Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold141
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: 2772588
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 118404 characters in sequence are not A, C, G, or T
File 17 of 18
Found at i:2622026 original size:22 final size:22
Alignment explanation
Indices: 2621967--2622034 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
2621957 AAATATAGAT
2621967 ATTTATTATTTAAATTTAATTATAA
1 ATTT-TTATTT-AATTTAATT-TAA
** *
2621992 AAATTTA-TAAATTTAATTTAA
1 ATTTTTATTTAATTTAATTTAA
2622013 ATTTTTATTTAATTTAAATTTA
1 ATTTTTATTTAATTT-AATTTA
2622035 TATAAAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 8 0.23
22 15 0.43
23 7 0.20
24 3 0.09
25 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTTTATTTAATTTAATTTAA
Found at i:2623821 original size:22 final size:22
Alignment explanation
Indices: 2623756--2623821 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 22
2623746 ATAAATAAAA
*
2623756 AATTTTATATAATATTAATTAT-T
1 AATTTTTTA-AAT-TTAATTATAT
* * ** *
2623779 AATGTATTAAAAATAAATATAT
1 AATTTTTTAAATTTAATTATAT
2623801 AATTTTTTAAATTTAATTATA
1 AATTTTTTAAATTTAATTATA
2623822 ATTTATAAAA
Statistics
Matches: 31, Mismatches: 11, Indels: 3
0.69 0.24 0.07
Matches are distributed among these distances:
21 6 0.19
22 19 0.61
23 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
AATTTTTTAAATTTAATTATAT
Found at i:2626395 original size:21 final size:19
Alignment explanation
Indices: 2626361--2626437 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 19
2626351 TTTTCAAAAA
*
2626361 AAATA-TTTGTATGAAAATT
1 AAATATTTTTTATG-AAATT
*
2626380 AAACTATTTTTTATGAAACT
1 AAA-TATTTTTTATGAAATT
*
2626400 GAAT-TTTTTTAATGAAATT
1 AAATATTTTTT-ATGAAATT
*
2626419 AAATATTTTCTTATAAAAT
1 AAATATTTT-TTATGAAAT
2626438 CAGTCGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
18 6 0.13
19 14 0.30
20 18 0.38
21 9 0.19
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (19 bp):
AAATATTTTTTATGAAATT
Found at i:2626427 original size:19 final size:18
Alignment explanation
Indices: 2626361--2626427 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 18
2626351 TTTTCAAAAA
*
2626361 AAATATTTGTATGAAAATT
1 AAATATTTTTATG-AAATT
*
2626380 AAACTATTTTTTATGAAACT
1 AAA-TA-TTTTTATGAAATT
* *
2626400 GAATTTTTTTAATGAAATT
1 AAATATTTTT-ATGAAATT
2626419 AAATATTTT
1 AAATATTTT
2626428 CTTATAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
18 5 0.13
19 18 0.47
20 8 0.21
21 7 0.18
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (18 bp):
AAATATTTTTATGAAATT
Found at i:2626596 original size:23 final size:22
Alignment explanation
Indices: 2626555--2626600 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2626545 AATTTCTGAC
* * *
2626555 AAAATTTTTGTTGATAATAGTTT
1 AAAATTTTTATCGAAAATA-TTT
2626578 AAAATTTTTATCGAAAATATTT
1 AAAATTTTTATCGAAAATATTT
2626600 A
1 A
2626601 TTTATAATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (22 bp):
AAAATTTTTATCGAAAATATTT
Found at i:2626837 original size:314 final size:312
Alignment explanation
Indices: 2626455--2627049 Score: 1066
Period size: 314 Copynumber: 1.9 Consensus size: 312
2626445 AAAAAGTAAT
*
2626455 TTTCATAACTAAAAAATAATTTTTTTTATTTCGATTGAAAATTAATATTTTTTATAAAAATGATT
1 TTTCATAACTAAAAAATAATTTTTTTTATTTCGATTGAAAATTAATATTTTCTATAAAAATGATT
2626520 TTGGAGGGAAATTTTTCACCAAAACAATTTCTGACAAAATTTTTGTTGATAATAGTTTAAAATTT
66 TTGGAGGGAAATTTTTCACCAAAACAATTTCTGACAAAATTTTTGTTGATAATAGTTTAAAATTT
2626585 TTATCGAAAATATTTATTTATAATGCAATGTTTATTGGGAAGTGAACCAAATCATCAAAACTTTT
131 TTATCGAAAATATTTATTTATAATGCAATGTTTATTGGGAAGTGAACCAAATCATC--AA-TTTT
* * *
2626650 TGATAGACTTTTTTGTTGGAAAAAACCAATATTTTGTTGAAAATACTTCTTACGTAGAAGTTGAT
193 TGATAGACTTTTTTGTTGGAAAAAACCAATATTTTGTTAAAAATACTTCTTACATAAAAGTTGAT
2626715 TGCCGATGCCCCTTCTCTCATTTCCTTTTGATTCCAAATCTCTTTTCTCTCCAAC
258 TGCCGATGCCCCTTCTCTCATTTCCTTTTGATTCCAAATCTCTTTTCTCTCCAAC
2626770 TTTCATAACTAAAAAATAA-TTTTTTTATTTCGATTGAAAATTAATATTTTCTATAAAAATGATT
1 TTTCATAACTAAAAAATAATTTTTTTTATTTCGATTGAAAATTAATATTTTCTATAAAAATGATT
* *
2626834 TTGGAGGGAAATTTTTCACCCAAACAATTTTTGACAAAATTTTTGTTGATAATAGTTTAAAATTT
66 TTGGAGGGAAATTTTTCACCAAAACAATTTCTGACAAAATTTTTGTTGATAATAGTTTAAAATTT
2626899 TTATCGAAAATATTTATTTATAATGCAATGTTTATTGGGAAGTGAACCAAATCATCAATTTTTGA
131 TTATCGAAAATATTTATTTATAATGCAATGTTTATTGGGAAGTGAACCAAATCATCAATTTTTGA
* * *
2626964 TGGAGTTTTTTGTTGGAAAAAACCAATATTTTGTTAAAAATACTTCTTCCATAAAAGTTGATTGC
196 TAGACTTTTTTGTTGGAAAAAACCAATATTTTGTTAAAAATACTTCTTACATAAAAGTTGATTGC
*
2627029 CGATGCCCCTTCTCTCTTTTC
261 CGATGCCCCTTCTCTCATTTC
2627050 TCTCCAACTT
Statistics
Matches: 270, Mismatches: 10, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
311 86 0.32
312 2 0.01
314 163 0.60
315 19 0.07
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.42
Consensus pattern (312 bp):
TTTCATAACTAAAAAATAATTTTTTTTATTTCGATTGAAAATTAATATTTTCTATAAAAATGATT
TTGGAGGGAAATTTTTCACCAAAACAATTTCTGACAAAATTTTTGTTGATAATAGTTTAAAATTT
TTATCGAAAATATTTATTTATAATGCAATGTTTATTGGGAAGTGAACCAAATCATCAATTTTTGA
TAGACTTTTTTGTTGGAAAAAACCAATATTTTGTTAAAAATACTTCTTACATAAAAGTTGATTGC
CGATGCCCCTTCTCTCATTTCCTTTTGATTCCAAATCTCTTTTCTCTCCAAC
Found at i:2626910 original size:23 final size:22
Alignment explanation
Indices: 2626869--2626914 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2626859 AATTTTTGAC
* * *
2626869 AAAATTTTTGTTGATAATAGTTT
1 AAAATTTTTATCGAAAATA-TTT
2626892 AAAATTTTTATCGAAAATATTT
1 AAAATTTTTATCGAAAATATTT
2626914 A
1 A
2626915 TTTATAATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (22 bp):
AAAATTTTTATCGAAAATATTT
Found at i:2629576 original size:13 final size:13
Alignment explanation
Indices: 2629558--2629582 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2629548 GCCAGTTTCA
2629558 TGTATCGATACAT
1 TGTATCGATACAT
2629571 TGTATCGATACA
1 TGTATCGATACA
2629583 AAGTAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2629917 original size:19 final size:19
Alignment explanation
Indices: 2629893--2629959 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
2629883 ATTCAACGAT
2629893 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
2629912 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
2629926 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
2629944 TTGTATCGATACATAA
1 TTGTATCGATACATAA
2629960 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 27 0.64
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:2629930 original size:32 final size:32
Alignment explanation
Indices: 2629894--2629956 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
2629884 TTCAACGATT
2629894 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
2629926 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
2629957 TAATTAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:2629931 original size:13 final size:13
Alignment explanation
Indices: 2629913--2629937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2629903 ACATAAGTGT
2629913 TGTATCGATACAA
1 TGTATCGATACAA
2629926 TGTATCGATACA
1 TGTATCGATACA
2629938 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2630018 original size:13 final size:13
Alignment explanation
Indices: 2630000--2630024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2629990 ATTACTCAAA
2630000 TGTATCGATACAT
1 TGTATCGATACAT
2630013 TGTATCGATACA
1 TGTATCGATACA
2630025 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2635848 original size:20 final size:21
Alignment explanation
Indices: 2635820--2635858 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2635810 TCTGGGTTTT
2635820 TTCAGATGTATCAATACATCA
1 TTCAGATGTATCAATACATCA
*
