Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 160 of 187
Found at i:47315745 original size:91 final size:91
Alignment explanation
Indices: 47315592--47315791 Score: 262
Period size: 91 Copynumber: 2.2 Consensus size: 91
47315582 TAAGAGCATT
*
47315592 GGCTTAATTG-CTTTTTTGAAAAAATTTGAGGGTCTTTTTGATAAATTTTAAAAGTTCAAGTGCC
1 GGCTTAATTGTTTTTTTTGAAAAAATTTGAGGGTCTTTTTGATAAATTTTAAAAGTTCAAGTGCC
47315656 CAATTAAGTGAAAA-AAAAA-AGCAGG
66 CAATTAAGTGAAAATAAAAAGAG-AGG
* * * ** *
47315681 GGCTTAATTGTTTTTTATTGAAGAAGTTTGAGGGTCTTTTTTATGCATTTTGAAAGTTCAAGTGC
1 GGCTTAATTGTTTTTT-TTGAAAAAATTTGAGGGTCTTTTTGATAAATTTTAAAAGTTCAAGTGC
* *
47315746 TCAATTGAGTGAAAATAAAAAGAGAGG
65 CCAATTAAGTGAAAATAAAAAGAGAGG
*
47315773 GGTTTAATTGCTTTTTTTT
1 GGCTTAATTG-TTTTTTTT
47315792 TTTAAATTCG
Statistics
Matches: 96, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
89 10 0.10
90 4 0.04
91 55 0.57
92 19 0.20
93 8 0.08
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (91 bp):
GGCTTAATTGTTTTTTTTGAAAAAATTTGAGGGTCTTTTTGATAAATTTTAAAAGTTCAAGTGCC
CAATTAAGTGAAAATAAAAAGAGAGG
Found at i:47316385 original size:18 final size:20
Alignment explanation
Indices: 47316346--47316389 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
47316336 TTTCATAAAA
*
47316346 TTATAACAAAAATTTGACTT
1 TTATAACAAAAATTTGAATT
47316366 TTATAA-AAAAATTT-AATT
1 TTATAACAAAAATTTGAATT
47316384 TTATAA
1 TTATAA
47316390 TTTTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.39
19 8 0.35
20 6 0.26
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (20 bp):
TTATAACAAAAATTTGAATT
Found at i:47316532 original size:12 final size:12
Alignment explanation
Indices: 47316502--47316533 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
47316492 CATATTTTAT
47316502 TTTTATTTATAA
1 TTTTATTTATAA
47316514 -TTT-TTTATAA
1 TTTTATTTATAA
47316524 TTTTATTTAT
1 TTTTATTTAT
47316534 TTTTTATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 7 0.39
11 6 0.33
12 5 0.28
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTATTTATAA
Found at i:47319276 original size:3 final size:3
Alignment explanation
Indices: 47319268--47319293 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
47319258 TTCAAAACAA
47319268 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
47319294 AAGATAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:47319430 original size:18 final size:19
Alignment explanation
Indices: 47319407--47319443 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
47319397 ATTTAAAAAA
47319407 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
47319425 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
47319444 GAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:47319449 original size:18 final size:21
Alignment explanation
Indices: 47319412--47319455 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
47319402 AAAAATATAA
*
47319412 ATTTTGGAATTTTTATAAA-T
1 ATTTTGGAATTTTGATAAATT
47319432 ATTTT-GAATTTTGA-AAATT
1 ATTTTGGAATTTTGATAAATT
47319451 ATTTT
1 ATTTT
47319456 TATTTTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 14 0.64
20 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (21 bp):
ATTTTGGAATTTTGATAAATT
Found at i:47320356 original size:19 final size:20
Alignment explanation
Indices: 47320332--47320378 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
47320322 ACTAGATCGA
47320332 TTAACCGAATTAAATCAA-T
1 TTAACCGAATTAAATCAATT
* *
47320351 TTAACCG-ATTAATTTAATT
1 TTAACCGAATTAAATCAATT
47320370 TTAACCGAA
1 TTAACCGAA
47320379 ATTTACACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.33
19 15 0.62
20 1 0.04
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (20 bp):
TTAACCGAATTAAATCAATT
Found at i:47322479 original size:9 final size:10
Alignment explanation
Indices: 47322460--47322516 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
47322450 TAAGATTAAG
47322460 TTTTAAATAA
1 TTTTAAATAA
47322470 TTTT-AATAA
1 TTTTAAATAA
** *
47322479 TTTTTTATAT
1 TTTTAAATAA
*
47322489 TTTTAAATAT
1 TTTTAAATAA
*
47322499 TTTTATAATTA
1 TTTTA-AATAA
47322510 TTTTAAA
1 TTTTAAA
47322517 AAAAATCACA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
9 9 0.23
10 22 0.56
11 8 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTTAAATAA
Found at i:47322716 original size:94 final size:91
Alignment explanation
Indices: 47322618--47322850 Score: 245
Period size: 94 Copynumber: 2.5 Consensus size: 91
47322608 TTTATTATTA
* * ****
47322618 TTTTGCACTCAATTGGGTACTTAAACTTTCAAAATACATCAAAAAGGCCCTTAAACTT-TTTCAA
1 TTTTGCACTCAATTGGGTACTTGAACTTTCAAAATACATCAAAAAGGCCCTCAAACTTAAAAAAA
* * * * *
47322682 AAAAAGCAATTAAGCTGCTGCTTTTTTTCT
66 AAAAAGCAATTAA-AT-C-ACTGTTCTT-G
* * * * *
47322712 TTTTGCACTCAATTGAGTACTTGAACTGTCAAAATGCATCAAAAAAGTCCTCAAACTTAAAAAAA
1 TTTTGCACTCAATTGGGTACTTGAACTTTCAAAATACATCAAAAAGGCCCTCAAACTTAAAAAAA
47322777 AAAAAGCAATTAAATCACTGTTCTTG
66 AAAAAGCAATTAAATCACTGTTCTTG
* * *
47322803 TTTTGCAC-AAATTGGGTACTTGAACATCCAAAATACATCAAAAAGGCC
1 TTTTGCACTCAATTGGGTACTTGAACTTTCAAAATACATCAAAAAGGCC
47322851 TGGGAAGGAT
Statistics
Matches: 114, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
90 32 0.28
91 8 0.07
92 6 0.05
93 1 0.01
94 52 0.46
95 15 0.13
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.31
Consensus pattern (91 bp):
TTTTGCACTCAATTGGGTACTTGAACTTTCAAAATACATCAAAAAGGCCCTCAAACTTAAAAAAA
AAAAAGCAATTAAATCACTGTTCTTG
Found at i:47323605 original size:6 final size:6
Alignment explanation
Indices: 47323594--47323620 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
47323584 AATTGAGTAC
47323594 AAAACA AAAACA AAAACA AAAACA AAA
1 AAAACA AAAACA AAAACA AAAACA AAA
47323621 GCTTAATTAC
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:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:47330680 original size:14 final size:16
Alignment explanation
Indices: 47330661--47330695 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
47330651 TTCTAATAAA
47330661 AATTTAA-AAAA-TAG
1 AATTTAATAAAATTAG
47330675 AATTTAATAAAATTAG
1 AATTTAATAAAATTAG
47330691 AATTT
1 AATTT
47330696 TTTTATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 4 0.21
16 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (16 bp):
AATTTAATAAAATTAG
Found at i:47330751 original size:19 final size:19
Alignment explanation
Indices: 47330696--47330752 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
47330686 ATTAGAATTT
*
47330696 TTTTATAAAAATCTTAAAA
1 TTTTATAAAAATCATAAAA
*** * **
47330715 AGATAAAAAAATTGTAAAA
1 TTTTATAAAAATCATAAAA
47330734 TTTTATAAAAATCATAAAA
1 TTTTATAAAAATCATAAAA
47330753 AATTAACGAC
Statistics
Matches: 26, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (19 bp):
TTTTATAAAAATCATAAAA
Found at i:47330985 original size:84 final size:81
Alignment explanation
Indices: 47330890--47331043 Score: 204
Period size: 84 Copynumber: 1.9 Consensus size: 81
47330880 TTTTTATAAA
47330890 AAAAATTTACAAAATTTATATTTCTTTAC-ATTTTGTATAATTTTCTTATAACTTTATAAAATTT
1 AAAAATTTACAAAATTTATATTTCTTTACGATTTT-TAT-ATTTT-TTATAA-TTTATAAAATTT
47330954 -ATATTTTTTACGATTATTAT
62 GA-ATTTTTTACGATTATTAT
** * * *
47330974 AAAAATTTACAATTTTTATATTTTTTTACGATTTTTATATTTTTTATAATTTTTAATATTTGAAT
1 AAAAATTTACAAAATTTATATTTCTTTACGATTTTTATATTTTTTATAATTTATAAAATTTGAAT
47331039 TTTTT
66 TTTTT
47331044 TAATTAAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
81 17 0.27
82 7 0.11
83 5 0.08
84 29 0.46
85 5 0.08
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (81 bp):
AAAAATTTACAAAATTTATATTTCTTTACGATTTTTATATTTTTTATAATTTATAAAATTTGAAT
TTTTTACGATTATTAT
Found at i:47331001 original size:19 final size:19
Alignment explanation
Indices: 47330979--47331034 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
47330969 ATTATAAAAA
47330979 TTTACAATTTTTATATTTT
1 TTTACAATTTTTATATTTT
*
47330998 TTTACGATTTTTATA-TTT
1 TTTACAATTTTTATATTTT
*
47331016 TTTATAATTTTTAATATTT
1 TTTACAATTTTT-ATATTT
47331035 GAATTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 13 0.41
19 17 0.53
20 2 0.06
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTACAATTTTTATATTTT
Found at i:47331025 original size:37 final size:38
Alignment explanation
Indices: 47330942--47331034 Score: 100
Period size: 37 Copynumber: 2.5 Consensus size: 38
47330932 TTCTTATAAC
**
47330942 TTTATAAAATTTATA-TTTTTTACGATTATTATAAAAA
1 TTTATAATTTTTATATTTTTTTACGATTATTATAAAAA
* * ***
47330979 TTTACAATTTTTATATTTTTTTACGATTTTTAT-ATTT
1 TTTATAATTTTTATATTTTTTTACGATTATTATAAAAA
