Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004582.1 Hibiscus syriacus cultivar Beakdansim tig00010223_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: 111260
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:139 original size:22 final size:22
Alignment explanation
Indices: 104--147 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
94 ATTATTTCAC
*
104 TTTCATTTCATTTCATAGCATGT
1 TTTCACTTCATTTCATA-CATGT
127 TTTCACTT-ATTTCATACATGT
1 TTTCACTTCATTTCATACATGT
148 ATCATTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 8 0.40
23 7 0.35
ACGTcount: A:0.23, C:0.18, G:0.07, T:0.52
Consensus pattern (22 bp):
TTTCACTTCATTTCATACATGT
Found at i:6356 original size:2 final size:2
Alignment explanation
Indices: 6349--6375 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6339 TTGTTTACAT
6349 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6376 CCTTTCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6647 original size:68 final size:68
Alignment explanation
Indices: 6527--6656 Score: 183
Period size: 68 Copynumber: 1.9 Consensus size: 68
6517 ACTCAATGGT
*
6527 ACTTAATCGTTCATCTAACTGGCATAATTGACACCTTTTTGCCAATTTCACAGTTAGGCCTTAAA
1 ACTTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTTCACAGTTAGGCCTTAAA
6592 GAC
66 GAC
* * * *
6595 ACTTAGTCTTTCATCTAGCTGGCAT-ATATGACACCTTTCTGTC-ATTTGCACAGTTAGGCCTT
1 ACTTAATCGTTCATCTAACTGGCATAAT-TGACACCTTTCTGCCAATTT-CACAGTTAGGCCTT
6657 TACATCTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
67 6 0.11
68 49 0.89
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (68 bp):
ACTTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTTCACAGTTAGGCCTTAAA
GAC
Found at i:7190 original size:157 final size:157
Alignment explanation
Indices: 7004--7286 Score: 485
Period size: 157 Copynumber: 1.8 Consensus size: 157
6994 TTTCAACTTT
** **
7004 GGCATCATTTCATTCCAATAATGCACCCATATGCATTATTATGTTATGTTGATAATGTACCCATA
1 GGCATCATTTCATGACAATAATGCACCCATATGCATTATTATGTTATGCCGATAATGTACCCATA
7069 TACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATTATTCTTTTATGCCG
66 TACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATTATTCTTTTATGCCG
7134 ATAATTTACCCATATACATATAGTTAA
131 ATAATTTACCCATATACATATAGTTAA
* * * * *
7161 GGCATCCTTTCATGACATTAATGCACCCATATGCATTATTATTTTATGCCGATAATGTGCTCATA
1 GGCATCATTTCATGACAATAATGCACCCATATGCATTATTATGTTATGCCGATAATGTACCCATA
7226 TACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATTATTCTTTTAT
66 TACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATTATTCTTTTAT
7287 TCATTAGTTT
Statistics
Matches: 117, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
157 117 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (157 bp):
GGCATCATTTCATGACAATAATGCACCCATATGCATTATTATGTTATGCCGATAATGTACCCATA
TACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATTATTCTTTTATGCCG
ATAATTTACCCATATACATATAGTTAA
Found at i:7206 original size:78 final size:79
Alignment explanation
Indices: 6976--7286 Score: 444
Period size: 79 Copynumber: 3.9 Consensus size: 79
6966 TTTTATGTTA
* * * * ** * * *
6976 ATAATGCACCCATATGCATTTCAACTTTGGCATCATTTCATTCCAATAATGCACCCATATGCATT
1 ATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATT
* **
7041 ATTATGTTATGTTG
66 ATTATTTTATGCCG
7055 ATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATT
1 ATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATT
*
7120 ATTCTTTTATGCCG
66 ATTATTTTATGCCG
* * *
7134 ATAATTTACCCATATACATAT-AGTTAAGGCATCCTTTCATGACATTAATGCACCCATATGCATT
1 ATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATT
7198 ATTATTTTATGCCG
66 ATTATTTTATGCCG
* *
7212 ATAATGTGCTCATATACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATT
1 ATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATT
*
7277 ATTCTTTTAT
66 ATTATTTTAT
7287 TCATTAGTTT
Statistics
Matches: 208, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
78 72 0.35
79 136 0.65
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.37
Consensus pattern (79 bp):
ATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATT
ATTATTTTATGCCG
Found at i:7800 original size:35 final size:35
Alignment explanation
Indices: 7737--7806 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
7727 TTCGTTCAAG
* *
7737 GTGGTATCGATACCTTCCTTAAGGTATCAGTACCC
1 GTGGTATCGATACATTCCTTAAGATATCAGTACCC
* * *
7772 GTGGTATCGATACATTTCTTCATATATCAGTACCC
1 GTGGTATCGATACATTCCTTAAGATATCAGTACCC
7807 TTGGAATGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (35 bp):
GTGGTATCGATACATTCCTTAAGATATCAGTACCC
