Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006089.1 Hibiscus syriacus cultivar Beakdansim tig00014439_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: 128867
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4352 original size:22 final size:22
Alignment explanation
Indices: 4280--4379 Score: 94
Period size: 23 Copynumber: 4.4 Consensus size: 22
4270 GAATCGAGGG
* *
4280 TTCTATGCGGTCCTTTGCGACAA
1 TTCTATGTGGTCCTTCG-GACAA
*
4303 TTCTATGTGGTCTTTCGGGACAA
1 TTCTATGTGGTCCTTC-GGACAA
*
4326 TTCTACGTGGTCCTTCGGACAA
1 TTCTATGTGGTCCTTCGGACAA
* *
4348 ATCTATGTGG-CACTTCGGTTCATA
1 TTCTATGTGGTC-CTTCGG-ACA-A
4372 TTCTATGT
1 TTCTATGT
4380 AGCACTTCGG
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.02
22 20 0.31
23 34 0.53
24 9 0.14
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (22 bp):
TTCTATGTGGTCCTTCGGACAA
Found at i:4379 original size:24 final size:24
Alignment explanation
Indices: 4324--4407 Score: 84
Period size: 24 Copynumber: 3.6 Consensus size: 24
4314 CTTTCGGGAC
* *
4324 AATTCTACGTGGTC-CTTCGG-ACA
1 AATTCTATGTGG-CACTTCGGTGCA
*
4347 AA-TCTATGTGGCACTTCGGTTCA
1 AATTCTATGTGGCACTTCGGTGCA
* *
4370 TATTCTATGTAGCACTTCGGTGCA
1 AATTCTATGTGGCACTTCGGTGCA
*
4394 AATTCTACGTGGCA
1 AATTCTATGTGGCA
4408 TTTTTTGACT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 1 0.02
22 14 0.28
23 5 0.10
24 30 0.60
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (24 bp):
AATTCTATGTGGCACTTCGGTGCA
Found at i:11134 original size:45 final size:46
Alignment explanation
Indices: 11085--11192 Score: 123
Period size: 45 Copynumber: 2.4 Consensus size: 46
11075 GAGTTGAGGG
* ***
11085 TTTTATGTGGTCATTCGGGATAATTCTATGTGGTCCTTC-GGACAA
1 TTTTATGTGGTCATTCGGGACAATTCTACACGGTCCTTCGGGACAA
* *
11130 TTTTATGTGGTCCTTCGAGACAATTCTACACGGTCCTTCGGGACAA
1 TTTTATGTGGTCATTCGGGACAATTCTACACGGTCCTTCGGGACAA
*
11176 -TCTATGTGG-CACTTCGG
1 TTTTATGTGGTCA-TTCGG
11193 TGCATATTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
44 1 0.02
45 45 0.87
46 6 0.12
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (46 bp):
TTTTATGTGGTCATTCGGGACAATTCTACACGGTCCTTCGGGACAA
Found at i:11136 original size:22 final size:22
Alignment explanation
Indices: 11085--11154 Score: 95
Period size: 22 Copynumber: 3.1 Consensus size: 22
11075 GAGTTGAGGG
* *
11085 TTTTATGTGGTCATTCGGGATAA
1 TTTTATGTGGTCCTTC-GGACAA
*
11108 TTCTATGTGGTCCTTCGGACAA
1 TTTTATGTGGTCCTTCGGACAA
11130 TTTTATGTGGTCCTTCGAGACAA
1 TTTTATGTGGTCCTTCG-GACAA
11153 TT
1 TT
11155 CTACACGGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 21 0.50
23 21 0.50
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (22 bp):
TTTTATGTGGTCCTTCGGACAA
Found at i:11190 original size:22 final size:23
Alignment explanation
Indices: 11088--11192 Score: 117
Period size: 23 Copynumber: 4.7 Consensus size: 23
11078 TTGAGGGTTT
* *
11088 TATGTGGTCATTCGGGATAATTC
1 TATGTGGTCCTTCGGGACAATTC
*
11111 TATGTGGTCCTTC-GGACAATTT
1 TATGTGGTCCTTCGGGACAATTC
*
11133 TATGTGGTCCTTCGAGACAATTC
1 TATGTGGTCCTTCGGGACAATTC
***
11156 TACACGGTCCTTCGGGACAA-TC
1 TATGTGGTCCTTCGGGACAATTC
11178 TATGTGG-CACTTCGG
1 TATGTGGTC-CTTCGG
11193 TGCATATTTA
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
21 1 0.01
22 32 0.47
23 35 0.51
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACAATTC
Found at i:11212 original size:23 final size:22
Alignment explanation
Indices: 11181--11223 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
11171 GACAATCTAT
*
11181 GTGGCACTTCGGTGCATATTTAC
1 GTGGAACTTCGGTGCA-ATTTAC
11204 GTGGAACTTCGGTGCAATTT
1 GTGGAACTTCGGTGCAATTT
11224 CTATGCGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.35
Consensus pattern (22 bp):
GTGGAACTTCGGTGCAATTTAC
Found at i:12590 original size:16 final size:16
Alignment explanation
Indices: 12569--12601 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12559 AATAAAATGC
12569 AATAAT-ATAAATAATA
1 AATAATAAT-AATAATA
12585 AATAATAATAATAATA
1 AATAATAATAATAATA
12601 A
1 A
12602 TAACCTGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:13398 original size:2 final size:2
Alignment explanation
Indices: 13391--13424 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
13381 CAATAAGTGA
13391 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
13425 TCCCAATCTA
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:14210 original size:31 final size:29
Alignment explanation
Indices: 14154--14241 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 29
14144 GAACAAAATG
14154 TAAATTTTGAAAGTTTAGTGG-CCAAAGAA
1 TAAATTTTGAAAGTTTAG-GGACCAAAGAA
* *
14183 TAAAGTTTGGAAACGTTTAGGGACCAAAAGGA
1 TAAA-TTTTGAAA-GTTTAGGGACC-AAAGAA
*
14215 T-AATTTTCAAAAGTTTAGGGACCAAAG
1 TAAATTTT-GAAAGTTTAGGGACCAAAG
14242 TGTAATTTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
29 8 0.16
30 23 0.46
31 13 0.26
32 6 0.12
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (29 bp):
TAAATTTTGAAAGTTTAGGGACCAAAGAA
Found at i:14251 original size:29 final size:30
Alignment explanation
Indices: 14197--14258 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
14187 GTTTGGAAAC
14197 GTTTAGGGACCAAAAGGATAATTTTCAAAA
1 GTTTAGGGACCAAAAGGATAATTTTCAAAA
14227 GTTTAGGGACC-AAAGTG-TAATTTTCAAAA
1 GTTTAGGGACCAAAAG-GATAATTTTCAAAA
14256 GTT
1 GTT
14259 AGGAGTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.31
Consensus pattern (30 bp):
GTTTAGGGACCAAAAGGATAATTTTCAAAA
Found at i:17744 original size:21 final size:21
Alignment explanation
Indices: 17714--17899 Score: 118
Period size: 21 Copynumber: 9.0 Consensus size: 21
17704 GATTTACATA
* *
17714 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
17735 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
* *
17756 TT--CGTTACGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
17775 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
17798 TT--CATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
