Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_046778
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: 99864
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Found at i:18418 original size:19 final size:20
Alignment explanation
Indices: 18376--18418 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
18366 GGATGTTGGT
* *
18376 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
18396 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
18415 CATG
1 CATG
18419 GAGGAGTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
CATGACTATCGAAAAGTTCA
Left flanking sequence: Indices 17876 -- 18375
GAGCTAAAAATGCATTTTTTTTCTTTTTTCTTTTCATTTCCAATTTTTCCATTTTTAAATTTATG
GGAGACTTGTCATATTTAGAATCTTTCTGTGGTGTGCTTTGTTTTTTATTATTCTGTACATTTTT
TTTATCATTCAAATATAGGCGCGATACGTGGGCAAACAAGGAGCGTAGGCTTGAAATAGAGGAAA
AAAGAAAACCGCGTAAGCGAGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTAACAAAAGA
AAGAAACAAAGAAATAAAAAGAAAGAAAATTTTTACTTTTTCTCTCTTTCAAATAAATCAAAAAT
ATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAAAAAGCCAAAATTTTGG
CTTTTTATTCTCTGCTTGCTTTTTTGCAAGCTTATTCTTTCGTCCTCGAAAATATTTGGAATAGA
TTTTTTCTTGTTCGCGCCTTACCAAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 18419 -- 18918
GAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCAGCTTATGCGCGATCA
TCTCGTGTTTAAGCTCACGCCATGTGGGCGTGAACTCTGGTTGAATTCGGGTTTTAAATCCCGCC
GCTGAGATGCTCAGTCGACTCTTGAACCTTAATAGGAAGACGGCTTCTTCCTAAATTAGTGCAAA
AGGTTCAAGGACTTAGGATGAACTTAATGTGAATGAGTATAAGCTTCGCTGCTCAAAAACACCCA
GTATTGACCACACTGAGAGACTTGCCAATGGCAAGAAAGGCCGCGGGTAACGCTAGTTGGCGAAA
TAGCGTTAAGCATTCCTAGCAATACGGAAAGAGAGGTCGTGATGATATCATCTACGTTCGTACTG
TTCCTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGAATAATTCCCATTAAGTT
CCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAACA
Found at i:24254 original size:20 final size:19
Alignment explanation
Indices: 24211--24261 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
24201 AAGAAAACCG
24211 GAAAAAACCGTTTAAGAGC
1 GAAAAAACCGTTTAAGAGC
24230 GAAAAAACCGTTTAAGAGC
1 GAAAAAACCGTTTAAGAGC
*
24249 GAAAAAAACGTTT
1 GAAAAAACCGTTT
24262 TTAGTTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.49, C:0.14, G:0.20, T:0.18
Consensus pattern (19 bp):
GAAAAAACCGTTTAAGAGC
Left flanking sequence: Indices 23711 -- 24210
AAATATAGTCAAAAATCTTAGGTTGTAACTTTATTATAAGCAGATTAGTTGATGTTTTATTCAAT
TCATATAAAAAGTGCCAAACATTGGGAACTATCCCAACAAAAGTAACGAAAAAAAACGGGAAGAA
GCAAAAACCACTTAAGTAAAAGAATTTGTTGTATTTTTTTCTTTGTTCTTCATAACAGCTAGGAA
