Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 15 of 45
Found at i:2808695 original size:16 final size:17
Alignment explanation
Indices: 2808642--2808687 Score: 67
Period size: 16 Copynumber: 2.7 Consensus size: 17
2808632 TTTATTTATG
2808642 TTATATTTATATTATATT
1 TTATA-TTATATTATATT
*
2808660 TTA-ATTATATCATATT
1 TTATATTATATTATATT
2808676 TTATATTATATT
1 TTATATTATATT
2808688 TTAATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 14 0.56
17 8 0.32
18 3 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TTATATTATATTATATT
Found at i:2808700 original size:11 final size:12
Alignment explanation
Indices: 2808636--2808699 Score: 62
Period size: 11 Copynumber: 5.2 Consensus size: 12
2808626 TATTAATTTA
*
2808636 TTTATGTTATA-
1 TTTATATTATAT
2808647 TTTATATTATAT
1 TTTATATTATAT
2808659 TTTAATTATATCATAT
1 TTT-A-TAT-T-ATAT
2808675 TTTATATTATAT
1 TTTATATTATAT
2808687 TTTA-ATTAT-T
1 TTTATATTATAT
2808697 TTT
1 TTT
2808700 TTATGTTAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
10 4 0.09
11 15 0.32
12 11 0.23
13 2 0.04
14 6 0.13
15 2 0.04
16 7 0.15
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:2809080 original size:19 final size:19
Alignment explanation
Indices: 2809046--2809102 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
2809036 AAGAAATCAA
*
2809046 TTTAAGAATGATTAATTTT
1 TTTAAGAGTGATTAATTTT
2809065 TTCTAA-AGAT-ATTAATTTT
1 TT-TAAGAG-TGATTAATTTT
2809084 TTTAAGAGTGATTAATTTT
1 TTTAAGAGTGATTAATTTT
2809103 AAAAAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 4 0.12
19 25 0.76
20 4 0.12
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTAAGAGTGATTAATTTT
Found at i:2809558 original size:7 final size:7
Alignment explanation
Indices: 2809546--2809572 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2809536 GGAACTTCAA
2809546 TGGCAAT
1 TGGCAAT
2809553 TGGCAAT
1 TGGCAAT
2809560 TGGCAAT
1 TGGCAAT
2809567 TGGCAA
1 TGGCAA
2809573 GTCATCTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (7 bp):
TGGCAAT
Found at i:2811940 original size:25 final size:24
Alignment explanation
Indices: 2811878--2811940 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
2811868 TTTTATTATT
*
2811878 ATTTTATCAATTATTAATTAATATA
1 ATTTTAT-AATTATTAATAAATATA
* * *
2811903 ACTTTAATCATTATTTATAAATATA
1 A-TTTTATAATTATTAATAAATATA
2811928 ATTTTGATAATTA
1 ATTTT-ATAATTA
2811941 ATAAGTGAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
24 3 0.10
25 22 0.73
26 5 0.17
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (24 bp):
ATTTTATAATTATTAATAAATATA
Found at i:2812645 original size:37 final size:38
Alignment explanation
Indices: 2812587--2812658 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
2812577 ATTTTAAAAT
*
2812587 TTTTTATATATATTTTGAAAGATAATATTTTTATATTA
1 TTTTTATATATATTTTAAAAGATAATATTTTTATATTA
*
2812625 TTTTTAT-TA-ATATTTAAAAGATTATATTTTTATA
1 TTTTTATATATAT-TTTAAAAGATAATATTTTTATA
2812659 CTCATATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 2 0.06
37 22 0.71
38 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (38 bp):
TTTTTATATATATTTTAAAAGATAATATTTTTATATTA
Found at i:2813808 original size:2 final size:2
Alignment explanation
Indices: 2813801--2813840 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2813791 AGGGTAATAC
2813801 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
2813841 TCTTCCACCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2816221 original size:27 final size:27
Alignment explanation
Indices: 2816172--2816232 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
2816162 ATTTATATAA
* *
2816172 TATTCATATTTTTTATTAAATTTTAAT
1 TATTTATATTTTTTATTAAATTTCAAT
* **
2816199 TATTTATATTTTTTGTTGTATTTCAAT
1 TATTTATATTTTTTATTAAATTTCAAT
2816226 TATTTAT
1 TATTTAT
2816233 TTTGATTTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (27 bp):
TATTTATATTTTTTATTAAATTTCAAT
Found at i:2816416 original size:22 final size:22
Alignment explanation
Indices: 2816386--2816427 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2816376 TTAATTTTTA
**
2816386 AAAAAATTATTTATTTATATTT
1 AAAAAATTATAAATTTATATTT
*
2816408 AAAATATTATAAATTTATAT
1 AAAAAATTATAAATTTATAT
2816428 AATTTTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAAAAATTATAAATTTATATTT
Found at i:2816477 original size:22 final size:21
Alignment explanation
Indices: 2816452--2816519 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 21
2816442 TAATAGTTTA
2816452 TTTTATATAACTTTTAATATAT
1 TTTTATATAA-TTTTAATATAT
*
2816474 TTTTATAT--TTAT-ATATAT
1 TTTTATATAATTTTAATATAT
*
2816492 TTATAT-TAATTTTTAAT-TAT
1 TTTTATATAA-TTTTAATATAT
2816512 TTTTATAT
1 TTTTATAT
2816520 TATAATTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
17 1 0.03
18 11 0.30
19 3 0.08
20 11 0.30
21 3 0.08
22 8 0.22
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTATATAATTTTAATATAT
Found at i:2816489 original size:16 final size:16
Alignment explanation
Indices: 2816468--2816498 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2816458 ATAACTTTTA
*
2816468 ATATATTTTTATATTT
1 ATATATATTTATATTT
2816484 ATATATATTTATATT
1 ATATATATTTATATT
2816499 AATTTTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATATATATTTATATTT
Found at i:2816503 original size:28 final size:27
Alignment explanation
Indices: 2816437--2816506 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 27
2816427 TAATTTTTTA
*
2816437 TATATTAATAGTTTATTTTATATAACTT
1 TATATTAAT-TTTTATTTTATATAACTT
*
2816465 T-TAATATATTTTTATATTTATATATA-TT
1 TATATTA-ATTTTTAT-TTTATATA-ACTT
2816493 TATATTAATTTTTA
1 TATATTAATTTTTA
2816507 ATTATTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
27 9 0.26
28 21 0.60
29 5 0.14
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (27 bp):
TATATTAATTTTTATTTTATATAACTT
Found at i:2817240 original size:2 final size:2
Alignment explanation
Indices: 2817233--2817264 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2817223 GTAAACAAAA
2817233 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2817265 GGACAAAGGT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2817291 original size:13 final size:13
Alignment explanation
Indices: 2817275--2817302 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2817265 GGACAAAGGT
2817275 AAAAGGTAAAGAA
1 AAAAGGTAAAGAA
2817288 AAAAGGTAAAGAA
1 AAAAGGTAAAGAA
2817301 AA
1 AA
2817303 CAGGGCTTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.07
Consensus pattern (13 bp):
AAAAGGTAAAGAA
Found at i:2818507 original size:21 final size:21
Alignment explanation
Indices: 2818481--2818521 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2818471 ATTTATTATA
2818481 TATTTTATTT-TTATATTTAAT
1 TATTTT-TTTATTATATTTAAT
2818502 TATTTTTTTATTATATTTAA
1 TATTTTTTTATTATATTTAA
2818522 AATATATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TATTTTTTTATTATATTTAAT
Found at i:2823860 original size:20 final size:20
Alignment explanation
Indices: 2823810--2823860 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2823800 GCTTATAATA
*
2823810 ATATAAAAAAATTTGTATTT
1 ATATAAAAATATTTGTATTT
* *
2823830 AAATAAAAATATTTTTA-TT
1 ATATAAAAATATTTGTATTT
2823849 ATATAAATAATA
1 ATATAAA-AATA
2823861 ATTTAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATATAAAAATATTTGTATTT
Found at i:2824199 original size:21 final size:20
Alignment explanation
