Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 37
Found at i:2208853 original size:22 final size:22
Alignment explanation
Indices: 2208779--2208845 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
2208769 TTATGGACAT
2208779 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2208801 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2208823 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2208845 A
1 A
2208846 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:2209812 original size:2 final size:2
Alignment explanation
Indices: 2209805--2209834 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2209795 AGGATATTAA
2209805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2209835 TAAGTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2215670 original size:28 final size:28
Alignment explanation
Indices: 2215637--2215693 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
2215627 CTACCGGTGC
* *
2215637 TTTTAAGTATTGACTCGACAACATAATA
1 TTTTAAGCACTGACTCGACAACATAATA
2215665 TTTTAAGCACTGACTCGACAACATAATA
1 TTTTAAGCACTGACTCGACAACATAATA
2215693 T
1 T
2215694 AAATAAGGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.33
Consensus pattern (28 bp):
TTTTAAGCACTGACTCGACAACATAATA
Found at i:2217376 original size:2 final size:2
Alignment explanation
Indices: 2217371--2217445 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
2217361 ACACACACAC
2217371 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2217413 AT 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 AT A
2217446 GTGCGAGTGA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2222288 original size:22 final size:22
Alignment explanation
Indices: 2222263--2222305 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2222253 ATTAGAATGA
*
2222263 TAAATAAATATTTTATTTTTAC
1 TAAATAAATATTTAATTTTTAC
**
2222285 TAAATACGTATTTAATTTTTA
1 TAAATAAATATTTAATTTTTA
2222306 TACTAGTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (22 bp):
TAAATAAATATTTAATTTTTAC
Found at i:2224665 original size:24 final size:24
Alignment explanation
Indices: 2224635--2224708 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
2224625 TTTTTTCGTA
2224635 TTTTAAAATTTTATAAATTTATTT
1 TTTTAAAATTTTATAAATTTATTT
*
2224659 TTTTAAAATTTTATAAAATTA-TT
1 TTTTAAAATTTTATAAATTTATTT
* * * *
2224682 ATTTAGAATTTTGTAAATTTATCT
1 TTTTAAAATTTTATAAATTTATTT
2224706 TTT
1 TTT
2224709 AACATAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 19 0.45
24 23 0.55
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (24 bp):
TTTTAAAATTTTATAAATTTATTT
Found at i:2224691 original size:23 final size:23
Alignment explanation
Indices: 2224636--2224703 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
2224626 TTTTTCGTAT
*
2224636 TTTAAAATTTTATAAATTTATTTT
1 TTTAAAATTTTATAAATTTA-TTA
*
2224660 TTTAAAATTTTATAAAATTATTA
1 TTTAAAATTTTATAAATTTATTA
* *
2224683 TTTAGAATTTTGTAAATTTAT
1 TTTAAAATTTTATAAATTTAT
2224704 CTTTTAACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (23 bp):
TTTAAAATTTTATAAATTTATTA
Found at i:2224709 original size:23 final size:22
Alignment explanation
Indices: 2224635--2224710 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 22
2224625 TTTTTTCGTA
2224635 TTTTAAAATTTTATAAATTTATTT
1 TTTTAAAATTTTATAAATTTA--T
*
2224659 TTTTAAAATTTTATAAAATTAT
1 TTTTAAAATTTTATAAATTTAT
* *
2224681 TATTTAGAATTTTGTAAATTTAT
1 T-TTTAAAATTTTATAAATTTAT
2224704 CTTTTAA
1 -TTTTAA
2224711 CATAAAATCT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.04
23 22 0.49
24 21 0.47
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (22 bp):
TTTTAAAATTTTATAAATTTAT
Found at i:2224901 original size:3 final size:3
Alignment explanation
Indices: 2224893--2224920 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2224883 GGAAGCAGCT
2224893 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2224921 CAATGCTGGT
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:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2227870 original size:14 final size:14
Alignment explanation
Indices: 2227851--2227881 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2227841 ATTAAAATCG
*
2227851 AAATAAAAAAGAGT
1 AAATAAAAAAGAAT
2227865 AAATAAAAAAGAAT
1 AAATAAAAAAGAAT
2227879 AAA
1 AAA
2227882 GGAAAATTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (14 bp):
AAATAAAAAAGAAT
Found at i:2228644 original size:25 final size:25
Alignment explanation
Indices: 2228615--2228669 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 25
2228605 AAAATGACAT
2228615 ACTATTTCGAAAAT-AAT-AATAAAAA
1 ACTATTT-GAAAATAAATAAAT-AAAA
2228640 ACTA-TTGAAAATAAATAAATAAAA
1 ACTATTTGAAAATAAATAAATAAAA
2228664 ACTATT
1 ACTATT
2228670 AAAAATTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 6 0.22
24 13 0.48
25 8 0.30
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (25 bp):
ACTATTTGAAAATAAATAAATAAAA
Found at i:2228651 original size:23 final size:24
Alignment explanation
Indices: 2228623--2228675 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
2228613 ATACTATTTC
2228623 GAAAAT-AAT-AATAAAAAACTATT
1 GAAAATAAATAAAT-AAAAACTATT
2228646 GAAAATAAATAAATAAAAACTATT
1 GAAAATAAATAAATAAAAACTATT
*
2228670 AAAAAT
1 GAAAAT
2228676 TCAAAACAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 6 0.22
24 18 0.67
25 3 0.11
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (24 bp):
GAAAATAAATAAATAAAAACTATT
Found at i:2228937 original size:20 final size:20
Alignment explanation
Indices: 2228912--2228960 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
2228902 TTTTATTGTG
*
2228912 AGTGGAGGGAGACAAGGACT
1 AGTGGAGGCAGACAAGGACT
2228932 AGTGGAGGCAGACAAGGACT
1 AGTGGAGGCAGACAAGGACT
2228952 AGTGGAGGC
1 AGTGGAGGC
2228961 TTGGTGGCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.45, T:0.10
Consensus pattern (20 bp):
AGTGGAGGCAGACAAGGACT
Found at i:2229772 original size:170 final size:170
Alignment explanation
Indices: 2229585--2230174 Score: 1117
Period size: 170 Copynumber: 3.5 Consensus size: 170
2229575 TGCTGGTGGA
* *
2229585 CACGATATCCTTCGTCGTGAAGTTAAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAA
*
2229650 GTTGAAATTGGCTCTGAATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
66 GTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
2229715 ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
131 ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
*
2229755 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTTGAGTCCAATATCCTTCGTCGTGAA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAA
2229820 GTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
66 GTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
*
2229885 ATCTTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
131 ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
2229925 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAA
2229990 GTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
66 GTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
2230055 ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
131 ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
*
2230095 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTTGTGAA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAA
*
2230160 GTTGAAATTGACTCT
66 GTTGAAATTGGCTCT
2230175 AGTTAGAACC
Statistics
Matches: 411, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
170 411 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (170 bp):
CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAA
GTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
Found at i:2229779 original size:46 final size:44
Alignment explanation
Indices: 2229712--2229827 Score: 130
Period size: 44 Copynumber: 2.6 Consensus size: 44
2229702 CTTTGAATTG
* *
2229712 GATATCCTTCG-CTGTAAAGTTGAAATCCAAT-GTTGTTTGTGAG-CAC
1 GATATCCTTCGTC-GTGAAGTTGAAAT-C-ATGGATGTTT-TGAGTC-C
*
2229758 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTTGAGTCC
1 GATATCCTTCGTCGTGAAGTTGAAATCATGGATGTTTTGAGTCC
*
2229802 AATATCCTTCGTCGTGAAGTTGAAAT
1 GATATCCTTCGTCGTGAAGTTGAAAT
2229828 TGGCTCTGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
44 31 0.49
45 8 0.13
46 23 0.37
47 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (44 bp):
GATATCCTTCGTCGTGAAGTTGAAATCATGGATGTTTTGAGTCC
Found at i:2231013 original size:6 final size:6
Alignment explanation
Indices: 2230981--2231021 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
2230971 ACCCTAAACA
*
2230981 TTTTTC TCTTTT- TTGTTC TTTTT- TTTTTC TTTTTC TTTTTC
1 TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
2231022 GACTTAGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 8 0.27
6 18 0.60
7 4 0.13
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:2231019 original size:12 final size:11
Alignment explanation
Indices: 2230981--2231021 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
2230971 ACCCTAAACA
2230981 TTTTTCTCTTTT
1 TTTTTCT-TTTT
*
2230993 TTGTTCTTTTT
1 TTTTTCTTTTT
2231004 TTTTTCTTTTT
1 TTTTTCTTTTT
2231015 CTTTTTC
1 -TTTTTC
2231022 GACTTAGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 14 0.54
12 12 0.46
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:2237759 original size:39 final size:39
Alignment explanation
Indices: 2237705--2237784 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
2237695 TTAACAGTAG
* *
2237705 ATGCAGCTTTCCCTTTGGTAGAGGATGAGTCAC-CGGGTA
1 ATGCAACTTTCCCTTTAGTAGAGGATGAGTC-CTCGGGTA
*
2237744 ATGCAACTTTCCCTTTAGTAGCGGATGAGTCCTCGGGTA
1 ATGCAACTTTCCCTTTAGTAGAGGATGAGTCCTCGGGTA
2237783 AT
1 AT
2237785 ACTCCGGGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.03
39 36 0.97
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (39 bp):
ATGCAACTTTCCCTTTAGTAGAGGATGAGTCCTCGGGTA
Found at i:2240357 original size:17 final size:18
Alignment explanation
Indices: 2240337--2240381 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
2240327 AAAAAGTTAG
2240337 TAAAAAAAATAAAC-AAA
