Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009373.1 Hibiscus syriacus cultivar Beakdansim tig00113244_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: 59370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2710 original size:41 final size:41
Alignment explanation
Indices: 2665--2805 Score: 232
Period size: 41 Copynumber: 3.5 Consensus size: 41
2655 ATTCGAGTTG
2665 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
2706 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* * *
2747 CATTTCGCGTTGCGATAGTCT--ACAGCGCGTTACGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
2787 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
2806 CTACGGTTGT
Statistics
Matches: 96, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
40 35 0.36
41 60 0.62
42 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:2715 original size:20 final size:20
Alignment explanation
Indices: 2690--2802 Score: 109
Period size: 20 Copynumber: 5.6 Consensus size: 20
2680 TAGTTGAAAA
2690 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
2710 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
2731 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
** * **
2751 TCGCGTTGCGATAGTCTACA
1 TCGCGTTGCGATTTTCCATT
* *
2771 GCGCGTTACGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
2791 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2803 AGTCTACGGT
Statistics
Matches: 68, Mismatches: 24, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
20 53 0.78
21 15 0.22
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:2975 original size:5 final size:6
Alignment explanation
Indices: 2913--2972 Score: 81
Period size: 6 Copynumber: 10.5 Consensus size: 6
2903 AAGACGTATT
* *
2913 ACCACT ACCACT ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2960 ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACC
2973 CGAGACAAGA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
5 15 0.28
6 38 0.72
ACGTcount: A:0.30, C:0.53, G:0.13, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:2983 original size:5 final size:5
Alignment explanation
Indices: 2973--3013 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
2963 CGACCCGACC
* *
2973 CGAGA CAAGA CGAGA CGAGA CGAGA CTAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
3014 CGCGGCGGCG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.39, C:0.22, G:0.37, T:0.02
Consensus pattern (5 bp):
CGAGA
Found at i:3651 original size:20 final size:20
Alignment explanation
Indices: 3626--3698 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
3616 ACTGTAGACT
3626 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
3646 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
3667 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
3687 ATCACAACGCGA
1 ATCGCAACGCGA
3699 TTTTTCAACT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:3668 original size:41 final size:42
Alignment explanation
Indices: 3623--3724 Score: 188
Period size: 41 Copynumber: 2.5 Consensus size: 42
3613 ACAACTGTAG
*
3623 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA-TTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTTCA
3664 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTTCA
3706 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
3725 CAACGAATTT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
41 34 0.58
42 25 0.42
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (42 bp):
ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTTCA
Found at i:3821 original size:41 final size:41
Alignment explanation
Indices: 3762--3864 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
3752 GTTGCGATTT
* *
3762 CAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTC
1 CAACTATCGCAACCCGAAATGGAAAAACGCAACGCGATCTC
* * * *
3803 CAACTATCGTAACCCGAAATGGAAAAACTCAACGCGATTTT
1 CAACTATCGCAACCCGAAATGGAAAAACGCAACGCGATCTC
**
3844 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACCCGAAATG
3865 CAACGTGAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.18
Consensus pattern (41 bp):
CAACTATCGCAACCCGAAATGGAAAAACGCAACGCGATCTC
Found at i:3913 original size:141 final size:141
Alignment explanation
Indices: 3626--3903 Score: 407
Period size: 141 Copynumber: 2.0 Consensus size: 141
3616 ACTGTAGACT
* * * *
3626 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCA
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACCCGAAATGGAAAAACA
**
3691 CAACGCGATTTTTCAACTATCGCAACGCGAAATGCAACGAATTTGCGATGATGGAGATCGCGTTG
66 CAACGCGATTTTTCAACTATCGCAACGCGAAATGCAACGAATTTGCGATGATGGAGATCGCAATG
* *
3756 CGATTTCAACT
