Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008447.1 Hibiscus syriacus cultivar Beakdansim tig00111252_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: 276830
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:730 original size:34 final size:31
Alignment explanation
Indices: 669--737 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 31
659 CCTTACAAAC
*
669 TCCCTAGTTTTTCCGGGATAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAACTAGAACCTT
*
700 TCCCTAGATTTTACACGGGATTAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGA-TAACTAGAACCTT
734 TCCC
1 TCCC
738 CTTTACAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 7 0.21
32 5 0.15
33 5 0.15
34 16 0.48
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (31 bp):
TCCCTAGTTTTACCGGGATAACTAGAACCTT
Found at i:1063 original size:21 final size:22
Alignment explanation
Indices: 1015--1075 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
1005 TGCCCAAAAT
1015 GGGGGGAATCGGTACCCCTTCATA
1 GGGGGGAATCGGTA-CCC-TCATA
1039 ---GGGAATCGGTACCCTCA-A
1 GGGGGGAATCGGTACCCTCATA
*
1057 GGGGGGAATCGGTTCCCTC
1 GGGGGGAATCGGTACCCTC
1076 CGAGTAATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
18 1 0.03
19 3 0.09
20 3 0.09
21 26 0.79
ACGTcount: A:0.20, C:0.26, G:0.34, T:0.20
Consensus pattern (22 bp):
GGGGGGAATCGGTACCCTCATA
Found at i:1150 original size:34 final size:35
Alignment explanation
Indices: 1112--1190 Score: 108
Period size: 34 Copynumber: 2.3 Consensus size: 35
1102 AAACCATGCA
1112 GGGGGAATCTATACCC-GAGGAATCGATACCCC-TG
1 GGGGGAATCTATACCCAG-GGAATCGATACCCCATG
* *
1146 GGGGGAATCTGTTCCCAGGGAATCGATACCCCATG
1 GGGGGAATCTATACCCAGGGAATCGATACCCCATG
*
1181 GGAGGAATCT
1 GGGGGAATCT
1191 GTTCCCATGG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
34 28 0.70
35 12 0.30
ACGTcount: A:0.25, C:0.24, G:0.32, T:0.19
Consensus pattern (35 bp):
GGGGGAATCTATACCCAGGGAATCGATACCCCATG
Found at i:1195 original size:35 final size:34
Alignment explanation
Indices: 1130--1197 Score: 118
Period size: 35 Copynumber: 2.0 Consensus size: 34
1120 CTATACCCGA
*
1130 GGAATCGATACCCCTGGGGGGAATCTGTTCCCAG
1 GGAATCGATACCCCTGGGAGGAATCTGTTCCCAG
1164 GGAATCGATACCCCATGGGAGGAATCTGTTCCCA
1 GGAATCGATACCCC-TGGGAGGAATCTGTTCCCA
1198 TGGGGGGGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 14 0.44
35 18 0.56
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (34 bp):
GGAATCGATACCCCTGGGAGGAATCTGTTCCCAG
Found at i:1199 original size:19 final size:20
Alignment explanation
Indices: 1175--1212 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1165 GAATCGATAC
1175 CCCAT-GGGAGGAATCTGTT
1 CCCATGGGGAGGAATCTGTT
*
1194 CCCATGGGGGGGAATCTGT
1 CCCATGGGGAGGAATCTGT
1213 ACCCCCTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.18, C:0.21, G:0.37, T:0.24
Consensus pattern (20 bp):
CCCATGGGGAGGAATCTGTT
Found at i:38050 original size:40 final size:40
Alignment explanation
Indices: 37993--38073 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
37983 CCGTAGTGCA
*
37993 ACACATAAGGTCATGCCCACCATATACACCAAAGTGTATT
1 ACACATAAGGTCATGCCCACCATATACACCAAAGCGTATT
* *
38033 ACACATAAGGTCGTGCCCACCATATACACCGAAGCGTATT
1 ACACATAAGGTCATGCCCACCATATACACCAAAGCGTATT
38073 A
1 A
38074 TAAACCTGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (40 bp):
ACACATAAGGTCATGCCCACCATATACACCAAAGCGTATT
Found at i:39044 original size:29 final size:29
Alignment explanation
Indices: 39001--39064 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
38991 TCTTCATCAA
* * *
39001 TTTTCCAAAATTTACGAATTTATCCCCAAC
1 TTTT-CAAAACTTACGAAATGATCCCCAAC
*
39031 TTTTCAAAACTTACGAAATGATCCCCAAT
1 TTTTCAAAACTTACGAAATGATCCCCAAC
39060 TTTTC
1 TTTTC
39065 TAAGGCTTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (29 bp):
TTTTCAAAACTTACGAAATGATCCCCAAC
Found at i:42918 original size:20 final size:20
Alignment explanation
Indices: 42880--42923 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
42870 ATAACCTATG
* *
42880 AAATAATTTAATAATTAGAT
1 AAATAATTAAATAATTAGAC
42900 AAATAATATAAATAA-TAGAC
1 AAATAAT-TAAATAATTAGAC
42920 AAAT
1 AAAT
42924 CTAGACAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (20 bp):
AAATAATTAAATAATTAGAC
Found at i:57684 original size:20 final size:20
Alignment explanation
Indices: 57638--57686 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
57628 AATACCTCAT
*
57638 TATCGATATTGACTTACTGAG
1 TATCGATATTGACCTAC-GAG
*
57659 TTTCGATATTAGACCTA-GAG
1 TATCGATATT-GACCTACGAG
57679 TATCGATA
1 TATCGATA
57687 CTCCTTGAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 10 0.42
21 9 0.38
22 5 0.21
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (20 bp):
TATCGATATTGACCTACGAG
Found at i:66389 original size:59 final size:59
Alignment explanation
Indices: 66316--66449 Score: 205
Period size: 59 Copynumber: 2.3 Consensus size: 59
66306 TAGCAGGATG
* * *
66316 CATATTCGGGTTAGCACTAAAGGATACTTAGTGAAAATGGTTAGCACGACCTTATGTGT
1 CATATTCGGGTTAGCACCAAAGGATACCTAGTGAAAATGGTGAGCACGACCTTATGTGT
* * * *
66375 CATATTCGAGTTAGCACCAAAGGATACCTAGTGCAGATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGTTAGCACCAAAGGATACCTAGTGAAAATGGTGAGCACGACCTTATGTGT
66434 CATATTCGGGTTAGCA
1 CATATTCGGGTTAGCA
66450 TTTTCGTACA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 67 1.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (59 bp):
CATATTCGGGTTAGCACCAAAGGATACCTAGTGAAAATGGTGAGCACGACCTTATGTGT
Found at i:67175 original size:47 final size:47
Alignment explanation
Indices: 67063--67460 Score: 653
Period size: 47 Copynumber: 8.6 Consensus size: 47
67053 TAATATTCAT
*
67063 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATACC-TAA
1 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAA
* * *
67109 TGCATCATTTCATGCATTTTCAATTATGGGATCTGTTCATGCCTTAA
1 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAA
*
67156 TGCATCCTTTCATGAATTTTCAATTATGGCATCCGTTCATGCCTTAA
1 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAA
*
67203 TGCATCCTTTCATGCATATTCAATTATGGCATCCGTTCATGCCTTAA
1 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAA
* *
67250 TGCATCCTTTCATGCATTTTCAATTATTGCCTCCGTTCATGCCTTAA
1 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAA
67297 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAA
1 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAA
* *
67344 TGCATCCTTTCATGCA-TTTCAA--ATGGCATTCGTTCATACCTTAA
1 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAA
* *
67388 TGCATCATTTCATGCATTTTCAATTATGGCATACGTTCATGCCTTAA
1 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAA
67435 TGCATCC-TTCATGCATTTTCAATTAT
1 TGCATCCTTTCATGCATTTTCAATTAT
67461 AATTTGATTT
Statistics
Matches: 327, Mismatches: 21, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
44 35 0.11
45 6 0.02
46 64 0.20
47 222 0.68
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (47 bp):
TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAA
Found at i:67245 original size:94 final size:94
Alignment explanation
Indices: 67063--67799 Score: 671
Period size: 94 Copynumber: 7.8 Consensus size: 94
67053 TAATATTCAT
67063 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATACC-TAATGCATCATTTCATGCATT
1 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATACCTTAATGCATCATTTCATGCATT
* *
67127 TTCAATTATGGGATCTGTTCATGCCTTAA
66 TTCAATTATGGCATCCGTTCATGCCTTAA
* * * *
67156 TGCATCCTTTCATGAATTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATA
1 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATACCTTAATGCATCATTTCATGCATT
67221 TTCAATTATGGCATCCGTTCATGCCTTAA
66 TTCAATTATGGCATCCGTTCATGCCTTAA
* * * *
67250 TGCATCCTTTCATGCATTTTCAATTATTGCCTCCGTTCATGCCTTAATGCATCCTTTCATGCATT
1 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATACCTTAATGCATCATTTCATGCATT
67315 TTCAATTATGGCATCCGTTCATGCCTTAA
66 TTCAATTATGGCATCCGTTCATGCCTTAA
*
67344 TGCATCCTTTCATGCA-TTTCAA--ATGGCATTCGTTCATACCTTAATGCATCATTTCATGCATT
1 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATACCTTAATGCATCATTTCATGCATT
*
67406 TTCAATTATGGCATACGTTCATGCCTTAA
