Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009074.1 Hibiscus syriacus cultivar Beakdansim tig00112507_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: 2143704
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1288816 original size:116 final size:114
Alignment explanation
Indices: 1288560--1289136 Score: 751
Period size: 116 Copynumber: 5.1 Consensus size: 114
1288550 TCTCCTTCTG
* * * *
1288560 TGATAGAATT-ATGCAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAG
1 TGATAGAATTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * *
1288624 ATGAGTTCTTCTCATTATGAACTT-CTCTGAAAATGTTGATCCATCTAA
66 ATGAGTTCTTCTCATTATGAACTTACTCTGGAAATGCTGATCCATCAAA
* * * *
1288672 TGATGGATTTGA-GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTT-TCTCTTCCTTCTTCA
1 TGATAGAATTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCA
* *
1288735 GATGACGAGTTCTTCTCATTACGAACTCTAC-CTGGTAATGCTGATCCATCAAA
65 GAT---GAGTTCTTCTCATTATGAACT-TACTCTGGAAATGCTGATCCATCAAA
*
1288788 TGAT-GAATTCATGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
1 TGATAGAATTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * * *
1288852 ATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGCTGATCCATCTAA
66 ATGAGTTCTTCTCATTATGAACTTACTCTGGAAATGCTGATCCATCAAA
* * * *
1288901 TGATCGATTTGA-GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTT-TCTCTTCCTTCTTCA
1 TGATAGAATTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCA
* *
1288964 GATGACGAGTTCTTCTCATTACGAACTCTAC-CTGGTAATGCTGATCCATCAAA
65 GAT---GAGTTCTTCTCATTATGAACT-TACTCTGGAAATGCTGATCCATCAAA
*
1289017 TGAT-GAATTCATGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
1 TGATAGAATTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* *
1289081 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAA
66 ATGAGTTCTTCTCATTATGAACTTACTCTGGAAATGCTGATCCATCAAA
1289130 TGATAGA
1 TGATAGA
1289137 TTTGAGTCTT
Statistics
Matches: 405, Mismatches: 40, Indels: 38
0.84 0.08 0.08
Matches are distributed among these distances:
111 1 0.00
112 60 0.15
113 137 0.34
114 7 0.02
115 30 0.07
116 165 0.41
117 5 0.01
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (114 bp):
TGATAGAATTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTTACTCTGGAAATGCTGATCCATCAAA
Found at i:1288979 original size:229 final size:228
Alignment explanation
Indices: 1288560--1289142 Score: 1035
Period size: 229 Copynumber: 2.5 Consensus size: 228
1288550 TCTCCTTCTG
* * * * *
1288560 TGATAGAATT-ATGCAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAG
1 TGAT-GAATTCATGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* *
1288624 ATGAGTTCTTCTCATTATGAAC-TTCTCTGAAAATGTTGATCCATCTAATGATGGATTTGAGCAA
65 ATGAGTTCTTCTCATTATGAACTTTCTCTGAAAA-GCTGATCCATCTAATGATAGATTTGAGCAA
1288688 AAGGTTGAACAAGCTCTTCTCATTATGAACTTTCTCTTCCTTCTTCAGATGACGAGTTCTTCTCA
129 AAGGTTGAACAAGCTCTTCTCATTATGAACTTTCTCTTCCTTCTTCAGATGACGAGTTCTTCTCA
1288753 TTACGAACTCTACCTGGTAATGCTGATCCATCAAA
194 TTACGAACTCTACCTGGTAATGCTGATCCATCAAA
1288788 TGATGAATTCATGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCATGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
1288853 TGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGCTGATCCATCTAATGATCGATTTGAGCAAA
66 TGAGTTCTTCTCATTATGAACTTTCTCT-GAAAAGCTGATCCATCTAATGATAGATTTGAGCAAA
1288918 AGGTTGAACAAGCTCTTCTCATTATGAACTTTCTCTTCCTTCTTCAGATGACGAGTTCTTCTCAT
130 AGGTTGAACAAGCTCTTCTCATTATGAACTTTCTCTTCCTTCTTCAGATGACGAGTTCTTCTCAT
1288983 TACGAACTCTACCTGGTAATGCTGATCCATCAAA
195 TACGAACTCTACCTGGTAATGCTGATCCATCAAA
1289017 TGATGAATTCATGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCATGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
1289082 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATAGATTTGAG
66 TGAGTTCTTCTCATTATGAACTTTCTCT-GAAAAGCTGATCCATCTAATGATAGATTTGAG
1289143 TCTTTGCTAA
Statistics
Matches: 342, Mismatches: 10, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
227 5 0.01
228 75 0.22
229 257 0.75
230 5 0.01
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (228 bp):
TGATGAATTCATGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
TGAGTTCTTCTCATTATGAACTTTCTCTGAAAAGCTGATCCATCTAATGATAGATTTGAGCAAAA
GGTTGAACAAGCTCTTCTCATTATGAACTTTCTCTTCCTTCTTCAGATGACGAGTTCTTCTCATT
ACGAACTCTACCTGGTAATGCTGATCCATCAAA
Found at i:1290187 original size:83 final size:83
Alignment explanation
Indices: 1289938--1290599 Score: 1233
Period size: 83 Copynumber: 8.0 Consensus size: 83
1289928 TTTACTATGA
1289938 GCAAATTCATCTT-TCAAATTCAATGATTGG-TCTG-CCAAACCAGATCAGATAACTCAAAGAAC
1 GCAAATTCATCTTCT-AAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAAC
1290000 ACTTCCAGAAGATGCTATTG
64 ACTTCCAGAAGATGCTATTG
*
1290020 GCAAATTCATCTTCTAAACTCAATGATT-GTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1290084 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
1290102 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1290167 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
*
1290185 GCAAATTCATCTTTTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1290250 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
1290268 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1290333 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
1290351 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1290416 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
*
1290434 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGACCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1290499 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
* *
1290517 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGACCAGATAATTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1290582 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
1290600 AGTCTCTTTT
Statistics
Matches: 570, Mismatches: 6, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
81 1 0.00
82 101 0.18
83 468 0.82
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (83 bp):
GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTG
Found at i:1303670 original size:3 final size:3
Alignment explanation
Indices: 1303662--1303750 Score: 142
Period size: 3 Copynumber: 29.7 Consensus size: 3
1303652 TTAATATATT
* *
1303662 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1303710 TAA TAA TAA TAA TAA TAA TAA TAA TTA TTA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1303751 TAAATTAATT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1307578 original size:24 final size:25
Alignment explanation
Indices: 1307542--1307593 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1307532 AATGAAATTA
* *
1307542 AAAAATAGCTAAA-GATAAAATCCT
1 AAAAATAGCTAAATCATAAAATCAT
**
1307566 AAAAATATTTAAATCATAAAATCAT
1 AAAAATAGCTAAATCATAAAATCAT
1307591 AAA
1 AAA
1307594 GATAAACAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.62, C:0.10, G:0.04, T:0.25
Consensus pattern (25 bp):
AAAAATAGCTAAATCATAAAATCAT
Found at i:1310046 original size:22 final size:22
Alignment explanation
Indices: 1310003--1310050 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
1309993 CGTATAATTA
* *
1310003 TAAATTACTTAAAAATTTAAAGG
1 TAAATTACTTAAAAA-TAAAAAG
*
1310026 TAAATTA-TTTAAAATAAAAAG
1 TAAATTACTTAAAAATAAAAAG
1310047 TAAA
1 TAAA
1310051 CTATACAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 9 0.41
22 6 0.27
23 7 0.32
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.33
Consensus pattern (22 bp):
TAAATTACTTAAAAATAAAAAG
Found at i:1313741 original size:52 final size:52
Alignment explanation
Indices: 1313663--1313777 Score: 203
Period size: 52 Copynumber: 2.2 Consensus size: 52
1313653 TCGATCACTG
*
1313663 AAATTAATTTCACTTCGGATACCAACCCTTGTAACTTTCTCTTCTCTCTGAT
1 AAATTAATTTCACTTCGGATACCAACCCTTATAACTTTCTCTTCTCTCTGAT
*
1313715 AAATTAATTTCACTTCGGATACCAACCCTTATAACTTTCTCTTCTCTCTGGT
1 AAATTAATTTCACTTCGGATACCAACCCTTATAACTTTCTCTTCTCTCTGAT
*
1313767 GAATTAATTTC
1 AAATTAATTTC
1313778 CTAAGCCAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.41
Consensus pattern (52 bp):
AAATTAATTTCACTTCGGATACCAACCCTTATAACTTTCTCTTCTCTCTGAT
Found at i:1316085 original size:23 final size:22
Alignment explanation
Indices: 1316058--1316114 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
1316048 TAATTAATGG
*
1316058 TATTTTTAAATTTAACTTTTTA
1 TATTTTTAAATTTAAATTTTTA
*
1316080 -ATATTTTAATATTTTAAATTTTTG
1 TAT-TTTTAA-A-TTTAAATTTTTA
1316104 TATTTTTAAAT
1 TATTTTTAAAT
1316115 AAGTAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
21 2 0.07
22 7 0.24
23 2 0.07
24 16 0.55
25 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
TATTTTTAAATTTAAATTTTTA
Found at i:1316107 original size:15 final size:16
Alignment explanation
Indices: 1316058--1316114 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
1316048 TAATTAATGG
1316058 TATTTTTAAA-TTTAA
1 TATTTTTAAATTTTAA
*
1316073 -CTTTTTAATATTTTAA
1 TATTTTTAA-ATTTTAA
**
1316089 TA-TTTTAAATTTTTG
1 TATTTTTAAATTTTAA
1316104 TATTTTTAAAT
1 TATTTTTAAAT
1316115 AAGTAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 7 0.21
15 8 0.24
16 19 0.56
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (16 bp):
TATTTTTAAATTTTAA
Found at i:1318061 original size:1 final size:1
Alignment explanation
Indices: 1318057--1318153 Score: 50
Period size: 1 Copynumber: 97.0 Consensus size: 1
1318047 ATAAAAAATG
* ** ** * * * * * *
1318057 AAAAAAGAAAAAAAAATGAAAAATGAAAAAGAAAAATAAAGAAAAAAAAAATAAAGAAAAAAAAT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
1318122 AGAAAAAAAATAGAAAAAAAAAGAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1318154 TAGAAAACAA
Statistics
Matches: 66, Mismatches: 30, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (1 bp):
