Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001328.1 Hibiscus syriacus cultivar Beakdansim tig00002593_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: 68922
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1228 original size:8 final size:8
Alignment explanation
Indices: 1217--1263 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
1207 AATTTTCTTA
1217 TTTTATTT
1 TTTTATTT
1225 TTTTAATTT
1 TTTT-ATTT
*
1234 TCTTA-TT
1 TTTTATTT
*
1241 TTAT-TTT
1 TTTTATTT
1248 TTTTATTT
1 TTTTATTT
1256 TTTTATTT
1 TTTTATTT
1264 GATTTATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
7 9 0.28
8 16 0.50
9 7 0.22
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTATTT
Found at i:1230 original size:22 final size:22
Alignment explanation
Indices: 1205--1275 Score: 106
Period size: 22 Copynumber: 3.2 Consensus size: 22
1195 CGAAAGGTAA
1205 TTAATTTTCTTATTTTATTTTT
1 TTAATTTTCTTATTTTATTTTT
1227 TTAATTTTCTTATTTTATTTTT
1 TTAATTTTCTTATTTTATTTTT
* * * *
1249 TTTATTTTTTTATTTGATTTAT
1 TTAATTTTCTTATTTTATTTTT
1271 TTAAT
1 TTAAT
1276 ATTATTTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (22 bp):
TTAATTTTCTTATTTTATTTTT
Found at i:1269 original size:17 final size:17
Alignment explanation
Indices: 1239--1272 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1229 AATTTTCTTA
**
1239 TTTTATTTTTTTTATTT
1 TTTTATTTGATTTATTT
1256 TTTTATTTGATTTATTT
1 TTTTATTTGATTTATTT
1273 AATATTATTT
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:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTATTTGATTTATTT
Found at i:1271 original size:31 final size:32
Alignment explanation
Indices: 1217--1288 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 32
1207 AATTTTCTTA
*
1217 TTTTATTTTTTTAATTTTCTTATTT-TATTTT
1 TTTTATTTTTTTAATTTTCTTATTTATATTAT
1248 TTTTATTTTTTT-ATTTGAT-TTATTTAATATTAT
1 TTTTATTTTTTTAATTT--TCTTATTT-ATATTAT
1281 TTTTATTT
1 TTTTATTT
1289 CTTATCTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 4 0.11
31 18 0.50
32 1 0.03
33 13 0.36
ACGTcount: A:0.19, C:0.01, G:0.01, T:0.78
Consensus pattern (32 bp):
TTTTATTTTTTTAATTTTCTTATTTATATTAT
Found at i:3389 original size:13 final size:13
Alignment explanation
Indices: 3371--3395 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3361 TTTTGAGGCA
3371 TTTTTTGAATTTG
1 TTTTTTGAATTTG
3384 TTTTTTGAATTT
1 TTTTTTGAATTT
3396 TCTCATATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (13 bp):
TTTTTTGAATTTG
Found at i:5698 original size:240 final size:240
Alignment explanation
Indices: 5233--5855 Score: 875
Period size: 240 Copynumber: 2.6 Consensus size: 240
5223 TCGAGATTGT
* * * *
5233 ATTTCAACTTCACAATAAAGGATATCT-AACTC-AAAGCACATACAATACTTGGATTTCAACTTC
1 ATTTCAACTTCACGACAAAGGATAT-TGGACTCGAAA-CA-ATACAA-GCTTGGATTTCAACTTC
* * * * * *
5296 ACGGCGAAGGATA-T----TCAAGGTTCAACTTCACAACGAATGGGTTATCTACGATTTTAGCTT
62 ACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAATGGGTCATCCACGATTTCAACTT
* * * *
5356 CACGACGAATGATATCGTGTCAACTCTAGATTGGATTTCAACTTCACGACGAATGATATCCAATT
127 CACGACGAAGGATATTGTGCCAACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATT
* * * *
5421 CAAAGCTCAACTTCACGGCGAAGGGGCTTCCCAGTTTCATTCATATCCA
192 CAAAGCTCAACTTCAAGGCGAAAGGGCTTCCCAGTTTCATTCAGAGCCA
5470 ATTTCAACTTCACGACAAAGGATATTGGACTCGAAACAATACAAGCTTGGATTTCAACTTCACGA
1 ATTTCAACTTCACGACAAAGGATATTGGACTCGAAACAATACAAGCTTGGATTTCAACTTCACGA
* *
5535 CGAAGGATATTCAAGTCAAGGCTCAACTTCAGAACGAATGGGTCATCCACGATTTCAACTTCATG
66 CGAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAATGGGTCATCCACGATTTCAACTTCACG
5600 ACGAAGGATATTGTGCCAACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAA
131 ACGAAGGATATTGTGCCAACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAA
* *
5665 GCTCAACTTCAAGGCTAAAGGGCTTCCCAGTTTCATTCAGAGCTA
196 GCTCAACTTCAAGGCGAAAGGGCTTCCCAGTTTCATTCAGAGCCA
* * * *
5710 ATTTCAACTTTACGGCGAAGGATATTGGACTCGAAACAATACAAGCTTGAATTTCAACTTCACGA
