Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MW477238
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: 224590
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Found at i:23157 original size:41 final size:41
Alignment explanation
Indices: 23100--23179 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
23090 TTTCTCGAGT
*
23100 ATTTTCTAATACAGAACGCTTAGTAATATCATTCAATTATC
1 ATTTTCTAATACAGAACGCTTACTAATATCATTCAATTATC
23141 ATTTTCTAATACAGAACGCTTACTAATATCATTCAATTA
1 ATTTTCTAATACAGAACGCTTACTAATATCATTCAATTA
23180 GCATAGAATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (41 bp):
ATTTTCTAATACAGAACGCTTACTAATATCATTCAATTATC
Left flanking sequence: Indices 22600 -- 23099
TTCAGTGGCATGTTTCGGTCCTCTTCCCCATTACTTAGAAAAAGTGAGCCACCGGTTCAGGTACA
AGATACTATCATTACCGCCTGGACAATTAGACATCCAACCCGTAATCGCAACGACCCAATTGCAA
GAGCGGAGCTCTACCAACTGAGCTATATCCCCAGTCAGGTACGACCCCTAATAGAGTAAAACAGG
TCTCTCTCTATAGCAGGTCTCTTTTTTACTTTCTGCATTTATAGAGTGTGGATACACTGGAGGAC
TCTACTAGGTTGTAGGGCAACATGGAGCTGTGTTAGGCACTTCATGTTTAAAAGATTCCAAGTCC
ATCTACAGAGGACCCTTTCAGAGGGCTAATTATGGATGCCCAATCCCGGAAAGCATGAGGATGTT
GATTGATTCCAGCCTCTCACTGTCTGTTATGGGTTAGTAGAGTCTAACAGTCCCACAGGGTGCCG
ACCCACGGTATAGTATTTTAGTATACAGGAATACCTTTCTCGAGT
Right flanking sequence: Indices 23180 -- 23679
GCATAGAATGATGGAATGATTGAATGCTCTATTATCGTTCGTATTCAGATTATTCATCTATGGAA
TGATTGAATGCTCTATTATCTAAGTCTTCATATTATCCATATATGCAAGAATAGGTATTCTAGAT
ACTGTGCAAAATCCAGGATTTTACTCTGGTTTTAAACCCTATATTGAGATATGATTTGGAATAAT
TTTTTTCGTATTCAGAAACCCTCTAATACTGATTGGATATTGAACTCTCATGAGTACTTGCCTCC
TGTCGGAAATGAAGATCGAGAAAAGGTCATCAAATTCTGGGTTTCATTTTACGATGATGCTATAA
GAAAATGTGAGATCACTAACATTAAGAAATGTGTTCCTATGAAAAATGACTTCGTATATAAACAG
ATCATATTCAAACGTCTTGACCATCATCGTGGTACGAATCCTAGCGATGATGTATTACGAGAAAT
ACAAAAATTCATCGAAGAGTCAACTTTTGAGTTTGATGAGAAGTC
Found at i:24064 original size:15 final size:15
Alignment explanation
Indices: 24045--24079 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
24035 GCTAAAACCT
24045 GCGATGATAAAGCCA
1 GCGATGATAAAGCCA
*
24060 TCGATGATAAAGCCA
1 GCGATGATAAAGCCA
24075 GCGAT
1 GCGAT
24080 AAGGCTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (15 bp):
GCGATGATAAAGCCA
Left flanking sequence: Indices 23545 -- 24044
GAAAAATGACTTCGTATATAAACAGATCATATTCAAACGTCTTGACCATCATCGTGGTACGAATC
CTAGCGATGATGTATTACGAGAAATACAAAAATTCATCGAAGAGTCAACTTTTGAGTTTGATGAG
AAGTCTATGTATAAAACAGTTCCAAACGTAATCTCTGATATGATTAAGAAAGCAAATCAGTCTGC
GTCTCCTGCTGATTGTTCTGCAAAGGATTATCTTTTGTCGAGTACAAAACTAACTGCTGAAGAGA
AAGAATCACTTAATGTGTTTAGTAATTATACGTTGGAAGTCTTAATAGTACATGTGTTAAGTACT
TTGTTTAATGCAGTAGAATCGAATTCAGTTATTCGTCTATCGACTTTAGTAGATCGTTTAGATGC
TGCTGTTCGTTCACAGATCACATTATTAATGAGGCGCAAATTTCAGAGAGAATGTACTCTCGAAG
CTCCTGAACTACCCATCGTTAAAGCAATAACTCGCGCTAAAACCT
Right flanking sequence: Indices 24080 -- 24579
