Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008590.1 Hibiscus syriacus cultivar Beakdansim tig00111539_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: 253679
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:2031 original size:21 final size:20
Alignment explanation
Indices: 2005--2048 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1995 GATTTCTGGG
* *
2005 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCC-TT
2026 CAAGGGGAACCGATACCCTT
1 CAAGGGGAACCGATACCCTT
2046 CAA
1 CAA
2049 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (20 bp):
CAAGGGGAACCGATACCCTT
Found at i:3119 original size:15 final size:14
Alignment explanation
Indices: 3080--3122 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
3070 ATAAGCAATG
3080 TGACTATAAGTATA
1 TGACTATAAGTATA
* *
3094 TGTGCTTTAAGTGATA
1 TG-ACTATAAGT-ATA
3110 TGACTATAAGTAT
1 TGACTATAAGTAT
3123 TTCTATTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
14 4 0.17
15 14 0.61
16 5 0.22
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.40
Consensus pattern (14 bp):
TGACTATAAGTATA
Found at i:3762 original size:23 final size:22
Alignment explanation
Indices: 3703--3769 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
3693 TATGGACATC
*
3703 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
3725 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
3747 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
3770 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:5874 original size:14 final size:14
Alignment explanation
Indices: 5794--5886 Score: 50
Period size: 14 Copynumber: 6.6 Consensus size: 14
5784 TAAAGGTAAT
*
5794 AAATAAAATAA-GA
1 AAATAAAATAACTA
* *
5807 AAAGACAAATAAAT-
1 AAATA-AAATAACTA
5821 AAATAAAATACACTA
1 AAATAAAATA-ACTA
* **
5836 AAATTAAAAGAGAAAA
1 AAA-TAAAATA-ACTA
*
5852 AAAT-GAATAACTA
1 AAATAAAATAACTA
5865 AAATAAAAT-ACTA
1 AAATAAAATAACTA
5878 AAATTAAAA
1 AAA-TAAAA
5887 AGGAAAAAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
13 22 0.37
14 23 0.38
15 4 0.07
16 11 0.18
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.18
Consensus pattern (14 bp):
AAATAAAATAACTA
Found at i:5906 original size:41 final size:43
Alignment explanation
Indices: 5821--5925 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 43
5811 ACAAATAAAT
5821 AAATAAAATACACTAAAATTAAAAGAGAAAAAAATGAATAACTA
1 AAATAAAATA-ACTAAAATTAAAAGAGAAAAAAATGAATAACTA
*
5865 AAATAAAAT-ACTAAAATTAAAA-AGGAAAAAATGAATAACTA
1 AAATAAAATAACTAAAATTAAAAGAGAAAAAAATGAATAACTA
* * *
5906 AATTGAAATAAATTAAAATT
1 AAATAAAAT-AACTAAAATT
5926 GATGGATTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
41 25 0.45
42 13 0.24
43 8 0.15
44 9 0.16
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.22
Consensus pattern (43 bp):
AAATAAAATAACTAAAATTAAAAGAGAAAAAAATGAATAACTA
Found at i:8574 original size:24 final size:24
Alignment explanation
Indices: 8547--8607 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
8537 TTGAAAATAT
* *
8547 TATTATTATTTAAATGTGATGTAC
1 TATTATTATTTAAATATGATGTAA
* * *
8571 TATTGTTGTTTTAATATGATGTAA
1 TATTATTATTTAAATATGATGTAA
*
8595 TTTTAATTATTTA
1 TATT-ATTATTTA
8608 CTTTGATAAT
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (24 bp):
TATTATTATTTAAATATGATGTAA
Found at i:9055 original size:14 final size:14
Alignment explanation
Indices: 9036--9080 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
9026 CCAAAAATAT
*
9036 AATTCATTTTCCAG
1 AATTCATTTTCCAA
*
9050 AATTCATTTTCAAA
1 AATTCATTTTCCAA
9064 AATTCATTTTCCGAA
1 AATTCATTTTCC-AA
9079 AA
1 AA
9081 CTATTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 23 0.85
15 4 0.15
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (14 bp):
AATTCATTTTCCAA
Found at i:9086 original size:28 final size:28
Alignment explanation
Indices: 9036--9089 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
9026 CCAAAAATAT
* *
9036 AATTCATTTTCCAGAATTCATTTTCAAA
1 AATTCATTTTCCAAAACTCATTTTCAAA
9064 AATTCATTTTCCGAAAACT-ATTTTCA
1 AATTCATTTTCC-AAAACTCATTTTCA
9090 GTGAAACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.43
Consensus pattern (28 bp):
AATTCATTTTCCAAAACTCATTTTCAAA
Found at i:19698 original size:2 final size:2
Alignment explanation
Indices: 19691--19715 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19681 TCATAAAATT
19691 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
19716 TTACAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20793 original size:3 final size:3
Alignment explanation
Indices: 20785--20814 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
20775 AAACCACCCC
20785 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20815 GAAGAAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20819 original size:3 final size:3
Alignment explanation
Indices: 20813--20976 Score: 321
Period size: 3 Copynumber: 55.0 Consensus size: 3
20803 TAATAATAAT
20813 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
20861 -AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
20908 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
20956 AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG
20977 GTATTATATA
Statistics
Matches: 160, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
2 2 0.01
3 158 0.99
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:23286 original size:68 final size:68
Alignment explanation
Indices: 23177--23383 Score: 405
Period size: 68 Copynumber: 3.0 Consensus size: 68
23167 GCAAAGGCTA
23177 AAAGAAGAAAAGATTAAGTAGATGAGCGTGAAGCTTCATCTTCATTGTCATCTTCTCCATGCTGA
1 AAAGAAGAAAAGATTAAGTAGATGAGCGTGAAGCTTCATCTTCATTGTCATCTTCTCCATGCTGA
23242 CAG
66 CAG
23245 AAAGAAGAAAAGATTAAGTAGATGAGCGTGAAGCTTCATCTTCATTGTCATCTTCTCCATGCTGA
1 AAAGAAGAAAAGATTAAGTAGATGAGCGTGAAGCTTCATCTTCATTGTCATCTTCTCCATGCTGA
23310 CAG
66 CAG
*
23313 AAAGAAGAAAAGATTAAGTAGATGAGCGTGAAGCTTCATCTTCATTATCATCTTCTCCATGCTGA
1 AAAGAAGAAAAGATTAAGTAGATGAGCGTGAAGCTTCATCTTCATTGTCATCTTCTCCATGCTGA
23378 CAG
66 CAG
23381 AAA
1 AAA
23384 AGTTACGCAA
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 138 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (68 bp):
AAAGAAGAAAAGATTAAGTAGATGAGCGTGAAGCTTCATCTTCATTGTCATCTTCTCCATGCTGA
CAG
Found at i:25011 original size:11 final size:11
Alignment explanation
Indices: 24997--25089 Score: 96
Period size: 11 Copynumber: 8.2 Consensus size: 11
24987 GCTTAAGTCA
24997 AGCTTGAATCG
1 AGCTTGAATCG
**
25008 AGCTCACAATCG
1 AGCT-TGAATCG
25020 AGCTTGAATCG
1 AGCTTGAATCG
**
25031 AGCTCACAATCG
1 AGCT-TGAATCG
25043 AGCTTGAATCG
1 AGCTTGAATCG
25054 AGCTTGAATCG
1 AGCTTGAATCG
**
25065 AGCTCAAAATCG
1 AGCT-TGAATCG
*
25077 AGCTTCAATCG
1 AGCTTGAATCG
25088 AG
1 AG
25090 TCTCGAGCTT
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
11 40 0.60
12 27 0.40
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (11 bp):
AGCTTGAATCG
Found at i:25023 original size:23 final size:23
Alignment explanation
Indices: 24997--25057 Score: 122
Period size: 23 Copynumber: 2.7 Consensus size: 23
24987 GCTTAAGTCA
24997 AGCTTGAATCGAGCTCACAATCG
1 AGCTTGAATCGAGCTCACAATCG
25020 AGCTTGAATCGAGCTCACAATCG
1 AGCTTGAATCGAGCTCACAATCG
25043 AGCTTGAATCGAGCT
1 AGCTTGAATCGAGCT
25058 TGAATCGAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (23 bp):
AGCTTGAATCGAGCTCACAATCG
Found at i:25053 original size:34 final size:34
Alignment explanation
Indices: 25003--25089 Score: 138
Period size: 34 Copynumber: 2.5 Consensus size: 34
24993 GTCAAGCTTG
* *
25003 AATCGAGCTCACAATCGAGCTTGAATCGAGCTCAC
1 AATCGAGCT-TCAATCGAGCTTGAATCGAGCTCAA
*
25038 AATCGAGCTTGAATCGAGCTTGAATCGAGCTCAA
1 AATCGAGCTTCAATCGAGCTTGAATCGAGCTCAA
25072 AATCGAGCTTCAATCGAG
1 AATCGAGCTTCAATCGAG
25090 TCTCGAGCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
34 39 0.81
35 9 0.19
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (34 bp):
AATCGAGCTTCAATCGAGCTTGAATCGAGCTCAA
Found at i:25137 original size:30 final size:31
Alignment explanation
Indices: 25092--25164 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
25082 CAATCGAGTC
25092 TCGAGCTTC-AGTCGAACTTTTGAAT-TT-T-TT
1 TCGAG-TTCGAGTCGAA-TTTT-AATATTATCTT
*
25122 TTGAGTTCGAGTCGAATTTTAATATTATCTT
1 TCGAGTTCGAGTCGAATTTTAATATTATCTT
25153 TCGAGTTCGAGT
1 TCGAGTTCGAGT
25165 TGAGCTTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
28 3 0.08
29 9 0.24
30 12 0.32
31 13 0.35
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (31 bp):
TCGAGTTCGAGTCGAATTTTAATATTATCTT
