Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_052709
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: 562920
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:349 original size:13 final size:13
Alignment explanation
Indices: 327--361 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
317 ATCAGACAAT
327 AATAAGAATAATA
1 AATAAGAATAATA
*
340 AATAATAATAATA
1 AATAAGAATAATA
353 AA-AAGAATA
1 AATAAGAATA
362 TTCATGAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (13 bp):
AATAAGAATAATA
Left flanking sequence: Indices 1 -- 326
GAGTCAGCTCACTTTCAAGCAAATCAACAAAATAACTTATAGTAAAAGGAAACCAGATAAACATG
ACAATAGTCTTTCGACGCAAAATTCACATAGATAAGAGCAAGAGAACAAGATTCACAATATTTCA
AGAGAACCCACACAAAAAAGGGAACGGGATACCGTTATATTGGGTCAAGGTTTGCACACTCCAAC
TCCCACTCTCAATGCCTTTATTTAGGTCAAGCTCCAACAGGTAGATTACACTAAAAGAAATCCAC
TCAGACACCTTTTTCACTTATTTCTTTTGAGAAAGACATTTTCATATACTGGTTCAATCAGACAA
T
Right flanking sequence: Indices 362 -- 861
TTCATGAGGATGTTGAAGATTTATTCACATCTTTATTAGAGCAAGGGTTGATCGAGCTTCCCGAA
CCTAAGAGACCGGATGAGGTGGGACGAGTAGGAGATCCCAAATACTGTAATTCCATCGGGTTATT
TGTCATCCGATAGATTATTGTTGAGTTCTTAAAGTGAAAAAAGTTTGAAAATGATGGTGTCATTG
AAATAGACCCTCCTAAGCAACCTGTGGTCACTTCAAATGCTTGTAATAGTTGGAGATATTCTTTG
CCCGATAGCTGAGATCTCGCCAAGCATAGCCTATATCTAGATCTAGTTCTAGCACCGGAAGAGCA
ATTTCAGAGGATCTCACAAAATATGATGAAAGATATATTCAAGGAGAATGGAGCACTCGTGTTAG
CCAAAGGAGTAGGGAAGTCTGGTTTGGGCAACTCCTTATACTGAGACTTGCAAGAGCCGGTGGAA
AAAAATCCTTATGATCCGGTAGAAGCTGGAGCTGTGGAAAATCAA
Found at i:100337 original size:15 final size:15
Alignment explanation
Indices: 100317--100347 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
100307 ATAAAAAATA
100317 TAAAAAAGAAAAAGGC
1 TAAAAAA-AAAAAGGC
100333 TAAAAAAAAAAAGGC
1 TAAAAAAAAAAAGGC
100348 ACTCATCAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.71, C:0.06, G:0.16, T:0.06
Consensus pattern (15 bp):
TAAAAAAAAAAAGGC
Left flanking sequence: Indices 99817 -- 100316
AGGCTGGGCTGCGTACTTTTCGGCGCCCACCTTTTCTTTAGGTGTTGGGGCAAGCCCCAGGAAAG
TCTAGGTTGGCTCCCAGCTCCATCTCGGTCGGCATCCTGCTCTCGAGGGAATGGAGTCCTGGAGC
GAACTACTCATTGCTGTCTTGCCCAAGGAAGGGCATTTGGAACATTCTTTTTAGGGAGGGAAAAC
GTGGTTGACAAGCCACTTCGAGGAGGCGACTGGAGTGCTTTCATCAAATAATGCATGTGGGCTGA
GCCATTCCCATCCCGACGTGGTGGCCCGATTCGGCCTGGCCTGGTCGGGAAGAGATTCACATAGA
GACAGACTACTGTTATCTGGGAATATCTTTCTATGTTAGCTAGCGGGGGCGGGCTTTGCTTTCCT
ATGGTAGTCCCGCGGCGGCCTCTGACCGTCCGTCCCGTCTCATCTTGATTTGGCTATACTTGTAT
GTAGCCAGCCATGTTAGCTTCACATGAGAGCCTTTATAAAAAATA
Right flanking sequence: Indices 100348 -- 100847