TCAAAAAACACCAGATTTGATAACTTAAAAAAGGGAATAAAAAATAAAAGCATGATATTAGAGAA
ATAGTAACATACGTGCTTAAGGCCTCCGTTAATTGTGTACAAATAAAACCTGAATAAGAAAGAAT
AAGAAAGGATTTCGCTGACAAAAAAAACAAATCTTCTGAAAACCAATAACACGTAAACCATGTTA
AACTGAAGCAAATCAATATCCAAAAAAAACGAATTCTAACTTCTTTCAGAATAGTTTTAAATAAA
AAATTCGTCATATTTCATTGTGTGTTAAACCTAATAAGAAAACCG
Right flanking sequence: Indices 24262 -- 24761
TTAGTTTTTAGTTTTTAGTTGGGTTGGCTTTTACTGCGCCCGGCAAAGTGTGCAATCAATCGTAA
GGCCCTACCAAGATTTTCTTTTCATTTCATTAGTAGTTAAGGGTTCGCCTCTAGAATTTTACTAC
ATTTAAGTCATTCATCATAATGCAATTACTATGTACTAAAACCGTATTACAGCCCAGCATTTCTA
TTTAATTGATGGCATAGAGCGCATATAGCCACAAAAATCTATGGCTAAGGGAATCTATGGCTAAG
GGAATCTATGGCTAAGGGAATCTATGGCTAAATCATGAATGAAGGTTAGTATTGTACTGCATTCT
TAGCTCAGTTGGATAGAGCAACAACCTTCTAAGTTGAAGGTCACAGGTTCAAATCCTGTAGGATG
CTTAAAGAAAGTGCATAATGAATGAATCAATAATATATACCAACGATATATGCATCTATCCAACC
CACATCCAACATCAAATATCCAACACGCGCGGAAATAAATAATTT
Found at i:24513 original size:16 final size:16
Alignment explanation
Indices: 24492--24552 Score: 122
Period size: 16 Copynumber: 3.8 Consensus size: 16
24482 TAGCCACAAA
24492 AATCTATGGCTAAGGG
1 AATCTATGGCTAAGGG
24508 AATCTATGGCTAAGGG
1 AATCTATGGCTAAGGG
24524 AATCTATGGCTAAGGG
1 AATCTATGGCTAAGGG
24540 AATCTATGGCTAA
1 AATCTATGGCTAA
24553 ATCATGAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (16 bp):
AATCTATGGCTAAGGG
Left flanking sequence: Indices 23992 -- 24491
GCCTCCGTTAATTGTGTACAAATAAAACCTGAATAAGAAAGAATAAGAAAGGATTTCGCTGACAA
AAAAAACAAATCTTCTGAAAACCAATAACACGTAAACCATGTTAAACTGAAGCAAATCAATATCC
AAAAAAAACGAATTCTAACTTCTTTCAGAATAGTTTTAAATAAAAAATTCGTCATATTTCATTGT
GTGTTAAACCTAATAAGAAAACCGGAAAAAACCGTTTAAGAGCGAAAAAACCGTTTAAGAGCGAA
AAAAACGTTTTTAGTTTTTAGTTTTTAGTTGGGTTGGCTTTTACTGCGCCCGGCAAAGTGTGCAA
TCAATCGTAAGGCCCTACCAAGATTTTCTTTTCATTTCATTAGTAGTTAAGGGTTCGCCTCTAGA
ATTTTACTACATTTAAGTCATTCATCATAATGCAATTACTATGTACTAAAACCGTATTACAGCCC
AGCATTTCTATTTAATTGATGGCATAGAGCGCATATAGCCACAAA
Right flanking sequence: Indices 24553 -- 25052
ATCATGAATGAAGGTTAGTATTGTACTGCATTCTTAGCTCAGTTGGATAGAGCAACAACCTTCTA
AGTTGAAGGTCACAGGTTCAAATCCTGTAGGATGCTTAAAGAAAGTGCATAATGAATGAATCAAT
AATATATACCAACGATATATGCATCTATCCAACCCACATCCAACATCAAATATCCAACACGCGCG
GAAATAAATAATTTTTTATTTATTTTGGGGGAGAGTGGCCGAGTGGTTAAAAGCGACAGACTGTA
AATCTGTTGAAGGTTTTCTACGTAGGTTCGAATCCTGCCTCTCCCATATACGACGAAGCAAAGCA
AAGCAAAGCACTTGTTGCACTTGTGCGACGAAGCAAGCACTTGTGCGACGAAGCACTTGTTGCAC
TTGTTTTTGTGCGACGAAGCAAGCACTTGTTTTTGTGCTTATCCTTTCATGCAATTAAATAGAGT
GGAACTTTCTCAGAAACATATTGAATGCTTTGCATATTGAATGCT
Found at i:24919 original size:20 final size:20