Found at i:26427 original size:14 final size:14
Alignment explanation
Indices: 26408--26457 Score: 82
Period size: 14 Copynumber: 3.6 Consensus size: 14
26398 TTTTTAATTA
26408 AAAAAATATTTTTT
1 AAAAAATATTTTTT
*
26422 AAAAAATATTTTTA
1 AAAAAATATTTTTT
26436 AAAAAATATTTTTT
1 AAAAAATATTTTTT
*
26450 TAAAAATA
1 AAAAAATA
26458 AATTTCTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAAAATATTTTTT
Found at i:26470 original size:28 final size:28
Alignment explanation
Indices: 26405--26462 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
26395 TTTTTTTTAA
**
26405 TTAAAAAAATATTTTTTAAAAAATATTT
1 TTAAAAAAATATTTTTTAAAAAATAAAT
*
26433 TTAAAAAAATATTTTTTTAAAAATAAAT
1 TTAAAAAAATATTTTTTAAAAAATAAAT
26461 TT
1 TT
26463 CTAAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TTAAAAAAATATTTTTTAAAAAATAAAT
Found at i:27097 original size:60 final size:59
Alignment explanation
Indices: 27028--27160 Score: 187
Period size: 60 Copynumber: 2.2 Consensus size: 59
27018 TCAACTGACT
* * *
27028 ATTTTGTAACTTTTAATAGTCGATGGACTCAACAAAGCAACACCCTATAGTCGAAGGATC
1 ATTTGGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACCCTATAGTCG-AGGACC
* * *
27088 ATTTGGTAACTTTTAATAGTTGAGGGACTCAACAAATCATCACCCTATAGTCGAGGACC
1 ATTTGGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACCCTATAGTCGAGGACC
27147 ATTTGTGT-ACTTTT
1 ATTTG-GTAACTTTT
27161 GCCCGAGTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
59 16 0.24
60 50 0.76
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (59 bp):
ATTTGGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACCCTATAGTCGAGGACC
Found at i:27503 original size:15 final size:15
Alignment explanation
Indices: 27483--27537 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 15
27473 ATGTAATAGA
27483 AATAAATATTATTTT
1 AATAAATATTATTTT
*
27498 AAT-AA-ATCATTTT
1 AATAAATATTATTTT
27511 AA-AATTATATTATTTT
1 AATAA--ATATTATTTT
*
27527 CATAAATATTA
1 AATAAATATTA
27538 GAAAGAAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
13 10 0.31
14 2 0.06
15 10 0.31
16 8 0.25
17 2 0.06
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (15 bp):
AATAAATATTATTTT
Found at i:31335 original size:2 final size:2
Alignment explanation
Indices: 31328--31382 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
31318 TTTCTAATAC
31328 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31370 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
31383 CACAATTTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33259 original size:26 final size:26
Alignment explanation
Indices: 33229--33286 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
33219 AATCATCTCA
33229 TTAATGTTGGTCCATGCTCTACAATT
1 TTAATGTTGGTCCATGCTCTACAATT
*
33255 TTAATGTTGGTCCATGCTCTACAGTT
1 TTAATGTTGGTCCATGCTCTACAATT
33281 TATAAT
1 T-TAAT
33287 CATCTCATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (26 bp):
TTAATGTTGGTCCATGCTCTACAATT
Found at i:33309 original size:39 final size:39
Alignment explanation
Indices: 33255--33359 Score: 201
Period size: 39 Copynumber: 2.7 Consensus size: 39
33245 CTCTACAATT
*
33255 TTAATGTTGGTCCATGCTCTACAGTTTATAATCATCTCA
1 TTAATGTTGGTCCATGCTCTACAATTTATAATCATCTCA
33294 TTAATGTTGGTCCATGCTCTACAATTTATAATCATCTCA
1 TTAATGTTGGTCCATGCTCTACAATTTATAATCATCTCA
33333 TTAATGTTGGTCCATGCTCTACAATTT
1 TTAATGTTGGTCCATGCTCTACAATTT
33360 TCTGATGGCT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (39 bp):
TTAATGTTGGTCCATGCTCTACAATTTATAATCATCTCA
Found at i:34823 original size:31 final size:31
Alignment explanation
Indices: 34788--34866 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 31
34778 CAGTTACGTC
* * *
34788 GGGGACCATATTGCAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATATTA
*
34819 GGGGACCATATTTACAAACAGACTAAATATTA
1 GGGGACCATA-TTGCAAACAGACTAAATATTA
**
34851 GGGGATTATATTGCAA
1 GGGGACCATATTGCAA
34867 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 15 0.38
32 25 0.62
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATATTA
Found at i:35523 original size:18 final size:18
Alignment explanation
Indices: 35450--35525 Score: 53
Period size: 18 Copynumber: 4.1 Consensus size: 18
35440 CCCATATGTT
*
35450 ATATATAATATATATAATA
1 ATATATAAT-TATAAAATA
* * * *
35469 TTTTTTAATTAAAAAATA
1 ATATATAATTATAAAATA
* * *
35487 GTTTATAATTAATTTAAATA
1 ATATATAATT-A-TAAAATA
35507 ATATATAATTATAAAATA
1 ATATATAATTATAAAATA
35525 A
1 A
35526 AAAATTTATA
Statistics
Matches: 43, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
18 22 0.51
19 8 0.19
20 13 0.30
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (18 bp):
ATATATAATTATAAAATA
Found at i:35581 original size:183 final size:184
Alignment explanation
Indices: 35281--35654 Score: 637
Period size: 183 Copynumber: 2.0 Consensus size: 184
35271 ATAAAAATTA
*
35281 AATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATAAATAATTATAAAATAAAAAT
1 AATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATAAATAATTATAAAATAAAAAA
*
35346 TTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTAT
66 TTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTCAAAAGTTATTGGATCTTAAATTAT
35411 TAATTGGGTTTTAAATTATTTGGGCTT-AGCCCATATGTTATATATAATATATAT
131 TAATTGGGTTTTAAATTATTTGGG-TTGAGCCCATATGTTATATATAATATATAT
*
35465 AATATTTTTTAATT-AAAAAATAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAA
1 AATATTTTTTAATTCAAAAAA-AGTTTATAATTAATTTAAATAATAAATAATTATAAAATAAAAA
*
35529 ATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTCAAAAGTTATTGGATCTTAAATTA
65 ATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTCAAAAGTTATTGGATCTTAAATTA
* * *
35593 TTAATTGTGTTTTTAATTATTTGGGTTGAGCCCATATGTTATATATAATATATTT
130 TTAATTGGGTTTTAAATTATTTGGGTTGAGCCCATATGTTATATATAATATATAT
*
35648 AAAATTT
1 AATATTT
35655 AAAATTTAAT
Statistics
Matches: 180, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
182 2 0.01
183 116 0.64
184 62 0.34
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.47
Consensus pattern (184 bp):
AATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATAAATAATTATAAAATAAAAAA
TTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTCAAAAGTTATTGGATCTTAAATTAT
TAATTGGGTTTTAAATTATTTGGGTTGAGCCCATATGTTATATATAATATATAT
Found at i:45045 original size:22 final size:21
Alignment explanation
Indices: 45016--45057 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
45006 TGATCAAATG
45016 ATATTATTTTAGT-ATTTTTAT
1 ATATTATTTT-GTGATTTTTAT
45037 ATATATATTTTGTGATTTTTA
1 ATAT-TATTTTGTGATTTTTA
45058 GGTAGAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
ATATTATTTTGTGATTTTTAT
Found at i:45980 original size:21 final size:21
Alignment explanation
Indices: 45954--45998 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
45944 GAATTCTGGG
* *
45954 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
45975 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
45996 CAA
1 CAA
45999 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:47734 original size:23 final size:22
Alignment explanation
Indices: 47675--47741 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
47665 TATGGACATC
*
47675 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
47697 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
47719 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
47742 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:50841 original size:21 final size:21
Alignment explanation
Indices: 50815--50859 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
50805 GAATTCTGGG
* *
50815 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
50836 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
50857 CAA
1 CAA
50860 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:52611 original size:23 final size:22
Alignment explanation
Indices: 52552--52618 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
52542 TATGGACATC
*
52552 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
52574 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
52596 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
52619 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:53733 original size:76 final size:75
Alignment explanation
Indices: 53649--53797 Score: 176
Period size: 76 Copynumber: 2.0 Consensus size: 75
53639 TAAACTCAAG
* *
53649 TTTAGGATAATATTTTAAACATTATAT-TTTACCTTT-GTATTTTAGTTTAAATAGGTTTTTAGT
1 TTTAGGATAATATTTT-AACATTATATCTTTA-CTTTAGTATTTCAGTTGAAATAGG-TTTTAGT
