Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009343.1 Hibiscus syriacus cultivar Beakdansim tig00113123_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: 2141224
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:1777902 original size:15 final size:15
Alignment explanation
Indices: 1777853--1777902 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1777843 ATTATTCTAT
*
1777853 TTTTTTATTAAAGTC
1 TTTTTTATTAAAGTA
1777868 TTTTTTATTATTAA--A
1 TTTTTTATTA--AAGTA
*
1777883 GTTTTTATTAAAGTA
1 TTTTTTATTAAAGTA
1777898 TTTTT
1 TTTTT
1777903 CATTTATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
15 24 0.86
17 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (15 bp):
TTTTTTATTAAAGTA
Found at i:1780278 original size:21 final size:21
Alignment explanation
Indices: 1780254--1780309 Score: 94
Period size: 21 Copynumber: 2.6 Consensus size: 21
1780244 TATATAGTCG
1780254 TTGGGGATGTTTTGGAGCCGT
1 TTGGGGATGTTTTGGAGCCGT
*
1780275 TTGGGGATGATTTGGAGCCGT
1 TTGGGGATGTTTTGGAGCCGT
1780296 TTGGGGATGATTTT
1 TTGGGGATG-TTTT
1780310 TCTACTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 29 0.91
22 3 0.09
ACGTcount: A:0.12, C:0.07, G:0.41, T:0.39
Consensus pattern (21 bp):
TTGGGGATGTTTTGGAGCCGT
Found at i:1780364 original size:21 final size:21
Alignment explanation
Indices: 1780338--1780408 Score: 124
Period size: 21 Copynumber: 3.4 Consensus size: 21
1780328 CCATAATAGG
1780338 GGGTATCGGTACCCCATCATA
1 GGGTATCGGTACCCCATCATA
1780359 GGGTATCGGTACCCCATCATA
1 GGGTATCGGTACCCCATCATA
* *
1780380 AGGTATCGATACCCCATCATA
1 GGGTATCGGTACCCCATCATA
1780401 GGGTATCG
1 GGGTATCG
1780409 ATACTCCTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (21 bp):
GGGTATCGGTACCCCATCATA
Found at i:1781055 original size:13 final size:13
Alignment explanation
Indices: 1781039--1781094 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 13
1781029 TGAAAAATAT
1781039 TTTAATAAAAAAC
1 TTTAATAAAAAAC
1781052 TTTAATAATAAAAAAGAC
1 -TT--TAAT-AAAAA-AC
*
1781070 TTTAATACAAAAC
1 TTTAATAAAAAAC
1781083 TTTAATAAAAAA
1 TTTAATAAAAAA
1781095 TATAGAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 13 0.36
14 6 0.17
15 4 0.11
16 4 0.11
17 7 0.19
18 2 0.06
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (13 bp):
TTTAATAAAAAAC
Found at i:1781060 original size:16 final size:18
Alignment explanation
Indices: 1781041--1781076 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1781031 AAAAATATTT
1781041 TAAT-AAAAA-ACTTTAA
1 TAATAAAAAAGACTTTAA
1781057 TAATAAAAAAGACTTTAA
1 TAATAAAAAAGACTTTAA
1781075 TA
1 TA
1781077 CAAAACTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 5 0.28
18 9 0.50
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (18 bp):
TAATAAAAAAGACTTTAA
Found at i:1781181 original size:15 final size:15
Alignment explanation
Indices: 1781161--1781189 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1781151 AGAATTGATA
1781161 TATTTAGACTAACCT
1 TATTTAGACTAACCT
1781176 TATTTAGACTAACC
1 TATTTAGACTAACC
1781190 CATAAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (15 bp):
TATTTAGACTAACCT
Found at i:1781813 original size:13 final size:13
Alignment explanation
Indices: 1781795--1781858 Score: 74
Period size: 13 Copynumber: 4.5 Consensus size: 13
1781785 TATTTCTATA
1781795 TTTTTTATTAAAG
1 TTTTTTATTAAAG
1781808 TTTTTTATTAAAG
1 TTTTTTATTAAAG
1781821 TATTTTTTATTATTAAAG
1 ----TTTT-TTATTAAAG
1781839 TTTTTTATTAAAG
1 TTTTTTATTAAAG
1781852 TATTTTT
1 T-TTTTT
1781859 CATTTATTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
13 23 0.51
14 9 0.20
17 4 0.09
18 9 0.20
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (13 bp):
TTTTTTATTAAAG
Found at i:1781837 original size:31 final size:30
Alignment explanation
Indices: 1781795--1781858 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 30
1781785 TATTTCTATA
1781795 TTTTTTATTAAAGTTTTTTATTAAAGTATT
1 TTTTTTATTAAAGTTTTTTATTAAAGTATT
1781825 TTTTATTATTAAAGTTTTTTATTAAAGTATT
1 TTTT-TTATTAAAGTTTTTTATTAAAGTATT
1781856 TTT
1 TTT
1781859 CATTTATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (30 bp):
TTTTTTATTAAAGTTTTTTATTAAAGTATT
Found at i:1782142 original size:144 final size:145
Alignment explanation
Indices: 1781880--1782155 Score: 419
Period size: 144 Copynumber: 1.9 Consensus size: 145
1781870 TCAATATGGT
* * * * * * *
1781880 AATAATCGTTCGTATTTATTTTCTCCGATCTGTCGCCGTCCACCGTCCTATCGTTCTGATTTTTC
1 AATAACCGTTCGGACTTATTTTCTCCGATCCGCCGCCGTCCACCGTCCGATCGTCCTGA-TTTTC
* *
1781945 AGTATGTTGTTCGTGTTGGCCTTGTGCAACTTTTCACCGTTCGGAACGTTGATCGGAGATCCCGA
65 AGTATGTTGTTCGTATTGGCCTTGCGCAACTTTTCACCGTTCGGAACGTTGATCGGAGATCCCGA
1782010 TCTCCGTAAAGAGGCC
130 TCTCCGTAAAGAGGCC
* * *
1782026 AATAACCGTTCGGACTTATTTTCTCCGATCCGCCGCTGTTCACTGTCCGATCGTCCTGA-TTTCA
1 AATAACCGTTCGGACTTATTTTCTCCGATCCGCCGCCGTCCACCGTCCGATCGTCCTGATTTTCA
*
1782090 GTATGTTGTTCGTATTGGCCTTGCGCAACTTTTCACTGTTCGGAACGTTGATCGGAGATCCCGAT
66 GTATGTTGTTCGTATTGGCCTTGCGCAACTTTTCACCGTTCGGAACGTTGATCGGAGATCCCGAT
1782155 C
131 C
1782156 GCCGGCGAAA
Statistics
Matches: 117, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
144 68 0.58
146 49 0.42
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (145 bp):
AATAACCGTTCGGACTTATTTTCTCCGATCCGCCGCCGTCCACCGTCCGATCGTCCTGATTTTCA
GTATGTTGTTCGTATTGGCCTTGCGCAACTTTTCACCGTTCGGAACGTTGATCGGAGATCCCGAT
CTCCGTAAAGAGGCC
Found at i:1782328 original size:14 final size:15
Alignment explanation
Indices: 1782302--1782331 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1782292 TCGTGGGTTT
1782302 TTTAATGGGGTTTTA
1 TTTAATGGGGTTTTA
*
1782317 TTTAATGGGTTTTTA
1 TTTAATGGGGTTTTA
1782332 GTGGATGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
TTTAATGGGGTTTTA
Found at i:1782468 original size:32 final size:32
Alignment explanation
Indices: 1782432--1782501 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
1782422 AGTACCCATT
*
1782432 TTTATTTCTTTGTCC-CTCATATACCCTACACC
1 TTTATTTCTTTG-CCGCCCATATACCCTACACC
*
1782464 TTTATTTCTTTGCCGCCCATATACCTTACACC
1 TTTATTTCTTTGCCGCCCATATACCCTACACC
*
1782496 ATTATT
1 TTTATT
1782502 AAAAAAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 2 0.06
32 32 0.94
ACGTcount: A:0.20, C:0.31, G:0.04, T:0.44
Consensus pattern (32 bp):
TTTATTTCTTTGCCGCCCATATACCCTACACC
Found at i:1786912 original size:62 final size:62
Alignment explanation
Indices: 1786836--1786958 Score: 246
Period size: 62 Copynumber: 2.0 Consensus size: 62
1786826 ATGAAATGAT
1786836 AAACAAAATCATGAATTATAGTCAATACTGCTATAAAATATTTACACCAAGAATTTTAAAAA
1 AAACAAAATCATGAATTATAGTCAATACTGCTATAAAATATTTACACCAAGAATTTTAAAAA
1786898 AAACAAAATCATGAATTATAGTCAATACTGCTATAAAATATTTACACCAAGAATTTTAAAA
1 AAACAAAATCATGAATTATAGTCAATACTGCTATAAAATATTTACACCAAGAATTTTAAAA
1786959 CAGGGTGTAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.29
Consensus pattern (62 bp):
AAACAAAATCATGAATTATAGTCAATACTGCTATAAAATATTTACACCAAGAATTTTAAAAA
Found at i:1789563 original size:14 final size:14
Alignment explanation
Indices: 1789546--1789585 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
1789536 TCTTCTTTTT
1789546 TTATTTATATTATA
1 TTATTTATATTATA
*
1789560 TTATTTTTATTATA
1 TTATTTATATTATA
1789574 TATATCTTATAT
1 T-TAT-TTATAT
1789586 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:1789577 original size:2 final size:2
Alignment explanation
Indices: 1789570--1789613 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
1789560 TTATTTTTAT
*
1789570 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
1789611 TA T
1 TA T
1789614 GTATGTATGA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
1 2 0.05
2 34 0.89
3 2 0.05
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1789902 original size:17 final size:18
Alignment explanation
Indices: 1789870--1789904 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1789860 ATTTTTATTT
1789870 CTTTTTAATTTCTTTTAC
1 CTTTTTAATTTCTTTTAC
*
1789888 CTTTTTTATTT-TTTTAC
1 CTTTTTAATTTCTTTTAC
1789905 TCCATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (18 bp):
CTTTTTAATTTCTTTTAC
Found at i:1793044 original size:19 final size:19
Alignment explanation
Indices: 1793022--1793070 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
1793012 ATCAGAATAA
1793022 AAAGAAAAA-AGAAAAAAAC
1 AAAGAAAAATA-AAAAAAAC
1793041 AAAGAGAAAATAAAAAAAAC
1 AAAGA-AAAATAAAAAAAAC
*
1793061 AAAGGAAAAT
1 AAAGAAAAAT
1793071 TGAAGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 10 0.37
20 16 0.59
21 1 0.04
ACGTcount: A:0.80, C:0.04, G:0.12, T:0.04
Consensus pattern (19 bp):
AAAGAAAAATAAAAAAAAC
Found at i:1793079 original size:20 final size:20
Alignment explanation
Indices: 1793033--1793070 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1793023 AAGAAAAAAG
1793033 AAAAAAACAAAGAGAAAATA
1 AAAAAAACAAAGAGAAAATA
1793053 AAAAAAACAAAG-GAAAAT
1 AAAAAAACAAAGAGAAAAT
1793071 TGAAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.79, C:0.05, G:0.11, T:0.05
Consensus pattern (20 bp):
AAAAAAACAAAGAGAAAATA
Found at i:1793253 original size:69 final size:69
Alignment explanation
Indices: 1793142--1793275 Score: 234
Period size: 69 Copynumber: 1.9 Consensus size: 69
1793132 GATTCAAACT
*
1793142 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTTCAAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
1793207 ACAA
66 ACAA
*
1793211 ATGAGATTGATCAAGCACAATTA-TTTCTAAATCACTGAATCACTTCACTCGAAGATCATAGAGC
1 ATGAGATTGATCAAGCACAATCATTTTC-AAATCACTGAATCACTTCACTCGAAGATCATAGAGC
1793275 A
65 A
1793276 TCAAGAGAGA
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 4 0.06
69 58 0.94
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTTCAAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
ACAA
Found at i:1793703 original size:24 final size:24
Alignment explanation
Indices: 1793676--1793724 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1793666 CGATCGTACG
