Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007800.1 Hibiscus syriacus cultivar Beakdansim tig00110114_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: 4652821
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 23
Found at i:3660055 original size:60 final size:60
Alignment explanation
Indices: 3660008--3660343 Score: 246
Period size: 60 Copynumber: 5.5 Consensus size: 60
3659998 TTCTTTTTAA
3660008 CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTCTAAATCG
* * * * * * * *
3660068 CGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTCTAAATCG
* * * * *
3660128 CATTGCGATTTTCTTCTAAATCGCGTTACGACTCTCTCAATCGCATTGCGATTCTATAAATCG
1 CGTTGCGA--TT-TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTCTAAATCG
* * * * * * * ** ** *
3660191 CATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAAATCGCGTTGCGA--TTC-TCTCAATCGCATTGCGATTTTCTAA-ATCG
* * * *** ** *
3660255 CGTTGCGATTTTCT--TTTGACCGTTGCGATTTTCTTTTTAACGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG--CGTTGCGATTCTCTCAATCGCATTGCGATTTTCTAAATCG
* *
3660315 CGTTGCGATTTT-GATATCGCGTTGCGATT
1 CGTTGCGATTTTCTAAATCGCGTTGCGATT
3660344 TTATTGGTCA
Statistics
Matches: 212, Mismatches: 53, Indels: 23
0.74 0.18 0.08
Matches are distributed among these distances:
59 10 0.05
60 87 0.41
61 20 0.09
62 8 0.04
63 66 0.31
64 21 0.10
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.39
Consensus pattern (60 bp):
CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTCTAAATCG
Found at i:3660184 original size:83 final size:83
Alignment explanation
Indices: 3660010--3660237 Score: 372
Period size: 83 Copynumber: 2.8 Consensus size: 83
3660000 CTTTTTAACG
* * *
3660010 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGA--TT-TTCTAAATCGCGTT
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
* *
3660072 GCGATTCTCTCAATCGCA
66 ACGACTCTCTCAATCGCA
*
3660090 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTT
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
3660155 ACGACTCTCTCAATCGCA
66 ACGACTCTCTCAATCGCA
*
3660173 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
3660238 GCGAACTTGG
Statistics
Matches: 137, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
80 42 0.31
82 2 0.01
83 93 0.68
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (83 bp):
TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
ACGACTCTCTCAATCGCA
Found at i:3660335 original size:19 final size:20
Alignment explanation
Indices: 3660295--3660345 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
3660285 TTCTTTTTAA
*
3660295 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
3660315 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
3660334 CGTTGCGATTTT
1 CGTTGCGATTTT
3660346 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:3661871 original size:59 final size:60
Alignment explanation
Indices: 3661806--3661924 Score: 213
Period size: 59 Copynumber: 2.0 Consensus size: 60
3661796 ATAAAGTCAA
*
3661806 ATTAATATTTTCGTATAATTGAATAAATATTATACCATTTTCTCATTTT-CTTTTTTAAT
1 ATTAATATTTTCGTATAATTGAATAAATATTATAACATTTTCTCATTTTCCTTTTTTAAT
*
3661865 ATTAATATTTTCGTATAATTGAATAAATGTTATAACATTTTCTCATTTTCCTTTTTTAAT
1 ATTAATATTTTCGTATAATTGAATAAATATTATAACATTTTCTCATTTTCCTTTTTTAAT
3661925 TGTGTACTCA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 47 0.82
60 10 0.18
ACGTcount: A:0.32, C:0.10, G:0.04, T:0.54
Consensus pattern (60 bp):
ATTAATATTTTCGTATAATTGAATAAATATTATAACATTTTCTCATTTTCCTTTTTTAAT
Found at i:3664370 original size:2 final size:2
Alignment explanation
Indices: 3664363--3664391 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3664353 ATGCAAATGA
3664363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3664392 GCTTAGGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3668880 original size:21 final size:21
Alignment explanation
Indices: 3668806--3668882 Score: 61
Period size: 20 Copynumber: 3.8 Consensus size: 21
3668796 TGCAACACAG
* * *
3668806 TTTCCAAATTCGCAACTC-AG
1 TTTCTAAATTCGCAACGCGAA
*
3668826 TTTCTGAAA-TCGCAATGCGAA
1 TTTCT-AAATTCGCAACGCGAA
** *
3668847 TTTCT-TTTTCGCAACGCGAT
1 TTTCTAAATTCGCAACGCGAA
3668867 TTTCTAAATTCGCAAC
1 TTTCTAAATTCGCAAC
3668883 ACAGAAGTCA
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
20 26 0.60
21 17 0.40
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (21 bp):
TTTCTAAATTCGCAACGCGAA
Found at i:3668943 original size:26 final size:26
Alignment explanation
Indices: 3668914--3668963 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3668904 CGCATTTATT
* * *
3668914 TTCGCAACACGAATTTTATTTTCGAA
1 TTCGAAACACGAATATTAATTTCGAA
3668940 TTCGAAACACGAATATTAATTTCG
1 TTCGAAACACGAATATTAATTTCG
3668964 CAACACAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (26 bp):
TTCGAAACACGAATATTAATTTCGAA
Found at i:3668945 original size:19 final size:20
Alignment explanation
Indices: 3668895--3668937 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
3668885 AGAAGTCAAA
* *
3668895 TTCGCAAAACGCA-TTTATT
1 TTCGCAACACGAATTTTATT
3668914 TTCGCAACACGAATTTTATT
1 TTCGCAACACGAATTTTATT
3668934 TTCG
1 TTCG
3668938 AATTCGAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.40
Consensus pattern (20 bp):
TTCGCAACACGAATTTTATT
Found at i:3669085 original size:22 final size:22
Alignment explanation
Indices: 3669058--3669130 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
3669048 TCACTCTCTA
*
3669058 CGGCGACATCCGTACCCATCTC
1 CGGCGACATCCGTCCCCATCTC
*
3669080 TGGCGACATCCGTCCCCATCTC
1 CGGCGACATCCGTCCCCATCTC
* *
3669102 CGGCGACATTCGTCCCCATATC
1 CGGCGACATCCGTCCCCATCTC
*
3669124 CGACGAC
1 CGGCGAC
3669131 CCCCTCCATC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.18, C:0.44, G:0.19, T:0.19
Consensus pattern (22 bp):
CGGCGACATCCGTCCCCATCTC
Found at i:3669558 original size:20 final size:19
Alignment explanation
Indices: 3669524--3669561 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3669514 CGCATTGCGA
3669524 ATTTTGTGTTACGAATTTC
1 ATTTTGTGTTACGAATTTC
*
3669543 ATTTTCGTGTTGCGAATTT
1 ATTTT-GTGTTACGAATTT
3669562 AAGTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.53
Consensus pattern (19 bp):
ATTTTGTGTTACGAATTTC
Found at i:3669568 original size:20 final size:20
Alignment explanation
Indices: 3669529--3669568 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3669519 TGCGAATTTT
* *
3669529 GTGTTACGAATTTCATTTTC
1 GTGTTACGAATTTAAGTTTC
*
3669549 GTGTTGCGAATTTAAGTTTC
1 GTGTTACGAATTTAAGTTTC
3669569 AAAAACTACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.47
Consensus pattern (20 bp):
GTGTTACGAATTTAAGTTTC
Found at i:3671097 original size:42 final size:42
Alignment explanation
Indices: 3671038--3671191 Score: 200
Period size: 42 Copynumber: 3.7 Consensus size: 42
3671028 ATGAGCACCT
* * * **
3671038 TCCACTTCGACACCGAGATCCATCACCTCATCGAGCCTCTTC
1 TCCACCTCGACACCGAGAGCCATCACCTGATCGAGCCAATTC
* * * * *
3671080 TCCACTTCCACACCGAGATCCATCACCTGATCGAGTCGATTC
1 TCCACCTCGACACCGAGAGCCATCACCTGATCGAGCCAATTC
*
3671122 TCCACCTCGACACCGAGAGCCATCACCTGATCTAGCCAATTC
1 TCCACCTCGACACCGAGAGCCATCACCTGATCGAGCCAATTC
*
3671164 TCCACCTCGACACCGAGAGCCATAACCT
1 TCCACCTCGACACCGAGAGCCATCACCT
3671192 ATTCCATCAC
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 100 1.00
ACGTcount: A:0.25, C:0.41, G:0.14, T:0.21
Consensus pattern (42 bp):
TCCACCTCGACACCGAGAGCCATCACCTGATCGAGCCAATTC
Found at i:3671356 original size:21 final size:21
Alignment explanation
Indices: 3671305--3671439 Score: 114
Period size: 21 Copynumber: 6.4 Consensus size: 21
3671295 AGTTATATGT
3671305 TTTACGTGATGAGGTCA-GTGC
1 TTTACGTGATGAGGT-AGGTGC
** *
3671326 TTTATATGATGAGGTCGGTGC
1 TTTACGTGATGAGGTAGGTGC
**
3671347 TTTACGTGATGA-CAATGGTGC
1 TTTACGTGATGAGGTA-GGTGC
* ** *
3671368 ATGGCGTGATGAAGTAGG-GTC
1 TTTACGTGATGAGGTAGGTG-C
* *
3671389 TTTACGTGGTGAGGTAGTTGC
1 TTTACGTGATGAGGTAGGTGC
3671410 TTTACGTGATGAGGTAGGTGC
1 TTTACGTGATGAGGTAGGTGC
*
3671431 TCTACGTGA
1 TTTACGTGA
3671440 GATTGTTTTA
Statistics
Matches: 87, Mismatches: 22, Indels: 10
0.73 0.18 0.08
Matches are distributed among these distances:
20 1 0.01
21 84 0.97
22 2 0.02
ACGTcount: A:0.20, C:0.12, G:0.35, T:0.33
Consensus pattern (21 bp):
TTTACGTGATGAGGTAGGTGC
Found at i:3671783 original size:21 final size:21
Alignment explanation
Indices: 3671723--3671853 Score: 97
Period size: 21 Copynumber: 6.3 Consensus size: 21
3671713 AAAGAAGCTT
* * *
3671723 GATCCATCTACCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
*
3671744 GATCCACCTCCCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
* ** *
3671765 GATTCACCTTTCATCGTTCAA
1 GATCCACCTCCCATCGTTCAG
** *
3671786 GA-GGACCCTCCCATCGTTCAA
1 GATCCA-CCTCCCATCGTTCAG
** *
3671807 GAGGC-CC-CCCATCGTTTAG
1 GATCCACCTCCCATCGTTCAG
*
3671826 GATCCACCTCCCATCATTCAG
1 GATCCACCTCCCATCGTTCAG
3671847 GATCCAC
1 GATCCAC
3671854 ATTCCATACT
Statistics
Matches: 88, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
19 13 0.15
20 5 0.06
21 69 0.78
22 1 0.01
ACGTcount: A:0.22, C:0.36, G:0.15, T:0.27
Consensus pattern (21 bp):
GATCCACCTCCCATCGTTCAG
Found at i:3671860 original size:21 final size:21
Alignment explanation
Indices: 3671814--3671860 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3671804 CAAGAGGCCC
* * *
3671814 CCCATCGTTTAGGATCCACCT
1 CCCATCATTCAGGATCCACAT
3671835 CCCATCATTCAGGATCCACAT
1 CCCATCATTCAGGATCCACAT
*
3671856 TCCAT
1 CCCAT
3671861 ACTATGTAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.38, G:0.11, T:0.28
Consensus pattern (21 bp):
CCCATCATTCAGGATCCACAT
Found at i:3674094 original size:37 final size:37
Alignment explanation
Indices: 3674041--3674145 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
3674031 CCATTTTGTC
3674041 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
3674078 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
3674115 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
3674146 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:3674651 original size:20 final size:20
Alignment explanation
Indices: 3674626--3674663 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3674616 TTTTTTATTA
3674626 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
3674646 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
3674664 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:3680842 original size:106 final size:106
Alignment explanation
Indices: 3680715--3681778 Score: 1653
Period size: 106 Copynumber: 10.0 Consensus size: 106
3680705 ATATCGTGCC
* * * * * *
3680715 ACTCGAGACAACACAAGTTCAACTTCACAACGAAAGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
3680780 AATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
3680821 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
3680886 AATTTCATAGCCAATTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* **
3680927 ACTCCAGACAACGCAAGTTCAACTTCACGACGAATGGACCGCTGGTTGTCAATAAACAACTTCAT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
3680992 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
3681033 ACTCCAGACAACGTAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
3681098 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
3681139 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
3681204 AATTTCAAAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
