Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003023.1 Hibiscus syriacus cultivar Beakdansim tig00006290_pilon, 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: 86091
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2590 original size:16 final size:17
Alignment explanation
Indices: 2569--2610 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
2559 ATCCTAAGTC
2569 AAAGAAGAA-AAA-GAAA
1 AAAGAA-AAGAAAGGAAA
2585 AAAGAAAAGAAAGGAAA
1 AAAGAAAAGAAAGGAAA
2602 AAAGGAAAA
1 AAA-GAAAA
2611 ATGTTAGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 2 0.09
16 9 0.39
17 7 0.30
18 5 0.22
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAGAAAAGAAAGGAAA
Found at i:2596 original size:18 final size:18
Alignment explanation
Indices: 2577--2610 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2567 TCAAAGAAGA
2577 AAAAGAAAAAA-GAAAAG
1 AAAAGAAAAAAGGAAAAG
*
2594 AAAGGAAAAAAGGAAAA
1 AAAAGAAAAAAGGAAAA
2611 ATGTTAGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAGGAAAAG
Found at i:3634 original size:60 final size:63
Alignment explanation
Indices: 3476--3642 Score: 207
Period size: 65 Copynumber: 2.7 Consensus size: 63
3466 AATTTACTCG
* * * *
3476 AGATTGGATTTCAACTTCACAACGAATGATATCCAACACAAAGCCAATTTGGTGAAACTTACTCA
1 AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAAC-TAAT-A
** *
3541 AGATTTTATTTCAACTTCA-AGACGAAGGATATCCAACTCAAAACCAATTTGGTTAAAC-AAT-
1 AGATTGGATTTCAACTTCACA-ACGAAGGATATCCAACTCAAAACCAATTTGGTGAAACTAATA
*
3602 A-CTTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAA
1 AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAA
3643 GCTCAACTTC
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
60 35 0.39
61 2 0.02
63 2 0.02
64 1 0.01
65 50 0.56
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.27
Consensus pattern (63 bp):
AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAACTAATA
Found at i:5665 original size:13 final size:14
Alignment explanation
Indices: 5649--5683 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
5639 TTCCTCTGTA
5649 TTTTATTTTTA-TT
1 TTTTATTTTTAGTT
*
5662 TTTTATCTTTAGTT
1 TTTTATTTTTAGTT
5676 TTTTATTT
1 TTTTATTT
5684 CTTTATAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.80
Consensus pattern (14 bp):
TTTTATTTTTAGTT
Found at i:5672 original size:19 final size:20
Alignment explanation
Indices: 5617--5761 Score: 117
Period size: 19 Copynumber: 7.2 Consensus size: 20
5607 TTACTATTAT
5617 TTTCTTTAT-TTTATTTTTA
1 TTTCTTTATCTTTATTTTTA
5636 TTTTTCCTCTGTAT-TTTATTTTTA
1 --TTT-CT-T-TATCTTTATTTTTA
5660 TTT-TTTATCTTTAGTTTTTTA
1 TTTCTTTATCTTTA--TTTTTA
**
5681 TTTCTTTATAGTTA-TTTTA
1 TTTCTTTATCTTTATTTTTA
*
5700 TTTCTTTATCTTCATTTTT-
1 TTTCTTTATCTTTATTTTTA
5719 TTTCATTT-TCTTTATATTTT-
1 TTTC-TTTATCTTTAT-TTTTA
5739 TTCTCTTTATCTTTA-TTTTA
1 TT-TCTTTATCTTTATTTTTA
5759 TTT
1 TTT
5762 ATTTTTGTTT
Statistics
Matches: 105, Mismatches: 6, Indels: 28
0.76 0.04 0.20
Matches are distributed among these distances:
18 3 0.03
19 36 0.34
20 19 0.18
21 20 0.19
22 13 0.12
23 1 0.01
24 13 0.12
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTCTTTATCTTTATTTTTA
Found at i:5689 original size:35 final size:36
Alignment explanation
Indices: 5650--5884 Score: 116
Period size: 40 Copynumber: 6.4 Consensus size: 36
5640 TCCTCTGTAT
*
5650 TTTATTTTTATTTTTTATCTTTAGTTT-TTTATTTC
1 TTTATTTTTATTTTTTATCTTTATTTTATTTATTTC
* *
5685 TTTATAGTTATTTTATTTCTTTATCTTCATTTTTTTTCATTTTC
1 -TT-TA--T-TTTTATTT-TTTATCTTTATTTTATTT-A-TTTC
5729 TTTATATTTT-TTCTCTTTATCTTTATTTTATTTATTT-
1 TTTAT-TTTTATT-T-TTTATCTTTATTTTATTTATTTC
* *
5766 TTGT-TTTATT-TGTTTTATCTTTGTTTTATTTA--T-
1 TT-TATTT-TTATTTTTTATCTTTATTTTATTTATTTC
* * *
5799 TTTA--TTTACTTTCTTATCTTTACTTTATTTTTTTCC
1 TTTATTTTTA-TTTTTTATCTTTATTTTATTTATTT-C
** * *
5835 TTTATCATTGTTTTCTCTATC-TTATTTTCTTTATTTC
1 TTTATTTTTATTTT-T-TATCTTTATTTTATTTATTTC
*
5872 ATT-TTTTTATTTT
1 TTTATTTTTATTTT
5885 CTTTATTTTC
Statistics
Matches: 156, Mismatches: 21, Indels: 44