2635841 TTCA-ATGTATCGATACAT
1 TTCAGATGTATCAATACAT
2635859 TCTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (21 bp):
TTCAGATGTATCAATACATCA
Found at i:2637788 original size:20 final size:20
Alignment explanation
Indices: 2637763--2637837 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
2637753 TTTTACCCAG
2637763 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
2637783 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
2637803 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
2637823 ATGTATCGATACATT
1 ATGTATCGATACATT
2637838 ATGTCTTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2637823 original size:40 final size:39
Alignment explanation
Indices: 2637763--2637840 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 39
2637753 TTTTACCCAG
*
2637763 ATGTATCGATACATTTTTCAATGTATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATGTATCGATACAT-TATGA
*
2637803 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATGTATCGATACATTATG
2637841 TCTTTTTACC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATGTATCGATACATTATGA
Found at i:2645551 original size:20 final size:20
Alignment explanation
Indices: 2645519--2645576 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
2645509 CTACTGTCAG
2645519 TTTATTATATCGATACAATTC
1 TTTATT-TATCGATACAATTC
2645540 TTTATTTATCGATACAATTC
1 TTTATTTATCGATACAATTC
* *
2645560 TTCATGTATCGATACAA
1 TTTATTTATCGATACAA
2645577 AGCAATATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 29 0.83
21 6 0.17
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.45
Consensus pattern (20 bp):
TTTATTTATCGATACAATTC
Found at i:2647097 original size:34 final size:34
Alignment explanation
Indices: 2647052--2647121 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
2647042 TATGCTAAAT
*
2647052 ACTTAGGGGAATGATAGACAGAAATAGTTAAAAA
1 ACTTAGCGGAATGATAGACAGAAATAGTTAAAAA
*
2647086 ACTTAGCGGAATGATAGACAGAAATGGTTAAAAA
1 ACTTAGCGGAATGATAGACAGAAATAGTTAAAAA
2647120 AC
1 AC
2647122 CCATGACGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.49, C:0.09, G:0.23, T:0.20
Consensus pattern (34 bp):
ACTTAGCGGAATGATAGACAGAAATAGTTAAAAA
Found at i:2648750 original size:2 final size:2
Alignment explanation
Indices: 2648743--2648767 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2648733 ACTATAAAAT
2648743 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 T
2648768 TACAAGTTGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2650701 original size:11 final size:11
Alignment explanation
Indices: 2650687--2650724 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
2650677 AATTTAAAAT
2650687 TAATTGATAAA
1 TAATTGATAAA
* *
2650698 TAATTTAAAAA
1 TAATTGATAAA
2650709 TAATTGATAAA
1 TAATTGATAAA
2650720 TAATT
1 TAATT
2650725 TAAAAGACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (11 bp):
TAATTGATAAA
Found at i:2650705 original size:22 final size:22
Alignment explanation
Indices: 2650677--2650729 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
2650667 TTAAATATCA
*
2650677 AATTTAAAATTAATTGATAAAT
1 AATTTAAAAATAATTGATAAAT
2650699 AATTTAAAAATAATTGATAAAT
1 AATTTAAAAATAATTGATAAAT
2650721 AATTTAAAA
1 AATTTAAAA
2650730 GACTTACGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
AATTTAAAAATAATTGATAAAT
Found at i:2651057 original size:32 final size:32
Alignment explanation
Indices: 2651016--2651132 Score: 92
Period size: 34 Copynumber: 3.3 Consensus size: 32
2651006 GTTAAATTTT
2651016 AATTATTTTTTATAAATTAATAAAAATTTAAA
1 AATTATTTTTTATAAATTAATAAAAATTTAAA
*
2651048 AATTA-TTTTTATTAATATTTATATAATTTATAATTAAATTA
1 AATTATTTTTTA-TAA-A-TTA-ATAA---A-AATTTAA--A
**
2651089 AATTATTACTTATAAATTAATAAAAATTTTAAAA
1 AATTATTTTTTATAAATTAATAAAAA-TTT-AAA
2651123 AATTATTTTT
1 AATTATTTTT
2651133 ATATTAATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 24
0.69 0.06 0.25
Matches are distributed among these distances:
31 6 0.09
32 8 0.12
33 1 0.02
34 14 0.21
35 7 0.11
36 2 0.03
38 5 0.08
39 9 0.14
40 1 0.02
41 9 0.14
42 4 0.06
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (32 bp):
AATTATTTTTTATAAATTAATAAAAATTTAAA
Found at i:2651105 original size:73 final size:75
Alignment explanation
Indices: 2651007--2651170 Score: 237
Period size: 73 Copynumber: 2.2 Consensus size: 75
2650997 TCGAGTTAAG
* **
2651007 TTAAATTTTAATTATTTTTTATAAATTAATAAAAA-TTT-AAAAATTA-TTTT-TATTAATATTT
1 TTAAA-TTAAATTATTACTTATAAATTAATAAAAATTTTAAAAAATTATTTTTATATTAATATTT
2651068 ATATAATTTATAA
65 ATAT--TTTATAA
2651081 TTAAATTAAATTATTACTTATAAATTAATAAAAATTTTAAAAAATTATTTTTATATTAATATTTA
1 TTAAATTAAATTATTACTTATAAATTAATAAAAATTTTAAAAAATTATTTTTATATTAATATTTA
2651146 TATTTTATAA
66 TATTTTATAA
2651156 TTAAATTAAAATTAT
1 TTAAATT-AAATTAT
2651171 ATTCAAAATT
Statistics
Matches: 82, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
73 26 0.32
74 8 0.10
75 22 0.27
76 11 0.13
77 15 0.18
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.52
Consensus pattern (75 bp):
TTAAATTAAATTATTACTTATAAATTAATAAAAATTTTAAAAAATTATTTTTATATTAATATTTA
TATTTTATAA
Found at i:2652466 original size:20 final size:20
Alignment explanation
Indices: 2652441--2652502 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 20
2652431 TGGTGAACAA
2652441 TTTTATTATTAAAAAAATAT
1 TTTTATTATTAAAAAAATAT
2652461 TTTTATTTATTAAATAAAATAAT
1 TTTTA-TTATTAAA-AAAAT-AT
*
2652484 ATTT-TT-TTAAAAAAATAT
1 TTTTATTATTAAAAAAATAT
2652502 T
1 T
2652503 AATTAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 2 0.05
19 5 0.14
20 10 0.27
21 10 0.27
22 5 0.14
23 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTTATTATTAAAAAAATAT
Found at i:2652478 original size:25 final size:24
Alignment explanation
Indices: 2652442--2652489 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
2652432 GGTGAACAAT
*
2652442 TTTATTATTAAAAAAATATTTTTA
1 TTTATTAATAAAAAAATATTTTTA
*
2652466 TTTATTAAATAAAATAATATTTTT
1 TTTATT-AATAAAAAAATATTTTT
2652490 TTAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTATTAATAAAAAAATATTTTTA
Found at i:2652537 original size:28 final size:28
Alignment explanation
Indices: 2652474--2652538 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
2652464 TATTTATTAA
*
2652474 ATAAA-ATAA-TATTTTTTTAAAAAAAT
1 ATAAATATAATTATTTTATTAAAAAAAT
*
2652500 ATTAAT-TAATTATTATTATTAAAAAAAT
1 ATAAATATAATTATT-TTATTAAAAAAAT
2652528 -TAAATATAATT
1 ATAAATATAATT
2652539 TATCTAAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 7 0.22
27 8 0.25
28 17 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
ATAAATATAATTATTTTATTAAAAAAAT
Found at i:2652826 original size:18 final size:18
Alignment explanation
Indices: 2652803--2652844 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2652793 GTAAATTTTT
2652803 TTAAAAAAAATTAAGTAA
1 TTAAAAAAAATTAAGTAA
* * *
2652821 TTAAAAAATATTTATTAA
1 TTAAAAAAAATTAAGTAA
2652839 TTAAAA
1 TTAAAA
2652845 TTTTAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
TTAAAAAAAATTAAGTAA
Found at i:2652854 original size:17 final size:18
Alignment explanation
Indices: 2652842--2652889 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 18
2652832 TTATTAATTA
2652842 AAATTTTAAATTAAATAT
1 AAATTTTAAATTAAATAT
2652860 AAATTTT--ATT-AATAT
1 AAATTTTAAATTAAATAT
* *
2652875 TAATTTTATATTAAA
1 AAATTTTAAATTAAA
2652890 ATTATTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 11 0.42
16 3 0.12
17 3 0.12
18 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATTTTAAATTAAATAT
Found at i:2652870 original size:33 final size:34
Alignment explanation
Indices: 2652826--2652889 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
2652816 AGTAATTAAA
2652826 AAATATTTATTAAT-TAAAATTTTAAATTAAATAT
