Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 32 of 65
Found at i:6461826 original size:24 final size:24
Alignment explanation
Indices: 6461799--6461848 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
6461789 AACAATTATA
6461799 AAAAATA-AAAAAAAAAGTAAAAAC
1 AAAAATAGAAAAAAAAA-TAAAAAC
* *
6461823 AAAAATAGAATAAAAAATAAATAC
1 AAAAATAGAAAAAAAAATAAAAAC
6461847 AA
1 AA
6461849 GTACAAGGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.12
Consensus pattern (24 bp):
AAAAATAGAAAAAAAAATAAAAAC
Found at i:6471724 original size:33 final size:33
Alignment explanation
Indices: 6471682--6471748 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
6471672 GTTATGTAGC
6471682 GTACTTCCCTTCAAAACCTCTTGAACTAAAAAG
1 GTACTTCCCTTCAAAACCTCTTGAACTAAAAAG
6471715 GTACTTCCCTTCAAAACCTCTTGAACTAAAAAG
1 GTACTTCCCTTCAAAACCTCTTGAACTAAAAAG
6471748 G
1 G
6471749 ACGACTTGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.27, G:0.10, T:0.27
Consensus pattern (33 bp):
GTACTTCCCTTCAAAACCTCTTGAACTAAAAAG
Found at i:6474412 original size:19 final size:19
Alignment explanation
Indices: 6474388--6474424 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
6474378 TAGCTGCCAC
6474388 CGGAAAATTTAGTAATGGG
1 CGGAAAATTTAGTAATGGG
6474407 CGGAAAATTTAGTAATGG
1 CGGAAAATTTAGTAATGG
6474425 CCTTCATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (19 bp):
CGGAAAATTTAGTAATGGG
Found at i:6488445 original size:44 final size:48
Alignment explanation
Indices: 6488379--6488475 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 48
6488369 TTATTTTCGT
6488379 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCAGTTAGG-TTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCAGTTAGGATTTA
* * *
6488426 TTTTT-GAAT-AA-GCATGCGAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCAGTTAGGATTTA
6488471 TTTTT
1 TTTTT
6488476 ATGGATAACA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
44 27 0.59
45 10 0.22
46 4 0.09
47 5 0.11
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (48 bp):
TTTTTCGAATAAATGCATGCGAACTAGATATCATGCAGTTAGGATTTA
Found at i:6498235 original size:22 final size:20
Alignment explanation
Indices: 6498201--6498247 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
6498191 AAGAAAAAGA
6498201 AGAAAAAATGAAAAAGGGAAG
1 AGAAAAAATGAAAAA-GGAAG
*
6498222 AGAACAAATGGAAAAAGGAAG
1 AGAAAAAAT-GAAAAAGGAAG
6498243 A-AAAA
1 AGAAAA
6498248 GAGAAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 3 0.13
21 14 0.61
22 6 0.26
ACGTcount: A:0.68, C:0.02, G:0.26, T:0.04
Consensus pattern (20 bp):
AGAAAAAATGAAAAAGGAAG
Found at i:6498275 original size:27 final size:27
Alignment explanation
Indices: 6498184--6498264 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
6498174 TGGAAAAAAC
* *
6498184 AAAAAGAAAGAAAAAGAAGAAAAAATG-
1 AAAAAGGAAGAAAAAG-AGAACAAATGA
*
6498211 AAAAAGG--G---AAGAGAACAAATGG
1 AAAAAGGAAGAAAAAGAGAACAAATGA
6498233 AAAAAGGAAGAAAAAGAGAA-AAATGA
1 AAAAAGGAAGAAAAAGAGAACAAATGA
6498259 AAAAAG
1 AAAAAG
6498265 AGAAATAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
21 9 0.20
22 10 0.22
24 1 0.02
25 1 0.02
26 11 0.24
27 13 0.29
ACGTcount: A:0.72, C:0.01, G:0.23, T:0.04
Consensus pattern (27 bp):
AAAAAGGAAGAAAAAGAGAACAAATGA
Found at i:6499467 original size:51 final size:51
Alignment explanation
Indices: 6499402--6499811 Score: 685
Period size: 51 Copynumber: 8.0 Consensus size: 51
6499392 AAGCAAATTC
6499402 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
6499453 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
6499504 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
6499555 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
6499606 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
6499657 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
* * * **
6499708 GTTCGTTGAGGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCT
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
** * * * *
6499759 GTTTATTGAATATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGAC
1 GTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
6499812 CCGTTTTATT
Statistics
Matches: 342, Mismatches: 13, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
51 309 0.90
54 2 0.01
55 31 0.09
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (51 bp):
GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
Found at i:6499849 original size:56 final size:56
Alignment explanation
Indices: 6499416--6499918 Score: 246
Period size: 51 Copynumber: 9.6 Consensus size: 56
6499406 GTTGAAGATT
* * * ** **
6499416 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
6499467 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
6499518 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
6499569 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
6499620 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** ** *
6499671 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAGGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * * * * *
6499722 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTG-TTTATTGAATATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
*
6499777 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * *
6499833 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
*
6499888 GAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGC
6499919 AGGCTCGTCA
Statistics
Matches: 419, Mismatches: 25, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
51 295 0.70
54 3 0.01
55 69 0.16
56 51 0.12
57 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (56 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
Found at i:6499919 original size:55 final size:55
Alignment explanation
Indices: 6499722--6499920 Score: 217
Period size: 55 Copynumber: 3.6 Consensus size: 55
6499712 GTTGAGGATT
* * * * * * *
6499722 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACC-TGTTTATTGAATATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGT-TTTATTGAAGATTGTTC
* *
6499777 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGA-CCGTTTTATTGAAGATTGTTC
* *
6499833 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
*
6499888 GAGTCTTATACT-TCCTGAAGGAATAGGGAGCAG
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGCAG
6499921 GCTCGTCATT
Statistics
Matches: 124, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
54 1 0.01
55 69 0.56
56 52 0.42
57 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (55 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGTTTTATTGAAGATTGTTC
Found at i:6499935 original size:55 final size:55
Alignment explanation
Indices: 6499723--6499945 Score: 186
Period size: 55 Copynumber: 4.0 Consensus size: 55
6499713 TTGAGGATTG
* * * * * * * *
6499723 AGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC-CTGT-TTATTGAATATTTTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACAC-GTATTA-TGAAGATTGTTCA
* * * *
6499778 AGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTAAAGATTGTTCA
1 AGTCT-TATACTCTCTGAAGGAATAGAGAGCAGACACGTATTA-TGAAGATTGTTCA
* * *
6499834 AGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTATGAAGATTGTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTATTATGAAGATTGTTCA
* * * *
6499889 AGTCTTATACT-TCCTGAAGGAATAGGGAGCAGGCTCGTCATT-TGAAGATTTTTCA
1 AGTCTTATACTCT-CTGAAGGAATAGAGAGCAGACACGT-ATTATGAAGATTGTTCA
6499944 AG
1 AG
6499946 AATTTATCCT
Statistics
Matches: 142, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
54 1 0.01
55 87 0.61
56 53 0.37
57 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (55 bp):
AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTATTATGAAGATTGTTCA
Found at i:6516720 original size:32 final size:32
Alignment explanation
Indices: 6516679--6516754 Score: 152
Period size: 32 Copynumber: 2.4 Consensus size: 32
6516669 ACTACCGGCA
6516679 TATTCGTTTGCATGTCATTTTAATCTTGTGTG
1 TATTCGTTTGCATGTCATTTTAATCTTGTGTG
6516711 TATTCGTTTGCATGTCATTTTAATCTTGTGTG
1 TATTCGTTTGCATGTCATTTTAATCTTGTGTG
6516743 TATTCGTTTGCA
1 TATTCGTTTGCA
6516755 GTGGAGGACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.16, C:0.13, G:0.18, T:0.53
Consensus pattern (32 bp):
TATTCGTTTGCATGTCATTTTAATCTTGTGTG
Found at i:6517600 original size:19 final size:19
Alignment explanation
Indices: 6517576--6517614 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
6517566 GCGATATGTC
*
6517576 TCGTCTTTTTTGTTTCGTT
1 TCGTCTTATTTGTTTCGTT
*
6517595 TCGTCTTATTTGTTTTGTT
1 TCGTCTTATTTGTTTCGTT
6517614 T
1 T
6517615 GTGAAGGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.03, C:0.13, G:0.15, T:0.69
Consensus pattern (19 bp):
TCGTCTTATTTGTTTCGTT
Found at i:6523574 original size:41 final size:41
Alignment explanation
Indices: 6523529--6523641 Score: 124
Period size: 41 Copynumber: 2.8 Consensus size: 41
6523519 GCGAACATAT
* ** *
6523529 AAATCGCAACGCG-ATTC-TGACTATCGCAACGAGTATCCGTA
1 AAATCGCAACGCGTATTCGT-A-AATCGCAACGACAATACGTA
6523570 AAATCGCAACGCGTATTCGTAAATCGCAACGACAATACGTA
1 AAATCGCAACGCGTATTCGTAAATCGCAACGACAATACGTA
* *
6523611 AAATCGCAACG-ATAATACGTAAATCGCAACG
1 AAATCGCAACGCGT-ATTCGTAAATCGCAACG
6523642 CGTATCTGTA
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
40 1 0.02
41 56 0.89
42 5 0.08
43 1 0.02
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
AAATCGCAACGCGTATTCGTAAATCGCAACGACAATACGTA
Found at i:6523593 original size:61 final size:61
Alignment explanation
Indices: 6523551--6523673 Score: 187
Period size: 61 Copynumber: 2.0 Consensus size: 61
6523541 GATTCTGACT
*
6523551 ATCGCAACGAGT-ATCCGTAAAATCGCAACGCGTAT-TCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGA-TAATACGT-AAATCGCAACGCGTATCT-GTAAATCGCAACGACAATACGTAAA
*
6523613 ATCGCAACGATAATACGTAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAA
1 ATCGCAACGATAATACGTAAATCGCAACGCGTATCTGTAAATCGCAACGACAATACGTAAA
6523674 TAGCAATGCG
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
61 41 0.72
62 16 0.28
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.20
Consensus pattern (61 bp):
ATCGCAACGATAATACGTAAATCGCAACGCGTATCTGTAAATCGCAACGACAATACGTAAA
Found at i:6523595 original size:20 final size:20
Alignment explanation
Indices: 6523551--6523721 Score: 150
Period size: 20 Copynumber: 8.4 Consensus size: 20
6523541 GATTCTGACT
* *
6523551 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATACGT-AA
*
6523572 ATCGCAACGCGTATTCGTAA
1 ATCGCAACGCGTATACGTAA
*
6523592 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATACGT-AA
*
6523613 ATCGCAACG-ATAATACGTAA
