Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 96 of 214
Found at i:27740401 original size:25 final size:25
Alignment explanation
Indices: 27740239--27740446 Score: 88
Period size: 25 Copynumber: 8.3 Consensus size: 25
27740229 CTTGCTTGAA
*
27740239 CTTCCCGA-TATATGGCT-ATCTAGAG
1 CTTCCC-ATTATATGGCTCATAT-GAG
* * **
27740264 CTTCCCGATTA-ATGGATCTTCGGAG
1 CTTCCC-ATTATATGGCTCATATGAG
* * **
27740289 CTACCCGTTAT-TGGCTCGCATGAG
1 CTTCCCATTATATGGCTCATATGAG
* * *
27740313 CTTCCTAAT-TATGGCT-ATTATTAG
1 CTTCCCATTATATGGCTCA-TATGAG
* * * * *
27740337 CTTCCCGTTATATAGCCCGTATAAG
1 CTTCCCATTATATGGCTCATATGAG
* *
27740362 CTTCCCGTTACATGGCTCATATGAG
1 CTTCCCATTATATGGCTCATATGAG
* *
27740387 CTTCCCATTATATGGCTCGAGAGAGAG
1 CTTCCCATTATATGGCTC-ATA-TGAG
* *
27740414 CTTCCCGTT-TATGTGCTCACATGAG
1 CTTCCCATTATATG-GCTCATATGAG
27740439 CATTCCCA
1 C-TTCCCA
27740447 AATATGAATT
Statistics
Matches: 135, Mismatches: 37, Indels: 21
0.70 0.19 0.11
Matches are distributed among these distances:
23 1 0.01
24 31 0.23
25 71 0.53
26 17 0.13
27 15 0.11
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.33
Consensus pattern (25 bp):
CTTCCCATTATATGGCTCATATGAG
Found at i:27743011 original size:41 final size:41
Alignment explanation
Indices: 27742889--27743024 Score: 167
Period size: 41 Copynumber: 3.4 Consensus size: 41
27742879 ACCAGTTTGG
* * *
27742889 CACCCAGTGCCTCATC-AGATAAT-TCGAAGTAATAAATTGA
1 CACCCAGTGTCTCATCGAGTTAATCT-GAAGTAGTAAATTGA
* * *
27742929 CACACAGTGTCTCATCG-GTTAAACTG-A--AGTAAATTGG
1 CACCCAGTGTCTCATCGAGTTAATCTGAAGTAGTAAATTGA
27742966 CACCCAGTGTCTCATCGAGTTAATCTGAAGTAGTAAATTGA
1 CACCCAGTGTCTCATCGAGTTAATCTGAAGTAGTAAATTGA
27743007 CACCCAGTGTCTCATCGA
1 CACCCAGTGTCTCATCGA
27743025 CTCGAAATCA
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
37 24 0.30
38 8 0.10
39 2 0.02
40 19 0.23
41 28 0.35
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (41 bp):
CACCCAGTGTCTCATCGAGTTAATCTGAAGTAGTAAATTGA
Found at i:27743227 original size:24 final size:24
Alignment explanation
Indices: 27743182--27743228 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
27743172 TATATATACC
27743182 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
27743206 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
27743229 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:27744014 original size:10 final size:10
Alignment explanation
Indices: 27744001--27744033 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
27743991 TTTGTTTTAT
27744001 TATAATATAA
1 TATAATATAA
27744011 TATAATATAA
1 TATAATATAA
27744021 TATAATAT-A
1 TATAATATAA
27744030 TATA
1 TATA
27744034 CTTAATACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TATAATATAA
Found at i:27744021 original size:15 final size:14
Alignment explanation
Indices: 27744001--27744033 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
27743991 TTTGTTTTAT
27744001 TATAATATAATATAA
1 TATAATATAATAT-A
27744016 TATAATATAATATA
1 TATAATATAATATA
27744030 TATA
1 TATA
27744034 CTTAATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TATAATATAATATA
Found at i:27749503 original size:14 final size:16
Alignment explanation
Indices: 27749484--27749515 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
27749474 GCTTGGGCCC
27749484 AAAATAAA-A-CCAAA
1 AAAATAAATAGCCAAA
27749498 AAAATAAATAGCCAAA
1 AAAATAAATAGCCAAA
27749514 AA
1 AA
27749516 TAACAGTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 1 0.06
16 7 0.44
ACGTcount: A:0.75, C:0.12, G:0.03, T:0.09
Consensus pattern (16 bp):
AAAATAAATAGCCAAA
Found at i:27750770 original size:18 final size:20
Alignment explanation
Indices: 27750728--27750771 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
27750718 TTTTATTTCT
27750728 TTATCTTTATATATGTATATA
1 TTAT-TTTATATATGTATATA
27750749 TTATTTTA-ATATGTAT-TA
1 TTATTTTATATATGTATATA
27750767 TTATT
1 TTATT
27750772 CTAAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.30
19 8 0.35
20 4 0.17
21 4 0.17
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (20 bp):
TTATTTTATATATGTATATA
Found at i:27751302 original size:19 final size:21
Alignment explanation
Indices: 27751270--27751315 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
27751260 TATTTATCTT
27751270 TTATTTACTGTTGT-TCA-CG
1 TTATTTACTGTTGTATCATCG
27751289 TTATTTAC-GCTTGTATCATCG
1 TTATTTACTG-TTGTATCATCG
27751310 -TATTTA
1 TTATTTA
27751316 TTATTGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.04
19 12 0.50
20 9 0.38
21 2 0.08
ACGTcount: A:0.20, C:0.15, G:0.13, T:0.52
Consensus pattern (21 bp):
TTATTTACTGTTGTATCATCG
Found at i:27756048 original size:83 final size:85
Alignment explanation
Indices: 27755948--27756141 Score: 329
Period size: 83 Copynumber: 2.3 Consensus size: 85
27755938 GCCACTAGTC
* *
27755948 CTATCTCCCTAAGTAGCAGTGGAGTAGGTTGAAGATTGTAGATC-T-TCTTCTTGTACTGGCAGT
1 CTATCTCCCTAAGTAGCAGTGGAGTAGGTTAAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGT
27756011 GAAGCAGATCGAAAACAAGT
66 GAAGCAGATCGAAAACAAGT
27756031 CTATCTCCCTAAGTAGCAGTGGAGTAGGTTAAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGT
1 CTATCTCCCTAAGTAGCAGTGGAGTAGGTTAAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGT
27756096 GAAGCAGATCGAAAACAAGT
66 GAAGCAGATCGAAAACAAGT
*
27756116 CTCATCTCCCTGAAGTTGCAGTGGAG
1 CT-ATCTCCCT-AAGTAGCAGTGGAG
27756142 CAGACTGAAG
Statistics
Matches: 104, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
83 43 0.41
84 1 0.01
85 39 0.38
86 8 0.08
87 13 0.12
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (85 bp):
CTATCTCCCTAAGTAGCAGTGGAGTAGGTTAAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGT
GAAGCAGATCGAAAACAAGT
Found at i:27756174 original size:45 final size:44
Alignment explanation
Indices: 27756119--27756647 Score: 183
Period size: 44 Copynumber: 11.8 Consensus size: 44
27756109 AACAAGTCTC
27756119 ATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAACATT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAAC-TT
* * * **
27756164 ATCTCTCTGAAGTTGCGGTGGAGCAGACTGAAGATAGCGAGTCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAAC-AAACTT
* * * * * *
27756209 ATTTCCCTAAAGTTGCAGCGGAACAAATTGAAGCTATAA-ATTACCGATCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG--ATAACA--A---A-CTT
* * * *
27756260 ATCTCTCTGAAGTTGCAGTAGAGCAGA-T---CATATCAAACCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAA-CTT
** * * * *
27756301 ATCTTTCTGAAGTTGCAGTAGAGTATG-TTAAAG-TAACAAACCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCA-GACTGAAGATAACAAA-CTT
* ** *
27756345 ATCCCCCT-AAGTTGCAGTAGG-GCAGGTTGAAGAT-ACAAGTCTT
1 ATCTCCCTGAAGTTGCAGT-GGAGCAGACTGAAGATAACAA-ACTT
* * *
27756388 ATCTCCCTGAAGTTGCAGTGAAGCAGACTGAA-ACT-ACTAATCCT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA-TAAC-AAACTT
* * * * * *
27756432 ATCTCCCTGAAGTTACAGTAGAGCGGATTAAAACGAT-A-AATCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAA-GATAACAAACTT
** ** * * ** ** *
27756476 ATAC-CTTTGAAGTTGCAAAGGGTCGGATTAAATCTTATCATTTCAAATTTT
1 AT-CTCCCTGAAGTTGC--A--GT-GGAGCAGA-CTGAAGATAACAAA-CTT
* ** **
27756527 ATCTCCCTGAAGTCGCAGTGGAGCAGGTTGAAGAT-ACAGGTCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACA-AACTT
* * * * *
27756571 ATCTCCATGAAGCTGCAGTGGAGCAGATTGAAG-TTACAAGTCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAA-ACTT
27756615 ATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
1 ATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
27756648 TTTATTTATT
Statistics
Matches: 357, Mismatches: 87, Indels: 81
0.68 0.17 0.15
Matches are distributed among these distances:
41 27 0.08
42 3 0.01
43 34 0.10
44 152 0.43
45 75 0.21
46 10 0.03
47 6 0.02
48 4 0.01
49 5 0.01
50 5 0.01
51 36 0.10
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
ATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAACTT
Found at i:27756648 original size:44 final size:44
Alignment explanation
Indices: 27756525--27756649 Score: 187
Period size: 44 Copynumber: 2.8 Consensus size: 44
27756515 ATTTCAAATT
* * * *
27756525 TTATCTCCCTGAAGTCGCAGTGGAGCAGGTTGAAGATACAGGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAGTC
* *
27756569 TTATCTCCATGAAGCTGCAGTGGAGCAGATTGAAGTTACAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAGTC
*
27756613 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTT
27756650 TATTTATTAT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 72 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAGTC
Found at i:27756685 original size:33 final size:33
Alignment explanation
Indices: 27756648--27756710 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
27756638 CAGACTGAAG
27756648 TTTATTTATTATCTTGCATAATTGATTCGTCTT
1 TTTATTTATTATCTTGCATAATTGATTCGTCTT
27756681 TTTATTTATTATCTTGCATAATTGATTCGT
1 TTTATTTATTATCTTGCATAATTGATTCGT
27756711 TTTAATTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.11, G:0.10, T:0.57
Consensus pattern (33 bp):
TTTATTTATTATCTTGCATAATTGATTCGTCTT
Found at i:27771670 original size:19 final size:19
Alignment explanation
Indices: 27771642--27771681 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
27771632 ATTAATTTTG
* *
27771642 ATCAAGTAAAATTAAATTA
1 ATCAAATAAAATAAAATTA
27771661 ATCAAATAAAATAAAATTA
1 ATCAAATAAAATAAAATTA
27771680 AT
1 AT
27771682 ATGATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (19 bp):
ATCAAATAAAATAAAATTA
Found at i:27773611 original size:17 final size:17
Alignment explanation
Indices: 27773591--27773623 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27773581 ATAGGGTTAG
27773591 TATGCGCGCTTGTACGA
1 TATGCGCGCTTGTACGA
*
27773608 TATGCGTGCTTGTACG
1 TATGCGCGCTTGTACG
27773624 GGATTTGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.21, G:0.30, T:0.33
Consensus pattern (17 bp):
TATGCGCGCTTGTACGA
Found at i:27773687 original size:20 final size:21
Alignment explanation
Indices: 27773664--27773715 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
27773654 TTTCGGTATT
27773664 CCTGTTTGCACTA-CGGTGCC
1 CCTGTTTGCACTATCGGTGCC
* **