Alignment explanation
Indices: 24894--24932 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
24884 AGCACTTGTT
24894 GCACTTGTGCGACGAAGCAA
1 GCACTTGTGCGACGAAGCAA
24914 GCACTTGTGCGACGAAGCA
1 GCACTTGTGCGACGAAGCA
24933 CTTGTTGCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.26, G:0.31, T:0.15
Consensus pattern (20 bp):
GCACTTGTGCGACGAAGCAA
Left flanking sequence: Indices 24394 -- 24893
TTAAGTCATTCATCATAATGCAATTACTATGTACTAAAACCGTATTACAGCCCAGCATTTCTATT
TAATTGATGGCATAGAGCGCATATAGCCACAAAAATCTATGGCTAAGGGAATCTATGGCTAAGGG
AATCTATGGCTAAGGGAATCTATGGCTAAATCATGAATGAAGGTTAGTATTGTACTGCATTCTTA
GCTCAGTTGGATAGAGCAACAACCTTCTAAGTTGAAGGTCACAGGTTCAAATCCTGTAGGATGCT
TAAAGAAAGTGCATAATGAATGAATCAATAATATATACCAACGATATATGCATCTATCCAACCCA
CATCCAACATCAAATATCCAACACGCGCGGAAATAAATAATTTTTTATTTATTTTGGGGGAGAGT
GGCCGAGTGGTTAAAAGCGACAGACTGTAAATCTGTTGAAGGTTTTCTACGTAGGTTCGAATCCT
GCCTCTCCCATATACGACGAAGCAAAGCAAAGCAAAGCACTTGTT
Right flanking sequence: Indices 24933 -- 25432
CTTGTTGCACTTGTTTTTGTGCGACGAAGCAAGCACTTGTTTTTGTGCTTATCCTTTCATGCAAT
TAAATAGAGTGGAACTTTCTCAGAAACATATTGAATGCTTTGCATATTGAATGCTTTGCATACAT
ATTGAATGCTTTGGTATTCGAGCCCTCTCCGAACCGTACGAGATAGTCGCCCATCATACGGCTCT
CCAATTCAACCTCTATGACGCCACCTTTTAAGCTTCTAAGATTGAAGACACAATAAATACAATAT
GGTTTTTAGTATATCCCTTTTTCGGTTTTATATTTTGCGTGGAGTATCTCTTCCACTCATAGATT
GTTTCCATGCTTCCATCTGGGTGTCCGTGATACCGCAAAAAAAAAATATATATATATATTTTTTT
TTTTTGCTTATGAAAGTAAGTCTTCAAAAAGGCGTTTTCCATTTTCGGCTTCTCATTCTGCTTTG
TTCGCATAGCAAATGGCAGCATGTAGATTCGTTTTGTGCTGAACT
Found at i:25065 original size:20 final size:17
Alignment explanation
Indices: 25023--25075 Score: 72
Period size: 16 Copynumber: 3.0 Consensus size: 17
25013 TTTCTCAGAA
25023 ACATATTGAATGCTTTG
1 ACATATTGAATGCTTTG
25040 -CATATTGAATGCTTTG
1 ACATATTGAATGCTTTG
25056 CATACATATTGAATGCTTTG
1 ---ACATATTGAATGCTTTG
25076 GTATTCGAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 16 0.50
20 16 0.50
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (17 bp):
ACATATTGAATGCTTTG
Left flanking sequence: Indices 24523 -- 25022
GAATCTATGGCTAAGGGAATCTATGGCTAAATCATGAATGAAGGTTAGTATTGTACTGCATTCTT
AGCTCAGTTGGATAGAGCAACAACCTTCTAAGTTGAAGGTCACAGGTTCAAATCCTGTAGGATGC
TTAAAGAAAGTGCATAATGAATGAATCAATAATATATACCAACGATATATGCATCTATCCAACCC
ACATCCAACATCAAATATCCAACACGCGCGGAAATAAATAATTTTTTATTTATTTTGGGGGAGAG
TGGCCGAGTGGTTAAAAGCGACAGACTGTAAATCTGTTGAAGGTTTTCTACGTAGGTTCGAATCC
TGCCTCTCCCATATACGACGAAGCAAAGCAAAGCAAAGCACTTGTTGCACTTGTGCGACGAAGCA
AGCACTTGTGCGACGAAGCACTTGTTGCACTTGTTTTTGTGCGACGAAGCAAGCACTTGTTTTTG
