Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_51.0, 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: 10072460
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 70252 characters in sequence are not A, C, G, or T
File 7 of 20
Found at i:2434828 original size:11 final size:11
Alignment explanation
Indices: 2434804--2434835 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
2434794 TTGCTTTGAC
2434804 TAAATATC-TA
1 TAAATATCATA
2434814 TAAATATCATA
1 TAAATATCATA
2434825 TAAATAT-ATA
1 TAAATATCATA
2434835 T
1 T
2434836 GAATTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAATATCATA
Found at i:2437146 original size:17 final size:16
Alignment explanation
Indices: 2437124--2437157 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2437114 TATTTTTAAA
*
2437124 TTTTTATTTTAAAATAT
1 TTTTTATTAT-AAATAT
2437141 TTTTTATTATAAATAT
1 TTTTTATTATAAATAT
2437157 T
1 T
2437158 AAATAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTATTATAAATAT
Found at i:2437849 original size:20 final size:21
Alignment explanation
Indices: 2437790--2437849 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 21
2437780 ATAATTTTTA
2437790 AAAATAATTTTTTATTAAATAATT
1 AAAATAA--TTTTA-TAAATAATT
* * *
2437814 AATATAA-TTAAAAAATAA-T
1 AAAATAATTTTATAAATAATT
2437833 AAAATAATTTTATAAAT
1 AAAATAATTTTATAAAT
2437850 CTCATTCGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
19 7 0.24
20 13 0.45
21 3 0.10
24 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATAATTTTATAAATAATT
Found at i:2437881 original size:9 final size:9
Alignment explanation
Indices: 2437867--2437900 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2437857 GATTTTATTC
*
2437867 AAATTTTTA
1 AAATTTTTT
2437876 AAATTTTTT
1 AAATTTTTT
*
2437885 TAATTTTTT
1 AAATTTTTT
2437894 AAATTTT
1 AAATTTT
2437901 CAATCCATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
AAATTTTTT
Found at i:2438176 original size:15 final size:16
Alignment explanation
Indices: 2438156--2438190 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2438146 CTGTTATGTG
*
2438156 AATTTT-ATTTTTAAT
1 AATTTTAATTTTTAAA
2438171 AATTTTAATTTTTAAA
1 AATTTTAATTTTTAAA
2438187 AATT
1 AATT
2438191 AAAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTAATTTTTAAA
Found at i:2440572 original size:19 final size:22
Alignment explanation
Indices: 2440523--2440566 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
2440513 GATCATGAAA
*
2440523 ATTTATTAATTAATTGAAATATT
1 ATTTATTAATAAATT-AAATATT
2440546 ATTTATTAATAAATT-AATATT
1 ATTTATTAATAAATTAAATATT
2440567 TTATTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
23 14 0.70
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTTATTAATAAATTAAATATT
Found at i:2452507 original size:15 final size:15
Alignment explanation
Indices: 2452487--2452519 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2452477 AGAACCTACA
2452487 TATTTT-ATATATTTT
1 TATTTTAAT-TATTTT
2452502 TATTTTAATTATTTT
1 TATTTTAATTATTTT
2452517 TAT
1 TAT
2452520 CAACACTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTTTAATTATTTT
Found at i:2452972 original size:5 final size:5
Alignment explanation
Indices: 2452936--2452971 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
2452926 ATTCACACGT
* *
2452936 CCTAG ACTAG CCTAG CCTAG CCTAG CCTAG CTTAG C
1 CCTAG CCTAG CCTAG CCTAG CCTAG CCTAG CCTAG C
2452972 TCCATTCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.22
Consensus pattern (5 bp):
CCTAG
Found at i:2455381 original size:33 final size:33
Alignment explanation
Indices: 2455333--2455403 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
2455323 ACAGAAATAA
*
2455333 GTGATCCAATGCCACAAGAAGGTGGTCATAAAT
1 GTGATCCAATGCCACAAGAAGGAGGTCATAAAT
* * *
2455366 GTGATGCAATTCCACACGAAGGAGGTCATAAAT
1 GTGATCCAATGCCACAAGAAGGAGGTCATAAAT
2455399 GTGAT
1 GTGAT
2455404 AGCCAACCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (33 bp):
GTGATCCAATGCCACAAGAAGGAGGTCATAAAT
Found at i:2456361 original size:5 final size:5
Alignment explanation
Indices: 2456351--2456376 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2456341 TTGTCCTTCA
2456351 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
2456377 TTTTTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:2456844 original size:15 final size:17
Alignment explanation
Indices: 2456824--2456856 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2456814 GATTTATGCG
2456824 TTTTAAAA-A-AATATT
1 TTTTAAAACAGAATATT
2456839 TTTTAAAACAGAATATT
1 TTTTAAAACAGAATATT
2456856 T
1 T
2456857 ATTTTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTTAAAACAGAATATT
Found at i:2465486 original size:22 final size:22
Alignment explanation
Indices: 2465456--2465499 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2465446 TGTTAAATAT
2465456 TAAAATTTATTAAATATTAAAA
1 TAAAATTTATTAAATATTAAAA
* *
2465478 TAAATTTTATTAAATTTTAAAA
1 TAAAATTTATTAAATATTAAAA
2465500 AGGAGGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAAATTTATTAAATATTAAAA
Found at i:2471926 original size:17 final size:17
Alignment explanation
Indices: 2471904--2471936 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2471894 TTATTTCTTC
*
2471904 TTTTTCTTTTTATTTTG
1 TTTTTCATTTTATTTTG
2471921 TTTTTCATTTTATTTT
1 TTTTTCATTTTATTTT
2471937 CTATAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTCATTTTATTTTG
Found at i:2476032 original size:21 final size:21
Alignment explanation
Indices: 2476008--2476050 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2475998 GGCAATAATA
*
2476008 AAATTGCTTTTCACAAT-TCAG
1 AAATTGCTTGTCA-AATCTCAG
2476029 AAATTGCTTGTCAAATCTCAG
1 AAATTGCTTGTCAAATCTCAG
2476050 A
1 A
2476051 CAGTGTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (21 bp):
AAATTGCTTGTCAAATCTCAG
Found at i:2488454 original size:3 final size:3
Alignment explanation
Indices: 2488446--2488471 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2488436 ATTTTAATTG
2488446 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
2488472 TAAGAATTCA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2497506 original size:2 final size:2
Alignment explanation
Indices: 2497499--2497523 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2497489 TACTAATCTC
2497499 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2497524 TTATTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2514373 original size:16 final size:16
Alignment explanation
Indices: 2514354--2514394 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2514344 TTGAAACATT
**
2514354 TTTTTTAAAAATTTTA
1 TTTTTTAAAAAAATTA
2514370 TTTTTTAAAAAAATTA
1 TTTTTTAAAAAAATTA
2514386 TTTTCTTAA
1 TTTT-TTAA
2514395 GAGCTTCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTTTAAAAAAATTA
Found at i:2515236 original size:80 final size:80
Alignment explanation
Indices: 2515088--2515254 Score: 187
Period size: 80 Copynumber: 2.1 Consensus size: 80
2515078 CATGAGTTCC
* *
2515088 ATTTATGAGATTGTAACATGTACGCCATGAGATGTAAGTGTTAAGTATATCATGTACACTATGAG
1 ATTTATGAGATTATAACATGTACGCCATGAGATGTAAGTGTTAAGTATATCATATACACTATGAG
*
2515153 CTAAACATG-TGATTG
66 CTAAACATGATGA-TA
* * * * * *
2515168 ATTTATGAGGTTATGAA-ATGTATGCCATGAGATGTATGTGTTGAG-ATAGTTATATACATTATG
1 ATTTATGAGATTAT-AACATGTACGCCATGAGATGTAAGTGTTAAGTATA-TCATATACACTATG
* *
2515231 GGCTAAGCATGATGATA
64 AGCTAAACATGATGATA
2515248 ATTTATG
1 ATTTATG
2515255 GAAATGTTAT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
79 3 0.04
80 65 0.89
81 5 0.07
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (80 bp):
ATTTATGAGATTATAACATGTACGCCATGAGATGTAAGTGTTAAGTATATCATATACACTATGAG
CTAAACATGATGATA
Found at i:2520705 original size:51 final size:51
Alignment explanation
Indices: 2520608--2520738 Score: 122
Period size: 51 Copynumber: 2.5 Consensus size: 51
2520598 ATCAAAAAGT
* * *
2520608 AAGAATCT-TTTATGGATTG-AGTGGGTTATAGCTTGATCTCATAAAAAAAA
1 AAGAATCTCTTTGTGGATTGTA-AGGGTTATAGCTTGATCTCAGAAAAAAAA
* * * **
2520658 AAGAATCTCTTTGTGGATTGTAAGGGTTATCGTTTGATCTCGGAAAAAAGG
1 AAGAATCTCTTTGTGGATTGTAAGGGTTATAGCTTGATCTCAGAAAAAAAA
* * *
2520709 AAGAATCCCATTGTGAATTGTGTAAGGGTT
1 AAGAATCTCTTTGTGGA-T-TGTAAGGGTT
2520739 TTCGCTTCCC
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
50 8 0.12
51 46 0.70
52 2 0.03
53 10 0.15
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.34
Consensus pattern (51 bp):
AAGAATCTCTTTGTGGATTGTAAGGGTTATAGCTTGATCTCAGAAAAAAAA
Found at i:2524343 original size:25 final size:25
Alignment explanation
Indices: 2524315--2524365 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2524305 TTTTTCATTA
*
2524315 AATGTCAACCACATTTCAATTATAT
1 AATGACAACCACATTTCAATTATAT
* * *
2524340 AATGACCACCACATTTTAGTTATAT
1 AATGACAACCACATTTCAATTATAT
2524365 A
1 A
2524366 TCAATACCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (25 bp):
AATGACAACCACATTTCAATTATAT
Found at i:2524659 original size:29 final size:30
Alignment explanation
Indices: 2524587--2524671 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 30
2524577 AGAATCATAT
*
2524587 CATTGATCGGAGTAATCTCTTGATGGTCGG
1 CATTGCTCGGAGTAATCTCTTGATGGTCGG
* * *
2524617 CATAGCTTGGAGTAATCTCTT-ATCGG-GGG
1 CATTGCTCGGAGTAATCTCTTGAT-GGTCGG
* *
2524646 CATTGCTCGAAGTAATCTCTCGATGG
1 CATTGCTCGGAGTAATCTCTTGATGG
2524672 GCATCATCAC
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
29 23 0.51
30 22 0.49
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (30 bp):
CATTGCTCGGAGTAATCTCTTGATGGTCGG
Found at i:2540379 original size:10 final size:10
Alignment explanation
Indices: 2540364--2540406 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
2540354 CTCTTGGCAA
2540364 ACATACATAT
1 ACATACATAT
2540374 ACATACATAT
