Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000032.1 Hibiscus syriacus cultivar Beakdansim tig00000053_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: 55575
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:2368 original size:34 final size:34
Alignment explanation
Indices: 2325--2420 Score: 156
Period size: 34 Copynumber: 2.8 Consensus size: 34
2315 GTTCAAGCTG
*
2325 TGAATGACAAAAAGAATAGAGTTATTATTTTTAT
1 TGAATGACAAAAAGAATAGAGTTATTATTTATAT
*
2359 TGAATGACAAAAAGAATGGAGTTATTATTTATAT
1 TGAATGACAAAAAGAATAGAGTTATTATTTATAT
* *
2393 TGGATGACAAAAAGAATAGAGTTGTTAT
1 TGAATGACAAAAAGAATAGAGTTATTAT
2421 CTGTATTTCA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (34 bp):
TGAATGACAAAAAGAATAGAGTTATTATTTATAT
Found at i:2635 original size:34 final size:34
Alignment explanation
Indices: 2596--2664 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
2586 TTTCAAGCTG
*
2596 TGAATGACAAAAAGAATAAAGTTATTATTTATAT
1 TGAATGACAAAAAGAATAAAGTTATTATCTATAT
*
2630 TGAATGACAAAAAGAATAGAGTTATTATCTATAT
1 TGAATGACAAAAAGAATAAAGTTATTATCTATAT
2664 T
1 T
2665 TCAATTACTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (34 bp):
TGAATGACAAAAAGAATAAAGTTATTATCTATAT
Found at i:2881 original size:34 final size:34
Alignment explanation
Indices: 2838--2906 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
2828 GTTCAAGCTG
*
2838 TGAATGACAAAAAGAATAGAGTTATTATTTATAT
1 TGAATGACAAAAAGAATAGAGTTATTATCTATAT
2872 TGAATGACAAAAAGAATAGAGTTATTATCTATAT
1 TGAATGACAAAAAGAATAGAGTTATTATCTATAT
2906 T
1 T
2907 TCAATTACTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.35
Consensus pattern (34 bp):
TGAATGACAAAAAGAATAGAGTTATTATCTATAT
Found at i:2901 original size:242 final size:241
Alignment explanation
Indices: 2359--3075 Score: 1266
Period size: 242 Copynumber: 3.0 Consensus size: 241
2349 TTATTTTTAT
* * * *
2359 TGAATGACAAAAAGAATGGAGTTATTATTTATATTGGATGACAAAAAGAATAGAGTTGTTATCTG
1 TGAATGACAAAAAGAATAGAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
2424 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
66 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
*
2489 TTTAC-AAACA-AAATACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
131 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
* *
2552 GTACATTGCATCAGTGTATATCTTAAGTGTTAT-TT-TTCAAGCTG
196 GTACATTGCATCAGTGTATATCTTTAGTGTTTTGTTGTTCAAGCTG
*
2596 TGAATGACAAAAAGAATAAAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
1 TGAATGACAAAAAGAATAGAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
* * *
2661 TATTTCAATTACTCATGTAACAATATTTTTGCAACACCTATACTTCTTCTGCCTTTGTTTGTAAC
66 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
2726 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
131 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
*
2791 GTACATTGCATCATTGTATATCTTTAGTGTTGTTGTTGTTCAAGCTG
196 GTACATTGCATCAGTGTATATCTTTAGTGTT-TTGTTGTTCAAGCTG
2838 TGAATGACAAAAAGAATAGAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
1 TGAATGACAAAAAGAATAGAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
2903 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
66 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
2968 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
131 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
*
3033 GTACATTGCATCAGTGTATATC-TTA-AGTTTTGTTGTTCAAGCT
196 GTACATTGCATCAGTGTATATCTTTAGTGTTTTGTTGTTCAAGCT
3076 TCAAATGTTC
Statistics
Matches: 457, Mismatches: 18, Indels: 8
0.95 0.04 0.02
Matches are distributed among these distances:
237 127 0.28
238 5 0.01
239 95 0.21
240 4 0.01
241 5 0.01
242 221 0.48
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (241 bp):
TGAATGACAAAAAGAATAGAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
GTACATTGCATCAGTGTATATCTTTAGTGTTTTGTTGTTCAAGCTG
Found at i:3273 original size:196 final size:194
Alignment explanation
Indices: 2903--3281 Score: 528
Period size: 196 Copynumber: 1.9 Consensus size: 194
2893 TTATTATCTA
* **
2903 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
1 TATTTCAATTACTAATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTAATTTGTAGC
* *
2968 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
