Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000536.1 Hibiscus syriacus cultivar Beakdansim tig00001033_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: 82734
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2275 original size:9 final size:9
Alignment explanation
Indices: 2261--2301 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
2251 AAATGGCAAT
2261 CATTCTTTA
1 CATTCTTTA
*
2270 CATTCTTCA
1 CATTCTTTA
*
2279 CATTTTTTA
1 CATTCTTTA
2288 CATTCTTTA
1 CATTCTTTA
*
2297 TATTC
1 CATTC
2302 ATTATTCTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (9 bp):
CATTCTTTA
Found at i:5791 original size:7 final size:7
Alignment explanation
Indices: 5774--5807 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
5764 GAGTTGAGAA
5774 AAAAAAG
1 AAAAAAG
*
5781 AAAAAGAA
1 AAAAA-AG
5789 AAAAAAG
1 AAAAAAG
5796 AAAAAAG
1 AAAAAAG
5803 AAAAA
1 AAAAA
5808 TTGAAAGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:5793 original size:16 final size:16
Alignment explanation
Indices: 5770--5807 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
5760 AGAGGAGTTG
5770 AGAAAAAAAAG-AAAA
1 AGAAAAAAAAGAAAAA
5785 AGAAAAAAAAGAAAAA
1 AGAAAAAAAAGAAAAA
5801 AGAAAAA
1 AGAAAAA
5808 TTGAAAGGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAAGAAAAA
Found at i:7045 original size:20 final size:20
Alignment explanation
Indices: 6983--7045 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
6973 CAATGGAATG
*
6983 GTTCATAATGAGAATAACTT
1 GTTCATAATGAGAAGAACTT
* * *
7003 TTTCAAAGAGGGAGAAGAA---
1 GTTCATA-A-TGAGAAGAACTT
7022 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
7042 GTTC
1 GTTC
7046 GACCTTTTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 10
0.65 0.15 0.21
Matches are distributed among these distances:
17 8 0.26
18 1 0.03
19 5 0.16
20 9 0.29
21 1 0.03
22 7 0.23
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.29
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:7337 original size:121 final size:121
Alignment explanation
Indices: 7123--7663 Score: 581
Period size: 121 Copynumber: 4.5 Consensus size: 121
7113 AAGAAATCGA
* * *
7123 AAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTTGGTCAAATTCCATCACAGAAGGAGGTG
1 AAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTTGCTCAAAATCCATCACAGAATGAGGTG
* * * * *
7188 GATCGACATTTCCAATGGAATGGTTCATAATAAGAAAAACTC-ATCTGAAGAGGGAG
66 GATCAACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCGATCCGAAGA-GGAG
*
7244 AAGAAGTTCATAATGAGAAGAACTTGTTCGATCTTTTTGCTCAAAATCCATCACAGAATGAGGTG
1 AAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTTGCTCAAAATCCATCACAGAATGAGGTG
* * * * *
7309 GATCAACATTTCCAATGGAAGGGTTCATAATGAGTAGAACTTG-TCCAAATACAGAG
66 GATCAACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCGATCCGAAGA-GGAG
* *
7365 AAGAAGTTCATAATGAGAAGAACTTGTTC-ATCCTTTTTGCTCAAAATTCATCATAGAATGAGGT
1 AAGAAGTTCATAATGAGAAGAACTTGTTCGA-CCTTTTTGCTCAAAATCCATCACAGAATGAGGT
* * ** * *
7429 AGATCGACATTTCCAATGGAAGTATTAATAATGATAAGAACTCGA-CCGAATGAGGAG
65 GGATCAACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCGATCCGAA-GAGGAG
* * * * * * * * *
7486 GATAAGTTCATAATAAGAATAAATTATTCGACCTTTTTGCTCAAAATCCATCACAAAAAGAGGTA
1 AAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTTGCTCAAAATCCATCACAGAATGAGGTG
* * *
7551 TAT-AGGCATTTCCAAT-GAAGGGTTCATAATGAGAAGAA-TCTATCCG-A-AGG-G
66 GATCA-ACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCGATCCGAAGAGGAG
* * * *
7602 -AGAAGTTCATAATGAGAA-ACATTTGTTC-AAC-ATTTGCTCAAAAT-CATCACAAAATGAGGT
1 AAGAAGTTCATAATGAGAAGA-ACTTGTTCGACCTTTTTGCTCAAAATCCATCACAGAATGAGGT
7662 GG
65 GG
7664 GATAGCACTA
Statistics
Matches: 356, Mismatches: 56, Indels: 25
0.81 0.13 0.06
Matches are distributed among these distances:
112 15 0.04
113 12 0.03
114 3 0.01
115 22 0.06
116 1 0.00
117 3 0.01
119 4 0.01
120 22 0.06
121 272 0.76
122 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (121 bp):
AAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTTGCTCAAAATCCATCACAGAATGAGGTG
GATCAACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCGATCCGAAGAGGAG
Found at i:7393 original size:20 final size:20
Alignment explanation
Indices: 7331--7395 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
7321 CAATGGAAGG
*
7331 GTTCATAATGAGTAGAACTT
1 GTTCATAATGAGAAGAACTT
*
7351 GTCCA-AATACAGAGAAGAA---
1 GTTCATAAT---GAGAAGAACTT
7370 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
7390 GTTCAT
1 GTTCAT
7396 CCTTTTTGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
17 8 0.23
19 7 0.20
20 13 0.37
22 7 0.20
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:7563 original size:242 final size:241
Alignment explanation
Indices: 6935--7588 Score: 693
Period size: 242 Copynumber: 2.8 Consensus size: 241
6925 TTCTTACATA
* * * * * * * *
6935 CTCAAAATCCATCACAAAAGGAGGTGGATCGATATTTCCAATGGAATGGTTCATAATGAGAATAA
1 CTCAAATTCCATCACAGAAGGAGGTAGATCGACATTTCCAATGGAATGATTAATAATAAGAAAAA
** * * * * *
7000 CTTTTTCAAAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTTGCTCAAAATC
66 CTCATCCGAAGAGGGAGAAGAAGTTCATAATAAGAAGAAATTATTCGACCTTTTTGCTCAAAATC
* * * * * *
7065 CATCATAGAATG-TGT--ATCAACATTTCAAATGGAATGGTTCATAAT--G-AGAA---G---AA
131 CATCACAAAAAGAGGTAGATCAACATTTCCAAT-GAAGGGTTCATAATGAGAAGAACTTGTCCAA
7118 AT-C-GA-AAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTTG
195 ATACAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTTG
* * * *