1 TAAAAAAAATAAACGAAA
*
2240354 TAAAAAAAAT-GACGAAA
1 TAAAAAAAATAAACGAAA
*
2240371 GAAAAAAAATA
1 TAAAAAAAATA
2240382 CAAAAAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 2 0.08
17 22 0.92
ACGTcount: A:0.78, C:0.04, G:0.07, T:0.11
Consensus pattern (18 bp):
TAAAAAAAATAAACGAAA
Found at i:2242056 original size:22 final size:23
Alignment explanation
Indices: 2242028--2242078 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
2242018 CATACATTTC
2242028 GAAAATAAT-AATAAAAACTATT
1 GAAAATAATAAATAAAAACTATT
2242050 GAAAATAATAAATAAAAACTATT
1 GAAAATAATAAATAAAAACTATT
*
2242073 AAAAAT
1 GAAAAT
2242079 TCAAAACAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (23 bp):
GAAAATAATAAATAAAAACTATT
Found at i:2242110 original size:17 final size:17
Alignment explanation
Indices: 2242053--2242112 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
2242043 AACTATTGAA
*
2242053 AATAATAAATAAAAACT
1 AATAATAAATAAAAAAT
* * *
2242070 ATTAA-AAATTCAAAACAG
1 AATAATAAA-T-AAAAAAT
2242088 AA-AATAAATAAAAAAT
1 AATAATAAATAAAAAAT
2242104 AATAATAAA
1 AATAATAAA
2242113 AATAAAGAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
16 10 0.31
17 14 0.44
18 8 0.25
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.22
Consensus pattern (17 bp):
AATAATAAATAAAAAAT
Found at i:2242118 original size:23 final size:23
Alignment explanation
Indices: 2242029--2242114 Score: 70
Period size: 23 Copynumber: 3.7 Consensus size: 23
2242019 ATACATTTCG
**
2242029 AAAATAATAATAAAAACT-ATTG
1 AAAATAATAATAAAAACTAATAA
*
2242051 AAAATAATAAATAAAAACTATTAA
1 AAAATAAT-AATAAAAACTAATAA
* *
2242075 AAATTCAA-AACAGAAAA-TAAATAA
1 AAAAT-AATAATA-AAAACT-AATAA
2242099 AAAATAATAATAAAAA
1 AAAATAATAATAAAAA
2242115 TAAAGAAACT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
22 8 0.16
23 20 0.40
24 20 0.40
25 2 0.04
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (23 bp):
AAAATAATAATAAAAACTAATAA
Found at i:2242340 original size:19 final size:20
Alignment explanation
Indices: 2242316--2242363 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
2242306 TTTTATTGTG
*
2242316 AGTGGAGGGAGAC-AGGACT
1 AGTGGAGGCAGACAAGGACT
2242335 AGTGGAGGCAGACAAGGACT
1 AGTGGAGGCAGACAAGGACT
2242355 AGTGGAGGC
1 AGTGGAGGC
2242364 TTGGTGGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.31, C:0.12, G:0.46, T:0.10
Consensus pattern (20 bp):
AGTGGAGGCAGACAAGGACT
Found at i:2245419 original size:35 final size:35
Alignment explanation
Indices: 2245380--2245451 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
2245370 TAAACTAAAA
*
2245380 AATAAATCTATTCATCAAATCACAT-TACTTATTAT
1 AATAAATCTATTCACCAAATCACATGT-CTTATTAT
*
2245415 AATAAATCTATTCACCAAATGACATGTCTTATTAT
1 AATAAATCTATTCACCAAATCACATGTCTTATTAT
2245450 AA
1 AA
2245452 ATTAGATCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 33 0.97
36 1 0.03
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.38
Consensus pattern (35 bp):
AATAAATCTATTCACCAAATCACATGTCTTATTAT
Found at i:2249015 original size:17 final size:16
Alignment explanation
Indices: 2248981--2249023 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
2248971 GTTAATTGTT
* *
2248981 AAAAATAAATATTTTA
1 AAAAATATATATTATA
2248997 AAAAATATATAATTATA
1 AAAAATATAT-ATTATA
*
2249014 AATAATATAT
1 AAAAATATAT
2249024 GAATGTAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAAATATATATTATA
Found at i:2255500 original size:12 final size:12
Alignment explanation
Indices: 2255483--2255507 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2255473 TATCATCAAG
2255483 GAATTTATGAGT
1 GAATTTATGAGT
2255495 GAATTTATGAGT
1 GAATTTATGAGT
2255507 G
1 G
2255508 CTCTTATCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (12 bp):
GAATTTATGAGT
Found at i:2256498 original size:186 final size:186
Alignment explanation
Indices: 2256184--2256554 Score: 742
Period size: 186 Copynumber: 2.0 Consensus size: 186
2256174 TAGCTTTAAA
2256184 AATTCATGAAAAAACATCCATTGACAAATTCAGCAAACTTTTTCCAATTCCATTCAGTCCAAGCA
1 AATTCATGAAAAAACATCCATTGACAAATTCAGCAAACTTTTTCCAATTCCATTCAGTCCAAGCA
2256249 GACTTTTCTCTGCTGACTATTTATCCTCAATTAGTAACTGCTTGAAGGTAATTTTTTATGCATCT
66 GACTTTTCTCTGCTGACTATTTATCCTCAATTAGTAACTGCTTGAAGGTAATTTTTTATGCATCT
2256314 ATACATCGTTATTGAGAAAATTAAGGTTTAAATATGTTCTAAAGTTTTTTTGGTAG
131 ATACATCGTTATTGAGAAAATTAAGGTTTAAATATGTTCTAAAGTTTTTTTGGTAG
2256370 AATTCATGAAAAAACATCCATTGACAAATTCAGCAAACTTTTTCCAATTCCATTCAGTCCAAGCA
1 AATTCATGAAAAAACATCCATTGACAAATTCAGCAAACTTTTTCCAATTCCATTCAGTCCAAGCA
2256435 GACTTTTCTCTGCTGACTATTTATCCTCAATTAGTAACTGCTTGAAGGTAATTTTTTATGCATCT
66 GACTTTTCTCTGCTGACTATTTATCCTCAATTAGTAACTGCTTGAAGGTAATTTTTTATGCATCT
2256500 ATACATCGTTATTGAGAAAATTAAGGTTTAAATATGTTCTAAAGTTTTTTTGGTA
131 ATACATCGTTATTGAGAAAATTAAGGTTTAAATATGTTCTAAAGTTTTTTTGGTA
2256555 TGTAACATGA
Statistics
Matches: 185, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
186 185 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (186 bp):
AATTCATGAAAAAACATCCATTGACAAATTCAGCAAACTTTTTCCAATTCCATTCAGTCCAAGCA
GACTTTTCTCTGCTGACTATTTATCCTCAATTAGTAACTGCTTGAAGGTAATTTTTTATGCATCT
ATACATCGTTATTGAGAAAATTAAGGTTTAAATATGTTCTAAAGTTTTTTTGGTAG
Found at i:2261659 original size:63 final size:63
Alignment explanation
Indices: 2261579--2261698 Score: 188
Period size: 63 Copynumber: 1.9 Consensus size: 63
2261569 TAATGACATC
* *
2261579 TTTTAATTTAAAATATTCAAAA-GATATAAATTCATTTTACTATACAAATTTAAATAGATATTA
1 TTTTAATTTAAAATATTCAAAAGGATAT-AATTAATTTTAATATACAAATTTAAATAGATATTA
**
2261642 TTTTAATTTAAAATATTCAAAAGGATATAATTAATTTTAATATTTAAATTTAAATAG
1 TTTTAATTTAAAATATTCAAAAGGATATAATTAATTTTAATATACAAATTTAAATAG
2261699 GTAACAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
63 47 0.90
64 5 0.10
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (63 bp):
TTTTAATTTAAAATATTCAAAAGGATATAATTAATTTTAATATACAAATTTAAATAGATATTA
Found at i:2261679 original size:34 final size:32
Alignment explanation
Indices: 2261579--2261682 Score: 101
Period size: 34 Copynumber: 3.2 Consensus size: 32
2261569 TAATGACATC
2261579 TTTTAATTTAAAATATTCAAAAGATATAAATTCA
1 TTTTAATTTAAAATATTCAAAAGATAT-AATT-A
* *
2261613 TTTTACTATACAAAT-TT-AAATAG--AT-ATTA
1 TTTTAATTTA-AAATATTCAAA-AGATATAATTA
2261642 TTTTAATTTAAAATATTCAAAAGGATATAATTAA
1 TTTTAATTTAAAATATTCAAAA-GATATAATT-A
2261676 TTTTAAT
1 TTTTAAT
2261683 ATTTAAATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
28 4 0.07
29 12 0.21
30 7 0.12
32 4 0.07
33 6 0.11
34 20 0.35
35 4 0.07
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (32 bp):
TTTTAATTTAAAATATTCAAAAGATATAATTA
Found at i:2269212 original size:22 final size:22
Alignment explanation
Indices: 2269160--2269212 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
2269150 GAAACATGTC
*
2269160 AAAA-TATAATAATTTTAAAAA
1 AAAATTATAATAATTTAAAAAA
*
2269181 AAAGTATATAA-AATTTAAAAAA
1 AAAAT-TATAATAATTTAAAAAA
2269203 TAAAATTATA
1 -AAAATTATA
2269213 TATTATATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 3 0.12
22 14 0.54
23 9 0.35
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAATTATAATAATTTAAAAAA
Found at i:2271134 original size:2 final size:2
Alignment explanation
Indices: 2271127--2271157 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2271117 AGTCTTCCTG
2271127 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2271158 GATTGGATGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2272079 original size:2 final size:2
Alignment explanation
Indices: 2272074--2272369 Score: 152
Period size: 2 Copynumber: 156.5 Consensus size: 2
2272064 TATATTTTTT
2272074 TA TA TA T- TA T- TA TA TA -A TA TGA GT- TA TA TA GTA TA TA GTA
1 TA TA TA TA TA TA TA TA TA TA TA T-A -TA TA TA TA -TA TA TA -TA
* *
2272114 TA TA TA GTG TA T- TA TA GTA TA TA TA TA T- TA TA TA GTA TG TA
1 TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA
*
2272155 T- TA TA TA TA T- TA TA -A TA TA T- TG TA TA T- TA TA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2272190 TA T- TA TA GTA TA GTA TA TA TA T- TA TA T- TA T- TA T- TA TA GTA
1 TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* *
2272230 TA TA TT TA T- TA TA TA T- TA TA T- TA GT- TA TG TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* *
2272268 CTA TA GTA TA TA TA TA TA TT TA TA T- TA TA TA T- TA CTT TA TA
1 -TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
2272309 TA TA GTA TA TA -A TA T- TA TT TA TA TA T- TA T- TA T- 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
2272347 T- TA TA T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2272370 TTATTACAAT
Statistics
Matches: 230, Mismatches: 17, Indels: 94
0.67 0.05 0.28
Matches are distributed among these distances:
1 32 0.14
2 173 0.75
3 24 0.10
4 1 0.00
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2272115 original size:26 final size:24
Alignment explanation
Indices: 2272100--2272298 Score: 75
Period size: 23 Copynumber: 8.2 Consensus size: 24
2272090 ATATGAGTTA
2272100 TATAGTATATAGTAT-ATATAGTGTA
1 TATAGTATATA-TATAATATAGT-TA
*
2272125 TTATAGTATATATATATTATATAGTATG
1 -TATAGTATATATATA--ATATAGT-TA
*
2272153 TATTA-TATATATTATAATATA-TTG
1 TA-TAGTATATA-TATAATATAGTTA
2272177 TATA-T-TATAT-TAATAT--TATA
1 TATAGTATATATATAATATAGT-TA
*
2272197 GTATAGTATATATATTATATTA-TTA
1 -TATAGTATATATATAATA-TAGTTA
*
2272222 TTATAGTATATATTTATTATATA-TTA
1 -TATAGTATATA--TATAATATAGTTA
* * *
2272248 TATTAGT-TATGTATTATATA-CTA
1 TA-TAGTATATATATAATATAGTTA
*
2272271 TAGTA-TATATATATATTTATA-TTA
1 TA-TAGTATATATATA-ATATAGTTA
2272295 TATA
1 TATA
2272299 TTACTTTATA
Statistics
Matches: 144, Mismatches: 12, Indels: 37
0.75 0.06 0.19
Matches are distributed among these distances:
19 1 0.01
20 7 0.05
21 5 0.03
22 6 0.04
23 31 0.22
24 16 0.11
25 23 0.16
26 26 0.18
27 15 0.10
28 14 0.10
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.52
Consensus pattern (24 bp):
TATAGTATATATATAATATAGTTA
Found at i:2272184 original size:118 final size:109
Alignment explanation
Indices: 2272060--2272369 Score: 278
Period size: 113 Copynumber: 2.7 Consensus size: 109
