Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019557.1 Corchorus olitorius cultivar O-4 contig19590, 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: 107903
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:708 original size:22 final size:22
Alignment explanation
Indices: 672--714 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
662 TTTTCCGCAA
* *
672 CAAGTCCTGGGCAGGAGTTGTC
1 CAAGTCCTGGACAGGACTTGTC
*
694 CAAGTCCTTGACAGGACTTGT
1 CAAGTCCTGGACAGGACTTGT
715 TCTGAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (22 bp):
CAAGTCCTGGACAGGACTTGTC
Found at i:775 original size:50 final size:50
Alignment explanation
Indices: 693--814 Score: 181
Period size: 50 Copynumber: 2.4 Consensus size: 50
683 CAGGAGTTGT
* * * *
693 CCAAGTCCTTGACAGGACTTGTTCTGAATTTTCTTCCGTTTTTCAACAGA
1 CCAAGTCCTGGGCAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCAACAGA
* *
743 CCAAGTCCTGGGCAGGAGTTGTTCTTATTTTTCTTCCGTCTTTCAACAGA
1 CCAAGTCCTGGGCAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCAACAGA
*
793 CCAGGTCCTGGGCAGGAGTTGT
1 CCAAGTCCTGGGCAGGAGTTGT
815 CAAGTCCTGG
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (50 bp):
CCAAGTCCTGGGCAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCAACAGA
Found at i:823 original size:21 final size:21
Alignment explanation
Indices: 797--836 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
787 AACAGACCAG
*
797 GTCCTGGGCAGGAGTTGTCAA
1 GTCCTGGGCAGGACTTGTCAA
818 GTCCTGGGCAGGACTTGTC
1 GTCCTGGGCAGGACTTGTC
837 CTGTTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25
Consensus pattern (21 bp):
GTCCTGGGCAGGACTTGTCAA
Found at i:1774 original size:26 final size:26
Alignment explanation
Indices: 1745--1795 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
1735 ATTATTAAAA
1745 TATTTTATTTAGAAAAAGTCAATTTT
1 TATTTTATTTAGAAAAAGTCAATTTT
*
1771 TATTTTATTTAGAAAAATTCAATTT
1 TATTTTATTTAGAAAAAGTCAATTT
1796 CTACAGTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (26 bp):
TATTTTATTTAGAAAAAGTCAATTTT
Found at i:3715 original size:14 final size:15
Alignment explanation
Indices: 3687--3716 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3677 TAAACAACCT
3687 CCACCCCTACAAAAA
1 CCACCCCTACAAAAA
*
3702 CCACCCTTACAAAAA
1 CCACCCCTACAAAAA
3717 TAGAACATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.43, G:0.00, T:0.10
Consensus pattern (15 bp):
CCACCCCTACAAAAA
Found at i:4820 original size:23 final size:23
Alignment explanation
Indices: 4790--4836 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
4780 TTAGATTTTT
4790 TTACTTTCATAAGTTCAATAAAG
1 TTACTTTCATAAGTTCAATAAAG
4813 TTACTTTCATAAGTTCAATAAAG
1 TTACTTTCATAAGTTCAATAAAG
4836 T
1 T
4837 CTACCTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (23 bp):
TTACTTTCATAAGTTCAATAAAG
Found at i:15828 original size:35 final size:34
Alignment explanation
Indices: 15769--15846 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 34
15759 TTTATAAGAC
15769 TAATCATTC-TTTTTTTTTTAAAAAAAAAGACTA
1 TAATCATTCTTTTTTTTTTTAAAAAAAAAGACTA
*
15802 TAATCATTCTTTTTTTTTTTTTAAAAAAAAGACTA
1 TAATCATTC-TTTTTTTTTTTAAAAAAAAAGACTA
15837 TAATCATTCT
1 TAATCATTCT
15847 ATTTGAACAT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
33 9 0.21
34 1 0.02
35 32 0.76
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (34 bp):
TAATCATTCTTTTTTTTTTTAAAAAAAAAGACTA
Found at i:16494 original size:16 final size:16
Alignment explanation
Indices: 16473--16504 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
16463 AAGAAATTAA
16473 TCAATTACCAAAATAG
1 TCAATTACCAAAATAG
16489 TCAATTACCAAAATAG
1 TCAATTACCAAAATAG
16505 GGCAGGGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (16 bp):
TCAATTACCAAAATAG
Found at i:17304 original size:11 final size:11
Alignment explanation
Indices: 17288--17338 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
17278 AAGGGCTGAA
17288 ATTAATTAATT
1 ATTAATTAATT
*
17299 ATTAATTAAAT
1 ATTAATTAATT
*
17310 AATAA-TAATT
1 ATTAATTAATT
17320 ATTGAA-TAATT
1 ATT-AATTAATT
17331 ATT-ATTAA
1 ATTAATTAA
17339 AAATCCCACA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
9 1 0.03
10 9 0.26
11 24 0.71
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (11 bp):
ATTAATTAATT
Found at i:31269 original size:54 final size:54
Alignment explanation
Indices: 31187--31294 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
31177 GCCGCCCAAC
31187 TTGCAATTTATGCAATTAAGGGCTTGGCACTCTAGGGTTTTTTAAATTCTAGCT
1 TTGCAATTTATGCAATTAAGGGCTTGGCACTCTAGGGTTTTTTAAATTCTAGCT
31241 TTGCAATTTATGCAATTAAGGGCTTGGCACTCTAGGGTTTTTTAAATTCTAGCT
1 TTGCAATTTATGCAATTAAGGGCTTGGCACTCTAGGGTTTTTTAAATTCTAGCT
31295 AATTGGGTAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (54 bp):
TTGCAATTTATGCAATTAAGGGCTTGGCACTCTAGGGTTTTTTAAATTCTAGCT