66 TTTACAAAACAGAAAGACTTGGAAAAAGAAAAAGATCGATGGACCAATTGACGTTGATGCTAAAC
* * * * *
3033 GTACATTGCATCAGTGTATATCTTAAGTTTTGTTGTTCAAGCTTCAAATGTTCATGTAACTTTG
131 GTACATGGAATCAGTGTACATCTTAAGTGTTGTTATTCAAGCTTCAAATGTTCATGTAACTTTG
* *
3097 TATTTCAATTACTAATGTAACAATATTG-TGTTAACACCTATACTTCTTTTGTCTTACAATTTGT
1 TATTTCAATTACTAATGTAACAATATTGTTG-CAACACCTATACTTCTTCTGTCTT--AATTTGT
* ** *
3161 AGCTTTACAAAATC-GCAAGACTTGGAAAAAGAAAAAGATCGATTTACTAATTGACGTTGATGCT
63 AGCTTTACAAAA-CAGAAAGACTTGGAAAAAGAAAAAGATCGATGGACCAATTGACGTTGATGCT
* * * *
3225 AAACGTACATGGAATCAGTTTACATCTTAGGTGTTGTTATTGAAGCTTCTAATGTTC
127 AAACGTACATGGAATCAGTGTACATCTTAAGTGTTGTTATTCAAGCTTCAAATGTTC
3282 TTCATTTAAC
Statistics
Matches: 161, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
193 2 0.01
194 49 0.30
196 109 0.68
197 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (194 bp):
TATTTCAATTACTAATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTAATTTGTAGC
TTTACAAAACAGAAAGACTTGGAAAAAGAAAAAGATCGATGGACCAATTGACGTTGATGCTAAAC
GTACATGGAATCAGTGTACATCTTAAGTGTTGTTATTCAAGCTTCAAATGTTCATGTAACTTTG
Found at i:8569 original size:89 final size:89
Alignment explanation
Indices: 8462--8633 Score: 326
Period size: 89 Copynumber: 1.9 Consensus size: 89
8452 CGCTCCCAGA
*
8462 TTCTTTATCCAGTTCAAGGCATTAGCTGTCTCCAAAATTAACCAACCTTTCTATCCCACTCAGAT
1 TTCTTTATCCAGTTCAAGGCATTAGCTGTCTCCAAAATTAACCAACCTTTCCATCCCACTCAGAT
*
8527 ATGGGAGAATTACAGTAATTTGTT
66 ATGGGAAAATTACAGTAATTTGTT
8551 TTCTTTATCCAGTTCAAGGCATTAGCTGTCTCCAAAATTAACCAACCTTTCCATCCCACTCAGAT
1 TTCTTTATCCAGTTCAAGGCATTAGCTGTCTCCAAAATTAACCAACCTTTCCATCCCACTCAGAT
8616 ATGGGAAAATTACAGTAA
66 ATGGGAAAATTACAGTAA
8634 AATTATGTCT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 81 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.33
Consensus pattern (89 bp):
TTCTTTATCCAGTTCAAGGCATTAGCTGTCTCCAAAATTAACCAACCTTTCCATCCCACTCAGAT
ATGGGAAAATTACAGTAATTTGTT
Found at i:10347 original size:16 final size:16
Alignment explanation
Indices: 10326--10359 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
10316 ATTGACTCTT
*
10326 AAGGAATTGGAATCTG
1 AAGGAATTGAAATCTG
10342 AAGGAATTGAAATCTG
1 AAGGAATTGAAATCTG
10358 AA
1 AA
10360 TATGAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.24
Consensus pattern (16 bp):
AAGGAATTGAAATCTG
Found at i:10931 original size:28 final size:29
Alignment explanation
Indices: 10871--10956 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 29
10861 AAGCCCGAAC
*
10871 CCGAATATCACACTTAAAAAATC-CGA-T
1 CCGAATATCACACTTAAAAAAACTCGACT
*
10898 CCGAATATTACACTTAAAAAAACTCGACT
1 CCGAATATCACACTTAAAAAAACTCGACT
* * *
10927 -TGAATATCAAACTTAACAAAA-TCGAC-
1 CCGAATATCACACTTAAAAAAACTCGACT
10953 CCGA
1 CCGA
10957 CCCGATCCCA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
27 28 0.57
28 20 0.41
29 1 0.02
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.22
Consensus pattern (29 bp):
CCGAATATCACACTTAAAAAAACTCGACT
Found at i:11006 original size:30 final size:30
Alignment explanation
Indices: 10953--11052 Score: 148
Period size: 30 Copynumber: 3.3 Consensus size: 30
10943 CAAAATCGAC
*
10953 CCGACCCGATCCCAATTTTTTTTAAAAAAAAA
1 CCGACCCGATCCCGA--TTTTTTAAAAAAAAA
10985 CCGACCCGATCCCGATTTTTTAAAAAAAAA
1 CCGACCCGATCCCGATTTTTTAAAAAAAAA
* *
11015 CCGACCCGATCCCGGTTTTTTTAAAAAAAA
1 CCGACCCGATCCCGATTTTTTAAAAAAAAA
11045 -CGACCCGA
1 CCGACCCGA
11053 ATATCACACT
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
29 8 0.12
30 43 0.66
32 14 0.22
ACGTcount: A:0.37, C:0.28, G:0.11, T:0.24
Consensus pattern (30 bp):
CCGACCCGATCCCGATTTTTTAAAAAAAAA
Found at i:11929 original size:99 final size:100
Alignment explanation
Indices: 11822--12220 Score: 410
Period size: 99 Copynumber: 3.9 Consensus size: 100
11812 TCTTATTGTC
* * *
11822 TTGCTGTAAATTTAGTTTATTTGCTTCTTTGTTTCAATTGATCATA-TCAGTCTTGTTTATGGAT
1 TTGCTGTAAATTTAGTTTATTTGATTCTTTGTTTCAATTGATCATATTCAGTCTTGCTTCTGGAT
11886 TTACTGTTTGTTGCAAAATTATTGGTTGTTTTTTT
66 TTACTGTTTGTTGCAAAATTATTGGTTGTTTTTTT
* *
11921 TTGCTGTAAATTTAGTTTATTTGCTTCTTTGATTT-AATTGATCAT-GTCAGTCTTGCTTCTGGA
1 TTGCTGTAAATTTAGTTTATTTGATTCTTTG-TTTCAATTGATCATATTCAGTCTTGCTTCTGGA
* *
