Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003986.1 Hibiscus syriacus cultivar Beakdansim tig00008673_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: 132993
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1176 original size:1 final size:1
Alignment explanation
Indices: 1170--1195 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1160 GCATGGACTT
1170 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
1196 ATAATACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1403 original size:18 final size:18
Alignment explanation
Indices: 1382--1418 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1372 CTTAAGAAAG
1382 TTTTAATAGTTCCATTAC
1 TTTTAATAGTTCCATTAC
*
1400 TTTTAATAGTTTCATTAC
1 TTTTAATAGTTCCATTAC
1418 T
1 T
1419 AGTAATGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.14, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTTAATAGTTCCATTAC
Found at i:1424 original size:18 final size:18
Alignment explanation
Indices: 1385--1424 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1375 AAGAAAGTTT
**
1385 TAATAGTTCCATTACTTT
1 TAATAGTTCCATTACTAG
*
1403 TAATAGTTTCATTACTAG
1 TAATAGTTCCATTACTAG
1421 TAAT
1 TAAT
1425 GGAACTTTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47
Consensus pattern (18 bp):
TAATAGTTCCATTACTAG
Found at i:2148 original size:6 final size:6
Alignment explanation
Indices: 2049--2147 Score: 136
Period size: 6 Copynumber: 17.2 Consensus size: 6
2039 CCGTCTCGTC
2049 TCGTCGG TCG-GG TCG-GG TCG-GG TCG-GG TCG-GG TCGTGG TCGTGG
1 TCGT-GG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
*
2093 TCGTGG TCGTGG TCGTGG TCGTGG TAGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
*
2141 TAGTGG T
1 TCGTGG T
2148 AATGGTAATG
Statistics
Matches: 88, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
5 25 0.28
6 60 0.68
7 3 0.03
ACGTcount: A:0.02, C:0.16, G:0.52, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:2153 original size:6 final size:6
Alignment explanation
Indices: 2083--2172 Score: 90
Period size: 6 Copynumber: 15.0 Consensus size: 6
2073 GGGTCGGGTC
* * * * * * *
2083 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTA GTGGTC GTGGTC
1 GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA
* * *
2131 GTGGTC GTGGTA GTGGTA ATGGTA ATGGTA GTGGTA GTGGTA
1 GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA
2173 TTACGTGTCT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 79 1.00
ACGTcount: A:0.10, C:0.09, G:0.48, T:0.33
Consensus pattern (6 bp):
GTGGTA
Found at i:2153 original size:18 final size:18
Alignment explanation
Indices: 2069--2172 Score: 113
Period size: 18 Copynumber: 5.9 Consensus size: 18
2059 GGTCGGGTCG
*
2069 GGTCG-GGTCG-GGTCGT
1 GGTCGTGGTCGTGGTAGT
*
2085 GGTCGTGGTCGTGGTCGT
1 GGTCGTGGTCGTGGTAGT
2103 GGTCGTGGTCGTGGTAGT
1 GGTCGTGGTCGTGGTAGT
*
2121 GGTCGTGGTCGTGGTCGT
1 GGTCGTGGTCGTGGTAGT
* ** *
2139 GGTAGTGGTAATGGTAAT
1 GGTCGTGGTCGTGGTAGT
* *
2157 GGTAGTGGTAGTGGTA
1 GGTCGTGGTCGTGGTA
2173 TTACGTGTCT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
16 5 0.06
17 5 0.06
18 68 0.87
ACGTcount: A:0.09, C:0.11, G:0.49, T:0.32
Consensus pattern (18 bp):
GGTCGTGGTCGTGGTAGT
Found at i:2313 original size:21 final size:21
Alignment explanation
Indices: 2289--2446 Score: 180
Period size: 21 Copynumber: 7.6 Consensus size: 21
2279 TTTGGAATAA
2289 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
2310 ATCGCAATGCGAA-TAT-GTA-A
1 ATCGCAACGCGAACT-TCG-ACT
* *
2330 ATCGCAATGCGATA-GTCGACT
1 ATCGCAACGCGA-ACTTCGACT
* *
2351 ATCGCAATGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
2372 ATCGCAACGCGAACTTAGACT
1 ATCGCAACGCGAACTTCGACT
*
2393 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
2414 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
2435 ATCGCAATGCGA
1 ATCGCAACGCGA
2447 TTTACATATT
Statistics
Matches: 120, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.14
21 103 0.86
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:2393 original size:42 final size:42
Alignment explanation
Indices: 2264--2446 Score: 223
Period size: 42 Copynumber: 4.4 Consensus size: 42
2254 TGCGATTTTG
* *
