Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_039531
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 520764
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:94875 original size:18 final size:18
Alignment explanation
Indices: 94852--94889 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
94842 ATCACTAACT
*
94852 AATACTAATCTAATAGAA
1 AATACTAATATAATAGAA
94870 AATACTAATATAATAGAA
1 AATACTAATATAATAGAA
94888 AA
1 AA
94890 GAACTTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (18 bp):
AATACTAATATAATAGAA
Left flanking sequence: Indices 94352 -- 94851
CAAAGATCTTACCATTTCCAAAGGAACTGGAGTTCCATCTCTTTTCCATTTCCATTCAAGAGTTC
TTATGTGTTTCCACGCCCCTTTGATACCCCGAAAAATGGACAAATTCCTTTTCTTAGGAACACAT
ACAGGATTCGTCACTCCAAAAAAGGATAATGGTAACCCCACCATTAACTACTTCATTTATGAATT
TCATAGTAATAGAAATACATGTCCCACCGAGACAGAATTTAGAACTTGCTATCCTCTTTCCTAGC
AGGCAAAGATTTACCTCCGTGGAAAGGATGATTCATTTGGATCGACATGAGAGTCCAACTACATT
GCATTGCCAGAATCCATGTTGTATATTTGAAAGAGGTTGACCTCCTTCCTTCTCTCATCGTACAA
TCCTCTTCCCGACGAGTCCCCTTTCTCCTCGGTCCACAGAGACAAAATGTAGGACTGGTGCCAAC
AGTTCATCACGGAAGAAAGGACTCACTGAGCCGGGATCACTAACT
Right flanking sequence: Indices 94890 -- 95389
GAACTTGTATACTTTCCCCGGTTCTGTTGCTACCGCGGGCTTTACGCAATCGATCGGATCATATA
GATATCCCTTCAACACAACATAGGTCATCGAAAGGATCTCGGAGACCCACCAAAGCACGAAAGCC
AGGATCTTTCAGAAAAAGGATTCCTATTCGAAGAGTGCATAACCGCATGGATAAGCTCACACTAA
CCCGTCAATTTGGGATCCAATTCGGGATTTTCCTTGGGAGGTATCGGGAAGGAATTGGAATGTAA
TAATATCGATTCATACAGAAGAAAAGGTTCTCTATTGATTTAAACGCTGTACCTATGGGATAGGG
ATAGAGGAAGAGGAAAAACCGAAGATTTCACATAGTACTTTTTTTTGATCGAAAAAAAAAAATGG
AAAGTGTTCAATTGGAACATGAAAACATGACTGAATTGGTCCTAGTTACTCTTCGGGACAGAGTG
GAAGAAGGGAGGAGATTCTAGAACGAGGGAAGGGATCCAATGACT
Found at i:105380 original size:15 final size:15
Alignment explanation
Indices: 105360--105389 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
105350 TTCCGTCACT
105360 TCTGGGATTAAGGGA
1 TCTGGGATTAAGGGA
*
105375 TCTGGGCTTAAGGGA
1 TCTGGGATTAAGGGA
105390 GTTCCCCCGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.10, G:0.40, T:0.27
Consensus pattern (15 bp):
TCTGGGATTAAGGGA
Left flanking sequence: Indices 104860 -- 105359
TGTTTCAGTTCCCATCTGGTGAGAAGAAGCTCTTTGCTTTGAAAGCTTTTTCGTAGGCAGCAAGC
AGTGGTAGGCTAGAAGGAAGCGCAGGAACTTCCGGGATTAAGGAAAGTAACCCGAGGGTAGTAGG
TTACAGAATCCGATTTGTGGCATCTTTCCTTGTCCGATTTGTTAGAGAAGGACTTATTTCAAAAA
AAGTTCTATAAGAATAGGGCAACTCCATTCAATAGGGAGGGAGGCATGGAATGGATGCTTCCCCT
TTCAGTGCAGGAAGGACTGCTTGGTGAAATGACGTACTTAGGATTCCCTCACTGTCAAGCAAGGG
AGTGACGAGAGGGTATCAAAACCACTCTTTAGAAAGATAGCCTACATTGAACCAAAGGAGTGATC
CCCACTCCGAATGAGATGTCGTATACGCAAATGCTCTTTCCGTTGCAGGCATAAGCGCTGCAAAC
ATGGCTACTTCCGCTCTTTTCGGAAGAGAAGATAGTTCCGTCACT
Right flanking sequence: Indices 105390 -- 105889
GTTCCCCCGAGGGAAAGACAGTCAATAGGAATTCTCTCTACTCTAGAACCCATAGGCCTAGGAGC
AATAGACTGAAGAGGTACGGCATCTGTAACAAAGTCAGTAACAAAGGGAGAAGGAAGAAAATCCA
GTGATAGTCTTTGGGACTTCTCCGGTGCTCTCTTTCCTGTAGTCGGAATCTCTGGTATCATCTTT
TCCAACTAATGCCAGATCTGATTCAATAGGAACAGAACCTTCTACCCCGTCTGGTATTCACGAAA
AGGAAAAGGAAGTCAGGGAATGAGCTAGAATATACCTGATGTTTGCAATTCTTACTGTCCTTCAA
GCCTTAGTAAGGCAAGTGACTCCGTACTTCCTTTTTTTCTATCCCTAGTATCGTACTCAACAAAA
GGGAAGAACCCTTGTTCAAGCCGGATTCTTGGAGCCTTCGGGATAGCATACCCTAATCCGAACGA
TTAAGTAGGAGGTTCTACTTTAGAGTTGTTGAACTGTTGAAGGCG
Found at i:112424 original size:5 final size:5
Alignment explanation
Indices: 112414--112447 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
112404 CCGGCTCTCC
*
112414 TTATA TTATA TTATA TTAGA TTATAA TTATA TTA
1 TTATA TTATA TTATA TTATA TTAT-A TTATA TTA
112448 AATAGAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (5 bp):
TTATA
Left flanking sequence: Indices 111914 -- 112413
GAGTCAGATGAATGCGCAGGGGATTCTTACTAAGACTAGCACCGGATTCTCCACATGCAGTTGCA
GAATTAGCACTCTCGGATTCATTCTTCCTAACAGCAGGGGATTTGCCCACTACTAGAACGAGGAC
CTAGCGACTTTGCAAGCATTCCAGGCTAGGCACCTAAGAGCGGTTATTCCTCCAACAAGTTCTTC
TGGGCTACGCTAAACCTTCAAGCCTTCCACCAGCGGATGAATACAGAATCTATCCCCTCTGCGCA