2272050 TTATTATATA
2272060 ATATTATATTTTTTTATATATTATTATATAATATGAGTTATATAGTATATAGTATATATAGTGTA
1 ATATTATATTTTTTTATATA-TATTATATAATAT-A-TTATATA-TATATAGTATATATA-T-TA
* *
2272125 TTATAGTATATATATATTATATAGTATGTATTATA-TATATTATAATATATTGT
60 TTATA-TATATATATATTATATAGTATATACTATAGTATA-TAT-ATATATT-T
* * *
2272178 ATATTATATTAATATTATAGTATAGTATATATATTATATTAT-TAT-TATAGTATATAT-TTATT
1 ATATTATATT-TTTTTATA-TATA-T-TATATAATATATTATATATATATAGTATATATATTATT
* *
2272240 ATATAT-TATATTAGTTATGTATTATATACTATAGTATATATATATATTT
62 ATATATATATA-TA-TTATATAGTATATACTATAGTATATATATATATTT
* * *
2272289 ATATTATATATTACTTTATATATAGTATATAATATTATT-TATATAT-TATTAT-TAT-TTATTA
1 ATATTATAT-TT-TTTTATATATATTATATAATA-TATTATATATATATAGTATATATATTATTA
2272350 TATTATATATATATATATAT
63 TA-TATATATATAT-TATAT
2272370 TTATTACAAT
Statistics
Matches: 163, Mismatches: 14, Indels: 38
0.76 0.07 0.18
Matches are distributed among these distances:
109 21 0.13
110 21 0.13
111 23 0.14
112 18 0.11
113 25 0.15
114 5 0.03
116 12 0.07
117 1 0.01
118 12 0.07
119 12 0.07
120 4 0.02
121 9 0.06
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (109 bp):
ATATTATATTTTTTTATATATATTATATAATATATTATATATATATAGTATATATATTATTATAT
ATATATATATTATATAGTATATACTATAGTATATATATATATTT
Found at i:2272337 original size:7 final size:7
Alignment explanation
Indices: 2272051--2272370 Score: 184
Period size: 7 Copynumber: 44.6 Consensus size: 7
2272041 CGTTCGAGAT
2272051 TATTATA
1 TATTATA
*
2272058 TAATATTA
1 TATTA-TA
2272066 TATT-T-
1 TATTATA
*
2272071 TTTTATA
1 TATTATA
2272078 TATTATTA
1 TATTA-TA
*
2272086 TATAATA
1 TATTATA
2272093 TGAGTTATA
1 T-A-TTATA
*
2272102 TAGTATA
1 TATTATA
*
2272109 TAGTATA
1 TATTATA
*
2272116 TA-TAGTG
1 TATTA-TA
2272123 TATTATA
1 TATTATA
2272130 GTATATATA
1 -TAT-TATA
2272139 TATTATA
1 TATTATA
* *
2272146 TAGTATG
1 TATTATA
2272153 TATTATA
1 TATTATA
2272160 TA-TAT-
1 TATTATA
*
2272165 TATAATA
1 TATTATA
*
2272172 TATTGTA
1 TATTATA
2272179 TA-T-TA
1 TATTATA
2272184 TATTA-A
1 TATTATA
2272190 TATTATA
1 TATTATA
2272197 GTA-TAGTA
1 -TATTA-TA
2272205 TATATATTA
1 TAT-TA-TA
2272214 TATTAT-
1 TATTATA
2272220 TATTATA
1 TATTATA
*
2272227 GTATATATT
1 -TAT-TATA
2272236 TATTATA
1 TATTATA
2272243 TATTATA
1 TATTATA
*
2272250 TTAGTTATG
1 -TA-TTATA
2272259 TATTATA
1 TATTATA
2272266 TACTATAGTA
1 TA-T-TA-TA
2272276 TATATATA
1 TAT-TATA
2272284 TATT-TA
1 TATTATA
2272290 TATTATA
1 TATTATA
*
2272297 TATTACTT
1 TATTA-TA
2272305 TA-TATA
1 TATTATA
*
2272311 TAGTATA
1 TATTATA
*
2272318 TAATAT-
1 TATTATA
2272324 TATTTATA
1 TA-TTATA
2272332 TATTAT-
1 TATTATA
*
2272338 TATTATT
1 TATTATA
2272345 TATTATA
1 TATTATA
2272352 T-TATATA
1 TAT-TATA
2272359 TATATATA
1 TAT-TATA
2272367 TATT
1 TATT
2272371 TATTACAATA
Statistics
Matches: 252, Mismatches: 26, Indels: 70
0.72 0.07 0.20
Matches are distributed among these distances:
5 9 0.04
6 41 0.16
7 112 0.44
8 57 0.23
9 29 0.12
10 4 0.02
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (7 bp):
TATTATA
Found at i:2272396 original size:26 final size:26
Alignment explanation
Indices: 2272277--2272389 Score: 80
Period size: 26 Copynumber: 4.5 Consensus size: 26
2272267 ACTATAGTAT
* * *
2272277 ATATATATATTTATATTATATATTACT
1 ATATATATATATATA-TATTTATTACA
* *
2272304 TTATATATAGTATATA-ATATTATT--T
1 ATATATATA-TATATATAT-TTATTACA
*
2272329 ATATAT-TAT-TAT-TATTTATTATA
1 ATATATATATATATATATTTATTACA
*
2272352 TTATATATATATATATATTTATTACA
1 ATATATATATATATATATTTATTACA
2272378 ATAT-TAT-TATAT
1 ATATATATATATAT
2272390 TTGTATTAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
21 5 0.07
22 5 0.07
23 6 0.09
24 10 0.14
25 12 0.17
26 15 0.21
27 12 0.17
28 5 0.07
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.57
Consensus pattern (26 bp):
ATATATATATATATATATTTATTACA
Found at i:2272397 original size:58 final size:58
Alignment explanation
Indices: 2272287--2272406 Score: 140
Period size: 58 Copynumber: 2.1 Consensus size: 58
2272277 ATATATATAT
* *
2272287 TTATATTATATATTACTTTATATATAGTATATAATATTATTTATATATTATTATTATTTA
1 TTATATTATATATTACTATATATATAGTATACAATATTATTTATATATTATTA--ATTTA
* *
2272347 TTATATTATATA-TA-TATATATAT-TTATTACAATATTA-TTATATTTGTATTAATTTA
1 TTATATTATATATTACTATATATATAGTA-TACAATATTATTTATATAT-TATTAATTTA
2272403 TTAT
1 TTAT
2272407 TTTAGGTTCA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
56 9 0.17
57 9 0.17
58 22 0.41
59 2 0.04
60 12 0.22
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (58 bp):
TTATATTATATATTACTATATATATAGTATACAATATTATTTATATATTATTAATTTA
Found at i:2272407 original size:11 final size:12
Alignment explanation
Indices: 2272139--2272407 Score: 79
Period size: 11 Copynumber: 22.3 Consensus size: 12
2272129 AGTATATATA
*
2272139 TATTATATAGTAT
1 TATTATAT-TTAT
*
2272152 GTATTATATATAT
1 -TATTATATTTAT
2272165 TATAATATATTGTA-
1 TAT--TATATT-TAT
*
2272179 TATTATA-TTAA
1 TATTATATTTAT
* *
2272190 TATTATAGTATAG
1 TATTATA-TTTAT
2272203 TATATATATTATAT
1 TAT-TATATT-TAT
* *
2272217 TATTAT-TATAG
1 TATTATATTTAT
2272228 TA-TATATTTAT
1 TATTATATTTAT
2272239 TA-TATATTATAT
1 TATTATATT-TAT
* *
2272251 TAGT-TATGTAT
1 TATTATATTTAT
*
2272262 TATATACTATAGTAT
1 TAT-TA-TAT-TTAT
2272277 ATATATATATTTA-
1 -TAT-TATATTTAT
*
2272290 TATTATATATTAC
1 TATTATAT-TTAT
* *
2272303 T-TTATATATAG
1 TATTATATTTAT
*
2272314 TA-TATA-ATAT
1 TATTATATTTAT
*
2272324 TATT-TATATAT
1 TATTATATTTAT
2272335 TATTATTATTTAT
1 TATTA-TATTTAT
*
2272348 TA-TATTATATAT
1 TATTA-TATTTAT
2272360 ATATATATATTTAT
1 -TAT-TATATTTAT
*
2272374 TA-CA-A--TAT
1 TATTATATTTAT
*
2272382 TATTATATTT-G
1 TATTATATTTAT
2272393 TATTA-ATTTAT
1 TATTATATTTAT
2272404 TATT
1 TATT
2272408 TTAGGTTCAA
Statistics
Matches: 201, Mismatches: 23, Indels: 65
0.70 0.08 0.22
Matches are distributed among these distances:
8 5 0.02
9 1 0.00
10 18 0.09
11 59 0.29
12 39 0.19
13 26 0.13
14 36 0.18
15 11 0.05
16 6 0.03
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (12 bp):
TATTATATTTAT
Found at i:2274709 original size:45 final size:45
Alignment explanation
Indices: 2274574--2274702 Score: 215
Period size: 45 Copynumber: 2.9 Consensus size: 45
2274564 TATAAAATCT
*
2274574 CTTACCATTT-ATCTCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTGTTC-CATAAGCTCGTAAGCTTATTTTACCAATATA
* *
2274619 CTTACCTTTTGTACCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAATATA
2274664 CTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACC
1 CTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACC
2274703 TGTATACCAT
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
45 77 0.99
46 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:2274916 original size:59 final size:59
Alignment explanation
Indices: 2274796--2274917 Score: 163
Period size: 59 Copynumber: 2.1 Consensus size: 59
2274786 CTAACCCGAG
* * ** *
2274796 TATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAGTCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGTCCCAAA
* ** *
2274855 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTATTCCCAAA
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGTCCCAAA
2274914 TATG
1 TATG
2274918 CAGACTGCTG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (59 bp):
TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGTCCCAAA
Found at i:2279837 original size:9 final size:9
Alignment explanation
Indices: 2279823--2279916 Score: 71
Period size: 10 Copynumber: 9.8 Consensus size: 9
2279813 GGCTGCTGGA
2279823 AACCGGTTT
1 AACCGGTTT
2279832 AACCGGTTT
1 AACCGGTTT
2279841 AACCGGTTTT
1 AACCGG-TTT
2279851 CAACCGGTTCT
1 -AACCGGTT-T
*
2279862 GACCGGTTT
1 AACCGGTTT
*
2279871 CAACCGGTTCG
1 -AACCGGTT-T
*
2279882 AACCAGTTT
1 AACCGGTTT
* *
2279891 GACCGGTCTG
1 AACCGGT-TT
*
2279901 AATCGGTTT
1 AACCGGTTT
*
2279910 GACCGGT
1 AACCGGT
2279917 CTGACCCGAC
Statistics
Matches: 66, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
9 27 0.41
10 32 0.48
11 7 0.11
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:2279857 original size:20 final size:20
Alignment explanation
Indices: 2279823--2279890 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
2279813 GGCTGCTGGA
2279823 AACCGGTTT-AACCGGTT-T
1 AACCGGTTTCAACCGGTTCT
2279841 AACCGGTTTTCAACCGGTTCT
1 AACCGG-TTTCAACCGGTTCT
* *
2279862 GACCGGTTTCAACCGGTTCG
1 AACCGGTTTCAACCGGTTCT
*
2279882 AACCAGTTT
1 AACCGGTTT
2279891 GACCGGTCTG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.14
19 3 0.07
20 28 0.65
21 6 0.14
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (20 bp):
AACCGGTTTCAACCGGTTCT
Found at i:2279897 original size:19 final size:20
Alignment explanation
Indices: 2279853--2279920 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 20
2279843 CCGGTTTTCA
* *
2279853 ACCGGTTCTG-ACCGGTTTCA
1 ACCGGTTCTGAACCAGTTT-G
2279873 ACCGGTTC-GAACCAGTTTG
1 ACCGGTTCTGAACCAGTTTG
* *
2279892 ACCGG-TCTGAATCGGTTTG
1 ACCGGTTCTGAACCAGTTTG
2279911 ACCGG-TCTGA
1 ACCGGTTCTGA
2279921 CCCGACCCGA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 2 0.05
19 25 0.60
20 15 0.36
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (20 bp):
ACCGGTTCTGAACCAGTTTG
Found at i:2279907 original size:29 final size:30
Alignment explanation
Indices: 2279852--2279908 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
2279842 ACCGGTTTTC
* *
2279852 AACCGGTTCTGACCGGTTTCAACCGGTTCG
1 AACCAGTTCTGACCGGTCTCAACCGGTTCG
* *
2279882 AACCAGTT-TGACCGGTCTGAATCGGTT
1 AACCAGTTCTGACCGGTCTCAACCGGTT
2279909 TGACCGGTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 16 0.70
30 7 0.30
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (30 bp):
AACCAGTTCTGACCGGTCTCAACCGGTTCG
Found at i:2279940 original size:17 final size:17
Alignment explanation
Indices: 2279918--2279956 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2279908 TTGACCGGTC
2279918 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
2279935 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
2279952 TGACC
1 TGACC
2279957 GTTACTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:2287173 original size:22 final size:22
