Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008106.1 Hibiscus syriacus cultivar Beakdansim tig00110641_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: 540947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:205198 original size:27 final size:24
Alignment explanation
Indices: 205149--205202 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
205139 AGGCGCCGCA
*
205149 TCATCCTTAGATAACCGGACTTCC
1 TCATCATTAGATAACCGGACTTCC
*
205173 TCATCATTAGATAACCGGACTTCT
1 TCATCATTAGATAACCGGACTTCC
205197 TCATCA
1 TCATCA
205203 CGTAGGAGCC
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:0.28, C:0.30, G:0.11, T:0.31
Consensus pattern (24 bp):
TCATCATTAGATAACCGGACTTCC
Found at i:205411 original size:3 final size:3
Alignment explanation
Indices: 205405--205452 Score: 64
Period size: 3 Copynumber: 16.0 Consensus size: 3
205395 TTTTTCTGGG
205405 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TGT- TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T-TA
205450 TTA
1 TTA
205453 CAAGCCTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 3 0.07
3 34 0.83
4 4 0.10
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:207007 original size:17 final size:16
Alignment explanation
Indices: 206974--207010 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
206964 TTATGTATGA
206974 ATATATTTTACATATT
1 ATATATTTTACATATT
*
206990 ATATATTTATATATATT
1 ATATATTT-TACATATT
207007 ATAT
1 ATAT
207011 TAAGTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATATTTTACATATT
Found at i:208806 original size:28 final size:28
Alignment explanation
Indices: 208766--208822 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
208756 CAATAATAAT
208766 ACGCTTAAGACTAACATGTTATTGATTG
1 ACGCTTAAGACTAACATGTTATTGATTG
208794 ACGCTTAAGACTAACATGTTATTGATTG
1 ACGCTTAAGACTAACATGTTATTGATTG
208822 A
1 A
208823 TGACAATGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (28 bp):
ACGCTTAAGACTAACATGTTATTGATTG
Found at i:227178 original size:47 final size:49
Alignment explanation
Indices: 227051--227180 Score: 135
Period size: 47 Copynumber: 2.7 Consensus size: 49
227041 ATATAAATTT
* *
227051 CTTACC-TTTTATCCCATAAGCTCATAAGCTTA--TTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
* ** *
227097 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTTTTTCAATATA
1 CTTACCATTT-AATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
* **
227147 CTTGCCA-TT-ATTCTGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
227181 GTATGGTTAC
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
46 6 0.09
47 25 0.36
48 20 0.29
49 2 0.03
50 17 0.24
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (49 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
Found at i:231227 original size:20 final size:20
Alignment explanation
Indices: 231202--231243 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
231192 TCTCTTTTTC
231202 TTTTCTTTCTCGTTTTCATT
1 TTTTCTTTCTCGTTTTCATT
*
231222 TTTTCTTTTTCGTTTTCATT
1 TTTTCTTTCTCGTTTTCATT
231242 TT
1 TT
231244 CATTTTCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.05, C:0.17, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTTCTTTCTCGTTTTCATT
Found at i:231231 original size:26 final size:25
Alignment explanation
Indices: 231196--231249 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
231186 TTTTTTTCTC
*
231196 TTTTTCTTTTC-TTTCTCGTTTTCAT
1 TTTTTCTTTTCGTTT-TCATTTTCAT
231221 TTTTTCTTTTTCGTTTTCATTTTCAT
1 TTTTTC-TTTTCGTTTTCATTTTCAT
231247 TTT
1 TTT
231250 CTATTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 6 0.23
26 17 0.65
27 3 0.12
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTTTCTTTTCGTTTTCATTTTCAT
Found at i:231237 original size:7 final size:6
Alignment explanation
Indices: 231189--231284 Score: 54
Period size: 6 Copynumber: 15.3 Consensus size: 6
231179 TCTCTCATTT
* * *
231189 TTTTCTC TTTTTC -TTTTC TTTCTC GTTTTC ATTTTTTC TTTTTC GTTTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC --TTTTTC TTTTTC TTTTTC
* * *
231239 ATTTTC ATTTTC TATTTT- TTTCTTC TTCTGTT- TTTTTC TTCTTC TT
1 TTTTTC TTTTTC T-TTTTC TTT-TTC TT-T-TTC TTTTTC TTTTTC TT
231285 ATAATATATA
Statistics
Matches: 72, Mismatches: 9, Indels: 17
0.73 0.09 0.17
Matches are distributed among these distances:
5 9 0.12
6 43 0.60
7 12 0.17
8 8 0.11
ACGTcount: A:0.04, C:0.19, G:0.03, T:0.74
Consensus pattern (6 bp):
TTTTTC
Found at i:232389 original size:6 final size:6
Alignment explanation
Indices: 232378--232402 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
232368 ACACTTGTAT
232378 CATGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC C
232403 CATAGGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:235674 original size:7 final size:7
Alignment explanation
Indices: 235662--235692 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
235652 GTCAAAGAAA
235662 GTCAACG
1 GTCAACG
235669 GTCAACG
1 GTCAACG
235676 GTCAACG
1 GTCAACG
235683 GTCAACG
1 GTCAACG
235690 GTC
1 GTC
235693 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:235710 original size:22 final size:22
Alignment explanation
Indices: 235682--235724 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
235672 AACGGTCAAC
235682 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
235704 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
235725 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:235739 original size:9 final size:9
Alignment explanation
Indices: 235721--235838 Score: 110
Period size: 9 Copynumber: 12.3 Consensus size: 9
235711 GGTCGGGTCG
*
235721 GGTCAGACC
1 GGTCAAACC
235730 GGTCAAACC
1 GGTCAAACC
*
235739 GGTTCAGACC
1 GG-TCAAACC
235749 GGTCAAACC
1 GGTCAAACC
*
235758 GGTTCGAACC
1 GG-TCAAACC
*
235768 GGTTGAAACC
1 GG-TCAAACC
235778 GGTCAAACC
1 GGTCAAACC
*
235787 GGTTGAAACC
1 GG-TCAAACC
235797 GGTCAAACC
1 GGTCAAACC
235806 GGTCAGAACC
1 GGTCA-AACC
*
235816 GGTTGAAAACC
1 GG-T-CAAACC
*
235827 GGTTAAACC
1 GGTCAAACC
235836 GGT
1 GGT
235839 TTCCAGCAGC
Statistics
Matches: 92, Mismatches: 11, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
9 45 0.49
10 39 0.42
11 7 0.08
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:235745 original size:19 final size:19
Alignment explanation
Indices: 235727--235839 Score: 122
Period size: 19 Copynumber: 5.8 Consensus size: 19
235717 GTCGGGTCAG
*
235727 ACCGGTCAAACCGGTTCAG
1 ACCGGTCAAACCGGTTCAA
*
235746 ACCGGTCAAACCGGTTCGA
1 ACCGGTCAAACCGGTTCAA
*
235765 ACCGGTTGAAACCGG-TCAA
1 ACCGG-TCAAACCGGTTCAA
*
235784 ACCGGTTGAAACCGG-TCAA
1 ACCGG-TCAAACCGGTTCAA
*
235803 ACCGGTCAGAACCGGTTGAAA
1 ACCGGTCA-AACCGGTT-CAA
*
235824 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
235840 TCCAGCAGCC
Statistics
Matches: 83, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
18 2 0.02
19 55 0.66
20 17 0.20
21 9 0.11
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAA
Found at i:235778 original size:29 final size:28
Alignment explanation
Indices: 235746--235838 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
235736 ACCGGTTCAG
* **
235746 ACCGGTCAAACCGGTTCGAACCGGTTGAA
1 ACCGGTCAAACCGGTTCAAACCGG-TTCA
*
235775 ACCGGTCAAACCGGTTGAAACCGG-TCAA
1 ACCGGTCAAACCGGTTCAAACCGGTTC-A
* *
235803 ACCGGTCAGAACCGGTTGAAAACCGGTTAA
1 ACCGGTCA-AACCGGTT-CAAACCGGTTCA
235833 ACCGGT
1 ACCGGT
235839 TTCCAGCAGC
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
28 9 0.17
29 30 0.56
30 14 0.26
31 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (28 bp):
ACCGGTCAAACCGGTTCAAACCGGTTCA
Found at i:235779 original size:48 final size:49
Alignment explanation
Indices: 235727--235839 Score: 176
Period size: 48 Copynumber: 2.3 Consensus size: 49
235717 GTCGGGTCAG
*
235727 ACCGGTCAAACCGGTTCAGACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAAACCGGTCAAACCGG-TCAGAACCGGTTGAAA
*
235775 ACCGGTCAAACCGGTTGAAACCGGTCAAACCGGTCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAAACCGGTCAAACCGGTCAGAACCGGTTGAAA
*
235824 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
235840 TCCAGCAGCC
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
47 2 0.03
48 41 0.68
49 17 0.28
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (49 bp):
ACCGGTCAAACCGGTTCAAACCGGTCAAACCGGTCAGAACCGGTTGAAA
Found at i:243005 original size:7 final size:7
Alignment explanation
Indices: 242993--243023 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
242983 GTCAAAGAAA
242993 GTCAACG
1 GTCAACG
243000 GTCAACG
1 GTCAACG
243007 GTCAACG
1 GTCAACG
243014 GTCAACG
1 GTCAACG
243021 GTC
1 GTC
243024 GGGTCAGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:243041 original size:22 final size:22
Alignment explanation
Indices: 243013--243055 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
243003 AACGGTCAAC
243013 GGTCAACGGTCGGGTCAGGTCG
1 GGTCAACGGTCGGGTCAGGTCG
*
243035 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCAGGTC
243056 AGACCGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCAGGTCG
Found at i:243076 original size:19 final size:19
Alignment explanation
Indices: 243058--243151 Score: 109
Period size: 19 Copynumber: 4.8 Consensus size: 19
243048 GTCGGGTCAG
*
243058 ACCGGTCAAACCGGTTCAG
1 ACCGGTCAAACCGGTTCAA
243077 ACCGGTCAAACCGGTTCAA
1 ACCGGTCAAACCGGTTCAA
* *
243096 ATCGGTTGAAACCGG-TCAA
1 ACCGG-TCAAACCGGTTCAA
*
243115 ACCGGTCAGAACCGGTTGAAA
1 ACCGGTCA-AACCGGTT-CAA
*
243136 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
243152 TCCAGCAGCC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
18 2 0.03
19 36 0.56
20 17 0.27
21 9 0.14
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.18
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAA
Found at i:243082 original size:10 final size:9
Alignment explanation
Indices: 243052--243150 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
243042 GGTCGGGTCG
*
243052 GGTCAGACC
1 GGTCAAACC
243061 GGTCAAACC
1 GGTCAAACC
*
243070 GGTTCAGACC
1 GG-TCAAACC
243080 GGTCAAACC
1 GGTCAAACC
*
243089 GGTTCAAATC
1 GG-TCAAACC
*
243099 GGTTGAAACC
1 GG-TCAAACC
243109 GGTCAAACC
1 GGTCAAACC
243118 GGTCAGAACC
1 GGTCA-AACC
*
243128 GGTTGAAAACC
1 GG-T-CAAACC
*
243139 GGTTAAACC
1 GGTCAAACC
243148 GGT
1 GGT
243151 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:243109 original size:29 final size:28
Alignment explanation
Indices: 243053--243150 Score: 115
Period size: 29 Copynumber: 3.4 Consensus size: 28
243043 GTCGGGTCGG
* * *
243053 GTCAGACCGGTCAAACCGGTTCAGACCG
1 GTCAAACCGGTCAAACCGGTTAAAACCG
* *
243081 GTCAAACCGGTTCAAATCGGTTGAAACCG
1 GTCAAACCGG-TCAAACCGGTTAAAACCG
243110 GTCAAACCGGTCAGAACCGGTTGAAAACCG
1 GTCAAACCGGTCA-AACCGGTT-AAAACCG
*
243140 GTTAAACCGGT
1 GTCAAACCGGT
243151 TTCCAGCAGC
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
28 12 0.20
29 32 0.53
30 16 0.27
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.17
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTAAAACCG
Found at i:250201 original size:225 final size:224
Alignment explanation
Indices: 249807--250212 Score: 523
Period size: 225 Copynumber: 1.8 Consensus size: 224
249797 TCAGCATGGA
* *
249807 GGAGCTAGTTTCTAATTAACGTTTTCAGGCTAAATCTCAACTTCATAACGAAGGATTCTTGACCC
1 GGAGCTAGTTTCCAATCAACGTTTTCAGGCTAAATCTCAACTTCATAACGAAGGATTCTTGACCC
* * * * ***
249872 AGAAATGCATCCATAACTGACTGCATTTTTGTTTAACTCAGCGACGAAAAGCCATCTTCTAGTTA
66 AGAAATGCATCCAGAACTGACT-CATTTTTGCTTAACTCAACGACGAAAAGCCATCTTCCAACAA
* * *
249937 AATCACTTTAAAGTTAATCTCAACTTCATGATGGAGGATAATGGGTTCGAAAACCAATTTGGATT
130 AACCACTTCAAAGTTAATCTCAACTCCATGATGGAGGATAATGGGTTCGAAAACCAATTTGGATT
250002 CGGCTACATTCTAGCTTAGCTTAAAGACAG
195 CGGCTACATTCTAGCTTAGCTTAAAGACAG
* * *
250032 GGAGCTAGTTTCCAATCAACGTTTTCAGGCTAAGTCTCAACTTCATGAC-AGATGATTCTTGACC
1 GGAGCTAGTTTCCAATCAACGTTTTCAGGCTAAATCTCAACTTCATAACGA-AGGATTCTTGACC
* ** *
