Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_065024
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: 416511
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Found at i:31713 original size:21 final size:20
Alignment explanation
Indices: 31687--31747 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
31677 AATTCTTCCA
31687 ATTAATTTAATGATTAATAAT
1 ATTAATTTAAT-ATTAATAAT
*
31708 ATTAATATATATATTAATTAA-
1 ATTAATTTA-ATATTAA-TAAT
*
31729 ATTAA-TTAATATTATTAAT
1 ATTAATTTAATATTAATAAT
31748 CATTTAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
18 3 0.09
19 6 0.18
20 2 0.06
21 18 0.53
22 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTAATTTAATATTAATAAT
Left flanking sequence: Indices 31187 -- 31686
ATGCTATTTAGTGTATTTTAAATTAAGTTCTTTTCTTTCTAAGAGGTGGAATAGAATAACCCGGT
TGAAGCGTAATGATCATACGTCTGTAATGCATTGTATGTCCCTTAATAGATCGCACTCTTCTACC
CTTTATCGGGAGTCTATGACTATTCATAGCTATTACCTTGACACCAAAGAAGAGTTCGACCCAAT
GCTTTATTTCTGTCTTAGTTGCTCCCGATTCGACATTAAAAGTATATTGATTTTTCCCCAATAAC
CGAATACTTTTGTCTGTAAATACTGCATTTTTTATTCCATTCATAAATCTATTTTCTTCCCTATG
AGTTCTAGTCTCAATAAAACTACTAGTTTTTTATTGTTCATATATAACCACACCAATTCGTTATG
TATGGATGATGAGATTCCATTGATACAGAGCCAATCGTTCTTTTTTCTCTGATAGATGGTCTGGA
TTCAAATCCTACTGAGAGGTCCAGTAGAGATCCGAAATTCTTCCA
Right flanking sequence: Indices 31748 -- 32247
CATTTAAATCTAATTGAAGTTTAGTAATTCTGGTTTTTGGAGAGAGGGTTCCATTGGCGTGCATC
CAGTAGGAATTGAACCTACGACTTCGCCAATTATGAGTTGGGCGCTTTAACCATTCAGCCATGGA
TGCTTCGGGGGAATCCTCGTACCTGGTGAATAACCAAATTCCAATTGAAATGAAATCTTTTAGAT
AAATCAATGCATTATAGGAGGTTTAAATACAAATGCATCAAATCAAATACTGGATTTTCGAATTG
AGAGAGATCCGGAATTCTCGCGATTTCTTATATTCATGGACTCAAATTAATTCAGCGGTATCTTT
CATTCACATTTTTTTCTATCAAGAGAGTTTTATCAAACTCTTGGACTCCCGAATTTGGAGTATCC
TACTTTCACGCAATTCACAGGGTTTAACAAGCAATCGATATTTCACGATCAAGAATGTAGTATTC
TTTGTAGTAGCGATCCTTCTATATCGTATTAACAATCGAAAGATG
Found at i:35405 original size:9 final size:9
Alignment explanation
Indices: 35393--35418 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
35383 CTATAGTTAC
35393 GATAGTGAT
1 GATAGTGAT
35402 GATAGTGAT
1 GATAGTGAT
35411 GATAGTGA
1 GATAGTGA
35419 GGATTTCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (9 bp):
GATAGTGAT
Left flanking sequence: Indices 34893 -- 35392
TCAAATCTTTGATGATTCCATCCTACATGATTGAGTTGCGAAAACTTCTGGATAGGTATCCTACA
TCGGGACTTCATTCTTTCTGGTTAAAGAATTTCTTTCTAGTTGCTCTTGAACAATTAGCAAATTT
TATAGAAGAAAGACGGATATTCCTTGCTCATTATCAGACAATAACCTATTCACAAACCCCGCGGG
TGGCTAGTAGTTTTGATTTCCCATCCAATGCGAAACCCTTTTCGCTCCGCTTAGCCCAACCCCTA
GGAGGGGGTATTTTAGTGATTGGTTCTATAGGAACTGGACGATCCTTTTTGGTCAAATACCTAGC
GAAAAACTCTTATGTTCCTTTCATTACAGTATTTCTGAACAAGTTCCTGGATAACCATCCTAAGG
GTATTAATATTGATGAGAATGATAGTGAAGAGAAAATTTTTGATGATAGAGAGGGTACCATTTAC