17817 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
* * *
17840 TT--CATTGTGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
17859 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
17882 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
17900 AATCGCAACG
Statistics
Matches: 124, Mismatches: 29, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
19 39 0.31
21 59 0.48
23 26 0.21
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:17796 original size:42 final size:42
Alignment explanation
Indices: 17718--17896 Score: 290
Period size: 42 Copynumber: 4.3 Consensus size: 42
17708 TACATATTCG
17718 CATTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* *
17758 CGTTACGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* *
17800 CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
17842 CATTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
17884 CGTTGCGATAGTC
1 CATTGCGATAGTC
17897 CAAAATCGCA
Statistics
Matches: 126, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 27 0.21
41 2 0.02
42 97 0.77
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (42 bp):
CATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:18000 original size:6 final size:6
Alignment explanation
Indices: 17989--18021 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
17979 GACACGTTTT
*
17989 ACCACG ACCACG ACCACG ACCACG ATCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
18022 TGACCTGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.33, C:0.48, G:0.15, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:18663 original size:21 final size:20
Alignment explanation
Indices: 18637--18703 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
18627 ATTTTGGACT
18637 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTT-GAATAA
*
18658 ATCGCAACGCGAACTTTGACT--
1 ATCGCAA--CGAA-TTTGAATAA
18679 ATCGCAACGAATTTTGAATAA
1 ATCGCAACGAA-TTTGAATAA
18700 ATCG
1 ATCG
18704 TAATGCGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
19 10 0.26
21 18 0.47
23 7 0.18
24 3 0.08
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGAATTTGAATAA
Found at i:18692 original size:42 final size:42
Alignment explanation
Indices: 18633--18769 Score: 197
Period size: 42 Copynumber: 3.3 Consensus size: 42
18623 TGCGATTTTG
*
18633 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * * *
18675 GACTATCGCAACGAATTTTGAATAAATCGTAATGCGAAATTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
18717 GACTATCGCAACGAATTAGG-A-AAATCGCAACGTGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
18757 GACTATCGCAACG
1 GACTATCGCAACG
18770 CGAACTTCGA
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
40 28 0.33
41 1 0.01
42 55 0.65
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:18748 original size:61 final size:59
Alignment explanation
Indices: 18679--18830 Score: 169
Period size: 61 Copynumber: 2.5 Consensus size: 59
18669 AACTTTGACT
* * * * *
18679 ATCGCAACGAATTTTGAATAAATCGTAATGCGAAATTCGACTATCGCAACGAATTAGGAAA
1 ATCGCAACGAACTTCGAAT--ATCGCAACGCGAAATTCGACTATCACAACGAATTAGGAAA
* * *
18740 ATCGCAACGTGAACTTCGACTATCGCAACGCGAACTTCGACTATCACAACGAATTTGGAAA
1 ATCGCAAC--GAACTTCGAATATCGCAACGCGAAATTCGACTATCACAACGAATTAGGAAA
*
18801 ATCGCAACGCGAACTTCGACTATCGCAACG
1 ATCGCAA--CGAACTTCGAATATCGCAACG
18831 AATTTGGAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
61 70 0.89
63 9 0.11
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (59 bp):
ATCGCAACGAACTTCGAATATCGCAACGCGAAATTCGACTATCACAACGAATTAGGAAA
Found at i:18766 original size:21 final size:20
Alignment explanation
Indices: 18658--18870 Score: 121
Period size: 21 Copynumber: 10.4 Consensus size: 20
18648 TTTGGAATAA
*
18658 ATCGCAACGCGAACTTTGACT
1 ATCGCAACG-GAACTTCGACT
* * *
18679 ATCGCAAC-GAATTTTGAAT
1 ATCGCAACGGAACTTCGACT
* * *
18698 AAATCGTAATGCGAAATTCGACT
1 --ATCGCAACG-GAACTTCGACT
* **
18721 ATCGCAAC-GAA-TTAGGAAA
1 ATCGCAACGGAACTT-CGACT
18740 ATCGCAACGTGAACTTCGACT
1 ATCGCAACG-GAACTTCGACT
18761 ATCGCAACGCGAACTTCGACT
1 ATCGCAACG-GAACTTCGACT
* * * **
18782 ATCACAAC-GAATTTGGAAA
1 ATCGCAACGGAACTTCGACT
18801 ATCGCAACGCGAACTTCGACT
1 ATCGCAACG-GAACTTCGACT
* * **
18822 ATCGCAAC-GAATTTGGAAA
1 ATCGCAACGGAACTTCGACT
* *
18841 ATCACAACGTGAACTTGGACT
1 ATCGCAACG-GAACTTCGACT
18862 ATCGCAACG
1 ATCGCAACG
18871 CGAATATGTA
Statistics
Matches: 145, Mismatches: 35, Indels: 24
0.71 0.17 0.12
Matches are distributed among these distances:
18 2 0.01
19 50 0.34
21 83 0.57
22 2 0.01
23 8 0.06
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGGAACTTCGACT
Found at i:18805 original size:40 final size:40
Alignment explanation
Indices: 18761--18870 Score: 184
Period size: 40 Copynumber: 2.8 Consensus size: 40
18751 AACTTCGACT
*
18761 ATCGCAACGCGAACTTCGACTATCACAACGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
18801 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
* * *
18841 ATCACAACGTGAACTTGGACTATCGCAACG
1 ATCGCAACGCGAACTTCGACTATCGCAACG
18871 CGAATATGTA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (40 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
Found at i:18849 original size:101 final size:103
Alignment explanation
Indices: 18658--18874 Score: 339
Period size: 101 Copynumber: 2.1 Consensus size: 103
18648 TTTGGAATAA
* * * *
18658 ATCGCAACGCGAACTTTGACTATCGCAACGAATTTTGAATAAATCGTAATGCGAAATTCGACTAT
1 ATCGCAACGCGAACTTCGACTATCACAACGAATTTTGAATAAATCGCAACGCGAAATTCGACTAT
*
18723 CGCAACGAATTAGGAAAATCGCAACGTGAACTTCGACT
66 CGCAACGAATTAGGAAAATCACAACGTGAACTTCGACT
* *
18761 ATCGCAACGCGAACTTCGACTATCACAACGAA-TTTGGA-AAATCGCAACGCGAACTTCGACTAT
1 ATCGCAACGCGAACTTCGACTATCACAACGAATTTTGAATAAATCGCAACGCGAAATTCGACTAT
* *
18824 CGCAACGAATTTGGAAAATCACAACGTGAACTTGGACT
66 CGCAACGAATTAGGAAAATCACAACGTGAACTTCGACT
18862 ATCGCAACGCGAA
1 ATCGCAACGCGAA
18875 TATGTAAATC
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
101 70 0.67
102 5 0.05
103 30 0.29
