Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 109 of 345
Found at i:29283309 original size:29 final size:30
Alignment explanation
Indices: 29283277--29283333 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
29283267 TCAATTAAGT
29283277 CTCTAAACGAAAA-TT-GCAATCAATTGATC
1 CTCTAAAC-AAAAGTTAGCAATCAATTGATC
* *
29283306 CTCTAATCAAAAGTTAGTAATCAATTGA
1 CTCTAAACAAAAGTTAGCAATCAATTGA
29283334 GCCCTTGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 9 0.38
30 11 0.46
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.30
Consensus pattern (30 bp):
CTCTAAACAAAAGTTAGCAATCAATTGATC
Found at i:29288847 original size:10 final size:9
Alignment explanation
Indices: 29288824--29288883 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
29288814 TATTAAAAAT
29288824 ATTTTTATA
1 ATTTTTATA
29288833 ATTTTTATA
1 ATTTTTATA
* *
29288842 CCTTTTAATA
1 -ATTTTTATA
*
29288852 A--TTTCTA
1 ATTTTTATA
29288859 ATTTTTATA
1 ATTTTTATA
* *
29288868 TTTTTTAAA
1 ATTTTTATA
29288877 ATTTTTA
1 ATTTTTA
29288884 ATTTTTAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
7 5 0.13
9 27 0.69
10 7 0.18
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:29288864 original size:26 final size:25
Alignment explanation
Indices: 29288831--29288890 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 25
29288821 AATATTTTTA
29288831 TAATTTTTATACCTTTTAATAATTTC
1 TAATTTTTATACCTTTTAA-AATTTC
** *
29288857 TAATTTTTATATTTTTTAAAATTTT
1 TAATTTTTATACCTTTTAAAATTTC
29288882 TAATTTTTA
1 TAATTTTTA
29288891 AAAGATTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (25 bp):
TAATTTTTATACCTTTTAAAATTTC
Found at i:29288890 original size:16 final size:18
Alignment explanation
Indices: 29288858--29288893 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
29288848 AATAATTTCT
29288858 AATTTTTATATTTTTTAA
1 AATTTTTATATTTTTTAA
29288876 AATTTTTA-A-TTTTTAA
1 AATTTTTATATTTTTTAA
29288892 AA
1 AA
29288894 GATTAATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 1 0.06
18 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTTTATATTTTTTAA
Found at i:29291548 original size:39 final size:40
Alignment explanation
Indices: 29291439--29291573 Score: 227
Period size: 40 Copynumber: 3.4 Consensus size: 40
29291429 TCCAATTTCT
29291439 AGCACAAAGCCTGCGGGATTTAACCCGGATATCTATTACC
1 AGCACAAAGCCTGCGGGATTTAACCCGGATATCTATTACC
* *
29291479 AGCACAAAGACTGCGGGATTTAGCCCGGATATCTATTACC
1 AGCACAAAGCCTGCGGGATTTAACCCGGATATCTATTACC
* *
29291519 AGCAC-AAGCCTGCCGGATTTAACCCGGATATCTATTGCC
1 AGCACAAAGCCTGCGGGATTTAACCCGGATATCTATTACC
29291558 AGCACAAAGCCTGCGG
1 AGCACAAAGCCTGCGG
29291574 ACTATAAGTC
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
39 35 0.40
40 52 0.60
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (40 bp):
AGCACAAAGCCTGCGGGATTTAACCCGGATATCTATTACC
Found at i:29294272 original size:23 final size:21
Alignment explanation
Indices: 29294246--29294297 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
29294236 AAAACGATAA
29294246 AAATATTATTTATATCAAACAGT
1 AAATATTATTT-T-TCAAACAGT
** *
29294269 AAATGGTATTTTTCAAACTGT
1 AAATATTATTTTTCAAACAGT
29294290 AAATATTA
1 AAATATTA
29294298 ACTTATTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 14 0.58
22 1 0.04
23 9 0.38
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (21 bp):
AAATATTATTTTTCAAACAGT
Found at i:29299613 original size:57 final size:58
Alignment explanation
Indices: 29299472--29299617 Score: 136
Period size: 57 Copynumber: 2.5 Consensus size: 58
29299462 AGCTCGCAAC
* * *
29299472 TATTCTCATATTAG-GGTTTGAACTTTTTTCTAGTCCAAGTTAGCCCCTAAACTTAATAAT
1 TATTCTCACATT-GCGGCTTGAAC-TTTTT-TAGTCCAAGTTAGCCCCTAAACTTAACAAT
* * * * * *
29299532 TGTTCTCACATTGCGGC-CGAAACTTTTTT-GTTCAAGTTAGGCCTTAAACTTGACAAT
1 TATTCTCACATTGCGGCTTG-AACTTTTTTAGTCCAAGTTAGCCCCTAAACTTAACAAT
* *
29299589 TATTCTCACGTTGGGGCTTGAACTTTTTT
1 TATTCTCACATTGCGGCTTGAACTTTTTT
29299618 TAACCAAGTC
Statistics
Matches: 70, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
57 46 0.66
58 2 0.03
59 7 0.10
60 15 0.21
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (58 bp):
TATTCTCACATTGCGGCTTGAACTTTTTTAGTCCAAGTTAGCCCCTAAACTTAACAAT
Found at i:29299724 original size:30 final size:30
Alignment explanation
Indices: 29299657--29299725 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
29299647 AAAACCTTAA
*
29299657 AGTTCAAGCCTAATATGGGAACAATTGCTT
1 AGTTTAAGCCTAATATGGGAACAATTGCTT
**
29299687 AACTTAAGCCTTAATATGGGAACAATTGC-T
1 AGTTTAAGCC-TAATATGGGAACAATTGCTT
29299717 AGTTTAAGC
1 AGTTTAAGC
29299726 TCCAACATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (30 bp):
AGTTTAAGCCTAATATGGGAACAATTGCTT
Found at i:29301707 original size:2 final size:2
Alignment explanation
Indices: 29301696--29301728 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
29301686 GCATACACCT
29301696 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29301729 GCAACTGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:29311224 original size:13 final size:14
Alignment explanation
Indices: 29311194--29311227 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
29311184 AATCAAATGG
29311194 AATTAATTTTGATTC
1 AATTAATTTT-ATTC
29311209 AATTAATTTT-TTC
1 AATTAATTTTATTC
29311222 AATTAA
1 AATTAA
29311228 ACGAAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
15 10 0.53
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (14 bp):
AATTAATTTTATTC
Found at i:29313051 original size:2 final size:2
Alignment explanation
Indices: 29313044--29313076 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29313034 AAAATTCTAT
29313044 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29313077 TTGATGTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29370074 original size:21 final size:21
Alignment explanation
Indices: 29370050--29370093 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
29370040 TACGGTACGT
29370050 ATACACTGTGTTTACAATTTG
1 ATACACTGTGTTTACAATTTG
29370071 ATACACTGTGTTTACAATTTG
1 ATACACTGTGTTTACAATTTG
29370092 AT
1 AT
29370094 TCTAGTACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (21 bp):
ATACACTGTGTTTACAATTTG
Found at i:29371020 original size:17 final size:19
Alignment explanation
Indices: 29370995--29371032 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
29370985 AATAAATAAT
*
29370995 AATATATAAA-ATCTT-AA
1 AATACATAAACATCTTCAA
29371012 AATACATAAACATCTTCAA
1 AATACATAAACATCTTCAA
29371031 AA
1 AA
29371033 AAATATAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 5 0.28
19 4 0.22
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (19 bp):
AATACATAAACATCTTCAA
Found at i:29371042 original size:19 final size:19
Alignment explanation
Indices: 29370992--29371042 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
29370982 GACAATAAAT
*
29370992 AATAATATATAAAATCTTAA
1 AATAA-ATATAACATCTTAA
*
29371012 AATACATA-AACATCTTCAA
1 AATAAATATAACATCTT-AA
29371031 AA-AAATATAACA
1 AATAAATATAACA
29371043 ATAAATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 11 0.42
19 11 0.42
20 4 0.15
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (19 bp):
AATAAATATAACATCTTAA
Found at i:29377853 original size:2 final size:2
Alignment explanation
Indices: 29377846--29377872 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29377836 TGAGGGTTGA
29377846 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
29377873 AGAAAATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29379576 original size:126 final size:126
Alignment explanation
Indices: 29379344--29379847 Score: 592
Period size: 126 Copynumber: 4.0 Consensus size: 126
29379334 TTTTTGCAAG
* * *
29379344 AATAATTCTGAGTAAACGTTTCTGAACAAATAGTGTCGAAAAACGATTCAAGCAGAATGCACTGT
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCG-AAAACGCTTCAAGCAGGATGCACTGT
* * *
29379409 CAGCAAAATTTGTGGAAAAAGCTCC-ACATGGACGTTCTTTTGTTACAATAGTTCGTAGAAA
65 CAGCAAAATTTCTGGAAAAAGCTCCTACGTGGACGCTCTTTTGTTACAATAGTTCGTAGAAA
* *
29379470 AATAATTCTGAGTAGACGTTTTTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCATTGTC
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTC
* * * * * **
29379535 AGCAAAATTTTTGGAAAAAGCTCCTATGTGGATGCTCTTTTGCTACAATAATTTATAGAAA
66 AGCAAAATTTCTGGAAAAAGCTCCTACGTGGACGCTCTTTTGTTACAATAGTTCGTAGAAA
* * * *
