Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_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: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 30
Found at i:2154431 original size:55 final size:55
Alignment explanation
Indices: 2154383--2154947 Score: 668
Period size: 55 Copynumber: 10.4 Consensus size: 55
2154373 AGGGTAGGTC
* ** *
2154383 GGACTTGAACAATCTTTGGAAAACGGGTCTGCTCCCTATTCTTTCAGGGAGTATA
1 GGACTCGAACAATCTTCAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATA
* * *
2154438 GGACTCGAACAATCTTCAAAAAACATGTCTTCTCCCTATTCTTTCAGGGAGTATA
1 GGACTCGAACAATCTTCAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATA
* * * *
2154493 GAACTCGAACAATCTTCAGCAAATGTGTCCGCTCCCTATTCTTTCAGGGAGTA-A
1 GGACTCGAACAATCTTCAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATA
* *
2154547 TGGACTCGAACAATCTTCA-ACAAACGTGT-TCGTTCCCTATTCTTTCCGGGAGTATA
1 -GGACTCGAACAATCTTCAGA-AAACGTGTCT-GCTCCCTATTCTTTCAGGGAGTATA
*
2154603 AGACTCGAACAATCTTCA-ACAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATA
1 GGACTCGAACAATCTTCAGA-AAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATA
* * * *
2154658 GGAGTCGAACAATCTTCAGCAAATGTGTCCGCTCCCTATTCTTTCAGGGAGTATA
1 GGACTCGAACAATCTTCAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATA
* * *
2154713 GGACTCGAACAATCTTCAGCAAACGTGTCCGCTCCCTATTCTTTCAGAGAGTATA
1 GGACTCGAACAATCTTCAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATA
* * * *
2154768 GGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAAGGAATAAA
1 GGACTCGAACAATCTTCAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATA
** * *
2154823 AAACTCAAACAATCTTCA-ACAA-------GCTCCCTATTCTTTCAGGGAGTATA
1 GGACTCGAACAATCTTCAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATA
* * ** * *
2154870 GTAATCGAACAATCTTCATCAAATGTGTATGCTCCCTATTCTTTCAGGGAGTATA
1 GGACTCGAACAATCTTCAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATA
* * *
2154925 GGAGTCAAACAATCTTCATAAAA
1 GGACTCGAACAATCTTCAGAAAA
2154948 TGATTCTGCT
Statistics
Matches: 442, Mismatches: 54, Indels: 28
0.84 0.10 0.05
Matches are distributed among these distances:
47 36 0.08
48 2 0.00
54 3 0.01
55 399 0.90
56 2 0.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (55 bp):
GGACTCGAACAATCTTCAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATA
Found at i:2154642 original size:165 final size:165
Alignment explanation
Indices: 2154413--2154942 Score: 756
Period size: 165 Copynumber: 3.3 Consensus size: 165
2154403 AAACGGGTCT
* * *
2154413 GCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAAAAAACATGTCTTCTCCCTATT
1 GCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATT
2154478 CTTTCAGGGAGTATAGAACTCGAACAATCTTCAGCAAATGTGTCCGCTCCCTATTCTTTCAGGGA
66 CTTTCAGGGAGTATAGAACTCGAACAATCTTCAGCAAATGTGTCCGCTCCCTATTCTTTCAGGGA
2154543 GTA-ATGGACTCGAACAATCTTCAACAAACGTGTTC
131 GTATA-GGACTCGAACAATCTTCAACAAACGTGTTC
* * *
2154578 GTTCCCTATTCTTTCCGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATT
1 GCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATT
* *
2154643 CTTTCAGGGAGTATAGGAGTCGAACAATCTTCAGCAAATGTGTCCGCTCCCTATTCTTTCAGGGA
66 CTTTCAGGGAGTATAGAACTCGAACAATCTTCAGCAAATGTGTCCGCTCCCTATTCTTTCAGGGA
* *
2154708 GTATAGGACTCGAACAATCTTCAGCAAACGTGTCC
131 GTATAGGACTCGAACAATCTTCAACAAACGTGTTC
* *
2154743 GCTCCCTATTCTTTCAGAGAGTATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATT
1 GCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATT
* * * * * *
2154808 CTTTCAAGGAATAAAAAACTCAAACAATCTTCAAC-AA-------GCTCCCTATTCTTTCAGGGA
66 CTTTCAGGGAGTATAGAACTCGAACAATCTTCAGCAAATGTGTCCGCTCCCTATTCTTTCAGGGA
* * * *
2154865 GTATAGTAATCGAACAATCTTCATCAAATGTGTAT-
131 GTATAGGACTCGAACAATCTTCAACAAACGTGT-TC
* *
2154900 GCTCCCTATTCTTTCAGGGAGTATAGGAGTCAAACAATCTTCA
1 GCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCA
2154943 TAAAATGATT
Statistics
Matches: 332, Mismatches: 31, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
157 89 0.27
164 2 0.01
165 240 0.72
166 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (165 bp):
GCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATT
CTTTCAGGGAGTATAGAACTCGAACAATCTTCAGCAAATGTGTCCGCTCCCTATTCTTTCAGGGA
GTATAGGACTCGAACAATCTTCAACAAACGTGTTC
Found at i:2154933 original size:102 final size:102
Alignment explanation
Indices: 2154743--2154942 Score: 292
Period size: 102 Copynumber: 2.0 Consensus size: 102
2154733 AAACGTGTCC
* *
2154743 GCTCCCTATTCTTTCAGAGAGTATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATT
1 GCTCCCTATTCTTTCAGAGAGTATAGGAATCGAACAATCTTCAGCAAACGTGTATGCTCCCTATT
2154808 CTTTCAAGGAATAAAAAACTCAAACAATCTTCAACAA
66 CTTTCAAGGAATAAAAAACTCAAACAATCTTCAACAA
* * * *
2154845 GCTCCCTATTCTTTCAGGGAGTATAGTAATCGAACAATCTTCATCAAATGTGTATGCTCCCTATT
1 GCTCCCTATTCTTTCAGAGAGTATAGGAATCGAACAATCTTCAGCAAACGTGTATGCTCCCTATT
* * * ** *
2154910 CTTTCAGGGAGTATAGGAGTCAAACAATCTTCA
66 CTTTCAAGGAATAAAAAACTCAAACAATCTTCA
2154943 TAAAATGATT
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
102 86 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (102 bp):
GCTCCCTATTCTTTCAGAGAGTATAGGAATCGAACAATCTTCAGCAAACGTGTATGCTCCCTATT
CTTTCAAGGAATAAAAAACTCAAACAATCTTCAACAA
Found at i:2155512 original size:55 final size:55
Alignment explanation
Indices: 2155448--2155949 Score: 504
Period size: 55 Copynumber: 9.3 Consensus size: 55
2155438 GGGTAGGTCA
* * * * *
2155448 GACTTGAACAATCTTTGGAAAATGGGTATGCTCCCTATTCTTTCAGGGAGTATAG
1 GACTCGAACAATCTTTAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATAG
* * * * *
2155503 GACTCGAACAATCTTCAAAAAACATGTCTTCTCCCTATTCTTTCAGGGAGTATAA
1 GACTCGAACAATCTTTAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATAG
* * *
2155558 GACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATTCTTTCAGGGAGTA-ATG
1 GACTCGAACAATCTTTAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATA-G
* * * * *
2155613 GACTCGAACAATCTTCA-ACAAACGTGTTTGTTCCCTATTCTTTCCGGGAGTATAA
1 GACTCGAACAATCTTTAGA-AAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATAG
* *
2155668 GACTCGAACAATCTTCA-ACAAACGTGTCTGCACCCTATTCTTTCAGGGAGTATAG
1 GACTCGAACAATCTTTAGA-AAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATAG
* * * * *
2155723 GACTCGAACAATCTTCAGCAAATGTGTCCGCTTCCTATTCTTTCAGGGAGTATAG
1 GACTCGAACAATCTTTAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATAG
* * * * * *
2155778 GACTCGAACAATCTTGAGCAAACGTGTCCGCTCCCTATTCTTTCAGGGAATAAAA
1 GACTCGAACAATCTTTAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATAG
* * * * *
2155833 AACTCAAACAATCTTCA-ACAA-------GCTCCCTATTTTTTCAGGGAGTATAG
1 GACTCGAACAATCTTTAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATAG
* * * * * *
2155880 GAATCGGACAATCTTCAGCAAATGTGTATGCTCCCTATTCTTTCAGGGAGTATAG
1 GACTCGAACAATCTTTAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATAG
* *
2155935 GAGTCAAACAATCTT
1 GACTCGAACAATCTT
2155950 CATAAAATGA
Statistics
Matches: 378, Mismatches: 57, Indels: 24
0.82 0.12 0.05
Matches are distributed among these distances:
47 35 0.09
48 2 0.01
54 3 0.01
55 337 0.89
56 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (55 bp):
GACTCGAACAATCTTTAGAAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATAG
Found at i:2155627 original size:110 final size:109
Alignment explanation
Indices: 2155447--2155956 Score: 586
Period size: 110 Copynumber: 4.7 Consensus size: 109
2155437 AGGGTAGGTC
* ** * * *
2155447 AGACTTGAACAATCTTTGGAAAATGGGTATGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAAC
1 AGACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAAC
2155512 AATCTTCAAAAAACATGTCTTCTCCCTATTCTTTCAGGGAGTATA
66 AATCTTCAAAAAACATGT-TTCTCCCTATTCTTTCAGGGAGTATA
2155557 AGACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATTCTTTCAGGGAGTA-ATGGACTCGAA
1 AGACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATTCTTTCAGGGAGTATA-GGACTCGAA
* * * *
2155621 CAATCTTCAACAAACGTGTTTGTTCCCTATTCTTTCCGGGAGTATA
65 CAATCTTCAAAAAACATGTTT-CTCCCTATTCTTTCAGGGAGTATA
* * *
2155667 AGACTCGAACAATCTTCAACAAACGTGTCTGCACCCTATTCTTTCAGGGAGTATAGGACTCGAAC
1 AGACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAAC
** ** ** *
2155732 AATCTTCAGCAAATGTGTCCGCTTCCTATTCTTTCAGGGAGTATA
66 AATCTTCAAAAAACATGT-TTCTCCCTATTCTTTCAGGGAGTATA
* * * * * * ** *
2155777 GGACTCGAACAATCTTGAGCAAACGTGTCCGCTCCCTATTCTTTCAGGGAATAAAAAACTCAAAC
1 AGACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAAC
* *
2155842 AATCTTC----AACAAG---CTCCCTATTTTTTCAGGGAGTATA
66 AATCTTCAAAAAACATGTTTCTCCCTATTCTTTCAGGGAGTATA
* * * * * *
2155879 GGAATCGGACAATCTTCAGCAAATGTGTATGCTCCCTATTCTTTCAGGGAGTATAGGAGTCAAAC
1 AGACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAAC
*
2155944 AATCTTCATAAAA
66 AATCTTCAAAAAA
2155957 TGAGTCTGTT
Statistics
Matches: 346, Mismatches: 46, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
102 83 0.24
106 5 0.01
109 3 0.01
110 254 0.73
111 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (109 bp):
AGACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAAC
AATCTTCAAAAAACATGTTTCTCCCTATTCTTTCAGGGAGTATA
Found at i:2155706 original size:165 final size:162
Alignment explanation
Indices: 2155477--2155951 Score: 656
Period size: 165 Copynumber: 2.9 Consensus size: 162
2155467 AAATGGGTAT
* *
2155477 GCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAAAAAACATGTCTTCTCCCTATT
1 GCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAAC-TGTC-TC-CCCTATT
*
2155542 CTTTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATTCTTTCAGGGA
63 CTTTCAGGGAGTATAGGACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATTCTTTCAGGGA
**
2155607 GTA-ATGGACTCGAACAATCTTCAACAAACGTGTTT
128 GTATA-GGACTCGAACAATCTTCAACAAACGTGTCC
* *
2155642 GTTCCCTATTCTTTCCGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCACCCTATT
1 GCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAAC-TGTCT-C-CCCTATT
* *
2155707 CTTTCAGGGAGTATAGGACTCGAACAATCTTCAGCAAATGTGTCCGCTTCCTATTCTTTCAGGGA
63 CTTTCAGGGAGTATAGGACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATTCTTTCAGGGA
* *
2155772 GTATAGGACTCGAACAATCTTGAGCAAACGTGTCC
128 GTATAGGACTCGAACAATCTTCAACAAACGTGTCC
* * * * *
2155807 GCTCCCTATTCTTTCAGGGAATAAAAAACTCAAACAATCTTCAAC-AA--G-CT-CCCTATTTTT
1 GCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACTGTCTCCCCTATTCTT
* * *
2155867 TCAGGGAGTATAGGAATCGGACAATCTTCAGCAAATGTGTATGCTCCCTATTCTTTCAGGGAGTA
66 TCAGGGAGTATAGGACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATTCTTTCAGGGAGTA
* *
2155932 TAGGAGTCAAACAATCTTCA
131 TAGGACTCGAACAATCTTCA
2155952 TAAAATGAGT
Statistics
Matches: 280, Mismatches: 28, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
157 86 0.31
160 2 0.01
161 1 0.00
164 3 0.01
165 187 0.67
166 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (162 bp):
GCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACTGTCTCCCCTATTCTT
TCAGGGAGTATAGGACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATTCTTTCAGGGAGTA
TAGGACTCGAACAATCTTCAACAAACGTGTCC
Found at i:2155942 original size:102 final size:102
Alignment explanation
Indices: 2155756--2155951 Score: 284
Period size: 102 Copynumber: 1.9 Consensus size: 102
2155746 GTGTCCGCTT
* * *
2155756 CCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTGAGCAAACGTGTCCGCTCCCTATTCTTT
1 CCTATTCTTTCAGGGAGTATAGGAATCGAACAATCTTCAGCAAACGTGTACGCTCCCTATTCTTT
2155821 CAGGGAATAAAAAACTCAAACAATCTTCAACAAGCTC
66 CAGGGAATAAAAAACTCAAACAATCTTCAACAAGCTC
* * * *
2155858 CCTATTTTTTCAGGGAGTATAGGAATCGGACAATCTTCAGCAAATGTGTATGCTCCCTATTCTTT
1 CCTATTCTTTCAGGGAGTATAGGAATCGAACAATCTTCAGCAAACGTGTACGCTCCCTATTCTTT
* * ** *
2155923 CAGGGAGTATAGGAGTCAAACAATCTTCA
66 CAGGGAATAAAAAACTCAAACAATCTTCA
2155952 TAAAATGAGT
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