Found at i:8904 original size:12 final size:12
Alignment explanation
Indices: 8887--8928 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
8877 ATTAAGGTAC
8887 TACTAATAATAA
1 TACTAATAATAA
8899 TACTAAT-ATAAA
1 TACTAATAAT-AA
8911 TA-TAATAATAA
1 TACTAATAATAA
*
8922 TAATAAT
1 TACTAAT
8929 TGTAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (12 bp):
TACTAATAATAA
Found at i:9134 original size:30 final size:30
Alignment explanation
Indices: 9100--9169 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
9090 TAGCATGTTC
* *
9100 CATTCACTTCATTTATTTCATAACATCTAT
1 CATTCACTTAATTCATTTCATAACATCTAT
* * * *
9130 CATTCATTTAATTCATTTCGTAACCTGTAT
1 CATTCACTTAATTCATTTCATAACATCTAT
9160 CATTCACTTA
1 CATTCACTTA
9170 TCACAATCTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.46
Consensus pattern (30 bp):
CATTCACTTAATTCATTTCATAACATCTAT
Found at i:9217 original size:2 final size:2
Alignment explanation
Indices: 9206--9237 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9196 TAAAGTATTG
9206 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9238 CTCAATGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15395 original size:72 final size:74
Alignment explanation
Indices: 15204--15482 Score: 492
Period size: 74 Copynumber: 3.8 Consensus size: 74
15194 TGTTACAAGA
* * *
15204 GAGAGAGAGATGCATGTTGAAGATCATAGAGACTAACAGGGTATAAGAAAAAGAAGTGAAGCATT
1 GAGAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAAAGTAGTGAAGCATT
*
15269 AGAGACAGG
66 AGAGAGAGG
15278 GAGAGAGATATGCATGTTGAAGATCATGGAGACTTAACA-GGTATAAGAAAAAGTAGTGAAGCAT
1 GAGAGAGATATGCATGTTGAAGATCATGGAGAC-TAACAGGGTATAAGAAAAAGTAGTGAAGCAT
15342 TAGAGAGA-G
65 TAGAGAGAGG
15351 G-GAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAAAGTAGTGAAGCATT
1 GAGAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAAAGTAGTGAAGCATT
15415 AGAGAGAGG
66 AGAGAGAGG
15424 GAGAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAAAGTAGTGA
1 GAGAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAAAGTAGTGA
15483 TGTATTTATA
Statistics
Matches: 197, Mismatches: 4, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
71 5 0.03
72 64 0.32
73 4 0.02
74 119 0.60
75 5 0.03
ACGTcount: A:0.43, C:0.07, G:0.31, T:0.19
Consensus pattern (74 bp):
GAGAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAAAGTAGTGAAGCATT
AGAGAGAGG
Found at i:15470 original size:146 final size:146
Alignment explanation
Indices: 15201--15482 Score: 503
Period size: 146 Copynumber: 1.9 Consensus size: 146
15191 TGATGTTACA
15201 AGAGAGAGAGAGATGCATGTTGAAGATCATAGAGACTAACAGGGTATAAGAAAAAGAAGTGAAGC
1 AGAGAGAGAGAGATGCATGTTGAAGATCATAGAGACTAACAGGGTATAAGAAAAAGAAGTGAAGC
15266 ATTAGAGACAGGGAGAGAGATATGCATGTTGAAGATCATGGAGACTTAACAGGTATAAGAAAAAG
66 ATTAGAGACAGGGAGAGAGATATGCATGTTGAAGATCATGGAGACTTAACAGGTATAAGAAAAAG
15331 TAGTGAAGCATTAGAG
131 TAGTGAAGCATTAGAG
* * * *
15347 AGAGGGAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAAAGTAGTGAAGC
1 AGAGAGAGAGAGATGCATGTTGAAGATCATAGAGACTAACAGGGTATAAGAAAAAGAAGTGAAGC
*
15412 ATTAGAGAGAGGGAGAGAGATATGCATGTTGAAGATCATGGAGAC-TAACAGGGTATAAGAAAAA
66 ATTAGAGACAGGGAGAGAGATATGCATGTTGAAGATCATGGAGACTTAACA-GGTATAAGAAAAA
15476 GTAGTGA
130 GTAGTGA
15483 TGTATTTATA
Statistics
Matches: 130, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
145 5 0.04
146 125 0.96
ACGTcount: A:0.43, C:0.07, G:0.31, T:0.19
Consensus pattern (146 bp):
AGAGAGAGAGAGATGCATGTTGAAGATCATAGAGACTAACAGGGTATAAGAAAAAGAAGTGAAGC
ATTAGAGACAGGGAGAGAGATATGCATGTTGAAGATCATGGAGACTTAACAGGTATAAGAAAAAG
TAGTGAAGCATTAGAG
Found at i:18429 original size:24 final size:24
Alignment explanation
Indices: 18378--18429 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
18368 AAAGTTGGAA
*
18378 TTGGAAGGATTCAAACTTGGGACT
1 TTGGAAGGATTCAAACTTGGGACG
*
18402 TTGGAAGGATTCAAACTTGGGCCG
1 TTGGAAGGATTCAAACTTGGGACG
18426 TTGG
1 TTGG
18430 GTTGTCAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.33, T:0.29
Consensus pattern (24 bp):
TTGGAAGGATTCAAACTTGGGACG
Found at i:18624 original size:30 final size:29
Alignment explanation
Indices: 18580--18702 Score: 89
Period size: 30 Copynumber: 4.3 Consensus size: 29
18570 ATCCTAAGTC
18580 AAAAA-ATA-TATTTTTTATTCAACTTATT
1 AAAAATATATTATTTTTTATT-AACTTATT
* *
18608 AAAAATATATTATTTTTATTTTAACTTA-G
1 AAAAATATATTATTTTT-TATTAACTTATT
* * *
18637 AAATATATTTTATTCTTATATTAAC-T-TT
1 AAAAATATATTATT-TTTTATTAACTTATT
*
18665 AAAAATATATTTAATTCTATTATTAAC-T-TT
1 AAAAATATA-TT-ATT-TTTTATTAACTTATT
18695 AAAAATAT
1 AAAAATAT
18703 TTTTTATTAT
