Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005266.1 Hibiscus syriacus cultivar Beakdansim tig00011909_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: 103611
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:5225 original size:2 final size:2
Alignment explanation
Indices: 5218--5254 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5208 GACGAAGAAA
5218 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
5255 AAAAACATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7678 original size:13 final size:14
Alignment explanation
Indices: 7667--7695 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7657 ATAACAAACG
7667 AAAATTGAAAACTA
1 AAAATTGAAAACTA
7681 AAAATTGAAAA-TA
1 AAAATTGAAAACTA
7694 AA
1 AA
7696 TTAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.21
Consensus pattern (14 bp):
AAAATTGAAAACTA
Found at i:8922 original size:23 final size:23
Alignment explanation
Indices: 8871--8922 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
8861 CAATCTGTTT
8871 ATTGGACCTTCTAGAAGTTACTA
1 ATTGGACCTTCTAGAAGTTACTA
* * * *
8894 ACTGGACCTTGTAGAAGTTGCTG
1 ATTGGACCTTCTAGAAGTTACTA
8917 ATTGGA
1 ATTGGA
8923 TGCCACATCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (23 bp):
ATTGGACCTTCTAGAAGTTACTA
Found at i:10190 original size:31 final size:31
Alignment explanation
Indices: 10154--10263 Score: 107
Period size: 31 Copynumber: 3.4 Consensus size: 31
10144 TTAGGTCTAT
*
10154 AAGGAATTACCAGTCAATGTTGAACCTATAA
1 AAGGAATTACCAGTCAATGCTGAACCTATAA
*
10185 AAGGAATTACCAG-CAGA-GACTGAACCTACCAGA
1 AAGGAATTACCAGTCA-ATG-CTGAACCTA-TA-A
* *
10218 GATAGGAATTACCAGTCGATGCTGAACCTATAC
1 -A-AGGAATTACCAGTCAATGCTGAACCTATAA
*
10251 AAGGAATGACCAG
1 AAGGAATTACCAG
10264 CAGCGACTGA
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
30 3 0.05
31 33 0.51
32 2 0.03
33 1 0.02
34 2 0.03
35 22 0.34
36 2 0.03
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (31 bp):
AAGGAATTACCAGTCAATGCTGAACCTATAA
Found at i:10228 original size:35 final size:34
Alignment explanation
Indices: 10186--10298 Score: 110
Period size: 35 Copynumber: 3.4 Consensus size: 34
10176 AACCTATAAA
10186 AGGAATTACCAGCAGAGACTGAACCTACCAGAGAT
1 AGGAATTACCAGCAGAGACTGAACCT-CCAGAGAT
* *
10221 AGGAATTACCAGTC-GATG-CTGAACCT--ATACA-
1 AGGAATTACCAG-CAGA-GACTGAACCTCCAGAGAT
* *
10252 AGGAATGACCAGCAGCGACTGAACCTGCCAGAGAT
1 AGGAATTACCAGCAGAGACTGAACCT-CCAGAGAT
*
10287 AGAAATTACCAG
1 AGGAATTACCAG
10299 TCGATGTTGA
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
30 2 0.03
31 20 0.32
32 3 0.05
34 3 0.05
35 32 0.52
36 2 0.03
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (34 bp):
AGGAATTACCAGCAGAGACTGAACCTCCAGAGAT
Found at i:10337 original size:66 final size:66
Alignment explanation
Indices: 10158--10342 Score: 257
Period size: 66 Copynumber: 2.8 Consensus size: 66
10148 GTCTATAAGG
* *
10158 AATTACCAGTCAATGTTGAACCTATAAAAGGAATTACCAGCAGA-GACTGAACCTACCAGAGATA
1 AATTACCAGTCGATGTTGAACCTATACAAGGAATTACCAGCA-ACGACTGAACCTACCAGAGATA
*
10222 GG
65 GA
* * * *
10224 AATTACCAGTCGATGCTGAACCTATACAAGGAATGACCAGCAGCGACTGAACCTGCCAGAGATAG
1 AATTACCAGTCGATGTTGAACCTATACAAGGAATTACCAGCAACGACTGAACCTACCAGAGATAG
10289 A
66 A
* *
10290 AATTACCAGTCGATGTTGAACCTA-ATCAATGAATTACTAGCAACGACTGAACC
1 AATTACCAGTCGATGTTGAACCTATA-CAAGGAATTACCAGCAACGACTGAACC
10343 CGTTAGAGTC
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
65 1 0.01
66 104 0.99
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (66 bp):
AATTACCAGTCGATGTTGAACCTATACAAGGAATTACCAGCAACGACTGAACCTACCAGAGATAG
A
Found at i:17491 original size:35 final size:33
Alignment explanation
Indices: 17442--17530 Score: 94
Period size: 33 Copynumber: 2.7 Consensus size: 33
17432 CAAAAAATTG
*
17442 TTTTCAAAAC-TATAATATATGTTTTAAATCGTA
1 TTTTCAAAACATATAATATATGTTTTAAACCG-A
*
17475 TTTTCAAAACCATATAATATGT-TTTTAAACCGA
1 TTTTCAAAA-CATATAATATATGTTTTAAACCGA
*
17508 TTTTTAAAA-ATATATATTATATG
1 TTTTCAAAACATATA-A-TATATG
17531 CTTAGAAAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
31 5 0.11
32 1 0.02
33 22 0.47
34 10 0.21
