Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008056.1 Hibiscus syriacus cultivar Beakdansim tig00110551_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: 2370532
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 13
Found at i:1526949 original size:20 final size:21
Alignment explanation
Indices: 1526924--1526966 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
1526914 ACTTAAATTC
1526924 TTAACATTTATATGATA-ATA
1 TTAACATTTATATGATATATA
1526944 TTAACATTTATATGATATATA
1 TTAACATTTATATGATATATA
1526965 TT
1 TT
1526967 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (21 bp):
TTAACATTTATATGATATATA
Found at i:1531763 original size:28 final size:28
Alignment explanation
Indices: 1531732--1531791 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1531722 CGGTATATAC
* *
1531732 ATATTAAAAATATTA-TTGTTTCATTTTT
1 ATATT-AAAATATTATTTATTTAATTTTT
* *
1531760 ATATTATAGTATTATTTATTTAATTTTT
1 ATATTAAAATATTATTTATTTAATTTTT
1531788 ATAT
1 ATAT
1531792 AATATATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (28 bp):
ATATTAAAATATTATTTATTTAATTTTT
Found at i:1539604 original size:19 final size:19
Alignment explanation
Indices: 1539576--1539614 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1539566 TTCATTATTA
*
1539576 TTATTTTTATTTTTATTTT
1 TTATTCTTATTTTTATTTT
1539595 TTATTCTTATTTTTATTTT
1 TTATTCTTATTTTTATTTT
1539614 T
1 T
1539615 ACTATTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (19 bp):
TTATTCTTATTTTTATTTT
Found at i:1539612 original size:6 final size:6
Alignment explanation
Indices: 1539570--1539615 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
1539560 TGGTCCTTCA
* *
1539570 TTATTA TTATTT TTATTT TTATTTT TTATTC TTATTT TTATTT TTA
1 TTATTT TTATTT TTATTT TTA-TTT TTATTT TTATTT TTATTT TTA
1539616 CTATTTGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
6 30 0.83
7 6 0.17
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (6 bp):
TTATTT
Found at i:1539830 original size:26 final size:28
Alignment explanation
Indices: 1539801--1539858 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
1539791 TAATACTACG
1539801 TTTTATTATTTTT-ATTGT-ATTTTTTA
1 TTTTATTATTTTTGATTGTGATTTTTTA
* * *
1539827 TTTTCTTATTTTTGTTTGTGTTTTTTTA
1 TTTTATTATTTTTGATTGTGATTTTTTA
1539855 TTTT
1 TTTT
1539859 CTTTAATTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 12 0.44
27 4 0.15
28 11 0.41
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.79
Consensus pattern (28 bp):
TTTTATTATTTTTGATTGTGATTTTTTA
Found at i:1539838 original size:14 final size:13
Alignment explanation
Indices: 1539820--1539862 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1539810 TTTTATTGTA
1539820 TTTTTTATTTTCT
1 TTTTTTATTTTCT
* *
1539833 TATTTTTGTTTGTGT
1 T-TTTTTATTT-TCT
1539848 TTTTTTATTTTCT
1 TTTTTTATTTTCT
1539861 TT
1 TT
1539863 AATTCCATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 5 0.21
14 16 0.67
15 3 0.12
ACGTcount: A:0.07, C:0.05, G:0.07, T:0.81
Consensus pattern (13 bp):
TTTTTTATTTTCT
Found at i:1539911 original size:4 final size:4
Alignment explanation
Indices: 1539892--1539979 Score: 78
Period size: 4 Copynumber: 22.2 Consensus size: 4
1539882 TCTTTATTCG
* * *
1539892 TATT T-TT TACTT TATT TATT TATT TATT TATT TATT TGTT TTTT TTTT
1 TATT TATT TA-TT TATT TATT TATT TATT TATT TATT TATT TATT TATT
1539940 TA-T T-TT TATT T-TT T-TT TATTT TATTT TATTT TATT TATT T
1 TATT TATT TATT TATT TATT TA-TT TA-TT TA-TT TATT TATT T
1539980 TTTTTTCCTT
Statistics
Matches: 75, Mismatches: 3, Indels: 12
0.83 0.03 0.13
Matches are distributed among these distances:
3 13 0.17
4 44 0.59
5 18 0.24
ACGTcount: A:0.17, C:0.01, G:0.01, T:0.81
Consensus pattern (4 bp):
TATT
Found at i:1539915 original size:20 final size:20
Alignment explanation
Indices: 1539809--1539982 Score: 88
Period size: 20 Copynumber: 8.2 Consensus size: 20
1539799 CGTTTTATTA
*
1539809 TTTTTATTGTATTT-TTTAT
1 TTTTTATTTTATTTATTTAT
* * *
1539828 TTTCTTATTTTTGTTTGTGT-T
1 TTT-TTA-TTTTATTTATTTAT
* *
1539849 TTTTTATTTTCTTTAATTCCAT
1 TTTTTATTTTATTT-ATT-TAT
*
1539871 TCTTTT-TTCCTTCTTTATTCGTAT
1 T-TTTTATT--TTATTTATT--TAT
*
1539895 TTTTTACTTTATTTATTTAT
1 TTTTTATTTTATTTATTTAT
* *
1539915 TTATTTA-TTTATTTGTTTTTT
1 TT-TTTATTTTATTT-ATTTAT
*
1539936 TTTTTATTTTTATTT-TTTTT
1 TTTTTA-TTTTATTTATTTAT
1539956 TATTTTATTTTATTTTATTTAT
1 T-TTTTATTTTA-TTTATTTAT
1539978 TTTTT
1 TTTTT
1539983 TTTCCTTTTT
Statistics
Matches: 123, Mismatches: 14, Indels: 34
0.72 0.08 0.20
Matches are distributed among these distances:
19 10 0.08
20 34 0.28
21 32 0.26
22 26 0.21
23 11 0.09
24 10 0.08
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (20 bp):
TTTTTATTTTATTTATTTAT
Found at i:1539982 original size:16 final size:15
Alignment explanation
Indices: 1539906--1539985 Score: 92
Period size: 16 Copynumber: 5.2 Consensus size: 15
1539896 TTTTACTTTA
1539906 TTTA-TTTATTTATTT
1 TTTATTTTATTT-TTT
*
1539921 ATTTATTTGTTTTTTTT
1 -TTTATTT-TATTTTTT
1539938 TTTATTTTTATTTTTT
1 TTTA-TTTTATTTTTT
*
1539954 TTTATTTTATTTTAT
1 TTTATTTTATTTTTT
1539969 TTTA-TTTATTTTTT
1 TTTATTTTATTTTTT
1539983 TTT
1 TTT
1539986 CCTTTTTTTC
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
14 12 0.21
15 14 0.25
16 19 0.33
17 8 0.14
18 4 0.07
ACGTcount: A:0.15, C:0.00, G:0.01, T:0.84
Consensus pattern (15 bp):
TTTATTTTATTTTTT
Found at i:1539991 original size:20 final size:19
Alignment explanation
Indices: 1539894--1539980 Score: 83
Period size: 19 Copynumber: 4.6 Consensus size: 19
1539884 TTTATTCGTA
*
1539894 TTTTTTACTTTATTTATTT
1 TTTTTTATTTTATTTATTT
*
1539913 ATTTATTTA-TTTATTTGTTT
1 -TTT-TTTATTTTATTTATTT
1539933 TTTTTT-TTATT-TTTATTT
1 TTTTTTATT-TTATTTATTT
1539951 TTTTTTATTTTATTT-TATT
1 TTTTTTATTTTATTTAT-TT
*
1539970 TTATTTATTTT
1 TTTTTTATTTT
1539981 TTTTTCCTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
18 19 0.33
19 22 0.38
20 13 0.22
21 4 0.07
ACGTcount: A:0.16, C:0.01, G:0.01, T:0.82
Consensus pattern (19 bp):
TTTTTTATTTTATTTATTT
Found at i:1541442 original size:105 final size:105
Alignment explanation
Indices: 1541260--1541468 Score: 400
Period size: 105 Copynumber: 2.0 Consensus size: 105
1541250 CATCACCACC
* *
1541260 AATCTTTCACCCTCATTTTTTGTGAACATCGAATAATCAAATTTACTCTGCTGATATCCTGCAGC
1 AATCTTTCACCCTCATTTTTTGTGAACATAGAATAATCAAATTTACTCTGCTAATATCCTGCAGC
1541325 TGCCAATGCTTCAGTAGGCTTTAAATTCCACTGTCGTGAT
66 TGCCAATGCTTCAGTAGGCTTTAAATTCCACTGTCGTGAT
1541365 AATCTTTCACCCTCATTTTTTGTGAACATAGAATAATCAAATTTACTCTGCTAATATCCTGCAGC
1 AATCTTTCACCCTCATTTTTTGTGAACATAGAATAATCAAATTTACTCTGCTAATATCCTGCAGC
1541430 TGCCAATGCTTCAGTAGGCTTTAAATTCCACTGTCGTGA
66 TGCCAATGCTTCAGTAGGCTTTAAATTCCACTGTCGTGA
1541469 GGCTTGTTTC
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 102 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (105 bp):
AATCTTTCACCCTCATTTTTTGTGAACATAGAATAATCAAATTTACTCTGCTAATATCCTGCAGC
TGCCAATGCTTCAGTAGGCTTTAAATTCCACTGTCGTGAT
Found at i:1547499 original size:153 final size:156
Alignment explanation
Indices: 1547307--1547616 Score: 574
Period size: 153 Copynumber: 2.0 Consensus size: 156
1547297 AATTGAAATA
1547307 AGTAATAAATTCAAGGACTAATGATTGGATATTTTGTGTTAGGAGTTGCAAAGAAGAAAGAGAAG
1 AGTAATAAATTCAAGGACTAATGATTGGATATTTTGTGTTAGGAGTTGCAAAGAAGAAAGAGAAG
1547372 AAGGATAATATGGTTTTTTTGCTAGTATATGGATTTTATATCCATTTTATATTAAGATGAT-A-T
66 AAGGATAATATGGTTTTTTTGCTAGTATATGGATTTTATATCCATTTTATATTAAGATGATAAGT
1547435 GGAGAAAGGAA-AAAA-TTGGATATTT
131 GGAG-AAGGAAGAAAATTTGGATATTT
1547460 AGTAATAAATTCAAGGACTAATGATTGGATATTTTGTGTTAGGAGTTGCAAAGAAGAAAGAGAAG
1 AGTAATAAATTCAAGGACTAATGATTGGATATTTTGTGTTAGGAGTTGCAAAGAAGAAAGAGAAG
1547525 AAGGATAATATGGTTTTTTTGCTAGTATATGGATTTTATATCCATTTTATATTAAGATGATAAGT
66 AAGGATAATATGGTTTTTTTGCTAGTATATGGATTTTATATCCATTTTATATTAAGATGATAAGT
1547590 GGAGAAGGAAGGAAAATTTGGATATTT
131 GGAGAAGGAA-GAAAATTTGGATATTT
1547617 GGTTATTCTC
Statistics
Matches: 152, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
153 126 0.83
154 7 0.05
155 5 0.03
156 4 0.03
157 10 0.07
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (156 bp):
AGTAATAAATTCAAGGACTAATGATTGGATATTTTGTGTTAGGAGTTGCAAAGAAGAAAGAGAAG
AAGGATAATATGGTTTTTTTGCTAGTATATGGATTTTATATCCATTTTATATTAAGATGATAAGT
GGAGAAGGAAGAAAATTTGGATATTT
Found at i:1548348 original size:20 final size:20
Alignment explanation
Indices: 1548325--1548368 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
1548315 GAAGTATCGC
1548325 TACTGTTGAGGTAGTACCGA
1 TACTGTTGAGGTAGTACCGA
1548345 TACTGTTGAGGTAGTACCGA
1 TACTGTTGAGGTAGTACCGA
1548365 TACT
1 TACT
1548369 ACTAAGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (20 bp):
TACTGTTGAGGTAGTACCGA
Found at i:1555951 original size:21 final size:21
Alignment explanation
Indices: 1555909--1555952 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1555899 ACTCTGGGAG
* *
1555909 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
1555930 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
1555951 CT
1 CT
1555953 CTTCCTCTGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:1557067 original size:17 final size:17
Alignment explanation
Indices: 1557045--1557077 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1557035 ATTTTCAAAG
1557045 TGATGCACCGATGCACA
1 TGATGCACCGATGCACA
1557062 TGATGCACCGATGCAC
1 TGATGCACCGATGCAC
1557078 CAATCCATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.18
Consensus pattern (17 bp):
TGATGCACCGATGCACA
Found at i:1558042 original size:24 final size:24
Alignment explanation
Indices: 1557997--1558048 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1557987 GGGATACTCC
* *
1557997 TACGGGGTCCTTAGGGACAAATTA
1 TACGGAGTCCTTAGAGACAAATTA
* * *
1558021 TACGGAGTCCTTCGAGAGAAATTC
1 TACGGAGTCCTTAGAGACAAATTA
1558045 TACG
1 TACG
1558049 TGGCACTTCG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (24 bp):
TACGGAGTCCTTAGAGACAAATTA
Found at i:1560481 original size:23 final size:23