AGTCTTTTACCTAGTAACGAGAATCCGGATAGTAACTATAGTTAC
Right flanking sequence: Indices 35419 -- 35918
GGATTTCGACCGTGACCTTGATAGGAAGCTCAAGTTTATAACTATAAAAGATGTGCTACCTAGGG
ATCTGATACCGGAAATAGACCGATTTTTGATCACCCTTCAATTCGAATTAGCAAAAGCAATGTCT
CCTTGTATAATTTGGATTCCAAACATTCATGATCTGAATATGAATGAGTCAAATGACTTATCCCT
TGGTCTATTCGTGAACTATCTCTCTAGGGATAGTCAAAGATGTTCCACTGGAAAGATTCTTGTTA
TTGCTTCAACTCATATTCCCCAAAAGGTAGATCCCGCTCTAATCGCTCCGGATAAATTAAATACA
TGCATTAAGATACGAAGGCTTCTTATTCCACAACAACGAAAGCACTTTTTTACTCTTTCATATAC
GAGGGGATTTCACTTGGAAAAGAAAATGTTCCATACTAATGGATTTGGGTCCATAACGATGGGTT
CCAATGTACGAGATCTTGTAGCACTTACCAATGAGGCCCTATCAA
Found at i:38065 original size:13 final size:13
Alignment explanation
Indices: 38047--38071 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38037 AAAGATAGAG
38047 ATATTATATATTT
1 ATATTATATATTT
38060 ATATTATATATT
1 ATATTATATATT
38072 CGATAAAAAG
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATATTATATATTT
Left flanking sequence: Indices 37547 -- 38046
GTCATTGATTGAATAGGTAAGTCACCAATCTCTAAAACAGACTATGTAATGTCCTTTATCCGTTG
GTTTACGGGTGGTAATTTTACTAGAGGTTTCTATTGTAACCCTGTGTGATTCCTGTTCAAGCATA
TAATTCGGCGGGTGCAGGGCGGACTTTTTCAAAACGGACTCTCCATTCATTAGATCCAGAAAATC
ATCAAAATTTTGTGACCTGCTGGCGAACTTATTCCAATTCAATAAGAAATCTCAATATTATGCCT
TGAAGAGGACTCGAACCTCCACGCTGTTTAGCACGAGATTTTGAGTCTCGCGTGTCTACCATTTC
ACCACCAAGGCATCTTCAAAGTGAATTGTATTCCATAAATATGATATCTATTTAGTGTTATGTAT
GGAATACATGAAAAAAGTGGAATTTGAAAGTTTTTTTATTGATCGGTCCTGTCATATAGGCCCGA
GTCGGACATCCAATTGGTTCGATTTGAATTATCCGAAAGATAGAG
Right flanking sequence: Indices 38072 -- 38571
CGATAAAAAGTGGACAATCTAACCTATTTTTGGCTTCAATTTCAATAGAAAGAAGCCAAAATAGG
TTAAAGGGTCTTAAAAAAGGAGAGATATTTAAAAAGCATACGCCTATTCCCAATCCTAAATGGAA
TGACGCAGAGATCTATATGTAAGCAGAGTATCCATTTAGATACGCTCGAATGTATATAATCCTAT
CCTATTGTCGTCCGCTATGGAATGAACTTATAATCATGAAATCGACTCGATCGTCAGATTATAGA
TTATAAGTTCATAACCCTAGCCCATTCCCATTTTGGGTGGAACAGATCTACTAATTCTTTGATTC
CAGTTAGTAAAGATAAGAGTTGATAAGAATTGAACTTATAAATAGATAGATTCTAGAAGCTAAAA
AAGGGTATCCTGAGCAATTTCAATAATGGGGTTCATTGATATTCCTGGTATAGTAGATGCTATCA
CACATATAATCATACTCAATTCGATGGAATTGTTTGATCTTAAAC
Found at i:115866 original size:21 final size:21
Alignment explanation
Indices: 115837--115876 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
115827 AACGTTCGCT
115837 TTCTCCTCTTCCTCTCAAATA
1 TTCTCCTCTTCCTCTCAAATA
* *
115858 TTCTTCTCTTGCTCTCAAA
1 TTCTCCTCTTCCTCTCAAA
115877 AACTCGCACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.35, G:0.03, T:0.45
Consensus pattern (21 bp):
TTCTCCTCTTCCTCTCAAATA
Left flanking sequence: Indices 115337 -- 115836
TAGCGTACTTCTACATATCCACTCAGAGGAAGGTCTTTTCGTAATGGATGACCCTCGAAACCATA
