Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002822.1 Hibiscus syriacus cultivar Beakdansim tig00005804_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: 92225
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1223 original size:3 final size:3
Alignment explanation
Indices: 1215--1241 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1205 AACCTATTAC
1215 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1242 TTATTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1246 original size:3 final size:3
Alignment explanation
Indices: 1240--1273 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1230 ATAATAATAA
1240 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1274 TTAAATAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2136 original size:27 final size:26
Alignment explanation
Indices: 2083--2142 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
2073 CATATAATAA
* **
2083 ATATATAATATAAATATATGTTCAAT
1 ATATATAATATAAACATAAATTCAAT
*
2109 ACTATATAATATAAACATAAATTTAAT
1 A-TATATAATATAAACATAAATTCAAT
2136 ATATATA
1 ATATATA
2143 TAACGGTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (26 bp):
ATATATAATATAAACATAAATTCAAT
Found at i:2974 original size:84 final size:85
Alignment explanation
Indices: 2821--3306 Score: 617
Period size: 84 Copynumber: 5.9 Consensus size: 85
2811 CGCTGTCATC
* * * *
2821 GAGCTGAATGGAATC-AACTCTAAGGTTTTTGTTGACA-A-AACCCTTATTGCCTTGACCTATG-
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
2882 TGTAAATTTGATATGCCCTT
66 TGTAAATTTGATATGCCCTT
* *
2902 GAGCTGAATGGAATCGAACTCGAAGGTTTTTCTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
2967 TGT-AATTTGATATGCTCTT
66 TGTAAATTTGATATGCCCTT
* * * * *
2986 GAGTTGAATGTAATCAAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGT
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
3051 TGTAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCCTT
* * *
3071 GAGATGAATGTAATCGAACTCGAAGG--TTT-TTG--AGATATCCCTTCT-GTCCTT--G-TATG
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCG-CCTTGAGCTATG
3127 CTGTAAATTCT-ATATGCCCTT
65 CTGTAAATT-TGATATGCCCTT
* *
3148 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGATAGATAACCCTTCTCG-CTTGAACTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
3212 TGTAAATTTGATATGCCCTT
66 TGTAAATTTGATATGCCCTT
* * * * * *
3232 GAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTAACAGATAGCCCTTCTCACATTGAACTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
3297 TTTAAATTTG
66 TGTAAATTTG
3307 CTGGGAGATA
Statistics
Matches: 354, Mismatches: 33, Indels: 32
0.84 0.08 0.08
Matches are distributed among these distances:
77 45 0.13
78 2 0.01
79 3 0.01
80 19 0.05
81 18 0.05
82 35 0.10
83 6 0.02
84 165 0.47
85 61 0.17
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (85 bp):
GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
TGTAAATTTGATATGCCCTT
Found at i:3242 original size:161 final size:161
Alignment explanation
Indices: 2821--3282 Score: 587
Period size: 161 Copynumber: 2.8 Consensus size: 161
2811 CGCTGTCATC
* * * *
2821 GAGCTGAATGGAATCAACTCTAAGGTTTTTGTTGACA-A-AACCCTTATTGCCTTGACCTATGTG
1 GAGCTGAATGGAATCAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCG-CTTGAACTATGTG
*
2884 TAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTCTTGACAGATAGCCCT
65 TAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGG--TTT-TTGA-AGATAGCCCT
*
2949 TCTCGCCTTGAGCTATGCTGTAATTTGATATGCTCTT
126 TCTCGCCTT-AGCTATGCTGTAATTTGATATGCCCTT
* * * *
2986 GAGTTGAATGTAATCAAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGT
1 GAGCTGAATGGAATC-AACTCGAAGGTTTTTGTTGACAGATAACCCTTCTC-GCTTGAACTATG-
* * *
3051 TGTAAATTTGATATGCCTTTGAGATGAATGTAATCGAACTCGAAGGTTTTTG-AGATATCCCTTC
63 TGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGAAGATAGCCCTTC
3115 T-GTCCTT-G-TATGCTGTAAATTCT-ATATGCCCTT
128 TCG-CCTTAGCTATGCTGT-AATT-TGATATGCCCTT
*
3148 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGATAGATAACCCTTCTCGCTTGAACTATGCT
1 GAGCTGAATGGAATC-AACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCTTGAACTATG-T
3213 GTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTAACAGATAGCCC
64 GTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTG---A-AGATAGCCC
3278 TTCTC
125 TTCTC
3283 ACATTGAACT
Statistics
Matches: 261, Mismatches: 22, Indels: 26
0.84 0.07 0.08
Matches are distributed among these distances:
161 68 0.26
162 61 0.23
163 2 0.01
164 16 0.06
165 13 0.05
166 36 0.14
167 4 0.02
168 18 0.07
169 43 0.16
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (161 bp):
GAGCTGAATGGAATCAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCTTGAACTATGTGT
AAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGAAGATAGCCCTTCTCG
CCTTAGCTATGCTGTAATTTGATATGCCCTT
Found at i:9181 original size:23 final size:21
Alignment explanation
Indices: 9155--9261 Score: 94
Period size: 23 Copynumber: 4.9 Consensus size: 21
9145 GTAAAATATT
9155 TTAAAAAAAAACAAAAAACTGAA
1 TTAAAAAAAAA-AAAAAA-TGAA
*
9178 TT--AAAAAAGAAAAAATGAA