Found at i:32342 original size:13 final size:13
Alignment explanation
Indices: 32324--32349 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32314 CTTGGCATGA
32324 GTGATGATTTTTG
1 GTGATGATTTTTG
32337 GTGATGATTTTTG
1 GTGATGATTTTTG
32350 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:32732 original size:19 final size:18
Alignment explanation
Indices: 32710--32760 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
32700 GGGCTGAAAT
32710 TAATTATTTATTAATTAAA
1 TAATTA-TTATTAATTAAA
* * *
32729 TAATAATTATTTTATTGAA
1 TAATTATTA-TTAATTAAA
32748 TAATTATTATTAA
1 TAATTATTATTAA
32761 AAATCCCACA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTATTATTAATTAAA
Found at i:34746 original size:43 final size:43
Alignment explanation
Indices: 34682--34782 Score: 166
Period size: 43 Copynumber: 2.3 Consensus size: 43
34672 TGACCAATTT
34682 GACTTGCAATTTTAATTACAAACCCATGTTTCGCTTCCCTTTA
1 GACTTGCAATTTTAATTACAAACCCATGTTTCGCTTCCCTTTA
* * *
34725 GATTTGCAATTTTAATTACAAACCTATGTTTCGTTTCCCTTTA
1 GACTTGCAATTTTAATTACAAACCCATGTTTCGCTTCCCTTTA
*
34768 GACTTGTAATTTTAA
1 GACTTGCAATTTTAA
34783 AGATCTTTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.44
Consensus pattern (43 bp):
GACTTGCAATTTTAATTACAAACCCATGTTTCGCTTCCCTTTA
Found at i:34806 original size:22 final size:22
Alignment explanation
Indices: 34779--34821 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
34769 ACTTGTAATT
34779 TTAAAGATCTTTAATTATTTTA
1 TTAAAGATCTTTAATTATTTTA
*
34801 TTAAAGGTCTTTAATTATTTT
1 TTAAAGATCTTTAATTATTTT
34822 CGTTTCACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.56
Consensus pattern (22 bp):
TTAAAGATCTTTAATTATTTTA
Found at i:41367 original size:233 final size:233
Alignment explanation
Indices: 40957--41425 Score: 929
Period size: 233 Copynumber: 2.0 Consensus size: 233
40947 GATGTTGGAC
40957 CAATTTCCCTAATATACTAATTTTAAGTCCTCGGATATGATTTTATTACTGCTAAAAGCAAATAT
1 CAATTTCCCTAATATACTAATTTTAAGTCCTCGGATATGATTTTATTACTGCTAAAAGCAAATAT
41022 TAACTTTGTCAAGTGACTTCTTGGTTGTTACGTGCATCAATGTGTTTTAATTCATACATATGGAT
66 TAACTTTGTCAAGTGACTTCTTGGTTGTTACGTGCATCAATGTGTTTTAATTCATACATATGGAT
*
41087 GCTGGGAGTATGATCATTTTAAGCTCCATTTTGCCCCTACTTAAATATTAGATTGGCCATTGTTA
131 GCTGGGAGTATGATCATTTTAAGCTCCATTTTGCCCCTACATAAATATTAGATTGGCCATTGTTA
41152 TGCAGGAATTAAATAAGAATATAATGGTTGATGACAAA
196 TGCAGGAATTAAATAAGAATATAATGGTTGATGACAAA
41190 CAATTTCCCTAATATACTAATTTTAAGTCCTCGGATATGATTTTATTACTGCTAAAAGCAAATAT
1 CAATTTCCCTAATATACTAATTTTAAGTCCTCGGATATGATTTTATTACTGCTAAAAGCAAATAT
41255 TAACTTTGTCAAGTGACTTCTTGGTTGTTACGTGCATCAATGTGTTTTAATTCATACATATGGAT
66 TAACTTTGTCAAGTGACTTCTTGGTTGTTACGTGCATCAATGTGTTTTAATTCATACATATGGAT
41320 GCTGGGAGTATGATCATTTTAAGCTCCATTTTGCCCCTACATAAATATTAGATTGGCCATTGTTA
131 GCTGGGAGTATGATCATTTTAAGCTCCATTTTGCCCCTACATAAATATTAGATTGGCCATTGTTA
41385 TGCAGGAATTAAATAAGAATATAATGGTTGATGACAAA
196 TGCAGGAATTAAATAAGAATATAATGGTTGATGACAAA
41423 CAA
1 CAA
41426 GATGGTAGAT
Statistics
Matches: 235, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
233 235 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (233 bp):
CAATTTCCCTAATATACTAATTTTAAGTCCTCGGATATGATTTTATTACTGCTAAAAGCAAATAT
TAACTTTGTCAAGTGACTTCTTGGTTGTTACGTGCATCAATGTGTTTTAATTCATACATATGGAT
GCTGGGAGTATGATCATTTTAAGCTCCATTTTGCCCCTACATAAATATTAGATTGGCCATTGTTA
TGCAGGAATTAAATAAGAATATAATGGTTGATGACAAA
Found at i:45470 original size:6 final size:6
Alignment explanation
Indices: 45433--45459 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
45423 CCCCCTTCTC
45433 TTTTAA TTTTAA TTTTAA TTTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTT
45460 ATTTTATTTT
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:50895 original size:31 final size:32
Alignment explanation
Indices: 50835--50902 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 32
50825 TTCAAAGAAC
* * * *
50835 ATTTTGTCCTACTTTGTCAAAATTTGAGGGTT
1 ATTTTATCCTACTATGTCAAAATTCGAGGGCT
*
50867 ATTTTATCCTTCTATGTC-AAATTCGAGGGCT
1 ATTTTATCCTACTATGTCAAAATTCGAGGGCT
50898 ATTTT
1 ATTTT
50903 GTCTATCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 16 0.52
32 15 0.48
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.47
Consensus pattern (32 bp):
ATTTTATCCTACTATGTCAAAATTCGAGGGCT
Found at i:53775 original size:59 final size:60
Alignment explanation
Indices: 53658--53788 Score: 140
Period size: 60 Copynumber: 2.2 Consensus size: 60
53648 TTTCTTGGGA
* * * ** * * *
53658 GAAATTATCCCGATTTTGATAGTTTAAGGGTGAAAGTTTCAAATTAAAAGTGAAA-GGGG
1 GAAATTGTCCCTATTTTGATAGTTAAAGACTGAAAGTTCCAAAATAAAAATGAAAGGGGG
**
53717 GAAATTGTCCCTATTTTGATAGATTAAAGACTGAAAGTTCCAAAATAAAAAT-TCAGGGGG
1 GAAATTGTCCCTATTTTGATAG-TTAAAGACTGAAAGTTCCAAAATAAAAATGAAAGGGGG
*
53777 GAAAATGTCCCT
1 GAAATTGTCCCT
53789 TTTGTAAAAG
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 21 0.36
60 38 0.64