ATCTGTTGATATACGGCGTAGATCCGGATGATTGATGGAAGAAACACCAAACATATCCCAAACTT
CTCGCTCCCACCGGCCGGCTGATGGAAATAGACTGACTACCGGAGATATTCGTGTTACTTCGTCT
GCACTGGTTTGTACACGAATGCGTGAGTTATACCGAGTACTCAGTAAATTATAGACCACTTCAAA
TCTTCGTTTTCGAGAGGGATAATCAACTCCGCAAATATCGATCGAAACTTGAACCCTTGTATAGG
TATGCAATTTAAGAAAGCACAATAATTGAAATAGGCAGTCCGTTTTGGTAGAAATATTATTACCA
TGTTGCGATCTTTCAAAACTGGTAAACCATTTGTCGCCGCCTGCGGGAAAAGACCACCACACACA
ATAGATTAATAAGAATTGGCTATCCATATAAAGATAACGTTCGCT
Right flanking sequence: Indices 115877 -- 116376
AACTCGCACCAGCGTGCCATGATTCTATATGAACAGTCAAAGTGATCCGCTTTACTTTCTTTTAG
CAAAGCTAGAAAAATGAAGAAGGACTTGTTCCGGTTGGTTGATCCGGAAAGATACGGGACAAACG
AAACTGGAAACAGCGAATTTCTCGGGAGCAAGATTAACTACCTAGACCGACCTGCTCTTATCTAA
TTCCATAAACACAACGAGACTTTACTGAATGACTTGATCGATCGTACTGTACTAGATAGACCATA
ATCCTTTCATACGCAATTCCTCGATGCCAATCTCGCACTTGATACGCAATAAAGACCTGGCTTTC
TTCAAAGGACGGATAGGATCTTAGCCTACCAGGGACCGGCTCTATGAGCACGGGCGGTGGTTTCT
CGATCAACTTTCTGATTCAGACTAAGAAAGAAAAGACAGTGAAGAGCAGGGATTTGTCACATATA
TATTTGATGATATTTCATTCATAGCAAGGTTCTTTTTGTTTTCCA
Found at i:151854 original size:20 final size:20
Alignment explanation
Indices: 151817--151854 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
151807 GTGGGGCTTC
*
151817 CAAGATGTGAATGTGGAGCT
1 CAAGATGTGAATGGGGAGCT
151837 CAAGATGATG-ATGGGGAG
1 CAAGATG-TGAATGGGGAG
151855 AAAATGGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.32, C:0.08, G:0.39, T:0.21
Consensus pattern (20 bp):
CAAGATGTGAATGGGGAGCT
Left flanking sequence: Indices 151317 -- 151816
ATCCTTGAATATACAATTCATGAGCTTGGAAATGGGTCCCCTGAAGTGAGGTAATGGCTCTTGTA
GATACCCAGGTTATCTAGGGTGCCTGGTAATGATGTACTTTATGTTTATGTATGTGTACAAGAAT
GTGATTCAAAACCAGTGGACTTGGCAATACATGTGAAGGAGTGGGGACTAATGGATGAAATGGAG
CAGGTATTGACATTCATTTGCAAGCTGACACCAAATTTTGTTGACATTAAATCTTAGTTGAGAGA
TCCACCTTGTGGTGAGATTGTCATGGTTCCACTGCATGCAACTGTTGGAGATTTTAAGCAAGCTG
CTGAGGCGGAAACTTACTGCATTGCAGAAAGGCTTATAGTGACAGACATCACAGAATTGATGGGT
GTGAGTGATGAGGAAGTGCTCTTTGGGTTAATCCAGTCAGGTGTGGAGCTTTGTGTGAGGGGAAT
TGCTATAGACTTGTGTACTCCTTTGAAGTCTCAGGGTGGGGCTTC
Right flanking sequence: Indices 151855 -- 152354
AAAATGGTGGCTTGTGAGGTATGGCAACATACACGATGTTGTGGTATAGTGCCACCACTGTTTGT
GTGCACTGGGTGCTGTGATTCACTTGTACCCCCAAGGATTGAATCCGCATTTGGTATGGATTGTG
CTGATATTTTTCTGATTTCACCAGAGGAGTATGGATATGGGTACTGAGCTTGATTACCATTGCAA
CAGTGTTTGTTGACTTGTTTCTGTGAACGTACTTTTTGAAACGTTCATTTTAGGATGTGTAGGAG
AGCTCTTAAATCTGACATTTATATTGATAAATGCATAGGCTTGATTCGGGTGTGTATGATTTTTC
TTTGAACCAGGGTCAAGGGACCTAACAGTAGGAAGGGTTAGTGCAGAAAGACTAACATGCTTTGC
AGAAGATAGGCTCCTTATATGTGATGGCATGGATCCTAGAGTTTTTTTTAAACAATGTTTGTTGC
CAAATCAGTAAGAAATGGGTCTCTTTCTGATAAGAAAGCATGCTT
Found at i:265160 original size:18 final size:19
Alignment explanation