Statistics
Matches: 77, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
28 13 0.17
29 23 0.30
30 38 0.49
31 3 0.04
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (29 bp):
AAAAATATATTATTTTTTATTAACTTATT
Found at i:18673 original size:57 final size:56
Alignment explanation
Indices: 18581--18731 Score: 148
Period size: 57 Copynumber: 2.7 Consensus size: 56
18571 TCCTAAGTCA
* * * *
18581 AAAAATATATTTT-TTAT-TCAACTTATTAAAAATATATTATTTTTATT-TTAAC-TT
1 AAAAATATTTTTTATTATATTAAC-T-TTAAAAATATATTAATTCTATTATTAACTTT
*
18635 AGAAATATATTTTATTCTTATATTAACTTTAAAAATATATTTAATTCTATTATTAACTTT
1 A-AAA-ATATTTT-TTATTATATTAACTTTAAAAATATA-TTAATTCTATTATTAACTTT
* * *
18695 AAAAATATTTTTTATTATCTTAACTTCAAATATATAT
1 AAAAATATTTTTTATTATATTAACTTTAAAAATATAT
18732 ATATATATAT
Statistics
Matches: 81, Mismatches: 8, Indels: 14
0.79 0.08 0.14
Matches are distributed among these distances:
54 1 0.01
55 3 0.04
56 7 0.09
57 34 0.42
58 21 0.26
59 12 0.15
60 3 0.04
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.52
Consensus pattern (56 bp):
AAAAATATTTTTTATTATATTAACTTTAAAAATATATTAATTCTATTATTAACTTT
Found at i:18731 original size:2 final size:2
Alignment explanation
Indices: 18724--18763 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
18714 TTAACTTCAA
18724 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
18764 TATTCTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18938 original size:29 final size:30
Alignment explanation
Indices: 18807--18993 Score: 158
Period size: 29 Copynumber: 6.3 Consensus size: 30
18797 TATTATTATC
*
18807 TAAAGTTAATAAAATAATAAAATATATTATT
1 TAAAGTTAATAAAAGAATAAAATATATT-TT
* * *
18838 TGAAGTTAAGT-TAATAA-AAAATATATTTT
1 TAAAGTTAA-TAAAAGAATAAAATATATTTT
* * *
18867 TAAA-CTAATAAAAGAAGAAAATATATCTT
1 TAAAGTTAATAAAAGAATAAAATATATTTT
*
18896 TAAAGTT-ATCATAAGAATAAAATATA-TTT
1 TAAAGTTAAT-AAAAGAATAAAATATATTTT
*
18925 TAAAGTTAA-AATAAAAATAAAATATA--TT
1 TAAAGTTAATAA-AAGAATAAAATATATTTT
18953 TAATATGTTGAATAAAA-AATAAAATATATTTTT
1 TAA-A-GTT-AATAAAAGAATAAAATATA-TTTT
18986 TAAAGTTA
1 TAAAGTTA
18994 GGATATGAAT
Statistics
Matches: 129, Mismatches: 13, Indels: 29
0.75 0.08 0.17
Matches are distributed among these distances:
27 1 0.01
28 13 0.10
29 45 0.35
30 41 0.32
31 20 0.16
32 4 0.03
33 5 0.04
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (30 bp):
TAAAGTTAATAAAAGAATAAAATATATTTT
Found at i:18947 original size:59 final size:59
Alignment explanation
Indices: 18807--18993 Score: 152
Period size: 59 Copynumber: 3.1 Consensus size: 59
18797 TATTATTATC
* * ** *
18807 TAAAGTTAATAAAATAATAAAATATATTATTTGAAGTTAAGTTAATAAAAAATATATTTT
1 TAAAGTTAATAAAAAAATAAAATATA-TATTTAAAGTTAACATAAGAAAAAATATATTTT
* * * * *
18867 TAAA-CTAATAAAAGAAGAAAATATATCTTTAAAGTTATCATAAGAATAAAATATA-TTT
1 TAAAGTTAATAAAAAAATAAAATATATATTTAAAGTTAACATAAGAA-AAAATATATTTT
* *
18925 TAAAGTTAA-AATAAAAAT-AAA-ATATATTTAATATGTTGA-ATAAAAAATAAAATATATTTTT
1 TAAAGTTAATAA-AAAAATAAAATATATATTTAA-A-GTTAACAT-AAGAA-AAAATATA-TTTT
18986 TAAAGTTA
1 TAAAGTTA
18994 GGATATGAAT
Statistics
Matches: 103, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
57 9 0.09
58 30 0.29
59 49 0.48
60 4 0.04
61 11 0.11
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (59 bp):
TAAAGTTAATAAAAAAATAAAATATATATTTAAAGTTAACATAAGAAAAAATATATTTT
Found at i:21614 original size:13 final size:14
Alignment explanation
Indices: 21591--21620 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
21581 TTCCCATTAT
21591 AGACGTGCATATGA
1 AGACGTGCATATGA
21605 AGAC-TGCATATGA
1 AGACGTGCATATGA
21618 AGA
1 AGA
21621 TTGTCCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:21893 original size:15 final size:15
Alignment explanation
Indices: 21873--22075 Score: 237
Period size: 15 Copynumber: 13.5 Consensus size: 15
21863 TGAAAAAAAT
21873 ATAAAATACAATAAC
1 ATAAAATACAATAAC
*
21888 ATAAAATACAATAAT
1 ATAAAATACAATAAC
* * *
21903 ACAATATATAATAAC
1 ATAAAATACAATAAC
*
21918 ATAAAATACAATACC
1 ATAAAATACAATAAC
* *
21933 AGAAAATA-ATATAAT
1 ATAAAATACA-ATAAC
21948 ATAAAATACAATAAC
1 ATAAAATACAATAAC
* **
21963 ATGAAATACAATGCC
1 ATAAAATACAATAAC
*
21978 AGAAAATACAATAAC
1 ATAAAATACAATAAC
*
21993 ATAAAATACAATACC
1 ATAAAATACAATAAC
* *
22008 AAAAAATACAATAAT
1 ATAAAATACAATAAC
*
22023 ATAAAATATAATAAC
1 ATAAAATACAATAAC
*
22038 ATAAAATACAATATC
1 ATAAAATACAATAAC
*
22053 ATAAAATACAATACC
1 ATAAAATACAATAAC
22068 ATAAAATA
1 ATAAAATA
22076 TGATATCACA
Statistics
Matches: 154, Mismatches: 32, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
14 1 0.01