Indices: 2824171--2824220 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
2824161 TAATATATAA
*
2824171 ATTTAAATT-ATTTATTATTT
1 ATTTAAATTCATATATTA-TT
2824191 ATATTAAATTCATATATTATT
1 AT-TTAAATTCATATATTATT
2824212 ATTTAAATT
1 ATTTAAATT
2824221 TAAATTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 9 0.33
21 11 0.41
22 7 0.26
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTAAATTCATATATTATT
Found at i:2824262 original size:17 final size:18
Alignment explanation
Indices: 2824217--2824288 Score: 60
Period size: 17 Copynumber: 4.0 Consensus size: 18
2824207 TTATTATTTA
*
2824217 AATTTAAATTAAATAATATT
1 AATTTAAATTTAATAA-A-T
* *
2824237 ATCTTTAAATTTACTAAA-
1 A-ATTTAAATTTAATAAAT
2824255 AATTTAAATTTAATAAAT
1 AATTTAAATTTAATAAAT
*
2824273 AA-TTAACTTTAA-AAAT
1 AATTTAAATTTAATAAAT
2824289 TAAAGTTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
16 4 0.09
17 23 0.52
18 3 0.07
20 2 0.05
21 12 0.27
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTTAAATTTAATAAAT
Found at i:2825786 original size:127 final size:127
Alignment explanation
Indices: 2825560--2825818 Score: 421
Period size: 127 Copynumber: 2.0 Consensus size: 127
2825550 TCACAAGAAT
* * * *
2825560 GATAATACCCCAGTAGACTGGCTGCAGTTATCCACTTAACTCTTCATGGTTATATGGTGTACAGC
1 GATAATACCCCAGTAGACTGCCTGCAGTTATCCACTTAACTCTTCATGGCTAAATGGTGTAAAGC
2825625 TTAGATCAACCCTCCAAACCCAGAACATTTAATCAATCTAGCCATGATCATGAGATGCTATA
66 TTAGATCAACCCTCCAAACCCAGAACATTTAATCAATCTAGCCATGATCATGAGATGCTATA
* * * *
2825687 GATAATACTCCAGTAGGCTGCCTGCAGTTATTCAGTTAAAC-CTTCATGGCTAAATGGTGTAAAG
1 GATAATACCCCAGTAGACTGCCTGCAGTTATCCACTT-AACTCTTCATGGCTAAATGGTGTAAAG
*
2825751 CTTAGATCAACCCTCCAAACCCAGAACATTTAATCAATCTAGCCATGATGATGAGATGCTATA
65 CTTAGATCAACCCTCCAAACCCAGAACATTTAATCAATCTAGCCATGATCATGAGATGCTATA
2825814 GATAA
1 GATAA
2825819 ACCAAAAGAC
Statistics
Matches: 122, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
127 119 0.98
128 3 0.02
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (127 bp):
GATAATACCCCAGTAGACTGCCTGCAGTTATCCACTTAACTCTTCATGGCTAAATGGTGTAAAGC
TTAGATCAACCCTCCAAACCCAGAACATTTAATCAATCTAGCCATGATCATGAGATGCTATA
Found at i:2833835 original size:2 final size:2
Alignment explanation
Indices: 2833828--2833862 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2833818 TACTACTCGA
2833828 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2833863 ATAAGTAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2834562 original size:29 final size:29
Alignment explanation
Indices: 2834528--2834596 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
2834518 TATATATATG
** *
2834528 TTAAAATTTATACATAAATTATTATCATA
1 TTAAAATTTATACATAAAAAATTATAATA
2834557 TTAAAATTTATACATAAAAAATTATAATA
1 TTAAAATTTATACATAAAAAATTATAATA
2834586 TTAAAATTTAT
1 TTAAAATTTAT
2834597 TTGTACTTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
TTAAAATTTATACATAAAAAATTATAATA
Found at i:2834577 original size:15 final size:16
Alignment explanation
Indices: 2834530--2834596 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 16
2834520 TATATATGTT
2834530 AAAATTTATACATA-A
1 AAAATTTATACATATA
** *
2834545 ATTA-TTAT-CATATT
1 AAAATTTATACATATA
2834559 AAAATTTATACATA-A
1 AAAATTTATACATATA
*
2834574 AAAA-TTATA-ATATT
1 AAAATTTATACATATA
2834588 AAAATTTAT
1 AAAATTTAT
2834597 TTGTACTTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
13 7 0.17
14 15 0.38
15 14 0.35
16 4 0.10
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAATTTATACATATA
Found at i:2834703 original size:18 final size:20
Alignment explanation
Indices: 2834680--2834719 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
2834670 TTACATATGA
*
2834680 TTATATACATAT-TAA-ATT
1 TTATATAAATATATAATATT
2834698 TTATATAAATATATAATATT
1 TTATATAAATATATAATATT
2834718 TT
1 TT
2834720 TTATTTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 3 0.16
20 5 0.26
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATATAAATATATAATATT
Found at i:2837444 original size:25 final size:23
Alignment explanation
Indices: 2837416--2837476 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 23
2837406 ATTCATTCAA
*
2837416 ATTAAATTTTAAATTATTTATTTT
1 ATTAAATTTTAAATAATTT-TTTT
2837440 GATTAAATTTTAAATAATTTTTTT
1 -ATTAAATTTTAAATAATTTTTTT
*
2837464 A-AAAATTTTAAAT
1 ATTAAATTTTAAAT
2837477 CAAATTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 11 0.32
23 1 0.03
24 4 0.12
25 18 0.53
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTAAATTTTAAATAATTTTTTT
Found at i:2837531 original size:39 final size:39
Alignment explanation
Indices: 2837488--2837570 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 39
2837478 AAATTAATTA
**
2837488 AATTTAAATTAT-TTTA-TAATAATAAAAATATTTTGTATT
1 AATTTAAATTATAAATATTAAT-ATAAAAATATTTT-TATT
*
2837527 AATTT-GATTATAAATATTAATATAAAAATATTTTTATT
1 AATTTAAATTATAAATATTAATATAAAAATATTTTTATT
2837565 AATTTA
1 AATTTA
2837571 TAAAAAAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
38 14 0.37
39 20 0.53
40 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (39 bp):
AATTTAAATTATAAATATTAATATAAAAATATTTTTATT
Found at i:2843871 original size:32 final size:32
Alignment explanation
Indices: 2843834--2843931 Score: 83
Period size: 32 Copynumber: 3.0 Consensus size: 32
2843824 AAATATATAG
2843834 ATTTATTGTTTTAATTTTAATATAAAATTAAA
1 ATTTATTGTTTTAATTTTAATATAAAATTAAA
** ** *
2843866 ATTTATAATTTTAATTTTTTTATTAAA-T-AA
1 ATTTATTGTTTTAATTTTAATATAAAATTAAA
** *
2843896 ATTTATTTATGTTTTAAGATTAATAAAAAATTAAA
1 ATTTA--T-TGTTTTAATTTTAATATAAAATTAAA
2843931 A
1 A
2843932 ATTAAAAAAA
Statistics
Matches: 48, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
30 7 0.15
31 1 0.02
32 23 0.48
33 13 0.27
34 1 0.02
35 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (32 bp):
ATTTATTGTTTTAATTTTAATATAAAATTAAA
Found at i:2844492 original size:8 final size:8
Alignment explanation
Indices: 2844481--2844518 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
2844471 AGAGTCTGAT
*
2844481 ATATATAT
1 ATATATAG
2844489 ATATATAG
1 ATATATAG
2844497 ATATAT-G
1 ATATATAG
2844504 AATATATAG
1 -ATATATAG
2844513 ATATAT
1 ATATAT
2844519 GGATGGACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
7 1 0.04
8 25 0.93
9 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (8 bp):
ATATATAG
Found at i:2844502 original size:16 final size:16
Alignment explanation
Indices: 2844489--2844519 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2844479 ATATATATAT
2844489 ATATATAGATATATGA
1 ATATATAGATATATGA
2844505 ATATATAGATATATG
1 ATATATAGATATATG
2844520 GATGGACGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (16 bp):
ATATATAGATATATGA
Found at i:2848081 original size:76 final size:76
Alignment explanation
Indices: 2847954--2848105 Score: 259
Period size: 76 Copynumber: 2.0 Consensus size: 76
2847944 TCTCTTTAGC
* *
2847954 GTCTTTCATGGTCTTATTTCCTTCTTTGACAGGCATACTCATAAACGCTTTGTGGTCTCATTTTC
1 GTCTTTCATGGTCTTATTTCCTTCTTTGACAGGCATACTCATAAACACTTTGTGGACTCATTTTC
2848019 CTTTTGTCATT
66 CTTTTGTCATT
* * *
2848030 GTCTTTCATGGTTTTTTTTCCTTCTTTGACAGGCATACTTATAAACACTTTGTGGACTCATTTTC
1 GTCTTTCATGGTCTTATTTCCTTCTTTGACAGGCATACTCATAAACACTTTGTGGACTCATTTTC
2848095 CTTTTGTCATT
66 CTTTTGTCATT
2848106 TGTGCTAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.16, C:0.21, G:0.14, T:0.49