Indices: 265137--265172 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
265127 GCGAAAGCTA
265137 ACCTCGG-ATCAAGTCAAC
1 ACCTCGGAATCAAGTCAAC
265155 ACCTCGGAATCAAGTCAA
1 ACCTCGGAATCAAGTCAA
265173 GTAATCGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.36, C:0.31, G:0.17, T:0.17
Consensus pattern (19 bp):
ACCTCGGAATCAAGTCAAC
Left flanking sequence: Indices 264637 -- 265136
GGCTTTCCCTTTCTTTCAGTTTTCAAGAGATTAGTCCCGCGAGATCGTGATCTAGTTCTTTCGTA
TAGCTCAAAAAGCAAAATAGTGATTTCGATCGTAAGTAAGCTGAAGGGAGTCCGCAAGACTGGTG
AATCCACTAGGGAAGAATTCTGGCAGTTCGCGAGCCAGTACTTTAGTTATTAGTGCCCTCGAAGG
TTATCGAATTCTAAGCTTTCTTCTCAGCCCTTCACCAGGTATAGGCTCAGGAAGCAAGCAACAAC
TGCTGCGGATCCTGGAACGAAATGAGAATTATCAATAGGCTTTTCTTTTGTACTCGAGTTCAAAT
CATTGGTCCGGGGTAAAGGAATGAGATCCTAAGGAAGCAATGCTAAAGTAATACCGTCCGGAGAC
TATTAGGGAATTCGGGTTAGAAGAATTCTACTCAAACAAAGTCAAGGTTGTGAGCCACGACACTT
CTCTTCTAATATCCCGAGGGAAGGTCAAGTCGAAAGCGAAAGCTA
Right flanking sequence: Indices 265173 -- 265672
GTAATCGGTTGAACGCGGTCTAGGTATAAGTATTCCTATTCCTGCGTTGTGCCGGAAGTCTTTAA
GACTTTCTTGATGCGGAGTAGCTATTGAATATTATAAAGTTCAGCAGTCCAGGCGGGTGTTCATT
TGCAGTTGCTGGTCGGGGATGGAAAGAAAGATGAATAGTTCGGTTGGCCTTGGCCGGAGATGGAG
ACACAGGTGGGTAGGTAGAGAATACCTAGGGGCGCGAGACAACTCTCTCTAAGGAACTCGACAAA
ATAGCCCCGTAACTTCGGGAGAAGGGGTGCCTGGTCACTGCGACCCCCTTTGTGAGGCAGGCAGC
CCGTTCAAAGTAGAACCAAGTAGAAATGTTCCTAAGATGGAACCCTACCCTCCTTATGACCTGTT
TTCTAACCTTTTTAATGGAGTGCATCCACTCATTCTAACCGAGAAGCCTCTGGGGTACTTCTTAA
TGCTTAACTCAAGGAGTTTCTACTATACGCTTCGGGTCTGACCTT
Found at i:287425 original size:17 final size:17
Alignment explanation
Indices: 287399--287433 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
287389 GACCCTCTTC
*
287399 CAAGACAAGATTATGGG
1 CAAGACAAGATTAGGGG
*
287416 CAAGAGAAGATTAGGGG
1 CAAGACAAGATTAGGGG
287433 C
1 C
287434 TATTCGAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.11, G:0.34, T:0.14
Consensus pattern (17 bp):
CAAGACAAGATTAGGGG
Left flanking sequence: Indices 286899 -- 287398
GCAGGAGCTCGGACTGAGTCTAGTTTAGGTCCATCCGAGGGTTTGCCTTTTCCTTCTGCACTTCT
TCACTTTTCTGCTTGGGTGCTCTCCCCCGAGTGAAGGCATAAGCCGTAGCCGTAGACAGTCACTA
GCACTAGTTTGATCGCTATGCCATTCTCGGCAACGATGTGGTGATAGCTGATCGACGAGTTGCTT
CGGTCTACCTTGTTGAATCATCTACATTGATTGAGGACTCGATGTCAGAATGCATTCTTCGAGAC
CCTGTTGTAGAAGTTTTCATCTAGTTCCTGTAGCTAGTCGTAGATGCATATTATAGCTGCTATCG
GATCAGAGGTTCGGGGGATTGATTTTGAACTATATTATTTATTTCTAAATAATTCCTGTTGGATC
TCTTGCTTTCAAGTTCTCTTAGTAGTATCCTCCTAAGCCTAGTCCAGCTGTCCTTGTTATTGCCC
CTCCGGTTCTGGTTCCGGTTGCTGTGGGTCCAGTCGACCCTCTTC
Right flanking sequence: Indices 287434 -- 287933
TATTCGAGTACTTCTTCCTCCCGAGATTGCTTTTCTTGTTATCAAAAGTCAGGGGCAGGATAAGA
AATAGAGAATCCCCCTATCGATCCCTATCGAGCCAGCCCAGGCTAGGAAATCTCCCTTAGTTTAA
