Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 40 of 172
Found at i:12692443 original size:14 final size:14
Alignment explanation
Indices: 12692426--12692459 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12692416 AAGATTTTTG
*
12692426 AATTATAATTTATT
1 AATTATAATTAATT
12692440 AATTATAATTAATT
1 AATTATAATTAATT
*
12692454 AGTTAT
1 AATTAT
12692460 TAGCTCAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
AATTATAATTAATT
Found at i:12705558 original size:71 final size:69
Alignment explanation
Indices: 12705434--12705578 Score: 254
Period size: 71 Copynumber: 2.1 Consensus size: 69
12705424 TGTACCACGT
*
12705434 CATCACCTGAAAATTTATATAATTTTTTTTTTAATTTTCAGGTGATGGTGTAGCACAATCACAAA
1 CATCACCTGAAAATTTATATAATTTTTTTTTTAATTTTCAAGTGATGGTGTAGCACAATCACAAA
12705499 GTGC
66 GTGC
*
12705503 CATCACCTGAAAATTTATATAATATATTTTTTTTAATTTTCAAGTGATGGTGTAGCTCAATCACA
1 CATCACCTGAAAATTTATATAAT-T-TTTTTTTTAATTTTCAAGTGATGGTGTAGCACAATCACA
12705568 AAGTGC
64 AAGTGC
12705574 CATCA
1 CATCA
12705579 TCAAACTTTC
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
69 23 0.32
70 1 0.01
71 48 0.67
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (69 bp):
CATCACCTGAAAATTTATATAATTTTTTTTTTAATTTTCAAGTGATGGTGTAGCACAATCACAAA
GTGC
Found at i:12706672 original size:17 final size:17
Alignment explanation
Indices: 12706650--12706682 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12706640 GCAAACAAAA
12706650 AAGTCA-AACAGAAAACC
1 AAGTCAGAA-AGAAAACC
12706667 AAGTCAGAAAGAAAAC
1 AAGTCAGAAAGAAAAC
12706683 ATACCTCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.61, C:0.18, G:0.15, T:0.06
Consensus pattern (17 bp):
AAGTCAGAAAGAAAACC
Found at i:12710353 original size:15 final size:15
Alignment explanation
Indices: 12710333--12710362 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12710323 CCGTCAACAA
12710333 AGGCTATGTTCATCT
1 AGGCTATGTTCATCT
12710348 AGGCTATGTTCATCT
1 AGGCTATGTTCATCT
12710363 CTAACCTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (15 bp):
AGGCTATGTTCATCT
Found at i:12710820 original size:28 final size:29
Alignment explanation
Indices: 12710789--12710866 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 29
12710779 TATTATTATT
*
12710789 TATATAAATATATAAATTA-ATTATAAAG
1 TATATAAATAAATAAATTACATTATAAAG
* * *
12710817 TATATTATTAAATTAATTACATTATAAA-
1 TATATAAATAAATAAATTACATTATAAAG
*
12710845 TATTATATTAAGAAATAAATTA
1 TA-TATA--AATAAATAAATTA
12710867 AATAAAGACA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
28 17 0.45
29 11 0.29
31 10 0.26
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (29 bp):
TATATAAATAAATAAATTACATTATAAAG
Found at i:12710866 original size:31 final size:28
Alignment explanation
Indices: 12710800--12710867 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
12710790 ATATAAATAT
**
12710800 ATAAATTAATTATAAAGTATATTATTAA
1 ATAAATTAATTATAAAGTATATTAAGAA
* *
12710828 ATTAATTACATTATAAATATTATATTAAGAA
1 ATAAATTA-ATTAT-AA-AGTATATTAAGAA
12710859 ATAAATTAA
1 ATAAATTAA
12710868 ATAAAGACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 5 0.16
30 3 0.09
31 17 0.53
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (28 bp):
ATAAATTAATTATAAAGTATATTAAGAA
Found at i:12711089 original size:11 final size:11
Alignment explanation
Indices: 12711073--12711098 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12711063 AGAAAGAGAC
12711073 GAAACAGGGGA
1 GAAACAGGGGA
12711084 GAAACAGGGGA
1 GAAACAGGGGA
12711095 GAAA
1 GAAA
12711099 GAAAGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:12712196 original size:37 final size:39
Alignment explanation
Indices: 12712137--12712232 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
12712127 CGGATAGATT
* * * *
12712137 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
12712174 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
12712213 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
12712233 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:12721227 original size:18 final size:17
Alignment explanation
Indices: 12721204--12721237 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12721194 ATTACATCCA
12721204 AATAAAACTCTCAATTAT
1 AATAAAACTCT-AATTAT
*
12721222 AATAAAATTCTAATTA
1 AATAAAACTCTAATTA
12721238 ATCCAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (17 bp):
AATAAAACTCTAATTAT
Found at i:12749535 original size:48 final size:48
Alignment explanation
Indices: 12749461--12749650 Score: 213
Period size: 48 Copynumber: 4.0 Consensus size: 48
12749451 CATTAGGGAA
* *
12749461 TACATTGATTTGGCTTCGGGACATGATATTAGCACTTTGGGTGCGAGT
1 TACATTGATTTGGCTTCGGGCCATGATATTAGCACTTAGGGTGCGAGT
* * ** * *
12749509 TATATTGATTTGGCTTCAGGCCATGATATCGGTACTTAGGGTGTGAGCT
1 TACATTGATTTGGCTTCGGGCCATGATATTAGCACTTAGGGTGCGAG-T
* * * *
12749558 T-CATTGATTTGG-TTTGGGCCATGATATTATCACTTCGGGTGCGAGA
1 TACATTGATTTGGCTTCGGGCCATGATATTAGCACTTAGGGTGCGAGT
** * *
12749604 TACATTGAGATGGCTTCGGGCCATGATATGAGCACTTAGTGTGCGAG
1 TACATTGATTTGGCTTCGGGCCATGATATTAGCACTTAGGGTGCGAG
12749651 ACTTCTGAGT
Statistics
Matches: 114, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
46 1 0.01
47 34 0.30
48 77 0.68
49 2 0.02
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.34
Consensus pattern (48 bp):
TACATTGATTTGGCTTCGGGCCATGATATTAGCACTTAGGGTGCGAGT
Found at i:12752916 original size:14 final size:14
Alignment explanation
Indices: 12752897--12752924 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12752887 GATTCTCCAC
12752897 AGTTTTTCTTTTAA
1 AGTTTTTCTTTTAA
12752911 AGTTTTTCTTTTAA
1 AGTTTTTCTTTTAA
12752925 GGGAAAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.64
Consensus pattern (14 bp):
AGTTTTTCTTTTAA
Found at i:12754241 original size:69 final size:67
Alignment explanation
Indices: 12754153--12754290 Score: 204
Period size: 69 Copynumber: 2.0 Consensus size: 67
12754143 TGATTAAACT
* * *
12754153 TAATCAGTTTACTATTAAATTAATATAATACTGATAAAGATAAATATTAGATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAATATAATACT-ATAAAGATAAATATTAAATTAAATTTAATATT
12754218 AAGA
65 -AGA
* * *
12754222 TAATCACTTTAATATTAAATTAATATAATACTATTAAGATAAGTATTAAATTTAATTTAATATTA
1 TAATCACTTTAATATTAAATTAATATAATACTATAAAGATAAATATTAAATTAAATTTAATATTA
12754287 GA
66 GA
12754289 TA
1 TA
12754291 TATTAAAATA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 5 0.08
68 28 0.44
69 30 0.48
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (67 bp):
TAATCACTTTAATATTAAATTAATATAATACTATAAAGATAAATATTAAATTAAATTTAATATTA
GA
Found at i:12754249 original size:25 final size:26
Alignment explanation
Indices: 12754210--12754258 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
12754200 TAGATTAAAT
12754210 TTAATATTAAGATAATCACT-TTAATA
1 TTAATATTAAGATAAT-ACTATTAATA
*
12754236 TTAA-ATTAATATAATACTATTAA
1 TTAATATTAAGATAATACTATTAA
12754259 GATAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 14 0.67
26 4 0.19
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (26 bp):
TTAATATTAAGATAATACTATTAATA
Found at i:12754303 original size:68 final size:69
Alignment explanation
Indices: 12754165--12754306 Score: 189
Period size: 68 Copynumber: 2.1 Consensus size: 69
12754155 ATCAGTTTAC
* **
12754165 TATTAAATTAATATAATACTGATAAAGATAAATATTAGATTAAATTTAATATTAAGATAATCACT
1 TATTAAATTAATATAATACTGATAAAGATAAATATTAAATTAAATTTAATATTAAGATAATCAAA
*
12754230 TTAA
66 ATAA
* * * *
12754234 TATTAAATTAATATAATACT-ATTAAGATAAGTATTAAATTTAATTTAATATT-AGATATATTAA
1 TATTAAATTAATATAATACTGATAAAGATAAATATTAAATTAAATTTAATATTAAGATA-ATCAA
12754297 AATAA
65 AATAA
12754302 TATTA
1 TATTA
12754307 TTTTGGAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
67 5 0.08
68 39 0.61
69 20 0.31
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.42
Consensus pattern (69 bp):
TATTAAATTAATATAATACTGATAAAGATAAATATTAAATTAAATTTAATATTAAGATAATCAAA
ATAA
Found at i:12767188 original size:17 final size:17
Alignment explanation
Indices: 12767163--12767198 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12767153 ATAGTAGTAC
12767163 ATTAATATTAATTATTA
1 ATTAATATTAATTATTA
* *
12767180 ATTATTATTATTTATTA
1 ATTAATATTAATTATTA
12767197 AT
1 AT
12767199 ATACTAGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTAATATTAATTATTA
Found at i:12767379 original size:16 final size:17
Alignment explanation
Indices: 12767352--12767384 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12767342 TATTATAATC
12767352 TATATCATAATAATAGT
1 TATATCATAATAATAGT
*
12767369 TATAT-ATAATAGTAGT
1 TATATCATAATAATAGT
12767385 ACATATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATCATAATAATAGT
Found at i:12767653 original size:30 final size:32
Alignment explanation
Indices: 12767575--12767653 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 32
12767565 CCATATATTT
* *
12767575 TATTATAAT-TTATATTATTACAATAGTTATA
1 TATTATAATATTATTTTAATACAATAGTTATA
12767606 TATGTATTAATA-T-TTTTAATA-AA-AGTTATA
1 TAT-TA-TAATATTATTTTAATACAATAGTTATA
12767636 TATTATAATATTATTTTA
1 TATTATAATATTATTTTA
12767654 TGTATTAGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
28 5 0.12
29 3 0.07
30 15 0.37
31 5 0.12
32 8 0.20
33 5 0.12
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (32 bp):
TATTATAATATTATTTTAATACAATAGTTATA
Found at i:12771847 original size:53 final size:53
Alignment explanation
Indices: 12771785--12771891 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
12771775 TAATGGTATA
*
12771785 TAGCACATAATTATTAATTTGATATTTTTCTAATTTATGGTATTAATAATACG