1 ATCGCAACGCGT-ATACGTAA
6523633 ATCGCAACGCGTAT-CTGTAA
1 ATCGCAACGCGTATAC-GTAA
* *
6523653 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATACGTAA
* * *
6523673 ATAGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATACGTAA
* * *
6523693 ATTGCAATGCGAATACGTAA
1 ATCGCAACGCGTATACGTAA
*
6523713 ATCGTAACG
1 ATCGCAACG
6523722 TGATTTTTAA
Statistics
Matches: 124, Mismatches: 19, Indels: 15
0.78 0.12 0.09
Matches are distributed among these distances:
19 1 0.01
20 87 0.70
21 36 0.29
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGTATACGTAA
Found at i:6523668 original size:40 final size:41
Alignment explanation
Indices: 6523551--6523721 Score: 186
Period size: 40 Copynumber: 4.2 Consensus size: 41
6523541 GATTCTGACT
* * * *
6523551 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATTCGTAA
1 ATCGCAACGCGTATCCGTAAAATCGCAACGAGAATACGTAA
* * *
6523592 ATCGCAACGAC-AATACGTAAAATCGCAACGATAATACGTAA
1 ATCGCAACG-CGTATCCGTAAAATCGCAACGAGAATACGTAA
*
6523633 ATCGCAACGCGTATCTGT-AAATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAAATCGCAACGAGAATACGTAA
* * * * *
6523673 ATAGCAATGCGTATCCGT-AAATTGCAATGCGAATACGTAA
1 ATCGCAACGCGTATCCGTAAAATCGCAACGAGAATACGTAA
*
6523713 ATCGTAACG
1 ATCGCAACG
6523722 TGATTTTTAA
Statistics
Matches: 108, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
40 62 0.57
41 46 0.43
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGTATCCGTAAAATCGCAACGAGAATACGTAA
Found at i:6524363 original size:21 final size:20
Alignment explanation
Indices: 6524285--6524360 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
6524275 TTCTAAACTT
*
6524285 AAAATCGCAACATGAAAATG
1 AAAATCGCAACAAGAAAATG
* *
6524305 AAAATCGTAACACGAAAATG
1 AAAATCGCAACAAGAAAATG
** * *
6524325 ACTATCACAACGAGAGAAATG
1 AAAATCGCAACAAGA-AAATG
6524346 AAAATCGCAACAAGA
1 AAAATCGCAACAAGA
6524361 GAATCGCAAC
Statistics
Matches: 43, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.54, C:0.17, G:0.16, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACAAGAAAATG
Found at i:6524377 original size:33 final size:33
Alignment explanation
Indices: 6524340--6524420 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
6524330 CACAACGAGA
6524340 GAAATGAAAATCGCAACAAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACAAGAGAATCGCAACGC
* * *
6524373 GAAATGAAAATCGCAACGAGATAATCGCAATGC
1 GAAATGAAAATCGCAACAAGAGAATCGCAACGC
**
6524406 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
6524421 TTGCGATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.48, C:0.21, G:0.20, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACAAGAGAATCGCAACGC
Found at i:6524438 original size:19 final size:19
Alignment explanation
Indices: 6524416--6524561 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
6524406 GAAACCAAAA
*
6524416 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
6524435 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
6524454 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
6524468 TCTCGTTGCGGTTTTCATT
1 TCGCGTTGCGATTTTCATT
6524487 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
6524501 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
6524520 TACGCGTTGTGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
* *
6524540 CTCTCGTTGCAATTTTCATT
1 -TCGCGTTGCGATTTTCATT
6524560 TC
1 TC
6524562 AACCAAAAGA
Statistics
Matches: 99, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
14 19 0.19
16 5 0.05
17 5 0.05
19 40 0.40
20 29 0.29
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:6524488 original size:33 final size:33
Alignment explanation
Indices: 6524438--6524533 Score: 138
Period size: 33 Copynumber: 2.9 Consensus size: 33
6524428 TTTCATTTCG
*
6524438 CGTTGCGATTTTAATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
6524471 CGTTGCGGTTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
** *
6524504 CGTTGCGATAGTCATTTACGCGTTGTGATT
1 CGTTGCGATTTTCATTT-CGCGTTGCGATT
6524534 TTCATTCTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
33 45 0.80
34 11 0.20
ACGTcount: A:0.11, C:0.21, G:0.24, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:6524547 original size:20 final size:20
Alignment explanation
Indices: 6524421--6524559 Score: 67
Period size: 20 Copynumber: 7.7 Consensus size: 20
6524411 CAAAATCGCA
*
6524421 TTGCGATTTTCATT-TCGCG
1 TTGCGATTTTCATTCTCTCG
* *
6524440 TTGCGATTTTAATT-TCGCG
1 TTGCGATTTTCATTCTCTCG
6524459 TTGCG------ATTCTCTCG
1 TTGCGATTTTCATTCTCTCG
* *
6524473 TTGCGGTTTTCATT-TCGCG
1 TTGCGATTTTCATTCTCTCG
6524492 TTGCG------ATTCTCTCG
1 TTGCGATTTTCATTCTCTCG
** *
6524506 TTGCGATAGTCATT-TACGCG
1 TTGCGATTTTCATTCT-CTCG
*
6524526 TTGTGATTTTCATTCTCTCG
1 TTGCGATTTTCATTCTCTCG
*
6524546 TTGCAATTTTCATT
1 TTGCGATTTTCATT
6524560 TCAACCAAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 31
0.69 0.08 0.23
Matches are distributed among these distances:
13 6 0.06
14 18 0.19
19 33 0.35
20 35 0.38
21 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (20 bp):
TTGCGATTTTCATTCTCTCG
Found at i:6526419 original size:94 final size:94
Alignment explanation
Indices: 6526258--6526637 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
6526248 TAGATTGCTT
* *
6526258 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
6526323 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
* *
6526352 AGTAAATTTATTCGGTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
6526417 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
6526446 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
6526511 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
6526540 AGTAAATTTGTTCAGTTGTTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
6526605 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
6526633 AGTAA
1 AGTAA
6526638 TGCAATCCAT
Statistics
Matches: 272, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
93 26 0.10
94 246 0.90
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:6526741 original size:19 final size:19
Alignment explanation
Indices: 6526728--6526804 Score: 92
Period size: 19 Copynumber: 4.3 Consensus size: 19
6526718 AATGACTATT
6526728 GCAACGCGAAATGAAATTC
1 GCAACGCGAAATGAAATTC
*
6526747 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAATTC
*
6526766 GCAA--CGAGA-G-AA-TC
1 GCAACGCGAAATGAAATTC
*
6526780 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAATTC
6526799 GCAACG
1 GCAACG
6526805 AAAAAATCGC
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
14 6 0.12
15 2 0.04
16 5 0.10
17 5 0.10
18 2 0.04
19 30 0.60
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
GCAACGCGAAATGAAATTC
Found at i:6526812 original size:14 final size:14
Alignment explanation
Indices: 6526760--6526818 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
6526750 ACGCGAAATG
*
6526760 AAAATCGCAACGAG
1 AAAATCGCAACGAA
*
6526774 AGAATCGCAACGCGAAA
1 AAAATCGCAA--CG-AA
6526791 TGAAAATCGCAACGAA
1 --AAAATCGCAACGAA
6526807 AAAATCGCAACG
1 AAAATCGCAACG
6526819 TGAAACTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 21 0.57
16 4 0.11
17 3 0.08
19 9 0.24
ACGTcount: A:0.49, C:0.22, G:0.20, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:6526833 original size:33 final size:33
Alignment explanation
Indices: 6526745--6526823 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
6526735 GAAATGAAAT
* *
6526745 TCGCAACGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAAAA
6526778 TCGCAACGCGAAATGAAAATCGCAACGAAAAAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAAAA
*
6526811 TCGCAACGTGAAA
1 TCGCAACGCGAAA
6526824 CTATAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.10
Consensus pattern (33 bp):
TCGCAACGCGAAATGAAAATCGCAACGAAAAAA
Found at i:6526920 original size:19 final size:19
Alignment explanation
Indices: 6526830--6526912 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
6526820 GAAACTATAA
*
6526830 TCGCGTTGCAATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
6526849 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
6526863 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
6526882 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
6526901 TCGCGTTGCGAT
1 TCGCGTTGCGAT
6526913 AGTCATTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
14 9 0.17
16 3 0.06
17 3 0.06
19 39 0.72
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:6530354 original size:24 final size:24
Alignment explanation
Indices: 6530327--6530380 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
6530317 TTGAAAAAAC
6530327 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
6530351 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
6530375 ATCAAA
1 ATCAAA
6530381 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:6531144 original size:20 final size:19
Alignment explanation
Indices: 6531121--6531450 Score: 338
Period size: 20 Copynumber: 16.5 Consensus size: 19
6531111 CATAATCTCG
6531121 TTGCGATTTACAGATTCGCA
1 TTGCGATTTAC-GATTCGCA
6531141 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACG-ATTCGCA
*
6531161 TTACGATTTACGTATTCGCA
1 TTGCGATTTACG-ATTCGCA
6531181 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACG-ATTCGCA
6531201 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACG-ATTCGCA
6531221 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACG-ATTCGCA
6531241 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACG-ATTCGCA
*
6531261 TTGCGATTTACGGATACGCA
1 TTGCGATTTAC-GATTCGCA
6531281 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACG-ATTCGCA
*
6531301 TTGCGATTTACGGATACGCA
1 TTGCGATTTAC-GATTCGCA
* * * *
6531321 TTGCAATTTATGTATTCTCG
1 TTGCGATTTACG-ATTCGCA
*
6531341 TTGCGATTTACAGATACGCA
1 TTGCGATTTAC-GATTCGCA
* * *
6531361 TTGCGATTTACTTATTCTCG
1 TTGCGATTTAC-GATTCGCA
* * *
6531381 TTGCGATTTATGGATACGCG
1 TTGCGATTTA-CGATTCGCA
*
6531401 TTGCGATTTTACGTATT-GTCG
1 TTGCGA-TTTACG-ATTCG-CA
* *
6531422 TTGCGATTTACGGATACGCG
1 TTGCGATTTAC-GATTCGCA
6531442 TTGCGATTT
1 TTGCGATTT
6531451 TACGGATACT
Statistics
Matches: 271, Mismatches: 27, Indels: 24
0.84 0.08 0.07
Matches are distributed among these distances:
19 3 0.01
20 249 0.92
21 19 0.07
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (19 bp):
TTGCGATTTACGATTCGCA
Found at i:6531146 original size:40 final size:40
Alignment explanation
Indices: 6531121--6531450 Score: 414
Period size: 40 Copynumber: 8.2 Consensus size: 40
6531111 CATAATCTCG
6531121 TTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTAC-GTATTCGCATTGCGATTTACGTATTCGCA
*