3681245 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
3681310 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
3681351 ACTCCAGACAAAGCAAGTTCAAATTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
3681416 AATTTCAAAGCCAATTTCAACTTCACAACGAAGGATGTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
3681457 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * * *
3681522 AATTTTAGAGTCAATTTCAACTTCACAGTGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * *
3681563 ACTCAAGACAACAAAAGTTCAACTTCACGACGAATGGACTGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
3681628 AATTTCAGAGTCAATTTCGACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
3681669 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
3681734 AATTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
3681775 ACTC
1 ACTC
3681779 GGAACAATGC
Statistics
Matches: 878, Mismatches: 79, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
105 1 0.00
106 877 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:3682562 original size:37 final size:37
Alignment explanation
Indices: 3682510--3682613 Score: 163
Period size: 37 Copynumber: 2.8 Consensus size: 37
3682500 CTTTTCGTCC
3682510 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
3682547 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
3682584 TACTATGATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
3682614 CCACAAGCAC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:3683134 original size:20 final size:20
Alignment explanation
Indices: 3683109--3683146 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3683099 ATTATTATTA
3683109 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
3683129 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
3683147 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:3683151 original size:17 final size:17
Alignment explanation
Indices: 3683129--3683175 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 17
3683119 ATATATATGC
3683129 TTTTACTTTTTTATATA
1 TTTTACTTTTTTATATA
*
3683146 TTTTACTCATTTTTTATCTA
1 TTTTA--C-TTTTTTATATA
3683166 TTTT-CTTTTT
1 TTTTACTTTTT
3683176 ATCTTTATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 5 0.19
17 6 0.23
19 1 0.04
20 14 0.54
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTACTTTTTTATATA
Found at i:3686056 original size:20 final size:20
Alignment explanation
Indices: 3686031--3686094 Score: 128
Period size: 20 Copynumber: 3.2 Consensus size: 20
3686021 GAACACGTTG
3686031 GCATTGGTTAATGCATAGAT
1 GCATTGGTTAATGCATAGAT
3686051 GCATTGGTTAATGCATAGAT
1 GCATTGGTTAATGCATAGAT
3686071 GCATTGGTTAATGCATAGAT
1 GCATTGGTTAATGCATAGAT
3686091 GCAT
1 GCAT
3686095 ATGTTTGGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (20 bp):
GCATTGGTTAATGCATAGAT
Found at i:3692996 original size:19 final size:20
Alignment explanation
Indices: 3692960--3693003 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
3692950 AAATTTGGCG
3692960 GTTTTTCCAGTTTTTTTCT-
1 GTTTTTCCAGTTTTTTTCTA
3692979 GTTTTTCCTAG-TTTTTTCTA
1 GTTTTTCC-AGTTTTTTTCTA
3692999 GTTTT
1 GTTTT
3693004 CAGCTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.07, C:0.14, G:0.11, T:0.68
Consensus pattern (20 bp):
GTTTTTCCAGTTTTTTTCTA
Found at i:3714608 original size:3 final size:3
Alignment explanation
Indices: 3714600--3714663 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
3714590 TCTATTCCTT
3714600 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3714648 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
3714664 GGTTTATATC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3716021 original size:20 final size:20
Alignment explanation
Indices: 3715996--3716039 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3715986 TAGATTTGAT
3715996 TAAAAA-ATAATTAATAAAAA
1 TAAAAATATAA-TAATAAAAA
*
3716016 TAAAAATATAATAATAATAA
1 TAAAAATATAATAATAAAAA
3716036 TAAA
1 TAAA
3716040 TAGATGACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
TAAAAATATAATAATAAAAA
Found at i:3717921 original size:17 final size:17
Alignment explanation
Indices: 3717899--3717944 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
3717889 GCGGGGTTAA
*
3717899 TTTAAAAAAAAATATTT
1 TTTAAAATAAAATATTT
*
3717916 TTT-AAATATAATATTT
1 TTTAAAATAAAATATTT
3717932 TTTAAAATAAAAT
1 TTTAAAATAAAAT
3717945 CTTTAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAAATAAAATATTT
Found at i:3717930 original size:16 final size:16
Alignment explanation
Indices: 3717909--3717960 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
3717899 TTTAAAAAAA
3717909 AATATTTTTTAAATAT
1 AATATTTTTTAAATAT
3717925 AATATTTTTTAAA-AT
1 AATATTTTTTAAATAT
* * *
3717940 AAAATCTTTAAAATTAT
1 AATATTTTTTAAA-TAT
3717957 AATA
1 AATA
3717961 CAACACATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 12 0.40
16 13 0.43
17 5 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATTTTTTAAATAT
Found at i:3726533 original size:26 final size:25
Alignment explanation
Indices: 3726486--3726546 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
3726476 TTAAAATAAT
3726486 AATAAGTAATAAAACAAAATAAGAAA
1 AATAAGTAATAAAACAAAATAA-AAA
* *
3726512 AATAAGTAGATAAAAC-AGATAAATA
1 AATAAGTA-ATAAAACAAAATAAAAA
3726537 AATAA-TAATA
1 AATAAGTAATA
3726547 TATAAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 3 0.09
24 2 0.06
25 7 0.22
26 13 0.41
27 7 0.22
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.20
Consensus pattern (25 bp):
AATAAGTAATAAAACAAAATAAAAA
Found at i:3732667 original size:30 final size:29
Alignment explanation
Indices: 3732633--3732692 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
3732623 ATATAATCAA
*
3732633 TAAATTTTATTCAACAAATAATTATTAAAT
1 TAAATTTAATTCAACAAATAATT-TTAAAT
* **
3732663 TAAATTTAATTTAATTAATAATTTTAAAT
1 TAAATTTAATTCAACAAATAATTTTAAAT
3732692 T
1 T
3732693 TTCTAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (29 bp):
TAAATTTAATTCAACAAATAATTTTAAAT
Found at i:3733651 original size:20 final size:21
Alignment explanation
Indices: 3733601--3733656 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 21
3733591 GGTACCACAT
*
3733601 GAACAATATCGATACTGTTCA
1 GAACAATATCGATACTGTTAA
* * *
3733622 -TATAACATCGATACTG-TAA
1 GAACAATATCGATACTGTTAA
*
3733641 GAACAATATCGGTACT
1 GAACAATATCGATACT
3733657 ACGTTCGTGA
Statistics
Matches: 26, Mismatches: 8, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (21 bp):
GAACAATATCGATACTGTTAA
Found at i:3734870 original size:5 final size:5
Alignment explanation
Indices: 3734860--3734885 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3734850 TCAATTTATC
3734860 TTTAA TTTAA TTTAA TTTAA TTTAA T
1 TTTAA TTTAA TTTAA TTTAA TTTAA T
3734886 AAATTAACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:3740813 original size:174 final size:172
Alignment explanation
Indices: 3740523--3740868 Score: 674
Period size: 174 Copynumber: 2.0 Consensus size: 172
3740513 TCAAAAAGCT
3740523 TAAACGATGTCGTTTTGTTGATGAAAAAAATGTTTTTTATGATATTTGAACCATAGAGCTATAGA
1 TAAACGATGTCGTTTTGTTGATGAAAAAAATGTTTTTTATGATATTTGAACCATAGAGCTATAGA
3740588 AAGGAAAGTTAAACACTCAACTACCTAGCTAACTCAATAACTTGTTATAACTTTAACAAAACTAT
66 AAGGAAAGTTAAACACTCAACTACCTAGCTAACTCAATAACTTGTTATAACTTTAACAAAACTAT
3740653 TATAAATGTTAAATAACAATTTAATTTTTTTAATTTTTATGAAC
131 TATAAATGTTAAATAACAA-TTAA-TTTTTTAATTTTTATGAAC
3740697 TAAACGATGTCGTTTTGTTGATGAAAAAAATGTTTTTTATGATATTTGAACCATAGAGCTATAGA
1 TAAACGATGTCGTTTTGTTGATGAAAAAAATGTTTTTTATGATATTTGAACCATAGAGCTATAGA
3740762 AAGGAAAGTTAAACACTCAACTACCTAGCTAACTCAATAACTTGTTATAACTTTAACAAAACTAT
66 AAGGAAAGTTAAACACTCAACTACCTAGCTAACTCAATAACTTGTTATAACTTTAACAAAACTAT
3740827 TATAAATGTTAAATAACAATTAATTTTTTAATTTTTATGAAC
131 TATAAATGTTAAATAACAATTAATTTTTTAATTTTTATGAAC
3740869 ACAATCTTCA
Statistics
Matches: 172, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
172 19 0.11
173 4 0.02
174 149 0.87
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (172 bp):
TAAACGATGTCGTTTTGTTGATGAAAAAAATGTTTTTTATGATATTTGAACCATAGAGCTATAGA
AAGGAAAGTTAAACACTCAACTACCTAGCTAACTCAATAACTTGTTATAACTTTAACAAAACTAT
TATAAATGTTAAATAACAATTAATTTTTTAATTTTTATGAAC
Found at i:3741136 original size:16 final size:16
Alignment explanation
Indices: 3741115--3741149 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
3741105 CCTTTTTGGC
3741115 AACCAAACATATATTT
1 AACCAAACATATATTT
3741131 AACCAAACATATATTT
1 AACCAAACATATATTT
3741147 AAC
1 AAC
3741150 AAATATTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (16 bp):
AACCAAACATATATTT
Found at i:3742940 original size:6 final size:6
Alignment explanation
Indices: 3742931--3742957 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3742921 ATAGGGAACA
3742931 AGATCG AGATCG AGATCG AGATCG AGA
1 AGATCG AGATCG AGATCG AGATCG AGA
3742958 CAGAAGTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.33, T:0.15
Consensus pattern (6 bp):
AGATCG
Found at i:3744022 original size:35 final size:35
Alignment explanation
Indices: 3743943--3744023 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
3743933 ACCGAATTAA
* *
3743943 ACGGGGACGGGAAAAATCGTTTATGTTAAACGAAG
1 ACGGGGATGGGAAAAACCGTTTATGTTAAACGAAG
* * *
3743978 ACAGAGATGGGAAAAACCGTTTATGTTAAACGAGG
1 ACGGGGATGGGAAAAACCGTTTATGTTAAACGAAG
3744013 ACGGGGATGGG
1 ACGGGGATGGG
3744024 TTTAGTAATC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.36, C:0.11, G:0.35, T:0.19
Consensus pattern (35 bp):
ACGGGGATGGGAAAAACCGTTTATGTTAAACGAAG
Found at i:3751870 original size:43 final size:42
Alignment explanation
Indices: 3751810--3752039 Score: 202
Period size: 43 Copynumber: 5.4 Consensus size: 42
3751800 AAATTTTTAT
* * *
3751810 TTTTTATATTTATAATTGAGGCCTCTAATTTTTGTAATCCCAC
1 TTTTTATCTTTATAATTGAGGCC-CTAATTTTTTTAATCTCAC
* * *
3751853 CTTTTATCTTTATAATTG-GGCCCTTATTTTTTTTAATCAT-ATT
1 TTTTTATCTTTATAATTGAGGCCC-TAATTTTTTTAATC-TCA-C
* * * *
3751896 TTTTTATATTTATAATTGATGACTCTAATTTTTTTCAATCTCAT
1 TTTTTATCTTTATAATTGA-GGCCCTAATTTTTTT-AATCTCAC
* *
3751940 TTTTTATCTTTATAATTGATGCCCCTAA-GTTTTTAAT-TCAC
1 TTTTTATCTTTATAATTGA-GGCCCTAATTTTTTTAATCTCAC
* *
3751981 TTTTTACCTTTATAATTGAGGTCCCTAATTTTTTCAATCAT-AC
1 TTTTTATCTTTATAATTGAGG-CCCTAATTTTTTTAATC-TCAC
3752024 TTTTTA-CTTTTATAAT
1 TTTTTATC-TTTATAAT
3752040 CTAATCCCCT
Statistics
Matches: 155, Mismatches: 20, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
40 1 0.01
41 28 0.18
42 28 0.18
43 53 0.34
44 37 0.24
45 8 0.05
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.54
Consensus pattern (42 bp):
TTTTTATCTTTATAATTGAGGCCCTAATTTTTTTAATCTCAC
Found at i:3751985 original size:87 final size:86
Alignment explanation
Indices: 3751807--3752019 Score: 229
Period size: 86 Copynumber: 2.5 Consensus size: 86
3751797 TTCAAATTTT
* *
3751807 TATTTTTTATATTTATAATTGAGGCCTCTAATTTTTGT-AATCCCACCTTTTATCTTTATAATTG
1 TATTTTTTATATTTATAATTGAGGACTCTAATTTTTTTCAATCCCACCTTTTATCTTTATAATTG
* **
3751871 GGCCCTTATTTTTTTTAATCA
66 GGCCCCTATAGTTTTTAATCA
* * **
3751892 TATTTTTTTATATTTATAATTGATGACTCTAATTTTTTTCAATCTCATTTTTTATCTTTATAATT
1 TA-TTTTTTATATTTATAATTGAGGACTCTAATTTTTTTCAATCCCACCTTTTATCTTTATAATT
*
3751957 GATGCCCCTA-AGTTTTTAAT--
65 G-GGCCCCTATAGTTTTTAATCA
* ** * *
3751977 TCACTTTTTACCTTTATAATTGAGGTCCCTAA-TTTTTTCAATC
1 T-ATTTTTTATATTTATAATTGAGGACTCTAATTTTTTTCAATC
3752020 ATACTTTTTA
Statistics
Matches: 108, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