66 TTCAATTATGGCATCCGTTCATGCCTTAA
* ** *** * * * * **
67435 TGCATCC-TTCATGCATTTTCAATTAT--AATTTGATT--TAGAGTAGTTCAT-ACTCTAAAAC-
1 TGCATCCTTTCATGCATTTTCAATTATGGCATCCG-TTCATACCTTAATGCATCA-TTTCATGCA
* * ** *
67493 TTATTCAAAATAT-TC-T-TTTTCATGCTTGTAAAA
64 TT-TTC-AATTATGGCATCCGTTCATGCCT-T--AA
* ** * ** ** * * * * *
67526 TATCATAATCAAATT-ATGAAACATATAAT-AATT-TAAACAATCTAATTGAATATCATCATCTC
1 T-GC---ATC-CTTTCATG---CAT-T-TTCAATTAT-GGC-ATC-CGTT-CATACCTTAAT-GC
* * *
67588 ATCCTTTCATGCATTTTCAATTATTGCCTCCGTTCATGCCTTAA
51 ATCATTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAA
* *
67632 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATT
1 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATACCTTAATGCATCATTTCATGCATT
** *
67697 TTCAATTATGGCATTTGTTCATACCTTAA
66 TTCAATTATGGCATCCGTTCATGCCTTAA
* * * *
67726 TGCATCATTTCATGCATTTTCAATTATGGCATACGTTCATGCCTTAATGCATCCTTTCATGCATT
1 TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATACCTTAATGCATCATTTCATGCATT
67791 TTCAATTAT
66 TTCAATTAT
67800 AAATTTGATT
Statistics
Matches: 530, Mismatches: 75, Indels: 77
0.78 0.11 0.11
Matches are distributed among these distances:
88 8 0.02
89 5 0.01
90 24 0.05
91 88 0.17
92 3 0.01
93 49 0.09
94 264 0.50
95 9 0.02
96 5 0.01
97 6 0.01
98 6 0.01
99 8 0.02
100 5 0.01
101 3 0.01
102 6 0.01
103 4 0.01
105 1 0.00
106 12 0.02
107 12 0.02
108 4 0.01
109 8 0.02
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (94 bp):
TGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATACCTTAATGCATCATTTCATGCATT
TTCAATTATGGCATCCGTTCATGCCTTAA
Found at i:67645 original size:20 final size:20
Alignment explanation
Indices: 67620--67693 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 20
67610 ATTGCCTCCG
67620 TTCATGCCTTAATGCATCCT
1 TTCATGCCTTAATGCATCCT
* *
67640 TTCATGCATTTTCAATTATGGCATCCG
1 TTCATGC--CTT--A--AT-GCATCCT
67667 TTCATGCCTTAATGCATCCT
1 TTCATGCCTTAATGCATCCT
67687 TTCATGC
1 TTCATGC
67694 ATTTTCAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
20 20 0.47
21 2 0.05
22 2 0.05
23 1 0.02
24 1 0.02
25 2 0.05
26 2 0.05
27 13 0.30
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (20 bp):
TTCATGCCTTAATGCATCCT
Found at i:67656 original size:47 final size:47
Alignment explanation
Indices: 67587--67799 Score: 363
Period size: 47 Copynumber: 4.5 Consensus size: 47
67577 ATCATCATCT
* *
67587 CATCCTTTCATGCATTTTCAATTATTGCCTCCGTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
67634 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
** *
67681 CATCCTTTCATGCATTTTCAATTATGGCATTTGTTCATACCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
* *
67728 CATCATTTCATGCATTTTCAATTATGGCATACGTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
67775 CATCCTTTCATGCATTTTCAATTAT
1 CATCCTTTCATGCATTTTCAATTAT
67800 AAATTTGATT
Statistics
Matches: 156, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 156 1.00
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.43
Consensus pattern (47 bp):
CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
Found at i:67671 original size:27 final size:27
Alignment explanation
Indices: 67633--67767 Score: 82
Period size: 27 Copynumber: 5.5 Consensus size: 27
67623 ATGCCTTAAT
*
67633 GCATCCTTTCATGCATTTTCAATTATG
1 GCATCCGTTCATGCATTTTCAATTATG
*
67660 GCATCCGTTCATGC--CTT--A--AT-
1 GCATCCGTTCATGCATTTTCAATTATG
*
67680 GCATCCTTTCATGCATTTTCAATTATG
1 GCATCCGTTCATGCATTTTCAATTATG
** **
67707 GCATTTGTTCAT--ACCTT--A--AT-
1 GCATCCGTTCATGCATTTTCAATTATG
**
67727 GCATCATTTCATGCATTTTCAATTATG
1 GCATCCGTTCATGCATTTTCAATTATG
*
67754 GCATACGTTCATGC
1 GCATCCGTTCATGC
67768 CTTAATGCAT
Statistics
Matches: 77, Mismatches: 17, Indels: 28
0.63 0.14 0.23
Matches are distributed among these distances:
20 22 0.29
21 4 0.05
22 5 0.06
23 2 0.03
24 2 0.03
25 5 0.06
26 4 0.05
27 33 0.43
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (27 bp):
GCATCCGTTCATGCATTTTCAATTATG
Found at i:67880 original size:338 final size:338
Alignment explanation
Indices: 67252--67928 Score: 1265
Period size: 338 Copynumber: 2.0 Consensus size: 338
67242 TGCCTTAATG
67252 CATCCTTTCATGCATTTTCAATTATTGCCTCCGTTCATGCCTTAATGCATCCTTTCATGCATTTT
1 CATCCTTTCATGCATTTTCAATTATTGCCTCCGTTCATGCCTTAATGCATCCTTTCATGCATTTT
67317 CAATTATGGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTCAAATGGCATTCGTTCATA
66 CAATTATGGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTCAAATGGCATTCGTTCATA
67382 CCTTAATGCATCATTTCATGCATTTTCAATTATGGCATACGTTCATGCCTTAATGCATCCTTCAT
131 CCTTAATGCATCATTTCATGCATTTTCAATTATGGCATACGTTCATGCCTTAATGCATCCTTCAT
67447 GCATTTTCAATTATAATTTGATTTAGAGTAGTTCATACTCTAAAACTTATTCAAAATATTCTTTT
196 GCATTTTCAATTATAATTTGATTTAGAGTAGTTCATACTCTAAAACTTATTCAAAATATTCTTTT
67512 TCATGCTTGTAAAATATCATAATCAAATTATGAAACATATA-ATAATTTAAACAATCT-AATTGA
261 TCATGCTTGTAAAATATCATAATCAAATTATGAAACATATATATAATTTAAACAATCTAAATTGA
67575 ATA-TCATCATCT
326 ATATTCATCATCT
67587 CATCCTTTCATGCATTTTCAATTATTGCCTCCGTTCATGCCTTAATGCATCCTTTCATGCATTTT
1 CATCCTTTCATGCATTTTCAATTATTGCCTCCGTTCATGCCTTAATGCATCCTTTCATGCATTTT
*
67652 CAATTATGGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATGGCATTTGTTC
66 CAATTATGGCATCCGTTCATGCCTTAATGCATCCTTTCATGCA-TTTCAA--ATGGCATTCGTTC
67717 ATACCTTAATGCATCATTTCATGCATTTTCAATTATGGCATACGTTCATGCCTTAATGCATCCTT
128 ATACCTTAATGCATCATTTCATGCATTTTCAATTATGGCATACGTTCATGCCTTAATGCATCC-T
67782 TCATGCATTTTCAATTATAAATTTGATTTAGAGTAGTTCATACTCTAAAACTTATTC-AAATATT
192 TCATGCATTTTCAATTAT-AATTTGATTTAGAGTAGTTCATACTCTAAAACTTATTCAAAATATT
67846 C-TTTTCATGCTTGTAAAATATCATAATCAAATTATGAAACATATATATAATTTAAACAATCTAA
256 CTTTTTCATGCTTGTAAAATATCATAATCAAATTATGAAACATATATATAATTTAAACAATCTAA
67910 ATTGAATATTCATCATCT
321 ATTGAATATTCATCATCT
67928 C
1 C
67929 TCATACTTAC
Statistics
Matches: 333, Mismatches: 1, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
335 108 0.32
336 6 0.02
338 119 0.36
339 43 0.13
340 47 0.14
341 10 0.03
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (338 bp):
CATCCTTTCATGCATTTTCAATTATTGCCTCCGTTCATGCCTTAATGCATCCTTTCATGCATTTT
CAATTATGGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTCAAATGGCATTCGTTCATA
CCTTAATGCATCATTTCATGCATTTTCAATTATGGCATACGTTCATGCCTTAATGCATCCTTCAT
GCATTTTCAATTATAATTTGATTTAGAGTAGTTCATACTCTAAAACTTATTCAAAATATTCTTTT
TCATGCTTGTAAAATATCATAATCAAATTATGAAACATATATATAATTTAAACAATCTAAATTGA
ATATTCATCATCT
Found at i:78189 original size:98 final size:99
Alignment explanation
Indices: 78076--78279 Score: 383
Period size: 98 Copynumber: 2.1 Consensus size: 99
78066 CAACTAATAA
78076 TATTATGCCATATATTAATTAATTTACATATAATTAATTATTGGCAAAAAGGCATCTGAGGTCTC
1 TATT-TGCCATATATTAATTAATTTACATATAATTAATTATTGGCAAAAAGGCATCTGAGGTCTC
78141 TCAACTTTC-CAAAAAACCAATGTGACCCTCATCC
65 TCAACTTTCTCAAAAAACCAATGTGACCCTCATCC
*
78175 TATTTGCCATATATTAATTAATTTACATATAATTAATTATTGGCAAAAAGGCATCTGATGTCTCT
1 TATTTGCCATATATTAATTAATTTACATATAATTAATTATTGGCAAAAAGGCATCTGAGGTCTCT
78240 CAACTTTCTCAAAAAACCAATGTGACCCTCATCC
66 CAACTTTCTCAAAAAACCAATGTGACCCTCATCC
78274 TATTTG
1 TATTTG
78280 TTTATCAATG
Statistics
Matches: 103, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
98 68 0.66
99 35 0.34
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (99 bp):
TATTTGCCATATATTAATTAATTTACATATAATTAATTATTGGCAAAAAGGCATCTGAGGTCTCT
CAACTTTCTCAAAAAACCAATGTGACCCTCATCC
Found at i:80433 original size:25 final size:25
Alignment explanation
Indices: 80405--80459 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
80395 AATATTTTAT
80405 ATATAAT-TAATATAAAAAATATAAA
1 ATATAATAT-ATATAAAAAATATAAA
* **
80430 ATATTATATATATAATTAATATAAA
1 ATATAATATATATAAAAAATATAAA
80455 ATATA
1 ATATA
80460 TAAAATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
ATATAATATATATAAAAAATATAAA
Found at i:80433 original size:34 final size:34
Alignment explanation
Indices: 80393--80478 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 34
80383 CCCAAACCCG
*
80393 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
*
80427 AAAATATTATATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