Consensus pattern (76 bp):
GTCTTTCATGGTCTTATTTCCTTCTTTGACAGGCATACTCATAAACACTTTGTGGACTCATTTTC
CTTTTGTCATT
Found at i:2850491 original size:21 final size:21
Alignment explanation
Indices: 2850465--2850504 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2850455 TATTCATTAA
2850465 ATTTTTAAAAAATTA-ATTTTT
1 ATTTTT-AAAAATTATATTTTT
*
2850486 ATTTTTTAAAATTATATTT
1 ATTTTTAAAAATTATATTT
2850505 AAAACAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAAATTATATTTTT
Found at i:2850609 original size:22 final size:22
Alignment explanation
Indices: 2850584--2850627 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2850574 TATATATATT
* *
2850584 TATTTAATATTTACATTTTTAA
1 TATTAAATATTTACAATTTTAA
*
2850606 TATTAAATATTTATAATTTTAA
1 TATTAAATATTTACAATTTTAA
2850628 AAAATATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTAAATATTTACAATTTTAA
Found at i:2850653 original size:19 final size:19
Alignment explanation
Indices: 2850631--2850723 Score: 62
Period size: 21 Copynumber: 4.6 Consensus size: 19
2850621 ATTTTAAAAA
2850631 ATATATTTTATATATAAAT
1 ATATATTTTATATATAAAT
** *
2850650 ATATTGACATTATATGTAAAT
1 ATA-T-ATTTTATATATAAAT
* *
2850671 AT-TAAATATATATATAAAT
1 ATAT-ATTTTATATATAAAT
*
2850690 ATATTTATATTTATATTTATAAT
1 ATA--TAT-TTTATATATA-AAT
2850713 ATATATTTTAT
1 ATATATTTTAT
2850724 TAACAATTAA
Statistics
Matches: 56, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
19 17 0.30
20 6 0.11
21 18 0.32
22 9 0.16
23 6 0.11
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (19 bp):
ATATATTTTATATATAAAT
Found at i:2850664 original size:21 final size:20
Alignment explanation
Indices: 2850638--2850694 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
2850628 AAAATATATT
*
2850638 TTATATATAAATATATTGACA
1 TTATATATAAATATATT-AAA
*
2850659 TTATATGT-AA-ATATTAAA
1 TTATATATAAATATATTAAA
2850677 TATATATATAAATATATT
1 T-TATATATAAATATATT
2850695 TATATTTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 3 0.10
19 11 0.37
20 4 0.13
21 12 0.40
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (20 bp):
TTATATATAAATATATTAAA
Found at i:2850690 original size:12 final size:12
Alignment explanation
Indices: 2850669--2850718 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
2850659 TTATATGTAA
2850669 ATAT-TAAATAT
1 ATATATAAATAT
2850680 ATATATAAATAT
1 ATATATAAATAT
* **
2850692 ATTTATATTTAT
1 ATATATAAATAT
*
2850704 ATTTAT-AATAT
1 ATATATAAATAT
2850715 ATAT
1 ATAT
2850719 TTTATTAACA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 10 0.31
12 22 0.69
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATATATAAATAT
Found at i:2850714 original size:21 final size:21
Alignment explanation
Indices: 2850560--2850723 Score: 52
Period size: 22 Copynumber: 7.5 Consensus size: 21
2850550 AATAATTTAT
2850560 TTTATATTTAGTATTATATATATTTA
1 TTTATATTTA-TATT-TATA-A--TA
* *
2850586 TTTAATATTTACATTTTTAATA
1 TTT-ATATTTATATTTATAATA
* *
2850608 TTAAATATTTATAATTT-TAAAA
1 TT-TATATTTAT-ATTTATAATA
** *
2850630 AATATATTT-TATATATAAATA
1 TTTATATTTATATTTAT-AATA
* *
2850651 TATTGACA-TTATATGTA-AATA
1 T-TT-ATATTTATATTTATAATA
* * * *
2850672 -TTAAATATATATATAAATATA
1 TTTATATTTATATTTATA-ATA
2850693 TTTATATTTATATTTATAATA
1 TTTATATTTATATTTATAATA
*
2850714 TATAT-TTTAT
1 TTTATATTTAT
2850724 TAACAATTAA
Statistics
Matches: 104, Mismatches: 22, Indels: 30
0.67 0.14 0.19
Matches are distributed among these distances:
18 2 0.02
19 12 0.12
20 8 0.08
21 23 0.22
22 31 0.30
23 11 0.11
24 1 0.01
25 3 0.03
26 6 0.06
27 7 0.07
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTATATTTATATTTATAATA
Found at i:2851452 original size:19 final size:20
Alignment explanation
Indices: 2851405--2851452 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
2851395 GAAAATATTT
2851405 TATTTATTAAAAGTAATTATA
1 TATTTATTAAAAG-AATTATA
*
2851426 TTTTTATTAATAA-AATTA-A
1 TATTTATTAA-AAGAATTATA
2851445 TATTTATT
1 TATTTATT
2851453 TAAATTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 8 0.33
20 5 0.21
21 9 0.38
22 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TATTTATTAAAAGAATTATA
Found at i:2858734 original size:2 final size:2
Alignment explanation
Indices: 2858727--2858757 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2858717 AAAGAATGGG
*
2858727 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2858758 CATACATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2858752 original size:16 final size:16
Alignment explanation
Indices: 2858731--2858765 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2858721 AATGGGATAT
*
2858731 ATATATATATATATAC
1 ATATATATATACATAC
2858747 ATATATATATACATAC
1 ATATATATATACATAC
2858763 ATA
1 ATA
2858766 AGTGGGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATATATATACATAC
Found at i:2858758 original size:12 final size:12
Alignment explanation
Indices: 2858727--2858761 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
2858717 AAAGAATGGG
*
2858727 ATATATATATAT
1 ATATATACATAT
2858739 ATATATACATAT
1 ATATATACATAT
2858751 ATATATACATA
1 ATATATACATA
2858762 CATAAGTGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATATACATAT
Found at i:2859913 original size:24 final size:26
Alignment explanation
Indices: 2859886--2859938 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
2859876 ATCTATAGTC
*
2859886 TTTAATCTTTTAT-TTT-AATTATAT
1 TTTAATCTTTAATGTTTAAATTATAT
*
2859910 TTTAATCTTTAATGTTTAAATTATTT
1 TTTAATCTTTAATGTTTAAATTATAT
2859936 TTT
1 TTT
2859939 TTAGATCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 12 0.48
25 3 0.12
26 10 0.40
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (26 bp):
TTTAATCTTTAATGTTTAAATTATAT
Found at i:2860538 original size:30 final size:30
Alignment explanation
Indices: 2860483--2860553 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
2860473 AATTTTATTT
*
2860483 AAATAAAT-TTTTATATTTTTATTACAATC
1 AAATAAATCTTTAATATTTTTATTACAATC
*
2860512 AAATAAATCTTTAATATTTATT-TTACACTC
1 AAATAAATCTTTAATATTT-TTATTACAATC
2860542 AAATAAACTCTT
1 AAATAAA-TCTT
2860554 AAACTTTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 8 0.22
30 23 0.62
31 6 0.16
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.46
Consensus pattern (30 bp):
AAATAAATCTTTAATATTTTTATTACAATC
Found at i:2860605 original size:30 final size:30
Alignment explanation
Indices: 2860542--2860607 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
2860532 TTTTACACTC
* *
2860542 AAATAAACTCTTAAACTTTAAATTTTACTT
1 AAATAAACTCTTAAACTTTAAATTATACCT
*
2860572 AAATAAACTCTTAACCTTT-AATATATACCT
1 AAATAAACTCTTAAACTTTAAAT-TATACCT
2860602 AAATAA
1 AAATAA
2860608 GTCCTTAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 3 0.09
30 29 0.91
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (30 bp):
AAATAAACTCTTAAACTTTAAATTATACCT
Found at i:2860856 original size:23 final size:23
Alignment explanation
Indices: 2860824--2860877 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
2860814 GACTTATATA
*
2860824 AATAATTTTAAAGTATAATATTT
1 AATAAATTTAAAGTATAATATTT
* *
2860847 AATAAATTTAAATTTTAATATTT
1 AATAAATTTAAAGTATAATATTT
2860870 -ATAAATTT
1 AATAAATTT
2860878 TTTTATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 8 0.29
23 20 0.71
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
AATAAATTTAAAGTATAATATTT
Found at i:2863263 original size:12 final size:12