1 AAATATTTATTAATAT-AAATTTTAAATTAAATAT
* *
2652860 AAAT-TTTATTAATATTAATTTTATATTAAA
1 AAATATTTATTAATATAAATTTTAAATTAAA
2652890 ATTATTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 22 0.81
34 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
AAATATTTATTAATATAAATTTTAAATTAAATAT
Found at i:2652879 original size:15 final size:15
Alignment explanation
Indices: 2652826--2652883 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 15
2652816 AGTAATTAAA
2652826 AAATATTTATTAAT-T
1 AAAT-TTTATTAATAT
2652841 AAAATTTTAAATTAAATAT
1 -AAATTTT--ATT-AATAT
2652860 AAATTTTATTAATAT
1 AAATTTTATTAATAT
*
2652875 TAATTTTAT
1 AAATTTTAT
2652884 ATTAAAATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
15 16 0.43
16 7 0.19
17 3 0.08
18 10 0.27
19 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AAATTTTATTAATAT
Found at i:2652991 original size:4 final size:4
Alignment explanation
Indices: 2652982--2653016 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
2652972 AAAACTGAGT
2652982 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2653017 GTTACAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2653213 original size:15 final size:15
Alignment explanation
Indices: 2653188--2653227 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
2653178 AGTTTTTCTT
2653188 TTTCTTTTTCTTTTCC
1 TTTC-TTTTCTTTTCC
2653204 TTTCTTTTCTTTTCC
1 TTTCTTTTCTTTTCC
*
2653219 TTTCATTTC
1 TTTCTTTTC
2653228 CCTCTCGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTCTTTTCTTTTCC
Found at i:2658284 original size:18 final size:18
Alignment explanation
Indices: 2658252--2658287 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2658242 ATCGTATAAA
2658252 TTAAATAAATTTAAATAT
1 TTAAATAAATTTAAATAT
2658270 TTAAA-AAATTATAAATAT
1 TTAAATAAATT-TAAATAT
2658288 CTCACCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAATAAATTTAAATAT
Found at i:2660161 original size:25 final size:26
Alignment explanation
Indices: 2660133--2660184 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
2660123 ATTTATGTAA
2660133 TAAAAAATAAATTTAATT-TTGATAT
1 TAAAAAATAAATTTAATTATTGATAT
*** *
2660158 TAAATTTTAAATTTAATTATTTATAT
1 TAAAAAATAAATTTAATTATTGATAT
2660184 T
1 T
2660185 TAACTTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
TAAAAAATAAATTTAATTATTGATAT
Found at i:2660192 original size:26 final size:25
Alignment explanation
Indices: 2660140--2660199 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
2660130 TAATAAAAAA
*
2660140 TAAATTTAATTTTGATATTAAATTT
1 TAAATTTAATTTTGATATTAAACTT
* *
2660165 TAAATTTAATTATTTATATTTAACTT
1 TAAATTTAATT-TTGATATTAAACTT
*
2660191 TAAAATTAA
1 TAAATTTAA
2660200 ATTGAGGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 11 0.37
26 19 0.63
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (25 bp):
TAAATTTAATTTTGATATTAAACTT
Found at i:2660886 original size:23 final size:22
Alignment explanation
Indices: 2660860--2660902 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
2660850 ACGATATTAA
*
2660860 AAATATAATAATA-AAATTTAATG
1 AAAT-TAA-AATATAAAGTTAATG
2660883 AAATTAAAATATAAAGTTAA
1 AAATTAAAATATAAAGTTAA
2660903 AATTTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (22 bp):
AAATTAAAATATAAAGTTAATG
Found at i:2661893 original size:16 final size:17
Alignment explanation
Indices: 2661872--2661909 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
2661862 GGATTCAATC
2661872 ATTTTATATTTAAA-TT
1 ATTTTATATTTAAATTT
2661888 ATTTTATATTTAAATTT
1 ATTTTATATTTAAATTT
2661905 ATTTT
1 ATTTT
2661910 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTATATTTAAATTT
Found at i:2661956 original size:16 final size:15
Alignment explanation
Indices: 2661922--2661975 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
2661912 AAAAAATTTT
* *
2661922 AATTTTTTTAGTTTG
1 AATTTTTTGAGTTTA
2661937 AATTTATTTGAGTTTA
1 AATTT-TTTGAGTTTA
*
2661953 AATTTTTT-ACGCTTA
1 AATTTTTTGA-GTTTA
2661968 AATTTTTT
1 AATTTTTT
2661976 TTAATTTAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.03
15 20 0.59
16 13 0.38
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (15 bp):
AATTTTTTGAGTTTA
Found at i:2662214 original size:20 final size:20
Alignment explanation
Indices: 2662177--2662215 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2662167 CTATTTTTAA
** *
2662177 TATATTTATTTATTAAATTC
1 TATATTTACATATAAAATTC
2662197 TATATTTACATATAAAATT
1 TATATTTACATATAAAATT
2662216 GATTTTTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATTTACATATAAAATTC
Found at i:2662229 original size:18 final size:18
Alignment explanation
Indices: 2662201--2662245 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
2662191 AAATTCTATA
*
2662201 TTTACATATAAAATTGATT
1 TTTA-ATATAAAATTAATT
* *
2662220 TTTTATATAAAGTTAATT
1 TTTAATATAAAATTAATT
2662238 TTTAATAT
1 TTTAATAT
2662246 TTATTATTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (18 bp):
TTTAATATAAAATTAATT
Found at i:2662261 original size:15 final size:15
Alignment explanation
Indices: 2662241--2662294 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
2662231 GTTAATTTTT
2662241 AATATTTATTATTAC
1 AATATTTATTATTAC
*
2662256 AATATTAGATATTTTTTA-
1 AATATT---TA-TTATTAC
2662274 AATATTTATTATTAC
1 AATATTTATTATTAC
2662289 AATATT
1 AATATT
2662295 AGATATTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 5 0.16
15 14 0.44
18 8 0.25
19 5 0.16
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (15 bp):
AATATTTATTATTAC
Found at i:2662280 original size:33 final size:32
Alignment explanation
Indices: 2662236--2662301 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 32
2662226 ATAAAGTTAA
2662236 TTTTTAATATTTATTATTACAATATTAGATAT
1 TTTTTAATATTTATTATTACAATATTAGATAT
2662268 TTTTTAAATATTTATTATTACAATATTAGATAT
1 TTTTT-AATATTTATTATTACAATATTAGATAT
2662301 T
1 T
2662302 ACAAATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 5 0.15
33 28 0.85
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (32 bp):
TTTTTAATATTTATTATTACAATATTAGATAT
Found at i:2662301 original size:18 final size:18
Alignment explanation
Indices: 2662247--2662302 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
2662237 TTTTAATATT
2662247 TATTATTACAATATTAGA
1 TATTATTACAATATTAGA
*
2662265 TATTTTTTA-AATATT---
1 TA-TTATTACAATATTAGA
2662280 TATTATTACAATATTAGA
1 TATTATTACAATATTAGA
2662298 TATTA
1 TATTA
2662303 CAAATTAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 5 0.16
15 8 0.26
18 13 0.42
19 5 0.16
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (18 bp):
TATTATTACAATATTAGA
Found at i:2662396 original size:27 final size:29
Alignment explanation
Indices: 2662363--2662431 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 29
2662353 TATCATATTC
2662363 ATTTTTTTGTATTGTG-TTGTATT-T-TA
1 ATTTTTTTGTATTGTGTTTGTATTGTATA
2662389 ATTATTTTT-TAGTTGTGTTTGTATTGTATA
1 ATT-TTTTTGTA-TTGTGTTTGTATTGTATA
*
2662419 ATTTTGTTGTATT
1 ATTTTTTTGTATT
2662432 TAAAATTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
26 5 0.14
27 10 0.28
28 7 0.19
29 7 0.19
30 7 0.19
ACGTcount: A:0.17, C:0.00, G:0.16, T:0.67
Consensus pattern (29 bp):
ATTTTTTTGTATTGTGTTTGTATTGTATA
Found at i:2662441 original size:18 final size:18
Alignment explanation
Indices: 2662407--2662440 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2662397 TTAGTTGTGT
*
2662407 TTGTATTGTATAATTTTG
1 TTGTATTGTAAAATTTTG
2662425 TTGTATT-TAAAATTTT
1 TTGTATTGTAAAATTTT
2662441 TATTTCTGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.62
Consensus pattern (18 bp):
TTGTATTGTAAAATTTTG
Found at i:2663975 original size:18 final size:17
Alignment explanation