35 9 0.19
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (33 bp):
TTTTCAAAACATATAATATATGTTTTAAACCGA
Found at i:21107 original size:22 final size:22
Alignment explanation
Indices: 21061--21109 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
21051 TAACTTTTCG
*
21061 GTCAAAGTCAACGGTCAGACTA
1 GTCAAAGTCAACGGTCAGACCA
*
21083 GTCAAAGTCAATGGTCTA-ACCA
1 GTCAAAGTCAACGGTC-AGACCA
21105 GTCAA
1 GTCAA
21110 CTCTGACCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (22 bp):
GTCAAAGTCAACGGTCAGACCA
Found at i:22708 original size:23 final size:23
Alignment explanation
Indices: 22674--22730 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
22664 TTTATAAATA
22674 CAAAAGTAAAATTTTACAATATT
1 CAAAAGTAAAATTTTACAATATT
*
22697 CAAGAGTAAAATTTTACAATATT
1 CAAAAGTAAAATTTTACAATATT
22720 CAAAAGTAAAA
1 CAAAAGTAAAA
22731 CAAATTTCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (23 bp):
CAAAAGTAAAATTTTACAATATT
Found at i:24842 original size:18 final size:17
Alignment explanation
Indices: 24810--24843 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
24800 TCTTAGAAAT
*
24810 ACTTTAGGTTATTTTAC
1 ACTTTAGGGTATTTTAC
24827 ACTTTAGGGGTATTTTA
1 ACTTTA-GGGTATTTTA
24844 GTCATTTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.50
Consensus pattern (17 bp):
ACTTTAGGGTATTTTAC
Found at i:25794 original size:20 final size:20
Alignment explanation
Indices: 25769--25837 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 20
25759 GGGGAATTGG
*
25769 TACCCCCTGGGGGTAATCTA
1 TACCCCCTGGGGGGAATCTA
* *
25789 T-TCCCCTAGGGGGGAATCTG
1 TACCCCCT-GGGGGGAATCTA
*
25809 TACCCCCTGGGGGAGAATCTG
1 TACCCCCTGGGGG-GAATCTA
25830 TACCCCCT
1 TACCCCCT
25838 AGGAAATCTG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 5 0.12
20 17 0.40
21 20 0.48
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.23
Consensus pattern (20 bp):
TACCCCCTGGGGGGAATCTA
Found at i:25815 original size:21 final size:20
Alignment explanation
Indices: 25758--25837 Score: 92
Period size: 20 Copynumber: 4.0 Consensus size: 20
25748 CCGTTAGACA
25758 GGGGGAAT-TGGTACCCCCTG
1 GGGGGAATCT-GTACCCCCTG
* * *
25778 GGGGTAATCTAT-TCCCCTAG
1 GGGGGAATCTGTACCCCCT-G
25798 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
25818 GGGGAGAATCTGTACCCCCT
1 GGGG-GAATCTGTACCCCCT
25838 AGGAAATCTG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
19 5 0.10
20 24 0.48
21 21 0.42
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.23
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:29214 original size:21 final size:20
Alignment explanation
Indices: 29167--29271 Score: 97
Period size: 21 Copynumber: 5.0 Consensus size: 20
29157 CCGTTAGACA
*
29167 GGGGGAATCGGTATCCCCTGG
1 GGGGGAATC-GTACCCCCTGG
29188 GAGGGGAATCGATACCCCCTGG
1 G-GGGGAATCG-TACCCCCTGG
*
29210 GGGGGAATCTGTTCCCCCT--
1 GGGGGAATC-GTACCCCCTGG
* *
29229 AGGGGAATCTGTACCCCTTGG
1 GGGGGAATC-GTACCCCCTGG
*
29250 GGGGGAATCGGTACCCCATGG
1 GGGGGAATC-GTACCCCCTGG
29271 G
1 G
29272 CAATCTGATT
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
19 16 0.23
21 36 0.51
22 19 0.27
ACGTcount: A:0.17, C:0.26, G:0.38, T:0.19
Consensus pattern (20 bp):
GGGGGAATCGTACCCCCTGG
Found at i:29251 original size:18 final size:19
Alignment explanation
Indices: 29211--29251 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
29201 ACCCCCTGGG
*
29211 GGGGAATCTGTTCCCCCTA
1 GGGGAATCTGTTACCCCTA
*
29230 GGGGAATCTG-TACCCCTT
1 GGGGAATCTGTTACCCCTA
29248 GGGG
1 GGGG
29252 GGGAATCGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.15, C:0.27, G:0.34, T:0.24
Consensus pattern (19 bp):
GGGGAATCTGTTACCCCTA
Found at i:29252 original size:19 final size:19
Alignment explanation
Indices: 29210--29271 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
29200 TACCCCCTGG
* *
29210 GGGGGAATCTGTTCCCCCT
1 GGGGGAATCTGTACCCCAT
* *
29229 AGGGGAATCTGTACCCCTT
1 GGGGGAATCTGTACCCCAT
*
29248 GGGGGGGAATCGGTACCCCAT
1 --GGGGGAATCTGTACCCCAT
29269 GGG
1 GGG
29272 CAATCTGATT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 19 0.54
21 16 0.46