11984 TTTACTGTATGTTGCAAAATTATTGGTTATTTATTTATTTATTTATT
65 TTTACTGTTTGTTGCAAAATTATTGG--------TT-GTT-TTT-TT
* * * * * * *
12031 TTGCTTTTAAATTTAGTTTATTTGATTGTATGTTTC-TTTCGATCGTATTCAGTCATGCTTCTTG
1 TTGC-TGTAAATTTAGTTTATTTGATTCTTTGTTTCAATT-GATCATATTCAGTCTTGCTTCTGG
* * *
12095 TTTTATTGTTTGTTGCAAAAATATTGGTTGTTTTTTT
64 ATTTACTGTTTGTTGCAAAATTATTGGTTGTTTTTTT
* * ** * *
12132 TTGCTTTAAATTTAGTTTATTTGATTGTTTGTTTCTCTCGATCATATTCAGTCTTGCTTCTGGTT
1 TTGCTGTAAATTTAGTTTATTTGATTCTTTGTTTCAATTGATCATATTCAGTCTTGCTTCTGGAT
* *
12197 TTAACTTTTTGTTGCGAAATTATT
66 TT-ACTGTTTGTTGCAAAATTATT
12221 AGTTTGTCGA
Statistics
Matches: 253, Mismatches: 28, Indels: 36
0.80 0.09 0.11
Matches are distributed among these distances:
99 81 0.32
100 58 0.23
101 24 0.09
102 3 0.01
103 2 0.01
104 2 0.01
107 2 0.01
108 2 0.01
109 3 0.01
110 11 0.04
111 28 0.11
112 37 0.15
ACGTcount: A:0.19, C:0.10, G:0.15, T:0.56
Consensus pattern (100 bp):
TTGCTGTAAATTTAGTTTATTTGATTCTTTGTTTCAATTGATCATATTCAGTCTTGCTTCTGGAT
TTACTGTTTGTTGCAAAATTATTGGTTGTTTTTTT
Found at i:12109 original size:112 final size:100
Alignment explanation
Indices: 12029--12220 Score: 287
Period size: 100 Copynumber: 1.9 Consensus size: 100
12019 TATTTATTTA
* * * *
12029 TTTTGCTTTTAAATTTAGTTTATTTGATTGTATGTTTCTTTCGATCGTATTCAGTCATGCTTCTT
1 TTTTGC-TTTAAATTTAGTTTATTTGATTGTATGTTTCTCTCGATCATATTCAGTCTTGCTTCTG
*
12094 GTTTTATTGTTTGTTGCAAAAATATTGGTTGTTTTT
65 GTTTTATTGTTTGTTGCAAAATTATTGGTTGTTTTT
*
12130 TTTTGCTTTAAATTTAGTTTATTTGATTGTTTGTTTCTCTCGATCATATTCAGTCTTGCTTCTGG
1 TTTTGCTTTAAATTTAGTTTATTTGATTGTATGTTTCTCTCGATCATATTCAGTCTTGCTTCTGG
*
12195 TTTTAACTT-TTTGTTGCGAAATTATT
66 TTTT-A-TTGTTTGTTGCAAAATTATT
12221 AGTTTGTCGA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
100 58 0.71
101 22 0.27
102 2 0.02
ACGTcount: A:0.18, C:0.10, G:0.15, T:0.57
Consensus pattern (100 bp):
TTTTGCTTTAAATTTAGTTTATTTGATTGTATGTTTCTCTCGATCATATTCAGTCTTGCTTCTGG
TTTTATTGTTTGTTGCAAAATTATTGGTTGTTTTT
Found at i:20988 original size:20 final size:21
Alignment explanation
Indices: 20948--20995 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
20938 GAAAAGTTTT
20948 ATAAAATATAATTATATAAAA
1 ATAAAATATAATTATATAAAA
20969 ATAAAAT-TAACTTA-ATAAAA
1 ATAAAATATAA-TTATATAAAA
20989 ACTAAAA
1 A-TAAAA
20996 GGTATAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
ATAAAATATAATTATATAAAA
Found at i:21983 original size:21 final size:20
Alignment explanation
Indices: 21897--22054 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
21887 AAATGACCAA
**
21897 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
21916 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
21936 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
21956 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
21977 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
21998 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
22018 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
22039 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
22055 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:22045 original size:20 final size:20
Alignment explanation
Indices: 22021--22214 Score: 210
Period size: 20 Copynumber: 9.7 Consensus size: 20
22011 CGATTTTCCA
** *
22021 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
22041 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
22061 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
22081 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
22101 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
22121 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
22141 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
22161 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
22181 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
22201 AAATCGCAACGCGA
1 AAATCGCAACGCGA
22215 TATTTAAAGC
Statistics
Matches: 149, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 148 0.99
21 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:22632 original size:33 final size:33
Alignment explanation
Indices: 22593--22663 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
22583 TTCACTTAGA
* *
