Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005996.1 Corchorus capsularis cultivar CVL-1 contig06014, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 128247
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:4624 original size:21 final size:21
Alignment explanation
Indices: 4598--4639 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4588 GTGCAAGTGA
*
4598 CCGGCCATGCGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
*
4619 CCGGCCACGTGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
4640 GCCCGCGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.29, G:0.33, T:0.19
Consensus pattern (21 bp):
CCGGCCACGCGACTTGGAGAT
Found at i:9926 original size:31 final size:30
Alignment explanation
Indices: 9885--9977 Score: 84
Period size: 30 Copynumber: 3.1 Consensus size: 30
9875 TTTCAAGGGA
*
9885 GAGGGGATGATGTGCCAAGGGCTTATCATG
1 GAGGGAATGATGTGCCAAGGGCTTATCATG
*
9915 GTCA-TGAATGATGCAT-CCAA-GGCTTATCATG
1 G--AGGGAATGATG--TGCCAAGGGCTTATCATG
* * *
9946 GAGGGAATGATGCGCCAAGGACTTACCATG
1 GAGGGAATGATGTGCCAAGGGCTTATCATG
9976 GA
1 GA
9978 CTTGAAGACA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
29 5 0.10
30 20 0.40
31 19 0.38
32 5 0.10
33 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (30 bp):
GAGGGAATGATGTGCCAAGGGCTTATCATG
Found at i:12767 original size:20 final size:20
Alignment explanation
Indices: 12742--12782 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
12732 CCTAACTTAG
12742 TTTTAAAGACAGTTTTCCAT
1 TTTTAAAGACAGTTTTCCAT
*
12762 TTTTAAAGGCAGTTTTCCAT
1 TTTTAAAGACAGTTTTCCAT
12782 T
1 T
12783 CATCACCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (20 bp):
TTTTAAAGACAGTTTTCCAT
Found at i:16736 original size:21 final size:21
Alignment explanation
Indices: 16697--16745 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
16687 TAAATGCTTT
**
16697 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
16719 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
16740 A-GAAGC
1 AGGAAGC
16746 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:18661 original size:33 final size:33
Alignment explanation
Indices: 18619--18702 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
18609 TTTCAATGCT
**
18619 ATCAACCAAAACACGATTATTTGCAATGCTATG
1 ATCAACCAAAACAAAATTATTTGCAATGCTATG
* **
18652 ATCAACCAAAATAAAATTATTTTTAATGCTATG
1 ATCAACCAAAACAAAATTATTTGCAATGCTATG
* *
18685 TTCAACCAAAACAGAATT
1 ATCAACCAAAACAAAATT
18703 GTTTTCATCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (33 bp):
ATCAACCAAAACAAAATTATTTGCAATGCTATG
Found at i:22303 original size:982 final size:981
Alignment explanation
Indices: 20423--22385 Score: 3800
Period size: 982 Copynumber: 2.0 Consensus size: 981
20413 AGCTCTGATT
*
20423 ACCAATTGATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAAC
1 ACCAATTGATACGAATATAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAAC
20488 TTGAATCACCAAACTTCTAGATGTGTATGTCGACAATCTTCACTTGATAAATCTTCCTTCGTTCG
66 TTGAATCACCAAACTTCTAGATGTGTATGTCGACAATCTTCACTTGATAAATCTTCCTTCGTTCG
20553 TCGGCCTTAGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAACAACC
131 TCGGCCTTAGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAACAACC
20618 AAGCAATCACAACTTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCTAAGTTTGCTCAAA
196 AAGCAATCACAACTTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCTAAGTTTGCTCAAA
*
20683 CTAGAACAATGAAGCCAAAGAAATCGATGTGTGTATAAACCTCTCAACTTTATTGATAACTTGAC
261 CTAGAACAATGAAGCCAAAGAAATCGATGTGGGTATAAACCTCTCAACTTTATTGATAACTTGAC
20748 TTCCTTTTACAAGAGATATTGGTGGCCTTATATAGTGATAGGGTCAACCAAAATCCTAAAATAAA
326 TTCCTTTTACAAGAGATATTGGTGGCCTTATATAGTGATAGGGTCAACCAAAATCCTAAAATAAA
20813 TCCTAATTTTCGTCCAAATATAAGGGCTAGGGAAAAACTAGTCCAAACCCAACTAGGAAAAGGAA
391 TCCTAATTTTCGTCCAAATATAAGGGCTAGGGAAAAACTAGTCCAAACCCAACTAGGAAAAGGAA
20878 ATAAAGACATAATTAAACAAGGATTGGACTTAGTCAACCAAGGCCCAATCCAAATAAGGTCCAAA
456 ATAAAGACATAATTAAACAAGGATTGGACTTAGTCAACCAAGGCCCAATCCAAATAAGGTCCAAA
*
20943 CTTAAAAATAAGCTAATCTAAGATAGAATTAAGCCCAAACAAAGATAACTAATGATAATGGGCTC
521 CTTAAAAATAAGCTAATCTAAGATAGAACTAAGCCCAAACAAAGATAACTAATGATAATGGGCTC
21008 ATGCCATGATGTCAATCCGGCCATCTAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGAT
586 ATGCCATGATGTCAATCCGGCCATCTAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGAT
21073 TTGTAATTTCTTGCCCAAATCATCACCAAAGCTCTTCAATTGAACTTCAATGATCTTCAAGTCTT
651 TTGTAATTTCTTGCCCAAATCATCACCAAAGCTCTTCAATTGAACTTCAATGATCTTCAAGTCTT
*
21138 CAAGATGAGTTCGAACAAGGCCCATGAGTGCATTCTTGAATCTCTTAGCTCTTGCTCTTGTCATC
716 CAAGATGAGTTCGAACAAGGCCCATGAGTGCATCCTTGAATCTCTTAGCTCTTGCTCTTGTCATC
21203 GGACCTAATGGCATCTTCAAAGGATCAAATGGCATCTTAATGGCATCTTCTTGGTGAATTACGAT
781 GGACCTAATGGCATCTTCAAAGGATCAAATGGCATCTTAATGGCATCTTCTTGGTGAATTACGAT
*
21268 TCCATCCTCTCCTTTAAGCTTGTCCATGCTTCGTTGCAGCCCTTGATCATCCTTTCCATGCTCTC
846 TCCATCCTCTCCTTTAAGCTTGTCCATGCTTCCTTGCAGCCCTTGATCATCCTTTCCATGCTCTC
21333 CATGCTTGTCTTCAAGTCTATAATAAGTCCTTGGCGCATAATTCCTTCCATGATAAGCCTAGGGC
911 CATGCTTGTCTTCAAGTCTATAATAAGTCCTTGGCGCATAATTCCTTCCATGATAAGCCTAGGGC
21398 GCATCA
976 GCATCA
21404 ACCAATTGATACGAATATAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAAC
1 ACCAATTGATACGAATATAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAAC
21469 TTGAATCACCAAACTTCTAGATGTGTATGTCGACAATCTTCACTTGATAAATCTTCCTTCGTTCG
66 TTGAATCACCAAACTTCTAGATGTGTATGTCGACAATCTTCACTTGATAAATCTTCCTTCGTTCG
21534 TCGGCCTTAGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAACAACC
131 TCGGCCTTAGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAACAACC
21599 AAGCAATCACAACTTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCTAAGTTTGCTCAAA
196 AAGCAATCACAACTTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCTAAGTTTGCTCAAA
*
21664 CTAGAACAATGAAGCCAAAGAAATCGATGTGGGTATAAACCTCTCAACTTTATTGATTAAGTTGA
261 CTAGAACAATGAAGCCAAAGAAATCGATGTGGGTATAAACCTCTCAACTTTATTGA-TAACTTGA
21729 CTTCCTTTTACAAGAGATATTGGTGGCCTTATATAGTGATAGGGTCAACCAAAATCCTAAAATAA
325 CTTCCTTTTACAAGAGATATTGGTGGCCTTATATAGTGATAGGGTCAACCAAAATCCTAAAATAA
***
21794 ATCCTAATTTTCGTCCAAATATAAGGGCTAGGGAAAAACTAGTCCTTGCCCAACTAGGAAAAGGA
390 ATCCTAATTTTCGTCCAAATATAAGGGCTAGGGAAAAACTAGTCCAAACCCAACTAGGAAAAGGA
21859 AATAAAGACATAATTAAACAAGGATTGGACTTAGTCAACCAAGGCCCAATCCAAATAAGGTCCAA
455 AATAAAGACATAATTAAACAAGGATTGGACTTAGTCAACCAAGGCCCAATCCAAATAAGGTCCAA
*
21924 ATTTAAAAATAAGCTAATCTAAGATAGAACTAAGCCCAAACAAAGATAACTAATGATAATGGGCT
520 ACTTAAAAATAAGCTAATCTAAGATAGAACTAAGCCCAAACAAAGATAACTAATGATAATGGGCT
21989 CATGCCATGATGTCAATCCGGCCATCTAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGA
585 CATGCCATGATGTCAATCCGGCCATCTAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGA
*
22054 TTTGTAATTTCTTGCCCAAATCATCACCAAAGCTCTTCAATTGAACTTCAATGGTCTTCAAGTCT
650 TTTGTAATTTCTTGCCCAAATCATCACCAAAGCTCTTCAATTGAACTTCAATGATCTTCAAGTCT
22119 TCAAGATGAGTTCGAACAAGGCCCATGAGTGCATCCTTGAATCTCTTAGCTCTTGCTCTTGTCAT
715 TCAAGATGAGTTCGAACAAGGCCCATGAGTGCATCCTTGAATCTCTTAGCTCTTGCTCTTGTCAT
22184 CGGACCTAATGGCATCTTCAAAGGATCAAATGGCATCTTAATGGCATCTTCTTGGTGAATTACGA
780 CGGACCTAATGGCATCTTCAAAGGATCAAATGGCATCTTAATGGCATCTTCTTGGTGAATTACGA
22249 TTCCATCCTCTCCTTTAAGCTTGTCCATGCTTCCTTGCAGCCCTTGATCATCCTTTCCATGCTCT
845 TTCCATCCTCTCCTTTAAGCTTGTCCATGCTTCCTTGCAGCCCTTGATCATCCTTTCCATGCTCT
* *
22314 CCATGCTTGTCTTCAAGTCTATAATAAGTCCTTGGCGTATAATTCCTTCCATGATAAGCCTTGGG
910 CCATGCTTGTCTTCAAGTCTATAATAAGTCCTTGGCGCATAATTCCTTCCATGATAAGCCTAGGG
22379 CGCATCA
975 CGCATCA
22386 GTATGCAAAG
Statistics
Matches: 968, Mismatches: 13, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
981 314 0.32
982 654 0.68
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (981 bp):
ACCAATTGATACGAATATAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAAC
TTGAATCACCAAACTTCTAGATGTGTATGTCGACAATCTTCACTTGATAAATCTTCCTTCGTTCG
TCGGCCTTAGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAACAACC
AAGCAATCACAACTTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCTAAGTTTGCTCAAA
CTAGAACAATGAAGCCAAAGAAATCGATGTGGGTATAAACCTCTCAACTTTATTGATAACTTGAC
TTCCTTTTACAAGAGATATTGGTGGCCTTATATAGTGATAGGGTCAACCAAAATCCTAAAATAAA
TCCTAATTTTCGTCCAAATATAAGGGCTAGGGAAAAACTAGTCCAAACCCAACTAGGAAAAGGAA
ATAAAGACATAATTAAACAAGGATTGGACTTAGTCAACCAAGGCCCAATCCAAATAAGGTCCAAA
CTTAAAAATAAGCTAATCTAAGATAGAACTAAGCCCAAACAAAGATAACTAATGATAATGGGCTC
ATGCCATGATGTCAATCCGGCCATCTAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGAT
TTGTAATTTCTTGCCCAAATCATCACCAAAGCTCTTCAATTGAACTTCAATGATCTTCAAGTCTT
CAAGATGAGTTCGAACAAGGCCCATGAGTGCATCCTTGAATCTCTTAGCTCTTGCTCTTGTCATC
GGACCTAATGGCATCTTCAAAGGATCAAATGGCATCTTAATGGCATCTTCTTGGTGAATTACGAT
TCCATCCTCTCCTTTAAGCTTGTCCATGCTTCCTTGCAGCCCTTGATCATCCTTTCCATGCTCTC
CATGCTTGTCTTCAAGTCTATAATAAGTCCTTGGCGCATAATTCCTTCCATGATAAGCCTAGGGC
GCATCA
Found at i:24794 original size:21 final size:21
Alignment explanation
Indices: 24768--24809 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
24758 GTACAAGTGA
*
24768 CCGGCCATGCGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
24789 CCGGCCACGCGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
24810 GCCCGCGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.33, T:0.17
Consensus pattern (21 bp):
CCGGCCACGCGACTTGGAGAT
Found at i:24895 original size:33 final size:33
Alignment explanation
Indices: 24792--24895 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 33
24782 TGGAGATCCG
* * *
24792 GCCACGCGACTTGGAGATGCCCGCGCAACACCCT
1 GCCACGCGACATGGAGATGCCCG-GCCACAACCT
* * *
24826 -CCATGCAACATGGAGATGCCCGGCCATC-ACCA
1 GCCACGCGACATGGAGATGCCCGGCCA-CAACCT
**
24858 GCCACGCGACATGGCCATGCCCGGCCACAACCT
1 GCCACGCGACATGGAGATGCCCGGCCACAACCT
24891 GCCAC
1 GCCAC
24896 ATGATCCTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
32 6 0.11
33 50 0.89
ACGTcount: A:0.23, C:0.42, G:0.24, T:0.11
Consensus pattern (33 bp):
GCCACGCGACATGGAGATGCCCGGCCACAACCT
Found at i:25927 original size:10 final size:10
Alignment explanation
Indices: 25902--25938 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
25892 AGTTATATCG
25902 AAAAATATAAA
1 AAAAATA-AAA
*
25913 CAAAATAAAA
1 AAAAATAAAA
25923 AAAAATAAAA
1 AAAAATAAAA
25933 AAAAAT
1 AAAAAT
25939 TCGACCAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.75
11 6 0.25
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:30549 original size:21 final size:21
Alignment explanation
Indices: 30524--30564 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
30514 CAATCAAGCA
30524 AATCA-AGCAACTCAAAGCATC
1 AATCATAGCAA-TCAAAGCATC
*
30545 AATCATAGTAATCAAAGCAT
1 AATCATAGCAATCAAAGCAT
30565 ATGAGTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.49, C:0.22, G:0.10, T:0.20
Consensus pattern (21 bp):
AATCATAGCAATCAAAGCATC
Found at i:32777 original size:21 final size:20
Alignment explanation
Indices: 32753--32790 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
32743 AGAAAAACAC
32753 AATTTTTTTCCATTTTTTTCA
1 AATTTTTTT-CATTTTTTTCA
32774 AATTTTTTTC-TTTTTTT
1 AATTTTTTTCATTTTTTT
32791 TAATCGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 1 0.06
21 9 0.53
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.74
Consensus pattern (20 bp):
AATTTTTTTCATTTTTTTCA
Found at i:38210 original size:6 final size:7
Alignment explanation
Indices: 38175--38225 Score: 79
Period size: 7 Copynumber: 7.4 Consensus size: 7
38165 TTAAATTCAT
38175 GTTTAGG
1 GTTTAGG
38182 GTTTAGG
1 GTTTAGG
38189 GTTTTAGG
1 G-TTTAGG
38197 GTTTAGG
1 GTTTAGG
38204 G-TTAGG
1 GTTTAGG
38210 G-TTAGG
1 GTTTAGG
38216 GTTTAGG
1 GTTTAGG
38223 GTT
1 GTT
38226 GCCTAAAGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.29
7 23 0.55
8 7 0.17
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:53581 original size:16 final size:16
Alignment explanation
Indices: 53556--53586 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53546 TTGCTTTGCT
53556 TTGCTCTGATTGATTA
1 TTGCTCTGATTGATTA
*
53572 TTGCTTTGATTGATT
1 TTGCTCTGATTGATT
53587 GCCTATTCCT
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:0.16, C:0.10, G:0.19, T:0.55
Consensus pattern (16 bp):
TTGCTCTGATTGATTA
Found at i:53593 original size:20 final size:21
Alignment explanation
Indices: 53551--53593 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
53541 TTGCATTGCT
* *
53551 TTGCTTTGCTCTGATTGATTA
1 TTGCTTTGATCTGATTGACTA
*
53572 TTGCTTTGAT-TGATTGCCTA
1 TTGCTTTGATCTGATTGACTA
53592 TT
1 TT
53594 CCTTGATTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.53
Consensus pattern (21 bp):
TTGCTTTGATCTGATTGACTA
Found at i:53708 original size:22 final size:19
Alignment explanation
Indices: 53683--53732 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 19
53673 ATGCCATGGA
53683 TGCTATGATTGATGCTTTGAAT
1 TGCT-TGATTG-TGC-TTGAAT
*
53705 TGCTTGAAT-TGCTTGAAT
1 TGCTTGATTGTGCTTGAAT
53723 TGCTTGATTG
1 TGCTTGATTG
53733 GGTCGACACT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 14 0.56
19 3 0.12
21 4 0.16
22 4 0.16
ACGTcount: A:0.20, C:0.10, G:0.24, T:0.46
Consensus pattern (19 bp):
TGCTTGATTGTGCTTGAAT
Found at i:53713 original size:9 final size:9
Alignment explanation
Indices: 53699--53729 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
53689 GATTGATGCT
53699 TTGAATTGC
1 TTGAATTGC
53708 TTGAATTGC
1 TTGAATTGC
53717 TTGAATTGC
1 TTGAATTGC
53726 TTGA
1 TTGA
53730 TTGGGTCGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.45
Consensus pattern (9 bp):
TTGAATTGC
Found at i:54635 original size:32 final size:31
Alignment explanation
Indices: 54578--54637 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
54568 TTTACCCAAA
*
54578 AAAAAAGTTAACAAGCTTTTTCTTTTAGCAC
1 AAAAAAGTTAACAAGCTTTTGCTTTTAGCAC
*
54609 AAAAAAGTTCACAAG-TTTGGTGCTTTTAG
1 AAAAAAGTTAACAAGCTTT--TGCTTTTAG
54638 ATTAAACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 3 0.12
31 14 0.56
32 8 0.32
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (31 bp):
AAAAAAGTTAACAAGCTTTTGCTTTTAGCAC
Found at i:55321 original size:11 final size:11
Alignment explanation
Indices: 55305--55337 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
55295 GAAGTTCGTG
55305 TTTGAAGATTT
1 TTTGAAGATTT
*
55316 TTTGAAGATAT
1 TTTGAAGATTT
55327 TTTGAAGATTT
1 TTTGAAGATTT
55338 GAAGACTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (11 bp):
TTTGAAGATTT
Found at i:58067 original size:29 final size:29
Alignment explanation
Indices: 57985--58071 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
57975 AAAAAAAAAC
*
57985 TCTAAATAGCGGCGTCTGGACGCCACTAT
1 TCTAAATAGCGGCGTCTGGACGCCGCTAT
58014 TCTAAATAGCGGCGTCTGGACGCCGCTAT
1 TCTAAATAGCGGCGTCTGGACGCCGCTAT
* *
58043 TCTAAATAGCGGCGTCTAGAAGCCGCTAT
1 TCTAAATAGCGGCGTCTGGACGCCGCTAT
58072 ATATAATTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.24
Consensus pattern (29 bp):
TCTAAATAGCGGCGTCTGGACGCCGCTAT
Found at i:61971 original size:90 final size:90
Alignment explanation
Indices: 61815--62159 Score: 528
Period size: 90 Copynumber: 3.8 Consensus size: 90
61805 CTTGAAGAAT
** * *
61815 GCCCCCAAGGGGCTCAACGCTAGTTGGCAAGGCGATCAACAAGATTTGACCCTGACCTAGCATGG
1 GCCCCCAAGGGGCTCAACGCTAGCAGGCAGGGCGATCGACAAGATTTGACCCTGACCTAGCATGG
*
61880 CCCCCTACTTATGGGAATGACGAAC
66 CCCCCAACTTATGGGAATGACGAAC
* *
61905 GCCCCCAAGGGGCTCAACGCTAGCAGGCGGGGCGATCGACAAGATTTGACCCTGACCTAGCTTGG
1 GCCCCCAAGGGGCTCAACGCTAGCAGGCAGGGCGATCGACAAGATTTGACCCTGACCTAGCATGG
61970 CCCCCAACTTATGGGAATGACGAAC
66 CCCCCAACTTATGGGAATGACGAAC
* * * * *
61995 GCCCCCAAGGGACTTAATGCCAGCAGGCAGGGCGATCGACAAGATTTGAGCCTGACCTAGCATGG
1 GCCCCCAAGGGGCTCAACGCTAGCAGGCAGGGCGATCGACAAGATTTGACCCTGACCTAGCATGG
* **
62060 CCGCCTTCTTATGGGAATGACGAAC
66 CCCCCAACTTATGGGAATGACGAAC
* * *
62085 GCCCCCAAGGGGCTCAACGCTAGCGGGCAGGGTGATTGACAAGATTTGACCCTGACCTAGCATGG
1 GCCCCCAAGGGGCTCAACGCTAGCAGGCAGGGCGATCGACAAGATTTGACCCTGACCTAGCATGG
62150 CCCCCAACTT
66 CCCCCAACTT