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.22
Consensus pattern (103 bp):
ATCGCAACGCGAACTTCGACTATCACAACGAATTTTGAATAAATCGCAACGCGAAATTCGACTAT
CGCAACGAATTAGGAAAATCACAACGTGAACTTCGACT
Found at i:18859 original size:61 final size:60
Alignment explanation
Indices: 18725--18874 Score: 178
Period size: 61 Copynumber: 2.5 Consensus size: 60
18715 TCGACTATCG
* **
18725 CAACGAA-TTAGGAAAATCGCAACGTGAACTTCGACTATCGCAACGCGAACTTCGACTATCA
1 CAACGAACTT-GGAAAATCGCAACGCGAACTTCGACTATCGCAAC-CGAACTTCGAAAATCA
* * *
18786 CAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAA-CGAATTTGGAAAATCA
1 CAACGAACTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACCGAACTTCGAAAATCA
**
18845 CAACGTGAACTTGGACTATCGCAACGCGAA
1 CAAC--GAACTTGGAAAATCGCAACGCGAA
18875 TATGTAAATC
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
59 16 0.21
61 60 0.77
62 2 0.03
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (60 bp):
CAACGAACTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACCGAACTTCGAAAATCA
Found at i:18912 original size:21 final size:21
Alignment explanation
Indices: 18883--18935 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
18873 AATATGTAAA
*
18883 TCGCATTGCGATAGTCCAAAT
1 TCGCGTTGCGATAGTCCAAAT
* *
18904 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAAT
*
18925 TCGTGTTGCGA
1 TCGCGTTGCGA
18936 ATCTGGAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAAT
Found at i:27320 original size:23 final size:22
Alignment explanation
Indices: 27281--27342 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
27271 AAATTACACA
*
27281 AAAACAGAAAATAAATAAAAAAGT
1 AAAA-AGATAATAAATAAAAAA-T
*
27305 AAAAAGATAATAAATAATAAAT
1 AAAAAGATAATAAATAAAAAAT
*
27327 -AAAACATAATAAATAA
1 AAAAAGATAATAAATAA
27343 TAAACCAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 15 0.43
22 1 0.03
23 15 0.43
24 4 0.11
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (22 bp):
AAAAAGATAATAAATAAAAAAT
Found at i:27321 original size:7 final size:7
Alignment explanation
Indices: 27290--27346 Score: 62
Period size: 7 Copynumber: 7.9 Consensus size: 7
27280 AAAAACAGAA
27290 AATAAAT
1 AATAAAT
*
27297 AAAAAAGT
1 AATAAA-T
*
27305 AAAAAGAT
1 AATAA-AT
27313 AATAAAT
1 AATAAAT
27320 AATAAAT
1 AATAAAT
27327 AA-AACAT
1 AATAA-AT
27334 AATAAAT
1 AATAAAT
27341 AATAAA
1 AATAAA
27347 CCAATATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
6 2 0.05
7 28 0.64
8 13 0.30
9 1 0.02
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (7 bp):
AATAAAT
Found at i:27335 original size:21 final size:23
Alignment explanation
Indices: 27290--27346 Score: 82
Period size: 21 Copynumber: 2.6 Consensus size: 23
27280 AAAAACAGAA
* *
27290 AATAAATAAAAAAGTAAAAAGAT
1 AATAAATAATAAAGTAAAAACAT
27313 AATAAATAATAAA-T-AAAACAT
1 AATAAATAATAAAGTAAAAACAT
27334 AATAAATAATAAA
1 AATAAATAATAAA
27347 CCAATATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 19 0.59
22 1 0.03
23 12 0.38
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (23 bp):
AATAAATAATAAAGTAAAAACAT
Found at i:27454 original size:37 final size:37
Alignment explanation
Indices: 27388--27710 Score: 323
Period size: 37 Copynumber: 8.9 Consensus size: 37
27378 TATAATATAT
* * *
27388 AAATATTTTTAAAAACTATATA--ACATATATTTTCA
1 AAATGTTTTCAAAAACTATATATTATATATATTTTCA
* *
27423 AATTGTTTTCAAAAATTATATATTATATATATTTTTTCA
1 AAATGTTTTCAAAAACTATATATTATATATA--TTTTCA
27462 AAATGTTTTCAAAAACTATATA-TATAT-TA-----A
1 AAATGTTTTCAAAAACTATATATTATATATATTTTCA
* *
27492 AAATATTTGT-AAAAACTATAT-T-ATATATATATTCA
1 AAATGTTT-TCAAAAACTATATATTATATATATTTTCA
** *
27527 AAATACTTTCAAAAACTATATATTATATATGTTTTCA
1 AAATGTTTTCAAAAACTATATATTATATATATTTTCA
* *
27564 AAATGTTTTTCAAAAACTATATATTATATAT-GTTTGA
1 AAATG-TTTTCAAAAACTATATATTATATATATTTTCA
*
27601 ATAATGTTTTCAAAAACTATATATTATATATTTTTTCAA
1 A-AATGTTTTCAAAAACTATATATTATATATATTTTC-A
*
27640 AACAT-TTTTTAAAAACTATATATTATATATATTTTCA
1 AA-ATGTTTTCAAAAACTATATATTATATATATTTTCA
* *
27677 AAACGCTTTCAAAAACTATATATATATTATATAT
1 AAATGTTTTCAAAAACTATATAT-TA-TATATAT
27711 ATATATATAT
Statistics
Matches: 243, Mismatches: 22, Indels: 42
0.79 0.07 0.14
Matches are distributed among these distances:
29 4 0.02
30 21 0.09
31 1 0.00
34 1 0.00
35 37 0.15
36 2 0.01
37 72 0.30
38 68 0.28
39 37 0.15
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (37 bp):
AAATGTTTTCAAAAACTATATATTATATATATTTTCA
Found at i:27471 original size:39 final size:38
Alignment explanation
Indices: 27388--27710 Score: 292
Period size: 38 Copynumber: 8.9 Consensus size: 38
27378 TATAATATAT
* * *
27388 AAATATTTTTAAAAACTAT--ATA-ACATATATTTTCA
1 AAATGTTTTCAAAAACTATATATATATATATATTTTCA
* * *
27423 AATTGTTTTCAAAAATTATATATTATATATATTTTTTCA
1 AAATGTTTTCAAAAACTATATA-TATATATATATTTTCA
27462 AAATGTTTTCAAAAACTATATATATAT-TA-A-----A
1 AAATGTTTTCAAAAACTATATATATATATATATTTTCA
*
27493 AATAT-TTGT-AAAAACTATAT-TATATATATA--TTCA
1 AA-ATGTTTTCAAAAACTATATATATATATATATTTTCA
** *
27527 AAATACTTTCAAAAACTATATAT-TATATATGTTTTCA
1 AAATGTTTTCAAAAACTATATATATATATATATTTTCA
* *
27564 AAATGTTTTTCAAAAACTATATAT-TATATAT-GTTTGA
1 AAATG-TTTTCAAAAACTATATATATATATATATTTTCA
*
27601 ATAATGTTTTCAAAAACTATATAT-TATATATTTTTTCAA
1 A-AATGTTTTCAAAAACTATATATATATATATATTTTC-A
*
27640 AACAT-TTTTTAAAAACTATATAT-TATATATATTTTCA
1 AA-ATGTTTTCAAAAACTATATATATATATATATTTTCA
* *
27677 AAACGCTTTCAAAAACTATATATATATTATATAT
1 AAATGTTTTCAAAAACTATATATATA-TATATAT
27711 ATATATATAT
Statistics
Matches: 241, Mismatches: 24, Indels: 42
0.79 0.08 0.14
Matches are distributed among these distances:
29 5 0.02
30 13 0.05
31 7 0.03
32 2 0.01
33 2 0.01
34 5 0.02
35 33 0.14
36 2 0.01
37 60 0.25
38 70 0.29
39 42 0.17
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (38 bp):
AAATGTTTTCAAAAACTATATATATATATATATTTTCA
Found at i:27484 original size:30 final size:30
Alignment explanation
Indices: 27448--27550 Score: 100
Period size: 30 Copynumber: 3.3 Consensus size: 30
27438 TTATATATTA
*
