Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_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: 9057482
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 37
Found at i:3660313 original size:31 final size:31
Alignment explanation
Indices: 3660239--3660305 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
3660229 ATACTATAAT
*
3660239 ATATATATATATATATATAATACACTTAAATA
1 ATATA-ATATATATATATAATACACTTAAAAA
**
3660271 ATATAATATATATATAT-ATATGCTTACAAAA
1 ATATAATATATATATATAATACACTTA-AAAA
3660302 ATAT
1 ATAT
3660306 GTTATATACC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.23
31 19 0.61
32 5 0.16
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.40
Consensus pattern (31 bp):
ATATAATATATATATATAATACACTTAAAAA
Found at i:3662264 original size:111 final size:111
Alignment explanation
Indices: 3661915--3662340 Score: 633
Period size: 111 Copynumber: 3.8 Consensus size: 111
3661905 TAAATGATCA
* * * * *
3661915 GTTCCACTGTCACTCAAGGG-ATATCAAATCTGGGGATGAGAGGGATCTATTCCGCTTCTTCTAA
1 GTTCCGCTGTCACTC-AGGGAATATCAAATCTTGGAAT-AGAGTGATCTATTCCACTTCTTCT-A
* *
3661979 AGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATTGGGGTAGACTT
63 AGGGAATATCAGATCTGGAGGAGTTGATCCATTGAATCGGGGTAGACTT
* *
3662028 GTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAATAGGGTGATCTGTTCCACTTCTTCTAA-G
1 GTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAATAGAGTGATCTATTCCACTTCTTCTAAGG
3662092 GAATATCAGATCTGGAGGAGTTGATCCATTGAATCGGGGTAGACTT
66 GAATATCAGATCTGGAGGAGTTGATCCATTGAATCGGGGTAGACTT
* * *
3662138 GCTCCGCTGTCACTCAGAGAATATCAAATCTTGGAATATAGTGATCTATTCCACTTCTTCTAAGG
1 GTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAATAGAGTGATCTATTCCACTTCTTCTAAGG
* *
3662203 GAATATCAGATCTGGAGGAGTTAATCCATTGAATCAGGGTAGACTT
66 GAATATCAGATCTGGAGGAGTTGATCCATTGAATCGGGGTAGACTT
* * * *
3662249 GTTCTGATGTTACTCAGGGAATATCAAATCTTGGAATATG-GTGATCTGTTCCACTTCTTCTAAG
1 GTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAATA-GAGTGATCTATTCCACTTCTTCTAAG
3662313 GGAATATCAGATCTGGAGGAGTTGATCC
65 GGAATATCAGATCTGGAGGAGTTGATCC
3662341 GTTCCGCTGT
Statistics
Matches: 286, Mismatches: 24, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
110 103 0.36
111 130 0.45
112 24 0.08
113 29 0.10
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.31
Consensus pattern (111 bp):
GTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAATAGAGTGATCTATTCCACTTCTTCTAAGG
GAATATCAGATCTGGAGGAGTTGATCCATTGAATCGGGGTAGACTT
Found at i:3675433 original size:2 final size:2
Alignment explanation
Indices: 3675426--3675452 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3675416 ATGCATAAAT
3675426 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 T
3675453 TTATGTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3675599 original size:2 final size:2
Alignment explanation
Indices: 3675571--3675641 Score: 53
Period size: 2 Copynumber: 37.5 Consensus size: 2
3675561 TTCTACATAC
* * * *
3675571 TA TA -A TA TA TT TA TA TT TA TA TT TA TA TA TA TA TA -A TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3675611 CT- TA AA TA -A TA TA -A TA TA TA TA TA TA TA TA T
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3675642 GCTTACAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
1 5 0.09
2 48 0.91
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3675655 original size:33 final size:31
Alignment explanation
Indices: 3675594--3675655 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
3675584 TATTTATATT
*
3675594 TATATATATATAATACACTTAAATAATATAA
1 TATATATATATAATACACTTAAAAAATATAA
**
3675625 TATATATATATATATATGCTTACAAAAATAT
1 TATATATATATA-ATACACTTA-AAAAATAT
3675656 GTTATATACC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 12 0.46
32 7 0.27
33 7 0.27
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (31 bp):
TATATATATATAATACACTTAAAAAATATAA
Found at i:3675662 original size:33 final size:30
Alignment explanation
Indices: 3675589--3675663 Score: 78
Period size: 33 Copynumber: 2.4 Consensus size: 30
3675579 ATTTATATTT
*
3675589 ATATTTATATATATATAATACACTTAAATA
1 ATATTTATATATATATAATACACTTAAAAA
* **
3675619 ATATAATATATATATATATATATGCTTACAAAA
1 ATAT-TTATATATATATA-ATACACTTA-AAAA
3675652 ATATGTTATATA
1 ATAT-TTATATA
3675664 CCGTATATGT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 4 0.11
31 12 0.33
32 7 0.19
33 13 0.36
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (30 bp):
ATATTTATATATATATAATACACTTAAAAA
Found at i:3681258 original size:254 final size:255
Alignment explanation
Indices: 3680798--3681285 Score: 951
Period size: 254 Copynumber: 1.9 Consensus size: 255
3680788 GCAATTTTGT
3680798 CCATTGTTTATGTTGGATCAATTTTCGAACATTGATAGTTTATTTACTAACGATTTGAGGAATTC
1 CCATTGTTTATGTTGGATCAATTTTCGAACATTGATAGTTTATTTACTAACGATTTGAGGAATTC
3680863 TTTTAACCCAAAATGAAACAATGATGTTAATATGTATTTTTACCCAAAATAATAGGAGTTAAACT
66 TTTTAACCCAAAATGAAACAATGATGTTAATATGTATTTTTACCCAAAATAATAGGAGTTAAACT
*
3680928 AATTATTTTACGAAACGTTAAATGTATTTTTGACGTTATACTAATAGCATGGTATTAGTATGAGG
131 AATTATTTTACGAAACGTTAAATGTATTTTTGACATTATACTAATAGCATGGTATTAGTATGAGG
3680993 TGATCACATCATATTTCTTTAAGATATTTCTTAGTCATTGATTACTCATACATCCTGCGG
196 TGATCACATCATATTTCTTTAAGATATTTCTTAGTCATTGATTACTCATACATCCTGCGG
3681053 CCATTGTTTATGTTGGATCAATTTTCGAACATTGATAGTTTATTTACTAACGATTTGAGGAATTC
1 CCATTGTTTATGTTGGATCAATTTTCGAACATTGATAGTTTATTTACTAACGATTTGAGGAATTC
*
3681118 TTTTAACCCAAAATGAAACATTGATGTTAATATGTA-TTTTACCCAAAATAATAGGAGTTAAACT
66 TTTTAACCCAAAATGAAACAATGATGTTAATATGTATTTTTACCCAAAATAATAGGAGTTAAACT
3681182 AATTATTTTACGAAACGTTAAATGTATTTTTGACATTATACTAATAGCATGGTATTAGTATGAGG
131 AATTATTTTACGAAACGTTAAATGTATTTTTGACATTATACTAATAGCATGGTATTAGTATGAGG
3681247 TGATCACATCATATTTCTTTAAGATATTTCTTAGTCATT
196 TGATCACATCATATTTCTTTAAGATATTTCTTAGTCATT
3681286 AATAACTTAC
Statistics
Matches: 231, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
254 131 0.57
255 100 0.43
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (255 bp):
CCATTGTTTATGTTGGATCAATTTTCGAACATTGATAGTTTATTTACTAACGATTTGAGGAATTC
TTTTAACCCAAAATGAAACAATGATGTTAATATGTATTTTTACCCAAAATAATAGGAGTTAAACT
AATTATTTTACGAAACGTTAAATGTATTTTTGACATTATACTAATAGCATGGTATTAGTATGAGG
TGATCACATCATATTTCTTTAAGATATTTCTTAGTCATTGATTACTCATACATCCTGCGG
Found at i:3681881 original size:23 final size:23
Alignment explanation
Indices: 3681855--3681914 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
3681845 ATAAAGCACA
* *
3681855 ATAATATATTAGGTATCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
3681878 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
3681901 ATAATAAAATAGGT
1 ATAATATAATAGGT
3681915 TAATTACTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:3681983 original size:87 final size:87
Alignment explanation
Indices: 3681837--3682001 Score: 260
Period size: 87 Copynumber: 1.9 Consensus size: 87
3681827 TATTTAACCG
* *
3681837 GAAACATTATAAAGCACAATAATATATTAGGTATCGCTTATATAATGTAATAGGTAGCGCTTATA
1 GAAACATTATAAAGCACAATAACATATTAGGTATCGCTTATATAACGTAATAGGTAGCGCTTATA
3681902 TAATAAAATAGGTTAATTACTA
66 TAATAAAATAGGTTAATTACTA
* *
3681924 GAAACATTATCAATCACAATAACATATTAGGTA-CTGCTTATATAACGTAATAGGTAGCGCTTAT
1 GAAACATTATAAAGCACAATAACATATTAGGTATC-GCTTATATAACGTAATAGGTAGCGCTTAT
**
3681988 ATAATGTAATAGGT
65 ATAATAAAATAGGT
3682002 AGCGCTTATA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
86 1 0.01
87 70 0.99
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.33
Consensus pattern (87 bp):
GAAACATTATAAAGCACAATAACATATTAGGTATCGCTTATATAACGTAATAGGTAGCGCTTATA
TAATAAAATAGGTTAATTACTA
Found at i:3681992 original size:110 final size:110
Alignment explanation
Indices: 3681864--3682066 Score: 379
Period size: 110 Copynumber: 1.8 Consensus size: 110
3681854 AATAATATAT
*
3681864 TAGGTATCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAAC
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAAC
*
3681929 ATTATCAATCACAATAACATATTAGGTACTGCTTATATAACGTAA
66 ATTATCAAGCACAATAACATATTAGGTACTGCTTATATAACGTAA
*
3681974 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAAC
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAAC
3682039 ATTATCAAGCACAATAACATATTAGGTA
66 ATTATCAAGCACAATAACATATTAGGTA
3682067 GCGTTTGTAA
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 90 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (110 bp):
TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAAC
ATTATCAAGCACAATAACATATTAGGTACTGCTTATATAACGTAA
Found at i:3682013 original size:25 final size:23
Alignment explanation
Indices: 3681942--3682014 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
3681932 ATCAATCACA
* *
3681942 ATAACATATTAGGTA-CTGCTTAT
1 ATAACGTAATAGGTAGC-GCTTAT
3681965 ATAACGTAATAGGTAGCGCTTAT
1 ATAACGTAATAGGTAGCGCTTAT
*
3681988 ATAATGTAATAGGTAGCGCTTAT
1 ATAACGTAATAGGTAGCGCTTAT
3682011 ATAA
1 ATAA
3682015 TAAAATAGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 45 0.98
24 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (23 bp):
ATAACGTAATAGGTAGCGCTTAT
Found at i:3682015 original size:23 final size:23
Alignment explanation
Indices: 3681951--3682024 Score: 105
Period size: 23 Copynumber: 3.2 Consensus size: 23