TTAGTCTCTCCAACCCGCCTAGTCAAAAGCCCTTTTTTTAGTTTAACCTGAATATAAAGAGACCT
TCTTTCTATTGGGAGGACTAGTCTTTTTGCGTAAGCCGCCTTGCTCTAAGAATCATCTCTTCTCC
CCGCGAGGGAGTAGCCTTTGCCAAAGAAGCGCTAATTACTTGTTGCATTGCCTGCGTTAGGAGAT
GAGTGCACTTGAGAAGAATGAGACATGGGAAAAAGAAGTTAAAACAAACAAAAAAGGGGCCAGAA
CATCAGAAGGTGGTAGACAATTTAGAGAGCTTGGAGGAAAAGATCAAGACCATCAAGGGTATAGA
GAGGCACCAAGTTCGCAGAGATCTGCTTCTTCTCAGACAGCTCCC
Found at i:319513 original size:30 final size:32
Alignment explanation
Indices: 319477--319706 Score: 183
Period size: 33 Copynumber: 7.2 Consensus size: 32
319467 GTCCACTGAT
319477 AGTATGTCCATTGATAC-GACTAACC-G-GGAC
1 AGTATGTCCATTGATACAG-CTAACCGGCGGAC
* **
319507 AGTATGT-CAGTGGATACAGCTAACCCGGCGGTT
1 AGTATGTCCA-TTGATACAGCTAA-CCGGCGGAC
* **
319540 AGTATGT-CAGTGGATACAGCTAACCCGGCGGTT
1 AGTATGTCCA-TTGATACAGCTAA-CCGGCGGAC
* *
319573 AGTATGTCCATTGATACAGCT-TCCCG-GGAC
1 AGTATGTCCATTGATACAGCTAACCGGCGGAC
**
319603 AGTATGTCCATTGATACAGCTAACCCGGCGGTT
1 AGTATGTCCATTGATACAGCTAA-CCGGCGGAC
* **
319636 AGTATGT-CAGTGGATACAGCTAACCCGGCGGTT
1 AGTATGTCCA-TTGATACAGCTAA-CCGGCGGAC
* *
319669 AGTATGTCCATTGATACAGCT-TCCCG-GGAC
1 AGTATGTCCATTGATACAGCTAACCGGCGGAC
319699 AGTATGTC
1 AGTATGTC
319707 AGTGGATCCT
Statistics
Matches: 171, Mismatches: 18, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
29 2 0.01
30 50 0.29
31 9 0.05
32 6 0.04
33 100 0.58
34 4 0.02
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (32 bp):
AGTATGTCCATTGATACAGCTAACCGGCGGAC
Left flanking sequence: Indices 318977 -- 319476
GTAATGAATTCTCGGAAGCTCTTTCTTAATCTGATAGAAAGTGGTTCCTTATTCTCGGCACCTAT
CAAAGTCATGTAATCCCTGTGTACTTGTTATCGAAGCAGCACCCTTTTTCAAATTCGATGCTTTA
CTTTCAGCTCAGAGAATTCACTTCTTCGGTCGTTCAGAGATGTAGGGGTTGCCGCTCCTATGCGG
TGGGTTCGACTCCCCAACGAGATATGTAACAAATTTCGTATAGTATTGAAATAAAATTAGGGCTG
GCCAGAATCTCTAAAAGAAGCCGCCCTTCTTCCTTTGAAATCTTTCTCCCATTCCTTCCGTTGGT
CAACAACCAACCACAACTCAATAGAATGAATTCTGAACTATAAAGGAGAAGTGAACCGTTCAGGC
AAGCGAAGCGGTTTGCTTTGATAAAATAATCATTTCATATAGAATCATTCATGTCAAGCTGGTTA
ATAACTTTTTTGATGTCTCATTTCACTAACTCCGTGTCCACTGAT
Right flanking sequence: Indices 319707 -- 320206
AGTGGATCCTGCCCCAGTCCCCTCCAGTCCCCCCGCTTCTTCCTCGGTTGATAGGGTAGGGATTT
TTGAAGACCATCCTGGTCTTGATCCCTGCAATGAGCGCGTGGTAGAACTTCAAGCTCAAATACGC
GCAAAAGTCTCTGAATTAATGCCTACTCAGAGTGAGCAAGAGGTTCTCGCAGCGGCCGAAGCTTT
ACATGCCGAAAGCCGCGATATCTCTTTTCTGCAGCGTATTTTGGAGGATTTGACGGCTGGGGGAA
CTGAGAGTGAGAGCTTTCGGGAGGCCCATAATTTTTTAGTAACGATTGCTCCTTGTGATGCAGCG
GAACCGTGGCAATTAGGATTTCAAGACGCAGCAACACCTATGATGCAAGGAATAATAGACTTACA
TCACGATATCTTTTTCTTCCTCATTCTGATTTTGGTTTTCGTATCACGGATCTTGGTTCGCGCTT
TATGGCATTTCCACTATAAAAAAAATCCAATCCCGCAAAGGATTG
Found at i:319549 original size:33 final size:33
Alignment explanation