1 TTAAAAAAAAAAAAAAATGAA
*
9197 -TAAAAAGAAAAAAAAATGGAAA
1 TTAAAAAAAAAAAAAAAT-G-AA
*
9219 TTAAAAAAAAAAATAAATGAA
1 TTAAAAAAAAAAAAAAATGAA
*
9240 ATAATATAAAAAACAAAAAATG
1 TTAA-A-AAAAAA-AAAAAATG
9262 TTAGCTAAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.01
19 4 0.06
20 18 0.26
21 12 0.17
22 4 0.06
23 23 0.33
24 7 0.10
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (21 bp):
TTAAAAAAAAAAAAAAATGAA
Found at i:9183 original size:22 final size:21
Alignment explanation
Indices: 9158--9261 Score: 90
Period size: 20 Copynumber: 4.8 Consensus size: 21
9148 AAATATTTTA
9158 AAAAAAAACAAAAAACTG-AATT
1 AAAAAAAA-AAAAAA-TGAAATT
*
9180 -AAAAAAGAAAAAATG-AA-T
1 AAAAAAAAAAAAAATGAAATT
9198 AAAAAGAAAAAAAAATGGAAATT
1 AAAAA-AAAAAAAAAT-GAAATT
9221 AAAAAAAAAAATAAATGAAATAAT
1 AAAAAAAAAAA-AAATGAAAT--T
*
9245 ATAAAAAACAAAAAATG
1 A-AAAAAAAAAAAAATG
9262 TTAGCTAAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
18 1 0.01
19 8 0.11
20 15 0.21
21 7 0.10
22 13 0.19
23 10 0.14
24 7 0.10
25 9 0.13
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.13
Consensus pattern (21 bp):
AAAAAAAAAAAAAATGAAATT
Found at i:9201 original size:41 final size:45
Alignment explanation
Indices: 9156--9261 Score: 125
Period size: 41 Copynumber: 2.4 Consensus size: 45
9146 TAAAATATTT
*
9156 TAAAAAAAAACAAAAAACT-G-AATT-AAAAAAGAAA-AAATG-AA
1 TAAAAAAAAACAAAAAA-TGGAAATTAAAAAAAAAAATAAATGAAA
*
9197 TAAAAAGAAA-AAAAAATGGAAATTAAAAAAAAAAATAAATGAAA
1 TAAAAAAAAACAAAAAATGGAAATTAAAAAAAAAAATAAATGAAA
9241 TAATATAAAAAACAAAAAATG
1 TAA-A-AAAAAACAAAAAATG
9262 TTAGCTAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
39 1 0.02
40 7 0.13
41 13 0.24
42 9 0.17
43 5 0.09
44 5 0.09
45 1 0.02
46 5 0.09
47 8 0.15
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (45 bp):
TAAAAAAAAACAAAAAATGGAAATTAAAAAAAAAAATAAATGAAA
Found at i:9203 original size:17 final size:20
Alignment explanation
Indices: 9160--9209 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
9150 ATATTTTAAA
*
9160 AAAAAACAAAAAACTGAATT
1 AAAAAAGAAAAAACTGAATT
9180 AAAAAAGAAAAAA-TGAA-T
1 AAAAAAGAAAAAACTGAATT
9198 -AAAAAGAAAAAA
1 AAAAAAGAAAAAA
9210 AAATGGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 12 0.41
18 1 0.03
19 4 0.14
20 12 0.41
ACGTcount: A:0.78, C:0.04, G:0.08, T:0.10
Consensus pattern (20 bp):
AAAAAAGAAAAAACTGAATT
Found at i:9219 original size:26 final size:24
Alignment explanation
Indices: 9190--9261 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 24
9180 AAAAAAGAAA
9190 AAATGAATAAAAAGAAAAAAAAATGG
1 AAAT-AATAAAAA-AAAAAAAAATGG
9216 AAAT--TAAAAAAAAAAATAAAT-G
1 AAATAATAAAAAAAAAAA-AAATGG
*
9238 AAATAATATAAAAAACAAAAAATG
1 AAATAATA-AAAAAAAAAAAAATG
9262 TTAGCTAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
22 11 0.28
23 10 0.25
24 6 0.15
25 9 0.22
26 4 0.10
ACGTcount: A:0.75, C:0.01, G:0.08, T:0.15
Consensus pattern (24 bp):
AAATAATAAAAAAAAAAAAAATGG
Found at i:17924 original size:16 final size:16
Alignment explanation
Indices: 17903--17943 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
17893 ACGATCTATT
17903 TGCCGAAATGGATTTG
1 TGCCGAAATGGATTTG
17919 TGCCGAAATGGATTTG
1 TGCCGAAATGGATTTG
*
17935 TGACGAAAT
1 TGCCGAAAT
17944 CGAACAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (16 bp):
TGCCGAAATGGATTTG
Found at i:19610 original size:19 final size:19
Alignment explanation
Indices: 19588--19645 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
19578 TTTATGGGTA
*
19588 ATTATTATATTTTTTTATT
1 ATTATTATATTTTTTTACT
* ***
19607 ATTATTTTATTTCCCTACT
1 ATTATTATATTTTTTTACT
*
19626 ATTATTATAATTTTTT-CT
1 ATTATTATATTTTTTTACT
19644 AT
1 AT
19646 ATTTAATTAT
Statistics
Matches: 29, Mismatches: 10, Indels: 1
0.73 0.25 0.03
Matches are distributed among these distances:
18 4 0.14
19 25 0.86
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTATTATATTTTTTTACT
Found at i:19854 original size:16 final size:16
Alignment explanation
Indices: 19833--19865 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19823 ATTTTTATAA
19833 TATTATTTATTT-TCTT
1 TATTATTT-TTTCTCTT
19849 TATTATTTTTTCTCTT
1 TATTATTTTTTCTCTT
19865 T
1 T
19866 CTTTCTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTATTTTTTCTCTT
Found at i:19940 original size:29 final size:27
Alignment explanation
Indices: 19879--19941 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 27
19869 TCTATTTTTC
19879 ATTTATTTATTATTAATAATTTTTAGT
1 ATTTATTTATTATTAATAATTTTTAGT
19906 ATTTTATTCTATTA-TATATACATTTTTTA-T
1 A-TTTATT-TATTATTA-ATA-A-TTTTTAGT
19936 ATTTAT
1 ATTTAT
19942 AAATATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
27 1 0.03
28 8 0.26
29 13 0.42
30 3 0.10
31 6 0.19
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (27 bp):
ATTTATTTATTATTAATAATTTTTAGT
Found at i:19941 original size:21 final size:21
Alignment explanation
Indices: 19917--19956 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19907 TTTTATTCTA
*
19917 TTATATATACATTTTTTATAT
1 TTATAAATACATTTTTTATAT
**
19938 TTATAAATATTTTTTTTAT