ACGTcount: A:0.16, C:0.26, G:0.37, T:0.21
Consensus pattern (19 bp):
GGGGGAATCTGTACCCCAT
Found at i:30450 original size:22 final size:20
Alignment explanation
Indices: 30410--30450 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
30400 TTCAATAATT
*
30410 ACCTTAATCAATCCAAAACA
1 ACCTTAATCAAACCAAAACA
30430 ACCTTAATCATAAACCAAAAC
1 ACCTTAATC--AAACCAAAAC
30451 CAACAGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (20 bp):
ACCTTAATCAAACCAAAACA
Found at i:40410 original size:57 final size:57
Alignment explanation
Indices: 40273--40392 Score: 186
Period size: 57 Copynumber: 2.1 Consensus size: 57
40263 GATAGCTCCC
* * ** *
40273 ATTCTGCAGGGGATTCCACTGATTAGGCCTTTCTCGTTGAGAATAACCCTGGTCCTG
1 ATTCTGCTGAGGATTCCACTGATTAGGAATTTCTCGTTGAGAATAACCCTGGCCCTG
*
40330 ATTCTGCTGAGGATTCCACTGATTAGGAATTTCTCGTTGAGAATAACCGTGGCCCTG
1 ATTCTGCTGAGGATTCCACTGATTAGGAATTTCTCGTTGAGAATAACCCTGGCCCTG
40387 ATTCTG
1 ATTCTG
40393 GCGGGTATTC
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.33
Consensus pattern (57 bp):
ATTCTGCTGAGGATTCCACTGATTAGGAATTTCTCGTTGAGAATAACCCTGGCCCTG
Found at i:45741 original size:23 final size:23
Alignment explanation
Indices: 45715--45783 Score: 120
Period size: 23 Copynumber: 3.0 Consensus size: 23
45705 AGCTCCACTG
*
45715 AATTACAGCTGCCTTAATTTGAC
1 AATTGCAGCTGCCTTAATTTGAC
*
45738 AATTGCAACTGCCTTAATTTGAC
1 AATTGCAGCTGCCTTAATTTGAC
45761 AATTGCAGCTGCCTTAATTTGAC
1 AATTGCAGCTGCCTTAATTTGAC
45784 TCTTAACAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (23 bp):
AATTGCAGCTGCCTTAATTTGAC
Found at i:47052 original size:15 final size:18
Alignment explanation
Indices: 47008--47052 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
46998 CCTAAAGTAC
47008 TATTA-TTGATAATAAAT
1 TATTATTTGATAATAAAT
*
47025 TATTATTTAATAAT-AAT
1 TATTATTTGATAATAAAT
47042 T-TT-TTTGATAA
1 TATTATTTGATAA
47053 ACCAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 7 0.28
16 2 0.08
17 9 0.36
18 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (18 bp):
TATTATTTGATAATAAAT
Found at i:54738 original size:15 final size:16
Alignment explanation
Indices: 54712--54741 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54702 ATAACAATTA
54712 TATCACTTTCATTTCT
1 TATCACTTTCATTTCT
54728 TATCA-TTTCATTTC
1 TATCACTTTCATTTC
54742 CTTCATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.23, G:0.00, T:0.57
Consensus pattern (16 bp):
TATCACTTTCATTTCT
Found at i:61988 original size:20 final size:19
Alignment explanation
Indices: 61921--62071 Score: 151
Period size: 20 Copynumber: 7.7 Consensus size: 19
61911 GAATAACCAA
61921 CAAATTCGCAACACGATTT
1 CAAATTCGCAACACGATTT
61940 CAAATTCGCAACACGATTT
1 CAAATTCGCAACACGATTT
* *
61959 CAAATTCGCAACACGAACTC
1 CAAATTCGCAACACG-ATTT
*
61979 CAATTTCGCAACAC-ATTT
1 CAAATTCGCAACACGATTT
* *
61997 CTAAATTCGCAACTCAGTTTT
1 C-AAATTCGCAACAC-GATTT
*
62018 CAAATTCGCAACTCGAATTT
1 CAAATTCGCAACACG-ATTT
*** *
62038 CTTTTTCGCAACTCGATTTT
1 CAAATTCGCAACACGA-TTT
*
62058 TAAATTCGCAACAC
1 CAAATTCGCAACAC
62072 AAGAGTCCTT
Statistics
Matches: 109, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
18 3 0.03
19 47 0.43
20 55 0.50
21 4 0.04
ACGTcount: A:0.33, C:0.27, G:0.09, T:0.30
Consensus pattern (19 bp):
CAAATTCGCAACACGATTT
Found at i:62026 original size:39 final size:40
Alignment explanation
Indices: 61922--62071 Score: 148
Period size: 39 Copynumber: 3.8 Consensus size: 40
61912 AATAACCAAC
61922 AAATTCGCAACACG-ATTTCAAATTCGCAACACGATTTC-
1 AAATTCGCAACACGAATTTCAAATTCGCAACACGATTTCT
* * *
61960 AAATTCGCAACACGAACTCCAATTTCGCAACAC-ATTTCT
1 AAATTCGCAACACGAATTTCAAATTCGCAACACGATTTCT
* * *
61999 AAATTCGCAACTC-AGTTTTCAAATTCGCAACTCGAATTTCT
1 AAATTCGCAACACGA-ATTTCAAATTCGCAACACG-ATTTCT
** * * *
62040 -TTTTCGCAACTCGATTTTTAAATTCGCAACAC
1 AAATTCGCAACACGAATTTCAAATTCGCAACAC
62072 AAGAGTCCTT
Statistics
Matches: 93, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
38 20 0.22
39 40 0.43
40 26 0.28
41 7 0.08
ACGTcount: A:0.33, C:0.27, G:0.09, T:0.31
Consensus pattern (40 bp):
AAATTCGCAACACGAATTTCAAATTCGCAACACGATTTCT