250096 CAGAAATGCATCCAGAACTGACT-ATATTTTGACTTAACTCAACGTCGTTAGGCCATCTTCCAAC
65 CAGAAATGCATCCAGAACTGACTCAT-TTTTG-CTTAACTCAACGACGAAAAGCCATCTTCCAAC
* * * *
250160 AAAACCTCTTCGAA-TTCAATCTCAACTCCATGA-GAGAGGATATTTGGTTCGAA
128 AAAACCACTTCAAAGTT-AATCTCAACTCCATGATG-GAGGATAATGGGTTCGAA
250213 TTCAATCCAG
Statistics
Matches: 153, Mismatches: 23, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
223 2 0.01
224 9 0.06
225 142 0.93
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (224 bp):
GGAGCTAGTTTCCAATCAACGTTTTCAGGCTAAATCTCAACTTCATAACGAAGGATTCTTGACCC
AGAAATGCATCCAGAACTGACTCATTTTTGCTTAACTCAACGACGAAAAGCCATCTTCCAACAAA
ACCACTTCAAAGTTAATCTCAACTCCATGATGGAGGATAATGGGTTCGAAAACCAATTTGGATTC
GGCTACATTCTAGCTTAGCTTAAAGACAG
Found at i:250780 original size:26 final size:25
Alignment explanation
Indices: 250747--250874 Score: 102
Period size: 26 Copynumber: 5.0 Consensus size: 25
250737 ATATAAATAA
250747 TTTTAAAAAATATATATTATATAGT
1 TTTTAAAAAATATATATTATATAGT
* **
250772 TTTT-GAAAATATATAATATATATAAC
1 TTTTAAAAAATATAT-AT-TATATAGT
* *
250798 TTTT-GAAAACATAT-TT-TATAGT
1 TTTTAAAAAATATATATTATATAGT
250820 TTTTAAAAATATAATACATATTATATAGT
1 TTTTAAAAA-AT-AT--ATATTATATAGT
* *
250849 TTTTAATATATATATATATATATAGT
1 TTTTAAAAAATATATAT-TATATAGT
250875 ATACATATTA
Statistics
Matches: 83, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
22 8 0.10
23 4 0.05
24 11 0.13
25 12 0.14
26 27 0.33
27 4 0.05
28 4 0.05
29 13 0.16
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (25 bp):
TTTTAAAAAATATATATTATATAGT
Found at i:250869 original size:29 final size:29
Alignment explanation
Indices: 250806--250874 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
250796 ACTTTTGAAA
*
250806 ACATATTTTATAGTTTTTAAAAATATAAT
1 ACATATTATATAGTTTTTAAAAATATAAT
*
250835 ACATATTATATAGTTTTT-AATATAT-AT
1 ACATATTATATAGTTTTTAAAAATATAAT
*
250862 ATATA-TATATAGT
1 ACATATTATATAGT
250875 ATACATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.22
27 6 0.16
28 6 0.16
29 17 0.46
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (29 bp):
ACATATTATATAGTTTTTAAAAATATAAT
Found at i:250888 original size:3 final size:3
Alignment explanation
Indices: 250880--250907 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
250870 ATAGTATACA
250880 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
250908 TTCTTTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:253165 original size:61 final size:62
Alignment explanation
Indices: 253070--253243 Score: 230
Period size: 61 Copynumber: 2.9 Consensus size: 62
253060 TTCAGTTTAA
* *
253070 CACTATAGTGTATATAAAGGACACTTGGTGCATATGGTGGGCACA-ACCTTATGTGTATTAG
1 CACTATAGTGTATATAAAGAACACTTAGTGCATATGGTGGGCACAGACCTTATGTGTATTAG
* * *
253131 CACTATAGTGTATACAGAGAACACTTAGTGCATATGGTGGG-AAAGACCTTATGTGTATTAG
1 CACTATAGTGTATATAAAGAACACTTAGTGCATATGGTGGGCACAGACCTTATGTGTATTAG
* * * *
253192 AAATATAGTGTATATAAAGGAA-ACTTAGTGCATATAGTGGGCAC-GACATTAT
1 CACTATAGTGTATATAAA-GAACACTTAGTGCATATGGTGGGCACAGACCTTAT
253244 TTATATTGGC
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
60 2 0.02
61 92 0.94
62 4 0.04
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.30
Consensus pattern (62 bp):
CACTATAGTGTATATAAAGAACACTTAGTGCATATGGTGGGCACAGACCTTATGTGTATTAG
Found at i:258583 original size:10 final size:10
Alignment explanation
Indices: 258568--258598 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
258558 ATCTCCCAAC
258568 TTCAATTCCA
1 TTCAATTCCA
258578 TTCAATTCCA
1 TTCAATTCCA
*
258588 ATCAATTCCA
1 TTCAATTCCA
258598 T
1 T
258599 ACCAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
TTCAATTCCA
Found at i:261494 original size:42 final size:42
Alignment explanation
Indices: 261448--261585 Score: 107
Period size: 42 Copynumber: 3.1 Consensus size: 42
261438 ATATGATGTG
261448 TATATGTTCAAAAGAAAAGTAATTGATGATAATCATGACATA
1 TATATGTTCAAAAGAAAAGTAATTGATGATAATCATGACATA
** * * * * ** *
261490 TATATAAAGTGTCAAGCTGATATATTTATTAAATGATGAAT-ATGATGTG
1 TATAT---GT-TCAA-AAGA-AAAGTAATT-GATGAT-AATCATGACATA
*
261539 TATATGTTAAAAAGAAAAGTAATTGATGATAATCATGACATA
1 TATATGTTCAAAAGAAAAGTAATTGATGATAATCATGACATA
261581 TATAT
1 TATAT
261586 AAAGTGTCAA
Statistics
Matches: 68, Mismatches: 19, Indels: 18
0.65 0.18 0.17
Matches are distributed among these distances:
41 3 0.04
42 20 0.29
43 6 0.09
44 2 0.03
45 5 0.07
46 6 0.09
47 2 0.03
48 6 0.09
49 15 0.22
50 3 0.04
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (42 bp):
TATATGTTCAAAAGAAAAGTAATTGATGATAATCATGACATA
Found at i:261526 original size:91 final size:91
Alignment explanation
Indices: 261418--261600 Score: 357
Period size: 91 Copynumber: 2.0 Consensus size: 91
261408 CATGATAGTT
*
261418 ATATATTTATTAAATGATGAATATGATGTGTATATGTTCAAAAGAAAAGTAATTGATGATAATCA
1 ATATATTTATTAAATGATGAATATGATGTGTATATGTTAAAAAGAAAAGTAATTGATGATAATCA
261483 TGACATATATATAAAGTGTCAAGCTG
66 TGACATATATATAAAGTGTCAAGCTG
261509 ATATATTTATTAAATGATGAATATGATGTGTATATGTTAAAAAGAAAAGTAATTGATGATAATCA
1 ATATATTTATTAAATGATGAATATGATGTGTATATGTTAAAAAGAAAAGTAATTGATGATAATCA
261574 TGACATATATATAAAGTGTCAAGCTG
66 TGACATATATATAAAGTGTCAAGCTG
261600 A
1 A
261601 GTGCAATGCA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (91 bp):
ATATATTTATTAAATGATGAATATGATGTGTATATGTTAAAAAGAAAAGTAATTGATGATAATCA
TGACATATATATAAAGTGTCAAGCTG
Found at i:261793 original size:22 final size:22
Alignment explanation
Indices: 261766--261812 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
261756 ATCATTGTTT
*
261766 TATATATGATGTTTATCATGAA
1 TATATATAATGTTTATCATGAA
261788 TATATATAATGTTTATCATGAA
1 TATATATAATGTTTATCATGAA
261810 TAT
1 TAT
261813 TATTTTGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (22 bp):
TATATATAATGTTTATCATGAA
Found at i:269776 original size:21 final size:21
Alignment explanation
Indices: 269727--269785 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
269717 GAGGATTGGT
* *
269727 ATACCAAA-GATTGAGTATCC
1 ATACCAAAGGCTTGAGTATCA
269747 ATACCAAAGGCTTGA-TATCA
1 ATACCAAAGGCTTGAGTATCA
*
269767 ATACCTAAAGTGGTTGAGT
1 ATACC-AAAG-GCTTGAGT
269786 GAGTTCATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 17 0.53
21 9 0.28
22 5 0.16
23 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (21 bp):
ATACCAAAGGCTTGAGTATCA
Found at i:273231 original size:31 final size:28
Alignment explanation
Indices: 273161--273232 Score: 74
Period size: 31 Copynumber: 2.5 Consensus size: 28
273151 CAAATTTTGG
*
273161 TTAATGACTAAAATTAAATTTTAAAAGT
1 TTAAGGACTAAAATTAAATTTTAAAAGT
* *
273189 TT-AGTGGCTAAATTATAAACTTTATAAAAGT
1 TTAAG-GACTAAAAT-TAAA-TTT-TAAAAGT
273220 TTAAGGACTAAAA
1 TTAAGGACTAAAA
273233 ATGTAATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
27 1 0.03
28 9 0.26
29 4 0.12
30 3 0.09
31 15 0.44
32 2 0.06
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (28 bp):
TTAAGGACTAAAATTAAATTTTAAAAGT
Found at i:295980 original size:148 final size:151
Alignment explanation
Indices: 295797--296092 Score: 530
Period size: 150 Copynumber: 2.0 Consensus size: 151
295787 TGAACTCTTC
295797 TCATACCTTGGTTATTCACCAAAGCTCCTGTCTTTATACACCCTAAC-AAATGGGGTTGTTAAAC
1 TCATACCTTGGTTATTCACCAAAGCTCCTGTCTTTATACACCCTAACAAAATGGGGTTGTTAAAC
*
295861 GCA-ACACAAATATCTTTTAGAGGGGCCCATGCTCTTAGATTCTA-T-TC-TGTTCCTATCAAAT
66 GCACACAAAAATATCTTTTAGAGGGGCCCATGCTCTTAGATTCTATTCTCATGTTCCTATCAAAT
295922 ATTGGGGTAATGTGTTTTTCT
131 ATTGGGGTAATGTGTTTTTCT
295943 TCATACCTTGGTATTATTCACCAAAGCTCCTGTCTTTATACACCCTAACAAAATGGGGTTGTTAA
1 TCATACCTTGG--TTATTCACCAAAGCTCCTGTCTTTATACACCCTAACAAAATGGGGTTGTTAA
296008 ACGCACACAAAAATATCTTTTAGAGGGGCCCATGCTCTTAGATTCTATTCTCATGTTCCTATCAA
64 ACGCACACAAAAATATCTTTTAGAGGGGCCCATGCTCTTAGATTCTATTCTCATGTTCCTATCAA
296073 ATATTGGGGTAATGTGTTTT
129 ATATTGGGGTAATGTGTTTT
296093 AACAGCTATT
Statistics
Matches: 142, Mismatches: 1, Indels: 7
0.95 0.01 0.05
Matches are distributed among these distances:
146 11 0.08
148 36 0.25
149 20 0.14
150 40 0.28
151 1 0.01
152 2 0.01
153 32 0.23
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (151 bp):
TCATACCTTGGTTATTCACCAAAGCTCCTGTCTTTATACACCCTAACAAAATGGGGTTGTTAAAC
GCACACAAAAATATCTTTTAGAGGGGCCCATGCTCTTAGATTCTATTCTCATGTTCCTATCAAAT
ATTGGGGTAATGTGTTTTTCT
Found at i:296512 original size:3 final size:3
Alignment explanation
Indices: 296504--296532 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
296494 TTATCTTCCC
296504 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
296533 GTATCACCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:296652 original size:18 final size:18
Alignment explanation
Indices: 296602--296652 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
296592 CACTTGCTCC
*
296602 ACCTCAAAATCAATGTCT
1 ACCTCAAAATCAGTGTCT
296620 ACCTCAAAATCAGTGTCT
1 ACCTCAAAATCAGTGTCT
*
296638 ACCTCAAAATTAGTG
1 ACCTCAAAATCAGTG
296653 ACTGCTCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.27
Consensus pattern (18 bp):
ACCTCAAAATCAGTGTCT
Found at i:298256 original size:43 final size:43
Alignment explanation
Indices: 298208--298294 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
298198 TAAGAAGGCT
298208 TGATACAAACTAAACATATCAAGACAGGGAAAAAACAAGAAGA
1 TGATACAAACTAAACATATCAAGACAGGGAAAAAACAAGAAGA
298251 TGATACAAACTAAACATATCAAGACAGGGAAAAAACAAGAAGA
1 TGATACAAACTAAACATATCAAGACAGGGAAAAAACAAGAAGA
298294 T
1 T
298295 TTAATGTGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.57, C:0.14, G:0.16, T:0.13
Consensus pattern (43 bp):
TGATACAAACTAAACATATCAAGACAGGGAAAAAACAAGAAGA
Found at i:311603 original size:1 final size:1
Alignment explanation
Indices: 311597--311621 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
311587 ATCTGATGTG
311597 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
311622 GCTTATAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:319905 original size:24 final size:24
Alignment explanation
Indices: 319832--319905 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
319822 TGCTATATTT
*
319832 TTATTTTCTTTTATTTTGGTCACTA
1 TTATTTT-TTTTATTTTGATCACTA
* * * *
319857 TT-TTTATTTATAATCTAATCACTA
1 TTATTT-TTTTTATTTTGATCACTA
*
319881 TTATTTTTTTTATTTTGATCTCTA
1 TTATTTTTTTTATTTTGATCACTA
319905 T
1 T
319906 GCTTTACTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
24 31 0.84
25 6 0.16
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.64
Consensus pattern (24 bp):
TTATTTTTTTTATTTTGATCACTA
Found at i:319989 original size:25 final size:26
Alignment explanation
Indices: 319958--320018 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
319948 AATCTTCTGA
*
319958 TATATTTTATTTTA-GTCCTTTACTT
1 TATATTTTATTTTATGTCATTTACTT
* *
319983 TATATTTTAATTTATTTCATTTACTT
1 TATATTTTATTTTATGTCATTTACTT
320009 T-TA-TTTATTT
1 TATATTTTATTT
320019 AATTTCAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 6 0.19
25 15 0.48
26 10 0.32
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (26 bp):
TATATTTTATTTTATGTCATTTACTT
Found at i:320033 original size:14 final size:14
Alignment explanation
Indices: 320016--320051 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
320006 CTTTTATTTA
320016 TTTAATTTCAGTT-C
1 TTTAATTTCA-TTAC
320030 TTTAATTTCATTAC
1 TTTAATTTCATTAC
320044 TTTAATTT
1 TTTAATTT
320052 TCTATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 2 0.10
14 19 0.90
ACGTcount: A:0.25, C:0.11, G:0.03, T:0.61
Consensus pattern (14 bp):
TTTAATTTCATTAC
Found at i:322293 original size:14 final size:14
Alignment explanation
Indices: 322266--322302 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
322256 GTTGCATTTA
322266 CATTTTCA--TTTG
1 CATTTTCATTTTTG
322278 CATTTTCATTTTTG
1 CATTTTCATTTTTG
*
322292 CATTTGCATTT
1 CATTTTCATTT
322303 GCATATTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 8 0.36
14 14 0.64
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.59
Consensus pattern (14 bp):
CATTTTCATTTTTG