22593 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
22626 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
22659 TTTCA
1 TTTCA
22664 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:22800 original size:41 final size:38
Alignment explanation
Indices: 22736--22852 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
22726 TTCAATTTGC
* *
22736 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
22774 AGAATGACTGTCGCAACGAGAGAAATGACAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
22815 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
22848 AGAAT
1 AGAAT
22853 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.45, C:0.18, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:22816 original size:21 final size:21
Alignment explanation
Indices: 22743--22818 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
22733 TGCAGAAGAG
* *
22743 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGACAA
**
22764 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGACAA
22784 TCGCAACGAGAGAAATGACAA
1 TCGCAACGAGAGAAATGACAA
22805 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
22819 TCGCAACGCG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGACAA
Found at i:22822 original size:14 final size:14
Alignment explanation
Indices: 22803--22859 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
22793 GAGAAATGAC
22803 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
22817 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
22836 AATCGCAACGAGAG
1 AATCGCAACGAGAG
22850 AATCGCAACG
1 AATCGCAACG
22860 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:22840 original size:33 final size:33
Alignment explanation
Indices: 22795--22875 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
22785 CGCAACGAGA
*
22795 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
22828 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
22861 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
22876 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:22893 original size:19 final size:19
Alignment explanation
Indices: 22871--22968 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
22861 GAAACCAAAA
*
22871 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
22890 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
22904 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
22923 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
22937 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
22956 TCGCGTTGCGATT
1 TCGCGTTGCGATT
22969 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 20 0.33
16 4 0.07
17 5 0.08
19 32 0.52
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:22912 original size:14 final size:14
Alignment explanation
Indices: 22893--22982 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
22883 TTTCATTTCG
22893 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
22907 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
22926 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
22940 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
22957 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
22973 CGTTGCGATT
1 CGTTGCGATT
22983 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 2 0.03
16 7 0.11
17 7 0.11
18 2 0.03
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:22922 original size:33 final size:33
Alignment explanation
Indices: 22876--22990 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
22866 CAAAATCGCA
*
22876 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
22909 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
22942 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
22975 TTGCGATTTTCATTTC
1 TTGCGATTGTCATTTC
22991 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
Found at i:24847 original size:93 final size:93
Alignment explanation
Indices: 24688--25160 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
24678 TAGATTGCTT
*
24688 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24753 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24781 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24846 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24873 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24938 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