29379596 AATAATTCTGAGTAGACATTTCTGAACAAATAGTGTCGAAAAAGCTTCAAGTAGGATGCATTGTC
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTC
* * * *
29379661 AGTAAAATTTCTGTAAAAAACT-CTCACGTGGACGCTCTTTT-TCTACAGTAGTTCGTAGAAA
66 AGCAAAATTTCTGGAAAAAGCTCCT-ACGTGGACGCTCTTTTGT-TACAATAGTTCGTAGAAA
* * * * *
29379722 AATAATTTTGA-TAGACGTTTCTGAAC-AA-AGTGTTGAAAACGCTTCAAGGATGATGCACTATC
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTC
* * * * * * *
29379784 AGTAAAATTTC-GAAAAAAAAGCTCCCACGTGGAC-TTTTTTTGCTACAGTAGTTCGTAGAAA
66 AGCAAAATTTCTG--GAAAAAGCTCCTACGTGGACGCTCTTTTGTTACAATAGTTCGTAGAAA
29379845 AAT
1 AAT
29379848 GAGGTTATAA
Statistics
Matches: 328, Mismatches: 43, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
122 1 0.00
123 65 0.20
124 17 0.05
125 64 0.20
126 181 0.55
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (126 bp):
AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTC
AGCAAAATTTCTGGAAAAAGCTCCTACGTGGACGCTCTTTTGTTACAATAGTTCGTAGAAA
Found at i:29383948 original size:14 final size:15
Alignment explanation
Indices: 29383931--29383963 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
29383921 TTATATACAT
29383931 AATACAT-AATACTA
1 AATACATAAATACTA
29383945 AATA-ATAAATACTA
1 AATACATAAATACTA
29383959 AATAC
1 AATAC
29383964 TGAATATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.12
14 15 0.88
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (15 bp):
AATACATAAATACTA
Found at i:29384871 original size:47 final size:46
Alignment explanation
Indices: 29384796--29384923 Score: 150
Period size: 47 Copynumber: 2.7 Consensus size: 46
29384786 ATGCAAACAT
** *
29384796 CATAAATGAAAAAAAAATCAAGCAGTATTGAAATTGTAATTATAA-TTG
1 CATAAATG-AAAAAAAATCAAATAGTATTGAAATAG-AATTA-AATTTG
*
29384844 CATAAATGAATAAAAATCAAATAGTATTGCAAATAGAATTAAATTTG
1 CATAAATGAAAAAAAATCAAATAGTATTG-AAATAGAATTAAATTTG
* *
29384891 CATAAATGAAAAAAATATCGAATAGTTTTGAAA
1 CATAAATGAAAAAAA-ATCAAATAGTATTGAAA
29384924 ATTTAAAATT
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
46 2 0.03
47 43 0.61
48 25 0.36
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (46 bp):
CATAAATGAAAAAAAATCAAATAGTATTGAAATAGAATTAAATTTG
Found at i:29385068 original size:11 final size:11
Alignment explanation
Indices: 29385052--29385107 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 11
29385042 AACAAACAAA
29385052 TTTGATAGAAC
1 TTTGATAGAAC
*
29385063 TTTGATAGAAT
1 TTTGATAGAAC
* * *
29385074 TTTGAGAAAAT
1 TTTGATAGAAC
*
29385085 TTTAAT-GAAC
1 TTTGATAGAAC
29385095 TTTGATAG-AC
1 TTTGATAGAAC
29385105 TTT
1 TTT
29385108 TGAAGGGAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
10 12 0.33
11 24 0.67
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (11 bp):
TTTGATAGAAC
Found at i:29390970 original size:19 final size:20
Alignment explanation
Indices: 29390934--29390971 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29390924 CAATTAAATG
29390934 ATAATTACATACATATTCTT
1 ATAATTACATACATATTCTT
*
29390954 ATAATTACA-AGATATTCT
1 ATAATTACATACATATTCT
29390972 ATTTTAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (20 bp):
ATAATTACATACATATTCTT
Found at i:29393750 original size:12 final size:12
Alignment explanation
Indices: 29393733--29393766 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
29393723 CGGCCCGCCC
29393733 ATATTAATTTTT
1 ATATTAATTTTT
*
29393745 ATATTATTTTTT
1 ATATTAATTTTT
29393757 ATA-TAATTTT
1 ATATTAATTTT
29393767 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:29394005 original size:11 final size:11
Alignment explanation
Indices: 29393974--29394013 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
29393964 ATAATAACAA
*
29393974 CAAAATAGTAG
1 CAAAATAATAG
*
29393985 CAACATAATAG
1 CAAAATAATAG
*
29393996 TAAAATAATAG
1 CAAAATAATAG
29394007 CAAAATA
1 CAAAATA
29394014 GGGAGAAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.20
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:29394567 original size:2 final size:2
Alignment explanation
Indices: 29394560--29394584 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29394550 TACTTCACCA
29394560 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
29394585 GGTAAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29398863 original size:30 final size:29
Alignment explanation
Indices: 29398769--29398870 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
29398759 TATAGTGAAT
* * *
29398769 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
29398798 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
29398826 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
29398856 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
29398871 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:29400993 original size:82 final size:82
Alignment explanation
Indices: 29400792--29400993 Score: 296
Period size: 82 Copynumber: 2.5 Consensus size: 82
29400782 GAATTCTTTG
* * * *
29400792 TATTTTTGGAATTTAATTCTCTTACATTTATTTTAAGAAATTTAGCCTCTTTATTTTTTGAATTT
1 TATTTTTAGAATTTAATCCTCTTACATTTATTTTAAGGAATTTAGCCTCTTTATTTTCTGAATTT
29400857 AAAAATACAAATTCAAT
66 AAAAATACAAATTCAAT
* * * * * *
29400874 TATTATTAGAATTTAATCCCCTTATATTTATTTTAAGGAATTTAGTCTTTTTATTTTCTGGATTT
1 TATTTTTAGAATTTAATCCTCTTACATTTATTTTAAGGAATTTAGCCTCTTTATTTTCTGAATTT
*
29400939 GAAAATACAAATTCAAT
66 AAAAATACAAATTCAAT
*
29400956 TATTTTTAGAATTCAATCCTCTTACATTTATTTTAAGG
1 TATTTTTAGAATTTAATCCTCTTACATTTATTTTAAGG
29400994 TTATTTCTCG
Statistics
Matches: 105, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 105 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (82 bp):
TATTTTTAGAATTTAATCCTCTTACATTTATTTTAAGGAATTTAGCCTCTTTATTTTCTGAATTT
AAAAATACAAATTCAAT
Found at i:29401852 original size:16 final size:17
Alignment explanation
Indices: 29401833--29401885 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
29401823 CTCTTTTCTC
29401833 TTCT-ATCTCTTTCGTT
1 TTCTCATCTCTTTCGTT
*
29401849 TTCTCCATCACTTCTTCG-T
1 TTCT-CATCTC-T-TTCGTT
29401868 TTCTCATCTCTTTCGTT
1 TTCTCATCTCTTTCGTT
29401885 T
1 T
29401886 GCAATGCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 8 0.27
17 3 0.10
18 9 0.30
19 6 0.20
20 4 0.13
ACGTcount: A:0.08, C:0.30, G:0.06, T:0.57
Consensus pattern (17 bp):
TTCTCATCTCTTTCGTT
Found at i:29410068 original size:12 final size:12
Alignment explanation
Indices: 29410051--29410077 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
29410041 AGAGGATTTT
29410051 TTTATTTTTTAA
1 TTTATTTTTTAA
29410063 TTTATTTTTTAA
1 TTTATTTTTTAA
29410075 TTT
1 TTT
29410078 TTAAATTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTATTTTTTAA
Found at i:29410071 original size:20 final size:20
Alignment explanation
Indices: 29410046--29410085 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29410036 AGTTGAGAGG
* *
29410046 ATTTTTTTATTTTTTAATTT
1 ATTTTTTAATTTTTAAATTT
29410066 ATTTTTTAATTTTTAAATTT
1 ATTTTTTAATTTTTAAATTT
29410086 GCTTTAGCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (20 bp):
ATTTTTTAATTTTTAAATTT
Found at i:29410422 original size:41 final size:41
Alignment explanation
Indices: 29410377--29410467 Score: 166
Period size: 41 Copynumber: 2.2 Consensus size: 41
29410367 AACTAAAAGT
29410377 GAAAATTTTAAAGAAATGATATTGTAAAAATAGATGTCGTA
1 GAAAATTTTAAAGAAATGATATTGTAAAAATAGATGTCGTA
29410418 GAAAATTTTAAAGAAATGATATTGTAAAAATAGATGTCGTA
1 GAAAATTTTAAAGAAATGATATTGTAAAAATAGATGTCGTA
29410459 -AAAGATTTT
1 GAAA-ATTTT
29410468 GTCGTTCATT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 3 0.06
41 46 0.94
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.33
Consensus pattern (41 bp):
GAAAATTTTAAAGAAATGATATTGTAAAAATAGATGTCGTA
Found at i:29411698 original size:10 final size:10
Alignment explanation
Indices: 29411673--29411705 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
29411663 ATTAAATTAA
29411673 AATTTATTTT
1 AATTTATTTT
29411683 --TTTATTTT
1 AATTTATTTT
29411691 AATTTATTTT
1 AATTTATTTT
29411701 AATTT
1 AATTT
29411706 TTAATATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.38
10 13 0.62
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
AATTTATTTT
Found at i:29414038 original size:10 final size:10
Alignment explanation
Indices: 29414000--29414047 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
29413990 GTTAATAGGT
29414000 TTTATATT-A
1 TTTATATTAA
29414009 -TT-TATTAA