47331016 TTTATAATTTTTAATATTT
1 TTTATAATTTTT-ATATTT
47331035 GAATTTTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
37 24 0.52
38 22 0.48
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.61
Consensus pattern (38 bp):
TTTATAATTTTTATATTTTTTTACGATTATTATAAAAA
Found at i:47331206 original size:87 final size:87
Alignment explanation
Indices: 47331115--47331318 Score: 223
Period size: 87 Copynumber: 2.3 Consensus size: 87
47331105 AGTTTTTAAT
* * *
47331115 AAAAGCAGGTACTTAATTACTTTTTTTTTTAA-GTTTGAGGATCTTTTTGATGCATTTTGAAAGT
1 AAAAGCAGG-ACTTAATT-CTTTTTTTTTTAAGGTTTGAGGACCTTTTTGATACATTTTGAAAAT
* *
47331179 TCAAGTACTCAATTGAGTAC-AAA
64 TCAAGTACCCAAATGAGTACAAAA
* * * *** *
47331202 AAAAGTAGAAGCTTAATTGTTTTTTTGAAAAGGTTTGAGGGCCTTTTTGATACATTTTGAAAATT
1 AAAAGCAGGA-CTTAATTCTTTTTTTTTTAAGGTTTGAGGACCTTTTTGATACATTTTGAAAATT
*
47331267 CAAGTACCCAAATGAGTGCAAAA
65 CAAGTACCCAAATGAGTACAAAA
* *
47331290 AAAAGCAGGAGTGTAATTGTTTTTTTTTT
1 AAAAGCAGGACT-TAATTCTTTTTTTTTT
47331319 TATTATTTGA
Statistics
Matches: 94, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
86 10 0.11
87 60 0.64
88 24 0.26
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (87 bp):
AAAAGCAGGACTTAATTCTTTTTTTTTTAAGGTTTGAGGACCTTTTTGATACATTTTGAAAATTC
AAGTACCCAAATGAGTACAAAA
Found at i:47331732 original size:16 final size:18
Alignment explanation
Indices: 47331711--47331746 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
47331701 TTTCATATAG
47331711 TATAAAT-TAA-ATAATA
1 TATAAATATAATATAATA
47331727 TATAAATATAATATAATA
1 TATAAATATAATATAATA
47331745 TA
1 TA
47331747 AACTTGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TATAAATATAATATAATA
Found at i:47331988 original size:20 final size:20
Alignment explanation
Indices: 47331959--47332007 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
47331949 ACCACTTCAA
*
47331959 TTTAATTTTTGT-TATTTATC
1 TTTAATTTTT-TCTATCTATC
*
47331979 TTTTATTTTTTCTATCTATC
1 TTTAATTTTTTCTATCTATC
47331999 TTTAATTTT
1 TTTAATTTT
47332008 GTTTTCAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTAATTTTTTCTATCTATC
Found at i:47335342 original size:19 final size:19
Alignment explanation
Indices: 47335318--47335355 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
47335308 ATAGTGGGAT
47335318 GAACGATGAACTATTCATC
1 GAACGATGAACTATTCATC
47335337 GAACGATGAACTATTCATC
1 GAACGATGAACTATTCATC
47335356 TTTCTTGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (19 bp):
GAACGATGAACTATTCATC
Found at i:47339461 original size:141 final size:141
Alignment explanation
Indices: 47339203--47339484 Score: 361
Period size: 141 Copynumber: 2.0 Consensus size: 141
47339193 GTGACTCGTA
**
47339203 TACTTTGATGTAAGTAAAAGTTCGAGTTCAAATAGATAAACAACCAAAAGTTGATGCGTCGGGTA
1 TACTTTGATGTAAGTAAAACCTCGAGTTCAAATAGATAAACAACCAAAAGTTGATGCGTCGGGTA
* * * * *
47339268 TACAACTTCTGAAGTATGTAGAGTCATTCATAATAGTAGAATTTATAGCCCGAGAAATGATTAAA
66 TACAACTTCTGAAGTATGTAGAGTCATTCACAACAGTAGAATTCATAACCCGAGAAATGAGTAAA
47339333 TGATATCCTTT
131 TGATATCCTTT
** * * *
47339344 TACTTTGATGTAAGTAAAAACCT-GAGTTCAAATAGATAAGGAATCGAAAA-TTGGTGCGTTGGG
1 TACTTTGATGTAAGT-AAAACCTCGAGTTCAAATAGATAAACAA-CCAAAAGTTGATGCGTCGGG
** * * * * *
47339407 TATATGACTTCTGCAGTATGTAGTGTCATTCACAACAGTGGAATTCATAACCCGAGACATGGGTA
64 TATACAACTTCTGAAGTATGTAGAGTCATTCACAACAGTAGAATTCATAACCCGAGAAATGAGTA
47339472 AATGATATCCTTT
129 AATGATATCCTTT
47339485 CATTAGCATT
Statistics
Matches: 120, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
141 110 0.92
142 10 0.08
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (141 bp):
TACTTTGATGTAAGTAAAACCTCGAGTTCAAATAGATAAACAACCAAAAGTTGATGCGTCGGGTA
TACAACTTCTGAAGTATGTAGAGTCATTCACAACAGTAGAATTCATAACCCGAGAAATGAGTAAA
TGATATCCTTT
Found at i:47341386 original size:17 final size:18
Alignment explanation
Indices: 47341350--47341393 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
47341340 AATTAATAAT
*
47341350 TTGAAATAGAAAATGGTA
1 TTGAAATAGAAAATGCTA
*
47341368 TTGAAAT-GACAATGCTA
1 TTGAAATAGAAAATGCTA
47341385 TTGAAATAG
1 TTGAAATAG
47341394 CAAGTGAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
TTGAAATAGAAAATGCTA
Found at i:47345051 original size:49 final size:50
Alignment explanation
Indices: 47344970--47345169 Score: 225
Period size: 49 Copynumber: 4.1 Consensus size: 50
47344960 CTCTTATTTA
* *
47344970 GCTCTTTTGAGCATCCCATTATATGGCTCTCATGAGCTTCCCGATTAATG
1 GCTCTTTTGAGCTTCCCGTTATATGGCTCTCATGAGCTTCCCGATTAATG
* *
47345020 GCTCTTTTGAGCTTTCCGTT-TATGGCTCTCATGAGCTTCCTGATTAATG
1 GCTCTTTTGAGCTTCCCGTTATATGGCTCTCATGAGCTTCCCGATTAATG
** * *
47345069 GCTC-TCCGAAGCTTCCCGGTAT-TGGCTCGCATGAGCTTCCCGATT-ATG
1 GCTCTTTTG-AGCTTCCCGTTATATGGCTCTCATGAGCTTCCCGATTAATG
* *
47345117 GCT-TTTATGAACTTCCCGTTACATGGCTCAT-ATGAGCTTCCCG-TTATATG
1 GCTCTTT-TGAGCTTCCCGTTATATGGCTC-TCATGAGCTTCCCGATTA-ATG
47345167 GCT
1 GCT
47345170 TAGAAGAGCT
Statistics
Matches: 126, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
48 21 0.17
49 81 0.64
50 24 0.19
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.36
Consensus pattern (50 bp):
GCTCTTTTGAGCTTCCCGTTATATGGCTCTCATGAGCTTCCCGATTAATG
Found at i:47345074 original size:25 final size:25
Alignment explanation
Indices: 47344977--47345188 Score: 172
Period size: 25 Copynumber: 8.6 Consensus size: 25
47344967 TTAGCTCTTT
*
47344977 TGAGCATCCC-ATTATATGGCTCTCA
1 TGAGCTTCCCGATTA-ATGGCTCTCA
**
47345002 TGAGCTTCCCGATTAATGGCTCTTT
1 TGAGCTTCCCGATTAATGGCTCTCA
* *
47345027 TGAGCTTTCCG-TTTATGGCTCTCA
1 TGAGCTTCCCGATTAATGGCTCTCA
*
47345051 TGAGCTTCCTGATTAATGGCTCTC-
1 TGAGCTTCCCGATTAATGGCTCTCA
* * * *
47345075 CGAAGCTTCCCG-GTATTGGCTCGCA
1 TG-AGCTTCCCGATTAATGGCTCTCA
* *
47345100 TGAGCTTCCCGATT-ATGGCTTTTA
1 TGAGCTTCCCGATTAATGGCTCTCA
*
47345124 TGAACTTCCCG-TTACATGGCTCAT-A
1 TGAGCTTCCCGATTA-ATGGCTC-TCA
*
47345149 TGAGCTTCCCG-TTATATGGCT-TAGA
1 TGAGCTTCCCGATTA-ATGGCTCT-CA
*
47345174 AGAGCTTCCCGATTA
1 TGAGCTTCCCGATTA
47345189 CATGCTCATA
Statistics
Matches: 150, Mismatches: 26, Indels: 21
0.76 0.13 0.11
Matches are distributed among these distances:
23 3 0.02
24 54 0.36
25 85 0.57
26 8 0.05
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (25 bp):
TGAGCTTCCCGATTAATGGCTCTCA
Found at i:47345132 original size:73 final size:74
Alignment explanation
Indices: 47345027--47345188 Score: 170
Period size: 73 Copynumber: 2.2 Consensus size: 74
47345017 ATGGCTCTTT
* * * * *
47345027 TGAGCTTTCCGTTTATGGCTCTCATGAGCTTCCTGATTA-ATGGCTC-TCCGAAGCTTCCCGGTA
1 TGAGCTTCCCGATTATGGCTCTCATGAACTTCCCG-TTACATGGCTCATACG-AGCTTCCCGGTA
*
47345090 T-TGGC-TCGCA
64 TATGGCTTAG-A
* * * *
47345100 TGAGCTTCCCGATTATGGCTTTTATGAACTTCCCGTTACATGGCTCATATGAGCTTCCCGTTATA
1 TGAGCTTCCCGATTATGGCTCTCATGAACTTCCCGTTACATGGCTCATACGAGCTTCCCGGTATA
47345165 TGGCTTAGA
66 TGGCTTAGA
*
47345174 AGAGCTTCCCGATTA
1 TGAGCTTCCCGATTA
47345189 CATGCTCATA
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
72 3 0.04
73 48 0.65
74 21 0.28
75 2 0.03
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.35
Consensus pattern (74 bp):
TGAGCTTCCCGATTATGGCTCTCATGAACTTCCCGTTACATGGCTCATACGAGCTTCCCGGTATA
TGGCTTAGA
Found at i:47345196 original size:50 final size:49
Alignment explanation
Indices: 47345099--47345200 Score: 134
Period size: 50 Copynumber: 2.1 Consensus size: 49
47345089 ATTGGCTCGC
** *
47345099 ATGAGCTTCCCGATTATGGCTTTTATGAACTTCCCGTTACATGGCTCAT
1 ATGAGCTTCCCGATTATGGCTTAGAAGAACTTCCCGTTACATGGCTCAT
* *
47345148 ATGAGCTTCCCGTTATATGGCTTAGAAGAGCTTCCCGATTACAT-GCTCAT
1 ATGAGCTTCCCGAT-TATGGCTTAGAAGAACTTCCCG-TTACATGGCTCAT
47345198 ATG
1 ATG
47345201 GGCATACCTG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
49 13 0.28
50 27 0.59
51 6 0.13
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.34
Consensus pattern (49 bp):
ATGAGCTTCCCGATTATGGCTTAGAAGAACTTCCCGTTACATGGCTCAT
Found at i:47346504 original size:39 final size:39
Alignment explanation
Indices: 47346407--47346506 Score: 155
Period size: 39 Copynumber: 2.6 Consensus size: 39
47346397 TTTTTACAAG
* * *
47346407 TTAAGCTTAGACGAGCAACCTGATGTGATGTGTTGTAGT
1 TTAAGCTTGGACGAGCAACTTGATGTGATGTGTTATAGT
* *
47346446 TTAAGCTTGGATGGGCAACTTGATGTGATGTGTTATAGT
1 TTAAGCTTGGACGAGCAACTTGATGTGATGTGTTATAGT
47346485 TTAAGCTTGGACGAGCAACTTG
1 TTAAGCTTGGACGAGCAACTTG
47346507 GTGTAATTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.34
Consensus pattern (39 bp):
TTAAGCTTGGACGAGCAACTTGATGTGATGTGTTATAGT
Found at i:47348665 original size:13 final size:13
