Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000609.1 Hibiscus syriacus cultivar Beakdansim tig00001182_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: 67995
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:10085 original size:21 final size:19
Alignment explanation
Indices: 10014--10127 Score: 57
Period size: 20 Copynumber: 5.6 Consensus size: 19
10004 ATTTCCAGAT
* *
10014 TCGCAACGCGATTTTGACCA
1 TCGCAATGCGATTTTGA-AA
*
10034 TCGCATTGCGATTTTCGAAA
1 TCGCAATGCGATTTT-GAAA
**
10054 TACGCGTTGCGATTTTAGATAA
1 T-CGCAATGCGATTTT-GA-AA
* *
10076 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGATTTTG-AAA
* * * *
10096 GCGCAATACGAATATGTAAA
1 TCGCAATGCGATTTTG-AAA
*
10116 TCGCAACGCGAT
1 TCGCAATGCGAT
10128 AACACGTGAT
Statistics
Matches: 75, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
20 44 0.59
21 28 0.37
22 3 0.04
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (19 bp):
TCGCAATGCGATTTTGAAA
Found at i:10102 original size:20 final size:20
Alignment explanation
Indices: 10077--10126 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
10067 TTTAGATAAT
10077 CGCAATGCGAATATGTAAAG
1 CGCAATGCGAATATGTAAAG
* *
10097 CGCAATACGAATATGTAAAT
1 CGCAATGCGAATATGTAAAG
*
10117 CGCAACGCGA
1 CGCAATGCGA
10127 TAACACGTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
CGCAATGCGAATATGTAAAG
Found at i:10140 original size:21 final size:21
Alignment explanation
Indices: 10115--10189 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
10105 GAATATGTAA
10115 ATCGCAACGCGATAACACGTG
1 ATCGCAACGCGATAACACGTG
* *
10136 ATCGCAACACGAT-TCTGAC-T-
1 ATCGCAACGCGATAAC--ACGTG
*
10156 ATCGCAACGCGATAATACGTG
1 ATCGCAACGCGATAACACGTG
*
10177 ATGGCAACGCGAT
1 ATCGCAACGCGAT
10190 TCTGACTATC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
19 2 0.05
20 14 0.33
21 25 0.58
22 2 0.05
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGATAACACGTG
Found at i:10160 original size:41 final size:41
Alignment explanation
Indices: 10115--10205 Score: 155
Period size: 41 Copynumber: 2.2 Consensus size: 41
10105 GAATATGTAA
10115 ATCGCAACGCGATAACACGTGATCGCAACACGATTCTGACT
1 ATCGCAACGCGATAACACGTGATCGCAACACGATTCTGACT
* * *
10156 ATCGCAACGCGATAATACGTGATGGCAACGCGATTCTGACT
1 ATCGCAACGCGATAACACGTGATCGCAACACGATTCTGACT
10197 ATCGCAACG
1 ATCGCAACG
10206 AAATTCTGAC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGATAACACGTGATCGCAACACGATTCTGACT
Found at i:10161 original size:20 final size:20
Alignment explanation
Indices: 10136--10221 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 20
10126 ATAACACGTG
10136 ATCGCAACACGATTCTGACT
1 ATCGCAACACGATTCTGACT
* **
10156 ATCGCAACGCGATAAT-ACGT
1 ATCGCAACACGATTCTGAC-T
* *
10176 GATGGCAACGCGATTCTGACT
1 -ATCGCAACACGATTCTGACT
*
10197 ATCGCAACGA-AATTCTGACT
1 ATCGCAAC-ACGATTCTGACT
10217 ATCGC
1 ATCGC
10222 GTTGCGATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
19 2 0.04
20 35 0.66
21 14 0.26
22 2 0.04
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAACACGATTCTGACT
Found at i:10473 original size:26 final size:22
Alignment explanation
Indices: 10390--10462 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
10380 CTACGACGAC
* *
10390 ATCCGTCCTCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGGCGAA
* *
10412 ATCCATCCCCATTTCCGGCGAA
1 ATCCGTCCCCATCTCCGGCGAA
10434 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGGCGAA
10456 ATCCGTC
1 ATCCGTC
10463 TATCTCCATC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.21, C:0.42, G:0.15, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGGCGAA
Found at i:10824 original size:33 final size:34
Alignment explanation
Indices: 10779--10861 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 34
10769 CGCAACGAAA
10779 AAATTCGCGTTGCGATTATCTCGTTGCAATAG-C
1 AAATTCGCGTTGCGATTATCTCGTTGCAATAGTC
* * *
10812 CATTTCGCGTTGCGATTATCTCGTTGCGATAGTC
1 AAATTCGCGTTGCGATTATCTCGTTGCAATAGTC
10846 AAATTCGCGTTGCGAT
1 AAATTCGCGTTGCGAT
10862 AATCATTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 29 0.66
34 15 0.34
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (34 bp):