Alignment explanation
Indices: 2287145--2287209 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
2287135 TGACTGGTCT
2287145 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
2287167 GACCCGACCCGACCGTTGATCC
1 GACCCGACCCGACCGTTGACCC
*
2287189 GACTCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
2287210 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:2290569 original size:22 final size:22
Alignment explanation
Indices: 2290541--2290585 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2290531 TTGTCGAGTT
2290541 TTCTATGTTAAAAGTTATAAGA
1 TTCTATGTTAAAAGTTATAAGA
2290563 TTCTATGTTAAAAGTTATAAGA
1 TTCTATGTTAAAAGTTATAAGA
2290585 T
1 T
2290586 GATTCGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (22 bp):
TTCTATGTTAAAAGTTATAAGA
Found at i:2295512 original size:30 final size:31
Alignment explanation
Indices: 2295465--2295544 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 31
2295455 TCGAAAGTGA
* *
2295465 TGGCA-GTGACATGTCATCAC-TTTAGA-ATG
1 TGGCATGTGACATATCATCACATTGA-ACATG
*
2295494 TGGCATGTGGCATATCATCACATTGAACATG
1 TGGCATGTGACATATCATCACATTGAACATG
*
2295525 TGAG-ATGTGCCATATCATCA
1 TG-GCATGTGACATATCATCA
2295545 GTTTTGACAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
29 5 0.12
30 14 0.33
31 23 0.53
32 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (31 bp):
TGGCATGTGACATATCATCACATTGAACATG
Found at i:2304105 original size:12 final size:12
Alignment explanation
Indices: 2304075--2304107 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2304065 ACAACATATT
2304075 ATAATAATT-AGC
1 ATAAT-ATTAAGC
2304087 ATAATATTAAGC
1 ATAATATTAAGC
2304099 ATAATATTA
1 ATAATATTA
2304108 CTTCCCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 3 0.15
12 17 0.85
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (12 bp):
ATAATATTAAGC
Found at i:2304602 original size:84 final size:83
Alignment explanation
Indices: 2304498--2304759 Score: 341
Period size: 84 Copynumber: 3.1 Consensus size: 83
2304488 ACTCTTTAGT
* *
2304498 AAGTTGAGAAGATAAATCAGGGTTTATTTCGGCAGAAGATCTCCAAGCAGCAACATTAGAATATT
1 AAGTTGAGAAGGTAAATCAGGGTTTATTTCGACAGAAGATCTCCAAGCAGCAACATTAGAATATT
2304563 TATCCTCCAATTTCTTGAC
66 TATCCT-CAATTTCTTGAC
* * * * *
2304582 AAGTTGAGAAGGCAAGTCAGGATTGATTTCGACAGAAGATCTCCAAGCAGCAACATTAGCATATT
1 AAGTTGAGAAGGTAAATCAGGGTTTATTTCGACAGAAGATCTCCAAGCAGCAACATTAGAATATT
* * *
2304647 CATCCTCGAGTTCTTTGAC
66 TATCCTCAATTTC-TTGAC
*
2304666 AAGTTGAG-AGGATAATTC-GGGATTT-TTATCGACAGAAGATCTCCAAGCAGCAACATTAGAAT
1 AAGTTGAGAAGG-TAAATCAGGG-TTTATT-TCGACAGAAGATCTCCAAGCAGCAACATTAGAAT
*
2304728 ATTTATCCTCAAGTTCCTTGAC
63 ATTTATCCTCAA-TTTCTTGAC
2304750 AAGTTGAGAA
1 AAGTTGAGAA
2304760 AACTCTTTCA
Statistics
Matches: 153, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
83 12 0.08
84 138 0.90
85 3 0.02
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (83 bp):
AAGTTGAGAAGGTAAATCAGGGTTTATTTCGACAGAAGATCTCCAAGCAGCAACATTAGAATATT
TATCCTCAATTTCTTGAC
Found at i:2310844 original size:20 final size:20
Alignment explanation
Indices: 2310819--2310892 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
2310809 TTTTCCCAAT
*
2310819 TCGCAATGCGAATAAATAAA
1 TCGCAACGCGAATAAATAAA
**
2310839 TCGCAACGCGAATTGGGA-AAA
1 TCGCAACGCGAA-T-AAATAAA
* * *
2310860 TCGCAATGCAAATAAGTAAA
1 TCGCAACGCGAATAAATAAA
2310880 TCGCAACGCGAAT
1 TCGCAACGCGAAT
2310893 TGGGAAAATC
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
20 26 0.63
21 14 0.34
22 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAATAAA
Found at i:2310862 original size:21 final size:21
Alignment explanation
Indices: 2310836--2310911 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
2310826 GCGAATAAAT
2310836 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* * ** *
2310857 AAATCGCAATGC-AAATAAGT
1 AAATCGCAACGCGAATTGGGA
2310877 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
2310898 AAATCGCAATGCGA
1 AAATCGCAACGCGA
2310912 TACTGACTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:2310864 original size:41 final size:41
Alignment explanation
Indices: 2310819--2310911 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
2310809 TTTTCCCAAT
2310819 TCGCAATGCGAATAAATAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAATAAATCGCAACGCGAATTGGGAAAA
* *
2310860 TCGCAATGCAAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAATAAATCGCAACGCGAATTGGGAAAA
2310901 TCGCAATGCGA
1 TCGCAATGCGA
2310912 TACTGACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAATAAATCGCAACGCGAATTGGGAAAA
Found at i:2310925 original size:20 final size:20
Alignment explanation
Indices: 2310900--2311034 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
2310890 AATTGGGAAA
2310900 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
2310920 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * **
2310940 ATCGCAATGCGATAATAAAAA
1 ATCGCAATGCGATACT-GACT
* * *
2310961 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
2310981 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
2311001 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
2311021 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
2311035 TTTCAAAGCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
19 2 0.02
20 69 0.72
21 25 0.26
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:2310944 original size:61 final size:61
Alignment explanation
Indices: 2310897--2311028 Score: 183
Period size: 61 Copynumber: 2.2 Consensus size: 61
2310887 GCGAATTGGG
* * * *
2310897 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAA
* * * *
2310958 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAA
*
2311019 ATAATCGCAA
1 AAAATCGCAA
2311029 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAA
Found at i:2311230 original size:22 final size:22
Alignment explanation
Indices: 2311202--2311245 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2311192 CACTCTCTCA
2311202 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2311224 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2311246 TATCTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2311534 original size:20 final size:20
Alignment explanation
Indices: 2311509--2311546 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2311499 CGATTCTCTC
2311509 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
2311529 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
2311547 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:2312887 original size:18 final size:18
Alignment explanation
Indices: 2312866--2312910 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2312856 TCCACTTCGG
*
2312866 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
2312884 GAGCTATCACTTCACCCA
1 GAGCCATCACCTCACCCA
2312902 GAGCCATCA
1 GAGCCATCA
2312911 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2313444 original size:19 final size:20
Alignment explanation
Indices: 2313390--2313456 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
2313380 TAGTTTTATT
* *
2313390 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2313410 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
2313430 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
2313449 TCGCAACG
1 TCGCAACG
2313457 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2313502 original size:19 final size:19
Alignment explanation
Indices: 2313390--2313510 Score: 92
Period size: 19 Copynumber: 6.6 Consensus size: 19
2313380 TAGTTTTATT
* **
2313390 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
2313410 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
2313430 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2313449 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
2313463 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
2313481 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2313500 TCGCAATGCGA
1 TCGCAACGCGA
2313511 TTTGTGTTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 18 0.21
19 26 0.31
20 24 0.29
21 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2313608 original size:20 final size:19
Alignment explanation
Indices: 2313517--2313620 Score: 87
Period size: 19 Copynumber: 5.7 Consensus size: 19
2313507 GCGATTTGTG
*
2313517 TTTCGCGTTGCGAT-TTCA
1 TTTCGCGTTGCGATAGTCA
2313535 TTTCGCGTTGCG--A-T--
1 TTTCGCGTTGCGATAGTCA
**
2313549 TTT-GTCGTTGCGATTTTCA
1 TTTCG-CGTTGCGATAGTCA
* * *
2313568 TTTCGCATTGTGATAGCCA
1 TTTCGCGTTGCGATAGTCA
2313587 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATAGTCA
2313607 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
2313621 TTTAAGTTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
13 1 0.01
14 10 0.15
16 1 0.01
17 1 0.01
18 12 0.18
19 26 0.38
20 17 0.25
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.42
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:2314077 original size:19 final size:19
Alignment explanation
Indices: 2314055--2314122 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
2314045 ATCGCAACGA
2314055 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2314074 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2314093 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
2314107 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
2314123 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:2314135 original size:52 final size:52
Alignment explanation
Indices: 2314024--2314122 Score: 162
Period size: 52 Copynumber: 1.9 Consensus size: 52
2314014 CAAGAGGCCC
* ***
2314024 AAATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGA
2314076 AAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGA
2314123 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13
Consensus pattern (52 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGA
Found at i:2314198 original size:20 final size:20
Alignment explanation
Indices: 2314141--2314198 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
2314131 TCGCATTGCG
* *
2314141 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