27773684 CCTGTCTGCAC-ATTTGTGCC
1 CCTGTTTGCACTATCGGTGCC
27773704 CCTGTTTGCACT
1 CCTGTTTGCACT
27773716 TCTATGCATC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.10, C:0.35, G:0.21, T:0.35
Consensus pattern (21 bp):
CCTGTTTGCACTATCGGTGCC
Found at i:27776662 original size:17 final size:17
Alignment explanation
Indices: 27776640--27776687 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
27776630 AATCGCCACC
27776640 AATATTCTTTGGTTTCT
1 AATATTCTTTGGTTTCT
*
27776657 AATATTTCATTT-GTTTTT
1 AATA-TTC-TTTGGTTTCT
*
27776675 TATATTCTTTGGT
1 AATATTCTTTGGT
27776688 ATGTAATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 3 0.12
17 9 0.35
18 11 0.42
19 3 0.12
ACGTcount: A:0.19, C:0.08, G:0.10, T:0.62
Consensus pattern (17 bp):
AATATTCTTTGGTTTCT
Found at i:27777634 original size:33 final size:33
Alignment explanation
Indices: 27777597--27777681 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
27777587 CGCACGGTTC
* *
27777597 TGTGAAATGATAACAAATAT-CACCTTTTCATTT
1 TGTGAAATGATAACAAATATACAAC-TTTAATTT
* *
27777630 TGTGAAATTATAACAGAT-TACAACTTTAATTT
1 TGTGAAATGATAACAAATATACAACTTTAATTT
* *
27777662 TGTGAAGTGATAATAAATAT
1 TGTGAAATGATAACAAATAT
27777682 TGACTAGCAT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
32 22 0.52
33 20 0.48
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (33 bp):
TGTGAAATGATAACAAATATACAACTTTAATTT
Found at i:27780000 original size:40 final size:39
Alignment explanation
Indices: 27779956--27780214 Score: 268
Period size: 40 Copynumber: 6.6 Consensus size: 39
27779946 GCTCCTCGTT
*
27779956 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGT-ATCTCGCA
* * *
27779996 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTATCTCGCA
*
27780036 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCG-A
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTATCTCGCA
*
27780074 CAAATGCCTTCGGG-CTTAGCCC-GAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTATCTCGCA
*
27780112 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTATCTCGCA
* * *
27780151 CAAATGCCTTC-GGATCTTAGTCCGGATATTGTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGG-TATAGT-ATC-TCGCA
27780192 C-AA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
27780215 ACATCATTCA
Statistics
Matches: 195, Mismatches: 14, Indels: 21
0.85 0.06 0.09
Matches are distributed among these distances:
37 14 0.07
38 48 0.25
39 61 0.31
40 65 0.33
41 7 0.04
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTATCTCGCA
Found at i:27780114 original size:76 final size:79
Alignment explanation
Indices: 27779956--27780215 Score: 313
Period size: 76 Copynumber: 3.3 Consensus size: 79
27779946 GCTCCTCGTT
* *
27779956 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTCGGGACTTAACCC
*
27780019 GGATTTAGTAACTCGCA
63 GGAATTAGTAACTCGCA
*
27780036 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCG-ACAAATGCCTTCGGG-CTTAGCCC-GA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGACTTAACCCGGA
*
27780098 ATTAGTATCTCGCA
66 ATTAGTAACTCGCA
**
27780112 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
27780176 ATATT-GTCACTTAGCA
65 A-ATTAGTAAC-TCGCA
27780192 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
27780216 CATCATTCAA
Statistics
Matches: 162, Mismatches: 9, Indels: 19
0.85 0.05 0.10
Matches are distributed among these distances:
76 53 0.33
77 19 0.12
78 33 0.20
79 34 0.21
80 23 0.14
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGACTTAACCCGGA
ATTAGTAACTCGCA
Found at i:27780150 original size:39 final size:39
Alignment explanation
Indices: 27779956--27780215 Score: 311
Period size: 39 Copynumber: 6.6 Consensus size: 39
27779946 GCTCCTCGTT
* *
27779956 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
27779996 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
27780036 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCG-A
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
27780074 CAAATGCCTTCGGGCTTAGCCC-GAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
27780112 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* * *
27780151 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TCGCA
27780192 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
27780216 CATCATTCAA
Statistics
Matches: 200, Mismatches: 11, Indels: 19
0.87 0.05 0.08
Matches are distributed among these distances:
37 14 0.07
38 46 0.23
39 68 0.34
40 61 0.31
41 11 0.05
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:27788022 original size:40 final size:40
Alignment explanation
Indices: 27787978--27788239 Score: 328
Period size: 39 Copynumber: 6.7 Consensus size: 40
27787968 GCTCCTCGTT
* *
27787978 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
27788018 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
27788058 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
27788097 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
27788136 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
27788175 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
27788216 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27788240 CATCATTCAA
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 126 0.62
40 64 0.32
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:27791956 original size:16 final size:16
Alignment explanation
Indices: 27791935--27791984 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 16
27791925 ATATTTAGTC
27791935 ATATAATAAATTATTA
1 ATATAATAAATTATTA
*
27791951 ATATAAT---GTATTA
1 ATATAATAAATTATTA
*
27791964 AAATAATAAATTATTGA
1 ATATAATAAATTATT-A
27791981 ATAT
1 ATAT
27791985 TTCAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 11 0.42
16 11 0.42
17 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:27792843 original size:20 final size:20
Alignment explanation
Indices: 27792818--27792855 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27792808 ACTTCTTGAT
*
27792818 TCAACTTTCTTTTTCATTCA
1 TCAACTTTCTCTTTCATTCA
27792838 TCAACTTTCTCTTTCATT
1 TCAACTTTCTCTTTCATT
27792856 AATTTTATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.55
Consensus pattern (20 bp):
TCAACTTTCTCTTTCATTCA
Found at i:27795788 original size:14 final size:15
Alignment explanation
Indices: 27795769--27795801 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
27795759 AGAAGCTGGG
27795769 AGAAGAGAAG-AGAA
1 AGAAGAGAAGAAGAA
27795783 AGAAGAGAAGAAGAA
1 AGAAGAGAAGAAGAA
27795798 AGAA
1 AGAA
27795802 AAAATACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AGAAGAGAAGAAGAA
Found at i:27800599 original size:75 final size:75
Alignment explanation
Indices: 27800513--27800653 Score: 205
Period size: 75 Copynumber: 1.9 Consensus size: 75
27800503 AATAGGAAGA
* *
27800513 ACATATAATGC-AGGTAT-TAAAGGATGCTAGTGTATTAATGCAAAACATTAAACAAAGATGCAT
1 ACATATAATGCAAGCT-TCTAAA-GATGCAAGTGTATTAATGCAAAACATTAAACAAAGATGCAT
27800576 TTAATAAACAAG
64 TTAATAAACAAG
* * *
27800588 ACATTTAATGCAAGCTTCTAAAGATGCAATTGTATTAATGCAAAACATTAATCAAAGATGCATTT
1 ACATATAATGCAAGCTTCTAAAGATGCAAGTGTATTAATGCAAAACATTAAACAAAGATGCATTT
27800653 A
66 A
27800654 TCCAACAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
75 52 0.88
76 7 0.12
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (75 bp):
ACATATAATGCAAGCTTCTAAAGATGCAAGTGTATTAATGCAAAACATTAAACAAAGATGCATTT
AATAAACAAG
Found at i:27801187 original size:25 final size:25
Alignment explanation
Indices: 27801159--27801228 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
27801149 TATGTATGCC
* *
27801159 GCCTTTGTGACGTATTCTGTATGTT
1 GCCTTTATGGCGTATTCTGTATGTT
* *
27801184 GCCTTTATGGCGTACTCTATATGTT
1 GCCTTTATGGCGTATTCTGTATGTT
* *
27801209 CCCCTTATGGCGTATTCTGT
1 GCCTTTATGGCGTATTCTGT
27801229 TTGGCTCTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (25 bp):
GCCTTTATGGCGTATTCTGTATGTT
Found at i:27813146 original size:16 final size:15
Alignment explanation
Indices: 27813125--27813195 Score: 67
Period size: 16 Copynumber: 4.7 Consensus size: 15
27813115 CCCTTGCATG
27813125 TGCGAACCCCCTTACA
1 TGCGAACCCCCTTA-A
*
27813141 TGCGAACCCAC-TATA
1 TGCGAACCCCCTTA-A
*
27813156 GGCGAA-CCCCTT-A
1 TGCGAACCCCCTTAA
27813169 TGCGAACCCCCTATAA
1 TGCGAACCCCCT-TAA
27813185 GTGCGAACCCC
1 -TGCGAACCCC
27813196 TGCTTGCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
13 6 0.13
14 8 0.18
15 10 0.22
16 11 0.24
17 10 0.22
ACGTcount: A:0.27, C:0.39, G:0.17, T:0.17
Consensus pattern (15 bp):
TGCGAACCCCCTTAA
Found at i:27813162 original size:15 final size:14
Alignment explanation
Indices: 27813142--27813196 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 14
27813132 CCCCTTACAT
27813142 GCGAACCCACTATAG
1 GCGAACCC-CTATAG
*
27813157 GCGAACCCCT-TAT
1 GCGAACCCCTATAG
27813170 GCGAACCCCCTATAAG
1 GCGAA-CCCCTAT-AG
27813186 TGCGAACCCCT
1 -GCGAACCCCT
27813197 GCTTGCAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 7 0.21
14 7 0.21
15 9 0.26
16 6 0.18
17 5 0.15
ACGTcount: A:0.27, C:0.38, G:0.18, T:0.16
Consensus pattern (14 bp):
GCGAACCCCTATAG
Found at i:27813175 original size:13 final size:13
Alignment explanation
Indices: 27813125--27813178 Score: 54
Period size: 15 Copynumber: 3.8 Consensus size: 13
27813115 CCCTTGCATG
27813125 TGCGAACCCCCTTACA
1 TGCGAA-CCCCTT--A
27813141 TGCGAACCCACTATA
1 TGCGAACCC-CT-TA
*
27813156 GGCGAACCCCTTA
1 TGCGAACCCCTTA
27813169 TGCGAACCCC
1 TGCGAACCCC
27813179 CTATAAGTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 11 0.32
14 2 0.06
15 12 0.35
16 8 0.24
17 1 0.03
ACGTcount: A:0.26, C:0.41, G:0.17, T:0.17
Consensus pattern (13 bp):
TGCGAACCCCTTA
Found at i:27813176 original size:28 final size:31
Alignment explanation
Indices: 27813124--27813196 Score: 98
Period size: 30 Copynumber: 2.4 Consensus size: 31
27813114 CCCCTTGCAT
27813124 GTGCGAACCCCCTTACATGCGAACCCACTAT-A
1 GTGCGAA-CCCCTTA-ATGCGAACCCACTATAA
*
27813156 G-GCGAACCCCTT-ATGCGAACCCCCTATAA
1 GTGCGAACCCCTTAATGCGAACCCACTATAA
27813185 GTGCGAACCCCT
1 GTGCGAACCCCT
