Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_pilon, whole genome shotgun sequence
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: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 29
Found at i:3509417 original size:19 final size:19
Alignment explanation
Indices: 3509376--3509446 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 19
3509366 CTTTCACATT
* * * *
3509376 TCATAATTTATTTCCAAAT
1 TCATAACTTATTTTCAGAC
*
3509395 TCATAACTTATTTTTAGAC
1 TCATAACTTATTTTCAGAC
* * * *
3509414 TCATAGCTTACTGTCAGAT
1 TCATAACTTATTTTCAGAC
*
3509433 TCATATCTTATTTT
1 TCATAACTTATTTT
3509447 AAAATTCATA
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.48
Consensus pattern (19 bp):
TCATAACTTATTTTCAGAC
Found at i:3517229 original size:30 final size:31
Alignment explanation
Indices: 3517173--3517250 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
3517163 TAAATTTTAG
** *
3517173 TAGTGACTAAAACAT-AAATTTTGAAA-GTT
1 TAGTGACTAAAGTATAAAATTTGGAAAGGTT
3517202 TAGTGACTAAAGTATAAAATTTGGAAAGGTT
1 TAGTGACTAAAGTATAAAATTTGGAAAGGTT
* *
3517233 TAGGGACCAAAGTGATAA
1 TAGTGACTAAAGT-ATAA
3517251 CTTTTCCAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.32
30 10 0.24
31 14 0.34
32 4 0.10
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (31 bp):
TAGTGACTAAAGTATAAAATTTGGAAAGGTT
Found at i:3518463 original size:19 final size:20
Alignment explanation
Indices: 3518420--3518465 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
3518410 TACTATGCTG
* * *
3518420 GAAATTAATGTTTGAGTGTT
1 GAAATTGATGTTAGAATGTT
3518440 GAAATTGATGTTAGAATG-T
1 GAAATTGATGTTAGAATGTT
3518459 GAAATTG
1 GAAATTG
3518466 GATTATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:3536904 original size:32 final size:31
Alignment explanation
Indices: 3536868--3536944 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
3536858 CGGGGCCGTG
*
3536868 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
3536900 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
3536931 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
3536945 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:3536927 original size:63 final size:63
Alignment explanation
Indices: 3536821--3536944 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
3536811 CCCTAAGGGA
* * ** *
3536821 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
3536884 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
3536945 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:3537860 original size:17 final size:17
Alignment explanation
Indices: 3537821--3537860 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3537811 GAAAGTCAAC
*
3537821 GGTCAACGGTCGGGTCG
1 GGTCAGCGGTCGGGTCG
3537838 GGTCAGCGGTCGGGTCG
1 GGTCAGCGGTCGGGTCG
3537855 GGTCAG
1 GGTCAG
3537861 ACCGGTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.10, C:0.23, G:0.50, T:0.17
Consensus pattern (17 bp):
GGTCAGCGGTCGGGTCG
Found at i:3537873 original size:9 final size:9
Alignment explanation
Indices: 3537855--3537993 Score: 98
Period size: 9 Copynumber: 14.3 Consensus size: 9
3537845 GGTCGGGTCG
*
3537855 GGTCAGACC
1 GGTCAAACC
3537864 GGTCAAACC
1 GGTCAAACC
*
3537873 GGCTCAGACC
1 GG-TCAAACC
*
3537883 GGTCAAATC
1 GGTCAAACC
* *
3537892 GATTCAGACC
1 G-GTCAAACC
3537902 GGTCAAACC
1 GGTCAAACC
*
3537911 GGTTCGAACC
1 GG-TCAAACC
*
3537921 GGTTGAAACC
1 GG-TCAAACC
3537931 GGTCAAACC
1 GGTCAAACC
3537940 GGTCAGAACC
1 GGTCA-AACC
*
3537950 GGTTGAAAACC
1 GG-T-CAAACC
3537961 GGTCAGAACC
1 GGTCA-AACC
*
3537971 GGTTGAAAACC
1 GG-T-CAAACC
*
3537982 GGTTAAACC
1 GGTCAAACC
3537991 GGT
1 GGT
3537994 TTCCAGCAGC
Statistics
Matches: 104, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
9 44 0.42
10 44 0.42
11 14 0.13
12 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:3537879 original size:19 final size:19
Alignment explanation
Indices: 3537857--3537994 Score: 118
Period size: 19 Copynumber: 7.1 Consensus size: 19
3537847 TCGGGTCGGG
*
3537857 TCAGACCGGTCAAACCGGC
1 TCAGACCGGTCAAACCGGT
* *
3537876 TCAGACCGGTCAAATCGAT
1 TCAGACCGGTCAAACCGGT
3537895 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
3537914 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
3537933 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* *
3537953 TGAAAACCGGTCAGAACCGGT
1 T-CAGACCGGTCA-AACCGGT
* * *
3537974 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
3537994 T
1 T
3537995 TCCAGCAGCC
Statistics
Matches: 103, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
18 3 0.03
19 53 0.51
20 17 0.17
21 30 0.29
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:3537931 original size:29 final size:29
Alignment explanation
Indices: 3537899--3537993 Score: 124
Period size: 29 Copynumber: 3.2 Consensus size: 29
3537889 ATCGATTCAG
3537899 ACCGGTCAAACCGGTTCGAACCGGTTGAA
1 ACCGGTCAAACCGGTTCGAACCGGTTGAA
3537928 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
3537958 ACCGGTCAGAACCGGTT-GAAAACCGGTT-AA
1 ACCGGTCA-AACCGGTTCG--AACCGGTTGAA
3537988 ACCGGT
1 ACCGGT
3537994 TTCCAGCAGC
Statistics
Matches: 60, Mismatches: 0, Indels: 11
0.85 0.00 0.15
Matches are distributed among these distances:
28 2 0.03
29 24 0.40
30 19 0.32
31 6 0.10
32 9 0.15
ACGTcount: A:0.31, C:0.26, G:0.27, T:0.16
Consensus pattern (29 bp):
ACCGGTCAAACCGGTTCGAACCGGTTGAA
Found at i:3537961 original size:21 final size:21
Alignment explanation
Indices: 3537935--3537994 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
3537925 GAAACCGGTC
3537935 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
3537956 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
3537977 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
3537995 TCCAGCAGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 8 0.21
21 30 0.79
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:3539969 original size:21 final size:21
Alignment explanation
Indices: 3539921--3539966 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
3539911 CCAATCATTG
3539921 TTTTGTATAGGTCGTGCACTGA
1 TTTTGTATAGGTCGTG-ACTGA
3539943 TTTTGTATAGG-CTGTG-CTGA
1 TTTTGTATAGGTC-GTGACTGA
3539963 TTTT
1 TTTT
3539967 TGTTTATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.35
21 1 0.04
22 14 0.61
ACGTcount: A:0.15, C:0.11, G:0.26, T:0.48
Consensus pattern (21 bp):
TTTTGTATAGGTCGTGACTGA
Found at i:3541433 original size:2 final size:2
Alignment explanation
Indices: 3541426--3541453 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3541416 TTCAAAACTA
3541426 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3541454 GATTATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3542109 original size:39 final size:39
Alignment explanation
Indices: 3542065--3542168 Score: 95
Period size: 39 Copynumber: 2.7 Consensus size: 39
3542055 TCCTGTACAC
*
3542065 CAGTAAGGGCTTACCCTGTACA-AAAAGCAAAGGAGCCTA
1 CAGTAAGGACTTACCCTGTACACAAAA-CAAAGGAGCCTA
* ** * * * * *
3542104 CAGTAAGGTCTTGTCATGTGCACAAAACAGATGAGCCTG
1 CAGTAAGGACTTACCCTGTACACAAAACAAAGGAGCCTA
3542143 CAGTAAGGACTTACCCTG-AGCACAAA
1 CAGTAAGGACTTACCCTGTA-CACAAA
3542169 GCCAAGAAGT
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
39 46 0.92
40 4 0.08
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (39 bp):
CAGTAAGGACTTACCCTGTACACAAAACAAAGGAGCCTA
Found at i:3543666 original size:50 final size:49
Alignment explanation
Indices: 3543589--3543997 Score: 552
Period size: 49 Copynumber: 8.3 Consensus size: 49
3543579 TTATGAATAA
* *
3543589 ATAAAAGGTTCCACTAATGAAAGTTAAATTCATAACGGTGCATTTTCGGC
1 ATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCA-TTTCGGC
* **
3543639 ATAAAAGGTGCCACTAATGAAAATTAAATGCATAACGACGCATTTCGGC
1 ATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGGC
* * * * * *
3543688 ATAAAATGTGTCACTAATGGAAGTTAAATGCATAACAGTGTATTTTTGGC
1 ATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCA-TTTCGGC
* * *
3543738 ATAAAAGGTGCCACAAATGAAAGTTAAATGCATAACAGTGCATTTCAGC
1 ATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGGC
* ** *
3543787 ATAAAAGGTGTCACTAATGAAAGTTAAATGCATAACGGTAAATTTTCGAC
1 ATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCA-TTTCGGC
* * *
3543837 ATAAAAGGTGCCACTAATGAAAGTTAAATGCATACCGATGCATTTCAGC
1 ATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGGC
*
3543886 ATAAAAGGTGTCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGGC
1 ATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGGC
*
3543935 ATAAAAGGT--CACTAATGAAAGTTAAATGCATAACGGTGCATTTTAGGC
1 ATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCA-TTTCGGC
*
3543983 ATAAAAGGTGTCACT
1 ATAAAAGGTGCCACT
3543998 CATGTTATTC
Statistics
Matches: 314, Mismatches: 40, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
47 31 0.10
48 15 0.05
49 142 0.45
50 126 0.40
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (49 bp):
ATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGGC
Found at i:3543765 original size:99 final size:99
Alignment explanation
Indices: 3543589--3543997 Score: 612
Period size: 99 Copynumber: 4.2 Consensus size: 99
3543579 TTATGAATAA
*
3543589 ATAAAAGGT-TCCACTAATGAAAGTTAAATTCATAACGGTGCATTTTCGGCATAAAAGGTGCCAC
1 ATAAAAGGTGT-CACTAATGAAAGTTAAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCAC
* * *
3543653 TAATGAAAATTAAATGCATAACGACGCATTTCGGC
65 TAATGAAAGTTAAATGCATAACGATGCATTTCAGC
* * * * * *
3543688 ATAAAATGTGTCACTAATGGAAGTTAAATGCATAACAGTGTATTTTTGGCATAAAAGGTGCCACA
1 ATAAAAGGTGTCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCACT
3543753 AATGAAAGTTAAATGCATAAC-AGTGCATTTCAGC
66 AATGAAAGTTAAATGCATAACGA-TGCATTTCAGC
** *
3543787 ATAAAAGGTGTCACTAATGAAAGTTAAATGCATAACGGTAAATTTTCGACATAAAAGGTGCCACT
1 ATAAAAGGTGTCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCACT
*
3543852 AATGAAAGTTAAATGCATACCGATGCATTTCAGC
66 AATGAAAGTTAAATGCATAACGATGCATTTCAGC
3543886 ATAAAAGGTGTCACTAATGAAAGTTAAATGCATAACGGTGCA-TTTCGGCATAAAAGGT--CACT
1 ATAAAAGGTGTCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCACT
* *
3543948 AATGAAAGTTAAATGCATAACGGTGCATTTTAGGC
66 AATGAAAGTTAAATGCATAACGATGCATTTCA-GC
3543983 ATAAAAGGTGTCACT
1 ATAAAAGGTGTCACT
3543998 CATGTTATTC
Statistics
Matches: 281, Mismatches: 25, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
96 33 0.12
97 17 0.06
98 16 0.06
99 213 0.76
100 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (99 bp):
ATAAAAGGTGTCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCACT
AATGAAAGTTAAATGCATAACGATGCATTTCAGC
Found at i:3544518 original size:22 final size:21
Alignment explanation
Indices: 3544493--3544542 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
3544483 TAATTTTTTG
3544493 TATTATGT-TACAAAGAATGTTT
1 TATTAT-TATACAAA-AATGTTT
*
3544515 TATTATTATACCAAAATGTTT
1 TATTATTATACAAAAATGTTT
*
3544536 TTTTATT
1 TATTATT
3544543 TTCGAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (21 bp):
TATTATTATACAAAAATGTTT
Found at i:3547798 original size:14 final size:14
Alignment explanation
Indices: 3547752--3547791 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
3547742 TTTGGTCCTA
3547752 AAATAAATTTAAAT
1 AAATAAATTTAAAT
3547766 AAATAAATTTAAAT
1 AAATAAATTTAAAT
3547780 AAATAAATTTAA
1 AAATAAATTTAA
3547792 TCCAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATAAATTTAAAT
Found at i:3551768 original size:21 final size:21
Alignment explanation
Indices: 3551718--3551779 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
3551708 TTCAACATGA
*
3551718 CTTAACCTTTTGATTAAAAGA
1 CTTAACCTTTTGATTAAAAGG
**
3551739 CTTCTCCTTTTGATTAAAAGG
1 CTTAACCTTTTGATTAAAAGG
*
