Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001535.1 Hibiscus syriacus cultivar Beakdansim tig00003012_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: 74863
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2409 original size:20 final size:20
Alignment explanation
Indices: 2364--2419 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
2354 TGGAATAAAT
** *
2364 AATCGCAACGCGAATTGGGAA
1 AATCGCAACGCGAA-TAAGTA
*
2385 AATCGCAATGCGAATAAGTA
1 AATCGCAACGCGAATAAGTA
2405 AATCGCAACGCGAAT
1 AATCGCAACGCGAAT
2420 TGGGAAAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (20 bp):
AATCGCAACGCGAATAAGTA
Found at i:2412 original size:41 final size:40
Alignment explanation
Indices: 2348--2438 Score: 148
Period size: 41 Copynumber: 2.3 Consensus size: 40
2338 TTTTCCCAAT
2348 TCGCAATG-GAATAAATAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAATAATCGCAACGCGAATTGGGAAAA
*
2387 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAAT-AATCGCAACGCGAATTGGGAAAA
*
2428 TCGCAGTGCGA
1 TCGCAATGCGA
2439 TACTGATCGC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 8 0.17
40 7 0.15
41 33 0.69
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.18
Consensus pattern (40 bp):
TCGCAATGCGAATAAATAATCGCAACGCGAATTGGGAAAA
Found at i:2438 original size:21 final size:21
Alignment explanation
Indices: 2364--2432 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
2354 TGGAATAAAT
2364 AATCGCAACGCGAATTGGGAA
1 AATCGCAACGCGAATTGGGAA
* ** *
2385 AATCGCAATGCGAA-TAAGTA
1 AATCGCAACGCGAATTGGGAA
2405 AATCGCAACGCGAATTGGGAA
1 AATCGCAACGCGAATTGGGAA
2426 AATCGCA
1 AATCGCA
2433 GTGCGATACT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.41
21 23 0.59
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.16
Consensus pattern (21 bp):
AATCGCAACGCGAATTGGGAA
Found at i:2491 original size:20 final size:20
Alignment explanation
Indices: 2466--2511 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2456 TAATAAAAAA
* *
2466 TCGCAACGAGGTACTTACTT
1 TCGCAACGAGATACTGACTT
*
2486 TCGCAACGCGATACTGACTT
1 TCGCAACGAGATACTGACTT
2506 TCGCAA
1 TCGCAA
2512 ACGATAATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (20 bp):
TCGCAACGAGATACTGACTT
Found at i:2731 original size:22 final size:21
Alignment explanation
Indices: 2703--2751 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
2693 ACTCTCACCC
2703 CATCTCCGACGAAATCCGTCCT
1 CATCTCCGACGAAATCCGT-CT
*
2725 CATCTCCGGCGAAATCCGTCT
1 CATCTCCGACGAAATCCGTCT
2746 -ATCTCC
1 CATCTCC
2752 ATCTCTCAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 6 0.23
21 2 0.08
22 18 0.69
ACGTcount: A:0.20, C:0.41, G:0.14, T:0.24
Consensus pattern (21 bp):
CATCTCCGACGAAATCCGTCT
Found at i:4322 original size:18 final size:18
Alignment explanation
Indices: 4301--4344 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
4291 TCCACTTCGG
* *
4301 GAGCCATTACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
4319 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
4337 GAG-CATCA
1 GAGCCATCA
4345 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.27, C:0.41, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:4791 original size:48 final size:49
Alignment explanation
Indices: 4703--4799 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 49
4693 ATTCATTCGG
4703 TTGCTGCCAATACTGCTAAACTGTTTTGTTAGTATTTGTTTTTGGTTTT
1 TTGCTGCCAATACTGCTAAACTGTTTTGTTAGTATTTGTTTTTGGTTTT
4752 TTGCTGCCAATACTGCTAAA-TGTTTTGTTAGTATTTGTTTTTGGTTTT
1 TTGCTGCCAATACTGCTAAACTGTTTTGTTAGTATTTGTTTTTGGTTTT
4800 GTTTTGTCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 28 0.58
49 20 0.42
ACGTcount: A:0.16, C:0.11, G:0.19, T:0.54
Consensus pattern (49 bp):
TTGCTGCCAATACTGCTAAACTGTTTTGTTAGTATTTGTTTTTGGTTTT
Found at i:4922 original size:19 final size:19
Alignment explanation
Indices: 4869--4933 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
4859 TAGTTTACTT
*
4869 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGACTA
* *
4889 TCGCAACGCGGAATGGCTA
1 TCGCAACGCGAAATGACTA
* *
4908 TCGCAATGCGAAATGA-AA
1 TCGCAACGCGAAATGACTA
4926 TCGCAACG
1 TCGCAACG
4934 ACAAAATCGC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 8 0.22
19 20 0.54
20 9 0.24
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:4942 original size:14 final size:14
Alignment explanation
Indices: 4923--4979 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
4913 ATGCGAAATG
4923 AAATCGCAACGACA
1 AAATCGCAACGACA
*
4937 AAATCGCAATGCGAAA
1 AAATCGCAA--CGACA
4953 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
4969 AAATCGCAACG
1 AAATCGCAACG
4980 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:4948 original size:32 final size:32
Alignment explanation
Indices: 4907--4996 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
4897 CGGAATGGCT
4907 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
4939 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
*
4971 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATG-AAATCGCAA
4997 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 47 0.84
33 9 0.16
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:4990 original size:19 final size:19
Alignment explanation
Indices: 4869--5001 Score: 65
Period size: 19 Copynumber: 7.6 Consensus size: 19
4859 TAGTTTACTT
* **
4869 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
* ***
4889 TCGCAACGCGGAATGGCTA
1 TCGCAACGCGAAATGAAAA
*
4908 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
4926 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
4940 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
4958 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
4972 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
4991 TCGCAATGCGA
1 TCGCAACGCGA
5002 TTTGTGTTTC
Statistics
Matches: 89, Mismatches: 12, Indels: 25
0.71 0.10 0.20
Matches are distributed among these distances:
14 20 0.22
16 8 0.09
18 18 0.20
19 34 0.38
20 9 0.10
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:5032 original size:14 final size:14
Alignment explanation
Indices: 5013--5070 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
5003 TTGTGTTTCG
5013 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
5027 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
5043 CGCATTGCAATTTTGT
1 CG--TTGCGATTTTGT
5059 CGTTGCGATTTT
1 CGTTGCGATTTT
