Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003605.1 Hibiscus syriacus cultivar Beakdansim tig00007624_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: 122085
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:9501 original size:252 final size:256
Alignment explanation
Indices: 9054--9561 Score: 900
Period size: 252 Copynumber: 2.0 Consensus size: 256
9044 TTCAAATGCG
9054 TATCTGTAATGGGAAGTAACCACTACAAATAAATTCATGCGTAAAAATCTCTGCATATAGACAGA
1 TATCTGTAATGGGAAGTAACCACTACAAATAAATTCATGCGTAAAAATCTCTGCATATAGACAGA
9119 AAAAGTAAGTACCGACTAAATTTAAAAAGAGGAAACATACAGAAAATGATACCCAGTAGTCAGTG
66 AAAAGTAAGTACCGACTAAATTTAAAAAGAGGAAACATACAGAAAATGATACCCAGTAGTCAGTG
9184 ATAGCAAGCTACGATAAGGTAAAAAGTCAAATGGGTTAAAACCTAAACTAAGACAAAACTACTCC
131 ATAGCAAGCTACGATAAGGTAAAAAGTCAAATGGGTTAAAACCTAAACTAAGACAAAACTACTCC
*
9249 GCTACCCTAGTTCTAAGCCTTTATAAATTCCAATGAAAG-ATCGTAT-AAAAGTAGAAGTC
196 GCTACCCTAGTTCTAAGCCTTTATAAATTCCAATGAAAGAACCGTATAAAAAGTAGAAGTC
*
9308 TATCTGTAATGGGAAGTAATCACTACAAATAAATTCATGCGTAAAAATCTCTGCATATAGACAG-
1 TATCTGTAATGGGAAGTAACCACTACAAATAAATTCATGCGTAAAAATCTCTGCATATAGACAGA
* * *
9372 AAAAGTAAGTCCCGACT-AATTTAAAAAGAGGAAACATGCAGAAAATGATACCCATTAGTCAGTG
66 AAAAGTAAGTACCGACTAAATTTAAAAAGAGGAAACATACAGAAAATGATACCCAGTAGTCAGTG
*
9436 ATAGCAAGCTACGATAAGGTAAAAAGTCAAATGGGTTAAAACCTAAACTAAGGA-AAAATTACTC
131 ATAGCAAGCTACGATAAGGTAAAAAGTCAAATGGGTTAAAACCTAAACTAA-GACAAAACTACTC
* *
9500 CGCTACCTTAGTTCTAAGCCTTTATAAATTCCAATGACAGAACCGTATAAAAAGTAGAAGTC
195 CGCTACCCTAGTTCTAAGCCTTTATAAATTCCAATGAAAGAACCGTATAAAAAGTAGAAGTC
9562 ATGGAATTTA
Statistics
Matches: 243, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
252 143 0.59
253 24 0.10
254 76 0.31
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (256 bp):
TATCTGTAATGGGAAGTAACCACTACAAATAAATTCATGCGTAAAAATCTCTGCATATAGACAGA
AAAAGTAAGTACCGACTAAATTTAAAAAGAGGAAACATACAGAAAATGATACCCAGTAGTCAGTG
ATAGCAAGCTACGATAAGGTAAAAAGTCAAATGGGTTAAAACCTAAACTAAGACAAAACTACTCC
GCTACCCTAGTTCTAAGCCTTTATAAATTCCAATGAAAGAACCGTATAAAAAGTAGAAGTC
Found at i:13986 original size:13 final size:13
Alignment explanation
Indices: 13968--14019 Score: 59
Period size: 13 Copynumber: 3.7 Consensus size: 13
13958 ACAATCATAT
13968 AATATAAATTTTA
1 AATATAAATTTTA
13981 AATATATTACATTTTA
1 AATATA--A-ATTTTA
*
13997 AATATAAAATTTA
1 AATATAAATTTTA
14010 AATATTAAAT
1 AATA-TAAAT
14020 CAATTTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 15 0.45
14 5 0.15
15 1 0.03
16 12 0.36
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (13 bp):
AATATAAATTTTA
Found at i:14205 original size:14 final size:14
Alignment explanation
Indices: 14188--14219 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
14178 GTTTTTAATT
*
14188 TTTTAGTATTTTAA
1 TTTTAATATTTTAA
14202 TTTTAATATTTTAA
1 TTTTAATATTTTAA
14216 TTTT
1 TTTT
14220 TGATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTTAATATTTTAA
Found at i:16773 original size:21 final size:20
Alignment explanation
Indices: 16726--16773 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
16716 ATTTTGGAAT
16726 TTAAAATTTGTTATTTAAGA
1 TTAAAATTTGTTATTTAAGA
* *
16746 TTTAAATTT-TTAATCTTAATA
1 TTAAAATTTGTT-AT-TTAAGA
16767 TTAAAAT
1 TTAAAAT
16774 AAAAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 10 0.43
21 11 0.48
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (20 bp):
TTAAAATTTGTTATTTAAGA
Found at i:18941 original size:31 final size:31
Alignment explanation
Indices: 18906--18986 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
18896 TTTTTTAAAC
*
18906 TTACAAAATAGTTATTAAATTTATTGAA-TTA
1 TTACAAAATAGTTATTAAATTTA-TCAATTTA
* *
18937 TTACAAAATAGTCATTAAATTTATCAATTTT
1 TTACAAAATAGTTATTAAATTTATCAATTTA
* *
18968 TTACAAAGTAATTATTAAA
1 TTACAAAATAGTTATTAAA
18987 CCAGATTGTC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 3 0.07
31 40 0.93
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (31 bp):