TGCTTATCCTTTCATGCAATTAAATAGAGTGGAACTTTCTCAGAA
Right flanking sequence: Indices 25076 -- 25575
GTATTCGAGCCCTCTCCGAACCGTACGAGATAGTCGCCCATCATACGGCTCTCCAATTCAACCTC
TATGACGCCACCTTTTAAGCTTCTAAGATTGAAGACACAATAAATACAATATGGTTTTTAGTATA
TCCCTTTTTCGGTTTTATATTTTGCGTGGAGTATCTCTTCCACTCATAGATTGTTTCCATGCTTC
CATCTGGGTGTCCGTGATACCGCAAAAAAAAAATATATATATATATTTTTTTTTTTTGCTTATGA
AAGTAAGTCTTCAAAAAGGCGTTTTCCATTTTCGGCTTCTCATTCTGCTTTGTTCGCATAGCAAA
TGGCAGCATGTAGATTCGTTTTGTGCTGAACTTTTTTTGATTACTGTGCTTCGTTCTATAGGGCT
CCCAGTTTCGGTTCCATCAATGGTCCTCTTTTGTTCGATATTGGTGTCATCGATTCAGGTTCCGC
TGCCCTAATCGGATATAAAGCATCATTCATGAGTTTAGGTTGCCC
Found at i:34724 original size:130 final size:130
Alignment explanation
Indices: 34491--34725 Score: 371
Period size: 130 Copynumber: 1.8 Consensus size: 130
34481 TGTGAGAAGG
* * *
34491 CCGCAGTAGAAAGCGCATTGCGCTTTCTACTGCGGCCTTCTCTCTTCATCCAATTTGTTTGAAAA
1 CCGCAGTACAAAGCCCATTGCGCTTTCTACGGCGGCCTTCTCTCTTCATCCAATTTGTTTGAAAA
* *
34556 TGAATTATTGAAAAAACAATCAAGGAATTGTGAAAAGATTATGCTTTTTTGTTTTTTTTATACGC
66 TGAATGATGGAAAAAACAATCAAGGAATTGTGAAAAGATTATGCTTTTTTGTTTTTTTTATACGC
* ** *
34621 CCGCAGTACAACGCCCATTGCTTTTTCTACGGCGGCCTTCTCTCTTCATCCAATTTGTTTGAAAT
1 CCGCAGTACAAAGCCCATTGCGCTTTCTACGGCGGCCTTCTCTCTTCATCCAATTTGTTTGAAAA
* *
34686 TGAATGATGGAAAAACCATTCAAGGAATTGTGAAAAGATT
66 TGAATGATGGAAAAAACAATCAAGGAATTGTGAAAAGATT
34726 GGAAAATCTT
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
130 94 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (130 bp):
CCGCAGTACAAAGCCCATTGCGCTTTCTACGGCGGCCTTCTCTCTTCATCCAATTTGTTTGAAAA
TGAATGATGGAAAAAACAATCAAGGAATTGTGAAAAGATTATGCTTTTTTGTTTTTTTTATACGC
Left flanking sequence: Indices 33991 -- 34490
TTAAGTGGCCTGGATTTTCTTATGCCTTTTTTTTTCTATCAGATGTTCTTTATTCTTATCCTTTT
CGGAAAAATATGTACAAAATGCATAAACCTTCGTCTTCAAGCCTGAATGCACCCGCTCCAGTAAA
TGACCTGACTAGAAGGCAAGCCCGCCATTCTGAAGTATGAATAGAAGTCTCATTGGCGAATATTT
TGGTAGTGACTAGTGAGGTAGGTGCAATTCCTACTGTATCCAAAATAATGCATCGGATGAATGCC
TAGGCATTGAGAAGGAAGGACGCTTTCAAGGGCGAAACGCCATGGGGAGATACCGTCTGTGATCC
ATGGATCTCCAATCGGGAAACCGTATCCAAGCGGGGCGGCGCATTAGTGTGCTGCGCTCTGTTTT
GGACTTTCAAAACTTAGCGAACTGAAACATCTAAGTAGCTAAAGGAAAGGAAATCAACCGAGACT
CCGTTAGTAGCGGCGAGCGAAAGCGGATTAGGCTTTGTGAGAAGG
Right flanking sequence: Indices 34726 -- 35225
GGAAAATCTTGCCAAAGAAGGTGATAGCCCTGTAAATTTTTTCTTATGGTTCGACTCAATAAGTA
AAACGCGGATACCGTGTTTGAATTATGATCGCTCTTATGTGACCAAGGGGGACCACCCTCTAAGC
CTAAGTATTCCTCAGTGACCAATAGCGTACAAGTACCGTGAGGGAAAGGTGAAAAGAACCCTAAG
