Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003608.1 Hibiscus syriacus cultivar Beakdansim tig00007635_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: 83467
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:5413 original size:141 final size:142
Alignment explanation
Indices: 5158--5455 Score: 544
Period size: 141 Copynumber: 2.1 Consensus size: 142
5148 GCAAATAGAG
*
5158 AATAATTTTCCCATTAAATTTATTGAGTCGCTTCAATGGTTAAAAAAAGTGTTATTCTCTCTTGA
1 AATAATTTTCCCATTAAATTTATTGAGTCGCTTCAATGGTTAAAAAAAGTGTTATTCTCTCCTGA
*
5223 TGTTCTAGATTCAAACATGTGTACATTGTCAATAATTAAGAAAGATCATAAATATATACTACATT
66 TGTTCTAGATTCAAACATGTGTACATTGTCAATAATTAAGAAAGATCATAAACATATACTACATT
5288 ATAATCACCCAT
131 ATAATCACCCAT
*
5300 -ATAATTTTCCCATTAAATTTATTGAGTCGCTTCAATGGTTTAAAAAAGTGTTATTCTCTCCTGA
1 AATAATTTTCCCATTAAATTTATTGAGTCGCTTCAATGGTTAAAAAAAGTGTTATTCTCTCCTGA
*
5364 TGTTCTAGATTCAAACATGTGTACATTGTCAATAATTAAGAAATATCATAAACATATACTACATT
66 TGTTCTAGATTCAAACATGTGTACATTGTCAATAATTAAGAAAGATCATAAACATATACTACATT
5429 ATAATCACCCAT
131 ATAATCACCCAT
*
5441 AATAATTTTTCCATT
1 AATAATTTTCCCATT
5456 TATGAGCGAA
Statistics
Matches: 150, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
141 137 0.91
142 13 0.09
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (142 bp):
AATAATTTTCCCATTAAATTTATTGAGTCGCTTCAATGGTTAAAAAAAGTGTTATTCTCTCCTGA
TGTTCTAGATTCAAACATGTGTACATTGTCAATAATTAAGAAAGATCATAAACATATACTACATT
ATAATCACCCAT
Found at i:6064 original size:27 final size:28
Alignment explanation
Indices: 6010--6064 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
6000 GATGACATAC
*
6010 TAACATTATAGTTTATTTTTTTAACAAT
1 TAACATTACAGTTTATTTTTTTAACAAT
6038 TAACATTACAGTTTA-TTTTTTAACAAT
1 TAACATTACAGTTTATTTTTTTAACAAT
6065 GAATAATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (28 bp):
TAACATTACAGTTTATTTTTTTAACAAT
Found at i:12589 original size:31 final size:31
Alignment explanation
Indices: 12549--12624 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
12539 AAAATATAAT
*
12549 AGGGTCAAAAATGATAAATTGGGTCTACTAC
1 AGGGACAAAAATGATAAATTGGGTCTACTAC
12580 AGGGACAAAAATGATAAATTGGGTCTACTAC
1 AGGGACAAAAATGATAAATTGGGTCTACTAC
*
12611 ATGGACAAAAATGA
1 AGGGACAAAAATGA
12625 CCCTTAATCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.22
Consensus pattern (31 bp):
AGGGACAAAAATGATAAATTGGGTCTACTAC
Found at i:13905 original size:21 final size:21
Alignment explanation
Indices: 13879--13923 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
13869 GATTTCTGGG
* *
13879 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
13900 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
13921 CAA
1 CAA
13924 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:14754 original size:31 final size:31
Alignment explanation
Indices: 14716--14840 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
14706 AGGGTCGAGG
*
14716 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
14747 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
14778 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
14809 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
14840 G
1 G
14841 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:18020 original size:21 final size:21
Alignment explanation
Indices: 17994--18038 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17984 GATTTCTGGG
* *
17994 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
18015 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
18036 CAA
1 CAA
18039 TCGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:18873 original size:31 final size:31
Alignment explanation
Indices: 18835--18959 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
18825 AGGGTCGAGG
18835 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
18866 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
18897 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
18928 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
18959 G
1 G
18960 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:20120 original size:23 final size:23
Alignment explanation
Indices: 20088--20139 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
20078 GTGTTCATTA
* * *
20088 GTTTAGCGTTCACGAATATATTC
1 GTTTAACGTTCACAAAAATATTC
*
20111 GTTTAACGTTCACAAAAATGTTC