Alignment explanation
Indices: 1560449--1560492 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1560439 TTATGAAAAT
1560449 ATATTAATTTAAATATAAATAAG
1 ATATTAATTTAAATATAAATAAG
* **
1560472 ATATTTATTTATTTATAAATA
1 ATATTAATTTAAATATAAATA
1560493 TCAGAAAAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATTAATTTAAATATAAATAAG
Found at i:1560694 original size:11 final size:12
Alignment explanation
Indices: 1560679--1560707 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1560669 AAAACATAAT
1560679 TAAAATAATTTA
1 TAAAATAATTTA
1560691 -AAAATAATTTA
1 TAAAATAATTTA
1560702 TAAAAT
1 TAAAAT
1560708 TTATAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAAATAATTTA
Found at i:1560827 original size:2 final size:2
Alignment explanation
Indices: 1560820--1560848 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1560810 ACTAAAATCA
1560820 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1560849 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1561976 original size:39 final size:38
Alignment explanation
Indices: 1561915--1561990 Score: 107
Period size: 39 Copynumber: 2.0 Consensus size: 38
1561905 ACCTGGCAGT
*
1561915 GCTAGAAGCTACTGCAACTGATGCGTGGAGGGGCTGCTC
1 GCTAGAAGCTACTGCAAATGATGCGTGG-GGGGCTGCTC
* * *
1561954 GCTAGAAGCTGCTGGAAATGATGCGTTGGGGGCTGCT
1 GCTAGAAGCTACTGCAAATGATGCGTGGGGGGCTGCT
1561991 GGATGGAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 9 0.27
39 24 0.73
ACGTcount: A:0.20, C:0.20, G:0.38, T:0.22
Consensus pattern (38 bp):
GCTAGAAGCTACTGCAAATGATGCGTGGGGGGCTGCTC
Found at i:1562549 original size:139 final size:138
Alignment explanation
Indices: 1562238--1562577 Score: 427
Period size: 139 Copynumber: 2.5 Consensus size: 138
1562228 CTAGCAAAAA
* * * *
1562238 GTTGAACAAATTCTTATCATTATGAACTTCTTCTTCTTTTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * * * *
1562303 CTCCTTCTGGAAATGCTGATCTTCAAAAGAGGCATTTGTTGATTCAACTCCATATGTGATGAATT
66 CTCCTTCTGAAAATACTGATCCTCAAAAGAGGCATTTGTTCATTCAACTCCATAGGAGATGAATC
* *
1562368 AAGGTAGG
131 AAGGCAAG
1562376 GTTGAACAAAATT-TTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAAC-AAATTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGA
* * * *
1562440 ATTTCCTT-TGAAAATATTGATCCTCAAATGAGGTTC-TTCT-TTCATTCAATTCCATAGGAGAT
65 A-CTCCTTCTGAAAATACTGATCCTCAAAAGAGG--CATT-TGTTCATTCAACTCCATAGGAGAT
*
1562502 GAATCAATGCAAG
126 GAATCAAGGCAAG
* *
1562515 GTTGAACAAGTTCTTCTTATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATG
1 GTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATG
1562578 TACTTCACCT
Statistics
Matches: 176, Mismatches: 20, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
138 79 0.45
139 95 0.54
140 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (138 bp):
GTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
CTCCTTCTGAAAATACTGATCCTCAAAAGAGGCATTTGTTCATTCAACTCCATAGGAGATGAATC
AAGGCAAG
Found at i:1562791 original size:123 final size:123
Alignment explanation
Indices: 1562512--1562836 Score: 413
Period size: 123 Copynumber: 2.6 Consensus size: 123
1562502 GAATCAATGC
* * *
1562512 AAGGTTGAACAAGTTCTTCTTATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * * ** * *
1562577 GTAC-TTCACCTAGAAATAGCTCTGCTGCTCTATCTTTTTTTGGAAATGGAGTCAAGCAA
66 GAACTTTC-TCTGGAAATAGCTCTGCTGATCTATCTCCTTCTGG-AATAGAGTCAAGCAA
*
1562636 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * *
1562701 GAACTTTCTCTGGAAA-AGTTGGTGTTGATCTATCTCCTTCTGTG-ATAGAGTCATGCAA
66 GAACTTTCTCTGGAAATAGCT-CTGCTGATCTATCTCCTTCTG-GAATAGAGTCAAGCAA
* * * *
1562759 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATCTTCAGATAAATTCTTCTTATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1562824 GAACTTTCTCTGG
66 GAACTTTCTCTGG
1562837 CATCCATCGG
Statistics
Matches: 177, Mismatches: 21, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
123 88 0.50
124 85 0.48
125 4 0.02
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTTTCTCTGGAAATAGCTCTGCTGATCTATCTCCTTCTGGAATAGAGTCAAGCAA
Found at i:1563092 original size:73 final size:73
Alignment explanation
Indices: 1562994--1563166 Score: 274
Period size: 73 Copynumber: 2.4 Consensus size: 73
1562984 GAGGTCTTAT
* * *
1562994 CATCTTGCACTGTAGGGCTTACAGATGACATTGAGGCTTTAAGATCAAAAAGCTCCCAAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACACTGAGGCTTTAAGATCAAAAAGCTCCCAAAGGCTT
1563059 TTTAAAAA
66 TTTAAAAA
* * *
1563067 CATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACACTGAGGCTTTAAGATCAAAAAGCTCCCAAAGGCTT
* *
1563132 TTTGAAAG
66 TTTAAAAA
1563140 CATCATGCACTGTAGGTCTTACAGATG
1 CATCATGCACTGTAGGTCTTACAGATG
1563167 TGGGAAATAG
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 91 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (73 bp):
CATCATGCACTGTAGGTCTTACAGATGACACTGAGGCTTTAAGATCAAAAAGCTCCCAAAGGCTT
TTTAAAAA
Found at i:1563884 original size:22 final size:22
Alignment explanation
Indices: 1563827--1563884 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
1563817 AATAAAACTT
*
1563827 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
1563849 TCATCTTTGGAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
1563871 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
1563885 TGTAGATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:1574981 original size:12 final size:12
Alignment explanation
Indices: 1574953--1574989 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1574943 TTTGGTAATC
1574953 CCCGACCCGATTA
1 CCCGACCCGA-TA
*
1574966 CCCGCCCCGATA
1 CCCGACCCGATA
1574978 CCCGACCCGATA
1 CCCGACCCGATA
1574990 AATATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.22, C:0.51, G:0.16, T:0.11
Consensus pattern (12 bp):
CCCGACCCGATA
Found at i:1576716 original size:29 final size:29
Alignment explanation
Indices: 1576684--1576740 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1576674 TGTTTAATCA
1576684 GTTTCTAATTTGTATCTTGTATTTATTTG
1 GTTTCTAATTTGTATCTTGTATTTATTTG
*
1576713 GTTTCTAATTTGTATGTTGTATTTATTT
1 GTTTCTAATTTGTATCTTGTATTTATTT
1576741 CAGTCTATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.18, C:0.05, G:0.14, T:0.63
Consensus pattern (29 bp):
GTTTCTAATTTGTATCTTGTATTTATTTG
Found at i:1583472 original size:21 final size:21
Alignment explanation
Indices: 1583448--1583487 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1583438 CATATTGAAG
1583448 AATTCAAGA-TCAAGAATCAGA
1 AATTC-AGATTCAAGAATCAGA
*
1583469 AATTCAGATTCCAGAATCA
1 AATTCAGATTCAAGAATCA
1583488 AGAGTCATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.23
Consensus pattern (21 bp):
AATTCAGATTCAAGAATCAGA
Found at i:1584576 original size:23 final size:24
Alignment explanation
Indices: 1584533--1584582 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
1584523 TTGTAAACGA
1584533 ATTTATATATAAATATATTATATT
1 ATTTATATATAAATATATTATATT
* *
1584557 ATTTATA-ATACATATGTTATATT
1 ATTTATATATAAATATATTATATT
1584580 ATT
1 ATT
1584583 ACTAATGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTTATATATAAATATATTATATT
Found at i:1585750 original size:19 final size:19
Alignment explanation
Indices: 1585726--1585766 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1585716 AATTTGGTCC
1585726 TTTATTATTATTATTATTT
1 TTTATTATTATTATTATTT
* *
1585745 TTTATTTTTATTTTTATTT
1 TTTATTATTATTATTATTT
1585764 TTT
1 TTT
1585767 CTATTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTATTATTATTATTATTT
Found at i:1585755 original size:13 final size:13
Alignment explanation
Indices: 1585733--1585816 Score: 51
Period size: 14 Copynumber: 6.0 Consensus size: 13
1585723 TCCTTTATTA
*
1585733 TTATTATTATTTT
1 TTATTTTTATTTT
1585746 TTATTTTTATTTT
1 TTATTTTTATTTT
*
1585759 TATTTTTTCTATTTT
1 T-TATTTT-TATTTT
* **
1585774 TTCTTTCTGGTTTT
1 TTATTT-TTATTTT
* *
1585788 TGTGTTTTTATATTA
1 T-TATTTTTAT-TTT
1585803 TTATTTATTATTTT
1 TTATTT-TTATTTT
1585817 CTCCTAACGT
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
13 13 0.24
14 22 0.41
15 19 0.35
ACGTcount: A:0.15, C:0.04, G:0.05, T:0.76
Consensus pattern (13 bp):
TTATTTTTATTTT
Found at i:1585773 original size:7 final size:6
Alignment explanation
Indices: 1585726--1585765 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
1585716 AATTTGGTCC
* *
1585726 TTTATT ATTATT ATTATTT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTA-TT TTTATT TTTATT TTTATT TTT
1585766 TCTATTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:1585956 original size:3 final size:3
Alignment explanation
Indices: 1585896--1585942 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
1585886 GCATATATAT
* *
1585896 TTA TT- TTA TTA CTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1585943 CTACATTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1586067 original size:24 final size:24
Alignment explanation
Indices: 1586038--1586084 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1586028 TCTTTATTCT
1586038 TATTTT-TACTTTGTTTTATTTATA
1 TATTTTGT-CTTTGTTTTATTTATA
* *
1586062 TATTTTGTTTTTGTTTTTTTTAT
1 TATTTTGTCTTTGTTTTATTTAT
1586085 TTTTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.77
Consensus pattern (24 bp):
TATTTTGTCTTTGTTTTATTTATA
Found at i:1586072 original size:28 final size:28
Alignment explanation
Indices: 1586041--1586095 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
1586031 TTATTCTTAT
1586041 TTTTACTTTGTTTTATTTATATATTTTG
1 TTTTACTTTGTTTTATTTATATATTTTG
** * * *
1586069 TTTTTGTTTTTTTTATTTTTATTTTTT
1 TTTTACTTTGTTTTATTTATATATTTT
1586096 TCTTTTTTTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.13, C:0.02, G:0.05, T:0.80
Consensus pattern (28 bp):
TTTTACTTTGTTTTATTTATATATTTTG
Found at i:1586087 original size:14 final size:14
Alignment explanation
Indices: 1586037--1586102 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
1586027 TTCTTTATTC
1586037 TTATTTTTACTTTGTT
1 TTATTTTTA-TTT-TT
*
1586053 TTATTTATATATTTTG
1 TTATTT-T-TATTTTT
*
1586069 TT-TTTGT-TTTTT
