Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 94 of 433
Found at i:28463703 original size:37 final size:37
Alignment explanation
Indices: 28463653--28463790 Score: 249
Period size: 37 Copynumber: 3.7 Consensus size: 37
28463643 AAATATATTC
28463653 CGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTT
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTT
*
28463690 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTT
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTT
*
28463727 CGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTT
*
28463764 CGGGTAAGACCCGATAACTACGTGTGG
1 CGGGTAAGACCCGATGACTACGTGTGG
28463791 GGACTATTCG
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (37 bp):
CGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTT
Found at i:28464923 original size:46 final size:47
Alignment explanation
Indices: 28464776--28464951 Score: 168
Period size: 50 Copynumber: 3.7 Consensus size: 47
28464766 TGGGGTAAGG
* *
28464776 TGCCGATGCCATGTCCCAGACATGGTCTTACAC-AA-GC-TCTAGCATA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAACACATCTCG-A-A
* * *
28464822 TTTGTGCCGATGTCGTGTCCCAGACATGGTCTTACACTGACACATCTCGAA
1 ----TGCCGATGCCATGTCCCAGACATGGTCTTACACTAACACATCTCGAA
* *
28464873 -GCCGATG-CATGTTCCAGACAT-GTCTTACACTAACAGTCGTCTC-AA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAACA--CATCTCGAA
28464918 TGCCGATGCCATGTCCCAGACATGGTCTTACACT
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACT
28464952 GGCTCTCATA
Statistics
Matches: 108, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
44 13 0.12
45 14 0.13
46 19 0.18
47 13 0.12
48 10 0.09
50 31 0.29
51 2 0.02
52 2 0.02
53 4 0.04
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.27
Consensus pattern (47 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTAACACATCTCGAA
Found at i:28468347 original size:80 final size:80
Alignment explanation
Indices: 28468263--28468411 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
28468253 TATGGTAACC
* * * *
28468263 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
28468327 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
28468343 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
28468408 CCGG
66 CCGG
28468412 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:28468353 original size:40 final size:38
Alignment explanation
Indices: 28468304--28468411 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
28468294 ATCACGATTT
*
28468304 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
28468344 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
28468384 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
28468412 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:28476459 original size:80 final size:80
Alignment explanation
Indices: 28476375--28476523 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
28476365 TATGGTAACC
* * * *
28476375 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
28476439 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
28476455 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
28476520 CCGG
66 CCGG
28476524 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:28476465 original size:40 final size:38
Alignment explanation
Indices: 28476416--28476523 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
28476406 ATCACGATTT
*
28476416 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
28476456 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
28476496 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
28476524 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:28479718 original size:40 final size:40
Alignment explanation
Indices: 28479616--28479781 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
28479606 AAATTGAATG
* * * * *
28479616 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAATT
* ***
28479656 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAATT
* * *
28479696 ATATCCGGGCTAAGACCCGAAGGC-A-CGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAATT
* * *
28479734 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTA-GTAATT
28479774 ATATCCGG
1 ATATCCGG
28479782 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
38 31 0.30
39 2 0.02
40 70 0.68
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAATT
Found at i:28487683 original size:40 final size:40
Alignment explanation
Indices: 28487624--28487765 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
28487614 AAATTGAATG
* * *
28487624 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
28487664 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
28487704 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
28487744 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
28487766 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:28487766 original size:40 final size:39
Alignment explanation
Indices: 28487663--28487791 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
28487653 TGCTGGAAAT
* * *
28487663 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
28487703 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
28487743 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
28487783 TATATCCGG
1 TATATCCGG
28487792 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:28490103 original size:29 final size:29
Alignment explanation
Indices: 28490069--28490127 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
28490059 AGTTTAATTT
28490069 ACAAGTCTAGGGGCAAAAATGTAATTTTG
1 ACAAGTCTAGGGGCAAAAATGTAATTTTG
* *
28490098 ACAAGTTTAGGGGCAAAATTGTAATTTTG
1 ACAAGTCTAGGGGCAAAAATGTAATTTTG
28490127 A
1 A
28490128 AAAAATATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (29 bp):
ACAAGTCTAGGGGCAAAAATGTAATTTTG
Found at i:28496305 original size:44 final size:44
Alignment explanation
Indices: 28496239--28496331 Score: 168
Period size: 44 Copynumber: 2.1 Consensus size: 44
28496229 TGTAAAAAGA
*
28496239 AAGAGGATCTCTTTGCGTCACTCCTCTTAATGGGATGAAACCTT
1 AAGAGGATCTCTTTGCGCCACTCCTCTTAATGGGATGAAACCTT
28496283 AAGAGGATCTCTTTGCGCCACTCCTCTTAATGGGATGAAACCTT
1 AAGAGGATCTCTTTGCGCCACTCCTCTTAATGGGATGAAACCTT
*
28496327 CAGAG
1 AAGAG
28496332 AGAAAGCAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.29
Consensus pattern (44 bp):
AAGAGGATCTCTTTGCGCCACTCCTCTTAATGGGATGAAACCTT
Found at i:28497190 original size:17 final size:16
Alignment explanation
Indices: 28497127--28497191 Score: 53
Period size: 16 Copynumber: 4.0 Consensus size: 16
28497117 TTAATTGACG
*
28497127 ATAA-AAATATAAATAT
1 ATAATAAATATATAT-T
*
28497143 ATATTAAATATATA-T
1 ATAATAAATATATATT
* *
28497158 ATACACAAAAATATATT
1 ATA-ATAAATATATATT
28497175 ATAATAAATATAATATT
1 ATAATAAATAT-ATATT
28497192 TTATTCAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
15 4 0.11
16 17 0.45
17 17 0.45
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAATAAATATATATT
Found at i:28497313 original size:18 final size:17
Alignment explanation
Indices: 28497286--28497322 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
28497276 AATATCACAT
*
28497286 TAATACTATTATTATAA
1 TAATACTATTATTAAAA
28497303 TAATAACTATTATTAAAA
1 TAAT-ACTATTATTAAAA
28497321 TA
1 TA
28497323 TTATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATACTATTATTAAAA
Found at i:28500249 original size:168 final size:169
Alignment explanation
Indices: 28499982--28500293 Score: 414
Period size: 168 Copynumber: 1.8 Consensus size: 169
28499972 AAACACATTC
* * * * *
28499982 TAAAATTTGTTAATGTTCTGCATAAAGGATGCAACTTCACTTGTTTTTGTTTAGGAATTCTCAGT
1 TAAAATTTGTTAATGTTCTGCATAAA-GAGGCAACTGCACTTGTTTTTATTGAGGAATTCTCAGC
* * **
28500047 ATGTGACAGATAACAAATCAATCCTACAAATAACTTGTATTGTTAGTAATCAATTCTATTTTTGA
65 ATGTGACAGATAACAAATCAATCATACAAATAACTTG--TCGTTAGTAATCAATTCTATAGTTGA
* *
28500112 TTTCAAGACAGTTAACCAAAGGCAATATCACTGACTTTGTTT
128 TTACAAGACACTTAACCAAAGGCAATATCACTGACTTTGTTT
* *
28500154 TAAAATTTGTTAATGTTCTGCA-AAA-AGGCAACTGCACTTGTTTTTATTGA-GAATTCTTAGCG
1 TAAAATTTGTTAATGTTCTGCATAAAGAGGCAACTGCACTTGTTTTTATTGAGGAATTCTCAGCA
* ** * *
28500216 TGTGACAGCTTTCAGATCAATCATATAAATAACTTGTCGTTAGTAATCAATTCTATAGTTGATTA
66 TGTGACAGATAACAAATCAATCATACAAATAACTTGTCGTTAGTAATCAATTCTATAGTTGATTA
28500281 CAAGACACTTAAC
131 CAAGACACTTAAC
28500294 TGTGTTTCAT
Statistics
Matches: 122, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
166 37 0.30
168 39 0.32
169 21 0.17
171 3 0.02
172 22 0.18
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (169 bp):
TAAAATTTGTTAATGTTCTGCATAAAGAGGCAACTGCACTTGTTTTTATTGAGGAATTCTCAGCA
TGTGACAGATAACAAATCAATCATACAAATAACTTGTCGTTAGTAATCAATTCTATAGTTGATTA
CAAGACACTTAACCAAAGGCAATATCACTGACTTTGTTT
Found at i:28505170 original size:69 final size:69
Alignment explanation
Indices: 28505059--28505197 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
28505049 CAAGACTCTA
*
28505059 TCAGCCCTACCACCACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
1 TCAGCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
28505124 CCTG
66 CCTG
28505128 TCAGCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
1 TCAGCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
28505193 CCTG
66 CCTG
28505197 T
1 T
28505198 TTTTCCTATC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.28, C:0.32, G:0.13, T:0.27
Consensus pattern (69 bp):
TCAGCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
CCTG
Found at i:28514678 original size:2 final size:2
Alignment explanation
Indices: 28514673--28514704 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28514663 ACCACACATA
28514673 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28514705 GTATGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28514772 original size:206 final size:203
Alignment explanation
Indices: 28514486--28514862 Score: 648
Period size: 206 Copynumber: 1.8 Consensus size: 203
28514476 ATATTTGACT
*
28514486 TATATATATATATATATATATGTGTGTGTGCACGCCATATAATATTTATTGTATTAATTTTGGTG
1 TATATATATATATATATATATGTGTGTGTGCACGCCATATAATATTTATTGTATTAATTTCGGTG
28514551 AATCGATTAATTAATTACTTTTGAACTGAATTAATTGATAATTAAATTTTTAATTGATCTCGATT
66 AATCGATTAATTAATTACTTTTGAACTGAATTAATTGATAATTAAATTTTTAATTGATCTCGATT
*
28514616 GAATTAATTTCAATGACCGATCGATTTACTAAATTA-ATTTGATTTTAACCACACATAATATATA
131 GAATTAATTTCAATGACCGATCAATTTACTAAATTATATTTGATTTTAACCACACATAATATATA
28514680 TATATATA
196 TATATATA
* *
28514688 TATATATATATATATATGTATGTGTGTGTGCGCGCGCGCCATATAATATTTATTGTATTAATTTC
1 TATATATATATATATATATATGTGTGTGT----GCACGCCATATAATATTTATTGTATTAATTTC
* * *
28514753 GGTGAATTGATTGATTAATTATTTTTGAACTGAATTAATTGATAATTAAATTTTTAATTGATCTC
62 GGTGAATCGATTAATTAATTACTTTTGAACTGAATTAATTGATAATTAAATTTTTAATTGATCTC
28514818 GATTGAATTAATTTCAATGACCGATCAATTTACTAAATTATATTT