1 ATTTCAACTTCACGACAAAGGATATTGGACTCGAAACAATACAAGCTTGGATTTCAACTTCACGA
* * * *
5775 CGAAGGATATTCAAGTTAAGGCTCAACTTCACAAAGAATGAGCCATCCACGATTTCAACTTCACG
66 CGAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAATGGGTCATCCACGATTTCAACTTCACG
5840 ACGAAGGGA-ATTGTGC
131 ACGAA-GGATATTGTGC
5856 TCACCAGTAA
Statistics
Matches: 346, Mismatches: 32, Indels: 13
0.88 0.08 0.03
Matches are distributed among these distances:
235 28 0.08
236 8 0.02
237 29 0.08
238 3 0.01
240 275 0.79
241 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (240 bp):
ATTTCAACTTCACGACAAAGGATATTGGACTCGAAACAATACAAGCTTGGATTTCAACTTCACGA
CGAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAATGGGTCATCCACGATTTCAACTTCACG
ACGAAGGATATTGTGCCAACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAA
GCTCAACTTCAAGGCGAAAGGGCTTCCCAGTTTCATTCAGAGCCA
Found at i:5921 original size:124 final size:124
Alignment explanation
Indices: 5760--6107 Score: 527
Period size: 124 Copynumber: 2.8 Consensus size: 124
5750 ACAAGCTTGA
* * * * *
5760 ATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTCAACTTCACAAAGAATGAGCCATCCAC
1 ATTTCAACTTCACGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGAATGGGCCATCCAC
* * * *
5825 GATTTCAACTTCACGACGAAGGGAATTGTGCTCACCAGTAACATTCATCTTTAGATTGG
66 GATTTCAACTTCACGACGAAGGGAATCGTGCCCACCAGCAACATTCATCTTCAGATTGG
* * *
5884 ATTTCAACTTCATGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGTAGGGGCCATCCAC
1 ATTTCAACTTCACGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGAATGGGCCATCCAC
* *
5949 GGTTTCAACTTCACGACGAAGGGAATCGTTCCCACCAGCAACATTCATCTTCAGATTGG
66 GATTTCAACTTCACGACGAAGGGAATCGTGCCCACCAGCAACATTCATCTTCAGATTGG
* * *
6008 ATTTCAACTTCACGACGAAGGATTTCCAATTCAAGGCTCAACTTCACAACGAATGGGCCCTCCAC
1 ATTTCAACTTCACGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGAATGGGCCATCCAC
6073 GATTTCAACTTCACGACGAA-GGATATCGTGCCCAC
66 GATTTCAACTTCACGACGAAGGGA-ATCGTGCCCAC
6108 AAGAAGCAAT
Statistics
Matches: 201, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
123 3 0.01
124 198 0.99
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (124 bp):
ATTTCAACTTCACGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGAATGGGCCATCCAC
GATTTCAACTTCACGACGAAGGGAATCGTGCCCACCAGCAACATTCATCTTCAGATTGG
Found at i:6306 original size:84 final size:84
Alignment explanation
Indices: 6158--6590 Score: 593
Period size: 84 Copynumber: 5.2 Consensus size: 84
6148 GATATCGTGT
* * *
6158 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCAAGTTCGACTA
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* * *
6223 CGCTAATCTCCAAAGCACA
66 CGCTCAGCTCCAAGGCACA
* * * * * * *
6242 TTATTTGTAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAATACCTTCGAGTTTGACTA
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
6307 CGCTCAGCT-CAAGGCACA
66 CGCTCAGCTCCAAGGCACA
* * *
6325 TCATTTGCAACATAGCTCAAGGAAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
6390 CGCTCAGCTCCAAGGCACA
66 CGCTCAGCTCCAAGGCACA
* * * * *
6409 TCATTTGAAGTATAACTCAAGG-ATAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACT
1 TCATTTGCAGCATAGCTCAAGGCA-AGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACT
*
6473 ACGCTCAGCTCCAAGGCACG
65 ACGCTCAGCTCCAAGGCACA
*
6493 TCATTTGCTA-CATAGCTCAAGGCAATAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACT
1 TCATTTGC-AGCATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACT
* *
6557 ACCCTCAGCTCTAAGGCACA
65 ACGCTCAGCTCCAAGGCACA
*
6577 TTATTTGCAGCATA
1 TCATTTGCAGCATA
6591 TCTTAGGTCG
Statistics
Matches: 303, Mismatches: 41, Indels: 10
0.86 0.12 0.03
Matches are distributed among these distances:
83 74 0.24
84 227 0.75
85 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (84 bp):
TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACA
Found at i:6438 original size:167 final size:168
Alignment explanation
Indices: 6158--6590 Score: 688
