Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004043.1 Hibiscus syriacus cultivar Beakdansim tig00008833_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: 60924
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:760 original size:145 final size:145
Alignment explanation
Indices: 495--761 Score: 331
Period size: 145 Copynumber: 1.8 Consensus size: 145
485 GGGAGCCTAC
* * * *
495 CTACCAAGGAGACCAGCCAGACATCTACCTGCTGAGGTAACAAGTTGGACTCGAGACGATTTGAC
1 CTACCAAGGAGACCAGCCAAACATCTACCTGCTAAAGTAACAAGTTGGACTCGAGACGATTCGAC
*** * * ** *
560 GTTGAAGCCAACAATTAAAGATCGCGAACTAGCTTGAAAGATTTCTAGAAATAGGAGGTGAATTA
66 GCCAAAGACAACAATTAAAGATCACGAACTAGCTCAAAAGATCTCTAGAAATAGGAGGTGAATTA
625 GGAGATAGGGAGTAT
131 GGAGATAGGGAGTAT
* * * * *
640 CTACCAAGGAGACGATCCAAACATTTTCCTGCTAAAGTAACAAGTTGGACTCGAGACGATTCGAT
1 CTACCAAGGAGACCAGCCAAACATCTACCTGCTAAAGTAACAAGTTGGACTCGAGACGATTCGAC
* *
705 GCCAAAGACAACAATTAAAGATCATGAAAC-AGCTCAAAAGA-CTCTTGAAAGTAGGAG
66 GCCAAAGACAACAATTAAAGATCACG-AACTAGCTCAAAAGATCTCTAGAAA-TAGGAG
762 ATGAGGTAGA
Statistics
Matches: 101, Mismatches: 19, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
144 7 0.07
145 91 0.90
146 3 0.03
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (145 bp):
CTACCAAGGAGACCAGCCAAACATCTACCTGCTAAAGTAACAAGTTGGACTCGAGACGATTCGAC
GCCAAAGACAACAATTAAAGATCACGAACTAGCTCAAAAGATCTCTAGAAATAGGAGGTGAATTA
GGAGATAGGGAGTAT
Found at i:1398 original size:26 final size:27
Alignment explanation
Indices: 1368--1430 Score: 110
Period size: 26 Copynumber: 2.4 Consensus size: 27
1358 AATCAAATGA
1368 ATTATAGATTCTCTTAATTC-TCAAGT
1 ATTATAGATTCTCTTAATTCTTCAAGT
*
1394 ATTATAGATTCTTTTAATTCTTCAAGT
1 ATTATAGATTCTCTTAATTCTTCAAGT
1421 ATTATAGATT
1 ATTATAGATT
1431 ACTAATGAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 19 0.54
27 16 0.46
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (27 bp):
ATTATAGATTCTCTTAATTCTTCAAGT
Found at i:2081 original size:10 final size:10
Alignment explanation
Indices: 2068--2094 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2058 ATAAAAGAAA
2068 AGAAAAAAAG
1 AGAAAAAAAG
2078 AGAAAAAAAG
1 AGAAAAAAAG
2088 AGAAAAA
1 AGAAAAA
2095 GCAAAGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAG
Found at i:2107 original size:20 final size:18
Alignment explanation
Indices: 2061--2124 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
2051 GGCGGGGATA
* *
2061 AAAG-AAAAGAAAAAAAG
1 AAAGAAAAAGAGAAAAAC
2078 AGAA-AAAAAGAGAAAAAGC
1 A-AAGAAAAAGAGAAAAA-C
*
2097 AAAGAAGAA-AGAAAAAC
1 AAAGAAAAAGAGAAAAAC
2114 AAAGAAAAAGA
1 AAAGAAAAAGA
2125 TGACAAGAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
17 10 0.26
18 23 0.61
19 5 0.13
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAGAGAAAAAC
Found at i:3634 original size:36 final size:36
Alignment explanation
Indices: 3571--3764 Score: 176
Period size: 37 Copynumber: 5.3 Consensus size: 36
3561 ATCTCACTTG
* **
3571 AAACATAAATTTATCTCACTCAAGATAGTTTTCCTTA
1 AAACA-AAATTTATCTCGCTTGAGATAGTTTTCCTTA
* * *
3608 AAACAAACTTTGTCTCGCTTGAGATAG-TTTCACTTG
1 AAACAAAATTTATCTCGCTTGAGATAGTTTTC-CTTA
* * *
3644 AAACAAAAATTTATCTCACTCGAGATAGTTTTTCTTA
1 AAAC-AAAATTTATCTCGCTTGAGATAGTTTTCCTTA
* * * * **
3681 AAACAAACTTTGTCTCGCTTGAGACAGCTTTCACTCG
1 AAACAAAATTTATCTCGCTTGAGATAGTTTTC-CTTA
* * *
3718 AAATAAAATTTATCTCTCTTGAGATAGTTTTTCTTA
1 AAACAAAATTTATCTCGCTTGAGATAGTTTTCCTTA
3754 AAAC-AAATTTA
1 AAACAAAATTTA
3765 ATTTTGCTCA
Statistics
Matches: 122, Mismatches: 31, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
35 11 0.09
36 50 0.41
37 58 0.48
38 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (36 bp):