27448 TATATATTTTTTCAAAATGTTTTCAAAAAC
1 TATATATTTTTTCAAAATATTTTCAAAAAC
* * *
27478 TATATATATATTAAAAATATTTGT-AAAAAC
1 TATATATTTTTTCAAAATATTT-TCAAAAAC
*
27508 TATATTATATATATATTCAAAATACTTTCAAAAAC
1 TATA-TAT-T-T-T-TTCAAAATATTTTCAAAAAC
27543 TATATATT
1 TATATATT
27551 ATATATGTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
30 28 0.48
31 4 0.07
33 2 0.03
34 4 0.07
35 20 0.34
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.44
Consensus pattern (30 bp):
TATATATTTTTTCAAAATATTTTCAAAAAC
Found at i:27613 original size:75 final size:75
Alignment explanation
Indices: 27508--27703 Score: 263
Period size: 75 Copynumber: 2.6 Consensus size: 75
27498 TTGTAAAAAC
** **
27508 TATATTATATATA-TATTCAAAATACTTTCAAAAACTATATATTATATATGTTTTCAAAATGTTT
1 TATATTATATATAGT-TTCAAAACGCTTTCAAAAACTATATATTATATATGTTTTCAAAACATTT
27572 TTCAAAAACTA
65 TTCAAAAACTA
* * * *
27583 TATATTATATAT-GTTTGAATAATGTTTTCAAAAACTATATATTATATATTTTTTCAAAACATTT
1 TATATTATATATAGTTTCAA-AACGCTTTCAAAAACTATATATTATATATGTTTTCAAAACATTT
*
27647 TTTAAAAACTA
65 TTCAAAAACTA
*
27658 TATATTATATATATTTTCAAAACGCTTTCAAAAACTATATA-TATAT
1 TATATTATATATAGTTTCAAAACGCTTTCAAAAACTATATATTATAT
27704 TATATATATA
Statistics
Matches: 107, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
74 9 0.08
75 93 0.87
76 5 0.05
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (75 bp):
TATATTATATATAGTTTCAAAACGCTTTCAAAAACTATATATTATATATGTTTTCAAAACATTTT
TCAAAAACTA
Found at i:27749 original size:2 final size:2
Alignment explanation
Indices: 27693--27730 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
27683 TTTCAAAAAC
27693 TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27731 GTTTTCTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:28020 original size:29 final size:29
Alignment explanation
Indices: 27978--28045 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
27968 AGAATAGAGG
27978 GGGACGACTTCTTGTTGTTGAGCCATACT
1 GGGACGACTTCTTGTTGTTGAGCCATACT
28007 GGGACGACTTCTTGTTGTTGAGCCATACT
1 GGGACGACTTCTTGTTGTTGAGCCATACT
28036 GTGGACGACT
1 G-GGACGACT
28046 CAAGAATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 30 0.79
30 8 0.21
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (29 bp):
GGGACGACTTCTTGTTGTTGAGCCATACT
Found at i:28626 original size:124 final size:124
Alignment explanation
Indices: 28372--28631 Score: 400
Period size: 124 Copynumber: 2.1 Consensus size: 124
28362 CTTCCTCGTG
* * * *
28372 AAGTTGAAATCGTGGATTGCTCCTTCGCTGTGAAGTTAAGCTTTGAATTGGATGTTCTTCGTTGT
1 AAGTTGAAATTGTGGATGGCTCCTTCGCTGTGAAGTTAAGCTTTAAATTGGATGTACTTCGTTGT
28437 GAAGTTGAAATCCAATCTTGTAAATTGTCTCGCCTCAAGTTTAATATATTTCATTGTGA
66 GAAGTTGAAATCCAATCTTGTAAATTGTCTCGCCTCAAGTTTAATATATTTCATTGTGA
* *
28496 AA-TTGAAATTGTGGATGGCTCCTTCGCTGTGAAGTTGAGCTTTAAATTGGATGTCACTTTGTTG
1 AAGTTGAAATTGTGGATGGCTCCTTCGCTGTGAAGTTAAGCTTTAAATTGGATGT-ACTTCGTTG
* * *
28560 TGAAGTTGAAATCCAATCTTGTAAATTG-CATCGCTTCGATTTTAATATATTTCATTGT-A
65 TGAAGTTGAAATCCAATCTTGTAAATTGTC-TCGCCTCAAGTTTAATATATTTCATTGTGA
28619 AAGTTGAAATTGT
1 AAGTTGAAATTGT
28632 CTCTAACAAG
Statistics
Matches: 124, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
123 52 0.42
124 72 0.58
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (124 bp):
AAGTTGAAATTGTGGATGGCTCCTTCGCTGTGAAGTTAAGCTTTAAATTGGATGTACTTCGTTGT
GAAGTTGAAATCCAATCTTGTAAATTGTCTCGCCTCAAGTTTAATATATTTCATTGTGA
Found at i:28804 original size:22 final size:22
Alignment explanation
Indices: 28777--28835 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
28767 TGATGACTCT
28777 TGATTCTAGAATCTTGAATTTC
1 TGATTCTAGAATCTTGAATTTC
28799 TGATTCTAGAATCTTGAATTTC
1 TGATTCTAGAATCTTGAATTTC
*
28821 TGATTCTTG-ATCTTG
1 TGATTCTAGAATCTTG
28836 GATTCTTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 6 0.17
22 30 0.83
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (22 bp):
TGATTCTAGAATCTTGAATTTC
Found at i:38377 original size:14 final size:14
Alignment explanation
Indices: 38358--38385 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38348 TTCGGGAGTC
38358 GTTACAGTCAAGGA
1 GTTACAGTCAAGGA
38372 GTTACAGTCAAGGA
1 GTTACAGTCAAGGA
38386 AGGATTAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (14 bp):
GTTACAGTCAAGGA
Found at i:39105 original size:30 final size:30
Alignment explanation
Indices: 39071--39137 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
39061 CATTAAGGGC
39071 AAAAATGGAATTTCTTATTGAATGGAATAA
1 AAAAATGGAATTTCTTATTGAATGGAATAA
39101 AAAAATGGAATTTCTTATTGAATGGAATAA
1 AAAAATGGAATTTCTTATTGAATGGAATAA
39131 AAAAATG
1 AAAAATG
39138 TCATTATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.49, C:0.03, G:0.16, T:0.31
Consensus pattern (30 bp):
AAAAATGGAATTTCTTATTGAATGGAATAA
Found at i:40896 original size:33 final size:33
Alignment explanation
Indices: 40854--40916 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
40844 CCTAGTACAG
40854 ATGGTGGACACGACCTTATGTGTCATACGGGTT
1 ATGGTGGACACGACCTTATGTGTCATACGGGTT
40887 ATGGTGGACACGACCTTATGTGTCATACGG
1 ATGGTGGACACGACCTTATGTGTCATACGG
40917 ATTAGCACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACGGGTT
Found at i:41017 original size:20 final size:20
Alignment explanation
Indices: 40980--41022 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
40970 TATATTTGGC
* *
40980 TATTGTCTATTGTTTATGAT
1 TATTGTCTATGGTATATGAT
*
41000 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATATGAT
41020 TAT
1 TAT
41023 GGAATAATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.19, T:0.56
Consensus pattern (20 bp):
TATTGTCTATGGTATATGAT
Found at i:41138 original size:46 final size:45
Alignment explanation
Indices: 41034--41219 Score: 293
Period size: 46 Copynumber: 4.1 Consensus size: 45
41024 GAATAATGAC
41034 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGG-ATAAATGGT
1 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTATAAATGGT
* *
41078 AAGTATATTTGTAAAATAAGCTTACGAGCTTATGGTATTAAATGGT