TTACAAAATAGTTATTAAATTTATCAATTTA
Found at i:22840 original size:3 final size:3
Alignment explanation
Indices: 22834--22860 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
22824 TAAATCAATA
22834 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
22861 TGAAGGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:23688 original size:35 final size:34
Alignment explanation
Indices: 23612--23689 Score: 122
Period size: 33 Copynumber: 2.3 Consensus size: 34
23602 TGTAGTTGAT
*
23612 GTATTTTTTTTATTAAAATAGGTGCCTACCTAAA
1 GTATTTTTTTTATTAAAATAGGTACCTACCTAAA
**
23646 GTA-TTTTTTTATTAAAATAGGTACCTGTCTAAA
1 GTATTTTTTTTATTAAAATAGGTACCTACCTAAA
23679 GTATTTTTTTT
1 GTATTTTTTTT
23690 TATTGTCCTC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 30 0.75
34 10 0.25
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50
Consensus pattern (34 bp):
GTATTTTTTTTATTAAAATAGGTACCTACCTAAA
Found at i:24592 original size:60 final size:60
Alignment explanation
Indices: 24528--24655 Score: 179
Period size: 60 Copynumber: 2.1 Consensus size: 60
24518 ATTGGTCCAT
* *
24528 AAACTTTTGAACATTTTAATTTCATCCCT-AAACTATGACTCC-CATTCTAAATTAGTCCCC
1 AAACTTTTGAACATTTCAAATTCA-CCCTCAAACTATGAC-CCTCATTCTAAATTAGTCCCC
* * *
24588 AAACTTTTGAACATTTCAAATTCACCCTCAAACTGTGACCCTTATTCTAGATTAGTCCCC
1 AAACTTTTGAACATTTCAAATTCACCCTCAAACTATGACCCTCATTCTAAATTAGTCCCC
24648 AAACTTTT
1 AAACTTTT
24656 AAATATTCCA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
59 6 0.10
60 55 0.90
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (60 bp):
AAACTTTTGAACATTTCAAATTCACCCTCAAACTATGACCCTCATTCTAAATTAGTCCCC
Found at i:24802 original size:59 final size:59
Alignment explanation
Indices: 24703--24842 Score: 158
Period size: 59 Copynumber: 2.4 Consensus size: 59
24693 TTCAAAGTTA
* * * *** *
24703 AAATTAGAATATTTAAAAGTTTGGGGATCAATATAGAATGAAGGTTATAATTTGAGGATG
1 AAATTAGAATATTCAAAAGTTTGGGAATCAATATAAAATGAA-AACATAATTTAAGGATG
* * *
24763 -AATTGGAATATTCAAAAGTTTGGAGAAT-AATTTAAAATGAAAACATAGTTTAAGGATG
1 AAATTAGAATATTCAAAAGTTTGG-GAATCAATATAAAATGAAAACATAATTTAAGGATG
24821 AAATTAGAATATTCAAAAGTTT
1 AAATTAGAATATTCAAAAGTTT
24843 AGGATTCACT
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
58 12 0.18
59 52 0.78
60 3 0.04
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.33
Consensus pattern (59 bp):
AAATTAGAATATTCAAAAGTTTGGGAATCAATATAAAATGAAAACATAATTTAAGGATG
Found at i:29178 original size:13 final size:13
Alignment explanation
Indices: 29160--29184 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29150 TCAAAGGAAC
29160 AAAAAAAAAACTA
1 AAAAAAAAAACTA
29173 AAAAAAAAAACT
1 AAAAAAAAAACT
29185 TGATAAATGA
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:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAAAAAAAACTA
Found at i:40658 original size:50 final size:50
Alignment explanation
Indices: 40588--40689 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
40578 CCAAATATTG
*
40588 AAGAAAGAACAATTTTATCAAACATCTAAGAGCACTTAACTCCTCAAGAA
1 AAGAAAGAACAATTTTATCAAACATCTAAGAACACTTAACTCCTCAAGAA
40638 AAGAAAGAACAATTTTATCAAACATCTAAGAACACTTAACTCCTCAAGAA
1 AAGAAAGAACAATTTTATCAAACATCTAAGAACACTTAACTCCTCAAGAA
40688 AA
1 AA
40690 CATTATTAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.50, C:0.20, G:0.09, T:0.22
Consensus pattern (50 bp):
AAGAAAGAACAATTTTATCAAACATCTAAGAACACTTAACTCCTCAAGAA
Found at i:46471 original size:48 final size:48
Alignment explanation
Indices: 46400--46496 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
46390 AAGAAGGCTG
46400 TAGCAGAATATTTTAACATCATATATTTTGAAATTTATTCTTATTATA
1 TAGCAGAATATTTTAACATCATATATTTTGAAATTTATTCTTATTATA
*
46448 TAGCAGAATATTTTAACATCATATATTTTGAAATTTGTTCTTATTATA
1 TAGCAGAATATTTTAACATCATATATTTTGAAATTTATTCTTATTATA
46496 T
1 T
46497 CATCTAGATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.48
Consensus pattern (48 bp):
TAGCAGAATATTTTAACATCATATATTTTGAAATTTATTCTTATTATA