Found at i:62157 original size:21 final size:19
Alignment explanation
Indices: 61925--62163 Score: 83
Period size: 20 Copynumber: 12.2 Consensus size: 19
61915 AACCAACAAA
* **
61925 TTCGCAACACGATTTCAAA
1 TTCGCAACACGATTTTATT
* **
61944 TTCGCAACACGATTTCAAA
1 TTCGCAACACGATTTTATT
* ** *
61963 TTCGCAACACGAACTCCAAT
1 TTCGCAACACG-ATTTTATT
**
61983 TTCGCAACAC-ATTTCTAAA
1 TTCGCAACACGATTT-TATT
* **
62002 TTCGCAACTC-AGTTTTCAAA
1 TTCGCAACACGA-TTTT-ATT
*
62022 TTCGCAACTCGAATTTCT-TT
1 TTCGCAACACG-ATTT-TATT
* **
62042 TTCGCAACTCGATTTTTAAA
1 TTCGCAACACGA-TTTTATT
* **
62062 TTCGCAACACAAGA-GTCCTT
1 TTCGCAACAC--GATTTTATT
* *
62082 TTCGCAACAAGATTTTATAA
1 TTCGCAACACGATTTTAT-T
**
62102 TTCGCAA-AGCGCGTTTATT
1 TTCGCAACA-CGATTTTATT
62121 TTCGCAACACGATTTTTATT
1 TTCGCAACACGA-TTTTATT
*
62141 TTCGCAACGCGGATTTTATT
1 TTCGCAACAC-GATTTTATT
62161 TTC
1 TTC
62164 AAAATCGAAA
Statistics
Matches: 173, Mismatches: 30, Indels: 33
0.73 0.13 0.14
Matches are distributed among these distances:
18 4 0.02
19 57 0.33
20 103 0.60
21 5 0.03
22 4 0.02
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (19 bp):
TTCGCAACACGATTTTATT
Found at i:62814 original size:34 final size:34
Alignment explanation
Indices: 62756--62824 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
62746 TAGTTTTCGC
* * *
62756 GTTGCGAATTTCGTGTTGCAAATTTCATTTTCAA
1 GTTGCGAATTTCATGTTGCAAATTTAAGTTTCAA
* **
62790 GTTGCGATTTTCATGTTGTGAATTTAAGTTTCAA
1 GTTGCGAATTTCATGTTGCAAATTTAAGTTTCAA
62824 G
1 G
62825 AATAAACTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (34 bp):
GTTGCGAATTTCATGTTGCAAATTTAAGTTTCAA
Found at i:64249 original size:42 final size:42
Alignment explanation
Indices: 64183--64309 Score: 164
Period size: 42 Copynumber: 3.0 Consensus size: 42
64173 CCCTACTTTT
* * *
64183 TCATCGAGTCGATTCTTCAGTTCGACACCGAGATGCATCACC
1 TCATCGAGTCGATTCTACACTTCGACACCGAGATACATCACC
* * *
64225 TCATCGAGTCGATTCTCCACTTCGACACCAAGATCCATCACC
1 TCATCGAGTCGATTCTACACTTCGACACCGAGATACATCACC
* * **
64267 TGATCGAGTCGATTCTATACCACGACACCGAGATACATCACC
1 TCATCGAGTCGATTCTACACTTCGACACCGAGATACATCACC
64309 T
1 T
64310 ATTCCATCAC
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.27, C:0.33, G:0.16, T:0.24
Consensus pattern (42 bp):
TCATCGAGTCGATTCTACACTTCGACACCGAGATACATCACC
Found at i:64495 original size:63 final size:62
Alignment explanation
Indices: 64439--64620 Score: 202
Period size: 63 Copynumber: 2.9 Consensus size: 62
64429 TGATGAGTTA
64439 GGTGCTTTATGTGATGAGGTCAGTGCTTTACGTGATGAGGTCGGTACTTTACGTGATGACAAT
1 GGTGCTTTATGTGATGAGGT-AGTGCTTTACGTGATGAGGTCGGTACTTTACGTGATGACAAT
* ** * * * * * * ** *
64502 GGTGCATGGTGTGATGAGGTAGGGTCTTTACGTGGTGAGTTAGCTATTTTGTGTGATAACAAT
1 GGTGCTTTATGTGATGAGGTAGTG-CTTTACGTGATGAGGTCGGTACTTTACGTGATGACAAT
* * *
64565 GGTGCTTTATGTGGTGAGGTAGTTGCTTTACGTGATGAGGTCGGTGCTCTACGTGA
1 GGTGCTTTATGTGATGAGGTAG-TGCTTTACGTGATGAGGTCGGTACTTTACGTGA
64621 GATTGTTTCA
Statistics
Matches: 91, Mismatches: 26, Indels: 4
0.75 0.21 0.03
Matches are distributed among these distances:
62 3 0.03
63 87 0.96
64 1 0.01
ACGTcount: A:0.19, C:0.11, G:0.35, T:0.36
Consensus pattern (62 bp):
GGTGCTTTATGTGATGAGGTAGTGCTTTACGTGATGAGGTCGGTACTTTACGTGATGACAAT
Found at i:64612 original size:21 final size:21
Alignment explanation
Indices: 64409--64620 Score: 117
Period size: 21 Copynumber: 10.1 Consensus size: 21
64399 ACCTCCACAG
* *
64409 GATGAGTTAGGTGCTTTATGT
1 GATGAGGTAGGTGCTTTACGT
* *
64430 GATGAGTTAGGTGCTTTATGT
1 GATGAGGTAGGTGCTTTACGT
64451 GATGAGGTCA-GTGCTTTACGT
1 GATGAGGT-AGGTGCTTTACGT
* *
64472 GATGAGGTCGGTACTTTACGT
1 GATGAGGTAGGTGCTTTACGT
** * ***
64493 GATGA-CAATGGTGCATGGTGT
1 GATGAGGTA-GGTGCTTTACGT
64514 GATGAGGTAGG-GTCTTTACGT
1 GATGAGGTAGGTG-CTTTACGT
* * * ** **
64535 GGTGAGTTAGCTATTTTGTGT
1 GATGAGGTAGGTGCTTTACGT
*** *
64556 GAT-AACAATGGTGCTTTATGT
1 GATGAGGTA-GGTGCTTTACGT
* *
64577 GGTGAGGTAGTTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* *
64598 GATGAGGTCGGTGCTCTACGT
1 GATGAGGTAGGTGCTTTACGT
64619 GA
1 GA
64621 GATTGTTTCA
Statistics
Matches: 140, Mismatches: 43, Indels: 16
0.70 0.22 0.08