80461 AAAATATATATATATATA
1 AAAATAT-TATATATATA
80479 TAATCGGGGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 39 0.80
35 10 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:82860 original size:33 final size:33
Alignment explanation
Indices: 82820--82917 Score: 187
Period size: 33 Copynumber: 3.0 Consensus size: 33
82810 CCCATATGCA
*
82820 AAGTTGGCCACCAACCAAGATGAATTTTCCAGT
1 AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
82853 AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
82886 AAGTTGGCCACCAACCAAGATGAATTTTCCAA
1 AAGTTGGCCACCAACCAAGATGAATTTTCCAA
82918 CTTGTCAAAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.23
Consensus pattern (33 bp):
AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
Found at i:87833 original size:15 final size:15
Alignment explanation
Indices: 87813--87845 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
87803 CGTAGGACCC
87813 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
87828 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
87843 CTA
1 CTA
87846 TTATACCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:87994 original size:23 final size:26
Alignment explanation
Indices: 87957--88025 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
87947 TTCTCTTGTG
87957 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
87981 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
88006 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
88026 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:88007 original size:12 final size:12
Alignment explanation
Indices: 87990--88025 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
87980 TATCATGTTC
87990 TCATATCACATG
1 TCATATCACATG
*
88002 TCATATCACATA
1 TCATATCACATG
88014 TCATATCACATG
1 TCATATCACATG
88026 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:88516 original size:64 final size:64
Alignment explanation
Indices: 88397--88539 Score: 173
Period size: 64 Copynumber: 2.2 Consensus size: 64
88387 TATTGATGGG
* * **
88397 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGGATGCACCGATGCACTACTT
1 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAGATGCACCGATGCACTACCA
** * *
88461 ATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAAA-AGAGTGCATCGATGCACTACC
1 ATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATTAAAGAGA-TGCACCGATGCACTACC
88524 A
64 A
*
88525 ATGCATCGATACACC
1 ATGCATCGATGCACC
88540 TTCAAACAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 2 0.03
64 58 0.88
65 6 0.09
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAGATGCACCGATGCACTACCA
Found at i:94895 original size:23 final size:26
Alignment explanation
Indices: 94858--94926 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
94848 TTCTCTTGTG
94858 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
94882 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
94907 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
94927 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:94908 original size:12 final size:12
Alignment explanation
Indices: 94891--94926 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
94881 TATCATGTTC
94891 TCATATCACATG
1 TCATATCACATG
*
94903 TCATATCACATA
1 TCATATCACATG
94915 TCATATCACATG
1 TCATATCACATG
94927 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:95342 original size:64 final size:63
Alignment explanation
Indices: 95234--95416 Score: 244
Period size: 64 Copynumber: 2.9 Consensus size: 63
95224 TAATGAAGGT
* * ** * *
95234 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTATTATTAATGGG
* **
95298 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTT-ATTATTAATGGG
*
95362 ATGCATCGATGCACTACTT-TGCATCGATGCATGAATTGCATTCGATGTTT-TTATT
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATT
95417 TTAAAAGAGT
Statistics
Matches: 106, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
61 5 0.05
63 31 0.29
64 70 0.66
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATTAATGGG
Found at i:95430 original size:63 final size:64
Alignment explanation
Indices: 95234--95441 Score: 217
Period size: 64 Copynumber: 3.3 Consensus size: 64
95224 TAATGAAGGT
* * ** ** * * * *
95234 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTGATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
* * *
95298 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
** *
95362 ATGCATCGATGCACTACTT-TGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATTAAAGAG
95424 AGTGCATCGATGCACTAC
1 A-TGCATCGATGCACTAC
95442 CAATGTATCG
Statistics
Matches: 126, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
62 2 0.02
63 48 0.38
64 76 0.60
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:101640 original size:15 final size:15
Alignment explanation
Indices: 101620--101652 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
101610 CGTAGGACCC
101620 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
101635 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
101650 CTA
1 CTA
101653 TTATACCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:101801 original size:23 final size:26
Alignment explanation
Indices: 101764--101832 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
101754 TTCTCTTGTG
101764 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
101788 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
101813 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
101833 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:101814 original size:12 final size:12
Alignment explanation
Indices: 101797--101832 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
101787 TATCATGTTC
101797 TCATATCACATG
1 TCATATCACATG
*
101809 TCATATCACATA
1 TCATATCACATG
101821 TCATATCACATG
1 TCATATCACATG
101833 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:102249 original size:64 final size:63
Alignment explanation
Indices: 102141--102323 Score: 235
Period size: 64 Copynumber: 2.9 Consensus size: 63
102131 TAATGAAGGT
* * ** * *
102141 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTATTATTAATGGG
* **
102205 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTT-ATTATTAATGGG
* *
102269 ATGCATCGATGTACTACTT-TGCATCGATGCATGAATTGCATTCGATGTTT-TTATT
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATT
102324 TTAAAAGAGT
Statistics
Matches: 105, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
61 5 0.05
63 31 0.30
64 69 0.66
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATTAATGGG
Found at i:102337 original size:63 final size:64
Alignment explanation
Indices: 102141--102348 Score: 208
Period size: 64 Copynumber: 3.3 Consensus size: 64
102131 TAATGAAGGT
* * ** ** * * * *
102141 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTGATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
* * *
102205 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
* ** *
102269 ATGCATCGATGTACTACTT-TGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATTAAAGAG
102331 AGTGCATCGATGCACTAC
1 A-TGCATCGATGCACTAC
102349 CAATGTATCG
Statistics
Matches: 124, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
62 2 0.02
63 47 0.38
64 75 0.60
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:103486 original size:37 final size:33
Alignment explanation
Indices: 103438--103520 Score: 103
Period size: 33 Copynumber: 2.4 Consensus size: 33
103428 ATATTTTAGG
103438 AACCAAAGATGAAATTCCCATATGCAAAGTTGGCCACC
1 AACC-AAGATGAAATTCCCA-AT---AAGTTGGCCACC
* *
103476 AACCAAGATGAATTTTCCAATAAGTTGGCCACC
1 AACCAAGATGAAATTCCCAATAAGTTGGCCACC
103509 AACCAAGATGAA
1 AACCAAGATGAA
103521 TTTTCCAACT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
33 24 0.56
36 2 0.05
37 13 0.30
38 4 0.09
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (33 bp):
AACCAAGATGAAATTCCCAATAAGTTGGCCACC
Found at i:103504 original size:33 final size:33
Alignment explanation
Indices: 103464--103528 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
103454 CCCATATGCA