1 ACATACATAT
2540384 ACATACATAT
1 ACATACATAT
*
2540394 AGAT--ATAT
1 ACATACATAT
2540402 ACATA
1 ACATA
2540407 TACATGAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
8 7 0.23
10 23 0.77
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.30
Consensus pattern (10 bp):
ACATACATAT
Found at i:2542830 original size:33 final size:33
Alignment explanation
Indices: 2542793--2542872 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
2542783 CGTGAGGCTG
*
2542793 ATGTGACATGTTAAAATATTATAATTAATTATA
1 ATGTGACATGTTAAAATATTATAATTAATGATA
* * * *
2542826 ATGTGATATGTTGATATATTATAATTGATGATA
1 ATGTGACATGTTAAAATATTATAATTAATGATA
*
2542859 ATATGACATGTTAA
1 ATGTGACATGTTAA
2542873 TTTGGCATGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.42
Consensus pattern (33 bp):
ATGTGACATGTTAAAATATTATAATTAATGATA
Found at i:2549803 original size:17 final size:17
Alignment explanation
Indices: 2549777--2549828 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
2549767 ATAAATTTTG
*
2549777 AAAAAC-TTTTCAAAAA
1 AAAAACTTTTTTAAAAA
2549793 AAAAACTTTTTTTAAAAA
1 AAAAAC-TTTTTTAAAAA
2549811 ATAAAA-TTTTTTAAAAA
1 A-AAAACTTTTTTAAAAA
2549828 A
1 A
2549829 GAGCTTCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 6 0.19
17 12 0.38
18 10 0.31
19 4 0.12
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAAACTTTTTTAAAAA
Found at i:2565816 original size:22 final size:23
Alignment explanation
Indices: 2565791--2565837 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
2565781 ATTGCTATGC
*
2565791 ATTACAATAAGAACTAAG-CTAA
1 ATTACAATAAAAACTAAGCCTAA
* *
2565813 ATTACTATAAAAATTAAGCCTAA
1 ATTACAATAAAAACTAAGCCTAA
2565836 AT
1 AT
2565838 AACTCTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.28
Consensus pattern (23 bp):
ATTACAATAAAAACTAAGCCTAA
Found at i:2566230 original size:12 final size:13
Alignment explanation
Indices: 2566205--2566230 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2566195 AATACCTATG
2566205 TTATAAATTTTTT
1 TTATAAATTTTTT
2566218 TTATAAATTTTTT
1 TTATAAATTTTTT
2566231 AAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATAAATTTTTT
Found at i:2573794 original size:71 final size:71
Alignment explanation
Indices: 2573653--2573879 Score: 310
Period size: 71 Copynumber: 3.2 Consensus size: 71
2573643 TCATAAAGCC
* * * * *
2573653 TAGTCAACTAGAGAGGAAGCATAGTCGACCCTGTTGCAAAAAAAATAAAGAAAATCAAGTTCAAA
1 TAGTCAACTATAGAGGAAGCATAGTCGACCTTGTT-CCAAAAAGATCAAGAAAATCAAGTTCAAA
2573718 ATAGTCA
65 ATAGTCA
* * *
2573725 TAGTCAACTATAGAGTAAGCACAGTCGACCTTATTCCAAAAAGATCAAGAAAATCAAGTTCAAAA
1 TAGTCAACTATAGAGGAAGCATAGTCGACCTTGTTCCAAAAAGATCAAGAAAATCAAGTTCAAAA
2573790 TAGTCA
66 TAGTCA
* * * *
2573796 TAGTCGACTATAGAGGAAGCATAATCGATCTTGTTCCAAAAAGATCAAGAAAATCAAGTTGAAGA
1 TAGTCAACTATAGAGGAAGCATAGTCGACCTTGTTCCAAAAAGATCAAGAAAATCAAGTTCAA-A
*
2573861 ATAGCCA
65 ATAGTCA
*
2573868 TAGTCGACTATA
1 TAGTCAACTATA
2573880 AAAAAGGTAT
Statistics
Matches: 138, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
71 89 0.64
72 49 0.36
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.22
Consensus pattern (71 bp):
TAGTCAACTATAGAGGAAGCATAGTCGACCTTGTTCCAAAAAGATCAAGAAAATCAAGTTCAAAA
TAGTCA
Found at i:2573972 original size:21 final size:22
Alignment explanation
Indices: 2573932--2573973 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2573922 GTCAACTTTA
*
2573932 AGAAGCCATAGTTGATTATAAG
1 AGAAGCCATAGTTGACTATAAG
*
2573954 AGAAG-CATAGTTGGCTATAA
1 AGAAGCCATAGTTGACTATAA
2573974 AAGGTCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (22 bp):
AGAAGCCATAGTTGACTATAAG
Found at i:2574559 original size:50 final size:51
Alignment explanation
Indices: 2574470--2574598 Score: 154
Period size: 50 Copynumber: 2.5 Consensus size: 51
2574460 GCTTCCTAAC
* ** **
2574470 AAAAAGCAAGAAT-CTTTTGTGGATTGTGTGGGTTATCGCTTGATCCTGT-
1 AAAAAGCAAGAATCCCTTTGTGGATTGTAAGAATTATCGCTTGATCCTGTG
* *
2574519 AAAAAGCAAGAATCCCTTTGTGGATTGTAAGAATTCTCGCTTGATTCTGTG
1 AAAAAGCAAGAATCCCTTTGTGGATTGTAAGAATTATCGCTTGATCCTGTG
* *
2574570 AAAAAGCAAAAATCCCCGTTGTGGATTGT
1 AAAAAGCAAGAAT-CCCTTTGTGGATTGT
2574599 GTAATGGTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
49 13 0.19
50 29 0.43
51 12 0.18
52 14 0.21
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (51 bp):
AAAAAGCAAGAATCCCTTTGTGGATTGTAAGAATTATCGCTTGATCCTGTG
Found at i:2585556 original size:21 final size:21
Alignment explanation
Indices: 2585515--2585561 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2585505 TTTTATAGAG
* *
2585515 TTATTTTAATTTTATGTTTAT
1 TTATTTTAATTTGATGATTAT
2585536 TTATTTTAATTTGGAT-ATTAT
1 TTATTTTAATTT-GATGATTAT
2585557 TTATT
1 TTATT
2585562 AGTTTTTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (21 bp):
TTATTTTAATTTGATGATTAT
Found at i:2592237 original size:21 final size:21
Alignment explanation
Indices: 2592154--2592230 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
2592144 ATTAATACAA
*
2592154 TTCATGACAAAGATAGATGCC
1 TTCATGACAAAGACAGATGCC
*
2592175 TTCATGATAAAGACAGATGCC
1 TTCATGACAAAGACAGATGCC
*
2592196 TTCATGATAAAGACAGATGCC
1 TTCATGACAAAGACAGATGCC
*
2592217 TTTATGACAAAGAC
1 TTCATGACAAAGAC
2592231 TAATGCCATC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (21 bp):
TTCATGACAAAGACAGATGCC
Found at i:2601569 original size:18 final size:19
Alignment explanation
Indices: 2601532--2601571 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
2601522 ATTCCATCAA
*
2601532 AAACAATTTAATTCAAAAG
1 AAACAATTTAATTAAAAAG
*
2601551 AAACAATTT-TTTAAAAAG
1 AAACAATTTAATTAAAAAG
2601569 AAA
1 AAA
2601572 GTACATTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (19 bp):
AAACAATTTAATTAAAAAG
Found at i:2610562 original size:112 final size:112
Alignment explanation
Indices: 2610411--2610621 Score: 323
Period size: 112 Copynumber: 1.9 Consensus size: 112
2610401 AAATGGAAGC
* * *
2610411 AACATCTTATACGGGGTCTGTAATTCTGATAACTATTGATTTGTTAGTAAATGAAGCATAATCTT
1 AACATCTTATACGGGCTCTGTAATTCTGATAACTATTGATTTGTTAGTAAATAAAGCAGAATCTT
*
2610476 AAGTTGGTTTACAACTTAAGTTTAAAGTCTAAAGTTTAGTCATCTTT
66 AAGTTGGTTTACAACTTAAATTTAAAGTCTAAAGTTTAGTCATCTTT
* * * * * *
2610523 AACATCTTTTATGGGCTCTGTATTTCTGATAACTGTTGATTTGTTAGTAAATAAATCAGAGTCTT
1 AACATCTTATACGGGCTCTGTAATTCTGATAACTATTGATTTGTTAGTAAATAAAGCAGAATCTT
*
2610588 AAGTTGGTTTACACCTTAAATTTAAAGTCTAAAG
66 AAGTTGGTTTACAACTTAAATTTAAAGTCTAAAG
2610622 CGTGGTATGG
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
112 88 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (112 bp):
AACATCTTATACGGGCTCTGTAATTCTGATAACTATTGATTTGTTAGTAAATAAAGCAGAATCTT
AAGTTGGTTTACAACTTAAATTTAAAGTCTAAAGTTTAGTCATCTTT
Found at i:2612625 original size:14 final size:13
Alignment explanation
Indices: 2612599--2612633 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
2612589 CAAATTCAAA
2612599 TAACTAAACTAAT
1 TAACTAAACTAAT
2612612 TAACTAATACTAAT
1 TAACTAA-ACTAAT
2612626 TAACTAAA
1 TAACTAAA
2612634 ATTTAAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAACTAAACTAAT
Found at i:2614411 original size:21 final size:21
Alignment explanation
Indices: 2614376--2614421 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
2614366 CTCTTGAAGT
2614376 AATTTAAAATAAAATAAACTAA
1 AATTTAAAATAAAAT-AACTAA
* *
2614398 AATTT-AACTAAAATAACTTA
1 AATTTAAAATAAAATAACTAA
2614418 AATT
1 AATT
2614422 AATTACTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 8 0.36
22 5 0.23
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTTAAAATAAAATAACTAA
Found at i:2615467 original size:16 final size:15
Alignment explanation
Indices: 2615437--2615490 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
2615427 AACAACATAA
2615437 AATT-AAAAT-AACT
1 AATTAAAAATAAACT
2615450 AACTTAAAAATAAACT
1 AA-TTAAAAATAAACT
*
2615466 AATTATAAA-AAA--
1 AATTAAAAATAAACT
2615478 AATTAAAAATAAA
1 AATTAAAAATAAA
2615491 GAAATTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
12 8 0.23
13 5 0.14
14 5 0.14
15 11 0.31
16 6 0.17
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
AATTAAAAATAAACT
Found at i:2615489 original size:27 final size:28
Alignment explanation
Indices: 2615436--2615511 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 28
2615426 AAACAACATA
*
2615436 AAATTA-AAATAACTAACTTAAAAATAAAC
1 AAATTATAAATAA--AAATTAAAAATAAAC
* *
2615465 TAATTATAAA-AAAAATTAAAAATAAAG
1 AAATTATAAATAAAAATTAAAAATAAAC
*
2615492 AAATTATAAATGAAAATTAA
1 AAATTATAAATAAAAATTAA
2615512 GGACTTAGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 22 0.55
28 8 0.20
29 7 0.17
30 3 0.08
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (28 bp):
AAATTATAAATAAAAATTAAAAATAAAC
Found at i:2619520 original size:80 final size:79
Alignment explanation
Indices: 2619436--2619590 Score: 202
Period size: 80 Copynumber: 1.9 Consensus size: 79
2619426 ATTTCATAAT
* ** *
2619436 CTCATAAATCATTCACATGCTTGGCCCATAGTGTACATCATATGCTTAACACATACAACTCATGG
1 CTCATAAATCATCCACATGCTTAACCCATAGTGTACATCATATGCTCAACACATACAACTCAT-G
2619501 CATACATGTCACAAG
65 CATACATGTCACAAG
* * * * * * *
2619516 CTCATAATTCATCCACTTGCTTAACTCATATTGTACATGATATGCTCAACAGATACAACTTATGC
1 CTCATAAATCATCCACATGCTTAACCCATAGTGTACATCATATGCTCAACACATACAACTCATGC
2619581 ATACATGTCA
66 ATACATGTCA
2619591 TAATTCATCC
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
79 12 0.19
80 52 0.81
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (79 bp):
CTCATAAATCATCCACATGCTTAACCCATAGTGTACATCATATGCTCAACACATACAACTCATGC
ATACATGTCACAAG
Found at i:2619600 original size:71 final size:71
Alignment explanation
Indices: 2619517--2619671 Score: 190
Period size: 71 Copynumber: 2.2 Consensus size: 71
2619507 TGTCACAAGC
* *
2619517 TCATAATTCATCCACTTGCTTAA-CTCATATTGTACATGATATGC-TCAACAGATACAACTTAT-