1 TTATAAATACATTTTTTAT
19957 TTTTTTTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATAAATACATTTTTTATAT
Found at i:20055 original size:16 final size:16
Alignment explanation
Indices: 20036--20092 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
20026 ACACTTTACT
20036 TTTTATTATCTTTTTA
1 TTTTATTATCTTTTTA
* *
20052 TTTTTTTCTCTTTTATA
1 TTTTATTATCTTTT-TA
*
20069 TATT-TTATCTTCATTTA
1 TTTTATTATCTT--TTTA
20086 TTTTATT
1 TTTTATT
20093 TATTTTCACT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 18 0.56
17 10 0.31
18 4 0.12
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTATTATCTTTTTA
Found at i:20055 original size:17 final size:17
Alignment explanation
Indices: 20030--20076 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 17
20020 TTTTTAACAC
20030 TTTACTTTTTATTATCTT
1 TTTA-TTTTTATTATCTT
*
20048 TTTATTTTT-TTCTCTT
1 TTTATTTTTATTATCTT
20064 TTATATATTTTAT
1 TT-TAT-TTTTAT
20077 CTTCATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 8 0.32
17 8 0.32
18 8 0.32
19 1 0.04
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTTTATTATCTT
Found at i:20094 original size:19 final size:19
Alignment explanation
Indices: 20045--20114 Score: 58
Period size: 19 Copynumber: 3.7 Consensus size: 19
20035 TTTTTATTAT
*
20045 CTTTTTAT-TTT-T-TTCT
1 CTTTTTATATTTATCTTCA
20061 CTTTTATATATTTTATCTTCA
1 CTTTT-TATA-TTTATCTTCA
* *
20082 -TTTATTTTATTTATTTTCA
1 CTTT-TTATATTTATCTTCA
20101 CTTTTTATATTTAT
1 CTTTTTATATTTAT
20115 AAATATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
16 5 0.12
17 3 0.07
19 21 0.49
20 10 0.23
21 4 0.09
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (19 bp):
CTTTTTATATTTATCTTCA
Found at i:20128 original size:38 final size:40
Alignment explanation
Indices: 20046--20133 Score: 103
Period size: 38 Copynumber: 2.3 Consensus size: 40
20036 TTTTATTATC
* **
20046 TTTTTATTT-TTTTCTCTTTTATATATTTTATCTTCATTT
1 TTTTTATTTATTTTCACTTTTATATATTTTATAATCATTT
*
20085 ATTTTATTTATTTTCACTTTT-TATA-TTTATAAAT-ATTT
1 TTTTTATTTATTTTCACTTTTATATATTTTAT-AATCATTT
20123 TTTTTATTTAT
1 TTTTTATTTAT
20134 CCTATTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
38 19 0.45
39 13 0.31
40 10 0.24
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (40 bp):
TTTTTATTTATTTTCACTTTTATATATTTTATAATCATTT
Found at i:28346 original size:124 final size:123
Alignment explanation
Indices: 28129--28563 Score: 562
Period size: 124 Copynumber: 3.6 Consensus size: 123
28119 TCGAAGAAAC
* *
28129 ATTCATCTTTAGATTGGATTTTAACTTCACGACGAAGGATATCTAATTCAAGGCTCAACTTCACA
1 ATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACA
* * * *
28194 ACAAATGGGTCGTCCACGATTTTAACTTCACGAAGAAGGATATCGTGCCCACCAGCAA
66 ACGAATGGGCCATCCACGATTTCAACTTCACGAAGAAGGATATCGTGCCCACCAGCAA
* **
28252 CATTCATCTTTAGATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTTGC
1 -ATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCAC
* * *
28317 AACGAATGGGCCATCTACGATTTCAACTTCACGAAGAAAGAAATCGTGCCCACCAGCGAA
65 AACGAATGGGCCATCCACGATTTCAACTTCACGAAGAAGGATATCGTGCCCACCAGC-AA
* * * * * *
28377 ATTCATCTTTGGATTGGATTTCAACTTTACGAAGAAGGATATCCAATTCCAGGTTTAACTTCACA
1 ATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACA
* * * * *
28442 ATGAAGGGGCCATCCACTATTTCAACTTCACGAAGAAGGATATTGTGCCCA-TA-C-A
66 ACGAATGGGCCATCCACGATTTCAACTTCACGAAGAAGGATATCGTGCCCACCAGCAA
* *
28497 A--C-TC--TAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCATA
1 ATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACA
*
28557 GCGAATG
66 ACGAATG
28564 AGCTTTCCAG
Statistics
Matches: 271, Mismatches: 39, Indels: 11
0.84 0.12 0.03
Matches are distributed among these distances:
115 52 0.19
117 2 0.01
118 1 0.00
120 2 0.01
122 1 0.00
123 1 0.00
124 210 0.77
125 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (123 bp):
ATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACA
ACGAATGGGCCATCCACGATTTCAACTTCACGAAGAAGGATATCGTGCCCACCAGCAA
Found at i:30415 original size:18 final size:18
Alignment explanation
Indices: 30392--30439 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
30382 AGTATTTATA
30392 TATATATATATAATTATTTT
1 TATAT-TAT-TAATTATTTT
*
30412 TATATTATTATTTATTTT
1 TATATTATTAATTATTTT
*
30430 CTTTATTATT
1 -TATATTATT
30440 TATTCTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.36
19 11 0.44
20 5 0.20
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TATATTATTAATTATTTT
Found at i:30435 original size:16 final size:16
Alignment explanation
Indices: 30416--30521 Score: 62
Period size: 16 Copynumber: 6.7 Consensus size: 16
30406 TATTTTTATA
30416 TTATTATTTATTTTCT
1 TTATTATTTATTTTCT
*
30432 TTATTATTTATTCTCT
1 TTATTATTTATTTTCT
* * *
30448 TTCTT-TATGTTTTCAT
1 TTATTATTTATTTTC-T
30464 TTATT-TATTATTATTACT
1 TTATTAT-TTATT-TT-CT
* *
30482 TT-TTA-GTATTTTAT
1 TTATTATTTATTTTCT
*
30496 TCTATTATATATTTT-T
1 T-TATTATTTATTTTCT
30512 TTA-TATTTAT
1 TTATTATTTAT
30522 GCATATTTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
14 8 0.11
15 11 0.16
16 34 0.49
17 11 0.16
18 5 0.07
19 1 0.01
