Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007845.1 Hibiscus syriacus cultivar Beakdansim tig00110201_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: 2731752
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 6 of 13
Found at i:1119376 original size:13 final size:13
Alignment explanation
Indices: 1119358--1119393 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
1119348 ATTATTATAG
1119358 TAATAATAAAATA
1 TAATAATAAAATA
1119371 TAATAAATAAAATA
1 TAAT-AATAAAATA
1119385 -AATAATAAA
1 TAATAATAAA
1119394 TAATGGGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.27
13 7 0.32
14 9 0.41
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAATAATAAAATA
Found at i:1119389 original size:16 final size:14
Alignment explanation
Indices: 1119358--1119396 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
1119348 ATTATTATAG
1119358 TAAT-AATAAAATA
1 TAATAAATAAAATA
1119371 TAATAAATAAAATAAA
1 TAATAAATAAAAT--A
1119387 TAATAAATAA
1 TAATAAATAA
1119397 TGGGTAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 8 0.35
16 11 0.48
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
TAATAAATAAAATA
Found at i:1121876 original size:65 final size:65
Alignment explanation
Indices: 1121800--1121931 Score: 264
Period size: 65 Copynumber: 2.0 Consensus size: 65
1121790 GTACTTTGTC
1121800 ATCTATAATATTTTTTCAAATAATTTCATTTTTAGCATATATTTACATAAAATCAATTTAATTAT
1 ATCTATAATATTTTTTCAAATAATTTCATTTTTAGCATATATTTACATAAAATCAATTTAATTAT
1121865 ATCTATAATATTTTTTCAAATAATTTCATTTTTAGCATATATTTACATAAAATCAATTTAATTAT
1 ATCTATAATATTTTTTCAAATAATTTCATTTTTAGCATATATTTACATAAAATCAATTTAATTAT
1121930 AT
1 AT
1121932 TTAAAATGTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (65 bp):
ATCTATAATATTTTTTCAAATAATTTCATTTTTAGCATATATTTACATAAAATCAATTTAATTAT
Found at i:1121923 original size:33 final size:32
Alignment explanation
Indices: 1121817--1121923 Score: 110
Period size: 33 Copynumber: 3.3 Consensus size: 32
1121807 ATATTTTTTC
1121817 AAATAATTTCATTTTTAGCATATATTTACATA
1 AAATAATTTCATTTTTAGCATATATTTACATA
* * * ** *
1121849 AAATCAATTT-AATTATATCTATAATATTT-TTTC
1 AAAT-AATTTCATTTTTAGC-AT-ATATTTACATA
1121882 AAATAATTTCATTTTTAGCATATATTTACATA
1 AAATAATTTCATTTTTAGCATATATTTACATA
1121914 AAATCAATTT
1 AAAT-AATTT
1121924 AATTATATTT
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
31 6 0.11
32 22 0.39
33 23 0.40
34 6 0.11
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (32 bp):
AAATAATTTCATTTTTAGCATATATTTACATA
Found at i:1122088 original size:15 final size:15
Alignment explanation
Indices: 1122068--1122100 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1122058 TCTCAAAGTT
1122068 AACCCTAAA-CTCTAA
1 AACCCTAAATC-CTAA
1122083 AACCCTAAATCCTAA
1 AACCCTAAATCCTAA
1122098 AAC
1 AAC
1122101 TCATAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.18
Consensus pattern (15 bp):
AACCCTAAATCCTAA
Found at i:1123331 original size:129 final size:130
Alignment explanation
Indices: 1123183--1123448 Score: 489
Period size: 129 Copynumber: 2.1 Consensus size: 130
1123173 ACCTTTAAAC
* *
1123183 TTGTATTTTCTTAAATTTAAGAGTGGATTAATTTTTTTATAATTTAAATATTATATTTTAAATTT
1 TTGTATTTTCTTAAATTTAAGAGTGGATTAATTTTTTTATAATTTAAATATGATATTATAAATTT
1123248 TATTCTGTCATCAATTATATATGTATAATAGTAAAGGTTTAATTTTAGATTAAAC-AATTATTAT
66 TATTCTGTCATCAATTATATATGTATAATAGTAAAGGTTTAATTTTAGATTAAACAAATTATTAT
1123312 TTGTATTTTCTTAAATTTAAGAGTGGATTAATTTTTTTATAATTTAAATATGATATTATAAATTT
1 TTGTATTTTCTTAAATTTAAGAGTGGATTAATTTTTTTATAATTTAAATATGATATTATAAATTT
* *
1123377 TATTCTGTCATCATTTATATATGTATAATATTAAAGGTTTAATTTTAGATTAAACAAATTATTAT
66 TATTCTGTCATCAATTATATATGTATAATAGTAAAGGTTTAATTTTAGATTAAACAAATTATTAT
1123442 TTGTATT
1 TTGTATT
1123449 GATATTGTTA
Statistics
Matches: 132, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
129 116 0.88
130 16 0.12
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.52
Consensus pattern (130 bp):
TTGTATTTTCTTAAATTTAAGAGTGGATTAATTTTTTTATAATTTAAATATGATATTATAAATTT
TATTCTGTCATCAATTATATATGTATAATAGTAAAGGTTTAATTTTAGATTAAACAAATTATTAT
Found at i:1124542 original size:73 final size:73
Alignment explanation
Indices: 1124423--1124569 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
1124413 ACATATTGGA
1124423 CGGAATGCGAAATTTGGCTTGCAAAATGGACAACAGGGAAGCATAGAAGTTACTCGTCCTTGATA
1 CGGAATGCGAAATTTGGCTTGCAAAATGGACAACAGGGAAGCATAGAAGTTACTCGTCCTTGATA
1124488 TAAACATC
66 TAAACATC
1124496 CGGAATGCGAAATTTGGCTTGCAAAATGGACAACAGGGAAGCATAGAAGTTACTCGTCCTTGATA
1 CGGAATGCGAAATTTGGCTTGCAAAATGGACAACAGGGAAGCATAGAAGTTACTCGTCCTTGATA
1124561 TAAACATC
66 TAAACATC
1124569 C
1 C
1124570 CTTCATCCAC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (73 bp):
CGGAATGCGAAATTTGGCTTGCAAAATGGACAACAGGGAAGCATAGAAGTTACTCGTCCTTGATA
TAAACATC
Found at i:1137224 original size:162 final size:162
Alignment explanation
Indices: 1136957--1137286 Score: 507
Period size: 162 Copynumber: 2.0 Consensus size: 162
1136947 TTTCCTGATT
* * *
1136957 CATTTGTATCCTTCTTGACTGAAGAAGATACATCACTGTAATCTCCACTTGCTGGTTGAGATTGA
1 CATTTGTATCCTTCTTGACTGAAGAAGAAACATCACCGTAATCTCCACTTGCTGATTGAGATTGA
* * * *
1137022 ACTATATCCCCGGACTTGTGCATATTGCCTAAAGGCTGAGATTCTGATCCCTGTCCAGCAGTAGC
66 ACTACATCCCCAGACTTGTGCATATCGCCTAAAGGCTGAGATTCTGATCCCTGTCCAGCAATAGC
* * *
1137087 TTTCTCCGAGCCAACTTGATTGGTATCAGTCC
131 TTTCTCCGACCCAACTTGATTGCTATCAATCC
* * *
1137119 CATTTGTATCCTTCTTGACTGAAGAAGAAATATCACCGTGATTTCCACTTGCTGATTGAGATTGA
1 CATTTGTATCCTTCTTGACTGAAGAAGAAACATCACCGTAATCTCCACTTGCTGATTGAGATTGA
* * * *
1137184 CCTACATCCCCAGACTTTTGCATATCGTCTGAAGGCTGAGATTCTGATCCCTGTCCAGCAATAGC
66 ACTACATCCCCAGACTTGTGCATATCGCCTAAAGGCTGAGATTCTGATCCCTGTCCAGCAATAGC
1137249 TTTCTCCGACCCAACTTGATTGCTATCAATCC
131 TTTCTCCGACCCAACTTGATTGCTATCAATCC
1137281 CATTTG
1 CATTTG
1137287 CCAAATCCTG
Statistics
Matches: 151, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
162 151 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (162 bp):
CATTTGTATCCTTCTTGACTGAAGAAGAAACATCACCGTAATCTCCACTTGCTGATTGAGATTGA
ACTACATCCCCAGACTTGTGCATATCGCCTAAAGGCTGAGATTCTGATCCCTGTCCAGCAATAGC
TTTCTCCGACCCAACTTGATTGCTATCAATCC
Found at i:1141870 original size:26 final size:26
Alignment explanation
Indices: 1141830--1141903 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
1141820 AGCACATGTC
** *
1141830 ACACACCGAAATACATCACTAACGTG
1 ACACACCGATGTACACCACTAACGTG
*
1141856 ACACATCGATGTACACCACTAACGTG
1 ACACACCGATGTACACCACTAACGTG
**
1141882 ACACACCGATACACACCACTAA
1 ACACACCGATGTACACCACTAA
1141904 TTAAAATGTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.41, C:0.34, G:0.11, T:0.15
Consensus pattern (26 bp):
ACACACCGATGTACACCACTAACGTG
Found at i:1142554 original size:2 final size:2
Alignment explanation
Indices: 1142549--1142583 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1142539 AGTGTGTGTG
1142549 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1142584 GAACTTATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1142933 original size:43 final size:42
Alignment explanation
Indices: 1142881--1143256 Score: 445
Period size: 43 Copynumber: 8.8 Consensus size: 42
1142871 TGAGAACAAA
* * *
1142881 AAACGCCGCAATAGGTCAAGATCTATCGCGGCGTTTTTGGAGC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
* * *
1142924 AAACGCCGCAAAAGATCGATATCTATAGCGGCGTTTTT-TAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
1142966 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
* *
1143009 AAACGCCGCAAAAGGTTAGACCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
* **
1143052 AAACGCCGCAAAAGGTCAGACCTATAGCGATGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
* * * *
1143094 AAACGCCGCAAAACGTTAGATCTATAGTGTCGTTTTTTGGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCG-TTTTTGGAAC
* *
1143137 AAACGTCGCAAAAGGTCAATATCTATAGCGGCG-TTTTGGAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
* * * * *
1143179 AAACGCCGTAAACGGACAGATCTATAGCGGCGTTTTT-TATATA
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-A-C
1143222 AAACGCCGCAAAAGGGT-AGATCTATAGCGGCGTTT
1 AAACGCCGCAAAA-GGTCAGATCTATAGCGGCGTTT
1143257 GTATCTAAAT
Statistics
Matches: 288, Mismatches: 37, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
41 34 0.12
42 74 0.26
43 166 0.58
44 14 0.05
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
Found at i:1142983 original size:85 final size:84
Alignment explanation
Indices: 1142881--1143256 Score: 440
Period size: 85 Copynumber: 4.4 Consensus size: 84
1142871 TGAGAACAAA
* * * * *
1142881 AAACGCCGCAATAGGTCAAGATCTATCGCGGCGTTTTTGGAGCAAACGCCGCAAAAGATCGATAT
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGAT-TAGAT
1142946 CTATAGCGGCGTTTTTTA-AC
64 CTATAGCGGCGTTTTTTATAC
* *
1142966 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTTAGACC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGATTAGATC
*
1143031 TATAGCGGCGTTTTTGGATAC
65 TATAGCGGCGTTTTT-TATAC
* **
1143052 AAACGCCGCAAAAGGTCAGACCTATAGCGATGTTTTTGGAACAAACGCCGCAAAACG-TTAGATC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAA-GATTAGATC
* *
1143116 TATAGTGTCGTTTTTTGGA-AC
65 TATAGCGGCGTTTTTT--ATAC
* * * * *
1143137 AAACGTCGCAAAAGGTCAATATCTATAGCGGCG-TTTTGGAACAAACGCCGTAAACGGA-CAGAT
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA-AGATTAGAT
*
1143200 CTATAGCGGCGTTTTTTATATA
64 CTATAGCGGCGTTTTTTATA-C
1143222 AAACGCCGCAAAAGGGT-AGATCTATAGCGGCGTTT
1 AAACGCCGCAAAA-GGTCAGATCTATAGCGGCGTTT
1143257 GTATCTAAAT
Statistics
Matches: 250, Mismatches: 28, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
83 1 0.00
84 55 0.22
85 139 0.56
86 55 0.22
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (84 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATTAGATCT
ATAGCGGCGTTTTTTATAC
Found at i:1143055 original size:128 final size:125
