Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003924.1 Hibiscus syriacus cultivar Beakdansim tig00008483_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: 1466330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 4 of 5
Found at i:1033963 original size:44 final size:44
Alignment explanation
Indices: 1033881--1033993 Score: 120
Period size: 44 Copynumber: 2.5 Consensus size: 44
1033871 GCTACTTTTC
* *
1033881 TATGTGCAAGGGTAAGACCTTATCGTTACCGCAAGCTCCTTTGT
1 TATGTGCAAGGGTAAGACCTTACCGTTACCACAAGCTCCTTTGT
* * * * **
1033925 TATGTGTAAGGGTAAGATCTTACCGTTATCACAGGCTCCTCTACT
1 TATGTGCAAGGGTAAGACCTTACCGTTACCACAAGCTCCT-TTGT
*
1033970 T-TGTGCACAGGATAAGACCTTACC
1 TATGTGCA-AGGGTAAGACCTTACC
1033994 ATAGGCTCCT
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
44 39 0.70
45 17 0.30
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (44 bp):
TATGTGCAAGGGTAAGACCTTACCGTTACCACAAGCTCCTTTGT
Found at i:1034011 original size:39 final size:39
Alignment explanation
Indices: 1033957--1034072 Score: 169
Period size: 39 Copynumber: 3.0 Consensus size: 39
1033947 CCGTTATCAC
* * *
1033957 AGGCTCCTCTACTTTGTGCACAGGATAAGACCTTACCAT
1 AGGCTCCTCGACTTTGTGCTCAGGATAAGTCCTTACCAT
* *
1033996 AGGCTCCTCGGCTTTGTGCTCAGGATAAGTCCTTACCGT
1 AGGCTCCTCGACTTTGTGCTCAGGATAAGTCCTTACCAT
* *
1034035 AGGCTCCTCGACTTTGTACTCAGGGTAAGTCCTTACCA
1 AGGCTCCTCGACTTTGTGCTCAGGATAAGTCCTTACCA
1034073 CAAACTCTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 68 1.00
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (39 bp):
AGGCTCCTCGACTTTGTGCTCAGGATAAGTCCTTACCAT
Found at i:1034151 original size:43 final size:43
Alignment explanation
Indices: 1034085--1034457 Score: 485
Period size: 43 Copynumber: 8.7 Consensus size: 43
1034075 AACTCTTTTT
* * *
1034085 CTATTTGCAAGGATAAGACCTTACTGTTTCCCAGGCTCCTTTA
1 CTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTCCTTTG
*
1034128 CTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTCCTCTG
1 CTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTCCTTTG
* *
1034171 CTATGTGCAAGAATAAGACCTTACCGTTTCCTAGGCTCCTTTG
1 CTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTCCTTTG
* * * *
1034214 CTATATGCAAGGATAAGACCTTATCATTTCCCAGGCTCATTTG
1 CTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTCCTTTG
* *
1034257 ATATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTCCATTG
1 CTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTCCTTTG
* * * * * * *
1034300 CAATGTGCAAGAATAAGACCCTATCGTTTCCTAGGCTCATATG
1 CTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTCCTTTG
* * * * *
1034343 CTATATGCAAGGATAAGACCTTACCATTTCCCATGCTCATTTA
1 CTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTCCTTTG
* * *
1034386 CTATGTGCAAGGATAAGACCTTACAGTTTCCTAGGCTCTTTTG
1 CTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTCCTTTG
* *
1034429 CTATGTGCAAGGGTAAGACCTTATCGTTT
1 CTATGTGCAAGGATAAGACCTTACCGTTT
1034458 TTGTAGGCTC
Statistics
Matches: 282, Mismatches: 48, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 282 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (43 bp):
CTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTCCTTTG
Found at i:1034244 original size:129 final size:127
Alignment explanation
Indices: 1034085--1034457 Score: 550
Period size: 129 Copynumber: 2.9 Consensus size: 127
1034075 AACTCTTTTT
* * *
1034085 CTATTTGCAAGGATAAGACCTTACTGTTTCCCAGGCTCCTTTACTATGTGCAAGGATAAGACCTT
1 CTATATGCAAGGATAAGACCTTAC-ATTTCCCAGGCTCATTTACTATGTGCAAGGATAAGACCTT
* * *
1034150 ACCGTTTCCCAGGCTCCTCTGCTATGTGCAAGAATAAGACCTTACCGTTTCCTAGGCTCCTTTG
65 ACCGTTTCCCAGGCTCCT-TGCTATGTGCAAGAATAAGACCTTATCGTTTCCTAGGCTCATATG
1034214 CTATATGCAAGGATAAGACCTTATCATTTCCCAGGCTCATTTGA-TATGTGCAAGGATAAGACCT
1 CTATATGCAAGGATAAGACCTTA-CATTTCCCAGGCTCATTT-ACTATGTGCAAGGATAAGACCT
* *
1034278 TACCGTTTCCCAGGCTCCATTGCAATGTGCAAGAATAAGACCCTATCGTTTCCTAGGCTCATATG
64 TACCGTTTCCCAGGCTCC-TTGCTATGTGCAAGAATAAGACCTTATCGTTTCCTAGGCTCATATG
*
1034343 CTATATGCAAGGATAAGACCTTACCATTTCCCATGCTCATTTACTATGTGCAAGGATAAGACCTT
1 CTATATGCAAGGATAAGACCTTA-CATTTCCCAGGCTCATTTACTATGTGCAAGGATAAGACCTT
* * * **
1034408 ACAGTTTCCTAGGCTCTTTTGCTATGTGCAAGGGTAAGACCTTATCGTTT
65 ACCGTTTCCCAGGCTC-CTTGCTATGTGCAAGAATAAGACCTTATCGTTT
1034458 TTGTAGGCTC
Statistics
Matches: 222, Mismatches: 17, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
128 1 0.00
129 218 0.98
130 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (127 bp):
CTATATGCAAGGATAAGACCTTACATTTCCCAGGCTCATTTACTATGTGCAAGGATAAGACCTTA
CCGTTTCCCAGGCTCCTTGCTATGTGCAAGAATAAGACCTTATCGTTTCCTAGGCTCATATG
Found at i:1036059 original size:42 final size:42
Alignment explanation
Indices: 1036012--1036261 Score: 371
Period size: 42 Copynumber: 6.0 Consensus size: 42
1036002 GAGCCTAGGA
* * *
1036012 AAACTGTAAGGTTTATCCTT-GCACACAGCAAAGGGGCTTGGG
1 AAACTGTAAGGCTTA-CCTTCGCACACAGCAAAGGGACCTGGG
* * *
1036054 AAACTGTAAGGCTTACCCTT-GCACACAACAAAGGAACCTGGT
1 AAACTGTAAGGCTTA-CCTTCGCACACAGCAAAGGGACCTGGG
* *
1036096 AAACTGTAAGGCTTACATTCGCACACAGCAAATGGACCTGGG
1 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGG
*
1036138 AAACTGTAAGGCTTACCCTT-GCACACAGCAAAGGGACCTGGT
1 AAACTGTAAGGCTTA-CCTTCGCACACAGCAAAGGGACCTGGG
1036180 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGG
1036222 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTG
1 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTG
1036262 ATAATACTTC
Statistics
Matches: 189, Mismatches: 16, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
41 7 0.04
42 179 0.95
43 3 0.02
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (42 bp):
AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGG
Found at i:1037201 original size:17 final size:17
Alignment explanation
Indices: 1037179--1037216 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1037169 AGTCAACAAC
*
1037179 GGTCAACGGTCGGGTCG
1 GGTCAACGGTAGGGTCG
1037196 GGTCAACGGTAGGGTCG
1 GGTCAACGGTAGGGTCG
1037213 GGTC
1 GGTC
1037217 GGGTCGGGTC
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:0.13, C:0.21, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTAGGGTCG
Found at i:1042323 original size:40 final size:40
Alignment explanation
Indices: 1042279--1042360 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
1042269 ACCGTAGTGC
1042279 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1042319 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1042359 TA
1 TA
1042361 TAAACCTGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1048426 original size:14 final size:14
Alignment explanation
Indices: 1048407--1048435 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1048397 AATAGTACCC
1048407 GAATAGTGAACAGT
1 GAATAGTGAACAGT
1048421 GAATAGTGAACAGT
1 GAATAGTGAACAGT
1048435 G
1 G
1048436 GGGGAATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.31, T:0.21
Consensus pattern (14 bp):
GAATAGTGAACAGT
Found at i:1049117 original size:40 final size:40
Alignment explanation
Indices: 1049073--1049234 Score: 306
Period size: 40 Copynumber: 4.0 Consensus size: 40
1049063 ACCGTAGTGC
*
1049073 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
1049113 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1049153 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1049193 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1049233 TA
1 TA
1049235 TAAACCTGCA
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 119 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1054816 original size:18 final size:18
Alignment explanation
Indices: 1054793--1054827 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1054783 CAGTTAACGA
1054793 TCAACGGGTCGAGTCGGG
1 TCAACGGGTCGAGTCGGG
*
1054811 TCAACGGGTCGGGTCGG
1 TCAACGGGTCGAGTCGG
1054828 ACCGATCAAA
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:0.14, C:0.23, G:0.46, T:0.17
Consensus pattern (18 bp):
TCAACGGGTCGAGTCGGG
Found at i:1069806 original size:24 final size:24
Alignment explanation
Indices: 1069778--1069824 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1069768 TATCTAATTT
*
1069778 CTGATTTGAATTATGTTATGATAC
1 CTGATATGAATTATGTTATGATAC
*
1069802 CTGATATGAATTCTGTTATGATA
1 CTGATATGAATTATGTTATGATA
1069825 TATGGCCTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.45
Consensus pattern (24 bp):
CTGATATGAATTATGTTATGATAC
Found at i:1077321 original size:23 final size:23
Alignment explanation
Indices: 1077288--1077334 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1077278 CATACATATA
*
1077288 GTCATCCCCATGAGCAATGTTAT
1 GTCATCACCATGAGCAATGTTAT
1077311 GTCATCACCATGAGCAATGTTAT
1 GTCATCACCATGAGCAATGTTAT
1077334 G
1 G
1077335 ACCGTTACAT
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:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (23 bp):
GTCATCACCATGAGCAATGTTAT
Found at i:1083017 original size:24 final size:24
Alignment explanation
Indices: 1082990--1083065 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
1082980 TATATCAAAA
1082990 ATCAAAACATAAATC-AGGTCAAGT
1 ATCAAAACA-AAATCTAGGTCAAGT
* *