24966 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
25031 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
25059 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
25124 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
25152 AGTAAATTT
1 AGTAAATTT
25161 ATCCATTCAA
Statistics
Matches: 376, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 92 0.24
93 284 0.76
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:24918 original size:185 final size:186
Alignment explanation
Indices: 24688--25160 Score: 921
Period size: 185 Copynumber: 2.5 Consensus size: 186
24678 TAGATTGCTT
*
24688 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24753 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
24818 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTC-TTTGGTTGAA
131 GTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
24873 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24938 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
25003 GTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
25059 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
25124 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
25161 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
185 173 0.61
186 112 0.39
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:25244 original size:19 final size:19
Alignment explanation
Indices: 25204--25332 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
25194 TAGTTTACTT
* *
25204 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
25224 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
25243 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
25262 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
*
25276 TCGCAAAGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
25295 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
25309 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
25328 TCGCA
1 TCGCA
25333 TTGAAGAGGT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:25287 original size:33 final size:32
Alignment explanation
Indices: 25240--25332 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
25230 CGCGAAACCA
**
25240 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
25272 AGAATCGCAAAGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
25305 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
25333 TTGAAGAGGT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 2 0.04
33 53 0.96
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:25330 original size:52 final size:52
Alignment explanation
Indices: 25204--25332 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
25194 TAGTTTACTT
** *
25204 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAAAGCGAAACCAAAATCGCAACGCGAAA
* * *
25256 T-G-AAAATCGCAACGACAGAATCGCAAAGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAAAGCGAAACCAAAATCGCAACG-CGAA-A
*
25309 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
25333 TTGAAGAGGT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 41 0.67
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAAAGCGAAACCAAAATCGCAACGCGAAA
Found at i:26984 original size:19 final size:19
Alignment explanation
Indices: 26960--27059 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
26950 AAAATTGACT
26960 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
26979 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
26998 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
27012 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27031 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
27051 ATCGCAATG
1 ATCGCAATG
27060 GGAGAATCGC
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.53
20 18 0.25
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:27089 original size:53 final size:53
Alignment explanation
Indices: 26960--27073 Score: 203
Period size: 53 Copynumber: 2.2 Consensus size: 53
26950 AAAATTGACT
26960 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
