Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015978.1 Corchorus olitorius cultivar O-4 contig16011, 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: 37781
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:210 original size:17 final size:17
Alignment explanation
Indices: 164--202 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
154 AAACCATGTA
* *
164 ATCTTTCATCACCGGTG
1 ATCTTGCATCACTGGTG
181 ATCTTGCATCACTGGTG
1 ATCTTGCATCACTGGTG
198 ATCTT
1 ATCTT
203 AGATCACTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (17 bp):
ATCTTGCATCACTGGTG
Found at i:3633 original size:14 final size:14
Alignment explanation
Indices: 3614--3640 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3604 AATGATTATA
3614 AAAGCAATAATAAG
1 AAAGCAATAATAAG
3628 AAAGCAATAATAA
1 AAAGCAATAATAA
3641 AGGCAATACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.11, T:0.15
Consensus pattern (14 bp):
AAAGCAATAATAAG
Found at i:5330 original size:31 final size:31
Alignment explanation
Indices: 5295--5355 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
5285 GAATTTCTTT
* *
5295 CTATTATTTTTCCATTTCGTTTTGTTGTTTC
1 CTATTATATTTCCATTTCGTTATGTTGTTTC
*
5326 CTATTATATTTCCATTTTGTTATGTTGTTT
1 CTATTATATTTCCATTTCGTTATGTTGTTT
5356 TCTTGGTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.13, C:0.13, G:0.10, T:0.64
Consensus pattern (31 bp):
CTATTATATTTCCATTTCGTTATGTTGTTTC
Found at i:5884 original size:21 final size:20
Alignment explanation
Indices: 5859--5901 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 20
5849 TAAAAATAAA
5859 TAATT-ATAAAAATGTTGAATT
1 TAATTAATAAAAA--TTGAATT
5880 TAATTAAATAAAAATTGAATT
1 TAATT-AATAAAAATTGAATT
5901 T
1 T
5902 TTCATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 13 0.65
23 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (20 bp):
TAATTAATAAAAATTGAATT
Found at i:9052 original size:2 final size:2
Alignment explanation
Indices: 9045--9082 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
9035 TTTCATATCC
* *
9045 AT AT AT AT AC AC AT AT AT AT AT AT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9083 ATACATTGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:9503 original size:2 final size:2
Alignment explanation
Indices: 9496--9530 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9486 ATAATTATCC
9496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9531 AGTAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10898 original size:29 final size:31
Alignment explanation
Indices: 10866--10933 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
10856 ATGCAATTTG
10866 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
* *
10895 GGATATAATGTTACGAAAAGCGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
10926 GGATATAA
1 GGATATAA
10934 TCTGTTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 13 0.37
30 4 0.11
31 18 0.51
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.22
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Found at i:11088 original size:31 final size:31
Alignment explanation
Indices: 11053--11127 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
11043 CTAACTGATT
**
11053 ATATCCTTAATTGCTTGAAATCGAAAACCTC
1 ATATCCTTAATTGCTTGAAATAAAAAACCTC
* * *
11084 ATATCCTTAATTACTTGAAATAAAAAACGTT
1 ATATCCTTAATTGCTTGAAATAAAAAACCTC
11115 ATATCCTTAATTG
1 ATATCCTTAATTG
11128 TTTGTTTTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (31 bp):
ATATCCTTAATTGCTTGAAATAAAAAACCTC
Found at i:12041 original size:16 final size:16
Alignment explanation
Indices: 12022--12052 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12012 ACATTCTAAG
12022 AATACATTTTTCTACT
1 AATACATTTTTCTACT
12038 AATACATTTTTCTAC
1 AATACATTTTTCTAC