Alignment explanation
Indices: 47348647--47348677 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
47348637 ATTTTAAACT
47348647 TTTAAAATTATTA
1 TTTAAAATTATTA
47348660 TTTAAAATTATTA
1 TTTAAAATTATTA
47348673 TTTAA
1 TTTAA
47348678 TGTTTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTAAAATTATTA
Found at i:47350684 original size:14 final size:14
Alignment explanation
Indices: 47350665--47350694 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
47350655 TGAGTCTTTC
47350665 TATTTTGATCAATT
1 TATTTTGATCAATT
47350679 TATTTTGATCAATT
1 TATTTTGATCAATT
47350693 TA
1 TA
47350695 GGTATCTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (14 bp):
TATTTTGATCAATT
Found at i:47354793 original size:23 final size:23
Alignment explanation
Indices: 47354767--47354811 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
47354757 AGCACATGCA
47354767 AGCTAATACTAGAGATGATGATG
1 AGCTAATACTAGAGATGATGATG
*
47354790 AGCTAATGCTAGAGATGATGAT
1 AGCTAATACTAGAGATGATGAT
47354812 TACTTAGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.27
Consensus pattern (23 bp):
AGCTAATACTAGAGATGATGATG
Found at i:47355420 original size:8 final size:8
Alignment explanation
Indices: 47355407--47355431 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
47355397 ATTTTACTAT
47355407 ATATAAAA
1 ATATAAAA
47355415 ATATAAAA
1 ATATAAAA
47355423 ATATAAAA
1 ATATAAAA
47355431 A
1 A
47355432 AAACAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
ATATAAAA
Found at i:47360887 original size:9 final size:9
Alignment explanation
Indices: 47360873--47360955 Score: 50
Period size: 9 Copynumber: 9.2 Consensus size: 9
47360863 TAGTTTAATT
47360873 AATTTTATA
1 AATTTTATA
*
47360882 AATTTTTTA
1 AATTTTATA
*
47360891 ATAATTTATTA
1 A-ATTTTA-TA
*
47360902 GATTTT-TA
1 AATTTTATA
*
47360910 TATTTT-TA
1 AATTTTATA
47360918 TAATATTTAT-
1 -AAT-TTTATA
47360928 AATTTTAATA
1 AATTTT-ATA
47360938 AA-TTTA-A
1 AATTTTATA
47360945 AATTTTATA
1 AATTTTATA
47360954 AA
1 AA
47360956 AAATATTAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
7 3 0.05
8 17 0.29
9 22 0.38
10 13 0.22
11 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (9 bp):
AATTTTATA
Found at i:47360926 original size:17 final size:16
Alignment explanation
Indices: 47360906--47360955 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
47360896 TTATTAGATT
47360906 TTTATATTTTTATAATA
1 TTTATATTTTTATAA-A
*
47360923 TTTATAATTTTAATAAA
1 TTTAT-ATTTTTATAAA
* *
47360940 TTTAAAATTTTATAAA
1 TTTATATTTTTATAAA
47360956 AAATATTAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 9 0.32
17 10 0.36
18 9 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTATATTTTTATAAA
Found at i:47372506 original size:29 final size:27
Alignment explanation
Indices: 47372451--47372512 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
47372441 AATTTCAAAA
* *
47372451 AAAATTATAAAACTATTTTTAAAATTT
1 AAAATTATAAAAATATTTTAAAAATTT
47372478 AAAATTATAAAAATATTCTTAAATAATTT
1 AAAATTATAAAAATATT-TTAAA-AATTT
*
47372507 TAAATT
1 AAAATT
47372513 CTTTTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 16 0.53
28 4 0.13
29 10 0.33
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (27 bp):
AAAATTATAAAAATATTTTAAAAATTT
Found at i:47374316 original size:22 final size:22
Alignment explanation
Indices: 47374269--47374317 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
47374259 TATATCTAAC
47374269 ATTTAGAATTTTGATTTCATAG
1 ATTTAGAATTTTGATTTCATAG
47374291 -TTTAGAATTTTTGGATTT-A-AG
1 ATTTAGAA-TTTT-GATTTCATAG
47374312 ATTTAG
1 ATTTAG
47374318 GATTATTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
21 9 0.38
22 10 0.42
23 5 0.21
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (22 bp):
ATTTAGAATTTTGATTTCATAG
Found at i:47376240 original size:24 final size:23
Alignment explanation
Indices: 47376213--47376275 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 23
47376203 GATTTGTCCT
47376213 TTTTTATT-TTTCTTTCATTTTAAG
1 TTTTTATTATTTCTTT--TTTTAAG
47376237 TTTTTATTTATTTACTTTTTTTAAG
1 TTTTTA-TTATTT-CTTTTTTTAAG
*
47376262 TTTTTTTTATTTCT
1 TTTTTATTATTTCT
47376276 CCTTATTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
23 2 0.06
24 12 0.34
25 14 0.40
26 3 0.09
27 4 0.11
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (23 bp):
TTTTTATTATTTCTTTTTTTAAG
Found at i:47376240 original size:25 final size:24
Alignment explanation
Indices: 47376212--47376275 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 24
47376202 TGATTTGTCC
47376212 TTTTTTATT-TTTCTTTCATTTTAAG
1 TTTTTTATTATTTCTTT--TTTTAAG
47376237 -TTTTTATTTATTTACTTTTTTTAAG
1 TTTTTTA-TTATTT-CTTTTTTTAAG
47376262 TTTTTT-TTATTTCT
1 TTTTTTATTATTTCT
47376276 CCTTATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
23 2 0.06
24 12 0.34
25 9 0.26
26 8 0.23
27 4 0.11
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (24 bp):
TTTTTTATTATTTCTTTTTTTAAG
Found at i:47376246 original size:4 final size:4
Alignment explanation
Indices: 47376239--47376315 Score: 50
Period size: 4 Copynumber: 18.5 Consensus size: 4
47376229 ATTTTAAGTT
* * *
47376239 TTTA TTTA TTTA CTTTT TTTAA GTT- TTT- TTTA TTTC TCCTTA TTTA
1 TTTA TTTA TTTA -TTTA TTT-A TTTA TTTA TTTA TTTA T--TTA TTTA
* *
47376285 TTTA TTTTA TTTA TTTG TTTA TTTG TTTA TT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TT
47376316 ATTGGTTTTG
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
3 5 0.09
4 40 0.70
5 9 0.16
6 3 0.05
ACGTcount: A:0.17, C:0.05, G:0.04, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:47376390 original size:34 final size:35
Alignment explanation
Indices: 47376340--47376420 Score: 112
Period size: 35 Copynumber: 2.3 Consensus size: 35
47376330 TTTTGAAATG
* *
47376340 TTTTATAATATTATTTTTTAAAA-TTTTAATTA-TA
1 TTTTTTAA-ATTATTTTTTAAAATTTTTAAATATTA
47376374 TATTTTTAAATTATTTTTTAAAATTTTTAAATATTA
1 T-TTTTTAAATTATTTTTTAAAATTTTTAAATATTA
47376410 TTTTTTAAATT
1 TTTTTTAAATT
47376421 TTAAATATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
34 15 0.36
35 24 0.57
36 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (35 bp):
TTTTTTAAATTATTTTTTAAAATTTTTAAATATTA
Found at i:47376397 original size:13 final size:12
Alignment explanation
Indices: 47376376--47376420 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
47376366 TAATTATATA
47376376 TTTTTAAATTAT
1 TTTTTAAATTAT
47376388 TTTTTAAA--AT
1 TTTTTAAATTAT
*
47376398 TTTTAAATATTAT
1 TTTTTAA-ATTAT
47376411 TTTTTAAATT
1 TTTTTAAATT
47376421 TTAAATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 8 0.29
11 1 0.04
12 11 0.39
13 8 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTTTAAATTAT
Found at i:47376408 original size:57 final size:56
Alignment explanation
Indices: 47376330--47376436 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 56
47376320 GTTTTGAAAA
*
47376330 TTTTGAAATGTTTTATAATATTATTTTTTAAAATTTTAATTATATATTTTTAAATTATT
1 TTTTAAAATGTTTTATAATATTATTTTTT-AAATTTTAA--ATATATTTTTAAATTATT
47376389 TTTTAAAAT-TTTTA-AATATTATTTTTTAAATTTTAAATATATTTTTAA
1 TTTTAAAATGTTTTATAATATTATTTTTTAAATTTTAAATATATTTTTAA
47376437 TAATATAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
54 12 0.26
56 9 0.19
57 13 0.28
58 5 0.11
59 8 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (56 bp):
TTTTAAAATGTTTTATAATATTATTTTTTAAATTTTAAATATATTTTTAAATTATT
Found at i:47376413 original size:23 final size:22
Alignment explanation
Indices: 47376375--47376434 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
47376365 TTAATTATAT
47376375 ATTTTT-AA-ATTATTTTTTAAA
1 ATTTTTAAATATTATTTTTT-AA
47376396 ATTTTTAAATATTATTTTTTAA
1 ATTTTTAAATATTATTTTTTAA
47376418 A-TTTTAAATA-TATTTTT
1 ATTTTTAAATATTATTTTT
47376435 AATAATATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.19
21 15 0.41
22 5 0.14
23 10 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTTTAAATATTATTTTTTAA
Found at i:47376715 original size:18 final size:18
Alignment explanation
Indices: 47376674--47376728 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
47376664 AAAATAAAAT
* *
47376674 AATTTGTTAAAAAAAGATT
1 AATTTGTT-AAAAAATATA
*
47376693 TATTTGTTAAAAAATATA
1 AATTTGTTAAAAAATATA
* *
47376711 AATTTATTTAAAAATATA
1 AATTTGTTAAAAAATATA
47376729 TATTAAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 23 0.77
19 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
AATTTGTTAAAAAATATA
Found at i:47376737 original size:14 final size:14
Alignment explanation