1793676 AATTCCTTGATAAGGCATCACACA
1 AATTCCTTGATAAGGCATCACACA
*
1793700 AATTCCTTGATAAGGCATCGCACA
1 AATTCCTTGATAAGGCATCACACA
1793724 A
1 A
1793725 TCCGAGCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.24
Consensus pattern (24 bp):
AATTCCTTGATAAGGCATCACACA
Found at i:1794261 original size:32 final size:31
Alignment explanation
Indices: 1794224--1794311 Score: 113
Period size: 32 Copynumber: 2.7 Consensus size: 31
1794214 GGAACAATGA
1794224 GGGCATCTTTGAAGATTCAACATCAAATATTG
1 GGGCATCTTTG-AGATTCAACATCAAATATTG
* * *
1794256 GGGCATTTTTTTAGATTCAACATCGAATATTG
1 GGGCA-TCTTTGAGATTCAACATCAAATATTG
*
1794288 GGGCATCTTTGGGAATTCAACATC
1 GGGCATCTTTGAG-ATTCAACATC
1794312 CTGATGCAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
31 5 0.10
32 39 0.81
33 4 0.08
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (31 bp):
GGGCATCTTTGAGATTCAACATCAAATATTG
Found at i:1795010 original size:106 final size:106
Alignment explanation
Indices: 1794887--1795220 Score: 420
Period size: 106 Copynumber: 3.2 Consensus size: 106
1794877 ATATCGTGCC
* * *
1794887 ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGGACAACTGGTTGTGAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
* *
1794952 AATTTCATAGCCAATTTCAACTTCATAAG-GAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCA-CAGCGAAGGATATTGG
* * *
1794993 ACTCGAGACAACACAAGTTCAACTTCATAACGAATGGACGACTGGTTGTCAACAAATAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
1795058 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * *
1795099 ACTCGAGATAGCACATA-CTCAACTTCACAGCAAAGGGGCGACTGGCTGTCAACAAACAATTTCT
1 ACTCGAGACAACACA-AGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCC
* * * * * *
1795163 TAGTTCCAGAGCCAATTTTAACTTCACGGCGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1795205 ACTCGAAACAATACAA
1 ACTCGAGACAACACAA
1795221 ATTACTTGGA
Statistics
Matches: 197, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
105 3 0.02
106 193 0.98
107 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1795550 original size:65 final size:65
Alignment explanation
Indices: 1795438--1795595 Score: 210
Period size: 65 Copynumber: 2.4 Consensus size: 65
1795428 TTTTGGAACT
*
1795438 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAATATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAATATTTCCCTTGAAAC
* * * * ** *
1795503 GAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTGAATCTGTTTCCCTTGAAA
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAATATTTCCCTTGAAA
1795567 C
65 C
* *
1795568 AAATTTCGTCTCCCTTGAGACATTTTCT
1 AAATTTTGTCTCCCTTGAGACAGTTTCT
1795596 TTTGGAACTA
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
64 3 0.04
65 76 0.96
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (65 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAATATTTCCCTTGAAAC
Found at i:1795624 original size:167 final size:165
Alignment explanation
Indices: 1795356--1795706 Score: 551
Period size: 167 Copynumber: 2.1 Consensus size: 165
1795346 GACAGTTTCC
* * * *
1795356 AAGTTTCCCTTGAAACAAAATATTTAAATCTGTTTTCATTGAAACTAATTTCGTCTCCCTTTAGA
1 AAGTTTCTCTTGAAACAAAATATTTAAATCTGTTTCCATTGAAACAAATTTCGTCTCCCTTGAGA
1795421 CATTTTCTTTTGGAACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTG-A
66 CATTTTCTTTTGGAACTAAATTTTGTCTCCCTTGAGACAGTTTCTC-TGAAAC-TAAACA-TGAA
*
1795485 AAATATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGA
128 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGA
* * * *
1795523 TAGTTTCTCTTGAAACAAAATCTTTGAATCTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
1 AAGTTTCTCTTGAAACAAAATATTTAAATCTGTTTCCATTGAAACAAATTTCGTCTCCCTTGAGA
* * * *
1795588 CATTTTCTTTTGGAACTAAGTTTTGTTTCTCTTGAGATAGTTTCTCTGAAACTAAACATGAAAAA
66 CATTTTCTTTTGGAACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTGAAACTAAACATGAAAAA
1795653 CATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGA
131 CATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGA
1795688 AAGTTTCTCTTGAAACAAA
1 AAGTTTCTCTTGAAACAAA
1795707 TTTCGTCTCC
Statistics
Matches: 169, Mismatches: 14, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
164 2 0.01
165 62 0.37
166 6 0.04
167 99 0.59
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (165 bp):
AAGTTTCTCTTGAAACAAAATATTTAAATCTGTTTCCATTGAAACAAATTTCGTCTCCCTTGAGA
CATTTTCTTTTGGAACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTGAAACTAAACATGAAAAA
CATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGA
Found at i:1795685 original size:100 final size:102
Alignment explanation
Indices: 1795506--1795723 Score: 239
Period size: 100 Copynumber: 2.2 Consensus size: 102
1795496 TTGAAATGAA
* * *
1795506 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAATCTGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTATGAAACTATTTCCCTTGAAACAAA
1795571 TTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAG
66 TTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAG
* * **
1795608 TTTTGTTTCTCTTGAGATAGTTTCTC-TGAAACTAAA-C-ATGAAAAAC-ATTTCCCTTGAAATG
1 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTATG--AAACTATTTCCCTTGAAACA
* * * * * * *
1795669 AATTTTGTCTCTCTTGAGAAAGTTTCTCTTGAAAC-AAA
64 AATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAG
* *
1795707 TTTCGTCTCCCTTGAGA
1 TTTTGTCTCTCTTGAGA
1795724 CATTTTCTTT
Statistics
Matches: 97, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
99 18 0.19
100 42 0.43
101 12 0.12
102 25 0.26
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (102 bp):
TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTATGAAACTATTTCCCTTGAAACAAA
TTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAG
Found at i:1795715 original size:136 final size:138
Alignment explanation
Indices: 1795554--1795870 Score: 505
Period size: 136 Copynumber: 2.3 Consensus size: 138
1795544 CTTTGAATCT
*
1795554 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAGTTTTGTTTCTC
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAGTTTTGTCTCTC
*
1795619 TTGAGATAGTTTCTC-TGAAAC-TAAACA-TGAAAAACATTTCCCTTGAAATGAATTTTGTCTCT
66 TTGAGATAGTTTCTCTTGAAACATAAACATTG-AAAACATTTCCATTGAAATGAATTTTGTCTCT
*
1795681 CTTGAGAAA
130 CTCGAGAAA
*
1795690 GTTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAGTTTTGTCTCTC
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAGTTTTGTCTCTC
*
1795755 TTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCATTGAGATGAATTTTGTCTCTC
66 TTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCATTGAAATGAATTTTGTCTCTC
*
1795820 TCGAGATA
131 TCGAGAAA
* ** *
1795828 GGTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCT
1 GTTTCCCTTGAAAC-AAATTTCGTCTCCCTTGAGACATTTTCT
1795871 CTTGAAACAT
Statistics
Matches: 166, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
136 78 0.47
137 6 0.04
138 55 0.33
139 27 0.16
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (138 bp):
GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAGTTTTGTCTCTC
TTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCATTGAAATGAATTTTGTCTCTC
TCGAGAAA
Found at i:1795759 original size:37 final size:36
Alignment explanation
Indices: 1795655--1795777 Score: 138
Period size: 36 Copynumber: 3.4 Consensus size: 36
1795645 ATGAAAAACA
* **
1795655 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGAAAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAAAG
* * * *
1795691 TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAT
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAAAG
* * * *
1795727 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGAAAG
1795764 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
1795778 TAAACATTGA
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
36 41 0.59
37 29 0.41
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.43
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAAAG
Found at i:1795862 original size:238 final size:240
Alignment explanation
Indices: 1795506--1795971 Score: 602
Period size: 238 Copynumber: 1.9 Consensus size: 240
1795496 TTGAAATGAA
* * * *
1795506 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAATCTGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCATTGAAACTATTTCCATTGAAACAAA
* ** ** * * * * * * *
1795571 TTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAGTTTTGTTTCTCTTGAGATAGTTTCTC-T
66 TTTCGTCTCCCTCGAGACAGGTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTCTT
* * *
1795635 GAAAC-TAAACA-TGAAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGAA-AGTTTCTC
131 GAAACATAAACATTG-AAAACATTTCCCTTGAAATGAATTTTGTCACTCATGA-AATAGTTTCCC
*
1795697 TTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAG
194 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
* **
1795744 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAA-CATTGAAAAC-ATTTCCATTGAGATG
1 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCATTG-AAACTATTTCCATTGAAACA
* * *
1795807 AATTTTGTCTCTCTCGAGATAGGTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTC
64 AATTTCGTCTCCCTCGAGACAGGTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTC
1795872 TTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCACTCATGAAATAGTTTCCC
129 TTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCACTCATGAAATAGTTTCCC
* *
1795937 TTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCT
194 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCT
1795972 CTTGAAGCAT
Statistics
Matches: 194, Mismatches: 28, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
238 98 0.51
239 14 0.07
240 80 0.41
241 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (240 bp):
TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCATTGAAACTATTTCCATTGAAACAAA
TTTCGTCTCCCTCGAGACAGGTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTCTT
GAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCACTCATGAAATAGTTTCCCTT
GAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
Found at i:1795875 original size:37 final size:37
Alignment explanation
Indices: 1795807--1795879 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 37
1795797 CATTGAGATG
* * *
1795807 AATTTTGTCTCTCTCGAGATAGGTTCCCTTGAAACAA
1 AATTTTATCTCCCTCGAGACAGGTTCCCTTGAAACAA
* * *
1795844 AATTTTATCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTATCTCCCTCGAGACAGGTTCCCTTGAAACA
1795880 TAAACATTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (37 bp):
AATTTTATCTCCCTCGAGACAGGTTCCCTTGAAACAA
Found at i:1795881 original size:102 final size:101
Alignment explanation
Indices: 1795744--1796008 Score: 388
Period size: 102 Copynumber: 2.6 Consensus size: 101
1795734 TGGAACTAAG
* * *
1795744 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCATTGAGATGAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCATTGAAATGAA
* *
1795809 TTTTGTCTCTC-TCGAGATAGGTTCCCTTGAAACAAAA
66 TTTTGTCACTCAT-GAAATAGGTTCCCTTGAAA-AAAA
* *
1795846 TTTTATCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCATTGAAATGAA
* *
1795911 TTTTGTCACTCATGAAATAGTTTCCCTTGAAATAAA
66 TTTTGTCACTCATGAAATAGGTTCCCTTGAAAAAAA
* * *
1795947 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAGCATAAACTTTGAAAACAGTTTCCTTTGAAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA-TTTCCATTGAAA
1796009 CAAAATCTTT
Statistics
Matches: 148, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
101 49 0.33
102 98 0.66
103 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.37
Consensus pattern (101 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCATTGAAATGAA
TTTTGTCACTCATGAAATAGGTTCCCTTGAAAAAAA
Found at i:1795969 original size:36 final size:36
Alignment explanation
Indices: 1795890--1795977 Score: 106
Period size: 36 Copynumber: 2.5 Consensus size: 36
1795880 TAAACATTGA
* *
1795890 AAACA-TTTCCCTTGAAATGAATTTTGTCACTCATG
1 AAACAGTTTCCCTTGAAATAAATTTTGTCACCCATG
* * *
1795925 AAATAGTTTCCCTTGAAATAAATTTTGTCTCCCTTG
1 AAACAGTTTCCCTTGAAATAAATTTTGTCACCCATG
* *
1795961 AGACAGTTTCTCTTGAA
1 AAACAGTTTCCCTTGAA
1795978 GCATAAACTT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 4 0.09
36 40 0.91
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (36 bp):
AAACAGTTTCCCTTGAAATAAATTTTGTCACCCATG
Found at i:1795997 original size:30 final size:30
Alignment explanation
Indices: 1795963--1796021 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1795953 CTCCCTTGAG
*
1795963 ACAGTTT-CTCTTGAAGCATAAA-CTTTGAAA
1 ACAGTTTCCT-TTGAAACA-AAATCTTTGAAA
1795993 ACAGTTTCCTTTGAAACAAAATCTTTGAA
1 ACAGTTTCCTTTGAAACAAAATCTTTGAA
1796022 TATGTTTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 21 0.81
31 2 0.08
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (30 bp):
ACAGTTTCCTTTGAAACAAAATCTTTGAAA
Found at i:1796090 original size:34 final size:34
Alignment explanation
Indices: 1796046--1796143 Score: 110
Period size: 36 Copynumber: 2.8 Consensus size: 34
1796036 AACAAATCTC
* * *
1796046 GTCTCCCTTGAGACAGTTTCTTTTGGAAGT-TTTT
1 GTCTCTCTTGAGACAGTTTCTCTT-GAAATATTTT
1796080 GTCTCTCTTGAGACAGTTTCTCTTGAAATAAATTTT
1 GTCTCTCTTGAGACAGTTTCTCTTGAAAT--ATTTT
*
1796116 GTCTCTCTTGAGATAGTTTC-CATTGAAA
1 GTCTCTCTTGAGACAGTTTCTC-TTGAAA
1796144 CTTCAATCTT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
33 4 0.07
34 22 0.39
35 1 0.02
36 29 0.52
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.44
Consensus pattern (34 bp):
GTCTCTCTTGAGACAGTTTCTCTTGAAATATTTT
Found at i:1796225 original size:36 final size:35
Alignment explanation
Indices: 1796163--1796246 Score: 127
Period size: 36 Copynumber: 2.4 Consensus size: 35
1796153 TTGAATACAT
* *
1796163 TTTCTCTTG-AA-ACATAAAAAACCTTTGAAATTG
1 TTTCTCTTGAAACACAAAAAAAACCTTTGAAAATG
1796196 TTTCTCTTGAAACACAAAAAAAAACCTTTGAAAATG
1 TTTCTCTTGAAACAC-AAAAAAAACCTTTGAAAATG
1796232 TTTCTCTTGAAACAC
1 TTTCTCTTGAAACAC
1796247 CAAACCCTCG
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
33 9 0.20
34 2 0.04
35 2 0.04
36 33 0.72
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.33
Consensus pattern (35 bp):
TTTCTCTTGAAACACAAAAAAAACCTTTGAAAATG
Found at i:1796390 original size:84 final size:85
Alignment explanation
Indices: 1796254--1796411 Score: 212
Period size: 84 Copynumber: 1.9 Consensus size: 85
1796244 CACCAAACCC
* * * * *
1796254 TCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACATCATAACTCAAGGCTAGAAGGGT
1 TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACATCATAACTCAAGGCAACAAGGGC
1796319 TATCTGTCACCAAAAGACCT
66 TATCTGTCACCAAAAGACCT
** * *
1796339 TCGAGTTCGACTATGCTCAGC-TCTAAGGCACATCATTTACAGT-ATAGCTCAAGGCAACAAGGG
1 TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACA-TCATAACTCAAGGCAACAAGGG
1796402 CTATCTGTCA
65 CTATCTGTCA
1796412 ATAAAATTGT
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
84 44 0.70
85 19 0.30
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (85 bp):
TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACATCATAACTCAAGGCAACAAGGGC
TATCTGTCACCAAAAGACCT
Found at i:1797470 original size:20 final size:19
Alignment explanation
Indices: 1797447--1797519 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 19
1797437 ATTTCGTCCC
1797447 ATATATATATTTTTAATTAT
1 ATATATATATTTTT-ATTAT
* *
1797467 ATATAT-TCCTCTTTTTTTATTT
1 ATATATAT-AT-TTTTATTA--T
1797489 ATATTATATTATTTTTATTAT
1 ATA-TATA-TATTTTTATTAT
1797510 ATATATATAT
1 ATATATATAT
1797520 ATATGTATAG
Statistics
Matches: 42, Mismatches: 4, Indels: 15
0.69 0.07 0.25
Matches are distributed among these distances:
19 4 0.10
20 14 0.33
21 8 0.19
22 4 0.10
23 10 0.24
24 1 0.02
25 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (19 bp):
ATATATATATTTTTATTAT
Found at i:1797500 original size:14 final size:14
Alignment explanation
Indices: 1797483--1797521 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1797473 TCCTCTTTTT
1797483 TTATTTATATTATA
1 TTATTTATATTATA
*
1797497 TTATTTTTATTATA
1 TTATTTATATTATA
*
1797511 TATATATATAT
1 T-TATTTATAT
1797522 ATGTATAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:1797871 original size:19 final size:18
Alignment explanation
Indices: 1797849--1797896 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
1797839 TATCTGTGTC
1797849 TTTATTTTTTAACATTTTA
1 TTTATTTTTTAA-ATTTTA
* *
1797868 TTTATTTTGTTTATTTTTA
1 TTTATTTT-TTAAATTTTA
1797887 -TTATTTTTTA
1 TTTATTTTTTA
1797897 CGTGTTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 2 0.08
18 7 0.28
19 13 0.52
20 3 0.12
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTATTTTTTAAATTTTA
Found at i:1802957 original size:231 final size:231
Alignment explanation
Indices: 1802554--1803015 Score: 924
Period size: 231 Copynumber: 2.0 Consensus size: 231
1802544 CTCGGGTGGT
1802554 CTCTGTCGCTGGAAAGGTTCTCCTTAGAAGTTTAATTGGATATGAAGAAAATCTCTTTCATATTT
1 CTCTGTCGCTGGAAAGGTTCTCCTTAGAAGTTTAATTGGATATGAAGAAAATCTCTTTCATATTT
1802619 TAATTTATATTGAATCTATATATAAGGGAGATGTCCTCAATGTGCAGGCTTTTCTCATCACAAAC
66 TAATTTATATTGAATCTATATATAAGGGAGATGTCCTCAATGTGCAGGCTTTTCTCATCACAAAC
1802684 CTCGAGCCCATAATGTTCTGGGAATTTGTATCTCTCATACTTGGAGGTTTAGGGTATCCAAGGTA
131 CTCGAGCCCATAATGTTCTGGGAATTTGTATCTCTCATACTTGGAGGTTTAGGGTATCCAAGGTA
1802749 AAGCCCCTTGATTTTAATAATGGGCAAAGTGTGACA
196 AAGCCCCTTGATTTTAATAATGGGCAAAGTGTGACA
1802785 CTCTGTCGCTGGAAAGGTTCTCCTTAGAAGTTTAATTGGATATGAAGAAAATCTCTTTCATATTT
1 CTCTGTCGCTGGAAAGGTTCTCCTTAGAAGTTTAATTGGATATGAAGAAAATCTCTTTCATATTT
1802850 TAATTTATATTGAATCTATATATAAGGGAGATGTCCTCAATGTGCAGGCTTTTCTCATCACAAAC
66 TAATTTATATTGAATCTATATATAAGGGAGATGTCCTCAATGTGCAGGCTTTTCTCATCACAAAC
1802915 CTCGAGCCCATAATGTTCTGGGAATTTGTATCTCTCATACTTGGAGGTTTAGGGTATCCAAGGTA
131 CTCGAGCCCATAATGTTCTGGGAATTTGTATCTCTCATACTTGGAGGTTTAGGGTATCCAAGGTA
1802980 AAGCCCCTTGATTTTAATAATGGGCAAAGTGTGACA
196 AAGCCCCTTGATTTTAATAATGGGCAAAGTGTGACA
1803016 TGTCATTTAT
Statistics
Matches: 231, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
231 231 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (231 bp):
CTCTGTCGCTGGAAAGGTTCTCCTTAGAAGTTTAATTGGATATGAAGAAAATCTCTTTCATATTT
TAATTTATATTGAATCTATATATAAGGGAGATGTCCTCAATGTGCAGGCTTTTCTCATCACAAAC
CTCGAGCCCATAATGTTCTGGGAATTTGTATCTCTCATACTTGGAGGTTTAGGGTATCCAAGGTA
AAGCCCCTTGATTTTAATAATGGGCAAAGTGTGACA
Found at i:1808646 original size:2 final size:2
Alignment explanation
Indices: 1808639--1808680 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1808629 GGGTTTCAGT
1808639 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1808681 AGTTTCGTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1816253 original size:46 final size:44
Alignment explanation
Indices: 1816201--1816312 Score: 145
Period size: 44 Copynumber: 2.5 Consensus size: 44
1816191 TCGGTTATTA
* *
1816201 TGTTGTTCAGACCATT-CATTTTTCCCGGATACTTATATATTGATTT
1 TGTTGTTCACACC-TTCCATTTTTCCCGGATAC-T-TATATCGATTT
* *
1816247 TGTTGTTCCCACCTTCCATTTTTCCCGGATACTTGTATCGATTT
1 TGTTGTTCACACCTTCCATTTTTCCCGGATACTTATATCGATTT
*
1816291 TGTTGTTCCCACCTTCCATTTT
1 TGTTGTTCACACCTTCCATTTT
1816313 CCGGGTACAG
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
44 31 0.51
45 3 0.05
46 27 0.44
ACGTcount: A:0.16, C:0.24, G:0.12, T:0.47
Consensus pattern (44 bp):
TGTTGTTCACACCTTCCATTTTTCCCGGATACTTATATCGATTT
Found at i:1816303 original size:44 final size:46
Alignment explanation
Indices: 1816217--1816312 Score: 160
Period size: 44 Copynumber: 2.1 Consensus size: 46
1816207 TCAGACCATT
*
1816217 CATTTTTCCCGGATACTTATATATTGATTTTGTTGTTCCCACCTTC
1 CATTTTTCCCGGATACTTATATATCGATTTTGTTGTTCCCACCTTC
*
1816263 CATTTTTCCCGGATAC-T-TGTATCGATTTTGTTGTTCCCACCTTC
1 CATTTTTCCCGGATACTTATATATCGATTTTGTTGTTCCCACCTTC
1816307 CATTTT
1 CATTTT
1816313 CCGGGTACAG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 31 0.65
45 1 0.02
46 16 0.33