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (60 bp):
GAAATTGTCCCTATTTTGATAGTTAAAGACTGAAAGTTCCAAAATAAAAATGAAAGGGGG
Found at i:54866 original size:17 final size:17
Alignment explanation
Indices: 54844--54879 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
54834 ATACAAAGAG
54844 CTATCTAGTATAACAAA
1 CTATCTAGTATAACAAA
* *
54861 CTATCTGGTGTAACAAA
1 CTATCTAGTATAACAAA
54878 CT
1 CT
54880 TTACAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (17 bp):
CTATCTAGTATAACAAA
Found at i:58447 original size:178 final size:178
Alignment explanation
Indices: 58110--58593 Score: 522
Period size: 178 Copynumber: 2.7 Consensus size: 178
58100 ATATTTTTTT
* * ** * * *
58110 ATACTTGAAGCATTAAATTTAACTTTTGACTCATTCATGAAAGTTGTAGATCATGAAAC-AACTT
1 ATACTTGAAACATCAAATTTAACTTTCAAGTCCTACATGAAAGTTGTAGATCATGAAACAAAC-T
* * * * * *
58174 TTTAACAGACACTTGAATCACCTCGATCGGATATATAGAA-AAAAATTTATGTGATATTAAGTAG
65 TTTAACAGACACTTGAATCATCTCAATCGGACATCTAGAACAAAAA-TTATGTAACATTAAGTAG
* * * * * * * *
58238 GCCGTCCATTCTTGCTAACTAAAAAAACTAATATTTCAGAAGCATTTTGG
129 ACAGTCAACTCTCGCTAACCAAAAAAACTAATATTTCAAAAGCATTTTAG
* * * * *
58288 ATACTTTAAACGTCAAATTTAGCTTTCGAGTTCTACATGAAAGTTGTAGATCATGAAACAAACTT
1 ATACTTGAAACATCAAATTTAACTTTCAAGTCCTACATGAAAGTTGTAGATCATGAAACAAACTT
* * *
58353 TTAATAGACACTTAAATCATCTCAATCGGACATCTAGAACAAAACTTATGTAACATTAAGTAGAC
66 TTAACAGACACTTGAATCATCTCAATCGGACATCTAGAACAAAAATTATGTAACATTAAGTAGAC
* * * *
58418 AGTCAACTCTCGCTAACCGACACAACTAATTTTTCAAAAGCATTTTAG
131 AGTCAACTCTCGCTAACCAAAAAAACTAATATTTCAAAAGCATTTTAG
* * ** **
58466 ATACTTGAAACATCAAATTTAACTTTCAAGTCCTTCATGAAAGTTGTATATCATGAATTAATGTT
1 ATACTTGAAACATCAAATTTAACTTTCAAGTCCTACATGAAAGTTGTAGATCATGAAACAAACTT
* * *
58531 TTAACAGACACTTGAATCACTGCAATCAAACTGACATCTAGAGCAAAAATTATGTAACATTAA
66 TTAACAGACACTTGAATCA-T-C--TCAATCGGACATCTAGAACAAAAATTATGTAACATTAA
58594 AATAAAAATT
Statistics
Matches: 252, Mismatches: 48, Indels: 8
0.82 0.16 0.03
Matches are distributed among these distances:
178 209 0.83
179 8 0.03
180 1 0.00
182 34 0.13
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (178 bp):
ATACTTGAAACATCAAATTTAACTTTCAAGTCCTACATGAAAGTTGTAGATCATGAAACAAACTT
TTAACAGACACTTGAATCATCTCAATCGGACATCTAGAACAAAAATTATGTAACATTAAGTAGAC
AGTCAACTCTCGCTAACCAAAAAAACTAATATTTCAAAAGCATTTTAG
Found at i:59125 original size:41 final size:40
Alignment explanation
Indices: 59064--59146 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 40
59054 TTGATTTCAT
59064 TAATTATGTAAAAGAAAATTACTTAAAAGTACTGTATATA
1 TAATTATGTAAAAGAAAATTACTTAAAAGTACTGTATATA
59104 TAATATATGTAAAAGAAAATTACTTAAAAGTACTGTATATA
1 TAAT-TATGTAAAAGAAAATTACTTAAAAGTACTGTATATA
59145 TA
1 TA
59147 TAATAATAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 4 0.10
41 38 0.90
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.35
Consensus pattern (40 bp):
TAATTATGTAAAAGAAAATTACTTAAAAGTACTGTATATA
Found at i:60399 original size:13 final size:13
Alignment explanation
Indices: 60381--60407 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
60371 AGTATAATGG
60381 CGACTTGTTTTGT
1 CGACTTGTTTTGT
60394 CGACTTGTTTTGT
1 CGACTTGTTTTGT
60407 C
1 C
60408 ATTATTAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.19, G:0.22, T:0.52
Consensus pattern (13 bp):
CGACTTGTTTTGT
Found at i:66590 original size:12 final size:13
Alignment explanation
Indices: 66562--66591 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
66552 GTTAGAGAGG
66562 AAAAGGGAAAATA
1 AAAAGGGAAAATA
66575 AAAAGGGAAAATA
1 AAAAGGGAAAATA
66588 AAAA
1 AAAA
66592 TACAGCTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (13 bp):
AAAAGGGAAAATA
Found at i:77250 original size:155 final size:155
Alignment explanation
Indices: 77050--77341 Score: 394
Period size: 155 Copynumber: 1.9 Consensus size: 155
77040 CCGAAAGTAT
* * * * *
77050 TTGAGGCCTAAATGGTGTATAACATCAACCAAAATAACTAAAGAACAACAAAT-AAACCCCAAAT
1 TTGAGCCCTAAATGGTGCATAACATCAACCAAAACAACCAAAGAACAAC-AATCAAACCCCAAAA
*
77114 ACATCAAAAATTACAAACAATATTC-TGCAAAAACCCAATCCCGAAACCTTGTACCC-AAAA-AA
65 ACATAAAAAATTACAAA-AATATTCTTG-AAAAACCCAATCCCGAAACCTTGT-CCCAAAAATAA
77176 AACCCAAATAGGTGCAAACCCCAAATGTC
127 AACCCAAATAGGTGCAAACCCCAAATGTC
* * * **
77205 TTGAGCCCTAAATGGTGCATCACATCAACGAAAACAACCCAAGAACAACAATCCTGACCCCAAAA
1 TTGAGCCCTAAATGGTGCATAACATCAACCAAAACAACCAAAGAACAACAAT-CAAACCCCAAAA
* *
77270 ACATAAAAAATTACCAAAATATTCTTGAAAAACCCAATCTCGAAACCTTGTCCCAAAAATAAAAC
65 ACATAAAAAATTACAAAAATATTCTTGAAAAACCCAATCCCGAAACCTTGTCCCAAAAATAAAAC
77335 CCAAATA
130 CCAAATA
77342 TATAAAGTAA
Statistics
Matches: 119, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
154 6 0.05
155 76 0.64
156 37 0.31
ACGTcount: A:0.48, C:0.26, G:0.09, T:0.17
Consensus pattern (155 bp):
TTGAGCCCTAAATGGTGCATAACATCAACCAAAACAACCAAAGAACAACAATCAAACCCCAAAAA