1 TTTATATTAA
*
29414017 TTTAT-CTAA
1 TTTATATTAA
29414026 TTTATATTAA
1 TTTATATTAA
*
29414036 TTTATATAAA
1 TTTATATTAA
29414046 TT
1 TT
29414048 GATTGAATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
7 4 0.12
8 3 0.09
9 10 0.31
10 15 0.47
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTATATTAA
Found at i:29414238 original size:26 final size:27
Alignment explanation
Indices: 29414202--29414265 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
29414192 TTTTTCCTGG
* *
29414202 AATAATATAAAAATA-TTATTTA-TCGA
1 AATAATATAAAAAAATTTAATTACT-GA
29414228 AATAATATAAAAAAATTTAATTACTGA
1 AATAATATAAAAAAATTTAATTACTGA
29414255 AATAATATAAA
1 AATAATATAAA
29414266 TTGTGTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 14 0.41
27 19 0.56
28 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (27 bp):
AATAATATAAAAAAATTTAATTACTGA
Found at i:29414458 original size:27 final size:26
Alignment explanation
Indices: 29414415--29414475 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
29414405 TGTCATGGCG
* * *
29414415 AAATTTTAGAAATTTTATTTATTTTTT
1 AAATTTTAGAAAGTTTAATT-TTTTAT
29414442 AAATTTTA-AAGAGTTTAATTTTTTAT
1 AAATTTTAGAA-AGTTTAATTTTTTAT
*
29414468 AATTTTTA
1 AAATTTTA
29414476 TTTAAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (26 bp):
AAATTTTAGAAAGTTTAATTTTTTAT
Found at i:29415805 original size:20 final size:21
Alignment explanation
Indices: 29415780--29415833 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
29415770 TTTTTTCACA
*
29415780 TTTTAAATAAAAATAAAA-AT
1 TTTTAAATAAAAAAAAAATAT
29415800 TTTTAAA-AAATAAAAAAATAT
1 TTTTAAATAAA-AAAAAAATAT
29415821 TTTTAAAATAAAA
1 TTTT-AAATAAAA
29415834 TTATAAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 3 0.10
20 13 0.45
21 6 0.21
22 4 0.14
23 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TTTTAAATAAAAAAAAAATAT
Found at i:29415816 original size:19 final size:20
Alignment explanation
Indices: 29415779--29415833 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
29415769 ATTTTTTCAC
29415779 ATTTTAAATAAA-AATAAAAAT
1 ATTTTAAA-AAATAA-AAAAAT
29415800 -TTTTAAAAAATAAAAAAAT
1 ATTTTAAAAAATAAAAAAAT
*
29415819 ATTTT-TAAAATAAAA
1 ATTTTAAAAAATAAAA
29415834 TTATAAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTTTAAAAAATAAAAAAAT
Found at i:29415848 original size:52 final size:51
Alignment explanation
Indices: 29415788--29415887 Score: 114
Period size: 52 Copynumber: 1.9 Consensus size: 51
29415778 CATTTTAAAT
* *
29415788 AAAAATAAAAATTTTTAAAAA-ATAAAAAAATATTTTTAAAATA-AAATTATA
1 AAAAAT-AAAATCTTTAAAAATA-AAAAAAATATTTTAAAAATATAAATTATA
* *
29415839 AAAAGATAAACTCTTTAAAATTCAAAAAAAATATTTTAAAAATATAAAT
1 AAAA-ATAAAATCTTTAAAAAT-AAAAAAAATATTTTAAAAATATAAAT
29415888 ATTTTAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
51 15 0.37
52 21 0.51
53 5 0.12
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (51 bp):
AAAAATAAAATCTTTAAAAATAAAAAAAATATTTTAAAAATATAAATTATA
Found at i:29416103 original size:29 final size:29
Alignment explanation
Indices: 29416044--29416116 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
29416034 GTTCCCAGAG
*
29416044 TTCATATTATTCTGATAATTAAATTTTTT
1 TTCATATTATTCTGATAAATAAATTTTTT
29416073 TTCATATTATTCT-AGTAAAT-AATTTTATT
1 TTCATATTATTCTGA-TAAATAAATTTT-TT
*
29416102 TTCATGTTATTCTGA
1 TTCATATTATTCTGA
29416117 AAAAGAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 7 0.18
29 31 0.79
30 1 0.03
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.56
Consensus pattern (29 bp):
TTCATATTATTCTGATAAATAAATTTTTT
Found at i:29418966 original size:2 final size:2
Alignment explanation
Indices: 29418959--29418999 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
29418949 CTTTGAAATT
29418959 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29419000 CACATAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29420196 original size:17 final size:17
Alignment explanation
Indices: 29420174--29420206 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29420164 AGTGGCTCGA
29420174 CCCATAAACAAGTCTAG
1 CCCATAAACAAGTCTAG
*
29420191 CCCATATACAAGTCTA
1 CCCATAAACAAGTCTA
29420207 CAAAGTAGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.30, G:0.09, T:0.21
Consensus pattern (17 bp):
CCCATAAACAAGTCTAG
Found at i:29423855 original size:2 final size:2
Alignment explanation
Indices: 29423848--29423885 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
29423838 TATGTACTAA
29423848 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
29423886 GCATACACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:29426841 original size:31 final size:29
Alignment explanation
Indices: 29426791--29426850 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
29426781 CTTAAGAACC
* **
29426791 TAATAACTTATTAAAACTTTTGAATAGTT
1 TAATAACTTATGAAAACTTTCAAATAGTT
29426820 TAATAACTTGAATGAAAACTTTCAAATAGTT
1 TAATAACTT--ATGAAAACTTTCAAATAGTT
29426851 CAGTGACTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 9 0.35
31 17 0.65
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.40
Consensus pattern (29 bp):
TAATAACTTATGAAAACTTTCAAATAGTT
Found at i:29431135 original size:21 final size:22
Alignment explanation
Indices: 29431111--29431151 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
29431101 AAAAAGAATA
29431111 AAAATTATAAAAAA-TAATTTT
1 AAAATTATAAAAAATTAATTTT
*
29431132 AAAATTTTAAAAAATTAATT
1 AAAATTATAAAAAATTAATT
29431152 AAATGCTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATTATAAAAAATTAATTTT
Found at i:29435287 original size:33 final size:33
Alignment explanation
Indices: 29435250--29435349 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
29435240 TGAATAGGAT
* *
29435250 TAAATCAACTAGTCGGATTTGTTAAATTGAGAA
1 TAAATTAACTAGTCGGATTTGTTAAATTGAAAA
* *
29435283 TAAATTAATTAGTCGGATTTATTAAATTGAAAA
1 TAAATTAACTAGTCGGATTTGTTAAATTGAAAA
**
29435316 TAAATTAACTAGTCAAATTTGTTAAATTGAAAA
1 TAAATTAACTAGTCGGATTTGTTAAATTGAAAA
29435349 T
1 T
29435350 CAGTTGATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (33 bp):
TAAATTAACTAGTCGGATTTGTTAAATTGAAAA
Found at i:29436318 original size:3 final size:3
Alignment explanation
Indices: 29436310--29436342 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
29436300 GTAGCACGTT
29436310 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
29436343 AAAATTTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:29437596 original size:45 final size:45
Alignment explanation
Indices: 29437546--29437634 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
29437536 ACTGAAGGAT
29437546 GATGAAGATCTAATACAAGTAACTTTGATTTTCTCTTCTTTTTGA
1 GATGAAGATCTAATACAAGTAACTTTGATTTTCTCTTCTTTTTGA
29437591 GATGAAGATCTAATACAAGTAACTTTGATTTTCTCTTCTTTTTG
1 GATGAAGATCTAATACAAGTAACTTTGATTTTCTCTTCTTTTTG
29437635 GGTTCAAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.45
Consensus pattern (45 bp):
GATGAAGATCTAATACAAGTAACTTTGATTTTCTCTTCTTTTTGA
Found at i:29441569 original size:2 final size:2
Alignment explanation
Indices: 29441564--29441588 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29441554 GTGCGTGGAA
29441564 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
29441589 TCCATCACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:29442961 original size:22 final size:22
Alignment explanation
Indices: 29442936--29443002 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
29442926 GTGAGATAAA
29442936 GAAATATGAGTTGATGGTACAT
1 GAAATATGAGTTGATGGTACAT
* *
29442958 G-AA-AT-A-TTGA-GATA-AA
1 GAAATATGAGTTGATGGTACAT
*
29442974 CAAATATGAGTTGATGGTACAT
1 GAAATATGAGTTGATGGTACAT
29442996 GAAATAT
1 GAAATAT
29443003 TGATATAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
16 1 0.03
17 5 0.15
18 6 0.18
19 2 0.06
20 6 0.18
21 5 0.15
22 8 0.24
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.30
Consensus pattern (22 bp):
GAAATATGAGTTGATGGTACAT
Found at i:29442979 original size:38 final size:38
Alignment explanation
Indices: 29442927--29443010 Score: 150
Period size: 38 Copynumber: 2.2 Consensus size: 38
29442917 CCTAATTATG
*
29442927 TGAGATAAAGAAATATGAGTTGATGGTACATGAAATAT
1 TGAGATAAACAAATATGAGTTGATGGTACATGAAATAT
29442965 TGAGATAAACAAATATGAGTTGATGGTACATGAAATAT
1 TGAGATAAACAAATATGAGTTGATGGTACATGAAATAT
*
29443003 TGATATAA
1 TGAGATAA