Alignment explanation
Indices: 2863230--2863264 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2863220 ATGGCGCGTA
2863230 TGCGACTGTGAC
1 TGCGACTGTGAC
*
2863242 TGTGACTGTGAC
1 TGCGACTGTGAC
*
2863254 TGCGAATGTGA
1 TGCGACTGTGA
2863265 ATGTTGCTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (12 bp):
TGCGACTGTGAC
Found at i:2866221 original size:2 final size:2
Alignment explanation
Indices: 2866214--2866257 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2866204 GAGAACTGAA
*
2866214 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG CG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2866256 AG
1 AG
2866258 GGTGAAATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2866604 original size:2 final size:2
Alignment explanation
Indices: 2866597--2866621 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2866587 CTGACTCTAA
2866597 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
2866622 GCTCGCCCTC
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:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2867753 original size:3 final size:3
Alignment explanation
Indices: 2867747--2867774 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2867737 TATAAATATT
2867747 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
2867775 CCTCCAATCT
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):
ATG
Found at i:2868716 original size:5 final size:5
Alignment explanation
Indices: 2868682--2868737 Score: 55
Period size: 5 Copynumber: 11.6 Consensus size: 5
2868672 ATATAAGGTG
* * *
2868682 GAAAA GAAGGA GAAAA -AAAA -AAAA GAAAA GAAAA G-AAA GGAAA GGAAA
1 GAAAA GAA-AA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
2868730 GAAAA GAA
1 GAAAA GAA
2868738 GGGACAGGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
4 12 0.27
5 29 0.64
6 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:2868746 original size:19 final size:19
Alignment explanation
Indices: 2868703--2868747 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
2868693 GAAAAAAAAA
*
2868703 AAAGAAAAGAAAAGAAAGG
1 AAAGGAAAGAAAAGAAAGG
*
2868722 AAAGGAAAGAAAAGAAGGG
1 AAAGGAAAGAAAAGAAAGG
*
2868741 ACAGGAA
1 AAAGGAA
2868748 CAGATTGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (19 bp):
AAAGGAAAGAAAAGAAAGG
Found at i:2869709 original size:33 final size:34
Alignment explanation
Indices: 2869633--2869722 Score: 89
Period size: 33 Copynumber: 2.7 Consensus size: 34
2869623 CACTAAAAGC
*
2869633 TTATT-TTTATAATTTTAAATAT-ATTAAAATAATT
1 TTATTATTTATAA--TTAAATTTAATTAAAATAATT
* *
2869667 ATATAATTTATAATTAAATTTAATTAAAAT-ATT
1 TTATTATTTATAATTAAATTTAATTAAAATAATT
*
2869700 TTATTATTTA-AATAATAATTTAA
1 TTATTATTTATAATTA-AATTTAA
2869723 ATTGAAACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
32 4 0.09
33 25 0.53
34 11 0.23
35 7 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
TTATTATTTATAATTAAATTTAATTAAAATAATT
Found at i:2870028 original size:18 final size:19
Alignment explanation
Indices: 2870002--2870038 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2869992 TCTTTTTCTT
*
2870002 TTTTTAAAAAAAAA-AAAA
1 TTTTAAAAAAAAAATAAAA
2870020 TTTTAAAAAAAAAATAAAA
1 TTTTAAAAAAAAAATAAAA
2870039 AGAAGAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
TTTTAAAAAAAAAATAAAA
Found at i:2871597 original size:13 final size:13
Alignment explanation
Indices: 2871579--2871611 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2871569 AAAAAACTAT
2871579 GATGCAAGAAACA
1 GATGCAAGAAACA
2871592 GATGCAAGAAACA
1 GATGCAAGAAACA
*
2871605 AATGCAA
1 GATGCAA
2871612 CAAAATACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.55, C:0.15, G:0.21, T:0.09
Consensus pattern (13 bp):
GATGCAAGAAACA
Found at i:2876235 original size:3 final size:3
Alignment explanation
Indices: 2876227--2876251 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2876217 GGGACGGCTT
2876227 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2876252 ATTTTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2879617 original size:2 final size:2
Alignment explanation
Indices: 2879605--2879640 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2879595 ATCTCCCTCC
* *
2879605 CT CT CT GT CT CT CT CT CT CT CT CT CT CT CC CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2879641 GGTTACTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:2880383 original size:2 final size:2
Alignment explanation
Indices: 2880376--2880405 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2880366 AGGGAAGAAA
2880376 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2880406 TATTTTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2882888 original size:25 final size:26
Alignment explanation
Indices: 2882807--2882899 Score: 76
Period size: 25 Copynumber: 3.8 Consensus size: 26
2882797 TGTTTTAATC
*
2882807 ATATATAA-ATATTTATA-TTAGTTTT
1 ATAT-TAATATATTTATATTTAGATTT
* *
2882832 AATATTAATA-ATTTATATTATATAATT
1 -ATATTAATATATTTATATT-TAGATTT
2882859 -T-TTAATATATTTATATTTA-ATTT
1 ATATTAATATATTTATATTTAGATTT
2882882 ATATTAATAT-TTTA-ATTT
1 ATATTAATATATTTATATTT
2882900 TTTATAATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
23 7 0.12
24 13 0.23
25 27 0.47
26 6 0.11
27 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
ATATTAATATATTTATATTTAGATTT
Found at i:2882906 original size:50 final size:51
Alignment explanation
Indices: 2882815--2882912 Score: 121
Period size: 50 Copynumber: 1.9 Consensus size: 51
2882805 TCATATATAA
*
2882815 ATATTTATATTAGTTTTAATATTAATAATTTATATTATATAAT-TTTTAAT
1 ATATTTATATTAGATTTAATATTAATAATTTATATTATATAATATTTTAAT
* * *
2882865 ATATTTATATTTA-ATTT-ATATTAATATTTTAATTTTTTATAATATTTT
1 ATATTTATA-TTAGATTTAATATTAATAATTT-ATATTATATAATATTTT
2882913 CAAAATTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
49 12 0.29
50 22 0.54
51 7 0.17
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (51 bp):
ATATTTATATTAGATTTAATATTAATAATTTATATTATATAATATTTTAAT
Found at i:2885350 original size:2 final size:2
Alignment explanation
Indices: 2885343--2885378 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2885333 ATTTGAGTTG
*
2885343 AT AT AT AT AT AT AT AT AT GT 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
2885379 TATGCACAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2885806 original size:32 final size:29
Alignment explanation
Indices: 2885757--2885830 Score: 82
Period size: 32 Copynumber: 2.6 Consensus size: 29
2885747 AAATTAATAC
*
2885757 AATAATATTTATAAATTTATATTAACATA
1 AATAATATTTATAAATTTATATAAACATA
*
2885786 AATAATGATTTATTAAAATTTATATAAATAT-
1 AATAAT-ATTTA-T-AAATTTATATAAACATA
2885817 AA-AATATTT-TAAAT
1 AATAATATTTATAAAT
2885831 ATAATTATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
26 4 0.10
27 1 0.03
29 10 0.25
30 8 0.20
31 3 0.08
32 14 0.35
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (29 bp):
AATAATATTTATAAATTTATATAAACATA
Found at i:2885818 original size:6 final size:6
Alignment explanation
Indices: 2885807--2885875 Score: 63
Period size: 6 Copynumber: 11.7 Consensus size: 6
2885797 ATTAAAATTT
* * *
2885807 ATATAA ATATAA A-AT-A TTTTAA ATATAA TTATAA TATAATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA -AT-ATAA ATATAA
*
2885855 ATAT-G ATATAA ATATAA ATAT
1 ATATAA ATATAA ATATAA ATAT
2885876 GTAAATTATG