1 GTTTAACGTTCACAAAAATATTC
20134 GTTTAA
1 GTTTAA
20140 AGTTTGTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (23 bp):
GTTTAACGTTCACAAAAATATTC
Found at i:21251 original size:28 final size:28
Alignment explanation
Indices: 21207--21268 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
21197 ATGAGTAATT
*
21207 AAAAAAATATTAGGTATCTAATTGCACA
1 AAAAAAATATTAAGTATCTAATTGCACA
* *
21235 AAAAAAATCTTAAGTATCTAATTGCATA
1 AAAAAAATATTAAGTATCTAATTGCACA
21263 AAAAAA
1 AAAAAA
21269 GAAGTCAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (28 bp):
AAAAAAATATTAAGTATCTAATTGCACA
Found at i:26055 original size:32 final size:33
Alignment explanation
Indices: 26009--26075 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
25999 AGAGGTGTAG
26009 TTAGCTTCTCCC-TTTTGGCTGTCAAAGAGTCA
1 TTAGCTTCTCCCTTTTTGGCTGTCAAAGAGTCA
* * *
26041 TTAGGTTCTCCCTTTTTGGCTGTCGATGAGTCA
1 TTAGCTTCTCCCTTTTTGGCTGTCAAAGAGTCA
26074 TT
1 TT
26076 TCAATCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 11 0.35
33 20 0.65
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (33 bp):
TTAGCTTCTCCCTTTTTGGCTGTCAAAGAGTCA
Found at i:31840 original size:36 final size:34
Alignment explanation
Indices: 31794--31912 Score: 132
Period size: 36 Copynumber: 3.3 Consensus size: 34
31784 TTTGAAAAAC
*
31794 ATATAATATATACTTTTAAAAAATCGATTTTTGAAA
1 ATATATTATATACTTTT--AAAATCGATTTTTGAAA
* * *
31830 ATATATTATATAGTTTTGAAAGCGATTTTTGAAA
1 ATATATTATATACTTTTAAAATCGATTTTTGAAA
31864 ATATAAATTATATAGTCTTTTAAAAT-GATTTTTGAAA
1 ATAT--ATTATATA--CTTTTAAAATCGATTTTTGAAA
31901 ATATATATATAT
1 ATATAT-TATAT
31913 TATATAATTT
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
34 19 0.27
35 2 0.03
36 28 0.39
37 15 0.21
38 7 0.10
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (34 bp):
ATATATTATATACTTTTAAAATCGATTTTTGAAA
Found at i:31861 original size:34 final size:35
Alignment explanation
Indices: 31813--31912 Score: 130
Period size: 37 Copynumber: 2.8 Consensus size: 35
31803 ATACTTTTAA
31813 AAAATCGATTTTTGAAAATATATTATATAGT-TTTG
1 AAAA-CGATTTTTGAAAATATATTATATAGTCTTTG
* *
31848 AAAGCGATTTTTGAAAATATAAATTATATAGTCTTTT
1 AAAACGATTTTTGAAAATAT--ATTATATAGTCTTTG
*
31885 AAAATGATTTTTGAAAATATATATATAT
1 AAAACGATTTTTGAAAATATAT-TATAT
31913 TATATAATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
34 16 0.28
35 5 0.09
36 15 0.26
37 21 0.37
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (35 bp):
AAAACGATTTTTGAAAATATATTATATAGTCTTTG
Found at i:31947 original size:113 final size:111
Alignment explanation
Indices: 31822--32116 Score: 298
Period size: 113 Copynumber: 2.6 Consensus size: 111
31812 AAAAATCGAT
* *
31822 TTTTG-AAA-ATATATTATATAGTTTTGAAAGCGATTTTTG-AAA-ATATAAAT--TATATAGTC
1 TTTTGAAAATATATATTATATAGTTTTGAAAAC-A-TTTTGAAAACATATAAATAATATATAAT-
* * * *
31881 TTTTAAAATGATTTTTGAAAATATATATATATTATATAATTTTTGAAAACA
63 TTTAAAAAT-A-TTTTGAAAACATATATATAATATATAATTTATGAAAACA
* * * *
31932 TTTTTAAAGGTATATAATATATAGTTTTGAAAACATTTTGAAAACATATATATAATATATAATTT
1 TTTTGAAA-ATATATATTATATAGTTTTGAAAACATTTTGAAAACATATAAATAATATATAATTT
*
31997 TAAAAATATTTTGAAAACATATATATAATATATAGTTTATGAAAACA
65 TAAAAATATTTTGAAAACATATATATAATATATAATTTATGAAAACA
* *** *
32044 TTTTGAAAATATATATAATATATATTTTTTGAAAACATTTTTTTAA-ATATATATAATATATAAG
1 TTTTGAAAATATATAT--TATATA-GTTTTGAAAACATTTTGAAAACATATAAATAATATATAA-
*
32108 TTTTGAAAA
62 TTTTAAAAA
32117 CGTTTTTGAA
Statistics
Matches: 155, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
110 4 0.03
111 13 0.08
112 46 0.30
113 52 0.34
114 33 0.21
115 7 0.05
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.44
Consensus pattern (111 bp):
TTTTGAAAATATATATTATATAGTTTTGAAAACATTTTGAAAACATATAAATAATATATAATTTT
AAAAATATTTTGAAAACATATATATAATATATAATTTATGAAAACA
Found at i:31984 original size:38 final size:37
Alignment explanation
Indices: 31830--32127 Score: 275
Period size: 38 Copynumber: 7.9 Consensus size: 37
31820 ATTTTTGAAA
* *
31830 ATATATTATATAGTTTTGAAAGCGATTTTTG-AAAATAT
1 ATATAATATATAGTTTTGAAAAC-A-TTTTGAAAAATAT
* * *
31868 A-A-ATTATATAGTCTTTTAAAATGATTTTTGAAAATATAT
1 ATATAATATATAGT-TTTGAAAA-CA-TTTTGAAAA-ATAT
* * * **
31907 ATATATTATATAATTTTTGAAAACATTTT--TAAAGGT
1 ATATAATATAT-AGTTTTGAAAACATTTTGAAAAATAT
31943 ATATAATATATAGTTTTGAAAACATTTTGAAAACATAT
1 ATATAATATATAGTTTTGAAAACATTTTGAAAA-ATAT
* * *