5071 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:5056 original size:32 final size:33
Alignment explanation
Indices: 5008--5083 Score: 127
Period size: 32 Copynumber: 2.3 Consensus size: 33
4998 GCGATTTGTG
* *
5008 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
5040 TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
5073 TTTCGCATTGC
1 TTTCGCATTGC
5084 GATAGCCATT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 25 0.61
33 16 0.39
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
Found at i:5085 original size:19 final size:19
Alignment explanation
Indices: 5029--5086 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 19
5019 GATTTTGTCG
5029 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
5047 TTGC-AATTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
5061 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5080 TTGCGAT
1 TTGCGAT
5087 AGCCATTTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 11
0.69 0.07 0.24
Matches are distributed among these distances:
14 4 0.13
15 4 0.13
16 4 0.13
17 5 0.16
18 7 0.23
19 7 0.23
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5093 original size:19 final size:20
Alignment explanation
Indices: 5071--5114 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5061 TTGCGATTTT
5071 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
5090 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
5110 CATTT
1 CATTT
5115 TGTGTTGCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:5123 original size:19 final size:19
Alignment explanation
Indices: 5059--5125 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
5049 GCAATTTTGT
**
5059 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
5078 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
5098 CGTTGCGATAGTCATTTTG
1 CGTTGCGATAGTCATTTCG
*
5117 TGTTGCGAT
1 CGTTGCGAT
5126 TTTAAGTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:9758 original size:19 final size:19
Alignment explanation
Indices: 9734--9819 Score: 111
Period size: 19 Copynumber: 4.5 Consensus size: 19
9724 TTCCACGCAA
*
9734 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
9753 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
9772 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
9791 TGCGATAGTT-ATTTCCGCGT
1 TGCGAT-TTTGATTT-CGCGT
9811 TGCGATTTT
1 TGCGATTTT
9820 CATTCTCGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
19 48 0.79
20 13 0.21
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:10368 original size:20 final size:20
Alignment explanation
Indices: 10339--10452 Score: 140
Period size: 20 Copynumber: 5.7 Consensus size: 20
10329 CGCTATGTAA
* *
10339 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
10359 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
10380 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
10400 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
10420 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
10440 ATCGCATTGCGAT
1 ATCGCATTGCGAT
10453 TTTCCCAATT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.04
20 65 0.79
21 12 0.15
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:10563 original size:21 final size:21
Alignment explanation
Indices: 10523--10563 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
10513 ATTGTATACC
**
10523 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
10544 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
10564 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:19274 original size:29 final size:30
Alignment explanation
Indices: 19242--19299 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
19232 TTTTTTTCAA
*
19242 AATTACGAAAATAGCACCATTTT-AAAATT
1 AATTACCAAAATAGCACCATTTTCAAAATT
*
19271 AATTACCAATATAGCACCATTTTCAAAAT
1 AATTACCAAAATAGCACCATTTTCAAAAT
19300 ATTTACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.31
Consensus pattern (30 bp):
AATTACCAAAATAGCACCATTTTCAAAATT
Found at i:19349 original size:22 final size:23
Alignment explanation
Indices: 19315--19359 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
19305 CTAAAATGTC
*
19315 ATTTTTTAAAAAAAGTACGAAAAT
1 ATTTTTT-AAAAAAGTACAAAAAT
*
19339 ATTTTTT-AAAAATTACAAAAA
1 ATTTTTTAAAAAAGTACAAAAA
19360 ATAGCACCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (23 bp):
ATTTTTTAAAAAAGTACAAAAAT
Found at i:20827 original size:15 final size:15
Alignment explanation
Indices: 20791--20887 Score: 82
Period size: 15 Copynumber: 6.6 Consensus size: 15
20781 ACAAATTATC
*
20791 TTAAATTTAAAAT-T
1 TTAAATATAAAATAT
20805 TTAAATATAAAATAT
1 TTAAATATAAAATAT
*
20820 TGAAATATTCAAAAT-T
1 TTAAATA-T-AAAATAT
20836 TTAAATATAAAAATAT
1 TTAAATAT-AAAATAT
20852 TTAAA-ATAAAA-A-
1 TTAAATATAAAATAT
20864 TTAAATTACTAAAA-A-
1 TTAAA-TA-TAAAATAT
20879 TTAAATATA
1 TTAAATATA
20888 TATTAAAAAC
Statistics
Matches: 72, Mismatches: 4, Indels: 15
0.79 0.04 0.16
Matches are distributed among these distances:
12 5 0.07
13 3 0.04
14 19 0.26
15 26 0.36
16 14 0.19
17 5 0.07
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (15 bp):
TTAAATATAAAATAT
Found at i:20834 original size:24 final size:24
Alignment explanation
Indices: 20807--20868 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
20797 TTAAAATTTT
**
20807 AAATATAAAATATTGAAATATTCA
1 AAATATAAAATATAAAAATATTCA
* * *
20831 AAATTTTAAATATAAAAATATTTA
1 AAATATAAAATATAAAAATATTCA
20855 AAATA-AAAAT-TAAA
1 AAATATAAAATATAAA
20869 TTACTAAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
22 4 0.13
23 4 0.13
24 23 0.74
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
AAATATAAAATATAAAAATATTCA
Found at i:21677 original size:2 final size:2
Alignment explanation
Indices: 21665--21694 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
21655 ATTATTAAAA
*
21665 AT AT TT 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
21695 TCCACTAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:26016 original size:21 final size:21
Alignment explanation
Indices: 25965--26017 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
25955 ATTATGACTA
*
25965 TCGCAAAGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
25986 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
26007 TCGCAATGCGA
1 TCGCAATGCGA
26018 AAAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:26050 original size:21 final size:21
