Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006386.1 Hibiscus syriacus cultivar Beakdansim tig00015381_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: 86801
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1072 original size:21 final size:21
Alignment explanation
Indices: 1039--1183 Score: 149
Period size: 21 Copynumber: 6.9 Consensus size: 21
1029 TGCGATTTTG
*
1039 GACTATCGTAACGAATTTGGA
1 GACTATCGCAACGAATTTGGA
*
1060 GACTACCGCAACGAATTTGGA
1 GACTATCGCAACGAATTTGGA
*
1081 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAATTTGGA
*
1102 GACTATCGCAACGCGAACTT-G-
1 GACTATCGCAA--CGAATTTGGA
1123 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAATTTGGA
*
1144 -A-TAAATCGCAACGCAAACTT-G-
1 GACT--ATCGCAACG--AATTTGGA
1165 GACTATCGCAACGAATTTG
1 GACTATCGCAACGAATTTG
1184 AAAAATCGCA
Statistics
Matches: 106, Mismatches: 7, Indels: 23
0.78 0.05 0.17
Matches are distributed among these distances:
19 11 0.10
20 2 0.02
21 78 0.74
22 3 0.03
23 12 0.11
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (21 bp):
GACTATCGCAACGAATTTGGA
Found at i:1094 original size:42 final size:41
Alignment explanation
Indices: 1036--1257 Score: 188
Period size: 42 Copynumber: 5.3 Consensus size: 41
1026 CGTTGCGATT
* *
1036 TTGGACTATCGTAACGAATTTGGAGACTACCGCAA-CGAAT
1 TTGGACTATCGCAACGAATTTGGAGACTACCGCAACCGAAC
* *
1076 TTGGAGACTATCGCAACGAACTTGGAGACTATCGCAACGCGAAC
1 TT-G-GACTATCGCAACGAATTTGGAGACTACCGCAAC-CGAAC
* *
1120 TTGGACTATCGCAACGAATTTGGA-A-TAAATCGCAACGCAAAC
1 TTGGACTATCGCAACGAATTTGGAGACT--ACCGCAAC-CGAAC
** *
1162 TTGGACTATCGCAACGAATTT-GA-AAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAGACTACCGCAAC-CGAAC
* * * *
1202 TTCGACTATCGCAACGCGAACTT--AGACTATCGCAATGCGAAC
1 TTGGACTATCGCAA--CGAATTTGGAGACTACCGCAA-CCGAAC
1244 TTGGACTATCGCAA
1 TTGGACTATCGCAA
1258 TGCGAATATG
Statistics
Matches: 157, Mismatches: 14, Indels: 20
0.82 0.07 0.10
Matches are distributed among these distances:
40 29 0.18
41 6 0.04
42 115 0.73
43 1 0.01
44 6 0.04
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (41 bp):
TTGGACTATCGCAACGAATTTGGAGACTACCGCAACCGAAC
Found at i:1106 original size:63 final size:60
Alignment explanation
Indices: 1036--1183 Score: 167
Period size: 63 Copynumber: 2.4 Consensus size: 60
1026 CGTTGCGATT
*
1036 TTGGACTATCGTAACGAATTTGGAGACTACCGCAACGAATTTGGAGACT-ATCGCAACG-AAC
1 TTGGACTATCGCAACGAATTTGG-GACTACCGCAACGAATTTGGA-A-TAATCGCAACGAAAC
* *
1097 TTGGAGACTATCGCAACGCGAACTT-GGACTATCGCAACGAATTTGGAATAAATCGCAACGCAAA
1 TT-G-GACTATCGCAA--CGAATTTGGGACTACCGCAACGAATTTGGAAT-AATCGCAACG-AAA
1161 C
60 C
1162 TTGGACTATCGCAACGAATTTG
1 TTGGACTATCGCAACGAATTTG
1184 AAAAATCGCA
Statistics
Matches: 74, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
61 9 0.12
62 2 0.03
63 50 0.68
64 2 0.03
65 11 0.15
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (60 bp):
TTGGACTATCGCAACGAATTTGGGACTACCGCAACGAATTTGGAATAATCGCAACGAAAC
Found at i:1212 original size:21 final size:21
Alignment explanation
Indices: 1081--1263 Score: 189
Period size: 21 Copynumber: 8.8 Consensus size: 21
1071 CGAATTTGGA
1081 GACTATCGCAA--CGAACTTGG
1 GACTATCGCAACGCGAACTT-G
1101 AGACTATCGCAACGCGAACTTG
1 -GACTATCGCAACGCGAACTTG
*
1123 GACTATCGCAA--CGAATTTG
1 GACTATCGCAACGCGAACTTG
* *
1142 GAATAAATCGCAACGCAAACTTG
1 GACT--ATCGCAACGCGAACTTG
*
1165 GACTATCGCAA--CGAATTTG
1 GACTATCGCAACGCGAACTTG
* ** *
1184 AAAAATCGCAACGCGAACTTC
1 GACTATCGCAACGCGAACTTG
*
1205 GACTATCGCAACGCGAACTTA
1 GACTATCGCAACGCGAACTTG