1 TCATAATTCATCCACATGCTTAACCT-ATA-TGTACATGATAT-CTTCAACAGATACAACTCATG
2619579 GCATACATG
63 GCATACATG
* * *
2619588 TCATAATTCATCCACATGCTTAGCCTATCATGTACATGATATCTTTAACAGATACATCTCATGGC
1 TCATAATTCATCCACATGCTTAACCTAT-ATGTACATGATATCTTCAACAGATACAACTCATGGC
2619653 ATACATG
65 ATACATG
*
2619660 TTATAATCTCAT
1 TCATAAT-TCAT
2619672 AAGTGGAAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
70 1 0.01
71 50 0.68
72 18 0.25
73 4 0.05
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.35
Consensus pattern (71 bp):
TCATAATTCATCCACATGCTTAACCTATATGTACATGATATCTTCAACAGATACAACTCATGGCA
TACATG
Found at i:2620035 original size:73 final size:73
Alignment explanation
Indices: 2619950--2620094 Score: 290
Period size: 73 Copynumber: 2.0 Consensus size: 73
2619940 GATAAACTAT
2619950 TCTTTAAAATATTATTTCATCATGCACAGCAAATCATTCCCATAAAAATTATTCTCACTTTACAT
1 TCTTTAAAATATTATTTCATCATGCACAGCAAATCATTCCCATAAAAATTATTCTCACTTTACAT
2620015 ATTAAAAC
66 ATTAAAAC
2620023 TCTTTAAAATATTATTTCATCATGCACAGCAAATCATTCCCATAAAAATTATTCTCACTTTACAT
1 TCTTTAAAATATTATTTCATCATGCACAGCAAATCATTCCCATAAAAATTATTCTCACTTTACAT
2620088 ATTAAAA
66 ATTAAAA
2620095 TACTTGAAGA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (73 bp):
TCTTTAAAATATTATTTCATCATGCACAGCAAATCATTCCCATAAAAATTATTCTCACTTTACAT
ATTAAAAC
Found at i:2621769 original size:2 final size:2
Alignment explanation
Indices: 2621762--2621789 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2621752 TATATGCTTT
2621762 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2621790 AGGTAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2625918 original size:27 final size:26
Alignment explanation
Indices: 2625866--2625941 Score: 70
Period size: 27 Copynumber: 3.0 Consensus size: 26
2625856 TTATTCTATT
*
2625866 TTTAAATATTAATAATTTATAATTTA
1 TTTAAATATTAATAATTAATAATTTA
*
2625892 TTTAAAGTATTAA-ATATTAATATTTTA
1 TTTAAA-TATTAATA-ATTAATAATTTA
*
2625919 -TTATAAT-TTAATCATTAA-AATTT
1 TTTA-AATATTAATAATTAATAATTT
2625942 TAAAATACTA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
24 4 0.10
25 9 0.21
26 11 0.26
27 18 0.43
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (26 bp):
TTTAAATATTAATAATTAATAATTTA
Found at i:2626037 original size:42 final size:41
Alignment explanation
Indices: 2625903--2626017 Score: 205
Period size: 41 Copynumber: 2.8 Consensus size: 41
2625893 TTAAAGTATT
*
2625903 AAATATTAATATTTTATTATAATTTAATCATTAAAATTTTA
1 AAATACTAATATTTTATTATAATTTAATCATTAAAATTTTA
2625944 AAATACTAATATTTTATTATAATTTAATCATTAAAATTTTA
1 AAATACTAATATTTTATTATAATTTAATCATTAAAATTTTA
2625985 AAATACTAATATTTTATTTATAATTTAAT-ATTA
1 AAATACTAATATTTTA-TTATAATTTAATCATTA
2626018 TTATGATTAA
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
41 60 0.83
42 12 0.17
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.50
Consensus pattern (41 bp):
AAATACTAATATTTTATTATAATTTAATCATTAAAATTTTA
Found at i:2632445 original size:2 final size:2
Alignment explanation
Indices: 2632438--2632484 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2632428 AAAGCGGAGG
2632438 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2632480 AT AT A
1 AT AT A
2632485 ACACGACACT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2634053 original size:6 final size:7
Alignment explanation
Indices: 2634036--2634060 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2634026 AGCAGAGGTT
2634036 TTTTTTC
1 TTTTTTC
2634043 TTTTTTC
1 TTTTTTC
2634050 TTTTTTC
1 TTTTTTC
2634057 TTTT
1 TTTT
2634061 CCTTTCATTA
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:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:2638236 original size:20 final size:21
Alignment explanation
Indices: 2638199--2638242 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
2638189 TTAACACTTG
* * *
2638199 ATTAATTTTATTTTAATCA-A
1 ATTAATTTGATATAAATCATA
2638219 ATTAATTTGATATAAATCATA
1 ATTAATTTGATATAAATCATA
2638240 ATT
1 ATT
2638243 TATAATTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTAATTTGATATAAATCATA
Found at i:2645106 original size:18 final size:17
Alignment explanation
Indices: 2645074--2645107 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2645064 AAAAAAATGG
*
2645074 ATAAAAAAATCATAATC
1 ATAAAAAAATAATAATC
2645091 ATAAAAAAATAAATAAT
1 ATAAAAAAAT-AATAAT
2645108 TCAAAGGTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAAAAAAATAATAATC
Found at i:2651424 original size:20 final size:19
Alignment explanation
Indices: 2651396--2651435 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2651386 AACCCGATTG
*
2651396 ATTAATATAATAGTTGTTAT
1 ATTAATATAAGA-TTGTTAT
*
2651416 ATTATTATAAGATTGTTAT
1 ATTAATATAAGATTGTTAT
2651435 A
1 A
2651436 CTACATCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (19 bp):
ATTAATATAAGATTGTTAT
Found at i:2660735 original size:112 final size:112
Alignment explanation
Indices: 2660538--2660759 Score: 275
Period size: 112 Copynumber: 2.0 Consensus size: 112
2660528 TGAGAATGCG
2660538 TAAAGAATATTTTCTTAAATGAACACTACTTATTCCCTCTAAATTCTTTTCAAAAGAGCAACAAT
1 TAAAGAATATTTTCTTAAATGAACACTACTTATTCCCTCTAAATTCTTTTCAAAAGAGCAACAAT
* **
2660603 TCGATCAACCAAAATGGGAGTTTGGTCATTTTACACATTAATGGGGT
66 TCGACCAACCAAAATGGGAGTTTGACCATTTTACACATTAATGGGGT
* * * * * ***
2660650 TAAAGAATATTTTCTTGAATG-ACGAGTACTTATTCCCTTTAGATTGTTTTCAAAAGAGCAATGG
1 TAAAGAATATTTTCTTAAATGAAC-ACTACTTATTCCCTCTAAATTCTTTTCAAAAGAGCAACAA
* ** * * *
2660714 TTCGGCCAATTAAGATGGGAGTTTGACCATTTTGCACCTTAATGGG
65 TTCGACCAACCAAAATGGGAGTTTGACCATTTTACACATTAATGGG
2660760 ATTTCTAACC
Statistics
Matches: 92, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
111 2 0.02
112 90 0.98
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (112 bp):
TAAAGAATATTTTCTTAAATGAACACTACTTATTCCCTCTAAATTCTTTTCAAAAGAGCAACAAT
TCGACCAACCAAAATGGGAGTTTGACCATTTTACACATTAATGGGGT
Found at i:2670247 original size:27 final size:28
Alignment explanation
Indices: 2670204--2670262 Score: 111
Period size: 27 Copynumber: 2.1 Consensus size: 28
2670194 TTAAAAAAAA
2670204 TTAATAAAAAAATTAATCATAGTAATTT
1 TTAATAAAAAAATTAATCATAGTAATTT
2670232 TTAAT-AAAAAATTAATCATAGTAATTT
1 TTAATAAAAAAATTAATCATAGTAATTT
2670259 TTAA
1 TTAA
2670263 AATCAGTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (28 bp):
TTAATAAAAAAATTAATCATAGTAATTT
Found at i:2677595 original size:31 final size:30
Alignment explanation
Indices: 2677547--2677604 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
2677537 TTATATAAAT
* *
2677547 TATAATAAAAGATTAAATACAATATTTTCG
1 TATAATAAAAAATTAAATACAAAATTTTCG
*
2677577 TATAATACAAAAATTAAATTCAAAATTT
1 TATAATA-AAAAATTAAATACAAAATTT
2677605 GGTAGACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.36
Consensus pattern (30 bp):
TATAATAAAAAATTAAATACAAAATTTTCG
Found at i:2678432 original size:3 final size:3
Alignment explanation
Indices: 2678418--2678447 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2678408 TAAAATGTCC
*
2678418 CAT CAT CTT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
2678448 AGTACCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (3 bp):
CAT
Found at i:2679205 original size:2 final size:2
Alignment explanation
Indices: 2679198--2679229 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2679188 TAAATGGTGC
2679198 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2679230 TCTTTGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2679691 original size:13 final size:12
Alignment explanation
Indices: 2679655--2679691 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2679645 TTGAATGTAT
*
2679655 AAAAAGTGAAAA
1 AAAAAATGAAAA
2679667 AAAAAATGAAAA
1 AAAAAATGAAAA
*
2679679 AAAAAATGTAAA
1 AAAAAATGAAAA
2679691 A
1 A
2679692 GACATCATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (12 bp):
AAAAAATGAAAA
Found at i:2681861 original size:18 final size:18
Alignment explanation
Indices: 2681834--2681871 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2681824 ATTAACTAGC
2681834 ATAATCATAAATAAT-TTA
1 ATAATCAT-AATAATCTTA
*
2681852 ATAATGATAATAATCTTA
1 ATAATCATAATAATCTTA
2681870 AT
1 AT
2681872 TTCTAGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (18 bp):
ATAATCATAATAATCTTA
Found at i:2682155 original size:19 final size:19
Alignment explanation
Indices: 2682116--2682155 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2682106 AATTTGTAGG
* **
2682116 AAATCAATAAGTAATCTCT
1 AAATAAATAAGTAATAACT
2682135 AAATAAATAAGTAATAACT
1 AAATAAATAAGTAATAACT
2682154 AA
1 AA
2682156 CTTTATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (19 bp):
AAATAAATAAGTAATAACT
Found at i:2702615 original size:21 final size:21
Alignment explanation
Indices: 2702578--2702642 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
2702568 AAGATCTTGA
*
2702578 TATATTTA-A-TTACTTATAT
1 TATATTTATATTTATTTATAT
2702597 TATATTTATATTTATTTATAT
1 TATATTTATATTTATTTATAT
* *
2702618 AATTTTTAATATTCTATCTTATAT
1 TATATTT-ATATT-TAT-TTATAT
2702642 T
1 T
2702643 TATAAAACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 8 0.22
20 1 0.03
21 14 0.38
22 5 0.14
23 3 0.08
24 6 0.16
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATTTATATTTATTTATAT
Found at i:2704438 original size:10 final size:10
Alignment explanation
Indices: 2704416--2704461 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
2704406 AATCTATTTC
*
2704416 CATATAT-TC
1 CATATATATA
2704425 CATATATATA
1 CATATATATA
2704435 CATATATATA
1 CATATATATA
*
2704445 CATATAT-TC
1 CATATATATA
2704454 CATATATA
1 CATATATA
2704462 ATATTATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
9 15 0.45
10 18 0.55
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.41
Consensus pattern (10 bp):
CATATATATA