AAAGGGAGTGCAATAGAAAACCTGAAATCCGATGCAAACAATCAGTCGAAGGACAAAGTAGGCTA
AGTCTAAATAGCGAGAAAGAAGAGATTGTGTTCTCTTTTGCGCTTCGTTATTCAGAACTTTCCAC
TCTAACGGCGTACCTTTTGCATAATGGGTCAGCGAGTAAATGGACACAGCAAGCTTAAGCCATTA
GGTGTAGGCGCAATGAAGTTGAAAGTAAATAAAGAATATAGTTGTTTCTATTTGACCCGAAACTG
AGTGATCTAGCCATGAGCAGGTTGAAGAGAGCTCTAACGGGCCTT
Found at i:40866 original size:81 final size:81
Alignment explanation
Indices: 40731--40880 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
40721 AAAATACTCG
*
40731 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
40796 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
40812 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
40876 CCAAG
65 CCAAG
40881 TGAGCTTAGG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
81 63 0.97
82 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (81 bp):
CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 40231 -- 40730
GGACAACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTAGAAATAAC
ACCAGTATTTCAACAACTTTTTGAGCTCATTTTTTACCCATATAATTCTTTATGTTTTTGTTTGA
ATAAGCCAATTCATGCTTCACCCACAAGACGCAAGGAGGGCGAAGACGCAAGGAAGGTTACTTAG
TCACCAGAGGATAACCACTTAGTAACCCCCACTTTGCCAATTAAATTAAGGCTTTATTAACAGAA
CTGGGGCGCGTAGTTTATAGCGAAGCTTTTTTTTTTTTCAATATTTTGGGAAATCCTCCAAAAAT
ATTTTTTGCTGCGAAAAGCAGCGCCCTCAAAGATTGTAAAGATTTAAGCTAATGGATGATTTGTT
TTTTTGGCGAATAACGGGATTTGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATT
AAGTTATACTCGCCCTTTTTTCTAATTCAAACATTAAAATACTCG
Right flanking sequence: Indices 40881 -- 41380
TGAGCTTAGGGAAGCGAAGCGCAGAATGGAAACACAATCTTTTTGTTTCGTTTTATCTTTGCCAT
TTCATTTTATAGACATCTCCGGCTTATTCCGGCTCGGCTGAATCTGCGGCATTTTTTCAAATATT
TGAAAAATCTATAGTCCTCTGTCTTAAGGTGTGTAGAGACTCCTTTTTATTGATTTATACCAGTC
TATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTAATCTAACCATGGTTGCCTTGGCA
ATGGCAATGACTTTTATACAATATGCAGAATACTCCAAAACCTCTATTTAGAACTAAAAGAATAT
AATGCTTTTTTATAAAAAAATCATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACATAGT
TTTGCCATCTATATAATAGAATAGAATAAGAAATAATAAGTTGGCGAGGAAGTAAAAATATATAT
ATATCTATCTATATATATATATATTTTTTTTTATTCTGTGGTCTT
Found at i:60831 original size:10 final size:10
Alignment explanation
Indices: 60815--60855 Score: 73
Period size: 10 Copynumber: 4.1 Consensus size: 10
60805 TAGCAGTAAA
60815 GAGCGTTATT
1 GAGCGTTATT
*
60825 CAGCGTTATT
1 GAGCGTTATT
60835 GAGCGTTATT
1 GAGCGTTATT
60845 GAGCGTTATT
1 GAGCGTTATT
60855 G
1 G
60856 GTGGGTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.20, C:0.12, G:0.29, T:0.39
Consensus pattern (10 bp):