Indices: 2663954--2663988 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2663944 CATCGAAAAA
2663954 ATTAATATCATAAAAATT
1 ATTAATAT-ATAAAAATT
*
2663972 ATTAATATATTAAAATT
1 ATTAATATATAAAAATT
2663989 TATATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTAATATATAAAAATT
Found at i:2663991 original size:18 final size:18
Alignment explanation
Indices: 2663954--2664001 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
2663944 CATCGAAAAA
2663954 ATTAATATCA-TAAAAATT
1 ATTAATAT-ATTAAAAATT
*
2663972 ATTAATATATTAAAATTT
1 ATTAATATATTAAAAATT
2663990 ATATAAATATAT
1 AT-T-AATATAT
2664002 CACTTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 1 0.04
18 17 0.65
19 1 0.04
20 7 0.27
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTAATATATTAAAAATT
Found at i:2664133 original size:16 final size:16
Alignment explanation
Indices: 2664109--2664150 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2664099 AATATGGATA
*
2664109 TTTTAAATTTAAAT-T
1 TTTTGAATTTAAATCT
*
2664124 GTTTTGAATTCAAATCT
1 -TTTTGAATTTAAATCT
2664141 TTTTGAATTT
1 TTTTGAATTT
2664151 TTTCAAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (16 bp):
TTTTGAATTTAAATCT
Found at i:2665126 original size:18 final size:16
Alignment explanation
Indices: 2665078--2665131 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 16
2665068 TATATATTTC
2665078 AAAATCTATAT-AATAT
1 AAAAT-TATATAAATAT
2665094 -AAATTAT-TAATATATT
1 AAAATTATATAA-ATA-T
2665110 AAAATGTATATAAATAT
1 AAAAT-TATATAAATAT
2665127 AAAAT
1 AAAAT
2665132 ACTAACACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.03
14 4 0.12
15 7 0.22
16 1 0.03
17 10 0.31
18 6 0.19
19 3 0.09
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAATTATATAAATAT
Found at i:2668590 original size:14 final size:15
Alignment explanation
Indices: 2668552--2668602 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
2668542 TTATATATTT
* *
2668552 TAAAATTTATATAAA
1 TAAAATTAATATATA
2668567 TAAATTATTAATATAT-
1 TAAA--ATTAATATATA
*
2668583 TAAAATTATTATATA
1 TAAAATTAATATATA
2668598 TAAAA
1 TAAAA
2668603 AATTTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 9 0.30
15 9 0.30
16 4 0.13
17 8 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAATTAATATATA
Found at i:2668604 original size:17 final size:17
Alignment explanation
Indices: 2668559--2668616 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
2668549 TTTTAAAATT
2668559 TATATAAATAAATTATTA
1 TATATAAA-AAATTATTA
*
2668577 -ATATATTAAAATTATTA
1 TATATA-AAAAATTATTA
2668594 TATATAAAAAATT-TTA
1 TATATAAAAAATTATTA
*
2668610 AATATAA
1 TATATAA
2668617 TGAAAATATC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
16 9 0.26
17 20 0.57
18 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TATATAAAAAATTATTA
Found at i:2668654 original size:15 final size:16
Alignment explanation
Indices: 2668627--2668657 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2668617 TGAAAATATC
2668627 ATAAAATATATATAAT
1 ATAAAATATATATAAT
2668643 ATAAAA-ATATATAAT
1 ATAAAATATATATAAT
2668658 TTGTTATGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAAATATATATAAT
Found at i:2669133 original size:9 final size:9
Alignment explanation
Indices: 2669119--2669143 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2669109 AAAAAAGTCT
2669119 TATTATATA
1 TATTATATA
2669128 TATTATATA
1 TATTATATA
2669137 TATTATA
1 TATTATA
2669144 AAGTTGAAAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATTATATA
Found at i:2669891 original size:32 final size:33
Alignment explanation
Indices: 2669855--2669925 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
2669845 ATATTGTATT
* *
2669855 TTATATAAATTTTTATATATTAATA-ACTTATA
1 TTATATAAATTATGATATATTAATATACTTATA
* * *
2669887 TTATATAAATTATGATATATTTATATATTTATG
1 TTATATAAATTATGATATATTAATATACTTATA
2669920 TTATAT
1 TTATAT
2669926 TTTTATTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
32 22 0.67
33 11 0.33
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (33 bp):
TTATATAAATTATGATATATTAATATACTTATA
Found at i:2669907 original size:19 final size:19
Alignment explanation
Indices: 2669883--2669927 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2669873 ATTAATAACT
2669883 TATA-TTATATAAATTATGA
1 TATATTTATAT-AATTATGA
* *
2669902 TATATTTATATATTTATGT
1 TATATTTATATAATTATGA
2669921 TATATTT
1 TATATTT
2669928 TTATTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
TATATTTATATAATTATGA
Found at i:2669942 original size:14 final size:13
Alignment explanation
Indices: 2669907--2669945 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2669897 TATGATATAT
*
2669907 TTATATATTTATG
1 TTATATTTTTATG
*
2669920 TTATATTTTTATT
1 TTATATTTTTATG
2669933 TTATTATTTTTAT
1 TTA-TATTTTTAT
2669946 ATCGTATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (13 bp):
TTATATTTTTATG
Found at i:2671555 original size:20 final size:20
Alignment explanation
Indices: 2671530--2671616 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
2671520 TTATTAAAAA
2671530 AAAGGATAAAAAAGGAAATG
1 AAAGGATAAAAAAGGAAATG
*
2671550 AAAGGAT-AAAAAGGAAAGG
1 AAAGGATAAAAAAGGAAATG
*
2671569 AAAATGA-AAAAAAGGAAAT-
1 -AAAGGATAAAAAAGGAAATG
*
2671588 AAA--TTAAAAAAGGAAATGG
1 AAAGGATAAAAAAGGAAAT-G
*
2671607 AAAGGTTAAA
1 AAAGGATAAA
2671617 TTAAAGGAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
17 12 0.21
18 3 0.05
19 14 0.25
20 22 0.39
21 5 0.09
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (20 bp):
AAAGGATAAAAAAGGAAATG
Found at i:2671887 original size:23 final size:23
Alignment explanation
Indices: 2671861--2671908 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
2671851 ATAAATTAAA
2671861 AAAGAAAATGAA-AAAGATAAATT
1 AAAGAAAATGAAGAAAGA-AAATT
*
2671884 AAAGGAAATGAATGAAAGAAAATT
1 AAAGAAAATGAA-GAAAGAAAATT
2671908 A
1 A
2671909 TAAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 11 0.50
24 6 0.27
25 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (23 bp):
AAAGAAAATGAAGAAAGAAAATT
Found at i:2672464 original size:40 final size:40
Alignment explanation
Indices: 2672408--2672530 Score: 140
Period size: 40 Copynumber: 3.1 Consensus size: 40
2672398 ATCAACATTT
*
2672408 TTAAAATTAATTCGTTTAAATTTAAAATGATATGACATAA
1 TTAAAATTAATTCGTTTAAATTTAAAATGATATGACACAA
* * * *
2672448 TTAAAATTAATCCGTTTATATTTAATACGATATGACACAA
1 TTAAAATTAATTCGTTTAAATTTAAAATGATATGACACAA
* * * * *
2672488 TTAAAATTGATTAGTTTACA-TTAAATATGATATGGCACGA
1 TTAAAATTAATTCGTTTAAATTTAAA-ATGATATGACACAA
2672528 TTA
1 TTA
2672531 CGACACCAAA
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
39 4 0.06
40 65 0.94
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (40 bp):
TTAAAATTAATTCGTTTAAATTTAAAATGATATGACACAA
Found at i:2675674 original size:40 final size:41
Alignment explanation
Indices: 2675613--2675701 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 41
2675603 AATGGCCAAG
* *
2675613 AAAAATAACAAAATTAAAATAACT-AAAAAAATACTACTAC
1 AAAAACAACAAAATTAAAATAACTGAAAAAAATAATACTAC
*
2675653 AAAAACAACAAAA-TAAGAATAATTGAAAAAAATAATACTAC
1 AAAAACAACAAAATTAA-AATAACTGAAAAAAATAATACTAC
*
2675694 AACAACAA
1 AAAAACAA
2675702 GAAATCTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 3 0.07
40 18 0.42
41 22 0.51
ACGTcount: A:0.69, C:0.12, G:0.02, T:0.17
Consensus pattern (41 bp):
AAAAACAACAAAATTAAAATAACTGAAAAAAATAATACTAC
Found at i:2676918 original size:33 final size:33
Alignment explanation
Indices: 2676881--2676944 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 33
2676871 ACAAGCTATG
2676881 TATCGATACATT-T-CTTCATGTATCGATACAATA
1 TATCGATACATTATAC--CATGTATCGATACAATA
2676914 TATCGATACATTATACCATGTATCGATACAA
1 TATCGATACATTATACCATGTATCGATACAA
