Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001629.1 Hibiscus syriacus cultivar Beakdansim tig00003243_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: 77033
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1432 original size:19 final size:20
Alignment explanation
Indices: 1408--1454 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
1398 CACGGAATGT
1408 AAGATTACCAATGAGAAT-A
1 AAGATTACCAATGAGAATAA
*
1427 AAGATTATCAATGAGAATAA
1 AAGATTACCAATGAGAATAA
1447 AAGATTAC
1 AAGATTAC
1455 TAGAGAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.23
Consensus pattern (20 bp):
AAGATTACCAATGAGAATAA
Found at i:4105 original size:45 final size:46
Alignment explanation
Indices: 4039--4133 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 46
4029 CATGTTATTT
* * *
4039 TTTAACGGAATTAACATTTTGGAGTAAACAAAATAACGATTTAAGC
1 TTTAACGGAATTAACAGTTTGGAGTAAACAAAATAACCATTTAAAC
* * * *
4085 TTTAA-GGAATTAACAGTTTGGATTAATCGAGATAACCATTTAAAC
1 TTTAACGGAATTAACAGTTTGGAGTAAACAAAATAACCATTTAAAC
4130 TTTA
1 TTTA
4134 GGGAGCAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 37 0.88
46 5 0.12
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.34
Consensus pattern (46 bp):
TTTAACGGAATTAACAGTTTGGAGTAAACAAAATAACCATTTAAAC
Found at i:13598 original size:15 final size:16
Alignment explanation
Indices: 13574--13604 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
13564 GGTTATTTTT
13574 AATAT-TTTTTTAAAA
1 AATATGTTTTTTAAAA
13589 AATATGTTTTTTAAAA
1 AATATGTTTTTTAAAA
13605 TAAAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
AATATGTTTTTTAAAA
Found at i:13615 original size:17 final size:16
Alignment explanation
Indices: 13574--13616 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
13564 GGTTATTTTT
13574 AATATTTTTTTAAAAAA
1 AATA-TTTTTTAAAAAA
* *
13591 TATGTTTTTTAAAATAA
1 AATATTTTTTAAAA-AA
13608 AATATTTTT
1 AATATTTTT
13617 ATTTTTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
AATATTTTTTAAAAAA
Found at i:14505 original size:28 final size:28
Alignment explanation
Indices: 14465--14534 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
14455 ATAGGATTTG
14465 TCCCGAAGGACCACATATAACACATATA
1 TCCCGAAGGACCACATATAACACATATA
*
14493 TCCCGAAGGACCACATATAACATATATA
1 TCCCGAAGGACCACATATAACACATATA
*
14521 TCCCGAAAGACCAC
1 TCCCGAAGGACCAC
14535 TCCTTAAGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.17
Consensus pattern (28 bp):
TCCCGAAGGACCACATATAACACATATA
Found at i:26154 original size:38 final size:35
Alignment explanation
Indices: 26100--26218 Score: 121
Period size: 38 Copynumber: 3.2 Consensus size: 35
26090 ATACATATAT
* *
26100 ATATATATATAATATAGTTTTGAAAACATATTCGAAA
1 ATATATATATTATATAGTTTTAAAAACAT-TT-GAAA
* *
26137 CATTTATATATTATATAGTTTTTAAAACACTTTGAAA
1 -ATATATATATTATATAGTTTTAAAAACA-TTTGAAA
* *
26174 ATAAATATAATATATAGTTTTAAAAACATTTTTGAAA
1 ATATATATATTATATAGTTTTAAAAACA--TTTGAAA
26211 ACTATATA
1 A-TATATA
26219 ATTTTGAAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
36 24 0.35
37 12 0.17
38 32 0.46
39 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (35 bp):
ATATATATATTATATAGTTTTAAAAACATTTGAAA
Found at i:26218 original size:36 final size:35
Alignment explanation
Indices: 26100--26220 Score: 109
Period size: 36 Copynumber: 3.3 Consensus size: 35
26090 ATACATATAT
* *