1 TAGCACATAATTATTAATTTGATATTTTTCCAATTTATGGTATTAATAATACG
12771838 TAGCACATAATTATTAATTTGATATTTTTCCAATTTATGGTATTAATAATACG
1 TAGCACATAATTATTAATTTGATATTTTTCCAATTTATGGTATTAATAATACG
12771891 T
1 T
12771892 CAGTTTTTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (53 bp):
TAGCACATAATTATTAATTTGATATTTTTCCAATTTATGGTATTAATAATACG
Found at i:12772725 original size:21 final size:21
Alignment explanation
Indices: 12772701--12772744 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
12772691 TTGCTTCTAT
12772701 GGTTTCTAAGTTCTCTCTAAA
1 GGTTTCTAAGTTCTCTCTAAA
12772722 GGTTTCTAAGTTCTCTCTAAA
1 GGTTTCTAAGTTCTCTCTAAA
12772743 GG
1 GG
12772745 GTCTTTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (21 bp):
GGTTTCTAAGTTCTCTCTAAA
Found at i:12776710 original size:4 final size:4
Alignment explanation
Indices: 12776701--12776743 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
12776691 ACGGTTTCTT
12776701 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT
12776744 ATCTCAAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:12793600 original size:26 final size:26
Alignment explanation
Indices: 12793569--12793621 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
12793559 GAGACTCTGT
12793569 CATACAAACACAATACATCAATAATG
1 CATACAAACACAATACATCAATAATG
12793595 CATACAAACACAATACATCAATAATG
1 CATACAAACACAATACATCAATAATG
12793621 C
1 C
12793622 CATCTACAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.53, C:0.25, G:0.04, T:0.19
Consensus pattern (26 bp):
CATACAAACACAATACATCAATAATG
Found at i:12796267 original size:48 final size:47
Alignment explanation
Indices: 12796198--12796345 Score: 170
Period size: 48 Copynumber: 3.1 Consensus size: 47
12796188 AGGCTATCAA
* * * *
12796198 CATCGATATGTGATCCCATGTAAGACCATGTCTAGGACATGACATTGG
1 CATCGACATATGATCCCATGTAAGACCATATCT-GGACATGGCATTGG
* * * *
12796246 CATCGACCTATGATCCTATGTAAGACCATTTTTGGGACATGGCATTGG
1 CATCGACATATGATCCCATGTAAGACCATATCT-GGACATGGCATTGG
* * *
12796294 CATCGATATGTGATCCCATGTAAGACCATATCTGGAATATGGCATTGG
1 CATCGACATATGATCCCATGTAAGACCATATCTGG-ACATGGCATTGG
12796342 CATC
1 CATC
12796346 CTACCATGTG
Statistics
Matches: 84, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
47 2 0.02
48 82 0.98
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (47 bp):
CATCGACATATGATCCCATGTAAGACCATATCTGGACATGGCATTGG
Found at i:12798505 original size:43 final size:43
Alignment explanation
Indices: 12798457--12798613 Score: 158
Period size: 43 Copynumber: 3.7 Consensus size: 43
12798447 AACATATACA
* * * *
12798457 ATGCCAACGTCCTAGACGTGGTCTTATATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCG
* * *
12798500 ATGCC-ACTGTCCCAGACAAGGTCTTACACGAAATCAGATA-CG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAATCAAATATCG
* * * * *
12798542 ATGTCGATGTCCCAGACATGGTCTTACACGTAAAACAGAA-GTCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGT-AATCA-AATATCG
12798586 ATGCCAACGTCCCAGACATGGTCTTACA
1 ATGCCAACGTCCCAGACATGGTCTTACA
12798614 TGATAACACA
Statistics
Matches: 92, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
42 29 0.32
43 35 0.38
44 28 0.30
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCG
Found at i:12805478 original size:90 final size:94
Alignment explanation
Indices: 12805323--12805543 Score: 249
Period size: 93 Copynumber: 2.4 Consensus size: 94
12805313 GATTTGTGCA
* * * ** *
12805323 CCAGTATGAGACCATGTCTGGGACATGGCATCGGCATCCAGACG-AGGGCTAGTGTAAGACTTGT
1 CCAGTATAAGACCATGTCTGGGACATGGCATCGAC-T-AAGA-GTAGTACTAGTGTAAGACATGT
* * * *
12805387 CTGGGACATGCTTC-A-GC-CATATTATGAGTG
63 CTAGGACATGCATCAACACGCATA-TATGAGAG
12805417 CCAG-AGTAAGA-CATGTCTGGGACAT-GCATCGACTAAGAGTAGTACTAGTGTAAGACATGTCT
1 CCAGTA-TAAGACCATGTCTGGGACATGGCATCGACTAAGAGTAGTACTAGTGTAAGACATGTCT
12805479 AGGACATGCATCAACACGCATATATGAGAG
65 AGGACATGCATCAACACGCATATATGAGAG
*
12805509 CCAGTATAAGACCATGTCTGGGGCATGGCATCGAC
1 CCAGTATAAGACCATGTCTGGGACATGGCATCGAC
12805544 AATTTATCCC
Statistics
Matches: 108, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
89 1 0.01
90 32 0.30
91 2 0.02
92 24 0.22
93 33 0.31
94 16 0.15
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.23
Consensus pattern (94 bp):
CCAGTATAAGACCATGTCTGGGACATGGCATCGACTAAGAGTAGTACTAGTGTAAGACATGTCTA
GGACATGCATCAACACGCATATATGAGAG
Found at i:12812518 original size:130 final size:130
Alignment explanation
Indices: 12812357--12812607 Score: 355
Period size: 130 Copynumber: 1.9 Consensus size: 130
12812347 ACGAGATTTG
* *
12812357 ATATTTGACAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGTAATTTCGCGTTTGCTCAAAAT
1 ATATTTGACAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTT--CGATTGCTCAAAAT
* * *
12812422 AATCGAATATCAC-TTCAAAATTTCACTCATGTATT-TTAAAATCCCTT-AAACGAAGGCGATAC
64 AATCAAATATC-CTTTCAAAATTTCACTCAGGTATTCTAAAAATCCCTTAAAACGAAGGCGATAC
12812484 GCA
128 GCA
* * * *
12812487 ATATTTGGCAATTCGTGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCGATTGTTTAAAATAA
1 ATATTTGACAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCGATTGCTCAAAATAA
* *
12812552 TCAAATATCCTTTCAAAATTTCACTCAGGTCTTCTAAAAATCCTTTAAAACGAAGG
66 TCAAATATCCTTTCAAAATTTCACTCAGGTATTCTAAAAATCCCTTAAAACGAAGG
12812608 TAATACTCGG
Statistics
Matches: 107, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
127 1 0.01
128 41 0.38
129 10 0.09
130 55 0.51
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (130 bp):
ATATTTGACAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCGATTGCTCAAAATAA
TCAAATATCCTTTCAAAATTTCACTCAGGTATTCTAAAAATCCCTTAAAACGAAGGCGATACGCA
Found at i:12812629 original size:130 final size:128
Alignment explanation
Indices: 12812357--12812658 Score: 347
Period size: 130 Copynumber: 2.3 Consensus size: 128
12812347 ACGAGATTTG
* *
12812357 ATATTTGACAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGTAATTTCGCGTTTGCTCAAAAT
1 ATATTTGACAATTCG-GGAATCGTGCCCTAACGTGTTGGGTTGCAATTTC-CGATTGCTCAAAAT
* * * *
12812422 AATCGAATATCACTTCAAAATTTCACTCATGTATTTTAAAATCCCTTAAACGAAGGCGATACGCA
64 AATCAAATATCACTTCAAAATTTCACTCAGGTATTTAAAAATCCCTTAAACGAAGGCAATACGCA
* * *
12812487 ATATTTGGCAATTCGTGGAATCGTGCCCTAACGTGTTGGGTTGCAATTT-CGATTGTTTAAAATA
1 ATATTTGACAATTCG-GGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCCGATTGCTCAAAATA
* * * *
12812551 ATCAAATATC-CTTTCAAAATTTCACTCAGGTCTTCTAAAAATCCTTTAAAACGAAGGTAATACT
65 ATCAAATATCAC-TTCAAAATTTCACTCAGGTATT-TAAAAATCCCTT-AAACGAAGGCAATACG
*
12812615 CG
127 CA
* * * * * * *
12812617 GTGTTTGACAATTCGAGAATCATGCCTTATCGTGCTGGGTTG
1 ATATTTGACAATTCGGGAATCGTGCCCTAACGTGTTGGGTTG
12812659 TGATTTCTCG
Statistics
Matches: 146, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
127 1 0.01
128 41 0.28
129 32 0.22
130 72 0.49
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (128 bp):
ATATTTGACAATTCGGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCCGATTGCTCAAAATAA
TCAAATATCACTTCAAAATTTCACTCAGGTATTTAAAAATCCCTTAAACGAAGGCAATACGCA
Found at i:12812975 original size:130 final size:130
Alignment explanation
Indices: 12812734--12812968 Score: 337
Period size: 130 Copynumber: 1.8 Consensus size: 130
12812724 CTTAAAAACA
* * * * *
12812734 AAGATGATGTTCAATGTTTGGTGATTTGAGAATCGTGCCCTATCGTGCTGGGTTGCACTTTTTTA
1 AAGAAGATGTTCAATGTTTGGCGATTTGAGAATCGAGCCCTATCGTGCTAGGTTGCACTTTTTCA
* * *
12812799 TTGGTCCAAAACAATTGAAGATCCCTTCGGAACTTCACTCACATTTTCTAAAATCTTTCAAAATG
66 TTGGCCCAAAACAATCGAAGATCCCTTCGGAACTTCACACACATTTTCTAAAATCTTTCAAAATG
*
12812864 AAGAAGATGTTCGATGTTTGGCGATTTGAGAATCGAGCCCTATCGTGCTAGGTTGCACTTTTTCA
1 AAGAAGATGTTCAATGTTTGGCGATTTGAGAATCGAGCCCTATCGTGCTAGGTTGCACTTTTTCA
* * * *
12812929 TTTGCCCAAAATAATCGAATATCTCCTT-GGAATTTCACAC
66 TTGGCCCAAAACAATCGAAGATC-CCTTCGGAACTTCACAC
12812969 GTATTTTATA
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
130 87 0.96
131 4 0.04
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (130 bp):
AAGAAGATGTTCAATGTTTGGCGATTTGAGAATCGAGCCCTATCGTGCTAGGTTGCACTTTTTCA
TTGGCCCAAAACAATCGAAGATCCCTTCGGAACTTCACACACATTTTCTAAAATCTTTCAAAATG
Found at i:12841386 original size:9 final size:9
Alignment explanation
Indices: 12841372--12841448 Score: 75
Period size: 9 Copynumber: 8.6 Consensus size: 9
12841362 ATAAGTATAA
12841372 AATTAACCG
1 AATTAACCG
**
12841381 AATTAACTA
1 AATTAACCG
12841390 AATTAACCG
1 AATTAACCG
* *
12841399 AATTAATCA
1 AATTAACCG
*
12841408 AATTGACCG
1 AATTAACCG
12841417 AATT-ACCTG
1 AATTAACC-G
*
12841426 AATTAATCG
1 AATTAACCG
*
12841435 AATTAATCG
1 AATTAACCG
12841444 AATTA
1 AATTA
12841449 TTTGTATAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
8 3 0.05
9 51 0.91
10 2 0.04
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (9 bp):
AATTAACCG
Found at i:12841394 original size:18 final size:18
Alignment explanation
Indices: 12841371--12841440 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 18
12841361 AATAAGTATA
12841371 AAATTAACCGAATTAACT
1 AAATTAACCGAATTAACT
12841389 AAATTAACCGAATTAA-T
1 AAATTAACCGAATTAACT
* *
12841406 CAAATTGACCGAATTACCT
1 -AAATTAACCGAATTAACT
* *
12841425 GAATTAATCGAATTAA
1 AAATTAACCGAATTAA
12841441 TCGAATTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
17 1 0.02
18 42 0.95
19 1 0.02
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTAACCGAATTAACT
Found at i:12841418 original size:36 final size:36
Alignment explanation
Indices: 12841371--12841448 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
12841361 AATAAGTATA
12841371 AAATTAACCGAATTAACTAAATTAACCGAATTAATC
1 AAATTAACCGAATTAACTAAATTAACCGAATTAATC