2676945 ATAGTGATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (33 bp):
TATCGATACATTATACCATGTATCGATACAATA
Found at i:2676929 original size:20 final size:20
Alignment explanation
Indices: 2676906--2676943 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2676896 TCATGTATCG
2676906 ATACAATATATCGATACATT
1 ATACAATATATCGATACATT
* *
2676926 ATACCATGTATCGATACA
1 ATACAATATATCGATACA
2676944 AATAGTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (20 bp):
ATACAATATATCGATACATT
Found at i:2677018 original size:19 final size:19
Alignment explanation
Indices: 2676974--2677046 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
2676964 TGCCAGTTTT
**
2676974 ATGTATCGATACAATTTGTCC
1 ATGTATCGATACAA--TGAAC
2676995 ATGTATCGATACAATGAAC
1 ATGTATCGATACAATGAAC
* *
2677014 ATGTATCGATACAAAGCAGC
1 ATGTATCGATACAATG-AAC
2677034 ATGTATCGATACA
1 ATGTATCGATACA
2677047 TCTTGGTGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
19 18 0.38
20 15 0.32
21 14 0.30
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (19 bp):
ATGTATCGATACAATGAAC
Found at i:2677590 original size:17 final size:17
Alignment explanation
Indices: 2677564--2677633 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
2677554 GTTTTCATTT
2677564 TTCT-CCCCTTAAAAAA
1 TTCTCCCCCTTAAAAAA
**
2677580 TTCTCCCCCTTAAACGA
1 TTCTCCCCCTTAAAAAA
* **
2677597 TTATCTCCTTTTAAAAAA
1 TTCTC-CCCCTTAAAAAA
2677615 TTCTCCCCCTTAAACAAA
1 TTCTCCCCCTTAAA-AAA
2677633 T
1 T
2677634 ATCTTCTCCC
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
16 4 0.10
17 21 0.51
18 16 0.39
ACGTcount: A:0.33, C:0.31, G:0.01, T:0.34
Consensus pattern (17 bp):
TTCTCCCCCTTAAAAAA
Found at i:2679535 original size:13 final size:13
Alignment explanation
Indices: 2679514--2679555 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2679504 AAATAGTACC
* *
2679514 CAATATATCAATA
1 CAATGTATCGATA
2679527 CAATGTATCGATA
1 CAATGTATCGATA
*
2679540 CAAAGTATCGATA
1 CAATGTATCGATA
2679553 CAA
1 CAA
2679556 GGAATGTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.26
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2683843 original size:13 final size:13
Alignment explanation
Indices: 2683825--2683851 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2683815 TACAATAAAC
2683825 ATGTATCGATACA
1 ATGTATCGATACA
2683838 ATGTATCGATACA
1 ATGTATCGATACA
2683851 A
1 A
2683852 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2683866 original size:33 final size:32
Alignment explanation
Indices: 2683806--2683870 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
2683796 CAATTTGTCC
2683806 ATGTATCGATACAATAAACATGTATCGATACA
1 ATGTATCGATACAATAAACATGTATCGATACA
*
2683838 ATGTATCGATACAA-AGCAGCATGTATCGATACA
1 ATGTATCGATACAATA--AACATGTATCGATACA
2683871 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 1 0.03
32 14 0.47
33 15 0.50
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (32 bp):
ATGTATCGATACAATAAACATGTATCGATACA
Found at i:2685190 original size:13 final size:13
Alignment explanation
Indices: 2685172--2685209 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2685162 TTAACTTTTC
* *
2685172 TATTATTTAATGA
1 TATTATATAATAA
2685185 TATTATATAATAA
1 TATTATATAATAA
2685198 TATTATATAATA
1 TATTATATAATA
2685210 TTGAAATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
TATTATATAATAA
Found at i:2687169 original size:29 final size:29
Alignment explanation
Indices: 2687123--2687178 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
2687113 ATATTGAGGT
*
2687123 TAATATCAATTAAGGATAATTTTGTAAAA
1 TAATATCAATTAAAGATAATTTTGTAAAA
2687152 TAATATCAA-TAGAAGATAATTTTGTAA
1 TAATATCAATTA-AAGATAATTTTGTAA
2687179 TAAAAACCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.38
Consensus pattern (29 bp):
TAATATCAATTAAAGATAATTTTGTAAAA
Found at i:2689569 original size:9 final size:9
Alignment explanation
Indices: 2689542--2689598 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
2689532 CATTTTTCTC
2689542 TTCTTTGTTCT
1 TTCTTT-TT-T
*
2689553 TTCATTTTT
1 TTCTTTTTT
2689562 TTCTTTTTT
1 TTCTTTTTT
*
2689571 TTCATTTTTG
1 TTC-TTTTTT
* *
2689581 CTATTTTTT
1 TTCTTTTTT
2689590 TTCTTTTTT
1 TTCTTTTTT
2689599 CTTTCTTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
9 24 0.65
10 8 0.22
11 5 0.14
ACGTcount: A:0.05, C:0.12, G:0.04, T:0.79
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:2689575 original size:18 final size:18
Alignment explanation
Indices: 2689542--2689602 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
2689532 CATTTTTCTC
2689542 TTCTTTGTTCTTTCATTTTT
1 TTCTTT-TT-TTTCATTTTT
2689562 TTCTTTTTTTTCATTTTT
1 TTCTTTTTTTTCATTTTT
* *
2689580 GCTATTTTTTTTC--TTTT
1 -TTCTTTTTTTTCATTTTT
2689597 TTCTTT
1 TTCTTT
2689603 CTTTATTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 4 0.11
17 4 0.11
18 10 0.28
19 12 0.33
20 6 0.17
ACGTcount: A:0.05, C:0.13, G:0.03, T:0.79
Consensus pattern (18 bp):
TTCTTTTTTTTCATTTTT
Found at i:2693738 original size:30 final size:32
Alignment explanation
Indices: 2693702--2693769 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 32
2693692 TATAATTTTA
* * *
2693702 ATATATATTAATATTATATATAAA-TAA-GAT
1 ATATATACTAAAATTATACATAAACTAATGAT
*
2693732 ATATATACTAAAATTATACATAAACTAATGGT
1 ATATATACTAAAATTATACATAAACTAATGAT
2693764 ATATAT
1 ATATAT
2693770 TTAGTACACA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 21 0.66
31 3 0.09
32 8 0.25
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (32 bp):
ATATATACTAAAATTATACATAAACTAATGAT
Found at i:2702256 original size:17 final size:17
Alignment explanation
Indices: 2702223--2702256 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2702213 GTTTTAAGAT
**
2702223 AAAAATTGAAATGGTAA
1 AAAAATTGAAAAAGTAA
2702240 AAAAATTGAAAAAGTAA
1 AAAAATTGAAAAAGTAA
2702257 TAATTATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.21
Consensus pattern (17 bp):
AAAAATTGAAAAAGTAA
Found at i:2702319 original size:88 final size:89
Alignment explanation
Indices: 2702181--2702356 Score: 293
Period size: 88 Copynumber: 2.0 Consensus size: 89
2702171 TTTGTTAAGT
*
2702181 TTTGATTTTCTTCCTTTATGTTGTTTTTGTTTGTTTTAAGATAAAAATTGAAATGGT-AAAAAAA
1 TTTGATTTTCTTCCTTTATGCTGTTTTTGTTTGTTTTAAGATAAAAATTGAAAT-GTAAAAAAAA
* *
2702245 TTG-AAAAAGTAATAATTATAATAA
65 TAGAAAAAAATAATAATTATAATAA
2702269 TTTGATTTTCTTCCTTTATGCTGTTTTTGTTTGTTTTAAGATAAAAATTGAAATGTAAAAAAAAA
1 TTTGATTTTCTTCCTTTATGCTGTTTTTGTTTGTTTTAAGATAAAAATTGAAATGT-AAAAAAAA
2702334 TAGAAAAAAATAATAATTATAAT
65 TAGAAAAAAATAATAATTATAAT
2702357 TATTATTAAA
Statistics
Matches: 82, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
87 2 0.02
88 53 0.65
89 9 0.11
90 18 0.22
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.44
Consensus pattern (89 bp):
TTTGATTTTCTTCCTTTATGCTGTTTTTGTTTGTTTTAAGATAAAAATTGAAATGTAAAAAAAAT
AGAAAAAAATAATAATTATAATAA
Found at i:2703827 original size:28 final size:29
Alignment explanation
Indices: 2703764--2703829 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
2703754 AAAGAAAGTT
* *
2703764 TTTAATTAAACAAAAATAAAAATTTGAGAA
1 TTTAATT-AACAAAAATAAAAATTTAAAAA
* * *
2703794 TGTAATTAA-AAAAATAACACTTTAAAAA
1 TTTAATTAACAAAAATAAAAATTTAAAAA
2703822 TTTAATTA
1 TTTAATTA
2703830 GATGTAATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 22 0.73
29 2 0.07
30 6 0.20
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (29 bp):
TTTAATTAACAAAAATAAAAATTTAAAAA
Found at i:2704546 original size:19 final size:18
Alignment explanation
Indices: 2704524--2704566 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
2704514 TTTATAATAA
2704524 ATTTTAA-AAAATATATATT
1 ATTTTAATAAAA-AT-TATT