6531161 TTACGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
6531201 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
* *
6531241 TTGCGATTTACGTATTCGCATTGCGATTTACGGATACGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
* *
6531281 TTGCGATTTACGTATTCGCATTGCGATTTACGGATACGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
* * * * *
6531321 TTGCAATTTATGTATTCTCGTTGCGATTTACAG-ATACGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTAC-GTATTCGCA
* * * * * * *
6531361 TTGCGATTTACTTATTCTCGTTGCGATTTATGGATACGCG
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
* * * *
6531401 TTGCGATTTTACGTATT-GTCGTTGCGATTTACGGATACGCG
1 TTGCGA-TTTACGTATTCG-CATTGCGATTTACGTATTCGCA
6531442 TTGCGATTT
1 TTGCGATTT
6531451 TACGGATACT
Statistics
Matches: 269, Mismatches: 16, Indels: 10
0.91 0.05 0.03
Matches are distributed among these distances:
39 2 0.01
40 230 0.86
41 37 0.14
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (40 bp):
TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
Found at i:6531198 original size:60 final size:60
Alignment explanation
Indices: 6531121--6531450 Score: 414
Period size: 60 Copynumber: 5.5 Consensus size: 60
6531111 CATAATCTCG
*
6531121 TTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCGCATTACGATTTACGTATTCGCA
1 TTGCGATTTAC-GTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
6531181 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
* *
6531241 TTGCGATTTACGTATTCGCATTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
* * * * * * *
6531301 TTGCGATTTACGGATACGCATTGCAATTTATGTATTCTCGTTGCGATTTACAG-ATACGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTAC-GTATTCGCA
* * * * * * * *
6531361 TTGCGATTTACTTATTCTCGTTGCGATTTATGGATACGCGTTGCGATTTTACGTATT-GTCG
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGA-TTTACGTATTCG-CA
* * *
6531422 TTGCGATTTACGGATACGCGTTGCGATTT
1 TTGCGATTTACGTATTCGCATTGCGATTT
6531451 TACGGATACT
Statistics
Matches: 238, Mismatches: 27, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
59 1 0.00
60 203 0.85
61 34 0.14
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (60 bp):
TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
Found at i:6531483 original size:41 final size:41
Alignment explanation
Indices: 6531181--6531491 Score: 152
Period size: 40 Copynumber: 7.7 Consensus size: 41
6531171 CGTATTCGCA
* * * * * * * *
6531181 TTGCGATTTACGTATTCGCATTGCGA-TTTACGTATTCGCA
1 TTGCGATTCACGAATACGCGTTGCGATTTTACGGATACTCG
* * * * * * * *
6531221 TTGCGATTTACGTATTCGCATTGCGA-TTTACGTATTCGCA
1 TTGCGATTCACGAATACGCGTTGCGATTTTACGGATACTCG
* * * * * * *
6531261 TTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCGCA
1 TTGCGATTCACGAATACGCGTTGCGATTTTACGGATACTCG
* * * * * * *
6531301 TTGCGATTTACGGATACGCATTGC-AATTTATGTATTCTCG
1 TTGCGATTCACGAATACGCGTTGCGATTTTACGGATACTCG
* * ** *
6531341 TTGCGATTTAC-AGATACGCATTGCGA-TTTACTTATTCTCG
1 TTGCGATTCACGA-ATACGCGTTGCGATTTTACGGATACTCG
* * * * **
6531381 TTGCGATTTATGGATACGCGTTGCGATTTTACGTATTGTCG
1 TTGCGATTCACGAATACGCGTTGCGATTTTACGGATACTCG
* *
6531422 TTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCG
1 TTGCGATTCACGAATACGCGTTGCGATTTTACGGATACTCG
6531463 TTGCGATAGTCA-GAAT-CGCGTTGCGATTT
1 TTGCGAT--TCACGAATACGCGTTGCGATTT
6531492 ATATGTTCGC
Statistics
Matches: 245, Mismatches: 19, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.00
40 169 0.69
41 70 0.29
42 3 0.01
43 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (41 bp):
TTGCGATTCACGAATACGCGTTGCGATTTTACGGATACTCG
Found at i:6531501 original size:20 final size:20
Alignment explanation
Indices: 6531478--6531532 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
6531468 ATAGTCAGAA
*
6531478 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
6531498 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
6531518 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
6531533 GGAAAATTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.13, C:0.18, G:0.24, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:6531616 original size:20 final size:19
Alignment explanation
Indices: 6531567--6531620 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
6531557 ATTCTTCATA
6531567 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
6531586 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
6531607 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
6531621 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:6533383 original size:18 final size:18
Alignment explanation
Indices: 6533357--6533412 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
6533347 ATTCGTCATG
*
6533357 AGATGAAGACTTAAGCAA
1 AGATAAAGACTTAAGCAA
* *
6533375 AGATAAAGACTCAAGAAA
1 AGATAAAGACTTAAGCAA
* *
6533393 AGATAAGGAC-TCAGCAA
1 AGATAAAGACTTAAGCAA
6533410 AGA
1 AGA
6533413 GAATGAAGCA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 7 0.23
18 24 0.77
ACGTcount: A:0.54, C:0.12, G:0.21, T:0.12
Consensus pattern (18 bp):
AGATAAAGACTTAAGCAA
Found at i:6533424 original size:14 final size:15
Alignment explanation
Indices: 6533405--6533433 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6533395 ATAAGGACTC
6533405 AGCAAAGA-GAATGA
1 AGCAAAGATGAATGA
6533419 AGCAAAGATGAATGA
1 AGCAAAGATGAATGA
6533434 GACAGTGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.07, G:0.28, T:0.10
Consensus pattern (15 bp):
AGCAAAGATGAATGA
Found at i:6534356 original size:21 final size:21
Alignment explanation
Indices: 6534330--6534386 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
6534320 TAGGATGAAC
6534330 AATATCGATACTGATGCAATT
1 AATATCGATACTGATGCAATT
*
6534351 AGTATCGATACTGATGCAATT
1 AATATCGATACTGATGCAATT
6534372 AATATCGATACTGAT
1 AATATCGATACTGAT
6534387 ATGGGTATCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (21 bp):
AATATCGATACTGATGCAATT
Found at i:6534916 original size:54 final size:54
Alignment explanation
Indices: 6534845--6535144 Score: 528
Period size: 54 Copynumber: 5.6 Consensus size: 54
6534835 GCACTATGTT
*
6534845 TGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTGTATG
1 TGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTGTATG
*
6534899 TGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTGTATA
1 TGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTGTATG
* *
6534953 TGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTGTGTG
1 TGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTGTATG
*
6535007 TGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTGTATG
1 TGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTGTATG
*
6535061 TGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTGTGTG
1 TGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTGTATG
* *
6535115 TGCAACTTAATAAATTCATAATGAGTTTAT
1 TGCAACTTAAGAAATTCATAATAAGTTTAT
6535145 AACTGGTAAT
Statistics
Matches: 236, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 236 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (54 bp):
TGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTGTATG
Found at i:6536633 original size:116 final size:116
Alignment explanation
Indices: 6536297--6536861 Score: 649
Period size: 116 Copynumber: 4.9 Consensus size: 116
6536287 AGTAGAAGGA
* *
6536297 TTCATAATGAGAAGAACTCATCCAACGAAGGGGAAGAAGTTCATAATGAGAAGAACTTGTTCAGA
1 TTCATAATGAGAAGAACTCATCCAACAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAGA
* * *
6536362 ACTTGACACATCAATCAT-ACAAGGAGGTGGATCAACATTTTTGAGGAA-TGG
66 ACTCGACACATCCATC-TCACAAGGAGGTGGATCAACATTTCTGAGGAAGT-G
* * * * * *
6536413 TTCATAATGAGAAAAACTCATCCAAC-GAGGGGAA-AATATTCATAATGAGAATAACTTGTTTAG
1 TTCATAATGAGAAGAACTCATCCAACAAAGGAGAAGAA-GTTCATAATGAGAAGAACTTGTTCAG
* * ** *
6536476 AACTCAACACATCCATCGCACAATAAGGTGGATCAAAATTTCTGAGGAAGTG
65 AACTCGACACATCCATCTCACAAGGAGGTGGATCAACATTTCTGAGGAAGTG
* * * *
6536528 TTCATAATGAGAAGAACTCACCCAACAAAAGAGAAGAAGTTCATAATGAGAAGAACATGTTCATA
1 TTCATAATGAGAAGAACTCATCCAACAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAGA
* * * * *
6536593 ACTCGATATATCCATCTCATAATGAGGTAGATCAACATTTCTGAGGAAG-G
66 ACTCGACACATCCATCTCACAAGGAGGTGGATCAACATTTCTGAGGAAGTG
** ** * *
6536643 TTTCATAATGAGAAGAACTCATGAAATGAGGGAGAAGAAGTTCATAATGGGAAGAACTTGTTCAG
1 -TTCATAATGAGAAGAACTCATCCAACAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAG
* * *
6536708 AACTCGACACATCCATCGCACAAGGAGGTGGATCAACATTTATGAGGAAATG
65 AACTCGACACATCCATCTCACAAGGAGGTGGATCAACATTTCTGAGGAAGTG
* * * **
6536760 TTCATAATGAGAAGAACTCATCTAA-AGAGGGAGAAGAAGTTTATAACAAGAAGAACTTGTTCAG
1 TTCATAATGAGAAGAACTCATCCAACA-AAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAG
** *
6536824 AACTCGGTACATCCAT-TACACAAAGAGGTGGATCAACA
65 AACTCGACACATCCATCT-CACAAGGAGGTGGATCAACA
6536862 AAGAGTTCGT
Statistics
Matches: 380, Mismatches: 60, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
114 2 0.01
115 96 0.25
116 279 0.73
117 3 0.01
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (116 bp):
TTCATAATGAGAAGAACTCATCCAACAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAGA
ACTCGACACATCCATCTCACAAGGAGGTGGATCAACATTTCTGAGGAAGTG
Found at i:6536778 original size:232 final size:231
Alignment explanation
Indices: 6536297--6536861 Score: 726
Period size: 232 Copynumber: 2.4 Consensus size: 231
6536287 AGTAGAAGGA
* *
6536297 TTCATAATGAGAAGAACTCATCCAACGAAGGGGAAGAAGTTCATAATGAGAAGAACTTGTTCAGA
1 TTCATAATGAGAAGAACTCATCCAACAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAGA
* * * * *
6536362 ACTTGACACATCAATCAT-ACAAGGAGGTGGATCAACATTTTTGAGGAATGGTTCATAATGAGAA
66 ACTCGATACATCCATC-TCACAAAGAGGTGGATCAACATTTCTGAGGAATGGTTCATAATGAGAA
* * *
6536426 AAACTCATCCAACGAGGGGAAAATATTCATAATGAGAATAACTTGTTTAGAACTCAACACATCCA
130 AAACTCATCAAACGAGGGGAAAATATTCATAATGAGAAGAACTTGTTCAGAACTCAACACATCCA
* * *
6536491 TCGCACAATAAGGTGGATCAAAATTTCTGAGGAAGTG
195 TCGCACAAGAAGGTGGATCAAAATTTATGAGGAAATG
* * * *
6536528 TTCATAATGAGAAGAACTCACCCAACAAAAGAGAAGAAGTTCATAATGAGAAGAACATGTTCATA
1 TTCATAATGAGAAGAACTCATCCAACAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAGA
* * * *
6536593 ACTCGATATATCCATCTCATAATGAGGTAGATCAACATTTCTGAGGAA-GGTTTCATAATGAGAA
66 ACTCGATACATCCATCTCACAAAGAGGTGGATCAACATTTCTGAGGAATGG-TTCATAATGAGAA
* * * * * *
6536657 GAACTCATGAAATGAGGGAGAAGAA-GTTCATAATGGGAAGAACTTGTTCAGAACTCGACACATC
130 AAACTCATCAAACGAGGG-GAA-AATATTCATAATGAGAAGAACTTGTTCAGAACTCAACACATC
* *
6536721 CATCGCACAAGGAGGTGGATCAACATTTATGAGGAAATG
193 CATCGCACAAGAAGGTGGATCAAAATTTATGAGGAAATG
* * * **
6536760 TTCATAATGAGAAGAACTCATCTAA-AGAGGGAGAAGAAGTTTATAACAAGAAGAACTTGTTCAG