AAGGCTAAAACCAGAGCTAAACCCCGCCGCAGACATTTTATCTTCGGCACTGTATTAGTTGAATT
CATGCAAAAAAGGGATTTGATAGAAGTCTCGCATATTGGTAATATTGAGGATGAGCCTATCCGCA
AGAAAGGTGGTGATTTCTATATCGCTAAACATCAGAATGTACACTGTAAATTTCCCGTCTCTGAT
TTGCCTATCAGGTTTAGTTTACCTATGGTATGCAAACCAGAAGATTGGAAAAGTATTCTCCCTGA
AAATCAACAGCCTAAGTATCTATCACATCTAAGGGGTGGTTACTTAAGTAGTTTAACGGCTGATA
TAGACGAGCGTTACCGTTTATTAAGCTCTCATAATATAGATCATTTTTATATAGAATTAAATAAG
AATTCTAAAATCTTATGTAATATCATGAATAAACTACAAAGTCAACCATTTAAAATAAATAGTCT
TTTCTTAAAATATATTCGAGAAAATGAGTCTATATTGGTAGAGCA
Found at i:26824 original size:15 final size:15
Alignment explanation
Indices: 26821--26852 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
26811 TAAAGACTAT
26821 GACTATGACTATAAA
1 GACTATGACTATAAA
26836 GACTATGACTATAAA
1 GACTATGACTATAAA
26851 GA
1 GA
26853 TGATGGTTAT
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:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (15 bp):
GACTATGACTATAAA
Left flanking sequence: Indices 26321 -- 26820
AAAAAAGTAGTTACTTTGATTATGATGAATTGTATTCGCGTATTAGAAATACAACATATGATGCT
CCACATCAGTCTTTGATTAGAGCTACACATTGTATAGACCCAGGCTTCACCGTTCTGGAAATCGA
CTTAATCGCCCTATCTGTTTTAGATCTTCTAATTCGTTATGTCTTCTCATCGGTAGAAGGTTATT
CCAAATTCAATATGATCTTCACCCTAGTTGATAAGGATGGTAAGGATATTACATATAATATATGT
AATGCAATACCATTGACTTCACTAGATGGTAGCGCGTTCTTTCCTTATAAGGATATCTTTCGTTA
TATATATAGGGCTGTTATCCAGGTTTTTGAGAAGTACAAGGGTGTTTGCATTACCAAAATCTCCC
TGCGTATCTTTATAACTGAGAAAAATCATGAAAAACATCTCTCAAAAGATGAAATCATAAAGGTA
CTTGATGCCCTTTTTGAGGATCTTTCTCATGACTATAAAGACTAT
Right flanking sequence: Indices 26853 -- 27352
TGATGGTTATGGCAAGCAGCTTCTTCTTTCTAAGGTTTTTAAGGACAAAGTTCGAAGAGATGTAA
AACCCCCTGTTGCTAAACCTATTTCTAATAAGAAACGTAATTATAATAGCAATATATCGCAAATC
ATTTCTTCAAAGAAAAAGGGTGTTACACCTTTTCTAGTGGCCGATATTGAGACAATCCTTCATAA
GGATGATACGGGGATGGAAGTGCAGACTCCATACGCAGTAGGTTTACTGGTGGTTCTACCTGAAA
AGGAAGTGGATAAAGCGGATATTATGACTTTCTATAGTGAGGATTTCTTTTACAAAGAATTCTAT
TCATCCTTCAAAGATAGGAGCGATAAGATCCTATATGAGATGGTTAAACGGATTGATTTATTAGT
TAATAAACAGTATAAGACAGCTAAGTCTATATACTTCCATAACTTATCACGATTCGATGGAATAA
TATTGCTTAAGCACTTAATCTGTCGTCATCCATACTACATAATTA
Found at i:26830 original size:21 final size:21
Alignment explanation
Indices: 26804--26847 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
26794 GATCTTTCTC
26804 ATGACTATAAAGACTATGACT
1 ATGACTATAAAGACTATGACT
26825 ATGACTATAAAGACTATGACT
1 ATGACTATAAAGACTATGACT
26846 AT
1 AT
26848 AAAGATGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (21 bp):
ATGACTATAAAGACTATGACT
Left flanking sequence: Indices 26304 -- 26803
TTCCTACTGTACTACAGAAAAAAGTAGTTACTTTGATTATGATGAATTGTATTCGCGTATTAGAA
ATACAACATATGATGCTCCACATCAGTCTTTGATTAGAGCTACACATTGTATAGACCCAGGCTTC
ACCGTTCTGGAAATCGACTTAATCGCCCTATCTGTTTTAGATCTTCTAATTCGTTATGTCTTCTC
ATCGGTAGAAGGTTATTCCAAATTCAATATGATCTTCACCCTAGTTGATAAGGATGGTAAGGATA