CTAACAGGGAAAGCTACTCTTCAATAGTATATGCCGCAAATCCTATGTTTGGGGTGACCATGAAC
ACACTGCTTGAGACCCTTCTTTCGTGAGACAGTTGTGATTCCGCTTTCACTAATAGAAAGGTGGG
ACAGCTTTCAATAGAACATAGAGCTCTGCCCTTTTTTACCCTCTCTAGACAAACTCTCTACCCCT
GCGCGCTTGGGAACGCACTATAGCCCTGCTTGAAGCCGGCTCTCC
Right flanking sequence: Indices 112448 -- 112947
AATAGAACATTTTCTTTTCCAGAATCAATAGAAAAAAGAATTCCTTTGCGGCTTACCGCTTACCT
ATCTTTCTCAAAACCCTCTCCTGGCTAGCTTTCCAATCGCAGGCTTACTTGCTTTCCTTGACTTA
ACTTCCCAATTGACAAGAAGGGGAACCGAAGCTAGGCACGAAGAAGGGAAAGAGTTTAGTTCTTG
TCAGTGACAAATGTCCTTTCGTTGGCCATAATTCTTCGCTATAACCCATGTTTCATCACATGAAC
GATAGATTATTCATTGGAGTGCCTATCGCTCGATATATGGAATAATTTCTCTAAACAACCCTGCC
TTCCCTCCGAGTTTACTTTACTGGAGTAGCTCCTGGACTTGCTTTGTTGACTGGACTAGCCATTG
GAGGGAAAGAAATGCCCATTTGTCGGCTTGAGGTGAGGAAAAAGACACCCCTTGCCTTTGACTTA
CATCGGCTGGAAGCGGGAACAACATATCGATCGGTTGGAGGAATT
Found at i:112444 original size:16 final size:15
Alignment explanation
Indices: 112418--112447 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
112408 CTCTCCTTAT
112418 ATTATATTATATTAG
1 ATTATATTATATTAG
112433 ATTATAATTATATTA
1 ATTAT-ATTATATTA
112448 AATAGAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATTATATTATATTAG
Left flanking sequence: Indices 111918 -- 112417
CAGATGAATGCGCAGGGGATTCTTACTAAGACTAGCACCGGATTCTCCACATGCAGTTGCAGAAT
TAGCACTCTCGGATTCATTCTTCCTAACAGCAGGGGATTTGCCCACTACTAGAACGAGGACCTAG
CGACTTTGCAAGCATTCCAGGCTAGGCACCTAAGAGCGGTTATTCCTCCAACAAGTTCTTCTGGG
CTACGCTAAACCTTCAAGCCTTCCACCAGCGGATGAATACAGAATCTATCCCCTCTGCGCACTAA
CAGGGAAAGCTACTCTTCAATAGTATATGCCGCAAATCCTATGTTTGGGGTGACCATGAACACAC
TGCTTGAGACCCTTCTTTCGTGAGACAGTTGTGATTCCGCTTTCACTAATAGAAAGGTGGGACAG
CTTTCAATAGAACATAGAGCTCTGCCCTTTTTTACCCTCTCTAGACAAACTCTCTACCCCTGCGC
GCTTGGGAACGCACTATAGCCCTGCTTGAAGCCGGCTCTCCTTAT
Right flanking sequence: Indices 112448 -- 112947
AATAGAACATTTTCTTTTCCAGAATCAATAGAAAAAAGAATTCCTTTGCGGCTTACCGCTTACCT
ATCTTTCTCAAAACCCTCTCCTGGCTAGCTTTCCAATCGCAGGCTTACTTGCTTTCCTTGACTTA
ACTTCCCAATTGACAAGAAGGGGAACCGAAGCTAGGCACGAAGAAGGGAAAGAGTTTAGTTCTTG
TCAGTGACAAATGTCCTTTCGTTGGCCATAATTCTTCGCTATAACCCATGTTTCATCACATGAAC
GATAGATTATTCATTGGAGTGCCTATCGCTCGATATATGGAATAATTTCTCTAAACAACCCTGCC
TTCCCTCCGAGTTTACTTTACTGGAGTAGCTCCTGGACTTGCTTTGTTGACTGGACTAGCCATTG
GAGGGAAAGAAATGCCCATTTGTCGGCTTGAGGTGAGGAAAAAGACACCCCTTGCCTTTGACTTA
CATCGGCTGGAAGCGGGAACAACATATCGATCGGTTGGAGGAATT
Found at i:116336 original size:6 final size:6
Alignment explanation
Indices: 116325--116349 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
116315 CGATCACCCT
116325 ATTCGA ATTCGA ATTCGA ATTCGA A
1 ATTCGA ATTCGA ATTCGA ATTCGA A
116350 AGCTCCAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (6 bp):
ATTCGA
Left flanking sequence: Indices 115825 -- 116324
GTCGTTATGTAGGTGGGACGGTACGAATTCATAAAAGACCTTGCCCACACGCTATGGCGAGATAG
GATCGATTACATATAGAAAGAGAACCTTGGAAATGCTATCTATTTACTCGACTCACTCAAAGCCA
GGTCTGGTCTTAAGCCGGACAAGATATTCTGACTGGGCTAGGCGTCATACTAAGTTTACCCGCAC
ATTAGTGAAAGTGGAACTAGACTTTGATCTCTTTTCAGATCATATAAAAGACCTTGACATAACCT
AAAACCCAATCCAACTTAGACAGAAAAGATGCCAGCCACAACTCTTATAGGCTTTATTGGTAAGC
TAATACTCATACTAAGGTGCCCTAGAAGAGAAGGGCTTTAGCGCAACACATTTTCGGATCAAAAC
AAAAGAAAAACCAGGAGGATAGAAAGCAGTAGTGGTGCCATTCATTACCTTTTCCTTTGTAATCT
CCACTCAACTCGATGGGTCTCTCATTGGAACGATCCGATCACCCT
Right flanking sequence: Indices 116350 -- 116849
AGCTCCAACAATGAGGAATCTCCCAAAAGGGAAGGGGATGAAGACGAATTTGATAGCGGTCCTTC
TAACTCACTCTTCGGGTTCAGCTAGTCGGGACAAACCAAGAAGAATAGGTCTTTCTGAGCACCTT
TAGCTAGAAGCTTGATAGCCCATTGTTATACCTGAGTCTATAGCTTTGGCAGCAACTGATCTCTC
TCTTTATTGTTTCCGAAGATGACTGAGAAAATCTTTTATGAAAAGATTTTTGATACTTAGCTTAT
TTCCCTTTGCCCTTAAGAATCTTGCTTTAGATAAAGGCAGATAAACTAGAGAAGTACATCATATC
TACCCGTCAAAGTCACCTATGAATGACTCCGGATTCCATATTGGATCTTAGCCAACTGATTAGAC
TCCAGAGTCTTAGCTTTCTTCTTCAGTAAGAAATGGACTTAGACCATATTCACTTCCATAAAGCT
TTTTAAGGCTCGCTCGACTTCTTTATCTCGCTTCCTTACTCCTAT
Found at i:128189 original size:12 final size:12
Alignment explanation