29443011 TGAATTAACT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.30
Consensus pattern (38 bp):
TGAGATAAACAAATATGAGTTGATGGTACATGAAATAT
Found at i:29444149 original size:31 final size:31
Alignment explanation
Indices: 29444106--29444169 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
29444096 CCTTTTCATA
29444106 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* **
29444137 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
29444168 TT
1 TT
29444170 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:29444433 original size:23 final size:24
Alignment explanation
Indices: 29444372--29444522 Score: 245
Period size: 24 Copynumber: 6.4 Consensus size: 24
29444362 CTGGAGGCCT
*
29444372 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
29444397 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
29444421 AGCCC-TTTAATAACT-GGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
29444443 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
29444467 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
29444491 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
29444514 AGCCCTTTT
1 AGCCCTTTT
29444523 TCACTTCCTC
Statistics
Matches: 120, Mismatches: 3, Indels: 7
0.92 0.02 0.05
Matches are distributed among these distances:
22 12 0.10
23 41 0.34
24 63 0.52
25 4 0.03
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:29444461 original size:70 final size:71
Alignment explanation
Indices: 29444372--29444522 Score: 259
Period size: 70 Copynumber: 2.1 Consensus size: 71
29444362 CTGGAGGCCT
29444372 AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTAATAACT-
1 AGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTAATAACTG
29444436 GGGCATA
65 GGGCATA
* * *
29444443 AGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGG
1 AGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGG
29444508 GGCATA
66 GGCATA
29444514 AGCCCTTTT
1 AGCCCTTTT
29444523 TCACTTCCTC
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
70 56 0.74
71 20 0.26
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (71 bp):
AGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGG
GGCATA
Found at i:29444596 original size:20 final size:20
Alignment explanation
Indices: 29444571--29444637 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
29444561 TTATGATTAC
29444571 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
29444591 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
29444611 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
29444631 ACCATGT
1 ATCATGT
29444638 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:29444602 original size:11 final size:11
Alignment explanation
Indices: 29444571--29444626 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
29444561 TTATGATTAC
29444571 ATCATGTGCAT
1 ATCATGTGCAT
*
29444582 ATCA--TACAT
1 ATCATGTGCAT
29444591 ATCATGTGCAT
1 ATCATGTGCAT
*
29444602 ATCA--TACAT
1 ATCATGTGCAT
*
29444611 GTCATGTGCAT
1 ATCATGTGCAT
29444622 ATCAT
1 ATCAT
29444627 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:29444706 original size:25 final size:25
Alignment explanation
Indices: 29444674--29444721 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29444664 ATACATAAAC
* * *
29444674 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
29444699 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
29444722 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:29452239 original size:30 final size:31
Alignment explanation
Indices: 29452203--29452265 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
29452193 CCTTTTCATA
29452203 TTTCATA-TTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
29452233 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
29452264 TT
1 TT
29452266 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:29452552 original size:23 final size:24
Alignment explanation
Indices: 29452449--29452567 Score: 179
Period size: 24 Copynumber: 5.0 Consensus size: 24
29452439 GCTTTATCAT
*
29452449 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
29452474 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
29452498 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
29452522 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
29452545 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
29452568 TCACTTCCTC
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
23 22 0.25
24 53 0.61
25 12 0.14
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:29452563 original size:47 final size:48
Alignment explanation
Indices: 29452449--29452567 Score: 179
Period size: 47 Copynumber: 2.5 Consensus size: 48
29452439 GCTTTATCAT
*
29452449 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTTA
* *
29452498 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTA
29452545 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
29452568 TCACTTCCTC
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
47 27 0.41
48 27 0.41
49 12 0.18
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTA
Found at i:29452640 original size:20 final size:20
Alignment explanation
Indices: 29452615--29452681 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
29452605 TTATGATTAC
29452615 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
29452635 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
29452655 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
29452675 ACCATGT
1 ATCATGT
29452682 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:29452646 original size:11 final size:11
Alignment explanation
Indices: 29452615--29452670 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
29452605 TTATGATTAC
29452615 ATCATGTGCAT
1 ATCATGTGCAT
*
29452626 ATCA--TACAT
1 ATCATGTGCAT
29452635 ATCATGTGCAT
1 ATCATGTGCAT
*
29452646 ATCA--TACAT
1 ATCATGTGCAT
*
29452655 GTCATGTGCAT
1 ATCATGTGCAT
29452666 ATCAT
1 ATCAT
29452671 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:29456176 original size:8 final size:8
Alignment explanation
Indices: 29456163--29456189 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
29456153 TTGTAAACTT
29456163 TAATAAAA
1 TAATAAAA
29456171 TAATAAAA
1 TAATAAAA
29456179 TAATAAAA
1 TAATAAAA
29456187 TAA
1 TAA
29456190 ACATTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
TAATAAAA
Found at i:29458686 original size:16 final size:15
Alignment explanation
Indices: 29458652--29458696 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
29458642 TGTATTTACT
* *
29458652 TATTATTTAAATAAA
1 TATTATTTATATTAA
29458667 TATTATTATATATTAA
1 TATTATT-TATATTAA
29458683 TATTATTTTATATT
1 TATTA-TTTATATT
29458697 GGTTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 7 0.27
16 17 0.65
17 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTATTTATATTAA
Found at i:29459024 original size:26 final size:24
Alignment explanation
Indices: 29458995--29459044 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
29458985 TAAAAAAAAA
*
29458995 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
29459021 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
29459045 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:29459056 original size:22 final size:21
Alignment explanation
Indices: 29458988--29459073 Score: 59
Period size: 21 Copynumber: 3.9 Consensus size: 21
29458978 ATTTCATTAA
*
29458988 AAAAAAAAT-TTAAAAATATAAT
1 AAAAAAAATATT-AAAACA-AAT
* *
29459010 AAATCAAATATATTTAAAA-ACAT
1 AAA--AAAAATA-TTAAAACAAAT
29459033 AAAAACAAATATTAAAACAAAT
1 AAAAA-AAATATTAAAACAAAT
* *
29459055 AAAAATAATACTAAAACAA
1 AAAAAAAATATTAAAACAA
29459074 TTCTTAAAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
21 20 0.38
22 15 0.29
23 5 0.10
24 6 0.12
25 4 0.08
26 2 0.04
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAAAATATTAAAACAAAT
Found at i:29459150 original size:15 final size:16
Alignment explanation
Indices: 29459120--29459152 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
29459110 AAATGGTTAT
29459120 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
29459137 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
29459152 A
1 A
29459153 AAAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:29459415 original size:16 final size:16
Alignment explanation