TTACATATAATATATGTAATGCAATACCATTGACTTCACTAGATGGTAGCGCGTTCTTTCCTTAT
AAGGATATCTTTCGTTATATATATAGGGCTGTTATCCAGGTTTTTGAGAAGTACAAGGGTGTTTG
CATTACCAAAATCTCCCTGCGTATCTTTATAACTGAGAAAAATCATGAAAAACATCTCTCAAAAG
ATGAAATCATAAAGGTACTTGATGCCCTTTTTGAGGATCTTTCTC
Right flanking sequence: Indices 26848 -- 27347
AAAGATGATGGTTATGGCAAGCAGCTTCTTCTTTCTAAGGTTTTTAAGGACAAAGTTCGAAGAGA
TGTAAAACCCCCTGTTGCTAAACCTATTTCTAATAAGAAACGTAATTATAATAGCAATATATCGC
AAATCATTTCTTCAAAGAAAAAGGGTGTTACACCTTTTCTAGTGGCCGATATTGAGACAATCCTT
CATAAGGATGATACGGGGATGGAAGTGCAGACTCCATACGCAGTAGGTTTACTGGTGGTTCTACC
TGAAAAGGAAGTGGATAAAGCGGATATTATGACTTTCTATAGTGAGGATTTCTTTTACAAAGAAT
TCTATTCATCCTTCAAAGATAGGAGCGATAAGATCCTATATGAGATGGTTAAACGGATTGATTTA
TTAGTTAATAAACAGTATAAGACAGCTAAGTCTATATACTTCCATAACTTATCACGATTCGATGG
AATAATATTGCTTAAGCACTTAATCTGTCGTCATCCATACTACAT
Found at i:29092 original size:27 final size:27
Alignment explanation
Indices: 29055--29111 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
29045 ATGCTGACAG
29055 AGAATCTGATAGATCAGGCAATCATTC
1 AGAATCTGATAGATCAGGCAATCATTC
*
29082 AGAATCTGATAGCTCAGGCAATCATTC
1 AGAATCTGATAGATCAGGCAATCATTC
29109 AGA
1 AGA
29112 CTCTAGCCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (27 bp):
AGAATCTGATAGATCAGGCAATCATTC
Left flanking sequence: Indices 28555 -- 29054
ATAGTTCTTGGTAGCCCACTCTCAGATGAGATGGTATCTTCTTCAGTCTTAGGTAAATTGAAGCT
AGAAGATAAAATAGTTAGTGGGGTCTTTTTAGCACCTAAATCCTATTACTATATTACTAAAGATG
GTAAAGATGTAATAAAACACAAGGGTCCAGCAAAACAATATGTTGACATTGATTGGTTTGAAAAC
CAATATGCTAACAGAAAAAACAAGAAAAGTGTACCGTATTCTACTCCCTTTGGTGTTGATTGGAA
TAAACTTCAGATTGTTAAGAAAACTACGAATCTTGCGATGAATGTGGATGTCGGTACCAAAAGGA
AAGTGGTATACACTGAAAATAATGTTTGGTTGGAGACCGTACCCTTTAAAGTGGAAAACTTAAAT
GATTGCTCTAAGCAGGACTTGATATACATTATCAATATTCTCAATAATGAGAAAGATTCTAATTC
AAGCCTAAATACCACGCCTGAAACATATCAGAGTGATGCTGACAG
Right flanking sequence: Indices 29112 -- 29611
CTCTAGCCCTGGCTACGGCAGTGATAATGAAAGCTATGATAATAGCAATAGCTCTGGTAGTGATT
CAGGCTCTGGCAGTGACAATAAGAGTTGTACCCCGAAGGATAATGATAAAGAAACGAAGGATGGG
AAGGATGGCAATGGCAGCTACTATGAGAGCAACAACTATGATACAGAAAGCAACAGCAACACAAG
TGCGCGGGAAAGCAACAACTATGATAGCACAGAAGAGAGCAGCTCTGGTAGTGATTCAGGCTCTG
GCAGTGACAATAAGAATGAAATCATACCTCCTATAGATGATAAAGAAGATGAGACTACTAACACT
TCTGATAACCATTCTTCAACTACGCCTACGGATGGCAAGAAAGAGACAGAAAGCAGCAACTATGA
TGATAGCACTTCTTCGCCAACCATTGATGATAGAACTTCGACTAATGCACCTTATAGCACTTATG
AGAACCCTAGCTCTGGCAATGATAGTGATTCAGACGGCTACGCCA
Found at i:31895 original size:37 final size:36
Alignment explanation
Indices: 31846--31916 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 36
31836 CCAGTGACTA
31846 CTAACCATTCTGAAACTAGCTCTGGCAATGATAGCT
1 CTAACCATTCTGAAACTAGCTCTGGCAATGATAGCT
31882 CTAACCCATTCTGAAACTAGCTCTGGCAATGATAG
1 CTAA-CCATTCTGAAACTAGCTCTGGCAATGATAG
31917 TGATGAAGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 4 0.12
