Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008935.1 Hibiscus syriacus cultivar Beakdansim tig00112253_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: 1775090
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:1052185 original size:33 final size:33
Alignment explanation
Indices: 1052042--1052410 Score: 400
Period size: 30 Copynumber: 11.2 Consensus size: 33
1052032 TTAAAAACTA
* * *
1052042 TATACTATACGTTTTCAAAACTATTTTAAAAAC
1 TATATTATATGTTTTCAAAATTATTTTAAAAAC
* *
1052075 --TATT-TACGTTTTCAAAACTATTTTAAAAAC
1 TATATTATATGTTTTCAAAATTATTTTAAAAAC
*
1052105 --TATT-TACGTTTTCAAAATTATTTTAAAAAC
1 TATATTATATGTTTTCAAAATTATTTTAAAAAC
*
1052135 TATA-TACA--TTTTCAAAATTATTTTAAAAAC
1 TATATTATATGTTTTCAAAATTATTTTAAAAAC
1052165 TATATTATATGTTTTCAAAATTATTTTAAAAAC
1 TATATTATATGTTTTCAAAATTATTTTAAAAAC
** *
1052198 GGTATTATATGTTTTCAAAATTATTTTAAAAAT
1 TATATTATATGTTTTCAAAATTATTTTAAAAAC
1052231 TATATTATATGTTTTCAAAATTATTTTAAAAAAC
1 TATATTATATGTTTTCAAAATTATTTT-AAAAAC
***
1052265 TATATACTATATGTTTTCAAAA-CCGTTTAAAAAC
1 TATAT--TATATGTTTTCAAAATTATTTTAAAAAC
*
1052299 TATATATTATATGTTTTCAAAACTATTTTTTAAAAAC
1 --TATATTATATGTTTTCAAAA-T-TATTTTAAAAAC
* *
1052336 TATA-TATTATTTTTTTCAAAATTATCTTAAAAAC
1 TATATTA-TA-TGTTTTCAAAATTATTTTAAAAAC
*
1052370 TATATGCTATATGTTTTCAAAAATAGTTTTAAAAAC
1 TATAT--TATATGTTTTCAAAATTA-TTTTAAAAAC
1052406 TATAT
1 TATAT
1052411 ATTATACGTT
Statistics
Matches: 294, Mismatches: 22, Indels: 37
0.83 0.06 0.10
Matches are distributed among these distances:
30 81 0.28
31 7 0.02
32 3 0.01
33 77 0.26
34 47 0.16
35 22 0.07
36 46 0.16
37 11 0.04
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (33 bp):
TATATTATATGTTTTCAAAATTATTTTAAAAAC
Found at i:1061449 original size:55 final size:55
Alignment explanation
Indices: 1061367--1061916 Score: 472
Period size: 55 Copynumber: 10.0 Consensus size: 55
1061357 GAAAACATGG
* * * * ** *
1061367 TTTT-TGAAGATTATTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGGTCCG
1 TTTTCTGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAAGGAGCAGACCCA
* * * * * * *
1061421 TTTTCTGAAGATTTTTCAAGTTCTATACTCCCTCAAAGAAGAGGGAACATACCCA
1 TTTTCTGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAAGGAGCAGACCCA
* **
1061476 TTTT-TCAAAGATTGTTCGAGTCCTATACTCTTTGAAAGAAGAAGGAG-AGGACCCA
1 TTTTCT-GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAAGGAGCA-GACCCA
* * *
1061531 TTTT-TCGAAGATTGTTCGAGCCCTATACTCCTTGAAA-AAGAAGGAGCAGACCCG
1 TTTTCT-GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAAGGAGCAGACCCA
* * * * * * *
1061585 TTTGCCGAAGATTGCTCGAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACACG
1 TTTTCTGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAAGGAGCAGACCCA
* * *
1061640 TTTGTC-AAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAG-AGGACACA
1 TTT-TCTGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAAGGAGCA-GACCCA
* * * * * * * *
1061695 TTTACCGAAAATTGTTCGAGTCATATACTCCTTGAAA-AATAAGGAGCGGACCCG
1 TTTTCTGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAAGGAGCAGACCCA
* * * ** * * *
1061749 TTTTATGAAGATCGTTCAAGTCCTATACTCTTTGAAAGACGAAGGAGCGGACACA
1 TTTTCTGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAAGGAGCAGACCCA
* * * **
1061804 TTTACTGAAGATTGTTCGAGTCCCCTATACTCCCTTAAAGAA-AAGGGAACAGATGCA
1 TTTTCTGAAGATTGTTCGAGT--CCTATACTCCCTGAAAGAAGAA-GGAGCAGACCCA
* *
1061861 TTTTTTGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAG-AGGAAACAGACCCA
1 TTTTCTGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAAGG-AGCAGACCCA
1061916 T
1 T
1061917 CCTTCGAATA
Statistics
Matches: 405, Mismatches: 75, Indels: 31
0.79 0.15 0.06
Matches are distributed among these distances:
54 95 0.23
55 265 0.65
56 3 0.01
57 42 0.10
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (55 bp):
TTTTCTGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAAGGAGCAGACCCA
Found at i:1061620 original size:109 final size:110
Alignment explanation
Indices: 1061372--1061902 Score: 527
Period size: 109 Copynumber: 4.8 Consensus size: 110
1061362 CATGGTTTTT
* * * * ** * *
1061372 GAAGATTATTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGGTCC-GTTTTCTGAAGATTTT
1 GAAGATTGTTCGAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACCCATTTTTC-GAAGATTGT
* * * * * * * **
1061436 TCAAGTTCTATACTCCCTCAAAGAAGAGGGAACATACCCATTTTTC
65 TCGAGTCCTATACTCCCTGAAAGAAGAAGGAGCAGACACATTTACC
* * *
1061482 AAAGATTGTTCGAGTCCTATACTCTTTGAAAGAAGAAGGAGAGGACCCATTTTTCGAAGATTGTT
1 GAAGATTGTTCGAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACCCATTTTTCGAAGATTGTT
* * * * *
1061547 CGAGCCCTATACTCCTTGAAA-AAGAAGGAGCAGACCCGTTTGCC
66 CGAGTCCTATACTCCCTGAAAGAAGAAGGAGCAGACACATTTACC
* * * * *
1061591 GAAGATTGCTCGAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACACGTTTGTCAAAGATTGTT
1 GAAGATTGTTCGAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACCCATTTTTCGAAGATTGTT
*
1061656 CGAGTCCTATACTCCCTGAAAGAAGAGGGAG-AGGACACATTTACC
66 CGAGTCCTATACTCCCTGAAAGAAGAAGGAGCA-GACACATTTACC
* * * * *
1061701 GAAAATTGTTCGAGTCATATACTCCTTGAAA-AATAAGGAGCGGACCCGTTTTAT-GAAGATCGT
1 GAAGATTGTTCGAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACCCATTTT-TCGAAGATTGT
* ** * * *
1061764 TCAAGTCCTATACTCTTTGAAAGACGAAGGAGCGGACACATTTACT
65 TCGAGTCCTATACTCCCTGAAAGAAGAAGGAGCAGACACATTTACC
* * ** *
1061810 GAAGATTGTTCGAGTCCCCTATACTCCCTT-AAAGAA-AAGGGAACAGATGCATTTTTTGAAGAT
1 GAAGATTGTTCGAGT--CCTATACT-CCTTGAAAGAAGAA-GGAGCGGACCCATTTTTCGAAGAT
1061873 TGTTCGAGTCCTATACTCCCTGAAAGAAGA
62 TGTTCGAGTCCTATACTCCCTGAAAGAAGA
1061903 GGAAACAGAC
Statistics
Matches: 347, Mismatches: 63, Indels: 20
0.81 0.15 0.05
Matches are distributed among these distances:
109 171 0.49
110 110 0.32
111 18 0.05
112 48 0.14
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (110 bp):
GAAGATTGTTCGAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACCCATTTTTCGAAGATTGTT
CGAGTCCTATACTCCCTGAAAGAAGAAGGAGCAGACACATTTACC
Found at i:1061650 original size:164 final size:164
Alignment explanation
Indices: 1061367--1061902 Score: 580
Period size: 164 Copynumber: 3.3 Consensus size: 164
1061357 GAAAACATGG
* * * **
1061367 TTTTT-GAAGATTATTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGGTCCGTTTTCTGAAG
1 TTTTTCGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAAGGAGCGGACCCGTTTTCTGAAG
* * * * * * ** *
1061431 ATTTTTCAAGTTCTATACTCCCTCAAAGAAGAGGGAACATACCCATTTTTCAAAGATTGTTCGAG
66 ATTGTTCAAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACACA-TTTTCAAAGATTGTTCGAG
* *
1061496 TCCTATACTCTTTGAAAGAAGAAGGAGAGGACCCA
130 TCCTATACTCCTTGAAAGAAGAAGGAGAGGACACA
* * * * *
1061531 TTTTTCGAAGATTGTTCGAGCCCTATACTCCTTGAAA-AAGAAGGAGCAGACCCGTTTGCCGAAG
1 TTTTTCGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAAGGAGCGGACCCGTTTTCTGAAG
* * *
1061595 ATTGCTCGAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACACGTTTGTCAAAGATTGTTCGAG
66 ATTGTTCAAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACACATTT-TCAAAGATTGTTCGAG
* *
1061660 TCCTATACTCCCTGAAAGAAGAGGGAGAGGACACA
130 TCCTATACTCCTTGAAAGAAGAAGGAGAGGACACA
** * * * * *
1061695 TTTACCGAAAATTGTTCGAGTCATATACTCCTTGAAA-AATAAGGAGCGGACCCGTTTTATGAAG
1 TTTTTCGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAAGGAGCGGACCCGTTTTCTGAAG
* * * * *
1061759 ATCGTTCAAGTCCTATACTCTTTGAAAGACGAAGGAGCGGACACATTTACTGAAGATTGTTCGAG
66 ATTGTTCAAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACACATTTTC-AAAGATTGTTCGAG
* **
1061824 TCCCCTATACTCCCTT-AAAGAA-AAGG-GAACAGATGCA
130 T--CCTATACT-CCTTGAAAGAAGAAGGAG-A-GGACACA
*
1061861 TTTTTTGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGA
1 TTTTTCGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGA
1061903 GGAAACAGAC
Statistics
Matches: 307, Mismatches: 56, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
163 4 0.01
164 217 0.71
165 31 0.10
166 49 0.16
167 6 0.02
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (164 bp):
TTTTTCGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAAGGAGCGGACCCGTTTTCTGAAG
ATTGTTCAAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACACATTTTCAAAGATTGTTCGAGT
CCTATACTCCTTGAAAGAAGAAGGAGAGGACACA
Found at i:1063092 original size:29 final size:29
Alignment explanation
Indices: 1063050--1063166 Score: 216
Period size: 29 Copynumber: 4.0 Consensus size: 29
1063040 AAAATGTTTT
1063050 TGGGTGTCCAATCACACCCTAATCAAAGA
1 TGGGTGTCCAATCACACCCTAATCAAAGA
1063079 TGGGTGTCCAATCACACCCTAATCAAAGA
1 TGGGTGTCCAATCACACCCTAATCAAAGA
1063108 TGGGTGTCCAATCACACCCTAATCAAAGA
1 TGGGTGTCCAATCACACCCTAATCAAAGA
* *
1063137 TGTGTGCCCAATCACACCCTAATCAAAGA
1 TGGGTGTCCAATCACACCCTAATCAAAGA
1063166 T
1 T
1063167 TGATGGCGAC
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 86 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.21
Consensus pattern (29 bp):
TGGGTGTCCAATCACACCCTAATCAAAGA
Found at i:1064866 original size:3 final size:3
Alignment explanation
Indices: 1064858--1064928 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
1064848 TATAGTATAA
1064858 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1064906 ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT
1064929 ATTTTTACAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1081389 original size:25 final size:25
Alignment explanation
Indices: 1081361--1081410 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1081351 TCAAGTAGTT
1081361 GCCCCAAGTTGAATGTTGGTATAAC
1 GCCCCAAGTTGAATGTTGGTATAAC
1081386 GCCCCAAGTTGAATGTTGGTATAAC
1 GCCCCAAGTTGAATGTTGGTATAAC
1081411 ACCAACTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (25 bp):
GCCCCAAGTTGAATGTTGGTATAAC
Found at i:1085356 original size:21 final size:20
Alignment explanation
Indices: 1085332--1085396 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
1085322 ACTTTGAAAC
1085332 AAATGGATTTCAAAGTTTGGT
1 AAATGG-TTTCAAAGTTTGGT
*
1085353 AAAT-GTTTC----TTT-GA
1 AAATGGTTTCAAAGTTTGGT
1085367 AAATGGTTTTCAAAGTTTGGT
1 AAATGG-TTTCAAAGTTTGGT
1085388 AAAT-GTTTC
1 AAATGGTTTC
1085397 TTTGAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 16
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 4 0.11
19 8 0.23
20 5 0.14
21 9 0.26
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (20 bp):