102 82 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (102 bp):
CCTATTCTTTCAGGGAGTATAGGAATCGAACAATCTTCAGCAAACGTGTACGCTCCCTATTCTTT
CAGGGAATAAAAAACTCAAACAATCTTCAACAAGCTC
Found at i:2157517 original size:38 final size:38
Alignment explanation
Indices: 2157454--2157653 Score: 213
Period size: 38 Copynumber: 5.2 Consensus size: 38
2157444 CCATCAATAG
* * *
2157454 TGCCCTAACATTACTTTATATTGGTACGAGCCTTCAAAA
1 TGCCCCAACATTA-TTTATACTGGTACGAGCCCTCAAAA
* * * * *
2157493 TGCCCCAACATTATTTATATTGGTACAAACCTTTAAAA
1 TGCCCCAACATTATTTATACTGGTACGAGCCCTCAAAA
* * *
2157531 TACCCCAACATTATCTTATACTAGTACGGGCCCTCAAAA
1 TGCCCCAACATTAT-TTATACTGGTACGAGCCCTCAAAA
* * * *
2157570 TTCCTCAATATTATTTATACTGGTACGTGCCCTCAAAA
1 TGCCCCAACATTATTTATACTGGTACGAGCCCTCAAAA
* *
2157608 T-CCCCAACATTAACTTATACTGGTACGGGCCCTCAAAA
1 TGCCCCAACATT-ATTTATACTGGTACGAGCCCTCAAAA
2157646 TGCCCCAA
1 TGCCCCAA
2157654 TATGGGTACT
Statistics
Matches: 137, Mismatches: 21, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
37 8 0.06
38 83 0.61
39 46 0.34
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (38 bp):
TGCCCCAACATTATTTATACTGGTACGAGCCCTCAAAA
Found at i:2157638 original size:76 final size:77
Alignment explanation
Indices: 2157460--2157656 Score: 245
Period size: 77 Copynumber: 2.6 Consensus size: 77
2157450 ATAGTGCCCT
* * * * *
2157460 AACATT-ACTTTATATTGGTACGAGCCTTCAAAATGCCCCAACATTATTTATATTGGTACAAACC
1 AACATTAAC-TTATACTGGTACGGGCCCTCAAAATGCCCCAATATTATTTATACTGGTACAAACC
* *
2157524 TTTAAAATACCCC
65 CTCAAAATACCCC
* * * * ***
2157537 AACATTATCTTATACTAGTACGGGCCCTCAAAATTCCTCAATATTATTTATACTGGTACGTGCCC
1 AACATTAACTTATACTGGTACGGGCCCTCAAAATGCCCCAATATTATTTATACTGGTACAAACCC
2157602 TCAAAAT-CCCC
66 TCAAAATACCCC
2157613 AACATTAACTTATACTGGTACGGGCCCTCAAAATGCCCCAATAT
1 AACATTAACTTATACTGGTACGGGCCCTCAAAATGCCCCAATAT
2157657 GGGTACTCGT
Statistics
Matches: 101, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
76 44 0.44
77 56 0.55
78 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (77 bp):
AACATTAACTTATACTGGTACGGGCCCTCAAAATGCCCCAATATTATTTATACTGGTACAAACCC
TCAAAATACCCC
Found at i:2164704 original size:18 final size:18
Alignment explanation
Indices: 2164681--2164727 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
2164671 GCTATACAAG
2164681 TGTGACTATTCCAAGACT
1 TGTGACTATTCCAAGACT
2164699 TGTGACTATTCCAAGACT
1 TGTGACTATTCCAAGACT
*
2164717 TGTGCCTATTC
1 TGTGACTATTC
2164728 TAGATATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (18 bp):
TGTGACTATTCCAAGACT
Found at i:2164996 original size:20 final size:22
Alignment explanation
Indices: 2164972--2165041 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 22
2164962 ATATCTAGAG
* *
2164972 TTAATTAAATATAT-GTTTTAA
1 TTAATTAAATATATAATTTCAA
*
2164993 -TAATTCAGAATATTTAATTTCAA
1 TTAATT-A-AATATATAATTTCAA
2165016 TTAATTAAATATAT-ATTT-AA
1 TTAATTAAATATATAATTTCAA
2165036 TTAATT
1 TTAATT
2165042 TAAAATAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
20 13 0.32
21 5 0.12
22 12 0.29
23 6 0.15
24 5 0.12
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (22 bp):
TTAATTAAATATATAATTTCAA
Found at i:2165021 original size:24 final size:20
Alignment explanation
Indices: 2164956--2165041 Score: 75
Period size: 22 Copynumber: 4.0 Consensus size: 20
2164946 TACGCTACTA
*
2164956 AAATATATATCTAGAGTTAATT
1 AAATATATATTTA-A-TTAATT
*
2164978 AAATATATGTTTTAA-TAATT
1 AAATATAT-ATTTAATTAATT
*
2164998 CAGAATATTTAATTTCAATTAATT
1 -A-AATATAT-ATTT-AATTAATT
2165022 AAATATATATTTAATTAATT
1 AAATATATATTTAATTAATT
2165042 TAAAATAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
20 13 0.25
21 5 0.09
22 24 0.45
23 6 0.11
24 5 0.09
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (20 bp):
AAATATATATTTAATTAATT
Found at i:2165118 original size:90 final size:88
Alignment explanation
Indices: 2165006--2165179 Score: 276
Period size: 89 Copynumber: 2.0 Consensus size: 88
2164996 TTCAGAATAT
* *
2165006 TTAATTTCAATTAATTAAATATATATTTAATTAATTTAAAATAATAAAATCCCTAATATGAATAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAA-CCCTAATATGAATAG
*
2165071 GGTAACTTGGATATAAAAGGATTA
65 AGTAACTTGGATATAAAAGGATTA
* *
2165095 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGAATAG
*
2165160 AGTAACTTGGCTATAAAAGG
65 AGTAACTTGGATATAAAAGG
2165180 GTGTGTTAGG
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 39 0.50
90 39 0.50
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGAATAGA
GTAACTTGGATATAAAAGGATTA
Found at i:2175274 original size:21 final size:21
Alignment explanation
Indices: 2175250--2175290 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2175240 GAATCGAATA
*
2175250 TAAAATTTGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
2175271 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
2175291 AACTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:2181522 original size:22 final size:21
Alignment explanation
Indices: 2181480--2181519 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2181470 GAGTTTGTTT
*
2181480 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2181501 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2181520 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2183721 original size:21 final size:21
Alignment explanation
Indices: 2183697--2183737 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2183687 GAATCGAATA
*
2183697 TAAAATTTGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
2183718 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
2183738 AACTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:2193096 original size:24 final size:22
Alignment explanation
Indices: 2193052--2193106 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
2193042 CATGCTCCAT
2193052 AGAAGAAAAAAACAGTAGTTCGG
1 AGAA-AAAAAAACAGTAGTTCGG
* *
2193075 AAGAAAAAAAAAGATGTTGTTCGG
1 -AGAAAAAAAAACA-GTAGTTCGG
2193099 -GAAAAAAA
1 AGAAAAAAA
2193107 GAGAAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 8 0.29
23 8 0.29
24 12 0.43
ACGTcount: A:0.56, C:0.05, G:0.24, T:0.15
Consensus pattern (22 bp):
AGAAAAAAAAACAGTAGTTCGG
Found at i:2194404 original size:12 final size:12
Alignment explanation
Indices: 2194387--2194411 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2194377 TATCTTTAAA
2194387 TTAAATTAATTT
1 TTAAATTAATTT
2194399 TTAAATTAATTT
1 TTAAATTAATTT
2194411 T
1 T
2194412 ATTGAGTTTA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTAAATTAATTT
Found at i:2195377 original size:21 final size:21
Alignment explanation
Indices: 2195353--2195392 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2195343 AATTAGTCAT
2195353 TTAATACTTCAAATTGACCTG
1 TTAATACTTCAAATTGACCTG
** *
2195374 TTAATTTTTCGAATTGACC
1 TTAATACTTCAAATTGACC
2195393 ATTCATTATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (21 bp):
TTAATACTTCAAATTGACCTG
Found at i:2197295 original size:6 final size:6
Alignment explanation
Indices: 2197260--2197288 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2197250 AATTATTGGG
2197260 TGGGGA TGGGGA TGGGGA TGGGGA TGGGG
1 TGGGGA TGGGGA TGGGGA TGGGGA TGGGG
2197289 GAAGGGGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.69, T:0.17
Consensus pattern (6 bp):
TGGGGA
Found at i:2198449 original size:30 final size:30
Alignment explanation
Indices: 2198409--2198489 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
2198399 GGACCCGGAG
* ** *
2198409 AAGCCTAAAGAGGCGGAGAAGAAGTCCGAT
1 AAGCCGAAAGAGGCGGAGAAGAAACCCGAA
2198439 AAGCCGAAAGAGGCCGG-GAAGAAACCCGAA
1 AAGCCGAAAGAGG-CGGAGAAGAAACCCGAA
* *
2198469 AAGCCGAAAGAAGCTGAGAAG
1 AAGCCGAAAGAGGCGGAGAAG
2198490 CCTAAAGAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.05
30 38 0.88
31 3 0.07
ACGTcount: A:0.43, C:0.19, G:0.33, T:0.05
Consensus pattern (30 bp):
AAGCCGAAAGAGGCGGAGAAGAAACCCGAA
Found at i:2198527 original size:48 final size:50
Alignment explanation
Indices: 2198475--2198601 Score: 154
Period size: 51 Copynumber: 2.6 Consensus size: 50
2198465 CGAAAAGCCG
* *
2198475 AAAGAAGCTGAGAAGCCTAAAGAGTCGGGG-G-AGAAGGCCGATAAACCA
1 AAAGAAGCTGAGAAGCCTAAAGAGTCGGGGAGAAAAAGGCCGAGAAACCA
*
2198523 AAAGAAGCTGAGAAGCCTAAAGAGGGT-GGGGAGAAAAAGGCTGAGAAACCA
1 AAAGAAGCTGAGAAGCCTAAAGA--GTCGGGGAGAAAAAGGCCGAGAAACCA
* *
2198574 AAAGAAGCGGAGAAACAC-AAAGAGTCGG
1 AAAGAAGCTGAGAAGC-CTAAAGAGTCGG
2198602 CGCCCGCGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
48 23 0.34
49 6 0.09
50 5 0.07
51 33 0.49
52 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.34, T:0.07
Consensus pattern (50 bp):
AAAGAAGCTGAGAAGCCTAAAGAGTCGGGGAGAAAAAGGCCGAGAAACCA
Found at i:2198729 original size:21 final size:18
Alignment explanation
Indices: 2198700--2198755 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
2198690 TGGTGCTGGG
*
2198700 CCTAGTTATTATGGTGGA
1 CCTAGCTATTATGGTGGA
2198718 CCTAGCTATTATGGTGGA
1 CCTAGCTATTATGGTGGA
* *
2198736 CCTAGCTACTACGGTGGA
1 CCTAGCTATTATGGTGGA
2198754 CC
1 CC
2198756 ACCTCAACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (18 bp):
CCTAGCTATTATGGTGGA
Found at i:2201060 original size:21 final size:20
Alignment explanation
Indices: 2201007--2201133 Score: 119
Period size: 21 Copynumber: 5.9 Consensus size: 20
2200997 AAAGTTTGGC
2201007 CAAAAGGGATCGATCTTCTTTT
1 CAAAAGGGATCGATC--CTTTT
* *
2201029 TAAAAGAGATCGATCCTTTAT
1 CAAAAGGGATCGATCCTTT-T
*
2201050 GAAAAGGGATCGATCCTTTT
1 CAAAAGGGATCGATCCTTTT
* *
2201070 GCAAAATGGATCAATCCTTTT
1 -CAAAAGGGATCGATCCTTTT
*
2201091 ACAAAAGGTTGGATCAATCCTTTT
1 -CAAAA-G--GGATCGATCCTTTT
2201115 ACAAAAGGGATCGATCCTT
1 -CAAAAGGGATCGATCCTT
2201134 GTCCTTAAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
20 5 0.06
21 51 0.57
22 13 0.14
23 1 0.01
24 20 0.22
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (20 bp):
CAAAAGGGATCGATCCTTTT
Found at i:2201108 original size:24 final size:23
Alignment explanation
Indices: 2201056--2201122 Score: 93
Period size: 24 Copynumber: 3.0 Consensus size: 23
2201046 TTATGAAAAG
* *
2201056 GGATCGATCCTTTTGCAAAA--T
1 GGATCAATCCTTTTACAAAAGGT
2201077 GGATCAATCCTTTTACAAAAGGTT
1 GGATCAATCCTTTTACAAAAGG-T
2201101 GGATCAATCCTTTTACAAAAGG
1 GGATCAATCCTTTTACAAAAGG
2201123 GATCGATCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
21 18 0.44
24 23 0.56
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (23 bp):
GGATCAATCCTTTTACAAAAGGT
Found at i:2201957 original size:21 final size:20
Alignment explanation
Indices: 2201924--2202005 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 20
2201914 TTTTTTGCTC
* *
2201924 AAAAGATTGATCCCCTAGAA
1 AAAAGATCGATCCCTTAGAA
* *
2201944 AAAAGGATCGATCCCTTTGACC
1 AAAA-GATCGATCCCTTAGA-A
2201966 AAAAGATCGATCCCTTTTA-AA
1 AAAAGATCGATCCC--TTAGAA
2201987 AAAAGATCGATCCCTTAGA
1 AAAAGATCGATCCCTTAGA
2202006 CAACAGTGAG
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
19 3 0.06
20 5 0.10
21 36 0.71
22 5 0.10
23 2 0.04
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (20 bp):
AAAAGATCGATCCCTTAGAA
Found at i:2201988 original size:42 final size:42
Alignment explanation
Indices: 2201923--2202002 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
2201913 ATTTTTTGCT
* *
2201923 CAAAAGATTGATCCCCTAGAAAAAAGGATCGATCCCTTTGAC
1 CAAAAGATCGATCCCCTAGAAAAAAAGATCGATCCCTTTGAC
* **
2201965 CAAAAGATCGATCCCTTTTAAAAAAAGATCGATCCCTT
1 CAAAAGATCGATCCCCTAGAAAAAAAGATCGATCCCTT
2202003 AGACAACAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (42 bp):
CAAAAGATCGATCCCCTAGAAAAAAAGATCGATCCCTTTGAC
Found at i:2204672 original size:20 final size:20
Alignment explanation
Indices: 2204647--2204696 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2204637 TTTGAGTTAA
2204647 TTAAAATATGCTTAAAGTGT