Found at i:322297 original size:6 final size:6
Alignment explanation
Indices: 322257--322306 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
322247 AATACCTTCG
* * *
322257 TTGCAT TTACAT TTTCAT TTGCAT TTTCATTT TTGCAT TTGCAT TTGCAT
1 TTGCAT TTGCAT TTGCAT TTGCAT TTGCA--T TTGCAT TTGCAT TTGCAT
322307 ATTTGCATAG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
6 32 0.86
8 5 0.14
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.56
Consensus pattern (6 bp):
TTGCAT
Found at i:322297 original size:20 final size:20
Alignment explanation
Indices: 322257--322314 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
322247 AATACCTTCG
322257 TTGCATTTACA-TTTT-CAT
1 TTGCATTTACATTTTTGCAT
*
322275 TTGCATTTTCATTTTTGCAT
1 TTGCATTTACATTTTTGCAT
* *
322295 TTGCATTTGCATATTTGCAT
1 TTGCATTTACATTTTTGCAT
322315 AGTTACATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
18 10 0.29
19 4 0.11
20 21 0.60
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (20 bp):
TTGCATTTACATTTTTGCAT
Found at i:324320 original size:13 final size:13
Alignment explanation
Indices: 324298--324336 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
324288 TGCTCAAAGT
*
324298 AAGAAGAAGAAAA
1 AAGAAAAAGAAAA
324311 AAGAAAAAGAAAAA
1 AAGAAAAAG-AAAA
324325 AAGAAAAA-AAAA
1 AAGAAAAAGAAAA
324337 TTGAATATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 4 0.17
13 8 0.33
14 12 0.50
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:327035 original size:20 final size:20
Alignment explanation
Indices: 327010--327094 Score: 82
Period size: 20 Copynumber: 4.2 Consensus size: 20
327000 GCATGATGCT
327010 TAAATCCTTAGGGTCATCAG
1 TAAATCCTTAGGGTCATCAG
*
327030 TAAATCTTTAGGGTCATCAG
1 TAAATCCTTAGGGTCATCAG
* * * * *
327050 TAAGTCTTTTGAGT-ATGATG
1 TAAATCCTTAGGGTCATCA-G
327070 CTTAAATCCTTAGGGTCATCAG
1 --TAAATCCTTAGGGTCATCAG
327092 TAA
1 TAA
327095 GTCTTTTGAG
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
19 3 0.06
20 34 0.67
22 11 0.22
23 3 0.06
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
TAAATCCTTAGGGTCATCAG
Found at i:327077 original size:42 final size:42
Alignment explanation
Indices: 327030--327190 Score: 225
Period size: 42 Copynumber: 3.8 Consensus size: 42
327020 GGGTCATCAG
*
327030 TAAATCTTTAGGGTCATCAGTAAGTCTTTTGAGTATGATGCT
1 TAAATCTTTAGGGTCATCAGTAAGTCTTTTGAGCATGATGCT
*
327072 TAAATCCTTAGGGTCATCAGTAAGTCTTTTGAGCATGATGCT
1 TAAATCTTTAGGGTCATCAGTAAGTCTTTTGAGCATGATGCT
* * * * *
327114 TAAATCATTCGTGTCATCAGTAAATCTTTCGAGCATGATGCT
1 TAAATCTTTAGGGTCATCAGTAAGTCTTTTGAGCATGATGCT
* *
327156 TAAATCCTTTA-GGTCATCTGTAAGTCTTTCGAGCA
1 TAAAT-CTTTAGGGTCATCAGTAAGTCTTTTGAGCA
327191 AGATAATAAG
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 103 0.97
43 3 0.03
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (42 bp):
TAAATCTTTAGGGTCATCAGTAAGTCTTTTGAGCATGATGCT
Found at i:327159 original size:22 final size:22
Alignment explanation
Indices: 327096--327161 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
327086 CATCAGTAAG
*
327096 TCTTTTGAGCATGATGCTTAAA
1 TCTTTCGAGCATGATGCTTAAA
* * *
327118 TCATTCGTGTCATCA-G--TAAA
1 TCTTTCGAG-CATGATGCTTAAA
327138 TCTTTCGAGCATGATGCTTAAA
1 TCTTTCGAGCATGATGCTTAAA
327160 TC
1 TC
327162 CTTTAGGTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
19 4 0.12
20 12 0.36
22 13 0.39
23 4 0.12
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (22 bp):
TCTTTCGAGCATGATGCTTAAA
Found at i:327398 original size:37 final size:34
Alignment explanation
Indices: 327315--327399 Score: 89
Period size: 37 Copynumber: 2.4 Consensus size: 34
327305 CCCGAAATAG
* *
327315 AAATTTTATTTCACTCGAGATAGTTTCTTAAAAC
1 AAATTTTATCTCACTCGAGATAGTTTCTCAAAAC
* * * *
327349 AAACTTTGTCTCACTTGAGATAATTTTCCCTCAAAAC
1 AAATTTTATCTCACTCGAGAT-AGTTT--CTCAAAAC
327386 AAATTTTATCTCAC
1 AAATTTTATCTCAC
327400 CTAAGACAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
34 17 0.43
35 4 0.10
37 19 0.47
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (34 bp):
AAATTTTATCTCACTCGAGATAGTTTCTCAAAAC
Found at i:327779 original size:123 final size:123
Alignment explanation
Indices: 327559--328486 Score: 1366
Period size: 123 Copynumber: 7.6 Consensus size: 123
327549 TTCAATGGGA
* * * *
327559 GAGTTCATAATGAAAAGAACTCATCTGAAAAGGAAGAAGAAATTCATAATGAGAAGAACTTGGTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
327624 AACCTTTTGCTCAACTCTATCGCAGAAGGAGATAGATCAACATTAACATTTCCAGAAG
66 AACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAACATCAACATTTCCAGAAG
* * * *
327682 GAGTTCATAATGAGAAGAACTCATCCGAAGAGGAAGAAAAAGTTCTTAATGAGAAGAACTTGGTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * *
327747 AACCTTTTGCTCGAGTCTATCGCAGAATGAGATAGATCAGCATCAACATTTCCAAAAG
66 AACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAACATCAACATTTCCAGAAG
* * * * * *
327805 GAGTTTATAATGAGAAGAACCCATATAAAAAGGAAGACGAAGTTCATAAT--G-AGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
327867 AACCTTTTGCTCGACTCTATCACAGAAGGAGATAGAT-AAGCATCAACATTTCCAGAAG
66 AACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAA-CATCAACATTTCCAGAAG
327925 GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * *
327990 AACCTTTTGCTCAACTCTATCGCAGAAGGAGATAGATCAACATCAATATTTCCAAAAT
66 AACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAACATCAACATTTCCAGAAG
* *
328048 GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * * * * *
328113 AACCTTTTACTCGACTCTATCACAGAAAGAGATAGATCAGCATAAATATTTCTAGAAA
66 AACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAACATCAACATTTCCAGAAG
328171 GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * * *
328236 AACCTTTTTCTCGACTCTATC-CTAGAAGGAGATAAATTAA-ATTCAAAATTTTCAAAAG
66 AACCTTTTGCTCGACTCTATCGC-AGAAGGAGATAGATCAACA-TCAACATTTCCAGAAG
*
328294 GACTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
328359 AACCTTTTGCTCGACTCTATCGCAGAAGGAGATAAATCAACATCAATATTTCCAGAAG
66 AACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAACATCAACATTTCCAGAAG
* *
328417 AAGTTCATAATGAGAATAACTCATCTGAAGAGGAAGAAG-AGTTCATAATGAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
328481 AACCTT
66 AACCTT
328487 AGCTCGATTC
Statistics
Matches: 725, Mismatches: 71, Indels: 19
0.89 0.09 0.02
Matches are distributed among these distances:
119 1 0.00
120 105 0.14
121 1 0.00
122 34 0.05
123 580 0.80
124 4 0.01
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (123 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAACATCAACATTTCCAGAAG
Found at i:328229 original size:246 final size:246
Alignment explanation
Indices: 327559--329179 Score: 1396
Period size: 246 Copynumber: 6.4 Consensus size: 246
327549 TTCAATGGGA
* * *
327559 GAGTTCATAATGAAAAGAACTCATCTGAAAAGGAAGAAGAAATTCATAATGAGAAGAACTTGGTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * *
327624 AACCTTTTGCTCAACTCTATCGCAGAAGGAGATAGATCAACATTAACATTTCCAGAAGGAGTTCA
66 AACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCCAGAAAGAGTTCA
* * * *
327689 TAATGAGAAGAACTCATCCGAAGAGGAAGAAAAAGTTCTTAATGAGAAGAACTTGGTCAACCTTT
131 TAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
* * * *
327754 TGCTCGAGTCTATCGCAGAATGAGATAGATCAGCATCAACATTTCCAAAAG
196 TGCTCGACTCTATCGCAGAAGGAGATAGATCAACATCAAAATTTCCAAAAG
* * * * *
327805 GAGTTTATAATGAGAAGAACCCATATAAAAAGGAAGACGAAGTTCATAAT--G-AGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
327867 AACCTTTTGCTCGACTCTATCACAGAAGGAGATAGAT-AAGCATCAACATTTCCAGAAGGAGTTC
66 AACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAA-CATCAACATTTCCAGAAAGAGTTC
327931 ATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
130 ATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
* * *
327996 TTGCTCAACTCTATCGCAGAAGGAGATAGATCAACATCAATATTTCCAAAAT
195 TTGCTCGACTCTATCGCAGAAGGAGATAGATCAACATCAAAATTTCCAAAAG
* * *
328048 GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * * *
328113 AACCTTTTACTCGACTCTATCACAGAAAGAGATAGATCAGCATAAATATTTCTAGAAAGAGTTCA
66 AACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCCAGAAAGAGTTCA
328178 TAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
131 TAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
* * * *
328243 TTCTCGACTCTATC-CTAGAAGGAGATAAATTAA-ATTCAAAATTTTCAAAAG
196 TGCTCGACTCTATCGC-AGAAGGAGATAGATCAACA-TCAAAATTTCCAAAAG
* *
328294 GACTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * *
328359 AACCTTTTGCTCGACTCTATCGCAGAAGGAGATAAATCAACATCAATATTTCCAG-AAGAAGTTC
66 AACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCCAGAAAG-AGTTC
*
328423 ATAATGAGAATAACTCATCTGAAGAGGAAGAAG-AGTTCATAATGAGAAGAACTTGTTCAACC-T
130 ATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
* * * *
328486 TAGCTCGATTCATCCCATAT-GGAGTTAAGTCA-ATAACACCTCATTTGAGGCATCAAAATTTCC
195 TTGCTCGA--C-T--C-TATCGCAG--AAG-GAGAT-AGA--TCA----A--CATCAAAATTTCC
*
328549 AGAAG
242 AAAAG
* * * * * * *
328554 AAGTTCATAATTAGAAGAACTTATTTGAAGAGGAAGAAAAAGTTCAAAATGAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * * * *
328619 AACCTTGT-CTTGATTC-ATCGCATATAGAGTTGAATCAGTGACACCTAACTTGAGGAATCAACA
66 AACCTTTTGCTCGACTCTATCACAGA-AG-G-AG-AT-A--G--ATC-AAC-------ATCAACA
* * *
328682 TTTCCAG-AAGAAGTTCTTAATGAGAAGAACTCATCTGAAGAGGATGAAAAAGTTCATAATGAGA
114 TTTCCAGAAAG-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
* * * ** * * *
328746 AGAACTTGTTCAA-CTTTAGCTC-AATTTATCATATATGGAG-TTGAATCACTAACACCTCACTC
178 AGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAG-AT--C--A-A---CA-TC
328808 GAGGGATCAATATTTCCAATGAA-
233 -----A--AA-ATTTCCAA--AAG
* *** * * *
328831 GAGTTCAAAATGAGAAGAACTTGCCCGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTCC
1 GAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* ** * * * * *
328896 AACCTTTTGCTTGA-TCTATTGCATAAGAAGATAAATCAACATCAATATTT--ATAAGGAGAGTT
66 AACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCCAGAA--AGAGTT
* ** * * * *
328958 CATAGTGAGAAGAACTCATCCAAAGAGGGAA-TATAAGTTTATAATGAGAAAAACTTGTTCAACC
129 CATAATGAGAAGAACTCATCTGAAGA-GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
** * * ** * * *
329022 TTTTGCGAGATTCCATCATAGAATGAGATGGATCAACAT-----TTT-CAATGAAA
193 TTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAACATCAAAATTTCCAA--AAG
* * * * *
329072 GAGTTCATAATAAGAAGAACTCGTCCGGAAAA-GAATAATAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCAT-CTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* ** * *
329136 CATCCTTTTGCTTTA-TCTATCACAG-AGGAAAAGAGATCAACATC
65 CAACCTTTTGCTCGACTCTATCACAGAAGG-AGATAGATCAACATC
329180 GATATTGTCA
Statistics
Matches: 1149, Mismatches: 148, Indels: 161
0.79 0.10 0.11
Matches are distributed among these distances:
240 9 0.01
241 84 0.07
242 7 0.01
243 219 0.19
244 8 0.01
245 35 0.03
246 362 0.32
247 2 0.00
249 3 0.00
250 3 0.00
251 5 0.00
252 3 0.00
254 3 0.00
255 2 0.00
258 9 0.01
259 10 0.01
260 81 0.07
261 65 0.06
262 13 0.01
263 15 0.01
264 2 0.00
265 1 0.00
266 1 0.00
267 8 0.01
268 10 0.01
269 6 0.01
270 1 0.00
272 1 0.00
273 2 0.00
274 2 0.00
275 56 0.05
276 41 0.04
277 66 0.06
278 14 0.01
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (246 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCCAGAAAGAGTTCA
TAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
TGCTCGACTCTATCGCAGAAGGAGATAGATCAACATCAAAATTTCCAAAAG
Found at i:328332 original size:366 final size:363
Alignment explanation
Indices: 327562--328486 Score: 1381
Period size: 366 Copynumber: 2.5 Consensus size: 363
327552 AATGGGAGAG
* * * *
327562 TTCATAATGAAAAGAACTCATCTGAAAAGGAAGAAGAAATTCATAATGAGAAGAACTTGGTCAAC
1 TTCATAATGAGAAGAACTCATCTGAAGAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* *
327627 CTTTTGCTCAACTCTATCGCAGAAGGAGATAGATCAACATTAACATTTCCAGAAGGAGTTCATAA
65 CTTTTGCTCAACTCTATCGCAGAAGGAGATAGATCAACATCAATATTTCCAGAA-GAGTTCATAA
* * * * *
327692 TGAGAAGAACTCATCCGAAGAGGAAGAAAAAGTTCTTAATGAGAAGAACTTGGTCAACCTTTTGC