103464 AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
103497 AAGTTGGCCACCAACCAAGATGAATTTTCCAA
1 AAGTTGGCCACCAACCAAGATGAATTTTCCAA
103529 CTTGCCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (33 bp):
AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
Found at i:108905 original size:45 final size:45
Alignment explanation
Indices: 108837--108935 Score: 155
Period size: 45 Copynumber: 2.2 Consensus size: 45
108827 TATAAAATCT
* *
108837 CTTACCATTTATCCCATAAGCTCGTAAGCTTA-TTTACCAATATA
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATACA
108881 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATACA
1 CTTACCATTT-ATACCATAAGCTCGTAAGCTTATTTTACCAATACA
*
108927 CTTGCCATT
1 CTTACCATT
108936 ATTCAATAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
44 10 0.20
45 21 0.42
46 19 0.38
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.36
Consensus pattern (45 bp):
CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATACA
Found at i:109117 original size:59 final size:59
Alignment explanation
Indices: 109025--109153 Score: 159
Period size: 59 Copynumber: 2.2 Consensus size: 59
109015 CATAGTGCTA
* * * * **
109025 TCCCGAGTATGACATATAATGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTAAAG
1 TCCCGAATATGACACATAATGTCGTGCCCACCATATACACTAGGTATCCTTAAGTAAAG
* * ** *
109084 TCCCGAATATGACACATAATGTTGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAATGTCGTGCCCACCATATACACTAGGTATCCTTAAGTAAAG
109143 TCCCGAATATG
1 TCCCGAATATG
109154 CAGCCTGCTG
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (59 bp):
TCCCGAATATGACACATAATGTCGTGCCCACCATATACACTAGGTATCCTTAAGTAAAG
Found at i:120904 original size:23 final size:24
Alignment explanation
Indices: 120878--120928 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
120868 GACTTTTTGG
* *
120878 TGAAATGA-ATTAACTATTTTTCA
1 TGAAAAGACATTAACTAATTTTCA
*
120901 TGAAAAGACTTTAACTAATTTTCA
1 TGAAAAGACATTAACTAATTTTCA
120925 TGAA
1 TGAA
120929 TAAAGAGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (24 bp):
TGAAAAGACATTAACTAATTTTCA
Found at i:126059 original size:23 final size:23
Alignment explanation
Indices: 126033--126083 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
126023 CTTTTTTGGG
*
126033 TGAAATGATTTAACTATTTTTCA
1 TGAAATGACTTAACTATTTTTCA
* *
126056 TGAAAAGACTTAACTTTTTTTCA
1 TGAAATGACTTAACTATTTTTCA
126079 T-AAAT
1 TGAAAT
126084 AGAGATGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (23 bp):
TGAAATGACTTAACTATTTTTCA
Found at i:127028 original size:13 final size:13
Alignment explanation
Indices: 127010--127034 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
127000 TTTGATTTTA
127010 ATTATATTATATC
1 ATTATATTATATC
127023 ATTATATTATAT
1 ATTATATTATAT
127035 TGTATCGTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTATATTATATC
Found at i:127044 original size:5 final size:5
Alignment explanation
Indices: 127036--127104 Score: 129
Period size: 5 Copynumber: 13.8 Consensus size: 5
127026 ATATTATATT
*
127036 GTATC GTATC GTATC GTATC GTTTC GTATC GTATC GTATC GTATC GTATC
1 GTATC GTATC GTATC GTATC GTATC GTATC GTATC GTATC GTATC GTATC
127086 GTATC GTATC GTATC GTAT
1 GTATC GTATC GTATC GTAT
127105 TATATTATAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 62 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (5 bp):
GTATC
Found at i:129573 original size:2 final size:2
Alignment explanation
Indices: 129568--129624 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
129558 TGTGTGTGTG
129568 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
129610 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
129625 GATTGTATAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:136636 original size:2 final size:2
Alignment explanation
Indices: 136631--136671 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
136621 TGTGTGTGTG
* *
136631 TA TA TA TA TA TA TA TA TA GA TA TA GA TA TA TA 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
136672 GATTGTGTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:137058 original size:22 final size:22
Alignment explanation
Indices: 137009--137059 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
136999 ACACATACAT
137009 ATGATATGTGACAGAAGAGAAG
1 ATGATATGTGACAGAAGAGAAG
* *
137031 A-AATATGTGATCATAAGAGAA-
1 ATGATATGTGA-CAGAAGAGAAG
137052 ATGATATG
1 ATGATATG
137060 AATACATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.47, C:0.04, G:0.25, T:0.24
Consensus pattern (22 bp):
ATGATATGTGACAGAAGAGAAG
Found at i:145018 original size:14 final size:15
Alignment explanation
Indices: 145001--145034 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
144991 TCGATTATCT
*
145001 TTATTTTTTAA-TTA
1 TTATTTCTTAATTTA
145015 TTATTTCTTAATTTA
1 TTATTTCTTAATTTA
145030 TTATT
1 TTATT
145035 CGCCATGCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATTTCTTAATTTA
Found at i:157579 original size:35 final size:36
Alignment explanation
Indices: 157498--157601 Score: 174
Period size: 35 Copynumber: 2.9 Consensus size: 36
157488 TAAAATCGTC
*
157498 ATTTACAATACTAGTGGGATAACCTAATTTGAGCGT
1 ATTTACAATACTAGTGGGATAACCTAATTTGAGCAT
*
157534 ATTTGCAATACTAGTGGGATAACCTAATTT-AGCAT
1 ATTTACAATACTAGTGGGATAACCTAATTTGAGCAT
*
157569 ATTTTCAATACTAGTGGGATAACCTAATTTGAG
1 ATTTACAATACTAGTGGGATAACCTAATTTGAG
157602 TCATTATCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 33 0.52
36 31 0.48
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (36 bp):
ATTTACAATACTAGTGGGATAACCTAATTTGAGCAT
Found at i:157624 original size:16 final size:17
Alignment explanation
Indices: 157597--157631 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
157587 ATAACCTAAT
*
157597 TTGAGTCATTATCAACA
1 TTGAGTCATTATAAACA
157614 TTGAG-CATTATAAACA
1 TTGAGTCATTATAAACA
157630 TT
1 TT
157632 CCCCCAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (17 bp):
TTGAGTCATTATAAACA
Found at i:162981 original size:35 final size:36
Alignment explanation
Indices: 162902--163002 Score: 150
Period size: 35 Copynumber: 2.8 Consensus size: 36
162892 AAAATCGTCA
*
162902 TTTCTAATACTAGTGGGATAACCTAATTTGAGCATAT
1 TTTC-AATACTAGTGGGATAACCTAATTTGAACATAT
*
162939 TTGCAATACTAGTGGGATAACCTAATTT-AACATAT
1 TTTCAATACTAGTGGGATAACCTAATTTGAACATAT
* *
162974 TTTCAATACTAGTGAGATAATCTAATTTG
1 TTTCAATACTAGTGGGATAACCTAATTTG
163003 TGTCACTATC
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
35 31 0.53
36 24 0.41
37 3 0.05
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (36 bp):
TTTCAATACTAGTGGGATAACCTAATTTGAACATAT
Found at i:165567 original size:15 final size:15
Alignment explanation
Indices: 165549--165578 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
165539 AAAACCATGT
165549 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
165564 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
165579 GAAATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:165585 original size:15 final size:15
Alignment explanation
Indices: 165552--165586 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
165542 ACCATGTTAG
* *
165552 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
165567 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
165582 ATAAA
1 ATAAA
165587 TTAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:165710 original size:9 final size:9
Alignment explanation
Indices: 165685--165710 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
165675 ATAAAAAATA
165685 AAGAAAAAG
1 AAGAAAAAG
165694 AAGAAAAAG
1 AAGAAAAAG
165703 AAGAAAAA
1 AAGAAAAA
165711 AAAATATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:165727 original size:17 final size:16
Alignment explanation
Indices: 165707--165807 Score: 51
Period size: 18 Copynumber: 5.8 Consensus size: 16
165697 AAAAAGAAGA
165707 AAAAAAAATATAGAAAT
1 AAAAAAAATATA-AAAT
*
165724 AAAACAAATAAATAAAAT
1 AAAA-AAA-ATATAAAAT
*
165742 AATAATAAAAAAGTAAAAAT
1 AA-AA-AAAATA-T-AAAAT
* * *
165762 AATATATATATAAAAT
1 AAAAAAAATATAAAAT
*
165778 -AAAAAAATAAAAAAAGT
1 AAAAAAAAT-ATAAAA-T
