Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 124 of 203
Found at i:39366814 original size:20 final size:20
Alignment explanation
Indices: 39366791--39366836 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
39366781 ATGTACGTAT
*
39366791 ATATATTATACTTTCTATAC
1 ATATATTATAATTTCTATAC
* *
39366811 ATATTTTATAATTTCTATAT
1 ATATATTATAATTTCTATAC
39366831 ATATAT
1 ATATAT
39366837 AATCATTATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATATTATAATTTCTATAC
Found at i:39366876 original size:100 final size:101
Alignment explanation
Indices: 39366728--39366939 Score: 336
Period size: 100 Copynumber: 2.1 Consensus size: 101
39366718 TTTTTAAGTT
* * * * *
39366728 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
*
39366793 A-TATTATACTTTCTATACATATTTTATAATTTCTA
66 AGTATTATACTTTCTATACACATTTTATAATTTCTA
39366828 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
*
39366893 ATGTATTATACTTTCTATCCACATTTTATAATTTCTA
66 A-GTATTATACTTTCTATACACATTTTATAATTTCTA
*
39366930 TATATGTATA
1 TATATATATA
39366940 TTTTCTTTAT
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
100 61 0.60
102 41 0.40
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.53
Consensus pattern (101 bp):
TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
AGTATTATACTTTCTATACACATTTTATAATTTCTA
Found at i:39371687 original size:29 final size:29
Alignment explanation
Indices: 39371655--39371724 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
39371645 GAACAAACCA
* *
39371655 AAACAAAATAGAGTAGAACAACACATTTC
1 AAACAAAATAGAGCAGAACAACACAATTC
* *
39371684 AAACAGAACAGAGCAGAACAACACAATTC
1 AAACAAAATAGAGCAGAACAACACAATTC
39371713 AAACAAAATAGA
1 AAACAAAATAGA
39371725 ACCGAATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.59, C:0.19, G:0.11, T:0.11
Consensus pattern (29 bp):
AAACAAAATAGAGCAGAACAACACAATTC
Found at i:39371751 original size:20 final size:20
Alignment explanation
Indices: 39371722--39371764 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
39371712 CAAACAAAAT
*
39371722 AGAACCGAATA-AAGCAGAGC
1 AGAACAGAATAGAA-CAGAGC
39371742 AGAACAGAATAGAACAGAGC
1 AGAACAGAATAGAACAGAGC
39371762 AGA
1 AGA
39371765 GCAATGCTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.53, C:0.16, G:0.26, T:0.05
Consensus pattern (20 bp):
AGAACAGAATAGAACAGAGC
Found at i:39371762 original size:25 final size:25
Alignment explanation
Indices: 39371734--39371784 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
39371724 AACCGAATAA
39371734 AGCAGAGCAGA-ACAGAATAGAACAG
1 AGCAGAGCA-ATACAGAATAGAACAG
* *
39371759 AGCAGAGCAATGCTGAATAGAACAG
1 AGCAGAGCAATACAGAATAGAACAG
39371784 A
1 A
39371785 ACAGGATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.49, C:0.16, G:0.27, T:0.08
Consensus pattern (25 bp):
AGCAGAGCAATACAGAATAGAACAG
Found at i:39383798 original size:19 final size:20
Alignment explanation
Indices: 39383774--39383859 Score: 75
Period size: 20 Copynumber: 4.2 Consensus size: 20
39383764 TACAGAGTAC
* *
39383774 GCCACAAAGGC-AATATAAT
1 GCCACAAAGGCTAACAAAAT
*
39383793 GCCACAATGGCTAACAAAAT
1 GCCACAAAGGCTAACAAAAT
*
39383813 GTCACAAAGGCCTAATCAAAAT
1 GCCACAAAGG-CTAA-CAAAAT
* *
39383835 ACGCCATAAAGACTAACAAAAT
1 --GCCACAAAGGCTAACAAAAT
39383857 GCC
1 GCC
39383860 CCCAAGCACC
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
19 10 0.19
20 17 0.31
21 4 0.07
22 12 0.22
23 4 0.07
24 7 0.13
ACGTcount: A:0.47, C:0.24, G:0.14, T:0.15
Consensus pattern (20 bp):
GCCACAAAGGCTAACAAAAT
Found at i:39394150 original size:18 final size:18
Alignment explanation
Indices: 39394127--39394161 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
39394117 TAGGCTAACT
39394127 AAGTATATTGAAACTCTC
1 AAGTATATTGAAACTCTC
39394145 AAGTATATTGAAACTCT
1 AAGTATATTGAAACTCT
39394162 AATTAATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (18 bp):
AAGTATATTGAAACTCTC
Found at i:39398439 original size:20 final size:20
Alignment explanation
Indices: 39398395--39398439 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
39398385 TTAAATTTTA
*
39398395 ATTAAAATTAGAAAAAAATT
1 ATTAAAAATAGAAAAAAATT
*
39398415 A-TAAAAATAGTAAAAAATT
1 ATTAAAAATAGAAAAAAATT
39398434 ATTAAA
1 ATTAAA
39398440 TTTTATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (20 bp):
ATTAAAAATAGAAAAAAATT
Found at i:39398474 original size:10 final size:10
Alignment explanation
Indices: 39398408--39398499 Score: 59
Period size: 10 Copynumber: 9.4 Consensus size: 10
39398398 AAAATTAGAA
39398408 AAAAAT-TAT
1 AAAAATATAT
39398417 AAAAATAGTA-
1 AAAAATA-TAT
39398427 AAAAAT-TAT
1 AAAAATATAT
* * *
39398436 TAAATTTTAT
1 AAAAATATAT
*
39398446 AAAAAT-CAT
1 AAAAATATAT
39398455 -AAAATATAT
1 AAAAATATAT
* *
39398464 AGAAATGTAT
1 AAAAATATAT
*
39398474 AAAAATATAGA
1 AAAAATATA-T
39398485 AAAGAATATAT
1 AAA-AATATAT
39398496 AAAA
1 AAAA
39398500 TTTTATAAAG
Statistics
Matches: 63, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
8 7 0.11
9 14 0.22
10 28 0.44
11 8 0.13
12 6 0.10
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.29
Consensus pattern (10 bp):
AAAAATATAT
Found at i:39398494 original size:20 final size:18
Alignment explanation
Indices: 39398453--39398488 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39398443 TATAAAAATC
*
39398453 ATAAAATATATAGAAATGT
1 ATAAAA-ATATAGAAAAGT
39398472 ATAAAAATATAGAAAAG
1 ATAAAAATATAGAAAAG
39398489 AATATATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (18 bp):
ATAAAAATATAGAAAAGT
Found at i:39398537 original size:10 final size:10
Alignment explanation
Indices: 39398512--39398570 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
39398502 TTATAAAGTC
*
39398512 GTAAGAAAAT
1 GTAAAAAAAT
39398522 GATAAAAAAAT
1 G-TAAAAAAAT
39398533 GTAAAAAAAT
1 GTAAAAAAAT
* * *
39398543 AT-AAAATAC
1 GTAAAAAAAT
39398552 GTAAAAAAAT
1 GTAAAAAAAT
*
39398562 -TATAAAAAT
1 GTAAAAAAAT
39398571 TATCATACCA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 14 0.36
10 16 0.41
11 9 0.23
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
GTAAAAAAAT
Found at i:39398546 original size:20 final size:20
Alignment explanation
Indices: 39398511--39398569 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
39398501 TTTATAAAGT
*
39398511 CGTAAGAAAATGATAAAAAAA
1 CGTAAAAAAAT-ATAAAAAAA
* *
39398532 TGTAAAAAAATAT-AAAATA
1 CGTAAAAAAATATAAAAAAA
39398551 CGTAAAAAAATTATAAAAA
1 CGTAAAAAAA-TATAAAAA
39398570 TTATCATACC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 14 0.44
20 5 0.16
21 13 0.41
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.20
Consensus pattern (20 bp):
CGTAAAAAAATATAAAAAAA
Found at i:39398578 original size:27 final size:26
Alignment explanation
Indices: 39398524--39398604 Score: 65
Period size: 27 Copynumber: 3.0 Consensus size: 26
39398514 AAGAAAATGA
* **
39398524 TAAAAAAATGTAAAAAAATATAAAATAC
1 TAAAAAAAT-TATAAAAAT-TATCATAC
39398552 GTAAAAAAATTATAAAAATTATCATAC
1 -TAAAAAAATTATAAAAATTATCATAC
* *
39398579 CAAAAGAAGATTAT-AAAATTTTCATA
1 TAAAA-AA-ATTATAAAAATTATCATA
39398605 ACTTTTATTG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 4 0.09
27 19 0.42
28 13 0.29
29 9 0.20
ACGTcount: A:0.62, C:0.06, G:0.05, T:0.27
Consensus pattern (26 bp):
TAAAAAAATTATAAAAATTATCATAC
Found at i:39398794 original size:20 final size:20
Alignment explanation
Indices: 39398771--39398812 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
39398761 TTTTTTATGA
39398771 TTTTCATGA-AATTTTACAAT
1 TTTTCAT-ATAATTTTACAAT
* *
39398791 TTTTTATATATTTTTACAAT
1 TTTTCATATAATTTTACAAT
39398811 TT
1 TT
39398813 ATATATATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTCATATAATTTTACAAT
Found at i:39398803 original size:19 final size:18
Alignment explanation
Indices: 39398781--39398821 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
39398771 TTTTCATGAA
*
39398781 ATTTTACAATTTTTTATAT
1 ATTTTACAA-TTTATATAT
39398800 ATTTTTACAATTTATATAT
1 A-TTTTACAATTTATATAT
39398819 ATT
1 ATT
39398822 CTAATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 10 0.50
20 8 0.40
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTACAATTTATATAT
Found at i:39398875 original size:10 final size:9
Alignment explanation
Indices: 39398756--39398902 Score: 59
Period size: 9 Copynumber: 16.1 Consensus size: 9
39398746 TGATGCATTC
39398756 TATAATTTTT
1 TATAA-TTTT
*
39398766 TATGATTTT
1 TATAATTTT
* *
39398775 CATGAAATTT
1 TAT-AATTTT
*
39398785 TACAATTTTT
1 TATAA-TTTT
39398795 TATATATTTT
1 TATA-ATTTT
* *
39398805 TACAATTTA
1 TATAATTTT
*
39398814 TAT-A-TAT
1 TATAATTTT
*
39398821 TCTAATTTT
1 TATAATTTT
* **
39398830 AATTTTTTT
1 TATAATTTT
39398839 TAT-ATTTT
1 TATAATTTT
*
39398847 TAATAAGTTT
1 T-ATAATTTT
*
39398857 AATAATTTT
1 TATAATTTT
*
39398866 TATAACTTT
1 TATAATTTT
* *
39398875 TATTGATTAT
1 TA-TAATTTT
*
39398885 TAT-TTTTT
1 TATAATTTT
39398893 TATAATTTT
1 TATAATTTT
39398902 T
1 T
39398903 GTCACACGTG
Statistics
Matches: 96, Mismatches: 32, Indels: 19
0.65 0.22 0.13
Matches are distributed among these distances:
7 3 0.03
8 13 0.14
9 47 0.49
10 32 0.33
11 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (9 bp):
TATAATTTT
Found at i:39400625 original size:96 final size:96
Alignment explanation
Indices: 39400251--39400605 Score: 586
Period size: 96 Copynumber: 3.7 Consensus size: 96
39400241 GCCTTATCCT
* * * *
39400251 ACAATGGAACCCCACTACTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
39400316 CAGGCTTGACGTGGGGCTTTCTGGTTGTGAA
66 CAGGCTTGACGTGGGGCTTTCTGGTTGTGAA
39400347 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
*
39400412 CAGGCTTGACATGGGGCTTTCTGGTTGTGAA
66 CAGGCTTGACGTGGGGCTTTCTGGTTGTGAA
*
39400443 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACATGGAAGATTCTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
*
39400508 CAGGCTTGACGTGGGGCTTTCTGG-CGCTGAA
66 CAGGCTTGACGTGGGGCTTTCTGGTTG-TGAA
* * * * *
39400539 ACAAAGGAACCTCAGTATTGTTGTCTTAATGAAGTGTCCTATGAATATAGGGAAAATTTTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
39400604 CA
66 CA
39400606 AGTTTGATGT
Statistics
Matches: 245, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
95 1 0.00
96 244 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (96 bp):
ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
CAGGCTTGACGTGGGGCTTTCTGGTTGTGAA
Found at i:39406935 original size:124 final size:124