7162 GTCAAATTCCATCACAGAAGGAGGTGGATCGACATTTCCAATGGAATGGTTCATAATAAGAAAAA
1 CTCAAATTCCATCACAGAAGGAGGTAGATCGACATTTCCAATGGAATGATTAATAATAAGAAAAA
* * * * *
7227 CTCATCTGAAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGATCTTTTTGCTCAAAATC
66 CTCATCCGAAGAGGGAGAAGAAGTTCATAATAAGAAGAAATTATTCGACCTTTTTGCTCAAAATC
* * * *
7292 CATCACAGAATGAGGTGGATCAACATTTCCAATGGAAGGGTTCATAATGAGTAGAACTTGTCCAA
131 CATCACAAAAAGAGGTAGATCAACATTTCCAAT-GAAGGGTTCATAATGAGAAGAACTTGTCCAA
7357 ATACAGAGAAGAAGTTCATAATGAGAAGAACTTGTTC-ATCCTTTTTG
195 ATACAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGA-CCTTTTTG
* * * * *
7404 CTCAAAATT-CATCATAGAATGAGGTAGATCGACATTTCCAATGGAA-GTATTAATAATGATAAG
1 CTC-AAATTCCATCACAGAAGGAGGTAGATCGACATTTCCAATGGAATG-ATTAATAATAAGAAA
* * *
7467 AACTCGA-CCGAATGA-GGAGGATAAGTTCATAATAAGAATAAATTATTCGACCTTTTTGCTCAA
64 AACTC-ATCCGAA-GAGGGAGAAGAAGTTCATAATAAGAAGAAATTATTCGACCTTTTTGCTCAA
* *
7530 AATCCATCACAAAAAGAGGTATAT-AGGCATTTCCAATGAAGGGTTCATAATGAGAAGAA
127 AATCCATCACAAAAAGAGGTAGATCA-ACATTTCCAATGAAGGGTTCATAATGAGAAGAA
7589 TCTATCCGAA
Statistics
Matches: 367, Mismatches: 39, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
227 129 0.35
228 2 0.01
230 28 0.08
232 1 0.00
233 4 0.01
236 1 0.00
239 4 0.01
240 1 0.00
241 26 0.07
242 163 0.44
243 8 0.02
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (241 bp):
CTCAAATTCCATCACAGAAGGAGGTAGATCGACATTTCCAATGGAATGATTAATAATAAGAAAAA
CTCATCCGAAGAGGGAGAAGAAGTTCATAATAAGAAGAAATTATTCGACCTTTTTGCTCAAAATC
CATCACAAAAAGAGGTAGATCAACATTTCCAATGAAGGGTTCATAATGAGAAGAACTTGTCCAAA
TACAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTTG
Found at i:7715 original size:27 final size:27
Alignment explanation
Indices: 7685--7736 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
7675 TAACAATGTT
7685 TACAGTGGAAGGAGCTCATTCAAACAA
1 TACAGTGGAAGGAGCTCATTCAAACAA
*
7712 TACAGTGGAAGGATCTCATTCAAAC
1 TACAGTGGAAGGAGCTCATTCAAAC
7737 GAGTGAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (27 bp):
TACAGTGGAAGGAGCTCATTCAAACAA
Found at i:7757 original size:18 final size:18
Alignment explanation
Indices: 7730--7793 Score: 103
Period size: 18 Copynumber: 3.6 Consensus size: 18
7720 AAGGATCTCA
*
7730 TTCA-AACGAGTGAAAAG
1 TTCATAACGAGCGAAAAG
7747 TTCATAACGAGCGAAAAG
1 TTCATAACGAGCGAAAAG
*
7765 TTTATAACGAGCGAAAAG
1 TTCATAACGAGCGAAAAG
7783 TTCATAACGAG
1 TTCATAACGAG
7794 AAGAATTTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
17 4 0.09
18 39 0.91
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (18 bp):
TTCATAACGAGCGAAAAG
Found at i:7919 original size:3 final size:3
Alignment explanation
Indices: 7911--7985 Score: 116
Period size: 3 Copynumber: 25.0 Consensus size: 3
7901 ATTTTTTACC
* *
7911 ATT ATT ATT TTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T GTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
7958 ATT ATAT ATT ATT ATT ATT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT
7986 TACATAAGTC
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
2 1 0.02
3 62 0.94
4 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:9798 original size:15 final size:15
Alignment explanation
Indices: 9749--9800 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
9739 TATTCGATTG
9749 ATTTAA-TTTTT-TT
1 ATTTAATTTTTTGTT
* *
9762 ATTTAAATTTTTGCT
1 ATTTAATTTTTTGTT
9777 ATTTAATTTTTTGTT
1 ATTTAATTTTTTGTT
9792 ATTTAATTT
1 ATTTAATTT
9801 ATGCCTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
13 6 0.18
14 5 0.15
15 23 0.68
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (15 bp):
ATTTAATTTTTTGTT
Found at i:12241 original size:139 final size:139
Alignment explanation
Indices: 11813--12385 Score: 685
Period size: 139 Copynumber: 4.2 Consensus size: 139
11803 GAATAATTTT
* * *
11813 ATAATTGATTAAAATTTATTAGGATAAATATTAGAGCCTCCACTTTAGGCTTAATTTCAATTTTA
1 ATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCACTTTAGGCTTAATTTCAATCTTA
* * * * * * *
11878 GTCCTTAAATTTAAGTGAATTCTT-A-GT-GTCCTTGCTTTTGCTCGAGGTTTCATTTTCATTAT
66 GTCCTTAAATTTAGGGGAATTCTTAATTTGGTCCTCGCTTTTGCTCAAGGTTCCATTTTAATTAT
* ***
11940 TCAAATTTT
131 TCGAATCAC
* * * * *
11949 ATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCATTTTAGGCTTAACTTCAAACCTG
1 ATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCACTTTAGGCTTAATTTCAATCTTA
* *
12014 GTCCTTAAATTTAGGGGAATT-TTAATTTGG-CCATTGCTTTTGCTCAAGGTTTCATTTTAATTA
66 GTCCTTAAATTTAGGGGAATTCTTAATTTGGTCC-TCGCTTTTGCTCAAGGTTCCATTTTAATTA
*
12077 TTCGGATCAC
130 TTCGAATCAC
* * * *
12087 ATAATTGATTGAAATTAATTAGG-TTGATAACTAGAGCCTCCACTTTAGGTTTAATTTCACA-CT
1 ATAATTGATTAAAATTAATTAGGATTAAT-ATTAGAGCCTCCACTTTAGGCTTAATTTCA-ATCT
* *
12150 TACTCCTTAAATTTAGGGGAATTTTTAATTTGGTCCTCGCTTTTGC-CTAAGGTTCCATTTTAAT
64 TAGTCCTTAAATTTAGGGGAATTCTTAATTTGGTCCTCGCTTTTGCTC-AAGGTTCCATTTTAAT
12214 TATTCGAATCAC
128 TATTCGAATCAC
* * * *
12226 ATAATTAATTAAAATTGATTAGGATTAATATTAGAGCCTCCACTTTAAGCTTAATTTCAATTTTA
1 ATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCACTTTAGGCTTAATTTCAATCTTA
** * *
12291 GAGCTTAAATTTAGGTGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAATTAT
66 GTCCTTAAATTTAGGGGAATTCTTAATTTGGTCCTCGCTTTTGCTCAAGGTTCCATTTTAATTAT
* *
12356 TTGAATCAA
131 TCGAATCAC
* * *
12365 AGAATTGGTTAAAATTGATTA
1 ATAATTGATTAAAATTAATTA
12386 AGTTAATTTT
Statistics
Matches: 376, Mismatches: 49, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
135 2 0.01
136 77 0.20
137 7 0.02
138 106 0.28
139 177 0.47