2264 GACTATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAATGCGAACTTGGACT--ATCGCAACGCGAACTTC
* * * *
2306 GACTATCGCAATGCGAA-TATGTA-AATCGCAATGCGATA-GTC
1 GACTATCGCAATGCGAACT-TGGACTATCGCAACGCGA-ACTTC
*
2347 GACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTA
1 GACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTC
*
2389 GACTATCGCAACGCGAACTTGGACTATCGCAACGCGAACTTC
1 GACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTC
2431 GACTATCGCAATGCGA
1 GACTATCGCAATGCGA
2447 TTTACATATT
Statistics
Matches: 122, Mismatches: 12, Indels: 14
0.82 0.08 0.09
Matches are distributed among these distances:
41 34 0.28
42 80 0.66
43 1 0.01
44 7 0.06
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (42 bp):
GACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTC
Found at i:2518 original size:21 final size:21
Alignment explanation
Indices: 2455--2529 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 21
2445 GATTTACATA
2455 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
2476 TTCACAATGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
**
2497 TTCGCATTGCGATAGTTGAAG
1 TTCGCATTGCGATAGTCCAAG
*
2518 TTCGCGTTGCGA
1 TTCGCATTGCGA
2530 ATCTGGAAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:6190 original size:16 final size:18
Alignment explanation
Indices: 6171--6208 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
6161 TGGCAGATCC
*
6171 AAATCCAGAA-GGGGAA-
1 AAATCAAGAACGGGGAAG
6187 AAATCAAGAACGGGGAAG
1 AAATCAAGAACGGGGAAG
6205 AAAT
1 AAAT
6209 ATTTTACCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 6 0.32
18 4 0.21
ACGTcount: A:0.53, C:0.11, G:0.29, T:0.08
Consensus pattern (18 bp):
AAATCAAGAACGGGGAAG
Found at i:12663 original size:28 final size:28
Alignment explanation
Indices: 12631--12713 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
12621 TATAATCCCT
12631 TGCAGAATCAGGACAGGA-ACTATGCCCA
1 TGCAGAATCAGGAC-GGAGACTATGCCCA
12659 TGCAGAATCAGGACGGAGACTATGCCCA
1 TGCAGAATCAGGACGGAGACTATGCCCA
* * *
12687 TGCAGAATCAGGATGGAAATTATGCCC
1 TGCAGAATCAGGACGGAGACTATGCCC
12714 TCCATAGAGC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
27 3 0.06
28 48 0.94
ACGTcount: A:0.34, C:0.23, G:0.27, T:0.17
Consensus pattern (28 bp):
TGCAGAATCAGGACGGAGACTATGCCCA
Found at i:13171 original size:26 final size:26
Alignment explanation
Indices: 13130--13180 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
13120 GCACAAAACG
13130 CCGCAATAGGTCGAGATATTTAGCGA
1 CCGCAATAGGTCGAGATATTTAGCGA
* * *
13156 CCGCAATAGTTTGAGATCTTTAGCG
1 CCGCAATAGGTCGAGATATTTAGCG
13181 GTTTTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (26 bp):
CCGCAATAGGTCGAGATATTTAGCGA
Found at i:14107 original size:43 final size:43
Alignment explanation
Indices: 14046--14154 Score: 209
Period size: 43 Copynumber: 2.5 Consensus size: 43
14036 CATCAACGCC
14046 GCTAAAAGTCATAATATATAGTGATGATTTTCACACAAACTCA
1 GCTAAAAGTCATAATATATAGTGATGATTTTCACACAAACTCA
14089 GCTAAAAGTCATAATATATAGTGATGATTTTCACACAAACTCA
1 GCTAAAAGTCATAATATATAGTGATGATTTTCACACAAACTCA
*
14132 GCTAAAAGTCATGATATATAGTG
1 GCTAAAAGTCATAATATATAGTG
14155 GCATTTTTTA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (43 bp):
GCTAAAAGTCATAATATATAGTGATGATTTTCACACAAACTCA
Found at i:50357 original size:60 final size:60
Alignment explanation
Indices: 50286--50434 Score: 156
Period size: 60 Copynumber: 2.5 Consensus size: 60
50276 AAATTTAAAT
* * * * * * *
50286 TCTT-AAATTTTAAAATATTTTAATTTTATTATTAAATTATAACTATTATTTTAAATTAG
1 TCTTCAAATTTTAAAACATTTCAATTTCATTATTAAACTATAACCATCATTTTAAATTAA
* * * *
50345 TCTTCAAATTTTATAACATTTCAATTTCATTCTTAAACTATGACCCTCATTTTAAATTAA
1 TCTTCAAATTTTAAAACATTTCAATTTCATTATTAAACTATAACCATCATTTTAAATTAA
* ** *
50405 TCTCCAAATTTTTGAACATTTCAACTTCAT
1 TCTTCAAATTTTAAAACATTTCAATTTCAT
50435 CCCAAACTAT
Statistics
Matches: 74, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
59 4 0.05
60 70 0.95
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.48
Consensus pattern (60 bp):
TCTTCAAATTTTAAAACATTTCAATTTCATTATTAAACTATAACCATCATTTTAAATTAA
Found at i:51305 original size:2 final size:2
Alignment explanation
Indices: 51294--51330 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
51284 ATCCTAACCC