37 30 0.88
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (36 bp):
CTAACCATTCTGAAACTAGCTCTGGCAATGATAGCT
Left flanking sequence: Indices 31346 -- 31845
CTTTTAAGCGGATCAAAGACCTAGATGACCCGTAGACAACATCATATACGCGGTAAACTAGCGTA
ATGCTAGCACTTAACCTTGCCGCTAACCTAGAGAGATTGGCACTCTTCTTCTCGACGAGAAGATT
GAGAGTCATGTGCCCTAGTAGAGAGCTGATTCGTCTAGCCGTTTAGGAGCTATAGACTGAGCTTT
TACCTCTTGCTAGCAAGCAACTAGCCCTGCCTATAGGTTAAGGTTAGGTTCCACCCTCTCAGCCT
TTCCAAGCCAAGATTCTACTCTATCTTATCTTCTTTTCCAAAAGAAATGTAGAAAATACATTCTA
TGGCTAGAATTGAGCGTTATATCGCCATTATGATAACACATGGGTGTTACTTACATTCAAGCCTA
AACGTAGGATAGAAGCTAAAGAAAGCTGTCATTGGAACTAAATTAGCTACTTCATAAGAACAGAA
AGCTACTCACTTAGAAACTCTTAGAGTTTTGGATGCCAGTGACTA
Right flanking sequence: Indices 31917 -- 32416
TGATGAAGACTCTGGCAACAAGGACAACAATAACAATAGCACTTCTGATAACCATTCTTCTGATA
GCTACTCTGGCAACAATGATGATAGCACTTCTTATAGCAGCCATGACAAAGGCAACAAAGAGACA
GAAGCAAGAACTGTTCGTTCAGATGGCAATGGCAGCTACTATGATAGCACTTCTTATAGTACAGA
TGACAAGACTACTAACCATTCTGAAACTAGCTCTAGCTCTGGCACTACTTCTTCAACTAGCTCAG
GTGGCAACGATAGATCTGGCGGCAACGATAGCAATAACGATAGCAGTAATAACGATAGCTGCTCA
GGTGGCTCTGAAACTAGCTCTAGCGGCAACAAAGACGAGGTAAACGAAGCAACATATTGACTTGT
TAGCCGTAGGCAGTGTAGTCTATCTTAGGCCTACTTCCTTGCTTTCAACCTCTTCCTTGGTGCCA
CCGTGAGCAAGTGCTTTAAGAATCTCTCCAAGGCTATGCAAAATC
Found at i:32835 original size:14 final size:14
Alignment explanation
Indices: 32818--32846 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
32808 TGAACTCAAG
32818 ACTCTTAACTCGGA
1 ACTCTTAACTCGGA
32832 ACTCTTAACTCGGA
1 ACTCTTAACTCGGA
32846 A
1 A
32847 GCTCGCATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (14 bp):
ACTCTTAACTCGGA
Left flanking sequence: Indices 32318 -- 32817
AGTGTAGTCTATCTTAGGCCTACTTCCTTGCTTTCAACCTCTTCCTTGGTGCCACCGTGAGCAAG
TGCTTTAAGAATCTCTCCAAGGCTATGCAAAATCCAGCCTATGCTCTAATATCGTATATAACTCG
GAACTCGGAACTCTTGACTCGGAGTCAATTCCTCTCCTACCTCTTACGATCCTCTCCTTGGACCT
AGCCTCAACTCAGGGCAACCTTTTTAGCTCGCTTTGCCTCTGACGAGATACTTTCCTGCGGAACC
TCACATCCGAGAATAACATTTCTATTCTCTTAATCATCATAATCAGTCTTTGTATCATAGTTGTT
GCTAGAGCAGCTATCATTGTAACCGGAGCTAGCTCTATTCTTTCTATAAGACCACCAGAGAAATC
TCGTATAGAATACCTAGAGTTGGGGGCACTGGTCACTTGTGATGGTTAGCATCTTATTTAGCTAC
GGGTGTTCTCAATGGGTACCACCCCGGTCCTAAAATGAACTCAAG
Right flanking sequence: Indices 32847 -- 33346
GCTCGCATACCAAAGATAGACTCAAGTCTTCACTTGCTTTCAACAAGATGCTCTTTCAGCCTCAC
AAGGGAGAATGACGGGGATAAGGCTCTATTCCTCAAGTTGTAGTCTTACCGTTAATTGCATTCTA
AGAAGACAACTTCTCAGTCTAGAAGCCTTGGTACCACTGTTCAGGCAAAGAGCCTCTTCCGAGAT
ACTACTACACCTCACAGCAATACAGCTCTTTCTAAACAGAGCGAAGCTATGGCACTAATAAATAA
TAAAATGAATATTCTCAGAAAGATCTTATATAAGAAAGAACCTAACAACATTGCATTCTATACGC
TCTTTCTTTTATCACTCACTAGCCATAAGAGCATATAGAGCTAGTACAGCAAGTCTTGCTATTGA
CTTTATATAGCTTATATAGTAGCTATGCGGAATCAAGTACAGCTAGAGTTGCTTCTTTCTTTTCT
TTTGCACTTCTTTACACCATTAGAGAACTTCTTCTTTCTTCTTCT