1 TTCATAATGAGAAGAACTCATCCAACA-AAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAG
*
6536824 AACTCGGTACATCCAT-TACACAAAGAGGTGGATCAACA
65 AACTCGATACATCCATCT-CACAAAGAGGTGGATCAACA
6536862 AAGAGTTCGT
Statistics
Matches: 286, Mismatches: 42, Indels: 11
0.84 0.12 0.03
Matches are distributed among these distances:
230 3 0.01
231 126 0.44
232 155 0.54
233 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (231 bp):
TTCATAATGAGAAGAACTCATCCAACAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAGA
ACTCGATACATCCATCTCACAAAGAGGTGGATCAACATTTCTGAGGAATGGTTCATAATGAGAAA
AACTCATCAAACGAGGGGAAAATATTCATAATGAGAAGAACTTGTTCAGAACTCAACACATCCAT
CGCACAAGAAGGTGGATCAAAATTTATGAGGAAATG
Found at i:6538625 original size:2 final size:2
Alignment explanation
Indices: 6538618--6538642 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6538608 ATTTGCGTGC
6538618 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
6538643 ATGTATACTC
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:6540508 original size:21 final size:21
Alignment explanation
Indices: 6540460--6540517 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
6540450 ACTCTCATTT
*
6540460 TGAATATCGAT-CTTCTATGA
1 TGAATATCGATACTACTATGA
6540480 -GAAATATCGATACTACTAT-A
1 TG-AATATCGATACTACTATGA
*
6540500 TGAAGTATCGATAATACT
1 TGAA-TATCGATACTACT
6540518 TCCTATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 1 0.03
20 12 0.38
21 19 0.59
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (21 bp):
TGAATATCGATACTACTATGA
Found at i:6542519 original size:30 final size:29
Alignment explanation
Indices: 6542480--6542538 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
6542470 GAGAATTTAC
* *
6542480 ATGAACTACGTGATTACATGTATATGTGA
1 ATGAACTACGAGATTACATGAATATGTGA
* *
6542509 ATGAAGCTACGAGTTTATATGAATATGTGA
1 ATGAA-CTACGAGATTACATGAATATGTGA
6542539 TATGTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGAACTACGAGATTACATGAATATGTGA
Found at i:6542786 original size:45 final size:46
Alignment explanation
Indices: 6542737--6542835 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 46
6542727 CTTAAGGAAT
* *
6542737 TTTCTACGTGGTC-CTTAGGGAC-A-TCTTATATGGCACTTCGGTGCA
1 TTTCTACGCGG-CACTTAGGGACAATTC-TACATGGCACTTCGGTGCA
* *
6542782 TTTCTACGCGGCACTTAGGTACAATTCTACGTGGCACTTCGGTGCA
1 TTTCTACGCGGCACTTAGGGACAATTCTACATGGCACTTCGGTGCA
*
6542828 TTTATACG
1 TTTCTACG
6542836 AGCTGTGGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
44 1 0.02
45 18 0.39
46 25 0.54
47 2 0.04
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (46 bp):
TTTCTACGCGGCACTTAGGGACAATTCTACATGGCACTTCGGTGCA
Found at i:6542835 original size:23 final size:23
Alignment explanation
Indices: 6542767--6542835 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
6542757 ACATCTTATA
6542767 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * * *
6542790 CGGCACTTAGGTACAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
6542813 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
6542836 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:6543223 original size:2 final size:2
Alignment explanation
Indices: 6543216--6543264 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
6543206 ATGCAATAAG
6543216 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6543258 TA TA TA T
1 TA TA TA T
6543265 GTTTAGATGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6544559 original size:22 final size:21
Alignment explanation
Indices: 6544510--6544589 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 21
6544500 AATAAGATTA
6544510 CCCAGGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
* *
6544531 CCCAGGGGTTACCGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
* * *
6544552 CCCAAGGGGAACATA-T-CCC
1 CCCAGGGGGTACAGATTCCCC
* *
6544571 CCTAGGGGGTACCGATTCC
1 CCCAGGGGGTACAGATTCC
6544590 TCCCTGTCTA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
19 13 0.29
20 2 0.04
21 30 0.67
ACGTcount: A:0.20, C:0.38, G:0.26, T:0.16
Consensus pattern (21 bp):
CCCAGGGGGTACAGATTCCCC
Found at i:6544980 original size:34 final size:32
Alignment explanation
Indices: 6544941--6545010 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 32
6544931 TTTTGTAAAG
*
6544941 GGGAAA-GATTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAATG-TTCTAGCTTAGCCCG-G-AAAAACTA
*
6544975 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAATGTTCTAGCTTAGCCCGGAAAAACTA
6545007 GGGA
1 GGGA
6545011 GTTAGTAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 20 0.61
35 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (32 bp):
GGGAAATGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:6546004 original size:15 final size:14
Alignment explanation
Indices: 6545982--6546025 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
6545972 GATGATGGTG
6545982 AAGGAAGATGAAGAA
1 AAGGAAGA-GAAGAA
*
6545997 AGGGAAGAGAAGAA
1 AAGGAAGAGAAGAA
*
6546011 AAGCAAGAAGAAGAA
1 AAGGAAG-AGAAGAA
6546026 GAATGAGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.61, C:0.02, G:0.34, T:0.02
Consensus pattern (14 bp):
AAGGAAGAGAAGAA
Found at i:6547996 original size:21 final size:21
Alignment explanation
Indices: 6547967--6548027 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
6547957 AATCAGATTG
*
6547967 CCCATGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
*
6547988 CCCAGGGGGAACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
* *
6548009 CCCAGGGAGTACCGATTCC
1 CCCAGGGGGTACAGATTCC
6548028 TCCCTGTCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (21 bp):
CCCAGGGGGTACAGATTCCCC
Found at i:6548420 original size:34 final size:32
Alignment explanation
Indices: 6548381--6548450 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 32
6548371 TTTTGTAAAG
*
6548381 GGGAAA-GATTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAATG-TTCTAGCTTAGCCCG-G-AAAAACTA
*
6548415 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAATGTTCTAGCTTAGCCCGGAAAAACTA
6548447 GGGA
1 GGGA
6548451 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 20 0.61
35 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (32 bp):
GGGAAATGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:6552285 original size:30 final size:29
Alignment explanation
Indices: 6552246--6552304 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
6552236 GAGAATTTAC
* *
6552246 ATGAACTACGTGATTACATGTATATGTGA
1 ATGAACTACGAGATTACATGAATATGTGA
* *
6552275 ATGAAGCTACGAGTTTATATGAATATGTGA
1 ATGAA-CTACGAGATTACATGAATATGTGA
6552305 TACGTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGAACTACGAGATTACATGAATATGTGA
Found at i:6552562 original size:23 final size:23
Alignment explanation
Indices: 6552535--6552602 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
6552525 CATTTTATAT
6552535 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * **
6552558 GGCACTTAGGTGCAATTCTACAT
1 GGCACTTCGGTGCATTTCTACGC
*
6552581 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
6552603 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:6557815 original size:23 final size:23
Alignment explanation
Indices: 6557789--6557833 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6557779 CACCACAGCT
*
6557789 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
6557812 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
6557834 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:6566814 original size:75 final size:74
Alignment explanation
Indices: 6566722--6567098 Score: 374
Period size: 75 Copynumber: 5.0 Consensus size: 74
6566712 TAAAATATAT
* * * *
6566722 ATACATTTCGAAAATATATATATTATATAGTTTTGAAAA-ATTTTGAAAACATATATAATGTATA
1 ATAC-TTTAGAAAATATATATAATATATAGTTTTAAAAACATTTTGAAAACATATATAATATATA
6566786 GTTTTTGAAA
65 GTTTTTGAAA
* * **
6566796 ATGCTTGAGAAAATATATATAATATATAGTTTTAAAAATCATTTTGAAAATTTATATAATATATA
1 ATACTTTAGAAAATATATATAATATATAGTTTTAAAAA-CATTTTGAAAACATATATAATATATA
*
6566861 GTTTTGGAAA
65 GTTTTTGAAA
* * * *
6566871 CAT--TTTTGAAAATTTATACAATATATAGTTTTAAAAACATTTTGAAAACATTTATATATTATA
1 -ATACTTTAGAAAATATATATAATATATAGTTTTAAAAACATTTTGAAAACA--TATATAATATA
6566934 TAGTTTTT-AAA
63 TAGTTTTTGAAA
* * *
6566945 A-ACATTTTGAAAATATATATAATATATAGTTTTTTTAAAACATTTTTG-AAA-ATATATATTAT
1 ATAC-TTTAGAAAATATATATAATATATAG--TTTTAAAAACA-TTTTGAAAACATATATAATAT
*
6567007 ATAGTTTTTTAAA
62 ATAGTTTTTGAAA
* * * * ** *
6567020 ACATTTTAGAAAATACATATAATATATAGTTTTTAAAAAAACATTTTGGAAATTTATATATTATA
1 ATACTTTAGAAAATATATATAATATATAG-TTTT--AAAAACATTTTGAAAACATATATAATATA
6567085 T-GTTTTTGAAA
63 TAGTTTTTGAAA
6567096 ATA
1 ATA
6567099 TTTTTATATA
Statistics
Matches: 259, Mismatches: 27, Indels: 32
0.81 0.08 0.10
Matches are distributed among these distances:
73 42 0.16
74 60 0.23
75 103 0.40
76 24 0.09
77 25 0.10
78 5 0.02
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (74 bp):
ATACTTTAGAAAATATATATAATATATAGTTTTAAAAACATTTTGAAAACATATATAATATATAG
TTTTTGAAA
Found at i:6566845 original size:37 final size:37
Alignment explanation
Indices: 6566724--6567118 Score: 391
Period size: 37 Copynumber: 10.7 Consensus size: 37
6566714 AAATATATAT
* * *
6566724 ACATTTCGAAAATATATATATTATATAG-TTTTGAAA
1 ACATTTTGAAAATATATATAATATATAGTTTTTAAAA
* *
6566760 A-ATTTTGAAAACATATATAATGTATAGTTTTTGAAAA
1 ACATTTTGAAAATATATATAATATATAGTTTTT-AAAA
* **
6566797 TGC-TTGAGAAAATATATATAATATATAG-TTTTAAAA
1 -ACATTTTGAAAATATATATAATATATAGTTTTTAAAA
* **
6566833 ATCATTTTGAAAATTTATATAATATATAG-TTTTGGAA
1 A-CATTTTGAAAATATATATAATATATAGTTTTTAAAA
* *
6566870 ACATTTTTGAAAATTTATACAATATATAG-TTTTAAAA
1 ACA-TTTTGAAAATATATATAATATATAGTTTTTAAAA
* *
6566907 ACATTTTGAAAACATTTATATATTATATAGTTTTTAAAA
1 ACATTTTG-AAA-ATATATATAATATATAGTTTTTAAAA
*
6566946 ACATTTTGAAAATATATATAATATATAGTTTTTTTAAA
1 ACATTTTGAAAATATATATAATATATAG-TTTTTAAAA
*
6566984 ACATTTTTGAAAATATATAT--TATATAGTTTTTTAAA
1 ACA-TTTTGAAAATATATATAATATATAGTTTTTAAAA
*
6567020 ACATTTTAGAAAATACATATAATATATAGTTTTTAAAAAA
1 ACATTTT-GAAAATATATATAATATATAGTTTTT--AAAA
* * * *
6567060 ACATTTTGGAAATTTATATATTATAT-GTTTTTGAAA
1 ACATTTTGAAAATATATATAATATATAGTTTTTAAAA
* *
6567096 ATATTTT---TATATATATAATATAT
1 ACATTTTGAAAATATATATAATATAT
6567119 TATTATTATT
Statistics
Matches: 307, Mismatches: 35, Indels: 37
0.81 0.09 0.10
Matches are distributed among these distances:
33 13 0.04
35 26 0.08
36 49 0.16
37 94 0.31
38 68 0.22
39 47 0.15
40 10 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (37 bp):
ACATTTTGAAAATATATATAATATATAGTTTTTAAAA
Found at i:6566934 original size:112 final size:110
Alignment explanation
Indices: 6566724--6567118 Score: 430