Indices: 47376715--47376761 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
47376705 AATATAAATT
* *
47376715 TATTTAAAAATATA
1 TATTAAAAAATAAA
47376729 TATTAAAAAATAAA
1 TATTAAAAAATAAA
* *
47376743 AAATAAAAAATAAA
1 TATTAAAAAATAAA
47376757 TATTA
1 TATTA
47376762 TAACTGGTCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TATTAAAAAATAAA
Found at i:47376750 original size:6 final size:7
Alignment explanation
Indices: 47376732--47376756 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
47376722 AAATATATAT
47376732 TAAAAAA
1 TAAAAAA
47376739 TAAAAAA
1 TAAAAAA
47376746 TAAAAAA
1 TAAAAAA
47376753 TAAA
1 TAAA
47376757 TATTATAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:47379431 original size:30 final size:30
Alignment explanation
Indices: 47379390--47379522 Score: 135
Period size: 30 Copynumber: 4.4 Consensus size: 30
47379380 GTCGCAGAGC
* *
47379390 AGTTCACATCACCTGGACATGGGTGGTTCA
1 AGTTCATATCACCTGGACATGGGTGGTTCG
* *
47379420 AGTTCATATCACCCGGACATGGGCTGCTT-G
1 AGTTCATATCACCTGGACATGGG-TGGTTCG
* *
47379450 AGTTCATATCACCTGGATATGGGTGATTCG
1 AGTTCATATCACCTGGACATGGGTGGTTCG
* * *
47379480 ATTTCATATCA-CTCGGACATAGGCGGTTCG
1 AGTTCATATCACCT-GGACATGGGTGGTTCG
* *
47379510 AGTTTATTTCACC
1 AGTTCATATCACC
47379523 CAGAGCAACC
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
29 6 0.07
30 73 0.87
31 5 0.06
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (30 bp):
AGTTCATATCACCTGGACATGGGTGGTTCG
Found at i:47379522 original size:60 final size:60
Alignment explanation
Indices: 47379390--47379503 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
47379380 GTCGCAGAGC
* * *
47379390 AGTTCACATCACCTGGACATGGGTGGTTCAAGTTCATATCACCCGGACATGGGCTGCTTG
1 AGTTCATATCACCTGGACATGGGTGATTCAAGTTCATATCACCCGGACATAGGCTGCTTG
* * * *
47379450 AGTTCATATCACCTGGATATGGGTGATTCGATTTCATATCACTCGGACATAGGC
1 AGTTCATATCACCTGGACATGGGTGATTCAAGTTCATATCACCCGGACATAGGC
47379504 GGTTCGAGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.29
Consensus pattern (60 bp):
AGTTCATATCACCTGGACATGGGTGATTCAAGTTCATATCACCCGGACATAGGCTGCTTG
Found at i:47382442 original size:81 final size:82
Alignment explanation
Indices: 47382345--47382498 Score: 231
Period size: 82 Copynumber: 1.9 Consensus size: 82
47382335 ATATTTAAAA
* * * * *
47382345 TTAAAAAAATTTAAAA-TATACATTTAACATA-TATAAAACAAATAATAAATTTGAAAGGTCATA
1 TTAAAAAAATTAAAAATTA-AAAATTAAAATATTATAAAACAAATAATAAATTTAAAAGGTCATA
47382408 TCTTTAAAAATAATATAT
65 TCTTTAAAAATAATATAT
*
47382426 TTAAAAAAATTAAAAATTAAAAATTAAAATATTATAAAACTAATAATAAATTTAAAAGGTCATAT
1 TTAAAAAAATTAAAAATTAAAAATTAAAATATTATAAAACAAATAATAAATTTAAAAGGTCATAT
47382491 CTTTAAAA
66 CTTTAAAA
47382499 TATTAAAATG
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 24 0.37
82 41 0.63
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (82 bp):
TTAAAAAAATTAAAAATTAAAAATTAAAATATTATAAAACAAATAATAAATTTAAAAGGTCATAT
CTTTAAAAATAATATAT
Found at i:47382447 original size:6 final size:7
Alignment explanation
Indices: 47382430--47382464 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
47382420 ATATATTTAA
47382430 AAAAATT
1 AAAAATT
47382437 AAAAATT
1 AAAAATT
47382444 AAAAATT
1 AAAAATT
47382451 AAAATATT
1 AAAA-ATT
47382459 ATAAAA
1 A-AAAA
47382465 CTAATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 18 0.69
8 5 0.19
9 3 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAAATT
Found at i:47382580 original size:14 final size:14
Alignment explanation
Indices: 47382561--47382587 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47382551 AACTTTTAAA
47382561 TTTTAAAAAATATT
1 TTTTAAAAAATATT
47382575 TTTTAAAAAATAT
1 TTTTAAAAAATAT
47382588 ATTTAAAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTTAAAAAATATT
Found at i:47382592 original size:13 final size:14
Alignment explanation
Indices: 47382562--47382595 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
47382552 ACTTTTAAAT
*
47382562 TTTAAAAAATATTT
1 TTTAAAAAATATTA
47382576 TTTAAAAAATA-TA
1 TTTAAAAAATATTA
47382589 TTTAAAA
1 TTTAAAA
47382596 TTTTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTAAAAAATATTA
Found at i:47382604 original size:22 final size:23
Alignment explanation
Indices: 47382575--47382618 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 23
47382565 AAAAAATATT
47382575 TTTTAAAAAAT-ATATT-TAAAA
1 TTTTAAAAAATAATATTATAAAA
47382596 TTTTAAAAAATAATATTATAAAA
1 TTTTAAAAAATAATATTATAAAA
47382619 CATTTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 11 0.52
22 5 0.24
23 5 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTTAAAAAATAATATTATAAAA
Found at i:47382730 original size:24 final size:24
Alignment explanation
Indices: 47382679--47382731 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
47382669 GGACAAATAA
* *
47382679 AAAAACTTAAAAAAGTAAATAAAT
1 AAAAACTTAAAAAAGAAAAAAAAT
47382703 AAAAACTT-AAAAAGAAAAAAAAT
1 AAAAACTTAAAAAAGAAAAAAAAT
47382726 GAAAAA
1 -AAAAA
47382732 GGACAAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (24 bp):
AAAAACTTAAAAAAGAAAAAAAAT
Found at i:47396681 original size:2 final size:2
Alignment explanation
Indices: 47396674--47396708 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
47396664 ATATCTTCTT
47396674 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47396709 TCCACTCACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47397117 original size:22 final size:23
Alignment explanation
Indices: 47397066--47397118 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
47397056 TTTAATTTAG
*
47397066 GTACTTTA-TAATTTATAAAATT
1 GTACTTTAGTAATTGATAAAATT
* *
47397088 TTAATTTAGTAA-TGATAAAATT
1 GTACTTTAGTAATTGATAAAATT
47397110 GTACTTTAG
1 GTACTTTAG
47397119 CCTCCTAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (23 bp):
GTACTTTAGTAATTGATAAAATT
Found at i:47399288 original size:3 final size:3
Alignment explanation
Indices: 47399282--47399308 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
47399272 GATGATGACT
47399282 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
47399309 AAGTCTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:47408508 original size:2 final size:2
Alignment explanation
Indices: 47408463--47408489 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47408453 GGGGAGGGGG
47408463 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
47408490 GAGGAAACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:47411280 original size:25 final size:24
Alignment explanation
Indices: 47411233--47411284 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
47411223 GTCATTAGGG
* *
47411233 TTACCGATTCTAGCTCTTATGAGC
1 TTACCGATACTAGCTCGTATGAGC
*
47411257 TTACCGATACTCAGCTCGTGTGAGC
1 TTACCGATACT-AGCTCGTATGAGC
47411282 TTA
1 TTA
47411285 TCGTTATTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (24 bp):
TTACCGATACTAGCTCGTATGAGC
Found at i:47411299 original size:25 final size:25
Alignment explanation
Indices: 47411252--47411299 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
47411242 CTAGCTCTTA
*
47411252 TGAGCTTACCGATACTCAGCTCGTG
1 TGAGCTTACCGATACTCAACTCGTG
* * *
47411277 TGAGCTTATCGTTATTCAACTCG
1 TGAGCTTACCGATACTCAACTCG
47411300 GAGGAGCTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (25 bp):
TGAGCTTACCGATACTCAACTCGTG
Found at i:47415743 original size:19 final size:20
Alignment explanation
Indices: 47415701--47415743 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
47415691 AAAGGTAAGT
* *
47415701 GTTTTTATATATTTTTTATA
1 GTTTTTATATATTATATATA
47415721 -TTTTTATATA-TATATATA
1 GTTTTTATATATTATATATA
47415739 GTTTT
1 GTTTT
47415744 ATTTTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
GTTTTTATATATTATATATA
Found at i:47415859 original size:40 final size:40
Alignment explanation
Indices: 47415814--47415891 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
47415804 GTAAAAAAGA
47415814 AAAGACCTTTTGAACGTTTTTTACTTCTCTTCTCTCTGCT
1 AAAGACCTTTTGAACGTTTTTTACTTCTCTTCTCTCTGCT
47415854 AAAGACCTTTTGAACGTTTTTTACTTCTCTTCTCTCTG
1 AAAGACCTTTTGAACGTTTTTTACTTCTCTTCTCTCTG
47415892 TTTTGTCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.18, C:0.24, G:0.10, T:0.47
Consensus pattern (40 bp):
AAAGACCTTTTGAACGTTTTTTACTTCTCTTCTCTCTGCT
Found at i:47417691 original size:52 final size:54
Alignment explanation
Indices: 47417628--47417831 Score: 219
Period size: 52 Copynumber: 3.9 Consensus size: 54
47417618 ACTGGCCACA
* * *
47417628 ACCCTAAATTTTTTT-A-TCT-GATAAAGGGTTGTCAGCCATCAGTGTCCCAAT