Indices: 29459346--29459420 Score: 59
Period size: 16 Copynumber: 4.7 Consensus size: 16
29459336 ATGTATTTAA
29459346 TTAT-TAAT-AGATAT
1 TTATATAATAAGATAT
*
29459360 TTATTATTTATAAAGATAT
1 TTA-TA-TAAT-AAGATAT
*
29459379 TTAT-TAATTAAG-TAA
1 TTATATAA-TAAGATAT
*
29459394 TTATATTATAAGATAT
1 TTATATAATAAGATAT
29459410 TTATATAATAA
1 TTATATAATAA
29459421 ATAAATTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
14 3 0.06
15 11 0.23
16 19 0.40
17 4 0.09
18 1 0.02
19 9 0.19
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (16 bp):
TTATATAATAAGATAT
Found at i:29459434 original size:32 final size:32
Alignment explanation
Indices: 29459362--29459424 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
29459352 ATAGATATTT
*
29459362 ATTAT-TTATAAAGATATTTATTAATTAAGTA
1 ATTATATTATAAAGATATTTATTAATTAAATA
29459393 ATTATATTAT-AAGATATTTATATAA-TAAATA
1 ATTATATTATAAAGATATTTAT-TAATTAAATA
29459424 A
1 A
29459425 ATTTAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 22 0.76
32 7 0.24
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (32 bp):
ATTATATTATAAAGATATTTATTAATTAAATA
Found at i:29459529 original size:2 final size:2
Alignment explanation
Indices: 29459517--29459573 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
29459507 TTGATGTTAT
29459517 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29459558 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
29459574 GTTAAAACAT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29460749 original size:45 final size:47
Alignment explanation
Indices: 29460678--29460784 Score: 130
Period size: 45 Copynumber: 2.3 Consensus size: 47
29460668 AAGTGTTGCT
* *
29460678 TTACTGTTACTGTTTCGGATTAGTTCCGAA-GAGGTACTC-CGTACC-
1 TTACTGTTACTGTTCCAGATTAGTTCC-AATGAGGTACTCGCGTACCG
* *
29460723 TTACTGTTACTGTTCCAGATTTGTTCCAATGAGGTACTCTGTGTACCG
1 TTACTGTTACTGTTCCAGATTAGTTCCAATGAGGTACTC-GCGTACCG
*
29460771 CTACTGTTACTGTT
1 TTACTGTTACTGTT
29460785 ACTGTTACCA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
44 2 0.04
45 33 0.62
47 5 0.09
48 13 0.25
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (47 bp):
TTACTGTTACTGTTCCAGATTAGTTCCAATGAGGTACTCGCGTACCG
Found at i:29467346 original size:51 final size:51
Alignment explanation
Indices: 29467269--29467365 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
29467259 TAGATACACG
29467269 GTGGCCTTCACATAGTACCATCCTTGTAG-CCAAAGCAATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCATCCTTGT-GTCCAAAGCAATTTTATTCACAAA
**
29467320 GTGGCCTTCACATAGTACCA-CACTTGTGTCCAAAGTTATTTTATTC
1 GTGGCCTTCACATAGTACCATC-CTTGTGTCCAAAGCAATTTTATTC
29467366 CTAAGGTTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
50 2 0.05
51 40 0.95
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCATCCTTGTGTCCAAAGCAATTTTATTCACAAA
Found at i:29467445 original size:52 final size:52
Alignment explanation
Indices: 29467389--29467556 Score: 248
Period size: 52 Copynumber: 3.2 Consensus size: 52
29467379 AAGAAATTTC
*
29467389 TCACTTAGCACCA-TGCCATGGACTTATTTCACTTAGATGCCGTGGACTTATT
1 TCACTTAGCA-CATTGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
*
29467441 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
* *
29467493 TCACTTAGCACATTGCCATGGTCTTATTTTACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAG---A-TGCCATGGACTTATT
29467549 TCACTTAG
1 TCACTTAG
29467557 ATGTCATGGT
Statistics
Matches: 106, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
51 2 0.02
52 81 0.76
55 1 0.01
56 22 0.21
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (52 bp):
TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
Found at i:29467466 original size:28 final size:27
Alignment explanation
Indices: 29467389--29467585 Score: 232
Period size: 28 Copynumber: 7.5 Consensus size: 27
29467379 AAGAAATTTC
29467389 TCACTTAGCACCATGCCATGGACTTATT
1 TCACTTAGCA-CATGCCATGGACTTATT
*
29467417 TCACTTAG---ATGCCGTGGACTTATT
1 TCACTTAGCACATGCCATGGACTTATT
29467441 TCACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
*
29467469 TCACTTAG---ATGCCATGGTCTTATT
1 TCACTTAGCACATGCCATGGACTTATT
*
29467493 TCACTTAGCACATTGCCATGGTCTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
*
29467521 TTACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
* *
29467549 TCACTTAG---ATGTCATGGTCTTATT
1 TCACTTAGCACATGCCATGGACTTATT
*
29467573 TCAATTAGCACAT
1 TCACTTAGCACAT
29467586 TGCTATGGTC
Statistics
Matches: 149, Mismatches: 9, Indels: 23
0.82 0.05 0.13
Matches are distributed among these distances:
24 65 0.44
25 2 0.01
27 4 0.03
28 78 0.52
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (27 bp):
TCACTTAGCACATGCCATGGACTTATT
Found at i:29467565 original size:52 final size:54
Alignment explanation
Indices: 29467402--29467593 Score: 206
Period size: 52 Copynumber: 3.7 Consensus size: 54
29467392 CTTAGCACCA
* *
29467402 TGCCATGGACTTATTTCACTTAG---A-TGCCGTGGACTTATTTCACTTAGCACAT
1 TGCCATGGTCTTATTTCACTTAGCACATTGCCATGGACTTATTTCACTTAG--CAT
* *
29467454 TGCCATGGACTTATTTCACTTAG---A-TGCCATGGTCTTATTTCACTTAGCACAT
1 TGCCATGGTCTTATTTCACTTAGCACATTGCCATGGACTTATTTCACTTAG--CAT
*
29467506 TGCCATGGTCTTATTTTACTTAGCACATTGCCATGGACTTATTTCACTTAG-A-
1 TGCCATGGTCTTATTTCACTTAGCACATTGCCATGGACTTATTTCACTTAGCAT
* * *
29467558 TGTCATGGTCTTATTTCAATTAGCACATTGCTATGG
1 TGCCATGGTCTTATTTCACTTAGCACATTGCCATGG
29467594 TCTAACCACG
Statistics
Matches: 127, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
52 103 0.81
53 1 0.01
55 1 0.01
56 22 0.17
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (54 bp):
TGCCATGGTCTTATTTCACTTAGCACATTGCCATGGACTTATTTCACTTAGCAT
Found at i:29467583 original size:80 final size:80
Alignment explanation
Indices: 29467401--29467596 Score: 292
Period size: 80 Copynumber: 2.5 Consensus size: 80
29467391 ACTTAGCACC
* * * *
29467401 ATGCCATGGACTTATTTCACTTAG---A-TGCCGTGGACTTATTTCACTTAGCACATTGCCATGG
1 ATGCCATGGTCTTATTTCAATTAGCACATTGCCATGGTCTTATTTCACTTAGCACATTGCCATGG
29467462 ACTTATTTCACTTAG
66 ACTTATTTCACTTAG
* *
29467477 ATGCCATGGTCTTATTTCACTTAGCACATTGCCATGGTCTTATTTTACTTAGCACATTGCCATGG
1 ATGCCATGGTCTTATTTCAATTAGCACATTGCCATGGTCTTATTTCACTTAGCACATTGCCATGG
29467542 ACTTATTTCACTTAG
66 ACTTATTTCACTTAG
* *
29467557 ATGTCATGGTCTTATTTCAATTAGCACATTGCTATGGTCT
1 ATGCCATGGTCTTATTTCAATTAGCACATTGCCATGGTCT
29467597 AACCACGATC
Statistics
Matches: 109, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
76 23 0.21
79 1 0.01
80 85 0.78
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.39
Consensus pattern (80 bp):
ATGCCATGGTCTTATTTCAATTAGCACATTGCCATGGTCTTATTTCACTTAGCACATTGCCATGG
ACTTATTTCACTTAG
Found at i:29476141 original size:60 final size:60
Alignment explanation
Indices: 29476069--29476185 Score: 175
Period size: 60 Copynumber: 1.9 Consensus size: 60
29476059 TAGTCACCTA
* *
29476069 AACTATTAGTAAATTT-TTTATCTGGTCA-TCTAACTATGAAAAGTTACAAAATGGTCATCT
1 AACTATTAGTAAATTTCTTT-TCTGGTAACT-TAACTATGAAAAGTTACAAAATCGTCATCT
*
29476129 AACTATTAGTAAATTTCTTTTTTGGTAACTTAACTATGAAAAGTTACAAAATCGTCA
1 AACTATTAGTAAATTTCTTTTCTGGTAACTTAACTATGAAAAGTTACAAAATCGTCA
29476186 CCCAATTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
60 48 0.92
61 4 0.08
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (60 bp):
AACTATTAGTAAATTTCTTTTCTGGTAACTTAACTATGAAAAGTTACAAAATCGTCATCT
Found at i:29476456 original size:62 final size:60
Alignment explanation
Indices: 29476381--29476516 Score: 186
Period size: 62 Copynumber: 2.2 Consensus size: 60
29476371 GACAAAATTG
29476381 AATAGTTTA-GTGACCATTTTGTAACTATTCATG-GTTGGGTAACCAAAAAAAAGAAATTTACT
1 AATAG-TTAGGTGACCATTTTGTAACTATTCA-GAGTTGGGTAACC--AAAAAAGAAATTTACT
* * *
29476443 AATAGTTAGGTGACCATTTTGTAGCTTTTCAGAGTTGGGTGACCAAAAAAGAAATTTACT
1 AATAGTTAGGTGACCATTTTGTAACTATTCAGAGTTGGGTAACCAAAAAAGAAATTTACT
*
29476503 AATATTTAGGTGAC
1 AATAGTTAGGTGAC
29476517 TACTAGCGTG
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
60 29 0.43
61 4 0.06
62 35 0.51
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (60 bp):
AATAGTTAGGTGACCATTTTGTAACTATTCAGAGTTGGGTAACCAAAAAAGAAATTTACT
Found at i:29488246 original size:14 final size:14
Alignment explanation
Indices: 29488227--29488259 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
29488217 TGAGGTTGAC
29488227 TCTTTCAAAAGAAG
1 TCTTTCAAAAGAAG
*
29488241 TCTTTCGAAAGAAG
1 TCTTTCAAAAGAAG