62160 GTAGGCGATG
Statistics
Matches: 227, Mismatches: 28, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 227 1.00
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (90 bp):
GCCCCCAAGGGGCTCAACGCTAGCAGGCAGGGCGATCGACAAGATTTGACCCTGACCTAGCATGG
CCCCCAACTTATGGGAATGACGAAC
Found at i:62413 original size:46 final size:46
Alignment explanation
Indices: 62339--62461 Score: 158
Period size: 45 Copynumber: 2.7 Consensus size: 46
62329 AGCATAGTCG
* * * *
62339 AACCCAAAAAGGGGTGAACACCCAAAATATTCGAAATTACATACCA
1 AACCCAAAAAGGGGCGAACGCCCAAAATATTCCAAACTACATACCA
* * * * *
62385 AACCTAAAAATGGGCGAGCGTCCAAAATA-TCCAAACTACATACCG
1 AACCCAAAAAGGGGCGAACGCCCAAAATATTCCAAACTACATACCA
62430 AACCCAAAAAGGGGCGAACGCCCAAAATATTC
1 AACCCAAAAAGGGGCGAACGCCCAAAATATTC
62462 AAGTGTGCAT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
45 38 0.60
46 25 0.40
ACGTcount: A:0.45, C:0.26, G:0.15, T:0.14
Consensus pattern (46 bp):
AACCCAAAAAGGGGCGAACGCCCAAAATATTCCAAACTACATACCA
Found at i:63218 original size:44 final size:43
Alignment explanation
Indices: 63110--63485 Score: 542
Period size: 44 Copynumber: 8.7 Consensus size: 43
63100 GAAAACATGG
** * * *
63110 GTCGATCGACCACATCACATTCAAAAGAAGAAGAAAGGAAGTG
1 GTCGATCGACCACATCACATTCAAACCAAGAAGAAAGTAACTA
* **
63153 GTCGATCGACCGCATTTCATTCAAACCAAGAAGAAATGTAACTA
1 GTCGATCGACCACATCACATTCAAACCAAGAAGAAA-GTAACTA
63197 GTCGATCGACCACATCACATTCAAACCAAGAAGAAATGTAACTA
1 GTCGATCGACCACATCACATTCAAACCAAGAAGAAA-GTAACTA
* *
63241 GTCGACCGATCACATCACATTCAAACCAAGAAGAAATGTAACTA
1 GTCGATCGACCACATCACATTCAAACCAAGAAGAAA-GTAACTA
* **
63285 GTCGACCGACCACATCACATTCAAACCAAGAAGAAAAG-AACCG
1 GTCGATCGACCACATCACATTCAAACCAAGAAG-AAAGTAACTA
63328 GTCGATCGACCACATCACATTCAAACCAAGAAGAGAAGTAACTA
1 GTCGATCGACCACATCACATTCAAACCAAGAAGA-AAGTAACTA
*
63372 GTCGATCGACCACATCACATTCAAACCAAG-CG-AAGTAACTA
1 GTCGATCGACCACATCACATTCAAACCAAGAAGAAAGTAACTA
*
63413 GTCGATCGACCACATCACATTAAAACCAAGAAGAAAAGTAACTA
1 GTCGATCGACCACATCACATTCAAACCAAGAAG-AAAGTAACTA
63457 GTCGATCGACCACATCACATTCAAACCAA
1 GTCGATCGACCACATCACATTCAAACCAA
63486 AAAGGAAAAA
Statistics
Matches: 303, Mismatches: 23, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
41 38 0.13
42 2 0.01
43 70 0.23
44 190 0.63
45 3 0.01
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.16
Consensus pattern (43 bp):
GTCGATCGACCACATCACATTCAAACCAAGAAGAAAGTAACTA
Found at i:63257 original size:131 final size:131
Alignment explanation
Indices: 63110--63485 Score: 562
Period size: 131 Copynumber: 2.9 Consensus size: 131
63100 GAAAACATGG
** * * * * **
63110 GTCGATCGACCACATCACATTCAAAAGAAGAAGAAAGGAAGTGGTCGATCGACCGCATTTCATTC
1 GTCGATCGACCACATCACATTCAAACCAAGAAGAAAGTAACTAGTCGATCGACCACATCACATTC
*
63175 AAACCAAGAAGAAATGTAACTAGTCGATCGACCACATCACATTCAAACCAAGAAGA-AATGTAAC
66 AAACCAAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACCAAGAAGAGAA-GTAAC
63239 TA
130 TA
* * *
63241 GTCGACCGATCACATCACATTCAAACCAAGAAGAAATGTAACTAGTCGACCGACCACATCACATT
1 GTCGATCGACCACATCACATTCAAACCAAGAAGAAA-GTAACTAGTCGATCGACCACATCACATT
**
63306 CAAACCAAGAAGAAAAG-AACCGGTCGATCGACCACATCACATTCAAACCAAGAAGAGAAGTAAC
65 CAAACCAAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACCAAGAAGAGAAGTAAC
63370 TA
130 TA
* *
63372 GTCGATCGACCACATCACATTCAAACCAAG-CG-AAGTAACTAGTCGATCGACCACATCACATTA
1 GTCGATCGACCACATCACATTCAAACCAAGAAGAAAGTAACTAGTCGATCGACCACATCACATTC
63435 AAACCAAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACCAA
66 AAACCAAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACCAA
63486 AAAGGAAAAA
Statistics
Matches: 221, Mismatches: 21, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
128 43 0.19
129 34 0.15
130 1 0.00
131 104 0.47
132 39 0.18
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.16
Consensus pattern (131 bp):
GTCGATCGACCACATCACATTCAAACCAAGAAGAAAGTAACTAGTCGATCGACCACATCACATTC
AAACCAAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACCAAGAAGAGAAGTAACT
A
Found at i:64088 original size:229 final size:227
Alignment explanation
Indices: 63589--64125 Score: 840
Period size: 229 Copynumber: 2.4 Consensus size: 227
63579 CACCCAAGCC
* * * *
63589 GAAGAAAGGAAAAATGTGTCGAATGACCAAAATCACATTCATGCCGAAATGATCAAAGAAGAAAG
1 GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGGTTAAAGAAGAAAG
* *
63654 GAGAAATGCGTCGAACGACCAAAATCACGTTCACGCCGAAATGCTCAAAGAAGAATGAGAAATGT
66 GAGAAATGCGTCGAACGACCAAAATCACGTTCACGCCGAAATGATCAAAGAAGAAGGAGAAATGT
** *
63719 GTCGAACGACCAAAATCATGTTCATGCCGAAATGATCAAAGTAGAAAGGAGAAATGCGTCGAACG
131 GTCGAACGACCAAAATCACATTCATGCCGAAATGATCAAAGAAGAAAGGAGAAATGCGTCGAACG
* *
63784 ACCAAAATCACGTTCATGCCGAAATGGTCAAA
196 ACCAAAATCACATTCATGCCGAAATGATCAAA
*
63816 GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGGTTAAAGAAGAAAT
1 GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGGTTAAAGAAGAAAG
* * *
63881 GAGAAATGTGTCGAACGACCAAAATCACGTTCATGTCGAAATGATCAAAGAAGAAAGGAGAAATG
66 GAGAAATGCGTCGAACGACCAAAATCACGTTCACGCCGAAATGATCAAAGAAG-AAGGAGAAATG
* * * * *
63946 TGTCGAATGACCAAGATCACATTCATGCCGAAAATGGTTAAAGAAGAAAGGAGAAATGTGTCGAA
130 TGTCGAACGACCAAAATCACATTCATGCCG-AAATGATCAAAGAAGAAAGGAGAAATGCGTCGAA
*
64011 TGACCAAAATCACATTCATGCCGAAATGATCAAA
194 CGACCAAAATCACATTCATGCCGAAATGATCAAA
*
64045 GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACTTTCATGCCGAAATGGTTAAAGAAGAAAG
1 GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGGTTAAAGAAGAAAG
**
64110 GAGAAACACGTCGAAC
66 GAGAAATGCGTCGAAC
64126 AATCAAGTTG
Statistics
Matches: 282, Mismatches: 26, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
227 109 0.39
228 36 0.13
229 137 0.49
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.17
Consensus pattern (227 bp):
GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGGTTAAAGAAGAAAG
GAGAAATGCGTCGAACGACCAAAATCACGTTCACGCCGAAATGATCAAAGAAGAAGGAGAAATGT
GTCGAACGACCAAAATCACATTCATGCCGAAATGATCAAAGAAGAAAGGAGAAATGCGTCGAACG
ACCAAAATCACATTCATGCCGAAATGATCAAA
Found at i:64125 original size:57 final size:57
Alignment explanation
Indices: 63589--64115 Score: 804
Period size: 57 Copynumber: 9.2 Consensus size: 57
63579 CACCCAAGCC
* *
63589 GAAGAAAGGAAAAATGTGTCGAATGACCAAAATCACATTCATGCCGAAATGATCAAA
1 GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGATCAAA
* * * *
63646 GAAGAAAGGAGAAATGCGTCGAACGACCAAAATCACGTTCACGCCGAAATGCTCAAA
1 GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGATCAAA
* **
63703 GAAG-AATGAGAAATGTGTCGAACGACCAAAATCATGTTCATGCCGAAATGATCAAA
1 GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGATCAAA
* * * *
63759 GTAGAAAGGAGAAATGCGTCGAACGACCAAAATCACGTTCATGCCGAAATGGTCAAA
1 GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGATCAAA
* *
63816 GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGGTTAAA
1 GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGATCAAA
* * *
63873 GAAGAAATGAGAAATGTGTCGAACGACCAAAATCACGTTCATGTCGAAATGATCAAA
1 GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGATCAAA
* * * *
63930 GAAGAAAGGAGAAATGTGTCGAATGACCAAGATCACATTCATGCCGAAAATGGTTAAA
1 GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACATTCATGCCG-AAATGATCAAA
*
63988 GAAGAAAGGAGAAATGTGTCGAATGACCAAAATCACATTCATGCCGAAATGATCAAA
1 GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGATCAAA
* * *
64045 GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACTTTCATGCCGAAATGGTTAAA
1 GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGATCAAA
64102 GAAGAAAGGAGAAA
1 GAAGAAAGGAGAAA
64116 CACGTCGAAC
Statistics
Matches: 429, Mismatches: 39, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
56 50 0.12
57 325 0.76
58 54 0.13
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (57 bp):
GAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGATCAAA
Found at i:64520 original size:49 final size:49
Alignment explanation
Indices: 64467--64577 Score: 145
Period size: 49 Copynumber: 2.3 Consensus size: 49
64457 ATGCGGCGTG
* *