140 7 0.02
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (139 bp):
ATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCACTTTAGGCTTAATTTCAATCTTA
GTCCTTAAATTTAGGGGAATTCTTAATTTGGTCCTCGCTTTTGCTCAAGGTTCCATTTTAATTAT
TCGAATCAC
Found at i:12304 original size:277 final size:275
Alignment explanation
Indices: 11813--12385 Score: 679
Period size: 277 Copynumber: 2.1 Consensus size: 275
11803 GAATAATTTT
* * *
11813 ATAATTGATTAAAATTTATTAGGATAAATATTAGAGCCTCCACTTTAGGCTTAATTTCAATTTTA
1 ATAATTGATTAAAATTAATTAGGATAAATACTAGAGCCTCCACTTTAGGCTTAATTTCAATCTTA
* * * * * *
11878 GTCCTTAAATTTAAGTGAATTCTTAGTGTCCTTGCTTTTGCTCGAGGTTTCATTTTCATTATTCA
66 CTCCTTAAATTTAAGGGAATTCTTAGTGTCCTCGCTTTTGCTCAAGGTTCCATTTTAATTATTCA
*** * * *
11943 AATTTTATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCATTTTAGGCTTAACTTCA
131 AATCACATAATTAATTAAAATTAATTAGGATTAATATTAGAGCCTCCACTTTAAGCTTAACTTCA
* * * *
12008 AACCTGGTCCTTAAATTTAGGGGAATT-TTAATTTGG-CCATTGCTTTTGCTCAAGGTTTCATTT
196 AACCTAGACCTTAAATTTAGGGGAATTCTTAATTTGGTCC-TCGCTTTTGCTCAAGGTTCCATTT
12071 TAATTATTCGGATCAC
260 TAATTATTCGGATCAC
* ** *
12087 ATAATTGATTGAAATTAATTAGG-TTGATAACTAGAGCCTCCACTTTAGGTTTAATTTCACA-CT
1 ATAATTGATTAAAATTAATTAGGATAAAT-ACTAGAGCCTCCACTTTAGGCTTAATTTCA-ATCT
* * *
12150 TACTCCTTAAATTTAGGGGAATTTTTAATTTGGTCCTCGCTTTTGC-CTAAGGTTCCATTTTAAT
64 TACTCCTTAAATTTAAGGGAATTCTT-A-GT-GTCCTCGCTTTTGCTC-AAGGTTCCATTTTAAT
* *
12214 TATTCGAATCACATAATTAATTAAAATTGATTAGGATTAATATTAGAGCCTCCACTTTAAGCTTA
125 TATTCAAATCACATAATTAATTAAAATTAATTAGGATTAATATTAGAGCCTCCACTTTAAGCTTA
* *** * * *
12279 ATTTCAATTTTAGAGCTTAAATTTAGGTGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTC
190 ACTTCAAACCTAGACCTTAAATTTAGGGGAATTCTTAATTTGGTCCTCGCTTTTGCTCAAGGTTC
* * *
12344 CATTTTAATTATTTGAATCAA
255 CATTTTAATTATTCGGATCAC
* * *
12365 AGAATTGGTTAAAATTGATTA
1 ATAATTGATTAAAATTAATTA
12386 AGTTAATTTT
Statistics
Matches: 249, Mismatches: 42, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
273 3 0.01
274 72 0.29
275 2 0.01
276 2 0.01
277 108 0.43
278 60 0.24
279 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (275 bp):
ATAATTGATTAAAATTAATTAGGATAAATACTAGAGCCTCCACTTTAGGCTTAATTTCAATCTTA
CTCCTTAAATTTAAGGGAATTCTTAGTGTCCTCGCTTTTGCTCAAGGTTCCATTTTAATTATTCA
AATCACATAATTAATTAAAATTAATTAGGATTAATATTAGAGCCTCCACTTTAAGCTTAACTTCA
AACCTAGACCTTAAATTTAGGGGAATTCTTAATTTGGTCCTCGCTTTTGCTCAAGGTTCCATTTT
AATTATTCGGATCAC
Found at i:12565 original size:22 final size:22
Alignment explanation
Indices: 12540--12588 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
12530 TAATATTAGA
12540 GCCTACATTTTTAGGTTTAATT
1 GCCTACATTTTTAGGTTTAATT
12562 GCCTACATTTTTAGGTTTAATT
1 GCCTACATTTTTAGGTTTAATT
12584 GCCTA
1 GCCTA
12589 GGTTCTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.47
Consensus pattern (22 bp):
GCCTACATTTTTAGGTTTAATT
Found at i:13588 original size:83 final size:80
Alignment explanation
Indices: 13483--13702 Score: 215
Period size: 80 Copynumber: 2.7 Consensus size: 80
13473 CTTTAGCGGT
* * *
13483 GTTTCTTTATAAACACCACAATAGGGTTCATCTATAGTGTCTTTTTTTAGAAAAACGCCGCAACA
1 GTTTCTATATAAACACCGCAATA-GGTTCATCTATAGTGAC-TTTTTTA-AAAAACGCCGCAACA
*
13548 GAGTAGTACTTCACCGGC
63 GAGTAGTACTTAACCGGC
* * * * * * * * *
13566 GTTTCTATACAAACACCGCAATAGGTCCATCTATAGTGGCATTTTTAATAAACGTCGTAACATAT
1 GTTTCTATATAAACACCGCAATAGGTTCATCTATAGTGACTTTTTTAAAAAACGCCGCAACAGAG
*
13631 TAGTACTTAAGCGGC
66 TAGTACTTAACCGGC
* * * * *
13646 GTTTTTATGTAAACGCCGCAATAAGGTTCACCTATAGTGACATTTTTTCAATAAACG
1 GTTTCTATATAAACACCGCAAT-AGGTTCATCTATAGTGAC-TTTTTT-AAAAAACG
13703 TTATAACAGA
Statistics
Matches: 113, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
80 44 0.39
81 21 0.19
82 20 0.18
83 28 0.25
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (80 bp):
GTTTCTATATAAACACCGCAATAGGTTCATCTATAGTGACTTTTTTAAAAAACGCCGCAACAGAG
TAGTACTTAACCGGC
Found at i:13665 original size:80 final size:80
Alignment explanation
Indices: 13472--13857 Score: 245
Period size: 82 Copynumber: 4.7 Consensus size: 80
13462 CAAAATGGTA
* * * * * *
13472 ACTTTAGCGGTGTTTCTT-TATAAACACCACAATAGGGTTCATCTATAGTGTCTTTTTTTAGAAA
1 ACTTAAGCGGCGTTT-TTATATAAACACCGCAATA-GGTTCATCTATAGTGAC-ATTTTTA-ATA
* * *
13536 AACGCCGCAACAGAGTAGT
62 AACGTCGTAACAGATTAGT
* * * * * *
13555 ACTTCACCGGCGTTTCTATACAAACACCGCAATAGGTCCATCTATAGTGGCATTTTTAATAAACG
1 ACTTAAGCGGCGTTTTTATATAAACACCGCAATAGGTTCATCTATAGTGACATTTTTAATAAACG
*
13620 TCGTAACATATTAGT
66 TCGTAACAGATTAGT
* * *
13635 ACTTAAGCGGCGTTTTTATGTAAACGCCGCAATAAGGTTCACCTATAGTGACATTTTTTCAATAA
1 ACTTAAGCGGCGTTTTTATATAAACACCGCAAT-AGGTTCATCTATAGTGACA-TTTTT-AATAA
** **
13700 ACGTTATAACAGATTAAA
63 ACGTCGTAACAGATTAGT
* * * * * * * * * *
13718 ACTTTAGCGGCATTTTTATACAAAC-GCGATAATAGAGTTCACCTATAATGGCTTTTTTCAGTAA
1 ACTTAAGCGGCGTTTTTATATAAACACCG-CAATAG-GTTCATCTATAGTGACATTTTT-AATAA
** * *
13782 ACACCGCAATAGATTAGT
63 ACGTCGTAACAGATTAGT
** * * ** * * *
13800 ACTTTCGCGGTGTTTTTATACAAACATTGTAATAGGGTTCACCTATAGTGGCATTTTT
1 ACTTAAGCGGCGTTTTTATATAAACACCGCAATA-GGTTCATCTATAGTGACATTTTT
13858 TCTCACGAAC
Statistics
Matches: 242, Mismatches: 53, Indels: 17
0.78 0.17 0.05
Matches are distributed among these distances:
80 44 0.18
81 22 0.09
82 92 0.38
83 84 0.35
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (80 bp):
ACTTAAGCGGCGTTTTTATATAAACACCGCAATAGGTTCATCTATAGTGACATTTTTAATAAACG
TCGTAACAGATTAGT
Found at i:13727 original size:83 final size:82
Alignment explanation