1 TTATTTTTATTTTT
1586081 TTATTTTTATTTTT
1 TTATTTTTATTTTT
*
1586095 TTCTTTTT
1 TTATTTTT
1586103 TTGGATATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
12 6 0.15
13 5 0.12
14 12 0.29
15 3 0.07
16 9 0.22
17 4 0.10
18 2 0.05
ACGTcount: A:0.12, C:0.03, G:0.05, T:0.80
Consensus pattern (14 bp):
TTATTTTTATTTTT
Found at i:1586101 original size:22 final size:21
Alignment explanation
Indices: 1586037--1586104 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
1586027 TTCTTTATTC
* *
1586037 TTATTTTTACTTTGTTTTATTT
1 TTATTTTTA-TTTTTTTTTTTT
* * *
1586059 ATATATTTTGTTTTTGTTTTTT
1 TTAT-TTTTATTTTTTTTTTTT
1586081 TTATTTTTATTTTTTTCTTTTT
1 TTATTTTTATTTTTTT-TTTTT
1586103 TT
1 TT
1586105 GGATATTAGT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
21 10 0.28
22 22 0.61
23 4 0.11
ACGTcount: A:0.12, C:0.03, G:0.04, T:0.81
Consensus pattern (21 bp):
TTATTTTTATTTTTTTTTTTT
Found at i:1586103 original size:15 final size:15
Alignment explanation
Indices: 1586037--1586096 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
1586027 TTCTTTATTC
*
1586037 TTATTTTTACTTTGTT
1 TTATTTTTA-TTTTTT
* *
1586053 TTA--TTTATATATT
1 TTATTTTTATTTTTT
* *
1586066 TTGTTTTTGTTTTTT
1 TTATTTTTATTTTTT
1586081 TTATTTTTATTTTTT
1 TTATTTTTATTTTTT
1586096 T
1 T
1586097 CTTTTTTTGG
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
13 6 0.18
14 4 0.12
15 21 0.62
16 3 0.09
ACGTcount: A:0.13, C:0.02, G:0.05, T:0.80
Consensus pattern (15 bp):
TTATTTTTATTTTTT
Found at i:1590075 original size:23 final size:23
Alignment explanation
Indices: 1590041--1590128 Score: 79
Period size: 23 Copynumber: 3.9 Consensus size: 23
1590031 GAGTCGAGGG
*
1590041 TTCTACGCGGTCCTTCGGGATAA
1 TTCTACGTGGTCCTTCGGGATAA
* * * *
1590064 TTCTACATGGTCCTTTGGGACAT
1 TTCTACGTGGTCCTTCGGGATAA
* *
1590087 TTCTACGCGATCCTTC-GGATAA
1 TTCTACGTGGTCCTTCGGGATAA
* * *
1590109 TACTATGTGGTCATTCGGGA
1 TTCTACGTGGTCCTTCGGGA
1590129 CATTTATATG
Statistics
Matches: 48, Mismatches: 16, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
22 15 0.31
23 33 0.69
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGATAA
Found at i:1590108 original size:45 final size:46
Alignment explanation
Indices: 1590041--1590133 Score: 125
Period size: 45 Copynumber: 2.0 Consensus size: 46
1590031 GAGTCGAGGG
* * * *
1590041 TTCTACGCGGTCCTTCGGGATAATTCTACATGGTCCTTTGGGACAT
1 TTCTACGCGATCCTTCGGGATAATACTACATGGTCATTCGGGACAT
**
1590087 TTCTACGCGATCCTTC-GGATAATACTATGTGGTCATTCGGGACAT
1 TTCTACGCGATCCTTCGGGATAATACTACATGGTCATTCGGGACAT
1590132 TT
1 TT
1590134 ATATGTGAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
45 26 0.63
46 15 0.37
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (46 bp):
TTCTACGCGATCCTTCGGGATAATACTACATGGTCATTCGGGACAT
Found at i:1590170 original size:24 final size:24
Alignment explanation
Indices: 1590130--1590210 Score: 119
Period size: 24 Copynumber: 3.4 Consensus size: 24
1590120 CATTCGGGAC
*
1590130 ATTTATATGTGAG-ACTTCGGTGCA
1 ATTTATACGTG-GCACTTCGGTGCA
*
1590154 ATTTCTACGTGGCACTTCGGTGCA
1 ATTTATACGTGGCACTTCGGTGCA
*
1590178 ATTTTTACGTGGCACTTCGGTGCA
1 ATTTATACGTGGCACTTCGGTGCA
1590202 ATTTATACG
1 ATTTATACG
1590211 AGCTGTGGTG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
23 1 0.02
24 51 0.98
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (24 bp):
ATTTATACGTGGCACTTCGGTGCA
Found at i:1598773 original size:18 final size:20
Alignment explanation
Indices: 1598740--1598779 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1598730 GTGAAGTGGG
1598740 TGTTCAAGAAAAAGAT-GAA
1 TGTTCAAGAAAAAGATAGAA
*
1598759 TGTTCAAG-GAAAGATAGAA
1 TGTTCAAGAAAAAGATAGAA
1598778 TG
1 TG
1598780 GTACAAAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.47, C:0.05, G:0.25, T:0.23
Consensus pattern (20 bp):
TGTTCAAGAAAAAGATAGAA
Found at i:1613027 original size:22 final size:21
Alignment explanation
Indices: 1612985--1613024 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1612975 GAGTTTATTT
*
1612985 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1613006 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1613025 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1616639 original size:2 final size:2
Alignment explanation
Indices: 1616632--1616676 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
1616622 TCCATATTTT
* *
1616632 TA TA TA TA TA TA CA TA TA TA T- TA T- TA TT TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1616671 TA TA TA
1 TA TA TA
1616677 GTTTGCAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1616732 original size:40 final size:37
Alignment explanation
Indices: 1616664--1616930 Score: 140
Period size: 38 Copynumber: 7.5 Consensus size: 37
1616654 ATTATTTATA
* ** **
1616664 TATATATTATATAGTTTGCAAATGATTTTCGAAAATAT
1 TATATAATATATAGTTTTTAAAACATTTT-GAAAATAT
1616702 GTATATAATATATAAGTTTTTAAAACATTTTAGAAAATA-
1 -TATATAATATAT-AGTTTTTAAAACATTTT-GAAAATAT
* * *
1616741 TATATCATATATAGTTTTTAAAATAATTTGTGAAAA-CT
1 TATATAATATATAGTTTTTAAAA-CATTT-TGAAAATAT
*
1616779 TATATAATATATAGTTTTGAAAACA--TT-----TA-
1 TATATAATATATAGTTTTTAAAACATTTTGAAAATAT
* *
1616808 TATAT--TATATAG-TTTTAAAACCTTTTTG-AAA-AC
1 TATATAATATATAGTTTTTAAAA-CATTTTGAAAATAT
* * * * * *
1616841 TATATAGTACATAATTTTGAAAACTTTTTTTAAAA-A-
1 TATATAATATATAGTTTTTAAAAC-ATTTTGAAAATAT
* * *
1616877 TATATAATATATAGATTTTAAAATATTTTTAAAA-A-
1 TATATAATATATAGTTTTTAAAACATTTTGAAAATAT
*
1616912 TATATATTATATAGTTTTT
1 TATATAATATATAGTTTTT
1616931 TTGAAATAAT
Statistics
Matches: 182, Mismatches: 28, Indels: 40
0.73 0.11 0.16
Matches are distributed among these distances:
26 7 0.04
27 8 0.04
29 7 0.04
32 1 0.01
33 5 0.03
34 1 0.01
35 34 0.19
36 30 0.16
37 16 0.09
38 41 0.23
39 12 0.07
40 20 0.11
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (37 bp):
TATATAATATATAGTTTTTAAAACATTTTGAAAATAT
Found at i:1616751 original size:36 final size:34
Alignment explanation
Indices: 1616703--1616930 Score: 129
Period size: 36 Copynumber: 6.6 Consensus size: 34
1616693 CGAAAATATG
1616703 TATATAATATATAAGTTTTTAAAACATTTTAGAAAA
1 TATAT-ATATATAAGTTTTTAAAACATTTT-GAAAA
*
1616739 TATATATCATATATAGTTTTTAAAATAATTTGTGAAAA
1 TATATAT-ATATA-AGTTTTTAAAA-CATTT-TGAAAA
*
1616777 CT-TATATAATATATAGTTTTGAAAACA-TTT----A
1 -TATATAT-ATATA-AGTTTTTAAAACATTTTGAAAA
*
1616808 TATAT-TATAT-AG-TTTTAAAACCTTTTTGAAAA
1 TATATATATATAAGTTTTTAAAA-CATTTTGAAAA
* * * *
1616840 CTATATAGTACATAA-TTTTGAAAACTTTTTTTAAAA
1 -TATATA-TATATAAGTTTTTAAAAC-ATTTTGAAAA
* * *
1616876 -ATATATAATATATAGATTTTAAAATATTTTTAAAA
1 TATATAT-ATATA-AGTTTTTAAAACATTTTGAAAA
1616911 -ATATATATTATATAGTTTTT
1 TATATATA-TATA-AGTTTTT
1616931 TTGAAATAAT
Statistics
Matches: 155, Mismatches: 15, Indels: 45
0.72 0.07 0.21
Matches are distributed among these distances:
26 7 0.05
27 3 0.02
28 3 0.02
29 4 0.03
30 2 0.01
31 4 0.03
32 1 0.01
33 6 0.04
34 10 0.06
35 35 0.23
36 36 0.23
37 12 0.08
38 30 0.19
39 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (34 bp):
TATATATATATAAGTTTTTAAAACATTTTGAAAA
Found at i:1616799 original size:25 final size:26
Alignment explanation
Indices: 1616771--1616828 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 26
1616761 AAATAATTTG
1616771 TGAAAAC-TTATATAATATATAGTTT
1 TGAAAACATTATATAATATATAGTTT
*
1616796 TGAAAACATTTATATATTATATAGTTT
1 TGAAAACA-TTATATAATATATAGTTT
1616823 T-AAAAC
1 TGAAAAC
1616829 CTTTTTGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 7 0.23
26 5 0.17
27 18 0.60
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (26 bp):
TGAAAACATTATATAATATATAGTTT
Found at i:1616864 original size:62 final size:66
Alignment explanation
Indices: 1616739--1616864 Score: 161
Period size: 62 Copynumber: 2.0 Consensus size: 66
1616729 TTTTAGAAAA
* *
1616739 TATATATCATATATAGTTTTTAAAATAATTTGTGAAAACTTATATAATATATAGTTTTGAAAACA
1 TATATAT-ATATATAGTTTTTAAAATAATTTGTGAAAACTTATATAATACATAATTTTGAAAACA
1616804 TT
65 TT
** * *
1616806 TATATAT-TATATAG-TTTTAAAA-CCTTTTTGAAAAC-TATATAGTACATAATTTTGAAAAC
1 TATATATATATATAGTTTTTAAAATAATTTGTGAAAACTTATATAATACATAATTTTGAAAAC
1616865 TTTTTTTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
62 21 0.40
63 10 0.19
64 8 0.15
65 7 0.13
67 7 0.13
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (66 bp):
TATATATATATATAGTTTTTAAAATAATTTGTGAAAACTTATATAATACATAATTTTGAAAACAT
T
Found at i:1616938 original size:37 final size:35
Alignment explanation
Indices: 1616806--1616930 Score: 128
Period size: 35 Copynumber: 3.5 Consensus size: 35
1616796 TGAAAACATT
* ** *
1616806 TATATATTATATAG-TTTTAAAACCTTTTTGAAAAC
1 TATATAATATATAGATTTTAAAATATTTTT-AAAAA
* * *
1616841 TATATAGTACATA-ATTTTGAAAACTTTTTTTAAAAA
1 TATATAATATATAGATTTT-AAAA-TATTTTTAAAAA
1616877 TATATAATATATAGATTTTAAAATATTTTTAAAAA
1 TATATAATATATAGATTTTAAAATATTTTTAAAAA
* *
1616912 TATATATTATATAGTTTTT
1 TATATAATATATAGATTTT
1616931 TTGAAATAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
35 43 0.57
36 23 0.30
37 10 0.13
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (35 bp):
TATATAATATATAGATTTTAAAATATTTTTAAAAA
Found at i:1616965 original size:16 final size:16
Alignment explanation
Indices: 1616936--1616973 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1616926 TTTTTTTGAA
1616936 ATAATTATATATATAT
1 ATAATTATATATATAT
1616952 ATAA-TATATA-ATAT
1 ATAATTATATATATAT
*
1616966 ATTATTAT
1 ATAATTAT
1616974 TATTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 7 0.35
15 9 0.45
16 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATAATTATATATATAT
Found at i:1618293 original size:23 final size:23
Alignment explanation
Indices: 1618267--1618311 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1618257 TATATATTCA
1618267 TTATTATTATTATTT-TTTACTTC
1 TTATTA-TATTATTTCTTTACTTC
*
1618290 TTATTATATTTTTTCTTTACTT
1 TTATTATATTATTTCTTTACTT
1618312 TTCTTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (23 bp):
TTATTATATTATTTCTTTACTTC