1083014 ATCATATCAAAATCTAGGTCAAGT
1 ATCAAAACAAAATCTAGGTCAAGT
* * * * *
1083038 ATCATATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCTAGGTCAAGT
1083062 ATCA
1 ATCA
1083066 GATCAGAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.11
24 41 0.89
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (24 bp):
ATCAAAACAAAATCTAGGTCAAGT
Found at i:1083070 original size:24 final size:24
Alignment explanation
Indices: 1083007--1083140 Score: 119
Period size: 24 Copynumber: 5.6 Consensus size: 24
1082997 CATAAATCAG
* * * *
1083007 GTCAAGTATCATATCAAAATCTAG
1 GTCAAGTATCAGATCAGAATCCAA
*
1083031 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
1083055 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
*
1083079 GTC-AGATATCAGATCA-AGATCCAT
1 GTCAAG-TATCAGATCAGA-ATCCAA
* * *
1083103 GTCAAGTTTCAGATAAGAATTCAA
1 GTCAAGTATCAGATCAGAATCCAA
* **
1083127 ATCAAAAATCAGAT
1 GTCAAGTATCAGAT
1083141 AAATATTCAT
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
23 3 0.03
24 87 0.94
25 3 0.03
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:1089120 original size:18 final size:18
Alignment explanation
Indices: 1089097--1089133 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1089087 CAACGGTCAA
1089097 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1089115 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1089133 C
1 C
1089134 AGGTAAACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.24, G:0.49, T:0.16
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1089133 original size:13 final size:13
Alignment explanation
Indices: 1089091--1089120 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1089081 AACGGTCAAC
1089091 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1089104 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1089117 GGTC
1 GGTC
1089121 GGGTCAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1089157 original size:31 final size:31
Alignment explanation
Indices: 1089090--1089158 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1089080 CAACGGTCAA
* * *
1089090 CGGTCAACGGGTCGGGTCAACGGGTCGGGTC
1 CGGTCAACGGGTCAGGTAAACGGGTCGGGAC
* *
1089121 GGGTCAACGGGTCAGGTAAACGGGTCGTGAC
1 CGGTCAACGGGTCAGGTAAACGGGTCGGGAC
1089152 CGGTCAA
1 CGGTCAA
1089159 AACGGTCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.16
Consensus pattern (31 bp):
CGGTCAACGGGTCAGGTAAACGGGTCGGGAC
Found at i:1089166 original size:9 final size:9
Alignment explanation
Indices: 1089152--1089200 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
1089142 GGGTCGTGAC
1089152 CGGTCAAAA
1 CGGTCAAAA
1089161 CGGTCAAAA
1 CGGTCAAAA
1089170 CCGGTTCAAAA
1 -CGG-TCAAAA
* *
1089181 CCGGTTAAAC
1 -CGGTCAAAA
1089191 CGGTCAAAA
1 CGGTCAAAA
1089200 C
1 C
1089201 CGGTTTTCAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 17 0.50
10 7 0.21
11 10 0.29
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (9 bp):
CGGTCAAAA
Found at i:1089178 original size:20 final size:18
Alignment explanation
Indices: 1089150--1089200 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
1089140 ACGGGTCGTG
1089150 ACCGGTCAAAACGGTCAAA
1 ACCGGTCAAAACGGT-AAA
*
1089169 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAA-CGGTAAA
1089189 ACCGGTCAAAAC
1 ACCGGTCAAAAC
1089201 CGGTTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 11 0.38
20 13 0.45
21 4 0.14
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (18 bp):
ACCGGTCAAAACGGTAAA
Found at i:1089201 original size:19 final size:19
Alignment explanation
Indices: 1089150--1089205 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1089140 ACGGGTCGTG
*
1089150 ACCGGTCAAAA-CGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
1089169 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
1089189 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
1089206 TTCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 13 0.38
21 4 0.12
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:1096285 original size:13 final size:13
Alignment explanation
Indices: 1096267--1096303 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1096257 ACCTGTCAAC
*
1096267 GGTCAACGGGTCG
1 GGTCAACGGGTCA
1096280 GGTCAACGGGTCA
1 GGTCAACGGGTCA
*
1096293 GGTAAACGGGT
1 GGTCAACGGGT
1096304 AAACGGGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.43, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCA
Found at i:1096336 original size:10 final size:10
Alignment explanation
Indices: 1096316--1096370 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
1096306 ACGGGTCGTG
1096316 ACCGGTC-AA
1 ACCGGTCAAA
1096325 ACCGGTCAAA
1 ACCGGTCAAA
1096335 ACCGGTTCAAA
1 ACCGG-TCAAA
*
1096346 ACCGGT-TAA
1 ACCGGTCAAA
1096355 ACCGGTCAAA
1 ACCGGTCAAA
1096365 ACCGGT
1 ACCGGT
1096371 TTTCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:1096371 original size:19 final size:19
Alignment explanation
Indices: 1096316--1096371 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1096306 ACGGGTCGTG
*
1096316 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
1096335 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
1096355 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
1096372 TTCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:1101218 original size:25 final size:27
Alignment explanation
Indices: 1101183--1101232 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
1101173 AACAAAAAGA
*
1101183 AAACTTTGATA-C-TAGCGATATTTAT
1 AAACTTGGATATCATAGCGATATTTAT
*
1101208 AAACTTGGATATCATAGTGATATTT
1 AAACTTGGATATCATAGCGATATTT
1101233 CTATTTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 1 0.05
27 10 0.48
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (27 bp):
AAACTTGGATATCATAGCGATATTTAT
Found at i:1101413 original size:21 final size:20
Alignment explanation
Indices: 1101374--1101413 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1101364 TCAAAATCCG
*
1101374 ATATAAATGATTTTATATTT
1 ATATAAATGATTATATATTT
*
1101394 ATATAAATTTATTATATATT
1 ATATAAA-TGATTATATATT
1101414 AGGTGGTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATATAAATGATTATATATTT
Found at i:1104336 original size:24 final size:24
Alignment explanation
Indices: 1104309--1104384 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
1104299 TATATCAAAA
* *
1104309 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAAGTCAAGT
* *
1104333 ATCATATCAGAAATCAAGTCAAGT
1 ATCAAAACAGAAATCAAGTCAAGT
* * *
1104357 AACATATCAG-AATCCAAGTCAAGT
1 ATCAAAACAGAAAT-CAAGTCAAGT
1104381 ATCA
1 ATCA
1104385 GATCAAAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAAATCAAGTCAAGT
Found at i:1104389 original size:24 final size:24
Alignment explanation
Indices: 1104326--1104437 Score: 138
Period size: 24 Copynumber: 4.7 Consensus size: 24
1104316 CATAAATCAG
*
1104326 GTCAAGTATCATATCAGAAAT-CAA
1 GTCAAGTATCAGATCAG-AATCCAA
* *
1104350 GTCAAGTAACATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
* *
1104374 GTCAAGTATCAGATCAAAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
*
1104398 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
1104422 GTCAAGTATCAGATCA
1 GTCAAGTATCAGATCA
1104438 TAATTCAAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.06
24 72 0.91
25 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:1104457 original size:48 final size:48
Alignment explanation
Indices: 1104326--1104459 Score: 130
Period size: 48 Copynumber: 2.8 Consensus size: 48
1104316 CATAAATCAG
* * * *
1104326 GTCAAGTATCATATCAGAAAT-CAAGTCAAGTAA-CATATCAGAATCCAA
1 GTCAAGTATCAGATCA-AAATCCAAATC-AGAAATCAGATCAGAATCCAA
** * *
1104374 GTCAAGTATCAGATCAAAATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAAATCAGAAATCAGATCAGAATCCAA
* *
1104422 GTCAAGTATCAGATCATAATTCAAATC-GAAAATCAGAT
1 GTCAAGTATCAGATCAAAATCCAAATCAG-AAATCAGAT
1104460 AAAATATTCA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
47 8 0.11
48 64 0.89
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATCAAAATCCAAATCAGAAATCAGATCAGAATCCAA
Found at i:1107011 original size:13 final size:13
Alignment explanation
Indices: 1106993--1107020 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1106983 GGTCAACGGC
1106993 TCAACGGGTCGGG
1 TCAACGGGTCGGG
1107006 TCAACGGGTCGGG
1 TCAACGGGTCGGG
1107019 TC
1 TC
1107021 GGGTCGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.25, G:0.43, T:0.18
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:1107602 original size:12 final size:12
Alignment explanation
Indices: 1107585--1107617 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1107575 ATAGGGAAAA
1107585 TCTAGAAAATTT
1 TCTAGAAAATTT
1107597 TCTAGAAAATTT
1 TCTAGAAAATTT
1107609 TCTAGAAAA
1 TCTAGAAAA
1107618 CATACGGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (12 bp):
TCTAGAAAATTT
Found at i:1109147 original size:24 final size:24
Alignment explanation
Indices: 1109120--1109171 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1109110 AACGGATATA
*
1109120 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