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.70
Consensus pattern (16 bp):
TTATTATTTATTTTCT
Found at i:30515 original size:20 final size:20
Alignment explanation
Indices: 30490--30537 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
30480 CTTTTTAGTA
*
30490 TTTTATTCTAT-TATATATTT
1 TTTTATTCTATGCATAT-TTT
*
30510 TTTTATATTTATGCATATTTT
1 TTTTAT-TCTATGCATATTTT
30531 TTTTATT
1 TTTTATT
30538 TTTTATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 7 0.29
21 13 0.54
22 4 0.17
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTATTCTATGCATATTTT
Found at i:30518 original size:27 final size:27
Alignment explanation
Indices: 30463--30519 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
30453 TATGTTTTCA
30463 TTTATTTATTATTATTACTTTTTAGTAT
1 TTTATTTATTATTATTA-TTTTTAGTAT
30491 TTTATTCTATTATATATT-TTTTTA-TAT
1 TTTATT-TATTAT-TATTATTTTTAGTAT
30518 TT
1 TT
30520 ATGCATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 5 0.19
28 12 0.44
29 6 0.22
30 4 0.15
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (27 bp):
TTTATTTATTATTATTATTTTTAGTAT
Found at i:30644 original size:24 final size:28
Alignment explanation
Indices: 30617--30676 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
30607 ACACTTTACT
30617 TTTTATTATCTT-T-TT-ATTT-TTTTA
1 TTTTATTATCTTATCTTCATTTATTTTA
*
30641 TTTTATATATTTTATCTTCATTTATTTTA
1 TTTTAT-TATCTTATCTTCATTTATTTTA
30670 TTTTATT
1 TTTTATT
30677 CATTTTCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 6 0.20
25 5 0.17
26 1 0.03
27 2 0.07
28 5 0.17
29 11 0.37
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (28 bp):
TTTTATTATCTTATCTTCATTTATTTTA
Found at i:39929 original size:127 final size:130
Alignment explanation
Indices: 39767--40030 Score: 401
Period size: 127 Copynumber: 2.0 Consensus size: 130
39757 AAAAAATAGC
* *
39767 AGTTAACAGAGTCCGAATCATAATAATACAGATCATACCCTGGATCGGGTCACCACAAGGTCGAA
1 AGTTAACAAAGTCCGAATCATAATAATACAGATCATACCATGGATCGGGTCACCACAAGGTCGAA
* *
39832 TAAAATATTAG-A-AAT-AATAAATAAATAAACAAAGGTTAGAGTGCAATAAAATAAAAGTCAGT
66 TAAAATAATAGAACAATAAATAAATAAATAAACAAAGGTTAAAGTGCAATAAAATAAAAGTCAGT
* *
39894 AGTTAGCAAAGTCCGAATCATAATAATATC-GATCATACCATGGATCTGGTCACCACAAGGTCGA
1 AGTTAACAAAGTCCGAATCATAATAATA-CAGATCATACCATGGATCGGGTCACCACAAGGTCGA
** *
39958 ATCGAATAATAGAAACAATAAATAAATAAATAAACAAAGGTTAAAGTGCAATAAAATAAAAGTTA
65 ATAAAATAATAG-AACAATAAATAAATAAATAAACAAAGGTTAAAGTGCAATAAAATAAAAGTCA
40023 GT
129 GT
40025 AGTTAA
1 AGTTAA
40031 TATGCAATAA
Statistics
Matches: 122, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
127 67 0.55
128 1 0.01
129 1 0.01
130 3 0.02
131 50 0.41
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.23
Consensus pattern (130 bp):
AGTTAACAAAGTCCGAATCATAATAATACAGATCATACCATGGATCGGGTCACCACAAGGTCGAA
TAAAATAATAGAACAATAAATAAATAAATAAACAAAGGTTAAAGTGCAATAAAATAAAAGTCAGT
Found at i:43282 original size:18 final size:18
Alignment explanation
Indices: 43259--43293 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43249 TTCCATCCGG
*
43259 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
43277 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
43294 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:44650 original size:45 final size:45
Alignment explanation
Indices: 44600--44689 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
44590 AAAATGCAAC
44600 AATTGAAAATGCATTGGACCCCACGACAATT-TCAGCACCGAAAGT
1 AATTGAAAATGCATTGGACCCCACGACAATTGT-AGCACCGAAAGT
* * * * *
44645 AATTGATAATTCATTGGCCCCCACGGCAATTGTAGGACCGAAAGT
1 AATTGAAAATGCATTGGACCCCACGACAATTGTAGCACCGAAAGT
44690 CACATTGGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 38 0.97
46 1 0.03
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.22
Consensus pattern (45 bp):
AATTGAAAATGCATTGGACCCCACGACAATTGTAGCACCGAAAGT
Found at i:45696 original size:25 final size:25
Alignment explanation
Indices: 45662--45710 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
45652 ATTCGATGAA
45662 GAAGAAGAGAGACATGGAGGAGGAG
1 GAAGAAGAGAGACATGGAGGAGGAG
*
45687 GAAGAAGAGAGATATGGAGGAGGA
1 GAAGAAGAGAGACATGGAGGAGGA
45711 AGATGAGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.47, T:0.06
Consensus pattern (25 bp):
GAAGAAGAGAGACATGGAGGAGGAG
Found at i:45705 original size:22 final size:23
Alignment explanation
Indices: 45662--45718 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 23
45652 ATTCGATGAA
45662 GAAGAAGAGAGACATGGAGGAGGAG
1 GAAGAAGAGAGACAT-G-GGAGGAG
*
45687 GAAGAAGAGAGATAT-GGAGGAG
1 GAAGAAGAGAGACATGGGAGGAG
*
45709 GAAGATGAGA
1 GAAGAAGAGA
45719 AGGAGCAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 16 0.53
25 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.46, T:0.07
Consensus pattern (23 bp):
GAAGAAGAGAGACATGGGAGGAG
Found at i:48915 original size:18 final size:18
Alignment explanation
Indices: 48892--48926 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48882 TTCCATCCGG
*
48892 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