Found at i:2704469 original size:29 final size:30
Alignment explanation
Indices: 2704416--2704474 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
2704406 AATCTATTTC
2704416 CATATATTCCATATATATACATAT-ATATA
1 CATATATTCCATATATATACATATAATATA
*
2704445 CATATATTCCATATATAATA-TTATAATATA
1 CATATATTCCATATAT-ATACATATAATATA
2704475 ATTTTATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (30 bp):
CATATATTCCATATATATACATATAATATA
Found at i:2710440 original size:23 final size:22
Alignment explanation
Indices: 2710408--2710477 Score: 86
Period size: 23 Copynumber: 2.9 Consensus size: 22
2710398 TAAATTATAA
2710408 ATAAAATATTAATATTTAAATT
1 ATAAAATATTAATATTTAAATT
2710430 ATCAAAATATTAATATTTTAAATAAATT
1 AT-AAAATATTAATA--TT---TAAATT
2710458 ATAAAATATTAATATTTAAA
1 ATAAAATATTAATATTTAAA
2710478 AATAAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
22 6 0.14
23 12 0.29
25 4 0.10
27 12 0.29
28 8 0.19
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (22 bp):
ATAAAATATTAATATTTAAATT
Found at i:2710442 original size:42 final size:42
Alignment explanation
Indices: 2710323--2710455 Score: 112
Period size: 42 Copynumber: 3.1 Consensus size: 42
2710313 AAAAATTAAT
* * * *
2710323 TAAAAGTATTAATATTTTAATCA-CAATTATAGTTAATTTATAAA
1 TAAAA-TATTAATATTTAAATTATCAA-AATA-TTAAATTATAAA
* *
2710367 TACAATATTAATATTTTAAAATT-T--TAATGATTAAATTATAAA
1 TAAAATATTAATA-TTT-AAATTATCAAAAT-ATTAAATTATAAA
*
2710409 TAAAATATTAATATTTAAATTATCAAAATATTAATATTTTAAA
1 TAAAATATTAATATTTAAATTATCAAAATATTAA-ATTATAAA
2710452 TAAA
1 TAAA
2710456 TTATAAAATA
Statistics
Matches: 72, Mismatches: 9, Indels: 17
0.73 0.09 0.17
Matches are distributed among these distances:
40 5 0.07
41 4 0.06
42 30 0.42
43 23 0.32
44 7 0.10
45 3 0.04
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (42 bp):
TAAAATATTAATATTTAAATTATCAAAATATTAAATTATAAA
Found at i:2710467 original size:27 final size:29
Alignment explanation
Indices: 2710424--2710483 Score: 97
Period size: 27 Copynumber: 2.1 Consensus size: 29
2710414 TATTAATATT
*
2710424 TAAATTATCAAAATATTAATATTT-TAAA
1 TAAATTATCAAAATATTAATATTTAAAAA
2710452 TAAATTAT-AAAATATTAATATTTAAAAA
1 TAAATTATCAAAATATTAATATTTAAAAA
2710480 TAAA
1 TAAA
2710484 AATAAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAATTATCAAAATATTAATATTTAAAAA
Found at i:2710481 original size:16 final size:15
Alignment explanation
Indices: 2710370--2710478 Score: 57
Period size: 15 Copynumber: 7.1 Consensus size: 15
2710360 TTATAAATAC
2710370 AATATTAATATTTTAA
1 AATATTAATA-TTTAA
*
2710386 AATTTTAATGA-TTAA
1 AATATTAAT-ATTTAA
*
2710401 ATTA-TAA-A--TAA
1 AATATTAATATTTAA
2710412 AATATTAATATTTAA
1 AATATTAATATTTAA
* * *
2710427 ATTATCAAAATATTAA
1 AATATTAATAT-TTAA
* *
2710443 TATTTTAAATAAATTATAA
1 AATATT-AAT--ATT-TAA
2710462 AATATTAATATTTAA
1 AATATTAATATTTAA
2710477 AA
1 AA
2710479 ATAAAAATAA
Statistics
Matches: 69, Mismatches: 14, Indels: 21
0.66 0.13 0.20
Matches are distributed among these distances:
11 6 0.09
12 4 0.06
13 1 0.01
14 3 0.04
15 22 0.32
16 17 0.25
17 3 0.04
18 4 0.06
19 9 0.13
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (15 bp):
AATATTAATATTTAA
Found at i:2710488 original size:27 final size:25
Alignment explanation
Indices: 2710383--2710489 Score: 87
Period size: 26 Copynumber: 4.2 Consensus size: 25
2710373 ATTAATATTT
* *
2710383 TAAAATTTTAATGA-TTAAATTATAAA
1 TAAAATATTAAT-ATTTAAA-TAAAAA
*
2710409 TAAAATATTAATATTTAAAT---TA
1 TAAAATATTAATATTTAAATAAAAA
*
2710431 TCAAAATATTAATATTTTAAATAAATTA
1 T-AAAATATTAATA-TTTAAATAAA-AA
2710459 TAAAATATTAATATTTAAAAATAAAAA
1 TAAAATATTAATATTT--AAATAAAAA
2710486 TAAA
1 TAAA
2710490 TAATCATAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 17
0.78 0.03 0.19
Matches are distributed among these distances:
22 2 0.03
23 12 0.17
24 7 0.10
25 2 0.03
26 19 0.28
27 17 0.25
28 10 0.14
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (25 bp):
TAAAATATTAATATTTAAATAAAAA
Found at i:2710587 original size:16 final size:17
Alignment explanation
Indices: 2710560--2710605 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
2710550 AATTATAAAT
* *
2710560 AAAATATTAATATTTAA
1 AAAATAATAATATATAA
2710577 AAAATAA-AATA-ATAA
1 AAAATAATAATATATAA
2710592 AAAATAATAATATA
1 AAAATAATAATATA
2710606 AAGAATAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 10 0.40
16 8 0.32
17 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATAATAATATATAA
Found at i:2710592 original size:15 final size:14
Alignment explanation
Indices: 2710574--2710614 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
2710564 TATTAATATT
2710574 TAAAAAATAAAATAA
1 TAAAAAATAAAAT-A
2710589 TAAAAAATAATAATA
1 TAAAAAATAA-AATA
*
2710604 TAAAGAATAAA
1 TAAAAAATAAA
2710615 GTGTATTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 1 0.04
15 20 0.83
16 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (14 bp):
TAAAAAATAAAATA
Found at i:2711959 original size:16 final size:17
Alignment explanation
Indices: 2711918--2711959 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2711908 GAAATTAAAA
2711918 TTTAGAT-TTTGATTCT
1 TTTAGATATTTGATTCT
*
2711934 TTTA-AAATTTGATT-T
1 TTTAGATATTTGATTCT
2711949 TTTAGATATTT
1 TTTAGATATTT
2711960 TTATTGAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.26, C:0.02, G:0.10, T:0.62
Consensus pattern (17 bp):
TTTAGATATTTGATTCT
Found at i:2712176 original size:21 final size:20
Alignment explanation
Indices: 2712151--2712189 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
2712141 ATGGAAGAAC
2712151 ATCTATTGATAGATCGGACCT
1 ATCTATTGATAGAT-GGACCT
2712172 ATCTATTGATAGATGGAC
1 ATCTATTGATAGATGGAC
2712190 AATAAAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (20 bp):
ATCTATTGATAGATGGACCT
Found at i:2713224 original size:69 final size:69
Alignment explanation
Indices: 2713108--2713244 Score: 229
Period size: 69 Copynumber: 2.0 Consensus size: 69
2713098 TCTCGAAAAT
* * * *
2713108 TTTAATCTACCTGTACCCATGTGATCACGAGCAATCCCAACATTGCCTGCTTCTTCCAGATTACC
1 TTTAATCGACCTATACCCATGTGATCACGAGCAATCCCAACAATGCCTGCTTCTCCCAGATTACC
2713173 AGCG
66 AGCG
*
2713177 TTTAATCGACCTATACCCATGTGATCATGAGCAATCCCAACAATGCCTGCTTCTCCCAGATTACC
1 TTTAATCGACCTATACCCATGTGATCACGAGCAATCCCAACAATGCCTGCTTCTCCCAGATTACC
2713242 AGC
66 AGC
2713245 TGACACCCCT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (69 bp):
TTTAATCGACCTATACCCATGTGATCACGAGCAATCCCAACAATGCCTGCTTCTCCCAGATTACC
AGCG
Found at i:2730384 original size:36 final size:36
Alignment explanation
Indices: 2730335--2730419 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
2730325 TTATGTGTTT
* *
2730335 AAGGGTCAGATGTGAGACGTCATACCAAACAT-GTA
1 AAGGGCCAAATGTGAGACGTCATACCAAACATGGTA
* * *
2730370 CAAGGGCCAAATGTGGGACGTTATACCACACATGGTA
1 -AAGGGCCAAATGTGAGACGTCATACCAAACATGGTA
*
2730407 AA-GGCAAAATGTG
1 AAGGGCCAAATGTG
2730420 GGGTATTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
35 10 0.24
36 29 0.69
37 3 0.07
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (36 bp):
AAGGGCCAAATGTGAGACGTCATACCAAACATGGTA
Found at i:2743780 original size:27 final size:27
Alignment explanation
Indices: 2743731--2743982 Score: 168
Period size: 27 Copynumber: 9.3 Consensus size: 27
2743721 ATGTGATAAT
***
2743731 TAAATTTTTCAACATGTTATGTAACAAC
1 TAAA-TTTTCAACATGACGTGTAACAAC
*
2743759 TAAATTTTCAATATGACGTGTAACAAC
1 TAAATTTTCAACATGACGTGTAACAAC
* * **
2743786 TATATTTTTCAATATGGTGTGTAACAA-
1 TA-AATTTTCAACATGACGTGTAACAAC
** *** *
2743813 TAAACCTTCAACATGGTATGTAACAGC
1 TAAATTTTCAACATGACGTGTAACAAC
* *
2743840 TACATTTTTCAACATGACGTATAACAAC
1 TA-AATTTTCAACATGACGTGTAACAAC
* * * * *
2743868 TACATTTTTCGACATGACATATAATAAC
1 TA-AATTTTCAACATGACGTGTAACAAC
* * *
2743896 TAAATTTTCAACATGATGTATAACAAT
1 TAAATTTTCAACATGACGTGTAACAAC
* * *
2743923 TACATTTTCAACATGGCATGTAACAA-
1 TAAATTTTCAACATGACGTGTAACAAC
* * * *
2743949 T-AATTTTCAATATAACGTATAACAAT
1 TAAATTTTCAACATGACGTGTAACAAC
2743975 TAAATTTT
1 TAAATTTT
2743983 AAAACATGGT
Statistics
Matches: 178, Mismatches: 41, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
25 18 0.10
26 20 0.11
27 71 0.40
28 69 0.39
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (27 bp):
TAAATTTTCAACATGACGTGTAACAAC
Found at i:2743807 original size:28 final size:27
Alignment explanation
Indices: 2743733--2744018 Score: 159
Period size: 27 Copynumber: 10.6 Consensus size: 27
2743723 GTGATAATTA
* *
2743733 AATTTTTCAACATGTTATGTAACAACT
1 AATTTTTCAACATGATGTGTAACAACT
* * *
2743760 AAATTTTCAATATGACGTGTAACAACT
1 AATTTTTCAACATGATGTGTAACAACT
* *
2743787 ATATTTTTCAATATGGTGTGTAACAA-T
1 A-ATTTTTCAACATGATGTGTAACAACT
*** * * *
2743814 AAACCTTCAACATGGTATGTAACAGCT
1 AATTTTTCAACATGATGTGTAACAACT
* *
2743841 ACATTTTTCAACATGACGTATAACAACT
1 A-ATTTTTCAACATGATGTGTAACAACT
* ** * *
2743869 ACATTTTTCGACATGACATATAATAACT
1 A-ATTTTTCAACATGATGTGTAACAACT
* * *
2743897 AAATTTTCAACATGATGTATAACAATT
1 AATTTTTCAACATGATGTGTAACAACT
***
2743924 ACA-TTTTCAACATGGCATGTAACAA-T
1 A-ATTTTTCAACATGATGTGTAACAACT
* * * * *
2743950 AA-TTTTCAATATAACGTATAACAATT
1 AATTTTTCAACATGATGTGTAACAACT
** * *
2743976 AAATTTTAAAACATGGTATGTAAC-ACT
1 -AATTTTTCAACATGATGTGTAACAACT
*
2744003 ATATTTTTTAACATGA
1 A-ATTTTTCAACATGA
2744019 CCTTTATCAT
Statistics
Matches: 199, Mismatches: 52, Indels: 16
0.75 0.19 0.06
Matches are distributed among these distances:
25 18 0.09
26 22 0.11
27 81 0.41
28 78 0.39
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (27 bp):
AATTTTTCAACATGATGTGTAACAACT
Found at i:2744554 original size:24 final size:25
Alignment explanation
Indices: 2744506--2744555 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
2744496 AATTGTATAA
*
2744506 TTCTATCTTTTAATTTATTTCTTTT