127 GATTGAATTAATTTCAATGACCGATCAATTTACTAAATTATATTT
28514863 TAGTGTTTAG
Statistics
Matches: 163, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
202 28 0.17
206 131 0.80
207 4 0.02
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.45
Consensus pattern (203 bp):
TATATATATATATATATATATGTGTGTGTGCACGCCATATAATATTTATTGTATTAATTTCGGTG
AATCGATTAATTAATTACTTTTGAACTGAATTAATTGATAATTAAATTTTTAATTGATCTCGATT
GAATTAATTTCAATGACCGATCAATTTACTAAATTATATTTGATTTTAACCACACATAATATATA
TATATATA
Found at i:28516686 original size:33 final size:34
Alignment explanation
Indices: 28516619--28516687 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 34
28516609 AATAAAATTT
*
28516619 AAATATTTTTAAATTACATTAATAATAAATAATA
1 AAATATATTTAAATTACATTAATAATAAATAATA
* * *
28516653 AAATATATTTAAATTA-TTTTATATTAAATAATA
1 AAATATATTTAAATTACATTAATAATAAATAATA
28516686 AA
1 AA
28516688 TAAAATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 16 0.52
34 15 0.48
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (34 bp):
AAATATATTTAAATTACATTAATAATAAATAATA
Found at i:28516699 original size:24 final size:22
Alignment explanation
Indices: 28516668--28516723 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
28516658 TATTTAAATT
28516668 ATTTTATATTAAATAATAAATAAA
1 ATTTTATATT-AATAA-AAATAAA
* *
28516692 ATTTTATATTTATGAAAATAAA
1 ATTTTATATTAATAAAAATAAA
*
28516714 ATTATATATT
1 ATTTTATATT
28516724 TATTAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 16 0.55
23 3 0.10
24 10 0.34
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTTTATATTAATAAAAATAAA
Found at i:28516713 original size:22 final size:22
Alignment explanation
Indices: 28516685--28516726 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
28516675 ATTAAATAAT
*
28516685 AAATAAAATTTTATATTTATGA
1 AAATAAAATTATATATTTATGA
28516707 AAATAAAATTATATATTTAT
1 AAATAAAATTATATATTTAT
28516727 TAAATTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
AAATAAAATTATATATTTATGA
Found at i:28539917 original size:24 final size:25
Alignment explanation
Indices: 28539854--28539991 Score: 80
Period size: 24 Copynumber: 5.8 Consensus size: 25
28539844 GGACTCACCG
* * *
28539854 CAGCTCGTATGAGCTTACCGATATTT
1 CAGCTCATATGAGCTTA-CTATGTTT
* * * *
28539880 TAGTTCGTAAGAGCTTACTAT-TTT
1 CAGCTCATATGAGCTTACTATGTTT
*
28539904 CAGTTCAT-TGGAGCTTA--ATGTTT
1 CAGCTCATAT-GAGCTTACTATGTTT
28539927 CAGCTCATATGAGCTTAC--TG-TT
1 CAGCTCATATGAGCTTACTATGTTT
* *
28539949 CAGCTCGGTA-GAGCTTACTGT-TTT
1 CAGCTC-ATATGAGCTTACTATGTTT
28539973 CAGCTCA-ATAGAGCTTACT
1 CAGCTCATAT-GAGCTTACT
28539992 GTTCATCAGC
Statistics
Matches: 92, Mismatches: 10, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
22 19 0.21
23 21 0.23
24 35 0.38
25 3 0.03
26 14 0.15
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (25 bp):
CAGCTCATATGAGCTTACTATGTTT
Found at i:28539992 original size:24 final size:24
Alignment explanation
Indices: 28539889--28540016 Score: 120
Period size: 24 Copynumber: 5.4 Consensus size: 24
28539879 TTAGTTCGTA
* * *
28539889 AGAGCTTACTATTTTCAGTTCATT
1 AGAGCTTACTGTTTTCAGCTCAAT
* *
28539913 GGAGCTTAATG-TTTCAGCTC-AT
1 AGAGCTTACTGTTTTCAGCTCAAT
**
28539935 ATGAGCTTACTG--TTCAGCTCGGT
1 A-GAGCTTACTGTTTTCAGCTCAAT
28539958 AGAGCTTACTGTTTTCAGCTCAAT
1 AGAGCTTACTGTTTTCAGCTCAAT
* *
28539982 AGAGCTTACTGTTCATCAGCTCAAG
1 AGAGCTTACTGTT-TTCAGCTCAAT
28540007 AGGAGCTTAC
1 A-GAGCTTAC
28540017 CGATCATGGC
Statistics
Matches: 86, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
22 19 0.22
23 19 0.22
24 30 0.35
25 10 0.12
26 8 0.09
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (24 bp):
AGAGCTTACTGTTTTCAGCTCAAT
Found at i:28540023 original size:26 final size:25
Alignment explanation
Indices: 28539972--28540023 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
28539962 CTTACTGTTT
* * *
28539972 TCAGCTCAATAGAGCTTACTGTTCA
1 TCAGCTCAAGAGAGCTTACCGATCA
28539997 TCAGCTCAAGAGGAGCTTACCGATCA
1 TCAGCTCAAGA-GAGCTTACCGATCA
28540023 T
1 T
28540024 GGCTCGAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (25 bp):
TCAGCTCAAGAGAGCTTACCGATCA
Found at i:28540139 original size:20 final size:19
Alignment explanation
Indices: 28540116--28540168 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
28540106 TAGCGGGCAC
28540116 AATTATTGTTTATATAGATG
1 AATTATTGTTTATATA-ATG
** *
28540136 AATTACGGTTTACA-AATG
1 AATTATTGTTTATATAATG
28540154 AATTATTGTTTATAT
1 AATTATTGTTTATAT
28540169 GATATATGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 14 0.54
19 1 0.04
20 11 0.42
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (19 bp):
AATTATTGTTTATATAATG
Found at i:28547638 original size:29 final size:28
Alignment explanation
Indices: 28547604--28547706 Score: 136
Period size: 29 Copynumber: 3.6 Consensus size: 28
28547594 TAATCGATCA
*
28547604 CGCACACTTAGTGCCATGTGATTTAAGCT
1 CGCACACTTAGTGCCAT-TAATTTAAGCT
*
28547633 CGCACACATAGTGCCATATAATTTAAGCT
1 CGCACACTTAGTGCCAT-TAATTTAAGCT
28547662 CGCACACTTAGTGCCA-TACATTTCAAGCT
1 CGCACACTTAGTGCCATTA-ATTT-AAGCT
*
28547691 TGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
28547707 ATCTCGTCAC
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
27 2 0.03
28 4 0.06
29 61 0.91
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCCATTAATTTAAGCT
Found at i:28554363 original size:12 final size:12
Alignment explanation
Indices: 28554348--28554374 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28554338 TATTTCCCCC
28554348 TTTATATTTTTT
1 TTTATATTTTTT
28554360 TTTATATTTTTT
1 TTTATATTTTTT
28554372 TTT
1 TTT
28554375 GTTCCAGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTATATTTTTT
Found at i:28555797 original size:29 final size:28
Alignment explanation
Indices: 28555763--28555865 Score: 136
Period size: 29 Copynumber: 3.6 Consensus size: 28
28555753 TAATCGATCA
*
28555763 CGCACACTTAGTGCCATGTGATTTAAGCT
1 CGCACACTTAGTGCCAT-TAATTTAAGCT
*
28555792 CGCACACATAGTGCCATATAATTTAAGCT
1 CGCACACTTAGTGCCAT-TAATTTAAGCT
28555821 CGCACACTTAGTGCCA-TACATTTCAAGCT
1 CGCACACTTAGTGCCATTA-ATTT-AAGCT
*
28555850 TGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
28555866 ATCTCGTCAC
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
27 2 0.03
28 4 0.06
29 61 0.91
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCCATTAATTTAAGCT
Found at i:28558517 original size:55 final size:53
Alignment explanation
Indices: 28558409--28558576 Score: 151
Period size: 55 Copynumber: 3.1 Consensus size: 53
28558399 ATTAGGGTTT
* * * * *
28558409 AAGGATACCATGTAAGGCCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGC
1 AAGGAAACCATGCAAGACCATGCCAAGACATGGC-ATTGATAA-G-TTCATAAGGC
* *
28558464 AAGGAAATCATGCAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGAAACCATGCAAGACCATGCCAAGACATGGCATTGATAAGTT-C-ATAAGGC
** * * * *
28558519 AAAGG-CCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGAAACCATGCAAGACCATGCCAAGACATGGCATTGATAAGTTCATAAGGC
28558572 AAGGA
1 AAGGA
28558577 TACTACGTAA
Statistics
Matches: 93, Mismatches: 15, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
52 6 0.06
53 9 0.10
54 8 0.09
55 66 0.71
56 4 0.04
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (53 bp):
AAGGAAACCATGCAAGACCATGCCAAGACATGGCATTGATAAGTTCATAAGGC
Found at i:28558862 original size:16 final size:16
Alignment explanation
Indices: 28558841--28558871 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28558831 ATAAATTTGA
28558841 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
28558857 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
28558872 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:28562386 original size:38 final size:38
Alignment explanation
Indices: 28562343--28562651 Score: 474
Period size: 38 Copynumber: 8.1 Consensus size: 38
28562333 CAAGGCCTGA
* * *
28562343 ATATAATACCAGTACTAGGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
28562381 ATATAATACCAGCACGAAGCCTGCAGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
28562419 ATATAATACCAGCACGAAGCCTGCTGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* *
28562457 ATATAATACCAGCACGAAGCCTGTGGGATTTAACCCAG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* * *
28562495 ATATATTACCAGCACGAAGCCTGTGGGATTTAACCCAG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
28562533 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
28562571 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* * *
28562609 ATATAATACCAGCATGAAGCTTGCGGGTCTTTAAGCCCGG
1 ATATAATACCAGCACGAAGCCTGCGGG-ATTTAA-CCCGG
28562649 ATA
1 ATA
28562652 CACATCAAAT
Statistics
Matches: 254, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
38 241 0.95
39 5 0.02
40 8 0.03
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
Found at i:28562990 original size:43 final size:44
Alignment explanation
Indices: 28562929--28563014 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 44
28562919 TAACATTTCA
*
28562929 TTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCG-ATATCG
1 TTTCACCGGCATTATAGCCTGCTAGGCCCAAAGCCCGAATATCG
*
28562972 TTTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGAATATC
1 TTTCACCGGCATTATAGCCTGCTAGGCCCAAAGCCCGAATATC
28563015 ATATTTTGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 35 0.88
44 5 0.12
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.24
Consensus pattern (44 bp):
TTTCACCGGCATTATAGCCTGCTAGGCCCAAAGCCCGAATATCG
Found at i:28566869 original size:23 final size:23
Alignment explanation
Indices: 28566843--28566927 Score: 68
Period size: 23 Copynumber: 3.7 Consensus size: 23
28566833 CGAACAATAC
*
28566843 GCTCTAATGAGCTGAAACGGAAA
1 GCTCTAATGAGCTGAAACGGTAA
* *
28566866 GCTCT-ATCAAGCTG-AACAGTAA
1 GCTCTAAT-GAGCTGAAACGGTAA
* * *
28566888 GCTC-ATACGAGTTGAAATGGTAA
1 GCTCTA-ATGAGCTGAAACGGTAA
*
28566911 GCTCCAATGAGCTGAAA
1 GCTCTAATGAGCTGAAA
28566928 ATAGAAAGCT
Statistics
Matches: 47, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
22 16 0.34
23 30 0.64
24 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (23 bp):
GCTCTAATGAGCTGAAACGGTAA
Found at i:28569586 original size:22 final size:22
Alignment explanation
Indices: 28569556--28569627 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
28569546 AGCTTATCGT
28569556 TTCAGCTCG-TATGAGCTTACTA
1 TTCAGCTCGATA-GAGCTTACTA
* *
28569578 TTCATCTCGATAGAGTTTACTA
1 TTCAGCTCGATAGAGCTTACTA
* *
28569600 TTTTCAGCTCAATAGAGCTTACTG
1 --TTCAGCTCGATAGAGCTTACTA
28569624 TTCA
1 TTCA
28569628 TCAGCTCAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
22 21 0.51
23 2 0.05
24 18 0.44
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (22 bp):
TTCAGCTCGATAGAGCTTACTA
Found at i:28569614 original size:24 final size:25
Alignment explanation
Indices: 28569520--28569647 Score: 74
Period size: 24 Copynumber: 5.4 Consensus size: 25