AAATGGTTTCAAAGTTTGGT
Found at i:1085378 original size:35 final size:36
Alignment explanation
Indices: 1085323--1085432 Score: 168
Period size: 35 Copynumber: 3.0 Consensus size: 36
1085313 TGGCAACCAA
*
1085323 CTTTGAAACAAATGGATTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AA-AAATGGTTTTCAAAGTTTGGTAAATGTTT
1085361 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
1085396 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
1085433 GTTGATTTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
35 33 0.49
36 8 0.12
37 22 0.32
38 5 0.07
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1087232 original size:35 final size:36
Alignment explanation
Indices: 1087188--1087288 Score: 177
Period size: 35 Copynumber: 2.8 Consensus size: 36
1087178 CAACTTTTAG
1087188 AAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG-A
1 AAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAA
1087223 AAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAA
1 AAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAA
*
1087259 AAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 AAATGG-TTTTCAAAGTTTGGTAAATGTTT
1087289 GTTGATTTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
35 34 0.54
36 7 0.11
37 22 0.35
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.46
Consensus pattern (36 bp):
AAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAA
Found at i:1088549 original size:25 final size:26
Alignment explanation
Indices: 1088521--1088569 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1088511 AATATATTTT
*
1088521 TTTCTTTC-AAAATTTTATAAGTTTA
1 TTTCTCTCTAAAATTTTATAAGTTTA
1088546 TTTCTCTCTAAAATTTTATAAGTT
1 TTTCTCTCTAAAATTTTATAAGTT
1088570 AATTCGTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (26 bp):
TTTCTCTCTAAAATTTTATAAGTTTA
Found at i:1092836 original size:23 final size:23
Alignment explanation
Indices: 1092805--1092860 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
1092795 GGAGCCGATT
1092805 ACCACCTCGCGAAAGAGACGTCC
1 ACCACCTCGCGAAAGAGACGTCC
* *
1092828 ACCGCCTCGCGAAAGAGACGTCT
1 ACCACCTCGCGAAAGAGACGTCC
1092851 ACCACCTCGC
1 ACCACCTCGC
1092861 TGAGCAGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.27, C:0.41, G:0.21, T:0.11
Consensus pattern (23 bp):
ACCACCTCGCGAAAGAGACGTCC
Found at i:1093037 original size:3 final size:3
Alignment explanation
Indices: 1093029--1093117 Score: 99
Period size: 3 Copynumber: 30.0 Consensus size: 3
1093019 CATTTGGTTT
* * * * * *
1093029 TTA TTA TTA TTT TTA TTA TTT TTA TTT TTA TTA CTA TTA TTA TTT TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1093077 TTA TTA ATA TTA TTA TTA TTA TTA ATA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1093118 CAGATACAAC
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
2 2 0.03
3 69 0.97
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1095099 original size:149 final size:146
Alignment explanation
Indices: 1094938--1095206 Score: 434
Period size: 149 Copynumber: 1.8 Consensus size: 146
1094928 AAAATAATCA
* *
1094938 TATTTTAATATTTATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCCT
1 TATTTTAATATTTATTTATTTTTTAATATTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTCCT
*
1095003 TTTATGATA-TTCTTAAATAAATAAATATCATATT-TTTATAAATTATATATATATTAATTTATT
66 TTTATGATATTTC-TAAATAAATAAATAT--T-TTATTTATAAA-TATATATAAATTAATTTATT
1095066 TAATTATTTTTAGAAAGATGT
126 TAATTATTTTTAGAAAGATGT
*
1095087 TATTTTAATATTTATTTATTTTTTAATATTAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCT
1 TATTTTAATATTTATTTATTTTTTAATATTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTCCT
*
1095152 TTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATTAAT
66 TTTATGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATTAAT
1095207 AGATTTTCTT
Statistics
Matches: 113, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
146 16 0.14
147 9 0.08
149 85 0.75
150 3 0.03
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (146 bp):
TATTTTAATATTTATTTATTTTTTAATATTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTCCT
TTTATGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATTAATTTATTTAATT
ATTTTTAGAAAGATGT
Found at i:1095739 original size:26 final size:26
Alignment explanation
Indices: 1095710--1095768 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
1095700 CTTTCAAATT
*
1095710 TTTTATTACTTATTATTTT-TATA-TTA
1 TTTTATTA-ATATT-TTTTATATATTTA
*
1095736 TTTTATTAATATTTTTTATTTATTTA
1 TTTTATTAATATTTTTTATATATTTA
1095762 TTTTATT
1 TTTTATT
1095769 CAAGTATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.14
25 7 0.24
26 18 0.62
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTATTAATATTTTTTATATATTTA
Found at i:1102944 original size:114 final size:114
Alignment explanation
Indices: 1102744--1102963 Score: 350
Period size: 114 Copynumber: 1.9 Consensus size: 114
1102734 CCACTTCTCG
*
1102744 TAGTAGAAATAAGGAGACCAAATAGCATCTTCTGGAAGAGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCAAATAGCATCTTCTGGAAGAGTTCTTTGAGTTATCTGATCTGATTC
* ** * *
1102809 GGTATGAACCGTAAAACCAATCATTGGATTTGAAATATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
* * *
1102858 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCAAATAGCATCTTCTGGAAGAGTTCTTTGAGTTATCTGATCTGATTC
*
1102923 GGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
1102964 CTGCATGATC
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 96 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCAAATAGCATCTTCTGGAAGAGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
Found at i:1105104 original size:54 final size:54
Alignment explanation
Indices: 1105022--1105133 Score: 179
Period size: 54 Copynumber: 2.1 Consensus size: 54
1105012 CAATAATTGA
* * **
1105022 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGAAGAAACCACAGGAAAGGATGAATGCGCCGTCAAATGTTTTAC
*
1105076 GAACATCTGAGAAGAAGCCACAGGAAAGGATGAATGCGCCGTCAAATGTTTTAC
1 GAACATCTGAGAAGAAACCACAGGAAAGGATGAATGCGCCGTCAAATGTTTTAC
1105130 GAAC
1 GAAC
1105134 CTGCTATTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (54 bp):
GAACATCTGAGAAGAAACCACAGGAAAGGATGAATGCGCCGTCAAATGTTTTAC
Found at i:1105531 original size:22 final size:22
Alignment explanation
Indices: 1105500--1105554 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1105490 ATCTACACTC
* *
1105500 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAAATTCCCTT
* *
1105522 TTTAAAGATGACAAATTCTCTT
1 TTCAAAGATGACAAATTCCCTT
1105544 TTCAAAGATGA
1 TTCAAAGATGA
1105555 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAAATTCCCTT
Found at i:1106179 original size:113 final size:113
Alignment explanation
Indices: 1105988--1106286 Score: 546
Period size: 113 Copynumber: 2.6 Consensus size: 113
1105978 ATTTCTGGAA
*
1105988 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA-AAGTTCATAATGAGAAAAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
1106052 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
66 CAACTTTTCACTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
*
1106100 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1106165 CAACTTTTCACTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
66 CAACTTTTCACTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
*
1106213 GAGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1106278 CAATCTTTT
66 CAA-CTTTT
1106287 GCATGATTCT
Statistics
Matches: 180, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
112 38 0.21
113 137 0.76
114 5 0.03
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACTTTTCACTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
Found at i:1106633 original size:3 final size:3
Alignment explanation
Indices: 1106625--1106710 Score: 110
Period size: 3 Copynumber: 30.0 Consensus size: 3
1106615 ATTTGGTTTT
* *
1106625 TTA TTA TTA TATA TTA TTT TTA TT- TTA TTA CTA TTA TTA TTA TT-
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1106669 TT- TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1106711 CATATATAAC
Statistics
Matches: 74, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
2 10 0.14
3 61 0.82
4 3 0.04
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1108703 original size:148 final size:146
Alignment explanation
Indices: 1108532--1108800 Score: 409
Period size: 148 Copynumber: 1.8 Consensus size: 146
1108522 AAAATAATCA
*
1108532 TATTTTAATATTATTTATTTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACATAGAAGTCATT
1 TATTTTAATATTATTTATTTTTTAATATTAAGAAAAGAGCTGTCTTAAAGCACATAGAAGTCATT
* *
1108597 TTCTGATA-TTCTTAAATAAATAAATATCATATT-TTTATAAAT-TATATATATATTAATTTATT
66 TTCTGATATTTC-TAAATAAATAAATAT--T-TTATTTACAAATATATATATAAATTAATTTATT
1108659 TAATTATTTTATATAGATGT
127 TAATTATTTTATATAGATGT
* * * *
1108679 TATTTTAATATTTATTTATTTTTTAATATTAAGAAAAGAGTTGTCTTAAGGTACCTAGAAGTCAT
1 TATTTTAATA-TTATTTATTTTTTAATATTAAGAAAAGAGCTGTCTTAAAGCACATAGAAGTCAT
1108744 TTTCTGATATTTCTAAATAAATAAATATTTTATTTACAAATATATATATAAATTAAT
65 TTTCTGATATTTCTAAATAAATAAATATTTTATTTACAAATATATATATAAATTAAT
1108801 AGATTTTCTT
Statistics
Matches: 111, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
145 2 0.02
146 9 0.08
147 24 0.22
148 73 0.66
149 3 0.03
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (146 bp):
TATTTTAATATTATTTATTTTTTAATATTAAGAAAAGAGCTGTCTTAAAGCACATAGAAGTCATT
TTCTGATATTTCTAAATAAATAAATATTTTATTTACAAATATATATATAAATTAATTTATTTAAT
TATTTTATATAGATGT
Found at i:1118069 original size:17 final size:17
Alignment explanation
Indices: 1118017--1118082 Score: 78
Period size: 18 Copynumber: 3.8 Consensus size: 17
1118007 ATAATGTAAA
1118017 ATTATCGGTGGGAATAAG
1 ATTATCGGT-GGAATAAG
* *
1118035 ATTATAGGTGAAAATAAG
1 ATTATCGGTG-GAATAAG
*
1118053 ATTACCGGTGGAATAAG
1 ATTATCGGTGGAATAAG
*
1118070 ATTATCGATGGAA
1 ATTATCGGTGGAA
1118083 AGATTATTGG
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
17 18 0.45
18 22 0.55
ACGTcount: A:0.39, C:0.06, G:0.27, T:0.27
Consensus pattern (17 bp):
ATTATCGGTGGAATAAG
Found at i:1119131 original size:208 final size:206
Alignment explanation
Indices: 1118756--1119172 Score: 759
Period size: 208 Copynumber: 2.0 Consensus size: 206