Indices: 319507--319713 Score: 243
Period size: 33 Copynumber: 6.5 Consensus size: 33
319497 TAACCGGGAC
319507 AGTATGTCAGTGGATACAGCTAACCCGGCGGTT
1 AGTATGTCAGTGGATACAGCTAACCCGGCGGTT
319540 AGTATGTCAGTGGATACAGCTAACCCGGCGGTT
1 AGTATGTCAGTGGATACAGCTAACCCGGCGGTT
* * **
319573 AGTATGTCCA-TTGATACAGCT-TCCC-G-GGAC
1 AGTATGT-CAGTGGATACAGCTAACCCGGCGGTT
*
319603 AGTATGTCCA-TTGATACAGCTAACCCGGCGGTT
1 AGTATGT-CAGTGGATACAGCTAACCCGGCGGTT
319636 AGTATGTCAGTGGATACAGCTAACCCGGCGGTT
1 AGTATGTCAGTGGATACAGCTAACCCGGCGGTT
* * **
319669 AGTATGTCCA-TTGATACAGCT-TCCC-G-GGAC
1 AGTATGT-CAGTGGATACAGCTAACCCGGCGGTT
319699 AGTATGTCAGTGGAT
1 AGTATGTCAGTGGAT
319714 CCTGCCCCAG
Statistics
Matches: 154, Mismatches: 13, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
29 2 0.01
30 36 0.23
31 5 0.03
32 9 0.06
33 98 0.64
34 4 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (33 bp):
AGTATGTCAGTGGATACAGCTAACCCGGCGGTT
Left flanking sequence: Indices 319007 -- 319506
CTGATAGAAAGTGGTTCCTTATTCTCGGCACCTATCAAAGTCATGTAATCCCTGTGTACTTGTTA
TCGAAGCAGCACCCTTTTTCAAATTCGATGCTTTACTTTCAGCTCAGAGAATTCACTTCTTCGGT
CGTTCAGAGATGTAGGGGTTGCCGCTCCTATGCGGTGGGTTCGACTCCCCAACGAGATATGTAAC
AAATTTCGTATAGTATTGAAATAAAATTAGGGCTGGCCAGAATCTCTAAAAGAAGCCGCCCTTCT
TCCTTTGAAATCTTTCTCCCATTCCTTCCGTTGGTCAACAACCAACCACAACTCAATAGAATGAA
TTCTGAACTATAAAGGAGAAGTGAACCGTTCAGGCAAGCGAAGCGGTTTGCTTTGATAAAATAAT
CATTTCATATAGAATCATTCATGTCAAGCTGGTTAATAACTTTTTTGATGTCTCATTTCACTAAC
TCCGTGTCCACTGATAGTATGTCCATTGATACGACTAACCGGGAC
Right flanking sequence: Indices 319714 -- 320213
CCTGCCCCAGTCCCCTCCAGTCCCCCCGCTTCTTCCTCGGTTGATAGGGTAGGGATTTTTGAAGA
CCATCCTGGTCTTGATCCCTGCAATGAGCGCGTGGTAGAACTTCAAGCTCAAATACGCGCAAAAG
TCTCTGAATTAATGCCTACTCAGAGTGAGCAAGAGGTTCTCGCAGCGGCCGAAGCTTTACATGCC
GAAAGCCGCGATATCTCTTTTCTGCAGCGTATTTTGGAGGATTTGACGGCTGGGGGAACTGAGAG
TGAGAGCTTTCGGGAGGCCCATAATTTTTTAGTAACGATTGCTCCTTGTGATGCAGCGGAACCGT
GGCAATTAGGATTTCAAGACGCAGCAACACCTATGATGCAAGGAATAATAGACTTACATCACGAT
ATCTTTTTCTTCCTCATTCTGATTTTGGTTTTCGTATCACGGATCTTGGTTCGCGCTTTATGGCA
TTTCCACTATAAAAAAAATCCAATCCCGCAAAGGATTGTTCATGG
Found at i:319640 original size:96 final size:97
Alignment explanation
Indices: 319476--319713 Score: 412
Period size: 96 Copynumber: 2.5 Consensus size: 97
319466 TGTCCACTGA
**
319476 TAGTATGTCCATTGATAC-GACTAACCGGGACAGTATGT-CAGTGGATACAGCTAACCCGGCGGT
1 TAGTATGTCCATTGATACAG-CTTCCCGGGACAGTATGTCCAGTGGATACAGCTAACCCGGCGGT
319539 TAGTATGTCAGTGGATACAGCTAACCCGGCGGT
65 TAGTATGTCAGTGGATACAGCTAACCCGGCGGT
*
319572 TAGTATGTCCATTGATACAGCTTCCCGGGACAGTATGTCCA-TTGATACAGCTAACCCGGCGGTT
1 TAGTATGTCCATTGATACAGCTTCCCGGGACAGTATGTCCAGTGGATACAGCTAACCCGGCGGTT
319636 AGTATGTCAGTGGATACAGCTAACCCGGCGGT
