Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_027406
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: 668584
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Found at i:3921 original size:36 final size:36
Alignment explanation
Indices: 3879--4419 Score: 1082
Period size: 36 Copynumber: 15.0 Consensus size: 36
3869 CCTATGTCTT
3879 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
3915 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
3951 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
3987 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4023 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4059 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4095 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4131 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4167 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4203 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4239 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4275 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4311 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4347 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4383 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4419 T
1 T
4420 TTTCTTGGTA
Statistics
Matches: 505, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 505 1.00
ACGTcount: A:0.47, C:0.14, G:0.25, T:0.14
Consensus pattern (36 bp):
TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
Left flanking sequence: Indices 3379 -- 3878
AAAACAGGTACTGATAACAAAGTACAAGCCCTAGCTTTTAAGCCGAAGAAAGAAGCAATCATACT
CCTTAAACAGAAAGATATTGCACTTCAAAATCGTTACTAGAAGCACTACAAGCGCACTTCCTATC
TAAACAAACCAAAGCAGAAAAAGCACCTCCCTCCCGGATAAAGAGCAAGTGTGCGAGAGAATAGA
ACTGAGCATCAAGGCTGCAAGACAGAAGGAAGGTTCCTGCGTGCAGGAAAGCTTTTTCACCGTCC
ATTGGGTATTTGTCTTTATCTCGCTCTCCCAACTAACTCAGACTTATGATAGGCGGGCTCAATTC
CAGATATTGACCTCTGGGGATCCTTCTCTTTGAATTCCCGGTCTTCCGTTTTCTTCCTTGGTTCC
ACCCTTCCATTCATGAAGCAGATCGCCGGGAAGGCTTTTTCTCAAGCATAAAACGAGAGACCCGA
TCACATTGATCGACAAACAAAACTCCCGATAGAAGCCTATGTCTT
Right flanking sequence: Indices 4420 -- 4919
TTTCTTGGTATTCACGCTCATCGGACTGAAGTTGGTCCTCATTTATCTCAGCAGAAGTCTTTCAT
GATCTTTTCATAAAGTTGAATCTAGCCAATGCAAACTCAACTCAGTTAGTACTCCTATATCAATC
GTTGTCGCTGCCTTCTCAAGATGACGGGTAACCCCTTTCTTTAGGAGGATCCATCTCTTTATCGC
AGCATGGTAGGAGCCTTGCATTATTTAAGCATGACAGGGCCGGACATTGCCTTTGCCGTAAGCAT
TTGAAGCCAATTCCTCAATTGCCGCCCAGTACATCGTAAAGTGGATCGATCGATATCTTAAGGGA
ACTTCTCATTATGTCTTTTACCTCTTCTTCTGAGCTAGAGTTACATGCTTATGCTGATTGGGGTC
CTTGTCTTGATAGTCGACGTTCTCTTTCTGGGTATGCTCTCCTTTTTCTTGCCTAATCTCCTTTC
CTAAAACTCTGCGCTTCTCTTTTGAATCTTCTCACCCCGCCTAGC
Found at i:80389 original size:24 final size:24
Alignment explanation
Indices: 80347--80395 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
80337 ATTCGGATTC
* *
80347 GTTACTTGGGGCTGATGAGGATGA
1 GTTACTTCGGGCTCATGAGGATGA
* *
80371 GTTACTTCGGGCTCCTGAGGGTGA
1 GTTACTTCGGGCTCATGAGGATGA
80395 G