15 152 0.99
16 1 0.01
ACGTcount: A:0.64, C:0.12, G:0.02, T:0.22
Consensus pattern (15 bp):
ATAAAATACAATAAC
Found at i:24433 original size:102 final size:102
Alignment explanation
Indices: 24309--24529 Score: 244
Period size: 102 Copynumber: 2.2 Consensus size: 102
24299 GGCATATTGC
* * * * * *
24309 CATATGAGTTCTGGATGGATTGTTAAGTAGATGACATTTTGATGTTGGGGTCAAAGAAGTTAAAA
1 CATATGAGTTTTGAATGAATTGTTAAGTAGATGACATTTCGATGTTGAGGCCAAAGAAGTTAAAA
*
24374 TATGAATACATTCCCCTTGAACTCAAAGGAATATTAT
66 GATGAATACATTCCCCTTGAACTCAAAGGAATATTAT
** ** * *
24411 CATATGAGTTTTGAATGAATTGTTGTGTCTATGGCATTTCGATGTTGAGGCCAAAGAAGTTGAAA
1 CATATGAGTTTTGAATGAATTGTTAAGTAGATGACATTTCGATGTTGAGGCCAAAGAAGTTAAAA
* * * * ** * *
24476 GATGAATGCCTTCCTCTTGGACTTGAATGCATATTAT
66 GATGAATACATTCCCCTTGAACTCAAAGGAATATTAT
*
24513 CATATGGGTTTTGAATG
1 CATATGAGTTTTGAATG
24530 GACTATTGTG
Statistics
Matches: 97, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
102 97 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.35
Consensus pattern (102 bp):
CATATGAGTTTTGAATGAATTGTTAAGTAGATGACATTTCGATGTTGAGGCCAAAGAAGTTAAAA
GATGAATACATTCCCCTTGAACTCAAAGGAATATTAT
Found at i:24557 original size:102 final size:101
Alignment explanation
Indices: 24346--24562 Score: 245
Period size: 102 Copynumber: 2.1 Consensus size: 101
24336 TAGATGACAT
* * *
24346 TTTGATGTTGGGGTCAAAGAAGTTAAAATATGAATACATTCCCCTTGAACTCAAAGGAATATTAT
1 TTTGATGTTGAGGCCAAAGAAGTTAAAAGATGAATACATTCCCCTTGAACTCAAAGGAATATTAT
* * * **
24411 CATATGAGTTTTGAATGAATTGTTGTGTCTATGGCA
66 CATATGAGTTTTGAATGAACTATTGTGTCGATGAAA
* * * * * ** * *
24447 TTTCGATGTTGAGGCCAAAGAAGTTGAAAGATGAATGCCTTCCTCTTGGACTTGAATGCATATTA
1 TTT-GATGTTGAGGCCAAAGAAGTTAAAAGATGAATACATTCCCCTTGAACTCAAAGGAATATTA
* *
24512 TCATATGGGTTTTGAATGGACTATTGTGTCGATGAAAA
65 TCATATGAGTTTTGAATGAACTATTGTGTCGATG-AAA
24550 TTTGATGTTGAGG
1 TTTGATGTTGAGG
24563 TTGAAGAAGT
Statistics
Matches: 95, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
101 3 0.03
102 88 0.93
103 4 0.04
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (101 bp):
TTTGATGTTGAGGCCAAAGAAGTTAAAAGATGAATACATTCCCCTTGAACTCAAAGGAATATTAT
CATATGAGTTTTGAATGAACTATTGTGTCGATGAAA
Found at i:24602 original size:102 final size:102
Alignment explanation
Indices: 24338--24603 Score: 239
Period size: 102 Copynumber: 2.6 Consensus size: 102
24328 TTGTTAAGTA
* * * * * * * * * **
24338 GATGACATTTTGATGTTGGGGTCAAAGAAGTTAAAATATGAATACATTCCCCTTGAACTCAAAGG
1 GATGAAATTTCGATGTTGAGGCCAAAGAAGTTGAAAGAAGAATACCTCCCCCTTGAACTTGAAGG
* *
24403 AATATTATCATATGAGTTTTGAATGAATTGTTGTGTC
66 AATATTATCATATGAGTTTTGAATGAACTATTGTGTC
* ** * * * * * *
24440 TATGGCATTTCGATGTTGAGGCCAAAGAAGTTGAAAGATGAATGCCTTCCTCTTGGACTTGAATG
1 GATGAAATTTCGATGTTGAGGCCAAAGAAGTTGAAAGAAGAATACCTCCCCCTTGAACTTGAAGG
* * *
24505 CATATTATCATATGGGTTTTGAATGGACTATTGTGTC
66 AATATTATCATATGAGTTTTGAATGAACTATTGTGTC
*** *
24542 GATGAAAATTT-GATGTTGAGGTTGAAGAAGTTGACAA-AAGAATATCTCCCCCTTGAACTTGA
1 GATG-AAATTTCGATGTTGAGGCCAAAGAAGTTGA-AAGAAGAATACCTCCCCCTTGAACTTGA
24604 GGGATGTTTG
Statistics
Matches: 131, Mismatches: 31, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
102 125 0.95
103 6 0.05
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.34
Consensus pattern (102 bp):
GATGAAATTTCGATGTTGAGGCCAAAGAAGTTGAAAGAAGAATACCTCCCCCTTGAACTTGAAGG
AATATTATCATATGAGTTTTGAATGAACTATTGTGTC
Found at i:25225 original size:39 final size:38
Alignment explanation
Indices: 25177--25258 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 38
25167 GATATAAAAA
* * *
25177 ATTTGAGAGTTTTAGATTTCAAGAGAATAGATGTAGAG
1 ATTTTAGAGTTTTAGATTTCAAGAGAATAAAGGTAGAG
*
25215 AGTTTTAGAGTTTTGGATTTCAAGAGAATAAAGGTAGAG
1 A-TTTTAGAGTTTTAGATTTCAAGAGAATAAAGGTAGAG
25254 ATTTT
1 ATTTT
25259 GAAAGTGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 5 0.13
39 34 0.87
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (38 bp):
ATTTTAGAGTTTTAGATTTCAAGAGAATAAAGGTAGAG
Found at i:25922 original size:191 final size:191
Alignment explanation
Indices: 25359--25934 Score: 569
Period size: 191 Copynumber: 3.0 Consensus size: 191
25349 AATGATACAC
* * * * **
25359 TATGAAATGACAAAGATTCTATACAAAATGTGAAAAAGTTTCTTGTGAAAAGCAACAACCCCTTT
1 TATGAAATGACAGAGATTCTATGCAAAAGGTGAAAAAG-TTCTTGTGAAAAGCATCTTCCCCTTT
* * * * *
25424 TTATAGAGATTCTCTGCATGAATCACTCAATTTCATGTACATATAATGTTTCTATATGGGGAACT
65 TTATAGAGATTCTCTACATTAATCACTCAATTT-ATCTACATATAATGTTCCTCTATGGGGAACT
* * *
25489 ATTCATCCCAA-ATATCTTCATGCTTGATGGGATGAGACATTAGTGTCTCAAACTAATGGACAC
129 ATTCATCCCAATATATC-TCATGCTTGATGGGATGAGACATTAGTGTCTCAAATTAATAGACAT
