Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008891.1 Hibiscus syriacus cultivar Beakdansim tig00112157_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: 94095
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3373 original size:3 final size:3
Alignment explanation
Indices: 3365--3403 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3355 GCTTCAGAGT
3365 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3404 CACAGCTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:7163 original size:111 final size:112
Alignment explanation
Indices: 7035--7237 Score: 329
Period size: 112 Copynumber: 1.8 Consensus size: 112
7025 TAACCTTACA
* **
7035 TAAATAAATTTGATAATAAATTAAAAATCA-GGAAAATAATATTTTTCATAAATTATAATCACAA
1 TAAATAAATTTAATAATAAATTAAAAATCATAAAAAATAATATTTTTCATAAATTATAATCACAA
*
7099 ATATTTTC-TCTATCCTACTAAATGTATCTATTATTGACTTTTAAAGT
66 ATA-TTTCATCTATCCCACTAAATGTATCTATTATTGACTTTTAAAGT
*
7146 TAAATAAATTTAATAATACATTAAAAATCATAAAAAATAATATTTTTCATAAATTATAATCACAA
1 TAAATAAATTTAATAATAAATTAAAAATCATAAAAAATAATATTTTTCATAAATTATAATCACAA
*
7211 GTATTTCATCTATCCCACTAAATGTAT
66 ATATTTCATCTATCCCACTAAATGTAT
7238 ACTTTTAAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
111 32 0.38
112 52 0.62
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (112 bp):
TAAATAAATTTAATAATAAATTAAAAATCATAAAAAATAATATTTTTCATAAATTATAATCACAA
ATATTTCATCTATCCCACTAAATGTATCTATTATTGACTTTTAAAGT
Found at i:13157 original size:59 final size:58
Alignment explanation
Indices: 13056--13175 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 58
13046 GAAGGGTTGG
* *
13056 TTAGAGCCATATTATGAATTTTTCTTTTCATTGCGACTAGGAGGGTTTGATAGGACAC
1 TTAGAGCCATATTATGAATTTTTCTTTTCATTGCGACTAGGAGGGCTCGATAGGACAC
*
13114 TTAGAGCCATATTAT-CATGTTTTCCTTTTCATTGCGACTAGGAGGGCTCGATAGGACAC
1 TTAGAGCCATATTATGAAT-TTTT-CTTTTCATTGCGACTAGGAGGGCTCGATAGGACAC
13173 TTA
1 TTA
13176 TCCATCTATT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
57 2 0.04
58 19 0.33
59 36 0.63
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.37
Consensus pattern (58 bp):
TTAGAGCCATATTATGAATTTTTCTTTTCATTGCGACTAGGAGGGCTCGATAGGACAC
Found at i:13322 original size:12 final size:12
Alignment explanation
Indices: 13294--13328 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
13284 TATCTTTTGT
13294 TTATCTTG-TTC
1 TTATCTTGTTTC
*
13305 TAATCTTGTTTC
1 TTATCTTGTTTC
13317 TTATCTTGTTTC
1 TTATCTTGTTTC
13329 CAGCACTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.11, C:0.17, G:0.09, T:0.63
Consensus pattern (12 bp):
TTATCTTGTTTC
Found at i:13708 original size:22 final size:26
Alignment explanation
Indices: 13655--13709 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 26
13645 CTAATTTTTC
13655 AAGAAAAGAAGAAGAAAAAGGCCGAA
1 AAGAAAAGAAGAAGAAAAAGGCCGAA
13681 AA-AAAAGAA-AA-AAAAAGG-C-AA
1 AAGAAAAGAAGAAGAAAAAGGCCGAA
13702 AAGAAAAG
1 AAGAAAAG
13710 TCACAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.14
22 6 0.21
23 7 0.25
24 2 0.07
25 7 0.25
26 2 0.07
ACGTcount: A:0.73, C:0.05, G:0.22, T:0.00
Consensus pattern (26 bp):
AAGAAAAGAAGAAGAAAAAGGCCGAA
Found at i:13708 original size:23 final size:25
Alignment explanation
Indices: 13658--13709 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 25
13648 ATTTTTCAAG
*
13658 AAAAGAAGAAGAAAAAGGCCGAAAA
1 AAAAGAAGAAGAAAAAGGCCAAAAA
*
13683 AAAAGAA-AA-AAAAAGG-CAAAAG
1 AAAAGAAGAAGAAAAAGGCCAAAAA
13705 AAAAG
1 AAAAG
13710 TCACAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.36
23 7 0.28
24 2 0.08
25 7 0.28
ACGTcount: A:0.73, C:0.06, G:0.21, T:0.00
Consensus pattern (25 bp):
AAAAGAAGAAGAAAAAGGCCAAAAA
Found at i:17711 original size:50 final size:54
Alignment explanation
Indices: 17657--17792 Score: 163
Period size: 59 Copynumber: 2.5 Consensus size: 54
17647 CACACTCCAA
*
17657 TTTGCCTTTTCATTGTGACTAAGAGGG-T-T-GG-TTAGAGCCATATTATCGAG
1 TTTGCCTTTTCATTGCGACTAAGAGGGTTATAGGATTAGAGCCATATTATCGAG
* *
17707 TTTGCCTTTTCATTGCGACTATGAGGGTTCGATAGGACACTTAGAGCCATATTATCGTG
1 TTTGCCTTTTCATTGCGACTAAGAGGGTT--ATAGG--A-TTAGAGCCATATTATCGAG