Found at i:35717 original size:41 final size:41
Alignment explanation
Indices: 35655--35734 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
35645 CATTCTATGC
*
35655 TAATTGAATGATATTAGTAAGCGTTCTGTATTAGAAAATGA
1 TAATTGAATGATATTACTAAGCGTTCTGTATTAGAAAATGA
35696 TAATTGAATGATATTACTAAGCGTTCTGTATTAGAAAAT
1 TAATTGAATGATATTACTAAGCGTTCTGTATTAGAAAAT
35735 ACTCGAGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.38
Consensus pattern (41 bp):
TAATTGAATGATATTACTAAGCGTTCTGTATTAGAAAATGA
Left flanking sequence: Indices 35155 -- 35654
CTAATTACATTACGAGGATAATGATGTATATGTATATGTTTAGTTATACTAGAAGAAAGGCTACG
AGGAATTCGACGAGATACAATTTTTGAGGATGATGATTCACCAGCATTATCATTATCATACAGAG
AGAGTTCTTCAAGCTTATCCGTTATTTTAGATACACCCAAAGCACGAGCATTTTTGGAGATCAAA
GAGCCTATTGTAGATCTCATATACCGTATGTTCATATAGCAATATCCCGGAACAGTGCGTGAAGG
AGTGATAATAGAACACGGAACAACAGACACATAAGAATAACGACTGACAGACAGACTCAACATAG
CAAATTCATTTTTTTAACAGAGTAAAATCCTGGATTTTGCACAGTATCTAGAATACCTATTCTTG
CATATATGGATAATATGAAGACTTAGATAATAGAGCATTCAATCATTCCATAGATGAATAATCTG
AATACGAACGATAATAGAGCATTCAATCATTCCATCATTCTATGC
Right flanking sequence: Indices 35735 -- 36234
ACTCGAGAAAGGTATTCCTGTATACTAAAATACTATACCGTGAGGCCGCCACCCTGTGGGTCTGG
TATACTACTACAACCCATAACAGCAGTGAGAGGCTGGAATCAATCGACATCCTCTATGCTTTCCG
GGATTGGGCATCAATACAATAAGGCTAGGCCTATATATATGACTTGGAATTTTACACCGTGGAAG
CGCCTAACCAGCTCCAGGTGGCCCTTCACCTAATAGAATCTACCAGTGATCCACACTCTAAAAGT
TAAAGCATTAGATTATATTTCTAAAAGTCAAGCTCAAACTTCTATAGAGATAGACCTAATATTAC
TCTATAAGGGGACAGCCAGAGGGTTACATATTTTAAGGATGCTTTCACTGATCCAGATCTGCTGT
TCCGCCTACAAAAAGGGATAGAGGAAAAAAGCGATAATATTACGGCCTCACTTAATTCTGAGCTT
GTCCAAGCCTGCCCAGTATCTAATGTACCCCCGCAGAAGCAGCTT
Found at i:49720 original size:16 final size:16
Alignment explanation
Indices: 49699--49733 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
49689 AGTCGCTACA
49699 GAGTAGACTTGAAACC
1 GAGTAGACTTGAAACC
49715 GAGTAGACTTGAAACC
1 GAGTAGACTTGAAACC
49731 GAG
1 GAG
49734 CGGGAACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (16 bp):
GAGTAGACTTGAAACC
Left flanking sequence: Indices 49199 -- 49698
GGCCTATGTTTGCTTTGCTTAGCAGCTGCTCTAAGTGAGTATTCCTAAGCAAGATAGCTTTGTTG
CTCTCCTTTTGATGGTTTAGTGATCTGAGTTCTAGCTTTTGAGTTAGCTCTTTGTCCGGTAAGTT
ATATCAGTTATCTTTTAGTTGCAACATAGCTGTAGCTCTCTGCTTCTATTGCATAGTAATTTCTC
TAGGAGAGGTCAAAAAGGGCGATTTCGTCACGTTTTGGTGACCTGTGATACCTCGGCCGGCTGGT
CCGAAGAAGTGGCAGCAGCATGCAACGTATTGGTGTTTCGGGAAGAAGGCTTGGATACGTAGTTC
GTATTGTCTATTGGCTCCCAATTATCATTGCCTATCCGCTCGAAGCCTTAAAGTAAAAGACTGGG
GAAGTCCATCAATACTGATCGTAGACAATTGACATTAAGTGGGAAGAGTAGACTTCAAGTATTGG
ACTTGCGTGAGTTGGTCGGGTCAAGGACCTGGGGCAGTCGCTACA
Right flanking sequence: Indices 49734 -- 50233
CGGGAACATGGCGGGTAGTAGCCTTTAACAGTGCTGGTCTACCCCGATTTTCTTTCCGGGACTGA
AAGACTTGGTTTCGCCACCCCTATTTCATTAGTAGAGCTCTATTGAGAAAGACCTTGGAATTGGC
CAATCACCAAGGGTTAGCATTCTGTTATAACGAATAGAACGAAAGATTGCCCCTTATTTGCTAAG