1109144 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
1109168 TCAA
1 TCAA
1109172 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:1109243 original size:72 final size:71
Alignment explanation
Indices: 1109149--1109281 Score: 189
Period size: 72 Copynumber: 1.9 Consensus size: 71
1109139 TCAGGTCAAG
*
1109149 TATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAAGTC-AAATATCAGATCAAAATCC
1 TATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAAATCGAAA-ATCAGAT-AAAATCC
1109213 ATGTCAGA
64 ATGTCAGA
* * *
1109221 TATCATATCAG-AATCCATGTCAAGTATCAGATCAGAATTCAAATCGAAAATCAGATAAAAT
1 TATCATATCAGAAAT-CAGGTCAAGTAACAGATCAGAATCCAAATCGAAAATCAGATAAAAT
1109282 ATTCATGTGA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
71 8 0.15
72 44 0.80
73 3 0.05
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (71 bp):
TATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAAATCGAAAATCAGATAAAATCCAT
GTCAGA
Found at i:1109258 original size:24 final size:24
Alignment explanation
Indices: 1109143--1109258 Score: 137
Period size: 24 Copynumber: 4.8 Consensus size: 24
1109133 CATAAATCAG
* *
1109143 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* *
1109167 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
* *
1109191 GTCAAATATCAGATCAAAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
1109215 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
1109239 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
1109259 TCAAATCGAA
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
23 4 0.05
24 72 0.92
25 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:1113854 original size:25 final size:27
Alignment explanation
Indices: 1113819--1113868 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1113809 AAAAAAAAGA
*
1113819 AAACTTTGATA-C-TAGCGATATTTAT
1 AAACTTGGATATCATAGCGATATTTAT
1113844 AAACTTGGATATCATAGCGATATTT
1 AAACTTGGATATCATAGCGATATTT
1113869 CTATTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 1 0.05
27 11 0.50
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (27 bp):
AAACTTGGATATCATAGCGATATTTAT
Found at i:1114049 original size:21 final size:20
Alignment explanation
Indices: 1114010--1114049 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1114000 TCAAAATCCG
*
1114010 ATATAAATGATTTTATATTT
1 ATATAAATGATTATATATTT
*
1114030 ATATAAATTTATTATATATT
1 ATATAAA-TGATTATATATT
1114050 AGGTGGTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATATAAATGATTATATATTT
Found at i:1115861 original size:25 final size:27
Alignment explanation
Indices: 1115826--1115875 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1115816 AAAAAAAAGA
*
1115826 AAACTTTGATA-C-TAGCGATATTTAT
1 AAACTTGGATATCATAGCGATATTTAT
1115851 AAACTTGGATATCATAGCGATATTT
1 AAACTTGGATATCATAGCGATATTT
1115876 CTATTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 1 0.05
27 11 0.50
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (27 bp):
AAACTTGGATATCATAGCGATATTTAT
Found at i:1116056 original size:21 final size:20
Alignment explanation
Indices: 1116017--1116056 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1116007 TCAAAATCCG
*
1116017 ATATAAATGATTTTATATTT
1 ATATAAATGATTATATATTT
*
1116037 ATATAAATTTATTATATATT
1 ATATAAA-TGATTATATATT
1116057 AGGTGGTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATATAAATGATTATATATTT
Found at i:1120119 original size:21 final size:20
Alignment explanation
Indices: 1120080--1120119 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1120070 TCAAAATCCG
*
1120080 ATATAAATGATTTTATATTT
1 ATATAAATGATTATATATTT
*
1120100 ATATAAATTTATTATATATT
1 ATATAAA-TGATTATATATT
1120120 AGGTGGTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATATAAATGATTATATATTT
Found at i:1120756 original size:46 final size:46
Alignment explanation
Indices: 1120689--1120776 Score: 176
Period size: 46 Copynumber: 1.9 Consensus size: 46
1120679 CGATCAATAC
1120689 TAATGATATCTCATGAACATAGCGTAACAAAGCTATTCTTATCTTG
1 TAATGATATCTCATGAACATAGCGTAACAAAGCTATTCTTATCTTG
1120735 TAATGATATCTCATGAACATAGCGTAACAAAGCTATTCTTAT
1 TAATGATATCTCATGAACATAGCGTAACAAAGCTATTCTTAT
1120777 ATTTGCAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (46 bp):
TAATGATATCTCATGAACATAGCGTAACAAAGCTATTCTTATCTTG
Found at i:1131499 original size:9 final size:10
Alignment explanation
Indices: 1131449--1131503 Score: 69
Period size: 9 Copynumber: 5.6 Consensus size: 10
1131439 AACGCTGGAA
1131449 ACCGGTTTTG
1 ACCGGTTTTG
*
1131459 ACCGG-TTTA
1 ACCGGTTTTG
*
1131468 ACCGGCTTTG
1 ACCGGTTTTG
1131478 AACCGGTTTTG
1 -ACCGGTTTTG
1131489 ACCGG-TTTG
1 ACCGGTTTTG
1131498 ACCGGT
1 ACCGGT
1131504 CACGACCCGT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
9 17 0.44
10 13 0.33
11 9 0.23
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.33
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:1131524 original size:13 final size:13
Alignment explanation
Indices: 1131506--1131536 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1131496 TGACCGGTCA
1131506 CGACCCGTTGACC
1 CGACCCGTTGACC
1131519 CGACCCGTTGACC
1 CGACCCGTTGACC
1131532 CGACC
1 CGACC
1131537 TGACCTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.48, G:0.23, T:0.13
Consensus pattern (13 bp):
CGACCCGTTGACC
Found at i:1131536 original size:18 final size:18
Alignment explanation
Indices: 1131515--1131549 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1131505 ACGACCCGTT
1131515 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
* *
1131533 GACCTGACCTGTTGACC
1 GACCCGACCCGTTGACC
1131550 GTTGACCGGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:1131618 original size:29 final size:29
Alignment explanation
Indices: 1131557--1131623 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
1131547 ACCGTTGACC
** *
1131557 GGTGCTATTCTGGGAATTAATTCAGTTTT
1 GGTGCTATTCTGGGAATTAATTCAGAATG
*
1131586 GGTGCTATTCTGGGAATTAATT-TGAAATG
1 GGTGCTATTCTGGGAATTAATTCAG-AATG
1131615 GGTGCTATT
1 GGTGCTATT
1131624 TTGGTAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.22, C:0.09, G:0.27, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCAGAATG
Found at i:1138729 original size:13 final size:13
Alignment explanation
Indices: 1138711--1138749 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1138701 TGACCGGTCA
*
1138711 CGACCCGTTTACC
1 CGACCCGTTGACC
1138724 CGACCCGTTGACC
1 CGACCCGTTGACC
*
1138737 CGACCTGTTGACC
1 CGACCCGTTGACC
1138750 GTTGACCGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.15, C:0.44, G:0.21, T:0.21
Consensus pattern (13 bp):
CGACCCGTTGACC
Found at i:1146086 original size:13 final size:13
Alignment explanation
Indices: 1146064--1146093 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1146054 GGGTTAACCC
*
1146064 GACCCGACCCGTT
1 GACCCAACCCGTT
1146077 GACCCAACCCGTT
1 GACCCAACCCGTT
1146090 GACC
1 GACC
1146094 GTTGACCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.13
Consensus pattern (13 bp):
GACCCAACCCGTT
Found at i:1157609 original size:31 final size:32
Alignment explanation
Indices: 1157552--1157629 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 32
1157542 TTGAGGCCAT
*
1157552 GGGGCCTACCTAAGAACACATCTTAGGGCCGC
1 GGGGCCTACCTAAGAACACATCTTAGGGCAGC
* **
1157584 GGGGCCTACCTGAGAA-TGATCTTAGGGCAGC
1 GGGGCCTACCTAAGAACACATCTTAGGGCAGC
* *
1157615 AGAGCCTACCTAAGA
1 GGGGCCTACCTAAGA
1157630 GTCACATTAG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.62
32 15 0.38
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (32 bp):
GGGGCCTACCTAAGAACACATCTTAGGGCAGC
Found at i:1164692 original size:29 final size:28
Alignment explanation
Indices: 1164561--1164694 Score: 128
Period size: 29 Copynumber: 4.6 Consensus size: 28
1164551 TCCACATTCG
**
1164561 AAAATTCCCAGAATGTCATTTTTTTCAA
1 AAAATTCCCAGAATGTCACCTTTTTCAA
* *
1164589 AATAATT-CCAAAATTGTCA-TTTTCTTCAA
1 AA-AATTCCCAGAA-TGTCACCTTT-TTCAA
* * *
1164618 AATAATCCCCATAATGACACCTTTTTCATA
1 AA-AATTCCCAGAATGTCACCTTTTTCA-A
*
1164648 AAAATTCCCATAATGTCACCTTTTTCACA
1 AAAATTCCCAGAATGTCACCTTTTTCA-A
1164677 AAAATTCCCAGAATGTCA
1 AAAATTCCCAGAATGTCA
1164695 TTGGGTCGGT
Statistics
Matches: 91, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
28 11 0.12
29 69 0.76
30 11 0.12
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.35
Consensus pattern (28 bp):
AAAATTCCCAGAATGTCACCTTTTTCAA
Found at i:1171878 original size:57 final size:56
Alignment explanation
Indices: 1171810--1171975 Score: 176
Period size: 57 Copynumber: 2.9 Consensus size: 56
1171800 AAAATGTAAT
* * *
1171810 ATTTTTCAAAATAATTTCCTGAATGTCATTTTTTTTCAAAATAATTCCCATATTGTC
1 ATTTTTCAAAATAATTTCCTGAATGTCA-TTTTTTTCAAAATAATTCCCAGAATATC
* *
1171867 ATTTTTCAAAATAA-TTACTAGAATATCATTTTTTT-AAAATAATTCCCAGAATATC
1 ATTTTTCAAAATAATTTCCT-GAATGTCATTTTTTTCAAAATAATTCCCAGAATATC
* * * * * *
1171922 ATCTTTTTCACAA-AATTCCCAGAATGTTATCTTTTTCACAATAATTCCCAGAAT
1 A--TTTTTCAAAATAATTTCCTGAATGTCATTTTTTTCAAAATAATTCCCAGAAT
1171976 GTCACCTATT
Statistics
Matches: 91, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
55 18 0.20
56 25 0.27
57 48 0.53