26100 ATATATATATAATATAGTTTTGAAAACATATTCGAAA
1 ATATATA-AT-ATATAGTTTTAAAAACATATTTGAAA
* * *
26137 CATTTATATATTATATAGTTTTTAAAACA-CTTTGAAA
1 -A--TATATAATATATAGTTTTAAAAACATATTTGAAA
*
26174 ATAAATATAATATATAGTTTTAAAAACATTTTTGAAA
1 AT--ATATAATATATAGTTTTAAAAACATATTTGAAA
26211 ACTATATAAT
1 A-TATATAAT
26221 TTTGAAAGCG
Statistics
Matches: 70, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
34 1 0.01
36 30 0.43
37 14 0.20
38 18 0.26
39 1 0.01
40 6 0.09
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (35 bp):
ATATATAATATATAGTTTTAAAAACATATTTGAAA
Found at i:29601 original size:19 final size:19
Alignment explanation
Indices: 29577--29622 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
29567 ACTTAGACAT
29577 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
29596 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
29615 TTTGCATT
1 TTTGCATT
29623 CACATTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Found at i:33222 original size:84 final size:84
Alignment explanation
Indices: 33029--33479 Score: 515
Period size: 84 Copynumber: 5.4 Consensus size: 84
33019 TAAACAAACT
* * ** * *
33029 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
33090 CTCAGCTTCGAGGGCACATC
66 CTCAGC-TCCAAGGCACATC
33110 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
33175 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* * * * * * *
33194 ATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTTCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
33259 ATCAGCT-CAATGGCACATC
66 CTCAGCTCCAA-GGCACATC
* * ** * *
33278 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
33339 CTCAGCTTCGAGGGCACATC
66 CTCAGC-TCCAAGGCACATC
* * * *
33359 ATTTGCAGCATAACTTAAGTGGAGAAGGGTTATCTTCCAATCAGAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
33424 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* * *
33443 ATTTGCAACACAACTTAAGTCTAGAAGGGTTATCTGC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGC
33480 TAAAGACCTT
Statistics
Matches: 307, Mismatches: 52, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
80 24 0.08
81 75 0.24
82 1 0.00
83 3 0.01
84 152 0.50
85 52 0.17
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (84 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATC
Found at i:33417 original size:165 final size:161
Alignment explanation
Indices: 33029--33501 Score: 538
Period size: 165 Copynumber: 2.9 Consensus size: 161
33019 TAAACAAACT
* * * ** *
33029 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-A-AAGACCCCCGAGTTCGATTAC-AC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACAAGACCTTCGAGTTCGACTACGA-
*
33091 TCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAG
65 TCAGC-TC-AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG----CCAAAG
* * *
33156 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATC
124 ACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATC
* * * * *
33194 ATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTTCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAAC--AAGACCTTCGAGTTCGACTACG
* * *
33259 ATCAGCTCAATGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
64 ATCAGCTCAA-GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCT
* * *
33324 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
128 TCGAGTTCGATTACACTCAGC-TCCAAGGCACATC
*