165795 AAAAAAATATATA
1 AAAAAAA-ATATA
165808 TATAAATTAA
Statistics
Matches: 64, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
15 5 0.08
16 10 0.16
17 6 0.09
18 23 0.36
19 13 0.20
20 7 0.11
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAAAAAATATAAAAT
Found at i:165775 original size:40 final size:37
Alignment explanation
Indices: 165731--165814 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 37
165721 AATAAAACAA
*
165731 ATAAATAAAATAATAATAAAAAAGTAAAAATAATATATAT
1 ATAAATAAAAAAAT-A-AAAAAAGTAAAAA-AATATATAT
165771 ATAAAATAAAAAAATAAAAAAAGTAAAAAAATATATAT
1 AT-AAATAAAAAAATAAAAAAAGTAAAAAAATATATAT
165809 ATAAAT
1 ATAAAT
165815 TAATAAAACT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
37 4 0.10
38 11 0.26
39 13 0.31
40 3 0.07
41 11 0.26
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (37 bp):
ATAAATAAAAAAATAAAAAAAGTAAAAAAATATATAT
Found at i:165783 original size:24 final size:22
Alignment explanation
Indices: 165706--165787 Score: 69
Period size: 25 Copynumber: 3.5 Consensus size: 22
165696 GAAAAAGAAG
*
165706 AAAAAAAAAT-ATAGAA-ATAA
1 AAAAAAAAATAATATAATATAA
* *
165726 AACAAATAAATAAAATAATAATAA
1 AA-AAAAAAATAATATAAT-ATAA
165750 AAAAGTAAAAATAATATATATATAA
1 AAAA--AAAAATAATATA-ATATAA
165775 AATAAAAAAATAA
1 AA-AAAAAAATAA
165788 AAAAAGTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 2 0.04
21 7 0.14
22 4 0.08
23 2 0.04
24 14 0.29
25 16 0.33
26 4 0.08
ACGTcount: A:0.76, C:0.01, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAAAAAAATAATATAATATAA
Found at i:165801 original size:49 final size:49
Alignment explanation
Indices: 165667--165801 Score: 130
Period size: 49 Copynumber: 2.7 Consensus size: 49
165657 ATAGTAAGTA
*
165667 AAAT-AAATATAAAAAATAAAGAAAAAGAAGAAAAAGAAGAAAAAAAAATATAG
1 AAATAAAATA-AAAAAAT-AA-AAAAAGTA-AAAAA-AAGAAAAAAAAATATAG
* * * * * *
165720 AAATAAAACAAATAAATAAAATAA-TAATAAAAAAGTAAAAATAATATAT
1 AAATAAAATAAAAAAATAAAAAAAGTAA-AAAAAAGAAAAAAAAATATAG
*
165769 ATATAAAATAAAAAAATAAAAAAAGTAAAAAAA
1 AAATAAAATAAAAAAATAAAAAAAGTAAAAAAA
165802 TATATATATA
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
49 40 0.59
50 8 0.12
51 4 0.06
52 2 0.03
53 10 0.15
54 4 0.06
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.16
Consensus pattern (49 bp):
AAATAAAATAAAAAAATAAAAAAAGTAAAAAAAAGAAAAAAAAATATAG
Found at i:165804 original size:38 final size:41
Alignment explanation
Indices: 165733--165873 Score: 134
Period size: 38 Copynumber: 3.5 Consensus size: 41
165723 TAAAACAAAT
*
165733 AAATAAAATAATAATAAAAAAGTAAAAATAATATATATATA
1 AAATAAAAAAATAATAAAAAAGTAAAAATAATATATATATA
165774 AAATAAAAAAAT-A-AAAAAAGTAAAAA-AATATATATATA
1 AAATAAAAAAATAATAAAAAAGTAAAAATAATATATATATA
* * *
165812 AATTAATAAAACTGATAATAAAAAA-T-AATAT-ATTTATATATA
1 AAATAA-AAAA---ATAATAAAAAAGTAAAAATAATATATATATA
* *
165854 TAATCTAAAAAA-AATAAAAA
1 AAAT-AAAAAAATAATAAAAA
165874 TATATACTAA
Statistics
Matches: 85, Mismatches: 7, Indels: 19
0.77 0.06 0.17
Matches are distributed among these distances:
38 25 0.29
39 18 0.21
40 1 0.01
41 11 0.13
42 21 0.25
43 3 0.04
44 6 0.07
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.27
Consensus pattern (41 bp):
AAATAAAAAAATAATAAAAAAGTAAAAATAATATATATATA
Found at i:166252 original size:37 final size:37
Alignment explanation
Indices: 166202--166291 Score: 103
Period size: 36 Copynumber: 2.5 Consensus size: 37
166192 GCTTGTGGAA
*
166202 CCTATCTTTAGGAGTTTAAAACATAGAAAAATTCTAT
1 CCTATTTTTAGGAGTTTAAAACATAGAAAAATTCTAT
* * * * *
166239 CCTATTTTTAGGAG-TTGAATCCTAGCAGAATTCTAT
1 CCTATTTTTAGGAGTTTAAAACATAGAAAAATTCTAT
166275 CCTATTTTT-GAGAGTTT
1 CCTATTTTTAG-GAGTTT
166292 GAATCCTAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 1 0.02
36 29 0.64
37 15 0.33
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (37 bp):
CCTATTTTTAGGAGTTTAAAACATAGAAAAATTCTAT
Found at i:166278 original size:36 final size:37
Alignment explanation
Indices: 166231--166300 Score: 117
Period size: 36 Copynumber: 1.9 Consensus size: 37
166221 AACATAGAAA
166231 AATTCTATCCTATTTTT-AGGAG-TTGAATCCTAGCAG
1 AATTCTATCCTATTTTTGA-GAGTTTGAATCCTAGCAG
166267 AATTCTATCCTATTTTTGAGAGTTTGAATCCTAG
1 AATTCTATCCTATTTTTGAGAGTTTGAATCCTAG
166301 TAGGACGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
36 20 0.62
37 12 0.38
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (37 bp):
AATTCTATCCTATTTTTGAGAGTTTGAATCCTAGCAG
Found at i:166947 original size:100 final size:104
Alignment explanation
Indices: 166761--167183 Score: 351
Period size: 106 Copynumber: 4.0 Consensus size: 104
166751 AATATTGTTC
* * * ** * * * *
166761 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCACTATGAAGTTGAAATTGACTCTGAAATC--GAAAATGCTTGTTGACA
* * * * *
166826 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
64 ATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
166867 CGAGTCTAATATCCTTCACTATGAAGTTGAAATTGACTCTG-AA-CG-AAAT-CTTGTTGACAAT
1 CGAGTCCAATATCCTTCACTATGAAGTTGAAATTGACTCTGAAATCGAAAATGCTTGTTGACAAT
166928 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** * * * * *
166967 CGAGTCCAATATCCTTCGTTGTGAAGTTGACATTGGCTCTGAAATTTGAAAAATGTTTGTTGACA
1 CGAGTCCAATATCCTTCACTATGAAGTTGAAATTGACTCTGAAA-TCG-AAAATGCTTGTTGACA
* * *
167032 ACCAACTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 ATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * **
167073 CGAGTGGCACGATATCC-TC-CGTCGTGGAGTTGAAATCG-CGGATGAAA-CTGAAAAGTTG-TT
1 CGAGT--C-CAATATCCTTCAC-T-ATGAAGTTGAAATTGAC-TCTGAAATC-GAAAA--TGCTT
* **
167133 CGTTGACAACCAGTTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
57 -GTTGACAATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
167182 CG
1 CG
167184 GGTAGCACGA
Statistics
Matches: 267, Mismatches: 34, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
100 80 0.30
101 5 0.02
102 1 0.00
103 1 0.00
104 1 0.00
105 6 0.02
106 87 0.33
107 4 0.01
108 8 0.03
109 74 0.28
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (104 bp):
CGAGTCCAATATCCTTCACTATGAAGTTGAAATTGACTCTGAAATCGAAAATGCTTGTTGACAAT
CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:167156 original size:109 final size:108
Alignment explanation
Indices: 166919--167379 Score: 477
Period size: 109 Copynumber: 4.4 Consensus size: 108
166909 ACGAAATCTT
* * *
166919 GTTGACAATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT--C-CAATATCC
1 GTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTAGCACGATATCC
* * * * * * *
166981 TTCGTTGTGAAGTTGACATTGGCTCTGAAATTTGAAAAATGTTT
66 TCCGTCGTGGAGTTGAAATTGGCGCTGAAA-TTGAAAATTGTTC
* *
167025 GTTGACAACCAACTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCACGATATCC
1 GTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTAGCACGATATCC
* * *
167090 TCCGTCGTGGAGTTGAAA-TCGCGGATGAAACTGAAAAGTTGTTC
66 TCCGTCGTGGAGTTGAAATTGGC-GCTGAAATTGAAAA-TTGTTC
*** *
167134 GTTGACAACCAGTTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCC
1 GTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTAGCACGATATCC
** * * *
167199 TCCGTCGTGGAGTTGAAATTGGTTCTGGAATTGGGAAGTTGTTC
66 TCCGTCGTGGAGTTGAAATTGGCGCTGAAATT-GAAAATTGTTC
* * *
167243 GTTGACAACC-A--G-----TC---GTGAAGTTGAACTTGCGTTGTCTCGGGTAGCATGATATCC
1 GTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTAGCACGATATCC
** * *
167297 TCCGTCGTGGAGTTGAAATTGGTTCCGAAATTGGGAAATTGTT-
66 TCCGTCGTGGAGTTGAAATTGGCGCTGAAATT-GAAAATTGTTC
*
167340 GTTGGCAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTG
1 GTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTG
167380 ACTCTAGCTA
Statistics
Matches: 304, Mismatches: 33, Indels: 34
0.82 0.09 0.09
Matches are distributed among these distances:
97 9 0.03
98 79 0.26
100 1 0.00
101 2 0.01
105 2 0.01
106 51 0.17
108 25 0.08
109 130 0.43
110 5 0.02
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (108 bp):
GTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTAGCACGATATCC
TCCGTCGTGGAGTTGAAATTGGCGCTGAAATTGAAAATTGTTC
Found at i:167283 original size:98 final size:97
Alignment explanation
Indices: 167159--167350 Score: 321