48910 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
48927 GTCCTTCGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:50052 original size:42 final size:45
Alignment explanation
Indices: 50006--50092 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 45
49996 CAAATGCAAC
50006 AATTGAAAATGCATTGG-ACCCACAC-AATT-CAGCACCGAAAGT
1 AATTGAAAATGCATTGGCACCCACACAAATTACAGCACCGAAAGT
* * * * *
50048 AATTGATAATTCATTGGCCCCCACGCAAATTACAGGACCGAAAGT
1 AATTGAAAATGCATTGGCACCCACACAAATTACAGCACCGAAAGT
50093 CACATTGGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 15 0.41
43 6 0.16
44 4 0.11
45 12 0.32
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (45 bp):
AATTGAAAATGCATTGGCACCCACACAAATTACAGCACCGAAAGT
Found at i:50806 original size:28 final size:28
Alignment explanation
Indices: 50766--50820 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
50756 TGCATTCGAT
50766 GAAGAAGAAGAGAGATATGGAGGAGGAG
1 GAAGAAGAAGAGAGATATGGAGGAGGAG
50794 GAAGAAGAAGAGAGATATGGAGGAGGA
1 GAAGAAGAAGAGAGATATGGAGGAGGA
50821 AGATGAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.45, T:0.07
Consensus pattern (28 bp):
GAAGAAGAAGAGAGATATGGAGGAGGAG
Found at i:51749 original size:135 final size:130
Alignment explanation
Indices: 51525--51884 Score: 402
Period size: 132 Copynumber: 2.7 Consensus size: 130
51515 GTTCTGGTCG
* * *
51525 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGATCGATGACACT-ATTCCTACG
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACA-TGGTTCCTACG
* * * *
51589 TGATGAGGACATCTTGGCCATCTTTAGGCATGATGATAACACGGTTCCTGCGCGATGAGGATGGC
65 TGATGAGG--ATGTTGGCCATCTTTAGG---GATGATAACACGGTTCCTACGCGATAAGGATGAC
*
51654 TGGTTA
125 TAGTTA
* * * * * *
51660 TCTAGGGGTGACACGGCTCCTACGTTATCAGAAGATCTAGTCGGGGGGATGACATGGTTCCTACG
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTC-GGTGGATGACATGGTTCCTACG
* * *
51725 TGATGAGGATGGATGACCATCTTTAGGGATGATAACACGGTTCCTACGTGATAAGGATGACTAGT
65 TGATGAGGAT-GTTGGCCATCTTTAGGGATGATAACACGGTTCCTACGCGATAAGGATGACTAGT
51790 TA
129 TA
* * * * * *
51792 TTTAAGGGTGATC-CGACTCCTACGTGATGAGGAGATCTGGTTGGTGGAT-ATACGGTTCCTACA
1 TCTAAGGGTGA-CACGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACATGGTTCCTACG
51855 TGATGAGGATAGTTGGCCATCTTTAGGGAT
65 TGATGAGGAT-GTTGGCCATCTTTAGGGAT
51885 AAATGTTTCA
Statistics
Matches: 189, Mismatches: 32, Indels: 13
0.81 0.14 0.06
Matches are distributed among these distances:
130 38 0.20
131 6 0.03
132 67 0.35
133 1 0.01
134 2 0.01
135 51 0.27
136 24 0.13
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (130 bp):
TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACATGGTTCCTACGT
GATGAGGATGTTGGCCATCTTTAGGGATGATAACACGGTTCCTACGCGATAAGGATGACTAGTTA
Found at i:52039 original size:21 final size:20
Alignment explanation
Indices: 51965--52041 Score: 127
Period size: 20 Copynumber: 3.8 Consensus size: 20
51955 GTTTCAAGAG
*
51965 AAACTGTCTCAAGGGAGACA
1 AAACTGTCTCAAGGGAGGCA
51985 AAACTGTCTCAAGGGAGGCA
1 AAACTGTCTCAAGGGAGGCA
52005 AAACTGTCTCAAGGGAGGCA
1 AAACTGTCTCAAGGGAGGCA
*
52025 AAACTTGTTTCAAGGGA
1 AAAC-TGTCTCAAGGGA
52042 AACAATCTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
20 43 0.80
21 11 0.20
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18
Consensus pattern (20 bp):
AAACTGTCTCAAGGGAGGCA
Found at i:52084 original size:106 final size:106
Alignment explanation
Indices: 51899--52093 Score: 293
Period size: 106 Copynumber: 1.8 Consensus size: 106
51889 GTTTCAAGAG
*
51899 AAACTGTCTCAAGAGAGACAAAATTCATTTAAAGGGAAACGATCTCAAAGATGGGTGTTTCAAGA
1 AAACTGTCTCAAGAGAGACAAAATTCATTTAAAGGGAAACAATCTCAAAGATGGGTGTTTCAAGA
51964 GAAACTGTCTCAAGGGAGACAAAACTGTCTCAAGGGAGGCA
66 GAAACTGTCTCAAGGGAGACAAAACTGTCTCAAGGGAGGCA
* * * * * * *
52005 AAACTGTCTCAAGGGAGGCAAAACTT-GTTTCAAGGGAAACAATCTCAAAGGTTGGTGTTTCATG
1 AAACTGTCTCAAGAGAGACAAAA-TTCATTTAAAGGGAAACAATCTCAAAGATGGGTGTTTCAAG
*
52069 AGAAACTGTCTCAAGGGAGATAAAA
65 AGAAACTGTCTCAAGGGAGACAAAA
52094 TTTGTTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
106 77 0.97
107 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (106 bp):
AAACTGTCTCAAGAGAGACAAAATTCATTTAAAGGGAAACAATCTCAAAGATGGGTGTTTCAAGA
GAAACTGTCTCAAGGGAGACAAAACTGTCTCAAGGGAGGCA
Found at i:52299 original size:102 final size:99
Alignment explanation
Indices: 52068--52311 Score: 242
Period size: 102 Copynumber: 2.4 Consensus size: 99
52058 GGTGTTTCAT
* * * * * *
52068 GAGAAACTGTCTCAAGGGAGATAAAATTTGTTTCAAGAGAAATAATTTAAAAGTTTGTCTTAAGG
1 GAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAAAAACTCAAAAGTTTGTCTAAAGG
* * *
52133 AAGATTGTCTCAAGTGAGACAAAGTTTGTTTTGA
66 AAAAATGTCTCAAGCGAGACAAAGTTTGTTTTGA
* ** * * **
52167 GAAAAACAATCTCAAGTGAGATC-AACTTTGTTTCAAGTTAAACAAACTCAAAA-TTTGTATCTC
1 GAGAAACTGTCTCAAGCGAGA-CAAAATTTGTTTCAAGAGAAA-AAACTCAAAAGTTTG--TCT-
52230 AAAGGAAAAATGTCTCAAGCGAGACGAAA-TTTGTTTTGA
61 AAAGGAAAAATGTCTCAAGCGAGAC-AAAGTTTGTTTTGA
* **
52269 GAGAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAA
1 GAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAAA
52312 CTGTCTCAAG