Alignment explanation
Indices: 1142881--1143256 Score: 461
Period size: 128 Copynumber: 2.9 Consensus size: 125
1142871 TGAGAACAAA
* * * *
1142881 AAACGCCGCAATAGGTCAAGATCTATCGCGGCGTTTTTGGAGCAAACGCCGCAAAAGATCGATAT
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATC-AGAT
1142946 CTATAGCGGCGTTTTTTAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
65 CTATAGCGGCGTTTTTTAACAAACGCCGCAAAAGGT-AGATCTATAGCGGCGTTTTTGGA-AC
* * * *
1143009 AAACGCCGCAAAAGGT-TAGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGAC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGATCAGAT
** * * * *
1143073 CTATAGCGATGTTTTTGGAACAAACGCCGCAAAACGTTAGATCTATAGTGTCGTTTTTTGGAAC
65 CTATAGCGGCGTTTTT-TAACAAACGCCGCAAAA-GGTAGATCTATAGCGGCG-TTTTTGGAAC
* * * *
1143137 AAACGTCGCAAAAGGTCAATATCTATAGCGGCG-TTTTGGAACAAACGCCGTAAACGGA-CAGAT
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA-AGATCAGAT
*
1143200 CTATAGCGGCGTTTTTTATATAAAACGCCGCAAAAGGGTAGATCTATAGCGGCGTTT
65 CTATAGCGGCGTTTTTTA-A-CAAACGCCGCAAAA-GGTAGATCTATAGCGGCGTTT
1143257 GTATCTAAAT
Statistics
Matches: 210, Mismatches: 30, Indels: 17
0.82 0.12 0.07
Matches are distributed among these distances:
126 1 0.00
127 72 0.34
128 114 0.54
129 23 0.11
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (125 bp):
AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATCAGATC
TATAGCGGCGTTTTTTAACAAACGCCGCAAAAGGTAGATCTATAGCGGCGTTTTTGGAAC
Found at i:1145244 original size:18 final size:18
Alignment explanation
Indices: 1145221--1145265 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1145211 CCAGGGTCAT
1145221 CATCAAAGTTGCCGACAA
1 CATCAAAGTTGCCGACAA
1145239 CATCAAAGTTGCCGACAA
1 CATCAAAGTTGCCGACAA
1145257 CATCAAAGT
1 CATCAAAGT
1145266 ATAGAACAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.40, C:0.27, G:0.16, T:0.18
Consensus pattern (18 bp):
CATCAAAGTTGCCGACAA
Found at i:1148171 original size:41 final size:41
Alignment explanation
Indices: 1148100--1148506 Score: 368
Period size: 41 Copynumber: 10.0 Consensus size: 41
1148090 ACGTTTATCC
* * *
1148100 TAAAAATGCCACAAAAGTAC-AGTATTTAGCGGCGTTTGTA
1 TAAAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTTTGTA
* * *
1148140 TAAAAGCGCCA-TAAAAATACTAGTCTATAGCGGCGTTTGT-
1 TAAAAACGCCACT-AAAGTACTAGTCTTTAGCGGCGTTTGTA
** *
1148180 TCAAAAAATACCACTAAAGAAC-AGTACTTTAGCGGCGTTTGT-
1 T--AAAAACGCCACTAAAGTACTAGT-CTTTAGCGGCGTTTGTA
* * *
1148222 TCAAAAACACCACTAAAGTAC-AGTATTTTAGCGGCATTTGTA
1 T-AAAAACGCCACTAAAGTACTAGT-CTTTAGCGGCGTTTGTA
* * * *
1148264 TAAAAACGCCACAAAAGTACTAGTCTATAGCGGTGTTTTTCA
1 TAAAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTTTGT-A
* *
1148306 -AAAAACGCCACTAAAGTAC-ATTCTTTAACGGCGTTTGTA
1 TAAAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTTTGTA
* * * * *
1148345 TAAAAACGCCACTAAAATACTAATCTATAGCGGCGCTTGTTT
1 TAAAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTTTG-TA
* * * *
1148387 TGAAAACGCCACTAAA-TAATA-TACTTTGGCGACGTTTGTA
1 TAAAAACGCCACTAAAGTACTAGT-CTTTAGCGGCGTTTGTA
* *
1148427 TGAAAATGCCACTAAAGTAC-AGTCTTTAGCGGCGTTTGTA
1 TAAAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTTTGTA
* * *
1148467 TAAAAACGCCACTAAAGTACTAGTATTTAACGACGTTTGT
1 TAAAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTTTGT
1148507 TCTAGAAATG
Statistics
Matches: 299, Mismatches: 52, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
39 1 0.00
40 99 0.33
41 149 0.50
42 49 0.16
43 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (41 bp):
TAAAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTTTGTA
Found at i:1163081 original size:22 final size:22
Alignment explanation
Indices: 1163034--1163089 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1163024 TTATTTCAGT
* *
1163034 CTTTATGGCACGTTTTCTCTGC
1 CTTTATGGCACGTTCTCTCTGA
1163056 CTTTATGGCACGTTCTCATCT-A
1 CTTTATGGCACGTTCTC-TCTGA
*
1163078 CTTTTTGGCACG
1 CTTTATGGCACG
1163090 CTTTTGGTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 27 0.90
23 3 0.10
ACGTcount: A:0.12, C:0.27, G:0.18, T:0.43
Consensus pattern (22 bp):
CTTTATGGCACGTTCTCTCTGA
Found at i:1165884 original size:7 final size:7
Alignment explanation
Indices: 1165848--1165897 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
1165838 TGAAAACGAT
1165848 TAAATAA
1 TAAATAA
*
1165855 -AAAAAA
1 TAAATAA
1165861 TAAA-AA
1 TAAATAA
*
1165867 CAAA-AA
1 TAAATAA
*
1165873 CAAATAA
1 TAAATAA
1165880 TAAATAA
1 TAAATAA
1165887 TAAATAA
1 TAAATAA
1165894 TAAA
1 TAAA
1165898 AAAGAATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 16 0.42
7 22 0.58
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (7 bp):
TAAATAA
Found at i:1165891 original size:14 final size:13
Alignment explanation
Indices: 1165848--1165899 Score: 61
Period size: 14 Copynumber: 4.0 Consensus size: 13
1165838 TGAAAACGAT
*
1165848 TAAATAAAAAAAA
1 TAAATAATAAAAA
*
1165861 TAAA-AACAAAAA
1 TAAATAATAAAAA
*
1165873 CAAATAATAAATAA
1 TAAATAATAAA-AA
1165887 TAAATAATAAAAA
1 TAAATAATAAAAA
1165900 AGAATAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.30
13 11 0.33
14 12 0.36
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (13 bp):
TAAATAATAAAAA
Found at i:1165920 original size:5 final size:5
Alignment explanation
Indices: 1165910--1165961 Score: 70
Period size: 5 Copynumber: 10.2 Consensus size: 5
1165900 AGAATAAAAG
*
1165910 AATAT AATAT AATAT AATAT AATAT AGTAT AATAT -ATAT ATATAT ATATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT A-ATAT A-ATAT
1165961 A
1 A
1165962 TTTATAAACT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
4 4 0.09
5 28 0.65
6 11 0.26
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (5 bp):
AATAT
Found at i:1165948 original size:2 final size:2
Alignment explanation
Indices: 1165911--1165967 Score: 61
Period size: 2 Copynumber: 30.5 Consensus size: 2
1165901 GAATAAAAGA
1165911 AT AT A- AT AT A- AT AT A- AT AT A- AT AT AGT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
*
1165949 AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT A
1165968 AACTTGTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
1 5 0.11
2 40 0.85
3 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1165987 original size:35 final size:35
Alignment explanation
Indices: 1165946--1166175 Score: 122
Period size: 35 Copynumber: 6.4 Consensus size: 35
1165936 GTATAATATA
1165946 TATATATATATATATATTTATAAACTTGTTTTAAAAC
1 TATATATATATATAT-TTTA-AAACTTGTTTTAAAAC
*
1165983 TATATATAATATATATTTCAAAGA-TAT-TTTTAAAA-
1 TATATAT-ATATATATTTTAAA-ACT-TGTTTTAAAAC
** *
1166018 TCATATAT-TATATAATTTTAAAAAATGTTTTCAAAC
1 T-ATATATATATAT-ATTTTAAAACTTGTTTTAAAAC
*
1166054 TATATGT-TATATAGTTTTCAAAAC--GTTTTAAAAC
1 TATATATATATATA-TTTT-AAAACTTGTTTTAAAAC
* * * ** *
1166088 TATAT-TATATGT-TTTCAAAA-ATGTTTTTTTAGC
1 TATATATATATATATTTTAAAACTTG-TTTTAAAAC
*
1166121 TATATATTATATATATTTTCAAAA-TATTTTTTAAAAAAC
1 TATATA-TATATATATTTT-AAAACT-TGTTTT--AAAAC
*
1166160 TATACAATATATATAT
1 TATA-TATATATATAT
1166176 ATATATATAT
Statistics
Matches: 151, Mismatches: 20, Indels: 42
0.71 0.09 0.20
Matches are distributed among these distances:
31 4 0.03
32 4 0.03
33 12 0.08
34 26 0.17
35 35 0.23
36 25 0.17
37 20 0.13
38 9 0.06
39 15 0.10
40 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (35 bp):
TATATATATATATATTTTAAAACTTGTTTTAAAAC
Found at i:1166088 original size:34 final size:34
Alignment explanation
Indices: 1165973--1166386 Score: 208
Period size: 37 Copynumber: 12.1 Consensus size: 34
1165963 TTATAAACTT
*
1165973 GTTTTAAAACTATATATAATATA-TATTTCAAAGATA
1 GTTTTAAAACTATATATTATATAGT-TTTCAAA-A-A
* * *
1166009 TTTTTAAAA-TCATATATTATATAATTTTAAAAAA
1 GTTTTAAAACT-ATATATTATATAGTTTTCAAAAA
* * *
1166043 TGTTTTCAAACTATATGTTATATAGTTTTCAAAAC
1 -GTTTTAAAACTATATATTATATAGTTTTCAAAAA
1166078 GTTTTAAAAC--TATATTATAT-GTTTTCAAAAA
1 GTTTTAAAACTATATATTATATAGTTTTCAAAAA
** * *
1166109 TGTTTTTTTAGCTATATATTATATATATTTTCAAAATA
1 -G-TTTTAAAACTATATATTATATA-GTTTTCAAAA-A
* * * * *
1166147 TTTTTTAAAAAACTATACA--ATATA--TAT-ATATA
1 -GTTTT--AAAACTATATATTATATAGTTTTCAAAAA
* * * *
1166179 --TAT-ATA-TATATA-TATATA-TATTAAAAAA
1 GTTTTAAAACTATATATTATATAGTTTTCAAAAA
*
1166207 -TTTCAAAACTATATATTATATAAG-TTTC----A
1 GTTTTAAAACTATATATTATAT-AGTTTTCAAAAA
*
1166236 -TTTTAAAACTATATATTATATAAGTTTTCAAAAT
1 GTTTTAAAACTATATATTATAT-AGTTTTCAAAAA
1166270 GATTTTAAAAACTATATATTATATATGTTTTCTAAAAA
1 G-TTTT-AAAACTATATATTATATA-GTTTTC-AAAAA
* *
1166308 TGTTTTAAAAACTACATATTATATAGTTTTCACAAGTA
1 -GTTTT-AAAACTATATATTATATAGTTTTCA-AA-AA
* * *
1166346 TTTTTAAAAACTATATATTATATACATTTTCAAAAT
1 GTTTT-AAAACTATATATTATATA-GTTTTCAAAAA
1166382 GTTTT
1 GTTTT
1166387 TTTTTTAAAA
Statistics
Matches: 295, Mismatches: 47, Indels: 72
0.71 0.11 0.17
Matches are distributed among these distances:
25 5 0.02
26 7 0.02
27 1 0.00
28 3 0.01
29 27 0.09
30 6 0.02
31 16 0.05
32 16 0.05
33 11 0.04
34 12 0.04
35 38 0.13
36 36 0.12
37 74 0.25
38 35 0.12
39 8 0.03
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (34 bp):
GTTTTAAAACTATATATTATATAGTTTTCAAAAA
Found at i:1166124 original size:67 final size:70
Alignment explanation
Indices: 1165945--1166144 Score: 185
Period size: 71 Copynumber: 2.8 Consensus size: 70
1165935 AGTATAATAT
** * * *
1165945 ATATATATATATATATATTTATAAACTTGTTTTAAAACTATATATAATATATA-TTTCAAAGATA
1 ATATAT-TATATA-AT-TTTA-AAAAATGTTTTCAAACTATATATTATATATATTTTCAAA-A-C
*
1166009 TTTTTAAAATC
60 GTTTTAAAATC
* *
1166020 ATATATTATATAATTTTAAAAAATGTTTTCAAACTATATGTTATATA-GTTTTCAAAACGTTTTA
1 ATATATTATATAATTTTAAAAAATGTTTTCAAACTATATATTATATATATTTTCAAAACGTTTTA
1166084 AAA-C
66 AAATC
* * ** *
1166088 -TATATTATAT-GTTTTCAAAAATGTTTTTTTAGCTATATATTATATATATTTTCAAAA
1 ATATATTATATAATTTTAAAAAATG-TTTTCAAACTATATATTATATATATTTTCAAAA
1166145 TATTTTTTAA
Statistics