129 TGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTAC
* * * * *
327757 TCGAGTCTATCGCAGAATGAGATAGATCAGCATCAACATTTCCAAAAGGAGTTTATAATGAGAAG
194 TCGACTCTATCACAGAAAGAGATAGATCAGCATAAACATTTCCAAAAGGAGTTCATAATGAGAAG
*
327822 AACCCATATAAAAAGGAAGACGAAGTTCATAATGAGAACTTGTTCAACCTTTTGCTCGACTCTAT
259 AACCCATATAAAAAGGAAGAAGAAGTTCATAATGAGAACTTGTTCAACCTTTTGCTCGACTCTAT
* * * *
327887 CACAGAAGGAGATAGATAAGCATCAACATTTCCAGAAGGAG
324 CACAGAAGGAGATAAATAA-CATCAAAATTTCCAAAAGGAC
327928 TTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
1 TTCATAATGAGAAGAACTCATCTGAAGAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
*
327993 CTTTTGCTCAACTCTATCGCAGAAGGAGATAGATCAACATCAATATTTCCAAAATGAGTTCATAA
65 CTTTTGCTCAACTCTATCGCAGAAGGAGATAGATCAACATCAATATTTCCAGAA-GAGTTCATAA
* *
328058 TGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTAC
129 TGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTAC
* *
328123 TCGACTCTATCACAGAAAGAGATAGATCAGCATAAATATTTCTAGAAA-GAGTTCATAATGAGAA
194 TCGACTCTATCACAGAAAGAGATAGATCAGCATAAACATTTCCA-AAAGGAGTTCATAATGAGAA
* * * * *
328187 GAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTTCTCGACT
258 GAACCCATATAAAAAGGAAGAAGAAGTTCATAAT--G-AGAACTTGTTCAACCTTTTGCTCGACT
*
328252 CTATC-CTAGAAGGAGATAAATTAA-ATTCAAAATTTTCAAAAGGAC
320 CTATCAC-AGAAGGAGATAAA-TAACA-TCAAAATTTCCAAAAGGAC
328297 TTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
1 TTCATAATGAGAAGAACTCATCTGAAGAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* *
328362 CTTTTGCTCGACTCTATCGCAGAAGGAGATAAATCAACATCAATATTTCCAGAAGAAGTTCATAA
65 CTTTTGCTCAACTCTATCGCAGAAGGAGATAGATCAACATCAATATTTCCAGAAG-AGTTCATAA
*
328427 TGAGAATAACTCATCTGAAGAGGAAGAAG-AGTTCATAATGAGAAGAACTTGTTCAACCTT
129 TGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
328487 AGCTCGATTC
Statistics
Matches: 512, Mismatches: 39, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
366 262 0.51
367 3 0.01
368 33 0.06
369 211 0.41
370 3 0.01
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (363 bp):
TTCATAATGAGAAGAACTCATCTGAAGAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
TTTTGCTCAACTCTATCGCAGAAGGAGATAGATCAACATCAATATTTCCAGAAGAGTTCATAATG
AGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTC
GACTCTATCACAGAAAGAGATAGATCAGCATAAACATTTCCAAAAGGAGTTCATAATGAGAAGAA
CCCATATAAAAAGGAAGAAGAAGTTCATAATGAGAACTTGTTCAACCTTTTGCTCGACTCTATCA
CAGAAGGAGATAAATAACATCAAAATTTCCAAAAGGAC
Found at i:328649 original size:138 final size:138
Alignment explanation
Indices: 328399--328901 Score: 645
Period size: 138 Copynumber: 3.6 Consensus size: 138
328389 GATAAATCAA
* *
328399 CATCAATATTTCCAGAAGAAGTTCATAATGAGAATAACTCATCTGAAGAGGAAG-AAGAGTTCAT
1 CATCAATATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCAT
*
328463 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCCCATATGGAGTT-AAGTCAATAACACCT
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAA-TCAATAACACCT
*
328527 CATTTGAGG
130 CACTTGAGG
* * * * *
328536 CATCAAAATTTCCAGAAGAAGTTCATAATTAGAAGAACTTATTTGAAGAGGAAGAAAAAGTTCAA
1 CATCAATATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCAT
* * * * *
328601 AATGAGAAGAACTTGTTCAACCTT-GTCTTGATTCATCGCATATAGAGTTGAATCAGTGACACCT
66 AATGAGAAGAACTTGTTCAACCTTAG-CTCGATTCATCACATATGGAGTTGAATCAATAACACCT
*
328665 AACTTGAGG
130 CACTTGAGG
* * * *
328674 AATCAACATTTCCAGAAGAAGTTCTTAATGAGAAGAACTCATCTGAAGAGGATGAAAAAGTTCAT
1 CATCAATATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCAT
* * * * *
328739 AATGAGAAGAACTTGTTCAACTTTAGCTCAATTTATCATATATGGAGTTGAATCACTAACACCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAATAACACCTC
*
328804 ACTCGAGG
131 ACTTGAGG
* * *** * *
328812 GATCAATATTTCCAATGAAG-AGTTCAAAATGAGAAGAACTTGCCCGAAGAGGAAGAAGAAGTTC
1 CATCAATATTTCC-A-GAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTC
*
328876 ATAATGAGAAGAACTTGTCCAACCTT
64 ATAATGAGAAGAACTTGTTCAACCTT
328902 TTGCTTGATC
Statistics
Matches: 315, Mismatches: 45, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
137 50 0.16
138 197 0.63
139 64 0.20
140 4 0.01
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (138 bp):
CATCAATATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAATAACACCTC
ACTTGAGG
Found at i:330734 original size:25 final size:26
Alignment explanation
Indices: 330705--330766 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 26
330695 AATCTTCTGA
330705 TATATTTTATTTTA-GTCATTTACTT
1 TATATTTTATTTTATGTCATTTACTT
*
330730 TATATTTTAATTTATGTCATTTACTT
1 TATATTTTATTTTATGTCATTTACTT
*
330756 TTTA-TTTATTT
1 TATATTTTATTT
330767 AATTTCAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 19 0.58
26 14 0.42
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.66
Consensus pattern (26 bp):
TATATTTTATTTTATGTCATTTACTT
Found at i:330749 original size:26 final size:25
Alignment explanation
Indices: 330705--330762 Score: 89
Period size: 26 Copynumber: 2.3 Consensus size: 25
330695 AATCTTCTGA
*
330705 TATATTTTATTTTAGTCATTTACTT
1 TATATTTTAATTTAGTCATTTACTT
330730 TATATTTTAATTTATGTCATTTACTT
1 TATATTTTAATTTA-GTCATTTACTT
*
330756 TTTATTT
1 TATATTT
330763 ATTTAATTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 13 0.43
26 17 0.57
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.66
Consensus pattern (25 bp):
TATATTTTAATTTAGTCATTTACTT
Found at i:330783 original size:14 final size:14
Alignment explanation
Indices: 330764--330799 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
330754 TTTTTATTTA
330764 TTTAATTTCAGTT-C
1 TTTAATTTCA-TTAC
330778 TTTAATTTCATTAC
1 TTTAATTTCATTAC
330792 TTTAATTT
1 TTTAATTT
330800 TCTATTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 2 0.10
14 19 0.90
ACGTcount: A:0.25, C:0.11, G:0.03, T:0.61
Consensus pattern (14 bp):
TTTAATTTCATTAC
Found at i:335650 original size:24 final size:24
Alignment explanation
Indices: 335585--335652 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
335575 TACAGAGGCC
*
335585 TGTGCTTTTGCAGCATACGAAACT
1 TGTGCTTTTGCAGCATATGAAACT
*
335609 TGTGCTTTTGCAGCATATGAAGCT
1 TGTGCTTTTGCAGCATATGAAACT
*
335633 TGTGCTTTTGTAGCATATGA
1 TGTGCTTTTGCAGCATATGA
335653 GTCCCCTTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (24 bp):
TGTGCTTTTGCAGCATATGAAACT
Found at i:336913 original size:42 final size:42
Alignment explanation
Indices: 336854--336948 Score: 190
Period size: 42 Copynumber: 2.3 Consensus size: 42
336844 TCTATTGGAA
336854 TTTTCAGCTTCTAACTCTCTTAATCTTTATTTCAGTTCTTCT
1 TTTTCAGCTTCTAACTCTCTTAATCTTTATTTCAGTTCTTCT
336896 TTTTCAGCTTCTAACTCTCTTAATCTTTATTTCAGTTCTTCT
1 TTTTCAGCTTCTAACTCTCTTAATCTTTATTTCAGTTCTTCT
336938 TTTTCAGCTTC
1 TTTTCAGCTTC
336949 AAATTCCTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.16, C:0.24, G:0.05, T:0.55
Consensus pattern (42 bp):
TTTTCAGCTTCTAACTCTCTTAATCTTTATTTCAGTTCTTCT
Found at i:339511 original size:10 final size:10
Alignment explanation
Indices: 339498--339528 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
339488 AAAATAGTTA
339498 AAAAATAAAT
1 AAAAATAAAT
339508 AAAAATAAAT
1 AAAAATAAAT
339518 AAAAATTAAAT
1 AAAAA-TAAAT
339529 GAATAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.75
11 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:339541 original size:28 final size:29
Alignment explanation
Indices: 339501--339555 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
339491 ATAGTTAAAA
*
339501 AATAAATAAAAATAAATAAAAATTAAATG
1 AATAAATAAAAATAAAGAAAAATTAAATG
* *
339530 AATAAA-AGAAATAAAGGAAAATTAAA
1 AATAAATAAAAATAAAGAAAAATTAAA
339556 ATTAAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (29 bp):
AATAAATAAAAATAAAGAAAAATTAAATG
Found at i:339544 original size:34 final size:35
Alignment explanation
Indices: 339499--339570 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 35
339489 AAATAGTTAA
*
339499 AAAATAAATAAA-AATAAATAAAAATT-AAATGAAT
1 AAAAGAAATAAAGAA-AAATAAAAATTAAAATGAAT
* * *
339533 AAAAGAAATAAAGGAAAATTAAAATTAAAATGATT
1 AAAAGAAATAAAGAAAAATAAAAATTAAAATGAAT
339568 AAA
1 AAA
339571 TTGGAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 21 0.66
35 11 0.34
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (35 bp):
AAAAGAAATAAAGAAAAATAAAAATTAAAATGAAT
Found at i:340769 original size:34 final size:34
Alignment explanation
Indices: 340732--340833 Score: 96
Period size: 37 Copynumber: 2.7 Consensus size: 34
340722 GTGTATAAAT
* *
340732 ATAATAATAATATAATACTAATTTATAATACTATATA
1 ATAATAATAATAT-ATA-TAATATATAACA-TATATA
*
340769 ACTATATAATAATATATATAATATATAACATAAATA
1 A-TA-ATAATAATATATATAATATATAACATATATA
340805 ATAATAAGCTTAATATATATATATATATA
1 ATAATAA---TAATATATATA-ATATATA
340834 TACTTTAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
34 4 0.07
35 2 0.04
36 6 0.11
37 22 0.39
38 12 0.21
39 10 0.18
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (34 bp):
ATAATAATAATATATATAATATATAACATATATA
Found at i:340776 original size:18 final size:19
Alignment explanation
Indices: 340725--340833 Score: 77
Period size: 18 Copynumber: 5.7 Consensus size: 19
340715 AAATATAGTG
340725 TATA-AATATAATAATAATA
1 TATATAATAT-ATAATAATA
* *
340744 TAATACTAATTTATAATACTA
1 T-ATA-TAATATATAATAATA
*
340765 TATA-ACTATATAATAATA
1 TATATAATATATAATAATA
*
340783 TATATAATATATAA-CATA
1 TATATAATATATAATAATA
340801 -A-ATAATA-ATAAGCTTAATA
1 TATATAATATATAA---TAATA
340820 TATATATATATATA
1 TATATA-ATATATA
340834 TACTTTAAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 20
0.71 0.08 0.20
Matches are distributed among these distances:
15 4 0.06
16 6 0.09
17 1 0.01
18 18 0.26
19 12 0.17
20 7 0.10
21 12 0.17
22 7 0.10
23 3 0.04
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (19 bp):
TATATAATATATAATAATA
Found at i:340823 original size:28 final size:27
Alignment explanation
Indices: 340730--340810 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 27
340720 TAGTGTATAA
* *
340730 ATATAATA-ATAA-TATAATACTAATTT
1 ATATAATATATAACTA-AATAATAATAT
* *
340756 ATAATACTATATAACTATATAATAATAT
1 AT-ATAATATATAACTAAATAATAATAT
340784 ATATAATATATAACATAAATAATAATA
1 ATATAATATATAAC-TAAATAATAATA
340811 AGCTTAATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
26 2 0.04
27 16 0.36
28 25 0.56
29 2 0.04
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (27 bp):
ATATAATATATAACTAAATAATAATAT
Found at i:340871 original size:26 final size:26
Alignment explanation
Indices: 340818--340889 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
340808 ATAAGCTTAA
340818 TATATATATATATATATACTTTAAAAAAT
1 TATATA-ATATAT-TATA-TTTAAAAAAT
**
340847 TATATAATATATTATATTTTCAAAAT
1 TATATAATATATTATATTTAAAAAAT
* *
340873 CATATAATATGTTATAT
1 TATATAATATATTATAT
340890 ATATATTACA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 23 0.59
27 4 0.10
28 6 0.15
29 6 0.15
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (26 bp):
TATATAATATATTATATTTAAAAAAT
Found at i:340922 original size:20 final size:20
Alignment explanation
Indices: 340899--341009 Score: 73
Period size: 22 Copynumber: 5.1 Consensus size: 20
340889 TATATATTAC
340899 ATATGTTTTTAAAAAACTATAT
1 ATATG-TTTT-AAAAACTATAT
*
340921 ATATGTTTTCAAAACTATATAAT
1 ATATGTTTTAAAAAC--TAT-AT
340944 AATATGTTTT-AAAACTATACT
1 -ATATGTTTTAAAAACTATA-T
* *
340965 ATATATTTTCAAAAACCATAT
1 ATATGTTTT-AAAAACTATAT
*
340986 ATTAT-TTTTGATCAAACTATAT
1 A-TATGTTTT-A-AAAACTATAT
341008 AT
1 AT
341010 TATCATGTAT
Statistics
Matches: 74, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
20 14 0.19
21 16 0.22
22 28 0.38
23 7 0.09
24 9 0.12
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (20 bp):
ATATGTTTTAAAAACTATAT
Found at i:342023 original size:4 final size:4
Alignment explanation
Indices: 342014--342040 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
342004 TAACATTGCA
342014 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
342041 GAGTGAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:343950 original size:15 final size:15