Period size: 167 Copynumber: 2.6 Consensus size: 168
6148 GATATCGTGT
*
6158 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCAAGTTCGACTA
1 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* * * * *
6223 CGCTAATCTCCAAAGCACATTATTTGTAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAA
66 CGCTCAGCTCCAAGGCACATTATTTGAAGCATAACTCAAGGATAGAAGGGTTATCTGCCAACAAA
* *
6288 ATACCTTCGAGTTTGACTACGCTCAGCT-CAAGGCACA
131 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACA
*
6325 TCATTTGCAACATAGCTCAAGGAAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* *
6390 CGCTCAGCTCCAAGGCACATCATTTGAAGTATAACTCAAGGATAGAAGGGTTATCTGCCAACAAA
66 CGCTCAGCTCCAAGGCACATTATTTGAAGCATAACTCAAGGATAGAAGGGTTATCTGCCAACAAA
* *
6455 AGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACG
131 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACA
* * *
6493 TCATTTGCTACATAGCTCAAGGCAATAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* * *
6558 CCCTCAGCTCTAAGGCACATTATTTGCAGCATA
66 CGCTCAGCTCCAAGGCACATTATTTGAAGCATA
6591 TCTTAGGTCG
Statistics
Matches: 243, Mismatches: 22, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
167 146 0.60
168 97 0.40
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (168 bp):
TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACATTATTTGAAGCATAACTCAAGGATAGAAGGGTTATCTGCCAACAAA
AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACA
Found at i:6607 original size:84 final size:84
Alignment explanation
Indices: 6158--6724 Score: 590
Period size: 84 Copynumber: 6.7 Consensus size: 84
6148 GATATCGTGT
* * * * *
6158 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCAAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* * *
6223 CGCTAATCTCCAAAGCACA
66 CGCTCAGCTCCAAGGCACA
* * * * *
6242 TTATTTGTAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAATACCTTCGAGTTTGACTA
1 TCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
6307 CGCTCAGCT-CAAGGCACA
66 CGCTCAGCTCCAAGGCACA
* * * * *
6325 TCATTTGCAACATAGCTCAAGGAAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
6390 CGCTCAGCTCCAAGGCACA
66 CGCTCAGCTCCAAGGCACA
* * *
6409 TCATTTGAAGTATAACTCAAGG-ATAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACT
1 TCATTTGCAGCATAACTCAAGGCA-AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
*
6473 ACGCTCAGCTCCAAGGCACG
65 ACGCTCAGCTCCAAGGCACA
* * *
6493 TCATTTGCTA-CATAGCTCAAGGCAATAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACT
1 TCATTTGC-AGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
* *
6557 ACCCTCAGCTCTAAGGCACA
65 ACGCTCAGCTCCAAGGCACA
* * * * * * * * * * *
6577 TTATTTGCAGCATATCT-TAGGTCGAGAAGGGATATCTACCAACCAAAGACCATCAAGTTCAATT
1 TCATTTGCAGCATAACTCAAGG-CAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
** *
6641 ACATTCAGCT-CAAGGACATA
65 ACGCTCAGCTCCAAGG-CACA
* * * * * *
6661 TCAAATTTACAACATAACCCAAGGCGAGAAAGGTTATCTGTCAAACAAAA-A-CTGTCGAGTTCG
1 TC--ATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTG-CCAACAAAAGACCT-TCGAGTTCG
6724 A
62 A
6725 TTCCATTCAG
Statistics
Matches: 400, Mismatches: 71, Indels: 22
0.81 0.14 0.04
Matches are distributed among these distances:
83 81 0.20
84 273 0.68
85 3 0.01
86 33 0.08
87 10 0.03
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (84 bp):
TCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACA
Found at i:6651 original size:168 final size:167
Alignment explanation
Indices: 6158--6659 Score: 679
Period size: 167 Copynumber: 3.0 Consensus size: 167
6148 GATATCGTGT
*
6158 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCAAGTTCGACTA
1 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* * * *
6223 CGCTAATCTCCAAAGCACATTATTTGTAGCATAACTCAAGG-CTAGAAGGGTTATCTGCCAACAA
66 CGCTCAGCTCCAAGGCACATTATTTGAAGCATAACTCAAGGTC-AGAAGGGTTATCTGCCAACAA
* *
6287 AATACCTTCGAGTTTGACTACGCTCAGCTCAAGGCACA
130 AAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGCACA
*