Alignment explanation
Indices: 39406715--39407064 Score: 601
Period size: 124 Copynumber: 2.8 Consensus size: 124
39406705 TTATTTCGAG
*
39406715 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACTAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
*
39406780 AAATCGTGCTCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
66 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
* *
39406839 TTGACGTTTTTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAAAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
39406904 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTTGGTTATGTAAGAAATAATTTTTT
66 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
* * *
39406963 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTATACCAGGATGTTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
39407028 AAATCGCGCCCTCATGGACGCGATTTTGCTACAGTAG
66 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTAG
39407065 CAAGTTTGGG
Statistics
Matches: 212, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
124 212 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
Found at i:39409142 original size:17 final size:17
Alignment explanation
Indices: 39409120--39409158 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
39409110 ACCAACATGG
39409120 GTATTTAGTCTATAACT
1 GTATTTAGTCTATAACT
39409137 GTATTTAGTCTATAACT
1 GTATTTAGTCTATAACT
39409154 GTATT
1 GTATT
39409159 ATTATCTCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (17 bp):
GTATTTAGTCTATAACT
Found at i:39411011 original size:37 final size:37
Alignment explanation
Indices: 39410961--39411039 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
39410951 TTATTACGAA
* * *
39410961 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
39410998 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
39411035 GTCTT
1 GTCTT
39411040 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:39414574 original size:40 final size:40
Alignment explanation
Indices: 39414514--39414633 Score: 159
Period size: 40 Copynumber: 3.0 Consensus size: 40
39414504 GCCCGAATAC
* * * *
39414514 ACGTCACCAGCATGATTGCTCTTCGGGATTTAGCACGGAT
1 ACGTCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
* * *
39414554 ATGTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
1 ACGTCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
* *
39414594 ACATCGCTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACGTCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
39414634 TTAGTAATTC
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
ACGTCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
Found at i:39414616 original size:80 final size:80
Alignment explanation
Indices: 39414522--39414674 Score: 200
Period size: 80 Copynumber: 1.9 Consensus size: 80
39414512 ACACGTCACC
* * * *
39414522 AGCATGATTGCTCTTCGGGATTTAGCACGGATAT-GTCACTAGCACGAATGCTCTTCGGAACTTA
1 AGCATGAATGCTCTTCGGGACTTAGCACGGATATAGTAACTAGCACCAATGC-CTTCGGAACTTA
39414586 GCCCGGATACATCGCT
65 GCCCGGATACATCGCT
* * * * *
39414602 AGCATGAATGCTCTTCGGGACTTAGCCCGGATTTAGTAATTCGCACCAATGCCTTCGGATCTTAG
1 AGCATGAATGCTCTTCGGGACTTAGCACGGATATAGTAACTAGCACCAATGCCTTCGGAACTTAG
*
39414667 TCCGGATA
66 CCCGGATA
39414675 TGGTCACTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
80 49 0.79
81 13 0.21
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (80 bp):
AGCATGAATGCTCTTCGGGACTTAGCACGGATATAGTAACTAGCACCAATGCCTTCGGAACTTAG
CCCGGATACATCGCT
Found at i:39414658 original size:40 final size:39
Alignment explanation
Indices: 39414534--39414712 Score: 116
Period size: 40 Copynumber: 4.5 Consensus size: 39
39414524 CATGATTGCT
* * *
39414534 CTTCGGGATTTAGCACGGATAT-GTC-ACTAGCACGAATGC
1 CTTC-GGACTTAGCCCGGATATAGTCAATTAGCAC-AATGC
* ** *
39414573 TCTTCGGAACTTAGCCCGGATACA-TC-GCTAGCATGAATGC
1 -CTTCGG-ACTTAGCCCGGATATAGTCAATTAGCA-CAATGC
* *
39414613 TCTTCGGGACTTAGCCCGGATTTAGT-AATTCGCACCAATGC
1 -CTTC-GGACTTAGCCCGGATATAGTCAATTAGCA-CAATGC
* * * *
39414654 CTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAAGC
1 CTTCGGA-CTTAGCCCGGATATAGTCAATTAGCACAATGC
39414694 CTTCAGGACTTAGCCCGGA
1 CTTC-GGACTTAGCCCGGA
39414713 CATCATTCGA
Statistics
Matches: 111, Mismatches: 19, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
39 5 0.05
40 85 0.77
41 21 0.19
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.26
Consensus pattern (39 bp):
CTTCGGACTTAGCCCGGATATAGTCAATTAGCACAATGC
Found at i:39415059 original size:29 final size:29
Alignment explanation
Indices: 39415020--39415098 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
39415010 CTTAATAATC
*
39415020 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
39415050 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
39415079 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
39415099 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:39420157 original size:51 final size:51
Alignment explanation
Indices: 39420091--39420212 Score: 185
Period size: 51 Copynumber: 2.4 Consensus size: 51
39420081 TTTAAAAAAT
*
39420091 GAAATTGAGGGGAAATTGAAATTAAATATGGAT-TTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGG-TCTTGAGAGAATTTTGGAAG
*
39420142 GAAATTGAGAGGAAATTGAAATTAAATATGGTCTTTAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGTCTTGAGAGAATTTTGGAAG
39420193 GAAATTTG-GAAGGAAATTGA
1 GAAA-TTGAG-AGGAAATTGA
39420213 GAGAATTAGA
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
50 1 0.02
51 52 0.79
52 13 0.20
ACGTcount: A:0.42, C:0.01, G:0.28, T:0.30
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGTCTTGAGAGAATTTTGGAAG
Found at i:39420202 original size:12 final size:12
Alignment explanation
Indices: 39420185--39420210 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39420175 TTTAGAGAAT
39420185 TTTGGAAGGAAA
1 TTTGGAAGGAAA
39420197 TTTGGAAGGAAA
1 TTTGGAAGGAAA
39420209 TT
1 TT
39420211 GAGAGAATTA
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:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (12 bp):
TTTGGAAGGAAA
Found at i:39420888 original size:30 final size:30
Alignment explanation
Indices: 39420852--39420911 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
39420842 TATTTTATTA
39420852 TTAATTTTGTTATTATTTTAAAGACATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
*
39420882 TTAATTTTGTTATTATTTTAGAGACATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
39420912 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGACATTTG
Found at i:39421056 original size:12 final size:12
Alignment explanation
Indices: 39421035--39421068 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39421025 TATATATTTT
*
39421035 AAAATTATATAA
1 AAAATAATATAA
39421047 AAAATAATATAA
1 AAAATAATATAA
*
39421059 AAATTAATAT
1 AAAATAATAT
39421069 GGGCAGGTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:39426070 original size:42 final size:43
Alignment explanation
Indices: 39425964--39426078 Score: 133
Period size: 42 Copynumber: 2.7 Consensus size: 43
39425954 TCGTACAACA
* * * *
39425964 CCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAACGATG
1 CCAATGTCCCAGACATGGTCTTACACGTAATCAAATAACGACG
* * * * *
39426007 CCACTGTCCCAAACAGGGTCTTACACGTAATCATAT-ACGGCG
1 CCAATGTCCCAGACATGGTCTTACACGTAATCAAATAACGACG
*
39426049 CCAATGTCCCAGACATGGTCTTACAGGTAA
1 CCAATGTCCCAGACATGGTCTTACACGTAA
39426079 ATCTCAAATT
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
42 30 0.51
43 29 0.49
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
CCAATGTCCCAGACATGGTCTTACACGTAATCAAATAACGACG
Found at i:39430022 original size:39 final size:40
Alignment explanation
Indices: 39429927--39430188 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
39429917 TTGAATGATG
*
39429927 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
39429965 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
39430006 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
39430045 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
39430084 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
39430123 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
39430162 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
39430189 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:39437956 original size:40 final size:39
Alignment explanation
Indices: 39437925--39438134 Score: 233
Period size: 40 Copynumber: 5.3 Consensus size: 39
39437915 GGACTAAGAT
* *
39437925 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
39437965 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
39438005 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* ** *
39438045 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGAT-ACAAATCCGGGTTAAGTC
* * * * *
39438085 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
39438124 CCGAAGGCATT
1 CCGAAGGCATT
39438135 TGAACGAGGA
Statistics
Matches: 153, Mismatches: 13, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
39 33 0.22
40 117 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:39438088 original size:120 final size:120
Alignment explanation
Indices: 39437872--39438134 Score: 300
Period size: 120 Copynumber: 2.2 Consensus size: 120
39437862 TTGAATGCTG
* *
39437872 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
39437936 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
39437992 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* ** * * * *
39438055 TCGTGCGAGTTGTTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
39438111 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
39438135 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
119 38 0.32
120 73 0.61
121 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:39438154 original size:79 final size:80
Alignment explanation
Indices: 39437925--39438169 Score: 228
Period size: 80 Copynumber: 3.1 Consensus size: 80
39437915 GGACTAAGAT
* * * * * * * ** *
39437925 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGA-GATAC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-ACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGA-GC
39437988 TAAATCCGGGTTAAGTC
64 TAAATCCGGGTTAAGTC
* * * ** ** *
39438005 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
39438070 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * *
39438085 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