53712 ATTTTAATTAAGT
63 ATTTTAATTAAGT
* * * * * *
53725 TTTAGGATATTATTTTTATATTTTATCTTTATTTTAGGTATTTCAGTTGAAATAGGTTTTAGTGT
1 TTTAGGATAATATTTTAACATTATATCTTTACTTTA-GTATTTCAGTTGAAATAGGTTTTAGTAT
53790 TTTAATTA
65 TTTAATTA
53798 GGATTTAGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
75 10 0.16
76 35 0.56
77 17 0.27
ACGTcount: A:0.29, C:0.03, G:0.12, T:0.56
Consensus pattern (75 bp):
TTTAGGATAATATTTTAACATTATATCTTTACTTTAGTATTTCAGTTGAAATAGGTTTTAGTATT
TTAATTAAGT
Found at i:54786 original size:19 final size:19
Alignment explanation
Indices: 54762--54804 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
54752 TTATCACACT
54762 AAAACGTAGTGCATTAACC
1 AAAACGTAGTGCATTAACC
54781 AAAACGTAGTGCATTAACC
1 AAAACGTAGTGCATTAACC
54800 AAAAC
1 AAAAC
54805 CGTGAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.21, G:0.14, T:0.19
Consensus pattern (19 bp):
AAAACGTAGTGCATTAACC
Found at i:56458 original size:15 final size:16
Alignment explanation
Indices: 56440--56469 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56430 TTTTTTGTAA
56440 TTTGT-TTTTTTATTT
1 TTTGTGTTTTTTATTT
56455 TTTGTGTTTTTTATT
1 TTTGTGTTTTTTATT
56470 ATATATAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.83
Consensus pattern (16 bp):
TTTGTGTTTTTTATTT
Found at i:71574 original size:16 final size:17
Alignment explanation
Indices: 71535--71575 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
71525 AATATGAGTA
71535 AATAAATCAAAGATAAAG
1 AATAAAT-AAAGATAAAG
*
71553 AA-AAATAAAGA-AAAT
1 AATAAATAAAGATAAAG
71568 AATAAATA
1 AATAAATA
71576 GATAACTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.24
16 10 0.48
17 4 0.19
18 2 0.10
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.17
Consensus pattern (17 bp):
AATAAATAAAGATAAAG
Found at i:73775 original size:105 final size:105
Alignment explanation
Indices: 73597--74056 Score: 848
Period size: 105 Copynumber: 4.4 Consensus size: 105
73587 GTGTTGTTTC
73597 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
73662 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* ** *
73702 GAGTCCAATATCCCTCGTTGTGAAGCAGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
* *
73767 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
*
73807 GAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
73872 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
73912 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
73977 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
74017 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
74057 GGTAAAACCT
Statistics
Matches: 342, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 342 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
Found at i:85301 original size:4 final size:4
Alignment explanation
Indices: 85292--85388 Score: 51
Period size: 4 Copynumber: 25.0 Consensus size: 4
85282 GACAATATAC
** * * * *
85292 ATAA ATAA ATGG ATAA ATAA ATAA ACAA ATATGA GTAA ATAA ATCA A-AG
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA--A ATAA ATAA ATAA ATAA
* * * *
85341 ATAA A-GA A-AA ATAA A-GA A-AA ATAA ATAA ATAG ATAA CTAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
85385 ATAA
1 ATAA
85389 GATGAGGAAA
Statistics
Matches: 68, Mismatches: 20, Indels: 10
0.69 0.20 0.10
Matches are distributed among these distances:
3 9 0.13
4 56 0.82
6 3 0.04
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:85356 original size:10 final size:10
Alignment explanation
Indices: 85341--85365 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
85331 TAAATCAAAG
85341 ATAAAGAAAA
1 ATAAAGAAAA
85351 ATAAAGAAAA
1 ATAAAGAAAA
85361 ATAAA
1 ATAAA
85366 TAAATAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (10 bp):
ATAAAGAAAA
Found at i:88657 original size:35 final size:35
Alignment explanation
Indices: 88598--88665 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
88588 AACGCACACG
*
88598 GAAAACTAACATAGTGAATAGCTGAATAACACATA
1 GAAAACTAACATAGTGAATAGCTGAAGAACACATA
* *
88633 GAAAACTGACATAGTGACCT-GCTGAAGAACACA
1 GAAAACTAACATAGTGA-ATAGCTGAAGAACACA
88666 ACCCAAACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 28 0.97
36 1 0.03
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (35 bp):
GAAAACTAACATAGTGAATAGCTGAAGAACACATA
Found at i:111107 original size:13 final size:13
Alignment explanation
Indices: 111089--111173 Score: 98
Period size: 13 Copynumber: 7.2 Consensus size: 13
111079 AAAATGGTGA
111089 TTAATGGTTAGGG
1 TTAATGGTTAGGG
111102 TTAATGGTTA-GG
1 TTAATGGTTAGGG
111114 ------GTTAGGG
1 TTAATGGTTAGGG
111121 TTAATGGTTAGGG
1 TTAATGGTTAGGG
*
111134 TT-AGGGTTAGGG
1 TTAATGGTTAGGG
111146 TTAA-GGTTAGGG
1 TTAATGGTTAGGG
111158 TTAATGGTTAGGG
1 TTAATGGTTAGGG
111171 TTA
1 TTA
111174 GGAATAATGG
Statistics
Matches: 62, Mismatches: 1, Indels: 18
0.77 0.01 0.22
Matches are distributed among these distances:
6 4 0.06
7 2 0.03
12 25 0.40
13 31 0.50
ACGTcount: A:0.22, C:0.00, G:0.40, T:0.38
Consensus pattern (13 bp):
TTAATGGTTAGGG
Found at i:111116 original size:6 final size:6
Alignment explanation
Indices: 111094--111204 Score: 114
Period size: 6 Copynumber: 17.8 Consensus size: 6
111084 GGTGATTAAT
* *
111094 GGTTAG GGTTAAT GGTTAG GGTTAG GGTTAAT GGTTAG GGTTAG GGTTAG
1 GGTTAG GGTT-AG GGTTAG GGTTAG GGTT-AG GGTTAG GGTTAG GGTTAG
* * * * *
111144 GGTTAA GGTTAG GGTTAAT GGTTAG GGTTAG GAATAAT GGTTAG GGTTAG
1 GGTTAG GGTTAG GGTT-AG GGTTAG GGTTAG G-GTTAG GGTTAG GGTTAG
*
111194 AGTTAG GGTTA
1 GGTTAG GGTTA
111205 AGATTAAGGT
Statistics
Matches: 85, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
6 67 0.79
7 18 0.21
ACGTcount: A:0.23, C:0.00, G:0.41, T:0.35
Consensus pattern (6 bp):
GGTTAG
Found at i:111118 original size:19 final size:19
Alignment explanation
Indices: 111094--111198 Score: 158
Period size: 19 Copynumber: 5.6 Consensus size: 19
111084 GGTGATTAAT
111094 GGTTAGGGTTAATGGTTAG
1 GGTTAGGGTTAATGGTTAG
111113 GGTTAGGGTTAATGGTTAG
1 GGTTAGGGTTAATGGTTAG
* *
111132 GGTTAGGGTT-AGGGTTAA
1 GGTTAGGGTTAATGGTTAG
111150 GGTTAGGGTTAATGGTTAG
1 GGTTAGGGTTAATGGTTAG
**
111169 GGTTAGGAATAATGGTTAG
1 GGTTAGGGTTAATGGTTAG
*
111188 GGTTAGAGTTA
1 GGTTAGGGTTA
111199 GGGTTAAGAT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
18 16 0.21
19 60 0.79
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (19 bp):
GGTTAGGGTTAATGGTTAG
Found at i:111155 original size:37 final size:38
Alignment explanation
Indices: 111094--111198 Score: 140
Period size: 37 Copynumber: 2.8 Consensus size: 38
111084 GGTGATTAAT
* *
111094 GGTTAGGGTTAATGGTTAGGGTTAGGGTTAATGGTTAG
1 GGTTAGGGTTAAGGGTTAAGGTTAGGGTTAATGGTTAG
111132 GGTTAGGGTT-AGGGTTAAGGTTAGGGTTAATGGTTAG
1 GGTTAGGGTTAAGGGTTAAGGTTAGGGTTAATGGTTAG
** * * *
111169 GGTTAGGAATAATGGTTAGGGTTAGAGTTA
1 GGTTAGGGTTAAGGGTTAAGGTTAGGGTTA
111199 GGGTTAAGAT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
37 33 0.56
38 26 0.44
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (38 bp):
GGTTAGGGTTAAGGGTTAAGGTTAGGGTTAATGGTTAG
Found at i:111155 original size:56 final size:56
Alignment explanation
Indices: 111089--111216 Score: 202
Period size: 56 Copynumber: 2.3 Consensus size: 56
111079 AAAATGGTGA
** *
111089 TTAATGGTTAGGGTTAATGGTTAGGGTTAGGGTTAATGGTTAGGGTTAGGGTTAGGG
1 TTAA-GGTTAGGGTTAATGGTTAGGGTTAGGAATAATGGTTAGGGTTAGAGTTAGGG
111146 TTAAGGTTAGGGTTAATGGTTAGGGTTAGGAATAATGGTTAGGGTTAGAGTTAGGG
1 TTAAGGTTAGGGTTAATGGTTAGGGTTAGGAATAATGGTTAGGGTTAGAGTTAGGG
* *
111202 TTAAGATTAAGGTTA
1 TTAAGGTTAGGGTTA
111217 CAATTACAAG
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
56 62 0.94
57 4 0.06
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.36
Consensus pattern (56 bp):
TTAAGGTTAGGGTTAATGGTTAGGGTTAGGAATAATGGTTAGGGTTAGAGTTAGGG
Found at i:114046 original size:30 final size:32
Alignment explanation
Indices: 114006--114065 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 32
113996 TTTATAAAAG
114006 TTTTCTCTTTTTACTTTTCAAG-TTT-TTTTCA
1 TTTTCTC-TTTTACTTTTCAAGCTTTGTTTTCA
*
114037 TTTT-TCTTTTATTTTTCAAGCTTTGTTTT
1 TTTTCTCTTTTACTTTTCAAGCTTTGTTTT
114066 TAAAATGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 13 0.50
30 5 0.19
31 8 0.31
ACGTcount: A:0.12, C:0.13, G:0.05, T:0.70
Consensus pattern (32 bp):
TTTTCTCTTTTACTTTTCAAGCTTTGTTTTCA
Found at i:114684 original size:18 final size:17
Alignment explanation
Indices: 114663--114704 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
114653 CTTTAATTGC
114663 TTTTACTTA-TTTAATCAT