6325 TCATTTGCAACATAGCTCAAGGAAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* *
6390 CGCTCAGCTCCAAGGCACATCATTTGAAGTATAACTCAAGGAT-AGAAGGGTTATCTGCCAACAA
66 CGCTCAGCTCCAAGGCACATTATTTGAAGCATAACTCAAGG-TCAGAAGGGTTATCTGCCAACAA
* *
6454 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACG
130 AAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACA
* * *
6493 TCATTTGCTACATAGCTCAAGGCAATAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* * * * * * * *
6558 CCCTCAGCTCTAAGGCACATTATTTGCAGCATATCT-TAGGTCGAGAAGGGATATCTACCAACCA
66 CGCTCAGCTCCAAGGCACATTATTTGAAGCATAACTCAAGGTC-AGAAGGGTTATCTGCCAACAA
* * * * **
6622 AAGACCATCAAGTTCAATTACATTCAGCTCAAGG-ACA
130 AAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGCACA
6659 T
1 T
6660 ATCAAATTTA
Statistics
Matches: 296, Mismatches: 34, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
166 4 0.01
167 153 0.52
168 139 0.47
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (167 bp):
TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACATTATTTGAAGCATAACTCAAGGTCAGAAGGGTTATCTGCCAACAAA
AGACCTTCGAGTTCGACTACGCTCAGCTCAAGGCACA
Found at i:7062 original size:3 final size:3
Alignment explanation
Indices: 7056--7105 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
7046 AACAATTACC
* *
7056 TAT TAT TAT TAT TATT TGT TAT TAT TAT TAT AAT TAT T-T TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
7101 T-T TAT
1 TAT TAT
7106 AAGGCCCATG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.85
4 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:7081 original size:22 final size:20
Alignment explanation
Indices: 7056--7107 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
7046 AACAATTACC
* *
7056 TATTATTATTATTATT-TGT
1 TATTATTATTATAATTATTT
7075 TATTATTATTATAATTATTT
1 TATTATTATTATAATTATTT
7095 TATTATT-TTATAA
1 TATTATTATTATAA
7108 GGCCCATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 21 0.70
20 9 0.30
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TATTATTATTATAATTATTT
Found at i:9096 original size:12 final size:12
Alignment explanation
Indices: 9079--9105 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
9069 GAATTGAATT
9079 TTTAAATTTCAA
1 TTTAAATTTCAA
9091 TTTAAATTTCAA
1 TTTAAATTTCAA
9103 TTT
1 TTT
9106 TCGCAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTAAATTTCAA
Found at i:10048 original size:23 final size:23
Alignment explanation
Indices: 10013--10056 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
10003 CAATATATAT
*
10013 ATATATATATATTTATAAATAAG
1 ATATATATATATTTAGAAATAAG
* *
10036 ATATTTATTTATTTAGAAATA
1 ATATATATATATTTAGAAATA
10057 TCATAAAAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
ATATATATATATTTAGAAATAAG
Found at i:10211 original size:142 final size:140
Alignment explanation
Indices: 10015--10268 Score: 413
Period size: 142 Copynumber: 1.8 Consensus size: 140
10005 ATATATATAT
*
10015 ATATATATATTTATAAATAAGATATTTATTTATTTAGAAATATCATAAAAGGACTTCTAGGTGCT
1 ATATATATATTTATAAATAAGATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCT
* *
10080 TTAAGACAACTCATTTCTTAATATTAAAAAAATAAATAAATATTAAAAAATAATTTTCTAAAAAA
66 TTAAGACAACACATTTATTAATATT-AAAAAATAAATAAATATTAAAAAATAATTTTCTAAAAAA
10145 ATAATAAATTA
130 ATAATAAATTA
*
10156 ATATATA-ATTTATAAAAATAGGATATTTATTTATTTA-AGAATATCAGAAAAGGACTTCTAGGT
1 ATATATATATTTAT--AAATAAGATATTTATTTATTTAGA-AATATCAGAAAAGGACTTCTAGGT
*
10219 GCTTTAAGACAGCACATTTATTAATATTAAAAAATAAATAAATATTAAAA
63 GCTTTAAGACAACACATTTATTAATATTAAAAAATAAATAAATATTAAAA
10269 TATGATTATT
Statistics
Matches: 105, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
140 6 0.06
141 30 0.29
142 69 0.66
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.37
Consensus pattern (140 bp):
ATATATATATTTATAAATAAGATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCT
TTAAGACAACACATTTATTAATATTAAAAAATAAATAAATATTAAAAAATAATTTTCTAAAAAAA
TAATAAATTA
Found at i:10482 original size:16 final size:16