*
17766 TTTGCCTTTTCATTGCGACTAGGAGGG
1 TTTGCCTTTTCATTGCGACTAAGAGGG
17793 CTCGATAGGA
Statistics
Matches: 73, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
50 25 0.34
51 1 0.01
54 1 0.01
55 2 0.03
59 44 0.60
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.37
Consensus pattern (54 bp):
TTTGCCTTTTCATTGCGACTAAGAGGGTTATAGGATTAGAGCCATATTATCGAG
Found at i:17780 original size:59 final size:59
Alignment explanation
Indices: 17688--17808 Score: 215
Period size: 59 Copynumber: 2.1 Consensus size: 59
17678 AGAGGGTTGG
* *
17688 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTATGAGGGTTCGATAGGACAC
1 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGCTCGATAGGACAC
*
17747 TTAGAGCCATATTATCGTGTTTGCCTTTTCATTGCGACTAGGAGGGCTCGATAGGACAC
1 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGCTCGATAGGACAC
17806 TTA
1 TTA
17809 TCCATCTATT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (59 bp):
TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGCTCGATAGGACAC
Found at i:19661 original size:2 final size:2
Alignment explanation
Indices: 19654--19680 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19644 TCAACTTTGT
19654 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19681 GTTAGGATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20236 original size:13 final size:13
Alignment explanation
Indices: 20218--20242 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20208 TAGTCGTTTA
20218 AGATTTTGAGATC
1 AGATTTTGAGATC
20231 AGATTTTGAGAT
1 AGATTTTGAGAT
20243 ATCACAATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
AGATTTTGAGATC
Found at i:21604 original size:17 final size:18
Alignment explanation
Indices: 21576--21615 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
21566 AAATTTTCAA
21576 TAAAACTATATAAAAATT
1 TAAAACTATATAAAAATT
* *
21594 TAAAA-TATATAATAGTT
1 TAAAACTATATAAAAATT
21611 TAAAA
1 TAAAA
21616 ATTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (18 bp):
TAAAACTATATAAAAATT
Found at i:22125 original size:23 final size:24
Alignment explanation
Indices: 22099--22150 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
22089 ATTTATGTCA
22099 TTGTGACACAC-TTTTCTATGCTC
1 TTGTGACACACTTTTTCTATGCTC
** *
22122 TTGTGGTACACTTTTTCTCTGCTC
1 TTGTGACACACTTTTTCTATGCTC
22146 TTGTG
1 TTGTG
22151 GCACGTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.12, C:0.23, G:0.17, T:0.48
Consensus pattern (24 bp):
TTGTGACACACTTTTTCTATGCTC
Found at i:22144 original size:24 final size:23
Alignment explanation
Indices: 22106--22151 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
22096 TCATTGTGAC
22106 ACACTTTTCTATGCTCTTGTGGT
1 ACACTTTTCTATGCTCTTGTGGT
*
22129 ACACTTTTTCTCTGCTCTTGTGG
1 ACAC-TTTTCTATGCTCTTGTGG
22152 CACGTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (23 bp):
ACACTTTTCTATGCTCTTGTGGT
Found at i:24565 original size:3 final size:3
Alignment explanation
Indices: 24557--24589 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
24547 GAACCGAACT
*
24557 AGA AGA AGA AGA AAA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
24590 GAGATTCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:29695 original size:24 final size:24
Alignment explanation
Indices: 29650--29695 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
29640 AGCATTTTTA
* *
29650 TTTTACTTTTTCATTTTTTTATAG
1 TTTTACTTGTTCATTTTCTTATAG
29674 TTTTACTTGTT-ATTTTCCTTAT
1 TTTTACTTGTTCATTTT-CTTAT
29696 CTTTTTCAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.15, C:0.11, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTTACTTGTTCATTTTCTTATAG
Found at i:39827 original size:13 final size:13
Alignment explanation
Indices: 39811--39846 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
39801 GAATGAAAAT
39811 GAGAATGAATTAG
1 GAGAATGAATTAG
39824 GAGAATGAATTAG
1 GAGAATGAATTAG
39837 GAGAATGAAT
1 GAGAATGAAT
39847 CTATCTAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (13 bp):
GAGAATGAATTAG
Found at i:39989 original size:26 final size:27
