17
0.78 0.11 0.10
Matches are distributed among these distances:
26 5 0.04
27 14 0.11
28 10 0.08
29 80 0.63
30 15 0.12
31 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (29 bp):
GTGATATTTTGGGAATTATTTTGAAAAAT
Found at i:132926 original size:30 final size:31
Alignment explanation
Indices: 132891--132948 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
132881 AGTTATAAAG
* * *
132891 TGGTGGATTTAATT-AATATTTTGAAAGAAA
1 TGGTGGATTAAATTGAAAATTTTCAAAGAAA
132921 TGGTGGATTAAATTGAAAATTTTCAAAG
1 TGGTGGATTAAATTGAAAATTTTCAAAG
132949 TTTGCAGACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.38
Consensus pattern (31 bp):
TGGTGGATTAAATTGAAAATTTTCAAAGAAA
Found at i:143839 original size:24 final size:25
Alignment explanation
Indices: 143811--143864 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
143801 GAATATTTTA
*
143811 TCTGATTTCC-GATTTGAATTTTGT
1 TCTGATTACCTGATTTGAATTTTGT
143835 TCTGA-TACCTGATTTGAATTTTGT
1 TCTGATTACCTGATTTGAATTTTGT
*
143859 TATGAT
1 TCTGAT
143865 ATCTAACCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (25 bp):
TCTGATTACCTGATTTGAATTTTGT
Done.