1 TTTTA-TTATTTTAAT-AT
114681 TTTTATTATTTTAATA-
1 TTTTATTATTTTAATAT
114697 TTTTATTA
1 TTTTATTA
114705 CCAAAATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.35
17 4 0.17
18 11 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATTATTTTAATAT
Found at i:119635 original size:82 final size:82
Alignment explanation
Indices: 119534--119697 Score: 328
Period size: 82 Copynumber: 2.0 Consensus size: 82
119524 GCATCTTGTT
119534 CTTATTAGTAGTGGAGATTTGATTTACTTGCAGGCTTATGGTAATATCGTGTCGATTCTGACATT
1 CTTATTAGTAGTGGAGATTTGATTTACTTGCAGGCTTATGGTAATATCGTGTCGATTCTGACATT
119599 GAGCGTTTCTTTACCCC
66 GAGCGTTTCTTTACCCC
119616 CTTATTAGTAGTGGAGATTTGATTTACTTGCAGGCTTATGGTAATATCGTGTCGATTCTGACATT
1 CTTATTAGTAGTGGAGATTTGATTTACTTGCAGGCTTATGGTAATATCGTGTCGATTCTGACATT
119681 GAGCGTTTCTTTACCCC
66 GAGCGTTTCTTTACCCC
119698 AAACACATTG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (82 bp):
CTTATTAGTAGTGGAGATTTGATTTACTTGCAGGCTTATGGTAATATCGTGTCGATTCTGACATT
GAGCGTTTCTTTACCCC
Found at i:121115 original size:18 final size:18
Alignment explanation
Indices: 121074--121111 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
121064 TTATTTTTAC
*
121074 TTTAATTGCTTTTACTTA
1 TTTAATCGCTTTTACTTA
121092 TTTAATCGCTTTTA-TTA
1 TTTAATCGCTTTTACTTA
121109 TTT
1 TTT
121112 TAATATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.21, C:0.11, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTAATCGCTTTTACTTA
Found at i:122515 original size:22 final size:22
Alignment explanation
Indices: 122498--122541 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
122488 GAATTTCATG
122498 TAGATTAATTATCTATTTCACA
1 TAGATTAATTATCTATTTCACA
122520 TAGATTAATTATCTATTTCACA
1 TAGATTAATTATCTATTTCACA
122542 ACTTAGTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (22 bp):
TAGATTAATTATCTATTTCACA
Found at i:130349 original size:33 final size:33
Alignment explanation
Indices: 130307--130374 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
130297 GCAAAGTTAT
130307 CAATGCTTTTGTGCTGTTTTTGAGTACAGATAG
1 CAATGCTTTTGTGCTGTTTTTGAGTACAGATAG
130340 CAATGCTTTTGTGCTGTTTTTGAGTACAGATAG
1 CAATGCTTTTGTGCTGTTTTTGAGTACAGATAG
130373 CA
1 CA
130375 TCATGTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.41
Consensus pattern (33 bp):
CAATGCTTTTGTGCTGTTTTTGAGTACAGATAG
Found at i:149578 original size:50 final size:49
Alignment explanation
Indices: 149475--149652 Score: 216
Period size: 50 Copynumber: 3.6 Consensus size: 49
149465 CACATACTAG
* *
149475 AAAAAATGTAGCACTT--CACATACTTATATCGGTGTAAGTGAATAAAAT
1 AAAAAATGTAGCACTTAACACATACTTACAT-GGTGTAAGTAAATAAAAT
*
149523 AAAAAAATTGTAGCACTTAACATATACTTACATGGTGTAAGTAAATAAAAT
1 -AAAAAA-TGTAGCACTTAACACATACTTACATGGTGTAAGTAAATAAAAT
* * * * *
149574 AAAAAAGTATAACACTTAATACATATTTACATAGTGTAAGTAAATAAAAT
1 AAAAAA-TGTAGCACTTAACACATACTTACATGGTGTAAGTAAATAAAAT
*
149624 AAAAAAATGTAGCACTTAATACATACTTA
1 -AAAAAATGTAGCACTTAACACATACTTA
149653 AACCGATGTA
Statistics
Matches: 112, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
49 6 0.05
50 72 0.64
51 23 0.21
52 11 0.10
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (49 bp):
AAAAAATGTAGCACTTAACACATACTTACATGGTGTAAGTAAATAAAAT
Found at i:152781 original size:15 final size:15
Alignment explanation
Indices: 152761--152790 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
152751 CTAATATTGG
*
152761 ATTTTTCATATTTTT
1 ATTTTTCAGATTTTT
152776 ATTTTTCAGATTTTT
1 ATTTTTCAGATTTTT
152791 TAATAGAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (15 bp):
ATTTTTCAGATTTTT
Found at i:153039 original size:68 final size:68
Alignment explanation
Indices: 152966--153101 Score: 245
Period size: 68 Copynumber: 2.0 Consensus size: 68
152956 TATCTCTGTC
152966 TTTGTGATACGTTTTTCATTTTTATCGGTCGTTTGACAGTTCTTTTATTTTTGTTTTGTCAAGGT
1 TTTGTGATACGTTTTTCATTTTTATCGGTCGTTTGACAGTTCTTTTATTTTTGTTTTGTCAAGGT
153031 TTG
66 TTG
** *
153034 TTTGTGATACGTTTTTTGTTTTTATCGGTCGTTTGACAGTTCTTTTATTTTTGTTTTGTCAGGGT
1 TTTGTGATACGTTTTTCATTTTTATCGGTCGTTTGACAGTTCTTTTATTTTTGTTTTGTCAAGGT
153099 TTG
66 TTG
153102 ATTAGATGAC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.12, C:0.10, G:0.21, T:0.58
Consensus pattern (68 bp):
TTTGTGATACGTTTTTCATTTTTATCGGTCGTTTGACAGTTCTTTTATTTTTGTTTTGTCAAGGT
TTG
Found at i:153085 original size:35 final size:35
Alignment explanation
Indices: 152984--153090 Score: 98
Period size: 35 Copynumber: 3.1 Consensus size: 35
152974 ACGTTTTTCA
152984 TTTTTATCGGTCGTTTGACAGTTCTTTTATTTTTG
1 TTTTTATCGGTCGTTTGACAGTTCTTTTATTTTTG
* * ** * *
153019 TTTTGTCA-AGGTTTGTTTGTGA-TAC--GT-TTTTTG
1 TTTT-T-ATCGG-TCGTTTGACAGTTCTTTTATTTTTG
153052 TTTTTATCGGTCGTTTGACAGTTCTTTTATTTTTG
1 TTTTTATCGGTCGTTTGACAGTTCTTTTATTTTTG
153087 TTTT
1 TTTT
153091 GTCAGGGTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 16
0.65 0.15 0.20
Matches are distributed among these distances:
31 8 0.15
32 5 0.10
33 10 0.19
34 2 0.04
35 14 0.27
36 5 0.10
37 8 0.15
ACGTcount: A:0.11, C:0.09, G:0.19, T:0.61
Consensus pattern (35 bp):
TTTTTATCGGTCGTTTGACAGTTCTTTTATTTTTG
Found at i:156146 original size:49 final size:49
Alignment explanation
Indices: 156091--156189 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
156081 CCATGCTTGA
* * *
156091 ATTCTGAAAAAACTAGTTGTGGATATATCTCATTGTTATATTCATTCTT
1 ATTCTGAAAAAACTAGTTATCGATATATCTCATCGTTATATTCATTCTT
156140 ATTCTGAAAAAACTAGTTATCGATATATCTCATCGTTATATTCATTCTT
1 ATTCTGAAAAAACTAGTTATCGATATATCTCATCGTTATATTCATTCTT
156189 A
1 A
156190 CGTTAGTATT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.43
Consensus pattern (49 bp):
ATTCTGAAAAAACTAGTTATCGATATATCTCATCGTTATATTCATTCTT
Found at i:159733 original size:31 final size:31
Alignment explanation
Indices: 159695--159763 Score: 138
Period size: 31 Copynumber: 2.2 Consensus size: 31
159685 TCATATAAAT
159695 CATGTATTTAAGTAGTTACATCTGCATAGTG
1 CATGTATTTAAGTAGTTACATCTGCATAGTG
159726 CATGTATTTAAGTAGTTACATCTGCATAGTG
1 CATGTATTTAAGTAGTTACATCTGCATAGTG
159757 CATGTAT
1 CATGTAT
159764 ATTGTCAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (31 bp):
CATGTATTTAAGTAGTTACATCTGCATAGTG
Found at i:161261 original size:23 final size:23
Alignment explanation
Indices: 161217--161315 Score: 108
Period size: 23 Copynumber: 4.3 Consensus size: 23
161207 TGTTGTTATG
** * *
161217 GTTTATGTTTGTTTGTTTTGTTC
1 GTTTATGTTCATTTATTGTGTTC
* *
161240 ATTTATATTCATTTATTGTGTTC
1 GTTTATGTTCATTTATTGTGTTC
* *
161263 GTTTACGTTCGTTTATTGTGTTC
1 GTTTATGTTCATTTATTGTGTTC
*
161286 GTTTATGTTCATTCATTTGTGTTC
1 GTTTATGTTCATTTA-TTGTGTTC
161310 GTTTAT
1 GTTTAT
161316 CATTTAAATG
Statistics
Matches: 62, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
23 48 0.77
24 14 0.23
ACGTcount: A:0.12, C:0.09, G:0.17, T:0.62
Consensus pattern (23 bp):
GTTTATGTTCATTTATTGTGTTC
Found at i:161285 original size:13 final size:13
Alignment explanation
Indices: 161251--161291 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
161241 TTTATATTCA
161251 TTTATTGTGTTCG
1 TTTATTGTGTTCG
*
161264 TTTA---CGTTCG
1 TTTATTGTGTTCG
161274 TTTATTGTGTTCG
1 TTTATTGTGTTCG
161287 TTTAT
1 TTTAT
161292 GTTCATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
10 9 0.39
13 14 0.61
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.61
Consensus pattern (13 bp):
TTTATTGTGTTCG
Found at i:161285 original size:46 final size:47
Alignment explanation
Indices: 161217--161314 Score: 126
Period size: 46 Copynumber: 2.1 Consensus size: 47
161207 TGTTGTTATG
* * * * *
161217 GTTTATGTTTGTTTGTTTTGTTCATTTATATTCATTTA-TTGTGTTC
1 GTTTACGTTCGTTTATTGTGTTCATTTATATTCATTCATTTGTGTTC
* *
161263 GTTTACGTTCGTTTATTGTGTTCGTTTATGTTCATTCATTTGTGTTC
1 GTTTACGTTCGTTTATTGTGTTCATTTATATTCATTCATTTGTGTTC
161310 GTTTA
1 GTTTA
161315 TCATTTAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 31 0.70
47 13 0.30
ACGTcount: A:0.12, C:0.09, G:0.17, T:0.61
Consensus pattern (47 bp):
GTTTACGTTCGTTTATTGTGTTCATTTATATTCATTCATTTGTGTTC
Found at i:162466 original size:20 final size:21
Alignment explanation
Indices: 162443--162489 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
162433 AATTTGTAAA
162443 TCGCAACA-CAAAAGTCAAAT
1 TCGCAACAGCAAAAGTCAAAT
* *
162463 TCGCAA-AGCGATAGTCAAAT
1 TCGCAACAGCAAAAGTCAAAT
162483 TCGCAAC
1 TCGCAAC
162490 GTGGAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.17
Consensus pattern (21 bp):
TCGCAACAGCAAAAGTCAAAT
Found at i:162517 original size:19 final size:19
Alignment explanation