Alignment explanation
Indices: 343930--343972 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
343920 GTCCTTGTAC
343930 TTATTTTATTTTATG
1 TTATTTTATTTTATG
343945 TTA-TTTATTTTACTG
1 TTATTTTATTTTA-TG
*
343960 TT-TTATATTTTAT
1 TTATTTTATTTTAT
343973 TATTTACTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (15 bp):
TTATTTTATTTTATG
Found at i:343953 original size:14 final size:13
Alignment explanation
Indices: 343933--343972 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 13
343923 CTTGTACTTA
343933 TTTTATTTTATGT
1 TTTTATTTTATGT
343946 TATTTATTTTACTGT
1 T-TTTATTTTA-TGT
343961 TTTATATTTTAT
1 TTT-TATTTTAT
343973 TATTTACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.04
14 12 0.50
15 11 0.46
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (13 bp):
TTTTATTTTATGT
Found at i:347765 original size:8 final size:7
Alignment explanation
Indices: 347762--347859 Score: 52
Period size: 8 Copynumber: 12.1 Consensus size: 7
347752 GCAAAAATAG
347762 AAAAGAAA
1 AAAAG-AA
347770 AAAAGATA
1 AAAAGA-A
347778 GAAAAGAA
1 -AAAAGAA
347786 AGAAAGAA
1 A-AAAGAA
*
347794 AAAGAAAA
1 AAA-AGAA
347802 AAACAGAAA
1 AAA-AG-AA
347811 AAATAGAA
1 AAA-AGAA
347819 AAACAGAA
1 AAA-AGAA
347827 AAAAGGGAGA
1 AAAA--GA-A
347837 AAAGAGAA
1 AAA-AGAA
*
347845 GAAAGAA
1 AAAAGAA
*
347852 AGAAGAA
1 AAAAGAA
347859 A
1 A
347860 GAAAACCGAT
Statistics
Matches: 73, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
7 15 0.21
8 36 0.49
9 17 0.23
10 4 0.05
11 1 0.01
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:347787 original size:13 final size:13
Alignment explanation
Indices: 347763--347864 Score: 61
Period size: 12 Copynumber: 7.6 Consensus size: 13
347753 CAAAAATAGA
347763 AAAGAAAA-AAAG
1 AAAGAAAAGAAAG
*
347775 ATAGAAAAGAAAG
1 AAAGAAAAGAAAG
*
347788 AAAGAAAAAGAAAAA
1 AAAG-AAAAG-AAAG
347803 AACAGAAAA-AATAG
1 AA-AGAAAAGAA-AG
* *
347817 AAA-AACAGAAAA
1 AAAGAAAAGAAAG
347829 AAGGGAGAAAAGAGAAG
1 AA---AGAAAAGA-AAG
347846 AAAG-AAAG-AAG
1 AAAGAAAAGAAAG
347857 AAAGAAAA
1 AAAGAAAA
347865 CCGATCAAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 24
0.69 0.08 0.24
Matches are distributed among these distances:
11 7 0.10
12 16 0.23
13 16 0.23
14 10 0.14
15 10 0.14
16 7 0.10
17 4 0.06
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (13 bp):
AAAGAAAAGAAAG
Found at i:347804 original size:9 final size:9
Alignment explanation
Indices: 347754--347830 Score: 59
Period size: 9 Copynumber: 8.6 Consensus size: 9
347744 AAGATATAGC
*
347754 AAAAATAGA
1 AAAAAAAGA
*
347763 AAAGAAA-A
1 AAAAAAAGA
* *
347771 AAAGATAGA
1 AAAAAAAGA
*
347780 AAAGAAAGA
1 AAAAAAAGA
347789 AAGAAAAAGA
1 AA-AAAAAGA
347799 AAAAAACAGA
1 AAAAAA-AGA
*
347809 AAAAATAG-
1 AAAAAAAGA
*
347817 AAAAACAGA
1 AAAAAAAGA
347826 AAAAA
1 AAAAA
347831 GGGAGAAAAG
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
8 14 0.25
9 27 0.47
10 16 0.28
ACGTcount: A:0.79, C:0.03, G:0.14, T:0.04
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:347820 original size:17 final size:18
Alignment explanation
Indices: 347754--347830 Score: 79
Period size: 17 Copynumber: 4.3 Consensus size: 18
347744 AAGATATAGC
347754 AAAAATAGAAAAGA-A-A
1 AAAAATAGAAAAGACAGA
*
347770 AAAAGATAGAAAAGAAAGA
1 AAAA-ATAGAAAAGACAGA
* *
347789 AAGAAAAAGAAAAAAACAGA
1 AA-AAATAG-AAAAGACAGA
347809 AAAAATAGAAAA-ACAGA
1 AAAAATAGAAAAGACAGA
347826 AAAAA
1 AAAAA
347831 GGGAGAAAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
16 4 0.08
17 20 0.38
18 5 0.10
19 11 0.21
20 12 0.23
ACGTcount: A:0.79, C:0.03, G:0.14, T:0.04
Consensus pattern (18 bp):
AAAAATAGAAAAGACAGA
Found at i:347839 original size:18 final size:17
Alignment explanation
Indices: 347792--347850 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
347782 AGAAAGAAAG
*
347792 AAAAAGAAAAAAACAGA
1 AAAAAGAGAAAAACAGA
*
347809 AAAAATAGAAAAACAGA
1 AAAAAGAGAAAAACAGA
* *
347826 AAAAAGGGAGAAAAGAGA
1 AAAAAGAGA-AAAACAGA
*
347844 AGAAAGA
1 AAAAAGA
347851 AAGAAGAAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
17 22 0.65
18 12 0.35
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (17 bp):
AAAAAGAGAAAAACAGA
Found at i:348199 original size:13 final size:13
Alignment explanation
Indices: 348170--348203 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
348160 CCTCAGGGTT
*
348170 AATTTTATTTGTAA
1 AATTTT-TTTCTAA
348184 AATTTTTTTCTAA
1 AATTTTTTTCTAA
348197 AATTTTT
1 AATTTTT
348204 AATGCATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (13 bp):
AATTTTTTTCTAA
Found at i:350010 original size:113 final size:113
Alignment explanation
Indices: 349812--350032 Score: 347
Period size: 113 Copynumber: 2.0 Consensus size: 113
349802 GATTGTTTTA
*
349812 AAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGACGATTTTCAATGAAGTTTTATAAGAACA
1 AAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGACGATTTTCAATGAAGTTTTATAAGAACA
*
349877 TAAGCTCGAGAGACCAACGTGATATGTAGGGGTTCCTTGATGACAACT
66 TAAGCTCAAGAGACCAACGTGATATGTAGGGGTTCCTTGATGACAACT
* * *
349925 AAGAAACTAAGCCTGATTTTCAGGGGGTTT-TTTATGATGATTTTCAATGAATTTTTATAAGAA-
1 AAGAAACTAAGCCTGATTTTCA-GGGGTTTCTTGATGACGATTTTCAATGAAGTTTTATAAGAAC
* *
349988 ACTAAGTTCAAGGGACCAACGTGATATGTAGGGGTTCCTTGATGA
65 A-TAAGCTCAAGAGACCAACGTGATATGTAGGGGTTCCTTGATGA
350033 AGATTTTCAA
Statistics
Matches: 99, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
112 1 0.01
113 91 0.92
114 7 0.07
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.33
Consensus pattern (113 bp):
AAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGACGATTTTCAATGAAGTTTTATAAGAACA
TAAGCTCAAGAGACCAACGTGATATGTAGGGGTTCCTTGATGACAACT
Found at i:350038 original size:71 final size:71
Alignment explanation
Indices: 349958--350103 Score: 265
Period size: 71 Copynumber: 2.1 Consensus size: 71
349948 GGGGTTTTTT
* *
349958 ATGATGATTTTCAATGAATTTTTATAAGAAACTAAGTTCAAGGGACCAACGTGATATGTAGGGGT
1 ATGAAGATTTTCAATGAATTTTTATAAGAAACTAAGCTCAAGGGACCAACGTGATATGTAGGGGT
350023 TCCTTG
66 TCCTTG
*
350029 ATGAAGATTTTCAATGAATTTTTATAAGAAACTAAGCTCGAGGGACCAACGTGATATGTAGGGGT
1 ATGAAGATTTTCAATGAATTTTTATAAGAAACTAAGCTCAAGGGACCAACGTGATATGTAGGGGT
350094 TCCTTG
66 TCCTTG
350100 ATGA
1 ATGA
350104 CAAATAAGAA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (71 bp):
ATGAAGATTTTCAATGAATTTTTATAAGAAACTAAGCTCAAGGGACCAACGTGATATGTAGGGGT
TCCTTG
Found at i:350481 original size:42 final size:41
Alignment explanation
Indices: 350398--350518 Score: 116
Period size: 42 Copynumber: 2.9 Consensus size: 41
350388 AAGGGTTTCT
* * *
350398 TGATGAGTAAGTCCTTTGGGCCATCAATATGTCTTTCGAGCA
1 TGATG-GTAAGTCCTTCGGGCCATCAATAAGACTTTCGAGCA
** *
350440 TGATGTGTAAGTCCTTCGGGCCATTTATAAGACTTTTGAGCA
1 TGATG-GTAAGTCCTTCGGGCCATCAATAAGACTTTCGAGCA
* * ** * *
350482 AGATGATAAAACCTTCGGGCCATCCATAAGACCTTCG
1 TGATGGTAAGTCCTTCGGGCCATCAATAAGACTTTCG
350519 GGCAGGATAT
Statistics
Matches: 64, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
41 25 0.39
42 39 0.61
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (41 bp):
TGATGGTAAGTCCTTCGGGCCATCAATAAGACTTTCGAGCA
Found at i:352109 original size:14 final size:14
Alignment explanation
Indices: 352090--352128 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
352080 CGTTTCTAAT
352090 TTATTATAATTTTA
1 TTATTATAATTTTA
*
352104 TTATTAT-ATTTTT
1 TTATTATAATTTTA
*
352117 TTATTTTAATTT
1 TTATTATAATTT
352129 AGTCACTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATTATAATTTTA
Found at i:352229 original size:51 final size:50
Alignment explanation
Indices: 352126--352254 Score: 190
Period size: 51 Copynumber: 2.6 Consensus size: 50
352116 TTTATTTTAA
*
352126 TTTAGTCACTGTTAGTTTCTGATTTAGTACTGTTATTTTAATTTTTACAT
1 TTTAGTCATTGTTAGTTTCTGATTTAGTACTGTTATTTTAATTTTTACAT
*
352176 TTTAGTCATTGTTAGTTTCTGATTTAGCTACTGTTATTTTAATTTTTGCAT
1 TTTAGTCATTGTTAGTTTCTGATTTAG-TACTGTTATTTTAATTTTTACAT
*
352227 TTTGGTCACTAT-TTA-TTTCTGATTTAGT
1 TTTAGTCA-T-TGTTAGTTTCTGATTTAGT
352255 TACTAACTTT
Statistics
Matches: 73, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
50 27 0.37
51 41 0.56
52 4 0.05
53 1 0.01
ACGTcount: A:0.20, C:0.10, G:0.13, T:0.57
Consensus pattern (50 bp):
TTTAGTCATTGTTAGTTTCTGATTTAGTACTGTTATTTTAATTTTTACAT
Found at i:356485 original size:22 final size:21
Alignment explanation
Indices: 356437--356490 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
356427 GACCGTTGAA
356437 TAGGGGGAATCAGTACCTCCT
1 TAGGGGGAATCAGTACCTCCT
*
356458 TAGGGGGAATCTGTACCTCCT
1 TAGGGGGAATCAGTACCTCCT
*
356479 TGGGGGGGAATC
1 T-AGGGGGAATC
356491 GGTTCCCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 21 0.70
22 9 0.30
ACGTcount: A:0.20, C:0.20, G:0.35, T:0.24
Consensus pattern (21 bp):
TAGGGGGAATCAGTACCTCCT
Found at i:356562 original size:22 final size:21
Alignment explanation
Indices: 356536--356579 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
356526 AAACCATTCA
356536 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGT-CCCCCTTGG
*
356558 GGGGGAATCGGTTCCCCTTGG
1 GGGGGAATCGGTCCCCCTTGG
356579 G
1 G
356580 CAATCTGCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.11, C:0.25, G:0.43, T:0.20
Consensus pattern (21 bp):
GGGGGAATCGGTCCCCCTTGG
Found at i:359185 original size:22 final size:23
Alignment explanation
Indices: 359138--359195 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
359128 TCCCTCCAGT
*
359138 GGGAATCAGTTCCCCTTCAAAGG
1 GGGAATCGGTTCCCCTTCAAAGG
359161 GGGAATCGGTTCCCCTTC-AAGG
1 GGGAATCGGTTCCCCTTCAAAGG
* *
359183 GGGTATCGATTCC
1 GGGAATCGGTTCC
359196 TCCTGCACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.21, C:0.26, G:0.29, T:0.24
Consensus pattern (23 bp):
GGGAATCGGTTCCCCTTCAAAGG
Found at i:360720 original size:51 final size:51
Alignment explanation
Indices: 360646--360747 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
360636 AAACTGTATA
360646 CATTCACCCATGGGGAAAAGAAGATTACTTTAGCTCCACTTTCACCAAAGC
1 CATTCACCCATGGGGAAAAGAAGATTACTTTAGCTCCACTTTCACCAAAGC
* *
360697 CATTCACCCATGGGGCAAGGAAGATTACTTTAGCTCCACTTTCACCAAAGC
1 CATTCACCCATGGGGAAAAGAAGATTACTTTAGCTCCACTTTCACCAAAGC
360748 AAATACATGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
CATTCACCCATGGGGAAAAGAAGATTACTTTAGCTCCACTTTCACCAAAGC
Found at i:362457 original size:49 final size:49
Alignment explanation
Indices: 362366--362509 Score: 207
Period size: 49 Copynumber: 2.9 Consensus size: 49
362356 GAATACCATG
* * * *
362366 AGTGACACCTTTTATGCTGAAAATTCACTATTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCG-AAATGCACTGTTATGCATTTAACTTTCATT
* *
362416 AGTGGCACCTTTTATGCCGAAATGCACGGTTATGCAATTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACTGTTATGCATTTAACTTTCATT
* *
362465 AGTGGCACTTTTTATGCCGAAATGCATTGTTATGCATTTAACTTT
1 AGTGGCACCTTTTATGCCGAAATGCACTGTTATGCATTTAACTTT
362510 TATTTGTGAG
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
49 67 0.80
50 17 0.20
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (49 bp):
AGTGGCACCTTTTATGCCGAAATGCACTGTTATGCATTTAACTTTCATT
Found at i:391541 original size:112 final size:111
Alignment explanation
Indices: 391344--391571 Score: 384
Period size: 112 Copynumber: 2.0 Consensus size: 111
391334 CGAAGTGCTG
* *
391344 AAATGGTAATTCACCTCATTATGAATACCATGGGTGGCCCCTTTTATGCCGAAAATGCACCGTTA
1 AAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCGAAAATGCACCATTA
* * *
391409 TGAATTAAGCAAAATCGATCGATAACTTTCATACACGAAGTATGTCA
66 TGAATTAAACAAAATCGATCGAT-ACTATCATACACAAAGTATGTCA
391456 AAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCGAAAATGCACCATTA
1 AAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCGAAAATGCACCATTA
* *
391521 TGCATTAAACAAAATCGATCGATACTATCATGCACAAAGTATGTCA
66 TGAATTAAACAAAATCGATCGATACTATCATACACAAAGTATGTCA
391567 AAATG
1 AAATG
391572 CACCTATAAC
Statistics
Matches: 109, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