33359 ATTTGCAGCATAACTTAAGTGGAGAAGGGTTATCTTCCAATCAGAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAA-CA-AGACCTTCGAGTTCGACTACG
* * * * * *
33424 CTCAGCTCCAAGGCATATCATTTGCAACACAACTTAAGTCTAGAAGGGTTATCTGCTAAAGACCT
64 ATCAGCT-CAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCT
*
33489 TTGAGTTCGATTA
128 TCGAGTTCGATTA
33502 TATTCAACTT
Statistics
Matches: 260, Mismatches: 38, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
164 28 0.11
165 159 0.61
166 5 0.02
167 1 0.00
168 44 0.17
169 22 0.08
170 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (161 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACAAGACCTTCGAGTTCGACTACGAT
CAGCTCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCTTCG
AGTTCGATTACACTCAGCTCCAAGGCACATC
Found at i:33584 original size:249 final size:247
Alignment explanation
Indices: 33051--33569 Score: 713
Period size: 249 Copynumber: 2.1 Consensus size: 247
33041 GCTTAAGTCG
* *
33051 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGC
1 AGAAGGGCTATCTGCAAAAAACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGC
33116 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
66 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
* *
33181 TCCAAGGCATATCATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTTCCAACAAAAGACCTTT
131 TCCAAGGCATATCATTTGCAACACAACTTAAGTCTACAAGGGTTATCTT-C-ACAAAAGACCTTT
* * * * * * * *
33246 GAGTTCGACTACGATCAGCTCAATGGCACATCATTTGCAGCATAGCTTAAGTCG
194 GAGTTCGACTACGATCAACTCAATGGCAAATCACTTACAGAATAGCTCAAGGCA
* *
33300 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGC
1 AGAAGGGCTATCTGCAAAAAACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGC
* * * *
33365 AGCATAACTTAAGTGGAGAAGGGTTATCTTCCAATCAGAGACCTTCGAGTTCGACTACGCTCAGC
66 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
* * *
33430 TCCAAGGCATATCATTTGCAACACAACTTAAGTCTAGAAGGGTTATC-T-GCTAAAGACCTTTGA
131 TCCAAGGCATATCATTTGCAACACAACTTAAGTCTACAAGGGTTATCTTCACAAAAGACCTTTGA
* * *
33493 GTTCGATTA-TATTCAACTTAGA-GGCAAATCAAGCTTACAGAATAGCTCAAGGCA
196 GTTCGACTACGA-TCAACTCA-ATGGCAAATC-A-CTTACAGAATAGCTCAAGGCA
*
33547 AGAAGGGTTATCTGTCAATAAAA
1 AGAAGGGCTATCTG-CAA-AAAA
33570 TTGTCGAGTT
Statistics
Matches: 241, Mismatches: 23, Indels: 12
0.87 0.08 0.04
Matches are distributed among these distances:
244 1 0.00
245 34 0.14
246 2 0.01
247 28 0.12
248 3 0.01
249 173 0.72
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (247 bp):
AGAAGGGCTATCTGCAAAAAACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGC
AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
TCCAAGGCATATCATTTGCAACACAACTTAAGTCTACAAGGGTTATCTTCACAAAAGACCTTTGA
GTTCGACTACGATCAACTCAATGGCAAATCACTTACAGAATAGCTCAAGGCA
Found at i:34123 original size:2 final size:2
Alignment explanation
Indices: 34118--34164 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
34108 TCTCATTTTT
* *
34118 TA TA TA TA CA CA 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
34160 -A TA TA
1 TA TA TA
34165 GTTTTGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:34195 original size:38 final size:36
Alignment explanation
Indices: 34149--34249 Score: 114
Period size: 38 Copynumber: 2.8 Consensus size: 36
34139 ATATATATAT
*
34149 ATATATATATAATATAGTTTTGAAAACATATTTGAAA
1 ATATATATATAATATAGTTTTTAAAACA-ATTTGAAA
* * * *
34186 CATTTATATATTAGATAGTTTTTAAAACACTTTGAAA