Matches: 107, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
66 11 0.10
67 28 0.26
68 10 0.09
69 8 0.07
70 1 0.01
71 31 0.29
72 4 0.04
73 2 0.02
74 6 0.06
75 6 0.06
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (70 bp):
ATATATTATATAATTTTAAAAAATGTTTTCAAACTATATATTATATATATTTTCAAAACGTTTTA
AAATC
Found at i:1166171 original size:2 final size:2
Alignment explanation
Indices: 1166166--1166199 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1166156 AAACTATACA
1166166 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1166200 TAAAAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1166238 original size:29 final size:29
Alignment explanation
Indices: 1166206--1166262 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1166196 ATATTAAAAA
1166206 ATTTCAAAACTATATATTATATAAGTTTC
1 ATTTCAAAACTATATATTATATAAGTTTC
*
1166235 ATTTTAAAACTATATATTATATAAGTTT
1 ATTTCAAAACTATATATTATATAAGTTT
1166263 TCAAAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (29 bp):
ATTTCAAAACTATATATTATATAAGTTTC
Found at i:1166295 original size:75 final size:75
Alignment explanation
Indices: 1166216--1166369 Score: 179
Period size: 75 Copynumber: 2.1 Consensus size: 75
1166206 ATTTCAAAAC
*** *
1166216 TATATATTATATAAGTTTCATTTT-AAAACTATATATTATATAAGTTTTCAAAA-TGA-TTTTAA
1 TATATATTATATAAAAAT-ATTTTAAAAACTACATATTATAT-AGTTTTCAAAAGT-ATTTTTAA
1166278 AAACTATATATTA
63 AAACTATATATTA
* * * * *
1166291 TATATGTTTTCTAAAAATGTTTTAAAAACTACATATTATATAGTTTTCACAAGTATTTTTAAAAA
1 TATATATTATATAAAAATATTTTAAAAACTACATATTATATAGTTTTCAAAAGTATTTTTAAAAA
1166356 CTATATATTA
66 CTATATATTA
1166366 TATA
1 TATA
1166370 CATTTTCAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
74 15 0.22
75 52 0.78
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (75 bp):
TATATATTATATAAAAATATTTTAAAAACTACATATTATATAGTTTTCAAAAGTATTTTTAAAAA
CTATATATTA
Found at i:1166376 original size:75 final size:72
Alignment explanation
Indices: 1166236--1166386 Score: 207
Period size: 75 Copynumber: 2.1 Consensus size: 72
1166226 ATAAGTTTCA
* **
1166236 TTTTAAAACTATATATTATATAAGTTTTCAAAATGATTTTAAAAACTATATATTATATATGTTTT
1 TTTTAAAACTACATATTATATAAGTTTTCAAAATGATTTTAAAAACTATATATTATATACATTTT
1166301 CTAAAAATG
66 C--AAAATG
*
1166310 TTTTAAAAACTACATATTATAT-AGTTTTCACAA-GTATTTTTAAAAACTATATATTATATACAT
1 TTTT-AAAACTACATATTATATAAGTTTTCAAAATG-A-TTTTAAAAACTATATATTATATACAT
1166373 TTTCAAAATG
63 TTTCAAAATG
1166383 TTTT
1 TTTT
1166387 TTTTTTAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
73 11 0.16
74 15 0.21
75 44 0.63
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (72 bp):
TTTTAAAACTACATATTATATAAGTTTTCAAAATGATTTTAAAAACTATATATTATATACATTTT
CAAAATG
Found at i:1166467 original size:18 final size:17
Alignment explanation
Indices: 1166440--1166479 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
1166430 TTGCAAACAA
1166440 TATAATATATATATATG
1 TATAATATATATATATG
1166457 TATAGATATATATATATG
1 TATA-ATATATATATATG
1166475 TATAA
1 TATAA
1166480 AATAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (17 bp):
TATAATATATATATATG
Found at i:1187826 original size:21 final size:21
Alignment explanation
Indices: 1187802--1187860 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
1187792 TTCGTTCAAG
1187802 ATGGGGAATCGATTCCCATTC
1 ATGGGGAATCGATTCCCATTC
1187823 ATGGGGAATCGATTCCCATTC
1 ATGGGGAATCGATTCCCATTC
* * *
1187844 ATAGGGTATCGGTTCCC
1 ATGGGGAATCGATTCCC
1187861 TCTACCCAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (21 bp):
ATGGGGAATCGATTCCCATTC
Found at i:1187966 original size:19 final size:19
Alignment explanation
Indices: 1187922--1187966 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1187912 TTCTTTTATT
*
1187922 TTAAACACCTACCATGTCA
1 TTAAACCCCTACCATGTCA
1187941 TTAAACCCCTACCATGTCA
1 TTAAACCCCTACCATGTCA
1187960 TTAAACC
1 TTAAACC
1187967 TAACCACCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.33, G:0.04, T:0.27
Consensus pattern (19 bp):
TTAAACCCCTACCATGTCA
Found at i:1195598 original size:2 final size:2
Alignment explanation
Indices: 1195591--1195623 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1195581 AGCTGATTCG
1195591 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1195624 TGAAATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1195613 original size:15 final size:15
Alignment explanation
Indices: 1195593--1195622 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1195583 CTGATTCGAT
1195593 ATATATATATATATA
1 ATATATATATATATA
1195608 ATATATATATATATA
1 ATATATATATATATA
1195623 TTGAAATGAA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:1195613 original size:17 final size:17
Alignment explanation
Indices: 1195591--1195623 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1195581 AGCTGATTCG
1195591 ATATATATATATATATA
1 ATATATATATATATATA
1195608 ATATATATATATATAT
1 ATATATATATATATAT
1195624 TGAAATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:1195801 original size:2 final size:2
Alignment explanation
Indices: 1195796--1195828 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1195786 ACTTTATATA
1195796 CT CT CT CT CT CT -T CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1195829 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:1198725 original size:12 final size:12
Alignment explanation
Indices: 1198692--1198726 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1198682 TTTAAATAAT
*
1198692 AAAATTGATAAAA
1 AAAATT-ATTAAA
1198705 AAAATTATTAAA
1 AAAATTATTAAA
1198717 AAAATTATTA
1 AAAATTATTA
1198727 TTTTTATCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (12 bp):
AAAATTATTAAA
Found at i:1198876 original size:21 final size:21
Alignment explanation
Indices: 1198851--1198894 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1198841 AAAAATATTA
* *
1198851 AAAAATATTAATATTTTAGAT
1 AAAAATAATAATATTTTAAAT
1198872 AAAAATAATAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
1198893 AA
1 AA
1198895 TGTTTTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAAT
Found at i:1204815 original size:18 final size:18
Alignment explanation
Indices: 1204792--1204843 Score: 104
Period size: 18 Copynumber: 2.9 Consensus size: 18
1204782 ATATAACACA
1204792 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
1204810 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
1204828 TATGTCCCGAAGGACC
1 TATGTCCCGAAGGACC
1204844 GCGTAAACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.27, C:0.33, G:0.23, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:1205199 original size:19 final size:20
Alignment explanation
Indices: 1205174--1205219 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
1205164 CCTATAATCA
1205174 TTTATATCTATACCACATAG
1 TTTATATCTATACCACATAG
1205194 -TTATATCTATACCACATAG
1 TTTATATCTATACCACATAG
1205213 TTTATAT
1 TTTATAT
1205220 AACTTTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.43
Consensus pattern (20 bp):
TTTATATCTATACCACATAG
Found at i:1205683 original size:24 final size:20
Alignment explanation
Indices: 1205630--1205687 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1205620 TTCCCCTTGA
*
1205630 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
1205650 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
1205673 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1205688 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1205762 original size:64 final size:64
Alignment explanation
Indices: 1205675--1205835 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 64
1205665 TCTTTAACAT
* * *
1205675 GTGCATCGATGCACTACC-CATGCATCGATACACCAATCACCTTCGATGTTTTCA-TTTTAAGGG
1 GTGCATCGATGCACT-CCTTATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTAA-GG
1205738 G
64 G
* * *** * *
1205739 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTGTATTCGATGTTTCCATTTTTTATGG
1 GTGCATCGATGCACTCCTTATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTAAGGG
* * *
1205803 GTGCATCGATGCACTTCTTGTACATCGATACAC
1 GTGCATCGATGCACTCCTTATGCATCGATACAC
1205836 ACTGAACAAT
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
63 2 0.02
64 74 0.91
65 5 0.06
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTCCTTATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:1207601 original size:21 final size:22
Alignment explanation
Indices: 1207577--1207625 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
1207567 TATTAGAAAC
1207577 ATTATTATTTC-TAT-TGATTTT
1 ATTATTATTTCTTATATG-TTTT
1207598 ATTATT-TTTCTTATATGTTTT
1 ATTATTATTTCTTATATGTTTT
1207619 ATTATTA
1 ATTATTA
1207626 ATGAACATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.16
21 19 0.76
22 2 0.08
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (22 bp):
ATTATTATTTCTTATATGTTTT
Found at i:1224860 original size:61 final size:61
Alignment explanation
Indices: 1224765--1224886 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
1224755 CCCCTTTTGC
1224765 TCTTTTGGGTTTTCAGAGGGTGAACTTACTTTAACAATTTCATTAAGAGTCTACTTAAATG
1 TCTTTTGGGTTTTCAGAGGGTGAACTTACTTTAACAATTTCATTAAGAGTCTACTTAAATG
1224826 TCTTTTGGGTTTTCAGAGGGTGAACTTACTTTAACAATTTCATTAAGAGTCTACTTAAATG
1 TCTTTTGGGTTTTCAGAGGGTGAACTTACTTTAACAATTTCATTAAGAGTCTACTTAAATG
1224887 GGGATGCTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (61 bp):
TCTTTTGGGTTTTCAGAGGGTGAACTTACTTTAACAATTTCATTAAGAGTCTACTTAAATG
Found at i:1225103 original size:14 final size:14
Alignment explanation
Indices: 1225084--1225127 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
1225074 TGTGTTTTTG
1225084 TTTATATGCAGAAA
1 TTTATATGCAGAAA
1225098 TTTATATGCAGAAA
1 TTTATATGCAGAAA
* *
1225112 TTTATTTGTAGAAA
1 TTTATATGCAGAAA
1225126 TT
1 TT
1225128 ACTCCCTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.43
Consensus pattern (14 bp):