Alignment explanation
Indices: 26024--26079 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
26014 GCGAAAAAGT
26024 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
26045 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
*
26066 AAATCGCAACGCGA
1 AAATCGCAATGCGA
26080 TACTGACTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (21 bp):
AAATCGCAATGCGAATTTGGA
Found at i:26092 original size:41 final size:41
Alignment explanation
Indices: 26065--26196 Score: 140
Period size: 41 Copynumber: 3.2 Consensus size: 41
26055 GCGAATTTGG
*
26065 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACACGATACTGACTATCGCAACGCGATAATAC
* * * *
26106 AAAATCGCAACACGATACTGACTTTCGCAACTCGATACT-T
1 AAAATCGCAACACGATACTGACTATCGCAACGCGATAATAC
** * * * * *
26146 AATTTCGCAACTCAATACTGACTTTCGCAATGAGATAATAC
1 AAAATCGCAACACGATACTGACTATCGCAACGCGATAATAC
*
26187 ATAATCGCAA
1 AAAATCGCAA
26197 TGCAATTTTC
Statistics
Matches: 73, Mismatches: 17, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
40 31 0.42
41 42 0.58
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACACGATACTGACTATCGCAACGCGATAATAC
Found at i:26093 original size:20 final size:20
Alignment explanation
Indices: 26068--26175 Score: 92
Period size: 20 Copynumber: 5.3 Consensus size: 20
26058 AATTTGGAAA
26068 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
26088 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
26109 ATCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
26129 TTCGCAACTCGATACTTAAT
1 ATCGCAACGCGATACTGACT
* * *
26149 TTCGCAACTCAATACTGACT
1 ATCGCAACGCGATACTGACT
*
26169 TTCGCAA
1 ATCGCAA
26176 TGAGATAATA
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.03
20 55 0.75
21 14 0.19
22 2 0.03
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:26397 original size:22 final size:22
Alignment explanation
Indices: 26369--26412 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
26359 CACTCTCTCA
26369 CCCATCTCCGAAGAAATCCGTC
1 CCCATCTCCGAAGAAATCCGTC
**
26391 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGAAGAAATCCGTC
26413 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.43, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGAAGAAATCCGTC
Found at i:28642 original size:20 final size:20
Alignment explanation
Indices: 28617--28669 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
28607 TAGTTTACTT
*
28617 TCGCAATACGAAAAT-GACTA
1 TCGCAATGCGAAAATGGA-TA
* *
28637 TCGCAACGCGGAAATGGATA
1 TCGCAATGCGAAAATGGATA
28657 TCGCAATGCGAAA
1 TCGCAATGCGAAA
28670 TGAAAATTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAAAATGGATA
Found at i:28732 original size:14 final size:14
Alignment explanation
Indices: 28713--28770 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
28703 TGTGTTTCGT
*
28713 GTTGCGATTTTGTC
1 GTTGCGATTTTATC
28727 GTTGCGATTTTCATTTC
1 GTTGCGATTTT-A--TC
28744 GCATTGCGATTTTATC
1 G--TTGCGATTTTATC
28760 GTTGCGATTTT
1 GTTGCGATTTT
28771 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 21 0.55
16 3 0.08
17 3 0.08
18 1 0.03
19 10 0.26
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.50
Consensus pattern (14 bp):
GTTGCGATTTTATC
Found at i:28744 original size:33 final size:33
Alignment explanation
Indices: 28714--28786 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
28704 GTGTTTCGTG
*
28714 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTATCGTTGCGATTTTCATTTCGCA
28747 TTGCGATTTTATCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTATCGTTGCGATTTTCATTTCGCA
28780 TTGCGAT
1 TTGCGAT
28787 AGCCATTTCC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.14, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTATCGTTGCGATTTTCATTTCGCA
Found at i:28805 original size:20 final size:20
Alignment explanation
Indices: 28759--28845 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
28749 GCGATTTTAT
**
28759 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
* *
28778 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTCCG
28798 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
28818 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
28838 CGTTGCGA
1 CGTTGCGA
28846 AAGTAAGTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
19 13 0.22
20 47 0.78
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:28856 original size:20 final size:19
Alignment explanation
Indices: 28772--28871 Score: 83
Period size: 20 Copynumber: 5.1 Consensus size: 19
28762 TGCGATTTTC
* * **
28772 ATTTCGCATTGCGATAGCC
1 ATTTCGCGTTGCGAAAGTA
* *
28791 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGAAAGTA
*
28811 ATTTCCGCGTTGCGATAGTCA
1 ATTT-CGCGTTGCGAAAGT-A
*
28832 TTTTCGCGTTGCGAAAGTA
1 ATTTCGCGTTGCGAAAGTA
*
28851 AGTTTCGTGTTGCGAAAGTA
1 A-TTTCGCGTTGCGAAAGTA
28871 A
1 A
28872 ACTATTCTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
19 5 0.07
20 63 0.89
21 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (19 bp):
ATTTCGCGTTGCGAAAGTA
Found at i:28863 original size:40 final size:40
Alignment explanation
Indices: 28772--28865 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
28762 TGCGATTTTC
* * *
28772 ATTT-CGCATTGCGATAGCCATTTCCGCGTTGCGATAGTC
1 ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
* *
28811 ATTTCCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTA
1 ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
*
28851 AGTTT-CGTGTTGCGA
1 A-TTTCCGCGTTGCGA
28866 AAGTAAACTA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 4 0.09
40 40 0.85
41 3 0.06
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (40 bp):
ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
Found at i:29273 original size:21 final size:20
Alignment explanation
Indices: 29213--29273 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
29203 GACTCACCTG
29213 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGTCCCCT
* ** * *
29233 CCAATCGTTCAAAAGGCCCCT
1 TC-ATCCCTCAAGAGTCCCCT
29254 ATCATCCCTCAAGAGTCCCC
1 -TCATCCCTCAAGAGTCCCC
29274 CCCACCGTTC
Statistics
Matches: 29, Mismatches: 10, Indels: 3
0.69 0.24 0.07
Matches are distributed among these distances:
20 1 0.03
21 27 0.93
22 1 0.03
ACGTcount: A:0.25, C:0.43, G:0.11, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGTCCCCT
Found at i:29300 original size:41 final size:42
Alignment explanation