Alignment explanation
Indices: 39933--39991 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
39923 GTAAAAACCC
**
39933 ATATTTTTAATTTAGTCACTAAAATTC
1 ATATTTTTAATTTAGTCACTAAAATAA
* *
39960 ATATTTTTAATTTAGTTACT-TAATAA
1 ATATTTTTAATTTAGTCACTAAAATAA
39986 ATATTT
1 ATATTT
39992 ATTTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (27 bp):
ATATTTTTAATTTAGTCACTAAAATAA
Found at i:41279 original size:9 final size:9
Alignment explanation
Indices: 41265--41298 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
41255 TAGGGATAAA
41265 ATTTATTTT
1 ATTTATTTT
41274 ATTTATTTT
1 ATTTATTTT
*
41283 ATTGATTTTT
1 ATTTA-TTTT
41293 ATTTAT
1 ATTTAT
41299 CTGGATAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (9 bp):
ATTTATTTT
Found at i:42133 original size:25 final size:25
Alignment explanation
Indices: 42099--42151 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
42089 TGCATAATCT
42099 ACTGGTTGATGTAGATTATTCATCA
1 ACTGGTTGATGTAGATTATTCATCA
42124 ACTGGTTGATGTAGATTATTCATCA
1 ACTGGTTGATGTAGATTATTCATCA
42149 ACT
1 ACT
42152 ATATCAACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (25 bp):
ACTGGTTGATGTAGATTATTCATCA
Found at i:42230 original size:24 final size:24
Alignment explanation
Indices: 42203--42248 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
42193 CGATACCCAG
42203 CTTCAGTGGTTGACAATAATACAA
1 CTTCAGTGGTTGACAATAATACAA
42227 CTTCAGTGGTTGACAATAATAC
1 CTTCAGTGGTTGACAATAATAC
42249 CGTTGGTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (24 bp):
CTTCAGTGGTTGACAATAATACAA
Found at i:49586 original size:31 final size:31
Alignment explanation
Indices: 49548--49611 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
49538 TAAAACATGA
49548 TCATTTTCGTTTTTATTTAATTAAGATGTGG
1 TCATTTTCGTTTTTATTTAATTAAGATGTGG
49579 TCATTTTCGTTTTTATTTAATTAAGATGTGG
1 TCATTTTCGTTTTTATTTAATTAAGATGTGG
49610 TC
1 TC
49612 GTAACGGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.08, G:0.16, T:0.55
Consensus pattern (31 bp):
TCATTTTCGTTTTTATTTAATTAAGATGTGG
Found at i:50930 original size:32 final size:32
Alignment explanation
Indices: 50887--50963 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
50877 GAGAAATTGA
*
50887 TTTTTTTAGTTCGGTTTAG-TTTGATAATTCAG
1 TTTTTTCAGTTCGG-TTAGATTTGATAATTCAG
*
50919 TTTTTTCAGTTCGGTTCGATTTGATAATTCAG
1 TTTTTTCAGTTCGGTTAGATTTGATAATTCAG
*
50951 TTTTTTCGGTTCG
1 TTTTTTCAGTTCG
50964 ATTTGTCAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 3 0.07
32 38 0.93
ACGTcount: A:0.16, C:0.10, G:0.19, T:0.55
Consensus pattern (32 bp):
TTTTTTCAGTTCGGTTAGATTTGATAATTCAG
Found at i:56035 original size:37 final size:38
Alignment explanation
Indices: 55967--56045 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 38
55957 CTCATGCTCG
*
55967 GAAGGCTTACTGATGAATTTGCTTCACTACTCTTCCGT
1 GAAGACTTACTGATGAATTTGCTTCACTACTCTTCCGT
* * * *
56005 GAAGACTTA-TGATGGATTTGTTTCATTACTCTTCTGT
1 GAAGACTTACTGATGAATTTGCTTCACTACTCTTCCGT
56042 GAAG
1 GAAG
56046 GCTTTAGAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 28 0.78
38 8 0.22
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (38 bp):
GAAGACTTACTGATGAATTTGCTTCACTACTCTTCCGT
Found at i:56109 original size:116 final size:116
Alignment explanation
Indices: 55901--56214 Score: 448
Period size: 116 Copynumber: 2.7 Consensus size: 116
55891 TATCAAATCT
* * *
55901 TGGATTTGCTTCACTAATCTTTTGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCCTCATGCTC
1 TGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCATGCTC
*
55966 GGAAGGCTTACTGATGAATTTGCTTCACTACTCTTCCGTGAAGACTTATGA
66 GGAAGGCTTACTGATGAATTTGCTTCACTACTCTTCCGTGAAGACTTAAGA
* * * * * * *
56017 TGGATTTGTTTCATTACTCTTCTGTGAAGGCTTTAGAAGGCCCGAAGGACTTAATCATCATGTTT
1 TGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCATGCTC
* * * * * *
56082 GGAATGTTTACTGATGGATTTGTTTCACTACTCTTCGGTGAAGGCTTAAGA
66 GGAAGGCTTACTGATGAATTTGCTTCACTACTCTTCCGTGAAGACTTAAGA
* *
56133 TTGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCATGCTC
1 TGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCATGCTC
*
56198 GGAAGGCTTACAGATGA
66 GGAAGGCTTACTGATGA
56215 CCCGAAGGGT
Statistics
Matches: 168, Mismatches: 30, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
116 168 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (116 bp):
TGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCATGCTC
GGAAGGCTTACTGATGAATTTGCTTCACTACTCTTCCGTGAAGACTTAAGA
Found at i:56148 original size:37 final size:37
Alignment explanation
Indices: 56098--56170 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
56088 TTTACTGATG
*
56098 GATTTGTTTCACTACTCTTCGGTGAAGGCTTAAGATT
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATT
56135 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
56171 GGCCCGGAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (37 bp):
GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATT
Found at i:56236 original size:42 final size:42
Alignment explanation
Indices: 56158--56269 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
56148 ACTCTTCGGT
* *
56158 GAAGGCTTA-AGATGGCCCGGAGGACTTAATCATCATGCTCG
1 GAAGGCTTACAGATGGCCCGAAGGACTTAAGCATCATGCTCG
* ** *
56199 GAAGGCTTACAGATGACCCGAAGGGTTTAAGCCTCATGCTCG
1 GAAGGCTTACAGATGGCCCGAAGGACTTAAGCATCATGCTCG
* *
56241 G-AGGACTTACTGATGGCCCGAAAGACTTA
1 GAAGG-CTTACAGATGGCCCGAAGGACTTA
56270 TAAATTTTGG
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 12 0.21
42 46 0.79
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21
Consensus pattern (42 bp):
GAAGGCTTACAGATGGCCCGAAGGACTTAAGCATCATGCTCG
Found at i:58508 original size:8 final size:8
Alignment explanation
Indices: 58490--58556 Score: 86
Period size: 8 Copynumber: 8.8 Consensus size: 8
58480 CAATTTTATT
58490 TCTTTTT-
1 TCTTTTTC
58497 TCTTTTTC
1 TCTTTTTC
*
58505 TCTTTTTT
1 TCTTTTTC
58513 TCTTTTT-
1 TCTTTTTC
58520 TCTTTTTC
1 TCTTTTTC
*
58528 TCTTTTTT
1 TCTTTTTC
58536 TCTTTTTC
1 TCTTTTTC
*
58544 T-TTTTTT
1 TCTTTTTC
58551 TCTTTT
1 TCTTTT
58557 CTTTTTATCT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
7 20 0.38
8 33 0.62
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TCTTTTTC
Found at i:58510 original size:15 final size:15
Alignment explanation
Indices: 58488--58569 Score: 98
Period size: 15 Copynumber: 5.5 Consensus size: 15
58478 ATCAATTTTA
58488 TTTCTTTTT-TCTTT
1 TTTCTTTTTCTCTTT
*
58502 TTCTCTTTTTTTCTTT
1 TT-TCTTTTTCTCTTT
58518 TTTCTTTTTCTCTTTT
1 TTTCTTTTTCTC-TTT
*
58534 TTTCTTTTTCTTTTT
1 TTTCTTTTTCTCTTT
58549 TTTC-TTTTCT-TTT
1 TTTCTTTTTCTCTTT
*
58562 TATCTTTT
1 TTTCTTTT
58570 CTTTCATTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
13 6 0.10
14 11 0.18
15 23 0.38
16 21 0.34
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTCTTTTTCTCTTT
Found at i:58518 original size:23 final size:23
Alignment explanation
Indices: 58483--58569 Score: 126
Period size: 23 Copynumber: 3.8 Consensus size: 23
58473 GTTTGATCAA
58483 TTTTATTTCTTTTTTCTTTTTCTC
1 TTTT-TTTCTTTTTTCTTTTTCTC
58507 TTTTTTTCTTTTTTCTTTTTCTC
1 TTTTTTTCTTTTTTCTTTTTCTC
58530 TTTTTTTC-TTTTTCTTTTT-T-
1 TTTTTTTCTTTTTTCTTTTTCTC
*
58550 TTCTTTTCTTTTTATCTTTT
1 TTTTTTTCTTTTT-TCTTTT
58570 CTTTCATTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
20 7 0.12
21 5 0.08
22 17 0.28
23 27 0.45
24 4 0.07
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (23 bp):
TTTTTTTCTTTTTTCTTTTTCTC
Found at i:58540 original size:31 final size:30
Alignment explanation
Indices: 58488--58581 Score: 113
Period size: 29 Copynumber: 3.1 Consensus size: 30
58478 ATCAATTTTA
*
58488 TTTCTTTTTTCTTTTTCTCTTTTTTTCTTT
1 TTTCTTTTTTCTTTTTATCTTTTTTTCTTT
*
58518 TTTCTTTTTCTCTTTTT-T-TCTTTTTCTTT
1 TTTCTTTTT-TCTTTTTATCTTTTTTTCTTT
58547 TTT-TTCTTTTCTTTTTATCTTTTCTTTCATTT
1 TTTCTT-TTTTCTTTTTATCTTTT-TTTC-TTT
58579 TTT
1 TTT
58582 GCTATATTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
28 9 0.16
29 17 0.30
30 13 0.23
31 11 0.20
32 6 0.11
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (30 bp):
TTTCTTTTTTCTTTTTATCTTTTTTTCTTT
Found at i:58567 original size:8 final size:7
Alignment explanation