1 TTAAAATATGCTTAAAGTGT
* * *
2204667 TTAAAATGTGTTTAAAGTTT
1 TTAAAATATGCTTAAAGTGT
*
2204687 TTTAAATATG
1 TTAAAATATG
2204697 AAAAATACTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.46
Consensus pattern (20 bp):
TTAAAATATGCTTAAAGTGT
Found at i:2204790 original size:19 final size:21
Alignment explanation
Indices: 2204762--2204815 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
2204752 TAATGTTCAT
*
2204762 AGTTTGGAAA-TTTT-TTAAG
1 AGTTTTGAAACTTTTATTAAG
2204781 AGTTTTGAAACTTTTATTAAG
1 AGTTTTGAAACTTTTATTAAG
2204802 A-TTTCTGAAACTTT
1 AGTTT-TGAAACTTT
2204816 ACAAAAGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 9 0.29
20 7 0.23
21 15 0.48
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (21 bp):
AGTTTTGAAACTTTTATTAAG
Found at i:2204934 original size:20 final size:20
Alignment explanation
Indices: 2204893--2204935 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2204883 TTTAATTAAG
*
2204893 AGTTTCGAAACTTTCATCAA
1 AGTTTCGAAACTTTCAACAA
* *
2204913 AGTTTTGAAACTTTCAAGAA
1 AGTTTCGAAACTTTCAACAA
2204933 AGT
1 AGT
2204936 GTGTTTAAAA
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:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (20 bp):
AGTTTCGAAACTTTCAACAA
Found at i:2204987 original size:20 final size:20
Alignment explanation
Indices: 2204942--2204987 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2204932 AAGTGTGTTT
* *
2204942 AAAAGTTTCTATACTTTCAC
1 AAAAGTTTCGAAACTTTCAC
*
2204962 -AAAGTTTCGAAACTTTCTC
1 AAAAGTTTCGAAACTTTCAC
2204981 AAAAGTT
1 AAAAGTT
2204988 AACGGATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (20 bp):
AAAAGTTTCGAAACTTTCAC
Found at i:2208687 original size:4 final size:4
Alignment explanation
Indices: 2208678--2208774 Score: 167
Period size: 4 Copynumber: 24.2 Consensus size: 4
2208668 TGTATAGTAA
2208678 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * *
2208726 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAC ATAC ATAT TTAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
2208774 A
1 A
2208775 AGCATGAGAT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 89 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (4 bp):
ATAT
Found at i:2208689 original size:6 final size:6
Alignment explanation
Indices: 2208678--2208774 Score: 167
Period size: 6 Copynumber: 16.2 Consensus size: 6
2208668 TGTATAGTAA
2208678 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * *
2208726 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAC ATACAT ATTTAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
2208774 A
1 A
2208775 AGCATGAGAT
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 86 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATAT
Found at i:2208693 original size:10 final size:10
Alignment explanation
Indices: 2208678--2208774 Score: 167
Period size: 10 Copynumber: 9.7 Consensus size: 10
2208668 TGTATAGTAA
2208678 ATATATATAT
1 ATATATATAT
2208688 ATATATATAT
1 ATATATATAT
2208698 ATATATATAT
1 ATATATATAT
2208708 ATATATATAT
1 ATATATATAT
2208718 ATATATATAT
1 ATATATATAT
2208728 ATATATATAT
1 ATATATATAT
2208738 ATATATATAT
1 ATATATATAT
2208748 ATATATATAT
1 ATATATATAT
* *
2208758 ATACATACAT
1 ATATATATAT
*
2208768 ATTTATA
1 ATATATA
2208775 AGCATGAGAT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 83 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (10 bp):
ATATATATAT
Found at i:2209580 original size:23 final size:23
Alignment explanation
Indices: 2209546--2209589 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2209536 TGGAGAACAT
2209546 GGCGGCGAAGCAGTTGGAGTAGA
1 GGCGGCGAAGCAGTTGGAGTAGA
*
2209569 GGCGGCGGAGCAGTTGGAGTA
1 GGCGGCGAAGCAGTTGGAGTA
2209590 AAGAATCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.14, G:0.50, T:0.14
Consensus pattern (23 bp):
GGCGGCGAAGCAGTTGGAGTAGA
Found at i:2215255 original size:14 final size:14
Alignment explanation
Indices: 2215236--2215269 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2215226 GAGGCGCGAC
2215236 TAGATGTTGAAGAA
1 TAGATGTTGAAGAA
2215250 TAGATGTTGAAGAA
1 TAGATGTTGAAGAA
*
2215264 TCGATG
1 TAGATG
2215270 GTATACGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.29, T:0.29
Consensus pattern (14 bp):
TAGATGTTGAAGAA
Found at i:2215306 original size:7 final size:7
Alignment explanation
Indices: 2215296--2215320 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2215286 AAGCTAGAAG
2215296 GGCTGCT
1 GGCTGCT
2215303 GGCTGCT
1 GGCTGCT
2215310 GGCTGCT
1 GGCTGCT
2215317 GGCT
1 GGCT
2215321 TGATAATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.28, G:0.44, T:0.28
Consensus pattern (7 bp):
GGCTGCT
Found at i:2220236 original size:138 final size:137
Alignment explanation
Indices: 2219971--2220252 Score: 379
Period size: 138 Copynumber: 2.1 Consensus size: 137
2219961 GTCGTAGGTG
* ** *
2219971 CATTTCGACATAAATTGTGTATAATGGTTATCGGTCGATTTTGTGTAATGCATAACGGTGCATTT
1 CATTTCGACATAAATTATGTATAAAAGTTATCGATCGATTTTGTGTAATGCATAACGGTGCATTT
** * * * *
2220036 TTGTATCAGTAATATGTGTACTTTCGGCACTAGATGTGCAACCATGGTATTTATAATGAGTTTGT
66 TCATATCAGTAATATATGTACTTTCGACACTAGATGTGCAACCATGGAATTCATAATGAGTTTGT
2220101 GAATTAC
131 GAATTAC
* *
2220108 CATTTCGACATATAATTATGTATAAAAGTTATCGATCGATTTTGT-TAAATGCATAATGGTGTAT
1 CATTTCGACATA-AATTATGTATAAAAGTTATCGATCGATTTTGTGT-AATGCATAACGGTGCAT
* * *
2220172 TTTCATATCAGTACTATATGTACTTTCTACACTATG-TGTGCATCCATGGAATTCATAATGAGTT
64 TTTCATATCAGTAATATATGTACTTTCGACACTA-GATGTGCAACCATGGAATTCATAATGAGTT
*
2220236 TGTGAATTTC
128 TGTGAATTAC
2220246 CATTTCG
1 CATTTCG
2220253 GCACTTAGGT
Statistics
Matches: 126, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
137 13 0.10
138 112 0.89
139 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (137 bp):
CATTTCGACATAAATTATGTATAAAAGTTATCGATCGATTTTGTGTAATGCATAACGGTGCATTT
TCATATCAGTAATATATGTACTTTCGACACTAGATGTGCAACCATGGAATTCATAATGAGTTTGT
GAATTAC
Found at i:2221284 original size:31 final size:31
Alignment explanation
Indices: 2221246--2221370 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
2221236 CCCGAAGGAC
* * *
2221246 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
2221277 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2221308 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2221339 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2221370 C
1 C
2221371 CCTCGACCCT
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2223152 original size:29 final size:29
Alignment explanation
Indices: 2223111--2223176 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
2223101 AATTATGTCT
* * *
2223111 ACTTTTGATAATTAGATGGCATGTATTTG
1 ACTTATGAAAATTAGATGGAATGTATTTG
***
2223140 ACTTATGAAAATTTTCTGGAATGTATTTG
1 ACTTATGAAAATTAGATGGAATGTATTTG
2223169 ACTTATGA
1 ACTTATGA
2223177 TTAGTGTAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (29 bp):
ACTTATGAAAATTAGATGGAATGTATTTG
Found at i:2223503 original size:3 final size:3
Alignment explanation
Indices: 2223495--2223522 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2223485 TGAATGAATC
2223495 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2223523 TTAAAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2224957 original size:3 final size:3
Alignment explanation
Indices: 2224951--2224988 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2224941 ATTATTATTA
2224951 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
2224989 TGACTCGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:2225402 original size:3 final size:3
Alignment explanation
Indices: 2225394--2225419 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2225384 TTAATAAGCA
2225394 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2225420 ATATTGAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2226780 original size:3 final size:3
Alignment explanation
Indices: 2226772--2226836 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
2226762 AGGATTGGTT
2226772 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2226820 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
2226837 TGGTATTTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2226942 original size:5 final size:5
Alignment explanation
Indices: 2226932--2227023 Score: 175
Period size: 5 Copynumber: 18.4 Consensus size: 5
2226922 ACTAGATTAG
*
2226932 GGTTA GGTTA GGTTA GGTTA GGCTA GGTTA GGTTA GGTTA GGTTA GGTTA
1 GGTTA GGTTA GGTTA GGTTA GGTTA GGTTA GGTTA GGTTA GGTTA GGTTA
2226982 GGTTA GGTTA GGTTA GGTTA GGTTA GGTTA GGTTA GGTTA GG
1 GGTTA GGTTA GGTTA GGTTA GGTTA GGTTA GGTTA GGTTA GG
2227024 CTTAAGGTTT
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 85 1.00
ACGTcount: A:0.20, C:0.01, G:0.41, T:0.38
Consensus pattern (5 bp):
GGTTA
Found at i:2227140 original size:17 final size:17
Alignment explanation
Indices: 2227118--2227171 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
2227108 TGGATCTGTA
2227118 AATAAATAA-AAAATATT
1 AATAAA-AATAAAATATT
*
2227135 AATAAAAATAAAGTATT
1 AATAAAAATAAAATATT
* *
2227152 AATAATAATTAAATA-T
1 AATAAAAATAAAATATT
2227168 AATA
1 AATA
2227172 TTTATACTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 7 0.22
17 25 0.78
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
AATAAAAATAAAATATT
Found at i:2231915 original size:129 final size:129
Alignment explanation
Indices: 2231738--2232022 Score: 527
Period size: 129 Copynumber: 2.2 Consensus size: 129
2231728 ATACAAAGGA
* ***
2231738 AGTGCATCGATGTACCCATTAAA-AATGGAAACATCGAATGCAGTTAGTGCATCAATGCATAAGG
1 AGTGCATCGATGCACATGTTAAAGAATGGAAACATCGAATGCAGTTAGTGCATCAATGCATAAGG
2231802 AGTGCATCGATGCACCTCCTTAAAATGAAAACATCGAAGGTGATTGGTGTATCGATGCATGGGT
66 AGTGCATCGATGCACCTCCTTAAAATGAAAACATCGAAGGTGATTGGTGTATCGATGCATGGGT
2231866 AGTGCATCGATGCACATGTTAAAGAATGGAAACATCGAATGCAGTTAGTGCATCAATGCATAAGG
1 AGTGCATCGATGCACATGTTAAAGAATGGAAACATCGAATGCAGTTAGTGCATCAATGCATAAGG
2231931 AGTGCATCGATGCACCTCCTTAAAATGAAAACATCGAAGGTGATTGGTGTATCGATGCATGGGT
66 AGTGCATCGATGCACCTCCTTAAAATGAAAACATCGAAGGTGATTGGTGTATCGATGCATGGGT
2231995 AGTGCATCGATGCACATGTTAAAGAATG
1 AGTGCATCGATGCACATGTTAAAGAATG
2232023 CATCGATGCA
Statistics
Matches: 152, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
128 19 0.12
129 133 0.88
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (129 bp):
AGTGCATCGATGCACATGTTAAAGAATGGAAACATCGAATGCAGTTAGTGCATCAATGCATAAGG
AGTGCATCGATGCACCTCCTTAAAATGAAAACATCGAAGGTGATTGGTGTATCGATGCATGGGT
Found at i:2232009 original size:64 final size:65
Alignment explanation
Indices: 2231733--2231968 Score: 288
Period size: 64 Copynumber: 3.7 Consensus size: 65
2231723 TATCGATACA
* * *
2231733 AAGGAAGTGCATCGATGTACC-CATTAAAAATGGAAACATCGAATGCAGTTAGTGCATCAATGCA
1 AAGG-AGTGCATCGATGCACCTCCTTAAAAATGAAAACATCGAATGCAGTTAGTGCATCAATGCA
2231797 T
65 T
* * *
2231798 AAGGAGTGCATCGATGCACCTCCTT-AAAATGAAAACATCGAAGGTG-A-TTGGTGTATCGATGC
1 AAGGAGTGCATCGATGCACCTCCTTAAAAATGAAAACATCGAA--TGCAGTTAGTGCATCAATGC
2231860 AT
64 AT
* * * *
2231862 -GGGTAGTGCATCGATGCACAT-GTTAAAGAATGGAAACATCGAATGCAGTTAGTGCATCAATGC
1 AAGG-AGTGCATCGATGCACCTCCTTAAA-AATGAAAACATCGAATGCAGTTAGTGCATCAATGC
2231925 AT
64 AT
2231927 AAGGAGTGCATCGATGCACCTCCTT-AAAATGAAAACATCGAA
1 AAGGAGTGCATCGATGCACCTCCTTAAAAATGAAAACATCGAA
2231969 GGTGATTGGT
Statistics
Matches: 144, Mismatches: 17, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
63 6 0.04
64 78 0.54
65 54 0.38
66 6 0.04
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (65 bp):
AAGGAGTGCATCGATGCACCTCCTTAAAAATGAAAACATCGAATGCAGTTAGTGCATCAATGCAT
Found at i:2232042 original size:20 final size:22
Alignment explanation
Indices: 2231997--2232054 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