Found at i:1618385 original size:12 final size:11
Alignment explanation
Indices: 1618364--1618482 Score: 51
Period size: 12 Copynumber: 9.7 Consensus size: 11
1618354 TAATATTCTT
*
1618364 TTTATCTTTTA
1 TTTATTTTTTA
1618375 TTTCATTTTTTA
1 TTT-ATTTTTTA
1618387 TTTGTATTTATTTA
1 -TT-TATTT-TTTA
1618401 TTTATTTTCCGTTGA
1 TTTATTTT---TT-A
1618416 TTTA-TTTTTA
1 TTTATTTTTTA
* *
1618426 CTTATTTTTTTC
1 TTTA-TTTTTTA
*
1618438 TTTCTTTCCTTTAA
1 TTTATTT--TTT-A
*
1618452 TTTATTTCTTA
1 TTTATTTTTTA
* *
1618463 GTTATTTATTTG
1 TTTATTT-TTTA
1618475 TTTATTTT
1 TTTATTTT
1618483 CTATAACATT
Statistics
Matches: 82, Mismatches: 12, Indels: 28
0.67 0.10 0.23
Matches are distributed among these distances:
10 4 0.05
11 17 0.21
12 29 0.35
13 11 0.13
14 16 0.20
15 5 0.06
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.71
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:1618394 original size:18 final size:17
Alignment explanation
Indices: 1618362--1618407 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
1618352 TTTAATATTC
*
1618362 TTTTTATCTTTTATTTCAT
1 TTTTTAT-TTGTATTT-AT
1618381 TTTTTATTTGTATTTAT
1 TTTTTATTTGTATTTAT
1618398 TTATTTATTT
1 TT-TTTATTT
1618408 TCCGTTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 4 0.16
18 14 0.56
19 7 0.28
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTTATTTGTATTTAT
Found at i:1618432 original size:37 final size:38
Alignment explanation
Indices: 1618391--1618483 Score: 109
Period size: 37 Copynumber: 2.5 Consensus size: 38
1618381 TTTTTATTTG
*
1618391 TATTTATTTATTTATTTTCCGTTGATTTATTT-TTACT
1 TATTTATTTATTTATTTTCCGTTAATTTATTTCTTACT
* * * * *
1618428 TATTTTTTTCTTT-CTTTCCTTTAATTTATTTCTTAGT
1 TATTTATTTATTTATTTTCCGTTAATTTATTTCTTACT
*
1618465 TATTTATTTGTTTATTTTC
1 TATTTATTTATTTATTTTC
1618484 TATAACATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
36 15 0.33
37 26 0.58
38 4 0.09
ACGTcount: A:0.16, C:0.10, G:0.04, T:0.70
Consensus pattern (38 bp):
TATTTATTTATTTATTTTCCGTTAATTTATTTCTTACT
Found at i:1618570 original size:13 final size:13
Alignment explanation
Indices: 1618552--1618576 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1618542 CGAATGTTTT
1618552 AATTTTCAATTTA
1 AATTTTCAATTTA
1618565 AATTTTCAATTT
1 AATTTTCAATTT
1618577 TCACAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTTTCAATTTA
Found at i:1622007 original size:95 final size:94
Alignment explanation
Indices: 1621839--1622082 Score: 280
Period size: 95 Copynumber: 2.7 Consensus size: 94
1621829 TATAATATTA
* *
1621839 TATATATACAATAAATCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGA
1 TATATATACAATAAAGCTTGAGGTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGA
* * *
1621904 TAATATTCAGCTAGCCTGATAAAGGTAAT
66 TAAGATTCAACTAACCTGATAAAGGTAAT
*
1621933 TATACTATACAATAAAGCTTGAGCGT-TCCCTCTA-AGGCAATTGGTTAAATGCCCCGGCTTTAT
1 TATA-TATACAATAAAGCTTGAG-GTGTCCCTCTAGA-GCAATTGGTTAAACGCCCCGGCTTTAT
*
1621996 GGATAAGATTCAACTAACCTGATAAAGGT-GT
63 GGATAAGATTCAACTAACCTGATAAAGGTAAT
* * *
1622027 T-TATAT---ATTAAG--T----TGTCCCTCTAGAGCAATTGGTTAAACACCCCGACTTTATGGA
1 TATATATACAATAAAGCTTGAGGTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGA
1622082 T
66 T
1622083 CTAACTAGCT
Statistics
Matches: 134, Mismatches: 11, Indels: 21
0.81 0.07 0.13
Matches are distributed among these distances:
82 1 0.01
83 36 0.27
84 1 0.01
87 1 0.01
89 5 0.04
92 3 0.02
93 2 0.01
94 7 0.05
95 77 0.57
96 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGGTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGA
TAAGATTCAACTAACCTGATAAAGGTAAT
Found at i:1623360 original size:84 final size:82
Alignment explanation
Indices: 1623228--1624332 Score: 1003
Period size: 84 Copynumber: 13.3 Consensus size: 82
1623218 GCTCAAGGAA
* * * *
1623228 AGAAGGGTTATTTGTCAACAAAAGACCTTCAATTTCGACTACGCTCAGCTCGAAGGCACATCATT
1 AGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATT
* * * * *
1623293 TACAACATAGCTCAAGTCA
64 TGCAGCATAACTTAAGTCG
* * * * * * *
1623312 AGAAGGGCTATCTGTCACCCAAAGACCTTCGAGTTCAAATACGTTCAGCTCTAAGGCATATTATT
1 AGAAGGGTTATCTG-CA-CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATT
*
1623377 AGCAGCATAACTTAAGTCG
64 TGCAGCATAACTTAAGTCG
*
1623396 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATT
* * * *
1623461 TGTAGCATAAATTAAATCA
64 TGCAGCATAACTTAAGTCG
* * * ** * * **
1623480 AAAATGGCTATCTG--CCAAAG-CCTTCGAGTTCGGTTACACTCAGCTCAAAGGCACCAAGATTT
1 AGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCA-CATCATTT
*
1623542 GCAGTATAACTTAAGTCG
65 GCAGCATAACTTAAGTCG
* * * *
1623560 ATAAGGGTTATTTGCTAACCAAAGACCTTCGAGTTCGACTACGATCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGC--ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATT
*
1623625 TGTAGCATAACTTAAGTCG
64 TGCAGCATAACTTAAGTCG
* * * * *
1623644 AGAAGGGCTATCTG--CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT
1 AGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCGAAGGCACATCATTT
1623707 GCAGCATAACTTAAGTCG
65 GCAGCATAACTTAAGTCG
* * * * * *
1623725 AGAAGGGGTTATCTACCAACCAAAGACCTTTGAGTTCGACTATGCTCAGCTCCAAAGCACGTCAT
1 AGAA-GGGTTATCT-GC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCAT
* *
1623790 TTGCAACATAGCTTAAGTCG
63 TTGCAGCATAACTTAAGTCG
* ** * * * * * *
1623810 AGAAGGGCTATCTG--CCAAAGACCCCCTAGTTAGATTACACTCAGCTTTGACGGCACATCATTT
1 AGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCGAAGGCACATCATTT
* * * *
1623873 ACAGCATAACTCAAGGCT
65 GCAGCATAACTTAAGTCG
** * * *
1623891 AGAAGGGTTATCTGTCACCAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
1 AGAAGGGTTATCTG-CACC-AAAGACCTTCGAGTTCGACTACGCTCAGC-TCGAAGGCACATCAT
* * *
1623956 TTGTAGCATAACTCAAGTCT
63 TTGCAGCATAACTTAAGTCG
* *
1623976 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGTTCTAAGGCACATCATT
1 AGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATT
*
1624041 TGCAGCATAGCTTAAGTCG
64 TGCAGCATAACTTAAGTCG
* * * * * *
1624060 AGAAGGGATATCTG--CCAAAGACC-CCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT
1 AGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCGAAGGCACATCATTT
* * * *
1624122 ACAGCATAACTCAAGGCT
65 GCAGCATAACTTAAGTCG
* * *
1624140 AGAAGGGTTATCTGTCA-CAATGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTT
1 AGAAGGGTTATCTG-CACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATTT
* * *
1624204 GCAGCATAGCCTAAGTCA
65 GCAGCATAACTTAAGTCG
* * ** * * * **
1624222 AGAAGGGTTATCT--ATCGAAGACCCACAAGTTCGATTACACTCAGCTTCGGGGGCACATCATTT
1 AGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCGAAGGCACATCATTT
1624285 GCAGCATAACTTAAGTCG
65 GCAGCATAACTTAAGTCG
*
1624303 AGAAGGGTTATCTGCCAACCGAAGACCTTC
1 AGAAGGGTTATCTG-C-ACCAAAGACCTTC
1624333 AAGTCTGATT
Statistics
Matches: 824, Mismatches: 166, Indels: 61
0.78 0.16 0.06
Matches are distributed among these distances:
79 46 0.06
80 158 0.19
81 114 0.14
82 54 0.07
83 18 0.02
84 236 0.29
85 169 0.21
86 29 0.04
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (82 bp):
AGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATTTG
CAGCATAACTTAAGTCG
Found at i:1623792 original size:166 final size:165
Alignment explanation
Indices: 1623228--1624353 Score: 1022
Period size: 164 Copynumber: 6.8 Consensus size: 165
1623218 GCTCAAGGAA
* * * * * *
1623228 AGAAGGGTTATTTGTCAACAAAAGACCTTCAATTTCGACTACGCTCAGCTCGAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * * * **
1623293 TACAACATAGCTCAAGTCAAGAAGGGCTATCTGTCACCCAAAGACCTTCGAGTTCAAATACGTTC
66 TGCAGCATAACTCAAGTCAAGAAGGGCTATCTG---CCCAAAGACCTTCGAGTTCGATTACACTC
* * * *
1623358 AGCTCTAAGGCATATTATTAGCAGCATAACTTAAGTCG
128 AGCTCGAAGGCACATCATTTGCAGCATAACTTAAGTCG
1623396 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * * * * *
1623461 TGTAGCATAAATTAAATCAAAAATGGCTATCTG-CCAAAG-CCTTCGAGTTCGGTTACACTCAGC
66 TGCAGCATAACTCAAGTCAAGAAGGGCTATCTGCCCAAAGACCTTCGAGTTCGATTACACTCAGC
* ** *
1623524 TCAAAGGCACCAAGATTTGCAGTATAACTTAAGTCG
131 TCGAAGGCA-CATCATTTGCAGCATAACTTAAGTCG
* * * *
1623560 ATAAGGGTTATTTGCTAACCAAAGACCTTCGAGTTCGACTACGATCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * *
1623625 TGTAGCATAACTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCTCGAGTTCGATTACACTCAGC
66 TGCAGCATAACTCAAGTCAAGAAGGGCTATCTGCCCAAAGACCTTCGAGTTCGATTACACTCAGC
*
1623689 TTCGAGGGCACATCATTTGCAGCATAACTTAAGTCG
131 -TCGAAGGCACATCATTTGCAGCATAACTTAAGTCG
* * * * *
1623725 AGAAGGGGTTATCTACCAACCAAAGACCTTTGAGTTCGACTATGCTCAGCTCCAAAGCACGTCAT
1 AGAA-GGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* * * * ** * *
1623790 TTGCAACATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCCCTAGTTAGATTACACTCAG
65 TTGCAGCATAACTCAAGTCAAGAAGGGCTATCTGCCCAAAGACCTTCGAGTTCGATTACACTCAG
* * * * * *
1623854 CTTTGACGGCACATCATTTACAGCATAACTCAAGGCT
130 C-TCGAAGGCACATCATTTGCAGCATAACTTAAGTCG
* ** * * * *
1623891 AGAAGGGTTATCTGTC-ACCAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCA
1 AGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCA
* * * * *
1623955 TTTGTAGCATAACTCAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGC
64 TTTGCAGCATAACTCAAGTCAAGAAGGGCTATCTG-C--CCAAAGACCTTCGAGTTCGATTACAC
* * *
1624020 TCAGTTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCG
126 TCAGCTCGAAGGCACATCATTTGCAGCATAACTTAAGTCG
* * * * * * *
1624060 AGAAGGGATATCTG----CCAAAGACC-CCAAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
* * * * * * * *
1624120 TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACAATGACCTTCGAGTTCGACTACGCTCA
65 TTGCAGCATAACTCAAGTCAAGAAGGGCTATCTG-CCCAAAGACCTTCGAGTTCGATTACACTCA
* * * * *
1624185 GCTCCAAGGCATATCATTTGCAGCATAGCCTAAGTCA
129 GCTCGAAGGCACATCATTTGCAGCATAACTTAAGTCG
* * ** * * * ***
1624222 AGAAGGGTTATCT----ATCGAAGACCCACAAGTTCGATTACACTCAGCTTCGGGGGCACATCAT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
* * * * *
1624283 TTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCGAAGACCTTCAAG-TCTGATTACAC
65 TTGCAGCATAACTCAAGTCAAGAAGGGCTATCTG-C--CCAAAGACCTTCGAGTTC-GATTACAC