Indices: 128159--128198 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
128149 ATGAAAGCCA
* *
128159 AGGTCAAGAATA
1 AGGTCACGAATG
128171 AGGTCACGAATG
1 AGGTCACGAATG
*
128183 AGGTCACGGATG
1 AGGTCACGAATG
128195 AGGT
1 AGGT
128199 GGTCTATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.17
Consensus pattern (12 bp):
AGGTCACGAATG
Left flanking sequence: Indices 127659 -- 128158
AAGTAGGTACGGAAGCTAGGTACGGAACCTAAGTAAATATTCAATATATCCGGCATCCGTTCACT
ACTCTTCTCTTCTTTCCTTTTCATTATATGAAAACTAATACACCATGATGACAAAACAAAGAAAA
TTGCCAGGAATGGCAAAGCCAGGCAGGGCAAAAAATATGCATATGTACTGCATAAATGAGATTAT
GATAATAAGAAAGAATATGCAAGTCTTATCGAACGTTATATCATATATTCCTATGAGTCGAAATT
TTTGTAGTCATAAAAAGAATAATGGAAGATTATCTGGTTCGTTAGATTGGGTTGCGTACTATATC
GGGGAATCATACAATGAGTTATCTGATTTCTTTTCAGAATTGACTGCAATCAAAGTGATTGACAT
TCAGAAAAGAATAAAGGAGGGAACATACAACCAGTCGGTGCTTCGACTTAGCGTCTTCTACAATA
AAGGACTTATTTATGATGGTAAGTTCCACCACATAATGAAAGCCA
Right flanking sequence: Indices 128199 -- 128698
GGTCTATTTGTGTATCAATCCTTCACAAGAAGACAGCCTTGTGCTAATGGGGATCGGGCGTTTGT
TAAACAAACTCTTATTCCAGAAATTCATTTTTATGAATAAATCATTAGGCTATCGAACTACTCCA
AAAGAATATTATGATATAGTATGTGCGAGAGAGAATGTCTTAATGCTTTATAAATTCGACCTAAC
ACTGTCTATGATGACTATATATCGTGAAAGTCTTTTGTCTAAGCTTTCACATATAGTTCAGAATC
GCTATATTATGGAATTCGTAGGCAAATTCCTGTATTTACCTATCAAGGATGATACTGGAATAGAC
TTCACTGCCGATTTGGGAATTCACATTCCATCCTCCTTATTTATAAGTGAAGTACTACTGAATTT
TGTCTTAATAGACTTCGATAATGAATTTCAACGTTTATTTCCACAATTAGAGTATACTAGATATA
TACATGAAGTTTTAGTCTCTTTCCCCACTTCTGATAGTAAGAAAG
Found at i:137205 original size:10 final size:10
Alignment explanation
Indices: 137190--137217 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
137180 TGAAGAAATA
137190 TATTATATTC
1 TATTATATTC
137200 TATTATATTC
1 TATTATATTC
137210 TATTATAT
1 TATTATAT
137218 ATAGTAGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTATATTC
Left flanking sequence: Indices 136690 -- 137189
AGTCTGTCCGTTCGAGCAGTCTGTCGGAAAAGGTTGTAATCCCTCTCTTGGTGATAGTAGCTCTT
CATCAGTTTATAGTAGGAGCTGAGCTCTTCCGCTAGCTTACTAGCTCTGGTAGTAAGGCTCTTCG
GTCAATAGTTCCACTGGAAACTGCTTCCTGTATCACTGCTTTTCATTTTCTTTTCGCAAATCTCT
TCTTTCCGTCTAAAATTCCCTCCCTTTTGGGGCTGGAGCATTCTTCCTTTATTAGCCTAAGGGGA
GAAAGCGCTCTCCCCATATTAGCTTATCGATCAGGATCAAGTTCAAGCAAGGAATCCTAGACATC
CCTCAGGCTCGTTTAAATAAATTATTTGAGTAGTCTTTTTTTAGAGTATGACATTCTAATGTAAA
GCATTCGGTAGTCGTCAATCCATCCTTTTCTTTTATTTAACATGGGTGATAGTACGAGTGCTGCT
TTCAGATGCATTAAAACCCATTATTTGTAGCCTTTTGAAGAAATA
Right flanking sequence: Indices 137218 -- 137717
ATAGTAGAGGAAGGACGTAGCTGGCACAATCAGGGAAATGGAGGCACTAGCAGAAGCAGTTTTAG
GAGAATAAGTAGTCGTTTTTCCTGTTTCTGGGGAGGAGGATTTCCATTTTCATGGGGATAAAGCT
GTTGTTGAATCTTAATGAGGGAATCTAGTTACATCCTCCTATTCTCGAGCAAGAAGAGGACAGGC
CCGGTCAAGGCTTTCGGTTTTTCTTAAAAATACATATGCCGGTTGGCTCTTTCGCATCTTCGGTT
TCAGTTCTTCTTTTTAGAAATACATATCCGCTGGCTAACGGGGGAGGGGGCAATTCAGATTTCAT
ATAGAAAACTTGCACACGGAGAAAGAGAGGGAGTACACAAGAGAGGAGCCCATTGAGGAGAGGTG
CACAAATGACTTCTTTTTTTACAATTAAGAAGTCGCATACGAAGGAGGAGACGTGGGAGCTCTTT
CTGCCTGAGAACGTTGCATGGCTCGCACGAGAGTCCGCGGACCGG
Found at i:168890 original size:18 final size:18
Alignment explanation
Indices: 168867--168909 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
168857 CGCCCTTGTT
168867 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
168885 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
168903 GACTATG
1 GACTATG
168910 GCAGGGCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAACAGATCGC
Left flanking sequence: Indices 168367 -- 168866
CGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGAGAC
AGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTACCTT
AGGACAGTTAGAGTTACTGCCGCCGTTTACTGGGGCTTCCATTCAAAGCTTATAACACTTTTCCT
TCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGTCCT
GTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGAGAG
CACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAGCGC
CCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGATCGC
CCTCCCAATTCGAAGTTTTTTCCTGGAAGCCTAAACGCCCTTGTT
Right flanking sequence: Indices 168910 -- 169409
GCAGGGCGGTACGCTCTGCTCTCTCGCGACCTCTACTCTAATCAAAAGACTAAAGGCCCCTACTG
AAGATTCAAAAGGCGAGCACAGAAATGAGAAAAAGCTTGTAGACTCGTAAGGCTGAACGACACAT
TCGAAAACTAAAGCGCACACTAGAAAGTGCTTCGAAAGGTGTAAGCAGGTGCGCGGAGCCGGAGC
CCGGCATGTTCGCCCGCTGGGCCGAGTGTTCGCCCACTTCAAAGTCTTCGCCTTTAGATAAAGAA
AAGTGTCCGCCCCTTAGATCGCCAAACTACGACGAGAGTTTCGCCTTTTGAAGCGCCAGTCGCGT
AGGGCGACCGGGCCACGCCAAGTCAGAAAGGCTTTGATGACTCAAGGTTCATATTAGGGAAAGGA
GAGTGAGGGGAAGAGGCGACGAGAGTCGGCCCGATCATCCAATTCGCTCCAACAGACAGGCATAG
TTCTGTAGTCAAAGCAACTTCGTCACTTTCGTGTACCCATCGGAC
Found at i:213172 original size:24 final size:24
Alignment explanation
Indices: 213145--213190 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
213135 CGCTTACTCT
**
213145 AAGAACGACAAGGGCAGATAAGAC
1 AAGAACGACAACCGCAGATAAGAC
* *
213169 AAGAGCGGCAACCGCAGATAAG
1 AAGAACGACAACCGCAGATAAG
213191 CCCTTTCCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.46, C:0.20, G:0.30, T:0.04
Consensus pattern (24 bp):
AAGAACGACAACCGCAGATAAGAC
Left flanking sequence: Indices 212645 -- 213144
ATCGAGCGCCTCTTGAACGCGAAATTCATCAGGCCAATCCGTTACACGGAATGGCTGTCAAATAT
AGTCCCCGTTGTCAAGAAGAAAAGAAAAAAAAATACATCGGGCTGTGAGACTTCGAAAAGTGAGA
ATCCCAGTGTGAAAGACATTGATAGTTCTTATCTTATTCTATAGTAGTAACCCTCTCCTAAGTGC
TATCTTTTTTCCTTATTCCCGTTCTCTTATAAAGAATGGCTCTCTTCCCCTGGCCTCGTTCTCTC
TATCGATCTCACAAGTCTCTCTGGTATAGGCAAGGGCTCATCTGTTCTTTTTCCTTGATTTCCCA
CCTTAGCTTAGGGGCTTCCATTGGGCTGTCATCTAGCTAGGGCTATTTGAACTAGTTTCAAAAGG
CTTGATTGCCCCTTCCTTTGTCGTGGGCGTGGGCGTAGGAAATCCAAATCCCATTCGAAGAAGGT
CAAGTCACCTAGTACTACTACTACTGACTTTGCAGCGCTTACTCT
Right flanking sequence: Indices 213191 -- 213690
CCCTTTCCTTAATTCCATGGCCTTACTCCAACAGAAGAAATTGCAGCGGAGGCGTGAACATGAAC
AGGCCGCACTAGATAAGTATGCAGCGATACATCATAATAAGTTAGTTGATAGCCTAATTTCGGAA
GCTACATATGAGCTGGTAAACACGACTATAAATAGTAGCCCAGAGAAAGTGAGATGGCTAAAGGA
CAAAACATGACAAGACACATTATTCGTCCTTATCAGATTAAATAGAGCTGCCTTTATAAACTATA
AGTGGTTCATCATTTATGAATTGGAAGATGAAATCTTTCTCTGGTGATGAATGGAGAATAGGTCT
CCCTGTCTTTTCTATTCAGGAAGCAGATAATTGCTATTCCCAAGGAACGTTAGCTCTGGCGCCCT
ATCTATTTGATATTTGAATTTCTCTTGCTTTCTGAGTGAGGCAGTGGTCTTTCTTTCTTCTCAAG
TAGTGTAGGTGGTGAAGGGGATTTATATAAATAAAATAAAAAAAG
Found at i:233205 original size:12 final size:12
Alignment explanation
Indices: 233169--233208 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
233159 AACAAATCGG
233169 ATGTGCACATTC
1 ATGTGCACATTC
* *
233181 ATATTGAACATTC
1 AT-GTGCACATTC
233194 ATGTGCACATTC
1 ATGTGCACATTC
233206 ATG
1 ATG
233209 CAAGATCCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (12 bp):
ATGTGCACATTC
Left flanking sequence: Indices 232669 -- 233168
ACGACTCTCAAAGGAGATCTCTGAGGTTCTGTTGTGTTTATGTTCAGAGCTTCAAGAACTATCTG
ATCAGCAAAAGAACAATAGCGAGAGACTTTTCCGCATTTGGAGACATCCACAAACTGTTCTATCA
CCCTGTTCAGTAGGTAAGACTGAGAGTGGGATTTCCCTTAATAGCGTCTAAAGTTTCGTTCTTTC
CATACTTCCCATACTCAACAATGTAGCTTATATGGTATTAGGTGCACTAGAACTGGCATGATCGC
TTCTATATCTTCCATCTCCTAAACTACTACTACTATACTAATATACTAAAGGGGGCAAGCAAAGC
CCTTCTTAGAAAGCAATTAACTCTTAGCAATACTTCACCATCACCCCTAGTAAATGATGTAGGGA
GTGCAGAATCAACTAGGGCTAACCTCTCTTTAGCCTATCTGTCCTCATGCTAGCCAATCTCTGGC
AATTGGTCTATGGCAAGGGTCATATTCAAGATGTGAACAAATCGG
Right flanking sequence: Indices 233209 -- 233708
CAAGATCCGGTGCTCTCTTTGAAATATCCGCTCTTAGGATAGAAGAATAAGTTCGGAAGAGAAGA
AGTAGCAGAATCCGTCAGCTTGCCACAGAACTCATCCAGAAGGAGTATGCAGCCAGACTGACTAC
GGAGATAGAAAGAAGAGGATGTTTTGGGAAGATGAATCAATATTAAAGAAAGAATAGGTTGCTAG
AGAATCGGATCTTAGATAGTGCACGAATGAATGCATAGTGAAAGTCAGTCTTGGTCTTGGGGTAA
TATCATCTTTCCTGCCCCTAGGTCCTAGGTTGCAAGTCAGCTGCTCACTCTCTCTTTCTTCGAAT
TCGATGTCTTAAGCAGCATGTAGCAAAGATCGATTTGAGATTCTGGGACCTGAAAACAGAAGCTA
GAGTTGAACGATCTACTTTTCTATCCTGTGGTCCTATCCGAAAGAAGGTCTCTTCTTTATAGAAA
GTAGCCTGGTCTGTCTCTCAATCAGTCTGTCCAGTCAAGTCCTTG
Found at i:277370 original size:5 final size:5
Alignment explanation
Indices: 277360--277392 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