Found at i:46483 original size:23 final size:23
Alignment explanation
Indices: 46409--46483 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
46399 GTAGCAGAAT
46409 ATTTTAACATCATATATTTTGAA
1 ATTTTAACATCATATATTTTGAA
* * ***
46432 A-TTTATTC-TTATTATATAGCAGAA
1 ATTTTA-ACATCA-TATAT-TTTGAA
46456 TATTTTAACATCATATATTTTGAA
1 -ATTTTAACATCATATATTTTGAA
46480 ATTT
1 ATTT
46484 GTTCTTATTA
Statistics
Matches: 36, Mismatches: 10, Indels: 12
0.62 0.17 0.21
Matches are distributed among these distances:
22 6 0.17
23 11 0.31
24 6 0.17
25 7 0.19
26 6 0.17
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.49
Consensus pattern (23 bp):
ATTTTAACATCATATATTTTGAA
Found at i:49703 original size:272 final size:270
Alignment explanation
Indices: 49206--50547 Score: 1522
Period size: 272 Copynumber: 4.9 Consensus size: 270
49196 TGGGATTGAA
* * **
49206 CAAAAAAGATTTCAAGAAACATAAAGGAAGAATAACAAAGTTTAAAAATGACATCGTGAAAGCCT
1 CAAACAAGATTTCAAGAAACATAAAGGAAGAATAACCAAGTTTAAAAATGACATCAAGAAAGCCT
*
49271 TTAGTCAAACCTAAGATCTTATTTGAAGCAACAAATGTTTAACAATACCTTCAGCTGCTCATTTT
66 TTAGTCAAACCTAAGATCTTATTTGAAGCAACAAATGTCTAACAATACCTTCAGCTGCTCATTTT
* * ** * * * ** *
49336 CAGCAGTA-ATTTCTTTCATCAATTCAATGTCAATAATGGGAATCTCCTTAATTATAGGAACTAG
131 CAGCAGTAGGTTT-ATTCATCAATTCGTTGTCAATAACGGG-ATCTCCTGAACTGCAGGAACTTG
* * * *
49400 TTCAGTAATGCTT-TTTGTAGCTTCATGTTCCTCAACTAGTAACTCTTTTGTTTCTTGAACCTAC
194 TTCAGCAATG-TTCTTTGCAGCTTCACGTTCCTCAACTAGTAACTCTTTTGTTTCCTGAACCTAC
*
49464 AATGGCATTGTCC
258 AATGGCATTGTGC
* * ** *
49477 CAAACAAGATTTAAAGAAACATAAAGGAACAATAATTAAGTTTAAAAATGACATCAAAAAAAGCC
1 CAAACAAGATTTCAAGAAACATAAAGGAAGAATAACCAAGTTTAAAAATGACATC-AAGAAAGCC
* * * * *
49542 TTTAGTCAAACCTAAGATCTTATTTGAAGCAACAGATGTGTAAAAATACCTTTAGCTGCTCATTA
65 TTTAGTCAAACCTAAGATCTTATTTGAAGCAACAAATGTCTAACAATACCTTCAGCTGCTCATTT
* * * *
49607 TCAGCAGTTGGTTTATTCATCAATTCGTTGACAATGACGGAGCTCTCCTGAACTGCAGGAACTTG
130 TCAGCAGTAGGTTTATTCATCAATTCGTTGTCAATAACGG-GATCTCCTGAACTGCAGGAACTTG
**
49672 TTCAGCAATGTTCTTTGCAGCTTCGTGTTCCTCAACTAGTAACTCTTTTGTTTCCTGAACCTACA
194 TTCAGCAATGTTCTTTGCAGCTTCACGTTCCTCAACTAGTAACTCTTTTGTTTCCTGAACCTACA
* *
49737 ACGCCATTGTGC
259 ATGGCATTGTGC
49749 CAAACAAGATTTCAAGAAACATAAAGGAAGAATAACCAAG-TTAAAAATGACATCAAGAAAG-CT
1 CAAACAAGATTTCAAGAAACATAAAGGAAGAATAACCAAGTTTAAAAATGACATCAAGAAAGCCT
** * **
49812 TCTAGTCAAACCTAAGATCTTGTTCTTATTCAAAGCAACAAATGTCTAGCAATACCTTTTGCTGC
66 T-TAGTCAAACCTAAGA------TCTTATTTGAAGCAACAAATGTCTAACAATACCTTCAGCTGC
* * *
49877 TCATTTTCAGCAGTAGGTTCATTCATCAATTCGTT-TCCAATAACGAGGTTCTCCTGAACCGCAG
124 TCATTTTCAGCAGTAGGTTTATTCATCAATTCGTTGT-CAATAACG-GGATCTCCTGAACTGCAG
* * ** * *
49941 GAACTTGTTCAGCAATGTTCTTTTCAGCTTCACATTCCAGAACTAGTGACTCCTTTGTTTCCTGA
187 GAACTTGTTCAGCAATGTTCTTTGCAGCTTCACGTTCCTCAACTAGTAACTCTTTTGTTTCCTGA
* *
50006 ACCGACAATGTCATTGTGC
252 ACCTACAATGGCATTGTGC
* * * * * *
50025 GAAGCAAGATTTCAAGAAACATAAAGAAAGAACAACCAAGTTTAAAAATGACATCAACACAG-CT
1 CAAACAAGATTTCAAGAAACATAAAGGAAGAATAACCAAGTTTAAAAATGACATCAAGAAAGCCT
* * * ** * ** *
50089 TCAAATCAAGCCTATCTTATTCTTGTTCAAAGCAACAAATGTCTAACAATACCTTCGGCTGCTCA
66 T-TAGTCAAACCTA--AGA-TCTTATTTGAAGCAACAAATGTCTAACAATACCTTCAGCTGCTCA
* * *
50154 TTTTCAGCAGTAGGTTTACTCATCAATTCGTTGTCAATAACGGGTTCCTCCTGAACCGCAGGAAC
127 TTTTCAGCAGTAGGTTTATTCATCAATTCGTTGTCAATAACGGGAT-CTCCTGAACTGCAGGAAC
* * * * * * *
50219 TTGTTCAGAAATGTTCTTTTCGGCTTCAGGTTCCTCAACTAGTGACTCCTTTGTTTCCTGAACTT
191 TTGTTCAGCAATGTTCTTTGCAGCTTCACGTTCCTCAACTAGTAACTCTTTTGTTTCCTGAACCT
50284 ACAATGAG-ATTGTGC
256 ACAATG-GCATTGTGC
* * * *
50299 CAAGCAAGATTTCAAGAAACAT--A--AAGAACAGCCAAGTTTAAAAATGGCATCAAGAAAGCCT
1 CAAACAAGATTTCAAGAAACATAAAGGAAGAATAACCAAGTTTAAAAATGACATCAAGAAAGCCT
* *
50360 TTAGTCAAACCTAATATCTTATTTGAAGCAACAAATGTCTAAAAATACCTTCAGCTGCTCATTTT
66 TTAGTCAAACCTAAGATCTTATTTGAAGCAACAAATGTCTAACAATACCTTCAGCTGCTCATTTT
* * * * * *
50425 GAG-AGGTAAGTTTATTCATCAATTCATTGTCAATAGCTGGGATCTCCTTAA-TCGCGGGAACTT
