Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007205.1 Hibiscus syriacus cultivar Beakdansim tig00019033_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: 53688
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:4776 original size:3 final size:3
Alignment explanation
Indices: 4713--4760 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
4703 TTTGTGTGTA
*
4713 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4761 TTATTTGTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5075 original size:35 final size:36
Alignment explanation
Indices: 4998--5096 Score: 121
Period size: 36 Copynumber: 2.8 Consensus size: 36
4988 TAGTTTTTAT
* * *
4998 GTTTTCGAAAACATATAATACATAGTTAAAAAAATGA
1 GTTTT-GAAAACATATAATATATAGTTTAAAAAATCA
*
5035 TTTTTGAAAACATATAATATATAGTTTAAAAAA-CA
1 GTTTTGAAAACATATAATATATAGTTTAAAAAATCA
*
5070 GTTTTGAAGACATAT-ATAATATAGTTT
1 GTTTTGAAAACATATAAT-ATATAGTTT
5097 TTGAAAACAT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
34 2 0.04
35 23 0.42
36 26 0.47
37 4 0.07
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.36
Consensus pattern (36 bp):
GTTTTGAAAACATATAATATATAGTTTAAAAAATCA
Found at i:5149 original size:35 final size:34
Alignment explanation
Indices: 5036--5149 Score: 97
Period size: 35 Copynumber: 3.1 Consensus size: 34
5026 AAAAAATGAT
5036 TTTTGAAAACATATAATATATAG--TTTAAAAAACA
1 TTTTGAAAA-ATAT-ATATATAGTTTTTAAAAAACA
* *
5070 GTTTTGAAGACATATATAATATAGTTTTTGAAAACATATTA
1 -TTTTGAA-AAATATAT-ATATAGTTTTT-AAAA-A-A-CA
*
5111 TTTTGAAAAATTATATATATAGTTTTTTAAAAACA
1 TTTTGAAAAA-TATATATATAGTTTTTAAAAAACA
5146 TTTT
1 TTTT
5150 TTAAACATAA
Statistics
Matches: 65, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
34 2 0.03
35 22 0.34
36 2 0.03
37 4 0.06
38 7 0.11
39 14 0.22
40 13 0.20
41 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (34 bp):
TTTTGAAAAATATATATATAGTTTTTAAAAAACA
Found at i:5166 original size:40 final size:40
Alignment explanation
Indices: 5081--5178 Score: 105
Period size: 39 Copynumber: 2.5 Consensus size: 40
5071 TTTTGAAGAC
* *
5081 ATATATA-ATATAGTTTTTGAAAACATATTATTTTGAAAA
1 ATATATATATATAGTTTTTGAAAACACATTATTTTAAAAA
*
5120 AT-TATATATATAGTTTTTTAAAA-ACATT-TTTTAAACATA
1 ATATATATATATAGTTTTTGAAAACACATTATTTTAAA-A-A
*
5159 ATATATATTATAAAGTTTTT
1 ATATATA-TATATAGTTTTT
5179 AAATATACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
37 6 0.12
38 9 0.18
39 20 0.40
40 4 0.08
41 11 0.22
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (40 bp):
ATATATATATATAGTTTTTGAAAACACATTATTTTAAAAA
Found at i:5202 original size:10 final size:10
Alignment explanation
Indices: 5187--5215 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5177 TTAAATATAC
5187 ATATATTATT
1 ATATATTATT
5197 ATATATTATT
1 ATATATTATT
5207 AT-TATTATT
1 ATATATTATT
5216 TTACTTTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATATATTATT
Found at i:5256 original size:18 final size:18
Alignment explanation
Indices: 5211--5259 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
5201 ATTATTATTA
5211 TTAT-TTTACTTTCCTTTT
1 TTATCTTTA-TTTCCTTTT
* *
5229 TTCTCATTTATTTTCTTTT
1 TTATC-TTTATTTCCTTTT
5248 TTATCTTTATTT
1 TTATCTTTATTT
5260 AAGGTCGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.38
19 12 0.46
20 4 0.15
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.73
Consensus pattern (18 bp):
TTATCTTTATTTCCTTTT
Found at i:6442 original size:15 final size:14
Alignment explanation
Indices: 6422--6480 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 14
6412 ACCCTTGACT
6422 TTTAATTCTTTTCAA
1 TTTAATTCTTTT-AA
* *
6437 TTTAATCCTTTTAG
1 TTTAATTCTTTTAA