Period size: 112 Copynumber: 3.6 Consensus size: 110
6566714 AAATATATAT
* * * *
6566724 ACATTTCGAAAATATATATATTATATAG-TTTTGAAA-AATTTTGAAAACATATATAATGTATAG
1 ACATTTTGAAAATATATATAATATATAGTTTTTGAAACATTTTTG-AAA-ATATATAATATATAG
* *
6566787 TTTTTGAAA-ATGCTTGAGAAAATATATATAATATATAG-TTTTAAAA
64 TTTTTAAAACAT-TTTGAGAAAATATATATAATATATAGTTTTTAAAA
* * *
6566833 ATCATTTTGAAAATTTATATAATATATAGTTTTGGAAACATTTTTGAAAATTTATACAATATATA
1 A-CATTTTGAAAATATATATAATATATAGTTTTTGAAACATTTTTGAAAA--TATATAATATATA
* * *
6566898 GTTTTAAAAACATTTTGA-AAACATTTATATATTATATAGTTTTTAAAA
63 GTTTTTAAAACATTTTGAGAAA-ATATATATAATATATAGTTTTTAAAA
* *
6566946 ACATTTTGAAAATATATATAATATATAGTTTTTTTAAAACATTTTTGAAAATATATATTATATAG
1 ACATTTTGAAAATATATATAATATATAG--TTTTTGAAACATTTTTGAAAATATATAATATATAG
*
6567011 TTTTTTAAAACATTTT-AGAAAATACATATAATATATAGTTTTTAAAAAA
64 -TTTTTAAAACATTTTGAGAAAATATATATAATATATAGTTTTT--AAAA
* * * * *
6567060 ACATTTTGGAAATTTATATATTATAT-GTTTTTGAAA-ATATTTT-TATATATATAATATAT
1 ACATTTTGAAAATATATATAATATATAGTTTTTGAAACAT-TTTTGAAAATATATAATATAT
6567119 TATTATTATT
Statistics
Matches: 243, Mismatches: 28, Indels: 29
0.81 0.09 0.10
Matches are distributed among these distances:
109 1 0.00
110 40 0.16
111 25 0.10
112 102 0.42
113 29 0.12
114 46 0.19
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (110 bp):
ACATTTTGAAAATATATATAATATATAGTTTTTGAAACATTTTTGAAAATATATAATATATAGTT
TTTAAAACATTTTGAGAAAATATATATAATATATAGTTTTTAAAA
Found at i:6568511 original size:24 final size:26
Alignment explanation
Indices: 6568456--6568512 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
6568446 CTTGTATATA
*
6568456 TATATATATATATATTATTTTTGTAT
1 TATATATATATATATTATCTTTGTAT
* *
6568482 TATATATACTCTATATTATCTTT-TTT
1 TATATATA-TATATATTATCTTTGTAT
6568508 TATAT
1 TATAT
6568513 TTTATTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (26 bp):
TATATATATATATATTATCTTTGTAT
Found at i:6571788 original size:2 final size:2
Alignment explanation
Indices: 6571781--6571815 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6571771 AAATTATAAT
6571781 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 T
6571816 TCAATAAAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6571987 original size:95 final size:95
Alignment explanation
Indices: 6571807--6572005 Score: 272
Period size: 95 Copynumber: 2.1 Consensus size: 95
6571797 TATATATATA
* * * * *
6571807 TATATATATTCAATAAAGCTTGAGATGTCCCTCTAGAGCAATTGTTTAAACACTCCGGCTTTATG
1 TATA-ATATACAATAAAGCTTGAGATGTCCCTCTAGAGAAATTGGTTAAACACCCCAGCTTTATG
* *
6571872 GATGAGATTCAGCTATCCTGATAAAGGCGAT
65 GATAAGATTCAGCTAACCTGATAAAGGCGAT
* * *
6571903 TATAATATACAATAAAGTTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACGCCCCAGCTTTATGG
1 TATAATATACAATAAAGCTTGAGATGTCCCTCTAGAGAAATTGGTTAAACACCCCAGCTTTATGG
* * *
6571968 ATAATATTCAGTTAACCTGATAAAGGTGAT
66 ATAAGATTCAGCTAACCTGATAAAGGCGAT
6571998 TATAATAT
1 TATAATAT
6572006 TAAGTTGTCC
Statistics
Matches: 90, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
95 86 0.96
96 4 0.04
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Consensus pattern (95 bp):
TATAATATACAATAAAGCTTGAGATGTCCCTCTAGAGAAATTGGTTAAACACCCCAGCTTTATGG
ATAAGATTCAGCTAACCTGATAAAGGCGAT
Found at i:6573343 original size:84 final size:83
Alignment explanation
Indices: 6573181--6573915 Score: 813
Period size: 84 Copynumber: 8.8 Consensus size: 83
6573171 GGAACTATTG
* *
6573181 GCAGCATAGCTCAAGGCAAGAAGGGCTA-CATGCCAACAAAGACCTTCGAGTTCAATTACACTCA
1 GCAGCATAGCTCAAGGCAAGAAGGGTTATC-TGCCAACAAAGACCTTCGAGTTCGATTACACTCA
* *
6573245 ACTCAAAGGTACATCATTT
65 GCTCAAAGGCACATCATTT
* *
6573264 GCAGCATAGCTCAAGGCAAGAAGGGTTATCTACCAACAAGAGACCTTAGAGTTCGATTACACTCA
1 GCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAA-AGACCTTCGAGTTCGATTACACTCA
6573329 GCTCAAAGGCACATCATTT
65 GCTCAAAGGCACATCATTT
* * **
6573348 GCAGCATAACTCAAGGCAAAAAGGACTATCTG-C--CAAAGACCTTCGAGTTCGATTACACTCAG
1 GCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAG
6573410 CTCAAAGGCATCATCATTT
66 CTCAAAGGCA-CATCATTT
* * * *
6573429 GCAGTATAGCTCAAGTCAAAAAGGGTTATCT---ACCAAAGACCTTCGAGTTCGACTT-CACTCA
1 GCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGA-TTACACTCA
* *
6573490 GTTCCAAGGCACATCATTT
65 GCTCAAAGGCACATCATTT
* * * * *
6573509 GCAGCATAACTCAAGGCTAGAAGAGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGATTACACTCA
* * * *
6573574 ACTCTAAGGTATATCATTT
65 GCTCAAAGGCACATCATTT
* * * * * * *
6573593 GTAACATAGCTCAAGGCAAGAA-GGTCTATTTGCCAATAAAAGACCTTCAAGTTCGACTACGCTC
1 GCAGCATAGCTCAAGGCAAGAAGGGT-TATCTGCCAA-CAAAGACCTTCGAGTTCGATTACACTC
*
6573657 AGCTCAAAGGCATATCATTT
64 AGCTCAAAGGCACATCATTT
* * * ** * * *
6573677 GCAGAATAACTCAAGGCTAGAAGGGTTATCTGTTAATAAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGATTACACTCA
*
6573742 GCTCAATGGCACATCATTT
65 GCTCAAAGGCACATCATTT
** ** * * * *
6573761 GCATAATAGCTCAAGGTGAGAGGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTATAATCA
1 GCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGATTACACTCA
*
6573826 GCTCAAAGACACATCATTT
65 GCTCAAAGGCACATCATTT
* * * * *
6573845 GCAGCATAGCTCAAAGCGAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGATTCCATTCA
1 GCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGATTACACTCA
6573910 GCTCAA
65 GCTCAA
6573916 GGGCGTGTCA
Statistics
Matches: 557, Mismatches: 81, Indels: 27
0.84 0.12 0.04
Matches are distributed among these distances:
80 68 0.12
81 71 0.13
82 2 0.00
83 40 0.07
84 373 0.67
85 3 0.01
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (83 bp):
GCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAG
CTCAAAGGCACATCATTT
Found at i:6574752 original size:37 final size:36
Alignment explanation
Indices: 6574706--6575001 Score: 296
Period size: 37 Copynumber: 8.0 Consensus size: 36
6574696 ATGTATGAGA
*
6574706 AAATATATATAATATATAG-TTTTAAAAATCATTTTG
1 AAATTTATATAATATATAGTTTTTAAAAA-CATTTTG
* *
6574742 AAACCTTATATAATATATAG-TTTTGAAAACATTTTTG
1 AAA-TTTATATAATATATAGTTTTTAAAAACA-TTTTG
6574779 AAAATTTATATAATATATAG-TTTTAAAAACATTTTG
1 -AAATTTATATAATATATAGTTTTTAAAAACATTTTG
* *
6574815 AAAACATTTATATATTATATAGTTTTTAAAAACATTTTAA
1 --AA-ATTTATATAATATATAGTTTTTAAAAACATTTT-G
* *
6574855 AAATATATATAATATATAGTTTTTTTAAAACATTTTTG
1 AAATTTATATAATATATAG-TTTTTAAAAACA-TTTTG
* * *
6574893 AAA-ATATATATTATATAGTTTTTTAAAACATTTTAG
1 AAATTTATATAATATATAGTTTTTAAAAACATTTT-G
**
6574929 AAAATACATATAATATATAGTTTTTAAAAAACATTTTGG
1 -AAATTTATATAATATATAGTTTTT-AAAAACATTTT-G
* * *
6574968 AAATTTATATATTATAT-GTTTTTTAAAATATTTT
1 AAATTTATATAATATATAGTTTTTAAAAACATTTT
6575002 TTTATATATA
Statistics
Matches: 226, Mismatches: 21, Indels: 26
0.83 0.08 0.10
Matches are distributed among these distances:
35 4 0.02
36 32 0.14
37 93 0.41
38 67 0.30
39 30 0.13
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (36 bp):
AAATTTATATAATATATAGTTTTTAAAAACATTTTG
Found at i:6574752 original size:75 final size:73
Alignment explanation
Indices: 6574602--6575001 Score: 391
Period size: 75 Copynumber: 5.4 Consensus size: 73
6574592 TTCTAAAATA
* * * * * * * **
6574602 TATATACTATATAG-TTTCGGAAACA-TTTCGAAAAGATATATATTATATAGTTTT-GAAATTTT
1 TATATAATATATAGTTTTTGAAAACATTTTAGAAAATATATATAATATATAGTTTTAAAAACATT
*
6574664 TTGAAAACA
66 TTG-AAACT
* ** * *
6574673 TATATAATGTATAGTTTTTGAAAATGTATGAGAAAATATATATAATATATAGTTTTAAAAATCAT
1 TATATAATATATAGTTTTTGAAAACATTTTAGAAAATATATATAATATATAGTTTTAAAAA-CAT
6574738 TTTGAAACCT
65 TTTGAAA-CT
* *
6574748 TATATAATATATAG-TTTTGAAAACATTTTTGAAAATTTATATAATATATAGTTTTAAAAACATT
1 TATATAATATATAGTTTTTGAAAACATTTTAGAAAATATATATAATATATAGTTTTAAAAACATT
6574812 TTGAAAACATT
66 TTG-AAAC--T
* * *
6574823 TATATATTATATAGTTTTTAAAAACATTTTA-AAAATATATATAATATATAGTTTTTTTAAAACA
1 TATATAATATATAGTTTTTGAAAACATTTTAGAAAATATATATAATATATAG--TTTTAAAAACA
*
6574887 TTTTTGAAA-A
64 -TTTTGAAACT
* * *
6574897 TATATATTATATAGTTTTTTAAAACATTTTAGAAAATACATATAATATATAGTTTTTAAAAAACA
1 TATATAATATATAGTTTTTGAAAACATTTTAGAAAATATATATAATATATAG-TTTT-AAAAACA
*
6574962 TTTTGGAAATT
64 TTTT-GAAACT
* * *
6574973 TATATATTATAT-GTTTTTTAAAATATTTT
1 TATATAATATATAGTTTTTGAAAACATTTT
6575002 TTTATATATA
Statistics
Matches: 280, Mismatches: 33, Indels: 28
0.82 0.10 0.08
Matches are distributed among these distances:
71 12 0.04
72 7 0.03
73 32 0.11
74 88 0.31
75 97 0.35
76 26 0.09
77 13 0.05
78 5 0.02
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (73 bp):
TATATAATATATAGTTTTTGAAAACATTTTAGAAAATATATATAATATATAGTTTTAAAAACATT
TTGAAACT
Found at i:6574801 original size:112 final size:109
Alignment explanation
Indices: 6574596--6574989 Score: 401
Period size: 112 Copynumber: 3.6 Consensus size: 109
6574586 ACGATTTTCT
* *** * *
6574596 AAAATATATATACTATATAG-TTTCGGAAACATTTCGAAAAGA-TATATATTATATAGTTTTG-A
1 AAAATATATATAATATATAGTTTTTAAAAACATTTTGAAAA-ATTATATAATATATAGTTTTGAA
* * * *
6574658 AA-TTTTTTGAAAACATATATAATGTATAGTTTTTGAAAATGTATGAG
65 AACATTTTTG-AAA-ATATATAATATATAGTTTTTAAAAAT-TTTGAG
**
6574705 AAAATATATATAATATATAG-TTTTAAAAATCATTTTGAAACCTTATATAATATATAGTTTTGAA
1 AAAATATATATAATATATAGTTTTTAAAAA-CATTTTGAAAAATTATATAATATATAGTTTTGAA
*
6574769 AACATTTTTGAAAATTTATATAATATATAGTTTTAAAAACATTTTGA-
65 AACATTTTTGAAAA--TATATAATATATAGTTTTTAAAA-ATTTTGAG
* *
6574816 AAACATTTATATATTATATAGTTTTTAAAAACATTTT-AAAAATATATATAATATATAGTTTTTT
1 AAA-ATATATATAATATATAGTTTTTAAAAACATTTTGAAAAAT-TATATAATATATAG--TTTT
* *
6574880 TAAAACATTTTTGAAAATATATATTATATAGTTTTTTAAAACATTTT-AG
62 GAAAACATTTTTGAAAATATATAATATATAG-TTTTTAAAA-ATTTTGAG
* * * *
6574929 AAAATACATATAATATATAGTTTTTAAAAAACATTTTGGAAATTTATATATTATAT-GTTTT
1 AAAATATATATAATATATAGTTTTT-AAAAACATTTTGAAAAATTATATAATATATAGTTTT
6574990 TTAAAATATT
Statistics
Matches: 243, Mismatches: 26, Indels: 31
0.81 0.09 0.10
Matches are distributed among these distances:
109 25 0.10
110 32 0.13
111 13 0.05
112 99 0.41
113 50 0.21
114 24 0.10
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (109 bp):
AAAATATATATAATATATAGTTTTTAAAAACATTTTGAAAAATTATATAATATATAGTTTTGAAA
ACATTTTTGAAAATATATAATATATAGTTTTTAAAAATTTTGAG
Found at i:6575021 original size:3 final size:3
Alignment explanation
Indices: 6575015--6575060 Score: 65
Period size: 3 Copynumber: 14.3 Consensus size: 3
6575005 ATATATAATA
6575015 TAT TAT TAT TAT TAT TATT TAT TAT TAT TAAT TAT TATT TAT TAT T
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT T-AT TAT TA-T TAT TAT T
6575061 TGTTTGTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
3 31 0.77
4 9 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6575038 original size:10 final size:10
Alignment explanation
Indices: 6575015--6575060 Score: 76