*
1226 GACTATCGCAATGCGAACTTG
1 GACTATCGCAACGCGAACTTG
*
1247 GACTATCGCAATGCGAA
1 GACTATCGCAACGCGAA
1264 TATGTAAATC
Statistics
Matches: 136, Mismatches: 18, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
19 24 0.18
21 95 0.70
22 1 0.01
23 16 0.12
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (21 bp):
GACTATCGCAACGCGAACTTG
Found at i:1234 original size:82 final size:83
Alignment explanation
Indices: 1081--1257 Score: 225
Period size: 82 Copynumber: 2.1 Consensus size: 83
1071 CGAATTTGGA
** * * *
1081 GACTATCGCAACGAACTTGGAGACTATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAT
1 GACTATCGCAACGAACTTGGAGAAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTAGAAT
1146 AAATCGCAACGCAAACTTG
66 -AATCGCAACGCAAACTTG
*
1165 GACTATCGCAACGAA-TTTGA-AAAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTAGA
1 GACTATCGCAACGAACTTGGAGAAAATCGCAACGCGAACTTCGACTATCGCAA--CGAACTTAGA
* * *
1228 CT-ATCGCAATGCGAACTTG
64 ATAATCGCAACGCAAACTTG
1247 GACTATCGCAA
1 GACTATCGCAA
1258 TGCGAATATG
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
82 54 0.66
83 4 0.05
84 24 0.29
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (83 bp):
GACTATCGCAACGAACTTGGAGAAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTAGAAT
AATCGCAACGCAAACTTG
Found at i:4109 original size:21 final size:21
Alignment explanation
Indices: 4085--4131 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
4075 AATATGTGAA
4085 TCGCATTGCGATTTTCTAAAT
1 TCGCATTGCGATTTTCTAAAT
4106 TCGCATTGCGATTTTCTAAAT
1 TCGCATTGCGATTTTCTAAAT
4127 TCGCA
1 TCGCA
4132 CACTGAAGTC
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:0.23, C:0.21, G:0.15, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCTAAAT
Found at i:4147 original size:19 final size:19
Alignment explanation
Indices: 4123--4184 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
4113 GCGATTTTCT
4123 AAATTCGCACAC-TGAAGTC
1 AAATTCGCACACAT-AAGTC
*
4142 AAATTCACAACACATAAGTC
1 AAATTCGC-ACACATAAGTC
*
4162 AAATTCGCAATACATAAGTC
1 AAATTCGC-ACACATAAGTC
4182 AAA
1 AAA
4185 GCGCGTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.18
20 30 0.79
21 1 0.03
ACGTcount: A:0.47, C:0.23, G:0.10, T:0.21
Consensus pattern (19 bp):
AAATTCGCACACATAAGTC
Found at i:4160 original size:20 final size:20
Alignment explanation
Indices: 4137--4184 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
4127 TCGCACACTG
4137 AAGTCAAATTCACAACACAT
1 AAGTCAAATTCACAACACAT
* *
4157 AAGTCAAATTCGCAATACAT
1 AAGTCAAATTCACAACACAT
4177 AAGTCAAA
1 AAGTCAAA
4185 GCGCGTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.50, C:0.21, G:0.08, T:0.21
Consensus pattern (20 bp):
AAGTCAAATTCACAACACAT
Found at i:4750 original size:20 final size:20
Alignment explanation
Indices: 4725--4797 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
4715 CGCAAATTAG
4725 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
4745 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
* *
4765 GTTCGCGTTGCAATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
4785 TTTCGCATTGCGA
1 TTTCGCGTTGCGA
4798 ATTTAAGTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.47
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:4808 original size:20 final size:20
Alignment explanation
Indices: 4723--4808 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
4713 AACGCAAATT
*
4723 AGTTTCGCGTTGCGATTTTC
1 AGTTTCGCGTTGCGAATTTC
* *
4743 ATTTTCGCGTTGCGATTTTC
1 AGTTTCGCGTTGCGAATTTC