A
Found at i:1318062 original size:8 final size:7
Alignment explanation
Indices: 1318049--1318160 Score: 65
Period size: 8 Copynumber: 15.6 Consensus size: 7
1318039 CCTGAAGAAT
1318049 AAAAAATG
1 AAAAAA-G
1318057 AAAAAAG
1 AAAAAAG
1318064 --AAAA-
1 AAAAAAG
*
1318068 AAAAATG
1 AAAAAAG
*
1318075 AAAAATG
1 AAAAAAG
*
1318082 AAAAAGAA
1 AAAAA-AG
1318090 AAATAAAG
1 AAA-AAAG
*
1318098 AAAAAAA
1 AAAAAAG
1318105 AAATAAAG
1 AAA-AAAG
1318113 AAAAAA-
1 AAAAAAG
1318119 AATAGAAA-
1 AA-A-AAAG
1318127 AAAAATAG
1 AAAAA-AG
1318135 AAAAAA-
1 AAAAAAG
1318141 AAAGAAAG
1 AAA-AAAG
1318149 AAAAATAG
1 AAAAA-AG
1318157 AAAA
1 AAAA
1318161 CAAAATGGGG
Statistics
Matches: 85, Mismatches: 6, Indels: 26
0.73 0.05 0.22
Matches are distributed among these distances:
5 4 0.05
6 10 0.12
7 31 0.36
8 38 0.45
9 2 0.02
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (7 bp):
AAAAAAG
Found at i:1318152 original size:24 final size:23
Alignment explanation
Indices: 1318057--1318165 Score: 107
Period size: 24 Copynumber: 4.7 Consensus size: 23
1318047 ATAAAAAATG
1318057 AAAAA-AGAAAAAAAAATGAAAAA
1 AAAAATAGAAAAAAAAA-GAAAAA
* *
1318080 TGAAAA-AGAAAAATAAAGAAAAA
1 -AAAAATAGAAAAAAAAAGAAAAA
* * *
1318103 AAAAATAAAGAAAAAAAATAGAAA
1 AAAAATAGA-AAAAAAAAGAAAAA
*
1318127 AAAAATAGAAAAAAAAAG-AAAG
1 AAAAATAGAAAAAAAAAGAAAAA
*
1318149 AAAAATAGAAAACAAAA
1 AAAAATAGAAAAAAAAA
1318166 TGGGGGACCA
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
22 22 0.31
23 16 0.23
24 33 0.46
ACGTcount: A:0.83, C:0.01, G:0.10, T:0.06
Consensus pattern (23 bp):
AAAAATAGAAAAAAAAAGAAAAA
Found at i:1318165 original size:12 final size:11
Alignment explanation
Indices: 1318057--1318166 Score: 100
Period size: 11 Copynumber: 9.5 Consensus size: 11
1318047 ATAAAAAATG
1318057 AAAAA-AGAAA
1 AAAAATAGAAA
1318067 AAAAA-ATGAAA
1 AAAAATA-GAAA
*
1318078 AATGAAAAAGAAA
1 AA--AAATAGAAA
* *
1318091 AATAAAGAAAAA
1 AA-AAATAGAAA
1318103 AAAAATAAAGAAA
1 AAAAAT--AGAAA
1318116 AAAAATAGAAA
1 AAAAATAGAAA
1318127 AAAAATAGAAA
1 AAAAATAGAAA
1318138 AAAAA-AGAAA
1 AAAAATAGAAA
1318148 GAAAAATAGAAA
1 -AAAAATAGAAA
1318160 ACAAAAT
1 A-AAAAT
1318167 GGGGGACCAA
Statistics
Matches: 86, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
10 11 0.13
11 36 0.42
12 19 0.22
13 19 0.22
14 1 0.01
ACGTcount: A:0.82, C:0.01, G:0.10, T:0.07
Consensus pattern (11 bp):
AAAAATAGAAA
Found at i:1319698 original size:133 final size:133
Alignment explanation
Indices: 1319374--1319817 Score: 563
Period size: 134 Copynumber: 3.3 Consensus size: 133
1319364 ACAAACCGAA
* * *
1319374 CTCGATTTAATCTTCCCT-AAGTAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCTCTC
1 CTCGATTCAATCTTCCCTGAAG-AACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTC
* *
1319438 AAGAAGAAGCA-GAACATATCCCTTTCTTTTAAGATTTGATATTCCTTGAGTAACAGTGGAACAA
65 AAGAAGAAG-ATGAACATATCCCTTTCTTTCAAGATTTGATATTCCCTGAGTAACAGT-GAACAA
* * *
1319502 ATCAAA
128 GTCTAC
* *
1319508 CTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAA-AGTCCCCAGATCCGATTTTCCCTC
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACA-TCCCCAGATCTGATTTTCCCTC
* * *
1319572 AAGAAGAAGATGAACATATCCCTTTCTTTCAAGATTTTATGTTCCCTGAGAAACAGTGAACAAGT
65 AAGAAGAAGATGAACATATCCCTTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGAACAAGT
*
1319637 CTGC
130 CTAC
* * *
1319641 CGCGATTCAATCTTCCCTAAAGAACAGTGTAATGAATCAACATCCCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCA
* * ** ** *
1319706 AGAAGAAG-TGAAACAAATCCCTCTCTTTCAAGATTTGATATTATCAAAGTGACAGTTGAACAAG
66 AGAAGAAGATG-AACATATCCCTTTCTTTCAAGATTTGATATTCCCTGAGTAACAG-TGAACAAG
1319770 TCTAC
129 TCTAC
* * *
1319775 CTCGATTCAATCTTTCTTGAAGAACAATGGAATGAATCAACAT
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACAT
1319818 TTCTCGATCT
Statistics
Matches: 268, Mismatches: 36, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
132 2 0.01
133 109 0.41
134 154 0.57
135 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (133 bp):
CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCA
AGAAGAAGATGAACATATCCCTTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGAACAAGTC
TAC
Found at i:1319991 original size:3 final size:3
Alignment explanation
Indices: 1319983--1320009 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1319973 GTTTTCATCC
1319983 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1320010 CATTTCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1321263 original size:9 final size:9
Alignment explanation
Indices: 1321251--1321276 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1321241 GAATTCGGTT
1321251 AATTAACCG
1 AATTAACCG
1321260 AATTAACCG
1 AATTAACCG
1321269 AATTAACC
1 AATTAACC
1321277 AAAATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:1321676 original size:183 final size:183
Alignment explanation
Indices: 1321290--1321676 Score: 652
Period size: 183 Copynumber: 2.1 Consensus size: 183
1321280 ATTAAATTTT
* * *
1321290 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAAAATATGGGCTAAACCCAAACCATTTAAAACCCAATTAATAA
*
1321355 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAATTTTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
*
1321420 TATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTTAATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTAATTAAA
1321473 AAATATTAAATATATTATATATAAAATATGGGCTAAACCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAAAATATGGGCTAAACCCAAACCATTTAAAACCCAATTAATAA
* *
1321538 TTTAAGATCCAATAACTTTTAATCTTAAATCAATATTAATTAATTAAAAAATTTATCTAAAATTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAA-TTATATAAAATTT
*
1321603 TTATTTTATACTTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
130 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTT-AATTAAA
* *
1321657 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
1321677 AATTAGAAAA
Statistics
Matches: 192, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
183 126 0.66
184 66 0.34
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAAAATATGGGCTAAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTAATTAAA
Found at i:1335840 original size:21 final size:21
Alignment explanation
Indices: 1335816--1335858 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1335806 ATTCACTTTG
*
1335816 TTGGACTTAT-ATTGTTGGATT
1 TTGG-CTTATAATTATTGGATT
*
1335837 TTGGTTTATAATTATTGGATT
1 TTGGCTTATAATTATTGGATT
1335858 T
1 T
1335859 ACGATTGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.21, C:0.02, G:0.21, T:0.56
Consensus pattern (21 bp):
TTGGCTTATAATTATTGGATT
Found at i:1338347 original size:13 final size:13
Alignment explanation
Indices: 1338329--1338376 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
1338319 GTCATAAATC
*
1338329 TATGACGTGTATT
1 TATGACGCGTATT
* *
1338342 TATGACACGCATT
1 TATGACGCGTATT
1338355 TATGACGCGTATT
1 TATGACGCGTATT
1338368 TATGACGCG
1 TATGACGCG
1338377 AATTGAGCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (13 bp):
TATGACGCGTATT
Found at i:1340317 original size:2 final size:2
Alignment explanation
Indices: 1340304--1340345 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
1340294 ATATTTGGTG
1340304 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1340346 GTCCGCCAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1344117 original size:20 final size:22
Alignment explanation
Indices: 1344094--1344140 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
1344084 AAGGAGTACT
*
1344094 GATACTC-A-ATGTTTAGTATC
1 GATACTCTATATGGTTAGTATC
1344114 GATAC-CTATATGGTTAGTATC
1 GATACTCTATATGGTTAGTATC
1344135 GATACT
1 GATACT
1344141 GAGGTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 1 0.04
20 6 0.26
21 16 0.70
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (22 bp):
GATACTCTATATGGTTAGTATC
Found at i:1346970 original size:2 final size:2
Alignment explanation
Indices: 1346963--1347057 Score: 74
Period size: 2 Copynumber: 50.0 Consensus size: 2
1346953 TAAAAATAAT
* *
1346963 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA AA TT TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
1347003 TT TA AA T- TA AA TA TA TA TA TA TA TA -A TA TT TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1347043 -A TT TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA
1347058 CCCGACCCGA
Statistics
Matches: 70, Mismatches: 18, Indels: 10
0.71 0.18 0.10
Matches are distributed among these distances:
1 5 0.07
2 65 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1347017 original size:41 final size:41
Alignment explanation
Indices: 1346970--1347050 Score: 126
Period size: 41 Copynumber: 1.9 Consensus size: 41
1346960 AATTATATAT
1346970 ATATATATATATATATATATATAATAAATTTAATTTAAATTAA
1 ATATATATATATATA-ATAT-TAATAAATTTAATTTAAATTAA
* *
1347013 ATATATATATATATAATATTTATATATTTAATTTAAAT
1 ATATATATATATATAATATTAATAAATTTAATTTAAAT
1347051 ATATATACCC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 17 0.47
42 4 0.11
43 15 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (41 bp):
ATATATATATATATAATATTAATAAATTTAATTTAAATTAA
Found at i:1348000 original size:25 final size:26
Alignment explanation
Indices: 1347941--1348000 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 26
1347931 AATGTTATTA
*
1347941 TTTGAAATTATTTTTGGACACTACAC
1 TTTGAATTTATTTTTGGACACTACAC
* * *
1347967 ATT-ATATTTA-TTTTGGACATTAGAC
1 TTTGA-ATTTATTTTTGGACACTACAC
1347992 TTTGAATTT
1 TTTGAATTT
1348001 TGGTTTTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
25 20 0.74
26 7 0.26
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.48
Consensus pattern (26 bp):
TTTGAATTTATTTTTGGACACTACAC
Found at i:1350844 original size:24 final size:24
Alignment explanation