ACGTcount: A:0.16, C:0.25, G:0.11, T:0.48
Consensus pattern (46 bp):
CATTTTTCCCGGATACTTATATATCGATTTTGTTGTTCCCACCTTC
Found at i:1830323 original size:128 final size:127
Alignment explanation
Indices: 1830004--1830393 Score: 573
Period size: 127 Copynumber: 3.1 Consensus size: 127
1829994 AAAATTAACG
* **
1830004 GTTAACAGAGTCCGAACCATAATAATACGGATCATACCCCGGATCGGGTCACCACAAGGCCGAAT
1 GTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGCCGAAT
* ** * *
1830069 CAAATAATAGAAACAACAAATAAATAAATAACTGTTAGAATGTAATAAAATAAAAATTAGTA
66 CAAATAATAGAAACAATAAATAAATAAATAAAGGTTAGAATGCAATAAAATAAAAGTTAGTA
* *
1830131 GTTAACAGAGTCCGAACCATAATAATGTAGATCATACCCCGGATCGGGTCACCACAAGGCCGAAT
1 GTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGCCGAAT
* * ** *
1830196 CTAATAATAGAAACAATAAATAAATAAACAAAGGTTAGAGCGCAATAAAAATAAAAGTCAGTA
66 CAAATAATAGAAACAATAAATAAATAAATAAAGGTTAGAATGCAAT-AAAATAAAAGTTAGTA
* * *
1830259 GTTAGCATAGTCCGAACCATAATAATGTGGATCATACCCCGGATCTGGTCACCACAAGGTCGAAT
1 GTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGCCGAAT
* * * *
1830324 CGAATAATAGAAACAATAAATAAATAAATAATGGTTAGAATGCAATAAGATAAAAGTTAGCA
66 CAAATAATAGAAACAATAAATAAATAAATAAAGGTTAGAATGCAATAAAATAAAAGTTAGTA
1830386 GTTAGCAG
1 GTTAGCAG
1830394 TGACCAAATT
Statistics
Matches: 235, Mismatches: 27, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
127 120 0.51
128 115 0.49
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (127 bp):
GTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGCCGAAT
CAAATAATAGAAACAATAAATAAATAAATAAAGGTTAGAATGCAATAAAATAAAAGTTAGTA
Found at i:1831963 original size:133 final size:134
Alignment explanation
Indices: 1831594--1832068 Score: 794
Period size: 134 Copynumber: 3.6 Consensus size: 134
1831584 AGTGACACAA
* * *
1831594 CTCCTACATGAT-AAGGAGGTCTGGTCAG-GGATGACACGGCTCATACGTGATGAAGAGTTATGG
1 CTCCTACGTGATGAA-GAGATCTGGTCGGTGGATGACACGGCTCATACGTGATGAAGAGTTATGG
*
1831657 CCATCTTTAGGAAGGGTGATAACTCGGTTCCTACACGATGAGGACGGCTGGTTATCTATGGTTGA
65 CCATCTTTAGGAAGGGTGATAACTCGGTTCCTACATGATGAGGACGGCTGGTTATCTATGGTTGA
1831722 CACGG
130 CACGG
*
1831727 CTCCTACGTGATGAAGAGATCTGGTCGGTGGATGTCACGGCTCATACGTGATGAAGAGTTATGGC
1 CTCCTACGTGATGAAGAGATCTGGTCGGTGGATGACACGGCTCATACGTGATGAAGAGTTATGGC
*
1831792 CATCTTTAGGAAGGGTGATAACTCGGTTCCTACATGATGAGGACGACTGGTTATCTATGGTTGAC
66 CATCTTTAGGAAGGGTGATAACTCGGTTCCTACATGATGAGGACGGCTGGTTATCTATGGTTGAC
*
1831857 ATGG
131 ACGG
* * *
1831861 CTCCTACGTGATGAAGAGATCTGGT-GGTGGATGACACGACTTATACGTGATGAAGAGTTCTGGC
1 CTCCTACGTGATGAAGAGATCTGGTCGGTGGATGACACGGCTCATACGTGATGAAGAGTTATGGC
*
1831925 CATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGAC
66 CATCTTTAGGAAGGGTGATAACTCGGTTCCTACATGATGAGGACGGCTGGTTATCTATGGTTGAC
*
1831990 ACGA
131 ACGG
* *
1831994 CTCCTACGTGATGAAGAGATCTGGTCGGTGGATGACACGGCTCATAGGTGATGAAGAGTTCTGGC
1 CTCCTACGTGATGAAGAGATCTGGTCGGTGGATGACACGGCTCATACGTGATGAAGAGTTATGGC
1832059 CATCTTTAGG
66 CATCTTTAGG
1832069 GATACTGATT
Statistics
Matches: 321, Mismatches: 18, Indels: 5
0.93 0.05 0.01
Matches are distributed among these distances:
133 147 0.46
134 174 0.54
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (134 bp):
CTCCTACGTGATGAAGAGATCTGGTCGGTGGATGACACGGCTCATACGTGATGAAGAGTTATGGC
CATCTTTAGGAAGGGTGATAACTCGGTTCCTACATGATGAGGACGGCTGGTTATCTATGGTTGAC
ACGG
Found at i:1832114 original size:29 final size:29
Alignment explanation
Indices: 1832077--1832137 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
1832067 GGGATACTGA
1832077 TTTCAAAAGAAACCA-ACTCAAAGATGATG
1 TTTCAAAAGAAA-CAGACTCAAAGATGATG
*
1832106 TTTCAAAAGAAACAGACTCAAGGATGATG
1 TTTCAAAAGAAACAGACTCAAAGATGATG
1832135 TTT
1 TTT
1832138 TTTAAAAGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (29 bp):
TTTCAAAAGAAACAGACTCAAAGATGATG
Found at i:1832410 original size:64 final size:64
Alignment explanation
Indices: 1832300--1832439 Score: 174
Period size: 64 Copynumber: 2.2 Consensus size: 64
1832290 CAAAGATGGT
1832300 AAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTTAAAAGAAACTATCTCAAAAGAGACA
1 AAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTC-TAAAAGAAACTATCTCAAAAGAGACA
* * * * * * * *
1832365 AAATTTTGTTTCCCAAAGAAATATATTCAATGATTTTTC-AAAAGAAATTGTCTCAATATAGACA
1 AAATTTTGTTT-CCAAAGAAACAAACTCAAAGATTTTTCTAAAAGAAACTATCTCAAAAGAGACA
*
1832429 AAACTTTGTTT
1 AAATTTTGTTT
1832440 TTCAGAAAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
64 31 0.48
65 11 0.17
66 23 0.35
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.34
Consensus pattern (64 bp):
AAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTAAAAGAAACTATCTCAAAAGAGACA
Found at i:1832676 original size:31 final size:31
Alignment explanation
Indices: 1832605--1832679 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
1832595 TCAAAATTCG
* * *
1832605 TTTCAAGGGAAAC-GACTCAAAGATGGTTTTA
1 TTTCAAGAGAAACAAACTCAAAGAT-GTTTGA
1832636 TTTCAAGAGAAACAAACTCAAAGAT-TTTGA
1 TTTCAAGAGAAACAAACTCAAAGATGTTTGA
*
1832666 TTTTCTAGAGAAAC
1 -TTTCAAGAGAAAC
1832680 TGCCTCAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 4 0.11
31 24 0.63
32 10 0.26
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (31 bp):
TTTCAAGAGAAACAAACTCAAAGATGTTTGA
Found at i:1833010 original size:19 final size:16
Alignment explanation
Indices: 1832971--1833003 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1832961 CTGTCTCAAG
1832971 TGAGACAAAGTTTGTT
1 TGAGACAAAGTTTGTT
1832987 TGAGACAAAGTTTGTT
1 TGAGACAAAGTTTGTT
1833003 T
1 T
1833004 TTTGAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.39
Consensus pattern (16 bp):
TGAGACAAAGTTTGTT
Found at i:1833038 original size:53 final size:51
Alignment explanation
Indices: 1832937--1833040 Score: 131
Period size: 53 Copynumber: 2.0 Consensus size: 51
1832927 TGTTTTAAAC
*
1832937 GAGACAAAATTTGTTTTTAAAAAACTGTCTCAAGTGAGACAAAGTTTGTTT
1 GAGACAAAATTTGTTTTTAAAAAACTGTCTCAAGTGAGACAAACTTTGTTT
* *
1832988 GAGACAAAGTTTGTTTTTTGAGAAAAC-GATCTCAAGTGAGATC-AACTTTGTTT
1 GAGACAAAATTTG-TTTTT-AAAAAACTG-TCTCAAGTGAGA-CAAACTTTGTTT
1833041 AATGTGAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
51 12 0.26
52 6 0.13
53 27 0.59
54 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.36
Consensus pattern (51 bp):
GAGACAAAATTTGTTTTTAAAAAACTGTCTCAAGTGAGACAAACTTTGTTT
Found at i:1833657 original size:4 final size:4
Alignment explanation
Indices: 1833650--1833714 Score: 82
Period size: 4 Copynumber: 16.8 Consensus size: 4
1833640 TTTATATATA
* *
1833650 ATGT ATGT ATG- -TGT ATAT ATGT TTGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1833696 ATGT ATGT AT-T GATGT ATG
1 ATGT ATGT ATGT -ATGT ATG
1833715 CTTTTCTCGA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 2 0.04
3 1 0.02
4 49 0.92
5 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
ATGT
Found at i:1835092 original size:21 final size:21
Alignment explanation
Indices: 1835050--1835092 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1835040 GTTCTGGGCT
*
1835050 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
1835071 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
1835092 A
1 A
1835093 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1835145 original size:20 final size:20
Alignment explanation
Indices: 1835120--1835157 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1835110 GAACGCTAGA
*
1835120 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
1835140 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
1835158 TAAAAAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:1835963 original size:103 final size:103
Alignment explanation
Indices: 1835635--1835955 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
1835625 GTAGAGGGTC
1835635 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAACTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAACTCTGGTGAGACACATAC
*
1835700 TTGATCCTTGGCATATGTATATGATTCTTAAGAAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1835738 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAACTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAACTCTGGTGAGACACATAC
1835803 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* * *
1835841 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGTACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAACTCTGGTGAGACACATAC
*
1835906 TTGATCCTTGGCATATGTATATGATCCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1835944 TATGTGGTCCTT
1 TATGTGGTCCTT
1835956 ATGGACATTA
Statistics
Matches: 212, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAACTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1836006 original size:23 final size:23
Alignment explanation
Indices: 1835972--1836034 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
1835962 ATTATTATAT
1835972 GGCA-TTACGGTGCAATTCTACGC
1 GGCACTTA-GGTGCAATTCTACGC
*
1835995 GGCACTCT-GGTGCAATTCTACGT
1 GGCACT-TAGGTGCAATTCTACGC
1836018 GGCACTTAGGTGCAATT
1 GGCACTTAGGTGCAATT
1836035 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
22 1 0.03
23 33 0.92
24 1 0.03
25 1 0.03
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTTAGGTGCAATTCTACGC
Found at i:1840091 original size:19 final size:19
Alignment explanation
Indices: 1840054--1840108 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 19
1840044 TCTTTGTCTA
* *
1840054 TGCTCCTTGTTTTCT-TTT
1 TGCTCTTTGTTTTTTCTTT
1840072 TGCTCTTTGTTTTTTCTTT
1 TGCTCTTTGTTTTTTCTTT
1840091 TG--CTTTGATTTTTTCTTT
1 TGCTCTTTG-TTTTTTCTTT
1840109 GTTTCTTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.15
18 23 0.70
19 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.11, T:0.71
Consensus pattern (19 bp):
TGCTCTTTGTTTTTTCTTT
Found at i:1840113 original size:26 final size:24
Alignment explanation
Indices: 1840084--1840164 Score: 83
Period size: 27 Copynumber: 3.1 Consensus size: 24
1840074 CTCTTTGTTT