28569510 TTATCTTGTA
* *
28569520 AGAGCTTACTGTT-TTCAGCTCATT
1 AGAGCTTACTATTCTTCAGCTCAAT
* ** *
28569544 GGAGCTTA-TCGT-TTCAGCTC-GT
1 AGAGCTTACTATTCTTCAGCTCAAT
* *
28569566 ATGAGCTTACTA---TTCATCTCGAT
1 A-GAGCTTACTATTCTTCAGCTCAAT
*
28569589 AGAGTTTACTATT-TTCAGCTCAAT
1 AGAGCTTACTATTCTTCAGCTCAAT
* * *
28569613 AGAGCTTACTGTTCATCAGCTCAAG
1 AGAGCTTACTATTCTTCAGCTCAAT
28569638 AGGAGCTTAC
1 A-GAGCTTAC
28569648 CGATCATGGC
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
22 17 0.21
23 19 0.23
24 28 0.34
25 10 0.12
26 8 0.10
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (25 bp):
AGAGCTTACTATTCTTCAGCTCAAT
Found at i:28569654 original size:26 final size:25
Alignment explanation
Indices: 28569603--28569654 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
28569593 TTTACTATTT
* * *
28569603 TCAGCTCAATAGAGCTTACTGTTCA
1 TCAGCTCAAGAGAGCTTACCGATCA
28569628 TCAGCTCAAGAGGAGCTTACCGATCA
1 TCAGCTCAAGA-GAGCTTACCGATCA
28569654 T
1 T
28569655 GGCTCGAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (25 bp):
TCAGCTCAAGAGAGCTTACCGATCA
Found at i:28570105 original size:15 final size:15
Alignment explanation
Indices: 28570085--28570114 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28570075 AGAAAGAATT
*
28570085 AAGAAATGAAAAAAA
1 AAGAAAAGAAAAAAA
28570100 AAGAAAAGAAAAAAA
1 AAGAAAAGAAAAAAA
28570115 TGAGCATGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (15 bp):
AAGAAAAGAAAAAAA
Found at i:28571288 original size:29 final size:29
Alignment explanation
Indices: 28571255--28571415 Score: 155
Period size: 29 Copynumber: 5.6 Consensus size: 29
28571245 TTGACGAGAT
28571255 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* *
28571284 TGGCACTGAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
28571313 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* ** * * ***
28571342 CGGCACTGGGTGTGCGAGCTCGAAGGCTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * *
28571371 TGGCACTATGTGTACGGGCT-TAAATCGA-A
1 TGGCACTAAGTGTGCGTGCTGGAAAT--ATA
28571400 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
28571416 AAATCGAGTA
Statistics
Matches: 107, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
28 2 0.02
29 105 0.98
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:28571373 original size:58 final size:58
Alignment explanation
Indices: 28571251--28571383 Score: 171
Period size: 58 Copynumber: 2.3 Consensus size: 58
28571241 TACGTTGACG
* * *
28571251 AGAT-TGGCACTAAGTGTGCGTGCTGGAAATATATGGCACTGAGTGTGCATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTGAGTGTGCATGCTCGAA
* *
28571308 ATATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTGGGTGTGCGA-GCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTGAGTGTGC-ATGCTCGAA
* * *
28571366 GGCTATGGCACTATGTGT
1 AGATATGGCACTAAGTGT
28571384 ACGGGCTTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
57 3 0.05
58 61 0.94
59 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTGAGTGTGCATGCTCGAA
Found at i:28579945 original size:40 final size:40
Alignment explanation
Indices: 28579901--28580029 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
28579891 TGCTGGAAAT
* * *
28579901 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
* *
28579941 TATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGAC
* * *
28579981 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGA-GTGAC
28580021 TATATCCGG
1 TATATCCGG
28580030 TTATATTCCG
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
39 4 0.05
40 71 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
Found at i:28587144 original size:40 final size:40
Alignment explanation
Indices: 28587100--28587228 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
28587090 TGCTGGAAAT
* * *
28587100 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
* *
28587140 TATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGAC
* * *
28587180 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGA-GTGAC
28587220 TATATCCGG
1 TATATCCGG
28587229 TTATATTCCG
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
39 4 0.05
40 71 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
Found at i:28589614 original size:27 final size:27
Alignment explanation
Indices: 28589580--28589674 Score: 111
Period size: 27 Copynumber: 3.5 Consensus size: 27
28589570 AGTTCAAAGA
28589580 GACATTAAACACAAGATAGTCCGATGG
1 GACATTAAACACAAGATAGTCCGATGG
* * *
28589607 GACATTAAACACGAGATAG-CCTGACGA
1 GACATTAAACACAAGATAGTCC-GATGG
* *
28589634 GACATTAAACATAGGATAGTCCGATGG
1 GACATTAAACACAAGATAGTCCGATGG
* *
28589661 AACACTAAACACAA
1 GACATTAAACACAA
28589675 AATGGTCCAT
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
26 2 0.04
27 50 0.93
28 2 0.04
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (27 bp):
GACATTAAACACAAGATAGTCCGATGG
Found at i:28589848 original size:181 final size:181
Alignment explanation
Indices: 28589530--28589880 Score: 447
Period size: 181 Copynumber: 1.9 Consensus size: 181
28589520 AGGTTAGATT
28589530 GTGTAAAACCATAGCTAAAAGACATTATGGCATCATAGACAGTTCAAAGAGACATTAAACACAAG
1 GTGTAAAACCATAGCTAAAAGACATTATGGCATCATAGACAGTTCAAAGAGACATTAAACACAAG
* * * *
28589595 ATAGTCCGATGGGACATTAAACACGAGATAGCCTGACGAGACATTAAACATAGGATAGTCCGATG
66 ATAGTCCGATGGGACATTAAACACGAGATAGCCTAACGAGACATTAAACACAAGATAGTCCAATG
* *
28589660 GAACACTAAACACAAAATGGTCCA-TTAGGATGGTAAACACGGGGGTATATC
131 AAACACTAAACACAAAATGGTCCACTGA-GATGGTAAACACGGGGGTATATC
* * * * * * * * * *
28589711 GTGTAAGACTATAGCTACAAGACGTTCTGGCATCATAGATAG-TCTGACGATACATTAAACACAG
1 GTGTAAAACCATAGCTAAAAGACATTATGGCATCATAGACAGTTC-AAAGAGACATTAAACACAA
* * * * *
28589775 GATAGTTCGATGGGACATTAAACATGGGATAGTCTAAC-AGGACATTAAGCACAAGATAGTCCAA
65 GATAGTCCGATGGGACATTAAACACGAGATAGCCTAACGA-GACATTAAACACAAGATAGTCCAA
* *
28589839 TGAAACACTAAACACAAGATGGTCTACTGAGATGGTAAACAC
129 TGAAACACTAAACACAAAATGGTCCACTGAGATGGTAAACAC
28589881 AGAATTATAT
Statistics
Matches: 144, Mismatches: 23, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
180 3 0.02
181 139 0.97
182 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (181 bp):
GTGTAAAACCATAGCTAAAAGACATTATGGCATCATAGACAGTTCAAAGAGACATTAAACACAAG
ATAGTCCGATGGGACATTAAACACGAGATAGCCTAACGAGACATTAAACACAAGATAGTCCAATG
AAACACTAAACACAAAATGGTCCACTGAGATGGTAAACACGGGGGTATATC
Found at i:28593898 original size:30 final size:29
Alignment explanation
Indices: 28593804--28593905 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
28593794 TATAGTGAAT
* * *
28593804 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
28593833 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
28593861 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
28593891 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
28593906 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:28613947 original size:42 final size:43
Alignment explanation
Indices: 28613846--28614002 Score: 181
Period size: 43 Copynumber: 3.7 Consensus size: 43
28613836 AGCTCGTACA
*
28613846 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATAAAAAATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATAAAAAATCG
* ** * *
28613889 ATGCCACTGTCCCAGACAAGGTCTTACATGTAATCAAATAT-G
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATAAAAAATCG
* * * *
28613931 ATGCCAATGTCCCAGACGTGGTCTTACACGTAAATCATAAGTCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGT-AATAAAAAATCG
** *
28613975 ATGCCAACATCCCATACGTGGTCTTACA
1 ATGCCAATGTCCCAGACGTGGTCTTACA
28614003 CGATAACACA
Statistics
Matches: 96, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
42 28 0.29
43 42 0.44
44 26 0.27
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACATGTAATAAAAAATCG
Found at i:28621583 original size:23 final size:24
Alignment explanation
Indices: 28621546--28621590 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
28621536 CTTCCTTTGA
28621546 AAAAAAAAAGAAAACAAAAAGATG
1 AAAAAAAAAGAAAACAAAAAGATG
* *
28621570 AAAAAAATAG-AAACAGAAAGA
1 AAAAAAAAAGAAAACAAAAAGA
28621591 AAACCACCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.78, C:0.04, G:0.13, T:0.04
Consensus pattern (24 bp):
AAAAAAAAAGAAAACAAAAAGATG
Found at i:28621906 original size:18 final size:17
Alignment explanation
Indices: 28621879--28621930 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
28621869 TTTTATTTTT
28621879 GTTTATTTTTGTTTTAGG
1 GTTTA-TTTTGTTTTAGG
*
28621897 GTTTAGTTTTG-GTTAGG
1 GTTTA-TTTTGTTTTAGG
*
28621914 GATTATTTTGTTTTAGG
1 GTTTATTTTGTTTTAGG
28621931 CCATTAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 5 0.17
17 14 0.48
18 10 0.34
ACGTcount: A:0.13, C:0.00, G:0.27, T:0.60
Consensus pattern (17 bp):
GTTTATTTTGTTTTAGG
Found at i:28622390 original size:79 final size:78
Alignment explanation
Indices: 28622307--28622564 Score: 318
Period size: 79 Copynumber: 3.3 Consensus size: 78
28622297 AGGATTAGTA
* ** * *
28622307 GCTTCAATCTACCCTACTGGAGATGGGATTTACTATCTTCAGTCTGCTCCACTGCAGCTTTAGGG
1 GCTTCAATCTACCC-ACTGCAGATGGGATTTGTTGTCTTCAGTCTGCTCCACTGCAACTTTAGGG
* *
28622372 AGATAAGGTTGGCG
65 AGATAAGGCTGGTG
** **
28622386 GCTTCAATCTGTTCCACTGCAGATGGGATTTGTTGTCTTCAGTCTGCTCTGCTGCAACTTTAGGG
1 GCTTCAATCT-ACCCACTGCAGATGGGATTTGTTGTCTTCAGTCTGCTCCACTGCAACTTTAGGG
*
28622451 AGGTAAGGCTGGTG
65 AGATAAGGCTGGTG
** * * *
28622465 GCTTCAATCTACTCCACAACATATGGGATTTGTTGTCTTCAGTCTGCTCCACTGCAACTTCAAGG
1 GCTTCAATCTAC-CCACTGCAGATGGGATTTGTTGTCTTCAGTCTGCTCCACTGCAACTTTAGGG
28622530 AGATAAGGCTGGTG
65 AGATAAGGCTGGTG
*
28622544 GCTTCAATCTACTCCATTGCA
1 GCTTCAATCTAC-CCACTGCA
28622565 ACTTTAGGAA
Statistics
Matches: 152, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
79 150 0.99
80 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (78 bp):
GCTTCAATCTACCCACTGCAGATGGGATTTGTTGTCTTCAGTCTGCTCCACTGCAACTTTAGGGA
GATAAGGCTGGTG
Found at i:28622756 original size:143 final size:143
Alignment explanation
Indices: 28622498--28623298 Score: 1021
Period size: 143 Copynumber: 5.6 Consensus size: 143
28622488 TGGGATTTGT
* * *
28622498 TGTCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTACTCCATTG
1 TGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTG
* * ** * * * *
28622563 CAACTTTAGGAAGATAAGATTTGCCATAATTTATAGCTTTAATATGTTCCACTGCAATG-CTAGA
66 CAACTTCAAGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGTC-AGG
* *
28622627 GAAATAAAATTCGC
130 GAAATAAGATTCAC
* * * *
28622641 TGTCTTCAGTCTGCTCCTCTTCAACTTTAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTA
1 TGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTG
* ** * * * * * *
28622706 TAACTTCTGGAAGATGAGATCCGCCATAACTCGTAGCTTCAATCTATTCCACTGCAACGTCGGGG
66 CAACTTCAAGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGTCAGGG
***
28622771 AAATAAGATTTGT
131 AAATAAGATTCAC
* * * * *