1624347 TCAGCTC
126 TCAGCTC
1624354 AGAGGCAAAC
Statistics
Matches: 818, Mismatches: 125, Indels: 33
0.84 0.13 0.03
Matches are distributed among these distances:
162 78 0.10
163 93 0.11
164 195 0.24
165 112 0.14
166 193 0.24
168 83 0.10
169 40 0.05
170 24 0.03
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (165 bp):
AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAGCATAACTCAAGTCAAGAAGGGCTATCTGCCCAAAGACCTTCGAGTTCGATTACACTCAGC
TCGAAGGCACATCATTTGCAGCATAACTTAAGTCG
Found at i:1624967 original size:20 final size:20
Alignment explanation
Indices: 1624942--1624991 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1624932 AATTTTCGTC
*
1624942 CATATATTTTTTTATATATA
1 CATATATATTTTTATATATA
*
1624962 CATATATATTTTTATTTATA
1 CATATATATTTTTATATATA
*
1624982 TATATTATAT
1 CATA-TATAT
1624992 AGTTTACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
CATATATATTTTTATATATA
Found at i:1625048 original size:40 final size:37
Alignment explanation
Indices: 1624980--1625122 Score: 146
Period size: 38 Copynumber: 3.8 Consensus size: 37
1624970 TTTTTATTTA
* ** **
1624980 TATATATTATATAGTTTACAAATGATTTTCGAAAATAT
1 TATATAATATATAGTTTTTAAAACATTTT-GAAAATAT
1625018 GTATATAATATATAAGTTTTTAAAACATTTTAGAAAATA-
1 -TATATAATATAT-AGTTTTTAAAACATTTT-GAAAATAT
* *
1625057 TATATCATATATAGTTTTTAAAATCATTTTTAAAA-ACT
1 TATATAATATATAGTTTTTAAAA-CATTTTGAAAATA-T
*
1625095 TATATAATATATAGTTTTGAAAACATTT
1 TATATAATATATAGTTTTTAAAACATTT
1625123 ATCTATTATA
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
36 1 0.01
37 20 0.22
38 38 0.42
39 11 0.12
40 20 0.22
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (37 bp):
TATATAATATATAGTTTTTAAAACATTTTGAAAATAT
Found at i:1625067 original size:36 final size:36
Alignment explanation
Indices: 1625019--1625246 Score: 136
Period size: 35 Copynumber: 6.6 Consensus size: 36
1625009 CGAAAATATG
1625019 TATATA-ATATATAAGTTTTTAAAACATTTTAGAAAA-
1 TATATATATATAT-AGTTTTTAAAACATTTTA-AAAAC
1625055 TATATATCATATATAGTTTTTAAAATCATTTTTAAAAAC
1 TATATAT-ATATATAGTTTTTAAAA-CA-TTTTAAAAAC
*
1625094 T-TATATAATATATAGTTTTGAAAACA--TT------
1 TATATAT-ATATATAGTTTTTAAAACATTTTAAAAAC
* * *
1625122 TATCTAT-TATATAG-TTTTAAAACCTTTTTGAAAAC
1 TATATATATATATAGTTTTTAAAA-CATTTTAAAAAC
* * *
1625157 TATACAGTACATA-A-TTTTGAAAACATTTTTTAAAAA-
1 TATATA-TATATATAGTTTTTAAAACA--TTTTAAAAAC
*
1625193 TATATA-ATATATA-TATTTTAAAATATTTTTAAAAA-
1 TATATATATATATAGT-TTTTAAAACA-TTTTAAAAAC
1625228 TATATAT-TATATAGTTTTT
1 TATATATATATATAGTTTTT
1625247 TGGAAATAAT
Statistics
Matches: 153, Mismatches: 15, Indels: 49
0.71 0.07 0.23
Matches are distributed among these distances:
26 7 0.05
27 8 0.05
28 1 0.01
29 6 0.04
34 6 0.04
35 33 0.22
36 29 0.19
37 24 0.16
38 33 0.22
39 6 0.04
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (36 bp):
TATATATATATATAGTTTTTAAAACATTTTAAAAAC
Found at i:1625085 original size:38 final size:37
Alignment explanation
Indices: 1624978--1625246 Score: 153
Period size: 36 Copynumber: 7.6 Consensus size: 37
1624968 TATTTTTATT
* ** ** *
1624978 TATATATATTATATAGTTTACAAATGATTTTCGAAAA
1 TATATATAATATATAGTTTTTAAAACATTTTAGAAAA
1625015 TATGTATATAATATATAAGTTTTTAAAACATTTTAGAAAA
1 TA--TATATAATATAT-AGTTTTTAAAACATTTTAGAAAA
*
1625055 TATATATCATATATAGTTTTTAAAATCATTTTTA-AAAA
1 TATATATAATATATAGTTTTTAAAA-CA-TTTTAGAAAA
*
1625093 CT-TATATAATATATAGTTTTGAAAACA--TT------
1 -TATATATAATATATAGTTTTTAAAACATTTTAGAAAA
* * *
1625122 TATCTAT--TATATAG-TTTTAAAACCTTTTTGAAAA
1 TATATATAATATATAGTTTTTAAAACATTTTAGAAAA
* * * * * * **
1625156 -CTATACAGTACATAATTTTGAAAACATTTTTTAAAA
1 TATATATAATATATAGTTTTTAAAACATTTTAGAAAA
*
1625192 -ATATATAATATATA-TATTTTAAAATATTTTTA-AAAA
1 TATATATAATATATAGT-TTTTAAAACA-TTTTAGAAAA
1625228 TATATAT--TATATAGTTTTT
1 TATATATAATATATAGTTTTT
1625247 TGGAAATAAT
Statistics
Matches: 183, Mismatches: 27, Indels: 46
0.71 0.11 0.18
Matches are distributed among these distances:
26 8 0.04
27 7 0.04
28 3 0.02
29 4 0.02
33 3 0.02
34 2 0.01
35 16 0.09
36 40 0.22
37 25 0.14
38 38 0.21
39 17 0.09
40 20 0.11
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (37 bp):
TATATATAATATATAGTTTTTAAAACATTTTAGAAAA
Found at i:1625118 original size:25 final size:25
Alignment explanation
Indices: 1625084--1625144 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 25
1625074 TTAAAATCAT
1625084 TTTTAAAA-ACTTATATAATATATAG
1 TTTTAAAACA-TTATATAATATATAG
* *
1625109 TTTTGAAAACATTTATCTATTATATAG
1 TTTT-AAAACA-TTATATAATATATAG
1625136 TTTTAAAAC
1 TTTTAAAAC
1625145 CTTTTTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.13
26 9 0.29
27 18 0.58
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.46
Consensus pattern (25 bp):
TTTTAAAACATTATATAATATATAG
Found at i:1625181 original size:62 final size:65
Alignment explanation
Indices: 1625064--1625184 Score: 167
Period size: 62 Copynumber: 1.9 Consensus size: 65
1625054 ATATATATCA
* * *
1625064 TATATAGTTTTTAAAATCATTTTTAAAAACTTATATAATATATAGTTTTGAAAACATTTATCTAT
1 TATATAGTTTTTAAAATCATTTTTAAAAACTTATACAATACATAATTTTGAAAACATTTATCTAT
* * *
1625129 TATATAG-TTTTAAAA-CCTTTTTGAAAAC-TATACAGTACATAATTTTGAAAACATTT
1 TATATAGTTTTTAAAATCATTTTTAAAAACTTATACAATACATAATTTTGAAAACATTT
1625185 TTTAAAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
62 24 0.48
63 11 0.22
64 8 0.16
65 7 0.14
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (65 bp):
TATATAGTTTTTAAAATCATTTTTAAAAACTTATACAATACATAATTTTGAAAACATTTATCTAT
Found at i:1625224 original size:35 final size:36
Alignment explanation
Indices: 1625129--1625277 Score: 124
Period size: 37 Copynumber: 4.1 Consensus size: 36
1625119 ATTTATCTAT
* * * *
1625129 TATATAGTTTT-AAAACCTTTTTGAAAACTATACAGTA
1 TATATA-TTTTGAAAACATTTTT-AAAAATATATAATA
*
1625166 CATA-ATTTTGAAAACATTTTTTAAAAATATATAATA
1 TATATATTTTGAAAACA-TTTTTAAAAATATATAATA
* *
1625202 TATATATTTT-AAAATATTTTTAAAAATATATATTA
1 TATATATTTTGAAAACATTTTTAAAAATATATAATA
* * * * * *
1625237 TATAGTTTTTTGGAAATAATTTTATATATATATAATA
1 TATA-TATTTTGAAAACATTTTTAAAAATATATAATA
1625274 TATA
1 TATA
1625278 ATATATTATT
Statistics
Matches: 93, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
35 26 0.28
36 30 0.32
37 37 0.40
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (36 bp):
TATATATTTTGAAAACATTTTTAAAAATATATAATA
Found at i:1626704 original size:18 final size:16
Alignment explanation
Indices: 1626673--1626718 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
1626663 TTATTATTCT
*
1626673 TTTTTTCTTTTATTTCA
1 TTTTTTATTTTATTT-A
1626690 TTTTTTATTTGTATTTA
1 TTTTTTATTT-TATTTA
1626707 TTTATTTATTTT
1 TTT-TTTATTTT
1626719 CGTTGATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTTTTATTTTATTTA
Found at i:1626727 original size:14 final size:14
Alignment explanation
Indices: 1626708--1626746 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1626698 TTGTATTTAT
*
1626708 TTATTTATTTTC-G
1 TTATTTATTTTCAC
1626721 TTGATTTATTTTCAC
1 TT-ATTTATTTTCAC
1626736 TTATTTATTTT
1 TTATTTATTTT
1626747 ATTTTTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 2 0.09
14 19 0.83
15 2 0.09
ACGTcount: A:0.18, C:0.08, G:0.05, T:0.69
Consensus pattern (14 bp):
TTATTTATTTTCAC
Found at i:1626750 original size:45 final size:44
Alignment explanation
Indices: 1626681--1626798 Score: 109
Period size: 45 Copynumber: 2.7 Consensus size: 44
1626671 CTTTTTTTCT
* * * *
1626681 TTTA-TTTCATTTTTTATTTGTATTTATTTATTTATTTTCGTTGA
1 TTTATTTTCATTATTTATTT-TATTTATTTATTCATTTCCGTTAA
* * *
1626725 TTTATTTTCACTTATTTATTTTATTTTTTTCTTCATTTCCTTTAA
1 TTTATTTTCA-TTATTTATTTTATTTATTTATTCATTTCCGTTAA
* *
1626770 TTTA-TTTC-TTAGTTA-TTTATTTGTTTATT
1 TTTATTTTCATTATTTATTTTATTTATTTATT
1626799 TTCTCTAACA
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
41 12 0.19
42 6 0.10
44 8 0.13
45 27 0.44
46 9 0.15
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.70
Consensus pattern (44 bp):
TTTATTTTCATTATTTATTTTATTTATTTATTCATTTCCGTTAA
Found at i:1627959 original size:24 final size:24
Alignment explanation
Indices: 1627930--1627983 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
1627920 TAGTCACCAC
*
1627930 TGCCACTTAGAATATGCACC-AAA
1 TGCCACGTAGAATATGCACCGAAA
1627953 GTGCCACGTAGAATATGCACCGAAA
1 -TGCCACGTAGAATATGCACCGAAA
1627978 TGCCAC
1 TGCCAC
1627984 ATAGGTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.19
Consensus pattern (24 bp):
TGCCACGTAGAATATGCACCGAAA
Found at i:1628713 original size:20 final size:20
Alignment explanation
Indices: 1628670--1628718 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1628660 TTCAATTATT
* **
1628670 GTATCGATACCTCAACCTTG
1 GTATCGATACCTCAACATCA
*
1628690 GTATCGATACCTCCACATCA
1 GTATCGATACCTCAACATCA
1628710 GTATCGATA
1 GTATCGATA
1628719 TTACTTCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (20 bp):
GTATCGATACCTCAACATCA
Found at i:1631077 original size:17 final size:16
Alignment explanation
Indices: 1631057--1631107 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1631047 AATTAGGTCC
1631057 TTATAATTATTTTATAT
1 TTATAATTATTTT-TAT
*
1631074 TTATATTTATTTTTAT
1 TTATAATTATTTTTAT
* * *
1631090 TTTTTACTATTTTTAT
1 TTATAATTATTTTTAT
1631106 TT
1 TT
1631108 TTTTACTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 17 0.59
17 12 0.41
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATAATTATTTTTAT
Found at i:1631100 original size:16 final size:17
Alignment explanation
Indices: 1631081--1631118 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1631071 TATTTATATT
1631081 TATTTTTA-TTTTTTAC
1 TATTTTTATTTTTTTAC
1631097 TATTTTTATTTTTTTAC
1 TATTTTTATTTTTTTAC
1631114 TATTT
1 TATTT
1631119 GTTGCTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTTTTATTTTTTTAC
Found at i:1632789 original size:20 final size:20
Alignment explanation
Indices: 1632764--1632856 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
1632754 TTTTCCCAAT
1632764 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1632784 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