Indices: 13562--13859 Score: 253
Period size: 82 Copynumber: 3.6 Consensus size: 82
13552 AGTACTTCAC
* * * * *
13562 CGGCGTTTCTATACAAACACCGCAATAGGTCCATCTATAGTGGCA-TTTTT-AATAAACGTCGTA
1 CGGCGTTTTTATACAAACGCCGCAATAGGTTCACCTATAGTGGCATTTTTTCAATAAACGTCATA
* **
13625 ACATATTAGTACTTAAG
66 ACAGATTAAAACTTAAG
** * *
13642 CGGCGTTTTTATGTAAACGCCGCAATAAGGTTCACCTATAGTGACATTTTTTCAATAAACGTTAT
1 CGGCGTTTTTATACAAACGCCGCAAT-AGGTTCACCTATAGTGGCATTTTTTCAATAAACGTCAT
*
13707 AACAGATTAAAACTTTAG
65 AACAGATTAAAACTTAAG
* * * * ** *
13725 CGGCATTTTTATACAAACG-CGATAATAGAGTTCACCTATAATGGC-TTTTTTCAGTAAACACCG
1 CGGCGTTTTTATACAAACGCCG-CAATAG-GTTCACCTATAGTGGCATTTTTTCAATAAACGTCA
* * ** **
13788 CAATAGATTAGTACTTTCG
64 TAACAGATTAAAACTTAAG
* *** *
13807 CGGTGTTTTTATACAAACATTGTAATAGGGTTCACCTATAGTGGCATTTTTTC
1 CGGCGTTTTTATACAAACGCCGCAATA-GGTTCACCTATAGTGGCATTTTTTC
13860 TCACGAACAC
Statistics
Matches: 176, Mismatches: 34, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
80 22 0.12
81 16 0.09
82 72 0.41
83 66 0.38
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (82 bp):
CGGCGTTTTTATACAAACGCCGCAATAGGTTCACCTATAGTGGCATTTTTTCAATAAACGTCATA
ACAGATTAAAACTTAAG
Found at i:13906 original size:84 final size:81
Alignment explanation
Indices: 13629--13911 Score: 216
Period size: 82 Copynumber: 3.4 Consensus size: 81
13619 GTCGTAACAT
* ** * * *
13629 ATTAGTACTTAAGCGGCGTTTTTATGTAAACGCCG-CAATA-AGGTTCACCTATAGTGACATTTT
1 ATTAGTACTTTAGCGGCGTTTTTATACAAACG-CGATAATAGA-GTTCACCTATAATGGC-TTTT
* *** * *
13692 TTCAATAAACGTTATAACAG
63 TTC-AGAAACACCACAATAG
** *
13712 ATTAAAACTTTAGCGGCATTTTTATACAAACGCGATAATAGAGTTCACCTATAATGGCTTTTTTC
1 ATTAGTACTTTAGCGGCGTTTTTATACAAACGCGATAATAGAGTTCACCTATAATGGCTTTTTTC
*
13777 AGTAAACACCGCAATAG
66 AG-AAACACCACAATAG
* * ** * *
13794 ATTAGTACTTTCGCGGTGTTTTTATACAAACATTG-TAATAGGGTTCACCTATAGTGGCATTTTT
1 ATTAGTACTTTAGCGGCGTTTTTATACAAAC-GCGATAATAGAGTTCACCTATAATGGC--TTTT
13858 TCTCACG-AACACCACAATAG
63 T-TCA-GAAACACCACAATAG
* *
13878 -TGTAGTGCTTTAGCGCCGTTTTTATACAAACGCG
1 AT-TAGTACTTTAGCGGCGTTTTTATACAAACGCG
13912 CAATAGCTTT
Statistics
Matches: 159, Mismatches: 32, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
81 1 0.01
82 64 0.40
83 47 0.30
84 43 0.27
85 3 0.02
86 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (81 bp):
ATTAGTACTTTAGCGGCGTTTTTATACAAACGCGATAATAGAGTTCACCTATAATGGCTTTTTTC
AGAAACACCACAATAG
Found at i:17377 original size:11 final size:11
Alignment explanation
Indices: 17361--17403 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
17351 CTCATAATTG
*
17361 AAAGAAAACCA
1 AAAGAAAACCT
*
17372 AAAGAAAAACTT
1 AAAG-AAAACCT
17384 AAAGAAAACCT
1 AAAGAAAACCT
*
17395 AATGAAAAC
1 AAAGAAAAC
17404 TTGATTTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.67, C:0.14, G:0.09, T:0.09
Consensus pattern (11 bp):
AAAGAAAACCT
Found at i:26447 original size:42 final size:42
Alignment explanation
Indices: 26381--26664 Score: 277
Period size: 42 Copynumber: 6.7 Consensus size: 42
26371 TAATTAGCGG
* *
26381 CATTTGTATCCAAAAAACACCGCTATAGATCTGACCTTTTGCGA
1 CATTTGT-TCC-AAAAACGCCGCTATAGATCTAACCTTTTGCGA
* * * * * * *
26425 CGTTTGTTACAAAATCGTCGCTATAGACCTAACTTTTTAC-A
1 CATTTGTTCCAAAAACGCCGCTATAGATCTAACCTTTTGCGA
*
26466 GCATTTGTATCCAAAAACGCCGCTATAGATCTAACCTTTTGCGG
1 -CATTTGT-TCCAAAAACGCCGCTATAGATCTAACCTTTTGCGA
* * * *
26510 CGTTTGTTCCAAAAACGACGCTATAGATCTGACTTTTTGC-A
1 CATTTGTTCCAAAAACGCCGCTATAGATCTAACCTTTTGCGA
** * *
26551 GCGA-TTGTTCCAAAAAAACCGCTATAGATCTCAATCTTTTGCGG
1 -C-ATTTGTTCCAAAAACGCCGCTATAGATCT-AACCTTTTGCGA
* * *
26595 CATTTGTTCCAAAAACGCTGCTATAGATCTGACCTTTTGCGG
1 CATTTGTTCCAAAAACGCCGCTATAGATCTAACCTTTTGCGA
* *
26637 CATTTGTTCCAAAAATGCCGCTACAGAT
1 CATTTGTTCCAAAAACGCCGCTATAGAT
26665 AAAGAACTTT
Statistics
Matches: 194, Mismatches: 38, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
41 1 0.01
42 120 0.62
43 67 0.35
44 6 0.03
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.32
Consensus pattern (42 bp):
CATTTGTTCCAAAAACGCCGCTATAGATCTAACCTTTTGCGA
Found at i:26532 original size:85 final size:83
Alignment explanation
Indices: 26380--26684 Score: 351
Period size: 85 Copynumber: 3.6 Consensus size: 83
26370 GTAATTAGCG
* * * *
26380 GCATTTGTATCCAAAAAACACCGCTATAGATCTGACCTTTTGCGACGTTTGTTACAAAATCGTCG
1 GCATTTGT-TCC-AAAAACACCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCCAAAAACG-CG
* * *
26445 CTATAGACCTAACTTTTTACA
63 CTATAGATCTGACTTTTTGCA
*
26466 GCATTTGTATCCAAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCCAAAAACGACGC
1 GCATTTGT-TCCAAAAACACCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCCAAAAACG-CGC
26531 TATAGATCTGACTTTTTGCA
64 TATAGATCTGACTTTTTGCA
* * *
26551 GCGA-TTGTTCCAAAAAAACCGCTATAGATCTCAATCTTTTGCGGCATTTGTTCCAAAAACGCTG
1 GC-ATTTGTTCCAAAAACACCGCTATAGATCT-AACCTTTTGCGGCGTTTGTTCCAAAAACGC-G
* *
26615 CTATAGATCTGACCTTTTGCG
63 CTATAGATCTGACTTTTTGCA
** * ** *
26636 GCATTTGTTCCAAAAATGCCGCTACAGATAAAGAACTTTTGCGGCGTTT
1 GCATTTGTTCCAAAAACACCGCTATAGATCTA-ACCTTTTGCGGCGTTT
26685 TTTATTCTCA
Statistics
Matches: 192, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
84 24 0.12
85 155 0.81
86 13 0.07
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (83 bp):
GCATTTGTTCCAAAAACACCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCCAAAAACGCGCTA
TAGATCTGACTTTTTGCA
Found at i:26659 original size:127 final size:127
Alignment explanation
Indices: 26377--26664 Score: 357
Period size: 127 Copynumber: 2.3 Consensus size: 127