4763 A-TGTTCGCGTTGC-AATTTTC
1 AGT-TTCGCGTTGCGAA-TTTC
* * *
4783 ATTTTCGCATTGCGAATTTA
1 AGTTTCGCGTTGCGAATTTC
4803 AGTTTC
1 AGTTTC
4809 AGAAACTACT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
19 2 0.04
20 52 0.91
21 3 0.05
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.47
Consensus pattern (20 bp):
AGTTTCGCGTTGCGAATTTC
Found at i:6578 original size:63 final size:64
Alignment explanation
Indices: 6472--6611 Score: 178
Period size: 63 Copynumber: 2.2 Consensus size: 64
6462 TTAGGGGAGT
* * *
6472 TACGTGATGAGGT-CGGTGCTTTGCGTCATGAGGTCGGTATTTTACGTGAAGACAATGGTGCGC
1 TACGTGATGAGGTACGGTGCTTTACGTCATGAGGTCGGTATTTTACGCGAAGACAATGATGCGC
** * *
6535 TACGTGATGAGGTACGGT-CTTTACGTGGTGAGGT-GGATGTTTTACGCGATGACAATGATGCGC
1 TACGTGATGAGGTACGGTGCTTTACGTCATGAGGTCGG-TATTTTACGCGAAGACAATGATGCGC
*
6598 TACGTGGTGAGGTA
1 TACGTGATGAGGTA
6612 TATACTTTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
62 2 0.03
63 61 0.91
64 4 0.06
ACGTcount: A:0.20, C:0.14, G:0.36, T:0.30
Consensus pattern (64 bp):
TACGTGATGAGGTACGGTGCTTTACGTCATGAGGTCGGTATTTTACGCGAAGACAATGATGCGC
Found at i:6620 original size:63 final size:63
Alignment explanation
Indices: 6472--6631 Score: 173
Period size: 63 Copynumber: 2.5 Consensus size: 63
6462 TTAGGGGAGT
* * * * * *
6472 TACGTGATGAGGT-CGGTGCTTTGCGTCATGAGGTCGG-TATTTTACGTGAAGACAATGGTGCGC
1 TACGTGATGAGGTACGAT-CTTTACGTGATGAGGT-GGATGTTTTACGCGAAGACAATGATGCGC
* * *
6535 TACGTGATGAGGTACGGTCTTTACGTGGTGAGGTGGATGTTTTACGCGATGACAATGATGCGC
1 TACGTGATGAGGTACGATCTTTACGTGATGAGGTGGATGTTTTACGCGAAGACAATGATGCGC
* *
6598 TACGTGGTGAGGTA-TATACTTTACGTGATGAGGT
1 TACGTGATGAGGTACGAT-CTTTACGTGATGAGGT
6632 AGCTGCTCTA
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
62 3 0.04
63 76 0.92
64 4 0.05
ACGTcount: A:0.21, C:0.14, G:0.34, T:0.31
Consensus pattern (63 bp):
TACGTGATGAGGTACGATCTTTACGTGATGAGGTGGATGTTTTACGCGAAGACAATGATGCGC
Found at i:6974 original size:42 final size:42
Alignment explanation
Indices: 6918--7049 Score: 160
Period size: 42 Copynumber: 3.2 Consensus size: 42
6908 GAAGAAGCCC
* * * *
6918 GATGCACCTGTCATCGTTCAAGAGGCATATCCTATCGTTCAA
1 GATGCCCCTGTCATCGTTCAAGAGGCACATCCCACCGTTCAA
* * *
6960 GATGCCCCTCTCATCGTTCAAGAGGCCCCTCCCACCGTTCAA
1 GATGCCCCTGTCATCGTTCAAGAGGCACATCCCACCGTTCAA
* *
7002 GAGGCCCCTGTCATCGTTCAAGAGGTC-CCTCCCACCGTTCAA
1 GATGCCCCTGTCATCGTTCAAGAGG-CACATCCCACCGTTCAA
7044 GA-GCCC
1 GATGCCC
7050 GATTCACATG
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
41 4 0.05
42 75 0.94
43 1 0.01
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.23
Consensus pattern (42 bp):
GATGCCCCTGTCATCGTTCAAGAGGCACATCCCACCGTTCAA
Found at i:6975 original size:21 final size:21
Alignment explanation
Indices: 6929--7046 Score: 137
Period size: 21 Copynumber: 5.6 Consensus size: 21
6919 ATGCACCTGT
***
6929 CATCGTTCAAGAGGCATATCC
1 CATCGTTCAAGAGGCCCCTCC
* * *
6950 TATCGTTCAAGATGCCCCTCT
1 CATCGTTCAAGAGGCCCCTCC
6971 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* **
6992 CACCGTTCAAGAGGCCCCTGT
1 CATCGTTCAAGAGGCCCCTCC
*
7013 CATCGTTCAAGAGGTCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
7034 CACCGTTCAAGAG
1 CATCGTTCAAGAG
7047 CCCGATTCAC
Statistics
Matches: 80, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 80 1.00
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:8438 original size:14 final size:14
Alignment explanation
Indices: 8419--8455 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
8409 GCTTGTTTAA
8419 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