2314161 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
2314181 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
2314199 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:2315285 original size:24 final size:24
Alignment explanation
Indices: 2315258--2315311 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2315248 GTATTCGAAA
* *
2315258 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
2315282 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
2315306 TTTGAT
1 TTTGAT
2315312 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:2315503 original size:12 final size:12
Alignment explanation
Indices: 2315486--2315510 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2315476 ATATAATCCT
2315486 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2315498 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2315510 G
1 G
2315511 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2317077 original size:21 final size:21
Alignment explanation
Indices: 2317011--2317077 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2317001 GTGAATCGGG
*
2317011 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2317031 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2317053 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2317074 CTCT
1 CTCT
2317078 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2317096 original size:42 final size:41
Alignment explanation
Indices: 2317011--2317133 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
2317001 GTGAATCGGG
* * * * *
2317011 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
2317053 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
2317095 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
2317134 TGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:2319217 original size:33 final size:33
Alignment explanation
Indices: 2319160--2319258 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
2319150 ACGAGATAAT
*
2319160 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
2319194 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
2319227 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
2319259 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:2319252 original size:19 final size:19
Alignment explanation
Indices: 2319135--2319319 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
2319125 TCTTTTGGTT
*
2319135 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
2319154 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
2319174 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
2319192 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
2319208 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
2319226 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2319241 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
2319261 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2319280 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2319299 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2319318 GA
1 GA
2319320 TTTTGGTTTC
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 62 0.45
20 45 0.33
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2319273 original size:39 final size:38
Alignment explanation
Indices: 2319230--2319319 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
2319220 GCGACCAGAC
2319230 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
2319269 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
2319307 AATCGCAATGCGA
1 AATCGCAACGCGA
2319320 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:2319348 original size:19 final size:19
Alignment explanation
Indices: 2319315--2319395 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
2319305 AAAATCGCAA
**
2319315 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
2319334 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
2319353 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
2319367 TGCGATAGTTATTTTCGCGT
1 TGCGATTTTTA-TTTCGCGT
2319387 TGCGATTTT
1 TGCGATTTT
2319396 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 22 0.44
20 12 0.24
ACGTcount: A:0.11, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:2319925 original size:20 final size:20
Alignment explanation
Indices: 2319900--2319952 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2319890 GCGCTATGTA
2319900 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
2319920 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
2319940 TATCTCGTTGCGA
1 AATCGCGTTGCGA
2319953 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:2319986 original size:20 final size:20
Alignment explanation
Indices: 2319961--2320014 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2319951 GATTTTGTAT
2319961 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
2319981 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
2320001 TATCGCATTGCGAT
1 TATCGCATTGCGAT
2320015 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:2319999 original size:61 final size:61
Alignment explanation
Indices: 2319901--2320017 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
2319891 CGCTATGTAA
* * * * *
2319901 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
2319962 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
2320018 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:2320033 original size:61 final size:61
Alignment explanation
Indices: 2319901--2320035 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
2319891 CGCTATGTAA
* * * * * ** *
2319901 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
2319962 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
2320024 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
2320036 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:2322754 original size:65 final size:65
Alignment explanation
Indices: 2322673--2322813 Score: 264
Period size: 65 Copynumber: 2.2 Consensus size: 65
2322663 AGTTAAGTTA
2322673 TTTGAGTTTCTATACAATTTTTTTATAATTATTTTATAGCATTATGATAAGGATTGATTTTGATT
1 TTTGAGTTTCTATACAATTTTTTTATAATTATTTTATAGCATTATGATAAGGATTGATTTTGATT
*
2322738 TTTGAGTTTCTATACAATTTTTTTATAATTATTTTATAGTATTATGATAAGGATTGATTTTGATT
1 TTTGAGTTTCTATACAATTTTTTTATAATTATTTTATAGCATTATGATAAGGATTGATTTTGATT
*
2322803 TTTGATTTTCT
1 TTTGAGTTTCT
2322814 CTAACCATAT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 74 1.00
ACGTcount: A:0.28, C:0.04, G:0.12, T:0.56
Consensus pattern (65 bp):
TTTGAGTTTCTATACAATTTTTTTATAATTATTTTATAGCATTATGATAAGGATTGATTTTGATT
Found at i:2322938 original size:26 final size:28
Alignment explanation
Indices: 2322894--2322948 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
2322884 ATATATCAAA
2322894 TACAATATAAAATTAT-AA-AATATATT
1 TACAATATAAAATTATAAAGAATATATT
* * *
2322920 TACAATATTATATTTTAAAGAATATATT
1 TACAATATAAAATTATAAAGAATATATT
2322948 T
1 T
2322949 TGAAGGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 13 0.54
27 2 0.08
28 9 0.38
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (28 bp):
TACAATATAAAATTATAAAGAATATATT
Found at i:2324067 original size:478 final size:477
Alignment explanation
Indices: 2323162--2324594 Score: 2512
Period size: 478 Copynumber: 3.0 Consensus size: 477
2323152 GGACTTAAAT
* * *
2323162 TGAAGGTTAAATTGAAGAAATAAGAAAATCATGAAGAAA-TGAGGGATTAAATTGAAAAATTAAA
1 TGAAGTTTGAATTGAAGAAATAAGAAAATCAT-AAAAAATTGAGGGATTAAATTGAAAAATTAAA
2323226 AAACTATTATCAAAAAGATGAATTGAAAGCACATATGTATTTTACTATAGTTTAGGAGCATGTGA
65 AAACTATTATCAAAAAGATGAATTGAAAGCACATATGTATTTTACTATAGTTTAGGAGCATGTGA
2323291 TTCAAATTTGGTTAAAAACGGACTTAAAATGAAGGAGGAATTGAAGGAATAATGAAATCGATAAC
130 TTCAAATTTGGTTAAAAACGGACTTAAAATGAAGGAGGAATTGAAGGAATAATGAAATCGATAAC
* *
2323356 TAAATCGCAAAATTGTCAAAATAGGCAATCACATTTTTTATTTTTCGAGTAACTGGAAATTTTTA
195 TAAATCGCAAAACTGTCAAAATAGGCAATCACATTTTTTATTTTTCGAGTAACTTGAAATTTTTA
*
2323421 AATTTCAACTCAAAAATCGAATTGATAATTTGAGTTGACTCGAATAACTCAAAATTAGGGGAAAA
260 AATTTCAACTCAAAAATCGAATTGATAATTTGAGTTGACTCGAATAACTCAAAATTA-GGAAAAA
* * *
2323486 AAGCGATTTTTTAAGTTGATACGAGTTTTGCTCACCCCTAACTTAAATTACAATAAAATATGAAT
324 AATCGATTTTTCAAGTCGATACGAGTTTTGCTCACCCCTAACTTAAATTACAATAAAATATGAAT
**
2323551 ATTAATACATGCTTTGTCTCTTTTGATAAATGAAAACACTGTAATATAAAGGGTTAGATAATATT
389 ATTAATACATGCTTTGTCTCTTTTGATAAATGAAAACACTGTAATATAAAGGGAGAGATAATATT
2323616 TGATGTATTATTAATGAATTAGAA
454 TGATGTATTATTAATGAATTAGAA
* *
2323640 TGAAGTTTGAATTGAATAAATAAGAAAATCATAAAAAATTGAGGGATTAAATTGAAAAATTTAAA
1 TGAAGTTTGAATTGAAGAAATAAGAAAATCATAAAAAATTGAGGGATTAAATTGAAAAATTAAAA
2323705 AACTATTATCAAAAAGATGAATTGAAAGCACATATGTATTTTACTATAGTTTAGGAGCATGTGAT
66 AACTATTATCAAAAAGATGAATTGAAAGCACATATGTATTTTACTATAGTTTAGGAGCATGTGAT
*
2323770 TCAAATTTGGTTAAAAACGGACTTAAAATGAAGGAGGAATTGAAGGAATAATGAAATCGGTAACT
131 TCAAATTTGGTTAAAAACGGACTTAAAATGAAGGAGGAATTGAAGGAATAATGAAATCGATAACT
2323835 AAATCGCAAAACTGTCAAAATAGGCAATCACATTTTTTATTTTTCGAGTAACTTGAAATTTTTAA
196 AAATCGCAAAACTGTCAAAATAGGCAATCACATTTTTTATTTTTCGAGTAACTTGAAATTTTTAA
2323900 ATTTCAACTCAAAAATCGAATTGATAATTTGAGTTGACTCGAATAACTCAAAATTAGGAAAAAAA
261 ATTTCAACTCAAAAATCGAATTGATAATTTGAGTTGACTCGAATAACTCAAAATTAGGAAAAAAA
**
2323965 TTTAATTTTTCAAGTCGATACGAGTTTTGCTCACCCCTAACTTAAATTACAATAAAATATGAATA
326 -TCGATTTTTCAAGTCGATACGAGTTTTGCTCACCCCTAACTTAAATTACAATAAAATATGAATA
2324030 TTAATACATGCTTTGTCTCTTTTGATAAATGAAAACACTGTAATATAAAGGGAGAGATAATATTT
390 TTAATACATGCTTTGTCTCTTTTGATAAATGAAAACACTGTAATATAAAGGGAGAGATAATATTT
2324095 GATGTATTATTAATGAATTAGAA
455 GATGTATTATTAATGAATTAGAA
* * * * *
2324118 TGAAGTTTGAATTGAAGAAATAAGAAATTTATGAAAATTTGAGGGACTAAATTGAAAAATTAAAA
1 TGAAGTTTGAATTGAAGAAATAAGAAAATCATAAAAAATTGAGGGATTAAATTGAAAAATTAAAA
*
2324183 AACTATTATAAAAAAGATGAATTGAAAGCACATATGTATTTTACTATAGTTTAGGAGCATGTGAT
66 AACTATTATCAAAAAGATGAATTGAAAGCACATATGTATTTTACTATAGTTTAGGAGCATGTGAT
* ** *
2324248 TTAAATTTGGTTAAAAAAAAGACTTAAAATGAAAGAGGAATTGAAGGAATAATGAAATC-ATGAA
131 TCAAATTTGGTT-AAAAACGGACTTAAAATGAAGGAGGAATTGAAGGAATAATGAAATCGAT-AA
*