26367 AAGGTAATTA
* * ***
26377 GCGGCATTTGTATCCAAAAAACACCGCTATAGATCTGACCTTTTGCGACGTTTGTTACAAAATCG
1 GCGGCATTTGT-TCC-AAAAACGCCGCTATAGATCTGACCTTTTGCGACGATTGTTACAAAAAAA
*
26442 TCGCTATAGACCTAACTTTTTACAGCATTTGTATCCAAAAACGCCGCTATAGATCTAACCTTTT
64 CCGCTATAGACCTAACTTTTTACAGCATTTGTATCCAAAAACGCCGCTATAGATCTAACCTTTT
* * * *
26506 GCGGCGTTTGTTCCAAAAACGACGCTATAGATCTGACTTTTTGC-AGCGATTGTTCCAAAAAAAC
1 GCGGCATTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGA-CGATTGTTACAAAAAAAC
* * * * *
26570 CGCTATAGATCTCAA-TCTTTTGCGGCATTTGT-TCCAAAAACGCTGCTATAGATCTGACCTTTT
65 CGCTATAGACCT-AACT-TTTTACAGCATTTGTATCCAAAAACGCCGCTATAGATCTAACCTTTT
* *
26633 GCGGCATTTGTTCCAAAAATGCCGCTACAGAT
1 GCGGCATTTGTTCCAAAAACGCCGCTATAGAT
26665 AAAGAACTTT
Statistics
Matches: 137, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
126 1 0.01
127 108 0.79
128 18 0.13
129 10 0.07
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (127 bp):
GCGGCATTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGACGATTGTTACAAAAAAACC
GCTATAGACCTAACTTTTTACAGCATTTGTATCCAAAAACGCCGCTATAGATCTAACCTTTT
Found at i:28189 original size:28 final size:28
Alignment explanation
Indices: 28157--28213 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
28147 CCGCCTTTAT
28157 TTTCAAGCA-CTGACTCGACAACATAATG
1 TTTCAAGCATCTG-CTCGACAACATAATG
* *
28185 TTTCAAGCATTTGCTCTACAACATAATG
1 TTTCAAGCATCTGCTCGACAACATAATG
28213 T
1 T
28214 AATCAGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (28 bp):
TTTCAAGCATCTGCTCGACAACATAATG
Found at i:28413 original size:2 final size:2
Alignment explanation
Indices: 28406--28441 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28396 CACATAGTGT
28406 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28442 CGAACCATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29348 original size:3 final size:3
Alignment explanation
Indices: 29340--29384 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
29330 GATATTCTAT
* *
29340 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29385 CATTATAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:30882 original size:22 final size:23
Alignment explanation
Indices: 30852--30905 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
30842 GCCATGACAT
*
30852 TTGTATATAGTTTA-TTTTAATCA
1 TTGT-TATAGTTTAGGTTTAATCA
*
30875 TTGTTATA-TTTAGGTTTAATTA
1 TTGTTATAGTTTAGGTTTAATCA
30897 TTGTT-TAGT
1 TTGTTATAGT
30906 CCTCTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 6 0.22
22 17 0.63
23 4 0.15
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.59
Consensus pattern (23 bp):
TTGTTATAGTTTAGGTTTAATCA
Found at i:31072 original size:30 final size:30
Alignment explanation
Indices: 31024--31109 Score: 104
Period size: 29 Copynumber: 2.9 Consensus size: 30
31014 GATATTTATG
31024 TTTTTAGTCCCTTT-AGTTTCTGTTTTTGTT
1 TTTTTAGT-CCTTTAAGTTTCTGTTTTTGTT
*
31054 TTTTTAATCCTTTAAGTTTCTG-TTTTGTT
1 TTTTTAGTCCTTTAAGTTTCTGTTTTTGTT
* * * *
31083 GTTTTAGTCCTGTAAATTTCTATTTTT
1 TTTTTAGTCCTTTAAGTTTCTGTTTTT
31110 ACTATTTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
29 29 0.60
30 19 0.40
ACGTcount: A:0.13, C:0.12, G:0.12, T:0.64
Consensus pattern (30 bp):
TTTTTAGTCCTTTAAGTTTCTGTTTTTGTT
Found at i:37551 original size:2 final size:2
Alignment explanation
Indices: 37540--37590 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
37530 TGCATAATAC
*
37540 TA TA TA -A TA TA TA TA TA TA TA TA -A TA CTA TA TA -A TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
37580 TA TA -A TA TA TA
1 TA TA TA TA TA TA
37591 ACAGTATAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
1 4 0.10
2 36 0.86
3 2 0.05
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:37558 original size:13 final size:13
Alignment explanation
Indices: 37533--37669 Score: 64
Period size: 13 Copynumber: 9.6 Consensus size: 13
37523 TAATAAATGC
37533 ATAATACTATATA-
1 ATAATA-TATATAT
37546 ATATATATATATAT
1 ATA-ATATATATAT
37560 ATAATACTATATAAT
1 ATAATA-TATAT-AT
37575 ATAA-ATATAATAT
1 ATAATATAT-ATAT
* *
37588 ATAACAGTATAATGT
1 ATAATA-TAT-ATAT
*
37603 ATACACACTATATAAT
1 ATA-ATA-TATAT-AT
*
37619 GTAAGTATATAT-T
1 ATAA-TATATATAT
*
37632 ATAAATATGTAATAT
1 AT-AATATAT-ATAT
*
37647 AATACATATATAGAT
1 -ATA-ATATATATAT
37662 ATAATATA
1 ATAATATA
37670 CATAAGTCAC
Statistics
Matches: 100, Mismatches: 9, Indels: 30
0.72 0.06 0.22
Matches are distributed among these distances:
13 32 0.32
14 22 0.22
15 29 0.29
16 17 0.17
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:37568 original size:27 final size:28
Alignment explanation
Indices: 37533--37591 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
37523 TAATAAATGC
*
37533 ATAATACTATATAATATATATAT-ATAT
1 ATAATACTATATAATATAAATATAATAT
37560 ATAATACTATATAATATAAATATAATAT
1 ATAATACTATATAATATAAATATAATAT
37588 ATAA
1 ATAA
37592 CAGTATAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (28 bp):
ATAATACTATATAATATAAATATAATAT
Found at i:37694 original size:5 final size:5
Alignment explanation
Indices: 37678--39616 Score: 3658
Period size: 5 Copynumber: 392.2 Consensus size: 5
37668 TACATAAGTC
37678 ACATA A-ATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
37727 ACATA ACATA ACATA ACATA ACATA ACATA AC--A ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
37775 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACAT- ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
