Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MF611848
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: 352767
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:5912 original size:18 final size:19
Alignment explanation
Indices: 5883--5920 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
5873 TCAGAACTCG
5883 AAGTCAGAACTCCTTCTCT
1 AAGTCAGAACTCCTTCTCT
5902 AAGTC-GAACTCCTTCTCT
1 AAGTCAGAACTCCTTCTCT
5920 A
1 A
5921 TTTCACTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.32
Consensus pattern (19 bp):
AAGTCAGAACTCCTTCTCT
Left flanking sequence: Indices 5383 -- 5882
TAGCTCTGTGATTTGTTGAATAGTGCACTTCTACTCTTTTTGGGAAAGGAAGGGAAGAAGTCCTT
CTTCGCCGTATCTAGCTCCTGGAAAGAAATCGCATTGAAAAGCCCGATCTAGGTCATCCAAGTAG
AAATTTAAGAAAATAGGGTACAGGTGGCAGTCCTTTGTTTGGCAATACATTCTCTCCGGACTCAG
TTACAACTGTAATTTCCATATATGAAGCAATTAGCTCCATCAGAAATGGATCCTTTACTGCAAAT
GAGACTTTCCAAGAGTCTTGCGGCGGAAGCATGATGGCAAAGCAAGTTCAGCCTTCCCCCAGCCA
GAAATAGAAATGTGAGCTAGGTAATCTCTTTAACTCTTCTCCTTTCTACATGCGAAAGAACAAGG
ACCCTCTTTTCATTGAAAATAAAATTTATCATTCCAACAAGAGACGTTAGAAGGACTTTTTCCCT
GGGATCTACTATTCTAGAATAGAAAAACTACAAACTCAGAACTCG
Right flanking sequence: Indices 5921 -- 6420
TTTCACTTCCTATTATTTATGTCTTGTAAGAGAAGGAATACAGTAAGGCCTTCTAGAGGCTGCTG
GGCGATTTGAGAAAACTTAAACCTTAAAAGAAAGCCTTTTTTCGATAAAAGTCTATTGGGCGCGA
GAGGCGCTCTAGACTGACGGAGGTGAACTAGCATAGATGTCTTTCCTTGGATTCCCTCTACGCTA
CGATCTTTTGACTGGAGTTAAGTCGTAACAAGGTCCAGTAGTATCCAGCTTGCCTCACGAAAGGG
ATCAACTTAGGAAGTTTGAAAGAGAAGATAAGGCCTCAACTATTGGCCCTTAAGGCCGCTATTCC
TGATCACTTTTTTGGTCTCCTGAAGTCTATACTAATACTGAGGGGGTCAGAGTAGCTGTCTCGTA
CTCTGGGAACAAATGTGATTCCCATTCGTTAAGATACTTGCCCCACCACTGAAGTCGATTGAGAC
TGATATTCGCATCTATGAGGACAAGCAAGAGAAGATAATAGAATT
Found at i:11397 original size:22 final size:22
Alignment explanation
Indices: 11372--11421 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
11362 CGTTTACTTC
11372 ACTTTTATCATATATCAATGAT
1 ACTTTTATCATATATCAATGAT
11394 ACTTTTATCATATATCAATGAT
1 ACTTTTATCATATATCAATGAT
11416 ACTTTT
1 ACTTTT
11422 TCTCACATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.34, C:0.14, G:0.04, T:0.48
Consensus pattern (22 bp):
ACTTTTATCATATATCAATGAT
Left flanking sequence: Indices 10872 -- 11371
AGAATAAAAAGAAAAAACCTAATTACACTAGCTAAACTCTAGAACAGAAGTGTGCAAGCTTCAAG
CATTCGAAGGGAAGAAGCTTAATGTGTTATTGTTTTGTTCGCTTTCAATAAAGAAGTCAGATAGA
AGGACTAGATTGAGTTTAGGCCGTTAAGGGCTAAGAGAGAGGTCGTTACAAAAAGAATTTAGTGA
TTTACTTAAGACTTGAATTAAGGGTTCTGGGAAGACTTTTGAAGGTCTTCGCATGCTTAATGGGA
TCTTTTCTAAGATGAAATTAATCATGTTCGACGGTTTAACTAAGGAGATGGATCATCATCATCTT
GGTCTTTGATGTGCTTCTGTTCTTGTTGTTCCTTTTTATATAAATTTGGGAACATTGTTCATTTA
GCCAAAAATGCCCTCAGTATTAAAGATAATGTCTTTCTTTTATAATAATGTTGGGCCCTACCTTG
TCTCCCTTCCCCCCGGCTCATCCCTTTGACCGGTCCGTTTACTTC
Right flanking sequence: Indices 11422 -- 11921
TCTCACATTGGAATGCTTTGCATGATTTTGATCTTGTACCCACGGTGCGGTAGACTGAACACCAA
TATGAGATAGGTTGCAGCTATAGTCAGAACTGAACCTGGCAAATTTCGTAATTATGACCCCGGTA
GCGAAGGAGACAGCAAATGGATGGAAATTCTCCACTTGACTTTATGGCTGCCGCCGCTTCTATCT
CCGGCGCTCTGAATATCGGGTATGATTGTTACTTTCTTTGCCTGCCCCACTCCCACCCACCTCTT
CCGAAAAGACAAGCTTACCTCGAGCATTCATTACATATGATATATCGAGAGTTCAAGACCATAAC
GTAATTCTTTTAGATAATGCCGATAAGCAAGTAGACAAGTTGATTGATTGGATTGGAGGTTCAAG
AATGTAAGAAAGAGGGATAAGACCGAGGCCTCGGACTCTCTAGACTCCTCTGGTCTCTCTCGACC
GAGTGAACATGCCCACTACCTTCTTGGATCAAGGGCTTTCATAGA
Found at i:12822 original size:14 final size:14
Alignment explanation
Indices: 12803--12829 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12793 GTTATACGGG
12803 ATTAGCTCATTACA
1 ATTAGCTCATTACA
12817 ATTAGCTCATTAC
1 ATTAGCTCATTAC
12830 GAGGTCTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (14 bp):
ATTAGCTCATTACA
Left flanking sequence: Indices 12303 -- 12802
GGTACCAAAGATGGTGCGCCTTCAGAGGTGGGGCCCCAGTGCAGCTCTCAAAGGTTAAGATCTTT