39438149 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
39438163 CCGAAGG
1 CCGAAGG
39438170 TACGTGATTT
Statistics
Matches: 138, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
78 14 0.10
79 46 0.33
80 75 0.54
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:39455363 original size:15 final size:15
Alignment explanation
Indices: 39455343--39455401 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 15
39455333 AAAATATTTG
39455343 AAATATTTTAATATA
1 AAATATTTTAATATA
*
39455358 AAATA-TTTAATTTCA
1 AAATATTTTAATAT-A
*
39455373 AAATATAATTTAAAATA
1 AAATAT--TTTAATATA
39455390 AAATATTTTAAT
1 AAATATTTTAAT
39455402 TAATTTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 7 0.19
15 16 0.44
17 7 0.19
18 6 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATATTTTAATATA
Found at i:39455427 original size:24 final size:24
Alignment explanation
Indices: 39455378--39455428 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
39455368 TTTCAAAATA
*
39455378 TAATTTAAAATAAAATATTTTAAT
1 TAATTTAAAATAAAATATTATAAT
*
39455402 TAATTTAATATAAAATAATTAT-AT
1 TAATTTAAAATAAAAT-ATTATAAT
39455426 TAA
1 TAA
39455429 CAATATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TAATTTAAAATAAAATATTATAAT
Found at i:39455472 original size:16 final size:16
Alignment explanation
Indices: 39455453--39455523 Score: 51
Period size: 16 Copynumber: 4.4 Consensus size: 16
39455443 TATATATTTT
39455453 TATTTTTATTAAATTA
1 TATTTTTATTAAATTA
*
39455469 TA--TTTAAT-AATTA
1 TATTTTTATTAAATTA
39455482 TATTTAAATATGATTAAATTA
1 TATTT---T-T-ATTAAATTA
*
39455503 TTTTTTTATTAAATTA
1 TATTTTTATTAAATTA
39455519 T-TTTT
1 TATTTT
39455524 AATAATAATC
Statistics
Matches: 44, Mismatches: 3, Indels: 17
0.69 0.05 0.27
Matches are distributed among these distances:
13 7 0.16
14 5 0.11
15 5 0.11
16 12 0.27
17 1 0.02
18 2 0.05
19 1 0.02
20 2 0.05
21 9 0.20
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (16 bp):
TATTTTTATTAAATTA
Found at i:39455482 original size:13 final size:13
Alignment explanation
Indices: 39455464--39455488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39455454 ATTTTTATTA
39455464 AATTATATTTAAT
1 AATTATATTTAAT
39455477 AATTATATTTAA
1 AATTATATTTAA
39455489 ATATGATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTATATTTAAT
Found at i:39455706 original size:44 final size:46
Alignment explanation
Indices: 39455638--39455726 Score: 112
Period size: 44 Copynumber: 2.0 Consensus size: 46
39455628 TTACAACATC
* *
39455638 ATTCTATTCAACCAAACACATGAA-TACT-ACTACAATTCTATTCT
1 ATTCCATTCAACCAAACACATGAATTACTAACTACAACTCTATTCT
* *
39455682 ATTCCATTCAACTAAACA-ATTGAATTACTAATTACAACTCTATTC
1 ATTCCATTCAACCAAACACA-TGAATTACTAACTACAACTCTATTC
39455727 CATTATAGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 1 0.03
44 20 0.53
45 4 0.11
46 13 0.34
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (46 bp):
ATTCCATTCAACCAAACACATGAATTACTAACTACAACTCTATTCT
Found at i:39459622 original size:71 final size:71
Alignment explanation
Indices: 39459506--39459663 Score: 217
Period size: 71 Copynumber: 2.2 Consensus size: 71
39459496 AAAAGAAAGA
* * * ** * * *
39459506 GTATCGTGATATCAACACCTTGGAATTGCGATACCTTTAATAGTATTGAAGAATGGAGACATCTT
1 GTATCGCGATATCCACACCTTGGAATCGCGATACCTCAAACAGTATTGAAGAATGGAGACACCCT
*
39459571 TCAGTG
66 TCAATG
* *
39459577 GTATCGCGATATCCACACCTTGGAATCGTGATACCTCAAACAGTATTGAAGAATGGGGACACCCT
1 GTATCGCGATATCCACACCTTGGAATCGCGATACCTCAAACAGTATTGAAGAATGGAGACACCCT
39459642 TCAATG
66 TCAATG
39459648 GTATCGCGATATCCAC
1 GTATCGCGATATCCAC
39459664 CTTTCCAAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 76 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (71 bp):
GTATCGCGATATCCACACCTTGGAATCGCGATACCTCAAACAGTATTGAAGAATGGAGACACCCT
TCAATG
Found at i:39459753 original size:22 final size:22
Alignment explanation
Indices: 39459700--39459754 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
39459690 CACTGCCTAA
*
39459700 GGTATCGTGATATCCTCTTATG
1 GGTATCGCGATATCCTCTTATG
*** * *
39459722 AAAATTGCGATATCTTCTTATG
1 GGTATCGCGATATCCTCTTATG
39459744 GGTATCGCGAT
1 GGTATCGCGAT
39459755 GTAACAGCCC
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (22 bp):
GGTATCGCGATATCCTCTTATG
Found at i:39462398 original size:13 final size:13
Alignment explanation
Indices: 39462380--39462404 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39462370 TAACTTATAT
39462380 GTGTGAAAATTTC
1 GTGTGAAAATTTC
39462393 GTGTGAAAATTT
1 GTGTGAAAATTT
39462405 TATCATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:39474078 original size:26 final size:25
Alignment explanation
Indices: 39474049--39474106 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 25
39474039 TTCATCTGAA
39474049 AATATGAGGCACACTCCACAAATTGT
1 AATAT-AGGCACACTCCACAAATTGT
39474075 AATAACATAGGCACACTCCACAAATTGT
1 AAT---ATAGGCACACTCCACAAATTGT
39474103 AATA
1 AATA
39474107 ACATACTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
25 1 0.03
26 3 0.10
28 23 0.79
29 2 0.07
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.22
Consensus pattern (25 bp):
AATATAGGCACACTCCACAAATTGT
Found at i:39474086 original size:28 final size:28
Alignment explanation
Indices: 39474055--39474111 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
39474045 TGAAAATATG
39474055 AGGCACACTCCACAAATTGTAATAACAT
1 AGGCACACTCCACAAATTGTAATAACAT
39474083 AGGCACACTCCACAAATTGTAATAACAT
1 AGGCACACTCCACAAATTGTAATAACAT
39474111 A
1 A
39474112 CTTATTTACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.21
Consensus pattern (28 bp):
AGGCACACTCCACAAATTGTAATAACAT
Found at i:39476877 original size:26 final size:26
Alignment explanation
Indices: 39476848--39476904 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
39476838 AACACGTCAG
*
39476848 AAAAGGAAGCCATTGTGGTATAATAT
1 AAAAGGAAGCCATTGTGGCATAATAT
*
39476874 AAAAGGAAGCCTTTGTGGCATAATAT
1 AAAAGGAAGCCATTGTGGCATAATAT
39476900 AAAAG
1 AAAAG
39476905 AAACCCTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.25
Consensus pattern (26 bp):
AAAAGGAAGCCATTGTGGCATAATAT
Found at i:39476918 original size:26 final size:26
Alignment explanation
Indices: 39476867--39476919 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
39476857 CCATTGTGGT
* * * *
39476867 ATAATATAAAAGGAAGCCTTTGTGGC
1 ATAATATAAAAGAAACCCTCTCTGGC
39476893 ATAATATAAAAGAAACCCTCTCTGGC
1 ATAATATAAAAGAAACCCTCTCTGGC
39476919 A
1 A
39476920 AAACTCGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (26 bp):
ATAATATAAAAGAAACCCTCTCTGGC
Found at i:39480174 original size:18 final size:19
Alignment explanation
Indices: 39480138--39480184 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
39480128 GAATAAAAGA
39480138 AAAAGAAAGC-AAAGAATCG
1 AAAAGAAA-CAAAAGAATCG
39480157 AAAAGAAACAAAAG-ATCG
1 AAAAGAAACAAAAGAATCG
39480175 AGAAA-AAACA
1 A-AAAGAAACA
39480185 GAAAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.68, C:0.11, G:0.17, T:0.04
Consensus pattern (19 bp):
AAAAGAAACAAAAGAATCG
Found at i:39484747 original size:43 final size:44
Alignment explanation
Indices: 39484677--39484818 Score: 157
Period size: 43 Copynumber: 3.3 Consensus size: 44
39484667 TTTTTCAAAT
* * *
39484677 AAACGCCGCTATAGATCAT-TACTTTTAGCGGCGCTTTTAT-ATC
1 AAACACCGCTAAAGATCATGTTC-TTTAGCGGCGCTTTTATCATC
* * *
39484720 AAACGCCGCTAAAGGTCATGTTCTTTAGCAGCGCTTTTATCA-C
1 AAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTATCATC
* * * *
39484763 AAACACCACTAAAGAACATGATCTTTAGCGGCGCTTTTTTCAT-
1 AAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTATCATC
39484806 AAACACCGCTAAA
1 AAACACCGCTAAA
39484819 AGTATCGTTC
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
43 81 0.96
44 3 0.04
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (44 bp):
AAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTATCATC
Found at i:39484831 original size:43 final size:42
Alignment explanation
Indices: 39484700--39484832 Score: 142
Period size: 43 Copynumber: 3.1 Consensus size: 42
39484690 GATCATTACT
* *
39484700 TTTAGCGGCGCTTTTAT-ATCAAACGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGCTTTTATCAT-AAACACCGCTAAAAGT-ATGTTC
* * * ** *
39484743 TTTAGCAGCGCTTTTATCACAAACACCACTAAAGAACATGATC
1 TTTAGCGGCGCTTTTATCATAAACACCGCTAAA-AGTATGTTC
*
39484786 TTTAGCGGCGCTTTTTTCATAAACACCGCTAAAAGTATCGTTC
1 TTTAGCGGCGCTTTTATCATAAACACCGCTAAAAGTAT-GTTC
39484829 TTTA
1 TTTA
39484833 ATGGCGTTTT
Statistics
Matches: 72, Mismatches: 15, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
42 3 0.04
43 68 0.94
44 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (42 bp):
TTTAGCGGCGCTTTTATCATAAACACCGCTAAAAGTATGTTC
Found at i:39485165 original size:21 final size:21
Alignment explanation
Indices: 39485141--39485190 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
39485131 TTCTATTCTG
39485141 CTCTGCTTCCCTCGCTGCTGC
1 CTCTGCTTCCCTCGCTGCTGC
39485162 CTCTGCTTCCCTCGCTGCTGC
1 CTCTGCTTCCCTCGCTGCTGC
39485183 CTCTGCTT
1 CTCTGCTT
39485191 TAAGTTGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.00, C:0.46, G:0.18, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCTGC
Found at i:39490654 original size:9 final size:9
Alignment explanation
Indices: 39490640--39491007 Score: 127
Period size: 9 Copynumber: 40.0 Consensus size: 9
39490630 TAAGTATAAT
39490640 TAAGTTATG
1 TAAGTTATG
39490649 TAAGTTATG
1 TAAGTTATG
39490658 TAAGTTATG
1 TAAGTTATG
* * *
39490667 ATATGATATA
1 -TAAGTTATG
*
39490677 T-ATTTATG
1 TAAGTTATG
39490685 TAAGTTA--
1 TAAGTTATG
39490692 TAAG-TATG
1 TAAGTTATG
39490700 ATTAAGTTATG
1 --TAAGTTATG
39490711 TAAGTTATG
1 TAAGTTATG
* *
39490720 TGAGTTACG
1 TAAGTTATG
39490729 TAAGTTATG
1 TAAGTTATG
* *
39490738 ATATGATATATATA
1 -TA--A-GT-TATG
39490752 TAAGTTAT-
1 TAAGTTATG
39490760 TAAGTTATG
1 TAAGTTATG
*
39490769 TAAGATATG
1 TAAGTTATG
*
39490778 TGAGTTATG
1 TAAGTTATG
* *
39490787 ATATGATATATA
1 -TAAG-T-TATG
* *
39490799 TAAGTAATT
1 TAAGTTATG
39490808 TAAGAATTTTATG
1 TAAG----TTATG
*
39490821 TATG-TATG
1 TAAGTTATG
*
39490829 TGAGTTATG
1 TAAGTTATG
39490838 TAAGTTATG
1 TAAGTTATG
* * *
39490847 ATATGATATA
1 -TAAGTTATG
*
39490857 T-ATTTATG
1 TAAGTTATG
39490865 T-A-TTATG
1 TAAGTTATG
39490872 TAAGTTATGG
1 TAAGTTAT-G
* *
39490882 TATGATATATA
1 TAAG-T-TATG
39490893 TAAGTTAT-
1 TAAGTTATG
*
39490901 TAGGTTATG
1 TAAGTTATG