3681941 AATAACATAT
*
3681951 TAGGTA-CTGCTTATATAACGTAA
1 TAGGTAGC-GCTTATATAATGTAA
3681974 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
**
3681997 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATGTAA
3682020 TAGGT
1 TAGGT
3682025 TAATTACTGG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 46 0.98
24 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATGTAA
Found at i:3682098 original size:21 final size:21
Alignment explanation
Indices: 3682074--3682129 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
3682064 GTAGCGTTTG
* *
3682074 TAAAATATCGTTACATTTTTA
1 TAAAGTATCGATACATTTTTA
3682095 TAAAGTATCGATACATTTTTA
1 TAAAGTATCGATACATTTTTA
3682116 TAAAGTATCGATAC
1 TAAAGTATCGATAC
3682130 TTTATAGGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (21 bp):
TAAAGTATCGATACATTTTTA
Found at i:3682575 original size:20 final size:21
Alignment explanation
Indices: 3682551--3682597 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
3682541 AAATTACATA
3682551 ACTTTAAAAAAAAT-ATAGAT
1 ACTTTAAAAAAAATGATAGAT
* * *
3682571 CCTTTTATAAAAATGATAGAT
1 ACTTTAAAAAAAATGATAGAT
3682592 ACTTTA
1 ACTTTA
3682598 CAATATAACA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.36
Consensus pattern (21 bp):
ACTTTAAAAAAAATGATAGAT
Found at i:3682764 original size:111 final size:112
Alignment explanation
Indices: 3682564--3682820 Score: 417
Period size: 111 Copynumber: 2.3 Consensus size: 112
3682554 TTAAAAAAAA
*
3682564 TATAGATCCTTTTATAAAAATGATAGATACTTTACAATATAACAGGCAAAAAATATGACAAAACC
1 TATAGATCCTTTTATAAAAATGATAGATACTTTACAATATAACAGGCAAAAAATATGACAAAACA
3682629 AGTTTCATTATGACAAAACCGATAAAATTTACCTAATATGTTGAAAG
66 AGTTTCATTATGACAAAACCGATAAAATTTACCTAATATGTTGAAAG
* * * * *
3682676 TATAAATCCTTTTATAAAAAGGATAGATACTTTACAATATAACATG-TAAAAATATGACAAAATA
1 TATAGATCCTTTTATAAAAATGATAGATACTTTACAATATAACAGGCAAAAAATATGACAAAACA
*
3682740 AGTTTCATTATGACAAAATCGATAAAATTTACCTAATATGTTGAAAG
66 AGTTTCATTATGACAAAACCGATAAAATTTACCTAATATGTTGAAAG
* *
3682787 TATAGATACTTTTTATAAAAATGATCGATACTTT
1 TATAGAT-CCTTTTATAAAAATGATAGATACTTT
3682821 TTTGAAAGTT
Statistics
Matches: 133, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
111 67 0.50
112 66 0.50
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (112 bp):
TATAGATCCTTTTATAAAAATGATAGATACTTTACAATATAACAGGCAAAAAATATGACAAAACA
AGTTTCATTATGACAAAACCGATAAAATTTACCTAATATGTTGAAAG
Found at i:3683447 original size:111 final size:112
Alignment explanation
Indices: 3683266--3683513 Score: 383
Period size: 111 Copynumber: 2.2 Consensus size: 112
3683256 GTATTGATAC
* *
3683266 TTTATAAAAATGTATCGATATTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTA
1 TTTATAAAAAAG-ATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTA
3683331 TGACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTATA-A-ATCAT
65 TGACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTATAGATAT-AT
* * *
3683378 TTTATAAAAAAGATAGATACTTTACAATATAATAGGTAAAATTATGACAAAACCAGTTTCATTAT
1 TTTATAAAAAAGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTAT
* * *
3683443 GACAAAACCGGTAAATTTTACCTGATATGTTGAAAGTATAGATATTT
66 GACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTATAGATATAT
3683490 TTTATAAAAAAAGATCGATACTTT
1 TTTAT-AAAAAAGATCGATACTTT
3683514 TTTAAAGTTA
Statistics
Matches: 124, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
111 87 0.70
112 18 0.15
113 19 0.15
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.33
Consensus pattern (112 bp):
TTTATAAAAAAGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTAT
GACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTATAGATATAT
Found at i:3684196 original size:22 final size:22
Alignment explanation
Indices: 3684171--3684244 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 22
3684161 AATAAAGCGT
3684171 AATAAAGAAAATATGTAAATAA
1 AATAAAGAAAATATGTAAATAA
*
3684193 AATAAATAAAATA--TAAA-AA
1 AATAAAGAAAATATGTAAATAA
*
3684212 AA-CAAGAAAA-ATG-AAAT-A
1 AATAAAGAAAATATGTAAATAA
* *
3684230 AATAAATAAAGTATG
1 AATAAAGAAAATATG
3684245 AGAAACTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
17 1 0.02
18 12 0.29
19 9 0.22
20 7 0.17
22 12 0.29
ACGTcount: A:0.70, C:0.01, G:0.08, T:0.20
Consensus pattern (22 bp):
AATAAAGAAAATATGTAAATAA
Found at i:3684327 original size:32 final size:33
Alignment explanation
Indices: 3684257--3684331 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 33
3684247 AAACTAATAG
* * *
3684257 TAAATAAT-ATATATATATATGAAATGATGATA
1 TAAAAAATGATATATATAAATGAAATGATGACA
3684289 TAAAAAAGTGATATATATAAAT-AAAT-ATGTACA
1 TAAAAAA-TGATATATATAAATGAAATGATG-ACA
3684322 T-AAAAATGAT
1 TAAAAAATGAT
3684332 GAAGCATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
31 4 0.11
32 14 0.38
33 8 0.22
34 11 0.30
ACGTcount: A:0.56, C:0.01, G:0.09, T:0.33
Consensus pattern (33 bp):
TAAAAAATGATATATATAAATGAAATGATGACA
Found at i:3694388 original size:20 final size:20
Alignment explanation
Indices: 3694360--3694398 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3694350 CCGCCTCGTC
* *
3694360 GCCGTCGTTGAACGGCGACG
1 GCCGCCGTTCAACGGCGACG
*
3694380 GCCGCCGTTCATCGGCGAC
1 GCCGCCGTTCAACGGCGAC
3694399 AAAATCACGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.36, G:0.36, T:0.15
Consensus pattern (20 bp):
GCCGCCGTTCAACGGCGACG
Found at i:3703421 original size:3 final size:3
Alignment explanation
Indices: 3703413--3703447 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
3703403 CATCTTCATG
* *
3703413 CTT CTT CTT CTC CTT CTC CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
3703448 CGCCATCGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (3 bp):
CTT
Found at i:3703436 original size:18 final size:18
Alignment explanation
Indices: 3703413--3703448 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3703403 CATCTTCATG
3703413 CTTCTTCTTCTCCTTCTC
1 CTTCTTCTTCTCCTTCTC
*
3703431 CTTCTTCTTCTTCTTCTC
1 CTTCTTCTTCTCCTTCTC
3703449 GCCATCGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (18 bp):
CTTCTTCTTCTCCTTCTC
Found at i:3703572 original size:12 final size:12
Alignment explanation
Indices: 3703555--3703588 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
3703545 ATCGGCCTCT
3703555 CCCTTGTGCTCG
1 CCCTTGTGCTCG
3703567 CCCTTGTGCTCG
1 CCCTTGTGCTCG
3703579 CCCTTGTGCT
1 CCCTTGTGCT
3703589 TCTCCTCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.41, G:0.24, T:0.35
Consensus pattern (12 bp):
CCCTTGTGCTCG
Found at i:3709866 original size:29 final size:29
Alignment explanation
Indices: 3709815--3710033 Score: 239
Period size: 29 Copynumber: 7.6 Consensus size: 29
3709805 CACATTCGAA
* ***
3709815 AATTACAAAAATATCACAT-TTTTTTTAAT
1 AATTACCAAAATATCA-ATGTTTTAAAAAT
*
3709844 AATGACCAAAATATCAATGTTTTAAAAAT
1 AATTACCAAAATATCAATGTTTTAAAAAT
* *
3709873 AATTACCATAATATC-ATCGATTTAAAAAT
1 AATTACCAAAATATCAAT-GTTTTAAAAAT
* **
3709902 AATTACTAAAATATCACCGTTTTAAAAAT
1 AATTACCAAAATATCAATGTTTTAAAAAT
*
3709931 AATTACCAAAATATC-ATCATTTTAAAAAT
1 AATTACCAAAATATCAAT-GTTTTAAAAAT
* *
3709960 AATTACCAAAATATCATTGTTTTTAAAAT
1 AATTACCAAAATATCAATGTTTTAAAAAT
3709989 AATTACCAAAATAT-AATCGTTTTAAAAAT
1 AATTACCAAAATATCAAT-GTTTTAAAAAT
* *
3710018 AATTTCTAAAATATCA
1 AATTACCAAAATATCA
3710034 CCGGGTCGGG
Statistics
Matches: 159, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
28 6 0.04
29 151 0.95
30 2 0.01
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.37
Consensus pattern (29 bp):
AATTACCAAAATATCAATGTTTTAAAAAT
Found at i:3709888 original size:58 final size:58
Alignment explanation
Indices: 3709815--3710033 Score: 271
Period size: 58 Copynumber: 3.8 Consensus size: 58
3709805 CACATTCGAA
* *** *
3709815 AATTACAAAAATATCA-CATTTTTTTTAATAATGACCAAAATATCAATGTTTTAAAAAT
1 AATTACCAAAATATCATCA-TTTTAAAAATAATTACCAAAATATCAATGTTTTAAAAAT
* * **
3709873 AATTACCATAATATCATCGA-TTTAAAAATAATTACTAAAATATCACCGTTTTAAAAAT
1 AATTACCAAAATATCATC-ATTTTAAAAATAATTACCAAAATATCAATGTTTTAAAAAT
* *
3709931 AATTACCAAAATATCATCATTTTAAAAATAATTACCAAAATATCATTGTTTTTAAAAT
1 AATTACCAAAATATCATCATTTTAAAAATAATTACCAAAATATCAATGTTTTAAAAAT
* * * *
3709989 AATTACCAAAATATAATCGTTTTAAAAATAATTTCTAAAATATCA
1 AATTACCAAAATATCATCATTTTAAAAATAATTACCAAAATATCA
3710034 CCGGGTCGGG
Statistics
Matches: 140, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
57 1 0.01
58 137 0.98
59 1 0.01
60 1 0.01
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.37
Consensus pattern (58 bp):
AATTACCAAAATATCATCATTTTAAAAATAATTACCAAAATATCAATGTTTTAAAAAT
Found at i:3710021 original size:87 final size:86
Alignment explanation
Indices: 3709841--3710033 Score: 269
Period size: 87 Copynumber: 2.2 Consensus size: 86
3709831 CATTTTTTTT
* * *
3709841 AATAATGACCAAAATATCAATGTTTTAAAAATAATTACCATAATATCATCGATTTAAAAATAATT
1 AATAATTACCAAAATATC-ATATTTTAAAAATAATTACCAAAATATCATCGATTTAAAAATAATT
* *
3709906 ACTAAAATATCACCGTTTTAAA
65 ACCAAAATATAACCGTTTTAAA
* * *
3709928 AATAATTACCAAAATATCATCATTTTAAAAATAATTACCAAAATATCATTGTTTTTAAAATAATT
1 AATAATTACCAAAATATCAT-ATTTTAAAAATAATTACCAAAATATCATCGATTTAAAAATAATT
*
3709993 ACCAAAATATAATCGTTTTAAA
65 ACCAAAATATAACCGTTTTAAA
* *
3710015 AATAATTTCTAAAATATCA