1 G
80396 GAATCCGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.41, T:0.29
Consensus pattern (24 bp):
GTTACTTCGGGCTCATGAGGATGA
Left flanking sequence: Indices 79847 -- 80346
CAAAAAGTTTAAATTGTCAGTTTCATCCTCTTTATGAGCCTGAGATCATAATCATATGGGTCAAC
AATTCTCATTTCTTAGTTACAGAAAGCCCTTCTCAAGGAAGTAAGCCAAAAGCCACTCATCTGAG
CCAGCGGATTCTCATTCTGCTGTGCCGGTGCGCAAAGCAAGCACGCTTAGACTGCGATGTGCAAT
CTTTGGTCTGCCTATCATTGTCCATTAAGGGCTGACTCCGCTAGGCAAGAGGACCACTACTGGGA
TTATTCAACTACTAACTGATGACCAGGGGACTACTCTGCTTCTTCCACTACTGATATTGACCGAC
CTGTTGAGAGGATAGCAACAGGAGAAAGAAAAAAAAGAAGTCGAGTTAGGTTCTGTTCTAGTATG
TAAGCATCTCTTTCCTCGGTCGATTCGTCTGCTCATTCAGCGTATGATTCTTATCCTACTTCCGA
TAAGTCTTATGAAACGAATTCGGCTGGAGATAGGCATTCGGATTC
Right flanking sequence: Indices 80396 -- 80895
GAATCCGTTGTTTCGGGATAAACTTGATATGTTAGTTCGGCCTCGGCTTCTTAGGATGATGCCTG
TGCAATGTATGATCCATCGGATTCTTTTTATTCTATTCTCGGTGCGTTGTTCTTCAGCGAATGAA
AGAAACCGCTGATTCCAAAGTTCCTTCATCAGATTTGGGTGCTTTTGAAAGAGCTGCTTCTGCGA
ATGACTCAACTGATACTACTCAAAAATTTCCCACATGGAAGGAAATGGGATTTTTGAGAAAAGGG
GTTGGGAACCATCGAAGGACTAGCAACCTGACAGTCCTAAGCAACCTTGAACCAACAACGTTACA
TATACCATACTGCTATAGAAGACATGAGTACCAGTTAGACTACGGGACGCGTACACCCGAAATTG
GTGAGCTACTTACTGCCCCTTAAGTCAAGAGAATAATAGTACTTTCAGCAAAGGATATCGTAACT
ATGGCGAATACGTTTTTCTTGCTTTCCACATACCCGGAATGCGAA
Found at i:97772 original size:26 final size:26
Alignment explanation
Indices: 97738--97795 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
97728 TTCCATACTT
* *
97738 AGAGAAAGATTTTAAGTTAAGAGAAG
1 AGAGAAAGATTTTAAGTCAAGAAAAG
97764 AGAGAAAGATTTTAAGTCAAGAAAAG
1 AGAGAAAGATTTTAAGTCAAGAAAAG
97790 A-AGAAA
1 AGAGAAA
97796 ACTGCCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (26 bp):
AGAGAAAGATTTTAAGTCAAGAAAAG
Left flanking sequence: Indices 97238 -- 97737
CTATCCGTCCCTTTTGCTAGAGTAAGTAATTCCCTTCCCTTTTGTTTGCCAGCGTAGCGCATTGA
TCATTGAAGTGGGGGCTAGGCGAGGGCATGGTCTACTTTTTGTTCTGAAATGACTAAGTACGGCT
TGGCTTCAGCTCGTGGGACTGGTTCTCTAGAAAAAGTCCCAAACCCCACATCCTGCAGTCCGCCT
GGATTCGATTCGCTTTTAGTAATTATATTACATTATATATATAAGTAATTAGAAGCTAAAGAGAA
ATTCAATATTACCATATTCTACCGCTCAACTAACGCTATGTGATCCGGTCAAGATGAATCGATCG
AATTTCACAGCTGAGGAGGCAAAGGGAGGCAAAGCGAGAGGTTCTGAAAGAAAAGACTTTATAGA
ACCTTACTCACACGATACGGGGATGGGCCTACACAAGCAGAAGGAAGAGCTATTAGCTTGTCGGC
GTAACGAATGAACTATCGGATGGTAGGCTAACTGCTTCCATACTT
Right flanking sequence: Indices 97796 -- 98295
ACTGCCTTTTTTTTGAATTGAAGGAGGAGTCGCGCATTCGTCTGCAGCGTATAGTATAGTAGCTT
CAATGGAAATCCGTTTGAATTGATGATTTTTCACCTGATTCCCCCAAAACCGTAGAAGCTCAGAT
CGGGGTTTAGCGATAACCTGAGATCCTTTATTCTGTCTCCACTTCTGAGCCGACCGAGCCTGAAG
CCAATATGTATGAAAGAAACCAATCAACGCAGGAATGGAGTTCGTAGCGAGAAGATAAAGTTCCT
CGCCTGAGAAGCACTTCACTGGGTAATAAAAAAAGCTACCTAAAAGATCTTATTACCTTTACTCT
AAGATGCTATAAGATAATTGGGAATCTTTTAGCCGCTATTCCCGCACTATTGTAAACCAGCTTGA
TAAAGGGTAGTGGTAGAGTCTCAGTACCACTGAAAGTGCGATAGTCGGGCAAACAATCTCCTCTT
TTTATCATATCATATAAGGTAGGGTATTGTATATATGGAAATTCA
Found at i:155779 original size:21 final size:21
Alignment explanation