6451 TTTAA-T-TTTTAA
1 TTTAATTCTTTTAA
*
6463 TTTTTATTCTTTT-A
1 -TTTAATTCTTTTAA
6477 TTTA
1 TTTA
6481 TTTAATTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
12 5 0.14
13 7 0.20
14 8 0.23
15 15 0.43
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTAATTCTTTTAA
Found at i:15626 original size:3 final size:3
Alignment explanation
Indices: 15577--15606 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
15567 TTTGTATGTA
15577 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
15607 TTATTTGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17372 original size:24 final size:24
Alignment explanation
Indices: 17326--17374 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
17316 AGTTTAATTT
*
17326 TTTTTATTTCTTTTAATTATTTAA
1 TTTTTATTTATTTTAATTATTTAA
*
17350 TTTTTATTTAATTTT-ATTGTTTAA
1 TTTTTATTT-ATTTTAATTATTTAA
17374 T
1 T
17375 AGTTGTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTTTATTTATTTTAATTATTTAA
Found at i:18392 original size:18 final size:18
Alignment explanation
Indices: 18365--18406 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
18355 TGGGGTAGGA
*
18365 ATTTTTATTTTCATTAT-T
1 ATTTTAATTTTCATT-TCT
*
18383 ATTTTAATTTTTATTTCT
1 ATTTTAATTTTCATTTCT
18401 ATTTTA
1 ATTTTA
18407 CTAACTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTAATTTTCATTTCT
Found at i:18405 original size:12 final size:12
Alignment explanation
Indices: 18364--18398 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
18354 GTGGGGTAGG
18364 AATTTTTATTTT
1 AATTTTTATTTT
* *
18376 CATTATTATTTT
1 AATTTTTATTTT
18388 AATTTTTATTT
1 AATTTTTATTT
18399 CTATTTTACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (12 bp):
AATTTTTATTTT
Found at i:30028 original size:2 final size:2
Alignment explanation
Indices: 30021--30053 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
30011 ATAAAATGAT
30021 TA TA TA TA 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 TA TA TA TA T
30054 TAAATATCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31878 original size:3 final size:3
Alignment explanation
Indices: 31859--31926 Score: 86
Period size: 3 Copynumber: 22.3 Consensus size: 3
31849 GTAAAAAATG
*
31859 ATA ATA A-A AAA ATTA ATA ATA ATA AT- ATAA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
31904 ATA ATA ATA ATAA ATA ATA ATA A
1 ATA ATA ATA AT-A ATA ATA ATA A
31927 CCCAGAAAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
2 4 0.07
3 48 0.81
4 7 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:32560 original size:41 final size:42
Alignment explanation
Indices: 32515--32596 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
32505 TGGAGGTCTT
* * *
32515 ATAGATGGCACAAATGACTT-ATCATCTTGCTCGAAAGACTG
1 ATAGATGACACAAAGGACTTAATCATCATGCTCGAAAGACTG
* *
32556 ATAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACT
1 ATAGATGACACAAAGGACTTAATCATCATGCTCGAAAGACT
32597 TACTGATGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 16 0.46
42 19 0.54
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (42 bp):
ATAGATGACACAAAGGACTTAATCATCATGCTCGAAAGACTG
Found at i:32771 original size:257 final size:257
Alignment explanation
Indices: 32065--33253 Score: 1481
Period size: 257 Copynumber: 4.7 Consensus size: 257
32055 AGATAACCTA
**
32065 AAGGATTTAATCATCATGCTCGATGGACTTACTGATGGCCCGAAGGACTTACTAATTTTGGGAAA
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAA-TTTGGGAAA
* * * *
32130 TAGTTTATTGAGTAAGAAACTTTGGAAATTGCTTTCTTACTTTTCAAAAATTTCATTTTCTAAAA
65 TAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAA
** * **
32195 ACATTAAATGAGAAACTTTGGAAATCACTTTCTCTCTTTTCGAAAATCATGTGGAAACATACTAC
130 ACATTAAATGAGAAACTTTGGAAATCACTTTCT-AATTTTCAAAAATCATGTGGAAACAT-CTTG
** * *
32260 CT-GAAGGTCTTATAGATGGCCTGAAGGACTTATCATCTTGCTCTAAAGA---A-AGATGACTCG
193 CTCGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCG
* * *
32320 AAGAATTTAATTATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTACTAATTTGGGAAAT
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTGGGAAAT
32385 AGTTTACTGGGTAAGAAAC--T-----T---TTTCTTACTTTTCAAAAATTTCATTTTCTGAAAA
66 AGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAA
*** * * * *
32440 CATTAAATGAGAAACTTTGGAAATTGTTTTCTCATTTTTCGAGAATAATGTGGAAACATCCTT-C
131 CATTAAATGAGAAACTTTGGAAATCACTTTCT-AATTTTCAAAAATCATGTGGAAACAT-CTTGC
* * * * * *
32504 TTGGAGGTCTTATAGATGGCACAAATGACTTATCATCTTGCTCGAAAGACTGATAGATGACCCA
194 TCGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCG
* * *
32568 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCTCGAAGGATTTACCAATTTGGGAAAT
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTGGGAAAT
* *
32633 AGTTTACT-GGTAAGAAACTTTGGAAATCGCTTTCTTACATTTAAAAAATTTCATTTTCTGAAAA
66 AGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAA
*
32697 CATTAAATGAGAAACTTTGGAAATCACTTTCTAAATTTTCAAAAATCATGTGGAAACATGTTGCT
131 CATTAAATGAGAAACTTTGGAAATCACTTTCT-AATTTTCAAAAATCATGTGGAAACATCTTGCT
* *
32762 CGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAAACAGACAGATGACCCG
195 CGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCG
* * * * * *
32825 AAGGATTTAATCATCATGCTCAAAAAATTTAATGATGGCCCGAAGGACTTATTAATTTTGGAAAT
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTGGGAAAT
* * *
32890 AATTTACTGGGTAAGAAACTTAGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTT-TAGAAC
66 AGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCT-GAAA
* ** * *
32954 ACACTAAATGAGAAACTTTAAAAATCGCTTTCTAATTTTGCAAAAATCATGTGGAAACATCATGC
130 ACATTAAATGAGAAACTTTGGAAATCACTTTCTAATTTT-CAAAAATCATGTGGAAACATCTTGC
* * * * *
33019 CCGAAGGTCTTATAGATGGCCCGAAGGATTTATTATCTTGCTCGAAAGACTTACAGATGACCCG
194 TCGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCG
* * * * *
33083 AAGGATTTAAGCATCATGCTTGAAAGACTTACT-A--ACCCGAAAGACTTAC-ATATTTTGGAAA
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTA-ATTTGGGAAA
* * * *
33144 TAGTTTACTGGGTAAGAAACTTTGTAAATCACTTTATTACTTTTTAAAAATTTCATTTTCAT-AA
65 TAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTC-TGAA
* *
33208 AAGATTTAAATGAGAAACTTTGGAAATCGA-TTTCTCATTTTCAAAA
129 AACA-TTAAATGAGAAACTTTGGAAATC-ACTTTCTAATTTTCAAAA
33254 CAACTTAATG
Statistics
Matches: 811, Mismatches: 99, Indels: 48
0.85 0.10 0.05
Matches are distributed among these distances:
243 2 0.00
244 128 0.16
247 12 0.01
248 75 0.09
249 1 0.00
252 1 0.00
254 29 0.04
255 134 0.17
256 32 0.04
257 212 0.26
258 185 0.23
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (257 bp):
AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTGGGAAAT
AGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAA
CATTAAATGAGAAACTTTGGAAATCACTTTCTAATTTTCAAAAATCATGTGGAAACATCTTGCTC
GAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCG
Found at i:33089 original size:41 final size:42
Alignment explanation
Indices: 33011--33114 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 42
33001 CATGTGGAAA
* * * * * *
33011 CATCATGCCCGAAGGTCTTATAGATGGCCCGAAGGATTT-AT
1 CATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAG
* *
33052 TATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAG
1 CATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAG
*
33094 CATCATGCTTGAAAGACTTAC
1 CATCATGCTCGAAAGACTTAC