Statistics
Matches: 113, Mismatches: 25, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
99 37 0.33
100 7 0.06
101 5 0.04
102 61 0.54
103 3 0.03
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (99 bp):
GAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAAAAACTCAAAAGTTTGTCTAAAGG
AAAAATGTCTCAAGCGAGACAAAGTTTGTTTTGA
Found at i:52299 original size:138 final size:137
Alignment explanation
Indices: 52136--52458 Score: 330
Period size: 138 Copynumber: 2.3 Consensus size: 137
52126 CTTAAGGAAG
* * * **
52136 ATTGTCTCAAGTGAGACAAAGTTTGTTTTGAGAAAAACAATCTCAAG-TGAGATC-AACTTTGTT
1 ATTGTCTCAAGCGAGACAAAATTTGTTTTGAGAAAAACAATCTCAAGCT-AGA-CAAAATTCATT
*
52199 TCAAGTTAAACAAAC-TCAAAATTTGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTG
64 TCAAGTAAAAC-AACTTCAAAATTTGTAT-TCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTG
52263 TTTTG-AGAGAA
127 TTTTGAAGA-AA
* **
52274 ATTGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAACTGTCTCAAGCTAGACAAAATTCATTT
1 ATTGTCTCAAGCGAGACAAAATTTGTTTTGAGA-AAAACAATCTCAAGCTAGACAAAATTCATTT
** * ** * * * *
52339 CAAGTAAAACAACTTTGAAATTTGTGTTCCGAGGGAAAATTTCTCAAGTGAGATGAAATTTGTTT
65 CAAGTAAAACAACTTCAAAATTTGTATTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGTTT
*
52404 TTAAGAAA
130 TGAAGAAA
* * * * * *
52412 ATTATCTCTAGCGAGACGACACTTTGTTTCGAGAGAAACAATCTCAA
1 ATTGTCTCAAGCGAGAC-AAAATTTGTTTTGAGAAAAACAATCTCAA
52459 AGGCAACAAA
Statistics
Matches: 151, Mismatches: 28, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
138 94 0.62
139 56 0.37
140 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (137 bp):
ATTGTCTCAAGCGAGACAAAATTTGTTTTGAGAAAAACAATCTCAAGCTAGACAAAATTCATTTC
AAGTAAAACAACTTCAAAATTTGTATTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTT
GAAGAAA
Found at i:52328 original size:37 final size:37
Alignment explanation
Indices: 52234--52333 Score: 148
Period size: 36 Copynumber: 2.7 Consensus size: 37
52224 TATCTCAAAG
*
52234 GAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAGA
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAGA
* *
52271 G-AAATTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAGA
* *
52307 GAAAACTGTCTCAAGCTAGACAAAATT
1 GAAAAATGTCTCAAGCGAGACAAAATT
52334 CATTTCAAGT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 33 0.58
37 24 0.42
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (37 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAGA
Found at i:53513 original size:16 final size:16
Alignment explanation
Indices: 53492--53524 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53482 GCGTCCTTTT
*
53492 TGATCTTTTGGTGAAC
1 TGATCTTCTGGTGAAC
53508 TGATCTTCTGGTGAAC
1 TGATCTTCTGGTGAAC
53524 T
1 T
53525 AATTCTGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.42
Consensus pattern (16 bp):
TGATCTTCTGGTGAAC
Found at i:53657 original size:16 final size:17
Alignment explanation
Indices: 53636--53684 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
53626 ATTTTTCCAT
53636 TTTTCTCTTTG-TTTTC
1 TTTTCTCTTTGATTTTC
*
53652 TTTTCTTTTTGATTTTTC
1 TTTTCTCTTTGA-TTTTC
**
53670 TTTTGGCTTTGATTT
1 TTTTCTCTTTGATTT
53685 GATCTTTGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 10 0.37
17 3 0.11
18 14 0.52
ACGTcount: A:0.04, C:0.12, G:0.10, T:0.73
Consensus pattern (17 bp):
TTTTCTCTTTGATTTTC
Found at i:54994 original size:114 final size:114
Alignment explanation
Indices: 54794--55028 Score: 330
Period size: 114 Copynumber: 2.1 Consensus size: 114
54784 TCGTAGTTGA
**
54794 CCATTATGATCCTGACGTTGCACTTCACAGTGCTCATGTGAAAGTCCACGATTGTTGATGATATG
1 CCATTATGATCCTGACGTCACACTTCACAGTGCTCATGTGAAAGTCCACGATTGTTGATGATATG
* *
54859 GCTAATGACATGGTAGATGGGCTAAAATTAAGCAAAAAGGCACCTCATG
66 GCTAATGACATGGTAGATGGGCTAAAAATAAGCAAAAAGGCACCTCAAG
* * * * *
54908 CCATTATGATCTTGACGTCACACTTTAC-GATGTTGATGTGACAGTCCACGATTGTT-AGTGATA
1 CCATTATGATCCTGACGTCACACTTCACAG-TGCTCATGTGAAAGTCCACGATTGTTGA-TGATA
* *
54971 TGTCTAATGACATGGTAGATGGGCTAAAAATATGCAAAAAGGCACCTCAAG
64 TGGCTAATGACATGGTAGATGGGCTAAAAATAAGCAAAAAGGCACCTCAAG
*
55022 CCCTTAT
1 CCATTAT
55029 ACTTTCCAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
113 2 0.02
114 105 0.98
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (114 bp):
CCATTATGATCCTGACGTCACACTTCACAGTGCTCATGTGAAAGTCCACGATTGTTGATGATATG
GCTAATGACATGGTAGATGGGCTAAAAATAAGCAAAAAGGCACCTCAAG
Found at i:57172 original size:2 final size:2
Alignment explanation
Indices: 57161--57191 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
57151 AAAATATAAA
57161 AT AT -T 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
57192 TGGGGCGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:58117 original size:32 final size:34
Alignment explanation
Indices: 58081--58148 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 34
58071 AAAGATAAAT
*
58081 TTATAATTTGAATCTTAAATT-TTTTCTTA-TGA
1 TTATAATTTGAATATTAAATTATTTTCTTAGTGA
*
58113 TTATAATTTGAATATTAAATTATTTTTTTAGTGA
1 TTATAATTTGAATATTAAATTATTTTCTTAGTGA
58147 TT
1 TT