1118746 ATATACCAGA
1118756 GAGCTATTTCATTATTATTATATAGTTAATTTTAATCAGTGTCAGTGATTGGCATTCCCTAAACA
1 GAGCTATTTCATTATTATTATATAGTTAATTTTAATCAGTGTCAGTGATTGGCATTCCCTAAACA
1118821 GACAGTACAGTGGATGTAGGCAGAGAAGCAAAAGAAACGTGCCATTATATACACATTTCAGCTTA
66 GACAGTACAGTGGATGTAGGCAGAGAAGCAAAAGAAACGTGCCATTATATACACATTTCAGCTTA
1118886 CAACACTGTGAATTTCTCTGTGAATATAAGAATTCTTTCAAAGGAAGAAGCATGAAGCTGGCGAT
131 CAACACTGTGAATTTCTCTGTGAATATAAGAATTCTTTCAAAGGAAGAAGCATGAAGCTGGCGAT
1118951 G-CTGACGGTG
196 GCCTGACGGTG
*
1118961 GAGCTATTTTATTATTA-TAT-TAGTTAATTTTAATCAGTGTCAATCAGTGATTGGCATTTCCCT
1 GAGCTATTTCATTATTATTATATAGTTAATTTTAATCAGTG----TCAGTGATTGGCA-TTCCCT
1119024 AAACAGACAGTACAGTGGATGTAGGCAGAGAAGCAAAAGAAACGTGCCATTATATACACATTTCA
61 AAACAGACAGTACAGTGGATGTAGGCAGAGAAGCAAAAGAAACGTGCCATTATATACACATTTCA
1119089 GCTTACAACACTGTGAATTTCTCTGTGAATATAAGAATTCTTTCAAAGGAAGAAGCATGAAGCTG
126 GCTTACAACACTGTGAATTTCTCTGTGAATATAAGAATTCTTTCAAAGGAAGAAGCATGAAGCTG
1119154 GCGATGCCTGACGGTG
191 GCGATGCCTGACGGTG
1119170 GAG
1 GAG
1119173 GTGAAGAAGG
Statistics
Matches: 205, Mismatches: 1, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
203 19 0.09
204 3 0.01
205 16 0.08
207 13 0.06
208 142 0.69
209 12 0.06
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.30
Consensus pattern (206 bp):
GAGCTATTTCATTATTATTATATAGTTAATTTTAATCAGTGTCAGTGATTGGCATTCCCTAAACA
GACAGTACAGTGGATGTAGGCAGAGAAGCAAAAGAAACGTGCCATTATATACACATTTCAGCTTA
CAACACTGTGAATTTCTCTGTGAATATAAGAATTCTTTCAAAGGAAGAAGCATGAAGCTGGCGAT
GCCTGACGGTG
Found at i:1120149 original size:42 final size:42
Alignment explanation
Indices: 1120098--1120331 Score: 262
Period size: 42 Copynumber: 5.7 Consensus size: 42
1120088 GCCTGATCCT
* * * * * *
1120098 ATGGAGACTGACCAAAGTGTCGGAAACAGTGCGGCTAAGCCG
1 ATGGGGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCA
* * * * *
1120140 ATGGGGACTGACCGAGGTGTCCCAAAGAACGTGGCTAGGCCA
1 ATGGGGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCA
* * * *
1120182 ACGGGGACTGACCAAAGTGTGGCAAAGAATGTGGCAAAGCCG
1 ATGGGGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCA
* *
1120224 AT-GGG---GA-CAAAGTATCGCAAAGAATGTGACTAAGCCA
1 ATGGGGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCA
1120261 ATGGGGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCA
1 ATGGGGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCA
* *
1120303 ATGGAGACTGACCAAAGTGTCACAAAGAA
1 ATGGGGACTGACCAAAGTGTCGCAAAGAA
1120332 CTTGCCTGAG
Statistics
Matches: 157, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
37 27 0.17
38 5 0.03
41 5 0.03
42 120 0.76
ACGTcount: A:0.34, C:0.20, G:0.32, T:0.15
Consensus pattern (42 bp):
ATGGGGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCA
Found at i:1120351 original size:42 final size:42
Alignment explanation
Indices: 1120266--1120448 Score: 192
Period size: 42 Copynumber: 4.4 Consensus size: 42
1120256 AGCCAATGGG
* * *
1120266 GACTGACCAAAGTGTCGCAAAGAA-TGTGGCTAAGCC-AATGGA
1 GACTGACCAAAGTGTCACAAAGAACT-TGCCTGAGCCTAA-GGA
1120308 GACTGACCAAAGTGTCACAAAGAACTTGCCTGAGCCTAAGGA
1 GACTGACCAAAGTGTCACAAAGAACTTGCCTGAGCCTAAGGA
** * *
1120350 GACTGACCAAAAG-GTCACAAAGAGGTTGTCTGAGCCTATGGA
1 GACTGACC-AAAGTGTCACAAAGAACTTGCCTGAGCCTAAGGA
* * * * * **
1120392 GATTGATCATAGTATCACAAAGAGCTTGCCTGAATCTAAGGA
1 GACTGACCAAAGTGTCACAAAGAACTTGCCTGAGCCTAAGGA
1120434 GACTGACCAAAGTGT
1 GACTGACCAAAGTGT
1120449 TATCAACTGT
Statistics
Matches: 117, Mismatches: 20, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
41 3 0.03
42 107 0.91
43 7 0.06
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (42 bp):
GACTGACCAAAGTGTCACAAAGAACTTGCCTGAGCCTAAGGA
Found at i:1120359 original size:84 final size:84
Alignment explanation
Indices: 1120085--1120448 Score: 300
Period size: 84 Copynumber: 4.4 Consensus size: 84
1120075 TTACAAACAG
* * * * * * *
1120085 CTTGCCTGATCCTATGGAGACTGACCAAAGTGTCGGAAACAGTGCGGCTAAGCCGATGGGGACTG
1 CTTGCCTGAGCCTAAGGAGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCGATGGAGACTG
* * * *
1120150 ACCGAGGTGTCCCAAAGAA
66 ACCAAAGTATCACAAAGAA
* * * * *
1120169 CGTGGCT-AGGCC-AACGGGGACTGACCAAAGTGTGGCAAAGAATGTGGCAAAGCCGATGG-G--
1 CTTGCCTGA-GCCTAA-GGAGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCGATGGAGAC
*
1120229 -GA-CAAAGTATCGCAAAGAA
64 TGACCAAAGTATCACAAAGAA
* * * *
1120248 -TGTGACTAAGCC-AATGGGGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCAATGGAGAC
1 CT-TGCCTGAGCCTAA-GGAGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCGATGGAGAC
*
1120311 TGACCAAAGTGTCACAAAGAA
64 TGACCAAAGTATCACAAAGAA
* * * * * *
1120332 CTTGCCTGAGCCTAAGGAGACTGACCAAAAG-GTCACAAAG-AGGTTGTCTGAGCCTATGGAGAT
1 CTTGCCTGAGCCTAAGGAGACTGACC-AAAGTGTCGCAAAGAATG-TGGCTAAGCCGATGGAGAC
* * *
1120395 TGATCATAGTATCACAAAGAG
64 TGACCAAAGTATCACAAAGAA
**
1120416 CTTGCCTGAATCTAAGGAGACTGACCAAAGTGT
1 CTTGCCTGAGCCTAAGGAGACTGACCAAAGTGT
1120449 TATCAACTGT
Statistics
Matches: 228, Mismatches: 38, Indels: 28
0.78 0.13 0.10
Matches are distributed among these distances:
79 63 0.28
80 4 0.02
83 11 0.05
84 143 0.63
85 7 0.03
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.18
Consensus pattern (84 bp):
CTTGCCTGAGCCTAAGGAGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCGATGGAGACTG
ACCAAAGTATCACAAAGAA
Found at i:1121186 original size:2 final size:2
Alignment explanation
Indices: 1121179--1121215 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1121169 TACTTTTAAC
1121179 AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
1121216 TTCAAATTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1121872 original size:29 final size:29
Alignment explanation
Indices: 1121823--1121890 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
1121813 ATCCTACTAA
1121823 CAAAACCAAA-TGATCAGAAAGCTATTAC
1 CAAAACCAAATTGATCAGAAAGCTATTAC
1121851 CAAAACCAAATTGATCAGAAAGCTATTAC
1 CAAAACCAAATTGATCAGAAAGCTATTAC
1121880 CAAAACCAAAT
1 CAAAACCAAAT
1121891 ACGAACAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
28 10 0.26
29 29 0.74
ACGTcount: A:0.51, C:0.22, G:0.09, T:0.18
Consensus pattern (29 bp):
CAAAACCAAATTGATCAGAAAGCTATTAC
Found at i:1124865 original size:16 final size:15
Alignment explanation
Indices: 1124841--1124900 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 15
1124831 TACATTAGAT
*
1124841 TTAAAAAAACAATATA
1 TTAATAAAA-AATATA
*
1124857 TTAATAAAAAATGTTTA
1 TTAATAAAAAA--TATA
*
1124874 TAAAATAAAAAATATA
1 T-TAATAAAAAATATA
1124890 TTAATAAAAAA
1 TTAATAAAAAA
1124901 ACGCAAACAC
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
15 11 0.31
16 12 0.33
17 4 0.11
18 9 0.25
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (15 bp):
TTAATAAAAAATATA
Found at i:1124866 original size:19 final size:19
Alignment explanation
Indices: 1124842--1124902 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
1124832 ACATTAGATT
1124842 TAAAAAAACAATATATTAA
1 TAAAAAAACAATATATTAA
*
1124861 T---AAAA-AATGT-TT-A
1 TAAAAAAACAATATATTAA
*
1124874 TAAAATAAAAAATATATTAA
1 TAAAA-AAACAATATATTAA
1124894 TAAAAAAAC
1 TAAAAAAAC
1124903 GCAAACACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 14
0.65 0.06 0.29
Matches are distributed among these distances:
13 2 0.06
14 2 0.06
15 4 0.12
16 5 0.16
17 3 0.09
18 4 0.12
19 6 0.19
20 6 0.19
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (19 bp):
TAAAAAAACAATATATTAA
Found at i:1124867 original size:18 final size:17
Alignment explanation
Indices: 1124844--1124901 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
1124834 ATTAGATTTA
1124844 AAAAAACAATATATTAAT
1 AAAAAA-AATATATTAAT
** *
1124862 AAAAAATGTTTA-TAA-
1 AAAAAAAATATATTAAT
1124877 AATAAAAAATATATTAAT
1 AA-AAAAAATATATTAAT
1124895 AAAAAAA
1 AAAAAAA
1124902 CGCAAACACA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
15 2 0.06
16 10 0.32
17 11 0.35
18 8 0.26
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (17 bp):
AAAAAAAATATATTAAT
Found at i:1124896 original size:20 final size:18
Alignment explanation
Indices: 1124859--1124898 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
1124849 ACAATATATT
*
1124859 AATAAAAAATGTTTATAA
1 AATAAAAAATATTTATAA
1124877 AATAAAAAATATATTAATAA
1 AATAAAAAATAT-TT-ATAA
1124897 AA
1 AA
1124899 AAACGCAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 2 0.11
20 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (18 bp):
AATAAAAAATATTTATAA
Found at i:1126074 original size:33 final size:34
Alignment explanation
Indices: 1126015--1126104 Score: 155
Period size: 33 Copynumber: 2.7 Consensus size: 34
1126005 CTCATGTGCA
*
1126015 AAGTTGGCCACCTACCAAAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
1126049 AAGTTGGCCACCAACC-AAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
*
1126082 AAGTTGGTCACCAACCAAAGATG
1 AAGTTGGCCACCAACCAAAGATG
1126105 TCAACTTTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
33 32 0.60
34 21 0.40
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (34 bp):
AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
Found at i:1127921 original size:21 final size:21
Alignment explanation
Indices: 1127895--1127954 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
1127885 CTGTTGAAAC
*
1127895 TCCACCTATTTTGGAGTATGA
1 TCCACCTACTTTGGAGTATGA
* *
1127916 TCCACCTGCTTTGGTGTATGA
1 TCCACCTACTTTGGAGTATGA
* *
1127937 TCCACCTGCTGTGGAGTA
1 TCCACCTACTTTGGAGTA
1127955 CTACTTATCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.35
Consensus pattern (21 bp):
TCCACCTACTTTGGAGTATGA
Found at i:1132190 original size:29 final size:29
Alignment explanation
Indices: 1132158--1132226 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
1132148 ATCCTACTAA
1132158 CAAAACCAAATTGATCAGAAAGCTATTAC
1 CAAAACCAAATTGATCAGAAAGCTATTAC
1132187 CAAAACCAAATTGATCAGAAAGCTATTAC
1 CAAAACCAAATTGATCAGAAAGCTATTAC
1132216 CAAAACCAAAT
1 CAAAACCAAAT
1132227 ACGAACAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.51, C:0.22, G:0.09, T:0.19
Consensus pattern (29 bp):
CAAAACCAAATTGATCAGAAAGCTATTAC
Found at i:1135230 original size:15 final size:15
Alignment explanation
Indices: 1135210--1135263 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
1135200 TTAGATTTAA
1135210 AATAAACAATATATT