Alignment explanation
Indices: 10434--10490 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
10424 TATAAACATG
10434 TAAAATTAAAATATAAA
1 TAAAATTAAAA-ATAAA
*
10451 TAAACAATGACTAAAATAAA
1 T-AA-AATTA--AAAATAAA
*
10471 TAAAATTAAAAATTAA
1 TAAAATTAAAAATAAA
10487 TAAA
1 TAAA
10491 TAAAAGTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
16 11 0.33
17 1 0.03
18 6 0.18
19 6 0.18
20 6 0.18
21 3 0.09
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (16 bp):
TAAAATTAAAAATAAA
Found at i:11757 original size:3 final size:3
Alignment explanation
Indices: 11751--11797 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
11741 AATATTTTAT
* *
11751 TAA TAA TAA TAA TAA TAA TAA TAA -ATA TAA TAA TAT TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
11796 TA
1 TA
11798 GTAAAAGCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 1 0.03
3 38 0.95
4 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:12625 original size:74 final size:74
Alignment explanation
Indices: 12504--12679 Score: 289
Period size: 74 Copynumber: 2.4 Consensus size: 74
12494 GAGGTCTTAT
* * *
12504 CATCTTACACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAAAAGCTCCCAAAGGCT
1 CATCTTGCACTGTAGGTCTTACAGATGTCCCAGAGGCTTTAAATATCAAAAAGCTCCCAAAGGCT
12569 TTTTGAAAA
66 TTTTGAAAA
* *
12578 CATCTTGCACTGTAGGTCTTACAGATGTCCCAGAGGCTTTAAATATCAAAAAGCTCCCGAAGGTT
1 CATCTTGCACTGTAGGTCTTACAGATGTCCCAGAGGCTTTAAATATCAAAAAGCTCCCAAAGGCT
12643 TTTTGAAAA
66 TTTTGAAAA
* *
12652 CATCATGCACTGTAGGTTTTACAGATGT
1 CATCTTGCACTGTAGGTCTTACAGATGT
12680 GGGAAATAGT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 95 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (74 bp):
CATCTTGCACTGTAGGTCTTACAGATGTCCCAGAGGCTTTAAATATCAAAAAGCTCCCAAAGGCT
TTTTGAAAA
Found at i:13399 original size:22 final size:22
Alignment explanation
Indices: 13369--13410 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
13359 ATTTTTTAAG
*
13369 AAATTTATCATCTTTGAAGAGA
1 AAATCTATCATCTTTGAAGAGA
*
13391 AAATCTATCATTTTTGAAGA
1 AAATCTATCATCTTTGAAGA
13411 ATGTAGATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (22 bp):
AAATCTATCATCTTTGAAGAGA
Found at i:14455 original size:15 final size:16
Alignment explanation
Indices: 14436--14479 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 16
14426 CTATATATTT
14436 TTTTTTTCATTTTTCA
1 TTTTTTTCATTTTTCA
14452 -TTTTTTCA-TTTTCA
1 TTTTTTTCATTTTTCA
14466 TTTTTTTCATTTTT
1 TTTTTTTCATTTTT
14480 TAAGCATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 6 0.23
15 16 0.62
16 4 0.15
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTTCATTTTTCA
Found at i:14456 original size:8 final size:8
Alignment explanation
Indices: 14437--14480 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
14427 TATATATTTT
14437 TTTTTTCA
1 TTTTTTCA
14445 -TTTTTCA
1 TTTTTTCA
14452 TTTTTTCA
1 TTTTTTCA
14460 --TTTTCA
1 TTTTTTCA
14466 TTTTTTTCA
1 -TTTTTTCA
14475 TTTTTT
1 TTTTTT
14481 AAGCATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
6 6 0.19
7 7 0.22
8 13 0.41
9 6 0.19
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCA
Found at i:14479 original size:7 final size:7
Alignment explanation
Indices: 14438--14470 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
14428 ATATATTTTT
14438 TTTTTCA
1 TTTTTCA
14445 TTTTTCA
1 TTTTTCA
14452 TTTTTTCA
1 -TTTTTCA
14460 -TTTTCA
1 TTTTTCA
14466 TTTTT
1 TTTTT
14471 TTCATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
7 11 0.46
8 7 0.29
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCA
Found at i:21756 original size:14 final size:16
Alignment explanation
Indices: 21739--21770 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21729 ATTATTTTTT
21739 TGAAT-TTTAT-TTAA
1 TGAATGTTTATCTTAA
21753 TGAATGTTTATCTTAA
1 TGAATGTTTATCTTAA
21769 TG
1 TG
21771 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 5 0.31