1 AATAATTACCAAAATATCA
3710034 CCGGGTCGGG
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 2 0.02
87 92 0.98
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (86 bp):
AATAATTACCAAAATATCATATTTTAAAAATAATTACCAAAATATCATCGATTTAAAAATAATTA
CCAAAATATAACCGTTTTAAA
Found at i:3713800 original size:14 final size:15
Alignment explanation
Indices: 3713781--3713814 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
3713771 ACATAATACA
3713781 AGTTAAAAAA-ACAT
1 AGTTAAAAAAGACAT
3713795 AGTTAAAAAAGACAT
1 AGTTAAAAAAGACAT
3713810 AGTTA
1 AGTTA
3713815 CAATACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (15 bp):
AGTTAAAAAAGACAT
Found at i:3714924 original size:2 final size:2
Alignment explanation
Indices: 3714919--3714966 Score: 53
Period size: 2 Copynumber: 23.0 Consensus size: 2
3714909 TTTTTTAATC
*
3714919 AT AT AT GAT AT AT AT AT AT AT AT AT AT -T CAT AT AT GAT AT AC
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT AT
3714961 AT AT AT
1 AT AT AT
3714967 TATCATAGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 1 0.03
2 34 0.85
3 5 0.12
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3714979 original size:23 final size:25
Alignment explanation
Indices: 3714926--3714973 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3714916 ATCATATATG
*
3714926 ATAT-ATATATATATATATATTCAT
1 ATATGATATACATATATATATTCAT
3714950 ATATGATATACATATAT-TA-TCAT
1 ATATGATATACATATATATATTCAT
3714973 A
1 A
3714974 GTTGATGGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 6 0.27
25 11 0.50
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (25 bp):
ATATGATATACATATATATATTCAT
Found at i:3715125 original size:14 final size:16
Alignment explanation
Indices: 3715097--3715137 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3715087 CATGATACAA
*
3715097 ATTTAGTTTATATAAT
1 ATTTATTTTATATAAT
3715113 -TTTATTTTA-ATAAT
1 ATTTATTTTATATAAT
*
3715127 ATGTATTTTAT
1 ATTTATTTTAT
3715138 TTAAGGCGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (16 bp):
ATTTATTTTATATAAT
Found at i:3719255 original size:9 final size:8
Alignment explanation
Indices: 3719243--3719318 Score: 50
Period size: 9 Copynumber: 9.2 Consensus size: 8
3719233 AATATTTTAT
3719243 ATATAATTA
1 ATATAA-TA
*
3719252 ATATAAAA
1 ATATAATA
3719260 ATATAA-A
1 ATATAATA
*
3719267 ATATTATA
1 ATATAATA
3719275 TATATAATTA
1 -ATATAA-TA
*
3719285 ATATAAAAA
1 ATAT-AATA
3719294 ATATAA-A
1 ATATAATA
*
3719301 ATATTAT-
1 ATATAATA
3719308 ATATATATA
1 ATATA-ATA
3719317 AT
1 AT
3719319 CGGGGCGGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
7 16 0.30
8 12 0.22
9 22 0.41
10 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:3719268 original size:33 final size:34
Alignment explanation
Indices: 3719231--3719314 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
3719221 CCCGAACTCA
*
3719231 AAAATATTTTATATATAATTAATAT-AAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
3719264 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
3719298 AAAATATTATATATATA
1 AAAATATTATATATATA
3719315 TAATCGGGGC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 24 0.49
34 25 0.51
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:3724268 original size:3 final size:3
Alignment explanation
Indices: 3724260--3724293 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3724250 ATATACAAAC
3724260 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3724294 GTTAGCTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3728883 original size:6 final size:6
Alignment explanation
Indices: 3728872--3728980 Score: 218
Period size: 6 Copynumber: 18.2 Consensus size: 6
3728862 GACACGTATT
3728872 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3728920 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3728968 ACCACG ACCACG A
1 ACCACG ACCACG A
3728981 GACGAGACGA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 103 1.00
ACGTcount: A:0.34, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3728987 original size:5 final size:5
Alignment explanation
Indices: 3728977--3729018 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
3728967 GACCACGACC
3728977 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACG-G ACG
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACG
3729019 GCGGCGGCGG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.11
5 33 0.89
ACGTcount: A:0.38, C:0.21, G:0.40, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:3729650 original size:22 final size:22
Alignment explanation
Indices: 3729623--3729675 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
3729613 AATTTGGAAA
3729623 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
3729645 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
3729667 ATCGCAACG
1 ATCGCAACG
3729676 CGAAATGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:3729692 original size:20 final size:20
Alignment explanation
Indices: 3729667--3729780 Score: 102
Period size: 20 Copynumber: 5.6 Consensus size: 20
3729657 ACTGTAGACT
3729667 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
3729687 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
* *
3729708 ATCGTAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
* * ** *
3729728 ATCGCAACTCGAATTTTAACT
1 ATCGCAACGCGAAATGGAA-A
3729749 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
3729769 ATCGCAACGCGA
1 ATCGCAACGCGA
3729781 TTTTCAACTA
Statistics
Matches: 70, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 41 0.59
21 29 0.41
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:3729717 original size:41 final size:41
Alignment explanation
Indices: 3729664--3729807 Score: 227
Period size: 41 Copynumber: 3.5 Consensus size: 41
3729654 ACAACTGTAG
3729664 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* * *
3729705 ACTATCGTAACGCGAAATGAAAAATCGCAACTCGAATTTT-A
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCG-ATTTTCA
3729746 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* *
3729787 ACTATCGCAATGCGACATGGA
1 ACTATCGCAACGCGAAATGGA
3729808 CGCGATTTTC
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
40 5 0.05
41 83 0.89
42 5 0.05
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:3729752 original size:21 final size:21
Alignment explanation
Indices: 3729642--3729801 Score: 89
Period size: 21 Copynumber: 7.7 Consensus size: 21
3729632 ACAACTGTAG
* *
3729642 ACTATCGCAACGAC-AACTGTA
1 ACTATCGCAACG-CGAATTTTA
* **
3729663 GACTATCGCAACGCGAAATGGA
1 -ACTATCGCAACGCGAATTTTA
*
3729685 A-AATCGCAACGCG-ATTTTCA
1 ACTATCGCAACGCGAATTTT-A
* * *
3729705 ACTATCGTAACGCGAA-ATGA
1 ACTATCGCAACGCGAATTTTA
** *
3729725 AAAATCGCAACTCGAATTTTA
1 ACTATCGCAACGCGAATTTTA
* **
3729746 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTTTA
*
3729767 A-AATCGCAACGCG-ATTTTCA
1 ACTATCGCAACGCGAATTTT-A
*
3729787 ACTATCGCAATGCGA
1 ACTATCGCAACGCGA
3729802 CATGGACGCG
Statistics
Matches: 102, Mismatches: 28, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
19 4 0.04
20 39 0.38
21 41 0.40
22 18 0.18
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (21 bp):
ACTATCGCAACGCGAATTTTA
Found at i:3734160 original size:2 final size:2
Alignment explanation
Indices: 3734153--3734194 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3734143 TTATGACCTG
3734153 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
3734195 GTGTGTGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3736069 original size:11 final size:10
Alignment explanation
Indices: 3736054--3736087 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
3736044 AATTTTTCAG
3736054 ATTTTTTTGT
1 ATTTTTTTGT
3736064 ATTTTTTTGT
1 ATTTTTTTGT
*
3736074 ATTTTTTTAT
1 ATTTTTTTGT
3736084 ATTT
1 ATTT
3736088 GTAAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (10 bp):
ATTTTTTTGT
Found at i:3736086 original size:20 final size:19
Alignment explanation
Indices: 3736035--3736087 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
3736025 ATACTAATTT
3736035 TTTTTTTATAATTTTTCAGA
1 TTTTTTTAT-ATTTTTCAGA
* **
3736055 TTTTTTTGTATTTTTTTGTA
1 TTTTTTTATATTTTTCAG-A
3736075 TTTTTTTATATTT
1 TTTTTTTATATTT
3736088 GTAAAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.75
Consensus pattern (19 bp):
TTTTTTTATATTTTTCAGA
Found at i:3737585 original size:22 final size:22
Alignment explanation
Indices: 3737554--3737631 Score: 104
Period size: 22 Copynumber: 3.5 Consensus size: 22
3737544 AAACCACTAT
* *
3737554 GTCCCGAAGGACCACTAGATAC
1 GTCCCAAAGGACCACTGGATAC
*
3737576 GTCCCAAAGGACCAATGGATAC
1 GTCCCAAAGGACCACTGGATAC
3737598 GT-CCAGAAGGACCACTGGATAC
1 GTCCCA-AAGGACCACTGGATAC
*
3737620 GTCCCGAAGGAC
1 GTCCCAAAGGAC
3737632 TAATATACCA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 3 0.06
22 44 0.90
23 2 0.04
ACGTcount: A:0.32, C:0.29, G:0.26, T:0.13
Consensus pattern (22 bp):
GTCCCAAAGGACCACTGGATAC
Found at i:3743783 original size:31 final size:31
Alignment explanation
Indices: 3743745--3743805 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
3743735 AATTTATCTA
3743745 TATTTGTGAGTTATTTA-ATAATTTAATAATT