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.43
Consensus pattern (56 bp):
ATTTTTCAAAATAATTTCCTGAATGTCATTTTTTTCAAAATAATTCCCAGAATATC
Found at i:1171899 original size:28 final size:28
Alignment explanation
Indices: 1171793--1172008 Score: 186
Period size: 29 Copynumber: 7.6 Consensus size: 28
1171783 TACATTCGAA
* * *
1171793 AATTCTCAAAATGTAATATTTTTCAAAAT
1 AATTCCCAGAATGTCAT-TTTTTCAAAAT
* *
1171822 AATTTCCTGAATGTCATTTTTTTTCAAAAT
1 AATTCCCAGAATGTCA--TTTTTTCAAAAT
* *
1171852 AATTCCCATATTGTCA-TTTTTCAAAAT
1 AATTCCCAGAATGTCATTTTTTCAAAAT
* * * *
1171879 AATTACTAGAATATCATTTTTTTAAAAT
1 AATTCCCAGAATGTCATTTTTTCAAAAT
* *
1171907 AATTCCCAGAATATCATCTTTTTCACAA-
1 AATTCCCAGAATGTCAT-TTTTTCAAAAT
* *
1171935 AATTCCCAGAATGTTATCTTTTTCACAAT
1 AATTCCCAGAATGTCAT-TTTTTCAAAAT
* *
1171964 AATTCCCAGAATGTCACCTATTTCATAAA-
1 AATTCCCAGAATGTCA-TTTTTTCA-AAAT
*
1171993 AATTCCCAAAATGTCA
1 AATTCCCAGAATGTCA
1172009 CTGGGTCGGT
Statistics
Matches: 154, Mismatches: 26, Indels: 14
0.79 0.13 0.07
Matches are distributed among these distances:
27 22 0.14
28 51 0.33
29 55 0.36
30 25 0.16
31 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (28 bp):
AATTCCCAGAATGTCATTTTTTCAAAAT
Found at i:1171975 original size:85 final size:85
Alignment explanation
Indices: 1171811--1171975 Score: 190
Period size: 85 Copynumber: 1.9 Consensus size: 85
1171801 AAATGTAATA
* * * * * *
1171811 TTTTTCAAAATAATTTCCTGAATGTCATTTTTTTTCAAAATAATTCCCATATTGTCATTTTTCAA
1 TTTTTCAAAATAATTCCCAGAATATCATTCTTTTTCAAAATAATTCCCAGAATGTCATTTTTCAA
*
1171876 AATAATTACTAGAATATCAT
66 AATAATTACCAGAATATCAT
* * *
1171896 TTTTTTAAAATAATTCCCAGAATATCA-TCTTTTTCACAA-AATTCCCAGAATGTTATCTTTTTC
1 TTTTTCAAAATAATTCCCAGAATATCATTCTTTTTCAAAATAATTCCCAGAATGTCA--TTTTTC
* *
1171959 ACAATAATTCCCAGAAT
64 AAAATAATTACCAGAAT
1171976 GTCACCTATT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
83 13 0.20
84 10 0.15
85 43 0.65
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (85 bp):
TTTTTCAAAATAATTCCCAGAATATCATTCTTTTTCAAAATAATTCCCAGAATGTCATTTTTCAA
AATAATTACCAGAATATCAT
Found at i:1171987 original size:29 final size:29
Alignment explanation
Indices: 1171811--1172009 Score: 154
Period size: 28 Copynumber: 7.0 Consensus size: 29
1171801 AAATGTAATA
* * * **
1171811 TTTTTCAAAATAATTTCCTGAATGTCATTT
1 TTTTTCACAATAATTCCCAGAATGTCA-CC
* * *
1171841 TTTTTCAAAATAATTCCCATATTGTCA--
1 TTTTTCACAATAATTCCCAGAATGTCACC
* * * * *
1171868 TTTTTCAAAATAATTACTAGAATATCA-T
1 TTTTTCACAATAATTCCCAGAATGTCACC
* * * *
1171896 TTTTTTAAAATAATTCCCAGAATATCATC
1 TTTTTCACAATAATTCCCAGAATGTCACC
* *
1171925 TTTTTCACAA-AATTCCCAGAATGTTATC
1 TTTTTCACAATAATTCCCAGAATGTCACC
1171953 TTTTTCACAATAATTCCCAGAATGTCACC
1 TTTTTCACAATAATTCCCAGAATGTCACC
* * * *
1171982 TATTTCATAAAAATTCCCAAAATGTCAC
1 TTTTTCACAATAATTCCCAGAATGTCAC
1172010 TGGGTCGGTT
Statistics
Matches: 143, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
27 22 0.15
28 50 0.35
29 48 0.34
30 23 0.16
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.41
Consensus pattern (29 bp):
TTTTTCACAATAATTCCCAGAATGTCACC
Found at i:1172031 original size:18 final size:18
Alignment explanation
Indices: 1172005--1172043 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1171995 TTCCCAAAAT
* *
1172005 GTCACTGGGTCGGTTCGG
1 GTCAATGGGTCGGGTCGG
1172023 GTCAATGGGTCGGGTCGG
1 GTCAATGGGTCGGGTCGG
1172041 GTC
1 GTC
1172044 GGGTCGGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.21, G:0.46, T:0.26
Consensus pattern (18 bp):
GTCAATGGGTCGGGTCGG
Found at i:1183634 original size:12 final size:13
Alignment explanation
Indices: 1183587--1183656 Score: 53
Period size: 12 Copynumber: 5.8 Consensus size: 13
1183577 GATACATGAC
1183587 CTGA-ATTCTGTT
1 CTGATATTCTGTT
* *
1183599 CTAAT-TTCTGAT
1 CTGATATTCTGTT
* *
1183611 CTG-GATTATGTT
1 CTGATATTCTGTT
1183623 CTGATATT-TGTT
1 CTGATATTCTGTT
1183635 CTGA-ATTCTGTT
1 CTGATATTCTGTT
*
1183647 TTGAT-TTCTG
1 CTGATATTCTG
1183657 ATATCTCCGT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
11 3 0.07
12 39 0.87
13 3 0.07
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.53
Consensus pattern (13 bp):
CTGATATTCTGTT
Found at i:1187818 original size:12 final size:12
Alignment explanation
Indices: 1187785--1187823 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
1187775 TGACCTGAAT
1187785 TCTGTTCTGGAT-
1 TCTGTTCT-GATA
1187797 TCTGTTCTGATA
1 TCTGTTCTGATA
1187809 TCTGTTCTGATA
1 TCTGTTCTGATA
1187821 TCT
1 TCT
1187824 ATTATGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 3 0.12
12 23 0.88
ACGTcount: A:0.13, C:0.18, G:0.18, T:0.51
Consensus pattern (12 bp):
TCTGTTCTGATA
Found at i:1187831 original size:24 final size:24
Alignment explanation
Indices: 1187785--1187831 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1187775 TGACCTGAAT
* *
1187785 TCTGTTCTGGATTCTGTTCTGATA
1 TCTGTTCTGGATTCTATTATGATA
1187809 TCTGTTCT-GATATCTATTATGAT
1 TCTGTTCTGGAT-TCTATTATGAT
1187832 TTCTAATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.51
Consensus pattern (24 bp):
TCTGTTCTGGATTCTATTATGATA
Found at i:1200573 original size:30 final size:30
Alignment explanation
Indices: 1200537--1200598 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
1200527 ATAACCCGAC
* *
1200537 CCGACCCGACCCGTTTACCCGTCCCATTGA
1 CCGACCCGACCCGTTGACCCGACCCATTGA
* *
1200567 CCGACCCGACCTGTTGACCCGACCCGTTGA
1 CCGACCCGACCCGTTGACCCGACCCATTGA
1200597 CC
1 CC
1200599 CGTTGACCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.16, C:0.47, G:0.19, T:0.18
Consensus pattern (30 bp):
CCGACCCGACCCGTTGACCCGACCCATTGA
Found at i:1200587 original size:13 final size:13
Alignment explanation
Indices: 1200569--1200600 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1200559 CCCATTGACC
*
1200569 GACCCGACCTGTT
1 GACCCGACCCGTT
1200582 GACCCGACCCGTT
1 GACCCGACCCGTT
1200595 GACCCG
1 GACCCG
1200601 TTGACCGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.44, G:0.25, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1203122 original size:24 final size:24
Alignment explanation
Indices: 1203090--1203144 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
1203080 AAATATTTTA
1203090 TCTGATTTCTGACCTGAATTCTAT
1 TCTGATTTCTGACCTGAATTCTAT
* * *
1203114 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGACCTGAATTCTAT
1203138 TCTGATT
1 TCTGATT
1203145 CTGTTTTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.49
Consensus pattern (24 bp):
TCTGATTTCTGACCTGAATTCTAT
Found at i:1203146 original size:11 final size:11
Alignment explanation
Indices: 1203107--1203155 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
1203097 TCTGACCTGA
*
1203107 ATTCTATTCTG
1 ATTCTGTTCTG
*
1203118 ATTTCTGATCTGG
1 A-TTCTGTTCT-G
1203131 ATTCTGTTCTG
1 ATTCTGTTCTG
*
1203142 ATTCTGTTTTG
1 ATTCTGTTCTG
1203153 ATT
1 ATT
1203156 TCTGATATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 15 0.47
12 15 0.47
13 2 0.06
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.55
Consensus pattern (11 bp):
ATTCTGTTCTG
Found at i:1207844 original size:29 final size:29
Alignment explanation
Indices: 1207777--1207838 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
1207767 CTCAGGGCCT
* *
1207777 TATATGATGTGTTGGGCTGGGTGTATAAA
1 TATATGATGTGATGGGATGGGTGTATAAA
* *
1207806 TTTATGATGTGATGGGATGGG-GTATATA
1 TATATGATGTGATGGGATGGGTGTATAAA
1207834 TATAT
1 TATAT
1207839 ATATGTTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.26, C:0.02, G:0.32, T:0.40
Consensus pattern (29 bp):
TATATGATGTGATGGGATGGGTGTATAAA
Found at i:1209390 original size:80 final size:81
Alignment explanation
Indices: 1209227--1209390 Score: 303
Period size: 80 Copynumber: 2.0 Consensus size: 81
1209217 ATACAATATG
* *
1209227 ATTGGATTTTAATGATAACCCTTTTACATCAAAAAATTGTAATTGGTTACAATTAAAAAAAACTT
1 ATTGGATTTTAATGATAACCCTTTTACATCAAAAAATTGAAATCGGTTACAATTAAAAAAAACTT
1209292 AAGAATTCACATATTT
66 AAGAATTCACATATTT
1209308 ATTGGATTTTAATGATAACCCTTTTACATCAAAAAATT-AAATCGGTTACAATTAAAAAAAACTT
1 ATTGGATTTTAATGATAACCCTTTTACATCAAAAAATTGAAATCGGTTACAATTAAAAAAAACTT
1209372 AAGAATTCACATATTT
66 AAGAATTCACATATTT
1209388 ATT
1 ATT
1209391 TCAAAATCTG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
80 43 0.53
81 38 0.47
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.37
Consensus pattern (81 bp):
ATTGGATTTTAATGATAACCCTTTTACATCAAAAAATTGAAATCGGTTACAATTAAAAAAAACTT
AAGAATTCACATATTT
Found at i:1213623 original size:13 final size:12
Alignment explanation
Indices: 1213597--1213637 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
1213587 GATTTTGACC
*
1213597 TGACCCAACCGT
1 TGACCCGACCGT
1213609 TGACCCGACCCGT
1 TGACCCGA-CCGT
1213622 TGA-CCGACCGT
1 TGACCCGACCGT
1213633 TGACC
1 TGACC
1213638 GAGTGGTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 7 0.27
12 12 0.46
13 7 0.27
ACGTcount: A:0.20, C:0.41, G:0.22, T:0.17
Consensus pattern (12 bp):
TGACCCGACCGT
Found at i:1213634 original size:11 final size:11
Alignment explanation
Indices: 1213604--1213639 Score: 54
Period size: 11 Copynumber: 3.1 Consensus size: 11
1213594 ACCTGACCCA