1632804 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
1632825 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1632846 TCGCAATGCGA
1 TCGCAATGCGA
1632857 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1632806 original size:41 final size:41
Alignment explanation
Indices: 1632761--1632856 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
1632751 CGATTTTCCC
1632761 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1632802 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
1632843 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1632857 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:1632810 original size:21 final size:20
Alignment explanation
Indices: 1632764--1632856 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1632754 TTTTCCCAAT
*
1632764 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
1632784 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
1632804 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
1632825 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
1632846 TCGCAATGCGA
1 TCGCAATGCGA
1632857 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:1632869 original size:41 final size:41
Alignment explanation
Indices: 1632783--1632917 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
1632773 GAATAAGTAA
* * *
1632783 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
1632824 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
1632865 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
1632906 TTCGCAACGCGA
1 ATCGCAACGCGA
1632918 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:1632870 original size:20 final size:20
Alignment explanation
Indices: 1632845--1632938 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1632835 AATTGGGAAA
*
1632845 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1632865 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1632886 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1632906 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1632926 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1632939 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1633496 original size:19 final size:19
Alignment explanation
Indices: 1633458--1633524 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1633448 TTCGAGAATG
*
1633458 AAAATCGCAAAGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1633478 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1633497 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1633516 AAAATCGCA
1 AAAATCGCA
1633525 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1633542 original size:19 final size:19
Alignment explanation
Indices: 1633520--1633703 Score: 172
Period size: 19 Copynumber: 10.1 Consensus size: 19
1633510 GAAACCAAAA
*
1633520 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1633539 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1633558 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1633577 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1633596 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
1633610 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1633629 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
1633643 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
1633662 TCCGCGTTGCAATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1633682 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1633702 TC
1 TC
1633704 AACCAAAAGA
Statistics
Matches: 135, Mismatches: 18, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
14 18 0.13
16 4 0.03
17 5 0.04
19 79 0.59
20 28 0.21
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1633628 original size:33 final size:33
Alignment explanation
Indices: 1633591--1633678 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
1633581 GTTGCGATTT
*
1633591 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
1633624 TCATTTCGCGTTGCGATTCTCTCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
1633657 TCATTTCCGCGTTGCAATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1633679 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 37 0.73
34 14 0.27
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
Found at i:1633680 original size:20 final size:20
Alignment explanation
Indices: 1633657--1633703 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1633647 ATTGCGATAG
1633657 TCATTTCCGCGTTGCAATTC
1 TCATTTCCGCGTTGCAATTC
* * *
1633677 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCAATTC
1633697 TCATTTC
1 TCATTTC
1633704 AACCAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCAATTC
Found at i:1635777 original size:42 final size:42
Alignment explanation
Indices: 1635731--1635819 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
1635721 CCTATCGTTG
*
1635731 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTC
1 AAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCACCATTC
* * * *
1635773 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCATCATTC
1 AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
1635815 AAGAG
1 AAGAG
1635820 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.10
42 34 0.85
43 2 0.05
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (42 bp):
AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:1636506 original size:20 final size:19
Alignment explanation
Indices: 1636471--1636537 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1636461 GAAACTTAAA
1636471 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1636490 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1636510 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1636529 ATCGCAACG
1 ATCGCAACG
1636538 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1636545 original size:14 final size:14
Alignment explanation
Indices: 1636526--1636615 Score: 81
Period size: 14 Copynumber: 5.9 Consensus size: 14
1636516 ATGCGAAATG
*
1636526 AAAATCGCAACGAC
1 AAAATCGCAACGAA
1636540 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAA
*
1636556 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAA
1636572 AAAATCGCAACGCAAA
1 AAAATCGCAACG--AA
*
1636588 ATGAAATCGCAACGAT
1 A--AAATCGCAACGAA
1636604 AAAATCGCAACG
1 AAAATCGCAACG
1636616 CGAAACACAA
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 32 0.50
16 12 0.19
18 20 0.31
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:1636568 original size:32 final size:32
Alignment explanation
Indices: 1636510--1636620 Score: 186
Period size: 32 Copynumber: 3.4 Consensus size: 32
1636500 GGAAATGGCT
*
1636510 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1636543 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
* *
1636575 ATCGCAACGCAAAATGAAATCGCAACGATAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1636607 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1636621 CACAAATCGC
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 59 0.80
33 15 0.20
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:1636649 original size:19 final size:17
Alignment explanation
Indices: 1636627--1636722 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
1636617 GAAACACAAA
1636627 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
1636646 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
1636662 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
1636678 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
1636694 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
1636711 TCGCATTGCGAT
1 TCGC-TTGCGAT
1636723 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:1636668 original size:14 final size:14
Alignment explanation
Indices: 1636649--1636706 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1636639 TTTCATTTCG
1636649 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1636663 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1636679 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1636695 CGTTGCGATTTT
1 CGTTGCGATTTT
1636707 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1636713 original size:33 final size:33
Alignment explanation
Indices: 1636632--1636722 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1636622 ACAAATCGCA
1636632 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1636665 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
1636697 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
1636723 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:1636741 original size:20 final size:19
Alignment explanation
Indices: 1636707--1636761 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1636697 TTGCGATTTT
*
1636707 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1636726 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1636746 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1636762 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1637254 original size:18 final size:18
Alignment explanation
Indices: 1637228--1637272 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1637218 GTCGATCAGA
*
1637228 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
1637246 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
1637264 TGATGGCTC
1 TGATGGCTC
1637273 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:1638610 original size:20 final size:20
Alignment explanation
Indices: 1638585--1638622 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1638575 AATAGTTTCT
1638585 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1638605 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1638623 GAGAGATCGC
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1638910 original size:22 final size:22
Alignment explanation
Indices: 1638885--1638928 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1638875 GATTTAGATA