Indices: 155753--155799 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
155743 TTAAGGGATG
155753 TAACAGAAGTTTCAAGAGAAC
1 TAACAGAAGTTTCAAGAGAAC
155774 TAACAGAAGTTTCAAGAGAAC
1 TAACAGAAGTTTCAAGAGAAC
155795 TAACA
1 TAACA
155800 ATCGATGGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (21 bp):
TAACAGAAGTTTCAAGAGAAC
Left flanking sequence: Indices 155253 -- 155752
TTAAGACTGTTGCAATTGGTACAACTGCTTCAATGGGATAGAAGGAAACTGGCTAAAAAGGATTA
GAAATGGACTAGTAAGAGACTCCAATGTAACCTCAAACTTAAATTGGAACCCTAGGAGGGGCAAC
TTCCACTCTTTTTTTCACTCTTTCCATTGTCGTTTACTTTACGAAGCGAAGGAAATCAAAAGGTA
TGCCCATTTTATCGAGGAGAGGAATTACTAGCTCGCAGGCTTAAAAATGATAACTTCCTTCCTTG
CCCTCGAACCGACTATCCAACGGCATGGAACACTTAGCATTGGCCTATAACTCAAATTCCATTTT
ATAGCACGCCAACAGGAGGGGCTTCTTACAAAAGCACTCCAACAACTCGCTTGAACTTGAAGAGA
GAAGCAACTACTACTTCTCCATCAAAGGAAAAACAAGCATCGACTAAATAGAAGGCCCTTGAATC
TTATCGTTAGAGCGCTATCTACCCTTAAGACTTACTTAAGGGATG
Right flanking sequence: Indices 155800 -- 156299
ATCGATGGACTGGAAGGGCGAGAGACAGAACAGCAAAGAGAACTCAATCTAGAATTTCCACTCCT
TCTAAAACCCCAACCCCAAGTACGGCATTAGCAATTGAAGAGCTTAGTTAGGATGGGTGGAACTA
CAACCCCTCGAACAGGCTCGATAAAGTCTGGGAGATTAGATAAGCTGGCTAGGTATTTTTATATT
CTTTTTACTGAAAATGCACCGAAGGCAACTGCCATTGAAACTATATAGCTTTATATATAAAAGGG
AGAATTCCGCTCGAAAACCAGCCCTCTTCACACCAGTACCTCTGTCCCGACATTTGGTGAGATAG
GGGTAATGCCTACCAAAGGTAAAGGGGAGCCTTCATGCAAATCTATTGAAGGGTCACCTACGTTA
GCTGGTGCCCACAGTGCCAAAGTTTCAACCAAGATCCTTTGGCTCCGTGCTGGTAGCCGGCTTGT
TACTCCAGATTTTAGTGACAAGAACGTCTGTCACGTGCGTCCCTA
Found at i:206579 original size:21 final size:21
Alignment explanation
Indices: 206553--206595 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
206543 TCGACCTCTA
* *
206553 CAATCGGGCGAGGTACGAGAC
1 CAATCGGGCGAGGAAAGAGAC
206574 CAATCGGGCGAGGAAAGAGAC
1 CAATCGGGCGAGGAAAGAGAC
206595 C
1 C
206596 CCTTTTCCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.37, T:0.07
Consensus pattern (21 bp):
CAATCGGGCGAGGAAAGAGAC
Left flanking sequence: Indices 206053 -- 206552
ATTTTTCCCGCGCAAATCATTCTTCATCGCATAAGCCCATGACAAGTCATTTCCAGATGCTTCTT
TCGGAAGAGCACGGGAAAGCCTCAATTTGGTGGGATCAAGTCCAAGCAAGGCGTGAGCGGAAAGG
CAAAGGGAAGTACATGGGACAAGATGCGATCGAGGTTGCAGGATTCATTTCTACCCGAACATTAG
ACCCAAAGCTTGTTCCAAAGGTTTCACTTCGCTTTAAAGGATAGGAGGGAGAGAAGCGTACAAGA
AAGCCCCTACTCCTTAAAAAAAAAGTAGCAGAGTTCTACCAATTGTTTATTTGCAATGGCTTGAA
CGAATCCGACGCAGAATCCCTTGCTTGCTTGATAGGGCTTGAGGTTATAAATCCAAGATGAAATC
TCGATGCATCAGATGTGGAAAGTGGCCTATCAACTAGCTCTAAAGGCCGAGGAAAAGCTAAAGAG
AAGGACCACAAGGGGGCACCGAAGGTGATAGGGGATCGACCTCTA
Right flanking sequence: Indices 206596 -- 207095
CCTTTTCCCTTCCCTCAATATATATGGCACGCTTTACTAATATAATAGAAAGTCAAGGCTCCATC
CTACTCGTTGCCCAGAGCCTTGACTTGAGCATTGTACAAGCGCTTAAGGCTCCTTCGGGCCATGG
CCACAACTATTATATAAGGCAAGGCTTGGAAGCAAGCTACCAGCGCTTATCGGCGAGAACTAGGC
TTGGCTTGGTTAGTAGTGCCCGCCCATTTTGTCTCGCCCGCCTTAGGCCCATGAATTCTTCAGAG
CGGGGCGGCAGGCCGGCGGGCGGGGGCCATCACCGGACGGGGACCATCAAAGAAGTGCCTCGACG
CGCCGCAGCCACTACTTTGACTCCTTTTATGCAATTATGAACTCCACGGAACTTTCTCGATTCCA