1 TTCTATCTTTTAATTTATTACTTTT
* *
2744531 TTCTAT-TTTTATTTTATTAGTTTT
1 TTCTATCTTTTAATTTATTACTTTT
2744555 T
1 T
2744556 GAAATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.74
Consensus pattern (25 bp):
TTCTATCTTTTAATTTATTACTTTT
Found at i:2744658 original size:203 final size:206
Alignment explanation
Indices: 2744304--2744686 Score: 490
Period size: 202 Copynumber: 1.9 Consensus size: 206
2744294 TAGTCTAATG
* *
2744304 TTTTAATTCTATTTCCCTTTCCTATTTCTAATTTATTAGTTTTTGAAATAAATAAAAAATTCTTG
1 TTTTAATTCTATTTCCCTTTCCTATTTCTAATTTATTAGTTTTTG--A-AAATAAAAAATTCCTA
* * * * * *
2744369 ATATTGAGAATTTTTCAAAATCTCCCAAATGCTCATGGTAAAATTTTAGAAAATTTTCTCACCTA
63 ATATTAAAAATTTTCCAAAATCTCCCAAACGCTCATAGTAAAATTTTAGAAAATTCTCTCACCTA
* *
2744434 GAATTATCAAAAAGTCACTTTTGGTTTTCTTGAA-ATTTCATCATTGGAAAGCTTATTTATTTAA
128 GAATTATCAAAAAGCCACTTTTGATTTTCTT-AAGATTTCATCATTGGAAAGCTTATTTATTTAA
2744498 TTGTATAATTCTATC
192 TTGTATAATTCTATC
** * * *
2744513 TTTTAATT-TATTTCTTTTTTCTATTTTTATTTTATTAGTTTTTG-AAAT-AAAAATTCCTAAT-
1 TTTTAATTCTATTTCCCTTTCCTATTTCTAATTTATTAGTTTTTGAAAATAAAAAATTCCTAATA
* *
2744574 TTAAAAATTTTCCAAAATCTCTCAAACGCTCATAGTAAAATTTT-GAAAAATTCTCTCACGTAGA
66 TTAAAAATTTTCCAAAATCTCCCAAACGCTCATAGTAAAATTTTAG-AAAATTCTCTCACCTAG-
* * *
2744638 AATTCTCAAAAAGCCACTTTTGATTTTCTTAAGGTTTCATTATTGGAAA
129 AATTATCAAAAAGCCACTTTTGATTTTCTTAAGATTTCATCATTGGAAA
2744687 ACTTCTATCA
Statistics
Matches: 151, Mismatches: 20, Indels: 12
0.83 0.11 0.07
Matches are distributed among these distances:
201 1 0.01
202 55 0.36
203 52 0.34
204 4 0.03
208 31 0.21
209 8 0.05
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.45
Consensus pattern (206 bp):
TTTTAATTCTATTTCCCTTTCCTATTTCTAATTTATTAGTTTTTGAAAATAAAAAATTCCTAATA
TTAAAAATTTTCCAAAATCTCCCAAACGCTCATAGTAAAATTTTAGAAAATTCTCTCACCTAGAA
TTATCAAAAAGCCACTTTTGATTTTCTTAAGATTTCATCATTGGAAAGCTTATTTATTTAATTGT
ATAATTCTATC
Found at i:2750593 original size:14 final size:14
Alignment explanation
Indices: 2750557--2750599 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
2750547 TATTCATAAC
* *
2750557 CAAAAATGAGAAAA
1 CAAAAAAGACAAAA
2750571 CATAAAAAGACAAAA
1 CA-AAAAAGACAAAA
2750586 CAAAAAAGGACAAA
1 CAAAAAA-GACAAA
2750600 CCACACATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.72, C:0.12, G:0.12, T:0.05
Consensus pattern (14 bp):
CAAAAAAGACAAAA
Found at i:2757768 original size:2 final size:2
Alignment explanation
Indices: 2757761--2757791 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2757751 TCCCATGGCC
2757761 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 A
2757792 NNNNNNNNNN
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2759760 original size:3 final size:3
Alignment explanation
Indices: 2759752--2759781 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2759742 TACTAAAATT
*
2759752 ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2759782 TAAAGTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:2760624 original size:15 final size:15
Alignment explanation
Indices: 2760604--2760634 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2760594 TTTTAGTTAA
*
2760604 ATTTTATATTATTTT
1 ATTTTAAATTATTTT
2760619 ATTTTAAATTATTTT
1 ATTTTAAATTATTTT
2760634 A
1 A
2760635 AGAGTAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTAAATTATTTT
Found at i:2763153 original size:20 final size:20
Alignment explanation
Indices: 2763114--2763154 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2763104 TATTTTATGC
*
2763114 ATTATAATTTAATATTTAAT
1 ATTATAATTTAATATATAAT
2763134 ATTATAAATTTAA-ATATAAT
1 ATTAT-AATTTAATATATAAT
2763154 A
1 A
2763155 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTATAATTTAATATATAAT
Found at i:2777671 original size:19 final size:19
Alignment explanation
Indices: 2777647--2777684 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2777637 TTTTTATTTA
*
2777647 AATAAAAAAATTATATATT
1 AATAAAAAAATTAAATATT
*
2777666 AATAAATAAATTAAATATT
1 AATAAAAAAATTAAATATT
2777685 CAGATGTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AATAAAAAAATTAAATATT
Found at i:2790595 original size:45 final size:45
Alignment explanation
Indices: 2790546--2790683 Score: 144
Period size: 42 Copynumber: 3.2 Consensus size: 45
2790536 TTCGTTAGGT
* *
2790546 GATTACTTCGGATGATGATAATGTTTATGTTACCATGCATTGGGA
1 GATTACTTCGGATGATGATAATGTTTATGCTACCATCCATTGGGA
**
2790591 GATTAC-TCTGGATGATG--AA-GTTTATGCTACCATCCATTGTAA
1 GATTACTTC-GGATGATGATAATGTTTATGCTACCATCCATTGGGA
* * * *
2790633 TATTA-TTCCGGATGATGATGAT-ATTATGCTATCATCCATTGGGA
1 GATTACTT-CGGATGATGATAATGTTTATGCTACCATCCATTGGGA
2790677 GATTACT
1 GATTACT
2790684 CTTATGATGA
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
42 32 0.43
43 3 0.04
44 25 0.33
45 15 0.20
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (45 bp):
GATTACTTCGGATGATGATAATGTTTATGCTACCATCCATTGGGA
Found at i:2790907 original size:17 final size:17
Alignment explanation
Indices: 2790885--2790923 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2790875 ATTATCAAAT
2790885 ACGAGTGTGCCGTAAAG
1 ACGAGTGTGCCGTAAAG
2790902 ACGAGTGTGCCGTAAAG
1 ACGAGTGTGCCGTAAAG
2790919 ACGAG
1 ACGAG
2790924 ATTATGGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.31, C:0.18, G:0.36, T:0.15
Consensus pattern (17 bp):
ACGAGTGTGCCGTAAAG
Found at i:2794287 original size:20 final size:20
Alignment explanation
Indices: 2794262--2794303 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2794252 TGATACATTC
*
2794262 GAATCCCACCAGTACGATAA
1 GAATCCCACCAGTACAATAA
*
2794282 GAATCCCATCAGTACAATAA
1 GAATCCCACCAGTACAATAA
2794302 GA
1 GA
2794304 GGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.17
Consensus pattern (20 bp):
GAATCCCACCAGTACAATAA
Found at i:2795996 original size:3 final size:3
Alignment explanation
Indices: 2795988--2796015 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2795978 GAGTACTAAA
2795988 AGT AGT AGT AGT AGT AGT AGT AGT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT A
2796016 TTAAAAAAGA
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:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
AGT
Found at i:2810297 original size:24 final size:24
Alignment explanation
Indices: 2810270--2810322 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2810260 TCCAATTACC
* * *
2810270 CCACCGCCGCCTCATGTACACCCT
1 CCACCGCCACCCCATGTACACCCA
* *
2810294 CCACCTCCACCCCATGTACATCCA
1 CCACCGCCACCCCATGTACACCCA
2810318 CCACC
1 CCACC
2810323 AGCACCACTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.57, G:0.08, T:0.15
Consensus pattern (24 bp):
CCACCGCCACCCCATGTACACCCA
Found at i:2810328 original size:24 final size:24
Alignment explanation
Indices: 2810282--2810328 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
2810272 ACCGCCGCCT
* *
2810282 CATGTACACCCTCCACCTCCACCC
1 CATGTACACCCACCACCACCACCC
* *
2810306 CATGTACATCCACCACCAGCACC
1 CATGTACACCCACCACCACCACC
2810329 ACTTCCTCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.53, G:0.06, T:0.15
Consensus pattern (24 bp):
CATGTACACCCACCACCACCACCC
Found at i:2814350 original size:2 final size:2
Alignment explanation
Indices: 2814303--2814331 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2814293 TCTTTTAATT
2814303 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 T
2814332 TCTTGAGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2827235 original size:60 final size:61
Alignment explanation
Indices: 2827141--2827291 Score: 205
Period size: 60 Copynumber: 2.5 Consensus size: 61
2827131 TCCAACCTTT
* * * * * *
2827141 ACCTATCTCAAAATAAGTTCAATTTTAAAATTTTAGAATTCCTAAACTTAATCTAGGCTCG
1 ACCTATCACAAAACAAGTCCAATTTTAAAATTTTAGAACTCCTAAACTTAATCTAAGCTCA
* *
2827202 ACCTATCA-AAAACATGTCCAATTTTAAAATTTTAGAACTCCTAAACTTAATTTAAGCTCA
1 ACCTATCACAAAACAAGTCCAATTTTAAAATTTTAGAACTCCTAAACTTAATCTAAGCTCA
* *
2827262 ACCTATCACAAAACAAGTTCGATTTTAAAA
1 ACCTATCACAAAACAAGTCCAATTTTAAAA
2827292 CTTAAGCTAG
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 53 0.68
61 25 0.32
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (61 bp):
ACCTATCACAAAACAAGTCCAATTTTAAAATTTTAGAACTCCTAAACTTAATCTAAGCTCA
Found at i:2827978 original size:60 final size:60
Alignment explanation
Indices: 2827291--2827989 Score: 545
Period size: 60 Copynumber: 11.7 Consensus size: 60
2827281 CGATTTTAAA
* * ** * * * *
2827291 ACTTAAGCTAGGCTCGATCTATCTCATAACAGGTTCAATTTTAA-ACTCTTG-AGCTCTTAT
1 ACTTAATCTAGGCTCGATCTATCTCACAACAGGTTTGA-TTTAATA-TTTTGAAACTCCTAG
* * * * * * *
2827351 AC-GAAACTAGGCTC-AACTTATCTCATAATAGGTTCGATTTAATATTTTGAAACTCCTAA
1 ACTTAATCTAGGCTCGATC-TATCTCACAACAGGTTTGATTTAATATTTTGAAACTCCTAG
* * * * * *
2827410 ACTTAATCTAGACTCGA-CTTGTCTCACAAGAAGTTTGATTTGATATTTTGAAACTCTTAG
1 ACTTAATCTAGGCTCGATC-TATCTCACAACAGGTTTGATTTAATATTTTGAAACTCCTAG
* * * * * * ** *
2827470 ACTTAATCCAAGTTCGTTCTATATCATAACAGGTTCAATTTGATATTTTGAAACTCCTAG
1 ACTTAATCTAGGCTCGATCTATCTCACAACAGGTTTGATTTAATATTTTGAAACTCCTAG
* * * * * ** *
2827530 ACTTAATCTAGGC-CTAATTTATCTCACAGCAGGTTCGGTTTAATATTTAAAAACTCTTAG
1 ACTTAATCTAGGCTC-GATCTATCTCACAACAGGTTTGATTTAATATTTTGAAACTCCTAG
* * ** *
2827590 ACTTAATCTAGGCTTGA-CTTATCTCACAATAGGTTCAATTTAATATTTTGAAACTCTTAG
1 ACTTAATCTAGGCTCGATC-TATCTCACAACAGGTTTGATTTAATATTTTGAAACTCCTAG
* * * * * *
2827650 ACTTAATTTAGGCTGGATTTATCTCACAACAAGTTTGATTTAATACTTTGAAACTCCTAT
1 ACTTAATCTAGGCTCGATCTATCTCACAACAGGTTTGATTTAATATTTTGAAACTCCTAG
* * *
2827710 ACTTAATCTAGGCTTGACCTATCTCACAATAGGTTTGATTTAATATTTTGAAACTCCTAG
1 ACTTAATCTAGGCTCGATCTATCTCACAACAGGTTTGATTTAATATTTTGAAACTCCTAG
* * * ** * * *
2827770 ACTTAATCTAGGCTTGACCTATCTCACAATAGGTTCAATTTTAA-A-CTTAAGAACTCCTAA
1 ACTTAATCTAGGCTCGATCTATCTCACAACAGGTTTGA-TTTAATATTTTGA-AACTCCTAG
* * * * * * ** * *