CATAAAAAATTACAAAAATATTCTTGAAAAACCCAATCCCGAAACCTTGTCCCAAAAATAAAACC
CAAATAGGTGCAAACCCCAAATGTC
Found at i:82325 original size:2 final size:2
Alignment explanation
Indices: 82318--82347 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
82308 AATTGTGGTA
82318 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
82348 TGTTTGTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:85738 original size:176 final size:176
Alignment explanation
Indices: 85385--85852 Score: 559
Period size: 176 Copynumber: 2.6 Consensus size: 176
85375 GATCAAGCTT
* * * *
85385 ATTCGAGTGTCCATTAAAAGGTTGTCTCATGATCTACAACTTTCATGAAGGACTCAAAAACTAAA
1 ATTCAAGTGTCCATTAAAAGGTTGTC-CATAATCTACAACTTTCATGAAGGACTCGAAAGCTAAA
* *
85450 TTTAATGTTTCAAGTAT-CAAATCGCTTCTGAAAAATTAGTTGTTTCGGTTGACGGGAATGGACG
65 TTTAATGTTTCAAGTATAAAAAACGCTTCT-AAAAATTAGTTGTTTCGGTTGACGGGAATGGACG
* * * * * *
85514 GTCCATTTATTATTACTTAACTTTTGCTCCATATGTCTGATAGAGGTG
129 GTCCACTTAATATTACATAACTTTTGCCCCAGATGTCCGATAGAGGTG
* * * *
85562 ATTCAAGTGTCCCTTAAAAGATTGTCAATTATCTACAA-TTTCCATGAAGGACTCGAAAGCT-AA
1 ATTCAAGTGTCCATTAAAAGGTTGTCCATAATCTACAACTTT-CATGAAGGACTCGAAAGCTAAA
*
85625 TTTAATGTTTCAAATATAAAAAACGCTTGC-AAAATATTAGTTGTTTCGGTT-AGCGGGAATGGA
65 TTTAATGTTTCAAGTATAAAAAACGCTT-CTAAAA-ATTAGTTGTTTCGGTTGA-CGGGAATGGA
* * * *
85688 TGGTCTACTTAATATTACATAATTTTTGCCCCAGATGTCCGATTGAGGTG
127 CGGTCCACTTAATATTACATAACTTTTGCCCCAGATGTCCGATAGAGGTG
* ** * *
85738 ATTTAAGTGTTTATTAAAAGGTTGTTCCATAATCTACAACTTTCATGGAGGACTTGAAAGCTAAA
1 ATTCAAGTGTCCATTAAAAGGTTG-TCCATAATCTACAACTTTCATGAAGGACTCGAAAGCTAAA
* * * *
85803 TTTGATGTTTCAAGTATAAAAAATGCTTCTAAAAAATTTGTTATTTCGGT
65 TTTAATGTTTCAAGTATAAAAAACGCTTCT-AAAAATTAGTTGTTTCGGT
85853 GGACTGTCTA
Statistics
Matches: 247, Mismatches: 34, Indels: 19
0.82 0.11 0.06
Matches are distributed among these distances:
175 26 0.11
176 120 0.49
177 54 0.22
178 43 0.17
179 4 0.02
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (176 bp):
ATTCAAGTGTCCATTAAAAGGTTGTCCATAATCTACAACTTTCATGAAGGACTCGAAAGCTAAAT
TTAATGTTTCAAGTATAAAAAACGCTTCTAAAAATTAGTTGTTTCGGTTGACGGGAATGGACGGT
CCACTTAATATTACATAACTTTTGCCCCAGATGTCCGATAGAGGTG
Found at i:87585 original size:36 final size:36
Alignment explanation
Indices: 87545--87643 Score: 126
Period size: 36 Copynumber: 2.8 Consensus size: 36
87535 ATCTTGCTGA
* * *
87545 CCTAAGTTGCCTAATACTTGGCTATAATGCCATTAG
1 CCTAAGTCGCCTAATACTTGGCTATAACGCCACTAG
* **
87581 CCTAAGTCGCCTAATACTTGGCTTTAACGCTGCTAG
1 CCTAAGTCGCCTAATACTTGGCTATAACGCCACTAG
* *
87617 CCTAAGTCGCCCAATAATTGGCTATAA
1 CCTAAGTCGCCTAATACTTGGCTATAA
87644 AGTCGATGGC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (36 bp):
CCTAAGTCGCCTAATACTTGGCTATAACGCCACTAG
Found at i:87663 original size:36 final size:36
Alignment explanation
Indices: 87545--87714 Score: 105
Period size: 36 Copynumber: 4.8 Consensus size: 36
87535 ATCTTGCTGA
* * * * * *
87545 CCTAAGTTGCCTAATACTTGGCTATAATG-CCATTAG
1 CCTAAGTCGCCCAATAATTGGCTATAAAGTCGA-TGG
* * * * * *
87581 CCTAAGTCGCCTAATACTTGGCTTTAACG-CTGCTAG
1 CCTAAGTCGCCCAATAATTGGCTATAAAGTC-GATGG
87617 CCTAAGTCGCCCAATAATTGGCTATAAAGTCGATGG
1 CCTAAGTCGCCCAATAATTGGCTATAAAGTCGATGG
* * ** * *
87653 CCTTAA-TCG-CCGATATTTGGCTATAATTTTGTTGG
1 CC-TAAGTCGCCCAATAATTGGCTATAAAGTCGATGG
* *
87688 GCTAAGTCGCCCAATAATTGACTATAA
1 CCTAAGTCGCCCAATAATTGGCTATAA
87715 GTTGCTAGCC
Statistics
Matches: 108, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
34 3 0.03
35 24 0.22
36 77 0.71
37 4 0.04
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (36 bp):
CCTAAGTCGCCCAATAATTGGCTATAAAGTCGATGG
Found at i:87764 original size:71 final size:71
Alignment explanation
Indices: 87585--87774 Score: 193
Period size: 71 Copynumber: 2.7 Consensus size: 71
87575 CATTAGCCTA
* * *
87585 AGTCGCCTAATACTTGGCTTTAACGCTGCTAGCCTAAGTCGCCCAATAATTGGCTATAAAGTCGA
1 AGTCGCC-AATACTTGGCTTTAATGCTGCTGGCCTAAGTCGCCCAATAATTGACTATAAAGTCGA
* *
87650 TGGCCTT
65 TAGCCAT
* * * * ** * * * *
87657 AATCGCCGATATTTGGCTATAATTTTGTTGGGCTAAGTCGCCCAATAATTGACTAT-AAGTTGCT
1 AGTCGCCAATACTTGGCTTTAATGCTGCTGGCCTAAGTCGCCCAATAATTGACTATAAAGTCGAT
87721 AGCCAT
66 AGCCAT
* * *
87727 AGTCGCGCAATACTTGGTTTTAATGCCGCTGGCCTAAGTCGTCCAATA
1 AGTCGC-CAATACTTGGCTTTAATGCTGCTGGCCTAAGTCGCCCAATA
87775 CATACTAGCT
Statistics
Matches: 91, Mismatches: 26, Indels: 3
0.76 0.22 0.03
Matches are distributed among these distances:
70 15 0.16
71 70 0.77
72 6 0.07
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (71 bp):
AGTCGCCAATACTTGGCTTTAATGCTGCTGGCCTAAGTCGCCCAATAATTGACTATAAAGTCGAT
AGCCAT
Found at i:88538 original size:4 final size:4
Alignment explanation
Indices: 88529--88567 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
88519 ATTTTTGTGG
*
88529 ATAC ATAC ATAC ATAC ATAC ATGC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
88568 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:88726 original size:2 final size:2