AAACAAAATTTATCTCGCTTGAGATAGTTTTCCTTA
Found at i:3683 original size:73 final size:74
Alignment explanation
Indices: 3564--3760 Score: 308
Period size: 73 Copynumber: 2.7 Consensus size: 74
3554 AAGATTTATC
* * *
3564 TCACTTGAAACATAAATTTATCTCACTCAAGATAGTTTTCCTTAAAACAAACTTTGTCTCGCTTG
1 TCACTTGAAACAAAAATTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTTGTCTCGCTTG
*
3629 AGATAG-TT
66 AGACAGCTT
3637 TCACTTGAAACAAAAATTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTTGTCTCGCTTG
1 TCACTTGAAACAAAAATTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTTGTCTCGCTTG
3702 AGACAGCTT
66 AGACAGCTT
* * * *
3711 TCACTCGAAA-TAAAATTTATCTCTCTTGAGATAGTTTTTCTTAAAACAAA
1 TCACTTGAAACAAAAATTTATCTCACTCGAGATAGTTTTTCTTAAAACAAA
3761 TTTAATTTTG
Statistics
Matches: 115, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
73 104 0.90
74 11 0.10
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.37
Consensus pattern (74 bp):
TCACTTGAAACAAAAATTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTTGTCTCGCTTG
AGACAGCTT
Found at i:4034 original size:138 final size:137
Alignment explanation
Indices: 3776--4437 Score: 583
Period size: 139 Copynumber: 4.9 Consensus size: 137
3766 TTTTGCTCAA
* *
3776 ATTCATCGCATATGGAGTTGAATCTGTGACCCCTCACTAGAGGGATAAACATTTCCGGTGGAGAG
1 ATTCATCGCATATGGAGTTGAATAT-TGACCCCTCACTAGAGGGATCAACATTTCCGGTGGAGAG
* * * *
3841 TTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGATAAGAACTTGTTCAAC
65 TTCATAATGAGAA-AAATCATCTGATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
3906 CTTAGCTCG
129 CTTAGCTCG
* * * * * * **
3915 ATTCATCACATATGGAGCTGAATAATTGACCCCTCACTTGGGGGATCAATATTTCCAGAAGA-AG
1 ATTCATCGCATATGGAGTTGAAT-ATTGACCCCTCACTAGAGGGATCAACATTTCCGGTGGAGAG
*
3979 TTCATAATGAGAACAAATCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
65 TTCATAATGAGAA-AAATCATCTGATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
4044 CTTAGCTCG
129 CTTAGCTCG
*** * * *
4053 ATTCATCGCATATGGAGTTGAATCAGCAACCCTTCACTCGAGGGATCAACATTTCCGGTGGAGGG
1 ATTCATCGCATATGGAGTTGAAT-ATTGACCCCTCACTAGAGGGATCAACATTTCCGGTGGAGAG
* *
4118 TTCATAATGAGAAAAACTCATCTGATGAGGAAGAAGAATTTCATAATGAGAAGAACCTGTTCAAC
65 TTCATAATGAGAAAAA-TCATCTGATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
** *
4183 CTTTTTCTTG
129 C-TTAGCTCG
* * * * ** *
4193 AATAT-ATCACAGAAGGAGAT-AA-ATT-A------AC-------ATCAACATTTCCAATTGAGA
1 -AT-TCATCGCATATGGAGTTGAATATTGACCCCTCACTAGAGGGATCAACATTTCCGGTGGAGA
* * * * * * *
4241 GTTCATAATGGGAAGAACTTATCTGATGAGGGAGAAGAAGTTCATAATAAGAATAACTTTTTCAA
64 GTTCATAATGAGAA-AAATCATCTGATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
*
4306 CCTTAGCTCA
128 CCTTAGCTCG
* * * *
4316 ATTCATCGCATATGGAGTTGAATA-AGCAAACCCTCACTCGA-GGATTCAACATTTCCAGTGGAG
1 ATTCATCGCATATGGAGTTGAATATTG--ACCCCTCACTAGAGGGA-TCAACATTTCCGGTGGAG
* * ** * *
4379 AATTCATAATGAGAAGAACTCATCTGAAAAGAGAA-TAGAAGTTTATAATGAGAAGAACT
63 AGTTCATAATGAGAA-AAATCATCTGATGAG-GAAGAAGAAGTTCATAATGAGAAGAACT
4438 CATCCAAAGA
Statistics
Matches: 420, Mismatches: 76, Indels: 54
0.76 0.14 0.10
Matches are distributed among these distances:
121 1 0.00
122 13 0.03
123 6 0.01
124 72 0.17
125 2 0.00
126 1 0.00
131 2 0.00
132 2 0.00
137 1 0.00
138 124 0.30
139 172 0.41
140 10 0.02
141 13 0.03
142 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (137 bp):
ATTCATCGCATATGGAGTTGAATATTGACCCCTCACTAGAGGGATCAACATTTCCGGTGGAGAGT
TCATAATGAGAAAAATCATCTGATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
TAGCTCG
Found at i:4460 original size:39 final size:39
Alignment explanation
Indices: 4377--4471 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 39