* * * *
12841407 AAATTGACCGAATTACCTGAATTAATCGAATTAATC
1 AAATTAACCGAATTAACTAAATTAACCGAATTAATC
*
12841443 GAATTA
1 AAATTA
12841449 TTTGTATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.29
Consensus pattern (36 bp):
AAATTAACCGAATTAACTAAATTAACCGAATTAATC
Found at i:12841548 original size:13 final size:13
Alignment explanation
Indices: 12841532--12841556 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12841522 AATTTTTATG
12841532 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
12841545 ATTGGGTTGGGT
1 ATTGGGTTGGGT
12841557 TGGGTACTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:12841556 original size:18 final size:18
Alignment explanation
Indices: 12841533--12841567 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12841523 ATTTTTATGA
12841533 TTGGGTTGGGTAATTGGG
1 TTGGGTTGGGTAATTGGG
*
12841551 TTGGGTTGGGTACTTGG
1 TTGGGTTGGGTAATTGG
12841568 CTTAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.03, G:0.49, T:0.40
Consensus pattern (18 bp):
TTGGGTTGGGTAATTGGG
Found at i:12843270 original size:20 final size:20
Alignment explanation
Indices: 12843227--12843331 Score: 90
Period size: 20 Copynumber: 5.3 Consensus size: 20
12843217 ATTTCTATTT
*
12843227 GTATAACT-GTAATTCATTC
1 GTATAACTAGTAATTCATCC
* *
12843246 ATATAACTAGTAGTTCATCC
1 GTATAACTAGTAATTCATCC
* ** *
12843266 GTATAAATAGTTGTTCATCG
1 GTATAACTAGTAATTCATCC
*
12843286 GTAATAA-AAGTAATTCATCC
1 GT-ATAACTAGTAATTCATCC
12843306 GTATTAAC-AGTAATTCATCC
1 GTA-TAACTAGTAATTCATCC
*
12843326 ATATAA
1 GTATAA
12843332 ACACATATCT
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
19 11 0.16
20 55 0.79
21 4 0.06
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (20 bp):
GTATAACTAGTAATTCATCC
Found at i:12843638 original size:50 final size:45
Alignment explanation
Indices: 12843547--12843638 Score: 105
Period size: 50 Copynumber: 1.9 Consensus size: 45
12843537 TATCAAGCTG
*
12843547 AATACTAAGCTCACGAGCTGAAACGGTAAGCTCCAATGAGCTAAA
1 AATACTAAGCTCACGAGCTGAAACGGTAAGCTCCAACGAGCTAAA
*
12843592 AATAGTAAGCTCTTACGAGCTGATATATCGGTAAGCT-CATACGAGCT
1 AATACTAAGCTC--ACGAGCTGA-A-A-CGGTAAGCTCCA-ACGAGCT
12843639 GTGGTGAGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
45 11 0.28
47 9 0.23
48 1 0.03
49 3 0.08
50 15 0.38
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (45 bp):
AATACTAAGCTCACGAGCTGAAACGGTAAGCTCCAACGAGCTAAA
Found at i:12845699 original size:65 final size:65
Alignment explanation
Indices: 12845589--12845716 Score: 168
Period size: 65 Copynumber: 2.0 Consensus size: 65
12845579 AAAGAGTTGT
** * *
12845589 GTTTGTGTCTGCAACATATGCAGGATCACAACCGATCGCATAACAGGACACTCACAAAGAGCTAC
1 GTTTGTGTCCACAACATATGCAGGATCACAACCGATCGAATAACAGGACACTCAAAAAGAGCTAC
** * *
12845654 GTTTGTGTCCACAACATATGCAGGATCACAATTGATC-AATAAACAGTACGCTCAAAAAGAGCT
1 GTTTGTGTCCACAACATATGCAGGATCACAACCGATCGAAT-AACAGGACACTCAAAAAGAGCT
12845717 GCGGTAGTCG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
64 2 0.04
65 52 0.96
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (65 bp):
GTTTGTGTCCACAACATATGCAGGATCACAACCGATCGAATAACAGGACACTCAAAAAGAGCTAC
Found at i:12857412 original size:17 final size:19
Alignment explanation
Indices: 12857376--12857417 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
12857366 GTTTTTAGTT
*
12857376 AAGTTAGTTTTTTTTATAC
1 AAGTTAGTTTTTATTATAC
12857395 AAGTTAG-TTTTATT-TAC
1 AAGTTAGTTTTTATTATAC
*
12857412 ATGTTA
1 AAGTTA
12857418 AAGACTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 8 0.38
18 6 0.29
19 7 0.33
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.55
Consensus pattern (19 bp):
AAGTTAGTTTTTATTATAC
Found at i:12863849 original size:43 final size:43
Alignment explanation
Indices: 12863786--12863900 Score: 119
Period size: 43 Copynumber: 2.7 Consensus size: 43
12863776 CATTAGGATT
*
12863786 ATCGTTATGTGACT-ATGTGTAAGACCAT-GTCTAGGAC-ATTGGC
1 ATCGATATGTGA-TAATGTGTAAGACCATAG-CT-GGACTATTGGC
* * ** *
12863829 ATCGCTATTTGATTTTGTGTAAGACCATAGCTGGGCTATTGGC
1 ATCGATATGTGATAATGTGTAAGACCATAGCTGGACTATTGGC
*
12863872 ATCGATATGTGATAATATGTAAGACCATA
1 ATCGATATGTGATAATGTGTAAGACCATA
12863901 TCCGGGATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
42 4 0.07
43 55 0.92
44 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (43 bp):
ATCGATATGTGATAATGTGTAAGACCATAGCTGGACTATTGGC
Found at i:12865644 original size:28 final size:28
Alignment explanation
Indices: 12865611--12865685 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 28
12865601 ATTGCATGAC
*
12865611 TATGAATGTGCTTGGGCCTGACGGGCCA
1 TATGAATGTGATTGGGCCTGACGGGCCA
* *
12865639 TATGAATGTGATTAGGCCTGATGGGCCA
1 TATGAATGTGATTGGGCCTGACGGGCCA
*
12865667 TATGAATGAGATTGGGCCT
1 TATGAATGTGATTGGGCCT
12865686 AAAGAGGCCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.23, C:0.16, G:0.33, T:0.28
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTGACGGGCCA
Found at i:12868737 original size:43 final size:43
Alignment explanation
Indices: 12868669--12868769 Score: 114
Period size: 43 Copynumber: 2.3 Consensus size: 43
12868659 AGGCCATGTA
*** *
12868669 TGGGACATTGGCATTGTATTGTGATTACGTGTAAGA-CCAAGTC
1 TGGGACATTGGCATCACATTATGATTACGTGTAAGACCCAA-TC
** *
12868712 TGGGACATTGGCATCACATTATGATTTTGTGTAAGACCCTATC
1 TGGGACATTGGCATCACATTATGATTACGTGTAAGACCCAATC
*
12868755 TGGGACAGTGGCATC
1 TGGGACATTGGCATC
12868770 GATATGTGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 46 0.94
44 3 0.06
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
TGGGACATTGGCATCACATTATGATTACGTGTAAGACCCAATC
Found at i:12872483 original size:35 final size:35
Alignment explanation
Indices: 12872433--12872505 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
12872423 TGATAAGAAA
12872433 GTGACAGAAAAAAAGATCAAAACAGTACAAGTTGT
1 GTGACAGAAAAAAAGATCAAAACAGTACAAGTTGT
** *
12872468 GTGACA-AAAACAAAGATTGAATCAGTACAAGTTGT
1 GTGACAGAAAA-AAAGATCAAAACAGTACAAGTTGT
12872503 GTG
1 GTG
12872506 CGAGTATCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 4 0.12
35 30 0.88
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.21
Consensus pattern (35 bp):
GTGACAGAAAAAAAGATCAAAACAGTACAAGTTGT
Found at i:12873348 original size:60 final size:60
Alignment explanation
Indices: 12873272--12873392 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 60
12873262 GAAGCCTCTA
12873272 AGAAATGTATCTGAAGTCCATATTTTTCTAGGACTAGCCGGCTATTATAGATTATTTGTG
1 AGAAATGTATCTGAAGTCCATATTTTTCTAGGACTAGCCGGCTATTATAGATTATTTGTG
* *
12873332 AGAAATGTATCTGAAGTCCGTATTTTTCTGGGACTAGCCGGCTATTATAGATTATTTGTG
1 AGAAATGTATCTGAAGTCCATATTTTTCTAGGACTAGCCGGCTATTATAGATTATTTGTG
12873392 A
1 A
12873393 AAGGTTTCTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.38
Consensus pattern (60 bp):
AGAAATGTATCTGAAGTCCATATTTTTCTAGGACTAGCCGGCTATTATAGATTATTTGTG
Found at i:12876673 original size:43 final size:43
Alignment explanation
Indices: 12876617--12876731 Score: 126
Period size: 43 Copynumber: 2.7 Consensus size: 43
12876607 CATTAGGATT
*
12876617 ATCGTTATGTGATTACATGTAAGACCAT-GTCTGGGAC-ATTGGC
1 ATCGTTATGTGATTACATGTAAGACCATAG-CTGGG-CTATTAGC
* ***
12876660 ATCGTTATTTGATTTTTTGTAAGACCATAGCTGGGCTATTAGC
1 ATCGTTATGTGATTACATGTAAGACCATAGCTGGGCTATTAGC
* * *
12876703 ATTGATATGTGATAACATGTAAGACCATA
1 ATCGTTATGTGATTACATGTAAGACCATA
12876732 TCCGGGATAT
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
42 1 0.02
43 56 0.97
44 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.36
Consensus pattern (43 bp):
ATCGTTATGTGATTACATGTAAGACCATAGCTGGGCTATTAGC
Found at i:12877403 original size:11 final size:11
Alignment explanation
Indices: 12877387--12877411 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12877377 GAAGCATTAC
12877387 TGTATAGGTCT
1 TGTATAGGTCT
12877398 TGTATAGGTCT
1 TGTATAGGTCT
12877409 TGT
1 TGT
12877412 TTTATCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.28, T:0.48
Consensus pattern (11 bp):
TGTATAGGTCT
Found at i:12878649 original size:8 final size:8
Alignment explanation
Indices: 12878622--12878652 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
12878612 CCAAAATACA
12878622 GGCTTTTC
1 GGCTTTTC
*
12878630 GGCATTTC
1 GGCTTTTC
12878638 GGCTTTTC
1 GGCTTTTC
12878646 GGCTTTT
1 GGCTTTT
12878653 GCCGATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.03, C:0.23, G:0.26, T:0.48
Consensus pattern (8 bp):
GGCTTTTC
Found at i:12879441 original size:14 final size:15
Alignment explanation
Indices: 12879392--12879449 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
12879382 TCGGCTATGG
12879392 AGGAAAAGAAGAA-A
1 AGGAAAAGAAGAAGA
* *
12879406 A-G-AAAGTAGATGA
1 AGGAAAAGAAGAAGA
*
12879419 ATAGAAAAGAA-AAGA
1 A-GGAAAAGAAGAAGA
12879434 AGGAAAAGAAGAAGA
1 AGGAAAAGAAGAAGA
12879449 A
1 A
12879450 AAAACTGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
12 7 0.21
13 3 0.09
14 9 0.26
15 10 0.29
16 5 0.15
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (15 bp):
AGGAAAAGAAGAAGA
Found at i:12879447 original size:12 final size:11
Alignment explanation
Indices: 12879394--12879451 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
12879384 GGCTATGGAG
12879394 GAAAAGAAGAA
1 GAAAAGAAGAA
* * *
12879405 AAGAAAGTAGAT
1 GA-AAAGAAGAA
*
12879417 GAATAGAA-AA
1 GAAAAGAAGAA
12879427 GAAAAGAAG--
1 GAAAAGAAGAA
12879436 GAAAAGAAGAA
1 GAAAAGAAGAA
12879447 GAAAA
1 GAAAA
12879452 AACTGAATCC
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
9 9 0.26
10 8 0.23
11 10 0.29
12 8 0.23