29488255 TCTTT
1 TCTTT
29488260 GAAGTGTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (14 bp):
TCTTTCAAAAGAAG
Found at i:29493028 original size:17 final size:17
Alignment explanation
Indices: 29493003--29493037 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29492993 TAATGTTATT
29493003 GACAAAATAACCAAATG
1 GACAAAATAACCAAATG
* *
29493020 GACAGAATAACGAAATG
1 GACAAAATAACCAAATG
29493037 G
1 G
29493038 TTACAAGTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.14, G:0.20, T:0.11
Consensus pattern (17 bp):
GACAAAATAACCAAATG
Found at i:29495533 original size:24 final size:23
Alignment explanation
Indices: 29495480--29495533 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 23
29495470 AATTTTTTAT
* *
29495480 ATAAAAAAATTAAAATAAAATAC
1 ATAAAAAAACTAAAATAAAATAA
* *
29495503 ATCAAAAACACTAAAATAAATTAAA
1 AT-AAAAAAACTAAAATAAAAT-AA
29495528 ATAAAA
1 ATAAAA
29495534 TGTTTTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 2 0.08
24 20 0.80
25 3 0.12
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (23 bp):
ATAAAAAAACTAAAATAAAATAA
Found at i:29495736 original size:22 final size:22
Alignment explanation
Indices: 29495711--29495773 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
29495701 AAACAGTAGG
29495711 AAAACAGTA-AGAAAACAACTGC
1 AAAACAGTAGA-AAAACAACTGC
*
29495733 AAAACAGTGGAAAAACAACTGC
1 AAAACAGTAGAAAAACAACTGC
*
29495755 AAAACAGTGGAAAAACAAC
1 AAAACAGTAGAAAAACAAC
29495774 AACAAAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 38 0.97
23 1 0.03
ACGTcount: A:0.59, C:0.17, G:0.16, T:0.08
Consensus pattern (22 bp):
AAAACAGTAGAAAAACAACTGC
Found at i:29495780 original size:22 final size:22
Alignment explanation
Indices: 29495722--29495773 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
29495712 AAACAGTAAG
29495722 AAAACAACTGCAAAACAGTGGA
1 AAAACAACTGCAAAACAGTGGA
29495744 AAAACAACTGCAAAACAGTGGA
1 AAAACAACTGCAAAACAGTGGA
29495766 AAAACAAC
1 AAAACAAC
29495774 AACAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.58, C:0.19, G:0.15, T:0.08
Consensus pattern (22 bp):
AAAACAACTGCAAAACAGTGGA
Found at i:29495997 original size:1 final size:1
Alignment explanation
Indices: 29495991--29496020 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
29495981 TTTCAAAAGT
29495991 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29496021 CCACTTCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29499084 original size:16 final size:16
Alignment explanation
Indices: 29499063--29499102 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
29499053 TAATTAAAAC
29499063 ATAAATTCATAATATT
1 ATAAATTCATAATATT
* *
29499079 ATAAATTTATTATATT
1 ATAAATTCATAATATT
29499095 AT-AATTCA
1 ATAAATTCA
29499103 AAAAATTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAATTCATAATATT
Found at i:29502440 original size:15 final size:15
Alignment explanation
Indices: 29502420--29502453 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29502410 AAAAGAAAAT
29502420 AATTTATTATATTTA
1 AATTTATTATATTTA
* *
29502435 AATTTATTTTATTTC
1 AATTTATTATATTTA
29502450 AATT
1 AATT
29502454 AAAAGGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTTATTATATTTA
Found at i:29509719 original size:42 final size:42
Alignment explanation
Indices: 29509667--29509814 Score: 149
Period size: 42 Copynumber: 3.6 Consensus size: 42
29509657 GAGGCTAACT
* * *
29509667 GAAGCACATAAGTGCTAAACGGAAACCTGA-AAGGGTTAAACG
1 GAAGCTCATAAGAGCTAAACGGAAACC-CATAAGGGTTAAACG
*
29509709 GAAGCTCATAAGAGCTAAATGGAAACCCATAAGGGTTAAACG
1 GAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAAACG
* * * * * *
29509751 GAAGCTTATAAGAGCTGAACTGAAACCCGTAAAGGTT-AACT
1 GAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAAACG
* * *
29509792 GAAACTCATATGAG-TTAACGGAA
1 GAAGCTCATAAGAGCTAAACGGAA
29509815 GCTCGTGAGA
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
40 7 0.08
41 15 0.17
42 67 0.75
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAAACG
Found at i:29509727 original size:21 final size:21
Alignment explanation
Indices: 29509667--29509766 Score: 76
Period size: 21 Copynumber: 4.8 Consensus size: 21
29509657 GAGGCTAACT
* *
29509667 GAAGCACATAAGTGCTAAACG
1 GAAGCTCATAAGAGCTAAACG
* * * *
29509688 GAAACCTGA-AAGGGTTAAACG
1 G-AAGCTCATAAGAGCTAAACG
*
29509709 GAAGCTCATAAGAGCTAAATG
1 GAAGCTCATAAGAGCTAAACG
* * * *
29509730 GAAACCCATAAGGGTTAAACG
1 GAAGCTCATAAGAGCTAAACG
*
29509751 GAAGCTTATAAGAGCT
1 GAAGCTCATAAGAGCT
29509767 GAACTGAAAC
Statistics
Matches: 57, Mismatches: 20, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
20 5 0.09
21 48 0.84
22 4 0.07
ACGTcount: A:0.42, C:0.16, G:0.25, T:0.17
Consensus pattern (21 bp):
GAAGCTCATAAGAGCTAAACG
Found at i:29512262 original size:13 final size:13
Alignment explanation
Indices: 29512244--29512269 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29512234 TAAAGTATTT
29512244 TTTTTATTTTTTA
1 TTTTTATTTTTTA
29512257 TTTTTATTTTTTA
1 TTTTTATTTTTTA
29512270 ATAGTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:29517432 original size:23 final size:23
Alignment explanation
Indices: 29517406--29517454 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
29517396 TTACAATCCA
29517406 CTCACTTACAAATTTCAATAACT
1 CTCACTTACAAATTTCAATAACT
29517429 CTCACTTACAAATTTCAATAACT
1 CTCACTTACAAATTTCAATAACT
29517452 CTC
1 CTC
29517455 TAATAAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.35
Consensus pattern (23 bp):
CTCACTTACAAATTTCAATAACT
Found at i:29522505 original size:10 final size:10
Alignment explanation
Indices: 29522491--29522528 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
29522481 ATTTTAGCTT
*
29522491 TTATCTTTAT
1 TTATCTTTAA
29522501 TTATCTTTAA
1 TTATCTTTAA
29522511 TTATCTTTAA
1 TTATCTTTAA
29522521 TTATCTTT
1 TTATCTTT
29522529 TATAATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:29522508 original size:17 final size:17
Alignment explanation
Indices: 29522483--29522531 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 17
29522473 TACATTTAAT
*
29522483 TTTAGCTTTTATCTTTA
1 TTTATCTTTTATCTTTA
29522500 TTTATCTTTAATTATCTTTA
1 TTTATC-TT--TTATCTTTA
*
29522520 ATTATCTTTTAT
1 TTTATCTTTTAT
29522532 AATTTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 9 0.33
18 2 0.07
19 2 0.07
20 14 0.52
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTATCTTTTATCTTTA
Found at i:29533493 original size:3 final size:3
Alignment explanation
Indices: 29533487--29533740 Score: 105
Period size: 3 Copynumber: 85.3 Consensus size: 3
29533477 AAAATACAAC
* * * *
29533487 AAT AAT AAT AGT AA- AAG ATAT AAT AA- CAT AAT AAT -AT AAT AGT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * *
29533530 AAT AGT AAC AAT -AT GAC GAT AAT AGT AAA AAT AAT -AT ATT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * **
29533574 AAT AGT AAT AA- AAGT AGT GCT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
29533619 AAT AAT AAT AAT AAT AAT AAT AAT GAT GAT GAT -CT ATT AAGT TAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
* * * * *
29533664 AAT GAA- AAT AAT GAT AAT GAT GAT -AT ATT AGAT AAT AAT AGT AA-
1 AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
* *
29533708 AAT AAT AAGT AAC AAT AAT AAAT TAT AAT AAT A
1 AAT AAT AA-T AAT AAT AAT -AAT AAT AAT AAT A
29533741 GTGATGAGAA
Statistics
Matches: 189, Mismatches: 44, Indels: 36
0.70 0.16 0.13
Matches are distributed among these distances:
2 18 0.10
3 154 0.81
4 17 0.09
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29533493 original size:22 final size:22
Alignment explanation
Indices: 29533442--29533502 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
29533432 ATAAGTAAAT
* *
29533442 ACAAAAATAA-AGGAAAATATA
1 ACAAAAATAATAGAAAAATACA
* *
29533463 ATAACAATAATAGAAAAATACA
1 ACAAAAATAATAGAAAAATACA
* *
29533485 ACAATAATAATAGTAAAA
1 ACAAAAATAATAGAAAAA
29533503 GATATAATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.18
Consensus pattern (22 bp):
ACAAAAATAATAGAAAAATACA
Found at i:29533759 original size:16 final size:16
Alignment explanation
Indices: 29533740--29533771 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29533730 TTATAATAAT
29533740 AGTGATGAGAATAACA
1 AGTGATGAGAATAACA
*
29533756 AGTGATGATAATAACA
1 AGTGATGAGAATAACA