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
4 1 0.02
5 7 0.14
6 35 0.70
7 3 0.06
8 4 0.08
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (6 bp):
ATATAA
Found at i:2885830 original size:26 final size:28
Alignment explanation
Indices: 2885752--2885848 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 28
2885742 ATATAAAATT
*
2885752 AATACAATAATATTTATAAATTTATATTA
1 AATATAATAATATTT-TAAATTTATATTA
2885781 ACATA-AATAATGATTTATTAAAATTTATA-TA
1 A-ATATAATAAT-A-TT-TT-AAATTTATATTA
*
2885812 AATATAA-AATATTTTAAATATA-ATTA
1 AATATAATAATATTTTAAATTTATATTA
2885838 TAATATAATAA
1 -AATATAATAA
2885849 ATATAAATAT
Statistics
Matches: 58, Mismatches: 1, Indels: 19
0.74 0.01 0.24
Matches are distributed among these distances:
25 1 0.02
26 8 0.14
27 9 0.16
28 4 0.07
29 8 0.14
30 10 0.17
31 8 0.14
32 10 0.17
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (28 bp):
AATATAATAATATTTTAAATTTATATTA
Found at i:2885844 original size:11 final size:11
Alignment explanation
Indices: 2885828--2885871 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
2885818 AAATATTTTA
*
2885828 AATATAATTAT
1 AATATAAATAT
2885839 AATAT-AATA-
1 AATATAAATAT
2885848 AATATAAATAT
1 AATATAAATAT
*
2885859 GATATAAATAT
1 AATATAAATAT
2885870 AA
1 AA
2885872 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
9 5 0.18
10 7 0.25
11 16 0.57
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
AATATAAATAT
Found at i:2885873 original size:17 final size:17
Alignment explanation
Indices: 2885829--2885876 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
2885819 AATATTTTAA
*
2885829 ATATAATTAT-AATAT-
1 ATATAAATATAAATATG
2885844 A-ATAAATATAAATATG
1 ATATAAATATAAATATG
2885860 ATATAAATATAAATATG
1 ATATAAATATAAATATG
2885877 TAAATTATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 7 0.24
15 6 0.21
16 1 0.03
17 15 0.52
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (17 bp):
ATATAAATATAAATATG
Found at i:2886172 original size:16 final size:15
Alignment explanation
Indices: 2886151--2886180 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2886141 TCATTATATT
2886151 TATATATATTATATAC
1 TATATATATT-TATAC
2886167 TATATATATTTATA
1 TATATATATTTATA
2886181 TCAAATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATTTATAC
Found at i:2886455 original size:3 final size:3
Alignment explanation
Indices: 2886447--2886514 Score: 100
Period size: 3 Copynumber: 21.7 Consensus size: 3
2886437 TGTTTTTTAC
*
2886447 ATT ATT ATT ATT ATT ATTT ATT ATC ATTT ATT ATTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT A-TT ATT A-TT ATT ATT ATT ATT
2886495 ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
2886515 CGGGGGTAGT
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
3 52 0.87
4 8 0.13
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2886835 original size:20 final size:20
Alignment explanation
Indices: 2886812--2886852 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2886802 ATTTAATTTA
* *
2886812 ATTTTTAAATTTTTATTAAT
1 ATTTATAAATTTTTATAAAT
*
2886832 ATTTATATATTTTTATAAAT
1 ATTTATAAATTTTTATAAAT
2886852 A
1 A
2886853 ATCATTAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTATAAATTTTTATAAAT
Found at i:2890272 original size:2 final size:2
Alignment explanation
Indices: 2890265--2890292 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2890255 CAAACCTAAA
2890265 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
2890293 CACTTTGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2892108 original size:50 final size:51
Alignment explanation
Indices: 2892049--2892145 Score: 144
Period size: 50 Copynumber: 1.9 Consensus size: 51
2892039 ATCATTTATT
*
2892049 GGGATCAATTATTCTTCAG-AATAACCTTAG-AATTCAATCCTAGAACTTAC
1 GGGATCAATTATTCTTC-GCAATAACCTTAGAAATTCAATCCCAGAACTTAC
* *
2892099 GGGATCAATTTTTCTTCGCAATAGCCTTAGAAATTCAATCCCAGAAC
1 GGGATCAATTATTCTTCGCAATAACCTTAGAAATTCAATCCCAGAAC
2892146 CTCAATAGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
49 1 0.02
50 26 0.62
51 15 0.36
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (51 bp):
GGGATCAATTATTCTTCGCAATAACCTTAGAAATTCAATCCCAGAACTTAC
Found at i:2895786 original size:108 final size:108
Alignment explanation
Indices: 2895597--2895928 Score: 481
Period size: 108 Copynumber: 3.1 Consensus size: 108
2895587 TTGTGGCTTC
* * * *
2895597 TACTTCGAGTGTCTTCACTGTCACTGAACTTTTGAGGAGTTTCTGTGTTTTCTTTCCGGTTTATC
1 TACTTTGAGTGTCTTCATTGTCACTGAACTTTTGAGGAGTTTCTGTGTTTTCCTTCCGGCTTATC
2895662 TCTTGAGGAATTTGTGTGATTTCACTCGGGTTTATCCCTTGTG
66 TCTTGAGGAATTTGTGTGATTTCACTCGGGTTTATCCCTTGTG
* * *
2895705 TACTTTGAGTGTCTTCATTGCCACTGAACTTTTGAGGAATTTGTGT-TTTATCCTTCCGGCTTAT
1 TACTTTGAGTGTCTTCATTGTCACTGAACTTTTGAGGAGTTTCTGTGTTT-TCCTTCCGGCTTAT
* * *
2895769 C-CATTGAGGATTTTGTGTGTTTTCACTGGGGTTTATCCCTTGTG
65 CTC-TTGAGGAATTTGTGTGATTTCACTCGGGTTTATCCCTTGTG
* *
2895813 TACTTTGAGTGTCTTCATTGTCACAGAACTTTTGAGGAGTTTCTGTGTTTTCCTTCTGGCTTATC
1 TACTTTGAGTGTCTTCATTGTCACTGAACTTTTGAGGAGTTTCTGTGTTTTCCTTCCGGCTTATC
* * *
2895878 TCTTGAGGACTTTGTG-CATTTTCACTTGGGTTTATCCCTTGTG
66 TCTTGAGGAATTTGTGTGA-TTTCACTCGGGTTTATCCCTTGTG
2895921 TACTTTGA
1 TACTTTGA
2895929 CTGTTATCCC
Statistics
Matches: 200, Mismatches: 19, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
107 4 0.02
108 192 0.96
109 4 0.02
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.46
Consensus pattern (108 bp):
TACTTTGAGTGTCTTCATTGTCACTGAACTTTTGAGGAGTTTCTGTGTTTTCCTTCCGGCTTATC
TCTTGAGGAATTTGTGTGATTTCACTCGGGTTTATCCCTTGTG
Found at i:2898571 original size:6 final size:6
Alignment explanation
Indices: 2898560--2898586 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2898550 GCGCCGAGGT
2898560 AGGGGC AGGGGC AGGGGC AGGGGC AGG
1 AGGGGC AGGGGC AGGGGC AGGGGC AGG
2898587 CGCAAGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.15, G:0.67, T:0.00
Consensus pattern (6 bp):
AGGGGC
Found at i:2899301 original size:31 final size:31
Alignment explanation
Indices: 2899263--2899322 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2899253 TATAACATTG
* *
2899263 AAATAAAATATTAAGTAAAGCAAAGTGGCTT
1 AAATAAAATATGAAGTAAAGCAAACTGGCTT
2899294 AAATAAAATATGAAGTAAAGCAAACTGGC
1 AAATAAAATATGAAGTAAAGCAAACTGGC
2899323 AAGGGCACCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.53, C:0.08, G:0.17, T:0.22
Consensus pattern (31 bp):
AAATAAAATATGAAGTAAAGCAAACTGGCTT
Found at i:2901022 original size:99 final size:99
Alignment explanation
Indices: 2900851--2901049 Score: 398
Period size: 99 Copynumber: 2.0 Consensus size: 99
2900841 GTCCATGCTT
2900851 TAGAAACAAATCTTTATCTTAACCAATATCATATTCTCTGTTTAGAAAACAAGGATATAAAATCA
1 TAGAAACAAATCTTTATCTTAACCAATATCATATTCTCTGTTTAGAAAACAAGGATATAAAATCA
2900916 CTCAACTTAAGCATCGAATAGTTTTGCCTTGTAG
66 CTCAACTTAAGCATCGAATAGTTTTGCCTTGTAG
2900950 TAGAAACAAATCTTTATCTTAACCAATATCATATTCTCTGTTTAGAAAACAAGGATATAAAATCA
1 TAGAAACAAATCTTTATCTTAACCAATATCATATTCTCTGTTTAGAAAACAAGGATATAAAATCA
2901015 CTCAACTTAAGCATCGAATAGTTTTGCCTTGTAG
66 CTCAACTTAAGCATCGAATAGTTTTGCCTTGTAG
2901049 T
1 T
2901050 TACCCCCATG
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (99 bp):
TAGAAACAAATCTTTATCTTAACCAATATCATATTCTCTGTTTAGAAAACAAGGATATAAAATCA
CTCAACTTAAGCATCGAATAGTTTTGCCTTGTAG
Found at i:2903816 original size:21 final size:23
Alignment explanation
Indices: 2903783--2903824 Score: 54