3551760 CTTAACCTTTTCA-TAAAAGG
1 CTTAACCTTTTGATTAAAAGG
3551780 ATTTAATCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
20 7 0.20
21 28 0.80
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (21 bp):
CTTAACCTTTTGATTAAAAGG
Found at i:3551778 original size:20 final size:21
Alignment explanation
Indices: 3551718--3551794 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
3551708 TTCAACATGA
* *
3551718 CTTAACCTTTTGATTAAAAGA
1 CTTAACCTTTTCATTAAAAGG
** *
3551739 CTTCTCCTTTTGATTAAAAGG
1 CTTAACCTTTTCATTAAAAGG
3551760 CTTAACCTTTTCA-TAAAAGG
1 CTTAACCTTTTCATTAAAAGG
* *
3551780 ATTTAATCTTTTCAT
1 -CTTAACCTTTTCAT
3551795 GAAGAGAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
20 7 0.15
21 39 0.85
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (21 bp):
CTTAACCTTTTCATTAAAAGG
Found at i:3552658 original size:11 final size:11
Alignment explanation
Indices: 3552638--3552669 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3552628 ACAAGGGGAA
*
3552638 GAATCGATAAG
1 GAATCCATAAG
3552649 GAATCCATAAG
1 GAATCCATAAG
3552660 GAATCCATAA
1 GAATCCATAA
3552670 AAAGAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (11 bp):
GAATCCATAAG
Found at i:3553809 original size:23 final size:23
Alignment explanation
Indices: 3553754--3553829 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
3553744 CATTTGTGCT
* **
3553754 CATTTATTTAATATTCGTGAACA
1 CATTCATTTAATATTCGCAAACA
**
3553777 TGTTCATTTAATATTCGCAAACA
1 CATTCATTTAATATTCGCAAACA
* * *
3553800 CATTCGTTTAATGTTTGGCAAACAA
1 CATTCATTTAAT-ATTCGCAAAC-A
3553825 CATTC
1 CATTC
3553830 TCTTTTTATC
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 27 0.66
24 8 0.20
25 6 0.15
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (23 bp):
CATTCATTTAATATTCGCAAACA
Found at i:3556405 original size:19 final size:20
Alignment explanation
Indices: 3556362--3556407 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
3556352 TACTATGCTG
* * *
3556362 GAAATTATTGTTTGAGTGTT
1 GAAATTGTTGTTAGAATGTT
3556382 GAAATTGTTGTTAGAATG-T
1 GAAATTGTTGTTAGAATGTT
3556401 GAAATTG
1 GAAATTG
3556408 GATCAATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.43
Consensus pattern (20 bp):
GAAATTGTTGTTAGAATGTT
Found at i:3560182 original size:22 final size:21
Alignment explanation
Indices: 3560155--3560196 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
3560145 AAATAACTTT
3560155 TTGGTCAAAATCAACAGTCAAA
1 TTGGTCAAAATCAA-AGTCAAA
*
3560177 TTGGTCAAAGTCAAAGTCAA
1 TTGGTCAAAATCAAAGTCAA
3560197 CGGGTCTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (21 bp):
TTGGTCAAAATCAAAGTCAAA
Found at i:3561583 original size:30 final size:30
Alignment explanation
Indices: 3561526--3561665 Score: 96
Period size: 30 Copynumber: 4.7 Consensus size: 30
3561516 ATCGGATTAA
* * * *
3561526 CACTATAGTGTGTAAGCATACTAAGTGCAG
1 CACTGTAGTGTGTAAGGACACTTAGTGCAG
3561556 CACTGTAGTGTGTAAGGACACTTAGTGCA-
1 CACTGTAGTGTGTAAGGACACTTAGTGCAG
* *
3561585 TA-TG--GTG-G-ACACGAC-CTTATGTGCATTGG
1 CACTGTAGTGTGTA-AGGACACTTA-GTGCA---G
* *
3561614 CACTATAGTGTGTAGGGACACTTAGTGCAG
1 CACTGTAGTGTGTAAGGACACTTAGTGCAG
* *
3561644 CTCTGTAATGTGTAAGGACACT
1 CACTGTAGTGTGTAAGGACACT
3561666 CAGGGTATCT
Statistics
Matches: 84, Mismatches: 14, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
24 5 0.06
25 10 0.12
26 3 0.04
28 2 0.02
29 2 0.02
30 45 0.54
32 3 0.04
33 9 0.11
34 5 0.06
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (30 bp):
CACTGTAGTGTGTAAGGACACTTAGTGCAG
Found at i:3565159 original size:3 final size:3
Alignment explanation
Indices: 3565151--3565290 Score: 280
Period size: 3 Copynumber: 46.7 Consensus size: 3
3565141 ATAACAAATA
3565151 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3565199 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3565247 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3565291 CATAGACTGA
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 137 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3565726 original size:21 final size:21
Alignment explanation
Indices: 3565663--3565726 Score: 51
Period size: 25 Copynumber: 2.9 Consensus size: 21
3565653 ACAAACTTAT
3565663 AAAATTTAAGGAAATG--AAAAA
1 AAAATTTAA--AAATGATAAAAA
*
3565684 AAAATTAATAGAAAATACATAAAAA
1 AAAATT--TA-AAAAT-GATAAAAA
3565709 AAAATTTAAAAATGATAA
1 AAAATTTAAAAATGATAA
3565727 TTTTAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
21 10 0.29
22 9 0.26
23 4 0.11
24 1 0.03
25 11 0.31
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.22
Consensus pattern (21 bp):
AAAATTTAAAAATGATAAAAA
Found at i:3567080 original size:20 final size:20
Alignment explanation
Indices: 3567045--3567083 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3567035 ACCGAATCGG
**
3567045 TTTAACCCGACCTGAACCGA
1 TTTAACCCGAAATGAACCGA
3567065 TTTAACCCGAAATGAACCG
1 TTTAACCCGAAATGAACCG
3567084 TTGACCTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.21
Consensus pattern (20 bp):
TTTAACCCGAAATGAACCGA
Found at i:3567130 original size:22 final size:22
Alignment explanation
Indices: 3567105--3567157 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
3567095 CGGTCATATC
* *
3567105 GTTGACTTTGATCTATCTGACT
1 GTTGACTTTGACCGATCTGACT
*
3567127 GTTGACTTTGACCGGTCTGACT
1 GTTGACTTTGACCGATCTGACT
*
3567149 GTTGGCTTT
1 GTTGACTTT
3567158 TACTTTGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (22 bp):
GTTGACTTTGACCGATCTGACT
Found at i:3573770 original size:20 final size:20
Alignment explanation
Indices: 3573723--3573772 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3573713 GGTCCAGACA
*
3573723 GAACCGAACCCGTTTGACCT
1 GAACCGAACCCGTTTGAACT
*
3573743 G-ACTCGAACCGGTTTGAACT
1 GAAC-CGAACCCGTTTGAACT
3573763 GAACCGAACC
1 GAACCGAACC
3573773 ATTGACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.32, G:0.22, T:0.18
Consensus pattern (20 bp):
GAACCGAACCCGTTTGAACT
Found at i:3573799 original size:22 final size:22
Alignment explanation
Indices: 3573774--3573822 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
3573764 AACCGAACCA
3573774 TTGACCGGT-ATGACCGTTGACC
1 TTGACCGGTCA-GACCGTTGACC
*
3573796 TTGACCGGTCAGACCGTTGACT
1 TTGACCGGTCAGACCGTTGACC
3573818 TTGAC
1 TTGAC
3573823 TTTAACCGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (22 bp):
TTGACCGGTCAGACCGTTGACC
Found at i:3573879 original size:16 final size:17
Alignment explanation
Indices: 3573832--3573871 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
3573822 CTTTAACCGA
3573832 AAAAGTTCAAATTTTTG
1 AAAAGTTCAAATTTTTG
3573849 AAAAGTTCAAATTTTTG
1 AAAAGTTCAAATTTTTG
3573866 AAAAGT
1 AAAAGT
3573872 CATTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (17 bp):
AAAAGTTCAAATTTTTG
Found at i:3575802 original size:36 final size:36
Alignment explanation
Indices: 3575762--3575872 Score: 101
Period size: 36 Copynumber: 3.2 Consensus size: 36
3575752 TAATGAGCTC
3575762 GAGTCGAGCAAAATTTTAACGAGCTTAACGAGCAAT
1 GAGTCGAGCAAAATTTTAACGAGCTTAACGAGCAAT
* *
3575798 GAGTCGAGCAACAAATTTT------CTTAACGAG-TAC
1 GAGTCGAGC-A-AAATTTTAACGAGCTTAACGAGCAAT
* * * *
3575829 GAGGCAAACAAAATTTTAACGAGCTTAACGTGCAAT
1 GAGTCGAGCAAAATTTTAACGAGCTTAACGAGCAAT
3575865 GAGTCGAG
1 GAGTCGAG
3575873 TCGAGCAACA
Statistics
Matches: 55, Mismatches: 11, Indels: 18
0.65 0.13 0.21
Matches are distributed among these distances:
29 7 0.13
30 1 0.02
31 7 0.13
32 9 0.16
35 8 0.15
36 15 0.27
37 1 0.02
38 7 0.13
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (36 bp):
GAGTCGAGCAAAATTTTAACGAGCTTAACGAGCAAT
Found at i:3575841 original size:67 final size:67
Alignment explanation
Indices: 3575732--3575872 Score: 212
Period size: 67 Copynumber: 2.1 Consensus size: 67
3575722 TCATCAAAGA
* * * * *
3575732 AGTCGAGCAACACATTTTCTTAATGAGCTCGAGTCGAGCAAAATTTTAACGAGCTTAACGAGCAA
1 AGTCGAGCAACAAATTTTCTTAACGAGCTCGAGGCAAACAAAATTTTAACGAGCTTAACGAGCAA
3575797 TG
66 TG
*
3575799 AGTCGAGCAACAAATTTTCTTAACGAG-TACGAGGCAAACAAAATTTTAACGAGCTTAACGTGCA
1 AGTCGAGCAACAAATTTTCTTAACGAGCT-CGAGGCAAACAAAATTTTAACGAGCTTAACGAGCA
3575863 ATG
65 ATG
3575866 AGTCGAG
1 AGTCGAG
3575873 TCGAGCAACA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 1 0.01
67 66 0.99
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (67 bp):
AGTCGAGCAACAAATTTTCTTAACGAGCTCGAGGCAAACAAAATTTTAACGAGCTTAACGAGCAA
TG
Found at i:3577812 original size:23 final size:23
Alignment explanation
Indices: 3577785--3577852 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
3577775 ACAAAAAGGT
3577785 AGAGAAAAACATATCACAAATG-C
1 AGAGAAAAACATATCACAAA-GAC
* * * *
3577808 AGAGATAAACGTGTCATAAAGAC
1 AGAGAAAAACATATCACAAAGAC
3577831 AGAGATAAAA-ATATCACAAAGA
1 AGAGA-AAAACATATCACAAAGA
3577853 TGTAATTATT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
22 1 0.03
23 31 0.89
24 3 0.09
ACGTcount: A:0.56, C:0.13, G:0.16, T:0.15
Consensus pattern (23 bp):
AGAGAAAAACATATCACAAAGAC
Found at i:3582413 original size:50 final size:50
Alignment explanation
Indices: 3582293--3582470 Score: 275
Period size: 50 Copynumber: 3.5 Consensus size: 50
3582283 TTAGCAGTAA
* **
3582293 AGCGCGCCCCCTGCACCGCGCTATACGATGATTTGGCGCCACGTGGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGT-GGGTAT
*
3582344 AGCGCGTCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGTGGGTAT
3582394 AGCGCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGTGGGTAT
* * * *
3582444 AGCGCGGCCCTTGAAGCGCGCTATACG
1 AGCGCGCCCCCTGCACCGCGCTATACG
3582471 CCACGTAGGG
Statistics
Matches: 118, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 78 0.66
51 40 0.34
ACGTcount: A:0.15, C:0.34, G:0.33, T:0.17
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGTGGGTAT
Found at i:3582560 original size:49 final size:52
Alignment explanation
Indices: 3582481--3582604 Score: 175
Period size: 49 Copynumber: 2.5 Consensus size: 52
3582471 CCACGTAGGG
** *
3582481 GTATAGCGCGGATCAGGTACCAC-ACTATACCTTTACTCCT-A-ATAATTTT
1 GTATAGCGCGGGGCAGGTACCGCGACTATACCTTTACTCCTGACATAATTTT
3582530 GTATAGCGCGGGGCAGGTACCGCGAC-ATACCTTTACTCCTGACATAATTTT
1 GTATAGCGCGGGGCAGGTACCGCGACTATACCTTTACTCCTGACATAATTTT
* *
3582581 ATATAGCGCGGGGCAGATACCGCG
1 GTATAGCGCGGGGCAGGTACCGCG
3582605 TTTTGTATAA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
49 34 0.51
50 3 0.04
51 30 0.45
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.27
Consensus pattern (52 bp):
GTATAGCGCGGGGCAGGTACCGCGACTATACCTTTACTCCTGACATAATTTT
Found at i:3586074 original size:110 final size:111
Alignment explanation
Indices: 3585880--3586100 Score: 356
Period size: 110 Copynumber: 2.0 Consensus size: 111
3585870 ATTACAAAAA
* * * *
3585880 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
*
3585945 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCA-AGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGT-AGAGATAT
* *
3585991 TTAATTATTAATATAATAATCATGTATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
3586055 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
3586101 ATGATTTCCA
Statistics
Matches: 102, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
109 1 0.01
110 69 0.68
111 32 0.31
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
Found at i:3586198 original size:14 final size:14
Alignment explanation
Indices: 3586179--3586207 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3586169 TATTAAATAA
3586179 AGTAAAAATATTAT
1 AGTAAAAATATTAT
3586193 AGTAAAAATATTAT
1 AGTAAAAATATTAT
3586207 A
1 A
3586208 AAATATACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (14 bp):
AGTAAAAATATTAT
Found at i:3586816 original size:27 final size:28