277350 CCGGCTCTCC
*
277360 TTATA TTATA TTATA TTAGA TTATA TTATA TTA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTA
277393 AATAGAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (5 bp):
TTATA
Left flanking sequence: Indices 276860 -- 277359
AGAGTCAGATGAATGCGCAGGGGATTCTTACTAAGACTAGCACCGGATTCTCCACATGCAGTTGC
AGAATTAGCACTCTCGGATTCATTCTTCCTAACAGCAGGGATTTGCCCACTACTAGAACGAGGAC
CTAGCGACTTTGCAAGCATTCCAGGCTAGGCACCTAAGAGCGGTTATTCCTCCAACAAGTTCTTC
TGGGCTACGCTAAACCTTCAAGCCTTCCACCAGCGGATGAATACAGAATCTATCCCCTCTGCGCA
CTAACAGGGAAAGCTACTCTTCAATAGTATATGCCGCAAATCCTATGTTTGGGGTGACCATGAAC
ACACTGCTTGAGACCCTTCTTTCGTGAGACAGTTGTGATTCCGCTTTCACTAATAGAAAGGTGGG
ACAGCTTTCAATAGAACATAGAGCTCTGCCCTTTTTTACCCTCTCTAGACAAACTCTCTACCCCT
GCGCGCTTGGGAACGCACTATAGCCCTGCTTGAAGCCGGCTCTCC
Right flanking sequence: Indices 277393 -- 277892
AATAGAACATTTTCTTTTTCCAGAATCAATAGAAAAAAGAATTCCTTTGCGGCTTACCGCTTACC
TATCTTTCTCCAAAACCCTCTCCTGGCTAGCTTTCCAATCGCAGGCTTACTTGCTTTCCTTGACT
TAACTTCCCAATTGACAAGAAGGGGAACCGAAGCTAGGCACGAAGAAGGGAAAGAGTTTAGTTCT
TGTCAGTGACAAATGTCCTTTCGTTGGCCATAATTCTTCGCTATAACCCATGTTTCATCACATGA
ACGATAGATTATTCATTGGAGTGCCTATCGCTCGATATATGGAATAATTTCTCTAAACAACCCTG
CCTTCCCTCCGAGTTTACTTTACTGGAGTAGCTCCTGGACTTGCTTTGTTGACTGGACTAGCCAT
TGAGGGAAAGAAATGCCCATTTGTCGGCTTGAGGTGAGGAAAAAAGACACCCCTTGCCTTTTGAC
TTACATCGGCTGGAAGCGGGAACAACATATCGATCGGTTGGAGGA
Found at i:291612 original size:24 final size:24
Alignment explanation
Indices: 291570--291618 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
291560 ATTCGGATTC
* *
291570 GTTACTTGGGGCTGATGAGGATGA
1 GTTACTTCGGGCTCATGAGGATGA
* *
291594 GTTACTTCGGGCTCCTGAGGGTGA
1 GTTACTTCGGGCTCATGAGGATGA
291618 G
1 G
291619 GAATCCGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.41, T:0.29
Consensus pattern (24 bp):
GTTACTTCGGGCTCATGAGGATGA
Left flanking sequence: Indices 291070 -- 291569
GTGAAATTGTCAGTTTCATCCTCTTTATGAGCCTGAGATCATATGGGTCAACAATTCTCATTTCT
TAGTCACAGAAAGCCCTTCTCAAGGAAGTGAGCCAAGAGCCACTCATCTGAGCCAGCGGATTCTA
ATTCTGCTGTGCCGGTGCGCAAAGCAAGCAAAGCACGCTTAGACTGCGATGTGCAATCTTTGATC
TGCCTATCATTGTCCATTAAGGGCTGACTCCGCTAGGCAAGAGGACCACTACTGGGATTATTCAA
CTACTAACTGATGACCAGGGGACTACTCTGCTTCTTCCACTACTGATATTGACTGACCTGTTGAG
AGGATAGCAGCAGGAGAAAGAAAAAAAGAAGTAGAAGAGTTAGGTTCTGTTCTAGTGTGTAAGCA
TCTCTTTCCTCGGTCGATTCGTCTGCTCATTCAGCCTATGATTCTTATCCAATTGCTTCTTCCGA
TAAGTCTTATAAAACGAATTCGGCTGGAGATAGGCATTCGGATTC
Right flanking sequence: Indices 291619 -- 292118
GAATCCGTTGTTTCGAGAGAAACTTGATATGTTAGTTCGGCCTCGGCTTCCGGGAGAAATTCCTC
ATCAGCCGGTTCAGATTGAGAGGGAAAGAGCAGCCCTAGGCTCCGCTTCTTAGGATGATGCCTGT
GCAATGTATGATCCATCGGATTCTTTTTATTCGATTTTCGGTGCGTTGTTTTTCAGCGAATGAAA
GAAACCGCTGATTCCACAGTTCCTTCATCAGATTTGGGTGCTTTTGAAAGAGCTGCTTCTGCGAA
TGACTCAACGGATACTACTCAAAAATTTCCCATAGAATCTCATTGAAGGAAATGGTATTTTTGGG
AAAGGAGTGTAGGCTTGCTTCGCATAGGCTACACAAGCCAGGGTTGGGAACCATCGAAAGACTAG
CAACCTGACAGTCCTAAGCAACCTGGAACCAACAACGTTACATATACCATACTGCTATAGAAGAC
ATGAGTACCAGTTAGACTACGGGACGCGTACACCCGAAATTGGTG
Found at i:292285 original size:26 final size:26
Alignment explanation
Indices: 292245--292297 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
292235 CATGTGAACT
* *
292245 AAGCCCAGGGGATGAT-CTCGGATTGA
1 AAGCCCAAGGCATGATCCT-GGATTGA
292271 AAGCCCAAGGCATGATCCTGGATTGA
1 AAGCCCAAGGCATGATCCTGGATTGA
292297 A
1 A
292298 GGTCTGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.19
Consensus pattern (26 bp):
AAGCCCAAGGCATGATCCTGGATTGA
Left flanking sequence: Indices 291745 -- 292244
CTGTGCAATGTATGATCCATCGGATTCTTTTTATTCGATTTTCGGTGCGTTGTTTTTCAGCGAAT
GAAAGAAACCGCTGATTCCACAGTTCCTTCATCAGATTTGGGTGCTTTTGAAAGAGCTGCTTCTG
CGAATGACTCAACGGATACTACTCAAAAATTTCCCATAGAATCTCATTGAAGGAAATGGTATTTT
TGGGAAAGGAGTGTAGGCTTGCTTCGCATAGGCTACACAAGCCAGGGTTGGGAACCATCGAAAGA
CTAGCAACCTGACAGTCCTAAGCAACCTGGAACCAACAACGTTACATATACCATACTGCTATAGA
AGACATGAGTACCAGTTAGACTACGGGACGCGTACACCCGAAATTGGTGAGCTACTTACTGCCCC