31981 ATATAATATATAATTTTAAAAATATTTTGAAAACATAT
1 ATATAATATATAGTTTTGAAAACATTTTGAAAA-ATAT
32019 ATATAATATATAGTTTATGAAAACATTTTG-AAAATAT
1 ATATAATATATAGTTT-TGAAAACATTTTGAAAAATAT
* ***
32056 ATATAATATATATTTTTTGAAAACATTTTTTTAAATAT
1 ATATAATATATA-GTTTTGAAAACATTTTGAAAAATAT
*
32094 ATATAATATATAAGTTTTGAAAACGTTTTTGAAA
1 ATATAATATAT-AGTTTTGAAAAC-ATTTTGAAA
32128 TTTTGAGAAT
Statistics
Matches: 217, Mismatches: 28, Indels: 29
0.79 0.10 0.11
Matches are distributed among these distances:
35 16 0.07
36 22 0.10
37 46 0.21
38 89 0.41
39 26 0.12
40 2 0.01
41 14 0.06
42 2 0.01
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (37 bp):
ATATAATATATAGTTTTGAAAACATTTTGAAAAATAT
Found at i:32133 original size:20 final size:20
Alignment explanation
Indices: 32108--32147 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
32098 AATATATAAG
*
32108 TTTTGAAAACGTTTTTGAAA
1 TTTTGAAAACGTTTTAGAAA
* *
32128 TTTTGAGAATGTTTTAGAAA
1 TTTTGAAAACGTTTTAGAAA
32148 ATATATATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (20 bp):
TTTTGAAAACGTTTTAGAAA
Found at i:32196 original size:8 final size:8
Alignment explanation
Indices: 32183--32228 Score: 74
Period size: 8 Copynumber: 5.5 Consensus size: 8
32173 AATAGTATTC
32183 TTTTTTAT
1 TTTTTTAT
32191 TTTTTTATTT
1 TTTTTTA--T
32201 TTTTTTAT
1 TTTTTTAT
32209 TTTTTTAT
1 TTTTTTAT
32217 TTTTTTAT
1 TTTTTTAT
32225 TTTT
1 TTTT
32229 CAGGTCCAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
8 28 0.78
10 8 0.22
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTAT
Found at i:32196 original size:10 final size:10
Alignment explanation
Indices: 32178--32222 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 10
32168 TTAAAAATAG
*
32178 TATTCTTTTT
1 TATTTTTTTT
32188 TA--TTTTTT
1 TATTTTTTTT
32196 TATTTTTTTT
1 TATTTTTTTT
32206 TA--TTTTTT
1 TATTTTTTTT
32214 TATTTTTTT
1 TATTTTTTT
32223 ATTTTTCAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
8 15 0.50
10 15 0.50
ACGTcount: A:0.11, C:0.02, G:0.00, T:0.87
Consensus pattern (10 bp):
TATTTTTTTT
Found at i:32199 original size:18 final size:17
Alignment explanation
Indices: 32178--32228 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 17
32168 TTAAAAATAG
32178 TATTCTTTTTTATTTTTT
1 TATT-TTTTTTATTTTTT
32196 TATTTTTTTTTATTTTTT
1 TA-TTTTTTTTATTTTTT
32214 TA-TTTTTTTATTTTT
1 TATTTTTTTTATTTTT
32229 CAGGTCCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.41
18 17 0.53
19 2 0.06
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.86
Consensus pattern (17 bp):
TATTTTTTTTATTTTTT
Found at i:34469 original size:103 final size:103
Alignment explanation
Indices: 34285--34510 Score: 382
Period size: 103 Copynumber: 2.2 Consensus size: 103
34275 GTCGAGGGTC
* *
34285 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACACGTGTGAAGTCTGGTGAGACACATAC
* *
34350 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
34388 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACACGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACACGTGTGAAGTCTGGTGAGACACATAC
* *
34453 TTGATCCCTAGTATATGTATATGATTTTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
34491 TATGTGGTCCTT-ATGGACAT
1 TATGTGGTCCTTCA-GGACAT
34511 TATTATATGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
102 1 0.01
103 115 0.99
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACACGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:34585 original size:23 final size:23
Alignment explanation
Indices: 34509--34586 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
34499 CCTTATGGAC
*
34509 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
34533 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
34556 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
34579 ATTATATG
1 ATTATATG
34587 AGCTGTGGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:36265 original size:29 final size:31
Alignment explanation
Indices: 36208--36265 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
36198 TGAAATATTC
* **
36208 TTTTATATATTTTTTACTTCTTATTATTTTT
1 TTTTATATATTTTTTACTTCTCAGAATTTTT
36239 TTTTATAT-TTTTTTACTT-TCAGAATTT
1 TTTTATATATTTTTTACTTCTCAGAATTT
36266 AACATTTTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.25
30 10 0.42
31 8 0.33
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.71