1213604 ACCGTTGACCCG
1 ACCGTTGA-CCG
1213616 ACCCGTTGACCG
1 A-CCGTTGACCG
1213628 ACCGTTGACCG
1 ACCGTTGACCG
1213639 A
1 A
1213640 GTGGTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.48
12 5 0.22
13 7 0.30
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.17
Consensus pattern (11 bp):
ACCGTTGACCG
Found at i:1213808 original size:57 final size:57
Alignment explanation
Indices: 1213692--1213841 Score: 255
Period size: 57 Copynumber: 2.6 Consensus size: 57
1213682 AATTATCTTG
*
1213692 AAAAGGGTGTTATTTTTGTAATTATTTTTCAAAAGGTGCTATTTTAATAATTATTTCT
1 AAAAGGGTGTTATTTTTGTAATTATTTTT-AAAAGGTCCTATTTTAATAATTATTTCT
* *
1213750 AAAAGGGTGCTATTTTTGTAATTATTTTTAAAAGGTCCTATTTTAGTAATTATTTCT
1 AAAAGGGTGTTATTTTTGTAATTATTTTTAAAAGGTCCTATTTTAATAATTATTTCT
*
1213807 AAAAGGGTGTTATTTTCGTAATTATTTTTAAAAGG
1 AAAAGGGTGTTATTTTTGTAATTATTTTTAAAAGG
1213842 GTGATATTTT
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
57 59 0.68
58 28 0.32
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.48
Consensus pattern (57 bp):
AAAAGGGTGTTATTTTTGTAATTATTTTTAAAAGGTCCTATTTTAATAATTATTTCT
Found at i:1213852 original size:29 final size:29
Alignment explanation
Indices: 1213644--1213851 Score: 215
Period size: 29 Copynumber: 7.2 Consensus size: 29
1213634 GACCGAGTGG
* * ** *
1213644 TATTTTGGTAATTATTTTGAAAATTGTGG
1 TATTTTAGTAATTATTTTTAAAAGGGTGC
* * * *
1213673 TA-TTCAGGTAATTATCTTGAAAAGGGTGT
1 TATTTTA-GTAATTATTTTTAAAAGGGTGC
*
1213702 TATTTTTGTAATTATTTTTCAAAA-GGTGC
1 TATTTTAGTAATTATTTTT-AAAAGGGTGC
* *
1213731 TATTTTAATAATTATTTCTAAAAGGGTGC
1 TATTTTAGTAATTATTTTTAAAAGGGTGC
* *
1213760 TATTTTTGTAATTATTTTTAAAA-GGTCC
1 TATTTTAGTAATTATTTTTAAAAGGGTGC
* *
1213788 TATTTTAGTAATTATTTCTAAAAGGGTGT
1 TATTTTAGTAATTATTTTTAAAAGGGTGC
* *
1213817 TATTTTCGTAATTATTTTTAAAAGGGTGA
1 TATTTTAGTAATTATTTTTAAAAGGGTGC
1213846 TATTTT
1 TATTTT
1213852 CATAAAATGG
Statistics
Matches: 149, Mismatches: 25, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
28 31 0.21
29 112 0.75
30 6 0.04
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (29 bp):
TATTTTAGTAATTATTTTTAAAAGGGTGC
Found at i:1221231 original size:29 final size:28
Alignment explanation
Indices: 1221189--1221405 Score: 254
Period size: 29 Copynumber: 7.6 Consensus size: 28
1221179 TCGTTAACCG
* * *
1221189 GGTGGTATTTTGGTAATTATTTTGAAAA
1 GGTGCTATTTTTGTAATTATTTTTAAAA
* * * * *
1221217 TGGTGGTATTCTGGTAATTATCTTGAAAA
1 -GGTGCTATTTTTGTAATTATTTTTAAAA
1221246 TGGTGCTATTTTTGTAATTATTTTTAAAA
1 -GGTGCTATTTTTGTAATTATTTTTAAAA
* *
1221275 GGTGCTATTTTAGTAATTATTTCTAAAA
1 GGTGCTATTTTTGTAATTATTTTTAAAA
*
1221303 GGGTACTATTTTTGTAATTATTTTTAAAA
1 -GGTGCTATTTTTGTAATTATTTTTAAAA
* *
1221332 GGTGCTATTTTAGTAATTATTTCTAAAA
1 GGTGCTATTTTTGTAATTATTTTTAAAA
1221360 GGATGCTATTTTTGTAATTATTTTTAAAA
1 GG-TGCTATTTTTGTAATTATTTTTAAAA
* *
1221389 GGGTTCTATTTTCGTAA
1 -GGTGCTATTTTTGTAA
1221406 AACGGTTGAT
Statistics
Matches: 166, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
28 53 0.32
29 111 0.67
30 2 0.01
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.48
Consensus pattern (28 bp):
GGTGCTATTTTTGTAATTATTTTTAAAA
Found at i:1221315 original size:57 final size:58
Alignment explanation
Indices: 1221188--1221405 Score: 289
Period size: 57 Copynumber: 3.8 Consensus size: 58
1221178 ATCGTTAACC
* * * * * * * *
1221188 GGGTGGTATTTTGGTAATTATTTTGAAAATGGTGGTATTCTGGTAATTATCTT-GAAAA
1 GGGTGCTATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTAT-TTCTAAAA
*
1221246 TGGTGCTATTTTTGTAATTATTTTTAAAA-GGTGCTATTTTAGTAATTATTTCTAAAA
1 GGGTGCTATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTATTTCTAAAA
*
1221303 GGGTACTATTTTTGTAATTATTTTTAAAA-GGTGCTATTTTAGTAATTATTTCTAAAA
1 GGGTGCTATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTATTTCTAAAA
* * *
1221360 GGATGCTATTTTTGTAATTATTTTTAAAAGGGTTCTATTTTCGTAA
1 GGGTGCTATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTAGTAA
1221406 AACGGTTGAT
Statistics
Matches: 144, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
56 2 0.01
57 103 0.72
58 39 0.27
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.48
Consensus pattern (58 bp):
GGGTGCTATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTATTTCTAAAA
Found at i:1221367 original size:86 final size:85
Alignment explanation
Indices: 1221189--1221405 Score: 265
Period size: 86 Copynumber: 2.5 Consensus size: 85
1221179 TCGTTAACCG
* * * ** * *
1221189 GGTGGTATTTTGGTAATTATTTTGAAAATGGTGGTATTCTGGTAATTATCTTGAAAATGGTGCTA
1 GGTGCTATTTTAGTAATTATTTT-AAAAGGGTACTATTTTCGTAATTATCTTGAAAATGGTGCTA
* *
1221254 TTTTTGTAATTATTTTTAAAA
65 TTTTAGTAATTATTTCTAAAA
* * *
1221275 GGTGCTATTTTAGTAATTATTTCTAAAAGGGTACTATTTTTGTAATTATTTTTAAAA-GGTGCTA
1 GGTGCTATTTTAGTAATTATTT-TAAAAGGGTACTATTTTCGTAATTATCTTGAAAATGGTGCTA
1221339 TTTTAGTAATTATTTCTAAAA
65 TTTTAGTAATTATTTCTAAAA
* *
1221360 GGATGCTATTTTTGTAATTATTTTTAAAAGGGTTCTATTTTCGTAA
1 GG-TGCTATTTTAGTAATTA-TTTTAAAAGGGTACTATTTTCGTAA
1221406 AACGGTTGAT
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
85 28 0.25
86 82 0.72
87 4 0.04
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.48
Consensus pattern (85 bp):
GGTGCTATTTTAGTAATTATTTTAAAAGGGTACTATTTTCGTAATTATCTTGAAAATGGTGCTAT
TTTAGTAATTATTTCTAAAA
Found at i:1222143 original size:24 final size:24
Alignment explanation
Indices: 1222116--1222166 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1222106 ATTTTTTACG
* *
1222116 GGATTTTGACATGATACCTGACCT
1 GGATTTTGACATGATACATGACAT
* *
1222140 GGATTTTTATATGATACATGACAT
1 GGATTTTGACATGATACATGACAT
1222164 GGA
1 GGA
1222167 CTCTGATCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (24 bp):
GGATTTTGACATGATACATGACAT
Found at i:1228788 original size:57 final size:58
Alignment explanation
Indices: 1228662--1228873 Score: 243
Period size: 57 Copynumber: 3.7 Consensus size: 58
1228652 TCGTTAACCA
* * * * * * * *
1228662 GGTGGTATTTTGGTAATTATTTTGAAAATGGTGGTATTCT-GATAATTATCTT-GAAAAT
1 GGTGATATTTTCGTAATTATTTTTAAAAGGGTGCTATTTTAG-TAATTAT-TTCTAAAAG
1228720 GGTGATATTTTCGTAATTATTTTTAAAA-GGTGCTATTTTAGTAATTATTTCTAAAAG
1 GGTGATATTTTCGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTATTTCTAAAAG
* * *
1228777 GGTGTTATTTTCGTAATTATTTTT-AAATGGTGTTATTTTAGTAATTATTTCTAAAAG
1 GGTGATATTTTCGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTATTTCTAAAAG
* ** *
1228834 GATGCCATTTTTGTAATTATTTTTAAAAGGGTGCTATTTT
1 GGTGATATTTTCGTAATTATTTTTAAAAGGGTGCTATTTT
1228874 TCGTAAAATG
Statistics
Matches: 135, Mismatches: 15, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
56 5 0.04
57 91 0.67
58 39 0.29
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.49
Consensus pattern (58 bp):
GGTGATATTTTCGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTATTTCTAAAAG
Found at i:1228854 original size:86 final size:85
Alignment explanation
Indices: 1228668--1228879 Score: 248
Period size: 86 Copynumber: 2.4 Consensus size: 85
1228658 ACCAGGTGGT
* * * * *
1228668 ATTTTGGTAATTATTTTGAAAATGGTGGTATTCT-GATAATTATCTTGAAAATGGTGATATTTTC
1 ATTTTAGTAATTATTTT-AAAAGGGTGCTATTTTCG-TAATTATCTTGAAAATGGTGATATTTTA
* *
1228732 GTAATTATTTTTAAAAGGTGCT
64 GTAATTATTTCTAAAAGGTGCC
* ** *
1228754 ATTTTAGTAATTATTTCTAAAAGGGTGTTATTTTCGTAATTAT-TTTTAAATGGTGTTATTTTAG
1 ATTTTAGTAATTATTT-TAAAAGGGTGCTATTTTCGTAATTATCTTGAAAATGGTGATATTTTAG
1228818 TAATTATTTCTAAAAGGATGCC
65 TAATTATTTCTAAAAGG-TGCC
*
1228840 ATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTTCGTAA
1 ATTTTAGTAATTA-TTTTAAAAGGGTGCTA-TTTTCGTAA
1228880 AATGGTTGAT
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
85 33 0.30
86 62 0.57
87 14 0.13
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.49
Consensus pattern (85 bp):
ATTTTAGTAATTATTTTAAAAGGGTGCTATTTTCGTAATTATCTTGAAAATGGTGATATTTTAGT
AATTATTTCTAAAAGGTGCC
Found at i:1228874 original size:29 final size:29
Alignment explanation
Indices: 1228662--1228879 Score: 208
Period size: 29 Copynumber: 7.6 Consensus size: 29
1228652 TCGTTAACCA
* * * *
1228662 GGTGGTATTTTGGTAATTATTTTGAAAAT
1 GGTGCTATTTTTGTAATTATTTTTAAAAG
* * * * *
1228691 GGTGGTA-TTCTGATAATTATCTTGAAAAT
1 GGTGCTATTTTTG-TAATTATTTTTAAAAG
* *
1228720 GGTGATATTTTCGTAATTATTTTTAAAA-
1 GGTGCTATTTTTGTAATTATTTTTAAAAG
* *
1228748 GGTGCTATTTTAGTAATTATTTCTAAAAG
1 GGTGCTATTTTTGTAATTATTTTTAAAAG
* * *
1228777 GGTGTTATTTTCGTAATTATTTTT-AAAT
1 GGTGCTATTTTTGTAATTATTTTTAAAAG
* * *
1228805 GGTGTTATTTTAGTAATTATTTCTAAAAG
1 GGTGCTATTTTTGTAATTATTTTTAAAAG
* *
1228834 GATGCCATTTTTGTAATTATTTTTAAAAG
1 GGTGCTATTTTTGTAATTATTTTTAAAAG
1228863 GGTGCTATTTTTCGTAA
1 GGTGCTATTTTT-GTAA
1228880 AATGGTTGAT
Statistics
Matches: 159, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
28 53 0.33
29 99 0.62
30 7 0.04
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.48
Consensus pattern (29 bp):
GGTGCTATTTTTGTAATTATTTTTAAAAG
Found at i:1229625 original size:24 final size:24
Alignment explanation
Indices: 1229590--1229647 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
1229580 ATTTTTTATG
* *
1229590 GGATTTTGATATGATACTTGACCT
1 GGATTTTGATATGATACATGACAT
*