0.71 0.10 0.20
Matches are distributed among these distances:
30 2 0.01
31 1 0.01
32 18 0.12
33 3 0.02
34 1 0.01
35 18 0.12
36 16 0.10
37 14 0.09
38 19 0.12
39 8 0.05
40 32 0.21
41 12 0.08
42 5 0.03
43 3 0.02
44 4 0.03
ACGTcount: A:0.14, C:0.10, G:0.03, T:0.73
Consensus pattern (36 bp):
TTTATTTTTATTTTTTATCTTTATTTTATTTATTTC
Found at i:5700 original size:109 final size:108
Alignment explanation
Indices: 5538--5733 Score: 226
Period size: 109 Copynumber: 1.8 Consensus size: 108
5528 TTATCACTAT
* *
5538 TATTTTTTTTTTATTTTTTATTGTTATTTATTTCATTTTTAATGCTTTATTTATATGTATATCTT
1 TATTTTATTTTTATTTTTTATTGTTATTTATTTCATTTTTAATGCTTTATTTATATCTATATCTT
5603 -ATTTTTACTATT-ATTTTCTTTATTTTATTTTTATTTTTCCTCTG
66 CATTTTT--T-TTCATTTTCTTTATTTTATTTTTATTTTTCCTCTG
* * *
5647 TATTTTATTTTTATTTTTTATCT-TTAGTTT-TTT-ATTTCTTTATAG--TTATTTTATTTCTTT
1 TATTTTATTTTTATTTTTTAT-TGTTA-TTTATTTCATTT-TTAAT-GCTTTA-TTTATATCTAT
5707 ATCTTCATTTTTTTTCATTTTCTTTAT
61 ATCTTCATTTTTTTTCATTTTCTTTAT
5734 ATTTTTTCTC
Statistics
Matches: 75, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
107 2 0.03
108 19 0.25
109 43 0.57
110 11 0.15
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.72
Consensus pattern (108 bp):
TATTTTATTTTTATTTTTTATTGTTATTTATTTCATTTTTAATGCTTTATTTATATCTATATCTT
CATTTTTTTTCATTTTCTTTATTTTATTTTTATTTTTCCTCTG
Found at i:5764 original size:9 final size:9
Alignment explanation
Indices: 5647--5893 Score: 75
Period size: 9 Copynumber: 26.7 Consensus size: 9
5637 TTTTCCTCTG
5647 TATTTTATT
1 TATTTTATT
*
5656 T-TTATTTTT
1 TATT-TTATT
*
5665 TATCTTTAGT
1 TAT-TTTATT
5675 T-TTTTATT
1 TATTTTATT
* *
5683 TCTTTATAGT
1 TATTT-TATT
5693 TATTTTATT
1 TATTTTATT
*
5702 T-CTTTATCT
1 TATTTTAT-T
*
5711 TCATTTTTTT
1 T-ATTTTATT
*
5721 TCATTTTCTT
1 T-ATTTTATT
5731 TATATTT-TT
1 TAT-TTTATT
*
5740 TCTCTTTATCTT
1 TAT-TTTA--TT
5752 TATTTTATT
1 TATTTTATT
5761 TA--TT-TT
1 TATTTTATT
*
5767 TGTTTTATT
1 TATTTTATT
*
5776 TGTTTTATCTT
1 TATTTTA--TT
*
5787 TGTTTTATT
1 TATTTTATT
5796 TATTTTATT
1 TATTTTATT
* *
5805 TACTTT-CT
1 TATTTTATT
5813 TATCTTTACTT
1 TAT-TTTA-TT
5824 TATTTT-TT
1 TATTTTATT
**
5832 TCCTTTATCAT
1 TATTTTAT--T
* * *
5843 TGTTTTCTC
1 TATTTTATT
*
5852 TATCTTATT
1 TATTTTATT
5861 T-TCTTTATT
1 TAT-TTTATT
5870 TCATTTT-TT
1 T-ATTTTATT
*
5879 TATTTTCTT
1 TATTTTATT
5888 TATTTT
1 TATTTT
5894 CATTATTGTT
Statistics
Matches: 180, Mismatches: 31, Indels: 54
0.68 0.12 0.20
Matches are distributed among these distances:
6 3 0.02
7 2 0.01
8 30 0.17
9 80 0.44
10 32 0.18
11 29 0.16
12 4 0.02
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (9 bp):
TATTTTATT
Found at i:5775 original size:20 final size:20
Alignment explanation
Indices: 5750--5805 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
5740 TCTCTTTATC
5750 TTTATTTTATTTATTTTTGT
1 TTTATTTTATTTATTTTTGT
*
5770 TTTATTTGT-TTTATCTTTGT
1 TTTATTT-TATTTATTTTTGT
5790 TTTA-TTTATTTTATTT
1 TTTATTTTA-TTTATTT
5806 ACTTTCTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 27 0.87
21 1 0.03
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTATTTTATTTATTTTTGT
Found at i:5871 original size:22 final size:22
Alignment explanation
Indices: 5852--5899 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
5842 TTGTTTTCTC
5852 TATCTTATTTTCTTTATTTCAT
1 TATCTTATTTTCTTTATTTCAT
* *
5874 TTTTTTATTTTCTTTATTTTCAT
1 TATCTTATTTTCTTTA-TTTCAT
5897 TAT
1 TAT
5900 TGTTTTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (22 bp):
TATCTTATTTTCTTTATTTCAT
Found at i:5907 original size:23 final size:22
Alignment explanation
Indices: 5856--5909 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
5846 TTTCTCTATC
*
5856 TTATTTTCTTTATTTCATTTTT
1 TTATTTTCTTTATTTCATTTTG
5878 TTATTTTCTTTATTTTCATTATTG
1 TTATTTTCTTTA-TTTCATT-TTG
5902 TT-TTTTCT
1 TTATTTTCT
5910 CTCTAACACG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 12 0.41
23 13 0.45
24 4 0.14
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (22 bp):