Indices: 29210--29300 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
29200 CCCGACTCAC
* *
29210 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAAAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAAAGGCCA
* * *
29252 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAAAGGCCA
29293 CTGTCATC
1 CTGTCATC
29301 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 22 0.51
42 21 0.49
ACGTcount: A:0.23, C:0.42, G:0.14, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAAAGGCCA
Found at i:30743 original size:14 final size:14
Alignment explanation
Indices: 30709--30747 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
30699 TTGATTGTTT
30709 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
30723 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
30737 TGTTGATTTGT
1 AATTGATTTGT
30748 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:30933 original size:20 final size:20
Alignment explanation
Indices: 30910--31011 Score: 109
Period size: 20 Copynumber: 5.2 Consensus size: 20
30900 TTTCTAGTTA
30910 CGATAGCCATTTTCGCGTTG
1 CGATAGCCATTTTCGCGTTG
*** *
30930 CGATTTTCA-TTTCGCATTG
1 CGATAGCCATTTTCGCGTTG
*** *
30949 CGATTTTCA-TTTCGCATTG
1 CGATAGCCATTTTCGCGTTG
30968 CGATAGCCATTTTCGCGTTG
1 CGATAGCCATTTTCGCGTTG
*
30988 TGATAGCCATTTTCGCGTTG
1 CGATAGCCATTTTCGCGTTG
31008 CGAT
1 CGAT
31012 TTCCCCGTTG
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
19 34 0.48
20 37 0.52
ACGTcount: A:0.16, C:0.23, G:0.22, T:0.40
Consensus pattern (20 bp):
CGATAGCCATTTTCGCGTTG
Found at i:31250 original size:20 final size:19
Alignment explanation
Indices: 31225--31274 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
31215 TTGAAGATGA
31225 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTT-AGAATCTCG
**
31245 TTGCGAAAGTTAGAATCTCG
1 TTGCG-ATTTTAGAATCTCG
31265 TTGCGATTTT
1 TTGCGATTTT
31275 GTATTATCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 3 0.12
20 19 0.76
21 3 0.12
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (19 bp):
TTGCGATTTTAGAATCTCG
Found at i:31334 original size:21 final size:21
Alignment explanation
Indices: 31304--31356 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
31294 GTCAGTATCG
*
31304 CATTGTGATTTTCCAAATTCA
1 CATTGCGATTTTCCAAATTCA
31325 CATTGCGATTTTCCAAATTCA
1 CATTGCGATTTTCCAAATTCA
31346 CATTGCGATTT
1 CATTGCGATTT
31357 ACTTATTCGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (21 bp):
CATTGCGATTTTCCAAATTCA
Found at i:32185 original size:24 final size:24
Alignment explanation
Indices: 32158--32211 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
32148 GTATTCGAAA
*
32158 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
32182 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
32206 TTTGAT
1 TTTGAT
32212 GATGTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:32403 original size:12 final size:12
Alignment explanation
Indices: 32386--32410 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32376 ATATAATCCT
32386 GAAGAAGAAAAA
1 GAAGAAGAAAAA
32398 GAAGAAGAAAAA
1 GAAGAAGAAAAA
32410 G
1 G
32411 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:34760 original size:19 final size:19
Alignment explanation
Indices: 34738--34815 Score: 112
Period size: 19 Copynumber: 4.4 Consensus size: 19
34728 GGAAATTACT
34738 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
34757 ATCGCAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
34771 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
34790 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
34809 ATCGCAA
1 ATCGCAA
34816 CGAGGGAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
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 36 0.69
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:35031 original size:14 final size:14
Alignment explanation
Indices: 35012--35048 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
35002 CATCAATTAA
35012 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
35026 ACAAATCACCTTTT
1 ACAAATCAACTTTT
35040 ACAAATCAA
1 ACAAATCAA
35049 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:36850 original size:93 final size:90
Alignment explanation
Indices: 36740--36924 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
36730 ATTTCAAACT
36740 TTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAG
1 TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT-AAGAA-ACA-A-TTTAG
*
36804 CAGAATTGGCAGCAACAGAATAAATTTAC
62 CAGAATTGACAGCAACAGAATAAATTTAC
*
36833 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATAAACAATTTAGCAG
1 TTCAACCAAAAGACAAAAC-AAAAGACAAATACTAACTTCACAGTGTTAAGAAACAATTTAGCAG
* *
36898 TATTGACAGCAACCGAATAAATTTAC
65 AATTGACAGCAACAGAATAAATTTAC
36924 T
1 T
36925 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 32 0.37
92 1 0.01
93 22 0.26
94 4 0.05
95 27 0.31
ACGTcount: A:0.49, C:0.18, G:0.11, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAGAAACAATTTAGCAGA
ATTGACAGCAACAGAATAAATTTAC
Found at i:38676 original size:33 final size:33
Alignment explanation
Indices: 38625--38751 Score: 191
Period size: 33 Copynumber: 3.8 Consensus size: 33
38615 TTGAAATGAA
* *
38625 AATCGCAACGAGATAATGAAAATCGCAACGCGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGAGAG
* *
38659 AATCACAACGCGAAATGAAAATCGCAACAAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
* *
38692 AATCGCAACGCAAAATGAAAATTGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
38725 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
38752 TGCGATTTTG
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 72 0.87
34 11 0.13
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:39356 original size:20 final size:20
Alignment explanation
Indices: 39331--39421 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
39321 GCTATGTAAA
39331 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* *
39351 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
* ** *
39371 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATGTAAGTAT
* * * *
39391 TCGCGTTGCAATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
39411 TCGCATTGCGA
1 TCGCATTGCGA
39422 ATTATGAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
19 3 0.05
20 57 0.95
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:39435 original size:21 final size:21
Alignment explanation