8433 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
8447 TTGATTTGT
1 TTGATTTGT
8456 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:8445 original size:78 final size:78
Alignment explanation
Indices: 8328--8519 Score: 300
Period size: 78 Copynumber: 2.5 Consensus size: 78
8318 GGGTACACTT
* *
8328 TTTTTTCTTGTTTAATTGAATTT-T-ACA-TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAG
1 TTTTTGCTTGTTTAATTG-ATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAG
8390 GAAATAAGAATTAA
65 GAAATAAGAATTAA
* *
8404 TTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGT
1 TTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGG
**
8469 AAATAAGAATTGT
66 AAATAAGAATTAA
8482 TTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGT
1 TTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGT
8520 TGTTTATTTA
Statistics
Matches: 107, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
75 4 0.04
76 18 0.17
77 2 0.02
78 83 0.78
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.51
Consensus pattern (78 bp):
TTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGG
AAATAAGAATTAA
Found at i:8507 original size:37 final size:37
Alignment explanation
Indices: 8374--8508 Score: 110
Period size: 37 Copynumber: 3.5 Consensus size: 37
8364 AAAAGTTGAT
* * **
8374 TTGTTTAATTGATGAGGAAATAAGAATTAATTTTTGC
1 TTGTTTAATTGATGTGTAAATAAGAATTGTTTTTTGC
* * * *** *
8411 TTGTTTAATTGATTTGTAAA-AGTTGATTTGTAAAAGTTGAT
1 TTGTTTAATTGATGTGTAAATA--AGAATTGT--TTTTTG-C
8452 TTGTTTAATTGATGTGTAAATAAGAATTGTTTTTTGC
1 TTGTTTAATTGATGTGTAAATAAGAATTGTTTTTTGC
*
8489 TTGTTTAATTGATTTGTAAA
1 TTGTTTAATTGATGTGTAAA
8509 AGTTGATTTG
Statistics
Matches: 73, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
36 1 0.01
37 36 0.49
38 7 0.10
40 9 0.12
41 19 0.26
42 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.19, T:0.49
Consensus pattern (37 bp):
TTGTTTAATTGATGTGTAAATAAGAATTGTTTTTTGC
Found at i:8607 original size:20 final size:20
Alignment explanation
Indices: 8582--8620 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
8572 GTACACTTTC
8582 GCAACGCGAAAATCAAATTT
1 GCAACGCGAAAATCAAATTT
*
8602 GCAACGCGAAAGTCAAATT
1 GCAACGCGAAAATCAAATT
8621 CGCGTTGCGA
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:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
GCAACGCGAAAATCAAATTT
Found at i:8715 original size:20 final size:20
Alignment explanation
Indices: 8689--8733 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
8679 TAACGCGATA
*
8689 ATCGCGTTGTGAATTTGACT
1 ATCGCGTTGCGAATTTGACT
*
8709 TTCGCGTTGCGAATTTGACT
1 ATCGCGTTGCGAATTTGACT
8729 ATCGC
1 ATCGC
8734 AACGCAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (20 bp):
ATCGCGTTGCGAATTTGACT
Found at i:11406 original size:14 final size:15
Alignment explanation
Indices: 11370--11407 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
11360 GAAATCATTG
11370 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
11385 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
11400 AAAAATTA
1 AAAAATTA
11408 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:11579 original size:19 final size:20
Alignment explanation
Indices: 11555--11686 Score: 87
Period size: 20 Copynumber: 6.7 Consensus size: 20
11545 AACTAAAACC
11555 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAAATTGAAATTCG
11574 TGTTGCG-AATTCGAAAATT-G
1 TGTTGCGAAATT-G-AAATTCG
* *
11594 AGTTGCGAATTTGAAATTC-
1 TGTTGCGAAATTGAAATTCG