1 AATAAACAATATATT
* * *
1135225 AATAAAAAATGTTTATAA
1 AATAAACAA--TATAT-T
1135243 AATAAACAATATATT
1 AATAAACAATATATT
1135258 AATAAA
1 AATAAA
1135264 AAAACGCAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 14 0.47
16 4 0.13
17 4 0.13
18 8 0.27
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (15 bp):
AATAAACAATATATT
Found at i:1136450 original size:33 final size:34
Alignment explanation
Indices: 1136391--1136480 Score: 155
Period size: 33 Copynumber: 2.7 Consensus size: 34
1136381 CTCATGTGCA
*
1136391 AAGTTGGCCACCTACCAAAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
1136425 AAGTTGGCCACCAACC-AAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
*
1136458 AAGTTGGTCACCAACCAAAGATG
1 AAGTTGGCCACCAACCAAAGATG
1136481 TCAACTTTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
33 32 0.60
34 21 0.40
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (34 bp):
AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
Found at i:1138417 original size:21 final size:21
Alignment explanation
Indices: 1138391--1138450 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
1138381 CTGTTGAAAC
* *
1138391 TCCACCTATTTTGGAGTATGA
1 TCCACCTACTGTGGAGTATGA
*
1138412 TCCACCTGCTGTGGAGTATGA
1 TCCACCTACTGTGGAGTATGA
*
1138433 TCCACCTGCTGTGGAGTA
1 TCCACCTACTGTGGAGTA
1138451 CTACTTATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (21 bp):
TCCACCTACTGTGGAGTATGA
Found at i:1143174 original size:23 final size:23
Alignment explanation
Indices: 1143146--1143237 Score: 94
Period size: 23 Copynumber: 4.0 Consensus size: 23
1143136 ACATTTTATA
*
1143146 TGGCACTTTGGTGCATTTCTATG
1 TGGCACTTTGGTGCATTTCTACG
* * * * *
1143169 CGGCACTTAGGTACAATTCTACA
1 TGGCACTTTGGTGCATTTCTACG
* *
1143192 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTTGGTGCATTTCTACG
* *
1143215 TAGCACTTTGGTGCATTTATACG
1 TGGCACTTTGGTGCATTTCTACG
1143238 AGCTGTGGTG
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (23 bp):
TGGCACTTTGGTGCATTTCTACG
Found at i:1143602 original size:3 final size:3
Alignment explanation
Indices: 1143594--1143633 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
1143584 GATATACATG
1143594 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
1143634 GGAAACGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1151760 original size:42 final size:42
Alignment explanation
Indices: 1151709--1151947 Score: 298
Period size: 42 Copynumber: 5.7 Consensus size: 42
1151699 GCCTGATCCT
* * * * * *
1151709 ATGGAGACTGACCAAAGTGTCGGAAACAGTGCGGCTAAGCCG
1 ATGGGGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCA
* * * * *
1151751 ATGGGGACTGACCGAGGTGTCCCAAAGAACGTGGCTAGGCCA
1 ATGGGGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCA
* * * *
1151793 ACGGGGACTGACCAAAGTGTGGCAAAGAATGTGGCAAAGCCG
1 ATGGGGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCA
* * *
1151835 ATGGGGACTGACCAAAGTATCGCAAAGAATGTGACTGAGCCA
1 ATGGGGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCA
1151877 ATGGGGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCA
1 ATGGGGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCA
* *
1151919 ATGGAGACTGACCAAAGTGTCACAAAGAA
1 ATGGGGACTGACCAAAGTGTCGCAAAGAA
1151948 CTTGCCTGAG
Statistics
Matches: 165, Mismatches: 32, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 165 1.00
ACGTcount: A:0.33, C:0.20, G:0.32, T:0.15
Consensus pattern (42 bp):
ATGGGGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCA
Found at i:1151967 original size:42 final size:41
Alignment explanation
Indices: 1151798--1152064 Score: 207
Period size: 42 Copynumber: 6.4 Consensus size: 41
1151788 GGCCAACGGG
** * ** * * *
1151798 GACTGACCAAAGTGTGGCAAAGAATGTGGCAAAGCCGATGGG
1 GACTGACCAAAGTGTCACAAAGAAT-TGCCTGAGCCTAAGGA
* * * *
1151840 GACTGACCAAAGTATCGCAAAGAATGTGACTGAGCC-AATGGG
1 GACTGACCAAAGTGTCACAAAGAAT-TGCCTGAGCCTAA-GGA
* * *
1151882 GACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCC-AATGGA
1 GACTGACCAAAGTGTCACAAAGAAT-TGCCTGAGCCTAA-GGA
1151924 GACTGACCAAAGTGTCACAAAGAACTTGCCTGAGCCTAAGGA
1 GACTGACCAAAGTGTCACAAAGAA-TTGCCTGAGCCTAAGGA
* * *
1151966 GACTGACCAAAAG-GTCACAAAGAGGTTGTCTGAGCCTATGGA
1 GACTGACC-AAAGTGTCACAAAGA-ATTGCCTGAGCCTAAGGA
* * * * * **
1152008 GATTGATCATAGTATCACAAAGAGCTTGCCTGAATCTAAGGA
1 GACTGACCAAAGTGTCACAAAGA-ATTGCCTGAGCCTAAGGA
1152050 GACTGACCAAAGTGT
1 GACTGACCAAAGTGT
1152065 TATCAACTGT
Statistics
Matches: 190, Mismatches: 29, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
41 4 0.02
42 179 0.94
43 7 0.04
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.18
Consensus pattern (41 bp):
GACTGACCAAAGTGTCACAAAGAATTGCCTGAGCCTAAGGA
Found at i:1151987 original size:84 final size:84
Alignment explanation
Indices: 1151696--1152064 Score: 345
Period size: 84 Copynumber: 4.4 Consensus size: 84
1151686 TTACAAACAG
* * * * * * *
1151696 CTTGCCTGATCCTATGGAGACTGACCAAAGTGTCGGAAACAGTGCGGCTAAGCCGATGGGGACTG
1 CTTGCCTGAGCCTAAGGAGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCGATGGAGACTG
* * * *
1151761 ACCGAGGTGTCCCAAAGAA
66 ACCAAAGTATCACAAAGAA
* * * * * *
1151780 CGTGGCT-AGGCC-AACGGGGACTGACCAAAGTGTGGCAAAGAATGTGGCAAAGCCGATGGGGAC
1 CTTGCCTGA-GCCTAA-GGAGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCGATGGAGAC
*
1151843 TGACCAAAGTATCGCAAAGAA
64 TGACCAAAGTATCACAAAGAA
* * *
1151864 -TGTGACTGAGCC-AATGGGGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCAATGGAGAC
1 CT-TGCCTGAGCCTAA-GGAGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCGATGGAGAC
*
1151927 TGACCAAAGTGTCACAAAGAA
64 TGACCAAAGTATCACAAAGAA
* * * * * *
1151948 CTTGCCTGAGCCTAAGGAGACTGACCAAAAG-GTCACAAAG-AGGTTGTCTGAGCCTATGGAGAT
1 CTTGCCTGAGCCTAAGGAGACTGACC-AAAGTGTCGCAAAGAATG-TGGCTAAGCCGATGGAGAC
* * *
1152011 TGATCATAGTATCACAAAGAG
64 TGACCAAAGTATCACAAAGAA
**
1152032 CTTGCCTGAATCTAAGGAGACTGACCAAAGTGT
1 CTTGCCTGAGCCTAAGGAGACTGACCAAAGTGT
1152065 TATCAACTGT
Statistics
Matches: 238, Mismatches: 38, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
83 8 0.03
84 222 0.93
85 8 0.03
ACGTcount: A:0.32, C:0.21, G:0.29, T:0.18
Consensus pattern (84 bp):
CTTGCCTGAGCCTAAGGAGACTGACCAAAGTGTCGCAAAGAATGTGGCTAAGCCGATGGAGACTG
ACCAAAGTATCACAAAGAA
Found at i:1151988 original size:126 final size:126
Alignment explanation
Indices: 1151696--1151976 Score: 330
Period size: 126 Copynumber: 2.2 Consensus size: 126
1151686 TTACAAACAG
* * * * * *
1151696 CTTGCCTGATCCTATGGAGACTGACCAAAGTGTCGGAAACAGTGCGGCTAAGCCGATGGGGACTG
1 CTTGCCTGAGCCTATGGAGACTGACCAAAGTGTCGCAAAGAATGCGACTAAGCCAATGGGGACTG
* * * * **
1151761 ACCGAGGTGTCCCAAAGAACGTGGCTAGGCCAACGGGGACTGACCAAAGTGTGGCAAAGAA
66 ACCAAAGTGTCCCAAAGAACGTGGCTAAGCCAACGGAGACTGACCAAAGTGTCACAAAGAA
* ** * * * * *
1151822 -TGTGGCAAAGCCGATGGGGACTGACCAAAGTATCGCAAAGAATGTGACTGAGCCAATGGGGACT
1 CT-TGCCTGAGCCTATGGAGACTGACCAAAGTGTCGCAAAGAATGCGACTAAGCCAATGGGGACT
* * *
1151886 GACCAAAGTGTCGCAAAGAATGTGGCTAAGCCAATGGAGACTGACCAAAGTGTCACAAAGAA
65 GACCAAAGTGTCCCAAAGAACGTGGCTAAGCCAACGGAGACTGACCAAAGTGTCACAAAGAA
*
1151948 CTTGCCTGAGCCTAAGGAGACTGACCAAA
1 CTTGCCTGAGCCTATGGAGACTGACCAAA
1151977 AGGTCACAAA
Statistics
Matches: 124, Mismatches: 29, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
125 1 0.01
126 122 0.98
127 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.30, T:0.16
Consensus pattern (126 bp):
CTTGCCTGAGCCTATGGAGACTGACCAAAGTGTCGCAAAGAATGCGACTAAGCCAATGGGGACTG
ACCAAAGTGTCCCAAAGAACGTGGCTAAGCCAACGGAGACTGACCAAAGTGTCACAAAGAA
Found at i:1152808 original size:2 final size:2
Alignment explanation
Indices: 1152801--1152838 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1152791 TACTTTTAAC
1152801 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
1152839 TTCAAATTCT
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:1153476 original size:29 final size:29
Alignment explanation
Indices: 1153444--1153512 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
1153434 ATCCTACTAA
1153444 CAAAACCAAATTGATCAGAAAGCTATTAC
1 CAAAACCAAATTGATCAGAAAGCTATTAC
1153473 CAAAACCAAATTGATCAGAAAGCTATTAC
1 CAAAACCAAATTGATCAGAAAGCTATTAC
1153502 CAAAACCAAAT
1 CAAAACCAAAT
1153513 ACGAACAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.51, C:0.22, G:0.09, T:0.19
Consensus pattern (29 bp):
CAAAACCAAATTGATCAGAAAGCTATTAC
Found at i:1156495 original size:15 final size:15
Alignment explanation
Indices: 1156475--1156528 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
1156465 TTAGATTTAA
1156475 AATAAACAATATATT
1 AATAAACAATATATT
* * *
1156490 AATAAAAAATGTTTATAA
1 AATAAACAA--TATAT-T
1156508 AATAAACAATATATT
1 AATAAACAATATATT
1156523 AATAAA
1 AATAAA
1156529 AAAACGCAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 14 0.47
16 4 0.13
17 4 0.13
18 8 0.27
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (15 bp):
AATAAACAATATATT
Found at i:1156640 original size:2 final size:2
Alignment explanation
Indices: 1156635--1156660 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1156625 AACAGTTACC
1156635 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
1156661 CATAATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1157725 original size:33 final size:34
Alignment explanation
Indices: 1157666--1157739 Score: 132
Period size: 33 Copynumber: 2.2 Consensus size: 34
1157656 CTCATGTGCA
*
1157666 AAGTTGGCCACCTACCAAAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
1157700 AAGTTGGCCACCAACC-AAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
1157733 AAGTTGG
1 AAGTTGG
1157740 TCACAAAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 24 0.62
34 15 0.38
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (34 bp):
AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
Found at i:1159688 original size:21 final size:21
Alignment explanation
Indices: 1159662--1159721 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
1159652 CTGTTGAAAC
* *
1159662 TCCACCTATTTTGGAGTATGA
1 TCCACCTACTGTGGAGTATGA
*
1159683 TCCACCTGCTGTGGAGTATGA
1 TCCACCTACTGTGGAGTATGA
*
1159704 TCCACCTGCTGTGGAGTA
1 TCCACCTACTGTGGAGTA
1159722 CTACTTATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (21 bp):
TCCACCTACTGTGGAGTATGA
Found at i:1162565 original size:23 final size:23