**
39490910 TGGGTTATG
1 TAAGTTATG
* *
39490919 ATATGATATATA
1 -TAAG-T-TATG
39490931 TAAGTTAT-
1 TAAGTTATG
39490939 TAAGTTATG
1 TAAGTTATG
*
39490948 TATG-TATG
1 TAAGTTATG
*
39490956 TGAGTTATG
1 TAAGTTATG
39490965 TAAGTTATG
1 TAAGTTATG
* * *
39490974 ATATGATATA
1 -TAAGTTATG
*
39490984 T-ATTTATG
1 TAAGTTATG
39490992 T-A-TTATG
1 TAAGTTATG
39490999 TAAGTTATG
1 TAAGTTATG
39491008 GTATGATATA
Statistics
Matches: 266, Mismatches: 57, Indels: 72
0.67 0.14 0.18
Matches are distributed among these distances:
6 2 0.01
7 16 0.06
8 51 0.19
9 122 0.46
10 36 0.14
11 17 0.06
12 10 0.04
13 9 0.03
14 3 0.01
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:39490825 original size:47 final size:48
Alignment explanation
Indices: 39490702--39490964 Score: 136
Period size: 49 Copynumber: 5.7 Consensus size: 48
39490692 TAAGTATGAT
* * * * *
39490702 TAAGTTATGTAAGTTATGTGAGTTACGTAAGTTATGATATGATATATATA
1 TAAGTAAT-TAAGTTATGTAAGATATGTGAGTTATGATATGA-ATATATA
*
39490752 TAAGTTATTAAGTTATGTAAGATATGTGAGTTATGATATG-ATATATA
1 TAAGTAATTAAGTTATGTAAGATATGTGAGTTATGATATGAATATATA
* * *
39490799 TAAGTAATTTAAGAATTTTATGTATG-TATGTGAGTTATG-TAAG-TTATGATA
1 TAAGTAA-TTAAG----TTATGTAAGATATGTGAGTTATGATATGAATAT-ATA
* * * * *
39490850 TGA-T-A-TATATTTATGT-A-TTATGTAAGTTATGGTATG-ATATATA
1 TAAGTAATTA-AGTTATGTAAGATATGTGAGTTATGATATGAATATATA
* *
39490893 TAAG---TT-A-TTA-G---GTTATGTGGGTTATGATATG-ATATATA
1 TAAGTAATTAAGTTATGTAAGATATGTGAGTTATGATATGAATATATA
* *
39490931 TAAGTTATTAAGTTATGTATG-TATGTGAGTTATG
1 TAAGTAATTAAGTTATGTAAGATATGTGAGTTATG
39490965 TAAGTTATGA
Statistics
Matches: 173, Mismatches: 19, Indels: 46
0.73 0.08 0.19
Matches are distributed among these distances:
38 27 0.16
39 1 0.01
40 3 0.02
41 3 0.02
42 1 0.01
43 21 0.12
44 13 0.08
46 12 0.07
47 16 0.09
48 6 0.03
49 29 0.17
50 15 0.09
51 18 0.10
52 8 0.05
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (48 bp):
TAAGTAATTAAGTTATGTAAGATATGTGAGTTATGATATGAATATATA
Found at i:39490832 original size:51 final size:49
Alignment explanation
Indices: 39490702--39490837 Score: 139
Period size: 49 Copynumber: 2.7 Consensus size: 49
39490692 TAAGTATGAT
* * * * *
39490702 TAAGTTATGTAAGTTATGTGAGTTACGTAAGTTATGATATGATATATATA
1 TAAGTTAAG-AAGTTATGTAAGATATGTGAGTTATGATATGATATATATA
**
39490752 TAAGTTATTAAGTTATGTAAGATATGTGAGTTATGATATGATATATATAA
1 TAAGTTAAGAAGTTATGTAAGATATGTGAGTTATGATATGATATATAT-A
* * *
39490802 GTAATTTAAGAATTTTATGTATG-TATGTGAGTTATG
1 -TAAGTTAAGAA-GTTATGTAAGATATGTGAGTTATG
39490838 TAAGTTATGA
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
49 35 0.48
50 9 0.12
51 21 0.29
52 8 0.11
ACGTcount: A:0.36, C:0.01, G:0.20, T:0.43
Consensus pattern (49 bp):
TAAGTTAAGAAGTTATGTAAGATATGTGAGTTATGATATGATATATATA
Found at i:39490876 original size:34 final size:34
Alignment explanation
Indices: 39490644--39491020 Score: 177
Period size: 34 Copynumber: 11.0 Consensus size: 34
39490634 TATAATTAAG
39490644 TTATGTAAGTTATGTAAGTTATGATATGATATATAT
1 TTATGT-A-TTATGTAAGTTATGATATGATATATAT
* * * *
39490680 TTATGTAAGTTA--TAAG-TATGATTAAGTTATGTAAG
1 TTATGT-A-TTATGTAAGTTATGA-TATGATATAT-AT
*
39490715 TTATGTGAGTTACGTAAGTTATGATATGATATATAT
1 TTATGT-A-TTATGTAAGTTATGATATGATATATAT
* * *
39490751 ATAAG--TTAT-TAAGTTATG-TAAGATATGTGAGTTAT
1 TTATGTATTATGTAAGTTATGATATGATA--T-A--TAT
* * * ** *
39490786 GATATGATATATATAAGTAATTTAAGA-ATTTTATGTAT
1 -TTATG-TAT-TAT--GTAAGTTATGATATGATATATAT
*
39490824 GTATGTGAGTTATGTAAGTTATGATATGATATATAT
1 TTATGT-A-TTATGTAAGTTATGATATGATATATAT
*
39490860 TTATGTATTATGTAAGTTATGGTATGATATATAT
1 TTATGTATTATGTAAGTTATGATATGATATATAT
**
39490894 AAGTTAT-TAGGTTATGTGGGTTATGATATGATATATA-
1 ---TTATGTA--TTATGTAAGTTATGATATGATATATAT
* *
39490931 -TAAG--TTAT-TAAGTTATG-TATG---TAT-G
1 TTATGTATTATGTAAGTTATGATATGATATATAT
*
39490956 TGA-G--TTATGTAAGTTATGATATGATATATAT
1 TTATGTATTATGTAAGTTATGATATGATATATAT
*
39490987 TTATGTATTATGTAAGTTATGGTATGATATATAT
1 TTATGTATTATGTAAGTTATGATATGATATATAT
39491021 ATAAGTTATT
Statistics
Matches: 264, Mismatches: 38, Indels: 80
0.69 0.10 0.21
Matches are distributed among these distances:
25 8 0.03
26 10 0.04
27 4 0.02
28 4 0.02
29 7 0.03
30 13 0.05
31 11 0.04
32 5 0.02
33 8 0.03
34 63 0.24
35 25 0.09
36 36 0.14
37 23 0.09
38 32 0.12
39 1 0.00
40 3 0.01
41 1 0.00
43 10 0.04
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (34 bp):
TTATGTATTATGTAAGTTATGATATGATATATAT
Found at i:39490885 original size:21 final size:21
Alignment explanation
Indices: 39490872--39490938 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
39490862 ATGTATTATG
39490872 TAAGTTATGGTATGATATATA
1 TAAGTTATGGTATGATATATA
* *
39490893 TAAGTTAT--TA-GGT-TATG
1 TAAGTTATGGTATGATATATA
** *
39490910 TGGGTTATGATATGATATATA
1 TAAGTTATGGTATGATATATA
39490931 TAAGTTAT
1 TAAGTTAT
39490939 TAAGTTATGT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
17 9 0.26
18 2 0.06
19 4 0.12
20 2 0.06
21 17 0.50
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (21 bp):
TAAGTTATGGTATGATATATA
Found at i:39490909 original size:38 final size:37
Alignment explanation
Indices: 39490640--39490949 Score: 169
Period size: 38 Copynumber: 8.5 Consensus size: 37
39490630 TAAGTATAAT
39490640 TAAGTTATGTAAGTTATGTAAGTTATGATATGATATATA
1 TAAGTTAT-T-AGTTATGTAAGTTATGATATGATATATA
* *
39490679 T---TTATGTAAGTTA--TAAG-TATGAT-TAAGT-TATG
1 TAAGTTAT-T-AGTTATGTAAGTTATGATATGA-TATATA
*
39490711 TAAGTTATGTGAGTTACGTAAGTTATGATATGATATATATA
1 TAAGTTAT-T-AGTTATGTAAGTTATGATATG--ATATATA
*
39490752 TAAGTTATTAAGTTATGTAAGATATGTGAGTTATGATATGATA
1 TAAGTTATT-AGTTATGTAAG-T-TATGA--TATGATAT-ATA
* * * * ** *
39490795 T-A--TATAAGTAATTTAAG-AATTTTATG-TATGTA
1 TAAGTTATTAGTTATGTAAGTTATGATATGATATATA
*
39490827 T--G---TGAGTTATGTAAGTTATGATATGATATATA
1 TAAGTTATTAGTTATGTAAGTTATGATATGATATATA
*
39490859 T---TTATGTA-TTATGTAAGTTATGGTATGATATATA
1 TAAGTTAT-TAGTTATGTAAGTTATGATATGATATATA
**
39490893 TAAGTTATTAGGTTATGTGGGTTATGATATGATATATA
1 TAAGTTATTA-GTTATGTAAGTTATGATATGATATATA
39490931 TAAGTTATTAAGTTATGTA
1 TAAGTTATT-AGTTATGTA
39490950 TGTATGTGAG
Statistics
Matches: 213, Mismatches: 29, Indels: 59
0.71 0.10 0.20
Matches are distributed among these distances:
30 10 0.05
31 6 0.03
32 15 0.07
33 10 0.05
34 35 0.16
35 12 0.06
36 15 0.07
37 8 0.04
38 45 0.21
39 12 0.06
40 15 0.07
41 13 0.06
42 9 0.04
43 4 0.02
44 4 0.02
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (37 bp):
TAAGTTATTAGTTATGTAAGTTATGATATGATATATA
Found at i:39490919 original size:127 final size:128
Alignment explanation
Indices: 39490760--39491036 Score: 430
Period size: 127 Copynumber: 2.1 Consensus size: 128
39490750 TATAAGTTAT
* * *
39490760 TAAGTTATGTAAGATATGTGAGTTATGATATGATATATATAAGTAATTTAAGAATTTTATGTATG
1 TAAGTTAT-TAAGTTATGTGGGTTATGATATGATATATATAAG----TTAAGAA-GTTATGTATG
39490825 TATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGGTATG-ATA
60 TATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGGTATGAATA
39490889 TATA
125 TATA
* **
39490893 TAAGTTATTAGGTTATGTGGGTTATGATATGATATATATAAGTTATTAAGTTATGTATGTATGTG
1 TAAGTTATTAAGTTATGTGGGTTATGATATGATATATATAAGTTAAGAAGTTATGTATGTATGTG
39490958 AGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGGTATGATATATATA
66 AGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGGTATGA-ATATATA
39491022 TAAGTTATTAAGTTA
1 TAAGTTATTAAGTTA
39491037 AGATCCAAAG
Statistics
Matches: 135, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
127 70 0.52
128 5 0.04
129 21 0.16
132 31 0.23
133 8 0.06
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (128 bp):
TAAGTTATTAAGTTATGTGGGTTATGATATGATATATATAAGTTAAGAAGTTATGTATGTATGTG
AGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGGTATGAATATATA
Found at i:39491083 original size:9 final size:9
Alignment explanation
Indices: 39491069--39491154 Score: 75
Period size: 9 Copynumber: 9.3 Consensus size: 9
39491059 TCTTTAAAGG
*
39491069 TATGTAAAT
1 TATGTAAGT
39491078 TATGTAAGT
1 TATGTAAGT
*
39491087 TATGATATGAT
1 TATG-TAAG-T
39491098 TAT-TAAGT
1 TATGTAAGT
39491106 TATGTAAGT
1 TATGTAAGT
*
39491115 TATGTGAGT
1 TATGTAAGT
*
39491124 TAATGTAAAT
1 T-ATGTAAGT
*
39491134 TATATAAGT
1 TATGTAAGT
* *
39491143 TACGTAAAT
1 TATGTAAGT
39491152 TAT
1 TAT
39491155 ATATTCATTT
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
8 4 0.07
9 43 0.70
10 10 0.16
11 4 0.07
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.44
Consensus pattern (9 bp):
TATGTAAGT
Found at i:39491110 original size:37 final size:37
Alignment explanation
Indices: 39491069--39491154 Score: 104
Period size: 37 Copynumber: 2.3 Consensus size: 37
39491059 TCTTTAAAGG
*
39491069 TATGTAAATTATGTAAGTT-ATGATATGATTAT-TAAGT
1 TATGTAAATTATGTAAGTTAATG-TA-AATTATATAAGT
* *
39491106 TATGTAAGTTATGTGAGTTAATGTAAATTATATAAGT
1 TATGTAAATTATGTAAGTTAATGTAAATTATATAAGT
*
39491143 TACGTAAATTAT
1 TATGTAAATTAT
39491155 ATATTCATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
36 5 0.12
37 34 0.81
38 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.44
Consensus pattern (37 bp):
TATGTAAATTATGTAAGTTAATGTAAATTATATAAGT
Found at i:39491136 original size:28 final size:29
Alignment explanation
Indices: 39491069--39491144 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
39491059 TCTTTAAAGG
39491069 TATGTAAATTATGTAAGTTATGATATGAT
1 TATGTAAATTATGTAAGTTATGATATGAT
*
39491098 TAT-TAAGTTATGTAAGTTATG---TGAGT
1 TATGTAAATTATGTAAGTTATGATATGA-T
*
39491124 TAATGTAAATTATATAAGTTA
1 T-ATGTAAATTATGTAAGTTA
39491145 CGTAAATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
25 3 0.07
26 2 0.05
27 2 0.05
28 31 0.76
29 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (29 bp):
TATGTAAATTATGTAAGTTATGATATGAT
Found at i:39491295 original size:20 final size:20
Alignment explanation
Indices: 39491270--39491310 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
39491260 TAGAGTAAAC
39491270 TCAATTTTGCTTTCCTTGTA
1 TCAATTTTGCTTTCCTTGTA
39491290 TCAATTTTGCTTTCCTTGTA
1 TCAATTTTGCTTTCCTTGTA
39491310 T
1 T
39491311 TAGTGGGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.20, G:0.10, T:0.56
Consensus pattern (20 bp):
TCAATTTTGCTTTCCTTGTA
Found at i:39491495 original size:75 final size:75
Alignment explanation
Indices: 39491380--39491560 Score: 301
Period size: 75 Copynumber: 2.4 Consensus size: 75
39491370 TATATAAAAT
* *
39491380 AAAAAAAA-AAGACATTGAGTTGGCATTACAAGATACAATTAATTTGTCTATATTTATCAAAATA