* *
11613 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAAATTGAAATTC-G
* * *
11634 TGTTGCGAATTTG-ACTTCTT
1 TGTTGCGAAATTGAAATTC-G
* *
11654 TGTTGCGAATTTGGAAACT-G
1 TGTTGCGAAATT-GAAATTCG
*
11674 GGTTGCGAAATTG
1 TGTTGCGAAATTG
11687 GAGTTCACGT
Statistics
Matches: 93, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
18 4 0.04
19 32 0.34
20 34 0.37
21 21 0.23
22 2 0.02
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.37
Consensus pattern (20 bp):
TGTTGCGAAATTGAAATTCG
Found at i:11639 original size:40 final size:40
Alignment explanation
Indices: 11555--11647 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 40
11545 AACTAAAACC
* *
11555 TGTTGCGAAATT-AAATTCGTGTTGCGAATTCGAAAATTG
1 TGTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATTG
* *
11594 AGTTGCGAATTTGAAATTC-AGTTGCGAATTTG-AAATTCAG
1 TGTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATT--G
11634 TGTTGCGAATTTGA
1 TGTTGCGAATTTGA
11648 CTTCTTTGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
38 5 0.11
39 21 0.46
40 20 0.43
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.37
Consensus pattern (40 bp):
TGTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATTG
Found at i:11659 original size:20 final size:21
Alignment explanation
Indices: 11555--11666 Score: 112
Period size: 19 Copynumber: 5.6 Consensus size: 21
11545 AACTAAAACC
*
11555 TGTTGCGAAATT-AAATTC-G
1 TGTTGCGAATTTGAAATTCAG
*
11574 TGTTGCGAATTCGAAAATT--G
1 TGTTGCGAATTTG-AAATTCAG
*
11594 AGTTGCGAATTTGAAATTCA-
1 TGTTGCGAATTTGAAATTCAG
11614 -GTTGCGAATTTGAAATTCAG
1 TGTTGCGAATTTGAAATTCAG
* **
11634 TGTTGCGAATTTG-ACTTCTT
1 TGTTGCGAATTTGAAATTCAG
11654 TGTTGCGAATTTG
1 TGTTGCGAATTTG
11667 GAAACTGGGT
Statistics
Matches: 80, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
19 34 0.43
20 29 0.36
21 17 0.21
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (21 bp):
TGTTGCGAATTTGAAATTCAG
Found at i:14986 original size:41 final size:41
Alignment explanation
Indices: 14929--15008 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
14919 TATTTAAATA
* * *
14929 TATCTTTTTAAACATATATTCATTCAATGATTGAATACATG
1 TATCTTTTTAAACATATACTCATTCAAAGATGGAATACATG
*
14970 TATCTTTTTAAACATATACTCATTTAAAGATGGAATACA
1 TATCTTTTTAAACATATACTCATTCAAAGATGGAATACA
15009 AGATAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (41 bp):
TATCTTTTTAAACATATACTCATTCAAAGATGGAATACATG
Found at i:29040 original size:29 final size:29
Alignment explanation
Indices: 29008--29253 Score: 266
Period size: 29 Copynumber: 8.6 Consensus size: 29
28998 ACAGAATTAA
*
29008 TTACGAAACTAACACCCTTTTAAAAATAT
1 TTACGAAAATAACACCCTTTTAAAAATAT
* *
29037 TTACAAAAATAACA-CCTATT-AAAATAT
1 TTACGAAAATAACACCCTTTTAAAAATAT
*
29064 TTACGTAAATAACACCCTTTTAAAAATAT
1 TTACGAAAATAACACCCTTTTAAAAATAT
* *
29093 TTACGAAAATAATACCCTTTTAGAAATAT
1 TTACGAAAATAACACCCTTTTAAAAATAT
* *
29122 TTACGAAAATGACACCCTTTTAGAAATAT
1 TTACGAAAATAACACCCTTTTAAAAATAT
* ** *
29151 TTACAAAAATAACACATTTTTAACAATAT
1 TTACGAAAATAACACCCTTTTAAAAATAT
* *
29180 TTACGAAACTAACA-CCTTCTTAACAATAT
1 TTACGAAAATAACACCCTT-TTAAAAATAT
* * * *
29209 TTACGGAACTAACA-CATTCTTAAGAATAT
1 TTACGAAAATAACACCCTT-TTAAAAATAT
* *
29238 TTACAAAAATACCACC
1 TTACGAAAATAACACC
29254 ATAACCGAAA
Statistics
Matches: 185, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
27 19 0.10
28 12 0.06
29 153 0.83
30 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.31
Consensus pattern (29 bp):
TTACGAAAATAACACCCTTTTAAAAATAT