1 TATTTGTGAGTTATTTATA-AATTTAATAATT
*
3743776 TATTTGTGAGTTATTTTTAAATTTAATAAT
1 TATTTGTGAGTTATTTATAAATTTAATAAT
3743806 CTATCTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (31 bp):
TATTTGTGAGTTATTTATAAATTTAATAATT
Found at i:3755894 original size:13 final size:13
Alignment explanation
Indices: 3755876--3755900 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3755866 ATAGTTGAAC
3755876 AGTCTTCATATGT
1 AGTCTTCATATGT
3755889 AGTCTTCATATG
1 AGTCTTCATATG
3755901 CGTATCTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (13 bp):
AGTCTTCATATGT
Found at i:3764312 original size:21 final size:21
Alignment explanation
Indices: 3764270--3764312 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3764260 TTTCTAGGCT
* *
3764270 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
3764291 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
3764312 A
1 A
3764313 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:3764363 original size:19 final size:19
Alignment explanation
Indices: 3764339--3764375 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3764329 AAATGCTAGA
*
3764339 GGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCAG
*
3764358 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
3764376 CAATGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.35, G:0.30, T:0.11
Consensus pattern (19 bp):
GGGGAACCGATACCCCCAG
Found at i:3765041 original size:103 final size:103
Alignment explanation
Indices: 3764857--3765177 Score: 606
Period size: 103 Copynumber: 3.1 Consensus size: 103
3764847 GTAGAGGGTC
3764857 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
3764922 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
3764960 TATGTTGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
3765025 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
3765063 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACGTAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
3765128 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
3765166 TATGTGGTCCTT
1 TATGTGGTCCTT
3765178 ATGGACATTA
Statistics
Matches: 212, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:3765227 original size:23 final size:23
Alignment explanation
Indices: 3765194--3765256 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
3765184 ATTATTATAT
3765194 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
3765217 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
3765240 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
3765257 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:3772726 original size:3 final size:3
Alignment explanation
Indices: 3772718--3772760 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3772708 CTCCCTTCTC
3772718 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3772761 AATATTCACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3775160 original size:80 final size:81
Alignment explanation
Indices: 3775026--3775188 Score: 319
Period size: 80 Copynumber: 2.0 Consensus size: 81
3775016 TGTAAAAGAG
3775026 GTTTTTTTCCCCTCCAATTCGATGATTACTACAAACAAAAGGCTCTTTCTCTTTCAAAGCAATAC
1 GTTTTTTTCCCCTCCAATTCGATGATTACTACAAACAAAAGGCTCTTTCTCTTTCAAAGCAATAC
3775091 CAAGCAAATCCAATAC
66 CAAGCAAATCCAATAC
3775107 GTTTTTTT-CCCTCCAATTCGATGATTACTACAAACAAAAGGCTCTTTCTCTTTCAAAGCAATAC
1 GTTTTTTTCCCCTCCAATTCGATGATTACTACAAACAAAAGGCTCTTTCTCTTTCAAAGCAATAC
3775171 CAAGCAAATCCAATAC
66 CAAGCAAATCCAATAC
3775187 GT
1 GT
3775189 GTAAGATTTT
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 74 0.90
81 8 0.10
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.31
Consensus pattern (81 bp):
GTTTTTTTCCCCTCCAATTCGATGATTACTACAAACAAAAGGCTCTTTCTCTTTCAAAGCAATAC
CAAGCAAATCCAATAC
Found at i:3776314 original size:16 final size:16
Alignment explanation
Indices: 3776293--3776323 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3776283 TTTTTAGTCA
*
3776293 GTATGTTTAATTTTAC
1 GTATGTTTAAATTTAC
3776309 GTATGTTTAAATTTA
1 GTATGTTTAAATTTA
3776324 GTCATTGCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55
Consensus pattern (16 bp):
GTATGTTTAAATTTAC
Found at i:3778675 original size:64 final size:64
Alignment explanation
Indices: 3778574--3778702 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
3778564 TCTATATTTC
3778574 CTAGCCATGATCACATGCCAATGGTTCTTCACTGCATTATCAGTTCTGCCACTGAAAAGCCTAA
1 CTAGCCATGATCACATGCCAATGGTTCTTCACTGCATTATCAGTTCTGCCACTGAAAAGCCTAA
3778638 CTAGCCATGATCACATGCCAATGGTTCTTCACTGCATTATCAGTTCTGCCACTGAAAAGCCTAA
1 CTAGCCATGATCACATGCCAATGGTTCTTCACTGCATTATCAGTTCTGCCACTGAAAAGCCTAA
3778702 C
1 C
3778703 AATCATTGCC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (64 bp):
CTAGCCATGATCACATGCCAATGGTTCTTCACTGCATTATCAGTTCTGCCACTGAAAAGCCTAA
Found at i:3780656 original size:2 final size:2
Alignment explanation
Indices: 3780649--3780687 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3780639 TAATGTAATA
*
3780649 AT AT AT AT AT AT GT 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 AT AT AT AT AT A
3780688 GTTTTTGGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3785209 original size:2 final size:2
Alignment explanation
Indices: 3785202--3785240 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3785192 GTAAGACCAT
3785202 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
3785241 GAATTAATCA
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:3785330 original size:29 final size:28
Alignment explanation
Indices: 3785289--3785389 Score: 78
Period size: 29 Copynumber: 3.4 Consensus size: 28
3785279 TCTCATTTTA
*
3785289 AATTAATCTTTAAACTTTTAAACATTCT
1 AATTAATCCTTAAACTTTTAAACATTCT
* ** *
3785317 AATTATATCCTTAAA-TTGTGACTCTCTTTCT
1 AATTA-ATCCTTAAACTT-TTA--AACATTCT
*
3785348 AAATTAGTCCTTAAACTTTTAAACATTCT
1 -AATTAATCCTTAAACTTTTAAACATTCT
*
3785377 AATTCTATCCTTA
1 AATT-AATCCTTA
3785390 GACTATGCCC
Statistics
Matches: 54, Mismatches: 12, Indels: 13
0.68 0.15 0.16
Matches are distributed among these distances:
28 11 0.20
29 21 0.39
31 15 0.28
32 7 0.13
ACGTcount: A:0.34, C:0.18, G:0.03, T:0.46
Consensus pattern (28 bp):
AATTAATCCTTAAACTTTTAAACATTCT
Found at i:3785380 original size:60 final size:60
Alignment explanation
Indices: 3785270--3785477 Score: 267
Period size: 60 Copynumber: 3.5 Consensus size: 60
3785260 CATATTCTCT
* * * *
3785270 AACTATGAATCTCATTT-TAAATTAATCTTTAAACTTTTAAACATTCTAATTATATCCTTA
1 AACTATGACTCTC-TTTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTCTATCCTTA
* *
3785330 AATTGTGACTCTCTTTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTCTATCCTTA
1 AACTATGACTCTCTTTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTCTATCCTTA
* * * * * * *
3785390 GACTATGCCCCTCTTTCTTAATTAGTCCTTAAACTTTTGAACATTCTAATTCCATCCCTA
1 AACTATGACTCTCTTTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTCTATCCTTA
3785450 AACTATGAC-CATCTTTCTAAATTAGTCC
1 AACTATGACTC-TCTTTCTAAATTAGTCC
3785478 CTAATAGTCC
Statistics
Matches: 128, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
59 4 0.03
60 124 0.97
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.42
Consensus pattern (60 bp):
AACTATGACTCTCTTTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTCTATCCTTA
Found at i:3789761 original size:64 final size:64
Alignment explanation
Indices: 3789677--3789822 Score: 188
Period size: 64 Copynumber: 2.3 Consensus size: 64
3789667 CATTCATAAG
* * *
3789677 TGCATCGATGCATTCC-TTTAAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCA-TAGCTA
1 TGCATCGATGCA-TCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACCGATGCACAAG-TA
3789740 A
64 A
* * * *
3789741 TGCATCGATGCATCCTTTTAAAATAATAACATCGAATGCATTTTATGCACCGATGCACAAGTAG
1 TGCATCGATGCATCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACCGATGCACAAGTAA
3789805 TGCATCGATGCATACCTT
1 TGCATCGATGCAT-CCTT
3789823 CATTGAAAGA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
63 3 0.04
64 63 0.88
65 6 0.08
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACCGATGCACAAGTAA
Found at i:3790532 original size:30 final size:30
Alignment explanation
Indices: 3790496--3790559 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
3790486 AAGGAATATA
* *
3790496 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
3790526 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
3790556 TGGA
1 TGGA
3790560 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:3793948 original size:64 final size:64
Alignment explanation
Indices: 3793864--3794009 Score: 179
Period size: 64 Copynumber: 2.3 Consensus size: 64
3793854 CATTCATAAG
* * * *
3793864 TGCATCGATGCATTCC-TTTAAAAGAAGAACATTGAATGCCTTTGATGCATCGATGCA-TAGCTA
1 TGCATCGATGCA-TCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACCGATGCACAAG-TA
3793927 A
64 A
* * * *
3793928 TGCATCGATGCATCCTTTTAAAATAATAACATCGAATGCATTTTATGCACCGATGCACAAGTAG
1 TGCATCGATGCATCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACCGATGCACAAGTAA
3793992 TGCATCGATGCATACCTT
1 TGCATCGATGCAT-CCTT
3794010 CATTGAAAGA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
63 3 0.04
64 62 0.87
65 6 0.08
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACCGATGCACAAGTAA
Found at i:3794719 original size:30 final size:30
Alignment explanation
Indices: 3794683--3794746 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
3794673 AAGGAACATA
*
3794683 TGGATAGTTGCCGAGGATCTTTATAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * * *
3794713 TGGATAGTTATCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
3794743 TGGA
1 TGGA
3794747 CAGGTCCTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:3798450 original size:2 final size:2
Alignment explanation
Indices: 3798445--3798478 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3798435 TCGTTTTTTC
3798445 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3798479 AAATGAATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3800416 original size:22 final size:22
Alignment explanation
Indices: 3800384--3800451 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
3800374 ATAGTACTAT
*
3800384 ACAAT-ATGAACAGTACCGTGA
1 ACAATAATGAACAATACCGTGA
* *
3800405 ACAATAATGAACATTACCGTAA
1 ACAATAATGAACAATACCGTGA
* * *
3800427 ATAGTAATAAACAATACCGTGA
1 ACAATAATGAACAATACCGTGA
3800449 ACA
1 ACA
3800452 GTACCAAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 5 0.13
22 33 0.87
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.21
Consensus pattern (22 bp):
ACAATAATGAACAATACCGTGA
Found at i:3803485 original size:103 final size:103
Alignment explanation
Indices: 3803303--3803630 Score: 602
Period size: 103 Copynumber: 3.2 Consensus size: 103
3803293 GTAGAGGGTC
* *
3803303 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
3803368 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
3803406 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
*
3803471 TTGATCTTTTGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
3803509 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
*
3803574 TTGATCTTTGGCATATGTATATGATTATTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
3803612 TATGTGGTCCTTAGGGACA
1 TATGTGGTCCTTCGGGACA
3803631 ACTTTATATG
Statistics
Matches: 217, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 217 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:3803666 original size:23 final size:23
Alignment explanation
Indices: 3803640--3803707 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
3803630 AACTTTATAT
*
3803640 GGCACTTCGGTGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTACGC
* * * *
3803663 GGCACTACGGTGAAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
3803686 GACACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
3803708 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:3810546 original size:103 final size:103
Alignment explanation
Indices: 3810368--3810694 Score: 602
Period size: 103 Copynumber: 3.2 Consensus size: 103
3810358 GTAGAGGGTC
* *
3810368 TATGTGGTTCTTCGGGACATATATGTATT-TTTGGAACAGGTGTGAGGTCTGTTGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
3810432 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
* *
3810470 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACAGGTGTAAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
3810535 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
3810573 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
3810638 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
3810676 TATGTGGTCCTTAGGGACA
1 TATGTGGTCCTTCGGGACA
3810695 ACTTTATATG
Statistics
Matches: 217, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
102 27 0.12
103 190 0.88
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:3810730 original size:23 final size:23
Alignment explanation
Indices: 3810704--3810766 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
3810694 AACTTTATAT
*
3810704 GGCACTTCGGTGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
3810727 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
3810750 GGCACTTCGGTGCATTT
1 GGCACTTCGGTGCATTT
3810767 ATACAAGTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:3813425 original size:15 final size:15
Alignment explanation
Indices: 3813400--3813446 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
3813390 TTTGTATACC
3813400 ATAT-AATATTTAAT
1 ATATGAATATTTAAT
3813414 ATA-GATATATTT-AT
1 ATATGA-ATATTTAAT
*
3813428 ATATGAATATTTATT
1 ATATGAATATTTAAT
3813443 ATAT
1 ATAT
3813447 AATTCAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (15 bp):
ATATGAATATTTAAT
Found at i:3813437 original size:14 final size:14
Alignment explanation
Indices: 3813400--3813446 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
3813390 TTTGTATACC
3813400 ATAT-AATATTTA-
1 ATATGAATATTTAT
3813412 ATATAGATATATTTAT
1 ATAT-GA-ATATTTAT
3813428 ATATGAATATTTATT
1 ATATGAATATTTA-T
3813443 ATAT
1 ATAT
3813447 AATTCAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.13
14 8 0.27
15 14 0.47
16 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
ATATGAATATTTAT
Found at i:3823142 original size:8 final size:9
Alignment explanation
Indices: 3823118--3823143 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3823108 GATGTTGTTC
3823118 TGGAAAAAA
1 TGGAAAAAA
3823127 TGGAAAAAA
1 TGGAAAAAA
3823136 TGGAAAAA
1 TGGAAAAA
3823144 GAAACTTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.23, T:0.12
Consensus pattern (9 bp):
TGGAAAAAA
Found at i:3826186 original size:16 final size:17
Alignment explanation
Indices: 3826166--3826203 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3826156 GAATTCAGAA
**
3826166 CAAGAAATTTAAAAAAT
1 CAAGAAATAAAAAAAAT
3826183 -AAGAAATAAAAAAAAT
1 CAAGAAATAAAAAAAAT
3826199 CAAGA
1 CAAGA
3826204 CACCAACCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.71, C:0.05, G:0.08, T:0.16
Consensus pattern (17 bp):
CAAGAAATAAAAAAAAT
Found at i:3840201 original size:27 final size:27
Alignment explanation
Indices: 3840163--3840219 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
3840153 TGCAAATCGA
*
3840163 GGAAGCGGTGGAACATGAGGAAGTGCT
1 GGAAGCGGTGGAACACGAGGAAGTGCT
* *
3840190 GGAAGCGGTGGAACACGAGGTAGTGTT
1 GGAAGCGGTGGAACACGAGGAAGTGCT
3840217 GGA
1 GGA
3840220 TCACGTGCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.28, C:0.11, G:0.46, T:0.16
Consensus pattern (27 bp):
GGAAGCGGTGGAACACGAGGAAGTGCT
Found at i:3844172 original size:10 final size:11
Alignment explanation
Indices: 3844153--3844183 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
3844143 GACGTAGTTC
3844153 TTTTCTTTTTT
1 TTTTCTTTTTT
3844164 TTTTCTTTTTT
1 TTTTCTTTTTT
3844175 TTTTGCTTT
1 TTTT-CTTT
3844184 CTCTGTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:3846448 original size:23 final size:23
Alignment explanation
Indices: 3846422--3846471 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
3846412 TAAATCAACG
3846422 TGTTCGCAAATGCTAAACGAGCA
1 TGTTCGCAAATGCTAAACGAGCA
3846445 TGTTCGCAAATGCTAAACGAGCA
1 TGTTCGCAAATGCTAAACGAGCA
3846468 TGTT
1 TGTT
3846472 TACAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (23 bp):
TGTTCGCAAATGCTAAACGAGCA
Found at i:3846477 original size:23 final size:23
Alignment explanation
Indices: 3846422--3846478 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
3846412 TAAATCAACG
*
3846422 TGTTCGCAAATGCTAAACGAGCA
1 TGTTCACAAATGCTAAACGAGCA
*
3846445 TGTTCGCAAATGCTAAACGAGCA
1 TGTTCACAAATGCTAAACGAGCA
*
3846468 TGTTTACAAAT
1 TGTTCACAAAT
3846479 ATTAAATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (23 bp):
TGTTCACAAATGCTAAACGAGCA
Found at i:3846484 original size:23 final size:23
Alignment explanation
Indices: 3846428--3846495 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
3846418 AACGTGTTCG
* **
3846428 CAAATGCTAAACGAGCATGTTCG
1 CAAATACTAAACGAGCATGTTTA
*
3846451 CAAATGCTAAACGAGCATGTTTA
1 CAAATACTAAACGAGCATGTTTA
* * *
3846474 CAAATATTAAATGAACATGTTT
1 CAAATACTAAACGAGCATGTTT
3846496 GTGAACATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (23 bp):
CAAATACTAAACGAGCATGTTTA
Found at i:3856815 original size:402 final size:396
Alignment explanation
Indices: 3855458--3856839 Score: 1082
Period size: 399 Copynumber: 3.5 Consensus size: 396
3855448 CAATGTGGAA
* * * * *
3855458 CTGCCTGTTCTTGAAGC-A-A-CAGTAGAAGATATTGATTTAGCTTTCAAGAAACTTCAT---GT
1 CTGCCTGTTCTTGAAGCAAGATCA-TTGAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGG
* * * * * *
3855517 AGTGGATGTTGAGGAAGTAATTCTTCCGAGTATGATTGAGAATCAGCCGGATCATGCAGATACCA
65 AGTAGATGCTGAGGAAGTAATTCTT-CAAGCATGATTGAGAATCAGCTGGATCATGCAGATCCCA
** * * * * * * * *
3855582 AGTCGGATTTAACTGTTATCGAGGCGAGATCTCTGGAGGATATACACAATGCTTTGCAACAAGGT
129 CTTCAGAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAATGCTTTCCAAAAAGG-
* * ** * * *
3855647 A-CAGAACCTAATCCAGCT-CAGCTGCCACAGTCCACAGACTTGAAGAAA-GGATCATCAGAAGT
193 ACCAGAACGTAATCCAG-TGGAGCTGCTGCAGTCCACAAACATG-AGAAATGGATCAACAGAAGT
* * * * * *** ** * * *
3855709 GGAGCAGA-ATGTTGTAGTAGTATCTTCCAAAGAGATTGAAGTTAG-CAATGCCGTCTCTGATAT
256 AGAACA-ACATGATG-CG--GTTTCTAGTAAAGAGATTGAAGCCAGTC-AGGTCGTCTCTGGTAT
* ** * * **
3855772 TCAAGAAAGCTATGATAATGCTGCTGGTGAACCTGAAAATG---ATGAAGAAA-CTGAAGAACGA
316 TCAAGAAA---ATGAGAACACTGCAGCTGAACCAAAAAATGAATATGAAGAAATC-GAAGAA--A
*** *
3855833 -AAGGCGGAGACCAACTTGAAG