ACGCAACTTATCCTTTTGGAGCTGACGTAACAAACTACGCGAGCCTCCCAACGAAGCCAACATAA
ATCCGATCCAAATAAAAAAAATAAAAGGAAGTTTCATTATGGTGG
Found at i:256317 original size:17 final size:17
Alignment explanation
Indices: 256297--256332 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
256287 ATATCCTTAG
256297 CTTTCCTGTATCTCTTT
1 CTTTCCTGTATCTCTTT
* *
256314 CTTTCTTGTCTCTCTTT
1 CTTTCCTGTATCTCTTT
256331 CT
1 CT
256333 CTATCTTCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.31, G:0.06, T:0.61
Consensus pattern (17 bp):
CTTTCCTGTATCTCTTT
Left flanking sequence: Indices 255797 -- 256296
GGCAAGAAATGAAATCGAATAATTGTATGCCGATCGCGCCCTCTCTTTCAATTGAGCTGATCCCC
TCGCTTCTTTACCCGGTGACTTAAATTTCTATTCATTACTGGGCTATTCCCACGTACTCACTGAC
GAACTGTACTAATTGGTGGGTTGATCCAGGTAGCTCAGATCTGGGAATGTACTACAGGGAGCATC
CTGACTAGTCTCATTGACATTTAAATGAGCATCCTGTTCCCTTCTGCTTCAGCATAGTAGACCTA
TTCTCCGAGAAGGAAGACCCTGTCCAGAAAAGTGGATTTCCCTGCTGTAGTATGAGTTGAGAGGA
TCAGACTTACGGGGGAACCTTCTCTAGTCTAGGAGCATTTCCACTATGTCTGTGTTCTTTCAATG
CCCCTTCCCAAAGCAAAGCAGGAAGAAACCTATGGCGCATTCTTCTCTTTCAAAAAAGCTTTGGT
ATTGCGCCTTTCTGTGCTCCCTTTCGCCCTTCGTTATATCCTTAG
Right flanking sequence: Indices 256333 -- 256832
CTATCTTCCCATTCCTTGTAAGAAGTCCTAGGAGCCAAGACAGTAAGTAAGCCAGTCTTTGGTCT
TTTAGTAAGTCTTTCCCTTCCTTGTACTAAGTAAGTAGGGGATCCTTTCTTTCTTTTTAATATTC
TTTCTCTCCAGGCAAGCAAGGAAGTAAGCAAGTAAGGAAGGGGGTCTGTGATTAATAGGTAAGCC
TGTGCTGCTAGTGTTAAGCTAGTGGTAAGGCAGCAGTAGGCCAATAATCCTTCTTTATAAGAGTC
CTAAATCCTAGGGTCCTCGTAGTCCATTAGGAAGAAGGCAAAAGAGCTTACCTCTGAAGACTGAA
GGAACAAGCGATTACTCTAAACCAAAGCGAACGCGAAGGGGTATCGGTAGTCCCTTTACTTTATT
CCTTGGCAGGAATAGCGGAAATGGTAACTCCAAACCCTTGAGTGGCTGGTTGAATGGATTTGGGC
GTATCTTAAATAAGGTAATTGATTGATTGAGTTGTTTCTGGATAA
Found at i:298639 original size:16 final size:17
Alignment explanation
Indices: 298607--298652 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
298597 CATCCCTTGG
298607 GGTTAGTTCATTCTCTT
1 GGTTAGTTCATTCTCTT
*
298624 GGTTAGTTGA-TCTCTT
1 GGTTAGTTCATTCTCTT
* *
298640 GCTTAGTTTATTC
1 GGTTAGTTCATTC
298653 CATTTACTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.13, C:0.15, G:0.20, T:0.52
Consensus pattern (17 bp):
GGTTAGTTCATTCTCTT
Left flanking sequence: Indices 298107 -- 298606
CTTCTATCCCCTTACCGAATTCTCTGTCTGTAATATTAAGTGTTGTAATAAATGTTATAGTTGAA
AGAAATTCCACCTCCTCCTTTTTTTTTCTCATCCCTTAGCCTTAGCTCTTTGATGAGCTCTTCGA
GAGTAATGAAATAGGCGTAGGCTCGATGATTCTTGAAAGTGAATATCGCTCGCAATGGCCGCCCT
GAGAGTTGAACCCTTCAACGGATAATTTCGTATGCTAGCTCCAATGAGTAGTAGAGGAAAGCTCG
GCCTCAGTGCGTCCTACTTGTGTCGTGTTTTAAGCCTGCTATGCATTCTTGCTCCATCTACCATT
CCTGACAAGCCATTTCTGGTATGCCCGCTGCTTCGTCCAAAATGACTTAAAATCCATCCTATCTT
TATTGGGATCATACCCCCTTGGACTTTACTTTTTTTTTCTGTTTTAGGAATTTATCCCTGGGCTT
TCAATGGGACCATGCCTTGGATTTCAATCCGAGATCATCCCTTGG
Right flanking sequence: Indices 298653 -- 299152
CATTTACTGCCCCTCTTTTGCTTGATGAAAGACATCCTGGCAAAGGCCTTGTATATTAGTAAAAA
AGGGGACTTTAATGGGTCCGATGGCTCTTTGACTGGTGTGCCTGAAAATGTGATTGATAAATGGG
CTTTTGAAACTCGATTTGTCGCAACAAGAGGTATTGTCTCCGCCTTTTCAAGTAGGGATCATCTC