64467 CGACACAAAAAGAAGCAAAACAACCATGTGCTAACTA-CCAGGTGGCATA
1 CGACACAAAAAGAA-CAAAACAACCAAGTGCTAACTATCAAGGTGGCATA
* * *
64516 CGACACAAAAAGGAACAAGACAACCAAGTGCTAACTATCAATGTGGCGTA
1 CGACACAAAAA-GAACAAAACAACCAAGTGCTAACTATCAAGGTGGCATA
64566 CGAC-CAAAAAGA
1 CGACACAAAAAGA
64578 GCGCAGGGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
48 2 0.04
49 37 0.67
50 16 0.29
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (49 bp):
CGACACAAAAAGAACAAAACAACCAAGTGCTAACTATCAAGGTGGCATA
Found at i:64933 original size:45 final size:45
Alignment explanation
Indices: 64844--64936 Score: 123
Period size: 45 Copynumber: 2.1 Consensus size: 45
64834 ATATGAATGG
* ** * **
64844 AAGTACAACAAATCAAATACTCTCGGTCAAAATGTGGCGTACGAC
1 AAGTACAACAAATCAAAGACTCTCGGTCAAAAAATAGCACACGAC
*
64889 AAGTTCAACAAATCAAAGACTCTCGGTCAAAAAATAGCACACGAC
1 AAGTACAACAAATCAAAGACTCTCGGTCAAAAAATAGCACACGAC
64934 AAG
1 AAG
64937 CGACAATATA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.17
Consensus pattern (45 bp):
AAGTACAACAAATCAAAGACTCTCGGTCAAAAAATAGCACACGAC
Found at i:65081 original size:44 final size:45
Alignment explanation
Indices: 65018--65116 Score: 139
Period size: 44 Copynumber: 2.2 Consensus size: 45
65008 GGGAAGGAGG
* * *
65018 CAAACAAAAGATTCCCAATCACAAAGTGGTGT-GTGACAAGAAAA-
1 CAAACAAAAGACTCACAATCACAAAGTGGCGTAG-GACAAGAAAAC
65062 CAAACAAAAGACTCACAATCACAAAGTGGCGTAGGACAAGAAAAC
1 CAAACAAAAGACTCACAATCACAAAGTGGCGTAGGACAAGAAAAC
65107 CAAAACAAAA
1 C-AAACAAAA
65117 ACTATTAACC
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
44 39 0.80
45 2 0.04
46 8 0.16
ACGTcount: A:0.53, C:0.20, G:0.16, T:0.11
Consensus pattern (45 bp):
CAAACAAAAGACTCACAATCACAAAGTGGCGTAGGACAAGAAAAC
Found at i:65202 original size:58 final size:58
Alignment explanation
Indices: 65140--65262 Score: 187
Period size: 58 Copynumber: 2.1 Consensus size: 58
65130 AAGTGGCATT
* *
65140 CGACAACATAGAAAGGGAAGGAGACAAGTCAAAAATTCTCAATTGCAAAAGTGACGT-A
1 CGACAACATAGAAAGGGAAGGAGACAAATAAAAAATTCTCAATTGC-AAAGTGACGTGA
* *
65198 CGACAACATAGAAAGGGAATGAGACAAATAAAAAATTCTCAATTGCAAAGTGGCGTGA
1 CGACAACATAGAAAGGGAAGGAGACAAATAAAAAATTCTCAATTGCAAAGTGACGTGA
65256 -GACAACA
1 CGACAACA
65263 ATGGAAGGAG
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
57 16 0.27
58 44 0.73
ACGTcount: A:0.47, C:0.15, G:0.22, T:0.15
Consensus pattern (58 bp):
CGACAACATAGAAAGGGAAGGAGACAAATAAAAAATTCTCAATTGCAAAGTGACGTGA
Found at i:65745 original size:38 final size:38
Alignment explanation
Indices: 65694--66097 Score: 598
Period size: 38 Copynumber: 10.7 Consensus size: 38
65684 AATTGGTGCC
*
65694 AAGCTGACAAAATGTGTCGACCGCCACATCGCTCGACA
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACA
65732 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGAC-
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACA
* *
65769 AAGCTGACGAAATGTGTCGACCGCCACGTCCCTCGACA
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACA
* * *
65807 AAGTTGACAAAATGTGTCGATCGCCACGTCACTCGACA
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACA
*
65845 AAGCTGACAAAGTGTGTCGACCGCCACGTCGCTCGACA
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACA
*
65883 AAGCTGACAAAGTGTGTCGACCGCCACGTCGCTCGAC-
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACA
65920 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACA
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACA
* * *
65958 AAGCTGACAAAATGTGTCGACCACCACATCGCTTGACA
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACA
* * ** * *
65996 AATCTCATGAAATGTGTCGACCGCCACATCGCTCAACA
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACA
* * * *
66034 AAGCTGACCAAATGTGTCGACCACCACGTCGTTCAAC-
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACA
66071 AAGCTGACAAAATGTGTCGACCGCCAC
1 AAGCTGACAAAATGTGTCGACCGCCAC
66098 AGGCCACCTC
Statistics
Matches: 333, Mismatches: 31, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
37 96 0.29
38 237 0.71
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.17
Consensus pattern (38 bp):
AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACA
Found at i:65928 original size:113 final size:113
Alignment explanation
Indices: 65694--66097 Score: 598
Period size: 113 Copynumber: 3.6 Consensus size: 113
65684 AATTGGTGCC
*
65694 AAGCTGACAAAATGTGTCGACCGCCACATCGCTCGACAAAGCTGACAAAATGTGTCGACCGCCAC
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACAAAGCTGACAAAATGTGTCGACCGCCAC
*
65759 GTCGCTCGAC-AAGCTGACGAAATGTGTCGACCGCCACGTCCCTCGACA
66 GTCGCTCGACAAAGCTGAC-AAATGTGTCGACCGCCACGTCGCTCGACA
* * * *
65807 AAGTTGACAAAATGTGTCGATCGCCACGTCACTCGACAAAGCTGACAAAGTGTGTCGACCGCCAC
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACAAAGCTGACAAAATGTGTCGACCGCCAC
65872 GTCGCTCGACAAAGCTGACAAAGTGTGTCGACCGCCACGTCGCTCGAC-
66 GTCGCTCGACAAAGCTGACAAA-TGTGTCGACCGCCACGTCGCTCGACA
*
65920 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACAAAGCTGACAAAATGTGTCGACCACCAC
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACAAAGCTGACAAAATGTGTCGACCGCCAC
* * * * * * *
65985 ATCGCTTGACAAATCTCATGAAATGTGTCGACCGCCACATCGCTCAACA
66 GTCGCTCGACAAAGCTGA-CAAATGTGTCGACCGCCACGTCGCTCGACA
* * * *
66034 AAGCTGACCAAATGTGTCGACCACCACGTCGTTCAAC-AAGCTGACAAAATGTGTCGACCGCCAC
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACAAAGCTGACAAAATGTGTCGACCGCCAC
66098 AGGCCACCTC
Statistics
Matches: 264, Mismatches: 23, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
113 196 0.74
114 68 0.26
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.17
Consensus pattern (113 bp):
AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACAAAGCTGACAAAATGTGTCGACCGCCAC
GTCGCTCGACAAAGCTGACAAATGTGTCGACCGCCACGTCGCTCGACA
Found at i:65968 original size:151 final size:149
Alignment explanation
Indices: 65694--66097 Score: 610
Period size: 151 Copynumber: 2.7 Consensus size: 149
65684 AATTGGTGCC
65694 AAGCTGACAAAATGTGTCGACCGCCACATCGCTCGACAAAGCTGACAAAATGTGTCGACCGCCAC
1 AAGCTGAC-AAATGTGTCGACCGCCACATCGCTCGACAAAGCTGAC-AAATGTGTCGACCGCCAC
* *
65759 GTCGCTCGACAAGCTGACGAAATGTGTCGACCGCCACGTCCCTCGACAAAGTTGACAAAATGTGT
64 GTCGCTCGACAAGCTGACAAAATGTGTCGACCGCCACGTCCCTCGACAAAGCTGACAAAATGTGT
* * *
65824 CGATCGCCACGTCACTCGACA
129 CGACCACCACATCACTCGACA
*
65845 AAGCTGACAAAGTGTGTCGACCGCCACGTCGCTCGACAAAGCTGACAAAGTGTGTCGACCGCCAC
1 AAGCTGACAAA-TGTGTCGACCGCCACATCGCTCGACAAAGCTGACAAA-TGTGTCGACCGCCAC
*
65910 GTCGCTCGACAAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACAAAGCTGACAAAATGTGT
64 GTCGCTCGACAAGCTGACAAAATGTGTCGACCGCCACGTCCCTCGACAAAGCTGACAAAATGTGT
* *
65975 CGACCACCACATCGCTTGACA
129 CGACCACCACATCACTCGACA
* * * * *
65996 AATCTCATGAAATGTGTCGACCGCCACATCGCTCAACAAAGCTGACCAAATGTGTCGACCACCAC
1 AAGCTGA-CAAATGTGTCGACCGCCACATCGCTCGACAAAGCTGA-CAAATGTGTCGACCGCCAC
* *
66061 GTCGTTCAACAAGCTGACAAAATGTGTCGACCGCCAC
64 GTCGCTCGACAAGCTGACAAAATGTGTCGACCGCCAC
66098 AGGCCACCTC
Statistics
Matches: 232, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
150 6 0.03
151 219 0.94
152 7 0.03
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.17
Consensus pattern (149 bp):
AAGCTGACAAATGTGTCGACCGCCACATCGCTCGACAAAGCTGACAAATGTGTCGACCGCCACGT
CGCTCGACAAGCTGACAAAATGTGTCGACCGCCACGTCCCTCGACAAAGCTGACAAAATGTGTCG
ACCACCACATCACTCGACA
Found at i:66250 original size:23 final size:24
Alignment explanation
Indices: 66216--66265 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
66206 TTTAAATTCT
*
66216 AAAAAAATAAGAA-AAAAAAGCAA
1 AAAAAAAAAAGAAGAAAAAAGCAA
*
66239 AAAAAAAAAAGAAGCAAAAAGCAA
1 AAAAAAAAAAGAAGAAAAAAGCAA
66263 AAA
1 AAA
66266 GCAAACAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.82, C:0.06, G:0.10, T:0.02
Consensus pattern (24 bp):
AAAAAAAAAAGAAGAAAAAAGCAA
Found at i:66266 original size:17 final size:17
Alignment explanation
Indices: 66227--66258 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
66217 AAAAAATAAG
66227 AAAAAA-AAGCAAAAAA
1 AAAAAAGAAGCAAAAAA