Period size: 21 Copynumber: 1.9 Consensus size: 23
2903773 ATATATTATA
2903783 AAATATGATAATA-CATAAATAAT
1 AAATATGATAATATC-TAAATAAT
2903806 AAATAT-A-AATATCTAAATA
1 AAATATGATAATATCTAAATA
2903825 TATATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
21 10 0.56
22 2 0.11
23 6 0.33
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (23 bp):
AAATATGATAATATCTAAATAAT
Found at i:2904077 original size:22 final size:21
Alignment explanation
Indices: 2904038--2904081 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
2904028 AACCGGTGCA
* **
2904038 TTTATATTTTATTTTTATTATT
1 TTTATATTTAATAATTA-TATT
2904060 TTTATATTTAATAATTATATT
1 TTTATATTTAATAATTATATT
2904081 T
1 T
2904082 AAAATATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTATATTTAATAATTATATT
Found at i:2904079 original size:13 final size:14
Alignment explanation
Indices: 2904061--2904093 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2904051 TTTATTATTT
*
2904061 TTATATTTAATA-A
1 TTATATTTAAAATA
2904074 TTATATTTAAAATA
1 TTATATTTAAAATA
2904088 TTATAT
1 TTATAT
2904094 ATATATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTATATTTAAAATA
Found at i:2904102 original size:18 final size:18
Alignment explanation
Indices: 2904075--2904113 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2904065 ATTTAATAAT
*
2904075 TATATTTAAAATATTATA
1 TATATATAAAATATTATA
* *
2904093 TATATATAAATTTTTATA
1 TATATATAAAATATTATA
2904111 TAT
1 TAT
2904114 TAATAATATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATATATAAAATATTATA
Found at i:2904787 original size:22 final size:22
Alignment explanation
Indices: 2904714--2904792 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
2904704 TTAAATAAAA
* * *
2904714 TAAAATGATTTAATAAAAATTAA
1 TAAAAT-ATATAATATAAATTAT
* *
2904737 TAAATTATATAAATATATTAGTATAT
1 TAAAATATAT-AATATA--AAT-TAT
2904763 TAAAATATATAATATAAATTAT
1 TAAAATATATAATATAAATTAT
2904785 TAAAATAT
1 TAAAATAT
2904793 CAAAATTTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
22 14 0.31
23 12 0.27
25 8 0.18
26 11 0.24
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (22 bp):
TAAAATATATAATATAAATTAT
Found at i:2904798 original size:30 final size:27
Alignment explanation
Indices: 2904741--2904809 Score: 75
Period size: 30 Copynumber: 2.4 Consensus size: 27
2904731 AATTAATAAA
** *
2904741 TTATATAAATATATTAGTATATTAAAAT
1 TTATATAAAT-TATTAAAATATCAAAAT
2904769 ATATAATATAAATTATTAAAATATCAAAAT
1 -T-T-ATATAAATTATTAAAATATCAAAAT
2904799 TTATATAAATT
1 TTATATAAATT
2904810 TAATATATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
27 9 0.26
28 1 0.03
29 2 0.06
30 15 0.43
31 8 0.23
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (27 bp):
TTATATAAATTATTAAAATATCAAAAT
Found at i:2906388 original size:3 final size:3
Alignment explanation
Indices: 2906380--2906410 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2906370 CTTGGTTTGA
2906380 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2906411 TGAAGTAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2907457 original size:15 final size:16
Alignment explanation
Indices: 2907437--2907483 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
2907427 AATTTAAGTA
2907437 TAAATTTTATT-AATT
1 TAAATTTTATTAAATT
*
2907452 TAAA-TTAATTAAATT
1 TAAATTTTATTAAATT
2907467 TAAATTATTATTTAAAT
1 TAAATT-TTA-TTAAAT
2907484 AATACAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 5 0.19
15 12 0.46
16 1 0.04
17 2 0.08
18 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATTTTATTAAATT
Found at i:2912979 original size:14 final size:13
Alignment explanation
Indices: 2912950--2912991 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 13
2912940 GGTAAGAAAG
2912950 AAATTATAAATATTA
1 AAATT-TAAAT-TTA
2912965 AAATTTAAAATTTA
1 AAATTT-AAATTTA
2912979 AAATTTAAATTTA
1 AAATTTAAATTTA
2912992 TTAAATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 7 0.27
14 10 0.38
15 9 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATTTAAATTTA
Found at i:2913001 original size:7 final size:7
Alignment explanation
Indices: 2912957--2912991 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
2912947 AAGAAATTAT
2912957 AAATATTA
1 AAAT-TTA
2912965 AAATTTA
1 AAATTTA
2912972 AAATTTA
1 AAATTTA
2912979 AAATTT-
1 AAATTTA
2912985 AAATTTA
1 AAATTTA
2912992 TTAAATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 6 0.23
7 16 0.62
8 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAATTTA
Found at i:2918026 original size:17 final size:16
Alignment explanation
Indices: 2917999--2918068 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
2917989 AATGTTTACA
2917999 TTAAATAAAAATATTAAT
1 TTAAAT-AAAA-ATTAAT
* *
2918017 TTAAGTAAAAATTTAT
1 TTAAATAAAAATTAAT
2918033 TTAAATAAAAATTAA-
1 TTAAATAAAAATTAAT
*
2918048 --AAATTAAAAATTTAT
1 TTAAA-TAAAAATTAAT
2918063 TTAAAT
1 TTAAAT
2918069 TTAAATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
13 3 0.07
14 9 0.21
16 19 0.44
17 7 0.16
18 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (16 bp):
TTAAATAAAAATTAAT
Found at i:2918068 original size:24 final size:23
Alignment explanation
Indices: 2918041--2918087 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2918031 ATTTAAATAA
* *
2918041 AAATTAAAAATTAAAAATTTATTT
1 AAATT-AAAATAAAAAAATTATTT
*
2918065 AAATTTAAATAAAAAAATTATTT
1 AAATTAAAATAAAAAAATTATTT
2918088 GATTAGAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATTAAAATAAAAAAATTATTT
Found at i:2918084 original size:31 final size:30
Alignment explanation
Indices: 2918022--2918080 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
2918012 TTAATTTAAG
*
2918022 TAAAAATTTATTTAAATAAAAATTAAAAAT
1 TAAAAATTTATTTAAATAAAAATAAAAAAT
**
2918052 TAAAAATTTATTTAAATTTAAATAAAAAA
1 TAAAAATTTATTTAAATAAAAATAAAAAA
2918081 ATTATTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (30 bp):
TAAAAATTTATTTAAATAAAAATAAAAAAT
Found at i:2918999 original size:16 final size:16
Alignment explanation
Indices: 2918980--2919019 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2918970 TATTCAAACT
2918980 CGAAATGACCCGAATC
1 CGAAATGACCCGAATC
**
2918996 CGAAATGATTCGAATC
1 CGAAATGACCCGAATC
*
2919012 TGAAATGA
1 CGAAATGA
2919020 ACTGAACTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (16 bp):
CGAAATGACCCGAATC
Found at i:2922464 original size:33 final size:33
Alignment explanation
Indices: 2922417--2922482 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2922407 TTATAACTTA
* **
2922417 TAAATATTAAAATTAAATCAACACAAATAATAT
1 TAAAAATTAAAATTAAAAAAACACAAATAATAT
*
2922450 TAAAAATTAAAATTAAAAAAATACAAATAATAT
1 TAAAAATTAAAATTAAAAAAACACAAATAATAT
2922483 ATATATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (33 bp):
TAAAAATTAAAATTAAAAAAACACAAATAATAT
Found at i:2922517 original size:26 final size:24
Alignment explanation
Indices: 2922465--2922511 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2922455 ATTAAAATTA
2922465 AAAAAATACAAATAATATATATAT
1 AAAAAATACAAATAATATATATAT
2922489 AAAAAATACAAATAATATATATA
1 AAAAAATACAAATAATATATATA
2922512 GATAAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAAAATACAAATAATATATATAT
Found at i:2923420 original size:14 final size:14
Alignment explanation
Indices: 2923385--2923423 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2923375 AAATTATAAA