GAGCGTTATT
Left flanking sequence: Indices 60315 -- 60814
CATTAGGCAATTTACTTTATACCACCTATTTTGTTTTGTTTTTGGTTTCTAGTCTTATTTTATTA
GTAGCTATGATTGGAGCTATAGTACTTACTATGCATAAAACTACTCAAGTCAAAAGACAGGATGT
GTTCCGACAAAATGCTATAGATTTTAAAAATACTATCAAAAAAATCAGAGATATTTGAAGGCTTC
AGCTCTCTGAAGCCATTAAGAAGCTCAAAAAAAAAGGTATATATATTTTTTTTTGTACGCTTCTT
TTTTTTCTTGCCGTGCCTTTTCAATCTTTGCTTTTCTTTTGCACAAAGCAAAGAAAGCGGGTAAA
CCCCCGTCCTAGCTAAGGTTTTGCGGGACTAAAGTCCTTCTACCAATAATAAATATGGGGCGAAA
AGAACAAAAGCTAAATACAAAAATATATATAGCAGCAAACACAAAGAGTCAAAAGTGTTGGAGCA
GCTACCATTGCGGCAAGTAGTTTTCTATTTTGCTATAGCAGTAAA
Right flanking sequence: Indices 60856 -- 61355
GTGGGTAGTTTTCTATGCCATTTCTATGGCAGCTCGTTTTCTCTCTCAAGTTACTGCATTGCTAG
TAGGATGCATTTATCTTTTCTATTCAATCCAAACCCCTTTACTGCAACTTTTGTTGCTATTCGTG
TTCTCACTCATTCCGCAGTTAGCGCAAATGACTGTTAAGTGCGCTGAATATATTGATAGCTGAAT
ATATTGCTGAATATATTGATAGCGGTTAGCGCAAATATTGATAGCTGAATATATTGATACAGGAT
TTCGCTTTTTACGCAGCATACTATAGATTATGTCTAAGTTAGGTATGGATAAATCTTATGGTTAA
ACGCAATTCATTTTTGCGCTTAGCTTTCATGAATCATGGGTGTTCTATTTTAGCATAGCATCTAA
TTACTATGTTATTACATAATTAACAAGTTGCATAATCTGCGCTACACAACCTACATACTTACATC
CTAATAAGCCCGCGCCTTCGGCCCTACACTAAAGATGCATCATGC
Found at i:61049 original size:16 final size:16
Alignment explanation
Indices: 61028--61109 Score: 66
Period size: 16 Copynumber: 5.0 Consensus size: 16
61018 TGTTAAGTGC
61028 GCTGAATATATTGATA
1 GCTGAATATATTGATA
61044 GCTGAATATA-T--T-
1 GCTGAATATATTGATA
61056 GCTGAATATATTGATA
1 GCTGAATATATTGATA
61072 GCGGTTAGCGCAA-ATATTGATA
1 GC---T---G-AATATATTGATA
61094 GCTGAATATATTGATA
1 GCTGAATATATTGATA
61110 CAGGATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 24
0.69 0.00 0.31
Matches are distributed among these distances:
12 10 0.19
13 2 0.04
15 4 0.07
16 22 0.41
19 2 0.04
22 12 0.22
23 2 0.04
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (16 bp):
GCTGAATATATTGATA
Left flanking sequence: Indices 60528 -- 61027
AGAAGCTCAAAAAAAAAGGTATATATATTTTTTTTTGTACGCTTCTTTTTTTTCTTGCCGTGCCT
TTTCAATCTTTGCTTTTCTTTTGCACAAAGCAAAGAAAGCGGGTAAACCCCCGTCCTAGCTAAGG
TTTTGCGGGACTAAAGTCCTTCTACCAATAATAAATATGGGGCGAAAAGAACAAAAGCTAAATAC
AAAAATATATATAGCAGCAAACACAAAGAGTCAAAAGTGTTGGAGCAGCTACCATTGCGGCAAGT
AGTTTTCTATTTTGCTATAGCAGTAAAGAGCGTTATTCAGCGTTATTGAGCGTTATTGAGCGTTA
TTGGTGGGTAGTTTTCTATGCCATTTCTATGGCAGCTCGTTTTCTCTCTCAAGTTACTGCATTGC
TAGTAGGATGCATTTATCTTTTCTATTCAATCCAAACCCCTTTACTGCAACTTTTGTTGCTATTC
GTGTTCTCACTCATTCCGCAGTTAGCGCAAATGACTGTTAAGTGC
Right flanking sequence: Indices 61110 -- 61609