66243 AAAAAAGAAGCAAAAA
1 AAAAAAGAAGCAAAAA
66259 GCAAAAAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.84, C:0.06, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAGCAAAAAA
Found at i:66763 original size:17 final size:18
Alignment explanation
Indices: 66730--66769 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
66720 CAAAATTTGA
66730 CCCGAACCCGATAACCCG
1 CCCGAACCCGATAACCCG
66748 CCCGAACCCG-TAACCCG
1 CCCGAACCCGATAACCCG
66765 CCCGA
1 CCCGA
66770 CCTGACACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.25, C:0.53, G:0.17, T:0.05
Consensus pattern (18 bp):
CCCGAACCCGATAACCCG
Found at i:66809 original size:16 final size:16
Alignment explanation
Indices: 66790--66854 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
66780 GACGAAACCG
*
66790 TGACCCGTAACCC-AGA
1 TGACCCGGAACCCGA-A
66806 TGACCCGGAACCCGAA
1 TGACCCGGAACCCGAA
*
66822 TGACCC-GAGACCCGTA
1 TGACCCGGA-ACCCGAA
* *
66838 TAACCCGAAACCCGAA
1 TGACCCGGAACCCGAA
66854 T
1 T
66855 AACTCGAGAC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
15 2 0.05
16 37 0.90
17 2 0.05
ACGTcount: A:0.32, C:0.37, G:0.20, T:0.11
Consensus pattern (16 bp):
TGACCCGGAACCCGAA
Found at i:66856 original size:16 final size:16
Alignment explanation
Indices: 66808--66857 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
66798 AACCCAGATG
* *
66808 ACCCGGAACCCGAATG
1 ACCCGAAACCCGAATA
* *
66824 ACCCGAGACCCGTATA
1 ACCCGAAACCCGAATA
66840 ACCCGAAACCCGAATA
1 ACCCGAAACCCGAATA
66856 AC
1 AC
66858 TCGAGACATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.36, C:0.38, G:0.18, T:0.08
Consensus pattern (16 bp):
ACCCGAAACCCGAATA
Found at i:67015 original size:21 final size:22
Alignment explanation
Indices: 66968--67016 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
66958 AATACAATTT
66968 ATATTATTGTTATAATTTTACC
1 ATATTATTGTTATAATTTTACC
*
66990 A-ATTATTGTTATGATTTTA-C
1 ATATTATTGTTATAATTTTACC
67010 ATATTAT
1 ATATTAT
67017 AAATTGGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 22 0.88
22 1 0.04
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (22 bp):
ATATTATTGTTATAATTTTACC
Found at i:67555 original size:31 final size:31
Alignment explanation
Indices: 67486--67566 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
67476 GAATGACCTT
* *
67486 AAACCCGTATGACCCGAGACCCGAACGACCCG
1 AAACCCGAATAACCCGA-ACCCGAACGACCCG
* *
67518 AGACCCGAATAACCCGAACCC-AGATGACCCG
1 AAACCCGAATAACCCGAACCCGA-ACGACCCG
*
67549 AAACCCGAATTACCCGAA
1 AAACCCGAATAACCCGAA
67567 AAAACTGCAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.02
31 27 0.64
32 14 0.33
ACGTcount: A:0.36, C:0.38, G:0.19, T:0.07
Consensus pattern (31 bp):
AAACCCGAATAACCCGAACCCGAACGACCCG
Found at i:67566 original size:16 final size:16
Alignment explanation
Indices: 67473--67567 Score: 95
Period size: 16 Copynumber: 6.0 Consensus size: 16
67463 ACCCGAGTGT
**
67473 CCCGAATGACCTTAAA
1 CCCGAATGACCCGAAA
* *
67489 CCCGTATGACCCGAGA
1 CCCGAATGACCCGAAA
* *
67505 CCCGAACGACCCGAGA
1 CCCGAATGACCCGAAA
*
67521 CCCGAATAACCCG-AA
1 CCCGAATGACCCGAAA
67536 CCC-AGATGACCCGAAA
1 CCCGA-ATGACCCGAAA
*
67552 CCCGAATTACCCGAAA
1 CCCGAATGACCCGAAA
67568 AAACTGCATG
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
14 1 0.02
15 11 0.17
16 52 0.80
17 1 0.02
ACGTcount: A:0.35, C:0.38, G:0.18, T:0.09
Consensus pattern (16 bp):
CCCGAATGACCCGAAA
Found at i:67759 original size:26 final size:24
Alignment explanation
Indices: 67722--67788 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 24
67712 AGCCAGCTGG
*
67722 CACTCCACACGTGACCTCCAACGTA
1 CACTCCACACGTGACC-CCAACGGA
67747 CGACTCCACACGTGAACCCCAACGGA
1 C-ACTCCACACGTG-ACCCCAACGGA
67773 CACCTCCACACGTGAC
1 CA-CTCCACACGTGAC
67789 ATCGTGCATG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
25 4 0.11
26 31 0.82
27 3 0.08
ACGTcount: A:0.28, C:0.45, G:0.15, T:0.12
Consensus pattern (24 bp):
CACTCCACACGTGACCCCAACGGA
Found at i:72909 original size:22 final size:23
Alignment explanation
Indices: 72875--72932 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
72865 TCGCCGGGAT
* *
72875 TGTATCACTAAAAA-GTTGCCTA
1 TGTATTACCAAAAACGTTGCCTA
*
72897 TGTATTACCAAAAAACTTTGCCTA
1 TGTATTACC-AAAAACGTTGCCTA
*
72921 T-AATTACCAAAA
1 TGTATTACCAAAA
72933 CTTTACACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 11 0.37
23 11 0.37
24 8 0.27
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (23 bp):
TGTATTACCAAAAACGTTGCCTA
Found at i:72934 original size:21 final size:23
Alignment explanation
Indices: 72890--72936 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
72880 CACTAAAAAG
*
72890 TTGCCTATGTATTACCAAAAAACT
1 TTGCCTATGAATTACC-AAAAACT
72914 TTGCCTAT-AATTACC-AAAACT
1 TTGCCTATGAATTACCAAAAACT
72935 TT
1 TT
72937 ACACCAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
23 6 0.27
24 8 0.36
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (23 bp):
TTGCCTATGAATTACCAAAAACT
Found at i:73061 original size:22 final size:22
Alignment explanation
Indices: 73036--73538 Score: 138
Period size: 22 Copynumber: 22.7 Consensus size: 22
73026 TATGATCTCG
73036 TTATGAAATTTTGATAACCTTC
1 TTATGAAATTTTGATAACCTTC
* * *
73058 TTATGAAATTTTAATAACGATAC
1 TTATGAAATTTTGATAAC-CTTC
* * *
73081 -TATGAAATTTCGAGAACCTTT
1 TTATGAAATTTTGATAACCTTC
**
73102 TTAT-AAATTTTTTTTAACCTTC
1 TTATGAAA-TTTTGATAACCTTC
* *
73124 TTATGGAATTTTG-TCAACCTCC
1 TTATGAAATTTTGAT-AACCTTC
* * * * **
73146 CTAAGGAATTTTGA-AGATCTGA
1 TTATGAAATTTTGATA-ACCTTC
* * **
73168 ATACGAAATTTTGATAACCAAC
1 TTATGAAATTTTGATAACCTTC
* * * * *
73190 ACTATGAGATGTTGATAATCTCC
1 -TTATGAAATTTTGATAACCTTC
* * * *
73213 ATATGATATATTGATAACC-AC
1 TTATGAAATTTTGATAACCTTC
* * * *
73234 GTTATGAAAATTTCAAAACCTCC
1 -TTATGAAATTTTGATAACCTTC
* *
73257 ATATG-AATTGTT-AGTAATCAC-AC
1 TTATGAAATT-TTGA-TAA-C-CTTC
* *
73280 -TCTGAAATTTTGATAATCAC-AC
1 TTATGAAATTTTGATAA-C-CTTC
*
73302 -TATGAAATTGTGATAACC-TC
1 TTATGAAATTTTGATAACCTTC
*
73322 GTTATGAAATTTTGATAAATCTTC
1 -TTATGAAATTTTGAT-AACCTTC
* * *
73346 CTATAAAATTTTGATAAACCTCC
1 TTATGAAATTTTGAT-AACCTTC
* * * * *
73369 CTATAAAAATTTAATAACCTCC
1 TTATGAAATTTTGATAACCTTC
* **
73391 CTATGATTTTTTGATAA-CTTC
1 TTATGAAATTTTGATAACCTTC
* * * *
73412 ATTAAGAAATTTTGTTAATCTCC
1 -TTATGAAATTTTGATAACCTTC
* * ***
73435 CTATGAAATTTTGATCTACAGAC
1 TTATGAAATTTTGAT-AACCTTC
* *
73458 -TATGAAATTTTGATGACCCTC
1 TTATGAAATTTTGATAACCTTC
** *
73479 TTATGAAATTTTGA-AAAATAAAC
1 TTATGAAATTTTGATAACCT--TC
73502 -TATGAAATTTTGATAACCTTC
1 TTATGAAATTTTGATAACCTTC
*
73523 ATATGAAATTTTGATA
1 TTATGAAATTTTGATA
73539 TCCTCCCTGA
Statistics
Matches: 356, Mismatches: 96, Indels: 58
0.70 0.19 0.11
Matches are distributed among these distances:
20 2 0.01
21 20 0.06
22 259 0.73
23 72 0.20
24 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.39
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCTTC
Found at i:73712 original size:22 final size:22
Alignment explanation
Indices: 73663--74056 Score: 173
Period size: 22 Copynumber: 17.7 Consensus size: 22
73653 AATCACATTT
* ** *
73663 TGAAAATTTGATAAAATCTTTA
1 TGAAATTTTGATAACCTCTCTA
73685 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * * *
73707 TAAAATTTTGTTGACCCCTCCA
1 TGAAATTTTGATAACCTCTCTA
* * * *
73729 TGAAATTTTGTTGACCCCCCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
73751 TGAGATTTTGATTATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * * *
73773 TGTAATTTTGATAGCCTCGCTT
1 TGAAATTTTGATAACCTCTCTA
** *
73795 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTCTA
*
73817 TGAAATTTTGATAATCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
73839 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTCTA
* * *
73863 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTCTA
*
73885 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
* * *
73905 TCAAATTTTGGTATCC-CT-TA
1 TGAAATTTTGATAACCTCTCTA
* * *
73925 TAAAATTGAGACTTTTATAACCT-TAATA