2324312 CTAAATCGCAAAACTGTCAAAATAGGCAATCACATTTTTGATTTTTCGAGTAAC-TGAAATTTTT
194 CTAAATCGCAAAACTGTCAAAATAGGCAATCACATTTTTTATTTTTCGAGTAACTTGAAATTTTT
* *
2324376 AAATTTCAACTCAAAAATCGAATTGATAATTTGAGTTGACTCGAATAACTCTAAATTAAGAAAAA
259 AAATTTCAACTCAAAAATCGAATTGATAATTTGAGTTGACTCGAATAACTCAAAATTAGGAAAAA
*
2324441 AATCGATTTTTCAAGTCAATACGAGTTTTGCTCACCCCTAACTTAAATTACAATAAAATATGAAT
324 AATCGATTTTTCAAGTCGATACGAGTTTTGCTCACCCCTAACTTAAATTACAATAAAATATGAAT
* *
2324506 ATTAATACATGCTTTGTCTCTTTTGATAAATGAAAACATTGTAATATAAAGGGCGAGATAATATT
389 ATTAATACATGCTTTGTCTCTTTTGATAAATGAAAACACTGTAATATAAAGGGAGAGATAATATT
2324571 TGATGTATTATTAATGAATTAGAA
454 TGATGTATTATTAATGAATTAGAA
2324595 GATGATATAT
Statistics
Matches: 914, Mismatches: 37, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
477 160 0.18
478 656 0.72
479 98 0.11
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.32
Consensus pattern (477 bp):
TGAAGTTTGAATTGAAGAAATAAGAAAATCATAAAAAATTGAGGGATTAAATTGAAAAATTAAAA
AACTATTATCAAAAAGATGAATTGAAAGCACATATGTATTTTACTATAGTTTAGGAGCATGTGAT
TCAAATTTGGTTAAAAACGGACTTAAAATGAAGGAGGAATTGAAGGAATAATGAAATCGATAACT
AAATCGCAAAACTGTCAAAATAGGCAATCACATTTTTTATTTTTCGAGTAACTTGAAATTTTTAA
ATTTCAACTCAAAAATCGAATTGATAATTTGAGTTGACTCGAATAACTCAAAATTAGGAAAAAAA
TCGATTTTTCAAGTCGATACGAGTTTTGCTCACCCCTAACTTAAATTACAATAAAATATGAATAT
TAATACATGCTTTGTCTCTTTTGATAAATGAAAACACTGTAATATAAAGGGAGAGATAATATTTG
ATGTATTATTAATGAATTAGAA
Found at i:2325242 original size:21 final size:22
Alignment explanation
Indices: 2325213--2325255 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2325203 AGTTTTTAAA
*
2325213 AAAGGTTTTTT-TTATATTTTT
1 AAAGATTTTTTATTATATTTTT
*
2325234 AAAGATTTTTTATTTTATTTTT
1 AAAGATTTTTTATTATATTTTT
2325256 GAGTTTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AAAGATTTTTTATTATATTTTT
Found at i:2329960 original size:3 final size:3
Alignment explanation
Indices: 2329952--2329976 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2329942 TAACCTTAGA
2329952 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
2329977 TTCATTCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2337864 original size:20 final size:20
Alignment explanation
Indices: 2337841--2337884 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2337831 AATTATTAAA
*
2337841 TTATTATTATAATGATATTT
1 TTATTATTATAATCATATTT
* **
2337861 TTATTTTTATTTTCATATTT
1 TTATTATTATAATCATATTT
2337881 TTAT
1 TTAT
2337885 ATAATCTCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (20 bp):
TTATTATTATAATCATATTT
Found at i:2349105 original size:31 final size:30
Alignment explanation
Indices: 2349067--2349151 Score: 134
Period size: 31 Copynumber: 2.8 Consensus size: 30
2349057 TTTACCATTG
*
2349067 AATTTTAAATAAAATACTAATTTGATCTCTA
1 AATTTTAAATAAAATATTAATTTGATCT-TA
*
2349098 AATTTTAAATAAAATATTATTTTTGATCTTA
1 AATTTTAAATAAAATATTA-ATTTGATCTTA
2349129 AATTTTAAATAAAATATTAATTT
1 AATTTTAAATAAAATATTAATTT
2349152 AACTTTTAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
30 3 0.06
31 39 0.78
32 8 0.16
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (30 bp):
AATTTTAAATAAAATATTAATTTGATCTTA
Found at i:2352829 original size:6 final size:6
Alignment explanation
Indices: 2352818--2352845 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2352808 AAGTCGTCAT
2352818 TAGAGA TAGAGA TAGAGA TAGAGA TAGA
1 TAGAGA TAGAGA TAGAGA TAGAGA TAGA
2352846 TAAGGAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18
Consensus pattern (6 bp):
TAGAGA
Found at i:2353566 original size:21 final size:21
Alignment explanation
Indices: 2353526--2353579 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
2353516 CGATTTACAT
*
2353526 ATTCGCATTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
* **
2353547 GTTCGCGTTGCGATTTTCCAA
1 ATTCGCGTTGCGATAGTCCAA
2353568 ATT--CGTTGCGAT
1 ATTCGCGTTGCGAT
2353580 GTCTAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 9 0.32
21 19 0.68
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (21 bp):
ATTCGCGTTGCGATAGTCCAA
Found at i:2354446 original size:21 final size:21
Alignment explanation
Indices: 2354421--2354492 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
2354411 TTTGGAATAA
2354421 ATCGCAACGCGAACTTCGATT
1 ATCGCAACGCGAACTTCGATT
* *
2354442 ATCGCAA--CGAACTTCAAATAA
1 ATCGCAACGCGAACTTC-GAT-T
* * *
2354463 ATCACAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGATT
2354484 ATCGCAACG
1 ATCGCAACG
2354493 AATTTAGAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
19 8 0.21
20 2 0.05
21 21 0.54
22 1 0.03
23 7 0.18
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGATT
Found at i:2354533 original size:21 final size:21
Alignment explanation
Indices: 2354504--2354556 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2354494 ATTTAGAAAA
* *
2354504 TCGCATTGCGATAGTCGACGT
1 TCGCGTTGCGAGAGTCGACGT
*
2354525 TCGCGTTGCGAGAGTCGATGT
1 TCGCGTTGCGAGAGTCGACGT
2354546 TCGCGTTGCGA
1 TCGCGTTGCGA
2354557 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.15, C:0.23, G:0.34, T:0.28
Consensus pattern (21 bp):
TCGCGTTGCGAGAGTCGACGT
Found at i:2359735 original size:18 final size:18
Alignment explanation
Indices: 2359712--2359746 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2359702 CTAATAGGTT
2359712 TATATTTCAAGTGTATAG
1 TATATTTCAAGTGTATAG
*
2359730 TATATTTCAAGTTTATA
1 TATATTTCAAGTGTATA
2359747 TTTCCTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (18 bp):
TATATTTCAAGTGTATAG
Found at i:2367437 original size:20 final size:20
Alignment explanation
Indices: 2367399--2367438 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2367389 ATCCCGATTT
**
2367399 TACCGGTTTTCAGTTGGTTC
1 TACCGGTTTTCAGCCGGTTC
2367419 TACCGGTTTTCAGCCGGTTC
1 TACCGGTTTTCAGCCGGTTC
2367439 ATTACTAGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.25, G:0.25, T:0.40
Consensus pattern (20 bp):
TACCGGTTTTCAGCCGGTTC
Found at i:2370191 original size:26 final size:26
Alignment explanation
Indices: 2370155--2370210 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
2370145 CTGGGAAATC
*
2370155 CTCCATCCCACTTTCGCTTTTCAGAT
1 CTCCATACCACTTTCGCTTTTCAGAT
*
2370181 CTCCATACCACTTTCGCTTTTCGGAT
1 CTCCATACCACTTTCGCTTTTCAGAT
2370207 CTCC
1 CTCC
2370211 TTTGGTAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.14, C:0.39, G:0.09, T:0.38
Consensus pattern (26 bp):
CTCCATACCACTTTCGCTTTTCAGAT
Found at i:2378036 original size:124 final size:124
Alignment explanation
Indices: 2377816--2378059 Score: 461
Period size: 124 Copynumber: 2.0 Consensus size: 124
2377806 GCAATTGTTG
2377816 AAATATGGTAAGGGTAAATTACCATATTTAGTCATTGTACTTTAAAGTATTTATAAGATTAGTCC
1 AAATATGGTAAGGGTAAATTACCATATTTAGTCATTGTACTTTAAAGTATTTATAAGATTAGTCC
2377881 TTAAGCCTCAACTATAAATACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAGCTAGA
66 TTAAGCCTCAACTATAAATACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAGCTAGA
** *
2377940 AAATATGGTAAGGGTAAATTACCATATTTAGTCATTGTACTTTAGGGTATTTATAAGATTAGTCT
1 AAATATGGTAAGGGTAAATTACCATATTTAGTCATTGTACTTTAAAGTATTTATAAGATTAGTCC
2378005 TTAAGCCTCAACTATAAATACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAGC
66 TTAAGCCTCAACTATAAATACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAGC
2378060 ATTCTAGCTT
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
124 117 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.34
Consensus pattern (124 bp):
AAATATGGTAAGGGTAAATTACCATATTTAGTCATTGTACTTTAAAGTATTTATAAGATTAGTCC
TTAAGCCTCAACTATAAATACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAGCTAGA
Found at i:2383724 original size:27 final size:25
Alignment explanation
Indices: 2383683--2383733 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
2383673 AAGGGAAATT
*
2383683 AAGTTTGTAGCTAGACTATTCAAAAAA
1 AAGTTTGTAGATAGAC-ATT-AAAAAA
2383710 AAGTTTGTAGATAGACATTAAAAA
1 AAGTTTGTAGATAGACATTAAAAA
2383734 CATAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.22
26 3 0.13
27 15 0.65
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (25 bp):
AAGTTTGTAGATAGACATTAAAAAA
Found at i:2401198 original size:2 final size:2
Alignment explanation
Indices: 2401191--2401241 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2401181 TGCATTAGTG
2401191 TA TA TA TA 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 TA TA TA TA
2401233 TA TA TA TA T
1 TA TA TA TA T
2401242 GTGCATTAGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2409914 original size:39 final size:38
Alignment explanation
Indices: 2409860--2409973 Score: 155
Period size: 34 Copynumber: 3.1 Consensus size: 38
2409850 AAAGTCAAGT
* *
2409860 CTTCACCAAAGAGTAGTAAAGCAAATCCATTTTGTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCA-TCTGTAAGC
2409899 CTTCACCAAAGAGTAGTGAAGC--A-CCATCT-TAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATCTGTAAGC
**
2409933 CTTCACGGAAGAGTAGTGAAGCAAATCCATCTGTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATCTGTAAGC
2409971 CTT
1 CTT
2409974 TAGAGCAAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
34 25 0.37
35 2 0.03
36 4 0.06
37 7 0.10
38 8 0.12
39 21 0.31
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (38 bp):
CTTCACCAAAGAGTAGTGAAGCAAATCCATCTGTAAGC
Found at i:2410399 original size:215 final size:213
Alignment explanation
Indices: 2409963--2410401 Score: 682
Period size: 215 Copynumber: 2.1 Consensus size: 213
2409953 GCAAATCCAT
2409963 CTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGT
1 CTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGT
* * ** * * *
2410028 TTTTACATGAATTTGAAAATGAAAATTATGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATG
66 TTTCACATGAATTTAAAAATGAAAACGATGTTTTAAGAAGATGAAACTTTTAAAAACAAAGAATG
* * * * *
2410093 CGATTTTCAAAATTTCATAATTTATAAGTTCGTCGGGCTATCAGTAAGTCTTTCGAGCTTGATGT
131 CGATTTTCAAAATTTCACAATTTATAAGTCCGTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA
*
2410158 TTAAATCCTTCGGGTCAT
196 TTAAATCCTTCGGGTCAA
**
2410176 CTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAAACCTTCGGGTAGGATGT
1 CTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGT
*
2410241 TTTCACATGAATTTAAAAATGAAAAAACGATGTTTTGAGAAGATGAAACTTTTAAAAACAAAGAA
66 TTTCACATGAATTTAAAAATG--AAAACGATGTTTTAAGAAGATGAAACTTTTAAAAACAAAGAA
* *
2410306 TGCGATTTTCAAAATTTCACAATTTATAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGAT
129 TGCGATTTTCAAAATTTCACAATTTATAAGTCCGTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
2410371 GATTAAATCCTTCGGGT-AA
194 GATTAAATCCTTCGGGTCAA
2410390 CTGGTAAGCCTT
1 CT-GTAAGCCTT
2410402 CACGGAAGAG
Statistics
Matches: 205, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
213 82 0.40
214 3 0.01
215 120 0.59
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (213 bp):
CTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGT
TTTCACATGAATTTAAAAATGAAAACGATGTTTTAAGAAGATGAAACTTTTAAAAACAAAGAATG
CGATTTTCAAAATTTCACAATTTATAAGTCCGTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA
TTAAATCCTTCGGGTCAA
Found at i:2410479 original size:80 final size:80
Alignment explanation
Indices: 2410346--2410627 Score: 449
Period size: 80 Copynumber: 3.5 Consensus size: 80
2410336 TCCTTTGGGC
2410346 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
*
2410411 GTAGTGAAGTAAATT
66 GTAGTGAAGCAAATT
* * * ** *
2410426 CATCAGTAAGTCTTTCGAGCATGGTAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACCGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
**
2410491 GTAGTGAAGCAAACC
66 GTAGTGAAGCAAATT
2410506 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
2410571 GTAGTGAAGCAAATT
66 GTAGTGAAGCAAATT
* *
2410586 CATCAGTAAGTCTTTCGAGCAGGATG-TTGAAATCTTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATT-AAATCCTTCGGGT
2410628 CATCAGTAAG
Statistics
Matches: 182, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
79 2 0.01
80 180 0.99
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (80 bp):
CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
GTAGTGAAGCAAATT
Found at i:2410697 original size:42 final size:43
Alignment explanation
Indices: 2410585--2410688 Score: 158
Period size: 42 Copynumber: 2.5 Consensus size: 43
2410575 TGAAGCAAAT
*
2410585 TCATCAGTAAGTCTTTCGAGCAGGATG-TTGAAATCTTTCGGG
1 TCATCAGTAAGTCTTTCGAGCAGGATGATTGAAATCCTTCGGG
*
2410627 TCATCAGTAAGTCTTTCGAGCATGATGATT-AAATCCTTCGGG
1 TCATCAGTAAGTCTTTCGAGCAGGATGATTGAAATCCTTCGGG
**
2410669 TCATTTGTAAGTCTTTCGAG
1 TCATCAGTAAGTCTTTCGAG
2410689 TGAGATGATA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
42 55 0.96
43 2 0.04
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (43 bp):
TCATCAGTAAGTCTTTCGAGCAGGATGATTGAAATCCTTCGGG
Found at i:2411149 original size:53 final size:53
Alignment explanation
Indices: 2411091--2411459 Score: 452
Period size: 53 Copynumber: 6.9 Consensus size: 53
2411081 AGAATTACAC
* *
2411091 CAGAAGATTGTTCGAGTTCTACCCCCTGAAGCAAGAGGGAGTGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACCCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* * *
2411144 CAGAAGATTGTTCGAGTTCTACTCCCTGAAACAAGAGGGAGCGAACCTGTAAG
1 CAGAAGATTGTTCGAGTTCTACCCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* * * * *
2411197 TAGAAGATTATTCGAGTTATACCCCCTGAAGCAAGAGGGAGTGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACCCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* * *
2411250 CAGAAGATTGTTCGAGTTCTACTCCCTGAAACAAGAGGGAGCGAACCTGTAAG
1 CAGAAGATTGTTCGAGTTCTACCCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* *
2411303 TAGAAGATTATTCGAGTTCTACCCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
1 CAGAAGATTGTTCGAGTTCTACCCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* * * * * * ***
2411356 AAGAAGATTATTCGAGTTCTACTCCCTGAAGAAATAGGGAGCGAACCCATTTT
1 CAGAAGATTGTTCGAGTTCTACCCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* ** * *
2411409 TAGAAGATTGTTCGAGTTCCTTAATCCCGGAA-CAAGAGGGAGCGGACCCGT
1 CAGAAGATTGTTCGAGTT-C-TACCCCCTGAAGCAAGAGGGAGCGAACCCGT
2411460 CATTTGAAGA
Statistics
Matches: 272, Mismatches: 42, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
53 247 0.91
54 16 0.06
55 9 0.03
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACCCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
Found at i:2411277 original size:106 final size:106
Alignment explanation
Indices: 2411092--2411402 Score: 543
Period size: 106 Copynumber: 2.9 Consensus size: 106
2411082 GAATTACACC
*
2411092 AGAAGATTGTTCGAGTTCTACCCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAGAAGATTGTTC
1 AGAAGATTATTCGAGTTCTACCCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAGAAGATTGTTC
2411157 GAGTTCTACTCCCTGAAACAAGAGGGAGCGAACCTGTAAGT
66 GAGTTCTACTCCCTGAAACAAGAGGGAGCGAACCTGTAAGT
*
2411198 AGAAGATTATTCGAGTTATACCCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAGAAGATTGTTC
1 AGAAGATTATTCGAGTTCTACCCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAGAAGATTGTTC
2411263 GAGTTCTACTCCCTGAAACAAGAGGGAGCGAACCTGTAAGT
66 GAGTTCTACTCCCTGAAACAAGAGGGAGCGAACCTGTAAGT
* * * *
2411304 AGAAGATTATTCGAGTTCTACCCCCTGAAGCAAGAGGGAGCGAACCCGTAAGAAGAAGATTATTC
1 AGAAGATTATTCGAGTTCTACCCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAGAAGATTGTTC
*
2411369 GAGTTCTACTCCCTGAAGA-AATAGGGAGCGAACC
66 GAGTTCTACTCCCTGAA-ACAAGAGGGAGCGAACC
2411403 CATTTTTAGA
Statistics
Matches: 196, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
106 195 0.99
107 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.20
Consensus pattern (106 bp):
AGAAGATTATTCGAGTTCTACCCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAGAAGATTGTTC
GAGTTCTACTCCCTGAAACAAGAGGGAGCGAACCTGTAAGT
Found at i:2424970 original size:12 final size:12
Alignment explanation
Indices: 2424953--2424996 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
2424943 GCTCAATTGA
2424953 AGCTCGATTTTG
1 AGCTCGATTTTG
**
2424965 AGCTCGA-TTCA
1 AGCTCGATTTTG
*
2424976 AGCTCGATTGTG
1 AGCTCGATTTTG
2424988 AGCTCGATT
1 AGCTCGATT
2424997 CAAGCTCGAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.34
Consensus pattern (12 bp):
AGCTCGATTTTG
Found at i:2424978 original size:23 final size:23
Alignment explanation
Indices: 2424942--2425005 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
2424932 TCAAGACTCA
* * *
2424942 AGCTCAATTGAAGCTCGATTTTG
1 AGCTCGATTCAAGCTCGATTGTG
2424965 AGCTCGATTCAAGCTCGATTGTG
1 AGCTCGATTCAAGCTCGATTGTG
2424988 AGCTCGATTCAAGCTCGA
1 AGCTCGATTCAAGCTCGA
2425006 CTTAAGCTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (23 bp):
AGCTCGATTCAAGCTCGATTGTG
Found at i:2424981 original size:11 final size:11
Alignment explanation
Indices: 2424939--2425016 Score: 68
Period size: 11 Copynumber: 6.9 Consensus size: 11
2424929 AGCTCAAGAC
*
2424939 TCAAGCTCAAT
1 TCAAGCTCGAT
*
2424950 TGAAGCTCGATT
1 TCAAGCTCGA-T
**
2424962 TTGAGCTCGAT
1 TCAAGCTCGAT
2424973 TCAAGCTCGAT
1 TCAAGCTCGAT
**
2424984 TGTGAGCTCGAT
1 T-CAAGCTCGAT
2424996 TCAAGCTCGACT
1 TCAAGCTCGA-T
2425008 T-AAGCTCGA
1 TCAAGCTCGA
2425017 GGATGGGTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
11 34 0.63
12 20 0.37
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (11 bp):
TCAAGCTCGAT
Found at i:2426946 original size:15 final size:15
Alignment explanation
Indices: 2426926--2426963 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2426916 CTTAACCCCT
2426926 AACCCTTAACATATA
1 AACCCTTAACATATA
*
2426941 AACCCTAAACATATA
1 AACCCTTAACATATA
2426956 AA-CCTTAA
1 AACCCTTAA
2426964 ATCATATCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (15 bp):
AACCCTTAACATATA
Found at i:2426985 original size:7 final size:7
Alignment explanation
Indices: 2426975--2427204 Score: 51
Period size: 7 Copynumber: 32.7 Consensus size: 7
2426965 TCATATCACA
2426975 TAAACTC
1 TAAACTC
2426982 TAAACTC
1 TAAACTC
*
2426989 TAAACCC
1 TAAACTC
*
2426996 TAAACTA
1 TAAACTC
2427003 TAAAC-C
1 TAAACTC
2427009 TTAAA-TC
1 -TAAACTC
* *
2427016 ATATCAC-A
1 -TA-AACTC
2427024 TAAACTC
1 TAAACTC
2427031 TAAAACTC
1 T-AAACTC
* *
2427039 TGAATTC
1 TAAACTC
* *
2427046 TGACCTC
1 TAAACTC
2427053 TAAAC-C
1 TAAACTC
2427059 TTAAAC-C
1 -TAAACTC
2427066 TTAACAC-C
1 -TAA-ACTC
2427074 TAAAC-C
1 TAAACTC
2427080 ATAAAC-C
1 -TAAACTC
*
2427087 ATAAACAC
1 -TAAACTC
2427095 TAAACTC
1 TAAACTC
2427102 TAAAC-C
1 TAAACTC
2427108 TTAAA-TCC
1 -TAAACT-C
* *
2427116 TATTAC-A
1 TA-AACTC
2427123 TAAACTC
1 TAAACTC
*
2427130 TAAGCTC
1 TAAACTC
2427137 TAAAC-C
1 TAAACTC
2427143 ATAAA-TCC
1 -TAAACT-C
2427151 TAAAC-C
1 TAAACTC
2427157 TTAAA-TC
1 -TAAACTC
* *
2427164 ATATCAC-A
1 -TA-AACTC
2427172 TAAACTC
1 TAAACTC
*
2427179 TAAACCC
1 TAAACTC
2427186 TAAACTC
1 TAAACTC
*
2427193 TAAACCC
1 TAAACTC
2427200 TAAAC
1 TAAAC
2427205 CTTATCACAT
Statistics
Matches: 168, Mismatches: 30, Indels: 50
0.68 0.12 0.20
Matches are distributed among these distances:
6 13 0.08
7 139 0.83
8 16 0.10
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.26
Consensus pattern (7 bp):
TAAACTC
Found at i:2427014 original size:49 final size:49
Alignment explanation
Indices: 2426939--2427208 Score: 303
Period size: 49 Copynumber: 5.5 Consensus size: 49
2426929 CCTTAACATA
*
2426939 TAAACCCTAAACATATAAACCTTAAATCATATCACATAAACTCTAAACTC
1 TAAACCCTAAAC-TCTAAACCTTAAATCATATCACATAAACTCTAAACTC
*
2426989 TAAACCCTAAACTATAAACCTTAAATCATATCACATAAACTCTAAAACTC
1 TAAACCCTAAACTCTAAACCTTAAATCATATCACATAAACTCT-AAACTC
* ** * * * * * *
2427039 TGAATTCTGACCTCTAAACCTTAAACCTTAACACCTAAAC-CATAAAC-C
1 TAAACCCTAAACTCTAAACCTTAAATCATATCACATAAACTC-TAAACTC
* * * *
2427087 ATAAACACTAAACTCTAAACCTTAAATCCTATTACATAAACTCTAAGCTC
1 -TAAACCCTAAACTCTAAACCTTAAATCATATCACATAAACTCTAAACTC
* *
2427137 TAAACCATAAA-TCCTAAACCTTAAATCATATCACATAAACTCTAAACCC
1 TAAACCCTAAACT-CTAAACCTTAAATCATATCACATAAACTCTAAACTC
* *
2427186 TAAACTCTAAACCCTAAACCTTA
1 TAAACCCTAAACTCTAAACCTTA
2427209 TCACATAATT
Statistics
Matches: 183, Mismatches: 30, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
48 2 0.01
49 130 0.71
50 51 0.28
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.26
Consensus pattern (49 bp):
TAAACCCTAAACTCTAAACCTTAAATCATATCACATAAACTCTAAACTC
Found at i:2427078 original size:99 final size:99
Alignment explanation