ACTCATCAGTCGGCCCCTTTCCTATTCAGCCTTGCCACCTCTCCAGTTAAGAGAATAGGTCCCGC
GGCCGCCCGCCTGAATCTATACTAGCTGCCACGCACGACCCGAACGATTTCAGCGCCCCTCTCCA
GATAAGAAGCAAAGCGTGCCATCACCTACAGCCCTTTCCTCTGCCGGGGACTTCCATGAAATGAA
AACGGGCGGCATCGTCGTATGCTCGACATTTGTTGCCCTGGTTTATACCCCGGAGTACTCCTATG
GCCGATCTGTCACCCAACCTCCTTAAACAACCTAAAGGCTTGGCCCCGTTCCGTTTGGAGTTGGA
GAATGGGCCTTATGGCACGGCTTAGTCAGTTATTCTCGCAGATAAGATTCGGACCGCCACTTCTC
TGAAAGCATGGTTTTTGCCTCCCTCCTTGGAGTTCGTCCATTCGTTGGGCGATCCCTTGCTCTCA
CGTTCGAGTGTTTGCTCGTCGTTTAGGCCGGTGAGTGAGATTTCT
Found at i:166318 original size:28 final size:28
Alignment explanation
Indices: 166278--166335 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
166268 AACTTTTCAA
166278 TATAAAGAAAGACCTTGTACATCTGTCC
1 TATAAAGAAAGACCTTGTACATCTGTCC
166306 TATAAAGAAAGACCTTGTACATCTGTCC
1 TATAAAGAAAGACCTTGTACATCTGTCC
166334 TA
1 TA
166336 ACTTTGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (28 bp):
TATAAAGAAAGACCTTGTACATCTGTCC
Left flanking sequence: Indices 165778 -- 166277
AGGTAAGCAAGTGGGATAGCTGAAAGCTTTTGATATGGATCTTAAGTAAGCACAAACCTGTGATA
AAGGTAGTTTCCCCCTCTTGGCATTGTAGGAGTCATTCCAGTAGTTTCATTCCAAGCATAAAAAG
TACCCGCATTGAATTCGCCTTCGTGGCAGTCTCTTAGGCGTCAGATTTTAGGCAAGCAGAAGGAT
CAGATAAGACATAGATTTATTTTAGTGGGAGTTATCCATCTAGGTCAAGCGCTAATATATACATT
GATTTCCTTTAGAGTTGAGAGTAAAATAGCTAGAAGAAGGCTAGGAAGGTGGAAGAGAAATTACC
TATAATAAGAAAGAGAATCCAATTTTCTAATATGAATTTGAATGGATTCTCCACTAACTGGAAAA
CCTGCCAATCCACTCTTCCTTTTTGGTCTGCCACTACTGTCTTACTGAAGCTGGCTTGCCTTGCG
TAGATCAAAAACTTTTCAAACTGGCTTACTAATAGAACTTTTCAA
Right flanking sequence: Indices 166336 -- 166835
ACTTTGATAACACTGGAATACATACTTTACTTCCGCGGGTATTGGCTTTCGGGCTTGATGAGCTC
CACCTTAAAGAGAAAAAAAATGGGCCTACTGCATGGGTTAATGTTGATAGGATCTGGGAGATTGG
AAAAGACATCCCGGTAAATGTATTTCTTTTAATAAAGGAAAGCTTCCACGTCACATCCGATAGTC
TGATTGGACTTCTGCTGGAACTGGCTGGTCACACTCGGTAAGACTTTTTTTATCCTGTAAGACTG
GCTTTTAATAGAACCCCTAACATCTCTAAGAAAGCATCGACCCTCGCTGATGCTCGTACATACTT
TGATTTCCGACTAAATAAAAGAGGCTTTCTTTGCAGCATCCGTCTTGCAAGCAACCTATCCCCCT
ATATTAGATTAATCGGGTTACAAAAACTCTAACGGATATAGAGCCAACGGACGCTATGGATTTGT
TGTACCATTTTACGTGCTTGAACTCAGAACACACGCCATCCGATC
Found at i:202391 original size:19 final size:19
Alignment explanation
Indices: 202356--202394 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
202346 GAGCAAGCCC
*
202356 AAACAGAAGCAACAAGAAA
1 AAACAGAAGCAAAAAGAAA
202375 AAACA-AAGCAAGAAAGAAA
1 AAACAGAAGCAA-AAAGAAA
202394 A
1 A
202395 CAGCTCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.72, C:0.13, G:0.15, T:0.00
Consensus pattern (19 bp):
AAACAGAAGCAAAAAGAAA