27813197 GCTTGCAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
28 14 0.37
29 2 0.05
30 16 0.42
31 5 0.13
32 1 0.03
ACGTcount: A:0.26, C:0.38, G:0.18, T:0.18
Consensus pattern (31 bp):
GTGCGAACCCCTTAATGCGAACCCACTATAA
Found at i:27813441 original size:24 final size:24
Alignment explanation
Indices: 27813392--27813441 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
27813382 ATATACATAT
*
27813392 TGCGAACCTTATATGAATTAGTTG
1 TGCGAACCTTATATGAATTACTTG
27813416 TGCGAACC-TATGA-GAATTACTATG
1 TGCGAACCTTAT-ATGAATTACT-TG
27813440 TG
1 TG
27813442 AACCCTACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (24 bp):
TGCGAACCTTATATGAATTACTTG
Found at i:27815436 original size:28 final size:28
Alignment explanation
Indices: 27815403--27815506 Score: 88
Period size: 28 Copynumber: 3.7 Consensus size: 28
27815393 AAAATCTCTA
* *
27815403 TTAAAGGTAAGCATTTGTGGTGAACCTC
1 TTAAAGGTAAGCCTTTGTGGAGAACCTC
* * *
27815431 TTAAAGG-ATTGCCTTTGTGGAAAAACT-
1 TTAAAGGTA-AGCCTTTGTGGAGAACCTC
* *
27815458 TTAAAAAGGTAAGCCTTTGTAGCGAACCTC
1 TT--AAAGGTAAGCCTTTGTGGAGAACCTC
*
27815488 TTAAAGG-ACGCCTTTGTGG
1 TTAAAGGTAAGCCTTTGTGG
27815507 CAAATCTCTG
Statistics
Matches: 59, Mismatches: 12, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
27 13 0.22
28 25 0.42
29 18 0.31
30 3 0.05
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (28 bp):
TTAAAGGTAAGCCTTTGTGGAGAACCTC
Found at i:27815477 original size:57 final size:58
Alignment explanation
Indices: 27815381--27815515 Score: 170
Period size: 57 Copynumber: 2.4 Consensus size: 58
27815371 AAAAAAGGAC
* * *
27815381 ACGCCTTTGT-GAAAAATCTCTATTAAAGGTAAGCATTTGTGGTGAACCTCTTAAAGG
1 ACGCCTTTGTGGAAAAATCTCTATAAAAGGTAAGCATTTGTAGCGAACCTCTTAAAGG
* * *
27815438 ATTGCCTTTGTGGAAAAA-CTTTA-AAAAGGTAAGCCTTTGTAGCGAACCTCTTAAAGG
1 A-CGCCTTTGTGGAAAAATCTCTATAAAAGGTAAGCATTTGTAGCGAACCTCTTAAAGG
*
27815495 ACGCCTTTGTGG-CAAATCTCT
1 ACGCCTTTGTGGAAAAATCTCT
27815516 GAAAGGAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
55 3 0.05
56 13 0.20
57 32 0.48
58 12 0.18
59 6 0.09
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (58 bp):
ACGCCTTTGTGGAAAAATCTCTATAAAAGGTAAGCATTTGTAGCGAACCTCTTAAAGG
Found at i:27815504 original size:27 final size:27
Alignment explanation
Indices: 27815470--27815522 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
27815460 AAAAAGGTAA
* *
27815470 GCCTTTGTAGCGAACCTCTTAAAGGAC
1 GCCTTTGTAGCAAACCTCTGAAAGGAC
* *
27815497 GCCTTTGTGGCAAATCTCTGAAAGGA
1 GCCTTTGTAGCAAACCTCTGAAAGGA
27815523 AAACCTATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (27 bp):
GCCTTTGTAGCAAACCTCTGAAAGGAC
Found at i:27816525 original size:162 final size:162
Alignment explanation
Indices: 27816250--27816564 Score: 456
Period size: 162 Copynumber: 1.9 Consensus size: 162
27816240 GACACATGAA
*
27816250 GGACATGCAAAGTGTCTATTATGCTTAGACGTAATGAATCAGGTACTTAAGGTTTAATTCACTAA
1 GGACATGCAAAGCGTCTATTATGCTTAGACGTAATGAATCAGGTACTTAAGGTTTAATTCACTAA
* *
27816315 GTTATTATAAACTTATGAAGGTTATTTCATGTTTCAATTTGCAAAGAAG-TTAGCA-CTGAGGGA
66 GTAATTATAAACTTATGAAGGTTATTTCATGTTTCAAGTTGCAAAGAAGTTTA-CATC-GAGGGA
*
27816378 CAATGCCAGAGCTGTGCTAAAGGATTGGTAAGAT
129 CAATACCAGAGCTGTGCTAAAGGATTGGTAAGAT
* * *
27816412 GGACATGCGAAGCGTCTATTATGCTTAGATGTAATGAATTAGGTACTTAAGGTTTAATTCACTAA
1 GGACATGCAAAGCGTCTATTATGCTTAGACGTAATGAATCAGGTACTTAAGGTTTAATTCACTAA
* * * * * *
27816477 GTAATTATGAAA-TTATGAAGGTTATTTCGTGTTTTAGGTTGTAAAGAAGTTTACATCGGGGGAT
66 GTAATTAT-AAACTTATGAAGGTTATTTCATGTTTCAAGTTGCAAAGAAGTTTACATCGAGGGAC
*
27816541 AATACCAGGGCTGTGCTAAAGGAT
130 AATACCAGAGCTGTGCTAAAGGAT
27816565 CAACAAAATG
Statistics
Matches: 136, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
162 129 0.95
163 7 0.05
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (162 bp):
GGACATGCAAAGCGTCTATTATGCTTAGACGTAATGAATCAGGTACTTAAGGTTTAATTCACTAA
GTAATTATAAACTTATGAAGGTTATTTCATGTTTCAAGTTGCAAAGAAGTTTACATCGAGGGACA
ATACCAGAGCTGTGCTAAAGGATTGGTAAGAT
Found at i:27818488 original size:119 final size:120
Alignment explanation
Indices: 27818277--27818534 Score: 303
Period size: 119 Copynumber: 2.2 Consensus size: 120
27818267 AAATCACGTA
* * * * *
27818277 CCTTCGGAATTTAA-CCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAG
1 CCTTCGGGACTTAACCCGGATATAGCTACTCGTACAAATGCCTTCGGGACATAACCCGGTAATAG
* * *
27818341 TGACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAAC-TCGCACAAATG
66 TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTAGCACAAA-G
* * *
27818396 CCTTCGGGACTTAACCCGGATTTAG-TAACTCGTACCAATGCCTTCGGG-CTTAACCCGG-AATC
1 CCTTCGGGACTTAACCCGGATATAGCT-ACTCGTACAAATGCCTTCGGGACATAACCCGGTAAT-
* * *
27818458 AGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAAG
64 AGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAACTTAGCACAAAG
*
27818515 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
27818535 CATCATTCAA
Statistics
Matches: 119, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
118 5 0.04
119 78 0.66
120 36 0.30
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
CCTTCGGGACTTAACCCGGATATAGCTACTCGTACAAATGCCTTCGGGACATAACCCGGTAATAG
TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTAGCACAAAG
Found at i:27818534 original size:40 final size:40
Alignment explanation
Indices: 27818291--27818534 Score: 282
Period size: 40 Copynumber: 6.1 Consensus size: 40
27818281 CGGAATTTAA
** *
27818291 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
27818331 CCGGTTATAGTGACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
27818371 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
27818411 CCGGATTTAGTAACTCGTACCAATGCCTTCGGG-CTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
27818450 CCGGA-ATCAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATAT-AGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
27818490 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
27818530 CCGGA
1 CCGGA
27818535 CATCATTCAA
Statistics
Matches: 178, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
38 3 0.02
39 32 0.18
40 130 0.73
41 13 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:27825775 original size:119 final size:120
Alignment explanation
Indices: 27825599--27825821 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
27825589 TATTCGTTCA
** * *
27825599 AATGCCTTCGGGACATAGCCCGGTTATAGTGACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT
1 AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
* *
27825664 ATAGTGAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTCACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* *
27825719 AATGCCTTCGGG-CTTAGCCCAGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCC-GAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGG
* *
27825781 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTCACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
27825822 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 3 0.03
119 65 0.72
120 22 0.24
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
ATAGTCACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:27825821 original size:40 final size:40
Alignment explanation
Indices: 27825597--27825821 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
27825587 GCTATTCGTT
* * *
27825597 CAAATGCCTTCGGGACATAGCCCGGTTATAGTGACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
27825637 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTGACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
27825677 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
27825717 CCAATGCCTTCGGG-CTTAGCCCAGA-ATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
27825756 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
27825797 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27825822 CATCATTCAA
Statistics
Matches: 163, Mismatches: 16, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 31 0.19
40 118 0.72
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:27828630 original size:17 final size:17
Alignment explanation
Indices: 27828604--27828649 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
27828594 CTGATCCATT
*
27828604 CACACAGCCATGCGACC
1 CACACGGCCATGCGACC
*
27828621 CACACGGCCATGTGACC
1 CACACGGCCATGCGACC
*
27828638 CACACGACCATG
1 CACACGGCCATG
27828650 TGCTAGGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.28, C:0.43, G:0.20, T:0.09
Consensus pattern (17 bp):
CACACGGCCATGCGACC
Found at i:27830475 original size:8 final size:8
Alignment explanation
Indices: 27830462--27830536 Score: 60
Period size: 8 Copynumber: 8.4 Consensus size: 8
27830452 TTGTAGTTCT
27830462 TTTATATA
1 TTTATATA
*
27830470 TTTATAAA
1 TTTATATA
*
27830478 TTTTTAGTTGA
1 TTTATA--T-A
27830489 TTTATATA
1 TTTATATA
27830497 TTTATATA
1 TTTATATA
27830505 TTTATCATAAA
1 TTTAT-AT--A
27830516 TTTATAATA
1 TTTAT-ATA
27830525 TTTTATATA
1 -TTTATATA
27830534 TTT
1 TTT
27830537 TTCAAAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
8 29 0.53
9 7 0.13
10 5 0.09
11 14 0.25
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (8 bp):
TTTATATA
Found at i:27830485 original size:27 final size:28
Alignment explanation
Indices: 27830450--27830507 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
27830440 TCTAGACGTG
*
27830450 TTTTGTAGTTCTTTTATATATTTATAAA
1 TTTTGTAGTTCATTTATATATTTATAAA
* *
27830478 TTTT-TAGTTGATTTATATATTTATATA
1 TTTTGTAGTTCATTTATATATTTATAAA
27830505 TTT
1 TTT
27830508 ATCATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.64
Consensus pattern (28 bp):
TTTTGTAGTTCATTTATATATTTATAAA
Found at i:27830518 original size:27 final size:26
Alignment explanation
Indices: 27830462--27830550 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 26
27830452 TTGTAGTTCT
* * **
27830462 TTTATATATTTATAAATTTTTAGTTGA
1 TTTATATATTTATATATTTTCA-TAAA
27830489 TTTATATATTTATATATTTATCATAAA
1 TTTATATATTTATATATTT-TCATAAA
27830516 TTTATAATATTTTATATATTTTTCA-AAA
1 TTTAT-ATA-TTTATATA-TTTTCATAAA
27830544 TTT-TATA
1 TTTATATA
27830551 CACTTTTAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