37824 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
37874 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
37924 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
37974 ACATA ACATA ACATA ACATA ACATA AC--A ACATA ACATA ACATA ACA-A
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38021 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38071 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38121 ACATA ACATA ACATA ACATA AC--A ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38169 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38219 ACATA ACATA ACATA ACATA ACATA ACAT- ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38268 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38318 ACATA ACATA ACATA AC-TA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38367 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38417 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38467 ACATA ACATA ACATA ACATA ACATA ACATA ACATA AC--A ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38515 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACAT- ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38564 ACATA ACATA ACATA ACATA ACAT- ACATA ACATA ACA-A ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38612 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38662 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACA-A ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38711 ACATA AC--A ACATA ACATA AC-TA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38758 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38808 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38858 ACAT- ACATA ACATA ACATA ACATAA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACAT-A ACATA ACATA ACATA ACATA ACATA
38908 ACATA ACATA ACATAA CACATA ACATA ACATA ACATA ACATA ACAT- ACATA
1 ACATA ACATA ACAT-A -ACATA ACATA ACATA ACATA ACATA ACATA ACATA
38959 ACATA ACAT- ACATA ACATA ACATA ACATA ACATA ACA-A ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
39007 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
39057 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
39107 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
39157 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
39207 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
39257 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA A-ATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
39306 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
39356 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
39406 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
39456 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
39506 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
39556 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
* *
39606 ATATA ATATA A
1 ACATA ACATA A
39617 ACAATATATC
Statistics
Matches: 1905, Mismatches: 1, Indels: 56
0.97 0.00 0.03
Matches are distributed among these distances:
3 15 0.01
4 60 0.03
5 1819 0.95
6 7 0.00
7 4 0.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
ACATA
Found at i:39625 original size:16 final size:16
Alignment explanation
Indices: 39606--39636 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39596 ACATAACATA
39606 ATATAATATAAACAAT
1 ATATAATATAAACAAT
*
39622 ATATCATATAAACAA
1 ATATAATATAAACAA
39637 AGTCGGACGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (16 bp):
ATATAATATAAACAAT
Found at i:44761 original size:44 final size:44
Alignment explanation
Indices: 44677--44761 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
44667 TCCCACACAG
* * *
44677 AATGAAAGGAAATTAAATTCAAAAGGAGATGAAACGAAGTACCA
1 AATGAAAGAAAATTAAATTCAAAAGGAAATGAAACAAAGTACCA
* *
44721 AATGAAAGAAAATTAAATTCACAAGGAAATGAAATAAAGTA
1 AATGAAAGAAAATTAAATTCAAAAGGAAATGAAACAAAGTA
44762 AGAAGAAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.58, C:0.07, G:0.18, T:0.18
Consensus pattern (44 bp):
AATGAAAGAAAATTAAATTCAAAAGGAAATGAAACAAAGTACCA
Found at i:53020 original size:10 final size:10
Alignment explanation
Indices: 53005--53092 Score: 88
Period size: 11 Copynumber: 8.4 Consensus size: 10
52995 AAAATGATAA
*
53005 ATAATAACAT
1 ATAATAATAT
53015 ATAATAAATAT
1 ATAAT-AATAT
*
53026 ATAATACTAT
1 ATAATAATAT
53036 ATAATAAATAT
1 ATAAT-AATAT
53047 ATATATATATAT
1 ATA-ATA-ATAT
*
53059 ATAATATTAT
1 ATAATAATAT
*
53069 ATAATATAAAT
1 ATAATA-ATAT
53080 ATAAT-ATAT
1 ATAATAATAT
53089 ATAA
1 ATAA
53093 CGGTATAATG
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
9 7 0.11
10 23 0.35
11 27 0.41
12 9 0.14
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
ATAATAATAT
Found at i:53029 original size:21 final size:22
Alignment explanation
Indices: 53005--53091 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 22
52995 AAAATGATAA
53005 ATAATA-ACATATAATAAATAT
1 ATAATATACATATAATAAATAT
53026 AT-A-ATACTATATAATAAATAT
1 ATAATATAC-ATATAATAAATAT
* *
53047 ATATATATATATATAAT-ATTAT
1 ATA-ATATACATATAATAAATAT
* *
53069 ATAATATAAATATAATATATAT
1 ATAATATACATATAATAAATAT
53091 A
1 A
53092 ACGGTATAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
19 1 0.02
20 3 0.05
21 29 0.53
22 11 0.20
23 8 0.15
24 3 0.05
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAATATACATATAATAAATAT
Found at i:53038 original size:2 final size:2
Alignment explanation
Indices: 53013--53091 Score: 73