Indices: 2426954--2427132 Score: 254
Period size: 99 Copynumber: 1.8 Consensus size: 99
2426944 CCTAAACATA
* * *
2426954 TAAACCTTAAATCATATCACATAAACTC-TAAACTC-TAAACCCTAAACTATAAACCTTAAATCA
1 TAAACCTTAAACCATAACACATAAAC-CATAAAC-CATAAACACTAAACTATAAACCTTAAATCA
2427017 TATCACATAAACTCTAAAACTCTGAATTCTGACCTC
64 TATCACATAAACTCTAAAACTCTGAATTCTGACCTC
* * * *
2427053 TAAACCTTAAACCTTAACACCTAAACCATAAACCATAAACACTAAACTCTAAACCTTAAATCCTA
1 TAAACCTTAAACCATAACACATAAACCATAAACCATAAACACTAAACTATAAACCTTAAATCATA
*
2427118 TTACATAAACTCTAA
66 TCACATAAACTCTAA
2427133 GCTCTAAACC
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
98 2 0.03
99 68 0.97
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (99 bp):
TAAACCTTAAACCATAACACATAAACCATAAACCATAAACACTAAACTATAAACCTTAAATCATA
TCACATAAACTCTAAAACTCTGAATTCTGACCTC
Found at i:2427125 original size:35 final size:35
Alignment explanation
Indices: 2427086--2427152 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
2427076 AACCATAAAC
*
2427086 CATAAACACTAAACTCTAAACCTTAAATCCTATTA
1 CATAAACACTAAACTCTAAACCATAAATCCTATTA
* *
2427121 CATAAACTCTAAGCTCTAAACCATAAATCCTA
1 CATAAACACTAAACTCTAAACCATAAATCCTA
2427153 AACCTTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (35 bp):
CATAAACACTAAACTCTAAACCATAAATCCTATTA
Found at i:2427196 original size:21 final size:21
Alignment explanation
Indices: 2426973--2427205 Score: 87
Period size: 21 Copynumber: 11.0 Consensus size: 21
2426963 AATCATATCA
2426973 CATAAACTCTAAACTCTAAAC
1 CATAAACTCTAAACTCTAAAC
* * *
2426994 CCTAAACTATAAAC-CTTAAAT
1 CATAAACTCTAAACTC-TAAAC
* *
2427015 CATATCAC-ATAAACTCTAAAAC
1 CATA-AACTCTAAACTCT-AAAC
* * * *
2427037 TC-TGAATTCTGACCTCTAAAC
1 -CATAAACTCTAAACTCTAAAC
*
2427058 CTTAAAC-CTTAACAC-CTAAAC
1 CATAAACTC-TAA-ACTCTAAAC
*
2427079 CATAAAC-CATAAACACTAAAC
1 CATAAACTC-TAAACTCTAAAC
*
2427100 TC-TAAAC-CTTAAATC-CTATTA-
1 -CATAAACTC-TAAA-CTCTA-AAC
*
2427121 CATAAACTCTAAGCTCTAAAC
1 CATAAACTCTAAACTCTAAAC
*
2427142 CATAAA-TCCTAAAC-CTTAAAT
1 CATAAACT-CTAAACTC-TAAAC
* *
2427163 CATATCAC-ATAAACTCTAAAC
1 CATA-AACTCTAAACTCTAAAC
* *
2427184 CCTAAACTCTAAACCCTAAAC
1 CATAAACTCTAAACTCTAAAC
2427205 C
1 C
2427206 TTATCACATA
Statistics
Matches: 158, Mismatches: 31, Indels: 46
0.67 0.13 0.20
Matches are distributed among these distances:
20 12 0.08
21 125 0.79
22 20 0.13
23 1 0.01
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (21 bp):
CATAAACTCTAAACTCTAAAC
Found at i:2427205 original size:7 final size:7
Alignment explanation
Indices: 2427052--2427205 Score: 62
Period size: 7 Copynumber: 22.0 Consensus size: 7
2427042 ATTCTGACCT
2427052 CTAAACC
1 CTAAACC
*
2427059 TTAAA-C
1 CTAAACC
*
2427065 CTTAACAC
1 CTAAAC-C
2427073 CTAAACC
1 CTAAACC
*
2427080 ATAAACC
1 CTAAACC
* *
2427087 ATAAACA
1 CTAAACC
*
2427094 CTAAACT
1 CTAAACC
2427101 CTAAACC
1 CTAAACC
* *
2427108 TTAAATC
1 CTAAACC
*
2427115 CTATTA-C
1 CTA-AACC
* *
2427122 ATAAACT
1 CTAAACC
* *
2427129 CTAAGCT
1 CTAAACC
2427136 CTAAACC
1 CTAAACC
* *
2427143 ATAAATC
1 CTAAACC
2427150 CTAAACC
1 CTAAACC
* *
2427157 TTAAATC
1 CTAAACC
* *
2427164 AT-ATCAC
1 CTAAAC-C
* *
2427171 ATAAACT
1 CTAAACC
2427178 CTAAACC
1 CTAAACC
*
2427185 CTAAACT
1 CTAAACC
2427192 CTAAACC
1 CTAAACC
2427199 CTAAACC
1 CTAAACC
2427206 TTATCACATA
Statistics
Matches: 106, Mismatches: 35, Indels: 12
0.69 0.23 0.08
Matches are distributed among these distances:
6 6 0.06
7 91 0.86
8 9 0.08
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.24
Consensus pattern (7 bp):
CTAAACC
Found at i:2432325 original size:21 final size:19
Alignment explanation
Indices: 2432301--2432365 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 19
2432291 ATTTTGTTAG
2432301 TATTTTATTTAA---TTAT
1 TATTTTATTTAATTTTTAT
*
2432317 TATATTATTTAATTTTTTTAT
1 TATTTTATTTAA--TTTTTAT
2432338 TATTTTATTTAATTTTT-T
1 TATTTTATTTAATTTTTAT
2432356 TATTTT-TTTA
1 TATTTTATTTA
2432366 CAGTTATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
16 11 0.26
17 4 0.10
18 7 0.17
19 5 0.12
21 15 0.36
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTATTTAATTTTTAT
Found at i:2432343 original size:8 final size:8
Alignment explanation
Indices: 2432305--2432361 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
2432295 TGTTAGTATT
*
2432305 TTATTTAA
1 TTATTTTA
*
2432313 TTATTATA
1 TTATTTTA
*
2432321 TTATTTAA
1 TTATTTTA
*
2432329 TTTTTTTA
1 TTATTTTA
2432337 TTATTTTA
1 TTATTTTA
*
2432345 TTTAATTTTT
1 -TT-ATTTTA
2432355 TTATTTT
1 TTATTTT
2432362 TTTACAGTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
8 30 0.77
9 4 0.10
10 5 0.13
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTATTTTA
Found at i:2432347 original size:16 final size:16
Alignment explanation
Indices: 2432305--2432347 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
2432295 TGTTAGTATT
* *
2432305 TTATTTAATTATTATA
1 TTATTTAATTTTTTTA
2432321 TTATTTAATTTTTTTA
1 TTATTTAATTTTTTTA
*
2432337 TTATTTTATTT
1 TTATTTAATTT
2432348 AATTTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTATTTAATTTTTTTA
Found at i:2432643 original size:27 final size:27
Alignment explanation
Indices: 2432613--2432672 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
2432603 TTATAACTGC
*
2432613 AAAA-AAAATAATTAAATTAAATAATAA
1 AAAATAAAATAA-TAAAATAAATAATAA
* * *
2432640 AAAATTAAATAATAAAATAATTAATAC
1 AAAATAAAATAATAAAATAAATAATAA
2432667 AAAATA
1 AAAATA
2432673 TGATTAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.27
Consensus pattern (27 bp):
AAAATAAAATAATAAAATAAATAATAA
Found at i:2432658 original size:20 final size:21
Alignment explanation
Indices: 2432613--2432659 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
2432603 TTATAACTGC
2432613 AAAA-AAAATAATTAAATTAA
1 AAAATAAAATAATTAAATTAA
*
2432633 ATAATAAAA-AATTAAA-TAA
1 AAAATAAAATAATTAAATTAA
2432652 TAAAATAA
1 -AAAATAA
2432660 TTAATACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.13
20 16 0.70
21 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAATAAAATAATTAAATTAA
Found at i:2432665 original size:15 final size:15
Alignment explanation
Indices: 2432626--2432663 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
2432616 AAAAATAATT
2432626 AAATTAAATAATAAA
1 AAATTAAATAATAAA
2432641 AAATTAAATAATAAA
1 AAATTAAATAATAAA
2432656 ATAATTAA
1 A-AATTAA
2432664 TACAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATTAAATAATAAA
Found at i:2433626 original size:186 final size:186
Alignment explanation
Indices: 2433299--2433690 Score: 655
Period size: 186 Copynumber: 2.1 Consensus size: 186
2433289 ATTTCGAATT
* * *
2433299 TATATAA-AAATTAAATATTTTTGAATTCAAAAAAACAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTGAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
2433363 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
66 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
* *
2433428 TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGACTTAG-CTCATATGTTA
131 TTGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGACTAAGTC-CATATGTTA
* *
2433484 TATATAATATATTTAATATTTTTATAATTCAAAAAAACAGTTTCCAATTAATTTAAATAATATAT
1 TATATAATATATTTAATATTTTT-GAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATAT
*
2433549 AATTATAAAATAAAAATTTTATAT-AATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
65 AATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTT
*
2433613 ATTGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTAAGTCCATATGTTA
130 ATTGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGACTAAGTCCATATGTTA
*
2433670 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
2433691 AATTTCGGTT
Statistics
Matches: 194, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
185 7 0.04
186 124 0.64
187 63 0.32
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.46
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTTGAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
TTGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGACTAAGTCCATATGTTA
Found at i:2433984 original size:31 final size:32
Alignment explanation
Indices: 2433946--2434007 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
2433936 TTAATATACG
* *
2433946 GCTAAAAATA-GCGGTATCGGTTTTGTTATTA
1 GCTAAAAAAAGGCGGTATCGGTTTTATTATTA
2433977 GCTAAAAAAAGGCGGTATCGGTTTTATTATT
1 GCTAAAAAAAGGCGGTATCGGTTTTATTATT
2434008 GTTGTGCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 9 0.32
32 19 0.68
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.37
Consensus pattern (32 bp):
GCTAAAAAAAGGCGGTATCGGTTTTATTATTA
Found at i:2434536 original size:20 final size:20
Alignment explanation
Indices: 2434499--2434536 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2434489 ATTTATTAAC
*
2434499 AAAATATTAATATTATTTTT
1 AAAATATTAATATAATTTTT
2434519 AAAATATTAGA-ATAATTT
1 AAAATATTA-ATATAATTT
2434537 ATTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
AAAATATTAATATAATTTTT
Found at i:2434591 original size:28 final size:28
Alignment explanation
Indices: 2434556--2434645 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 28
2434546 TATTTATGTC
2434556 AATATTATTATTAAAATATTAT-ATCTAT
1 AATATTATTATTAAAATATTATGAT-TAT
* * * *
2434584 AATTTTATAAATAAAAAATTATGATTAT
1 AATATTATTATTAAAATATTATGATTAT
* ** *
2434612 TATATT-TTATTAAAATAAAATTATTAT
1 AATATTATTATTAAAATATTATGATTAT
2434639 AA-ATTAT
1 AATATTAT
2434646 ATTTATTATT
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
26 3 0.06
27 17 0.36
28 25 0.53
29 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
AATATTATTATTAAAATATTATGATTAT
Found at i:2434648 original size:31 final size:31
Alignment explanation
Indices: 2434585--2434653 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
2434575 TATATCTATA
*
2434585 ATTTTA-TAAATAAAAAATTATGATTATTAT
1 ATTTTATTAAATAAAAAATTATGATAATTAT
* *
2434615 ATTTTATTAAA-ATAAAATTATTATAAATTAT
1 ATTTTATTAAATAAAAAATTATGAT-AATTAT
2434646 A-TTTATTA
1 ATTTTATTA
2434654 TTTATTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTTTATTAAATAAAAAATTATGATAATTAT
Done.