1 ACCCAAAATTTTTTTAATTCTAGATAAAGGGGTGTCAGCCATCAGTGTCCCAGT
* * * *
47417679 ACCCCAAAATTTTTTTAATTCTGGA-AAAGAGGT-TCTAACCATCAGTGCCCCAGT
1 A-CCCAAAATTTTTTTAATTCTAGATAAAGGGGTGTC-AGCCATCAGTGTCCCAGT
* * *
47417733 ACCCAAAATTTTTTTAA-T-TAGATAAAGGGGTGTCGGCCATTAGTGTCCCAGC
1 ACCCAAAATTTTTTTAATTCTAGATAAAGGGGTGTCAGCCATCAGTGTCCCAGT
* *
47417785 ACCCAAAATTTTTTT-ATTC-AGATAAAGGGGTGCCGGCCATCAGTGTC
1 ACCCAAAATTTTTTTAATTCTAGATAAAGGGGTGTCAGCCATCAGTGTC
47417832 ATGACACCCC
Statistics
Matches: 129, Mismatches: 15, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
51 5 0.04
52 76 0.59
53 21 0.16
54 25 0.19
55 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (54 bp):
ACCCAAAATTTTTTTAATTCTAGATAAAGGGGTGTCAGCCATCAGTGTCCCAGT
Found at i:47417840 original size:52 final size:50
Alignment explanation
Indices: 47417599--47417831 Score: 166
Period size: 52 Copynumber: 4.5 Consensus size: 50
47417589 TCGAAATACA
* * * *
47417599 AAAGGGGTGTCGGCCATGCACTGGCCA-CAACCCTAAATTTTTTTATCT-GAT
1 AAAGGGGTGCCGGCCAT-CAGTGTCCAGC-ACCCAAAATTTTTTTAT-TAGAT
* * * ** *
47417650 AAAGGGTTGTCAGCCATCAGTGTCCCAATACCCCAAAATTTTTTTAATTCTGGA-
1 AAAGGGGTGCCGGCCATCAGTGT-CCAGCA-CCCAAAATTTTTTT-A-T-TAGAT
* * *** * *
47417704 AAAGAGGTTCTAACCATCAGTGCCCCAGTACCCAAAATTTTTTTAATTAGAT
1 AAAGGGGTGCCGGCCATCAGTG-TCCAGCACCCAAAATTTTTTT-ATTAGAT
* *
47417756 AAAGGGGTGTCGGCCATTAGTGTCCCAGCACCCAAAATTTTTTTATTCAGAT
1 AAAGGGGTGCCGGCCATCAGTGT-CCAGCACCCAAAATTTTTTTATT-AGAT
47417808 AAAGGGGTGCCGGCCATCAGTGTC
1 AAAGGGGTGCCGGCCATCAGTGTC
47417832 ATGACACCCC
Statistics
Matches: 146, Mismatches: 26, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
50 4 0.03
51 26 0.18
52 73 0.50
53 17 0.12
54 24 0.16
55 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (50 bp):
AAAGGGGTGCCGGCCATCAGTGTCCAGCACCCAAAATTTTTTTATTAGAT
Found at i:47417849 original size:52 final size:50
Alignment explanation
Indices: 47417717--47417852 Score: 148
Period size: 52 Copynumber: 2.6 Consensus size: 50
47417707 GAGGTTCTAA
* * * *
47417717 CCATCAGTGCCCCAGTACCCAAAATTTTTTTAATTAGATAAAGGGGTGTCGG
1 CCATCAGTG-TCCAGCACCC-AAATTTTTTTTATTAGATAAAGGGGTGCCGG
* *
47417769 CCATTAGTGTCCCAGCACCCAAAATTTTTTTATTCAGATAAAGGGGTGCCGG
1 CCATCAGTGT-CCAGCACCCAAATTTTTTTTATT-AGATAAAGGGGTGCCGG
*
47417821 CCATCAGTGT-CATGACACCCCAATTTTTTTTA
1 CCATCAGTGTCCA-G-CACCCAAATTTTTTTTA
47417853 AATATACCAG
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
50 2 0.03
51 13 0.18
52 56 0.79
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (50 bp):
CCATCAGTGTCCAGCACCCAAATTTTTTTTATTAGATAAAGGGGTGCCGG
Found at i:47418908 original size:25 final size:27
Alignment explanation
Indices: 47418864--47418925 Score: 103
Period size: 25 Copynumber: 2.4 Consensus size: 27
47418854 ATAAAAAATA
47418864 ACCAAAATAT-TATAATTTTTTTATTT
1 ACCAAAATATATATAATTTTTTTATTT
47418890 ACCAAAATATATAT-A-TTTTTTATTT
1 ACCAAAATATATATAATTTTTTTATTT
47418915 ACCAAAATATA
1 ACCAAAATATA
47418926 CTAAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
25 21 0.60
26 11 0.31
27 3 0.09
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.47
Consensus pattern (27 bp):
ACCAAAATATATATAATTTTTTTATTT
Found at i:47419099 original size:4 final size:4
Alignment explanation
Indices: 47419090--47419228 Score: 76
Period size: 4 Copynumber: 34.0 Consensus size: 4
47419080 GAAGGAGAGG
*
47419090 GAAA GAAA GAAA GAAA GAAA GAAA GGAATGA GAAA AAAA GAAA G-AA -AAA
1 GAAA GAAA GAAA GAAA GAAA GAAA -GAA--A GAAA GAAA GAAA GAAA GAAA
* * * * *
47419139 GAAG GAAA GAAAA GGAAA GGAG GAGA GAAAA AAAA GAAA G-AA G-AA GAAGA
1 GAAA GAAA G-AAA -GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAA-A
*
47419189 GGAAA GGAGAA GAAA -AAA GAAA G-AA -AAA GAAG GAAA GAAA
1 -GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
47419229 AGGAGAGGAG
Statistics
Matches: 106, Mismatches: 14, Indels: 30
0.71 0.09 0.20
Matches are distributed among these distances:
3 17 0.16
4 61 0.58
5 18 0.17
6 9 0.08
7 1 0.01
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:47419123 original size:27 final size:28
Alignment explanation
Indices: 47419093--47419145 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
47419083 GGAGAGGGAA
* *
47419093 AGAAAGAAAGAAAGAAAGA-AAGGAATG
1 AGAAAAAAAGAAAGAAAAAGAAGGAATG
47419120 AGAAAAAAAGAAAGAAAAAGAAGGAA
1 AGAAAAAAAGAAAGAAAAAGAAGGAA
47419146 AGAAAAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (28 bp):
AGAAAAAAAGAAAGAAAAAGAAGGAATG
Found at i:47419140 original size:41 final size:40
Alignment explanation
Indices: 47419095--47419295 Score: 170
Period size: 41 Copynumber: 5.1 Consensus size: 40
47419085 AGAGGGAAAG
47419095 AAAGAAAGAAAG-AAA-GAAAGGAATGAGAAAAAAAGAAAGAA
1 AAAGAAAGAAAGAAAAGGAAAGG-A-GAGAAAAAAA-AAAGAA
* *
47419136 AAAGAAGGAAAGAAAAGGAAAGGAGGAGAGAAAAAAAAG--
1 AAAGAAAGAAAGAAAAGGAAAGGA-GAGAAAAAAAAAAGAA
* *
47419175 AAAG-AAG-AAGAAGAGGAAAGGAGAAGAAAAAAGAAAGAA
1 AAAGAAAGAAAGAAAAGGAAAGGAG-AGAAAAAAAAAAGAA
* * *
47419214 AAAGAAGGAAAGAAAAGGAGAGGAGAAGAGAAAAAAAAGAA
1 AAAGAAAGAAAGAAAAGGAAAGGAG-AGAAAAAAAAAAGAA
* * * *
47419255 GAAG-AAG-AAGAAGAGGGAAGGA-A-AAAAAAAAGAAAAA
1 AAAGAAAGAAAGAAAAGGAAAGGAGAGAAAAAAAA-AAGAA
47419292 AAAG
1 AAAG
47419296 GTAATTTTTT
Statistics
Matches: 132, Mismatches: 20, Indels: 20
0.77 0.12 0.12
Matches are distributed among these distances:
36 8 0.06
37 33 0.25
38 2 0.02
39 20 0.15
40 4 0.03
41 46 0.35
42 13 0.10
43 6 0.05
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (40 bp):
AAAGAAAGAAAGAAAAGGAAAGGAGAGAAAAAAAAAAGAA
Found at i:47419182 original size:3 final size:3
Alignment explanation
Indices: 47419176--47419268 Score: 54
Period size: 3 Copynumber: 32.3 Consensus size: 3
47419166 AAAAAAAAGA
* * *
47419176 AAG AAG AAG AAG AGG AAAG GAG AAG AA- AA- AAG AAAG AAA AAG AAG
1 AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG
* * * * *
47419221 GA- AAG AA- AAG GAG -AG GAG AAG -AG AAA AAA AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
47419265 AAG A
1 AAG A
47419269 GGGAAGGAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
2 11 0.15
3 55 0.77
4 5 0.07
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:47419217 original size:78 final size:76
Alignment explanation
Indices: 47419095--47419295 Score: 282
Period size: 78 Copynumber: 2.6 Consensus size: 76
47419085 AGAGGGAAAG
*
47419095 AAAGAAAGAAAGAAAGAA-AGGAATGAG-AAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAG
1 AAAGAAAG-AAG-AAGAAGAGGAAGGAGAAAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAG
*
47419158 GAGGAGAGAAAAA
64 GAGAAGAGAAAAA
*
47419171 AAAGAAAGAAGAAGAAGAGGAAAGGAGAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAGAG
1 AAAGAAAGAAGAAGAAGAGG-AAGGAGAA-AAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAG
47419236 GAGAAGAGAAAAA
64 GAGAAGAGAAAAA
*
47419249 AAAGAAGAAGAAGAAGAAGAGGGAAGGAAAAAAAAAAGAAA-AAAAAG
1 AAAG-A-AAGAAGAAGAAGA-GGAAGGAGAAAAAAAAGAAAGAAAAAG
47419296 GTAATTTTTT
Statistics
Matches: 114, Mismatches: 4, Indels: 12
0.88 0.03 0.09
Matches are distributed among these distances:
74 5 0.04
75 6 0.05
76 13 0.11
77 1 0.01
78 56 0.49
79 11 0.10
80 20 0.18
81 2 0.02
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (76 bp):
AAAGAAAGAAGAAGAAGAGGAAGGAGAAAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGA
GAAGAGAAAAA
Found at i:47420362 original size:17 final size:17
Alignment explanation
Indices: 47420318--47420352 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
47420308 AGTTAAAATA
*
47420318 AAAAGAATAAAAGAAAC
1 AAAAGAAGAAAAGAAAC
47420335 AAAAGAAGAAAAGAAAC
1 AAAAGAAGAAAAGAAAC
47420352 A
1 A
47420353 GAATAGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.77, C:0.06, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAAGAAGAAAAGAAAC
Found at i:47421272 original size:24 final size:27
Alignment explanation
Indices: 47421245--47421313 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
47421235 GTGAATTTGT
*
47421245 GAAATAATTATTG-ATTG-AAATGTG-
1 GAAATAATGATTGAATTGAAAATGTGA
47421269 GAAA-AATGATTGAATTGAAAATGTGA
1 GAAATAATGATTGAATTGAAAATGTGA
**
47421295 GAAATTGTGATTGAATTGA
1 GAAATAATGATTGAATTGA
47421314 GAATATATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 7 0.18
24 8 0.21
25 7 0.18
26 4 0.11
27 12 0.32
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (27 bp):
GAAATAATGATTGAATTGAAAATGTGA
Found at i:47422645 original size:27 final size:27
Alignment explanation