Indices: 58488--58569 Score: 96
Period size: 7 Copynumber: 11.1 Consensus size: 7
58478 ATCAATTTTA
58488 TTTCTTT
1 TTTCTTT
58495 TTTCTTT
1 TTTCTTT
58502 TTCTCTTTT
1 TT-TC-TTT
58511 TTTCTTT
1 TTTCTTT
58518 TTTCTTT
1 TTTCTTT
58525 TTCTCTTT
1 TT-TCTTT
58533 TTT-TCTT
1 TTTCT-TT
58540 TTTCTTT
1 TTTCTTT
58547 TTT-TTCT
1 TTTCTT-T
58554 TTTCTTT
1 TTTCTTT
58561 TTATCTTT
1 TT-TCTTT
58569 T
1 T
58570 CTTTCATTTT
Statistics
Matches: 67, Mismatches: 0, Indels: 15
0.82 0.00 0.18
Matches are distributed among these distances:
6 3 0.04
7 39 0.58
8 20 0.30
9 5 0.07
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTCTTT
Found at i:58848 original size:2 final size:2
Alignment explanation
Indices: 58841--58870 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
58831 ACCACAAGGG
58841 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
58871 TTAAAAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60956 original size:12 final size:13
Alignment explanation
Indices: 60935--60966 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
60925 AAATGAATAT
60935 ATGC-AATGCT-A
1 ATGCAAATGCTAA
60946 ATGCAAATGCTAA
1 ATGCAAATGCTAA
60959 ATGCAAAT
1 ATGCAAAT
60967 ACAAAAGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 4 0.21
12 6 0.32
13 9 0.47
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.25
Consensus pattern (13 bp):
ATGCAAATGCTAA
Found at i:62724 original size:24 final size:24
Alignment explanation
Indices: 62696--62741 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
62686 ATAAGATATC
62696 AAAATGAAAAAAAGTAA-TAATAGA
1 AAAAT-AAAAAAAGTAATTAATAGA
* *
62720 AAAATAAATAAATTAATTAATA
1 AAAATAAAAAAAGTAATTAATA
62742 AGCTAATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.24
Consensus pattern (24 bp):
AAAATAAAAAAAGTAATTAATAGA
Found at i:67509 original size:7 final size:7
Alignment explanation
Indices: 67497--67526 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
67487 TGCAAATGTA
67497 AATTAAT
1 AATTAAT
67504 AATTAAT
1 AATTAAT
67511 AATTAAT
1 AATTAAT
67518 AA-TAAT
1 AATTAAT
67524 AAT
1 AAT
67527 GTGTTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AATTAAT
Found at i:67908 original size:37 final size:38
Alignment explanation
Indices: 67853--67935 Score: 150
Period size: 37 Copynumber: 2.2 Consensus size: 38
67843 GTCATTCTCG
67853 GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCCGT
1 GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCCGT
*
67891 GAAGGCTTA-TGATGGATTTGCTTCACTACTCTTCTGT
1 GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCCGT
67928 GAAGGCTT
1 GAAGGCTT
67936 TAGATGGCCT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 35 0.80
38 9 0.20
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.37
Consensus pattern (38 bp):
GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCCGT
Found at i:67941 original size:116 final size:116
Alignment explanation
Indices: 67787--68093 Score: 454
Period size: 116 Copynumber: 2.6 Consensus size: 116
67777 TATCAAATCT
* * *
67787 TGGATTTGCTTCACTAATCTTTGGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCGTCATTCTC
1 TGGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCATGCTC
* *
67852 GGAAGGCTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTATGA
66 GGAAGGCTTACTGATGCATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
* *
67903 TGGATTTGCTTCACTACTCTTCT-GTGAAGGCTTTAGATGGCCTGGAGGACTTAATCATCATGCT
1 TGGATTTGCTTCACTACTCTT-TGGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCATGCT
* * * *
67967 TGGAAGGCTTACTGGTGCATTTGTTTCACTACTCTTCGGTGAAGGCTTAAGA
65 CGGAAGGCTTACTGATGCATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
* * * *
68019 TTGATTTGTTTCACTACTCTTTGGTGAAGGCTTAAGATAGCCCGGAGGACTAAATCATCATGCTC
1 TGGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCATGCTC
*
68084 GAAAGGCTTA
66 GGAAGGCTTA
68094 TATATGACCC
Statistics
Matches: 170, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
115 1 0.01
116 168 0.99
117 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (116 bp):
TGGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCATGCTC
GGAAGGCTTACTGATGCATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
Found at i:68030 original size:37 final size:37
Alignment explanation
Indices: 67985--68056 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
67975 TTACTGGTGC
67985 ATTTGTTTCACTACTCTTCGGTGAAGGCTTAAGATTG
1 ATTTGTTTCACTACTCTTCGGTGAAGGCTTAAGATTG
*
68022 ATTTGTTTCACTACTCTTTGGTGAAGGCTTAAGAT
1 ATTTGTTTCACTACTCTTCGGTGAAGGCTTAAGAT
68057 AGCCCGGAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (37 bp):
ATTTGTTTCACTACTCTTCGGTGAAGGCTTAAGATTG
Found at i:70390 original size:6 final size:6
Alignment explanation
Indices: 70374--70438 Score: 77
Period size: 6 Copynumber: 11.5 Consensus size: 6
70364 TGATCAGTTT
*
70374 TTTTTC TTTTTTC TTTTT- TTCTT- TTTTTC TTTTTC TTTTTC -TTTTC
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
70420 TTTTTC -TTTTC -TTTTC TTT
1 TTTTTC TTTTTC TTTTTC TTT
70439 CATTTTTTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
5 23 0.43
6 24 0.45
7 6 0.11
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:70392 original size:16 final size:16
Alignment explanation
Indices: 70371--70446 Score: 72
Period size: 14 Copynumber: 4.9 Consensus size: 16
70361 GTTTGATCAG
70371 TTTTTTTTCTTTTTTC
1 TTTTTTTTCTTTTTTC
70387 -TTTTTTTC-TTTTT-
1 TTTTTTTTCTTTTTTC
*
70400 TTCTTTTTC-TTTTTC
1 TTTTTTTTCTTTTTTC
*
70415 TTTTCTTTT-TCTTTTC
1 TTTT-TTTTCTTTTTTC
*
70431 TTTTCTTTCATTTTTT
1 TTTTTTTTC-TTTTTT
70447 GCTATATCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
14 17 0.35
15 14 0.29
16 13 0.27
17 5 0.10
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTTCTTTTTTC
Found at i:70398 original size:22 final size:21
Alignment explanation
Indices: 70373--70446 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 21
70363 TTGATCAGTT
70373 TTTTTTCTTTTTTCTTTTTTTC
1 TTTTTT-TTTTTTCTTTTTTTC
70395 TTTTTTTCTTTTTCTTTTTCTT-
1 TTTTTTT-TTTTTCTTTTT-TTC
*
70417 TTCTTTTTCTTTTCTTTTCTTTC
1 TT-TTTTTTTTTTCTTTT-TTTC
*
70440 ATTTTTT
1 TTTTTTT
70447 GCTATATCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
21 1 0.02
22 35 0.78
23 9 0.20
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTTTTTTTTTCTTTTTTTC
Found at i:70401 original size:11 final size:11
Alignment explanation
Indices: 70371--70438 Score: 77
Period size: 11 Copynumber: 6.1 Consensus size: 11
70361 GTTTGATCAG
70371 TTTTTTTTCTT
1 TTTTTTTTCTT
70382 TTTTCTTTT-TT
1 TTTT-TTTTCTT
70393 TCTTTTTTTCTT
1 T-TTTTTTTCTT
70405 TTTCTTTTTCTT
1 TTT-TTTTTCTT
*
70417 TTCTTTTTC-T
1 TTTTTTTTCTT
*
70427 TTTCTTTTCTT
1 TTTTTTTTCTT
70438 T
1 T
70439 CATTTTTTGC
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
10 8 0.16
11 21 0.43
12 20 0.41
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:70445 original size:11 final size:10
Alignment explanation
Indices: 70371--70445 Score: 61
Period size: 10 Copynumber: 7.5 Consensus size: 10
70361 GTTTGATCAG
70371 TTTTT-TTTC
1 TTTTTCTTTC
70380 TTTTT-TCTT-
1 TTTTTCT-TTC
70389 TTTTTCTTT-
1 TTTTTCTTTC
*
70398 TTTTCTTTTTC
1 TTTT-TCTTTC
70409 TTTTTCTTTTC
1 TTTTTC-TTTC
70420 TTTTTCTTT-
1 TTTTTCTTTC
70429 TCTTTTCTTTC
1 T-TTTTCTTTC
70440 ATTTTT
1 -TTTTT
70446 TGCTATATCT
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
9 18 0.32
10 19 0.34
11 18 0.32
12 1 0.02
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:72767 original size:26 final size:25
Alignment explanation
Indices: 72727--72776 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
72717 GAATACATGC
* *
72727 AATGCTAATGCAAATGCTAAATGTA
1 AATGCTAATGCAAATACAAAATGTA
72752 AATGCTAAATGCAAATACAAAATGT
1 AATGCT-AATGCAAATACAAAATGT
72777 GTCATTCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (25 bp):
AATGCTAATGCAAATACAAAATGTA
Found at i:72775 original size:13 final size:13
Alignment explanation
Indices: 72723--72767 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
72713 AAATGAATAC
72723 ATGC-AATGCT-A
1 ATGCAAATGCTAA
72734 ATGCAAATGCTAA
1 ATGCAAATGCTAA
*
72747 ATGTAAATGCTAA