Found at i:29315 original size:59 final size:59
Alignment explanation
Indices: 29235--29366 Score: 201
Period size: 59 Copynumber: 2.2 Consensus size: 59
29225 TTCTTAAGAA
* * *
29235 TATTTACAAAAATACCACCATAACCGAAATTAATTTCGTATTAGTCATTCTTTTAAAAC
1 TATTTACAAAAATACCACCATAACAGAAATTAATTACATATTAGTCATTCTTTTAAAAC
* * *
29294 TATTTACAAAAATAGCTCCATAACATAAATTAATTACATATTAGTCATTCTTTTAAAAC
1 TATTTACAAAAATACCACCATAACAGAAATTAATTACATATTAGTCATTCTTTTAAAAC
29353 TATTTATCAAAAAT
1 TATTTA-CAAAAAT
29367 CTAAACCAAC
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
59 59 0.89
60 7 0.11
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.37
Consensus pattern (59 bp):
TATTTACAAAAATACCACCATAACAGAAATTAATTACATATTAGTCATTCTTTTAAAAC
Found at i:39378 original size:3 final size:3
Alignment explanation
Indices: 39370--39451 Score: 85
Period size: 3 Copynumber: 26.7 Consensus size: 3
39360 GGCCCGTTTG
* * *
39370 TAA TAA TAA TTAA TAA TAA TAT TAG TAA TAAA TAA TAA -AA TTAG TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA -TAA TAA
* *
39417 TTA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
39452 TTTAAATGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
2 2 0.03
3 57 0.86
4 7 0.11
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:40595 original size:451 final size:452
Alignment explanation
Indices: 39701--40695 Score: 1694
Period size: 451 Copynumber: 2.2 Consensus size: 452
39691 TCTTGATGAG
* * *
39701 TTCTTCTCATTATGAACTTCTTCCTCATTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTC
*
39766 -CTGGCAATGTTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTAT
62 TCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTAT
39830 GAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCC
127 GAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCC
39895 ATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTC
192 ATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTC
39960 TTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCA
257 TTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCA
*
40025 AACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
322 AACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCT
*
40090 CATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAA
387 CATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAAGTTGAACAA
40155 A
452 A
*
40156 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
* * *
40221 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAT
66 GCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAT
40286 TTCTTCTTCCTTC-TCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCA
131 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCA
40350 AGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
196 AGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
* * **
40415 GATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGATGATCCATC-AGATGATGGATTTGAAC
261 GATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAG-TGATGAATTCAAAC
40479 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCAT
325 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCAT
* * ** *
40544 TATGAACCTTCTCTGGCAATGATGATCCATC-AGATGATGGATTTGAACAAAAAGTTGAACAAG
390 TATGAACCTTCTCTGGCAATGATAATCCATCAAG-TGATGAATTCAAACAAAAAGTTGAACAAA
40607 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTCTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCT-TCTCT
* **
40671 GGAAATGTTGATCCATTGAATGATG
65 GGCAATGTTGATCCATCAAATGATG
40696 GATTTGAATC