Alignment explanation
Indices: 1162511--1162565 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
1162501 GACATTTTAT
* * *
1162511 ATGGCACTTTGGTGCATTTCTAT
1 ATGGCACTTAGGTGCAATTCTAC
** *
1162534 GCGGTACTTAGGTGCAATTCTAC
1 ATGGCACTTAGGTGCAATTCTAC
1162557 ATGGCACTT
1 ATGGCACTT
1162566 CGATGCATTT
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (23 bp):
ATGGCACTTAGGTGCAATTCTAC
Found at i:1162586 original size:23 final size:23
Alignment explanation
Indices: 1162560--1162603 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1162550 ATTCTACATG
1162560 GCACTTCGATGCATTTATACGTA
1 GCACTTCGATGCATTTATACGTA
* *
1162583 GCACTTTGGTGCATTTATACG
1 GCACTTCGATGCATTTATACG
1162604 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (23 bp):
GCACTTCGATGCATTTATACGTA
Found at i:1162971 original size:3 final size:3
Alignment explanation
Indices: 1162963--1163006 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1162953 GATATACATG
1162963 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1163007 TAGGAAATGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1179670 original size:14 final size:15
Alignment explanation
Indices: 1179643--1179672 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1179633 TTCTTTTCTC
1179643 TTTCTTTATTCATTT
1 TTTCTTTATTCATTT
1179658 TTTCTTT-TTCATTT
1 TTTCTTTATTCATTT
1179672 T
1 T
1179673 AACTTTTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTCTTTATTCATTT
Found at i:1183544 original size:17 final size:16
Alignment explanation
Indices: 1183513--1183546 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1183503 CACGTGAGGA
1183513 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1183529 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1183546 T
1 T
1183547 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1198434 original size:139 final size:139
Alignment explanation
Indices: 1198262--1198619 Score: 574
Period size: 139 Copynumber: 2.6 Consensus size: 139
1198252 GAAGCAAGCT
* * *
1198262 CAAGTTCTTCTCATTATGAACTTCTTTTCCCTTATCGGATGAGTTATTCTCATTATGAACTCTCT
1 CAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTCATTATGAACTCTCC
*
1198327 ACTGGAAAG-GTTGATCCCTCGAGTGAGGTTTTGCTGATTCAACTCCATATGTGACGAATCGAGC
66 ACTGG-AAGTGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGACGAATCGAGC
1198391 TAAGGTTGAA
130 TAAGGTTGAA
* *
1198401 CAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGAATGAGTTCTTCTCATTATAAACTCTCC
1 CAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTCATTATGAACTCTCC
* * *
1198466 ACTTGAAGTGTTGATCCCTCGAGTGAGGTGTTGCTGGTTCAACTCCATATGTGATGAATCGAGCT
66 ACTGGAAGTGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGACGAATCGAGCT
1198531 AAGGTTGAA
131 AAGGTTGAA
* *
1198540 CAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCC
1 CAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTCATTATGAACTCTCC
* * *
1198605 ATTTGAAATGTTGAT
66 ACTGGAAGTGTTGAT
1198620 TAGTTTACCA
Statistics
Matches: 203, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
138 3 0.01
139 200 0.99
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (139 bp):
CAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTCATTATGAACTCTCC
ACTGGAAGTGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGACGAATCGAGCT
AAGGTTGAA
Found at i:1199110 original size:21 final size:21
Alignment explanation
Indices: 1199056--1199105 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1199046 ATTTATCGTT
*
1199056 TGTATGAAACGATGAAATGTA
1 TGTATGAAAAGATGAAATGTA
* *
1199077 T-TATGCAAAGATGTAAATTTA
1 TGTATGAAAAGATG-AAATGTA
1199098 TGTATGAA
1 TGTATGAA
1199106 TGATGGTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 10 0.43
21 8 0.35
22 5 0.22
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.34
Consensus pattern (21 bp):
TGTATGAAAAGATGAAATGTA
Found at i:1199528 original size:20 final size:20
Alignment explanation
Indices: 1199497--1199569 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
1199487 GCATCATGCT
*
1199497 CGAAAGAATTACTAATGGCC
1 CGAAAGACTTACTAATGGCC
* *
1199517 CGAATGACTTACTCATCAT-GCT
1 CGAAAGACTTACT-A--ATGGCC
*
1199539 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTAATGGCC
*
1199559 CGAAGGACTTA
1 CGAAAGACTTA
1199570 ATATCTTGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 2 0.05
20 23 0.55
21 1 0.02
22 14 0.33
23 2 0.05
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (20 bp):
CGAAAGACTTACTAATGGCC
Found at i:1199534 original size:42 final size:42
Alignment explanation
Indices: 1199428--1199571 Score: 159
Period size: 42 Copynumber: 3.5 Consensus size: 42
1199418 GGGCTTATGG
* *
1199428 ATGGCCCGAATGACTTAAT-ATCTTGCTCGAAAGACTT-GTA
1 ATGGCCCGAATGACTTAATCATCATGCTCGAAAGACTTACTA
* * * * *
1199468 GATGACCC-AAAGAATTTAAGCATCATGCTCGAAAGAATTACTA
1 -ATGGCCCGAATG-ACTTAATCATCATGCTCGAAAGACTTACTA
* *
1199511 ATGGCCCGAATGACTTACTCATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAATGACTTAATCATCATGCTCGAAAGACTTACTA
*
1199553 ATGGCCCGAAGGACTTAAT
1 ATGGCCCGAATGACTTAAT
1199572 ATCTTGAGGC
Statistics
Matches: 83, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
40 3 0.04
41 11 0.13
42 64 0.77
43 5 0.06
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (42 bp):
ATGGCCCGAATGACTTAATCATCATGCTCGAAAGACTTACTA
Found at i:1199547 original size:22 final size:22
Alignment explanation
Indices: 1199488--1199551 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
1199478 AGAATTTAAG
*
1199488 CATCATGCTCGAAAGAATTACT
1 CATCATGCTCGAAAGACTTACT
* *
1199510 -A--ATGGCCCGAATGACTTACT
1 CATCAT-GCTCGAAAGACTTACT
1199530 CATCATGCTCGAAAGACTTACT
1 CATCATGCTCGAAAGACTTACT
1199552 GATGGCCCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
19 2 0.06
20 13 0.39
21 2 0.06
22 14 0.42
23 2 0.06
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.27
Consensus pattern (22 bp):
CATCATGCTCGAAAGACTTACT
Found at i:1199633 original size:4 final size:4
Alignment explanation
Indices: 1199624--1199790 Score: 334
Period size: 4 Copynumber: 41.8 Consensus size: 4
1199614 AAATCTATAA
1199624 CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG
1 CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG
1199672 CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG
1 CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG
1199720 CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG
1 CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG
1199768 CGTG CGTG CGTG CGTG CGTG CGT
1 CGTG CGTG CGTG CGTG CGTG CGT
1199791 ATGTATATTA
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 163 1.00
ACGTcount: A:0.00, C:0.25, G:0.50, T:0.25
Consensus pattern (4 bp):
CGTG
Found at i:1201584 original size:18 final size:18
Alignment explanation
Indices: 1201564--1201671 Score: 87
Period size: 18 Copynumber: 5.9 Consensus size: 18
1201554 TCTATTTTAT
* *
1201564 TCTTTTTTCTCTTTTTTT
1 TCTTTTTTTTCTTTTTTC
*
1201582 TCTTTTTCTTCTATTTTTTC
1 TCTTTTT-TT-TCTTTTTTC
*
1201602 TTTTTCTTTTTCTTTTTTC
1 TCTTT-TTTTTCTTTTTTC
*
1201621 TC-TGTTTTTCTGTTTTTC
1 TCTTTTTTTTCT-TTTTTC
*
1201639 TCTTTTTTTT-TTCTTTC
1 TCTTTTTTTTCTTTTTTC
*
1201656 T-TTCTTTTTTGTTTTT
1 TCTT-TTTTTTCTTTTT
1201672 GATTTCTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 14
0.75 0.10 0.14
Matches are distributed among these distances:
16 2 0.03
17 19 0.26
18 21 0.29
19 16 0.22
20 13 0.18
21 2 0.03
ACGTcount: A:0.01, C:0.16, G:0.03, T:0.81
Consensus pattern (18 bp):
TCTTTTTTTTCTTTTTTC
Found at i:1201619 original size:31 final size:31
Alignment explanation
Indices: 1201566--1201653 Score: 103
Period size: 31 Copynumber: 2.9 Consensus size: 31
1201556 TATTTTATTC
*
1201566 TTTTTTCTCTTT-TTTTTC-TTTTTCTTCTA
1 TTTTTTCTTTTTCTTTTTCTTTTTTCTTCTA
*
1201595 TTTTTTCTTTTTCTTTTTCTTTTTTC-TCTG
1 TTTTTTCTTTTTCTTTTTCTTTTTTCTTCTA
*
1201625 TTTTTCTGTTTTTCTCTTTT-TTTTTTCTT
1 TTTTT-TCTTTTTCT-TTTTCTTTTTTCTT
1201654 TCTTTCTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
29 11 0.22
30 14 0.27
31 21 0.41
32 5 0.10
ACGTcount: A:0.01, C:0.16, G:0.02, T:0.81
Consensus pattern (31 bp):
TTTTTTCTTTTTCTTTTTCTTTTTTCTTCTA
Found at i:1201643 original size:39 final size:38
Alignment explanation
Indices: 1201554--1201660 Score: 123
Period size: 38 Copynumber: 2.8 Consensus size: 38
1201544 GTTGAATTTG
*
1201554 TCTATTTTATTCTTTTTTCTCTT-TTTTTTCT-T-TTTCT
1 TCTATTTT-TTCTTTTTT-TTTTCTTTTTTCTCTGTTTCT
1201591 TCTATTTTTTCTTTTTCTTTTTCTTTTTTCTCTGTTT-T
1 TCTATTTTTTCTTTTT-TTTTTCTTTTTTCTCTGTTTCT
*
1201629 TCTGTTTTTCTCTTTTTTTTTTCTTTCTTTCT
1 TCTATTTTT-TCTTTTTTTTTTCTTT-TTTCT
1201661 TTTTTGTTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
36 11 0.18
37 17 0.27
38 19 0.31
39 15 0.24
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.79
Consensus pattern (38 bp):
TCTATTTTTTCTTTTTTTTTTCTTTTTTCTCTGTTTCT
Found at i:1201647 original size:48 final size:46
Alignment explanation
Indices: 1201563--1201665 Score: 129
Period size: 48 Copynumber: 2.2 Consensus size: 46
1201553 GTCTATTTTA
*
1201563 TTCTTTTTTCTCTTTTTTTTCTTTTTCTTCTATTTTTTCTT-TTTCTTT
1 TTCTTTTTTCTCTTTTTTCTCTTTTTCTTCTATTTTTT-TTCTTTC--T
* *
1201611 TTCTTTTTTCTCTGTTTTTCTGTTTTTC-TCTTTTTTTTTTCTTTCT
1 TTCTTTTTTCTCT-TTTTTCTCTTTTTCTTCTATTTTTTTTCTTTCT
1201657 TTCTTTTTT
1 TTCTTTTTT
1201666 GTTTTTGATT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
46 10 0.20
47 2 0.04
48 26 0.52
49 12 0.24
ACGTcount: A:0.01, C:0.17, G:0.02, T:0.81
Consensus pattern (46 bp):
TTCTTTTTTCTCTTTTTTCTCTTTTTCTTCTATTTTTTTTCTTTCT
Found at i:1201834 original size:2 final size:2
Alignment explanation
Indices: 1201827--1201858 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1201817 GGACAACAAG
*
1201827 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1201859 TTTTGAAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1211704 original size:8 final size:8
Alignment explanation
Indices: 1211691--1211731 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1211681 CTCATTTTCA
1211691 GAGAATTT
1 GAGAATTT
1211699 GAGAATTT
1 GAGAATTT
*
1211707 -AGAGTTT
1 GAGAATTT
*
1211714 GGGAATTT
1 GAGAATTT
1211722 GAGAATTT
1 GAGAATTT
1211730 GA
1 GA