29533772 GTAACAATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (16 bp):
AGTGATGAGAATAACA
Found at i:29533904 original size:16 final size:15
Alignment explanation
Indices: 29533875--29533917 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
29533865 TATACGTATG
*
29533875 AAAAATAATGATAGT
1 AAAAATAATAATAGT
29533890 AAAATATAATAATAGT
1 AAAA-ATAATAATAGT
*
29533906 AATAATAATAAT
1 AAAAATAATAAT
29533918 GGAATGAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
AAAAATAATAATAGT
Found at i:29534020 original size:3 final size:3
Alignment explanation
Indices: 29534012--29534041 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
29534002 ACACTACCAT
29534012 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29534042 TAGAAATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29534143 original size:3 final size:3
Alignment explanation
Indices: 29534135--29534172 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
29534125 AAATATACAC
29534135 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
29534173 TATTAAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:29534690 original size:25 final size:25
Alignment explanation
Indices: 29534647--29534703 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
29534637 AATCTCAAAA
29534647 AAAAGAAAAATCCCCTCTTGAATCTC
1 AAAA-AAAAATCCCCTCTTGAATCTC
* *
29534673 AAAAAAAAATCTCTTCTTGAATCTC
1 AAAAAAAAATCCCCTCTTGAATCTC
29534698 AAAAAA
1 AAAAAA
29534704 TTTCTTCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.25
Consensus pattern (25 bp):
AAAAAAAAATCCCCTCTTGAATCTC
Found at i:29534704 original size:22 final size:23
Alignment explanation
Indices: 29534652--29534711 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 23
29534642 CAAAAAAAAG
* *
29534652 AAAAATCCCCTCTTGAATCTCAAAA
1 AAAAATCTCTTCTTGAATCTC--AA
29534677 AAAAATCTCTTCTTGAATCTC-A
1 AAAAATCTCTTCTTGAATCTCAA
*
29534699 AAAAATTTCTTCT
1 AAAAATCTCTTCT
29534712 CTCCAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.41
25 19 0.59
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.33
Consensus pattern (23 bp):
AAAAATCTCTTCTTGAATCTCAA
Found at i:29535624 original size:205 final size:205
Alignment explanation
Indices: 29535260--29536049 Score: 1327
Period size: 205 Copynumber: 3.9 Consensus size: 205
29535250 AGATTTATTT
* * * * * * * * *
29535260 CTTCGATTTGATCCCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTTAACGTAAGCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAATCAC
** * * * * *
29535325 GCGAAAGCCAAATCAACTATG-ATTCGATTTGTTCCTTGTAAGCATAAGGATGCCAATCCATCTT
66 ATGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
*
29535389 GGATCCGCTTCAGCATAAACATCCGAAGGTGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
131 GGATCCGCTTCAGCATAAACATCTGAAGGTGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
29535454 AGATGCCAAA
196 AGATGCCAAA
29535464 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAATCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAATCAC
29535529 ATGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
66 ATGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
* *
29535594 GGATCTGCTTCAGCGA-AATCATCTGAAGGTGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTG
131 GGATCCGCTTCAGC-ATAAACATCTGAAGGTGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTG
29535658 AAGATGCCAAA
195 AAGATGCCAAA
29535669 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAATCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAATCAC
29535734 ATGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
66 ATGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
29535799 GGATCCGCTTCAGCATAAACATCTGAAGGTGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
131 GGATCCGCTTCAGCATAAACATCTGAAGGTGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
29535864 AGATGCCAAA
196 AGATGCCAAA
29535874 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAATCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAATCAC
29535939 ATGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
66 ATGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
* * *
29536004 GGATCTGCTTCAG--TGAAATCGTCTGAAGGCGAGATCTGCTATGTGT
131 GGATCCGCTTCAGCAT-AAA-CATCTGAAGGTGAGATCTGCTATGTGT
29536050 GGCCTATTAC
Statistics
Matches: 557, Mismatches: 24, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
203 1 0.00
204 78 0.14
205 477 0.86
206 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (205 bp):
CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAATCAC
ATGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
GGATCCGCTTCAGCATAAACATCTGAAGGTGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
AGATGCCAAA
Found at i:29544122 original size:15 final size:14
Alignment explanation
Indices: 29544080--29544129 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
29544070 ATAACTTTGA
*
29544080 ATGCAAATGATGTG
1 ATGCAAATGATGAG
29544094 ATG-AAATGTTATGAG
1 ATGCAAATG--ATGAG
29544109 ATGCAAATGCATGA-
1 ATGCAAATG-ATGAG
29544123 ATGCAAA
1 ATGCAAA
29544130 AAGAATATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.32
15 11 0.35
16 5 0.16
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (14 bp):
ATGCAAATGATGAG
Found at i:29547981 original size:3 final size:3
Alignment explanation
Indices: 29547975--29548213 Score: 75
Period size: 3 Copynumber: 80.3 Consensus size: 3
29547965 AAAATACAAC
* * * *
29547975 AAT AAT AAT AGT AA- AAG ATAT AAT AA- CAT AAT AAT -AT AAT AGT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * *
29548018 AAT AGT AAC AAT -AT GAC GAT AAT AGT AAA AAT AAT -AT ATT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * **
29548062 AAT AGT AAT AA- AAGT AGT GCT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
29548107 AAT AAT AAT GAT GAT GAT -CT ATT AAGT TAT AAT GAA- AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT -AAT AAT AAT AAT
* * * * *
29548152 AAT GAT GAT -AT ATT AGAT AAT AAT AGT AA- AAT AAT AAGT AAC AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
*
29548197 AAT AAAT TAT AAT AAT A
1 AAT -AAT AAT AAT AAT A
29548214 GTGATGAGAA
Statistics
Matches: 174, Mismatches: 44, Indels: 36
0.69 0.17 0.14
Matches are distributed among these distances:
2 18 0.10
3 139 0.80
4 17 0.10
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29547981 original size:22 final size:22
Alignment explanation
Indices: 29547930--29547990 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
29547920 ATAAGTAAAT
* *
29547930 ACAAAAATAA-AGGAAAATATA
1 ACAAAAATAATAGAAAAATACA
* *
29547951 ATAACAATAATAGAAAAATACA
1 ACAAAAATAATAGAAAAATACA
* *
29547973 ACAATAATAATAGTAAAA
1 ACAAAAATAATAGAAAAA
29547991 GATATAATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.18
Consensus pattern (22 bp):
ACAAAAATAATAGAAAAATACA
Found at i:29548232 original size:16 final size:16
Alignment explanation
Indices: 29548213--29548244 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29548203 TTATAATAAT
29548213 AGTGATGAGAATAACA
1 AGTGATGAGAATAACA
*
29548229 AGTGATGATAATAACA
1 AGTGATGAGAATAACA
29548245 GTAACAATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (16 bp):
AGTGATGAGAATAACA
Found at i:29548377 original size:16 final size:15
Alignment explanation
Indices: 29548348--29548390 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
29548338 TATACGTATG
*
29548348 AAAAATAATGATAGT
1 AAAAATAATAATAGT
29548363 AAAATATAATAATAGT
1 AAAA-ATAATAATAGT
*
29548379 AATAATAATAAT
1 AAAAATAATAAT
29548391 GGAATGAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
AAAAATAATAATAGT
Found at i:29548493 original size:3 final size:3
Alignment explanation
Indices: 29548485--29548520 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
29548475 ACACTACCAT
29548485 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29548521 TAGAAATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29548622 original size:3 final size:3
Alignment explanation
Indices: 29548614--29548657 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
29548604 AAATATACAC
29548614 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
29548658 TTAAAATGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:29549151 original size:30 final size:29
Alignment explanation
Indices: 29549115--29549187 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 29