16 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.53
Consensus pattern (16 bp):
TGAATGTTTATCTTAA
Found at i:21837 original size:15 final size:15
Alignment explanation
Indices: 21817--21848 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
21807 TGCAATGAAT
21817 AATGAATGTATGCAA
1 AATGAATGTATGCAA
21832 AATGAATGTATGCAA
1 AATGAATGTATGCAA
21847 AA
1 AA
21849 GGTATTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:25174 original size:26 final size:26
Alignment explanation
Indices: 25123--25201 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 26
25113 TTAATACTTG
25123 AAAATAA-A-ATAAAAATATTAAT-AA
1 AAAATAATATATAAAAATATT-ATGAA
*
25147 AAAATAATATATATAAATATTATGAA
1 AAAATAATATATAAAAATATTATGAA
*
25173 AATAATAACTATATAGAAAA-ATTTTGAA
1 AA-AATAA-TATATA-AAAATATTATGAA
25201 A
1 A
25202 GGAAAGAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
24 7 0.15
25 3 0.07
26 14 0.30
27 5 0.11
28 14 0.30
29 3 0.07
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (26 bp):
AAAATAATATATAAAAATATTATGAA
Found at i:25185 original size:24 final size:24
Alignment explanation
Indices: 25121--25185 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
25111 ATTTAATACT
*
25121 TGAAAATAA-AATAAAAATATTAA
1 TGAAAATAATAATATAAATATTAA
*
25144 TAAAAAATAATATATATAAATATT-A
1 T-GAAAATAATA-ATATAAATATTAA
25169 TGAAAATAATAACTATA
1 TGAAAATAATAA-TATA
25186 TAGAAAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
23 2 0.06
24 20 0.57
25 3 0.09
26 10 0.29
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (24 bp):
TGAAAATAATAATATAAATATTAA
Found at i:25185 original size:28 final size:26
Alignment explanation
Indices: 25123--25201 Score: 74
Period size: 28 Copynumber: 3.0 Consensus size: 26
25113 TTAATACTTG
*
25123 AAAATAA-A-ATAAAAATATTAAT-AA
1 AAAATAATATATAGAAATATT-ATGAA
*
25147 AAAATAATATATATAAATATTATGAA
1 AAAATAATATATAGAAATATTATGAA
* *
25173 AATAATAACTATATAGAAAAATTTTGAA
1 AA-AATAA-TATATAGAAATATTATGAA
25201 A
1 A
25202 GGAAAGAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
24 7 0.15
25 3 0.07
26 14 0.30
27 5 0.11
28 17 0.37
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (26 bp):
AAAATAATATATAGAAATATTATGAA
Found at i:26106 original size:22 final size:21
Alignment explanation
Indices: 26081--26125 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
26071 TAATAATAAT
26081 AACA-ATAATAATTAAATATATA
1 AACATATAA-AATTAAA-ATATA
*
26103 AACATGTAAAATTAAAATATA
1 AACATATAAAATTAAAATATA
26124 AA
1 AA
26126 TAAACAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 11 0.52
23 3 0.14
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (21 bp):
AACATATAAAATTAAAATATA
Found at i:27425 original size:3 final size:3
Alignment explanation
Indices: 27419--27463 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
27409 ATATTTTTAT
* *
27419 TAA TAA TAA TAA TAA TAA -ATA TAA TAA TAT TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
27464 AAGCAAATGG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 1 0.03
3 36 0.95
4 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:27446 original size:24 final size:24
Alignment explanation
Indices: 27401--27460 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
27391 GCCAGAAATG
** * *
27401 TAATAATAATATTTTTATTAATAA
1 TAATAATAATAAATATAATAATAA
*
27425 TAATAATAATAAATATAATAATAT
1 TAATAATAATAAATATAATAATAA
*
27449 TATTAATAATAA
1 TAATAATAATAA
27461 TAAAAGCAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATAATAATAAATATAATAATAA
Found at i:27460 original size:18 final size:18
Alignment explanation
Indices: 27401--27463 Score: 78
Period size: 18 Copynumber: 3.7 Consensus size: 18
27391 GCCAGAAATG
* *
27401 TAATAATAATATTTTTAT
1 TAATAATAATAATATTAT
27419 TAATAATAATAATA--AT
1 TAATAATAATAATATTAT
*
27435 AAAT-ATAATAATATTAT
1 TAATAATAATAATATTAT
27452 TAATAATAATAA
1 TAATAATAATAA
27464 AAGCAAATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