TTATTTTCTTTATTTCATTTTG
Found at i:6625 original size:13 final size:13
Alignment explanation
Indices: 6589--6627 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 13
6579 ATTATTAGTA
6589 ATTAAAATAAATT
1 ATTAAAATAAATT
6602 ATTAAGTAATAAATT
1 ATTAA--AATAAATT
6617 ATTAAAATAAA
1 ATTAAAATAAA
6628 ATGTAAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.46
15 13 0.54
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (13 bp):
ATTAAAATAAATT
Found at i:8041 original size:35 final size:35
Alignment explanation
Indices: 7995--8069 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
7985 AAAATACTTC
7995 AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGG
1 AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGG
* * *
8030 AATTTGGGGTTTAGAATGTAATTGAAGTGTTTTGG
1 AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGG
8065 AATTT
1 AATTT
8070 TGAACATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGG
Found at i:10168 original size:23 final size:23
Alignment explanation
Indices: 10140--10198 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
10130 TTTATATGGA
10140 ACTTCGGTGCATTTCTAGGCGGC
1 ACTTCGGTGCATTTCTAGGCGGC
* * * * *
10163 ACTTCGATGTATTTCTATGCTGT
1 ACTTCGGTGCATTTCTAGGCGGC
10186 ACTTCGGTGCATT
1 ACTTCGGTGCATT
10199 CTATACGAGT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (23 bp):
ACTTCGGTGCATTTCTAGGCGGC
Found at i:28037 original size:2 final size:2
Alignment explanation
Indices: 28026--28054 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28016 TTTGTCAATC
28026 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28055 AAATTTACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:28261 original size:13 final size:13
Alignment explanation
Indices: 28212--28276 Score: 76
Period size: 13 Copynumber: 5.0 Consensus size: 13
28202 AATGACGCGC
28212 AATGCGCGTCATA
1 AATGCGCGTCATA
* *
28225 AATGTGCGCCATA
1 AATGCGCGTCATA
**
28238 AATAAGCGTCATA
1 AATGCGCGTCATA
*
28251 AATGCGTGTCATA
1 AATGCGCGTCATA
*
28264 AATGCGCATCATA
1 AATGCGCGTCATA
28277 TATTTATGAC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:29127 original size:24 final size:24
Alignment explanation
Indices: 29095--29140 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
29085 ATAAATATCC
29095 TTAAAATTTTATAATAAACGAGCA
1 TTAAAATTTTATAATAAACGAGCA
29119 TTAAAATTTTATAATAAACGAG
1 TTAAAATTTTATAATAAACGAG
29141 AAAAATTCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.35
Consensus pattern (24 bp):
TTAAAATTTTATAATAAACGAGCA
Found at i:34735 original size:22 final size:22
Alignment explanation
Indices: 34710--34757 Score: 75
Period size: 19 Copynumber: 2.3 Consensus size: 22
34700 TTATGTTTAT
34710 TTCAACAACATTATTTCCCTAA
1 TTCAACAACATTATTTCCCTAA
34732 TT---CAACATTATTTCCCTAA
1 TTCAACAACATTATTTCCCTAA
34751 TTCAACA
1 TTCAACA
34758 TTAAAAAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 19 0.83
22 4 0.17
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38
Consensus pattern (22 bp):
TTCAACAACATTATTTCCCTAA
Found at i:34739 original size:19 final size:19
Alignment explanation
Indices: 34715--34760 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
34705 TTTATTTCAA
34715 CAACATTATTTCCCTAATT
1 CAACATTATTTCCCTAATT
34734 CAACATTATTTCCCTAATT
1 CAACATTATTTCCCTAATT
34753 CAACATTA
1 CAACATTA
34761 AAAAGACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.39
Consensus pattern (19 bp):
CAACATTATTTCCCTAATT
Found at i:37957 original size:147 final size:149
Alignment explanation
Indices: 37682--38608 Score: 825
Period size: 147 Copynumber: 6.2 Consensus size: 149
37672 ATAACAATCG
* * * *
37682 TTATGAGTGTGAATTGTTTTTAAAAAATTTGTACAAATTCGATG-TTTCTTATTCATAATATTAA
1 TTATGAGTGTGATTTGTTTCTAAAAAA-ATGTACAAATTCAATGTTTTCTTATTCATAATATTAA
* * * * * * * **
37746 ATTACGGTTAAGGTGTGTGTCA-TAGATATGATTATAACATCGCGATTGTGGATTCTACGTACGT
65 ATTACGGTTATGGTGTCTGTCACGAGATGTGATTACAATATCGCGATTGTGGATACTACAAACGT
*
37810 TACATAACGTCTAATGGTCA