1 AAAAAAAATAAGACTTTGAGTTGGCATTACAAGATACAATTAATTTGTCTATATTGATCAAAATA
*
39491444 AGTTAAATTA
66 AGTAAAATTA
* * *
39491454 AAAAAAAATAAGCCTTTGAGTTGGCATTACAATATATAATTAATTTGTCTATATTGATCAAAATA
1 AAAAAAAATAAGACTTTGAGTTGGCATTACAAGATACAATTAATTTGTCTATATTGATCAAAATA
39491519 AGTAAAATTA
66 AGTAAAATTA
39491529 AAAAAAAATAAGACTTTGAGTTGGCATTACAA
1 AAAAAAAATAAGACTTTGAGTTGGCATTACAA
39491561 AATAAATATA
Statistics
Matches: 99, Mismatches: 7, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
74 8 0.08
75 91 0.92
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (75 bp):
AAAAAAAATAAGACTTTGAGTTGGCATTACAAGATACAATTAATTTGTCTATATTGATCAAAATA
AGTAAAATTA
Found at i:39491790 original size:66 final size:65
Alignment explanation
Indices: 39491693--39491843 Score: 203
Period size: 66 Copynumber: 2.3 Consensus size: 65
39491683 TATAAAATCG
* ** * * * *
39491693 ATAATTTATTAAATTACATAAAAAATTGATAATTTATTGACATAAAATCAAATAAACTAATCAAA
1 ATAATTTATTCAATTA-ATCGATAATCGATAATTTATTCACATAAAACCAAATAAACTAATCAAA
39491758 C
65 C
* *
39491759 ATAATTTATTCAATTTAATCGATAATCGATAATTTATTCACATTAAACCGAATAAACTAATCAAA
1 ATAATTTATTCAA-TTAATCGATAATCGATAATTTATTCACATAAAACCAAATAAACTAATCAAA
39491824 C
65 C
39491825 ATAATTTATTCAATTAATC
1 ATAATTTATTCAATTAATC
39491844 AAATATATAA
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
65 6 0.08
66 66 0.88
67 3 0.04
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.36
Consensus pattern (65 bp):
ATAATTTATTCAATTAATCGATAATCGATAATTTATTCACATAAAACCAAATAAACTAATCAAAC
Found at i:39494311 original size:7 final size:7
Alignment explanation
Indices: 39494291--39494503 Score: 117
Period size: 7 Copynumber: 29.9 Consensus size: 7
39494281 ACTAATTAAT
39494291 CTAAACC
1 CTAAACC
*
39494298 TTAAACCC
1 CTAAA-CC
*
39494306 CTAACCC
1 CTAAACC
**
39494313 CTATCCC
1 CTAAACC
39494320 CTAAACC
1 CTAAACC
*
39494327 TTAAACC
1 CTAAACC
*
39494334 CTAAGCC
1 CTAAACC
39494341 CTTAAACC
1 C-TAAACC
39494349 CTAAACC
1 CTAAACC
*
39494356 TTAAACC
1 CTAAACC
*
39494363 TTAAACC
1 CTAAACC
39494370 CT-AACC
1 CTAAACC
*
39494376 CTTAAACT
1 C-TAAACC
39494384 CTAAACC
1 CTAAACC
*
39494391 CATAATCC
1 C-TAAACC
*
39494399 GTAAACC
1 CTAAACC
*
39494406 TTAAA--
1 CTAAACC
*
39494411 ATAGTAACTC
1 CTA--AAC-C
39494421 CTAAACC
1 CTAAACC
*
39494428 TTAAACC
1 CTAAACC
*
39494435 ATAAACC
1 CTAAACC
* *
39494442 ATAATCC
1 CTAAACC
*
39494449 CTAAATC
1 CTAAACC
*
39494456 TTAAACC
1 CTAAACC
* *
39494463 TTAAAAC
1 CTAAACC
39494470 CTAAACC
1 CTAAACC
* *
39494477 ATATACC
1 CTAAACC
39494484 CTAAACC
1 CTAAACC
* *
39494491 ATAAACT
1 CTAAACC
39494498 CTAAAC
1 CTAAAC
39494504 TATAATAATA
Statistics
Matches: 158, Mismatches: 38, Indels: 20
0.73 0.18 0.09
Matches are distributed among these distances:
5 2 0.01
6 5 0.03
7 126 0.80
8 23 0.15
10 2 0.01
ACGTcount: A:0.42, C:0.34, G:0.01, T:0.23
Consensus pattern (7 bp):
CTAAACC
Found at i:39494324 original size:29 final size:30
Alignment explanation
Indices: 39494291--39494362 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 30
39494281 ACTAATTAAT
**
39494291 CTAAACCTTAAACCCCTAA-CCCCTATCCC
1 CTAAACCTTAAACCCCTAAGCCCCTAAACC
*
39494320 CTAAACCTTAAA-CCCTAAGCCCTTAAACC
1 CTAAACCTTAAACCCCTAAGCCCCTAAACC
39494349 CTAAACCTTAAACC
1 CTAAACCTTAAACC
39494363 TTAAACCCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.16
29 31 0.82
30 1 0.03
ACGTcount: A:0.36, C:0.42, G:0.01, T:0.21
Consensus pattern (30 bp):
CTAAACCTTAAACCCCTAAGCCCCTAAACC
Found at i:39494974 original size:111 final size:113
Alignment explanation
Indices: 39494796--39495096 Score: 437
Period size: 114 Copynumber: 2.7 Consensus size: 113
39494786 GTTTTTAATT
* * * * *
39494796 TTTTTTGCGGCGTTTTTCAAA-AGCGTCGCTAATGCTCGACATATAGCGACATTTTTCAAAAAAG
1 TTTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCGTTTTTC-AACAAG
* *
39494860 CGCCGCTAATGCCACTAAAGCTCAACAT-AAA-ACGGCGTTGTGCTTAA
65 CGCCGCTAATGCCACTAAAGCTCAACATAAAACACGGCATTATGCTTAA
* *
39494907 TTTTTTGCGGCGTGTTTCAAAGAGCGCCACTAATGCTCGACCTATAGCGGCGTTTTTCAACAAGC
1 TTTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCGTTTTTCAACAAGC
*
39494972 GCCGCTAATTCCACTAAAGCTCAACATAAAACGACGGCATTATGCTTAA
66 GCCGCTAATGCCACTAAAGCTCAACATAAAAC-ACGGCATTATGCTTAA
* * * *
39495021 ATTTTAGCGGCGTTTTTCAAAGAGCGCCGCTAACGCTCGACCTATAGTGGCGTTTTTCAACAAGC
1 TTTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCGTTTTTCAACAAGC
39495086 GCCGCTAATGC
66 GCCGCTAATGC
39495097 ACGACATATT
Statistics
Matches: 169, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
111 52 0.31
112 34 0.20
114 83 0.49
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (113 bp):
TTTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCGTTTTTCAACAAGC
GCCGCTAATGCCACTAAAGCTCAACATAAAACACGGCATTATGCTTAA
Found at i:39495117 original size:40 final size:40
Alignment explanation
Indices: 39495025--39495157 Score: 124
Period size: 40 Copynumber: 3.3 Consensus size: 40
39495015 GCTTAAATTT
* * *
39495025 TAGCGGCGTTTTTCAA-AGAGCGCCGCTAACGCTCGACCTA
1 TAGCGGCGTTTTTCAACA-AGCGCCGCTAATGCACGACATA
*
39495065 TAGTGGCGTTTTTCAACAAGCGCCGCTAATGCACGACATA
1 TAGCGGCGTTTTTCAACAAGCGCCGCTAATGCACGACATA
* * * * * * * * *
39495105 TTGCGGCATTTTTCGACTATCGCCGCTAATTCCCAATATA
1 TAGCGGCGTTTTTCAACAAGCGCCGCTAATGCACGACATA
*
39495145 TAGCAGCGTTTTT
1 TAGCGGCGTTTTT
39495158 TTGTCCAAAC
Statistics
Matches: 75, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
40 74 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.29
Consensus pattern (40 bp):
TAGCGGCGTTTTTCAACAAGCGCCGCTAATGCACGACATA
Found at i:39495249 original size:10 final size:10
Alignment explanation
Indices: 39495231--39495264 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
39495221 AAGTCATTAA
*
39495231 AATCCTAATT
1 AATCTTAATT
39495241 AATCTTAATT
1 AATCTTAATT
*
39495251 AAACTTAATT
1 AATCTTAATT
39495261 AATC
1 AATC
39495265 ATCTATGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (10 bp):
AATCTTAATT
Found at i:39498620 original size:2 final size:2
Alignment explanation
Indices: 39498613--39498663 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
39498603 ATACCTTGGG
39498613 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
39498655 GT GT GT GT G
1 GT GT GT GT G
39498664 GGTGGTATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:39501417 original size:19 final size:19
Alignment explanation
Indices: 39501385--39501422 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
39501375 TATATACATT
39501385 TTTAGTTTTCAAA-TAAAA
1 TTTAGTTTTCAAATTAAAA
*
39501403 TTTAGTTTTTTAAATTAAAA
1 TTTAG-TTTTCAAATTAAAA
39501423 AATTAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 7 0.41
20 5 0.29
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (19 bp):
TTTAGTTTTCAAATTAAAA
Found at i:39506896 original size:43 final size:43
Alignment explanation
Indices: 39506835--39506922 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
39506825 CAGTAACAAA
39506835 CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
1 CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
39506878 CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
1 CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
39506921 CA
1 CA
39506923 GCGAGTGAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (43 bp):
CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
Found at i:39509648 original size:74 final size:74
Alignment explanation
Indices: 39509556--39509702 Score: 258
Period size: 74 Copynumber: 2.0 Consensus size: 74
39509546 TCTTCCTATC
39509556 AATAGATCACACGGTAGAGTTATTTATACAAATTTAAATATATAAATTTCATTTATTGTTATTCT
1 AATAGATCACACGGTAGAGTTATTTATACAAATTTAAATATATAAATTTCATTTATTGTTATTCT
39509621 ACTTAAAGG
66 ACTTAAAGG
* * * *
39509630 AATAGATGACTCGGTAGAGTTATTTATACAAATTTGAATATATAAGTTTCATTTATTGTTATTCT
1 AATAGATCACACGGTAGAGTTATTTATACAAATTTAAATATATAAATTTCATTTATTGTTATTCT
39509695 ACTTAAAG
66 ACTTAAAG
39509703 TAGTAAAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.41
Consensus pattern (74 bp):
AATAGATCACACGGTAGAGTTATTTATACAAATTTAAATATATAAATTTCATTTATTGTTATTCT
ACTTAAAGG
Found at i:39511040 original size:13 final size:14
Alignment explanation
Indices: 39511017--39511045 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
39511007 AAGATACACC
39511017 AAGATAATAAAAAA
1 AAGATAATAAAAAA
39511031 AAGA-AATAAAAAA
1 AAGATAATAAAAAA
39511044 AA
1 AA
39511046 TCAATATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (14 bp):
AAGATAATAAAAAA
Found at i:39511111 original size:11 final size:11
Alignment explanation
Indices: 39511095--39511126 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
39511085 ATACACGAAT
39511095 TCAAAATAGAC
1 TCAAAATAGAC
39511106 TCAAAATAGAC
1 TCAAAATAGAC
39511117 TCAAAATAGA
1 TCAAAATAGA
39511127 ATTAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.19
Consensus pattern (11 bp):
TCAAAATAGAC
Found at i:39511133 original size:11 final size:11
Alignment explanation
Indices: 39511095--39511135 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
39511085 ATACACGAAT
*
39511095 TCAAAATAGAC
1 TCAAAATAGAA
*
39511106 TCAAAATAGAC
1 TCAAAATAGAA
39511117 TCAAAATAGAA
1 TCAAAATAGAA
*
39511128 TTAAAATA
1 TCAAAATA
39511136 AGCATTGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.59, C:0.12, G:0.07, T:0.22
Consensus pattern (11 bp):
TCAAAATAGAA
Found at i:39512540 original size:15 final size:15
Alignment explanation
Indices: 39512520--39512550 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39512510 GATCCCCAAT
39512520 ACTTCAATCTGCCCC
1 ACTTCAATCTGCCCC
*
39512535 ACTTCAGTCTGCCCC
1 ACTTCAATCTGCCCC
39512550 A
1 A
39512551 TTGCAATTTT
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:0.19, C:0.45, G:0.10, T:0.26
Consensus pattern (15 bp):
ACTTCAATCTGCCCC
Found at i:39514953 original size:40 final size:40
Alignment explanation
Indices: 39514902--39515127 Score: 425
Period size: 40 Copynumber: 5.7 Consensus size: 40
39514892 CATTTGAATG
39514902 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAT
39514942 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAT
39514982 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAT
39515022 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAT
*
39515062 ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAT
* *