33115 TAACCCGAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 32 0.63
42 19 0.37
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAG
Found at i:41464 original size:2 final size:2
Alignment explanation
Indices: 41457--41540 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
41447 CATAAATGAT
41457 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41499 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41541 CATTGGACTT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43457 original size:15 final size:16
Alignment explanation
Indices: 43426--43463 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
43416 GTAAAAAACG
*
43426 ATAATAGAAATTAATA
1 ATAATATAAATTAATA
43442 ATAATATAAA-TAATA
1 ATAATATAAATTAATA
43457 ATAATAT
1 ATAATAT
43464 TATTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
ATAATATAAATTAATA
Found at i:47199 original size:13 final size:13
Alignment explanation
Indices: 47183--47216 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
47173 TTCTAGCAAA
47183 CATTTCTTCATTT
1 CATTTCTTCATTT
*
47196 CATTTTTTCATTT
1 CATTTCTTCATTT
47209 CATTTCTT
1 CATTTCTT
47217 TTACTATCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.65
Consensus pattern (13 bp):
CATTTCTTCATTT
Found at i:50871 original size:51 final size:53
Alignment explanation
Indices: 50758--50883 Score: 177
Period size: 51 Copynumber: 2.4 Consensus size: 53
50748 AAATATTTCA
* * * *
50758 CTTAGGGTGAAAACCCCAAA-GGTTCCTTAAGTAAAAAAAGCTTAAAAAGATG
1 CTTAGGGTGAAAACCCGAAAGGGTGCCTTAAATAAAAAAAGCTCAAAAAGATG
50810 CTTAGGGTGAAAACCCGAAAGGGTGCCTTAAAT-AAAAAAG-TCAAAAAGATG
1 CTTAGGGTGAAAACCCGAAAGGGTGCCTTAAATAAAAAAAGCTCAAAAAGATG
* *
50861 TTTAGAGTGAAAACCCGAAAGGG
1 CTTAGGGTGAAAACCCGAAAGGG
50884 CGCTCTAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
51 31 0.46
52 26 0.39
53 10 0.15
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (53 bp):
CTTAGGGTGAAAACCCGAAAGGGTGCCTTAAATAAAAAAAGCTCAAAAAGATG
Found at i:51624 original size:25 final size:24
Alignment explanation
Indices: 51572--51625 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
51562 AATCAAGAAC
*
51572 CAAGAATCAGGAAATCAGAATAAG
1 CAAGAATCAGGAAATCAGAAAAAG
*
51596 CAAGAATCA-GAAACGTCAGAAAAAT
1 CAAGAATCAGGAAA--TCAGAAAAAG
51621 CAAGA
1 CAAGA
51626 CTGACAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 4 0.15
24 9 0.35
25 13 0.50
ACGTcount: A:0.56, C:0.15, G:0.19, T:0.11
Consensus pattern (24 bp):
CAAGAATCAGGAAATCAGAAAAAG
Found at i:51929 original size:32 final size:32
Alignment explanation
Indices: 51888--52083 Score: 117
Period size: 32 Copynumber: 5.6 Consensus size: 32
51878 TCAATTTACA
51888 CTCAACTTCACGACGAATGAGTCACCTACGAT
1 CTCAACTTCACGACGAATGAGTCACCTACGAT
* *
51920 CTCAACTTCAGGACGAAGGATATCGTGC-CCAATA-GATT
1 CTCAACTTCACGACGAATG--A--GT-CACC--TACGA-T
* *
51958 GACTCAACTTCATGACGAAGGAGTCACCTACGAT
1 --CTCAACTTCACGACGAATGAGTCACCTACGAT
* * *
51992 TTCAACTTCACGACGAATGATATCATGCCTAATAGATT
1 CTCAACTTCACGACGAATGA-GTCA--CCT-A-CGA-T
* * *
52030 GACTCAACTTCATGACGTATGAGCCACCTACGAT
1 --CTCAACTTCACGACGAATGAGTCACCTACGAT
*
52064 TTCAACTTCACGACGAATGA
1 CTCAACTTCACGACGAATGA
52084 TATCGTGCCT
Statistics
Matches: 127, Mismatches: 17, Indels: 40
0.69 0.09 0.22
Matches are distributed among these distances:
32 51 0.40
33 3 0.02
34 5 0.04
35 8 0.06
36 10 0.08
37 8 0.06
38 5 0.04
39 2 0.02
40 35 0.28
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (32 bp):
CTCAACTTCACGACGAATGAGTCACCTACGAT
Found at i:51975 original size:40 final size:40
Alignment explanation
Indices: 51920--52115 Score: 126
Period size: 40 Copynumber: 5.3 Consensus size: 40