Indices: 1350812--1350857 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1350802 TATGGTTGGA
*
1350812 GAAGAAGAGGGAAGAGGAAGCATC
1 GAAGAAGAGAGAAGAGGAAGCATC
*
1350836 GAAGAAGAGAGACGAGGAAGCA
1 GAAGAAGAGAGAAGAGGAAGCA
1350858 GTGAGGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.09, G:0.41, T:0.02
Consensus pattern (24 bp):
GAAGAAGAGAGAAGAGGAAGCATC
Found at i:1355610 original size:24 final size:24
Alignment explanation
Indices: 1355578--1355623 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1355568 TATGGTTGGA
*
1355578 GAAGAAGAGGGAAGAGGAAGCATC
1 GAAGAAGAGAGAAGAGGAAGCATC
*
1355602 GAAGAAGAGAGACGAGGAAGCA
1 GAAGAAGAGAGAAGAGGAAGCA
1355624 GTGAGGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.09, G:0.41, T:0.02
Consensus pattern (24 bp):
GAAGAAGAGAGAAGAGGAAGCATC
Found at i:1357252 original size:33 final size:34
Alignment explanation
Indices: 1357205--1357269 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
1357195 TCAAATCATC
* *
1357205 ATTTTGTAACTTTTAATAATTAGAG-ACTCAATA
1 ATTTTATAACTTTTAAAAATTAGAGTACTCAATA
* *
1357238 ATTTTATAATTTTTAAAAATTGGAGTACTCAA
1 ATTTTATAACTTTTAAAAATTAGAGTACTCAA
1357270 CAAAACAGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (34 bp):
ATTTTATAACTTTTAAAAATTAGAGTACTCAATA
Found at i:1359440 original size:22 final size:21
Alignment explanation
Indices: 1359401--1359442 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1359391 AGTGAAAAAA
**
1359401 CCGGATCGATTTTTATCCGAT
1 CCGGATCGATTTAAATCCGAT
1359422 CCGGATCGGATTTAAATCCGA
1 CCGGATC-GATTTAAATCCGA
1359443 CTATGTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (21 bp):
CCGGATCGATTTAAATCCGAT
Found at i:1361944 original size:29 final size:29
Alignment explanation
Indices: 1361911--1361969 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1361901 GACTTGATAG
* * *
1361911 TTCAGCTCATTAAAAGGAGACTGAAACCT
1 TTCAGATCATTAAAAGGAGAATAAAACCT
*
1361940 TTCAGATCATTAAAGGGAGAATAAAACCT
1 TTCAGATCATTAAAAGGAGAATAAAACCT
1361969 T
1 T
1361970 AGGAATCGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (29 bp):
TTCAGATCATTAAAAGGAGAATAAAACCT
Found at i:1362545 original size:50 final size:48
Alignment explanation
Indices: 1362468--1362567 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 48
1362458 CAAAGTTAAC
1362468 ATAAATTTCTGTTAAAAAATCAAAAATCAAATACAAAATGAGAAATAA
1 ATAAATTTCTGTTAAAAAATCAAAAATCAAATACAAAATGAGAAATAA
1362516 ATAAATTTCTTGTTAAAAAAATCAAAAATCAAATACAAAATGAGAAATAA
1 ATAAATTTC-TGTT-AAAAAATCAAAAATCAAATACAAAATGAGAAATAA
1362566 AT
1 AT
1362568 GTGGCATAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 9 0.18
49 4 0.08
50 37 0.74
ACGTcount: A:0.60, C:0.08, G:0.06, T:0.26
Consensus pattern (48 bp):
ATAAATTTCTGTTAAAAAATCAAAAATCAAATACAAAATGAGAAATAA
Found at i:1366576 original size:3 final size:3
Alignment explanation
Indices: 1366570--1366621 Score: 88
Period size: 3 Copynumber: 17.3 Consensus size: 3
1366560 TCTCATACTC
1366570 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-T ATCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT
1366618 TCT T
1 TCT T
1366622 TTTGAGCAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 1 0.02
3 45 0.96
4 1 0.02
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:1370135 original size:15 final size:15
Alignment explanation
Indices: 1370109--1370185 Score: 100
Period size: 15 Copynumber: 5.1 Consensus size: 15
1370099 AACATACAGG
1370109 TAACAGTAGACCAGA
1 TAACAGTAGACCAGA
* *
1370124 TAATAATAGACCAGA
1 TAACAGTAGACCAGA
* *
1370139 TAATAGTAGACCATA
1 TAACAGTAGACCAGA
*
1370154 TAACAGTAGACCATA
1 TAACAGTAGACCAGA
*
1370169 TAACAGTATACCAGA
1 TAACAGTAGACCAGA
1370184 TA
1 TA
1370186 GTAGCAAACT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 55 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (15 bp):
TAACAGTAGACCAGA
Found at i:1373415 original size:34 final size:34
Alignment explanation
Indices: 1373366--1373430 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
1373356 TATTAAGGAG
1373366 GAGTTATGGAATTTATAAGC-T-TTGGAGTTAGA
1 GAGTTATGGAATTTATAAGCTTCTTGGAGTTAGA
*
1373398 GAGTTATTGGTAATTTATTAGCTTCTTGGAGTT
1 GAGTTA-TGG-AATTTATAAGCTTCTTGGAGTT
1373431 TTTGAATTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 6 0.21
33 3 0.11
34 10 0.36
35 1 0.04
36 8 0.29
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.43
Consensus pattern (34 bp):
GAGTTATGGAATTTATAAGCTTCTTGGAGTTAGA
Found at i:1378792 original size:24 final size:24
Alignment explanation
Indices: 1378765--1378820 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
1378755 ATTATTAAGG
1378765 AGGAGTTATGGAATTTATGAGTTT
1 AGGAGTTATGGAATTTATGAGTTT
1378789 AGGAGTTATGGAATTTATGAGTTT
1 AGGAGTTATGGAATTTATGAGTTT
*
1378813 GGGAGTTA
1 AGGAGTTA
1378821 GATAGTCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (24 bp):
AGGAGTTATGGAATTTATGAGTTT
Found at i:1380206 original size:14 final size:14
Alignment explanation
Indices: 1380184--1380225 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
1380174 AAGGGTTGCT
1380184 TCATATAGATCTCC
1 TCATATAGATCTCC
*
1380198 TCATCTAGATCTCC
1 TCATATAGATCTCC
*
1380212 TCATTTAGATCTCC
1 TCATATAGATCTCC
1380226 ATTCATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.24, C:0.31, G:0.07, T:0.38
Consensus pattern (14 bp):
TCATATAGATCTCC
Found at i:1392998 original size:41 final size:41
Alignment explanation
Indices: 1392953--1393136 Score: 151
Period size: 41 Copynumber: 4.4 Consensus size: 41
1392943 TTTATATCAC
* *
1392953 AAACGTCGCAATAGATTATAAATTTTACGGCGATTTAGCCA
1 AAACGCCGCAATAGATTATAAATTTTGCGGCGATTTAGCCA
** * * **
1392994 AAACGCCGCAATAGAGTGGTAAA-CTGGCGGC-ATTTTTTCCA
1 AAACGCCGCAATAGA-TTATAAATTTTGCGGCGA-TTTAGCCA
*
1393035 CAAACGCCGCAATAGAGTATAAATTTTGCGGCGATTTAGCCA
1 -AAACGCCGCAATAGATTATAAATTTTGCGGCGATTTAGCCA
* ** * *
1393077 AAACGTCGCAATAGAGTGGTAAA-TTAGCGGCGTTTTTA-CCA
1 AAACGCCGCAATAGA-TTATAAATTTTGCGGCG-ATTTAGCCA
*
1393118 CAAACGCCGCAATATATTA
1 -AAACGCCGCAATAGATTA
1393137 CACATATAGT
Statistics
Matches: 110, Mismatches: 25, Indels: 16
0.73 0.17 0.11
Matches are distributed among these distances:
40 1 0.01
41 55 0.50
42 53 0.48
43 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (41 bp):
AAACGCCGCAATAGATTATAAATTTTGCGGCGATTTAGCCA
Found at i:1393004 original size:83 final size:82
Alignment explanation
Indices: 1392910--1393136 Score: 301
Period size: 83 Copynumber: 2.7 Consensus size: 82
1392900 CTTTTTTGTA
* * * * *
1392910 AAAAAGCCGCAATAGGGTGATAAATTAGTGGCGTTTATATCACAAACGTCGCAATAGATTATAAA
1 AAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTT-TATCACAAACGCCGCAATAGATTATAAA
1392975 TTTTACGGCGATTTAGCC
65 TTTTACGGCGATTTAGCC
* * * * *
1392993 AAAACGCCGCAATAGAGTGGTAAACTGGCGGCATTTTTTCCACAAACGCCGCAATAGAGTATAAA
1 AAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTTAT-CACAAACGCCGCAATAGATTATAAA
*
1393058 TTTTGCGGCGATTTAGCC
65 TTTTACGGCGATTTAGCC
* * *
1393076 AAAACGTCGCAATAGAGTGGTAAATTAGCGGCGTTTTTACCACAAACGCCGCAATATATTA
1 AAAACGCCGCAATAGAGTGGTAAATTAGCGGCG-TTTTATCACAAACGCCGCAATAGATTA
1393137 CACATATAGT
Statistics
Matches: 123, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
82 2 0.02
83 117 0.95
84 4 0.03
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (82 bp):
AAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTTATCACAAACGCCGCAATAGATTATAAAT
TTTACGGCGATTTAGCC
Found at i:1393044 original size:42 final size:42
Alignment explanation
Indices: 1392915--1393131 Score: 164
Period size: 42 Copynumber: 5.2 Consensus size: 42
1392905 TTGTAAAAAA
* * * * * *
1392915 GCCGCAATAGGGTGATAAATTAGTGGCGTTTATATCACAAAC
1 GCCGCAATAGAGTGGTAAATTAGCGGCATTTTTACCACAAAC
* **
1392957 GTCGCAATAGA-TTATAAATTTTA-CGGCGA--TTTAGCCA-AAAC
1 GCCGCAATAGAGTGGTAAA--TTAGCGGC-ATTTTTA-CCACAAAC
* * *
1392998 GCCGCAATAGAGTGGTAAACTGGCGGCATTTTTTCCACAAAC
1 GCCGCAATAGAGTGGTAAATTAGCGGCATTTTTACCACAAAC
* *
1393040 GCCGCAATAGAGT-ATAAATTTTGCGGCGA--TTTAGCCA-AAAC
1 GCCGCAATAGAGTGGTAAA-TTAGCGGC-ATTTTTA-CCACAAAC
* *
1393081 GTCGCAATAGAGTGGTAAATTAGCGGCGTTTTTACCACAAAC
1 GCCGCAATAGAGTGGTAAATTAGCGGCATTTTTACCACAAAC
1393123 GCCGCAATA
1 GCCGCAATA
1393132 TATTACACAT
Statistics
Matches: 137, Mismatches: 22, Indels: 32
0.72 0.12 0.17
Matches are distributed among these distances:
40 2 0.01
41 63 0.46
42 68 0.50
43 4 0.03
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (42 bp):
GCCGCAATAGAGTGGTAAATTAGCGGCATTTTTACCACAAAC
Found at i:1393215 original size:41 final size:41
Alignment explanation
Indices: 1393117--1393384 Score: 298
Period size: 41 Copynumber: 6.5 Consensus size: 41
1393107 CGTTTTTACC
* *
1393117 ACAAACGCCGCAATA-TATTACA-CATATAGTGGCGTTTGTTCCT
1 ACAAACGCCGCAATAGTGTTA-ATCA-ATAGTGGCGTTT-TT-GT
1393160 A-AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTGT
1 ACAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTGT
*
1393200 ACAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAT
1 ACAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTGT
*
1393241 ACAAACGCCGTAATAGTGTTAATCAATAGTGGCGTTTTTAG-
1 ACAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTT-GT
** * *
1393282 ACAAACATCGCAATAGTGTTAAACAATAGTGGCGTTTAT-T
1 ACAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTGT
* * * *
1393322 AGCAAACGCCACAATAATG-TAATCAAAAGTGGCTTTTTTTGT
1 A-CAAACGCCGCAATAGTGTTAATCAATAGTGGC-GTTTTTGT
* *
1393364 ATAAACGCCGCAA-AATGTTAA
1 ACAAACGCCGCAATAGTGTTAA
1393385 ATATATAGTC
Statistics
Matches: 196, Mismatches: 20, Indels: 20
0.83 0.08 0.08
Matches are distributed among these distances:
40 19 0.10
41 142 0.72
42 28 0.14
43 7 0.04
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (41 bp):
ACAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTGT
Found at i:1394644 original size:41 final size:41
Alignment explanation
Indices: 1394598--1394708 Score: 114
Period size: 42 Copynumber: 2.7 Consensus size: 41
1394588 TTGATATTAG
1394598 GTGGCGTTTTTTAATAAACACCGCAATAGAATAGTTCCTTA
1 GTGGCGTTTTTTAATAAACACCGCAATAGAATAGTTCCTTA
* * * * * * * *
1394639 GTGGCGTTTTCGTAAAAAACGCAGTAATAGAGTAGTTCTTTT
1 GTGGCGTTTT-TTAATAAACACCGCAATAGAATAGTTCCTTA
* *
1394681 GCGGCGTTTTTAATATAAACACCGCAAT
1 GTGGCGTTTTTTA-ATAAACACCGCAAT
1394709 TGTCCTTTAA
Statistics
Matches: 53, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
41 11 0.21
42 42 0.79
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (41 bp):
GTGGCGTTTTTTAATAAACACCGCAATAGAATAGTTCCTTA
Found at i:1402837 original size:21 final size:21
Alignment explanation
Indices: 1402813--1402959 Score: 82
Period size: 21 Copynumber: 7.0 Consensus size: 21
1402803 ATGAAGCAAG
* *
1402813 GGAAGTAGAGAGAGCAGCAGT
1 GGAAGCAGAGAGAGCAGCAGC
**
1402834 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* * *
1402855 GGAAGCGGAGAAAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* * *
1402876 GGCAGCACAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* * * * *
1402897 GGTAGTACAGAGAGAAGCAAC
1 GGAAGCAGAGAGAGCAGCAGC
* * *
1402918 -GATAGCACAGAGAGAAGTAGC
1 GGA-AGCAGAGAGAGCAGCAGC
* *
1402939 -GACAGCACAGAGAGAAGCAGC
1 GGA-AGCAGAGAGAGCAGCAGC
1402960 ATATCAGCAT
Statistics
Matches: 103, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
20 1 0.01
21 102 0.99
ACGTcount: A:0.40, C:0.18, G:0.37, T:0.05
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:1402895 original size:42 final size:42
Alignment explanation
Indices: 1402844--1402957 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
1402834 GGAAGCAGCT
* ** * *
1402844 AGAGCAGCAGCGGAAGCGGAGAAAGAAGCAGCGGCAGCACAG
1 AGAGAAGCAGCGGAAGCACAGAAAGAAGCAACGACAGCACAG
* * * *
1402886 AGAGAAGCAGCGGTAGTACAGAGAGAAGCAACGATAGCACAG
1 AGAGAAGCAGCGGAAGCACAGAAAGAAGCAACGACAGCACAG
* *
1402928 AGAGAAGTAGC-GACAGCACAGAGAGAAGCA
1 AGAGAAGCAGCGGA-AGCACAGAAAGAAGCA
1402958 GCATATCAGC
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 1 0.02
42 58 0.98
ACGTcount: A:0.42, C:0.18, G:0.36, T:0.04
Consensus pattern (42 bp):
AGAGAAGCAGCGGAAGCACAGAAAGAAGCAACGACAGCACAG
Found at i:1402952 original size:23 final size:21
Alignment explanation
Indices: 1402867--1402957 Score: 101
Period size: 21 Copynumber: 4.3 Consensus size: 21
1402857 AAGCGGAGAA
* *
1402867 AGAAGCAGCGGCAGCACAGAG
1 AGAAGCAACGACAGCACAGAG
* ** *
1402888 AGAAGCAGCGGTAGTACAGAG
1 AGAAGCAACGACAGCACAGAG
*
1402909 AGAAGCAACGATAGCACAGAG
1 AGAAGCAACGACAGCACAGAG
* *
1402930 AGAAGTAGCGACAGCACAGAG
1 AGAAGCAACGACAGCACAGAG
1402951 AGAAGCA
1 AGAAGCA
1402958 GCATATCAGC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.43, C:0.19, G:0.34, T:0.04
Consensus pattern (21 bp):
AGAAGCAACGACAGCACAGAG
Found at i:1403632 original size:86 final size:86
Alignment explanation
Indices: 1403468--1403720 Score: 246
Period size: 86 Copynumber: 3.0 Consensus size: 86
1403458 TTTTCGATAC
* * * * * * * * *
1403468 AAACGCCGCTTAATC-TGAAAACCTACTGCGACG-TTTGGGGAGAAACGCCGCTAAACATCATCA
1 AAACGCCGC-TAAACATCAAAACCTACTGCGGCGTTTTAGTGACAAACGCAGCTAAATATCAACA
*
1403531 CCTATTGCGTCGTTTGTTGAAA
65 CCTATTGCGGCGTTTGTTGAAA
* *
1403553 AAACGCCG-TAAAATATCAACACCTACTGCGGCGTTTGTAAGT-A-AAACGCAGCTAAATATCAA
1 AAACGCCGCT-AAACATCAAAACCTACTGCGGCGTTT-T-AGTGACAAACGCAGCTAAATATCAA
* * **
1403615 CACCTACTGCGGCGTTTGTAGGGA
63 CACCTATTGCGGCGTTTGTTGAAA
* * * * *
1403639 AAACGCCGCTAAACATCAAAACCTATTGCTGCGTTTTTGTGACAAACGCTGCTAAATAACAACAC
1 AAACGCCGCTAAACATCAAAACCTACTGCGGCGTTTTAGTGACAAACGCAGCTAAATATCAACAC
1403704 CTATTGCGGCGTTTGTT
66 CTATTGCGGCGTTTGTT
1403721 CAACAAACAC
Statistics
Matches: 136, Mismatches: 24, Indels: 15
0.78 0.14 0.09
Matches are distributed among these distances:
83 1 0.01
84 4 0.03
85 25 0.18
86 102 0.75
87 3 0.02
88 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (86 bp):
AAACGCCGCTAAACATCAAAACCTACTGCGGCGTTTTAGTGACAAACGCAGCTAAATATCAACAC
CTATTGCGGCGTTTGTTGAAA
Found at i:1403674 original size:129 final size:128
Alignment explanation
Indices: 1403488--1403719 Score: 319
Period size: 129 Copynumber: 1.8 Consensus size: 128
1403478 TAATCTGAAA
**
1403488 ACCTACTGCGACGTTTGGGGAGAAACGCCGCTAAACATCATCACCTATTGCGTCGTTTGTTG-AA
1 ACCTACTGCGACGTTTGGGGAGAAACGCCGCTAAACATCAAAACCTATTGCGTCGTTT-TTGTAA
*
1403552 AAAACGCCG-TAAAATATCAACACCTACTGCGGCGTTTGTAAGTAAAACGCAGCTAAATATCAAC
65 AAAACGCCGCT-AAATAACAACACCTACTGCGGCGTTTGTAAGTAAAACGCAGCTAAATATCAAC
*
1403616 ACCTACTGCGGCGTTTGTAGGGA-AAACGCCGCTAAACATCAAAACCTATTGC-TGCGTTTTTGT
1 ACCTACTGCGACGTTTG--GGGAGAAACGCCGCTAAACATCAAAACCTATTGCGT-CGTTTTTGT
* * * *
1403679 GACAAACGCTGCTAAATAACAACACCTATTGCGGCGTTTGT
63 AAAAAACGCCGCTAAATAACAACACCTACTGCGGCGTTTGT
1403720 TCAACAAACA
Statistics
Matches: 91, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
128 20 0.22
129 66 0.73
130 5 0.05
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (128 bp):
ACCTACTGCGACGTTTGGGGAGAAACGCCGCTAAACATCAAAACCTATTGCGTCGTTTTTGTAAA
AAACGCCGCTAAATAACAACACCTACTGCGGCGTTTGTAAGTAAAACGCAGCTAAATATCAAC
Found at i:1403735 original size:43 final size:43
Alignment explanation
Indices: 1403366--1403720 Score: 215
Period size: 43 Copynumber: 8.3 Consensus size: 43
1403356 CCGAACTTTA
* * **
1403366 GCGGCGTTTATATG-AAAAACACCGCTAAAGCTCAACACCTATT
1 GCGGCGTTTGT-TGAAAAAACGCCGCTAAATATCAACACCTATT
* * * * * *
1403409 GCTGCGTTT-TTAATAAAAACGCCACTAATTCTTAAC-CCTTATT
1 GCGGCGTTTGTTGA-AAAAACGCCGCTAAATATCAACACC-TATT
** * * * * * * * *
1403452 GCTTCATTT-TCGATACAAACGCCGCTTAATCTGAAAACCTACT
1 GCGGCGTTTGTTGA-AAAAACGCCGCTAAATATCAACACCTATT
* * * * * *
1403495 GCGACGTTTG-GGGAGAAACGCCGCTAAACATCATCACCTATT
1 GCGGCGTTTGTTGAAAAAACGCCGCTAAATATCAACACCTATT
* *
1403537 GCGTCGTTTGTTGAAAAAACGCCG-TAAAATATCAACACCTACT
1 GCGGCGTTTGTTGAAAAAACGCCGCT-AAATATCAACACCTATT
* *
1403580 GCGGCGTTTG-T-AAGTAAAACGCAGCTAAATATCAACACCTACT
1 GCGGCGTTTGTTGAA--AAAACGCCGCTAAATATCAACACCTATT
* ** * *
1403623 GCGGCGTTTGTAGGGAAAACGCCGCTAAACATCAAAACCTATT
1 GCGGCGTTTGTTGAAAAAACGCCGCTAAATATCAACACCTATT
* * * * *
1403666 GCTGCGTTT-TTGTGACAAACGCTGCTAAATAACAACACCTATT
1 GCGGCGTTTGTTG-AAAAAACGCCGCTAAATATCAACACCTATT
1403709 GCGGCGTTTGTT
1 GCGGCGTTTGTT
1403721 CAACAAACAC
Statistics
Matches: 242, Mismatches: 56, Indels: 27
0.74 0.17 0.08
Matches are distributed among these distances:
41 3 0.01
42 37 0.15
43 197 0.81
44 5 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (43 bp):
GCGGCGTTTGTTGAAAAAACGCCGCTAAATATCAACACCTATT
Found at i:1404593 original size:25 final size:27
Alignment explanation
Indices: 1404542--1404595 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 27
1404532 TACACCAGAA
1404542 AAAAAGTAAGGAAAAGTTAACATTTTAAG
1 AAAAAGTAAGGAAAA--TAACATTTTAAG
1404571 AAAAAGTAA-GAAAA-AACATTTTAAG
1 AAAAAGTAAGGAAAATAACATTTTAAG
1404596 TTGTGCGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 11 0.44
28 5 0.20
29 9 0.36
ACGTcount: A:0.59, C:0.04, G:0.15, T:0.22
Consensus pattern (27 bp):
AAAAAGTAAGGAAAATAACATTTTAAG
Found at i:1408864 original size:14 final size:14
Alignment explanation
Indices: 1408847--1408891 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
1408837 AAAATATAAT
*
1408847 ATAAATATATATAC
1 ATAAGTATATATAC
1408861 ATAAGTATATATAC
1 ATAAGTATATATAC
* *
1408875 ATACGTGTATATAC
1 ATAAGTATATATAC
1408889 ATA
1 ATA
1408892 TCTATATAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.36
Consensus pattern (14 bp):
ATAAGTATATATAC
Found at i:1408899 original size:14 final size:13
Alignment explanation
Indices: 1408852--1408899 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
1408842 ATAATATAAA
*
1408852 TATATATACATAAG
1 TATATATACAT-AC
1408866 TATATATACATAC
1 TATATATACATAC
*
1408879 GTGTATATACATATC
1 -TATATATACATA-C
1408894 TATATA
1 TATATA
1408900 GGCCACCTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (13 bp):
TATATATACATAC
Found at i:1414394 original size:19 final size:19
Alignment explanation
Indices: 1414370--1414407 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1414360 GACTTTGATG
1414370 ATTTCTGCAGCCCCCCTTC
1 ATTTCTGCAGCCCCCCTTC
*
1414389 ATTTCTGCGGCCCCCCTTC
1 ATTTCTGCAGCCCCCCTTC
1414408 TTGGACTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.08, C:0.47, G:0.13, T:0.32
Consensus pattern (19 bp):
ATTTCTGCAGCCCCCCTTC
Found at i:1417668 original size:18 final size:19
Alignment explanation
Indices: 1417642--1417681 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1417632 CCTCTAAAAA
1417642 TTTAAAATTTT-TATATAT
1 TTTAAAATTTTCTATATAT
* *
1417660 TTTAGAATTTTCTATGTAT
1 TTTAAAATTTTCTATATAT
1417679 TTT
1 TTT
1417682 TTATTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTAAAATTTTCTATATAT
Found at i:1426477 original size:17 final size:17
Alignment explanation
Indices: 1426457--1426502 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
1426447 GCCATTGTAT
1426457 GAGCCGAGCCGCTGACC
1 GAGCCGAGCCGCTGACC
1426474 GAGCCGAGCCGCTGACC
1 GAGCCGAGCCGCTGACC
* *
1426491 AAGTCGAGCCGC
1 GAGCCGAGCCGC
1426503 GTTGATCGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.20, C:0.39, G:0.35, T:0.07
Consensus pattern (17 bp):
GAGCCGAGCCGCTGACC
Found at i:1429494 original size:23 final size:24
Alignment explanation
Indices: 1429456--1429508 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
1429446 ATCTCATTCA
1429456 CTATACATTTTCATATCACATGTT
1 CTATACATTTTCATATCACATGTT
1429480 CTATACA-TTTCATATCACATGTT
1 CTATACATTTTCATATCACATGTT
1429503 CATATA
1 C-TATA
1429509 AGCTCATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 17 0.61
24 11 0.39
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (24 bp):