Consensus pattern (31 bp):
TTTTATATATTTTTTACTTCTCAGAATTTTT
Found at i:41295 original size:117 final size:122
Alignment explanation
Indices: 41165--41382 Score: 306
Period size: 123 Copynumber: 1.8 Consensus size: 122
41155 AACAAAAATA
* *
41165 ATTTACATTTTTTTATTATTATGAATATCTAT-G-AAGAAT-TT-T-TACAATGTAAACAT-TTT
1 ATTTACATCTTTTTATTATTATGAATAT-TATAGTAA-AATGTTATGTAAAATGTAAACATATTT
41224 -TACATAAATTATGTAAAATTTAATATTAATTAAAATATCTTAAATTATAAACATTTTT
64 GTACATAAATTATGTAAAATTTAATATTAATTAAAATATCTTAAATTATAAACATTTTT
* * * *
41282 ATTTACATCTTTTTATTATTATGAATATTTTAGTTAAATGTTGATGTAAAATTTAAATATATTTG
1 ATTTACATCTTTTTATTATTATGAATATTATAGTAAAATGTT-ATGTAAAATGTAAACATATTTG
41347 TACATAAATTATGTAAAATTTAATATTAATTAAAAT
65 TACATAAATTATGTAAAATTTAATATTAATTAAAAT
41383 TAAAATAATA
Statistics
Matches: 87, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
116 2 0.02
117 31 0.36
118 3 0.03
120 1 0.01
121 11 0.13
122 3 0.03
123 36 0.41
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.48
Consensus pattern (122 bp):
ATTTACATCTTTTTATTATTATGAATATTATAGTAAAATGTTATGTAAAATGTAAACATATTTGT
ACATAAATTATGTAAAATTTAATATTAATTAAAATATCTTAAATTATAAACATTTTT
Found at i:41457 original size:15 final size:15
Alignment explanation
Indices: 41437--41467 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41427 CAACAAATAA
41437 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
41452 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
41467 A
1 A
41468 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:41640 original size:18 final size:19
Alignment explanation
Indices: 41617--41653 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
41607 CCAATAATCA
41617 TATTCT-CTGGTAATCTTT
1 TATTCTACTGGTAATCTTT
41635 TATTCTCACTGGTAATCTT
1 TATTCT-ACTGGTAATCTT
41654 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (19 bp):
TATTCTACTGGTAATCTTT
Found at i:42523 original size:20 final size:20
Alignment explanation
Indices: 42499--42554 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
42489 AATTCGAGTT
42499 GCGAATTTGAAAATCGCGTTA
1 GCGAATTTGAAAATCGCG-TA
*
42520 -CGAATTTGAAAATCGTGTA
1 GCGAATTTGAAAATCGCGTA
42539 GCGAATTTGGAAAATC
1 GCGAATTT-GAAAATC
42555 ACATGCGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 2 0.06
20 23 0.72
21 7 0.22
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (20 bp):
GCGAATTTGAAAATCGCGTA
Found at i:42639 original size:19 final size:19
Alignment explanation
Indices: 42617--42665 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
42607 GGAGTTTGCG
42617 TTGCGAATTTGAGATCGCA
1 TTGCGAATTTGAGATCGCA
42636 TTGCGAATTTGAGATCGCA
1 TTGCGAATTTGAGATCGCA
42655 TTGCGAATTTG
1 TTGCGAATTTG
42666 TTGGTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (19 bp):
TTGCGAATTTGAGATCGCA
Found at i:43366 original size:21 final size:21
Alignment explanation
Indices: 43340--43389 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
43330 TCCAGATTCA
43340 CAACGCGAACATCGACTATCG
1 CAACGCGAACATCGACTATCG
*
43361 CAACGCGAACTTCGACTATCG
1 CAACGCGAACATCGACTATCG
*
43382 CAATGCGA
1 CAACGCGA
43390 TTTTCCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.16
Consensus pattern (21 bp):
CAACGCGAACATCGACTATCG
Found at i:43446 original size:21 final size:21
Alignment explanation
Indices: 43421--43534 Score: 74
Period size: 21 Copynumber: 5.4 Consensus size: 21
43411 GTCCAAGTTT
*
43421 CGTTGCAATTTATTCCAAATC
1 CGTTGCGATTTATTCCAAATC
* *
43442 CGTTGCGA--TAGTCCAAGTTC
1 CGTTGCGATTTATTCCAA-ATC
*
43462 ACGTTGCGATTTATTCCAAATT
1 -CGTTGCGATTTATTCCAAATC
* * * *
43484 TGTTGC-A-ATAGTCCAAGTTC
1 CGTTGCGATTTATTCCAA-ATC
* *
43504 GCGTTGCGATTTATTACAAATT
1 -CGTTGCGATTTATTCCAAATC
43526 CGTTGCGAT
1 CGTTGCGAT
43535 AGTCCAAGTT
Statistics
Matches: 68, Mismatches: 17, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
19 14 0.21
20 4 0.06
21 34 0.50
22 3 0.04
23 13 0.19
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATC
Found at i:43480 original size:42 final size:42
Alignment explanation
Indices: 43385--43545 Score: 238
Period size: 42 Copynumber: 3.9 Consensus size: 42
43375 ACTATCGCAA
*
43385 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTT-TCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCACGT
* *
43424 TGCAATTTATTCCAAATCCGTTGCGATAGTCCAAGTTCACGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCACGT
* * *
43466 TGCGATTTATTCCAAATTTGTTGCAATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCACGT
*
43508 TGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTC
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTC
43546 CTTGCAATAG
Statistics
Matches: 108, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 4 0.04
40 2 0.02
41 27 0.25
42 75 0.69
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (42 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCACGT
Found at i:43555 original size:19 final size:19
Alignment explanation
Indices: 43486--43564 Score: 59
Period size: 19 Copynumber: 3.9 Consensus size: 19
43476 TCCAAATTTG
43486 TTGCAATAGTCCAAGTTCGC
1 TTGCAATAGTCCAAGTTC-C
* * * * *
43506 GTTGCGATTTATTACAAATTCG
1 -TTGC-A-ATAGTCCAAGTTCC
*
43528 TTGCGATAGTCCAAGTTCC
1 TTGCAATAGTCCAAGTTCC
*
43547 TTGCAATAGTCGAAGTTC
1 TTGCAATAGTCCAAGTTC
43565 GCGTTACGAT
Statistics
Matches: 43, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
19 25 0.58
21 8 0.19
22 1 0.02
23 9 0.21
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (19 bp):
TTGCAATAGTCCAAGTTCC
Found at i:43555 original size:61 final size:61
Alignment explanation
Indices: 43385--43602 Score: 232
Period size: 61 Copynumber: 3.6 Consensus size: 61
43375 ACTATCGCAA
* *
43385 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTTCGTTGCAATTTATTCCAA-ATC-CGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG-TTCGTTGCAA--TAGTCCAAGTTCGCGT
* * * * *
43445 TGCGA--TAGTCCAAGTTCACGTTGCGATTTATTCCAAATTTGTTGCAATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATT--CGTTGCGA--TAGTCCAAGTTCGTTGCAATAGTCCAAGTTCGCGT
* * *
43508 TGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCCTTGCAATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCAATAGTCCAAGTTCGCGT
*
43569 TACGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
43603 AATCACAACG
Statistics
Matches: 132, Mismatches: 17, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
59 1 0.01
60 12 0.09
61 69 0.52
62 10 0.08
63 25 0.19
64 7 0.05
65 8 0.06
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (61 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCAATAGTCCAAGTTCGCGT
Found at i:44471 original size:21 final size:21
Alignment explanation
Indices: 44447--44581 Score: 134
Period size: 21 Copynumber: 6.4 Consensus size: 21
44437 TTTGGAATAA
*
44447 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
44468 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* *
44489 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
44508 AAATCGCAAAGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
* *
44531 ATCGCAACG-G-ATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
* *
44550 AAATTGCAAAGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
44573 ATCGCAACG
1 ATCGCAACG
44582 AATTTGGAAA
Statistics
Matches: 92, Mismatches: 14, Indels: 16
0.75 0.11 0.13
Matches are distributed among these distances:
19 17 0.18
20 1 0.01
21 56 0.61
22 1 0.01
23 17 0.18
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:44493 original size:42 final size:43
Alignment explanation
Indices: 44447--44597 Score: 183
Period size: 42 Copynumber: 3.7 Consensus size: 43
44437 TTTGGAATAA
* * * *
44447 ATCGCAACGCGAACTTCGACT-ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAATTTGGAATAATCGCAAAGCGAACTTGGACT
44489 ATCGCAA--CGAATTTGGAATAAATCGCAAAGCGAACTTGGACT
1 ATCGCAACGCGAATTTGGAAT-AATCGCAAAGCGAACTTGGACT
*
44531 ATCGCAACG-G-ATTTGGAATAAATTGCAAAGCGAACTTGGACT
1 ATCGCAACGCGAATTTGGAAT-AATCGCAAAGCGAACTTGGACT
44573 ATCGCAA--CGAATTTGGAA-AATCGCA
1 ATCGCAACGCGAATTTGGAATAATCGCA
44598 TTGCGATAGT
Statistics
Matches: 97, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
40 15 0.15
41 1 0.01
42 80 0.82
43 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (43 bp):
ATCGCAACGCGAATTTGGAATAATCGCAAAGCGAACTTGGACT
Found at i:44522 original size:63 final size:63
Alignment explanation
Indices: 44419--44539 Score: 215
Period size: 63 Copynumber: 1.9 Consensus size: 63
44409 CGTTGCGATT
*
44419 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACAAATTTGGAATAAATCGCAAAGCGAACTTCGACTATCGCAACGCGAAC
* *
44482 TTGGACTATCGCAACGAATTTGGAATAAATCGCAAAGCGAACTTGGACTATCGCAACG