1 -ATATATATATAATATAGTTTTTAAAACAATTTGAAA
*
34223 ATAAATATA-ATATATAGTTTTTAAAAC
1 ATATATATATA-ATATAGTTTTTAAAAC
34250 GTTTTTAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
36 22 0.42
37 7 0.13
38 24 0.45
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (36 bp):
ATATATATATAATATAGTTTTTAAAACAATTTGAAA
Found at i:34240 original size:36 final size:36
Alignment explanation
Indices: 34151--34402 Score: 158
Period size: 36 Copynumber: 6.9 Consensus size: 36
34141 ATATATATAT
* **
34151 ATATATATAATATAGTTTTGAAAACATATTTGAAACATTT
1 ATATA-AT-ATATAGTTTTTAAAACAT-TTTGAAA-ATAA
* * *
34191 ATATATTAGATAGTTTTTAAAACACTTTGAAAATAA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
* *
34227 ATATAATATATAGTTTTTAAAACGTTTTTAAAA-AA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
* ** * *
34262 ATATATTATACGGTTTTAAAAAACATTTTTAAAATAA
1 ATATAATATATAGTTTT-TAAAACATTTTGAAAATAA
*** *
34299 ATATAAT-T-T--TTAAAAAGAAACATTTTGAAAACATAT
1 ATATAATATATAGTT-TTTA-AAACATTTTG-AAA-ATAA
* * * *
34335 ATATATTATATAGTTTTGAAATCATTTT-AAAA-AC
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
* *
34369 TTATAATATATAGTTTTAAAAACATTTTTGAAAA
1 ATATAATATATAGTTTTTAAAACA-TTTTGAAAA
34403 CTATATAATT
Statistics
Matches: 168, Mismatches: 32, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
33 4 0.02
34 30 0.18
35 24 0.14
36 61 0.36
37 16 0.10
38 24 0.14
39 2 0.01
40 7 0.04
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (36 bp):
ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
Found at i:34327 original size:106 final size:106
Alignment explanation
Indices: 34210--34414 Score: 247
Period size: 106 Copynumber: 1.9 Consensus size: 106
34200 ATAGTTTTTA
* * *
34210 AAACACTTTG-AAA-ATAAATATAATATATAGTTTTTAAAACGTTTTTAAAAAAATATATTATAC
1 AAACACTTTGAAAACATAAATATAATATATAGTTTTGAAAAC-ATTTTAAAAAAATATAATATAC
*
34273 GGTTTTAAAAAACATTTTT-AAAA-TAAATATAATTTTTAAAAAG
65 AGTTTT-AAAAACATTTTTGAAAACT--ATATAATTTTTAAAAAG
* * * * ** *
34316 AAACATTTTGAAAACATATATATATTATATAGTTTTGAAATCATTTTAAAAACTTATAATATATA
1 AAACACTTTGAAAACATAAATATAATATATAGTTTTGAAAACATTTTAAAAAAATATAATATACA
34381 GTTTTAAAAACATTTTTGAAAACTATATAATTTT
66 GTTTTAAAAACATTTTTGAAAACTATATAATTTT
34415 GAAAGCATTT
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
106 31 0.37
107 29 0.35
108 24 0.29
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (106 bp):
AAACACTTTGAAAACATAAATATAATATATAGTTTTGAAAACATTTTAAAAAAATATAATATACA
GTTTTAAAAACATTTTTGAAAACTATATAATTTTTAAAAAG
Found at i:34396 original size:72 final size:70
Alignment explanation
Indices: 34151--34409 Score: 208
Period size: 72 Copynumber: 3.6 Consensus size: 70
34141 ATATATATAT
* * * *
34151 ATATATATAATATAGTTTTGAAAACATATTTG-AAACATTTATATATTAGATAGTTTTTAAAACA
1 ATATA-AT-ATATAGTTTTAAAAACAT-TTTGAAAACATATATATATTATATAGTTTTAAAAACA
*
34215 CTTTGAAAATAA
63 -TTT--TAA-AA
* * * **
34227 ATATAATATATAGTTTTTAAAACGTTTTTAAAA-A-A-ATATATTATACGGTTTTAAAAAACATT
1 ATATAATATATAGTTTTAAAAACATTTTGAAAACATATATATATTATATAGTTTT-AAAAACATT
*
34289 TTTAAA
65 TTAAAA
* * *
34295 ATA-AATATA-ATTTTTAAAAAGAAACATTTTGAAAACATATATATATTATATAGTTTTGAAATC
1 ATATAATATATAGTTTT---AA-AAACATTTTGAAAACATATATATATTATATAGTTTTAAAAAC
34358 ATTTTAAAA
62 ATTTTAAAA
34367 ACTTATAATATATAGTTTTAAAAACATTTTTGAAAAC-TATATA
1 A--TATAATATATAGTTTTAAAAACA-TTTTGAAAACATATATA
34410 ATTTTGAAAG
Statistics
Matches: 149, Mismatches: 20, Indels: 32