131 CGAATTCAACG
* *
3767 ATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGTAACCCGAAATGGAAAAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACCCGAAATGGAAAAACA
*
3832 CAACGCGA-TTTTCAACTATCGCAATGCGAAATGCAACGTGAATTTGCGAT-AGTGGAGATCGCA
66 CAACGCGATTTTTCAACTATCGCAACGCGAAATGCAAC--GAATTTGCGATGA-TGGAGATCGCA
*
3895 ATGTGAATT
128 ATGCGAATT
3904 AGAGATCGCA
Statistics
Matches: 123, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
140 28 0.23
141 68 0.55
142 27 0.22
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (141 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACCCGAAATGGAAAAACA
CAACGCGATTTTTCAACTATCGCAACGCGAAATGCAACGAATTTGCGATGATGGAGATCGCAATG
CGAATTCAACG
Found at i:4716 original size:22 final size:22
Alignment explanation
Indices: 4667--4710 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4657 TATATATTGT
*
4667 ATGAATAGTACTGTGAACAGTA
1 ATGAATAGTACTGTGAACAATA
4689 ATGAATAGTA-TCGTGAACAATA
1 ATGAATAGTACT-GTGAACAATA
4711 TCGAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.27
Consensus pattern (22 bp):
ATGAATAGTACTGTGAACAATA
Found at i:4778 original size:21 final size:21
Alignment explanation
Indices: 4738--4804 Score: 82
Period size: 21 Copynumber: 3.1 Consensus size: 21
4728 CCAGAATTAA
* *
4738 ACAATGGTACCAATATCCTGCT
1 ACAAT-GTACCGATACCCTGCT
*
4760 ACAATGTACTGATACCCTGCT
1 ACAATGTACCGATACCCTGCT
4781 AC-ATGTACCGATACCCTTGCT
1 ACAATGTACCGATACCC-TGCT
4802 ACA
1 ACA
4805 GTAACTTTCG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 13 0.33
21 21 0.54
22 5 0.13
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (21 bp):
ACAATGTACCGATACCCTGCT
Found at i:8443 original size:26 final size:27
Alignment explanation
Indices: 8395--8447 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
8385 TGGATTTATA
8395 AAAATGCCCCTAAAGTGTAAAATGACC
1 AAAATGCCCCTAAAGTGTAAAATGACC
* *
8422 AAAATGCTCCT-AAGTGTTAAATGACC
1 AAAATGCCCCTAAAGTGTAAAATGACC
8448 TAAAGTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.23
Consensus pattern (27 bp):
AAAATGCCCCTAAAGTGTAAAATGACC
Found at i:10901 original size:13 final size:13
Alignment explanation
Indices: 10845--10914 Score: 63
Period size: 13 Copynumber: 5.4 Consensus size: 13
10835 AAATAGTAAG
*
10845 TAAAAAAAACAAA
1 TAAAAAAAATAAA
* * *
10858 TAATAAAATTATA
1 TAAAAAAAATAAA
10871 TAAAAAGAAA-AAGA
1 TAAAAA-AAATAA-A
10885 -AAAAAAAATAAA
1 TAAAAAAAATAAA
*
10897 TAAAACAAATAAA
1 TAAAAAAAATAAA
10910 TAAAA
1 TAAAA
10915 TAATAATAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
12 4 0.09
13 38 0.84
14 3 0.07
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (13 bp):
TAAAAAAAATAAA
Found at i:10963 original size:27 final size:27
Alignment explanation
Indices: 10903--10978 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 27
10893 TAAATAAAAC
* *
10903 AAATAAATAAAATAATAATAACAAAGT
1 AAATATATATAATAATAATAACAAAGT
10930 ACGAATATATATAATAAATAATAA-AAAGT
1 A--AATATATATAAT-AATAATAACAAAGT
*
10959 AAATATATATAA-ATTAATAA
1 AAATATATATAATAATAATAA
10979 ATTAAATGAC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
25 7 0.16
27 12 0.28
29 16 0.37
30 8 0.19
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.28
Consensus pattern (27 bp):
AAATATATATAATAATAATAACAAAGT
Found at i:11302 original size:22 final size:21
Alignment explanation
Indices: 11270--11325 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
11260 CAATAAAAAA
*
11270 AGAATAAATATATATAATGATAAT
1 AGAA-AAATATATAAAAT--TAAT
*
11294 A-AAAAATATAGAAAATTAAT
1 AGAAAAATATATAAAATTAAT
11314 AGAAAAATATAT
1 AGAAAAATATAT
11326 GTATAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 5 0.18
21 9 0.32
22 11 0.39
23 2 0.07
24 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (21 bp):
AGAAAAATATATAAAATTAAT
Found at i:11461 original size:12 final size:11
Alignment explanation
Indices: 11425--11478 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
11415 TACCATATAT
* *
11425 ATAACAAAAAA
1 ATAATAAAAGA
11436 ATAATATAAA-A
1 ATAATA-AAAGA
11447 ATAATAAAAGTA
1 ATAATAAAAG-A
*
11459 ATAATACAAGA
1 ATAATAAAAGA
11470 ATAATAAAA
1 ATAATAAAA
11479 AAAGAGAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.08
11 21 0.57
12 13 0.35
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (11 bp):
ATAATAAAAGA
Found at i:11472 original size:23 final size:23
Alignment explanation
Indices: 11435--11478 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
11425 ATAACAAAAA
*
11435 AATAATATAAAAATAATAAAAGT
1 AATAATACAAAAATAATAAAAGT
*
11458 AATAATACAAGAATAATAAAA
1 AATAATACAAAAATAATAAAA
11479 AAAGAGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (23 bp):