1840084 TTTCTTTTGCTTTGATTTTTTCTTTG
1 TTTCTTTT-CTTTG-TTTTTTCTTTG
1840110 TTTCTTTTCTCTTTGCTTTTTTCTTTG
1 TTTC-TTT-TCTTTG-TTTTTTCTTTG
1840137 CACTTT-TTTTCTTTGTTTTTTCTTTG
1 ---TTTCTTTTCTTTGTTTTTTCTTTG
1840163 TT
1 TT
1840165 ATTCTTTGTT
Statistics
Matches: 49, Mismatches: 1, Indels: 13
0.78 0.02 0.21
Matches are distributed among these distances:
23 2 0.04
26 15 0.31
27 25 0.51
28 4 0.08
30 3 0.06
ACGTcount: A:0.02, C:0.15, G:0.09, T:0.74
Consensus pattern (24 bp):
TTTCTTTTCTTTGTTTTTTCTTTG
Found at i:1840142 original size:19 final size:20
Alignment explanation
Indices: 1840105--1840142 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1840095 TTGATTTTTT
* *
1840105 CTTTGTTTCTTTTCTCTTTG
1 CTTTGTTTCTTTGCACTTTG
1840125 CTTT-TTTCTTTGCACTTT
1 CTTTGTTTCTTTGCACTTT
1840143 TTTTCTTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.03, C:0.21, G:0.08, T:0.68
Consensus pattern (20 bp):
CTTTGTTTCTTTGCACTTTG
Found at i:1840189 original size:71 final size:68
Alignment explanation
Indices: 1840075--1840204 Score: 167
Period size: 70 Copynumber: 1.9 Consensus size: 68
1840065 TTCTTTTTGC
*
1840075 TCTTTGTTTTTTCTTTTGCTTTGATTTTTTCTTTGTTTCTTTTCTCTTTGCTTTTTTCTTTGCAC
1 TCTTTGTTTTTTCTTTTGCTTTGATTTGTTCTTTGTTTCTTTT-TCTTTG-TTTTTT-TTTGCAC
1840140 TTTTTT
63 TTTTTT
**
1840146 TCTTTGTTTTTTC-TTTG-TTATTCTTTGTTCTTT-TTCTCTTTTTCTTTGTTTTTTTTTGC
1 TCTTTGTTTTTTCTTTTGCTT-TGATTTGTTCTTTGTT-TCTTTTTCTTTGTTTTTTTTTGC
1840205 TTCTTTTATG
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
67 5 0.09
68 6 0.11
69 10 0.19
70 20 0.37
71 13 0.24
ACGTcount: A:0.02, C:0.15, G:0.08, T:0.75
Consensus pattern (68 bp):
TCTTTGTTTTTTCTTTTGCTTTGATTTGTTCTTTGTTTCTTTTTCTTTGTTTTTTTTTGCACTTT
TTT
Found at i:1840222 original size:24 final size:21
Alignment explanation
Indices: 1840100--1840233 Score: 85
Period size: 21 Copynumber: 6.1 Consensus size: 21
1840090 TTGCTTTGAT
*
1840100 TTTTTCTTTGTTTCTTTTCTC
1 TTTTTCTTTGTTTTTTTTCTC
* ** *
1840121 -TTTGCTTT-TTTCTTTGCACTT
1 TTTTTCTTTGTTT-TTT-TTCTC
*
1840142 TTTTTCTTTGTTTTTTCTT-TG
1 TTTTTCTTTGTTTTTT-TTCTC
* *
1840163 TTATTCTTTGTTCTTTTTCTC
1 TTTTTCTTTGTTTTTTTTCTC
1840184 TTTTTCTTTGTTTTTTTTTGCTTC
1 TTTTTCTTTG-TTTTTTTT-C-TC
*
1840208 TTTTATGTTTGTTTTTCTTGTCTC
1 TTTT-TCTTTGTTTTT-TT-TCTC
1840232 TT
1 TT
1840234 CACTTTGATT
Statistics
Matches: 86, Mismatches: 16, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
19 3 0.03
20 11 0.13
21 27 0.31
22 17 0.20
23 4 0.05
24 15 0.17
25 8 0.09
26 1 0.01
ACGTcount: A:0.02, C:0.15, G:0.08, T:0.75
Consensus pattern (21 bp):
TTTTTCTTTGTTTTTTTTCTC
Found at i:1842346 original size:29 final size:31
Alignment explanation
Indices: 1842288--1842347 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 31
1842278 AAAATGACAC
* *
1842288 AAACAAAAGAGAAGAAATAAGTTGGTGTACAA
1 AAACAAAAGAGAAGAAACAAGTT-GAGTACAA
1842320 AAACAAAAGAGAA-AAACAAGTT-AGTACA
1 AAACAAAAGAGAAGAAACAAGTTGAGTACA
1842348 TGTAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 5 0.19
31 8 0.31
32 13 0.50
ACGTcount: A:0.60, C:0.08, G:0.18, T:0.13
Consensus pattern (31 bp):
AAACAAAAGAGAAGAAACAAGTTGAGTACAA
Found at i:1844657 original size:131 final size:132
Alignment explanation
Indices: 1844488--1844848 Score: 471
Period size: 128 Copynumber: 2.8 Consensus size: 132
1844478 AAAATTAACG
* **
1844488 GTTAACAGAGTCCGAACTATAATAATACGGATCATACCCCGGATCGGGTCACCACAAGGCCGAAT
1 GTTAACAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGCCGAAT
* * * *
1844553 CAAATAATAGAAACAACAAATAAATAAATAAATAACTGTTAGAATGTAAT-AAAATAAAAGTTAG
66 CAAATAATAGAAACAACAAATAAATAAATAAATAAATGTTAGAACGCAATAAAAATAAAAGTCAG
1844617 TA
131 TA
* *
1844619 GTTAACAGAGTCTGAACCATAATAATGTAGATCATACCCCGGATCGGGTCACCACAAGGCCGAAT
1 GTTAACAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGCCGAAT
* * *
1844684 CTAATAATAG--A-AAC-AATAAATAAATAAACAAATGTTAGAGCGCAATAAAAATAAAAGTCAG
66 CAAATAATAGAAACAACAAATAAATAAATAAATAAATGTTAGAACGCAATAAAAATAAAAGTCAG
1844745 TA
131 TA
* * * * * *** * *
1844747 GCTAGCAGAGTCCGAACCATAATAACGTGGATCATACTCCGAATCTAATCTCCACAAGGTCGAAT
1 GTTAACAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGCCGAAT
* *
1844812 CGAATAATAGAAACAATAAATAAATAAATAAATAAAT
66 CAAATAATAGAAACAACAAATAAATAAATAAATAAAT
1844849 AAATAAATAA
Statistics
Matches: 198, Mismatches: 27, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
127 27 0.14
128 80 0.40
129 1 0.01
130 1 0.01
131 71 0.36
132 18 0.09
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (132 bp):
GTTAACAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGCCGAAT
CAAATAATAGAAACAACAAATAAATAAATAAATAAATGTTAGAACGCAATAAAAATAAAAGTCAG
TA
Found at i:1844835 original size:4 final size:4
Alignment explanation
Indices: 1844826--1844858 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1844816 TAATAGAAAC
1844826 AATA AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA AATA A
1844859 TGGTTAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:1849025 original size:23 final size:23
Alignment explanation
Indices: 1848998--1849051 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
1848988 ATTTTACCCA
* *
1848998 TTAACTTTAGATAAAATATTATT
1 TTAACTCTAGATAAAATATTAAT
1849021 TTAACTCTAGATAAAATATTAAT
1 TTAACTCTAGATAAAATATTAAT
1849044 TTAACTCT
1 TTAACTCT
1849052 TTAACCTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (23 bp):
TTAACTCTAGATAAAATATTAAT
Found at i:1863350 original size:26 final size:26
Alignment explanation
Indices: 1863314--1863365 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1863304 TTTAAGGGAC
*
1863314 TTACCTTTATCATGTCATCTATTGAA
1 TTACCTTTATCATATCATCTATTGAA
1863340 TTACCTTTATCATATCATCTATTGAA
1 TTACCTTTATCATATCATCTATTGAA
1863366 CGGGTTTGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (26 bp):
TTACCTTTATCATATCATCTATTGAA
Found at i:1868186 original size:16 final size:16
Alignment explanation
Indices: 1868165--1868197 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1868155 GTACTTAAAC
1868165 TATCATTTTATCACAT
1 TATCATTTTATCACAT
1868181 TATCATTTTATCACAT
1 TATCATTTTATCACAT
1868197 T
1 T
1868198 CTTATTGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (16 bp):
TATCATTTTATCACAT
Found at i:1870089 original size:16 final size:17
Alignment explanation
Indices: 1870062--1870096 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1870052 AATATCATAG
1870062 TATTATTTTTTTGATAA
1 TATTATTTTTTTGATAA
1870079 TATTA-TTTTTTGATAA
1 TATTATTTTTTTGATAA
1870095 TA
1 TA
1870097 ATAATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (17 bp):
TATTATTTTTTTGATAA
Found at i:1870103 original size:17 final size:16
Alignment explanation
Indices: 1870068--1870104 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1870058 ATAGTATTAT
*
1870068 TTTTTTGATAATATTA
1 TTTTTTGATAATATAA
1870084 TTTTTTGATAATAATAA
1 TTTTTTGATAAT-ATAA
1870101 TTTT
1 TTTT
1870105 ATTTTGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTTTGATAATATAA
Found at i:1877499 original size:3 final size:3
Alignment explanation
Indices: 1877491--1877537 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
1877481 TTTTTTCATT
* *
1877491 TTA TTA TTA TTA TTA CTA TTA -TA TTA TTA TTTA TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
1877536 TT
1 TT
1877538 TATTTATTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1877525 original size:27 final size:27
Alignment explanation
Indices: 1877494--1877546 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1877484 TTTCATTTTA
1877494 TTATTATTATTACTA-TTATATTATTAT
1 TTATTATTATTACTATTTAT-TTATTAT
* *
1877521 TTATTTTTATTATTATTTATTTATTA
1 TTATTATTATTACTATTTATTTATTA
1877547 CAAACATGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (27 bp):
TTATTATTATTACTATTTATTTATTAT
Found at i:1879847 original size:182 final size:183
Alignment explanation
Indices: 1879541--1879908 Score: 672
Period size: 182 Copynumber: 2.0 Consensus size: 183
1879531 TATTTTTTAA
1879541 ATTATGTTTTCTTAAAAACTATTTTAAAAATTATTTTAGGTAGTTGACCTACCTAAACCAAAAAG
1 ATTATGTTTTCTTAAAAACTATTTTAAAAATTATTTTAGGTAGTTGACCTACCTAAACCAAAAAG
1879606 GTCAATGACTACTCCTAAAATATTCTAAATCAAAATCATTTATTTTTTCCGCTAAGTAAAATTTC
66 GTCAATGACTACTCCTAAAATATTCTAAATCAAAATCATTTATTTTTTCCGCTAAGTAAAATTTC
1879671 GT-CCCGAGCGAAAACCGGTTAC-TATTTATTTA-AATTTCGTTTC-TTACCTGT
131 GTGCCCGAGCGAAAACCGGTTACTTATTTATTTATAATTTCG--TCATTACCTGT
1879722 ATTATGTTTTCTTAAAAACTATTTTAAAAGATTATTTTAGGTAGTTGACCTACCTAAACCAAAAA
1 ATTATGTTTTCTTAAAAACTATTTTAAAA-ATTATTTTAGGTAGTTGACCTACCTAAACCAAAAA
1879787 GGTCAATGACTACTCCTAAAATATTCTAAATCAAAATCATTTATTTTTTCCGCTAAGTAAAATTT
65 GGTCAATGACTACTCCTAAAATATTCTAAATCAAAATCATTTATTTTTTCCGCTAAGTAAAATTT
*
1879852 CGTGCCCGGGCGAAAACCGGTTACTTATTTATTTATAATTTCGTCATTACCTGT
130 CGTGCCCGAGCGAAAACCGGTTACTTATTTATTTATAATTTCGTCATTACCTGT
1879906 ATT
1 ATT
1879909 TTATACATAT
Statistics
Matches: 181, Mismatches: 1, Indels: 7
0.96 0.01 0.04
Matches are distributed among these distances:
181 29 0.16
182 103 0.57
183 21 0.12
184 21 0.12
185 7 0.04
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.39
Consensus pattern (183 bp):
ATTATGTTTTCTTAAAAACTATTTTAAAAATTATTTTAGGTAGTTGACCTACCTAAACCAAAAAG
GTCAATGACTACTCCTAAAATATTCTAAATCAAAATCATTTATTTTTTCCGCTAAGTAAAATTTC
GTGCCCGAGCGAAAACCGGTTACTTATTTATTTATAATTTCGTCATTACCTGT
Found at i:1880300 original size:3 final size:3
Alignment explanation
Indices: 1880292--1880325 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1880282 TTTAATACAT
*
1880292 TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1880326 AAAAATCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1886088 original size:41 final size:41
Alignment explanation
Indices: 1886026--1886117 Score: 157
Period size: 41 Copynumber: 2.2 Consensus size: 41
1886016 TTTTTAAATT
* *
1886026 ATTTTCACGTGTATAGAAGGTCTTTGGAGGATGATATTCCC
1 ATTTTCATGTATATAGAAGGTCTTTGGAGGATGATATTCCC
*