4367 TTTCCAGTGG
*
4377 AGAA-TTCATAATGAGAAGAACTCATCTGAAAAGAGAAT
1 AGAAGTTCATAATGAGAAGAACTCATCAGAAAAGAGAAT
*
4415 AGAAGTTTATAATGAGAAGAACTCATCCAAAGAAAA-AGAA-
1 AGAAGTTCATAATGAGAAGAACTCAT-C--AGAAAAGAGAAT
4455 A-AAGTTCATAATGAGAA
1 AGAAGTTCATAATGAGAA
4472 CTTGTTCAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
38 4 0.08
39 35 0.70
40 2 0.04
41 4 0.08
42 5 0.10
ACGTcount: A:0.53, C:0.09, G:0.18, T:0.20
Consensus pattern (39 bp):
AGAAGTTCATAATGAGAAGAACTCATCAGAAAAGAGAAT
Found at i:5706 original size:23 final size:24
Alignment explanation
Indices: 5664--5709 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
5654 CACTAGGGGC
* *
5664 ACGTAGAATTTGTCCTGAAGGACT
1 ACGTAGAATATGTCCCGAAGGACT
5688 ACGTAGAA-ATGTCCCGAAGGAC
1 ACGTAGAATATGTCCCGAAGGAC
5710 CACATATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.22
Consensus pattern (24 bp):
ACGTAGAATATGTCCCGAAGGACT
Found at i:6013 original size:44 final size:44
Alignment explanation
Indices: 5961--6059 Score: 180
Period size: 44 Copynumber: 2.2 Consensus size: 44
5951 TATCATACTT
* *
5961 TCATGTAATCACATTTCTTTTTTCACATGCTTTATATCTTGTAC
1 TCATGTAATCACATATCTCTTTTCACATGCTTTATATCTTGTAC
6005 TCATGTAATCACATATCTCTTTTCACATGCTTTATATCTTGTAC
1 TCATGTAATCACATATCTCTTTTCACATGCTTTATATCTTGTAC
6049 TCATGTAATCA
1 TCATGTAATCA
6060 TATCACTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.46
Consensus pattern (44 bp):
TCATGTAATCACATATCTCTTTTCACATGCTTTATATCTTGTAC
Found at i:9816 original size:20 final size:20
Alignment explanation
Indices: 9791--9837 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
9781 CAAGTCCTTG
*
9791 TTGCATTTGCATCTCGCAT-T
1 TTGCATTTGCATAT-GCATAT
9811 TTGCATTTGCATATGCATAT
1 TTGCATTTGCATATGCATAT
9831 TTGCATT
1 TTGCATT
9838 AACATATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (20 bp):
TTGCATTTGCATATGCATAT
Found at i:9843 original size:20 final size:19
Alignment explanation
Indices: 9806--9844 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
9796 TTTGCATCTC
**
9806 GCATTTTGCATTTGCATAT
1 GCATTTTGCATTAACATAT
9825 GCATATTTGCATTAACATAT
1 GCAT-TTTGCATTAACATAT
9845 ACACATTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (19 bp):
GCATTTTGCATTAACATAT
Found at i:10865 original size:11 final size:11
Alignment explanation
Indices: 10849--10948 Score: 80
Period size: 11 Copynumber: 8.9 Consensus size: 11
10839 AGTATAAGAG
10849 CAAAGAAAAAA
1 CAAAGAAAAAA
10860 CAAAGAACAATGAA
1 CAAAGAA-AA--AA
*
10874 CAATGAAAAAA
1 CAAAGAAAAAA
*
10885 -AGAGCAAAGAAA
1 CAAAG-AAA-AAA
*
10897 AAAAG-AAAAA
1 CAAAGAAAAAA
* *
10907 TAAAGGAAAAA
1 CAAAGAAAAAA
10918 CAAAGAAAAAA
1 CAAAGAAAAAA
*
10929 CAAAG-AAAAC
1 CAAAGAAAAAA
10939 CAAAGAAAAA
1 CAAAGAAAAA
10949 GAGGATAAGA
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
10 18 0.25
11 37 0.51
12 5 0.07
13 5 0.07
14 8 0.11
ACGTcount: A:0.75, C:0.09, G:0.13, T:0.03
Consensus pattern (11 bp):
CAAAGAAAAAA
Found at i:10922 original size:21 final size:21
Alignment explanation
Indices: 10889--10948 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
10879 AAAAAAAGAG
10889 CAAAG-AAAA-AAAGAAAAATA
1 CAAAGAAAAACAAAGAAAAA-A
*
10909 -AAGGAAAAACAAAGAAAAAA
1 CAAAGAAAAACAAAGAAAAAA
*
10929 CAAAGAAAACCAAAGAAAAA
1 CAAAGAAAAACAAAGAAAAA
10949 GAGGATAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 3 0.09
20 5 0.15
21 26 0.76
ACGTcount: A:0.78, C:0.08, G:0.12, T:0.02
Consensus pattern (21 bp):
CAAAGAAAAACAAAGAAAAAA
Found at i:12499 original size:22 final size:22
Alignment explanation
Indices: 12458--12499 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12448 TTTAAACAAG