51294 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51331 TAAATTTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:56689 original size:16 final size:16
Alignment explanation
Indices: 56668--56708 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
56658 GCAAGTTATA
56668 TCAGCTGGAAGGTGTG
1 TCAGCTGGAAGGTGTG
56684 TCAGCTGGAAGGTGTG
1 TCAGCTGGAAGGTGTG
56700 TCAGCTGGA
1 TCAGCTGGA
56709 TCGGTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.20, C:0.15, G:0.41, T:0.24
Consensus pattern (16 bp):
TCAGCTGGAAGGTGTG
Found at i:60930 original size:228 final size:228
Alignment explanation
Indices: 60532--61005 Score: 664
Period size: 228 Copynumber: 2.1 Consensus size: 228
60522 CATTGGAATG
* * *
60532 CTGATTCTGGTAGGATTGTGGCACATGCACATTATTATCATTTCCTACAGCCATTGAAGATGATA
1 CTGATTCTGGTAGGATTGTGGCACATGCACATTATCACCATTTCCTACAGCCACTGAAGATGATA
* * * ** *
60597 CTCCGTTGATGTCGCACCATGGATAAGTAGAACGATTGTTCGAAAATTGATTGTTGCCGGTCACG
66 CTCCATAGATGTCACACCATGGATAAGTAGAACGAGCGTTCGAAAATTGATTGTTGCCGGTCAAG
* ** *
60662 AAAGGCGATCCGTTAACGACTTTCATCGGATTTTGTAACGAATTTCCCATTGAAGAGCCTGCATT
131 AAAGGCGATCCGTTAACGACATTCATCGGATTTTGTAACGAATCCCCCACTGAAGAGCCTGCATT
* *
60727 AAAATCTTGTTGAGAAGACCAAGAGTTGACATAT
196 AAAATCTTGTTGAAAAGACCAAGAGTTAACAT-T
*
60761 -TGATTCTGGTAGGATTGTGGCACGTGCACATTATCACCATTTCCTACAGCCACTGAAGATGATA
1 CTGATTCTGGTAGGATTGTGGCACATGCACATTATCACCATTTCCTACAGCCACTGAAGATGATA
* * ** * * * * *
60825 CTCCATAGATGTCACCCCGTGGATGCGTAGGATGAGCG-TCTGGAAATTGATTGTTTCTGGTCAA
66 CTCCATAGATGTCACACCATGGATAAGTAGAACGAGCGTTC-GAAAATTGATTGTTGCCGGTCAA
* *
60889 GAAAGTCGATCCGTTAACGACATTCATCGGATTTTGTAACGAATCCCCCACTGAAGAGGCTGCAT
130 GAAAGGCGATCCGTTAACGACATTCATCGGATTTTGTAACGAATCCCCCACTGAAGAGCCTGCAT
*
60954 TAAAATCTTGTTGAAAAGACCAAGCGTTAACATT
195 TAAAATCTTGTTGAAAAGACCAAGAGTTAACATT
60988 CTGATTCTGGTAGGATTG
1 CTGATTCTGGTAGGATTG
61006 CGGAGTTGAA
Statistics
Matches: 215, Mismatches: 28, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
227 3 0.01
228 212 0.99
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (228 bp):
CTGATTCTGGTAGGATTGTGGCACATGCACATTATCACCATTTCCTACAGCCACTGAAGATGATA
CTCCATAGATGTCACACCATGGATAAGTAGAACGAGCGTTCGAAAATTGATTGTTGCCGGTCAAG
AAAGGCGATCCGTTAACGACATTCATCGGATTTTGTAACGAATCCCCCACTGAAGAGCCTGCATT
AAAATCTTGTTGAAAAGACCAAGAGTTAACATT
Found at i:61460 original size:135 final size:135
Alignment explanation
Indices: 61165--61450 Score: 362
Period size: 135 Copynumber: 2.1 Consensus size: 135
61155 CCACCATCGG
* * * * *
61165 AGAAGCATTCAGAATTGAATGCGCATG-TGCAAATGCATACAATATATTGTTGTTTCCTTCCATT
1 AGAAGCATTCAGAATCGAATGTGCAGGCT-CAAATGCATACAATATATTGTTGTTTCCTGCCATG
* * *
61229 GATGGTGCTGCATTGACGTCTCGTCGATAATAACCCGCCACTGGAGAAACTCCATTAACAGCTTG
65 GATGGTGCTCCATTGACGTCTCGTCGATAAGAACCCGCCACTAGAGAAACTCCATTAACAGCTTG
* *
61294 CTGAGA
130 CGGACA
* * *
61300 AGAAGCATTCGGAATCGAATGTGCAGGCTCAAATGCATACATTGTATTGTTGTTTCCTGCCATGG
1 AGAAGCATTCAGAATCGAATGTGCAGGCTCAAATGCATACAATATATTGTTGTTTCCTGCCATGG
* * * *
61365 ATGGTGCTCCATTGATGTCTTGTCGATAAGAACCTGCCA-TCAGAGACACTCCATTAACAAG-TT
66 ATGGTGCTCCATTGACGTCTCGTCGATAAGAACCCGCCACT-AGAGAAACTCCATTAAC-AGCTT
61428 GCGGACA
129 GCGGACA
*
61435 ATAAGCATTCAGAATC
1 AGAAGCATTCAGAATC
61451 TGACTTGCAG
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
134 1 0.01
135 125 0.97
136 3 0.02
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (135 bp):
AGAAGCATTCAGAATCGAATGTGCAGGCTCAAATGCATACAATATATTGTTGTTTCCTGCCATGG
ATGGTGCTCCATTGACGTCTCGTCGATAAGAACCCGCCACTAGAGAAACTCCATTAACAGCTTGC
GGACA
Found at i:62858 original size:15 final size:14
Alignment explanation
Indices: 62819--62858 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
62809 GACTATTAGT
62819 TTTAAAATATTATA
1 TTTAAAATATTATA
*
62833 TTATAATATATTATA
1 TT-TAAAATATTATA
62848 TATTAAAATAT
1 T-TTAAAATAT
62859 AACATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 2 0.09
15 19 0.86
16 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAAAATATTATA
Found at i:63234 original size:21 final size:21
Alignment explanation
Indices: 63208--63261 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
63198 GCGTTGCATT
63208 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