1 TGAAA-T-----TTTGATAACCTCT-CTA
*
73953 TGAAATTTTGATAACCAT-ACTA
1 TGAAATTTTGATAACC-TCTCTA
* *
73975 TGAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTCTCTA
* *
73997 TGAAATATT-AGTAATCTC-CTTA
1 TGAAATTTTGA-TAACCTCTC-TA
* **
74019 TGAAATTTTGTTAACAACTCTA
1 TGAAATTTTGATAACCTCTCTA
74041 TGAAATTCTT-ATAACC
1 TGAAATT-TTGATAACC
74057 ATGCTATGGC
Statistics
Matches: 278, Mismatches: 68, Indels: 52
0.70 0.17 0.13
Matches are distributed among these distances:
20 13 0.05
21 33 0.12
22 195 0.70
23 4 0.01
24 6 0.02
25 12 0.04
26 8 0.03
27 1 0.00
28 6 0.02
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:74000 original size:44 final size:43
Alignment explanation
Indices: 73952--74076 Score: 108
Period size: 44 Copynumber: 2.8 Consensus size: 43
73942 TAACCTTAAT
**
73952 ATGAAATTTTGATAACCATACTATGAAATTTTGATAACCTCCCC
1 ATGAAATTTT-ATAACCATACTATGAAATTTTGATAACAACCCC
* * * * * *
73996 ATGAAATATTAGTAATC-TCCTTATGAAATTTTGTTAACAACTCT
1 ATGAAATTTTA-TAACCATAC-TATGAAATTTTGATAACAACCCC
* **
74040 ATGAAATTCTTATAACCATGCTATGGCATTTTGATAA
1 ATGAAATT-TTATAACCATACTATGAAATTTTGATAA
74077 TTTCTTTGAT
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
43 3 0.05
44 55 0.87
45 5 0.08
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (43 bp):
ATGAAATTTTATAACCATACTATGAAATTTTGATAACAACCCC
Found at i:74124 original size:22 final size:22
Alignment explanation
Indices: 74099--74298 Score: 122
Period size: 22 Copynumber: 8.8 Consensus size: 22
74089 CCTTTCCATA
*
74099 AAATTGTGATAACCACACTATG
1 AAATTTTGATAACCACACTATG
** *
74121 AAATTTCAATAACCATC-CTAAG
1 AAATTTTGATAACCA-CACTATG
* *
74143 AAATTTTAAATCACCTGATC-CTATG
1 AAATTTT-GATAACC--A-CACTATG
*
74168 AAATTTTGGTAACCACACTACTTCG
1 AAATTTTGATAACCACACTA--T-G
* **
74193 AGATTTTGATAACTTCTA-TATG
1 AAATTTTGATAACCAC-ACTATG
*
74215 AAATTTTGGTAACCACACTATG
1 AAATTTTGATAACCACACTATG
* *
74237 GAATTTTGATAACCTC-CTCATG
1 AAATTTTGATAACCACACT-ATG
* * *
74259 AAATTATAATAACCATC-TTATG
1 AAATTTTGATAACCA-CACTATG
74281 AAATTTTGATAACCACAC
1 AAATTTTGATAACCACAC
74299 AGAGACAAGA
Statistics
Matches: 136, Mismatches: 29, Indels: 26
0.71 0.15 0.14
Matches are distributed among these distances:
21 5 0.04
22 86 0.63
23 10 0.07
24 5 0.04
25 29 0.21
26 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.34
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATG
Found at i:74260 original size:44 final size:43
Alignment explanation
Indices: 74161--74294 Score: 135
Period size: 44 Copynumber: 3.0 Consensus size: 43
74151 AATCACCTGA
* *
74161 TCCTATGAAATTTTGGTAACCACACTACTTCGAGATTTTGATAACT
1 TCCTATGAAATTTTGGTAACCACACTA--TGGA-ATTTTGATAACC
*
74207 TCTATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC
1 TC-CTATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC
* ** * *
74251 TCCTCATGAAATTATAATAACCATC-TTATGAAATTTTGATAACC
1 TCCT-ATGAAATTTTGGTAACCA-CACTATGGAATTTTGATAACC
74295 ACACAGAGAC
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
43 1 0.01
44 45 0.59
45 4 0.05
46 2 0.03
47 24 0.32
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (43 bp):
TCCTATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC
Found at i:74498 original size:20 final size:20
Alignment explanation
Indices: 74460--74498 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
74450 TATTGACATT
74460 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
74480 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
74499 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:77325 original size:127 final size:127
Alignment explanation
Indices: 77171--77420 Score: 500
Period size: 127 Copynumber: 2.0 Consensus size: 127
77161 TTTTACACTA
77171 TTTTGTTAATATTTGTGTTTTTAGGTCTTGAAGACAAGAAAAGTGAAAACTTATTGTTTTTCACT
1 TTTTGTTAATATTTGTGTTTTTAGGTCTTGAAGACAAGAAAAGTGAAAACTTATTGTTTTTCACT
77236 CTTTTTGGAGCTATTCTGGAGACTTTTTACTCAACTATAGATTTAGCCATTTGGAATGTCCG
66 CTTTTTGGAGCTATTCTGGAGACTTTTTACTCAACTATAGATTTAGCCATTTGGAATGTCCG
77298 TTTTGTTAATATTTGTGTTTTTAGGTCTTGAAGACAAGAAAAGTGAAAACTTATTGTTTTTCACT
1 TTTTGTTAATATTTGTGTTTTTAGGTCTTGAAGACAAGAAAAGTGAAAACTTATTGTTTTTCACT
77363 CTTTTTGGAGCTATTCTGGAGACTTTTTACTCAACTATAGATTTAGCCATTTGGAATG
66 CTTTTTGGAGCTATTCTGGAGACTTTTTACTCAACTATAGATTTAGCCATTTGGAATG
77421 AAGATTTGAA
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 123 1.00
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (127 bp):
TTTTGTTAATATTTGTGTTTTTAGGTCTTGAAGACAAGAAAAGTGAAAACTTATTGTTTTTCACT
CTTTTTGGAGCTATTCTGGAGACTTTTTACTCAACTATAGATTTAGCCATTTGGAATGTCCG
Found at i:90180 original size:29 final size:30
Alignment explanation
Indices: 90105--90181 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
90095 TTTGACACCG
**
90105 AGTGCAAACCCACACTCAAATGCAATCCCA
1 AGTGCAAACCCACACTTGAATGCAATCCCA
90135 AGTGCAAACCCACACTTGAAT-CAA-CCCA
1 AGTGCAAACCCACACTTGAATGCAATCCCA
*
90163 AGTGCACAACCCGCACTTG
1 AGTGCA-AACCCACACTTG
90182 TAAAAACACA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 10 0.23
29 14 0.33
30 19 0.44
ACGTcount: A:0.36, C:0.36, G:0.13, T:0.14
Consensus pattern (30 bp):
AGTGCAAACCCACACTTGAATGCAATCCCA
Found at i:90545 original size:28 final size:28
Alignment explanation
Indices: 90513--90566 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
90503 GTCGCGCCAG
*
90513 TTGTTGA-CAGCTTTAGCGCGTCCGTACT
1 TTGTTGATC-GCTTCAGCGCGTCCGTACT
*
90541 TTGTTGATCGCTTCAGCGTGTCCGTA
1 TTGTTGATCGCTTCAGCGCGTCCGTA
90567 ATGTTTGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.13, C:0.24, G:0.26, T:0.37
Consensus pattern (28 bp):
TTGTTGATCGCTTCAGCGCGTCCGTACT
Found at i:94501 original size:8 final size:8
Alignment explanation
Indices: 94465--94499 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
94455 CAAATGAAGC
94465 CAAACACA
1 CAAACACA
94473 CAAACACA
1 CAAACACA
94481 CAAACACA
1 CAAACACA
*
94489 CAAGCACA
1 CAAACACA
94497 CAA
1 CAA
94500 GCGAGGCAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.60, C:0.37, G:0.03, T:0.00
Consensus pattern (8 bp):
CAAACACA
Found at i:95657 original size:50 final size:51
Alignment explanation
Indices: 95598--95824 Score: 248
Period size: 51 Copynumber: 4.5 Consensus size: 51
95588 GTTTAAGTCC
** *
95598 TTTAAGTAATTTGTTTATAAAGATTGGATTTTTAAGTAAAAGA-TGAATCT
1 TTTAAGTAATTTGTAAATAAAGATTGGATTTTTAAGTGAAAGATTGAATCT
* * * *
95648 TTCAAGTAATTTGTAAATAGAGATT-GATTTTTAATTGAAAGATT-AAGCT
1 TTTAAGTAATTTGTAAATAAAGATTGGATTTTTAAGTGAAAGATTGAATCT
* *
95697 TTTAAGTAATTTG-AGAGTAAAGATAGAGA-TTTTAAGTGAAAGATTGAATCT
1 TTTAAGTAATTTGTA-AATAAAGATTG-GATTTTTAAGTGAAAGATTGAATCT
* * * * *
95748 TTTAACTAATTTATACATAAAGACTGGATTTTTAAGTGAAAGATTAAATCT
1 TTTAAGTAATTTGTAAATAAAGATTGGATTTTTAAGTGAAAGATTGAATCT
* * *
95799 TTAAAGTAATGTGTGAATAAAGATTG
1 TTTAAGTAATTTGTAAATAAAGATTG
95825 AACTCTTACG
Statistics
Matches: 143, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
48 1 0.01
49 38 0.27
50 39 0.27
51 64 0.45
52 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.39
Consensus pattern (51 bp):
TTTAAGTAATTTGTAAATAAAGATTGGATTTTTAAGTGAAAGATTGAATCT
Found at i:96708 original size:41 final size:41
Alignment explanation
Indices: 96524--97160 Score: 477
Period size: 41 Copynumber: 14.8 Consensus size: 41
96514 GTCTTATTCT
* * *
96524 CAGTTTGTCCTTCC-CAGTCGAAAGGTGTTGTTTAGTTGCCTATTC
1 CAGTTTGCCCTTCCTCA-TCGGAAGGTGTTGTTTAGTT---T-TCC
* * * *
96569 TAGTTTGGCATTCCTCATCGGAAGGTGTTGTTTA-TATTCC
1 CAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAGTTTTCC
* *
96609 TAGTTTGCCCTTCCTCATCGGAAGGTGTCGTTTAGTTGCTTATTCC
1 CAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA---G-TT-TTCC
* *
96655 CAGTTTGCCCTTCCTCATAGGAAGGTGTTGTTTACTTTTCC
1 CAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAGTTTTCC
* *
96696 C-GTTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTTTCC
1 CAG-TTTGCCCTTCCTCATCGGAAGGTGTTGTTTAGTTTTCC
*
96737 CAGTTTGCCCTTCCTCATAGGAAGGTGTTGTTTAGTTTTCC