1 ATGCAAATGCTAA
72760 ATGCAAAT
1 ATGCAAAT
72768 ACAAAATGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 4 0.13
12 6 0.20
13 20 0.67
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (13 bp):
ATGCAAATGCTAA
Found at i:77257 original size:2 final size:2
Alignment explanation
Indices: 77246--77301 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
77236 GACTACACAT
77246 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
77287 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
77302 GCAATATACA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:81412 original size:21 final size:22
Alignment explanation
Indices: 81386--81431 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
81376 TCAATAAAAA
81386 TTTACCTAAAACATT-ATTTGT
1 TTTACCTAAAACATTAATTTGT
* *
81407 TTTACCTAAAATATTAATTTTT
1 TTTACCTAAAACATTAATTTGT
81429 TTT
1 TTT
81432 TAATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTACCTAAAACATTAATTTGT
Found at i:82398 original size:19 final size:20
Alignment explanation
Indices: 82316--82405 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 20
82306 ATTTTGATTT
*
82316 TGAAAAATGTGTTGCGATAG
1 TGAAAAACGTGTTGCGATAG
* * *
82336 T-TAAAATGTGTTGCGAGAG
1 TGAAAAACGTGTTGCGATAG
*
82355 TTTGAAAAACGTGTTGTTGTTATAG
1 --TGAAAAACGTGTTG-CG--ATAG
82380 TGAAAAA-GTGTTGCGATAG
1 TGAAAAACGTGTTGCGATAG
82399 TGAAAAA
1 TGAAAAA
82406 TCCAAAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
19 27 0.47
20 1 0.02
21 2 0.04
22 16 0.28
23 8 0.14
25 3 0.05
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (20 bp):
TGAAAAACGTGTTGCGATAG
Found at i:82722 original size:6 final size:6
Alignment explanation
Indices: 82706--82745 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
82696 CTCGAGGTAG
*
82706 GGTCG- GGTCGT GGTCGT GGTCTT GGTCGT GGTCGT GGTCG
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCG
82746 GAGAGTAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:82820 original size:20 final size:20
Alignment explanation
Indices: 82795--82842 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
82785 ATTCTGTACT
82795 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
82815 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
82835 ATCGCGTT
1 ATCGCGTT
82843 ATGATTCTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:84136 original size:23 final size:23
Alignment explanation
Indices: 84110--84179 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
84100 AAGGGTACTG
84110 ATGCAATTGATGTAAGTTTATTT
1 ATGCAATTGATGTAAGTTTATTT
** * *
84133 ATGC-A-TGA--TAAGGGTACTG
1 ATGCAATTGATGTAAGTTTATTT
*
84152 ATGCAGTTGATGTAAGTTTATTT
1 ATGCAATTGATGTAAGTTTATTT
84175 ATGCA
1 ATGCA
84180 TGATTAAGAA
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
19 11 0.32
21 6 0.18
22 1 0.03
23 16 0.47
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (23 bp):
ATGCAATTGATGTAAGTTTATTT
Found at i:84156 original size:42 final size:42
Alignment explanation
Indices: 84097--84183 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
84087 TGATCTGATG
84097 GATAAGGGTACTGATGCAATTGATGTAAGTTTATTTATGCAT
1 GATAAGGGTACTGATGCAATTGATGTAAGTTTATTTATGCAT
*
84139 GATAAGGGTACTGATGCAGTTGATGTAAGTTTATTTATGCAT
1 GATAAGGGTACTGATGCAATTGATGTAAGTTTATTTATGCAT
84181 GAT
1 GAT
84184 TAAGAATCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (42 bp):
GATAAGGGTACTGATGCAATTGATGTAAGTTTATTTATGCAT
Found at i:84624 original size:105 final size:107
Alignment explanation
Indices: 84485--84697 Score: 342
Period size: 105 Copynumber: 2.0 Consensus size: 107
84475 ATTACTACTC
84485 CCATTCGTTCATGTTTTGTTTTTTGGTGAATTCAGTGCTACTTTTTCTTCTATTGTATTAACATA
1 CCATTCGTTCA-GTTTTGTTTTTTGGTGAATTCAGTGCTAC-TTTTCTTCTATTGTATTAACATA
*
84550 GATGT-TTGGTTAATGTCTTAGCATTTGGAAAGTGTAGTCAAGT
64 GATGTATTGGTTAATGTCTTAGCATTTGGAAAGTGTAATCAAGT
* * *
84593 CCATTCGTTCA-TTTTG-TTTTTGGTGATTTCAGTGCTACTTTTCTTCTATTTTATTATCATAGA
1 CCATTCGTTCAGTTTTGTTTTTTGGTGAATTCAGTGCTACTTTTCTTCTATTGTATTAACATAGA
*
84656 TGTATTGGTTAATGTCTTAGTATTTGGAAAGTGTAATCAAGT