Indices: 47422615--47422670 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
47422605 AAAGAGGGTG
*
47422615 ATGGAGGGGAATAAAAAGGCGGCACCA
1 ATGGAGAGGAATAAAAAGGCGGCACCA
47422642 ATGGAGAGGAATAAAAAGGCGGCACCA
1 ATGGAGAGGAATAAAAAGGCGGCACCA
47422669 AT
1 AT
47422671 ATGTGGCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.34, T:0.09
Consensus pattern (27 bp):
ATGGAGAGGAATAAAAAGGCGGCACCA
Found at i:47427032 original size:10 final size:11
Alignment explanation
Indices: 47427015--47427043 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
47427005 TAAAAAATAC
47427015 CTTCTTTTTCT
1 CTTCTTTTTCT
47427026 C-TCTTTTTCT
1 CTTCTTTTTCT
47427036 CTTCTTTT
1 CTTCTTTT
47427044 CCACAGCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:47427243 original size:27 final size:27
Alignment explanation
Indices: 47427205--47427265 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
47427195 TTTTTTTGGT
*
47427205 ATATTTTGGTAAATAAAAAAAATTATA
1 ATATTTTAGTAAATAAAAAAAATTATA
*
47427232 ATATTTTAGTAAATAAAAAAAGTTATA
1 ATATTTTAGTAAATAAAAAAAATTATA
47427259 ATATTTT
1 ATATTTT
47427266 GGTTATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (27 bp):
ATATTTTAGTAAATAAAAAAAATTATA
Found at i:47427790 original size:30 final size:30
Alignment explanation
Indices: 47427754--47427810 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
47427744 CTTTTTTTGC
* * *
47427754 TGTTTTTTTATTATTTTGTTGCTATTTTCT
1 TGTTTTTTCACTATTTTGTTACTATTTTCT
47427784 TGTTTTTTCACTATTTTGTTACTATTT
1 TGTTTTTTCACTATTTTGTTACTATTT
47427811 CACAATTATA
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:0.12, C:0.09, G:0.09, T:0.70
Consensus pattern (30 bp):
TGTTTTTTCACTATTTTGTTACTATTTTCT
Found at i:47427997 original size:34 final size:34
Alignment explanation
Indices: 47427954--47428019 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
47427944 AGTAAAATAT
*
47427954 TTTTCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCGTAAAATGATTTACGGGAAAATATTTTAC
*
47427987 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACGGGAAAATATTTT
47428020 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:47433435 original size:15 final size:15
Alignment explanation
Indices: 47433405--47433444 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
47433395 TATGTTAACT
47433405 TAATATATATAAGTTA
1 TAATA-ATATAAGTTA
*
47433421 TAATAATATATGTTA
1 TAATAATATAAGTTA
47433436 TAATAATAT
1 TAATAATAT
47433445 TTAAAACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (15 bp):
TAATAATATAAGTTA
Found at i:47436962 original size:2 final size:2
Alignment explanation
Indices: 47436955--47437003 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
47436945 NNNNNNNNNN
47436955 TA TA TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47436998 TA TA TA
1 TA TA TA
47437004 CGTATTCAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:47437975 original size:43 final size:42
Alignment explanation
Indices: 47437919--47438047 Score: 138
Period size: 43 Copynumber: 3.0 Consensus size: 42
47437909 ATATCGTATA
*
47437919 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATAACG
1 ATGCCAACATCCCAGACGTGGTCTTACATGTAA-CACATAACG
**
47437962 ATGCC-ACTATCCCAGACAG-GGTCTTACATGTAAACACA-AGTTG
1 ATGCCAAC-ATCCCAGAC-GTGGTCTTACATGT-AACACATA-ACG
* *
47438005 ATGCCAACGTCCCAGACGTGGTCTTACATGATAACATATAACG
1 ATGCCAACATCCCAGACGTGGTCTTACATG-TAACACATAACG
47438048 GAATCCTATG
Statistics
Matches: 71, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
42 4 0.06
43 60 0.85
44 7 0.10
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (42 bp):
ATGCCAACATCCCAGACGTGGTCTTACATGTAACACATAACG
Found at i:47439173 original size:13 final size:13
Alignment explanation
Indices: 47439155--47439179 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47439145 CTCAAACAAT
47439155 AAATTTTCACACG
1 AAATTTTCACACG
47439168 AAATTTTCACAC
1 AAATTTTCACAC
47439180 ATATTGATTC
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:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:47440878 original size:51 final size:50
Alignment explanation
Indices: 47440713--47440895 Score: 206
Period size: 51 Copynumber: 3.6 Consensus size: 50
47440703 AGTGAAAGTG
*
47440713 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGGT
* * * * ** * *
47440764 A-GGTCGCATGTATAGTACTATGTGTAGGCTACTATGCATACCAGATAGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
* * * * *
47440813 TTCGATCACGTGTGTAGTACTATGTACAGGCTACTACGTGTATCGGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
47440864 AATGGTCACATGTGTAGTACTATGTGCAGGCT
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCT
47440896 GCTATGTGAA
Statistics
Matches: 103, Mismatches: 26, Indels: 6
0.76 0.19 0.04
Matches are distributed among these distances:
49 4 0.04
50 35 0.34
51 63 0.61
52 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
Found at i:47440961 original size:45 final size:45
Alignment explanation
Indices: 47440905--47440999 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
47440895 TGCTATGTGA
* *
47440905 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
*
47440950 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
47440995 ACCGA
1 ACCGA
47441000 GTATCTGTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:47444266 original size:22 final size:24
Alignment explanation
Indices: 47444222--47444272 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
47444212 TATTAATTTT
47444222 AAAATAATAATAGAATAATAATAA
1 AAAATAATAATAGAATAATAATAA
47444246 AAAATAA-AATCAGAA-AA-AATAA
1 AAAATAATAAT-AGAATAATAATAA
47444268 AAAAT
1 AAAAT
47444273 TTAATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 10 0.38
23 5 0.19
24 11 0.42
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (24 bp):
AAAATAATAATAGAATAATAATAA
Found at i:47444347 original size:30 final size:29
Alignment explanation
Indices: 47444278--47444355 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
47444268 AAAATTTAAT
47444278 AATTACATTTT-AGCCCTAACTTTTTCAAA
1 AATTACATTTTGA-CCCTAACTTTTTCAAA
* *
47444307 AATTATATTTTGACCCTAACTTTTCCTC-TA
1 AATTACATTTTGACCCTAACTTTT--TCAAA
*
47444337 AATTACATTTTGGCCCTAA
1 AATTACATTTTGACCCTAA
47444356 GAGTTTTGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 21 0.50
30 19 0.45
31 2 0.05
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.42
Consensus pattern (29 bp):
AATTACATTTTGACCCTAACTTTTTCAAA
Found at i:47444948 original size:17 final size:18
Alignment explanation
Indices: 47444916--47444950 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
47444906 AGAGTTTTGA
47444916 AAAAAAAGAGTAGGGAAAG
1 AAAAAAAGAG-AGGGAAAG
47444935 AAAAAAAGAG-GGGAAA
1 AAAAAAAGAGAGGGAAA
47444951 CACCGGTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (18 bp):
AAAAAAAGAGAGGGAAAG
Found at i:47445066 original size:17 final size:16
Alignment explanation
Indices: 47445053--47445087 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
47445043 GAAAAAAAGG
47445053 GAAAATAAATAAAAAAA
1 GAAAATAAA-AAAAAAA
47445070 GAAAATAAAAAAAGAAA
1 GAAAATAAAAAAA-AAA
47445087 G
1 G
47445088 GGAAACAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (16 bp):
GAAAATAAAAAAAAAA
Found at i:47445079 original size:12 final size:13
Alignment explanation
Indices: 47445059--47445086 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
47445049 AAGGGAAAAT
47445059 AAATAAAAAAAGA
1 AAATAAAAAAAGA
47445072 AAATAAAAAAAGA
1 AAATAAAAAAAGA
47445085 AA
1 AA
47445087 GGGAAACAAT
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:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (13 bp):
AAATAAAAAAAGA
Found at i:47457772 original size:93 final size:93
Alignment explanation
Indices: 47457661--47457849 Score: 378
Period size: 93 Copynumber: 2.0 Consensus size: 93
47457651 CAATTAGTAC
47457661 AGTTTATTAGTTAAAGTCTCCCTTGTTTCACTGATCGACTGTCCTAACCTCTCGTCACTAAAATT
1 AGTTTATTAGTTAAAGTCTCCCTTGTTTCACTGATCGACTGTCCTAACCTCTCGTCACTAAAATT
47457726 AAATTATCTCATTGTACAGACTTCATAT
66 AAATTATCTCATTGTACAGACTTCATAT
47457754 AGTTTATTAGTTAAAGTCTCCCTTGTTTCACTGATCGACTGTCCTAACCTCTCGTCACTAAAATT
1 AGTTTATTAGTTAAAGTCTCCCTTGTTTCACTGATCGACTGTCCTAACCTCTCGTCACTAAAATT
47457819 AAATTATCTCATTGTACAGACTTCATAT
66 AAATTATCTCATTGTACAGACTTCATAT
47457847 AGT
1 AGT
47457850 GTTCTCACTT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 96 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (93 bp):
AGTTTATTAGTTAAAGTCTCCCTTGTTTCACTGATCGACTGTCCTAACCTCTCGTCACTAAAATT