TGTCAAGGGCTCAAGCGCAAAGAATTCTCCTCCTGCTTCTTCTTTTTGCTCTTCTTCAGGCGAGA
TCGAATGAGCTCACAACCTTCATAATAAAAAGTAGATGTGCTCGTCGTAAGGAAAGCAAAGGAGA
GTCAAATAAATCCAAGAAGCCAAGCCCGCTTACGTCTGCCTTTCTTTAGGTAGGACTATTGAATA
AAGCCCTTGAATGGATCTTCTCTTTTTGAGTTACTAAGGAACATGGTTATCCTTTTATATATATA
GAAGTCCACTTCCACTAGAGTGTCTAGATTGCCGATTTATCCTTCCTTGCCTTCAGTCAATCCGT
GAAGTTTCTTTCTATTATTTAAAAAAAGAAATAGACAGGATTTATGAGTGTAGGTGTACTGGTTC
TATGCTAAAGTCTCATACTTCTTTCTTTTTAGGAGGTTATACGGG
Right flanking sequence: Indices 12830 -- 13329
GAGGTCTCATATCTTTTTAGAGTCCCAATCCCCCTTAGATATACATCAAAAAATCCAATAGAAAG
ACTTGAACTAGACTATCCGATCCAATAGAAAGACTTGAACTAGACTATCCGAATGGGATATCTTG
AATCCTTTGCTCTACCGACTGGCATATCTTGAATCCTTTGCTCTACCATGGATTGACTGGCATTA
GAAGGAAAGCGTATTACTTGAAGTGGATCTCCTATCTATATTCAACAGCTTGAAGAGGCACTATT
GGCTACATAGAAGTCATTGAAAGCTCTAAAGCTTACCTTGATCTAGAAGTCATTGAAAGCTCTAA
AGCTTACCTTGATCCAATACTTCCGGAAGACATGAATCCCTTTTACAGCTATAGTAGAGATGCAA
GTTCCACGCCTTTAATTACTTTCTTTTTAATCGCTAGTAAAGGATGACATTACTCTAACTAAGTC
TTTGTTTAAGGGTAAAGGAACTAACAAGACAGTAAAGGTGAGGAA
Found at i:12923 original size:32 final size:32
Alignment explanation
Indices: 12882--12946 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
12872 ACATCAAAAA
12882 ATCCAATAGAAAGACTTGAACTAGACTATCCG
1 ATCCAATAGAAAGACTTGAACTAGACTATCCG
12914 ATCCAATAGAAAGACTTGAACTAGACTATCCG
1 ATCCAATAGAAAGACTTGAACTAGACTATCCG
12946 A
1 A
12947 ATGGGATATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.22
Consensus pattern (32 bp):
ATCCAATAGAAAGACTTGAACTAGACTATCCG
Left flanking sequence: Indices 12382 -- 12881
GCGCAAAGAATTCTCCTCCTGCTTCTTCTTTTTGCTCTTCTTCAGGCGAGATCGAATGAGCTCAC
AACCTTCATAATAAAAAGTAGATGTGCTCGTCGTAAGGAAAGCAAAGGAGAGTCAAATAAATCCA
AGAAGCCAAGCCCGCTTACGTCTGCCTTTCTTTAGGTAGGACTATTGAATAAAGCCCTTGAATGG
ATCTTCTCTTTTTGAGTTACTAAGGAACATGGTTATCCTTTTATATATATAGAAGTCCACTTCCA
CTAGAGTGTCTAGATTGCCGATTTATCCTTCCTTGCCTTCAGTCAATCCGTGAAGTTTCTTTCTA
TTATTTAAAAAAAGAAATAGACAGGATTTATGAGTGTAGGTGTACTGGTTCTATGCTAAAGTCTC
ATACTTCTTTCTTTTTAGGAGGTTATACGGGATTAGCTCATTACAATTAGCTCATTACGAGGTCT
CATATCTTTTTAGAGTCCCAATCCCCCTTAGATATACATCAAAAA
Right flanking sequence: Indices 12947 -- 13446
ATGGGATATCTTGAATCCTTTGCTCTACCGACTGGCATATCTTGAATCCTTTGCTCTACCATGGA
TTGACTGGCATTAGAAGGAAAGCGTATTACTTGAAGTGGATCTCCTATCTATATTCAACAGCTTG
AAGAGGCACTATTGGCTACATAGAAGTCATTGAAAGCTCTAAAGCTTACCTTGATCTAGAAGTCA
TTGAAAGCTCTAAAGCTTACCTTGATCCAATACTTCCGGAAGACATGAATCCCTTTTACAGCTAT
AGTAGAGATGCAAGTTCCACGCCTTTAATTACTTTCTTTTTAATCGCTAGTAAAGGATGACATTA
CTCTAACTAAGTCTTTGTTTAAGGGTAAAGGAACTAACAAGACAGTAAAGGTGAGGAAAGAACTG
AACTAACTCAACTGTAAAGGAAAGGAGAGGTTATCAGAGCTTTTAACCTTTCCGATAGTCCAGTA
CCCCTAATGTCCGATAGTCCAGTACCCCTAATGTTAGTAGTTCAA
Found at i:12988 original size:31 final size:31
Alignment explanation
Indices: 12943--13006 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
12933 ACTAGACTAT
*
12943 CCGAATGGGATATCTTGAATCCTTTGCTCTA
1 CCGAATGGCATATCTTGAATCCTTTGCTCTA
*
12974 CCGACTGGCATATCTTGAATCCTTTGCTCTA
1 CCGAATGGCATATCTTGAATCCTTTGCTCTA
13005 CC
1 CC
13007 ATGGATTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.34
Consensus pattern (31 bp):
CCGAATGGCATATCTTGAATCCTTTGCTCTA
Left flanking sequence: Indices 12443 -- 12942
TCACAACCTTCATAATAAAAAGTAGATGTGCTCGTCGTAAGGAAAGCAAAGGAGAGTCAAATAAA
TCCAAGAAGCCAAGCCCGCTTACGTCTGCCTTTCTTTAGGTAGGACTATTGAATAAAGCCCTTGA
ATGGATCTTCTCTTTTTGAGTTACTAAGGAACATGGTTATCCTTTTATATATATAGAAGTCCACT
TCCACTAGAGTGTCTAGATTGCCGATTTATCCTTCCTTGCCTTCAGTCAATCCGTGAAGTTTCTT
TCTATTATTTAAAAAAAGAAATAGACAGGATTTATGAGTGTAGGTGTACTGGTTCTATGCTAAAG
TCTCATACTTCTTTCTTTTTAGGAGGTTATACGGGATTAGCTCATTACAATTAGCTCATTACGAG
GTCTCATATCTTTTTAGAGTCCCAATCCCCCTTAGATATACATCAAAAAATCCAATAGAAAGACT
TGAACTAGACTATCCGATCCAATAGAAAGACTTGAACTAGACTAT