27012 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
27065 ATCGCAATG
1 ATCGCAATG
27074 TGATTTTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.49
53 30 0.51
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:27097 original size:19 final size:19
Alignment explanation
Indices: 27075--27214 Score: 130
Period size: 19 Copynumber: 8.1 Consensus size: 19
27065 ATCGCAATGT
*
27075 GATTTTAATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
27094 GA--TT-ATCTCG--TTGC
1 GATTTTCATTTCGCATTGC
27108 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
27127 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
27146 GA--TTC-TCTCG--TTGC
1 GATTTTCATTTCGCATTGC
27160 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
27179 GA--TTC-TCTCG--TTGC
1 GATTTTCATTTCGCATTGC
27193 GATTTTCATTTCCGCATTGC
1 GATTTTCATTT-CGCATTGC
27213 GA
1 GA
27215 AATGTAATGG
Statistics
Matches: 99, Mismatches: 6, Indels: 31
0.73 0.04 0.23
Matches are distributed among these distances:
14 18 0.18
16 21 0.21
17 19 0.19
18 2 0.02
19 33 0.33
20 6 0.06
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:27132 original size:52 final size:52
Alignment explanation
Indices: 27066--27182 Score: 198
Period size: 52 Copynumber: 2.2 Consensus size: 52
27056 AATGGGAGAA
* *
27066 TCGCAATGTGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
* *
27118 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
27170 TCGCATTGCGATT
1 TCGCATTGCGATT
27183 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
Found at i:27160 original size:33 final size:33
Alignment explanation
Indices: 27123--27214 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
27113 TCATTTCGCA
27123 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
27156 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
27189 TTGCGATTTTCATTTCCGCATTGCGA
1 TTGCGATTTTCATTT-CGCATTGCGA
27215 AATGTAATGG
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 48 0.83
34 10 0.17
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:27161 original size:14 final size:14
Alignment explanation
Indices: 27142--27196 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
27132 TCATTTCGCA
27142 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
27156 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
27173 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
27189 TTGCGATT
1 TTGCGATT
27197 TTCATTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:27297 original size:19 final size:19
Alignment explanation
Indices: 27273--27370 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
27263 AAAATTGACT
27273 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27292 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
27311 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
27325 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27344 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
27364 ATCGCAA
1 ATCGCAA
27371 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:27402 original size:53 final size:53
Alignment explanation
Indices: 27273--27389 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
27263 AAAATTGACT
27273 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
27325 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
27378 ATCGCAATGCGA
1 ATCGCAATGCGA
27390 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:27407 original size:19 final size:19
Alignment explanation
Indices: 27379--27546 Score: 186
Period size: 19 Copynumber: 9.6 Consensus size: 19
27369 AACGAGAGAA
*
27379 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
27398 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
27414 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
27431 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
27450 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
27469 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
27485 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
27502 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
27518 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
27535 TCCGCATTGCGA
1 T-CGCATTGCGA
27547 AATGTAATGG
Statistics