130 TACATAACGTCTAACGGTCA
* * * *
37830 TTATGAGTGTGGTTTGTTT-TAAAAAAATATAAAAATTTAATGTTTTCTTATTCATAATATTAAA
1 TTATGAGTGTGATTTGTTTCTAAAAAAATGTACAAATTCAATGTTTTCTTATTCATAATATTAAA
* *
37894 TTACGGTTACGGTGTCTGTCACGA-ATGTGATTACAATATCACGATTGTGGATACTACAAACGTT
66 TTACGGTTATGGTGTCTGTCACGAGATGTGATTACAATATCGCGATTGTGGATACTACAAACG-T
*
37958 ACATAACTCATAACGGTCGATAACGGTCG
130 ---T-A--CATAAC-GTC--TAACGGTCA
* * * *
37987 TTATGAGTGTGATATATTTCTAAAAAAATTGTTCAAATTCAATGTTTTCTGATTCATAATATTAA
1 TTATGAGTGTGATTTGTTTCTAAAAAAA-TGTACAAATTCAATGTTTTCTTATTCATAATATTAA
* * * *
38052 ACTACGGTTATGGTGTTTGTCACG-GATGTGATTACAAATATCGCGATTGTGAATACTACATACG
65 ATTACGGTTATGGTGTCTGTCACGAGATGTGATTAC-AATATCGCGATTGTGGATACTACAAACG
* * *
38116 TTACATAATGTGTAACGATCA
129 TTACATAACGTCTAACGGTCA
* * * * * *
38137 TTAAGAGTTTGACTTGTTTCTAGAAAAATGTACAAATTCAAT-TTTTTTTATTCATTATATTAAA
1 TTATGAGTGTGATTTGTTTCTAAAAAAATGTACAAATTCAATGTTTTCTTATTCATAATATTAAA
** * * * * *
38201 TTATAGTTATGGTGTCTGTCACGA-ATGTAATTACAATATCGCGATTATAGATACTACAGATGTT
66 TTACGGTTATGGTGTCTGTCACGAGATGTGATTACAATATCGCGATTGTGGATACTACAAACGTT
* *
38265 ACATAATG-CGTAACGGTCG
131 ACATAACGTC-TAACGGTCA
* * * * * * *
38284 TTAGGAGTGTGATTTTATTTCTAAAAAATTGTATAAATAT-AATGTTATATAATTCATAATATTT
1 TTATGAGTGTGA-TTTGTTTCTAAAAAAATGTACAAAT-TCAATGTTTTCTTATTCATAATA-TT
** ** * * * * *
38348 ATAATTTATTGTTACAGTGTCTGTCTC-ATATGTGATTACAATATCGTGATTGTGAATACTACAG
63 A-AA-TTACGGTTATGGTGTCTGTCACGAGATGTGATTACAATATCGCGATTGTGGATACTACAA
* * *
38412 ACATTACATAAAGTGTAACGGTCA
126 ACGTTACATAACGTCTAACGGTCA
* * * * * * * *
38436 TTAGGAGTTTGATTTGTTTCTAAAAATATTTTTCAAATTCAATGTTTTCTGATTCATATTATCAA
1 TTATGAGTGTGATTTGTTTCTAAAAA-AATGTACAAATTCAATGTTTTCTTATTCATAATATTAA
* * ** * *
38501 ATTATGGTTATAGTAACTGTCAC-AGATGTGATTATAATATCGCGATTGTGGATACTAGAAACGT
65 ATTACGGTTATGGTGTCTGTCACGAGATGTGATTACAATATCGCGATTGTGGATACTACAAACGT
* *
38565 TACATAACG-CGTAACAGTCG
130 TACATAACGTC-TAACGGTCA
* *
38585 TTACGAGTGTGATTTGTCTCTAAA
1 TTATGAGTGTGATTTGTTTCTAAA
38609 GAACACGTTA
Statistics
Matches: 636, Mismatches: 114, Indels: 57
0.79 0.14 0.07
Matches are distributed among these distances:
146 11 0.02
147 128 0.20
148 89 0.14
149 114 0.18
150 34 0.05
151 20 0.03
152 105 0.17
153 5 0.01
154 6 0.01
155 4 0.01
156 1 0.00
157 23 0.04
158 8 0.01
159 63 0.10
160 25 0.04
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (149 bp):
TTATGAGTGTGATTTGTTTCTAAAAAAATGTACAAATTCAATGTTTTCTTATTCATAATATTAAA
TTACGGTTATGGTGTCTGTCACGAGATGTGATTACAATATCGCGATTGTGGATACTACAAACGTT
ACATAACGTCTAACGGTCA
Found at i:38236 original size:307 final size:298
Alignment explanation
Indices: 37679--38597 Score: 948
Period size: 307 Copynumber: 3.1 Consensus size: 298
37669 GATATAACAA
* * * * * *
37679 TCGTTATGAGTGTGA-ATTGTTTTTAAAAAATTTGTACAAATTCGATG-TTTCTTATTCATAATA
1 TCGTTATGAGTGTGATA-TATTTCTAAAAAAATTGTTCAAATTCAATGTTTTCTAATTCATAATA
* * * * * * * *
37742 TTAAATTACGGTTAAGGTGTGTGTCATAGATATGATTATAACATCGCGATTGTGGATTCTACGTA
65 TTAAATTACGGTTAAGGTGTCTGTCACAGATGTGATTACAATATCGCGATTGTGAATACTACATA
* * * * * * * *
37807 CGTTACATAACGTCTAATGGTCATTATGAGTGTGGTTTGTTT-TAAAAAAATATAAAAATTTAAT
130 CGTTACATAAAGTGTAACGGTCATTAAGAGTTTGATTTGTTTCT-AAAAAATATACAAATTCAAT
* * * *
37871 GTTTTCTTATTCATAATATTAAATTACGGTTACGGTGTCTGTCACGAATGTGATTACAATATCAC
194 GTTTTCTTATTCATTATATTAAATTATGGTTATGGTGTCTGTCACGAATGTGATTACAATATCGC
37936 GATTGTGGATACTACAAACGTTACATAACTCATAACGGTCGATAACGG
259 GATTGTGGATACTACAAACGTTACATAA--CAT----G-CG-TAACGG
*
37984 TCGTTATGAGTGTGATATATTTCTAAAAAAATTGTTCAAATTCAATGTTTTCTGATTCATAATAT
1 TCGTTATGAGTGTGATATATTTCTAAAAAAATTGTTCAAATTCAATGTTTTCTAATTCATAATAT
* * * *
38049 TAAACTACGGTTATGGTGTTTGTCACGGATGTGATTACAAATATCGCGATTGTGAATACTACATA
66 TAAATTACGGTTAAGGTGTCTGTCACAGATGTGATTAC-AATATCGCGATTGTGAATACTACATA
* * * *
38114 CGTTACATAATGTGTAACGATCATTAAGAGTTTGACTTGTTTCTAGAAAAATGTACAAATTCAAT
130 CGTTACATAAAGTGTAACGGTCATTAAGAGTTTGATTTGTTTCTA-AAAAATATACAAATTCAAT
* * *
38179 -TTTTTTTATTCATTATATTAAATTATAGTTATGGTGTCTGTCACGAATGTAATTACAATATCGC