Left flanking sequence: Indices 201856 -- 202355
TGATCTTCACTGGTCGGAGGCTAAGAGCTTTCTTTGACTCTGAGTCATATGGGATGGGTCCCTAC
TCTCACTATGACATAGTGGCCCAACGGTTCCTATGAAAGTCATAGCCGGACCTACTCTCCTCTCG
CCGATGGTTTGAGAGTTGCGTTGGCGTGACGCTAATCTACTGATATTCGAGTGCTTGAGTTTCAC
TCATGTAGAGATAACGAAGGGAAAGGGCATTTGAGGGAGAGCCCAACCCAAGGGAAGGGGCAAAG
AAAGGACCTGAGCACATTGACATCGAAGAAAAGGCCAATGAAAATAGGGAAAGTCCTATTCAAGC
CGCTTTACCGACGAGGTTAAAGAGCGGTAGCCCCTCCTTCGAGCAAGCAAGCGGCACTAAAAGCA
GGATGAAAGCAAGCAAGGAGTGTAAGCCACTTGCCCGATAGGGTAAGGAGCGGAGACCCTTCCTT
CATTCATTAAGTTTAGGGAGTCAGGGATAACAGAGGAGCAAGCCC
Right flanking sequence: Indices 202395 -- 202894
CAGCTCTTTGTCTTACTGTGCCCGAGGAAGGGAAGAAAGAAGATGACAGACAAAGCACAACGGAG
GAATGAACTTCAAGCATGGAGGGGGAAAGTAACGGCACTCAAAGCTGTCTTCCATCAACCAAGCA
TGAAACAGAAGCCATGGACTAAGATGACTGGACAGGAGCGATAAGCAGCTATCAGCCACTCGAAC
CAAGTTAGAGGTTTTTTTCATGAGAGTCTTTCTAACATTCTTCACCTGAACCCGGGAACAGCTTT
GACTTAGATACTCTATTGTCAGATAGTTGAATGGCACCGGGAATGGATTAGGGAGCAAAGGAGAT
TAGGGAAAGTCGAAAGCCCTTTTTCCAACTGAGAGGGGCAGGAGAAGGATAGAAAGGTAGTTTCC
TCCAGCAAGAGGGATGACTTCTTCCTTTCCGCAAATAACAAGCGCTTTTCTTCGCCACATCGCGT
ATAACGGGAATCGAACCCCCCTGCTGCTGGCGGGCGGATGGAGAA
Found at i:206228 original size:13 final size:13
Alignment explanation
Indices: 206210--206235 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
206200 AAGGAGTTTT
206210 CTCGTATTCTGTA
1 CTCGTATTCTGTA
206223 CTCGTATTCTGTA
1 CTCGTATTCTGTA
206236 TTAGCTCCTT
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:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
CTCGTATTCTGTA
Left flanking sequence: Indices 205710 -- 206209
ATGCGGCACACATGCTCTGAAGCGTGCTTTTACGCTCGATGATTCCCTCTTCAAGGTGTGTTCAG
TTAGAACGTTAAAAAGAAAGAGAGCGTTCAAGTTCAGGTGGTCGAATGCATTTTTCTGTACTGTA
GCAGGAATGGCTTTCCTGGGCCCTACTTTGTTTATGTATGCGTACGTGTAAACGCATTTACTTTC
TCTGACTCTGAGGGTAAATTGACTTCGGGAGCGGTAACGGATTTTCTCGATACTAAGTTTGCCGG
AAAGCACTTCACGTATAAGAGCTTGGGTCCCCGTATCCTTTGTTTGCCTTTTTACCTTCGGTAGG
AAACCATTATGGAAAGTGATCACACGAAAAGCAAAAAAGCGCTCTTCCTTCCGGCTTCTGGAAAG
ACTTGAGCCGATAGACGAACATTGGTCAATTTCAATTAAAGGTCGGCTACTAATTACAATTGTTG
GATTGAAAGCATCTCTCTTTCCGATTTCGTTTTCGAAGGAGTTTT
Right flanking sequence: Indices 206236 -- 206735
TTAGCTCCTTCCACGAATGAATAAGGTAAGGCTTCGATCTTTCGCTTTTGAGTTCGTCCGGAAGC
TCTAGTATGAGCCGGTGATTCCAGTCCGTCTCGGATGGAACTCCCACCTAAAAGGTCGTCTCTTG
TCGAACATCTCACCCAAGCGCTAGGTAATCCAATTTGGAGCATCGGTACTCGCCAGAGTTACAAG
TCGTTAAGCGACGCGAAAGAGTTGATCCATCGGATTGGGATTAGCCAGTCTTTGAGCTAGCCCTA
ATTGAATCTACCAAATAGGCAAATAGGCTAAAGAAGGGAAGCACCAACCATTCATTTGTCGAATC