Matches: 126, Mismatches: 7, Indels: 31
0.77 0.04 0.19
Matches are distributed among these distances:
14 18 0.14
16 21 0.17
17 19 0.15
18 2 0.02
19 60 0.48
20 6 0.05
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:27422 original size:33 final size:33
Alignment explanation
Indices: 27385--27546 Score: 261
Period size: 33 Copynumber: 4.7 Consensus size: 33
27375 AGAATCGCAA
27385 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
27418 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
27456 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
27489 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
27522 TGCGATTTTCATTTCCGCATTGCGA
1 TGCGATTTTCATTT-CGCATTGCGA
27547 AATGTAATGG
Statistics
Matches: 121, Mismatches: 2, Indels: 11
0.90 0.01 0.08
Matches are distributed among these distances:
33 72 0.60
34 10 0.08
35 7 0.06
36 7 0.06
38 25 0.21
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:27460 original size:71 final size:68
Alignment explanation
Indices: 27379--27546 Score: 268
Period size: 71 Copynumber: 2.4 Consensus size: 68
27369 AACGAGAGAA
*
27379 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA--
*
27444 TTCATT
64 TTC-TC
27450 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
27515 CTC
66 CTC
27518 TCG--TTGCGATTTTCATTTCCGCATTGCGA
1 TCGCATTGCGATTTTCATTT-CGCATTGCGA
27547 AATGTAATGG
Statistics
Matches: 94, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
66 15 0.16
67 10 0.11
68 4 0.04
69 3 0.03
71 62 0.66
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (68 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
CTC
Found at i:27493 original size:14 final size:14
Alignment explanation
Indices: 27474--27528 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
27464 TCATTTCGCA
27474 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
27488 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
27505 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
27521 TTGCGATT
1 TTGCGATT
27529 TTCATTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:27566 original size:332 final size:313
Alignment explanation
Indices: 26979--27737 Score: 1169
Period size: 313 Copynumber: 2.4 Consensus size: 313
26969 CGAAATGAAA
26979 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGGA
* * * *
27044 AATGAAAATCGCAATGGGAGAATCGCAATGTGATTTTAATTTCGCATTGCGA--------TT---
66 AATGAAAATCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
27098 A---TC---TCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
131 ATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
27155 GTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGAAATGT
196 GTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGAAATGT
*
27220 AATGGTTGATTTTGTTGATTTCAATCTGCATTATGTTGAAGGCAAAATTGACTATCGCAATGCGA
261 AATGGTTGATTTTGTTGATTTCAATATGCATTATGTTGAAGGC-AAA---A-T-T-G--A--C--
27285 AAT
313 --T
27288 GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATG
1 ----ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATG
27353 CGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTCTCTCGT
62 CGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTCTCTCGT
27418 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTC
127 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTC
27483 TCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGAA
192 TCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGAA
27548 ATGTAATGGTTGATTTTGTTGATTTCAATATGCATTATGTTGAAGGCAAAATTGACT
257 ATGTAATGGTTGATTTTGTTGATTTCAATATGCATTATGTTGAAGGCAAAATTGACT
27605 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGGA
27670 AATGAAAATCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
66 AATGAAAATCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
27735 ATT
131 ATT
27738 GTAATTTCCG
Statistics
Matches: 422, Mismatches: 5, Indels: 38
0.91 0.01 0.08
Matches are distributed among these distances:
313 246 0.58
317 1 0.00
321 3 0.01
323 1 0.00
324 1 0.00
325 1 0.00
326 1 0.00
327 3 0.01
328 1 0.00
330 3 0.01
331 3 0.01
332 158 0.37
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (313 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGGA
AATGAAAATCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
ATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
GTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGAAATGT
AATGGTTGATTTTGTTGATTTCAATATGCATTATGTTGAAGGCAAAATTGACT
Found at i:27673 original size:20 final size:19
Alignment explanation
Indices: 27605--27683 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 19
27595 AAAATTGACT
27605 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
27624 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
27638 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27657 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
27677 ATCGCAA
1 ATCGCAA
27684 CGAGAGAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 20 0.38
20 16 0.31
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:28618 original size:20 final size:20
Alignment explanation
Indices: 28368--28617 Score: 261
Period size: 20 Copynumber: 12.5 Consensus size: 20
28358 AAATTTCAGT
* * *
28368 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
28388 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
28408 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
28428 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
28448 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
28468 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
28488 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
28508 ATTGCGATTTACCCATAT-GC
1 GTTGCGATTTACGGAT-TCGC
*
28528 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
28548 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
28568 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
28588 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
28608 GTTGCGATTT
1 GTTGCGATTT
28618 TGTACTATCG
Statistics
Matches: 198, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:28648 original size:21 final size:20
Alignment explanation
Indices: 28584--28660 Score: 82
Period size: 21 Copynumber: 3.8 Consensus size: 20
28574 ATTTATGTGT
* *
28584 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCACAA
* *
28604 TCGCGTTGCGATTTTGTACTA
1 TCGCGTTGCGATTTT-CACAA
* *
28625 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTC-ACAA
28646 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
28661 GGAAACTGAT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 15 0.33
21 31 0.67
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCACAA
Found at i:28657 original size:42 final size:39
Alignment explanation
Indices: 28565--28661 Score: 122
Period size: 42 Copynumber: 2.4 Consensus size: 39
28555 TTTACGGATA
* * * *
28565 CGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTT-TGTCTTCGCATTGCGATTTTCAGAAT
28605 CGCGTTGCGATTTTGTACTATCGCATTGCGATTTTCAAGAAT
1 CGCGTTGCGATTTTGT-CT-TCGCATTGCGATTTTC-AGAAT
28647 CGCGTTGCGATTTTG
1 CGCGTTGCGATTTTG
28662 GAAACTGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
39 3 0.06
40 14 0.28
41 15 0.30
42 18 0.36
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.41
Consensus pattern (39 bp):
CGCGTTGCGATTTTGTCTTCGCATTGCGATTTTCAGAAT
Found at i:32876 original size:31 final size:32
Alignment explanation
Indices: 32841--32900 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
32831 AATAAGTACT
* * *
32841 TAGGAATTACAACACCCAAAAAC-TCCCTTAA
1 TAGGAAGTACAAAACCAAAAAACATCCCTTAA
*
32872 TAGGAAGTAGAAAACCAAAAAACATCCCT
1 TAGGAAGTACAAAACCAAAAAACATCCCT
32901 AAACAACAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 19 0.79
32 5 0.21
ACGTcount: A:0.48, C:0.25, G:0.10, T:0.17
Consensus pattern (32 bp):
TAGGAAGTACAAAACCAAAAAACATCCCTTAA
Found at i:39872 original size:35 final size:35
Alignment explanation
Indices: 39833--39903 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
39823 CATTCACACT
*
39833 TTTCTTATTTC-CCTTCTTCTTCCACGCCTAATTCC
1 TTTCTTATTTCTCCTT-TTCTTCCACGCATAATTCC
* *
39868 TTTCTTATTTCTCGTTTTCTTTCACGCATAATTCC
1 TTTCTTATTTCTCCTTTTCTTCCACGCATAATTCC
39903 T
1 T
39904 GTTAATAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 29 0.91
36 3 0.09
ACGTcount: A:0.13, C:0.31, G:0.04, T:0.52
Consensus pattern (35 bp):
TTTCTTATTTCTCCTTTTCTTCCACGCATAATTCC
Done.