1886067 ATTTTCATGTATATAGTAGGTCTTTGGAGGATGATATTCCC
1 ATTTTCATGTATATAGAAGGTCTTTGGAGGATGATATTCCC
1886108 ATTTTCATGT
1 ATTTTCATGT
1886118 TTGGATATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.41
Consensus pattern (41 bp):
ATTTTCATGTATATAGAAGGTCTTTGGAGGATGATATTCCC
Found at i:1891892 original size:43 final size:43
Alignment explanation
Indices: 1891638--1891880 Score: 387
Period size: 43 Copynumber: 5.7 Consensus size: 43
1891628 ATCATTCTGT
* *
1891638 ATGGGATCCTCTACGGAGAGCATCATCCTCGTCGCGATTTTGC
1 ATGGGATCCTCTACGGAGGGCATCATCCTCGTCCCGATTTTGC
* *
1891681 ATGGGATCCTCTATGGAGGGCATCTTCCTCGTCCCGATTTTGC
1 ATGGGATCCTCTACGGAGGGCATCATCCTCGTCCCGATTTTGC
* *
1891724 ATGTGATCCTCTACGGAGGGCATCATCCCCGTCCCGATTTTGC
1 ATGGGATCCTCTACGGAGGGCATCATCCTCGTCCCGATTTTGC
*
1891767 ATGGGATCCTCTACGGAGAGCATCATCCTCGTCCCGATTTTGC
1 ATGGGATCCTCTACGGAGGGCATCATCCTCGTCCCGATTTTGC
* ***
1891810 ATGGGATCATCTACGGAGGGCATCATCCTCGTCCCGATTCAAC
1 ATGGGATCCTCTACGGAGGGCATCATCCTCGTCCCGATTTTGC
1891853 ATGGGATCCTCTACGGAGGGCATCATCC
1 ATGGGATCCTCTACGGAGGGCATCATCC
1891881 ATGTCCTGAT
Statistics
Matches: 183, Mismatches: 17, Indels: 0
0.92 0.09 0.00
Matches are distributed among these distances:
43 183 1.00
ACGTcount: A:0.19, C:0.30, G:0.25, T:0.27
Consensus pattern (43 bp):
ATGGGATCCTCTACGGAGGGCATCATCCTCGTCCCGATTTTGC
Found at i:1895743 original size:2 final size:2
Alignment explanation
Indices: 1895738--1895766 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1895728 TTTTTTTAGT
1895738 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1895767 TATTGATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1895779 original size:3 final size:3
Alignment explanation
Indices: 1895764--1895840 Score: 111
Period size: 3 Copynumber: 25.7 Consensus size: 3
1895754 TATATATATA
* * *
1895764 TAT TAT TGA- TAT TAT TAT TAT TGT TGT TGT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1895809 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1895841 CACCACTCGG
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 1 0.01
3 68 0.97
4 1 0.01
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1895943 original size:18 final size:18
Alignment explanation
Indices: 1895920--1895960 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1895910 AACCCTAGCT
* *
1895920 ACCTCAGCTGCCAACGCC
1 ACCTCAGCTACCAACACC
1895938 ACCTCAGCTACCAACACC
1 ACCTCAGCTACCAACACC
1895956 ACCTC
1 ACCTC
1895961 TCCTCTGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.27, C:0.51, G:0.10, T:0.12
Consensus pattern (18 bp):
ACCTCAGCTACCAACACC
Found at i:1897497 original size:11 final size:12
Alignment explanation
Indices: 1897472--1897501 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
1897462 CCTTCTTAGG
1897472 ATTATTCGAATA
1 ATTATTCGAATA
1897484 ATTATTCG-ATA
1 ATTATTCGAATA
1897495 ATTATTC
1 ATTATTC
1897502 TTCATGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.47
Consensus pattern (12 bp):
ATTATTCGAATA
Found at i:1902310 original size:5 final size:6
Alignment explanation
Indices: 1902281--1902313 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1902271 TTTTATTTTG
1902281 TTTTCC TTTTCC TTTTCC TTTTCC -TTTCC TTTT
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTT
1902314 TTTTTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTCC
Found at i:1902340 original size:27 final size:27
Alignment explanation
Indices: 1902310--1902368 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
1902300 TTTCCTTTCC
* * *
1902310 TTTTTTTTTCTTTTTTCTTTATTGTGT
1 TTTTTTTTTCTTATTTCTTTATTCTAT
*
1902337 TTTTATTTTCTTATTTCTTTATTCTAT
1 TTTTTTTTTCTTATTTCTTTATTCTAT
1902364 TTTTT
1 TTTTT
1902369 ATTATTTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.80
Consensus pattern (27 bp):
TTTTTTTTTCTTATTTCTTTATTCTAT
Found at i:1902376 original size:10 final size:11
Alignment explanation
Indices: 1902347--1902395 Score: 59
Period size: 10 Copynumber: 4.5 Consensus size: 11
1902337 TTTTATTTTC
1902347 TTATTTCTTTAT
1 TTATTT-TTTAT
1902359 TCTATTTTTTA-
1 T-TATTTTTTAT
1902370 TTA-TTTTTAT
1 TTATTTTTTAT
1902380 TTA-TTTTTAT
1 TTATTTTTTAT
1902390 TTATTT
1 TTATTT
1902396 CTATTTTATC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 6 0.18
10 15 0.44
11 3 0.09
12 5 0.15
13 5 0.15
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (11 bp):
TTATTTTTTAT
Found at i:1902384 original size:20 final size:20
Alignment explanation
Indices: 1902338--1902401 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
1902328 TTATTGTGTT
*
1902338 TTTATTTTCTTATT-TCTTTA
1 TTTATTTT-TTATTATTTTTA
1902358 TTCTATTTTTTATTATTTTTA
1 TT-TATTTTTTATTATTTTTA
*
1902379 TTTA-TTTTTATTTATTTCTA
1 TTTATTTTTTA-TTATTTTTA
1902399 TTT
1 TTT
1902402 TATCTTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 6 0.15
20 20 0.51
21 13 0.33
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTATTTTTTATTATTTTTA
Found at i:1902400 original size:10 final size:10
Alignment explanation
Indices: 1902354--1902401 Score: 62
Period size: 10 Copynumber: 4.7 Consensus size: 10
1902344 TTCTTATTTC
1902354 TTTATTCTATT
1 TTTATT-TATT
1902365 TTT-TATTATT
1 TTTAT-TTATT
1902375 TTTATTTATT
1 TTTATTTATT
1902385 TTTATTTATT
1 TTTATTTATT
*
1902395 TCTATTT
1 TTTATTT
1902402 TATCTTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
10 29 0.85
11 5 0.15
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTATTTATT
Found at i:1910114 original size:208 final size:208
Alignment explanation
Indices: 1909753--1910157 Score: 693
Period size: 208 Copynumber: 1.9 Consensus size: 208
1909743 GTCATATATC
* *
1909753 ATCTGAGTAAGAAGTTCACCGATTGCGAGATTAGACATCCTCCTATCGAGAAAGTTTGTTGAGCT
1 ATCTGAGTAAGAAGTTCACCGATTGCGAGATTAGACATCCTCCAATCGAGAAAGTTTATTGAGCT
* * * * *
1909818 CTAGTCTGGGCTACAAATAGACTCAGGCAATATATATTGTATCACACTACTTGGCTGATTTCCAA
66 ATAGTCTGGGCTACAAAGAGACTCAGACAATACATATTGTATCACACTACTTGGATGATTTCCAA
*
1909883 GTTGAATCCTTTAAAGCACATGATGAGTGTACCTACTCTATCTGAAAGGTTAACCCGATGATAGA
131 GTTGAATCCTTTAAAGCACATGATGAGTGTACCTACTCTATCTGAAAGGTTAACCCGATGACAGA
1909948 TAGAAAGCCATCT
196 TAGAAAGCCATCT
* * * *
1909961 ATCTGAGTAAGAAGTTTACCGATTGCGAGGTTAGACATCCTCCAATCGAGAAGGTTTATTGTGCT
1 ATCTGAGTAAGAAGTTCACCGATTGCGAGATTAGACATCCTCCAATCGAGAAAGTTTATTGAGCT
1910026 ATAGTCTGGGCTACAAAGAGACTCAGACAATACATATTGTATCACACTACTTGGATGATTTCCAA
66 ATAGTCTGGGCTACAAAGAGACTCAGACAATACATATTGTATCACACTACTTGGATGATTTCCAA
*
1910091 GTTGAATCCTTTAAAGTACATGATGAGTGTACCTACTCTATCTGAAAGGTTAACCCGATGACAGA
131 GTTGAATCCTTTAAAGCACATGATGAGTGTACCTACTCTATCTGAAAGGTTAACCCGATGACAGA
1910156 TA
196 TA
1910158 CTATTGTCTG
Statistics
Matches: 184, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
208 184 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (208 bp):
ATCTGAGTAAGAAGTTCACCGATTGCGAGATTAGACATCCTCCAATCGAGAAAGTTTATTGAGCT
ATAGTCTGGGCTACAAAGAGACTCAGACAATACATATTGTATCACACTACTTGGATGATTTCCAA
GTTGAATCCTTTAAAGCACATGATGAGTGTACCTACTCTATCTGAAAGGTTAACCCGATGACAGA
TAGAAAGCCATCT
Found at i:1914722 original size:17 final size:18
Alignment explanation
Indices: 1914700--1914733 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1914690 TTCGGCCCTC
1914700 CAATTTAAT-TTTTATTT
1 CAATTTAATCTTTTATTT
*
1914717 CAATTTCATCTTTTATT
1 CAATTTAATCTTTTATT
1914734 ATTAATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (18 bp):
CAATTTAATCTTTTATTT
Found at i:1914745 original size:2 final size:2
Alignment explanation
Indices: 1914738--1914775 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1914728 TTTATTATTA
1914738 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
1914776 TTATCGATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1914875 original size:2 final size:2
Alignment explanation
Indices: 1914870--1914948 Score: 112
Period size: 2 Copynumber: 41.5 Consensus size: 2
1914860 TTTTTTCTTT
* *
1914870 TA TA TA TA TT TG TA TA TA TA TA TA TA TA TA TA T- 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
1914911 TA T- TA TA TA TA TA T- TA TA TA TA TA TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1914949 TTATTATTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
1 4 0.06
2 66 0.94
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1914902 original size:24 final size:23
Alignment explanation
Indices: 1914870--1914949 Score: 128
Period size: 22 Copynumber: 3.5 Consensus size: 23
1914860 TTTTTTCTTT
*
1914870 TATATATAT-TTGTATATATATA
1 TATATATATATTATATATATATA
1914892 TATATATATATTATATATATAT-
1 TATATATATATTATATATATATA
1914914 TATATATATATTATATATATATA
1 TATATATATATTATATATATATA
1914937 TATTATATATATT
1 TA-TATATATATT
1914950 TATTATTATT
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
22 31 0.57
23 13 0.24
24 10 0.19
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (23 bp):
TATATATATATTATATATATATA
Found at i:1914968 original size:9 final size:10
Alignment explanation
Indices: 1914872--1914968 Score: 91
Period size: 11 Copynumber: 9.8 Consensus size: 10
1914862 TTTTCTTTTA
1914872 TATATATT-T
1 TATATATTAT
1914881 GTATATA-TAT
1 -TATATATTAT
1914891 ATATATATATAT
1 -TATATAT-TAT
1914903 TATATATATAT
1 TATATAT-TAT
1914914 TATATATATAT
1 TATATAT-TAT
1914925 TATATA-TA-
1 TATATATTAT
1914933 TATATATTA-
1 TATATATTAT
1914942 TATATATTTAT
1 TATATA-TTAT
1914953 TAT-TATTAT
1 TATATATTAT
1914962 TAT-TATT
1 TATATATT
1914969 TTTCTAATAT
Statistics
Matches: 80, Mismatches: 1, Indels: 13
0.85 0.01 0.14
Matches are distributed among these distances:
8 6 0.08
9 22 0.28
10 18 0.22
11 31 0.39
12 3 0.04
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (10 bp):
TATATATTAT
Found at i:1915044 original size:16 final size:15
Alignment explanation
Indices: 1915024--1915080 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
1915014 TTCCTTTTTC
1915024 CTTTTTTTTTTATTGT
1 CTTTTTTTTTTATT-T
*
1915040 GTTTTATTTTCTTATTT
1 CTTTT-TTTT-TTATTT