28622784 TGTCTTTAGTCTGCTCCGCTGCAACTTCAGAGAGATAAGGCTAGTGGCTTCAATCTGCTCCCCTG
1 TGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTG
*
28622849 CAACTTCAAGAAAATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGTCAGGG
66 CAACTTCAAGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGTCAGGG
28622914 AAATAAGATTCAC
131 AAATAAGATTCAC
* * *
28622927 TGTCTTCAGTCTGCTCCACTGCAACTTCTGGAAGATAAGGCTGGTGGCTTCTATCTGCTCCACTG
1 TGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTG
* * * ** * *
28622992 CAACTTCAAGAAGATAAGATCC-ACAGTAATTTATACCTTTAATCCATTCTACTGTAACGTCAGG
66 CAACTTCAAGAAGATAAGATCCGCCA-TAATTTGTAGCTTTAATCTGTTCCACTGCAACGTCAGG
28623056 GAAATAAGATTCAC
130 GAAATAAGATTCAC
* * * * * *
28623070 TGTCTTCAGTCTACTCCGCTGCAACTTTAGGGAGATAAGGCTGATGGCTTCAATCTGCTCTATTG
1 TGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTG
* * * *
28623135 TAACTTCAAGAAGATAAGATCTGCCATAATTTGTAGCTTTAATCCGTTCCACTGCAATGTCAGGG
66 CAACTTCAAGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGTCAGGG
*
28623200 AAATAAGATTCAT
131 AAATAAGATTCAC
* * * *
28623213 TGTCTTCAATCTGCTCCCCTGCAACTTCAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCTACTG
1 TGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTG
*
28623278 CAACTTCAGGAAGATAAGATC
66 CAACTTCAAGAAGATAAGATC
28623299 TGCGATCTTC
Statistics
Matches: 565, Mismatches: 90, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
142 2 0.00
143 560 0.99
144 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (143 bp):
TGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTG
CAACTTCAAGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGTCAGGG
AAATAAGATTCAC
Found at i:28622866 original size:44 final size:45
Alignment explanation
Indices: 28622793--28623009 Score: 145
Period size: 44 Copynumber: 4.7 Consensus size: 45
28622783 TTGTCTTTAG
*
28622793 TCTGCTCCGCTGCAACTTC-AGAGAGATAAGGCT-AGTGGCTTCAA
1 TCTGCTCCACTGCAACTTCAAGA-AGATAAGGCTAAGTGGCTTCAA
* * * *
28622837 TCTGCTCCCCTGCAACTTCAAGAAAATAAGATCCGCCATAATTTGTAGCTTTAA
1 TCTGCTCCACTGCAACTTCAAGAAGATAAG----G-C-TAA---GTGGCTTCAA
* * * ** * * * *
28622891 TCTGTTCCACTGCAACGTCAGGGAA-ATAAGATTCACTGTCTTCAG
1 TCTGCTCCACTGCAACTTCA-AGAAGATAAGGCTAAGTGGCTTCAA
** * *
28622936 TCTGCTCCACTGCAACTTCTGGAAGATAAGGCT-GGTGGCTTCTA
1 TCTGCTCCACTGCAACTTCAAGAAGATAAGGCTAAGTGGCTTCAA
28622980 TCTGCTCCACTGCAACTTCAAGAAGATAAG
1 TCTGCTCCACTGCAACTTCAAGAAGATAAG
28623010 ATCCACAGTA
Statistics
Matches: 132, Mismatches: 28, Indels: 26
0.71 0.15 0.14
Matches are distributed among these distances:
44 62 0.47
45 31 0.23
48 3 0.02
49 1 0.01
50 1 0.01
51 1 0.01
54 30 0.23
55 3 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAAGAAGATAAGGCTAAGTGGCTTCAA
Found at i:28623297 original size:429 final size:428
Alignment explanation
Indices: 28622498--28623298 Score: 1131
Period size: 429 Copynumber: 1.9 Consensus size: 428
28622488 TGGGATTTGT
*
28622498 TGTCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTACTCCATTG
1 TGTCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTG
* * * * ** *
28622563 CAACTTTAGGAAGATAAGATTTGCCATAATTTATAGCTTTAATATGTTCCACTGCAATGCTAGAG
66 CAACTTCAAGAAGATAAGA-TTCCCATAATTTATACCTTTAATACATTCCACTGCAACGCTAGAG
* * * * *
28622628 AAATAAAATTCGCTGTCTTCAGTCTGCTCCTCTTCAACTTTAGGGAGATAAGGCTGGTGGCTTCA
130 AAATAAAATTCACTGTCTTCAGTCTACTCCGCTGCAACTTTAGGGAGATAAGGCTGATGGCTTCA
** * *
28622693 ATCTGCTCCACTATAACTTCTGGAAGATGAGATCCGCCATAACTCGTAGCTTCAATCTATTCCAC
195 ATCTGCTCCACTATAACTTCAAGAAGATAAGATCCGCCATAACTCGTAGCTTCAATCCATTCCAC
* ** * * *
28622758 TGCAACGTCGGGGAAATAAGATTTGTTGTCTTTAGTCTGCTCCGCTGCAACTTCAGAGAGATAAG
260 TGCAACGTCAGGGAAATAAGATTCATTGTCTTCAATCTGCTCCCCTGCAACTTCAGAGAGATAAG
*
28622823 GCTAGTGGCTTCAATCTGCTCCCCTGCAACTTCAAGAAAATAAGATCCGCCATAATTTGTAGCTT
325 GCTAGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAAATAAGATCCGCCATAATTTGTAGCTT
28622888 TAATCTGTTCCACTGCAACGTCAGGGAAATAAGATTCAC
390 TAATCTGTTCCACTGCAACGTCAGGGAAATAAGATTCAC
* * *
28622927 TGTCTTCAGTCTGCTCCACTGCAACTTC-TGGAAGATAAGGCTGGTGGCTTCTATCTGCTCCACT
1 TGTCTTCAGTCTGCTCCACTGCAACTTCAAGG-AGATAAGGCTGGTGGCTTCAATCTACTCCACT
* * *
28622991 GCAACTTCAAGAAGATAAGA-TCCACAGTAATTTATACCTTTAATCCATTCTACTGTAACG-TCA
65 GCAACTTCAAGAAGATAAGATTCC-CA-TAATTTATACCTTTAATACATTCCACTGCAACGCT-A
* *
28623054 GGGAAATAAGATTCACTGTCTTCAGTCTACTCCGCTGCAACTTTAGGGAGATAAGGCTGATGGCT
127 GAGAAATAAAATTCACTGTCTTCAGTCTACTCCGCTGCAACTTTAGGGAGATAAGGCTGATGGCT
* * * * * * * *
28623119 TCAATCTGCTCTATTGTAACTTCAAGAAGATAAGATCTGCCATAATTTGTAGCTTTAATCCGTTC
192 TCAATCTGCTCCACTATAACTTCAAGAAGATAAGATCCGCCATAACTCGTAGCTTCAATCCATTC
*
28623184 CACTGCAATGTCAGGGAAATAAGATTCATTGTCTTCAATCTGCTCCCCTGCAACTTCAGAGAGAT
257 CACTGCAACGTCAGGGAAATAAGATTCATTGTCTTCAATCTGCTCCCCTGCAACTTCAGAGAGAT
* * * *
28623249 AAGGCTGGTGGCTTCAATCTGCTCTACTGCAACTTCAGGAAGATAAGATC
322 AAGGCTAGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAAATAAGATC
28623299 TGCGATCTTC
Statistics
Matches: 323, Mismatches: 45, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
427 2 0.01
428 5 0.02
429 316 0.98
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (428 bp):
TGTCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTG
CAACTTCAAGAAGATAAGATTCCCATAATTTATACCTTTAATACATTCCACTGCAACGCTAGAGA
AATAAAATTCACTGTCTTCAGTCTACTCCGCTGCAACTTTAGGGAGATAAGGCTGATGGCTTCAA
TCTGCTCCACTATAACTTCAAGAAGATAAGATCCGCCATAACTCGTAGCTTCAATCCATTCCACT
GCAACGTCAGGGAAATAAGATTCATTGTCTTCAATCTGCTCCCCTGCAACTTCAGAGAGATAAGG
CTAGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAAATAAGATCCGCCATAATTTGTAGCTTT
AATCTGTTCCACTGCAACGTCAGGGAAATAAGATTCAC
Found at i:28625291 original size:40 final size:40
Alignment explanation
Indices: 28625232--28625365 Score: 144
Period size: 40 Copynumber: 3.4 Consensus size: 40
28625222 GCAAATTGTG
* *
28625232 ATATCCGGGCTAAGTCCCG-AGGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGG-CATTTATGCAAGTAATT
** **
28625272 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCAAGTAATT
* * * * *
28625312 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCATG
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCAAGTAATT
*
28625352 ATATCCGGGTTAAG
1 ATATCCGGGCTAAG
28625366 TCCCATAGGC
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 76 0.96
41 3 0.04
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCAAGTAATT
Found at i:28627814 original size:5 final size:5
Alignment explanation
Indices: 28627804--28627873 Score: 65
Period size: 5 Copynumber: 13.8 Consensus size: 5
28627794 CTTGGCCTCT
*
28627804 TTTTC TTTTC TTTTTTC TTTTC TTTT- TCTT- TTTTC TTTTC TTTTC TTTTTTC
1 TTTTC TTTTC --TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC --TTTTC
*
28627856 TTTTC TTTTA TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTT
28627874 TTGTAACACC
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
4 10 0.18
5 37 0.65
7 10 0.18
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTC
Found at i:28627824 original size:17 final size:17
Alignment explanation
Indices: 28627804--28627875 Score: 119
Period size: 17 Copynumber: 4.2 Consensus size: 17
28627794 CTTGGCCTCT
28627804 TTTTCTTTTCTTTTTTC
1 TTTTCTTTTCTTTTTTC
28627821 TTTTCTTTTTCTTTTTTC
1 TTTTC-TTTTCTTTTTTC
28627839 TTTTCTTTTCTTTTTTC
1 TTTTCTTTTCTTTTTTC
*
28627856 TTTTCTTTTATTTTTT-
1 TTTTCTTTTCTTTTTTC
28627872 TTTT
1 TTTT
28627876 GTAACACCCC
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
16 4 0.08
17 32 0.60
18 17 0.32
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTCTTTTCTTTTTTC
Found at i:28627871 original size:12 final size:12
Alignment explanation
Indices: 28627803--28627864 Score: 101
Period size: 12 Copynumber: 5.2 Consensus size: 12
28627793 CCTTGGCCTC
28627803 TTTTTCTTTTCT
1 TTTTTCTTTTCT
28627815 TTTTTCTTTTC-
1 TTTTTCTTTTCT
28627826 TTTTTCTTTT-T
1 TTTTTCTTTTCT
28627837 TCTTTTCTTTTCT
1 T-TTTTCTTTTCT
28627850 TTTTTCTTTTCT
1 TTTTTCTTTTCT
28627862 TTT
1 TTT
28627865 ATTTTTTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.23
12 34 0.72
13 2 0.04
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:28632786 original size:2 final size:2
Alignment explanation
Indices: 28632779--28632808 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28632769 CCAGATGTAC
28632779 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28632809 TATCAAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28633207 original size:43 final size:42
Alignment explanation
Indices: 28633152--28633323 Score: 152
Period size: 43 Copynumber: 4.0 Consensus size: 42
28633142 ATATCGTACA
* *
28633152 ATGCCAAC-GTCCCAGACGTGGTCTTACATGCTATCCCATATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACATG-TATCACATATCG
* * * * *
28633195 ATGCCACTGTCCCAAACAGGGTCTTTACACGAATCAAATA-CG
1 ATGCCACTGTCCCAGACATGGTC-TTACATGTATCACATATCG
* **
28633237 GTGATGA-TGTCCCAGACATGGTCTTACATGTAATCACATATCG
1 ATG-CCACTGTCCCAGACATGGTCTTACATGT-ATCACATATCG
* * *
28633280 ATGCCAATGTCCCAGACATGGTCTTACATGAGAACACATATCG
1 ATGCCACTGTCCCAGACATGGTCTTACATG-TATCACATATCG
28633323 A
1 A
28633324 AACCCTATGT
Statistics
Matches: 102, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
41 6 0.06
42 28 0.27
43 62 0.61
44 6 0.06
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (42 bp):
ATGCCACTGTCCCAGACATGGTCTTACATGTATCACATATCG
Found at i:28633260 original size:42 final size:44
Alignment explanation
Indices: 28633189--28633304 Score: 121
Period size: 42 Copynumber: 2.7 Consensus size: 44
28633179 ATGCTATCCC
* * * *
28633189 ATATCGATGCCACTGTCCCAAACAGGGTCTTTACACG-AATCAA
1 ATATCGATGACAATGTCCCAGACATGGTCTTTACACGTAATCAA
* ** * *
28633232 ATA-CGGTGATGATGTCCCAGACATGGTC-TTACATGTAATCAC
1 ATATCGATGACAATGTCCCAGACATGGTCTTTACACGTAATCAA
*
28633274 ATATCGATGCCAATGTCCCAGACATGGTCTT
1 ATATCGATGACAATGTCCCAGACATGGTCTT
28633305 ACATGAGAAC
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
41 6 0.11
42 26 0.46
43 24 0.42
44 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (44 bp):
ATATCGATGACAATGTCCCAGACATGGTCTTTACACGTAATCAA
Found at i:28633341 original size:43 final size:42
Alignment explanation
Indices: 28633243--28633334 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 42
28633233 TACGGTGATG
* **
28633243 ATGTCCCAGACATGGTCTTACATGTAATCACATATCGATGCCA
1 ATGT-CCAGACATGGTCTTACATGTAAACACATATCGAACCCA
*
28633286 ATGTCCCAGACATGGTCTTACATG-AGAACACATATCGAAACCCT
1 ATGT-CCAGACATGGTCTTACATGTA-AACACATATCG-AACCCA
28633330 ATGTC
1 ATGTC
28633335 ATGACATATG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 1 0.02
43 35 0.81
44 7 0.16
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (42 bp):
ATGTCCAGACATGGTCTTACATGTAAACACATATCGAACCCA
Found at i:28634582 original size:14 final size:14
Alignment explanation
Indices: 28634563--28634601 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