TCAAGTGTTATGATCCTCCATTTCTGCTCGGTAGTGGCCTAAGGCTCAATGATGGATCTTCCTAG
CTAAGGCTAGCATCTCATCCCAGCTTTCATCTTATTGCTTTGAGCTCTCTTTGCTTTGGGAAAGT
GTAAAAGTGTAACCTGCTGCTCCTTGATTTCACATAAACAACTGAGTGTCTTCTGCTCCTTTTGC
TCTTCGCTTTCTGTGTTTATTGATCTCCTGCCCACTCACATTCTCTTTCTTTATCGAATCCTTAT
AGGCAGATAGGACTACTCCTGCTTGCTCTTGGCCTTGGCTGCTTA
Found at i:325711 original size:26 final size:26
Alignment explanation
Indices: 325675--325727 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
325665 GGGACAAAGG
325675 CCTCGAATCCTGTCTTTGACGGCGAT
1 CCTCGAATCCTGTCTTTGACGGCGAT
325701 CCTCGAATCCTGTCTTTGACGGCGAT
1 CCTCGAATCCTGTCTTTGACGGCGAT
325727 C
1 C
325728 ATAGCGTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.32, G:0.23, T:0.30
Consensus pattern (26 bp):
CCTCGAATCCTGTCTTTGACGGCGAT
Left flanking sequence: Indices 325175 -- 325674
TCGCAGTGAGCGCTACCTAAGCACTGTTGAAGGCACTCAGAGAAGAGTGGAAAGAGTCCTAAGAG
GGCTTCTCACTAAGACTTTCGACTCACTGCCAAAAGCTCCTTCTTGTGCGCTAACGCTGGAAGGG
ATGGTTTTGGGTGGGGGAGAGATCACTGGAAGACTTAGTCGTTTAGATAGAGATAACATTTCTAT
AATAAAAAATATGGAACTCAGTACCCCCAGGCGTTCGCTAAATGCATTTCGCTTACAGTCACTAG
GAAGGGGTTCTAGTAACGAAAGATTCCTTCCATAGATAGGCCACATTTCTCATATTCATTTCAGT
GCTTTTGGTCTACCGTTTTGGAAAGCAGGGGCAAGTCAGGCATCATGCTTTCCTGGGGAGATCGT
TTCAATTTACATAATAGTTAAGCTTCGTGCTTGCTGTGAAAGTGATCTTCGTAATCAAGAGATGG
GGCGTTCTCTCTCCCTACTTAACTAACAAGCAATGGGGACAAAGG
Right flanking sequence: Indices 325728 -- 326227
ATAGCGTGTCACGCTGGGAAACTGATCGAATGTTTTCTGTCTCAATGTCAGTGTGAAAGTCCTAA
TATCTTTACGAGGTCGAAATAGCATCACAGAAAGAGCAGCCAGAACCTACTCCCAGTTGGCCAGC
ATCAAAGCATTCAAATGAAGAAGGAGTCCCCGTCCAACGGAGCACTAAGAAGCAAGGGACACATG
GACAAGAAATGGGTAAGGGGAAAATGAACTCATCGGTTAATAACCCAGTGTTTGGGACCAGAAGG
AAGGCATGGAACTCGAACTAGTGATTCCCTTGCGATCTTGTCTTCCTACTATAGAAGGATCAGAG
CCAGAAGTCCCTATAAAAGAAAAAAGTCCTAGGTGAATTTTTAGTTTTATTTGAAGAGTCTTACC
CCTACGGAATGAAAGAAAGTTTTATTCCGTAGGGGATAGTATCTGCATTTGCGTCTACTGAATAC
TATATTTCACATTGGGACGGCTATAGTCAATAGAGCCACTACCAC
Found at i:334261 original size:14 final size:14
Alignment explanation
Indices: 334242--334272 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
334232 TTTGAATTAT
334242 AATGCCACTAATCC
1 AATGCCACTAATCC
*
334256 AATGCCGCTAATCC
1 AATGCCACTAATCC
334270 AAT
1 AAT
334273 AGTTTAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.32, G:0.10, T:0.23
Consensus pattern (14 bp):
AATGCCACTAATCC
Left flanking sequence: Indices 333742 -- 334241
CTACGACATTCTGCTGGGCGTACTACCGCACTACCGGGATCCGACGCCGCTTCTTGTCTTGGGAA
AGATGCCTCGAAATTTCAAGGCCAAGCGCGAAGAAACTCGTTCCATGGTAGGACCGGTGGATGAA
GCCATCGCTATACTCCTAGACTCAAAGCCTAACGGAGACCAGCGCCCTATAAGCCCGCCATATGC
TTGGGAGGTAGACGAAAACCCCTTTCCGATAGGGTACCCGTTACCCAGCTTAAAAATCGTTAGAG
GCTTCGGCTTTTGTCAATGCCTGTCCATTTCCTGTTGTGGGCTGGGTTGTCAGGAAGTGAGCCCG
AGAGGGGCGTCCAGACGCGGGTCGAGTATGAATGCTTCCTTTATCCAAACAAGCTGTACTATTCC
TTTTCCACCGACCTTGGCTATTTGAGCTGCGGGTAACTAAGGCTCTACCCTTTCTGCCTTTCCTG
ATTACCTGATTGTTTTCCTGCTTCGCGAAAGTCTTTTTGAATTAT