15 9 0.24
16 5 0.13
17 5 0.13
18 19 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAATAATAATATTAT
Found at i:29536 original size:2 final size:2
Alignment explanation
Indices: 29529--29554 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29519 TTAATCTAAG
29529 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
29555 TTTGCACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29691 original size:2 final size:2
Alignment explanation
Indices: 29684--29733 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
29674 GTATTGTACT
29684 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
29726 TA TA TA TA
1 TA TA TA TA
29734 ATGCTAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30315 original size:2 final size:2
Alignment explanation
Indices: 30308--30350 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
30298 CCAGTTTGGG
30308 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
30350 T
1 T
30351 CACTTTAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36839 original size:27 final size:27
Alignment explanation
Indices: 36809--36865 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
36799 ATTCTCGTCT
*
36809 TTTTACATCATAAGG-GTATTTTCATAA
1 TTTTACATAAT-AGGAGTATTTTCATAA
*
36836 TTTTACCTAATAGGAGTATTTTCATAA
1 TTTTACATAATAGGAGTATTTTCATAA
36863 TTT
1 TTT
36866 ATTTTCCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (27 bp):
TTTTACATAATAGGAGTATTTTCATAA
Found at i:41048 original size:19 final size:19
Alignment explanation
Indices: 41024--41065 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
41014 TAAGTTACAA
41024 TTGATGAAGTT-ATGAGATT
1 TTGATGAAGTTGA-GAGATT
41043 TTGATGAAGTTGAGAGATT
1 TTGATGAAGTTGAGAGATT
41062 TTGA
1 TTGA
41066 ATTTATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (19 bp):
TTGATGAAGTTGAGAGATT
Found at i:41205 original size:13 final size:13
Alignment explanation
Indices: 41161--41205 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
41151 TACTTTTTAT
41161 ATTAATTATAATC
1 ATTAATTATAATC
*
41174 CTTATATTATAAATC
1 ATTA-ATTAT-AATC
41189 -TTAATTATAATC
1 ATTAATTATAATC
41201 ATTAA
1 ATTAA
41206 ATTAATTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 8 0.29
15 4 0.14
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTAATTATAATC
Found at i:42583 original size:2 final size:2
Alignment explanation
Indices: 42576--42686 Score: 94
Period size: 2 Copynumber: 57.0 Consensus size: 2
42566 GAATGCATAA
*
42576 AT AT AT AT AT AT GT AT ACT -T AT A- AT AT A- AGT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT
* *
42616 GA- AT AC AT A- AGT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 -AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42658 AT AT AT AT AT AT ACT -T AT A- AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
42687 GTGTGTGTAT
Statistics
Matches: 90, Mismatches: 6, Indels: 26
0.74 0.05 0.21
Matches are distributed among these distances:
1 8 0.09
2 77 0.86
3 5 0.06
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:42837 original size:29 final size:29
Alignment explanation
Indices: 42803--42895 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
42793 TATTATATTT
42803 ATATATTATAAGTATAATATATACTTATA
1 ATATATTATAAGTATAATATATACTTATA
* *
42832 TTATA-TACTTA-TATAAGTATATACTTATA
1 ATATATTA-TAAGTATAA-TATATACTTATA
* * * *
42861 ATGTATGCATAAGTATAATGTACA-TTATA
1 ATATAT-TATAAGTATAATATATACTTATA
42890 ATATAT
1 ATATAT
42896 ATACATGCAT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
28 7 0.14
29 31 0.62
30 6 0.12
31 6 0.12
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (29 bp):
ATATATTATAAGTATAATATATACTTATA
Found at i:42965 original size:128 final size:128
Alignment explanation
Indices: 42707--42975 Score: 299
Period size: 128 Copynumber: 2.1 Consensus size: 128
42697 AAGTATACAT
*
42707 TATACTTAAATAAGTATATACATATAATGAATGCATAAGTATAAATGTATAATATACATTATATA