63229 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
63250 TCGCGTAGCGAT
1 TCGCGTTGCGAT
63262 TTTCAAGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:63275 original size:20 final size:20
Alignment explanation
Indices: 63250--63293 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
63240 TAGTTGAAAA
63250 TCGCGTAGCGATTTTCAAGT
1 TCGCGTAGCGATTTTCAAGT
* *
63270 TCGCGTTGCGATTTTCCAGT
1 TCGCGTAGCGATTTTCAAGT
63290 TCGC
1 TCGC
63294 ATTGCGATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.36
Consensus pattern (20 bp):
TCGCGTAGCGATTTTCAAGT
Found at i:63298 original size:20 final size:20
Alignment explanation
Indices: 63257--63301 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
63247 AAATCGCGTA
*
63257 GCGATTTTCAAGTTCGCGTT
1 GCGATTTTCAAGTTCGCATT
*
63277 GCGATTTTCCAGTTCGCATT
1 GCGATTTTCAAGTTCGCATT
63297 GCGAT
1 GCGAT
63302 AGTCTACAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
GCGATTTTCAAGTTCGCATT
Found at i:63957 original size:5 final size:5
Alignment explanation
Indices: 63947--63973 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
63937 CCGCCGCCGC
63947 CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CG
63974 GGTCGGGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.37
Consensus pattern (5 bp):
CGTCT
Found at i:64005 original size:6 final size:6
Alignment explanation
Indices: 63974--64039 Score: 104
Period size: 6 Copynumber: 11.7 Consensus size: 6
63964 TCTCGTCTCG
63974 GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
64018 GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTC
64040 ATACGTGTCT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 20 0.33
6 40 0.67
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:64205 original size:41 final size:41
Alignment explanation
Indices: 64160--64249 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 41
64150 CTGTAGACTT
*
64160 TCGCAACAACAACTGTAGACTATCGCAA-CGAATTTGGAAAA
1 TCGCAACAACAACTGTAGACTATCGCAACCGAA-ATGGAAAA
**
64201 TCGCAATGACAACTGTAGACTATCGCAACGCGAAATGGAAAA
1 TCGCAACAACAACTGTAGACTATCGCAAC-CGAAATGGAAAA
64243 TCGCAAC
1 TCGCAAC
64250 GCGAAATGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 26 0.60
42 13 0.30
43 4 0.09
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.18
Consensus pattern (41 bp):
TCGCAACAACAACTGTAGACTATCGCAACCGAAATGGAAAA
Found at i:64226 original size:22 final size:22
Alignment explanation
Indices: 64137--64230 Score: 95
Period size: 22 Copynumber: 4.4 Consensus size: 22
64127 AATTTGGAAA
*
64137 ATCGCAACTACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
64159 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
64181 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
64200 ATCGCAATGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
64222 ATCGCAACG
1 ATCGCAACG
64231 CGAAATGGAA
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
19 12 0.22
20 2 0.04
21 2 0.04
22 39 0.71
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.21
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:64247 original size:20 final size:20
Alignment explanation
Indices: 64222--64273 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
64212 ACTGTAGACT
64222 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
64242 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
64262 ATCGCAACGCGA
1 ATCGCAACGCGA
64274 TTTTCAACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:64288 original size:21 final size:21
Alignment explanation
Indices: 64262--64315 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
64252 GAAATGGAAA
64262 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
64283 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
64304 ATCGCAACGCGA
1 ATCGCAACGCGA
64316 ATTTGCGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:64937 original size:24 final size:24
Alignment explanation
Indices: 64910--64961 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
64900 TTTATGGTCT
*
64910 TTTACGTTCGTTCATTTGTATTCG
1 TTTACGTTCGTTCATTTGTATTAG
*
64934 TTTACGTTCGTTCATTTGTGTTAG
1 TTTACGTTCGTTCATTTGTATTAG
64958 TTTA
1 TTTA
64962 TCATTTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.56