GAAAGCTTCGCCTACGACGTAACTCAGCGCGGTAAGCTCCATTTTGCTGGCGCTTGTTTAATTTA
AAGTGGTACGGTATCCCCATACTTTTCTAACTAAGTCAATTGAAAATGACATCGGCTAGTGAGCA
AACGAGCTTCCGAATTGGATCAAAGCCAAGAACCGAGGCGAGGTC
Found at i:246545 original size:14 final size:14
Alignment explanation
Indices: 246528--246556 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
246518 GACTACATCC
246528 ATCTATCCTACCTA
1 ATCTATCCTACCTA
246542 ATCTATCCTACCTA
1 ATCTATCCTACCTA
246556 A
1 A
246557 ACAGTAAGCC
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:0.34, G:0.00, T:0.34
Consensus pattern (14 bp):
ATCTATCCTACCTA
Left flanking sequence: Indices 246028 -- 246527
GAACAAATACTATTTATTAGCTTAGCCGGGAGAATCTAGTCATTTAGTCAGTTCATAACAATCTC
TGTAAAGCAAGGGGCAAAGCTTCTACGACAGCTTCTCCCTCATGTCATGTAGTCGTCGGCCTTCC
CGACGCCCCCCCTTCGTCGCTTCTGGCTAAGCATCTTTCGGCGGAGGAAAGGAGGCGACTAGTCG
CTTCTGGCGAAGCTGCGAGCCTACCCTGCCTACTTAAATAGCTTACGCTTACTCAGCCTAGTCTA
CTAAAAGAGGGCTACAGCAAGCAACGAAGTTGCCTTTGTTTGTTGTGGGTCGCGCCTCGCCGTAG
GCACTGAATGAATGAAATGAGTGGAGATCTTCCTTCCTCCTTTCAAATAACCAAGAACTTCGTTG
GTACTAGTGGCGAAGAAAAATCTTACCCCAAAAAAAGCAACTCGGAACCTAAAGAGAAGAGAGTT
CAGTCTACAAGAAGCTGGCAGAGCTTTAGCCATTGGACTACATCC
Right flanking sequence: Indices 246557 -- 247056
ACAGTAAGCCTTTTCTTGTTCGTTCTTCGAGCTAGTGGAGTCCTTCCGGCTAATGAAGATACTAC
TCCAGTCTTCCCATTCATTCACAGTGGATCCTTCCTTTTCCCTAAGAATTGAACGAACCAAGTTC
ACCTATACGAGAGTGAAGAATAAAACCCTACAATCAACTTCCCACTTTTGATGTCCCACGATTCT
GCTAGTTTAGAAACTAAAGAGAAAAACAGGCGTCAGAAAAGCGATAACTCAAAATTCTCCCCAAG
TAGGATTTGAACCTACGACCAGTCAGTTAACAGCCGACCGCTCTACCACTGAGCTACTGAGGAAG
AACTCCCTTAAGGAAGCCGACTCTCGTTCTTTGGACCAACCTATGACCGGGTTCGTCACTCTTTT
TTTTTCCCTTGATTGAAAGAGGCTAAGCGCGGTACATTGAGTAAAGGGAGGATTTGCTACATCGC
TACATCGGGCGGTGGGTGGCCCCTTCGAGAGTTGCGGGTCCTTGC
Found at i:278456 original size:22 final size:22
Alignment explanation
Indices: 278428--278472 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
278418 TGCGAAACTC
278428 AACCACTGAAATTGGTACACGA
1 AACCACTGAAATTGGTACACGA
278450 AACCACTGAAATTGGTACACGA
1 AACCACTGAAATTGGTACACGA
278472 A
1 A
278473 GGCTCCACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (22 bp):
AACCACTGAAATTGGTACACGA
Left flanking sequence: Indices 277928 -- 278427
CTGGCTATTGCTTTCTCACTCATTGATCAAGGGAAGAGGGTCGGGCACTTGAAAGCTATCGCTTG
AGATAAAGAACATATAGGTACAGAGCCCTTTCGGTAGGGGGTCTGGGTCCGTCTCAGTTCAGTAT
TGGAGTCCATTGTGTTGTGAGAATCTTTTAGAAATGCATTTGATCAAGAGGAAAGGATTGAACGA
CTGATCGACCAGGGAGAAAGCTACCTTTTTAATGTCCCTCCCAAAAAGTAGAACTTTCGGTCTAC
TCAGATAGGAAAGTCAAGTTCATGTGGAAGCTTCAGTCACAGGTGGGGAAGCAAGAGAGAGAGAA