2923385 TAAATATT-TTTA-
1 TAAATATTATTTAT
2923397 T-AAT-TTATTTAT
1 TAAATATTATTTAT
2923409 TAAATATTATTTAT
1 TAAATATTATTTAT
2923423 T
1 T
2923424 TATATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 2 0.09
11 7 0.30
12 2 0.09
13 3 0.13
14 9 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TAAATATTATTTAT
Found at i:2924721 original size:15 final size:16
Alignment explanation
Indices: 2924701--2924730 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2924691 AAATTTTAAA
2924701 AACTTGAAA-TAACCT
1 AACTTGAAACTAACCT
2924716 AACTTGAAACTAACC
1 AACTTGAAACTAACC
2924731 AGACCCGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.23
Consensus pattern (16 bp):
AACTTGAAACTAACCT
Found at i:2926433 original size:2 final size:2
Alignment explanation
Indices: 2926426--2926453 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2926416 TCCTACATTC
2926426 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
2926454 TGAGAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2932074 original size:2 final size:2
Alignment explanation
Indices: 2932067--2932094 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2932057 TTGACTCAGA
2932067 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
2932095 GTGCGCGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2932323 original size:2 final size:2
Alignment explanation
Indices: 2932318--2932354 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2932308 TAGCCATTTC
*
2932318 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT GT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2932355 AACTGACTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.03, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2933639 original size:11 final size:11
Alignment explanation
Indices: 2933613--2933654 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
2933603 TATTTAAAAG
*
2933613 TTAAATTTTTAT
1 TTAAA-TTTAAT
2933625 TTAAATTTAAT
1 TTAAATTTAAT
*
2933636 TTAAATATAA-
1 TTAAATTTAAT
2933646 TTAAATTTA
1 TTAAATTTA
2933655 TCAAATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 8 0.30
11 14 0.52
12 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:2938494 original size:17 final size:17
Alignment explanation
Indices: 2938472--2938516 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2938462 AACTAATGCT
2938472 TTTTAAAATTATT-AACA
1 TTTTAAAATTATTCAA-A
*
2938489 TTTTAAAATTTTTTCAAA
1 TTTTAAAA-TTATTCAAA
2938507 TTTTAAAATT
1 TTTTAAAATT
2938517 CCTCATCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 13 0.52
19 2 0.08
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTAAAATTATTCAAA
Found at i:2939102 original size:18 final size:17
Alignment explanation
Indices: 2939081--2939126 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
2939071 AATATATTAA
2939081 AATTTTTAATATAAATAT
1 AATTTTTAATATAAAT-T
*
2939099 AATTTTT-ATATTAATT
1 AATTTTTAATATAAATT
*
2939115 -ATATTTAATATA
1 AATTTTTAATATA
2939127 TTATATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 5 0.21
16 5 0.21
17 7 0.29
18 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTTTAATATAAATT
Found at i:2939112 original size:23 final size:23
Alignment explanation
Indices: 2939086--2939180 Score: 68
Period size: 23 Copynumber: 4.0 Consensus size: 23
2939076 ATTAAAATTT
2939086 TTAATATAAATATAATTTTTATA
1 TTAATATAAATATAATTTTTATA
* * *
2939109 TTAAT-TATATTTAATATATTATA
1 TTAATATAAATATAAT-TTTTATA
* * *
2939132 TTATATTTATTATATTATTTTTATA
1 TTA-ATATA-AATATAATTTTTATA
2939157 TTAATA-AATATATCATATTTTTAT
1 TTAATATAA-ATAT-A-ATTTTTAT
2939181 TATATCTAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
22 8 0.14
23 19 0.34
24 4 0.07
25 19 0.34
26 6 0.11
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (23 bp):
TTAATATAAATATAATTTTTATA
Found at i:2939116 original size:9 final size:9
Alignment explanation
Indices: 2939104--2939148 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
2939094 AATATAATTT
2939104 TTATATTAA
1 TTATATTAA
2939113 TTATATTTAA
1 TTATA-TTAA
2939123 -TATATTATA
1 TTATATTA-A
*
2939132 TTATATTTA
1 TTATATTAA
2939141 TTATATTA
1 TTATATTA
2939149 TTTTTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
8 3 0.10
9 18 0.58
10 10 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTATATTAA
Found at i:2939133 original size:5 final size:5
Alignment explanation
Indices: 2939104--2939159 Score: 64
Period size: 5 Copynumber: 11.6 Consensus size: 5
2939094 AATATAATTT
* *
2939104 TTATA TTA-A TTATA TT-TA ATATA TTATA TTATA TT-TA TTATA TTATTT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTA-TA
2939152 TTATA TTA
1 TTATA TTA
2939160 ATAAATATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
4 11 0.26
5 28 0.65
6 4 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:2939136 original size:19 final size:19
Alignment explanation
Indices: 2939105--2939176 Score: 78
Period size: 19 Copynumber: 3.9 Consensus size: 19
2939095 ATATAATTTT
2939105 TATATTA-ATTATATTTAA
1 TATATTATATTATATTTAA
*
2939123 TATATTATATTATATTTAT
1 TATATTATATTATATTTAA
*
2939142 TATATTAT-TTTTATATTAA
1 TATATTATATTATAT-TTAA
* *
2939161 TA-AATATATCATATTT
1 TATATTATATTATATTT
2939177 TTATTATATC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
18 18 0.40
19 27 0.60
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTTAA
Found at i:2939148 original size:14 final size:14
Alignment explanation
Indices: 2939104--2939155 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
2939094 AATATAATTT
*
2939104 TTATATTAATTATA
1 TTATATTTATTATA
*
2939118 TT-TAATATATTATA
1 TTAT-ATTTATTATA
2939132 TTATATTTATTATA
1 TTATATTTATTATA
*
2939146 TTATTTTTAT
1 TTATATTTAT
2939156 ATTAATAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 1 0.03
14 30 0.94
15 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATATTTATTATA
Found at i:2940527 original size:22 final size:23
Alignment explanation
Indices: 2940449--2940520 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 23
2940439 TTTAAAATAT
*
2940449 TTAT-AATTAAATTTGAATAATT-
1 TTATAAATTTAATTTGAAT-ATTA
*
2940471 TTATAATATTTAAATTG-AT-TTA
1 TTATAA-ATTTAATTTGAATATTA
*
2940493 TTAATGAATTTAATTTGAATATTA
1 TT-ATAAATTTAATTTGAATATTA
2940517 TTAT
1 TTAT
2940521 TATTTAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
21 2 0.05
22 15 0.38
23 10 0.25
24 13 0.32
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (23 bp):
TTATAAATTTAATTTGAATATTA
Found at i:2940675 original size:14 final size:14
Alignment explanation
Indices: 2940639--2940675 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2940629 AAATAAAAAT
2940639 TAAAATAT-ATTTA
1 TAAAATATAATTTA
2940652 -AAAATCATAATTTA
1 TAAAAT-ATAATTTA
2940666 TAAAATATAA
1 TAAAATATAA
2940676 AAAATAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.24
13 2 0.10
14 9 0.43
15 5 0.24
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAATATAATTTA
Found at i:2941796 original size:29 final size:28
Alignment explanation
Indices: 2941734--2941796 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 28
2941724 TTTATATCAC
* *
2941734 ATATAATTATTGTAATATAATTATTTAA
1 ATATAATTATTGTAATATAATTAGTGAA
* *
2941762 AAATAATTAATT-TATATATTATTAGTGAA
1 ATATAATT-ATTGTA-ATATAATTAGTGAA
2941791 ATATAA
1 ATATAA
2941797 AAATTATTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (28 bp):