Consensus pattern (24 bp):
TTTACGTTCGTTCATTTGTATTAG
Found at i:68092 original size:18 final size:18
Alignment explanation
Indices: 68065--68106 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
68055 CGGAATGTAA
* *
68065 GATTATCGGCGGGAATAG
1 GATTACCGGCAGGAATAG
*
68083 GATTACCGGCAGGAATAT
1 GATTACCGGCAGGAATAG
68101 GATTAC
1 GATTAC
68107 TGACAATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (18 bp):
GATTACCGGCAGGAATAG
Found at i:79195 original size:63 final size:62
Alignment explanation
Indices: 79110--79266 Score: 176
Period size: 63 Copynumber: 2.5 Consensus size: 62
79100 TTCCCCTCAC
* * * *
79110 AGTCAATACTTAACTTCCTCGTGAAGAGAAGTCAACTTTTTTTATTTCCTAACTC-CCTAG-AGG
1 AGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAACTTGTGTTATTT-CTAACTCTCC-AGTA-G
* * *
79173 AGTCAATCCTTGATTTCCTCGTGAAGAGATGTCAACTTGTGTTATTTCTTACTCTCCAGTAG
1 AGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAACTTGTGTTATTTCTAACTCTCCAGTAG
* *
79235 AGTCAA-CTTTTGACTTCCTCGTGAAGAAAAGT
1 AGTCAATC-CTTGACTTCCTCGTGAAGAGAAGT
79267 AAATATTGCA
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
61 1 0.01
62 35 0.44
63 44 0.55
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.36
Consensus pattern (62 bp):
AGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAACTTGTGTTATTTCTAACTCTCCAGTAG
Found at i:79593 original size:79 final size:82
Alignment explanation
Indices: 79412--79597 Score: 247
Period size: 79 Copynumber: 2.3 Consensus size: 82
79402 AACATTCAGT
* * *
79412 CTGATCTTCTCTGAATGAATA-ATGGAGCAGATATGTCTTCAAAATTGATCTGTATACCCGAAAA
1 CTGATCTTCTCTGAATAAATAGATGGAGCAGATACGTCTTCAAAATTGATATGTATACCCGAAAA
*
79476 AGTGGTAAAGATCCATA
66 AGTGGCAAAGATCCATA
* *
79493 CTGATCTTCTCTGAATTAATAGA-GGAGCAGATACGTCTT-TAAATTGATATGTATACCCG-AAA
1 CTGATCTTCTCTGAATAAATAGATGGAGCAGATACGTCTTCAAAATTGATATGTATACCCGAAAA
* * *
79555 AGTGGCACATATCCATT
66 AGTGGCAAAGATCCATA
*
79572 TTGATCTTCTCTGAATAAATAG-TGGA
1 CTGATCTTCTCTGAATAAATAGATGGA
79598 ACATATTCTT
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
79 39 0.42
80 18 0.19
81 35 0.38
82 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (82 bp):
CTGATCTTCTCTGAATAAATAGATGGAGCAGATACGTCTTCAAAATTGATATGTATACCCGAAAA
AGTGGCAAAGATCCATA
Found at i:79666 original size:36 final size:36
Alignment explanation
Indices: 79625--79786 Score: 126
Period size: 36 Copynumber: 4.7 Consensus size: 36
79615 GCAATCATCC
*
79625 AGCCTTCACAGAAGAGTAGTGAAGTAAATCATTCAA
1 AGCCTTCACAGAAGAGTAGTGAAGTAAATCATTCTA
* * * ** *
79661 AGCCTTTATA-AA-AG-AGT--AGTAAAACAACCCA
1 AGCCTTCACAGAAGAGTAGTGAAGTAAATCATTCTA
* * *
79692 A-CCTTCAC-GAAAGAATAGTGAAGTAAATCATTTTT
1 AGCCTTCACAG-AAGAGTAGTGAAGTAAATCATTCTA
* *
79727 AGCCTTCA-AGGAAGAGTAGTGAAGTAAATCATTTTT
1 AGCCTTCACA-GAAGAGTAGTGAAGTAAATCATTCTA
79763 AGCCTTCAC-GAAAGAGTAGTGAAG
1 AGCCTTCACAG-AAGAGTAGTGAAG
79787 CATGAACATA
Statistics
Matches: 99, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
30 5 0.05
31 13 0.13
32 1 0.01
33 6 0.06
34 2 0.02
35 12 0.12
36 59 0.60
37 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (36 bp):
AGCCTTCACAGAAGAGTAGTGAAGTAAATCATTCTA
Found at i:79966 original size:3 final size:3
Alignment explanation
Indices: 79958--80014 Score: 78
Period size: 3 Copynumber: 18.7 Consensus size: 3
79948 TTTCGTTTTA
* * *
79958 TAT TAT TAT TAT TAT TATT TAT TAC TAC TAT TAT TAT TAT TAG TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
80004 TAT TAT TAT TA
1 TAT TAT TAT TA
80015 CATAAACTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:84753 original size:3 final size:3
Alignment explanation
Indices: 84745--84834 Score: 171
Period size: 3 Copynumber: 29.7 Consensus size: 3
84735 ACTTAAAGCT
84745 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
84793 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGAA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AG
84835 GGTTAACTGC
Statistics
Matches: 86, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 83 0.97
4 3 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:84983 original size:69 final size:69
Alignment explanation
Indices: 84872--85011 Score: 271
Period size: 69 Copynumber: 2.0 Consensus size: 69
84862 GCGGGAGGTA
*