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (11 bp):
GAAAAGAAGAA
Found at i:12879448 original size:20 final size:22
Alignment explanation
Indices: 12879391--12879451 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 22
12879381 TTCGGCTATG
*
12879391 GAGGAAAAGAAGAAAAGAAAGTA
1 GAGGAAAAGAAGAAGA-AAAGTA
* *
12879414 GATGAATAGAA-AAGAAAAG-A
1 GAGGAAAAGAAGAAGAAAAGTA
12879434 -AGGAAAAGAAGAAGAAAA
1 GAGGAAAAGAAGAAGAAAA
12879452 AACTGAATCC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 8 0.25
20 8 0.25
21 4 0.12
22 3 0.09
23 9 0.28
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (22 bp):
GAGGAAAAGAAGAAGAAAAGTA
Found at i:12880378 original size:19 final size:18
Alignment explanation
Indices: 12880341--12880384 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
12880331 ATACATAGAG
12880341 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
12880358 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
12880377 TACTAATT
1 TAATAATT
12880385 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:12888101 original size:16 final size:16
Alignment explanation
Indices: 12888080--12888114 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
12888070 ATACCTCCAT
*
12888080 TCTCAGTAGTCTTCTA
1 TCTCAGCAGTCTTCTA
12888096 TCTCAGCAGTCTTCTA
1 TCTCAGCAGTCTTCTA
12888112 TCT
1 TCT
12888115 TAGAAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.29, G:0.11, T:0.43
Consensus pattern (16 bp):
TCTCAGCAGTCTTCTA
Found at i:12893040 original size:27 final size:27
Alignment explanation
Indices: 12893009--12893186 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
12892999 TAAATTGTAC
12893009 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
12893036 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
12893062 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
12893090 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
12893118 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
12893145 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
12893172 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12893187 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:12893123 original size:82 final size:81
Alignment explanation
Indices: 12893010--12893165 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
12893000 AAATTGTACA
* *
12893010 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
12893074 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
12893091 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
12893156 TGCGAGTTGA
65 TGCGAATTGA
12893166 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:12893177 original size:82 final size:81
Alignment explanation
Indices: 12893006--12893186 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
12892996 GATTAAATTG
* *
12893006 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
12893071 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
12893087 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
12893151 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
12893169 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
12893187 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:12895062 original size:39 final size:39
Alignment explanation
Indices: 12895005--12895134 Score: 188
Period size: 39 Copynumber: 3.3 Consensus size: 39
12894995 GTCTTTAGGC
*
12895005 CCGGATATATTTCTAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATATTTCCAGCACGTAGCCTGCGGACCTCAAGT
12895044 CCGGATATATTTCCAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATATTTCCAGCACGTAGCCTGCGGACCTCAAGT
* * * * *
12895083 CCTGATATGTTTCCAGCACATAGCCTACAGACCTCAAGT
1 CCGGATATATTTCCAGCACGTAGCCTGCGGACCTCAAGT
* *
12895122 CCAGATATGTTTC
1 CCGGATATATTTC
12895135 TAAATATCAT
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 84 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (39 bp):
CCGGATATATTTCCAGCACGTAGCCTGCGGACCTCAAGT
Found at i:12903810 original size:22 final size:21
Alignment explanation
Indices: 12903785--12903825 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
12903775 TAAAAAACCC
*
12903785 AAAAACAGGAAAAATAAAAAAT
1 AAAAAAAGGAAAAA-AAAAAAT
*
12903807 AAAAAAAGGAAGAAAAAAA
1 AAAAAAAGGAAAAAAAAAA
12903826 CCTCAGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.05
Consensus pattern (21 bp):
AAAAAAAGGAAAAAAAAAAAT
Found at i:12904861 original size:3 final size:3
Alignment explanation
Indices: 12904853--12904892 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
12904843 AATGTTTCGA
12904853 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
12904893 ATTTTATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:12907488 original size:87 final size:89
Alignment explanation
Indices: 12907350--12907523 Score: 271
Period size: 87 Copynumber: 2.0 Consensus size: 89
12907340 TAATGAGTTA
* * * *
12907350 TCTTATTAAGTGGGAGGTTTCAAACGTAGAAAAAGATTTGCAGCAGTGCATCTTTTTCTGTTATT
1 TCTTATTAAGTGAGAGGTTTAAAACGCAGAAAAAGATTTGCAGCAGTGCATCATTTTCTGTTATT
12907415 CGATCAAC-AAAGACAATGAGAAC
66 CGATCAACAAAAGACAATGAGAAC
*
12907438 TCTTATTAAGTGAGAGG-TTAAAATGCAGAAAAAGATTTGCAGCAGTGCATCATTTTCTGTTATT
1 TCTTATTAAGTGAGAGGTTTAAAACGCAGAAAAAGATTTGCAGCAGTGCATCATTTTCTGTTATT
* *
12907502 CGATCGACAAAAGATAATGAGA
66 CGATCAACAAAAGACAATGAGA
12907524 TGATGCAGGG
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
87 50 0.64
88 28 0.36
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (89 bp):
TCTTATTAAGTGAGAGGTTTAAAACGCAGAAAAAGATTTGCAGCAGTGCATCATTTTCTGTTATT
CGATCAACAAAAGACAATGAGAAC
Found at i:12913171 original size:28 final size:29
Alignment explanation
Indices: 12913140--12913213 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 29
12913130 TTAGCAGACA
* *
12913140 TTCCACATAAGATAGTTCGTGGCGGA-TT
1 TTCCGCATAAGATAGTCCGTGGCGGACTT
*
12913168 TTCCGCATAAGATAGTCCGTGGTGGACTT
1 TTCCGCATAAGATAGTCCGTGGCGGACTT
12913197 TT-CGCATAAGATAGTCC
1 TTCCGCATAAGATAGTCC
12913214 TTAGCAAACT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 38 0.90
29 4 0.10
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (29 bp):
TTCCGCATAAGATAGTCCGTGGCGGACTT
Found at i:12913224 original size:28 final size:29
Alignment explanation
Indices: 12913140--12913224 Score: 66
Period size: 28 Copynumber: 3.0 Consensus size: 29
12913130 TTAGCAGACA
* * * **
12913140 TTCCACATAAGATAGTTCGTGGCGGA-TT
1 TTCCGCATAAGATAGTCCGTAGCAAACTT
* ***
12913168 TTCCGCATAAGATAGTCCGTGGTGGACTT
1 TTCCGCATAAGATAGTCCGTAGCAAACTT
*
12913197 TT-CGCATAAGATAGTCCTTAGCAAACTT
1 TTCCGCATAAGATAGTCCGTAGCAAACTT
12913225 CCTTTTTCTG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
28 44 0.92
29 4 0.08
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (29 bp):
TTCCGCATAAGATAGTCCGTAGCAAACTT
Found at i:12920294 original size:26 final size:26
Alignment explanation
Indices: 12920265--12920316 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
12920255 GCTTGCCACA
12920265 CTTACTGCTACTGGTAGCTACGCTGC
1 CTTACTGCTACTGGTAGCTACGCTGC
* *
12920291 CTTACTGTTACTGGTAGCTTCGCTGC
1 CTTACTGCTACTGGTAGCTACGCTGC
12920317 GATGTAGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.29, G:0.23, T:0.35
Consensus pattern (26 bp):
CTTACTGCTACTGGTAGCTACGCTGC
Found at i:12928319 original size:26 final size:26
Alignment explanation
Indices: 12928290--12928341 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
12928280 CTTACCACAC
12928290 TTACTGCTACTGGCAGCTACGCTGCG
1 TTACTGCTACTGGCAGCTACGCTGCG
* *
12928316 TTACTGTTACTGGCAGCTTCGCTGCG
1 TTACTGCTACTGGCAGCTACGCTGCG
12928342 ATATAGGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.29, G:0.27, T:0.31
Consensus pattern (26 bp):
TTACTGCTACTGGCAGCTACGCTGCG
Found at i:12931609 original size:26 final size:26
Alignment explanation
Indices: 12931580--12931631 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
12931570 CTTACCACAC
12931580 TTACTGCTACTGGCAGCTACGCTGCG
1 TTACTGCTACTGGCAGCTACGCTGCG
* *
12931606 TTACTGTTACTGGCAGCTTCGCTGCG
1 TTACTGCTACTGGCAGCTACGCTGCG
12931632 ATATAGGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.29, G:0.27, T:0.31
Consensus pattern (26 bp):
TTACTGCTACTGGCAGCTACGCTGCG
Found at i:12933575 original size:43 final size:43
Alignment explanation
Indices: 12933508--12933634 Score: 168
Period size: 43 Copynumber: 3.0 Consensus size: 43
12933498 AAGTCTGAAC
* * * **
12933508 TCAT-TCACCGGCA-TCTCGCCTGCTAAGCTTGAAGCCCGATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATA
* *
12933549 TCATTTCACCGGTATTATAGCCTGCTAGGCCCGAAGCCCGATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATA
*
12933592 TTATCTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATA
12933635 ATATTATTCA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
41 4 0.05
42 8 0.11
43 63 0.84
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.24
Consensus pattern (43 bp):
TCATCTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATA
Found at i:12933674 original size:43 final size:46
Alignment explanation
Indices: 12933562--12933675 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 46
12933552 TTTCACCGGT
* *
12933562 ATTATAGCCTGCTAGGCCCGAAGCCCG---ATATTATCTCACCGGC
1 ATTAAAGCCTGCTAGGCCCGAAGCCCGATAATATTATCTCACCAGC
*
12933605 ATTATAGCCTGCTAGGCCCGAAGCCCGATAATATTAT-TCACCAGC
1 ATTAAAGCCTGCTAGGCCCGAAGCCCGATAATATTATCTCACCAGC
* *
12933650 -TTAAAGCTTGCTAGG-CCGAGGCCCGA
1 ATTAAAGCCTGCTAGGCCCGAAGCCCGA
12933676 ATATCACATT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
43 37 0.58