1 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTA-TAAATGGT
*
41124 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTATTAAATTGT
1 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTA-TAAATGGT
* * *
41170 AAGTATTTTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGT
1 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTATAAATGGT
41215 AAGTG
1 AAGTG
41220 ATTTTATTTT
Statistics
Matches: 130, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
44 33 0.25
45 12 0.09
46 85 0.65
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.34
Consensus pattern (45 bp):
AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTATAAATGGT
Found at i:45478 original size:26 final size:26
Alignment explanation
Indices: 45427--45478 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
45417 ACAAAAACAG
** *
45427 AAAATAAATAAAAAGTTAAAAGATAA
1 AAAATAAATAAAAAGACAAAAAATAA
45453 AAAATAAATAAAAA-ACAATAAAATAA
1 AAAATAAATAAAAAGACAA-AAAATAA
45479 TAAACCAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (26 bp):
AAAATAAATAAAAAGACAAAAAATAA
Found at i:45561 original size:24 final size:21
Alignment explanation
Indices: 45519--45561 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
45509 TATAGTATAA
45519 TATATAAATATTTTTAAAAAC
1 TATATAAATATTTTTAAAAAC
*
45540 TATATAACATATATTTTCAAAA
1 TATATAA-ATAT-TTTTAAAAA
45562 TGTTTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 8 0.42
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (21 bp):
TATATAAATATTTTTAAAAAC
Found at i:45654 original size:24 final size:26
Alignment explanation
Indices: 45605--45667 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
45595 TTTTTCAAAT
45605 TATTTTCAAAAACTATATATTATATA
1 TATTTTCAAAAACTATATATTATATA
45631 TATTTTCAAAAACTATATATTATATA
1 TATTTTCAAAAACTATATATTATATA
*
45657 TGTTTTCAAAA
1 TATTTTCAAAA
45668 TATTTTTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (26 bp):
TATTTTCAAAAACTATATATTATATA
Found at i:45695 original size:2 final size:2
Alignment explanation
Indices: 45682--45713 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
45672 TTTCAAAAAC
45682 TA TA TA TCA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
45714 TCAAAATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45711 original size:63 final size:61
Alignment explanation
Indices: 45573--45730 Score: 187
Period size: 63 Copynumber: 2.6 Consensus size: 61
45563 GTTTTCAAAA
* * *
45573 ATTATATATATATATA-TATAT-TTTTTTCAAATTATTTTCAAAAACTATATATTATATAT
1 ATTATATATATATATATTATATATGTTTTCAAAATATTTTCAAAAACTATATATCATATAT
* * *
45632 ATTTTCAAAAACTATATATTATATATGTTTTCAAAATATTTTTCAAAAACTATATATCATATAT
1 ATTAT-ATATA-TATATATTATATATGTTTTCAAAATA-TTTTCAAAAACTATATATCATATAT
*
45696 ATATATATATATATATATTCA-AAATGTTTTCAAAA
1 AT-TATATATATATATATT-ATATATGTTTTCAAAA
45731 ATTATATATT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
59 4 0.05
60 3 0.04
61 6 0.07
62 5 0.06
63 32 0.39
64 30 0.37
65 2 0.02
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.47
Consensus pattern (61 bp):
ATTATATATATATATATTATATATGTTTTCAAAATATTTTCAAAAACTATATATCATATAT
Found at i:45729 original size:51 final size:51
Alignment explanation
Indices: 45644--45746 Score: 145
Period size: 51 Copynumber: 2.0 Consensus size: 51
45634 TTTCAAAAAC
* * *
45644 TATATATTATATATGTTTTCAAAATATTTTTCAAAAACTATATATCATATA
1 TATATATTATATATATATTCAAAATAGTTTTCAAAAACTATATATCATATA
* *
45695 TATATATATATATATATATTCAAAAT-GTTTTCAAAAATTATATATTATATA
1 TATATAT-TATATATATATTCAAAATAGTTTTCAAAAACTATATATCATATA
45746 T
1 T
45747 TTTTTCAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 30 0.65
52 16 0.35
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.48
Consensus pattern (51 bp):
TATATATTATATATATATTCAAAATAGTTTTCAAAAACTATATATCATATA
Found at i:45770 original size:39 final size:38
Alignment explanation
Indices: 45642--45822 Score: 150
Period size: 39 Copynumber: 4.4 Consensus size: 38
45632 ATTTTCAAAA
*
45642 ACTATATATTATATATGTTTTCAAAATATTTTTCAAAA
1 ACTATATATTATATATTTTTTCAAAATATTTTTCAAAA
* *
45680 ACTATATATCATATATATATATATATATATATATTCAAAATGTTTTCAAAA
1 ACTATATAT--TATATAT-T-T-T-T-T-CA-A---AATAT-TTTTCAAAA
* *
45731 ATTATATATTATATATTTTTTCAAAATATTTTTTAAAAA
1 ACTATATATTATATATTTTTTCAAAATA-TTTTTCAAAA
* *
45770 ACTATGTATTATATATATTTTT-AAAATA-CTTTCAAAA
1 ACTATATATTATATAT-TTTTTCAAAATATTTTTCAAAA
45807 ACTATATATTATATAT
1 ACTATATATTATATAT
45823 ATGATTTCTA
Statistics
Matches: 116, Mismatches: 12, Indels: 31
0.73 0.08 0.19
Matches are distributed among these distances:
37 22 0.19
38 9 0.08
39 31 0.27
40 13 0.11
42 2 0.02
43 2 0.02
44 2 0.02
45 2 0.02
46 2 0.02
47 2 0.02
48 1 0.01
49 7 0.06
50 4 0.03
51 17 0.15
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.48
Consensus pattern (38 bp):
ACTATATATTATATATTTTTTCAAAATATTTTTCAAAA
Found at i:45823 original size:39 final size:39
Alignment explanation
Indices: 45524--45829 Score: 178
Period size: 37 Copynumber: 7.9 Consensus size: 39
45514 TATAATATAT
* *
45524 AAATATTTTTAAAAAC--TATA-TA-ACATATATTTTCA
1 AAATATTTTCAAAAACTATATATTATATATATATTTTCA
* *
45559 AAATGTTTTCAAAAATTATATATATATATATATATTTTTTTCA
1 AAATATTTTCAAAAACTATATAT-TATATATATA---TTTTCA
*
45602 AATTATTTTCAAAAACTATATA-T-TATATATATTTTCA
1 AAATATTTTCAAAAACTATATATTATATATATATTTTCA
* * ** * * *
45639 AAA-ACTAT-ATATTA-TATATGTTTTCA-AAATATTTTTCA
1 AAATATTTTCA-AAAACTATATATTAT-ATATATA-TTTTCA
* * * *
45677 AAA-ACTATAT-ATCATA-TATATATATATATATATATATTCA
1 AAATA-T-TTTCA-AAAACTATATAT-TATATATATATTTTCA
* *
45717 AAATGTTTTCAAAAATTATATATTATATAT-T-TTTTCA
1 AAATATTTTCAAAAACTATATATTATATATATATTTTCA
* *
45754 AAATATTTTTTAAAAAACTATGTATTATATATAT-TTTT-A
1 AAATA--TTTTCAAAAACTATATATTATATATATATTTTCA
*
45793 AAATACTTTCAAAAACTATATATTATATATATGATTT
1 AAATATTTTCAAAAACTATATATTATATATAT-ATTT
45830 CTAAAATTAT
Statistics
Matches: 213, Mismatches: 33, Indels: 46
0.73 0.11 0.16
Matches are distributed among these distances:
35 19 0.09