84 11 0.10
85 26 0.24
86 34 0.31
87 31 0.29
88 6 0.06
ACGTcount: A:0.24, C:0.15, G:0.07, T:0.54
Consensus pattern (86 bp):
TATTTTTTATATTTATAATTGAGGACTCTAATTTTTTTCAATCCCACCTTTTATCTTTATAATTG
GGCCCCTATAGTTTTTAATCA
Found at i:3751997 original size:41 final size:42
Alignment explanation
Indices: 3751904--3752039 Score: 150
Period size: 41 Copynumber: 3.2 Consensus size: 42
3751894 TTTTTTTATA
* * *
3751904 TTTATAATTGATGACTCTAATTTTTTTCAATCTCATTTTTTATC
1 TTTATAATTGATGACCCTAA-TTTTTTCAAT-TCACTTTTTACC
* *
3751948 TTTATAATTGATGCCCCTAAGTTTTT-AATTCACTTTTTACC
1 TTTATAATTGATGACCCTAATTTTTTCAATTCACTTTTTACC
* * *
3751989 TTTATAATTGAGGTCCCTAATTTTTTCAA-TCATACTTTTTACT
1 TTTATAATTGATGACCCTAATTTTTTCAATTC--ACTTTTTACC
3752032 TTTATAAT
1 TTTATAAT
3752040 CTAATCCCCT
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
41 35 0.44
42 5 0.06
43 22 0.28
44 18 0.22
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (42 bp):
TTTATAATTGATGACCCTAATTTTTTCAATTCACTTTTTACC
Found at i:3752050 original size:43 final size:42
Alignment explanation
Indices: 3751920--3752054 Score: 127
Period size: 43 Copynumber: 3.2 Consensus size: 42
3751910 ATTGATGACT
* *
3751920 CTAATTTTTTTCAATCTCATTTTTTA-TCTTTATAATTGATGCCC
1 CTAA-TTTTTTCAATCTCACTTTTTACT-TTTATAATTAAT-CCC
* * *
3751964 CTAAGTTTTT-AAT-TCACTTTTTACCTTTATAATTGAGGT-CC
1 CTAATTTTTTCAATCTCACTTTTTACTTTTATAATT-A-ATCCC
3752005 CTAATTTTTTCAATCAT-ACTTTTTACTTTTATAATCTAATCCC
1 CTAATTTTTTCAATC-TCACTTTTTACTTTTATAAT-TAATCCC
3752048 CTAATTT
1 CTAATTT
3752055 AATCATTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
41 29 0.39
42 7 0.09
43 33 0.44
44 6 0.08
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (42 bp):
CTAATTTTTTCAATCTCACTTTTTACTTTTATAATTAATCCC
Found at i:3754233 original size:60 final size:60
Alignment explanation
Indices: 3754169--3754282 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
3754159 TTTAAGGATT
* * * * *
3754169 AAATTGAAATATTCAAATGTTTAAGGATTAATTTAGAAA-GATATTTATAATTTAGGAATA
1 AAATTGAAATATTCAAAAGTTTAAGAACTAATTTA-AAATGAGAGTTATAATTTAGGAATA
*
3754229 AAATTGAAATATTTAAAAGTTTAAGAACTAATTTAAAATGAGAGTTATAATTTA
1 AAATTGAAATATTCAAAAGTTTAAGAACTAATTTAAAATGAGAGTTATAATTTA
3754283 AGAACATGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 3 0.06
60 44 0.94
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (60 bp):
AAATTGAAATATTCAAAAGTTTAAGAACTAATTTAAAATGAGAGTTATAATTTAGGAATA
Found at i:3758471 original size:31 final size:31
Alignment explanation
Indices: 3758433--3758512 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 31
3758423 AGAACCTCAA
* * *
3758433 AAACTGTCCATAGGTCCCAAAGAACCTAGGT
1 AAACTGTCCATATGTCCCAAAGAACATAGGC
* * **
3758464 AAACTGTCAATATGTTCCTTAGAACATAGGC
1 AAACTGTCCATATGTCCCAAAGAACATAGGC
*
3758495 ATACTGTCCATATGTCCC
1 AAACTGTCCATATGTCCC
3758513 GGAAGATATA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (31 bp):
AAACTGTCCATATGTCCCAAAGAACATAGGC
Found at i:3763271 original size:32 final size:31
Alignment explanation
Indices: 3763170--3763275 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
3763160 TAGGTCCCAA
* * ** *
3763170 AGAACATATGTAAACTGTCCATATGTTCCTT
1 AGAACATAGGTATACTGTAAATATGTTCCGT
** *
3763201 AGAACATAGGTATACTGTTCATATATTCCG-
1 AGAACATAGGTATACTGTAAATATGTTCCGT
* *
3763231 AAAGACATAGGTGATTCTGTAAATATGTTCCGT
1 AGA-ACATAGGT-ATACTGTAAATATGTTCCGT
3763264 AGAACATAGGTA
1 AGAACATAGGTA
3763276 AACCCTTGAC
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
30 2 0.03
31 34 0.56
32 23 0.38
33 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (31 bp):
AGAACATAGGTATACTGTAAATATGTTCCGT
Found at i:3775182 original size:5 final size:5
Alignment explanation
Indices: 3775172--3775240 Score: 70
Period size: 5 Copynumber: 13.8 Consensus size: 5
3775162 AAAAGGGGAA
**
3775172 AAAAT AAAAT AAAAT AAAAT -AAAT CAAAGG AAAAT AAAAT AAAAT -AAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT
**
3775221 CAAAGG AAAAT AAAAT AAAA
1 -AAAAT AAAAT AAAAT AAAA
3775241 ATATATCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
4 8 0.15
5 40 0.77
6 4 0.08
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:3775205 original size:25 final size:25
Alignment explanation
Indices: 3775177--3775250 Score: 130
Period size: 25 Copynumber: 2.9 Consensus size: 25
3775167 GGGAAAAAAT
3775177 AAAATAAAATAAAATAAATCAAAGG
1 AAAATAAAATAAAATAAATCAAAGG
3775202 AAAATAAAATAAAATAAATCAAAGG
1 AAAATAAAATAAAATAAATCAAAGG
*
3775227 AAAATAAAATAAAAATATATCAAA
1 AAAATAAAAT-AAAATAAATCAAA
3775251 TAAATCAAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 35 0.74
26 12 0.26
ACGTcount: A:0.73, C:0.04, G:0.05, T:0.18
Consensus pattern (25 bp):
AAAATAAAATAAAATAAATCAAAGG
Found at i:3775363 original size:10 final size:10
Alignment explanation
Indices: 3775281--3775380 Score: 63
Period size: 10 Copynumber: 10.5 Consensus size: 10
3775271 AAAAATAAAC
3775281 ATAAAAAATA
1 ATAAAAAATA
*
3775291 A-AAAAAA-G
1 ATAAAAAATA
*
3775299 ATAAATAAT-
1 ATAAAAAATA
3775308 A-AAAAAAT-
1 ATAAAAAATA
*
3775316 ATAAAGGAA-A
1 ATAAA-AAATA
**
3775326 ATAAATCA-A
1 ATAAAAAATA
3775335 ATAGAAAAATGA
1 ATA-AAAAAT-A
*
3775347 A-ATAAAATA
1 ATAAAAAATA
3775356 ATAAAAAATA
1 ATAAAAAATA
3775366 ATAAAAAATA
1 ATAAAAAATA
3775376 ATAAA
1 ATAAA
3775381 TGAATCAAAG
Statistics
Matches: 71, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
8 8 0.11
9 22 0.31
10 38 0.54
11 1 0.01
12 2 0.03
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (10 bp):
ATAAAAAATA
Found at i:3775364 original size:20 final size:19
Alignment explanation
Indices: 3775263--3775384 Score: 64
Period size: 18 Copynumber: 6.5 Consensus size: 19
3775253 AATCAAAGGG
3775263 AAAAATGTAAA-AATAAACATA
1 AAAAATG-AAATAA-AAA-ATA
3775284 AAAAAT-AAA-AAAAAGATA
1 AAAAATGAAATAAAAA-ATA
* *
3775302 AATAAT-AAA-AAAATATA
1 AAAAATGAAATAAAAAATA
**
3775319 AAGGA--AAATAAATCAAATA
1 AAAAATGAAATAAA--AAATA
3775338 GAAAAATGAAATAAAATAATA
1 -AAAAATGAAATAAAA-AATA
3775359 AAAAAT--AATAAAAAATA
1 AAAAATGAAATAAAAAATA
*
3775376 ATAAATGAA
1 AAAAATGAA
3775385 TCAAAGGAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
16 3 0.04
17 18 0.22
18 25 0.30
19 10 0.12
20 10 0.12
21 10 0.12
22 7 0.08
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.18
Consensus pattern (19 bp):
AAAAATGAAATAAAAAATA
Found at i:3776428 original size:3 final size:3
Alignment explanation
Indices: 3776415--3776451 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
3776405 AAAAAAGAAT
3776415 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3776452 AAGTAATAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:3776686 original size:37 final size:37
Alignment explanation
Indices: 3776544--3776905 Score: 486
Period size: 37 Copynumber: 9.8 Consensus size: 37
3776534 AAAAAATTCC
* *
3776544 AAAACTATATATTGTAT-AGTTTTCAAAAAT-TATTTT
1 AAAACTATATATTATATAATTTTTCAAAAATGT-TTTT
3776580 -AAA--A-ATATTATATAAGTTTTTCAAAAAAATGTTTTT
1 AAAACTATATATTATATAA-TTTTTC--AAAAATGTTTTT
*
3776616 AAAATTATATATTATATAATTTTTCAAAAAATGTTTTT
1 AAAACTATATATTATATAATTTTTC-AAAAATGTTTTT
3776654 AAAACTATATATTATATAATTTTTCAAAAATGTTTTT
1 AAAACTATATATTATATAATTTTTCAAAAATGTTTTT
3776691 AAAACTATATATTATATAATTTTTCAAAAATGTTTTT
1 AAAACTATATATTATATAATTTTTCAAAAATGTTTTT
3776728 AAAACTATATATTATATAATTTTTCAAAAATGTTTTT
1 AAAACTATATATTATATAATTTTTCAAAAATGTTTTT
* *
3776765 AAAACTATATATTATATAATTTTTTAAAAATATTTTT
1 AAAACTATATATTATATAATTTTTCAAAAATGTTTTT
* *
3776802 AAAACTATATATTATATAATTTTTCACAAATGTTTTA
1 AAAACTATATATTATATAATTTTTCAAAAATGTTTTT
* * * * **
3776839 AAAACCATATACTATATAAGTTTTC-AAATTGTTTCA
1 AAAACTATATATTATATAATTTTTCAAAAATGTTTTT
*
3776875 AAAACTATATAATATATAAATGTTTTCAAAA
1 AAAACTATATATTATAT-AAT-TTTTCAAAA
3776906 CTATATATTA
Statistics
Matches: 296, Mismatches: 18, Indels: 21
0.88 0.05 0.06
Matches are distributed among these distances:
32 8 0.03
33 2 0.01
34 5 0.02
35 3 0.01
36 33 0.11
37 182 0.61
38 42 0.14
39 10 0.03
40 11 0.04
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (37 bp):
AAAACTATATATTATATAATTTTTCAAAAATGTTTTT
Found at i:3776899 original size:63 final size:63
Alignment explanation
Indices: 3776829--3776967 Score: 176
Period size: 63 Copynumber: 2.2 Consensus size: 63
3776819 AATTTTTCAC
** *
3776829 AAATGTTTTAAAAACCATATACTATATA-AGTTTTCAAAT-TGTTTCAAAAACTATATAATATAT
1 AAATGTTTTAAAAACCATATACTATATATA-TTTAAAAATAT-TTTCAAAAACTATATAACATAT
* * *
3776892 AAATGTTTTCAAAACTATATATTATATATATTTAAAAATATTTTCAAAAACTATATAACATAT
1 AAATGTTTTAAAAACCATATACTATATATATTTAAAAATATTTTCAAAAACTATATAACATAT
*
3776955 AAAT-TTTCAAAAA
1 AAATGTTTTAAAAA
3776968 TCATTTTTTG
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
62 7 0.11
63 57 0.86
64 2 0.03
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.40
Consensus pattern (63 bp):
AAATGTTTTAAAAACCATATACTATATATATTTAAAAATATTTTCAAAAACTATATAACATAT
Found at i:3776920 original size:36 final size:36
Alignment explanation
Indices: 3776880--3776948 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
3776870 TTTCAAAAAC
* *
3776880 TATATA-ATATATAAATGTTTTC-AAAACTATATAT
1 TATATATATATAAAAATATTTTCAAAAACTATATAT
*
3776914 TATATATATTTAAAAATATTTTCAAAAACTATATA
1 TATATATATATAAAAATATTTTCAAAAACTATATA
3776949 ACATATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 6 0.20
35 13 0.43
36 11 0.37
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (36 bp):
TATATATATATAAAAATATTTTCAAAAACTATATAT
Found at i:3776955 original size:36 final size:37
Alignment explanation
Indices: 3776892--3776974 Score: 98
Period size: 36 Copynumber: 2.2 Consensus size: 37
3776882 TATAATATAT
* ** *
3776892 AAATGTTTTCAAAACTATATATTATATATA-TTT-AA
1 AAATATTTTCAAAACTATATAACATATAAATTTTCAA
3776927 AAATATTTTCAAAAACTATATAACATATAAATTTTCAA
1 AAATATTTTC-AAAACTATATAACATATAAATTTTCAA
3776965 AAATCATTTT
1 AAAT-ATTTT
3776975 TTGAAAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
35 9 0.22
36 17 0.43
37 3 0.08
38 6 0.15
39 5 0.12
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.42
Consensus pattern (37 bp):
AAATATTTTCAAAACTATATAACATATAAATTTTCAA
Found at i:3777766 original size:84 final size:84
Alignment explanation
Indices: 3777678--3778331 Score: 722
Period size: 84 Copynumber: 7.9 Consensus size: 84
3777668 GTTTACCTCT
* * * *
3777678 GAGCTGAGTGTAATCGAACTCGAAGGTCTTCGGTTGGCAGATAACCC-TCATCGACTTAAGCTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC-TCGACTTAAGTTAT
*
3777742 GCTGTAAATGATGTGCCTTG
65 GCTGCAAATGATGTGCCTTG
* * * *
3777762 GAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGGTTGACAGATAGCCCTTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
*
3777827 CTGCAAATGATGTGTCTTG
66 CTGCAAATGATGTGCCTTG
* *
3777846 GAGTTGAGCGTAGTCGAACTCGAAGGTATTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* *
3777911 CTACAAATGATATGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * * *
3777930 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-AGACAGATAACCCTTCTAGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
** *
3777994 GCTATAAATGATGTGCCCTCG
65 GCTGCAAATGATGTG-CCTTG
* * * * * *
3778015 AAGCTGAGTGTAATCGAACTTGAGGGTC--T--TTGGCAGGTAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
3778076 CTGCAAATGATGTGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * * *
3778095 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTT-ACAGATAACCCTTATAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * *
3778159 CTGTAAATGATGTACCCTCG
66 CTGCAAATGATGT-GCCTTG
* * * * * * *
3778179 AAGCTAAGTGTAATCGAACTC-AAGGGTC--T--TCGGCAGATATCCCTTCTCGACTTAAGCTAT
1 GAGCTGAGCGTAGTCGAACTCGAA-GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
*
3778239 GCTGCAAATAATGTGCCTTG
65 GCTGCAAATGATGTGCCTTG
* * * * * *
3778259 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-ATTGGCATATAACCCTTCTAGCCTTGAGTTACG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
3778323 CTGCAAATG
66 CTGCAAATG
3778332 TTGTCTTTAA
Statistics
Matches: 471, Mismatches: 84, Indels: 31
0.80 0.14 0.05
Matches are distributed among these distances:
80 53 0.11
81 72 0.15
82 4 0.01
83 69 0.15
84 239 0.51
85 34 0.07
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (84 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
CTGCAAATGATGTGCCTTG
Found at i:3777872 original size:168 final size:166
Alignment explanation
Indices: 3777624--3778331 Score: 851
Period size: 164 Copynumber: 4.3 Consensus size: 166
3777614 CGACTAATTT
* * * * * * * *
3777624 GTTGACAGATATCCCTTCTTGCCTTGAGCTATTCTATAAATTTGGTTTACCTCTG-AGCTGAGTG
1 GTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA--TGATGTGCCTC-GAAGCTGAGTG
*
3777688 TAATCGAACTCGAAGGTCTTCGGTTGGCAGATAACCC-TCATCGACTTAAGCTATGCTGTAAATG
63 TAATCGAACTCGAAGGTCTTC--TTGGCAGATAACCCTTC-TCGACTTAAGCTATGCTGCAAATG
*
3777752 ATGTGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTG
125 ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
* * * * * * * * * * * *
3777794 GTTGACAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCTTGGAGTTGAGCGTAG
1 GTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTCGAAGCTGAGTGTAA
* * * * *
3777859 TCGAACTCGAAGGTATTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATAT
66 TCGAACTCGAAGGT-CTT-CTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
3777924 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
129 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTG
* *
3777963 G-AGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTGTA
1 GTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG-CCTCGAAGCTGAGTGTA
* * * *
3778027 ATCGAACTTGAGGGTC-T-TTGGCAGGTAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
65 ATCGAACTCGAAGGTCTTCTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
3778090 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
130 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
* * *
3778127 GTT-ACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATGTACCCTCGAAGCTAAGTGTA
1 GTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT-GCCTCGAAGCTGAGTGTA
* *
3778191 ATCGAACTC-AAGGGTCTTC--GGCAGATATCCCTTCTCGACTTAAGCTATGCTGCAAATAATGT
65 ATCGAACTCGAA-GGTCTTCTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
3778253 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-
129 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
* * * * *
3778290 ATTGGCATATAACCCTTCTAGCCTTGAGTTACGCTGCAAATG
1 GTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
3778332 TTGTCTTTAA
Statistics
Matches: 467, Mismatches: 59, Indels: 30
0.84 0.11 0.05
Matches are distributed among these distances:
163 3 0.01
164 182 0.39
165 77 0.16
167 2 0.00
168 137 0.29
169 33 0.07
170 33 0.07
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (166 bp):
GTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTCGAAGCTGAGTGTAA
TCGAACTCGAAGGTCTTCTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
Found at i:3778198 original size:249 final size:252
Alignment explanation
Indices: 3777679--3778331 Score: 686
Period size: 249 Copynumber: 2.6 Consensus size: 252
3777669 TTTACCTCTG
* * *
3777679 AGCTGAGTGTAATCGAACTCGAAGGTC-TTCGGTTGGCAGATAACCCTCATCGACTTAAGCTATG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTCGGTAGACAGATAACCCTCATAGACTTAAGCTATG
* * * * * *
3777743 CTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGGTTGACAGATAGCC
66 CTATAAATGATGTGCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGG-TGACAGATAACC
* *
3777808 CTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCTTGGAGTTGAGCGTAGTCGAACTCGAAGGT
130 CTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
* * * * * *
3777873 ATTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGG
195 ATTTGGTTGACAGATAACCCTTATAGACTTAAGTTATGCTACAAATGATATCCCTCGA
* * * * * *
3777931 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-AGACAGATAACCCTTC-TAGCCTTGAGTTAT
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTCGGTAGACAGATAACCC-TCATAGACTTAAGCTAT
* * * *
3777994 GCTATAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTT-G-G-CAGGTAAC
65 GCTATAAATGATGTG-CCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGACAGATAAC
*
3778056 CCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
129 CCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
* * * ** *
3778121 TCTTTGGTT-ACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATGTACCCTCGA
194 TATTTGGTTGACAGATAACCCTTATAGACTTAAGTTATGCTACAAATGATAT-CCCTCGA
* * *
3778180 AGCTAAGTGTAATCGAACTC-AAGGGTC-TTC-G--G-CAGATATCCCTTC-TCGACTTAAGCTA
1 AGCTGAGTGTAATCGAACTCGAA-GGTCTTTCGGTAGACAGATAACCC-TCATAGACTTAAGCTA
** * * * * ** * *
3778238 TGCTGCAAATAATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTATTGGCATATAAC
64 TGCTATAAATGATGTGCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGACAGATAAC
* * * * *
3778303 CCTTCTAGCCTTGAGTTACGCTGCAAATG
129 CCTTCTCGACTTAAGCTATGCTGCAAATG
3778332 TTGTCTTTAA
Statistics
Matches: 334, Mismatches: 59, Indels: 21
0.81 0.14 0.05
Matches are distributed among these distances:
244 30 0.09
245 34 0.10
246 2 0.01
247 32 0.10
248 38 0.11
249 101 0.30
250 1 0.00
252 61 0.18
253 35 0.10
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (252 bp):
AGCTGAGTGTAATCGAACTCGAAGGTCTTTCGGTAGACAGATAACCCTCATAGACTTAAGCTATG
CTATAAATGATGTGCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCC
TTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTA
TTTGGTTGACAGATAACCCTTATAGACTTAAGTTATGCTACAAATGATATCCCTCGA
Found at i:3782294 original size:24 final size:24
Alignment explanation
Indices: 3782262--3782317 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
3782252 TGGTCGACTG
*
3782262 TTGACCGTTGACCGGCGTTAACCA
1 TTGATCGTTGACCGGCGTTAACCA
* *
3782286 TTGATCGTTGATCGGCGTTAACCG
1 TTGATCGTTGACCGGCGTTAACCA
3782310 TTGATCGT
1 TTGATCGT
3782318 CGTTGACCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (24 bp):
TTGATCGTTGACCGGCGTTAACCA
Found at i:3782313 original size:17 final size:17
Alignment explanation
Indices: 3782291--3782326 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3782281 AACCATTGAT
3782291 CGTTGATCGGCGTTAAC
1 CGTTGATCGGCGTTAAC
* *
3782308 CGTTGATCGTCGTTGAC
1 CGTTGATCGGCGTTAAC
3782325 CG
1 CG
3782327 GCCTTTGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.25, G:0.31, T:0.31
Consensus pattern (17 bp):
CGTTGATCGGCGTTAAC
Found at i:3784831 original size:80 final size:80
Alignment explanation
Indices: 3784698--3784857 Score: 293
Period size: 80 Copynumber: 2.0 Consensus size: 80
3784688 CCAGTCAACA
* * *
3784698 AACTCTTGTAATAGTGATTCTAATTTCTGGCACTCTATCGGTAAACTGAAGATTTGTGTTTCTCT
1 AACTCTTCTAATAGTGATTCTAATTTCCGGCACTCTATCGATAAACTGAAGATTTGTGTTTCTCT
3784763 GCCCGATAAGATTAT
66 GCCCGATAAGATTAT
3784778 AACTCTTCTAATAGTGATTCTAATTTCCGGCACTCTATCGATAAACTGAAGATTTGTGTTTCTCT
1 AACTCTTCTAATAGTGATTCTAATTTCCGGCACTCTATCGATAAACTGAAGATTTGTGTTTCTCT
3784843 GCCCGATAAGATTAT
66 GCCCGATAAGATTAT
3784858 CTTGTATCTC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (80 bp):
AACTCTTCTAATAGTGATTCTAATTTCCGGCACTCTATCGATAAACTGAAGATTTGTGTTTCTCT
GCCCGATAAGATTAT
Found at i:3785019 original size:24 final size:24
Alignment explanation
Indices: 3784932--3785026 Score: 84
Period size: 24 Copynumber: 4.0 Consensus size: 24
3784922 AATTTTTATT
* *
3784932 TGAATTATGTTTTGACATCTGATT
1 TGAATTATGTTTTGATATCTGATC
* * * * *
3784956 TGAAATCTGTTCTGAT-TCCTAACC
1 TGAATTATGTTTTGATAT-CTGATC
* *
3784980 TGGATTCTGTTTTGATATCTGATC
1 TGAATTATGTTTTGATATCTGATC
*
3785004 TGAATTATGTTTTGATTTCTGAT
1 TGAATTATGTTTTGATATCTGAT
3785027 ATCTCGGTTT
Statistics
Matches: 54, Mismatches: 15, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 52 0.96
25 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (24 bp):
TGAATTATGTTTTGATATCTGATC
Found at i:3785194 original size:2 final size:2
Alignment explanation
Indices: 3785187--3785225 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3785177 CGGATGGGGG
3785187 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3785226 TTAAAAGATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3787965 original size:3 final size:3
Alignment explanation
Indices: 3787954--3787995 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
3787944 AAAAAAGAAT
*
3787954 TAA TAAA TAA TAA TAA TAA TAA TAA -AA GTAA TAG TAA TAA TA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TA
3787996 TATATTCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 27 0.79
4 5 0.15
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:3788019 original size:23 final size:25
Alignment explanation
Indices: 3787988--3788034 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
3787978 AAAGTAATAG
*
3787988 TAATAATATATA-TTCTAAAATATA
1 TAATAATATATATTTCAAAAATATA
3788012 TAAT-ATATATATTTCAAAAATAT
1 TAATAATATATATTTCAAAAATAT
3788035 TTTTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (25 bp):
TAATAATATATATTTCAAAAATATA
Found at i:3788188 original size:37 final size:37
Alignment explanation
Indices: 3788072--3788357 Score: 309
Period size: 37 Copynumber: 7.8 Consensus size: 37
3788062 AAAAATTTCC
* * *
3788072 AAAACTCTATATTGTAT-AGTTTTCAAAAAT-TATTTT
1 AAAACTATATATTATATAATTTTTCAAAAATAT-TTTT
* *
3788108 AAAA-TAT-TA-TATA-AGTTTTTCAAAAAATGTTTTT
1 AAAACTATATATTATATAATTTTTC-AAAAATATTTTT
* * * *
3788142 AAAATTATATATTATATAATATTTCAAAATTTTTTTT
1 AAAACTATATATTATATAATTTTTCAAAAATATTTTT
*
3788179 AAAACTATATATTATATTAATTTTTCAAAAATGTTTTT
1 AAAACTATATATTATA-TAATTTTTCAAAAATATTTTT
3788217 AAAACTATATATTATATAATTTTTCAAAAATATTTTT
1 AAAACTATATATTATATAATTTTTCAAAAATATTTTT
* * *
3788254 AAAACTATATATTATATAAATTTTCACAAATATTTTA
1 AAAACTATATATTATATAATTTTTCAAAAATATTTTT
* * *
3788291 AAAATTATATACTATATAAGTTTTC-AAAAT-TTTTT
1 AAAACTATATATTATATAATTTTTCAAAAATATTTTT
*
3788326 AAAAACTATATAATATATAAATGTTTTCAAAA
1 -AAAACTATATATTATAT-AAT-TTTTCAAAA
3788358 CTATATATTA
Statistics
Matches: 214, Mismatches: 24, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
33 8 0.04
34 16 0.07
35 10 0.05
36 25 0.12
37 107 0.50
38 45 0.21
39 3 0.01
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (37 bp):
AAAACTATATATTATATAATTTTTCAAAAATATTTTT
Found at i:3788220 original size:75 final size:72
Alignment explanation
Indices: 3788079--3788446 Score: 334
Period size: 75 Copynumber: 5.1 Consensus size: 72
3788069 TCCAAAACTC
* * * *
3788079 TATATTGTATAGTTTTCAAAAATTATTTTAAAA-TAT-TA-TATA-AGTTTTTCAAAAAATGTTT
1 TATATTATATAATTTTC-AAAATTTTTTTAAAACTATATATTATATAATTTTTC-AAAAATGTTT
3788140 TTAAAATTA
64 TTAAAATTA
3788149 TATATTATATAATATTTCAAAATTTTTTTTAAAACTATATATTATATTAATTTTTCAAAAATGTT
1 TATATTATATAAT-TTTCAAAA-TTTTTTTAAAACTATATATTATA-TAATTTTTCAAAAATGTT
*
3788214 TTTAAAACTA
63 TTTAAAATTA
* * * *
3788224 TATATTATATAATTTTTCAAAAATATTTTTAAAACTATATATTATATAAATTTTCACAAATATTT