1 TTGGACTATCGCAACAAATTTGGAATAAATCGCAAAGCGAACTTCGACTATCGCAACG
44540 GATTTGGAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (63 bp):
TTGGACTATCGCAACAAATTTGGAATAAATCGCAAAGCGAACTTCGACTATCGCAACGCGAAC
Found at i:44622 original size:21 final size:21
Alignment explanation
Indices: 44593--44643 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
44583 ATTTGGAAAA
*
44593 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
44614 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
44635 TCGCGTTGC
1 TCGCGTTGC
44644 AAATCTGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:45834 original size:303 final size:303
Alignment explanation
Indices: 45282--46130 Score: 1470
Period size: 303 Copynumber: 2.8 Consensus size: 303
45272 TCAAGTATTT
*
45282 TACGACCCGAACCTTTCTCCCCAAGTACCCCACTCCAGGAAGGCGGAATACGTACGTGTGCGTGT
1 TACGACCCGAACCTTTCTCCCCAAGTACCCCACTCCAGGCAGGCGGAATACGTACGTGTGCGTGT
45347 GTTCGAGATAGAATAAAAAGAAAATAATCCGAAAAATAGGGGTGCAACACGAGGACTTCCCAGGA
66 GTTCGAGATAGAATAAAAAGAAAATAATCCGAAAAATAGGGGTGCAACACGAGGACTTCCCAGGA
45412 GGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGG
131 GGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGG
* *
45477 TGCATTAGTGCTGGTATGATCGCACCCGTCATGCCTTGCGCCCTTAATTTATTTAAGGCGTTTGT
196 TGCATTAGTGCTGGTATGATCGCACCCGTCATGCCTTGCGCCCTTAATTTATTTAAAGCGTTCGT
* * * *
45542 TTTCTTCCGGCCCGCACTTAAGGGAGTCGCAAAATTCGGATTC
261 TTTCTTACGGCCCACACTTAAGGGACTCGCAAAATTCAGATTC
* *
45585 TACGCCCCGAACCTTTATCCCCAAGTACCCCACTCCAGGCAGGCGGAATACGTACGTGTGCGTGT
1 TACGACCCGAACCTTTCTCCCCAAGTACCCCACTCCAGGCAGGCGGAATACGTACGTGTGCGTGT
* * *
45650 GTTCGAGATAGAATAAAAAGAAAATAATCCGAAAAAGAGGGATGCAACACAAGGACTTCCCAGGA
66 GTTCGAGATAGAATAAAAAGAAAATAATCCGAAAAATAGGGGTGCAACACGAGGACTTCCCAGGA
*
45715 GGTCACCCATCATAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGG
131 GGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGG
* * *
45780 TGCATTAGTGCTGGTATGATCGCACCCGTCATGCTTTGTGCTCTTAATTTATTTAAAGCGTTCGT
196 TGCATTAGTGCTGGTATGATCGCACCCGTCATGCCTTGCGCCCTTAATTTATTTAAAGCGTTCGT
* *
45845 TTTCTTACGGCCCACACTTAAGGGACTCGTAAAATTCATATTC
261 TTTCTTACGGCCCACACTTAAGGGACTCGCAAAATTCAGATTC
* *
45888 TACGACCCGAACCTTTCTCCCCAAGTACCCCACTCCAGGCATGCGGAATACGTACATGT--GTGT
1 TACGACCCGAACCTTTCTCCCCAAGTACCCCACTCCAGGCAGGCGGAATACGTACGTGTGCGTGT
*
45951 GTTCGATATAGAATAAAAAGAAAATAATCCGAAAAATAGGGGTGCAACACGAGGACTTCCCAGGA
66 GTTCGAGATAGAATAAAAAGAAAATAATCCGAAAAATAGGGGTGCAACACGAGGACTTCCCAGGA
*
46016 GGTCACCAATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGG
131 GGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGG
*
46081 TGCATTAGTGCTGGTATGATCGCACCCGTCATGCCTTGCG-CATTAATTTA
196 TGCATTAGTGCTGGTATGATCGCACCCGTCATGCCTTGCGCCCTTAATTTA
46131 AAAATAAAAA
Statistics
Matches: 514, Mismatches: 32, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
300 8 0.02
301 166 0.32
303 340 0.66
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (303 bp):
TACGACCCGAACCTTTCTCCCCAAGTACCCCACTCCAGGCAGGCGGAATACGTACGTGTGCGTGT
GTTCGAGATAGAATAAAAAGAAAATAATCCGAAAAATAGGGGTGCAACACGAGGACTTCCCAGGA
GGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGG
TGCATTAGTGCTGGTATGATCGCACCCGTCATGCCTTGCGCCCTTAATTTATTTAAAGCGTTCGT
TTTCTTACGGCCCACACTTAAGGGACTCGCAAAATTCAGATTC
Found at i:53831 original size:24 final size:24
Alignment explanation
Indices: 53795--53852 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
53785 ATTAAAATGA
**
53795 TAAACGAACACAAGTGAACGAACG
1 TAAACGAACACAAACGAACGAACG
* *
53819 TAAATGAATACAAACGAACGAACG
1 TAAACGAACACAAACGAACGAACG
*
53843 TAAACAAACA
1 TAAACGAACA
53853 TAAAATTAAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.55, C:0.19, G:0.16, T:0.10
Consensus pattern (24 bp):
TAAACGAACACAAACGAACGAACG
Found at i:54058 original size:14 final size:14
Alignment explanation
Indices: 54035--54073 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
54025 TGGGCTAAAT
*
54035 ATAAACGAACGAAC
1 ATAAACGAACAAAC
*
54049 ATAAATGAACAAAC
1 ATAAACGAACAAAC
54063 ATAAACGAACA
1 ATAAACGAACA
54074 GATTACTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.62, C:0.18, G:0.10, T:0.10
Consensus pattern (14 bp):
ATAAACGAACAAAC
Found at i:60438 original size:21 final size:21
Alignment explanation
Indices: 60414--60456 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
60404 ACGAACTCAG
*