AAATTCGCGTTGCGATTATCTCGTTGCAATAGTC
Found at i:10872 original size:20 final size:20
Alignment explanation
Indices: 10833--10901 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
10823 GCGATTATCT
* **
10833 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAATCATTTTCG
10853 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAATCATTTTCG
* * **
10873 TGTTGTGATTTTCATTTTCG
1 CGTTGCGATAATCATTTTCG
*
10893 TGTTGCGAT
1 CGTTGCGAT
10902 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.43
Consensus pattern (20 bp):
CGTTGCGATAATCATTTTCG
Found at i:10902 original size:20 final size:20
Alignment explanation
Indices: 10849--10904 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
10839 GATAGTCAAA
* **
10849 TTCGCGTTGCGATAATCATT
1 TTCGTGTTGCGATTTTCATT
*
10869 TTCGTGTTGTGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
10889 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
10905 AAGTTTCAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.12, C:0.14, G:0.21, T:0.52
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:10911 original size:20 final size:20
Alignment explanation
Indices: 10868--10911 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
10858 CGATAATCAT
* * *
10868 TTTCGTGTTGTGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
10888 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
10908 TTTC
1 TTTC
10912 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:12907 original size:20 final size:20
Alignment explanation
Indices: 12882--13041 Score: 146
Period size: 20 Copynumber: 8.6 Consensus size: 20
12872 AGAAGAATAG
* *
12882 TCGCAACACGAAAATGATTA
1 TCGCAACGCGAAAATGACTA
**
12902 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
*
12922 TCGCAACG-G--GAT-A--A
1 TCGCAACGCGAAAATGACTA
*
12936 TCGCAATGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
12956 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
12976 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
*
12996 TCGCAACG-G--GAT-A--A
1 TCGCAACGCGAAAATGACTA
*
13010 TCGCAATGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
13030 TCGCAACGCGAA
1 TCGCAACGCGAA
13042 TTTAGTTTCG
Statistics
Matches: 112, Mismatches: 16, Indels: 24
0.74 0.11 0.16
Matches are distributed among these distances:
14 16 0.14
15 2 0.02
16 2 0.02
17 6 0.05
18 2 0.02
19 2 0.02
20 82 0.73
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:13003 original size:74 final size:74
Alignment explanation
Indices: 12882--13041 Score: 302
Period size: 74 Copynumber: 2.2 Consensus size: 74
12872 AGAAGAATAG
* *
12882 TCGCAACACGAAAATGATTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGA
1 TCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGA
12947 AAATGACTA
66 AAATGACTA
12956 TCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGA
1 TCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGA
13021 AAATGACTA
66 AAATGACTA
13030 TCGCAACGCGAA
1 TCGCAACGCGAA
13042 TTTAGTTTCG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
74 84 1.00
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (74 bp):
TCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGA
AAATGACTA
Found at i:13094 original size:33 final size:34
Alignment explanation
Indices: 13052--13118 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
13042 TTTAGTTTCG
* *
13052 CGTTGCGATAGTC-ATTTCGCGTTGCGATTATCA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAATCA
13085 CGTTGCGATAGTCAAATTCGCGTTGCGATAATCA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAATCA
13119 TTTTCGTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAATCA
Found at i:13124 original size:20 final size:19
Alignment explanation
Indices: 13047--13121 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 19
13037 GCGAATTTAG
13047 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGTCA
13066 TTTCGCGTTGCGAT--T-A
1 TTTCGCGTTGCGATAGTCA
*
13082 --TCACGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTC-A
* *
13100 ATTCGCGTTGCGATAATCA
1 TTTCGCGTTGCGATAGTCA
13119 TTT
1 TTT
13122 TCGTGTTACG
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