2231987 GCATGGGTAG
2231997 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
2232021 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
2232041 TGTATCGATGCACT
1 TGCATCGATGCACT
2232055 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:2233212 original size:193 final size:193
Alignment explanation
Indices: 2232883--2233272 Score: 780
Period size: 193 Copynumber: 2.0 Consensus size: 193
2232873 ATAACAATAA
2232883 ATATATATTACATGTAAAGTATATGCTTTTGTGATATGAATTGTATTATATGTTATATAAGATGA
1 ATATATATTACATGTAAAGTATATGCTTTTGTGATATGAATTGTATTATATGTTATATAAGATGA
2232948 TGTGTATATTGCTTGATTAATTGAATCATATGTGGCTTAAAAGAATGAATATATGAGTATATGAT
66 TGTGTATATTGCTTGATTAATTGAATCATATGTGGCTTAAAAGAATGAATATATGAGTATATGAT
2233013 TATGAGACATAAATGATAAGAATATGGATAGTGGAATAAGGTTAGTAATGGAAATAGTGTGAG
131 TATGAGACATAAATGATAAGAATATGGATAGTGGAATAAGGTTAGTAATGGAAATAGTGTGAG
2233076 ATATATATTACATGTAAAGTATATGCTTTTGTGATATGAATTGTATTATATGTTATATAAGATGA
1 ATATATATTACATGTAAAGTATATGCTTTTGTGATATGAATTGTATTATATGTTATATAAGATGA
2233141 TGTGTATATTGCTTGATTAATTGAATCATATGTGGCTTAAAAGAATGAATATATGAGTATATGAT
66 TGTGTATATTGCTTGATTAATTGAATCATATGTGGCTTAAAAGAATGAATATATGAGTATATGAT
2233206 TATGAGACATAAATGATAAGAATATGGATAGTGGAATAAGGTTAGTAATGGAAATAGTGTGAG
131 TATGAGACATAAATGATAAGAATATGGATAGTGGAATAAGGTTAGTAATGGAAATAGTGTGAG
2233269 ATAT
1 ATAT
2233273 GTATATGTAT
Statistics
Matches: 197, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
193 197 1.00
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.37
Consensus pattern (193 bp):
ATATATATTACATGTAAAGTATATGCTTTTGTGATATGAATTGTATTATATGTTATATAAGATGA
TGTGTATATTGCTTGATTAATTGAATCATATGTGGCTTAAAAGAATGAATATATGAGTATATGAT
TATGAGACATAAATGATAAGAATATGGATAGTGGAATAAGGTTAGTAATGGAAATAGTGTGAG
Found at i:2233280 original size:6 final size:6
Alignment explanation
Indices: 2233269--2233990 Score: 1282
Period size: 6 Copynumber: 123.0 Consensus size: 6
2233259 ATAGTGTGAG
2233269 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
*
2233317 ATATGT ATATGT ATA--T ATATGT ATATGT ATATAT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
2233363 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
2233411 ATATGT ATA-GT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGTAT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATG--T
2233460 ATATGT A-ATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
2233507 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATA--T
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
*
2233553 ATATGT ATATGT ATATGT ATATG- -TATGT ATATGT ATATGT ATATAT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
2233599 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
2233647 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
2233695 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATA--T
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
2233741 ATATGT ATATGT ATATGT ATATGT ATATG- -TATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
2233787 ATATGT ATATG- -TATGT ATATGT -TATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
2233832 ATATGT ATATGT ATATGT ATATG- -TATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
2233878 ATATGT ATA-GT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
2233925 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
2233973 ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT
2233991 GTATATTACA
Statistics
Matches: 692, Mismatches: 4, Indels: 40
0.94 0.01 0.05
Matches are distributed among these distances:
4 28 0.04
5 20 0.03
6 638 0.92
8 6 0.01
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:2236787 original size:25 final size:25
Alignment explanation
Indices: 2236757--2236807 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2236747 AAATGCATGA
2236757 TTTATGAATGCGACATTAATAAATG
1 TTTATGAATGCGACATTAATAAATG
2236782 TTTATGAATGCGACATTAATAAATG
1 TTTATGAATGCGACATTAATAAATG
2236807 T
1 T
2236808 CATGTATAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (25 bp):
TTTATGAATGCGACATTAATAAATG
Found at i:2240331 original size:22 final size:22
Alignment explanation
Indices: 2240300--2240346 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2240290 ACAATAAAAT
*
2240300 TTTTATACATAAACATAAATAA
1 TTTTACACATAAACATAAATAA
*
2240322 TTTTACACATAAACCTAAATAA
1 TTTTACACATAAACATAAATAA
2240344 TTT
1 TTT
2240347 AAATAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTTACACATAAACATAAATAA
Found at i:2241878 original size:14 final size:14
Alignment explanation
Indices: 2241859--2241897 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2241849 TGGATCTGTA
* *
2241859 AATAAAAATATATT
1 AATAAAAATAAAGT
2241873 AATAAAAATAAAGT
1 AATAAAAATAAAGT
*
2241887 AATAATAATAA
1 AATAAAAATAA
2241898 TAATAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (14 bp):
AATAAAAATAAAGT
Found at i:2242837 original size:9 final size:9
Alignment explanation
Indices: 2242823--2242847 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2242813 AGCATAACAA
2242823 CTTCATCAT
1 CTTCATCAT
2242832 CTTCATCAT
1 CTTCATCAT
2242841 CTTCATC
1 CTTCATC
2242848 TACAAGGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.36, G:0.00, T:0.44
Consensus pattern (9 bp):
CTTCATCAT
Found at i:2243472 original size:10 final size:10
Alignment explanation
Indices: 2243457--2243482 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2243447 GCGCCTCAGA
2243457 GCCTCGCTGC
1 GCCTCGCTGC
2243467 GCCTCGCTGC
1 GCCTCGCTGC
2243477 GCCTCG
1 GCCTCG
2243483 GTACGCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.50, G:0.31, T:0.19
Consensus pattern (10 bp):
GCCTCGCTGC
Found at i:2246648 original size:2 final size:2
Alignment explanation
Indices: 2246641--2246675 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2246631 ATAATACGGC
2246641 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2246676 ATTAAGCAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2247096 original size:16 final size:16
Alignment explanation
Indices: 2247075--2247108 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2247065 GGCCAATTGT
*
2247075 GACCCAATATCACACG
1 GACCCAATAGCACACG
2247091 GACCCAATAGCACACG
1 GACCCAATAGCACACG
2247107 GA
1 GA
2247109 ACCATAAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.35, G:0.18, T:0.09
Consensus pattern (16 bp):
GACCCAATAGCACACG
Found at i:2247118 original size:16 final size:16
Alignment explanation
Indices: 2247078--2247112 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2247068 CAATTGTGAC
* *
2247078 CCAATATCACACGGAC
1 CCAATAGCACACGGAA
2247094 CCAATAGCACACGGAA
1 CCAATAGCACACGGAA
2247110 CCA
1 CCA
2247113 TAAGCATCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.37, G:0.14, T:0.09
Consensus pattern (16 bp):
CCAATAGCACACGGAA
Found at i:2247350 original size:16 final size:16
Alignment explanation
Indices: 2247329--2247362 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2247319 GGCCAATTGT
*
2247329 GACCCAATATCACACG
1 GACCCAATAGCACACG
2247345 GACCCAATAGCACACG
1 GACCCAATAGCACACG
2247361 GA
1 GA
2247363 ACCATAAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.35, G:0.18, T:0.09
Consensus pattern (16 bp):
GACCCAATAGCACACG
Found at i:2247372 original size:16 final size:16
Alignment explanation
Indices: 2247332--2247366 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2247322 CAATTGTGAC
* *
2247332 CCAATATCACACGGAC
1 CCAATAGCACACGGAA
2247348 CCAATAGCACACGGAA
1 CCAATAGCACACGGAA
2247364 CCA
1 CCA
2247367 TAAGCATCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.37, G:0.14, T:0.09
Consensus pattern (16 bp):
CCAATAGCACACGGAA
Found at i:2247491 original size:254 final size:255
Alignment explanation
Indices: 2247042--2247552 Score: 983
Period size: 254 Copynumber: 2.0 Consensus size: 255
2247032 TATATTTGGA
2247042 GGTGTCCCAGTCGGAAGCATAAAGGCCAATTGTGACCCAATATCACACGGACCCAATAGCACACG
1 GGTGTCCCAGTCGGAAGCATAAAGGCCAATTGTGACCCAATATCACACGGACCCAATAGCACACG
2247107 GAACCATAAGCATCAGGGGTGCACGTTCATGGTCCGTGCCATTTGACCCAACAACGGAACCCATA
66 GAACCATAAGCATCAGGGGTGCACGTTCATGGTCCGTGCCATTTGACCCAACAACGGAACCCATA
2247172 AGAGTCGCCGCCGCATCATCTCCGTTATGAACTCGGTAATCACCGCACATATCAGACACACCGCG
131 AGAGTCGCCGCCGCATCATCTCCGTTATGAACTCGGTAATCACCGCACATATCAGACACACCGCG
2247237 GGTGCGATAATGAGATACGGGACGCGTTCAAGGAAATACA-GGTTTCAAATAACATAGTC
196 GGTGCGATAATGAGATACGGGACGCGTTCAAGGAAATACAGGGTTTCAAATAACATAGTC
2247296 GGTGTCCCAGTCGGAAGCATAAAGGCCAATTGTGACCCAATATCACACGGACCCAATAGCACACG
1 GGTGTCCCAGTCGGAAGCATAAAGGCCAATTGTGACCCAATATCACACGGACCCAATAGCACACG
2247361 GAACCATAAGCATCAGGGGTGCACGTTCATGGTCCGTGCCATTTGACCCAACAACGGAA-CCATA
66 GAACCATAAGCATCAGGGGTGCACGTTCATGGTCCGTGCCATTTGACCCAACAACGGAACCCATA
2247425 AGAGTCGCCGCCGCATCAT-TCGACGTTATGAACTCGGTAATCACCGCACATATCAGACACACCG
131 AGAGTCGCCGCCGCATCATCTC--CGTTATGAACTCGGTAATCACCGCACATATCAGACACACCG
2247489 CGGGTGCGATAATGAGATACGGGACGCGTTCAAGGAAATACAGGGTTTCAAATAACATAGTC
194 CGGGTGCGATAATGAGATACGGGACGCGTTCAAGGAAATACAGGGTTTCAAATAACATAGTC
2247551 GG
1 GG
2247553 CGAGTCCGCT
Statistics
Matches: 254, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
252 2 0.01
253 24 0.09
254 207 0.81
255 21 0.08
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (255 bp):
GGTGTCCCAGTCGGAAGCATAAAGGCCAATTGTGACCCAATATCACACGGACCCAATAGCACACG
GAACCATAAGCATCAGGGGTGCACGTTCATGGTCCGTGCCATTTGACCCAACAACGGAACCCATA
AGAGTCGCCGCCGCATCATCTCCGTTATGAACTCGGTAATCACCGCACATATCAGACACACCGCG
GGTGCGATAATGAGATACGGGACGCGTTCAAGGAAATACAGGGTTTCAAATAACATAGTC
Found at i:2259605 original size:20 final size:21
Alignment explanation
Indices: 2259567--2259605 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2259557 AAAATATATA
**
2259567 TATATAAATTTTATTATAAAG
1 TATATAAATTTTAGAATAAAG
2259588 TATATAAA-TTTAGAATAA
1 TATATAAATTTTAGAATAA
2259606 TAAAGTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
TATATAAATTTTAGAATAAAG
Found at i:2259648 original size:14 final size:14
Alignment explanation
Indices: 2259629--2259659 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2259619 TTTCGATGTT
2259629 TTTTTATATAAATA
1 TTTTTATATAAATA
*
2259643 TTTTTATTTAAATA
1 TTTTTATATAAATA
2259657 TTT
1 TTT
2259660 AGAATTCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTATATAAATA
Found at i:2263433 original size:155 final size:155
Alignment explanation
Indices: 2263176--2263459 Score: 374
Period size: 155 Copynumber: 1.8 Consensus size: 155
2263166 AGACACTCTC
* * * * *
2263176 TTAAGCTTAATATTAGCTCAAATTCACACCTTCTTGATCAATTGCAGTTTTCTTCCTAAACAGAA
1 TTAACCTTAATATTAGCTCAAATTCACAACTTCTTGATCAATAGCAATTTTCTTCCTAAACAAAA
* * * * * *
2263241 TCTAAACTGACCAAAGCTTGATTGCAACTTGTGATACTTTAATCTTCT-CTCTTTCTAAGACAAA
66 ACTAAACTGACCAAAGCCTGATTACAACATGCGATACTTCAATCTTCTCCT-TTTCTAAGACAAA
2263305 CATTTACATAAATGCACTATTTCAAT
130 CATTTACATAAATGCACTATTTCAAT
* * * * *
2263331 TTAACCTTAATATTAGCTCCATTTCGCAACTTCTTGATTAATAGTAATTTTCTTCCTAAACAAAA
1 TTAACCTTAATATTAGCTCAAATTCACAACTTCTTGATCAATAGCAATTTTCTTCCTAAACAAAA
* *
2263396 ACTAAACTGA-CATAAGCCTGATTACAACATGCGATACTTCAATTTTCTCCTTTTCTGAGACAAA
66 ACTAAACTGACCA-AAGCCTGATTACAACATGCGATACTTCAATCTTCTCCTTTTCTAAGACAAA
2263460 TATATGTATA
Statistics
Matches: 109, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
154 2 0.02
155 105 0.96
156 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.36
Consensus pattern (155 bp):
TTAACCTTAATATTAGCTCAAATTCACAACTTCTTGATCAATAGCAATTTTCTTCCTAAACAAAA
ACTAAACTGACCAAAGCCTGATTACAACATGCGATACTTCAATCTTCTCCTTTTCTAAGACAAAC
ATTTACATAAATGCACTATTTCAAT
Found at i:2268643 original size:20 final size:20
Alignment explanation
Indices: 2268615--2268659 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2268605 CTCTTTTAAT
* *