GGAAGCTTGGTTCGACCAGACATTGATCCCCTCGGAAAAATCCCATGTTGATGGAGATCCATCCG
TTGGGGCACCATACCCCACCCACACCCAAATCAATGCTCGGCTAGCTTGTTTCTGATGACTATTT
GGGATTTTCCAAAAAGAAGAGGAAGATGACGGGAGTGCGAAACTC
Right flanking sequence: Indices 278473 -- 278972
GGCTCCACTATGCGGGTTCACCTCTTAATATCTTAAAAAACACGAAATGCGGGCTCAAGAGAAAG
CAAAGCGAAAGTTAGGAGATATAGGAGAACCATGGGTTGAGGACAAAGGGCATGATCAAACCGTC
TTTTCGGATGAGTACTTTGCTTCGGTACCGGGAGTCTGACAAATGAAGTGAACTCTACATTGACT
GCCTAGTACTCGACTCGGAAAGAAGACTCACTCACTGTGCTTTCATTTCATGACAAAGTGGCCGA
GAAAAGACCTTATTCTGTGTTGAAGCAAGAGGCATTAGGAATCCTAGGAAGAGCGCCAGAAAGAA
GCTCACTCAGTAGTGTGGTCTCATCGAGTCGGAGAGGAAGCATCAATCAGCGCATAGGGAATCCG
GTGAGAGTGCTCAACAGCAGCTCCCGGTTAAATCGATAGGCCGAAAGCTGATTTAGACAAAAAGA
TTTTTGGTTGGGAGGGATACATGTTCCCGTCCCAACGGAGTGATT
Found at i:373836 original size:28 final size:28
Alignment explanation
Indices: 373768--373824 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
373758 CAACTACCGA
373768 TATCTATTAATATCTTTTCTTATAATGT
1 TATCTATTAATATCTTTTCTTATAATGT
373796 TATCTATTAATATCTTTTCTTATAATGT
1 TATCTATTAATATCTTTTCTTATAATGT
373824 T
1 T
373825 GTTGTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.58
Consensus pattern (28 bp):
TATCTATTAATATCTTTTCTTATAATGT
Left flanking sequence: Indices 373268 -- 373767
TTCACGCAAATCCGAAGAAGTTATCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTC
TGGCCGGGCTTTCCTGAGGTATCTAATAACCTTGCTTCTGCTCGCCGCTGGCGCACCTCTCCTAA
CTATTGCCCATTTATTCTGGAATAATTTTTTTAGGAGGGACAATTTTACATATTTCTGCCAAATC
CTTCTATTATTAAGTACGGCTGGTACCATTTCGATGTGTTTCGATTCTTCCGAACAAGAGAGGTT
TGATGCTTTTGAATTCATTGTATTAATTCTACTTCCTACTCGCAGTATGCTCTTTATGATCTCGG
CTCATGATTCAATTGCCATGTATTTAGCTATTGAGCCTCAAAGTTTATGTTTTTATGTGATCGCA
GCATCAAAAAGAAAGTCTGAATTTTCCACGGAAGCCGGCTCGAAATATTTGATCTTAGGTGCATT
TCCCTCTGGAATCTTATTGTTTGGGTACGACCGGACAACTACCGA
Right flanking sequence: Indices 373825 -- 374324
GTTGTTAAATATATATATCGTAAACTACCGGATCGGGTATTACTTAGATGTGAAACTTGCAGACC
TCATTGGTTGTGATATTGATCGTCACGGGGGGAACGAAATCTAAGAATATATAGACTTGTAGAGA
CCCTCTATGTAGTTGTCTATCTAGGGCGATCGATCTACATCTTTCCCCATAGCCCTGGGGCTGTG
TCTCGATCTCCTACGTGCGAAATCTGAGGGACTAGTTCCTATGGAGATTCCCCTTGGTCTAATTC
CACGCCTTATGACGTTTCGAAAAGGGAGTCGGTGTGGCGTAAAGTGAAGATCACGGGAAGTAGAG
AAGAATTCCCTTTCTGGGGTATTCCGAAGGTGTAACCTAGACAACGAAAAAGGGGCCCGATACTT
CAACTAGAAGAGCGACCAGTTGGTTCACCAAACCCCGACCCAGCGTTACACGTTTTCCAGGTCCG
AAGGGATCCAGTGCCCAATTACCGACTCCTCCCGGAATTGCGTTA
Found at i:404730 original size:15 final size:16
Alignment explanation
Indices: 404700--404732 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