Alignment explanation
Indices: 3586762--3586822 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
3586752 TAAAAAATCA
3586762 AAAAGAAAAAAAGAACATAAACACAAGC
1 AAAAGAAAAAAAGAACATAAACACAAGC
* * *
3586790 GAAAGAAGAAAAGAA-ATAATA-AGAAGC
1 AAAAGAAAAAAAGAACATAA-ACACAAGC
3586817 AAAAGA
1 AAAAGA
3586823 TAGAGAGGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.70, C:0.08, G:0.16, T:0.05
Consensus pattern (28 bp):
AAAAGAAAAAAAGAACATAAACACAAGC
Found at i:3588120 original size:28 final size:28
Alignment explanation
Indices: 3588080--3588150 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
3588070 CCGAGAAATG
* *
3588080 AAGGCATTGAGAGGATTTCTTAAAAAAA
1 AAGGAATTGAGAGGATTTCCTAAAAAAA
3588108 AAGGAATTGAGAGGATTTCCTAAAAAAA
1 AAGGAATTGAGAGGATTTCCTAAAAAAA
*
3588136 AAGGTATTGAGAGGA
1 AAGGAATTGAGAGGA
3588151 CAAGAGAGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.46, C:0.06, G:0.25, T:0.23
Consensus pattern (28 bp):
AAGGAATTGAGAGGATTTCCTAAAAAAA
Found at i:3588342 original size:21 final size:24
Alignment explanation
Indices: 3588292--3588342 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 24
3588282 AATTGATTTG
*
3588292 AATTGTAGATTTTAAATAATTTAT
1 AATTATAGATTTTAAATAATTTAT
*
3588316 ATTTATAGA-TTTAAA-AA-TTAT
1 AATTATAGATTTTAAATAATTTAT
3588337 AATTAT
1 AATTAT
3588343 TCAAATCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 9 0.38
22 2 0.08
23 6 0.25
24 7 0.29
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (24 bp):
AATTATAGATTTTAAATAATTTAT
Found at i:3598414 original size:18 final size:19
Alignment explanation
Indices: 3598393--3598436 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3598383 GTTGTTTTTA
*
3598393 AAATAAAAG-ATAAGAATT
1 AAATAAAAGAAAAAGAATT
3598411 AAATAAAAGAAAAAGAATT
1 AAATAAAAGAAAAAGAATT
3598430 AAATAAA
1 AAATAAA
3598437 CAAATTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (19 bp):
AAATAAAAGAAAAAGAATT
Found at i:3599282 original size:5 final size:5
Alignment explanation
Indices: 3599272--3599362 Score: 73
Period size: 5 Copynumber: 17.8 Consensus size: 5
3599262 GTTAAGAGAA
* *
3599272 AAAAT AAAAT AAAAT -AAAT CAAAAT AAAAT -AAAT AGAAT GAAAA- AAAGTT
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT -AAAAT AAA-AT
*
3599322 CAAAA- AAAAT AAAAT AAAACG AAAAT AAAAT GAAAAT AAAA
1 -AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT -AAAAT AAAA
3599363 ACAAAAATAT
Statistics
Matches: 70, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
4 15 0.21
5 36 0.51
6 16 0.23
7 3 0.04
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:3599301 original size:11 final size:11
Alignment explanation
Indices: 3599272--3599368 Score: 75
Period size: 11 Copynumber: 9.4 Consensus size: 11
3599262 GTTAAGAGAA
3599272 AAAATAAAAT-
1 AAAATAAAATC
3599282 AAAAT-AAATC
1 AAAATAAAATC
3599292 AAAATAAAAT-
1 AAAATAAAATC
* *
3599302 -AAATAGAATG
1 AAAATAAAATC
*
3599312 AAAA-AAAGTTC
1 AAAATAAA-ATC
3599323 AAAA-AAAAT-
1 AAAATAAAATC
3599332 AAAATAAAA-C
1 AAAATAAAATC
*
3599342 GAAAATAAAATG
1 -AAAATAAAATC
*
3599354 AAAATAAAAAC
1 AAAATAAAATC
3599365 AAAA
1 AAAA
3599369 ATATAACGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
9 16 0.23
10 17 0.24
11 37 0.53
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.15
Consensus pattern (11 bp):
AAAATAAAATC
Found at i:3599379 original size:23 final size:22
Alignment explanation
Indices: 3599332--3599379 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
3599322 CAAAAAAAAT
* *
3599332 AAAATAAAACGAAAATAAAATG
1 AAAATAAAACAAAAATAAAACG
*
3599354 AAAATAAAAACAAAAATATAACG
1 AAAAT-AAAACAAAAATAAAACG
3599377 AAA
1 AAA
3599380 TGAGTTGCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (22 bp):
AAAATAAAACAAAAATAAAACG
Found at i:3600971 original size:29 final size:29
Alignment explanation
Indices: 3600929--3600991 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
3600919 CTTGGTTGAT
3600929 AAGTTGGTCTTTGATTT-TCCGCATAGCTG
1 AAGTTGGTCTTTGATTTAT-CGCATAGCTG
3600958 AAGTTGGTCTTTGATTTATCGCATAGCTG
1 AAGTTGGTCTTTGATTTATCGCATAGCTG
3600987 AAGTT
1 AAGTT
3600992 TGGGTGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 32 0.97
30 1 0.03
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (29 bp):
AAGTTGGTCTTTGATTTATCGCATAGCTG
Found at i:3602350 original size:19 final size:19
Alignment explanation
Indices: 3602314--3602376 Score: 92
Period size: 19 Copynumber: 3.4 Consensus size: 19
3602304 GTTGTTTTTA
*
3602314 AAATAAAAG-ATAAGAATT
1 AAATAAAAGAAAAAGAATT
*
3602332 AAATAAAAGAAAAATAATT
1 AAATAAAAGAAAAAGAATT
3602351 AAATAAAAGAAAAAGAATT
1 AAATAAAAGAAAAAGAATT
*
3602370 AATTAAA
1 AAATAAA
3602377 CAAATTAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
18 9 0.22
19 31 0.77
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (19 bp):
AAATAAAAGAAAAAGAATT
Found at i:3603087 original size:73 final size:76
Alignment explanation
Indices: 3602968--3603159 Score: 234
Period size: 76 Copynumber: 2.6 Consensus size: 76
3602958 TAAAACATCT
* * * * * *
3602968 TAAATCCTAATTAAAACACTTAAAA-CTATTTGAACTAAAATACCTAAAA-ATA-ATAATAT-TT
1 TAAATACTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATATA
*
3603029 AATATAATATTC-
65 AAAATAATA-TCA
*
3603041 TAAATTCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATATAA
1 TAAATACTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATATAA
3603106 AAATAATATCA
66 AAATAATATCA
*
3603117 TAAA-ACTAAATTAAAATACTAAAACATATTTAAACTAAAATAC
1 TAAATACT-AATTAAAATACTAAAACCTATTTAAACTAAAATAC
3603160 AAAGATAAAA
Statistics
Matches: 104, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
72 5 0.05
73 40 0.38
74 2 0.02
75 10 0.10
76 47 0.45
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.31
Consensus pattern (76 bp):
TAAATACTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATATAA
AAATAATATCA
Found at i:3603150 original size:24 final size:24
Alignment explanation
Indices: 3603049--3603159 Score: 82
Period size: 24 Copynumber: 4.5 Consensus size: 24
3603039 TCTAAATTCT
*
3603049 AATTAAAATACTAAAACCTATTTA
1 AATTAAAATACTAAAACATATTTA
* * *
3603073 AACTAAAATACCTAAAACAAATATAA
1 AATTAAAATA-CTAAAACATAT-TTA
* **
3603099 AATATAAAA-A-TAATATCATAAAACTA
1 AAT-TAAAATACTAA-AACAT--ATTTA
3603125 AATTAAAATACTAAAACATATTTA
1 AATTAAAATACTAAAACATATTTA
*
3603149 AACTAAAATAC
1 AATTAAAATAC
3603160 AAAGATAAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
24 25 0.38
25 17 0.26
26 14 0.22
27 9 0.14
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (24 bp):
AATTAAAATACTAAAACATATTTA
Found at i:3605665 original size:20 final size:20
Alignment explanation
Indices: 3605626--3605667 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3605616 TATGAGGTTT
*
3605626 TTAAGCCTTTCTGTTATGCA
1 TTAAGCCTTTCTATTATGCA
* *
3605646 TTAAGCCTTTTTATTTTGCA
1 TTAAGCCTTTCTATTATGCA
3605666 TT
1 TT
3605668 CAGTTATGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (20 bp):
TTAAGCCTTTCTATTATGCA
Found at i:3612379 original size:20 final size:20
Alignment explanation
Indices: 3612342--3612380 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3612332 CACACCAAAA
*
3612342 TCTCAAATCCTCTCAAATCT
1 TCTCAAATCCTCTAAAATCT
3612362 TCTCAAA-CCATCTAAAATC
1 TCTCAAATCC-TCTAAAATC
3612381 CCAAACCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (20 bp):
TCTCAAATCCTCTAAAATCT
Found at i:3614853 original size:17 final size:19
Alignment explanation
Indices: 3614826--3614860 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3614816 GATGCCACTC
3614826 ATTGTATCTAAT-ATTATA
1 ATTGTATCTAATAATTATA
3614844 ATTG-ATCTAATAATTAT
1 ATTGTATCTAATAATTAT
3614861 TGCTAACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (19 bp):
ATTGTATCTAATAATTATA
Found at i:3622657 original size:3 final size:3
Alignment explanation
Indices: 3622649--3622708 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
3622639 TATCAGCTCC
* * * * * * *
3622649 TGA TGA TGA TCA TGA TGG TGA TGA TCA TGA TGG TGG TGG TGA TGA CGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
3622697 TGA TGA TGA TGA
1 TGA TGA TGA TGA
3622709 GAGTGGGGAG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.27, C:0.05, G:0.37, T:0.32
Consensus pattern (3 bp):
TGA
Found at i:3622693 original size:15 final size:15
Alignment explanation
Indices: 3622652--3622683 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3622642 CAGCTCCTGA
3622652 TGATGATCATGATGG
1 TGATGATCATGATGG
3622667 TGATGATCATGATGG
1 TGATGATCATGATGG
3622682 TG
1 TG
3622684 GTGGTGATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.34, T:0.34
Consensus pattern (15 bp):
TGATGATCATGATGG
Found at i:3625093 original size:13 final size:14
Alignment explanation
Indices: 3625063--3625096 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3625053 AATATCTTTT
*
3625063 AAAATAATTTTAAG
1 AAAATAATTTTAAA
3625077 AAAATAA-TTTAAA
1 AAAATAATTTTAAA
3625090 AAAATAA
1 AAAATAA
3625097 AAATTTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
AAAATAATTTTAAA
Found at i:3626262 original size:21 final size:19
Alignment explanation
Indices: 3626224--3626269 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
3626214 AATTAATCAT
3626224 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
3626244 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
3626265 A-TAAT
1 ACTAAT
3626270 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:3639072 original size:82 final size:82
Alignment explanation
Indices: 3638928--3639284 Score: 516
Period size: 82 Copynumber: 4.4 Consensus size: 82
3638918 GGAAATATGG
* * *
3638928 TCCACTATTCTTTCAGGGGAGATCAGACTTGATATTTGCCTCTTTTTCGGGTAGTCAAATCAATT
1 TCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGATCAATT
*
3638993 TTGGAATACGGGTCTGC
66 TTGGAAGACGGGTCTGC
* * * *
3639010 TTCACTATTCATTCAAGGGAGATCAGACTTAATATGTGCCTCTTTTTCGGGAAGTCAGATCAATT
1 TCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGATCAATT
* *
3639075 TTGGAAGACGAGTATGC
66 TTGGAAGACGGGTCTGC
* * *
3639092 TCCACTATTCGTTCAGGGGAGATCAGAATTGATATGTGCCTCTTTTTCGGGTAGTGAGATCAATT
1 TCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGATCAATT
3639157 TTGGAAGACGGGTCTGC
66 TTGGAAGACGGGTCTGC
* ** * * *
3639174 TCCACTATTTATTCAGGCCAGATCAGACTTGATTTGTGCCTCTTTTTTGGGTAGCCAGATCAATT
1 TCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGATCAATT
*
3639239 TTGGAATACGGGTCTGC
66 TTGGAAGACGGGTCTGC
* *
3639256 TCCACTATTTATTCAGGGGATATCAGACT
1 TCCACTATTCATTCAGGGGAGATCAGACT
3639285 CGAGAAATCT
Statistics
Matches: 243, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 243 1.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (82 bp):
TCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGATCAATT
TTGGAAGACGGGTCTGC
Found at i:3639753 original size:90 final size:89
Alignment explanation
Indices: 3639368--3640097 Score: 585
Period size: 90 Copynumber: 8.2 Consensus size: 89
3639358 TACTCTTTGT
* * * * * *
3639368 GGGAGATCAGACTCGAGATTGATTTGCTTCGCTACTCTTTCGGGAAGACC-AATATT-AAATA-A
1 GGGAGATCAGACTCGAGATTGATTTGATTCACTA-TTTTTTGTGAAGACCAAAT-TTGAAATATT
* * *
3639430 GAATAATCTGTTCCTCTACTCTTCCG
64 GAAGAATCTGCTCCACTACTCTTCCG
* * * * * *
3639456 AGGAGATCAGACTCGAGATTGATTTGATTCACTATTTTTTTTGTAAGACAAAATCTGACATA-AG
1 GGGAGATCAGACTCGAGATTGATTTGATTCACTATTTTTTGTG-AAGACCAAATTTGAAATATTG
* * * *
3639520 AAGAATATACTCCTCTACTCTTCCA
65 AAGAATCTGCTCCACTACTCTTCCG
* ** * * *
3639545 GGGAGATCAGACTTGAGATTGATTTGATTCACT-TCTTTTTCAAGAAGACTAAATTTGACATA-A
1 GGGAGATCAGACTCGAGATTGATTTGATTCACTAT-TTTTT-GTGAAGACCAAATTTGAAATATT
* * * *
3639608 GAAAAATATGATCCACTACACTTCCG
64 GAAGAATCTGCTCCACTACTCTTCCG