AATAATACAAAAATAATAAAAGT
Found at i:11582 original size:9 final size:9
Alignment explanation
Indices: 11494--11588 Score: 52
Period size: 9 Copynumber: 10.1 Consensus size: 9
11484 GAAAGTAAAA
11494 AAATATAAT
1 AAATATAAT
11503 -AATAATAA-
1 AAAT-ATAAT
*
11511 AAATATAAA
1 AAATATAAT
11520 AAATATACAT
1 AAATATA-AT
*
11530 ATATATAAAT
1 AAATAT-AAT
* *
11540 AAGTAGAAT
1 AAATATAAT
* *
11549 AAAAGGAAAAT
1 -AAA-TATAAT
11560 ATAATAGTAA-
1 A-AATA-TAAT
11570 AAATATAAT
1 AAATATAAT
11579 AAATATAAT
1 AAATATAAT
11588 A
1 A
11589 GTAATAATAA
Statistics
Matches: 66, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
8 10 0.15
9 31 0.47
10 16 0.24
11 9 0.14
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.27
Consensus pattern (9 bp):
AAATATAAT
Found at i:12198 original size:37 final size:37
Alignment explanation
Indices: 12144--12247 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
12134 GTGCTTGTGG
* * *
12144 ATCATA-TCTTTAAGAGTTTAAATCATAGTAGAACTCT
1 ATCATAGT-TTTAGGAGTTTAAATCCTAGTAAAACTCT
* * * *
12181 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCATAGTTTTAGGAGTTTAAATCCTAGTAAAACTCT
*
12218 ATCATAGTTTTAGGAGTTTGAATCCTAGTA
1 ATCATAGTTTTAGGAGTTTAAATCCTAGTA
12248 TGACGAAAAG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 55 0.98
38 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (37 bp):
ATCATAGTTTTAGGAGTTTAAATCCTAGTAAAACTCT
Found at i:13477 original size:106 final size:106
Alignment explanation
Indices: 12982--14663 Score: 2357
Period size: 106 Copynumber: 15.9 Consensus size: 106
12972 ATCCTCCGTC
* * ** * * ** *
12982 GTGAAGTTGAAA-TGGCTTTGGAACCGTGAAATTGTTTGTTGACAACCAGCCATCCCTTCGTTGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
* * * *
13046 GAAGTTGAACTTGTGTTATCTCGAGTCCAATATCATTCGCT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* ** * *
13087 GTGAAGTTGAAATTGACTCTG-AA-TGA-AA--T-TTTGTTGACAATTAGCTG-CCTATTCGTCG
1 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC-CTTCGTCG
* * * * * *
13145 TGAAGTTGAGCTTGTGTTGCCTTGG-GTTCAAGATCATTCGCT
65 TGAAGTTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGCT
* * * * * *
13187 GAGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAACCAGCGGTCCCTTCATCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
* *
13252 GAAGTTGAATTTGCGTAAACTTGCGTTGTCTTGAGTCCAATATCCTACGCT
66 GAA---G---TT--G--AACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* * *
13303 GTGAAGTTGAAATTGGCTTTGAAA-TGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
* * *
13367 GAAGTTGAACTTGCGTTGTCTAGAGTTCAATATCCTTCGTT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* *
13408 GTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTGGTTGACAACCAGCGGTCCCTTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
13473 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* * * *
13514 GTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
*
13579 GAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* * * *
13620 GTTAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
*
13685 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
*
13726 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCATCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
13791 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* *
13832 GTGAAGTTGAAATTGGCTATGAAATTG-GAAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCG
1 GTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCG
*
13896 TGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCT
65 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* * *
13938 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
*
14003 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* *
14044 GTGAAGTTGAAATTGGCTCTGAAATTGATAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
* *
14109 GAAGTTGAACTTGCGTTGCCTGTAGTCCAATATCCTTCGCT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* *
14150 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
*
14215 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
14256 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
*
14321 GAAGTTGAACTTGCGTTGTTTGGAGTCCAATATCCTTCGCT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* *
14362 GTGAAGTTGAAATTGGCTATGAAATTG-GAAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCG
1 GTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCG
*
14426 TGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCT
65 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* * * * * *
14468 GTGAAGTTGAAATTAGATTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
* *