* *
12458 ATTTATCTCTCTTGAAATAGAA
1 ATTTATCTCACTCGAAATAGAA
*
12480 ATTTATCTCACTCGAGATAG
1 ATTTATCTCACTCGAAATAG
12500 TTTTTCTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (22 bp):
ATTTATCTCACTCGAAATAGAA
Found at i:12555 original size:73 final size:74
Alignment explanation
Indices: 12468--12662 Score: 304
Period size: 73 Copynumber: 2.6 Consensus size: 74
12458 ATTTATCTCT
* *
12468 CTTGAAATAGAAATTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTTGTCTCGCTTGAGA
1 CTTGAAATAGAAATTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACATTGTCTCGCTTAAGA
12533 C-TGTTTCA
66 CATGTTTCA
*
12541 CTTGAAATAGAAATTTATCTCTCTCGAGATAGTTTTTCTTAAAACAAACATTGTCTCGCTTAAGA
1 CTTGAAATAGAAATTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACATTGTCTCGCTTAAGA
*
12606 CATTTTTCA
66 CATGTTTCA
* * *
12615 CTCGAAACA-AAATTTTATCTCACTTGAGATAGTTTTTCTTAAAACAAA
1 CTTGAAATAGAAA-TTTATCTCACTCGAGATAGTTTTTCTTAAAACAAA
12663 TTTCATTTCT
Statistics
Matches: 112, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
73 66 0.59
74 46 0.41
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.38
Consensus pattern (74 bp):
CTTGAAATAGAAATTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACATTGTCTCGCTTAAGA
CATGTTTCA
Found at i:12928 original size:138 final size:139
Alignment explanation
Indices: 12678--13087 Score: 624
Period size: 138 Copynumber: 3.0 Consensus size: 139
12668 TTTCTCTCAA
* * * * *
12678 ATTCATTGCATATGGAGTTGAATCAGTGACCCATCACTCGAGGGATTAACATTTACAGTGGAAAG
1 ATTCATAGCATATGGAGTTGAATCAGCGACCCCTCACTCGAGGGATCAACATTTCCAGTGGAAAG
*
12743 TTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
66 TTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
12808 CTTAGCTCG
131 CTTAGCTCG
* * * **
12817 ATTCATCGCATATGGAGTTAAATCAGCGACCCCTCACTCGAGGGATCAATATTTCCAG-AAAAAG
1 ATTCATAGCATATGGAGTTGAATCAGCGACCCCTCACTCGAGGGATCAACATTTCCAGTGGAAAG
* ** * *
12881 TTCATAATGAGATGAACTCATCTAAAGAGGAAGAAGAAGTTCATAATGAGAATAACTTGTTCAAC
66 TTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
12946 CTTAGCTCG
131 CTTAGCTCG
* * * *
12955 ATTCATAGCATATGGAGTTGAATCAGCAACCTCTCACTCGATGGATCAACATTTCCAGTGGAGAG
1 ATTCATAGCATATGGAGTTGAATCAGCGACCCCTCACTCGAGGGATCAACATTTCCAGTGGAAAG
*
13020 TTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTTATAATGAGAAGAACTTGTTCAAC
66 TTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
13085 CTT
131 CTT
13088 TTGCTCGAAT
Statistics
Matches: 240, Mismatches: 30, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
138 124 0.52
139 116 0.48
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (139 bp):
ATTCATAGCATATGGAGTTGAATCAGCGACCCCTCACTCGAGGGATCAACATTTCCAGTGGAAAG
TTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
CTTAGCTCG
Found at i:13379 original size:39 final size:39
Alignment explanation
Indices: 13282--13379 Score: 126
Period size: 39 Copynumber: 2.5 Consensus size: 39
13272 TCCAGTGGAG
* * ** *
13282 AGTTCATAATGAGAAGAACACATCTGAAAAGGGAGATGA
1 AGTTCATAATGAGAAGAACTCATCCGAAAAGAAAGAAGA
*
13321 AGTTCATAATGAGAAGAACTCATCCGAAGAA-AAATAAGA
1 AGTTCATAATGAGAAGAACTCATCCGAA-AAGAAAGAAGA
13360 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
13380 TGTTCAACCT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 50 0.96
40 2 0.04
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.19
Consensus pattern (39 bp):
AGTTCATAATGAGAAGAACTCATCCGAAAAGAAAGAAGA
Found at i:14604 original size:29 final size:30
Alignment explanation
Indices: 14548--14605 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
14538 TTTTTTTATT
*
14548 TATTTTATTTCGATTTTTGCATGCTAATTTA