375 TAAGTAAGAGACCAACGTGAAG
* * *
3855854 CTACCTGTTCTTGAAGCAAGATCAATTGAAGATATTGTTTTGGCTTTTAAGCAACTTCATGAAGC
1 CTGCCTGTTCTTGAAGCAAGATC-ATTGAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGG
* * *
3855919 AGTGGATGCTGAGGAAATAATTCTTCCAAGCTTGATTGAGAATCAGCTGGATCATGCAGATCCCA
65 AGTAGATGCTGAGGAAGTAATTCTT-CAAGCATGATTGAGAATCAGCTGGATCATGCAGATCCCA
* * *
3855984 CTTCAGAATTACCTGTTGTCGAGGCAAGATCTCTTGAAGATATAAATAATGCTTTCCAAAAAGGA
129 CTTCAGAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAATGCTTTCCAAAAAGGA
* * * * * * *
3856049 CCAGAACTTAATCCAGTTGAGTTGCTGCAGTCTACAAACTTGAGGAATGGGTCAACAGAAGTAGA
194 CCAGAACGTAATCCAGTGGAGCTGCTGCAGTCCACAAACATGAGAAATGGATCAACAGAAGTAGA
* *** * * *
3856114 ACAGCATGATGCGGTTTCTAGTAAAGAGATTGAAGTTGGTGAGGTGGTCTCTGGTTTTCAAGAAA
259 ACAACATGATGCGGTTTCTAGTAAAGAGATTGAAGCCAGTCAGGTCGTCTCTGGTATTCAAGAAA
** * * * * * * *
3856179 ATGAGAATGCTGCTGCTGAATCAAAAAATGAATATGAAGCAATTGAAGAAATAGGTATGCTGACC
324 ATGAGAACACTGCAGCTGAACCAAAAAATGAATATGAAGAAATCGAAGAAATAAGTAAG-AGACC
* *
3856244 TATGT-ACAG
388 AACGTGA-AG
* * * * * ** *
3856253 CAGTCTGTCCGTAAAGCAAGATTGGTTGAAGATATTGATTTGGCTTTTAAGCAACTTCATGATGG
1 CTGCCTGTTCTTGAAGCAAGA-TCATTGAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGG
* * * * *
3856318 TGTTGGTGCTGAGGAAGTAATTCTTACAAGCATGATCGAGAATCAGCTGGATCATGCTGATCCCA
65 AGTAGATGCTGAGGAAGTAATTCTT-CAAGCATGATTGAGAATCAGCTGGATCATGCAGATCCCA
* * ** * *
3856383 CTCCAGAATTACCCGTTGTCGAGGCAAGATCTCTGGAGGATATACATAATGCTTTCCGGAAATGC
129 CTTCAGAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAATGCTTTCCAAAAAGGA
** ** * *
3856448 CCAGAACGTAATCCAGTGGAGCTGCCT-CTTTCCACTGACATGAGAAATGGATCATCAGACA-TG
194 CCAGAACGTAATCCAGTGGAGCTG-CTGCAGTCCACAAACATGAGAAATGGATCAACAGA-AGTA
* * * * *
3856511 GAGCAACATGATGTGGTTTCTGGTGAAGAGATTGAAGCCATTCATGG-CGTCTCTGGTATTCAAG
257 GAACAACATGATGCGGTTTCTAGTAAAGAGATTGAAGCCAGTCA-GGTCGTCTCTGGTATTCAAG
* * *
3856575 AAAATAGTCTGAACACTGCCAG-TGAACCAAAAAATGACTATGATGAAATCGAAGAAATGAAG-A
321 AAAAT-G--AGAACACTG-CAGCTGAACCAAAAAATGAATATGAAGAAATCGAAGAAAT-AAGTA
*
3856638 CAGAGACCAACGTGGAG
381 -AGAGACCAACGTGAAG
* *
3856655 CTGCCTGTTCTTGAAGCAAGATCATTGAAAGACATTGATTTGGCTTTTAAGCAACTCCATGAAGG
1 CTGCCTGTTCTTGAAGCAAGATCATTG-AAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGG
* * * * * * **
3856720 AGTAGATG-TCGAGGAAGTAACTCTTCTTACCATGATTGAGAATCACCAGGGTCATGCAGATAGC
65 AGTAGATGCT-GAGGAAGTAATTCTTC-AAGCATGATTGAGAATCAGCTGGATCATGCAGATCCC
* * * * *
3856784 AATTCTGATTTACCTGTTGTTGATGCAAGATCTCTGGAGGATATACATAATGCTTT
128 ACTTCAGAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAATGCTTT
3856840 TCAGCAAGGC
Statistics
Matches: 787, Mismatches: 166, Indels: 60
0.78 0.16 0.06
Matches are distributed among these distances:
396 41 0.05
397 2 0.00
398 5 0.01
399 357 0.45
400 8 0.01
401 13 0.02
402 356 0.45
403 5 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (396 bp):
CTGCCTGTTCTTGAAGCAAGATCATTGAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGA
GTAGATGCTGAGGAAGTAATTCTTCAAGCATGATTGAGAATCAGCTGGATCATGCAGATCCCACT
TCAGAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAATGCTTTCCAAAAAGGACC
AGAACGTAATCCAGTGGAGCTGCTGCAGTCCACAAACATGAGAAATGGATCAACAGAAGTAGAAC
AACATGATGCGGTTTCTAGTAAAGAGATTGAAGCCAGTCAGGTCGTCTCTGGTATTCAAGAAAAT
GAGAACACTGCAGCTGAACCAAAAAATGAATATGAAGAAATCGAAGAAATAAGTAAGAGACCAAC
GTGAAG
Found at i:3857330 original size:378 final size:373
Alignment explanation
Indices: 3856658--3857352 Score: 800
Period size: 378 Copynumber: 1.8 Consensus size: 373
3856648 CGTGGAGCTG
*
3856658 CCTGTTCTTGAAGCAAGATCATTGAAAGACATTGATTTGGCTTTTAAGCAACTCCATGAAGGAGT
1 CCTGTTCTTGAAGCAAAATCATTGAAAGACATTGATTTGGCTTTTAAGCAACTCCATGAAGGAGT
** * * *
3856723 AGATGTCGAGGAAGTAACTCTTCTTACCATGATTGAGAATCACCAGGGTCATGCAGATAGCAATT
66 AGATGTCGAGGAAGTAACTCTTCCAACCATGATTGAGAATCACCAGGGTCATACAGATACCAATC
* * * * ** * * *
3856788 CTGATTTACCTGTTGTTGATGCAAGATCTCTGGAGGATATACATAATGCTTTTCAGCAAGGCACC
131 CAGATTTACCTGTTGTCGACGCAAGATATCAAGAGGATATACATAACGCTTTTCAACAAAGCACC
* *
3856853 AAATCTAATCCAACTGAGCAGCCACATTCATCAGGAGAAGATCATGATGTGGTTTCTATGAATGA
196 AAATCTAATCCAACTGAGCAGCCAAATTCA-CAGGAGAAGA-CATGATGTGGTTTCAATGAATGA
* * * * * *
3856918 GATTGATGGTAGCAATGCCGTCTCAGGTATTCAAGAAACAAGCCAGAATGCTGCTGGTGAACCAA
259 GATTGAAGGTAGAAATGCAGCCTCAGGGATTCAAG-AACAAG--AGAATGCTCCTGGTGAACCAA
3856983 AAGATGAATATGAAGATAAGGAAGAAATAGAGATGGAGACCAAGGCGGCACTA
321 AAGATGAATATGAAGATAAGGAAGAAATAGAGATGGAGACCAAGGCGGCACTA
*
3857036 CCTGTTCTTGAAGCAAAATCAGTTG-AAGACATTGATTTGG-TTTTGAAGCAACTTCATGAAGGA
1 CCTGTTCTTGAAGCAAAATCA-TTGAAAGACATTGATTTGGCTTTT-AAGCAACTCCATGAAGGA
* * ** *
3857099 GTAGATGTGGAGGAAGTAATTCTTCCAAGTATGATTGAGAATCAGCAGGGTCATACAGATACCAA
64 GTAGATGTCGAGGAAGTAACTCTTCCAACCATGATTGAGAATCACCAGGGTCATACAGATACCAA
* * *
3857164 TCCAG-TATTACCTGTTGTCG-CGCCGAGATATCAAGAGGATTTTCATAACGCTTTTCAACAAAG
129 TCCAGAT-TTACCTGTTGTCGACG-CAAGATATCAAGAGGATATACATAACGCTTTTCAACAAAG
* * **
3857227 CCCCGAATCTAATCCTGCTGAGCTA-CCTAATAATTC-CA-G-GAAG-CATGATG-GAGTTTCAA
192 CACCAAATCTAATCCAACTGAGC-AGCC--A-AATTCACAGGAGAAGACATGATGTG-GTTTCAA
* * *
3857286 CTGAA-GAGATTGAAGTTAGTGAAAATGCAGCCTCCGGGATTCAAGAACATGAGAATGCTCCTGG
252 -TGAATGAGATTGAAGGTA--G-AAATGCAGCCTCAGGGATTCAAGAACAAGAGAATGCTCCTGG
3857350 TGA
313 TGA
3857353 GCCTAAACAG
Statistics
Matches: 265, Mismatches: 39, Indels: 29
0.80 0.12 0.09
Matches are distributed among these distances:
374 1 0.00
375 39 0.15
376 4 0.02
377 16 0.06
378 194 0.73
379 6 0.02
380 1 0.00
381 4 0.02
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (373 bp):
CCTGTTCTTGAAGCAAAATCATTGAAAGACATTGATTTGGCTTTTAAGCAACTCCATGAAGGAGT
AGATGTCGAGGAAGTAACTCTTCCAACCATGATTGAGAATCACCAGGGTCATACAGATACCAATC
CAGATTTACCTGTTGTCGACGCAAGATATCAAGAGGATATACATAACGCTTTTCAACAAAGCACC
AAATCTAATCCAACTGAGCAGCCAAATTCACAGGAGAAGACATGATGTGGTTTCAATGAATGAGA
TTGAAGGTAGAAATGCAGCCTCAGGGATTCAAGAACAAGAGAATGCTCCTGGTGAACCAAAAGAT
GAATATGAAGATAAGGAAGAAATAGAGATGGAGACCAAGGCGGCACTA
Found at i:3861280 original size:2 final size:2
Alignment explanation
Indices: 3861226--3861267 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3861216 CTAAATTTTA
3861226 AT AT AT AT AT AT AT AT -T 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
3861267 A
1 A
3861268 GTCATCCATA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3863832 original size:20 final size:19
Alignment explanation
Indices: 3863790--3863865 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 19
3863780 ATATAAATTT
3863790 TATA-TATAAACTATATAA
1 TATATTATAAACTATATAA
*
3863808 T-TATTATAAGCTATATATA
1 TATATTATAAACTATATA-A
***
3863827 TATATTAT-GTTTATATGAA
1 TATATTATAAACTATAT-AA
3863846 CTATATATATAAACTATATA
1 -TATAT-TATAAACTATATA
3863866 TGTAAACTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
17 2 0.05
18 13 0.30
19 8 0.18
20 12 0.27
21 4 0.09
22 5 0.11
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (19 bp):
TATATTATAAACTATATAA
Found at i:3863871 original size:13 final size:13
Alignment explanation
Indices: 3863779--3863875 Score: 68
Period size: 13 Copynumber: 6.9 Consensus size: 13
3863769 TATAAGTTTT
* *
3863779 TATATAAATTTTA
1 TATATAAACTATA
3863792 TATATAAACTATA
1 TATATAAACTATA
3863805 TAATTATTATAAGCTATA
1 T-A-TA-TA-AA-CTATA
* * *
3863823 TATATATATTATGTT
1 TATATAAACTA--TA
*
3863838 TATATGAACTATA
1 TATATAAACTATA
3863851 TATATAAACTATA
1 TATATAAACTATA
*
3863864 TATGTAAACTAT
1 TATATAAACTAT
3863876 GTAACAACCC
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
13 38 0.58
14 2 0.03
15 13 0.20
16 4 0.06
17 3 0.05
18 6 0.09
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (13 bp):
TATATAAACTATA
Found at i:3864692 original size:29 final size:29
Alignment explanation
Indices: 3864648--3864807 Score: 189
Period size: 29 Copynumber: 5.5 Consensus size: 29
3864638 CCCGACCCGA
* * *
3864648 TGATATTTTGGGAATTATTTTTAAAATGG
1 TGATATTTTGGTAATTATTTTGAAAAAGG
* *
3864677 TGATATTTTGGTAATTATTTCGGAAAAAATG
1 TGATATTTTGGTAATTATTT-TG-AAAAAGG
*
3864708 TGATATTTTGGTAATTATTTCG-AAAA-G
1 TGATATTTTGGTAATTATTTTGAAAAAGG
*
3864735 TGATATTTTGGTAGTTATTTTGAAAAAGG
1 TGATATTTTGGTAATTATTTTGAAAAAGG
* *
3864764 TGATATTTTGATAATTATTTTTAAAAAGG
1 TGATATTTTGGTAATTATTTTGAAAAAGG
* *
3864793 TGCTATTTTCGTAAT
1 TGATATTTTGGTAAT
3864808 AGTTGACTGT
Statistics
Matches: 113, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
27 21 0.19
28 8 0.07
29 58 0.51
30 1 0.01
31 25 0.22
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.46
Consensus pattern (29 bp):
TGATATTTTGGTAATTATTTTGAAAAAGG
Found at i:3866447 original size:2 final size:2
Alignment explanation
Indices: 3866436--3866477 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3866426 GTTTATAAAC
3866436 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3866477 T
1 T
3866478 TATTCAAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3866598 original size:17 final size:18
Alignment explanation
Indices: 3866576--3866630 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
3866566 TTAAGAAATT
*
3866576 TTGAGAA-TATAGGGAAA
1 TTGAGAATTAGAGGGAAA
3866593 TTGAGAATTTAGAGGGAAA
1 TTGAGAA-TTAGAGGGAAA
3866612 TTGAGAAATTTAGAGGGAA
1 TTGAG-AA-TTAGAGGGAA