Period size: 10 Copynumber: 4.7 Consensus size: 10
6575005 ATATATAATA
6575015 TATTATTA-T
1 TATTATTATT
6575024 TATTATTATT
1 TATTATTATT
6575034 TATTATTATT
1 TATTATTATT
*
6575044 AATTATTATT
1 TATTATTATT
6575054 TATTATT
1 TATTATT
6575061 TGTTTGTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
9 8 0.24
10 26 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TATTATTATT
Found at i:6575038 original size:13 final size:13
Alignment explanation
Indices: 6575015--6575061 Score: 69
Period size: 13 Copynumber: 3.6 Consensus size: 13
6575005 ATATATAATA
6575015 TATTA-TTATTAT
1 TATTATTTATTAT
6575027 TATTATTTATTAT
1 TATTATTTATTAT
*
6575040 TATTAATTATTATT
1 TATTATTTATTA-T
6575054 TATTATTT
1 TATTATTT
6575062 GTTTGTTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
12 5 0.16
13 18 0.58
14 8 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTATTTATTAT
Found at i:6576339 original size:30 final size:32
Alignment explanation
Indices: 6576296--6576355 Score: 90
Period size: 30 Copynumber: 1.9 Consensus size: 32
6576286 TTCAGTCCTT
6576296 TTTATGTTCTATTTTTA-TATTATCTTAATTTG
1 TTTATGTTCTATTTTTATTATTAT-TTAATTTG
6576328 TTTAT-TT-TATTTTTATTATTATTTAATT
1 TTTATGTTCTATTTTTATTATTATTTAATT
6576356 GATACTACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 14 0.52
31 8 0.30
32 5 0.19
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.70
Consensus pattern (32 bp):
TTTATGTTCTATTTTTATTATTATTTAATTTG
Found at i:6576438 original size:24 final size:24
Alignment explanation
Indices: 6576403--6576461 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
6576393 ATATACTCTA
*
6576403 TATTATCTTTTTTATATTTTA-TTT
1 TATTATC-TTTTTATATTTCATTTT
*
6576427 TATTAT-TATTTTCTATTTCATTTT
1 TATTATCT-TTTTATATTTCATTTT
*
6576451 TATTAACTTTT
1 TATTATCTTTT
6576462 GTCTATCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 1 0.03
23 10 0.34
24 17 0.59
25 1 0.03
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (24 bp):
TATTATCTTTTTATATTTCATTTT
Found at i:6587921 original size:3 final size:3
Alignment explanation
Indices: 6587915--6587941 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6587905 TAATTACAAC
6587915 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
6587942 CTTATTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6589428 original size:15 final size:14
Alignment explanation
Indices: 6589388--6589430 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
6589378 TTAAATCAAG
6589388 TAATTTTTAAATATT
1 TAATTTTTAAA-ATT
6589403 T-ATTTTATAAAATT
1 TAATTTT-TAAAATT
6589417 TAATTGTTTAAAAT
1 TAATT-TTTAAAAT
6589431 ATTTAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 9 0.36
15 14 0.56
16 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TAATTTTTAAAATT
Found at i:6592139 original size:31 final size:31
Alignment explanation
Indices: 6592101--6592206 Score: 149
Period size: 31 Copynumber: 3.4 Consensus size: 31
6592091 AAAGACGACC
* * *
6592101 CTTGGGTAGGCTCTGAGGCCCCAAGGACTTT
1 CTTGGGTAGGCTCCGAGGCACCAAGAACTTT
* *
6592132 CTTGGGTAGGCCCCGAGGCACCTAGAACTTT
1 CTTGGGTAGGCTCCGAGGCACCAAGAACTTT
* *
6592163 CTTAGGTAGGCTCCGAGGCACCGAGAACTTT
1 CTTGGGTAGGCTCCGAGGCACCAAGAACTTT
6592194 CTTGGGTAGGCTC
1 CTTGGGTAGGCTC
6592207 TCAAGCCCCA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.18, C:0.26, G:0.31, T:0.25
Consensus pattern (31 bp):
CTTGGGTAGGCTCCGAGGCACCAAGAACTTT
Found at i:6603640 original size:21 final size:21
Alignment explanation
Indices: 6603523--6603640 Score: 71
Period size: 21 Copynumber: 5.7 Consensus size: 21
6603513 ACGCGAAATA
**
6603523 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
6603543 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
6603563 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
6603584 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
6603605 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
*
6603626 AGAATCGCAACGCGA
1 AAAATCGCAACGCGA
6603641 ACACATAAAT
Statistics
Matches: 71, Mismatches: 23, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
19 1 0.01
20 24 0.34
21 44 0.62
22 2 0.03
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:6603653 original size:20 final size:20
Alignment explanation
Indices: 6603628--6603836 Score: 235
Period size: 20 Copynumber: 10.4 Consensus size: 20
6603618 GATTTTCCAG
* *
6603628 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
6603648 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
6603668 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
6603688 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
6603708 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
6603728 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
6603748 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
6603768 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
**
6603788 AATCGCAAC-AATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
6603808 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
6603828 AATCACAAC
1 AATCGCAAC
6603837 ACTGAAATTT
Statistics
Matches: 165, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.01
20 160 0.97
21 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:6604566 original size:24 final size:24
Alignment explanation
Indices: 6604527--6604573 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6604517 AAATTTGGTC
6604527 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
6604551 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
6604574 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:6604765 original size:12 final size:12
Alignment explanation
Indices: 6604748--6604772 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6604738 ATATAATCCT
6604748 GAAGAAGAAAAA
1 GAAGAAGAAAAA
6604760 GAAGAAGAAAAA
1 GAAGAAGAAAAA
6604772 G
1 G
6604773 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:6607105 original size:33 final size:34
Alignment explanation
Indices: 6607054--6607252 Score: 167
Period size: 33 Copynumber: 5.7 Consensus size: 34
6607044 CGGAAATTAC
* *
6607054 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
6607087 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
* * *
6607121 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AATGAAAATCGCAATGCGA-AAT-GAA
*
6607160 AAT-GCGGA-AATGAAAATCGCAATGCGAAATGAA
1 AATCGC-AACAATGAAAATCGCAATGCGAAATGAA
* *
6607193 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
6607226 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAA--C--AATGAAAATCGCAA
6607253 CGAGAGAATC
Statistics
Matches: 133, Mismatches: 15, Indels: 31
0.74 0.08 0.17
Matches are distributed among these distances:
32 2 0.02
33 57 0.43
34 35 0.26
35 1 0.01
36 1 0.01
37 1 0.01
38 14 0.11
39 21 0.16
40 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:6607131 original size:53 final size:52
Alignment explanation
Indices: 6607068--6607290 Score: 367
Period size: 53 Copynumber: 4.2 Consensus size: 52
6607058 GCAACGAGAG
* *
6607068 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
6607121 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
6607174 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
6607226 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
6607278 AATCACATTGCGA
1 AATCGCAATGCGA
6607291 TTCTCTCGTT
Statistics
Matches: 164, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
52 70 0.43
53 93 0.57
54 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:6607137 original size:19 final size:19
Alignment explanation
Indices: 6607068--6607281 Score: 225
Period size: 19 Copynumber: 12.2 Consensus size: 19
6607058 GCAACGAGAG
6607068 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
6607087 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
6607101 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
6607121 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
6607140 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
6607154 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
6607174 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
6607193 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
6607207 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
6607226 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
6607245 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
6607259 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
6607278 AATC
1 AATC
6607282 ACATTGCGAT
Statistics
Matches: 164, Mismatches: 9, Indels: 44
0.76 0.04 0.20
Matches are distributed among these distances:
14 42 0.26
15 3 0.02
16 6 0.04
17 8 0.05
18 2 0.01
19 74 0.45
20 29 0.18
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:6607211 original size:86 final size:84
Alignment explanation
Indices: 6607054--6607233 Score: 242
Period size: 86 Copynumber: 2.1 Consensus size: 84
6607044 CGGAAATTAC
6607054 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAA-GCGG-AATG
6607119 AAAATCGCAATGCGAAATGAA
64 AAAATCGCAATGCGAAATGAA
*
6607140 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAAAATCGCAAGCGG
*
6607203 -A-GAGAATCGCAATGCGAAATGAA
60 AATGAAAATCGCAATGCGAAATGAA
6607226 AATCGCAA
1 AATCGCAA
6607234 TGCGAAATGA
Statistics
Matches: 86, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
86 54 0.63
87 16 0.19
89 2 0.02
90 1 0.01
92 13 0.15
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (84 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAAGCGGAATGAA
AATCGCAATGCGAAATGAA
Found at i:6607263 original size:33 final size:33
Alignment explanation
Indices: 6607121--6607281 Score: 157
Period size: 33 Copynumber: 4.7 Consensus size: 33
6607111 CGGAAATGAA
6607121 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
6607154 AATCGCAATGCGGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
* * * *
6607187 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
6607226 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
6607259 AATCGCAATGCGAAATTAAAATC
1 AATCGCAATGCGAAATGAAAATC
6607282 ACATTGCGAT
Statistics
Matches: 104, Mismatches: 12, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
31 5 0.05
32 3 0.03
33 49 0.47
34 20 0.19
35 1 0.01
36 2 0.02
38 10 0.10
39 7 0.07
40 7 0.07
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:6607393 original size:52 final size:53
Alignment explanation
Indices: 6607283--6607396 Score: 221
Period size: 53 Copynumber: 2.2 Consensus size: 53
6607273 ATTAAAATCA
6607283 CATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