404690 TTCTATTCTA
*
404700 ATTATAGGATTCTATT
1 ATTATAGGATTATATT
404716 ATTATA-GATTATATT
1 ATTATAGGATTATATT
404731 AT
1 AT
404733 ATATTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (16 bp):
ATTATAGGATTATATT
Left flanking sequence: Indices 404200 -- 404699
GCAAGTTCAGTCTTTTCAGGGCGAGCTGACCGCAGAAACCGTAGACTTCCATGATGAACCCACCT
TAGCCACCTCCGATCAGACAGAAAGATGCGATCGTTAGAGATTCGACGATTCCCGGTTGGACCTA
TTCAAGCGATTGAACGAGATACTCGACAACTAGAAAGACGCACTTGAATACTGAATGCTATGAGG
AGAAAGAATGACTATCACCAACCATAAAGACGATAAAAGAAGGCACTCCCGTTCCCCCGAAATCA
TCTTCTGTGCGTGGTTATCCAATCATGATGTGGTAGGCTTAGTAGGGCTCGAACCTACAATCTAA
CCGTTATGAGCGGTACGTTTCAACCAATTAAACTATAAGCCCCTACAGATCTCTACATGCAATTC
GCTCACTTCGGGAAGAGCGGACGGAAGGCGACGGGGAGGCCTTTGCTCTATCTGCTTCTTCCTCT
TCTCAGGAATGAAGAATTAGATAAAAAAAAATGGATTCTATTCTA
Right flanking sequence: Indices 404733 -- 405232
ATATTATATATATAATATTCTATATCTATTATTAGAATGAATAATATAATTAAGCAAGCGGCCCT
TTTGCGACTCAAACTGCCGGTACGCTTTCCGGCTCGCAACGACTCAAACGGGCGGAGGCTCTCTA
TTTGCTTGCACTGCCGGCTGTTCGCCTTTAGTTAGAAGTAGAAGTCGCTCTTTGCCCCACACTTC
TAAAAAAGTATGGATTAATTCAGTAAGAAAAAAAAAACTTGGTTACGGGAACCGAAGGTTAGGCC
GACTACTTACTTTCTCCTTACCCTTAACAGGATTGTCTCCTACCGATCGAGGAAAGGCTTAGAAT
CCATGCTTTGACCGGTAATGTCCAATCTAAGAACGTCTTGTGCCTTTTCCTGGGCCCCCTTCATT
CTGACTTAGCTAATTCAATTCTTTCTATTTCTAATGGGCTTATACTTTTTTCTATATCCCCCGAG
AAAAGAAAGTCCTGCTATATCTAATGTATTTTTTCCAGGACCGCT
Found at i:413503 original size:14 final size:14
Alignment explanation
Indices: 413484--413512 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
413474 TTACTAATAT
413484 AATATAGAATATAA
1 AATATAGAATATAA
413498 AATATAGAATATAA
1 AATATAGAATATAA
413512 A
1 A
413513 GGAGGAGGAT
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:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (14 bp):
AATATAGAATATAA
Left flanking sequence: Indices 412984 -- 413483
CCGTGAAGTCTCCCTTTGGACTAAGAAATCGGCACAGAGTAGAATCGAACTGATGTAATGGGCGG
AACGCTCCCCTACCGATGCCTTAGGCCCAAAAAAGCTTTCTTTTTCCTCAGGGGAGACCAGGAGC
CATTGATTGAATCCTTCGAGCTAGTCGGCGAAGGGACCAATGAGTATGATAGAATAGATAGGAAT
GCCAGAGCGTCAATGAAATTCATGTTTTCCGGTTCTCCATTTATGAATAGAAAAGGTCTTGAAGC
CCAAAATCAAGTTTTTTTGGAAAGGAGTAAAGTCAGGCTTTCTTCAACATCTGTACTTGATCTAA
CCCTTTCTTTTGCTTGACTTTCGTTTTCAATAAGGCTACCCTATCGCGATAGACCACCTTACTCA
AATAGGGGGCATCTCGGGCATTGAAAGCAAGGAGACTGGAAAGGGCTGAGGTAAGGGATCGTGAG
CCATAAGCAGCAAGCACAGTATTCAAGTAAAGGCCTTACTAATAT
Right flanking sequence: Indices 413513 -- 414012
GGAGGAGGATTTGGATCAAGCTCATATTACTATCACATTACTATGTTAGGAGATAAAAGCCATTC
AATCCCCGGGAGCTCTTTTTCCCTAAAGCGAACGGTCTACTCAAGCTCAAGAAAAGTAGAAGTTG