Indices: 39411--39473 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
39401 ATTTACGTAT
* *
39411 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
39432 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
39452 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
39473 T
1 T
39474 TACATTGCCA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:39537 original size:20 final size:21
Alignment explanation
Indices: 39493--39544 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
39483 ATAGTCAGTA
*
39493 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
39514 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
39534 TCGCATTGCGA
1 TCGCATTGCGA
39545 ATCGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:39951 original size:14 final size:14
Alignment explanation
Indices: 39934--39960 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39924 TTTTATTTTA
39934 ATTTTTTTAAAAAT
1 ATTTTTTTAAAAAT
39948 ATTTTTTTAAAAA
1 ATTTTTTTAAAAA
39961 ATTAAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTTTTTAAAAAT
Found at i:40915 original size:21 final size:21
Alignment explanation
Indices: 40885--41091 Score: 160
Period size: 21 Copynumber: 10.0 Consensus size: 21
40875 GATTTACATA
*
40885 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
40906 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* ** *
40927 TTTGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
* *
40948 TT--CGTTGCGTTAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
40967 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
40990 TT--CGTTACGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
41009 TTCACGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
41032 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
41051 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
41074 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
41092 AATCGCAACA
Statistics
Matches: 147, Mismatches: 27, Indels: 26
0.74 0.14 0.13
Matches are distributed among these distances:
19 39 0.27
21 82 0.56
23 26 0.18
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:40939 original size:42 final size:41
Alignment explanation
Indices: 40910--41088 Score: 270
Period size: 42 Copynumber: 4.3 Consensus size: 41
40900 TCCAAGTTCG
*
40910 CGTTGCGATAGTCGAAGTTTGCGTTGCGATT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAATT
*
40950 CGTTGCGTTAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
* * * *
40992 CGTTACGATAGTCCAAGTTCACGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
41034 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
41076 CGTTGCGATAGTC
1 CGTTGCGATAGTC
41089 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:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAATT
Found at i:41842 original size:21 final size:21
Alignment explanation
Indices: 41816--42074 Score: 241
Period size: 21 Copynumber: 12.6 Consensus size: 21
41806 TTTGGAATAA
41816 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* * *
41837 ATCGCAA--TGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
41856 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
* **
41879 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
*
41898 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
*
41919 ATCGCAATGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* *
41940 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
41959 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
41982 ATCGCAA--CGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* * **
42001 ATCG-AA-ACGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
* *
42020 ATCACAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
42041 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
42062 ATCGCAATGCGAA
1 ATCGCAACGCGAA
42075 TATGTAAATC
Statistics
Matches: 190, Mismatches: 35, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
18 2 0.01
19 61 0.32
20 2 0.01
21 108 0.57
23 17 0.09
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:41902 original size:61 final size:60
Alignment explanation
Indices: 41858--42068 Score: 327
Period size: 61 Copynumber: 3.5 Consensus size: 60
41848 TTTGGAATAA
*
41858 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAAC-CGAACTTCGACT
*
41919 ATCGCAATGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGG-A-AAATCGCAAC-CGAACTTCGACT
* *
41982 ATCGCAA--CGAACTTGGACTATCGAAACGAATTTGGAAAATCACAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAAC-CGAACTTCGACT
42041 ATCGCAACGCGAACTTGGACTATCGCAA
1 ATCGCAACGCGAACTTGGACTATCGCAA
42069 TGCGAATATG
Statistics
Matches: 141, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
59 29 0.21
60 1 0.01
61 80 0.57
62 1 0.01
63 30 0.21
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (60 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACCGAACTTCGACT
Found at i:42059 original size:103 final size:103
Alignment explanation
Indices: 41802--42049 Score: 356
Period size: 103 Copynumber: 2.4 Consensus size: 103
41792 CCAGTCGTTG
*
41802 CGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAATGAATTTGGAATAAATCGCAACG
1 CGAATTTGG-A-AAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACG
* *
41867 CGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACG
64 CGAACTTCGACTATCGCAACGAACTTGGAAAATCGCAACA
* * ** *
41907 CGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCG
1 CGAATTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCG
**
41972 AACTTCGACTATCGCAACGAACTTGGACTATCG-AA-A
66 AACTTCGACTATCGCAACGAACTTGGAAAATCGCAACA
* *
42008 CGAATTTGGAAAATCACAACGCGAACTTCGACTATCGCAACG
1 CGAATTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACG
42050 CGAACTTGGA
Statistics
Matches: 126, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
101 35 0.28
102 2 0.02
103 81 0.64
104 1 0.01
105 7 0.06
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (103 bp):
CGAATTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCG
AACTTCGACTATCGCAACGAACTTGGAAAATCGCAACA
Found at i:42113 original size:21 final size:21
Alignment explanation
Indices: 42089--42135 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
42079 TAAATCGCAA
42089 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
42110 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
42131 TGCGA
1 TGCGA
42136 ATCTGGAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:43331 original size:22 final size:23