2704543 ATTTTAATTAAAAATTATT
1 ATTTTAA-TAAAAATTATT
2704562 ATTTT
1 ATTTT
2704567 GTATCAGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 16 0.73
20 2 0.09
21 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTAATAAAAATTATT
Found at i:2705940 original size:14 final size:15
Alignment explanation
Indices: 2705911--2705940 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2705901 GATTTAAAAG
2705911 TTTATAAAAGTTGAA
1 TTTATAAAAGTTGAA
2705926 TTTATAAAA-TTGAA
1 TTTATAAAAGTTGAA
2705940 T
1 T
2705941 AATATGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (15 bp):
TTTATAAAAGTTGAA
Found at i:2707892 original size:43 final size:43
Alignment explanation
Indices: 2707826--2707917 Score: 157
Period size: 43 Copynumber: 2.1 Consensus size: 43
2707816 TTCAAAGACA
*
2707826 TGTTTCTTATATTTGCAGGATCATACCCTCATATCCGTGTCAT
1 TGTTTCTTATATTTGCAGAATCATACCCTCATATCCGTGTCAT
*
2707869 TGTTTCTTATATTTGCAGAATCATACCCTTATATCCGTGTCAT
1 TGTTTCTTATATTTGCAGAATCATACCCTCATATCCGTGTCAT
*
2707912 TCTTTC
1 TGTTTC
2707918 GTTGAATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.45
Consensus pattern (43 bp):
TGTTTCTTATATTTGCAGAATCATACCCTCATATCCGTGTCAT
Found at i:2709264 original size:30 final size:30
Alignment explanation
Indices: 2709208--2709264 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
2709198 CTTTGAAGCG
* **
2709208 GGGTTTGGTTTAAATTTTAATTTCATTCGT
1 GGGTTTGGTTTAAATTTGAAAGTCATTCGT
2709238 GGGTTTGGTTTAAATTTGAAAGTCATT
1 GGGTTTGGTTTAAATTTGAAAGTCATT
2709265 TGAGTTATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (30 bp):
GGGTTTGGTTTAAATTTGAAAGTCATTCGT
Found at i:2709340 original size:26 final size:26
Alignment explanation
Indices: 2709306--2709406 Score: 69
Period size: 26 Copynumber: 3.8 Consensus size: 26
2709296 TATAATTTAA
*
2709306 AATATAATAAAAATTTAAAATTAATT
1 AATAAAATAAAAATTTAAAATTAATT
* ***
2709332 AATAAAATAATAATTTTTTATTAATT
1 AATAAAATAAAAATTTAAAATTAATT
* * * *
2709358 TATAAAATATATTATTTTAAAATAAAATT
1 AATAAAATA-A-AAATTTAAAAT-TAATT
*
2709387 AA-AAAATTAAAATTTTAAAA
1 AATAAAA-TAAAAATTTAAAA
2709407 AAATTATTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
26 29 0.50
27 10 0.17
28 12 0.21
29 7 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AATAAAATAAAAATTTAAAATTAATT
Found at i:2709380 original size:15 final size:17
Alignment explanation
Indices: 2709350--2709381 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2709340 AATAATTTTT
2709350 TATTAATTTATAAAATA
1 TATTAATTTATAAAATA
2709367 TATT-ATTT-TAAAATA
1 TATTAATTTATAAAATA
2709382 AAATTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTAATTTATAAAATA
Found at i:2716462 original size:16 final size:16
Alignment explanation
Indices: 2716437--2716489 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
2716427 ATAAATTATA
*
2716437 TAAAATATAAGATAAAT
1 TAAAA-ATAAAATAAAT
2716454 TAAAAATAATAA-AAAT
1 TAAAAATAA-AATAAAT
*
2716470 TAAAATTAAAAT-AAT
1 TAAAAATAAAATAAAT
2716485 TAAAA
1 TAAAA
2716490 TATTAACACA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 10 0.31
16 16 0.50
17 6 0.19
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
TAAAAATAAAATAAAT
Found at i:2716473 original size:21 final size:22
Alignment explanation
Indices: 2716449--2716495 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
2716439 AAATATAAGA
2716449 TAAATTAAAAATAA-TAAAA-AT
1 TAAATT-AAAATAATTAAAATAT
2716470 TAAAATTAAAATAATTAAAATAT
1 T-AAATTAAAATAATTAAAATAT
2716493 TAA
1 TAA
2716496 CACATTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 8 0.35
22 12 0.52
23 3 0.13
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAATTAAAATAATTAAAATAT
Found at i:2716908 original size:17 final size:17
Alignment explanation
Indices: 2716871--2716912 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2716861 GTTTATATGT
* *
2716871 AAATATTTATAAATTAT
1 AAATATTTATAAACTAA
*
2716888 AAATATTTATTAACTAA
1 AAATATTTATAAACTAA
2716905 AAAT-TTTA
1 AAATATTTA
2716913 AATATCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATATTTATAAACTAA
Found at i:2717453 original size:21 final size:23
Alignment explanation
Indices: 2717411--2717454 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
2717401 ATGTTATTAT
* *
2717411 TAAAAATATAAATAATTTAAAAA
1 TAAAAATATAAATAAATAAAAAA
2717434 TAAAAAT-T-AATAAATAAAAAA
1 TAAAAATATAAATAAATAAAAAA
2717455 GTTTTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAAAATATAAATAAATAAAAAA
Found at i:2717497 original size:13 final size:13
Alignment explanation
Indices: 2717480--2717510 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
2717470 TTAAAATTTA
2717480 AAAAAAAAAAGAGG
1 AAAAAAAAAA-AGG
2717494 AAAAAAAAAAAGG
1 AAAAAAAAAAAGG
2717507 AAAA
1 AAAA
2717511 GAAGGGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGG
Found at i:2717833 original size:16 final size:15
Alignment explanation
Indices: 2717812--2717869 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
2717802 CCTTTTTTCC
2717812 AAATTTTTTACATTTT
1 AAATTTTTTA-ATTTT
*
2717828 AAA-TTTTAAATTTT
1 AAATTTTTTAATTTT
* *
2717842 TATTTTTTTAATTTT
1 AAATTTTTTAATTTT
2717857 ATAGATTTTTTAA
1 A-A-ATTTTTTAA
2717870 CAATTTTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
14 6 0.18
15 15 0.45
16 4 0.12
17 8 0.24
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (15 bp):
AAATTTTTTAATTTT
Found at i:2717919 original size:17 final size:16
Alignment explanation
Indices: 2717897--2717935 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2717887 GAATGTTTTA
2717897 TAATTTCTTTATTGTT
1 TAATTTCTTTATTGTT
* *
2717913 TAGATTTTTTTATTTTT
1 TA-ATTTCTTTATTGTT
2717930 TAATTT
1 TAATTT
2717936 AAAAATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.72
Consensus pattern (16 bp):
TAATTTCTTTATTGTT
Found at i:2717929 original size:8 final size:8
Alignment explanation
Indices: 2717831--2717935 Score: 59
Period size: 8 Copynumber: 12.1 Consensus size: 8
2717821 ACATTTTAAA
*
2717831 TTTTAAAT
1 TTTTAATT
*
2717839 TTTTATTT
1 TTTTAATT
2717847 TTTTAATT
1 TTTTAATT
*
2717855 TTATAGATT
1 TTTTA-ATT
2717864 TTTTAACAATT
1 TTTT---AATT
*
2717875 TTTTATAAT
1 TTTTA-ATT
*
2717884 TTTGAATGT
1 TTTTAAT-T
2717893 TTTATAATT
1 TTT-TAATT
2717902 TCTTT-ATT
1 T-TTTAATT
*
2717910 GTTTAGATT
1 TTTTA-ATT
*
2717919 TTTTTATT
1 TTTTAATT
2717927 TTTTAATT
1 TTTTAATT
2717935 T
1 T
2717936 AAAAATTATT
Statistics
Matches: 74, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
7 3 0.04
8 33 0.45
9 25 0.34
10 5 0.07
11 7 0.09
12 1 0.01
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.68
Consensus pattern (8 bp):
TTTTAATT
Found at i:2717973 original size:18 final size:19
Alignment explanation
Indices: 2717939--2717983 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
2717929 TTAATTTAAA
2717939 AATTAT-TTTTATATTTTT
1 AATTATATTTTATATTTTT
2717957 AATTATATTTTA-ATTTTT
1 AATTATATTTTATATTTTT
2717975 -A-TATATTTT
1 AATTATATTTT
2717984 TAAGTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.31
17 1 0.04
18 12 0.46
19 5 0.19
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
AATTATATTTTATATTTTT
Found at i:2717991 original size:26 final size:26
Alignment explanation
Indices: 2717812--2717999 Score: 69
Period size: 27 Copynumber: 7.3 Consensus size: 26
2717802 CCTTTTTTCC
*
2717812 AAATTTTTTACA-TTTTAA-AT-TTT
1 AAATTTTTTATATTTTTAATATATTT
*
2717835 AAA-TTTTTATTTTTTTAAT-T-TTAT
1 AAATTTTTTATATTTTTAATATATT-T
* * *
2717859 AGATTTTTTAACAATTTTTTATA-ATTTT
1 AAATTTTTT-A-TATTTTTAATATA-TTT
* * * *
2717887 GAATGTTTTATAATTTCTTTAT-TGTTT
1 AAATTTTTTAT-ATTT-TTAATATATTT
*
2717914 AGATTTTTT-TATTTTT--TA-ATTT
1 AAATTTTTTATATTTTTAATATATTT
2717936 AAAAATTATTTTTATATTTTTAATTATATTT