60414 TGGATCTCCCAGTCGAAGGCC
1 TGGATCTCCCAGTCAAAGGCC
* *
60435 TGGATCTCTCTGTCAAAGGCC
1 TGGATCTCCCAGTCAAAGGCC
60456 T
1 T
60457 CTTTGAGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.30, G:0.26, T:0.26
Consensus pattern (21 bp):
TGGATCTCCCAGTCAAAGGCC
Found at i:62648 original size:175 final size:168
Alignment explanation
Indices: 62364--62708 Score: 510
Period size: 175 Copynumber: 2.0 Consensus size: 168
62354 TGGCCTGTGT
* * *
62364 TCTCAGGCATTCTGATATCTTTTCTTTTTCATTCGGGGAATCGTGCCTCTTGAAACCTTTGAATG
1 TCTCAGGCATGCTGATATCTTTTCTTTGTCATTCGGGAAATCGTGCCTCTTGAAACCTTTGAATG
* *
62429 TGTGTTTCTTTGCCTCTTTATGCCTTCTTATTTTTCCATAGGGGATTCTTCTTCTTCGCCGATCA
66 AGTGTTTCTTTGCCTCTTTATGCCTTCTTATTTTTCCATAGGGGATTCTTCTTCTGCGCCGATCA
* *
62494 TGATTACATCAGAGGATAAGTTTAGTCCTATCTTTATA
131 TGATTACATCAGAGGATAAGTTCAATCCTATCTTTATA
* *
62532 TCTCAGGCCTGCTGATATCTTTTCTTTGTCATTCGGGAAATCGTGCCTTGTTGATCTTGAGACCT
1 TCTCAGGCATGCTGATATCTTTTCTTTGTCATTCGGGAAATCGTGCC-------TCTTGAAACCT
* *
62597 TTGAATGAGTGTTTCTTTTCCTCTTTATGCCTTCTTCTTTTTCCATAGGGGATTCTTCTTCTGCG
59 TTGAATGAGTGTTTCTTTGCCTCTTTATGCCTTCTTATTTTTCCATAGGGGATTCTTCTTCTGCG
* *
62662 CCGATCATTATTACATCAGAGGATAAGTTCAATCCTGTCTTTATA
124 CCGATCATGATTACATCAGAGGATAAGTTCAATCCTATCTTTATA
62707 TC
1 TC
62709 ATTTCTTATA
Statistics
Matches: 157, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
168 43 0.27
175 114 0.73
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.43
Consensus pattern (168 bp):
TCTCAGGCATGCTGATATCTTTTCTTTGTCATTCGGGAAATCGTGCCTCTTGAAACCTTTGAATG
AGTGTTTCTTTGCCTCTTTATGCCTTCTTATTTTTCCATAGGGGATTCTTCTTCTGCGCCGATCA
TGATTACATCAGAGGATAAGTTCAATCCTATCTTTATA
Found at i:64043 original size:2 final size:2
Alignment explanation
Indices: 64036--64060 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
64026 AAGAACATAA
64036 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
64061 AACTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66726 original size:29 final size:29
Alignment explanation
Indices: 66684--66762 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
66674 CGGTGATAGA
* * *
66684 TATATTTATCGATCTAATACCAGTCAGAT
1 TATATTTTTCGATCTAACACCAGTCAGAC
* *
66713 TATATTTTTTGATCTAACACTAGTCAGAC
1 TATATTTTTCGATCTAACACCAGTCAGAC
66742 TATATTTTTCGATCTAACACC
1 TATATTTTTCGATCTAACACC
66763 CTTAGCAGTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.41
Consensus pattern (29 bp):
TATATTTTTCGATCTAACACCAGTCAGAC
Found at i:67134 original size:9 final size:9
Alignment explanation
Indices: 67122--67173 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
67112 TAATATTTTG
67122 TATTTAATT
1 TATTTAATT
*
67131 TATTTAA-G
1 TATTTAATT
67139 TATTTAATT
1 TATTTAATT
67148 TATTTAA--
1 TATTTAATT
* *
67155 TATTTTACT
1 TATTTAATT
67164 TATTTAATT
1 TATTTAATT
67173 T
1 T
67174 TTTTGCAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:67143 original size:17 final size:17
Alignment explanation
Indices: 67121--67170 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
67111 TTAATATTTT
67121 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
67138 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
67155 -TATTTTACTTATTTAA
1 GTATTTAATTTATTTAA
67171 TTTTTTTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:67166 original size:16 final size:16
Alignment explanation
Indices: 67130--67175 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
67120 TGTATTTAAT
* *
67130 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTTAC
67147 TTATTTAATATTTTAC
1 TTATTTAATATTTTAC
67163 TTATTTAAT-TTTT
1 TTATTTAATATTTT
67176 TTGCAGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTAATATTTTAC
Found at i:69051 original size:9 final size:9
Alignment explanation
Indices: 69039--69095 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
69029 TAATATTTTG
69039 TATTTAATT
1 TATTTAATT
*
69048 TATTTAA-G
1 TATTTAATT
69056 TATTTAATT
1 TATTTAATT
69065 TATTTAA--
1 TATTTAATT
*
69072 TATTTTATT
1 TATTTAATT
*
69081 TAATTAATT
1 TATTTAATT
*
69090 TTTTTA
1 TATTTA
69096 CAGATATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
7 6 0.16
8 7 0.18
9 25 0.66
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
TATTTAATT
Found at i:69060 original size:17 final size:17
Alignment explanation
Indices: 69038--69087 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