1229614 GGATTTTTATATGATACATGACAT
1 GGATTTTGATATGATACATGACAT
*
1229638 GGATTCTGAT
1 GGATTTTGAT
1229648 CAGCTACTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (24 bp):
GGATTTTGATATGATACATGACAT
Found at i:1230848 original size:26 final size:24
Alignment explanation
Indices: 1230819--1230866 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
1230809 CAATAGTTCT
1230819 CATACTATTTATATAAGATTTTTATC
1 CATACTATTT-T-TAAGATTTTTATC
* *
1230845 CATATTATTTTTTAGATTTTTA
1 CATACTATTTTTAAGATTTTTA
1230867 ATCATGTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 1 0.05
26 9 0.45
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.56
Consensus pattern (24 bp):
CATACTATTTTTAAGATTTTTATC
Found at i:1236119 original size:29 final size:28
Alignment explanation
Indices: 1236077--1236288 Score: 203
Period size: 29 Copynumber: 7.4 Consensus size: 28
1236067 TCGTTAACCG
* *
1236077 GGTGGTATTTTGGTAATTATTTTGAAAA
1 GGTGCTATTTTAGTAATTATTTTGAAAA
* * * * *
1236105 TGGTGGTATTCTGGTAATTATCTTGAAGAT
1 -GGTGCTATTTTAGTAATTATTTTGAA-AA
*
1236135 GGTGCTATTTTCA-TAATTATTTTTAAAA
1 GGTGCTATTTT-AGTAATTATTTTGAAAA
*
1236163 GGTGCTATTTTAGTAATTATTTCT-AGAAG
1 GGTGCTATTTTAGTAATTATTT-TGA-AAA
* *
1236192 GGTGCTATTTTCGTAATTATTTTTAAAA
1 GGTGCTATTTTAGTAATTATTTTGAAAA
*
1236220 GGTGTTATTTTAGTAATTATTTGTGAAAA
1 GGTGCTATTTTAGTAATTATTT-TGAAAA
* * * *
1236249 GATGTTATTTTTGTAATTATTTTTAAAA
1 GGTGCTATTTTAGTAATTATTTTGAAAA
1236277 GGGTGCTATTTT
1 -GGTGCTATTTT
1236289 CATAAAATGA
Statistics
Matches: 155, Mismatches: 20, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
27 1 0.01
28 50 0.32
29 103 0.66
30 1 0.01
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.49
Consensus pattern (28 bp):
GGTGCTATTTTAGTAATTATTTTGAAAA
Found at i:1236199 original size:57 final size:57
Alignment explanation
Indices: 1236076--1236288 Score: 234
Period size: 57 Copynumber: 3.7 Consensus size: 57
1236066 ATCGTTAACC
* * * * * * * *
1236076 GGGTGGTATTTTGGTAATTATTTTGAAAATGGTGGTATTCTGGTAATTATCT-TGAA
1 GGGTGCTATTTTCGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTATTTCTGAA
*
1236132 GATGGTGCTATTTTCATAATTATTTTTAAAA-GGTGCTATTTTAGTAATTATTTCTAGAA
1 G--GGTGCTATTTTCGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTATTTCT-GAA
* *
1236191 GGGTGCTATTTTCGTAATTATTTTTAAAA-GGTGTTATTTTAGTAATTATTTGTGAAA
1 GGGTGCTATTTTCGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTATTTCTG-AA
* * * *
1236248 AGATGTTATTTTTGTAATTATTTTTAAAAGGGTGCTATTTT
1 GGGTGCTATTTTCGTAATTATTTTTAAAAGGGTGCTATTTT
1236289 CATAAAATGA
Statistics
Matches: 135, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
56 2 0.01
57 94 0.70
58 35 0.26
59 4 0.03
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (57 bp):
GGGTGCTATTTTCGTAATTATTTTTAAAAGGGTGCTATTTTAGTAATTATTTCTGAA
Found at i:1236249 original size:86 final size:85
Alignment explanation
Indices: 1236077--1236289 Score: 232
Period size: 86 Copynumber: 2.5 Consensus size: 85
1236067 TCGTTAACCG
* * * * * * *
1236077 GGTGGTATTTTGGTAATTATTTTGAAAATGGTGGTATTCTGGTAATTATCTTGAAGATGGTGCTA
1 GGTGCTATTTTAGTAATTATTTT-AAAAGGGTGCTATTTTCGTAATTATCTTGAAGAAGGTGCTA
*
1236142 TTTTCATAATTATTTTTAAAA
65 TTTTCATAATTATTTTGAAAA
* * * *
1236163 GGTGCTATTTTAGTAATTATTTCTAGAAGGGTGCTATTTTCGTAATTATTTTTAA-AAGGTGTTA
1 GGTGCTATTTTAGTAATTATTT-TAAAAGGGTGCTATTTTCGTAATTATCTTGAAGAAGGTGCTA
1236227 TTTT-AGTAATTATTTGTGAAAA
65 TTTTCA-TAATTATTT-TGAAAA
* * *
1236249 GATGTTATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTC
1 GGTGCTATTTTAGTAATTA-TTTTAAAAGGGTGCTATTTTC
1236290 ATAAAATGAT
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
84 1 0.01
85 20 0.19
86 82 0.77
87 4 0.04
ACGTcount: A:0.28, C:0.05, G:0.19, T:0.48
Consensus pattern (85 bp):
GGTGCTATTTTAGTAATTATTTTAAAAGGGTGCTATTTTCGTAATTATCTTGAAGAAGGTGCTAT
TTTCATAATTATTTTGAAAA
Found at i:1237027 original size:24 final size:24
Alignment explanation
Indices: 1237000--1237072 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
1236990 TTTTTTTACG
1237000 GGATTTTGATATGATACTTGACCT
1 GGATTTTGATATGATACTTGACCT
* * *
1237024 GGATTTTTATATGATACATGACAT
1 GGATTTTGATATGATACTTGACCT
* *
1237048 GGATTCTGATCA-GCTACTTGACCT
1 GGATTTTGAT-ATGATACTTGACCT
1237072 G
1 G
1237073 AATTATGTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 39 0.98
25 1 0.03
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
GGATTTTGATATGATACTTGACCT
Found at i:1237096 original size:2 final size:2
Alignment explanation
Indices: 1237089--1237117 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1237079 GTTTTAAATT
1237089 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 T
1237118 CCGTTATGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1237806 original size:15 final size:15
Alignment explanation
Indices: 1237786--1237822 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1237776 GACGAGAACT
1237786 ACATGCTTGGTAATG
1 ACATGCTTGGTAATG
*
1237801 ACATGCTTGGTATTG
1 ACATGCTTGGTAATG
1237816 ACATGCT
1 ACATGCT
1237823 CCTCAACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (15 bp):
ACATGCTTGGTAATG
Found at i:1238727 original size:42 final size:41
Alignment explanation
Indices: 1238661--1238749 Score: 153
Period size: 42 Copynumber: 2.1 Consensus size: 41
1238651 GGCCTTATTT
1238661 ATTTTATTTATTTGTATAAGTAATTATTTCAGATGATTTTA
1 ATTTTATTTATTTGTATAAGTAATTATTTCAGATGATTTTA
1238702 ATTTTATATTATTTAGTATAA-TAATTATTTCAGATGATTTTA
1 ATTTTAT-TTATTT-GTATAAGTAATTATTTCAGATGATTTTA
1238744 ATTTTA
1 ATTTTA
1238750 CTTGAAAATG
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
41 7 0.15
42 33 0.72
43 6 0.13
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (41 bp):
ATTTTATTTATTTGTATAAGTAATTATTTCAGATGATTTTA
Found at i:1248129 original size:10 final size:10
Alignment explanation
Indices: 1248116--1248184 Score: 68
Period size: 10 Copynumber: 6.7 Consensus size: 10
1248106 CGACCCGACC
1248116 CGTTGACCAG
1 CGTTGACCAG
1248126 CGTTGACC-G
1 CGTTGACCAG
*
1248135 CGTTGACCTG
1 CGTTGACCAG
1248145 CGTTGACCAG
1 CGTTGACCAG
* *
1248155 AACTTTGACCGG
1 --CGTTGACCAG
*
1248167 CGTTGACCGG
1 CGTTGACCAG
1248177 CCGTTGAC
1 -CGTTGAC
1248185 TTTTTCTGGG
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
9 9 0.18
10 27 0.53
11 7 0.14
12 8 0.16
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (10 bp):
CGTTGACCAG
Found at i:1248140 original size:19 final size:19
Alignment explanation
Indices: 1248112--1248175 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
1248102 GACCCGACCC
1248112 GACC-CGTTGACCAGCGTT
1 GACCGCGTTGACCAGCGTT
*
1248130 GACCGCGTTGACCTGCGTT
1 GACCGCGTTGACCAGCGTT
* *
1248149 GACCAGAACTTTGACCGGCGTT
1 GACC-G--CGTTGACCAGCGTT
1248171 GACCG
1 GACCG
1248176 GCCGTTGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
18 4 0.10
19 17 0.44
20 1 0.03
21 1 0.03
22 16 0.41
ACGTcount: A:0.17, C:0.31, G:0.30, T:0.22
Consensus pattern (19 bp):
GACCGCGTTGACCAGCGTT
Found at i:1250496 original size:24 final size:24
Alignment explanation
Indices: 1250469--1250517 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1250459 GTTTTTTTTT
* *
1250469 ATTTCTGATTTGAATTTTGTTCTG
1 ATTTCTGATCTGAATTATGTTCTG
1250493 ATTTCTGATCTGAATTATGTTCTG
1 ATTTCTGATCTGAATTATGTTCTG
1250517 A
1 A
1250518 ATTATGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.20, C:0.10, G:0.16, T:0.53
Consensus pattern (24 bp):
ATTTCTGATCTGAATTATGTTCTG
Found at i:1250516 original size:12 final size:12
Alignment explanation
Indices: 1250479--1250525 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
1250469 ATTTCTGATT
*
1250479 TGAATTTTGTTC
1 TGAATTATGTTC
* * *
1250491 TGATTTCTGATC
1 TGAATTATGTTC
1250503 TGAATTATGTTC
1 TGAATTATGTTC
1250515 TGAATTATGTT
1 TGAATTATGTT
1250526 TTGATTTCTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.21, C:0.09, G:0.17, T:0.53
Consensus pattern (12 bp):
TGAATTATGTTC
Found at i:1256101 original size:23 final size:23
Alignment explanation
Indices: 1256054--1256097 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1256044 CACATTCTAC
*
1256054 AAATATTTACAAAACTAACACCT
1 AAATATTTACAAAAATAACACCT
*
1256077 AAAT-TTTACAAAAATATCACC
1 AAATATTTACAAAAATAACACC
1256098 CTAACATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.27
Consensus pattern (23 bp):
AAATATTTACAAAAATAACACCT
Found at i:1257944 original size:28 final size:28
Alignment explanation
Indices: 1257880--1257981 Score: 177
Period size: 28 Copynumber: 3.6 Consensus size: 28
1257870 ACCCGACCCG
1257880 GTGACATTTTGGGAATTATTTTGAAAAA
1 GTGACATTTTGGGAATTATTTTGAAAAA
1257908 GGTGACATTTTGGGAATTATTTTGAAAAA
1 -GTGACATTTTGGGAATTATTTTGAAAAA
* *
1257937 ATGACATTTTGGGAATTATTTTGAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAA
1257965 GTGACATTTTGGGAATT
1 GTGACATTTTGGGAATT
1257982 TTCGAATGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
28 42 0.60
29 28 0.40
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (28 bp):
GTGACATTTTGGGAATTATTTTGAAAAA
Found at i:1259000 original size:63 final size:63
Alignment explanation
Indices: 1258869--1259000 Score: 137
Period size: 63 Copynumber: 2.1 Consensus size: 63