CTATACATTTTCATATCACATGTT
Found at i:1429506 original size:13 final size:13
Alignment explanation
Indices: 1429460--1429507 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
1429450 CATTCACTAT
*
1429460 ACATTTTCATATC
1 ACATGTTCATATC
1429473 ACATGTTC-TAT-
1 ACATGTTCATATC
1429484 ACAT-TTCATATC
1 ACATGTTCATATC
1429496 ACATGTTCATAT
1 ACATGTTCATAT
1429508 AAGCTCATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
12 7 0.23
13 14 0.45
ACGTcount: A:0.31, C:0.21, G:0.04, T:0.44
Consensus pattern (13 bp):
ACATGTTCATATC
Found at i:1429515 original size:23 final size:23
Alignment explanation
Indices: 1429466--1429516 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1429456 CTATACATTT
**
1429466 TCATATCACATGTTCTATACATT
1 TCATATCACATGTTCTATACAGC
1429489 TCATATCACATGTTCATATA-AGC
1 TCATATCACATGTTC-TATACAGC
1429512 TCATA
1 TCATA
1429517 GTTCTTTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (23 bp):
TCATATCACATGTTCTATACAGC
Found at i:1430194 original size:20 final size:22
Alignment explanation
Indices: 1430169--1430226 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1430159 TTTCCCTTGA
1430169 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
1430189 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
1430212 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1430227 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:1430287 original size:64 final size:63
Alignment explanation
Indices: 1430214--1430375 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 63
1430204 TCTTTAACAT
* * * * *
1430214 GTGCATCGATGCACTACCCATGCATCGATACAC-AATTTCCTTCGATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACT-CCAATGCATCGATACACTAACTGCATTCGATGTTTCCATTTTTAA-GGG
* *
1430277 GATGCATCGATGCACTCCTAATGCATCGATGCACTAACTGCATTCGATGTTTCCATTTTTAATGG
1 G-TGCATCGATGCACTCC-AATGCATCGATACACTAACTGCATTCGATGTTTCCATTTTTAAGGG
**
1430342 GTGCATCGATGCACTTCCTGTGCATCGATACACT
1 GTGCATCGATGCAC-TCCAATGCATCGATACACT
1430376 TTGGAAATTT
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
63 3 0.04
64 53 0.63
65 22 0.26
66 6 0.07
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCAATGCATCGATACACTAACTGCATTCGATGTTTCCATTTTTAAGGG
Found at i:1430867 original size:20 final size:20
Alignment explanation
Indices: 1430842--1430881 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1430832 AACTTACCTT
1430842 TGCCATAGAGCTTACGGGAA
1 TGCCATAGAGCTTACGGGAA
*
1430862 TGCCATGGAGCTTACGGGAA
1 TGCCATAGAGCTTACGGGAA
1430882 GAGAAGAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.20
Consensus pattern (20 bp):
TGCCATAGAGCTTACGGGAA
Found at i:1431211 original size:22 final size:23
Alignment explanation
Indices: 1431171--1431240 Score: 90
Period size: 22 Copynumber: 3.0 Consensus size: 23
1431161 TAACGGAGAT
1431171 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATC-AAACAGAATTCAG
*
1431195 ATCAGATATC-AACAGAA-TCAAG
1 ATCAGAAATCAAACAGAATTC-AG
1431217 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCA-AACAGAATTCAG
1431241 TTGTATCAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 2 0.05
22 18 0.45
24 18 0.45
25 2 0.05
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (23 bp):
ATCAGAAATCAAACAGAATTCAG
Found at i:1433334 original size:14 final size:14
Alignment explanation
Indices: 1433307--1433340 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1433297 CAACGAGTCA
1433307 GGTC-AACGGGTCG
1 GGTCAAACGGGTCG
*
1433320 GGTCAAACGGTTCG
1 GGTCAAACGGGTCG
1433334 GGTCAAA
1 GGTCAAA
1433341 ACTGGGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.24, C:0.21, G:0.38, T:0.18
Consensus pattern (14 bp):
GGTCAAACGGGTCG
Found at i:1442889 original size:14 final size:14
Alignment explanation
Indices: 1442870--1442917 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1442860 AAATAAATCA
*
1442870 TGGTTTATGATCTC
1 TGGTTTCTGATCTC
* *
1442884 TGGTTTCTGTTCAC
1 TGGTTTCTGATCTC
* *
1442898 TGGATTCTGATCTT
1 TGGTTTCTGATCTC
1442912 TGGTTT
1 TGGTTT
1442918 TTAAAACCTT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.10, C:0.15, G:0.23, T:0.52
Consensus pattern (14 bp):
TGGTTTCTGATCTC
Found at i:1445504 original size:79 final size:80
Alignment explanation
Indices: 1445413--1445572 Score: 313
Period size: 79 Copynumber: 2.0 Consensus size: 80
1445403 CAATGTTTTA
1445413 TCTATCGATTCGATACAAAGTTTCATGTTTAAGTTTTCGTTTCTAACGT-AATTCATTTGTTATG
1 TCTATCGATTCGATACAAAGTTTCATGTTTAAGTTTTCGTTTCTAACGTAAATTCATTTGTTATG
1445477 TATCTGAGATATTAT
66 TATCTGAGATATTAT
1445492 TCTATCGATTCGATACAAAGTTTCATGTTTAAGTTTTCGTTTCTAACGTAAATTCATTTGTTATG
1 TCTATCGATTCGATACAAAGTTTCATGTTTAAGTTTTCGTTTCTAACGTAAATTCATTTGTTATG
1445557 TATCTGAGATATTAT
66 TATCTGAGATATTAT
1445572 T
1 T
1445573 GGACGTGGAA
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 49 0.61
80 31 0.39
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (80 bp):
TCTATCGATTCGATACAAAGTTTCATGTTTAAGTTTTCGTTTCTAACGTAAATTCATTTGTTATG
TATCTGAGATATTAT
Found at i:1449364 original size:17 final size:17
Alignment explanation
Indices: 1449342--1449374 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1449332 GCCATTACTG
1449342 GAAGAAG-AGAAGAAGAA
1 GAAGAAGTAG-AGAAGAA
1449359 GAAGAAGTAGAGAAGA
1 GAAGAAGTAGAGAAGA
1449375 GAGCATGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (17 bp):
GAAGAAGTAGAGAAGAA
Found at i:1450580 original size:2 final size:2
Alignment explanation
Indices: 1450573--1450599 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1450563 TCTATAGCGC
1450573 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1450600 TGACCTGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1453633 original size:40 final size:41
Alignment explanation
Indices: 1453578--1453655 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
1453568 CCAGTTATTA
1453578 TGTGTTTAAAGAGAT-AAAGTAAGCAAAGGTATAATAGTAC
1 TGTGTTTAAAGAGATAAAAGTAAGCAAAGGTATAATAGTAC
1453618 TGTGTTTAAAGAGATAAAAGTAAGCAAAGGTATAATAG
1 TGTGTTTAAAGAGATAAAAGTAAGCAAAGGTATAATAG
1453656 CATAACATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
40 15 0.41
41 22 0.59
ACGTcount: A:0.46, C:0.04, G:0.23, T:0.27
Consensus pattern (41 bp):
TGTGTTTAAAGAGATAAAAGTAAGCAAAGGTATAATAGTAC
Found at i:1456456 original size:15 final size:17
Alignment explanation
Indices: 1456425--1456456 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1456415 ATGTATTTTT
1456425 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
1456442 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
1456457 TTATATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:1456575 original size:13 final size:12
Alignment explanation
Indices: 1456556--1456595 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 12
1456546 AAAGGAAAAG
1456556 AAAAAGAAAATA
1 AAAAAGAAAATA
1456568 ACAAAAGAAAATA
1 A-AAAAGAAAATA
*
1456581 AAAAA-AAAACA
1 AAAAAGAAAATA
1456592 AAAA
1 AAAA
1456596 CCAAAAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 9 0.35
12 5 0.19
13 12 0.46
ACGTcount: A:0.85, C:0.05, G:0.05, T:0.05
Consensus pattern (12 bp):
AAAAAGAAAATA
Found at i:1456583 original size:29 final size:29
Alignment explanation
Indices: 1456537--1456594 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1456527 GAAAATAATG
* *
1456537 TAACAAAGAAAAGGAAAAGAAAAAGAAAA
1 TAACAAAGAAAAGGAAAAAAAAAACAAAA
*
1456566 TAACAAAAGAAAA-TAAAAAAAAAACAAAA
1 TAAC-AAAGAAAAGGAAAAAAAAAACAAAA
1456595 ACCAAAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.79, C:0.05, G:0.10, T:0.05
Consensus pattern (29 bp):
TAACAAAGAAAAGGAAAAAAAAAACAAAA
Found at i:1457945 original size:15 final size:17
Alignment explanation
Indices: 1457914--1457946 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1457904 ATGTATTTTT
1457914 ATCTATCTTGTAATTTA
1 ATCTATCTTGTAATTTA
1457931 ATCTA-CTTG-AATTTA
1 ATCTATCTTGTAATTTA
1457946 A
1 A
1457947 AAAAAATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (17 bp):
ATCTATCTTGTAATTTA
Found at i:1458480 original size:18 final size:17
Alignment explanation
Indices: 1458448--1458485 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
1458438 TTTAATTTAG
1458448 AATTTTAAATATTTATA
1 AATTTTAAATATTTATA
*
1458465 AATTTTCAAATTTTTATA
1 AATTTT-AAATATTTATA
1458483 AAT
1 AAT
1458486 ATTTTTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTTAAATATTTATA
Found at i:1458491 original size:12 final size:12
Alignment explanation
Indices: 1458474--1458505 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1458464 AAATTTTCAA
1458474 ATTTTTATAAAT
1 ATTTTTATAAAT
*
1458486 ATTTTTAGAAAT
1 ATTTTTATAAAT
1458498 ATTTTTAT
1 ATTTTTAT
1458506 TTAAACAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (12 bp):
ATTTTTATAAAT
Found at i:1461228 original size:20 final size:21
Alignment explanation
Indices: 1461191--1461231 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1461181 GGGAGAGAAG
1461191 GAAAAAATAAAGACGAAAAGA
1 GAAAAAATAAAGACGAAAAGA
1461212 GAAAAAATGAAA-A-GAAAAGA
1 GAAAAAAT-AAAGACGAAAAGA
1461232 CTTAGCTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 9 0.47
22 3 0.16
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (21 bp):
GAAAAAATAAAGACGAAAAGA
Found at i:1462162 original size:191 final size:183
Alignment explanation
Indices: 1461795--1462164 Score: 643
Period size: 191 Copynumber: 2.0 Consensus size: 183
1461785 GTGTTTACTA
*
1461795 TTCCTAGTTTAATGCATTTCAGTCATTGTCTGTCTTAATATTTGGTTTAATATCTGTTTAGGTTA
1 TTCCTAGTTTAATGCATTTCAGTCATAGTCTGTCTTAATATTTGGTTTAATATCTGTTTAGGTTA
1461860 TTGATTCATGATTATTTCATTTAGATCCATGTCTGTATATTAATAAAAATTAATATTTAGATCTG
66 TTGATTCATGATTATTTCATTTAGATCCATGTCTGTATATTAATAAAAATTAATATTTAGATCTG
1461925 GCTTCTAAATTGGTTTGACTTTTGTTTTTTGTCCTTTAAATATTATTTTCTAG