Right flanking sequence: Indices 13007 -- 13506
ATGGATTGACTGGCATTAGAAGGAAAGCGTATTACTTGAAGTGGATCTCCTATCTATATTCAACA
GCTTGAAGAGGCACTATTGGCTACATAGAAGTCATTGAAAGCTCTAAAGCTTACCTTGATCTAGA
AGTCATTGAAAGCTCTAAAGCTTACCTTGATCCAATACTTCCGGAAGACATGAATCCCTTTTACA
GCTATAGTAGAGATGCAAGTTCCACGCCTTTAATTACTTTCTTTTTAATCGCTAGTAAAGGATGA
CATTACTCTAACTAAGTCTTTGTTTAAGGGTAAAGGAACTAACAAGACAGTAAAGGTGAGGAAAG
AACTGAACTAACTCAACTGTAAAGGAAAGGAGAGGTTATCAGAGCTTTTAACCTTTCCGATAGTC
CAGTACCCCTAATGTCCGATAGTCCAGTACCCCTAATGTTAGTAGTTCAAGTTGAAAGAGAAAGA
CAAGCAAGAAGTACACGAATCCGGATCAGAGAATAGGTAACATGA
Found at i:13137 original size:36 final size:36
Alignment explanation
Indices: 13097--13168 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
13087 ATTGGCTACA
13097 TAGAAGTCATTGAAAGCTCTAAAGCTTACCTTGATC
1 TAGAAGTCATTGAAAGCTCTAAAGCTTACCTTGATC
13133 TAGAAGTCATTGAAAGCTCTAAAGCTTACCTTGATC
1 TAGAAGTCATTGAAAGCTCTAAAGCTTACCTTGATC
13169 CAATACTTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (36 bp):
TAGAAGTCATTGAAAGCTCTAAAGCTTACCTTGATC
Left flanking sequence: Indices 12597 -- 13096
TAAGGAACATGGTTATCCTTTTATATATATAGAAGTCCACTTCCACTAGAGTGTCTAGATTGCCG
ATTTATCCTTCCTTGCCTTCAGTCAATCCGTGAAGTTTCTTTCTATTATTTAAAAAAAGAAATAG
ACAGGATTTATGAGTGTAGGTGTACTGGTTCTATGCTAAAGTCTCATACTTCTTTCTTTTTAGGA
GGTTATACGGGATTAGCTCATTACAATTAGCTCATTACGAGGTCTCATATCTTTTTAGAGTCCCA
ATCCCCCTTAGATATACATCAAAAAATCCAATAGAAAGACTTGAACTAGACTATCCGATCCAATA
GAAAGACTTGAACTAGACTATCCGAATGGGATATCTTGAATCCTTTGCTCTACCGACTGGCATAT
CTTGAATCCTTTGCTCTACCATGGATTGACTGGCATTAGAAGGAAAGCGTATTACTTGAAGTGGA
TCTCCTATCTATATTCAACAGCTTGAAGAGGCACTATTGGCTACA
Right flanking sequence: Indices 13169 -- 13668
CAATACTTCCGGAAGACATGAATCCCTTTTACAGCTATAGTAGAGATGCAAGTTCCACGCCTTTA
ATTACTTTCTTTTTAATCGCTAGTAAAGGATGACATTACTCTAACTAAGTCTTTGTTTAAGGGTA
AAGGAACTAACAAGACAGTAAAGGTGAGGAAAGAACTGAACTAACTCAACTGTAAAGGAAAGGAG
AGGTTATCAGAGCTTTTAACCTTTCCGATAGTCCAGTACCCCTAATGTCCGATAGTCCAGTACCC
CTAATGTTAGTAGTTCAAGTTGAAAGAGAAAGACAAGCAAGAAGTACACGAATCCGGATCAGAGA
ATAGGTAACATGAACCGGGAGATGGGAATACCAATTACTCTATTGAACCGGGATAGAGAGATGCA
GGAACGTAGTAACTCGACTGAAAGGAGAGGGTAGAAGTGAGTCGACCAGCGGGAGAGGAACGAAC
GAGACTGATAAGGAGAGGTCGGAAGTGATTGGCACGGGAGCTCCT
Found at i:13166 original size:21 final size:21
Alignment explanation
Indices: 13106--13166 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
13096 ATAGAAGTCA
13106 TTGAAAGCTCTAAAGCTTACC
1 TTGAAAGCTCTAAAGCTTACC
*
13127 TTG--A--TCTAGAAG--T-CA
1 TTGAAAGCTCTA-AAGCTTACC
13142 TTGAAAGCTCTAAAGCTTACC
1 TTGAAAGCTCTAAAGCTTACC
13163 TTGA
1 TTGA
13167 TCCAATACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 16
0.62 0.04 0.33
Matches are distributed among these distances:
15 4 0.13
16 1 0.03
17 5 0.17
18 6 0.20
19 5 0.17
20 1 0.03
21 8 0.27
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (21 bp):
TTGAAAGCTCTAAAGCTTACC
Left flanking sequence: Indices 12606 -- 13105
TGGTTATCCTTTTATATATATAGAAGTCCACTTCCACTAGAGTGTCTAGATTGCCGATTTATCCT
TCCTTGCCTTCAGTCAATCCGTGAAGTTTCTTTCTATTATTTAAAAAAAGAAATAGACAGGATTT
ATGAGTGTAGGTGTACTGGTTCTATGCTAAAGTCTCATACTTCTTTCTTTTTAGGAGGTTATACG
GGATTAGCTCATTACAATTAGCTCATTACGAGGTCTCATATCTTTTTAGAGTCCCAATCCCCCTT
AGATATACATCAAAAAATCCAATAGAAAGACTTGAACTAGACTATCCGATCCAATAGAAAGACTT
GAACTAGACTATCCGAATGGGATATCTTGAATCCTTTGCTCTACCGACTGGCATATCTTGAATCC
TTTGCTCTACCATGGATTGACTGGCATTAGAAGGAAAGCGTATTACTTGAAGTGGATCTCCTATC
TATATTCAACAGCTTGAAGAGGCACTATTGGCTACATAGAAGTCA
Right flanking sequence: Indices 13167 -- 13666
TCCAATACTTCCGGAAGACATGAATCCCTTTTACAGCTATAGTAGAGATGCAAGTTCCACGCCTT
TAATTACTTTCTTTTTAATCGCTAGTAAAGGATGACATTACTCTAACTAAGTCTTTGTTTAAGGG
TAAAGGAACTAACAAGACAGTAAAGGTGAGGAAAGAACTGAACTAACTCAACTGTAAAGGAAAGG
AGAGGTTATCAGAGCTTTTAACCTTTCCGATAGTCCAGTACCCCTAATGTCCGATAGTCCAGTAC