44 13 0.20
45 7 0.11
46 7 0.11
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (46 bp):
ATTAAAGCCTGCTAGGCCCGAAGCCCGATAATATTATCTCACCAGC
Found at i:12935370 original size:14 final size:15
Alignment explanation
Indices: 12935341--12935370 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12935331 CAAAATTTAG
12935341 ACATGATACTTTCAC
1 ACATGATACTTTCAC
12935356 ACATGATAC-TTCAC
1 ACATGATACTTTCAC
12935370 A
1 A
12935371 TATAATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (15 bp):
ACATGATACTTTCAC
Found at i:12935744 original size:17 final size:16
Alignment explanation
Indices: 12935722--12935753 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
12935712 CACGATCACG
12935722 AATGATTTTATTATTTC
1 AATGATTTTA-TATTTC
12935739 AATGATTTTATATTT
1 AATGATTTTATATTT
12935754 GGGTTTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.59
Consensus pattern (16 bp):
AATGATTTTATATTTC
Found at i:12947420 original size:46 final size:46
Alignment explanation
Indices: 12947362--12947530 Score: 157
Period size: 46 Copynumber: 3.6 Consensus size: 46
12947352 TCTCATAGCT
12947362 GATGCATGTCCCAGACATGTCTTACACTAACTTATGTCTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAACTTATGTCTCGAGGCC
* * *
12947408 GATGCATGTCCCAGACACGTCTTACACTAGCAC-TA-GTCTCAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTA--ACTTATGTCTCGAGGCC
* * ** ** * *
12947454 GATGCCATGTCCTAGACATGGTCTTAAACTGGCTCTCAT-AAT-GTGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTAACT-T-ATGTCTCGAGGCC
12947502 GATGCATGTCCCAGACATGTCTTACACTA
1 GATGCATGTCCCAGACATGTCTTACACTA
12947531 GCTCATAATA
Statistics
Matches: 98, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
46 51 0.52
47 27 0.28
48 18 0.18
49 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTAACTTATGTCTCGAGGCC
Found at i:12947479 original size:94 final size:90
Alignment explanation
Indices: 12947323--12947532 Score: 212
Period size: 94 Copynumber: 2.3 Consensus size: 90
12947313 ACTGATGCCG
* * *
12947323 TGTCCCAGACATGGTCTTACACT-GACACATCTCATAGCTGATGCATGTCCCAGACATGTCTTAC
1 TGTCCCAGACA-CGTCTTACACTAG-CACATCTCATAGCCGATGCATGTCCCAGACATGTCTTAA
**
12947387 ACTAACT-T-ATGTCTCGAGGCCGATGCA
64 ACTAACTCTCAT-AAT-GAGGCCGATGCA
*
12947414 TGTCCCAGACACGTCTTACACTAGCACTAGTCTCA-ATGCCGATGCCATGTCCTAGACATGGTCT
1 TGTCCCAGACACGTCTTACACTAGCAC-A-TCTCATA-GCCGATG-CATGTCCCAGACAT-GTCT
** * *
12947478 TAAACTGGCTCTCATAATGTGGCTGATGCA
61 TAAACTAACTCTCATAATGAGGCCGATGCA
*
12947508 TGTCCCAGACATGTCTTACACTAGC
1 TGTCCCAGACACGTCTTACACTAGC
12947533 TCATAATAAC
Statistics
Matches: 100, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
90 13 0.13
91 14 0.14
92 11 0.11
93 13 0.13
94 45 0.45
95 2 0.02
96 2 0.02
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (90 bp):
TGTCCCAGACACGTCTTACACTAGCACATCTCATAGCCGATGCATGTCCCAGACATGTCTTAAAC
TAACTCTCATAATGAGGCCGATGCA
Found at i:12952381 original size:79 final size:81
Alignment explanation
Indices: 12952272--12952454 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
12952262 TACTCGTTCA
* *
12952272 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
12952335 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
12952352 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
12952415 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
12952431 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
12952455 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:12952454 original size:40 final size:40
Alignment explanation
Indices: 12952251--12952454 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
12952241 CGGAATTTAA
** *
12952251 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
12952291 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
12952331 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
12952370 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
12952410 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
12952450 CCGGA
1 CCGGA
12952455 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:12960807 original size:49 final size:49
Alignment explanation
Indices: 12960751--12960898 Score: 296
Period size: 49 Copynumber: 3.0 Consensus size: 49
12960741 GTTTTGCCCA
12960751 TGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
12960800 TGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
12960849 TGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
12960898 T
1 T
12960899 TGCCCATCAT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 99 1.00
ACGTcount: A:0.24, C:0.18, G:0.08, T:0.49
Consensus pattern (49 bp):
TGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:12968339 original size:53 final size:54
Alignment explanation
Indices: 12968136--12968341 Score: 188
Period size: 53 Copynumber: 3.9 Consensus size: 54
12968126 TTCCTTTTTA
* * * *
12968136 AACTTACCATTGCCATGTCTTGACATGGTCTTACGT-GGTATCATTGCCTTATG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGGTATCCTTGCCTTATG
* * * * * * *
12968189 AACTCACTATTGCCATGCCTTGGCAGGGTCTTACATAGG-ATCTTTGCCTTATAG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGGTATCCTTGCCTTAT-G
** ** * * *
12968243 TAGTTTATTAATGCCATGTCTTGACATGGCCTTACAT-GATATCCTTGCCTTATG
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGGTATCCTTGCCTTATG
12968297 AACTTACCAATGCCATGCCTT-AGCATGGTCTTAC-TGGGTATCCTT
1 AACTTACCAATGCCATGCCTTGA-CATGGTCTTACATGGGTATCCTT
12968342 AAACCCTAAT
Statistics
Matches: 122, Mismatches: 25, Indels: 12
0.77 0.16 0.08
Matches are distributed among these distances:
52 2 0.02
53 76 0.62
54 5 0.04
55 39 0.32
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.36
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGGTATCCTTGCCTTATG
Found at i:12976018 original size:101 final size:101
Alignment explanation
Indices: 12975877--12976211 Score: 670
Period size: 101 Copynumber: 3.3 Consensus size: 101
12975867 GACCTCCTAC
12975877 ATAGTGAAAAGTACATATATCAATAAATTAACATGAATTATTATTCGATGAAATTATTTGATTTG
1 ATAGTGAAAAGTACATATATCAATAAATTAACATGAATTATTATTCGATGAAATTATTTGATTTG
12975942 CGAAATGCATTTTTGAGCATCGAAATGCATCTCATT
66 CGAAATGCATTTTTGAGCATCGAAATGCATCTCATT
12975978 ATAGTGAAAAGTACATATATCAATAAATTAACATGAATTATTATTCGATGAAATTATTTGATTTG
1 ATAGTGAAAAGTACATATATCAATAAATTAACATGAATTATTATTCGATGAAATTATTTGATTTG
12976043 CGAAATGCATTTTTGAGCATCGAAATGCATCTCATT
66 CGAAATGCATTTTTGAGCATCGAAATGCATCTCATT
12976079 ATAGTGAAAAGTACATATATCAATAAATTAACATGAATTATTATTCGATGAAATTATTTGATTTG
1 ATAGTGAAAAGTACATATATCAATAAATTAACATGAATTATTATTCGATGAAATTATTTGATTTG
12976144 CGAAATGCATTTTTGAGCATCGAAATGCATCTCATT
66 CGAAATGCATTTTTGAGCATCGAAATGCATCTCATT
12976180 ATAGTGAAAAGTACATATATCAATAAATTAAC
1 ATAGTGAAAAGTACATATATCAATAAATTAAC
12976212 TATGGCAAAC
Statistics
Matches: 234, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 234 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (101 bp):
ATAGTGAAAAGTACATATATCAATAAATTAACATGAATTATTATTCGATGAAATTATTTGATTTG
CGAAATGCATTTTTGAGCATCGAAATGCATCTCATT
Found at i:12978085 original size:13 final size:13
Alignment explanation
Indices: 12978067--12978093 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12978057 ATGTTTTATT
12978067 AAATTTTAACTTA
1 AAATTTTAACTTA
12978080 AAATTTTAACTTA
1 AAATTTTAACTTA
12978093 A
1 A
12978094 CCTTTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTTTAACTTA
Found at i:12989805 original size:41 final size:41
Alignment explanation
Indices: 12989747--12989832 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
12989737 TGTGGATATT
12989747 TGAATTTGATAAGTTTTAAATGTTTAATAATTCTTTGGTGTA
1 TGAATTTGATAAGTTTTAAATGTTTAATAATTC-TTGGTGTA
*
12989789 TGAA-TTGATAAGTTTTAAATGTTTATTAATTCTTGGTGTA
1 TGAATTTGATAAGTTTTAAATGTTTAATAATTCTTGGTGTA
12989829 TGAA
1 TGAA
12989833 AGGTGATGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
40 12 0.28
41 27 0.63
42 4 0.09
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.49
Consensus pattern (41 bp):
TGAATTTGATAAGTTTTAAATGTTTAATAATTCTTGGTGTA
Found at i:12991732 original size:14 final size:14
Alignment explanation
Indices: 12991713--12991742 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12991703 TTTTTTGTTG
12991713 TTTTATACTGTTTA
1 TTTTATACTGTTTA
*
12991727 TTTTATGCTGTTTA
1 TTTTATACTGTTTA
12991741 TT
1 TT
12991743 ACGATTTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (14 bp):
TTTTATACTGTTTA
Found at i:12999058 original size:20 final size:20
Alignment explanation
Indices: 12999033--12999079 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
12999023 TAAAAATATG
12999033 ATTTAATAAGACAATGTGTA
1 ATTTAATAAGACAATGTGTA
12999053 ATTTAATAAGACAATGTGTA
1 ATTTAATAAGACAATGTGTA
12999073 ATTTAAT
1 ATTTAAT
12999080 GTTATTGCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (20 bp):
ATTTAATAAGACAATGTGTA
Found at i:12999383 original size:68 final size:67
Alignment explanation
Indices: 12999311--12999460 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
12999301 CATCATGTGT
* * * *
12999311 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
12999373 ATGTAG
62 ATGTAG
** * *
12999379 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
12999444 AG
66 AG
12999446 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
12999461 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:12999416 original size:64 final size:64
Alignment explanation
Indices: 12999335--12999518 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
12999325 AGACATTATG
* *