111 25 0.23
112 84 0.77
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (111 bp):
AAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCGAAAATGCACCATTA
TGAATTAAACAAAATCGATCGATACTATCATACACAAAGTATGTCA
Found at i:393340 original size:101 final size:100
Alignment explanation
Indices: 393231--394018 Score: 654
Period size: 101 Copynumber: 7.9 Consensus size: 100
393221 TTATTTTTTA
** * * * * *
393231 ATAATATAAACAATTTGATACATATAACCTAAACGGTTGACAATTAGAAAAGACGCAACCTACAA
1 ATAATATAAACGGTTTCAAACATATAACGTAAACAGTTGACAATTA-AAAAGATGCAACCTACAA
* * *
393296 TGTTATAATTATAAACCTGTTATGTCTTATTTTTGC
65 TGTTATACTTATAAACCTGTTTTGTCTTACTTTTGC
* * * * * * * *
393332 ATAATATAAATGTTTTCAAACATATAACTTAAA-TGACTGGCAATTAAAAA-AGGCTCTACCTAC
1 ATAATATAAACGGTTTCAAACATATAACGTAAACAG-TTGACAATTAAAAAGATG--CAACCTAC
* *
393395 AATGTTATACTTATAAATCTGTTTTGTCTTAATTTTGC
63 AATGTTATACTTATAAACCTGTTTTGTCTTACTTTTGC
* * * **
393433 ATAATATAAACGGTTTCAAACATATAACATAAACATTTGACAA-TAAAAAGGTGTTACCTACAAT
1 ATAATATAAACGGTTTCAAACATATAACGTAAACAGTTGACAATTAAAAAGATGCAACCTACAAT
* * *
393497 GTTATACTTATAAACCCGTTTTGTATT-CATTTTGT
66 GTTATACTTATAAACCTGTTTTGTCTTAC-TTTTGC
* ** * * * **
393532 ATAATATAAATGGTTTCAAACATATATTGTAAATAGTTGACAATAAAAAAAGGTGCAACCTATGA
1 ATAATATAAACGGTTTCAAACATATAACGTAAACAGTTGACAAT-TAAAAAGATGCAACCTACAA
*
393597 TGTTATACTTATAAACATGTTTTGTCTTACTTTTGC
65 TGTTATACTTATAAACCTGTTTTGTCTTACTTTTGC
* * * *
393633 ATAAT-TAAACGGTTTCAAACACATAACTTAAACAGTTGACAATTAGAAAAAAAGCACTACCTAC
1 ATAATATAAACGGTTTCAAACATATAACGTAAACAGTTGACAATTA-AAAAGATGCA--ACCTAC
* * * * * * *
393697 AATTTTATACTTATACATCTTTTTTGTTTTACATTTGT
63 AATGTTATACTTATAAACCTGTTTTGTCTTACTTTTGC
* * * **
393735 AT-ATATAAACAGTTT-ACTACATATAACGTAAATAGTTGATGATTAAAAA-ATGC-A-CTAC-A
1 ATAATATAAACGGTTTCA-AACATATAACGTAAACAGTTGACAATTAAAAAGATGCAACCTACAA
* * *
393794 TATAAT-GTTATAAACCTGTTTTGTCTTACTTTTGC
65 TGTTATACTTATAAACCTGTTTTGTCTTACTTTTGC
* * * * *
393829 ATAATATAAACGG-TTCTAAATATATAACCTAAACGGTTGACAAATAAAAGAGATG-ATACCTAT
1 ATAATATAAACGGTTTC-AAACATATAACGTAAACAGTTGACAATTAAAA-AGATGCA-ACCTAC
*
393892 AATGTTATACTTATAAACCTGTTTTGTATTACTTTTGC
63 AATGTTATACTTATAAACCTGTTTTGTCTTACTTTTGC
* * * * * * * ** * *
393930 ATAATATAAAC-ATTTTACTACATATAACGTAAACGGGTGAAAATTTAAAACGAAACTACCTATA
1 ATAATATAAACGGTTTCA-AACATATAACGTAAACAGTTGACAA-TTAAAAAGATGCAACCTACA
* *
393994 ACGTTATACTTA-AAACATGTTTTGT
64 ATGTTATACTTATAAACCTGTTTTGT
394019 GAATTGTCTG
Statistics
Matches: 549, Mismatches: 110, Indels: 57
0.77 0.15 0.08
Matches are distributed among these distances:
94 26 0.05
95 37 0.07
96 6 0.01
97 4 0.01
98 1 0.00
99 82 0.15
100 71 0.13
101 249 0.45
102 73 0.13
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.36
Consensus pattern (100 bp):
ATAATATAAACGGTTTCAAACATATAACGTAAACAGTTGACAATTAAAAAGATGCAACCTACAAT
GTTATACTTATAAACCTGTTTTGTCTTACTTTTGC
Found at i:393583 original size:200 final size:196
Alignment explanation
Indices: 393231--393939 Score: 684
Period size: 200 Copynumber: 3.6 Consensus size: 196
393221 TTATTTTTTA
** * * * * **
393231 ATAATATAAACAATTTGATACATATAACCTAAACGGTTGACAATTAGAAAAGACGCA-ACCTACA
1 ATAATATAAACGGTTTCAAACATATAACATAAACAGTTGACAA-TA-AAAAGGTG-ATACCTACA
* * * * *
393295 ATGTTATAATTATAAACCTGTTATGTCTTATTTTTGCATAATATAAATGTTTTCAAACATATAAC
63 ATGTTATACTTATAAACCTGTTTTGTATTACTTTTGCATAATATAAATGGTTTCAAACATATAA-
* *
393360 T-TAAAT-GACTGGCAATTAAAAAAGGCTCTACCTACAATGTTATACTTATAAATCTGTTTTGTC
127 TGTAAATAG-TTGACAATTAAAAAAGG-TC-ACCTAC-ATGTTATACTTATAAA-CTGTTTTGTC
*
393423 TTAATTTTGC
187 TTACTTTTGC
* *
393433 ATAATATAAACGGTTTCAAACATATAACATAAACATTTGACAATAAAAAGGTGTTACCTACAATG
1 ATAATATAAACGGTTTCAAACATATAACATAAACAGTTGACAATAAAAAGGTGATACCTACAATG
* * *
393498 TTATACTTATAAACCCGTTTTGTATT-CATTTTGTATAATATAAATGGTTTCAAACATATATTGT
66 TTATACTTATAAACCTGTTTTGTATTAC-TTTTGCATAATATAAATGGTTTCAAACATATAATGT
* *
393562 AAATAGTTGACAATAAAAAAAGGTGCAACCTATGATGTTATACTTATAAACATGTTTTGTCTTAC
130 AAATAGTTGACAATTAAAAAAGGT-C-ACCTA-CATGTTATACTTATAAAC-TGTTTTGTCTTAC
393627 TTTTGC
191 TTTTGC
* * ***
393633 ATAAT-TAAACGGTTTCAAACACATAACTTAAACAGTTGACAATTAGAAAAAAAGCACTACCTAC
1 ATAATATAAACGGTTTCAAACATATAACATAAACAGTTGACAA-TA-AAAAGGTG-A-TACCTAC
* * * * * * * ** *
393697 AATTTTATACTTATACATCTTTTTTGTTTTACATTTGTAT-ATATAAACAGTTT-ACTACATATA
62 AATGTTATACTTATAAACCTGTTTTGTATTACTTTTGCATAATATAAATGGTTTCA-AACATATA
* ** * * * *
393760 ACGTAAATAGTTGATGATTAAAAAATG-CA-CTACATATAAT-GTTATAAACCTGTTTTGTCTTA
126 ATGTAAATAGTTGACAATTAAAAAAGGTCACCTACATGTTATACTTATAAA-CTGTTTTGTCTTA
393822 CTTTTGC
190 CTTTTGC
* * * * *
393829 ATAATATAAACGG-TTCTAAATATATAACCTAAACGGTTGACAAATAAAAGAGATGATACCTATA
1 ATAATATAAACGGTTTC-AAACATATAACATAAACAGTTGAC-AATAAAA-AGGTGATACCTACA
393893 ATGTTATACTTATAAACCTGTTTTGTATTACTTTTGCATAATATAAA
63 ATGTTATACTTATAAACCTGTTTTGTATTACTTTTGCATAATATAAA
393940 CATTTTACTA
Statistics
Matches: 423, Mismatches: 65, Indels: 44
0.80 0.12 0.08
Matches are distributed among these distances:
195 39 0.09
196 45 0.11
197 38 0.09
198 5 0.01
199 38 0.09
200 135 0.32
201 9 0.02
202 75 0.18
203 38 0.09
204 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.37
Consensus pattern (196 bp):
ATAATATAAACGGTTTCAAACATATAACATAAACAGTTGACAATAAAAAGGTGATACCTACAATG
TTATACTTATAAACCTGTTTTGTATTACTTTTGCATAATATAAATGGTTTCAAACATATAATGTA
AATAGTTGACAATTAAAAAAGGTCACCTACATGTTATACTTATAAACTGTTTTGTCTTACTTTTG
C
Found at i:394575 original size:201 final size:191
Alignment explanation
Indices: 394308--394858 Score: 635
Period size: 201 Copynumber: 2.8 Consensus size: 191
394298 AAGCCTCTAA
* * * **
394308 TACAATGTTATACTTATAAACCTGTTTTGTTTTGCTTTTGAATAATATAAACAATTTCAAACATA
1 TACAATGTTATACTTATAAACCTGTTTTGTCTTACTTTTGCATAATATAAATGATTTCAAACATA
* * *
394373 TAACCTAAACAATTGATAATT-AAAAAAGGCGCTACCTATAATGTTATACTTATAAACATGTTTT
66 TAACCTAAACAATTGACAATTAAAAAAAGGCACTACCTACAATGTTATACTTATAAACATGTTTT
* * **
394437 GTTTTACATTTGCATAATATAAACGATTTACTACATACAACATAAACGATTAATGATTGAAAAA-
131 GTTTTACTTTTGCATAATATAAACG-GTT--T--ATA-AAC----A-G-TTAACAATT-AAAAAC
*
394501 GATGCTACC
183 GACGCTACC
* ** * *
394510 TATAATGTTATACTTATAAATTTGTTTT-TCTTACTTTTCCATAATATAAATGATTTCAGACATA
1 TACAATGTTATACTTATAAACCTGTTTTGTCTTACTTTTGCATAATATAAATGATTTCAAACATA
* * *
394574 T-ACCTAAACAGTTGACAATTAAAAAAATGTACTACCTACAATGTTATACTTATAAACATGTTTT
66 TAACCTAAACAATTGACAATTAAAAAAAGGCACTACCTACAATGTTATACTTATAAACATGTTTT
* * *
394638 GTCTTACTTTTGCATAATATAAATGGTTTATAAACAGTTGACAATTAAAAACGACGCTACC
131 GTTTTACTTTTGCATAATATAAACGGTTTATAAACAGTTAACAATTAAAAACGACGCTACC
* *
394699 TACAATGTTATACTTATAAACCTATTTTGTCTTACTTTTGCATAATATAAATGGTTTCAAACATA
1 TACAATGTTATACTTATAAACCTGTTTTGTCTTACTTTTGCATAATATAAATGATTTCAAACAT-
* * * * *
394764 ATAACATAAACGATTGACAATTAAAAAAAGACACTACCTACAATGTTATAC-TATTAAACCTATT
65 ATAACCTAAACAATTGACAATTAAAAAAAGGCACTACCTACAATGTTATACTTA-TAAACATGTT
* *
394828 TTGTTTTAGTTTTGCATAATATAAACAGTTT
129 TTGTTTTACTTTTGCATAATATAAACGGTTT
394859 CATACATATA
Statistics
Matches: 300, Mismatches: 43, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
188 5 0.02
189 38 0.13
190 33 0.11
191 5 0.02
192 77 0.26
195 3 0.01
196 3 0.01
198 1 0.00
200 19 0.06
201 91 0.30
202 25 0.08
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (191 bp):
TACAATGTTATACTTATAAACCTGTTTTGTCTTACTTTTGCATAATATAAATGATTTCAAACATA
TAACCTAAACAATTGACAATTAAAAAAAGGCACTACCTACAATGTTATACTTATAAACATGTTTT
GTTTTACTTTTGCATAATATAAACGGTTTATAAACAGTTAACAATTAAAAACGACGCTACC
Found at i:394661 original size:101 final size:100
Alignment explanation
Indices: 394221--394875 Score: 612
Period size: 100 Copynumber: 6.6 Consensus size: 100
394211 CTACTTTATT
* * **
394221 TTATAAACATGTTTTGTCTTACTTTTGCATAATATAAATGGTTTCAAATATATAACCTAAATGGT
1 TTATAAACATGTTTTGTCTTACTTTTGCATAATATAAATGATTTCAAACATATAACCTAAACAGT
* * *
394286 TGACAATTAAAAAAGCCTCTA-ATACAATGTTATAC
66 TGACAATTAAAAAA-ACGCTACCTACAATGTTATAC
* * * * ** *
394321 TTATAAACCTGTTTTGTTTTGCTTTTGAATAATATAAACAATTTCAAACATATAACCTAAACAAT
1 TTATAAACATGTTTTGTCTTACTTTTGCATAATATAAATGATTTCAAACATATAACCTAAACAGT
* * *
394386 TGATAATTAAAAAAGGCGCTACCTATAATGTTATAC
66 TGACAATTAAAAAA-ACGCTACCTACAATGTTATAC
* * * * * *
394422 TTATAAACATGTTTTGTTTTACATTTGCATAATATAAACGATTT-ACTACATACAACATAAAC-G
1 TTATAAACATGTTTTGTCTTACTTTTGCATAATATAAATGATTTCA-AACATATAACCTAAACAG
* ** * * *
394485 ATTAATGATTGAAAAAGATGCTACCTATAATGTTATAC
65 -TTGACAATT-AAAAAAACGCTACCTACAATGTTATAC
** * *
394523 TTATAAATTTGTTTT-TCTTACTTTTCCATAATATAAATGATTTCAGACATAT-ACCTAAACAGT
1 TTATAAACATGTTTTGTCTTACTTTTGCATAATATAAATGATTTCAAACATATAACCTAAACAGT
*
394586 TGACAATTAAAAAAATGTACTACCTACAATGTTATAC
66 TGACAATTAAAAAAACG--CTACCTACAATGTTATAC
*
394623 TTATAAACATGTTTTGTCTTACTTTTGCATAATATAAATG--GT------T-T-A--TAAACAGT
1 TTATAAACATGTTTTGTCTTACTTTTGCATAATATAAATGATTTCAAACATATAACCTAAACAGT
**
394676 TGACAATTAAAAACGACGCTACCTACAATGTTATAC
66 TGACAATT-AAAAAAACGCTACCTACAATGTTATAC
* * * *
394712 TTATAAACCTATTTTGTCTTACTTTTGCATAATATAAATGGTTTCAAACATAATAACATAAAC-G
1 TTATAAACATGTTTTGTCTTACTTTTGCATAATATAAATGATTTCAAACAT-ATAACCTAAACAG
*
394776 ATTGACAATTAAAAAAAGACACTACCTACAATGTTATAC
65 -TTGACAATT-AAAAAA-ACGCTACCTACAATGTTATAC
* * * * * *
394815 -TATTAAACCTATTTTGTTTTAGTTTTGCATAATATAAA-CAGTTTCATACATATAACCTAAA
1 TTA-TAAACATGTTTTGTCTTACTTTTGCATAATATAAATGA-TTTCAAACATATAACCTAAA
394876 TTATTATATA
Statistics
Matches: 465, Mismatches: 63, Indels: 52
0.80 0.11 0.09
Matches are distributed among these distances:
89 56 0.12
90 16 0.03
91 7 0.02
92 2 0.00
93 1 0.00
97 1 0.00
98 8 0.02
99 15 0.03
100 134 0.29
101 128 0.28
102 35 0.08
103 62 0.13
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (100 bp):
TTATAAACATGTTTTGTCTTACTTTTGCATAATATAAATGATTTCAAACATATAACCTAAACAGT
TGACAATTAAAAAAACGCTACCTACAATGTTATAC
Found at i:394716 original size:89 final size:89
Alignment explanation
Indices: 394578--394755 Score: 295
Period size: 89 Copynumber: 2.0 Consensus size: 89
394568 GACATATACC
* *
394578 TAAACAGTTGACAATTAAAAAAATGTACTACCTACAATGTTATACTTATAAACATGTTTTGTCTT
1 TAAACAGTTGACAATTAAAAAAACG-ACTACCTACAATGTTATACTTATAAACATATTTTGTCTT
394643 ACTTTTGCATAATATAAATGGTTTA
65 ACTTTTGCATAATATAAATGGTTTA
* *
394668 TAAACAGTTGACAATTAAAAACGACG-CTACCTACAATGTTATACTTATAAACCTATTTTGTCTT
1 TAAACAGTTGACAATTAAAAA-AACGACTACCTACAATGTTATACTTATAAACATATTTTGTCTT
394732 ACTTTTGCATAATATAAATGGTTT
65 ACTTTTGCATAATATAAATGGTTT
394756 CAAACATAAT
Statistics
Matches: 83, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
89 60 0.72
90 21 0.25
91 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (89 bp):
TAAACAGTTGACAATTAAAAAAACGACTACCTACAATGTTATACTTATAAACATATTTTGTCTTA
CTTTTGCATAATATAAATGGTTTA
Found at i:394806 original size:103 final size:101
Alignment explanation
Indices: 394667--394875 Score: 296
Period size: 103 Copynumber: 2.0 Consensus size: 101
394657 TAAATGGTTT
* *
394667 ATAAACAGTTGACAATTAAAAACGACGCTACCTACAATGTTATACT-TATAAACCTATTTTGTCT
1 ATAAACAGTTGACAATTAAAAAAGACACTACCTACAATGTTATACTAT-TAAACCTATTTTGTCT
**
394731 TACTTTTGCATAATATAAATGGTTTCAAACATAATAAC
65 TACTTTTGCATAATATAAACAGTTTCAAACAT-ATAAC
*
394769 ATAAAC-GATTGACAATTAAAAAAAGACACTACCTACAATGTTATACTATTAAACCTATTTTGTT
1 ATAAACAG-TTGACAATT-AAAAAAGACACTACCTACAATGTTATACTATTAAACCTATTTTGTC
* *
394833 TTAGTTTTGCATAATATAAACAGTTTCATACATATAAC
64 TTACTTTTGCATAATATAAACAGTTTCAAACATATAAC
*
394871 CTAAA
1 ATAAA
394876 TTATTATATA
Statistics
Matches: 96, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
101 1 0.01
102 24 0.25
103 70 0.73
104 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (101 bp):
ATAAACAGTTGACAATTAAAAAAGACACTACCTACAATGTTATACTATTAAACCTATTTTGTCTT
ACTTTTGCATAATATAAACAGTTTCAAACATATAAC
Found at i:394843 original size:192 final size:188
Alignment explanation
Indices: 394496--394852 Score: 504
Period size: 192 Copynumber: 1.9 Consensus size: 188
394486 TTAATGATTG
* * ** *
394496 AAAAAGATGCTACCTATAATGTTATACTTATAAATTTGTTTTTCTTACTTTTCCATAATATAAAT