14 11 0.24
16 2 0.04
17 1 0.02
18 1 0.02
19 17 0.37
20 14 0.30
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:13133 original size:20 final size:20
Alignment explanation
Indices: 13110--13163 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
13100 ATTCGCGTTG
* *
13110 CGATAATCATTTTCGTGTTA
1 CGATAATAAGTTTCGTGTTA
**
13130 CGATTTTAAGTTTCGTGTTA
1 CGATAATAAGTTTCGTGTTA
**
13150 CGATTTTAAGTTTC
1 CGATAATAAGTTTC
13164 AGAAACTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (20 bp):
CGATAATAAGTTTCGTGTTA
Found at i:13717 original size:42 final size:42
Alignment explanation
Indices: 13651--13756 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
13641 CTGTCATCGT
* *
13651 TCAAGAGGCCTCTCCTATCATTCAAGAGGCCCCTATCATCCC
1 TCAAGAGGCCCCTCCCATCATTCAAGAGGCCCCTATCATCCC
* * * **
13693 TCAAGAGTCCCCTCCCATCGTTCAAGAGGCCCCTGTCATCGT
1 TCAAGAGGCCCCTCCCATCATTCAAGAGGCCCCTATCATCCC
* * *
13735 TGAAGAGGTCCCTCCCAACATT
1 TCAAGAGGCCCCTCCCATCATT
13757 ATAGCCCGAT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.24
Consensus pattern (42 bp):
TCAAGAGGCCCCTCCCATCATTCAAGAGGCCCCTATCATCCC
Found at i:13725 original size:21 final size:21
Alignment explanation
Indices: 13645--13751 Score: 106
Period size: 21 Copynumber: 5.1 Consensus size: 21
13635 ACTCACCTGT
*
13645 CATCGTTCAAGAGGCCTCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * **
13666 TATCATTCAAGAGGCCCCTAT
1 CATCGTTCAAGAGGCCCCTCC
** *
13687 CATCCCTCAAGAGTCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
**
13708 CATCGTTCAAGAGGCCCCTGT
1 CATCGTTCAAGAGGCCCCTCC
* *
13729 CATCGTTGAAGAGGTCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
13750 CA
1 CA
13752 ACATTATAGC
Statistics
Matches: 66, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.23
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:15199 original size:36 final size:30
Alignment explanation
Indices: 15119--15184 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
15109 ATAAGAGTTG
* *
15119 ATTTGTTTAATTTATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTATT
15149 ATTTGTTTAATTGATGTGTAAATAATTATT
1 ATTTGTTTAATTGATGTGTAAATAATTATT
15179 ATTTGT
1 ATTTGT
15185 GCTTGTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTATT
Found at i:15359 original size:20 final size:20
Alignment explanation
Indices: 15334--15576 Score: 226
Period size: 20 Copynumber: 12.8 Consensus size: 20
15324 GTGATTTTCT
* *
15334 CGTTGCAATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
15354 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
15374 CGTTGTGATAGTCAAA-TCG
1 CGTTGCGATAGTCAAATTCG
15393 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
15413 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
* * *
15433 CTTTACGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
**
15452 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
15472 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
15486 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
15506 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
15526 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* *
15540 CGTTGCGATATTCAAATTCT
1 CGTTGCGATAGTCAAATTCG
15560 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
15577 GAATGTGTAA
Statistics
Matches: 182, Mismatches: 27, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
14 20 0.11
16 2 0.01
18 2 0.01
19 36 0.20
20 122 0.67
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:15410 original size:59 final size:57
Alignment explanation
Indices: 15334--15576 Score: 223
Period size: 59 Copynumber: 4.3 Consensus size: 57
15324 GTGATTTTCT
* * *
15334 CGTTGCAATAGTCAAATTCCCGTTGCGATAATCAAATTCGCGTTGTGATAGTCAAATCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT-AT-AAATTCGCGTTGCGATAGTCAAATCG
* * **
15393 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCTTTACGATAGTCATTTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATA--TAAATTCGCGTTGCGATAGTCAAATCG
** * *
15452 CGTTGCGATAGTCATTTTCGCATTGCGAT-T--A-TCCCGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATATAAATTCGCGTTGCGATAGTCAAA-TCG