* * ** ** *
25552 TATGACATGATAGAGATTCTCCGCAAAAGGTGAAAGAAGTTCTTGTGAAAATTAT-TTTCCCTTT
1 TATGAAATGACAGAGATTCTATGCAAAAGGTGAAA-AAGTTCTTGTGAAAAGCATCTTCCCCTTT
* * * * * * * * *
25616 TTACAAAGATTCTCTCCATTAACCAATTAATTTTATCTACATATAATGCTCCACTACGGGGAACT
65 TTATAGAGATTCTCTACATTAATCACTCAA-TTTATCTACATATAATGTTCCTCTATGGGGAACT
* * * * *
25681 ATTTA-CCCCAT-TATCTACACGCTTGATGGGATGAGATACTAGTGTCTCAAATTAATAGACAT
129 ATTCATCCCAATATATCT-CATGCTTGATGGGATGAGACATTAGTGTCTCAAATTAATAGACAT
* * *
25743 TATGAAATGGA-AGAGATTCTTTGCAAAAGGTGAAAAAGCTTCTTGCGAAAAGCGTCTTCCCCTT
1 TATGAAAT-GACAGAGATTCTATGCAAAAGGTGAAAAAG-TTCTTGTGAAAAGCATCTTCCCCTT
* * * *
25807 TTTGTAGAGATTCAT-TACATTAATCACTCAGA-TTATCTACAAATAATGTTCCTCTTTGGGGAG
64 TTTATAGAGATTC-TCTACATTAATCACTCA-ATTTATCTACATATAATGTTCCTCTATGGGGAA
* * *
25870 CTATTCATCCCAACTATATCT-ATGTTTGATGGGAT-AGACATT-GATATCTCAAATTAATAAAC
127 CTATTCATCCCAA-TATATCTCATGCTTGATGGGATGAGACATTAG-TGTCTCAAATTAATAGAC
25932 AT
190 AT
25934 T
1 T
25935 GTGACATGGC
Statistics
Matches: 307, Mismatches: 63, Indels: 28
0.77 0.16 0.07
Matches are distributed among these distances:
190 5 0.02
191 143 0.47
192 104 0.34
193 47 0.15
194 8 0.03
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (191 bp):
TATGAAATGACAGAGATTCTATGCAAAAGGTGAAAAAGTTCTTGTGAAAAGCATCTTCCCCTTTT
TATAGAGATTCTCTACATTAATCACTCAATTTATCTACATATAATGTTCCTCTATGGGGAACTAT
TCATCCCAATATATCTCATGCTTGATGGGATGAGACATTAGTGTCTCAAATTAATAGACAT
Found at i:35969 original size:17 final size:17
Alignment explanation
Indices: 35947--35986 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
35937 CTTTGGCAAC
35947 AACATTCAAAGTA-GATG
1 AACATTCAAA-TATGATG
35964 AACATTCAAATATGATG
1 AACATTCAAATATGATG
*
35981 CACATT
1 AACATT
35987 GAGATACAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (17 bp):
AACATTCAAATATGATG
Found at i:39519 original size:25 final size:25
Alignment explanation
Indices: 39490--39546 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
39480 TATATGAATA
39490 ATATGTGAGTATATATATATATATGT
1 ATATGTGAGTATATATATATATAT-T
* * *
39516 -TATGTGCGTATGTGTATATATATT
1 ATATGTGAGTATATATATATATATT
39540 ATATGTG
1 ATATGTG
39547 TGTGCATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (25 bp):
ATATGTGAGTATATATATATATATT
Found at i:39546 original size:17 final size:18
Alignment explanation
Indices: 39524--39561 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
39514 GTTATGTGCG
39524 TATGTGTAT-ATATATTA
1 TATGTGTATCATATATTA
*
39541 TATGTGTGTGCATATATTA
1 TATGTGTAT-CATATATTA
39560 TA
1 TA
39562 CTATATTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.50
Consensus pattern (18 bp):
TATGTGTATCATATATTA
Found at i:39550 original size:29 final size:30
Alignment explanation
Indices: 39498--39568 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
39488 TAATATGTGA
* *
39498 GTATATATATATATATGTTATGTGCGTATGT
1 GTATATATAT-TATATGTTATGTGCATATAT
*
39529 GTATATATATTATATG-TGTGTGCATATAT
1 GTATATATATTATATGTTATGTGCATATAT
39558 -TATACTATATT
1 GTATA-TATATT
39569 CTTATATGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 4 0.11
29 16 0.44
30 6 0.17
31 10 0.28
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.49
Consensus pattern (30 bp):
GTATATATATTATATGTTATGTGCATATAT
Found at i:48549 original size:10 final size:10
Alignment explanation
Indices: 48534--48576 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
48524 GCCGTCCGTC
*
48534 CGTCTCGTCT
1 CGTCTCGGCT
48544 CGTCTCGGCT
1 CGTCTCGGCT
*
48554 CGGCTCGGCT
1 CGTCTCGGCT
*
48564 CGGCTCGGCT
1 CGTCTCGGCT
48574 CGT
1 CGT
48577 GGTCGTGGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.00, C:0.40, G:0.33, T:0.28
Consensus pattern (10 bp):
CGTCTCGGCT
Found at i:48560 original size:15 final size:15
Alignment explanation
Indices: 48537--48576 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
48527 GTCCGTCCGT
*
48537 CTCGTCTCGTCTCGG
1 CTCGGCTCGTCTCGG
*
48552 CTCGGCTCGGCTCGG
1 CTCGGCTCGTCTCGG
48567 CTCGGCTCGT
1 CTCGGCTCGT
48577 GGTCGTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.40, G:0.33, T:0.28
Consensus pattern (15 bp):
CTCGGCTCGTCTCGG
Found at i:48584 original size:6 final size:6
Alignment explanation
Indices: 48573--48651 Score: 158
Period size: 6 Copynumber: 13.2 Consensus size: 6
48563 TCGGCTCGGC
48573 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
48621 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
48652 AATACGTGTC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:48951 original size:22 final size:22