1 CAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAGTTTTCC
* * *
96778 C-GTTTTGCCCTTCCCCACCGGAAGGTGTTTTTTAGTTTTCC
1 CAG-TTTGCCCTTCCTCATCGGAAGGTGTTGTTTAGTTTTCC
* * *
96819 CAGTTTGTCCTTCCCCA-CGAGAAGGTGTTGTCTAAGTCTACATTTCC
1 CAGTTTGCCCTTCCTCATCG-GAAGGTGTTGT-TTAG--T---TTTCC
* * *
96866 CAGTTTGCCCTT-CTCCACCGGAAGGTTTTGTCTAGTTCTTTAAATTCC
1 CAGTTTGCCCTTCCT-CATCGGAAGGTGTTGTTTAG----TT---TTCC
* * * *
96914 CAATTTGCTCTTCCCCATCGGAAGGTGTTGTTTAAGTCTACATTTAC
1 CAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTT-AG--T---TTTCC
*
96961 CAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAG-TTTCC
1 CAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAGTTTTCC
* * * *
97001 AATTTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGTTGTCTAATTAC
1 CAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA---GT-T--TTCC
* * * *
97048 TAGTTTACCCTTCCCCACCGGAAGGTGTTGTTTAG-TTT-C
1 CAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAGTTTTCC
* *
97087 CAGTCTTGCCCTTCCTCATTGGAAGGTATTGTTTAG-TTT-C
1 CAGT-TTGCCCTTCCTCATCGGAAGGTGTTGTTTAGTTTTCC
* *
97127 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA
1 CAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
97161 AGTTGCCTTA
Statistics
Matches: 488, Mismatches: 66, Indels: 82
0.77 0.10 0.13
Matches are distributed among these distances:
39 30 0.06
40 107 0.22
41 135 0.28
42 8 0.02
43 1 0.00
44 3 0.01
45 30 0.06
46 42 0.09
47 96 0.20
48 32 0.07
49 3 0.01
50 1 0.00
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.39
Consensus pattern (41 bp):
CAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAGTTTTCC
Found at i:96732 original size:87 final size:87
Alignment explanation
Indices: 96545--97487 Score: 591
Period size: 87 Copynumber: 10.7 Consensus size: 87
96535 TCCCAGTCGA
* * * * *
96545 AAGGTGTTGTTTAGTTGCCTATT-CTAGTTTGGCATTCCTCATCGGAAGGTGTTGTTTA-TATTC
1 AAGGTGTTGTTTAGTTGCTTATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTACTTTTC
* * *
96608 CTAG-TTTGCCCTTCCTCATCGG
66 C-CGTTTTGCCCTTCCCCACCGG
* *
96630 AAGGTGTCGTTTAGTTGCTTATTCCCAGTTTGCCCTTCCTCATAGGAAGGTGTTGTTTACTTTTC
1 AAGGTGTTGTTTAGTTGCTTATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTACTTTTC
96695 CCGTTTTGCCCTTCCCCACCGG
66 CCGTTTTGCCCTTCCCCACCGG
* *
96717 AAGGTGTTGTTTA---G-TT-TTCCCAGTTTGCCCTTCCTCATAGGAAGGTGTTGTTTAGTTTTC
1 AAGGTGTTGTTTAGTTGCTTATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTACTTTTC
96777 CCGTTTTGCCCTTCCCCACCGG
66 CCGTTTTGCCCTTCCCCACCGG
* * *
96799 AAGGTGTT-TTT--TAG-TT-TTCCCAGTTTGTCCTTCCCCA-CGAGAAGGTGTTGTCTAAGTCT
1 AAGGTGTTGTTTAGTTGCTTATTCCCAGTTTGCCCTTCCTCATCG-GAAGGTGTTG--T---T-T
* *
96858 ACATTTCCCAG-TTTGCCCTTCTCCACCGG
59 ACTTTTCCC-GTTTTGCCCTTCCCCACCGG
* * * * *
96887 AAGGTTTTGTCTAGTT-CTTTAAATTCCCAATTTGCTCTTCCCCATCGGAAGGTGTTGTTTAAGT
1 AAGGTGTTGTTTAGTTGC-TT--ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTT-A--
* *
96951 CTACATTTACCAG-TTTGCCCTTCCCCATCGG
60 CT---TTT-CCCGTTTTGCCCTTCCCCACCGG
* * * *
96982 AAGGTGTTGTTTA---G--T-TTCCAATTTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGTTGTC
1 AAGGTGTTGTTTAGTTGCTTATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA-CT-T-
** *
97041 TAATTAC-TAGTTTACCCTTCCCCACCGG
63 T--TCCCGT--TTTGCCCTTCCCCACCGG
* * *
97069 AAGGTGTTGTTTA---G--T-TT-CCAGTCTTGCCCTTCCTCATTGGAAGGTATTGTTTA-GTTT
1 AAGGTGTTGTTTAGTTGCTTATTCCCAGT-TTGCCCTTCCTCATCGGAAGGTGTTGTTTACTTTT
*
97126 CCAG-TTTGCCCTTCCCCACCGG
65 CCCGTTTTGCCCTTCCCCACCGG
* *
97148 AAGGTGTTGTTTAAGTTGCCTTATT-CCTGTTTTGCCCTT-CTCCACCGGAAGGTGTTGTTTAAG
1 AAGGTGTTGTTT-AGTTG-CTTATTCCCAG-TTTGCCCTTCCT-CATCGGAAGGTGTTG--T---
* *
97211 TTACCTTATTCCTGTTTTGCCCTTCCCTACCGG
57 TTA-CTT-TTCCCGTTTTGCCCTTCCCCACCGG
* * *
97244 AAGGTTTTGTTTAGATTGCCTTATTCCC-GTTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGT
1 AAGGTGTTGTTTAG-TTG-CTTATTCCCAG-TTTGCCCTTCCTCATCGGAAGGTGTTGTTT-A--
* *
97308 TGCCTTATTCACGTTTTGCCCTT-CCCAACGG
60 ---CTT-TTCCCGTTTTGCCCTTCCCCACCGG
* * * * *
97339 AAGTTGTTGTCTAAGTTGCCTTATT-CCTGTTTCACCCTTCCAT-ATCGGAAGGTGTTGTTTAGT
1 AAGGTGTTGT-TTAGTTG-CTTATTCCCAGTTT-GCCCTTCC-TCATCGGAAGGTGTTGTTTACT
* * * *
97402 TTTCCTGGTTTGCTCTTCCCTACCGG
62 TTTCCCGTTTTGCCCTTCCCCACCGG
* * *
97428 AAGGTGTTGTTTATTTTGTCTTATT-CCTGTTTCGCCCTTCC-CGATTGGAAGGTGTTGTTT
1 AAGGTGTTGTTTA-GTTG-CTTATTCCCAGTTT-GCCCTTCCTC-ATCGGAAGGTGTTGTTT
97488 TGCCATGATT
Statistics
Matches: 700, Mismatches: 85, Indels: 142
0.76 0.09 0.15
Matches are distributed among these distances:
79 29 0.04
80 1 0.00
81 5 0.01
82 105 0.15
83 5 0.01
84 4 0.01
85 22 0.03
86 40 0.06
87 151 0.22
88 47 0.07
89 62 0.09
90 3 0.00
91 3 0.00
92 7 0.01
93 1 0.00
94 8 0.01
95 114 0.16
96 90 0.13
97 3 0.00
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.41
Consensus pattern (87 bp):
AAGGTGTTGTTTAGTTGCTTATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTACTTTTC
CCGTTTTGCCCTTCCCCACCGG
Found at i:96936 original size:48 final size:47
Alignment explanation
Indices: 96604--97304 Score: 335
Period size: 48 Copynumber: 15.8 Consensus size: 47
96594 TGTTGTTTAT
* * * *
96604 ATTCCTAGTTTGCCCTTCCTCATCGGAAGGTGTCGTTTAGTTGCT--T
1 ATTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTT-CTACA
* *
96650 ATTCCCAGTTTGCCCTTCCTCATAGGAAGGTGTTGTTTA---CT---
1 ATTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTCTACA
* *
96691 TTTCCC-GTTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAG-T-T---
1 ATTCCCAG-TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTCTACA
* *
96733 -TTCCCAGTTTGCCCTTCCTCATAGGAAGGTGTTGTTTAG-T-T---
1 ATTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTCTACA
* *
96774 -TTCCC-GTTTTGCCCTTCCCCACCGGAAGGTGTTTTTTAG-T-T---
1 ATTCCCAG-TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTCTACA
* *
96815 -TTCCCAGTTTGTCCTTCCCCA-CGAGAAGGTGTTGTCTAAG-TCTACA
1 ATTCCCAGTTTGCCCTTCCCCATCG-GAAGGTGTTGT-TTAGTTCTACA
* * * * *
96861 TTTCCCAGTTTGCCCTTCTCCACCGGAAGGTTTTGTCTAGTTCTTTA-A
1 ATTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTC--TACA
* *
96909 ATTCCCAATTTGCTCTTCCCCATCGGAAGGTGTTGTTTAAG-TCTACA
1 ATTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTT-AGTTCTACA
* * *
96956 TTTACCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTT-TCCA
1 ATTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTCTACA
* * *
97002 A-T-----TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGTTGT-CTA
1 ATTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTCTAC-A
* * * *
97043 ATTACTAGTTTACCCTTCCCCACCGGAAGGTGTTGTTTAG---T---
1 ATTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTCTACA
* * *
97084 -TT-CCAGTCTTGCCCTTCCTCATTGGAAGGTATTGTTTAG---T---
1 ATTCCCAGT-TTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTCTACA
* *
97124 -TT-CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGC--CTT
1 ATTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTT-AGTT-CTAC-A
* * * *
97170 ATT-CCTGTTTTGCCCTTCTCCACCGGAAGGTGTTGTTTAAG-T-TACCTT
1 ATTCCCAG-TTTGCCCTTCCCCATCGGAAGGTGTTGTTT-AGTTCTA-C-A
* * * * *
97218 ATT-CCTGTTTTGCCCTTCCCTACCGGAAGGTTTTGTTTAGATTGC--CTT
1 ATTCCCAG-TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAG-TT-CTAC-A
*
97266 ATTCCC-GTTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA
1 ATTCCCAG-TTTGCCCTTCCCCATCGGAAGGTGTTGTTTA
97305 AGTTGCCTTA
Statistics
Matches: 552, Mismatches: 56, Indels: 92
0.79 0.08 0.13
Matches are distributed among these distances:
39 29 0.05
40 75 0.14
41 135 0.24
42 10 0.02
43 1 0.00
44 1 0.00
45 1 0.00
46 45 0.08
47 105 0.19
48 143 0.26
49 7 0.01
ACGTcount: A:0.15, C:0.26, G:0.20, T:0.40
Consensus pattern (47 bp):
ATTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTCTACA
Found at i:96953 original size:95 final size:95
Alignment explanation
Indices: 96781--96997 Score: 272
Period size: 95 Copynumber: 2.4 Consensus size: 95
96771 GTTTTCCCGT
** *
96781 TTTGCCCTTCCCCACCGGAAGGTGTT-T-T--TTAGTT---TTCCCAGTTTGTCCTTCCCCACGA