CCCTAATGTTAGTAGTTCAAGTTGAAAGAGAAAGACAAGCAAGAAGTACACGAATCCGGATCAGA
GAATAGGTAACATGAACCGGGAGATGGGAATACCAATTACTCTATTGAACCGGGATAGAGAGATG
CAGGAACGTAGTAACTCGACTGAAAGGAGAGGGTAGAAGTGAGTCGACCAGCGGGAGAGGAACGA
ACGAGACTGATAAGGAGAGGTCGGAAGTGATTGGCACGGGAGCTC
Found at i:13419 original size:24 final size:24
Alignment explanation
Indices: 13387--13435 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
13377 TTTTAACCTT
13387 TCCGATAGTCCAGTACCCCTAATG
1 TCCGATAGTCCAGTACCCCTAATG
13411 TCCGATAGTCCAGTACCCCTAATG
1 TCCGATAGTCCAGTACCCCTAATG
13435 T
1 T
13436 TAGTAGTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (24 bp):
TCCGATAGTCCAGTACCCCTAATG
Left flanking sequence: Indices 12887 -- 13386
ATAGAAAGACTTGAACTAGACTATCCGATCCAATAGAAAGACTTGAACTAGACTATCCGAATGGG
ATATCTTGAATCCTTTGCTCTACCGACTGGCATATCTTGAATCCTTTGCTCTACCATGGATTGAC
TGGCATTAGAAGGAAAGCGTATTACTTGAAGTGGATCTCCTATCTATATTCAACAGCTTGAAGAG
GCACTATTGGCTACATAGAAGTCATTGAAAGCTCTAAAGCTTACCTTGATCTAGAAGTCATTGAA
AGCTCTAAAGCTTACCTTGATCCAATACTTCCGGAAGACATGAATCCCTTTTACAGCTATAGTAG
AGATGCAAGTTCCACGCCTTTAATTACTTTCTTTTTAATCGCTAGTAAAGGATGACATTACTCTA
ACTAAGTCTTTGTTTAAGGGTAAAGGAACTAACAAGACAGTAAAGGTGAGGAAAGAACTGAACTA
ACTCAACTGTAAAGGAAAGGAGAGGTTATCAGAGCTTTTAACCTT
Right flanking sequence: Indices 13436 -- 13935
TAGTAGTTCAAGTTGAAAGAGAAAGACAAGCAAGAAGTACACGAATCCGGATCAGAGAATAGGTA
ACATGAACCGGGAGATGGGAATACCAATTACTCTATTGAACCGGGATAGAGAGATGCAGGAACGT
AGTAACTCGACTGAAAGGAGAGGGTAGAAGTGAGTCGACCAGCGGGAGAGGAACGAACGAGACTG
ATAAGGAGAGGTCGGAAGTGATTGGCACGGGAGCTCCTTTACCTTTAAGCGTTCTGGTAGGTATC
CGAAGCCAATACAGTCTAAGTGTGAGCCTGGCCGGCGCCTGAGGCCCCAGGACGTATATCAACTA
AAAAGTCTTATCTTTTAGAGAATAGCTTTAGGTTCTCCTTAATATATCTGTTAGGAAGCGAAGGA
TACCTTTGGTAAGGGATCCAAGCGCCTTAAGGTGCAGGTAAAGGGTAGCTCCTTTTATCTCTTTA
AAAGGGTAGCTACTCCTATCTCTTAAAGTGTTATGTAGCGCAGGA
Found at i:13910 original size:26 final size:26
Alignment explanation
Indices: 13865--13914 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
13855 AGGTGCAGGT
* **
13865 AAAGGGTAGCTCCTTTTATCTCTTTA
1 AAAGGGTAGCTACTCCTATCTCTTTA
13891 AAAGGGTAGCTACTCCTATCTCTT
1 AAAGGGTAGCTACTCCTATCTCTT
13915 AAAGTGTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (26 bp):
AAAGGGTAGCTACTCCTATCTCTTTA
Left flanking sequence: Indices 13365 -- 13864
GGTTATCAGAGCTTTTAACCTTTCCGATAGTCCAGTACCCCTAATGTCCGATAGTCCAGTACCCC
TAATGTTAGTAGTTCAAGTTGAAAGAGAAAGACAAGCAAGAAGTACACGAATCCGGATCAGAGAA
TAGGTAACATGAACCGGGAGATGGGAATACCAATTACTCTATTGAACCGGGATAGAGAGATGCAG
GAACGTAGTAACTCGACTGAAAGGAGAGGGTAGAAGTGAGTCGACCAGCGGGAGAGGAACGAACG
AGACTGATAAGGAGAGGTCGGAAGTGATTGGCACGGGAGCTCCTTTACCTTTAAGCGTTCTGGTA
GGTATCCGAAGCCAATACAGTCTAAGTGTGAGCCTGGCCGGCGCCTGAGGCCCCAGGACGTATAT
CAACTAAAAAGTCTTATCTTTTAGAGAATAGCTTTAGGTTCTCCTTAATATATCTGTTAGGAAGC
GAAGGATACCTTTGGTAAGGGATCCAAGCGCCTTAAGGTGCAGGT
Right flanking sequence: Indices 13915 -- 14414
AAAGTGTTATGTAGCGCAGGACCCCTTGGGGGCAGGTAACCCTAACTCCTTAACTCCTTACGCTA
AAGAAATGGATAGATAACTACCTATATCCCCTCCGGGTAAGAGTAGGACTGTAAGCTTGGGTGTT
TGCCCTGGCCTTGTAGCTACCCCTCAAAGGGGCGATTGTACAAAGACAGTTTCTAAGGAATCTAA
AGACTGAGCTACCCTTTTCCTTAGTAGTTTAGGAATCAAAAGTGCTGGTCTCGCCTTTCGTCTTT
CTTCCTATTTCCTAAGCGTGGCGAATCTGTATCGAGTCAGCTTCCTGCGGATCCGGCTTAAGAAG
TAAGAAATTTCCCTTTGTCGAGGGTATAGTAGTGAAACTTGAGTGGCAACTTCCCCAGCCTCATC
CGTTTTTCAAAATCGCATACTTAACCTCCCCAGAAACAACCCACATACCACTCTTTTTTCTGTTC
TAGGGATAAACCAGGAGGACAGGAAACCTAGGGGGGTGACCGACG
Found at i:26223 original size:13 final size:13
Alignment explanation
Indices: 26205--26231 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
26195 CATTACTATA
26205 GTGAATAGATAGG
1 GTGAATAGATAGG
26218 GTGAATAGATAGG
1 GTGAATAGATAGG
26231 G
1 G
26232 GCATTCCGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (13 bp):
GTGAATAGATAGG
Left flanking sequence: Indices 25705 -- 26204