1 --AAA-T-TTTTTATATTTTTAA-TATATTT
* *
2717967 TAATTTTTATATATTTTTAA-GTATTT
1 AAATTTTT-TATATTTTTAATATATTT
2717993 AAATTTT
1 AAATTTT
2718000 AATGAGTGTC
Statistics
Matches: 123, Mismatches: 19, Indels: 43
0.66 0.10 0.23
Matches are distributed among these distances:
22 10 0.08
23 12 0.10
24 7 0.06
25 10 0.08
26 18 0.15
27 32 0.26
28 24 0.20
29 4 0.03
30 2 0.02
31 4 0.03
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (26 bp):
AAATTTTTTATATTTTTAATATATTT
Found at i:2718723 original size:12 final size:12
Alignment explanation
Indices: 2718701--2718752 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
2718691 ATATTAAAAA
2718701 AATATTTTATATT
1 AATA-TTTATATT
2718714 AATATTTATAATT
1 AATATTTAT-ATT
2718727 AA-ATTTATATAAT
1 AATATTTATAT--T
*
2718740 AATATTTTTATT
1 AATATTTATATT
2718752 A
1 A
2718753 TTTAAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
11 2 0.06
12 13 0.38
13 12 0.35
14 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AATATTTATATT
Found at i:2718755 original size:23 final size:24
Alignment explanation
Indices: 2718703--2718765 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
2718693 ATTAAAAAAA
*
2718703 TATTT-TATATTAATATTTATAAT
1 TATTTATATAATAATATTTATAAT
*
2718726 TAAATTTATATAATAATATTT-TTAT
1 T--ATTTATATAATAATATTTATAAT
*
2718751 TATTTAAATAATAAT
1 TATTTATATAATAAT
2718766 TTAAGTTAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 14 0.41
25 8 0.24
26 12 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTTATATAATAATATTTATAAT
Found at i:2719424 original size:19 final size:19
Alignment explanation
Indices: 2719400--2719436 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2719390 AATATTTTTA
2719400 TTTAAAT-TTAATTATAAAT
1 TTTAAATATTAA-TATAAAT
2719419 TTTAAATATTAATATAAA
1 TTTAAATATTAATATAAA
2719437 AATAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAAATATTAATATAAAT
Found at i:2719958 original size:34 final size:35
Alignment explanation
Indices: 2719870--2719991 Score: 101
Period size: 36 Copynumber: 3.5 Consensus size: 35
2719860 AATAATTAAA
**
2719870 ATATAATATAAATGAATATA-TAAATGTATCAAAATTT
1 ATATAA-AT-AAT-AATATATTAAACATATCAAAATTT
2719907 ATAT-AA-AATAA-ATTATT-AACATATCAAAATTT
1 ATATAAATAATAATA-TATTAAACATATCAAAATTT
* * *
2719939 ATATAAATAATAATATATTAAACATAATTATAATAT
1 ATATAAATAATAATATATTAAACAT-ATCAAAATTT
* *
2719975 ATAAAAATTATAATATA
1 ATATAAATAATAATATA
2719992 AATATCTAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
31 1 0.01
32 21 0.30
33 6 0.08
34 9 0.13
35 7 0.10
36 23 0.32
37 4 0.06
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (35 bp):
ATATAAATAATAATATATTAAACATATCAAAATTT
Found at i:2720928 original size:15 final size:15
Alignment explanation
Indices: 2720910--2720958 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
2720900 TTTAAAAATT
2720910 ATATTTTAAATATAA
1 ATATTTTAAATATAA
*
2720925 ATATTTTAAAAAATAA
1 ATATTTT-AAATATAA
2720941 A-ATATTTAAATAATAA
1 ATAT-TTTAAAT-ATAA
2720957 AT
1 AT
2720959 TCAGATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATTTTAAATATAA
Found at i:2720948 original size:16 final size:17
Alignment explanation
Indices: 2720917--2720957 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
2720907 ATTATATTTT
2720917 AAATATAAATATTTTAAA
1 AAATA-AAATATTTTAAA
2720935 AAATAAAATA-TTTAAA
1 AAATAAAATATTTTAAA
*
2720951 TAATAAA
1 AAATAAA
2720958 TTCAGATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.55
17 5 0.23
18 5 0.23
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATAAAATATTTTAAA
Found at i:2721400 original size:18 final size:19
Alignment explanation
Indices: 2721360--2721413 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
2721350 AATATGTTAC
*
2721360 TTTTAAATTAATTAAAAAA
1 TTTTAAAATAATTAAAAAA
* *
2721379 TTTTAAAAT-ATTATAAAT
1 TTTTAAAATAATTAAAAAA
2721397 TTTTAAAA-AATTTAAAA
1 TTTTAAAATAA-TTAAAA
2721414 CATTGATGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTTAAAATAATTAAAAAA
Found at i:2721997 original size:74 final size:76
Alignment explanation
Indices: 2721835--2721999 Score: 176
Period size: 74 Copynumber: 2.2 Consensus size: 76
2721825 TATTTTAAAC
* * * * **
2721835 ATATAAAAATTAATATAA-ATACAACACGAACATATAATTTTTATTTTAAATTTAATCGTTATAA
1 ATAT-AAAATAAAT-TAAGATATAACACGAACATATAATTTTTATTCTAAATTAAATCACTATAA
* *
2721899 CAAATTATACAAA
64 CAAACTAAACAAA
* * *
2721912 ATATAAGATAAATTAAGATATAACACGAACATATAA-TTTT-TTCTAAATTAAATTACTATGACA
1 ATATAAAATAAATTAAGATATAACACGAACATATAATTTTTATTCTAAATTAAATCACTATAACA
2721975 AACTAAACAAA
66 AACTAAACAAA
2721986 ATA-AGAAATAAATT
1 ATATA-AAATAAATT
2722000 GAAACACGAC
Statistics
Matches: 74, Mismatches: 12, Indels: 7
0.80 0.13 0.08
Matches are distributed among these distances:
73 1 0.01
74 37 0.50
75 7 0.09
76 25 0.34
77 4 0.05
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.33
Consensus pattern (76 bp):
ATATAAAATAAATTAAGATATAACACGAACATATAATTTTTATTCTAAATTAAATCACTATAACA
AACTAAACAAA
Found at i:2723647 original size:29 final size:29
Alignment explanation
Indices: 2723614--2723673 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
2723604 AATATATAAA
*
2723614 TATTAATATAAAAATAAT-TTTTAAATTTT
1 TATTAATATAAAAATAATAATTT-AATTTT
* *
2723643 TATTAATTTATAAATAATAATTTAATTTT
1 TATTAATATAAAAATAATAATTTAATTTT
2723672 TA
1 TA
2723674 AAATTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TATTAATATAAAAATAATAATTTAATTTT
Found at i:2724240 original size:16 final size:16
Alignment explanation
Indices: 2724204--2724246 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2724194 TTAATATTTT
*
2724204 AAATATGAAATAACTC
1 AAATTTGAAATAACTC
* *
2724220 AAATTTGAATTAATTC
1 AAATTTGAAATAACTC
*
2724236 AAATTTTAAAT
1 AAATTTGAAAT
2724247 GATTTAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (16 bp):
AAATTTGAAATAACTC
Found at i:2724308 original size:7 final size:7
Alignment explanation
Indices: 2724271--2724315 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
2724261 TAATTTAATC
2724271 TTAAAAT
1 TTAAAAT
2724278 TTAATAAT
1 TTAA-AAT
2724286 TTAAATAT
1 TTAAA-AT
**
2724294 AAAAAAT
1 TTAAAAT
2724301 TTAAAAT
1 TTAAAAT
2724308 TTAAAAT
1 TTAAAAT
2724315 T
1 T
2724316 ATTTAAAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 20 0.62
8 12 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAAAAT
Found at i:2724312 original size:16 final size:17
Alignment explanation
Indices: 2724266--2724340 Score: 77
Period size: 17 Copynumber: 4.6 Consensus size: 17
2724256 TAAATTAATT
2724266 TAATCTTAAAATTT--AA
1 TAAT-TTAAAATTTAAAA
*
2724282 TAATTT-AAATATAAAA
1 TAATTTAAAATTTAAAA
2724298 -AATTTAAAATTTAAAA
1 TAATTTAAAATTTAAAA
* *
2724314 TTATTTAAAACTTAAAA
1 TAATTTAAAATTTAAAA
*
2724331 TAATTCAAAA
1 TAATTTAAAA
2724341 ATTCTTCAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
14 5 0.10
15 7 0.14
16 15 0.31
17 22 0.45
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATTTAAAATTTAAAA
Found at i:2724315 original size:14 final size:14
Alignment explanation
Indices: 2724271--2724315 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
2724261 TAATTTAATC
2724271 TTAAAATTTAATAAT
1 TTAAAATTTAA-AAT
**
2724286 TTAAATATAAAAAAT
1 TTAAA-ATTTAAAAT
2724301 TTAAAATTTAAAAT
1 TTAAAATTTAAAAT
2724315 T
1 T
2724316 ATTTAAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
14 8 0.32
15 13 0.52
16 4 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAAAATTTAAAAT
Found at i:2724329 original size:24 final size:22
Alignment explanation
Indices: 2724271--2724331 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 22
2724261 TAATTTAATC
2724271 TTAAAATTTAATAATTTAAATAT
1 TTAAAATTTAA-AATTTAAATAT