AAATTATCTCATTGTACAGACTTCATAT
Found at i:47459059 original size:27 final size:27
Alignment explanation
Indices: 47459021--47459076 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
47459011 AAACTAGACC
47459021 CAATAAAATATATGATGGAATCACCTA
1 CAATAAAATATATGATGGAATCACCTA
*
47459048 CAATAAAGTATATGATGGAATCACCTA
1 CAATAAAATATATGATGGAATCACCTA
47459075 CA
1 CA
47459077 CTTTCAGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.25
Consensus pattern (27 bp):
CAATAAAATATATGATGGAATCACCTA
Found at i:47462115 original size:77 final size:77
Alignment explanation
Indices: 47461906--47462423 Score: 718
Period size: 76 Copynumber: 6.7 Consensus size: 77
47461896 TTTCAAAAAA
* *
47461906 ATCAACTCATAATCCAAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTTCAATTTC
1 ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTTTTCAATTTC
*
47461971 TTTTTTTTTCAAAG
66 --TATTTTTCAAAG
* * * * *
47461985 ATCAACTCATAATTCGAGAGGTGAGTTGAGCTTCAGGTCACACGTCGAGGTATTTTTTCAATTTC
1 ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTTTTCAATTTC
*
47462050 TTTTTTTCAAAG
66 TATTTTTCAAAG
* * *
47462062 ATCAACTCATAATCCAAGAGGTGAGTTGAGCCTCGAGTCGCACGCCGAAGTATTTTTTCAATTTC
1 ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTTTTCAATTTC
*
47462127 TGTTTTTCAAAG
66 TATTTTTCAAAG
* **
47462139 ATCAACTCATAATCTGAGAGGTGAGTTGAGCCTCGGGTTACACGCCGAGGTA-TTTTTCAATTTC
1 ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTTTTCAATTTC
47462203 TATTTTTCAAAG
66 TATTTTTCAAAG
* * * * *
47462215 ATCAACTTATAATTCGAGAGGTGAGTTGAGTCTTGGGTCGCACGCCGAGGTA-TTTTTCAATCTC
1 ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTTTTCAATTTC
47462279 TATTTTTCAAAG
66 TATTTTTCAAAG
* * *
47462291 GTCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAAGCA-TTTTTCAATTTC
1 ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTTTTCAATTTC
*
47462355 TGTTTTTCAAAG
66 TATTTTTCAAAG
* * * * * *
47462367 ATCAACTCATAATCCGATAAGTGACTTGAGCCTCGGGTTGCATGCCAAGGTATTTTT
1 ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTTT
47462424 AAATTTCAGT
Statistics
Matches: 391, Mismatches: 47, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
76 201 0.51
77 130 0.33
79 60 0.15
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (77 bp):
ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTTTTCAATTTC
TATTTTTCAAAG
Found at i:47462989 original size:29 final size:30
Alignment explanation
Indices: 47462951--47463051 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
47462941 AAAATTTACT
* *
47462951 AATTATATTTTG-GCTCTAACTTTTTCTAA
1 AATTACATTTTGACCTCTAACTTTTTCTAA
* * *
47462980 AATTACATTTTGCCCCCTAACTTTTCCTAA
1 AATTACATTTTGACCTCTAACTTTTTCTAA
*
47463010 AATTATATTTTGACCTCTAAC-TTTTCTTAA
1 AATTACATTTTGACCTCTAACTTTTTC-TAA
47463040 AATTACATTTTG
1 AATTACATTTTG
47463052 GCCCCGTGAG
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 15 0.25
30 46 0.75
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.48
Consensus pattern (30 bp):
AATTACATTTTGACCTCTAACTTTTTCTAA
Found at i:47463774 original size:6 final size:6
Alignment explanation
Indices: 47463763--47463850 Score: 108
Period size: 6 Copynumber: 14.8 Consensus size: 6
47463753 AGGGTTAGAG
** * * *
47463763 AGAAAA AG-AAA AGAGGA GGAAAA AGAAAC A-AAAA AGAAAA GAAAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA -AGAAAA
47463810 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA
47463851 GGGAAACAGT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
5 9 0.13
6 55 0.80
7 5 0.07
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:47467980 original size:12 final size:11
Alignment explanation
Indices: 47467936--47467987 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
47467926 ACCCTAATTA
47467936 TTATAATTTTT
1 TTATAATTTTT
*
47467947 TTATAA--TAT
1 TTATAATTTTT
*
47467956 TTATAA-GTTT
1 TTATAATTTTT
47467966 TTATGAATTTTT
1 TTAT-AATTTTT
47467978 TTATAATTTT
1 TTATAATTTT
47467988 ATAAGTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 8 0.23
10 6 0.17
11 14 0.40
12 7 0.20
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (11 bp):
TTATAATTTTT
Found at i:47467987 original size:9 final size:9
Alignment explanation
Indices: 47467930--47468154 Score: 82
Period size: 10 Copynumber: 22.9 Consensus size: 9
47467920 ACATTAACCC
*
47467930 TAATTATTA
1 TAATTTTTA
47467939 TAATTTTTTTA
1 TAA--TTTTTA
*
47467950 TAATATTTA
1 TAATTTTTA
47467959 TAAGTTTTTA
1 TAA-TTTTTA
47467969 TGAATTTTTTTA
1 T-AA--TTTTTA
47467981 TAA-TTTTA
1 TAATTTTTA
*
47467989 TAAGTTTATA
1 TAA-TTTTTA
* *
47467999 GAAAGTTTTA
1 -TAATTTTTA
47468009 -AATATTTTAA
1 TAAT-TTTT-A
*
47468019 TACACTTTTA
1 TA-ATTTTTA
*
47468029 T-TTTTTTA
1 TAATTTTTA
*
47468037 GAATTTATTA
1 TAATTT-TTA
47468047 TAATTTTTA
1 TAATTTTTA
*
47468056 TAAACTTTTA
1 T-AATTTTTA
47468066 TGAAATTTTTAA
1 T--AATTTTT-A
*
47468078 TAATATTTA
1 TAATTTTTA
*
47468087 TAAGTTTTA
1 TAATTTTTA
*
47468096 -AATATTTA
1 TAATTTTTA
47468104 T-ATTTTTAA
1 TAATTTTT-A
*
47468113 TGATTTTTA
1 TAATTTTTA
47468122 TGAAATTATTTTTA
1 T---A--ATTTTTA
47468136 TAATTTTTTAA
1 TAA-TTTTT-A
47468147 TAATTTTT
1 TAATTTTT
47468155 TTAAATAAAA
Statistics
Matches: 165, Mismatches: 24, Indels: 53
0.68 0.10 0.22
Matches are distributed among these distances:
8 26 0.16
9 35 0.21
10 55 0.33
11 31 0.19
12 10 0.06
14 8 0.05
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (9 bp):
TAATTTTTA
Found at i:47467989 original size:30 final size:30
Alignment explanation
Indices: 47467936--47467995 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
47467926 ACCCTAATTA
47467936 TTATAATTTTTTTATAATATTTATAAGTTT
1 TTATAATTTTTTTATAATATTTATAAGTTT
47467966 TTATGAATTTTTTTATAAT-TTTATAAGTTT
1 TTAT-AATTTTTTTATAATATTTATAAGTTT
47467996 ATAGAAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (30 bp):
TTATAATTTTTTTATAATATTTATAAGTTT
Found at i:47468118 original size:16 final size:17
Alignment explanation
Indices: 47468078--47468118 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
47468068 AAATTTTTAA
47468078 TAATATTTATAAGTTTT
1 TAATATTTATAAGTTTT
*
47468095 AAATATTTAT-A-TTTT
1 TAATATTTATAAGTTTT
47468110 TAATGATTT
1 TAAT-ATTT
47468119 TTATGAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 7 0.33
16 5 0.24
17 9 0.43
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
TAATATTTATAAGTTTT
Found at i:47473274 original size:8 final size:8
Alignment explanation
Indices: 47473257--47473296 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
47473247 TCATCCCATC
47473257 AAAAATTTT
1 AAAAA-TTT
47473266 AAAAATTT
1 AAAAATTT
*
47473274 AAAAATAT
1 AAAAATTT
*
47473282 AAAAATAT
1 AAAAATTT
47473290 AAAAATT
1 AAAAATT
47473297 ATTTTGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 24 0.83
9 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAAATTT
Found at i:47476506 original size:30 final size:29
Alignment explanation
Indices: 47476473--47476528 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
47476463 AAAGGCCATT
47476473 TTTTTTCAA-AATTTACCGAAATGGGCCGG
1 TTTTTT-AATAATTTACCGAAATGGGCCGG
* *
47476502 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAATAATTTACCGAAATGGGCC
47476529 ATTTTCCGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (29 bp):
TTTTTTAATAATTTACCGAAATGGGCCGG
Found at i:47485509 original size:14 final size:14
Alignment explanation
Indices: 47485487--47485530 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
47485477 CTAAATCTTG
*
47485487 AACTCTGAACCTCA
1 AACTATGAACCTCA
* *
47485501 AACTTTGAACCTAA
1 AACTATGAACCTCA
*
47485515 AACTATAAACCTCA
1 AACTATGAACCTCA
47485529 AA
1 AA
47485531 TCATGAACAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.45, C:0.27, G:0.05, T:0.23
Consensus pattern (14 bp):
AACTATGAACCTCA
Found at i:47485662 original size:29 final size:29
Alignment explanation
Indices: 47485625--47485682 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
47485615 AAGTTTATAC
47485625 AATACGAACAAGAATTAATTAAAATTTAT
1 AATACGAACAAGAATTAATTAAAATTTAT
47485654 AATACGAACAAGAATTAATTAAAATTTAT
1 AATACGAACAAGAATTAATTAAAATTTAT
47485683 CTAAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (29 bp):
AATACGAACAAGAATTAATTAAAATTTAT
Found at i:47486210 original size:16 final size:16
Alignment explanation
Indices: 47486189--47486219 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47486179 ATATTATGAA
47486189 AAAAATAAAAATATTC
1 AAAAATAAAAATATTC
*
47486205 AAAAATACAAATATT
1 AAAAATAAAAATATT
47486220 TTTTCTTTTT