TGTGTTATTAGCATTTAGAGGGATTAACAAGGCACTGAAAGTGAAAGCTGTCTAACCGCTCTAAG
CCAGTTGTTGAAGTGAGTTAAGGTCTTTCTCTTTCCGAGTTCAGCCTGGGAGTTCGAAGAAGATT
AGTTCAATAGCCAAAGCGGACCAGAGAAGGTTAGTTTAATGATCCGCAGAGATAGATCAAAGAAA
AGCTGACCGAGGCAGAAAACAAAAGAATAAAAGGGAAAGAAAGTCAAGCTTGATTGGCTAAGAGA
CATAGGTAAGGTTTTTTACTGAAAGAGGTTTCACTCTTACATATACTTAGTATACGAATAAGAGA
AGAGCACCTACACCTACGCCTAAGAAGAGAACAAGTTCATCATCAACCGGAAGCTTGCAGCAACA
GGAAATCCAGTAATGCACGAAGGAGACAGAGATTAGTGAGCGTAGGTGATAGATCCAATAAGAGG
AGAGGCAGAGGGCAAATGAGTAGACGAAATTTTAGCATTACTATA
Right flanking sequence: Indices 26232 -- 26731
GCATTCCGCTAGCGTAAAGTGAAATATATATTATATAAGGAATGAAAGCCACTCCTGCTCTACTT
CCTTATAAGAGACTCGCTACTAAGGTTCTTAAAGGTGCGCTTTTCCTGGATTGCTATTCCAGCTT
GGCTTTCCTCGGGGAGGGAAACAAGCGGCTAAGCTAAAACTGTAACGAGTGTAGCTACGAAGGAA
TGCTTTCTCATTGAACAAAAAGAATAGCCGGTCTTTGTTTTTGCTGTTACAGAAGAAGCAGCTCT
TGGCCTTTTGCTTGGCACTAGGAAGAGAAAAGAAAGATCTTAGGGCTAGGCCCTTTAGGCCAATT
AAGAGATCAGACTTCACTTCAAGAACTAACGAAAATAGCCCTGATCAAGCGGAAGAAATGCTTGC
TCTCAGCTTTATGTTAGAAAAAGTCCGTTGCTATTGGACTTGGCTAGTAAGCCAAGAGGGAATCA
GTCTTAACTAAGCCAAAAGACTAGCGAACGAGGGGAAAAAGAAGC
Found at i:78023 original size:2 final size:2
Alignment explanation
Indices: 78016--78047 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
78006 AGGGCTATGC
78016 TA TA TA TA T- TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
78048 GAAGCAGCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 77516 -- 78015
GAAAATATAGATAGATACATCTTTGAAGGGGTCGTACGATCGATTGCTTTTTCACTGCCGGGCAG
GCATAACTAGTAACTTTACTCTTTCTAAACCCCCTTAGATGAGGCAAAGGCCGGAGCTGCTACAA
TAGCTTTAGCGGGAGCTGGAGGAAATAACACTGATAGATGGACGTGAGAAAGCTCTTTTATAATT
ATAAAATTTTTGTCTGGTATCGTGTGGTATATGGGCGGGAGGAGAATAAGAGTCTCGTCTCATCT
TTCAGCTGGAGTTAAGGCTCTCCTGTAAGAACTCTGGAAGGAATTGGTAGACAAAGCATAATGCT
TCTTACAAGCGAAAGAAAGATTAGCTCGATCCCAGGAGCGTAGATGGAATCTGTCGAGGAGCACT
TCTCGGGGTAGCATCGCCCAGGTTGAGAAGGAATCGCTTAGGTTTCTTCGGAACCAGAAGAATAG
GAATGATTACTTGACGTAATCTCAATATCAGAAAAAGGGCTATGC
Right flanking sequence: Indices 78048 -- 78547
GAAGCAGCGTCTCTATCTCTTAGTGAGCTAGCCGCTACTATAGTTTTAAGGGATTTGTGCAATGA
ATTCTTTTCTGCCAGTTTCGAGTGGGAGTCTAAATCAACCCATTTTAAAGCAAGATAGACCAAAC
GACTTTACTGTAGGAAGAATCCCAGAAGAGGTGATACACTGATTCTGGATGCAACTCACAAAGAC
AGCAAGTTTCATCATCAATAACTCTATCGTATTGAGAGCTCTTTTGATCCCATCCATTCCTTTAT
CGTCTGATCCAGTGATTAGTTAAGTTAGAAGAATGGAATTACTTCCATATGCGGGCAGATATGCA
TTAACAAGCTTATTGAAGGGAAGTTCCCCGCTCTCGAATAAAAAAGTAAGCTGACTATCCCGCAG
TGAGCGCTACCTAAGCACTGTTGAAGGCACTCAGAGAAGAGTGGAAAGAGTCCTAAGAGGGCTTC
TCACTAAGACTTTCGACTCCGATGCCTTTGAATCCGTTGATTGAA
Found at i:116194 original size:14 final size:14
Alignment explanation
Indices: 116175--116201 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
116165 TACTTGTGAT
116175 TTCATTTTCTTTGG
1 TTCATTTTCTTTGG
116189 TTCATTTTCTTTG
1 TTCATTTTCTTTG
116202 ATTTATCCGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.11, T:0.67
Consensus pattern (14 bp):
TTCATTTTCTTTGG
Left flanking sequence: Indices 115675 -- 116174
ATCCTAAACAAATAGAATCCCTTCCGGTCGGGAAGATGCAGATAAAAAAAAAGGCCAATAGCCTG
CTTCTACGGCATAAGCTTTAAAGAAGAAGAGAGCTATCATTTCATAAGAAAAATTTGTTGTTTAA
ATCTCAAAGGTATAGGTTAAATTTGGAACAGTAGTCATTTCAATCTTTTTTTTCGAAAGAAAAAT
CCGTCAATAAATGACGAACTCCATTATACAGATGATAGGACAGGGCTAAGGCAGTAATCTCGACG
GCGATTAGGATGAGCTTTGATGAATAAAAGAAGAATAGGTAGAAATTTTCATAGGTGAAGCAAAT
CAAACCTATTTTAAGACAAAGAAGATAAAAAAACAAAACTATAGTGACTAGGGAAGCTCCGGAAA
TTCTATGGGAAATTGGAAACGTCGAAGTGAGCTGTGGCTTATAAATAGGAAGATGAGGAGATAAC
GGGCGAAGGATATGCAATTTCTTATTATTAGAATTTACTTGTGAT
Right flanking sequence: Indices 116202 -- 116701
ATTTATCCGCTCCTCCCAAAAAAAGAGAAAGACTTTTCATTTAAATACGGGTTGTTGGCTTTTTT
CCAACAAAGACATGGGACACGTATATTGTTTCTATGACTATAATACGATATTTTCATTTAGCTAT
AGAGATCATAAGAATACTTTACTTTTCCCAACAGGTAAATTCGTAGGTGTGTATTTTAGCGAAGA