GATCAAACAGTCAAGGTCTGCCTAGCGAAATAAATAATGATAGTAGTTGTAGAGATCTACCCGCT
CATATGAGTTCCGTGAACAACAAAAATAAGGGCAGTTCTATCTTTCATCACCGATTAACAAGCTT
TCACGTTCCAAGGAATGACATGGCTGTTCAAGAACCCGTTCAAAACGCGGGAAAAAGAAATGCCT
AAAGTCACGAGTAGGTCCTCACGTCAGTTTAAATCGTCGCTTCGCTAATTGGATCTCTTTGGCGG
TTTACCGGGCAATGCCATCATTGACGTTAAGTTGCCAGTCTTTCG
Found at i:56953 original size:19 final size:20
Alignment explanation
Indices: 56925--56985 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
56915 TAATAGAACT
* *
56925 TAATTCTATT-ATATTTATA
1 TAATTCTATTAATAATAATA
*
56944 TAATTTTATTAATAATAATA
1 TAATTCTATTAATAATAATA
* * *
56964 TAATTATAATAATAATATTA
1 TAATTCTATTAATAATAATA
56984 TA
1 TA
56986 TAAACAAACA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
19 9 0.26
20 26 0.74
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATTCTATTAATAATAATA
Left flanking sequence: Indices 56425 -- 56924
CTGGTCAAAACTAAGGGCTGTCACCCTAGTACGCCGTTCCGCTGTTAAGAGCAGTCCCGCCTAAA
CCCCACTCACTAACGGCAAGCTGTCTCCATTCAGTTGTCTCCGTCTGCTACTATCATACTAAGGG
AAGTTGCCCTAGTAGCCATTATGTTTGAAAGTCCAGTACGCCCTTCTGTTGTTAGGAAAGTCAAG
CTGTCTACGTCAACTTCGAACCCACGAACTGTACTTGAAGCTGTCTCCTTCTGAGATTGCTATCC
CCTGACCGATAAAAGGACGATTCGAGGCCATACAAACGTGGTTCTAGTTACCCTTGCCTTTCCCC
AATGGGGATTCTATTTCCCGAATGTGGTACTTGGTTGGTTTCCTCATCCACTAAACTAGGTCCTT
GTAGCAAAGGATCTTTCCTAAAGAGTGCTGCAAACGATCGATTCTCATCCCCCGATGTAGTACTT
GTTGACCTATTCTATTCTCCTGCAAGCGAAAGGGCTAATAGAACT
Right flanking sequence: Indices 56986 -- 57485
TAAACAAACAATTTCTTTTTTTATCCAATTGTTCATTCCTGGGAAGAGGAAGAAGCAGATAGAGC
AAAGGCCTCCTCTTTCCGTCGGCTCTTCCCGAAGTGAGCGAATTGCATGTAGAGATCCGTAGGGG
CTTATAGTTTAATTGGTTGAAACGTACCGCTCATAACGGTTATATTGTAGGTTCGAGCCCTACTA
AGCCTACCACCCTCTTATCTTCACCTGATACAAGGCAGTCGAAGTCCCCGCCGCCCTGCAGATCT
CAATCTAGCGACGGGCACCTGGAACCACACTGCTGCCGCTGCCCTTCGGGCACGCCTCCTACGCT
TATCACTCACCTACGCTTTTGCAGCATGCCCCCTTCGGGCAATACGGCTTTATAAACGCGAAGCA
GCTTGTATTTTAAAAATACAAATGTCATCTGCTTTTATAAATTTGTGTAATACTCTCTGTGGGTG
TTCGACATGCTGTCGAAGGAATCCCAACCTTCCTTTAGTTGGTAG
Found at i:56966 original size:20 final size:20
Alignment explanation
Indices: 56941--56985 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
56931 TATTATATTT
* *
56941 ATATAATTTTATTAATAATA
1 ATATAATTATAATAATAATA
56961 ATATAATTATAATAATAATA
1 ATATAATTATAATAATAATA
*
56981 TTATA
1 ATATA
56986 TAAACAAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATAATTATAATAATAATA
Left flanking sequence: Indices 56441 -- 56940
GCTGTCACCCTAGTACGCCGTTCCGCTGTTAAGAGCAGTCCCGCCTAAACCCCACTCACTAACGG
CAAGCTGTCTCCATTCAGTTGTCTCCGTCTGCTACTATCATACTAAGGGAAGTTGCCCTAGTAGC
CATTATGTTTGAAAGTCCAGTACGCCCTTCTGTTGTTAGGAAAGTCAAGCTGTCTACGTCAACTT
CGAACCCACGAACTGTACTTGAAGCTGTCTCCTTCTGAGATTGCTATCCCCTGACCGATAAAAGG
ACGATTCGAGGCCATACAAACGTGGTTCTAGTTACCCTTGCCTTTCCCCAATGGGGATTCTATTT