** * * * *
15506 CGTTGCGATAGTCATTTTCGCATTGCGAT-T--A-TCCCGTTGCGATATTCAAATTCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATATAAATTCGCGTTGCGATAGTCAAA-TCG
15560 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
15577 GAATGTGTAA
Statistics
Matches: 162, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
53 14 0.09
54 71 0.44
56 1 0.01
58 1 0.01
59 74 0.46
60 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (57 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATATAAATTCGCGTTGCGATAGTCAAATCG
Found at i:15524 original size:54 final size:54
Alignment explanation
Indices: 15374--15573 Score: 242
Period size: 54 Copynumber: 3.6 Consensus size: 54
15364 ATCAAATTCG
* ** * *
15374 CGTTGTGATAGTCAAA-TCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCG--A-TT--A-TCC
* * *
15433 CTTTACGATAGTC-ATTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
15486 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
* *
15540 CGTTGCGATATTCAAATTCTCGTTGCGATAGTCA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCA
15574 AATGAATGTG
Statistics
Matches: 126, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
53 13 0.10
54 72 0.57
56 2 0.02
57 1 0.01
58 1 0.01
59 37 0.29
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
Found at i:18059 original size:24 final size:24
Alignment explanation
Indices: 18032--18078 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
18022 CAAAATCCGA
18032 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
18056 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
18079 AATACCGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:18921 original size:20 final size:20
Alignment explanation
Indices: 18893--19059 Score: 201
Period size: 20 Copynumber: 8.3 Consensus size: 20
18883 AATTCAGTGA
*
18893 TGCGTTAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
18913 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
**
18933 TGCGATCACGT-ATTATCGCGT
1 TGCGAT-A-GTCAGAATCGCGT
* * *
18954 TGCGATAGTAAGAACCTCGT
1 TGCGATAGTCAGAATCGCGT
18974 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
*
18994 TGCGATAGTCCGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
* *
19014 TGCGATAGCCCGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
* * *
19034 TGTGATAGTCCGAATCGTGT
1 TGCGATAGTCAGAATCGCGT
19054 TGCGAT
1 TGCGAT
19060 TTACATATTC
Statistics
Matches: 128, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
19 2 0.02
20 109 0.85
21 15 0.12
22 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:19077 original size:60 final size:60
Alignment explanation
Indices: 18903--19079 Score: 180
Period size: 60 Copynumber: 2.9 Consensus size: 60
18893 TGCGTTAGTC
* * *
18903 AGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGA-TCACGTATTATCGCGTTGCGATAGTA
1 AGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTACATA-T-TCGCGTTGCGATAGCA
* * * * *
18964 AGAACCTCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCCGA-A-TCGCGTTGCGATAGCC
1 AGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGAT-TTAC-ATATTCGCGTTGCGATAGCA
* * * * *
19024 CGAATCGCGTTGTGATAGTCCGAATCGTGTTGCGATTTACATATTCGCATTGCGAT
1 AGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCGTTGCGAT
19080 TTACATATTC
Statistics
Matches: 94, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
58 1 0.01
59 3 0.03
60 55 0.59
61 33 0.35
63 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (60 bp):
AGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCGTTGCGATAGCA
Found at i:19078 original size:20 final size:20
Alignment explanation
Indices: 19053--19120 Score: 127
Period size: 20 Copynumber: 3.4 Consensus size: 20
19043 CCGAATCGTG
19053 TTGCGATTTACATATTCGCA
1 TTGCGATTTACATATTCGCA
19073 TTGCGATTTACATATTCGCA
1 TTGCGATTTACATATTCGCA
*
19093 TTGCGATTTACATATTCGTA
1 TTGCGATTTACATATTCGCA
19113 TTGCGATT
1 TTGCGATT
19121 ATCTAAAATC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.43
Consensus pattern (20 bp):
TTGCGATTTACATATTCGCA
Found at i:19230 original size:19 final size:19
Alignment explanation
Indices: 19206--19242 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19196 TGCGATAATG