84872 ACGACAAGCATATTACTCAAAACGAAATAAAAGTTCGATGATTGTATTGCAAGTTTCAAAAGTTG
1 ACGACAAGCATATTACTCAAAACGAAATAAAAGTTCGATGATTGTATTACAAGTTTCAAAAGTTG
84937 GGTG
66 GGTG
84941 ACGACAAGCATATTACTCAAAACGAAATAAAAGTTCGATGATTGTATTACAAGTTTCAAAAGTTG
1 ACGACAAGCATATTACTCAAAACGAAATAAAAGTTCGATGATTGTATTACAAGTTTCAAAAGTTG
85006 GGTG
66 GGTG
85010 AC
1 AC
85012 CAAAATGCAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (69 bp):
ACGACAAGCATATTACTCAAAACGAAATAAAAGTTCGATGATTGTATTACAAGTTTCAAAAGTTG
GGTG
Found at i:85447 original size:47 final size:47
Alignment explanation
Indices: 85392--85537 Score: 274
Period size: 47 Copynumber: 3.1 Consensus size: 47
85382 ATCCTCCCTC
*
85392 CGACTCTGATCTGATCAGAATTTTAAAAATATAAACCCAACCTAATT
1 CGACTCTGATCTGATCAGAATTTTAAAAATATAAATCCAACCTAATT
85439 CGACTCTGATCTGATCAGAATTTTAAAAATATAAATCCAACCTAATT
1 CGACTCTGATCTGATCAGAATTTTAAAAATATAAATCCAACCTAATT
*
85486 CGACTCTGATTTGATCAGAATTTTAAAAATATAAATCCAACCTAATT
1 CGACTCTGATCTGATCAGAATTTTAAAAATATAAATCCAACCTAATT
85533 CGACT
1 CGACT
85538 ATGTATAAAA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 97 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.32
Consensus pattern (47 bp):
CGACTCTGATCTGATCAGAATTTTAAAAATATAAATCCAACCTAATT
Found at i:89819 original size:3 final size:3
Alignment explanation
Indices: 89811--89882 Score: 90
Period size: 3 Copynumber: 23.7 Consensus size: 3
89801 TTCCGTTTTA
* * * *
89811 TAT TAT TAT TAT TAC TAT TAT TAT TAT TATT TAT TAT TAC TAC TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
*
89857 TAT TAT TAT TAG TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
89883 CATAAACTCG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
3 59 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:102064 original size:79 final size:81
Alignment explanation
Indices: 101883--102064 Score: 242
Period size: 79 Copynumber: 2.3 Consensus size: 81
101873 AACATTCAGT
* * *
101883 CTGATCTTCTCTGAATGAATAGTGGAGCAGATATGTCTTCAAAATTGATCTATATACCCGAAAAA
1 CTGATCTTCTCTGAATAAATAGAGGAGCAGATACGTCTTCAAAATTGATCTATATACCCGAAAAA
*
101948 GTGGTAAAGATCCAGA
66 GTGGCAAAGATCCAGA
* * * *
101964 CTGATCTTCTCTGAATTAATAGAGGAGCAGATACGTCTT-TAAATTGATTTGTATACCCG-AAAA
1 CTGATCTTCTCTGAATAAATAGAGGAGCAGATACGTCTTCAAAATTGATCTATATACCCGAAAAA
* **
102027 GTGGCACAGATCCATT
66 GTGGCAAAGATCCAGA
*
102043 TTGATCTTCTCTGAATAAATAG
1 CTGATCTTCTCTGAATAAATAG
102065 TGGAACATAT
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
79 36 0.40
80 17 0.19
81 36 0.40
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (81 bp):
CTGATCTTCTCTGAATAAATAGAGGAGCAGATACGTCTTCAAAATTGATCTATATACCCGAAAAA
GTGGCAAAGATCCAGA
Found at i:102137 original size:36 final size:36
Alignment explanation
Indices: 102096--102221 Score: 102
Period size: 36 Copynumber: 3.7 Consensus size: 36
102086 TCAATCATCC
102096 AGCCTTCACGGAAGAGTAGTGAAGTAAATCATTCAA
1 AGCCTTCACGGAAGAGTAGTGAAGTAAATCATTCAA
* * * * ** *
102132 AGCCTTTA--TAAAAG-AGT--AGTAAAACAACCCA
1 AGCCTTCACGGAAGAGTAGTGAAGTAAATCATTCAA
* * ***
102163 A-CCTTCATGGAAGAATAGTGAAGTAAATCATTTTT
1 AGCCTTCACGGAAGAGTAGTGAAGTAAATCATTCAA
102198 AGCCTTCACGGAAGAGTAGTGAAG
1 AGCCTTCACGGAAGAGTAGTGAAG
102222 CGATACAAAT
Statistics
Matches: 65, Mismatches: 19, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
30 5 0.08
31 11 0.17
32 3 0.05
33 6 0.09
34 4 0.06
35 9 0.14
36 27 0.42
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (36 bp):
AGCCTTCACGGAAGAGTAGTGAAGTAAATCATTCAA
Found at i:102437 original size:3 final size:3
Alignment explanation
Indices: 102429--102509 Score: 108
Period size: 3 Copynumber: 26.7 Consensus size: 3
102419 TTTCGTTTTA
* *
102429 TAT TAT TAT TAT TAC TAT TAT TAA TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
* * *
102475 TAC TAC TAC TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
102510 CATAAACTTG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
3 68 0.96
4 3 0.04
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:107371 original size:15 final size:14
Alignment explanation
Indices: 107332--107371 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
107322 GACTATAAGT
107332 TTTAAAATATTATA
1 TTTAAAATATTATA
*
107346 TTATAATATATTATA
1 TT-TAAAATATTATA