66 AGTATGTCAGTGGATACAGCTAACCCGGCGGT
319668 TAGTATGTCCATTGATACAGCTTCCCGGGACAGTATGT-CAGTGGAT
1 TAGTATGTCCATTGATACAGCTTCCCGGGACAGTATGTCCAGTGGAT
319714 CCTGCCCCAG
Statistics
Matches: 135, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
95 2 0.01
96 130 0.96
97 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (97 bp):
TAGTATGTCCATTGATACAGCTTCCCGGGACAGTATGTCCAGTGGATACAGCTAACCCGGCGGTT
AGTATGTCAGTGGATACAGCTAACCCGGCGGT
Left flanking sequence: Indices 318976 -- 319475
AGTAATGAATTCTCGGAAGCTCTTTCTTAATCTGATAGAAAGTGGTTCCTTATTCTCGGCACCTA
TCAAAGTCATGTAATCCCTGTGTACTTGTTATCGAAGCAGCACCCTTTTTCAAATTCGATGCTTT
ACTTTCAGCTCAGAGAATTCACTTCTTCGGTCGTTCAGAGATGTAGGGGTTGCCGCTCCTATGCG
GTGGGTTCGACTCCCCAACGAGATATGTAACAAATTTCGTATAGTATTGAAATAAAATTAGGGCT
GGCCAGAATCTCTAAAAGAAGCCGCCCTTCTTCCTTTGAAATCTTTCTCCCATTCCTTCCGTTGG
TCAACAACCAACCACAACTCAATAGAATGAATTCTGAACTATAAAGGAGAAGTGAACCGTTCAGG
CAAGCGAAGCGGTTTGCTTTGATAAAATAATCATTTCATATAGAATCATTCATGTCAAGCTGGTT
AATAACTTTTTTGATGTCTCATTTCACTAACTCCGTGTCCACTGA
Right flanking sequence: Indices 319714 -- 320213
CCTGCCCCAGTCCCCTCCAGTCCCCCCGCTTCTTCCTCGGTTGATAGGGTAGGGATTTTTGAAGA
CCATCCTGGTCTTGATCCCTGCAATGAGCGCGTGGTAGAACTTCAAGCTCAAATACGCGCAAAAG
TCTCTGAATTAATGCCTACTCAGAGTGAGCAAGAGGTTCTCGCAGCGGCCGAAGCTTTACATGCC
GAAAGCCGCGATATCTCTTTTCTGCAGCGTATTTTGGAGGATTTGACGGCTGGGGGAACTGAGAG
TGAGAGCTTTCGGGAGGCCCATAATTTTTTAGTAACGATTGCTCCTTGTGATGCAGCGGAACCGT
GGCAATTAGGATTTCAAGACGCAGCAACACCTATGATGCAAGGAATAATAGACTTACATCACGAT
ATCTTTTTCTTCCTCATTCTGATTTTGGTTTTCGTATCACGGATCTTGGTTCGCGCTTTATGGCA
TTTCCACTATAAAAAAAATCCAATCCCGCAAAGGATTGTTCATGG
Found at i:319703 original size:63 final size:66
Alignment explanation
Indices: 319476--319713 Score: 275
Period size: 63 Copynumber: 3.7 Consensus size: 66
319466 TGTCCACTGA
319476 TAGTATGTCCATTGATAC-GACTAA-CC-G-GGACAGTATGTCAGTGGATACAGCTAACCCGGCG
1 TAGTATGTCCATTGATACAG-CTAACCCGGCGGACAGTATGTCAGTGGATACAGCTAACCCGGCG
319537 GT
65 GT
* ** * *
319539 TAGTATGT-CAGTGGATACAGCTAACCCGGCGGTTAGTATGTCCA-TTGATACAGCT-TCCC-G-
1 TAGTATGTCCA-TTGATACAGCTAACCCGGCGGACAGTATGT-CAGTGGATACAGCTAACCCGGC
*
319599 GGA
64 GGT
* **
319602 CAGTATGTCCATTGATACAGCTAACCCGGCGGTTAGTATGTCAGTGGATACAGCTAACCCGGCGG
1 TAGTATGTCCATTGATACAGCTAACCCGGCGGACAGTATGTCAGTGGATACAGCTAACCCGGCGG
319667 T
66 T
*
319668 TAGTATGTCCATTGATACAGCT-TCCC-G-GGACAGTATGTCAGTGGAT
1 TAGTATGTCCATTGATACAGCTAACCCGGCGGACAGTATGTCAGTGGAT
319714 CCTGCCCCAG
Statistics
Matches: 149, Mismatches: 15, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
62 4 0.03
63 83 0.56
64 10 0.07
65 8 0.05
66 42 0.28
67 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (66 bp):
TAGTATGTCCATTGATACAGCTAACCCGGCGGACAGTATGTCAGTGGATACAGCTAACCCGGCGG