26 3 0.06
27 26 0.48
28 11 0.20
29 11 0.20
30 3 0.06
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTATATATTTATATATTTTCATAAA
Found at i:27830548 original size:19 final size:20
Alignment explanation
Indices: 27830516--27830600 Score: 72
Period size: 19 Copynumber: 4.5 Consensus size: 20
27830506 TTATCATAAA
*
27830516 TTTATAATATTTTATATATT
1 TTTAAAATATTTTATATATT
* * *
27830536 TTTCAAA-ATTTTATACACT
1 TTTAAAATATTTTATATATT
*
27830555 TTTAAAATATTTTAT-TATA
1 TTTAAAATATTTTATATATT
27830574 TTT---ATATTTTATATATGT
1 TTTAAAATATTTTATATAT-T
*
27830592 TTGAAAATA
1 TTTAAAATA
27830601 ATAATATAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
16 9 0.18
17 3 0.06
18 2 0.04
19 20 0.41
20 12 0.24
21 3 0.06
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTAAAATATTTTATATATT
Found at i:27830558 original size:29 final size:29
Alignment explanation
Indices: 27830488--27830546 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
27830478 TTTTTAGTTG
*
27830488 ATTTAT-ATA-TTTATATATTTATCATAA
1 ATTTATAATATTTTATATATTTTTCATAA
27830515 ATTTATAATATTTTATATATTTTTCA-AA
1 ATTTATAATATTTTATATATTTTTCATAA
27830543 ATTT
1 ATTT
27830547 TATACACTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 6 0.21
28 9 0.31
29 14 0.48
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (29 bp):
ATTTATAATATTTTATATATTTTTCATAA
Found at i:27830640 original size:16 final size:17
Alignment explanation
Indices: 27830621--27830658 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
27830611 ATTCATATTT
27830621 TATAAAAAATT-TAAAA
1 TATAAAAAATTCTAAAA
*
27830637 TATATAAAATTGCTAAAA
1 TATAAAAAATT-CTAAAA
27830655 TATA
1 TATA
27830659 TTTATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (17 bp):
TATAAAAAATTCTAAAA
Found at i:27832327 original size:27 final size:27
Alignment explanation
Indices: 27832296--27832351 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
27832286 CATTACAAGT
* * *
27832296 GGGTTTGCCAGTTGAGTTGCGAATTGA
1 GGGTTTGCCAGTTAAGCTGCGAACTGA
27832323 GGGTTTGCCAGTTAAGCTGCGAACTGA
1 GGGTTTGCCAGTTAAGCTGCGAACTGA
27832350 GG
1 GG
27832352 TTCACTAGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.20, C:0.14, G:0.38, T:0.29
Consensus pattern (27 bp):
GGGTTTGCCAGTTAAGCTGCGAACTGA
Found at i:27833020 original size:12 final size:12
Alignment explanation
Indices: 27832988--27833019 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
27832978 AAGTGAGTTG
27832988 ATGTTTTTAAGT
1 ATGTTTTTAAGT
27833000 ATGTTTTTAAGT
1 ATGTTTTTAAGT
27833012 ATAGTTTT
1 AT-GTTTT
27833020 ATAACTTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.25, C:0.00, G:0.16, T:0.59
Consensus pattern (12 bp):
ATGTTTTTAAGT
Found at i:27836343 original size:19 final size:19
Alignment explanation
Indices: 27836319--27836365 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
27836309 GGATATATTT
*
27836319 TAAATCTTATTTAGTTAGA
1 TAAATCTTATTTAGGTAGA
27836338 TAAATCTTATTTAGGTAGA
1 TAAATCTTATTTAGGTAGA
27836357 TAAATCTTA
1 TAAATCTTA
27836366 GAATAAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (19 bp):
TAAATCTTATTTAGGTAGA
Found at i:27840922 original size:19 final size:19
Alignment explanation
Indices: 27840893--27840938 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
27840883 GGATATATTT
27840893 TAAAT-TTATTTAGGTGGA
1 TAAATCTTATTTAGGTGGA
27840911 TAAATCTTATTTAGGTGGA
1 TAAATCTTATTTAGGTGGA
27840930 TAAATCTTA
1 TAAATCTTA
27840939 GAATAAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.43
Consensus pattern (19 bp):
TAAATCTTATTTAGGTGGA
Found at i:27841587 original size:37 final size:37
Alignment explanation
Indices: 27841546--27841620 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
27841536 TTAACTAAGA
*
27841546 AAAAGGAAATAAAGCTGAGCTATATTAAATGCTATGG
1 AAAAGGAAATAAAGCTGAGCCATATTAAATGCTATGG
* *
27841583 AAAAGGAAATAGAGTTGAGCCATATTAAATGCTATGG
1 AAAAGGAAATAAAGCTGAGCCATATTAAATGCTATGG
27841620 A
1 A
27841621 TTAAAATGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.45, C:0.08, G:0.23, T:0.24
Consensus pattern (37 bp):
AAAAGGAAATAAAGCTGAGCCATATTAAATGCTATGG
Found at i:27849055 original size:18 final size:18
Alignment explanation
Indices: 27849032--27849073 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
27849022 ATGCACTTCG
27849032 TGCATTCCATACAAAACA
1 TGCATTCCATACAAAACA
* **
27849050 TGCATTCCATGCAACCCA
1 TGCATTCCATACAAAACA
27849068 TGCATT
1 TGCATT
27849074 TCATGTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.31, G:0.10, T:0.26
Consensus pattern (18 bp):
TGCATTCCATACAAAACA
Found at i:27854313 original size:12 final size:13
Alignment explanation
Indices: 27854288--27854317 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
27854278 TGAACTATAA
27854288 TTATTGCATTTAT
1 TTATTGCATTTAT
27854301 TTATTGC-TTTAT
1 TTATTGCATTTAT
27854313 TTATT
1 TTATT
27854318 CATGTATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (13 bp):
TTATTGCATTTAT
Found at i:27862084 original size:18 final size:17
Alignment explanation
Indices: 27862063--27862110 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
27862053 GCATTTCACA
27862063 CATTCCATGCAACCCATG
1 CATTCCATGCAA-CCATG
*
27862081 CATTTCATGCGAACCATG
1 CATTCCATGC-AACCATG
*
27862099 CATCCCATGCAA
1 CATTCCATGCAA
27862111 TGTGCTGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 2 0.08
18 22 0.85
19 2 0.08
ACGTcount: A:0.29, C:0.35, G:0.12, T:0.23
Consensus pattern (17 bp):
CATTCCATGCAACCATG
Found at i:27866415 original size:79 final size:82
Alignment explanation
Indices: 27866304--27866488 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 82
27866294 GCTACTCGTT
* * *
27866304 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCACACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTC-GGATCTTAACCC
* *
27866367 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* * **
27866384 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGATCTTAACCCG
* *
27866447 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
27866464 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27866489 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 53 0.59
80 34 0.38
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:27866488 original size:40 final size:41
Alignment explanation
Indices: 27866304--27866488 Score: 195
Period size: 40 Copynumber: 4.6 Consensus size: 41
27866294 GCTACTCGTT
* * *
27866304 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCA-CA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTAGCA
* * * *
27866344 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTAGCA
* *
27866384 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTTAGCA
* * *
27866423 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAACTTAGCA
27866464 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27866489 CATCATTCAA
Statistics
Matches: 121, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 75 0.62
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTAGCA
Found at i:27874472 original size:79 final size:82
Alignment explanation
Indices: 27874361--27874545 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
27874351 GCTACTCGTT
* * *
27874361 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
27874424 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
27874441 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
27874504 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
27874521 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27874546 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:27874545 original size:40 final size:40
Alignment explanation
Indices: 27874342--27874545 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
27874332 CGGAATTTAA
** *
27874342 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
27874382 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
27874422 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
27874461 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
27874501 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
27874541 CCGGA
1 CCGGA
27874546 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:27876769 original size:40 final size:40
Alignment explanation
Indices: 27876721--27876947 Score: 402
Period size: 40 Copynumber: 5.7 Consensus size: 40
27876711 GCAAACACAT
* * *
27876721 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
27876761 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
27876801 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
27876841 TTGCCTTCAGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
27876881 TTGCCTTC-GGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
27876920 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
27876948 TCCAATGCTC
Statistics
Matches: 180, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
39 39 0.22
40 141 0.78
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:27876935 original size:119 final size:120
Alignment explanation
Indices: 27876721--27876947 Score: 402
Period size: 119 Copynumber: 1.9 Consensus size: 120
27876711 GCAAACACAT
* *
27876721 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCAGGTCTTAACCCGGACATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
*
27876786 TATCATCTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
66 TATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
27876841 TTGCCTTCAGGTCTTAGCCCGGATATATCAACTCGCATAATTGCCTTC-GGTCTTAGCCCGGATA
1 TTGCCTTCAGGTCTTAACCCGGACATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
27876905 TATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATAT
66 TATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATAT
27876948 TCCAATGCTC
Statistics
Matches: 102, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
119 58 0.57
120 44 0.43
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.31
Consensus pattern (120 bp):
TTGCCTTCAGGTCTTAACCCGGACATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
TATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:27891928 original size:28 final size:28
Alignment explanation
Indices: 27891896--27892033 Score: 100
Period size: 28 Copynumber: 4.8 Consensus size: 28
27891886 GTAAAGGATT
*
27891896 TTTGTGGCTATCTCTGTTACAGGAAGCC
1 TTTGTGGCTATCTCTGTTAAAGGAAGCC
* * **
27891924 TTTGTGGCTTATGTTCATATTAAAAGGATTCC
1 TTTGTGGC-TAT-CTC-TGTT-AAAGGAAGCC
* * *
27891956 CTTGTGGCAATCTCTGATAAAGGAAGCC
1 TTTGTGGCTATCTCTGTTAAAGGAAGCC
*
27891984 TTTGTGG-TGATCTTTGTTAAAGGGAAGCC
1 TTTGTGGCT-ATCTCTGTTAAA-GGAAGCC
* *
27892013 TTTATAG-TGATCTCTGTTAAA
1 TTTGTGGCT-ATCTCTGTTAAA
27892034 ATGATGCCTT
Statistics
Matches: 85, Mismatches: 19, Indels: 11
0.74 0.17 0.10
Matches are distributed among these distances:
28 32 0.38
29 30 0.35
30 4 0.05
31 5 0.06
32 14 0.16
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (28 bp):
TTTGTGGCTATCTCTGTTAAAGGAAGCC
Found at i:27892010 original size:29 final size:28
Alignment explanation
Indices: 27891965--27892051 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 28
27891955 CCTTGTGGCA
* *
27891965 ATCTCTGATAAAGGAAGCCTTTGTGGTG
1 ATCTCTGTTAAAGGAAGCCTTTATGGTG
* *
27891993 ATCTTTGTTAAAGGGAAGCCTTTATAGTG
1 ATCTCTGTTAAA-GGAAGCCTTTATGGTG
* *
27892022 ATCTCTGTTAAAATGATGCCTTTATGGTG
1 ATCTCTGTT-AAAGGAAGCCTTTATGGTG
27892051 A
1 A
27892052 GACTCTAAAG
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 10 0.20
29 36 0.73
30 3 0.06
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (28 bp):
ATCTCTGTTAAAGGAAGCCTTTATGGTG
Found at i:27904601 original size:52 final size:52
Alignment explanation
Indices: 27904518--27904618 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
27904508 TAAGGAAACG
* * *
27904518 TAATGGACAGTAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
27904570 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
27904619 TATGTGCATG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:27907245 original size:27 final size:27
Alignment explanation
Indices: 27907189--27907261 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
27907179 TAGATGTTTG
* * * *
27907189 CCACAAAGGC-ATTCCTTCATGTTATG
1 CCACAAAGGCTTTTCTTTCATATTATA
27907215 CCACAAAGGCTTTTCTTTCATATTATA
1 CCACAAAGGCTTTTCTTTCATATTATA
27907242 CCACAAAGGCTTTTTCTTTC
1 CCACAAAGGC-TTTTCTTTC
27907262 CTAACGTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 10 0.24
27 22 0.54
28 9 0.22
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (27 bp):
CCACAAAGGCTTTTCTTTCATATTATA
Found at i:27907909 original size:23 final size:23
Alignment explanation
Indices: 27907879--27907927 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
27907869 AAAAGAACAA
27907879 AGAGAGTTGAATAACTCACAAAT
1 AGAGAGTTGAATAACTCACAAAT
27907902 AGAGAGTTGAATAACTCACAAAT
1 AGAGAGTTGAATAACTCACAAAT
27907925 AGA
1 AGA
27907928 TTAAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.20
Consensus pattern (23 bp):
AGAGAGTTGAATAACTCACAAAT
Found at i:27910204 original size:23 final size:23
Alignment explanation
Indices: 27910152--27910204 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
27910142 AACCTGGACA
* **
27910152 ACATTAAGACAATGTTTAAATGC
1 ACATTAAGACAAGGTTTAAACAC
27910175 ACATTAAGACAAGGTTTAAACAC
1 ACATTAAGACAAGGTTTAAACAC
*
27910198 ACTTTAA
1 ACATTAA
27910205 TTTGTAGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.28
Consensus pattern (23 bp):
ACATTAAGACAAGGTTTAAACAC
Found at i:27910353 original size:38 final size:39
Alignment explanation
Indices: 27910272--27910380 Score: 157
Period size: 38 Copynumber: 2.8 Consensus size: 39
27910262 AAGTATTGAA
* * *
27910272 GATGTTCAAACTATGACATAATTAAAGACCCATATTAAT
1 GATGTTCAAATTATGACATAATTAAATACTCATATTAAT
*
27910311 GATGTTCAGATTATGACATAATT-AATACTCATATTAAT
1 GATGTTCAAATTATGACATAATTAAATACTCATATTAAT
* *
27910349 GATGTTAAAATTATGGCATAATTAAATACTCA
1 GATGTTCAAATTATGACATAATTAAATACTCA
27910381 AACTATAATA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 33 0.53
39 29 0.47
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (39 bp):
GATGTTCAAATTATGACATAATTAAATACTCATATTAAT
Found at i:27912232 original size:15 final size:15
Alignment explanation
Indices: 27912169--27912237 Score: 52
Period size: 15 Copynumber: 4.4 Consensus size: 15
27912159 CCTTTTTCTC
27912169 TTTTTCAATTTCATTTT
1 TTTTTCAATTTC--TTT
27912186 ATTTTTC--TTTCTCTT
1 -TTTTTCAATTTCT-TT
** *
27912201 TTCTTTCAAGCTATTT
1 TT-TTTCAATTTCTTT
27912217 TTTTTCAATTTCTTT
1 TTTTTCAATTTCTTT
27912232 TTTTTC
1 TTTTTC
27912238 TCGCTCATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
14 3 0.07
15 22 0.54
16 8 0.20
17 2 0.05
18 6 0.15
ACGTcount: A:0.13, C:0.16, G:0.01, T:0.70
Consensus pattern (15 bp):
TTTTTCAATTTCTTT
Found at i:27914753 original size:30 final size:31
Alignment explanation
Indices: 27914719--27914778 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
27914709 AAACCTTTTA
*
27914719 TTTTTCCCCAAAATTTTTACTCCC-TCTCAC
1 TTTTTCCCCAAAACTTTTACTCCCTTCTCAC
* *
27914749 TTTTTCCCTAAAACTTTTATTCCCTTCTCA
1 TTTTTCCCCAAAACTTTTACTCCCTTCTCA
27914779 TCCTAGCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (31 bp):
TTTTTCCCCAAAACTTTTACTCCCTTCTCAC
Found at i:27923291 original size:58 final size:60
Alignment explanation
Indices: 27923226--27923342 Score: 148
Period size: 61 Copynumber: 2.0 Consensus size: 60
27923216 ATCACTTTAA
* * * *
27923226 TATTAAATTAATATAATACTTA-T-TCAGATAAATATTAGATGAAATTTAATATTAAATC
1 TATTAAATTAATAGAATACTTACTATAAGATAAATATTAAATGAAATTTAATACTAAATC
* **
27923284 TATTAAATTAATAGAATATTTATCTATAAGATAAATATTAAATTTAATTTAATACTAAA
1 TATTAAATTAATAGAATACTTA-CTATAAGATAAATATTAAATGAAATTTAATACTAAA
27923343 GATTCACTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
58 20 0.41
60 1 0.02
61 28 0.57
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (60 bp):
TATTAAATTAATAGAATACTTACTATAAGATAAATATTAAATGAAATTTAATACTAAATC
Found at i:27932587 original size:19 final size:19
Alignment explanation
Indices: 27932552--27932597 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
27932542 AAAGAAAGAC
*
27932552 AGAAAAATAAATC-AAAAA
1 AGAAAAAGAAATCAAAAAA
*
27932570 AGAAAAAGAGAATGAAAAAA
1 AGAAAAAGA-AATCAAAAAA
27932590 AGAAAAAG
1 AGAAAAAG
27932598 GAGATTGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 3 0.12
20 13 0.54
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (19 bp):
AGAAAAAGAAATCAAAAAA
Found at i:27938099 original size:22 final size:21
Alignment explanation
Indices: 27938068--27938109 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
27938058 TATTATGCAT
27938068 TATTAAACAGAAAACACTAAAG
1 TATTAAACAGAAAACA-TAAAG
*
27938090 TATTATACAGAAAACATAAA
1 TATTAAACAGAAAACATAAA
27938110 TGTGCTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.60, C:0.12, G:0.07, T:0.21
Consensus pattern (21 bp):
TATTAAACAGAAAACATAAAG
Found at i:27938856 original size:20 final size:20
Alignment explanation
Indices: 27938831--27938873 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
27938821 AATTTAACTT
*
27938831 CTTCTTTTCTTACTCT-CTTA
1 CTTCTTTACTTACT-TGCTTA
27938851 CTTCTTTACTTACTTGCTTA
1 CTTCTTTACTTACTTGCTTA
27938871 CTT
1 CTT
27938874 AAATAACTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.12, C:0.28, G:0.02, T:0.58
Consensus pattern (20 bp):
CTTCTTTACTTACTTGCTTA
Found at i:27939194 original size:50 final size:50
Alignment explanation
Indices: 27939128--27939359 Score: 338
Period size: 50 Copynumber: 4.6 Consensus size: 50
27939118 TCTATACTGT
** * * ** *
27939128 CAATGCCATAACCCAGATATTGTCTTACATGGGAGTTCTCATATCGGTGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGC
* **
27939178 CCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGC
* *
27939228 CAACGCCATGTCCCATACATGGTCTTACATGGGACCTCTCATCTCGGTGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGC
*
27939278 CAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGC
*
27939328 CAACGCCATGTCCCAGACATGGTCTTACATGG
1 CAATGCCATGTCCCAGACATGGTCTTACATGG
27939360 CTCACATATT
Statistics
Matches: 162, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 162 1.00
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGC
Found at i:27939830 original size:18 final size:18
Alignment explanation
Indices: 27939807--27939843 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
27939797 TTTCTATTCA
*
27939807 TACCTTTTTAAATTTTGT
1 TACCTTTCTAAATTTTGT
*
27939825 TACCTTTCTATATTTTGT
1 TACCTTTCTAAATTTTGT
27939843 T
1 T
27939844 TCATCATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.62
Consensus pattern (18 bp):
TACCTTTCTAAATTTTGT
Found at i:27947084 original size:45 final size:45
Alignment explanation
Indices: 27947020--27947207 Score: 331
Period size: 45 Copynumber: 4.2 Consensus size: 45
27947010 CATGAAATTA
27947020 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
27947065 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
27947110 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * *
27947155 AGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
27947200 AGGAAGCA
1 AGGAAGCA
27947208 CCATGGCCGA
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 137 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:27954009 original size:27 final size:28
Alignment explanation
Indices: 27953872--27954049 Score: 261
Period size: 28 Copynumber: 6.4 Consensus size: 28
27953862 GAGATTGGCG
* * * *
27953872 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
27953901 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
* *
27953929 CTAAGTGTGCAAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
27953957 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
27953985 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
27954012 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
27954039 CTGAGTGTGCG
1 CTAAGTGTGCG
27954050 GACTTAATAT
Statistics
Matches: 140, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
27 51 0.36
28 74 0.53
29 15 0.11
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:27957108 original size:40 final size:40