36 6 0.03
37 50 0.23
38 12 0.06
39 44 0.21
40 50 0.23
41 7 0.03
43 25 0.12
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (39 bp):
AAATATTTTCAAAAACTATATATTATATATATATTTTCA
Found at i:48984 original size:22 final size:23
Alignment explanation
Indices: 48958--49038 Score: 66
Period size: 22 Copynumber: 3.7 Consensus size: 23
48948 TAGATAACTA
*
48958 AAGTGCATTAGCACTAG-TATTG
1 AAGTGCATTAGCACTAGATATAG
*
48980 AAGTGTC-TCAGCACT-GATATAG
1 AAGTG-CATTAGCACTAGATATAG
*
49002 AAGTGCATTTGCACTA-ATACTA-
1 AAGTGCATTAGCACTAGATA-TAG
49024 AAGTGTC-TTAGCACT
1 AAGTG-CATTAGCACT
49039 GTTGAGAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
21 2 0.04
22 42 0.88
23 4 0.08
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (23 bp):
AAGTGCATTAGCACTAGATATAG
Found at i:49203 original size:20 final size:20
Alignment explanation
Indices: 49178--49215 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
49168 TACTGATCAT
49178 TTTAGTATCGATATCAAACC
1 TTTAGTATCGATATCAAACC
*
49198 TTTAGTATCGGTATCAAA
1 TTTAGTATCGATATCAAA
49216 ATCGGTCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (20 bp):
TTTAGTATCGATATCAAACC
Found at i:55233 original size:3 final size:3
Alignment explanation
Indices: 55225--55274 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
55215 TATTTACAAT
55225 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55273 AT
1 AT
55275 GGATAAGTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:55301 original size:23 final size:23
Alignment explanation
Indices: 55275--55331 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
55265 TAATAATAAT
55275 GGATAAGTGAGGACTTAAACCTA
1 GGATAAGTGAGGACTTAAACCTA
55298 GGATAAGTGAGGACTTAAACCTA
1 GGATAAGTGAGGACTTAAACCTA
55321 GG-TCAAGTGAG
1 GGAT-AAGTGAG
55332 AATATGAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 1 0.03
23 32 0.97
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.21
Consensus pattern (23 bp):
GGATAAGTGAGGACTTAAACCTA
Found at i:57648 original size:10 final size:9
Alignment explanation
Indices: 57618--57647 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
57608 AAGGTTATGA
57618 TTTGGGATT
1 TTTGGGATT
57627 TTTGGGATT
1 TTTGGGATT
*
57636 TTTGGGCTT
1 TTTGGGATT
57645 TTT
1 TTT
57648 TATAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.07, C:0.03, G:0.30, T:0.60
Consensus pattern (9 bp):
TTTGGGATT
Found at i:59026 original size:2 final size:2
Alignment explanation
Indices: 59019--59058 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
59009 CGAGATCCTT
59019 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59059 GTCTTCTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61444 original size:14 final size:14
Alignment explanation
Indices: 61409--61451 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
61399 AGTAAAATCC
61409 ATAAAATATCAAAG
1 ATAAAATATCAAAG
*
61423 ATATAATATCAAA-
1 ATAAAATATCAAAG
*
61436 ATGAAAATATCCAAG
1 AT-AAAATATCAAAG
61451 A
1 A
61452 ACCAAATACT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 2 0.08
14 21 0.88
15 1 0.04
ACGTcount: A:0.60, C:0.09, G:0.07, T:0.23
Consensus pattern (14 bp):
ATAAAATATCAAAG
Found at i:73411 original size:20 final size:21
Alignment explanation
Indices: 73386--73442 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
73376 CTGATTCAAT
*
73386 TAGTATCGATACCTA-TGAGG
1 TAGTATCGATACCTAGTAAGG
73406 TAGTATCGATACCATAGTAAGG
1 TAGTATCGATACC-TAGTAAGG
*
73428 -GGTATCGATACCTAG
1 TAGTATCGATACCTAG
73443 AAATATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.48
21 13 0.39
22 4 0.12
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCTAGTAAGG
Found at i:73593 original size:95 final size:96
Alignment explanation
Indices: 73405--73581 Score: 212
Period size: 95 Copynumber: 1.9 Consensus size: 96
73395 TACCTATGAG
* * * * *
73405 GTAGTATCGATACCATAGTAAGGGGTATCGATACCTAGAAATATTAAATCTAATATTGGTATCGA
1 GTAGTATCAATACCATAGTAAGGGGTATCAATACCTAGAAACATCAAACCTAATATTGGTATCGA
* *** *
73470 TACCGGTAGGGGGTATCAGTACAATAGTAGT
66 CACCCAAAAGGGGTATCAGTACAATAGTAGT
* * * * *
73501 GTAGTATCAATACCATGGTAA-GGGTATCAATACCTGGAAACATCGAACCTATTTTTGGTATCGA
1 GTAGTATCAATACCATAGTAAGGGGTATCAATACCTAGAAACATCAAACCTAATATTGGTATCGA
73565 CACCCAAAAGGGGTATC
66 CACCCAAAAGGGGTATC
73582 GGTATCATAG
Statistics
Matches: 66, Mismatches: 15, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
95 47 0.71
96 19 0.29
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.28
Consensus pattern (96 bp):
GTAGTATCAATACCATAGTAAGGGGTATCAATACCTAGAAACATCAAACCTAATATTGGTATCGA
CACCCAAAAGGGGTATCAGTACAATAGTAGT
Found at i:74021 original size:55 final size:55
Alignment explanation
Indices: 73953--74189 Score: 384
Period size: 55 Copynumber: 4.3 Consensus size: 55
73943 ATGTGTGTTG
73953 CAGGCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTA
1 CAGGCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTA
* *
74008 CAAGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTA
1 CAGGCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTA
* *
74063 CAGGCACTATGTGTGGATATTCACGAAATTCATCATGAGTTGATGAATCACCGTA
1 CAGGCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTA
* * * *
74118 TAGGCACTTTGTATGCATATTCACGAAATTCATCATGAGTCGATGAATCAGCGTA
1 CAGGCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTA
* *
74173 CATGCACTATGTGTGCA
1 CAGGCACTTTGTGTGCA
74190 GCCCACAGAA
Statistics
Matches: 166, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 166 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (55 bp):
CAGGCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTA
Found at i:74058 original size:27 final size:27
Alignment explanation
Indices: 74028--74113 Score: 68
Period size: 26 Copynumber: 3.1 Consensus size: 27
74018 GTGTGCATAT
*
74028 TCACGGAATTCATCATGAGTTGATGAA
1 TCACGAAATTCATCATGAGTTGATGAA
* ** * * *
74055 TCACCGTACAGGCA-CTATGTGTGGAT-AT
1 TCA-CG-AAATTCATC-ATGAGTTGATGAA
74083 TCACGAAATTCATCATGAGTTGATGAA