14533 GAAGTTTAACTTGCGTTGTCTAGAGTCCAATATCCTTCGCT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* * * * * * *
14574 GTTAAGTTGAAATTAGCTCCGAAATTG-GAAAATTG-TTGTTGACAACTAGCCGTCCCTTCGTTG
1 GTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCG
* *
14637 TGAAGTTGAACTTGTGTTGTCTTGAGT
65 TGAAGTTGAACTTGCGTTGTCTGGAGT
14664 GGCACGATAT
Statistics
Matches: 1429, Mismatches: 121, Indels: 54
0.89 0.08 0.03
Matches are distributed among these distances:
99 2 0.00
100 71 0.05
101 5 0.00
102 2 0.00
103 4 0.00
104 1 0.00
105 118 0.08
106 1129 0.79
107 5 0.00
109 3 0.00
112 3 0.00
114 1 0.00
115 41 0.03
116 44 0.03
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
Found at i:15511 original size:22 final size:22
Alignment explanation
Indices: 15485--15554 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
15475 TTATGTTTGG
15485 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
**
15507 TCAAAGGTTTGGCATGGGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
15529 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
15551 TCAA
1 TCAA
15555 CGATTTGATG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:16170 original size:6 final size:6
Alignment explanation
Indices: 16159--16217 Score: 55
Period size: 6 Copynumber: 9.0 Consensus size: 6
16149 TTTTTTGTCC
* *
16159 CTTTTT CTTTTT GATTTTT GTTCTTT CTTTTT CTTTTT CTTTTT GCTTCTTTT
1 CTTTTT CTTTTT -CTTTTT CTT-TTT CTTTTT CTTTTT CTTTTT -C-T-TTTT
16212 CTTTTT
1 CTTTTT
16218 TGTTTTTGCC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
6 27 0.60
7 12 0.27
8 2 0.04
9 4 0.09
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (6 bp):
CTTTTT
Found at i:16192 original size:26 final size:27
Alignment explanation
Indices: 16159--16217 Score: 86
Period size: 26 Copynumber: 2.2 Consensus size: 27
16149 TTTTTTGTCC
16159 CTTTTTCTTTTTGATTTTTG-TTC-TTT
1 CTTTTTCTTTTT-ATTTTTGCTTCTTTT
*
16185 CTTTTTCTTTTTCTTTTTGCTTCTTTT
1 CTTTTTCTTTTTATTTTTGCTTCTTTT
16212 CTTTTT
1 CTTTTT
16218 TGTTTTTGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 6 0.20
26 15 0.50
27 9 0.30
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (27 bp):
CTTTTTCTTTTTATTTTTGCTTCTTTT
Found at i:16208 original size:16 final size:16
Alignment explanation
Indices: 16159--16217 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
16149 TTTTTTGTCC
16159 CTTTTTCTTTTTGATT
1 CTTTTTCTTTTTGATT
*
16175 -TTTGTTCTTTCTT-TTT
1 CTTT-TTCTTT-TTGATT
*
16191 CTTTTTCTTTTTGCTT
1 CTTTTTCTTTTTGATT
16207 C-TTTTCTTTTT
1 CTTTTTCTTTTT
16218 TGTTTTTGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 15 0.41
16 17 0.46
17 5 0.14
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (16 bp):
CTTTTTCTTTTTGATT
Found at i:16211 original size:22 final size:23
Alignment explanation
Indices: 16159--16226 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 23
16149 TTTTTTGTCC
16159 CTTTTTCTTTTTGATTTTTGTTCTTT
1 CTTTTTCTTTTT-ATTTTTG--CTTT
*
16185 CTTTTTCTTTTTCTTTTTGC-TT
1 CTTTTTCTTTTTATTTTTGCTTT
*
16207 C-TTTTCTTTTTTGTTTTTGC
1 CTTTTTC-TTTTTATTTTTGC
16227 CCTTTTTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.13
22 15 0.38
23 1 0.03
25 6 0.15
26 12 0.31
ACGTcount: A:0.01, C:0.15, G:0.07, T:0.76
Consensus pattern (23 bp):
CTTTTTCTTTTTATTTTTGCTTT
Found at i:16231 original size:21 final size:21
Alignment explanation
Indices: 16187--16232 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
16177 TGTTCTTTCT
*
16187 TTTTCTTTTTCTTTTTGCTTC
1 TTTTCTTTTTCTTTTTGCTCC
*
16208 TTTTCTTTTTTGTTTTTGC-CC
1 TTTTC-TTTTTCTTTTTGCTCC
16229 TTTT
1 TTTT
16233 TGTTCTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (21 bp):
TTTTCTTTTTCTTTTTGCTCC
Found at i:16233 original size:22 final size:22
Alignment explanation
Indices: 16150--16233 Score: 57
Period size: 22 Copynumber: 3.7 Consensus size: 22
16140 TGCATGTGCT
*
16150 TTTTTG-TCCCTTTTTCTTTTTGA
1 TTTTTGCT-CCTTTTTCTTTTT-C
*
16173 TTTTTGTTCTTTCTTTTTCTTTTTC
1 TTTTTG--C-TCCTTTTTCTTTTTC
* *
16198 TTTTTGCTTC-TTTTCTTTTTTG
1 TTTTTGCTCCTTTTTC-TTTTTC
16220 TTTTTGC-CCTTTTT
1 TTTTTGCTCCTTTTT
16234 GTTCTGATTG
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
21 6 0.12
22 19 0.37
23 7 0.14
25 6 0.12
26 12 0.24
27 1 0.02
ACGTcount: A:0.01, C:0.17, G:0.07, T:0.75
Consensus pattern (22 bp):
TTTTTGCTCCTTTTTCTTTTTC
Found at i:20692 original size:23 final size:24
Alignment explanation
Indices: 20666--20773 Score: 73
Period size: 22 Copynumber: 4.5 Consensus size: 24
20656 AACAAATAAT
20666 AAATATATATAAAA-AAAAAAAGA
1 AAATATATATAAAACAAAAAAAGA
* *
20689 AAATA-A-ATAAAACAAATAAACA
1 AAATATATATAAAACAAAAAAAGA
* ** *
20711 AAATA-ATA-ATAACAAAGTACGA