T
Left flanking sequence: Indices 318976 -- 319475
AGTAATGAATTCTCGGAAGCTCTTTCTTAATCTGATAGAAAGTGGTTCCTTATTCTCGGCACCTA
TCAAAGTCATGTAATCCCTGTGTACTTGTTATCGAAGCAGCACCCTTTTTCAAATTCGATGCTTT
ACTTTCAGCTCAGAGAATTCACTTCTTCGGTCGTTCAGAGATGTAGGGGTTGCCGCTCCTATGCG
GTGGGTTCGACTCCCCAACGAGATATGTAACAAATTTCGTATAGTATTGAAATAAAATTAGGGCT
GGCCAGAATCTCTAAAAGAAGCCGCCCTTCTTCCTTTGAAATCTTTCTCCCATTCCTTCCGTTGG
TCAACAACCAACCACAACTCAATAGAATGAATTCTGAACTATAAAGGAGAAGTGAACCGTTCAGG
CAAGCGAAGCGGTTTGCTTTGATAAAATAATCATTTCATATAGAATCATTCATGTCAAGCTGGTT
AATAACTTTTTTGATGTCTCATTTCACTAACTCCGTGTCCACTGA
Right flanking sequence: Indices 319714 -- 320213
CCTGCCCCAGTCCCCTCCAGTCCCCCCGCTTCTTCCTCGGTTGATAGGGTAGGGATTTTTGAAGA
CCATCCTGGTCTTGATCCCTGCAATGAGCGCGTGGTAGAACTTCAAGCTCAAATACGCGCAAAAG
TCTCTGAATTAATGCCTACTCAGAGTGAGCAAGAGGTTCTCGCAGCGGCCGAAGCTTTACATGCC
GAAAGCCGCGATATCTCTTTTCTGCAGCGTATTTTGGAGGATTTGACGGCTGGGGGAACTGAGAG
TGAGAGCTTTCGGGAGGCCCATAATTTTTTAGTAACGATTGCTCCTTGTGATGCAGCGGAACCGT
GGCAATTAGGATTTCAAGACGCAGCAACACCTATGATGCAAGGAATAATAGACTTACATCACGAT
ATCTTTTTCTTCCTCATTCTGATTTTGGTTTTCGTATCACGGATCTTGGTTCGCGCTTTATGGCA
TTTCCACTATAAAAAAAATCCAATCCCGCAAAGGATTGTTCATGG
Found at i:346579 original size:16 final size:18
Alignment explanation
Indices: 346550--346583 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
346540 TCTTTATTGG
346550 CTCTATATTCATTTCATA
1 CTCTATATTCATTTCATA
346568 CTCTAT-TT-ATTTCATA
1 CTCTATATTCATTTCATA
346584 TAGTCAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (18 bp):
CTCTATATTCATTTCATA
Left flanking sequence: Indices 346050 -- 346549
CTCGGCCCAAGCAATGCCCCAAGACTCCCATGTCTTTCTTGGTTGGACCAACCCAACCGGTGATT
TCCAACAAGTCTCTCTTTTTTTTTGAGAGGCCATCTTTCTTGTCAAGTACCTCTTCAACTCTTTC
TTCAACTAGGTCGGACGCGCAAAGCGCTCCACCTGAGTTAGAGCGGGTATTTGATCGAATCTGTG
ATGAATACGCAGAGTGGGTGGTGAGAGCCGGTAAGCAATTACCCCCAGAATGGAGCATGCCGGAC
CTTGTTCGGACAGTGATTGGGGACGAGGCTATTCACATCCCAGGCTTTCTCAAGGATTCATATGT
TGATGTTATGTTACATGGACAAAATAGTTGGTTATGCAACGAGGTTTTTCAGTTTTTGGATTTTA
TTACCAGCTCGGTAATATAAACATAACATCTTAGTCTTTATAGAGCTGCGGCATTCCCCCTTACT
TTTTACTTTAATTGAAGTTTGATTGTGTTAATTGTTCTTTATTGG
Right flanking sequence: Indices 346584 -- 347083
TAGTCAATTTGGACTGACTTGTGGGGGGGGTCTCAGCCTCTGGACTTTGAGTGGATTTGCTGTTT
CGACAACGGCGCTGACAGTTCCAATCTGCCGGCGTTGGAATCGTCGTCAAGTTCCGAGTCTCTGG
CTACTTTTCGAAATGTTATCGCAGCAGAAAATGAAGCGGAAATATATGAGCGAATTAGGGTTCTC
GAGAACCAGCATTACTACAATATCCCCCCTCATAATAACCCGGGAGATTACGCGAGGCTGGTTCG
AGAGCACTTCGATCAAGCCCTAAACGTAGATCACTACAGGGAAATCTTTGATCGAGAGTATCTCG
AACTATGCGTATTAGAGAAAAAGGCCGGTCTGCAGGATAAAGTCTTCAATCTGATGCTTGATGAG
CAGAATCTTGCTCGAATTATGGAGCTATCTCCCTATTCAAATAGTTGGCAGGAAGCCTACGACTT
CATTCAGGAGAAGGTTTCCCCGCTTAGCTCCCTTTAACATGCCGC
Done.