Alignment explanation
Indices: 48926--48980 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
48916 TCAGGAGTTA
* *
48926 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
48948 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
48970 CGGGAGTTATA
1 CAGGAGTTATA
48981 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:54526 original size:5 final size:5
Alignment explanation
Indices: 54507--54555 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
54497 GTCCGTCTGT
* * *
54507 CTCGT CTCGT CTCGG CTCGG CACGG CTCGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
54556 TGGTCGTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.02, C:0.41, G:0.35, T:0.22
Consensus pattern (5 bp):
CTCGG
Found at i:54564 original size:6 final size:6
Alignment explanation
Indices: 54553--54637 Score: 125
Period size: 6 Copynumber: 14.2 Consensus size: 6
54543 TCGGCTCGGC
* * *
54553 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGTGG TCGAGG TCGAGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
* *
54601 TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
54638 AATACGTGTC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 75 1.00
ACGTcount: A:0.06, C:0.16, G:0.49, T:0.28
Consensus pattern (6 bp):
TCGTGG
Found at i:54937 original size:22 final size:22
Alignment explanation
Indices: 54912--54966 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
54902 TCAGGAGTTA
* *
54912 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
54934 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
54956 CGGGAGTTATA
1 CAGGAGTTATA
54967 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:57705 original size:2 final size:2
Alignment explanation
Indices: 57700--57846 Score: 271
Period size: 2 Copynumber: 74.5 Consensus size: 2
57690 TTCTCTCGTG
57700 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
*
57742 TA TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA -A 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
57783 TA TA TA TA TA TA TA -A 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
57824 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
57847 TTTAAAAATC
Statistics
Matches: 141, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
1 2 0.01
2 139 0.99
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:59069 original size:20 final size:21
Alignment explanation
Indices: 59044--59094 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
59034 AAAGTTTTGG
*
59044 ATCGATCCCTTCACC-ATATA
1 ATCGATCCCTTCACCAAAATA
* *
59064 ATCGATCCCTTTACCAAAATG
1 ATCGATCCCTTCACCAAAATA
59085 ATCGATCCCT
1 ATCGATCCCT
59095 CGATGAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.29, C:0.33, G:0.08, T:0.29
Consensus pattern (21 bp):
ATCGATCCCTTCACCAAAATA
Found at i:59090 original size:21 final size:21
Alignment explanation
Indices: 59043--59117 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
59033 GAAAGTTTTG
* *
59043 GATCGATCCCTTCACC-ATAT
1 GATCGATCCCTTTACCAAAAT
*
59063 AATCGATCCCTTTACCAAAAT
1 GATCGATCCCTTTACCAAAAT
** ** *
59084 GATCGATCCCTCGATGAAAAG
1 GATCGATCCCTTTACCAAAAT
59105 GATCGATCCCTTT
1 GATCGATCCCTTT
59118 CTTGCAACTG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.28
Consensus pattern (21 bp):
GATCGATCCCTTTACCAAAAT
Found at i:59201 original size:20 final size:20
Alignment explanation
Indices: 59175--59233 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
59165 GAAAGTTTTG
59175 GATCGATCCCTTCACCAAA-
1 GATCGATCCCTTCACCAAAC
*
59194 GAATCGATCCCTACACCAAAC
1 G-ATCGATCCCTTCACCAAAC
* *
59215 GATCGATCTCTTTACCAAA
1 GATCGATCCCTTCACCAAA
59234 AAGATTGATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.34, C:0.34, G:0.10, T:0.22
Consensus pattern (20 bp):
GATCGATCCCTTCACCAAAC
Found at i:62263 original size:16 final size:16
Alignment explanation
Indices: 62238--62268 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62228 CAATATTCAT
*
62238 TTTATTTTATTTTTTA
1 TTTATATTATTTTTTA
62254 TTTATATTATTTTTT
1 TTTATATTATTTTTT
62269 TAAAAATCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTATATTATTTTTTA
Found at i:62316 original size:23 final size:25
Alignment explanation
Indices: 62270--62318 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
62260 TTATTTTTTT
*
62270 AAAAATCCACATAAGAACTAATAAA
1 AAAAATCCACATAAGAAATAATAAA
*
62295 AAAAATTCACATAA-AAAT-ATAAA
1 AAAAATCCACATAAGAAATAATAAA
62318 A
1 A
62319 TTTAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 3 0.14
25 13 0.59