51910 CACCTACGAT
*
51920 CTCAACTTCAGGACGAAGGATATCGTGCCCAATAGATTGA
1 CTCAACTTCATGACGAAGGATATCGTGCCCAATAGATTGA
51960 CTCAACTTCATGACGAAGG--A--GT-CACC--TACGATT--
1 CTCAACTTCATGACGAAGGATATCGTGC-CCAATA-GATTGA
* * * *
51993 -TCAACTTCACGACGAATGATATCATGCCTAATAGATTGA
1 CTCAACTTCATGACGAAGGATATCGTGCCCAATAGATTGA
* *
52032 CTCAACTTCATGAC----G-TAT-GAG-CCACCTACGATT--
1 CTCAACTTCATGACGAAGGATATCGTGCCCA-ATA-GATTGA
* * *
52065 -TCAACTTCACGACGAATGATATCGTGCCTAATAGATTGA
1 CTCAACTTCATGACGAAGGATATCGTGCCCAATAGATTGA
52104 CTCAACTTCATG
1 CTCAACTTCATG
52116 GCAAATGAGT
Statistics
Matches: 117, Mismatches: 15, Indels: 48
0.65 0.08 0.27
Matches are distributed among these distances:
32 28 0.24
33 2 0.02
34 6 0.05
35 12 0.10
36 8 0.07
37 12 0.10
38 7 0.06
39 2 0.02
40 40 0.34
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (40 bp):
CTCAACTTCATGACGAAGGATATCGTGCCCAATAGATTGA
Found at i:52007 original size:72 final size:72
Alignment explanation
Indices: 51887--52132 Score: 384
Period size: 72 Copynumber: 3.4 Consensus size: 72
51877 TTCAATTTAC
* * * * *
51887 ACTCAACTTCACGACGAATGAGTCACCTACGATCTCAACTTCAGGACGAAGGATATCGTGCCCAA
1 ACTCAACTTCATGACGAATGAGTCACCTACGATTTCAACTTCACGACGAATGATATCGTGCCTAA
51952 TAGATTG
66 TAGATTG
* *
51959 ACTCAACTTCATGACGAAGGAGTCACCTACGATTTCAACTTCACGACGAATGATATCATGCCTAA
1 ACTCAACTTCATGACGAATGAGTCACCTACGATTTCAACTTCACGACGAATGATATCGTGCCTAA
52024 TAGATTG
66 TAGATTG
* *
52031 ACTCAACTTCATGACGTATGAGCCACCTACGATTTCAACTTCACGACGAATGATATCGTGCCTAA
1 ACTCAACTTCATGACGAATGAGTCACCTACGATTTCAACTTCACGACGAATGATATCGTGCCTAA
52096 TAGATTG
66 TAGATTG
* * *
52103 ACTCAACTTCATGGCAAATGAGTCATCTAC
1 ACTCAACTTCATGACGAATGAGTCACCTAC
52133 TACATAGCTT
Statistics
Matches: 158, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 158 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (72 bp):
ACTCAACTTCATGACGAATGAGTCACCTACGATTTCAACTTCACGACGAATGATATCGTGCCTAA
TAGATTG
Found at i:52634 original size:33 final size:36
Alignment explanation
Indices: 52596--52688 Score: 140
Period size: 33 Copynumber: 2.7 Consensus size: 36
52586 TTTTTAAATG
*
52596 GTTTTTGAAAACATAAATATATAG-TT-AAAAAACA
1 GTTTTTGAAAACATATATATATAGTTTAAAAAAACA
52630 -TTTTTGAAAACATATA-ATATAGTTTAAAAAAACA
1 GTTTTTGAAAACATATATATATAGTTTAAAAAAACA
52664 GTTTTTGAAAACATATATAATATAG
1 GTTTTTGAAAACATATAT-ATATAG
52689 GTTTTTTAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
32 6 0.11
33 17 0.32
34 8 0.15
35 16 0.30
37 6 0.11
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (36 bp):
GTTTTTGAAAACATATATATATAGTTTAAAAAAACA
Found at i:52669 original size:35 final size:34
Alignment explanation
Indices: 52559--52688 Score: 138
Period size: 35 Copynumber: 3.7 Consensus size: 34
52549 TAATAGATAT
* *** *
52559 AGTTTTTGAAAACATATAATATATAACTTTTTAAAT
1 AGTTTTTGAAAACATAT-ATATAT-AGTTAAAAAAC
* *
52595 GGTTTTTGAAAACATAAATATATAGTTAAAAAAC
1 AGTTTTTGAAAACATATATATATAGTTAAAAAAC
52629 A-TTTTTGAAAACATATA-ATATAGTTTAAAAAAAC
1 AGTTTTTGAAAACATATATATATAG-TT-AAAAAAC
52663 AGTTTTTGAAAACATATATAATATAG
1 AGTTTTTGAAAACATATAT-ATATAG
52689 GTTTTTTAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
32 6 0.08
33 17 0.21
34 14 0.17
35 22 0.28
36 15 0.19
37 6 0.08
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.38
Consensus pattern (34 bp):
AGTTTTTGAAAACATATATATATAGTTAAAAAAC
Found at i:52771 original size:3 final size:3
Alignment explanation
Indices: 52765--52789 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
52755 ATTATACACA
52765 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
52790 TTACTTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Done.