1211732 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1213416 original size:34 final size:31
Alignment explanation
Indices: 1213371--1213459 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
1213361 AAAATAATTC
*
1213371 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
1213405 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* * *
1213436 TATAAAATATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
1213460 AAATACTAAC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 6 0.13
32 16 0.35
33 2 0.04
34 22 0.48
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:1213436 original size:31 final size:33
Alignment explanation
Indices: 1213371--1213450 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
1213361 AAAATAATTC
* *
1213371 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
1213405 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
1213436 TATAAAATATAATAA
1 TA-AAAAAATAATAA
1213451 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.15
32 10 0.25
33 2 0.05
34 22 0.55
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:1214740 original size:24 final size:24
Alignment explanation
Indices: 1214713--1214758 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1214703 TATATGCTCG
*
1214713 TTTATTTTCGTTCATTTATGTTTA
1 TTTATGTTCGTTCATTTATGTTTA
1214737 TTTATGTTCGTTCATTTATGTT
1 TTTATGTTCGTTCATTTATGTT
1214759 CGTTCATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.15, C:0.09, G:0.11, T:0.65
Consensus pattern (24 bp):
TTTATGTTCGTTCATTTATGTTTA
Found at i:1214755 original size:14 final size:14
Alignment explanation
Indices: 1214713--1214774 Score: 87
Period size: 14 Copynumber: 4.7 Consensus size: 14
1214703 TATATGCTCG
*
1214713 TTTATTTTCGTTCA
1 TTTATGTTCGTTCA
1214727 TTTATG-T--TT-A
1 TTTATGTTCGTTCA
1214737 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
1214751 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
1214765 TTTATGTTCG
1 TTTATGTTCG
1214775 AACAAAAGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 7 0.16
11 3 0.07
13 3 0.07
14 30 0.70
ACGTcount: A:0.15, C:0.11, G:0.13, T:0.61
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:1215100 original size:27 final size:26
Alignment explanation
Indices: 1215031--1215158 Score: 97
Period size: 27 Copynumber: 4.9 Consensus size: 26
1215021 TTTGTGTTTG
*
1215031 TGTTGTTTGTTTATGTTCATTTATTA
1 TGTTTTTTGTTTATGTTCATTTATTA
*
1215057 TGTTCGTTCATTTGTTTATATTCATTTATTA
1 TG-T--TT--TTTGTTTATGTTCATTTATTA
*
1215088 TGTTTTTTCGTTTATGTTC--GT-TTA
1 TGTTTTTT-GTTTATGTTCATTTATTA
* *
1215112 CG---TTCGTTTATGTTCATTTATTA
1 TGTTTTTTGTTTATGTTCATTTATTA
*
1215135 TGTTTTTTCGTTTATGTTCGTTTA
1 TGTTTTTT-GTTTATGTTCATTTA
1215159 CGTTCGTTTA
Statistics
Matches: 79, Mismatches: 10, Indels: 25
0.69 0.09 0.22
Matches are distributed among these distances:
20 10 0.13
21 2 0.03
22 1 0.01
23 4 0.05
24 4 0.05
25 1 0.01
26 7 0.09
27 24 0.30
28 2 0.03
29 1 0.01
30 1 0.01
31 22 0.28
ACGTcount: A:0.14, C:0.09, G:0.14, T:0.63
Consensus pattern (26 bp):
TGTTTTTTGTTTATGTTCATTTATTA
Found at i:1215109 original size:10 final size:10
Alignment explanation
Indices: 1215054--1215168 Score: 88
Period size: 10 Copynumber: 12.3 Consensus size: 10
1215044 TGTTCATTTA
1215054 TTATGTTCGT
1 TTATGTTCGT
*
1215064 TCAT-TT-GT
1 TTATGTTCGT
* *
1215072 TTATATTCAT
1 TTATGTTCGT
1215082 TTAT-TAT-GT
1 TTATGT-TCGT
1215091 TT-T-TTCGT
1 TTATGTTCGT
1215099 TTATGTTCGT
1 TTATGTTCGT
*
1215109 TTACGTTCGT
1 TTATGTTCGT
*
1215119 TTATGTTCAT
1 TTATGTTCGT
1215129 TTAT-TAT-GT
1 TTATGT-TCGT
1215138 TT-T-TTCGT
1 TTATGTTCGT
1215146 TTATGTTCGT
1 TTATGTTCGT
*
1215156 TTACGTTCGT
1 TTATGTTCGT
1215166 TTA
1 TTA
1215169 AATGAACGAA
Statistics
Matches: 86, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
7 2 0.02
8 17 0.20
9 14 0.16
10 53 0.62
ACGTcount: A:0.14, C:0.10, G:0.14, T:0.62
Consensus pattern (10 bp):
TTATGTTCGT
Found at i:1215128 original size:47 final size:47
Alignment explanation
Indices: 1215054--1215168 Score: 189
Period size: 47 Copynumber: 2.5 Consensus size: 47
1215044 TGTTCATTTA
* *
1215054 TTATGTTCG-TT-CATTTGTTTATATTCATTTATTATGTTTTTTCGT
1 TTATGTTCGTTTACGTTCGTTTATATTCATTTATTATGTTTTTTCGT
*
1215099 TTATGTTCGTTTACGTTCGTTTATGTTCATTTATTATGTTTTTTCGT
1 TTATGTTCGTTTACGTTCGTTTATATTCATTTATTATGTTTTTTCGT
1215146 TTATGTTCGTTTACGTTCGTTTA
1 TTATGTTCGTTTACGTTCGTTTA
1215169 AATGAACGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
45 9 0.14
46 2 0.03
47 54 0.83
ACGTcount: A:0.14, C:0.10, G:0.14, T:0.62
Consensus pattern (47 bp):
TTATGTTCGTTTACGTTCGTTTATATTCATTTATTATGTTTTTTCGT
Found at i:1215207 original size:31 final size:32
Alignment explanation
Indices: 1215169--1215250 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 32
1215159 CGTTCGTTTA
*
1215169 AATGAACGAACATGAG-CAAGCTATATTCCTT
1 AATGAACGAACATGAGACAAACTATATTCCTT
1215200 AATGAACGAACATG-GACAAACTATATTCCTT
1 AATGAACGAACATGAGACAAACTATATTCCTT
*
1215231 AATGAACGAATATGA-ACAAA
1 AATGAACGAACATGAGACAAA
1215251 AAAAAATTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
30 1 0.02
31 46 0.98
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (32 bp):
AATGAACGAACATGAGACAAACTATATTCCTT
Found at i:1218331 original size:10 final size:11
Alignment explanation
Indices: 1218305--1218330 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1218295 ATGTAGACTC
1218305 AAAAATAATTA
1 AAAAATAATTA
1218316 AAAAATAATTA
1 AAAAATAATTA
1218327 AAAA
1 AAAA
1218331 TTTAAAGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAATAATTA
Found at i:1225644 original size:15 final size:15
Alignment explanation
Indices: 1225624--1225668 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
1225614 CATTACCTGT
1225624 CCCGCATCCGCCCGC
1 CCCGCATCCGCCCGC
1225639 CCCGCATCCGCCCGC
1 CCCGCATCCGCCCGC
* *
1225654 CCCACATCTGCCCGC
1 CCCGCATCCGCCCGC
1225669 TCAGCTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.09, C:0.64, G:0.18, T:0.09
Consensus pattern (15 bp):
CCCGCATCCGCCCGC
Found at i:1233029 original size:24 final size:24
Alignment explanation
Indices: 1233002--1233047 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1232992 CGTTCATTTA
*
1233002 CGTTCGTGAACGTTCGATTATGTT
1 CGTTCATGAACGTTCGATTATGTT
* **
1233026 CGTTTATGTTCGTTCGATTATG
1 CGTTCATGAACGTTCGATTATG
1233048 CTTGTTTATG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.46
Consensus pattern (24 bp):
CGTTCATGAACGTTCGATTATGTT
Found at i:1233054 original size:24 final size:24
Alignment explanation
Indices: 1233012--1233059 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1233002 CGTTCGTGAA
1233012 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
1233036 CGTTCGATTATGCTT-GTTTATGTT
1 CGTTCGATTATG-TTCGTTTATGTT
1233060 TATTCATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.54
Consensus pattern (24 bp):
CGTTCGATTATGTTCGTTTATGTT
Found at i:1234170 original size:16 final size:16
Alignment explanation
Indices: 1234149--1234199 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
1234139 GTCTCCAACG
1234149 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
1234165 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
1234181 TTTATATTCGT-TT-A
1 TTTATGTTCGTGTTCA
1234195 TTTAT
1 TTTAT
1234200 TAAATGAACG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
14 6 0.18
15 2 0.06
16 26 0.76
ACGTcount: A:0.16, C:0.10, G:0.14, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:1239538 original size:42 final size:41
Alignment explanation
Indices: 1239485--1239624 Score: 131
Period size: 42 Copynumber: 3.4 Consensus size: 41
1239475 AAAATACTAC
* * *
1239485 TTTAGCAGCGTTTTTTCAACAAACGCCGTAATAGAGTGGTA
1 TTTAGCGGCGTTTTTTCAACAAACGCCGCAATAGAGTAGTA
** * * * *
1239526 GTTTAGCGGCGTTTATAGC-TCAAACGCCGGAATATAGTTGT-
1 -TTTAGCGGCGTTT-TTTCAACAAACGCCGCAATAGAGTAGTA
* *
1239567 TTATAGTGGCATTTTTTCAACAAACGCCGCAATAGAGTAGTAA
1 TT-TAGCGGCGTTTTTTCAACAAACGCCGCAATAGAGTAGT-A
1239610 TTTAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
1239625 ATAGAAATGC
Statistics
Matches: 76, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
40 4 0.05
41 27 0.36
42 41 0.54
43 4 0.05
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTTCAACAAACGCCGCAATAGAGTAGTA
Found at i:1243890 original size:86 final size:85
Alignment explanation
Indices: 1243740--1243903 Score: 222
Period size: 85 Copynumber: 1.9 Consensus size: 85
1243730 CGTTTGTTTC
* * *
1243740 ATAGATATCGACCTTTTGCGGCATTTATTCCAAAAACGCCACTCTAGATCTAACCTTTTGCGGCG
1 ATAGATATCGACCTTTTGCGGCATTTATTCCAAAAACGCCACTATAGATATAACCTTTTACGGCG
1243805 TTTGTATCCAAAAATGCCTAA
66 TTTGT-TCCAAAAATGCCTAA
* *** * *
1243826 ATAGATATCGACCTTTT-CGGCATTTGTTCCAAAAACGCTGTTATTGATATCGACCTTTTACGGC
1 ATAGATATCGACCTTTTGCGGCATTTATTCCAAAAACGCCACTATAGATAT-AACCTTTTACGGC
1243890 GTTTGTTCCAAAAA
65 GTTTGTTCCAAAAA
1243904 CACCGCGATA
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
85 34 0.50
86 34 0.50
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.34
Consensus pattern (85 bp):
ATAGATATCGACCTTTTGCGGCATTTATTCCAAAAACGCCACTATAGATATAACCTTTTACGGCG
TTTGTTCCAAAAATGCCTAA
Found at i:1243924 original size:43 final size:43
Alignment explanation
Indices: 1243740--1243930 Score: 179
Period size: 43 Copynumber: 4.5 Consensus size: 43
1243730 CGTTTGTTTC
* *
1243740 ATAGATATCGACCTTTTGCGGCATTTATTCCAAAAACGCCACT
1 ATAGATATCGACCTTTTGCGGCATTTGTTCCAAAAACGCCGCT
* * * * * ***
1243783 CTAGATCT-AACCTTTTGCGGCGTTTGTATCCAAAAATGCCTAA
1 ATAGATATCGACCTTTTGCGGCATTTGT-TCCAAAAACGCCGCT
* *
1243826 ATAGATATCGACCTTTT-CGGCATTTGTTCCAAAAACGCTGTT
1 ATAGATATCGACCTTTTGCGGCATTTGTTCCAAAAACGCCGCT
* * * * *
1243868 ATTGATATCGACCTTTTACGGCGTTTGTTCCAAAAACACCGCG
1 ATAGATATCGACCTTTTGCGGCATTTGTTCCAAAAACGCCGCT
* * *
1243911 ATAGATCTTGACCTATTGCG
1 ATAGATATCGACCTTTTGCG
1243931 TCTTTTTTTT
Statistics
Matches: 116, Mismatches: 29, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
42 42 0.36
43 67 0.58
44 7 0.06
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (43 bp):
ATAGATATCGACCTTTTGCGGCATTTGTTCCAAAAACGCCGCT
Found at i:1245127 original size:6 final size:5
Alignment explanation
Indices: 1245090--1245120 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