Indices: 162477--162567 Score: 137
Period size: 19 Copynumber: 4.7 Consensus size: 19
162467 AAAGCGATAG
162477 TCAAATTCGCAACGTGGAATT
1 TCAAATTCGCAAC-T-GAATT
* *
162498 TTAAATTCGAAACTGAATT
1 TCAAATTCGCAACTGAATT
162517 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
162536 TTAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
162555 TCAAATTCGCAAC
1 TCAAATTCGCAAC
162568 ACAAATGTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 52 0.81
20 1 0.02
21 11 0.17
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:162543 original size:38 final size:40
Alignment explanation
Indices: 162477--162567 Score: 159
Period size: 38 Copynumber: 2.3 Consensus size: 40
162467 AAAGCGATAG
162477 TCAAATTCGCAACGTGGAATTTTAAATTCGAAACTGAATT
1 TCAAATTCGCAACGTGGAATTTTAAATTCGAAACTGAATT
*
162517 TCAAATTCGCAAC-T-GAATTTTAAATTCGCAACTGAATT
1 TCAAATTCGCAACGTGGAATTTTAAATTCGAAACTGAATT
162555 TCAAATTCGCAAC
1 TCAAATTCGCAAC
162568 ACAAATGTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 36 0.72
39 1 0.02
40 13 0.26
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (40 bp):
TCAAATTCGCAACGTGGAATTTTAAATTCGAAACTGAATT
Found at i:162724 original size:14 final size:15
Alignment explanation
Indices: 162705--162742 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
162695 TTCCCATCTC
162705 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
162719 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
162735 TAATTTTT
1 TAATTTTT
162743 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:163316 original size:12 final size:12
Alignment explanation
Indices: 163295--163328 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
163285 ACCACATTTC
*
163295 CAATACCAAACA
1 CAATATCAAACA
163307 CAATATCAAACA
1 CAATATCAAACA
*
163319 CAATCTCAAA
1 CAATATCAAA
163329 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:165798 original size:18 final size:18
Alignment explanation
Indices: 165775--165810 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
165765 AAACAAAAGG
*
165775 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
165793 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
165811 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:166121 original size:20 final size:20
Alignment explanation
Indices: 166096--166134 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
166086 ATGTTGCGAT
166096 CAACGCGAAAGTCAAATTCA
1 CAACGCGAAAGTCAAATTCA
166116 CAACGCGAAAGTCAAATTC
1 CAACGCGAAAGTCAAATTC
166135 GCAAACCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCA
Found at i:166192 original size:54 final size:54
Alignment explanation
Indices: 166133--166235 Score: 129
Period size: 54 Copynumber: 1.9 Consensus size: 54
166123 AAAGTCAAAT
166133 TCGCAAAC-CAAAAATCGCGTTGCGAATTTGACTTTC-TCATTGCGAATTTGACTA
1 TCGC-AACGCAAAAATCGCGTTGCGAATTTGACTTTCGT-ATTGCGAATTTGACTA
** ** *
166187 TCGCAACGCTTATTTCGCGTTGCGAATTTGACTTTCGTGTTGCGAATTT
1 TCGCAACGCAAAAATCGCGTTGCGAATTTGACTTTCGTATTGCGAATTT
166236 AACTTTCATG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
53 3 0.07
54 38 0.90
55 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.36
Consensus pattern (54 bp):
TCGCAACGCAAAAATCGCGTTGCGAATTTGACTTTCGTATTGCGAATTTGACTA
Found at i:166228 original size:20 final size:20
Alignment explanation
Indices: 166199--166248 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
166189 GCAACGCTTA
* *
166199 TTTCGCGTTGCGAATTTGAC
1 TTTCGTGTTGCGAATTTAAC
166219 TTTCGTGTTGCGAATTTAAC
1 TTTCGTGTTGCGAATTTAAC
*
166239 TTTCATGTTG
1 TTTCGTGTTG
166249 TACATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.46
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAC
Found at i:167038 original size:39 final size:39
Alignment explanation
Indices: 166995--167081 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
166985 TCCGATGCTC
* *
166995 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGCTGCCAAGCAAAAGAAA
*
167034 ATCAAAATCCAAATCTCATATGCTGCCAAGCAAAAGAAA
1 ATCAAAATCCAAAGCTCATATGCTGCCAAGCAAAAGAAA
167073 ATCAAAATC
1 ATCAAAATC
167082 TACAACTTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.48, C:0.22, G:0.13, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGCTGCCAAGCAAAAGAAA
Found at i:167275 original size:20 final size:20
Alignment explanation
Indices: 167252--167289 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
167242 ACACGAAAAT
*
167252 CAAATTCGTAACGCGAAAGC
1 CAAATTCGCAACGCGAAAGC
*
167272 CAAATTTGCAACGCGAAA
1 CAAATTCGCAACGCGAAA
167290 TAAGCGTTGC
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:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGC
Found at i:167336 original size:20 final size:20
Alignment explanation
Indices: 167313--167350 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
167303 AGTCAATTCG
167313 CAACGCAAAAGTAAAATTTA
1 CAACGCAAAAGTAAAATTTA
* *
167333 CAACGCGAAAGTCAAATT
1 CAACGCAAAAGTAAAATT
167351 CGCAAACCGA
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:0.18, G:0.13, T:0.18
Consensus pattern (20 bp):
CAACGCAAAAGTAAAATTTA
Found at i:167583 original size:65 final size:64
Alignment explanation
Indices: 167458--167579 Score: 169
Period size: 65 Copynumber: 1.9 Consensus size: 64
167448 TTTTAGAAAC
* *
167458 AACAAATCCACTTTTACAAATCAATTAAACAAGCAAATAATAATTCTTATTTACACATCAAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAA-CAAATAATAAATCTTATTTACACATCAAATTA
* * *
167523 AACAAATCAACTTTTACAAATCAATTAATC-A-AAA-AATAAATCTTATTTCCTCATCAA
1 AACAAATCAACTTTTACAAATCAATTAAACAACAAATAATAAATCTTATTTACACATCAA
167580 TCAACTTTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
61 20 0.38
62 3 0.06
64 1 0.02
65 28 0.54
ACGTcount: A:0.49, C:0.19, G:0.01, T:0.31
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAACAAATAATAAATCTTATTTACACATCAAATTA
Found at i:168968 original size:20 final size:21
Alignment explanation
Indices: 168943--168983 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
168933 TTGAACGGCG
168943 GACA-GGACCTCTTGAACGAT
1 GACAGGGACCTCTTGAACGAT
*
168963 GACAGGGGCCTCTTGAACGAT
1 GACAGGGACCTCTTGAACGAT
168984 AGGAGGCGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (21 bp):
GACAGGGACCTCTTGAACGAT
Found at i:168974 original size:21 final size:22
Alignment explanation
Indices: 168950--169006 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
168940 GCGGACAGGA
*
168950 CCTCTTGAACGATGA-CAGGGG
1 CCTCTTGAACGATGAGCAGGCG
*
168971 CCTCTTGAACGAT-AGGAGGCG
1 CCTCTTGAACGATGAGCAGGCG
*
168992 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
169007 TAGGTGCATC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (22 bp):
CCTCTTGAACGATGAGCAGGCG
Found at i:171176 original size:19 final size:20
Alignment explanation
Indices: 171141--171181 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
171131 AGAAGTTTCT
*
171141 GAAACTTAAATTCGCAACGC
1 GAAACTAAAATTCGCAACGC
171161 GAAACTAAAATT-GCAACGC
1 GAAACTAAAATTCGCAACGC
171180 GA
1 GA
171182 TTTTTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (20 bp):
GAAACTAAAATTCGCAACGC
Found at i:171693 original size:40 final size:41
Alignment explanation
Indices: 171636--171835 Score: 227
Period size: 40 Copynumber: 5.0 Consensus size: 41
171626 GCGTAAAAAT
* * *
171636 ATTTGACTT-TCGCGTTGCGAATTTGACTATCGTGTTACAA
1 ATTTGACTTATCGCGTTGCGAATTTGACTATCGCGTTGCGA
* *
171676 ATTTGACTTAT-GTGTTGCTAATTTGACTATCGCGTTGCGA
1 ATTTGACTTATCGCGTTGCGAATTTGACTATCGCGTTGCGA
* *
171716 ATTTGAC-TATCGCGTTGCGAATTTGACT-TTGTGTTGCGA
1 ATTTGACTTATCGCGTTGCGAATTTGACTATCGCGTTGCGA
* *
171755 ATTTAAC-TATCGCGTTGTGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTATCGCGTTGCGAATTTGACTATCGCGTTGCGA
* *
171795 ATTTGACTTAT-GTGTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 ATTTGACTTATCGCGTTGCGAATTTGAC-TA-TCGCGTTGCGA
171835 A
1 A
171836 ATTAGAAACT
Statistics
Matches: 137, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.01
39 43 0.31
40 88 0.64
41 4 0.03
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (41 bp):
ATTTGACTTATCGCGTTGCGAATTTGACTATCGCGTTGCGA
Found at i:171778 original size:59 final size:60
Alignment explanation
Indices: 171636--171835 Score: 280
Period size: 60 Copynumber: 3.4 Consensus size: 60
171626 GCGTAAAAAT
* * * * * *
171636 ATTTGACTTTCGCGTTGCGAATTTGACTATCGTGTTACAAATTTGACTTATGTGTTGCTA
1 ATTTAACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCGA
*
171696 ATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTT-TGTGTTGCGA