Alignment explanation
Indices: 43306--43350 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
43296 TAAATAAACC
*
43306 AATAATAATATTC-AGAATTAAA
1 AATAATAAAATTCGAGAATTAAA
* *
43328 AATATTAAAATTCGAGGATTAAA
1 AATAATAAAATTCGAGAATTAAA
43351 TTGTAAAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (23 bp):
AATAATAAAATTCGAGAATTAAA
Found at i:44549 original size:17 final size:16
Alignment explanation
Indices: 44510--44552 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
44500 AGGTTTAAAT
44510 TTTGGGCCTGGACAGG
1 TTTGGGCCTGGACAGG
* *
44526 TTATGGGCTTGGATCGGG
1 TT-TGGGCCTGGA-CAGG
44544 TTTGGGCCT
1 TTTGGGCCT
44553 CCAGGTTGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.09
17 15 0.68
18 5 0.23
ACGTcount: A:0.09, C:0.16, G:0.42, T:0.33
Consensus pattern (16 bp):
TTTGGGCCTGGACAGG
Found at i:44646 original size:17 final size:17
Alignment explanation
Indices: 44624--44656 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
44614 GGCCTGTAAA
44624 AATAATTAAT-TAATAAT
1 AATAA-TAATATAATAAT
44641 AATAATAATATAATAA
1 AATAATAATATAATAA
44657 ATGGGACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAATAATATAATAAT
Found at i:44856 original size:55 final size:55
Alignment explanation
Indices: 44779--44915 Score: 177
Period size: 55 Copynumber: 2.5 Consensus size: 55
44769 ATGGGAAATT
* * *
44779 TGCTCCACTCTTCTTTAAGGGAGATAAGATTCAAGAAATATTTGGAAAAC-GTATC
1 TGCTCCACTCTTCTTTAAGGGAGATAAGACTCAAGAAATATTTGAAAAACAG-ATA
* * * * * *
44834 TGCTTCACTATTCTTTCAGGGAGATAAGACTCGAGATATCTTTGAAAAACAGATA
1 TGCTCCACTCTTCTTTAAGGGAGATAAGACTCAAGAAATATTTGAAAAACAGATA
44889 TGCTCCACTCTTCTTTAAGGGAGATAA
1 TGCTCCACTCTTCTTTAAGGGAGATAA
44916 AATCCAAGGG
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
55 68 0.99
56 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (55 bp):
TGCTCCACTCTTCTTTAAGGGAGATAAGACTCAAGAAATATTTGAAAAACAGATA
Found at i:45000 original size:102 final size:102
Alignment explanation
Indices: 44822--46598 Score: 2000
Period size: 102 Copynumber: 17.4 Consensus size: 102
44812 AGAAATATTT
* * * * * * *
44822 GGAAAACGTATCTGCTTCACTATTCTTTCAGGGAGATAAGACTCGAGATATCTTTGAAAAACAGA
1 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGA
* *
44887 TATGCTCCACTCTTCTTTAAGGGAGATAAAATCCAAG
66 TATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * * * * * * *
44924 GGAAAATGGATCTGCTCCACTTTTCTCTCAAGGAGATAGGACTCGAGAGATGC-TTGTAAAACAG
1 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAAT-CTTTGTAAAACGG
* *
44988 ATATGCTTCACTCTTCTTTCAGGGAGATAAGATCCAAT
65 ATATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * *
45026 GGAAGGCGAATCTGCTCCACTCTTCTTTCAGGGATATAAGACTTGAGAAATCTTTGGAAAACGGA
1 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGA
* *
45091 TTTGCTCCACTCTTCTTTCAGGGAAATAAGATCCAAG
66 TATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * ** * * *
45128 GGAAGACGAATATGCTCCACTCTTTTTTCAGAAAGATAAGACTCGATAAATATTTGTAAAACAGA
1 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGA
*
45193 TCTGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
66 TATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* *
45230 GGAAGACGAATCTGCTCCACTCTTCTCTCAGGGAGATAAGACGCGAGAAATCTTTAG-AAAACGG
1 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTT-GTAAAACGG
* * * *
45294 ATCTTCTCCTCGCTTCTTTCAGGGAGATAAGATCCAAG
65 ATATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * * * *
45332 GGAAGACGAATATGCTCCACTATTCTTTCAGGGAGATAAAACTCGAGAGATCTTTGTAAAATGAA
1 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGA
*
45397 TATACTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
66 TATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * * * * *
45434 GGAAGATGAATTTG-TCCCGCTCTTCTTTCAGGAAGATAAGACTTGAGAAATCTTTGGAAAACGA
1 GGAAGACGAATCTGCT-CCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGG
* * *
45498 ATTTGCTTCACTCTTCTTTCAAGGAGATAAGATCCAAG
65 ATATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * *
45536 GGAAAACAAATCTGCTCCACTCTT-TTTCAAGGAGATAAGACTCGAGAAATCTTTGGAAAACGGA
1 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGA
* * *
45600 TATGCTTCACTCTTCTTTCAAGGAGATAAGATCCAAT
66 TATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * * * * *
45637 GGAAGACGAATATGTTCCACTCTTATTTCAGGGAGATAAAACTAGAGAAATCTTTGTAAAATGAA
1 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGA
* * *
45702 TCTTCTCTACTCTTCTTTCAGGGAGATAAGATCCAAG
66 TATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * *
45739 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATTCTAGAAATATTTGTAAAACGGA
1 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGA
* * * *
45804 TCTGCTCCACTCTTCTTTTAGGGAGATAAAATCTAAG
66 TATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * * *
45841 GGAAGACGAATCTGCTCCACTTTTCTTTCAAGGAGATAAGATTTGAGAAATCTTTGTAAAACAGA
1 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGA
* * *
45906 TCTACTCCACTCTTCTTTCAAGGAGATAAGATCCAAG
66 TATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* *
45943 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAA-AGTTCGAGAAATCTTTGTAAAACGA
1 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGA-CTCGAGAAATCTTTGTAAAACGG
* * *
46007 ATCTGCTCCACTCTTTTTTCAGGGAGATACGATCCAAG
65 ATATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * * * * * *
46045 GGAAGACAAATATTCTCCACTATTCTTTTAGGGAGATATGATTCAAGAAATCTTTGTAAAACGGA
1 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGA
* *
46110 TATGCTCCACTGTTCTTTTAGGGAGATAAGATCCAAG
66 TATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * * *
46147 GGAAGACGAATTTGCTCCACTCTTCTTTCTA-TGAGATAAGATTCAAGAAATCTTTGTAAAACGA
1 GGAAGACGAATCTGCTCCACTCTTCTTTC-AGGGAGATAAGACTCGAGAAATCTTTGTAAAACGG
* *
46211 ATTTGCTCCACTCTTCTTTCAGGGAGATAAAATCCAAG
65 ATATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * * * * * * * *
46249 GAAAGATGAATATTCTCCTCTCTTCTTTCAAGGAGATAAGA-TCTA-AGAA-------AAGATGA
1 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGA-AATCTTTGTAAAACGG
* * * *
46305 ATATGCTCCACTCTTATTTCAAGGAGATAAGATTCGAGAAATCTTT
65 ATATGCTCCACTCTTCTTTCAGGGAGATAAGA-TC---CAA----G
* * * * * * **
46351 GTAAAATGGATCTGCTCTACTCTTCTTTCAGGGAGATAAGATTCGAGAAATCTTTGTAAAACATA
1 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGA
* * * *
46416 TCTGCCCCACTATTCTTTCAGGGAGATAAGATCCATG
66 TATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * * * *
46453 GGAAGACGAATCTTCTTCACTATTCTTTTAGGGAGATAAGACTTGAGAAATCTTTGTAAAACAGA
1 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGA
* *
46518 TATGATCCATTCTTCTTTCAGGGAGATAAGATCCAAG
66 TATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* *
46555 GTAAGACGAATATGCTCCACTCTTCTTTCAGGGAGATAAGACTC
1 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTC
46599 AAAATTGATT
Statistics
Matches: 1417, Mismatches: 229, Indels: 58
0.83 0.13 0.03
Matches are distributed among these distances:
94 33 0.02
95 2 0.00
98 2 0.00
100 1 0.00
101 101 0.07
102 1234 0.87
103 10 0.01
104 1 0.00
106 1 0.00
109 2 0.00
110 30 0.02
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (102 bp):
GGAAGACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGA
TATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
Found at i:45813 original size:55 final size:55
Alignment explanation
Indices: 45744--46141 Score: 267
Period size: 55 Copynumber: 7.7 Consensus size: 55
45734 CCAAGGGAAG
45744 ACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATTCTAGAAATATTTGTAAA
1 ACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATTCTAGAAATATTTGTAAA
* * * * * *
45799 ACGGATCTGCTCCACTCTTCTTTTAGGGAGATAA-AATCT----A-A--GGGAAG
1 ACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATTCTAGAAATATTTGTAAA
* * *
45846 ACGAATCTGCTCCACTTTTCTTTCAAGGAGATAAGATT-TGAGAAATCTTTGTAAA
1 ACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATTCT-AGAAATATTTGTAAA
* * * * * *
45901 AC-AGATCTACTCCACTCTTCTTTCAAGGAGATAAGA-TC----CA-A--GGGAAG
1 ACGA-ATCTGCTCCACTCTTCTTTCAGGGAGATAAGATTCTAGAAATATTTGTAAA
* *
45948 ACGAATCTGCTCCACTCTTCTTTCAGGGAGATAA-AGTTCGAGAAATCTTTGTAAA
1 ACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGA-TTCTAGAAATATTTGTAAA
* * * * **
46003 ACGAATCTGCTCCACTCTTTTTTCAGGGAGATACGATCCAAGGGA-A---G-ACAA
1 ACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATTCTAGAAATATTTGTA-AA
* * * * * *
46054 A--TAT-T-CTCCACTATTCTTTTAGGGAGATATGATTCAAGAAATCTTTGTAAA
1 ACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATTCTAGAAATATTTGTAAA
* * * *
46105 ACGGATATGCTCCACTGTTCTTTTAGGGAGATAAGAT
1 ACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGAT
46142 CCAAGGGAAG
Statistics
Matches: 263, Mismatches: 48, Indels: 64
0.70 0.13 0.17
Matches are distributed among these distances:
46 1 0.00
47 96 0.37
48 6 0.02
49 3 0.01
50 3 0.01
51 8 0.03
52 3 0.01
53 2 0.01
54 7 0.03
55 133 0.51
56 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (55 bp):
ACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATTCTAGAAATATTTGTAAA
Found at i:46183 original size:47 final size:47
Alignment explanation
Indices: 46112--46337 Score: 204
Period size: 47 Copynumber: 4.6 Consensus size: 47
46102 AAAACGGATA
* * * *
46112 TGCTCCACTGTTCTTTTAGGGAGATAAGATCCAAGGGAAGACGAATT
1 TGCTCCACTCTTCTTTCAAGGAGATAAGATCCAAGGAAAGACGAATT
* * *
46159 TGCTCCACTCTTCTTTCTATGAGATAAGATTCAA-GAAATCTTTGTAAAACGAATT
1 TGCTCCACTCTTCTTTCAAGGAGATAAGATCCAAGGAAA-----G----ACGAATT
* * *
46214 TGCTCCACTCTTCTTTCAGGGAGATAAAATCCAAGGAAAGATGAATAT
1 TGCTCCACTCTTCTTTCAAGGAGATAAGATCCAAGGAAAGACGAAT-T
* * * * *
46262 T-CTCCTCTCTTCTTTCAAGGAGATAAGATCTAAGAAAAGATGAATA
1 TGCTCCACTCTTCTTTCAAGGAGATAAGATCCAAGGAAAGACGAATT
*
46308 TGCTCCACTCTTATTTCAAGGAGATAAGAT
1 TGCTCCACTCTTCTTTCAAGGAGATAAGAT
46338 TCGAGAAATC
Statistics
Matches: 146, Mismatches: 21, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
46 4 0.03
47 98 0.67
48 2 0.01
51 2 0.01
55 36 0.25
56 4 0.03
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (47 bp):
TGCTCCACTCTTCTTTCAAGGAGATAAGATCCAAGGAAAGACGAATT
Found at i:46238 original size:55 final size:55
Alignment explanation
Indices: 46152--46447 Score: 220
Period size: 55 Copynumber: 5.7 Consensus size: 55
46142 CCAAGGGAAG
*
46152 ACGAATTTGCTCCACTCTTCTTTCTA-TGAGATAAGATTCAAGAAATCTTTGTAAA
1 ACGAATTTGCTCCACTCTTCTTTC-AGGGAGATAAGATTCAAGAAATCTTTGTAAA
* *
46207 ACGAATTTGCTCCACTCTTCTTTCAGGGAGATAAAATCCAAG--------G-AAA
1 ACGAATTTGCTCCACTCTTCTTTCAGGGAGATAAGATTCAAGAAATCTTTGTAAA
* * * *
46253 GATGAATATT-CTCCTCTCTTCTTTCAAGGAGATAAGA-TCTAAG-AA-------AAG
1 -ACGAAT-TTGCTCCACTCTTCTTTCAGGGAGATAAGATTC-AAGAAATCTTTGTAAA
* * * * *
46301 ATGAATATGCTCCACTCTTATTTCAAGGAGATAAGATTCGAGAAATCTTTGTAAA
1 ACGAATTTGCTCCACTCTTCTTTCAGGGAGATAAGATTCAAGAAATCTTTGTAAA
* * * * *
46356 ATGGATCTGCTCTACTCTTCTTTCAGGGAGATAAGATTCGAGAAATCTTTGTAAA
1 ACGAATTTGCTCCACTCTTCTTTCAGGGAGATAAGATTCAAGAAATCTTTGTAAA
* * *
46411 AC-ATATCTGCCCCACTATTCTTTCAGGGAGATAAGAT
1 ACGA-ATTTGCTCCACTCTTCTTTCAGGGAGATAAGAT
46448 CCATGGGAAG
Statistics
Matches: 200, Mismatches: 24, Indels: 34
0.78 0.09 0.13
Matches are distributed among these distances:
46 5 0.03
47 66 0.33
48 8 0.04
54 1 0.00
55 120 0.60
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (55 bp):
ACGAATTTGCTCCACTCTTCTTTCAGGGAGATAAGATTCAAGAAATCTTTGTAAA
Found at i:46808 original size:62 final size:61
Alignment explanation
Indices: 46705--47196 Score: 492
Period size: 62 Copynumber: 8.0 Consensus size: 61
46695 TCTTTGCGAT
* * *
46705 GGAGTCAGGAATAGCAAAAGGTTGACTTCTCTTCACGAGGAAGTCAAGTATTGACTCTATTAG
1 GGAGTCAGGAATAACAAAA-GTTGACTTCTCTTCACGAGGAAGTCAAGTATTAACTCTACT-G
* * * * * *
46768 GGAGTCAGGGATAACAAAAATTTACTTCTCTTCACAAGGAAGTCAAATATTGACTCTACTGG
1 GGAGTCAGGAATAACAAAAGTTGACTTCTCTTCACGAGGAAGTCAAGTATTAACTCTACT-G
* * * * * *
46830 GGAGTCAGTG-ATAACAAATGTTTACTTCTCTTCATGAGGAAGTTAAGAATTGACTCTACTG
1 GGAGTCAG-GAATAACAAAAGTTGACTTCTCTTCACGAGGAAGTCAAGTATTAACTCTACTG
* * * * * * * * *
46891 AAGAGTAAGGGATAACAAAGGTTTACTTCTCTTTACGAGGAAGCCAAGTATTGACTTTACTGG
1 -GGAGTCAGGAATAACAAAAGTTGACTTCTCTTCACGAGGAAGTCAAGTATTAACTCTACT-G
* * *
46954 GGAGTCAGGGATAACAAAGGTTGACTTCTCTTCACGAGGAAGTCAAAG-ATTAACTCTATTG
1 GGAGTCAGGAATAACAAAAGTTGACTTCTCTTCACGAGGAAGTC-AAGTATTAACTCTACTG
* *
47015 GGAAGTCAGAAATAAC-AAAGAATGACTTCTCTTCACGAGGAAGTCAA-TGATTAACTCTACTG
1 GG-AGTCAGGAATAACAAAAG-TTGACTTCTCTTCACGAGGAAGTCAAGT-ATTAACTCTACTG
* * * *
47077 GGAGTCAGAAATAACAAAGAATT-ATTTCTCTTCATGAGGAAGTCAA-TGATTAACTCTACTG
1 GGAGTCAGGAATAACAAA-AGTTGACTTCTCTTCACGAGGAAGTCAAGT-ATTAACTCTACTG
* * * *
47138 AGGAGTCAGAAATAACAAAGGTTGACTTCTATTCACGAGGAAGTCAAGGATTAACTCTA
1 -GGAGTCAGGAATAACAAAAGTTGACTTCTCTTCACGAGGAAGTCAAGTATTAACTCTA
47197 GGAAACAAGA
Statistics
Matches: 368, Mismatches: 47, Indels: 29
0.83 0.11 0.07
Matches are distributed among these distances:
61 61 0.17
62 284 0.77
63 23 0.06
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (61 bp):
GGAGTCAGGAATAACAAAAGTTGACTTCTCTTCACGAGGAAGTCAAGTATTAACTCTACTG
Found at i:47045 original size:186 final size:185
Alignment explanation
Indices: 46721--47196 Score: 580
Period size: 186 Copynumber: 2.6 Consensus size: 185
46711 AGGAATAGCA
* * *
46721 AAAGGTTGACTTCTCTTCACGAGGAAGTCAAGTATTGACTCTATTAGGGAGTCAGGGATAACAAA
1 AAAGGTTTACTTCTCTTCACGAGGAAGTCAAGTATTGACTCTACTGGGGAGTCAGGGATAACAAA
** * * * * * ** *
46786 AATTTACTTCTCTTCACAAGGAAGTCAAATATTGACTCTACTGGGGAGTCAGTGATAACAAATGT
66 GGTTGACTTCTCTTCACGAGGAAGTCAAAGATTAACTCTACTGGGAAGTCAGAAATAACAAATGA
* * * * **
46851 TTACTTCTCTTCATGAGGAAGTTAA-GAATTGACTCTACTGAAGAGTAAGGGATAAC
131 TGACTTCTCTTCACGAGGAAGTCAATG-ATTAACTCTACTG-AGAGTAAGAAATAAC
* * *
46907 AAAGGTTTACTTCTCTTTACGAGGAAGCCAAGTATTGACTTTACTGGGGAGTCAGGGATAACAAA
1 AAAGGTTTACTTCTCTTCACGAGGAAGTCAAGTATTGACTCTACTGGGGAGTCAGGGATAACAAA
*
46972 GGTTGACTTCTCTTCACGAGGAAGTCAAAGATTAACTCTATTGGGAAGTCAGAAATAACAAA-GA
66 GGTTGACTTCTCTTCACGAGGAAGTCAAAGATTAACTCTACTGGGAAGTCAGAAATAACAAATG-
* *
47036 ATGACTTCTCTTCACGAGGAAGTCAATGATTAACTCTACTGGGAGTCAGAAATAAC
130 ATGACTTCTCTTCACGAGGAAGTCAATGATTAACTCTACTGAGAGTAAGAAATAAC
** * * * * **
47092 AAAGAATTATTTCTCTTCATGAGGAAGTCAA-TGATTAACTCTACTGAGGAGTCAGAAATAACAA
1 AAAGGTTTACTTCTCTTCACGAGGAAGTCAAGT-ATTGACTCTACTGGGGAGTCAGGGATAACAA
* *
47156 AGGTTGACTTCTATTCACGAGGAAGTCAAGGATTAACTCTA
65 AGGTTGACTTCTCTTCACGAGGAAGTCAAAGATTAACTCTA
47197 GGAAACAAGA
Statistics
Matches: 249, Mismatches: 38, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
184 1 0.00
185 102 0.41
186 145 0.58
187 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (185 bp):
AAAGGTTTACTTCTCTTCACGAGGAAGTCAAGTATTGACTCTACTGGGGAGTCAGGGATAACAAA
GGTTGACTTCTCTTCACGAGGAAGTCAAAGATTAACTCTACTGGGAAGTCAGAAATAACAAATGA
TGACTTCTCTTCACGAGGAAGTCAATGATTAACTCTACTGAGAGTAAGAAATAAC
Found at i:49511 original size:97 final size:96
Alignment explanation
Indices: 49345--49527 Score: 258
Period size: 97 Copynumber: 1.9 Consensus size: 96
49335 GCCAAGGAGT
* *
49345 AGGCTAGCTAAATCTTATCCATAAAGCCAGGGTGTTTAACCAATTTCTCTAGAGGGACAACTTAA
1 AGGCTAGCTAAATCTTATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTAA
*
49410 GCTTTATTATATATATTATAATCACCTTTATC
66 GCTTTATTATATACA-TATAATCACCTTTATC
* * * * * **
49442 AGGCTAGCTGAATCTTATCCATAAAGTCGGGGCGTTTAACTAATTGCTCTAGAGGGATAGTTTAA
1 AGGCTAGCTAAATCTTATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTAA
*
49507 GCTTTATTGTATACATATAAT
66 GCTTTATTATATACATATAAT
49528 ATTATATTCC
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
96 6 0.08
97 69 0.92
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (96 bp):
AGGCTAGCTAAATCTTATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTAA
GCTTTATTATATACATATAATCACCTTTATC
Found at i:55807 original size:3 final size:3
Alignment explanation
Indices: 55799--55844 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
55789 ATTTGGCCTG
* *
55799 TAA TAA TAA TTA T-T TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55845 ATGGGACAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
2 3 0.08
3 35 0.92
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:55824 original size:20 final size:20
Alignment explanation
Indices: 55799--55844 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
55789 ATTTGGCCTG
* *
55799 TAATAATAATTATTTAATAA
1 TAATAATAATAATATAATAA
55819 TAATAATAATAATATAATAA
1 TAATAATAATAATATAATAA
55839 TAATAA
1 TAATAA
55845 ATGGGACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATAATAATAATATAATAA
Found at i:59395 original size:16 final size:17
Alignment explanation
Indices: 59359--59409 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
59349 CAAATGTAAA
59359 TTAATAAATAATAATA--
1 TTAAT-AATAATAATATT
*
59375 ATAATAATAAT-ATATT
1 TTAATAATAATAATATT
*
59391 TTAATAATTATAATATT
1 TTAATAATAATAATATT
59408 TT
1 TT
59410 TTAAGTCCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 3 0.10
15 6 0.21
16 13 0.45
17 7 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAATAATAATAATATT
Found at i:59395 original size:19 final size:19
Alignment explanation
Indices: 59373--59413 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
59363 TAAATAATAA
59373 TAATAATAATAATATATTT
1 TAATAATAATAATATATTT
* *
59392 TAATAATTATAATATTTTT
1 TAATAATAATAATATATTT
59411 TAA
1 TAA
59414 GTCCGATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATAATAATAATATATTT
Found at i:61021 original size:31 final size:32
Alignment explanation
Indices: 60985--61061 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
60975 AATATCGCAC
* *
60985 TATTAATATAATATAACATATCATATTAA-AA
1 TATTAATATAATATAACACATCATATAAATAA
*
61016 TATTAATATAATATATCACATCATATAAATAA
1 TATTAATATAATATAACACATCATATAAATAA
* *
61048 TAATAAAATAATAT
1 TATTAATATAATAT
61062 GTCATTGTAG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 26 0.65
32 14 0.35
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (32 bp):
TATTAATATAATATAACACATCATATAAATAA
Found at i:69419 original size:29 final size:28
Alignment explanation
Indices: 69387--69470 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 28
69377 TATAAAATGT
69387 TCAATGTGATAACTGTACTTTTAAAATA
1 TCAATGTGATAACTGTACTTTTAAAATA
* *
69415 CTCAATATGAT-AC-GTACTTTGACAAAATA
1 -TCAATGTGATAACTGTACTTT--TAAAATA
* *
69444 TCTAATGTGATAGCTATAC-TTTAAAAT
1 TC-AATGTGATAACTGTACTTTTAAAAT
69471 TGTTCAATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
27 7 0.16
28 9 0.20
29 22 0.50
30 3 0.07
31 3 0.07
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (28 bp):
TCAATGTGATAACTGTACTTTTAAAATA
Found at i:69452 original size:58 final size:58
Alignment explanation
Indices: 69388--69513 Score: 164
Period size: 58 Copynumber: 2.2 Consensus size: 58
69378 ATAAAATGTT
* * *
69388 CAATGTGATAACTGTACTTTTAAAA-TACTCAATATGATACGTACTTTGACAAAATATC
1 CAATGTGATAACTATAC-TTTAAAATTACTCAATATGATACATACTTCGACAAAATATC
* * ** *
69446 TAATGTGATAGCTATACTTTAAAATTGTTCAATATGATACATACTTCGACAAGATATC
1 CAATGTGATAACTATACTTTAAAATTACTCAATATGATACATACTTCGACAAAATATC
69504 CAATGTGATA
1 CAATGTGATA
69514 TTTGAACTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 7 0.12
58 51 0.88
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (58 bp):
CAATGTGATAACTATACTTTAAAATTACTCAATATGATACATACTTCGACAAAATATC
Done.