28634553 GGCTATTACA
28634563 GTTTTTCTTTTTTT
1 GTTTTTCTTTTTTT
*
28634577 GTTTTTCTTTTCTT
1 GTTTTTCTTTTTTT
28634591 -TTTTTCTTTTT
1 GTTTTTCTTTTT
28634602 CTCTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (14 bp):
GTTTTTCTTTTTTT
Found at i:28634589 original size:19 final size:19
Alignment explanation
Indices: 28634565--28634614 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
28634555 CTATTACAGT
*
28634565 TTTTCTTTTTTTGTTTTTC
1 TTTTCTTTTTTTCTTTTTC
28634584 TTTTCTTTTTTTCTTTTTC
1 TTTTCTTTTTTTCTTTTTC
* *
28634603 TCTTATTTTTTT
1 TTTTCTTTTTTT
28634615 AAGTGAAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (19 bp):
TTTTCTTTTTTTCTTTTTC
Found at i:28637641 original size:28 final size:28
Alignment explanation
Indices: 28637597--28637697 Score: 114
Period size: 28 Copynumber: 3.6 Consensus size: 28
28637587 GCCCCTTTAA
* * * *
28637597 GCCCAATCTCATTCATATGGCCCAT-TG
1 GCCCAACCACATTCATATGGTCCATCAG
28637624 GCCACAACCACATTCATATGGTCCATCAG
1 GCC-CAACCACATTCATATGGTCCATCAG
* *
28637653 GCCCAATCATATTCATATGGTCCATCAG
1 GCCCAACCACATTCATATGGTCCATCAG
* *
28637681 GCCCAATCATATTCATA
1 GCCCAACCACATTCATA
28637698 GTCATGCAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 3 0.05
28 59 0.89
29 4 0.06
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.27
Consensus pattern (28 bp):
GCCCAACCACATTCATATGGTCCATCAG
Found at i:28637936 original size:16 final size:16
Alignment explanation
Indices: 28637915--28637945 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28637905 AAACTTCTGG
28637915 CTTTTCGGCATTTTGA
1 CTTTTCGGCATTTTGA
28637931 CTTTTCGGCATTTTG
1 CTTTTCGGCATTTTG
28637946 GGATTTACCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.19, G:0.19, T:0.52
Consensus pattern (16 bp):
CTTTTCGGCATTTTGA
Found at i:28652333 original size:3 final size:3
Alignment explanation
Indices: 28652327--28652403 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
28652317 ATAAATGATG
28652327 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28652375 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
28652404 GGTAAAATAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:28654771 original size:29 final size:29
Alignment explanation
Indices: 28654738--28654867 Score: 113
Period size: 29 Copynumber: 4.5 Consensus size: 29
28654728 GTGACGAGAT
28654738 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
28654767 TGGCACTAAGTGTGCATGCTGGAAAT-TA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
28654795 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
28654824 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
28654853 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
28654868 GAAATCGAGT
Statistics
Matches: 81, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
28 22 0.27
29 59 0.73
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:28662798 original size:29 final size:29
Alignment explanation
Indices: 28662765--28662923 Score: 171
Period size: 29 Copynumber: 5.5 Consensus size: 29
28662755 GTGACGAGAT
28662765 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
28662794 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
28662823 TGGCACTAAGTGTGCATGCTGGAAAT-TA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
28662851 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
28662880 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
28662909 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
28662924 GAAATCGAGT
Statistics
Matches: 110, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
28 22 0.20
29 88 0.80
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:28662835 original size:58 final size:58
Alignment explanation
Indices: 28662761--28662925 Score: 176
Period size: 57 Copynumber: 2.9 Consensus size: 58
28662751 TACGGTGACG
*
28662761 AGAT-TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGC-ATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGA-GCTCGAA
* * **
28662818 ATATATGGCACTAAGTGTGCATGCTGGAAAT-TACGGCACTGGGTGTGCGAGCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGAGCTCGAA
* * * ** * *
28662875 GGGTATGGCACTATGTGTGCGGGCT-TAAATCACATGGCACTAAGTGTGCGA
1 AGATATGGCACTAAGTGTGCATGCTGGAAAT-ATATGGCACTAAGTGTGCGA
28662926 AATCGAGTAT
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
56 4 0.05
57 42 0.48
58 42 0.48
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGAGCTCGAA
Found at i:28666710 original size:20 final size:20
Alignment explanation
Indices: 28666687--28666740 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
28666677 TAAAATTTTG
28666687 AATCTATCGATACTCAACAA
1 AATCTATCGATACTCAACAA
**
28666707 AATCTATCGATACTTGACAA
1 AATCTATCGATACTCAACAA
**
28666727 AAAGTATCGATACT
1 AATCTATCGATACT
28666741 AGATTGGTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (20 bp):
AATCTATCGATACTCAACAA
Found at i:28669961 original size:99 final size:101
Alignment explanation
Indices: 28669857--28670091 Score: 250
Period size: 103 Copynumber: 2.3 Consensus size: 101
28669847 TAAATAATAA
* *
28669857 TTATAT-AATAAAAATAATT-TTTA-TATAAATATATTT-AACAAAATG-ATAGATATAAAAAT-
1 TTATATAAATAAAAATAATTATTAATTAAAAATAT-TTTAAACAAAATGCATAGA-ATAAAAATA
** *
28669916 TATATGACTTCATTATATAATTACATATTTATTAATTTAT
64 TATAT--CTTCATTATATAATTACATATACACTAATTTAT
* *
28669956 TTATATAAATAAAGA-AATTATTAATTAAAAATATTTTAAACATAATGTCACATAGAATAAAAAT
1 TTATATAAATAAAAATAATTATTAATTAAAAATATTTTAAACAAAATG---CATAGAATAAAAAT
* * *
28670020 ATATATTTTTATTATATAATTACATATACACTATTTTAT
63 ATATATCTTCATTATATAATTACATATACACTAATTTAT
*
28670059 TTATATAAATAAAAATAGTTATTAATTGAAAAA
1 TTATATAAATAAAAATAATTATTAATT-AAAAA
28670092 ATGAATTAAA
Statistics
Matches: 113, Mismatches: 12, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
99 10 0.09
100 13 0.12
101 16 0.14
103 41 0.36
104 18 0.16
105 15 0.13
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.42
Consensus pattern (101 bp):
TTATATAAATAAAAATAATTATTAATTAAAAATATTTTAAACAAAATGCATAGAATAAAAATATA
TATCTTCATTATATAATTACATATACACTAATTTAT
Found at i:28670143 original size:12 final size:12
Alignment explanation
Indices: 28670128--28670152 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28670118 ATATTTATTA
28670128 ATTAAAAATTTT
1 ATTAAAAATTTT
28670140 ATTAAAAATTTT
1 ATTAAAAATTTT
28670152 A
1 A
28670153 AAAAAATTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTAAAAATTTT
Found at i:28672859 original size:18 final size:18
Alignment explanation
Indices: 28672836--28672870 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28672826 GAAAACACCA
28672836 TCATGATCAAGTTCATGG
1 TCATGATCAAGTTCATGG
*
28672854 TCATGATCATGTTCATG
1 TCATGATCAAGTTCATG
28672871 ATGTGATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (18 bp):
TCATGATCAAGTTCATGG
Found at i:28678215 original size:2 final size:2
Alignment explanation
Indices: 28678208--28678235 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28678198 TGTTTGTTTA
28678208 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28678236 GGAATTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28680900 original size:47 final size:47
Alignment explanation
Indices: 28680831--28681000 Score: 313
Period size: 47 Copynumber: 3.6 Consensus size: 47
28680821 AACAGCTCGT
28680831 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
28680878 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
28680925 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
28680972 AGTGTATATATGTGGTAAAGCCGAATGGC
1 AGTGTATATATGTGATAAGGCCTAATGGC
28681001 TAATGTGAAA
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 120 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:28681007 original size:47 final size:48
Alignment explanation
Indices: 28680831--28681250 Score: 317
Period size: 48 Copynumber: 8.8 Consensus size: 48
28680821 AACAGCTCGT
* * * **
28680831 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTG-ATGA-ATGTGAA
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAT-ACATGTGAA
* * * **
28680878 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTG-ATGA-ATGTGAA
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAT-ACATGTGAA
* * * **
28680925 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTG-ATGA-ATGTGAA
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAT-ACATGTGAA
**
28680972 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTG
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTG-AATACATGTGAA
* * **
28681021 A-TATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTG
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTG-AATACATGTGAA
* * * **
28681069 A-TATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATACATGTGTG
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTG-AATACATGTGAA
* * * * *
28681117 A-TATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTG-AATACATGTGAA
* * * * * *
28681165 A-TGTGTATATGTCGTAAAGCCGAATGGCGAATGTGAAATGCGTATGAGAT
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTG-AATAC--ATGTGAA
*
28681215 A-TG-A-ATATGTGGTAAAGCCGAATGGCTAATGAGAAT
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAT
28681251 GTTGTAACCT
Statistics
Matches: 342, Mismatches: 26, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
47 128 0.37
48 199 0.58
49 8 0.02
50 7 0.02
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (48 bp):
AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTGAATACATGTGAA
Found at i:28681037 original size:48 final size:48
Alignment explanation
Indices: 28680978--28681245 Score: 428
Period size: 48 Copynumber: 5.6 Consensus size: 48
28680968 TGAAAGTGTA
28680978 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTGATATG
28681026 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTGATATG
*
28681074 TATATGTGGTAAAGCCGAATGGATAATGTGAAATACATGTGTGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTGATATG
* * * *
28681122 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATGTG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTGATATG
* * * * * *
28681170 TATATGTCGTAAAGCCGAATGGCGAATGTGAAATGCGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTGATATG
*
28681218 AATATGTGGTAAAGCCGAATGGCTAATG
1 TATATGTGGTAAAGCCGAATGGCTAATG
28681246 AGAATGTTGT
Statistics
Matches: 205, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 205 1.00
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTGATATG
Found at i:28681344 original size:37 final size:37
Alignment explanation
Indices: 28681294--28681379 Score: 163
Period size: 37 Copynumber: 2.3 Consensus size: 37
28681284 GGAAATATAT
*
28681294 TCCGGGTGAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
28681331 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
28681368 TCCGGGTAAGAC