107361 TATTAAAATAT
1 T-TTAAAATAT
107372 AACATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 2 0.09
15 19 0.86
16 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAAAATATTATA
Found at i:107462 original size:2 final size:2
Alignment explanation
Indices: 107455--107479 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
107445 AAGTTTATCT
107455 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
107480 TATTGTAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:107728 original size:21 final size:21
Alignment explanation
Indices: 107702--107767 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
107692 GCGTTGCATT
107702 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
* ** **
107723 TCGCGTTGCGAT-TTTCCAGT
1 TCGCGTTGCGATAATTGAAAA
*
107743 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
107764 TCGC
1 TCGC
107768 ATTGTCTGGG
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:108444 original size:24 final size:24
Alignment explanation
Indices: 108417--108468 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
108407 TTTTATGGCT
* *
108417 TTTACGTTCGTTCATTTGTATTCG
1 TTTAAGTTCGTTCATTTGTATTAG
*
108441 TTTAAGTTCGTTCATTTGTGTTAG
1 TTTAAGTTCGTTCATTTGTATTAG
108465 TTTA
1 TTTA
108469 TCATTGAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.15, C:0.12, G:0.17, T:0.56
Consensus pattern (24 bp):
TTTAAGTTCGTTCATTTGTATTAG
Found at i:112401 original size:3 final size:3
Alignment explanation
Indices: 112393--112508 Score: 232
Period size: 3 Copynumber: 38.7 Consensus size: 3
112383 ACTTAAAGCT
112393 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
112441 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
112489 AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AG
112509 GGTTAACTGC
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 113 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:112657 original size:69 final size:69
Alignment explanation
Indices: 112546--112685 Score: 271
Period size: 69 Copynumber: 2.0 Consensus size: 69
112536 GCGGGAGGTA
*
112546 ACGACAAGCATATTACTCAAAACGAAATAAAAGTTCGATGATTGTATTGCAAGTTTCAAAAGTTG
1 ACGACAAGCATATTACTCAAAACGAAATAAAAGTTCGATGATTGTATTACAAGTTTCAAAAGTTG
112611 GGTG
66 GGTG
112615 ACGACAAGCATATTACTCAAAACGAAATAAAAGTTCGATGATTGTATTACAAGTTTCAAAAGTTG
1 ACGACAAGCATATTACTCAAAACGAAATAAAAGTTCGATGATTGTATTACAAGTTTCAAAAGTTG
112680 GGTG
66 GGTG
112684 AC
1 AC
112686 CAAAATGCAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (69 bp):
ACGACAAGCATATTACTCAAAACGAAATAAAAGTTCGATGATTGTATTACAAGTTTCAAAAGTTG
GGTG
Found at i:113151 original size:47 final size:47
Alignment explanation
Indices: 113096--113241 Score: 274
Period size: 47 Copynumber: 3.1 Consensus size: 47
113086 ATCCTCCCTC
*
113096 CGACTCTGATCTGATCAGAATTTTAAAAATATAAACCCAACCTAATT
1 CGACTCTGATCTGATCAGAATTTTAAAAATATAAATCCAACCTAATT
*
113143 CGACTCTGATCTGATCAGAATTTTAAAAATATAAATCCAACCTGATT
1 CGACTCTGATCTGATCAGAATTTTAAAAATATAAATCCAACCTAATT
113190 CGACTCTGATCTGATCAGAATTTTAAAAATATAAATCCAACCTAATT
1 CGACTCTGATCTGATCAGAATTTTAAAAATATAAATCCAACCTAATT
113237 CGACT
1 CGACT
113242 ATGTATAAAA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 96 1.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.31
Consensus pattern (47 bp):
CGACTCTGATCTGATCAGAATTTTAAAAATATAAATCCAACCTAATT
Found at i:117605 original size:3 final size:3
Alignment explanation
Indices: 117597--117694 Score: 117
Period size: 3 Copynumber: 32.7 Consensus size: 3
117587 TTTCGTTTTA
* * * *
117597 TAT TAT TAT TA- TAT TAT TAT TAT TAC TAT TAT TAA TAT TAA TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
117644 TAT TAT TATT TAT TAT TAC TAC TAT TAT TAT TAT TAG TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
117690 TAT TA
1 TAT TA
117695 CATAAACTCG
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.02
3 76 0.94
4 3 0.04
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:127059 original size:62 final size:63
Alignment explanation
Indices: 126903--127059 Score: 169
Period size: 63 Copynumber: 2.5 Consensus size: 63
126893 CCCTCACAGT
* * *
126903 CAATACTTAACTTCCTCGTGAAGAGAAGTCAACTTTTGTTATTTCCTAACTCCCTAGAGGAGC