2827830 ACTTAATCTAGACTCAACCAATCTTAAAACAGGTTTGATTTAA-AAATTGAGACTCTTAG
1 ACTTAATCTAGGCTCGATCTATCTCACAACAGGTTTGATTTAATATTTTGAAACTCCTAG
* * * * * * *
2827889 ACTTAATTTAGGTTTGATCTATCTCAAAACAGGTTTGATTTAAAATTTTGGAACACCTAG
1 ACTTAATCTAGGCTCGATCTATCTCACAACAGGTTTGATTTAATATTTTGAAACTCCTAG
* *
2827949 ACTTAATCTAGGCTCGATCTATCTTAAAACAGGTTTGATTT
1 ACTTAATCTAGGCTCGATCTATCTCACAACAGGTTTGATTT
2827990 TTTTAAAAAA
Statistics
Matches: 513, Mismatches: 112, Indels: 28
0.79 0.17 0.04
Matches are distributed among these distances:
58 11 0.02
59 87 0.17
60 408 0.80
61 7 0.01
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (60 bp):
ACTTAATCTAGGCTCGATCTATCTCACAACAGGTTTGATTTAATATTTTGAAACTCCTAG
Found at i:2833426 original size:42 final size:42
Alignment explanation
Indices: 2833366--2833448 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
2833356 TACCAAACCC
* * *
2833366 TTGACTTTCAAAATTGATTTTAATTTTTCACCATTTGAGGGT
1 TTGACTTTCAAAAGTGATTTTAATTCTTAACCATTTGAGGGT
**
2833408 TTGACTTTTGAAAGTGATTTTAATTCTTAACCATTTGAGGG
1 TTGACTTTCAAAAGTGATTTTAATTCTTAACCATTTGAGGG
2833449 GAAGGGGGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.46
Consensus pattern (42 bp):
TTGACTTTCAAAAGTGATTTTAATTCTTAACCATTTGAGGGT
Found at i:2836950 original size:12 final size:12
Alignment explanation
Indices: 2836933--2836957 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2836923 GCATTAGGTT
2836933 ATTAATTTCATG
1 ATTAATTTCATG
2836945 ATTAATTTCATG
1 ATTAATTTCATG
2836957 A
1 A
2836958 ATGAGTATGA
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:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (12 bp):
ATTAATTTCATG
Found at i:2841811 original size:252 final size:252
Alignment explanation
Indices: 2841351--2842024 Score: 876
Period size: 252 Copynumber: 2.7 Consensus size: 252
2841341 TTTTGAACTA
* * *
2841351 TTATTATTATTATTATTTAAAAAGTAAAATTTGCATATCATTAAATATTTTTAACCCGAGAATAT
1 TTATTATT-TT-TTATTTAAAAATTAAAATTTGTATATCATTAAATATTTTTAACCCAAGAATAT
*
2841416 AAATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTTACTTAATTGACTTGTTATGTTAAC
64 AAATTTAAATATTTATTTTTCACTAGAATTAGATTTTTTTTACTTAATTGACTTGTTATGTTAAC
* * * *
2841481 TTTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGCTTTTACATCAATT
129 TCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCTACATTTATAAACTTTTACATCAATT
* * *
2841546 GTTACAATTTTATGTCAAG-CTTATCTATGTC-AATTTTGAACTATTATTACTTTT-A-TC
194 ATTACAATTTTATGTCAAGACTTATCTATATCGAA-TTTGAACTATAATTA-TTTTCATTC
* ** *
2841603 TTTATTATTTTTTATTTAAAAATTAAAATTTGTATATCATTAAATACTTTTATTCTAAGAATATA
1 -TTATTATTTTTTATTTAAAAATTAAAATTTGTATATCATTAAATATTTTTAACCCAAGAATATA
* * *
2841668 AATTTAAA-ACTTTTTTTTTTCACTAGAATTAGATTTTTTTTACTTACTTTACTTGTTATGTTAA
65 AATTTAAATA--TTTATTTTTCACTAGAATTAGATTTTTTTTACTTAATTGACTTGTTATGTTAA
* * * *
2841732 CTCTCACACATTTACATTAAGATATAAAATTTAGTTATTCTACATTTATAAATTTTTACGTCAAT
128 CTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCTACATTTATAAACTTTTACATCAAT
* * * * *
2841797 TATTATAGTTTTATGTCAAGACTTTTTTATATCGAATTTGAATTATAATTATTTTCATTC
193 TATTACAATTTTATGTCAAGACTTATCTATATCGAATTTGAACTATAATTATTTTCATTC
* ** * *
2841857 TTATTATTCTTTATTTAAAAATTAAAAATTT-TATATGGTTAAACATTTTTAGCCCAAGAATATA
1 TTATTATTTTTTATTTAAAAATT-AAAATTTGTATATCATTAAATATTTTTAACCCAAGAATATA
* * **
2841921 AATTTAAATATTTGTTTTTCATTAGAATTAGA-TTTTTTTACTTAATTGACTTGTTACATTAACT
65 AATTTAAATATTTATTTTTCACTAGAATTAGATTTTTTTTACTTAATTGACTTGTTATGTTAACT
* * *
2841985 CTCATACATTTATGTTAAGATTTTAAATTTAGTTATTCTA
130 CTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCTA
2842025 GTTTTACGAG
Statistics
Matches: 367, Mismatches: 46, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
250 1 0.00
251 118 0.32
252 149 0.41
253 87 0.24
254 12 0.03
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.49
Consensus pattern (252 bp):
TTATTATTTTTTATTTAAAAATTAAAATTTGTATATCATTAAATATTTTTAACCCAAGAATATAA
ATTTAAATATTTATTTTTCACTAGAATTAGATTTTTTTTACTTAATTGACTTGTTATGTTAACTC
TCACACATTTACGTTAAGATTTAAAATTTAGTTATTCTACATTTATAAACTTTTACATCAATTAT
TACAATTTTATGTCAAGACTTATCTATATCGAATTTGAACTATAATTATTTTCATTC
Found at i:2842427 original size:26 final size:26
Alignment explanation
Indices: 2842391--2842448 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
2842381 TTACTAATTA
* *
2842391 ACCTTACAATATGGTCAAAAATGATG
1 ACCTTACAATAAGGTCAAAAATAATG
2842417 ACCTTACAATAAGGTCAAAAATAATG
1 ACCTTACAATAAGGTCAAAAATAATG
2842443 ACCTTA
1 ACCTTA
2842449 GTGTAGAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (26 bp):
ACCTTACAATAAGGTCAAAAATAATG
Found at i:2844890 original size:21 final size:23
Alignment explanation
Indices: 2844860--2844903 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2844850 TACACAATGC
2844860 TTTGTTAATTGAAA-ACCTTTTT
1 TTTGTTAATTGAAACACCTTTTT
*
2844882 TTTG-TAATTGAAACGCCTTTTT
1 TTTGTTAATTGAAACACCTTTTT
2844904 CTTTACCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.52
Consensus pattern (23 bp):
TTTGTTAATTGAAACACCTTTTT
Found at i:2847661 original size:21 final size:21
Alignment explanation
Indices: 2847635--2847700 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
2847625 GAGTATTACT
2847635 TTTAAATTTAAACAATTTAAA
1 TTTAAATTTAAACAATTTAAA
* ** *
2847656 TTTAAATGTAATTAATTCT-TA
1 TTTAAATTTAAACAATT-TAAA
*
2847677 TTTAAATTTAAACAAATTAAA
1 TTTAAATTTAAACAATTTAAA
2847698 TTT
1 TTT
2847701 CAATATGATG
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (21 bp):
TTTAAATTTAAACAATTTAAA
Found at i:2854841 original size:15 final size:16
Alignment explanation
Indices: 2854821--2854855 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
2854811 GGATATTACT
2854821 TTAAATTTAAATA-AA
1 TTAAATTTAAATATAA
2854836 TTAAATTTAAATATAA
1 TTAAATTTAAATATAA
2854852 TTAA
1 TTAA
2854856 TCTTTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAATTTAAATATAA
Found at i:2854845 original size:21 final size:21
Alignment explanation
Indices: 2854820--2854889 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
2854810 AGGATATTAC
2854820 TTTAAATTTAAATAAATTAAA
1 TTTAAATTTAAATAAATTAAA
* * **
2854841 TTTAAATAT-AATTAATCTTTA
1 TTTAAATTTAAATAAAT-TAAA
* * *
2854862 TTTAACTTTAAACAAACTAAA
1 TTTAAATTTAAATAAATTAAA
2854883 TTTAAAT
1 TTTAAAT
2854890 ATAATGGATA
Statistics
Matches: 35, Mismatches: 12, Indels: 4
0.69 0.24 0.08
Matches are distributed among these distances:
20 6 0.17
21 25 0.71
22 4 0.11
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTAAATTTAAATAAATTAAA
Found at i:2856146 original size:18 final size:17
Alignment explanation
Indices: 2856099--2856151 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
2856089 AAGGTCATGT
* *
2856099 CTTAATCTAAATAGACA
1 CTTAATTTAAATAGTCA
2856116 CTTAATTTAAATAGTCA
1 CTTAATTTAAATAGTCA
* *
2856133 CTTGAATTTGAATAATCA
1 CTT-AATTTAAATAGTCA
2856151 C
1 C
2856152 ATCTAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 18 0.58
18 13 0.42
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.36
Consensus pattern (17 bp):
CTTAATTTAAATAGTCA
Found at i:2856605 original size:24 final size:24
Alignment explanation
Indices: 2856578--2856631 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
2856568 ACAGTCACAC
2856578 TGAATATTCTAAAATGAGGCTATT
1 TGAATATTCTAAAATGAGGCTATT
*
2856602 TGAATATTCTAGAATGAGGCTATT
1 TGAATATTCTAAAATGAGGCTATT
2856626 T-AATAT
1 TGAATAT
2856632 AAAAATTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (24 bp):
TGAATATTCTAAAATGAGGCTATT
Found at i:2861615 original size:17 final size:18
Alignment explanation
Indices: 2861593--2861640 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
2861583 AAGTCATGTC
2861593 TTAATTTAAATAAATA-T
1 TTAATTTAAATAAATATT
*
2861610 TTAATTTAAATAATTATT
1 TTAATTTAAATAAATATT
*
2861628 TTAATTTAGATAA
1 TTAATTTAAATAA
2861641 TTATATCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTAATTTAAATAAATATT
Found at i:2861632 original size:18 final size:18
Alignment explanation
Indices: 2861593--2861644 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
2861583 AAGTCATGTC
*
2861593 TTAATTTAAATAAATA-T
1 TTAATTTAAATAATTATT
2861610 TTAATTTAAATAATTATT
1 TTAATTTAAATAATTATT
*
2861628 TTAATTTAGATAATTAT
1 TTAATTTAAATAATTAT
2861645 ATCTAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 15 0.47
18 17 0.53
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TTAATTTAAATAATTATT
Found at i:2862282 original size:29 final size:30
Alignment explanation
Indices: 2862250--2862326 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
2862240 TTTAATAAAG
*
2862250 TTTAAATTAATTTTTATTTTTTTATTAT-A
1 TTTAAATTAATTTTTATATTTTTATTATAA
* *
2862279 TTT-AATTAAATTTGTATATTTTTATTTTAA
1 TTTAAATT-AATTTTTATATTTTTATTATAA
* *
2862309 ATTAAATAAATTTTTATA
1 TTTAAATTAATTTTTATA
2862327 ATTAATAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 4 0.10
29 20 0.51
30 12 0.31
31 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (30 bp):
TTTAAATTAATTTTTATATTTTTATTATAA
Found at i:2874116 original size:29 final size:29
Alignment explanation
Indices: 2874061--2874117 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
2874051 GGATATTCAA
* * **
2874061 TATATCTTGCTTAGTTATTGTTTATATTG
1 TATATCTTGCTTAGCTACTGTAGATATTG
*
2874090 TATATCTTGTTTAGCTACTGTAGATATT
1 TATATCTTGCTTAGCTACTGTAGATATT
2874118 ATAAATATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.54
Consensus pattern (29 bp):
TATATCTTGCTTAGCTACTGTAGATATTG
Found at i:2884711 original size:3 final size:3
Alignment explanation
Indices: 2884705--2884731 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2884695 AGTAATTGAG
2884705 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
2884732 AGAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2885504 original size:28 final size:29