1245080 ATAATTCTCG
1245090 TAAAGA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAA-A TAAAA TAAAA TAAAA TAAAA TAAAA
1245121 ATGAAAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:1246012 original size:19 final size:19
Alignment explanation
Indices: 1245988--1246034 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
1245978 ATTATTTAGG
1245988 AGTGCATCGATGCATGACT
1 AGTGCATCGATGCATGACT
*
1246007 AGTGCATCGATGCATGCCT
1 AGTGCATCGATGCATGACT
*
1246026 TGTGCATCG
1 AGTGCATCG
1246035 GTACACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (19 bp):
AGTGCATCGATGCATGACT
Found at i:1246495 original size:137 final size:139
Alignment explanation
Indices: 1246245--1246524 Score: 483
Period size: 137 Copynumber: 2.0 Consensus size: 139
1246235 TTGGAGTAAT
*
1246245 ATTTTGATATTCAAATAATTGTATCGAATATACTTAGAGAATCATTTGTAAAATCTTAAAATTCA
1 ATTTTGATATTCAAATAATTATATCGAATATACTTAGAGAATCATTTGTAAAATCTTAAAATTCA
* * * *
1246310 TTTATCTTAATTTGTTATATCGAAACATCAAAAATGTTTTCAATAATCTCCC-CCTTTTTGATAT
66 TTTATATTAATTTGTTATATCAAAACATAAAAAATGTTTTCAACAATCTCCCACCTTTTTGATAT
1246374 AACAAAACC
131 AACAAAACC
*
1246383 ATTTTGATATTCGAATAATTATATCGAATATACTTAGAGAAT-ATTTGTAAAATCTTAAAATTCA
1 ATTTTGATATTCAAATAATTATATCGAATATACTTAGAGAATCATTTGTAAAATCTTAAAATTCA
*
1246447 TTTATATTAATTTGTTATATCAAAACATAAAAAATGTTTTCAACAATCTCCCACTTTTTTGATAT
66 TTTATATTAATTTGTTATATCAAAACATAAAAAATGTTTTCAACAATCTCCCACCTTTTTGATAT
1246512 AACAAAACC
131 AACAAAACC
1246521 ATTT
1 ATTT
1246525 GAGTAATTTT
Statistics
Matches: 134, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
137 70 0.52
138 64 0.48
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (139 bp):
ATTTTGATATTCAAATAATTATATCGAATATACTTAGAGAATCATTTGTAAAATCTTAAAATTCA
TTTATATTAATTTGTTATATCAAAACATAAAAAATGTTTTCAACAATCTCCCACCTTTTTGATAT
AACAAAACC
Found at i:1248864 original size:23 final size:23
Alignment explanation
Indices: 1248834--1248916 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
1248824 ATGCATTTAT
1248834 GAGTGCATCGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
* *
1248857 GAGTGCATCGGTGCATC-TTC-AT
1 GAGTGCATCGATGCA-CATTCAAG
* *
1248879 GA-TGTATCGATGCACATTTAAG
1 GAGTGCATCGATGCACATTCAAG
1248901 G-GATGCATCGATGCAC
1 GAG-TGCATCGATGCAC
1248917 TGTCATGTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
20 1 0.02
21 12 0.25
22 5 0.10
23 29 0.60
24 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (23 bp):
GAGTGCATCGATGCACATTCAAG
Found at i:1248893 original size:44 final size:44
Alignment explanation
Indices: 1248814--1248935 Score: 146
Period size: 44 Copynumber: 2.8 Consensus size: 44
1248804 AAAACATGAT
* *
1248814 GAGTGTATCGATGCAT-TT-ATGAGTGCATCGATGCACATTCAAG
1 GAGTGCATCGATGCATCTTCATGA-TGTATCGATGCACATTCAAG
* *
1248857 GAGTGCATCGGTGCATCTTCATGATGTATCGATGCACATTTAAG
1 GAGTGCATCGATGCATCTTCATGATGTATCGATGCACATTCAAG
1248901 G-GATGCATCGATGCA-CTGTCATG-TGTATCGATGCA
1 GAG-TGCATCGATGCATCT-TCATGATGTATCGATGCA
1248936 TTAATCACAA
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
43 29 0.41
44 37 0.53
45 4 0.06
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (44 bp):
GAGTGCATCGATGCATCTTCATGATGTATCGATGCACATTCAAG
Found at i:1255898 original size:20 final size:20
Alignment explanation
Indices: 1255873--1255929 Score: 114
Period size: 20 Copynumber: 2.9 Consensus size: 20
1255863 TAAATTATGC
1255873 ATCGATGCACTGCTACATTG
1 ATCGATGCACTGCTACATTG
1255893 ATCGATGCACTGCTACATTG
1 ATCGATGCACTGCTACATTG
1255913 ATCGATGCACTGCTACA
1 ATCGATGCACTGCTACA
1255930 GTACCACTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (20 bp):
ATCGATGCACTGCTACATTG
Found at i:1262048 original size:20 final size:20
Alignment explanation
Indices: 1262023--1262083 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
1262013 TTTTGGTGCA
*
1262023 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
1262043 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
1262064 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
1262084 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:1262092 original size:21 final size:21
Alignment explanation
Indices: 1262066--1262105 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1262056 CCCCCTTTGA
*
1262066 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1262087 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1262106 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1267678 original size:3 final size:3
Alignment explanation
Indices: 1267670--1267704 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1267660 AATTGTATTA
1267670 AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1267705 TTTGTAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1267692 original size:17 final size:17
Alignment explanation
Indices: 1267670--1267702 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1267660 AATTGTATTA
1267670 AATAATAATAATAATAT
1 AATAATAATAATAATAT
1267687 AATAATAATAATAATA
1 AATAATAATAATAATA
1267703 ATTTTGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATAATAATAATAT
Found at i:1270340 original size:14 final size:14
Alignment explanation
Indices: 1270323--1270355 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1270313 TTATATATTC
1270323 TAAAAATAAAAATA
1 TAAAAATAAAAATA
*
1270337 TAAAAATAAAATTA
1 TAAAAATAAAAATA
1270351 TAAAA
1 TAAAA
1270356 TTGCAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAAAATAAAAATA
Found at i:1270435 original size:42 final size:40
Alignment explanation
Indices: 1270369--1270461 Score: 105
Period size: 42 Copynumber: 2.3 Consensus size: 40
1270359 CAACTAAATT
* * *
1270369 TAAAATAATTTGAGATTAAAATAAATAATTTAAATTTTAAGG
1 TAAAATAATTTGAAAATAAAATAAAT--TTTAAATGTTAAGG
* * * *
1270411 TGAAATAATTTGAAAATAATATAAATTTTGAATGTTAGGG
1 TAAAATAATTTGAAAATAAAATAAATTTTAAATGTTAAGG
1270451 TAAAATAATTT
1 TAAAATAATTT
1270462 TAAATTACAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 21 0.49
42 22 0.51
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (40 bp):
TAAAATAATTTGAAAATAAAATAAATTTTAAATGTTAAGG
Found at i:1271474 original size:22 final size:22
Alignment explanation
Indices: 1271449--1271783 Score: 442
Period size: 22 Copynumber: 15.3 Consensus size: 22
1271439 CTATTTTAAA
1271449 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1271471 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
1271493 ATTTATTTTTAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
1271515 A-TTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
1271536 AATTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
**
1271558 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
1271579 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
***
1271602 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
*
1271624 ATTTATTTTAAAATATGGATTC
1 ATTTATTTTAAAATATGGATTG
* *
1271646 ATTTATTCTAAAATGTGGATTG
1 ATTTATTTTAAAATATGGATTG
*
1271668 ATTTATTTTAAAATGTGGATTG
1 ATTTATTTTAAAATATGGATTG
***
1271690 ATTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATGGATTG
1271711 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
*
1271734 ATTTATTTTAAAATATGGATTT
1 ATTTATTTTAAAATATGGATTG
*
1271756 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
1271778 ATTTAT
1 ATTTAT
1271784 GTTGAAAACA
Statistics
Matches: 271, Mismatches: 37, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
21 19 0.07
22 248 0.92
23 4 0.01
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.48
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:1272845 original size:22 final size:22
Alignment explanation
Indices: 1272819--1272979 Score: 202
Period size: 22 Copynumber: 7.3 Consensus size: 22
1272809 AACAACTTAA
1272819 TTTAAAATATGGATTGATTTAT
1 TTTAAAATATGGATTGATTTAT
***
1272841 TTT-AAA-ATGCGAAAAATTTTAT
1 TTTAAAATATG-GATTGA-TTTAT
1272863 TTTAAAATATGGATTGATTTAT
1 TTTAAAATATGGATTGATTTAT
*
1272885 TTTAAAATATAGATTGATTTAT
1 TTTAAAATATGGATTGATTTAT
** *
1272907 TTTAAAATATGGA-AAAATTATT
1 TTTAAAATATGGATTGATTTA-T
1272929 TTTAAAATATGGATTGATTTAT
1 TTTAAAATATGGATTGATTTAT
*
1272951 TTTAAATTATGGATTGATTTAT
1 TTTAAAATATGGATTGATTTAT
1272973 TTTAAAA
1 TTTAAAA
1272980 ACTTTATTAT
Statistics
Matches: 117, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
20 3 0.03
21 10 0.09
22 91 0.78
23 10 0.09
24 3 0.03
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.48
Consensus pattern (22 bp):
TTTAAAATATGGATTGATTTAT
Found at i:1272932 original size:66 final size:67
Alignment explanation
Indices: 1272819--1272980 Score: 267
Period size: 66 Copynumber: 2.4 Consensus size: 67
1272809 AACAACTTAA
*
1272819 TTTAAAATATGGATTGATTTATTTT-AAAATGCGAAAAATTTTATTTTAAAATATGGATTGATTT
1 TTTAAAATATGGATTGATTTATTTTAAAAATGCGAAAAATTATATTTTAAAATATGGATTGATTT
1272883 AT
66 AT
*
1272885 TTTAAAATATAGATTGATTTATTTTAAAATATG-GAAAAATTAT-TTTTAAAATATGGATTGATT
1 TTTAAAATATGGATTGATTTATTTTAAAA-ATGCGAAAAATTATATTTTAAAATATGGATTGATT
1272948 TAT
65 TAT
*
1272951 TTTAAATTATGGATTGATTTATTTTAAAAA
1 TTTAAAATATGGATTGATTTATTTTAAAAA
1272981 CTTTATTATT
Statistics
Matches: 90, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
65 1 0.01
66 74 0.82
67 12 0.13
68 3 0.03
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.48
Consensus pattern (67 bp):
TTTAAAATATGGATTGATTTATTTTAAAAATGCGAAAAATTATATTTTAAAATATGGATTGATTT
AT
Found at i:1274726 original size:17 final size:18
Alignment explanation
Indices: 1274693--1274726 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1274683 CCGTTACTAG
1274693 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
1274711 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
1274727 GACCGGTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:1275451 original size:23 final size:22
Alignment explanation
Indices: 1275425--1275467 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1275415 TATAAAAAAT
1275425 TATTTTTTATTAAATATTTTTGG
1 TATTTTTTATTAAAT-TTTTTGG
*
1275448 TATTTTTTATTTAATTTTTT
1 TATTTTTTATTAAATTTTTT
1275468 AAATAATTAT
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:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (22 bp):
TATTTTTTATTAAATTTTTTGG
Found at i:1275559 original size:17 final size:17
Alignment explanation