12053 CAAGCAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (16 bp):
AATACATTTTTCTACT
Found at i:12139 original size:16 final size:16
Alignment explanation
Indices: 12120--12152 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12110 TAAAAAGTTA
*
12120 TTTAAATAAAATATTT
1 TTTAAAAAAAATATTT
12136 TTTAAAAAAAATATTT
1 TTTAAAAAAAATATTT
12152 T
1 T
12153 CTTCTGAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTAAAAAAAATATTT
Found at i:12257 original size:60 final size:60
Alignment explanation
Indices: 12183--12296 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
12173 AGATGATAAG
*
12183 CAAGCAATTTAGGATATAACGTTTTCTGCCGCAAGCAATTAAGGATATAACGTTACAAAA
1 CAAGCAATTAAGGATATAACGTTTTCTGCCGCAAGCAATTAAGGATATAACGTTACAAAA
* *** *
12243 CAAGCAATTAAGGATATAACGTTTTTTGTTTCAAGCAATTAAGGATATGACGTT
1 CAAGCAATTAAGGATATAACGTTTTCTGCCGCAAGCAATTAAGGATATAACGTT
12297 TTTTTATTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (60 bp):
CAAGCAATTAAGGATATAACGTTTTCTGCCGCAAGCAATTAAGGATATAACGTTACAAAA
Found at i:12307 original size:32 final size:31
Alignment explanation
Indices: 12183--12324 Score: 144
Period size: 31 Copynumber: 4.6 Consensus size: 31
12173 AGATGATAAG
* * ****
12183 CAAGCAATTTAGGATATAACGTTTTCTGCCG
1 CAAGCAATTAAGGATATAACGTTTTTTATTT
** ***
12214 CAAGCAATTAAGGATATAACG--TTACAAAA
1 CAAGCAATTAAGGATATAACGTTTTTTATTT
*
12243 CAAGCAATTAAGGATATAACGTTTTTTGTTT
1 CAAGCAATTAAGGATATAACGTTTTTTATTT
*
12274 CAAGCAATTAAGGATATGACGTTTTTTTATTT
1 CAAGCAATTAAGGATATAACG-TTTTTTATTT
12306 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
12325 TCAGTTAGGG
Statistics
Matches: 92, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
29 23 0.25
31 42 0.46
32 27 0.29
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTTTATTT
Found at i:12517 original size:29 final size:31
Alignment explanation
Indices: 12443--12509 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
12433 CCTAACGGAC
12443 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
*
12474 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
12503 TATATCC
1 TATATCC
12510 CAAATTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGCTTTTCGTAACGT
Found at i:12941 original size:109 final size:109
Alignment explanation
Indices: 12750--12967 Score: 400
Period size: 109 Copynumber: 2.0 Consensus size: 109
12740 TAGTCATTTT
12750 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
* *
12815 ATTTAATAGGTTTAATTGAATAAACAACACAATTAATAATAATA
66 ATTTAATAGATTCAATTGAATAAACAACACAATTAATAATAATA
*
12859 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCATTTTGTATTGTTTGGTATGTGTGCTT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
*
12924 ATTTAATAGATTCAATTGAATAAACCACACAATTAATAATAATA
66 ATTTAATAGATTCAATTGAATAAACAACACAATTAATAATAATA
12968 TATATAATAG
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 105 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (109 bp):
GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
ATTTAATAGATTCAATTGAATAAACAACACAATTAATAATAATA
Found at i:15691 original size:2 final size:2
Alignment explanation
Indices: 15684--15719 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
15674 GCTTTCTGTC
15684 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
15720 ATTGAACTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:21440 original size:2 final size:2
Alignment explanation
Indices: 21433--21462 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21423 TTTGATACTG
21433 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
21463 TTGTACCAAC
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:24257 original size:218 final size:218
Alignment explanation
Indices: 23879--24272 Score: 626
Period size: 218 Copynumber: 1.8 Consensus size: 218
23869 TAAAAGGCTT