1 ATTTAACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCGA
*
171755 ATTTAACTATCGCGTTGTGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCG-
1 ATTTAACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCGA
*
171814 ATTT-ACAAATTCGCGTTGCGAA
1 ATTTAAC-TA-TCGCGTTGCGAA
171836 ATTAGAAACT
Statistics
Matches: 128, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
58 2 0.02
59 61 0.48
60 65 0.51
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (60 bp):
ATTTAACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCGA
Found at i:171814 original size:20 final size:20
Alignment explanation
Indices: 171636--171802 Score: 221
Period size: 20 Copynumber: 8.4 Consensus size: 20
171626 GCGTAAAAAT
*
171636 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
* * *
171656 ATTTGACTATCGTGTTACAA
1 ATTTGACTATCGCGTTGCGA
* *
171676 ATTTGACTTAT-GTGTTGCTA
1 ATTTGAC-TATCGCGTTGCGA
171696 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
171716 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
* *
171736 ATTTGACT-TTGTGTTGCGA
1 ATTTGACTATCGCGTTGCGA
* *
171755 ATTTAACTATCGCGTTGTGA
1 ATTTGACTATCGCGTTGCGA
171775 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
171795 ATTTGACT
1 ATTTGACT
171803 TATGTGTTGC
Statistics
Matches: 128, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.15
20 106 0.83
21 3 0.02
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:171855 original size:60 final size:59
Alignment explanation
Indices: 171645--171841 Score: 209
Period size: 59 Copynumber: 3.3 Consensus size: 59
171635 TATTTGACTT
* * * * * * * *
171645 TCGCGTTGCGAATTTGACTATCGTGTTACAAATTTGACTTATGTGTTGCTAATTTGACTA
1 TCGCGTTGCGAATTAGACAATCGCGTTGCGAATTTGACTT-TGTGTTGCGAATTTAAATA
* * *
171705 TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTGTGTTGCGAATTTAACTA
1 TCGCGTTGCGAATTAGACAATCGCGTTGCGAATTTGACTTTGTGTTGCGAATTTAAATA
* * *
171764 TCGCGTTGTGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCG-ATTTACAA-A
1 TCGCGTTGCGAATTAGACAATCGCGTTGCGAATTTGACTT-TGTGTTGCGAATTTA-AATA
171823 TTCGCGTTGCGAAATTAGA
1 -TCGCGTTGCG-AATTAGA
171842 AACTGGGTTG
Statistics
Matches: 124, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
59 62 0.50
60 56 0.45
61 6 0.05
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (59 bp):
TCGCGTTGCGAATTAGACAATCGCGTTGCGAATTTGACTTTGTGTTGCGAATTTAAATA
Found at i:171871 original size:20 final size:21
Alignment explanation
Indices: 171820--171875 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
171810 TGCGATTTAC
171820 AAATTCGCGTTGCGAAATTAG
1 AAATTCGCGTTGCGAAATTAG
* *
171841 AAACT-GGGTTGCGAAATT-G
1 AAATTCGCGTTGCGAAATTAG
*
171860 AAGTTCGCGTTGCGAA
1 AAATTCGCGTTGCGAA
171876 TTTGTTGGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.14
20 21 0.72
21 4 0.14
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (21 bp):
AAATTCGCGTTGCGAAATTAG
Found at i:173766 original size:17 final size:17
Alignment explanation
Indices: 173744--173799 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 17
173734 CCTTTGAAAA
173744 CAAACAATTATTACTAC
1 CAAACAATTATTACTAC
**
173761 CAAAC-ATCCTT-C-A-
1 CAAACAATTATTACTAC
*
173774 -AAAAAATTATTACTAC
1 CAAACAATTATTACTAC
173790 CAAACAATTA
1 CAAACAATTA
173800 AAATTAGTTG
Statistics
Matches: 28, Mismatches: 6, Indels: 10
0.64 0.14 0.23
Matches are distributed among these distances:
12 3 0.11
13 4 0.14
14 2 0.07
15 2 0.07
16 4 0.14
17 13 0.46
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (17 bp):
CAAACAATTATTACTAC
Found at i:173802 original size:26 final size:28
Alignment explanation
Indices: 173749--173802 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
173739 GAAAACAAAC
*
173749 AATTATTACTACCAAACATCCTTCAAAAA
1 AATTATTACTACCAAACA-CATTCAAAAA
173778 AATTATTACTACCAAACA-ATT-AAAA
1 AATTATTACTACCAAACACATTCAAAA
173803 TTAGTTGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 2 0.08
29 18 0.75
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (28 bp):
AATTATTACTACCAAACACATTCAAAAA
Found at i:174832 original size:20 final size:22
Alignment explanation
Indices: 174796--174842 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
174786 ATTAAATCCC
174796 TATTTTTATTGAATAAAAATAA
1 TATTTTTATTGAATAAAAATAA
* *
174818 TATTTTT-TT-AATAAATATAT
1 TATTTTTATTGAATAAAAATAA
174838 TATTT
1 TATTT
174843 CGAGTTGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 14 0.61
21 2 0.09
22 7 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTTTTATTGAATAAAAATAA
Found at i:180595 original size:9 final size:9
Alignment explanation
Indices: 180581--180655 Score: 53
Period size: 10 Copynumber: 7.8 Consensus size: 9
180571 GGCTGCTGGA
180581 AACCGGTTT
1 AACCGGTTT
180590 AACCGGTTTT
1 AACCGG-TTT
*
180600 CAACCAGTTCT
1 -AACCGGTT-T
*
180611 GACCGG-TT
1 AACCGGTTT
180619 AGACCGGTTT
1 A-ACCGGTTT
*
180629 CAACCGGTTCG
1 -AACCGGTT-T
180640 AACCGGTTT
1 AACCGGTTT
*
180649 GACCGGT
1 AACCGGT
180656 CTGACCCGAC
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
8 1 0.02
9 18 0.35
10 26 0.50
11 7 0.13
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (9 bp):
AACCGGTTT
Found at i:180644 original size:29 final size:30
Alignment explanation
Indices: 180581--180655 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 30
180571 GGCTGCTGGA
180581 AACCGGTTTA-ACCGGTTTTCAACCAGTTCTG
1 AACCGG-TTAGACCGG-TTTCAACCAGTTCTG
*
180612 -ACCGGTTAGACCGGTTTCAACCGGTTC-G
1 AACCGGTTAGACCGGTTTCAACCAGTTCTG
*
180640 AACCGGTTTGACCGGT
1 AACCGGTTAGACCGGT
180656 CTGACCCGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
28 1 0.03
29 29 0.73
30 10 0.25
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (30 bp):
AACCGGTTAGACCGGTTTCAACCAGTTCTG
Found at i:180682 original size:22 final size:22
Alignment explanation
Indices: 180656--180710 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
180646 TTTGACCGGT
180656 CTGACCCGACCCGACCGTTGAC
1 CTGACCCGACCCGACCGTTGAC
180678 CTGACCCGACCCGACCGTTGAC
1 CTGACCCGACCCGACCGTTGAC
*
180700 CCGACCCGACC
1 CTGACCCGACC
180711 GTTGACCGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.49, G:0.22, T:0.11
Consensus pattern (22 bp):
CTGACCCGACCCGACCGTTGAC
Found at i:180683 original size:17 final size:17
Alignment explanation
Indices: 180679--180717 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
180669 ACCGTTGACC
180679 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
180696 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
180713 TGACC
1 TGACC
180718 GCTGACCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:180717 original size:7 final size:7
Alignment explanation
Indices: 180707--180751 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
180697 GACCCGACCC
180707 GACCGTT
1 GACCGTT
*
180714 GACCGCT
1 GACCGTT
180721 GACCGTT
1 GACCGTT
180728 GACCGTT
1 GACCGTT
180735 GACCGTT
1 GACCGTT
180742 GACCGTT
1 GACCGTT
180749 GAC
1 GAC
180752 TTTCTTTGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.16, C:0.31, G:0.29, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:187243 original size:9 final size:9
Alignment explanation
Indices: 187229--187293 Score: 58
Period size: 10 Copynumber: 6.8 Consensus size: 9
187219 GGCTGCTGGA
187229 AACCGGTTT
1 AACCGGTTT
187238 AACCGGTTTT
1 AACCGG-TTT
*
187248 CAACCGGTTCG
1 -AACCGGTT-T
187259 AACCGGTTT
1 AACCGGTTT
* *
187268 GACCGGTTCG
1 AACCGGTT-T
187278 AACCGGTTT
1 AACCGGTTT
*
187287 GACCGGT
1 AACCGGT
187294 CTGACCCGAC
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
9 19 0.42
10 20 0.44
11 6 0.13
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (9 bp):
AACCGGTTT
Found at i:187254 original size:20 final size:21
Alignment explanation
Indices: 187229--187286 Score: 77
Period size: 19 Copynumber: 2.9 Consensus size: 21
187219 GGCTGCTGGA
*
187229 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCGAACCGGTTTTC
187249 AACCGGTTCGAACCGG-TTT-
1 AACCGGTTCGAACCGGTTTTC
*
187268 GACCGGTTCGAACCGGTTT
1 AACCGGTTCGAACCGGTTT
187287 GACCGGTCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.44
20 13 0.38
21 6 0.18
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (21 bp):
AACCGGTTCGAACCGGTTTTC
Found at i:187274 original size:19 final size:19
Alignment explanation
Indices: 187250--187293 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
187240 CCGGTTTTCA
187250 ACCGGTTCGAACCGGTTTG
1 ACCGGTTCGAACCGGTTTG
187269 ACCGGTTCGAACCGGTTTG
1 ACCGGTTCGAACCGGTTTG
187288 ACCGGT
1 ACCGGT