* * * *
3639634 GGGAGATCAGACTTGAGATTGATTTGATTCAATATATTTTTGTGAAGACCAAATTTTATATATTG
1 GGGAGATCAGACTCGAGATTGATTTGATTCACTAT-TTTTTGTGAAGACCAAATTTGAAATATTG
* * *
3639699 AAGAATCTGTTCCTCTACTCTTCTG
65 AAGAATCTGCTCCACTACTCTTCCG
* * *
3639724 GGGAGATCAGAATCGAGATTGATTTGATTCACTGCTTTTTTAG-AAAGACCAAATTTGAAATATT
1 GGGAGATCAGACTCGAGATTGATTTGATTCACT-ATTTTTT-GTGAAGACCAAATTTGAAATATT
* * **
3639788 GAAGAATCTGTTCCACTACCTTTTTTG
64 GAAGAATCTGCTCCACTA-CTCTTCCG
** ** * * * * * *
3639815 GGGAGATCCTACTCGAGATTGATTTTCTTCGCTACTCTTTTGTTAAGAACAAATCTAAAATATTG
1 GGGAGATCAGACTCGAGATTGATTTGATTCACTA-TTTTTTGTGAAGACCAAATTTGAAATATTG
*
3639880 AAGAATCTGCTCCACTACTCTTCTG
65 AAGAATCTGCTCCACTACTCTTCCG
* * * * * * * *
3639905 TGGTGATCAGACTCGAGATTGATTTGCTTCGCTACTCTTTCGTAAAGACCAAATATGAAATATTG
1 GGGAGATCAGACTCGAGATTGATTTGATTCACTA-TTTTTTGTGAAGACCAAATTTGAAATATTG
3639970 AAGAATCTGCTCCACTACTCTTCCG
65 AAGAATCTGCTCCACTACTCTTCCG
* ** * * * ** * * * *
3639995 TGGTTATCATACTCGAGATTGATTTGCTTCGCTACGCTTTTATGAAGGCCAAATCTGAAATA-AG
1 GGGAGATCAGACTCGAGATTGATTTGATTCACTA-TTTTTTGTGAAGACCAAATTTGAAATATTG
* * ***
3640059 AAGAATATGTTCCACTACTCTTTTA
65 AAGAATCTGCTCCACTACTCTTCCG
3640084 GGGAGATCAGACTC
1 GGGAGATCAGACTC
3640098 AAGTTTTTTT
Statistics
Matches: 535, Mismatches: 95, Indels: 23
0.82 0.15 0.04
Matches are distributed among these distances:
87 5 0.01
88 38 0.07
89 181 0.34
90 237 0.44
91 74 0.14
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (89 bp):
GGGAGATCAGACTCGAGATTGATTTGATTCACTATTTTTTGTGAAGACCAAATTTGAAATATTGA
AGAATCTGCTCCACTACTCTTCCG
Found at i:3639900 original size:181 final size:177
Alignment explanation
Indices: 3639334--3640097 Score: 694
Period size: 181 Copynumber: 4.3 Consensus size: 177
3639324 AGATTGAATA
* ** *
3639334 TGAAATAAGAAGAATATTCTCCTTTACTCTT-TGTGGGAGATCAGACTCGAGATTGATTTGCTTC
1 TGAAATAAGAAGAATATGCTCCACTACTCTTCTG-GGGAGATCAGACTCGAGATTGATTTGATTC
* * * * * * *
3639398 GCTACTCTTTCGGGAAGACC-AATATT-AAATAAGAATAATCTGTTCCTCTACTCTTCCGAGGAG
65 ACTACTTTTTCAGAAAGACCAAAT-TTGAAATAAGAAGAATCTGTTCCACTACTCTTCCGGGGAG
* *
3639461 ATCAGACTCGAGATTGATTTGATTCACTATTTTTTTTGTAAG-ACAAAATC
129 ATCAGACTCGAGATTGATTTGATTCACTATCTTTTGTG-AAGAAC-AAATC
* * * ** *
3639511 TGACATAAGAAGAATATACTCCTCTACTCTTCCAGGGAGATCAGACTTGAGATTGATTTGATTCA
1 TGAAATAAGAAGAATATGCTCCACTACTCTTCTGGGGAGATCAGACTCGAGATTGATTTGATTCA
* * * * * * *
3639576 CTTCTTTTTCA-AGAAGACTAAATTTGACATAAGAAAAATATGATCCACTACACTTCCGGGGAGA
66 CTACTTTTTCAGA-AAGACCAAATTTGAAATAAGAAGAATCTGTTCCACTACTCTTCCGGGGAGA
* * * * *
3639640 TCAGACTTGAGATTGATTTGATTCAATATATTTTTGTGAAGACCAAATT
130 TCAGACTCGAGATTGATTTGATTCACTAT-CTTTTGTGAAGAACAAATC
* * * * * * *
3639689 TTATATATTGAAGAATCTGTTCCTCTACTCTTCTGGGGAGATCAGAATCGAGATTGATTTGATTC
1 TGAAATA-AGAAGAATATGCTCCACTACTCTTCTGGGGAGATCAGACTCGAGATTGATTTGATTC
* * * * **
3639754 ACTGCTTTTTTAGAAAGACCAAATTTGAAATATTGAAGAATCTGTTCCACTACCTTTTTTGGGGA
65 ACTACTTTTTCAGAAAGACCAAATTTGAAATA-AGAAGAATCTGTTCCACTA-CTCTTCCGGGGA
** ** * *
3639819 GATCCTACTCGAGATTGATTTTCTTCGCTACTCTTTTGTTAAGAACAAATC
128 GATCAGACTCGAGATTGATTTGATTCACTA-TCTTTTGTGAAGAACAAATC
* * * * * *
3639870 TAAAATATTGAAGAATCTGCTCCACTACTCTTCTGTGGTGATCAGACTCGAGATTGATTTGCTTC
1 TGAAATA-AGAAGAATATGCTCCACTACTCTTCTGGGGAGATCAGACTCGAGATTGATTTGATTC
* * * * * * *
3639935 GCTACTCTTTC-GTAAAGACCAAATATGAAATATTGAAGAATCTGCTCCACTACTCTTCCGTGGT
65 ACTACTTTTTCAG-AAAGACCAAATTTGAAATA-AGAAGAATCTGTTCCACTACTCTTCCGGGGA
* * * * * * **
3639999 TATCATACTCGAGATTGATTTGCTTCGCTACGCTTTTATGAAGGCCAAATC
128 GATCAGACTCGAGATTGATTTGATTCACTA-TCTTTTGTGAAGAACAAATC
* * *
3640050 TGAAATAAGAAGAATATGTTCCACTACTCTTTTAGGGAGATCAGACTC
1 TGAAATAAGAAGAATATGCTCCACTACTCTTCTGGGGAGATCAGACTC
3640098 AAGTTTTTTT
Statistics
Matches: 482, Mismatches: 93, Indels: 22
0.81 0.16 0.04
Matches are distributed among these distances:
177 71 0.15
178 73 0.15
179 117 0.24
180 73 0.15
181 147 0.30
182 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (177 bp):
TGAAATAAGAAGAATATGCTCCACTACTCTTCTGGGGAGATCAGACTCGAGATTGATTTGATTCA
CTACTTTTTCAGAAAGACCAAATTTGAAATAAGAAGAATCTGTTCCACTACTCTTCCGGGGAGAT
CAGACTCGAGATTGATTTGATTCACTATCTTTTGTGAAGAACAAATC
Found at i:3640286 original size:62 final size:63
Alignment explanation
Indices: 3640187--3640857 Score: 505
Period size: 62 Copynumber: 11.0 Consensus size: 63
3640177 CCTTTCGTGA
* * * * * *
3640187 GGGAGTCGGGAATAACAAAAAGTTGACTTCTCATCACGAAG-AAGT-TAAGTATTGACTCTATTA
1 GGGAGTCAGGAATAAC-AAAGGTTGACTTCTCTTCACGAAGAAAGTCAAAG-ATTGACTCTACTG
** * * * *
3640250 CAGAGTCA-GAGATAACAAAGATTGACTTCTCTTCACG-AGGAAGTCAAGGATTGACTCTGCTG
1 GGGAGTCAGGA-ATAACAAAGGTTGACTTCTCTTCACGAAGAAAGTCAAAGATTGACTCTACTG
* * * * * *
3640312 GGGAGTCAGGAATATCAAAGATTGATTTCTCTTCACG-AGGAAGTCAAAGATTGGCTCCT-CTA
1 GGGAGTCAGGAATAACAAAGGTTGACTTCTCTTCACGAAGAAAGTCAAAGATTGACT-CTACTG
* * * * *
3640374 GGGAGTTAGGAATAACAAAGGTTGACTTCTCTGCATG-AGAAAATCAAGGATTGACTCTACTG
1 GGGAGTCAGGAATAACAAAGGTTGACTTCTCTTCACGAAGAAAGTCAAAGATTGACTCTACTG
* * * ** *
3640436 GAGAGTCAAGAATAACAAAGGTGGACTTCTCTTCTTG-AGAAAGTCAAAGATTAACTCTACTG
1 GGGAGTCAGGAATAACAAAGGTTGACTTCTCTTCACGAAGAAAGTCAAAGATTGACTCTACTG
* * *
3640498 TGGAGTCAAGAATAACAAAGGTTGACTTCTCTTCATG-AGAAAGTCAAAGATTGACTCTACT-
1 GGGAGTCAGGAATAACAAAGGTTGACTTCTCTTCACGAAGAAAGTCAAAGATTGACTCTACTG
* * *
3640559 GGGAGTCAGGAATAACAAAGGTTGACTTCTCTTTACG-AGAAAGTCAATGATTGGCTCCTA-TG
1 GGGAGTCAGGAATAACAAAGGTTGACTTCTCTTCACGAAGAAAGTCAAAGATTGACT-CTACTG
* * ** * * * **
3640621 GGGAGTTAGGAATAATAAAAATTGA-TT-TC-TC-TG-AGGAAGTCAGA-ATTGACTCTACCA
1 GGGAGTCAGGAATAACAAAGGTTGACTTCTCTTCACGAAGAAAGTCAAAGATTGACTCTACTG
* * ** * * * *
3640678 GGGAGTCAGGGATAATAAAAATTGACTTCTC-T----AAGGAAGTCAGA-ATTAACTCTACTA
1 GGGAGTCAGGAATAACAAAGGTTGACTTCTCTTCACGAAGAAAGTCAAAGATTGACTCTACTG
* * * * * *
3640735 GGGAGTCAGGGATAATAAAAGTTGACTTTTCTTCAC-AAGGAAGTTAAAGATTGACT-TCACTG
1 GGGAGTCAGGAATAACAAAGGTTGACTTCTCTTCACGAAGAAAGTCAAAGATTGACTCT-ACTG
* * * * * *
3640797 AGGAGTCAAGAAATAAAAAAAAGTTGACTTCTCTTCAC-AAGGAAGTCAAGGATTGACTCTA
1 GGGAGTC-AGGAAT-AACAAAGGTTGACTTCTCTTCACGAAGAAAGTCAAAGATTGACTCTA
3640858 GGAAACAAGA
Statistics
Matches: 509, Mismatches: 78, Indels: 41
0.81 0.12 0.07
Matches are distributed among these distances:
56 3 0.01
57 80 0.16
58 12 0.02
59 4 0.01
60 2 0.00
61 68 0.13
62 279 0.55
63 20 0.04
64 40 0.08
65 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (63 bp):
GGGAGTCAGGAATAACAAAGGTTGACTTCTCTTCACGAAGAAAGTCAAAGATTGACTCTACTG
Found at i:3640362 original size:29 final size:28
Alignment explanation
Indices: 3640265--3640364 Score: 76
Period size: 29 Copynumber: 3.3 Consensus size: 28
3640255 TCAGAGATAA
3640265 CAAAGATTGACTTCTCTTCACGAGGAAGT
1 CAAAGATTGA-TTCTCTTCACGAGGAAGT
* * ** *
3640294 CAAGGATTGACTCTGCTGGGGA-GTCAGGAATAT
1 CAAAGATTGATTCT-CT--TCACG--AGGAA-GT
3640327 CAAAGATTGATTTCTCTTCACGAGGAAGT
1 CAAAGATTGA-TTCTCTTCACGAGGAAGT
3640356 CAAAGATTG
1 CAAAGATTG
3640365 GCTCCTCTAG
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
28 3 0.06
29 21 0.40
30 6 0.11
31 2 0.04
32 6 0.11
33 12 0.23
34 3 0.06
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (28 bp):
CAAAGATTGATTCTCTTCACGAGGAAGT
Found at i:3640399 original size:124 final size:124
Alignment explanation
Indices: 3640136--3640857 Score: 596
Period size: 124 Copynumber: 5.8 Consensus size: 124
3640126 ATCAAATCAG
* * * * * * *
3640136 AAAGATTGATTTCTTTTCATGAAGAAGTCAAGAATTGACTCCCTTTCGTGAGGGAGTCGGGAATA
1 AAAGGTTGACTTCTCTTCATGAGGAAGTCAAGGATTGACT--C-TAC-TG-GGGAGTCAGGAATA
* * * * * **
3640201 ACAAAAAGTTGACTTCTCATCACGAAGAAGT-TAAGTATTGACTCTATTACAGAGTCA-GAGATA
61 ACAAAGA-TTGACTTCTCTTCACGAGGAAGTCAAAG-ATTGACTCTACTAGGGAGTCAGGA-ATA
3640264 AC
123 AC
* * * *
3640266 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTGCTGGGGAGTCAGGAATATCAAA
1 AAAGGTTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATAACAAA
* * *
3640331 GATTGATTTCTCTTCACGAGGAAGTCAAAGATTGGCTCCT-CTAGGGAGTTAGGAATAAC
66 GATTGACTTCTCTTCACGAGGAAGTCAAAGATTGACT-CTACTAGGGAGTCAGGAATAAC
* * * * *
3640390 AAAGGTTGACTTCTCTGCATGAGAAAATCAAGGATTGACTCTACTGGAGAGTCAAGAATAACAAA
1 AAAGGTTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATAACAAA
* * ** * * *
3640455 GGTGGACTTCTCTTCTTGAGAAAGTCAAAGATTAACTCTACT-GTGGAGTCAAGAATAAC
66 GATTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTAG-GGAGTCAGGAATAAC
* *
3640514 AAAGGTTGACTTCTCTTCATGAGAAAGTCAAAGATTGACTCTACT-GGGAGTCAGGAATAACAAA
1 AAAGGTTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATAACAAA
* * * * * * * *
3640578 GGTTGACTTCTCTTTACGAGAAAGTCAATGATTGGCTCCTA-TGGGGAGTTAGGAATAAT
66 GATTGACTTCTCTTCACGAGGAAGTCAAAGATTGACT-CTACTAGGGAGTCAGGAATAAC
** * ** * *
3640637 AAAAATTGA-TT-TC-TC-TGAGGAAGTC-AGAATTGACTCTACCAGGGAGTCAGGGATAATAAA
1 AAAGGTTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATAACAAA
* * * * *
3640697 AATTGACTTCTC-T-A--AGGAAGTCAGA-ATTAACTCTACTAGGGAGTCAGGGATAAT
66 GATTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTAGGGAGTCAGGAATAAC
* * ** * * * * *
3640751 AAAAGTTGACTTTTCTTCACAAGGAAGTTAAAGATTGACT-TCACTGAGGAGTCAAGAAATAAAA
1 AAAGGTTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCT-ACTGGGGAGTC-AGGAATAACA
* * *
3640815 AAAAGTTGACTTCTCTTCACAAGGAAGTCAAGGATTGACTCTA
64 AAGA-TTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTCTA
3640858 GGAAACAAGA
Statistics
Matches: 485, Mismatches: 85, Indels: 48
0.78 0.14 0.08
Matches are distributed among these distances:
113 3 0.01
114 28 0.06
115 10 0.02
116 2 0.00
117 3 0.01
118 21 0.04
119 52 0.11
120 13 0.03
121 12 0.02
122 3 0.01
123 71 0.15
124 184 0.38
125 34 0.07
126 11 0.02
127 2 0.00
128 1 0.00
130 35 0.07
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.27
Consensus pattern (124 bp):
AAAGGTTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATAACAAA
GATTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTAGGGAGTCAGGAATAAC
Found at i:3640465 original size:186 final size:186
Alignment explanation
Indices: 3640136--3640857 Score: 636
Period size: 186 Copynumber: 3.9 Consensus size: 186
3640126 ATCAAATCAG
* * * * *
3640136 AAAGATTGATTTCTTTTCATGAAGAAGTC-AAGAATTGACTCCCTTTCGTGAGGGAGTCGGGAAT
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAAG-ATTGACT--C-TAC-T-AGGGAGTCAGGAAT
* * * * **
3640200 AACAAAAAGTTGACTTCTCATCACGA-AGAAGTTAAGTATTGACTCTATTACAGAGTC-AGAGAT
60 AAC-AAAAGTTGACTTCTCTTCACGAGA-AAGTCAAGGATTGACTCTACTGGAGAGTCAAGA-AT
* *
3640263 AACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTGCTGGGGAGTCAGGAATATC
122 AACAAAAATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATATC
* * * *
3640328 AAAGATTGATTTCTCTTCACGAGGAAGTCAAAGATTGGCTCCT-CTAGGGAGTTAGGAATAACAA
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAAGATTGACT-CTACTAGGGAGTCAGGAATAACAA
* * * * **
3640392 AGGTTGACTTCTCTGCATGAGAAAATCAAGGATTGACTCTACTGGAGAGTCAAGAATAACAAAGG
65 AAGTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTCTACTGGAGAGTCAAGAATAACAAAAA
* ** * * * * * *
3640457 TGGACTTCTCTTCTTGAGAAAGTCAAAGATTAACTCTACTGTGGAGTCAAGAATAAC
130 TTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATATC
* *
3640514 AAAGGTTGACTTCTCTTCATGAGAAAGTCAAAGATTGACTCTACT-GGGAGTCAGGAATAACAAA
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAAGATTGACTCTACTAGGGAGTCAGGAATAACAAA
* * * * * * * *
3640578 GGTTGACTTCTCTTTACGAGAAAGTCAATGATTGGCTCCTA-TGGGGAGTTAGGAATAATAAAAA
66 AGTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACT-CTACTGGAGAGTCAAGAATAACAAAAA
* * ** *
3640642 TTGA-TT-TC-TC-TGAGGAAGTC-AGAATTGACTCTACCAGGGAGTCAGGGATAAT-
130 TTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAAT-ATC
* * * * *
3640694 AAAAATTGACTTCTC-T-A--AGGAAGTCAGA-ATTAACTCTACTAGGGAGTCAGGGATAATAAA