CCCGAATGTGGTACTTGGTTGGTTTCCTCATCCACTAAACTAGGTCCTTGTAGCAAAGGATCTTT
CCTAAAGAGTGCTGCAAACGATCGATTCTCATCCCCCGATGTAGTACTTGTTGACCTATTCTATT
CTCCTGCAAGCGAAAGGGCTAATAGAACTTAATTCTATTATATTT
Right flanking sequence: Indices 56986 -- 57485
TAAACAAACAATTTCTTTTTTTATCCAATTGTTCATTCCTGGGAAGAGGAAGAAGCAGATAGAGC
AAAGGCCTCCTCTTTCCGTCGGCTCTTCCCGAAGTGAGCGAATTGCATGTAGAGATCCGTAGGGG
CTTATAGTTTAATTGGTTGAAACGTACCGCTCATAACGGTTATATTGTAGGTTCGAGCCCTACTA
AGCCTACCACCCTCTTATCTTCACCTGATACAAGGCAGTCGAAGTCCCCGCCGCCCTGCAGATCT
CAATCTAGCGACGGGCACCTGGAACCACACTGCTGCCGCTGCCCTTCGGGCACGCCTCCTACGCT
TATCACTCACCTACGCTTTTGCAGCATGCCCCCTTCGGGCAATACGGCTTTATAAACGCGAAGCA
GCTTGTATTTTAAAAATACAAATGTCATCTGCTTTTATAAATTTGTGTAATACTCTCTGTGGGTG
TTCGACATGCTGTCGAAGGAATCCCAACCTTCCTTTAGTTGGTAG
Found at i:162793 original size:15 final size:16
Alignment explanation
Indices: 162775--162809 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
162765 AAAAGGAGGA
162775 AAAAG-AAAGACCACC
1 AAAAGTAAAGACCACC
*
162790 AAAAGTAACGACCACC
1 AAAAGTAAAGACCACC
162806 AAAA
1 AAAA
162810 TATGCATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.60, C:0.26, G:0.11, T:0.03
Consensus pattern (16 bp):
AAAAGTAAAGACCACC
Left flanking sequence: Indices 162275 -- 162774
GAACTACCGCCTGCATGAGCTCATCCATCCAAACTAAAGAAGACTTAGAAACCAAACCGAGTAGA
ATAAGAAAGACTACTTTAATGATAAAATAAGAAAAGATAGGAGCTCCCCATGGTAAGCGAAACAT
AATAAAACCCTGTACAGCTAAAGAAAAAGTAAGATGTAACCTGAGAGACTGTAAAATGTGAATTA
AAGAGAGAACAGAACCTTTAGTTACAAGGATGAAGATTACCAAAAATATTCTATTTTCTAACTCA
TTTACTTCAAGACTGGTTTTGAATGCCGCGAGAAAGAATCTCATCTCTAACGATATTTTGAATTC
TATTATTTCTGAAGCCGATAAACACAGGATCAAATGAGGGACTCCTGGCAGTTCCGGCCCGAGCG
TTAATCATTTTTATTGTGAACTAGATCCCTTTATGCGCCTGAAAGCAAATGAAAGAAGGACGCCC
TAACCCCCCTGAATGCACGCGTTAAAGGATAAAGGAAAAGGAGGA
Right flanking sequence: Indices 162810 -- 163309
TATGCATAGTTATTCGATCTTTTTTGATCAGACTTTTTATCAGTATCGTTGTACTGTTGATTACT
CGCCTGCTTTGGAACTGGGCTTGGCTTGGCTAGAAGGGACGAGCGACAGACAGTCTTCTTTTTCT
TAGTCTTCTCTATCTAAAGGGAGTTTCGATTCCGCAGAACCTATAGGAGCAATAGACGGAGTTAG
TGTGGTATAGCTGTTAGTAAGGCGTAGAGCAGTAGCGGTCTTCACTTTTCCTGTTACAGAATCGA
CTATAAACGCTGTTCATGGCACGGTTAGCGGTGAAAAAAAAAGAATAGCGATTGTTGAATCAGTT
TGCTCTTTCTACTTTGATTGCTCTTGTGAAGCTCTGAGGTGCGGTTTTATTCCTTTACTTTAGGA
GTAGGAGTGAAGGCAAGATCCTACTTTCAATCGAGTGAATAGCAGGCTTGTAGTTGAATCGAGAT
TGGCGATGAGTACAAGATCGAAAATCTTTCTCGCAGCTCGTGCTT
Found at i:179264 original size:18 final size:17
Alignment explanation
Indices: 179230--179273 Score: 70
Period size: 18 Copynumber: 2.5 Consensus size: 17
179220 AGGAATTTTT
*
179230 TTATTATTGTTTATATA
1 TTATTATTATTTATATA
179247 TTATTATTATTATATATA
1 TTATTATTATT-TATATA
179265 TTATTATTA
1 TTATTATTA
179274 ATAAAATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTATTATTATTTATATA
Left flanking sequence: Indices 178730 -- 179229