Indices: 1275537--1275594 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
1275527 GGTAGCATGG
1275537 CCGGTTCGCTAACCGGT
1 CCGGTTCGCTAACCGGT
1275554 CCGGTTCGCTAACCGGT
1 CCGGTTCGCTAACCGGT
*
1275571 CCGGTTCGTTAACCGGT
1 CCGGTTCGCTAACCGGT
1275588 CCGGTTC
1 CCGGTTC
1275595 TGAAAACCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.10, C:0.34, G:0.29, T:0.26
Consensus pattern (17 bp):
CCGGTTCGCTAACCGGT
Found at i:1281863 original size:25 final size:24
Alignment explanation
Indices: 1281825--1281873 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
1281815 AGAAAGTTAA
*
1281825 ATTTATATATAATCAGAACTAAAC
1 ATTTATATATAATCAAAACTAAAC
*
1281849 ATTTCATATTTAATCAAAACTAAAC
1 ATTT-ATATATAATCAAAACTAAAC
1281874 GTTATATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (24 bp):
ATTTATATATAATCAAAACTAAAC
Found at i:1285137 original size:19 final size:20
Alignment explanation
Indices: 1285097--1285138 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1285087 GATCAATCAT
*
1285097 TTTCTCTAAAGGATCGATTC
1 TTTCTCCAAAGGATCGATTC
*
1285117 TTTCTCCAAGGGATCGA-TC
1 TTTCTCCAAAGGATCGATTC
1285136 TTT
1 TTT
1285139 TTGAAAATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TTTCTCCAAAGGATCGATTC
Found at i:1285171 original size:20 final size:20
Alignment explanation
Indices: 1285127--1285175 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1285117 TTTCTCCAAG
* *
1285127 GGATCGATCTTTTTGAAAAT
1 GGATTGATCTTTTCGAAAAT
1285147 GGATTGATCTTTTCGAAAA-
1 GGATTGATCTTTTCGAAAAT
1285166 GTGATTGATC
1 G-GATTGATC
1285176 CTTTGCTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (20 bp):
GGATTGATCTTTTCGAAAAT
Found at i:1303555 original size:22 final size:22
Alignment explanation
Indices: 1303527--1303570 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1303517 TTTACCCAAA
1303527 TACCAGGAGAAACTGCTGCAAC
1 TACCAGGAGAAACTGCTGCAAC
1303549 TACCAGGAGAAACTGCTGCAAC
1 TACCAGGAGAAACTGCTGCAAC
1303571 CCCTCGTCGT
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:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (22 bp):
TACCAGGAGAAACTGCTGCAAC
Found at i:1304428 original size:16 final size:16
Alignment explanation
Indices: 1304407--1304438 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1304397 ACTTTATAAT
*
1304407 TATAAGATTCTGGTGC
1 TATAAGATTCTAGTGC
1304423 TATAAGATTCTAGTGC
1 TATAAGATTCTAGTGC
1304439 ATTTTCTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (16 bp):
TATAAGATTCTAGTGC
Found at i:1307829 original size:16 final size:16
Alignment explanation
Indices: 1307787--1307833 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1307777 TAACATGAAC
1307787 CAAAAGTAACCCGAAT
1 CAAAAGTAACCCGAAT
** *
1307803 TGAAATTAACCCGAAT
1 CAAAAGTAACCCGAAT
*
1307819 CAAAAGCAACCCGAA
1 CAAAAGTAACCCGAA
1307834 CCGAATTTAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.49, C:0.26, G:0.13, T:0.13
Consensus pattern (16 bp):
CAAAAGTAACCCGAAT
Found at i:1307872 original size:32 final size:32
Alignment explanation
Indices: 1307784--1307873 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
1307774 AACTAACATG
* * *
1307784 AACCAAAAGTAACCCGAATTGAAATTAACCCG
1 AACCAAAAGAAACCCGAATTGAATTTAACCCA
* * **
1307816 AATCAAAAGCAACCCGAACCGAATTTAACCCA
1 AACCAAAAGAAACCCGAATTGAATTTAACCCA
*
1307848 AACCGAAAGAAACCCGAATTGAATTT
1 AACCAAAAGAAACCCGAATTGAATTT
1307874 TTATCCGATT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.47, C:0.26, G:0.12, T:0.16
Consensus pattern (32 bp):
AACCAAAAGAAACCCGAATTGAATTTAACCCA
Found at i:1307893 original size:65 final size:64
Alignment explanation
Indices: 1307784--1307909 Score: 153
Period size: 65 Copynumber: 2.0 Consensus size: 64
1307774 AACTAACATG
* *
1307784 AACCAAAAGTAACCCGAATTGAAATTAACCCGAATCAAAAGCAACCCGAACCGAATTTAACCCA
1 AACCAAAAGAAACCCGAATTGAAATTAACCCGAATCAAAAGCAACCCGAACCAAATTTAACCCA
* * * * * * * *
1307848 AACCGAAAGAAACCCGAATTGAATTTTTATCCGATTCGAAAGCAACCTGAATCAAATTTAAC
1 AACCAAAAGAAACCCGAATTGAA-ATTAACCCGAATCAAAAGCAACCCGAACCAAATTTAAC
1307910 TTGACCCGAA
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
64 21 0.41
65 30 0.59
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.19
Consensus pattern (64 bp):
AACCAAAAGAAACCCGAATTGAAATTAACCCGAATCAAAAGCAACCCGAACCAAATTTAACCCA
Found at i:1308027 original size:18 final size:19
Alignment explanation
Indices: 1307988--1308043 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 19
1307978 TAATAAATTA
*
1307988 ATTTA-AATAAAATTGATA-
1 ATTTATAATAAAA-TAATAG
* *
1308006 ATTTATTA-AAAATATTAG
1 ATTTATAATAAAATAATAG
1308024 ATTTATAATAAAATAATAG
1 ATTTATAATAAAATAATAG
1308043 A
1 A
1308044 AAGTTTAAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
17 3 0.10
18 16 0.53
19 11 0.37
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
ATTTATAATAAAATAATAG
Found at i:1308539 original size:2 final size:2
Alignment explanation
Indices: 1308532--1308598 Score: 111
Period size: 2 Copynumber: 34.0 Consensus size: 2
1308522 ATTTTTACAA
1308532 AT AT AT AT CA- AT -T 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
1308573 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
1308599 TTAATTTTGA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.03
2 59 0.95
3 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1309293 original size:21 final size:21
Alignment explanation
Indices: 1309235--1309296 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
1309225 AAGTTAAAGC
* * *
1309235 GAGAGAATCAGAATGAGAAAT
1 GAGAGAAACAGAAAGAGAAGT
*
1309256 GAGAGAAACAGAGAGAGAAGT
1 GAGAGAAACAGAAAGAGAAGT
* *
1309277 GAGAGAACCACAAAGAGAAG
1 GAGAGAAACAGAAAGAGAAG
1309297 CTAGAAAAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.53, C:0.08, G:0.32, T:0.06
Consensus pattern (21 bp):
GAGAGAAACAGAAAGAGAAGT
Found at i:1309509 original size:28 final size:29
Alignment explanation
Indices: 1309469--1309540 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 29
1309459 TTATTCTAGT
* *
1309469 TGTTAAACTATATTACATTTCACTT-GAA
1 TGTTGAACTATATTACATTTCACTTAAAA
*
1309497 TGTTGAACTATATTATATTTCACTTAAAA
1 TGTTGAACTATATTACATTTCACTTAAAA
*
1309526 T-TTGAACTAAATTAC
1 TGTTGAACTATATTAC
1309541 TTTAATGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
28 35 0.92
29 3 0.08
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (29 bp):
TGTTGAACTATATTACATTTCACTTAAAA
Found at i:1309850 original size:42 final size:43
Alignment explanation
Indices: 1309798--1309894 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 43
1309788 ACAAAAATAT
* * *
1309798 CGCTATATGTCGAAACCTATTGGGGCGTTTATATAA-AAACGA
1 CGCTAAATGTCCAAACCTATTGGGGCGTTTATAAAAGAAACGA
* * * * * *
1309840 TGCTAAATGTCCTAACCTATTGTGGTGTTTGTAAAAGAAACGC
1 CGCTAAATGTCCAAACCTATTGGGGCGTTTATAAAAGAAACGA
1309883 CGCTAAATGTCC
1 CGCTAAATGTCC
1309895 TAACATGTTG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
42 28 0.64
43 16 0.36
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (43 bp):
CGCTAAATGTCCAAACCTATTGGGGCGTTTATAAAAGAAACGA
Found at i:1309892 original size:43 final size:42
Alignment explanation
Indices: 1309751--1309947 Score: 150
Period size: 43 Copynumber: 4.7 Consensus size: 42
1309741 TTTTTACTCT
1309751 AAAACGCCG-TAATATGTCCTAACCTA-TGT--TGTTTATAACA
1 AAAACGCCGCTAA-ATGTCCTAACCTATTGTGGTGTTTATAA-A
*** * ** * * *
1309791 AAAATATCGCTATATGTCGAAACCTATTGGGGCGTTTATATA
1 AAAACGCCGCTAAATGTCCTAACCTATTGTGGTGTTTATAAA
** *
1309833 AAAACGATGCTAAATGTCCTAACCTATTGTGGTGTTTGTAAA
1 AAAACGCCGCTAAATGTCCTAACCTATTGTGGTGTTTATAAA
* * * * *
1309875 AGAAACGCCGCTAAATGTCCTAACATGTTGTGGTATTTGTTAAC
1 A-AAACGCCGCTAAATGTCCTAACCTATTGTGGTGTTT-ATAAA
* * *
1309919 AAAACGTCGTTAAAGGTCCTAACCTATTG
1 AAAACGCCGCTAAATGTCCTAACCTATTG
1309948 CGGCATTTTT
Statistics
Matches: 119, Mismatches: 32, Indels: 9
0.74 0.20 0.06
Matches are distributed among these distances:
40 17 0.14
41 4 0.03
42 33 0.28
43 61 0.51
44 4 0.03
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (42 bp):
AAAACGCCGCTAAATGTCCTAACCTATTGTGGTGTTTATAAA
Found at i:1310513 original size:13 final size:14
Alignment explanation
Indices: 1310476--1310513 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
1310466 TTTGCATAAA
1310476 AATATTATTTTTGT
1 AATATTATTTTTGT
1310490 AAT-TTATTTTT-T
1 AATATTATTTTTGT
1310502 AATATTAATTTT
1 AATATT-ATTTT
1310514 AGAATTAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.18
13 10 0.45
14 8 0.36
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (14 bp):
AATATTATTTTTGT
Found at i:1311469 original size:31 final size:33
Alignment explanation
Indices: 1311431--1311492 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
1311421 GACCCGACCC
**
1311431 GAAAAAAA-TATAATTTTATCT-TATATATTTA
1 GAAAAAAATTATAATAATATCTCTATATATTTA
1311462 GAAAAAAATTATAATAATATCTCTATATATT
1 GAAAAAAATTATAATAATATCTCTATATATT
1311493 ATTTTTCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 8 0.30
32 11 0.41
33 8 0.30
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (33 bp):
GAAAAAAATTATAATAATATCTCTATATATTTA
Found at i:1312780 original size:29 final size:29
Alignment explanation
Indices: 1312721--1312777 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1312711 TTTATATTAA
* **
1312721 TTTAAAATTTTAATAATTATTTTTTCAAT
1 TTTAAAATTTTAATAATTAATTAATCAAT
*
1312750 TTTAAAATTTTAATTATTAAATTAATCA
1 TTTAAAATTTTAATAATT-AATTAATCA
1312778 TTTGAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 17 0.74
30 6 0.26
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (29 bp):
TTTAAAATTTTAATAATTAATTAATCAAT
Found at i:1314238 original size:2 final size:2
Alignment explanation
Indices: 1314231--1314259 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1314221 TTTCTTATGA
1314231 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1314260 CTTTTTTGAG
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1323294 original size:3 final size:3
Alignment explanation
Indices: 1323286--1323344 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
1323276 TTAAATCAAC
1323286 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1323333 ATA ATA ATA ATA
1 ATA ATA ATA ATA
1323345 CTTGATGTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.