ATATAATTATTGTAATATAATTAGTGAA
Found at i:2942332 original size:3 final size:3
Alignment explanation
Indices: 2942324--2942358 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2942314 CATGAATTAG
2942324 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2942359 TAGATCTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2950647 original size:17 final size:17
Alignment explanation
Indices: 2950622--2950655 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2950612 GCTTTTAGAG
*
2950622 ATTGTTGGGTTAGGGAT
1 ATTGATGGGTTAGGGAT
2950639 ATTGATGGGTTAGGGAT
1 ATTGATGGGTTAGGGAT
2950656 GGAAAAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.41, T:0.38
Consensus pattern (17 bp):
ATTGATGGGTTAGGGAT
Found at i:2950763 original size:81 final size:83
Alignment explanation
Indices: 2950647--2950810 Score: 201
Period size: 81 Copynumber: 2.0 Consensus size: 83
2950637 ATATTGATGG
*
2950647 GTTAGGGATGGAAAAAGATGGAAGCTTTTAGAGAGAGAGAAAAGATTTTAAGAGAAAGAA-A-TG
1 GTTAGGGATGGAAAAAGATGAAAGCTTTTA-AGAGAGAG-AAA-ATTTTAAGAGAAAGAATATTG
*
2950710 GGTTAAGACAGAGAGGGGAGT
63 GGTTAAGACAGAGACGGGAGT
* * * *
2950731 GTTAGGGAT-GAAGAGGATGAAAGCTTTT-AGAGAGAGAAATTTTTAAGAGATAGAATATTGGGT
1 GTTAGGGATGGAAAAAGATGAAAGCTTTTAAGAGAGAGAAAATTTTAAGAGAAAGAATATTGGGT
* *
2950794 TAGGAGAGAGACGGGAG
66 TAAGACAGAGACGGGAG
2950811 AGTCAAAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
79 14 0.20
80 4 0.06
81 27 0.39
83 16 0.23
84 9 0.13
ACGTcount: A:0.40, C:0.02, G:0.36, T:0.21
Consensus pattern (83 bp):
GTTAGGGATGGAAAAAGATGAAAGCTTTTAAGAGAGAGAAAATTTTAAGAGAAAGAATATTGGGT
TAAGACAGAGACGGGAGT
Found at i:2950850 original size:14 final size:14
Alignment explanation
Indices: 2950831--2950888 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
2950821 GAAAAAAAAA
*
2950831 TAAATATAATTTAT
1 TAAATATAATATAT
2950845 TAAATATAA-ATAT
1 TAAATATAATATAT
2950858 ATAAATAT-AT-T-T
1 -TAAATATAATATAT
2950870 GTAAATATTAATATAT
1 -TAAATA-TAATATAT
2950886 TAA
1 TAA
2950889 TTTTAGAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
12 7 0.19
13 6 0.17
14 18 0.50
15 4 0.11
16 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
TAAATATAATATAT
Found at i:2950882 original size:26 final size:28
Alignment explanation
Indices: 2950830--2950885 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
2950820 TGAAAAAAAA
*
2950830 ATAAATATAATTTATTAAATATAAATAT
1 ATAAATATAATTTAGTAAATATAAATAT
*
2950858 ATAAATAT-ATTT-GTAAATATTAATAT
1 ATAAATATAATTTAGTAAATATAAATAT
2950884 AT
1 AT
2950886 TAATTTTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 14 0.54
27 4 0.15
28 8 0.31
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
ATAAATATAATTTAGTAAATATAAATAT
Found at i:2953766 original size:2 final size:2
Alignment explanation
Indices: 2953759--2953802 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2953749 TCCTATTTGG
2953759 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
2953801 AT
1 AT
2953803 TTGTAAAGCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2959546 original size:13 final size:13
Alignment explanation
Indices: 2959514--2959555 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2959504 TTTTAAAACA
2959514 AAAATTATTC-TT
1 AAAATTATTCTTT
*
2959526 AATTATTATTCTTT
1 AA-AATTATTCTTT
2959540 AAAATTATT-TTT
1 AAAATTATTCTTT
2959552 AAAA
1 AAAA
2959556 ATTTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 9 0.35
13 13 0.50
14 4 0.15
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAATTATTCTTT
Found at i:2965766 original size:2 final size:2
Alignment explanation
Indices: 2965755--2965785 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2965745 TGTTGTCTGC
2965755 AT AT -T 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
2965786 TTAAATGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2966814 original size:28 final size:27
Alignment explanation
Indices: 2966782--2966846 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 27
2966772 CCTAAAATAC
*
2966782 TATATTATATTTAAAAATATTATATATT
1 TATATTATATTTAAAAATATTAAAT-TT
* *
2966810 TATA-TATAATTTTAATATATTAAATTT
1 TATATTAT-ATTTAAAAATATTAAATTT
*
2966837 TATATCATAT
1 TATATTATAT
2966847 AAATTTTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
27 11 0.35
28 20 0.65
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
TATATTATATTTAAAAATATTAAATTT
Found at i:2966851 original size:16 final size:15
Alignment explanation
Indices: 2966810--2966855 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
2966800 ATTATATATT
2966810 TATATAT-AATTTTA
1 TATATATAAATTTTA
2966824 -ATATATTAAATTTTA
1 TATATA-TAAATTTTA
2966839 TATCATATAAATTTTA
1 TAT-ATATAAATTTTA
2966855 T
1 T
2966856 CATTTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.18
14 1 0.04
15 7 0.25
16 12 0.43
17 3 0.11
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATATAAATTTTA
Found at i:2969685 original size:15 final size:16
Alignment explanation
Indices: 2969665--2969696 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2969655 TCACAAAAAA
2969665 TTAAAAAAATA-ATTT
1 TTAAAAAAATATATTT
2969680 TTAAAAAAATATATTT
1 TTAAAAAAATATATTT
2969696 T
1 T
2969697 ATGTGATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAAAAATATATTT
Found at i:2972086 original size:13 final size:13
Alignment explanation
Indices: 2972068--2972093 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2972058 CCTTCTGACC
2972068 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
2972081 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
2972094 AAACAAAGGG
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAAA
Found at i:2972090 original size:16 final size:16
Alignment explanation
Indices: 2972069--2972100 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2972059 CTTCTGACCC
2972069 AAAAAAAAAAAACAAA
1 AAAAAAAAAAAACAAA
2972085 AAAAAAAAAAAACAAA
1 AAAAAAAAAAAACAAA
2972101 GGGAGCCGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAACAAA
Found at i:2972757 original size:37 final size:37
Alignment explanation
Indices: 2972678--2972757 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
2972668 AAATTTAAAA
*
2972678 ATAAAATAAAATGATATATATTCTTTTAAATATATTT
1 ATAAAATAAAATGATATATATTCTTTTAAATATATCT
*
2972715 TTAAAATAAAAT-ATATAATAATT-TTTT-AATCATATCT
1 ATAAAATAAAATGATAT-AT-ATTCTTTTAAAT-ATATCT
2972752 ATAAAA
1 ATAAAA
2972758 ATTTTAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 7 0.19
37 27 0.73
38 3 0.08
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
ATAAAATAAAATGATATATATTCTTTTAAATATATCT
Found at i:2983606 original size:19 final size:19
Alignment explanation
Indices: 2983576--2983623 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
2983566 AAGTCATGCA
2983576 AGAAGAAATGAACTCTTTGC
1 AGAAG-AATGAACTCTTTGC
2983596 AGAAGAATGAACTCTTTGC
1 AGAAGAATGAACTCTTTGC
2983615 AGAAGAATG
1 AGAAGAATG
2983624 GTGTGTACGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 23 0.82
20 5 0.18
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (19 bp):
AGAAGAATGAACTCTTTGC
Found at i:2986236 original size:2 final size:2
Alignment explanation
Indices: 2986229--2986256 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2986219 AATCTAAGCT
2986229 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
2986257 GCCCAAATTC
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
Done.