*
1915057 CTTTATTTTTTTTTTT
1 CTTT-TTTTTTTATTT
*
1915073 ATTTTTTT
1 CTTTTTTT
1915081 CTATTTTATC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
15 4 0.12
16 12 0.35
17 12 0.35
18 6 0.18
ACGTcount: A:0.09, C:0.05, G:0.04, T:0.82
Consensus pattern (15 bp):
CTTTTTTTTTTATTT
Found at i:1915047 original size:39 final size:38
Alignment explanation
Indices: 1915002--1915075 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
1914992 TATAATATAT
* *
1915002 TTTTATTTTGTT-TTCCTTTTTCCTTTTTTTTTTATTGTG
1 TTTTATTTTCTTATTCCTTTAT--TTTTTTTTTTATTGTG
*
1915041 TTTTATTTTCTTATTTCTTTATTTTTTTTTTTATT
1 TTTTATTTTCTTATTCCTTTATTTTTTTTTTTATT
1915076 TTTTTCTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 13 0.42
39 11 0.35
40 7 0.23
ACGTcount: A:0.08, C:0.08, G:0.04, T:0.80
Consensus pattern (38 bp):
TTTTATTTTCTTATTCCTTTATTTTTTTTTTTATTGTG
Found at i:1915049 original size:27 final size:27
Alignment explanation
Indices: 1915001--1915063 Score: 65
Period size: 29 Copynumber: 2.3 Consensus size: 27
1914991 TTATAATATA
* * *
1915001 TTTTTATTTTGTTTTCCTTTTTCCTTTTT
1 TTTTTATTGTGTTTT-CATTTT-CTTATT
1915030 TTTTTATTGTGTTTT-ATTTTCTTATT
1 TTTTTATTGTGTTTTCATTTTCTTATT
*
1915056 TCTTTATT
1 TTTTTATT
1915064 TTTTTTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 12 0.40
27 4 0.13
29 14 0.47
ACGTcount: A:0.08, C:0.10, G:0.05, T:0.78
Consensus pattern (27 bp):
TTTTTATTGTGTTTTCATTTTCTTATT
Found at i:1915093 original size:40 final size:41
Alignment explanation
Indices: 1915025--1915127 Score: 106
Period size: 38 Copynumber: 2.5 Consensus size: 41
1915015 TCCTTTTTCC
*
1915025 TTTTTTTTTTATTGTGTTT-TATTTTCTTAT-TTCTT-TA-T
1 TTTTTTTTTTATT-TCTTTCTATTTTCTTATGTTCTTATACT
*
1915063 TTTTTTTTTTATTTTTTTCTATTTTATCTTATGTTCTTATACT
1 TTTTTTTTTTATTTCTTTCTA-TTT-TCTTATGTTCTTATACT
1915106 TGTCTTTATTTTTATTTCTTTC
1 T-T-TTT-TTTTTATTTCTTTC
1915128 ATGTTCTCTA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
37 4 0.07
38 15 0.28
39 3 0.06
40 6 0.11
41 5 0.09
42 2 0.04
43 2 0.04
44 1 0.02
45 3 0.06
46 13 0.24
ACGTcount: A:0.12, C:0.09, G:0.04, T:0.76
Consensus pattern (41 bp):
TTTTTTTTTTATTTCTTTCTATTTTCTTATGTTCTTATACT
Found at i:1920559 original size:2 final size:2
Alignment explanation
Indices: 1920554--1920627 Score: 78
Period size: 2 Copynumber: 36.5 Consensus size: 2
1920544 ATGTACACAG
* *
1920554 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT TGC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
* * *
1920596 TA TG TA CA CA GTA 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
1920628 TGGTTACTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 60 0.95
3 2 0.03
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1920564 original size:53 final size:54
Alignment explanation
Indices: 1920519--1920627 Score: 195
Period size: 53 Copynumber: 2.1 Consensus size: 54
1920509 TATTTTGAAT
*
1920519 TATATATATATATATATTTTTTGCTATGTACACAGTATATATATA-TATATATA
1 TATATATATATATATATATTTTGCTATGTACACAGTATATATATATTATATATA
1920572 TATATATATATATATATATTTTGCTATGTACACAGTATATATATA-TATATATA
1 TATATATATATATATATATTTTGCTATGTACACAGTATATATATATTATATATA
1920625 TAT
1 TAT
1920628 TGGTTACTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (54 bp):
TATATATATATATATATATTTTGCTATGTACACAGTATATATATATTATATATA
Found at i:1922570 original size:17 final size:17
Alignment explanation
Indices: 1922550--1922591 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
1922540 TTTATGCTAT
1922550 TTTGATGATTATTATGG
1 TTTGATGATTATTATGG
*
1922567 TTTGATGCTTATTATGG
1 TTTGATGATTATTATGG
1922584 TTT-ATGAT
1 TTTGATGAT
1922592 ACTTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.21, C:0.02, G:0.21, T:0.55
Consensus pattern (17 bp):
TTTGATGATTATTATGG
Found at i:1927624 original size:26 final size:26
Alignment explanation
Indices: 1927566--1927618 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
1927556 TTAGGACCGT
1927566 CCTTTTCATACACACCCATTATTGTA
1 CCTTTTCATACACACCCATTATTGTA
*
1927592 CCTTTTCAATACTCACCCATTATTGTA
1 CCTTTTC-ATACACACCCATTATTGTA
1927619 TTTTTCCCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.40
Consensus pattern (26 bp):
CCTTTTCATACACACCCATTATTGTA
Found at i:1930718 original size:31 final size:30
Alignment explanation
Indices: 1930681--1930766 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 30
1930671 AATTTCATTG
1930681 AATTTAGAGGTTAAATTGATATTTTATATA
1 AATTTAGAGGTTAAATTGATATTTTATATA
* *
1930711 AAGTTTAGGGGTTAAATT-AGTATTTTATGTA
1 AA-TTTAGAGGTTAAATTGA-TATTTTATATA
** *
1930742 AATTTTTAGGTCAAATTGATATTTT
1 AATTTAGAGGTTAAATTGATATTTT
1930767 GTCTAGGGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 20 0.43
31 27 0.57
ACGTcount: A:0.35, C:0.01, G:0.16, T:0.48
Consensus pattern (30 bp):
AATTTAGAGGTTAAATTGATATTTTATATA
Found at i:1948078 original size:11 final size:12
Alignment explanation
Indices: 1948061--1948106 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
1948051 TTTATTTGCA
1948061 ATTCTTTATCTT
1 ATTCTTTATCTT
1948073 -TTCTTTATCTT
1 ATTCTTTATCTT
* *
1948084 GTT-TTAATCTT
1 ATTCTTTATCTT
*
1948095 ATTTTTTATCTT
1 ATTCTTTATCTT
1948107 GTTTCCAGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.15, C:0.13, G:0.02, T:0.70
Consensus pattern (12 bp):
ATTCTTTATCTT
Found at i:1948105 original size:23 final size:22
Alignment explanation
Indices: 1948068--1948110 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1948058 GCAATTCTTT
1948068 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
1948090 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
1948111 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:1948396 original size:20 final size:20
Alignment explanation
Indices: 1948369--1948412 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1948359 TTTTTTTGAT
1948369 ATATATATATATGGATGGATGG
1 ATATAT-TA-ATGGATGGATGG
*
1948391 ATATATTAATGGGTGGATGG
1 ATATATTAATGGATGGATGG
1948411 AT
1 AT
1948413 GCTACGGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.30, T:0.36
Consensus pattern (20 bp):
ATATATTAATGGATGGATGG
Found at i:1956690 original size:29 final size:27
Alignment explanation
Indices: 1956648--1956701 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
1956638 CACAATTGAA
1956648 TTCACCCAAAGACGCCGAGAAATCTGG
1 TTCACCCAAAGACGCCGAGAAATCTGG
* *
1956675 TTCACCCCTAAAGACGTCGAGATATCT
1 TTCA-CCC-AAAGACGCCGAGAAATCT
1956702 CAAAACCCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 3 0.13
29 16 0.70
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (27 bp):
TTCACCCAAAGACGCCGAGAAATCTGG
Found at i:1960979 original size:60 final size:60
Alignment explanation
Indices: 1960860--1960998 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 60
1960850 ATATGAAAAA
* * * * * *
1960860 TTAGGTGACCATTTTGTAATTTTTAATAGTCAATAGACTCAACAAATAAGTGTCCTATAG
1 TTAGGGGACCATTATGTAACTTGTAATAATCAATAGACTCAACAAATAAGTATCCTATAG
* *
1960920 TTAGGGGACTATTATGTAACTTGTAATAATCAA-ATGACTCAACAAAATAA-TATCTTATAG
1 TTAGGGGACCATTATGTAACTTGTAATAATCAATA-GACTCAAC-AAATAAGTATCCTATAG
* *
1960980 ATAGAGGACCATCTATGTA
1 TTAGGGGACCAT-TATGTA
1960999 TTTTACCCAA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
59 1 0.02
60 52 0.80
61 12 0.18
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (60 bp):
TTAGGGGACCATTATGTAACTTGTAATAATCAATAGACTCAACAAATAAGTATCCTATAG
Found at i:1964705 original size:49 final size:50
Alignment explanation
Indices: 1964633--1964730 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 50
1964623 GACTTGTGTT
* ** *
1964633 TTTTTTTTCATTTGTTTATTGTTGTAGCAAAC-TTTTTTTGTTTTTATGA
1 TTTTTTGTCATTTGCGTATTGTTGTAGCAAACTTTTTTTTGTCTTTATGA
*
1964682 TTTTTTGTCATTTGCGTATTGTTGTAGCTAACTTTTTTTTGTCTTTATG
1 TTTTTTGTCATTTGCGTATTGTTGTAGCAAACTTTTTTTTGTCTTTATG
1964731 TATATATTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 28 0.65
50 15 0.35
ACGTcount: A:0.14, C:0.08, G:0.14, T:0.63
Consensus pattern (50 bp):
TTTTTTGTCATTTGCGTATTGTTGTAGCAAACTTTTTTTTGTCTTTATGA
Found at i:1964747 original size:17 final size:17
Alignment explanation
Indices: 1964725--1964757 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1964715 TTTTTTTGTC
*
1964725 TTTATGTATATATTTAT
1 TTTATGTATAAATTTAT
1964742 TTTATGTATAAATTTA
1 TTTATGTATAAATTTA
1964758 GCTTTCTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTATGTATAAATTTAT
Found at i:1968123 original size:33 final size:33
Alignment explanation
Indices: 1968086--1968158 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
1968076 ATCAACAGTG
1968086 TTTTTTCT-TCATTTGCTTATTGTTGTAGCAAAC
1 TTTTTT-TGTCATTTGCTTATTGTTGTAGCAAAC
**
1968119 TTTTTTTGTCATTTGCTTATTGTTGTAGTTAAC
1 TTTTTTTGTCATTTGCTTATTGTTGTAGCAAAC
1968152 TTTTTTT
1 TTTTTTT
1968159 TCTTTATGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 1 0.03
33 36 0.97
ACGTcount: A:0.15, C:0.11, G:0.12, T:0.62
Consensus pattern (33 bp):
TTTTTTTGTCATTTGCTTATTGTTGTAGCAAAC
Found at i:1968179 original size:15 final size:15
Alignment explanation
Indices: 1968156--1968185 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1968146 GTTAACTTTT
*
1968156 TTTTCTTTATGTATA
1 TTTTATTTATGTATA
1968171 TTTTATTTATGTATA
1 TTTTATTTATGTATA
1968186 AATTTAGCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (15 bp):
TTTTATTTATGTATA
Found at i:1979018 original size:20 final size:19
Alignment explanation
Indices: 1978989--1979027 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1978979 TTAATGGCTA
1978989 TCATTATTTACATTTCATTT
1 TCATTATTTACA-TTCATTT
* *
1979009 TCATTCTTTATATTCATTT
1 TCATTATTTACATTCATTT
1979028 CATAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (19 bp):
TCATTATTTACATTCATTT
Found at i:1982513 original size:11 final size:11
Alignment explanation
Indices: 1982497--1982534 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
1982487 ATGCTTGAAG
*
1982497 AAAAAAATGAA