Matches are distributed among these distances:
20 3 0.02
21 133 0.95
22 4 0.03
ACGTcount: A:0.19, C:0.10, G:0.34, T:0.36
Consensus pattern (21 bp):
GATGAGGTAGGTGCTTTACGT
Found at i:64982 original size:18 final size:18
Alignment explanation
Indices: 64959--64993 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
64949 TTCACCTCTT
64959 ATCGTTCAAGAGGCCCCC
1 ATCGTTCAAGAGGCCCCC
64977 ATCGTTCAAGAGGCCCC
1 ATCGTTCAAGAGGCCCC
64994 TCCCATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.37, G:0.23, T:0.17
Consensus pattern (18 bp):
ATCGTTCAAGAGGCCCCC
Found at i:65069 original size:21 final size:21
Alignment explanation
Indices: 64905--65075 Score: 127
Period size: 21 Copynumber: 8.3 Consensus size: 21
64895 GAAGAAGCCT
* * *
64905 GATCCACCTACCATTGTTCAA
1 GATCCACCTCCCATCGTTCAG
* *
64926 GATCCATCTCCCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
* ** *
64947 GATTCACCTCTTATCGTTCAA
1 GATCCACCTCCCATCGTTCAG
** *
64968 GA--GGCC-CCCATCGTTCAA
1 GATCCACCTCCCATCGTTCAG
* *
64986 GAGGCC-CCTCCCATCATTCAAG
1 GA-TCCACCTCCCATCGTTC-AG
* * *
65008 AAGCC-CCTCCCATCATTCAG
1 GATCCACCTCCCATCGTTCAG
*
65028 GATCCACCTCCCATCATTCAG
1 GATCCACCTCCCATCGTTCAG
65049 GATCCACCTCCCATCGTTCAG
1 GATCCACCTCCCATCGTTCAG
65070 GATCCA
1 GATCCA
65076 TATTTCATAC
Statistics
Matches: 124, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
18 12 0.10
19 2 0.02
20 7 0.06
21 101 0.81
22 2 0.02
ACGTcount: A:0.23, C:0.38, G:0.13, T:0.25
Consensus pattern (21 bp):
GATCCACCTCCCATCGTTCAG
Found at i:66637 original size:20 final size:20
Alignment explanation
Indices: 66612--66738 Score: 121
Period size: 20 Copynumber: 6.3 Consensus size: 20
66602 ATACGTTTAA
*
66612 GAAAATCAAATTCGCAACGC
1 GAAAATCAAATTCGCAACAC
*
66632 GAAAATCAAATTCGCAACTC
1 GAAAATCAAATTCGCAACAC
*
66652 -AATATTCAAATTCGCAACAC
1 GAA-AATCAAATTCGCAACAC
* * **
66672 GAAAATCGAATTCGTAACGT
1 GAAAATCAAATTCGCAACAC
*** **
66692 GAAAATCGGTTTCGCAATTC
1 GAAAATCAAATTCGCAACAC
*
66712 GAAAATCAAATTTGCAACAC
1 GAAAATCAAATTCGCAACAC
66732 GAAAATC
1 GAAAATC
66739 GCATTGCGAA
Statistics
Matches: 85, Mismatches: 20, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
19 2 0.02
20 81 0.95
21 2 0.02
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.22
Consensus pattern (20 bp):
GAAAATCAAATTCGCAACAC
Found at i:66706 original size:60 final size:60
Alignment explanation
Indices: 66612--66739 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
66602 ATACGTTTAA
* *
66612 GAAAATCAAATTCGCAACGCGAAAATCAAATTCGCAACTC-AATATTCAAATTCGCAACAC
1 GAAAATCGAATTCGCAACGCGAAAATCAAATTCGCAACTCGAA-AATCAAATTCGCAACAC
* * *** * *
66672 GAAAATCGAATTCGTAACGTGAAAATCGGTTTCGCAATTCGAAAATCAAATTTGCAACAC
1 GAAAATCGAATTCGCAACGCGAAAATCAAATTCGCAACTCGAAAATCAAATTCGCAACAC
66732 GAAAATCG
1 GAAAATCG
66740 CATTGCGAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 56 0.97
61 2 0.03
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.22
Consensus pattern (60 bp):
GAAAATCGAATTCGCAACGCGAAAATCAAATTCGCAACTCGAAAATCAAATTCGCAACAC
Found at i:72045 original size:103 final size:103
Alignment explanation
Indices: 71866--72091 Score: 373
Period size: 103 Copynumber: 2.2 Consensus size: 103
71856 GTCGAGGGTC
*
71866 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTAGAACATGTGTAAAGTCTGGTGAGACACATAC
71931 TTGATCCCTAGTATATATATATGATTATTAAGGAATGA
66 TTGATCCCTAGTATATATATATGATTATTAAGGAATGA
* * *
71969 TATGTGGTCTTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTAGAACATGTGTAAAGTCTGGTGAGACACATAC
* * *
72034 TTGATCCCTAGTATATGTATATGATTCTTTAGGAATGA
66 TTGATCCCTAGTATATATATATGATTATTAAGGAATGA
72072 TATGTGGTCCTT-ATGGACAT
1 TATGTGGTCCTTCA-GGACAT
72092 TATTATATGG
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCAGGACATATATGTATTCTTTAGAACATGTGTAAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATATATATGATTATTAAGGAATGA
Found at i:72167 original size:23 final size:23
Alignment explanation
Indices: 72099--72159 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
72089 CATTATTATA
*
72099 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
* *
72122 CGGCACTACGGTGTAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
72145 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
72160 TTTATATGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:73565 original size:20 final size:20
Alignment explanation
Indices: 73536--73622 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 20
73526 TTTATATACC
73536 AAAA-AAATTCATGTTGCAA
1 AAAAGAAATTCATGTTGCAA
73555 AAAAGAAATTCGA-GTTGCAA
1 AAAAGAAATTC-ATGTTGCAA
** * *
73575 AAAAGAAATTTGTGTTTCGA
1 AAAAGAAATTCATGTTGCAA
* * *
73595 AAAATAAATTCGTGTTGCGA
1 AAAAGAAATTCATGTTGCAA
73615 AAAAGAAA
1 AAAAGAAA
73623 ATCTAGTTGC
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
19 4 0.07
20 52 0.91
21 1 0.02
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.25
Consensus pattern (20 bp):
AAAAGAAATTCATGTTGCAA
Found at i:73584 original size:40 final size:40
Alignment explanation
Indices: 73536--73622 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
73526 TTTATATACC
73536 AAAA-AAATTCATGTTGCAAAAAAGAAATTCGAGTTGCAA
1 AAAAGAAATTCATGTTGCAAAAAAGAAATTCGAGTTGCAA
** * * * * *
73575 AAAAGAAATTTGTGTTTCGAAAAATAAATTCGTGTTGCGA
1 AAAAGAAATTCATGTTGCAAAAAAGAAATTCGAGTTGCAA
73615 AAAAGAAA
1 AAAAGAAA
73623 ATCTAGTTGC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 4 0.10
40 36 0.90
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.25
Consensus pattern (40 bp):
AAAAGAAATTCATGTTGCAAAAAAGAAATTCGAGTTGCAA
Found at i:73611 original size:60 final size:59
Alignment explanation
Indices: 73536--73716 Score: 163
Period size: 60 Copynumber: 3.0 Consensus size: 59
73526 TTTATATACC
* * *
73536 AAAAAAATTCATGTTGCAAAAAAGAAATTCGAGTTGCAAAAAAGAAATTTGTGTTTCGA
1 AAAAAAATTCATGTTGCAAAAAAGAAAATCGAGTTGCAAAAAAGAAATTCGTGTTGCGA
* * * ** *
73595 AAAATAAATTCGTGTTGCGAAAAAGAAAATCTAGTTGCGGAGAAGAAATTCGTGTTGCGA
1 AAAA-AAATTCATGTTGCAAAAAAGAAAATCGAGTTGCAAAAAAGAAATTCGTGTTGCGA
* ** *
73655 ATTCAAAAA-TCGA-GTTGCCAAATTA-AAAATCGTA-TTGCGAAAAAGAAATTCGTGTTGCGA
1 A--AAAAAATTC-ATGTTG-CAAAAAAGAAAATCG-AGTTGCAAAAAAGAAATTCGTGTTGCGA
73715 AA
1 AA
73717 TTGTCAAAAT
Statistics
Matches: 98, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
59 4 0.04
60 84 0.86
61 8 0.08
62 2 0.02
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (59 bp):
AAAAAAATTCATGTTGCAAAAAAGAAAATCGAGTTGCAAAAAAGAAATTCGTGTTGCGA
Found at i:73631 original size:20 final size:21
Alignment explanation
Indices: 73548--73716 Score: 106
Period size: 20 Copynumber: 8.4 Consensus size: 21
73538 AAAAATTCAT
* *
73548 GTTGCAAAAAAGAAATTCG-A
1 GTTGCGAAAAAGAAAATCGTA
* * *
73568 GTTGCAAAAAAGAAATTTGT-
1 GTTGCGAAAAAGAAAATCGTA
* * *
73588 GTTTCGAAAAATAAATTCGT-
1 GTTGCGAAAAAGAAAATCGTA
73608 GTTGCGAAAAAGAAAATC-TA
1 GTTGCGAAAAAGAAAATCGTA
* * *
73628 GTTGCGGAGAAGAAATTCGT-
1 GTTGCGAAAAAGAAAATCGTA
**
73648 GTTGCGAATTCA-AAAATCG-A
1 GTTGCGAA-AAAGAAAATCGTA
* *
73668 GTTGCCAAATTA-AAAATCGTA
1 GTTGCGAAA-AAGAAAATCGTA
*
73689 -TTGCGAAAAAGAAATTCGT-
1 GTTGCGAAAAAGAAAATCGTA
73708 GTTGCGAAA
1 GTTGCGAAA
73717 TTGTCAAAAT
Statistics
Matches: 119, Mismatches: 21, Indels: 18
0.75 0.13 0.11
Matches are distributed among these distances:
19 2 0.02
20 114 0.96
21 3 0.03
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (21 bp):
GTTGCGAAAAAGAAAATCGTA
Found at i:73773 original size:20 final size:19
Alignment explanation
Indices: 73640--73799 Score: 72
Period size: 20 Copynumber: 7.9 Consensus size: 19
73630 TGCGGAGAAG
*
73640 AAATTCGTGTTGCGAATTC
1 AAATTCGAGTTGCGAATTC
* * *
73659 AAAAATCGAGTTGCCAAATTA
1 -AAATTCGAGTTG-CGAATTC
* ***
73680 AAAATCGTA-TTGCGAAAAAG
1 AAATTCG-AGTTGCG-AATTC
*
73700 AAATTCGTGTTGCGAAATTGTC
1 AAATTCGAGTTGCG-AA-T-TC
* *
73722 AAAATCGAGTTGCGAATTT
1 AAATTCGAGTTGCGAATTC
* * *
73741 GACTTCTGTGTTGCGAATTCC
1 AAATTC-GAGTTGCGAATT-C
*
73762 AAATTCGAGTTGCGAAAAAT-
1 AAATTCGAGTTGCG--AATTC
73782 AAATTCGAGTTGCGAATT
1 AAATTCGAGTTGCGAATT
73800 TGAAAATTGA
Statistics
Matches: 104, Mismatches: 26, Indels: 22
0.68 0.17 0.14
Matches are distributed among these distances:
18 3 0.03
19 5 0.05
20 69 0.66
21 12 0.12