2268615 ATTTTATTTTAAAAATAAAA
1 ATTTAATTTCAAAAATAAAA
*
2268635 ATTTAATTTCATAAATAAAA
1 ATTTAATTTCAAAAATAAAA
2268655 ATTTA
1 ATTTA
2268660 TTAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTAATTTCAAAAATAAAA
Found at i:2269206 original size:16 final size:16
Alignment explanation
Indices: 2269185--2269226 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2269175 TGAGAAAAAT
2269185 TTAATTTAAATTTAAA
1 TTAATTTAAATTTAAA
*
2269201 TTAATTTAATTTTAAA
1 TTAATTTAAATTTAAA
*
2269217 ATAATGTTAA
1 TTAAT-TTAA
2269227 TAAATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTAATTTAAATTTAAA
Found at i:2273699 original size:50 final size:51
Alignment explanation
Indices: 2273627--2273961 Score: 301
Period size: 50 Copynumber: 6.8 Consensus size: 51
2273617 AATCATACTA
* * *
2273627 AAAAAAATATATAGCACTTAACACATACTTACACCGGTATAAGTGAATAAAAT
1 AAAAAAATGTA-A-CACTTAACACATACTTACACCGATGTAAGTGAATAAAAT
*
2273680 -AAAAAGTGTAACACTTAACACATACTTACACCGAT-TAAGTGAATAAAA-
1 AAAAAAATGTAACACTTAACACATACTTACACCGATGTAAGTGAATAAAAT
* * *
2273728 AAAAAAA--T---ACTTAACAC-TAC-TACACCAAATCTAAATGAATAAAAT
1 AAAAAAATGTAACACTTAACACATACTTACACC-GATGTAAGTGAATAAAAT
* * * * * *
2273773 AAAAAAATGTAGCATTTAACACATACTTATAACGGTGTAAGTAAATAAAAT
1 AAAAAAATGTAACACTTAACACATACTTACACCGATGTAAGTGAATAAAAT
* * *
2273824 AAAAAAAGTGTAGCACTT-A-ACATACTTATA-CGATGTAAGTGAATAAAGT
1 AAAAAAA-TGTAACACTTAACACATACTTACACCGATGTAAGTGAATAAAAT
* * * * *
2273873 AAAATATTGTAGCACTTAACACATACTTACA-CGGTGTAAG-AAAT-AAAT
1 AAAAAAATGTAACACTTAACACATACTTACACCGATGTAAGTGAATAAAAT
*
2273921 AAAAAAATGTAGA-ACTTAACACATACTTACA-TGATGTAAGT
1 AAAAAAATGTA-ACACTTAACACATACTTACACCGATGTAAGT
2273962 ATGTATATAT
Statistics
Matches: 237, Mismatches: 29, Indels: 36
0.78 0.10 0.12
Matches are distributed among these distances:
42 6 0.03
43 5 0.02
44 21 0.09
45 7 0.03
47 2 0.01
48 47 0.20
49 43 0.18
50 60 0.25
51 25 0.11
52 21 0.09
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (51 bp):
AAAAAAATGTAACACTTAACACATACTTACACCGATGTAAGTGAATAAAAT
Found at i:2274034 original size:2 final size:2
Alignment explanation
Indices: 2274027--2274057 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2274017 AGTATGTTTC
2274027 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 T
2274058 TAAGTTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2274212 original size:2 final size:2
Alignment explanation
Indices: 2274205--2274241 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2274195 AGTATGTTTC
2274205 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2274242 TAAGTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2281978 original size:18 final size:18
Alignment explanation
Indices: 2281952--2281998 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2281942 TTTTAATATT
* *
2281952 TTAATTTAAATTTACATA
1 TTAAATTAAATTCACATA
*
2281970 TTAAATTAAATTCACATC
1 TTAAATTAAATTCACATA
2281988 TTAACATTAAA
1 TTAA-ATTAAA
2281999 AAATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAATTAAATTCACATA
Found at i:2282076 original size:30 final size:29
Alignment explanation
Indices: 2282042--2282130 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 29
2282032 AATATATTTA
*
2282042 ATTTTAATTTGAAAAATATATTTTAATATT
1 ATTTTAATTT-AAAAATATATCTTAATATT
* * *
2282072 ATTTTAACTTAAAAATATATCTTATTCTT
1 ATTTTAATTTAAAAATATATCTTAATATT
*
2282101 -TTATTAATTTTTAAAATATATCTTAA-ATT
1 ATT-TTAA-TTTAAAAATATATCTTAATATT
2282130 A
1 A
2282131 AAATAAAAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
28 2 0.04
29 22 0.46
30 24 0.50
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (29 bp):
ATTTTAATTTAAAAATATATCTTAATATT
Found at i:2282174 original size:30 final size:28
Alignment explanation
Indices: 2282112--2282461 Score: 98
Period size: 30 Copynumber: 11.9 Consensus size: 28
2282102 TATTAATTTT
*
2282112 TAAAATATATCTTAAATTAAAATAAAAG
1 TAAAATATATCTTAAATTAAAATAAAAA
*
2282140 TAAAATATAT-TTCATAATTTAAGATAAAAA
1 TAAAATATATCTT-A-AA-TTAAAATAAAAA
* ** *
2282170 TAAAATAT-T-TTAAAGGTAAAATATGAT
1 TAAAATATATCTTAAA-TTAAAATAAAAA
* * ** * *
2282197 TAAAATAAAAATTTTAAGCTAAAATAAGAT
1 TAAAAT--ATATCTTAAATTAAAATAAAAA
* * * *
2282227 TAAAATATATTTTTTAAACTAAAATAAGAC
1 TAAAATATA--TCTTAAATTAAAATAAAAA
* * * *
2282257 TAGAATATATATTTTTAAGTTAAAATAAGAC
1 TA-AA-ATATA-TCTTAAATTAAAATAAAAA
* * ** * *
2282288 TAAAA-AAATTTTAAGCTAAAATAAGAT
1 TAAAATATATCTTAAATTAAAATAAAAA
* * * *
2282315 TAAAATATATTTTTTAAACTAAAATAAGAC
1 TAAAATATA--TCTTAAATTAAAATAAAAA
* * * *
2282345 TAGAATATATATTTTTAAGTTAAAATAAGAC
1 TA-AA-ATATA-TCTTAAATTAAAATAAAAA
* *
2282376 TAAAATATATTTTTTAAATAAAAATAAAAA
1 TAAAATATA--TCTTAAATTAAAATAAAAA
* * *
2282406 TAAATTATAT-TGAATAAGTTAAGATAAAAA
1 TAAAATATATCT---TAAATTAAAATAAAAA
*
2282436 TAAAATATACTTTTAATATTAAAATA
1 TAAAATATA-TCTTAA-ATTAAAATA
2282462 TGTATTTAAA
Statistics
Matches: 263, Mismatches: 36, Indels: 44
0.77 0.10 0.13
Matches are distributed among these distances:
27 40 0.15
28 19 0.07
29 15 0.06
30 129 0.49
31 49 0.19
32 11 0.04
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (28 bp):
TAAAATATATCTTAAATTAAAATAAAAA
Found at i:2282183 original size:16 final size:16
Alignment explanation
Indices: 2282164--2282213 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
2282154 TAATTTAAGA
2282164 TAAAAATAAAATATTT
1 TAAAAATAAAATATTT
** *
2282180 TAAAGGTAAAATATGAT
1 TAAAAATAAAATAT-TT
2282197 T-AAAATAAAA-ATTT
1 TAAAAATAAAATATTT
2282211 TAA
1 TAA
2282214 GCTAAAATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
14 2 0.08
15 3 0.12
16 19 0.73
17 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (16 bp):
TAAAAATAAAATATTT
Found at i:2282312 original size:88 final size:88
Alignment explanation
Indices: 2282203--2282380 Score: 356
Period size: 88 Copynumber: 2.0 Consensus size: 88
2282193 TGATTAAAAT
2282203 AAAAATTTTAAGCTAAAATAAGATTAAAATATATTTTTTAAACTAAAATAAGACTAGAATATATA
1 AAAAATTTTAAGCTAAAATAAGATTAAAATATATTTTTTAAACTAAAATAAGACTAGAATATATA
2282268 TTTTTAAGTTAAAATAAGACTAA
66 TTTTTAAGTTAAAATAAGACTAA
2282291 AAAAATTTTAAGCTAAAATAAGATTAAAATATATTTTTTAAACTAAAATAAGACTAGAATATATA
1 AAAAATTTTAAGCTAAAATAAGATTAAAATATATTTTTTAAACTAAAATAAGACTAGAATATATA
2282356 TTTTTAAGTTAAAATAAGACTAA
66 TTTTTAAGTTAAAATAAGACTAA
2282379 AA
1 AA
2282381 TATATTTTTT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (88 bp):
AAAAATTTTAAGCTAAAATAAGATTAAAATATATTTTTTAAACTAAAATAAGACTAGAATATATA
TTTTTAAGTTAAAATAAGACTAA
Found at i:2282319 original size:118 final size:119
Alignment explanation
Indices: 2282171--2282402 Score: 315
Period size: 118 Copynumber: 2.0 Consensus size: 119
2282161 AGATAAAAAT
* * * * *
2282171 AAAATATTTTAAAGGTAAAATATGATTAAAATAAAAATTTTAAGCTAAAATAAGATTAAAATATA
1 AAAAAATTTTAAAGCTAAAATAAGATTAAAATAAAAATTTTAAACTAAAATAAGACTAAAATATA
* * *
2282236 T-TTTTTAAACTAAAATAAGACTAGAATATATATTTTTAAGTTAAAATAAGACTA
66 TATTTTTAAACTAAAATAAGACTAAAATATAT-TTTTTAAATAAAAATAAGACTA
* ** *
2282290 AAAAAATTTT-AAGCTAAAATAAGATTAAAATATATTTTTTAAACTAAAATAAGACTAGAATATA
1 AAAAAATTTTAAAGCTAAAATAAGATTAAAATAAAAATTTTAAACTAAAATAAGACTAAAATATA
**
2282354 TATTTTTAAGTTAAAATAAGACTAAAATATATTTTTTAAATAAAAATAA
66 TATTTTTAAACTAAAATAAGACTAAAATATATTTTTTAAATAAAAATAA
2282403 AAATAAATTA
Statistics
Matches: 98, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
118 62 0.63
119 36 0.37
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.36
Consensus pattern (119 bp):
AAAAAATTTTAAAGCTAAAATAAGATTAAAATAAAAATTTTAAACTAAAATAAGACTAAAATATA
TATTTTTAAACTAAAATAAGACTAAAATATATTTTTTAAATAAAAATAAGACTA
Found at i:2282393 original size:61 final size:60
Alignment explanation
Indices: 2282174--2282416 Score: 246
Period size: 61 Copynumber: 4.1 Consensus size: 60
2282164 TAAAAATAAA
* * * * * ** * *
2282174 ATATTTTAAAGGTAAAATATGATTAAAATAAAAATTTTAAGCTAAAATAAGATTAAA-AT
1 ATATTTTTAAGCTAAAATAAGACTAAAATATATTTTTTAAACTAAAATAAGACTAAATAT
* * **
2282233 ATATTTTTTAAACTAAAATAAGACTAGAATATATATTTTTAAGTTAAAATAAGACTAAA-A-
1 ATA-TTTTTAAGCTAAAATAAGACTAAAATATAT-TTTTTAAACTAAAATAAGACTAAATAT
* *
2282293 A-AATTTTAAGCTAAAATAAGATTAAAATATATTTTTTAAACTAAAATAAGACTAGAATAT
1 ATATTTTTAAGCTAAAATAAGACTAAAATATATTTTTTAAACTAAAATAAGACTA-AATAT
* * *
2282353 ATATTTTTAAGTTAAAATAAGACTAAAATATATTTTTTAAA-TAAAAATAAAAATAAAT-T
1 ATATTTTTAAGCTAAAATAAGACTAAAATATATTTTTTAAACT-AAAATAAGACTAAATAT
2282412 ATATT
1 ATATT
2282417 GAATAAGTTA
Statistics
Matches: 155, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
57 20 0.13
58 28 0.18
59 11 0.07
60 28 0.18
61 68 0.44
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (60 bp):
ATATTTTTAAGCTAAAATAAGACTAAAATATATTTTTTAAACTAAAATAAGACTAAATAT
Found at i:2283441 original size:9 final size:9
Alignment explanation
Indices: 2283427--2283495 Score: 50
Period size: 9 Copynumber: 7.0 Consensus size: 9
2283417 ATATTAAACT
2283427 ACTATATAA
1 ACTATATAA
2283436 ACTATATATA
1 ACTATATA-A
*
2283446 TTAC-ATATGA
1 --ACTATATAA
2283456 ACTATATGTATAA
1 ACTATA--T--AA
2283469 ACTATATAA
1 ACTATATAA
*
2283478 ACTATGTAA
1 ACTATATAA
2283487 ACTATATAA
1 ACTATATAA
2283496 TATATATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
8 2 0.04
9 29 0.60
10 2 0.04
11 6 0.12
12 2 0.04
13 7 0.15
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.36
Consensus pattern (9 bp):
ACTATATAA
Found at i:2283485 original size:20 final size:20
Alignment explanation
Indices: 2283427--2283495 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 20
2283417 ATATTAAACT
* *
2283427 ACTATATAAACTATATATATT
1 ACTATATAAACTATGTATA-A
*
2283448 AC-ATATGAACTATATGTATAA
1 ACTATATAAAC--TATGTATAA
2283469 ACTATATAAACTATG--TAA
1 ACTATATAAACTATGTATAA
2283487 ACTATATAA
1 ACTATATAA
2283496 TATATATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
18 12 0.29
20 11 0.27
21 4 0.10
22 14 0.34
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.36
Consensus pattern (20 bp):
ACTATATAAACTATGTATAA
Found at i:2283521 original size:65 final size:62
Alignment explanation
Indices: 2283446--2283568 Score: 194
Period size: 65 Copynumber: 1.9 Consensus size: 62
2283436 ACTATATATA
*
2283446 TTACATATGAACTATATGTATAAACTATATAAAC-TATGTAAACTATATAATATATATATTTTAG
1 TTACATATGAACTATATATATAAACTATATAAACGTATG--AACTATAT-ATATATA-ATTTTAG
2283510 T
62 T
2283511 TTACATATGAACTATATATATAAACTATATAAACGTATGAACTATATATATATAATTT
1 TTACATATGAACTATATATATAAACTATATAAACGTATGAACTATATATATATAATTT
2283569 ATTAATGAAC
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
62 4 0.07
63 7 0.12
64 8 0.14
65 33 0.59
66 4 0.07
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.41
Consensus pattern (62 bp):
TTACATATGAACTATATATATAAACTATATAAACGTATGAACTATATATATATAATTTTAGT
Found at i:2283536 original size:13 final size:13
Alignment explanation
Indices: 2283515--2283626 Score: 50
Period size: 13 Copynumber: 8.2 Consensus size: 13
2283505 TTTAGTTTAC
*
2283515 ATATGAACTATAT
1 ATATAAACTATAT
2283528 ATATAAACTATAT
1 ATATAAACTATAT
*
2283541 AAACGTATGAACTATAT
1 --A--TATAAACTATAT
*
2283558 ATATATAA-TTTAT
1 ATATA-AACTATAT
*
2283571 -TAATGAACTATAT
1 AT-ATAAACTATAT
* **
2283584 AAACT-ATTTATAT
1 ATA-TAAACTATAT
* *
2283597 AGTATATACTACAT
1 A-TATAAACTATAT
2283611 ATATAAACTATAT
1 ATATAAACTATAT
2283624 ATA
1 ATA
2283627 CTATACAATT
Statistics
Matches: 72, Mismatches: 16, Indels: 22
0.65 0.15 0.20
Matches are distributed among these distances:
12 3 0.04
13 47 0.65
14 9 0.12
15 2 0.03
17 11 0.15
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.39
Consensus pattern (13 bp):
ATATAAACTATAT
Found at i:2283589 original size:65 final size:64
Alignment explanation
Indices: 2283448--2283597 Score: 180
Period size: 65 Copynumber: 2.3 Consensus size: 64
2283438 TATATATATT
* * **
2283448 ACATATGAACTATATGTATAAACTATATAAACTATGTAAACTATATAATATATATATTTTAGTTT