Alignment explanation
Indices: 2885472--2885550 Score: 97
Period size: 28 Copynumber: 2.7 Consensus size: 29
2885462 CTATTAAACA
2885472 ATATTTAAATAAATTTTTAT-TTTTTATT
1 ATATTTAAATAAATTTTTATATTTTTATT
* *
2885500 ATATTCAATTAAATTTTTATATTTTTATT
1 ATATTTAAATAAATTTTTATATTTTTATT
* * *
2885529 TTGAATTAAATAAATTCTTATA
1 AT-ATTTAAATAAATTTTTATA
2885551 ATTAATTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 18 0.43
29 9 0.21
30 15 0.36
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (29 bp):
ATATTTAAATAAATTTTTATATTTTTATT
Found at i:2891784 original size:15 final size:15
Alignment explanation
Indices: 2891733--2891787 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
2891723 CATTACAATA
*
2891733 CAATGTGATTAC-AG
1 CAATGTGATTGCAAG
*
2891747 CTAATGTAATTGCAAG
1 C-AATGTGATTGCAAG
*
2891763 TAATGTGATTGCAAG
1 CAATGTGATTGCAAG
2891778 CAATGTGATT
1 CAATGTGATT
2891788 ACAGGGAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 1 0.03
15 31 0.91
16 2 0.06
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (15 bp):
CAATGTGATTGCAAG
Found at i:2892038 original size:31 final size:29
Alignment explanation
Indices: 2891941--2892529 Score: 213
Period size: 27 Copynumber: 21.1 Consensus size: 29
2891931 TATAAGTTTA
* * *
2891941 ATATAT-TTTATTTTTTGTTATTAATTTTT
1 ATATATATATATTTTTTATT-TTTATTTTT
* ** *
2891970 ATATA-ATATCATTTCTTAAATATATTTTT
1 ATATATATAT-ATTTTTTATTTTTATTTTT
2891999 A-ATATATATATTTTTTATTTTTATTTATT
1 ATATATATATATTTTTTATTTTTATTT-TT
*
2892028 AT-TATATATATTTTATA-TTTTATTTTT
1 ATATATATATATTTTTTATTTTTATTTTT
*
2892055 A-ATATAT-TCATATTTTTATTATTAATTTTT
1 ATATATATAT-AT-TTTTTATT-TTTATTTTT
* ** *
2892085 ATATA-ATATCATTTCTTAAATATATTTTT
1 ATATATATAT-ATTTTTTATTTTTATTTTT
* *
2892114 A-ATGTCATATA--TTTTATTTTTATTTAT
1 ATATAT-ATATATTTTTTATTTTTATTTTT
* *
2892141 -TAT-TA-ATATTTTATA-TTTTATTTTA
1 ATATATATATATTTTTTATTTTTATTTTT
* * *
2892166 ATATATTTATA-TTTATATTATTAATTTTT
1 ATATATATATATTTTTTATT-TTTATTTTT
* ** *
2892195 ATATA-ATATCATATTTTAAATATATTTTT
1 ATATATATAT-ATTTTTTATTTTTATTTTT
* *
2892224 A-ATAT-CATATTTTTTATTTTT-TTATT
1 ATATATATATATTTTTTATTTTTATTTTT
* *
2892250 AT-TATAT-T-TTATATATTTTTA-TTTT
1 ATATATATATATTTTTTATTTTTATTTTT
* *
2892275 AT-T-TTTATA-TTTTTATTATTAATTTTT
1 ATATATATATATTTTTTATT-TTTATTTTT
* * ** *
2892302 ATATATAT-CATTTCTTAAATATA-TTTT
1 ATATATATATATTTTTTATTTTTATTTTT
*
2892329 A-ATGTCATATA--TTTTA-TTTTATTTATT
1 ATATAT-ATATATTTTTTATTTTTATTT-TT
*
2892356 AT-TATA-ATATTTTATA-TTTTATTTTT
1 ATATATATATATTTTTTATTTTTATTTTT
* * * *
2892382 A-ATATATTTATATTTATATTATTAATTTT
1 ATATATATATAT-TTTTTATTTTTATTTTT
* * ** *
2892411 ATATAAATATCATATTTTAAATATATTTTT
1 ATATATATAT-ATTTTTTATTTTTATTTTT
*
2892441 A-ATGTCATATA--TTTTATTTTTATTTATT
1 ATATAT-ATATATTTTTTATTTTTATTT-TT
* * *
2892469 ATTATAATTTTATATATTTTATTTTCATTTCTT
1 A-TAT-A-TATATATTTTTTATTTTTATTT-TT
*
2892502 -TA-ATAT-T-TTTTTTATTTATATATTTT
1 ATATATATATATTTTTTATTTTTAT-TTTT
2892528 AT
1 AT
2892530 TTTAATTTAT
Statistics
Matches: 411, Mismatches: 91, Indels: 118
0.66 0.15 0.19
Matches are distributed among these distances:
24 5 0.01
25 38 0.09
26 51 0.12
27 87 0.21
28 59 0.14
29 87 0.21
30 53 0.13
31 15 0.04
32 1 0.00
33 15 0.04
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.65
Consensus pattern (29 bp):
ATATATATATATTTTTTATTTTTATTTTT
Found at i:2892059 original size:23 final size:23
Alignment explanation
Indices: 2892014--2892407 Score: 132
Period size: 23 Copynumber: 18.0 Consensus size: 23
2892004 ATATATTTTT
2892014 TATTTT-TA-TTTATTATTATATA
1 TATTTTATATTTTATTATTA-ATA
*
2892036 TATTTTATATTTTATTTTTAATA
1 TATTTTATATTTTATTATTAATA
*
2892059 TA-TTCATATTTTTATTATTAAT-
1 TATTTTATA-TTTTATTATTAATA
* * *
2892081 T-TTTATATAATATCATTTCTTAAATA
1 TATTT-TAT-ATTTTA-TTATT-AATA
* *
2892107 TATTTT-TAATGTCATATATT--T-
1 TATTTTAT-ATTTTAT-TATTAATA
2892128 TATTTT-TA-TTTATTATT-A-A
1 TATTTTATATTTTATTATTAATA
2892147 TATTTTATATTTTATT-TTAATA
1 TATTTTATATTTTATTATTAATA
2892169 TA-TTTATATTTATATTATTAAT-
1 TATTTTATATTT-TATTATTAATA
*
2892191 T-TTTATATAATATCATATT-TTAA-A
1 TATTT-TAT-AT-T-TTATTATTAATA
* *
2892215 TA---TAT-TTTTAATA-TCATA
1 TATTTTATATTTTATTATTAATA
* *
2892233 TTTTTTATTTTTTTATTATT-AT-
1 TATTTTA-TATTTTATTATTAATA
*
2892255 -ATTTTATATATTT-TTATT-TTA
1 TATTTTATAT-TTTATTATTAATA
2892276 T-TTTTATATTTTTATTATTAAT-
1 TATTTTATA-TTTTATTATTAATA
* * *
2892298 T-TTTATATATATCATTTCTTAAATA
1 TATTT-TATATTTTA-TTATT-AATA
* *
2892323 TATTTTA-ATGTCATATATT--T-
1 TATTTTATATTTTAT-TATTAATA
2892343 TA-TTT-TA-TTTATTATT-ATAA
1 TATTTTATATTTTATTATTAAT-A
*
2892363 TATTTTATATTTTATTTTTAATA
1 TATTTTATATTTTATTATTAATA
2892386 TA-TTTATATTTATATTATTAAT
1 TATTTTATATTT-TATTATTAAT
2892408 TTTATATAAA
Statistics
Matches: 287, Mismatches: 30, Indels: 109
0.67 0.07 0.26
Matches are distributed among these distances:
17 9 0.03
18 11 0.04
19 14 0.05
20 17 0.06
21 50 0.17
22 50 0.17
23 71 0.25
24 36 0.13
25 21 0.07
26 5 0.02
27 3 0.01
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (23 bp):
TATTTTATATTTTATTATTAATA
Found at i:2892124 original size:64 final size:60
Alignment explanation
Indices: 2891928--2892142 Score: 223
Period size: 59 Copynumber: 3.6 Consensus size: 60
2891918 CTAATTATTA
** * *
2891928 AAATATAAGTTTAATATATTTTAT-TTTTTGTTATTAATTTTTATATAATATCATTTCTT
1 AAATATATTTTTAATATATATTATATTTTTATTATTAATTTTTATATAATATCATTTCTT
*
2891987 AAATATATTTTTAATATATA-TAT-TTTTTATT-TTTATTTATTAT-T-ATAT-ATATT-TT
1 AAATATATTTTTAATATATATTATATTTTTATTATTAATTT-TTATATAATATCAT-TTCTT
* * *
2892042 ATATTTTATTTTTAATATAT-TCATATTTTTATTATTAATTTTTATATAATATCATTTCTT
1 A-AATATATTTTTAATATATATTATATTTTTATTATTAATTTTTATATAATATCATTTCTT
*
2892102 AAATATATTTTTAATGTCATATATTTTATTTTTATTTATTA
1 AAATATATTTTTAA--T-ATATATTATATTTTTA-TTATTA
2892143 TTAATATTTT
Statistics
Matches: 128, Mismatches: 13, Indels: 25
0.77 0.08 0.15
Matches are distributed among these distances:
55 5 0.04
56 24 0.19
57 19 0.15
58 21 0.16
59 34 0.27
60 5 0.04
61 1 0.01
62 4 0.03
63 9 0.07
64 6 0.05
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (60 bp):
AAATATATTTTTAATATATATTATATTTTTATTATTAATTTTTATATAATATCATTTCTT
Found at i:2892162 original size:21 final size:21
Alignment explanation
Indices: 2892128--2892198 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
2892118 TCATATATTT
2892128 TATTTT-TA-TTTATTATTAA
1 TATTTTATATTTTATTATTAA
2892147 TATTTTATATTTTATT-TTAA
1 TATTTTATATTTTATTATTAA
2892167 TATATTTATATTTATATTATTAA
1 TAT-TTTATATTT-TATTATTAA
2892190 T-TTTTATAT
1 TATTTTATAT
2892199 AATATCATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.13
20 9 0.19
21 22 0.47
22 5 0.11
23 5 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTTATATTTTATTATTAA
Found at i:2892166 original size:20 final size:20
Alignment explanation
Indices: 2892128--2892641 Score: 135
Period size: 20 Copynumber: 25.2 Consensus size: 20
2892118 TCATATATTT
2892128 TATTTT-TA-TTTATTATTAA
1 TATTTTATATTTTATT-TTAA
2892147 TATTTTATATTTTATTTTAA
1 TATTTTATATTTTATTTTAA
2892167 TATATTTATATTTATATTATTAA
1 TAT-TTTATATTT-TATT-TTAA
* * *
2892190 T-TTTTATA---TAATATCA
1 TATTTTATATTTTATTTTAA
* *
2892206 TATTTTA-AATATATTTTTAA
1 TATTTTATATTTTA-TTTTAA
** *
2892226 TATCATATTTTTTATTTT--
1 TATTTTATATTTTATTTTAA
* *
2892244 T-TTAT-TATTATATTTTATA
1 TATTTTATATTTTATTTTA-A
*
2892263 TATTTT-TATTTTATTTTTA
1 TATTTTATATTTTATTTTAA
*
2892282 TATTTT-TATTATTAATTTTTA
1 TATTTTATATT-TT-ATTTTAA
* * **
2892303 TA-TATATCA-TTTCTTAAATA
1 TATTTTAT-ATTTTATTTTA-A
*
2892323 TATTTTA-ATGTCATATATTT--
1 TATTTTATAT-T-TTAT-TTTAA
*
2892343 TATTTTAT-TTATTATTATAA
1 TATTTTATATT-TTATTTTAA
2892363 TATTTTATATTTTATTTTTAA
1 TATTTTATATTTTA-TTTTAA
2892384 TATATTTATATTTATATTATTAA
1 TAT-TTTATATTT-TATT-TTAA
*
2892407 T-TTTATATAAATATCATATTTTAAA
1 TATTT-TAT--AT-T-TTATTTT-AA
*
2892432 TATATTTTTAATGTCATATATTTT-A
1 TAT-TTTAT-AT-T--T-TATTTTAA
*
2892457 T-TTTTAT-TTATTATTATAA
1 TATTTTATATT-TTATTTTAA
*
2892476 T-TTTATATATTTTATTTTCA
1 TATTT-TATATTTTATTTTAA
*
2892496 TTTCTTTAATATTTT-TTTT-A
1 TAT-TTT-ATATTTTATTTTAA
*
2892516 T-TTATATATTTTATTTTAA
1 TATTTTATATTTTATTTTAA
2892535 TTTATTTTACCTATATTATATAATGTTAA
1 --TATTTTA--TAT-TT-TAT--T-TTAA
*
2892564 TTTTTTATATTTTA--TT--
1 TATTTTATATTTTATTTTAA
2892580 TATTTTA-ATTTTATTCTT-A
1 TATTTTATATTTTATT-TTAA
*
2892599 TATTATATATTTTA-TTTAA
1 TATTTTATATTTTATTTTAA
*
2892618 TATTTT-TATTTTAATTATAA
1 TATTTTATATTTT-ATTTTAA
2892638 TATT
1 TATT
2892642 ATAAAATATT
Statistics
Matches: 379, Mismatches: 47, Indels: 137
0.67 0.08 0.24
Matches are distributed among these distances:
15 6 0.02
16 19 0.05
17 18 0.05
18 26 0.07
19 50 0.13
20 90 0.24
21 61 0.16
22 36 0.09
23 19 0.05
24 10 0.03
25 19 0.05
26 6 0.02
27 14 0.04
28 1 0.00
29 4 0.01
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (20 bp):
TATTTTATATTTTATTTTAA
Found at i:2892200 original size:110 final size:110
Alignment explanation
Indices: 2891937--2892517 Score: 778
Period size: 110 Copynumber: 5.2 Consensus size: 110
2891927 AAAATATAAG
*
2891937 TTTAATATATTT-TATTTTTTGTTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
1 TTTAATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
*
2892001 TAT-ATATATTTTTTATTTTTATTTATTATTATATATATTTTATATTTTATT
65 TGTCATATA--TTTTATTTTTATTTATTA-T-TA-ATATTTTATATTTTA-T
*
2892052 TTTAATATATTCATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
2892117 GTCATATATTTTATTTTTATTTATTATTAATATTTTATATTTTAT
66 GTCATATATTTTATTTTTATTTATTATTAATATTTTATATTTTAT
*
2892162 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTAA
* *
2892226 TATCATATTTTTTA-TTTT-TTTATTATT-ATATTTTATATATTTTTAT
65 TGTCATATATTTTATTTTTATTTATTATTAATA-TTT-TATA-TTTTAT
2892272 TTT-AT-T-TTTATATTTTTATTATTAATTTTTATAT-ATATCATTTCTTAAATATA-TTTTAAT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