0.74 0.10 0.16
Matches are distributed among these distances:
66 5 0.03
67 6 0.04
68 5 0.03
69 2 0.01
70 12 0.08
71 18 0.12
72 31 0.21
73 31 0.21
74 21 0.14
75 8 0.05
76 10 0.07
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.41
Consensus pattern (70 bp):
ATATAATATATAGTTTTAAAAACATTTTGAAAACATATATATATTATATAGTTTTAAAAACATTT
TAAAA
Found at i:34408 original size:29 final size:29
Alignment explanation
Indices: 34375--34431 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
34365 AAACTTATAA
*
34375 TATATAGTTTTAAAAACATTTTTGAAAAC
1 TATATAATTTTAAAAACATTTTTGAAAAC
* * *
34404 TATATAATTTTGAAAGCATTTTTTAAAA
1 TATATAATTTTAAAAACATTTTTGAAAA
34432 AAAATATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (29 bp):
TATATAATTTTAAAAACATTTTTGAAAAC
Found at i:34452 original size:66 final size:61
Alignment explanation
Indices: 34341--34473 Score: 160
Period size: 66 Copynumber: 2.1 Consensus size: 61
34331 ATATATATAT
* * ** *
34341 TATATAGTTTTGAAATCATTTTAAAAACTTATAATATATAGTTTTAAAA-ACATTTTTGAAAA
1 TATATAATTTTGAAAGCATTTTAAAAAAATATAATATATAATTTTAAAATAC--TTTTGAAAA
34403 CTATATAATTTTGAAAGCATTTTTTAAAAAAAATATAATATATAATTTTAAAATACTTTTGAAAA
1 -TATATAATTTTGAAAGCA--TTTT-AAAAAAATATAATATATAATTTTAAAATACTTTTGAAAA
34468 TATATA
1 TATATA
34474 TTATATAGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
63 16 0.26
64 6 0.10
65 13 0.21
66 24 0.39
67 2 0.03
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (61 bp):
TATATAATTTTGAAAGCATTTTAAAAAAATATAATATATAATTTTAAAATACTTTTGAAAA
Found at i:34536 original size:14 final size:14
Alignment explanation
Indices: 34519--34563 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
34509 TATTATCGTG
34519 TTATTTATTTTTAT
1 TTATTTATTTTTAT
34533 TTATTTATTTTTAT
1 TTATTTATTTTTAT
* *
34547 TAATTTTATTTTCAT
1 TTA-TTTATTTTTAT
34562 TT
1 TT
34564 TAATTGTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTTATTTTTAT
Found at i:35444 original size:13 final size:12
Alignment explanation
Indices: 35425--35455 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
35415 TGGGTTTCCT
35425 ACGGCGGCCGGC
1 ACGGCGGCCGGC
35437 AGCGGCGGCCGGC
1 A-CGGCGGCCGGC
35450 ACGGCG
1 ACGGCG
35456 TTGGCACGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.10, C:0.39, G:0.52, T:0.00
Consensus pattern (12 bp):
ACGGCGGCCGGC
Found at i:36955 original size:16 final size:17
Alignment explanation
Indices: 36934--36976 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
36924 TGTGTGGTTT
36934 TTTTTAAATATATAT-A
1 TTTTTAAATATATATAA
*
36950 TTTTTAATTTTATATATAA
1 TTTTTAA--ATATATATAA
36969 TTTTTAAA
1 TTTTTAAA
36977 ATTACCAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
16 7 0.32
18 7 0.32
19 8 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTTAAATATATATAA
Found at i:38629 original size:42 final size:43
Alignment explanation
Indices: 38577--38666 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 43
38567 TGATTGTAAG
* *
38577 TTTTTCAATATCACTTTGTGCCTTTATAATTGAGCT-CCTGAT
1 TTTTTCAATATCACTTTGTACCTTTATAATTGAGCTCCCTAAT
* * * *
38619 TTTTTCAATATCATTTTTTATCTTTATAATTGAGGTCCCTAAT
1 TTTTTCAATATCACTTTGTACCTTTATAATTGAGCTCCCTAAT
38662 TTTTT
1 TTTTT
38667 TTCCAATCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 31 0.76
43 10 0.24
ACGTcount: A:0.22, C:0.16, G:0.09, T:0.53
Consensus pattern (43 bp):