1 TATTTTATTTCGATTTTAGCAT-CTAATTTA
14579 TATTTTATTTC-ATTTTAGTCAT-TAATT
1 TATTTTATTTCGATTTTAG-CATCTAATT
14606 AATTTTGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 5 0.20
30 6 0.24
31 14 0.56
ACGTcount: A:0.24, C:0.09, G:0.07, T:0.60
Consensus pattern (30 bp):
TATTTTATTTCGATTTTAGCATCTAATTTA
Found at i:17677 original size:12 final size:12
Alignment explanation
Indices: 17660--17684 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17650 TAACAAAAGC
17660 AACAAAAAGAAA
1 AACAAAAAGAAA
17672 AACAAAAAGAAA
1 AACAAAAAGAAA
17684 A
1 A
17685 GAAAGAGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (12 bp):
AACAAAAAGAAA
Found at i:19427 original size:21 final size:22
Alignment explanation
Indices: 19377--19437 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 22
19367 GGAAAGAAGC
19377 CAAAGGACGTGACTCTTCAAGAAT
1 CAAAGGACGTGACTCTTC-A-AAT
* *
19401 CTAAGGATGTGACTCTTC-AAT
1 CAAAGGACGTGACTCTTCAAAT
*
19422 CAAAGGACATGA-TCTT
1 CAAAGGACGTGACTCTT
19438 TGGAGGACCA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 4 0.12
21 12 0.38
24 16 0.50
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (22 bp):
CAAAGGACGTGACTCTTCAAAT
Found at i:21585 original size:15 final size:15
Alignment explanation
Indices: 21548--21578 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21538 TCTTTGATAA
*
21548 CTATTCTATCCATTT
1 CTATTCTTTCCATTT
21563 CTATTCTTTCCATTT
1 CTATTCTTTCCATTT
21578 C
1 C
21579 CTTTCTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.29, G:0.00, T:0.55
Consensus pattern (15 bp):
CTATTCTTTCCATTT
Found at i:30064 original size:21 final size:21
Alignment explanation
Indices: 30022--30064 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
30012 TTTCTGGGCT
* *
30022 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
30043 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
30064 A
1 A
30065 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:30117 original size:20 final size:20
Alignment explanation
Indices: 30092--30129 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30082 GAATGCTAGA
*
30092 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
30112 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
30130 TAAAAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:30764 original size:23 final size:23
Alignment explanation
Indices: 30738--30792 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
30728 ACTACGGTGT
30738 AATTCTACGCGGCACTCCGGCGC
1 AATTCTACGCGGCACTCCGGCGC
* * *
30761 AATTCTACGTGGCACTTCGGTGC
1 AATTCTACGCGGCACTCCGGCGC
*
30784 AATTATACG
1 AATTCTACG
30793 AGCTGTGGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (23 bp):
AATTCTACGCGGCACTCCGGCGC
Found at i:31242 original size:2 final size:2
Alignment explanation
Indices: 31235--31266 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31225 TTGTATAACC
31235 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31267 GATTATTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33284 original size:3 final size:3
Alignment explanation
Indices: 33276--33305 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
33266 TAATTAACTT
*
33276 TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
33306 GTAGTAGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:35233 original size:39 final size:39
Alignment explanation
Indices: 35189--35267 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
35179 TAAGTTTCTT
35189 AAATCTTTCAAGTTTGAGGGAATGGGAAGGTTCCTGAAA
1 AAATCTTTCAAGTTTGAGGGAATGGGAAGGTTCCTGAAA
35228 AAATCTTTCAAGTTTGAGGGAATGGGAAGGTTCCTGAAA