1 TATACTTAAATAAGTATATACATATAATGAATGCATAAGTATAAATGTACAATATACATTATATA
* * * * * *
42772 TACATGAATTATATTCATACATATTATATTTATATATTATAAGTATAATATATACTTATATTA
66 TACATGAATTATATTCATACATATCATAGTAATATATTATAAGTATAATACACACATATATTA
* * * *
42835 TATACTTATATAAGTATATACTTATAATGTATGCATAAGTAT-AATGTACATTATA-A-TATATA
1 TATACTTAAATAAGTATATACATATAATGAATGCATAAGTATAAATGTACAATATACATTATATA
*
42897 TACATGCATTATATTATCATATCATTCATCATACGTAATATA-TAT-A-TAT-ATACACACATAT
66 TACATGAATTATA-T-TCATA-CA-T-ATCATA-GTAATATATTATAAGTATAATACACACATAT
42958 A-TA
125 ATTA
42961 TATA-TT--ATAAGTATA
1 TATACTTAAATAAGTATA
42976 ATGTATACTT
Statistics
Matches: 123, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
123 9 0.07
125 20 0.16
126 8 0.07
127 26 0.21
128 44 0.36
129 2 0.02
130 8 0.07
131 6 0.05
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.42
Consensus pattern (128 bp):
TATACTTAAATAAGTATATACATATAATGAATGCATAAGTATAAATGTACAATATACATTATATA
TACATGAATTATATTCATACATATCATAGTAATATATTATAAGTATAATACACACATATATTA
Found at i:42983 original size:34 final size:34
Alignment explanation
Indices: 42945--43009 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
42935 TATATATATA
42945 TATACACACA-TATATA-TATATTATAAGTATAATG
1 TATACACACATTATATACT-TA-TATAAGTATAATG
**
42979 TATACTTACATTATATACTTATATAAGTATA
1 TATACACACATTATATACTTATATAAGTATA
43010 TACATATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 18 0.67
35 8 0.30
36 1 0.04
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.42
Consensus pattern (34 bp):
TATACACACATTATATACTTATATAAGTATAATG
Found at i:48898 original size:15 final size:15
Alignment explanation
Indices: 48866--48907 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
48856 TCCGCTGAAC
*
48866 TTTATTTATTTATTA
1 TTTATTTATTTATCA
48881 TTTATTTATTGTA-CA
1 TTTATTTATT-TATCA
*
48896 TTTATTTTTTTA
1 TTTATTTATTTA
48908 ATTTTCTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 2 0.08
15 20 0.83
16 2 0.08
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTATTTATCA
Found at i:62289 original size:24 final size:24
Alignment explanation
Indices: 62261--62349 Score: 142
Period size: 24 Copynumber: 3.7 Consensus size: 24
62251 TTTCTATTAT
* *
62261 AATACCTGACTTGGATTCTGATCG
1 AATACTTGACCTGGATTCTGATCG
*
62285 GATACTTGACCTGGATTCTGATCG
1 AATACTTGACCTGGATTCTGATCG
*
62309 AATACTTGACCTGGATTCTGATAG
1 AATACTTGACCTGGATTCTGATCG
62333 AATACTTGACCTGGATT
1 AATACTTGACCTGGATT
62350 ATGTTTTGAT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (24 bp):
AATACTTGACCTGGATTCTGATCG
Found at i:63255 original size:26 final size:25
Alignment explanation
Indices: 63204--63255 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
63194 ACTTAATATC
* * *
63204 ATTTATAAAATTTTTTTTACTGAAA
1 ATTTATAAAATTTCTTTTAATAAAA
*
63229 ATTTATTAAATTATCTTTTAATAAAA
1 ATTTATAAAATT-TCTTTTAATAAAA
63255 A
1 A
63256 AAATTCACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (25 bp):
ATTTATAAAATTTCTTTTAATAAAA
Found at i:67921 original size:55 final size:57
Alignment explanation
Indices: 67732--67920 Score: 282
Period size: 55 Copynumber: 3.4 Consensus size: 57
67722 ACCATATCTC
*
67732 AACTTTTTGCACACGAAGTGCCAATACGAAAATTCATACACTTAGTATGAATTTCTT
1 AACTTTTTGCACACGAAGTGCCAATACGGAAATTCATACACTTAGTATGAATTTCTT
*
67789 AACTTTTTGCACACGAAGTGCCCAATACAGAAA-T--TACACTTAGTATGAA-TTCTT
1 AACTTTTTGCACACGAAGTG-CCAATACGGAAATTCATACACTTAGTATGAATTTCTT
*
67843 AATTTTTTGCACACGAAGTGCC-ATACGGAAATTCATACACTTAGTA-GAATTTCTT
1 AACTTTTTGCACACGAAGTGCCAATACGGAAATTCATACACTTAGTATGAATTTCTT
**
67898 AACTTTTTGCACACTTAGTGCCA
1 AACTTTTTGCACACGAAGTGCCA
67921 TTTTGTAATC
Statistics
Matches: 119, Mismatches: 7, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
52 8 0.07
53 3 0.03
54 27 0.23
55 50 0.42
57 21 0.18
58 10 0.08
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (57 bp):
AACTTTTTGCACACGAAGTGCCAATACGGAAATTCATACACTTAGTATGAATTTCTT
Done.