Period size: 98 Copynumber: 2.0 Consensus size: 97
167149 TCCCTTCGTT
*
167159 GTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGGAGTTGAAATTGGTTC
1 GTGAAGTTGAACTTGCGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGGAGTTGAAATTGGTTC
* * *
167224 TGGAATTGGGAAGTTGTTCGTTGACAACCAGTC
66 CGAAATTGGGAAATTGTT-GTTGACAACCAGTC
*
167257 GTGAAGTTGAACTTGCGTTGTCTCGGGTAGCATGATATCCTCCGTCGTGGAGTTGAAATTGGTTC
1 GTGAAGTTGAACTTGCGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGGAGTTGAAATTGGTTC
*
167322 CGAAATTGGGAAATTGTTGTTGGCAACCA
66 CGAAATTGGGAAATTGTTGTTGACAACCA
167351 ACCGTCCCTT
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
97 10 0.11
98 78 0.89
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.32
Consensus pattern (97 bp):
GTGAAGTTGAACTTGCGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGGAGTTGAAATTGGTTC
CGAAATTGGGAAATTGTTGTTGACAACCAGTC
Found at i:168040 original size:67 final size:67
Alignment explanation
Indices: 167960--168118 Score: 223
Period size: 67 Copynumber: 2.4 Consensus size: 67
167950 GAAACGAAAT
* *
167960 TTTGTTTTAAGGGAGATA-AAT-TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCATGGGAGAC
1 TTTGTTTCAAGGGA-A-ACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
168023 AAAA
64 AAAA
* * *
168027 TTTGTTTCGAGGGAAACAATCTCAAAGGTTTTGTGTTTTAAGAGAAACTGTCTCAAGGGAGACAA
1 TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
168092 AA
66 AA
**
168094 TTTGTTTCAAGGGAAATTATCTCAA
1 TTTGTTTCAAGGGAAACAATCTCAA
168119 GAGAGACGAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 77 0.94
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (67 bp):
TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
AA
Found at i:168117 original size:36 final size:36
Alignment explanation
Indices: 168077--168248 Score: 121
Period size: 36 Copynumber: 4.9 Consensus size: 36
168067 AGAGAAACTG
*
168077 TCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATTA
1 TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATTA
* **
168113 TCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGT-
1 TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAT-TA
* * * * *
168149 TTTC-A-A-TG-----TTTATGTTTC-AGGAGAAACTG
1 TCTCAAGAGAGACAAAATT-TGTTTCAAGG-GAAATTA
* *
168178 TCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTA
1 TCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAATTA
**
168215 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAAT
1 TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAT
168249 GTTTCCAATG
Statistics
Matches: 103, Mismatches: 19, Indels: 28
0.69 0.13 0.19
Matches are distributed among these distances:
28 6 0.06
29 11 0.11
30 1 0.01
32 1 0.01
33 1 0.01
34 1 0.01
35 1 0.01
36 47 0.46
37 29 0.28
38 5 0.05
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (36 bp):
TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATTA
Found at i:168212 original size:37 final size:37
Alignment explanation
Indices: 168161--168333 Score: 152
Period size: 37 Copynumber: 4.9 Consensus size: 37
168151 TCAATGTTTA
*
168161 TGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGG-GAAACTGTCTCAAGAGAGACAAAATTT
*
168198 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * **
168234 CATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
168262 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
168300 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
168334 CTCATTTCAA
Statistics
Matches: 105, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
27 3 0.03
28 2 0.02
29 11 0.10
30 5 0.05
35 4 0.04
36 14 0.13
37 58 0.55
38 8 0.08
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:168233 original size:102 final size:102
Alignment explanation
Indices: 168060--168436 Score: 630
Period size: 102 Copynumber: 3.7 Consensus size: 102
168050 AAAGGTTTTG
* *
168060 TGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAATTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
168124 ACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
168161 TGTTTCAGGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
168226 ACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
168263 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
168328 ACAAAACTCATTTCAAGGAAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * * *
168365 TGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAATTCTGTTTCGAGGGAAACTATCTCAAGCGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
168430 ATAAAAT
66 ACAAAAT
168437 CTTGTTTTAA
Statistics
Matches: 259, Mismatches: 16, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
101 32 0.12
102 227 0.88
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:168416 original size:37 final size:37
Alignment explanation
Indices: 168365--168458 Score: 109
Period size: 37 Copynumber: 2.5 Consensus size: 37
168355 TCAATGTTTA
* *
168365 TGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAATTC
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATTC
* *
168402 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAA-TC
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATTC
* * *
168438 TTGTTTTAAGAAAAACAATCT
1 -TGTTTCAAGAGAAACTATCT
168459 TGAGGGAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
36 2 0.04
37 45 0.96
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATTC
Found at i:169942 original size:183 final size:183
Alignment explanation
Indices: 169634--169983 Score: 646
Period size: 183 Copynumber: 1.9 Consensus size: 183
169624 GGTTTAACTA
*
169634 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTAGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
* **
169699 AGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
169764 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
*
169817 AAGGGTTCGTCTCATCACAAAGTCTTAGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTAGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
*
169882 AGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
169947 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
169984 CGGATTTAAT
Statistics
Matches: 161, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 161 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (183 bp):
AAGGGTTCATCTCATCACAAAGTCTTAGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
Found at i:173894 original size:15 final size:15
Alignment explanation
Indices: 173876--173905 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
173866 AAAACCATGT
173876 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
173891 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
173906 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:173912 original size:15 final size:15
Alignment explanation
Indices: 173879--173913 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
173869 ACCATGTTAG
* *
173879 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
173894 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
173909 ATAAA
1 ATAAA
173914 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:174060 original size:9 final size:9
Alignment explanation
Indices: 173993--174119 Score: 62
Period size: 9 Copynumber: 13.4 Consensus size: 9
173983 AAATAGTAAG
*
173993 TAAAATAAA
1 TAAAAAAAA
*
174002 TATAAAAAA
1 TAAAAAAAA
174011 TAAAGAAAAA
1 TAAA-AAAAA
*
174021 GAAGAAAAAGA
1 TAA-AAAAA-A
174032 -AGAAAAAAA
1 TA-AAAAAAA
* *
174041 T-ATAGAAA
1 TAAAAAAAA
*
174049 TAAAACAAA
1 TAAAAAAAA
174058 TAAAAAATAA
1 TAAAAAA-AA
*
174068 T-AAAAAAG
1 TAAAAAAAA
*
174076 TAAAATTAATA
1 TAAAA--AAAA
*
174087 TATATAAAAA
1 TA-AAAAAAA
174097 TAAAAAAAAA
1 T-AAAAAAAA
*
174107 TAAAAAAAG
1 TAAAAAAAA
174116 TAAA
1 TAAA
174120 TATATATATA
Statistics
Matches: 90, Mismatches: 16, Indels: 24
0.69 0.12 0.18
Matches are distributed among these distances:
8 8 0.09
9 41 0.46
10 31 0.34
11 8 0.09
12 2 0.02
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:174099 original size:39 final size:38
Alignment explanation
Indices: 174055--174174 Score: 120