2892332 GTCATATATTTTA-TTTTATTTATTATTATAATATTTTATATTTTATT
66 GTCATATATTTTATTTTTATTTATTA-T-TAATATTTTATATTTTA-T
*
2892379 TTTAATATATTTATATTTATATTATTAA-TTTTATATAAATATCATATT-TTAAATATATTTTTA
1 TTTAATATATTTATATTTTTATTATTAATTTTTATAT-AATATCAT-TTCTTAAATATATTTTTA
2892442 ATGTCATATATTTTATTTTTATTTATTATT-ATAATTTTATATATTTTAT
64 ATGTCATATATTTTATTTTTATTTATTATTAAT-A-TTT-TATATTTTAT
* * * *
2892491 TTTCATTTCTTTAATATTTTTTTTATT
1 TTTAATATATTT-ATATTTTTATTATT
2892518 TATATATTTT
Statistics
Matches: 426, Mismatches: 16, Indels: 50
0.87 0.03 0.10
Matches are distributed among these distances:
105 24 0.06
106 28 0.07
107 39 0.09
108 19 0.04
109 22 0.05
110 101 0.24
111 35 0.08
112 38 0.09
113 34 0.08
114 18 0.04
115 61 0.14
116 7 0.02
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.65
Consensus pattern (110 bp):
TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
GTCATATATTTTATTTTTATTTATTATTAATATTTTATATTTTAT
Found at i:2892393 original size:6 final size:6
Alignment explanation
Indices: 2892336--2892401 Score: 50
Period size: 5 Copynumber: 11.0 Consensus size: 6
2892326 TTTAATGTCA
* *
2892336 TATATT T-TATT T-TATT TATTATT ATAATATTT TATATT T-TATT TTTA-A
1 TATATT TATATT TATATT TA-TATT -T-ATA-TT TATATT TATATT TATATT
2892384 TATATT TATATT TATATT
1 TATATT TATATT TATATT
2892402 ATTAATTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
5 18 0.36
6 18 0.36
7 7 0.14
8 4 0.08
9 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATATT
Found at i:2892398 original size:217 final size:220
Alignment explanation
Indices: 2891937--2892517 Score: 867
Period size: 217 Copynumber: 2.6 Consensus size: 220
2891927 AAAATATAAG
* *
2891937 TTTAATATATTT-TATTTTTTGTTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTA
1 TTTAATATATTTATA-TTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTA
* * *
2892000 ATATATATATTTTTTATTTTTATTTATTATTATATATATTTTATATTTTATTTTTAATATATTCA
64 ATAT-CATATTTTTTATTTTTATTTATTATTATAT-T-TTATATATTTTA-TTTTAAT-TATTTA
2892065 TATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCATATATTTTA
124 TATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCATATATTTTA
2892130 TTTTTATTTATTATTAATATTTTATATTTTAT
189 TTTTTATTTATTATTAATATTTTATATTTTAT
2892162 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAAT
2892227 ATCATATTTTTTA-TTTT-TTTATTATTATATTTTATATATTTTTATTTT-ATT-TTTATATTTT
66 ATCATATTTTTTATTTTTATTTATTATTATATTTTATATA-TTTTATTTTAATTATTTATATTTT
2892288 TATTATTAATTTTTATAT-ATATCATTTCTTAAATATA-TTTTAATGTCATATATTTTA-TTTTA
130 TATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCATATATTTTATTTTTA
2892350 TTTATTATTATAATATTTTATATTTTATT
195 TTTATTA-T-TAATATTTTATATTTTA-T
2892379 TTTAATATATTTATATTTATATTATTAA-TTTTATATAAATATCATATTTTAAATATATTTTTAA
1 TTTAATATATTTATATTTATATTATTAATTTTTATAT-AATATCATATTTTAAATATATTTTTAA
* * * *
2892443 TGTCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTTCATTTCTTTAATAT
65 TATCATATTTTTTATTTTTATTTATTATTAT-ATTTTATATATTTTATTTT-AATTATTT-ATAT
*
2892508 TTTTTTTATT
127 TTTTATTATT
2892518 TATATATTTT
Statistics
Matches: 333, Mismatches: 9, Indels: 30
0.90 0.02 0.08
Matches are distributed among these distances:
214 12 0.04
215 21 0.06
216 44 0.13
217 95 0.29
218 5 0.02
219 22 0.07
220 20 0.06
221 8 0.02
222 16 0.05
223 17 0.05
224 10 0.03
225 59 0.18
226 4 0.01
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.65
Consensus pattern (220 bp):
TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAAT
ATCATATTTTTTATTTTTATTTATTATTATATTTTATATATTTTATTTTAATTATTTATATTTTT
ATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCATATATTTTATTTTTAT
TTATTATTAATATTTTATATTTTAT
Found at i:2892507 original size:22 final size:21
Alignment explanation
Indices: 2892477--2892518 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2892467 TTATTATAAT
2892477 TTTATATATTTTATTTTCATTTC
1 TTTATATATTTT-TTTT-ATTTC
2892500 TTTA-ATATTTTTTTTATTT
1 TTTATATATTTTTTTTATTT
2892519 ATATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 4 0.21
22 7 0.37
23 4 0.21
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTATATATTTTTTTTATTTC
Found at i:2892508 original size:17 final size:17
Alignment explanation
Indices: 2892450--2892616 Score: 97
Period size: 15 Copynumber: 10.1 Consensus size: 17
2892440 TAATGTCATA
2892450 TATTT-TAT-TTTTATT
1 TATTTATATATTTTATT
*
2892465 TA-TTATTATAATTTTATA
1 TATTTA-TAT-ATTTTATT
*
2892483 TATTT-TAT-TTTCATT
1 TATTTATATATTTTATT
* *
2892498 TCTTTA-ATATTTTTTT
1 TATTTATATATTTTATT
2892514 TATTTATATATTTTA-T
1 TATTTATATATTTTATT
* * **
2892530 T-TTAATTTATTTTACC
1 TATTTATATATTTTATT
* *
2892546 TATATTATATAATGTTAAT
1 TAT-TTATAT-ATTTTATT
2892565 T-TTT-TATATTTTATT
1 TATTTATATATTTTATT
2892580 TATTT-TA-ATTTTATTCT
1 TATTTATATATTTTA-T-T
2892597 TATATTATATATTTTATT
1 TAT-TTATATATTTTATT
2892615 TA
1 TA
2892617 ATATTTTTAT
Statistics
Matches: 116, Mismatches: 18, Indels: 33
0.69 0.11 0.20
Matches are distributed among these distances:
14 2 0.02
15 37 0.32
16 25 0.22
17 17 0.15
18 18 0.16
19 11 0.09
20 6 0.05
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (17 bp):
TATTTATATATTTTATT
Found at i:2892573 original size:49 final size:49
Alignment explanation
Indices: 2892515--2892643 Score: 133
Period size: 49 Copynumber: 2.7 Consensus size: 49
2892505 TATTTTTTTT
2892515 ATTT-ATATATTTTATTTTAATTT-ATTTTA-CCTATATTATATAATGTTA
1 ATTTAATATATTTTATTTTAATTTAATTTTATCCTATATTATAT-AT-TTA
** * * *
2892563 ATTTTTTATATTTTA-TTTATTTTAATTTTATTCTTATATTATATATTTT
1 ATTTAATATATTTTATTTTAATTTAATTTTA-TCCTATATTATATATTTA
*
2892612 ATTTAATAT-TTTTATTTTAATTATAATATTAT
1 ATTTAATATATTTTATTTTAATT-TAATTTTAT
2892644 AAAATATTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
48 16 0.24
49 31 0.46
50 9 0.13
51 11 0.16
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (49 bp):
ATTTAATATATTTTATTTTAATTTAATTTTATCCTATATTATATATTTA
Found at i:2892586 original size:217 final size:212
Alignment explanation
Indices: 2891937--2892658 Score: 657
Period size: 217 Copynumber: 3.3 Consensus size: 212
2891927 AAAATATAAG
* *
2891937 TTTAATATATTT-TATTTTTTGTTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTA
1 TTTAATATATTTATA-TTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTA
*
2892000 ATAT-ATATATTTTTTATTTTTATTTATTATTATATATATTT-TATATTTTATTTTTAATATATT
64 ATATCATATA--TTTTATTTTTATTTATTATTATA-AT-TTTATATATTTTA-TTTT-AT-TTTT
* * * * *
2892063 CATATTTTTATTA-TTA-AT-TTTTA-TATAATATCATTTCTTAAATATATT-TTTAATGTCATA
122 TATATTTTTTTTATTTATATATTTTATTTTAAT-TTA-TT-TT--ATATATTATATAATGT--TA
2892123 TATTTTATTTTTATTTATTATTAATATTTTATATTTTA-T
180 -A--TT-TTTTTA-TTATTATT--TATTTTATATTTTATT
2892162 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAAT
*
2892227 ATCATATTTTTTA-TTTT-TTTATTATTAT-ATTTTATATATTTTTATTTTA-TTTTTATATTTT
66 ATCATATATTTTATTTTTATTTATTATTATAATTTTATATA-TTTTATTTTATTTTTTATA-TTT
* * * * * *
2892288 TATTATTAATTTTTATATATATCATTTCTTAAATATATTTTA-ATGTCATAT-AT-TTTATTTTA
129 T-TT-TT-A--TTTATATATTTTA-TT-TT-AATTTATTTTATATATTATATAATGTTAATTTT-
*
2892350 TTTATTATTATAATATTTTATATTTTATT
185 TTTATTATTAT-TTATTTTATATTTTATT
2892379 TTTAATATATTTATATTTATATTATTAA-TTTTATATAAATATCATATTTTAAATATATTTTTAA
1 TTTAATATATTTATATTTATATTATTAATTTTTATAT-AATATCATATTTTAAATATATTTTTAA
*
2892443 TGTCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTTCATTTCTTTAATAT
65 TATCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTT-ATTT-TTT-ATAT
2892508 TTTTTTTATTTATATATTTTATTTTAATTTATTTTACCTATATTATATAATGTTAATTTTTTATA
127 TTTTTTTATTTATATATTTTATTTTAATTTATTTTA--TATATTATATAATGTTAATTTTTT-TA
2892573 TT-TTATTTATTTTA-ATTTTATT
189 TTATTATTTATTTTATATTTTATT
* * * * * *
2892595 CTT-ATAT-TATATATTT-TATT-TAATATTTTTATTTTAATTATAATATTATAAA-ATATTTTT
1 TTTAATATATTTATATTTATATTATTA-ATTTTTA-TATAA-TATCATATTTTAAATATATTTTT
2892655 AATA
63 AATA
2892659 AGGTAATAAA
Statistics
Matches: 425, Mismatches: 32, Indels: 91
0.78 0.06 0.17
Matches are distributed among these distances:
212 2 0.00
213 5 0.01
214 36 0.08
215 20 0.05
216 34 0.08
217 108 0.25
218 22 0.05
219 37 0.09
220 26 0.06
221 11 0.03
222 18 0.04
223 8 0.02
224 13 0.03
225 64 0.15
226 11 0.03
227 2 0.00
228 3 0.01
229 2 0.00
230 3 0.01
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (212 bp):
TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAAT
ATCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTTATTTTTTATATTTTT
TTTATTTATATATTTTATTTTAATTTATTTTATATATTATATAATGTTAATTTTTTTATTATTAT
TTATTTTATATTTTATT
Found at i:2892641 original size:39 final size:35
Alignment explanation
Indices: 2892569--2892644 Score: 89
Period size: 39 Copynumber: 2.1 Consensus size: 35
2892559 GTTAATTTTT
* *
2892569 TATATTTTATTTATTTTAATTTTATTCTTATATTA
1 TATATTTTATTTATTTTAATTTTATTATAATATTA
*
2892604 TATATTTTATTTAATATTTTTATTTTAATTATAATATTA
1 TATATTTTA-TT--TATTTTAATTTT-ATTATAATATTA
2892643 TA
1 TA
2892645 AAATATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 9 0.26
36 2 0.06
38 11 0.32
39 12 0.35
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (35 bp):
TATATTTTATTTATTTTAATTTTATTATAATATTA
Found at i:2892652 original size:30 final size:33
Alignment explanation
Indices: 2892588--2892655 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 33
2892578 TTTATTTTAA
* **
2892588 TTTTATTCTTATATTATATATTTTATTTAATAT
1 TTTTATTCTTATATTATATATATTATAAAATAT
2892621 TTTTATT-TTA-ATTATA-ATATTATAAAATAT
1 TTTTATTCTTATATTATATATATTATAAAATAT
2892651 TTTTA
1 TTTTA
2892656 ATAAGGTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 16 0.50
31 6 0.19
32 3 0.09
33 7 0.22
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (33 bp):
TTTTATTCTTATATTATATATATTATAAAATAT
Done.