Alignment explanation
Indices: 27957010--27957392 Score: 513
Period size: 40 Copynumber: 9.6 Consensus size: 40
27957000 TCCTCGTTCA
* * * ** *
27957010 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* *
27957049 AATGCCTTCGGGACATAACCCGGATTTAACAATTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
27957089 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
27957129 AATGCCTTCGGGACTTAATCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* *
27957169 AATGCCTTCGGGACTTAACCCGGATTTAGCAATTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
27957209 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
27957249 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
27957289 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
27957329 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
27957369 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
27957393 CAGCATTCAA
Statistics
Matches: 311, Mismatches: 28, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
39 36 0.12
40 267 0.86
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:27960138 original size:45 final size:45
Alignment explanation
Indices: 27960074--27960258 Score: 325
Period size: 45 Copynumber: 4.1 Consensus size: 45
27960064 CATGAAATTA
27960074 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
27960119 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
27960164 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * *
27960209 AGGAAGCATTTGGCCAACATCATGCATAATTTATGGAATAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
27960254 AGGAA
1 AGGAA
27960259 TCACCATGGC
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 134 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:27963469 original size:21 final size:22
Alignment explanation
Indices: 27963445--27963490 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
27963435 TTAAAAACAA
27963445 ATTAAACACTT-AACTAAATTT
1 ATTAAACACTTAAACTAAATTT
* *
27963466 ATTAAATACTTAAACTAATTTT
1 ATTAAACACTTAAACTAAATTT
27963488 ATT
1 ATT
27963491 CCAGCAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTAAACACTTAAACTAAATTT
Found at i:27967457 original size:18 final size:18
Alignment explanation
Indices: 27967436--27967470 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
27967426 TTTTTCTTTT
27967436 TCAATTT-TTTTCTCAATC
1 TCAATTTATTTT-TCAATC
27967454 TCAATTTATTTTTCAAT
1 TCAATTTATTTTTCAAT
27967471 TTATTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTATTTTTCAATC
Found at i:27967469 original size:12 final size:12
Alignment explanation
Indices: 27967454--27967479 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27967444 TTTCTCAATC
27967454 TCAATTTATTTT
1 TCAATTTATTTT
27967466 TCAATTTATTTT
1 TCAATTTATTTT
27967478 TC
1 TC
27967480 TTCATTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (12 bp):
TCAATTTATTTT
Found at i:27967527 original size:18 final size:18
Alignment explanation
Indices: 27967506--27967551 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
27967496 CACTTTTTCG
27967506 ATTTCTTTTTCTTTTGCA
1 ATTTCTTTTTCTTTTGCA
* *
27967524 ATTT-TTTTTCTTTTTCG
1 ATTTCTTTTTCTTTTGCA
*
27967541 TTTTCTTTTTC
1 ATTTCTTTTTC
27967552 AATTTCATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.07, C:0.15, G:0.04, T:0.74
Consensus pattern (18 bp):
ATTTCTTTTTCTTTTGCA
Found at i:27967544 original size:12 final size:11
Alignment explanation
Indices: 27967484--27967551 Score: 50
Period size: 12 Copynumber: 6.0 Consensus size: 11
27967474 TTTTTCTTCA
27967484 TTTTCTTTTTC
1 TTTTCTTTTTC
**
27967495 -TCACTTTTTC
1 TTTTCTTTTTC
*
27967505 GATTTCTTTTTC
1 -TTTTCTTTTTC
*
27967517 TTTTGCAATTTT-
1 TTTT-C-TTTTTC
27967529 TTTTCTTTTTC
1 TTTTCTTTTTC
27967540 GTTTTCTTTTTC
1 -TTTTCTTTTTC
27967552 AATTTCATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
10 12 0.27
11 4 0.09
12 24 0.55
13 4 0.09
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:27968375 original size:14 final size:14
Alignment explanation
Indices: 27968344--27968377 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
27968334 TTCAACTCTT
*
27968344 TTTTTTGCTCAATT
1 TTTTTTGCTCAATA
*
27968358 TTTTTTGCTCACTA
1 TTTTTTGCTCAATA
27968372 TTTTTT
1 TTTTTT
27968378 CGAATTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.15, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTTTTGCTCAATA
Found at i:27968377 original size:16 final size:14
Alignment explanation
Indices: 27968342--27968368 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27968332 CTTTCAACTC
27968342 TTTTTTTTGCTCAA
1 TTTTTTTTGCTCAA
27968356 TTTTTTTTGCTCA
1 TTTTTTTTGCTCA
27968369 CTATTTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.15, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTTTTTGCTCAA
Found at i:27969609 original size:20 final size:20
Alignment explanation
Indices: 27969584--27969628 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
27969574 TAAATACACA
27969584 TAATTAAAACT-AGACACAAT
1 TAATT-AAACTAAGACACAAT
**
27969604 TAATTAAGTTAAGACACAAT
1 TAATTAAACTAAGACACAAT
27969624 TAATT
1 TAATT
27969629 CGGTTGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (20 bp):
TAATTAAACTAAGACACAAT
Found at i:27971882 original size:15 final size:15
Alignment explanation
Indices: 27971862--27971892 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27971852 GGCTTCCGCC
27971862 AAATGTTTTATCTAG
1 AAATGTTTTATCTAG
*
27971877 AAATGTTTTATTTAG
1 AAATGTTTTATCTAG
27971892 A
1 A
27971893 GTAACATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.48
Consensus pattern (15 bp):
AAATGTTTTATCTAG
Found at i:27989418 original size:25 final size:24
Alignment explanation
Indices: 27989342--27989418 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
27989332 CAGCTTGTAT
* *
27989342 GAGCTTACTAATTTTAGCTCATGA
1 GAGCTTACCAATTTTAGCTCGTGA
*
27989366 GAGCTTACCAAATTTAGCTCGT-A
1 GAGCTTACCAATTTTAGCTCGTGA
*
27989389 CGAGCTTACCGATTTATAGCTCGTGA
1 -GAGCTTACCAATTT-TAGCTCGTGA
27989415 GAGC
1 GAGC
27989419 ATATTGATTC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
23 1 0.02
24 31 0.69
25 12 0.27
26 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (24 bp):
GAGCTTACCAATTTTAGCTCGTGA
Found at i:27989427 original size:25 final size:25
Alignment explanation
Indices: 27989380--27989446 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
27989370 TTACCAAATT
* * ** *
27989380 TAGCTCGTACGAGCTTACCGATTTA
1 TAGCTCGTAAGAGCATATTGATTCA
*
27989405 TAGCTCGTGAGAGCATATTGATTCA
1 TAGCTCGTAAGAGCATATTGATTCA
*
27989430 TAGCTTGTAAGAGCATA
1 TAGCTCGTAAGAGCATA
27989447 CATGTACAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (25 bp):
TAGCTCGTAAGAGCATATTGATTCA
Found at i:27998475 original size:8 final size:8
Alignment explanation
Indices: 27998464--27998488 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
27998454 TATAACATTA
27998464 TATTATAT
1 TATTATAT
27998472 TATTATAT
1 TATTATAT
27998480 TATTATAT
1 TATTATAT
27998488 T
1 T
27998489 TGAACTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATTATAT
Found at i:28000042 original size:20 final size:20
Alignment explanation
Indices: 28000017--28000079 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
28000007 ATAATCAGTA
28000017 CCCTTGATTGCACTTACGTG
1 CCCTTGATTGCACTTACGTG
* ** *
28000037 CCCTTGTTTGTGCTT-CGATA
1 CCCTTGATTGCACTTACG-TG
* *
28000057 CCCCTGATTGCACTTATGTG
1 CCCTTGATTGCACTTACGTG
28000077 CCC
1 CCC
28000080 CTGTTTATAC
Statistics
Matches: 31, Mismatches: 10, Indels: 4
0.69 0.22 0.09
Matches are distributed among these distances:
19 2 0.06
20 28 0.90
21 1 0.03
ACGTcount: A:0.13, C:0.32, G:0.19, T:0.37
Consensus pattern (20 bp):
CCCTTGATTGCACTTACGTG
Found at i:28000093 original size:40 final size:40
Alignment explanation
Indices: 28000015--28000093 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
28000005 TCATAATCAG
* * * *
28000015 TACCCTTGATTGCACTTACGTGCCCTTGTTTGTGCTTCGA
1 TACCCCTGATTGCACTTACGTGCCCCTGTTTATACTTCGA
*
28000055 TACCCCTGATTGCACTTATGTGCCCCTGTTTATACTTCG
1 TACCCCTGATTGCACTTACGTGCCCCTGTTTATACTTCG
28000094 GTAATTTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.14, C:0.29, G:0.18, T:0.39
Consensus pattern (40 bp):
TACCCCTGATTGCACTTACGTGCCCCTGTTTATACTTCGA
Found at i:28000642 original size:12 final size:12
Alignment explanation
Indices: 28000620--28000653 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
28000610 GCAAGTCAGG
28000620 TAGCTACACGGCC
1 TAGC-ACACGGCC
28000633 TAGCACACGGCC
1 TAGCACACGGCC
28000645 TAGCACACG
1 TAGCACACG
28000654 AGCGTGTGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.26, C:0.38, G:0.24, T:0.12
Consensus pattern (12 bp):
TAGCACACGGCC
Found at i:28001644 original size:23 final size:21
Alignment explanation
Indices: 28001614--28001657 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
28001604 CATGAGAATG
28001614 TCAATGCAAAGCTTTTTCAAAAA
1 TCAATGC-AAG-TTTTTCAAAAA
*
28001637 TCAATGCATGTTTTTCAAAAA
1 TCAATGCAAGTTTTTCAAAAA
28001658 CATTCCTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 2 0.10
23 7 0.35
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (21 bp):
TCAATGCAAGTTTTTCAAAAA
Found at i:28001934 original size:42 final size:42
Alignment explanation
Indices: 28001875--28001967 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
28001865 ATATTTTTAG
* *
28001875 TGGCATGCTTAACATGTGAATCAAATTTATAATCAACATAGT
1 TGGCATGCTAAACATGTGAATCAAATTTATAATCAACACAGT
* *
28001917 TGGCATGCTAAACATGTGAATCAAATTTATAATTAATACAGT
1 TGGCATGCTAAACATGTGAATCAAATTTATAATCAACACAGT
28001959 TGGCATGCT
1 TGGCATGCT
28001968 TAATATGGGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (42 bp):
TGGCATGCTAAACATGTGAATCAAATTTATAATCAACACAGT
Found at i:28003823 original size:52 final size:52
Alignment explanation
Indices: 28003740--28003840 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
28003730 TAAGGAAACG
* *
28003740 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCAGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCAGTTGAAGCTCAAACAA
*
28003792 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCAGTTGAAGCTCAAA
28003841 TATGTGCATG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCAGTTGAAGCTCAAACAA
Found at i:28013292 original size:79 final size:79
Alignment explanation
Indices: 28013169--28013346 Score: 243
Period size: 79 Copynumber: 2.3 Consensus size: 79
28013159 GGACTAAGAT
* *
28013169 CCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTA
1 CCGAAGGCATTTGTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACT-
*
28013234 ATTCCGGGCTAAG-C
65 ATACCGGGCTAAGTC
* ** *
28013248 CCGAAGGCATTTGTACGAGTTACTAAATTCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACT
1 CCGAAGGCATTTGTACGAGTTACTAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACT
*
28013312 ATACCGGGCTATGTC
65 ATACCGGGCTAAGTC
*
28013327 CCGAAGGCATTTGAACGAGT
1 CCGAAGGCATTTGTACGAGT
28013347 AGCTATATCC
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
78 12 0.14
79 76 0.86
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTA
TACCGGGCTAAGTC
Found at i:28013307 original size:40 final size:40
Alignment explanation
Indices: 28013116--28013339 Score: 244
Period size: 40 Copynumber: 5.7 Consensus size: 40
28013106 TTGAATGATG
** * *
28013116 TCCGGGCTAAGTCCCGAAGGC-TTTGTGATA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
*
28013156 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
* *
28013196 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
* *
28013236 TCCGGGCTAAG-CCCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * * *
28013275 TTCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
*
28013315 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28013340 AACGAGTAGC
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
39 55 0.34
40 97 0.60
41 9 0.06
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:28013370 original size:39 final size:39
Alignment explanation
Indices: 28013123--28013372 Score: 181
Period size: 40 Copynumber: 6.3 Consensus size: 39
28013113 ATGTCCGGGC
** * * *
28013123 TAAGTCCCGAAGGC-TTTGTGATAAGTGACCATATCCGGAC
1 TAAGTCCCGAAGGCATTTGT-ACGAGTTACTATATCCGG-T
* * * *
28013163 TAAGAT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGAC
1 TAAG-TCCCGAAGGCATTTGTACGAGTTACTATATCCGG-T
* * *
28013203 TAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGC
1 TAAG-TCCCGAAGGCATTTGTACGAGTTACTATA-TCC-GGT
* *
28013243 TAAG-CCCGAAGGCATTTGTACGAGTTACTAAATTCGGGT
1 TAAGTCCCGAAGGCATTTGTACGAGTTACTATA-TCCGGT
* *
28013282 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-CCGGGC
1 TAAGTCCCGAAGGCATTTGTACGAGTTACTATATCC-GGT
* *
28013321 TATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCCGGT
1 TAAGTCCCGAAGGCATTTGTACGAGTTA-CTATATCCGGT
* *
28013360 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
28013373 TACGTGATTT
Statistics
Matches: 178, Mismatches: 22, Indels: 21
0.81 0.10 0.10
Matches are distributed among these distances:
38 3 0.02
39 71 0.40
40 96 0.54
41 8 0.04
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (39 bp):
TAAGTCCCGAAGGCATTTGTACGAGTTACTATATCCGGT
Found at i:28020873 original size:40 final size:40
Alignment explanation
Indices: 28020685--28020908 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
28020675 TTGAATGATG
* * * *
28020685 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
28020725 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
28020765 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
28020805 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
28020844 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
28020884 -CCGGGCTATGTCCCAAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28020909 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 57 0.35
40 100 0.61
41 8 0.05
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28020915 original size:79 final size:78
Alignment explanation
Indices: 28020685--28020927 Score: 269
Period size: 79 Copynumber: 3.1 Consensus size: 78
28020675 TTGAATGATG
* * * *
28020685 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATA-CCGGGCTAAG-TCCCGAAGGCAT
28020748 TTGTGCGAGATACTAAA
63 TTGTGCGAG-TACTAAA
* * *
28020765 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCGAAGGCATT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACT-ATACCGGGCTAAGTCCCGAAGGCATT
28020828 TGTGCGAGTTACTAAA
64 TGTGCGAG-TACTAAA
* * *
28020844 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATACCGGGCTATGTCCCAAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATACCGGGCTAAGTCCCGAAGGCATTTG
** *
28020909 AACGAGTAGCTATA
66 TGCGAGTA-CTAAA
28020923 TCCGG
1 TCCGG
28020928 TTAAATTCCG
Statistics
Matches: 139, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
78 14 0.10
79 84 0.60
80 31 0.22
81 10 0.07
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (78 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTACTAAA
Found at i:28025376 original size:227 final size:227
Alignment explanation
Indices: 28024981--28025432 Score: 697
Period size: 227 Copynumber: 2.0 Consensus size: 227
28024971 TTAGTGTCTA
* * *
28024981 AAGTGTATCAATGTGTGTATTGAGGAAATGAACAAGTCTATTGTGAAAGAGTCTATTATGAGTAA
1 AAGTGTATCAATGTGTGTATGGAAGAAATGAACAAGTCTATTGTGAAAGAGTCTATCATGAGTAA
* *
28025046 GTCATATGTGAATAAGTCTGTCAAGTATAAGTCTGCATGAAGTGTTTATGTCGTCTAAAAGGGTC
66 GTCATATGTGAATAAGTCTGTCAAGTATAAGTCTGCATGAACTATTTATGTCGTCTAAAAGGGTC
* * * *
28025111 CGTCAAGAATAAAAACATGAATCTCTTAAAGGAAAAGTCCATGGCATTCTGAAGACCATATAGTC
131 CGTCAAGAACAAAAACATGAATCTCTAAAAGGAAAAGTCCATGGCACTCTAAAGACCATATAGTC
*
28025176 TAAGACCATGGCTGGGCTATGGCATCATATGG
196 TAAGACCATGGCTAGGCTATGGCATCATATGG
* *
28025208 AAGTGTATCAATGTGTGTATGGAAGATATGAACAAGTCTATTGTGAAAGAGTCTATCATGTGTAA
1 AAGTGTATCAATGTGTGTATGGAAGAAATGAACAAGTCTATTGTGAAAGAGTCTATCATGAGTAA
* * * * * * * * *
28025273 GTCATATGTGGATGAGTTTGTTAAGTATGAGTCTGCATGAACTATTTGTGTTGTCTAAAGGGGTT
66 GTCATATGTGAATAAGTCTGTCAAGTATAAGTCTGCATGAACTATTTATGTCGTCTAAAAGGGTC
* *
28025338 CTTCGAGAACAAAAACATGAATCTCTAAAAGGAAAAGTCCATGGCACTCTAAAGACCATATAGTC
131 CGTCAAGAACAAAAACATGAATCTCTAAAAGGAAAAGTCCATGGCACTCTAAAGACCATATAGTC
28025403 TAAGACCATGGCTAGGCTATGGCATCATAT
196 TAAGACCATGGCTAGGCTATGGCATCATAT
28025433 TTTAAAAATT
Statistics
Matches: 202, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
227 202 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (227 bp):
AAGTGTATCAATGTGTGTATGGAAGAAATGAACAAGTCTATTGTGAAAGAGTCTATCATGAGTAA
GTCATATGTGAATAAGTCTGTCAAGTATAAGTCTGCATGAACTATTTATGTCGTCTAAAAGGGTC
CGTCAAGAACAAAAACATGAATCTCTAAAAGGAAAAGTCCATGGCACTCTAAAGACCATATAGTC
TAAGACCATGGCTAGGCTATGGCATCATATGG
Found at i:28025573 original size:29 final size:29
Alignment explanation
Indices: 28025532--28025695 Score: 154
Period size: 29 Copynumber: 5.7 Consensus size: 29
28025522 AACACCAATT
* *
28025532 TCTG-TAAAAGGAATCTTTTGTGGCTATC
1 TCTGTTAAAAGGAAGCCTTTGTGGCTATC
* *
28025560 TCTGTTAACAGGAAGCCTTTGTGGCTATT
1 TCTGTTAAAAGGAAGCCTTTGTGGCTATC
* ** * *
28025589 TCTATTAAAAGGATTCCCTTGTGGCAATC
1 TCTGTTAAAAGGAAGCCTTTGTGGCTATC
28025618 TCTGTTAAAAGGAAGCCTTTGTGG-TGATC
1 TCTGTTAAAAGGAAGCCTTTGTGGCT-ATC
* * * *
28025647 TTTGTTAAAGGGAAGCCTTTATAG-TGATC
1 TCTGTTAAAAGGAAGCCTTTGTGGCT-ATC
* *
28025676 TCTGTTAAAATGATGCCTTT
1 TCTGTTAAAAGGAAGCCTTT
28025696 ATGGTGAGAC
Statistics
Matches: 110, Mismatches: 24, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
28 4 0.04
29 106 0.96
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (29 bp):
TCTGTTAAAAGGAAGCCTTTGTGGCTATC
Found at i:28025684 original size:87 final size:86
Alignment explanation
Indices: 28025527--28025685 Score: 189
Period size: 87 Copynumber: 1.8 Consensus size: 86
28025517 TCAAAAACAC
* * * * * *
28025527 CAATTTCTGTAAAAGGAATCTTTTGTGGCTATCTCTGTTAACAGGAAGCCTTTGTGGCTATTTCT
1 CAATCTCTGTAAAAGGAAGCCTTTGTGGCTATCTCTGTTAACAGGAAGCCTTTATAGCTATCTCT
28025592 ATTAAAAGGATTCCCTTGTGG
66 ATTAAAAGGATTCCCTTGTGG
*
28025613 CAATCTCTGTTAAAAGGAAGCCTTTGTGG-TGATCTTTGTTAA-AGGGAAGCCTTTATAG-TGAT
1 CAATCTCTG-TAAAAGGAAGCCTTTGTGGCT-ATCTCTGTTAACA-GGAAGCCTTTATAGCT-AT
*
28025675 CTCTGTTAAAA
62 CTCTATTAAAA
28025686 TGATGCCTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
86 11 0.18
87 50 0.82
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.37
Consensus pattern (86 bp):
CAATCTCTGTAAAAGGAAGCCTTTGTGGCTATCTCTGTTAACAGGAAGCCTTTATAGCTATCTCT
ATTAAAAGGATTCCCTTGTGG
Found at i:28026895 original size:21 final size:23
Alignment explanation
Indices: 28026850--28026896 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
28026840 TCACCTGCAA
* *
28026850 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
28026873 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
28026894 TAA
1 TAA
28026897 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:28040962 original size:27 final size:27
Alignment explanation
Indices: 28040906--28040978 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
28040896 TAGATGTTTG
* * * *
28040906 CCACAAAGGC-ATTCCTTCATGTTATG
1 CCACAAAGGCTTTTCTTTCATATTATA
28040932 CCACAAAGGCTTTTCTTTCATATTATA
1 CCACAAAGGCTTTTCTTTCATATTATA
28040959 CCACAAAGGCTTTTTCTTTC
1 CCACAAAGGC-TTTTCTTTC
28040979 CTAACGTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 10 0.24
27 22 0.54
28 9 0.22
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (27 bp):
CCACAAAGGCTTTTCTTTCATATTATA
Found at i:28041618 original size:23 final size:23
Alignment explanation
Indices: 28041588--28041636 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
28041578 AAAAGAACAA
28041588 AGAGAGTTGAATAACTCACAAAT
1 AGAGAGTTGAATAACTCACAAAT
28041611 AGAGAGTTGAATAACTCACAAAT
1 AGAGAGTTGAATAACTCACAAAT
28041634 AGA
1 AGA
28041637 TTAAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.20
Consensus pattern (23 bp):
AGAGAGTTGAATAACTCACAAAT
Found at i:28044033 original size:37 final size:39
Alignment explanation
Indices: 28043953--28044060 Score: 148
Period size: 37 Copynumber: 2.8 Consensus size: 39
28043943 AAGTATTGAA
* * *
28043953 GATGTTCAAACTATGACATAATTAAAGACCCATATTAAT