22 15 0.14
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.31
Consensus pattern (19 bp):
AAATTCGAGTTGCGAATTC
Found at i:73794 original size:40 final size:40
Alignment explanation
Indices: 73689--73816 Score: 116
Period size: 40 Copynumber: 3.1 Consensus size: 40
73679 AAAAATCGTA
* * *
73689 TTGCGAAAAAGAAATTCGTGTTGCGAAATTGTCAAAATCGAG
1 TTGCGAAAAATAAATTCGTGTTGCG-AATT-CCAAATTCGAG
** * *
73731 TTGCG-AATTTGACTTCTGTGTTGCGAATTCCAAATTCGAG
1 TTGCGAAAAATAAATTC-GTGTTGCGAATTCCAAATTCGAG
* **
73771 TTGCGAAAAATAAATTCGAGTTGCGAATTTGAAAATT-GAG
1 TTGCGAAAAATAAATTCGTGTTGCGAA-TTCCAAATTCGAG
73811 TTGCGA
1 TTGCGA
73817 TTTTGTAAAT
Statistics
Matches: 69, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
40 32 0.46
41 24 0.35
42 13 0.19
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (40 bp):
TTGCGAAAAATAAATTCGTGTTGCGAATTCCAAATTCGAG
Found at i:73811 original size:20 final size:19
Alignment explanation
Indices: 73723--73880 Score: 102
Period size: 20 Copynumber: 8.0 Consensus size: 19
73713 GAAATTGTCA
*
73723 AAATCGAGTTGCGAATTTG
1 AAATTGAGTTGCGAATTTG
** * **
73742 ACTTCTGTGTTGCGAATTCC
1 AAAT-TGAGTTGCGAATTTG
**
73762 AAATTCGAGTTGCGAAAAAT-
1 AAATT-GAGTTGCG-AATTTG
73782 AAATTCGAGTTGCGAATTTG
1 AAATT-GAGTTGCGAATTTG
*
73802 AAAATTGAGTTGCGATTTTG
1 -AAATTGAGTTGCGAATTTG
* *
73822 TAAATTGTGTTGCGAAATTG
1 -AAATTGAGTTGCGAATTTG
* * *
73842 GAGTTCGTGTTGCGAATTTG
1 AAATT-GAGTTGCGAATTTG
* *
73862 AAATCGCGTTGCGAATTTG
1 AAATTGAGTTGCGAATTTG
73881 TTGGTTATTT
Statistics
Matches: 107, Mismatches: 26, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
19 22 0.21
20 78 0.73
21 7 0.07
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.35
Consensus pattern (19 bp):
AAATTGAGTTGCGAATTTG
Found at i:73834 original size:60 final size:59
Alignment explanation
Indices: 73700--73881 Score: 152
Period size: 60 Copynumber: 3.0 Consensus size: 59
73690 TGCGAAAAAG
* * ** * **
73700 AAATTCGTGTTGCGAAATTGTCAAAATCGAGTTGCGAATTTGACTTCTGTGTTGCGAA-TTCC
1 AAATT-GTGTTGCGAAAATG--AAATTCGAGTTGCGAATTTGAAATC-GAGTTGCGAATTTGT
* * *
73762 AAATTCGAGTTGCGAAAAAT-AAATTCGAGTTGCGAATTTGAAAATTGAGTTGCGATTTTGT
1 AAATT-GTGTTGCG-AAAATGAAATTCGAGTTGCGAATTTG-AAATCGAGTTGCGAATTTGT
* * * * *
73823 AAATTGTGTTGCGAAATTGGAGTTCGTGTTGCGAATTTGAAATCGCGTTGCGAATTTGT
1 AAATTGTGTTGCGAAAATGAAATTCGAGTTGCGAATTTGAAATCGAGTTGCGAATTTGT
73882 TGGTTATTTT
Statistics
Matches: 98, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
59 21 0.21
60 51 0.52
61 9 0.09
62 13 0.13
63 4 0.04
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.36
Consensus pattern (59 bp):
AAATTGTGTTGCGAAAATGAAATTCGAGTTGCGAATTTGAAATCGAGTTGCGAATTTGT
Found at i:75835 original size:16 final size:16
Alignment explanation
Indices: 75814--75859 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 16
75804 CGTGAATTTT
75814 TTTAAATTTCGCACAA
1 TTTAAATTTCGCACAA
75830 TTTAAATTTCGTCGCACAA
1 TTTAAA-TT--TCGCACAA
75849 TTTAAATTTCG
1 TTTAAATTTCG
75860 TCACTGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 9 0.33
17 2 0.07
18 2 0.07
19 14 0.52
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (16 bp):
TTTAAATTTCGCACAA
Found at i:75846 original size:19 final size:19
Alignment explanation
Indices: 75822--75861 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
75812 TTTTTAAATT
75822 TCGCACAATTTAAATTTCG
1 TCGCACAATTTAAATTTCG
75841 TCGCACAATTTAAATTTCG
1 TCGCACAATTTAAATTTCG
75860 TC
1 TC
75862 ACTGAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.38
Consensus pattern (19 bp):
TCGCACAATTTAAATTTCG
Found at i:78184 original size:2 final size:2
Alignment explanation
Indices: 78177--78201 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
78167 ATATTATCAC
78177 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 T
78202 GATCATCTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:81550 original size:13 final size:13
Alignment explanation
Indices: 81532--81559 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
81522 TTCATACGAA
81532 AAAATCTGTTGTT
1 AAAATCTGTTGTT
81545 AAAATCTGTTGTT
1 AAAATCTGTTGTT
81558 AA