1 TCACGAAATTCATCATGAGTTGATGAA
74110 TCAC
1 TCAC
74114 CGTATAGGCA
Statistics
Matches: 41, Mismatches: 13, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
26 12 0.29
27 11 0.27
28 7 0.17
29 11 0.27
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (27 bp):
TCACGAAATTCATCATGAGTTGATGAA
Found at i:80348 original size:20 final size:20
Alignment explanation
Indices: 80319--80374 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
80309 ATATTCAATC
* *
80319 AGTATTGATACCTA-TGAGG
1 AGTATCGATACCTAGTAAGG
80338 TAGTATCGATACCATAGTAAGG
1 -AGTATCGATACC-TAGTAAGG
*
80360 GGTATCGATACCTAG
1 AGTATCGATACCTAG
80375 AAACATCGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
21 13 0.42
22 4 0.13
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (20 bp):
AGTATCGATACCTAGTAAGG
Found at i:80980 original size:55 final size:55
Alignment explanation
Indices: 80895--81128 Score: 389
Period size: 55 Copynumber: 4.3 Consensus size: 55
80885 TGTACTGCAG
80895 GCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACA-
1 GCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAT
*
80949 GACACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTACAT
1 G-CACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAT
* * * *
81005 GCACTATGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAAAG
1 GCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAT
*
81060 GCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCATACAT
1 GCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAT
*
81115 GCACTATGTGTGCA
1 GCACTTTGTGTGCA
81129 GCCCAAAGAA
Statistics
Matches: 168, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
54 1 0.01
55 166 0.99
56 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (55 bp):
GCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAT
Found at i:83077 original size:30 final size:30
Alignment explanation
Indices: 83041--83100 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
83031 ACTCCAATAT
83041 GAGTTACAAATGTCACATCAGAAATTCATA
1 GAGTTACAAATGTCACATCAGAAATTCATA
*
83071 GAGTTACAAATGTCATATCAGAAATTCATA
1 GAGTTACAAATGTCACATCAGAAATTCATA
83101 ATTGATCTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (30 bp):
GAGTTACAAATGTCACATCAGAAATTCATA
Found at i:83851 original size:40 final size:40
Alignment explanation
Indices: 83806--83911 Score: 140
Period size: 40 Copynumber: 2.6 Consensus size: 40
83796 ATAGGAGTCA
* * **
83806 AATATTTCACCATAGTGCTGAGGTCGAGCCTTGCTCATGT
1 AATATTGCAACATAGTGCTGAGGTCGAGCCTTGCTCACCT
* * *
83846 AATATTGCATCGTAGTGTTGAGGTCGAGCCTTGCTCACCT
1 AATATTGCAACATAGTGCTGAGGTCGAGCCTTGCTCACCT
*
83886 AATAATGCAACATAGTGCTGAGGTCG
1 AATATTGCAACATAGTGCTGAGGTCG
83912 GGCTTTACCC
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (40 bp):
AATATTGCAACATAGTGCTGAGGTCGAGCCTTGCTCACCT
Found at i:84200 original size:21 final size:22
Alignment explanation
Indices: 84166--84207 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
84156 AAAATAACAG
84166 TTATGATAAACATCATATGTAT
1 TTATGATAAACATCATATGTAT
84188 TTATGAT-AACATCATATGTA
1 TTATGATAAACATCATATGTA
84208 ATAAACAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (22 bp):
TTATGATAAACATCATATGTAT
Found at i:90104 original size:21 final size:23
Alignment explanation
Indices: 90078--90129 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
90068 TTCTAGAAAG
90078 GGAATTTTGGATATA-AATTA-A
1 GGAATTTTGGATATACAATTAGA
** *
90099 GGAATTCGGGTTATACAATTAGA
1 GGAATTTTGGATATACAATTAGA
90122 GGAATTTT
1 GGAATTTT
90130 AAAATTAGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 12 0.50
22 5 0.21
23 7 0.29
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.37
Consensus pattern (23 bp):
GGAATTTTGGATATACAATTAGA
Found at i:90879 original size:2 final size:2
Alignment explanation
Indices: 90874--90919 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
90864 ACACACACAA
90874 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90916 AT AT
1 AT AT
90920 TAAATATTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:91454 original size:2 final size:2
Alignment explanation
Indices: 91447--91471 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
91437 AAATAAAGTC
91447 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
91472 CTTTTAAAAA
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:92843 original size:78 final size:78
Alignment explanation
Indices: 92756--92904 Score: 237
Period size: 78 Copynumber: 1.9 Consensus size: 78
92746 ATATAGTAAG
*
92756 TAAACATTAAAAGAATGTAATTTTAATTACAACTCTTTTAATGGATATTTAATTTAGAA-TAATT
1 TAAACATTAAAAGAATGTAATTTGAATTACAACTCTTTTAATGGATATTTAATTT-GAATTAATT
92820 GAATAAGGATAAAA
65 GAATAAGGATAAAA
* * *
92834 TAAACATTAAAAGAATGTCATTTGGATTATAACTCTTTTAATGGATATTTAATTTGAATTAATTG
1 TAAACATTAAAAGAATGTAATTTGAATTACAACTCTTTTAATGGATATTTAATTTGAATTAATTG
*
92899 ATTAAG
66 AATAAG
92905 AATTTAATTA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
77 3 0.05
78 62 0.95
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (78 bp):
TAAACATTAAAAGAATGTAATTTGAATTACAACTCTTTTAATGGATATTTAATTTGAATTAATTG
AATAAGGATAAAA
Found at i:112192 original size:23 final size:23
Alignment explanation
Indices: 112162--112209 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
112152 AATTTATAAA
*
112162 ATTTAAAATTCTAAATGTAAATT
1 ATTTAAAATTTTAAATGTAAATT
112185 ATTTAAAATTTTAAATGTAAATT
1 ATTTAAAATTTTAAATGTAAATT
112208 AT
1 AT
112210 AAATTAGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (23 bp):
ATTTAAAATTTTAAATGTAAATT
Found at i:112192 original size:30 final size:31
Alignment explanation
Indices: 112158--112239 Score: 98
Period size: 30 Copynumber: 2.7 Consensus size: 31
112148 ATTTAATTTA
* * *
112158 TAAAATTTAAAATTCTAAA-TGTAAATTATT
1 TAAAATTTTAAATTCTAAATTATAAATTAGT
*
112188 TAAAATTTTAAA-TGTAAATTATAAATTAGT
1 TAAAATTTTAAATTCTAAATTATAAATTAGT
*
112218 TAAAATTTTAAA-TGTAAATTAT
1 TAAAATTTTAAATTCTAAATTAT