1 ACATATGAACTATATATATAAACTATATAAACTATG-AAACTATATAATATATATATTTTAATGA
2283513 ACATATGAACTATATATATAAACTATATAAACGTATG-AACTATAT-ATATATA-ATTTATTAAT
1 ACATATGAACTATATATATAAACTATATAAAC-TATGAAACTATATAATATATATA-TT-TTAAT
2283575 GA
63 GA
* *
2283577 ACTATATAAACTATTTATATA
1 AC-ATATGAACTATATATATA
2283598 GTATATACTA
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
62 1 0.01
63 9 0.12
64 14 0.19
65 47 0.63
66 4 0.05
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (64 bp):
ACATATGAACTATATATATAAACTATATAAACTATGAAACTATATAATATATATATTTTAATGA
Found at i:2283654 original size:31 final size:30
Alignment explanation
Indices: 2283619--2283752 Score: 76
Period size: 31 Copynumber: 4.3 Consensus size: 30
2283609 ATATATAAAC
2283619 TATATATACTATACAATTTACATATGAATTA
1 TATATATACTATA-AATTTACATATGAATTA
* * * *
2283650 TATATAAAAACTAT-AATTTATATATAAAATA
1 TATAT--ATACTATAAATTTACATATGAATTA
* *
2283681 TATACTATACT-TAATATTTATATACT-ATATAA
1 TATA-TATACTATAA-ATTTACATA-TGA-ATTA
* * * *
2283713 TATATATAGTTTACATTATTACATATGAACTA
1 TATATATACTATA-AAT-TTACATATGAATTA
2283745 TATATATA
1 TATATATA
2283753 AATTATATAA
Statistics
Matches: 80, Mismatches: 12, Indels: 21
0.71 0.11 0.19
Matches are distributed among these distances:
29 1 0.01
30 5 0.06
31 38 0.47
32 22 0.28
33 14 0.17
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.43
Consensus pattern (30 bp):
TATATATACTATAAATTTACATATGAATTA
Found at i:2283673 original size:18 final size:19
Alignment explanation
Indices: 2283640--2283682 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
2283630 TACAATTTAC
2283640 ATATGAATTATATATA-AAA
1 ATAT-AATTATATATATAAA
2283659 ACTATAATT-TATATATAAA
1 A-TATAATTATATATATAAA
2283678 ATATA
1 ATATA
2283683 TACTATACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 10 0.45
19 9 0.41
20 3 0.14
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
ATATAATTATATATATAAA
Found at i:2283823 original size:24 final size:24
Alignment explanation
Indices: 2283779--2283824 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2283769 TAGTTTACAT
**
2283779 ATAAACTATATATGTAGTTTATTA
1 ATAAACTATATAACTAGTTTATTA
2283803 ATAAACTATATAAACTA-TTTAT
1 ATAAACTATAT-AACTAGTTTAT
2283825 ATAGTATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (24 bp):
ATAAACTATATAACTAGTTTATTA
Found at i:2284052 original size:22 final size:21
Alignment explanation
Indices: 2284027--2284068 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2284017 GGATTCTACC
2284027 TAAAAATCAC-AAAATATATATA
1 TAAAAAT-ACTAAAATA-ATATA
2284049 TAAAAATACTAAAATAATAT
1 TAAAAATACTAAAATAATAT
2284069 CATTTGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAATACTAAAATAATATA
Found at i:2284210 original size:13 final size:13
Alignment explanation
Indices: 2284194--2284254 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 13
2284184 TACTATATAT
2284194 TATATATATAAAC
1 TATATATATAAAC
* * *
2284207 TATAT-TGTATAG
1 TATATATATAAAC
* * *
2284219 TTTACATATGAAC
1 TATATATATAAAC
*
2284232 TATATATAAAAAC
1 TATATATATAAAC
2284245 TATATATATA
1 TATATATATA
2284255 TATAAAGTGT
Statistics
Matches: 33, Mismatches: 14, Indels: 2
0.67 0.29 0.04
Matches are distributed among these distances:
12 7 0.21
13 26 0.79
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:2284217 original size:18 final size:18
Alignment explanation
Indices: 2284189--2284422 Score: 100
Period size: 18 Copynumber: 13.3 Consensus size: 18
2284179 TTATGTACTA
*
2284189 TATATTATATATATAAAC
1 TATATTGTATATATAAAC
* *
2284207 TATATTGTATAGTTTACA-
1 TATATTGTATA-TATAAAC
* * *
2284225 TATGAACTATATATAAAAAC
1 TAT--ATTGTATATATAAAC
* *
2284245 TATA-TATATATATAAAG
1 TATATTGTATATATAAAC
*
2284262 TGTA-TGTTATATATAAAC
1 TATATTG-TATATATAAAC
*
2284280 TATATAT-TATATAGT--TC
1 TATAT-TGTATATA-TAAAC
* *
2284297 -AT-TAGTATATTTAAAC
1 TATATTGTATATATAAAC
*
2284313 TATATAGTATATATAAAC
1 TATATTGTATATATAAAC
* *
2284331 TATATAT-TATATGGT--TC
1 TATAT-TGTATAT-ATAAAC
* *
2284348 -AT-TAGTATATATAACC
1 TATATTGTATATATAAAC
*
2284364 TATATAT-TATATATAAAT
1 TATAT-TGTATATATAAAC
* *
2284382 TATATAGTATACATAAAC
1 TATATTGTATATATAAAC
*
2284400 TATATGGTATATATAAAC
1 TATATTGTATATATAAAC
2284418 TATAT
1 TATAT
2284423 ATTATATAGT
Statistics
Matches: 161, Mismatches: 33, Indels: 44
0.68 0.14 0.18
Matches are distributed among these distances:
14 2 0.01
15 12 0.07
16 6 0.04
17 21 0.13
18 101 0.63
19 9 0.06
20 10 0.06
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (18 bp):
TATATTGTATATATAAAC
Found at i:2284325 original size:51 final size:51
Alignment explanation
Indices: 2284251--2284392 Score: 196
Period size: 51 Copynumber: 2.8 Consensus size: 51
2284241 AAACTATATA
* *
2284251 TATATATAAAGTGTAT-GTTATATATAAACTATATATTATATAGTTCATTAG
1 TATATATAAACTATATAG-TATATATAAACTATATATTATATAGTTCATTAG
* *
2284302 TATATTTAAACTATATAGTATATATAAACTATATATTATATGGTTCATTAG
1 TATATATAAACTATATAGTATATATAAACTATATATTATATAGTTCATTAG
* * * *
2284353 TATATATAACCTATATATTATATATAAATTATATAGTATA
1 TATATATAAACTATATAGTATATATAAACTATATATTATA
2284393 CATAAACTAT
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 80 0.99
52 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (51 bp):
TATATATAAACTATATAGTATATATAAACTATATATTATATAGTTCATTAG
Found at i:2284413 original size:87 final size:84
Alignment explanation
Indices: 2284269--2284459 Score: 285
Period size: 87 Copynumber: 2.2 Consensus size: 84
2284259 AAGTGTATGT
* **
2284269 TATATATAAACTATATATTATATAGTTCATTAGTATATTTAAACTATATAGTATATATAAACTAT
1 TATATATAACCTATATATTATATAGTTCATTAGTATACATAAACTATATAGTATATATAAACTAT
*
2284334 ATATTATATGGTTCATTAG
66 ATATTATATAGTTCATTAG
* *
2284353 TATATATAACCTATATATTATATA-TAAATTATATAGTATACATAAACTATATGGTATATATAAA
1 TATATATAACCTATATATTATATAGT---TCAT-TAGTATACATAAACTATATAGTATATATAAA
2284417 CTATATATTATATAGTTCATTAG
62 CTATATATTATATAGTTCATTAG
2284440 TATATATAACCTATATATTA
1 TATATATAACCTATATATTA
2284460 ATTTATTAAT
Statistics
Matches: 97, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
83 1 0.01
84 23 0.24
86 3 0.03
87 70 0.72
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (84 bp):
TATATATAACCTATATATTATATAGTTCATTAGTATACATAAACTATATAGTATATATAAACTAT
ATATTATATAGTTCATTAG
Found at i:2284428 original size:18 final size:18
Alignment explanation
Indices: 2284234--2284430 Score: 162
Period size: 18 Copynumber: 11.3 Consensus size: 18
2284224 ATATGAACTA
*
2284234 TATATAAAAACTATATA-
1 TATATATAAACTATATAG
* *
2284251 TATATATAAAGTGTAT-G
1 TATATATAAACTATATAG
2284268 TTATATATAAACTATATA-
1 -TATATATAAACTATATAG
**
2284286 T-TATAT-AGTTCAT-TAG
1 TATATATAAACT-ATATAG
*
2284302 TATATTTAAACTATATAG
1 TATATATAAACTATATAG
2284320 TATATATAAACTATATA-
1 TATATATAAACTATATAG
***
2284337 T-TATAT-GGTTCAT-TAG
1 TATATATAAACT-ATATAG
* *
2284353 TATATATAACCTATATAT
1 TATATATAAACTATATAG
*
2284371 TATATATAAATTATATAG
1 TATATATAAACTATATAG
* *
2284389 TATACATAAACTATATGG
1 TATATATAAACTATATAG
*
2284407 TATATATAAACTATATAT
1 TATATATAAACTATATAG
2284425 TATATA
1 TATATA
2284431 GTTCATTAGT
Statistics
Matches: 140, Mismatches: 27, Indels: 25
0.73 0.14 0.13
Matches are distributed among these distances:
15 7 0.05
16 16 0.11
17 28 0.20
18 89 0.64
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (18 bp):
TATATATAAACTATATAG
Found at i:2284558 original size:60 final size:60
Alignment explanation
Indices: 2284494--2284651 Score: 174
Period size: 60 Copynumber: 2.6 Consensus size: 60
2284484 TAATTGAAAG
* * *
2284494 AATTGGAAAATATATGAGGA-TCAAATTGAACAAATTTTAAATATGAAGCTTAAATTAATA
1 AATTGCAAAATAAATGAGGACT-AAATTGAACAAATTTTAAATATAAAGCTTAAATTAATA
* * ** *
2284554 AATTGCACATTAAATTTGGACTAAATTGAATAAATTTTAAATATAAAGCTTAAATTAATA
1 AATTGCAAAATAAATGAGGACTAAATTGAACAAATTTTAAATATAAAGCTTAAATTAATA
* * * **
2284614 TATTGCATCATTAAATTTGGACTAAATTGAACAAATTT
1 AATTGCA-AAATAAATGAGGACTAAATTGAACAAATTT
2284652 AAAACTAGAA
Statistics
Matches: 86, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
60 56 0.65
61 30 0.35
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (60 bp):
AATTGCAAAATAAATGAGGACTAAATTGAACAAATTTTAAATATAAAGCTTAAATTAATA
Found at i:2284654 original size:60 final size:60
Alignment explanation
Indices: 2284516--2284651 Score: 236
Period size: 60 Copynumber: 2.2 Consensus size: 60
2284506 TATGAGGATC
*
2284516 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGCACATTAAATTTGGACT
1 AAATTGAACAAATTTTAAATATAAAGCTTAAATTAATAAATTGCACATTAAATTTGGACT
* *
2284576 AAATTGAATAAATTTTAAATATAAAGCTTAAATTAATATATTGCATCATTAAATTTGGACT
1 AAATTGAACAAATTTTAAATATAAAGCTTAAATTAATAAATTGCA-CATTAAATTTGGACT
2284637 AAATTGAACAAATTT
1 AAATTGAACAAATTT
2284652 AAAACTAGAA
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
60 42 0.59
61 29 0.41
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (60 bp):
AAATTGAACAAATTTTAAATATAAAGCTTAAATTAATAAATTGCACATTAAATTTGGACT
Found at i:2285310 original size:18 final size:18
Alignment explanation
Indices: 2285273--2285427 Score: 103
Period size: 18 Copynumber: 8.6 Consensus size: 18
2285263 CTCTAAGCCT
*
2285273 AACCCGAACCTAAACCCG
1 AACCCGAACCCAAACCCG
*
2285291 AACCCGAACCCAAACTCG
1 AACCCGAACCCAAACCCG
** * *
2285309 AACTTGATCCTAAACCCG
1 AACCCGAACCCAAACCCG
* *
2285327 AAACCAAACCCAAACCCG
1 AACCCGAACCCAAACCCG
* * ** *
2285345 AACTCGATCCTTAACCCA
1 AACCCGAACCCAAACCCG
* *
2285363 AACCCAAACCCAAACCCA
1 AACCCGAACCCAAACCCG
** *
2285381 AACCTAAACCCAAACCCA
1 AACCCGAACCCAAACCCG
* * * *
2285399 AACCCAAACCTAAATCCA
1 AACCCGAACCCAAACCCG
*
2285417 AACCCAAACCC
1 AACCCGAACCC
2285428 TAACTAAGCC
Statistics
Matches: 107, Mismatches: 30, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 107 1.00
ACGTcount: A:0.43, C:0.43, G:0.05, T:0.08
Consensus pattern (18 bp):
AACCCGAACCCAAACCCG
Found at i:2285328 original size:36 final size:36
Alignment explanation
Indices: 2285281--2285408 Score: 151
Period size: 36 Copynumber: 3.7 Consensus size: 36
2285271 CTAACCCGAA
* * *
2285281 CCTAAACCCGAACCCGAACCCAAACTCGAACTTGAT
1 CCTAAACCCGAACCCAAACCCAAACCCGAACTCGAT
*
2285317 CCTAAACCCGAAACCAAACCCAAACCCGAACTCGAT
1 CCTAAACCCGAACCCAAACCCAAACCCGAACTCGAT
* *
2285353 CCTTAACCCAAACCCAAACCCAAACCC-AA----A-
1 CCTAAACCCGAACCCAAACCCAAACCCGAACTCGAT
*
2285383 CCTAAACCCAAACCCAAACCCAAACC
1 CCTAAACCCGAACCCAAACCCAAACC
2285409 TAAATCCAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
30 25 0.30
31 1 0.01
35 2 0.02
36 56 0.67
ACGTcount: A:0.42, C:0.44, G:0.05, T:0.09
Consensus pattern (36 bp):
CCTAAACCCGAACCCAAACCCAAACCCGAACTCGAT
Found at i:2285423 original size:6 final size:6
Alignment explanation
Indices: 2285320--2285427 Score: 119
Period size: 6 Copynumber: 18.0 Consensus size: 6
2285310 ACTTGATCCT
* * * * * *
2285320 AAACCC GAAA-CC AAACCC AAACCC GAACTC GATCCT TAACCC AAACCC
1 AAACCC -AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
* * *
2285368 AAACCC AAACCC AAACCT AAACCC AAACCC AAACCC AAACCT AAATCC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
2285416 AAACCC AAACCC
1 AAACCC AAACCC
2285428 TAACTAAGCC
Statistics
Matches: 85, Mismatches: 15, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
5 3 0.04
6 79 0.93
7 3 0.04
ACGTcount: A:0.46, C:0.44, G:0.03, T:0.06
Consensus pattern (6 bp):
AAACCC
Found at i:2295878 original size:6 final size:6
Alignment explanation
Indices: 2295869--2295898 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2295859 TGTTCATAGA
*
2295869 GAGTCT GAGTCC GAGTCC GAGTCC GAGTCC
1 GAGTCC GAGTCC GAGTCC GAGTCC GAGTCC
2295899 AAGTTCTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.30, G:0.33, T:0.20
Consensus pattern (6 bp):
GAGTCC
Found at i:2296976 original size:131 final size:131
Alignment explanation