CAGGATTTCGCTTTTTACGCAGCATACTATAGATTATGTCTAAGTTAGGTATGGATAAATCTTAT
GGTTAAACGCAATTCATTTTTGCGCTTAGCTTTCATGAATCATGGGTGTTCTATTTTAGCATAGC
ATCTAATTACTATGTTATTACATAATTAACAAGTTGCATAATCTGCGCTACACAACCTACATACT
TACATCCTAATAAGCCCGCGCCTTCGGCCCTACACTAAAGATGCATCATGCATGAAGATATGAAG
CACAAAAATTACCACTAAATTATCTATCAAGTACTGGGATACTTAGGTTCTTTTATTTGAACTTA
GGTTCTTTTATTTATCACCTACGGGAAAAAAAACAAGAATATACCAAATGAGTTTGAAAAATACA
TGGCTATTTCCAATTGGTTATTGTGACGCTGCGGAACCTTGGCAATTAGGATTTCAAGACGCAGC
AACACCTATGATGCAAGGAATAATTGAGTGCGCCTAGATATATCA
Found at i:61061 original size:12 final size:12
Alignment explanation
Indices: 61044--61068 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61034 TATATTGATA
61044 GCTGAATATATT
1 GCTGAATATATT
61056 GCTGAATATATT
1 GCTGAATATATT
61068 G
1 G
61069 ATAGCGGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (12 bp):
GCTGAATATATT
Left flanking sequence: Indices 60544 -- 61043
AGGTATATATATTTTTTTTTGTACGCTTCTTTTTTTTCTTGCCGTGCCTTTTCAATCTTTGCTTT
TCTTTTGCACAAAGCAAAGAAAGCGGGTAAACCCCCGTCCTAGCTAAGGTTTTGCGGGACTAAAG
TCCTTCTACCAATAATAAATATGGGGCGAAAAGAACAAAAGCTAAATACAAAAATATATATAGCA
GCAAACACAAAGAGTCAAAAGTGTTGGAGCAGCTACCATTGCGGCAAGTAGTTTTCTATTTTGCT
ATAGCAGTAAAGAGCGTTATTCAGCGTTATTGAGCGTTATTGAGCGTTATTGGTGGGTAGTTTTC
TATGCCATTTCTATGGCAGCTCGTTTTCTCTCTCAAGTTACTGCATTGCTAGTAGGATGCATTTA
TCTTTTCTATTCAATCCAAACCCCTTTACTGCAACTTTTGTTGCTATTCGTGTTCTCACTCATTC
CGCAGTTAGCGCAAATGACTGTTAAGTGCGCTGAATATATTGATA
Right flanking sequence: Indices 61069 -- 61568
ATAGCGGTTAGCGCAAATATTGATAGCTGAATATATTGATACAGGATTTCGCTTTTTACGCAGCA
TACTATAGATTATGTCTAAGTTAGGTATGGATAAATCTTATGGTTAAACGCAATTCATTTTTGCG
CTTAGCTTTCATGAATCATGGGTGTTCTATTTTAGCATAGCATCTAATTACTATGTTATTACATA
ATTAACAAGTTGCATAATCTGCGCTACACAACCTACATACTTACATCCTAATAAGCCCGCGCCTT
CGGCCCTACACTAAAGATGCATCATGCATGAAGATATGAAGCACAAAAATTACCACTAAATTATC
TATCAAGTACTGGGATACTTAGGTTCTTTTATTTGAACTTAGGTTCTTTTATTTATCACCTACGG
GAAAAAAAACAAGAATATACCAAATGAGTTTGAAAAATACATGGCTATTTCCAATTGGTTATTGT
GACGCTGCGGAACCTTGGCAATTAGGATTTCAAGACGCAGCAACA
Found at i:61435 original size:20 final size:20
Alignment explanation
Indices: 61410--61447 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
61400 GTACTGGGAT
61410 ACTTAGGTTCTTTTATTTGA
1 ACTTAGGTTCTTTTATTTGA
61430 ACTTAGGTTCTTTTATTT
1 ACTTAGGTTCTTTTATTT
61448 ATCACCTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.11, G:0.13, T:0.58
Consensus pattern (20 bp):
ACTTAGGTTCTTTTATTTGA
Left flanking sequence: Indices 60910 -- 61409
TGCATTGCTAGTAGGATGCATTTATCTTTTCTATTCAATCCAAACCCCTTTACTGCAACTTTTGT