TTTTTCAATATCACTTTGTACCTTTATAATTGAGCTCCCTAAT
Found at i:40450 original size:30 final size:30
Alignment explanation
Indices: 40389--40468 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
40379 GAAAAGTCAT
* * *
40389 AAATCGGTCACTAACGTTATTGTTTGATACA
1 AAAT-GGTCACTGACGTTATCGTATGATACA
* *
40420 ATATGGTCACTGACGTTATCGTATGTTACA
1 AAATGGTCACTGACGTTATCGTATGATACA
*
40450 AAATAGTCACTCGACGTTA
1 AAATGGTCACT-GACGTTA
40469 ACAATCATTA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 31 0.76
31 10 0.24
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (30 bp):
AAATGGTCACTGACGTTATCGTATGATACA
Found at i:59070 original size:2 final size:2
Alignment explanation
Indices: 59063--59105 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
59053 CAAATACAAT
59063 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
59105 A
1 A
59106 TATATATATA
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:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:59756 original size:22 final size:22
Alignment explanation
Indices: 59728--59772 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
59718 GAAAGTACTG
*
59728 TAGCAGGGGAATCGGTTCCCTA
1 TAGCAGGGGAACCGGTTCCCTA
59750 TAGCAGGGGAACCGGTTCCCTA
1 TAGCAGGGGAACCGGTTCCCTA
59772 T
1 T
59773 TTGTAATCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.22
Consensus pattern (22 bp):
TAGCAGGGGAACCGGTTCCCTA
Found at i:61989 original size:21 final size:20
Alignment explanation
Indices: 61950--61987 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
61940 AGAATGTCCA
61950 GGGGGTATCGATTCCCCCTG
1 GGGGGTATCGATTCCCCCTG
61970 GGGGGTATCGATTCCCCC
1 GGGGGTATCGATTCCCCC
61988 CTAAATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCCTG
Found at i:62351 original size:14 final size:15
Alignment explanation
Indices: 62334--62362 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
62324 TACATGATAT
62334 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
62348 GCATAAAACATAAGA
1 GCATAAAACATAAGA
62363 TATATGATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:66602 original size:23 final size:23
Alignment explanation
Indices: 66565--66626 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
66555 CAACTCATAT
*
66565 AAATGCACCGAAGTGCCACGTAG
1 AAATACACCGAAGTGCCACGTAG
* * *
66588 AATTACACCGTAGTGTCACGTAG
1 AAATACACCGAAGTGCCACGTAG
*
66611 AAATGCACCGAAGTGC
1 AAATACACCGAAGTGC
66627 TATATAAAGT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (23 bp):
AAATACACCGAAGTGCCACGTAG
Found at i:66981 original size:12 final size:12
Alignment explanation
Indices: 66964--66994 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
66954 ATGATTCACA
66964 TATCACAGAGCT
1 TATCACAGAGCT
66976 TATCACAGAGCT
1 TATCACAGAGCT
66988 TATCACA
1 TATCACA
66995 TATAATTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (12 bp):
TATCACAGAGCT
Found at i:68219 original size:35 final size:35
Alignment explanation
Indices: 68168--68249 Score: 155
Period size: 35 Copynumber: 2.3 Consensus size: 35
68158 CTACACCGTA
*
68168 TATCGATGCATCCCTTGACGGGTGCATCGATGCAC
1 TATCTATGCATCCCTTGACGGGTGCATCGATGCAC
68203 TATCTATGCATCCCTTGACGGGTGCATCGATGCAC
1 TATCTATGCATCCCTTGACGGGTGCATCGATGCAC
68238 TATCTATGCATC
1 TATCTATGCATC
68250 GGTACATAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (35 bp):
TATCTATGCATCCCTTGACGGGTGCATCGATGCAC
Done.