131 CAGCA-GTAGGTTTATTCATCAATTCGTTGTCAATAAC-GGGATCTCCTGAACT-GCAGGAACTT
* * * * *
50488 GTTCAGCAATGCTCTTTGCAGCTTCACGTTCCTTAACTAGCAAGTCTTGTGTTTCCTGAA
193 GTTCAGCAATGTTCTTTGCAGCTTCACGTTCCTCAACTAGTAACTCTTTTGTTTCCTGAA
50548 GCTGAAGTCG
Statistics
Matches: 924, Mismatches: 124, Indels: 50
0.84 0.11 0.05
Matches are distributed among these distances:
266 1 0.00
267 139 0.15
268 6 0.01
269 3 0.00
270 61 0.07
271 69 0.07
272 215 0.23
273 8 0.01
274 189 0.20
275 1 0.00
276 198 0.21
277 33 0.04
279 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (270 bp):
CAAACAAGATTTCAAGAAACATAAAGGAAGAATAACCAAGTTTAAAAATGACATCAAGAAAGCCT
TTAGTCAAACCTAAGATCTTATTTGAAGCAACAAATGTCTAACAATACCTTCAGCTGCTCATTTT
CAGCAGTAGGTTTATTCATCAATTCGTTGTCAATAACGGGATCTCCTGAACTGCAGGAACTTGTT
CAGCAATGTTCTTTGCAGCTTCACGTTCCTCAACTAGTAACTCTTTTGTTTCCTGAACCTACAAT
GGCATTGTGC
Found at i:50692 original size:96 final size:96
Alignment explanation
Indices: 50532--50843 Score: 387
Period size: 96 Copynumber: 3.2 Consensus size: 96
50522 AACTAGCAAG
* * * * * *
50532 TCTTGTGTTTCCTGAAGCTGAAGTCGCAGTTCGTGAAACTCAAGTTGCTT-TTCATT-CAAGGTA
1 TCTTTTGTTTGCTGAAGCTCAAGTTGCAGTTCATGAAACTCAAGTTGCTTCTT--TTGCAAAGTA
* *
50595 GATTCAAACCTTGCACTTTCCTCTTCTTGTAAC
64 GATTCAAACCTTGCACTTTCCTGTTCTAGTAAC
* * *
50628 TCTTTTGTTTTCTGAAGCTCAAGTTGCAGTTCCTGAAACTCAAGTTCCTTCTTTTGCAAAGTAGA
1 TCTTTTGTTTGCTGAAGCTCAAGTTGCAGTTCATGAAACTCAAGTTGCTTCTTTTGCAAAGTAGA
** * * *
50693 TTGTAACCTTTCAGTTTCCTGTGCTAGTAAC
66 TTCAAACCTTGCACTTTCCTGTTCTAGTAAC
* * *
50724 TCTTTTGATTGCTGAAGCTCAAGTTGCAGTTCATGAAACTCAAGTTGCTTCTTATG-AATAGAAG
1 TCTTTTGTTTGCTGAAGCTCAAGTTGCAGTTCATGAAACTCAAGTTGCTTCTTTTGCAA-AGTAG
*
50788 ATTCAAACCTTGCACTTTCCTGTTCTAGCAAC
65 ATTCAAACCTTGCACTTTCCTGTTCTAGTAAC
*
50820 TCTTTTGTTTGCAGAAGCTCAAGT
1 TCTTTTGTTTGCTGAAGCTCAAGT
50844 CCCAAATTCT
Statistics
Matches: 185, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
95 4 0.02
96 179 0.97
97 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (96 bp):
TCTTTTGTTTGCTGAAGCTCAAGTTGCAGTTCATGAAACTCAAGTTGCTTCTTTTGCAAAGTAGA
TTCAAACCTTGCACTTTCCTGTTCTAGTAAC
Found at i:51176 original size:66 final size:66
Alignment explanation
Indices: 51065--51336 Score: 445
Period size: 66 Copynumber: 4.1 Consensus size: 66
51055 CAGCTTGCAG
* * * * *
51065 TTCCTGAAACTCAAGTTGCTTCTTTTGCAAAGTAGATTCAAACCTTTCACTTTCCTGTTTTTTAG
1 TTCCTCAAACTCAAGTTGCATCTTCTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTGG
51130 A
66 A
* * *
51131 TTCCTCAAACTCAAGTTGCATCTTCTGTAAGGTAGATTCATACCTTGCACTTTCCTGTTTTTTGG
1 TTCCTCAAACTCAAGTTGCATCTTCTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTGG
51196 A
66 A
*
51197 TTCCTCAAACTCAAGTTGCATCTTCTGCAAAGTAGATTCAAACCTTGCATTTTCCTGTTTTTTGG
1 TTCCTCAAACTCAAGTTGCATCTTCTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTGG
51262 A
66 A
* *
51263 TTCCTCAAACTCAAGTTGCATCTTCTTCAAAGTAGATTCAAACTTTGCACTTTCCTGTTTTTTGG
1 TTCCTCAAACTCAAGTTGCATCTTCTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTGG
51328 A
66 A
51329 TTCCTCAA
1 TTCCTCAA
51337 GGTCAACCTG
Statistics
Matches: 191, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 191 1.00
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.41
Consensus pattern (66 bp):
TTCCTCAAACTCAAGTTGCATCTTCTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTGG
A
Found at i:57154 original size:15 final size:15
Alignment explanation
Indices: 57134--57166 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
57124 TAAAATCTTT
*
57134 TTTTCCCGTTCTTGA
1 TTTTCCCGTTCTAGA
57149 TTTTCCCGTTCTAGA
1 TTTTCCCGTTCTAGA
57164 TTT
1 TTT
57167 GGATCTGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.12, T:0.55
Consensus pattern (15 bp):
TTTTCCCGTTCTAGA
Found at i:60499 original size:6 final size:6
Alignment explanation
Indices: 60488--60594 Score: 187
Period size: 6 Copynumber: 17.8 Consensus size: 6
60478 ATCTGTCTAT
* *
60488 CGTGTA CGTGTA CGTGTA TGTGTA CGTGTA TGTGTA CGTGTA CGTGTA