1638885 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1638907 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1638929 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1639142 original size:20 final size:20
Alignment explanation
Indices: 1639117--1639210 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1639107 GATTATGTAT
1639117 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1639137 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
1639157 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
1639178 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1639198 TATCGCATTGCGA
1 TATCGCGTTGCGA
1639211 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1639182 original size:41 final size:42
Alignment explanation
Indices: 1639137--1639272 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
1639127 CGAAAGTCAG
* * * *
1639137 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
1639178 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
1639220 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
1639261 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
1639273 TTTACTTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.04
41 70 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:1639211 original size:20 final size:20
Alignment explanation
Indices: 1639097--1639211 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1639087 CGCTTTGAAA
*
1639097 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1639118 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1639138 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1639158 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1639179 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1639199 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1639212 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1639244 original size:20 final size:20
Alignment explanation
Indices: 1639200--1639292 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
1639190 ATAGTCAGTA
*
1639200 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
1639221 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
1639241 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
1639262 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
1639282 TCGCATTGCGA
1 TCGCATTGCGA
1639293 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:1639273 original size:41 final size:41
Alignment explanation
Indices: 1639200--1639295 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
1639190 ATAGTCAGTA
* *
1639200 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1639241 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1639282 TCGCATTGCGAATT
1 TCGCATTGCGAATT
1639296 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1650005 original size:77 final size:78
Alignment explanation
Indices: 1649879--1650034 Score: 289
Period size: 77 Copynumber: 2.0 Consensus size: 78
1649869 GCTTTGCTGG
1649879 AGTCCTCCTCCAGTCGATTTTTTAAGTTTAACGTGGATGGGGCTGTGAGT-TGTTGGGATGTTAG
1 AGTCCTCCTCCAGTCGATTTTTTAAGTTTAACGTGGATGGGGCTGTGAGTGTGTTGGGATGTTAG
1649943 CTGGAA-TGGGGA
66 CTGGAATTGGGGA
1649955 AGTCCTCCTCCAGTCGATTTTTTTAAGTTTAACGTGGATGGGGCTGTGAGTGTGTTGGGATGTTA
1 AGTCCTCCTCCAGTCGA-TTTTTTAAGTTTAACGTGGATGGGGCTGTGAGTGTGTTGGGATGTTA
1650020 GCTGGAATTGGGGA
65 GCTGGAATTGGGGA
1650034 A
1 A
1650035 TTCTAAGAGA
Statistics
Matches: 77, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
76 17 0.22
77 33 0.43
78 20 0.26
79 7 0.09
ACGTcount: A:0.19, C:0.13, G:0.34, T:0.35
Consensus pattern (78 bp):
AGTCCTCCTCCAGTCGATTTTTTAAGTTTAACGTGGATGGGGCTGTGAGTGTGTTGGGATGTTAG
CTGGAATTGGGGA
Found at i:1653217 original size:22 final size:23
Alignment explanation
Indices: 1653189--1653233 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
1653179 CTCTTGAATT
1653189 TCTAATTTGTT-TTTTTTTTAAA
1 TCTAATTTGTTATTTTTTTTAAA
1653211 TCTAATTTGTTATTTTTTTTAAA
1 TCTAATTTGTTATTTTTTTTAAA
1653234 AAAAAAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (23 bp):
TCTAATTTGTTATTTTTTTTAAA
Found at i:1656184 original size:16 final size:14
Alignment explanation
Indices: 1656163--1656203 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 14
1656153 CCTTGTACCA
1656163 TGTAGAAAACAAAC
1 TGTAGAAAACAAAC
*
1656177 TGTGTAGAAAACAGAC
1 --TGTAGAAAACAAAC
1656193 TGTAGAAAACA
1 TGTAGAAAACA
1656204 GACAAGTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.46
16 13 0.54
ACGTcount: A:0.51, C:0.12, G:0.20, T:0.17
Consensus pattern (14 bp):
TGTAGAAAACAAAC
Found at i:1656198 original size:14 final size:15
Alignment explanation
Indices: 1656163--1656206 Score: 63
Period size: 14 Copynumber: 2.9 Consensus size: 15
1656153 CCTTGTACCA
*
1656163 TGTAGAAAACAAACTG
1 TGTAGAAAACAGAC-G
1656179 TGTAGAAAACAGAC-
1 TGTAGAAAACAGACG
1656193 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
1656207 AAGTCTGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 14 0.52
16 13 0.48
ACGTcount: A:0.50, C:0.14, G:0.20, T:0.16
Consensus pattern (15 bp):
TGTAGAAAACAGACG
Found at i:1660948 original size:44 final size:44
Alignment explanation
Indices: 1660871--1660960 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
1660861 GTATCATTCT
* *
1660871 TTTTTTTTTGATAGGAATAGTAGGCCTCATTAAAAACCTCCCTC
1 TTTTTTTTTGATAAGAATAGAAGGCCTCATTAAAAACCTCCCTC
* * * * *
1660915 TTTTTTTTTGATAAGATTTGAAGGTCTCTTTAAAAACCTCCTTC
1 TTTTTTTTTGATAAGAATAGAAGGCCTCATTAAAAACCTCCCTC
1660959 TT
1 TT
1660961 GATTAATGGA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (44 bp):
TTTTTTTTTGATAAGAATAGAAGGCCTCATTAAAAACCTCCCTC
Found at i:1672312 original size:54 final size:56
Alignment explanation
Indices: 1672227--1672337 Score: 208
Period size: 54 Copynumber: 2.0 Consensus size: 56
1672217 AGTTTGCCAC
1672227 ACTGATACTCCAAAAAAACGGTTTGAAGAGTAAATGTATTGAGGTTATAAAAATGG
1 ACTGATACTCCAAAAAAACGGTTTGAAGAGTAAATGTATTGAGGTTATAAAAATGG
1672283 ACTGATACT-CAAAAAAACGG-TTGAAGAGTAAATGTATTGAGGTTATAAAAATGG
1 ACTGATACTCCAAAAAAACGGTTTGAAGAGTAAATGTATTGAGGTTATAAAAATGG
1672337 A
1 A
1672338 AGTCCCGAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
54 35 0.64
55 11 0.20
56 9 0.16
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.26
Consensus pattern (56 bp):
ACTGATACTCCAAAAAAACGGTTTGAAGAGTAAATGTATTGAGGTTATAAAAATGG
Found at i:1674787 original size:59 final size:58
Alignment explanation
Indices: 1674675--1674794 Score: 161
Period size: 59 Copynumber: 2.1 Consensus size: 58
1674665 GTCTCTCAAT
* ** *
1674675 TATAGGGTGTTGCTTTGTTGAGTCACTTGATATTAAAAGTTACAAAATGGTCACCCGAC
1 TATAGGATGTTGCTTTGTTGAGTCACCCGATACTAAAAGTTACAAAATGGTCA-CCGAC
* *
1674734 TATAGGATGTTGCTTTGTTGAGTCCCCCGACTACTAAAAGTTAC-AAATTGTCACCGAC
1 TATAGGATGTTGCTTTGTTGAGTCACCCGA-TACTAAAAGTTACAAAATGGTCACCGAC
1674792 TAT
1 TAT
1674795 TTATTATGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
58 8 0.15
59 34 0.63
60 12 0.22
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (58 bp):
TATAGGATGTTGCTTTGTTGAGTCACCCGATACTAAAAGTTACAAAATGGTCACCGAC
Found at i:1676098 original size:31 final size:31
Alignment explanation
Indices: 1676052--1676215 Score: 133
Period size: 31 Copynumber: 5.3 Consensus size: 31
1676042 TCCGATGACC
* * *
1676052 TAGGTAAACTATCCATATGTTCCTTAGAACA
1 TAGGTATACTGTCCATATGTTCCGTAGAACA
* **
1676083 TATGTATACTGTCCATATG-TCTCAAATG-ACA
1 TAGGTATACTGTCCATATGTTC-CGTA-GAACA
*
1676114 TAGGTAATTCTGTCCATATGTTCCGTAGAACA
1 TAGGT-ATACTGTCCATATGTTCCGTAGAACA
***
1676146 TAGGTATACTGTCCATATGTCTCAAAAG-ACA
1 TAGGTATACTGTCCATATGT-TCCGTAGAACA
1676177 TAGGTAATTA-TGTCCATATGTTCCGT--AACA
1 TAGGT-A-TACTGTCCATATGTTCCGTAGAACA
*
1676207 TATGTATAC
1 TAGGTATAC
1676216 CCTCGACTCT
Statistics
Matches: 106, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
28 2 0.02
29 1 0.01
30 9 0.08
31 50 0.47
32 40 0.38
33 4 0.04
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (31 bp):
TAGGTATACTGTCCATATGTTCCGTAGAACA
Found at i:1676132 original size:32 final size:32
Alignment explanation
Indices: 1676091--1676197 Score: 130
Period size: 32 Copynumber: 3.4 Consensus size: 32
1676081 CATATGTATA
1676091 CTGTCCATATGTCTCAAATGACATAGGTAATT
1 CTGTCCATATGTCTCAAATGACATAGGTAATT
** *
1676123 CTGTCCATATGT-TC-CGTAGAACATAGGT-ATA
1 CTGTCCATATGTCTCAAAT-G-ACATAGGTAATT
*
1676154 CTGTCCATATGTCTCAAAAGACATAGGTAATT
1 CTGTCCATATGTCTCAAATGACATAGGTAATT
*
1676186 ATGTCCATATGT
1 CTGTCCATATGT
1676198 TCCGTAACAT
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
30 1 0.02
31 25 0.40
32 36 0.58
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (32 bp):
CTGTCCATATGTCTCAAATGACATAGGTAATT
Found at i:1676144 original size:63 final size:63
Alignment explanation
Indices: 1676046--1676215 Score: 256
Period size: 63 Copynumber: 2.7 Consensus size: 63
1676036 ATAGGTTCCG
* * * *
1676046 ATGACCTAGGTAA-ACTATCCATATGTTCCTTAGAACATATGTATACTGTCCATATGTCTCAA
1 ATGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATATGTATACTGTCCATATGTCTCAA
*
1676108 ATGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAA
1 ATGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATATGTATACTGTCCATATGTCTCAA
* *
1676171 AAGACATAGGTAATTATGTCCATATGTTCCGT--AACATATGTATAC
1 ATGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATATGTATAC
1676216 CCTCGACTCT
Statistics
Matches: 99, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
61 12 0.12
62 12 0.12
63 75 0.76
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (63 bp):
ATGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATATGTATACTGTCCATATGTCTCAA
Found at i:1679330 original size:31 final size:31
Alignment explanation
Indices: 1679265--1679457 Score: 153
Period size: 31 Copynumber: 6.2 Consensus size: 31
1679255 ATAAAGATCC
* * *
1679265 TAGGT-AACTGTCTATAGGTTCCGAT-GAACC
1 TAGGTAAACTGTCCATATGTTCC-ATAGAACA
* *
1679295 TAGGTAAACTATCCATATGTTCCTTAGAACA
1 TAGGTAAACTGTCCATATGTTCCATAGAACA
* * *
1679326 TAGGTATACTGTCCATATGTCTCAAAAG-ACA