1 TATATTATATAA-TTTTC-AAAATTTTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTT
*
3788289 TAAAAATTA
64 TTAAAATTA
* *
3788298 TATACTATATAAGTTTTCAAAATTTTTTAAAAACTATATA--ATAT-A----T---AAATGTTTT
1 TATATTATATAA-TTTTCAAAATTTTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTT
* *
3788353 CAAAACTA
65 TAAAATTA
* ** ** *
3788361 TATATTATATATA-TTTAAAAATATTTTCAAAAACTATATAACATATAAATTTTCAAAAATCGTT
1 TATATTATATA-ATTTTCAAAAT-TTTTTTAAAACTATATATTATATAATTTTTCAAAAAT-GTT
3788425 TTCTGAAAATTA
63 TT-T-AAAATTA
3788437 TATATTATAT
1 TATATTATAT
3788447 TTTGACAAAA
Statistics
Matches: 251, Mismatches: 23, Indels: 42
0.79 0.07 0.13
Matches are distributed among these distances:
62 8 0.03
63 40 0.16
64 1 0.00
65 4 0.02
66 2 0.01
70 17 0.07
71 18 0.07
72 3 0.01
73 26 0.10
74 48 0.19
75 56 0.22
76 28 0.11
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (72 bp):
TATATTATATAATTTTCAAAATTTTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTT
AAAATTA
Found at i:3788347 original size:27 final size:27
Alignment explanation
Indices: 3788317--3788376 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
3788307 TAAGTTTTCA
3788317 AAATTTTTTAAAAACTATATAATATAT
1 AAATTTTTTAAAAACTATATAATATAT
* * *
3788344 AAATGTTTTCAAAACTATATATTATAT
1 AAATTTTTTAAAAACTATATAATATAT
*
3788371 ATATTT
1 AAATTT
3788377 AAAAATATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (27 bp):
AAATTTTTTAAAAACTATATAATATAT
Found at i:3788370 original size:63 final size:62
Alignment explanation
Indices: 3788281--3788418 Score: 165
Period size: 63 Copynumber: 2.2 Consensus size: 62
3788271 AAATTTTCAC
* * * * *
3788281 AAATATTTTAAAAATTATATACTATATA-AGTTTTCAAAAT-TTTTTAAAAACTATATAATATAT
1 AAAT-TTTTCAAAACTATATACTATATATA--TTTAAAAATATTTTCAAAAACTATATAACATAT
*
3788344 AAATGTTTTCAAAACTATATATTATATATATTTAAAAATATTTTCAAAAACTATATAACATAT
1 AAAT-TTTTCAAAACTATATACTATATATATTTAAAAATATTTTCAAAAACTATATAACATAT
3788407 AAA-TTTTCAAAA
1 AAATTTTTCAAAA
3788419 ATCGTTTTCT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
61 9 0.14
62 8 0.12
63 48 0.73
64 1 0.02
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (62 bp):
AAATTTTTCAAAACTATATACTATATATATTTAAAAATATTTTCAAAAACTATATAACATAT
Found at i:3788372 original size:36 final size:36
Alignment explanation
Indices: 3788332--3788400 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
3788322 TTTTAAAAAC
* *
3788332 TATATA-ATATATAAATGTTTTC-AAAACTATATAT
1 TATATATATATAAAAATATTTTCAAAAACTATATAT
*
3788366 TATATATATTTAAAAATATTTTCAAAAACTATATA
1 TATATATATATAAAAATATTTTCAAAAACTATATA
3788401 ACATATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 6 0.20
35 13 0.43
36 11 0.37
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (36 bp):
TATATATATATAAAAATATTTTCAAAAACTATATAT
Found at i:3788407 original size:36 final size:35
Alignment explanation
Indices: 3788344--3788412 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
3788334 TATAATATAT
* ** *
3788344 AAATGTTTTCAAAACTATATATTATATATATTTAA
1 AAATATTTTCAAAACTATATAACATATAAATTTAA
3788379 AAATATTTTCAAAAACTATATAACATATAAATTT
1 AAATATTTTC-AAAACTATATAACATATAAATTT
3788413 TCAAAAATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 9 0.31
36 20 0.69
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (35 bp):
AAATATTTTCAAAACTATATAACATATAAATTTAA
Found at i:3788903 original size:2 final size:2
Alignment explanation
Indices: 3788845--3788884 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3788835 GTATACTTGA
3788845 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
3788885 TTTTAATTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3791451 original size:2 final size:2
Alignment explanation
Indices: 3791446--3791529 Score: 97
Period size: 2 Copynumber: 44.5 Consensus size: 2
3791436 GAAAAACTTG
* *
3791446 TA TA TA TA TA TA TA TA TA -A TA TC T- TG 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
* *
3791486 TA TA TA TA TA -A TA TC T- TG 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
3791526 -A TA T
1 TA TA T
3791530 CTTGAACACA
Statistics
Matches: 73, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
1 5 0.07
2 68 0.93
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3791455 original size:26 final size:26
Alignment explanation
Indices: 3791426--3791519 Score: 89
Period size: 28 Copynumber: 3.4 Consensus size: 26
3791416 ATTTTTTCTT
*
3791426 TATATATATGGAAAAACTTGTATATA
1 TATATATATAGAAAAACTTGTATATA
* * *
3791452 TATATATATATAATATCTTGTATATATA
1 TATATATATAGAAAAACTTG--TATATA
*
3791480 TATATATATATATATAATATCTTGTATATA
1 TATATATATAGA-A-AA-A-CTTGTATATA
3791510 TATATATATA
1 TATATATATA
3791520 TATATAATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
26 16 0.29
28 18 0.32
29 1 0.02
30 17 0.30
32 4 0.07
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (26 bp):
TATATATATAGAAAAACTTGTATATA
Found at i:3791458 original size:24 final size:26
Alignment explanation
Indices: 3791426--3791526 Score: 80
Period size: 30 Copynumber: 3.7 Consensus size: 26
3791416 ATTTTTTCTT
*
3791426 TATATATATGGA-AA-AACTTGTATA
1 TATATATATAGATAATAACTTGTATA
* *
3791450 TATATATATATATAATATCTTGTATATA
1 TATATATATAGATAATAACTTG--TATA
*
3791478 TATATATATATATATATAATATCTTGTATA
1 TATATATATAGATA-AT-A-A-CTTGTATA
*
3791508 TATATATATATATATATAA
1 TATATATATAGATA-ATAA
3791527 TATCTTGAAC
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
24 10 0.15
25 2 0.03
26 5 0.08
28 19 0.29
29 3 0.05
30 22 0.34
32 4 0.06
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.47
Consensus pattern (26 bp):
TATATATATAGATAATAACTTGTATA
Found at i:3791543 original size:32 final size:31
Alignment explanation
Indices: 3791446--3791534 Score: 162
Period size: 30 Copynumber: 2.9 Consensus size: 31
3791436 GAAAAACTTG
3791446 TATATATATATATATATAATATCTTGTATATA
1 TATATATATATATATATAATATCTTG-ATATA
3791478 TATATATATATATATATAATATCTTG-TATA
1 TATATATATATATATATAATATCTTGATATA
3791508 TATATATATATATATATAATATCTTGA
1 TATATATATATATATATAATATCTTGA
3791535 ACACATATAA
Statistics
Matches: 56, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
30 30 0.54
32 26 0.46
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (31 bp):
TATATATATATATATATAATATCTTGATATA
Found at i:3792684 original size:2 final size:2
Alignment explanation
Indices: 3792677--3792716 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3792667 ACTCCCCTTA
3792677 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
3792717 GGTCTGTTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3795766 original size:83 final size:83
Alignment explanation
Indices: 3795624--3795802 Score: 349
Period size: 83 Copynumber: 2.2 Consensus size: 83
3795614 AAATTTATGA
3795624 ACCATTTATCGATTCCCCTCTTATTTCTTTAAAACGAAAATATTAGATTGAAAGCAATACATATA
1 ACCATTTATCGATTCCCCTCTTATTTCTTTAAAACGAAAATATTAGATTGAAAGCAATACATATA
3795689 TGTGATCAATATTATTAG
66 TGTGATCAATATTATTAG
*
3795707 ACCATTTATCGATTCCCCTCTTATTTCTTTAAAACGAAAATATTAGATTGAAAGTAATACATATA
1 ACCATTTATCGATTCCCCTCTTATTTCTTTAAAACGAAAATATTAGATTGAAAGCAATACATATA
3795772 TGTGATCAATATTATTAG
66 TGTGATCAATATTATTAG
3795790 ACCATTTATCGAT
1 ACCATTTATCGAT
3795803 AACTAGATGG
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 95 1.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (83 bp):
ACCATTTATCGATTCCCCTCTTATTTCTTTAAAACGAAAATATTAGATTGAAAGCAATACATATA
TGTGATCAATATTATTAG
Found at i:3799589 original size:21 final size:21
Alignment explanation
Indices: 3799565--3799629 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
3799555 AATACAAGCA
*
3799565 AGAGTCGAAGAGAAGCTTGAG
1 AGAGTCGAAGAGAAACTTGAG
3799586 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
3799607 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
3799628 AG
1 AG
3799630 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.40, C:0.11, G:0.34, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:3802162 original size:201 final size:201
Alignment explanation
Indices: 3801833--3802932 Score: 1514
Period size: 201 Copynumber: 5.6 Consensus size: 201
3801823 ACATATGCAT
* ** * * *
3801833 CCATAAGTATAATGTAATAGGTAAATTTTTAATGTAACTGGTATAAATATATCGGTTTTATGAGA
1 CCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGA
* * *
3801898 GAATATGTTTACAACATGTATCGACACTTTTTTAATTTTGTATCGATACTTTTGGTCCAGAATGG
66 GAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
* *
3801963 ATGCCAAAAAGGGTGAACGCATAAAATGTCGATACATTTTCAAAAAGTGTCGATTCCAGAAACAT
131 ATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATTCCAAAAACAT
3802028 CGAAAC
196 CGAAAC
* * * *
3802034 CCATAATTATAATGTAATAGGTAAATTTACAATATAACCGGTATAAATATATCAAATTTATGAGA
1 CCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGA
* *
3802099 TAATAGGTCTACAACATGTATCAACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
66 GAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
* * *
3802164 ATACCAAAAAGGGTGAACGCATAAAGTGTCGAT-C----CCAGAAA----C-A-T-C-AAAAC--
131 ATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATTCCAAAAACAT
*
3802214 CTATAA-
196 CGA-AAC
** * ** * * *
3802220 TTATAATGTA-ATAGGTAA-ATTTACAATGT--AAC-----CGGTATAAATATATCGATTTTATG
1 CCATAAT-TATA-ATGTAATAGGTA-AATTTACAATGTAACCGGTATAAATATACCGATTTTATG
*
3802276 AGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGCCGATACTTTTGGTCCAGAA
63 AGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAA
* * *
3802341 TGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAAA
128 TGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATTCCAAAAA
3802406 CATCGAAAC
193 CATCGAAAC
* *
3802415 CCATAATTATAATGTAATATGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAAA
1 CCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGA
* *
3802480 GAATAGGTCTACAATATGTATCGACATTTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATG
66 GAATAGGTCTACAACATGTATCGACA-CTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATG
*
3802545 GATGTCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGA-TCCTAAAAAC
130 GATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATTCC-AAAAAC
3802609 ATCGAAAC
194 ATCGAAAC
* * *
3802617 CCATAATTATAATGTAATAGCTAAATTCACAATGTAACCGGTATAAATATGCCGATTTTATGAGA
1 CCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGA
* * *
3802682 GAATAGGTCTACAACATGTATCGAAACGTTTTTAATTTTGTGTCGATACTTTTGGTCCAAAATGG
66 GAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
* *
3802747 ATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAATGTCGATCCCAAAAACAT
131 ATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATTCCAAAAACAT
*
3802812 CAAAAC
196 CGAAAC
* *
3802818 CCATAATTATAATGTAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGA
1 CCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGA
*
3802883 GAATAGGTCTACAACATGTATCGACACATTTTTAATTTTGTGTCGATACT
66 GAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACT
3802933 AATTTAAATA
Statistics
Matches: 793, Mismatches: 74, Indels: 64
0.85 0.08 0.07
Matches are distributed among these distances:
180 119 0.15
181 1 0.00
185 6 0.01
186 11 0.01
187 13 0.02
188 4 0.01
189 2 0.00
190 2 0.00
191 1 0.00
192 2 0.00
193 4 0.01
194 13 0.02
195 12 0.02
196 7 0.01
200 1 0.00
201 408 0.51
202 187 0.24
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (201 bp):
CCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGA
GAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
ATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATTCCAAAAACAT
CGAAAC
Found at i:3804416 original size:6 final size:6
Alignment explanation
Indices: 3804405--3804450 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
3804395 CAAGCGGTCA
* * *
3804405 ATGAAG ATGAAG ATGACG ATGAAG ATGATG ATGAAG ATGACG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
3804451 TGATCCAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.43, C:0.04, G:0.33, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:3804425 original size:12 final size:12
Alignment explanation
Indices: 3804405--3804450 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
3804395 CAAGCGGTCA
*
3804405 ATGAAGATGAAG
1 ATGACGATGAAG
3804417 ATGACGATGAAG
1 ATGACGATGAAG
*
3804429 ATGATGATGAAG
1 ATGACGATGAAG
3804441 ATGACGATGA
1 ATGACGATGA
3804451 TGATCCAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.43, C:0.04, G:0.33, T:0.20
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:3804451 original size:18 final size:18
Alignment explanation
Indices: 3804405--3804454 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
3804395 CAAGCGGTCA
* *
3804405 ATGAAGATGAAGATGACG
1 ATGAAGATGATGATGAAG
3804423 ATGAAGATGATGATGAAG
1 ATGAAGATGATGATGAAG
*
3804441 ATGACGATGATGAT
1 ATGAAGATGATGAT
3804455 CCAAACAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.42, C:0.04, G:0.32, T:0.22
Consensus pattern (18 bp):
ATGAAGATGATGATGAAG
Found at i:3806147 original size:251 final size:251
Alignment explanation
Indices: 3805721--3806214 Score: 701
Period size: 251 Copynumber: 2.0 Consensus size: 251
3805711 CTTAAAGTTT
* *
3805721 CCCATAAAGTGGCGATCCATATATAAAAAGTAACGACCCAAAAAACATCGAAACCCATAATTATA
1 CCCATAAAGTAGCGATACATATATAAAAAGTAACGACCCAAAAAACATCGAAACCCATAATTATA
* * *
3805786 ATGTAATGGGTAATTTTTCAATATAACCAGTATAAATATATCGGTTTTATGAAAAATATGTCTAC
66 ATGTAATCGGTAATTTTTCAACATAACCAGTATAAATATACCGGTTTTATGAAAAATATGTCTAC
* *
3805851 AACATTTATCGACACTTATTAGTATTGTGTCGATACATTTTGTCCAGAATGGATGCCAAAAAGGG
131 AACATGTATCGACACTTATTAATATTGTGTCGATACATTTTGTCCAGAATGGATGCCAAAAAGGG
* *
3805916 GGAAC-CTACAAAGTGTCGATACAGTTTCATAAAGTTTCGAT-CCAAAAGGGTTGCA
196 GGAACGC-ACAAAGTGTCGATACAGTTTCAAAAAGTGTCGATCCCAAAAGGGTTGCA
* * * **
3805971 CCCATAAAGTATCGATACATTTATTAAAAGTGTCGATCCC-AAAAACATCGAAACCCATAATTAT
1 CCCATAAAGTAGCGATACATATATAAAAAGTAACGA-CCCAAAAAACATCGAAACCCATAATTAT
* * *
3806035 AATGTAATCGGTAATTTTGT-AACATAACCGGTATACATATACCGGTTTTATGAGAGAATATGTC
65 AATGTAATCGGTAATTTT-TCAACATAACCAGTATAAATATACCGGTTTTATGA-AAAATATGTC
* * *
3806099 TATAATATGTATCGACACTTATTAATATTGTGTCGATA-ATTTTTGTCCATAATGGATGCCAAAA
128 TACAACATGTATCGACACTTATTAATATTGTGTCGATACA-TTTTGTCCAGAATGGATGCCAAAA
* * *
3806163 AGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAA
192 AGGGGGAACGCACAAAGTGTCGATACAGTTTCAAAAAGTGTCGATCCCAAAA
3806215 ACATCGAAAC
Statistics
Matches: 215, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
250 100 0.47
251 108 0.50
252 7 0.03
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (251 bp):
CCCATAAAGTAGCGATACATATATAAAAAGTAACGACCCAAAAAACATCGAAACCCATAATTATA
ATGTAATCGGTAATTTTTCAACATAACCAGTATAAATATACCGGTTTTATGAAAAATATGTCTAC
AACATGTATCGACACTTATTAATATTGTGTCGATACATTTTGTCCAGAATGGATGCCAAAAAGGG
GGAACGCACAAAGTGTCGATACAGTTTCAAAAAGTGTCGATCCCAAAAGGGTTGCA
Found at i:3809331 original size:200 final size:196
Alignment explanation
Indices: 3808846--3809578 Score: 708
Period size: 200 Copynumber: 3.6 Consensus size: 196
3808836 ACCTAAATAT
* * *
3808846 GTGTCGATACATTT-TATACAAGTATCGA-CCCAAAAAACATCAAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTATA-AAAAGTATCGATCCC-AAAAACATCGAAACCGATAATTATAATGTAA
* * * * * * *
3808909 TAGGTAAATTAACAATGTAAAC-AGTATAAATATACCAGTTAATTAGAAAACATGTCAACATAAT
64 TAGGTAAATTTACAATGTAACCGA-TATAAATATACCATTTTATGAGAAAATAGGTC-ACATAAT
* * *
3808973 GTATCGACACTTGTGTAATTGGTGTCGATACTTATTGTCCA-AGATGAAT-GCACAAATGAGGTG
127 GTATCGACACTTGT-TAATTTGTGTCGATACTT-TTGTCCAGA-ATGAATACCA-AAAAG-GGTG
3809036 C-ACTCATAAA
187 CAAC-CATAAA
* *
3809046 GTGTCGATACATTTATTAAAAGTATTCGATCCCAAAAACATCGAAACCGATAATTATAATGTATT
1 GTGTCGATACATTTATAAAAAGTA-TCGATCCCAAAAACATCGAAACCGATAATTATAATGTAAT
* *
3809111 AGGTAAATTTACAATGTAACCGATATAAATATACCAATTTTATGATAAAATAGGTCAGCATAAAG
65 AGGTAAATTTACAATGTAACCGATATAAATATACC-ATTTTATGAGAAAATAGGTCA-CATAATG
*
3809176 TATCGACACTTGATAAATTTGTGTCGATACTTTTGGTCCAGAATGAATACCAAAAAGGGTGCAAC
128 TATCGACACTTG-TTAATTTGTGTCGATACTTTT-GTCCAGAATGAATACCAAAAAGGGTGCAAC
3809241 CATAAA
191 CATAAA
* * * *
3809247 GTGTCGATACATTTATAAAAAGTATTGATCCCGAAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * ** * * *
3809312 GGTAAATTTTCAATGTAACCGGTATATTTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGT
66 GGTAAATTTACAATGTAACCGATATAAATATACC-ATTTTATGAGAAAATAGGTC-ACATAATGT
* * * *
3809377 ATCGACACGTTGTTAGTTTATGTCGATACTTTTTTCCAGAATGAAATATGAATGCCAAACCA-GG
129 ATCGACAC-TTGTTAATTTGTGTCGATACTTTTGTCCAGAATG--A-AT--A--CCAAA-AAGGG
*
3809441 TGCAAGCATAAA
185 TGCAACCATAAA
* ** ** * * *
3809453 GTGTTGATACATTTA-AAATTGTATCGATCTAAAAAACATCGTAACCGATAATAATAATGTTATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * ** **
3809517 GGTAAATTTACAATATTACTGGTATAAATATACCGGTTTACTTCGAAAATAGGTCAACATAA
66 GGTAAATTTACAATGTAACCGATATAAATATACCATTTTA-TGAGAAAATAGGTC-ACATAA
3809579 GCGCTACCTA
Statistics
Matches: 447, Mismatches: 64, Indels: 39
0.81 0.12 0.07
Matches are distributed among these distances:
199 9 0.02
200 135 0.30
201 107 0.24
202 71 0.16
203 4 0.01
204 6 0.01
205 82 0.18
206 32 0.07
207 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (196 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGATATAAATATACCATTTTATGAGAAAATAGGTCACATAATGTAT
CGACACTTGTTAATTTGTGTCGATACTTTTGTCCAGAATGAATACCAAAAAGGGTGCAACCATAA
A
Found at i:3809678 original size:87 final size:87
Alignment explanation
Indices: 3809575--3809735 Score: 304
Period size: 87 Copynumber: 1.9 Consensus size: 87
3809565 ATAGGTCAAC
*
3809575 ATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCC
1 ATAAGCGCTACATATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCC
3809640 GGTTAAATGCCTATTTTATTAT
66 GGTTAAATGCCTATTTTATTAT
*
3809662 ATAAGCGCTACATATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCC
1 ATAAGCGCTACATATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCC
3809727 GGTTAAATG
66 GGTTAAATG
3809736 ATACAACATT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (87 bp):
ATAAGCGCTACATATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCC
GGTTAAATGCCTATTTTATTAT
Found at i:3809707 original size:23 final size:23
Alignment explanation
Indices: 3809657--3809701 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3809647 TGCCTATTTT
*
3809657 ATTATATAAGCGCTACATATTAC
1 ATTATATAAGCGCTACATAATAC
*
3809680 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACATAATA
3809702 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACATAATAC
Found at i:3810208 original size:72 final size:72
Alignment explanation
Indices: 3810075--3810218 Score: 216
Period size: 72 Copynumber: 2.0 Consensus size: 72
3810065 TTTTTAAGTT
* * * * * * *
3810075 TAATAATTAAAAAATATTTTTAAACATATTTTTTTTTTCAAACACTCGAAAATATGGTAATTCAA
1 TAATAATTAAAAAATATTTTTAAACATAATTTTTTATTAAAAAACTCAAAAACATGATAATTCAA
3810140 TGGGCCC
66 TGGGCCC
*
3810147 TAATAATTAAAAAATATTTTTAAACATAATTTTTTATTAAAAAACTCAAAAACATGATAATTCAG
1 TAATAATTAAAAAATATTTTTAAACATAATTTTTTATTAAAAAACTCAAAAACATGATAATTCAA
3810212 TGGGCCC
66 TGGGCCC
3810219 CATTTTAATG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.37
Consensus pattern (72 bp):
TAATAATTAAAAAATATTTTTAAACATAATTTTTTATTAAAAAACTCAAAAACATGATAATTCAA
TGGGCCC
Found at i:3813806 original size:28 final size:28
Alignment explanation
Indices: 3813764--3813827 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
3813754 CTTTTATTAA
* *
3813764 ATCAAATTGCCTACTTTATACAATTTAT
1 ATCAAATAGCATACTTTATACAATTTAT
3813792 ATCAAATAGCATACTTTATACAATTTAT
1 ATCAAATAGCATACTTTATACAATTTAT
3813820 ATCAAATA
1 ATCAAATA
3813828 ATTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (28 bp):
ATCAAATAGCATACTTTATACAATTTAT
Found at i:3818310 original size:18 final size:18
Alignment explanation
Indices: 3818277--3818328 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
3818267 ACTTAGAATT
* *
3818277 TGTCTCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
3818295 TG-CCCAGAAGGACCACTA
1 TGTCCC-GAAGGACCACTA
3818313 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
3818329 ATATCACATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 2 0.07
18 25 0.83
19 3 0.10
ACGTcount: A:0.29, C:0.33, G:0.21, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3818559 original size:18 final size:18
Alignment explanation
Indices: 3818536--3818605 Score: 104
Period size: 18 Copynumber: 3.9 Consensus size: 18
3818526 ACTTAGAATT
3818536 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
*
3818554 TGTCCCGAATAACCACTA
1 TGTCCCGAATGACCACTA
*
3818572 TGTCTCGAATGACCACTA
1 TGTCCCGAATGACCACTA
* *
3818590 TGTTCCGAAGGACCAC
1 TGTCCCGAATGACCAC
3818606 ATATCACATA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:3820676 original size:49 final size:49
Alignment explanation
Indices: 3820621--3820982 Score: 151
Period size: 49 Copynumber: 7.4 Consensus size: 49
3820611 TGGGGTACTT
* * *
3820621 AAACCCTTTAAAGATTTTTGTTTGAGGG-TAGACTCGATTGGGAGTGCTC
1 AAACCCTTTGAAGATTTTTGTTTGAGGGCTAG-CTCGATTAGGAGCGCTC
* * * * * *
3820670 AAACCCTTTGTATATTTTTATTTGAGGGCTCGCTCGCTTAGGAGCGTTC
1 AAACCCTTTGAAGATTTTTGTTTGAGGGCTAGCTCGATTAGGAGCGCTC
* * * *** *
3820719 AAATCCTTTGGAGATTTTTGTTTG-GGGACGAGCTTTCTT-GAGAGCACTC
1 AAACCCTTTGAAGATTTTTGTTTGAGGG-CTAGCTCGATTAG-GAGCGCTC
* * * ** *
3820768 AAACCCTCTGGAGATTTTCGTTTGAGGGCCGGCTC-ACTTAGGAGTGCTC
1 AAACCCTTTGAAGATTTTTGTTTGAGGGCTAGCTCGA-TTAGGAGCGCTC
* * * * * ** ** * **
3820817 AAATCCTTTGGAGATTTTCGTTTAAAGGCGGGCTCTCTTGGGAGTACTC
1 AAACCCTTTGAAGATTTTTGTTTGAGGGCTAGCTCGATTAGGAGCGCTC
* * * * * * * *
3820866 GAACCATTTGGAGATTTTTATTTGAGGG-TGGGCTAGCTTGGGAGCGCTC
1 AAACCCTTTGAAGATTTTTGTTTGAGGGCT-AGCTCGATTAGGAGCGCTC
* * * * ** * * * *
3820915 GAACCATTT-ATAGATTTTCGTTTAAGGGCGGGCTTGCTTGGGAGCACTC
1 AAACCCTTTGA-AGATTTTTGTTTGAGGGCTAGCTCGATTAGGAGCGCTC
*
3820964 AAACCCTTTGAAGTTTTTT
1 AAACCCTTTGAAGATTTTT
3820983 AGGGCGGACT
Statistics
Matches: 243, Mismatches: 59, Indels: 22
0.75 0.18 0.07
Matches are distributed among these distances:
48 4 0.02
49 232 0.95
50 7 0.03
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (49 bp):
AAACCCTTTGAAGATTTTTGTTTGAGGGCTAGCTCGATTAGGAGCGCTC
Found at i:3820738 original size:98 final size:97
Alignment explanation
Indices: 3820632--3820983 Score: 284
Period size: 98 Copynumber: 3.6 Consensus size: 97
3820622 AACCCTTTAA
** * * *
3820632 AGATTTTTGTTTGAGGGTAGACTCGATTGGGAGTGCTCAAACCCTTTGTATATTTTTATTTGAGG
1 AGATTTTTGTTTGAGGG-AGACTCTCTTGGGAGTACTCAAACCCTTTGGAGATTTTTATTTGAGG
* *
3820697 GCTC-GCTCGCTTAGGAGCGTTCAAATCCTTTGG
65 GC-CGGCTCACTTAGGAGCGCTCAAATCCTTTGG
* * * * **
3820730 AGATTTTTGTTTG-GGGACGAGCTTTCTTGAGAGCACTCAAACCCTCTGGAGATTTTCGTTTGAG
1 AGATTTTTGTTTGAGGGA-GA-CTCTCTTGGGAGTACTCAAACCCTTTGGAGATTTTTATTTGAG
*
3820794 GGCCGGCTCACTTAGGAGTGCTCAAATCCTTTGG
64 GGCCGGCTCACTTAGGAGCGCTCAAATCCTTTGG
* * * * *
3820828 AGATTTTCGTTTAAAGGCG-GGCTCTCTTGGGAGTACTCGAACCATTTGGAGATTTTTATTTGAG
1 AGATTTTTGTTT-GAGG-GAGACTCTCTTGGGAGTACTCAAACCCTTTGGAGATTTTTATTTGAG