1 AAAAAGACGCTACCTACAATGTTATACTTATAAACCTATTTTTCTTACTTTTCCATAATATAAAT
* * *
394561 GATTTCAGACATATACCTAAACAGTTGACAATTAAAAAAATGTACTACCTACAATGTTATACTTA
66 GATTTCAAACATATACATAAACAGTTGACAATTAAAAAAATGCACTACCTACAATGTTATACTTA
*
394626 TAAACATGTTTTGTCTTACTTTTGCATAATATAAATGGTTTATAAACAGTTGACAATT
131 TAAACATATTTTGTCTTACTTTTGCATAATATAAATGGTTTATAAACAGTTGACAATT
*
394684 AAAAACGACGCTACCTACAATGTTATACTTATAAACCTATTTTGTCTTACTTTTGCATAATATAA
1 AAAAA-GACGCTACCTACAATGTTATACTTATAAACCTATTTT-TCTTACTTTTCCATAATATAA
*
394749 ATGGTTTCAAACATAATAACATAAAC-GATTGACAATTAAAAAAA-GACACTACCTACAATGTTA
64 ATGATTTCAAACAT-AT-ACATAAACAG-TTGACAATTAAAAAAATG-CACTACCTACAATGTTA
* * *
394812 TAC-TATTAAACCTATTTTGTTTTAGTTTTGCATAATATAAA
125 TACTTA-TAAACATATTTTGTCTTACTTTTGCATAATATAAA
394853 CAGTTTCATA
Statistics
Matches: 148, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
188 5 0.03
189 32 0.22
190 32 0.22
191 6 0.04
192 73 0.49
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (188 bp):
AAAAAGACGCTACCTACAATGTTATACTTATAAACCTATTTTTCTTACTTTTCCATAATATAAAT
GATTTCAAACATATACATAAACAGTTGACAATTAAAAAAATGCACTACCTACAATGTTATACTTA
TAAACATATTTTGTCTTACTTTTGCATAATATAAATGGTTTATAAACAGTTGACAATT
Found at i:395884 original size:144 final size:142
Alignment explanation
Indices: 395592--395969 Score: 474
Period size: 144 Copynumber: 2.6 Consensus size: 142
395582 TTAGTGTTTA
* * * * * **
395592 AAATATAAAATATCGATACTGA-TATAAAAATTATCGATACATGTTGAGGATAATTTTCTGA-AG
1 AAATAAAAAATATCGATATTGATTAT-AAAAGTCTCGATACATTTTGAGGATAATTTGATGACA-
* * ** *** *
395655 AACTGTCGAAATAAATAGTATCAGACTTATTGTCAAACGTACGATACTGGAAGTAAACTTAAATT
64 AACTTTCGAAATAAATTGTATCAGACTTATCATCAAACGTACGATACCAAAAGTAAACTTAAACT
*
395720 GAAACTACTACTTG
129 GAAACAACTACTTG
* *
395734 AAATAAAAGATATTGATACTT-ATTATAAAAGTCTCGATACATTTTGAGGATAATTTGATGCACA
1 AAATAAAAAATATCGATA-TTGATTATAAAAGTCTCGATACATTTTGAGGATAATTTGATG-ACA
395798 AACTTTCGAAATAAATTGTATCAGACTTATCATCAAACGTATCGATACCAAAAGTAAACTTAAAC
64 AACTTTCGAAATAAATTGTATCAGACTTATCATCAAACGTA-CGATACCAAAAGTAAACTTAAAC
395863 TGAAACAACTACTTG
128 TGAAACAACTACTTG
* *
395878 AAATAAAAAATATCGATATTGATTATAAAAGTCTTGATACATTTTGAGGACAATTTGATGTACAA
1 AAATAAAAAATATCGATATTGATTATAAAAGTCTCGATACATTTTGAGGATAATTTGATG-ACAA
* * *
395943 ACATTCGAAATAAATTATATCGGACTT
65 ACTTTCGAAATAAATTGTATCAGACTT
395970 TCCTATTTGA
Statistics
Matches: 204, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
142 45 0.22
143 44 0.22
144 115 0.56
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (142 bp):
AAATAAAAAATATCGATATTGATTATAAAAGTCTCGATACATTTTGAGGATAATTTGATGACAAA
CTTTCGAAATAAATTGTATCAGACTTATCATCAAACGTACGATACCAAAAGTAAACTTAAACTGA
AACAACTACTTG
Found at i:399645 original size:2 final size:2
Alignment explanation
Indices: 399638--399668 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
399628 TTGAAAGCAA
399638 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
399669 ACTAATACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:401751 original size:57 final size:57
Alignment explanation
Indices: 401663--401775 Score: 190
Period size: 57 Copynumber: 2.0 Consensus size: 57
401653 AGAAGATAAA
** *
401663 CAACTACATGCAGTTAGCTCTGTTAAGTGCCAAATGTTCCATCCTCCCGCATATGGG
1 CAACTACATGCAGTTAGAACTGTTAAGTGCCAAATGTTACATCCTCCCGCATATGGG
*
401720 CAACTACATGCATTTAGAACTGTTAAGTGCCAAATGTTACATCCTCCCGCATATGG
1 CAACTACATGCAGTTAGAACTGTTAAGTGCCAAATGTTACATCCTCCCGCATATGG
401776 AGGACCACTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (57 bp):
CAACTACATGCAGTTAGAACTGTTAAGTGCCAAATGTTACATCCTCCCGCATATGGG
Found at i:406021 original size:103 final size:103
Alignment explanation
Indices: 405842--406048 Score: 414
Period size: 103 Copynumber: 2.0 Consensus size: 103
405832 AGAAAATAAA
405842 AATAGTCAAATGTAAAGGGACTAATGATGAAATTATTCCATCATTAAAATTTTAGGCTGATTTTA
1 AATAGTCAAATGTAAAGGGACTAATGATGAAATTATTCCATCATTAAAATTTTAGGCTGATTTTA
405907 ACTTGATTTTACTTATGTCAGACGCATAGTTTAAGAGG
66 ACTTGATTTTACTTATGTCAGACGCATAGTTTAAGAGG
405945 AATAGTCAAATGTAAAGGGACTAATGATGAAATTATTCCATCATTAAAATTTTAGGCTGATTTTA
1 AATAGTCAAATGTAAAGGGACTAATGATGAAATTATTCCATCATTAAAATTTTAGGCTGATTTTA
406010 ACTTGATTTTACTTATGTCAGACGCATAGTTTAAGAGG
66 ACTTGATTTTACTTATGTCAGACGCATAGTTTAAGAGG
406048 A
1 A
406049 GAGAGAGAGA
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (103 bp):
AATAGTCAAATGTAAAGGGACTAATGATGAAATTATTCCATCATTAAAATTTTAGGCTGATTTTA
ACTTGATTTTACTTATGTCAGACGCATAGTTTAAGAGG
Found at i:406655 original size:130 final size:130
Alignment explanation
Indices: 406484--406750 Score: 525
Period size: 130 Copynumber: 2.1 Consensus size: 130
406474 TATTTTGTTA
406484 TATTATGACACTTATAAATGTAACGTTTTATTTGTGGTGTATTGTTGTTTAAGCATGTTTAAGTG
1 TATTATGACACTTATAAATGTAACGTTTTATTTGTGGTGTATTGTTGTTTAAGCATGTTTAAGTG
*
406549 ATATGATATTTAATAATTTAAATAATAAATTATTGTTAAACATATAAAATGATATAAAATGAACT
66 ATATGATATTTAATAATTTAAATAATAAATTATTGTTAAACATATAAAATGATATAAAATGAACC
406614 TATTATGACACTTATAAATGTAACGTTTTATTTGTGGTGTATTGTTGTTTAAGCATGTTTAAGTG
1 TATTATGACACTTATAAATGTAACGTTTTATTTGTGGTGTATTGTTGTTTAAGCATGTTTAAGTG
406679 ATATGATATTTAATAATTTAAATAATAAATTATTGTTAAACATATAAAATGATATAAAATGAACC
66 ATATGATATTTAATAATTTAAATAATAAATTATTGTTAAACATATAAAATGATATAAAATGAACC
406744 TATTATG
1 TATTATG
406751 CCCCTTAGAT
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 136 1.00
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.43
Consensus pattern (130 bp):
TATTATGACACTTATAAATGTAACGTTTTATTTGTGGTGTATTGTTGTTTAAGCATGTTTAAGTG
ATATGATATTTAATAATTTAAATAATAAATTATTGTTAAACATATAAAATGATATAAAATGAACC
Found at i:406790 original size:130 final size:130
Alignment explanation
Indices: 406521--406791 Score: 352
Period size: 130 Copynumber: 2.1 Consensus size: 130
406511 TTATTTGTGG
*
406521 TGTATTGTTGTTTAAGCATGTTTAAGTGATATGATATTTAATAATTTAAATAATAAATTATTGTT
1 TGTAATGTTGTTTAAGCATGTTTAAGTGATATGATATTTAATAATTTAAATAATAAATTATTGTT
* * ** ** * ***
406586 AAACATATAAAATGATATAAAATGAACTTATTATGACACTTATAAATGTAACGTTTTATTTGTGG
66 AAACATATAAAATGATATAAAATGAACCTATTATGACACCTATAAATGTAACAATGAATATGACC
*
406651 TGTATTGTTGTTTAAGCATGTTTAAGTGATATGATATTTAATAATTTAAATAATAAATTATTGTT
1 TGTAATGTTGTTTAAGCATGTTTAAGTGATATGATATTTAATAATTTAAATAATAAATTATTGTT
* *
406716 AAACATATAAAATGATATAAAATGAACCTATTATG-CCCCT-TAGAT-TATACAAATGAAGTATG
66 AAACATATAAAATGATATAAAATGAACCTATTATGACACCTATAAATGTA-AC-AATGAA-TATG
406778 ACC
128 ACC
406781 T-TAAATGTTGT
1 TGT-AATGTTGT
406792 GCGAAGAGAC
Statistics
Matches: 124, Mismatches: 13, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
127 2 0.02
128 6 0.05
129 6 0.05
130 110 0.89
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.41
Consensus pattern (130 bp):
TGTAATGTTGTTTAAGCATGTTTAAGTGATATGATATTTAATAATTTAAATAATAAATTATTGTT
AAACATATAAAATGATATAAAATGAACCTATTATGACACCTATAAATGTAACAATGAATATGACC
Found at i:407908 original size:18 final size:16
Alignment explanation
Indices: 407887--407930 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
407877 TAAATAAACA
407887 TTAAATAATATTGTATTT
1 TTAAATAATA-T-TATTT
*
407905 TTAAATGATATTATTT
1 TTAAATAATATTATTT
*
407921 TTAAAAAATA
1 TTAAATAATA
407931 GTCAAAGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 13 0.57
17 1 0.04
18 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
TTAAATAATATTATTT
Found at i:418905 original size:17 final size:17
Alignment explanation
Indices: 418885--418924 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
418875 TTTAACAATT
418885 ATATTATTTT-ATATTAA
1 ATATTATTTTCATA-TAA
*
418902 ATATTTTTTTCATATAA
1 ATATTATTTTCATATAA
418919 ATATTA
1 ATATTA
418925 AATATAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATTATTTTCATATAA
Found at i:419763 original size:2 final size:2
Alignment explanation
Indices: 419756--419789 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
419746 TATAAATAGT
419756 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
419790 ACAAACCAAC
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):
TA
Found at i:420122 original size:33 final size:33
Alignment explanation
Indices: 420085--420157 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
420075 ACACAACGTT
**
420085 AACCCTAATGTGCCGTTAGGAAAACCCAACTTG
1 AACCCTAATGTGCCGTTAGGAAAACCCAACGCG
420118 AACCCTAATGTGCCGTTAGGAAAACCCAACGCG
1 AACCCTAATGTGCCGTTAGGAAAACCCAACGCG
420151 AACCCTA
1 AACCCTA
420158 CTCTAGGGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.34, C:0.30, G:0.18, T:0.18
Consensus pattern (33 bp):
AACCCTAATGTGCCGTTAGGAAAACCCAACGCG
Found at i:427001 original size:164 final size:164
Alignment explanation
Indices: 426812--427142 Score: 646
Period size: 164 Copynumber: 2.0 Consensus size: 164
426802 GTATCTTCAA
426812 GGTTTTTGTACCCATAAAGATCAAGAAGATCGTGATGTTTGAGTTTAAGTCGACGATGAATATTG
1 GGTTTTTGTACCCATAAAGATCAAGAAGATCGTGATGTTTGAGTTTAAGTCGACGATGAATATTG
426877 ACACGATGAGCTCTTCTTTTTCGGTTATGTTAGCCCTATTGAGTAAAGGAATGTATCTCCTTATA
66 ACACGATGAGCTCTTCTTTTTCGGTTATGTTAGCCCTATTGAGT-AAGGAATGTATCTCCTTATA
426942 GTAGCCTTCAACTGAACTTCTACC-TGTCGAAGTC
130 GTAGCCTTCAACTGAACTTCTACCTTGTCGAAGTC
426976 GGTTTTTGTACCCATAAAGATCAAGAAGATCGTGATGTTTGAGTTTAAGTCGACGATGAATATTG
1 GGTTTTTGTACCCATAAAGATCAAGAAGATCGTGATGTTTGAGTTTAAGTCGACGATGAATATTG
427041 ACACGATGAGCTCTTCTTTTTCGGTTATGTTAGCCCTATTGAGTAAGGAATGTATCTCCTTATAG
66 ACACGATGAGCTCTTCTTTTTCGGTTATGTTAGCCCTATTGAGTAAGGAATGTATCTCCTTATAG
427106 TAGCCTTCAACTGAACTTCTACCTTGTCGAAGTC
131 TAGCCTTCAACTGAACTTCTACCTTGTCGAAGTC
427140 GGT
1 GGT
427143 GTAGTCGTAG
Statistics
Matches: 166, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
163 44 0.27
164 122 0.73
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (164 bp):
GGTTTTTGTACCCATAAAGATCAAGAAGATCGTGATGTTTGAGTTTAAGTCGACGATGAATATTG
ACACGATGAGCTCTTCTTTTTCGGTTATGTTAGCCCTATTGAGTAAGGAATGTATCTCCTTATAG
TAGCCTTCAACTGAACTTCTACCTTGTCGAAGTC
Found at i:448147 original size:35 final size:34
Alignment explanation
Indices: 448062--448148 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
448052 ATTTGGTATT
* *
448062 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATCG
* *
448096 TAAATGATAACCAAATTACAATAAATGATATTAAATCG
1 TAAAT-ACAACAAAATTACAAT-AA-GA-ATTAAATCG
448134 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
448149 ACTGATATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 22 0.50
36 3 0.07
37 5 0.11
38 9 0.20
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATCG
Found at i:448388 original size:18 final size:18
Alignment explanation
Indices: 448365--448399 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
448355 CTCGCTGTCA
448365 TCATCATCGTCGTCGTCG
1 TCATCATCGTCGTCGTCG
* *
448383 TCATCATTGTCTTCGTC
1 TCATCATCGTCGTCGTC
448400 ATCCTGAGAA
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:0.11, C:0.31, G:0.17, T:0.40
Consensus pattern (18 bp):
TCATCATCGTCGTCGTCG
Found at i:450786 original size:51 final size:50
Alignment explanation
Indices: 450653--450808 Score: 147
Period size: 51 Copynumber: 3.1 Consensus size: 50
450643 CCCTGTACCG
**
450653 CGCTATACCTCACGTGTCAGATAAA-CAGC-TATAGCGCGGAACAGGGGGCA
1 CGCTATACC-CACGTGT-AGCCAAATCAGCATATAGCGCGGAACAGGGGGCA
** * * * *
450703 CGCTATACCCACGTGTAAGCCATGTCAACATATAACGCGGTACAGGGGGCG
1 CGCTATACCCACGTGT-AGCCAAATCAGCATATAGCGCGGAACAGGGGGCA
** *
450754 CGCTATACCCCACGTGGT-GCCAAATCAGCATATAGCGCGGGGCAGGGAGCA
1 CGCTATA-CCCACGT-GTAGCCAAATCAGCATATAGCGCGGAACAGGGGGCA
450805 CGCT
1 CGCT
450809 TTACTGCTAC
Statistics
Matches: 85, Mismatches: 17, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
49 10 0.12
50 12 0.14
51 54 0.64
52 7 0.08
53 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.29, T:0.16
Consensus pattern (50 bp):
CGCTATACCCACGTGTAGCCAAATCAGCATATAGCGCGGAACAGGGGGCA
Found at i:452003 original size:35 final size:34
Alignment explanation
Indices: 451955--452036 Score: 110
Period size: 35 Copynumber: 2.4 Consensus size: 34