Alignment explanation
Indices: 88719--88744 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
88709 AGGTTGAAAC
88719 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
88745 TATGTGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93504 original size:21 final size:21
Alignment explanation
Indices: 93451--93505 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
93441 GCCTTCAGCA
93451 GCTTGC-GCCTGGGTGCTCAG
1 GCTTGCGGCCTGGGTGCTCAG
* * * * *
93471 GCCTACGGGCTGGGTGTTCAT
1 GCTTGCGGCCTGGGTGCTCAG
93492 GCTTGCGGCCTGGG
1 GCTTGCGGCCTGGG
93506 GGGGGGGGGG
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.05, C:0.27, G:0.42, T:0.25
Consensus pattern (21 bp):
GCTTGCGGCCTGGGTGCTCAG
Found at i:95905 original size:24 final size:24
Alignment explanation
Indices: 95872--95917 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
95862 TGGACTTGAA
95872 GATGACCATGGAGAGCATGGAGAG
1 GATGACCATGGAGAGCATGGAGAG
* **
95896 GATGAGCATGGATTGCATGGAG
1 GATGACCATGGAGAGCATGGAG
95918 GCATGGAGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.41, T:0.17
Consensus pattern (24 bp):
GATGACCATGGAGAGCATGGAGAG
Found at i:97124 original size:115 final size:116
Alignment explanation
Indices: 96921--97145 Score: 407
Period size: 115 Copynumber: 1.9 Consensus size: 116
96911 AAGAAGTAAG
96921 AAATTCTTAGGTGGTAATTTGTCTTCAATCTTCTTGTAGCTTCCTTCCTTCCCAAGCAACAACGC
1 AAATTCTTAGGTGGTAATTTGTCTTCAATCTTCTTGTAGCTTCCTTCCTTCCCAAGCAACAACGC
96986 CAAAATTGTGATCGAGTCATTGAACAATCACAAAATAAATCCCCACAAAAT
66 CAAAATTGTGATCGAGTCATTGAACAATCACAAAATAAATCCCCACAAAAT
* *
97037 AAATTCTTAGGTGGTAATTTGT-TTCAATCTTCTTGTTGCTTCCTTCCTTCCCAAGCAACGACGC
1 AAATTCTTAGGTGGTAATTTGTCTTCAATCTTCTTGTAGCTTCCTTCCTTCCCAAGCAACAACGC
* *
97101 CAAAATTGTGATCGAGTCGTTGAACAATCGCAAAATAAATCCCCA
66 CAAAATTGTGATCGAGTCATTGAACAATCACAAAATAAATCCCCA
97146 TAAACCTTTA
Statistics
Matches: 105, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
115 83 0.79
116 22 0.21
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (116 bp):
AAATTCTTAGGTGGTAATTTGTCTTCAATCTTCTTGTAGCTTCCTTCCTTCCCAAGCAACAACGC
CAAAATTGTGATCGAGTCATTGAACAATCACAAAATAAATCCCCACAAAAT
Found at i:99156 original size:15 final size:17
Alignment explanation
Indices: 99131--99162 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
99121 TACCTTATGG
99131 AGTCTTTGGAA-AGTGA
1 AGTCTTTGGAAGAGTGA
99147 AGTC-TTGGAAGAGTGA
1 AGTCTTTGGAAGAGTGA
99163 TATTGGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.31, C:0.06, G:0.34, T:0.28
Consensus pattern (17 bp):
AGTCTTTGGAAGAGTGA
Found at i:99604 original size:44 final size:43
Alignment explanation
Indices: 99537--99848 Score: 324
Period size: 44 Copynumber: 7.1 Consensus size: 43
99527 TACCCTTCAT
* *
99537 CATTGGAAGAAGGTGATAGTTTCGCAAACACCATATTCTTTTGA
1 CATTGGAA-AAGGTGATAGTTTCGCGAACACCATATGCTTTTGA
* * * *
99581 CATTGGGAAAAGGTGATAATTTCGCCAACATCATATGCCTTTGA
1 CATT-GGAAAAGGTGATAGTTTCGCGAACACCATATGCTTTTGA
* * * * *
99625 CATTGGGAGAGGGTGATAGTTTCGCGAATACCATATGTTTTTTA
1 CATT-GGAAAAGGTGATAGTTTCGCGAACACCATATGCTTTTGA
* *
99669 CCTT-GAAAGAGGGTGATAGTTTCGCGAACACCATATGCATTTGA
1 CATTGGAAA-A-GGTGATAGTTTCGCGAACACCATATGCTTTTGA
*
99713 CATTGGGAAAAGGTGATAGTTTCACGAACACCATATGCTTTTGA
1 CATT-GGAAAAGGTGATAGTTTCGCGAACACCATATGCTTTTGA
* * * *
99757 -TTTTGAAAGAGGGTGATAGTTTCGCGAACACCATATACCTTTGA
1 CATTGGAAA-A-GGTGATAGTTTCGCGAACACCATATGCTTTTGA
* * *
99801 CAAT-GAAATAGGGAGATAGTTTCGCGAACACCATATGCTTTTAA
1 CATTGGAAA-A-GGTGATAGTTTCGCGAACACCATATGCTTTTGA
99845 CATT
1 CATT
99849 AAAAGAAGTG
Statistics
Matches: 223, Mismatches: 37, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
42 7 0.03
43 3 0.01
44 203 0.91
45 6 0.03
46 4 0.02
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (43 bp):
CATTGGAAAAGGTGATAGTTTCGCGAACACCATATGCTTTTGA
Found at i:99686 original size:88 final size:88
Alignment explanation
Indices: 99537--99854 Score: 381
Period size: 88 Copynumber: 3.6 Consensus size: 88
99527 TACCCTTCAT
* * *
99537 CATTGGAAGAAGGTGATAGTTTCGCAAACACCATATTCTTTTGACATTGGGAAA-A-GGTGATAA
1 CATTGGAAGAAGGTGATAGTTTCGCGAACACCATATGCTTTTGACATT--GAAAGAGGGTGATAG
* *
99600 TTTCGCCAACATCATATGCCTTTGA
64 TTTCGCGAACACCATATGCCTTTGA
* * * * * *
99625 CATTGGGAGAGGGTGATAGTTTCGCGAATACCATATGTTTTTTACCTTGAAAGAGGGTGATAGTT
1 CATTGGAAGAAGGTGATAGTTTCGCGAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGTT
*
99690 TCGCGAACACCATATGCATTTGA
66 TCGCGAACACCATATGCCTTTGA
* **
99713 CATTGGGAA-AAGGTGATAGTTTCACGAACACCATATGCTTTTGATTTTGAAAGAGGGTGATAGT
1 CATT-GGAAGAAGGTGATAGTTTCGCGAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGT
*
99777 TTCGCGAACACCATATACCTTTGA
65 TTCGCGAACACCATATGCCTTTGA
* * * * * * *
99801 CAATGAAATAGGGAGATAGTTTCGCGAACACCATATGCTTTTAACATTAAAAGA
1 CATTGGAAGAAGGTGATAGTTTCGCGAACACCATATGCTTTTGACATTGAAAGA