TTTATATGCAGAAA
Found at i:1225349 original size:38 final size:38
Alignment explanation
Indices: 1225307--1225380 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
1225297 CTCCCCTTAT
** *
1225307 CTTATTACATATGGGAATAAGATTTTGTTATTGTTTAC
1 CTTATTACATATAAGAATAAAATTTTGTTATTGTTTAC
1225345 CTTATTACATATAAGAATAAAATTTTGTTATTGTTT
1 CTTATTACATATAAGAATAAAATTTTGTTATTGTTT
1225381 TTGTGGTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (38 bp):
CTTATTACATATAAGAATAAAATTTTGTTATTGTTTAC
Found at i:1227081 original size:281 final size:285
Alignment explanation
Indices: 1226544--1227083 Score: 1020
Period size: 281 Copynumber: 1.9 Consensus size: 285
1226534 AACGATGGTG
1226544 GTTGCCATTTTCTATTGTGAAATAATCGTTGTTCCCTTGTAAGAGTTATTGTCGTCCCTTTCTCT
1 GTTGCCATTTTCTATTGTGAAATAATCGTTGTTCCCTTGTAAGAGTTATTGTCGTCCCTTTCTCT
1226609 AACGCCCTTTTCGTAATATCCAACCAATGAAGACTGTGTTCCAGTGTTGGTCTTTCATCGGATAG
66 AACGCCCTTTTCGTAATATCCAACCAATGAAGACTGTGTTCCAGTGTTGGTCTTTCATCGGATAG
1226674 AGGGTTATTAAAAGCCACTGCATTTATAGAAATCCAAATATTCTATACCAACTCACCAAACAAAA
131 AGGGTTATTAAAAGCCACTGCATTTATAGAAATCCAAATATTCTATACCAACTCACCAAACAAAA
1226739 TATCCCAATCATCATTTTTTTCAATGTATTGAGTAGAATTGCACATGTTCATTGTTATCCAATCG
196 TATCCCAATCATCATTTTTTTCAATGTATTGAGTAGAATTGCACATGTTCATTGTTATCCAATCG
1226804 ACAATATTCATTTGAATAAACTCTT
261 ACAATATTCATTTGAATAAACTCTT
1226829 GTTGCCA-TTTCTA-T-TG-AATAATCGTTGTTCCCTTGTAAGAGTTATTGTCGTCCCTTTCTCT
1 GTTGCCATTTTCTATTGTGAAATAATCGTTGTTCCCTTGTAAGAGTTATTGTCGTCCCTTTCTCT
1226890 AACGCCCTTTTCGTAATATCCAACCAATGAAGACTGTGTTCCAGTGTTGGTCTTTCATCGGATAG
66 AACGCCCTTTTCGTAATATCCAACCAATGAAGACTGTGTTCCAGTGTTGGTCTTTCATCGGATAG
1226955 AGGGTTATTAAAAGCCACTGCATTTATAGAAATCCAAATATTCTATACCAACTCACCCAAACAAA
131 AGGGTTATTAAAAGCCACTGCATTTATAGAAATCCAAATATTCTATACCAACTCA-CCAAACAAA
1227020 ATATCCCAATCATCATTTTTTTTCAATGTATTGAGTAGAATTGCACATGTTCA-TG-TATCCAAT
195 ATATCCCAATCATCA-TTTTTTTCAATGTATTGAGTAGAATTGCACATGTTCATTGTTATCCAAT
1227083 C
259 C
1227084 CAACTCACCA
Statistics
Matches: 253, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
281 174 0.69
282 28 0.11
283 38 0.15
284 6 0.02
285 7 0.03
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (285 bp):
GTTGCCATTTTCTATTGTGAAATAATCGTTGTTCCCTTGTAAGAGTTATTGTCGTCCCTTTCTCT
AACGCCCTTTTCGTAATATCCAACCAATGAAGACTGTGTTCCAGTGTTGGTCTTTCATCGGATAG
AGGGTTATTAAAAGCCACTGCATTTATAGAAATCCAAATATTCTATACCAACTCACCAAACAAAA
TATCCCAATCATCATTTTTTTCAATGTATTGAGTAGAATTGCACATGTTCATTGTTATCCAATCG
ACAATATTCATTTGAATAAACTCTT
Found at i:1227145 original size:79 final size:83
Alignment explanation
Indices: 1227002--1227164 Score: 298
Period size: 79 Copynumber: 2.0 Consensus size: 83
1226992 ATATTCTATA
1227002 CCAACTCACCCAAACAAAATATCCCAATCATCATTTTTTTTCAATGTATTGAGTAGAATTGCACA
1 CCAACTCACCCAAACAAAATATCCCAATCATCATTTTTTTTCAATGTATTGAGTAGAATTGCACA
1227067 TGTTCA-TG-TATCCAAT
66 TGTTCATTGTTATCCAAT
1227083 CCAACTCA-CCAAACAAAATATCCCAATCATCA-TTTTTTTCAATGTATTGAGTAGAATTGCACA
1 CCAACTCACCCAAACAAAATATCCCAATCATCATTTTTTTTCAATGTATTGAGTAGAATTGCACA
1227146 TGTTCATTGTTATCCAAT
66 TGTTCATTGTTATCCAAT
1227164 C
1 C
1227165 GACAATATTC
Statistics
Matches: 80, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
79 37 0.46
80 26 0.32
81 17 0.21
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (83 bp):
CCAACTCACCCAAACAAAATATCCCAATCATCATTTTTTTTCAATGTATTGAGTAGAATTGCACA
TGTTCATTGTTATCCAAT
Found at i:1230963 original size:15 final size:15
Alignment explanation
Indices: 1230944--1230986 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1230934 ATACTATTAA
1230944 ATTAAATTATAAAAC
1 ATTAAATTATAAAAC
* *
1230959 GTTAAATTATAAAAT
1 ATTAAATTATAAAAC
1230974 ATTAAATATATAA
1 ATTAAAT-TATAA
1230987 TTATAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (15 bp):
ATTAAATTATAAAAC
Found at i:1230971 original size:22 final size:22
Alignment explanation
Indices: 1230946--1230996 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
1230936 ACTATTAAAT
1230946 TAAATTATAAAACGT-TA-AATTA
1 TAAATTATAAAA--TATATAATTA
* *
1230968 TAAAATATTAAATATATAATTA
1 TAAATTATAAAATATATAATTA
1230990 TAAATTA
1 TAAATTA
1230997 GTTAAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.04
21 2 0.08
22 21 0.88
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
TAAATTATAAAATATATAATTA
Found at i:1231140 original size:20 final size:20
Alignment explanation
Indices: 1231115--1231186 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
1231105 GATCGATAAT
1231115 TCGCAACGCGATCTCCAGTA
1 TCGCAACGCGATCTCCAGTA
** * *
1231135 TCGCAAATCAATTTCCAG-A
1 TCGCAACGCGATCTCCAGTA
* * *
1231154 TTCGCAACGCGAACTTCGACTA
1 -TCGCAACGCGATC-TCCAGTA
1231176 TCGCAACGCGA
1 TCGCAACGCGA
1231187 ACTTGGACTA
Statistics
Matches: 38, Mismatches: 11, Indels: 5
0.70 0.20 0.09
Matches are distributed among these distances:
19 1 0.03
20 22 0.58
21 14 0.37
22 1 0.03
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGATCTCCAGTA
Found at i:1231181 original size:21 final size:21
Alignment explanation
Indices: 1231155--1231207 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1231145 ATTTCCAGAT
1231155 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
1231176 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
1231197 TCGCAATGCGA
1 TCGCAACGCGA
1231208 TTTACATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:1231246 original size:21 final size:21
Alignment explanation
Indices: 1231216--1231651 Score: 280
Period size: 21 Copynumber: 21.0 Consensus size: 21
1231206 GATTTACATA
*
1231216 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
1231237 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
1231258 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1231277 TTCGTGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1231298 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
1231321 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
1231340 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
1231361 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
* *
1231382 TT--CATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1231401 TTCGCGTTGCGAT-TTCTTTCAAA
1 TTCGCGTTGCGATAGTC---CAAG
*
1231424 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
1231443 TTCGCGTTGCGATTTATTCAAAA
1 TTCGCGTTGCGA--TAGTCCAAG
1231466 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1231485 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* * *
1231508 TT--CATTGTGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1231527 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
1231550 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
1231569 TTCGCGTTGCGATTTATTCAAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
1231592 AT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1231611 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
1231634 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
1231652 AATCGCAATG
Statistics
Matches: 318, Mismatches: 65, Indels: 66
0.71 0.14 0.15
Matches are distributed among these distances:
19 79 0.25
20 2 0.01
21 182 0.57
22 2 0.01
23 53 0.17
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:1231335 original size:103 final size:102
Alignment explanation
Indices: 1231222--1231497 Score: 365
Period size: 103 Copynumber: 2.7 Consensus size: 102
1231212 CATATTCGCA
* * *
1231222 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGTGTTGC
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCAAAATTCGTTGCGATAGTCCAAGTTCG-GTTGC
1231287 GATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCG
65 GATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCG
** * * ** * *
1231325 TTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTC-ATTG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCAAAATT--CGTTGCGATAGTCCAAGTTCGGTTG
* * *
1231389 CGATAGTCGAAGTTCGCGTTGCGATTTCTTTCAAATTCG
64 CGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCG
1231428 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCAAAATTCGTTGCGATAGTCCAAGTTCGCGTT
1 TTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCAAAATTCGTTGCGATAGTCCAAGTTCG-GTT
1231493 GCGAT
63 GCGAT
1231498 TTATTCCAAA
Statistics
Matches: 146, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
103 116 0.79
104 1 0.01
105 29 0.20
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (102 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCAAAATTCGTTGCGATAGTCCAAGTTCGGTTGCG
ATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:1231651 original size:42 final size:42
Alignment explanation
Indices: 1231222--1231648 Score: 543
Period size: 42 Copynumber: 10.3 Consensus size: 42
1231212 CATATTCGCA
*
1231222 TTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
1231262 TTGCGATAGTCGAAGTTCGTGTTGCGA--TAGT-CAAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAA-TT--CG
* * * * * *
1231304 TTGCGATTTATTCCAAATT--CGTTGCGA--TAGTCGAAGTTCGCG
1 TTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT--CG
*
1231346 TTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCA
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
1231386 TTGCGATAGTCGAAGTTCGCGTTGCGATTTCTTTCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
1231428 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCAAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
1231470 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCA
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
1231512 TTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
1231554 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCAAAAATCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
1231596 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1231638 TTGCGATAGTC
1 TTGCGATAGTC