** * * **
3820892 GGTGGGCT-AGCTTGGGAGCGCTCGAA-CCATTTAT
64 GGCCGGCTCA-CTTAGGAGCGCTCAAATCC-TTTGG
* * * * * * *
3820926 AGATTTTCGTTTAAGGGCGGGCT-TGCTTGGGAGCACTCAAACCCTTTGAAGTTTTTTA
1 AGATTTTTGTTTGAGGG-AGACTCT-CTTGGGAGTACTCAAACCCTTTGGAGATTTTTA
3820984 GGGCGGACTC
Statistics
Matches: 206, Mismatches: 37, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
96 2 0.01
97 14 0.07
98 186 0.90
99 1 0.00
100 2 0.01
101 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.35
Consensus pattern (97 bp):
AGATTTTTGTTTGAGGGAGACTCTCTTGGGAGTACTCAAACCCTTTGGAGATTTTTATTTGAGGG
CCGGCTCACTTAGGAGCGCTCAAATCCTTTGG
Found at i:3821681 original size:138 final size:137
Alignment explanation
Indices: 3821427--3821826 Score: 440
Period size: 138 Copynumber: 2.9 Consensus size: 137
3821417 GGTGGGCTTG
* * * ** * **
3821427 CTTGAGAACTCTTAAACCCTTTGGATTTTTTTAGGGCATGCTCACTTGGGAGTGCTTAAACCCTT
1 CTTGAGAGCTCTCAAACCCTTTGGGTTTTTTTAGGGCGGGCTCACTTGGGGGAACTTAAACCCTT
* * *** * * *
3821492 TGGAGTTTTTTAGGGCAGACTTTCTTAGGAATGCTCGAACCTTTTGTAGATTTTTGTTTAAGGGC
66 TGGAGTTTTTTAGGGCAGACTCTCTTGGGAGCACTCGAACCCTTTGAAGATTTTTATTTAAGGGC
*
3821557 AGGATCA
131 AAGATCA
* * * * *
3821564 TTTGTGAGCTCTCAAACCCTTTGGGGTTTTTTAGGGTGGGCTCACTTGAGGGGCACTTAAACCCT
1 CTTGAGAGCTCTCAAACCCTTTGGGTTTTTTTAGGGCGGGCTCACTTG-GGGGAACTTAAACCCT
* *
3821629 TTTGAGTTTTTTAGGGCAGACTCTCTTGGGAGCACTCGAACCCTTTGAAGATTTTTATTTGAGGG
65 TTGGAGTTTTTTAGGGCAGACTCTCTTGGGAGCACTCGAACCCTTTGAAGATTTTTATTTAAGGG
*
3821694 CAAGCTCA
130 CAAGATCA
** * ** *
3821702 CTTGAGATTTCTCAATCCCTTTGGAGTTTTTTTAGGGCGGGCTTGCTTGGGGGAACTCAAACCCT
1 CTTGAGAGCTCTCAAACCCTTTGG-GTTTTTTTAGGGCGGGCTCACTTGGGGGAACTTAAACCCT
* ** * * * *
3821767 TTGGAGTTTTTTAAGGTGGACTCGCTTGGGAGCACTCAAACCCTTTGGAGATTTTCATTT
65 TTGGAGTTTTTTAGGGCAGACTCTCTTGGGAGCACTCGAACCCTTTGAAGATTTTTATTT
3821827 TGCTTTGCTT
Statistics
Matches: 218, Mismatches: 43, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
137 39 0.18
138 159 0.73
139 20 0.09
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (137 bp):
CTTGAGAGCTCTCAAACCCTTTGGGTTTTTTTAGGGCGGGCTCACTTGGGGGAACTTAAACCCTT
TGGAGTTTTTTAGGGCAGACTCTCTTGGGAGCACTCGAACCCTTTGAAGATTTTTATTTAAGGGC
AAGATCA
Found at i:3821816 original size:44 final size:44
Alignment explanation
Indices: 3821440--3821821 Score: 221
Period size: 44 Copynumber: 8.4 Consensus size: 44
3821430 GAGAACTCTT
* * ** *
3821440 AAACCCTTTGGATTTTTTTAGGGCATG-CTCACTTGGGAGTGCTT
1 AAACCCTTTGGAGTTTTTTAGGGC-GGACTCACTTGGGAGCACTC
* ** * ***
3821484 AAACCCTTTGGAGTTTTTTAGGGCAGACTTTCTTAGGAATGCTC
1 AAACCCTTTGGAGTTTTTTAGGGCGGACTCACTTGGGAGCACTC
* * * * * *
3821528 GAACCTTTTGTAGATTTTTGTTTAAGGGCAGGA-TCATTTGTGAGCTCTC
1 AAACCCTTTG--GA-GTTT-TTT-AGGGC-GGACTCACTTGGGAGCACTC
* * * * *
3821577 AAACCCTTTGGGGTTTTTTAGGGTGGGCTCACTTGAGGGGCACTT
1 AAACCCTTTGGAGTTTTTTAGGGCGGACTCACTTG-GGAGCACTC
* * *
3821622 AAACCCTTTTGAGTTTTTTAGGGCAGACTCTCTTGGGAGCACTC
1 AAACCCTTTGGAGTTTTTTAGGGCGGACTCACTTGGGAGCACTC
* * * * ***
3821666 GAACCCTTTGAAGATTTTTATTTGAGGGC-AAGCTCACTTGAGATTTCTC
1 AAACCCTTTG--GA-GTTT-TTT-AGGGCGGA-CTCACTTGGGAGCACTC
* * ** * *
3821715 AATCCCTTTGGAGTTTTTTTAGGGCGGGCTTGCTTGGGGGAACTC
1 AAACCCTTTGGAG-TTTTTTAGGGCGGACTCACTTGGGAGCACTC
* * *
3821760 AAACCCTTTGGAGTTTTTTAAGGTGGACTCGCTTGGGAGCACTC
1 AAACCCTTTGGAGTTTTTTAGGGCGGACTCACTTGGGAGCACTC
*
3821804 AAACCCTTTGGAGATTTT
1 AAACCCTTTGGAGTTTTT
3821822 CATTTTGCTT
Statistics
Matches: 254, Mismatches: 67, Indels: 34
0.72 0.19 0.10
Matches are distributed among these distances:
43 3 0.01
44 110 0.43
45 64 0.25
46 10 0.04
47 12 0.05
48 7 0.03
49 46 0.18
50 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (44 bp):
AAACCCTTTGGAGTTTTTTAGGGCGGACTCACTTGGGAGCACTC
Found at i:3824469 original size:20 final size:19
Alignment explanation
Indices: 3824446--3824500 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
3824436 ACAATGAAAC
*
3824446 ATAAAAAAATAGATAAATTT
1 ATAAAAAAATAGATAAA-AT
*
3824466 ATAAAAAAATATATAAAAT
1 ATAAAAAAATAGATAAAAT
3824485 -TAAAAAAATAGA-AAAA
1 ATAAAAAAATAGATAAAA
3824501 GAATTATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.12
18 11 0.34
19 1 0.03
20 16 0.50
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (19 bp):
ATAAAAAAATAGATAAAAT
Found at i:3826152 original size:36 final size:36
Alignment explanation
Indices: 3826105--3826178 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
3826095 ATTTATACCT
*
3826105 TATTTGTATGTTTATGTTTATGAAACTTGTGAAATA
1 TATTTGTATGTTTATGTTTATGAAACTTATGAAATA
3826141 TATTTGTATGTTTATGTTTATGAAACTTATGAAATA
1 TATTTGTATGTTTATGTTTATGAAACTTATGAAATA
3826177 TA
1 TA
3826179 GTCGAGTAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.50
Consensus pattern (36 bp):
TATTTGTATGTTTATGTTTATGAAACTTATGAAATA
Found at i:3831462 original size:22 final size:22
Alignment explanation
Indices: 3831437--3831486 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
3831427 TTTCTTTTGT
3831437 TAATGTAGATGTTTAATGTTTC
1 TAATGTAGATGTTTAATGTTTC
3831459 TAATGTAGATGTTTAATGTTTC
1 TAATGTAGATGTTTAATGTTTC
3831481 TAATGT
1 TAATGT
3831487 TATCATCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.28, C:0.04, G:0.18, T:0.50
Consensus pattern (22 bp):
TAATGTAGATGTTTAATGTTTC
Found at i:3832811 original size:28 final size:26
Alignment explanation
Indices: 3832763--3832817 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
3832753 GGTCGAGCTT
* * *
3832763 AGTCAACTAACTGAGTTAACTCGTTG
1 AGTCAACTAACAGAGTCAACTCATTG
3832789 AGTCAACTCGAACAGAGTCAACTCATTG
1 AGTCAACT--AACAGAGTCAACTCATTG
3832817 A
1 A
3832818 CTTTGAATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 8 0.33
28 16 0.67
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (26 bp):
AGTCAACTAACAGAGTCAACTCATTG
Found at i:3833412 original size:16 final size:16
Alignment explanation
Indices: 3833391--3833424 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3833381 GCCGTTATGA
*
3833391 TTTACTGATTTATTGT
1 TTTACTGATTGATTGT
*
3833407 TTTACTGGTTGATTGT
1 TTTACTGATTGATTGT
3833423 TT
1 TT
3833425 ATGAACTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.06, G:0.18, T:0.62
Consensus pattern (16 bp):
TTTACTGATTGATTGT
Found at i:3835209 original size:6 final size:6
Alignment explanation
Indices: 3835193--3835222 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
3835183 ATAATTTTGA
3835193 TAATAAT TAATAT TAATAT TAATAT TAATA
1 TAAT-AT TAATAT TAATAT TAATAT TAATA
3835223 AATGACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TAATAT
Found at i:3836488 original size:2 final size:2
Alignment explanation
Indices: 3836481--3836528 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
3836471 CATTTTTGCC
3836481 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
3836523 AT AT AT
1 AT AT AT
3836529 TTGAAATAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3842111 original size:15 final size:15
Alignment explanation
Indices: 3842091--3842147 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
3842081 AACCGGGTAT
3842091 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
* **
3842106 CGGGTACCTGCAAAATC
1 CGGGTACCCG-ATTA-C
*
3842123 CGGATACCCGATTAC
1 CGGGTACCCGATTAC
3842138 CGGGTACCCG
1 CGGGTACCCG
3842148 TAACATCCAG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 19 0.59
16 4 0.12
17 9 0.28
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:3847748 original size:14 final size:14
Alignment explanation
Indices: 3847731--3847824 Score: 52
Period size: 14 Copynumber: 6.6 Consensus size: 14
3847721 ATAAATAATA
3847731 AAAAATAAAGACAT
1 AAAAATAAAGACAT
* *
3847745 AAAAGTAAAGGC-T
1 AAAAATAAAGACAT
3847758 AAAAATTAAAGTACCA-
1 AAAAA-TAAAG-A-CAT
* *
3847774 AAAAATAAATA-AC
1 AAAAATAAAGACAT
*
3847787 AAAAATAAA-AGGAT
1 AAAAATAAAGA-CAT
*
3847801 AGAAATATAAATACAT
1 A-AAA-ATAAAGACAT
3847817 AAAAATAA
1 AAAAATAA
3847825 TGTAAATGCA
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
12 2 0.03
13 14 0.22
14 22 0.35
15 10 0.16
16 14 0.22
17 1 0.02
ACGTcount: A:0.68, C:0.06, G:0.09, T:0.17
Consensus pattern (14 bp):
AAAAATAAAGACAT
Found at i:3847798 original size:43 final size:42
Alignment explanation
Indices: 3847718--3847824 Score: 103
Period size: 43 Copynumber: 2.5 Consensus size: 42
3847708 TAAGTGCTAG
* * *
3847718 AATATAAATAATAAAAAATAAAGACATAAAAGTAAAGGCTAAA
1 AATATAAAT-ACAAAAAATAAAAACATAAAAGTAAAGGATAAA
*
3847761 AAT-TAAAGTACCAAAAAATAAATAACA-AAAA-TAAAAGGATAGA
1 AATATAAA-TA-CAAAAAATAAA-AACATAAAAGT-AAAGGATAAA
3847804 AATATAAATACATAAAAATAA
1 AATATAAATACA-AAAAATAA
3847825 TGTAAATGCA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
42 8 0.15
43 39 0.72
44 7 0.13
ACGTcount: A:0.68, C:0.06, G:0.07, T:0.19
Consensus pattern (42 bp):
AATATAAATACAAAAAATAAAAACATAAAAGTAAAGGATAAA
Found at i:3847836 original size:19 final size:19
Alignment explanation
Indices: 3847808--3847845 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3847798 GATAGAAATA
3847808 TAAATACATAAAAATAATG
1 TAAATACATAAAAATAATG
* *
3847827 TAAATGCATAAAATTAATG
1 TAAATACATAAAAATAATG
3847846 CTTAAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.29
Consensus pattern (19 bp):
TAAATACATAAAAATAATG
Found at i:3849261 original size:119 final size:119
Alignment explanation
Indices: 3848945--3849504 Score: 554
Period size: 119 Copynumber: 4.8 Consensus size: 119
3848935 AATCTCTTCT
* * ** *
3848945 TTATGAACTTCTTC-TCACTCTTCAGACGAGTTCTTCTCATTATGAA-CTTTCCATTGGAAAT-G
1 TTATGAACTTCTTCTTC-CTCCTCGGACGAGTTCTTCTCATTATGAACCCCTCCATTGGAAATAA
* * * *
3849007 CTGATCCACTTTATTCTGTGATGGATTT--G--AAAGGAAAC-AACAAAGTTCTTCTCA
65 C-GATCCACCTCATTCTGTGATGGATTTGAGTAAAAGG--TCGAAC-AAGTTATTCTCA
* * * * * ** * * *
3849061 TTATGAAC-T-TT-TT-CT--TAGGATGAGCTCTTCTCATTATGAACTCTTTTATTGAAAATGAT
1 TTATGAACTTCTTCTTCCTCCTCGGACGAGTTCTTCTCATTATGAACCCCTCCATTGGAAATAAC
* * *
3849120 GACCCACCTCCTTCTATGATGGATTTGAGTAAAAGGTCGAACAAGTTATTCTCA
66 GATCCACCTCATTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTATTCTCA
*
3849174 TTATGAACTTCTTCTTCCTCCTCGGATGAGTTCTTCTCATTATGAACCCCTCCATTGGAAATAAC
1 TTATGAACTTCTTCTTCCTCCTCGGACGAGTTCTTCTCATTATGAACCCCTCCATTGGAAATAAC
* * *
3849239 GATCCACCTCCTTCTGTAATGGATTTGAGTAAAAGGTCAAACAAGTTATTCTCA
66 GATCCACCTCATTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTATTCTCA
* * * * * * * *
3849293 TTGTGAACTTCTTATTCCTCATCGGACAATTTTTTCTCATTGTGAACCCCTCCATTGGAAATGAC
1 TTATGAACTTCTTCTTCCTCCTCGGACGAGTTCTTCTCATTATGAACCCCTCCATTGGAAATAAC
* * * * * *
3849358 AACCCACTTCATTCTGTGATAGATTTAAGTAAAAGGTCGAACAAATTATTCTCA
66 GATCCACCTCATTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTATTCTCA
* * * * **
3849412 TTATGAACTTCTTCTTCCTCCTCGGACAAGTTCTTCTTATTATGAATCCCTCTATTGGAAATATT
1 TTATGAACTTCTTCTTCCTCCTCGGACGAGTTCTTCTCATTATGAACCCCTCCATTGGAAATAAC
*
3849477 GATCCACCTCTTTCTGTGATGGATTTGA
66 GATCCACCTCATTCTGTGATGGATTTGA
3849505 ATCTGTAAAA
Statistics
Matches: 363, Mismatches: 67, Indels: 25
0.80 0.15 0.05
Matches are distributed among these distances:
110 21 0.06
111 31 0.09
112 2 0.01
113 21 0.06
114 7 0.02
115 8 0.02
116 10 0.03
117 2 0.01
119 261 0.72
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.37
Consensus pattern (119 bp):
TTATGAACTTCTTCTTCCTCCTCGGACGAGTTCTTCTCATTATGAACCCCTCCATTGGAAATAAC
GATCCACCTCATTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTATTCTCA
Found at i:3849309 original size:20 final size:19