Period size: 2 Copynumber: 42.5 Consensus size: 2
53003 AAATAATAAC
* *
53013 AT AT A- AT AA AT AT AT A- AT ACT AT AT A- AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
*
53053 AT AT AT AT A- AT AT -T AT AT A- AT AT AA AT AT A- 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
53091 A
1 A
53092 ACGGTATAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
1 7 0.11
2 54 0.86
3 2 0.03
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:53224 original size:7 final size:7
Alignment explanation
Indices: 53191--53260 Score: 56
Period size: 8 Copynumber: 9.9 Consensus size: 7
53181 CATAAATAAC
53191 ATAATAT
1 ATAATAT
*
53198 ATACTAT
1 ATAATAT
*
53205 ACAATAT
1 ATAATAT
53212 A-AATAT
1 ATAATAT
53218 AT--TAT
1 ATAATAT
53223 ATAATAT
1 ATAATAT
*
53230 AATATAAAT
1 -ATA-ATAT
53239 ATAATGAT
1 ATAAT-AT
53247 ATAATGAT
1 ATAAT-AT
53255 ATAATA
1 ATAATA
53261 AGTTTATATA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
5 5 0.10
6 6 0.12
7 17 0.33
8 21 0.40
9 3 0.06
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (7 bp):
ATAATAT
Found at i:53229 original size:32 final size:31
Alignment explanation
Indices: 53191--53260 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 31
53181 CATAAATAAC
*
53191 ATAATATATACTATACAATATAA-ATAT-ATTAT
1 ATAATATA-A-TATA-AATATAAGATATAATGAT
53223 ATAATATAATATAAATATAATGATATAATGAT
1 ATAATATAATATAAATATAA-GATATAATGAT
53255 ATAATA
1 ATAATA
53261 AGTTTATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
29 7 0.21
30 4 0.12
31 5 0.15
32 18 0.53
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (31 bp):
ATAATATAATATAAATATAAGATATAATGAT
Found at i:53233 original size:23 final size:24
Alignment explanation
Indices: 53207--53251 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
53197 TATACTATAC
*
53207 AATATAAATAT-ATTATATAATAT
1 AATATAAATATAATGATATAATAT
53230 AATATAAATATAATGATATAAT
1 AATATAAATATAATGATATAAT
53252 GATATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
AATATAAATATAATGATATAATAT
Found at i:57723 original size:24 final size:24
Alignment explanation
Indices: 57677--57723 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
57667 TTGAAAGGTC
* *
57677 ACAACCTTTCATGTAGGAAATGTA
1 ACAACCTTTCATGCAAGAAATGTA
* *
57701 ACAATCTTTCATGCAAGACATGT
1 ACAACCTTTCATGCAAGAAATGT
57724 CTCTTTAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (24 bp):
ACAACCTTTCATGCAAGAAATGTA
Found at i:60071 original size:35 final size:35
Alignment explanation
Indices: 60008--60174 Score: 169
Period size: 35 Copynumber: 4.8 Consensus size: 35
59998 ACTAGCAATA
* * **
60008 AGTCGCATTCATATAATTCACAGTAGTGAGTCATG
1 AGTCGCATTCAGATAATGCACAACAGTGAGTCATG
* * *
60043 AGTCACATTCAGATAGTACACAACAGTGAGTCATG
1 AGTCGCATTCAGATAATGCACAACAGTGAGTCATG
60078 AGGT-GCATTCAGATAATGCACAGA-AGTGAGTCAAT-
1 A-GTCGCATTCAGATAATGCACA-ACAGTGAGTC-ATG
* * *
60113 AGTCGCATTCAGTTAATGCACAACATTGAGTCTTG
1 AGTCGCATTCAGATAATGCACAACAGTGAGTCATG
* * *
60148 AGTTGTATTCAGATAATGCACATCAGT
1 AGTCGCATTCAGATAATGCACAACAGT
60175 TACAGTCATT
Statistics
Matches: 109, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
34 4 0.04
35 100 0.92
36 5 0.05
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (35 bp):
AGTCGCATTCAGATAATGCACAACAGTGAGTCATG
Found at i:60135 original size:70 final size:70
Alignment explanation
Indices: 60012--60169 Score: 201
Period size: 70 Copynumber: 2.3 Consensus size: 70
60002 GCAATAAGTC
* * * *
60012 GCATTCATATAATTCACAGTAGTGAGTCATGAGTCACATTCAGATAGTACACAACAGTGAGTCAT
1 GCATTCAGATAATGCACAGAAGTGAGTCATGAGTCACATTCAGATAATACACAACAGTGAGTCAT
60077 GAGGT
66 GAGGT
* * * * *
60082 GCATTCAGATAATGCACAGAAGTGAGTCAAT-AGTCGCATTCAGTTAATGCACAACATTGAGTCT
1 GCATTCAGATAATGCACAGAAGTGAGTC-ATGAGTCACATTCAGATAATACACAACAGTGAGTCA
*
60146 TGAGTT
65 TGAGGT
*
60152 GTATTCAGATAATGCACA
1 GCATTCAGATAATGCACA
60170 TCAGTTACAG
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
70 74 0.97
71 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (70 bp):
GCATTCAGATAATGCACAGAAGTGAGTCATGAGTCACATTCAGATAATACACAACAGTGAGTCAT
GAGGT
Found at i:67299 original size:82 final size:82
Alignment explanation
Indices: 67056--67427 Score: 509
Period size: 81 Copynumber: 4.6 Consensus size: 82
67046 TATTTTGGTA
* * * *
67056 GAATAATGTAGATTTTCTGACTCTCTAAAAATTTTAA-CTTATCTGAGTTAATGTGAAATGTCAA
1 GAATAGTGTAGATTCTCTGACTCTCTAAAATTTTTAAGTTTATCTGAGTTAATGTGAAATGTCAA
67120 TGAAAAGCAAAGGACGT
66 TGAAAAGCAAAGGACGT
* * * *
67137 GAATAGTATAGATTCTTTGACTCTCTAAAATTTTCAAG-TTATCTGAGTTGATGTGAAATGTCAA
1 GAATAGTGTAGATTCTCTGACTCTCTAAAATTTTTAAGTTTATCTGAGTTAATGTGAAATGTCAA
* *
67201 TGAAAAGTAAATGACGT
66 TGAAAAGCAAAGGACGT
* * *
67218 GAATAGTGTAGATTCTCTGACTCTATAAATTTTTTAAGTTTATCTGAGTTAATATGAAATGTCAA
1 GAATAGTGTAGATTCTCTGACTCTCTAAAATTTTTAAGTTTATCTGAGTTAATGTGAAATGTCAA
67283 TGAAAAGCAAAGGACGT
66 TGAAAAGCAAAGGACGT
* * * * * *
67300 GAATAGTATAGACTCTCTGACTCTCTAAAAATTTTCATTTTATCTGAGTTGATGTGAAATGTCAA
1 GAATAGTGTAGATTCTCTGACTCTCTAAAATTTTTAAGTTTATCTGAGTTAATGTGAAATGTCAA
*
67365 TGAAAAGCAAA-GACAT
66 TGAAAAGCAAAGGACGT
* *
67381 GAATAGTGTA-ACATCTCTGTCTCTCTAAAATTTTTAAGTTTATCTGA
1 GAATAGTGTAGA-TTCTCTGACTCTCTAAAATTTTTAAGTTTATCTGA
67428 AAAGCAAATG
Statistics
Matches: 254, Mismatches: 34, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
80 1 0.00
81 147 0.58
82 106 0.42
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (82 bp):
GAATAGTGTAGATTCTCTGACTCTCTAAAATTTTTAAGTTTATCTGAGTTAATGTGAAATGTCAA