Indices: 2296733--2297100 Score: 454
Period size: 131 Copynumber: 2.8 Consensus size: 131
2296723 ATAATTTTAA
* * *
2296733 AGAGAAAATGATAATATCTAATTATTTCCAATCGAGAAAAAATGACATTTCATGCCTTAAAACAA
1 AGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACAA
* ** * * *
2296798 TAATTTATTACCCCAATTGAAATGAAGAGATATCACTATTTCGTCTTAAAATTCAACATTGATTC
66 TCATTTATTATTCCAATCGAAATGAAGATATATCACTATTTCGTCTTAAAAATCAACATTGATTC
2296863 G
131 G
* * *
2296864 AGTA-AAAACGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 AG-AGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACA
* *
2296928 GTCATTTATTATTCCAATCGAAATGAAGATATATCACTA-TTCTGTCTTAAAAATCAATATTGAT
65 ATCATTTATTATTCCAATCGAAATGAAGATATATCACTATTTC-GTCTTAAAAATCAACATTGAT
2296992 TCG
129 TCG
* * * * ** * *
2296995 AGAGAAAATGGTAATATATGATTATTTCCAATCGAGAATAAATAACCTCTCATGCCGCAAATCAT
1 AGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACAA
* * * *
2297060 TCATGTATT-TCTCCAACCGAAATGAGGATATATTACTATTT
66 TCATTTATTAT-TCCAATCGAAATGAAGATATATCACTATTT
2297101 TCAATATCGA
Statistics
Matches: 204, Mismatches: 28, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
130 5 0.02
131 196 0.96
132 3 0.01
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (131 bp):
AGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACAA
TCATTTATTATTCCAATCGAAATGAAGATATATCACTATTTCGTCTTAAAAATCAACATTGATTC
G
Found at i:2299290 original size:15 final size:14
Alignment explanation
Indices: 2299270--2299300 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
2299260 TTCTTATGTT
2299270 AACAAGAATAGGACA
1 AACAAGAATAGG-CA
2299285 AACAAGAATAGGCA
1 AACAAGAATAGGCA
2299299 AA
1 AA
2299301 GACAAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.61, C:0.13, G:0.19, T:0.06
Consensus pattern (14 bp):
AACAAGAATAGGCA
Found at i:2300308 original size:224 final size:224
Alignment explanation
Indices: 2299918--2300366 Score: 898
Period size: 224 Copynumber: 2.0 Consensus size: 224
2299908 TAATTACAAT
2299918 TCAAATTTCAAGAGATTCTTTCAATTCAATAAACACTCTATGGTTTACATCTGTAGTGCTAATAA
1 TCAAATTTCAAGAGATTCTTTCAATTCAATAAACACTCTATGGTTTACATCTGTAGTGCTAATAA
2299983 AATCATTTCTCAACCATTTCTATAATTTATGTGGTTTGTATACCCATTACCAATATAACGATCCA
66 AATCATTTCTCAACCATTTCTATAATTTATGTGGTTTGTATACCCATTACCAATATAACGATCCA
2300048 TTTCCTCATTATAAAGTTCTTATGTTTATACACACATTTTGCATATGGAAATTCATACACTTAGT
131 TTTCCTCATTATAAAGTTCTTATGTTTATACACACATTTTGCATATGGAAATTCATACACTTAGT
2300113 ATGAATCTCTTAACGGTTTGCACACAAAG
196 ATGAATCTCTTAACGGTTTGCACACAAAG
2300142 TCAAATTTCAAGAGATTCTTTCAATTCAATAAACACTCTATGGTTTACATCTGTAGTGCTAATAA
1 TCAAATTTCAAGAGATTCTTTCAATTCAATAAACACTCTATGGTTTACATCTGTAGTGCTAATAA
2300207 AATCATTTCTCAACCATTTCTATAATTTATGTGGTTTGTATACCCATTACCAATATAACGATCCA
66 AATCATTTCTCAACCATTTCTATAATTTATGTGGTTTGTATACCCATTACCAATATAACGATCCA
2300272 TTTCCTCATTATAAAGTTCTTATGTTTATACACACATTTTGCATATGGAAATTCATACACTTAGT
131 TTTCCTCATTATAAAGTTCTTATGTTTATACACACATTTTGCATATGGAAATTCATACACTTAGT
2300337 ATGAATCTCTTAACGGTTTGCACACAAAG
196 ATGAATCTCTTAACGGTTTGCACACAAAG
2300366 T
1 T
2300367 GCCCAATAGG
Statistics
Matches: 225, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
224 225 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (224 bp):
TCAAATTTCAAGAGATTCTTTCAATTCAATAAACACTCTATGGTTTACATCTGTAGTGCTAATAA
AATCATTTCTCAACCATTTCTATAATTTATGTGGTTTGTATACCCATTACCAATATAACGATCCA
TTTCCTCATTATAAAGTTCTTATGTTTATACACACATTTTGCATATGGAAATTCATACACTTAGT
ATGAATCTCTTAACGGTTTGCACACAAAG
Found at i:2300499 original size:59 final size:58
Alignment explanation
Indices: 2300318--2300536 Score: 341
Period size: 59 Copynumber: 3.8 Consensus size: 58
2300308 TTTTGCATAT
* ** * *
2300318 GGAAATTCATACACTTAGTATGAATCTCTTAACGGTTTGCACACAAAGTGCCCAATAG
1 GGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACGAAGTGCCCAATAC
**
2300376 GGAAATTCATACACTTAACATGAATTTCTTAAC-TTTTGCACACGAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACGAAGTGCCCAATAC
*
2300433 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCAAACGAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAAC-TTTTTGCACACGAAGTGCCCAATAC
2300492 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAAC-TTTTTGCACAC
2300537 TTCATGCCAT
Statistics
Matches: 149, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
57 52 0.35
58 30 0.20
59 67 0.45
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.32
Consensus pattern (58 bp):
GGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACGAAGTGCCCAATAC
Found at i:2300521 original size:116 final size:116
Alignment explanation
Indices: 2300318--2300536 Score: 341
Period size: 116 Copynumber: 1.9 Consensus size: 116
2300308 TTTTGCATAT
* *
2300318 GGAAATTCATACACTTAGTATGAATCTCTTAACGGTTTGCACACAAAGTGCCCAATAGGGAAATT
1 GGAAATTCATACACTTAGTATGAATCTCTTAACGGTTTGCAAACAAAGTGCCCAATACGGAAATT
2300383 CATACACTTAACATGAATTTCTTAAC-TTTTGCACACGAAGTGCCCAATAC
66 CATACACTTAACATGAATTTCTTAACATTTTGCACACGAAGTGCCCAATAC
* ** *
2300433 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCAAACGAAGTGCCCAATACGGAAAT
1 GGAAATTCATACACTTAGTATGAATCTCTTAAC-GGTTTGCAAACAAAGTGCCCAATACGGAAAT
**
2300498 TCATACACTTAGTATGAATTTCTTAACATTTTTGCACAC
65 TCATACACTTAACATGAATTTCTTAACA-TTTTGCACAC
2300537 TTCATGCCAT
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
115 32 0.34
116 51 0.55
118 10 0.11
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.32
Consensus pattern (116 bp):
GGAAATTCATACACTTAGTATGAATCTCTTAACGGTTTGCAAACAAAGTGCCCAATACGGAAATT
CATACACTTAACATGAATTTCTTAACATTTTGCACACGAAGTGCCCAATAC
Found at i:2301069 original size:94 final size:95
Alignment explanation
Indices: 2300866--2301088 Score: 376
Period size: 94 Copynumber: 2.4 Consensus size: 95
2300856 TAGCTCTTAA
* * *
2300866 GTATCGATACCCCTACCATGGTAACGATACTACCATACTATGGTACCGATACCCCCTTCGGGTAC
1 GTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACCGATACCCCCTTCGGATAC
2300931 CGATACCAATTTTAGATTCGATGTGGCCTG
66 CGATACCAATTTTAGATTCGATGTGGCCTG
* * *
2300961 GTATCGATATCCTTACCATGGTATCGATACTACCATACTATGGTACCGATA-CCCCTTCTGATAT
1 GTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACCGATACCCCCTTCGGATAC
*
2301025 CGATACCAATTTTAGATTCGATGTTGCCTG
66 CGATACCAATTTTAGATTCGATGTGGCCTG
2301055 GTATCGATACCCTTACCATGGTATCGATACTACC
1 GTATCGATACCCTTACCATGGTATCGATACTACC
2301089 TCGTCGGTAT
Statistics
Matches: 120, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
94 72 0.60
95 48 0.40
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (95 bp):
GTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACCGATACCCCCTTCGGATAC
CGATACCAATTTTAGATTCGATGTGGCCTG
Found at i:2307546 original size:61 final size:59
Alignment explanation
Indices: 2307296--2307632 Score: 502
Period size: 59 Copynumber: 5.7 Consensus size: 59
2307286 TTCCCATATA
* ** * *
2307296 GAAATTCATACACTTAGTATGAATCTCTTAAC-GGTTTGTACACAAAGTGCCCAATACG
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACG
*
2307354 AAAATTCATACACTTAGTATGAATTTCTTAAC-TTTTT-CACACGAAGTGCCCAATACG
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACG
* * * *
2307411 GAAATTCATACACTTAATATGAATTTCTTAAAATTTTTGCACATGAAGTGCCCAATATG
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACG
*
2307470 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACATGAAAAGTGCCCAATACG
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACG--AAGTGCCCAATACG
* *
2307531 GAAATTCATACACTTAGTATGATTTTCTTAACATTTTTGCACACGAAGTGTCCAATACG
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACG
*
2307590 GAAATTCATACACTTAGTATGAA-TTCTTAACATTTTTTCACAC
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACAC
2307633 TTAGTGCCAT
Statistics
Matches: 256, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
57 47 0.18
58 57 0.22
59 96 0.38
61 56 0.22
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (59 bp):
GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACG
Found at i:2307561 original size:120 final size:116
Alignment explanation
Indices: 2307296--2307632 Score: 482
Period size: 120 Copynumber: 2.9 Consensus size: 116
2307286 TTCCCATATA
* ** * * *
2307296 GAAATTCATACACTTAGTATGAATCTCTTAACGGTTTGTACACA-AAGTGCCCAATACGAAAATT
1 GAAATTCATACACTTAGTATGAATTTCTTAA-AATTTTTGCACAGAAGTGCCCAATACGGAAATT
2307360 CATACACTTAGTATGAATTTCTTAAC-TTTTTCACACGAAGTGCCCAATACG
65 CATACACTTAGTATGAATTTCTTAACATTTTTCACACGAAGTGCCCAATACG
* *
2307411 GAAATTCATACACTTAATATGAATTTCTTAAAATTTTTGCACATGAAGTGCCCAATATGGAAATT
1 GAAATTCATACACTTAGTATGAATTTCTTAAAATTTTTGCACA-GAAGTGCCCAATACGGAAATT
*
2307476 CATACACTTAGTATGAATTTCTTAACATTTTTGCACATGAAAAGTGCCCAATACG
65 CATACACTTAGTATGAATTTCTTAACATTTTT-CACACG--AAGTGCCCAATACG
* * *
2307531 GAAATTCATACACTTAGTATGATTTTCTTAACATTTTTGCACACGAAGTGTCCAATACGGAAATT
1 GAAATTCATACACTTAGTATGAATTTCTTAAAATTTTTGCACA-GAAGTGCCCAATACGGAAATT
2307596 CATACACTTAGTATGAA-TTCTTAACATTTTTTCACAC
65 CATACACTTAGTATGAATTTCTTAACA-TTTTTCACAC
2307633 TTAGTGCCAT
Statistics
Matches: 199, Mismatches: 16, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
114 8 0.04
115 29 0.15
116 44 0.22
117 5 0.03
118 5 0.03
119 13 0.07
120 95 0.48
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (116 bp):
GAAATTCATACACTTAGTATGAATTTCTTAAAATTTTTGCACAGAAGTGCCCAATACGGAAATTC
ATACACTTAGTATGAATTTCTTAACATTTTTCACACGAAGTGCCCAATACG
Found at i:2308102 original size:74 final size:75
Alignment explanation
Indices: 2307954--2308112 Score: 241
Period size: 74 Copynumber: 2.1 Consensus size: 75
2307944 TAAAATTTCT
* * *
2307954 GTATCGATATTACCATACTATGGTATCGATACCCCCTTCGGGTATAGATACTAATTTTAGATTCG
1 GTATCGATACTACCATACTATGGTACCGATACCCCCTTCGGGTATAGATACCAATTTTAGATTCG
2308019 ATGTGGCCTG
66 ATGTGGCCTG
* *
2308029 GTATCGATACTACCATACTATGGTACCGATA-CCCTTTAC-GGTATCGATACCAATTTTAGATTC
1 GTATCGATACTACCATACTATGGTACCGATACCCCCTT-CGGGTATAGATACCAATTTTAGATTC
*
2308092 GATGTTGCCTG
65 GATGTGGCCTG
2308103 GTATCGATAC
1 GTATCGATAC
2308113 CCTTACCATG
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
74 47 0.61
75 30 0.39
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (75 bp):
GTATCGATACTACCATACTATGGTACCGATACCCCCTTCGGGTATAGATACCAATTTTAGATTCG
ATGTGGCCTG
Found at i:2308152 original size:74 final size:73
Alignment explanation
Indices: 2307954--2308132 Score: 189
Period size: 74 Copynumber: 2.4 Consensus size: 73
2307944 TAAAATTTCT
* * * * *** * *
2307954 GTATCGATATTACCATACTATGGTATCGATACCCCCTTCGGGTATAGATACTAATTTTAGATTCG
1 GTATCGATA-CACCATACCATGGTACCGATA-CCCTTTAAAGTATCGATACCAATTTTAGATTCG
2308019 ATGTGGCCTG
64 ATGTGGCCTG
* **
2308029 GTATCGATACTACCATACTATGGTACCGATACCCTTTACGGTATCGATACCAATTTTAGATTCGA
1 GTATCGATAC-ACCATACCATGGTACCGATACCCTTTAAAGTATCGATACCAATTTTAGATTCGA
*
2308094 TGTTGCCTG
65 TGTGGCCTG
* *
2308103 GTATCGATAC-CCTTACCATGGTATCGATAC
1 GTATCGATACACCATACCATGGTACCGATAC
2308133 TTATTCATAA
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
72 17 0.18
74 47 0.51
75 28 0.30
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (73 bp):
GTATCGATACACCATACCATGGTACCGATACCCTTTAAAGTATCGATACCAATTTTAGATTCGAT
GTGGCCTG
Found at i:2309147 original size:132 final size:133
Alignment explanation
Indices: 2308922--2309228 Score: 420
Period size: 132 Copynumber: 2.3 Consensus size: 133
2308912 AAATCCGGTT
* *
2308922 TGAAAATGTTAATTCATTCCATTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTG
1 TGAAAATGTTAATTCATTCCATTGTTCTTCAGGGAAGATTAAATCGAGGCAGACTTGTTCCACTG
* *
2308987 TTCCTCAAGGAATATCAAATCTGGAAAAAAGATGGATCTATTCC-GCTACTTGAAGGAAAATCAG
66 TTCCTCAAGGAAAATCAAATCTGGAAAAAAGAAGGATCTATTCCAGCTACTTGAAGGAAAATCAG
2309051 ATA
131 ATA
* * **
2309054 TGAAAATATTGATTCATTCTGTTGTTCTTCAGGGAAGATTAAATC-AGGGCAGACTTGTTCCACT
1 TGAAAATGTTAATTCATTCCATTGTTCTTCAGGGAAGATTAAATCGA-GGCAGACTTGTTCCACT
* * * *
2309118 GTTCCTTAGGGAAAATCAAATCTGGAAAAAAGAAGGATCTATTCCGTAGCTTCTTGAGGGAAAAT