12999335 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
12999399 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
12999464 AA
63 AA
* * * *
12999466 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
12999519 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:13004799 original size:19 final size:17
Alignment explanation
Indices: 13004761--13004798 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
13004751 CACAGTTTGG
*
13004761 CACATGATTGTGTGTCA
1 CACATGATTATGTGTCA
13004778 CACATGATTATGTGTCA
1 CACATGATTATGTGTCA
13004795 CACA
1 CACA
13004799 CTCGCTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (17 bp):
CACATGATTATGTGTCA
Found at i:13012828 original size:15 final size:13
Alignment explanation
Indices: 13012796--13012820 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13012786 AAGAAATATA
13012796 ATCTTATTTTATC
1 ATCTTATTTTATC
13012809 ATCTTATTTTAT
1 ATCTTATTTTAT
13012821 GTCATCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (13 bp):
ATCTTATTTTATC
Found at i:13018237 original size:28 final size:28
Alignment explanation
Indices: 13018204--13018278 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
13018194 ATTCCATGAC
*
13018204 TATGAATGTGATTGGGCTTGACCGGCCA
1 TATGAATGTGATTGGGCCTGACCGGCCA
* * **
13018232 TATGAAAGTGATTGGACCTGATGGGCCA
1 TATGAATGTGATTGGGCCTGACCGGCCA
*
13018260 TATGAATGAGATTGGGCCT
1 TATGAATGTGATTGGGCCT
13018279 AAAGGGGCCA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.28
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTGACCGGCCA
Found at i:13025826 original size:16 final size:16
Alignment explanation
Indices: 13025797--13025831 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
13025787 CCGACAAATC
*
13025797 CCGAATTGCCAAAAAG
1 CCGAAATGCCAAAAAG
*
13025813 CCGAAATGCTAAAAAG
1 CCGAAATGCCAAAAAG
13025829 CCG
1 CCG
13025832 GAAGTTTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.26, G:0.20, T:0.11
Consensus pattern (16 bp):
CCGAAATGCCAAAAAG
Found at i:13026081 original size:28 final size:28
Alignment explanation
Indices: 13026048--13026122 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
13026038 ATTGCATGAC
13026048 TATGAATGTGATTGGGCCTGACGGGCCA
1 TATGAATGTGATTGGGCCTGACGGGCCA
** * * **
13026076 TATGAAAATGATTAGGTCTGGTGGGCCA
1 TATGAATGTGATTGGGCCTGACGGGCCA
*
13026104 TATGAATGAGATTGGGCCT
1 TATGAATGTGATTGGGCCT
13026123 AAATGGGCCA
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.25, C:0.13, G:0.33, T:0.28
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTGACGGGCCA
Found at i:13035903 original size:17 final size:18
Alignment explanation
Indices: 13035870--13035903 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13035860 TTCATAGAAG
13035870 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
13035888 GGTTTTCAAT-AAAACA
1 GGTTTTCAATGAAAACA
13035904 CTTCAATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:13038156 original size:19 final size:19
Alignment explanation
Indices: 13038110--13038157 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
13038100 CCCATACTTG
*
13038110 AAGTTAGTTACAAACCCTA
1 AAGTAAGTTACAAACCCTA
*
13038129 AAATAAGTTACAAACCCTA
1 AAGTAAGTTACAAACCCTA
*
13038148 AAGTGAGTTA
1 AAGTAAGTTA
13038158 ATCTTCGTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (19 bp):
AAGTAAGTTACAAACCCTA
Found at i:13038218 original size:17 final size:18
Alignment explanation
Indices: 13038188--13038236 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
13038178 GATTTATGTC
* * *
13038188 ATTTGTTTATTTTTCTTT
1 ATTTATTTACTTTTCATT
13038206 ATTTATTT-CTTTTCATT
1 ATTTATTTACTTTTCATT
*
13038223 GTTTATTTACTTTT
1 ATTTATTTACTTTT
13038237 ATCTTCCAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.73
Consensus pattern (18 bp):
ATTTATTTACTTTTCATT
Found at i:13045261 original size:17 final size:17
Alignment explanation
Indices: 13045228--13045261 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
13045218 TTCTGGCGTA
13045228 GTTCTGGTTTATCGTGT
1 GTTCTGGTTTATCGTGT
13045245 GTTCTTGGTTTAT-GTGT
1 GTTC-TGGTTTATCGTGT
13045262 ACGCCATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.06, C:0.09, G:0.29, T:0.56
Consensus pattern (17 bp):
GTTCTGGTTTATCGTGT
Found at i:13048702 original size:48 final size:48
Alignment explanation
Indices: 13048631--13048725 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
13048621 TGTCTTGATG
*
13048631 ATGAATCCGGCTTCTGAGATGGATCAATCAGCTTCCTTTGAGTAATTA
1 ATGAATCCGACTTCTGAGATGGATCAATCAGCTTCCTTTGAGTAATTA
13048679 ATGAATCCGACTTCTGAGATGGATCAATCAGCTTCCTTTGAGTAATT
1 ATGAATCCGACTTCTGAGATGGATCAATCAGCTTCCTTTGAGTAATT
13048726 CCTTCCTTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (48 bp):
ATGAATCCGACTTCTGAGATGGATCAATCAGCTTCCTTTGAGTAATTA
Found at i:13057916 original size:46 final size:46
Alignment explanation
Indices: 13057849--13058064 Score: 287
Period size: 46 Copynumber: 4.7 Consensus size: 46
13057839 TGTAACCCGC
13057849 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
* *
13057895 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
* *
13057941 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCGT--TTGCAT
* * * *
13057991 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
13058034 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
13058065 TTCAGATGCC
Statistics
Matches: 149, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
42 1 0.01
43 7 0.05
45 2 0.01
46 102 0.68
47 27 0.18
48 3 0.02
50 6 0.04
51 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
Found at i:13058043 original size:93 final size:92
Alignment explanation
Indices: 13057849--13058074 Score: 289
Period size: 93 Copynumber: 2.4 Consensus size: 92
13057839 TGTAACCCGC
* * *
13057849 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCGTTTGCATCCATAAGTGAACTCAGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTTTACATCCAT-A-CGAACTCAGA
* *
13057912 CTCAACTCAACGAGCTCGGGCGTTCGCAT
64 CTCAACTCAACGAGCTCGGACATTCGCAT
*
13057941 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTC-T-CGAACTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCT--TTACATC-CATACGAACTCAG
* *
13058004 ACTCAACTCAACGAGTTCGGACATTTGCAT
63 ACTCAACTCAACGAGCTCGGACATTCGCAT
* *
13058034 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCC
13058075 CAAACATCCT
Statistics
Matches: 119, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
92 36 0.30
93 72 0.61
94 3 0.03
96 7 0.06
97 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (92 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTTTACATCCATACGAACTCAGACT
CAACTCAACGAGCTCGGACATTCGCAT
Found at i:13058089 original size:46 final size:46
Alignment explanation
Indices: 13057854--13058089 Score: 175
Period size: 46 Copynumber: 5.1 Consensus size: 46
13057844 CCCGCCCATA
* * * *
13057854 AGTGAACTCGGACTCAACTCAACGAGCTCGG--GCGTTTGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTATACATCC-T
* * * *
13057899 AAGTGAACTCAGACTCAACTCAACGAGCTCGG--GCGT-TCGCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAT-ACATCC-T
*
13057945 AAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTA--TACATC-CT
* * * *
13057995 --CGAACTCGGACTCAACTCAACGAGTTCGGA--CATTTGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTATACATCC-T
* * *
13058038 AAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCCAAACATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTATACATCCT
13058085 AGTGA
1 AGTGA
13058090 CATGTCACTT
Statistics
Matches: 161, Mismatches: 16, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
42 1 0.01
43 6 0.04
45 3 0.02
46 106 0.66
47 29 0.18
48 9 0.06
50 5 0.03
51 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTATACATCCT
Found at i:13063009 original size:206 final size:206
Alignment explanation
Indices: 13062648--13063203 Score: 817
Period size: 206 Copynumber: 2.7 Consensus size: 206
13062638 AAATATGCTT
* *
13062648 CTTCGATTTGTTCTCTGACAATACAGAGATGTCAAATCATCTTAGATTTGCTTCAGCGTTAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
** * * * *
13062713 GCAAAAACCAAATCAGCTATGTCTTTGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * * * * * *
13062778 GGATTTGCTTCAGTCTAATCATCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCCGTCGAATATG
131 GGATCTGCTTCAGTATAAACATCTGAAGGCTAGATCTGCTATGTATCTACCCTCCGTCAAATATG
*
13062843 GAGATGCCAAA
196 GAGACGCCAAA
*
13062854 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* * * *
13062919 GTGAAAGCTAAGTCAGCTATGAT-TTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCT
66 GTGAAAGCCAAATCAGCTATG-TCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
* *
13062983 TGGATCTGCTTCAGTATAAACATCTGAAGGCTAGATCTGTTATGTATCTACTCTCCGTCAAATAT
130 TGGATCTGCTTCAGTATAAACATCTGAAGGCTAGATCTGCTATGTATCTACCCTCCGTCAAATAT
13063048 GGAGACGCCAAA
195 GGAGACGCCAAA
* * * * * *
13063060 CTTTGATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGATTTACTTTATCGTAAGCAT
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
*
13063125 GTGAAAGCCAAATCAGCTATGTCTTCGATTTATTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
13063190 GGATCTTGCTTCAG
131 GGATC-TGCTTCAG
13063204 CCAGATCTGC
Statistics
Matches: 312, Mismatches: 35, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
205 1 0.00
206 302 0.97
207 9 0.03
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (206 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTGCTTCAGTATAAACATCTGAAGGCTAGATCTGCTATGTATCTACCCTCCGTCAAATATG
GAGACGCCAAA
Found at i:13075261 original size:57 final size:58