Period size: 39 Copynumber: 3.0 Consensus size: 38
174045 GAAATAAAAC
174055 AAATAAAAAATAATAAAAAAGTAAAATTAATATATATAA
1 AAATAAAAAATAATAAAAAAGTAAAATT-ATATATATAA
*
174094 AAATAAAAAAAAATAAAAAAAGT-AAA-TATATATATAA
1 AAATAAAAAATAAT-AAAAAAGTAAAATTATATATATAA
*
174131 ATTAATAAAACTGATAATAAAAAA-TAATATATTTATATATATAA
1 A--AATAAAA--AATAATAAAAAAGTAA-A-A-TTATATATATAA
174175 TCTAAAAAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 15
0.79 0.03 0.17
Matches are distributed among these distances:
37 11 0.16
38 1 0.01
39 24 0.35
40 15 0.22
41 5 0.07
42 1 0.01
44 11 0.16
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (38 bp):
AAATAAAAAATAATAAAAAAGTAAAATTATATATATAA
Found at i:174103 original size:40 final size:39
Alignment explanation
Indices: 174055--174187 Score: 116
Period size: 40 Copynumber: 3.4 Consensus size: 39
174045 GAAATAAAAC
174055 AAAT-AAAAAATAATAAAAAAGTAAAATTAATATATATAA
1 AAATAAAAAAATAATAAAAAAGTAAAATT-ATATATATAA
174094 AAATAAAAAAA-AATAAAAAAAGT-AAA-TATATATATAA
1 AAATAAAAAAATAAT-AAAAAAGTAAAATTATATATATAA
**
174131 ATTAATAAAACTGATAATAAAAAA-TAATATATT-TATATATATA
1 A--AATAAAA-AAATAATAAAAAAGTAA-A-ATTATATATATA-A
**
174174 ATCTAAAAAAATAA
1 AAATAAAAAAATAA
174188 AAATATATAC
Statistics
Matches: 77, Mismatches: 6, Indels: 21
0.74 0.06 0.20
Matches are distributed among these distances:
37 11 0.14
38 1 0.01
39 18 0.23
40 26 0.34
41 9 0.12
42 9 0.12
43 3 0.04
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (39 bp):
AAATAAAAAAATAATAAAAAAGTAAAATTATATATATAA
Found at i:174159 original size:10 final size:10
Alignment explanation
Indices: 174047--174114 Score: 52
Period size: 10 Copynumber: 6.8 Consensus size: 10
174037 AAAATATAGA
*
174047 AATAAAACA-
1 AATAAAAAAT
174056 AATAAAAAAT
1 AATAAAAAAT
174066 AATAAAAAAGT
1 AATAAAAAA-T
**
174077 AA-AATTAAT
1 AATAAAAAAT
174086 ATATATAAAAAT
1 A-ATA-AAAAAT
*
174098 AAAAAAAAAT
1 AATAAAAAAT
174108 AA-AAAAA
1 AATAAAAA
174115 GTAAATATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
9 15 0.31
10 22 0.46
11 6 0.12
12 5 0.10
ACGTcount: A:0.78, C:0.01, G:0.01, T:0.19
Consensus pattern (10 bp):
AATAAAAAAT
Found at i:174241 original size:23 final size:22
Alignment explanation
Indices: 174186--174247 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
174176 CTAAAAAAAT
174186 AAAAATATATAC-T-AAAGTAAA
1 AAAAATAT-TACATAAAAGTAAA
*
174207 AAAGAA-AATACATAAAATGTAAA
1 AAA-AATATTACATAAAA-GTAAA
174230 AAAAATATTACATGAAAA
1 AAAAATATTACAT-AAAA
174248 AAAAAGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 3 0.09
21 5 0.15
22 7 0.21
23 14 0.42
24 4 0.12
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.21
Consensus pattern (22 bp):
AAAAATATTACATAAAAGTAAA
Found at i:174587 original size:36 final size:37
Alignment explanation
Indices: 174515--174615 Score: 134
Period size: 36 Copynumber: 2.8 Consensus size: 37
174505 GTGCTTGTGG
* * * *
174515 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
*
174552 ATCCTATTTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
174588 ATCCTATTTTT-GAGAGTTTGAATCCTAG
1 ATCCTATTTTTAG-GAGTTTGAATCCTAG
174616 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 1 0.02
36 30 0.53
37 26 0.46
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:194613 original size:57 final size:57
Alignment explanation
Indices: 194501--194626 Score: 139
Period size: 57 Copynumber: 2.2 Consensus size: 57
194491 ATGACACACG
* * * * *
194501 AATGTGTGTCATCTTTTTTAATGATGTGTGCTTCAATGACACGTAATGTGAGTCATA
1 AATGTGTGTCATCTTATTTAATGACGGGAGCTTCAATGACACGTAATGCGAGTCATA
* * *
194558 CATGTGTGTCATCTTCATTT-ATGACGGGAGCTTCAATGACGC-TCAATGCGTGTCATA
1 AATGTGTGTCATCTT-ATTTAATGACGGGAGCTTCAATGACACGT-AATGCGAGTCATA
*
194615 AATGCGTGTCAT
1 AATGTGTGTCAT
194627 AAATGTGAGT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
56 1 0.02
57 53 0.93
58 3 0.05
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.37
Consensus pattern (57 bp):
AATGTGTGTCATCTTATTTAATGACGGGAGCTTCAATGACACGTAATGCGAGTCATA
Found at i:194620 original size:13 final size:13
Alignment explanation
Indices: 194602--194672 Score: 88
Period size: 13 Copynumber: 5.5 Consensus size: 13
194592 AATGACGCTC
194602 AATGCGTGTCATA
1 AATGCGTGTCATA
194615 AATGCGTGTCATA
1 AATGCGTGTCATA
* *
194628 AATGTGAGTCATA
1 AATGCGTGTCATA
* * *
194641 AATGTGAGTTATA
1 AATGCGTGTCATA
*
194654 AATGCGTGTCATC
1 AATGCGTGTCATA
194667 AATGCG
1 AATGCG
194673 CGTTATAGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (13 bp):
AATGCGTGTCATA
Found at i:198015 original size:65 final size:66
Alignment explanation
Indices: 197843--198069 Score: 357
Period size: 66 Copynumber: 3.5 Consensus size: 66
197833 GAATACCATG
* * * *
197843 AGTGGCACATTTTATGCCGATAATGCACCATTATGCATTAAACAAAATCGATCGATAATTTTCAT
1 AGTGGCACCTTTTATGTCGATAATGCACCGTTATGCATTAATCAAAATCGATCGATAATTTTCAT
197908 T
66 T
* * * *
197909 AGTGGCACCTTTTATGTCGATAATGCACCGTTATGCATTAATCAAAATCGATTGATTATTTTTAA
1 AGTGGCACCTTTTATGTCGATAATGCACCGTTATGCATTAATCAAAATCGATCGATAATTTTCAT
197974 T
66 T
* *
197975 AGTGGCA-TTTTTATGTTGATAATGCACCGTTATGCATTAATCAAAATCGATCGATAATTTTCAT
1 AGTGGCACCTTTTATGTCGATAATGCACCGTTATGCATTAATCAAAATCGATCGATAATTTTCAT
198039 T
66 T
198040 AGTGGCACCTTTTATGTCGATAATGCACCG
1 AGTGGCACCTTTTATGTCGATAATGCACCG
198070 ATGGCTCTCA
Statistics
Matches: 144, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
65 59 0.41
66 85 0.59
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (66 bp):
AGTGGCACCTTTTATGTCGATAATGCACCGTTATGCATTAATCAAAATCGATCGATAATTTTCAT
T
Found at i:201097 original size:2 final size:2
Alignment explanation
Indices: 201086--201126 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
201076 GAATTTAAGA
201086 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
201127 TATTTCAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:203301 original size:21 final size:20
Alignment explanation
Indices: 203262--203299 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
203252 TTCAAACAAC
203262 TTTTTTTTTCCATTTTTTCT
1 TTTTTTTTTCCATTTTTTCT
203282 TTTTTTTTTCCATTTTTT
1 TTTTTTTTTCCATTTTTT
203300 TCGAAATGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTTTTCCATTTTTTCT
Found at i:206631 original size:18 final size:19
Alignment explanation
Indices: 206608--206645 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
206598 TATTTAAGTG
*
206608 ATAAAAGCGA-TTAAATAA
1 ATAAAAGCAATTTAAATAA
206626 ATAAAAGCAATTTAAATAA
1 ATAAAAGCAATTTAAATAA
206645 A
1 A
206646 AATAAGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.24
Consensus pattern (19 bp):
ATAAAAGCAATTTAAATAA
Found at i:210511 original size:26 final size:26
Alignment explanation
Indices: 210482--210533 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
210472 TATTAAAAAC
210482 AAAACTTGAAAA-TAAAAGAGAAAAGA
1 AAAACTTGAAAAGTAAAA-AGAAAAGA
*
210508 AAAACTTGAAAAGTAAAAATAAAAGA
1 AAAACTTGAAAAGTAAAAAGAAAAGA
210534 GAAAGCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.69, C:0.04, G:0.13, T:0.13
Consensus pattern (26 bp):
AAAACTTGAAAAGTAAAAAGAAAAGA
Found at i:212535 original size:59 final size:59
Alignment explanation
Indices: 212444--212569 Score: 198
Period size: 59 Copynumber: 2.1 Consensus size: 59
212434 AGTGCAAAAT
* *
212444 CGAATTTGATACATAAGGTCATGCCCACCATATGCACTAGGTATCCTTTAGTGCAATCC
1 CGAATATGACACATAAGGTCATGCCCACCATATGCACTAGGTATCCTTTAGTGCAATCC
* * * *
212503 CGAATATGACACATAAGGTCGTTCCCATCATATGCACTAGGTATCCTTTAGTGCAATCT
1 CGAATATGACACATAAGGTCATGCCCACCATATGCACTAGGTATCCTTTAGTGCAATCC
212562 CGAATATG
1 CGAATATG
212570 CAACTTGTTG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (59 bp):
CGAATATGACACATAAGGTCATGCCCACCATATGCACTAGGTATCCTTTAGTGCAATCC
Found at i:212736 original size:2 final size:2
Alignment explanation
Indices: 212729--212754 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
212719 GCATAACAAC
212729 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
212755 TAGTAATCAA
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:220610 original size:12 final size:12
Alignment explanation