29549105 GATTTTTTGT
29549115 TCTTGAATCTCAAAAAAAAGAAAAATCCCC
1 TCTTGAATCTCAAAAAAAA-AAAAATCCCC
* *
29549145 TCTTGAATCTC---AAAAAAAAAATCTCT
1 TCTTGAATCTCAAAAAAAAAAAAATCCCC
29549171 TCTTGAATCTCAAAAAA
1 TCTTGAATCTCAAAAAA
29549188 TTTCTTCTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 19 0.50
27 5 0.13
29 3 0.08
30 11 0.29
ACGTcount: A:0.48, C:0.21, G:0.05, T:0.26
Consensus pattern (29 bp):
TCTTGAATCTCAAAAAAAAAAAAATCCCC
Found at i:29550449 original size:19 final size:19
Alignment explanation
Indices: 29550425--29550463 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
29550415 AAATCTAAAC
29550425 ATAATTTTTATAATTTTTT
1 ATAATTTTTATAATTTTTT
29550444 ATAATTTTTATAATTTTTT
1 ATAATTTTTATAATTTTTT
29550463 A
1 A
29550464 GGGAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATAATTTTTATAATTTTTT
Found at i:29550463 original size:10 final size:9
Alignment explanation
Indices: 29550425--29550461 Score: 65
Period size: 9 Copynumber: 4.0 Consensus size: 9
29550415 AAATCTAAAC
29550425 ATAATTTTT
1 ATAATTTTT
29550434 ATAATTTTTT
1 ATAA-TTTTT
29550444 ATAATTTTT
1 ATAATTTTT
29550453 ATAATTTTT
1 ATAATTTTT
29550462 TAGGGAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 18 0.67
10 9 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATAATTTTT
Found at i:29551283 original size:2 final size:2
Alignment explanation
Indices: 29551276--29551304 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29551266 CGACTTAATT
29551276 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29551305 TGATTTGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29560423 original size:21 final size:21
Alignment explanation
Indices: 29560382--29560423 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29560372 ATGATTTTCT
*
29560382 AATGCTAACTATTTCGATTAA
1 AATGCTAACTATTTAGATTAA
29560403 AATGCTAACATATTTAG-TTAA
1 AATGCTAAC-TATTTAGATTAA
29560424 TCATTTAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (21 bp):
AATGCTAACTATTTAGATTAA
Found at i:29560823 original size:29 final size:29
Alignment explanation
Indices: 29560776--29560831 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
29560766 TTTAATTCTT
* *
29560776 TTTAATAGTACAGGTACT-ATATTGATCTA
1 TTTAACAGTACAGGGACTAAT-TTGATCTA
*
29560805 TTTAACAGTAGAGGGACTAATTTGATC
1 TTTAACAGTACAGGGACTAATTTGATC
29560832 AAGTCCCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 21 0.91
30 2 0.09
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (29 bp):
TTTAACAGTACAGGGACTAATTTGATCTA
Found at i:29561955 original size:83 final size:81
Alignment explanation
Indices: 29561798--29561955 Score: 217
Period size: 83 Copynumber: 1.9 Consensus size: 81
29561788 ACATCTTCTG
* * **
29561798 TTATAACACATAACAATGCCATATATATAGACACGTAAGTATTTGCAATTCATCTTTGCTTATCC
1 TTATAACACATAACAATGCCATATATATAGACACATAAGTATTTGCAATTCATCTTTACTTAAAC
*
29561863 TACCGTGCAACCTCCA
66 TACCATGCAACCTCCA
* * *
29561879 TTATAACACGTAACAATGCCATATATATATACACTCATAAGTATTTGCAATTCATTTTTACTTAA
1 TTATAACACATAACAATGCCATATATATAGACA--CATAAGTATTTGCAATTCATCTTTACTTAA
*
29561944 ACTACTATGCAA
64 ACTACCATGCAA
29561956 TCTTAACATC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
81 31 0.47
83 35 0.53
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (81 bp):
TTATAACACATAACAATGCCATATATATAGACACATAAGTATTTGCAATTCATCTTTACTTAAAC
TACCATGCAACCTCCA
Found at i:29577385 original size:2 final size:2
Alignment explanation
Indices: 29577378--29577412 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
29577368 TCTTTTGTTT
*
29577378 TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29577413 CTTAGAGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29579328 original size:193 final size:193
Alignment explanation
Indices: 29578992--29579377 Score: 754
Period size: 193 Copynumber: 2.0 Consensus size: 193
29578982 TTCAAGCACG
29578992 TGTCCATAAGCATAGGTGCAACGTTGGTCGGCGGTACGGCTTGATATGATTGAAGTGGAACATGT
1 TGTCCATAAGCATAGGTGCAACGTTGGTCGGCGGTACGGCTTGATATGATTGAAGTGGAACATGT
29579057 GACTAATGTGTGATAATTATCCTATCGGGATTGGCATAGAGAAAAAGCAGAATTTATATTTTCTG
66 GACTAATGTGTGATAATTATCCTATCGGGATTGGCATAGAGAAAAAGCAGAATTTATATTTTCTG
* *
29579122 CTTCTATATGAATGCTGAGGAAAAAGAAGCTATAAAGTTTGAGAATTCAATCAAACCAGAAAT
131 CTTCTACATGAATGCTGAGGAAAAAGAAGCTATAAAGTTTGAGAATACAATCAAACCAGAAAT
29579185 TGTCCATAAGCATAGGTGCAACGTTGGTCGGCGGTACGGCTTGATATGATTGAAGTGGAACATGT
1 TGTCCATAAGCATAGGTGCAACGTTGGTCGGCGGTACGGCTTGATATGATTGAAGTGGAACATGT
29579250 GACTAATGTGTGATAATTATCCTATCGGGATTGGCATAGAGAAAAAGCAGAATTTATATTTTCTG
66 GACTAATGTGTGATAATTATCCTATCGGGATTGGCATAGAGAAAAAGCAGAATTTATATTTTCTG
29579315 CTTCTACATGAATGCTGAGGAAAAAGAAGCTATAAAGTTTGAGAATACAATCAAACCAGAAAT
131 CTTCTACATGAATGCTGAGGAAAAAGAAGCTATAAAGTTTGAGAATACAATCAAACCAGAAAT
29579378 AGATATCAGC
Statistics
Matches: 191, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
193 191 1.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (193 bp):
TGTCCATAAGCATAGGTGCAACGTTGGTCGGCGGTACGGCTTGATATGATTGAAGTGGAACATGT
GACTAATGTGTGATAATTATCCTATCGGGATTGGCATAGAGAAAAAGCAGAATTTATATTTTCTG
CTTCTACATGAATGCTGAGGAAAAAGAAGCTATAAAGTTTGAGAATACAATCAAACCAGAAAT
Found at i:29580017 original size:2 final size:2
Alignment explanation
Indices: 29580010--29580037 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29580000 ATGTGCCTTG
29580010 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
29580038 ATTGGAGGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29589217 original size:31 final size:31
Alignment explanation
Indices: 29589179--29589240 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
29589169 CTATCTCAGC
29589179 ATCAACTCCAACCAGCCTCACACCGATATGG
1 ATCAACTCCAACCAGCCTCACACCGATATGG
*
29589210 ATCAACTCCAAGCAGCCTCACACCGATATGG
1 ATCAACTCCAACCAGCCTCACACCGATATGG
29589241 CTAAGTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.37, G:0.15, T:0.16
Consensus pattern (31 bp):
ATCAACTCCAACCAGCCTCACACCGATATGG
Found at i:29594001 original size:42 final size:42
Alignment explanation
Indices: 29593899--29594038 Score: 122
Period size: 44 Copynumber: 3.3 Consensus size: 42
29593889 ATCTGTTCTG
* * *
29593899 CGTGTAAGACCAC-GTCTGAGACGTTGGCATCAATTTCTG-TTCT
1 CGTGTAAGACC-CTGTCTGAGACATTGGCATC-GTATCTGATT-T
* *
29593942 GCGTGTAAGACCATGTCTGAGACATTGGAATCGTATCTGATTT
1 -CGTGTAAGACCCTGTCTGAGACATTGGCATCGTATCTGATTT
* * * * *
29593985 CGTGTAAGACCCTGTCTGGGATAGTGGCATCGATATTTGATTA
1 CGTGTAAGACCCTGTCTGAGACATTGGCATCG-TATCTGATTT
*
29594028 CATGTAAGACC
1 CGTGTAAGACC
29594039 ACATCTGGGA
Statistics
Matches: 80, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
42 27 0.34
43 24 0.30
44 29 0.36
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (42 bp):
CGTGTAAGACCCTGTCTGAGACATTGGCATCGTATCTGATTT
Found at i:29594037 original size:43 final size:42
Alignment explanation
Indices: 29593945--29594039 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
29593935 CTGTTCTGCG
* * *
29593945 TGTAAGACCATGTCTGAGACATTGGAATCGTATCTGATTTCG
1 TGTAAGACCATGTCTGAGACAGTGGAATCGTATCTGATTACA
* * * * *
29593987 TGTAAGACCCTGTCTGGGATAGTGGCATCGATATTTGATTACA
1 TGTAAGACCATGTCTGAGACAGTGGAATCG-TATCTGATTACA
29594030 TGTAAGACCA
1 TGTAAGACCA
29594040 CATCTGGGAC
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 25 0.58
43 18 0.42
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (42 bp):
TGTAAGACCATGTCTGAGACAGTGGAATCGTATCTGATTACA
Found at i:29602406 original size:28 final size:28
Alignment explanation
Indices: 29602369--29602422 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
29602359 ACAAATTCAA
29602369 AAAAGAAT-AAAATTAAAATTGATAAAAT
1 AAAAGAATAAAAATT-AAATTGATAAAAT
* *
29602397 AAAAGTATAAAAATTAAATTTATAAA
1 AAAAGAATAAAAATTAAATTGATAAA
29602423 TTTTACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (28 bp):
AAAAGAATAAAAATTAAATTGATAAAAT
Found at i:29604488 original size:23 final size:21
Alignment explanation
Indices: 29604440--29604485 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 21
29604430 TTATTATTAA
*
29604440 AATATAAATTTAAAAAATCAT
1 AATATAAATTTAAAAAATAAT
29604461 AATATATAATATTATAAAAATAAT
1 AATATA-AAT-TTA-AAAAATAAT
29604485 A
1 A
29604486 TATGATTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 3 0.14
23 3 0.14
24 9 0.43
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AATATAAATTTAAAAAATAAT
Done.