1 AAATATATATAAAACAAAAAAAGA
* *
20733 ATAATATATATATATAATAAATAAAAGT
1 A-AATATATATA-A-AACAAA-AAAAGA
20761 AAATATATATAAA
1 AAATATATATAAA
20774 TTAATAAATT
Statistics
Matches: 64, Mismatches: 13, Indels: 14
0.70 0.14 0.15
Matches are distributed among these distances:
21 6 0.09
22 24 0.38
23 10 0.16
24 3 0.05
25 2 0.03
26 1 0.02
27 15 0.23
28 3 0.05
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (24 bp):
AAATATATATAAAACAAAAAAAGA
Found at i:21265 original size:12 final size:11
Alignment explanation
Indices: 21237--21277 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
21227 TATATATAAT
* *
21237 AATAATATAAA
1 AATAATACAAG
21248 AATAATACAAG
1 AATAATACAAG
21259 TAATAATACAAG
1 -AATAATACAAG
21271 AATAATA
1 AATAATA
21278 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:21315 original size:13 final size:13
Alignment explanation
Indices: 21297--21405 Score: 56
Period size: 13 Copynumber: 8.7 Consensus size: 13
21287 AGAAAGTAAA
21297 AAAATATAATAAT
1 AAAATATAATAAT
*
21310 AAAATATAAAAAT
1 AAAATATAATAAT
*
21323 ATACATAT-ATAAT
1 A-AAATATAATAAT
21336 ---ATA-AATAAGT
1 AAAATATAATAA-T
* **
21346 AGAATA-AA-AGG
1 AAAATATAATAAT
*
21357 AAAATATAATAGT
1 AAAATATAATAAT
21370 AAAA-ATAATAAT
1 AAAATATAATAAT
21382 AAATAATAGTAATAAT
1 -AA-AATA-TAATAAT
21398 AAAA-ATAA
1 AAAATATAA
21406 AATGCAAAGA
Statistics
Matches: 76, Mismatches: 8, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
9 7 0.09
10 1 0.01
11 5 0.07
12 13 0.17
13 31 0.41
14 9 0.12
15 3 0.04
16 7 0.09
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.27
Consensus pattern (13 bp):
AAAATATAATAAT
Found at i:21321 original size:21 final size:21
Alignment explanation
Indices: 21296--21340 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
21286 GAGAAAGTAA
21296 AAAAATATA-ATAATAAAATAT
1 AAAAATATACAT-ATAAAATAT
*
21317 AAAAATATACATATATAATAT
1 AAAAATATACATATAAAATAT
21338 AAA
1 AAA
21341 TAAGTAGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAATATACATATAAAATAT
Found at i:21390 original size:22 final size:22
Alignment explanation
Indices: 21362--21406 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
21352 AAAGGAAAAT
*
21362 ATAATAGTAAAAATAATAATAA
1 ATAATAGTAAAAATAAAAATAA
*
21384 ATAATAGTAATAATAAAAATAA
1 ATAATAGTAAAAATAAAAATAA
21406 A
1 A
21407 ATGCAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (22 bp):
ATAATAGTAAAAATAAAAATAA
Found at i:21396 original size:16 final size:15
Alignment explanation
Indices: 21375--21404 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
21365 ATAGTAAAAA
21375 TAATAATAAATAATAG
1 TAATAATAAA-AATAG
21391 TAATAATAAAAATA
1 TAATAATAAAAATA
21405 AAATGCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
TAATAATAAAAATAG
Found at i:21405 original size:53 final size:52
Alignment explanation
Indices: 21307--21407 Score: 118
Period size: 53 Copynumber: 1.9 Consensus size: 52
21297 AAAATATAAT
* *
21307 AATAAAATATAAAAATATACATATATAATATAAATAAGTAGAATAAAAGGAA
1 AATAAAATATAAAAATATACATAAATAATATAAATAAGTAAAATAAAAGGAA
*
21359 AATATAATAGTAAAAATAATA-ATAAATAATAGT-AATAA-TAAAAATAAAA
1 AATAAAATA-TAAAAAT-ATACATAAATAATA-TAAATAAGT-AAAATAAAA
21408 TGCAAAGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
52 9 0.21
53 29 0.69
54 4 0.10
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.26
Consensus pattern (52 bp):
AATAAAATATAAAAATATACATAAATAATATAAATAAGTAAAATAAAAGGAA
Found at i:22009 original size:37 final size:37
Alignment explanation
Indices: 21968--22071 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 37
21958 GTGCTTGTGG
* * *
21968 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAAAACTCT
* *
22005 ATCCTATTTTTAGGAGTTTAAATCCTAGAAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAAAACTCT
* *
22042 ATCCTATTTTTATGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTA
22072 CGACGAAAAG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAAAACTCT
Found at i:25653 original size:21 final size:20
Alignment explanation
Indices: 25617--25679 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
25607 AAAACCAGAA
25617 CCCTATGGGGGTATCGATTC
1 CCCTATGGGGGTATCGATTC
* *
25637 CCCTATAGGGGGAATCGGTTC
1 CCCTAT-GGGGGTATCGATTC
*
25658 CCTTATGGGGGTATCGATTC
1 CCCTATGGGGGTATCGATTC
25678 CC
1 CC
25680 TCTGCCAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.29
Consensus pattern (20 bp):
CCCTATGGGGGTATCGATTC
Found at i:34778 original size:46 final size:44
Alignment explanation
Indices: 34683--34786 Score: 140
Period size: 45 Copynumber: 2.3 Consensus size: 44
34673 GCACTAAGGA
34683 TGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCTTGG
1 TGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATA-CTTGG
*
34728 TGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATA-TTCAGAG
1 TGCATCGATGCATAAAATGCATTCGATG-TTTGAAAAATACTT--G-G
34774 TGCATCGATGCAT
1 TGCATCGATGCAT
34787 GGAGAGTGCA
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
43 2 0.04
45 34 0.63
46 18 0.33
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (44 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATACTTGG
Found at i:34794 original size:19 final size:19
Alignment explanation
Indices: 34770--34820 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
34760 GAAAATATTC
34770 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
34789 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
34808 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
34821 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:35237 original size:31 final size:31
Alignment explanation
Indices: 35199--35260 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
35189 ATTGATTTTG
35199 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
*
35230 AAAAACTTACTCTCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
35261 TTAAATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.34, G:0.03, T:0.27
Consensus pattern (31 bp):
AAAAACTTACTCCCCCTTACTATAGCACATC
Found at i:39725 original size:22 final size:21
Alignment explanation
Indices: 39699--39745 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
39689 AAGGTCAAAA
*
39699 ATCAAATTGTTTGAAAATTG-AT
1 ATCAAATGGTTT-AAAA-TGAAT
39721 ATC-AATGGTTTAAAATGAAT
1 ATCAAATGGTTTAAAATGAAT
39741 ATCAA
1 ATCAA
39746 TTACGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 8 0.36
22 3 0.14
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
ATCAAATGGTTTAAAATGAAT
Found at i:41912 original size:46 final size:44
Alignment explanation
Indices: 41817--41920 Score: 140
Period size: 45 Copynumber: 2.3 Consensus size: 44
41807 GCACTAAGGA
41817 TGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCTTGG
1 TGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATA-CTTGG
*
41862 TGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATA-TTCAGAG
1 TGCATCGATGCATAAAATGCATTCGATG-TTTGAAAAATACTT--G-G
41908 TGCATCGATGCAT
1 TGCATCGATGCAT
41921 GGAGAGTGCA
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
43 2 0.04
45 34 0.63
46 18 0.33
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (44 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATACTTGG
Found at i:41928 original size:19 final size:19
Alignment explanation
Indices: 41904--41954 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
41894 GAAAATATTC
41904 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
41923 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
41942 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
41955 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:42193 original size:12 final size:12
Alignment explanation
Indices: 42176--42211 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
42166 TCGAATATAA
42176 ATTTGTAAAATC
1 ATTTGTAAAATC
42188 ATTTGTAAAATC
1 ATTTGTAAAATC
42200 ATTTGTAAAATC
1 ATTTGTAAAATC
42212 TTAAAATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
ATTTGTAAAATC
Found at i:45162 original size:19 final size:20
Alignment explanation
Indices: 45135--45179 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
45125 ATTAGCAACA
*
45135 TAAT-AAAAATGATTCTATC
1 TAATAAAAAATGATCCTATC
*
45154 TAATTAAAAATGATCCTATC
1 TAATAAAAAATGATCCTATC
45174 TAATAA
1 TAATAA
45180 CTAATAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (20 bp):
TAATAAAAAATGATCCTATC
Found at i:45163 original size:20 final size:20
Alignment explanation
Indices: 45138--45177 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
45128 AGCAACATAA
*
45138 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
45158 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
45178 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:45269 original size:20 final size:20
Alignment explanation
Indices: 45244--45282 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
45234 TAATAGAATA
*
45244 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
45264 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
45283 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:45273 original size:52 final size:52
Alignment explanation
Indices: 45136--45283 Score: 262
Period size: 53 Copynumber: 2.8 Consensus size: 52
45126 TTAGCAACAT
45136 AATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
*