TGCAGCAAGTCGGGACTTCAATTCCTATCGTATCAGTTCGAGACAGTCAATTGTATCCCCCTCGA
CGCGAGGCCATCCAAAAGAATGAAGACGAGCTCACCCTGCAAGAAAACGGATGCAACAAGCAACG
ATTGAGCAGGGCGAATCCCTTACCCGGAGTCAAAATGCGCTGCGATCTAGCCTCTCTTGGCGCAC
CTACCTAATAGATAGAGATAAAGCTGAGGTAAGTAGTTAACTGACTAGTGCTTCCAGTCCAACAA
GTCTCCTATTTCCGAGTGAATTAGCAAGAGCACGACCCGCGACCTGTTATTCAGCGACATAAGAC
TTTTGTCGCCTAATCTTCCATTCCCCTCTACCTATGAGCTCCCAA
Found at i:461746 original size:13 final size:13
Alignment explanation
Indices: 461728--461753 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
461718 TCCTGCGAGC
461728 TTAGTTTATGAAT
1 TTAGTTTATGAAT
461741 TTAGTTTATGAAT
1 TTAGTTTATGAAT
461754 AATGCAGCAA
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:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTAGTTTATGAAT
Left flanking sequence: Indices 461228 -- 461727
AAGAATAGACGGAGACGAGACGTACGATTGAAATCACGTTTATGAAAGCAATGGCTCTTAGCCGA
CTAAGATGACCACATAGTGGTATACTACTTCACGTAATTCACGTAATTTTCCACTTTACCACTAT
CAGACTAGACCGGAGCTTTTGAATAGGGCTTTGAGGATAAAAAGACTAGCCGGAAAGCCATTCCC
CTGCTTGCGACCGCTGGACCACTTGGAATGATGGAAAAGAGAGTACAGAGAGCATTCCATATGGG
GCTTCCCATCGGGGCTACCATTTTATCAGGCCCGATCGAGGTTCTCTTCTTTCCCGTTCATATGA
AAAAGACCTGCAATGCTAATCTCGTTAGGCCACCCGAACCCATCGAACCGGAGTTAGATAGGTGA
AAAGATAACAAGACAACACCTGCCTATATCGCTCCTGTCTAAGCGAGCGAGACTTTTTCCATTGA
TATTTCCATATCATGTAGCGAGACTCCACTTTAGATCCTGCGAGC
Right flanking sequence: Indices 461754 -- 462253
AATGCAGCAATCGTAGGGTCGACAGTACCGGTGGGCTTTGAGCTACCAGAGCAAGGAGATAGAGC
TTGAGCTTTTCCTTCATGGACCAAGGCGACTCTCGTTAGCTCTACTTGGGCTTAGTGCGATTCGA
AACTGGGATTTTTTCTAGCCCGAAGAACGAACAAAGACAACAAGGAGCGACTGATAAGGAGCGGT
TCAAGCTTTCTGGCCATTCCAACTGCCTCCATTATTCTACTTTTTAAGCGCCATAAGCAGCCAAG
CATAGTGGTTCGCTCAAGCAATGGAGTTTGCGAAACTTCCGTTCCGGTAGTCCTTAACGCAAGGA
AATAGTAAGATCAGACCCTCGAATTCGATTACACACAAGCTGCCAAGTAAGCTCTCGAAAGAGCT
ACCTCAGAATGAAAGCTACATCAATCCAAAGGAATTCAATCCGTTATATCTCCACCTCGTAAAGC
CGTAACAGCATCGACTCATTAATGCGCCCTCAAGGGGCAGCCTAT
Found at i:469103 original size:16 final size:16
Alignment explanation
Indices: 469078--469109 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
469068 ACGATTTGAG
469078 ATTTTAGTTTCTTACC
1 ATTTTAGTTTCTTACC
*
469094 ATTTTTGTTTCTTACC
1 ATTTTAGTTTCTTACC
469110 GAGGTTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.19, G:0.06, T:0.59
Consensus pattern (16 bp):
ATTTTAGTTTCTTACC
Left flanking sequence: Indices 468578 -- 469077
AAAAAAGAAACTTTGGGATTGCTAAATCACCGATGAAATAAAGCAACGGAGCCACCATAGTATTT
TGTTTTTATTAATTCCTCCCAAGGAAAGGGTGGTCATTGTATCATTTACCGACCGAGGCTTTGTA