39515102 ATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATCCGGGCTAAGACCCGAAGGCAA
39515128 ATGTGTTTGC
Statistics
Matches: 183, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 183 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGAT
Found at i:39516877 original size:217 final size:218
Alignment explanation
Indices: 39516502--39516952 Score: 706
Period size: 217 Copynumber: 2.1 Consensus size: 218
39516492 GGGTGTTACA
* *
39516502 TAACTTCAGGGAGATAAGACTAGATACGATTTGCTCTCTGCAACTTCAAAGAGATAAGATCTGTC
1 TAACTTCAAGGAGATAAGACTAGATACGATCTGCTCTCTGCAACTTCAAAGAGATAAGATCTGTC
* * *
39516567 ATTTTAATCCGCTTTATTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCA
66 ATTTTAATCCACTTCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCA
*
39516632 ACTTCAGGGAGATAAGATTCACCATCTTCAGTCTGCCCCACTGCAACTTTAGGAGGATAAAACCT
131 ACTTCAGGGAGATAAGATTCACCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAAACCT
* * * **
39516697 GCTTTC-TCAGTCTGCTCCGTTG
196 GCTATCTTCAATCCGCTCCACTG
* *
39516719 TAACTTCAATGAGATAAGACTAGATACGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTC
1 TAACTTCAAGGAGATAAGACTAGATACGATCTGCTCTCTGCAACTTCAAAGAGATAAGATCTGTC
* *
39516784 ATTTTAATCCACTTCGCTGTAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCA
66 ATTTTAATCCACTTCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCA
* * * * *
39516849 ACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCCCATTGCAACTTCAGGGGGATAAGACTT
131 ACTTCAGGGAGATAAGATTCACCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAAACCT
39516914 GCTATCTTCAATCCGCTCCACTG
196 GCTATCTTCAATCCGCTCCACTG
*
39516937 TAACTTCAGGGAGATA
1 TAACTTCAAGGAGATA
39516953 GAATTTGTGA
Statistics
Matches: 211, Mismatches: 22, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
217 185 0.88
218 26 0.12
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (218 bp):
TAACTTCAAGGAGATAAGACTAGATACGATCTGCTCTCTGCAACTTCAAAGAGATAAGATCTGTC
ATTTTAATCCACTTCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCA
ACTTCAGGGAGATAAGATTCACCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAAACCT
GCTATCTTCAATCCGCTCCACTG
Found at i:39516899 original size:45 final size:45
Alignment explanation
Indices: 39516616--39516952 Score: 198
Period size: 45 Copynumber: 7.7 Consensus size: 45
39516606 TATTGGCTTT
*
39516616 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCACCATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCCATCTTC
* * * * * **
39516661 AGTCTGCCCCACTGCAACTTTA-GGAGGATAAAACCTGCTTTC-TC
1 AATCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCCATCTTC
* ** * ** * *
39516705 AGTCTGCTCCGTTGTAACTTCAATGAGATAAGACTAG--A--TAC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTC
* * * * *
39516746 GATCTGCT-CTCTGCAACTTCAGAGAGATAAGA-TCTGTCAT-TTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TGCCATCTTC
** * * * * * *
39516789 AATCCACTTCGCTGTAACTTCAGGGAGATAGGATTATTGGC-T-TT-
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA--CTTGCCATCTTC
39516833 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCCATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCCATCTTC
* * * * *
39516878 AGTCTGCCCCATTGCAACTTCAGGGGGATAAGACTTGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTC
* *
39516923 AATCCGCTCCACTGTAACTTCAGGGAGATA
1 AATCTGCTCCACTGCAACTTCAGGGAGATA
39516953 GAATTTGTGA
Statistics
Matches: 220, Mismatches: 55, Indels: 34
0.71 0.18 0.11
Matches are distributed among these distances:
39 1 0.00
40 20 0.09
41 9 0.04
42 3 0.01
43 7 0.03
44 79 0.36
45 94 0.43
46 6 0.03
47 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTC
Found at i:39525385 original size:15 final size:15
Alignment explanation
Indices: 39525344--39525396 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
39525334 AACTAATACA
39525344 AATAATAAT-ACTAAT
1 AATAATAATAAC-AAT
* * *
39525359 AATTATAGTAACATT
1 AATAATAATAACAAT
*
39525374 AATAATAATAACAAC
1 AATAATAATAACAAT
39525389 AATAATAA
1 AATAATAA
39525397 AAATAGTTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
15 28 0.93
16 2 0.07
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (15 bp):
AATAATAATAACAAT
Found at i:39529026 original size:32 final size:32
Alignment explanation
Indices: 39528985--39529048 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
39528975 AGCCTCTTGG
*
39528985 AATTTTCTTTCCCACCTATTGGCTTTGCTTCT
1 AATTTTCTTTCCCACCTATCGGCTTTGCTTCT
39529017 AATTTTCTTTCCCACCTATCGGCTTTGCTTCT
1 AATTTTCTTTCCCACCTATCGGCTTTGCTTCT
39529049 TTCTTCTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.12, C:0.30, G:0.09, T:0.48
Consensus pattern (32 bp):
AATTTTCTTTCCCACCTATCGGCTTTGCTTCT
Found at i:39532507 original size:34 final size:32
Alignment explanation
Indices: 39532461--39532527 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 32
39532451 TATAAGTAAG
39532461 TTTTTTTTAAAAAGAAATAAATTACATATTAA
1 TTTTTTTTAAAAAGAAATAAATTACATATTAA
39532493 TTTTTTTTAAAAAAAGAAATAAATTACATATTAA
1 TTTTTTTT--AAAAAGAAATAAATTACATATTAA
39532527 T
1 T
39532528 AAAATTGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 8 0.24
34 25 0.76
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (32 bp):
TTTTTTTTAAAAAGAAATAAATTACATATTAA
Found at i:39534202 original size:26 final size:26
Alignment explanation
Indices: 39534173--39534223 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
39534163 TTATTGAATT
* *
39534173 TATTT-ATTTGTTTTATTTGGTTTTTA
1 TATTTGATTTATTTTAATT-GTTTTTA
39534199 TATTTGATTTATTTTAATTGTTTTT
1 TATTTGATTTATTTTAATTGTTTTT
39534224 GGGTCGAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.73
Consensus pattern (26 bp):
TATTTGATTTATTTTAATTGTTTTTA
Found at i:39537309 original size:40 final size:39
Alignment explanation
Indices: 39537247--39537329 Score: 105
Period size: 41 Copynumber: 2.1 Consensus size: 39
39537237 CAATTTAACT
* * *
39537247 GATGAGACACTGGGAGTTAATTTACTACTTCAGATTTATTC
1 GATGAGACACTGGGAG-AAATTTAATACTTC-GAATTATTC
39537288 GATGAGACACTGGTGA-AAATTTAATACTTCGAATTATTC
1 GATGAGACACTGG-GAGAAATTTAATACTTCGAATTATTC
39537327 GAT
1 GAT
39537330 AAGGCACTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 11 0.29
40 12 0.32
41 13 0.34
42 2 0.05
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (39 bp):
GATGAGACACTGGGAGAAATTTAATACTTCGAATTATTC
Found at i:39537726 original size:17 final size:18
Alignment explanation
Indices: 39537696--39537730 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
39537686 AAATGTTGTT
39537696 TTAAATATTCAATTGTGC
1 TTAAATATTCAATTGTGC
*
39537714 TTAAA-ATTTAATTGTGC
1 TTAAATATTCAATTGTGC
39537731 CTATTATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (18 bp):
TTAAATATTCAATTGTGC
Found at i:39541887 original size:17 final size:18
Alignment explanation
Indices: 39541855--39541889 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
39541845 AAATGTGGTT
39541855 TTAAATATTCAATTGTGC
1 TTAAATATTCAATTGTGC
*
39541873 TTAAA-ATTTAATTGTGC
1 TTAAATATTCAATTGTGC
39541890 CTATTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (18 bp):
TTAAATATTCAATTGTGC
Found at i:39543059 original size:17 final size:18
Alignment explanation
Indices: 39543027--39543061 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
39543017 AAATGTGGTT
39543027 TTAAATATTCAATTGTGC
1 TTAAATATTCAATTGTGC
*
39543045 TTAAA-ATTTAATTGTGC
1 TTAAATATTCAATTGTGC
39543062 CTATTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (18 bp):
TTAAATATTCAATTGTGC
Found at i:39544150 original size:17 final size:18
Alignment explanation
Indices: 39544122--39544156 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
39544112 AAATGTGGTT
39544122 TTAAATATTTAATTGTGC
1 TTAAATATTTAATTGTGC
39544140 TTAAA-ATTTAATTGTGC
1 TTAAATATTTAATTGTGC
39544157 CTATTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAAATATTTAATTGTGC
Found at i:39557055 original size:17 final size:18
Alignment explanation
Indices: 39557025--39557059 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
39557015 AAATATTGTT
39557025 TTAAATATTCAATTGTGC
1 TTAAATATTCAATTGTGC
*
39557043 TTAAA-ATTTAATTGTGC
1 TTAAATATTCAATTGTGC
39557060 CTATTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (18 bp):
TTAAATATTCAATTGTGC
Found at i:39560529 original size:14 final size:15
Alignment explanation
Indices: 39560506--39560546 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
39560496 TCAACCTTTA
39560506 TTTTAATTTTAT-AT
1 TTTTAATTTTATCAT
*
39560520 TTTTAGTTTTATCA-
1 TTTTAATTTTATCAT
39560534 TTTTAATGTTTAT
1 TTTTAAT-TTTAT
39560547 GAAGATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (15 bp):
TTTTAATTTTATCAT
Found at i:39560734 original size:35 final size:35
Alignment explanation
Indices: 39560602--39560734 Score: 131
Period size: 35 Copynumber: 3.8 Consensus size: 35
39560592 TTTAAATGAG
* * * * *
39560602 TATATCCCAATCTTTTTAAGGTTGCCTTAAATATA
1 TATATCCCAACCTTTTTAAGGTTGTCTTAGACAAA
* * * * *
39560637 TTTATCCCAACCTTTTTGAGGTTGCCTTAGACTAG
1 TATATCCCAACCTTTTTAAGGTTGTCTTAGACAAA
* *
39560672 TATATCTCAACCTTTTTAGGGTTGTCTTAGACAAA
1 TATATCCCAACCTTTTTAAGGTTGTCTTAGACAAA
* * *
39560707 TCTATCCCAACCTTTTTAAAGTCGTCTT
1 TATATCCCAACCTTTTTAAGGTTGTCTT
39560735 TGACTTGGGC
Statistics
Matches: 78, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 78 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (35 bp):
TATATCCCAACCTTTTTAAGGTTGTCTTAGACAAA
Found at i:39562826 original size:6 final size:6
Alignment explanation
Indices: 39562815--39562843 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
39562805 TAATAAAACA
39562815 AATGGG AATGGG AATGGG AATGGG AATGG
1 AATGGG AATGGG AATGGG AATGGG AATGG
39562844 TAGTGGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.48, T:0.17
Consensus pattern (6 bp):
AATGGG
Found at i:39565416 original size:29 final size:30
Alignment explanation
Indices: 39565350--39565416 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
39565340 AAATATATTT
*
39565350 TTAT-ATTTTTATAATTTTTAAAGGTTAAA
1 TTATAATTTTTATAATTTTTAAAGGTCAAA
* *
39565379 TTA-ATTTTTTATCATTTTTAAA-GTCAAA
1 TTATAATTTTTATAATTTTTAAAGGTCAAA
39565407 TTATAATTTT
1 TTATAATTTT
39565417 AGCGTTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 8 0.25
29 24 0.75
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (30 bp):
TTATAATTTTTATAATTTTTAAAGGTCAAA
Found at i:39569816 original size:5 final size:5
Alignment explanation