99855 AGTGGCAATT
Statistics
Matches: 195, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
86 4 0.02
87 4 0.02
88 184 0.94
89 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (88 bp):
CATTGGAAGAAGGTGATAGTTTCGCGAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGTT
TCGCGAACACCATATGCCTTTGA
Found at i:99790 original size:132 final size:132
Alignment explanation
Indices: 99543--99848 Score: 405
Period size: 132 Copynumber: 2.3 Consensus size: 132
99533 TCATCATTGG
* * * *
99543 AAGAAGGTGATAGTTTCGCAAACACCATATTCTTTTGACATTGGGAAAAGGTGATAATTTCGCCA
1 AAGAGGGTGATAGTTTCGCGAACACCATATGCTTTTGACATTGGGAAAAGGTGATAATTTCACCA
* ** * *** * **
99608 ACATCATATGCCTTTGACATTGGGAGAGGGTGATAGTTTCGCGAATACCATATGTTTTTTACCTT
66 ACACCATATGCCTTTGACATTGAAAGAGGGTGATAGTTTCGCGAACACCATATACCTTTGACAAT
99673 GA
131 GA
* * *
99675 AAGAGGGTGATAGTTTCGCGAACACCATATGCATTTGACATTGGGAAAAGGTGATAGTTTCACGA
1 AAGAGGGTGATAGTTTCGCGAACACCATATGCTTTTGACATTGGGAAAAGGTGATAATTTCACCA
* **
99740 ACACCATATGCTTTTGATTTTGAAAGAGGGTGATAGTTTCGCGAACACCATATACCTTTGACAAT
66 ACACCATATGCCTTTGACATTGAAAGAGGGTGATAGTTTCGCGAACACCATATACCTTTGACAAT
99805 GA
131 GA
* * *
99807 AATAGGGAGATAGTTTCGCGAACACCATATGCTTTTAACATT
1 AAGAGGGTGATAGTTTCGCGAACACCATATGCTTTTGACATT
99849 AAAAGAAGTG
Statistics
Matches: 150, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
132 150 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (132 bp):
AAGAGGGTGATAGTTTCGCGAACACCATATGCTTTTGACATTGGGAAAAGGTGATAATTTCACCA
ACACCATATGCCTTTGACATTGAAAGAGGGTGATAGTTTCGCGAACACCATATACCTTTGACAAT
GA
Found at i:100277 original size:75 final size:73
Alignment explanation
Indices: 100124--100472 Score: 316
Period size: 72 Copynumber: 4.7 Consensus size: 73
100114 TGCTTAATCC
* * * * * * *
100124 TTTTTTAAGCTACATAGGATGTAGCCGTTGTAAG-CCTTTTTTGAAGTTGCATTTGTAT-AGGCG
1 TTTTTTAAGCTGCATAGGCTATAGGCGTTGTACGCCCTTTTTT-AAGCTGCA-TAGT-TGAGGCG
* *
100187 TTATACACCCCT
63 TTGTA-AGCCCT
* * *
100199 TTTTTTAAGCTACATAGGCTGTAGGCGTTTGTAAGCCCTTTTTTAAGCTGCATAG-T-AGGCGTT
1 TTTTTTAAGCTGCATAGGCTATAGGCG-TTGTACGCCCTTTTTTAAGCTGCATAGTTGAGGCGTT
100262 GTAAGCCCTT
65 GTAAGCCC-T
* * * * * * *
100272 TTTTTTAAGTTGCATAGGTTATAGACATTGTACCCCCTTTTTTGAGCTGCATAGGTTGTGGCCGT
1 TTTTTTAAGCTGCATAGGCTATAGGCGTTGTACGCCCTTTTTTAAGCTGCATA-GTTGAGG-CGT
100337 TGTAAGCCCT
64 TGTAAGCCCT
* * * * *
100347 TTTCTTAAGCTGCATTGGCTATAGGCGTTGTACGCCC-TTTTTAATCTACATAGGCTGCAGGCGT
1 TTTTTTAAGCTGCATAGGCTATAGGCGTTGTACGCCCTTTTTTAAGCTGCATA-GTTG-AGGCGT
100411 TGTAAG--CT
64 TGTAAGCCCT
* * *
100419 CTTTTTAAGCTGCATAGGCTATAGGCGTTGTACGCCCTCTTTTAAGCTACATAG
1 TTTTTTAAGCTGCATAGGCTATAGGCGTTGTACGCCCTTTTTTAAGCTGCATAG
100473 GCTAGAAGCA
Statistics
Matches: 232, Mismatches: 33, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
72 64 0.28
73 46 0.20
74 26 0.11
75 62 0.27
76 26 0.11
77 8 0.03
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (73 bp):
TTTTTTAAGCTGCATAGGCTATAGGCGTTGTACGCCCTTTTTTAAGCTGCATAGTTGAGGCGTTG
TAAGCCCT
Found at i:100314 original size:72 final size:74
Alignment explanation
Indices: 100195--100475 Score: 322
Period size: 72 Copynumber: 3.8 Consensus size: 74
100185 CGTTATACAC
* * * *
100195 CCCTTTTTTTAAGCTACATAGGCTGTAGGCGTTTGTAAGCCCTTTTTTAAGCTGCATA-G-T-AG
1 CCCTTTTTTTAAGCTGCATAGGCTATAGGCG-TTGTACGCCCTTTTTTAAGCTACATAGGCTGAG
100257 GCGTTGTAAG
65 GCGTTGTAAG
* * * * * * * * *
100267 CCCTTTTTTTTAAGTTGCATAGGTTATAGACATTGTACCCCCTTTTTTGAGCTGCATAGGTTGTG
1 CCC-TTTTTTTAAGCTGCATAGGCTATAGGCGTTGTACGCCCTTTTTTAAGCTACATAGGCTGAG
100332 GCCGTTGTAAG
65 G-CGTTGTAAG
* * *
100343 CCCTTTTCTTAAGCTGCATTGGCTATAGGCGTTGTACGCCC-TTTTTAATCTACATAGGCTGCAG
1 CCCTTTTTTTAAGCTGCATAGGCTATAGGCGTTGTACGCCCTTTTTTAAGCTACATAGGCTG-AG
100407 GCGTTGTAAG
65 GCGTTGTAAG
* *
100417 --CTCTTTTTAAGCTGCATAGGCTATAGGCGTTGTACGCCCTCTTTTAAGCTACATAGGCT
1 CCCTTTTTTTAAGCTGCATAGGCTATAGGCGTTGTACGCCCTTTTTTAAGCTACATAGGCT
100476 AGAAGCATCA
Statistics
Matches: 175, Mismatches: 27, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
72 62 0.35
73 40 0.23
74 26 0.15
75 35 0.20
76 12 0.07
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (74 bp):
CCCTTTTTTTAAGCTGCATAGGCTATAGGCGTTGTACGCCCTTTTTTAAGCTACATAGGCTGAGG
CGTTGTAAG
Found at i:100323 original size:37 final size:37
Alignment explanation
Indices: 100122--100473 Score: 216
Period size: 36 Copynumber: 9.5 Consensus size: 37
100112 TCTGCTTAAT
* * * * *
100122 CCTTTTTTAAGCTACATAGGATGTAGCCGTTGTAAG-
1 CCTTTTTTAAGCTGCATAGGTTATAGACGTTGTACGC
* ** * * *
100158 CCTTTTTTGAAGTTGCATTTG-TATAGGCGTTATACACC
1 CCTTTTTT-AAGCTGCATAGGTTATAGACGTTGTAC-GC
* * * * *
100196 CCTTTTTTTAAGCTACATAGGCTGTAGGCGTTTGTAAGC
1 CC-TTTTTTAAGCTGCATAGGTTATAGACG-TTGTACGC
* *
100235 CCTTTTTTAAGCTGCATA-G---TAGGCGTTGTAAGC
1 CCTTTTTTAAGCTGCATAGGTTATAGACGTTGTACGC
* * *
100268 CCTTTTTTTTAAGTTGCATAGGTTATAGACATTGTACCC