65 GTTCCTCAAGGAAAATCAAATCTGGAAAAAAGAAGGATCTATTCC--AGCTACTTGAAGGAAAAT
* *
2309183 CATATC
128 CAGATA
* * *
2309189 TGAAAATGTTTATTCATTCCATCGTTCTTTAGGGAAGATT
1 TGAAAATGTTAATTCATTCCATTGTTCTTCAGGGAAGATT
2309229 GAATTGAGTT
Statistics
Matches: 151, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
131 1 0.01
132 97 0.64
135 53 0.35
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (133 bp):
TGAAAATGTTAATTCATTCCATTGTTCTTCAGGGAAGATTAAATCGAGGCAGACTTGTTCCACTG
TTCCTCAAGGAAAATCAAATCTGGAAAAAAGAAGGATCTATTCCAGCTACTTGAAGGAAAATCAG
ATA
Found at i:2311605 original size:2 final size:2
Alignment explanation
Indices: 2311600--2311640 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2311590 TTATTGTGTG
2311600 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2311641 ATCTCCTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2314315 original size:11 final size:11
Alignment explanation
Indices: 2314295--2314328 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
2314285 AATGTGAAAA
2314295 GTAAATGCAAT
1 GTAAATGCAAT
*
2314306 GTAGATGCAAT
1 GTAAATGCAAT
2314317 GTAAATGCAAT
1 GTAAATGCAAT
2314328 G
1 G
2314329 CAAGGTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (11 bp):
GTAAATGCAAT
Found at i:2317686 original size:17 final size:18
Alignment explanation
Indices: 2317650--2317683 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2317640 TGGGTACCCA
2317650 AAAAAATATATGTCATTT
1 AAAAAATATATGTCATTT
2317668 AAAAAA-ATAT-TCATTT
1 AAAAAATATATGTCATTT
2317684 TAATTAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (18 bp):
AAAAAATATATGTCATTT
Found at i:2318346 original size:131 final size:128
Alignment explanation
Indices: 2318053--2318375 Score: 407
Period size: 131 Copynumber: 2.5 Consensus size: 128
2318043 AGAGAAAAAG
* *
2318053 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCATGCCTTAAAACAATCATTTATTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTA
** * **
2318118 CCCCAATTGAAATGAAATGATACTATTCCGACTTAAAATTCAATATTGCTTCCAGTCAAAACA
66 CCCCAATCAAAATGAAATGATACTATTCCGACTTAAAAATCAATATTGCTTCCAGAAAAAACA
* *
2318181 ATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATGTCTTAAAGCAATCATTTATTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTA
** * * *
2318246 TTCCAATCAAAATGAAGA-GATATCTCTATTTCGTCTTAAAAATCAATATTGAC-TCGAGAAAAA
66 CCCCAATCAAAATGAA-ATGATA---CTATTCCGACTTAAAAATCAATATTG-CTTCCAGAAAAA
**
2318309 ATG
126 ACA
* * * *
2318312 GTAATATCTGATTATTTCCAATCGAGAATAAATGATCTCTAATGCCTTAAAGCAATCATTTATT
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATT
2318376 TCTCCAACTG
Statistics
Matches: 168, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
128 77 0.46
129 1 0.01
131 89 0.53
132 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (128 bp):
ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTA
CCCCAATCAAAATGAAATGATACTATTCCGACTTAAAAATCAATATTGCTTCCAGAAAAAACA
Found at i:2323097 original size:130 final size:130
Alignment explanation
Indices: 2322860--2323121 Score: 497
Period size: 130 Copynumber: 2.0 Consensus size: 130
2322850 TTAATACGGA
2322860 CAGTTGATATGCAATTATCATCGCTAAAAGAGTAGAGGAGAGTCAACTCACTGGTTTTGGGGCTG
1 CAGTTGATATGCAATTATCATCGCTAAAAGAGTAGAGGAGAGTCAACTCACTGGTTTTGGGGCTG
* * *
2322925 GCTGGGTGATTCCATAGAGCTTGGAGCTTGGAGGAGGCCATTGAGTCGACACTTTTACTCTTCTT
66 GCTGGGTGATTCCATAGAGCTTGGAGCTTGGAGGACGACATTGAGTCGACACTTTAACTCTTCTT
2322990 CAGTTGATATGCAATTATCATCGCTAAAAGAGTAGAGGAGAGTCAACTCACTGGTTTTGGGGCTG
1 CAGTTGATATGCAATTATCATCGCTAAAAGAGTAGAGGAGAGTCAACTCACTGGTTTTGGGGCTG
2323055 GCTGGGTGATTCCATAGAGCTTGGAGCTTGGAGGACGACATTGAGTCGACACTTTAACTCTTCTT
66 GCTGGGTGATTCCATAGAGCTTGGAGCTTGGAGGACGACATTGAGTCGACACTTTAACTCTTCTT
2323120 CA
1 CA
2323122 ATAAAATGGA
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 129 1.00
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (130 bp):
CAGTTGATATGCAATTATCATCGCTAAAAGAGTAGAGGAGAGTCAACTCACTGGTTTTGGGGCTG
GCTGGGTGATTCCATAGAGCTTGGAGCTTGGAGGACGACATTGAGTCGACACTTTAACTCTTCTT
Found at i:2323858 original size:14 final size:15
Alignment explanation
Indices: 2323691--2323866 Score: 230
Period size: 15 Copynumber: 11.5 Consensus size: 15
2323681 TAATAAGGTT
2323691 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
2323706 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
2323721 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
2323736 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
2323751 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
2323766 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
2323781 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
2323796 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
2323811 AATTATTATAAATATGGA
1 ATTTATTTTAAA-AT--A
2323829 TTGATTT-TTTTAAAATA
1 ---ATTTATTTTAAAATA
2323846 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
2323860 ATTTATT
1 ATTTATT
2323867 AGTATGGATT
Statistics
Matches: 146, Mismatches: 8, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
14 16 0.11
15 115 0.79
16 2 0.01
17 1 0.01
18 1 0.01
19 2 0.01
20 6 0.04
21 3 0.02
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:2323887 original size:32 final size:32
Alignment explanation
Indices: 2323846--2324431 Score: 242
Period size: 32 Copynumber: 19.4 Consensus size: 32
2323836 TTTTAAAATA
2323846 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
2323878 ATTTA-TTT---TAA---A--A-TATGGATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
2323900 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
2323932 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
2323954 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
2323986 ATTTATTTT--A-AA---A-TA-TA--GATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
2324008 ATTTATTTTAAATAATTTATTTGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
** **
2324040 ATTTATTTTAAA-ATATGGATT-G-ATTTATT-
1 ATTTATTTTAAATA-ATTTATTAGTATGGATTG
* * * * *
2324069 ATTGTAGTTTTATGGATTGATTTATT--T-T-AAATA
1 ATT-TA-TTTTA---AATAATTTATTAGTATGGATTG
* * * **
2324102 ATTTATTTGTATGGATTGATTTATTTTAAAATATAAATTG
1 ATTTATTT-TA---AATAATTTA--TT--AGTATGGATTG
*
2324142 ATTTA--TT--AT--TGTAGTT-GTATGGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTG
*
2324168 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
2324200 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
2324222 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
2324254 ATTTAATTTAAATAATTTATTTGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* * *
2324286 ATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
1 ATTTATTTT-AAATA---ATTTA-TTAGTA-TGGA-TTG
** * ** * * * *
2324325 TATGGA-TTGATTTATTTTA-AAATATGAATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTG
2324356 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
2324388 ATTTATTTTAAATAATTTGTTTGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
2324420 ATTTATTTTAAA
1 ATTTATTTTAAA
2324432 ATATGGATTG
Statistics
Matches: 424, Mismatches: 55, Indels: 150
0.67 0.09 0.24
Matches are distributed among these distances:
22 54 0.13
23 12 0.03
24 3 0.01
25 7 0.02
26 22 0.05
28 12 0.03
29 11 0.03
30 18 0.04
31 36 0.08
32 192 0.45
33 12 0.03
34 8 0.02
35 3 0.01
36 4 0.01
37 5 0.01
38 8 0.02
39 6 0.01
40 11 0.03
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:2323909 original size:54 final size:54
Alignment explanation
Indices: 2323846--2324677 Score: 503
Period size: 54 Copynumber: 15.4 Consensus size: 54
2323836 TTTTAAAATA
*
2323846 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
2323900 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
2323954 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
2324008 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
2324062 ATTTA--TT--AT--TGTAGTT-TTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT--A-AA---A----TATGGATTG
* * * * ***
2324120 ATTTATTTT-AA-AA--TA-TA-AATTGATTTA-TTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAATATGGATTG
*
2324168 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * *
2324222 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTAATTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * ** * * * ***
2324272 ATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
** ** * ** * * *
2324334 ATTTATTTTAAA-ATATGAATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTG
* *
2324388 ATTTATTTTAAATAATTTGTTTGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
2324442 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * **
2324486 A-TTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTT-AAATAATTTATTAG
1 ATTTA-TTTTAAATAATTTA--TT--AGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * *** **
2324545 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTATTGTAGTTGTATAAATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
* ** *
2324602 ATTTATTTTAAATAATTTATTAGAATAAATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
2324656 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
2324678 TTGTAGTTGT
Statistics
Matches: 607, Mismatches: 104, Indels: 134
0.72 0.12 0.16
Matches are distributed among these distances:
43 3 0.00
44 4 0.01
46 1 0.00
47 5 0.01
48 61 0.10
49 6 0.01
50 26 0.04
51 4 0.01
52 8 0.01
53 7 0.01
54 342 0.56
55 25 0.04
56 15 0.02
57 24 0.04
58 42 0.07
59 12 0.02
60 7 0.01
61 2 0.00
62 13 0.02
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:2323914 original size:68 final size:66
Alignment explanation
Indices: 2323704--2323921 Score: 247
Period size: 60 Copynumber: 3.4 Consensus size: 66
2323694 TATTTTAAAA
* *
2323704 TAATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAATAATTTATTAT-AA-A---A
1 TAATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAATATGGA
2323764 -
66 T
2323764 TAATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAATATGGA
1 TAATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAATATGGA
2323829 T
66 T
* * ** * * * *
2323830 TGATTT-TTTTAAAATAATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
1 TAATTTATTTTAAAATAATTTATTATAAAATAATTTATT--T-TAAAATAAATTATTAT-AAATA
2323893 TGGAT
62 TGGAT
2323898 TAATTTATTTT-AAATAATTTATTA
1 TAATTTATTTTAAAATAATTTATTA
2323922 GTATGGATTG
Statistics
Matches: 135, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
60 54 0.40
61 2 0.01
62 1 0.01
64 13 0.10
65 18 0.13
66 6 0.04
67 10 0.07
68 27 0.20
69 4 0.03
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (66 bp):
TAATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAATATGGA
T
Found at i:2323921 original size:22 final size:22
Alignment explanation
Indices: 2323869--2323911 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2323859 AATTTATTAG
*
2323869 TATGGATTGATTTATTTTAAAA
1 TATGGATTAATTTATTTTAAAA
2323891 TATGGATTAATTTATTTTAAA
1 TATGGATTAATTTATTTTAAA
2323912 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGGATTAATTTATTTTAAAA
Found at i:2323939 original size:22 final size:22
Alignment explanation
Indices: 2323923--2323965 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2323913 AATTTATTAG
2323923 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2323945 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2323966 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2324002 original size:22 final size:22
Alignment explanation
Indices: 2323977--2324019 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2323967 AATTTATTAG
2323977 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
2323999 TATAGATTGATTTATTTTAAA
1 TATAGATTGATTTATTTTAAA
2324020 TAATTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TATAGATTGATTTATTTTAAAA
Done.