1231649 CAAAATCGCA
Statistics
Matches: 342, Mismatches: 33, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
39 5 0.01
40 64 0.19
41 2 0.01
42 260 0.76
43 3 0.01
44 8 0.02
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:1232269 original size:6 final size:6
Alignment explanation
Indices: 1232258--1232284 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1232248 TCTCGTCTTG
1232258 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1232285 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1232387 original size:19 final size:19
Alignment explanation
Indices: 1232363--1232434 Score: 83
Period size: 19 Copynumber: 3.6 Consensus size: 19
1232353 ATACCACCAG
1232363 ACGAATTTGGACTATCGCA
1 ACGAATTTGGACTATCGCA
*
1232382 ACGAATTTGGAATAAATCGCA
1 ACGAATTTGGACT--ATCGCA
1232403 ACGCGAACTTT-GACTATCGCA
1 A--CGAA-TTTGGACTATCGCA
1232424 ACGAATTTGGA
1 ACGAATTTGGA
1232435 AAATCCAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
18 3 0.07
19 18 0.40
21 14 0.31
23 7 0.16
24 3 0.07
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (19 bp):
ACGAATTTGGACTATCGCA
Found at i:1232894 original size:23 final size:23
Alignment explanation
Indices: 1232845--1232894 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
1232835 AATATTGTAT
* *
1232845 TTTAATTAAATTACATTTAGATT
1 TTTAATTAAATTACAATTAGATG
* * *
1232868 TTTAATTAATTTATAATTATATG
1 TTTAATTAAATTACAATTAGATG
1232891 TTTA
1 TTTA
1232895 GTACTTCATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTAATTAAATTACAATTAGATG
Found at i:1242167 original size:23 final size:23
Alignment explanation
Indices: 1242137--1242183 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1242127 GACTCGATCG
1242137 AATGATCAATCCTGACGTTAATA
1 AATGATCAATCCTGACGTTAATA
*
1242160 AATGATCACTCCTGACGTTAATA
1 AATGATCAATCCTGACGTTAATA
1242183 A
1 A
1242184 CACAACAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (23 bp):
AATGATCAATCCTGACGTTAATA
Found at i:1244120 original size:16 final size:16
Alignment explanation
Indices: 1244101--1244134 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1244091 CAATATACGA
1244101 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
1244117 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
1244133 AT
1 AT
1244135 TTAGACGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:1244208 original size:16 final size:18
Alignment explanation
Indices: 1244176--1244209 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1244166 TATTAATGTA
1244176 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
1244194 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
1244210 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:1244752 original size:21 final size:23
Alignment explanation
Indices: 1244707--1244753 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1244697 GTGTCACCAA
1244707 TAACATATATCATGATCATGTGT
1 TAACATATATCATGATCATGTGT
* *
1244730 TAACATATGTCA-GATCCTG-GT
1 TAACATATATCATGATCATGTGT
1244751 TAA
1 TAA
1244754 ATAATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (23 bp):
TAACATATATCATGATCATGTGT
Found at i:1244884 original size:130 final size:130
Alignment explanation
Indices: 1244680--1244927 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
1244670 AATTTTCTTC
* * *
1244680 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACATATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
1244745 CCTGGTTAAATAATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATAATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
1244810 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
1244875 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATAATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
1244928 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATAATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:1245374 original size:35 final size:35
Alignment explanation
Indices: 1245324--1245399 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
1245314 AATTGAATTT
* *
1245324 AATTGAATTATTTTGGAATTTAGGGTTGAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
* * *
1245359 AATTGATTTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
1245394 AATTGA
1 AATTGA
1245400 GGACTATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.34, C:0.01, G:0.25, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
Found at i:1251498 original size:7 final size:7
Alignment explanation
Indices: 1251486--1251510 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1251476 GATGTGGTAT
1251486 AAATTTA
1 AAATTTA
1251493 AAATTTA
1 AAATTTA
1251500 AAATTTA
1 AAATTTA
1251507 AAAT
1 AAAT
1251511 ATAACATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:1259790 original size:33 final size:34
Alignment explanation
Indices: 1259727--1259790 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
1259717 CAAGAGAAAC
*
1259727 GTGTTAAGAATAATCAATCAAACAAGAAACAAAT
1 GTGTTAAGAATAATCAAGCAAACAAGAAACAAAT
*
1259761 GTGTTAAGAATAATC-AGCAAACAATAAACA
1 GTGTTAAGAATAATCAAGCAAACAAGAAACA
1259791 CAACTTGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (34 bp):
GTGTTAAGAATAATCAAGCAAACAAGAAACAAAT
Found at i:1267855 original size:33 final size:32
Alignment explanation
Indices: 1267808--1267919 Score: 170
Period size: 33 Copynumber: 3.4 Consensus size: 32
1267798 TTTTAAACTT
1267808 TATTTCAATTATCGAACTTGGAAGTTTTTAAG
1 TATTTCAATTATCGAACTTGGAAGTTTTTAAG
* *
1267840 TATTTGAATTTATCGAACGTGGAAGTTTTTAAG
1 TATTTCAA-TTATCGAACTTGGAAGTTTTTAAG
* *
1267873 TATTTGAATTTATCGAACTTGGAAGTATTTAAG
1 TATTTCAA-TTATCGAACTTGGAAGTTTTTAAG
1267906 TATTTCAATTATCG
1 TATTTCAATTATCG
1267920 TAAACTTTGT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
32 13 0.18
33 61 0.82
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (32 bp):
TATTTCAATTATCGAACTTGGAAGTTTTTAAG
Found at i:1272030 original size:26 final size:26
Alignment explanation
Indices: 1271994--1272062 Score: 138
Period size: 26 Copynumber: 2.7 Consensus size: 26
1271984 CTTAAGGAGT
1271994 GGTCCTTCGGGACAAATACAGTCATA
1 GGTCCTTCGGGACAAATACAGTCATA
1272020 GGTCCTTCGGGACAAATACAGTCATA
1 GGTCCTTCGGGACAAATACAGTCATA
1272046 GGTCCTTCGGGACAAAT
1 GGTCCTTCGGGACAAAT
1272063 TTCATAGCCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (26 bp):
GGTCCTTCGGGACAAATACAGTCATA
Found at i:1274010 original size:21 final size:21
Alignment explanation
Indices: 1273985--1274026 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1273975 TCTGGGCAAG
*
1273985 GGGAATCGATACCCATTCAAA
1 GGGAACCGATACCCATTCAAA
*
1274006 GGGAACCGATACCCCTTCAAA
1 GGGAACCGATACCCATTCAAA
1274027 CGAACAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.29, G:0.19, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAA
Found at i:1275628 original size:23 final size:23
Alignment explanation
Indices: 1275598--1275654 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
1275588 ATTATATGGT
1275598 ACTACGGTGCAATTCTACGCGGC
1 ACTACGGTGCAATTCTACGCGGC
* *
1275621 ACTACGGTACAATTCTACGTGGC
1 ACTACGGTGCAATTCTACGCGGC
*
1275644 ACTTCGGTGCA
1 ACTACGGTGCA
1275655 TTTATATAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
ACTACGGTGCAATTCTACGCGGC
Found at i:1279871 original size:97 final size:96
Alignment explanation
Indices: 1279582--1279881 Score: 370
Period size: 97 Copynumber: 3.1 Consensus size: 96
1279572 TAATATCCAT
*
1279582 AAGGATCACAT-TCATTCCTTAAGAATCATTACATATGCCAAGGATCAAGTATGTGTCTCACCAG
1 AAGGACCACATATCATTCCTTAAGAAT-A-TACATATGCCAAGGATCAAGTATGT-TCTCACCAG
1279646 ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
63 ACTTCACACATGTTCCAAAGAAT--ATATATG-CCCG
*
1279683 AGATGACCAC--ATCATTCCTTAAGAATCTATACATA--CCAAGGA-CAAGTATG-TCTCA-CAG
1 A-AGGACCACATATCATTCCTTAAGAA--TATACATATGCCAAGGATCAAGTATGTTCTCACCAG
* * *
1279741 AC--CACACATGTT-CAAATAAACATATATGTCCG
63 ACTTCACACATGTTCCAAA-GAATATATATGCCCG
*
1279773 AAGGACCACATATCATTCCTTAAGAATATACATATGCCAAGGATCAAGTATGTATCTCACCATAC
1 AAGGACCACATATCATTCCTTAAGAATATACATATGCCAAGGATCAAGTATGT-TCTCACCAGAC
1279838 TTCACACATGTTCCAAAGAATATATATGCCCG
65 TTCACACATGTTCCAAAGAATATATATGCCCG
1279870 AAGGACCACATA
1 AAGGACCACATA
1279882 GACCTCTACC
Statistics
Matches: 173, Mismatches: 10, Indels: 36
0.79 0.05 0.16
Matches are distributed among these distances:
89 15 0.09
90 4 0.02
91 29 0.17
92 12 0.07
93 12 0.07
94 5 0.03
95 9 0.05
96 5 0.03
97 34 0.20
98 12 0.07
99 7 0.04
101 21 0.12
102 7 0.04
103 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (96 bp):
AAGGACCACATATCATTCCTTAAGAATATACATATGCCAAGGATCAAGTATGTTCTCACCAGACT
TCACACATGTTCCAAAGAATATATATGCCCG
Found at i:1280509 original size:19 final size:20
Alignment explanation
Indices: 1280472--1280509 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1280462 TTTTTTATCA
*
1280472 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1280492 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1280510 TATAGCGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1286625 original size:23 final size:22
Alignment explanation
Indices: 1286595--1286658 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
1286585 CAGCTCATAT
1286595 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
1286618 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
*
1286641 AATTACACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
1286659 TATAATAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:1286802 original size:103 final size:103
Alignment explanation
Indices: 1286674--1286994 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
1286664 TAATGTCCAT
1286674 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
1286739 GACTTCACACATGTTCCAAAGAATGCATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1286777 AATGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
1286842 GACCTCACACATGTTCCAAATAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1286880 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1286945 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1286983 AAGGACCACATA
1 AAGGACCACATA
1286995 GACCATCTAC
Statistics
Matches: 209, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 209 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1287513 original size:19 final size:20
Alignment explanation
Indices: 1287476--1287513 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1287466 TTTTTTATCA
*
1287476 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1287496 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1287514 TCTAGCGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1287565 original size:21 final size:21
Alignment explanation
Indices: 1287541--1287583 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1287531 TCATATTCGT
*
1287541 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
1287562 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
1287583 T
1 T
1287584 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:1304925 original size:13 final size:13
Alignment explanation
Indices: 1304909--1304946 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
1304899 TATTTTTATT
*
1304909 TTATAATATATAA
1 TTATAAAATATAA
1304922 TTATAAAAATATAA
1 TTAT-AAAATATAA
1304936 TTATAAAATAT
1 TTATAAAATAT
1304947 TTTTGAGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TTATAAAATATAA
Found at i:1307623 original size:23 final size:26
Alignment explanation
Indices: 1307569--1307630 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 26
1307559 GTGACTAAAA
1307569 TAAAATTAAAATATAATTAGAGATAATTT
1 TAAAA-TAAAATATAATTA-AGATAA-TT
1307598 TAAAATAAAA-ATAATT-AGATAA-T
1 TAAAATAAAATATAATTAAGATAATT
*
1307621 TAAAACAAAA
1 TAAAATAAAA
1307631 CAAAAATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 10 0.31
25 6 0.19
27 6 0.19
28 5 0.16
29 5 0.16
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (26 bp):
TAAAATAAAATATAATTAAGATAATT
Found at i:1318460 original size:2 final size:2
Alignment explanation
Indices: 1318453--1318534 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
1318443 AGGTTAGCTG
1318453 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1318495 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1318535 TATCACCAGT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1325795 original size:24 final size:25
Alignment explanation
Indices: 1325768--1325815 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
1325758 TATACCATAA
*
1325768 CAATGAAGAAGCAGTAAGC-CAAAC
1 CAATCAAGAAGCAGTAAGCACAAAC
1325792 CAATCAAGAAGCAGTAAGCACAAA
1 CAATCAAGAAGCAGTAAGCACAAA
1325816 TCAAAGAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.52, C:0.21, G:0.19, T:0.08
Consensus pattern (25 bp):
CAATCAAGAAGCAGTAAGCACAAAC
Found at i:1325819 original size:21 final size:23
Alignment explanation
Indices: 1325773--1325828 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
1325763 CATAACAATG
*
1325773 AAGAAGCAGTAAGCCAAACCAATC
1 AAGAAGCAGTAAGCC-AACAAATC
1325797 AAGAAGCAGTAAG-C-ACAAATC
1 AAGAAGCAGTAAGCCAACAAATC
1325818 AA-AGAGCAGTA
1 AAGA-AGCAGTA
1325829 TGCAAGATCG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.03
21 15 0.50
23 1 0.03
24 13 0.43
ACGTcount: A:0.52, C:0.20, G:0.20, T:0.09
Consensus pattern (23 bp):
AAGAAGCAGTAAGCCAACAAATC
Found at i:1329251 original size:23 final size:23
Alignment explanation
Indices: 1329225--1329273 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1329215 ATAAAGAACC
*
1329225 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAACAT-CCATT
*
1329248 AAAATAAAGTTTAAACATCCATT
1 AAAATAAAGCTTAAACATCCATT
1329271 AAA
1 AAA
1329274 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGCTTAAACATCCATT
Found at i:1332564 original size:26 final size:26
Alignment explanation
Indices: 1332535--1332626 Score: 115
Period size: 26 Copynumber: 3.8 Consensus size: 26
1332525 AAGAACTGAG
1332535 AGAGAAAAGTAAAAGTTAAAGATGAA
1 AGAGAAAAGTAAAAGTTAAAGATGAA
1332561 AGAGAAAAGTAAAAGTT-AA-A--AA
1 AGAGAAAAGTAAAAGTTAAAGATGAA
* *
1332583 TGA-AATAG-AAAAGTTAAAGATGAA
1 AGAGAAAAGTAAAAGTTAAAGATGAA
*
1332607 AGAGAAAAGAAAAAGTTAAA
1 AGAGAAAAGTAAAAGTTAAA
1332627 AATTTGAAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
20 7 0.12
21 6 0.11
22 5 0.09
24 5 0.09
25 6 0.11
26 27 0.48
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (26 bp):
AGAGAAAAGTAAAAGTTAAAGATGAA
Found at i:1332568 original size:20 final size:19
Alignment explanation
Indices: 1332559--1332615 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
1332549 GTTAAAGATG
1332559 AAAGA-GAAAAGTAAAAGTT
1 AAAGATGAAAAG-AAAAGTT
*
1332578 AAAAATGAAATAGAAAAGTT
1 AAAGATGAAA-AGAAAAGTT
1332598 AAAGATGAAAGAGAAAAG
1 AAAGATGAAA-AGAAAAG
1332616 AAAAAGTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.12
20 27 0.82
21 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.14
Consensus pattern (19 bp):
AAAGATGAAAAGAAAAGTT
Found at i:1332621 original size:20 final size:20
Alignment explanation
Indices: 1332578--1332621 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1332568 AGTAAAAGTT
* *
1332578 AAAA-ATGAAATAGAAAAGT
1 AAAAGATGAAAGAGAAAAGA
*
1332597 TAAAGATGAAAGAGAAAAGA
1 AAAAGATGAAAGAGAAAAGA
1332617 AAAAG
1 AAAAG
1332622 TTAAAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.11
Consensus pattern (20 bp):
AAAAGATGAAAGAGAAAAGA
Found at i:1332641 original size:28 final size:26
Alignment explanation
Indices: 1332535--1332643 Score: 104
Period size: 26 Copynumber: 4.3 Consensus size: 26
1332525 AAGAACTGAG
* *
1332535 AGAGAAAAGTAAAAGTTAAAGATGAA
1 AGAGAAAAGAAAAAGTTAAAAATGAA
*
1332561 AGAGAAAAGTAAAAGTTAAAAAT---
1 AGAGAAAAGAAAAAGTTAAAAATGAA
* *
1332584 -GA-AATAG-AAAAGTTAAAGATGAA
1 AGAGAAAAGAAAAAGTTAAAAATGAA
1332607 AGAGAAAAGAAAAAGTTAAAAATTTGAA
1 AGAGAAAAGAAAAAGTTAAAAA--TGAA
*
1332635 AGGGAAAAG
1 AGAGAAAAG
1332644 GGGTGATAGG
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
20 12 0.17
21 4 0.06
22 2 0.03
24 2 0.03
25 4 0.06
26 33 0.48
28 12 0.17
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (26 bp):
AGAGAAAAGAAAAAGTTAAAAATGAA
Found at i:1345974 original size:23 final size:23
Alignment explanation
Indices: 1345947--1345995 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1345937 TGGTGGTTGG
1345947 TTTAATGG-ATATTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
* *
1345970 TTTAATGGTATGTTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
1345993 TTT
1 TTT
1345996 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:1352813 original size:20 final size:20
Alignment explanation
Indices: 1352790--1352834 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1352780 TTAACTTTTT
*
1352790 CTTTTCTCTTTC-TTCCTTAA
1 CTTTTCTATTTCATT-CTTAA
*
1352810 CTTTTCTATTTCATTTTTAA
1 CTTTTCTATTTCATTCTTAA
1352830 CTTTT
1 CTTTT
1352835 ACTTTTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.13, C:0.22, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTCTATTTCATTCTTAA
Found at i:1354299 original size:23 final size:23
Alignment explanation
Indices: 1354272--1354320 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1354262 TGGTGGTTGG
1354272 TTTAATGG-ATATTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
* *
1354295 TTTAATGGTATGTTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
1354318 TTT
1 TTT
1354321 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:1362328 original size:21 final size:20
Alignment explanation
Indices: 1362264--1362334 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
1362254 ATTTATACAC
1362264 TTATTTATTTTTAAAATTAT
1 TTATTTATTTTTAAAATTAT
* *
1362284 TTAATTAATTTTT-ATA-TA-
1 TT-ATTTATTTTTAAAATTAT
*
1362302 AT-TTTATTTTCTAAAATTAT
1 TTATTTATTTT-TAAAATTAT
*
1362322 TTATTTATATTTA
1 TTATTTATTTTTA
1362335 GAACATATTC
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
16 7 0.18
17 1 0.03
18 3 0.08
19 4 0.11
20 7 0.18
21 16 0.42
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATTTATTTTTAAAATTAT
Found at i:1364132 original size:18 final size:18
Alignment explanation
Indices: 1364109--1364144 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1364099 ATTGATAAAT
1364109 AACAAAGTAAATCACCCC
1 AACAAAGTAAATCACCCC
1364127 AACAAAGTAAATCACCCC
1 AACAAAGTAAATCACCCC
1364145 GATGACCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.33, G:0.06, T:0.11
Consensus pattern (18 bp):
AACAAAGTAAATCACCCC
Found at i:1367287 original size:21 final size:21
Alignment explanation
Indices: 1367258--1367304 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1367248 ATTCTGACTA
1367258 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1367279 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
1367300 TCGCA
1 TCGCA
1367305 ACGCGATTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1367325 original size:20 final size:20
Alignment explanation
Indices: 1367300--1367393 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
1367290 TTTTCCTAAT
*
1367300 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
*
1367320 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
* *
1367340 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCG-ATTACGTAAA
* *
1367361 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
*
1367381 TCACAATGCGATT
1 TCGCAATGCGATT
1367394 TACATAGCGC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 45 0.74
21 16 0.26
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:1367362 original size:41 final size:41
Alignment explanation
Indices: 1367300--1367396 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