1 CC--TTTTTTAAGCTGCATAGGTTATAGACGTTGTACGC
* * * * *
100307 CCTTTTTTGAGCTGCATAGGTTGTGGCCGTTGTAAGC
1 CCTTTTTTAAGCTGCATAGGTTATAGACGTTGTACGC
* * *
100344 CCTTTTCTTAAGCTGCATTGGCTATAGGCGTTGTACGC
1 CCTTTT-TTAAGCTGCATAGGTTATAGACGTTGTACGC
* * * ** * *
100382 CC-TTTTTAATCTACATAGGCTGCAGGCGTTGTAAGC
1 CCTTTTTTAAGCTGCATAGGTTATAGACGTTGTACGC
* * *
100418 TC-TTTTTAAGCTGCATAGGCTATAGGCGTTGTACGC
1 CCTTTTTTAAGCTGCATAGGTTATAGACGTTGTACGC
* *
100454 CCTCTTTTAAGCTACATAGG
1 CCTTTTTTAAGCTGCATAGG
100474 CTAGAAGCAT
Statistics
Matches: 249, Mismatches: 53, Indels: 27
0.76 0.16 0.08
Matches are distributed among these distances:
33 10 0.04
34 6 0.02
35 15 0.06
36 75 0.30
37 60 0.24
38 51 0.20
39 28 0.11
40 4 0.02
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (37 bp):
CCTTTTTTAAGCTGCATAGGTTATAGACGTTGTACGC
Found at i:100326 original size:110 final size:112
Alignment explanation
Indices: 100144--100388 Score: 279
Period size: 110 Copynumber: 2.2 Consensus size: 112
100134 TACATAGGAT
* ** * *
100144 GTAGCCGTTGTAAG-CC-TTTTTTGAAGTTGCATTTGTATAGGCGTTATACACCCCTTTTTTTAA
1 GTAGGCGTTGTAAGCCCTTTTTTTGAAGTTGCATAGGTATAGACATTATACACCCCTTTTTTTAA
100207 GCTACATAGGCTGTAGG-CGTTTGTAAGCCCTTTT-TTAAGCTGCA-TA
66 GCTACATAGGCTGT-GGCCG-TTGTAAGCCCTTTTCTTAAGCTGCATTA
* * *
100253 GTAGGCGTTGTAAGCCCTTTTTTTTAAGTTGCATAGGTTATAGACATTGTAC-CCCC-TTTTTTG
1 GTAGGCGTTGTAAGCCCTTTTTTTGAAGTTGCATAGG-TATAGACATTATACACCCCTTTTTTTA
* * *
100316 AGCTGCATAGGTTGTGGCCGTTGTAAGCCCTTTTCTTAAGCTGCATTG
65 AGCTACATAGGCTGTGGCCGTTGTAAGCCCTTTTCTTAAGCTGCATTA
*
100364 GCTATAGGCGTTGTACGCCCTTTTT
1 G---TAGGCGTTGTAAGCCCTTTTT
100389 AATCTACATA
Statistics
Matches: 115, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
109 29 0.25
110 33 0.29
111 22 0.19
112 11 0.10
114 20 0.17
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (112 bp):
GTAGGCGTTGTAAGCCCTTTTTTTGAAGTTGCATAGGTATAGACATTATACACCCCTTTTTTTAA
GCTACATAGGCTGTGGCCGTTGTAAGCCCTTTTCTTAAGCTGCATTA
Found at i:101672 original size:68 final size:68
Alignment explanation
Indices: 101590--101795 Score: 340
Period size: 68 Copynumber: 3.0 Consensus size: 68
101580 TATCCTATGT
* *
101590 CAACTTCATCATACTGTCAATAGCTATGGTGTGTGTGCTGCACATGACAACGCCAAAAAGCAGTG
1 CAACTCCATCATACTGTCAATAGCTATGGTGTGTGTGCTGCACGTGACAACGCCAAAAAGCAGTG
101655 TCA
66 TCA
101658 CAACTCCATCATACTGTCAATAGCTATGGTGTGTGTGCTGCACGTGACAACGCCAAAAAGCAGTG
1 CAACTCCATCATACTGTCAATAGCTATGGTGTGTGTGCTGCACGTGACAACGCCAAAAAGCAGTG
101723 TCA
66 TCA
* * * *
101726 CAACTCCATCATATTGTCAATAGTTATGATGTGTGTGCGCTGCACGTGACAACGCCAAAAAGTAG
1 CAACTCCATCATACTGTCAATAGCTATG--GTGTGTGTGCTGCACGTGACAACGCCAAAAAGCAG
101791 TGTCA
64 TGTCA
101796 ACATGTACCA
Statistics
Matches: 130, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
68 92 0.71
70 38 0.29
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (68 bp):
CAACTCCATCATACTGTCAATAGCTATGGTGTGTGTGCTGCACGTGACAACGCCAAAAAGCAGTG
TCA
Found at i:102275 original size:2 final size:2
Alignment explanation
Indices: 102231--102260 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
102221 CTTGGGTGGC
102231 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
102261 CTCAGAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:103687 original size:435 final size:432
Alignment explanation
Indices: 102657--103701 Score: 1217
Period size: 435 Copynumber: 2.4 Consensus size: 432
102647 GTTGGCTTTT
102657 ATTTTTGTTTTT-TTT-TTCTATTTGTCCGATTAAGATGATTCAAGTGTCTATTAAAAGGTAATT
1 ATTTTT-TTTTTCTTTGTTCTATTTGT-CGATTAAGATGATTCAAGTGTCTATTAAAAGGTAATT
* * * *
102720 TCATGATCTACAATTTTCATTAAGAACTCAAAAG-TCAA-TTTTA-A--T--ATTCTAAAAAATA
64 TCATGATCTACAACTTTCATAAAG-ACTCAAAAGCT-AATTTTTATATTTCAATTCAAAAAAATG
* ** * * *
102778 CTTCCGAAATTTTGTGGTTTTGATTGCCGGTTAATTTAATATCGTATAATTTTTTGTCAACATGT
127 CTTCTGAAATTTTGT-GTTTCAATTGACGGTT-ATTTAATATCATATAA-TTTTCGTCAACATGT
* * *** * * * *
102843 CATATTGAAGTTATTGAAGTGTCGGTTAAAAGGTTATTGCATGATTTACGACCTTCATGAAGGAC
189 CATATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTACCACATAATCTACAACCTTCATGAAGAAC
** *
102908 CCGAAAGCTAAATTTGATCTACGAGTTTTGTGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGA
254 CCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGATTCAAAAGGGAATTTTTATGTTTCAAGA
* * *
102973 TCTCCATTAACAAACATATTTTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTT
319 TCTCCATTAACAAACATATTTTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTACTTT
* *
103038 ATACTACTTAGTCTTTTACAAATTCTATCTTAATCTAACGTTTAAGCTTC
384 ATACTACTTAGTCCTTTACAAATTCTATCTTAATCT-ACGTTTAAACTTC
* * * *
103088 TTTTTTTTTATTCTTTGTTCTATTTGTCGATTAAGTTGATTCATGTGTCTATAAAAAAGGTAATT
1 ATTTTTTTT-TTCTTTGTTCTATTTGTCGATTAAGATGATTCAAGTGTCTAT-TAAAAGGTAATT
* * * *
103153 TCATGATCTACAACTTTC--AAGGACTCAAAAACAAATTTTTATGTTTCAATTCAAAAAAATGCT