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAAGATTGACTCTACTAGGGAGTCAGGAATAACAAA
* * * * * *
3640754 AGTTGACTTTTCTTCACAAGGAAGTTAAAGATTGACT-TCACT-GAGGAGTCAAGAAATAAAAAA
66 AGTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTCT-ACTGGA-GAGTCAAG-AATAACAAA
*
3640817 AAGTTGACTTCTCTTCACAAGGAAGTCAAGGATTGACTCTA
128 AA-TTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTA
3640858 GGAAACAAGA
Statistics
Matches: 435, Mismatches: 78, Indels: 43
0.78 0.14 0.08
Matches are distributed among these distances:
174 1 0.00
175 13 0.03
176 62 0.14
177 10 0.02
178 5 0.01
179 3 0.01
180 36 0.08
181 12 0.03
182 10 0.02
183 14 0.03
184 2 0.00
185 71 0.16
186 137 0.31
187 19 0.04
188 1 0.00
189 1 0.00
190 1 0.00
191 2 0.00
192 32 0.07
193 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.27
Consensus pattern (186 bp):
AAAGATTGACTTCTCTTCATGAGGAAGTCAAAGATTGACTCTACTAGGGAGTCAGGAATAACAAA
AGTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTCTACTGGAGAGTCAAGAATAACAAAAAT
TGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATATC
Found at i:3640696 original size:57 final size:57
Alignment explanation
Indices: 3640621--3640762 Score: 221
Period size: 57 Copynumber: 2.5 Consensus size: 57
3640611 GGCTCCTATG
* * * * *
3640621 GGGAGTTAGGAATAATAAAAATTGATTTCTCTGAGGAAGTCAGAATTGACTCTACCA
1 GGGAGTCAGGGATAATAAAAATTGACTTCTCTAAGGAAGTCAGAATTAACTCTACCA
*
3640678 GGGAGTCAGGGATAATAAAAATTGACTTCTCTAAGGAAGTCAGAATTAACTCTACTA
1 GGGAGTCAGGGATAATAAAAATTGACTTCTCTAAGGAAGTCAGAATTAACTCTACCA
*
3640735 GGGAGTCAGGGATAATAAAAGTTGACTT
1 GGGAGTCAGGGATAATAAAAATTGACTT
3640763 TTCTTCACAA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 78 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (57 bp):
GGGAGTCAGGGATAATAAAAATTGACTTCTCTAAGGAAGTCAGAATTAACTCTACCA
Found at i:3642998 original size:19 final size:19
Alignment explanation
Indices: 3642959--3643008 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
3642949 TCATTTCCAC
*
3642959 TTTCTTATGTC-TTCAGAT
1 TTTCTTATGTCTTTCACAT
*
3642977 TTTCTTATGTCTTTCACCT
1 TTTCTTATGTCTTTCACAT
*
3642996 TTTTTTATGTCTT
1 TTTCTTATGTCTT
3643009 GAAAATGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.12, C:0.18, G:0.08, T:0.62
Consensus pattern (19 bp):
TTTCTTATGTCTTTCACAT
Found at i:3645767 original size:22 final size:21
Alignment explanation
Indices: 3645742--3645782 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3645732 AAAGATGCAA
*
3645742 AAATGTAAATGCGAAAATGTAG
1 AAATGGAAATGC-AAAATGTAG
*
3645764 AAATGGGAATGCAAAATGT
1 AAATGGAAATGCAAAATGT
3645783 GCAATACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.49, C:0.05, G:0.24, T:0.22
Consensus pattern (21 bp):
AAATGGAAATGCAAAATGTAG
Found at i:3650435 original size:3 final size:3
Alignment explanation
Indices: 3650429--3650465 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3650419 GATTATTATT
*
3650429 TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3650466 TATTATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:3650470 original size:3 final size:3
Alignment explanation
Indices: 3650464--3650492 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3650454 AATAATAATA
3650464 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3650493 AATAAAACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3665771 original size:2 final size:2
Alignment explanation
Indices: 3665640--3665759 Score: 224
Period size: 2 Copynumber: 60.5 Consensus size: 2
3665630 TAATAAATAA
3665640 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3665682 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3665724 AT AT AT AT AT AT AA AT -T AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3665760 ATGAATTATA
Statistics
Matches: 115, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 114 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3665885 original size:16 final size:15
Alignment explanation
Indices: 3665864--3665897 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3665854 TCTAAATAAT
*
3665864 TTTTAATATAATTTTA
1 TTTTAAAATAA-TTTA
3665880 TTTTAAAATAATTTA
1 TTTTAAAATAATTTA
3665895 TTT
1 TTT
3665898 ATTAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAAAATAATTTA
Found at i:3674435 original size:22 final size:20
Alignment explanation
Indices: 3674406--3674459 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
3674396 CAAAATGCAA
3674406 AAATTAAAATAACAGT-AGCT
1 AAATTAAAATAACAGTGA-CT
*
3674426 AAATCATAAACTAACAGTGACT
1 AAAT--TAAAATAACAGTGACT
3674448 AAATTAAAATAA
1 AAATTAAAATAA
3674460 AATAAAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 11 0.38
22 17 0.59
23 1 0.03
ACGTcount: A:0.57, C:0.11, G:0.07, T:0.24
Consensus pattern (20 bp):
AAATTAAAATAACAGTGACT
Found at i:3675862 original size:91 final size:91
Alignment explanation
Indices: 3675707--3676145 Score: 520
Period size: 91 Copynumber: 4.8 Consensus size: 91
3675697 AAAGTAATCA
* *
3675707 CCAAGGTTGAATAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
* * * *
3675772 ATAAACTCTACACAGGAAATGTTGGT
66 ATGAACTCTTCACAGGAAATATTGAT
* * * *
3675798 CCAAGGTCGAATAAGTTCTTCTCATTATGAACTTTTTCTCCCTCGTTGGATAAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
* * * * *
3675863 ATGAACTCTCCCCTGGGAATATTGAG
66 ATGAACTCTTCACAGGAAATATTGAT
** * *
3675889 CCAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATAAGTTCTTCTTATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
* * *
3675954 ATAAACTCTTCATTA-GAAATGTTGAT
66 ATGAACTCTTCA-CAGGAAATATTGAT
* * * * *
3675980 CAAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
** *
3676045 ATGAACTCTTCATTGGAAACATTGAT
66 ATGAACTCTTCACAGGAAATATTGAT
** * * * * *
3676071 AAAAGCTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCCCAGTCGGACGAGTTCTTCTCAT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC-GTTGGATGAGTTCTTCTCAT
3676136 TATGAACTCT
65 TATGAACTCT
3676146 CCATTTGAAA
Statistics
Matches: 299, Mismatches: 46, Indels: 5
0.85 0.13 0.01
Matches are distributed among these distances:
90 1 0.00
91 270 0.90
92 28 0.09
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (91 bp):
CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
ATGAACTCTTCACAGGAAATATTGAT
Found at i:3676038 original size:182 final size:182
Alignment explanation
Indices: 3675707--3676158 Score: 573
Period size: 182 Copynumber: 2.5 Consensus size: 182
3675697 AAAGTAATCA
*
3675707 CCAAGGTTGAATAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTCATT
* * * * * *
3675772 ATAAACTCTACA-CAGGAAATGTTGGTCCAAGGTCGAATAAGTTCTTCTCATTATGAACTTTTTC
66 ATAAACTCTACATTA-GAAATGTTGATCAAAGGTCGAACAAGTTATTCTCATTATGAACTTCTTC
* * * * *
3675836 TCCCTCGTTGGATAAGTTCTTCTCATTATGAACTCTCCCCTGGGAATATTGAG
130 TCCCTCATCGGATAAGTTCTTCTCATTATGAACTCTCCACTGGAAACATTGAG
** * * *
3675889 CCAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATAAGTTCTTCTTATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTCATT
* *
3675954 ATAAACTCTTCATTAGAAATGTTGATCAAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCT
66 ATAAACTCTACATTAGAAATGTTGATCAAAGGTCGAACAAGTTATTCTCATTATGAACTTCTTCT
* * * * *
3676019 CCTTCATCGGATGAGTTCTTCTCATTATGAACTCTTCATTGGAAACATTGAT
131 CCCTCATCGGATAAGTTCTTCTCATTATGAACTCTCCACTGGAAACATTGAG
** * * * * *
3676071 AAAAGCTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCCCAGTCGGACGAGTTCTTCTCAT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTC-GTTGGATGAGTTCTTCTCAT
* * *
3676136 TATGAACTCTCCATTTGAAATGT
65 TATAAACTCTACATTAGAAATGT
3676159 CAATCCCTCA
Statistics
Matches: 230, Mismatches: 38, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
182 193 0.84
183 37 0.16
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (182 bp):
CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTCATT
ATAAACTCTACATTAGAAATGTTGATCAAAGGTCGAACAAGTTATTCTCATTATGAACTTCTTCT
CCCTCATCGGATAAGTTCTTCTCATTATGAACTCTCCACTGGAAACATTGAG
Found at i:3676799 original size:75 final size:72
Alignment explanation
Indices: 3676671--3676813 Score: 178
Period size: 75 Copynumber: 1.9 Consensus size: 72
3676661 TTCTCTCGAT
* * * * *
3676671 TGAGATAAATTTTGTTTCAAGGGAAACTGTCTCCAGTGAGATAAAAATGGTTTTAAGAAAAACCA
1 TGAGATAAATTTTGTTTCAAGGGAAACTATCTCAAGCGAGACAAAAATGGTTTTAAGAAAAACAA
3676736 TCTCAAG
66 TCTCAAG
* ** *
3676743 TGAGATAAAATTTCTTGTTTGAAGGGAAACTATCTCAAGCGAGACAAATCTTGTTTTAAGAAAAA
1 TGAGAT-AAA-TT-TTGTTTCAAGGGAAACTATCTCAAGCGAGACAAAAATGGTTTTAAGAAAAA
3676808 CAATCT
63 CAATCT
3676814 TGAGTCAAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
72 6 0.10
73 3 0.05
74 2 0.03
75 48 0.81
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (72 bp):
TGAGATAAATTTTGTTTCAAGGGAAACTATCTCAAGCGAGACAAAAATGGTTTTAAGAAAAACAA
TCTCAAG
Found at i:3677066 original size:37 final size:36
Alignment explanation
Indices: 3676979--3677092 Score: 122
Period size: 36 Copynumber: 3.2 Consensus size: 36
3676969 TATTTCAATG
* * * *
3676979 GAAAAA-TGTCTCAAACGAGACGAAATTTGTTTTGA
1 GAAAAATTATCTCAAGCGAGACAAAATTTGTTTTAA
* * * *
3677014 GAGAAATTGTCTCAAGCGAGACAAAATTTATTTTTA
1 GAAAAATTATCTCAAGCGAGACAAAATTTGTTTTAA
* *
3677050 GATAAAATTATCTCAAGTGAGACAAAGTTTGTTTTAA
1 GA-AAAATTATCTCAAGCGAGACAAAATTTGTTTTAA
3677087 GAAAAA
1 GAAAAA
3677093 AAATATCAAG
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
35 5 0.08
36 31 0.47
37 30 0.45
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.31
Consensus pattern (36 bp):
GAAAAATTATCTCAAGCGAGACAAAATTTGTTTTAA
Found at i:3677102 original size:36 final size:37
Alignment explanation
Indices: 3677025--3677105 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
3677015 AGAAATTGTC
* * ** *
3677025 TCAAGCGAGACAAAATTTATTTTTAGATAAAATTATC
1 TCAAGTGAGACAAAATTTATTTTAAGATAAAAAAATA
* *
3677062 TCAAGTGAGACAAAGTTTGTTTTAAGA-AAAAAAATA
1 TCAAGTGAGACAAAATTTATTTTAAGATAAAAAAATA
3677098 TCAAGTGA
1 TCAAGTGA
3677106 TATAAATCCT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 14 0.38
37 23 0.62
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.31
Consensus pattern (37 bp):
TCAAGTGAGACAAAATTTATTTTAAGATAAAAAAATA
Found at i:3683311 original size:129 final size:129
Alignment explanation
Indices: 3683076--3683326 Score: 373
Period size: 129 Copynumber: 1.9 Consensus size: 129
3683066 CATACCCTCA
* * * *
3683076 AGCTTTAAAATGACTAAAATACCCTTGAGTTTTGGAATGACCTAATTACCCTAATGACTTGTATT
1 AGCTTTAAAATGACTAAAATAACCTTAAATTTTGGAATGACCTAATTACCCTAATGACTTGGATT
*
3683141 AAGTGAATTTCCTTTGGATAAGTTCTAAAAATACTATTAAGGCTTAAAAAACTATAATGTCTCG
66 AAGTGAATTGCCTTTGGATAAGTTCTAAAAATACTATTAAGGCTTAAAAAACTATAATGTCTCG
* *
3683205 AGCTTTAAAATGACTTAAATAACC-TAACATTTTGGAATGACCTAGA-TACCCTCATGACTTGGA
1 AGCTTTAAAATGACTAAAATAACCTTAA-ATTTTGGAATGACCTA-ATTACCCTAATGACTTGGA
* *
3683268 TTAAGTGAATTGCCTTTGGATAAGTTCTAGAAATACTGA-TAAGGCTTAAAACACTATAA
64 TTAAGTGAATTGCCTTTGGATAAGTTCTAAAAATACT-ATTAAGGCTTAAAAAACTATAA
3683327 CATCTATATG
Statistics
Matches: 110, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
128 2 0.02
129 106 0.96
130 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (129 bp):
AGCTTTAAAATGACTAAAATAACCTTAAATTTTGGAATGACCTAATTACCCTAATGACTTGGATT
AAGTGAATTGCCTTTGGATAAGTTCTAAAAATACTATTAAGGCTTAAAAAACTATAATGTCTCG
Found at i:3687708 original size:27 final size:27
Alignment explanation
Indices: 3687678--3687739 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
3687668 AAAATAACCG
*
3687678 AATACCCTTGAGATT-TAAAATGA-CTAA
1 AATACCCTTAAG-TTCTAAAATGACCT-A
3687705 AATACCCTTAAGTTCTAAAATGACCTA
1 AATACCCTTAAGTTCTAAAATGACCTA
3687732 AATACCCT
1 AATACCCT