45187 AATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCCAATAACTAATAG
1 AAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
*
45240 AATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
45284 TTTAATTTAG
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 3 0.03
52 44 0.48
53 45 0.49
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.32
Consensus pattern (52 bp):
AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
Found at i:47852 original size:20 final size:19
Alignment explanation
Indices: 47829--47882 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 19
47819 GTTGCGATTT
47829 AGAAAATCGCAACGTAAAAA
1 AGAAAATCGCAACGT-AAAA
*
47849 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAAC-GTAAAA
47869 AGAAAATCGCAACG
1 AGAAAATCGCAACG
47883 CGAGCTTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 1 0.03
20 29 0.91
21 2 0.06
ACGTcount: A:0.54, C:0.19, G:0.19, T:0.09
Consensus pattern (19 bp):
AGAAAATCGCAACGTAAAA
Found at i:47942 original size:20 final size:20
Alignment explanation
Indices: 47917--48170 Score: 301
Period size: 20 Copynumber: 12.4 Consensus size: 20
47907 TTTAGAAGAA
*
47917 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
*
47937 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
47957 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
47977 ATTCGCAACGCGATTTAGAAGAG
1 AATCGCAATGCGA-TT-G-AGAG
*
48000 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
*
48020 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
* *
48040 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
* *
48060 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
* *
48080 AATCGCAACGCGATTAAGAG
1 AATCGCAATGCGATTGAGAG
* *
48100 ATTCGCAACGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
48120 ATTCGCAACGCGATTTAGAAGAG
1 AATCGCAATGCGA-TT-G-AGAG
*
48143 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
48163 AATCGCAA
1 AATCGCAA
48171 CGTTGAAAAT
Statistics
Matches: 213, Mismatches: 15, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
20 172 0.81
21 6 0.03
22 5 0.02
23 30 0.14
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.22
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:48006 original size:83 final size:83
Alignment explanation
Indices: 47895--48134 Score: 333
Period size: 83 Copynumber: 2.9 Consensus size: 83
47885 AGCTTCCAAG
*
47895 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAAT
1 TTCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAAT
47960 CGCAATGCGATTGAGAGA
66 CGCAATGCGATTGAGAGA
47978 TTCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAAT
1 TTCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAAT
* *
48043 CGCAATGCGATTTATAGA
66 CGCAATGCGATTGAGAGA
* * * * * * * * * *
48061 ATCGCAATGCGATTT---ATAGAATCGCAACGCGATTAAGAGATTCGCAACGCGATTGAGAGATT
1 TTCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAAT
*
48123 CGCAACGCGATT
66 CGCAATGCGATT
48135 TAGAAGAGAA
Statistics
Matches: 143, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
80 50 0.35
83 93 0.65
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.24
Consensus pattern (83 bp):
TTCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAAT
CGCAATGCGATTGAGAGA
Found at i:48291 original size:6 final size:6
Alignment explanation
Indices: 48280--48317 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
48270 GACACGTATT
48280 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
48318 CGAGACGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.32, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:49029 original size:6 final size:6
Alignment explanation
Indices: 49013--49050 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
49003 TCTCGTCTCG
49013 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
49051 AATACGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:49161 original size:20 final size:20
Alignment explanation
Indices: 49138--49435 Score: 193
Period size: 20 Copynumber: 14.6 Consensus size: 20
49128 TTCTTTTTAA
49138 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
49158 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
49178 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
49198 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
49218 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
49238 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
49261 CGTTGCGAATCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
49281 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
49301 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
49321 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