194 GTTTTCTTATTCATTATATTAAATTATGGTTATGGTGTCTGTCACGAATGTGATTACAATATCGC
* * * *
38243 GATTATAGATACTACAGATGTTACAT-A-ATGCGTAACGG
259 GATTGTGGATACTACAAACGTTACATAACATGCGTAACGG
* * * *
38281 TCGTTAGGAGTGTGATTTTATTTCT-AAAAAATTGTAT-AAATAT-AATGTTATATAATTCATAA
1 TCGTTATGAGTGTGA-TATATTTCTAAAAAAATTGT-TCAAAT-TCAATGTTTTCTAATTCATAA
** * * *
38343 TATTTATAATTTATTGTTACA-GTGTCTGTCTCATATGTGATTACAATATCGTGATTGTGAATAC
63 TA-TTA-AA-TTACGGTTA-AGGTGTCTGTCACAGATGTGATTACAATATCGCGATTGTGAATAC
* * * * *
38407 TACAGACATTACATAAAGTGTAACGGTCATTAGGAGTTTGATTTGTTTCTAAAAATATTTTTCAA
124 TACATACGTTACATAAAGTGTAACGGTCATTAAGAGTTTGATTTGTTTCTAAAAA-A-TATACAA
* * * **
38472 ATTCAATGTTTTCTGATTCA-TATTATCAAATTATGGTTATAGTAACTGTCAC-AGATGTGATTA
187 ATTCAATGTTTTCTTATTCATTA-TATTAAATTATGGTTATGGTGTCTGTCACGA-ATGTGATTA
* * *
38535 TAATATCGCGATTGTGGATACTAGAAACGTTACATAAC--GCGTAACAG
250 CAATATCGCGATTGTGGATACTACAAACGTTACATAACATGCGTAACGG
*
38582 TCGTTACGAGTGTGAT
1 TCGTTATGAGTGTGAT
38598 TTGTCTCTAA
Statistics
Matches: 518, Mismatches: 77, Indels: 43
0.81 0.12 0.07
Matches are distributed among these distances:
297 52 0.10
298 19 0.04
299 68 0.13
300 41 0.08
301 93 0.18
302 1 0.00
303 2 0.00
305 40 0.08
306 49 0.09
307 136 0.26
308 17 0.03
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (298 bp):
TCGTTATGAGTGTGATATATTTCTAAAAAAATTGTTCAAATTCAATGTTTTCTAATTCATAATAT
TAAATTACGGTTAAGGTGTCTGTCACAGATGTGATTACAATATCGCGATTGTGAATACTACATAC
GTTACATAAAGTGTAACGGTCATTAAGAGTTTGATTTGTTTCTAAAAAATATACAAATTCAATGT
TTTCTTATTCATTATATTAAATTATGGTTATGGTGTCTGTCACGAATGTGATTACAATATCGCGA
TTGTGGATACTACAAACGTTACATAACATGCGTAACGG
Found at i:39476 original size:2 final size:2
Alignment explanation
Indices: 39469--39511 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
39459 TTGTTGAATG
39469 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39511 A
1 A
39512 ACACTCCTCG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42797 original size:45 final size:45
Alignment explanation
Indices: 42714--42801 Score: 133
Period size: 46 Copynumber: 2.0 Consensus size: 45
42704 AATATTAAGA
* *
42714 GGTACCGATACCCCTATGAATGGGTACCGATACCCCCTATGAATG
1 GGTACCGATACCCCTATGAATGGGTACCAATACACCCTATGAATG
*
42759 GGTACCGATACCCCCTATGAATGGGTATCAATA-ACCCTATGAA
1 GGTACCGATA-CCCCTATGAATGGGTACCAATACACCCTATGAA
42802 AGCTCAACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 19 0.49
46 20 0.51
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (45 bp):
GGTACCGATACCCCTATGAATGGGTACCAATACACCCTATGAATG
Found at i:42801 original size:22 final size:23
Alignment explanation
Indices: 42714--42785 Score: 137
Period size: 23 Copynumber: 3.2 Consensus size: 23
42704 AATATTAAGA
42714 GGTACCGATA-CCCCTATGAATG
1 GGTACCGATACCCCCTATGAATG
42736 GGTACCGATACCCCCTATGAATG
1 GGTACCGATACCCCCTATGAATG
42759 GGTACCGATACCCCCTATGAATG
1 GGTACCGATACCCCCTATGAATG
42782 GGTA
1 GGTA
42786 TCAATAACCC
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 10 0.20
23 39 0.80
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (23 bp):
GGTACCGATACCCCCTATGAATG
Found at i:42847 original size:19 final size:19
Alignment explanation
Indices: 42823--42859 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
42813 CGAATGCAAA
*
42823 AAGGGTATTGATACCATAC
1 AAGGGTATCGATACCATAC
42842 AAGGGTATCGATACCATA
1 AAGGGTATCGATACCATA
42860 GTGCAAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (19 bp):
AAGGGTATCGATACCATAC
Found at i:43277 original size:33 final size:33
Alignment explanation
Indices: 43240--43309 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
43230 TTTTGTAAAG
* * *
43240 GGGAAATGTTCTAGCTGATCCCATGAAAAGCTA
1 GGGAAAGGTTCTAGCTGAGCCCATGAAAAACTA
* * *
43273 GGGAAAGGTTCTAGTTTAGCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTGAGCCCATGAAAAACTA
43306 GGGA
1 GGGA
43310 GTTTGTAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTGAGCCCATGAAAAACTA
Found at i:45993 original size:18 final size:18