1 TCCGGGTAAGAC
28681380 TTCGTAATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:28683341 original size:40 final size:40
Alignment explanation
Indices: 28683275--28683666 Score: 617
Period size: 40 Copynumber: 9.8 Consensus size: 40
28683265 AAGAATTGAG
* * *
28683275 AGTGATATATCCAGG-CTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCC-GGACTAAGTTCCGAAGAGCATTCGTGCT
28683315 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
28683355 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
* *
28683395 AGTGATGTACCCGGATTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
*
28683435 AGTGATGTATCCGGATTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
*
28683475 AGTGATGTATCCAGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
28683515 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTC-TAGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGT-GCT
28683555 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
* * * * *
28683595 AGTAAGGCAACCGGACTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
* * *
28683635 AGTGATGTATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCA
28683667 ATCATGCTGG
Statistics
Matches: 329, Mismatches: 20, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
39 3 0.01
40 325 0.99
41 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
Found at i:28687201 original size:47 final size:47
Alignment explanation
Indices: 28687132--28687301 Score: 313
Period size: 47 Copynumber: 3.6 Consensus size: 47
28687122 AACAGCTCGT
28687132 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
28687179 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
28687226 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
28687273 AGTGTATATATGTGGTAAAGCCGAATGGC
1 AGTGTATATATGTGATAAGGCCTAATGGC
28687302 TAATGTGAAA
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 120 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:28687308 original size:47 final size:48
Alignment explanation
Indices: 28687132--28687551 Score: 317
Period size: 48 Copynumber: 8.8 Consensus size: 48
28687122 AACAGCTCGT
* * * **
28687132 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTG-ATGA-ATGTGAA
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAT-ACATGTGAA
* * * **
28687179 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTG-ATGA-ATGTGAA
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAT-ACATGTGAA
* * * **
28687226 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTG-ATGA-ATGTGAA
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAT-ACATGTGAA
**
28687273 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTG
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTG-AATACATGTGAA
* * **
28687322 A-TATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTG
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTG-AATACATGTGAA
* * * **
28687370 A-TATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATACATGTGTG
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTG-AATACATGTGAA
* * * * *
28687418 A-TATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTG-AATACATGTGAA
* * * * * *
28687466 A-TGTGTATATGTCGTAAAGCCGAATGGCGAATGTGAAATGCGTATGAGAT
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTG-AATAC--ATGTGAA
*
28687516 A-TG-A-ATATGTGGTAAAGCCGAATGGCTAATGAGAAT
1 AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAT
28687552 GTTGTAACCT
Statistics
Matches: 342, Mismatches: 26, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
47 128 0.37
48 199 0.58
49 8 0.02
50 7 0.02
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (48 bp):
AGTGTATATATGTGGTAAAGCCGAATGGCTAATGTGAATACATGTGAA
Found at i:28687338 original size:48 final size:48
Alignment explanation
Indices: 28687279--28687546 Score: 428
Period size: 48 Copynumber: 5.6 Consensus size: 48
28687269 TGAAAGTGTA
28687279 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTGATATG
28687327 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTGATATG
*
28687375 TATATGTGGTAAAGCCGAATGGATAATGTGAAATACATGTGTGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTGATATG
* * * *
28687423 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATGTG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTGATATG
* * * * * *
28687471 TATATGTCGTAAAGCCGAATGGCGAATGTGAAATGCGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTGATATG
*
28687519 AATATGTGGTAAAGCCGAATGGCTAATG
1 TATATGTGGTAAAGCCGAATGGCTAATG
28687547 AGAATGTTGT
Statistics
Matches: 205, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 205 1.00
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATGTGTGATATG
Found at i:28687645 original size:37 final size:37
Alignment explanation
Indices: 28687595--28687680 Score: 163
Period size: 37 Copynumber: 2.3 Consensus size: 37
28687585 GGAAATATAT
*
28687595 TCCGGGTGAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
28687632 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
28687669 TCCGGGTAAGAC
1 TCCGGGTAAGAC
28687681 TTCGTAATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:28691886 original size:12 final size:12
Alignment explanation
Indices: 28691869--28691895 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28691859 ATCAAAATCT
28691869 AAGCTAAAGTTG
1 AAGCTAAAGTTG
28691881 AAGCTAAAGTTG
1 AAGCTAAAGTTG
28691893 AAG
1 AAG
28691896 ATGACATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.26, T:0.22
Consensus pattern (12 bp):
AAGCTAAAGTTG
Found at i:28702289 original size:27 final size:28
Alignment explanation
Indices: 28702221--28702295 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
28702211 GGTTTAAAAT
* * *
28702221 TGTACAGCACTAAGTGTGCGAGTTTGAT
1 TGTATAGCACTAAGTGTGCGAGTCTGAA
*
28702249 TATATAGCACTAAGTGTGCGAG-CTGAA
1 TGTATAGCACTAAGTGTGCGAGTCTGAA
28702276 TGTATAGCACTAAGTGTGCG
1 TGTATAGCACTAAGTGTGCG
28702296 GATTCACTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 22 0.52
28 20 0.48
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (28 bp):
TGTATAGCACTAAGTGTGCGAGTCTGAA
Found at i:28703895 original size:24 final size:23
Alignment explanation
Indices: 28703849--28703904 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
28703839 TTGGTTATGG
*
28703849 TAAAGGTTAAATTAGTAATTTAA
1 TAAAGGTTAAAATAGTAATTTAA
* *
28703872 TAAATGTTAAAATAGT-A-TTAT
1 TAAAGGTTAAAATAGTAATTTAA
*
28703893 TAAAGGTAAAAA
1 TAAAGGTTAAAA
28703905 CATTAAAACA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 13 0.46
22 1 0.04
23 14 0.50
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (23 bp):
TAAAGGTTAAAATAGTAATTTAA
Found at i:28709154 original size:62 final size:62
Alignment explanation
Indices: 28709085--28709235 Score: 171
Period size: 62 Copynumber: 2.4 Consensus size: 62
28709075 AAACTTAAAT
* * * * * * * *
28709085 AGTGAGTTACGCGACTTGGGTACACGCCCGTGTCA-TTGATTGTGTGGTTTTATACCACA-AGC
1 AGTGAGTTACACGACCTAGGCACACGCCCGTGTCACTAG-CTATGTAGTTTTATACCACAGA-C
*
28709147 AGTGAGTTACACGACCTAGGCACACGCCCGTGTCCCTAGCTATGTAGTTTTATACCACAGAC
1 AGTGAGTTACACGACCTAGGCACACGCCCGTGTCACTAGCTATGTAGTTTTATACCACAGAC
* *
28709209 AGTGAGTTACACGACCCAGACACACGC
1 AGTGAGTTACACGACCTAGGCACACGC
28709236 TCGTATCCGT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
62 73 0.96
63 3 0.04
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (62 bp):
AGTGAGTTACACGACCTAGGCACACGCCCGTGTCACTAGCTATGTAGTTTTATACCACAGAC
Found at i:28709377 original size:24 final size:24
Alignment explanation
Indices: 28709345--28709392 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
28709335 TGAGTTACAT
*
28709345 GGCCAATCACACGCCTTGCCACAC
1 GGCCAATCACAAGCCTTGCCACAC
28709369 GGCCAATCACAAGCCTTGCCACAC
1 GGCCAATCACAAGCCTTGCCACAC
28709393 AGCCGTGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.44, G:0.17, T:0.12
Consensus pattern (24 bp):
GGCCAATCACAAGCCTTGCCACAC
Found at i:28711930 original size:33 final size:32
Alignment explanation
Indices: 28711891--28712027 Score: 100
Period size: 33 Copynumber: 4.2 Consensus size: 32
28711881 AAGGGTGGTA
* *
28711891 TTGAAAAGGAAAGGTATACTTTGTGTATACCAC
1 TTGAAAAGGAAAAGTACACTTTGTGT-TACCAC
* *
28711924 TTGAAAATGAAAAGTACACTATGTG-TA-CAC
1 TTGAAAAGGAAAAGTACACTTTGTGTTACCAC
** * * *
28711954 TTGAAAAGGTTATGTACACTTTGTGTGTACAAA
1 TTGAAAAGGAAAAGTACACTTTGTGT-TACCAC
** * *
28711987 TTGAAAAGGGTATGTACACTTCATGTG-TATCAC
1 TTGAAAAGGAAAAGTACACTT--TGTGTTACCAC
28712020 TTGAAAAG
1 TTGAAAAG
28712028 AGAATATGCA
Statistics
Matches: 84, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
30 23 0.27
31 2 0.02
32 2 0.02
33 53 0.63
35 4 0.05
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (32 bp):
TTGAAAAGGAAAAGTACACTTTGTGTTACCAC
Found at i:28716597 original size:69 final size:69
Alignment explanation
Indices: 28716407--28716598 Score: 203
Period size: 70 Copynumber: 2.8 Consensus size: 69
28716397 AATTGATGAG
* * *
28716407 TTGTTATATT-AAAAATGTCTTCATTTACGTTCGA-TTTAAATGCTTAATGTGTTGCTGTAAAGT
1 TTGTTATCTTAAAAAATGT-TTCATTTACG-TCAATTTTAAATGCTTAATGTGCTGCTGTAAAGT
28716470 GCTAAT
64 GCTAAT
* * * *
28716476 TTGTTATCTTAAAGAAATGTTTCACTCACGTTAATTTTAGATGCTTAATGTGCTGCTGTAAAAG-
1 TTGTTATCTTAAA-AAATGTTTCATTTACGTCAATTTTAAATGCTTAATGTGCTGCTGT-AAAGT
* *
28716540 GTTGAT
64 GCTAAT
* * *
28716546 TTGTTGTCTT-GAAAATGTGTTCATTTACGTCCATTTTAAATGCTTAATGTGCT
1 TTGTTATCTTAAAAAATGT-TTCATTTACGTCAATTTTAAATGCTTAATGTGCT
28716599 TTCCAAAAAT
Statistics
Matches: 102, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
68 6 0.06
69 41 0.40
70 45 0.44
71 10 0.10
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.44
Consensus pattern (69 bp):
TTGTTATCTTAAAAAATGTTTCATTTACGTCAATTTTAAATGCTTAATGTGCTGCTGTAAAGTGC
TAAT
Found at i:28718105 original size:40 final size:40
Alignment explanation
Indices: 28718050--28718248 Score: 107
Period size: 41 Copynumber: 4.9 Consensus size: 40
28718040 CAAAAATTGT
* *
28718050 AAAACACATAGCAATAGCGGCG-TTTTACCAAAAACGCCAC
1 AAAAAACAGAGCAATAGCGGCGATTTTA-CAAAAACGCCAC
* * * * *
28718090 TAAAAATAGAGCAATAGCTGCGATTTTTACTAAAACGCCGC
1 AAAAAACAGAGCAATAGCGGCGA-TTTTACAAAAACGCCAC
* * * * **
28718131 AAAAAACAGAGCATTAGTGGCGCTTTTTGC-AAAACGCCGTT
1 AAAAAACAGAGCAATAGCGGCG-ATTTTACAAAAACGCC-AC
* * * * ** *
28718172 AAAAACCAGA-CATTAGCGGTGCTTTTGGAAAAACGCCGC
1 AAAAAACAGAGCAATAGCGGCGATTTTACAAAAACGCCAC
* * * **
28718211 TAAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGC
1 -AAAAAACAGAGCAATAGCGGCGATTTTACAAAAACGC
28718249 TGCTAAAAAC
Statistics
Matches: 128, Mismatches: 24, Indels: 13
0.78 0.15 0.08
Matches are distributed among these distances:
39 5 0.04
40 52 0.41
41 66 0.52
42 5 0.04
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (40 bp):
AAAAAACAGAGCAATAGCGGCGATTTTACAAAAACGCCAC
Found at i:28718176 original size:41 final size:41