Alignment explanation
Indices: 3849284--3849339 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
3849274 GTCAAACAAG
3849284 TTATTCTCATTGTGAACTT
1 TTATTCTCATTGTGAACTT
* *
3849303 CTTATTCCTCATCG-GACAATT
1 -TTATT-CTCATTGTGA-ACTT
3849324 TT-TTCTCATTGTGAAC
1 TTATTCTCATTGTGAAC
3849340 CCCTCCATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
18 7 0.24
19 4 0.14
20 9 0.31
21 9 0.31
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.46
Consensus pattern (19 bp):
TTATTCTCATTGTGAACTT
Found at i:3850098 original size:102 final size:102
Alignment explanation
Indices: 3849760--3850260 Score: 558
Period size: 99 Copynumber: 5.0 Consensus size: 102
3849750 GAGATAGATT
* * * * * * *
3849760 TTTGTTTCAAGTGAAATAATTTCAAAATATGTGTTCCAAGGGGAATTATCT----CAAG-TAAAA
1 TTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAATTGTCTCAAGCAAGATGAAA
* * * *
3849820 TTGATTTTAAGAAAAACTATCTCAAATG--ATAAATT
66 TTGATTTTAAGAAAAACAATCTCAAGTGAAATTAATA
* * ** *
3849855 TTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAACTGCCTCAAAAAAGAGGAAA
1 TTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAATTGTCTCAAGCAAGATGAAA
* *
3849920 TTGATTTTAA-AAGAAACTATCTCAAGTGAGA-TAA-A
66 TTGATTTTAAGAA-AAACAATCTCAAGTGAAATTAATA
* * *
3849955 TTT-TTTCGAATGAAACAATCTCAAAATTTGTGTTTCGAGGGAAATTGTCTCAAGCAAGATGAAA
1 TTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAATTGTCTCAAGCAAGATGAAA
*
3850019 TTTATTTTAAGAAAAACAATCTCAAGTGAAATTAATA
66 TTGATTTTAAGAAAAACAATCTCAAGTGAAATTAATA
*
3850056 TTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAATTGTCTCAAGCGAGATGAAA
1 TTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAATTGTCTCAAGCAAGATGAAA
* * * *
3850121 TTGGTTTTAAGAAGAAAAAAACAATCTTAAGTGAGATCAAT-
66 TTGATTTT---AAG--AAAAACAATCTCAAGTGAAATTAATA
* * * * * *
3850162 CTTGTTTCGAGTGAAATAATTTTAAAATTTGTGTTTCAAGGCAAATTGTCTCAAGCGAGACGAAA
1 TTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAATTGTCTCAAGCAAGATGAAA
3850227 TTGATTTTAAGAAAAACAATCTCAAGTGAGAATT
66 TTGATTTTAAGAAAAACAATCTCAAGTGA-AATT
3850261 TTTTTCATAT
Statistics
Matches: 345, Mismatches: 43, Indels: 29
0.83 0.10 0.07
Matches are distributed among these distances:
95 43 0.12
99 83 0.24
100 35 0.10
101 23 0.07
102 66 0.19
103 3 0.01
105 3 0.01
106 67 0.19
107 22 0.06
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (102 bp):
TTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAATTGTCTCAAGCAAGATGAAA
TTGATTTTAAGAAAAACAATCTCAAGTGAAATTAATA
Found at i:3850253 original size:208 final size:201
Alignment explanation
Indices: 3849760--3850260 Score: 620
Period size: 208 Copynumber: 2.5 Consensus size: 201
3849750 GAGATAGATT
* * * * * *
3849760 TTTGTTTCAAGTGAAATAATTTCAAAATATGTGTTCCAAGGGGAATTATCTCAA--G-TA-AAAT
1 TTTGTTTCGAGTGAAATAATTTCAAAATTTGTGTTTCAAGGGAAATTGTCTCAAGCGAGAGAAAT
* * * *
3849821 TGATTTTAAGAAAAACTATCTCAAATG--ATAAATTTTTGTTTCGAGTGAAACAATTTCAAAATT
66 TGATTTTAAGAAAAACAATCTCAAGTGAAATTAATATTTGTTTCGAGTGAAACAATTTCAAAATT
*
3849884 TGTGTTTCAAGGGAAACTGCCTCAAAAAAGAGGAAATTGATTTTAAAAGAAACTATCTCAAGTGA
131 TGTGTTTCAAGGGAAACTGCCTCAAAAAAGAGGAAATTGATTTTAAAAGAAACAATCTCAAGTGA
3849949 GATAAA
196 GATAAA
* * * * *
3849955 TTT-TTTCGAATGAAACAATCTCAAAATTTGTGTTTCGAGGGAAATTGTCTCAAGCAAGATGAAA
1 TTTGTTTCGAGTGAAATAATTTCAAAATTTGTGTTTCAAGGGAAATTGTCTCAAGCGAGA-GAAA
*
3850019 TTTATTTTAAGAAAAACAATCTCAAGTGAAATTAATATTTGTTTCGAGTGAAACAATTTCAAAAT
65 TTGATTTTAAGAAAAACAATCTCAAGTGAAATTAATATTTGTTTCGAGTGAAACAATTTCAAAAT
* * *** * * *
3850084 TTGTGTTTCAAGGGAAATTGTCTCAAGCGAGATGAAATTGGTTTTAAGAAGAAAAAAACAATCTT
130 TTGTGTTTCAAGGGAAACTGCCTCAAAAAAGAGGAAATTGATTTTAA-AAG----AAACAATCTC
*
3850149 AAGTGAGATCAA
190 AAGTGAGATAAA
* *
3850161 TCTTGTTTCGAGTGAAATAATTTTAAAATTTGTGTTTCAAGGCAAATTGTCTCAAGCGAGACGAA
1 T-TTGTTTCGAGTGAAATAATTTCAAAATTTGTGTTTCAAGGGAAATTGTCTCAAGCGAGA-GAA
3850226 ATTGATTTTAAGAAAAACAATCTCAAGTGAGAATT
64 ATTGATTTTAAGAAAAACAATCTCAAGTGA-AATT
3850261 TTTTTCATAT
Statistics
Matches: 256, Mismatches: 35, Indels: 16
0.83 0.11 0.05
Matches are distributed among these distances:
194 41 0.16
195 3 0.01
197 1 0.00
199 28 0.11
201 73 0.29
202 3 0.01
206 20 0.08
207 2 0.01
208 81 0.32
209 4 0.02
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (201 bp):
TTTGTTTCGAGTGAAATAATTTCAAAATTTGTGTTTCAAGGGAAATTGTCTCAAGCGAGAGAAAT
TGATTTTAAGAAAAACAATCTCAAGTGAAATTAATATTTGTTTCGAGTGAAACAATTTCAAAATT
TGTGTTTCAAGGGAAACTGCCTCAAAAAAGAGGAAATTGATTTTAAAAGAAACAATCTCAAGTGA
GATAAA
Found at i:3853341 original size:20 final size:20
Alignment explanation
Indices: 3853316--3853371 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
3853306 GTGAAAGTTG
3853316 TCCCGAAGGACCTATGTATA
1 TCCCGAAGGACCTATGTATA
* * *
3853336 TCCCGAAGGATCTCTGTATG
1 TCCCGAAGGACCTATGTATA
* *
3853356 TCTCGAAAGACCTATG
1 TCCCGAAGGACCTATG
3853372 AACCCTCGAC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (20 bp):
TCCCGAAGGACCTATGTATA
Found at i:3863724 original size:20 final size:20
Alignment explanation
Indices: 3863699--3863797 Score: 76
Period size: 20 Copynumber: 4.7 Consensus size: 20
3863689 AATAAAGGTA
3863699 TGTATCGATGCACTCTATAG
1 TGTATCGATGCACTCTATAG
* *
3863719 TGTATCGATGCATCCCTTAACGAG
1 TGTATCGATGCA-CTC-T-A-TAG
* *
3863743 TGAATCGATGGACTATCTATAG
1 TGTATCGATGCAC--TCTATAG
3863765 TGTATCGATGCACTCCT-TA-
1 TGTATCGATGCACT-CTATAG
*
3863784 TGTATAGATGCACT
1 TGTATCGATGCACT
3863798 AATATCATTC
Statistics
Matches: 63, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
19 13 0.21
20 15 0.24
21 4 0.06
22 14 0.22
23 3 0.05
24 13 0.21
25 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (20 bp):
TGTATCGATGCACTCTATAG
Found at i:3865511 original size:2 final size:2
Alignment explanation
Indices: 3865504--3865539 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3865494 CTGATCACGA
3865504 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
3865540 TCCCCAAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3875592 original size:2 final size:2
Alignment explanation
Indices: 3875585--3875616 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3875575 CATGTTTAAC
*
3875585 CA CA CA CA CA CA CA CG CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3875617 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.50, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3876052 original size:24 final size:24
Alignment explanation
Indices: 3876000--3876044 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3875990 GAATTTCCAC
3876000 ATAG-ATTTGTCCCGAAGGACCAT
1 ATAGAATTTGTCCCGAAGGACCAT
3876023 ATAGAATTTGTCCCGAAGGACC
1 ATAGAATTTGTCCCGAAGGACC
3876045 TTGTAGAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (24 bp):
ATAGAATTTGTCCCGAAGGACCAT
Found at i:3881683 original size:29 final size:27
Alignment explanation
Indices: 3881621--3881698 Score: 79
Period size: 29 Copynumber: 2.8 Consensus size: 27
3881611 TTAAAGTACC
3881621 AAAAA-ATAAATAACA-AAAATAAAAGG
1 AAAAATATAAAT-ACATAAAATAAAAGG
3881647 ATAGAAATATAAATACATAAAAGTAAAGAGG
1 A-A-AAATATAAATACATAAAA-TAAA-AGG
* *
3881678 AAAAATGTAAATGCATAAAAT
1 AAAAATATAAATACATAAAAT
3881699 TAATGCTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 7 0.16
29 26 0.59
30 5 0.11
31 4 0.09
ACGTcount: A:0.67, C:0.04, G:0.12, T:0.18
Consensus pattern (27 bp):
AAAAATATAAATACATAAAATAAAAGG
Found at i:3886150 original size:39 final size:39
Alignment explanation
Indices: 3885956--3886151 Score: 214
Period size: 39 Copynumber: 5.0 Consensus size: 39
3885946 CCTGTACACC
* * * * *
3885956 CAGTAAGGGCTTACCCTGTGCACAAAGCAGAGAAGCCTA
1 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
* * * * * *
3885995 CAGTAAGGTCTTATCATGTGCACAAAGCAGAGGAGCTTG
1 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
* * *
3886034 CAGTAAGGACTTACCCAGAGCACAAAGCCAAGGAGCATG
1 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
** * *
3886073 TGGTAAGAACTTACCCTGAGCACAAA-CTCGATGAGCCTG
1 CAGTAAGGACTTACCCTGAGCACAAAGC-CGAGGAGCCTG
3886112 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
1 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
3886151 C
1 C
3886152 CGAAAACGGT
Statistics
Matches: 130, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
38 1 0.01
39 128 0.98
40 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.26, T:0.16
Consensus pattern (39 bp):
CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
Found at i:3886904 original size:25 final size:25
Alignment explanation
Indices: 3886867--3886920 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
3886857 TTTGTCAAAG
* *
3886867 TCAACGGTTGGTCAATGGTTAACGA
1 TCAACGGTCGGTCAATAGTTAACGA
3886892 TCAACGGTCGGTCAATAGTTAACGA
1 TCAACGGTCGGTCAATAGTTAACGA
3886917 TCAA
1 TCAA
3886921 TTGTTGAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (25 bp):
TCAACGGTCGGTCAATAGTTAACGA
Found at i:3887334 original size:17 final size:18
Alignment explanation
Indices: 3887309--3887342 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3887299 GATTTGTTTC
3887309 TAAAAAGAG-GAAAATAT
1 TAAAAAGAGAGAAAATAT
*
3887326 TAAAGAGAGAGAAAATA
1 TAAAAAGAGAGAAAATA
3887343 AATAATTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (18 bp):
TAAAAAGAGAGAAAATAT
Found at i:3887841 original size:18 final size:18
Alignment explanation
Indices: 3887818--3887855 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3887808 CATGGTGGTG
*
3887818 GCGTGGAGTTTTGGTGTA
1 GCGTGGAGTGTTGGTGTA
3887836 GCGTGGAGTGTTGGTGTA
1 GCGTGGAGTGTTGGTGTA
3887854 GC
1 GC
3887856 AGGGCATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.08, G:0.47, T:0.34
Consensus pattern (18 bp):
GCGTGGAGTGTTGGTGTA
Found at i:3891058 original size:46 final size:46
Alignment explanation
Indices: 3890991--3891083 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
3890981 TTTCAATGCC
*
3890991 CCTTGTTCCCTTAGGAATCCATACTTGTTTAATTTTAAAATGTTTT
1 CCTTGTTCCCTTAGGAATCCATACTTGTTTAATTTTAAAACGTTTT
3891037 CCTTGTTCCCTTAGGAATCCATACTTGTTTAATTTTAAAACGTTTT
1 CCTTGTTCCCTTAGGAATCCATACTTGTTTAATTTTAAAACGTTTT
3891083 C
1 C
3891084 TTTTCTTTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (46 bp):
CCTTGTTCCCTTAGGAATCCATACTTGTTTAATTTTAAAACGTTTT
Found at i:3891315 original size:19 final size:20
Alignment explanation
Indices: 3891271--3891318 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3891261 TCTAAATCAT
*
3891271 TTTTCAAAATTTCATTTTGC
1 TTTTCAAAATTCCATTTTGC
3891291 TTTTCAAAA-TCCAATTTTG-
1 TTTTCAAAATTCC-ATTTTGC
3891310 TTTTCAAAA
1 TTTTCAAAA
3891319 GAAATTCGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGC
Found at i:3893908 original size:21 final size:22
Alignment explanation
Indices: 3893882--3893924 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
3893872 GGGAGCATAT
* *
3893882 GGGTATTGATACT-CCTTTATA
1 GGGTATCGATACTACCTGTATA
3893903 GGGTATCGATACTACCTGTATA
1 GGGTATCGATACTACCTGTATA
3893925 AAACTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (22 bp):
GGGTATCGATACTACCTGTATA
Found at i:3896790 original size:20 final size:20
Alignment explanation
Indices: 3896765--3896819 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
3896755 AACCAGACAG
* *
3896765 GGGGTATCGGTACCCTTCGA
1 GGGGTATCGGTACCATTCAA
*
3896785 GGGGTATCGATACACATTCAA
1 GGGGTATCGGTAC-CATTCAA
*
3896806 GGTGTATCGGTACC
1 GGGGTATCGGTACC
3896820 GTTAAGAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (20 bp):
GGGGTATCGGTACCATTCAA
Done.