**
2724294 AAAAAATTTAAAATTTAAAATTAT
1 TTAAAATTTAAAATTT-AAA-TAT
*
2724318 TTAAAACTTAAAAT
1 TTAAAATTTAAAAT
2724332 AATTCAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 5 0.16
23 12 0.39
24 14 0.45
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAAAATTTAAAATTTAAATAT
Found at i:2725294 original size:20 final size:18
Alignment explanation
Indices: 2725259--2725304 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
2725249 GTATATCAAC
2725259 TTTTATTAATATTTAAATA
1 TTTT-TTAATATTTAAATA
*
2725278 TTTTTTAATATCATTAATTA
1 TTTTTTAATAT--TTAAATA
2725298 TTTTTTA
1 TTTTTTA
2725305 TTTATTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 4 0.17
20 13 0.54
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTTAATATTTAAATA
Found at i:2725337 original size:14 final size:14
Alignment explanation
Indices: 2725320--2725368 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
2725310 TATAATTTAA
2725320 AAAATATAAATATT
1 AAAATATAAATATT
2725334 AAAATATTAAAT-TT
1 AAAATA-TAAATATT
*
2725348 AATACTATAAA-ATT
1 AA-AATATAAATATT
2725362 AAAATAT
1 AAAATAT
2725369 TTTATTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
13 4 0.13
14 18 0.60
15 8 0.27
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAATATAAATATT
Found at i:2726305 original size:17 final size:17
Alignment explanation
Indices: 2726283--2726363 Score: 56
Period size: 17 Copynumber: 4.2 Consensus size: 17
2726273 TATAATTATA
2726283 TTTAAAATATTTTATTT
1 TTTAAAATATTTTATTT
2726300 TTTAAAA-ATTTTAATTT
1 TTTAAAATATTTT-ATTT
*
2726317 ATTAATAATTTATATTTTATTAAT
1 -TT--TAA--AATATTTTATT--T
2726341 TTTAAAATATTTATATATT
1 TTTAAAATATTT-TAT-TT
2726360 TTTA
1 TTTA
2726364 TATTAAATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 20
0.70 0.03 0.27
Matches are distributed among these distances:
16 5 0.10
17 11 0.22
18 2 0.04
19 11 0.22
20 6 0.12
21 4 0.08
22 4 0.08
23 7 0.14
24 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTAAAATATTTTATTT
Found at i:2726335 original size:32 final size:32
Alignment explanation
Indices: 2726288--2726386 Score: 81
Period size: 32 Copynumber: 3.0 Consensus size: 32
2726278 TTATATTTAA
* *
2726288 AATATTTTATTTTTTAAAAATTTTAATTTATT
1 AATAATTTATATTTTAAAAATTTTAATTTATT
** **
2726320 AATAATTTATATTTTATTAATTTTAAAATATT
1 AATAATTTATATTTTAAAAATTTTAATTTATT
* * *
2726352 TATATATTTTTATATTAAATTATATTTTAATTTAT
1 AATA-ATTTATATTTTAAA--A-ATTTTAATTTAT
2726387 ATTATATTCA
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
32 29 0.58
33 10 0.20
35 1 0.02
36 10 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (32 bp):
AATAATTTATATTTTAAAAATTTTAATTTATT
Found at i:2726337 original size:18 final size:17
Alignment explanation
Indices: 2726291--2726340 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
2726281 TATTTAAAAT
*
2726291 ATTTTATTTT-TTAAAA
1 ATTTTATTTTATTAATA
*
2726307 ATTTTAATTTATTAATA
1 ATTTTATTTTATTAATA
2726324 ATTTATATTTTATTAAT
1 ATTT-TATTTTATTAAT
2726341 TTTAAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 9 0.31
17 9 0.31
18 11 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTATTTTATTAATA
Found at i:2726670 original size:3 final size:3
Alignment explanation
Indices: 2726662--2726700 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2726652 TAAAGGTGAA
*
2726662 ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2726701 TTGAAATCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2728394 original size:22 final size:20
Alignment explanation
Indices: 2728351--2728401 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
2728341 TGGCAGGCTT
*
2728351 AAATTAATATTTATTTATTAAA
1 AAATT-ATATTTATTTAAT-AA
*
2728373 AAATTATTTTTATTTAAATAA
1 AAATTATATTTATTT-AATAA
2728394 AAATTATA
1 AAATTATA
2728402 AAATATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATTATATTTATTTAATAA
Found at i:2728875 original size:16 final size:16
Alignment explanation
Indices: 2728832--2728876 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
2728822 TTTCAAAATA
*
2728832 TAAAATAATTAAAACT
1 TAAAATAATTCAAACT
* *
2728848 TAAAATTAATTCGAATT
1 TAAAA-TAATTCAAACT
2728865 TAAAATAATTCA
1 TAAAATAATTCA
2728877 CGAGTCAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (16 bp):
TAAAATAATTCAAACT
Found at i:2729442 original size:21 final size:22
Alignment explanation
Indices: 2729413--2729459 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2729403 AAAATATTTT
*
2729413 TATATAAAT-TAAAT-TATAAAA
1 TATAAAAATATAAATATA-AAAA
*
2729434 TATAAAAATATTAATATAAAAA
1 TATAAAAATATAAATATAAAAA
2729456 TATA
1 TATA
2729460 TTTTAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 8 0.36
22 12 0.55
23 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TATAAAAATATAAATATAAAAA
Found at i:2729466 original size:13 final size:14
Alignment explanation
Indices: 2729432--2729458 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2729422 TAAATTATAA
2729432 AATATAAAAATATT
1 AATATAAAAATATT
2729446 AATATAAAAATAT
1 AATATAAAAATAT
2729459 ATTTTAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATATAAAAATATT
Found at i:2733161 original size:13 final size:13
Alignment explanation
Indices: 2733143--2733167 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2733133 TGTTCAAATA
2733143 TATGTCAAACATC
1 TATGTCAAACATC
2733156 TATGTCAAACAT
1 TATGTCAAACAT
2733168 GGGTAGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
TATGTCAAACATC
Found at i:2735531 original size:13 final size:14
Alignment explanation
Indices: 2735500--2735532 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
2735490 TTGTAATACG
2735500 ATAAAATAAATGAAT
1 ATAAAATAAAT-AAT
2735515 ATAAAATAAAT-AT
1 ATAAAATAAATAAT
2735528 ATAAA
1 ATAAA
2735533 TGAGATCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
15 11 0.61
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (14 bp):
ATAAAATAAATAAT
Found at i:2739250 original size:36 final size:38
Alignment explanation
Indices: 2739182--2739253 Score: 94
Period size: 36 Copynumber: 1.9 Consensus size: 38
2739172 TTTAATTAAT
* *
2739182 TAAAAATTATTTTTATTAAATTTAATTATAAATATTGA
1 TAAAAAATATTTTTATTAAATATAATTATAAATATTGA
* *
2739220 TAAAAAATA-TTTT-TTAAATATCATTTTAAATATT
1 TAAAAAATATTTTTATTAAATATAATTATAAATATT
2739254 AAAATAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 18 0.60
37 4 0.13
38 8 0.27
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (38 bp):
TAAAAAATATTTTTATTAAATATAATTATAAATATTGA
Found at i:2739791 original size:16 final size:15
Alignment explanation
Indices: 2739747--2739800 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
2739737 GAAGGTGATA
*
2739747 TTATAATTAT-TATT
1 TTATAATTATATTTT
*
2739761 TTATAATTTTAATTTT
1 TTATAATTAT-ATTTT
*
2739777 TTATAATTAATATTTA
1 TTATAATT-ATATTTT
2739793 TTATAATT
1 TTATAATT
2739801 GATTTGTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 9 0.27
16 23 0.70
17 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATAATTATATTTT
Found at i:2740381 original size:3 final size:3
Alignment explanation
Indices: 2740373--2740410 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2740363 CAATTTTTAA
2740373 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2740411 AGCAGATTGC
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2741523 original size:15 final size:15
Alignment explanation
Indices: 2741505--2741549 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
2741495 ATTATCTTAT
**
2741505 TAATTAATTAAATTA
1 TAATTAATTAAAAAA
*
2741520 TAATTAAATAAAAAA
1 TAATTAATTAAAAAA
*
2741535 TAATTACTTAAAAAA
1 TAATTAATTAAAAAA
2741550 GAAATTTGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
TAATTAATTAAAAAA
Done.