Statistics
Matches: 510, Mismatches: 26, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
450 6 0.01
451 373 0.73
452 97 0.19
455 34 0.07
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (452 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
GCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAT
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCA
AGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
GATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACA
AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAAGTTGAACAAA
Found at i:40703 original size:113 final size:113
Alignment explanation
Indices: 39701--40686 Score: 1667
Period size: 113 Copynumber: 8.7 Consensus size: 113
39691 TCTTGATGAG
* * * *
39701 TTCTTCTCATTATGAACTTCTTCCTCATTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTC
* * * *
39766 -CTGGCAATGTTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAA
62 TCTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
39817 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
39882 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
66 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
39930 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
39995 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
66 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
40043 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
40108 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
66 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
40156 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
40221 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
66 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
40269 TTCTTCTCATTATGAATTTCTTCTTCCTTC-TCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
40333 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
66 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
40381 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
* * **
40446 GCAATGATGATCCATC-AGATGATGGATTTGAACAAAAGGTTGAACAAA
66 GCAATGATAATCCATCAAG-TGATGAATTCAAACAAAAGGTTGAACAAA
*
40494 TTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
* * ** * *
40559 GCAATGATGATCCATC-AGATGATGGATTTGAACAAAAAGTTGAACAAG
66 GCAATGATAATCCATCAAG-TGATGAATTCAAACAAAAGGTTGAACAAA
*
40607 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTCTCTCT
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCT-TCTCT
* * *
40671 GGAAATGTTGATCCAT
65 GGCAATGATAATCCAT
40687 TGAATGATGG
Statistics
Matches: 847, Mismatches: 19, Indels: 11
0.97 0.02 0.01
Matches are distributed among these distances:
112 119 0.14
113 694 0.82
116 34 0.04
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
Found at i:41145 original size:22 final size:22
Alignment explanation
Indices: 41103--41154 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
41093 GATAAAGCTT
* *
41103 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTAAAAAGAGAATCTA
*
41125 TCATCTTTAAAAA-AGGGATCTA
1 TCATCTTTAAAAAGA-GAATCTA
*
41147 CCATCTTT
1 TCATCTTT
41155 GAAGAGTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:41601 original size:40 final size:40
Alignment explanation
Indices: 41545--41624 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
41535 TTTCAGCTTA
*
41545 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTATGTGG
* *
41585 GATGTAAAACATTTGACAACGCATTCATCCTTTTATGTGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTATGTGG
41625 ACTCTGCTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (40 bp):
GATGTAAAACACTTGACAACACATTCATCCTTTTATGTGG
Found at i:43999 original size:83 final size:83
Alignment explanation
Indices: 43859--44040 Score: 296
Period size: 83 Copynumber: 2.2 Consensus size: 83
43849 TTTATTTCTA
*
43859 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTATCCAACCAGATTAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTATCCAACCAGATCAGATAACTCAAA
43924 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
43942 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTT-T-TGCCAAACCAGATCAGATAACTCA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTAT-CC-AACCAGATCAGATAACTCA
44005 AAGAACACTTCCAGAAGATG
64 AAGAACACTTCCAGAAGATG
*
44025 CTATGAGCACATTCAT
1 CTATGAGCAAATTCAT
44041 TTGTTCCATT
Statistics
Matches: 92, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
81 1 0.01
82 3 0.03
83 88 0.96
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTATCCAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:49615 original size:14 final size:14
Alignment explanation
Indices: 49582--49634 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
49572 TGTGCAATAA
* *
49582 AAATGCAAAGATGCC
1 AAATGTAAATATG-C
49597 AAATGTAAATATGC
1 AAATGTAAATATGC
* *
49611 AAATGTAAAAATGT
1 AAATGTAAATATGC
49625 AAATGTAAAT
1 AAATGTAAAT
49635 TATTTAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
14 22 0.67
15 11 0.33
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.25
Consensus pattern (14 bp):
AAATGTAAATATGC
Found at i:53138 original size:3 final size:3
Alignment explanation
Indices: 53130--53229 Score: 112
Period size: 3 Copynumber: 32.7 Consensus size: 3
53120 GGCCCGTTTG
* * *
53130 TAA TAA TAA TTAA TAA TAA TAT TAG TAA TAAA TAA TAA -AA TTAG TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA -TAA TAA
* * *
53177 TTA TAA TTA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53225 TAA TA
1 TAA TA
53230 TTTAAATGAA
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.02
3 73 0.89
4 7 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:60386 original size:29 final size:29
Alignment explanation
Indices: 60354--60421 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
60344 GGAGACTCAA
60354 AACCCGAATTGCAATAACACGGATAGACT
1 AACCCGAATTGCAATAACACGGATAGACT
60383 AACCCGAATTGCAATAACACGGATAGACT
1 AACCCGAATTGCAATAACACGGATAGACT
60412 AACCCGAATT
1 AACCCGAATT
60422 ATTTAATTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.18
Consensus pattern (29 bp):
AACCCGAATTGCAATAACACGGATAGACT
Found at i:82790 original size:20 final size:20
Alignment explanation
Indices: 82751--82790 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
82741 ATTATTGAGC
* *
82751 TGGTTTTTATGTTCTGTGTT
1 TGGTTTTTAAGTTCTATGTT
*
82771 TGGTTTTTAAGTTTTATGTT
1 TGGTTTTTAAGTTCTATGTT
82791 GTAACAGAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.03, G:0.23, T:0.65
Consensus pattern (20 bp):
TGGTTTTTAAGTTCTATGTT
Found at i:83859 original size:16 final size:15
Alignment explanation
Indices: 83809--83860 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
83799 TTCAAATATG
* *
83809 AAAATGACTCAAAAC
1 AAAATGACCCAAACC
*
83824 AAACATGAACCAAACAC
1 AAA-ATGACCCAAAC-C
83841 AAAATGACCCAGAACC
1 AAAATGACCCA-AACC
83857 AAAA
1 AAAA
83861 AGGATCCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 3 0.10
16 20 0.67
17 7 0.23
ACGTcount: A:0.60, C:0.25, G:0.08, T:0.08
Consensus pattern (15 bp):
AAAATGACCCAAACC
Done.