112240 TTAAAATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
29 5 0.11
30 42 0.89
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.44
Consensus pattern (31 bp):
TAAAATTTTAAATTCTAAATTATAAATTAGT
Found at i:112223 original size:23 final size:22
Alignment explanation
Indices: 112197--112246 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
112187 TTAAAATTTT
112197 AAATGTAAATTATAAATTAGTTA
1 AAATGTAAA-TATAAATTAGTTA
* * *
112220 AAATTTTAAATGTAAATTATTTA
1 AAA-TGTAAATATAAATTAGTTA
112243 AAAT
1 AAAT
112247 AAATGGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 17 0.74
24 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (22 bp):
AAATGTAAATATAAATTAGTTA
Found at i:116706 original size:2 final size:2
Alignment explanation
Indices: 116699--116753 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
116689 GAACAAAAAC
116699 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
116741 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
116754 ACATCATACA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:116930 original size:23 final size:23
Alignment explanation
Indices: 116904--116992 Score: 81
Period size: 23 Copynumber: 3.9 Consensus size: 23
116894 CATTGAAGTG
116904 CCACTTAGAAATGTCCCGAAGGA
1 CCACTTAGAAATGTCCCGAAGGA
* * *
116927 CCACATAGATATGTCCTGAAGGA
1 CCACTTAGAAATGTCCCGAAGGA
* **
116950 CC-GTGTAGAAATGTCTTGAAGGA
1 CCACT-TAGAAATGTCCCGAAGGA
* * *
116973 CCACGTAGAATTATCCCGAA
1 CCACTTAGAAATGTCCCGAA
116993 TGACTGCGTA
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (23 bp):
CCACTTAGAAATGTCCCGAAGGA
Found at i:117004 original size:46 final size:46
Alignment explanation
Indices: 116909--117005 Score: 106
Period size: 46 Copynumber: 2.1 Consensus size: 46
116899 AAGTGCCACT
* * *
116909 TAGAAATGTCCCGAAGGACCACATAGATATGTCCTGAAGGACCGTG
1 TAGAAATGTCCCGAAGGACCACATAGATATATCCCGAAGGACCGCG
** * * *
116955 TAGAAATGTCTTGAAGGACCACGTAGA-ATTATCCCGAATGACTGCG
1 TAGAAATGTCCCGAAGGACCACATAGATA-TATCCCGAAGGACCGCG
117001 TAGAA
1 TAGAA
117006 CCCTTGACTC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
45 1 0.02
46 41 0.98
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.22
Consensus pattern (46 bp):
TAGAAATGTCCCGAAGGACCACATAGATATATCCCGAAGGACCGCG
Found at i:117175 original size:14 final size:14
Alignment explanation
Indices: 117156--117189 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
117146 TAGGTCAATG
117156 TCACATAACTTATA
1 TCACATAACTTATA
*
117170 TCACATAGCTTATA
1 TCACATAACTTATA
117184 TCACAT
1 TCACAT
117190 TTTCATGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (14 bp):
TCACATAACTTATA
Found at i:122246 original size:23 final size:22
Alignment explanation
Indices: 122220--122298 Score: 86
Period size: 23 Copynumber: 3.5 Consensus size: 22
122210 CACCGAGGTG
122220 CCACGTAGAAATGTCCCAAAGGA
1 CCACGTAGAAATGTCCCAAA-GA
* * *
122243 CCACATAGATATGTCCCGAATGA
1 CCACGTAGAAATGTCCC-AAAGA
* *
122266 CCGCGTAGAAATGTCTCGAAAGA
1 CCACGTAGAAATGTC-CCAAAGA
122289 CCACGTAGAA
1 CCACGTAGAA
122299 TTTCCCGAAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (22 bp):
CCACGTAGAAATGTCCCAAAGA
Found at i:122433 original size:16 final size:15
Alignment explanation
Indices: 122407--122495 Score: 56
Period size: 16 Copynumber: 5.8 Consensus size: 15
122397 TCCCATAGCT
122407 TATATCACATAGACA
1 TATATCACATAGACA
122422 TATATCCACATAGACCA
1 TATAT-CACATAGA-CA
* *
122439 T-TGTCACATAGA-T
1 TATATCACATAGACA
* * ***
122452 TATGTCATATTCTCA
1 TATATCACATAGACA
122467 TATAATCACATAGATCA
1 TAT-ATCACATAGA-CA
*
122484 TATAACACATAG
1 TATATCACATAG
122496 GTCATGTAGA
Statistics
Matches: 55, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
13 1 0.02
14 7 0.13
15 16 0.29
16 23 0.42
17 8 0.15
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.31
Consensus pattern (15 bp):
TATATCACATAGACA
Found at i:122500 original size:16 final size:17
Alignment explanation
Indices: 122464--122500 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
122454 TGTCATATTC
122464 TCATATAATCACATAGA
1 TCATATAATCACATAGA
*
122481 TCATATAA-CACATAGG
1 TCATATAATCACATAGA
122497 TCAT
1 TCAT
122501 GTAGAATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (17 bp):
TCATATAATCACATAGA
Found at i:123032 original size:17 final size:16
Alignment explanation
Indices: 122987--123033 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
122977 TACTTGTACA
122987 TTGGTATCGATAC-CC
1 TTGGTATCGATACTCC
*
123002 TTGGTAAT-GTTACTCC
1 TTGGT-ATCGATACTCC
123018 TTCGGTATCGATACTC
1 TT-GGTATCGATACTC
123034 TTTTAAGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 9 0.35
16 8 0.31
17 9 0.35
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (16 bp):
TTGGTATCGATACTCC
Found at i:127322 original size:43 final size:46
Alignment explanation
Indices: 127274--127384 Score: 129
Period size: 49 Copynumber: 2.4 Consensus size: 46
127264 GTAACCATGC
127274 AAATAAGCTTATGAGCTTACGGAA-T-AATGGCAAGTA-TTGAAAA
1 AAATAAGCTTATGAGCTTACGGAATTAAATGGCAAGTATTTGAAAA
* * * **
127317 AAATAAGCTTACGAGCTTATGGAATTTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTACGGAA--TTAAATGGCAAGTA-TTTGAAAA
127366 AAATAAGCTTATGAGCTTA
1 AAATAAGCTTATGAGCTTA
127385 TGGGATAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
43 22 0.39
46 1 0.02
47 10 0.18
49 23 0.41
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.32
Consensus pattern (46 bp):
AAATAAGCTTATGAGCTTACGGAATTAAATGGCAAGTATTTGAAAA
Found at i:127845 original size:22 final size:22
Alignment explanation
Indices: 127820--127894 Score: 150
Period size: 22 Copynumber: 3.4 Consensus size: 22
127810 AAAGGGGTAC
127820 CGATTCCCCTGCTACAGGGAAT
1 CGATTCCCCTGCTACAGGGAAT
127842 CGATTCCCCTGCTACAGGGAAT
1 CGATTCCCCTGCTACAGGGAAT
127864 CGATTCCCCTGCTACAGGGAAT
1 CGATTCCCCTGCTACAGGGAAT
127886 CGATTCCCC
1 CGATTCCCC
127895 AACTGTTCAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (22 bp):
CGATTCCCCTGCTACAGGGAAT
Done.