1 TAGGTAAACTGTCCATATGT-TCCATAGAACA
* *
1679357 TAGATAATTA-TGTCCATATGTTCCGTAGAACA
1 TAGGTAA--ACTGTCCATATGTTCCATAGAACA
* * * *
1679389 TAGGTATATTGTCCATATGTCTCAAAAG-ACA
1 TAGGTAAACTGTCCATATGT-TCCATAGAACA
* *
1679420 TAGGTAATTCTGTCCATATGTTCCGTAGAACA
1 TAGGTAA-ACTGTCCATATGTTCCATAGAACA
1679452 TAGGTA
1 TAGGTA
1679458 TACCCTCGAC
Statistics
Matches: 127, Mismatches: 26, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
30 7 0.06
31 72 0.57
32 47 0.37
33 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (31 bp):
TAGGTAAACTGTCCATATGTTCCATAGAACA
Found at i:1679376 original size:32 final size:32
Alignment explanation
Indices: 1679323--1679440 Score: 129
Period size: 32 Copynumber: 3.8 Consensus size: 32
1679313 GTTCCTTAGA
1679323 ACATAGGT-A-TACTGTCCATATGTCTCAAAAG
1 ACATAGGTAATTA-TGTCCATATGTCTCAAAAG
* ***
1679354 ACATAGATAATTATGTCCATATGT-TCCGTAG
1 ACATAGGTAATTATGTCCATATGTCTCAAAAG
1679385 AACATAGGT-A-TATTGTCCATATGTCTCAAAAG
1 -ACATAGGTAATTA-TGTCCATATGTCTCAAAAG
*
1679417 ACATAGGTAATTCTGTCCATATGT
1 ACATAGGTAATTATGTCCATATGT
1679441 TCCGTAGAAC
Statistics
Matches: 71, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
30 2 0.03
31 31 0.44
32 35 0.49
33 3 0.04
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (32 bp):
ACATAGGTAATTATGTCCATATGTCTCAAAAG
Found at i:1679377 original size:63 final size:63
Alignment explanation
Indices: 1679306--1679460 Score: 274
Period size: 63 Copynumber: 2.5 Consensus size: 63
1679296 AGGTAAACTA
*
1679306 TCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGATAATTATG
1 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGATAATTATG
* * *
1679369 TCCATATGTTCCGTAGAACATAGGTATATTGTCCATATGTCTCAAAAGACATAGGTAATTCTG
1 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGATAATTATG
1679432 TCCATATGTTCCGTAGAACATAGGTATAC
1 TCCATATGTTCCGTAGAACATAGGTATAC
1679461 CCTCGACTCA
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 87 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (63 bp):
TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGATAATTATG
Found at i:1682923 original size:31 final size:31
Alignment explanation
Indices: 1682858--1682987 Score: 106
Period size: 31 Copynumber: 4.2 Consensus size: 31
1682848 ATAAAGATCC
* * *
1682858 TAGGT-AACTGTCTATAGGTTCCGAT-GAACC
1 TAGGTAAACTGTCCATATGTTCC-ATAGAACA
* *
1682888 TAGGTAAACTATCCATATGTTCCTTAGAACA
1 TAGGTAAACTGTCCATATGTTCCATAGAACA
* * *
1682919 TAGGTATACTGTCCATATGTCTCAAAAG-ACA
1 TAGGTAAACTGTCCATATGT-TCCATAGAACA
* *
1682950 TAGATAATTA-TGTCCATATGTTCCGTAGAACA
1 TAGGTAA--ACTGTCCATATGTTCCATAGAACA
1682982 TAGGTA
1 TAGGTA
1682988 TACCCTCGAC
Statistics
Matches: 78, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
30 6 0.08
31 48 0.62
32 23 0.29
33 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (31 bp):
TAGGTAAACTGTCCATATGTTCCATAGAACA
Found at i:1687611 original size:31 final size:31
Alignment explanation
Indices: 1687537--1687730 Score: 173
Period size: 31 Copynumber: 6.2 Consensus size: 31
1687527 AAAGATCCTC
* * *
1687537 GGTA-ACTGTCTATAGGTTCCGAT-GAACCTA
1 GGTATACTGTCCATATGTTCC-ATAGAACATA
* * * *
1687567 GTTAAACTATCCATATGTTCCTTAGAACATA
1 GGTATACTGTCCATATGTTCCATAGAACATA
* *
1687598 GGTATACTGTCCATATGTCTCAAAAG-ACATA
1 GGTATACTGTCCATATGT-TCCATAGAACATA
*
1687629 GGTAATTA-TGTCCATATGTTCCGTAGAACATA
1 GGT-A-TACTGTCCATATGTTCCATAGAACATA
* *
1687661 GGTATACTGTCCATATGTCTCAAAAG-ACATA
1 GGTATACTGTCCATATGT-TCCATAGAACATA
* *
1687692 GGTAATTCTGTCCATATGTTCCGTAGAACATA
1 GGT-ATACTGTCCATATGTTCCATAGAACATA
1687724 GGTATAC
1 GGTATAC
1687731 CCTCGACTCT
Statistics
Matches: 131, Mismatches: 23, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
30 6 0.05
31 73 0.56
32 50 0.38
33 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (31 bp):
GGTATACTGTCCATATGTTCCATAGAACATA
Found at i:1687646 original size:32 final size:31
Alignment explanation
Indices: 1687593--1687710 Score: 150
Period size: 32 Copynumber: 3.7 Consensus size: 31
1687583 GTTCCTTAGA
1687593 ACATAGGTATACTGTCCATATGTCTCAAAAG
1 ACATAGGTATACTGTCCATATGTCTCAAAAG
***
1687624 ACATAGGTAATTA-TGTCCATATGT-TCCGTAG
1 ACATAGGT-A-TACTGTCCATATGTCTCAAAAG
1687655 AACATAGGTATACTGTCCATATGTCTCAAAAG
1 -ACATAGGTATACTGTCCATATGTCTCAAAAG
*
1687687 ACATAGGTAATTCTGTCCATATGT
1 ACATAGGT-ATACTGTCCATATGT
1687711 TCCGTAGAAC
Statistics
Matches: 74, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
30 2 0.03
31 32 0.43
32 38 0.51
33 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (31 bp):
ACATAGGTATACTGTCCATATGTCTCAAAAG
Found at i:1687656 original size:63 final size:63
Alignment explanation
Indices: 1687576--1687730 Score: 292
Period size: 63 Copynumber: 2.5 Consensus size: 63
1687566 AGTTAAACTA
*
1687576 TCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATTATG
1 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATTATG
*
1687639 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATTCTG
1 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATTATG
1687702 TCCATATGTTCCGTAGAACATAGGTATAC
1 TCCATATGTTCCGTAGAACATAGGTATAC
1687731 CCTCGACTCT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 90 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (63 bp):
TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATTATG
Found at i:1688835 original size:64 final size:64
Alignment explanation
Indices: 1688683--1688839 Score: 160
Period size: 64 Copynumber: 2.5 Consensus size: 64
1688673 CAATGAAAGT
* * * ** *
1688683 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATCACTGGG
1 ATGCATCGATGCACTACCTG-TGCATCGATGCATAAAATGCATTCGATGTTCTATTATAAAAGAG
* * * *
1688747 ATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATAAAAG
1688810 AG
63 AG
1688812 -TGCATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACCTGTGCATCGAT
1688840 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
63 1 0.01
64 60 0.79
65 15 0.20
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATGCATTCGATGTTCTATTATAAAAGAG
Found at i:1690696 original size:60 final size:60
Alignment explanation
Indices: 1690617--1690749 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 60
1690607 ATCATATGTC
* * * **
1690617 CTCAAACTATAACTCTCATTTTAAATT-GAT-CTCTAAAATTTTAAATGTTTCAATTTCAT-
1 CTCAAACTATGACTATCATTCTAAATTAG-TCCTC-AAAATTTTAAACATTTCAATTTCATA
* * *
1690676 CCCTAAACTATGACTATCATTCTAGATTAGTCCTCAAAATTTTGAACATTTCAATTTCATA
1 CTC-AAACTATGACTATCATTCTAAATTAGTCCTCAAAATTTTAAACATTTCAATTTCATA
1690737 CTCAAACTATGAC
1 CTCAAACTATGAC
1690750 CTTCATTATA
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
59 2 0.03
60 53 0.87
61 6 0.10
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.39
Consensus pattern (60 bp):
CTCAAACTATGACTATCATTCTAAATTAGTCCTCAAAATTTTAAACATTTCAATTTCATA
Found at i:1690769 original size:60 final size:61
Alignment explanation
Indices: 1690664--1690787 Score: 137
Period size: 60 Copynumber: 2.0 Consensus size: 61
1690654 ATTTTAAATG
* * *
1690664 TTTCAATTTCATCCCTAAACTATGACTATCATTCTAGATTAGTCCTCAAA-ATTTTGAACA
1 TTTCAATTTCATCCCTAAACTATGACTATCATTATAAACTAGTCCTCAAACATTTTGAACA
* * * * *
1690724 TTTCAATTTCAT-ACTCAAACTATGACCT-TCATTATAAACTGGTCCTTAAACTTTTTTAACA
1 TTTCAATTTCATCCCT-AAACTATGA-CTATCATTATAAACTAGTCCTCAAACATTTTGAACA
1690785 TTT
1 TTT
1690788 TGATTTTATC
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
59 2 0.04
60 38 0.72
61 13 0.25
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (61 bp):
TTTCAATTTCATCCCTAAACTATGACTATCATTATAAACTAGTCCTCAAACATTTTGAACA
Found at i:1691063 original size:31 final size:28
Alignment explanation
Indices: 1690981--1691078 Score: 76
Period size: 28 Copynumber: 3.4 Consensus size: 28
1690971 TAGAAGAGGG
*
1690981 TCATAGTTTAAGGATGAAA-TAGAATGT
1 TCATAGTTTAAGGATGAAATTAGAATGA
* * *
1691008 TCAAAAGTTTAACGACT-AATTTAGAATGAAAA
1 TC-ATAGTTTAAGGA-TGAAATTAGAATG---A
1691040 TCATAGTTTAAGGATGAAATTAGAAT-A
1 TCATAGTTTAAGGATGAAATTAGAATGA
*
1691067 TTCAAAGTTTAA
1 -TCATAGTTTAA
1691079 TGACTAATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
27 3 0.05
28 22 0.40
29 8 0.15
30 1 0.02
31 19 0.35
32 2 0.04
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (28 bp):
TCATAGTTTAAGGATGAAATTAGAATGA
Found at i:1691105 original size:59 final size:60
Alignment explanation
Indices: 1690977--1691108 Score: 171
Period size: 59 Copynumber: 2.2 Consensus size: 60
1690967 AACTTAGAAG
* **
1690977 AGGGTCATAGTTTAAGGATGAAATAGAATGTTCAAAAGTTTAACGACTAATTTAGAATGA
1 AGGGTCATAGTTTAAGGATGAAATAGAATATTCAAAAGTTTAACGACTAATTTAGAAACA
** *
1691037 A-AATCATAGTTTAAGGATGAAATTAGAATATTC-AAAGTTTAATGACTAATTTA-AAACA
1 AGGGTCATAGTTTAAGGATGAAA-TAGAATATTCAAAAGTTTAACGACTAATTTAGAAACA
*
1691095 AGGGTTATAGTTTA
1 AGGGTCATAGTTTA
1691109 GAGACATGAT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 4 0.07
59 47 0.77
60 10 0.16
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (60 bp):
AGGGTCATAGTTTAAGGATGAAATAGAATATTCAAAAGTTTAACGACTAATTTAGAAACA
Found at i:1695647 original size:27 final size:27
Alignment explanation
Indices: 1695617--1695686 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
1695607 ATTTAAGGAA
1695617 ATGGGTTTTTAGTTGATATGTTAGAAC
1 ATGGGTTTTTAGTTGATATGTTAGAAC
*
1695644 ATGGGTTTTTAGTTGATATGTTAGAAT
1 ATGGGTTTTTAGTTGATATGTTAGAAC
*
1695671 ATGAGTTTTTA-TTGAT
1 ATGGGTTTTTAGTTGAT
1695687 GTTTATTAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 5 0.12
27 36 0.88
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (27 bp):
ATGGGTTTTTAGTTGATATGTTAGAAC
Found at i:1696162 original size:22 final size:22
Alignment explanation
Indices: 1696122--1696163 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1696112 ACTGAAAGGG
*
1696122 AGTATCGGTACCATAGTATAGA
1 AGTATCGATACCATAGTATAGA
* *
1696144 AGTATCGATATCATGGTATA
1 AGTATCGATACCATAGTATA
1696164 AGTACCAATA
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:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTATCGATACCATAGTATAGA
Done.