3866631 TAGAAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
17 7 0.21
19 14 0.41
20 13 0.38
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.25
Consensus pattern (18 bp):
TTGAGAATTAGAGGGAAA
Found at i:3866608 original size:19 final size:20
Alignment explanation
Indices: 3866586--3866630 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
3866576 TTGAGAATAT
3866586 AGGGAAATTGAG-AATTTAG
1 AGGGAAATTGAGAAATTTAG
3866605 AGGGAAATTGAGAAATTTAG
1 AGGGAAATTGAGAAATTTAG
3866625 AGGGAA
1 AGGGAA
3866631 TAGAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (20 bp):
AGGGAAATTGAGAAATTTAG
Found at i:3866640 original size:46 final size:47
Alignment explanation
Indices: 3866545--3866649 Score: 115
Period size: 46 Copynumber: 2.3 Consensus size: 47
3866535 TTTTAATTTT
* * **
3866545 ATTTGGGAATTTAGAAGGAAATTAAGAAATTTTGAGAATATAGGGAA
1 ATTTGAGAATTTAGAAGGAAATTAAGAAATTTAGAGAATATAGAAAA
* * *
3866592 A-TTGAGAATTTAGAGGGAAATTGAGAAATTTAGAGGGA-ATAGAAAA
1 ATTTGAGAATTTAGAAGGAAATTAAGAAATTTAGA-GAATATAGAAAA
*
3866638 ATTTGGGAATTT
1 ATTTGAGAATTT
3866650 GGAGCCAAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
46 36 0.75
47 12 0.25
ACGTcount: A:0.44, C:0.00, G:0.27, T:0.30
Consensus pattern (47 bp):
ATTTGAGAATTTAGAAGGAAATTAAGAAATTTAGAGAATATAGAAAA
Found at i:3866641 original size:19 final size:20
Alignment explanation
Indices: 3866598--3866641 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
3866588 GGAAATTGAG
* *
3866598 AATTTAGAGGGAAATTGAGA
1 AATTTAGAGGGAAATAGAAA
3866618 AATTTAGAGGG-AATAGAAA
1 AATTTAGAGGGAAATAGAAA
3866637 AATTT
1 AATTT
3866642 GGGAATTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.27
Consensus pattern (20 bp):
AATTTAGAGGGAAATAGAAA
Found at i:3866897 original size:15 final size:15
Alignment explanation
Indices: 3866874--3866906 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3866864 GTATGTATGC
3866874 ATATATATAAACTAT
1 ATATATATAAACTAT
*
3866889 ATATGTATAAACTAT
1 ATATATATAAACTAT
3866904 ATA
1 ATA
3866907 AAATATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (15 bp):
ATATATATAAACTAT
Found at i:3867071 original size:7 final size:7
Alignment explanation
Indices: 3867059--3867139 Score: 81
Period size: 7 Copynumber: 11.6 Consensus size: 7
3867049 TTAAAAAAAA
3867059 CTAAACC
1 CTAAACC
3867066 CTAAACC
1 CTAAACC
3867073 CTAAACC
1 CTAAACC
*
3867080 TTAAACC
1 CTAAACC
*
3867087 CTAAATC
1 CTAAACC
*
3867094 CTAAACT
1 CTAAACC
*
3867101 TTAAACC
1 CTAAACC
* * *
3867108 ATACACA
1 CTAAACC
*
3867115 CTAAATC
1 CTAAACC
*
3867122 TTAAACC
1 CTAAACC
3867129 CTAAACC
1 CTAAACC
3867136 CTAA
1 CTAA
3867140 TATAAATAGA
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 57 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:3867084 original size:21 final size:21
Alignment explanation
Indices: 3867060--3867139 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
3867050 TAAAAAAAAC
3867060 TAAACCCTAAACCCTAAACCT
1 TAAACCCTAAACCCTAAACCT
* *
3867081 TAAACCCTAAATCCTAAACTT
1 TAAACCCTAAACCCTAAACCT
* * * *
3867102 TAAACCATACACACTAAATCT
1 TAAACCCTAAACCCTAAACCT
3867123 TAAACCCTAAACCCTAA
1 TAAACCCTAAACCCTAA
3867140 TATAAATAGA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAACCT
Found at i:3867844 original size:22 final size:21
Alignment explanation
Indices: 3867803--3867844 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3867793 AAAAATGCAC
3867803 TTAAGTGGGAAAAAAGAAAAA
1 TTAAGTGGGAAAAAAGAAAAA
* * *
3867824 TTAATTGGGGAAAAAGTAAAA
1 TTAAGTGGGAAAAAAGAAAAA
3867845 CCATTCAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.19
Consensus pattern (21 bp):
TTAAGTGGGAAAAAAGAAAAA
Found at i:3868282 original size:14 final size:14
Alignment explanation
Indices: 3868263--3868304 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
3868253 AACCCTAATT
3868263 ATAAACTCTAAACC
1 ATAAACTCTAAACC
*
3868277 ATAAACTTTAAACC
1 ATAAACTCTAAACC
*
3868291 ATAAACACTAAACC
1 ATAAACTCTAAACC
3868305 CTAATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAACTCTAAACC
Found at i:3868801 original size:16 final size:16
Alignment explanation
Indices: 3868739--3868804 Score: 69
Period size: 16 Copynumber: 4.1 Consensus size: 16
3868729 AAATATCAGA
**
3868739 TCAGGTTAAAAACATA
1 TCAGGTTAAAAACAGG
* *
3868755 TCATGTTAAAAACATG
1 TCAGGTTAAAAACAGG
* *
3868771 TGAGGTTGAAAACAGG
1 TCAGGTTAAAAACAGG
*
3868787 TCAGGTTGAAAACAGG
1 TCAGGTTAAAAACAGG
3868803 TC
1 TC
3868805 GGGTAATACC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (16 bp):
TCAGGTTAAAAACAGG
Found at i:3871272 original size:34 final size:34
Alignment explanation
Indices: 3871234--3871306 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
3871224 TAGTTTAAGC
3871234 TCTATAATATTTGTGGGTTTTATCTGGATATATT
1 TCTATAATATTTGTGGGTTTTATCTGGATATATT
3871268 TCTATAATATTTGTGGGTTTTATCTGGATATATT
1 TCTATAATATTTGTGGGTTTTATCTGGATATATT
3871302 TCTAT
1 TCTAT
3871307 TAATTTTCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.53
Consensus pattern (34 bp):
TCTATAATATTTGTGGGTTTTATCTGGATATATT
Found at i:3876555 original size:16 final size:17
Alignment explanation
Indices: 3876518--3876549 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3876508 AACACCATTT
3876518 ATTTAATA-TTTATATA
1 ATTTAATATTTTATATA
3876534 ATTTAATATTTTATAT
1 ATTTAATATTTTATAT
3876550 TTTTAAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTAATATTTTATATA
Found at i:3876997 original size:31 final size:31
Alignment explanation
Indices: 3876926--3876998 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
3876916 CTATTAAATA
* *
3876926 TTAACAAAAATATAAGGATATGTACAACATT
1 TTAACAAAATTATAAGGATATATACAACATT
3876957 TTAACAAAATTATTAAGGATATATACAACA-T
1 TTAACAAAATTA-TAAGGATATATACAACATT
3876988 TTAACAAAATT
1 TTAACAAAATT
3876999 CCATTTTTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 23 0.59
32 16 0.41
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.32
Consensus pattern (31 bp):
TTAACAAAATTATAAGGATATATACAACATT
Found at i:3877488 original size:18 final size:18
Alignment explanation
Indices: 3877465--3877521 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 18
3877455 AACAAAATGG
3877465 CTTTAGATTTCTAGGCAT
1 CTTTAGATTTCTAGGCAT
*
3877483 CTTTAG-GTT-TAGGACA-
1 CTTTAGATTTCTAGG-CAT
* *
3877499 ATTT-GATTTCTAGGCGT
1 CTTTAGATTTCTAGGCAT
3877516 CTTTAG
1 CTTTAG
3877522 TATTAGAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 10
0.66 0.11 0.23
Matches are distributed among these distances:
15 1 0.03
16 10 0.34
17 11 0.38
18 7 0.24
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.44
Consensus pattern (18 bp):
CTTTAGATTTCTAGGCAT
Found at i:3878562 original size:21 final size:21
Alignment explanation
Indices: 3878536--3878580 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3878526 GATTTCTGGG
* *
3878536 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3878557 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3878578 CAA
1 CAA
3878581 ACGACATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:3879395 original size:31 final size:31
Alignment explanation
Indices: 3879357--3879510 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
3879347 GGGTCGAGGG
3879357 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
3879388 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
3879419 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
3879450 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
3879481 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
3879511 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:3882569 original size:21 final size:21
Alignment explanation
Indices: 3882543--3882587 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3882533 GATTTCTGGG
* *
3882543 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3882564 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3882585 CAA
1 CAA
3882588 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:3883400 original size:31 final size:31
Alignment explanation
Indices: 3883362--3883515 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
3883352 GGGTCGAGGG
3883362 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
3883393 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
3883424 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
3883455 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
3883486 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
3883516 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:3885458 original size:2 final size:2
Alignment explanation
Indices: 3885453--3885477 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3885443 TTTACCCTTA
3885453 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3885478 AATAATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3886348 original size:19 final size:19
Alignment explanation
Indices: 3886308--3886351 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3886298 TTTAATAAGT
*
3886308 TAAAATTTAATATTAAACTA
1 TAAAATTTAATA-TAAAATA
3886328 TAAATATTTAATA-AAAATA
1 TAAA-ATTTAATATAAAATA
3886347 TAAAA
1 TAAAA
3886352 ATATTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.05