TTAAGTCAAGAGCTAGTAGTACTATCAGCAAAGGATATCGTAACTATGGCGAATACGTTTTTCTT
GCTTGCCACATACCCGGATGCGAACTAAGCAGGAACATGTGAACT
Right flanking sequence: Indices 292298 -- 292797
GGTCTGGAATTGTGGACACAGGGCGGAGGCATACCAGGCTTAATAACGACTAAAGACCATTGGAC
GACCGGGAAATAGCACTGAACAAGCAGGGGCTAAAAGCTTCTTCTACCCAGTCTTCTCCCATAGG
CTAAGAAGAGGGTCAATACGATCCCTTTGAGAAAGAACAAAAAATGAAACTATCAGAGCCATTGC
GGGTGATTTCGACTTCGAAAGCCATGAGCCCCATTCACGAAAGCCTACGGAACAAACTTGCTACT
TTTGATTAACTCGTCGCTACTTCTGACCCCTCTACGTACCCTCTCTTTCTCAATCTGACCCTTCC
ATGTACCCGACACTGATTCCCAAGCAGAGGGAGGAGAAGGAGGATCTTACAACTACATCATTTAT
TATTACAACATCTTACAACACTTAATATTACTATGAGAATGACAGAAGCCCGCTAAACAAGCACA
GATTGGTAAATAAGCACAGAAGCTGCTAAAAGCACATAAATAGGT
Found at i:319273 original size:16 final size:16
Alignment explanation
Indices: 319249--319283 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
319239 GTGGATATGG
*
319249 ATAACATATATTTTTT
1 ATAACATATATATTTT
*
319265 ATAAGATATATATTTT
1 ATAACATATATATTTT
319281 ATA
1 ATA
319284 TGGATCCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (16 bp):
ATAACATATATATTTT
Left flanking sequence: Indices 318749 -- 319248
GGATAGGCTGGTTCGCTTGAAGAGAATTTTGTCTATGATCAGCCCCGAATCATGTCATGCATGAA
CAGGCTCCGTAAGATCCAATCGAATCAGTGATTTGGCAGAATCCAGATTCTGTTTGTTCTATTTC
ACTTATGAAATCGTTTTCTTTATGTTTTAATAGTATGGAAATGCATTCATTTCCTCTGCATCGAC
CCGATTTATGATACTATCGGAGTGAAACAAGGGATCTAAAGAAGAATAGAGGCTAGAGTATATTA
GTAACAAGTAAACCTTTTGTATGTAAAAAGTTTCCAAATATTTTGGAGATAAATGCCAATCGCAA
GGTCTGAGACGACCCAGAGAGCATTTGATCATAATCCACTTGCTTTGTAAGCCTACTTGGGTATT
GAGCATTTATCTGTAAGAGCGGAATTCCTTGCAATGGATAGTTGCAACTCCGCAAAGGGGAATCT
AATACATTTTTTCTTACAGATTACAGAGAACCGCTGTGGATATGG
Right flanking sequence: Indices 319284 -- 319783
TGGATCCATTTGGTTTTTTTTATTCTTGCTCGAGCCGGATGATGAAAAATTATCATGTCCGGTTC
CTTCGGGGGATGAATCCATAAGAATTCACCTATCCTAATAACAAAAAAACCTGACTTGAATGATC
CTGTATTAAGAGCTAAATTGGCTAAAGGGATGGGTCATAATTATTACGGGGAACCCGCATGGCCC
AATGATCTGTTATATATTTTTCCAGTAGTAATTCTAGGTACTATTGCATCTAACATCGGCTTAGC
GGTTCTAGAACCATCAATGATTGGTGAACCGGCGGATCCATTTGCAACTCCTTTGGAAATATTAC
CTGAATGGTACTTTTTTCCCGTATTTCAAATACTTCGTACAGTACCCAATAAGTTCTTAGGTGTT
CTTTTAATGGTTTCAGTACCCGCGGGATTATTAACTGTGCCTTTTTTTATCCTGCCATTAGGGGA
AAGGGAGCTTGACTCATTTCATGCATAGGTAGGAAGAAAGCTCTT
Found at i:366719 original size:15 final size:15
Alignment explanation
Indices: 366679--366719 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
366669 TAATAGTAGT
366679 AGTAGTTCCAAAGCC
1 AGTAGTTCCAAAGCC
* *
366694 AGTCGTCCCAAAGCC
1 AGTAGTTCCAAAGCC
366709 AGTAGTTCCAA
1 AGTAGTTCCAA
366720 CCAAATCAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.20
Consensus pattern (15 bp):
AGTAGTTCCAAAGCC
Left flanking sequence: Indices 366179 -- 366678
AAGGATTACTTATACTTATATAGAAAAAAAGTCTCATTCCATCCTAAGAAAAGATTTTCGCAATC
CCTTCCAGGCCTACTCTTCTGACCCCTAAGAAAGTGGAAACTAAGGATTTCACTATAGAGGCCTT
ATAGATATAGACAGAGTCAGAGTCCTCAATAAATATTTTAGAAAGTCTTTCAAGGGAAGTGCTAG
CATTTCTCTTCTCTAAGTCCAACTCAAAGGAGCAAGCATCTTAGACTAATGCGGATCCGACCCTT
TGAGGCACCTTTACTACTTAAAGAAAAAGACAGGGGCGGGACGGGGTTTGGTGCGCTCTTCTCGG
CTCTAGCTCTACTTTCAATAACATGTGTTAAGCATGTAGCTAAATGGCATGTTGAAAGCCGAACT
AAACCTAGTTCTCCTAGGAAAGAGATTGGTTTCGAGTTCTAGTAGTTAGGCAGCATTGATTATTA
TTTCTAGTACATCCTTTATTTATTTTTATTTATAGTAATAGTAGT
Right flanking sequence: Indices 366720 -- 367219
CCAAATCAGCAACGCGAAGCGAAGGATAAATATCTTTGTTATTAGAAAGCAAGTCCGTCCCACGA
TTATAGTTATCTTATCTGTTAGTTGAAGCTAGCGGTGGGAAGCCAACCAACGATTCTAGTTCTGC
TTTTTCTGTTGAAAGCAAGCCGCCGGCGGACGGTATTTATTCAAAAGTTGTCGCTGAACCCTTCT
CTTCCTCCGATGAAGCAGTCGAGAAGTCAATGGAAAAGGTACCATACCCGCGGGGGATATCTCAA
TCGAAGTCTAAAAATCGAGAAACGTTCTAAATGCCCTTAAATCATCGTTTTAAGCCGCGTTCTGC
TGATTATGATTAGATAGTCAAATTCTCCATTGGACGCTTCAAATGACGATGACGCCCACTTTTTT
TAAAAAATGGATGAATTCTTCTAATTGAATTTAACGGATTCTGAGAAAGCGGATTTGTCTGCTTA
TTCAACGGATGAACCGGATTCTTCAACTGCAATTGAGGAAGCTGA
Found at i:390451 original size:24 final size:21
Alignment explanation
Indices: 390424--390467 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