Alignment explanation
Indices: 45970--46026 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 18
45960 CAACAATTGG
* *
45970 TAACAACTGATATCTTTT
1 TAACAATTGGTATCTTTT
*
45988 TAACAATTGGTACCTTTT
1 TAACAATTGGTATCTTTT
46006 GTAAACAATTGGTATCTTTT
1 -T-AACAATTGGTATCTTTT
46026 T
1 T
46027 CATTAAACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 15 0.45
19 2 0.06
20 16 0.48
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.46
Consensus pattern (18 bp):
TAACAATTGGTATCTTTT
Found at i:46270 original size:22 final size:22
Alignment explanation
Indices: 46245--46324 Score: 124
Period size: 22 Copynumber: 3.6 Consensus size: 22
46235 AAGAGGTACC
*
46245 GATACCCTTATGAATGGGTATT
1 GATACCCCTATGAATGGGTATT
46267 GATACCCCTATGAATGGGTATT
1 GATACCCCTATGAATGGGTATT
* *
46289 GATACCCCTATAAATGGGTATC
1 GATACCCCTATGAATGGGTATT
*
46311 AATACCCCTATGAA
1 GATACCCCTATGAA
46325 AGCTCAAACA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (22 bp):
GATACCCCTATGAATGGGTATT
Found at i:51234 original size:3 final size:3
Alignment explanation
Indices: 51226--51278 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
51216 TTTAATTACG
*
51226 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
51274 TTA TT
1 TTA TT
51279 TTACACTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:52654 original size:326 final size:326
Alignment explanation
Indices: 52072--52712 Score: 1077
Period size: 326 Copynumber: 2.0 Consensus size: 326
52062 CAAATGTCGC
* * * * *
52072 GTGCATGGGGTCTTCGGGAGTTAGTTGTCGTGGGTGTAGTGAGTGAAGAGAAGAGGGAGATGAAG
1 GTGCATGGGGTCTTCGGGAGTCAGCTGCCATGGGTGTAGTGAGTAAAGAGAAGAGGGAGATGAAG
52137 GAGTGTTAGGGTTAAGAGTTTCGAGCAGAATGAAAAATGAGTGGGGTATTAGACTTACTTTGTTA
66 GAGTGTTAGGGTTAAGAGTTTCGAGCAGAATGAAAAATGAGTGGGGTATTAGACTTACTTTGTTA
52202 TTTTGGTAAAATCACGCTAAGGTCCCTAGACCTTTAGCGTGTTTTTACGTTTCAGTCACCAAATC
131 TTTTGGTAAAATCACGCTAAGGTCCCTAGACCTTTAGCGTGTTTTTACGTTTCAGTCACCAAATC
*
52267 ATAGGTTAATTACCCATAGGTCCCTTAACTTTAGGAATCCATTTGTATTCTGGTAACTAATTTAG
196 ATAGGTTAATTACCCATAGATCCCTTAACTTTAGGAATCCATTTGTATTCTGGTAACTAATTTAG
52332 GGTTAAATTGATATTTGGGTCTTTGTCTTTAGCATAGGTAATATTTTGGTCAACTGCCAAATGTT
261 GGTTAAATTGATATTTGGGT-TTTGTCTTTAGCATAGGTAATATTTTGGTCAACTGCCAAATGTT
52397 AT
325 AT
52399 GTGCATGGGGTCTTCGGGAGTCAGCTGCCATGGGTGTAGTGAGTAAAGAGAAGAGGGAGATGAAG
1 GTGCATGGGGTCTTCGGGAGTCAGCTGCCATGGGTGTAGTGAGTAAAGAGAAGAGGGAGATGAAG
* * **
52464 GAGTGTTAGGGTTAAGATTTTCGGGTTGAATGAAAAATGAG-GGGGTATTAGACTTACTTTGTTA
66 GAGTGTTAGGGTTAAGAGTTTCGAGCAGAATGAAAAATGAGTGGGGTATTAGACTTACTTTGTTA
** * *
52528 TTTTGGTAAAATCACGCTAAGGTTTCTAGACCTTTAGCGTGTTTTTACGTTTCAGTCACTATATC
131 TTTTGGTAAAATCACGCTAAGGTCCCTAGACCTTTAGCGTGTTTTTACGTTTCAGTCACCAAATC
* * * *
52593 GTAGGTTAATTACCTATAGATCCCTTAACTTTAGGAATCTATTTGTATTCTGGTCACTAATTTAG
196 ATAGGTTAATTACCCATAGATCCCTTAACTTTAGGAATCCATTTGTATTCTGGTAACTAATTTAG
* * *
52658 GGTTAAATTGATGTTTGGGTTTTTTCTTTAGCATATGTAATATTTTGGTCAACTG
261 GGTTAAATTGATATTTGGGTTTTGTCTTTAGCATAGGTAATATTTTGGTCAACTG
52713 TTCATGGGGA
Statistics
Matches: 293, Mismatches: 21, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
325 33 0.11
326 163 0.56
327 97 0.33
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (326 bp):
GTGCATGGGGTCTTCGGGAGTCAGCTGCCATGGGTGTAGTGAGTAAAGAGAAGAGGGAGATGAAG
GAGTGTTAGGGTTAAGAGTTTCGAGCAGAATGAAAAATGAGTGGGGTATTAGACTTACTTTGTTA
TTTTGGTAAAATCACGCTAAGGTCCCTAGACCTTTAGCGTGTTTTTACGTTTCAGTCACCAAATC
ATAGGTTAATTACCCATAGATCCCTTAACTTTAGGAATCCATTTGTATTCTGGTAACTAATTTAG
GGTTAAATTGATATTTGGGTTTTGTCTTTAGCATAGGTAATATTTTGGTCAACTGCCAAATGTTA
T
Found at i:53525 original size:5 final size:5
Alignment explanation
Indices: 53512--53545 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
53502 CTCCTTTCAT
* *
53512 TTTTA TTTTG TTTTA TTTTA GTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
53546 TGTGGAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:54779 original size:18 final size:18
Alignment explanation