TGAAAAGCAAAGGACGT
Found at i:67386 original size:163 final size:163
Alignment explanation
Indices: 67056--67427 Score: 570
Period size: 163 Copynumber: 2.3 Consensus size: 163
67046 TATTTTGGTA
* * * * *
67056 GAATAATGTAGATTTTCTGACTCTCTAAAAATTTTAA-CTTATCTGAGTTAATGTGAAATGTCAA
1 GAATAGTGTAGATTCTCTGACTCTCTAAAATTTTTAAGTTTATCTGAGTTAATATGAAATGTCAA
* *
67120 TGAAAAGCAAAGGACGTGAATAGTATAGATTCTTTGACTCTCTAAAATTTTCAAGTTATCTGAGT
66 TGAAAAGCAAAGGACGTGAATAGTATAGACTCTCTGACTCTCTAAAATTTTCAAGTTATCTGAGT
* *
67185 TGATGTGAAATGTCAATGAAAAGTAAATGACGT
131 TGATGTGAAATGTCAATGAAAAGCAAATGACAT
* *
67218 GAATAGTGTAGATTCTCTGACTCTATAAATTTTTTAAGTTTATCTGAGTTAATATGAAATGTCAA
1 GAATAGTGTAGATTCTCTGACTCTCTAAAATTTTTAAGTTTATCTGAGTTAATATGAAATGTCAA
**
67283 TGAAAAGCAAAGGACGTGAATAGTATAGACTCTCTGACTCTCTAAAAATTTTCATTTTATCTGAG
66 TGAAAAGCAAAGGACGTGAATAGTATAGACTCTCTGACTCTCT-AAAATTTTCAAGTTATCTGAG
67348 TTGATGTGAAATGTCAATGAAAAGCAAA-GACAT
130 TTGATGTGAAATGTCAATGAAAAGCAAATGACAT
* *
67381 GAATAGTGTA-ACATCTCTGTCTCTCTAAAATTTTTAAGTTTATCTGA
1 GAATAGTGTAGA-TTCTCTGACTCTCTAAAATTTTTAAGTTTATCTGA
67428 AAAGCAAATG
Statistics
Matches: 190, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
162 33 0.17
163 111 0.58
164 46 0.24
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (163 bp):
GAATAGTGTAGATTCTCTGACTCTCTAAAATTTTTAAGTTTATCTGAGTTAATATGAAATGTCAA
TGAAAAGCAAAGGACGTGAATAGTATAGACTCTCTGACTCTCTAAAATTTTCAAGTTATCTGAGT
TGATGTGAAATGTCAATGAAAAGCAAATGACAT
Found at i:67459 original size:61 final size:60
Alignment explanation
Indices: 67365--67488 Score: 169
Period size: 61 Copynumber: 2.0 Consensus size: 60
67355 GAAATGTCAA
* **
67365 TGAAAAGCAAAGACATGAATAGTGTAACATCTCTGTCTCTCTAAAATTTTTAAGTTTATC
1 TGAAAAGCAAAGACATGAATAGTATAACATCTCTAACTCTCTAAAATTTTTAAGTTTATC
* * *
67425 TGAAAAGCAAATGACATGAATAGTATAGA-TTCTCTAACTCTCTAAAATTTTTCATTTTATC
1 TGAAAAGCAAA-GACATGAATAGTATA-ACATCTCTAACTCTCTAAAATTTTTAAGTTTATC
67486 TGA
1 TGA
67489 GTTGATGTGA
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 11 0.20
61 44 0.79
62 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (60 bp):
TGAAAAGCAAAGACATGAATAGTATAACATCTCTAACTCTCTAAAATTTTTAAGTTTATC
Found at i:67612 original size:25 final size:25
Alignment explanation
Indices: 67570--67632 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 25
67560 ATAGTGTAGA
*
67570 TCATGTTCAATCTTTTACACAACACAC
1 TCAT-TTC-ATCTCTTACACAACACAC
*
67597 TCCTTTCATCTCTTACACAACACAC
1 TCATTTCATCTCTTACACAACACAC
*
67622 TTATTTCATCT
1 TCATTTCATCT
67633 AACGAAATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 26 0.81
26 3 0.09
27 3 0.09
ACGTcount: A:0.29, C:0.32, G:0.02, T:0.38
Consensus pattern (25 bp):
TCATTTCATCTCTTACACAACACAC
Found at i:68247 original size:16 final size:16
Alignment explanation
Indices: 68223--68263 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
68213 ACACACATGT
68223 ACAATGACCTCCATGAC
1 ACAA-GACCTCCATGAC
*
68240 ATAAGACCTCCATGAC
1 ACAAGACCTCCATGAC
68256 ACAAGACC
1 ACAAGACC
68264 GTAGACATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.39, C:0.34, G:0.12, T:0.15
Consensus pattern (16 bp):
ACAAGACCTCCATGAC
Found at i:72917 original size:23 final size:22
Alignment explanation
Indices: 72891--72958 Score: 93
Period size: 21 Copynumber: 3.1 Consensus size: 22
72881 GGTTCTACGC
72891 GGTCCTTCGGGACAATTCTATGT
1 GGTCCTTCGGGAC-ATTCTATGT
* *
72914 GGTCCTTCGGGATA-TATATGT
1 GGTCCTTCGGGACATTCTATGT
*
72935 GGTCCTTTGGGACATTCTATGT
1 GGTCCTTCGGGACATTCTATGT
72957 GG
1 GG
72959 CACTTCGATG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.46
22 9 0.23
23 12 0.31
ACGTcount: A:0.16, C:0.18, G:0.29, T:0.37
Consensus pattern (22 bp):
GGTCCTTCGGGACATTCTATGT
Found at i:76772 original size:20 final size:20
Alignment explanation
Indices: 76717--76765 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
76707 GAAGTTGCAT
*
76717 GAACAATATTGGTACTTGAA
1 GAACAATATTGGTACTTAAA
76737 GAACAATATTGGTACTTAAA
1 GAACAATATTGGTACTTAAA
76757 GAACAATAT
1 GAACAATAT
76766 CGATACTGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (20 bp):
GAACAATATTGGTACTTAAA
Found at i:82342 original size:34 final size:31
Alignment explanation
Indices: 82290--82359 Score: 104
Period size: 34 Copynumber: 2.2 Consensus size: 31
82280 ACCTTACAAC
82290 TCCCTAGTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTCCGGGCTAAACTAGAACCTT
*
82321 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTT-C-CGGGCTAAACTAGAACCTT
82355 TCCCT
1 TCCCT
82360 TTACAAAGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
31 7 0.20
32 4 0.11
33 1 0.03
34 23 0.66
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (31 bp):
TCCCTAGTTTTCCGGGCTAAACTAGAACCTT
Found at i:82594 original size:20 final size:22
Alignment explanation
Indices: 82569--82608 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
82559 AGTCGTATAT
82569 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
82589 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
82609 TATACTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:82670 original size:21 final size:19
Alignment explanation
Indices: 82636--82676 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
82626 CCCATAATAG
82636 AGGGAATCGTACCCCTTCAT
1 AGGGAATCGTA-CCCTTCAT
*
82656 AGGGAGTCGATACCCTTCAT
1 AGGGAATCG-TACCCTTCAT
82676 A
1 A
82677 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (19 bp):
AGGGAATCGTACCCTTCAT
Done.