1 AAATCTTTCAAGTTTGAGGGAATGGGAAGGTTCCTGAAA
35267 A
1 A
35268 GGCCAGATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (39 bp):
AAATCTTTCAAGTTTGAGGGAATGGGAAGGTTCCTGAAA
Found at i:36130 original size:27 final size:26
Alignment explanation
Indices: 36066--36133 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
36056 GTATTTATTG
***
36066 GTTCGATTAACTAAATATTTTTACAA
1 GTTCGATTAACTAAATATTAAAACAA
36092 GTTCGATTAACTAAATA-TAAAACTAA
1 GTTCGATTAACTAAATATTAAAAC-AA
36118 CGTTCGATTAACTAAA
1 -GTTCGATTAACTAAA
36134 AACATTATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 3 0.08
26 19 0.51
27 15 0.41
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (26 bp):
GTTCGATTAACTAAATATTAAAACAA
Found at i:36303 original size:21 final size:21
Alignment explanation
Indices: 36289--36328 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
36279 CATCAGTATC
36289 ACCACCACCACCATCATCACA
1 ACCACCACCACCATCATCACA
*
36310 ACCACCATCACCATCATCA
1 ACCACCACCACCATCATCA
36329 TCGTCATCGC
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:0.38, C:0.50, G:0.00, T:0.12
Consensus pattern (21 bp):
ACCACCACCACCATCATCACA
Found at i:36324 original size:18 final size:18
Alignment explanation
Indices: 36286--36325 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
36276 CAGCATCAGT
* *
36286 ATCACCACCACCACCATC
1 ATCACAACCACCACCACC
*
36304 ATCACAACCACCATCACC
1 ATCACAACCACCACCACC
36322 ATCA
1 ATCA
36326 TCATCGTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.50, G:0.00, T:0.12
Consensus pattern (18 bp):
ATCACAACCACCACCACC
Found at i:37913 original size:21 final size:21
Alignment explanation
Indices: 37899--37938 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
37889 CATCAGTATC
37899 ACCACCACCACCATCATCACA
1 ACCACCACCACCATCATCACA
*
37920 ACCACCATCACCATCATCA
1 ACCACCACCACCATCATCA
37939 TCGTCATCGC
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:0.38, C:0.50, G:0.00, T:0.12
Consensus pattern (21 bp):
ACCACCACCACCATCATCACA
Found at i:37934 original size:18 final size:18
Alignment explanation
Indices: 37896--37935 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
37886 CAGCATCAGT
* *
37896 ATCACCACCACCACCATC
1 ATCACAACCACCACCACC
*
37914 ATCACAACCACCATCACC
1 ATCACAACCACCACCACC
37932 ATCA
1 ATCA
37936 TCATCGTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.50, G:0.00, T:0.12
Consensus pattern (18 bp):
ATCACAACCACCACCACC
Found at i:38500 original size:3 final size:3
Alignment explanation
Indices: 38492--38566 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
38482 TGGGTATCCT
* * * * * * *
38492 TTA TTA TTA TTA TTA TTA CTA CTA CTA CTA CTA CTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
38540 TTA TTA TTA TTA TTA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
38567 AATAATAATT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:45409 original size:3 final size:3
Alignment explanation
Indices: 45401--45425 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
45391 GTTGATAGAT
45401 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
45426 ACATTATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:46375 original size:40 final size:40
Alignment explanation
Indices: 46296--46445 Score: 106
Period size: 40 Copynumber: 3.6 Consensus size: 40
46286 ATCCAGAAGT
* **
46296 AATAAATGTGGGGCACTTTTGAAGGTCTTTATCAACAAGA
1 AATAAATGTGGGGCACTTTTGAAGGACCGTATCAACAAGA
* *
46336 AATAAATGTTGGGGCA-TTTTGAAGGACCGTATGAGCAAGA
1 AATAAATG-TGGGGCACTTTTGAAGGACCGTATCAACAAGA
* ** * *
46376 AATGATGAATG-GTGGGCACTTTTTAAGGTTCGTATCATCCAAAA
1 AAT-A--AATGTG-GGGCACTTTTGAAGGACCGTATCA-ACAAGA
* *