*
19206 GAGATCACGTTGCGATTTA
1 GAGATCACATTGCGATTTA
*
19225 GAGATCGCATTGCGATTT
1 GAGATCACATTGCGATTT
19243 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCACATTGCGATTTA
Found at i:24155 original size:2 final size:2
Alignment explanation
Indices: 24148--24173 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24138 TCTTCAAAAC
24148 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
24174 TGATGATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26698 original size:60 final size:59
Alignment explanation
Indices: 26571--26698 Score: 134
Period size: 60 Copynumber: 2.1 Consensus size: 59
26561 ATAGTCATAT
* ** * *
26571 GACCATTTTATAATTTTTAATAGTTGAGGGACTCAATAAAGCAATGTTTTATAGTAAGTG
1 GACCATTTTATAATTTTTAATAGTCGAGAAACTCAAAAAAG-AATGTTCTATAGTAAGTG
* * *
26631 TATCATTTTATAATTTTTAATAGTCGAGAAACTCAAAAAAG-ATGTACTCTATAATTAAG-G
1 GACCATTTTATAATTTTTAATAGTCGAGAAACTCAAAAAAGAATGT--TCTAT-AGTAAGTG
26691 GACCATTT
1 GACCATTT
26699 GTGTACTTTA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
58 4 0.07
60 46 0.84
61 5 0.09
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (59 bp):
GACCATTTTATAATTTTTAATAGTCGAGAAACTCAAAAAAGAATGTTCTATAGTAAGTG
Found at i:28125 original size:197 final size:189
Alignment explanation
Indices: 27800--28195 Score: 521
Period size: 197 Copynumber: 2.1 Consensus size: 189
27790 ATAAAGTTTC
*
27800 ACCCGACCCGAATATATGAATTAGAAACTCGACTCGAAATAATAAAAAAAAATTATTCAATAAAA
1 ACCCGACCCGAATATATGAATTAGAAACTCGACTCAAAATAATAAAAAAAAATTATTCAATAAAA
27865 ACATACTTAATTGAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAG
66 ACATACTTAATTGAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAG
*** * * * *
27930 GTAAAATTATATAT-TTTT-GGGTTGGGTCGGGTATTTTTCACCTTAAACCTGAATTTG
131 GTAAAATTATATATATTTTCGGGTCAAGTCGGGTATTTTTCACCCTAAACCCGAACTCG
*
27987 ACCCGACCCGAATATATGAATTAGAACCCTGACCAGAC-CTAAAATAATAAAAAAAATATTTTTA
1 ACCCGACCCGAATATATGAATTAGAA-ACT---C-GACTC-AAAATAATAAAAAAAA-A---TTA
* * *
28051 TTCAATAAAAATAGTGATTTAATTGAAAAAAATTATATATAGA-GGGTATTATTGTAATTATTGC
56 TTCAATAAAAACA-T-ACTTAATTGAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCC
* *
28115 TAAATATATAAGGTAAAATTATATATATTTTCGGGTCAATTTGGGTATTTTTCACCCTAAACCCG
119 TAAATATATAAGGTAAAATTATATATATTTTCGGGTCAAGTCGGGTATTTTTCACCCTAAACCCG
28180 AACTCG
184 AACTCG
*
28186 ACCTGACCCG
1 ACCCGACCCG
28196 TCCCGAATAT
Statistics
Matches: 180, Mismatches: 15, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
187 26 0.14
188 2 0.01
191 2 0.01
192 18 0.10
193 1 0.01
196 15 0.08
197 47 0.26
198 30 0.17
199 39 0.22
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (189 bp):
ACCCGACCCGAATATATGAATTAGAAACTCGACTCAAAATAATAAAAAAAAATTATTCAATAAAA
ACATACTTAATTGAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAG
GTAAAATTATATATATTTTCGGGTCAAGTCGGGTATTTTTCACCCTAAACCCGAACTCG
Found at i:30607 original size:58 final size:57
Alignment explanation
Indices: 30518--30634 Score: 189
Period size: 58 Copynumber: 2.0 Consensus size: 57
30508 AAATGCAATC
* *
30518 AAGTCCCCCTCTCACTTGCAGTGTCGCTGTTAGAATCATTACTCGTATATTTCTTGT
1 AAGTCCCCCACTCACTTGCAGTGTCGCTGTTAGAATAATTACTCGTATATTTCTTGT
* *
30575 AAGTCCCCCAACTGACTTGCAGTGTCGCTGTTAGAATAATTACTTGTATATTTCTTGT
1 AAGTCCCCC-ACTCACTTGCAGTGTCGCTGTTAGAATAATTACTCGTATATTTCTTGT
30633 AA
1 AA
30635 ATTGGATCGG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
57 9 0.16
58 46 0.84
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (57 bp):
AAGTCCCCCACTCACTTGCAGTGTCGCTGTTAGAATAATTACTCGTATATTTCTTGT
Found at i:34521 original size:14 final size:14
Alignment explanation
Indices: 34498--34527 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
34488 TTAATTGTTG
34498 TTAATAAATAATAA
1 TTAATAAATAATAA
*
34512 TTAATGAATAATAA
1 TTAATAAATAATAA
34526 TT
1 TT
34528 CATTTGATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (14 bp):
TTAATAAATAATAA
Found at i:35199 original size:2 final size:2
Alignment explanation
Indices: 35187--35236 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
35177 TGACCACAAT
*
35187 TA TA AA 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 TA
35229 TA TA TA TA