131 GCTTCTAAATTGGTTTGACTTTTGTTTTTTGTCCTTTAAATATTATTTTCTAG
1461978 TTCCTAGTTTAATGCATTTCAGTCATAGTCTGTTGTCTTAATATATTTGGTTTAATATCTGTTTT
1 TTCCTAGTTTAATGCATTTCAGTCATAGTC---TGTCTT-A-ATATTTGGTTTAATATCTG-TTT
1462043 AGGTTATTGATTCATGATTTATTTCATTTAGATCCATGTCTGTATATTAATAAAAAATTAATATT
60 AGGTTATTGATTCATGA-TTATTTCATTTAGATCCATGTCTGTATATTAAT-AAAAATTAATATT
1462108 TAGGATCTGGCTTCTAAATTGGTTTGACTTTTG-TTTTTGTCCTTTAAATATTATTTT
123 TA-GATCTGGCTTCTAAATTGGTTTGACTTTTGTTTTTTGTCCTTTAAATATTATTTT
1462165 GAAAGATAAA
Statistics
Matches: 177, Mismatches: 1, Indels: 10
0.94 0.01 0.05
Matches are distributed among these distances:
183 29 0.16
186 6 0.03
187 1 0.01
188 19 0.11
189 20 0.11
190 33 0.19
191 39 0.22
192 30 0.17
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (183 bp):
TTCCTAGTTTAATGCATTTCAGTCATAGTCTGTCTTAATATTTGGTTTAATATCTGTTTAGGTTA
TTGATTCATGATTATTTCATTTAGATCCATGTCTGTATATTAATAAAAATTAATATTTAGATCTG
GCTTCTAAATTGGTTTGACTTTTGTTTTTTGTCCTTTAAATATTATTTTCTAG
Found at i:1462371 original size:15 final size:15
Alignment explanation
Indices: 1462351--1462394 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1462341 TTTAATATTT
1462351 TTATTGTTAGACTCA
1 TTATTGTTAGACTCA
1462366 TTATTGTTAG--T-A
1 TTATTGTTAGACTCA
1462378 TTATTGTTTA-ACTCA
1 TTATTG-TTAGACTCA
1462393 TT
1 TT
1462395 GTTATTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 7 0.28
13 4 0.16
14 1 0.04
15 13 0.52
ACGTcount: A:0.25, C:0.09, G:0.11, T:0.55
Consensus pattern (15 bp):
TTATTGTTAGACTCA
Found at i:1463248 original size:27 final size:28
Alignment explanation
Indices: 1463194--1463248 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
1463184 CGAATCTCAT
* *
1463194 TCAATTTAATTCAAATTAATTCAAAATTG
1 TCAATTT-ATTCAAAATAAATCAAAATTG
*
1463223 TCAATTT-TTCAAAATAAATCATAATT
1 TCAATTTATTCAAAATAAATCAAAATT
1463249 ATTTTTAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 16 0.70
29 7 0.30
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (28 bp):
TCAATTTATTCAAAATAAATCAAAATTG
Found at i:1466221 original size:18 final size:17
Alignment explanation
Indices: 1466198--1466270 Score: 51
Period size: 18 Copynumber: 4.1 Consensus size: 17
1466188 AAATGAAAAG
1466198 AAAAAAGAGAGCAAAGAA
1 AAAAAAGAGAG-AAAGAA
* *
1466216 AAAAAAAAGAGCGAAGAGA
1 AAAAAAGAGAG-AAAGA-A
*
1466235 AAAGAAGA-A-AAGAGAA
1 AAAAAAGAGAGAA-AGAA
*
1466251 AAAGAAAGAAAGAAAGAA
1 AAA-AAAGAGAGAAAGAA
1466269 AA
1 AA
1466271 TGGATCAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
16 5 0.11
17 7 0.16
18 23 0.52
19 9 0.20
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAAAAGAGAGAAAGAA
Found at i:1466223 original size:20 final size:20
Alignment explanation
Indices: 1466192--1466267 Score: 84
Period size: 20 Copynumber: 3.7 Consensus size: 20
1466182 AAAGCAAAAT
1466192 GAAAAGAAAAAAGAGAGCAAA
1 GAAAAGAAAAAAGAGAG-AAA
*
1466213 GAAAA-AAAAAAGAGCGAAGA
1 GAAAAGAAAAAAGAGAGAA-A
*
1466233 GAAAAGAAGAAAAGAGAAAAA
1 GAAAAGAA-AAAAGAGAGAAA
1466254 G-AAAGAAAGAAAGA
1 GAAAAGAAA-AAAGA
1466268 AAATGGATCA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
19 3 0.06
20 27 0.56
21 9 0.19
22 9 0.19
ACGTcount: A:0.72, C:0.03, G:0.25, T:0.00
Consensus pattern (20 bp):
GAAAAGAAAAAAGAGAGAAA
Found at i:1466253 original size:34 final size:34
Alignment explanation
Indices: 1466195--1466259 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
1466185 GCAAAATGAA
*
1466195 AAGAAAAAAGAGAGCAAAGAAAAAAAAAAGAGCG
1 AAGAAAAAAGAGAGAAAAGAAAAAAAAAAGAGCG
* *
1466229 AAGAGAAAAGA-AGAAAAGAGAAAAAGAAAGA
1 AAGAAAAAAGAGAGAAAAGA-AAAAAAAAAGA
1466260 AAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 7 0.26
34 20 0.74
ACGTcount: A:0.72, C:0.03, G:0.25, T:0.00
Consensus pattern (34 bp):
AAGAAAAAAGAGAGAAAAGAAAAAAAAAAGAGCG
Found at i:1469142 original size:100 final size:101
Alignment explanation
Indices: 1468966--1469157 Score: 221
Period size: 100 Copynumber: 1.9 Consensus size: 101
1468956 AAGACGTGAA
** *
1468966 CATTTGAGATTGTTTCTCTTAAAAAACAAATTTCGTCTCACTTGAGACTGTTTCCCATAGAAATA
1 CATTTGAGATTGTTTCTCTTAAAAAACAAATTTCGTCTCACTTGAGAC-GCATCCCATAGAAACA
* *
1469031 AAAATTTTGAAATTGTTT-CACTTGAAATTTTTTTCCT
65 AAAATTGTGAAATT-TTTGCACCTGAAATTTTTTTCCT
* * * * *
1469068 CATTTGAGCTTGTTTCTC-T-CAAAATAAATTTCGTCTCGCTTGAGAC-CATCCTCATTCGAAAC
1 CATTTGAGATTGTTTCTCTTAAAAAACAAATTTCGTCTCACTTGAGACGCATCC-CA-TAGAAAC
*
1469130 ACAAATTGTGAAATTTTTGCACCTGAAA
64 AAAAATTGTGAAATTTTTGCACCTGAAA
1469158 CAAAATTGAT
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
98 3 0.04
99 5 0.07
100 50 0.66
101 1 0.01
102 17 0.22
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (101 bp):
CATTTGAGATTGTTTCTCTTAAAAAACAAATTTCGTCTCACTTGAGACGCATCCCATAGAAACAA
AAATTGTGAAATTTTTGCACCTGAAATTTTTTTCCT
Found at i:1469238 original size:36 final size:36
Alignment explanation
Indices: 1469196--1469265 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
1469186 CCTAAAAAGG
*
1469196 TTTTGTCTCGCTTGAGACAATTTCTCTTGAAACAAA
1 TTTTGTCTCGCTTGAGACAATTTCTCATGAAACAAA
*
1469232 TTTTGTCTCGCTTGAGACAGTTTCTCATGAAACA
1 TTTTGTCTCGCTTGAGACAATTTCTCATGAAACA
1469266 TAAACCTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (36 bp):
TTTTGTCTCGCTTGAGACAATTTCTCATGAAACAAA
Found at i:1471414 original size:75 final size:76
Alignment explanation
Indices: 1471328--1471533 Score: 332
Period size: 75 Copynumber: 2.8 Consensus size: 76
1471318 ATTTTAAATA
1471328 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGATTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGATTTTAGTATTTTAATTAAGTTTTA
1471393 GGATA-TATTT
66 GGATATTATTT
* *
1471403 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTAATTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGATTTTAGTATTTTAATTAAGTTTTA
1471468 GGATATTATTT
66 GGATATTATTT
* *
1471479 TTATA-TTTATC-TT-TTTTAGGTAGTTTAGTTTAAATA-ATTTTAAGTGTTTTAATTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGATTTT-AGTATTTTAATTA
1471534 GGATTTAAGA
Statistics
Matches: 123, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
72 4 0.03
73 33 0.27
74 2 0.02
75 74 0.60
76 10 0.08
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.58
Consensus pattern (76 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGATTTTAGTATTTTAATTAAGTTTTA
GGATATTATTT
Found at i:1472178 original size:17 final size:18
Alignment explanation
Indices: 1472156--1472197 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
1472146 CTTTCAATTA
1472156 TTTATTTAATTATT-TCT
1 TTTATTTAATTATTATCT
*
1472173 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
1472191 TTTATTT
1 TTTATTT
1472198 TAAAAGTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1472251 original size:27 final size:27
Alignment explanation
Indices: 1472220--1472286 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
1472210 TTAAAAACCC
1472220 TTTTTTATTTTACTACTATTATTTATTA
1 TTTTTTATTTTAC-ACTATTATTTATTA
* *
1472248 TTTTATTATTTT-CCCTTTTATTTATTA
1 TTTT-TTATTTTACACTATTATTTATTA
* *
1472275 TTATCTATTTTA
1 TTTTTTATTTTA
1472287 TTTTATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
26 6 0.18
27 15 0.45
28 5 0.15
29 7 0.21
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTTTTATTTTACACTATTATTTATTA
Found at i:1472270 original size:20 final size:20
Alignment explanation
Indices: 1472245--1472294 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1472235 CTATTATTTA
* *
1472245 TTATTTTATTATTTTCCCTT
1 TTATTTTATTATTATCCATT
*
1472265 TTA-TTTATTATTATCTATT
1 TTATTTTATTATTATCCATT
1472284 TTATTTTATTA
1 TTATTTTATTA
1472295 AATCTTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTTTATTATTATCCATT
Found at i:1472285 original size:19 final size:19
Alignment explanation
Indices: 1472236--1472294 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1472226 ATTTTACTAC
* *
1472236 TATTATTTATTAT-TTTAT
1 TATTATCTATTTTATTTAT
* **
1472254 TATTTTCCCTTTTATTTAT
1 TATTATCTATTTTATTTAT
1472273 TATTATCTATTTTATTTTAT
1 TATTATCTATTTTA-TTTAT
1472293 TA
1 TA
1472295 AATCTTTTCA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
18 8 0.26
19 16 0.52
20 7 0.23
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTATCTATTTTATTTAT
Found at i:1476689 original size:21 final size:21
Alignment explanation
Indices: 1476665--1476712 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1476655 TTACAATTTT
1476665 GTCATTCTTACTCTTGCGGTG
1 GTCATTCTTACTCTTGCGGTG
1476686 GTCATTCTTACTCTTGCGGTG
1 GTCATTCTTACTCTTGCGGTG
1476707 GTCATT
1 GTCATT
1476713 TTGGGCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.44
Consensus pattern (21 bp):
GTCATTCTTACTCTTGCGGTG
Found at i:1480639 original size:17 final size:18
Alignment explanation
Indices: 1480617--1480658 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
1480607 CTTTCAATTA
1480617 TTTATTTAATTATT-TCT
1 TTTATTTAATTATTATCT
*
1480634 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
1480652 TTTATTT
1 TTTATTT
1480659 TAAAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1480760 original size:17 final size:19
Alignment explanation
Indices: 1480720--1480760 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
1480710 ATTAGTTTCC
*
1480720 CTTTTATTTATTATTATAT
1 CTTTTATTTATTATTAAAT
*
1480739 ATTTTA-TT-TTATTAAAT
1 CTTTTATTTATTATTAAAT
1480756 CTTTT
1 CTTTT
1480761 CAACTTTACC
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
17 12 0.63
18 2 0.11
19 5 0.26
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
CTTTTATTTATTATTAAAT
Found at i:1485056 original size:38 final size:38
Alignment explanation
Indices: 1485013--1485150 Score: 154
Period size: 38 Copynumber: 3.7 Consensus size: 38
1485003 ATAATGTTCG
* * *
1485013 ATTATTTAAAAATTTATATTCAATTAAAATTCAGATAT
1 ATTATTTACAAATTTATATTCAATTAAAATACAAATAT