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTCTAGTTCTTTAAATTCCCAATTTGTCCTTCCCCACGA
*
96839 GAAGGTGTTGTCTAAGTCTACATTTCCCAG
66 GAAGGTGTTGTCTAAGTCTACATTTACCAG
* *
96869 TTTGCCCTTCTCCACCGGAAGGTTTTGTCTAGTTCTTTAAATTCCCAATTTG-CTCTTCCCCATC
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTCTAGTTCTTTAAATTCCCAATTTGTC-CTTCCCCA-C
*
96933 G-GAAGGTGTTGTTTAAGTCTACATTTACCAG
64 GAGAAGGTGTTGTCTAAGTCTACATTTACCAG
* *
96964 TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTCTAGTT
96998 TCCAATTTTG
Statistics
Matches: 109, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
88 24 0.22
89 1 0.01
90 1 0.01
92 4 0.04
94 1 0.01
95 76 0.70
96 2 0.02
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (95 bp):
TTTGCCCTTCCCCACCGGAAGGTGTTGTCTAGTTCTTTAAATTCCCAATTTGTCCTTCCCCACGA
GAAGGTGTTGTCTAAGTCTACATTTACCAG
Found at i:97150 original size:39 final size:39
Alignment explanation
Indices: 97049--97160 Score: 170
Period size: 40 Copynumber: 2.8 Consensus size: 39
97039 TCTAATTACT
*
97049 AGTTTACCCTTCCCCACCGGAAGGTGTTGTTTAGTTTCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTTCC
* ** *
97088 AGTCTTGCCCTTCCTCATTGGAAGGTATTGTTTAGTTTCC
1 AGT-TTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTTCC
97128 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA
97161 AGTTGCCTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
39 29 0.46
40 34 0.54
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (39 bp):
AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTTCC
Found at i:97311 original size:48 final size:48
Alignment explanation
Indices: 97130--97487 Score: 421
Period size: 48 Copynumber: 7.6 Consensus size: 48
97120 TAGTTTCCAG
97130 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCCTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCCTGT
* *
97178 TTTGCCCTTCTCCACCGGAAGGTGTTGTTTAAGTTACCTTATTCCTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCCTGT
* * *
97226 TTTGCCCTTCCCTACCGGAAGGTTTTGTTT-AGATTGCCTTATTCCCGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAG-TTGCCTTATTCCTGT
97274 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCAC-GT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTC-CTGT
* * *
97322 TTTGCCCTT-CCCAACGGAAGTTGTTGTCTAAGTTGCCTTATTCCTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCCTGT
** ** * *
97369 TTCACCCTTCCATATCGGAAGGTGTTGTTT-A---G--TT-TTCCTGG
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCCTGT
* * ** *
97410 TTTGCTCTTCCCTACCGGAAGGTGTTGTTTATTTTGTCTTATTCCTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCCTGT
* * **
97458 TTCGCCCTTCCCGATTGGAAGGTGTTGTTT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTT
97488 TGCCATGATT
Statistics
Matches: 266, Mismatches: 32, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
41 31 0.12
42 2 0.01
44 1 0.00
45 1 0.00
46 1 0.00
47 45 0.17
48 182 0.68
49 3 0.01
ACGTcount: A:0.13, C:0.25, G:0.20, T:0.42
Consensus pattern (48 bp):
TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCCTGT
Found at i:97460 original size:89 final size:88
Alignment explanation
Indices: 97322--97487 Score: 224
Period size: 89 Copynumber: 1.9 Consensus size: 88
97312 TTATTCACGT
* *
97322 TTTGCCCTTCCCAACGGAAGTTGTTGTCTAAGTTGCCTTATTCCTGTTTCACCCTTCCATATCGG
1 TTTGCCCTTCCCAACGGAAGGTGTTGTCTAAGTTGCCTTATTCCTGTTTCACCCTTCCAGATCGG
97387 AAGGTGTTGTTTAGTTTTCCTGG
66 AAGGTGTTGTTTAGTTTTCCTGG
* * * ** * * * *
97410 TTTGCTCTTCCCTACCGGAAGGTGTTGTTTATTTTGTCTTATTCCTGTTTCGCCCTTCCCGATTG
1 TTTGCCCTTCCC-AACGGAAGGTGTTGTCTAAGTTGCCTTATTCCTGTTTCACCCTTCCAGATCG
97475 GAAGGTGTTGTTT
65 GAAGGTGTTGTTT
97488 TGCCATGATT
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
88 11 0.17
89 55 0.83
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (88 bp):
TTTGCCCTTCCCAACGGAAGGTGTTGTCTAAGTTGCCTTATTCCTGTTTCACCCTTCCAGATCGG
AAGGTGTTGTTTAGTTTTCCTGG
Found at i:97467 original size:184 final size:188
Alignment explanation
Indices: 97130--97487 Score: 474
Period size: 184 Copynumber: 1.9 Consensus size: 188
97120 TAGTTTCCAG
* * **
97130 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCCTGTTTTGCCCTTCTCCACCG
1 TTTGCCCTTCCCCAACGGAAGGTGTTGTCTAAGTTGCCTTATTCCTGTTTCACCCTTCTCCACCG
* *
97195 GAAGGTGTTGTTTAAGTTACCTTATTCCTGTTTTGCCCTTCCCTACCGGAAGGTTTTGTTTAGAT
66 GAAGGTGTTGTTTAAG----CTTATTCCTGGTTTGCCCTTCCCTACCGGAAGGTGTTGTTTAGAT
*
97260 TGCCTTATTCCCGTTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCACGT
127 TGCCTTATTCCCGTTTCGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCACGT
* * *
97322 TTTGCCCTT-CCCAACGGAAGTTGTTGTCTAAGTTGCCTTATTCCTGTTTCACCCTTC-CATATC
1 TTTGCCCTTCCCCAACGGAAGGTGTTGTCTAAGTTGCCTTATTCCTGTTTCACCCTTCTC-CACC
* ** *
97385 GGAAGGTGTTGTTT-AG-TT-TTCCTGGTTTGCTCTTCCCTACCGGAAGGTGTTGTTTATTTTGT
65 GGAAGGTGTTGTTTAAGCTTATTCCTGGTTTGCCCTTCCCTACCGGAAGGTGTTGTTTAGATTGC
* * **
97447 CTTATTCCTGTTTCGCCCTTCCCGATTGGAAGGTGTTGTTT
130 CTTATTCCCGTTTCGCCCTTCCCCACCGGAAGGTGTTGTTT
97488 TGCCATGATT
Statistics
Matches: 147, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
184 74 0.50
185 2 0.01
190 3 0.02
191 59 0.40
192 9 0.06
ACGTcount: A:0.13, C:0.25, G:0.20, T:0.42
Consensus pattern (188 bp):
TTTGCCCTTCCCCAACGGAAGGTGTTGTCTAAGTTGCCTTATTCCTGTTTCACCCTTCTCCACCG
GAAGGTGTTGTTTAAGCTTATTCCTGGTTTGCCCTTCCCTACCGGAAGGTGTTGTTTAGATTGCC
TTATTCCCGTTTCGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCACGT
Found at i:113946 original size:21 final size:21
Alignment explanation
Indices: 113912--113952 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
113902 CAAAAACAAC
113912 CCTATTTTTATGGT-TATTTT
1 CCTATTTTTATGGTCTATTTT
*
113932 CCTATGTTTTTTGGTCTATTT
1 CCTAT-TTTTATGGTCTATTT
113953 ATTCTCTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.63
Consensus pattern (21 bp):
CCTATTTTTATGGTCTATTTT
Found at i:114155 original size:19 final size:18
Alignment explanation
Indices: 114131--114166 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
114121 TGAAGATTTC
114131 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
114150 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
114167 ATTAATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:123239 original size:33 final size:32
Alignment explanation
Indices: 123149--123256 Score: 108
Period size: 33 Copynumber: 3.3 Consensus size: 32
123139 AGCATAAGTG
* * * * *
123149 ACCGGCCACGCGACTTGGAGAAGCCCGCGCAAC
1 ACCGGCCACGCGACATGAACATGCCCG-GCCAC
* *
123182 ACCGGCCATGCGACATGAAGATGCCCGGCCATC
1 ACCGGCCACGCGACATGAACATGCCCGGCCA-C
**
123215 ACCGGCCACGCGACATGTCCATGCCCGGCCAC
1 ACCGGCCACGCGACATGAACATGCCCGGCCAC
123247 ACCCGGCCAC
1 A-CCGGCCAC
123257 ATGACTCGGC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 5 0.08
33 59 0.92
ACGTcount: A:0.22, C:0.43, G:0.27, T:0.08
Consensus pattern (32 bp):
ACCGGCCACGCGACATGAACATGCCCGGCCAC
Found at i:124202 original size:8 final size:8
Alignment explanation
Indices: 124189--124222 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
124179 ACCCTTCTTG
124189 AAAAATTC
1 AAAAATTC
124197 AAAAATTC
1 AAAAATTC
*
124205 AGAAACTTC
1 A-AAAATTC
124214 AAAAATTC
1 AAAAATTC
124222 A
1 A
124223 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:124311 original size:5 final size:5
Alignment explanation
Indices: 124301--124332 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
124291 ATTGAAAAAT
*
124301 ATAAA ATAAA ATAAA ATAAA ATAAA AAAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT
124333 TTGACCAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:124321 original size:15 final size:15
Alignment explanation
Indices: 124295--124332 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
124285 AGTTATATTG
*
124295 AAAAATATAAAATAA
1 AAAAAAATAAAATAA
*
124310 AATAAAATAAAATAA
1 AAAAAAATAAAATAA
124325 AAAAAAAT
1 AAAAAAAT
124333 TTGACCAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAAAATAAAATAA
Done.