3687740 CATGAGTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 2 0.06
27 28 0.88
28 2 0.06
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (27 bp):
AATACCCTTAAGTTCTAAAATGACCTA
Found at i:3690231 original size:44 final size:44
Alignment explanation
Indices: 3690168--3690253 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
3690158 TATGTCTTAT
*
3690168 CTATGTTGGAGCTATTACCAACATTTCAAACTTATTTCCTAAAA
1 CTATGTTGAAGCTATTACCAACATTTCAAACTTATTTCCTAAAA
* *
3690212 CTATGTTGAAGCTGTTACCAACATTTCCAACTTATTTCCTAA
1 CTATGTTGAAGCTATTACCAACATTTCAAACTTATTTCCTAA
3690254 TTTTTTATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.37
Consensus pattern (44 bp):
CTATGTTGAAGCTATTACCAACATTTCAAACTTATTTCCTAAAA
Found at i:3703660 original size:2 final size:2
Alignment explanation
Indices: 3703655--3703692 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
3703645 ATTCATATTA
*
3703655 AT AT AT AT AT TT GAT 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 AT AT AT AT AT A
3703693 CATACGTGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.97
3 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3703662 original size:19 final size:21
Alignment explanation
Indices: 3703638--3703684 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
3703628 CATGAATAAA
3703638 ATATATAATTCATAT-TA-AT
1 ATATATAATTCATATATATAT
* *
3703657 ATATATATTTGATATATATAT
1 ATATATAATTCATATATATAT
3703678 ATATATA
1 ATATATA
3703685 TATATATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 13 0.54
20 2 0.08
21 9 0.38
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
ATATATAATTCATATATATAT
Found at i:3723116 original size:12 final size:12
Alignment explanation
Indices: 3723073--3723127 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
3723063 CAAAGCATTT
3723073 TTATTTTACTTG
1 TTATTTTACTTG
3723085 TTCATTTT--TTG
1 TT-ATTTTACTTG
3723096 TATAGTTTTACTTG
1 T-TA-TTTTACTTG
*
3723110 TTATTTTCCTTG
1 TTATTTTACTTG
3723122 TT-TTTT
1 TTATTTT
3723128 CAGGTTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
11 9 0.24
12 17 0.46
13 7 0.19
14 4 0.11
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.69
Consensus pattern (12 bp):
TTATTTTACTTG
Found at i:3741657 original size:65 final size:65
Alignment explanation
Indices: 3741579--3741724 Score: 201
Period size: 65 Copynumber: 2.3 Consensus size: 65
3741569 ACCTAATTTG
3741579 ATTG-AACATCGAATGTTTTTGATGTACCGATGCACAGACCATGCATCAATGCACTCCAT-GTT-
1 ATTGAAACATCGAATGTTTTT-ATGTACCGATGCACAGACCATGCATCAATGCACTCC-TGGTTC
3741641 TT
64 TT
* * **
3741643 ATTGAAACAACGAATGCTTTTTATGTACCGATGCACAGTCCATGCATTGATGCACTCCTGGTTCT
1 ATTGAAACATCGAATG-TTTTTATGTACCGATGCACAGACCATGCATCAATGCACTCCTGGTTCT
3741708 T
65 T
3741709 -TTGAAACATCGAATGT
1 ATTGAAACATCGAATGT
3741725 AATTAGTGTA
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
64 6 0.08
65 60 0.82
66 7 0.10
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (65 bp):
ATTGAAACATCGAATGTTTTTATGTACCGATGCACAGACCATGCATCAATGCACTCCTGGTTCTT
Found at i:3743918 original size:16 final size:16
Alignment explanation
Indices: 3743882--3743919 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3743872 GTAGAATTCA
*
3743882 AATTTTTAATGATATC
1 AATTTTTAATGATAAC
3743898 AATTTTTAATGCATAAC
1 AATTTTTAATG-ATAAC
3743915 -ATTTT
1 AATTTT
3743920 CAAAAACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (16 bp):
AATTTTTAATGATAAC
Found at i:3747423 original size:57 final size:58
Alignment explanation
Indices: 3747322--3747447 Score: 164
Period size: 57 Copynumber: 2.2 Consensus size: 58
3747312 AAAAAAGTGA
* * **
3747322 TATTTTCATAAATATTTTTAAAAAGGTACTATTTTTGTAAATATTTTTAAAAGGGTGC
1 TATTTTCGTAAATATTTTTAAAAAGGTACTATGTTCATAAATATTTTTAAAAGGGTGC
* ** *
3747380 TATTTTCGTAAATA-TTTTAAAAATGTGTTATGTTCATAAATATTTTTAAAAGGGTGT
1 TATTTTCGTAAATATTTTTAAAAAGGTACTATGTTCATAAATATTTTTAAAAGGGTGC
*
3747437 TAGTTTCGTAA
1 TATTTTCGTAA
3747448 TTAATTTCTG
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
57 46 0.78
58 13 0.22
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (58 bp):
TATTTTCGTAAATATTTTTAAAAAGGTACTATGTTCATAAATATTTTTAAAAGGGTGC
Found at i:3747438 original size:29 final size:29
Alignment explanation
Indices: 3747287--3747435 Score: 147
Period size: 29 Copynumber: 5.1 Consensus size: 29
3747277 CCTACCCGTT
* * *
3747287 TGCTATTTTCGTTAATATTTTTTAAAAAAAAG
1 TGCTATTTTCATAAATA-TTTTT--AAAAAGG
*
3747319 TGATATTTTCATAAATATTTTTAAAAAGG
1 TGCTATTTTCATAAATATTTTTAAAAAGG
* ** *
3747348 TACTATTTTTGTAAATATTTTTAAAAGGG
1 TGCTATTTTCATAAATATTTTTAAAAAGG
* *
3747377 TGCTATTTTCGTAAATA-TTTTAAAAATG
1 TGCTATTTTCATAAATATTTTTAAAAAGG
* * *
3747405 TGTTATGTTCATAAATATTTTTAAAAGGG
1 TGCTATTTTCATAAATATTTTTAAAAAGG
3747434 TG
1 TG
3747436 TTAGTTTCGT
Statistics
Matches: 98, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
28 23 0.23
29 56 0.57
31 5 0.05
32 14 0.14
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (29 bp):
TGCTATTTTCATAAATATTTTTAAAAAGG
Found at i:3747934 original size:2 final size:2
Alignment explanation
Indices: 3747927--3747980 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
3747917 GATTTGATAA
3747927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3747969 GT AT AT AT AT AT
1 AT AT AT AT AT AT
3747981 CACTGAAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3750170 original size:13 final size:13
Alignment explanation
Indices: 3750152--3750190 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
3750142 GTATCATAAT
3750152 TTTTCAAACATTG
1 TTTTCAAACATTG
*
3750165 TTTTCAAA-ATTA
1 TTTTCAAACATTG
3750177 TTTTCAAACATTG
1 TTTTCAAACATTG
3750190 T
1 T
3750191 CAATCAGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (13 bp):
TTTTCAAACATTG
Found at i:3750182 original size:12 final size:13
Alignment explanation
Indices: 3750152--3750188 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
3750142 GTATCATAAT
*
3750152 TTTTCAAACATTG
1 TTTTCAAACATTA
3750165 TTTTCAAA-ATTA
1 TTTTCAAACATTA
3750177 TTTTCAAACATT
1 TTTTCAAACATT
3750189 GTCAATCAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.35, C:0.14, G:0.03, T:0.49
Consensus pattern (13 bp):
TTTTCAAACATTA
Found at i:3752407 original size:65 final size:64
Alignment explanation
Indices: 3752294--3752419 Score: 162
Period size: 65 Copynumber: 2.0 Consensus size: 64
3752284 ACACACCTAA
* * *
3752294 TTTTATTGAACATCAAATGCTTTTGATGTACCGATGAACAGGCCATGCATCGATGCACTCCATG
1 TTTTATTGAACATCAAATGCTTTTGATGTACCGATGAACAGACAATGCATCAATGCACTCCATG
* * * * * *
3752358 TTTTATTGAAACATCGAATGCTTTTGATGTTCCTATGCATAGACAATGCATCAATGTACTCC
1 TTTTATTG-AACATCAAATGCTTTTGATGTACCGATGAACAGACAATGCATCAATGCACTCC
3752420 TTCCTCTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
64 8 0.15
65 44 0.85
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (64 bp):
TTTTATTGAACATCAAATGCTTTTGATGTACCGATGAACAGACAATGCATCAATGCACTCCATG
Found at i:3754031 original size:18 final size:18
Alignment explanation
Indices: 3753991--3754032 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3753981 AAATCAGGTG
**
3753991 ATTTTAATAAAATATTTT
1 ATTTTAATAAAATATTCA
3754009 ATTTTAATAAAATA-TCA
1 ATTTTAATAAAATATTCA
3754026 AGTTTTA
1 A-TTTTA
3754033 GGGTCTATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
ATTTTAATAAAATATTCA
Found at i:3755060 original size:21 final size:22
Alignment explanation
Indices: 3755002--3755063 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
3754992 ATTCGAATTA
3755002 AAAATAAAATTACAAAA-TAAAT
1 AAAATAAAA-TACAAAATTAAAT
* *
3755024 TAAAT-AAATACTAAAATTGAAT
1 AAAATAAAATAC-AAAATTAAAT
3755046 AAAATAAAATA-AAAATTA
1 AAAATAAAATACAAAATTA
3755064 CAAATAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
20 3 0.09
21 13 0.39
22 12 0.36
23 5 0.15
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAATAAAATACAAAATTAAAT
Found at i:3755848 original size:2 final size:2
Alignment explanation
Indices: 3755841--3755886 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3755831 TACATCCAAG
3755841 TA TA TA 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
3755883 TA TA
1 TA TA
3755887 ATTTTTTGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3756216 original size:31 final size:29
Alignment explanation
Indices: 3756181--3756259 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 29
3756171 TGTTATTGCA
*
3756181 TGAAACAAGGGATTGTGGGGGTATTTGGTGT
1 TGAAA-AAGGGATTGTGGGGGT-GTTGGTGT
*
3756212 TGAAAAATGGGA-TG-GTGGGTGTTGGTGT
1 TGAAAAA-GGGATTGTGGGGGTGTTGGTGT
* *
3756240 TGAAATATGGGATAGTGGGG
1 TGAAA-AAGGGATTGTGGGG
3756260 TTTGAATAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
28 16 0.41
29 7 0.18
30 7 0.18
31 9 0.23
ACGTcount: A:0.24, C:0.01, G:0.44, T:0.30
Consensus pattern (29 bp):
TGAAAAAGGGATTGTGGGGGTGTTGGTGT
Found at i:3756249 original size:28 final size:28
Alignment explanation
Indices: 3756205--3756258 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
3756195 GTGGGGGTAT
*
3756205 TTGGTGTTGAAAAATGGGATGGTGGGTG
1 TTGGTGTTGAAAAATGGGATAGTGGGTG
*
3756233 TTGGTGTTGAAATATGGGATAGTGGG
1 TTGGTGTTGAAAAATGGGATAGTGGG
3756259 GTTTGAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.33
Consensus pattern (28 bp):
TTGGTGTTGAAAAATGGGATAGTGGGTG
Found at i:3756590 original size:91 final size:91
Alignment explanation
Indices: 3756435--3756776 Score: 452
Period size: 91 Copynumber: 3.8 Consensus size: 91
3756425 GAACAAAGTT
* * * *
3756435 GAACAAGTTCTTCTCATTATGAACTTCATCTTCCTCGTTGGATGAGTTATTCTCATTATGAACTC
1 GAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTGTTGGATGAGTTCTTCTCATTATGAACTC
** *
3756500 TCCACTGAAAACGTCAAGGCAAGGTC
66 TCCACTGGTAACGTCAAGGCAGGGTC
** * *
3756526 GAACAAACTATTCTAATTATGAACTTCTTCTTCCTTGTTGGATGAGTTCTTCTTATTATGAACTC
1 GAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTGTTGGATGAGTTCTTCTCATTATGAACTC
** * *
3756591 TATACTGGTAACTTCAAGACAGGGTC
66 TCCACTGGTAACGTCAAGGCAGGGTC
* *
3756617 GAACAAGTTAATATCATTATGAACTTCTTCTTCCTTGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTGTTGGATGAGTTCTTCTCATTATGAACTC
*
3756682 TCCACTGGTAACGTCAAGGTAGGGT-
66 TCCACTGGTAACGTCAAGGCAGGGTC
* * * ** *
3756707 TAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTGTCAGATGAGTTCTTCTCGTTATGAACT
1 GAACAAGTTATTCTCATTATGAACTTCTTCTTCCT-TGTTGGATGAGTTCTTCTCATTATGAACT
3756772 CTCCA
65 CTCCA
3756777 TTTGAAGTGT
Statistics
Matches: 216, Mismatches: 34, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
90 30 0.14
91 186 0.86
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (91 bp):
GAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTGTTGGATGAGTTCTTCTCATTATGAACTC
TCCACTGGTAACGTCAAGGCAGGGTC
Found at i:3757240 original size:66 final size:66
Alignment explanation
Indices: 3757170--3757298 Score: 190
Period size: 66 Copynumber: 2.0 Consensus size: 66
3757160 ACGAAATTTC
*
3757170 TTTCAAC-GAAAACAATCTCAAAGGTTGG-TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAAC
1 TTTCAACAG-AAACAATCTCAAAGG-TGGATGTTTCAAGAGAAAATGTCTCAAAAGAGACAAAAC
3757233 ATG
64 ATG
* * *
3757236 TTTCAACAGAAACAATCTCAAATGTGGATGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAAC
1 TTTCAACAGAAACAATCTCAAAGGTGGATGTTTCAAGAGAAAATGTCTCAAAAGAGACAAAAC
3757299 TCATTTCAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
65 3 0.05
66 53 0.93
67 1 0.02
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (66 bp):
TTTCAACAGAAACAATCTCAAAGGTGGATGTTTCAAGAGAAAATGTCTCAAAAGAGACAAAACAT
G
Found at i:3757323 original size:66 final size:67
Alignment explanation
Indices: 3757170--3757345 Score: 175
Period size: 66 Copynumber: 2.7 Consensus size: 67
3757160 ACGAAATTTC
* * * *