1 TA TA TA TA
35237 AAAGTAAGGG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:40341 original size:23 final size:22
Alignment explanation
Indices: 40308--40359 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
40298 ATAAATATTT
*
40308 TATTT-TATTTTAATTAAATTA
1 TATTTATATTTTAACTAAATTA
*
40329 TATTTATATTTTTAACTAATTTA
1 TATTTATA-TTTTAACTAAATTA
*
40352 TAATTATA
1 TATTTATA
40360 CGTTTAGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 5 0.19
22 2 0.08
23 19 0.73
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTATATTTTAACTAAATTA
Found at i:40365 original size:23 final size:23
Alignment explanation
Indices: 40316--40386 Score: 56
Period size: 23 Copynumber: 3.1 Consensus size: 23
40306 TTTATTTTAT
* * * **
40316 TTTAATTAAATTATATTTATATT
1 TTTAACTAATTTATAATTATACG
40339 TTTAACTAATTTATAATTATACG
1 TTTAACTAATTTATAATTATACG
* *
40362 TTT-AGTACTTTATAATT-TAACG
1 TTTAACTAATTTATAATTAT-ACG
40384 TTT
1 TTT
40387 TATAAATTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 1 0.03
22 18 0.45
23 21 0.52
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTAACTAATTTATAATTATACG
Found at i:41166 original size:29 final size:29
Alignment explanation
Indices: 41153--41222 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
41143 TTAACATCTA
41153 AAATTCTAAATTTTAAACTCTAAAATCAT
1 AAATTCTAAATTTTAAACTCTAAAATCAT
* * *
41182 AAATTCTAAATCTTAAAATATAAAACTC-T
1 AAATTCTAAATTTTAAACTCTAAAA-TCAT
41211 AATATTCTAAAT
1 AA-ATTCTAAAT
41223 ATGATATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 25 0.69
30 11 0.31
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (29 bp):
AAATTCTAAATTTTAAACTCTAAAATCAT
Found at i:41168 original size:22 final size:22
Alignment explanation
Indices: 41137--41200 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
41127 TTTTTTATTT
*
41137 TAAATCTTAACATCTAAAATTC-
1 TAAATTTTAA-ATCTAAAATTCA
41159 TAAATTTTAAACTCTAAAA-TCA
1 TAAATTTTAAA-TCTAAAATTCA
*
41181 TAAATTCTAAATCTTAAAAT
1 TAAATTTTAAATC-TAAAAT
41201 ATAAAACTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 5 0.14
22 31 0.86
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTTTAAATCTAAAATTCA
Found at i:43188 original size:22 final size:23
Alignment explanation
Indices: 43163--43205 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
43153 AGTATTAACC
43163 TAAAA-AGAATATGAAAAAAATT
1 TAAAATAGAATATGAAAAAAATT
* *
43185 TAAAATCGAATCTGAAAAAAA
1 TAAAATAGAATATGAAAAAAA
43206 ATAATATCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.65, C:0.05, G:0.09, T:0.21
Consensus pattern (23 bp):
TAAAATAGAATATGAAAAAAATT
Found at i:44041 original size:2 final size:2
Alignment explanation
Indices: 44034--44075 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
44024 GGCTACATGC
44034 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
44076 TCCTCTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44314 original size:18 final size:18
Alignment explanation
Indices: 44291--44325 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
44281 ATCCAAAATC
44291 TGTTCTGCAATGACATAT
1 TGTTCTGCAATGACATAT
*
44309 TGTTCTGCAATGGCATA
1 TGTTCTGCAATGACATA
44326 CTGCATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (18 bp):
TGTTCTGCAATGACATAT
Found at i:46338 original size:156 final size:159
Alignment explanation
Indices: 46050--46484 Score: 422
Period size: 156 Copynumber: 2.8 Consensus size: 159
46040 TGGAAGAGTC
* * * *
46050 GTATGCAATTTAGCTT-A-ACTCAACAACGAAGAGATATTTTTCAGCCAACTTAACCCGCATAGG
1 GTATGCAATTTAGCTTAAGACTCAACAACGATGAGCTATTTTCCAGCCAACTTAACCCGCAAAGG
* * ** * * * * * * * * *
46113 GTTTATAAATTTTTTG-GTCAAATTTAAACTTCACAACAAAGGACAATAAAATCGAAGAACATCC
66 ATTTA-CAGGTTTTTGAATCAAATTTAAACTTTACGACGAATGATATTGAACTCGAAGAACATCC
* * * * * *
46177 GAAATCGACTTAACTCGCAATGGATGAGTTA
130 AAAATCAACTTAACTCACAATGAAGGAG-GA
* * * * *
46208 -TATGCAATTTAGCTT-A-ACTCAACAACGATGAGTTATTTTCTAGCTAGC-TAACTCG-AAGAG
1 GTATGCAATTTAGCTTAAGACTCAACAACGATGAGCTATTTTCCAGCCAACTTAACCCGCAA-AG
* * * * *
46268 GGTTTGA-AGGTTTTTGAGTCAAATTTCAACTTTATGACGAA-GAATATTGGACTCGAAGAACAT
65 GATTT-ACAGGTTTTTGAATCAAATTTAAACTTTACGACGAATG-ATATTGAACTCGAAGAACAT