187294 CTGACCCGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.27, G:0.32, T:0.25
Consensus pattern (19 bp):
ACCGGTTCGAACCGGTTTG
Found at i:187298 original size:9 final size:9
Alignment explanation
Indices: 187230--187299 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
187220 GCTGCTGGAA
*
187230 ACCGGTTTA
1 ACCGGTTTG
*
187239 ACCGGTTTTCA
1 ACCGG-TTT-G
*
187250 ACCGGTTCG
1 ACCGGTTTG
187259 AACCGGTTTG
1 -ACCGGTTTG
*
187269 ACCGGTTCG
1 ACCGGTTTG
187278 AACCGGTTTG
1 -ACCGGTTTG
*
187288 ACCGGTCTG
1 ACCGGTTTG
187297 ACC
1 ACC
187300 CGACCCGACC
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
9 24 0.47
10 21 0.41
11 6 0.12
ACGTcount: A:0.17, C:0.29, G:0.27, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:187317 original size:17 final size:17
Alignment explanation
Indices: 187295--187333 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
187285 TTGACCGGTC
187295 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
187312 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
187329 TGACC
1 TGACC
187334 GTTGACCGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:187333 original size:7 final size:7
Alignment explanation
Indices: 187323--187367 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
187313 GACCCGACCC
187323 GACCGTT
1 GACCGTT
187330 GACCGTT
1 GACCGTT
*
187337 GACCGCT
1 GACCGTT
*
187344 GATCGTT
1 GACCGTT
187351 GACCGTT
1 GACCGTT
187358 GACCGTT
1 GACCGTT
187365 GAC
1 GAC
187368 TTTCTTTGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:190510 original size:21 final size:20
Alignment explanation
Indices: 190464--190508 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
190454 AATTAACTTT
*
190464 AAATTTTAAATTTTAAACCA
1 AAATTTTAAATTTAAAACCA
190484 ACAATTTTAAATTATAAAACTCA
1 A-AATTTTAAATT-TAAAAC-CA
190507 AA
1 AA
190509 TTCTAATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 1 0.05
21 11 0.52
22 6 0.29
23 3 0.14
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATTTTAAATTTAAAACCA
Found at i:191783 original size:17 final size:17
Alignment explanation
Indices: 191761--191793 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
191751 AATTAATATC
191761 ATTTAAATAATAAAATG
1 ATTTAAATAATAAAATG
*
191778 ATTTAATTAATAAAAT
1 ATTTAAATAATAAAAT
191794 TAATAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATTTAAATAATAAAATG
Found at i:191802 original size:17 final size:17
Alignment explanation
Indices: 191764--191807 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
191754 TAATATCATT
*
191764 TAAA-TAATAAAATGAT
1 TAAATTAATAAAATGAA
* *
191780 TTAATTAATAAAATTAA
1 TAAATTAATAAAATGAA
191797 TAAATTAATAA
1 TAAATTAATAA
191808 TATAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TAAATTAATAAAATGAA
Found at i:196775 original size:34 final size:34
Alignment explanation
Indices: 196730--196796 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
196720 AATAGAAATT
*
196730 ACAACTTCTCTC-GACCTAACAAGGAGAAAACAATA
1 ACAACTTCTCTCTGA--TAAAAAGGAGAAAACAATA
196765 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAGGAGAAAACAA
196797 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 23 0.79
35 4 0.14
36 2 0.07
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.19
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGGAGAAAACAATA
Found at i:203254 original size:3 final size:3
Alignment explanation
Indices: 203241--203289 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
203231 GGCTTAAAAA
* *
203241 TAT TA- TAT TAT TA- TATT TAT TAT TAT TAT TAA TGT TAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
203285 TAT TA
1 TAT TA
203290 GTAGCAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.85
4 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:203269 original size:18 final size:18
Alignment explanation
Indices: 203241--203289 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
203231 GGCTTAAAAA
203241 TATTA-TATTATTATAT-T
1 TATTATTATTATTA-ATGT
203258 TATTATTATTATTAATGT
1 TATTATTATTATTAATGT
203276 TATTATTATTATTA
1 TATTATTATTATTA
203290 GTAGCAGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.23
18 23 0.77
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TATTATTATTATTAATGT
Found at i:205443 original size:88 final size:87
Alignment explanation
Indices: 205294--205457 Score: 265
Period size: 88 Copynumber: 1.9 Consensus size: 87
205284 ATAGACCAAT
**
205294 TTTTGTCTTAAAAAATGATTTTTCTTAAAATTGTTTTTAAAAGATGTTTTTAGATATTCGACCTA
1 TTTTGTCTTAAAAAATGATTTTTCTTAAAATTGTTTTTAAAAGACATTTTTAGATATTCGACCTA
205359 CCTAACCCAAAGGCCGATCAAC
66 CCTAACCCAAAGGCCGATCAAC
* * *
205381 TTTTGTCTTAAAAAATGATTTTTCTTTAAATTATTTTTTAAAAGACATTTTTAGGTATTCGACCT
1 TTTTGTCTTAAAAAATGATTTTTCTTAAAATT-GTTTTTAAAAGACATTTTTAGATATTCGACCT
*
205446 GCCTAACCCAAA
65 ACCTAACCCAAA
205458 TGTCGATGGC
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
87 31 0.44
88 39 0.56
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (87 bp):
TTTTGTCTTAAAAAATGATTTTTCTTAAAATTGTTTTTAAAAGACATTTTTAGATATTCGACCTA
CCTAACCCAAAGGCCGATCAAC
Found at i:210401 original size:37 final size:37
Alignment explanation
Indices: 210341--210482 Score: 137
Period size: 37 Copynumber: 3.8 Consensus size: 37
210331 ACAACCTCAT
*
210341 TTAATACAGAGGATTTATCTCACTTGAGATTGTTTTTC
1 TTAAAACAGA-GATTTATCTCACTTGAGATTGTTTTTC
* *
210379 TTAAAAACAGA-ATTTGTCTCACTTGAGATAGTTTTTAC
1 TT-AAAACAGAGATTTATCTCACTTGAGATTGTTTTT-C
* * **
210417 TTGAAACAAGAAGATTTATTTCACTCAAGATTGTTTTTC
1 TTAAAAC-AG-AGATTTATCTCACTTGAGATTGTTTTTC
*
210456 TTAAAACA-AGATTTGA-CTCGCTTGAGA
1 TTAAAACAGAGATTT-ATCTCACTTGAGA
210483 CGATTTTTAC
Statistics
Matches: 84, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
36 13 0.15
37 28 0.33
38 8 0.10
39 15 0.18
40 20 0.24
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.39
Consensus pattern (37 bp):
TTAAAACAGAGATTTATCTCACTTGAGATTGTTTTTC
Found at i:210514 original size:76 final size:77
Alignment explanation
Indices: 210353--210530 Score: 211
Period size: 76 Copynumber: 2.3 Consensus size: 77
210343 AATACAGAGG
* ** * *
210353 ATTTATCTCACTTGAGATTGTTTTTCTTAAAAACAGAATTTGTCTCACTTGAGATAGTTTTTACT
1 ATTTATTTCACTCAAGATTGTTTTTCTTAAAAACAGAATTTGACTCACTTGAGAGAGTTTTTACT
** *
210418 TGAAACAAGAAG
66 CAAAACAAGAAC
*
210430 ATTTATTTCACTCAAGATTGTTTTTCTT-AAAACA-AGATTTGACTCGCTTGAGACGA-TTTTTA
1 ATTTATTTCACTCAAGATTGTTTTTCTTAAAAACAGA-ATTTGACTCACTTGAGA-GAGTTTTTA
*
210492 CTCAAAATAAG-AC
64 CTCAAAACAAGAAC
210505 ATTTCATTTCACTCAAGATTGTTTTT
1 ATTT-ATTTCACTCAAGATTGTTTTT
210531 AAAGAAGATT
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
75 6 0.07
76 56 0.64
77 26 0.30
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (77 bp):
ATTTATTTCACTCAAGATTGTTTTTCTTAAAAACAGAATTTGACTCACTTGAGAGAGTTTTTACT
CAAAACAAGAAC
Found at i:210585 original size:39 final size:39
Alignment explanation
Indices: 210531--210751 Score: 238
Period size: 39 Copynumber: 5.8 Consensus size: 39
210521 GATTGTTTTT
210531 AAAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAA
1 AAAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAA
*
210570 AAAGAATATTTTATCTCGCTTGAGATAGTTTCCCTCGAA
1 AAAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAA
* * * * *
210609 ACAGAAGATTTTGTATTGCTTGAGATAGTTTCTCTCGAA
1 AAAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAA
* * *
210648 ACAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTG--
1 AAAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAA
* * * * *
210685 AAACAA-ATCTT-TCTCTCTTGAGACAGTTTCCCTTGAA
1 AAAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAA
* * *
210722 ACAATAA-A-TGTATCTCGCTTGAGATGGTTT
1 A-AAGAAGATTTTATCTCGCTTGAGATAGTTT
210752 TTCTTAAAAC
Statistics
Matches: 156, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
35 22 0.14
36 4 0.03
37 6 0.04
38 20 0.13
39 104 0.67
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (39 bp):
AAAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAA
Found at i:210779 original size:74 final size:73
Alignment explanation
Indices: 210661--210800 Score: 192
Period size: 74 Copynumber: 1.9 Consensus size: 73
210651 GAAGATTTTG
* * *
210661 TCTCGCTTGAGATAGTTTCCCTTGAAACAAATCTTTCTCTCTTGAGACAGTTTCCCTTGAAACAA
1 TCTCGCTTGAGATAGTTTCCCTTAAAACAAATCTTTCTCGCTTGAGACAATTTCCCTTGAAACAA
210726 TAAATGTA
66 TAAATGTA
* ** *
210734 TCTCGCTTGAGATGGTTTTTCTTAAAACCAAT-TTCGTCTCGCTTGAGACAATTTCCCTTGAAAC
1 TCTCGCTTGAGATAGTTTCCCTTAAAACAAATCTT--TCTCGCTTGAGACAATTTCCCTTGAAAC
210798 AAT
64 AAT