1 CGTGTA CGTGTA CGTGTA CGTGTA CGTGTA CGTGTA CGTGTA CGTGTA
60536 CGTGTA CGTGTA CGTGTA CGTGTA CGTGTA CGTGTA CGTGTA CGTGTA
1 CGTGTA CGTGTA CGTGTA CGTGTA CGTGTA CGTGTA CGTGTA CGTGTA
*
60584 CGTGTA TGTGT
1 CGTGTA CGTGT
60595 CTGCACATAT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 96 1.00
ACGTcount: A:0.16, C:0.14, G:0.34, T:0.36
Consensus pattern (6 bp):
CGTGTA
Found at i:65793 original size:34 final size:34
Alignment explanation
Indices: 65728--65793 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
65718 GTACGTAAAA
* * * *
65728 ATAATATTTTTTATATACTTTCATTTAATGAAAG
1 ATAAAATTATTTATATACTTTAATGTAATGAAAG
65762 ATAAAATTATTTATATACTATTAATGT-ATGAA
1 ATAAAATTATTTATATACT-TTAATGTAATGAA
65794 TCTTGTGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 22 0.81
35 5 0.19
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (34 bp):
ATAAAATTATTTATATACTTTAATGTAATGAAAG
Found at i:67321 original size:14 final size:15
Alignment explanation
Indices: 67302--67339 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
67292 TTTCTGTCTA
67302 TATGCAGAGATTT-T
1 TATGCAGAGATTTAT
*
67316 TATGCAGGGATTTAT
1 TATGCAGAGATTTAT
67331 T-TGCAGAGA
1 TATGCAGAGA
67340 GTAATTCCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 19 0.90
15 2 0.10
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.37
Consensus pattern (15 bp):
TATGCAGAGATTTAT
Found at i:70244 original size:39 final size:39
Alignment explanation
Indices: 70201--70280 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
70191 TCTTGAGATT
*
70201 TTCTCAATTTG-CTTGAAGACG-TCATGTAATCGTGGAGTC
1 TTCTCAATTTGTC-TGAAGACGCT-ATGCAATCGTGGAGTC
* *
70240 TTCTCTATTTGTCTGAAGACGCTATGCAGTCGTGGAGTC
1 TTCTCAATTTGTCTGAAGACGCTATGCAATCGTGGAGTC
70279 TT
1 TT
70281 TATATTTAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 34 0.94
40 2 0.06
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (39 bp):
TTCTCAATTTGTCTGAAGACGCTATGCAATCGTGGAGTC
Found at i:70296 original size:39 final size:41
Alignment explanation
Indices: 70212--70300 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 41
70202 TCTCAATTTG
* * **
70212 CTTGAAGACG-TCATGTAATCGTGGAGTCTTCTCTATTTGT
1 CTTGAAGACGCTCATGCAATCGTGGAGTCTTCTATATTTAA
*
70252 C-TGAAGACGCT-ATGCAGTCGTGGAGTCTT-TATATTTAA
1 CTTGAAGACGCTCATGCAATCGTGGAGTCTTCTATATTTAA
70290 CTTGAAGACGC
1 CTTGAAGACGC
70301 GTGGGCACCT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
38 7 0.17
39 33 0.79
40 2 0.05
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (41 bp):
CTTGAAGACGCTCATGCAATCGTGGAGTCTTCTATATTTAA
Found at i:72395 original size:7 final size:7
Alignment explanation
Indices: 72373--72415 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
72363 TAATTAAAAT
72373 TATTTATA
1 TATTTA-A
*
72381 TTTTTAA
1 TATTTAA
72388 TATTTAA
1 TATTTAA
72395 TATTTAA
1 TATTTAA
72402 TATATTAA
1 TAT-TTAA
72410 TTATTT
1 -TATTT
72416 TATAATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 17 0.55
8 11 0.35
9 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (7 bp):
TATTTAA
Found at i:72399 original size:16 final size:16
Alignment explanation
Indices: 72373--72425 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 16
72363 TAATTAAAAT
72373 TATTT-ATATTTTTAA
1 TATTTAATATTTTTAA
72388 TATTTAATA--TTTAA
1 TATTTAATATTTTTAA
72402 TATATTAATTATTTTATAA
1 TAT-TTAA-TATTTT-TAA
72421 T-TTTA
1 TATTTA
72426 TGAGATGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 8 0.25
15 9 0.28
16 5 0.16
17 3 0.09
18 3 0.09
19 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTAATATTTTTAA
Found at i:73315 original size:37 final size:36
Alignment explanation
Indices: 73240--73315 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
73230 ATTTTTTATT
*
73240 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
73276 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
73313 TTT
1 TTT