1 AA
81560 TATATACACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (13 bp):
AAAATCTGTTGTT
Found at i:84199 original size:2 final size:2
Alignment explanation
Indices: 84192--84225 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
84182 TACTTTTTAA
84192 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
84226 TTAACTAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86685 original size:2 final size:2
Alignment explanation
Indices: 86678--86706 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
86668 TTATTTTTCA
86678 AT AT 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 AT AT A
86707 AGGGTTGCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:95454 original size:129 final size:129
Alignment explanation
Indices: 95224--95463 Score: 331
Period size: 129 Copynumber: 1.9 Consensus size: 129
95214 CGTTGATCGT
* * * *
95224 TGACTTTGACCAAAAATTTAAAATTTTTGAAAAGTCATATTTTATGTTATTCGACATTATGAGTC
1 TGACTTTGACCAAAAATTCAAAATTTTCGAAAAGTCATATTTTATGTTATTCGACATCATGAATC
* *
95289 CGAATCCGAAGTTCGTTTTTCAAAATTCAAACCCGAAAGCCTCGAAATTGTCAATAAAAAATGC
66 CGAATCCGAAGTTCGTTTTGCAAAATTCAAACCCGAAAGCCCCGAAATTGTCAATAAAAAATGC
** *
95353 TGACTTTGACCAAAAATTCAAAATTTTCGAAAAGTCATATTTTATGTT-TTCCGATGTCCTGAAT
1 TGACTTTGACCAAAAATTCAAAATTTTCGAAAAGTCATATTTTATGTTATT-CGACATCATGAAT
* * **
95417 CTGATTCCGAAGTTCGTTTTGGC-AAATTCTGACCCGAAAGCCCCGAA
65 CCGAATCCGAAGTTCGTTTT-GCAAAATTCAAACCCGAAAGCCCCGAA
95464 TCAGGCTCGT
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
128 2 0.02
129 93 0.97
130 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (129 bp):
TGACTTTGACCAAAAATTCAAAATTTTCGAAAAGTCATATTTTATGTTATTCGACATCATGAATC
CGAATCCGAAGTTCGTTTTGCAAAATTCAAACCCGAAAGCCCCGAAATTGTCAATAAAAAATGC
Found at i:96088 original size:44 final size:45
Alignment explanation
Indices: 96037--96135 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 45
96027 TCTATGACTT
* *
96037 GTAAGACCTTACCGTTTCCGCAGGCTTCC-CTGCTATGTGCA-AGG
1 GTAAGACCTTACCGTTACCGCAGGC-TCCTCTACTATGTGCACAGG
* * *
96081 GTAAGACCTCACTGTTACCGCAGGCTCCTCTACTTTGTGCACAGG
1 GTAAGACCTTACCGTTACCGCAGGCTCCTCTACTATGTGCACAGG
*
96126 ATAAGACCTT
1 GTAAGACCTT
96136 CCACATGCTC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
43 3 0.07
44 32 0.70
45 11 0.24
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.27
Consensus pattern (45 bp):
GTAAGACCTTACCGTTACCGCAGGCTCCTCTACTATGTGCACAGG
Found at i:101285 original size:18 final size:17
Alignment explanation
Indices: 101258--101304 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
101248 ATTGACCCGT
101258 CCGA-CGTTGACC-TGA
1 CCGATCGTTGACCGTGA
101273 CTCGATCCGTTGACCGTTGA
1 C-CGAT-CGTTGACCG-TGA
101293 CCGATCGTTGAC
1 CCGATCGTTGAC
101305 TTTGAGCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 3 0.11
18 15 0.56
19 4 0.15
20 4 0.15
ACGTcount: A:0.17, C:0.32, G:0.26, T:0.26
Consensus pattern (17 bp):
CCGATCGTTGACCGTGA
Found at i:102093 original size:39 final size:42
Alignment explanation
Indices: 102050--102136 Score: 117
Period size: 44 Copynumber: 2.1 Consensus size: 42
102040 GGAACATTTT
102050 CATATCTA-ATGTATT-ATT-TCGTTTGTACTCCAATACATA
1 CATATCTATATGTATTAATTATCGTTTGTACTCCAATACATA
* *
102089 CATATTTATTGTTGTATTAATTATCGTTTGTACTCCAATACATA
1 CATATCTA-T-ATGTATTAATTATCGTTTGTACTCCAATACATA
102133 CATA
1 CATA
102137 CATATTACAG
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
39 7 0.17
42 6 0.15
43 3 0.07
44 25 0.61
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.45
Consensus pattern (42 bp):
CATATCTATATGTATTAATTATCGTTTGTACTCCAATACATA
Found at i:102206 original size:39 final size:39
Alignment explanation
Indices: 102151--102227 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
102141 TTACAGTAGT
**
102151 AGGCTCCTCTTTTTTGTGCACAGGATAAGACCTTACCGC
1 AGGCTCCTCTGCTTTGTGCACAGGATAAGACCTTACCGC
*
102190 AGGCTCCTCTGCTTTGTGCACAGGGTAAGACCTTACCG
1 AGGCTCCTCTGCTTTGTGCACAGGATAAGACCTTACCG
102228 AGTGTACAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.29
Consensus pattern (39 bp):
AGGCTCCTCTGCTTTGTGCACAGGATAAGACCTTACCGC
Done.