1367290 TTTTCCTAAT
* * *
1367300 TCGCAACGCG-ATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATACGTAAA
*
1367340 TCGCAATGCGAATTAGGAAAATCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATACGTAAA
* *
1367381 TCACAATGCGATTTAC
1 TCGCAATGCGAATTAC
1367397 ATAGCGCCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 9 0.18
41 40 0.82
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCGCAACGCGAATACGTAAA
Found at i:1367972 original size:20 final size:20
Alignment explanation
Indices: 1367947--1368043 Score: 117
Period size: 20 Copynumber: 4.8 Consensus size: 20
1367937 TTCTAAACTT
*
1367947 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
*
1367967 AAAATCGTAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
1367987 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
1368008 AAAATCGCAACACG-AAATG
1 AAAATCGCAACACGAAAATG
*
1368027 AAAATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
1368044 CCAAAATCGC
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
19 18 0.28
20 31 0.48
21 16 0.25
ACGTcount: A:0.52, C:0.19, G:0.18, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:1368026 original size:19 final size:19
Alignment explanation
Indices: 1367947--1368054 Score: 108
Period size: 19 Copynumber: 5.5 Consensus size: 19
1367937 TTCTAAACTT
*
1367947 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACG-AAATG
*
1367967 AAAATCGTAACACGAAAATG
1 AAAATCGCAACACG-AAATG
** *
1367987 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-A-CGAAATG
1368008 AAAATCGCAACACGAAATG
1 AAAATCGCAACACGAAATG
* **
1368027 AAAATCGCAACGCGAAACC
1 AAAATCGCAACACGAAATG
1368046 AAAATCGCA
1 AAAATCGCA
1368055 TTGCGATTTT
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
19 31 0.42
20 27 0.36
21 15 0.20
22 1 0.01
ACGTcount: A:0.51, C:0.20, G:0.17, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACACGAAATG
Found at i:1368141 original size:20 final size:20
Alignment explanation
Indices: 1368079--1368134 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
1368069 TCGCGTTGCG
1368079 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
*
1368099 ATT-TCCGCGTTGCGATAGTC
1 ATTCT-CTCGTTGCGATAGTC
1368119 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
1368135 TTTCATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:1368264 original size:25 final size:26
Alignment explanation
Indices: 1368210--1368264 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
1368200 TTATGTTTAT
*
1368210 TGTTTTTGGTATATCTTCACATTGTA
1 TGTTTTTGGTATATCTTAACATTGTA
1368236 -GTTTTTGGTATATC-TAAC-TTGGTA
1 TGTTTTTGGTATATCTTAACATT-GTA
1368260 TGTTT
1 TGTTT
1368265 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 2 0.08
24 6 0.23
25 18 0.69
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (26 bp):
TGTTTTTGGTATATCTTAACATTGTA
Found at i:1370002 original size:94 final size:94
Alignment explanation
Indices: 1369838--1370217 Score: 602
Period size: 94 Copynumber: 4.1 Consensus size: 94
1369828 TAGATTGCTT
* * * * *
1369838 AGTAAATTTATTCGGTTGCTGTCAATACTGTTAAATTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1369903 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
* * *
1369932 AGTAAATTTATTCGGTTGATGCCAATTCTGCTAAACTATGTATTCTTTAACACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1369997 TTTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
1370026 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTAAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1370091 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
1370120 AGTAAATTTGTTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1370185 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1370213 AGTAA
1 AGTAA
1370218 TACAATCCAT
Statistics
Matches: 266, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
93 26 0.10
94 240 0.90
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1370327 original size:17 final size:16
Alignment explanation
Indices: 1370305--1370386 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 16
1370295 AAAAATGACT
1370305 ATCGCAATGCGAAATGA
1 ATCGCAA-GCGAAATGA
*
1370322 ATCGCAA-CGAGA-GA
1 ATCGCAAGCGAAATGA
*
1370336 ATCGCAACGAGAAATGAAA
1 ATCGCAA-GCGAAATG--A
*
1370355 ATCGCAA-CGAGA-GA
1 ATCGCAAGCGAAATGA
*
1370369 ATCGCAACACGAAATGA
1 ATCGCAA-GCGAAATGA
1370386 A
1 A
1370387 AATCGCAACG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
14 17 0.33
15 4 0.08
16 8 0.16
17 14 0.27
19 8 0.16
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (16 bp):
ATCGCAAGCGAAATGA
Found at i:1370339 original size:14 final size:14
Alignment explanation
Indices: 1370320--1370376 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
1370310 AATGCGAAAT
1370320 GAATCGCAACGAGA
1 GAATCGCAACGAGA
1370334 GAATCGCAACGAGAAA
1 GAATCGCAACGAG--A
1370350 TGAAAATCGCAACGAGA
1 -G--AATCGCAACGAGA
1370367 GAATCGCAAC
1 GAATCGCAAC
1370377 ACGAAATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 22 0.58
16 2 0.05
17 2 0.05
19 12 0.32
ACGTcount: A:0.46, C:0.21, G:0.25, T:0.09
Consensus pattern (14 bp):
GAATCGCAACGAGA
Found at i:1370359 original size:19 final size:19
Alignment explanation
Indices: 1370335--1370397 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
1370325 GCAACGAGAG
1370335 AATCGCAACGAGAAATGAA
1 AATCGCAACGAGAAATGAA
1370354 AATCGCAACGAG--A-G--
1 AATCGCAACGAGAAATGAA
1370368 AATCGCAAC-ACGAAATGAA
1 AATCGCAACGA-GAAATGAA
1370387 AATCGCAACGA
1 AATCGCAACGA
1370398 CAAAGACAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.03
14 10 0.27
16 2 0.05
17 2 0.05
19 21 0.57
20 1 0.03
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.10
Consensus pattern (19 bp):
AATCGCAACGAGAAATGAA
Found at i:1370363 original size:33 final size:33
Alignment explanation
Indices: 1370305--1370397 Score: 138
Period size: 33 Copynumber: 2.9 Consensus size: 33
1370295 AAAAATGACT
* *
1370305 ATCGCAATGCGAAATG--AATCGCAACGAGAGA
1 ATCGCAACGAGAAATGAAAATCGCAACGAGAGA
1370336 ATCGCAACGAGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGAGAAATGAAAATCGCAACGAGAGA
1370369 ATCGCAAC-ACGAAATGAAAATCGCAACGA
1 ATCGCAACGA-GAAATGAAAATCGCAACGA
1370398 CAAAGACAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
31 14 0.25
32 1 0.02
33 42 0.74
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (33 bp):
ATCGCAACGAGAAATGAAAATCGCAACGAGAGA
Found at i:1370961 original size:21 final size:21
Alignment explanation
Indices: 1370937--1371003 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1370927 TCATTCCTCG
1370937 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1370958 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1370979 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1371000 AGAG
1 AGAG
1371004 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1370961 original size:42 final size:42
Alignment explanation
Indices: 1370885--1371003 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1370875 GACTCGCCTG
* * * * * * *
1370885 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1370927 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1370969 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1371004 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1372156 original size:14 final size:14
Alignment explanation
Indices: 1372139--1372174 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1372129 TTGGTTAAGT
1372139 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1372153 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1372167 TGATTTGT
1 TGATTTGT
1372175 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1372318 original size:33 final size:33
Alignment explanation
Indices: 1372281--1372360 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
1372271 AAAAATGACT
* * *
1372281 ATCGCAATGCGAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1372314 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1372347 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1372361 CTAAATTCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1372337 original size:19 final size:19
Alignment explanation
Indices: 1372281--1372339 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1372271 AAAAATGACT
1372281 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1372300 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
1372314 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1372333 ATCGCAA
1 ATCGCAA
1372340 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 11 0.33
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 18 0.55
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1372388 original size:19 final size:19
Alignment explanation
Indices: 1372366--1372504 Score: 118
Period size: 19 Copynumber: 7.7 Consensus size: 19
1372356 CGAAACTAAA
1372366 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1372385 TTCGCTTTGCGA-TTTC--
1 TTCGCGTTGCGATTTTCAT
*
1372401 --CTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
1372418 TTCGCTTTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1372437 TTCCGCGTTGCGATATTAAT
1 TT-CGCGTTGCGATTTTCAT
1372457 ATTCGCGTTGCGATTTTCA-
1 -TTCGCGTTGCGATTTTCAT
1372476 ----CGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1372491 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
1372505 CTATCGTTGC
Statistics
Matches: 95, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
14 22 0.23
15 4 0.04
18 4 0.04
19 35 0.37
20 28 0.29
21 2 0.02
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1372412 original size:33 final size:33
Alignment explanation
Indices: 1372370--1372517 Score: 145
Period size: 33 Copynumber: 4.3 Consensus size: 33
1372360 ACTAAATTCG