Right flanking sequence: Indices 334273 -- 334772
AGTTTAGATATCCATGCACAGAGAAGCTGCTAGTCTTTTCGACTATGCCTTCCTTTCTAATTTTC
CTTCTTACAGGGCACGAACGGGAGCCTTTCTTTCCTAAGAAGGAATGTGGCGAAGAACCTGAAAG
TCTTTCTTCTTTTAATGCCCACAGATCCGCTGGAGGAAGGAAGCCAGGGAGACTTAGCATCCGAT
TATCGCAATATACTCTTTCTGGGAAATGTGCATGAAGAGTAATTCCATGTAGGCAGCTTATAGCC
TTCTTTCCTTGTTTTGTTGCACTCATTCACTCCGCAATTCCCTAAAGAAAGGGCAAGATAGAGTC
AAAAGGCAGAAGAAGAAGGGCTTTTCTTTGCTCTTCTTTCCAGGATTCCTTCTCATCGAGAGATG
CGGCATTACCGCTGTTGTCTCTATGCCTTTTTGCCTATCTTACTCTTTCTCGAGGGACAGATGCC
GATTATCCTACAATGCTTTTTTTAACATCTGAAAAAGCTTTTCTT
Found at i:384471 original size:26 final size:26
Alignment explanation
Indices: 384442--384519 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 26
384432 ATTCCTTTTC
384442 GGGAGCGATTCATCCTTCCCTTCACT
1 GGGAGCGATTCATCCTTCCCTTCACT
* * ** **
384468 GGGAGAGAATCAATAGATT-CCTTTTC-
1 GGGAGCGATTC-AT-CCTTCCCTTCACT
384494 GGGAGCGATTCATCCTTCCCTTCACT
1 GGGAGCGATTCATCCTTCCCTTCACT
384520 TTGCTTTGCC
Statistics
Matches: 36, Mismatches: 12, Indels: 8
0.64 0.21 0.14
Matches are distributed among these distances:
24 2 0.06
25 7 0.19
26 18 0.50
27 7 0.19
28 2 0.06
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.31
Consensus pattern (26 bp):
GGGAGCGATTCATCCTTCCCTTCACT
Left flanking sequence: Indices 383942 -- 384441
GCATCAAGCTGTTCGCAAGGGCCAACTTGATCCTCTTCCCCAGGGATCCCAGATGGGGGAACCTA
GGGGAGCCGCCGACTCCAACTACCGTCCATGTACGATCCATACTAGATCTGACCAACCGCCCATC
CTACCTCTTCTACGTTCTTGACAGCCCATCTTTGTCTCAGTAGAGTCTTTCAGTGGCATGTTTCG
GTCCTCTTCCCCATTACTTAGAAAAAGTGAGCCACCGGTTCAGGTACAAGATACTATCATTACCG
CCTGGACAATTAGACACCCAACCCGTAATCGCAACGACCCAATTGCAAGAGCGGAGCTCTACCAA
CTGAGCTATATCCCCCGAGCCAAGTGGAGCATGCATGAAGGAGTCAGATGCTTCTTCTATTCTTT
TCCTTGGCGCAGCTGGGCCATCCTGGACTTGAACCAGAGACCTCGCCCGTGAAGTAAATCATCGC
ACCTACGGTCCAACCAATTGGGAGAGAATCAATAGATTCCTTTTC
Right flanking sequence: Indices 384520 -- 385019
TTGCTTTGCCCAGCTAAACGCAAAGAGAACAATTGCTTCCTTCCTTAACTAAGTCAAAGAGCGGA
TTCGTACCATCCTGTTAAACAGTCGAGTTGCGGGAAAGAGATAGCATTCGCCACGTTCAAGCTAA
AAACTAGTTCGAACTAAAGTATTTATTCTATTAGGTAATTAGAAATATCGTAAGAGAAGAAGAAA
TGCCCAAAGACTCCCATGCTTTCCGTTGGTCAACAACCAATAAAAGTAAACTATAGTTTTTCACT
ACTCGTACAGTGAAAATGAAGTCTCTCCTTTTTTTGGGGGGAGCGGAGAATGAAAAGAATGAAAG
AAAAATGAAATTGTTTTCCACGGCTATTCAAAATTCAAAAGATTTTTTTTCAAAATGTTTGTCTT
GGCCTTGGCCAAAAACCGCTGGTTCTGCTACCGCTGGTTTTGCTATCGCTGGTTTAGCTACCGCT
GGTTCTTCTAATGACCTGGGGGTGGGGGGGCAAATGGAACCACCC
Found at i:384493 original size:52 final size:52
Alignment explanation
Indices: 384415--384519 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
384405 TCCAACCAAT
384415 TGGGAGAGAATCAATAGATTCCTTTTCGGGAGCGATTCATCCTTCCCTTCAC
1 TGGGAGAGAATCAATAGATTCCTTTTCGGGAGCGATTCATCCTTCCCTTCAC
384467 TGGGAGAGAATCAATAGATTCCTTTTCGGGAGCGATTCATCCTTCCCTTCAC
1 TGGGAGAGAATCAATAGATTCCTTTTCGGGAGCGATTCATCCTTCCCTTCAC
384519 T
1 T
384520 TTGCTTTGCC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (52 bp):
TGGGAGAGAATCAATAGATTCCTTTTCGGGAGCGATTCATCCTTCCCTTCAC