1 AAAAAAAAGAA
1982508 AAAAAAGAAGAA
1 AAAAAA-AAGAA
1982520 AAAAAAAAGAA
1 AAAAAAAAGAA
1982531 AAAA
1 AAAA
1982535 GAAGGGGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.03
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:1982518 original size:21 final size:21
Alignment explanation
Indices: 1982493--1982538 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1982483 TACTATGCTT
*
1982493 GAAGAAAAAAATGAA-AAAAAA
1 GAAGAAAAAAA-AAAGAAAAAA
1982514 GAAGAAAAAAAAAAGAAAAAA
1 GAAGAAAAAAAAAAGAAAAAA
1982535 GAAG
1 GAAG
1982539 GGGGGTTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (21 bp):
GAAGAAAAAAAAAAGAAAAAA
Found at i:1983673 original size:133 final size:130
Alignment explanation
Indices: 1983489--1983813 Score: 534
Period size: 133 Copynumber: 2.5 Consensus size: 130
1983479 AGTGGATCAG
* * *
1983489 CATTTCAATGGAGAGTTCATAATGAGAAGAA-GCATCCGACAGA-GAGAAGAAGTTCATAATGAG
1 CATTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGAGAAGAAGTTCATAATGAG
1983552 AAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCGCTTGAGGAA
66 AAGAGCTTG-TCGACCTATCACTCGATTCATG-CATTTCGAATCAGTGACACCTCGCTTGAGG-A
1983617 TTGA
128 -TGA
1983621 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCAT-ATG
1 CATTT-CAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAA-GGAGAAGAAGTTCATAATG
1983685 AGAAGAGCTTGTCGACCTATCACTCGATTCATGCATTTCGAATCAGTGACACCTCGCTTGAGGAT
64 AGAAGAGCTTGTCGACCTATCACTCGATTCATGCATTTCGAATCAGTGACACCTCGCTTGAGGAT
1983750 GA
129 GA
1983752 CATTTCAATGGAGAGTTCATAATGAGAAGAACTCATCC--AAAAGGAGAAGAAGTTCATAATGA
1 CATTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGAGAAGAAGTTCATAATGA
1983814 AGCTTGTTCG
Statistics
Matches: 185, Mismatches: 3, Indels: 14
0.92 0.01 0.07
Matches are distributed among these distances:
127 15 0.08
128 8 0.04
130 33 0.18
131 8 0.04
132 6 0.03
133 56 0.30
134 31 0.17
135 14 0.08
136 14 0.08
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (130 bp):
CATTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGAGAAGAAGTTCATAATGAG
AAGAGCTTGTCGACCTATCACTCGATTCATGCATTTCGAATCAGTGACACCTCGCTTGAGGATGA
Found at i:1985671 original size:115 final size:117
Alignment explanation
Indices: 1985426--1985660 Score: 431
Period size: 115 Copynumber: 2.0 Consensus size: 117
1985416 TAGACTTATA
1985426 TTTATGCATATTTTGATTTAGGCCACTAGTTTTTTTTAATTTACATGTTTATCTCACATTCATTT
1 TTTATGCATATTTTGATTTAGGCCACTAGTTTTTTTTAATTTACATGTTTATCTCACATTCATTT
1985491 AAATTTAGTCATTATTTCAAATATATATATTTTAAATTTATTACTTTGGCAT
66 AAATTTAGTCATTATTTCAAATATATATATTTTAAATTTATTACTTTGGCAT
1985543 TTTATGCATATTTTGATTTAGGCCA-TAG-TTTTTTTAATTTACATGTTTAATCTCACATTCA-T
1 TTTATGCATATTTTGATTTAGGCCACTAGTTTTTTTTAATTTACATGTTT-ATCTCACATTCATT
*
1985605 TAAATTTAGTCATTATTTCAAATATATATTTTTTAAATTTATTACTTTGGCAT
65 TAAATTTAGTCATTATTTCAAATATATATATTTTAAATTTATTACTTTGGCAT
1985658 TTT
1 TTT
1985661 GTTTTTATTT
Statistics
Matches: 116, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
115 76 0.66
116 15 0.13
117 25 0.22
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.53
Consensus pattern (117 bp):
TTTATGCATATTTTGATTTAGGCCACTAGTTTTTTTTAATTTACATGTTTATCTCACATTCATTT
AAATTTAGTCATTATTTCAAATATATATATTTTAAATTTATTACTTTGGCAT
Found at i:1990108 original size:15 final size:15
Alignment explanation
Indices: 1990084--1990120 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1990074 CACGTTGATT
1990084 AATT-TAATTAAAA-
1 AATTATAATTAAAAG
1990097 ATATTATAATTAAAAG
1 A-ATTATAATTAAAAG
1990113 AATTATAA
1 AATTATAA
1990121 CTCGTCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 1 0.05
14 3 0.14
15 16 0.76
16 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AATTATAATTAAAAG
Found at i:1994380 original size:60 final size:60
Alignment explanation
Indices: 1994267--1994381 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
1994257 ATAGTCGAGT
* * * *
1994267 GATCATTTTGTAACTTTTAATAGTCGGTAGACTTAACAAAATAATGCATTATAGTTAAAG
1 GATCATTTTGTAACTTTTAATAGTCGGAAGACTCAACAAAATAATACACTATAGTTAAAG
* * * *
1994327 GATCGTTTTGTAACTTTTAATAGT-TGAAGAACTCGACAAAATAATACCCTATAGT
1 GATCATTTTGTAACTTTTAATAGTCGGAAG-ACTCAACAAAATAATACACTATAGT
1994382 CTTAGGGTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 3 0.07
60 43 0.93
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (60 bp):
GATCATTTTGTAACTTTTAATAGTCGGAAGACTCAACAAAATAATACACTATAGTTAAAG
Found at i:1996040 original size:2 final size:2
Alignment explanation
Indices: 1996033--1996069 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1996023 TTGAGATTAA
1996033 AT AT 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 AT AT A
1996070 AAATTCTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1996462 original size:18 final size:17
Alignment explanation
Indices: 1996441--1996474 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1996431 TCAATGCATC
1996441 AAATATAAATTTATAAAA
1 AAATATAAATTT-TAAAA
*
1996459 AAATATATATTTTAAA
1 AAATATAAATTTTAAA
1996475 GTCAATCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATATAAATTTTAAAA
Found at i:1998259 original size:16 final size:16
Alignment explanation
Indices: 1998240--1998276 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1998230 AGACCAAAAC
1998240 AATAAAATAAAATAA-A
1 AATAAAAT-AAATAATA
1998256 AATAAAATAAATAATA
1 AATAAAATAAATAATA
1998272 AATAA
1 AATAA
1998277 TATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AATAAAATAAATAATA
Found at i:1998276 original size:11 final size:11
Alignment explanation
Indices: 1998243--1998273 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
1998233 CCAAAACAAT
1998243 AAAATAAAATA
1 AAAATAAAATA
1998254 AAAATAAAATA
1 AAAATAAAATA
1998265 AATAATAAA
1 AA-AATAAA
1998274 TAATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:1998349 original size:34 final size:35
Alignment explanation
Indices: 1998273--1998606 Score: 211
Period size: 34 Copynumber: 9.3 Consensus size: 35
1998263 TAAATAATAA
* * *
1998273 ATAATATAT-ATATACATAAATATTTTCAAAAAC-AT
1 ATAATATATAATTTTCA-AAATGTTTT-AAAAACTAT
* *
1998308 ATAATATATAAATTTCAAAATGTTTT-TAAACTAT
1 ATAATATATAATTTTCAAAATGTTTTAAAAACTAT
* ** *
1998342 ATAATATATGAATTTTTTCAACATGTTTTCAAAAAAAAG
1 ATAATATAT-AA--TTTTCAAAATGTTTT-AAAAACTAT
* *
1998381 ATTATATA-AATTTTCCCAAAACGTTTTAAAAACTAT
1 ATAATATATAATTTT--CAAAATGTTTTAAAAACTAT
*
1998417 ATAATATA-AATGTTTTCAAAATGTTTTCAAAAC--T
1 ATAATATATAA--TTTTCAAAATGTTTTAAAAACTAT
* *
1998451 ATAATATATATGTTTTCAAAAATGTTTTCAAAACTAT
1 ATAATATATA-ATTTTC-AAAATGTTTTAAAAACTAT
* *
1998488 AT-ATATA-AGTTTTCAAAATGATTTTAAAAATTAT
1 ATAATATATAATTTTCAAAATG-TTTTAAAAACTAT
* *
1998522 ATATTATATATATTTTCTAAAATGTTTTCTTTTAAAACTAT
1 ATAATATATA-ATTTTC-AAAATG---T-TTTAAAAACTAT
* ** * *
1998563 ATATTATATAATTTT-AAAAACTATTAAAAATTAT
1 ATAATATATAATTTTCAAAATGTTTTAAAAACTAT
*
1998597 ATATTATATA
1 ATAATATATA
1998607 CGTAGTTTCA
Statistics
Matches: 242, Mismatches: 33, Indels: 49
0.75 0.10 0.15
Matches are distributed among these distances:
33 10 0.04
34 63 0.26
35 46 0.19
36 40 0.17
37 32 0.13
38 14 0.06
39 11 0.05
40 6 0.02
41 20 0.08
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (35 bp):
ATAATATATAATTTTCAAAATGTTTTAAAAACTAT
Found at i:1998370 original size:37 final size:36
Alignment explanation
Indices: 1998301--1998549 Score: 184
Period size: 37 Copynumber: 7.0 Consensus size: 36
1998291 AATATTTTCA
*
1998301 AAAAC-ATATAATATATAA--ATTTCAAAATGTTTT
1 AAAACTATATAATATATAATGTTTTCAAAATGTTTT
* * *
1998334 TAAACTATATAATATATGAATTTTTTCAACATGTTTT
1 AAAACTATATAATATAT-AATGTTTTCAAAATGTTTT
* * * * * *
1998371 CAAAA-AAAAGATTATATAAAT-TTTCCCAAAACGTTTT
1 -AAAACTATATAATATAT-AATGTTT-TCAAAATGTTTT
1998408 AAAAACTATATAATATA-AATGTTTTCAAAATGTTTT
1 -AAAACTATATAATATATAATGTTTTCAAAATGTTTT
1998444 CAAAAC--TATAATATAT-ATGTTTTCAAAAATGTTTT
1 -AAAACTATATAATATATAATGTTTTC-AAAATGTTTT
1998479 CAAAAC--TAT-ATATATAA-GTTTTCAAAATGATTTT
1 -AAAACTATATAATATATAATGTTTTCAAAATG-TTTT
* * *
1998513 AAAAATTATATATTATAT-ATATTTTCTAAAATGTTTT
1 -AAAACTATATAATATATAATGTTTTC-AAAATGTTTT
1998550 CTTTTAAAAC
Statistics
Matches: 175, Mismatches: 24, Indels: 30
0.76 0.10 0.13
Matches are distributed among these distances:
33 10 0.06
34 48 0.27
35 22 0.13
36 25 0.14
37 54 0.31
38 16 0.09
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.43
Consensus pattern (36 bp):
AAAACTATATAATATATAATGTTTTCAAAATGTTTT
Found at i:1998440 original size:11 final size:11
Alignment explanation
Indices: 1998424--1998448 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1998414 TATATAATAT
1998424 AAATGTTTTCA
1 AAATGTTTTCA
1998435 AAATGTTTTCA
1 AAATGTTTTCA
1998446 AAA
1 AAA
1998449 CTATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:1998593 original size:75 final size:70
Alignment explanation
Indices: 1998381--1998624 Score: 201
Period size: 71 Copynumber: 3.3 Consensus size: 70
1998371 CAAAAAAAAG
* * * * * *
1998381 ATTATATAAATTTTCCCAAAACGTTTTAAAAACTATATAATATAAATGTTTTCAAAATG-TTTTC
1 ATTATATATATTTT-CAAAAATGTTTTCAAAACTATAT-ATATAAA--TTTTCAAAA-GATATTA
*
1998445 AAAACTATA-
61 AAAATTATAT
* * *
1998454 A-TATATATGTTTTCAAAAATGTTTTCAAAACTATATATATAAGTTTTCAAAATGATTTTAAAAA
1 ATTATATATATTTTCAAAAATGTTTTCAAAACTATATATATAAATTTTCAAAA-GATATTAAAAA
1998518 TTATAT
65 TTATAT
*
1998524 ATTATATATATTTTCTAAAATGTTTTCTTTTAAAACTATATATTATATAATTTT-AAAA-ACTAT
1 ATTATATATATTTTCAAAAATGTTTTC----AAAACTATATA-TATA-AATTTTCAAAAGA-TAT
1998587 TAAAAATTATAT
59 TAAAAATTATAT
*
1998599 ATTATATACGTAGTTTCAAAATATGT
1 ATTATATA--TATTTTCAAAA-ATGT
1998625 ATATATATAA
Statistics
Matches: 144, Mismatches: 14, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
68 11 0.08
69 12 0.08
70 7 0.05
71 43 0.30
72 10 0.07
73 1 0.01
74 1 0.01
75 33 0.23
76 8 0.06
77 14 0.10
78 4 0.03
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (70 bp):
ATTATATATATTTTCAAAAATGTTTTCAAAACTATATATATAAATTTTCAAAAGATATTAAAAAT
TATAT
Done.