Alignment explanation
Indices: 13075189--13075297 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 58
13075179 GCCCACTGAT
* *
13075189 CGATCTCGCACACATAGTGCTTGGTT-GAAGAACTCGCACACACAGTGCCTCAATTAC
1 CGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTCAATTAC
* * *
13075246 CGATTTCGCACACATAGTGCTCGGTTAAAAGAATTTGCACACACAGTGCCTC
1 CGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTC
13075298 TAATCATTCG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
57 24 0.52
58 22 0.48
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (58 bp):
CGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTCAATTAC
Found at i:13075541 original size:40 final size:40
Alignment explanation
Indices: 13075497--13075613 Score: 128
Period size: 40 Copynumber: 2.9 Consensus size: 40
13075487 GAATACACGT
* * *
13075497 CACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * * *
13075537 CACCAGCACGAATGCTCTTTGAGG-TTTAGCACGGATATAT
1 CACCAGCACGAATGCTCTTCG-GGACTTAGCCCGGATATAA
* * *
13075577 TACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
13075614 CATCACTAGT
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
39 1 0.02
40 59 0.95
41 2 0.03
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
Found at i:13075746 original size:40 final size:40
Alignment explanation
Indices: 13075701--13075857 Score: 172
Period size: 40 Copynumber: 3.9 Consensus size: 40
13075691 CGAATACACG
* * *
13075701 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* * * *
13075741 ACACCAGCACGAATGCTCTTTGAGG-TTTAGCACGGATATA
1 TCACCAGCACGAATGCTCTTCG-GGACTTAGCCCGGATATA
* * * * *
13075781 TTACTAGCACGAATGCTCTTCGGAACTTAGCCCGGGTACA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* *
13075821 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
13075858 CATCATCGAG
Statistics
Matches: 95, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
39 1 0.01
40 92 0.97
41 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
Found at i:13075772 original size:205 final size:205
Alignment explanation
Indices: 13075420--13075827 Score: 807
Period size: 205 Copynumber: 2.0 Consensus size: 205
13075410 AATTTGAATT
13075420 CGTATAGTAATGAACACTTAAACTTTGCTCAAATTACCGGCACGAAGCCTACTAGGCACGAAGGC
1 CGTATAGTAATGAACACTTAAACTTTGCTCAAATTACCGGCACGAAGCCTACTAGGCACGAAGGC
13075485 CCGAATACACGTCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAAT
66 CCGAATACACGTCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAAT
13075550 GCTCTTTGAGGTTTAGCACGGATATATTACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATAC
131 GCTCTTTGAGGTTTAGCACGGATATATTACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATAC
13075615 ATCACTAGTA
196 ATCACTAGTA
13075625 CGTATAGTAATGAACACTTAAACTTTGCTCAAATTACCGGCACGAAGCCTACTAGGCACGAAGGC
1 CGTATAGTAATGAACACTTAAACTTTGCTCAAATTACCGGCACGAAGCCTACTAGGCACGAAGGC
13075690 CCGAATACACGTCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAAT
66 CCGAATACACGTCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAAT
*
13075755 GCTCTTTGAGGTTTAGCACGGATATATTACTAGCACGAATGCTCTTCGGAACTTAGCCCGGGTAC
131 GCTCTTTGAGGTTTAGCACGGATATATTACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATAC
13075820 ATCACTAG
196 ATCACTAG
13075828 CATGAATGCT
Statistics
Matches: 202, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
205 202 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.23
Consensus pattern (205 bp):
CGTATAGTAATGAACACTTAAACTTTGCTCAAATTACCGGCACGAAGCCTACTAGGCACGAAGGC
CCGAATACACGTCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAAT
GCTCTTTGAGGTTTAGCACGGATATATTACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATAC
ATCACTAGTA
Found at i:13079306 original size:29 final size:28
Alignment explanation
Indices: 13079270--13079347 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
13079260 TCACGAGATT
13079270 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
13079300 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
13079327 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
13079348 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:13079565 original size:174 final size:174
Alignment explanation
Indices: 13079300--13079627 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
13079290 AAATTGTACA
*
13079300 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
13079365 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCAACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCAACTTTACCGAGTCAA
13079430 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* *
13079474 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
13079539 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCAACTTTACCGAGTCAA
13079604 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
13079628 ACCTTGAGTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCAACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:13081635 original size:49 final size:49
Alignment explanation
Indices: 13081524--13081667 Score: 229
Period size: 49 Copynumber: 3.0 Consensus size: 49
13081514 TCACATCCAT
* *
13081524 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
* *
13081571 ACTTTCACGTTCATCACATCGGCCATTAGACCTTATCACATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
13081620 ACTTTCACATTCATCACACCGGCCATTAGGCCTTATCACATATATATA
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
13081668 TATTCACATC
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
47 35 0.40
49 53 0.60
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (49 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
Found at i:13089624 original size:18 final size:19
Alignment explanation
Indices: 13089601--13089636 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13089591 ACTGGGCCAT
*
13089601 AAAA-TTTCATTCACATCA
1 AAAATTTTCATACACATCA
13089619 AAAATTTTCATACACATC
1 AAAATTTTCATACACATC
13089637 CATAATGTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTTTCATACACATCA
Found at i:13091600 original size:50 final size:50
Alignment explanation
Indices: 13091491--13091655 Score: 172
Period size: 50 Copynumber: 3.3 Consensus size: 50
13091481 AGATGCCAAC
* * * * * * * *
13091491 GCCATGTCCCAGACATTGTCTTACACT-A-GCTCACACATCAAAGTCGAT
1 GCCATGTCCCAGACATGGTCCTACAATGACTCTCATATATCAAGGCCGAT
*
13091539 GCCATGTCCCAGACATGGTCCTACAATGACTCTCATATATCGAGGCCGAT
1 GCCATGTCCCAGACATGGTCCTACAATGACTCTCATATATCAAGGCCGAT
* * * * * * *
13091589 GCCATGTCCCAGACATGGTCTTACACTGGCTCTTATCTGTCAATGCCGAT
1 GCCATGTCCCAGACATGGTCCTACAATGACTCTCATATATCAAGGCCGAT
13091639 GCCATGTCCCAGACATG
1 GCCATGTCCCAGACATG
13091656 TCTTACACTA
Statistics
Matches: 98, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
48 24 0.24
49 1 0.01
50 73 0.74
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCCTACAATGACTCTCATATATCAAGGCCGAT
Found at i:13091784 original size:44 final size:44
Alignment explanation
Indices: 13091718--13091805 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
13091708 ATTCTCAAGG
*
13091718 TTCAACCGGGAGTTTATGACGTTAAGTCTCATCATACATTACTC
1 TTCAACCGGGAGTTTATCACGTTAAGTCTCATCATACATTACTC
*
13091762 TTCAACGGGGAGTTTATCACGTTAAGTCTCATCATACATTACTC
1 TTCAACCGGGAGTTTATCACGTTAAGTCTCATCATACATTACTC
13091806 ATAGCCACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (44 bp):
TTCAACCGGGAGTTTATCACGTTAAGTCTCATCATACATTACTC
Found at i:13096486 original size:25 final size:26
Alignment explanation
Indices: 13096457--13096579 Score: 151
Period size: 26 Copynumber: 4.8 Consensus size: 26
13096447 CCTCTTTAAT
* **
13096457 AACTGGGGCA-AAGCCTTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
13096482 AACTGGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
* * **
13096507 AACTAGGGCATAAGCCCCTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
* *
13096533 ATCTGGGGCAGAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
13096559 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
13096580 GCACTTCCTC
Statistics
Matches: 82, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
25 31 0.38
26 51 0.62
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.26
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAATA
Found at i:13096568 original size:52 final size:51
Alignment explanation
Indices: 13096457--13096575 Score: 186
Period size: 52 Copynumber: 2.3 Consensus size: 51
13096447 CCTCTTTAAT
**
13096457 AACTGGGGCA-AAGCCTTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCCTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATA
* *
13096507 AACTAGGGCATAAGCCCCTTTCGGTAATCTGGGGCAGAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCCTTTCGGTAAACTGGGGCA-AAGCCCTTTTCAATA
13096559 AACTGGGGCATAAGCCC
1 AACTGGGGCATAAGCCC
13096576 TTTTGCACTT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 9 0.15
51 22 0.35
52 31 0.50
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (51 bp):
AACTGGGGCATAAGCCCCTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATA
Found at i:13096654 original size:20 final size:20
Alignment explanation
Indices: 13096629--13096703 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
13096619 TTATGATTAC
*
13096629 ATCATGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
13096649 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
13096669 ATCATGTGCATATCATATCAT
1 ATCATGTGCATATCATA-CAT
13096690 -TCATGT--ATATCATA
1 ATCATGTGCATATCATA
13096704 TCCCACGTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 8 0.15
20 42 0.79