46420 GAATAAATGTTGGGACATTTTTGAAG
1 -AATAAATG-TGGGGCACTTTTGAAG
46446 TCCCATATCA
Statistics
Matches: 86, Mismatches: 14, Indels: 17
0.74 0.12 0.15
Matches are distributed among these distances:
40 30 0.35
41 9 0.10
42 9 0.10
43 29 0.34
44 6 0.07
45 3 0.03
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (40 bp):
AATAAATGTGGGGCACTTTTGAAGGACCGTATCAACAAGA
Found at i:47802 original size:89 final size:88
Alignment explanation
Indices: 47663--48352 Score: 580
Period size: 89 Copynumber: 7.8 Consensus size: 88
47653 TTATCTTAGA
* * * * * *
47663 TTTGGTATTCCTGAAAGAGTAGAGAAGTAAATTAATCTCGAGTCTGATCTCCCCGGAAGAGTAGT
1 TTTGGTCTTCCTGAAAAAGTAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCTGGAAGAGTAGT
47728 GGAGCAGATTCTTCTTATGTAAAG
66 GGAGCAGATTCTTCTTAT-TAAAG
* * * * * *
47752 TTTGGTCTTCCTGAAAAAGCAGCGAATCAAATAAATCTTGAGTCTAATCTCCCCT-TAAGAGTAG
1 TTTGGTCTTCCTGAAAAAGTAGCGAAGCAAATCAATCTCGAGTCTGATCT-CCCTGGAAGAGTAG
* * *
47816 TGGAGCAGATTATTCTTATCACAAA
65 TGGAGCAGATTCTTCTTATTA-AAG
*
47841 TTTGGTCTTCCCT-AAAGAA-TAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTA
1 TTTGGTCTT-CCTGAAA-AAGTAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCTGGAAGAGTA
* * * ***
47904 GAGAAGCAGATTCTTCATATCCCAG
64 GTGGAGCAGATTCTTCTTATTAAAG
* ** * * * *
47929 ATTTGGTCTTCCCGAAAGCGTAACGAA-CAAAATCAATCTCGGGACTGATCTCCATGGAAGAGTA
1 -TTTGGTCTTCCTGAAAAAGTAGCGAAGC-AAATCAATCTCGAGTCTGATCTCCCTGGAAGAGTA
* * *
47993 GAGGAGCATATTCTTCTTATCCTAGA-
64 GTGGAGCAGATTCTTCTTAT--TAAAG
* * * * * * * *
48019 TTTAGTCTTCCCGACAGAGTAGAGAAGCAAATCAATCTCGATTCTGATCTCCCTGAAAGAGTAGA
1 TTTGGTCTTCCTGAAAAAGTAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCTGGAAGAGTAGT
**
48084 GGAGCAGAGTT-TTCTTATTTCAG
66 GGAGCAGA-TTCTTCTTATTAAAG
* * * *
48107 ATTTGGTTTTCC-CAAAAGAGTAGCGAAGCAAATCAATTTCGAGTTTGATCTCCCTGGAAGAGTA
1 -TTTGGTCTTCCTGAAAA-AGTAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCTGGAAGAGTA
* *
48171 GTGGAGTAGATTCTTCTTATGTCATA-
64 GTGGAGCAGATTCTTCTTAT-T-AAAG
* * * *
48197 TTTGGTCTTCATGAAAAAGCAGCGAATCAAATCAATCTCGAGTCTGATCTCCCTAGAAGAGTAGT
1 TTTGGTCTTCCTGAAAAAGTAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCTGGAAGAGTAGT
*
48262 ----CTGATTCTTCTTATGT-AAG
66 GGAGCAGATTCTTCTTAT-TAAAG
* ** * * *
48281 ATTTGGTCTTCCTGAAAAAAGTTGAAAAGAAAATCAATCTCAAGTCTGATCTCCACTGAAAGAAG
1 -TTTGGTCTTCCTG-AAAAAGTAGCGAAGCAAATCAATCTCGAGTCTGATCTCC-CTGGAAG-AG
48346 -AGTGGAG
62 TAGTGGAG
48353 TAAACCTTCC
Statistics
Matches: 482, Mismatches: 90, Indels: 56
0.77 0.14 0.09
Matches are distributed among these distances:
83 1 0.00
85 26 0.05
86 32 0.07
87 10 0.02
88 14 0.03
89 381 0.79
90 16 0.03
91 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (88 bp):
TTTGGTCTTCCTGAAAAAGTAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCTGGAAGAGTAGT
GGAGCAGATTCTTCTTATTAAAG
Found at i:48135 original size:267 final size:266
Alignment explanation
Indices: 47660--48260 Score: 688
Period size: 267 Copynumber: 2.2 Consensus size: 266
47650 ATCTTATCTT
* * * *
47660 AGATTTGGTATTCCTGAAAGAGTAGA-GAAGTAAATTAATCTCGAGTCTGATCTCCCCGGAAGAG
1 AGATTTGGTCTTCCTGAAAGAGTA-ACGAA-CAAATCAATCTCGAGTCTGATCTCCCTGGAAGAG
* * * * * *
47724 TAGTGGAGCAGATTCTTCTTATGTAAAGTTTGGTCTTCCTGAAAAAGCAGCGAATCAAATAAATC
64 TAGAGGAGCAGATTCTTCTTATCTAAAGTTTAGTCTTCCCGAAAAAGCAGAGAAGCAAATAAATC
* * * *
47789 TTGAGTCTAATCTCCCCTTAAGAGTAGTGGAGCAGATTATTCTTATCACAAATTTGGTCTTCCCT
129 TCGAGTCTAATCTCCCCTAAAGAGTAGAGGAGCAGATTATTCTTATCACAAATTTGGTCTTCCCA
47854 AAAGAATAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAGAAGCAGATTCTT
194 AAAGAATAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAGAAGCAGATTCTT
47919 CATATCCC
259 CATATCCC
* * * * *
47927 AGATTTGGTCTTCCCGAAAGCGTAACGAACAAAATCAATCTCGGGACTGATCTCCATGGAAGAGT
1 AGATTTGGTCTTCCTGAAAGAGTAACGAAC-AAATCAATCTCGAGTCTGATCTCCCTGGAAGAGT
* * * * * *
47992 AGAGGAGCATATTCTTCTTATCCTAGA-TTTAGTCTTCCCGACAGAGTAGAGAAGCAAATCAATC
65 AGAGGAGCAGATTCTTCTTAT-CTAAAGTTTAGTCTTCCCGAAAAAGCAGAGAAGCAAATAAATC
* * ** * *
48056 TCGATTCTGATCT-CCCTGAAAGAGTAGAGGAGCAGAGTT-TTCTTATTTCAGATTTGGTTTTCC
129 TCGAGTCTAATCTCCCCT-AAAGAGTAGAGGAGCAGA-TTATTCTTATCACAAATTTGGTCTTCC
* * * * * * *
48119 CAAAAGAGTAGCGAAGCAAATCAATTTCGAGTTTGATCTCCCTGGAAGAGTAGTGGAGTAGATTC
192 CAAAAGAATAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAGAAGCAGATTC
* **
48184 TTCTTATGTC
257 TTCATATCCC
* * * * * *
48194 ATATTTGGTCTTCATGAAAAAGCAGCGAATCAAATCAATCTCGAGTCTGATCTCCCTAGAAGAGT
1 AGATTTGGTCTTCCTGAAAGAGTAACGAA-CAAATCAATCTCGAGTCTGATCTCCCTGGAAGAGT
48259 AG
65 AG
48261 TCTGATTCTT
Statistics
Matches: 276, Mismatches: 52, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
266 5 0.02
267 265 0.96
268 6 0.02
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (266 bp):
AGATTTGGTCTTCCTGAAAGAGTAACGAACAAATCAATCTCGAGTCTGATCTCCCTGGAAGAGTA
GAGGAGCAGATTCTTCTTATCTAAAGTTTAGTCTTCCCGAAAAAGCAGAGAAGCAAATAAATCTC
GAGTCTAATCTCCCCTAAAGAGTAGAGGAGCAGATTATTCTTATCACAAATTTGGTCTTCCCAAA
AGAATAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAGAAGCAGATTCTTCA
TATCCC
Found at i:48601 original size:81 final size:81
Alignment explanation
Indices: 48320--48676 Score: 409
Period size: 82 Copynumber: 4.4 Consensus size: 81
48310 AAAATCAATC
* *
48320 TCAAGTCTGATCTCCACTGAAAGAAGAGTGGAGTAAA--C--CTTCCAAAATTGATCTGACTA-C
1 TCAAGTTTGATCTCC-CTGAAAGAAGAGTGGAGCAAACCCGTCTTCCAAAATTGATCTGACTACC
* *
48380 TGAAAAAGATGAACAAA
65 CGAAAAAGAGGAACAAA
* * * * * *
48397 TCAAGTTTGATCTCCCTGATAGAATAGTGGAGCAGACACGTCTCCCGAAATTGATCTGACTACCC
1 TCAAGTTTGATCTCCCTGAAAGAAGAGTGGAGCAAACCCGTCTTCCAAAATTGATCTGACTACCC
* *
48462 AAAAAAAAAGGAACAAA
66 -GAAAAAGAGGAACAAA
* * *
48479 TCAAGTATGATCTCCACTAAAAGAAGAGTGGAGCAAACCCGTCTTCCAAAATAGATCTGACTACC
1 TCAAGTTTGATCTCC-CTGAAAGAAGAGTGGAGCAAACCCGTCTTCCAAAATTGATCTGACTACC
* *
48544 CGAAAAGGAGGAACATA
65 CGAAAAAGAGGAACAAA
* * * * *
48561 TCAAATTTTATCTCCCTGAAAGAAGAGTGGTGCATACCCGTTTTCCAAAATTGATCTGACTACCC
1 TCAAGTTTGATCTCCCTGAAAGAAGAGTGGAGCAAACCCGTCTTCCAAAATTGATCTGACTACCC
* *
48626 GAAAAAGAAGAACAGA
66 GAAAAAGAGGAACAAA
* *
48642 TCAAGTCTGATCTCCCCTGAAATAAGAGTGGAGCA
1 TCAAGTTTGATCT-CCCTGAAAGAAGAGTGGAGCA
48677 GATTTCCCAT
Statistics
Matches: 232, Mismatches: 40, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
76 17 0.07
77 14 0.06
78 1 0.00
80 19 0.08
81 69 0.30
82 70 0.30
83 42 0.18
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.22
Consensus pattern (81 bp):
TCAAGTTTGATCTCCCTGAAAGAAGAGTGGAGCAAACCCGTCTTCCAAAATTGATCTGACTACCC
GAAAAAGAGGAACAAA
Found at i:52317 original size:22 final size:22
Alignment explanation
Indices: 52274--52318 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
52264 ATATTAGTTT
* *
52274 TTTTATAATCTAGAATGATTAG
1 TTTTAGAATCTAAAATGATTAG
52296 TTTTAGAATCTAAAAATG-TTAG
1 TTTTAGAATCT-AAAATGATTAG
52318 T
1 T
52319 GAACGCTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (22 bp):
TTTTAGAATCTAAAATGATTAG
Found at i:54740 original size:2 final size:2
Alignment explanation
Indices: 54733--54799 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
54723 TAATATCCCT
54733 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54775 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
54800 TAAAAGGTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.