58149 TCATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 20 0.62
33 7 0.22
34 5 0.16
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.57
Consensus pattern (34 bp):
TTATAATTTGAATATTAAATTATTTTCTTAGTGA
Found at i:58595 original size:21 final size:22
Alignment explanation
Indices: 58571--58627 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
58561 CATTTCAGCT
* *
58571 TGGTTTCGAAATTCCTT-TGCC
1 TGGTTTCGAAATCCCTTGTACC
*
58592 TGGTTTCGAAACCCCTTGTACC
1 TGGTTTCGAAATCCCTTGTACC
58614 TGGTTTC-AAATCCC
1 TGGTTTCGAAATCCC
58628 CCTGACTGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.37
Consensus pattern (22 bp):
TGGTTTCGAAATCCCTTGTACC
Found at i:58618 original size:22 final size:23
Alignment explanation
Indices: 58590--58649 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
58580 AATTCCTTTG
58590 CCTGGTTTCGAAA-CCCCTTGTA
1 CCTGGTTTCGAAAGCCCCTTGTA
* *
58612 CCTGGTTTC-AAATCCCCCTG-A
1 CCTGGTTTCGAAAGCCCCTTGTA
*
58633 -CTGGTTTCTAAAGCCCC
1 CCTGGTTTCGAAAGCCCC
58650 CGTCTGGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 8 0.24
21 11 0.32
22 15 0.44
ACGTcount: A:0.18, C:0.35, G:0.17, T:0.30
Consensus pattern (23 bp):
CCTGGTTTCGAAAGCCCCTTGTA
Found at i:58638 original size:20 final size:21
Alignment explanation
Indices: 58591--58666 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 21
58581 ATTCCTTTGC
* *
58591 CTGGTTTCGAAA-CCCCTTGTA
1 CTGGTTTCTAAATCCCCCTG-A
58612 CCTGGTTTC-AAATCCCCCTGA
1 -CTGGTTTCTAAATCCCCCTGA
* *
58633 CTGGTTTCTAAAGCCCCC-GT
1 CTGGTTTCTAAATCCCCCTGA
58653 CTGGTTTCTAAATC
1 CTGGTTTCTAAATC
58667 ACATGTTCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
20 22 0.46
21 12 0.25
22 14 0.29
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (21 bp):
CTGGTTTCTAAATCCCCCTGA
Found at i:59641 original size:6 final size:5
Alignment explanation
Indices: 59609--59640 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
59599 TTGAAATTTT
59609 ATTAA ATTAA ATTAA ATTAA ATTAAA ATTAA A
1 ATTAA ATTAA ATTAA ATTAA ATT-AA ATTAA A
59641 AAACCCCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATTAA
Found at i:64677 original size:15 final size:16
Alignment explanation
Indices: 64626--64687 Score: 63
Period size: 15 Copynumber: 3.8 Consensus size: 16
64616 TTATCTAATC
*
64626 TTAAAAATAAAAAATAA
1 TTAAAAATTAAAAAT-A
* *
64643 TTTGAAATTTAAAAATA
1 -TTAAAAATTAAAAATA
64660 TTAAAAATTAAAAA-A
1 TTAAAAATTAAAAATA
*
64675 TTAAAAGTTAAAA
1 TTAAAAATTAAAA
64688 CACCAAGCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
15 13 0.34
16 12 0.32
17 1 0.03
18 12 0.32
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
TTAAAAATTAAAAATA
Found at i:65684 original size:60 final size:58
Alignment explanation
Indices: 65596--65785 Score: 177
Period size: 60 Copynumber: 3.2 Consensus size: 58
65586 TGCATCACAG
* *
65596 TCCTCAAAGTATGAC-TCTATTTTAAATTAGTCTCTAAACTTTTAAATATTCCAATTTCA
1 TCCTCAAACTATGACTTC-ATTCTAAATTAGTC-CTAAACTTTTAAATATTCCAATTTCA
* * * *
65655 TCCTTAAACTATGACTATCATTCTAAATTAGTCCTCAAACTTTTGAATATTTCAATTTTA
1 TCCTCAAACTATGACT-TCATTCTAAATTAGTCCT-AAACTTTTAAATATTCCAATTTCA
* * * * * * *
65715 TCCCCAAACTTTAACCTTCATTCTAAACTGGTCCCTAAACTTTTTTAAACATTCCAGTTTCA
1 TCCTCAAACTATGA-CTTCATTCTAAATTAGT-CCTAAAC--TTTTAAATATTCCAATTTCA
65777 TCC-CAAACT
1 TCCTCAAACT
65786 TTATGTATAT
Statistics
Matches: 107, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
59 15 0.14
60 61 0.57
61 13 0.12
62 18 0.17
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.40
Consensus pattern (58 bp):
TCCTCAAACTATGACTTCATTCTAAATTAGTCCTAAACTTTTAAATATTCCAATTTCA
Found at i:65999 original size:29 final size:29
Alignment explanation
Indices: 65962--66017 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
65952 TAGAAAAAAG
*
65962 TTAATAGTTTAAGGATGAAATTAGAATGT
1 TTAAAAGTTTAAGGATGAAATTAGAATGT
* * *
65991 TTAAAAGTTTAATGATTAATTTAGAAT
1 TTAAAAGTTTAAGGATGAAATTAGAAT
66018 AAAAGTCATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (29 bp):
TTAAAAGTTTAAGGATGAAATTAGAATGT
Found at i:66012 original size:60 final size:60
Alignment explanation
Indices: 65915--66066 Score: 171
Period size: 60 Copynumber: 2.5 Consensus size: 60
65905 TGAATTTGGA
* * *
65915 GATGAAATTGGAATGTTCAAAATTTTGAGGACCAATTTAGAA-AAAAGTTAATAGTTTAAG
1 GATGAAATTGGAATGTTCAAAAGTTTAAGGACCAATTTAGAATAAAAG-TAATAGGTTAAG
* * * ** * *
65975 GATGAAATTAGAATGTTTAAAAGTTTAATGATTAATTTAGAATAAAAGTCATAGGTTGAG
1 GATGAAATTGGAATGTTCAAAAGTTTAAGGACCAATTTAGAATAAAAGTAATAGGTTAAG
* * *
66035 GATGAAATTGGAATATGCAAAAATTTAAGGAC
1 GATGAAATTGGAATGTTCAAAAGTTTAAGGAC
66067 TATTTTAATT
Statistics
Matches: 74, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
60 69 0.93
61 5 0.07
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.32
Consensus pattern (60 bp):
GATGAAATTGGAATGTTCAAAAGTTTAAGGACCAATTTAGAATAAAAGTAATAGGTTAAG
Found at i:67109 original size:2 final size:2
Alignment explanation
Indices: 67097--67136 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
67087 CAAATTAATC
* *
67097 AT AT CT AT AT AT AT AT AT CT 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