1258859 TAATGTGACT
* * * *
1258869 CTTAGGTAGGCTCTACGGCCCTGAGATCATTCTCGGGTAGGCCCTACGGCCCTAAGATGTGTT
1 CTTAGGTAGGCCCCACGGCCCTGAAATCATTCTCGGGTAGGCCCTACGGCCCTAAGATGTGTC
* * *
1258932 TTTAGGTAGGCCCCACGG-CCTCGAAATC-TATCTTGGGTAGGCTCT-CAGGCCCTAAGATGT-T
1 CTTAGGTAGGCCCCACGGCCCT-GAAATCAT-TCTCGGGTAGGCCCTAC-GGCCCTAAGATGTGT
1258993 CC
63 -C
1258995 CTTAGG
1 CTTAGG
1259001 ATAACTCTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
62 6 0.11
63 51 0.89
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (63 bp):
CTTAGGTAGGCCCCACGGCCCTGAAATCATTCTCGGGTAGGCCCTACGGCCCTAAGATGTGTC
Found at i:1259060 original size:25 final size:25
Alignment explanation
Indices: 1259008--1259060 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1258998 AGGATAACTC
* *
1259008 TTTTATGAGATTTACTGTAGTATAA
1 TTTTATGAGATTTACTGGACTATAA
* *
1259033 TTTTATGATATTTACTGGACTATGA
1 TTTTATGAGATTTACTGGACTATAA
1259058 TTT
1 TTT
1259061 GTTTAGTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (25 bp):
TTTTATGAGATTTACTGGACTATAA
Found at i:1261315 original size:18 final size:18
Alignment explanation
Indices: 1261292--1261330 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1261282 ATTAAAGGGG
1261292 GTGTTGACTCAAGCACAA
1 GTGTTGACTCAAGCACAA
*
1261310 GTGTTGACTCAAGCACCA
1 GTGTTGACTCAAGCACAA
1261328 GTG
1 GTG
1261331 ATGCTTCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (18 bp):
GTGTTGACTCAAGCACAA
Found at i:1286544 original size:20 final size:20
Alignment explanation
Indices: 1286519--1286556 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1286509 CAATTTATTC
1286519 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
1286539 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
1286557 TCCTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:1289218 original size:24 final size:24
Alignment explanation
Indices: 1289197--1289252 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1289187 TCATGATGTC
1289197 TCGATGCACATACAAAAAGATGCA
1 TCGATGCACATACAAAAAGATGCA
** *
1289221 TCGATGCACATACAAAGGGTTGCA
1 TCGATGCACATACAAAAAGATGCA
1289245 TCGATGCA
1 TCGATGCA
1289253 TTAAGCACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (24 bp):
TCGATGCACATACAAAAAGATGCA
Found at i:1294255 original size:64 final size:65
Alignment explanation
Indices: 1294183--1294362 Score: 186
Period size: 65 Copynumber: 2.8 Consensus size: 65
1294173 TGGAACACTT
* * * *
1294183 AGTGCATCGGTGCATTAAGTGTGCATCAATGCATAAAATG-AATTTGATGTTTTGAAT-AAGCCT
1 AGTGCATCGGTGCATGAAGTGTGCATCAATGCATAAAATGCAA-TCGATGTTTTCAATAAAACCT
1294246 A
65 A
** * *
1294247 AGTGCATCGAGT-CATGGTGTGTGCATCGATGCATAAAATGCAATCGATGTTTTCATTAAAACCT
1 AGTGCATCG-GTGCATGAAGTGTGCATCAATGCATAAAATGCAATCGATGTTTTCAATAAAACCT
*
1294311 G
65 A
* ** * * *
1294312 AGTGCATCGATGCATGAAGAATGCATCAATGCATAAACTACATTCGATGTT
1 AGTGCATCGGTGCATGAAGTGTGCATCAATGCATAAAATGCAATCGATGTT
1294363 CAATTTATTC
Statistics
Matches: 94, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
64 45 0.48
65 49 0.52
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (65 bp):
AGTGCATCGGTGCATGAAGTGTGCATCAATGCATAAAATGCAATCGATGTTTTCAATAAAACCTA
Found at i:1295578 original size:13 final size:13
Alignment explanation
Indices: 1295560--1295586 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1295550 CGCGTCATTT
1295560 ACGATCAATACTA
1 ACGATCAATACTA
1295573 ACGATCAATACTA
1 ACGATCAATACTA
1295586 A
1 A
1295587 GATATTCTTA
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:0.22, G:0.07, T:0.22
Consensus pattern (13 bp):
ACGATCAATACTA
Found at i:1298128 original size:13 final size:13
Alignment explanation
Indices: 1298110--1298149 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
1298100 CCCGACCCGA
1298110 CCGACCCGTTGAC
1 CCGACCCGTTGAC
*
1298123 CCGACCCGTGGAC
1 CCGACCCGTTGAC
*
1298136 CCAACCCGTTGAC
1 CCGACCCGTTGAC
1298149 C
1 C
1298150 GGGTGCTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.12
Consensus pattern (13 bp):
CCGACCCGTTGAC
Found at i:1298227 original size:29 final size:29
Alignment explanation
Indices: 1298150--1298247 Score: 110
Period size: 29 Copynumber: 3.4 Consensus size: 29
1298140 CCCGTTGACC
1298150 GGGTGCTATTTTGGGAATTAATTTGAAATA
1 GGGTGCTATTTTGGGAATTAATTTGAAA-A
* *
1298180 -GGTGATGTTTTGGGAATTAATTTGAAAA
1 GGGTGCTATTTTGGGAATTAATTTGAAAA
* * *
1298208 GGGTGCTATTATGGTG-ATTATTTTAAAAA
1 GGGTGCTATTTTGG-GAATTAATTTGAAAA
*
1298237 GGGTGTTATTT
1 GGGTGCTATTT
1298248 CTGTAAAATG
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
28 1 0.02
29 55 0.96
30 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.28, T:0.42
Consensus pattern (29 bp):
GGGTGCTATTTTGGGAATTAATTTGAAAA
Found at i:1305223 original size:17 final size:18
Alignment explanation
Indices: 1305186--1305226 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1305176 TTGACCGGTT
*
1305186 TTGATCCGACACGACCCG
1 TTGACCCGACACGACCCG
*
1305204 TTGACCCGACCCGA-CCG
1 TTGACCCGACACGACCCG
1305221 TTGACC
1 TTGACC
1305227 GTAGATCGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.20, C:0.41, G:0.22, T:0.17
Consensus pattern (18 bp):
TTGACCCGACACGACCCG
Found at i:1305319 original size:28 final size:29
Alignment explanation
Indices: 1305234--1305330 Score: 142
Period size: 29 Copynumber: 3.4 Consensus size: 29
1305224 ACCGTAGATC
* *
1305234 GGGTGCTATTTTGGGAATTAATTCGAAAT
1 GGGTGCTATTTTGGGAATTAATTTGAAAA
1305263 GGGTGCTATTTTGGGAATTAATTTGAAAA
1 GGGTGCTATTTTGGGAATTAATTTGAAAA
* * *
1305292 GGGTGCTA-TTTGGTAATTATTTTAAAAA
1 GGGTGCTATTTTGGGAATTAATTTGAAAA
1305320 GGGTGCTATTT
1 GGGTGCTATTT
1305331 CTGTAAAATG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
28 25 0.40
29 37 0.60
ACGTcount: A:0.28, C:0.05, G:0.27, T:0.40
Consensus pattern (29 bp):
GGGTGCTATTTTGGGAATTAATTTGAAAA
Found at i:1306624 original size:21 final size:21
Alignment explanation
Indices: 1306597--1306647 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1306587 TTGGATATAT
*
1306597 CTGTATTATTAATATTTTGTT
1 CTGTATTATTAATATTTTGTG
*
1306618 TTGTATTATTAATATTTTGTG
1 CTGTATTATTAATATTTTGTG
1306639 CTGTATTAT
1 CTGTATTAT
1306648 ATCTAATGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.04, G:0.12, T:0.61
Consensus pattern (21 bp):
CTGTATTATTAATATTTTGTG
Found at i:1311813 original size:44 final size:44
Alignment explanation
Indices: 1311750--1311849 Score: 119
Period size: 44 Copynumber: 2.3 Consensus size: 44
1311740 TTGTAAGTCT
* * * * * * * *
1311750 TTACCGTTTTCGCAGGCTCCTTTGCTATGTGCAAGGGTAATACC
1 TTACCGTTATCGCAAGCTCCTTTACAATGTACAAGGATAAGAAC
*
1311794 TTACCGTTATCGCAAGCTCCTTTACAATGTATAAGGATAAGAAC
1 TTACCGTTATCGCAAGCTCCTTTACAATGTACAAGGATAAGAAC
1311838 TTACCGTTATCG
1 TTACCGTTATCG
1311850 TAGGCTCATC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (44 bp):
TTACCGTTATCGCAAGCTCCTTTACAATGTACAAGGATAAGAAC
Found at i:1311985 original size:39 final size:39
Alignment explanation
Indices: 1311905--1311985 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 39
1311895 CTCGAATTTA
* * * *
1311905 TGCTCAGGGTAAGTCCTTACAGTAGGCTTCTCGGCTTTG
1 TGCTCAGGGTAAGTCCTTACAGCAGGCTCCTAGGCTATG
* *
1311944 TGCTCATGGTAAGTCCTTACCA-CAGGCTCCTATGCTATG
1 TGCTCAGGGTAAGTCCTTA-CAGCAGGCTCCTAGGCTATG
1311983 TGC
1 TGC
1311986 AAGGATAAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 33 0.94
40 2 0.06
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (39 bp):
TGCTCAGGGTAAGTCCTTACAGCAGGCTCCTAGGCTATG
Found at i:1312017 original size:43 final size:43
Alignment explanation
Indices: 1311964--1312090 Score: 200
Period size: 43 Copynumber: 3.0 Consensus size: 43
1311954 AAGTCCTTAC
* *
1311964 CACAGGCTCCTATGCTATGTGCAAGGATAAGACCTTACCGTTT
1 CACAAGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCGTTT
* * *
1312007 CCCATGCTCCTTTACTATGTGCAAGGATAAGACCTTACCGTTT
1 CACAAGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCGTTT
*
1312050 CACAAGCTCCTTTGCTATGTGTAAGGATAAGACCTTACCGT
1 CACAAGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCGT
1312091 ATAAGACCTT
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 76 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (43 bp):
CACAAGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCGTTT
Found at i:1312096 original size:15 final size:15
Alignment explanation
Indices: 1312076--1312105 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1312066 ATGTGTAAGG
1312076 ATAAGACCTTACCGT
1 ATAAGACCTTACCGT
1312091 ATAAGACCTTACCGT
1 ATAAGACCTTACCGT
1312106 TTCCCAGGCT
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:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (15 bp):
ATAAGACCTTACCGT
Found at i:1312126 original size:58 final size:58
Alignment explanation
Indices: 1312033--1312143 Score: 186
Period size: 58 Copynumber: 1.9 Consensus size: 58
1312023 ATGTGCAAGG
* *
1312033 ATAAGACCTTACCGTTTCACAAGCTCCTTTGCTATGTGTAAGGATAAGACCTTACCGT
1 ATAAGACCTTACCGTTTCACAAGCTCCTTTACTATGTGCAAGGATAAGACCTTACCGT
* *
1312091 ATAAGACCTTACCGTTTCCCAGGCTCCTTTACTATGTGCAAGGATAAGACCTT
1 ATAAGACCTTACCGTTTCACAAGCTCCTTTACTATGTGCAAGGATAAGACCTT