TGCTATTCGTGTTCTCACTCATTCCGCAGTTAGCGCAAATGACTGTTAAGTGCGCTGAATATATT
GATAGCTGAATATATTGCTGAATATATTGATAGCGGTTAGCGCAAATATTGATAGCTGAATATAT
TGATACAGGATTTCGCTTTTTACGCAGCATACTATAGATTATGTCTAAGTTAGGTATGGATAAAT
CTTATGGTTAAACGCAATTCATTTTTGCGCTTAGCTTTCATGAATCATGGGTGTTCTATTTTAGC
ATAGCATCTAATTACTATGTTATTACATAATTAACAAGTTGCATAATCTGCGCTACACAACCTAC
ATACTTACATCCTAATAAGCCCGCGCCTTCGGCCCTACACTAAAGATGCATCATGCATGAAGATA
TGAAGCACAAAAATTACCACTAAATTATCTATCAAGTACTGGGAT
Right flanking sequence: Indices 61448 -- 61947
ATCACCTACGGGAAAAAAAACAAGAATATACCAAATGAGTTTGAAAAATACATGGCTATTTCCAA
TTGGTTATTGTGACGCTGCGGAACCTTGGCAATTAGGATTTCAAGACGCAGCAACACCTATGATG
CAAGGAATAATTGAGTGCGCCTAGATATATCATCACGGTTGCAGAGCTCTGCTCCAACTCTGCCA
TATCTGCTCGAGCTGGCTATCGCCAGGATGTGAGCTACACAGGTGGGGCATCCTTCAATAAGATT
GCCCCGAAAGCATCATGTGAAACTCGCAGAACATTGAGACTGCCCTCACTAGGATGCTTCGACAA
AGCATAAGGAAAGATCAGGATAACAAACTTGATACGTGAATCTAGTCCATCCAATTCCGGGCCGT
ATGTCTGAAGCAGAATATCAAGGCATACGCGTGGATAGTAAGCCTGCACAAAACGGCCGAACTCG
CGCTCGATATCAATTGCGAACACGGGACTTGAGTCCCCACGTAGC
Found at i:74749 original size:13 final size:13
Alignment explanation
Indices: 74731--74756 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
74721 TTCTTTTTGG
74731 AAAGAAATTACAA
1 AAAGAAATTACAA
74744 AAAGAAATTACAA
1 AAAGAAATTACAA
74757 TTACAATACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAGAAATTACAA
Left flanking sequence: Indices 74231 -- 74730
AAACCCATCATTGCACTTTGTGAAAATGGGTTCCTGAATGCAGCTTCGCCCTTGGATGCTCACGC
CCTTGCCGGGATTACTCTAGCAATTACAGCGGGTATTTCAGGAATCCAGCGTCGGTCAAGAATTC
CGGATCAAACAAAGTTTCTGTCCAGAATTGTTGACCTAGGAGACCCCCAACAAATAGGGGCCCAT
GAACGTTTTGTTTGGTTCAATTGAATGATCACAGAAAGGCTTCTATTTGTATTTCGCTATTTGTT
GTTGTCGTCGCCATAATAGATTTCAATTCAATTGGATGCCGACAAAATAAAACAAATATTAAACA
ACAATAGAAATTGACTTCGTGTTGTTTGTCTTATTGACTTCTTTGTCTTATCAAAGAAGCAGCAT
ATATTGCTGCTAATCGTGTTGTCTTATTGACTTCGTGTTGTCTTATTCTCATTCTCTATTATGTT
CGCTGCGCACATAATAGCCTTTTAGAGTTCAGTTCTTCTTTTTGG
Right flanking sequence: Indices 74757 -- 75256
TTACAATACATTACAACATGTATTTGGCTATTACAAATACATCTTACAGCTATTATAATAAGCTT
CTTTCCTTTCTGTGGTCTTTTATTTCCGAAGTTTACTAAGTTTACAAGGCGCAAAGCGGAATTCG
TATATTTTTATTTGCAAATAATAATTAACATTTTAACATTTGCACTAGAGACTAAATGCTACACA
ACGTATTCACTGTGCTGCGCACATAATAGATTACCAATTTTGCAGCTTCACCCACAGAAAGGAAA
CTGAATATTCAGTTAATAATTTTCTCTAAGAAAAGAAAAGAACTAAAATATGCTTCGCTCTTTAA
CTCATGTTCTAATGTGTTTACTTCTTGGAAAAAAAGAGACGATTTGTGGATAACCAATCGTTTTT
CAAATCTCTGATAGCTACTTTACCAAAATGGATACATCAATTTCAAAAATCAAAACATGAAAATA
TATTATATACCAATCCTGATTACCTATTTCAATTATTATGGTTTT
Done.