451945 GTTGGTTGCC
*
451955 AAAAAAATGTATTGGATGGAGATACAATTACTATA
1 AAAAAAAT-TATTGGATGGAAATACAATTACTATA
* *
451990 AAAAAAATCTATTGGATGGAAATACAATTATTATG
1 AAAAAAAT-TATTGGATGGAAATACAATTACTATA
*
452025 AAATAAATTATT
1 AAAAAAATTATT
452037 CCCTTGATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 4 0.10
35 38 0.90
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (34 bp):
AAAAAAATTATTGGATGGAAATACAATTACTATA
Found at i:453958 original size:55 final size:56
Alignment explanation
Indices: 453892--454001 Score: 195
Period size: 56 Copynumber: 2.0 Consensus size: 56
453882 TTACCGATTC
453892 GGGTTCGTTCAAAGTTGTTTC-TTTTTCCTTCCCAATCTGCATAAACATTAAAAGT
1 GGGTTCGTTCAAAGTTGTTTCTTTTTTCCTTCCCAATCTGCATAAACATTAAAAGT
* *
453947 GGGTTCGTTCAAATTTGTTTCTTTTTTCCTTTCCAATCTGCATAAACATTAAAAG
1 GGGTTCGTTCAAAGTTGTTTCTTTTTTCCTTCCCAATCTGCATAAACATTAAAAG
454002 CAGGCCCGTC
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
55 20 0.38
56 32 0.62
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (56 bp):
GGGTTCGTTCAAAGTTGTTTCTTTTTTCCTTCCCAATCTGCATAAACATTAAAAGT
Found at i:454544 original size:29 final size:29
Alignment explanation
Indices: 454472--454545 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
454462 GTTCCAAACA
*
454472 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGACGACCTTG
* *
454501 TAGGTCGTCAAGCACTCCGGACGACCTTG
1 TAGGTCGCCATGCACTCCGGACGACCTTG
*
454530 TAGGTCGCCGTGCACT
1 TAGGTCGCCATGCACT
454546 TCTGCTCCTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.16, C:0.32, G:0.30, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGACGACCTTG
Found at i:454606 original size:21 final size:21
Alignment explanation
Indices: 454547--454606 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 21
454537 CCGTGCACTT
*
454547 CTGCTCCTCGCGTGATTCCTG
1 CTGCTCCTCGCGTGATTCCTC
* ** * *
454568 TTGCAACTGCACCT-ATTCCTC
1 CTGCTCCT-CGCGTGATTCCTC
454589 CTGCTCCTCGCGTGATTC
1 CTGCTCCTCGCGTGATTC
454607 ATCTTGCAAC
Statistics
Matches: 26, Mismatches: 11, Indels: 4
0.63 0.27 0.10
Matches are distributed among these distances:
20 3 0.12
21 20 0.77
22 3 0.12
ACGTcount: A:0.10, C:0.38, G:0.18, T:0.33
Consensus pattern (21 bp):
CTGCTCCTCGCGTGATTCCTC
Found at i:454606 original size:42 final size:42
Alignment explanation
Indices: 454547--454656 Score: 184
Period size: 42 Copynumber: 2.6 Consensus size: 42
454537 CCGTGCACTT
* * *
454547 CTGCTCCTCGCGTGATTCCTGTTGCAACTGCACCTATTCCTC
1 CTGCTCCTCGCGTGATTCATCTTGCAACTGAACCTATTCCTC
454589 CTGCTCCTCGCGTGATTCATCTTGCAACTGAACCTATTCCTC
1 CTGCTCCTCGCGTGATTCATCTTGCAACTGAACCTATTCCTC
*
454631 ATGCTCCTCGCGTGATTCATCTTGCA
1 CTGCTCCTCGCGTGATTCATCTTGCA
454657 GCTGCTCAGG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.15, C:0.35, G:0.16, T:0.34
Consensus pattern (42 bp):
CTGCTCCTCGCGTGATTCATCTTGCAACTGAACCTATTCCTC
Found at i:455177 original size:21 final size:21
Alignment explanation
Indices: 455146--455209 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
455136 AAATTTAGTA
455146 ATTAG-TTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
455166 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
455187 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
455208 AT
1 AT
455210 ATTATATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 5 0.12
21 36 0.88
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:455217 original size:28 final size:28
Alignment explanation
Indices: 455186--455239 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
455176 TAGTATAAAT
*
455186 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
455214 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
455240 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:455652 original size:14 final size:14
Alignment explanation
Indices: 455633--455659 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
455623 GTAATTTATT
455633 ATTTTTTGTTGTTC
1 ATTTTTTGTTGTTC
455647 ATTTTTTGTTGTT
1 ATTTTTTGTTGTT
455660 GTGTATGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (14 bp):
ATTTTTTGTTGTTC
Found at i:456037 original size:14 final size:13
Alignment explanation
Indices: 456012--456042 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
456002 TGAAATTATC
456012 TTATCTAATTTTT
1 TTATCTAATTTTT
456025 TTATCTAAATTTTT
1 TTATCT-AATTTTT
456039 TTAT
1 TTAT
456043 TTTTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATCTAATTTTT
Found at i:459004 original size:46 final size:47
Alignment explanation
Indices: 458949--459107 Score: 277
Period size: 46 Copynumber: 3.4 Consensus size: 47
458939 AATAATTATT
458949 TAGTAATGATTAGTAATAATGAAATTATTATATA-TTAATGATTTGG
1 TAGTAATGATTAGTAATAATGAAATTATTATATATTTAATGATTTGG
458995 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGG
1 TAGTAATGATTAGTAATAATGAAATTATTA-T-ATATTTAATGATTTGG
459044 TAGTAATGATTAGTAATAATGAAATTATTA-ATATTTAATGATTTGG
1 TAGTAATGATTAGTAATAATGAAATTATTATATATTTAATGATTTGG
459090 TAGTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
459108 TATTACTAAT
Statistics
Matches: 109, Mismatches: 0, Indels: 7
0.94 0.00 0.06
Matches are distributed among these distances:
46 55 0.50
47 9 0.08
48 3 0.03
49 42 0.39
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (47 bp):
TAGTAATGATTAGTAATAATGAAATTATTATATATTTAATGATTTGG
Found at i:459044 original size:49 final size:49
Alignment explanation
Indices: 458890--459107 Score: 267
Period size: 46 Copynumber: 4.6 Consensus size: 49
458880 TTTGATTTAG
* * * * *
458890 TAATGATTTGATAATCATGATT--TAATAATGAATTTA-TATTTAAAATT
1 TAATGATTTGGTAGTAATGATTAGTAATAATGAAATTATTA-TTAATATT
* *
458937 ATAATAATTAT-TTAGTAATGATTAGTAATAATGAAATTATTA-T-ATA-T
1 -TAATGATT-TGGTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
458984 TAATGATTTGGTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTTGGTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
459033 TAATGATTTGGTAGTAATGATTAGTAATAATG-AA--ATTATTAATATT
1 TAATGATTTGGTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
459079 TAATGATTTGGTAGTAATGATTTAGTAAT
1 TAATGATTTGGTAGTAATGA-TTAGTAAT
459108 TATTACTAAT
Statistics
Matches: 153, Mismatches: 8, Indels: 19
0.85 0.04 0.11
Matches are distributed among these distances:
45 1 0.01
46 69 0.45
47 10 0.07
48 23 0.15
49 35 0.23
50 13 0.08
51 2 0.01
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (49 bp):
TAATGATTTGGTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
Found at i:459063 original size:95 final size:96
Alignment explanation
Indices: 458890--459107 Score: 295
Period size: 95 Copynumber: 2.3 Consensus size: 96
458880 TTTGATTTAG
* * * * *
458890 TAATGATTTGATAATCATGATT--TAATAATGAATTTATATTTAAAATTATAATAATTATTTAGT
1 TAATGATTTGGTAGTAATGATTAGTAATAATGAAATTATATTTAAAATTATAATAATTATGTAGT
458953 AATGATTAGTAATAATGAAATTATT-ATATAT
66 AATGATTAGTAATAATGAAATTATTAATAT-T
* *
458984 TAATGATTTGGTAGTAATGATTAGTAATAATGAAATTAT-TATTAATATT-TAATGATT-TGGTA
1 TAATGATTTGGTAGTAATGATTAGTAATAATGAAATTATAT-TTAAAATTATAATAATTAT-GTA
459046 GTAATGATTAGTAATAATGAAATTATTAATATT
64 GTAATGATTAGTAATAATGAAATTATTAATATT
459079 TAATGATTTGGTAGTAATGATTTAGTAAT
1 TAATGATTTGGTAGTAATGA-TTAGTAAT
459108 TATTACTAAT
Statistics
Matches: 111, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
94 20 0.18
95 58 0.52
96 33 0.30
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (96 bp):
TAATGATTTGGTAGTAATGATTAGTAATAATGAAATTATATTTAAAATTATAATAATTATGTAGT
AATGATTAGTAATAATGAAATTATTAATATT
Found at i:459133 original size:14 final size:13
Alignment explanation
Indices: 459109--459478 Score: 136
Period size: 12 Copynumber: 30.0 Consensus size: 13
459099 TTTAGTAATT
459109 ATTACTAATAATGAA
1 ATTA-TAATAATG-A
459124 ATTATAATAATG-
1 ATTATAATAATGA
459136 ATT-TAATAATG-
1 ATTATAATAATGA
* * *
459147 ATTTTAATATTTA
1 ATTATAATAATGA
*
459160 ATGAT--T--TGA
1 ATTATAATAATGA
*
459169 A-TATTATTAATGA
1 ATTA-TAATAATGA
* *
459182 TTTGATAATAAT-C
1 ATT-ATAATAATGA
459195 ATTATAATAATG-
1 ATTATAATAATGA
459207 ATTAGTAATAAT--
1 ATTA-TAATAATGA
459219 -TTATAATAATG-
1 ATTATAATAATGA
459230 ATT-TAATAATG-
1 ATTATAATAATGA
* * *
459241 ATTTTAATATTTA
1 ATTATAATAATGA
* * *
459254 ATGAT-TTGATG-
1 ATTATAATAATGA
*
459265 ATT-TAGTAATGA
1 ATTATAATAATGA
* *
459277 TTTGATAATAAT-C
1 ATT-ATAATAATGA
459290 ATTATAATAATGA
1 ATTATAATAATGA
* *
459303 TTTAGTAATAAT-C
1 ATTA-TAATAATGA
459316 ATTATAATAATG-
1 ATTATAATAATGA
*
459328 ATT-TAATGAT-A
1 ATTATAATAATGA
*
459339 ATAATAATAAT-A
1 ATTATAATAATGA
*
459351 ATAATAATAAT-A
1 ATTATAATAATGA
*
459363 ATAATAATAAT-A
1 ATTATAATAATGA
*
459375 ATAATAATAAT-A
1 ATTATAATAATGA
*
459387 ATAATAATAATGA
1 ATTATAATAATGA
* *
459400 TTTAATAATAAT-C
1 ATT-ATAATAATGA
459413 ATTATAATAATGA
1 ATTATAATAATGA
* *
459426 TTTAATAGTAATG-
1 ATT-ATAATAATGA
*
459439 ATT-TAGTAATGA
1 ATTATAATAATGA
*
459451 TTTTATAATAATGA
1 -ATTATAATAATGA
* *
459465 TTTAATACTAATGA
1 ATT-ATAATAATGA
459479 TTTAATAGTT
Statistics
Matches: 280, Mismatches: 43, Indels: 65
0.72 0.11 0.17
Matches are distributed among these distances:
8 1 0.00
9 4 0.01
10 8 0.03
11 49 0.17
12 113 0.40
13 39 0.14
14 61 0.22
15 5 0.02
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.43
Consensus pattern (13 bp):
ATTATAATAATGA
Found at i:459150 original size:49 final size:49
Alignment explanation
Indices: 458912--459485 Score: 221
Period size: 49 Copynumber: 11.6 Consensus size: 49
458902 AATCATGATT
* * * *
458912 TAATAATGAATTTATATTTAA-AATTATAATAATTATTTAGTAATGATTAG
1 TAATAATGAAATTATA-ATAATGATT-TAATAATGATTTAGTAATGATTAG
* *
458962 TAATAATGAAATTATTAT-AT-A-TTAATGAT--TTGGTAGTAATGATTAG
1 TAATAATGAAATTATAATAATGATTTAATAATGATT--TAGTAATGATTAG
* *
459008 TAATAATGAAATTATTATTAAT-ATTTAATGAT--TTGGTAGTAATGATTAG
1 TAATAATGAAATTA-TAATAATGATTTAATAATGATT--TAGTAATGATTAG
* * *
459057 TAATAATGAAATTATTAATATTTAATGATTTGGTAGTAATGATTTAGTAATTATTAC
1 TAATAATGAAATTA-T-A-A--TAATGA-TT--TAATAATGATTTAGTAATGATTAG
459114 TAATAATGAAATTATAATAATGATTTAATAATGATTT--TAAT-ATT--
1 TAATAATGAAATTATAATAATGATTTAATAATGATTTAGTAATGATTAG
* * *
459158 TAATGATTTGAATATTAT--TAATGATTTGATAATAATCATTATAATAATGATTAG
1 TAAT-A-ATGAA-ATTATAATAATGA-TT--TAATAATGATT-TAGTAATGATTAG
459212 TAATAAT----TTATAATAATGATTTAATAATGATTT--TAAT-ATT--
1 TAATAATGAAATTATAATAATGATTTAATAATGATTTAGTAATGATTAG
* * * * *
459252 TAATGATTTGATGATT-TAGTAATGATTTGATAATAATCATTATAATAATGATTTAG
1 TAAT-A-ATGA-AATTATAATAATGA-TT--TAATAATGATT-TAGTAATGA-TTAG
* * * * * *
459308 TAATAAT--CATTATAATAATGATTTAATGAT-A-ATAATAAT-AATAA
1 TAATAATGAAATTATAATAATGATTTAATAATGATTTAGTAATGATTAG
* * * * * * *
459352 TAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATGATT--
1 TAATAATGA-AATTATAATAATGAT-TTAATAATGAT-TTAGTAATGATTAG
459402 TAATAAT-AATCATTATAATAATGATTTAATAGTAATGATTTAGTAATGATTTTA-
1 TAATAATGAA--ATTATAATAATGATTT-A-A-TAATGATTTAGTAATGA--TTAG
* *
459456 TAATAATG-ATTTAATACTAATGATTTAATA
1 TAATAATGAAATT-ATAATAATGATTTAATA
459486 GTTATTACTA
Statistics
Matches: 418, Mismatches: 40, Indels: 132
0.71 0.07 0.22
Matches are distributed among these distances:
40 4 0.01
41 1 0.00
42 4 0.01
43 4 0.01
44 15 0.04
45 9 0.02
46 67 0.16
47 32 0.08
48 25 0.06
49 79 0.19
50 38 0.09
51 29 0.07
52 33 0.08
53 20 0.05
54 17 0.04
55 4 0.01
56 5 0.01
57 30 0.07
59 2 0.00
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.44
Consensus pattern (49 bp):
TAATAATGAAATTATAATAATGATTTAATAATGATTTAGTAATGATTAG
Found at i:459163 original size:16 final size:18
Alignment explanation
Indices: 459142--459186 Score: 67
Period size: 16 Copynumber: 2.6 Consensus size: 18
459132 AATGATTTAA
*
459142 TAATGATTTTAATA-T-T
1 TAATGATTTGAATATTAT
459158 TAATGATTTGAATATTAT
1 TAATGATTTGAATATTAT
459176 TAATGATTTGA
1 TAATGATTTGA
459187 TAATAATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 13 0.50
17 1 0.04
18 12 0.46
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (18 bp):
TAATGATTTGAATATTAT
Done.