1312144 CCTGTTTCCC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (58 bp):
ATAAGACCTTACCGTTTCACAAGCTCCTTTACTATGTGCAAGGATAAGACCTTACCGT
Found at i:1312152 original size:43 final size:43
Alignment explanation
Indices: 1312091--1312187 Score: 133
Period size: 43 Copynumber: 2.3 Consensus size: 43
1312081 ACCTTACCGT
*
1312091 ATAAGACCTTACCGTTTCCCAGGCTCCTTTACTATGTGCAAGG
1 ATAAGACCTTACCGTTTCCCAGGCTCCTTTACTATGTGAAAGG
* **
1312134 ATAAGACCTT-CCTGTTTCCCAGGCTCTTTTGTTATGTGAAAGG
1 ATAAGACCTTACC-GTTTCCCAGGCTCCTTTACTATGTGAAAGG
*
1312177 GTAAGACCTTA
1 ATAAGACCTTA
1312188 TCATTTTTGC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
42 2 0.04
43 45 0.96
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (43 bp):
ATAAGACCTTACCGTTTCCCAGGCTCCTTTACTATGTGAAAGG
Found at i:1312170 original size:101 final size:101
Alignment explanation
Indices: 1311990--1312187 Score: 317
Period size: 101 Copynumber: 2.0 Consensus size: 101
1311980 ATGTGCAAGG
*
1311990 ATAAGACCTTACCGTTTCCCATGCTCCTTTACTATGTGCAAGGATAAGACCTTACCGTTTCACAA
1 ATAAGACCTTACCGTTTCCCAGGCTCCTTTACTATGTGCAAGGATAAGACCTTACCGTTTCACAA
*
1312055 GCTCCTTTGCTATGTGTAAGGATAAGACCTTACCGT
66 GCTCCTTTGCTATGTGAAAGGATAAGACCTTACCGT
*
1312091 ATAAGACCTTACCGTTTCCCAGGCTCCTTTACTATGTGCAAGGATAAGACCTT-CCTGTTTCCCA
1 ATAAGACCTTACCGTTTCCCAGGCTCCTTTACTATGTGCAAGGATAAGACCTTACC-GTTTCACA
* * * *
1312155 GGCTCTTTTGTTATGTGAAAGGGTAAGACCTTA
65 AGCTCCTTTGCTATGTGAAAGGATAAGACCTTA
1312188 TCATTTTTGC
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
100 2 0.02
101 87 0.98
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (101 bp):
ATAAGACCTTACCGTTTCCCAGGCTCCTTTACTATGTGCAAGGATAAGACCTTACCGTTTCACAA
GCTCCTTTGCTATGTGAAAGGATAAGACCTTACCGT
Found at i:1313710 original size:29 final size:29
Alignment explanation
Indices: 1313668--1313851 Score: 148
Period size: 29 Copynumber: 6.4 Consensus size: 29
1313658 CAACCCTACC
*
1313668 AGGTGACATTTTGGGAATTATTTTGAAAA
1 AGGTGATATTTTGGGAATTATTTTGAAAA
*
1313697 AGGTGATATTTTGGAAATTATTTTGAAAA
1 AGGTGATATTTTGGGAATTATTTTGAAAA
* * *
1313726 A-GTGACATTTTGGG-ATT-TTTTTAAATT
1 AGGTGATATTTTGGGAATTATTTTGAAA-A
* * * *
1313753 A-GTTACATTCTGGTAATTA-TTTGTAAAA
1 AGGTGATATTTTGGGAATTATTTTG-AAAA
* * *
1313781 TGATGCTATTTTGGGAATTA-TTTGTAAAA
1 AGGTGATATTTTGGGAATTATTTTG-AAAA
* *
1313810 TGGTGATATTTTGGTAATTATTTT-ACATAA
1 AGGTGATATTTTGGGAATTATTTTGA-A-AA
1313840 AGGTGATATTTT
1 AGGTGATATTTT
1313852 TGTAATTTTC
Statistics
Matches: 125, Mismatches: 22, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
26 7 0.06
27 14 0.11
28 18 0.14
29 70 0.56
30 16 0.13
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (29 bp):
AGGTGATATTTTGGGAATTATTTTGAAAA
Found at i:1320902 original size:11 final size:11
Alignment explanation
Indices: 1320888--1320917 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1320878 AATTAAGTTT
1320888 TAATTTTAAAA
1 TAATTTTAAAA
1320899 TAATTTTAAAA
1 TAATTTTAAAA
*
1320910 CAATTTTA
1 TAATTTTA
1320918 CAAAGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:1322876 original size:13 final size:13
Alignment explanation
Indices: 1322860--1322889 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1322850 CCGTTCACCC
1322860 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1322873 GACCCGACCTGTT
1 GACCCGACCCGTT
1322886 GACC
1 GACC
1322890 GTTGAACGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1335349 original size:24 final size:25
Alignment explanation
Indices: 1335321--1335374 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
1335311 GAATATTTTA
*
1335321 TCTGATTTCC-GATTTGAATTTTGT
1 TCTGATTACCTGATTTGAATTTTGT
1335345 TCTGA-TACCTGATTTGAATTTTGT
1 TCTGATTACCTGATTTGAATTTTGT
*
1335369 TATGAT
1 TCTGAT
1335375 ATCTAACCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (25 bp):
TCTGATTACCTGATTTGAATTTTGT
Found at i:1353649 original size:17 final size:18
Alignment explanation
Indices: 1353627--1353660 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1353617 TTGAATGTTC
*
1353627 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
1353644 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
1353661 ACAGAATGGA
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:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:1355433 original size:79 final size:79
Alignment explanation
Indices: 1355301--1355523 Score: 286
Period size: 79 Copynumber: 2.8 Consensus size: 79
1355291 AGTCCTTACA
* *
1355301 GACCTAAGGATATATTGGGTAGGCCCCAAGGCATATCCTTAGGTTGGTTCCCTTTGTTGTGTGCA
1 GACCTAAGGATATCTTGGGTA-GCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGTTGTGTGCA
1355366 TAAGGTAACCCTACG
65 TAAGGTAACCCTACG
* * * * * *
1355381 GACCTAAGAATATCTTGGGTAGCCCCAAGGTATATCCTCAGGTTGGTTCCCTTAGCTGCGTGCTT
1 GACCTAAGGATATCTTGGGTAGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGTTGTGTGCAT
1355446 AAGGTAACCCTACG
66 AAGGTAACCCTACG
** * **
1355460 GATATAAGGATGTCCTTGGGTAGATCCAAGGTATATCCTTAGGTTGGCTTCCCTTT-TTGCTGTG
1 GACCTAAGGATAT-CTTGGGTAGCCCCAAGGTATATCCTTAGGTTGG-TTCCCTTTGTTG-TGTG
1355524 TGCTGAGGGC
Statistics
Matches: 122, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
79 61 0.50
80 51 0.42
81 10 0.08
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (79 bp):
GACCTAAGGATATCTTGGGTAGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGTTGTGTGCAT
AAGGTAACCCTACG
Found at i:1359874 original size:24 final size:24
Alignment explanation
Indices: 1359847--1359905 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
1359837 ATTTCTAATT
*
1359847 TGAATTTTGTTATGATACCTGATC
1 TGAATTTTGTTATGATACCTGACC
* *
1359871 TGAATTCTT-TTCTGATATCTGACC
1 TGAATT-TTGTTATGATACCTGACC
*
1359895 TGAATTATGTT
1 TGAATTTTGTT
1359906 TTCATTTCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 26 0.90
25 2 0.07
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (24 bp):
TGAATTTTGTTATGATACCTGACC
Found at i:1366649 original size:12 final size:12
Alignment explanation
Indices: 1366632--1366656 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1366622 TGTAAACATA
1366632 ACCATGTTTAGG
1 ACCATGTTTAGG
1366644 ACCATGTTTAGG
1 ACCATGTTTAGG
1366656 A
1 A
1366657 AAGTTTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (12 bp):
ACCATGTTTAGG
Found at i:1399455 original size:13 final size:13
Alignment explanation
Indices: 1399436--1399472 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1399426 GTCACAATCC
1399436 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1399449 TACCCGACCCGTT
1 GACCCGACCCGTT
1399462 GACCCGACCCG
1 GACCCGACCCG
1399473 ACCCGTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1399472 original size:31 final size:31
Alignment explanation
Indices: 1399434--1399498 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1399424 CGGTCACAAT
* *
1399434 CCGACCCGACCCGTTTACCCGACCCGTTGAC
1 CCGACCCGACCCGTTGACCCGACCCGTTCAC
**
1399465 CCGACCCGACCCGTTGACTTGACCCGTTCAC
1 CCGACCCGACCCGTTGACCCGACCCGTTCAC
1399496 CCG
1 CCG
1399499 TTGACCGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.15, C:0.48, G:0.20, T:0.17
Consensus pattern (31 bp):
CCGACCCGACCCGTTGACCCGACCCGTTCAC
Found at i:1399515 original size:8 final size:7
Alignment explanation
Indices: 1399475--1399525 Score: 52
Period size: 8 Copynumber: 7.1 Consensus size: 7
1399465 CCGACCCGAC
1399475 CCGTTGA
1 CCGTTGA
1399482 -C-TTGA
1 CCGTTGA
*
1399487 CCCGTTCA
1 -CCGTTGA
1399495 CCCGTTGA
1 -CCGTTGA
1399503 CCGTTGA
1 CCGTTGA
1399510 CTCGTTGA
1 C-CGTTGA
1399518 CCGTTGA
1 CCGTTGA
1399525 C
1 C
1399526 TGGCGTTGAC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 4 0.11
6 1 0.03
7 16 0.42
8 17 0.45
ACGTcount: A:0.14, C:0.33, G:0.24, T:0.29
Consensus pattern (7 bp):
CCGTTGA
Found at i:1399515 original size:15 final size:15
Alignment explanation
Indices: 1399483--1399536 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
1399473 ACCCGTTGAC
* *
1399483 TTGACCCGTTCACCCG
1 TTGA-CCGTTGACTCG
1399499 TTGACCGTTGACTCG
1 TTGACCGTTGACTCG
1399514 TTGACCGTTGACTGGCG
1 TTGACCGTTGACT--CG
1399531 TTGACC
1 TTGACC
1399537 ACTGTTGACC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 22 0.65
16 4 0.12
17 8 0.24
ACGTcount: A:0.13, C:0.31, G:0.26, T:0.30
Consensus pattern (15 bp):
TTGACCGTTGACTCG
Found at i:1400851 original size:18 final size:18
Alignment explanation
Indices: 1400825--1400860 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1400815 TCGAAATGAC
*
1400825 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1400843 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1400861 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1402014 original size:24 final size:23
Alignment explanation
Indices: 1401987--1402042 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
1401977 AATTATTTTA
* *
1401987 TCTGATTTTCGACTTGAATTCTGT
1 TCTGATTTT-GACCTGAATTCTAT
**
1402011 TCTGATACATGACCTGAATTCTAT
1 TCTGAT-TTTGACCTGAATTCTAT
1402035 TCTGATTT
1 TCTGATTT
1402043 CTGATATGGA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.46
Consensus pattern (23 bp):
TCTGATTTTGACCTGAATTCTAT
Done.