Left flanking sequence: Indices 383915 -- 384414
TCGCTCAAAGGGTTGAAGGGAGATAGTGCATCAAGCTGTTCGCAAGGGCCAACTTGATCCTCTTC
CCCAGGGATCCCAGATGGGGGAACCTAGGGGAGCCGCCGACTCCAACTACCGTCCATGTACGATC
CATACTAGATCTGACCAACCGCCCATCCTACCTCTTCTACGTTCTTGACAGCCCATCTTTGTCTC
AGTAGAGTCTTTCAGTGGCATGTTTCGGTCCTCTTCCCCATTACTTAGAAAAAGTGAGCCACCGG
TTCAGGTACAAGATACTATCATTACCGCCTGGACAATTAGACACCCAACCCGTAATCGCAACGAC
CCAATTGCAAGAGCGGAGCTCTACCAACTGAGCTATATCCCCCGAGCCAAGTGGAGCATGCATGA
AGGAGTCAGATGCTTCTTCTATTCTTTTCCTTGGCGCAGCTGGGCCATCCTGGACTTGAACCAGA
GACCTCGCCCGTGAAGTAAATCATCGCACCTACGGTCCAACCAAT
Right flanking sequence: Indices 384520 -- 385019
TTGCTTTGCCCAGCTAAACGCAAAGAGAACAATTGCTTCCTTCCTTAACTAAGTCAAAGAGCGGA
TTCGTACCATCCTGTTAAACAGTCGAGTTGCGGGAAAGAGATAGCATTCGCCACGTTCAAGCTAA
AAACTAGTTCGAACTAAAGTATTTATTCTATTAGGTAATTAGAAATATCGTAAGAGAAGAAGAAA
TGCCCAAAGACTCCCATGCTTTCCGTTGGTCAACAACCAATAAAAGTAAACTATAGTTTTTCACT
ACTCGTACAGTGAAAATGAAGTCTCTCCTTTTTTTGGGGGGAGCGGAGAATGAAAAGAATGAAAG
AAAAATGAAATTGTTTTCCACGGCTATTCAAAATTCAAAAGATTTTTTTTCAAAATGTTTGTCTT
GGCCTTGGCCAAAAACCGCTGGTTCTGCTACCGCTGGTTTTGCTATCGCTGGTTTAGCTACCGCT
GGTTCTTCTAATGACCTGGGGGTGGGGGGGCAAATGGAACCACCC
Found at i:384944 original size:15 final size:15
Alignment explanation
Indices: 384924--384980 Score: 80
Period size: 15 Copynumber: 3.8 Consensus size: 15
384914 TTGGCCAAAA
384924 ACCGCTGGTTCTGCT
1 ACCGCTGGTTCTGCT
*
384939 ACCGCTGGTTTTGCT
1 ACCGCTGGTTCTGCT
*
384954 ATCGCTGGTT-TAGCT
1 ACCGCTGGTTCT-GCT
384969 ACCGCTGGTTCT
1 ACCGCTGGTTCT
384981 TCTAATGACC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
14 1 0.03
15 35 0.95
16 1 0.03
ACGTcount: A:0.09, C:0.28, G:0.26, T:0.37
Consensus pattern (15 bp):
ACCGCTGGTTCTGCT
Left flanking sequence: Indices 384424 -- 384923
ATCAATAGATTCCTTTTCGGGAGCGATTCATCCTTCCCTTCACTGGGAGAGAATCAATAGATTCC
TTTTCGGGAGCGATTCATCCTTCCCTTCACTTTGCTTTGCCCAGCTAAACGCAAAGAGAACAATT
GCTTCCTTCCTTAACTAAGTCAAAGAGCGGATTCGTACCATCCTGTTAAACAGTCGAGTTGCGGG
AAAGAGATAGCATTCGCCACGTTCAAGCTAAAAACTAGTTCGAACTAAAGTATTTATTCTATTAG
GTAATTAGAAATATCGTAAGAGAAGAAGAAATGCCCAAAGACTCCCATGCTTTCCGTTGGTCAAC
AACCAATAAAAGTAAACTATAGTTTTTCACTACTCGTACAGTGAAAATGAAGTCTCTCCTTTTTT
TGGGGGGAGCGGAGAATGAAAAGAATGAAAGAAAAATGAAATTGTTTTCCACGGCTATTCAAAAT
TCAAAAGATTTTTTTTCAAAATGTTTGTCTTGGCCTTGGCCAAAA
Right flanking sequence: Indices 384981 -- 385480
TCTAATGACCTGGGGGTGGGGGGGCAAATGGAACCACCCCAACCACCCATCGTCCCCAGCCCCCT
TGAGCAATTTGAGATTGTGCCATTGATTGATTTGAAGATTGGAAACTTGTATTTCTCATTCACAA
ATCCATCTTTGTTTATGCTGCTAACTCTCAGTTTGTTCCTACTTCTGGTTCATTTTGTTACTAAA
AAGGGAGGAGGAAAGTTAGTACCAAATGCTTGGCAATCCTTGGTAGAGCTTATTTATGATTTCGT
GCTGAACCCGGTAAACGAACAAATAGGCGGTCTTTCCAGTAATGTGAAACAAAAGTATTTCCCTT
GCATCTCGGTCACTTTTACTTTTTCGTTATTTCGTAATCCCCAGGGTATGATACCTTATAGCTTC
ACAGTTACAAGTCATTTTCTCATTACTTTGGGTCTCTCATTTTCTCTTTTTATTGGCATTACTAT
AGTGGGATTTCAAAGAAATGGGATACATTTTTTAAGCTTTTTATT
Found at i:570565 original size:15 final size:15
Alignment explanation