* * * * *
1485051 GTTATTTACGAATTTATATTCAACTGAAATAGAAATAT
1 ATTATTTACAAATTTATATTCAATTAAAATACAAATAT
* **
1485089 ATTATTTACGAATTTATATTTGATT-AAATACAAATAT
1 ATTATTTACAAATTTATATTCAATTAAAATACAAATAT
*
1485126 ATTA-TTACAAATTTATATTCGATTA
1 ATTATTTACAAATTTATATTCAATTA
1485151 TTATACAATT
Statistics
Matches: 84, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
36 18 0.21
37 15 0.18
38 51 0.61
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (38 bp):
ATTATTTACAAATTTATATTCAATTAAAATACAAATAT
Found at i:1485245 original size:8 final size:8
Alignment explanation
Indices: 1485233--1485280 Score: 60
Period size: 8 Copynumber: 6.0 Consensus size: 8
1485223 TATGGTTAAA
*
1485233 CACAAGTA
1 CACAAGTT
1485241 CACAAGTT
1 CACAAGTT
*
1485249 CAAAAGTT
1 CACAAGTT
*
1485257 GACAAGTT
1 CACAAGTT
1485265 CACAAGTT
1 CACAAGTT
*
1485273 AACAAGTT
1 CACAAGTT
1485281 TTCACAATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.23
Consensus pattern (8 bp):
CACAAGTT
Found at i:1485268 original size:24 final size:24
Alignment explanation
Indices: 1485234--1485280 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1485224 ATGGTTAAAC
1485234 ACAAGTACACAAGTTCAA-AAGTTG
1 ACAAGTACACAAGTT-AACAAGTTG
*
1485258 ACAAGTTCACAAGTTAACAAGTT
1 ACAAGTACACAAGTTAACAAGTT
1485281 TTCACAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (24 bp):
ACAAGTACACAAGTTAACAAGTTG
Found at i:1488271 original size:26 final size:28
Alignment explanation
Indices: 1488219--1488272 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
1488209 ACAGAAGTCA
* *
1488219 AATTCGCAAAGCACGAATTTTATTTTCG
1 AATTCGCAAAGCACGAATATTAATTTCG
*
1488247 AATTCG-AAA-CATGAATATTAATTTCG
1 AATTCGCAAAGCACGAATATTAATTTCG
1488273 CAACACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 14 0.61
27 3 0.13
28 6 0.26
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (28 bp):
AATTCGCAAAGCACGAATATTAATTTCG
Found at i:1488816 original size:20 final size:20
Alignment explanation
Indices: 1488791--1488831 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1488781 GTGATTTTAG
*
1488791 TTTTCGTGTTGCGAATTTCA
1 TTTTCGAGTTGCGAATTTCA
*
1488811 TTTTCGAGTTGCGATTTTCA
1 TTTTCGAGTTGCGAATTTCA
1488831 T
1 T
1488832 GTTGCGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.51
Consensus pattern (20 bp):
TTTTCGAGTTGCGAATTTCA
Found at i:1490438 original size:42 final size:42
Alignment explanation
Indices: 1490333--1490480 Score: 188
Period size: 42 Copynumber: 3.5 Consensus size: 42
1490323 TCCCCACTTT
* * ** * *
1490333 GACACCGAGATCCATCAACCTCATCGAGCCTCTTCTCCACTTC
1 GACACCGAGAGCCATC-ACCTGATCGAGCCGATTCTACACCTC
* * * *
1490376 GACACTGAGATCCATTACCTGATCAAGCCGATTCTACACCTC
1 GACACCGAGAGCCATCACCTGATCGAGCCGATTCTACACCTC
*
1490418 GACACCGAGAGCCATCACCTGATCGAGTCGATTCTACACCTC
1 GACACCGAGAGCCATCACCTGATCGAGCCGATTCTACACCTC
1490460 GACACCGAGAGCCATCACCTG
1 GACACCGAGAGCCATCACCTG
1490481 TTCCATCACA
Statistics
Matches: 92, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 78 0.85
43 14 0.15
ACGTcount: A:0.26, C:0.37, G:0.16, T:0.20
Consensus pattern (42 bp):
GACACCGAGAGCCATCACCTGATCGAGCCGATTCTACACCTC
Found at i:1490605 original size:21 final size:21
Alignment explanation
Indices: 1490579--1490639 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1490569 ACCTCCACGG
1490579 GATGAGTTAGGTGCTTTACGT
1 GATGAGTTAGGTGCTTTACGT
* *
1490600 GATGAGGTCA-GTGTTTTACGT
1 GATGA-GTTAGGTGCTTTACGT
* *
1490621 GATGAGGTCGGTGCTTTAC
1 GATGAGTTAGGTGCTTTAC
1490640 CTCGACACCG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.03
21 28 0.88
22 3 0.09
ACGTcount: A:0.18, C:0.11, G:0.34, T:0.36
Consensus pattern (21 bp):
GATGAGTTAGGTGCTTTACGT
Found at i:1490763 original size:183 final size:183
Alignment explanation
Indices: 1490455--1490822 Score: 736
Period size: 183 Copynumber: 2.0 Consensus size: 183
1490445 TCGATTCTAC
1490455 ACCTCGACACCGAGAGCCATCACCTGTTCCATCACATCATCGAGCCTCTTCTCCAATATCACCTC
1 ACCTCGACACCGAGAGCCATCACCTGTTCCATCACATCATCGAGCCTCTTCTCCAATATCACCTC
1490520 ATGATAGTCGACCGAAAAAGATGCCACGATATTTATCTCCCCGTTCTCCACCTCCACGGGATGAG
66 ATGATAGTCGACCGAAAAAGATGCCACGATATTTATCTCCCCGTTCTCCACCTCCACGGGATGAG
1490585 TTAGGTGCTTTACGTGATGAGGTCAGTGTTTTACGTGATGAGGTCGGTGCTTT
131 TTAGGTGCTTTACGTGATGAGGTCAGTGTTTTACGTGATGAGGTCGGTGCTTT
1490638 ACCTCGACACCGAGAGCCATCACCTGTTCCATCACATCATCGAGCCTCTTCTCCAATATCACCTC
1 ACCTCGACACCGAGAGCCATCACCTGTTCCATCACATCATCGAGCCTCTTCTCCAATATCACCTC
1490703 ATGATAGTCGACCGAAAAAGATGCCACGATATTTATCTCCCCGTTCTCCACCTCCACGGGATGAG
66 ATGATAGTCGACCGAAAAAGATGCCACGATATTTATCTCCCCGTTCTCCACCTCCACGGGATGAG
1490768 TTAGGTGCTTTACGTGATGAGGTCAGTGTTTTACGTGATGAGGTCGGTGCTTT
131 TTAGGTGCTTTACGTGATGAGGTCAGTGTTTTACGTGATGAGGTCGGTGCTTT
1490821 AC
1 AC
1490823 GTGACAACAA
Statistics
Matches: 185, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
183 185 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (183 bp):
ACCTCGACACCGAGAGCCATCACCTGTTCCATCACATCATCGAGCCTCTTCTCCAATATCACCTC
ATGATAGTCGACCGAAAAAGATGCCACGATATTTATCTCCCCGTTCTCCACCTCCACGGGATGAG
TTAGGTGCTTTACGTGATGAGGTCAGTGTTTTACGTGATGAGGTCGGTGCTTT
Found at i:1490788 original size:21 final size:21
Alignment explanation
Indices: 1490762--1490826 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
1490752 ACCTCCACGG
1490762 GATGAGTTAGGTGCTTTACGT
1 GATGAGTTAGGTGCTTTACGT
* *
1490783 GATGAGGTCA-GTGTTTTACGT
1 GATGA-GTTAGGTGCTTTACGT
* *
1490804 GATGAGGTCGGTGCTTTACGT
1 GATGAGTTAGGTGCTTTACGT
1490825 GA
1 GA
1490827 CAACAATGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 1 0.03
21 32 0.89
22 3 0.08
ACGTcount: A:0.18, C:0.11, G:0.35, T:0.35
Consensus pattern (21 bp):
GATGAGTTAGGTGCTTTACGT
Found at i:1490889 original size:42 final size:41
Alignment explanation
Indices: 1490843--1490948 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 41
1490833 TGGTGCATGG
* *
1490843 CGTGATGAGGTAGG-GTCTTTATGTGGTGAGGTAGCTGTTTTA
1 CGTGATGA-GTAGGTGT-TTTACGTGGTGAGGTAGCTGCTTTA
** *
1490885 CGTGATGAAAATGGTGTTTTACGTGGTGAGGTATCTGCTTTA
1 CGTGATGAGTA-GGTGTTTTACGTGGTGAGGTAGCTGCTTTA
* *
1490927 CGTGATGATGTAGATGCTTTAC
1 CGTGATGA-GTAGGTGTTTTAC
1490949 ATGAGAATGT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
41 1 0.02
42 48 0.92
43 3 0.06
ACGTcount: A:0.20, C:0.09, G:0.33, T:0.38
Consensus pattern (41 bp):
CGTGATGAGTAGGTGTTTTACGTGGTGAGGTAGCTGCTTTA
Found at i:1490926 original size:21 final size:21
Alignment explanation
Indices: 1490902--1490948 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1490892 AAAATGGTGT
* **
1490902 TTTACGTGGTGAGGTATCTGC
1 TTTACGTGATGAGGTAGATGC
*
1490923 TTTACGTGATGATGTAGATGC
1 TTTACGTGATGAGGTAGATGC
1490944 TTTAC
1 TTTAC
1490949 ATGAGAATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40
Consensus pattern (21 bp):
TTTACGTGATGAGGTAGATGC
Found at i:1491350 original size:21 final size:21
Alignment explanation
Indices: 1491236--1491367 Score: 124
Period size: 21 Copynumber: 6.3 Consensus size: 21
1491226 GAAGAAGCCC
* *
1491236 GATCCACCTACCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
*
1491257 GATCCACCTCCCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
* * ** *
1491278 GATTCACTTGTCATCGTTCAA
1 GATCCACCTCCCATCGTTCAG
* *
1491299 GAGTCC-CATCCCATCGTTCAA
1 GA-TCCACCTCCCATCGTTCAG
*
1491320 GAGGCC-CCTCCCATCGTTCAG
1 GA-TCCACCTCCCATCGTTCAG
*
1491341 GATCCACCTCCCACCGTTCAG
1 GATCCACCTCCCATCGTTCAG
1491362 GATCCA
1 GATCCA
1491368 TATGACATTC
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
20 2 0.02
21 89 0.96
22 2 0.02
ACGTcount: A:0.21, C:0.37, G:0.16, T:0.26
Consensus pattern (21 bp):
GATCCACCTCCCATCGTTCAG
Found at i:1492969 original size:20 final size:20
Alignment explanation
Indices: 1492944--1492982 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1492934 TCAAGTTGCG
*
1492944 ATTTTCGCGTTGCGGATTTT
1 ATTTTCGCGTTGCGAATTTT
1492964 ATTTTCGCGTTGCGAATTT
1 ATTTTCGCGTTGCGAATTT
1492983 GAGTTACGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.15, G:0.23, T:0.49
Consensus pattern (20 bp):
ATTTTCGCGTTGCGAATTTT
Found at i:1492976 original size:34 final size:34
Alignment explanation
Indices: 1492899--1492978 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 34
1492889 AAAAATAAAA
* *
1492899 TTCGCGTTGCGATTTTTGTGTTGCGAATTTGAGT
1 TTCGCGTTGCGATTTTCGCGTTGCGAATTTGAGT
* ** * * *
1492933 ATCAAGTTGCGATTTTCGCGTTGCGGATTTTATT
1 TTCGCGTTGCGATTTTCGCGTTGCGAATTTGAGT
1492967 TTCGCGTTGCGA
1 TTCGCGTTGCGA
1492979 ATTTGAGTTA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.14, C:0.15, G:0.28, T:0.44
Consensus pattern (34 bp):
TTCGCGTTGCGATTTTCGCGTTGCGAATTTGAGT
Found at i:1495537 original size:24 final size:24
Alignment explanation
Indices: 1495510--1495555 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1495500 AAAATCCGAT
1495510 TATTGACCAAGATCAAAGTTCGGG
1 TATTGACCAAGATCAAAGTTCGGG
*
1495534 TATTGACCAAGATCAAATTTCG
1 TATTGACCAAGATCAAAGTTCG
1495556 AATACTGACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (24 bp):
TATTGACCAAGATCAAAGTTCGGG
Found at i:1495564 original size:24 final size:24
Alignment explanation
Indices: 1495513--1495564 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1495503 ATCCGATTAT
** *
1495513 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
1495537 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
1495561 TGAC
1 TGAC
1495565 TAATACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:1496513 original size:20 final size:20
Alignment explanation
Indices: 1496488--1496715 Score: 110
Period size: 20 Copynumber: 11.3 Consensus size: 20
1496478 AAATAAAAGC
1496488 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
*
1496508 TGTTGCG-AATTCAAAAATCG
1 TGTTGCGAAATT-AAAATTCG
* * *
1496528 AGTTGCGAAAATAAAATTCA