46331 CCAAAATCAACTTAACTCACAATGAAGGAGGA
128 CCAAAATCAACTTAACTCACAATGAAGGAGGA
* *
46363 GTCTGCAATTTAGTTTAAGTACTCAACAACGATGAGCTATTTTCCAGCCAACTTAACCCGCAAAG
1 GTATGCAATTTAGCTTAAG-ACTCAACAACGATGAGCTATTTTCCAGCCAACTTAACCCGCAAAG
*
46428 GATTTACAGGTTTTTTAATCAAATTTAAACTTTACGACGAATGATATTGAACTCGAA
65 GATTTACAGGTTTTTGAATCAAATTTAAACTTTACGACGAATGATATTGAACTCGAA
46485 AATTGACTTA
Statistics
Matches: 226, Mismatches: 39, Indels: 22
0.79 0.14 0.08
Matches are distributed among these distances:
155 10 0.04
156 85 0.38
157 44 0.19
159 29 0.13
160 55 0.24
161 3 0.01
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (159 bp):
GTATGCAATTTAGCTTAAGACTCAACAACGATGAGCTATTTTCCAGCCAACTTAACCCGCAAAGG
ATTTACAGGTTTTTGAATCAAATTTAAACTTTACGACGAATGATATTGAACTCGAAGAACATCCA
AAATCAACTTAACTCACAATGAAGGAGGA
Found at i:47303 original size:85 final size:85
Alignment explanation
Indices: 47140--47346 Score: 256
Period size: 85 Copynumber: 2.4 Consensus size: 85
47130 AATATCCAAA
* * * * *
47140 AAACGCCGCAAAACATCGAGATCTATAGCGGCATTTTTGGAACAAACACCGTAAAAGGTCATATA
1 AAACGCCGCAAAAGATTGAGATCTATAGCGGCGTTTTTGGAACAAACACCGCAAAAGGTCAGATA
*
47205 TATATCGACGTTTTTGGAAC
66 TATAGCGACGTTTTTGGAAC
* * ** *
47225 AAACACCGCAAAAGATTGAGATCTATAGTGGCGTTTTTGGAACAAACGTCGCAAAAGGTCAGATT
1 AAACGCCGCAAAAGATTGAGATCTATAGCGGCGTTTTTGGAACAAACACCGCAAAAGGTCAGATA
*
47290 TATAGC-AGTGTTTTTGGAAC
66 TATAGCGA-CGTTTTTGGAAC
* * *
47310 AAACGCCGCAAATG-GTCAGATCTATAGCGGCGTTTTT
1 AAACGCCGCAAAAGATTGAGATCTATAGCGGCGTTTTT
47347 TATACAAAAT
Statistics
Matches: 104, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
84 21 0.20
85 83 0.80
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (85 bp):
AAACGCCGCAAAAGATTGAGATCTATAGCGGCGTTTTTGGAACAAACACCGCAAAAGGTCAGATA
TATAGCGACGTTTTTGGAAC
Found at i:47354 original size:42 final size:42
Alignment explanation
Indices: 47140--47346 Score: 234
Period size: 42 Copynumber: 4.9 Consensus size: 42
47130 AATATCCAAA
** *
47140 AAACGCCGCAAAACATCGAGATCTATAGCGGCATTTTTGGAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
* * * * * *
47183 AAACACCGTAAAAGGTCATATATATATCGACGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
* * * *
47225 AAACACCGCAAAAGATTGAGATCTATAGTGGCGTTTTTGGAAC
1 AAACGCCGCAAAAG-GTCAGATCTATAGCGGCGTTTTTGGAAC
* * * *
47268 AAACGTCGCAAAAGGTCAGATTTATAGCAGTGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
*
47310 AAACGCCGCAAATGGTCAGATCTATAGCGGCGTTTTT
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTT
47347 TATACAAAAT
Statistics
Matches: 133, Mismatches: 30, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
42 87 0.65
43 46 0.35
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
Found at i:49373 original size:12 final size:13
Alignment explanation
Indices: 49350--49378 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
49340 TATGAGTTAT
49350 ATATGTTTATATG
1 ATATGTTTATATG
49363 ATATG-TTATATG
1 ATATGTTTATATG
49375 ATAT
1 ATAT
49379 TTGATTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (13 bp):
ATATGTTTATATG
Found at i:49706 original size:30 final size:30
Alignment explanation
Indices: 49651--49708 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
49641 AGAGTCGAGG
* *
49651 GTTACCTATGTCCTTCGGGACATATGGACA
1 GTTACCTATGTCCTCCGGAACATATGGACA
* *
49681 GTTACCTATGTTCTCCGGAATATATGGA
1 GTTACCTATGTCCTCCGGAACATATGGA
49709 TAGGTCCTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (30 bp):
GTTACCTATGTCCTCCGGAACATATGGACA
Found at i:53432 original size:40 final size:40
Alignment explanation
Indices: 53387--53570 Score: 217
Period size: 40 Copynumber: 4.6 Consensus size: 40
53377 AAAAGTAAAG
* *
53387 ACTAAAGTACAGGATTTAGCGGCATTTATATAAAAACACC
1 ACTAAAGTACAGTATTTAGCGGCATTTATATAAAAACGCC
* * * *
53427 ACTAAAGTATAATTTTTAGCGGCGTTTATATAAAAACGCC
1 ACTAAAGTACAGTATTTAGCGGCATTTATATAAAAACGCC
* * * * *
53467 ACTAAAGTATGAGTATTTAGCGGCGTTTGTA-AAAAATGTC
1 ACTAAAGTA-CAGTATTTAGCGGCATTTATATAAAAACGCC
* *
53507 ACTAAAGTACTAGTATTTAGCGGTATTTATATAAAAATGCC
1 ACTAAAGTAC-AGTATTTAGCGGCATTTATATAAAAACGCC
*
53548 ACTAATGTACAGTATTTAGCGGC
1 ACTAAAGTACAGTATTTAGCGGC
53571 GTGGCGTTTG
Statistics