1 CATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
6607336 CATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCG
1 CATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
6607388 CATTGCGAT
1 CATTGCGAT
6607397 AGTCATTTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.49
53 31 0.51
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (53 bp):
CATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
Found at i:6607404 original size:19 final size:19
Alignment explanation
Indices: 6607299--6607396 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
6607289 GATTCTCTCG
6607299 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
6607319 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
6607338 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
6607352 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
6607371 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
6607390 TTGCGAT
1 TTGCGAT
6607397 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:6607522 original size:14 final size:14
Alignment explanation
Indices: 6607503--6607539 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
6607493 CATCAATTAC
6607503 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
6607517 ACAAATCATCTTTT
1 ACAAATCAACTTTT
6607531 ACAAATCAA
1 ACAAATCAA
6607540 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:6609563 original size:14 final size:14
Alignment explanation
Indices: 6609512--6609567 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
6609502 GCGAAATGAA
*
6609512 AATCGCAACGACAG
1 AATCGCAACGAAAG
6609526 AATCG-AATGCGAAATG
1 AATCGCAA--CGAAA-G
6609542 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
6609558 AATCGCAACG
1 AATCGCAACG
6609568 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
13 2 0.06
14 15 0.43
15 4 0.11
16 2 0.06
17 5 0.14
18 5 0.14
19 2 0.06
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:6609576 original size:33 final size:33
Alignment explanation
Indices: 6609493--6609584 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
6609483 GCGAAACCAA
*
6609493 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
6609526 AATCG-AATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
6609558 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
6609585 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.48, C:0.21, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:6609582 original size:19 final size:19
Alignment explanation
Indices: 6609456--6609589 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
6609446 TAGTTTACTT
* *
6609456 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
6609476 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
6609495 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
6609514 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
6609528 TCG-AATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
6609546 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
6609560 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
6609579 TCGCAATGCGA
1 TCGCAACGCGA
6609590 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 23
0.75 0.06 0.18
Matches are distributed among these distances:
13 2 0.02
14 13 0.14
15 4 0.04
16 8 0.08
17 10 0.11
18 5 0.05
19 41 0.43
20 12 0.13
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:6609601 original size:19 final size:19
Alignment explanation
Indices: 6609585--6609680 Score: 103
Period size: 19 Copynumber: 5.3 Consensus size: 19
6609575 AAAATCGCAA
6609585 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
6609604 TGCGATTCT--TTT---GT
1 TGCGATTTTGGTTTCGCGT
**
6609618 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
6609637 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
6609656 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
6609676 TGCGA
1 TGCGA
6609681 AAGTAAACTA
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
14 10 0.15
16 3 0.05
17 3 0.05
19 36 0.55
20 13 0.20
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:6609844 original size:93 final size:93
Alignment explanation
Indices: 6609728--6610010 Score: 532
Period size: 93 Copynumber: 3.1 Consensus size: 93
6609718 ATGGATTGCA
6609728 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
6609792 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
6609820 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
* *
6609885 TAGTAGAATTGGCAGCAACCAAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
6609913 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
6609978 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
6610006 TTACT
1 TTACT
6610011 AAGCAATCTA
Statistics
Matches: 185, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
92 4 0.02
93 181 0.98
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:6611757 original size:21 final size:21
Alignment explanation
Indices: 6611701--6611765 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
6611691 TCTTTTGGTT
6611701 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
6611722 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
*
6611742 GAAATAAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
6611763 GAA
1 GAA
6611766 TCGCAACGCG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.49, C:0.15, G:0.25, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:6611829 original size:14 final size:14
Alignment explanation
Indices: 6611807--6611863 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
6611797 TTTGGTTTCG
*
6611807 CGTTACGATTCTCT
1 CGTTGCGATTCTCT
*
6611821 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
6611840 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
6611854 CGTTGCGATT
1 CGTTGCGATT
6611864 TTCATTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:6611839 original size:33 final size:33
Alignment explanation
Indices: 6611791--6611871 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
6611781 AAAATCGCAA
**
6611791 TGCGATTTTGGTTTCGCGTTACGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
*
6611824 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
6611857 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
6611872 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.10, C:0.22, G:0.21, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
Found at i:6611874 original size:21 final size:21
Alignment explanation
Indices: 6611848--6611923 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
6611838 CGCGTTGCGA
6611848 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
6611869 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
6611889 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
6611910 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
6611924 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:6611904 original size:41 final size:41
Alignment explanation
Indices: 6611847--6611924 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
6611837 TCGCGTTGCG
*
6611847 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
6611888 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
6611925 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:6612045 original size:33 final size:33
Alignment explanation
Indices: 6612003--6612073 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
6611993 AATACTAACT
6612003 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
6612036 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
6612069 TGAAA
1 TGAAA
6612074 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:6612478 original size:20 final size:20
Alignment explanation
Indices: 6612453--6612626 Score: 226
Period size: 20 Copynumber: 8.7 Consensus size: 20
6612443 CTTTAAATAT
6612453 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
6612473 CGCGTTACGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
6612495 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
6612514 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
6612534 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
6612554 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
6612574 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
6612594 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
6612614 CGCGTTGCGATTT
1 CGCGTTGCGATTT
6612627 TAATATTCGC
Statistics
Matches: 134, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.01
20 116 0.87
21 14 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:6612635 original size:20 final size:21
Alignment explanation
Indices: 6612594--6612645 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
6612584 TTTACGGATA
* *
6612594 CGCGTTGCGA-TTTATGTGTT
1 CGCGTTGCGATTTTATATATT
6612614 CGCGTTGCGATTTTA-ATATT
1 CGCGTTGCGATTTTATATATT
6612634 CGCGTTGCGATT
1 CGCGTTGCGATT
6612646 CTGGAAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.13, C:0.17, G:0.27, T:0.42
Consensus pattern (21 bp):
CGCGTTGCGATTTTATATATT
Found at i:6612706 original size:42 final size:43
Alignment explanation
Indices: 6612613--6612711 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 43
6612603 ATTTATGTGT
* *
6612613 TCGCGTTGCG-ATTT-TAATATTCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTCTGCAAAA
** * *
6612654 TCGCAATGCGAATTTGTACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTCTGCAA-AA
*
6612696 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
6612712 GAAACTGATT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
41 11 0.24
42 31 0.67
43 4 0.09
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.36
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTCTGCAAAA
Found at i:6612946 original size:8 final size:8
Alignment explanation
Indices: 6612933--6612982 Score: 57
Period size: 8 Copynumber: 6.2 Consensus size: 8
6612923 AAATGATATT
6612933 TTAAATTA
1 TTAAATTA
6612941 TTAAATTA
1 TTAAATTA
*
6612949 ATAAGATT-
1 TTAA-ATTA
6612957 TTAAATTA
1 TTAAATTA
6612965 TTAAATTA
1 TTAAATTA
* *
6612973 ATAAAATA
1 TTAAATTA
6612981 TT
1 TT
6612983 TTATGTGCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
7 3 0.09
8 29 0.83
9 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (8 bp):
TTAAATTA
Found at i:6612957 original size:24 final size:24
Alignment explanation
Indices: 6612930--6612976 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
6612920 TAAAAATGAT
6612930 ATTTTAAATTATTAAATTAATAAG
1 ATTTTAAATTATTAAATTAATAAG
6612954 ATTTTAAATTATTAAATTAATAA
1 ATTTTAAATTATTAAATTAATAA
6612977 AATATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