Indices: 39569806--39570172 Score: 734
Period size: 5 Copynumber: 73.4 Consensus size: 5
39569796 TAAATTTTAT
39569806 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
39569856 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
39569906 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
39569956 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
39570006 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
39570056 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
39570106 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
39570156 ATATA ATATA ATATA AT
1 ATATA ATATA ATATA AT
39570173 CAATGAATAA
Statistics
Matches: 362, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 362 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:39571470 original size:34 final size:34
Alignment explanation
Indices: 39571432--39571497 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
39571422 CGACGGTGCC
39571432 TTGGTGTGGTGTAATTATCGCTCTATTAAGCCTT
1 TTGGTGTGGTGTAATTATCGCTCTATTAAGCCTT
* * *
39571466 TTGGTGTGGTGTAGTTATCGCTTTATTGAGCC
1 TTGGTGTGGTGTAATTATCGCTCTATTAAGCC
39571498 ATTGGATGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.15, C:0.14, G:0.27, T:0.44
Consensus pattern (34 bp):
TTGGTGTGGTGTAATTATCGCTCTATTAAGCCTT
Found at i:39571508 original size:34 final size:34
Alignment explanation
Indices: 39571432--39571509 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
39571422 CGACGGTGCC
*
39571432 TTGGTGTGGTGTAATTATCGCTCTATTAAGCCTT
1 TTGGTGTGGTGTAATTATCGCTCTATTAAGCCTA
* * *
39571466 TTGGTGTGGTGTAGTTATCGCTTTATTGAGCC-A
1 TTGGTGTGGTGTAATTATCGCTCTATTAAGCCTA
39571499 TTGGATGTGGT
1 TTGG-TGTGGT
39571510 CTATTGAGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 4 0.10
34 35 0.90
ACGTcount: A:0.15, C:0.12, G:0.29, T:0.44
Consensus pattern (34 bp):
TTGGTGTGGTGTAATTATCGCTCTATTAAGCCTA
Found at i:39580903 original size:6 final size:6
Alignment explanation
Indices: 39580892--39580919 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39580882 TTTTCGTTAC
39580892 CAGTAT CAGTAT CAGTAT CAGTAT CAGT
1 CAGTAT CAGTAT CAGTAT CAGTAT CAGT
39580920 TTAGGCCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (6 bp):
CAGTAT
Found at i:39581476 original size:17 final size:18
Alignment explanation
Indices: 39581441--39581478 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
39581431 GACTCATGTT
39581441 ACATGCCCATGTGGGCCC
1 ACATGCCCATGTGGGCCC
*
39581459 ACATGCCCGTGT-GGCCC
1 ACATGCCCATGTGGGCCC
39581476 ACA
1 ACA
39581479 CGACCCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.18, C:0.39, G:0.26, T:0.16
Consensus pattern (18 bp):
ACATGCCCATGTGGGCCC
Found at i:39586011 original size:20 final size:21
Alignment explanation
Indices: 39585976--39586017 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39585966 CCCCTTCAGT
* *
39585976 TTAAAAATTTTCATATTTTTC
1 TTAAAAATTCTCATATGTTTC
39585997 TTAAAAATTCT-ATATGTTTC
1 TTAAAAATTCTCATATGTTTC
39586017 T
1 T
39586018 GATTTAGTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (21 bp):
TTAAAAATTCTCATATGTTTC
Found at i:39592651 original size:34 final size:34
Alignment explanation
Indices: 39592609--39592677 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
39592599 ACATGGCTAT
39592609 ACACACTTTGATCATCAACCACTCATACATTTCC
1 ACACACTTTGATCATCAACCACTCATACATTTCC
39592643 ACACACTTTGATCATCAACCACTCATACATTTCC
1 ACACACTTTGATCATCAACCACTCATACATTTCC
39592677 A
1 A
39592678 TACTTCCATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (34 bp):
ACACACTTTGATCATCAACCACTCATACATTTCC
Found at i:39596208 original size:26 final size:26
Alignment explanation
Indices: 39596132--39596200 Score: 102
Period size: 26 Copynumber: 2.7 Consensus size: 26
39596122 CCCAACAAAA
*
39596132 TTTTGACAATTTTACCCATGGTAAAG
1 TTTTGACGATTTTACCCATGGTAAAG
* * *
39596158 TTTTGATGATTTTACACGTGGTAAAG
1 TTTTGACGATTTTACCCATGGTAAAG
39596184 TTTTGACGATTTTACCC
1 TTTTGACGATTTTACCC
39596201 TTAGTAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.42
Consensus pattern (26 bp):
TTTTGACGATTTTACCCATGGTAAAG
Found at i:39610776 original size:19 final size:20
Alignment explanation
Indices: 39610746--39610793 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
39610736 TTGCTGTTAT
*
39610746 TATTTCTTTATTTTTGTTTA
1 TATTTCTTTATTTTGGTTTA
*
39610766 TATTT-TTTATTTTGGTTTT
1 TATTTCTTTATTTTGGTTTA
*
39610785 TTTTTCTTT
1 TATTTCTTT
39610794 CAGTCATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.10, C:0.04, G:0.06, T:0.79
Consensus pattern (20 bp):
TATTTCTTTATTTTGGTTTA
Found at i:39611032 original size:3 final size:3
Alignment explanation
Indices: 39611024--39611086 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
39611014 ACTGTTTCTC
* * *
39611024 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT TTT GTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39611072 ATTT ATT -TT ATT ATT
1 A-TT ATT ATT ATT ATT
39611087 TATTTCATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:39616664 original size:46 final size:46
Alignment explanation
Indices: 39616593--39616890 Score: 234
Period size: 49 Copynumber: 6.4 Consensus size: 46
39616583 CATATCAAAC
* *
39616593 CTTATCTCCCTGAAGTTGCAGTGGAACAGGTTAAAAATAAAACAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAACAAAACAAT
* * * *
39616639 CTTATCTCCCTGAAGTTGCAATGGAACAGATTGAAGACAAGCTACATAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAACAA--AACA-AT
**
39616688 CTTATCTCCCTGAAGTTGCAGT-GAAGCAGATTAAAGCCACAAAC---
1 CTTATCTCCCTGAAGTTGCAGTGGAA-CAGATTAAAAACA-AAACAAT
* * * *
39616732 CTTATCTCCCTGAAATTGCAGTGGAACAGGTTAAAAATAAACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAACAAAACAAT
* * * ** * *
39616778 CTTATCTCCCTGAAGTTGTAGTGGAGCAAATTGAAGATGGGCTACA-AAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATT-AA-A--AACAAAACAAT
* * **
39616827 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCACAAAC---
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAACA-AAACAAT
*
39616871 CTTATCTCCTTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCA
39616891 TTAGAGCAGG
Statistics
Matches: 202, Mismatches: 35, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
43 3 0.01
44 48 0.24
45 5 0.02
46 64 0.32
47 3 0.01
48 11 0.05
49 66 0.33
50 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (46 bp):
CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAACAAAACAAT
Found at i:39616704 original size:49 final size:48
Alignment explanation
Indices: 39616593--39616861 Score: 252
Period size: 46 Copynumber: 5.7 Consensus size: 48
39616583 CATATCAAAC
* *
39616593 CTTATCTCCCTGAAGTTGCAGTGGAACAGGTTAAAAATAA--AACAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAATAAGCTACAAT
* * * *
39616639 CTTATCTCCCTGAAGTTGCAATGGAACAGATTGAAGACAAGCTACATAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAATAAGCTACA-AT
* *
39616688 CTTATCTCCCTGAAGTTGCAGT-GAAGCAGATT----A-AAGCCACAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAA-CAGATTAAAAATAAGCTAC-AAT
* * *
39616732 CTTATCTCCCTGAAATTGCAGTGGAACAGGTTAAAAATAAAC--CAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAATAAGCTACAAT
* * * * * **
39616778 CTTATCTCCCTGAAGTTGTAGTGGAGCAAATTGAAGATGGGCTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAATAAGCTAC-AAT
* *
39616827 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAA
39616862 GCCACAAACC
Statistics
Matches: 182, Mismatches: 27, Indels: 25
0.78 0.12 0.11
Matches are distributed among these distances:
44 33 0.18
45 5 0.03
46 69 0.38
47 1 0.01
48 8 0.04
49 66 0.36
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (48 bp):
CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAATAAGCTACAAT
Found at i:39616722 original size:95 final size:90
Alignment explanation
Indices: 39616593--39616805 Score: 232
Period size: 93 Copynumber: 2.3 Consensus size: 90
39616583 CATATCAAAC
* * *
39616593 CTTATCTCCCTGAAGTTGCAGTGGAA-CAGGTTAAAAATA-AAACAATCTTATCTCCCTGAAGTT
1 CTTATCTCCCTGAAGTTGCAGT-GAAGCAGATTAAAAACACAAAC---CTTATCTCCCTGAAATT
* * *
39616656 GCAATGGAACAGATTGAAGACAAGCTACATAT
62 GCAATGGAACAGATTAAAAACAAAC--CA-AT
** *
39616688 CTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCACAAACCTTATCTCCCTGAAATTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAAACACAAACCTTATCTCCCTGAAATTGCAA
* *
39616753 TGGAACAGGTTAAAAATAAACCAAT
66 TGGAACAGATTAAAAACAAACCAAT
* *
39616778 CTTATCTCCCTGAAGTTGTAGTGGAGCA
1 CTTATCTCCCTGAAGTTGCAGTGAAGCA
39616806 AATTGAAGAT
Statistics
Matches: 103, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
90 28 0.27
91 2 0.02
93 35 0.34
94 3 0.03
95 31 0.30
96 4 0.04
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (90 bp):
CTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAAACACAAACCTTATCTCCCTGAAATTGCAA
TGGAACAGATTAAAAACAAACCAAT
Found at i:39616751 original size:44 final size:45
Alignment explanation
Indices: 39616588--39616994 Score: 224
Period size: 44 Copynumber: 8.9 Consensus size: 45
39616578 CAGATCATAT
* ***
39616588 CAAACCTTATCTCCCTGAAGTTGCAGTGGAA-CAGGTTAAAAATAA
1 CAAACCTTATCTCCCTGAAGTTGCAGT-GAAGCAGATTAAAAGCCA
* * * *
39616633 AACAATCTTATCTCCCTGAAGTTGCAATGGAA-CAGATTGAAGACAAGCTA
1 CA-AACCTTATCTCCCTGAAGTTGCAGT-GAAGCAGATT--A-A-AAGCCA
* *
39616683 CATATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATT-AAAGCCA
1 CAAACCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAAGCCA
* * ***
39616727 CAAACCTTATCTCCCTGAAATTGCAGTGGAA-CAGGTTAAAAATAAA
1 CAAACCTTATCTCCCTGAAGTTGCAGT-GAAGCAGATT-AAAAGCCA
* * * * * * *
39616773 CCAATCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTGAAGATGGGCTA
1 CAAACCTTATCTCCCTGAAGTTGCAGTGAAGCAGATT-AA-A--AGCCA
* * *
39616822 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAGCCA
1 CAAACCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAAGCCA
* * * * **
39616866 CAAACCTTATCTCCTTGAAGTTGCA-TTAGAGCAGGTT-GAAGATA
1 CAAACCTTATCTCCCTGAAGTTGCAGTGA-AGCAGATTAAAAGCCA
* * * * *
39616910 CCAATCTTATCTCCCT-ATAGTTTCAGT-AGAGCATATT-AAAGCTA
1 CAAACCTTATCTCCCTGA-AGTTGCAGTGA-AGCAGATTAAAAGCCA
* * * *
39616954 CTAA-TTCTATCTCCTTGAAGTTGCAGTGCAGCAGATTAAAA
1 CAAACCT-TATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAA
39616995 CGATGAATCC
Statistics
Matches: 283, Mismatches: 59, Indels: 40
0.74 0.15 0.10
Matches are distributed among these distances:
43 3 0.01
44 128 0.45
45 12 0.04
46 66 0.23
47 2 0.01
48 4 0.01
49 64 0.23
50 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (45 bp):
CAAACCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAAGCCA
Found at i:39616754 original size:139 final size:139
Alignment explanation
Indices: 39616588--39616993 Score: 522
Period size: 139 Copynumber: 3.0 Consensus size: 139
39616578 CAGATCATAT
*
39616588 CAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGGTTAAAAATAAAACAATCTTATCTCCCTGAA
1 CAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGGTTAAAAATAAACCAATCTTATCTCCCTGAA
* * *
39616653 GTTGCAATGGAACAGATTGAAGACAAGCTACATATCTTATCTCCCTGAAGTTGCAGTGAAGCAGA
66 GTTGCAGTGGAGCAAATTGAAGACAAGCTACATATCTTATCTCCCTGAAGTTGCAGTGAAGCAGA
39616718 TTAAAGCCA
131 TTAAAGCCA
*
39616727 CAAACCTTATCTCCCTGAAATTGCAGTGGAACAGGTTAAAAATAAACCAATCTTATCTCCCTGAA
1 CAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGGTTAAAAATAAACCAATCTTATCTCCCTGAA
* *** * * *
39616792 GTTGTAGTGGAGCAAATTGAAGATGGGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGA
66 GTTGCAGTGGAGCAAATTGAAGACAAGCTACATATCTTATCTCCCTGAAGTTGCAGTGAAGCAGA
39616857 TTAAAGCCA
131 TTAAAGCCA
* * * * * *
39616866 CAAACCTTATCTCCTTGAAGTTGCATTAGAGCAGGTTGAAGAT--ACCAATCTTATCTCCCT-AT
1 CAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGGTTAAAAATAAACCAATCTTATCTCCCTGA-
* * * * * * *
39616928 AGTTTCAGTAGAGCATATTAAAG-CTA-CTA-AT-TC-TATCTCCTTGAAGTTGCAGTGCAGCAG
65 AGTTGCAGTGGAGCAAATTGAAGACAAGCTACATATCTTATCTCCCTGAAGTTGCAGTGAAGCAG
39616988 ATTAAA
130 ATTAAA
39616994 ACGATGAATC
Statistics
Matches: 235, Mismatches: 31, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
132 30 0.13
133 2 0.01
134 1 0.00
135 3 0.01
136 1 0.00
137 35 0.15
139 163 0.69
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (139 bp):
CAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGGTTAAAAATAAACCAATCTTATCTCCCTGAA
GTTGCAGTGGAGCAAATTGAAGACAAGCTACATATCTTATCTCCCTGAAGTTGCAGTGAAGCAGA
TTAAAGCCA
Found at i:39616838 original size:95 final size:92
Alignment explanation
Indices: 39616636--39616861 Score: 258
Period size: 95 Copynumber: 2.4 Consensus size: 92
39616626 AAAATAAAAC
* * * *
39616636 AATCTTATCTCCCTGAAGTTGCAATGGAACAGATTGAAGACAAGCTACATATCTTATCTCCCTGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAACAAAC-ACATATCTTATCTCCCTGA
*
39616701 AGTTGCAGTGAAGCAGATTAAAGCCACA
65 AGTTGCAGTGAAGCAAATTAAAGCCACA
* * * *
39616729 AACCTTATCTCCCTGAAATTGCAGTGGAACAGGTTAAAAATAAAC-CA-ATCTTATCTCCCTGAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAACAAACACATATCTTATCTCCCTGAA
* * *
39616792 GTTGTAGTGGAGCAAATTGAAGATGGGCTACA
66 GTTGCAGTGAAGCAAATT-AA-A---GCCACA
* *
39616824 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAA
39616862 GCCACAAACC
Statistics
Matches: 111, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
90 31 0.28
91 4 0.04
92 1 0.01
93 37 0.33
95 38 0.34
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (92 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAACAAACACATATCTTATCTCCCTGAA
GTTGCAGTGAAGCAAATTAAAGCCACA
Found at i:39616987 original size:88 final size:88
Alignment explanation
Indices: 39616549--39616980 Score: 228
Period size: 93 Copynumber: 4.8 Consensus size: 88
39616539 ATAAATTACA
* * * * * * *
39616549 AATCTTATATCTCTGAAGTTGCAGTAGAGCAGATCATA---TCAAACCTTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTACAGTAGAGCAGATTAAAGCCACAAACCTTATCTCCTTGAAGTTG
* * * * *
39616611 CAGTGGAACAGGTTAAAAATAAAAC
66 CAGTAGAGCAGGTTGAAGAT--ACC
* * * * * * * *
39616636 AATCTTATCTCCCTGAAGTTGCAATGGAACAGATTGAAGACAAGCTACATATCTTATCTCCCTGA
1 AATCTTATCTCCCTGAAGTTACAGTAGAGCAGATT----A-AAGCCACAAACCTTATCTCCTTGA
* * ** *
39616701 AGTTGCAGT-GAAGCAGATTAAAGCCACA
61 AGTTGCAGTAG-AGCAGGTTGAAGATACC
* * * * * * *** * * *
39616729 AACCTTATCTCCCTGAAATTGCAGTGGAACAGGTTAAAAATAAACCAATCTTATCTCCCTGAAGT
1 AATCTTATCTCCCTGAAGTTACAGTAGAGCAGATT--AAAGCCACAAACCTTATCTCCTTGAAGT
* * ** *
39616794 TGTAGTGGAGCAAATTGAAGATGGGCTACA
64 TGCAGTAGAGCAGGTTGAAGA-----TACC
*
39616824 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCACAAACCTTATCTCCTTGAAGTTG
1 AATCTTATCTCCCTGAAGTTACAGTAGAGCAGATTAAAGCCACAAACCTTATCTCCTTGAAGTTG
*
39616889 CATTAGAGCAGGTTGAAGATACC
66 CAGTAGAGCAGGTTGAAGATACC
* * * * *
39616912 AATCTTATCTCCCT-ATAGTTTCAGTAGAGCATATTAAAGCTACTAA-TTCTATCTCCTTGAAGT
1 AATCTTATCTCCCTGA-AGTTACAGTAGAGCAGATTAAAGCCACAAACCT-TATCTCCTTGAAGT
39616975 TGCAGT
64 TGCAGT
39616981 GCAGCAGATT
Statistics
Matches: 272, Mismatches: 56, Indels: 33
0.75 0.16 0.09
Matches are distributed among these distances:
87 31 0.11
88 61 0.22
90 37 0.14
91 4 0.01
92 1 0.00
93 70 0.26
94 1 0.00
95 67 0.25
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (88 bp):
AATCTTATCTCCCTGAAGTTACAGTAGAGCAGATTAAAGCCACAAACCTTATCTCCTTGAAGTTG
CAGTAGAGCAGGTTGAAGATACC
Found at i:39627481 original size:6 final size:6
Alignment explanation
Indices: 39627470--39627500 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
39627460 AATTTTCTGA
39627470 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC C
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC C
39627501 GCTACATCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CTCTCC
Found at i:39633430 original size:13 final size:14
Alignment explanation
Indices: 39633399--39633430 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
39633389 TAGCCATTTT
39633399 TATTTTTCTTTTAA
1 TATTTTTCTTTTAA
39633413 TATTTTTCTTTTAA
1 TATTTTTCTTTTAA
39633427 -ATTT
1 TATTT
39633431 AATTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTTTTCTTTTAA
Found at i:39636543 original size:22 final size:23
Alignment explanation
Indices: 39636500--39636557 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
39636490 CTGAGTTGGT
*
39636500 AAACGGTAAGCTCTATCAAGCT-
1 AAACGGTAAGCTCCATCAAGCTA
* *
39636522 GAACGGTAAGCTCCGT-AGAGCTA
1 AAACGGTAAGCTCCATCA-AGCTA
39636545 AAACGGTAAGCTC
1 AAACGGTAAGCTC
39636558 ATAAGAGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.03
22 17 0.57
23 12 0.40
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.19
Consensus pattern (23 bp):
AAACGGTAAGCTCCATCAAGCTA
Found at i:39636564 original size:23 final size:22
Alignment explanation
Indices: 39636499--39636589 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 22
39636489 CCTGAGTTGG
*
39636499 TAAACGGTAAGCTCTATCA-AGC
1 TAAACGGTAAGCTC-ATAAGAGC
* *
39636521 TGAACGGTAAGCTCCGT-AGAGC
1 TAAACGGTAAGCT-CATAAGAGC
*
39636543 TAAAACGGTAAGCTCATAAGAGT
1 T-AAACGGTAAGCTCATAAGAGC
* *
39636566 TGAAACGATAAGCTCATACGAGC
1 T-AAACGGTAAGCTCATAAGAGC
39636589 T
1 T
39636590 GTGGTGAGTC
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.02
22 19 0.34
23 36 0.64
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (22 bp):
TAAACGGTAAGCTCATAAGAGC
Found at i:39639086 original size:17 final size:17
Alignment explanation
Indices: 39639052--39639085 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
39639042 GACCATGTTA
39639052 TAATTTCTTTGATATTT
1 TAATTTCTTTGATATTT
*
39639069 TAATTT-TTTTATATTT
1 TAATTTCTTTGATATTT
39639085 T
1 T
39639086 TCAAAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TAATTTCTTTGATATTT
Found at i:39642355 original size:89 final size:88
Alignment explanation
Indices: 39642169--39642365 Score: 216
Period size: 89 Copynumber: 2.2 Consensus size: 88
39642159 TCTGTTCCAT
* * * ** ** *
39642169 TGCAACATCAAGGTGATAAGACTGGTGTCTTCGATCTGCTTCTCTGCTGGTACAGGAAGACAAGA
1 TGCAAC-TCAAGGAGATAAGACTGCTATCTTCGATCTGCTTCGATGCCAGTACAGGAAAACAAGA
* ** * *
39642234 TCTGCTATCTTTAGTCTTCACCGC
65 TCTACTATCTTTAACCTACACCAC
39642258 TGCAACTCAAGGAGATAAGACTTGCTATCTTCGATCTGCTTCGATGCCAGTACAGGAAAACAAGA
1 TGCAACTCAAGGAGATAAGAC-TGCTATCTTCGATCTGCTTCGATGCCAGTACAGGAAAACAAGA
*
39642323 TCTACTAT-TTTCAACCTACTCCAC
65 TCTACTATCTTT-AACCTACACCAC
* *
39642347 TGCTACTCAGGGAGATAAG
1 TGCAACTCAAGGAGATAAG
39642366 GCTTTATAGT
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
88 17 0.19
89 73 0.81
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (88 bp):
TGCAACTCAAGGAGATAAGACTGCTATCTTCGATCTGCTTCGATGCCAGTACAGGAAAACAAGAT
CTACTATCTTTAACCTACACCAC
Found at i:39649905 original size:3 final size:3
Alignment explanation
Indices: 39649897--39649934 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
39649887 ATAAGGAAAC
39649897 AAT AAT AAT AA- AAT AAT AAT AAT AGATT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT A
39649935 TTAAACTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 26 0.81
4 2 0.06
5 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:39649911 original size:11 final size:12
Alignment explanation
Indices: 39649897--39649934 Score: 51
Period size: 11 Copynumber: 3.1 Consensus size: 12
39649887 ATAAGGAAAC
39649897 AATAATAATAA-
1 AATAATAATAAT
39649908 AATAATAATAAT
1 AATAATAATAAT
39649920 AGATTAATAATAAT
1 A-A-TAATAATAAT
39649934 A
1 A
39649935 TTAAACTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.46
12 1 0.04
13 1 0.04
14 11 0.46
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
AATAATAATAAT
Found at i:39649914 original size:14 final size:14
Alignment explanation
Indices: 39649897--39649934 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
39649887 ATAAGGAAAC
39649897 AATAATAATAAAAT
1 AATAATAATAAAAT
* *
39649911 AATAATAATAGATT
1 AATAATAATAAAAT
39649925 AATAATAATA
1 AATAATAATA
39649935 TTAAACTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
AATAATAATAAAAT
Found at i:39653757 original size:30 final size:30
Alignment explanation
Indices: 39653723--39653785 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
39653713 ACATTTGAGG
*
39653723 TAGATTCTTAAGTATTATGTGACACAGGTT
1 TAGATTCTCAAGTATTATGTGACACAGGTT
39653753 TAGATTCTCAAGTATTATGTGACACAGGTT
1 TAGATTCTCAAGTATTATGTGACACAGGTT
39653783 TAG
1 TAG
39653786 CTCGGACTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (30 bp):
TAGATTCTCAAGTATTATGTGACACAGGTT
Found at i:39655698 original size:21 final size:21
Alignment explanation
Indices: 39655673--39655712 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
39655663 AGAAAAGGGC
39655673 TTAATCGTGTAAA-ATGAAAAT
1 TTAATCGT-TAAATATGAAAAT
*
39655694 TTAATGGTTAAATATGAAA
1 TTAATCGTTAAATATGAAA
39655713 TTGCCTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.35
Consensus pattern (21 bp):
TTAATCGTTAAATATGAAAAT
Done.