64 TCATGATCTACAACTTTCATAAAGACTCAAAAGCTAATTTTTATATTTCAATTCAAAAAAATGCT
* ** * * *
103216 TCCT-AAATTTGGTCGTTTCAATTGTTGGTCTATTTAATACCATATAATTTTCGATCCACGTGTC
129 T-CTGAAATTTTGT-GTTTCAATTGACGGT-TATTTAATATCATATAATTTTCG-TCAACATGT-
* *
103280 CA-ATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTACCATATAATCTACAACTTTCATGAAGAAC
189 CATATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTACCACATAATCTACAACCTTCATGAAGAAC
** *
103344 CCGAAAG-TTTATTTGATTTACGAGTTTCATGAAGGATTCAAAAGGGAATTTTTATGTTTCAAGA
254 CCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGATTCAAAAGGGAATTTTTATGTTTCAAGA
* * *
103408 TCTCCATTAACAAATAT-TTTCTTATTTGAATTAGTTATTAAATCACCCTCATACTTTTCTATTT
319 TCTCCATTAACAAACATATTT-TTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTACTT
*
103472 TATGCTACTTAGTCCTTTACAAATTCTATCTT-A-CT-CGATTTAACACTTC
383 TATACTACTTAGTCCTTTACAAATTCTATCTTAATCTACG-TTTAA-ACTTC
* *
103521 ATTTTTTTTTTCTTTGTTCTATTTGTCTAATTAAGATAATTCAAGTGTCTATTAAAAGGTAATTT
1 ATTTTTTTTTTCTTTGTTCTATTTGTC-GATTAAGATGATTCAAGTGTCTATTAAAAGGTAATTT
* * * *
103586 TATAATTTACAACTTTCATGAAAGACTCAAAAGCTAATTTTTATATTTCAATTCGAAAAAATGCT
65 CATGATCTACAACTTTCAT-AAAGACTCAAAAGCTAATTTTTATATTTCAATTCAAAAAAATGCT
* * ** *
103651 TTTGAAATTTTGTGATTTCCATTGACAATGTATTTAATATCATATTATTTT
129 TCTGAAATTTTGTG-TTTCAATTGACGGT-TATTTAATATCATATAATTTT
103702 TTATCCAGAT
Statistics
Matches: 516, Mismatches: 74, Indels: 44
0.81 0.12 0.07
Matches are distributed among these distances:
430 13 0.03
431 16 0.03
432 75 0.15
433 72 0.14
434 7 0.01
435 217 0.42
436 112 0.22
437 4 0.01
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (432 bp):
ATTTTTTTTTTCTTTGTTCTATTTGTCGATTAAGATGATTCAAGTGTCTATTAAAAGGTAATTTC
ATGATCTACAACTTTCATAAAGACTCAAAAGCTAATTTTTATATTTCAATTCAAAAAAATGCTTC
TGAAATTTTGTGTTTCAATTGACGGTTATTTAATATCATATAATTTTCGTCAACATGTCATATTA
AAGTTATTCAAGTGTCGGTTAAAAGGTTACCACATAATCTACAACCTTCATGAAGAACCCGAAAG
CTAAATTTGATCTACGAGTTTCATGAAGGATTCAAAAGGGAATTTTTATGTTTCAAGATCTCCAT
TAACAAACATATTTTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTACTTTATACTAC
TTAGTCCTTTACAAATTCTATCTTAATCTACGTTTAAACTTC
Found at i:107365 original size:68 final size:69
Alignment explanation
Indices: 107288--107479 Score: 187
Period size: 68 Copynumber: 2.8 Consensus size: 69
107278 TAAGAGAAAT
* * *
107288 AAGCAAAACAACAACATTTTGAACAACAAAACAACAACA-TTTGAACAGAAAAATAGCA-ATATT
1 AAGCAAAACAACAACATTTTAAACAACAAAACAACAACATTTTGAACAGAAAAACAACAGA-ATT
*
107351 TTGAA
65 TTCAA
* * * * *
107356 AAGCAAAACAACAATATTTTAAACAGCAAAACAACAGCATTTTGAATAGCAAAACAACAGAATTT
1 AAGCAAAACAACAACATTTTAAACAACAAAACAACAACATTTTGAACAGAAAAACAACAGAATTT
107421 TCAA
66 TCAA
* * * * * * *
107425 CAGC--AA-AACAACATTTTAAATAGCAAAATAGCAACATTTTCAACAAAGAAAACAA
1 AAGCAAAACAACAACATTTTAAACAACAAAACAACAACATTTTGAACAGA-AAAACAA
107480 AAACTGTCCA
Statistics
Matches: 102, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
66 32 0.31
67 9 0.09
68 35 0.34
69 25 0.25
70 1 0.01
ACGTcount: A:0.55, C:0.17, G:0.08, T:0.19
Consensus pattern (69 bp):
AAGCAAAACAACAACATTTTAAACAACAAAACAACAACATTTTGAACAGAAAAACAACAGAATTT
TCAA
Found at i:107400 original size:46 final size:45
Alignment explanation
Indices: 107289--107437 Score: 176
Period size: 46 Copynumber: 3.3 Consensus size: 45
107279 AAGAGAAATA
*
107289 AGCAAAACAACAACATTTTGAACAA-CAAAACAACAACA-TTTGAAC
1 AGCAAAACAACAACATTTTGAA-AAGCAAAACAACAA-ATTTTAAAC
* * * *
107334 AGAAAAATAGCAATATTTTGAAAAGCAAAACAACAATATTTTAAAC
1 AGCAAAACAACAACATTTTGAAAAGCAAAACAACAA-ATTTTAAAC
* * *
107380 AGCAAAACAACAGCATTTTGAATAGCAAAACAACAGAATTTTCAAC
1 AGCAAAACAACAACATTTTGAAAAGCAAAACAACA-AATTTTAAAC
107426 AGCAAAACAACA
1 AGCAAAACAACA
107438 TTTTAAATAG
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
44 2 0.02
45 30 0.34
46 55 0.62
47 1 0.01
ACGTcount: A:0.55, C:0.18, G:0.09, T:0.18
Consensus pattern (45 bp):
AGCAAAACAACAACATTTTGAAAAGCAAAACAACAAATTTTAAAC
Found at i:107459 original size:23 final size:23
Alignment explanation
Indices: 107289--107469 Score: 158
Period size: 23 Copynumber: 8.0 Consensus size: 23
107279 AAGAGAAATA
*
107289 AGCAAAACAACAACATTTTGAAC
1 AGCAAAACAACAACATTTTAAAC
* *
107312 AACAAAACAACAACA-TTTGAAC
1 AGCAAAACAACAACATTTTAAAC
* * * *
107334 AGAAAAATAGCAATATTTTGAAA-
1 AGCAAAACAACAACATTTT-AAAC
*
107357 AGCAAAACAACAATATTTTAAAC
1 AGCAAAACAACAACATTTTAAAC
* * *
107380 AGCAAAACAACAGCATTTTGAAT
1 AGCAAAACAACAACATTTTAAAC
*
107403 AGCAAAACAACAGA-ATTTTCAAC
1 AGCAAAACAACA-ACATTTTAAAC
*
107426 AGC--AA-AACAACATTTTAAAT
1 AGCAAAACAACAACATTTTAAAC
* * *
107446 AGCAAAATAGCAACATTTTCAAC
1 AGCAAAACAACAACATTTTAAAC
107469 A
1 A
107470 AAGAAAACAA
Statistics
Matches: 128, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.01
20 14 0.11
21 2 0.02
22 22 0.17
23 87 0.68
24 2 0.02
ACGTcount: A:0.54, C:0.18, G:0.08, T:0.20
Consensus pattern (23 bp):
AGCAAAACAACAACATTTTAAAC
Done.