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:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATAAAAATATTC
Found at i:47486388 original size:12 final size:12
Alignment explanation
Indices: 47486373--47486407 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
47486363 TTTTTACTTA
47486373 AATTTTTTTTAT
1 AATTTTTTTTAT
47486385 AATTTTTGTTTAT
1 AATTTTT-TTTAT
*
47486398 GATTTTTTTT
1 AATTTTTTTT
47486408 GAACCTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (12 bp):
AATTTTTTTTAT
Found at i:47488546 original size:14 final size:14
Alignment explanation
Indices: 47488524--47488567 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
47488514 CTAAATCTTG
*
47488524 AACTCTGAACCTCA
1 AACTATGAACCTCA
* *
47488538 AACTTTGAACCTAA
1 AACTATGAACCTCA
*
47488552 AACTATAAACCTCA
1 AACTATGAACCTCA
47488566 AA
1 AA
47488568 TCATGAACAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.45, C:0.27, G:0.05, T:0.23
Consensus pattern (14 bp):
AACTATGAACCTCA
Found at i:47488882 original size:7 final size:7
Alignment explanation
Indices: 47488870--47488902 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
47488860 GTTATACACA
47488870 TATAAGG
1 TATAAGG
47488877 TATAAGG
1 TATAAGG
47488884 TATAAGG
1 TATAAGG
47488891 TATAAGG
1 TATAAGG
47488898 TATAA
1 TATAA
47488903 TATTATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.30
Consensus pattern (7 bp):
TATAAGG
Found at i:47490160 original size:13 final size:14
Alignment explanation
Indices: 47490138--47490168 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
47490128 AGTATATATA
47490138 AAAAAGTAAAAAAC
1 AAAAAGTAAAAAAC
47490152 AAAAA-TAAAAAAC
1 AAAAAGTAAAAAAC
47490165 AAAA
1 AAAA
47490169 CATATGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.84, C:0.06, G:0.03, T:0.06
Consensus pattern (14 bp):
AAAAAGTAAAAAAC
Found at i:47490946 original size:5 final size:5
Alignment explanation
Indices: 47490938--47490971 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
47490928 TCGTTATTTT
*
47490938 AAATA AAATA AAATGA AAATA AAAGA AAATA AAA
1 AAATA AAATA AAAT-A AAATA AAATA AAATA AAA
47490972 AAATATGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (5 bp):
AAATA
Found at i:47490972 original size:16 final size:16
Alignment explanation
Indices: 47490938--47490972 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
47490928 TCGTTATTTT
* *
47490938 AAATAAAATAAAATGA
1 AAATAAAAGAAAATAA
47490954 AAATAAAAGAAAATAA
1 AAATAAAAGAAAATAA
47490970 AAA
1 AAA
47490973 AATATGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (16 bp):
AAATAAAAGAAAATAA
Found at i:47490983 original size:26 final size:26
Alignment explanation
Indices: 47490938--47490987 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
47490928 TCGTTATTTT
47490938 AAATAAAATAAAATGAAAATAAAAGA
1 AAATAAAATAAAATGAAAATAAAAGA
*
47490964 AAATAAAA-AAATATGGAAATAAAA
1 AAATAAAATAAA-ATGAAAATAAAA
47490988 ACAATAGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (26 bp):
AAATAAAATAAAATGAAAATAAAAGA
Found at i:47491953 original size:15 final size:15
Alignment explanation
Indices: 47491935--47491965 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
47491925 CAAACTACCT
47491935 GCTAATAGACTAACA
1 GCTAATAGACTAACA
47491950 GCTAATAGACTAACA
1 GCTAATAGACTAACA
47491965 G
1 G
47491966 AATTTAGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (15 bp):
GCTAATAGACTAACA
Found at i:47497323 original size:16 final size:16
Alignment explanation
Indices: 47497302--47497337 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
47497292 AAACAAATTA
*
47497302 ATATAAGCAAATATTT
1 ATATAAACAAATATTT
47497318 ATATAAACAAATATTT
1 ATATAAACAAATATTT
47497334 ATAT
1 ATAT
47497338 TTATGTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.39
Consensus pattern (16 bp):
ATATAAACAAATATTT
Found at i:47500764 original size:31 final size:31
Alignment explanation
Indices: 47500707--47500765 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
47500697 AACAACTCAT
*
47500707 TGACTTAAATAAAAGCTTTTGAATAGTTCAG
1 TGACTTAAATAAAAGCTTTAGAATAGTTCAG
47500738 TGACTTAAATGAAAA-CTTTCAG-ATAGTT
1 TGACTTAAAT-AAAAGCTTT-AGAATAGTT
47500766 AAATGATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (31 bp):
TGACTTAAATAAAAGCTTTAGAATAGTTCAG
Found at i:47504518 original size:19 final size:18
Alignment explanation
Indices: 47504491--47504529 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
47504481 ATTAAAATTT
*
47504491 TAAAAATCAAAATTTAAAC
1 TAAAAATC-AAATTCAAAC
*
47504510 TAAAGATCAAATTCAAAC
1 TAAAAATCAAATTCAAAC
47504528 TA
1 TA
47504530 TTTATACGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.26
Consensus pattern (18 bp):
TAAAAATCAAATTCAAAC
Found at i:47506382 original size:16 final size:16
Alignment explanation
Indices: 47506361--47506399 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
47506351 TTATGTGTAT
47506361 GGTAAG-CAAATAATAA
1 GGTAAGTCAAAT-ATAA
*
47506377 GGTAAGTGAAATATAA
1 GGTAAGTCAAATATAA
47506393 GGTAAGT
1 GGTAAGT
47506400 ATTATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.49, C:0.03, G:0.26, T:0.23
Consensus pattern (16 bp):
GGTAAGTCAAATATAA
Found at i:47506509 original size:36 final size:38
Alignment explanation
Indices: 47506471--47506549 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 38
47506461 ATATTGACTT
* *
47506471 GAAAATGGAAAAGT-AAATTTGAATTGAATTGTG-A-TT
1 GAAAATGAAAAAGTGAAA-TTGAATTGAAATGTGAATTT
*
47506507 GAAAGTGAAAAAGTGAAATTGAATTGAAATGTGAATTT
1 GAAAATGAAAAAGTGAAATTGAATTGAAATGTGAATTT
47506545 GAAAA
1 GAAAA
47506550 GTATGTGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 26 0.72
37 4 0.11
38 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.29
Consensus pattern (38 bp):
GAAAATGAAAAAGTGAAATTGAATTGAAATGTGAATTT
Found at i:47506799 original size:20 final size:22
Alignment explanation
Indices: 47506743--47506805 Score: 94
Period size: 23 Copynumber: 2.9 Consensus size: 22
47506733 CTTTGCCTAC
47506743 CAGGCACTTTATGTGTCGTACAT
1 CAGGCACTTTATGTGTCGTA-AT
*
47506766 CAGGCACTTTATGTGTCGT-TT
1 CAGGCACTTTATGTGTCGTAAT
47506787 CAGGCAC-TTATGTGTCGTA
1 CAGGCACTTTATGTGTCGTA
47506806 TACTGATTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
20 11 0.29
21 8 0.21
23 19 0.50
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.37
Consensus pattern (22 bp):
CAGGCACTTTATGTGTCGTAAT
Found at i:47508864 original size:17 final size:17
Alignment explanation
Indices: 47508842--47508876 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
47508832 AAATACATAG
47508842 ATAAATACTA-TAATAAT
1 ATAAATA-TAGTAATAAT
47508859 ATAAATATAGTAATAAT
1 ATAAATATAGTAATAAT
47508876 A
1 A
47508877 AGAATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (17 bp):
ATAAATATAGTAATAAT
Found at i:47509844 original size:2 final size:2
Alignment explanation
Indices: 47509839--47509884 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
47509829 GTTTATGCTT
47509839 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47509881 TA TA
1 TA TA
47509885 ATNNNNNNNN
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47521981 original size:16 final size:16
Alignment explanation
Indices: 47521960--47521990 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
47521950 ATAACTAATC
47521960 GGTATTAATCATTCCG
1 GGTATTAATCATTCCG
47521976 GGTATTAATCATTCC
1 GGTATTAATCATTCC
47521991 AGTTTTGAAC
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:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (16 bp):
GGTATTAATCATTCCG
Found at i:47522189 original size:41 final size:41
Alignment explanation
Indices: 47522133--47522215 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
47522123 AAAAAAGAAT
47522133 GAATCAAACAATCCCAGTTAGAAGAAGATAGGTATAACCCA
1 GAATCAAACAATCCCAGTTAGAAGAAGATAGGTATAACCCA
*
47522174 GAATCAAACAATCCCAGTTAGAAGATGATAGGTATAACCCA
1 GAATCAAACAATCCCAGTTAGAAGAAGATAGGTATAACCCA
47522215 G
1 G
47522216 CTAAGCTTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.18
Consensus pattern (41 bp):
GAATCAAACAATCCCAGTTAGAAGAAGATAGGTATAACCCA
Found at i:47527541 original size:14 final size:14
Alignment explanation
Indices: 47527522--47527552 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
47527512 TATTTATTGT
47527522 TATTTGAAGAATAA
1 TATTTGAAGAATAA
47527536 TATTTGAAGAATAA
1 TATTTGAAGAATAA
47527550 TAT
1 TAT
47527553 GGAATACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (14 bp):
TATTTGAAGAATAA
Done.