Matches: 122, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
40 88 0.72
41 34 0.28
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (40 bp):
ACTAAAGTACAGTATTTAGCGGCATTTATATAAAAACGCC
Found at i:53537 original size:81 final size:79
Alignment explanation
Indices: 53387--53572 Score: 228
Period size: 81 Copynumber: 2.3 Consensus size: 79
53377 AAAAGTAAAG
* * * *** * *
53387 ACTAAAGTACAGGATTTAGCGGCATTTATATAAAAACACCACTAAAGTATAATTTTTAGCGGCGT
1 ACTAAAGTACAGTATTTAGCGGCGTTTGTA-AAAAATGTCACTAAAGTATAATATTTAGCGGCAT
53452 TTATATAAAAACGCC
65 TTATATAAAAACGCC
* * *
53467 ACTAAAGTATGAGTATTTAGCGGCGTTTGTAAAAAATGTCACTAAAGTACTAGTATTTAGCGGTA
1 ACTAAAGTA-CAGTATTTAGCGGCGTTTGTAAAAAATGTCACTAAAGTA-TAATATTTAGCGGCA
*
53532 TTTATATAAAAATGCC
64 TTTATATAAAAACGCC
*
53548 ACTAATGTACAGTATTTAGCGGCGT
1 ACTAAAGTACAGTATTTAGCGGCGT
53573 GGCGTTTGTT
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
80 39 0.43
81 51 0.57
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (79 bp):
ACTAAAGTACAGTATTTAGCGGCGTTTGTAAAAAATGTCACTAAAGTATAATATTTAGCGGCATT
TATATAAAAACGCC
Found at i:58659 original size:12 final size:12
Alignment explanation
Indices: 58637--58682 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
58627 ATCAATTTTT
58637 TTATCTTTTAAAA
1 TTAT-TTTTAAAA
58650 TTATTTTTAAAA
1 TTATTTTTAAAA
*
58662 TTA-TTTTGAAA
1 TTATTTTTAAAA
58673 TGTATTTTTA
1 T-TATTTTTA
58683 GGTATTTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 8 0.28
12 13 0.45
13 8 0.28
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (12 bp):
TTATTTTTAAAA
Found at i:59431 original size:19 final size:21
Alignment explanation
Indices: 59407--59447 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
59397 ATTAAGATTG
59407 ATTAATATTTT-T-ATTTTTA
1 ATTAATATTTTATAATTTTTA
59426 ATTAATATTTTATAATTTTTA
1 ATTAATATTTTATAATTTTTA
59447 A
1 A
59448 ATATTTTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.55
20 1 0.05
21 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTAATATTTTATAATTTTTA
Found at i:59981 original size:2 final size:2
Alignment explanation
Indices: 59970--60003 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
59960 TAATTATACC
59970 TA TA TA -A 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 T
60004 TTATTAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60688 original size:21 final size:21
Alignment explanation
Indices: 60648--60763 Score: 81
Period size: 21 Copynumber: 5.3 Consensus size: 21
60638 TTAAATATAA
*
60648 AAATATAAAAATATTGAAAAAT
1 AAATATAAAAATACT-AAAAAT
60670 AAATATAAAAATACTAAAAAT
1 AAATATAAAAATACTAAAAAT
* * * *
60691 AAAAATTAAATTACTATATATAT
1 AAATATAAAAATACTA-A-AAAT
* *
60714 ATATATTAAAAATGCTAAAAAT
1 AAATA-TAAAAATACTAAAAAT
* * **
60736 -ATTATTAAAATTTTAAAAAAT
1 AAATATAAAAATACT-AAAAAT
60757 AAATATA
1 AAATATA
60764 TATATTATAA
Statistics
Matches: 71, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
20 7 0.10
21 27 0.38
22 22 0.31
23 7 0.10
24 8 0.11
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.33
Consensus pattern (21 bp):
AAATATAAAAATACTAAAAAT
Found at i:60689 original size:9 final size:8
Alignment explanation
Indices: 60640--60695 Score: 57
Period size: 8 Copynumber: 7.2 Consensus size: 8
60630 TTTAAATTTT
60640 AAATATAA
1 AAATATAA
60648 AAATATAA
1 AAATATAA
*
60656 AAATATTGA
1 AAATA-TAA
60665 AAA-AT--
1 AAATATAA
60670 AAATATAA
1 AAATATAA
60678 AAATACTAA
1 AAATA-TAA
60687 AAATA-AA
1 AAATATAA
60694 AA
1 AA
60696 TTAAATTACT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
5 3 0.07
6 2 0.05
7 5 0.12
8 19 0.45
9 13 0.31
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (8 bp):
AAATATAA
Found at i:61195 original size:2 final size:2
Alignment explanation
Indices: 61184--61235 Score: 72
Period size: 2 Copynumber: 26.5 Consensus size: 2
61174 ATTATATAAC
*
61184 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TG
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61226 TA TA -A TA TA T
1 TA TA TA TA TA T
61236 CGTTTTAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 2 0.04
2 41 0.91
3 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Done.