ATTTCTTTATGCACGCGACTTGGCTTCAGCTCTCGAACCGGTTATCAACCAAGCTACAAGCAAAA
CTAAGGCGGAAAGTAGTACGGTTGGGTCCTTTTTGCTTTCCCTTGGGATTAAAGCAATGTTCAGA
AGATCGGATCAGAGAATTTCAGTTACGCTAAGTTCATGAACTCTTTCAGACTCTCTCTCTATGAT
CGAGTCAGACCCTTGTTCGCTTGTTAGCTCGTCTCCTTTCGTATATAAAGGCTCAACTGTTCTGT
AAAGGACTGCTCCTAAGGCTTCAGCTAGCAGAGCACTTAAGACAG
Found at i:213838 original size:13 final size:13
Alignment explanation
Indices: 213820--213844 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
213810 CGTTCGTGCC
213820 AGCAAGAAAACGG
1 AGCAAGAAAACGG
213833 AGCAAGAAAACG
1 AGCAAGAAAACG
213845 TATGTGCGGC
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:0.56, C:0.16, G:0.28, T:0.00
Consensus pattern (13 bp):
AGCAAGAAAACGG
Left flanking sequence: Indices 213320 -- 213819
ATCCCTAAAGAGATGCCTAAAGGGCACAAAACCAAAACAGGGGTTAAAGATGGCACGGTTTCCGC
TTTCCCGGTTTGATCAGGTGGCAGCTGTCGGGGTACTGGTAACTAGCTTTGGTGCCTCTCTCTTC
TTCTCTAACGGCTGTCGGCCTGCGTGGTCTTGAATAGTGGTTCCTCGGTTGCCTGAAGGTCTCTT
TGAGGTTTAAAGGGGCTGGCTACAGGCGGTATTCGTCTTTGGCTAAGGAAAAGAAAACCTCAATA
TAACCGACACTGGTATAGGCACGTTTTGGTGGCCTTCTCGCCTTTCTAGGCCTCTCCTCTTAATA
GGGTGAGTTACACTTATTAGTATGAGCCTGCCCTGCCTGCTCGTTAGCTGTAGGCTTGAACCCCT
AACCCGTCTAAGGCCCTGTCTAAGGCAAGGTCCTTGCTTGTTGGCTGGCTTTCTATCGTTAGCGC
AGGAGGAAGATTGCTGACGGATTCCTTCTTCTTCTCGTTCGTGCC
Right flanking sequence: Indices 213845 -- 214344
TATGTGCGGCTAACGCACCACGTGCGTAGCTGCTCGAGCGAAGCGAGAGGAGAAGTCGAACGAAC
TGGTAATATAATAGAATACATAACGCGCTGGAGATAAATCAACCAGAAATCCTTAAGCTCAAGCT
CCAGTTCAGTGAGCAAAGAAGAAAGCAGGTATGAAATCATTCTAAGCGAAAGGAGCGGTGGAAGC
AGTGGCTAAGCTTCGATAATGTCTAATTTCCTTCTTAATAAGGCCGGCCTACCTTGATATGAGGG
TATGAAGTATCTCGACCAGAGGGAGAGGGTATGGAGTTATCTGAATATGCTTTAGCTGTAACAGC
GGGAGTAGAAAAGCAGCTGTAATTCTTTGGTTTGGAAAAGGCCGATTCTCAGCCCATGGGTATTC
GAAAAGGCCTTAGTTGCCCGGTTAGTAAATGTCCCCCCACTCTCCTGGGGTTCAATAAGAAGGAT
TTCTCCCCGGAAGTAACTGAACTTGAGCTAGGGAAAGATTAAGAC
Found at i:227643 original size:13 final size:13
Alignment explanation
Indices: 227625--227651 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
227615 ACTAATATAT
227625 ATAGACCTAATAA
1 ATAGACCTAATAA
227638 ATAGACCTAATAA
1 ATAGACCTAATAA
227651 A
1 A
227652 GTAATACTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (13 bp):
ATAGACCTAATAA
Left flanking sequence: Indices 227125 -- 227624
TCCACTTTAGGAAGCAATATTGATGATTAATGAAACCCTACGGGTTTTCAAGCATAAATCCCGGG
AAAAGACCCACTTGTAGGTGCCATGAGACGAGACGGGATAGAGCCTGAGACCCCGATGTCAGTAA
AGAAAAACTACCGTTTTTCATTCCTCATTAAATGACTAATTCTACCTTCTCCTACTTCTCCAACT
TCTGCTTCTGCGGATTCCGCTTACCCTGAAACTGATTCTGAAACTTCATCAAATACTGCAACTGA
TTCTGTCCATGAAACTGATTCCTATTCAACTGATTCCGAAACTGATTCGGCAACAGAAACTTCTT
CTACTGATGCTGATGCTGCTTCTTCTGCTGATTCTTCTCCTACAATCGGCTCCGGTCCGGAGGAA
GGCACAAACGATAGTAAGTCAGTTGCTAGTAAGTCTCTGTCTTAGTAGTTCGGTGCCCTTCGCGA
GACCCTGTAGAGCGAAAAAGACATCAATCATACCTACTAATATAT
Right flanking sequence: Indices 227652 -- 228151
GTAATACTCACAGATCGAAAGACGGCAGCGCTTGGGAGATGCTAAGGTAGGGTTACGTTTTATGG
TAGGGTATGGTTCGAGATATTGCTAAATTAAGTACATGAATTTTCTTATTTCACCGGAGGGGAGG
AGAGTGAAGGGACACCTGATCTTGATCTGATTAGTAGTAAAGTCGCTAAGGCCCTAGACTAATAA
TTGTTCTCGGCTGCCCTACACTAATAAGGCAAGGAAGAAGGGCCTTAGGCCAACGACGGGGGATA
GGGCCAACGACTGGTTACGGGATAGGGACTGAATAGCTACTGACTGATGGACCGATGGGTTCCGG
AAGGTTGGCTGGCAAGGATGGTTGGCGAAGAAGATCTAAGGTCTGCTGAGGGCGTAGAATAGAAG
GTGGGCTCGAATTGGCTCGAAGGTTGGGGGGAAAGGGGTTGGTGTGGTCTCACTCAAAGAAGCAG
CCGAGCCAGAGCCTTTAGTTGATGTCTTTTCGGTAGCAGTCCCAA
Found at i:237293 original size:26 final size:27
Alignment explanation
Indices: 237256--237307 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
237246 TTTGTTGCGA
*
237256 AAGATGGAATAAGTAAT-CTGCAATGG
1 AAGATGGAATAACTAATGCTGCAATGG
* *
237282 AAGATGGGATAACTAATGCTGGAATG
1 AAGATGGAATAACTAATGCTGCAATG
237308 AATAAGTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.40, C:0.08, G:0.29, T:0.23