Alignment explanation
Indices: 28718121--28718338 Score: 307
Period size: 41 Copynumber: 5.4 Consensus size: 41
28718111 GATTTTTACT
* * * *
28718121 AAAACGCCGC-AAAAAACAGAGCATTAGTGGCGCTTTTTGC
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGA
* *
28718161 AAAACGCCGTTAAAAACCAGA-CATTAGCGGTGCTTTTGGA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGA
28718201 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGA
* *
28718242 AAAACGCTGCTAAAAACCAGAGTATTAGCGGCGCTTTT-GA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGA
* * *
28718282 TAAAACGTCGCTAAAAACCAGAACATTAGCGGCGCTTTTGGT
1 -AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGA
28718324 AAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
28718339 GTCATATAAC
Statistics
Matches: 158, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
40 46 0.29
41 111 0.70
42 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGA
Found at i:28718509 original size:7 final size:7
Alignment explanation
Indices: 28718494--28718547 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
28718484 TTAATTATCA
*
28718494 TTATAGT
1 TTATGGT
28718501 TTATGGT
1 TTATGGT
28718508 TTATGGT
1 TTATGGT
* *
28718515 TTAAGAT
1 TTATGGT
*
28718522 ATATGGT
1 TTATGGT
*
28718529 TTAGGGT
1 TTATGGT
*
28718536 TTAAGGT
1 TTATGGT
28718543 TTATG
1 TTATG
28718548 AGTTAACTAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (7 bp):
TTATGGT
Found at i:28718526 original size:21 final size:21
Alignment explanation
Indices: 28718502--28718586 Score: 89
Period size: 21 Copynumber: 3.9 Consensus size: 21
28718492 CATTATAGTT
*
28718502 TATGGTTTATGGTTTAAGATA
1 TATGGTTTAGGGTTTAAGATA
* *
28718523 TATGGTTTAGGGTTTAAGGTT
1 TATGGTTTAGGGTTTAAGATA
**
28718544 TATGAGTTAACTATAGTTTAAGATA
1 TATG-GTT---TAGGGTTTAAGATA
28718569 TATGGTTTAGGGTTTAAG
1 TATGGTTTAGGGTTTAAG
28718587 GTTTAGGAGT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
21 31 0.61
22 3 0.06
24 3 0.06
25 14 0.27
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (21 bp):
TATGGTTTAGGGTTTAAGATA
Found at i:28718565 original size:46 final size:46
Alignment explanation
Indices: 28718513--28718602 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
28718503 ATGGTTTATG
*
28718513 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTATGAGTTAACTATA
1 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAACTATA
28718559 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAACTA
1 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAACTA
28718603 GTATTTGAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (46 bp):
GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAACTATA
Found at i:28718754 original size:7 final size:7
Alignment explanation
Indices: 28718629--28718757 Score: 59
Period size: 7 Copynumber: 18.1 Consensus size: 7
28718619 GATGATGTAT
28718629 GGGTTTA
1 GGGTTTA
*
28718636 GGGATTA
1 GGGTTTA
* *
28718643 TGATTTA
1 GGGTTTA
28718650 GGGTTTAA
1 GGGTTT-A
28718658 GGG-TTA
1 GGGTTTA
28718664 GGG-TT-
1 GGGTTTA
28718669 GGAGTTTA
1 GG-GTTTA
* *
28718677 TGGTGTAA
1 GGGT-TTA
* *
28718685 CGGTTTG
1 GGGTTTA
*
28718692 GGGTTAA
1 GGGTTTA
*
28718699 GGGTTAA
1 GGGTTTA
28718706 GGGTTTA
1 GGGTTTA
*
28718713 GAGTTTA
1 GGGTTTA
*
28718720 GTGTTTA
1 GGGTTTA
*
28718727 TGGG-ATA
1 -GGGTTTA
*
28718734 TGGGTTAA
1 -GGGTTTA
28718742 GAGGTTTA
1 G-GGTTTA
28718750 GGGTTTA
1 GGGTTTA
28718757 G
1 G
28718758 ATTAATTAGT
Statistics
Matches: 92, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
5 2 0.02
6 7 0.08
7 64 0.70
8 19 0.21
ACGTcount: A:0.21, C:0.01, G:0.40, T:0.39
Consensus pattern (7 bp):
GGGTTTA
Found at i:28719577 original size:16 final size:18
Alignment explanation
Indices: 28719556--28719590 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
28719546 GGTTAATTTA
28719556 TAATTTA-TTC-ACTATT
1 TAATTTACTTCTACTATT
28719572 TAATTTACTTCTACTATT
1 TAATTTACTTCTACTATT
28719590 T
1 T
28719591 TTAGTGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 3 0.18
18 7 0.41
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATTTACTTCTACTATT
Found at i:28720440 original size:30 final size:30
Alignment explanation
Indices: 28720385--28720544 Score: 222
Period size: 29 Copynumber: 5.5 Consensus size: 30
28720375 ATAGTGAATC
28720385 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
28720414 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
28720444 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
*
28720473 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
28720501 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
28720531 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28720545 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.18
29 48 0.40
30 47 0.39
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:28720477 original size:59 final size:57
Alignment explanation
Indices: 28720385--28720544 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 57
28720375 ATAGTGAATC
*
28720385 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
28720444 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
28720501 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
28720545 CAATCTTGTC
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 50 0.54
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:28728355 original size:30 final size:30
Alignment explanation
Indices: 28728300--28728459 Score: 222
Period size: 29 Copynumber: 5.5 Consensus size: 30
28728290 ATAGTGAATC
28728300 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
28728329 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
28728359 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
*
28728388 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
28728416 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
28728446 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28728460 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.18
29 48 0.40
30 47 0.39
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:28728392 original size:59 final size:57
Alignment explanation
Indices: 28728300--28728459 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 57
28728290 ATAGTGAATC
*
28728300 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
28728359 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
28728416 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
28728460 CAATCTTGTC
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 50 0.54
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:28731085 original size:15 final size:15
Alignment explanation
Indices: 28731065--28731095 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28731055 TTGAAGGTAA
28731065 CCTACTGGTTTTCTT
1 CCTACTGGTTTTCTT
28731080 CCTACTGGTTTTCTT
1 CCTACTGGTTTTCTT
28731095 C
1 C
28731096 TAATTCAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.29, G:0.13, T:0.52
Consensus pattern (15 bp):
CCTACTGGTTTTCTT
Found at i:28732355 original size:23 final size:23
Alignment explanation
Indices: 28732310--28732355 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
28732300 GAAATTGAGA
**
28732310 TGTTAATTGAGGTGTATAAATGT
1 TGTTAATTGAAATGTATAAATGT
28732333 TGTTAATTGAAATGT-TAATATGT
1 TGTTAATTGAAATGTATAA-ATGT
28732356 GTGTGTGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.46
Consensus pattern (23 bp):
TGTTAATTGAAATGTATAAATGT
Found at i:28732760 original size:23 final size:23
Alignment explanation
Indices: 28732734--28733111 Score: 317
Period size: 23 Copynumber: 16.4 Consensus size: 23
28732724 AAATGTTGTT
28732734 AATTG-AGATGTTAAAGTGCTGCA
1 AATTGAAG-TGTTAAAGTGCTGCA
* * *
28732757 AATTAAAGTGTTTAAA-TGTTGTA
1 AATTGAAGTG-TTAAAGTGCTGCA
*
28732780 AATTGAACTGTTAAAGTGCTGCA
1 AATTGAAGTGTTAAAGTGCTGCA
*
28732803 AATTGAAGTGTTAAAGTGCTGTA
1 AATTGAAGTGTTAAAGTGCTGCA
* * *
28732826 AATTGGAGTGTTTAAGTACTGCA
1 AATTGAAGTGTTAAAGTGCTGCA
* *
28732849 AATTGAAGTGTT-TAGTTGCTGGA
1 AATTGAAGTGTTAAAG-TGCTGCA
* **
28732872 AATTG-AGATGTTTAAA-TGTTGTT
1 AATTGAAG-TG-TTAAAGTGCTGCA
*
28732895 AATTGAAATGTTAAAGTGCTGCA
1 AATTGAAGTGTTAAAGTGCTGCA
* *
28732918 AATTGAAGTGTTTTAA-TGCTGTA
1 AATTGAAGTG-TTAAAGTGCTGCA
28732941 AATTGAAGTGTTAAAGTGCTGCA
1 AATTGAAGTGTTAAAGTGCTGCA
* * **
28732964 AATTGAAGCGGTTAAA-TGTTGTT
1 AATTGAAG-TGTTAAAGTGCTGCA
*
28732987 AATTGAAATGTTAAAGTGCTGCA
1 AATTGAAGTGTTAAAGTGCTGCA
* *
28733010 AATTGAAGTGTTTGAA-TGCTGTA
1 AATTGAAGTG-TTAAAGTGCTGCA
** **
28733033 AATTGAAGTGCTATAAA-TATTGTT
1 AATTGAAGTG-T-TAAAGTGCTGCA
*
28733057 AATTGAAATGTTAAAGTGCTGCA
1 AATTGAAGTGTTAAAGTGCTGCA
* *
28733080 AATTGAAGTGTTTGAA-TGCTGTA
1 AATTGAAGTG-TTAAAGTGCTGCA
28733103 AATTGAAGT
1 AATTGAAGT
28733112 TGTGGATTAT
Statistics
Matches: 283, Mismatches: 55, Indels: 34
0.76 0.15 0.09
Matches are distributed among these distances:
22 28 0.10
23 210 0.74
24 44 0.16
25 1 0.00
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.37
Consensus pattern (23 bp):
AATTGAAGTGTTAAAGTGCTGCA
Found at i:28733070 original size:92 final size:91
Alignment explanation
Indices: 28732750--28733111 Score: 363
Period size: 92 Copynumber: 3.9 Consensus size: 91
28732740 GATGTTAAAG
* * * *
28732750 TGCTGCAAATTAAAGTGTTTAAATGTTGTAAATTGAACTGTTAAAGTGCTGCAAATTGAAGTGTT
1 TGCTGCAAATTGAAGTGTTTAAATGCTGTAAATTGAAATGTTAAAGTGCTGCAAATTGAAATGTT
* *
28732815 AAAGTGCTGTAAATTGGAGTGTTTAA
66 AAAGTGCTGCAAATTGAAGTGTTTAA
* ** * * * **
28732841 GTACTGCAAATTGAAGTGTTTAGTTGCTGGAAATTGAGATGTTTAAA-TGTTGTTAATTGAAATG
1 -TGCTGCAAATTGAAGTGTTTAAATGCTGTAAATTGAAATG-TTAAAGTGCTGCAAATTGAAATG
28732905 TTAAAGTGCTGCAAATTGAAGTGTTTTAA
64 TTAAAGTGCTGCAAATTGAAGTG-TTTAA
* * ** * **
28732934 TGCTGTAAATTGAAGTG-TTAAAGTGCTGCAAATTGAAGCGGTTAAA-TGTTGTTAATTGAAATG
1 TGCTGCAAATTGAAGTGTTTAAA-TGCTGTAAATTGAA-ATGTTAAAGTGCTGCAAATTGAAATG
28732997 TTAAAGTGCTGCAAATTGAAGTGTTTGAA
64 TTAAAGTGCTGCAAATTGAAGTGTTT-AA
* * ** * *
28733026 TGCTGTAAATTGAAGTGCTATAAATATTGTTAATTGAAATGTTAAAGTGCTGCAAATTGAAGTGT
1 TGCTGCAAATTGAAGTG-TTTAAATGCTGTAAATTGAAATGTTAAAGTGCTGCAAATTGAAATG-
* *
28733091 TTGAA-TGCTGTAAATTGAAGT
64 TTAAAGTGCTGCAAATTGAAGT
28733112 TGTGGATTAT
Statistics
Matches: 226, Mismatches: 35, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
91 6 0.03
92 163 0.72
93 49 0.22
94 8 0.04
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (91 bp):
TGCTGCAAATTGAAGTGTTTAAATGCTGTAAATTGAAATGTTAAAGTGCTGCAAATTGAAATGTT
AAAGTGCTGCAAATTGAAGTGTTTAA
Found at i:28735028 original size:19 final size:19
Alignment explanation
Indices: 28735005--28735051 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
28734995 ATTTAATCTA
*
28735005 ATTTTTATTATTTA-TTTT
1 ATTTTTATTATATATTTTT
* *
28735023 AGTTTTGATTCTATATTTTT
1 A-TTTTTATTATATATTTTT
28735043 ATTTTTATT