ATTTTAAATTATTAAATTAATAAG
Found at i:6621901 original size:45 final size:44
Alignment explanation
Indices: 6621833--6621933 Score: 132
Period size: 45 Copynumber: 2.3 Consensus size: 44
6621823 AAAGAGTTAC
* * * *
6621833 GAAATAAGTTGGGTAATGCTGGTAATAGCTCCAATATAGT-ATTA
1 GAAATAAGTTGGGTAATACTGGTAATAACTCCAACATAGTGA-GA
*
6621877 GGAAATAAGTTGGGTAATATTGGTAATAACTCCAACATAGTGAGA
1 -GAAATAAGTTGGGTAATACTGGTAATAACTCCAACATAGTGAGA
6621922 GAAATAAGTTGG
1 GAAATAAGTTGG
6621934 AATTACAACA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 12 0.24
45 37 0.74
46 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.29
Consensus pattern (44 bp):
GAAATAAGTTGGGTAATACTGGTAATAACTCCAACATAGTGAGA
Found at i:6622757 original size:30 final size:31
Alignment explanation
Indices: 6622718--6622789 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
6622708 ACAACACACT
* * * *
6622718 AAAGAAAACAAAAACCC-TCACAGCAGAAGC
1 AAAGGAAACAAAAACCCATCACAACAAAAAC
*
6622748 AAAGGAAACAAAAGCCCATCACAACAAAAAC
1 AAAGGAAACAAAAACCCATCACAACAAAAAC
6622779 AAA-GAAACAAA
1 AAAGGAAACAAA
6622790 TATAGGGGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 23 0.64
31 13 0.36
ACGTcount: A:0.62, C:0.24, G:0.11, T:0.03
Consensus pattern (31 bp):
AAAGGAAACAAAAACCCATCACAACAAAAAC
Found at i:6623091 original size:22 final size:22
Alignment explanation
Indices: 6623066--6623109 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
6623056 TATTGGTTTA
6623066 ATTATAAATTTAGTCCTTCAAC
1 ATTATAAATTTAGTCCTTCAAC
6623088 ATTATAAATTTAGTCCTTCAAC
1 ATTATAAATTTAGTCCTTCAAC
6623110 TTTGAAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (22 bp):
ATTATAAATTTAGTCCTTCAAC
Found at i:6623155 original size:28 final size:27
Alignment explanation
Indices: 6623112--6623187 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 27
6623102 CCTTCAACTT
6623112 TGAAGTATTGAAGTTACTTAATGAAATC
1 TGAAGTATTGAAGTTACTTAA-GAAATC
* *
6623140 T-ATAGTATTGAAGTTACTCTAAGATATT
1 TGA-AGTATTGAAGTTACT-TAAGAAATC
*
6623168 TGAAGTCTTGAAGTTACTTA
1 TGAAGTATTGAAGTTACTTA
6623188 TAAAATTTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 3 0.07
28 35 0.83
29 4 0.10
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (27 bp):
TGAAGTATTGAAGTTACTTAAGAAATC
Found at i:6623249 original size:22 final size:22
Alignment explanation
Indices: 6623224--6623280 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
6623214 CCTAAGAAAC
*
6623224 TGGTATATCGTACTAATTTATA
1 TGGTACATCGTACTAATTTATA
6623246 TGGTACATCGTACTAATTTATA
1 TGGTACATCGTACTAATTTATA
6623268 TGGTACATCGTAC
1 TGGTACATCGTAC
6623281 CGGAGCAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (22 bp):
TGGTACATCGTACTAATTTATA
Found at i:6625825 original size:12 final size:13
Alignment explanation
Indices: 6625803--6625831 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6625793 GTTAGTTCTC
6625803 TTTTCTCTTTGTT
1 TTTTCTCTTTGTT
6625816 TTTTCT-TTTGTT
1 TTTTCTCTTTGTT
6625828 TTTT
1 TTTT
6625832 GATAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:6625879 original size:23 final size:23
Alignment explanation
Indices: 6625849--6625909 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
6625839 ATAATTCTGG
6625849 CTGTGTTGCACGTTTATCTCCGC
1 CTGTGTTGCACGTTTATCTCCGC
* * *
6625872 CTGTGTTGCGCGTTTATCTCTGT
1 CTGTGTTGCACGTTTATCTCCGC
* *
6625895 CTTTGTGGCACGTTT
1 CTGTGTTGCACGTTT
6625910 TTCTATTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.07, C:0.25, G:0.25, T:0.44
Consensus pattern (23 bp):
CTGTGTTGCACGTTTATCTCCGC
Found at i:6627286 original size:20 final size:20
Alignment explanation
Indices: 6627257--6627314 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
6627247 AACGTGATTT
6627257 CAAATTCGCAACACGAACTC
1 CAAATTCGCAACACGAACTC
* **
6627277 CAATTTCGCAACAC-AGTTTC
1 CAAATTCGCAACACGA-ACTC
6627297 CAAATTCGCAACACGAAC
1 CAAATTCGCAACACGAAC
6627315 ATGGAAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.38, C:0.33, G:0.10, T:0.19
Consensus pattern (20 bp):
CAAATTCGCAACACGAACTC
Found at i:6630773 original size:22 final size:20
Alignment explanation
Indices: 6630710--6630761 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
6630700 AATAATTAAC
6630710 AATTTGAAAAATGAGTTGCG
1 AATTTGAAAAATGAGTTGCG
6630730 AATTTGAAAAATGAGTTGCG
1 AATTTGAAAAATGAGTTGCG
*
6630750 AATTTGACAAAT
1 AATTTGAAAAAT
6630762 TCGTGTTGCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (20 bp):
AATTTGAAAAATGAGTTGCG
Found at i:6634977 original size:76 final size:75
Alignment explanation
Indices: 6634893--6635108 Score: 272
Period size: 76 Copynumber: 2.9 Consensus size: 75
6634883 ATTTTAAATA
* *
6634893 TTATATTTTATCTTTTTTTTAGGTATTTTAATTTAAATAAGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTTTTTTAGGTATTTTAGTTTAAAT-AGTTTTAGTATTTTAATTAAGATTTA
*
6634958 AGATATTATTT
65 AAATATTATTT
* * *
6634969 TTATATTTTATCTTTGTTTTAGGTAATTTAGTTTAAATAGATTTTAGTATTTTAATTAGGATTTA
1 TTATATTTTATCTTTTTTTTAGGTATTTTAGTTTAAATAG-TTTTAGTATTTTAATTAAGATTTA
6635034 AAATATTATTT
65 AAATATTATTT
** * * * * * *
6635045 AAAAATATTAT-TATTTTTTAGGTATTTTAGTTTAAATAGTTTAAATAGTTTTAATTAGGATTTA
1 TTATATTTTATCTTTTTTTTAGGTATTTTAGTTTAAATAGTTTTAGTA-TTTTAATTAAGATTTA
6635109 TGATGTTTTA
Statistics
Matches: 123, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
74 6 0.05
75 43 0.35
76 74 0.60
ACGTcount: A:0.33, C:0.01, G:0.10, T:0.56
Consensus pattern (75 bp):
TTATATTTTATCTTTTTTTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAAGATTTAA
AATATTATTT
Found at i:6635807 original size:20 final size:20
Alignment explanation
Indices: 6635782--6635831 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
6635772 TTACTATTTA
6635782 TTATTTTATTATT-TCCCT-TT
1 TTATTTTATTATTAT--CTATT
6635802 TTA-TTTATTATTATCTATT
1 TTATTTTATTATTATCTATT
6635821 TTATTTTATTA
1 TTATTTTATTA
6635832 AATATTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.07
19 14 0.52
20 11 0.41
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTTTATTATTATCTATT
Found at i:6644220 original size:13 final size:13
Alignment explanation
Indices: 6644199--6644233 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
6644189 CCCACTTACT
6644199 TTTCACTTTTCAC
1 TTTCACTTTTCAC
* *
6644212 TTTCTCTTTTTAC
1 TTTCACTTTTCAC
6644225 TTTCACTTT
1 TTTCACTTT
6644234 CTAGTTTCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTCACTTTTCAC
Found at i:6646829 original size:20 final size:20
Alignment explanation
Indices: 6646804--6646846 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6646794 TCTAAGAGCC
*
6646804 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
6646824 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
6646844 CAT
1 CAT
6646847 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:6650528 original size:26 final size:26
Alignment explanation
Indices: 6650499--6650553 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 26
6650489 GATAGTGTAA
6650499 CGTAATGTGGCAGCAAATAG-AGATGT
1 CGTAATGTGGCAGCAAAT-GTAGATGT
6650525 CGTAATGTGGCAGCAAATGTAGATGT
1 CGTAATGTGGCAGCAAATGTAGATGT
6650551 CGT
1 CGT
6650554 GGCAAAGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 1 0.04
26 27 0.96
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (26 bp):
CGTAATGTGGCAGCAAATGTAGATGT
Found at i:6651711 original size:23 final size:23
Alignment explanation
Indices: 6651675--6651738 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
6651665 CAGCTCATAT
6651675 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* *
6651698 AATTGCACCTAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
6651721 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
6651739 TATAAGATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:6657111 original size:20 final size:20
Alignment explanation
Indices: 6657088--6657125 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6657078 CAAAAGACCT
*
6657088 CATAGATGTTCCAAAGGATA
1 CATAGATGTCCCAAAGGATA
*
6657108 CATATATGTCCCAAAGGA
1 CATAGATGTCCCAAAGGA
6657126 CCGTGTAGAC
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:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (20 bp):
CATAGATGTCCCAAAGGATA
Found at i:6657284 original size:30 final size:29
Alignment explanation
Indices: 6657231--6657289 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
6657221 TGTAAACATA
* *
6657231 TCACATATTCATATAAACTCGTAGCTTCAT
1 TCACATATACATATAAACACGTAG-TTCAT
* *
6657261 TCACATATACATTTAATCACGTAGTTCAT
1 TCACATATACATATAAACACGTAGTTCAT
6657290 GTAAATTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (29 bp):
TCACATATACATATAAACACGTAGTTCAT
Found at i:6669700 original size:23 final size:25
Alignment explanation
Indices: 6669647--6669701 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
6669637 TAATTCTCCT
*
6669647 CTTTTTTCTCTCCTCTTCGTCTCTTC
1 CTTTTTTCTCTCCTATTC-TCTCTTC
*
6669673 C-TTTTTCTCTTCTATT-TCT-TTC
1 CTTTTTTCTCTCCTATTCTCTCTTC
6669695 CTTTTTT
1 CTTTTTT
6669702 TATCACTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 4 0.15
23 8 0.31
25 13 0.50
26 1 0.04
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.65
Consensus pattern (25 bp):
CTTTTTTCTCTCCTATTCTCTCTTC
Found at i:6678697 original size:11 final size:11
Alignment explanation
Indices: 6678681--6678736 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
6678671 ATTTTCGTCC
6678681 TATTATATATA
1 TATTATATATA
*
6678692 TATTAT-TATTT
1 TATTATATA-TA
*
6678703 TATTATACATA
1 TATTATATATA
6678714 TATT-TATAT-
1 TATTATATATA
6678723 TA-TATATATA
1 TATTATATATA
6678733 TATT
1 TATT
6678737 TTTTACAGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
8 1 0.03
9 7 0.19
10 8 0.22
11 19 0.53
12 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTATATATA
Found at i:6678725 original size:17 final size:16
Alignment explanation
Indices: 6678698--6678733 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
6678688 TATATATTAT
6678698 TATTTTATTATACATA
1 TATTTTATTATACATA
*
6678714 TATTTATATTATATATA
1 TATTT-TATTATACATA
6678731 TAT
1 TAT
6678734 ATTTTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTTATTATACATA
Found at i:6678741 original size:22 final size:21
Alignment explanation
Indices: 6678684--6678739 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
6678674 TTCGTCCTAT
* *
6678684 TATATATATATTATTATTTTA
1 TATATATATATTTTTATATTA
* *
6678705 T-TATACATATATTTATATTA
1 TATATATATATTTTTATATTA
6678725 TATATATATATTTTT
1 TATATATATATTTTT
6678740 TACAGACCCA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TATATATATATTTTTATATTA
Done.