Consensus pattern (27 bp):
AAGATGGAATAACTAATGCTGCAATGG
Left flanking sequence: Indices 236756 -- 237255
TTCTTTTTGATACCGCCTTTTTGGCTATTCTCGTAAATAAGCATTTCTTGGAAGCGAGGATCAAC
CCCTCTTTGTTGGTGTCTAAAATCCCGCACTTTTAGTATTCTTTCGACGATCTATCCGATTTCTA
AGTGAACCTAGTCTTATGCCTAAGACATGAAGGTAAAGTCGTAGATGACGCCTACTTCCTTTCGA
ATGCTTTCGAATGAGACTTGAACCAGAATCGTTTTCTAAGAAAGAAGGGGCTTTAGCCAATAAAG
CATGCTATAGCTTCAGGGGCGATCGATTTAGTAGGGGTGGATCGAGGCGCTTTTTAGCGGACAGC
ATAAATGTAATACGGTGACCAAAAAGAGACAAGAAAACGAGGTCGAAAATGGTAGGTAGGTATTA
CATCACCGGGAACAAGATTCTTTCACACGAATTCGGAACTTGGCTCGATCATCAAAAAAAGTCAT
CGTTGCCGTTTTACGCTTTTTTGGCATGTTCTCTTTTTGTTGCGA
Right flanking sequence: Indices 237308 -- 237807
AATAAGTTTCTATATATAACCTCTAAACCCACTTTCCTTGCGTCAGTGTCCTTATACACTCGCCC
TATTCTTTTTGAAATAGATCTGGGCGGAAATGTCTTATTATATCTTATATCTAAGATATACATCT
TTGAGCAAGAAATCCCCATTTGAATGATTTACAATCGATATCATTACTCATACTGAAACTGAAAA
AGTCGTCTTTTTTAAGATCCAAGAAATTCCAGTACCTAGATAAAACTTTTGAATCTTCTTTCGCC
CTTTTAATTGACATAGACCCCCGCCCTCTAATAAAATGAGGATGCTACATTGGGACTTAGTCGGG
ATAGCTCAGCTGGTAGAGCAGAGGACTGAAAATCCTCGTGTCACCAGTTCCAATCAGGTTCCTGG
CACATGATTAATTTGGATGAGTCTCTCTTGAATAAATTAATTGATATGAATCGACATCCCTATTC
ATTTTGAGTTTGGATCATAACACATACTTTTATCCATCTCGCCGA
Found at i:244753 original size:29 final size:29
Alignment explanation
Indices: 244699--244758 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
244689 CCAATTTATT
* *
244699 TTATTATTAATATTAATAATATTAATTAA
1 TTATTATTAATATAAATAATAATAATTAA
*
244728 TTATTATTGAT-TAAATAATAAATAATTAA
1 TTATTATTAATATAAATAAT-AATAATTAA
244757 TT
1 TT
244759 TTAAATTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
TTATTATTAATATAAATAATAATAATTAA
Left flanking sequence: Indices 244199 -- 244698
AAGAACTCAATAGAATATAGAATAAGGATATACAAACAAGAACCAATCCTAACGAAAAGGCCGAA
AAAATGGGATTGGGAAGTAATACTACTCCTAGACCTCCTAAGATCAGACCCGATCCCAGAAAGAC
TAAAATAAAATCATGCATTGGCCCGGGTAAATCCATAAAATCCAAATCTCAATATTTCATGATTT
TATTGACCTGACCAGGAAAAAAGAAGTAACTCCATTTTTTTTTTGTTTATGATACTTCTTAACTT
AAACGTAATTAAATAAATAAAATTGGAACAGATGCGGGCGGGTTGATATATATAGTGTTATTAGC
CCTAATCATTCAATATCTGGAAAATTGTTTGAAAATATATATATTACTCTAATATAAATAGAAAA
TCTAAATATAGAAATACATTTTTCATCAAAATGAAATGACAAGTTTAAACAACTTTTTCAAAGCC
TTATTTTGAGAGATGCAACCTAATTTCATTTATTTCCAATTTATT
Right flanking sequence: Indices 244759 -- 245258
TTAAATTGAATTGTTAATTGGGGATTTTTTTGAATTGAGAGGTTTAAGTTTAACTATTTTATATT
TTATTTCTATTGGAGGCGAATTCGAAATTGTGCGAATTGTGTAATCATCAATTACTGACGTTGGT
AACCGACCCAAAGCAATTTGATTAGAATTAAATTCGTGACGATCATAACTTGAAAGTTCATATTC
TTCAGTCATTGATAAACAATTTGTTGGACAATACTCAACGCAATTACCACAAAATATACAGATTA
AAAAAAAAATACTGTAATTAAACAATCGTTTCTTTCGAATATCACTTTCCAATTTCCAATCTACA
ACAGGTGGATCTATAGGACATACACGAACGCATACTTCACAAGCAATGCATTTATCAAATTCAAA
GTGAATTCGGCCCCGGAAACGTTCCGACGTAATTAGTTTTTCGTAGGGATATTGAATAGTTATAG
GTAAACGATTCGCGTGAGACAGGGTAATCGCGAAACCTTGACCGA
Found at i:253259 original size:23 final size:21
Alignment explanation
Indices: 253217--253284 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
253207 ACTTCCTTTC
253217 TTTTTGTCCAAGTCACTTCTT
1 TTTTTGTCCAAGTCACTTCTT
**
253238 TTTTTGTCCAAGTTGCTT-TT
1 TTTTTGTCCAAGTCACTTCTT
* * *
253258 CTTTTTGTCTAACTCACTTCCT
1 -TTTTTGTCCAAGTCACTTCTT
253280 TTTTT
1 TTTTT
253285 CTGTGTGAGT
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 252717 -- 253216
CCAAAAAGAGTGGTATTTGCTAGCAACAACATAATGGAGGCAGTCAATCAATACAGATTGATCCG
AAATCAGATTCAAATCCCATATAGTACCTCTGGGTACATAAGAAATGTATTGAATCGATTCTTTT
TAATGAATAGATCCGATCGCAACTTCGAATATGGAATTCAAAGGGATCAAATAGGAAAGGATACT
CTTAATCATAGAACTATAATGAAATATAGGATCAACCAACATTTATCGAATTTGAAAAAGAGTCA
GAAGAAATGGTTCGATCCCCTTATTTGGATTTCTCGAACCGAGAGATCCATGAATCGGAATCCTG
ATGCATATAGATACAAATGGTCCAGTCCAATGGGAGCAAGAATTTCCAGGAACATTTCGTTTCTG