390414 GTTGAATGCT
390424 TTCCTATTCAAGACATACTACCAA
1 TTCCT-TTCAAG-C-TACTACCAA
*
390448 TTCCTTTGAAGCTACTACCA
1 TTCCTTTCAAGCTACTACCA
390468 TTACCGAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 1 0.05
23 5 0.26
24 5 0.26
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.32
Consensus pattern (21 bp):
TTCCTTTCAAGCTACTACCAA
Left flanking sequence: Indices 389924 -- 390423
ATTGAATTTGAAGAAGCTGTTACATGAAGGATTTACCGAGGAAGATCTCATAAGGGCAGGGAAAT
CTCATAGGAGAAGAAAGCTTTTGGGTTAGCAATAACCGGTCTTTCTGGTCTTGTTGTCATATCCC
TTGCTTGAGTAACCTTAGCTATAGAATCCGCCTTACCTTCTCCTTACCTTGGCCTTACCCGTTCG
ATTGATTGTTCTAACAGAAAAGTCGTTTCGTTAAGTCGAATTAAAAGGTCAGTTTTGTCAGTGAT
TAAATGGAAAGGGGGAGCGGTTCGGGCCTACTCTTGAACTTTGAGGCTAATTAAAAGCCGAAACA
AAAGGCCAAATATCGGCATGTAACTGAGAAAGATGGGATTCGGTCAACAAAGAAATTAAAACACT
CCCTTCTTTCTGTCGACAATGATGAAAACCAGATCGAACTCTAAAGTCAAGCCTTTCACTTCATT
GTTCAAGCTCTGGAACATGGGTGAAGTTCATACATGTTGAATGCT
Right flanking sequence: Indices 390468 -- 390967
TTACCGAAGCTGGCTTGCTTGTTTTGCGGTTGGGGTTTTGAAACCAGAGAAAGAAGATCCGGTTG
GGCTTGCTAGCGATGGGAGATTAGTCACCGGAAGACTTGCTAGCTTGCTCTTTCAAAAGCTCATA
CGGTGTGTCTTCTACTCCTCTCCCGATACGACTTATTTCCTGACCGTTCCCTCGTGCTTTTTTCA
AGGAAGGTTGCTTAGACTACCAACCTTGATTGACCGAAAGGCAGGCTCAAGCTTGAGTTGTCTCT
GCTTGGATTCGCTGGACTCTGTCTGGGTTCGTCTAGCTTTGCATTGCTTGCCTGGCTTAGACTGG
GTGAATTTCCCCCCTTTGAAAGCTCCATACTTTACCCTCCAACAAGACCACAACTCAATTAAGTC
AGCTTTCTGCCCTCCACTACCAAAAGACGTGGAGACCCGTTTATCTCGTCAGCTTCTTACTTAAG
GCTACATTTACGTCACTTCCTTGAACTCACTTAAGGAAATCCCAA
Found at i:394004 original size:24 final size:24
Alignment explanation
Indices: 393951--394004 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
393941 AAACCTATAT
* *
393951 CACGAATTGGTTCACGTAGGAATG
1 CACGTATTGGTTCACGTAAGAATG
**
393975 GGCGTATTGGTTCACGTAAGAATG
1 CACGTATTGGTTCACGTAAGAATG
393999 CACGTA
1 CACGTA
394005 GAATACCAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (24 bp):
CACGTATTGGTTCACGTAAGAATG
Left flanking sequence: Indices 393451 -- 393950
TAGATAATGAAGATCTGATTCTAGGTTATGTTTCAGGAAGGATACGACGTGGTTTTATACGGATC
CTACCGGGAGATAAAGTTAAAATTGAAATAAGCCGTTATGATTCAACTAAAGGACGTATAATTTA
TAGACTCCACAACAAGGATTCAAACGATTAAGTAGTTTTTCAAGTTCAACATTACGGAATACTAT
TCGGGGTTCAAAAATTCAAGAAACTTCTTTTCTTCAAAAGAATGGATTCAGAATTTAAGTAAGGA
ATGACAAATATGAAAATAAGGGCCTCTGTTCGTAAAATTTGTGAAAAATGTCGACTGATCCGTAG
GCGGGGACGAATTTTTTTCCAACCCGAAACATAAACAACGACAAGGATAATCATTCTACTAAAAA
GTTCTAAAGGACTAGGATTCAATGTAAACAAAAAAAATTACATGAAATGGATATATCCATATATT
TCTGACTCATATTTATGAGATGATAAAATATGGCAAAACCTATAT
Right flanking sequence: Indices 394005 -- 394504
GAATACCAAAGGGAGTTATTCATGTTCAAGCAAGTTTCAACAATACCATTGTGACTGTTACAGAT
GTACGAGGTCGAGTGGTTTCTTGGGCCTCTGCTGGTACTTGTGGATTCAGGGGTACAAAAAGAGG
GACACCATTTGCTGCTCAAACCGCAGCAGGAAATGCTATTCGTACAGTCGTTGATCAAGGTATGC
AACGAGCAGAAGTCATGATAAAGGGTCCTGGTCTTGGAAGGGATGCAGCATTACGAGCTATTCGT
AGAAGTGGTATACTACTAAGTTTCGTACGGGATGTAACCCCTATGCCACATAATGGCTGTAGACC
TCCTAAAAAAAGACGTGTGTAGAAATAAAATAACCATTGACGAGATTGCAAGAGAAATAAATGAT
CTGATTAATTATCTACAATATTCCTATGGTTCGAGAGAAAATAAGAGTATCTACTCAGACACTGC
AGTGGAAGTGTGTTGAATCAAGAACAGATAGTAAGCACCTTTATT
Found at i:468424 original size:19 final size:19
Alignment explanation
Indices: 468400--468437 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
468390 TCAAGTTTTT
468400 TAAGTGTAGCTCTACTAAA
1 TAAGTGTAGCTCTACTAAA
468419 TAAGTGTAGCTCTACTAAA
1 TAAGTGTAGCTCTACTAAA
468438 GTAGTCGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
TAAGTGTAGCTCTACTAAA
Left flanking sequence: Indices 467900 -- 468399
AAAGAATTTTTGCTACCCTGCCTGATTATGAAGAGCTTCGAGTCTATCGGGAGAGGATGTGGTGG
TAACCCCGTCTAGAGCCGGGCGTCCAGCCGTGTAAGAAGACTCACTTTAGCCACTATAGCGACTT
CACTCTCAACTCTAGCGGATAAGTACTCTCCATCCACTTCCCCCTTTCCGTATGCCCAAAAGCTC
GCCCGCCCGGTTTATGAGCCCCTTTCCGATTCCCTCACCCAATCTCATGAGAAGCAAGCCCAGCA
GGCCCTGCCTTAACCTGTCCCCAGACAGTCAGCCCTCACCAGGCTGCTGGCATTGCTAAATGCTC
TGCCATGAAGCAAGCTTTCCCGAATACGACAGATGCGGAAGTGGGGAAGCCGGAAGTCGCTAAAG