3757170 TTTCAAC-GAAAACAATCTCAAAGGT-TGGTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAAC
1 TTTCAACAG-AAACAATCTCAAAGATGTGGTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAAC
*
3757233 ATG
65 ATA
3757236 TTTCAACAGAAACAATCTC-AA-ATGTGGATGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAAC
1 TTTCAACAGAAACAATCTCAAAGATGTGG-TGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAAC
3757299 -TCA
65 AT-A
** ** * *
3757302 TTTCAAGGGGAAATGAT-TCAAAGATTTTGTGTTTCAAGGGAAAC
1 TTTCAA-CAGAAACAATCTCAAAGATGTGGTGTTTCAAGGGAAAC
3757346 GTTTTCAAAG
Statistics
Matches: 92, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
64 1 0.01
65 6 0.07
66 57 0.62
67 24 0.26
68 4 0.04
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (67 bp):
TTTCAACAGAAACAATCTCAAAGATGTGGTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAACA
TA
Found at i:3757410 original size:36 final size:36
Alignment explanation
Indices: 3757360--3757520 Score: 133
Period size: 36 Copynumber: 4.6 Consensus size: 36
3757350 TCAAAGTTTA
* * *
3757360 TGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
3757396 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * *
3757432 CATTTTAAGGGAAAC-GTTTTC-A-A-AG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
*
3757460 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATGT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT-T
*
3757498 TGTTTCAAGGGAGACTGTCTCAA
1 TGTTTCAAGGGAAACTGTCTCAA
3757521 TGGAGACTAT
Statistics
Matches: 95, Mismatches: 18, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
28 2 0.02
29 14 0.15
30 2 0.02
31 1 0.01
32 2 0.02
33 2 0.02
34 1 0.01
35 1 0.01
36 47 0.49
37 22 0.23
38 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:3757471 original size:101 final size:102
Alignment explanation
Indices: 3757337--3757520 Score: 325
Period size: 101 Copynumber: 1.8 Consensus size: 102
3757327 TTTGTGTTTC
* *
3757337 AAGGGAAACGTTTTCAAAGTTTATGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAAT-TTGTTT
1 AAGGGAAACGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATGTTGTTT
3757401 CAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTT
66 CAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTT
3757438 AAGGGAAACGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATGTTGTTT
1 AAGGGAAACGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATGTTGTTT
* *
3757503 CAAGGGAGACTGTCTCAA
66 CAAGGGAAACTATCTCAA
3757521 TGGAGACTAT
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 56 0.72
102 22 0.28
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (102 bp):
AAGGGAAACGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATGTTGTTT
CAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTT
Found at i:3757525 original size:15 final size:15
Alignment explanation
Indices: 3757502--3757542 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
3757492 AAATGTTGTT
*
3757502 TCAAGGGAGACTGTC
1 TCAAGGGAGACTATC
*
3757517 TCAATGGAGACTATC
1 TCAAGGGAGACTATC
3757532 TCAAGGGAGAC
1 TCAAGGGAGAC
3757543 AAAACTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.20
Consensus pattern (15 bp):
TCAAGGGAGACTATC
Found at i:3757607 original size:39 final size:39
Alignment explanation
Indices: 3757526--3757825 Score: 440
Period size: 39 Copynumber: 7.7 Consensus size: 39
3757516 CTCAATGGAG
* * * *
3757526 ACTATCTCAAGGGAGACAAAA-CTTTATGTTTTGAGGGGA
1 ACTATCTCAAGCGAGACAAAATC-TTCTGTTTCGAGGGAA
* * *
3757565 ACTATCTCAAGCGAGATAAAATCTTCTATTTCAAGGGAA
1 ACTATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAA
3757604 ACTATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAA
1 ACTATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAA
* * *
3757643 ACTATCTCAAGGGAAACAAAATCTTCTGTTTCAAGGGAA
1 ACTATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAA
*
3757682 ACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAA
1 ACTATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAA
* * *
3757721 ACTCTCTCAAGTGAGACAAAATCTTATGTTTCGAGGGAA
1 ACTATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAA
*
3757760 ACTATCTCAAGCGAGACAAAATCTTCAGTTTCGAGGGAA
1 ACTATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAA
*
3757799 ACTATCTCAAGCGAGATAAAATCTTCT
1 ACTATCTCAAGCGAGACAAAATCTTCT
3757826 TTAAAAAAAT
Statistics
Matches: 233, Mismatches: 27, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
39 232 1.00
40 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (39 bp):
ACTATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAA
Found at i:3757884 original size:72 final size:73
Alignment explanation
Indices: 3757797--3757973 Score: 184
Period size: 76 Copynumber: 2.4 Consensus size: 73
3757787 GTTTCGAGGG
*
3757797 AAACTATCTCAAGCGAGATAAAATCTTCTTT-AAAAA-AATCTTGAGTGAAATGAAAT-GTCTTC
1 AAACTTTCTCAAGCGAGA-AAAATCTTCTTTAAAAAATAATCTTGAGTGAAAT-AAATCGTCTTC
*
3757859 TTTTAAGTAA
64 TTTCAAGTAA
* *
3757869 AAACTTTCTCAAGCGAGACAAATCTAGT-TTTAAGAAAAATAATCTTGAGTGAAATAAATCTTCT
1 AAACTTTCTCAAGCGAGAAAAATCT--TCTTT-A-AAAAATAATCTTGAGTGAAATAAATCGTCT
* *
3757933 TGTTTCGAGTAA
62 TCTTTCAAGTAA
*
3757945 AAA-TTGTCTCAAGCGAGACAAAATATTCT
1 AAACTT-TCTCAAGCGAGA-AAAATCTTCT
3757974 GTTTCAAGGA
Statistics
Matches: 87, Mismatches: 8, Indels: 16
0.78 0.07 0.14
Matches are distributed among these distances:
71 6 0.07
72 20 0.23
73 1 0.01
75 12 0.14
76 43 0.49
77 5 0.06
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (73 bp):
AAACTTTCTCAAGCGAGAAAAATCTTCTTTAAAAAATAATCTTGAGTGAAATAAATCGTCTTCTT
TCAAGTAA
Found at i:3757995 original size:39 final size:39
Alignment explanation
Indices: 3757951--3758026 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
3757941 GTAAAAATTG
*
3757951 TCTCAAGCGAGACAAAATATTCT-GTTTCAAGGAAAACTA
1 TCTCAAGCGAGACAAAATATTCTAG-TTCAAGCAAAACTA
*
3757990 TCTCAAGCGAGACAAAATCTTCTAGTTCAAGCAAAAC
1 TCTCAAGCGAGACAAAATATTCTAGTTCAAGCAAAAC
3758027 AACTCTTGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 33 0.97
40 1 0.03
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (39 bp):
TCTCAAGCGAGACAAAATATTCTAGTTCAAGCAAAACTA
Found at i:3762793 original size:12 final size:13
Alignment explanation
Indices: 3762763--3762828 Score: 55
Period size: 13 Copynumber: 4.8 Consensus size: 13
3762753 ATATTAATCC
3762763 AAATTAAAAAATA
1 AAATTAAAAAATA
*
3762776 AAATTACAAAAT-
1 AAATTAAAAAATA
3762788 AAATTAAATAAACACTA
1 AAATT-AA-AAA-A-TA
3762805 AAATTGAATAAAATA
1 AAATT-AA-AAAATA
3762820 AAA-TAAAAA
1 AAATTAAAAA
3762829 TTATAAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
12 8 0.18
13 14 0.31
14 4 0.09
15 6 0.13
16 2 0.04
17 11 0.24
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.23
Consensus pattern (13 bp):
AAATTAAAAAATA
Found at i:3762828 original size:21 final size:21
Alignment explanation
Indices: 3762763--3762851 Score: 64
Period size: 21 Copynumber: 4.3 Consensus size: 21
3762753 ATATTAATCC
*
3762763 AAATTAA-AAAATAAAATTACA
1 AAATTAATAAAATAAAACTA-A
* *
3762784 AAATAAATTAAATAAACACT-A
1 AAATTAATAAAATAAA-ACTAA
3762805 AAATTGAATAAAATAAAA-TAA
1 AAATT-AATAAAATAAAACTAA
*
3762826 AAATT-AT-AAATAATAA-TAG
1 AAATTAATAAAATAA-AACTAA
3762845 AAATTAA
1 AAATTAA
3762852 ATTTTCAAGG
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
18 6 0.11
19 11 0.20
20 2 0.04
21 18 0.32
22 17 0.30
23 2 0.04
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (21 bp):
AAATTAATAAAATAAAACTAA
Found at i:3762843 original size:19 final size:18
Alignment explanation
Indices: 3762815--3762850 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3762805 AAATTGAATA
3762815 AAATAAAATAAAAATTAT
1 AAATAAAATAAAAATTAT
*
3762833 AAATAATAATAGAAATTA
1 AAATAA-AATAAAAATTA
3762851 AATTTTCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAATAAAATAAAAATTAT
Found at i:3763927 original size:31 final size:28
Alignment explanation
Indices: 3763892--3763961 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
3763882 ATGAAGCAAT
3763892 GGATGGTGGGGGTATTTAGTGTTGAAAAATG
1 GGATGGTGGGGG---TTAGTGTTGAAAAATG
* * *
3763923 GGATGGTGGGCGTTGGTGTTGAAATATG
1 GGATGGTGGGGGTTAGTGTTGAAAAATG
3763951 GGATGGTGGGG
1 GGATGGTGGGG
3763962 TTTGCATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 24 0.69
31 11 0.31
ACGTcount: A:0.20, C:0.01, G:0.49, T:0.30
Consensus pattern (28 bp):
GGATGGTGGGGGTTAGTGTTGAAAAATG
Found at i:3765446 original size:11 final size:12
Alignment explanation
Indices: 3765391--3765475 Score: 61
Period size: 12 Copynumber: 7.2 Consensus size: 12
3765381 ACCCTTTTAC
*
3765391 TATTATTTTCTT
1 TATTATTTTATT
*
3765403 TATTTTCTTTATT
1 TATTAT-TTTATT
3765416 TATTATTTT-TT
1 TATTATTTTATT
*
3765427 TGTTCATTTTATT
1 TATT-ATTTTATT
*
3765440 T-TTATTTT-TA
1 TATTATTTTATT
*
3765450 TATT-TTTTATC
1 TATTATTTTATT
* *
3765461 TAATATGTTATT
1 TATTATTTTATT
3765473 TAT
1 TAT
3765476 ATGTTAATAT
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
10 6 0.11
11 16 0.28
12 22 0.39
13 13 0.23
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (12 bp):
TATTATTTTATT
Found at i:3765447 original size:20 final size:20
Alignment explanation
Indices: 3765401--3765447 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
3765391 TATTATTTTC
*
3765401 TTTATTTTCTTTATTTATTA
1 TTTATTTTCTTCATTTATTA
*
3765421 TTT-TTTTGTTCATTTTATT-
1 TTTATTTTCTTCA-TTTATTA
3765440 TTTATTTT
1 TTTATTTT
3765448 TATATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTATTTTCTTCATTTATTA
Found at i:3765551 original size:41 final size:43
Alignment explanation
Indices: 3765498--3765580 Score: 118
Period size: 41 Copynumber: 2.0 Consensus size: 43
3765488 ATATGTTACC
*
3765498 CTTTTATATTGTTTTATATTATATAC-ATATCTGTATT-TTATT
1 CTTTTATATTGTTTTATATTAAATACTATATCT-TATTATTATT
*
3765540 CTTTT-TATTGTTTTTTATTAAATACTATATCTTATTATTAT
1 CTTTTATATTGTTTTATATTAAATACTATATCTTATTATTAT
3765581 ATATATGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 22 0.59
42 15 0.41
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.63
Consensus pattern (43 bp):
CTTTTATATTGTTTTATATTAAATACTATATCTTATTATTATT
Found at i:3769158 original size:84 final size:84
Alignment explanation
Indices: 3769007--3769906 Score: 1034
Period size: 84 Copynumber: 10.9 Consensus size: 84
3768997 TCCAGTACAA
* * * * *
3769007 CATAACTCAAGGCAAAAAGGGTTATCTGTCAAC-AAATACCTTCGAGTTTGATTACACTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
3769071 AAAGGCACATCATTTGTAG
66 AAAGGCACATCATTTGCAG
**** * * * *
3769090 CATAGCTCAAAATGAGAAGGGTTATCTACCAACAAAAGACATTGGAGTTCAATTACACTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
3769155 AAAGGCGCATCATTTACAG
66 AAAGGCACATCATTTGCAG
* * * * *
3769174 CATAACTCAAGTCTAA-AAGGGTTATATGTCAAC-AAAGACCTTCGAGTTCGATTACAGTCAGCT
1 CATAGCTCAAGGC-AAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCT
*
3769237 CAAAGGCACATCATTTGTAG
65 CAAAGGCACATCATTTGCAG
* * * * * *
3769257 CATAACTCAAGGTAAGAAGGGTTATCTTCCAACAAAAGTCCTTCGAGTTCGATTCCATTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
3769322 AAAGGCATATCATTTGCAG
66 AAAGGCACATCATTTGCAG
* * *
3769341 CATAGCTCAAGGTAAGAAGGGCTATCTG-C--C-AAAGACCTTCGAGTTCGATTACAATCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* * *
3769402 AATGGCATATCATTTACAG
66 AAAGGCACATCATTTGCAG
* * * * *
3769421 CATAGATCAAGGAAATAAGTGTTATCTGCCAA-TAAAGACCTTCGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
3769485 AAAGACACATCATTTGCAG
66 AAAGGCACATCATTTGCAG
* * * * *
3769504 CATAGCTCAATGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCAAGTTCGAATACACTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
3769569 AAAGGCACATCATTTGCAA
66 AAAGGCACATCATTTGCAG