21 3 0.06
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:13096660 original size:11 final size:11
Alignment explanation
Indices: 13096629--13096684 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
13096619 TTATGATTAC
13096629 ATCATGTGCAT
1 ATCATGTGCAT
* *
13096640 TTCA--TACAT
1 ATCATGTGCAT
13096649 ATCATGTGCAT
1 ATCATGTGCAT
*
13096660 ATCA--TACAT
1 ATCATGTGCAT
13096669 ATCATGTGCAT
1 ATCATGTGCAT
13096680 ATCAT
1 ATCAT
13096685 ATCATTCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:13096702 original size:9 final size:10
Alignment explanation
Indices: 13096646--13096702 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
13096636 GCATTTCATA
13096646 CATATCATGT
1 CATATCATGT
*
13096656 GCATATCAT-A
1 -CATATCATGT
13096666 CATATCATGT
1 CATATCATGT
*
13096676 GCATATCATAT
1 -CATATCATGT
13096687 CAT-TCATGT
1 CATATCATGT
13096696 -ATATCAT
1 CATATCAT
13096703 ATCCCACGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 2 0.05
9 17 0.44
10 3 0.08
11 17 0.44
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (10 bp):
CATATCATGT
Found at i:13098089 original size:30 final size:30
Alignment explanation
Indices: 13098025--13098081 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
13098015 GCAAAAATTG
13098025 TAAAACACAGAGCAATAGCGGCGTTTTTGC
1 TAAAACACAGAGCAATAGCGGCGTTTTTGC
*
13098055 TAAAA-ACTGAGCAATAGCGGCGTTTTT
1 TAAAACACAGAGCAATAGCGGCGTTTTT
13098082 TGTTAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (30 bp):
TAAAACACAGAGCAATAGCGGCGTTTTTGC
Found at i:13098098 original size:41 final size:40
Alignment explanation
Indices: 13098053--13098304 Score: 281
Period size: 41 Copynumber: 6.2 Consensus size: 40
13098043 CGGCGTTTTT
* * * *
13098053 GCTAAAAACTGAGCAAT-AGCGGCGTTTTTTGTTAAAATGCC
1 GCTAAAAACAGAGC-ATCAGCGGCG-CTTTTGGTAAAACGCC
*
13098094 GCTAAAAACAGAGCATTAGCGGCGCTTTTGGTAAAACGCC
1 GCTAAAAACAGAGCATCAGCGGCGCTTTTGGTAAAACGCC
* * * *
13098134 GCTAAAGACCAGAGCATCAACGGTGCTTTTGGTGAAACGCC
1 GCTAAA-AACAGAGCATCAGCGGCGCTTTTGGTAAAACGCC
* * *
13098175 GCTAAAAACCAGAGCATCAGCGGCGTTTTTGGTGAAATGCC
1 GCTAAAAA-CAGAGCATCAGCGGCGCTTTTGGTAAAACGCC
* * *
13098216 GCTAAAGACCAGAGCATCAGCGGCACTTTTGGTAAAATGCC
1 GCTAAA-AACAGAGCATCAGCGGCGCTTTTGGTAAAACGCC
* *
13098257 GCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCC
1 GCTAAA-AACAGAGCATCAGCGGCGCTTTTGGTAAAACGCC
*
13098298 ACTAAAA
1 GCTAAAA
13098305 GTCATGTAAC
Statistics
Matches: 185, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
40 23 0.12
41 161 0.87
42 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (40 bp):
GCTAAAAACAGAGCATCAGCGGCGCTTTTGGTAAAACGCC
Found at i:13098203 original size:123 final size:122
Alignment explanation
Indices: 13098053--13098304 Score: 355
Period size: 123 Copynumber: 2.1 Consensus size: 122
13098043 CGGCGTTTTT
* * *
13098053 GCTAAAAACTGAGCAATAGCGGCGTTTTTTGTTAAAATGCCGCTAAA-AACAGAGCATTAGCGGC
1 GCTAAAAACAGAGCAATAGCGGCG-TTTTTGGTAAAATGCCGCTAAAGAACAGAGCATCAGCGGC
* * *
13098117 GCTTTTGGTAAAACGCCGCTAAAGACCAGAGCATCAACGGTGCTTTTGGTGAAACGCC
65 ACTTTTGGTAAAACGCCGCTAAAGACCAGAGCATCAACGGCGCTTTTGGTAAAACGCC
* *
13098175 GCTAAAAACCAGAGC-ATCAGCGGCGTTTTTGGTGAAATGCCGCTAAAGACCAGAGCATCAGCGG
1 GCTAAAAA-CAGAGCAAT-AGCGGCGTTTTTGGTAAAATGCCGCTAAAGAACAGAGCATCAGCGG
* * *
13098239 CACTTTTGGTAAAATGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCC
64 CACTTTTGGTAAAACGCCGCTAAAGACCAGAGCATCAACGGCGCTTTTGGTAAAACGCC
*
13098298 ACTAAAA
1 GCTAAAA
13098305 GTCATGTAAC
Statistics
Matches: 115, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
122 30 0.26
123 85 0.74
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (122 bp):
GCTAAAAACAGAGCAATAGCGGCGTTTTTGGTAAAATGCCGCTAAAGAACAGAGCATCAGCGGCA
CTTTTGGTAAAACGCCGCTAAAGACCAGAGCATCAACGGCGCTTTTGGTAAAACGCC
Found at i:13098205 original size:82 final size:82
Alignment explanation
Indices: 13098079--13098303 Score: 326
Period size: 82 Copynumber: 2.8 Consensus size: 82
13098069 TAGCGGCGTT
* *
13098079 TTTTGTTAAAATGCCGCTAAAAA-CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAGAC
1 TTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAGAC
**
13098143 CAGAGCATCAACGGTGC
66 CAGAGCATCAACGGCAC
* * * * *
13098160 TTTTGGTGAAACGCCGCTAAAAACCAGAGCATCAGCGGCGTTTTTGGTGAAATGCCGCTAAAGAC
1 TTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAGAC
*
13098225 CAGAGCATCAGCGGCAC
66 CAGAGCATCAACGGCAC
* * *
13098242 TTTTGGTAAAATGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCACTAAA
1 TTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAA
13098304 AGTCATGTAA
Statistics
Matches: 125, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
81 20 0.16
82 105 0.84
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.22
Consensus pattern (82 bp):
TTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAGAC
CAGAGCATCAACGGCAC
Found at i:13098943 original size:24 final size:24
Alignment explanation
Indices: 13098916--13098964 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
13098906 CATATATTTA
13098916 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTTTATATAAAAATTAAT
13098940 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTTTATATAAAAATTAAT
13098964 T
1 T
13098965 GTTATTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
TTAAAAGTTTATATAAAAATTAAT
Found at i:13099355 original size:21 final size:21
Alignment explanation
Indices: 13099329--13099368 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
13099319 AATCATTGAT
*
13099329 AAATAAATAAGAAAACATTAA
1 AAATAAATAAAAAAACATTAA
13099350 AAATAAATAAAAAAACATT
1 AAATAAATAAAAAAACATT
13099369 TGATATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (21 bp):
AAATAAATAAAAAAACATTAA
Found at i:13099832 original size:14 final size:13
Alignment explanation
Indices: 13099783--13099834 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
13099773 CTTAATTTTT
13099783 TATTTATAAAAACCA
1 TATTTATAAAAA--A
13099798 -ATTTATAAAAAA
1 TATTTATAAAAAA
* *
13099810 TAGTAATAAAAAA
1 TATTTATAAAAAA
13099823 TATTTTATAAAA
1 TA-TTTATAAAA
13099835 TTACTTAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 1 0.03
13 12 0.39
14 18 0.58
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (13 bp):
TATTTATAAAAAA
Found at i:13104393 original size:30 final size:31
Alignment explanation
Indices: 13104359--13104429 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 31
13104349 TGATTCTATA
*
13104359 TTTATATTT-AATCTA-ATGTTTATTATTTAT
1 TTTATATTTGAATCTATATGTTTAAT-TTTAT
* * *
13104389 TTTATTTTTGATTCTATATTTTTAATTTTAT
1 TTTATATTTGAATCTATATGTTTAATTTTAT
13104420 TTT-TATTTGA
1 TTTATATTTGA
13104430 TAATGAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 14 0.41
31 13 0.38
32 7 0.21
ACGTcount: A:0.25, C:0.03, G:0.04, T:0.68
Consensus pattern (31 bp):
TTTATATTTGAATCTATATGTTTAATTTTAT
Found at i:13104410 original size:14 final size:12
Alignment explanation
Indices: 13104372--13104424 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
13104362 ATATTTAATC
13104372 TAATGTTTATTATT
1 TAAT-TTTATT-TT
13104386 T-ATTTTATTTT
1 TAATTTTATTTT
*
13104397 TGATTCTATATTTT
1 TAATT-T-TATTTT
13104411 TAATTTTATTTT
1 TAATTTTATTTT
13104423 TA
1 TA
13104425 TTTGATAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
11 3 0.09
12 17 0.49
13 4 0.11
14 11 0.31
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (12 bp):
TAATTTTATTTT
Found at i:13104605 original size:43 final size:43
Alignment explanation
Indices: 13104543--13104648 Score: 167
Period size: 43 Copynumber: 2.5 Consensus size: 43
13104533 TTTAAAATTT
* *
13104543 CATGACCTTTAGTGGCGTTTGTGAGAAAAGCGCCGCTAAAGGC
1 CATGACCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGC
* * *
13104586 CATGACCTTTAGCGACGTTTGTGGGAAAAGCGCCGCTAAAAGT
1 CATGACCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGC
13104629 CATGACCTTTAGCGGCGTTT
1 CATGACCTTTAGCGGCGTTT
13104649 TTTCAAATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (43 bp):
CATGACCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGC
Found at i:13115894 original size:43 final size:43
Alignment explanation
Indices: 13115832--13115976 Score: 236
Period size: 43 Copynumber: 3.4 Consensus size: 43
13115822 TCAATGAACT
* * *
13115832 CGCACACTTAGTGCTAATTAATTAACCGAAGCTATAATTGTAT
1 CGCACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTAC
*
13115875 CACACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTAC
1 CGCACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTAC
*
13115918 CGCACACTTAGTGCCAATTAATTAGCCAAAGCTATAATTGTAC
1 CGCACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTAC
*
13115961 CGCACACTTAATGCCA
1 CGCACACTTAGTGCCA
13115977 GTACATTAAA
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 95 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (43 bp):
CGCACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTAC
Found at i:13122240 original size:6 final size:6
Alignment explanation
Indices: 13122224--13122259 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
13122214 AGTCCCTTTC
*
13122224 TTTTTA CTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
13122260 CCTTTCTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:13123263 original size:4 final size:4
Alignment explanation
Indices: 13123256--13123280 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
13123246 CTTAAAAAAA
13123256 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
13123281 TTAGTAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Done.