67137 GCAAGTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68854 original size:26 final size:26
Alignment explanation
Indices: 68795--68861 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
68785 TTTATTCTCA
*
68795 TAAAAATTTATAAGTTTATCTATTTC
1 TAAAATTTTATAAGTTTATCTATTTC
*
68821 TAAAATTTTATAAGCTTT-TCTCTTTC
1 TAAAATTTTATAAG-TTTATCTATTTC
* *
68847 TAACATTTTAGAAGT
1 TAAAATTTTATAAGT
68862 GTCTCCTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 1 0.03
26 32 0.89
27 3 0.08
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.49
Consensus pattern (26 bp):
TAAAATTTTATAAGTTTATCTATTTC
Found at i:79508 original size:20 final size:19
Alignment explanation
Indices: 79479--79520 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
79469 AAAATGCATG
79479 TTTTTTAGAATTATGCACT
1 TTTTTTAGAATTATGCACT
79498 TTTTATTAGAATTATGCACT
1 TTTT-TTAGAATTATGCACT
79518 TTT
1 TTT
79521 CCAGCAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.55
Consensus pattern (19 bp):
TTTTTTAGAATTATGCACT
Found at i:80357 original size:33 final size:32
Alignment explanation
Indices: 80315--80406 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 32
80305 ATGAACATAA
*
80315 CATAACATGAACTTTCATGGTAAGAACTTGTAT
1 CATAACATGAACTTTCATGG-AAGAACTTATAT
80348 CATAACATGAACTTTCATGGAATGAACTTATAT
1 CATAACATGAACTTTCATGGAA-GAACTTATAT
*
80381 CATAACATGAATTTTCATGGCAAGAA
1 CATAACATGAACTTTCATGG-AAGAA
80407 TGATCTCATA
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
32 2 0.04
33 51 0.93
34 2 0.04
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (32 bp):
CATAACATGAACTTTCATGGAAGAACTTATAT
Found at i:80359 original size:18 final size:17
Alignment explanation
Indices: 80338--80391 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
80328 TTCATGGTAA
80338 GAACTTGTATCATAACAT
1 GAACTT-TATCATAACAT
*
80356 GAAC-TT-TCATGGA-AT
1 GAACTTTATCAT-AACAT
80371 GAACTTATATCATAACAT
1 GAACTT-TATCATAACAT
80389 GAA
1 GAA
80392 TTTTCATGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 10 0.34
16 3 0.10
17 3 0.10
18 13 0.45
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (17 bp):
GAACTTTATCATAACAT
Found at i:81162 original size:50 final size:50
Alignment explanation
Indices: 81078--81262 Score: 196
Period size: 50 Copynumber: 3.7 Consensus size: 50
81068 ATTATACCAT
* * * *
81078 TGAACTTATCACATAATTACACCAGTAAAATTTAACACATATCATATCAA
1 TGAACTTAACACATAATTACACTAGTGAACTTTAACACATATCATATCAA
* * * *
81128 TGAACTTAACATATAATTACACTAGTCAACTTTAACACATA--ATATTAG
1 TGAACTTAACACATAATTACACTAGTGAACTTTAACACATATCATATCAA
* * * * *
81176 TGAACTTAATACATAATTATAC-ATGTGAACTTAAATACATATCATGTCAA
1 TGAACTTAACACATAATTACACTA-GTGAACTTTAACACATATCATATCAA
* * *
81226 TCAACTTAACACATAATTACTCTAGTGAATTTTAACA
1 TGAACTTAACACATAATTACACTAGTGAACTTTAACA
81263 TGTATTTACA
Statistics
Matches: 108, Mismatches: 23, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
47 1 0.01
48 38 0.35
50 68 0.63
51 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (50 bp):
TGAACTTAACACATAATTACACTAGTGAACTTTAACACATATCATATCAA
Found at i:81181 original size:23 final size:22
Alignment explanation
Indices: 81150--81192 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
81140 ATAATTACAC
81150 TAGTCAACTTTAACACATAATAT
1 TAGTCAAC-TTAACACATAATAT
* *
81173 TAGTGAACTTAATACATAAT
1 TAGTCAACTTAACACATAAT
81193 TATACATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (22 bp):
TAGTCAACTTAACACATAATAT
Found at i:81189 original size:22 final size:24
Alignment explanation
Indices: 81128--81216 Score: 74
Period size: 26 Copynumber: 3.6 Consensus size: 24
81118 ATCATATCAA
* * *
81128 TGAACTTAACATATAATTACACTAG
1 TGAACTTAATACATAATTATA-TAG
* *
81153 TCAACTTTAACACATAA-TAT-TAG
1 TGAAC-TTAATACATAATTATATAG
*
81176 TGAACTTAATACATAATTATACATG
1 TGAACTTAATACATAATTATATA-G
81201 TGAACTTAAATACATA
1 TGAACTT-AATACATA
81217 TCATGTCAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
22 10 0.19
23 10 0.19
24 1 0.02
25 14 0.26
26 18 0.34
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.34
Consensus pattern (24 bp):
TGAACTTAATACATAATTATATAG
Found at i:81688 original size:31 final size:31
Alignment explanation
Indices: 81653--81728 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
81643 TCAAAAAACA
* *
81653 TAAGATATGGTTACTTTCATTTTTATTTTAT
1 TAAGATATGGTCACTTTCATTTTTATTTAAT
* *
81684 TAAGATATGATCATTTTCATTTTTATTTAAT
1 TAAGATATGGTCACTTTCATTTTTATTTAAT
*
81715 TAAGATGTGGTCAC
1 TAAGATATGGTCAC
81729 CCCGAGTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.51
Consensus pattern (31 bp):
TAAGATATGGTCACTTTCATTTTTATTTAAT
Found at i:84337 original size:19 final size:20
Alignment explanation
Indices: 84296--84346 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
84286 GAAACCCCTT
*
84296 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
84316 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
84335 TGAAGATACATG
1 TGAAAATACATG
84347 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Done.