73316 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:76030 original size:17 final size:17
Alignment explanation
Indices: 76008--76061 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
75998 TTTAAGTATT
76008 AAACTTTTAATTTTTCA
1 AAACTTTTAATTTTTCA
* *
76025 AAAC--TTAATGTCT-A
1 AAACTTTTAATTTTTCA
*
76039 AAACTTTTAGTTTTTCA
1 AAACTTTTAATTTTTCA
76056 AAACTT
1 AAACTT
76062 AACGTTACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 5 0.17
15 7 0.24
16 6 0.21
17 11 0.38
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (17 bp):
AAACTTTTAATTTTTCA
Found at i:80337 original size:23 final size:23
Alignment explanation
Indices: 80298--80347 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
80288 TGTTCGTTTA
* *
80298 TTTATTGTTCTCGAACAT-TTTG
1 TTTATTGTTCTCAAACATGTTCG
*
80320 TTTATATGTTTTCAAACATGTTCG
1 TTTAT-TGTTCTCAAACATGTTCG
80344 TTTA
1 TTTA
80348 ACATTCGTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.22
23 11 0.48
24 7 0.30
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.54
Consensus pattern (23 bp):
TTTATTGTTCTCAAACATGTTCG
Found at i:82404 original size:14 final size:14
Alignment explanation
Indices: 82385--82421 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
82375 CATCAATTAA
82385 ACAAATCAACTTTT
1 ACAAATCAACTTTT
* *
82399 ACAAATTACCTTTT
1 ACAAATCAACTTTT
82413 ACAAATCAA
1 ACAAATCAA
82422 TTAAACAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:83836 original size:21 final size:21
Alignment explanation
Indices: 83770--83836 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
83760 GTGAATCAGG
*
83770 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
83790 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
83812 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
83833 CTCT
1 CTCT
83837 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:83855 original size:42 final size:41
Alignment explanation
Indices: 83770--83891 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 41
83760 GTGAATCAGG
* * * * *
83770 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
83812 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
83854 CTCTTCAACGAT-AGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
83892 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
41 24 0.36
42 39 0.58
43 4 0.06
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:85967 original size:33 final size:33
Alignment explanation
Indices: 85910--86008 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
85900 ACGAGATAAT
*
85910 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
85944 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
85977 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
86009 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:86002 original size:19 final size:19
Alignment explanation
Indices: 85885--86107 Score: 250
Period size: 19 Copynumber: 12.1 Consensus size: 19
85875 TCTTTTGGTT
*
85885 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
85904 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
85924 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
85942 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
85958 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
85976 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
85991 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
86011 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
86030 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
86049 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
86068 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
86087 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
86106 GA
1 GA
86108 TTTTGGTTTC
Statistics
Matches: 176, Mismatches: 15, Indels: 26
0.81 0.07 0.12
Matches are distributed among these distances:
14 19 0.11
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.02
19 100 0.57
20 45 0.26