AGCAGAAGAGCCGCCTTCAAGTAATGTTTGATCGATTACGTATTAATCAATATTCGATTGATTGG
TCTGAGGTTATCGACAAAAAAGATTTGTCTAAGCCACTTCCTTTC
Right flanking sequence: Indices 253285 -- 253784
CTGTGTGAGTTTCGGGAATATCCCCTTTCATAGGTCCGAGATGATCTACATCTATGAATTGAAAG
GTCCGAATGATCAACTCTGCAATCAGTTGTTAGAATCAATAGGTCTTCAAATTGTTCATTTGAAA
AAATGGAAACCCTTCTTATTGGATGATCATGATACTTCCCAAAAATATAAATTCTTGATCAATGG
AGGAACAATATCACCATTTTTGTTCAATAAGATACCAAAGTGGATGATTGACTCATTCCATACTA
GAAATAATCGCAGGAAATCCTTTGATAACACGGATTCCTATTTCTCAATGATATTCCACGATCAA
GACAATTGGCTGAATCCCGTGAAACCATTTCATAGAAGTTCATTGATATCTTCTTTTTATAAAGC
AAATCGACTTCGATTCTTGAATAATCCACATCACTTCTGCTTCTATTGGAACACAAGATTCCCCT
TTTCTGTGGAAAAGGCCCGTATCAATAATTATGATTTTACGTATG
Found at i:319822 original size:15 final size:16
Alignment explanation
Indices: 319796--319831 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
319786 CACTACCTTA
319796 TACTAGTAAAATGGCG
1 TACTAGTAAAATGGCG
319812 TACTA-TAAAATGGCG
1 TACTAGTAAAATGGCG
319827 TACTA
1 TACTA
319832 AAGGTGCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (16 bp):
TACTAGTAAAATGGCG
Left flanking sequence: Indices 319296 -- 319795
GCCCAAGCCTTCTCGAGCCCTTTTTTTTTGAGTCAGATAATGCCCTAGGCCTTCGATGAGCCTTC
CCCATGGTTTAAAGAGCTTGCCCTAGCGCCGAACCCTTTTCGGCCTAACGAGGGCTTTTTTTTCT
TCCTCTGCATTTTTAGGATGATATAGAATTTCGATCTGACAGTGACACGTGTATAAATATAAGCG
GTCAAACCATCTCCCCATCTCAAGGTAACCGCCTACGGCCCCTCTGCTGTCTCGTCGACCTTTCC
CTTCGATGATTCGTTCAAACAAAATGTCATGCTTCGTGCTTCGCACCCCTCGCATTTTCAGTGGA
TTCTTCCCAACTTCGAGAGTGAAATTGATCCGACTAACCAAGCAACGGTTAGTTGTGCGGTAGCG
TAAAGGGTGCGATAGTAATAGGAGAAAGACTAAGAAAAGTCTTTCCGGGTTATGCCATAAAGACG
CATTAAGCTCCTTGATCGCTTAGAGCCCCTCGATACACTACCTTA
Right flanking sequence: Indices 319832 -- 320331
AAGGTGCTCTCCTTACGTCAGTTAACAAAGTAAGGGAGATTTGGATACCAAACTGGACTGGACAA
CTAACCAATTCTGTCTCGCATTCTCTTTTTCAAAGACTTCCTTCGTGAATGGAATCTCCCAACTT
GTGTAAGTCGAAATCCGTTACCTATAAAAAAAGTATAAGATCGAGCTACGAAGTTGGTTGGCCAT
GTATTGATACCGCATTTAGTGTACTTGAATCGCGGGCAAGTGCCTTCCACTCGAACTCCAACTGA
TAGAAGTTCTTGCTCGGGAAAAAATATCTGTTTTACCTGCCCATGAATCGTAGCGTAGATCTTTC
TTCTCCTTAGGTCTCTAGCTTGATCATCTCTTAGCATTCCATGATCGGTCCGTATGTCCTTCTTT
AGGAGTTGAGCAGCCCTCTTCGCGGGTATAGGCCCTGGCCCAATTTCACAAGCACAGCAAATAGC
CAATTCCGCCCCATGTATTCAATTATAAAATTCTCCTGGTTTGCA
Found at i:321458 original size:20 final size:20
Alignment explanation
Indices: 321433--321472 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
321423 GATAGCCCAT
*
321433 TTATACAGAATGGTAAAGGG
1 TTATACAGAATGGCAAAGGG
321453 TTATACAGAATGGCAAAGGG
1 TTATACAGAATGGCAAAGGG
321473 GACCTCTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (20 bp):
TTATACAGAATGGCAAAGGG
Left flanking sequence: Indices 320933 -- 321432
CTTTATCTTCGTATTAGCCCTTATTCGGCGATTCAAACCCGAAATCCAATACAGAAGGGAATGCA
AGCAGTGAGGTTACCCCTTAGGGCGGATGAAAGAGGATTCCCGGACTTGAAACTGGCAAAAGCTC
TTATTTGTCATTCCCGCTCAATTTTCTAAATTGAGTAGGGCAAATTCTCAAGCCTTCGAGCCTTC
TTTTCTTTTGATTGGTAGAGTAGCCTATAACTCTTGAAGAACCGGAAAGAGGAGATGAGGGACCA
CTTCGAGGATTCCTCCCCCAAAGCGGTAATTAATTACTAGTTAACTTAACAAAGTGAAATCTACA
ATTTTTTGACAAACAAGATGTTGCGGAGACAGGATTGGAACCCGTGACCTCAAGGTTATGAGCCT
TGCGAGCTACCAAACTGCTCTACCCCGCGATGAAGAGAAGAACTGAAAACTAATAGATAACCAAG
TTCTGTATAACCCTTTACCATATCTGTACAAATAGGATAGCCCAT
Right flanking sequence: Indices 321473 -- 321972
GACCTCTACGATCACCGACCCTAGAATTGAAATCAAGAGTTAATCCTTACCAACTCGATCTTGTT
GCTCCTGGCAACAAACATGCATCAACCATTTCACGAAGTATATGTCCGGATAGTCCAAAGTCTCG
ATAATTAGCTCTCGGCCGTCCAGTCGCAAAACAACGTCGATGAAGGCGTGTAGCTGCGCTATTCC
GTGGTGGGGATTGTAACTTTCTATAAATTTCCCATTTCTCACTCAATGACGGAACTTTGCTTATT
TCTTTTTTTTGAGGATTGACGAATCAAATGATATTTCTGTTCTAATTTATTCCTCTTCTTCTCCC
GCTGAATCAAACCTTTCCTTGCCATAATGGTTCAGTTCCAATTAGTATCCATGATACAAGTCGAA
TCCTAGATGTAGAAATATAAGAAGGTGGCCCTCTATCTATCGAAAGAAATGATCTTTTCGCGGAT
ACAAGACATCCAAAAAAGAATTCCAAATTTAACCAACCGACGTAG
Done.