1 GATGTTCAAATTATGACATAATTAAATACTCATATTAAT
*
28043992 GATGTTCAGATTATGACAT-ATT-AATACTCATATTAAT
1 GATGTTCAAATTATGACATAATTAAATACTCATATTAAT
* *
28044029 GATGTTAAAATTATGGCATAATTAAATACTCA
1 GATGTTCAAATTATGACATAATTAAATACTCA
28044061 ACTATAATAA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
37 29 0.48
38 6 0.10
39 25 0.42
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (39 bp):
GATGTTCAAATTATGACATAATTAAATACTCATATTAAT
Found at i:28063105 original size:33 final size:33
Alignment explanation
Indices: 28063068--28063133 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
28063058 AATATCAAAA
*
28063068 ACTTGAAAACAGGGGTCACATTTAATGTTAATG
1 ACTTGAAAACAGGGGTCACATTTAATATTAATG
28063101 ACTTGAAAACAGGGGTCACATTTAATATTAATG
1 ACTTGAAAACAGGGGTCACATTTAATATTAATG
28063134 GGCAACACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (33 bp):
ACTTGAAAACAGGGGTCACATTTAATATTAATG
Found at i:28065312 original size:43 final size:41
Alignment explanation
Indices: 28065255--28065455 Score: 206
Period size: 43 Copynumber: 4.8 Consensus size: 41
28065245 AAATTCAGTG
*
28065255 ATACGGGGAATCAGCACATAGCAACCCCTTTCACAGT-AAAA
1 ATACGGGGAATCAGCACTTAGCAACCCCTTT-ACAGTCAAAA
* * * **
28065296 AGTACGGTGGATTCAGCACTTAGCAACCACCTTTATATTCAGTA
1 A-TACGG-GGAATCAGCACTTAGCAACC-CCTTTACAGTCAAAA
* * * * *
28065340 ATACGGGGAATCAGCACATAGCAGCCCCTTTCGCAATCAAAG
1 ATACGGGGAATCAGCACTTAGCAACCCCTTT-ACAGTCAAAA
* *
28065382 ATACGGTGGAATCAGCACTTAGCAACCACCTTTAAAGTCAATA
1 ATACGG-GGAATCAGCACTTAGCAACC-CCTTTACAGTCAAAA
*
28065425 ATTCGGGGAATCAGCACTTAGCAACCCCTTT
1 ATACGGGGAATCAGCACTTAGCAACCCCTTT
28065456 TTATCCAATG
Statistics
Matches: 130, Mismatches: 23, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
41 11 0.08
42 52 0.40
43 54 0.42
44 13 0.10
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (41 bp):
ATACGGGGAATCAGCACTTAGCAACCCCTTTACAGTCAAAA
Found at i:28065359 original size:85 final size:85
Alignment explanation
Indices: 28065216--28065455 Score: 340
Period size: 85 Copynumber: 2.8 Consensus size: 85
28065206 ATCCGTTACT
* * *
28065216 CGGTGGATTCAACACTTAACAACCACC-TTAAATTCAGTGATACGGGGAATCAGCACATAGCAAC
1 CGGTGGATTCAGCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAAC
*
28065280 CCCTTTCACAGTAAAA-AGTA
66 CCCTTTCACAATAAAAGA-TA
* *
28065300 CGGTGGATTCAGCACTTAGCAACCACCTTTATATTCAGTAATACGGGGAATCAGCACATAGCAGC
1 CGGTGGATTCAGCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAAC
* *
28065365 CCCTTTCGCAATCAAAGATA
66 CCCTTTCACAATAAAAGATA
* * * * *
28065385 CGGTGGAATCAGCACTTAGCAACCACCTTTAAAGTCAATAATTCGGGGAATCAGCACTTAGCAAC
1 CGGTGGATTCAGCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAAC
28065450 CCCTTT
66 CCCTTT
28065456 TTATCCAATG
Statistics
Matches: 139, Mismatches: 15, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
84 25 0.18
85 113 0.81
86 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (85 bp):
CGGTGGATTCAGCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAAC
CCCTTTCACAATAAAAGATA
Found at i:28065386 original size:42 final size:40
Alignment explanation
Indices: 28065255--28065455 Score: 197
Period size: 42 Copynumber: 4.8 Consensus size: 40
28065245 AAATTCAGTG
* * *
28065255 ATACGGGGAATCAGCACATAGCAACCCCTTTCACAGTAAAA
1 ATACGGGGAATCAGCACTTAGCAACCCCTTT-ACAATCAAA
* * * *
28065296 AGTACGGTGGATTCAGCACTTAGCAACCACCTTTATATTCAGTA
1 A-TACGG-GGAATCAGCACTTAGCAACC-CCTTTACAATCA-AA
* * *
28065340 ATACGGGGAATCAGCACATAGCAGCCCCTTTCGCAATCAAA
1 ATACGGGGAATCAGCACTTAGCAACCCCTTT-ACAATCAAA
28065381 GATACGGTGGAATCAGCACTTAGCAACCACCTTTA-AAGTCAATA
1 -ATACGG-GGAATCAGCACTTAGCAACC-CCTTTACAA-TCAA-A
*
28065425 ATTCGGGGAATCAGCACTTAGCAACCCCTTT
1 ATACGGGGAATCAGCACTTAGCAACCCCTTT
28065456 TTATCCAATG
Statistics
Matches: 133, Mismatches: 17, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
41 12 0.09
42 54 0.41
43 54 0.41
44 13 0.10
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (40 bp):
ATACGGGGAATCAGCACTTAGCAACCCCTTTACAATCAAA
Found at i:28071247 original size:75 final size:77
Alignment explanation
Indices: 28071068--28071263 Score: 272
Period size: 75 Copynumber: 2.6 Consensus size: 77
28071058 TGGATTCAGT
* *
28071068 ACTTAGCAAGCACCAATGATTCGGGGAATCACCACTTAGCAACCCCTTTTCACATTCAAAAATAC
1 ACTTAGCAACCACCAATGATTCGGGGAATCAACACTTAGCAACCCCTTTTCACATTCAAAAATAC
*
28071133 GATGGAATCAGC
66 GATGGAATAAGC
* * ** * *
28071145 ACTTAGCAACCACCAATGAATCAGGGAATCAGTACTTAGCAACCCC-TTTCACATT-TAAGATAC
1 ACTTAGCAACCACCAATGATTCGGGGAATCAACACTTAGCAACCCCTTTTCACATTCAAAAATAC
*
28071208 GGT-GAGATAAGC
66 GATGGA-ATAAGC
28071220 ACTTAGCAACCACCAATGATTCGGGGAATCAACACTTAGCAACC
1 ACTTAGCAACCACCAATGATTCGGGGAATCAACACTTAGCAACC
28071264 GCTTGGGGGA
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
74 2 0.02
75 53 0.50
76 9 0.09
77 41 0.39
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (77 bp):
ACTTAGCAACCACCAATGATTCGGGGAATCAACACTTAGCAACCCCTTTTCACATTCAAAAATAC
GATGGAATAAGC
Found at i:28071261 original size:33 final size:33
Alignment explanation
Indices: 28071219--28071365 Score: 99
Period size: 33 Copynumber: 4.4 Consensus size: 33
28071209 GTGAGATAAG
28071219 CACTTAGCAACCACCAATGATTCGGGGAATCAA
1 CACTTAGCAACCACCAATGATTCGGGGAATCAA
* *
28071252 CACTTAGC-A--ACC---GCTTGGGGGAATCAA
1 CACTTAGCAACCACCAATGATTCGGGGAATCAA
* * * * *
28071279 CACTTAGTAACCCCCTTCACATTTAAAATACGGTGGAATCAG
1 CACTTAGCAA-CCAC--CA-A--T--GATTCGG-GGAATCAA
*
28071321 CACTTAGCAACCACCAATGATTCGGGGAATCAG
1 CACTTAGCAACCACCAATGATTCGGGGAATCAA
28071354 CACTTAGCAACC
1 CACTTAGCAACC
28071366 CCCTTTATAT
Statistics
Matches: 86, Mismatches: 13, Indels: 30
0.67 0.10 0.23
Matches are distributed among these distances:
27 20 0.23
28 1 0.01
30 3 0.03
31 1 0.01
32 1 0.01
33 29 0.34
34 5 0.06
36 1 0.01
38 1 0.01
39 2 0.02
41 6 0.07
42 16 0.19
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.20
Consensus pattern (33 bp):
CACTTAGCAACCACCAATGATTCGGGGAATCAA
Found at i:28071323 original size:102 final size:102
Alignment explanation
Indices: 28071168--28071365 Score: 317
Period size: 102 Copynumber: 1.9 Consensus size: 102
28071158 CAATGAATCA
** * *
28071168 GGGAATCAGTACTTAGCAACCCCTTTCACATTTAAGATACGGTGAGATAAGCACTTAGCAACCAC
1 GGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGAGATAAGCACTTAGCAACCAC
28071233 CAATGATTCGGGGAATCAACACTTAGCAACCGCTTGG
66 CAATGATTCGGGGAATCAACACTTAGCAACCGCTTGG
* *
28071270 GGGAATCAACACTTAGTAACCCCCTTCACATTTAAAATACGGTG-GAATCAGCACTTAGCAACCA
1 GGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGAG-ATAAGCACTTAGCAACCA
*
28071334 CCAATGATTCGGGGAATCAGCACTTAGCAACC
65 CCAATGATTCGGGGAATCAACACTTAGCAACC
28071366 CCCTTTATAT
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 1 0.01
102 87 0.99
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (102 bp):
GGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGAGATAAGCACTTAGCAACCAC
CAATGATTCGGGGAATCAACACTTAGCAACCGCTTGG
Found at i:28074690 original size:12 final size:12
Alignment explanation
Indices: 28074673--28074714 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
28074663 CTCTAATGTT
28074673 ACACGGGCAAGG
1 ACACGGGCAAGG
*
28074685 ACACGGGTAAGG
1 ACACGGGCAAGG
**
28074697 ACACGGGGTAGG
1 ACACGGGCAAGG
28074709 ACACGG
1 ACACGG
28074715 TCATGTGTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.31, C:0.21, G:0.43, T:0.05
Consensus pattern (12 bp):
ACACGGGCAAGG
Found at i:28085289 original size:20 final size:20
Alignment explanation
Indices: 28085266--28085332 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
28085256 AAAATACATT
28085266 CAGGGGTACTGAAGTACAAA
1 CAGGGGTACTGAAGTACAAA
* * * *
28085286 CAGGGGCAC-GTATGTGCAATT
1 CAGGGGTACTG-AAGTACAA-A
* *
28085307 TAGGGGTGCTGAAGTACAAA
1 CAGGGGTACTGAAGTACAAA
28085327 CAGGGG
1 CAGGGG
28085333 CACGCATGTG
Statistics
Matches: 33, Mismatches: 11, Indels: 6
0.66 0.22 0.12
Matches are distributed among these distances:
19 1 0.03
20 19 0.58
21 12 0.36
22 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.36, T:0.18
Consensus pattern (20 bp):
CAGGGGTACTGAAGTACAAA
Found at i:28085319 original size:41 final size:41
Alignment explanation
Indices: 28085267--28085471 Score: 216
Period size: 41 Copynumber: 5.0 Consensus size: 41
28085257 AAATACATTC
*
28085267 AGGGGTACTGAAGTACAAACAGGGGCACGTATGTGCAATTT
1 AGGGGTACTGAAGTACAAACAGGGGCACGCATGTGCAATTT
* *
28085308 AGGGGTGCTGAAGTACAAACAGGGGCACGCATGTGTAATTT
1 AGGGGTACTGAAGTACAAACAGGGGCACGCATGTGCAATTT
* ** *
28085349 AGGGGGTAAC-GAAGTACAAACAGGTGCACATATGTGCAATTC
1 A-GGGGT-ACTGAAGTACAAACAGGGGCACGCATGTGCAATTT
* * ** * * *
28085391 AAGGGTACCGAAGTACAAACAAAGGAACACATGTGTAATTT
1 AGGGGTACTGAAGTACAAACAGGGGCACGCATGTGCAATTT
* * *
28085432 AGGGGTA-TCGAAGTAGAAACAGGGGCGCGAATGTGCAATT
1 AGGGGTACT-GAAGTACAAACAGGGGCACGCATGTGCAATT
28085472 CAGCAATAAT
Statistics
Matches: 133, Mismatches: 27, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
40 2 0.02
41 97 0.73
42 33 0.25
43 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.20
Consensus pattern (41 bp):
AGGGGTACTGAAGTACAAACAGGGGCACGCATGTGCAATTT
Found at i:28085372 original size:83 final size:82
Alignment explanation
Indices: 28085267--28085473 Score: 263
Period size: 83 Copynumber: 2.5 Consensus size: 82
28085257 AAATACATTC
* * * * **
28085267 AGGGGT-ACTGAAGTACAAACAGGGGCACGTATGTGCAATTTAGGGGTGCTGAAGTACAAACAGG
1 AGGGGTAAC-GAAGTACAAACAGGGGCACGTATGTGCAATTCAAGGGTACCGAAGTACAAACAAA
* *
28085331 GGCACGCATGTGTAATTT
65 GGAACACATGTGTAATTT
* *
28085349 AGGGGGTAACGAAGTACAAACAGGTGCACATATGTGCAATTCAAGGGTACCGAAGTACAAACAAA
1 A-GGGGTAACGAAGTACAAACAGGGGCACGTATGTGCAATTCAAGGGTACCGAAGTACAAACAAA
28085414 GGAACACATGTGTAATTT
65 GGAACACATGTGTAATTT
* * * *
28085432 AGGGGTATCGAAGTAGAAACAGGGGCGCGAATGTGCAATTCA
1 AGGGGTAACGAAGTACAAACAGGGGCACGTATGTGCAATTCA
28085474 GCAATAATCA
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
82 36 0.34
83 69 0.64
84 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.20
Consensus pattern (82 bp):
AGGGGTAACGAAGTACAAACAGGGGCACGTATGTGCAATTCAAGGGTACCGAAGTACAAACAAAG
GAACACATGTGTAATTT
Done.