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:86136 original size:19 final size:19
Alignment explanation
Indices: 86103--86183 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
86093 AAAATCGCAA
**
86103 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
86122 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
86141 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
86155 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
86175 TGCGATTTT
1 TGCGATTTT
86184 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:86785 original size:21 final size:21
Alignment explanation
Indices: 86756--86848 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
86746 ATAGTAAGTA
86756 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
86777 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
86797 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
86818 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
86838 TCGCATTGCGA
1 TCGCATTGCGA
86849 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:86786 original size:41 final size:41
Alignment explanation
Indices: 86695--86829 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
86685 GCTATGTAAA
* * * ** *
86695 TCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
86735 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
86777 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
86818 TCGCGTTGCGAT
1 TCGCGTTGCGAT
86830 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:86830 original size:41 final size:41
Alignment explanation
Indices: 86756--86848 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
86746 ATAGTAAGTA
86756 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
86797 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
86838 TCGCATTGCGA
1 TCGCATTGCGA
86849 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:89007 original size:71 final size:73
Alignment explanation
Indices: 88883--89028 Score: 278
Period size: 71 Copynumber: 2.0 Consensus size: 73
88873 ACTCATGCTC
88883 CACTATACATTAGGGGCCCAAGTTATTTTTTTAGGGGCTCTTATTTTTTATTTACTTAGGACCTT
1 CACTATACATTAGGGGCCCAAGTTATTTTTTTAGGGGCTCTTATTTTTTATTTACTTAGGACCTT
88948 TAAAATGT
66 TAAAATGT
88956 CACTATACATTAGGGGCCCAAG-T-TTTTTTTAGGGGCTCTTATTTTTTATTTACTTAGGACCTT
1 CACTATACATTAGGGGCCCAAGTTATTTTTTTAGGGGCTCTTATTTTTTATTTACTTAGGACCTT
89019 TAAAATGT
66 TAAAATGT
89027 CA
1 CA
89029 GGTTTCTCCA
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
71 50 0.68
72 1 0.01
73 22 0.30
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (73 bp):
CACTATACATTAGGGGCCCAAGTTATTTTTTTAGGGGCTCTTATTTTTTATTTACTTAGGACCTT
TAAAATGT
Found at i:94653 original size:30 final size:28
Alignment explanation
Indices: 94630--94684 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
94620 CGGTGATCGG
94630 TATATTTACTGATCTAACACCGGTCAGAT
1 TATATTTACTGATCTAACACCGGT-AGAT
* *
94659 TATATTTCCTGATCTAACACCCGTAG
1 TATATTTACTGATCTAACACCGGTAG
94685 CAGTAAAGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.35
Consensus pattern (28 bp):
TATATTTACTGATCTAACACCGGTAGAT
Found at i:94901 original size:10 final size:10
Alignment explanation
Indices: 94886--94926 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
94876 TTTTATCACA
94886 TCAAATTCTC
1 TCAAATTCTC
94896 TCAAATTCTC
1 TCAAATTCTC
94906 T-AAATTTCTC
1 TCAAA-TTCTC
*
94916 TCAAATACTC
1 TCAAATTCTC
94926 T
1 T
94927 ATCTTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (10 bp):
TCAAATTCTC
Found at i:94978 original size:13 final size:14
Alignment explanation
Indices: 94950--94978 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
94940 ATATTTTATA
94950 ATATTTTTACTATT
1 ATATTTTTACTATT
94964 ATATTTTTACT-TT
1 ATATTTTTACTATT
94977 AT
1 AT
94979 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Found at i:95184 original size:111 final size:112
Alignment explanation
Indices: 95052--95274 Score: 403