ACGTcount: A:0.67, C:0.12, G:0.02, T:0.18
Consensus pattern (25 bp):
AAAAATCCACATAAGAAATAATAAA
Found at i:62962 original size:31 final size:31
Alignment explanation
Indices: 62926--62994 Score: 138
Period size: 31 Copynumber: 2.2 Consensus size: 31
62916 CGTTATCGGC
62926 GCAATCGTCCGTTTTTTGTTTAGTTACGGAT
1 GCAATCGTCCGTTTTTTGTTTAGTTACGGAT
62957 GCAATCGTCCGTTTTTTGTTTAGTTACGGAT
1 GCAATCGTCCGTTTTTTGTTTAGTTACGGAT
62988 GCAATCG
1 GCAATCG
62995 ACCGCGATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.42
Consensus pattern (31 bp):
GCAATCGTCCGTTTTTTGTTTAGTTACGGAT
Found at i:64387 original size:73 final size:73
Alignment explanation
Indices: 64266--64424 Score: 237
Period size: 73 Copynumber: 2.2 Consensus size: 73
64256 CGTACCAGGG
* * *
64266 ATTTGAATAACGGGTATCGTGTTCGTGTAATAGCCGTTTCAGACGGCATCTTTACCGTTATATGA
1 ATTTGAATAGCGGGTATCGTGTTCGTGTAATAACCGTTTCAGACGGCATCTTTACCGTTATATAA
* *
64331 TAACTGCT
66 CAACCGCT
* *
64339 ATTTGAATAGCGGGTATCGTGTTCGTGTAATAACCGTTTCAGATGGCATCTTTACCTTTATATAA
1 ATTTGAATAGCGGGTATCGTGTTCGTGTAATAACCGTTTCAGACGGCATCTTTACCGTTATATAA
*
64404 CGACCGCT
66 CAACCGCT
*
64412 ATTTCAATAGCGG
1 ATTTGAATAGCGG
64425 ACCACTATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (73 bp):
ATTTGAATAGCGGGTATCGTGTTCGTGTAATAACCGTTTCAGACGGCATCTTTACCGTTATATAA
CAACCGCT
Found at i:81892 original size:56 final size:55
Alignment explanation
Indices: 81722--81897 Score: 171
Period size: 56 Copynumber: 3.2 Consensus size: 55
81712 AGTTAACGAT
* *
81722 TGACACCTCTGTTTAGTTAAAAATGACTGAGCACCTCTGTTCTTCAGTCTAGAAAC
1 TGACACCTCT-ATTAGTTAAAAATGACTGAGCACCTCTGTCCTTCAGTCTAGAAAC
* * * * * * * *
81778 TGGCACCTCTGCTTTG-T---AATGATTGAGCACCTCTGTCCTTTAATCGACAAAC
1 TGACACCTCT-ATTAGTTAAAAATGACTGAGCACCTCTGTCCTTCAGTCTAGAAAC
* * * *
81830 TAACACCTCTATATAGTTAAAAATGACTGAGCCCCTCTGTGCTTCAGTCTAGAATC
1 TGACACCTCTAT-TAGTTAAAAATGACTGAGCACCTCTGTCCTTCAGTCTAGAAAC
81886 TGACACCTCTAT
1 TGACACCTCTAT
81898 GCTTTATAAG
Statistics
Matches: 93, Mismatches: 22, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
51 1 0.01
52 39 0.42
53 1 0.01
55 1 0.01
56 51 0.55
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (55 bp):
TGACACCTCTATTAGTTAAAAATGACTGAGCACCTCTGTCCTTCAGTCTAGAAAC
Found at i:82117 original size:11 final size:11
Alignment explanation
Indices: 82101--82126 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
82091 TCAAACAGGG
82101 AACAAGCATCA
1 AACAAGCATCA
82112 AACAAGCATCA
1 AACAAGCATCA
82123 AACA
1 AACA
82127 GGGAACAAGC
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:0.58, C:0.27, G:0.08, T:0.08
Consensus pattern (11 bp):
AACAAGCATCA
Found at i:83372 original size:40 final size:39
Alignment explanation
Indices: 83323--83399 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 39
83313 GTTAGTTGAC
* *
83323 TACTTGTATGTTAGATGAATCGACTA-GAGTTAGGGATGGG
1 TACTAGTATGATAGATGAATCGA-TAGGA-TTAGGGATGGG
*
83363 TACTAGTATGATAGATGAATTGATAGGATTAGGGATG
1 TACTAGTATGATAGATGAATCGATAGGATTAGGGATG
83400 AACACGAGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 11 0.33
40 22 0.67
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.32
Consensus pattern (39 bp):
TACTAGTATGATAGATGAATCGATAGGATTAGGGATGGG
Found at i:86054 original size:22 final size:23
Alignment explanation
Indices: 86002--86053 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 23
85992 ATAAAAATAT
86002 TAATTATTAAAATATATTGATTAA
1 TAATT-TTAAAATATATTGATTAA
86026 TAATTTTAAAA-ATA-TGA-TAA
1 TAATTTTAAAATATATTGATTAA
86046 TATATTTT
1 TA-ATTTT
86054 TTAGTATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.19
21 8 0.30
22 3 0.11
23 6 0.22
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
TAATTTTAAAATATATTGATTAA
Found at i:86214 original size:23 final size:23
Alignment explanation
Indices: 86153--86216 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 23
86143 TTTATAATAT
* *
86153 TTATTAATTTTAAAAAAATATAA
1 TTATTAATTTTTAAAATATATAA
** *
86176 TTA--AATAATTAAAATATATTA
1 TTATTAATTTTTAAAATATATAA
86197 TTATTAATTTTTAAAATATA
1 TTATTAATTTTTAAAATATA
86217 ATATAATATT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
21 16 0.50
23 16 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTATTAATTTTTAAAATATATAA
Found at i:86258 original size:24 final size:25
Alignment explanation
Indices: 86205--86270 Score: 82
Period size: 24 Copynumber: 2.6 Consensus size: 25
86195 TATTATTAAT
86205 TTTTAA-AATATAATATAATATTCTTA
1 TTTTAATAATAT-A-ATAATATTCTTA
* *
86231 TTTTATTATTATAATAATA-TCTTA
1 TTTTAATAATATAATAATATTCTTA
86255 TTTTAATAATATAATA