1372370 CGTTGCGATTTTCATTTCGCTTTGCGATTTCCT
1 CGTTGCGATTTTCATTTCGCTTTGCGATTTCCT
*
1372403 CGTTGCGATTTTCATTTCGCTTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCTTTGC----G--ATTTCCT
* * * * *
1372442 CGTTGCGATATTAATATTCGCGTTGCGATTTTCA
1 CGTTGCGATTTTCAT-TTCGCTTTGCGATTTCCT
* *
1372476 CGTTGCGATTTTCATTTCGCATTGCGA-TTCTAT
1 CGTTGCGATTTTCATTTCGCTTTGCGATTTC-CT
1372509 CGTTGCGAT
1 CGTTGCGAT
1372518 AGACATTAAG
Statistics
Matches: 95, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
32 2 0.02
33 45 0.47
34 18 0.19
36 1 0.01
37 1 0.01
39 19 0.20
40 9 0.09
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCTTTGCGATTTCCT
Found at i:1372481 original size:14 final size:14
Alignment explanation
Indices: 1372462--1372489 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1372452 TTAATATTCG
1372462 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
1372476 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
1372490 TTTCGCATTG
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:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTTTCA
Found at i:1372486 original size:73 final size:72
Alignment explanation
Indices: 1372368--1372503 Score: 209
Period size: 73 Copynumber: 1.9 Consensus size: 72
1372358 AAACTAAATT
* * * * *
1372368 CGCGTTGCGATTTTCATTTCGCTTTGCGATTTCCTCGTTGCGATTTTCATTTCGCTTTGCGATAG
1 CGCGTTGCGATATTAATTTCGCGTTGCGATTTCCACGTTGCGATTTTCATTTCGCATTGCGATAG
1372433 TCATTTC
66 TCATTTC
*
1372440 CGCGTTGCGATATTAATATTCGCGTTGCGATTTTCACGTTGCGATTTTCATTTCGCATTGCGAT
1 CGCGTTGCGATATTAAT-TTCGCGTTGCGATTTCCACGTTGCGATTTTCATTTCGCATTGCGAT
1372504 TCTATCGTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
72 15 0.26
73 42 0.74
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.43
Consensus pattern (72 bp):
CGCGTTGCGATATTAATTTCGCGTTGCGATTTCCACGTTGCGATTTTCATTTCGCATTGCGATAG
TCATTTC
Found at i:1375068 original size:24 final size:24
Alignment explanation
Indices: 1375034--1375087 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1375024 CTGAAAAATC
1375034 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1375058 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1375082 ATCAAA
1 ATCAAA
1375088 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1375101 original size:24 final size:24
Alignment explanation
Indices: 1375034--1375101 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1375024 CTGAAAAATC
* * *
1375034 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1375058 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1375082 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1375102 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1375990 original size:20 final size:20
Alignment explanation
Indices: 1375967--1376004 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1375957 ATTTACAGAT
* *
1375967 TCGCAATGTGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
1375987 TCGCAATGCGAATACGTA
1 TCGCAATGCGAATACGTA
1376005 TTCGCGTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1376022 original size:20 final size:20
Alignment explanation
Indices: 1375999--1376076 Score: 156
Period size: 20 Copynumber: 3.9 Consensus size: 20
1375989 GCAATGCGAA
1375999 TACGTATTCGCGTTGCGATT
1 TACGTATTCGCGTTGCGATT
1376019 TACGTATTCGCGTTGCGATT
1 TACGTATTCGCGTTGCGATT
1376039 TACGTATTCGCGTTGCGATT
1 TACGTATTCGCGTTGCGATT
1376059 TACGTATTCGCGTTGCGA
1 TACGTATTCGCGTTGCGA
1376077 ATTAGGAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (20 bp):
TACGTATTCGCGTTGCGATT
Found at i:1376022 original size:40 final size:41
Alignment explanation
Indices: 1375978--1376064 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 41
1375968 CGCAATGTGA
1375978 TTACGTAAATCGCAATGCGA-ATACGTATTCGCGTTGCGAT
1 TTACGTAAATCGCAATGCGATATACGTATTCGCGTTGCGAT
* ** *
1376018 TTACGT-ATTCGCGTTGCGATTTACGTATTCGCGTTGCGAT
1 TTACGTAAATCGCAATGCGATATACGTATTCGCGTTGCGAT
1376058 TTACGTA
1 TTACGTA
1376065 TTCGCGTTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
39 10 0.24
40 31 0.76
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
TTACGTAAATCGCAATGCGATATACGTATTCGCGTTGCGAT
Found at i:1376118 original size:21 final size:21
Alignment explanation
Indices: 1376072--1376118 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1376062 GTATTCGCGT
1376072 TGCGAATTAGGAAAATCGCAA
1 TGCGAATTAGGAAAATCGCAA
* * * *
1376093 CGCGAATTTGGGAAATCGTAA
1 TGCGAATTAGGAAAATCGCAA
1376114 TGCGA
1 TGCGA
1376119 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (21 bp):
TGCGAATTAGGAAAATCGCAA
Found at i:1379644 original size:49 final size:50
Alignment explanation
Indices: 1379586--1379821 Score: 338
Period size: 49 Copynumber: 4.8 Consensus size: 50
1379576 CACCATCACA
* * *
1379586 CAGACGTGCTAAATCATCATTAAAAGTAGTACCACTGA-CACAAAGACGT
1 CAGACGTGCTAAATCATCATTAATAGTAGCACCACTCATCACAAAGACGT
* * * * * *
1379635 TAGACGTGCTAAATAATCAGTAATAGTAGCACCAC-CGTCACAAAGATGC
1 CAGACGTGCTAAATCATCATTAATAGTAGCACCACTCATCACAAAGACGT
1379684 CAGACGTGCTAAATCATCATTAATAGTAGCACCA-TCATCACAAAGACGT
1 CAGACGTGCTAAATCATCATTAATAGTAGCACCACTCATCACAAAGACGT
1379733 CAGACGTGCTAAATCATCATTAATAGTAGCACCA-TCATCACAAAGACGT
1 CAGACGTGCTAAATCATCATTAATAGTAGCACCACTCATCACAAAGACGT
* *
1379782 CAGACGTACTAAATCATCAGTAATAGTAGCACCAC-CATCA
1 CAGACGTGCTAAATCATCATTAATAGTAGCACCACTCATCA
1379822 GTGCTAAATC
Statistics
Matches: 167, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
49 167 1.00
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.21
Consensus pattern (50 bp):
CAGACGTGCTAAATCATCATTAATAGTAGCACCACTCATCACAAAGACGT
Found at i:1379726 original size:98 final size:98
Alignment explanation
Indices: 1379586--1379997 Score: 413
Period size: 98 Copynumber: 4.3 Consensus size: 98
1379576 CACCATCACA
* * * *
1379586 CAGACGTGCTAAATCATCATTAAAAGTAGTACCACTGA-CACAAAGACGTTAGACGTGCTAAATA
1 CAGACGTGCTAAATCATCATTAATAGTAGCACCA-TCATCACAAAGACGTCAGACGTGCTAAATA
* *
1379650 ATCAGTAATAGTAGCACCACCGTCACAAAGATGC
65 ATCAGTAATAGTAGCACCACCATCACAAAGACGC
*
1379684 CAGACGTGCTAAATCATCATTAATAGTAGCACCATCATCACAAAGACGTCAGACGTGCTAAATCA
1 CAGACGTGCTAAATCATCATTAATAGTAGCACCATCATCACAAAGACGTCAGACGTGCTAAATAA
* * *
1379749 TCATTAATAGTAGCACCATCATCACAAAGACGT
66 TCAGTAATAGTAGCACCACCATCACAAAGACGC
* * *
1379782 CAGACGTACTAAATCATCAGTAATAGTAGCA-C--CA-C-C----A--TC--A-GTGCTAAATCA
1 CAGACGTGCTAAATCATCATTAATAGTAGCACCATCATCACAAAGACGTCAGACGTGCTAAATAA
** * * *
1379833 TCGTTAATAGTAGCACCACCGTCACAAAGATGT
66 TCAGTAATAGTAGCACCACCATCACAAAGACGC
*
1379866 CAGACGTATGCTAAATCATCATTAATAGTAGCACGTACACTATCGTCACAAAGACGTCAGACGTG
1 CAGACG--TGCTAAATCATCATTAATAGTAG--C--AC-C-ATCATCACAAAGACGTCAGACGTG
* * * **
1379931 CTAAATCATCATTAATAGTAGCACCACTATCACAAAGACAT
58 CTAAATAATCAGTAATAGTAGCACCACCATCACAAAGACGC
*
1379972 CAGACGTGCTAAATCATCATTTATAG
1 CAGACGTGCTAAATCATCATTAATAG
1379998 ACGTCAGACG
Statistics
Matches: 266, Mismatches: 25, Indels: 40
0.80 0.08 0.12
Matches are distributed among these distances:
84 46 0.17
85 1 0.00
86 21 0.08
87 2 0.01
88 1 0.00
89 1 0.00
90 1 0.00
92 1 0.00
93 1 0.00
94 1 0.00
95 3 0.01
96 1 0.00
97 4 0.02
98 114 0.43
101 1 0.00
103 2 0.01
104 19 0.07
105 1 0.00
106 45 0.17
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.23
Consensus pattern (98 bp):
CAGACGTGCTAAATCATCATTAATAGTAGCACCATCATCACAAAGACGTCAGACGTGCTAAATAA
TCAGTAATAGTAGCACCACCATCACAAAGACGC
Found at i:1379948 original size:55 final size:51
Alignment explanation
Indices: 1379822--1379997 Score: 234
Period size: 49 Copynumber: 3.4 Consensus size: 51
1379812 ACCACCATCA
* *
1379822 GTGCTAAATCATCGTTAATAGTAGCACCAC--CGTCACAAAGATGTCAGAC
1 GTGCTAAATCATCATTAATAGTAGCACCACTACGTCACAAAGACGTCAGAC
1379871 GTATGCTAAATCATCATTAATAGTAGCACGTACACTATCGTCACAAAGACGTCAGAC
1 G--TGCTAAATCATCATTAATAGTAGCAC---CACTA-CGTCACAAAGACGTCAGAC
*
1379928 GTGCTAAATCATCATTAATAGTAGCACCACTA--TCACAAAGACATCAGAC
1 GTGCTAAATCATCATTAATAGTAGCACCACTACGTCACAAAGACGTCAGAC
*
1379977 GTGCTAAATCATCATTTATAG
1 GTGCTAAATCATCATTAATAG
1379998 ACGTCAGACG
Statistics
Matches: 115, Mismatches: 4, Indels: 16
0.85 0.03 0.12
Matches are distributed among these distances:
49 37 0.32
51 25 0.22
52 5 0.04
54 3 0.03
55 26 0.23
57 19 0.17
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (51 bp):
GTGCTAAATCATCATTAATAGTAGCACCACTACGTCACAAAGACGTCAGAC
Found at i:1379954 original size:190 final size:182
Alignment explanation
Indices: 1379640--1379990 Score: 553
Period size: 190 Copynumber: 1.9 Consensus size: 182
1379630 GACGTTAGAC
1379640 GTGCTAAATAATCAGTAATAGTAGCACCACCGTCACAAAGATGCCAGACGTGCTAAATCATCATT
1 GTGCTAAATAATCAGTAATAGTAGCACCACCGTCACAAAGATGCCAGACGTGCTAAATCATCATT
1379705 AATAGTAGCACCATCATCACAAAGACGTCAGACGTGCTAAATCATCATTAATAGTAGCACCA-TC
66 AATAGTAGCACCATCATCACAAAGACGTCAGACGTGCTAAATCATCATTAATAGTAGCACCACT-
*
1379769 ATCACAAAGACGTCAGACGTACTAAATCATCAGTAATAGTAGCACCACCATCA
130 ATCACAAAGACATCAGACGTACTAAATCATCAGTAATAGTAGCACCACCATCA
* *
1379822 GTGCTAAATCATC-GTTAATAGTAGCACCACCGTCACAAAGATGTCAGACGTATGCTAAATCATC
1 GTGCTAAATAATCAG-TAATAGTAGCACCACCGTCACAAAGATGCCAGACG--TGCTAAATCATC
*
1379886 ATTAATAGTAGCACGTACACTATCGTCACAAAGACGTCAGACGTGCTAAATCATCATTAATAGTA
63 ATTAATAGTAG--C--AC-C-ATCATCACAAAGACGTCAGACGTGCTAAATCATCATTAATAGTA
*
1379951 GCACCACTATCACAAAGACATCAGACGTGCTAAATCATCA
122 GCACCACTATCACAAAGACATCAGACGTACTAAATCATCA
1379991 TTTATAGACG
Statistics
Matches: 154, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
181 1 0.01
182 46 0.30
184 23 0.15
186 1 0.01
188 2 0.01
189 1 0.01
190 79 0.51
191 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.23
Consensus pattern (182 bp):
GTGCTAAATAATCAGTAATAGTAGCACCACCGTCACAAAGATGCCAGACGTGCTAAATCATCATT
AATAGTAGCACCATCATCACAAAGACGTCAGACGTGCTAAATCATCATTAATAGTAGCACCACTA
TCACAAAGACATCAGACGTACTAAATCATCAGTAATAGTAGCACCACCATCA
Done.