* * * *
3769588 CATAGCTCAAGGCAAGAAGGGCTATCTG-C--C-AAAGTCCTTCGAGTTCAATTACACTCATCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
3769649 AAAGGCATATCATTTGCAG
66 AAAGGCACATCATTTGCAG
* * * * *
3769668 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAAAAAAATACCTTCAAGTTCGATTCCATTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
3769733 AAAGACACATCATTTGCAG
66 AAAGGCACATCATTTGCAG
* * * *
3769752 CATGGCTCAAGGCAAGAAGGGTTATCTACCAATAAAAGACCTTCGAGTTTGATTACACTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
3769817 AAATGCACATCATTTGCAG
66 AAAGGCACATCATTTGCAG
* * * * * * * * * *
3769836 TATAGCTCAAGGAAAGAAGGGCTATCTGTCGAC-AAATACCTTCAAGTTCAATTTCATTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
3769900 AAGGGCA
66 AAAGGCA
3769907 TGTTAAAGTC
Statistics
Matches: 687, Mismatches: 117, Indels: 26
0.83 0.14 0.03
Matches are distributed among these distances:
80 138 0.20
81 4 0.01
82 2 0.00
83 195 0.28
84 347 0.51
85 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (84 bp):
CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
AAAGGCACATCATTTGCAG
Found at i:3769283 original size:167 final size:167
Alignment explanation
Indices: 3769007--3769906 Score: 1014
Period size: 167 Copynumber: 5.4 Consensus size: 167
3768997 TCCAGTACAA
* * * * *
3769007 CATAACTCAAGGCAAA-AAGGGTTATCTGTCAACAAATACCTTCGAGTTTGATTACACTCAGCTC
1 CATAGCTCAA-GCAAAGAAGGGCTATCTGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTC
* **** * *
3769071 AAAGGCACATCATTTGTAGCATAGCTCAAAATGAGAAGGGTTATCTACCAACAAAAGACATTGGA
65 AAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTACCAACAAAAGACCTTCGA
* * *
3769136 GTTCAATTACACTCAGCTCAAAGGCGCATCATTTACAG
130 GTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAG
* * * * * *
3769174 CATAACTCAAGTCTAA-AAGGGTTATATGTCAACAAAGACCTTCGAGTTCGATTACAGTCAGCTC
1 CATAGCTCAAG-CAAAGAAGGGCTATCTGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTC
* * * * *
3769238 AAAGGCACATCATTTGTAGCATAACTCAAGGTAAGAAGGGTTATCTTCCAACAAAAGTCCTTCGA
65 AAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTACCAACAAAAGACCTTCGA
* * *
3769303 GTTCGATTCCATTCAGCTCAAAGGCATATCATTTGCAG
130 GTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAG
** * *
3769341 CATAGCTCAAGGTAAGAAGGGCTATCTG-C--CAAAGACCTTCGAGTTCGATTACAATCAGCTCA
1 CATAGCTCAAGCAAAGAAGGGCTATCTGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTCA
* * * * * * * * *
3769403 ATGGCATATCATTTACAGCATAGATCAAGGAAATAAGTGTTATCTGCCAA-TAAAGACCTTCGAG
66 AAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTACCAACAAAAGACCTTCGAG
*
3769467 TTCGATTACACTCAGCTCAAAGACACATCATTTGCAG
131 TTCGATTACACTCAGCTCAAAGGCACATCATTTGCAG
* * *
3769504 CATAGCTCAATGC-GAGAAGGGCTATCTGCCAACAAAAGACCTTCAAGTTCGAATACACTCAGCT
1 CATAGCTCAA-GCAAAGAAGGGCTATCTGTCAAC-AAAGACCTTCAAGTTCGATTACACTCAGCT
* * * *
3769568 CAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATCT-GC--C-AAAGTCCTTCG
64 CAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTACCAACAAAAGACCTTCG
* * *
3769629 AGTTCAATTACACTCATCTCAAAGGCATATCATTTGCAG
129 AGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAG
* * * * * *
3769668 CATAGCTCAAGGC-AAGAAGGGTTATCTGCCAAAAAAATACCTTCAAGTTCGATTCCATTCAGCT
1 CATAGCTCAA-GCAAAGAAGGGCTATCTGTC-AACAAAGACCTTCAAGTTCGATTACACTCAGCT
* * *
3769732 CAAAGACACATCATTTGCAGCATGGCTCAAGGCAAGAAGGGTTATCTACCAATAAAAGACCTTCG
64 CAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTACCAACAAAAGACCTTCG
* *
3769797 AGTTTGATTACACTCAGCTCAAATGCACATCATTTGCAG
129 AGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAG
* * * * * * *
3769836 TATAGCTCAAGGAAAGAAGGGCTATCTGTCGACAAATACCTTCAAGTTCAATTTCATTCAGCTCA
1 CATAGCTCAAGCAAAGAAGGGCTATCTGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTCA
*
3769901 AGGGCA
66 AAGGCA
3769907 TGTTAAAGTC
Statistics
Matches: 629, Mismatches: 90, Indels: 28
0.84 0.12 0.04
Matches are distributed among these distances:
163 69 0.11
164 215 0.34
165 3 0.00
166 7 0.01
167 267 0.42
168 68 0.11
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (167 bp):
CATAGCTCAAGCAAAGAAGGGCTATCTGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTCA
AAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTACCAACAAAAGACCTTCGAG
TTCGATTACACTCAGCTCAAAGGCACATCATTTGCAG
Found at i:3769484 original size:247 final size:247
Alignment explanation
Indices: 3769007--3769907 Score: 1110
Period size: 247 Copynumber: 3.6 Consensus size: 247
3768997 TCCAGTACAA
* * *
3769007 CATAACTCAAGGCAAAAAGGGTTATCTGT-CAAC-AAATACCTTCGAGTTTGATTACACTCAGCT
1 CATAACTCAAGGCAAGAAGGGTTATCT-TCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCT
* ** * * * * *
3769070 CAAAGGCACATCATTTGTAGCATAGCTCAAAATGAGAAGGGTTATCTACCAACAAAAGACATTGG
65 CAAAGGCACATCATTTGCAGCATAGCTCAAGGTAAGAAGGGCTATCT-GC-AC-AAAGACCTTCG
** **
3769135 AGTTCAATTACACTCAGCTCAAAGGCGCATCATTTACAGCATA-ACTCAAGTCTAAAAGGGTTAT
127 AGTTCAATTACACTCAGCTCAAAGGCATATCATTTACAGCATAGA-TCAAG-GAAAAAGGGTTAT
* * * * * *
3769199 ATGTCAACAAAGACCTTCGAGTTCGATTACAGTCAGCTCAAAGGCACATCATTTGTAG
190 CTGCCAAAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACATCATTTGCAG
* * * *
3769257 CATAACTCAAGGTAAGAAGGGTTATCTTCCAACAAAAGTCCTTCGAGTTCGATTCCATTCAGCTC
1 CATAACTCAAGGCAAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
3769322 AAAGGCATATCATTTGCAGCATAGCTCAAGGTAAGAAGGGCTATCTGC-CAAAGACCTTCGAGTT
66 AAAGGCACATCATTTGCAGCATAGCTCAAGGTAAGAAGGGCTATCTGCACAAAGACCTTCGAGTT
* * * *
3769386 CGATTACAATCAGCTCAATGGCATATCATTTACAGCATAGATCAAGGAAATAAGTGTTATCTGCC
131 CAATTACACTCAGCTCAAAGGCATATCATTTACAGCATAGATCAAGGAAA-AAGGGTTATCTGCC
*
3769451 AATAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACATCATTTGCAG
195 AAAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACATCATTTGCAG
* * * * * * *
3769504 CATAGCTCAATGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCAAGTTCGAATACACTCAGCTC
1 CATAACTCAAGGCAAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* * *
3769569 AAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATCTGC-CAAAGTCCTTCGAGTT
66 AAAGGCACATCATTTGCAGCATAGCTCAAGGTAAGAAGGGCTATCTGCACAAAGACCTTCGAGTT
* * * *
3769633 CAATTACACTCATCTCAAAGGCATATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCC
131 CAATTACACTCAGCTCAAAGGCATATCATTTACAGCATAGATCAAGG-AAAAAGGGTTATCTGCC
* * * *
3769698 AAAAAAATACCTTCAAGTTCGATTCCATTCAGCTCAAAGACACATCATTTGCAG
195 -AAAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACATCATTTGCAG
** * * *
3769752 CATGGCTCAAGGCAAGAAGGGTTATCTACCAATAAAAGACCTTCGAGTTTGATTACACTCAGCTC
1 CATAACTCAAGGCAAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* * * * *
3769817 AAATGCACATCATTTGCAGTATAGCTCAAGGAAAGAAGGGCTATCTGTCGACAAATACCTTCAAG
66 AAAGGCACATCATTTGCAGCATAGCTCAAGGTAAGAAGGGCTATCTG-C-ACAAAGACCTTCGAG
* * *
3769882 TTCAATTTCATTCAGCTCAAGGGCAT
129 TTCAATTACACTCAGCTCAAAGGCAT
3769908 GTTAAAGTCA
Statistics
Matches: 564, Mismatches: 78, Indels: 17
0.86 0.12 0.03
Matches are distributed among these distances:
246 2 0.00
247 280 0.50
248 151 0.27
249 2 0.00
250 30 0.05
251 99 0.18
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (247 bp):
CATAACTCAAGGCAAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
AAAGGCACATCATTTGCAGCATAGCTCAAGGTAAGAAGGGCTATCTGCACAAAGACCTTCGAGTT
CAATTACACTCAGCTCAAAGGCATATCATTTACAGCATAGATCAAGGAAAAAGGGTTATCTGCCA
AAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACATCATTTGCAG
Found at i:3770157 original size:217 final size:217
Alignment explanation
Indices: 3769779--3770216 Score: 795
Period size: 217 Copynumber: 2.0 Consensus size: 217
3769769 AGGGTTATCT
* * *
3769779 ACCAATAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAATGCACATCATTTGCAGTATAGCTC
1 ACCAATAAAAGACCTTCAAGTTTGATTACACTCAGCTCAAAAGCACATCATTTGCAGCATAGCTC
3769844 AAGGAAAGAAGGGCTATCTGTCGACAAATACCTTCAAGTTCAATTTCATTCAGCTCAAGGGCATG
66 AAGGAAAGAAGGGCTATCTGTCGACAAATACCTTCAAGTTCAATTTCATTCAGCTCAAGGGCATG
* * *
3769909 TTAAAGTCACATCATAGTTTAAGTTGAGAAAAGCTATCTATCAATAAAATTTTTGAGTTCGATTC
131 TTAAAGTCACATCATAGTTTAAGTCGAGAAAAACTATCTATCAATAAAATTTTCGAGTTCGATTC
*
3769974 CATTCAGCTCGATGATACATAA
196 CATTCAGCTCGATGACACATAA
3769996 ACCAATAAAAGACCTTCAAGTTTGATTACACTCAGCTCAAAAGCACATCATTTGCAGCATAGCTC
1 ACCAATAAAAGACCTTCAAGTTTGATTACACTCAGCTCAAAAGCACATCATTTGCAGCATAGCTC
3770061 AAGGAAAGAAGGGCTATCTGTCGACAAATACCTTCAAGTTCAATTTCATTCAGCTCAAGGGCATG
66 AAGGAAAGAAGGGCTATCTGTCGACAAATACCTTCAAGTTCAATTTCATTCAGCTCAAGGGCATG
*
3770126 TTAAAGTCACATCATAGTTTAAGTCGAGAAAAACTATCTATCAATAAAATTTTCGAGTTCGATTT
131 TTAAAGTCACATCATAGTTTAAGTCGAGAAAAACTATCTATCAATAAAATTTTCGAGTTCGATTC
*
3770191 CATTCATCTCGATGACACATAA
196 CATTCAGCTCGATGACACATAA
3770213 ACCA
1 ACCA
3770217 CACTACTTCC
Statistics
Matches: 212, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
217 212 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (217 bp):
ACCAATAAAAGACCTTCAAGTTTGATTACACTCAGCTCAAAAGCACATCATTTGCAGCATAGCTC
AAGGAAAGAAGGGCTATCTGTCGACAAATACCTTCAAGTTCAATTTCATTCAGCTCAAGGGCATG
TTAAAGTCACATCATAGTTTAAGTCGAGAAAAACTATCTATCAATAAAATTTTCGAGTTCGATTC
CATTCAGCTCGATGACACATAA
Found at i:3772029 original size:68 final size:63
Alignment explanation
Indices: 3771897--3772047 Score: 162
Period size: 66 Copynumber: 2.3 Consensus size: 63
3771887 CCTTTTTTAT
* * *
3771897 TATTTTATATTATATACATATATGTATTTTTTTATTATTGTTTTATTGTTTTTTATTAAATAA
1 TATTTTATATTATATATATATATATATTTTTTTATTATTATTTTATTGTTTTTTATTAAATAA
*
3771960 TATATCTTATTATTATATATATGTATATATTTTACTTTATTATTATTTT-TTGGTTTCTTT-TTA
1 TAT-T-TTA-TATTATATATATATATATATTTT--TTTATTATTATTTTATT-GTTT-TTTATTA
**
3772023 CCTAA
59 AATAA
3772028 TATTTTATATGTATATATAT
1 TATTTTATAT-TATATATAT
3772048 TTTTATTGTT
Statistics
Matches: 74, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
63 3 0.04
64 1 0.01
65 6 0.08
66 32 0.43
67 3 0.04
68 26 0.35
69 3 0.04
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (63 bp):
TATTTTATATTATATATATATATATATTTTTTTATTATTATTTTATTGTTTTTTATTAAATAA
Found at i:3772216 original size:7 final size:7
Alignment explanation
Indices: 3772197--3772237 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
3772187 TTGATGTTTG
3772197 CTTTTTT
1 CTTTTTT
3772204 -TGTTTTT
1 CT-TTTTT
3772211 CTTTTTT
1 CTTTTTT
*
3772218 CGTTTTT
1 CTTTTTT
3772225 C-TTTTT
1 CTTTTTT
3772231 CTTTTTT
1 CTTTTTT
3772238 TACCTAATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
6 7 0.23
7 22 0.73
8 1 0.03
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (7 bp):
CTTTTTT
Found at i:3772216 original size:14 final size:14
Alignment explanation
Indices: 3772197--3772230 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3772187 TTGATGTTTG
*
3772197 CTTTTTTTGTTTTT
1 CTTTTTTCGTTTTT
3772211 CTTTTTTCGTTTTT
1 CTTTTTTCGTTTTT
3772225 CTTTTT
1 CTTTTT
3772231 CTTTTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (14 bp):
CTTTTTTCGTTTTT
Found at i:3772229 original size:20 final size:20
Alignment explanation
Indices: 3772200--3772237 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3772190 ATGTTTGCTT
*
3772200 TTTTTGTTTTTCTTTTTTCG
1 TTTTTCTTTTTCTTTTTTCG
3772220 TTTTTCTTTTTCTTTTTT
1 TTTTTCTTTTTCTTTTTT
3772238 TACCTAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (20 bp):
TTTTTCTTTTTCTTTTTTCG
Found at i:3772280 original size:24 final size:24
Alignment explanation
Indices: 3772253--3772298 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3772243 AATAGTTATA
*
3772253 TATT-TTTAGTTTTAGTTTTTTCAT
1 TATTATTT-GTTTTAATTTTTTCAT
*
3772277 TATTATTTTTTTTAATTTTTTC
1 TATTATTTGTTTTAATTTTTTC
3772299 TTTCTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (24 bp):
TATTATTTGTTTTAATTTTTTCAT
Done.