Indices: 54756--54796 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
54746 AAAGAGTGGC
54756 GAGCTAGACGTACGAGAG
1 GAGCTAGACGTACGAGAG
*
54774 GAGCTAGACGTCCGAGAG
1 GAGCTAGACGTACGAGAG
54792 GAGCT
1 GAGCT
54797 GTGAGCTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.20, G:0.39, T:0.12
Consensus pattern (18 bp):
GAGCTAGACGTACGAGAG
Found at i:60710 original size:5 final size:6
Alignment explanation
Indices: 60691--60721 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
60681 TTATTTTTCC
60691 TTTATT TTTATT TTTATT TTTA-T TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TT
60722 GTAGATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:60710 original size:11 final size:11
Alignment explanation
Indices: 60681--60721 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
60671 AATAATTTTA
**
60681 TTATTTTTCCT
1 TTATTTTTATT
60692 TTATTTTTATTT
1 TTATTTTTA-TT
60704 TTATTTTTATT
1 TTATTTTTATT
60715 TTATTTT
1 TTATTTT
60722 GTAGATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:60875 original size:24 final size:25
Alignment explanation
Indices: 60829--60876 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
60819 GAAAAATTCT
*
60829 TTTTGATTTATTCATTTTTCTTTTA
1 TTTTGATTTATTCATTTTACTTTTA
60854 TTTT-ATTTATT-ATTTTAACTTTT
1 TTTTGATTTATTCATTTT-ACTTTT
60877 CTTTCTCCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (25 bp):
TTTTGATTTATTCATTTTACTTTTA
Found at i:61393 original size:17 final size:16
Alignment explanation
Indices: 61371--61404 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
61361 TAAAATTAGT
61371 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
61388 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
61404 A
1 A
61405 TCCTCATGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:75196 original size:3 final size:3
Alignment explanation
Indices: 75188--75237 Score: 55
Period size: 3 Copynumber: 15.7 Consensus size: 3
75178 GGGTATTTTG
* *
75188 TAA TAA TAAA TAAA TAA TAA TATT TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA T-AA T-AA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
75236 TA
1 TA
75238 TAAGAGTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 33 0.80
4 8 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:75219 original size:27 final size:25
Alignment explanation
Indices: 75181--75234 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 25
75171 TTGGTTTGGG
*
75181 TATTTTGTAATAATAAATAAATAATAA
1 TATTTTATAATAAT-AAT-AATAATAA
75208 TATTTTATAATAATAATAATAATAA
1 TATTTTATAATAATAATAATAATAA
75233 TA
1 TA
75235 ATATAAGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 10 0.38
26 3 0.12
27 13 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
TATTTTATAATAATAATAATAATAA
Found at i:77451 original size:49 final size:49
Alignment explanation
Indices: 77387--77481 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
77377 CCACTTCTAC
77387 CCCAACTTAAATTCACATGTATAGTTAACCTTTCTCAGTCAACTTCCAT
1 CCCAACTTAAATTCACATGTATAGTTAACCTTTCTCAGTCAACTTCCAT
*
77436 CCCAACTTAAATTCACATGTATAGTTAAGCTTTCTCAGTCAACTTC
1 CCCAACTTAAATTCACATGTATAGTTAACCTTTCTCAGTCAACTTC
77482 TTCGACTAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.35
Consensus pattern (49 bp):
CCCAACTTAAATTCACATGTATAGTTAACCTTTCTCAGTCAACTTCCAT
Found at i:77534 original size:86 final size:85
Alignment explanation
Indices: 77428--77676 Score: 426
Period size: 86 Copynumber: 2.9 Consensus size: 85
77418 TTCTCAGTCA
*
77428 ACTTCCATCCCAACTTAAATTCACATGTATAGTTAAGCTTTCTCAGTCAACTTCTTCGACTAGAG
1 ACTTCTATCCCAACTTAAATTCACATGTATAGTTAA-CTTTCTCAGTCAACTTCTTCGACTAGAG
77493 TTTCTTTTCTTCTTTTTAAAT
65 TTTCTTTTCTTCTTTTTAAAT
* *
77514 ACTTCTATCCCAACTTAAATTCACATGTTTGGTTAACTTTTCTCAGTCAACTTCTTCGACTAGAG
1 ACTTCTATCCCAACTTAAATTCACATGTATAGTTAAC-TTTCTCAGTCAACTTCTTCGACTAGAG
77579 TTTCTTTTCTTCTTTTTAAAT
65 TTTCTTTTCTTCTTTTTAAAT
* *
77600 ACTTCTATCCCAACTTAAATCCACGTGTATAGTTAACCTTTCTCAGTCAACTTCTTCGACTAGAG
1 ACTTCTATCCCAACTTAAATTCACATGTATAGTTAA-CTTTCTCAGTCAACTTCTTCGACTAGAG