Indices: 220593--220618 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
220583 TGAGCCTGAA
220593 CAGCCCGAGGAG
1 CAGCCCGAGGAG
220605 CAGCCCGAGGAG
1 CAGCCCGAGGAG
220617 CA
1 CA
220619 AGCACAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.35, G:0.38, T:0.00
Consensus pattern (12 bp):
CAGCCCGAGGAG
Found at i:222483 original size:34 final size:34
Alignment explanation
Indices: 222440--222508 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
222430 ATAAATATCA
222440 TGCCAATGCGAACAAGGTAGACTGATCGCAAGGC
1 TGCCAATGCGAACAAGGTAGACTGATCGCAAGGC
222474 TGCCAATGCGAACAAGGTAGACTGATCGCAAGGC
1 TGCCAATGCGAACAAGGTAGACTGATCGCAAGGC
222508 T
1 T
222509 TCCTAAGGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.23, G:0.29, T:0.16
Consensus pattern (34 bp):
TGCCAATGCGAACAAGGTAGACTGATCGCAAGGC
Found at i:222564 original size:2 final size:2
Alignment explanation
Indices: 222557--222586 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
222547 TTTGAAATAC
222557 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
222587 TCTTAAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:225428 original size:2 final size:2
Alignment explanation
Indices: 225421--225454 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
225411 TTTGAAATAC
225421 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
225455 TCTTAAATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:225496 original size:7 final size:7
Alignment explanation
Indices: 225486--225510 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
225476 CATTTAGTAT
225486 TTTTAAA
1 TTTTAAA
225493 TTTTAAA
1 TTTTAAA
225500 TTTTAAA
1 TTTTAAA
225507 TTTT
1 TTTT
225511 CAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:231934 original size:2 final size:2
Alignment explanation
Indices: 231927--231959 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
231917 AATACTACAC
231927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
231960 TCTTAAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:232050 original size:3 final size:3
Alignment explanation
Indices: 232042--232089 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
232032 TATTAAAATA
* * *
232042 TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAA TAT TAA TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
232088 TA
1 TA
232090 ATTTACATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 36 0.95
4 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:233903 original size:2 final size:2
Alignment explanation
Indices: 233896--233953 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
233886 TACGTGTAAG
233896 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
233938 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
233954 TATTAAAATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:239017 original size:21 final size:21
Alignment explanation
Indices: 238988--239028 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
238978 AAGGGAGAAG
*
238988 AAAATGATAGAAAGTAAAAGT
1 AAAAAGATAGAAAGTAAAAGT
*
239009 AAAAAGATAGAAAGTGAAAG
1 AAAAAGATAGAAAGTAAAAG
239029 GTGAAAACGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (21 bp):
AAAAAGATAGAAAGTAAAAGT
Found at i:252376 original size:52 final size:52
Alignment explanation
Indices: 252232--252379 Score: 176
Period size: 52 Copynumber: 2.8 Consensus size: 52
252222 GGATGTTCAT
* *
252232 ATGATCCATGT-AGGGCATCATGAAGGTTCACATCAGTATGAAAAAGACAGAA
1 ATGATCCATGTGA-GGCATCATGAAGGTTCACATCAGCATGAAAAAGACAAAA
* * * *
252284 ATGATCCATGTGGGGCATCATAAAGATTCACATCAACATGAAAAAGACAAAA
1 ATGATCCATGTGAGGCATCATGAAGGTTCACATCAGCATGAAAAAGACAAAA
* *
252336 ATTATCCATGTGAGGCAT-ATTGAAGGCTCACA-CTAGCATGAAAA
1 ATGATCCATGTGAGGCATCA-TGAAGGTTCACATC-AGCATGAAAA
252380 GGTTGGGATA
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
51 2 0.02
52 79 0.98
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (52 bp):
ATGATCCATGTGAGGCATCATGAAGGTTCACATCAGCATGAAAAAGACAAAA
Found at i:253728 original size:40 final size:40
Alignment explanation
Indices: 253680--254156 Score: 774
Period size: 40 Copynumber: 11.9 Consensus size: 40
253670 CATTTAATAT
*
253680 AGAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCTTGAAAC
* *
253720 ATAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCTTGAAAC
253760 AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCTTGAAAC
*
253800 AGAATATTTTATCTCGTTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCTTGAAAC
*
253840 AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCCTGAAAC
1 AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCTTGAAAC
*
253880 AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCCTGAAAC
1 AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCTTGAAAC
253920 AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCTTGAAAC
*
253960 AGAAGATTTTATATCGTTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCTTGAAAC
* * **
254000 ATAAGATTCTATCTCACTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCTTGAAAC
* **
254040 GGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCTTGAAAC
** *
254080 AGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAAT
1 AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCTTGAAAC
** *
254120 AGAAGATTTTATCTCACTCAAGATTTTTTTTCCTTGA
1 AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCTTGA
254157 TTACACGTCA
Statistics
Matches: 416, Mismatches: 21, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 416 1.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.42
Consensus pattern (40 bp):
AGAAGATTTTATCTCGTTCAAGATTGTTTTTCCTTGAAAC
Found at i:253885 original size:23 final size:23
Alignment explanation
Indices: 253859--253927 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
253849 TATCTCGTTC
253859 AAGATTGTTTTTCCCTGAAACAG
1 AAGATTGTTTTTCCCTGAAACAG
* * **
253882 AAGA-T-TTTATCTC-G-TTC--
1 AAGATTGTTTTTCCCTGAAACAG
253899 AAGATTGTTTTTCCCTGAAACAG
1 AAGATTGTTTTTCCCTGAAACAG
253922 AAGATT
1 AAGATT
253928 TTATCTCGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 4 0.12
18 1 0.03
19 7 0.22
20 2 0.06
21 7 0.22
22 1 0.03
23 10 0.31
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (23 bp):
AAGATTGTTTTTCCCTGAAACAG
Found at i:256714 original size:28 final size:26
Alignment explanation
Indices: 256672--256727 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 26
256662 GGTGGTTAAA
*
256672 TTATTTTATTATAAATTATAATTTTATT
1 TTATTTTATTATAAA-AATAA-TTTATT
*
256700 TTATTTTATTTTAAAAATAATTTATT
1 TTATTTTATTATAAAAATAATTTATT
256726 TT
1 TT
256728 CTTGAAGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 8 0.31
27 4 0.15
28 14 0.54
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTATTTTATTATAAAAATAATTTATT
Found at i:257608 original size:152 final size:151
Alignment explanation
Indices: 257322--257615 Score: 454
Period size: 152 Copynumber: 1.9 Consensus size: 151
257312 GCTTGCCTAG
*
257322 AGGGATTGTGTCATATCCAACCCATACGTTTTAATCAAGTTAGTCAATCGCATCCAATACCTAGT
1 AGGGATTGTGTCATATCCAACCAATACGTTTTAATCAAGTTAGT-AATCGCATCCAATACCTAGT
*
257387 CAAATTTGATAGATGAAATATCTGACCCTACTAACGATGTTTTCATGCTGAATTTTAAGAAAAAT
65 CAAATTTGATAGATGAAATATCTGAACCTACTAACGATGTTTTCATGCTGAATTTTAAGAAAAAT
257452 ATTTGTTTTTTCTAATCTTAGA
130 ATTTGTTTTTTCTAATCTTAGA
*
257474 AGGGATTGTGTCATAT-CAACCAATACGTTTTAATCAAGTTATGT-GTCGCATCCAATACCTAGT
1 AGGGATTGTGTCATATCCAACCAATACGTTTTAATCAAGTTA-GTAATCGCATCCAATACCTAGT
*
257537 CAAATATGTTGCTAGATGAAAATATCT-AACCTACTAACGATG-TTTCATGCTGAATTTTTAAGA
65 C-AA-AT-TTGATAGATG-AAATATCTGAACCTACTAACGATGTTTTCATGCTGAA-TTTTAAGA
257600 AAAA-ATTTGTTTTTTC
125 AAAATATTTGTTTTTTC
257616 ACCTATACGT
Statistics
Matches: 132, Mismatches: 4, Indels: 12
0.89 0.03 0.08
Matches are distributed among these distances:
150 19 0.14
151 26 0.20
152 44 0.33
153 35 0.27
154 8 0.06
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (151 bp):
AGGGATTGTGTCATATCCAACCAATACGTTTTAATCAAGTTAGTAATCGCATCCAATACCTAGTC
AAATTTGATAGATGAAATATCTGAACCTACTAACGATGTTTTCATGCTGAATTTTAAGAAAAATA
TTTGTTTTTTCTAATCTTAGA
Done.