GAAATGCGGCAGGGTCTTCAAGCCCCACGCTCGATTCTCGAGATTCATGGGGCGTCTCGCGAAGA
TCTTCGATCGCTATCGCAAGAATATAGCGATCGAAGAGCTATCGCTCCGCTGCTTCGCGTTTATA
AAGCCGTATTGCCCGAAGGGGGCATGCTTCAAAAGCGTAGGTGAGTGATAAGCGTAGGAGGCGTG
CCCGAAGGGCAGCGGCAGCAGTGTGGTTCCAGGTGCCCGTCGCTAGATTGAGATCTGCAGGGCGG
CGGGGACTTCGACTGCCTTGTATCAGGTGAAGATAAGAGGGTGGTAGGCTTAGTAGGGCTCGAAC
CTACAATATAACCGTTATGAGCGGTACGTTTCAACCAATTAAACTATAAGCCCCTACGGATCTCT
ACATGCAATTCGCTCGCTTCGGGAAGAGCGGACGGAAAGAGGAGGCCTTTGCTCTATCTGCTTCT
TCCTCTTCCCAGGAATGAACAATTGGATAAAAAAAAGGAATTTTT
Right flanking sequence: Indices 179274 -- 179773
ATAAAATGATAAAAATAGAATAGAATTAAGTTCTATTAGCCCTTTCGCGACTCAAACTGCCGGTA
CGCTTTCCGGCTCGCAATGGCTCAAACGGGCGGGGGCTCTCTATTTGCTTGCAATGCCGGTTCTT
CGCCTTTAGTTAGAAGTAGAAGTAGAGGGCGCCATTTGCCCCACACTTCATAAAAAGTAGAAGTG
AGAAAGAAAAACTTGGTTACGGGAACGGCCGACTACTTTAGTATAGCTACACCTATAAAAGGTTT
TCCTACCCCTTCTCCTTTCTGTCAATGTTGCCAATTCCCAGAATACTAATGTACCCTCGTGTATA
CAGCTGTCCAACTACTTTCTTCCTCCGACTTATTTAGTAACTTCCGGCTTCCCCACTTCCGCATC
TGTCGTATTCGGGAGAGCTTGCTTCGTAGCGGAGCATTTAGCAATGCCAGCAGCCTGGTGAGGGC
TGGCTGTCTGGGGACAGGTTAAAGCAGGGCCTGCTGGGCTTGCTT
Found at i:212176 original size:23 final size:21
Alignment explanation
Indices: 212130--212197 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
212120 ATTTCGTTTC
212130 TTTTTGTCCAAGTCACTTCTT
1 TTTTTGTCCAAGTCACTTCTT
**
212151 TTTTTGTCCAAGTTGCTT-TT
1 TTTTTGTCCAAGTCACTTCTT
* * *
212171 CTTTTTGTCTAACTCACTTCCT
1 -TTTTTGTCCAAGTCACTTCTT
212193 TTTTT
1 TTTTT
212198 CTTTGTGAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.05
21 35 0.92
22 1 0.03
ACGTcount: A:0.12, C:0.22, G:0.09, T:0.57
Consensus pattern (21 bp):
TTTTTGTCCAAGTCACTTCTT
Left flanking sequence: Indices 211630 -- 212129
TATTTGCTAGCAACAACCTAATGGAGGCAGTCAATCAATATAGATTGATCCAAAATCTGATTCAA
ATCCAATATAGCACCTATAGGTACATAAGAAATGTATTGAATCGATTCTTTTTAATGAATAGATC
CGATCGCAACTTCGAATATGGAATTCAAAGGGATCAAATAGGAAAGGATACTCTGAATCGTAGAA
ATCATAGAAATAGAATGAAATATATGATCAACCAACATTTATCGAATTTTAAAAAGAGTCAGAAG
AGATGTTTCGATCCTCTTATTTTGATTTCTCGAACCGAGAGATCCATGAATCGGGATCCTGATGC
ATATAGATACAAATGGTCCAATGGGAGCCATAATTTCCAGGAACATTTGGACCATTTCGTTTCTG
AGCAGAAGAGCCGTTTTCGAGTAGTGTTCGATCGATTACGTATTAATCAATATTCGATTGATTGG
TCTGAGGTTATTGACAAAAAAGGTTTGTCTAAGCCATTTCGTTTC
Right flanking sequence: Indices 212198 -- 212697
CTTTGTGAGTTTCGGGAATATCCCCATTCATAGGTCCGAGATCTACATCTATGAATTGAAAGGTC
CGAATGATCAACTCTGCAATCAGTTGTTAGAATCAATAGGTCTTCAAATCGTTCATTTTAAAAAA
TTGAAACCCTTCTTATTGGATGATCATGATACTTCCCAAAAATCGAAATTCTTGATCAATGGAGG
AACAATATCACCGTTTTTGTTCAATAAGATACCAAAGTGGATGATTGACTCATTCCATACTAGAA
ATAATCGTAGGAAATCCTTTGCTAACACGGATTCCTATTTCTCAACGATATTTCACGATCAAGAC
TATTGGCTGAATCCCGTGAAACCATTTCATAGAAGTTCATTGATATCTTCTTTTTATAAAGCAAA
TCAACTTCGATTCTTGAATAATCCACATCACTTATGCTTCTATTGTAATAAAAGATTCCCTTTTT
TTTATGTGGAAAAGGCCCGTATCAATAATTATGATTTTACGTATG
Done.