GACTCTCTATTTTTCTTCGGTAAAAGTGAATTCTCTTGTAGAGCCGTATGCAATGCGCAAGCAAT
GCCTGTACGGTTGTTCAATTCTATTATTATCTTATATCATCAGGGTAATGATCCATCAACCTATA
GCTGCTTTTTATGAAGCACAAATAGGAGAATTTGTCCTGGAAGCGGAAGAACTACTGAAACTGCG
CGAAATCCTCACAAGGGTTTATGCACAAAGAACAGGCAAACCCTTATGGGTTGTATCTGAAGACA
TGGAAAGGGATGTTTTTATGTCAGCAGCAGAAGCCCAAGTTCATGGAATTGTTGATCTTGTAGCA
GTTGCATAAAAAATAGCAGGAATTTCACACAAATCACGATTTGAG
Right flanking sequence: Indices 469110 -- 469609
GAGGTTTCATATTCTATATTCTATTAATTTGAATTTTATTAATTTTAATAAAATATTAAAATAGA
ATAGGAATATAGAAAAAATTCATAATCATCCGGTTAGGATCGATCTAAACCAGCCCATTATGCAT
ACGATTCAACATGCCAACTATTAAACAACTTATTAGAAACACAAGACAGCCAATCAGAAATGTCA
CCAAATCCCCCGCTCTCGGGGGATGCCCTCAGCGCCGAGGGACATGTACTAGGGTGTATGTGCGA
CTCGTTCAGATTGTGGTTTTTTTCAATTGAAAATGCGAAAGAATTCCCCATTGGTAGCAAATGAT
TATCTGTTAAGCAGGGCAAATCTTATTTAAATTAAAATAAAAAGCCGAAAATGGATGCCTCTACT
CTTGCAAGAACGGACTAACAAGGTCAACTAATCCGCATAATTAAATACCGTTACTGTAAAAACGG
ATCTCGTTGTGAAAAACCTACTACTGGGGAGGGTAGAGCCAAAAA
Found at i:524929 original size:24 final size:24
Alignment explanation
Indices: 524902--524949 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
524892 AACTTGCAAA
*
524902 CATAACCAGGCAGTGAGGTATCTT
1 CATAACCAGGCAGTGAGGAATCTT
* *
524926 CATACCCAGGCGGTGAGGAATCTT
1 CATAACCAGGCAGTGAGGAATCTT
524950 AAGGGGAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (24 bp):
CATAACCAGGCAGTGAGGAATCTT
Left flanking sequence: Indices 524402 -- 524901
GGCCAAATCAGGTCTTGTAATATACTGCAGGGCTCCAACGATGCTTCTGTACAGAGATGGATTAT
GAAATGGAGTAGAAGAGACTGCAGCAGAGGACTGATTTTAAAGTTAATTGGAGAAGAGCAGGGCT
TACAATTCAGCATAGCAGCTCTCTGGAGGAGATCCAACGCATATTTTTGCTGTGTTAAAAAAAGT
CCACGATCATTCTTGTCTTGAGTACCTCAATGCCAAGAAAATAGTTCAAGTTCCCGAGGTTCTTT
ATAGCGGAGCACTTAATTCAGTGATTAGAGTGGAGATATAAGAGGTATCACTGCCAGTTATAATA
ATATCATCCACATAAACCGCAAGAATTGTAGTTCGCAAACTGTTAGTTTGAATAAATAACGAGGA
ATCACTACGGCTCATAAGAAAGCCTTTACTGATTAAAAAGCTATAAAACTTATCATACCAAGCGC
GTGATGCCTGTTTAAGACCATACAATGCTTTCTGCAACTTGCAAA
Right flanking sequence: Indices 524950 -- 525449
AAGGGGAGGGGTTGGTAGTGAAGGGAAGTCCAGGGCTGTGTCTGATCAGCTTACTGGGAGAATTC
CAGGCGAGGGAGTATTGGTAAGGTTATGGAGGAAAGAGGAAATAGGATTTTGGGCATCTCTCGTT
GCTTCGGATGTTTATGAGAAAGAAGCTTCTCACAGATATTGACTTTTAGATAGATACCAGCATCG
TATCTTAATTAGCAGTTTCTTGAACTTGGTTGCACTCGTAAAGCAGCTTAAGAGAGCAACGAAAG
ACGGAGCGGTGATATTTCATGACTAGCAAGTGGAGGATCATTCCAGGCTCTAATTCAGTCTCTGA
TGGCGTAGCTGATGTGTCATGCTAGGAAGCTGAGCTAGGGCATTTCTTCTTTCGGTTTAAGTGTT
GTGAAAACCCTCCTCTCCGCTTCTGGCAGCATAGAAGGAAGCTTGGGGGAAAGGTCTAAGTGCAA
GCATTGAGTCAAACTGATTCAGGTATAGCAATGTAGTTCTTGTCT
Done.