49344 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
*** **
49365 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTAAATCG
49385 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
49405 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
49424 CGTTGCGATTTT
1 CGTTGCGATTTT
49436 ATTGGTCATT
Statistics
Matches: 226, Mismatches: 45, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
19 17 0.08
20 163 0.72
21 14 0.06
22 4 0.02
23 28 0.12
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:49184 original size:40 final size:40
Alignment explanation
Indices: 49138--49351 Score: 230
Period size: 40 Copynumber: 5.2 Consensus size: 40
49128 TTCTTTTTAA
* * *
49138 CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCG
1 CGTTGCGATTCTCTAAATCGCATTGCGATTCTCTAAATCG
* * * *
49178 CATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCG
1 CGTTGCGATTCTCTAAATCGCATTGCGATTCTCTAAATCG
* * *
49218 CATTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCG
1 CGTTGCGATTCTCTAAATCGCATTGCGA--TTC-TCTAAATCG
* * *
49261 CGTTGCGAATCTCTCAATCGCATTGCGATTCTATAAATCG
1 CGTTGCGATTCTCTAAATCGCATTGCGATTCTCTAAATCG
* * *
49301 CATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCG
1 CGTTGCGATTCTCTAAATCGCATTGCGA--TTC-TCTAAATCG
49344 CGTTGCGA
1 CGTTGCGA
49352 ACTTGGAAGC
Statistics
Matches: 149, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
40 93 0.62
41 3 0.02
42 6 0.04
43 47 0.32
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (40 bp):
CGTTGCGATTCTCTAAATCGCATTGCGATTCTCTAAATCG
Found at i:49280 original size:83 final size:83
Alignment explanation
Indices: 49140--49352 Score: 288
Period size: 83 Copynumber: 2.6 Consensus size: 83
49130 CTTTTTAACG
* * * * * *
49140 TTGCGATTTTCTAAATCGCGTTGCGA--TTC-TCTCAATCGCATTGCGATTCTATAAATCGCATT
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGAATCTATAAATCGCATT
* * *
49202 GCGATTCTCTCAGTCGCA
66 GCGATTCTATAAATCGCA
* * *
49220 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCATT
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGAATCTATAAATCGCATT
49285 GCGATTCTATAAATCGCA
66 GCGATTCTATAAATCGCA
*
49303 TTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGAA
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGAA
49353 CTTGGAAGCT
Statistics
Matches: 116, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
80 22 0.19
82 3 0.03
83 91 0.78
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (83 bp):
TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGAATCTATAAATCGCATT
GCGATTCTATAAATCGCA
Found at i:51688 original size:19 final size:20
Alignment explanation
Indices: 51661--51705 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
51651 ATTAGCAACA
*
51661 TAAT-AAAAATGATTCTATC
1 TAATAAAAAATGATCCTATC
*
51680 TAATTAAAAATGATCCTATC
1 TAATAAAAAATGATCCTATC
51700 TAATAA
1 TAATAA
51706 CTAATAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (20 bp):
TAATAAAAAATGATCCTATC
Found at i:51689 original size:20 final size:20
Alignment explanation
Indices: 51664--51703 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
51654 AGCAACATAA
*
51664 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
51684 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
51704 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:51746 original size:20 final size:21
Alignment explanation
Indices: 51717--51756 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
51707 TAATAGAATA
*
51717 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
51738 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
51757 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:51795 original size:20 final size:20
Alignment explanation
Indices: 51770--51808 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
51760 TAATAGAATA
*
51770 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
51790 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
51809 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:51799 original size:52 final size:52
Alignment explanation
Indices: 51662--51809 Score: 271
Period size: 53 Copynumber: 2.8 Consensus size: 52
51652 TTAGCAACAT
51662 AATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
51713 AATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
*
51766 AATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
51810 TTTAATTTAG
Statistics
Matches: 94, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
51 3 0.03
52 45 0.48
53 46 0.49
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (52 bp):
AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
Done.