1 TGTTGCGAAATTAAAATTCG
* *
1496548 TGTTGCG-AATTAGAAAATCT
1 TGTTGCGAAATTA-AAATTCG
* ** *
1496568 TGTTACGAAAAGGAAACTT-G
1 TGTTGCG-AAATTAAAATTCG
* **
1496588 TGTTGCGAATTTAAAAACCG
1 TGTTGCGAAATTAAAATTCG
* *
1496608 CGTTGCG-AATTCAAAAATCG
1 TGTTGCGAAATT-AAAATTCG
* *
1496628 AGTTGCGAATTTAAAATTCCG
1 TGTTGCGAAATTAAAATT-CG
* *
1496649 TATTTCG-AA-TACCAAATTCG
1 TGTTGCGAAATTA--AAATTCG
* ** *
1496669 CGTTGCGAAATTGGAGTTCG
1 TGTTGCGAAATTAAAATTCG
*
1496689 TGTTGCGAATTTGAAAA-TCG
1 TGTTGCGAAATT-AAAATTCG
*
1496709 CGTTGCG
1 TGTTGCG
1496716 TAAAAGAAAT
Statistics
Matches: 150, Mismatches: 44, Indels: 28
0.68 0.20 0.13
Matches are distributed among these distances:
19 18 0.12
20 105 0.70
21 23 0.15
22 4 0.03
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:1496533 original size:40 final size:40
Alignment explanation
Indices: 1496489--1496643 Score: 145
Period size: 40 Copynumber: 3.9 Consensus size: 40
1496479 AATAAAAGCT
*
1496489 GTTGCGAAATTAAAATTCGTGTTGCGAATTCAAAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTTAAAAATCGA
* * **
1496529 GTTGCGAAAATAAAATTCATGTTGCGAA-TTAGAAAATCTT
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTTA-AAAATCGA
* ** * * *
1496569 GTTACGAAAAGGAAACTT-GTGTTGCGAATTTAAAAACCGC
1 GTTGCG-AAATTAAAATTCGTGTTGCGAATTTAAAAATCGA
* *
1496609 GTTGCG-AATTCAAAAATCGAGTTGCGAATTTAAAA
1 GTTGCGAAATT-AAAATTCGTGTTGCGAATTTAAAA
1496644 TTCCGTATTT
Statistics
Matches: 91, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
38 2 0.02
39 6 0.07
40 72 0.79
41 11 0.12
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGTGTTGCGAATTTAAAAATCGA
Found at i:1496674 original size:41 final size:40
Alignment explanation
Indices: 1496589--1496677 Score: 97
Period size: 41 Copynumber: 2.2 Consensus size: 40
1496579 GGAAACTTGT
* *
1496589 GTTGCGAATTTAAAAACCGCGTTGCGAATTCAAAAATCGA
1 GTTGCGAATTTAAAAACCGCATTGCGAATACAAAAATCGA
* * * * * *
1496629 GTTGCGAATTTAAAATTCCGTATTTCGAATACCAAATTCGC
1 GTTGCGAATTTAAAA-ACCGCATTGCGAATACAAAAATCGA
1496670 GTTGCGAA
1 GTTGCGAA
1496678 ATTGGAGTTC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 15 0.38
41 25 0.62
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (40 bp):
GTTGCGAATTTAAAAACCGCATTGCGAATACAAAAATCGA
Found at i:1496753 original size:20 final size:21
Alignment explanation
Indices: 1496720--1496779 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 21
1496710 GTTGCGTAAA
*
1496720 AGAAATTCGCATTGCAAATTC
1 AGAAATTCGAATTGCAAATTC
*
1496741 AGAAA-TCGAATTGCGAATTC
1 AGAAATTCGAATTGCAAATTC
* **
1496761 -CAAATTCGCGTTGCAAATT
1 AGAAATTCGAATTGCAAATT
1496780 TGGAAACTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 3 0.09
20 24 0.75
21 5 0.16
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (21 bp):
AGAAATTCGAATTGCAAATTC
Found at i:1497202 original size:17 final size:19
Alignment explanation
Indices: 1497170--1497208 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
1497160 CCACATAATC
1497170 TTTCTCTTTCTCTTTTTCA
1 TTTCTCTTTCTCTTTTTCA
*
1497189 TTTC-CTTT-TCTTTTTGA
1 TTTCTCTTTCTCTTTTTCA
1497206 TTT
1 TTT
1497209 TATTTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 4 0.21
19 4 0.21
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTCTCTTTCTCTTTTTCA
Found at i:1498730 original size:2 final size:2
Alignment explanation
Indices: 1498723--1498753 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1498713 AATATGAAGC
*
1498723 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1498754 AACCTCAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1500138 original size:22 final size:21
Alignment explanation
Indices: 1500102--1500142 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1500092 CAGTAATTAG
1500102 ATTATTTTATTTTATGTATTCA
1 ATTATTTTATTTTAT-TATTCA
1500124 ATTATTTT-TTGTTATTATT
1 ATTATTTTATT-TTATTATT
1500143 TTCGTAGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (21 bp):
ATTATTTTATTTTATTATTCA
Found at i:1500850 original size:22 final size:21
Alignment explanation
Indices: 1500814--1500854 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1500804 CAGTAATTAG
1500814 ATTATTTTATTTTATGTATTCA
1 ATTATTTTATTTTAT-TATTCA
1500836 ATTATTTT-TTGTTATTATT
1 ATTATTTTATT-TTATTATT
1500855 TTCGTAGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (21 bp):
ATTATTTTATTTTATTATTCA
Found at i:1501368 original size:19 final size:20
Alignment explanation
Indices: 1501326--1501369 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1501316 CTCTTTTAAT
* *
1501326 ATTTTATTTTATAAATAAAC
1 ATTTAATTTCATAAATAAAC
*
1501346 ATTTAATTTCATAGATAAA-
1 ATTTAATTTCATAAATAAAC
1501365 ATTTA
1 ATTTA
1501370 TTAAAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTTAATTTCATAAATAAAC
Found at i:1502304 original size:16 final size:16
Alignment explanation
Indices: 1502268--1502310 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1502258 CTTTTCTTAT
*
1502268 TTTATTTATAATGTTA
1 TTTATTTATTATGTTA
1502284 TTTATTTATTAT-TTA
1 TTTATTTATTATGTTA
*
1502299 TATTATATATTA
1 T-TTATTTATTA
1502311 GATAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTATTTATTATGTTA
Found at i:1509668 original size:42 final size:43
Alignment explanation
Indices: 1509606--1509688 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 43
1509596 ATGCACGTCA
*
1509606 GTTTCTAAAGCAGCAGTTTGTTGACCTTCATTA-TTCCAAAAC
1 GTTTCTAAAGCAGCAATTTGTTGACCTTCATTATTTCCAAAAC
* *
1509648 GTTTCTAAAGCTGCAATTTGTTGACTTTCATTATTTCCAAA
1 GTTTCTAAAGCAGCAATTTGTTGACCTTCATTATTTCCAAA
1509689 CTGCTCTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 30 0.81
43 7 0.19
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (43 bp):
GTTTCTAAAGCAGCAATTTGTTGACCTTCATTATTTCCAAAAC
Found at i:1510853 original size:15 final size:14
Alignment explanation
Indices: 1510837--1510879 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1510827 AATTAAAATA
1510837 AAATTATAAAATTT
1 AAATTATAAAATTT
*
1510851 AAATTGTAAAAATTT
1 AAATTAT-AAAATTT
*
1510866 AGATTACTAAAATT
1 AAATTA-TAAAATT
1510880 AAGACTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 6 0.25
15 17 0.71
16 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (14 bp):
AAATTATAAAATTT
Found at i:1510987 original size:13 final size:14
Alignment explanation
Indices: 1510969--1510998 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1510959 CAAATTAATA
1510969 TATATTTT-AAAAT
1 TATATTTTAAAAAT
1510982 TATATTTTAAAAAT
1 TATATTTTAAAAAT
1510996 TAT
1 TAT
1510999 TAAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATATTTTAAAAAT
Found at i:1511297 original size:82 final size:82
Alignment explanation
Indices: 1511160--1511323 Score: 328
Period size: 82 Copynumber: 2.0 Consensus size: 82
1511150 GAATCACTGA
1511160 TGTTGTGTTCTGTTATCGGCACAATCGACCGTTTTCCCATTAAATTATGGGCGTAACATTATGAG
1 TGTTGTGTTCTGTTATCGGCACAATCGACCGTTTTCCCATTAAATTATGGGCGTAACATTATGAG
1511225 ATTGGTGTAAATCTATG
66 ATTGGTGTAAATCTATG
1511242 TGTTGTGTTCTGTTATCGGCACAATCGACCGTTTTCCCATTAAATTATGGGCGTAACATTATGAG
1 TGTTGTGTTCTGTTATCGGCACAATCGACCGTTTTCCCATTAAATTATGGGCGTAACATTATGAG
1511307 ATTGGTGTAAATCTATG
66 ATTGGTGTAAATCTATG
1511324 ACCCACCGCA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (82 bp):
TGTTGTGTTCTGTTATCGGCACAATCGACCGTTTTCCCATTAAATTATGGGCGTAACATTATGAG
ATTGGTGTAAATCTATG
Found at i:1514599 original size:18 final size:18
Alignment explanation
Indices: 1514576--1514621 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1514566 ATTCATGCAT
1514576 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
1514594 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
1514612 TTATTTCATT
1 TTAGTTCATT
1514622 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:1516490 original size:276 final size:277
Alignment explanation
Indices: 1515948--1516502 Score: 1053
Period size: 276 Copynumber: 2.0 Consensus size: 277
1515938 TTCCCTTCTT
*
1515948 ATAACGTTGTTTGTACATTTTCAGTCTTCAAACAAAGCATTGCAAAGTTCTTACTAGAATCACGA
1 ATAACGTTGTTTGTACATTTTCAGTCTTCAAACAAAGCACTGCAAAGTTCTTACTAGAATCACGA
*
1516013 TCGGACAACGTCGTATATGACTCGGAACATATAATCGGGATCGTATCATTTGGTATCAGAGTTAG
66 TCGGACAACATCGTATATGACTCGGAACATATAATCGGGATCGTATCATTTGGTATCAGAGTTAG
1516078 CCGATTCAGTAAGCGTTCCGTATCATTTATTGAAGGCCATTCATGTTCTAGCAAGGGGACATGCA
131 CCGATTCAGTAAGCGTTCCGTATCATTTATTGAAGGCCATTCATGTTCTAGCAAGGGGACATGCA
1516143 ATAACCATCATTCAAACTTAGCATTCAAGGCCTTTATCATCTTTTGAAGGCTGATCATTTCTCAA
196 ATAACCATCATTCAAACTTAGCATTCAAGGCCTTTATCATCTTTTGAAGGCTGATCATTTCTCAA
1516208 GGAACAAGC-ATGAAGG
261 GGAACAAGCAATGAAGG
1516224 ATAACGTTGTTTGTACATTTTCAGTCTTCAAACAAAGCACTGCAAAGTTCTTACTAGAATCACGA
1 ATAACGTTGTTTGTACATTTTCAGTCTTCAAACAAAGCACTGCAAAGTTCTTACTAGAATCACGA
1516289 TCGGACAACATCGTATATGACTCGGAACATATAATCGGGATCGTATCATTTGGTATCAGAGTTAG
66 TCGGACAACATCGTATATGACTCGGAACATATAATCGGGATCGTATCATTTGGTATCAGAGTTAG
1516354 CCGATTCAGTAAGCGTTCCGTATCATTTATTGAAGGCCATTCATGTTCTAGCAAGGGGACATGCA
131 CCGATTCAGTAAGCGTTCCGTATCATTTATTGAAGGCCATTCATGTTCTAGCAAGGGGACATGCA
1516419 ATAACCATCATTCAAAACTTAGCATTCAAGGCCTTTATCATCTTTTGAAGGCTGAT-A-TTCTCA
196 ATAACCATCATTC-AAACTTAGCATTCAAGGCCTTTATCATCTTTTGAAGGCTGATCATTTCTCA
1516482 AGGGAACAAGCAATGAAGG
260 A-GGAACAAGCAATGAAGG
1516501 AT
1 AT
1516503 GATTTTATTT
Statistics
Matches: 274, Mismatches: 2, Indels: 5
0.98 0.01 0.02
Matches are distributed among these distances:
275 7 0.03
276 216 0.79
277 51 0.19
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (277 bp):
ATAACGTTGTTTGTACATTTTCAGTCTTCAAACAAAGCACTGCAAAGTTCTTACTAGAATCACGA
TCGGACAACATCGTATATGACTCGGAACATATAATCGGGATCGTATCATTTGGTATCAGAGTTAG
CCGATTCAGTAAGCGTTCCGTATCATTTATTGAAGGCCATTCATGTTCTAGCAAGGGGACATGCA
ATAACCATCATTCAAACTTAGCATTCAAGGCCTTTATCATCTTTTGAAGGCTGATCATTTCTCAA
GGAACAAGCAATGAAGG
Done.