19 9 0.41
20 4 0.18
21 8 0.36
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAATTTAATATAAAATA
Found at i:3886617 original size:37 final size:37
Alignment explanation
Indices: 3886576--3886650 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
3886566 CATAATACTT
3886576 GAAGAAAATAGAAAATTAGGGTGGATTTGGAGAAGTG
1 GAAGAAAATAGAAAATTAGGGTGGATTTGGAGAAGTG
3886613 GAAGAAAATAGAAAATTAGGGTGGATTTGGAGAAGTG
1 GAAGAAAATAGAAAATTAGGGTGGATTTGGAGAAGTG
3886650 G
1 G
3886651 GCATAGGGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.36, T:0.21
Consensus pattern (37 bp):
GAAGAAAATAGAAAATTAGGGTGGATTTGGAGAAGTG
Found at i:3888532 original size:2 final size:2
Alignment explanation
Indices: 3888525--3888550 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3888515 CAATTTCCAA
3888525 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
3888551 TCAGCTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3895514 original size:12 final size:12
Alignment explanation
Indices: 3895497--3895521 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3895487 AATACATATG
3895497 AAATATTATAAA
1 AAATATTATAAA
3895509 AAATATTATAAA
1 AAATATTATAAA
3895521 A
1 A
3895522 CGAAAGACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATATTATAAA
Found at i:3896289 original size:24 final size:21
Alignment explanation
Indices: 3896256--3896304 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
3896246 TGTTTAAGAA
*
3896256 TTATATTATGGTCTAAATCATTTG
1 TTATAATAT-GTCTAAA--ATTTG
*
3896280 TTATAATATGTGTAAAATTTG
1 TTATAATATGTCTAAAATTTG
3896301 TTAT
1 TTAT
3896305 GGAAAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
23 6 0.26
24 8 0.35
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (21 bp):
TTATAATATGTCTAAAATTTG
Found at i:3898968 original size:2 final size:2
Alignment explanation
Indices: 3898961--3898988 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3898951 ACACATTATC
3898961 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
3898989 TATTGTCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3906389 original size:19 final size:19
Alignment explanation
Indices: 3906331--3906392 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
3906321 TATATTTTAA
*
3906331 ATATTAAATAATTT-TTAA
1 ATATTAAATAATTTATTAT
* *
3906349 ATGA-TAAATATTTTA-AATT
1 AT-ATTAAATAATTTATTA-T
3906368 ATATTAAATAATTTATTAT
1 ATATTAAATAATTTATTAT
3906387 ATATTA
1 ATATTA
3906393 TTTTATTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
18 13 0.38
19 20 0.59
20 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
ATATTAAATAATTTATTAT
Found at i:3906809 original size:84 final size:83
Alignment explanation
Indices: 3906684--3906850 Score: 235
Period size: 84 Copynumber: 2.0 Consensus size: 83
3906674 TATCGCAAAC
* * * * *
3906684 TTTTATGATAAGTACAAAGAGAATATCTTTTGTCAAATGTGACAAGTCTTCATGACTATGTAAAG
1 TTTTATGATAAATACAAAGAGAATATATTTTATCAAATGTGACAAGTCTTCATAACTAAGTAAAG
*
3906749 TTAAGACTAATTTAATAG
66 TTAAGACTAAATTAATAG
* * *
3906767 TTTTATGATCAAATACAAAGAGAATGTATTTTATCAAGTGTGACAAGTCTTCATAATTAAGTAAA
1 TTTTATGAT-AAATACAAAGAGAATATATTTTATCAAATGTGACAAGTCTTCATAACTAAGTAAA
*
3906832 GTTAAGATTAAATTAATAG
65 GTTAAGACTAAATTAATAG
3906851 AATAATGATC
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
83 9 0.12
84 64 0.88
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (83 bp):
TTTTATGATAAATACAAAGAGAATATATTTTATCAAATGTGACAAGTCTTCATAACTAAGTAAAG
TTAAGACTAAATTAATAG
Found at i:3912183 original size:25 final size:22
Alignment explanation
Indices: 3912155--3912201 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
3912145 TTTTTAACTC
3912155 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
3912180 AATCTAATCCTAAAAGATAATA
1 AATCTAATCCTAAAAAATAATA
3912202 CATCATCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 6 0.29
24 3 0.14
25 4 0.19
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.32
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:3914223 original size:2 final size:2
Alignment explanation
Indices: 3914216--3914247 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3914206 TTCTAAACTA
3914216 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
3914248 TTCTTTAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3914929 original size:2 final size:2
Alignment explanation
Indices: 3914922--3914948 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3914912 ATATAATTTC
3914922 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 T
3914949 GCTTCATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3917051 original size:30 final size:31
Alignment explanation
Indices: 3916981--3917075 Score: 129
Period size: 31 Copynumber: 3.1 Consensus size: 31
3916971 AAGAGTCGAG
*
3916981 GGTTACCTATGTCCTTCGAGACATATGGACA
1 GGTTACCTATGTCCTTCGGGACATATGGACA
* *
3917012 GGATACCTATGTCCTTCGGGATATATGGACA
1 GGTTACCTATGTCCTTCGGGACATATGGACA
* * *
3917043 -GTTACCTATGTTCTTCGGAACATATGGATA
1 GGTTACCTATGTCCTTCGGGACATATGGACA
3917073 GGT
1 GGT
3917076 CCTTCGGGAC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 25 0.45
31 30 0.55
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (31 bp):
GGTTACCTATGTCCTTCGGGACATATGGACA
Found at i:3920298 original size:24 final size:26
Alignment explanation
Indices: 3920257--3920365 Score: 81
Period size: 24 Copynumber: 4.5 Consensus size: 26
3920247 TTATGATTAC
* *
3920257 TACTAAT-TTTATAATATT-TTAAAT
1 TACTAATAATTATTATATTATTAAAT
3920281 TACTAATAATTATT-TATTATT-AA-
1 TACTAATAATTATTATATTATTAAAT
* *
3920304 TACTTAATAATT-TTATATTAATAATT
1 TAC-TAATAATTATTATATTATTAAAT
* * *
3920330 TATTAATAATTAGTA-ATAATTAAAT
1 TACTAATAATTATTATATTATTAAAT
*
3920355 TA-TAATTATTA
1 TACTAATAATTA
3920366 CTAATAATGA
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
23 5 0.07
24 35 0.51
25 24 0.35
26 4 0.06
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (26 bp):
TACTAATAATTATTATATTATTAAAT
Found at i:3920316 original size:21 final size:21
Alignment explanation
Indices: 3920284--3920326 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 21
3920274 TTTAAATTAC
3920284 TAATAATTATTTATTATTAATACT
1 TAATAA-T-TTTA-TATTAATACT
3920308 TAATAATTTTATATTAATA
1 TAATAATTTTATATTAATA
3920327 ATTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
23 1 0.05
24 6 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATAATTTTATATTAATACT
Found at i:3920365 original size:14 final size:15
Alignment explanation
Indices: 3920296--3920365 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 15
3920286 ATAATTATTT
3920296 ATTATTAATACTTAATA
1 ATTATTAA-A-TTAATA
*
3920313 ATT-TTATATTAATA
1 ATTATTAAATTAATA
*
3920327 ATTTATTAATAATTAGTA
1 A-TTATT-A-AATTAATA
*
3920345 ATAATTAAATT-ATA
1 ATTATTAAATTAATA
3920359 ATTATTA
1 ATTATTA
3920366 CTAATAATGA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
14 15 0.35
15 7 0.16
16 6 0.14
17 8 0.19
18 7 0.16
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (15 bp):
ATTATTAAATTAATA
Found at i:3920370 original size:24 final size:25
Alignment explanation
Indices: 3920275--3920413 Score: 92
Period size: 24 Copynumber: 5.7 Consensus size: 25
3920265 TTATAATATT
* * * *
3920275 TTAAATTACTAATAATTATTTATTA
1 TTAAATTAATAATAATTACTAATAA
* *
3920300 TTAATACTTAATAAT-TTTA-TATTAA
1 TTAA-A-TTAATAATAATTACTAATAA
* * *
3920325 -TAATTTATTAATAATTAGTAATAA
1 TTAAATTAATAATAATTACTAATAA
*
3920349 TTAAATT-ATAATTATTACTAATAA
1 TTAAATTAATAATAATTACTAATAA
* *
3920373 -TGATTTAATAATAATTACTAATAA
1 TTAAATTAATAATAATTACTAATAA
* *
3920397 TT-ATTTAATAATGATTA
1 TTAAATTAATAATAATTA
3920414 AATATTTAAA
Statistics
Matches: 90, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
22 7 0.08
23 7 0.08
24 52 0.58
25 13 0.14
26 4 0.04
27 7 0.08
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (25 bp):
TTAAATTAATAATAATTACTAATAA
Found at i:3920381 original size:11 final size:11
Alignment explanation
Indices: 3920367--3920417 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
3920357 TAATTATTAC
3920367 TAATAATGATT
1 TAATAATGATT
*
3920378 TAATAATAATT
1 TAATAATGATT
*
3920389 ACTAATAATTATT
1 --TAATAATGATT
3920402 TAATAATGATT
1 TAATAATGATT
*
3920413 AAATA
1 TAATA
3920418 TTTAAATAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
11 24 0.71
13 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (11 bp):
TAATAATGATT
Found at i:3920499 original size:22 final size:22
Alignment explanation
Indices: 3920466--3920507 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3920456 ATAGTTGAAC
3920466 TTATAACAAGTCGAATTTATAT
1 TTATAACAAGTCGAATTTATAT
3920488 TTATAA-ATAGTCGAATTTAT
1 TTATAACA-AGTCGAATTTAT
3920508 TCTTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (22 bp):
TTATAACAAGTCGAATTTATAT
Found at i:3920505 original size:16 final size:16
Alignment explanation
Indices: 3920444--3920486 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
3920434 TCAATTTAAA
3920444 TCGAATTTATAA-ATAG
1 TCGAATTTATAACA-AG
* *
3920460 TTGAACTTATAACAAG
1 TCGAATTTATAACAAG
3920476 TCGAATTTATA
1 TCGAATTTATA
3920487 TTTATAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (16 bp):
TCGAATTTATAACAAG
Done.