69028 TTAATATTTT
69038 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
69055 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
69072 -TATTTTATTTAATTAA
1 GTATTTAATTTATTTAA
69088 TTTTTTTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:72396 original size:30 final size:29
Alignment explanation
Indices: 72334--72409 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
72324 TTCTGCAAAG
* * *
72334 GGTGTTAGATCGAGAAATATAGTCTGAAC
1 GGTGTTTGATCGGGAAATATAGTCTCAAC
72363 GGTGTTTGATCGGGAAATATATTGT-TCAAC
1 GGTGTTTGATCGGGAAATATA--GTCTCAAC
*
72393 GGTGATAT-ATCGGGAAA
1 GGTG-TTTGATCGGGAAA
72410 ATCGCCATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 19 0.47
30 17 0.43
31 4 0.10
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (29 bp):
GGTGTTTGATCGGGAAATATAGTCTCAAC
Found at i:75033 original size:36 final size:36
Alignment explanation
Indices: 74926--75034 Score: 173
Period size: 36 Copynumber: 3.0 Consensus size: 36
74916 ACATCGGTTT
*
74926 ATCTTGAACCTCACCTATATCCTTCACTTGAAGACA
1 ATCTTGAACCTCACCTATATCCTTCACTTGAAGACG
* *
74962 ATCTTAAACCTCATCTATATCCTTCACTTGAAGACG
1 ATCTTGAACCTCACCTATATCCTTCACTTGAAGACG
* *
74998 ATCTTGAACCTCACCCATATCCATCACTTGAAGACG
1 ATCTTGAACCTCACCTATATCCTTCACTTGAAGACG
75034 A
1 A
75035 CTAGTGAGGT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.31, C:0.30, G:0.09, T:0.29
Consensus pattern (36 bp):
ATCTTGAACCTCACCTATATCCTTCACTTGAAGACG
Found at i:79803 original size:22 final size:23
Alignment explanation
Indices: 79768--79815 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
79758 TTCATGTACT
79768 TGAGAGTCGAAAAACA-TAACGG
1 TGAGAGTCGAAAAACATTAACGG
* *
79790 TGAGATTCGGAAAACATTAACGG
1 TGAGAGTCGAAAAACATTAACGG
79813 TGA
1 TGA
79816 CACTTGGTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.19
Consensus pattern (23 bp):
TGAGAGTCGAAAAACATTAACGG
Found at i:81675 original size:23 final size:22
Alignment explanation
Indices: 81631--81675 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
81621 AATCTCATAG
*
81631 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
81653 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
81676 AAATGTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:83124 original size:102 final size:104
Alignment explanation
Indices: 82958--83171 Score: 362
Period size: 102 Copynumber: 2.1 Consensus size: 104
82948 GTCCTTCGGA
* *
82958 AATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCATTGGCATATG
1 AATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCACTAGCATATG
83023 TATATGATTCTTAAGGAATGATATGTGGTCCTT-TGGGAC
66 TATATGATTCTTAAGGAATGATATGTGGTCCTTAT-GGAC
* *
83062 -ATATATGTA-TCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGTATATG
1 AATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCACTAGCATATG
83125 TATATGATTCTTAAGGAATGATATGTGGTCCTTATGGAC
66 TATATGATTCTTAAGGAATGATATGTGGTCCTTATGGAC
83164 AATATATG
1 AATATATG
83172 ATATGCAATT
Statistics
Matches: 104, Mismatches: 4, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
102 87 0.84
103 17 0.16
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (104 bp):
AATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCACTAGCATATG
TATATGATTCTTAAGGAATGATATGTGGTCCTTATGGAC
Found at i:83201 original size:21 final size:22
Alignment explanation
Indices: 83175--83226 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
83165 ATATATGATA
83175 TGCAATTCTACACGGCACT-CG
1 TGCAATTCTACACGGCACTCCG
**
83196 TGCAA-TCTACGTGGCACTCCG
1 TGCAATTCTACACGGCACTCCG
83217 TGCAATTCTA
1 TGCAATTCTA
83227 TGTGGTGCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 11 0.41
21 12 0.44
22 4 0.15
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (22 bp):
TGCAATTCTACACGGCACTCCG
Found at i:83242 original size:24 final size:21
Alignment explanation
Indices: 83188--83242 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 21
83178 AATTCTACAC
83188 GGCAC-TCGTGCAATCTACGT
1 GGCACTTCGTGCAATCTACGT
* *
83208 GGCACTCCGTGCAATTCTATGT
1 GGCACTTCGTGCAA-TCTACGT
83230 GGTGCACTTCGTG
1 -G-GCACTTCGTG
83243 GCACTCGGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 6 0.21
23 1 0.04
24 9 0.32
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.29
Consensus pattern (21 bp):
GGCACTTCGTGCAATCTACGT
Done.