77665 TTTCTTTTCTTC
65 TTTCTTTTCTTC
77677 ATTTATGTAT
Statistics
Matches: 154, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
85 1 0.01
86 152 0.99
87 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.43
Consensus pattern (85 bp):
ACTTCTATCCCAACTTAAATTCACATGTATAGTTAACTTTCTCAGTCAACTTCTTCGACTAGAGT
TTCTTTTCTTCTTTTTAAAT
Found at i:77698 original size:3 final size:3
Alignment explanation
Indices: 77690--77719 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
77680 TATGTATTTA
77690 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
77720 TGGTAGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:79574 original size:3 final size:3
Alignment explanation
Indices: 79568--79666 Score: 67
Period size: 3 Copynumber: 31.0 Consensus size: 3
79558 TAATATTATT
* * * *
79568 TAA TAA TAA TAT TAT TAA TAA T-A TATA TATA TAA TAA CATG TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TA-A TAA -TAA
*
79616 TAA TAA TAA TAA TAA TAA T-A TGA TAA TAA TAGCA TATA TAA TTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA--A TA-A TAA -TAA TAA
79664 TAA
1 TAA
79667 AAATGGATAA
Statistics
Matches: 80, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.05
3 56 0.70
4 17 0.21
5 3 0.04
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:79579 original size:16 final size:16
Alignment explanation
Indices: 79558--79623 Score: 68
Period size: 16 Copynumber: 4.3 Consensus size: 16
79548 TTGAGCTTTG
79558 TAATATTATTTAATAA
1 TAATATTATTTAATAA
79574 TAATATTA-TTAATAA
1 TAATATTATTTAATAA
*
79589 T-ATA-TATAT-ATAA
1 TAATATTATTTAATAA
* *
79602 TAACATGTAATTAATAA
1 TAATAT-TATTTAATAA
79619 TAATA
1 TAATA
79624 ATAATAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
13 7 0.17
14 6 0.15
15 8 0.20
16 11 0.28
17 8 0.20
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
TAATATTATTTAATAA
Found at i:79619 original size:42 final size:44
Alignment explanation
Indices: 79567--79666 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 44
79557 GTAATATTAT
* * * *
79567 TTAATAATAATATTATTAATAATATATATATATAATA-ACATGTAA
1 TTAATAATAATAATAATAATAATAT-GATA-ATAATACACATATAA
*
79612 TTAATAATAATAATAATAATAATATGATAATAATAGCATATATAA
1 TTAATAATAATAATAATAATAATATGATAATAATA-CACATATAA
79657 TTAATAATAA
1 TTAATAATAA
79667 AAATGGATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 6 0.12
44 3 0.06
45 39 0.81
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (44 bp):
TTAATAATAATAATAATAATAATATGATAATAATACACATATAA
Found at i:79935 original size:42 final size:42
Alignment explanation
Indices: 79884--79965 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
79874 AAAGACTTAT
*
79884 CATCTTGCTCGAAAGACTGACAGATAACCCGAAGGATTTAAA
1 CATCATGCTCGAAAGACTGACAGATAACCCGAAGGATTTAAA
* *
79926 CATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTA
1 CATCATGCTCGAAAGACTGACAGATAACCCGAAGGATTTA
79966 CAAATTTGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTGACAGATAACCCGAAGGATTTAAA
Found at i:79966 original size:20 final size:20
Alignment explanation
Indices: 79903--79967 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 20
79893 CGAAAGACTG
*
79903 ACAGATAACCCGAAGGATTT
1 ACAGATGACCCGAAGGATTT
* * * *
79923 AAACATCATG-CTCGAAAGACTT
1 --ACA-GATGACCCGAAGGATTT
79945 ACAGATGACCCGAAGGATTT
1 ACAGATGACCCGAAGGATTT
79965 ACA
1 ACA
79968 AATTTGTGGG
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
19 3 0.09
20 15 0.47
22 12 0.38
23 2 0.06
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (20 bp):
ACAGATGACCCGAAGGATTT
Found at i:85677 original size:24 final size:24
Alignment explanation
Indices: 85645--85695 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
85635 TGCTGATCCT
85645 CATGTATCTTTTTCCAGTAGCAAG
1 CATGTATCTTTTTCCAGTAGCAAG
85669 CATGTATCTTTTTCCAGTAGCAAG
1 CATGTATCTTTTTCCAGTAGCAAG
85693 CAT
1 CAT
85696 CAGTATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (24 bp):
CATGTATCTTTTTCCAGTAGCAAG
Done.