1 TTTTAATAATATAATA
86271 TAATTCTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
24 19 0.54
25 6 0.17
26 6 0.17
27 4 0.11
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
TTTTAATAATATAATAATATTCTTA
Found at i:86261 original size:16 final size:16
Alignment explanation
Indices: 86236--86266 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
86226 TCTTATTTTA
86236 TTATTATAATAATATC
1 TTATTATAATAATATC
*
86252 TTATTTTAATAATAT
1 TTATTATAATAATAT
86267 AATATAATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTATAATAATATC
Found at i:90509 original size:22 final size:22
Alignment explanation
Indices: 90473--90535 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
90463 TGATTGTTGC
*
90473 ATATGA-TGTTATCATGAATAT
1 ATATGATTTTTATCATGAATAT
90494 ATATGATTTTTATCAT-ATATAT
1 ATATGATTTTTATCATGA-ATAT
90516 ATATGATTTTTATCATGAAT
1 ATATGATTTTTATCATGAAT
90536 GTTATTTTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 7 0.18
22 30 0.79
23 1 0.03
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (22 bp):
ATATGATTTTTATCATGAATAT
Found at i:90997 original size:44 final size:45
Alignment explanation
Indices: 90906--91014 Score: 184
Period size: 45 Copynumber: 2.4 Consensus size: 45
90896 GGAATATGGT
*
90906 TTATGGAATAATGGAAAGTGTATTGGTAAAAATAAGCTTACGAGC
1 TTATGGAATAATGGTAAGTGTATTGGTAAAAATAAGCTTACGAGC
90951 TTATGGAATAATGGTAAGTGTATTGGT-AAAATAAGCTTACGAGC
1 TTATGGAATAATGGTAAGTGTATTGGTAAAAATAAGCTTACGAGC
*
90995 TTATGGGATAAATGGTAAGT
1 TTATGGAAT-AATGGTAAGT
91015 AAATTGATTA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
44 25 0.41
45 36 0.59
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.31
Consensus pattern (45 bp):
TTATGGAATAATGGTAAGTGTATTGGTAAAAATAAGCTTACGAGC
Found at i:91417 original size:12 final size:12
Alignment explanation
Indices: 91400--91424 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
91390 TTTTCTGAAA
91400 TTACTGTAGCAG
1 TTACTGTAGCAG
91412 TTACTGTAGCAG
1 TTACTGTAGCAG
91424 T
1 T
91425 GTATCGATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (12 bp):
TTACTGTAGCAG
Found at i:97221 original size:22 final size:21
Alignment explanation
Indices: 97187--97227 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
97177 TGATTATTGC
97187 ATATGTTGTTATCATGAATAT
1 ATATGTTGTTATCATGAATAT
*
97208 ATATGATTTTTATCATGAAT
1 ATATG-TTGTTATCATGAAT
97228 GTTATTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (21 bp):
ATATGTTGTTATCATGAATAT
Found at i:97687 original size:44 final size:45
Alignment explanation
Indices: 97596--97704 Score: 175
Period size: 45 Copynumber: 2.4 Consensus size: 45
97586 TGGAATATGG
*
97596 TTATGGAATAATGGAAAGTGTATTGGTAAAAATAAACTTACGAGC
1 TTATGGAATAATGGTAAGTGTATTGGTAAAAATAAACTTACGAGC
*
97641 TTATGGAATAATGGTAAGTGTATTGGT-AAAATAAGCTTACGAGC
1 TTATGGAATAATGGTAAGTGTATTGGTAAAAATAAACTTACGAGC
*
97685 TTATGGGATAAATGGTAAGT
1 TTATGGAAT-AATGGTAAGT
97705 AAATTGATAA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 24 0.40
45 36 0.60
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.31
Consensus pattern (45 bp):
TTATGGAATAATGGTAAGTGTATTGGTAAAAATAAACTTACGAGC
Found at i:106603 original size:12 final size:13
Alignment explanation
Indices: 106556--106634 Score: 58
Period size: 14 Copynumber: 6.0 Consensus size: 13
106546 AACTTATAGA
*
106556 AATAATATTTTAAT
1 AATAATA-TTAAAT
106570 AATAATATTAACAT
1 AATAATATTAA-AT
106584 AAATAATATTAAAT
1 -AATAATATTAAAT
*
106598 AA-AATATT--CT
1 AATAATATTAAAT
*
106608 AAT-ATTTTAAAAAT
1 AATAATATT--AAAT
106622 AATAATATTAAAT
1 AATAATATTAAAT
106635 TATTGAACAT
Statistics
Matches: 52, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
10 7 0.13
12 6 0.12
13 9 0.17
14 15 0.29
15 15 0.29
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
AATAATATTAAAT
Found at i:106603 original size:15 final size:15
Alignment explanation
Indices: 106570--106600 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
106560 ATATTTTAAT
106570 AATAATATTAACATA
1 AATAATATTAACATA
106585 AATAATATTAA-ATA
1 AATAATATTAACATA
106599 AA
1 AA
106601 ATATTCTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAATATTAACATA
Found at i:106981 original size:21 final size:21
Alignment explanation
Indices: 106941--106981 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
106931 AATACATAAT
* *
106941 AGTACCGATACTGCTCAAGAC
1 AGTACCAATACTACTCAAGAC
*
106962 AGTACCAATACTACTTAAGA
1 AGTACCAATACTACTCAAGA
106982 GGTTTGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (21 bp):
AGTACCAATACTACTCAAGAC
Done.