Period size: 112 Copynumber: 2.0 Consensus size: 112
95042 TGGAAATCAT
*
95052 ATATCTCTACACTTTGCTGATACGGTAACA-TTTTAACGTTTTAATTTAATTTAAATTATTAGTA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTTAACGTTTTAATTTAATTTAAATTATTAGTA
*
95116 ATATTTAGTTGATTTATTTAATGCATAATTATTAGATTAAGAATTAA
66 ATAATTAGTTGATTTATTTAATGCATAATTATTAGATTAAGAATTAA
95163 ATATCTCGACACTTTGCTGATACGGTAACATTTTTAACGTTTTAATTTAATTTAAATTATTAGTA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTTAACGTTTTAATTTAATTTAAATTATTAGTA
* *
95228 GTAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 ATAATTAGTTGATTTATTTAATGCATAATTATTAGATTAAGAATTAA
95275 TTTTTGTAAT
Statistics
Matches: 107, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
111 29 0.27
112 78 0.73
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.45
Consensus pattern (112 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTTAACGTTTTAATTTAATTTAAATTATTAGTA
ATAATTAGTTGATTTATTTAATGCATAATTATTAGATTAAGAATTAA
Found at i:96837 original size:18 final size:18
Alignment explanation
Indices: 96781--96838 Score: 98
Period size: 18 Copynumber: 3.2 Consensus size: 18
96771 CCAGCAGCCA
*
96781 CCGCATCCATATATGATG
1 CCGCAACCATATATGATG
*
96799 CCACAACCATATATGATG
1 CCGCAACCATATATGATG
96817 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
96835 CCGC
1 CCGC
96839 CATCGCCTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:97196 original size:9 final size:9
Alignment explanation
Indices: 97182--97229 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
97172 GATTTACGAT
97182 GACGATGAC
1 GACGATGAC
97191 GACGATGAC
1 GACGATGAC
*
97200 GA-TAGTGAC
1 GACGA-TGAC
*
97209 GACGACGAC
1 GACGATGAC
*
97218 GACGACGAC
1 GACGATGAC
97227 GAC
1 GAC
97230 AGCGAGGAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
8 1 0.03
9 32 0.94
10 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.33, T:0.08
Consensus pattern (9 bp):
GACGATGAC
Found at i:98589 original size:50 final size:50
Alignment explanation
Indices: 98514--98648 Score: 234
Period size: 50 Copynumber: 2.7 Consensus size: 50
98504 GTTCGTAACC
*
98514 TGATCAAAAAATGTATAACTTACTAACTTGCTTTCTTTGCAAAATTAAAA
1 TGATCAAAAAATGTATACCTTACTAACTTGCTTTCTTTGCAAAATTAAAA
98564 TGATCAAAAAATGTATACCTTACTAACTTGCTTTCTTTGCAAAATTAAAA
1 TGATCAAAAAATGTATACCTTACTAACTTGCTTTCTTTGCAAAATTAAAA
* * *
98614 TAATAAAAAAATGTATACCTTACTAACTTGTTTTC
1 TGATCAAAAAATGTATACCTTACTAACTTGCTTTC
98649 ACTTACCCAT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 81 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (50 bp):
TGATCAAAAAATGTATACCTTACTAACTTGCTTTCTTTGCAAAATTAAAA
Found at i:102265 original size:21 final size:20
Alignment explanation
Indices: 102227--102265 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
102217 TATCCATCCG
*
102227 TTTTCATTTTGATCATCAAT
1 TTTTCATTTTGATAATCAAT
*
102247 TTTTCAATTTTGTTAATCA
1 TTTTC-ATTTTGATAATCA
102266 GTCAACCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTTCATTTTGATAATCAAT
Found at i:103788 original size:17 final size:16
Alignment explanation
Indices: 103755--103792 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
103745 TTTTAATAAA
*
103755 TAAA-TTTAGTTTTAT
1 TAAATTTTAGTTTGAT
103770 TAAATTTTATGTTTGAT
1 TAAATTTTA-GTTTGAT
103787 TAAATT
1 TAAATT
103793 AAATTCTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 4 0.20
17 12 0.60
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (16 bp):
TAAATTTTAGTTTGAT
Found at i:118681 original size:24 final size:25
Alignment explanation
Indices: 118649--118697 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 25
118639 GAGCAGCTCG
118649 AAAATATAATATATTAATAT-TTAAAA
1 AAAATA-AAT-TATTAATATATTAAAA
118675 AAAATAAATTATTAATATATTAA
1 AAAATAAATTATTAATATATTAA
118698 CATTTATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.41
25 7 0.32
26 6 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AAAATAAATTATTAATATATTAAAA
Done.