1 CAATCCTTGACTTCCTCGTGAAGAGAAGTCAACTTGTGTTATTTCCTAACTCCCTAGAGGAGC
* * * * *
126966 CAATCCTTGATTTCCTCATGAAGAGATGTCAACTTGTGTTATTT-CTGACTCTCC-AGTA-GAGT
1 CAATCCTTGACTTCCTCGTGAAGAGAAGTCAACTTGTGTTATTTCCTAACTC-CCTAG-AGGAGC
* *
127028 CAA-CTTTTGACTTCCTCGTGAAGAAAAGTCAA
1 CAATC-CTTGACTTCCTCGTGAAGAGAAGTCAA
127060 TATTGCAGAT
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
61 1 0.01
62 36 0.46
63 41 0.53
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (63 bp):
CAATCCTTGACTTCCTCGTGAAGAGAAGTCAACTTGTGTTATTTCCTAACTCCCTAGAGGAGC
Found at i:127373 original size:79 final size:81
Alignment explanation
Indices: 127202--127390 Score: 247
Period size: 79 Copynumber: 2.4 Consensus size: 81
127192 AACATTCAGT
* * * *
127202 CTGATATTCTCTGAATGAATAGTGGAGCAGATATGTCTTCAAAATTGATCTGTATACCCGAAAAA
1 CTGATCTTCTCTGAATAAATAGTGGAACAGATACGTCTTCAAAATTGATCTGTATACCCGAAAAA
*
127267 GTGGTAAAGATCCAGA
66 GTGGCAAAGATCCAGA
* * * *
127283 CTGATCTTCTCTGAATTAATAGAGGAACAGATACGTCTT-TAAATTGATTTGTATACCCG-AAAA
1 CTGATCTTCTCTGAATAAATAGTGGAACAGATACGTCTTCAAAATTGATCTGTATACCCGAAAAA
* **
127346 GTGGCACAGATCCATT
66 GTGGCAAAGATCCAGA
*
127362 TTGATCTTCTCTGAATAAATAGTGGAACA
1 CTGATCTTCTCTGAATAAATAGTGGAACA
127391 TATTCTTATT
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
79 42 0.45
80 18 0.19
81 34 0.36
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (81 bp):
CTGATCTTCTCTGAATAAATAGTGGAACAGATACGTCTTCAAAATTGATCTGTATACCCGAAAAA
GTGGCAAAGATCCAGA
Found at i:127456 original size:36 final size:36
Alignment explanation
Indices: 127415--127576 Score: 156
Period size: 36 Copynumber: 4.7 Consensus size: 36
127405 GCAATCATCC
*
127415 AGCCTTCACGGAAGAGTAGTGAAGTAAATCATTCAA
1 AGCCTTCACGGAAGAGTAGTGAAGTAAATCATTCTA
* * * * ** *
127451 AGCCTTTA--TAAAAG-AGT--AGTAAAACAACCCA
1 AGCCTTCACGGAAGAGTAGTGAAGTAAATCATTCTA
* * *
127482 A-CCTTCACGGAAGAATAGTGAAGTAAATCATTTTT
1 AGCCTTCACGGAAGAGTAGTGAAGTAAATCATTCTA
* * *
127517 AGCCTTCACGGAAGAGTAATGAAGTAAATCATTTTT
1 AGCCTTCACGGAAGAGTAGTGAAGTAAATCATTCTA
127553 AGCCTTCACGGAAGAGTAGTGAAG
1 AGCCTTCACGGAAGAGTAGTGAAG
127577 CGATACAAAT
Statistics
Matches: 100, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
30 5 0.05
31 11 0.11
32 3 0.03
33 6 0.06
34 4 0.04
35 9 0.09
36 62 0.62
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (36 bp):
AGCCTTCACGGAAGAGTAGTGAAGTAAATCATTCTA
Found at i:127592 original size:36 final size:36
Alignment explanation
Indices: 127483--127612 Score: 127
Period size: 36 Copynumber: 3.6 Consensus size: 36
127473 AACAACCCAA
* * ** *
127483 CCTTCACGGAAGAATAGTGAAGTAAATCATTTTTAG
1 CCTTCACGGAAGAGTAGTGAAGGAAATCAAATCTAG
* * ** *
127519 CCTTCACGGAAGAGTAATGAAGTAAATCATTTTTAG
1 CCTTCACGGAAGAGTAGTGAAGGAAATCAAATCTAG
*
127555 CCTTCACGGAAGAGTAGTGAAGCGATA-CAAATCTAG
1 CCTTCACGGAAGAGTAGTGAAG-GAAATCAAATCTAG
* *
127591 CCTTCACGAAAGATTAGTGAAG
1 CCTTCACGGAAGAGTAGTGAAG
127613 TAGGAACATA
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
36 81 0.98
37 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (36 bp):
CCTTCACGGAAGAGTAGTGAAGGAAATCAAATCTAG
Found at i:127792 original size:3 final size:3
Alignment explanation
Indices: 127784--127848 Score: 87
Period size: 3 Copynumber: 21.7 Consensus size: 3
127774 TTTCGTTTTA
* *
127784 TAT TAT TAT TAT TA- TAT TAT TAT TATT TAT TAC TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
*
127829 TAT TAG TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
127849 CATAAACTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:131975 original size:58 final size:59
Alignment explanation
Indices: 131908--132036 Score: 163
Period size: 59 Copynumber: 2.2 Consensus size: 59
131898 TAGTCGAATT
* * *
131908 ATCATTTTATAACTTTTAATATTAGGA-GACTCAACAAAACAATATTTTATAATCGAGAG
1 ATCATTTTATAACTTTTAATAGTAGAAGGACTCAACAAAACAATACTTTATAATCGA-AG
* * * *
131967 A-CATTTTATAACTTTTAGTAGTCGAAGGACTTAACAAAACAATGCTTTATAATCGAAG
1 ATCATTTTATAACTTTTAATAGTAGAAGGACTCAACAAAACAATACTTTATAATCGAAG
132025 ATCATTTGTATA
1 ATCATTT-TATA
132037 TTTTATCTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
58 24 0.40
59 32 0.53
60 4 0.07
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (59 bp):
ATCATTTTATAACTTTTAATAGTAGAAGGACTCAACAAAACAATACTTTATAATCGAAG
Done.