1 ATTTTTATT
28735052 TTAATTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.04
19 17 0.74
20 5 0.22
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72
Consensus pattern (19 bp):
ATTTTTATTATATATTTTT
Found at i:28735248 original size:43 final size:43
Alignment explanation
Indices: 28735187--28735292 Score: 185
Period size: 43 Copynumber: 2.5 Consensus size: 43
28735177 TTTTAAATTT
*
28735187 CATGACTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGC
1 CATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGC
*
28735230 CATGACCTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGC
1 CATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGC
*
28735273 CATAACCTTTAGCGGCGTTT
1 CATGACCTTTAGCGGCGTTT
28735293 TTTTCAAATA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (43 bp):
CATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGC
Found at i:28739123 original size:51 final size:51
Alignment explanation
Indices: 28739044--28739148 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
28739034 ATCGAGGTCT
*
28739044 ATAACAACAAAATTAACTCATTACTACACTACATTATACATTTCAAGTTTA
1 ATAACAACAAAATTAACTCATTAATACACTACATTATACATTTCAAGTTTA
28739095 ATAACAACAAAATTAACTCATTAATACACTACATTATACATTTCAAGTTTA
1 ATAACAACAAAATTAACTCATTAATACACTACATTATACATTTCAAGTTTA
28739146 ATA
1 ATA
28739149 TCTTCCACTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (51 bp):
ATAACAACAAAATTAACTCATTAATACACTACATTATACATTTCAAGTTTA
Found at i:28745644 original size:23 final size:23
Alignment explanation
Indices: 28745618--28745661 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
28745608 CATGCTAATA
28745618 ATAAATGCAATC-ATTATGCATTC
1 ATAAAT-CAATCAATTATGCATTC
*
28745641 ATAAATCATTCAATTATGCAT
1 ATAAATCAATCAATTATGCAT
28745662 ATTAGGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (23 bp):
ATAAATCAATCAATTATGCATTC
Found at i:28751130 original size:32 final size:32
Alignment explanation
Indices: 28751094--28751176 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 32
28751084 ACACTATATG
* * *
28751094 TGTACACTTGAAAAGGTTATCTACACTTTGTA
1 TGTACACTTGAAAAGGGTATCTACAATTCGTA
* * * *
28751126 TGTACAAATTGAAAAGGGTATGTTCAATTCGTG
1 TGTAC-ACTTGAAAAGGGTATCTACAATTCGTA
28751159 TGTATCACTTGAAAAGGG
1 TGTA-CACTTGAAAAGGG
28751177 AATGTGCACC
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 5 0.12
33 35 0.85
34 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.34
Consensus pattern (32 bp):
TGTACACTTGAAAAGGGTATCTACAATTCGTA
Found at i:28757040 original size:62 final size:61
Alignment explanation
Indices: 28756974--28757136 Score: 197
Period size: 62 Copynumber: 2.6 Consensus size: 61
28756964 TCGAAAACTT
*
28756974 AAACAGTAAGTTACATAGCCTGGACATACGCCCGTGTCCCT-GACCGTGTGGTTTTATACCAC
1 AAACAGTGAGTTACAT-GCCTGGACATACGCCCGTGTCCCTAG-CCGTGTGGTTTTATACCAC
* *
28757036 AAACAGTGAGTTACACGGCCTAGGCACAT--GCCCGTGTCCCTAGCCGTGTGGTTTTATGCCAC
1 AAACAGTGAGTTACA-TGCCT-GG-ACATACGCCCGTGTCCCTAGCCGTGTGGTTTTATACCAC
** *
28757098 AAACAGTGAGTTACACTGCCCAGACACACGCCCGTGTCC
1 AAACAGTGAGTTACA-TGCCTGGACATACGCCCGTGTCC
28757137 GTTGCTTGTG
Statistics
Matches: 88, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
60 3 0.03
61 1 0.01
62 77 0.88
63 3 0.03
64 4 0.05
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.23
Consensus pattern (61 bp):
AAACAGTGAGTTACATGCCTGGACATACGCCCGTGTCCCTAGCCGTGTGGTTTTATACCAC
Found at i:28762506 original size:31 final size:31
Alignment explanation
Indices: 28762471--28762536 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
28762461 TTTCAATTTA
28762471 GTCACTAACATTTTAGATCATTTCTATTTTG
1 GTCACTAACATTTTAGATCATTTCTATTTTG
* ** ** *
28762502 GTCACTTATGTTTTAGATTGTTTCTGTTTTG
1 GTCACTAACATTTTAGATCATTTCTATTTTG
28762533 GTCA
1 GTCA
28762537 GTCTTGGTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.20, C:0.14, G:0.15, T:0.52
Consensus pattern (31 bp):
GTCACTAACATTTTAGATCATTTCTATTTTG
Found at i:28769983 original size:35 final size:35
Alignment explanation
Indices: 28769937--28770008 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
28769927 CATATATATA
*
28769937 ATTATAATGCATATAATATAAATTGTAAATACCAT
1 ATTATAATGCATATAATATAAATTATAAATACCAT
*
28769972 ATTATAATGCATATAATCTAAATTATAAATACCAT
1 ATTATAATGCATATAATATAAATTATAAATACCAT
28770007 AT
1 AT
28770009 GAACTAACCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.38
Consensus pattern (35 bp):
ATTATAATGCATATAATATAAATTATAAATACCAT
Found at i:28771387 original size:59 final size:59
Alignment explanation
Indices: 28771295--28771412 Score: 200
Period size: 59 Copynumber: 2.0 Consensus size: 59
28771285 AAGCCGGTAA
* *
28771295 AGACCAGGACCTTTAGCGGTGCTTTTATAAAAAACGCCGCTAAATACCTGTACTTTTAG
1 AGACCAGGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACCTGTACTTTTAG
* *
28771354 AGACCAGGACCTTTAGCGGCGCTTTTATAAAAAATGCCGCTAGAGACCTGTACTTTTAG
1 AGACCAGGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACCTGTACTTTTAG
28771413 CGGCGCTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (59 bp):
AGACCAGGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACCTGTACTTTTAG
Found at i:28771412 original size:43 final size:43
Alignment explanation
Indices: 28771351--28771481 Score: 190
Period size: 43 Copynumber: 3.0 Consensus size: 43
28771341 CCTGTACTTT
* * *
28771351 TAGAGACCAGGACCTTTAGCGGCGCTTTTATAAAAAATGCCGC
1 TAGAGACCTGTACTTTTAGCGGCGCTTTTATAAAAAATGCCGC
28771394 TAGAGACCTGTACTTTTAGCGGCGCTTTTATAAAAAATGCCGC
1 TAGAGACCTGTACTTTTAGCGGCGCTTTTATAAAAAATGCCGC
* * * * *
28771437 TAAAGACATGTACTTTTAGCGACGCTTTTTTAAAAAACGCCGC
1 TAGAGACCTGTACTTTTAGCGGCGCTTTTATAAAAAATGCCGC
28771480 TA
1 TA
28771482 ATTTGCCCAG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 80 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (43 bp):
TAGAGACCTGTACTTTTAGCGGCGCTTTTATAAAAAATGCCGC
Found at i:28771412 original size:102 final size:103
Alignment explanation
Indices: 28771263--28771455 Score: 271
Period size: 102 Copynumber: 1.9 Consensus size: 103
28771253 GCCACAAAAA
* * *
28771263 TTAGCGGCGTTTTTTAGAAAAAAAGCCGGTAAAGACCAGGACCTTTAGCGGTGCTTTTATAAAAA
1 TTAGCGGCGTCTTTTAGAAAAAAAGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTATAAAAA
* *
28771328 ACGCCGCTAAATACCTGTACTTTTAGAGACCAGGACCT
66 ACGCCGCTAAAGACATGTACTTTTAGAGACCAGGACCT
* * * * * *
28771366 TTAGCGGCG-CTTTTATAAAAAATGCCGCTAGAGACCTGTACTTTTAGCGGCGCTTTTATAAAAA
1 TTAGCGGCGTCTTTTAGAAAAAAAGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTATAAAAA
*
28771430 ATGCCGCTAAAGACATGTACTTTTAG
66 ACGCCGCTAAAGACATGTACTTTTAG
28771456 CGACGCTTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
102 69 0.88
103 9 0.12
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (103 bp):
TTAGCGGCGTCTTTTAGAAAAAAAGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTATAAAAA
ACGCCGCTAAAGACATGTACTTTTAGAGACCAGGACCT
Found at i:28771482 original size:43 final size:43
Alignment explanation
Indices: 28771365--28771482 Score: 191
Period size: 43 Copynumber: 2.7 Consensus size: 43
28771355 GACCAGGACC
* *
28771365 TTTAGCGGCGCTTTTATAAAAAATGCCGCTAGAGACCTGTACT
1 TTTAGCGGCGCTTTTATAAAAAATGCCGCTAAAGACATGTACT
28771408 TTTAGCGGCGCTTTTATAAAAAATGCCGCTAAAGACATGTACT
1 TTTAGCGGCGCTTTTATAAAAAATGCCGCTAAAGACATGTACT
* * *
28771451 TTTAGCGACGCTTTTTTAAAAAACGCCGCTAA
1 TTTAGCGGCGCTTTTATAAAAAATGCCGCTAA
28771483 TTTGCCCAGT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTATAAAAAATGCCGCTAAAGACATGTACT
Found at i:28771822 original size:21 final size:21
Alignment explanation
Indices: 28771776--28771823 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
28771766 TCCTGTTCTG
* *
28771776 CTCCACCTCCCTCGTTGCTGC
1 CTCCGCCTCCCTCGCTGCTGC
28771797 CTCCGCCTCCCTCGCTGCTGC
1 CTCCGCCTCCCTCGCTGCTGC
28771818 CTCCGC
1 CTCCGC
28771824 TCTAAGTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.02, C:0.56, G:0.17, T:0.25
Consensus pattern (21 bp):
CTCCGCCTCCCTCGCTGCTGC
Found at i:28772410 original size:18 final size:18
Alignment explanation
Indices: 28772378--28772415 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
28772368 TACAATATAG
28772378 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
28772397 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
28772414 TA
1 TA
28772416 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:28778992 original size:28 final size:28
Alignment explanation
Indices: 28778945--28779026 Score: 128
Period size: 28 Copynumber: 2.9 Consensus size: 28
28778935 ATGTTGTTGA
* * *
28778945 ATACTCAATGTCTTGCACACTAAGTGCC
1 ATACTCGATATCTCGCACACTAAGTGCC
*
28778973 ATACTCGATATCTCGTACACTAAGTGCC
1 ATACTCGATATCTCGCACACTAAGTGCC
28779001 ATACTCGATATCTCGCACACTAAGTG
1 ATACTCGATATCTCGCACACTAAGTG
28779027 TAATACATAG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (28 bp):
ATACTCGATATCTCGCACACTAAGTGCC
Found at i:28779147 original size:40 final size:40
Alignment explanation
Indices: 28779013--28779149 Score: 166
Period size: 40 Copynumber: 3.4 Consensus size: 40
28779003 ACTCGATATC
** * ** * * *
28779013 TCGCACACTAAGTGTAATACATAGCTAAAGCTATCTCAAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCAATGTCGAA
* * *
28779053 TCACACACTAAGTGTCATATATAGCCGAAGCTATGTCGAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCAATGTCGAA
*
28779093 TCGCACACTAAGTGCCATATATAGCCGAAGCAATGTCGAG
1 TCGCACACTAAGTGCCATATATAGCCGAAGCAATGTCGAA
28779133 TCGCACACTAAGTGCCA
1 TCGCACACTAAGTGCCA
28779150 CAATGGCCAA
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 86 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATATATAGCCGAAGCAATGTCGAA
Found at i:28796801 original size:13 final size:13
Alignment explanation
Indices: 28796783--28796812 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
28796773 TTGAAATGTT
28796783 TAAAATGTAAGGG
1 TAAAATGTAAGGG
28796796 TAAAATGTAAGGG
1 TAAAATGTAAGGG
28796809 TAAA
1 TAAA
28796813 TTTGGTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (13 bp):
TAAAATGTAAGGG
Found at i:28805406 original size:40 final size:40
Alignment explanation
Indices: 28805310--28805528 Score: 278
Period size: 40 Copynumber: 5.5 Consensus size: 40
28805300 CGAATGGTAT
* * * *
28805310 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAAA
* *
28805351 CCGGG-TCAATTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* *
28805391 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* *
28805431 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* * * *
28805471 CCGGGCTAATTCCCGAAGGCAATTGTGCGAATTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
*
28805511 CCGGGCTATGTCCCGAAG
1 CCGGGCTAAGTCCCGAAG
28805529 ACAATCGAGC
Statistics
Matches: 159, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
40 134 0.84
41 25 0.16
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
Done.