Indices: 570545--570574 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
570535 CCAGTATATT
570545 ATTTTATTTCACTTA
1 ATTTTATTTCACTTA
570560 ATTTTATTTCACTTA
1 ATTTTATTTCACTTA
570575 GCCTGCCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTATTTCACTTA
Left flanking sequence: Indices 570045 -- 570544
TTTTTCATTTTAAATTGAAGTTTGACTCTGATTAGATCCTTAGCGCAAGCGCTAAGTAAGCAAGC
TACCTTATGTAATGTAAAAAAAACCGAGGAAAATAACGTCAAGTAGAAACGAACAAGGTCTTACG
GCACGATCGATCACTATATCTTTTCTTTTTTTTTTTTTTTTTATGGAAAGAGGGGATGATACGTG
GCGTGGTATACCTAATCGTTTGGTCAACGAGACGTACGTAAGTCGACATAGCTCCATGTATATGT
TCTTTGGAGCTAGAACCCATAAATAGAATGAAATAATGGTGAGCCTAGGGCGACGAATATGGCTC
AAGGGTGTCTATACAAAGCCCTTCTCTTATTCATTCAAAGGGCCAATGCACCAGCCAGCCGGTGT
GGTGGCGAACACGCTGTGCTGTAAGCCAAGCTGTTCACCTTGTAGACGGAGGAGATATAGAAAGT
GTGCCGTGCGTGATTCAAAAGATTCTATAGTAGCACCAGTATATT
Right flanking sequence: Indices 570575 -- 571074
GCCTGCCTCCCCCATGACTTTCCGGACCAACCAACCCAGATCTGCCCTCGCAAGTCTCTCTGCAT
TTTGGGAGCAGAGCATGCAAAATCGATCGAGCAATGGATGGATCTTAGAAGAATTCCACTTTGAA
CGGCACGACTCTTTCTATTTTTTCGCTGGAATTCATTTTGTCTCCCCTCCTCTTTCAATCGACAC
ACTCGACGCAGATAGCTCCGGTGGCCCCGGCTTCTGCCTCTATCAGGCGGCGGCAGCCCCCACCT
CCACAGCCACAGCATGGAGGAGCAGCTCCTTAATCCGCACTACAACCAATCCAAATTATCTCCGG
ATCGATATATGATGATGCTAAACCGAGACCGAGATAGAGAAAGAGGGCTGTCCCTTTGTTGGCTT
TTCGAAAAAAAGCACTCATAGGAATGGTGCGAATTCCCATGTTCTTTTTAGTCTCGCTTGGTTTC
GAGAGCCTCCCCCTCCCCGTCTCTTACTCGTCTTTTGAAAGCCGT
Found at i:583425 original size:19 final size:19
Alignment explanation
Indices: 583389--583430 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
583379 CTTCAGATAT
*
583389 TTTTATTTCTTTTATTTTA
1 TTTTATTTCTTTGATTTTA
*
583408 TTTTATTT-TTTGACTTTTC
1 TTTTATTTCTTTGA-TTTTA
583427 TTTT
1 TTTT
583431 GGTGCTGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTATTTCTTTGATTTTA
Left flanking sequence: Indices 582889 -- 583388
TGAAGCAGCCTAGCATCACTTTAGATAGAAGCAGAATGGATAACTTACAACTGAAAGTAAGTTCT
TCGGATCGATATCTCGTACGACGTAATGGAGATCTTGGTCTAGATCCGGTGGTTCGCAGAATTCG
GGACCTAACGATGTTCGGTTCGTCCCATGAACGGGAGCGGACAATTCCCTTTTCGGGGAATGGCT
GCAATCACAAGCAAGTGATTGAATGAGTGGGGGGCTCCGAAAGCACATGCGGGATAAGCAGGTAT
TTCAGGAGACGGTCTAAAAATGGGTCCGATTCAAAAAAAAAAAAGAGAACTCTCAACAAGCTGGA
ACTAATCAAGATCAATAGGAAGAGGAGTTAGCTAGGAATCTATTGACAAAGTTCATGCACCTATA
TGGAAGGGCTGTTTTGTTGATGTATTCCTGTCGAGAATGAAGAAGAAGAAAAAGAGCCTTTTCAA
CCGGCCCAGATCTATTATCACGAACCCTAAAATTTCTTCAGATAT
Right flanking sequence: Indices 583431 -- 583930
GGTGCTGCTACTGTTCAACTCCATACTAACATTTTTAAATTCCTATCATCATCGTCGCAGCTTGC
GAGTTTGAGGAAGATAAGGTCGATTCGAGGGAGGTGCAGCAAGCCCTCCCCCCGGTGCCGGAAGC
TTCTGAGCCACTACCACTAGCTCAGGAGCCTGTTTCTCCTTCGTTTGAAATCCAAGCTGCTGAAG
TCAACCAAGAGGACATCTGGAGGGAGTTGGAGCAGCAGGAGCAACCGGCACCAACGGGTGGAGCT
AAGCTAACAAGGCCTCACATATGCGAAAGCTCACCCCATTGGAAAATCAGGTAGCTGACCTTATT
ATCGATTTACGAAAATCCGAAGTACCCTCACCTAATAAGATTCAACAAATCGTCGAAATGCTCGA
AGAAGAAAGAATATGGTCTGGAAAAGCTGCGCACAATCAAAAAGCACAACCAACAATATGGCAGA
AAGAGTGTATTTTTTAGGAACTCCAAGGAGTGCTTTAATATGTTC
Done.