AAGTCGGAGGAAGAAAGCAGTTAGGCAACAGTATGCACAATAAGGGTACATTAGTATCCTGGGAA
TTGACAACATTGACAGAAAGGGGAAGGGGTAAGAATCAAGTTTTT
Right flanking sequence: Indices 468438 -- 468937
GTAGTCGGCCTAACCTTCGGTTCCCGTAACCAAGTTTCTCTTTCTCACTCCTTATGTACTTTTTC
TTACTTCATCCATACTTTTTCTTTTTGAAGTGTAGGGCAAAGGGCGCTCTCTACTTTCACTTCTA
ACTAAAGGCGAACAGCCGGCTTTGCAAGCAAATAGAGAGCCCCCGCCCGTTTGAGTCGCGAAAGG
GCCGCTTACTTAATTAAAATAATTATTTATAAGAAAATAATAAGATAATTAAGATTCTATATCTA
TCTATAAACAATTGGAAAATATATAGAATTTATAAATATATAATTCTATTTATAAATTGTTCATT
CCTGGGAAGAGGAAGAAACAGATAGAGCAAAGGCCTTCTCTTTCCGTCCGCTCTTCCCGAAGTGA
GAGAATTGCATGTAAAGATCCGTAAGGGCTTATAGTTTAATTGGTTGAAACGTACCGCTCATAAC
GGTTATATTGTAGGTTCGAGCCCTACTAAGCCTACTACCCTCTTC
Found at i:504908 original size:20 final size:20
Alignment explanation
Indices: 504883--504926 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
504873 TATACGATGG
* *
504883 GTCTTATTATTAAGACTATA
1 GTCTTAATAATAAGACTATA
504903 GTCTTAATAATAAGACTATA
1 GTCTTAATAATAAGACTATA
504923 GTCT
1 GTCT
504927 AGTAAGCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (20 bp):
GTCTTAATAATAAGACTATA
Left flanking sequence: Indices 504383 -- 504882
ATCAGAAGCTTTTTCTACATCCATATGATCTACTAAAGTGAAAGTAGATCGTGCCCATATAATGA
AAGCAGATCTTGGTCCATGGGCTCATTCTCAATTAGTCTTCCTGGACTATGTTTCTTACCCACCC
CTGCTAGCATAAAAACAAGAGCTTTTCGGGCAGCGAGTCACATGTTGGAATGTCAGGATGTGGAA
TTTCGTTATTGAGATTAGATTAGTGATTAGTCACACCTACCGTAACCTATATGGGTAAGGTTAAG
CAGCTGACTTCGCCCCAAAGATGAGACTAGGAGAGTTGCATGCTCAAATGTGATCAATTGTAAAC
AAGCTCTTGTACATCCAAAGCTTCTTCAAAGCCCGTCCCAAAGCACTTCTCGGAGGTGAAACCGA
CGGAGGACTTCACCCTTATCTTTTAAAGAATGGCCTTTACGGCGCCCTATGCCGATTCCCACTTT
CACTCTTTTGCCTCGAGACTTCCTAGGGAAAAAAGTATACGATGG
Right flanking sequence: Indices 504927 -- 505426
AGTAAGCTGTTCTCAATGGGCTTAGCGAAGTTCTCGCCGTTCAGCAGTGGAATATTCCCATGATA
TAGTCGCTCAGTCATTTGTGAATTCCTTTCTTGAGTCCAGGATATCGGAAATAACATCTATAAAG
AGTTGCCGGAACCGGTGCTACACCAAAGCATGGGCTTTTTCTTTCTCAATTTCTTTTTAATTACA
TGACTGGGAATCTTCCTTCTCTTCTTTTTTAGTCGGTATTCGCCTCAAGATGGACATACACCAAT
CATGGTAGGGTCTGAGTAGGCATTGTTTAACATAATTGCCTATAGCGAAGACCCGTCGTTTTCCG
CCACCTTCACAGCCTTCGTTTGTTACGGGTTCGATTCTTTGGTTGCGCGGAAAGGTAATGTCAAC
TAGTGTTGAACAGCCCTTTTCCATATCCGGTTCTTTGTCCGGGGAGATCAAATTACCGGAAGAAC
TAATGATCATAGACCAATGACCAGCCAACTTTCCTGGTGATGCAA
Found at i:509791 original size:39 final size:39
Alignment explanation
Indices: 509737--509812 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
509727 TTTTCTATTC
*
509737 ACTCATGATCTGGCCTGGTCGACCCGATCATGATATTTG
1 ACTCATGATCTGGCCTGGTCGACCCAATCATGATATTTG
*
509776 ACTCATGATCTGGCCTGGTTGACCCAATCATGATATT
1 ACTCATGATCTGGCCTGGTCGACCCAATCATGATATT
509813 GAAGGATGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (39 bp):
ACTCATGATCTGGCCTGGTCGACCCAATCATGATATTTG
Left flanking sequence: Indices 509237 -- 509736
CACACCTGTGTAGAGTAGATCGTTCAACACCTGTGGCACAAACCCATTTTTGACCTATTGGTCCT
AGTATCATAGGCGACCGAACGGCCGCCCCCTAATTACTAGACCGACCAGCTATAATAATTCCATA
AACACCTAGCGAAGATATGGCAAACAAATAAAGTAGCCCTATGTTCGGATCTGACAATACCATAC
CATAATCAAAAGGTACAACGGCCCGAGCAACCAGACTTAGCATAAATGTAGCCACTGGAGCCATT
CTAAAAAGGGAGAAATTAGCACTACTTGGTGAAATAGGTTCTTTTAGAATCAATTTCAAACCATC
TGCTAGAGGTTGTAACAATCCGAACGATCCCACTACATCAGGACCCTTTCGACGTTGCACAAAAG
CCATTACTTTACGTTCAGCTAGCACTAAAAAGGCTACTCCTAGTAGAAGTGGTAGAATTATTCCA
AGTATTTCCGCTGGAACAGCTATGTACGTTTTCGATTTTCTATTC
Right flanking sequence: Indices 509813 -- 510312
GAAGGATGGGACCTTTTCTCGAAAAACTCCGGATCTCGATAAGAGTTGAAGATAGTGCAAGATCG
AATCCTCTTACCTTACTTCGAATAGAATCTTAGCCTGCCTCACTTGCTTTCTTTACTGCATAAGG
TTTCGTAATAAAAAGCGAAGTCAAGGGATTTCCTTCTAACTAGTGGCCGAGAGTAAGCAAGCTAC
ATGGACCAGAAGGAAAGGTGGAGGACCTGATTCCAAAAAGAATAATCACTCATCCTCGTCTGAAA
ATCTTCTTTCAGAAAGAAGATTTTCGCTAAACCGTAATAGAAAGGGAAAAAGGGATTGGCTTTCT
ATTACGGTTTTTCCTGTTGCCCAGGTTCCTGACTAGGCGATTATGATTCCCTACATCATTCTTAC
TAGTTATCAGAGGGCATAGTGACTCTCGGACCTACTCGCTTTCTTAGAAGCAGCCTTTGATTAAA
GCTCACTTGGAACTTGCTTGTTTGGAACCCTGTCCCTCTGAAACT
Done.