210801 TTCTCTCTCT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
72 2 0.03
73 27 0.47
74 29 0.50
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.36
Consensus pattern (73 bp):
TCTCGCTTGAGATAGTTTCCCTTAAAACAAATCTTTCTCGCTTGAGACAATTTCCCTTGAAACAA
TAAATGTA
Found at i:210799 original size:15 final size:15
Alignment explanation
Indices: 210775--210850 Score: 53
Period size: 15 Copynumber: 4.7 Consensus size: 15
210765 TTTCGTCTCG
*
210775 CTTGAGACAATTTCC
1 CTTGAAACAATTTCC
210790 CTTGAAACAATTTCTCTCTC
1 CTTGAAACAA--T-T-TC-C
* * *
210810 TCTTGAGACAGTTTCT
1 -CTTGAAACAATTTCC
*
210826 CTTGAAACAGTTTCC
1 CTTGAAACAATTTCC
210841 CTTGAAACAA
1 CTTGAAACAA
210851 GAAATGTATC
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
15 31 0.65
17 3 0.06
18 2 0.04
19 3 0.06
20 1 0.02
21 8 0.17
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.36
Consensus pattern (15 bp):
CTTGAAACAATTTCC
Found at i:210815 original size:36 final size:36
Alignment explanation
Indices: 210538--210839 Score: 175
Period size: 39 Copynumber: 8.1 Consensus size: 36
210528 TTTAAAGAAG
* * *
210538 ATTT-TATCTCGCTTGAGATAGTTTCCCTCGAAAAAGA
1 ATTTCTATCTCGCTTGAGACAGTTTCCCTTG--AAACA
* * *
210575 ATATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAA
1 AT-TTCTATCTCGCTTGAGACAGTTTCCCTTGAAAC---A
* * * *
210615 GATTTTGTAT-T-GCTTGAGATAGTTTCTCTCGAAACAGAA
1 -A-TTTCTATCTCGCTTGAGACAGTTTCCCTTGAAAC---A
* *
210654 GATTT-TGTCTCGCTTGAGATAGTTTCCCTTGAAACA
1 -ATTTCTATCTCGCTTGAGACAGTTTCCCTTGAAACA
* * *
210690 A-ATCTTTCTCTCTTGAGACAGTTTCCCTTGAAACA
1 ATTTCTATCTCGCTTGAGACAGTTTCCCTTGAAACA
* * ** ** *
210725 ATAAATGTATCTCGCTTGAGATGGTTTTTCTTAAAACCA
1 AT--TTCTATCTCGCTTGAGACAGTTTCCCTTGAAA-CA
* *
210764 ATTTC-GTCTCGCTTGAGACAATTTCCCTTGAAACA
1 ATTTCTATCTCGCTTGAGACAGTTTCCCTTGAAACA
* * *
210799 ATTTCTCTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 ATTTCTATCTCGCTTGAGACAGTTTCCCTTGAAACA
*
210835 GTTTC
1 ATTTC
210840 CCTTGAAACA
Statistics
Matches: 218, Mismatches: 32, Indels: 31
0.78 0.11 0.11
Matches are distributed among these distances:
34 1 0.00
35 37 0.17
36 52 0.24
37 8 0.04
38 30 0.14
39 81 0.37
40 2 0.01
41 6 0.03
42 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (36 bp):
ATTTCTATCTCGCTTGAGACAGTTTCCCTTGAAACA
Found at i:211456 original size:12 final size:13
Alignment explanation
Indices: 211433--211465 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
211423 GGCTTAAAAA
211433 ATATTATATTATT
1 ATATTATATTATT
211446 ATATT-TATTATT
1 ATATTATATTATT
211458 ATTATTAT
1 A-TATTAT
211466 TAGTAGTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.44
13 9 0.50
14 1 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATATTATATTATT
Found at i:213636 original size:88 final size:87
Alignment explanation
Indices: 213483--213657 Score: 280
Period size: 88 Copynumber: 2.0 Consensus size: 87
213473 AAGCACAGAC
** *
213483 CAACTTTTGTCTTAAAAACGATTTTTTCTTAAAATTGTTTTTAAAAGATGTTTTTAGGTGTTCGA
1 CAACTTTTGTCTTAAAAACGATTTTTTCTTAAAATTGTTTTTAAAAGACATTTTTAGGTATTCGA
213548 CCTACCTAACCCAAAGGCCGAT
66 CCTACCTAACCCAAAGGCCGAT
*
213570 CAACTTTTGTCTTAAAAAATGA-TTTTTCTTAAAATTGTTTTTTAAAAGACATTTTTAGGTATTC
1 CAACTTTTGTCTT-AAAAACGATTTTTTCTTAAAATTG-TTTTTAAAAGACATTTTTAGGTATTC
*
213634 GACCTACCTAACCCAAAGGTCGAT
64 GACCTACCTAACCCAAAGGCCGAT
213658 GGCGACTCTA
Statistics
Matches: 81, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
87 28 0.35
88 53 0.65
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (87 bp):
CAACTTTTGTCTTAAAAACGATTTTTTCTTAAAATTGTTTTTAAAAGACATTTTTAGGTATTCGA
CCTACCTAACCCAAAGGCCGAT
Found at i:217283 original size:12 final size:12
Alignment explanation
Indices: 217266--217292 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
217256 AATGATTTTA
217266 TTTATAATTAGT
1 TTTATAATTAGT
217278 TTTATAATTAGT
1 TTTATAATTAGT
217290 TTT
1 TTT
217293 TGAATCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (12 bp):
TTTATAATTAGT
Found at i:224673 original size:18 final size:18
Alignment explanation
Indices: 224650--224684 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
224640 TTCCATCCGG
*
224650 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
224668 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
224685 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:226013 original size:18 final size:18
Alignment explanation
Indices: 225987--226057 Score: 80
Period size: 18 Copynumber: 4.2 Consensus size: 18
225977 AACGGTCAAT
*
225987 GGGTCAACGGGTCGGGTC
1 GGGTAAACGGGTCGGGTC
226005 GGGTAAA-----CGGGTC
1 GGGTAAACGGGTCGGGTC
226018 GGGTAAACGGGTCGGGTC
1 GGGTAAACGGGTCGGGTC
* *
226036 GGGTCAACGGTTCGGGTC
1 GGGTAAACGGGTCGGGTC
226054 GGGT
1 GGGT
226058 TGTGACCGGT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
13 13 0.29
18 32 0.71
ACGTcount: A:0.14, C:0.18, G:0.49, T:0.18
Consensus pattern (18 bp):
GGGTAAACGGGTCGGGTC
Found at i:226015 original size:13 final size:13
Alignment explanation
Indices: 225999--226034 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
225989 GTCAACGGGT
225999 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
226012 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
226025 CGGGTCGGGT
1 CGGGTCGGGT
226035 CGGGTCAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:226029 original size:31 final size:31
Alignment explanation
Indices: 225987--226052 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
225977 AACGGTCAAT
*
225987 GGGTCAACGGGTCGGGTCGGGTAAACGGGTC
1 GGGTAAACGGGTCGGGTCGGGTAAACGGGTC
* *
226018 GGGTAAACGGGTCGGGTCGGGTCAACGGTTC
1 GGGTAAACGGGTCGGGTCGGGTAAACGGGTC
226049 GGGT
1 GGGT
226053 CGGGTTGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.15, C:0.18, G:0.48, T:0.18
Consensus pattern (31 bp):
GGGTAAACGGGTCGGGTCGGGTAAACGGGTC
Found at i:229844 original size:18 final size:18
Alignment explanation
Indices: 229821--229855 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
229811 TTCCATCCGG
*
229821 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
229839 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
229856 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:231157 original size:8 final size:8
Alignment explanation
Indices: 231124--231178 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
231114 TCAAAGTTTT
231124 GGTCAACAG
1 GGTCAAC-G
231133 TGGTCAACG
1 -GGTCAACG
231142 ACGGTCAACG
1 --GGTCAACG
231152 GGTCAAC-
1 GGTCAACG
*
231159 GGTCAATG
1 GGTCAACG
231167 GGTCAACG
1 GGTCAACG
231175 GGTC
1 GGTC
231179 GGGTCGGGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 6 0.15
8 18 0.45
9 1 0.03
10 15 0.38
ACGTcount: A:0.25, C:0.24, G:0.35, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:231162 original size:15 final size:15
Alignment explanation
Indices: 231142--231175 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
231132 GTGGTCAACG
231142 ACGGTCAACGGGTCA
1 ACGGTCAACGGGTCA
*
231157 ACGGTCAATGGGTCA
1 ACGGTCAACGGGTCA
231172 ACGG
1 ACGG
231176 GTCGGGTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.24, G:0.35, T:0.15
Consensus pattern (15 bp):
ACGGTCAACGGGTCA
Found at i:231192 original size:18 final size:18
Alignment explanation
Indices: 231166--231223 Score: 98
Period size: 18 Copynumber: 3.2 Consensus size: 18
231156 AACGGTCAAT
231166 GGGTCAACGGGTCGGGTC
1 GGGTCAACGGGTCGGGTC
* *
231184 GGGTAAACGGGTCGGGTT
1 GGGTCAACGGGTCGGGTC
231202 GGGTCAACGGGTCGGGTC
1 GGGTCAACGGGTCGGGTC
231220 GGGT
1 GGGT
231224 TGTGACTGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.12, C:0.17, G:0.52, T:0.19
Consensus pattern (18 bp):
GGGTCAACGGGTCGGGTC
Found at i:235025 original size:18 final size:18
Alignment explanation
Indices: 235002--235036 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
234992 TTCCATCCGG
*
235002 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
235020 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
235037 GTCCTTTTCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:236354 original size:18 final size:18
Alignment explanation
Indices: 236333--236390 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
236323 GACGGTCAAT
236333 GGGTCAACGGGTCGGGTC
1 GGGTCAACGGGTCGGGTC
*
236351 GGGTCAACGGGTCAGGTC
1 GGGTCAACGGGTCGGGTC
236369 GGGTCAACGGGTCGGGTC
1 GGGTCAACGGGTCGGGTC
236387 GGGT
1 GGGT
236391 TGTGACAGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.12, C:0.21, G:0.50, T:0.17
Consensus pattern (18 bp):
GGGTCAACGGGTCGGGTC
Done.