66 TGTATTGGTTAATGTCTTAGCATTTGGAAAGTGTAATCAAGT
84698 ACAGAATCCC
Statistics
Matches: 99, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
104 26 0.26
105 57 0.58
106 5 0.05
108 11 0.11
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (107 bp):
CCATTCGTTCAGTTTTGTTTTTTGGTGAATTCAGTGCTACTTTTCTTCTATTGTATTAACATAGA
TGTATTGGTTAATGTCTTAGCATTTGGAAAGTGTAATCAAGT
Found at i:86064 original size:20 final size:21
Alignment explanation
Indices: 86039--86077 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
86029 GGCTGCTGGA
*
86039 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCGAACCGGTTTTC
86059 AACCGGTTCGAACCGGTTT
1 AACCGGTTCGAACCGGTTT
86078 GACCGGTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.31
Consensus pattern (21 bp):
AACCGGTTCGAACCGGTTTTC
Found at i:86127 original size:17 final size:17
Alignment explanation
Indices: 86105--86160 Score: 94
Period size: 17 Copynumber: 3.3 Consensus size: 17
86095 TTGACCGATC
*
86105 TGACCCGACCCAACCGT
1 TGACCCGACCCGACCGT
*
86122 TGACCCAACCCGACCGT
1 TGACCCGACCCGACCGT
86139 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
86156 TGACC
1 TGACC
86161 GTTGACCGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.21, C:0.46, G:0.20, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:86160 original size:7 final size:7
Alignment explanation
Indices: 86150--86180 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
86140 GACCCGACCC
86150 GACCGTT
1 GACCGTT
86157 GACCGTT
1 GACCGTT
86164 GACCGTT
1 GACCGTT
86171 GACCGTT
1 GACCGTT
86178 GAC
1 GAC
86181 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:93282 original size:10 final size:9
Alignment explanation
Indices: 93267--93363 Score: 97
Period size: 10 Copynumber: 10.3 Consensus size: 9
93257 CGGTTTTCAA
93267 ACCGGTTCTG
1 ACCGGTT-TG
93277 ACCGGTTTG
1 ACCGGTTTG
*
93286 ACCGGTTTCA
1 ACCGGTTT-G
93296 ACCGGTTTG
1 ACCGGTTTG
93305 AACCGGTTTG
1 -ACCGGTTTG
*
93315 ACCGGTCTG
1 ACCGGTTTG
93324 AACCGGTTTG
1 -ACCGGTTTG
*
93334 A-CGGTCTG
1 ACCGGTTTG
*
93342 AGCTGGTTTG
1 A-CCGGTTTG
*
93352 ACCGGTCTG
1 ACCGGTTTG
93361 ACC
1 ACC
93364 CGACCCGACC
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
8 7 0.10
9 28 0.38
10 38 0.52
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:93291 original size:19 final size:18
Alignment explanation
Indices: 93267--93363 Score: 106
Period size: 19 Copynumber: 5.2 Consensus size: 18
93257 CGGTTTTCAA
*
93267 ACCGGTTCTGACCGGTTTG
1 ACCGGTT-TGACCGGTCTG
* *
93286 ACCGGTTTCAACCGGTTTG
1 ACCGGTTT-GACCGGTCTG
93305 AACCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTCTG
93324 AACCGGTTTGA-CGGTCTG
1 -ACCGGTTTGACCGGTCTG
*
93342 AGCTGGTTTGACCGGTCTG
1 A-CCGGTTTGACCGGTCTG
93361 ACC
1 ACC
93364 CGACCCGACC
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
17 1 0.01
18 17 0.25
19 43 0.62
20 8 0.12
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (18 bp):
ACCGGTTTGACCGGTCTG
Found at i:93309 original size:29 final size:29
Alignment explanation
Indices: 93245--93334 Score: 110
Period size: 29 Copynumber: 3.0 Consensus size: 29
93235 TGGTGCTGGA
* *
93245 AACCGGTTTAAACGGTTTTCAAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTC-AACCGGTT-TG
93277 -ACCGGTTTGACCGGTTTCAACCGGTTTG
1 AACCGGTTTGACCGGTTTCAACCGGTTTG
* *
93305 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 AACCGGTTTGACCGGTTTCAACCGGTTTG
93334 A
1 A
93335 CGGTCTGAGC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
28 2 0.04
29 35 0.66
30 4 0.08
31 12 0.23
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (29 bp):
AACCGGTTTGACCGGTTTCAACCGGTTTG
Found at i:93382 original size:17 final size:17
Alignment explanation
Indices: 93360--93397 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
93350 TGACCGGTCT
93360 GACCCGACCCGACCGTG
1 GACCCGACCCGACCGTG
*
93377 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTG
93394 GACC
1 GACC
93398 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.47, G:0.26, T:0.08
Consensus pattern (17 bp):
GACCCGACCCGACCGTG
Done.