* *
23879 AAACATTAATTAAAAACAATTAAGGAAGGGAAATGGGTAATTACAAAAAAGGGTAGCAGGAAAAG
1 AAACATTAATTAAAAACAATTAAGGAAGGGAAATGAGTAATTACAAAAAAGGGTAACAGGAAAAG
* * *** * * *
23944 GAAGGGGAGAAATTCATATAGGGGCTTTTTAGTCATTTGAAAAGTGAGATAAGACCAAAAAAAGG
66 GAAGGGGAGAAACTCATAGAGGGGCTTTTTAGTCATCCAAAAAGTGAGAAAAAACCAAAAAAAGC
*
24009 CAAAAAGTGGCACCACATTAATCCTCAATTTGGCCTTTTAATAATTATCCTGGGTACTGAATCGG
131 CAAAAAGTGGCAACACATTAATCCTCAATTTGGCCTTTTAATAATTATCCTGGGTACTGAATCGG
24074 TGAGAGGAAAAAAGAAAGGGGGG
196 TGAGAGGAAAAAAGAAAGGGGGG
* * *
24097 AAACATTGATTAAAAACAATTAAGGAAGTGAAATGAGTAATTACAAAAAAGTGTAACAGGAAAAG
1 AAACATTAATTAAAAACAATTAAGGAAGGGAAATGAGTAATTACAAAAAAGGGTAACAGGAAAAG
*
24162 GAAGGGGAGAAACTCATAGAGGGGCTTTTTAGTCATCCAAAAAGTGAGAAAAAACCAAAAGAAGC
66 GAAGGGGAGAAACTCATAGAGGGGCTTTTTAGTCATCCAAAAAGTGAGAAAAAACCAAAAAAAGC
* * *
24227 CAAAAGGTGGTAACACATTAATCCTCAATTTGGCCTTTTAGTAATT
131 CAAAAAGTGGCAACACATTAATCCTCAATTTGGCCTTTTAATAATT
24273 TCCCTGGTAA
Statistics
Matches: 158, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
218 158 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (218 bp):
AAACATTAATTAAAAACAATTAAGGAAGGGAAATGAGTAATTACAAAAAAGGGTAACAGGAAAAG
GAAGGGGAGAAACTCATAGAGGGGCTTTTTAGTCATCCAAAAAGTGAGAAAAAACCAAAAAAAGC
CAAAAAGTGGCAACACATTAATCCTCAATTTGGCCTTTTAATAATTATCCTGGGTACTGAATCGG
TGAGAGGAAAAAAGAAAGGGGGG
Found at i:24313 original size:21 final size:21
Alignment explanation
Indices: 24289--24332 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
24279 GTAACTAAAA
24289 ATAATATATAGTAGTATATAT
1 ATAATATATAGTAGTATATAT
*
24310 ATAATATATATTAGTATATAT
1 ATAATATATAGTAGTATATAT
24331 AT
1 AT
24333 GAGACAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
ATAATATATAGTAGTATATAT
Found at i:28758 original size:22 final size:23
Alignment explanation
Indices: 28730--28775 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
28720 ATGTTGTTTT
28730 TTTTTGG-CCAAAACACTCTTTA
1 TTTTTGGCCCAAAACACTCTTTA
*
28752 TTTTTGGCCCACAACACTCTTTA
1 TTTTTGGCCCAAAACACTCTTTA
28775 T
1 T
28776 GTTGTTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.24, C:0.26, G:0.09, T:0.41
Consensus pattern (23 bp):
TTTTTGGCCCAAAACACTCTTTA
Found at i:28964 original size:60 final size:59
Alignment explanation
Indices: 28871--29030 Score: 232
Period size: 60 Copynumber: 2.7 Consensus size: 59
28861 CTAATTGTTC
* * *
28871 AAATAAGGGCCTAACGTTTGCCAAAATACTCAAATAAGGGTCTGATCTTTTAATTTGGCA
1 AAATAAGGGCCTAACGTTTG-CAAAATGCTCAAATAAGGGACCGATCTTTTAATTTGGCA
* *
28931 AAATAAGGGCCTAAAGTTATTG-AAAATGCTCAAATAAGGGACCGATCTTTTAATTTGGCC
1 AAATAAGGGCCTAACG-T-TTGCAAAATGCTCAAATAAGGGACCGATCTTTTAATTTGGCA
28991 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
1 AAATAAGGGCCTAACGTTTG-CAAAATGCTCAAATAAGGG
29031 CCTGGCATCA
Statistics
Matches: 90, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
58 3 0.03
59 1 0.01
60 82 0.91
61 1 0.01
62 3 0.03
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (59 bp):
AAATAAGGGCCTAACGTTTGCAAAATGCTCAAATAAGGGACCGATCTTTTAATTTGGCA
Found at i:29028 original size:31 final size:30
Alignment explanation
Indices: 28869--29033 Score: 92
Period size: 31 Copynumber: 5.5 Consensus size: 30
28859 GGCTAATTGT
*
28869 TCAAATAAGGGCCTAACGTTTGCCAAAATAC
1 TCAAATAAGGGCCTAACGTTTG-CAAAATGC
* * * **
28900 TCAAATAAGGGTCTGATC-TTT-TAATTTGGC
1 TCAAATAAGGGCCT-AACGTTTGCAAAAT-GC
* *
28930 -AAAATAAGGGCCTAAAGTTATTG-AAAATGC
1 TCAAATAAGGGCCTAACG-T-TTGCAAAATGC
* * * **
28960 TCAAATAAGGGACCGATC-TTT-TAATTTGGC
1 TCAAATAAGGG-CCTAACGTTTGCAAAAT-GC
28990 -CAAATAAGGGCCTAACGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAACGTTTG-CAAAATGC
29020 TCAAATAAGGGCCT
1 TCAAATAAGGGCCT
29034 GGCATCAGTT
Statistics
Matches: 97, Mismatches: 23, Indels: 28
0.66 0.16 0.19
Matches are distributed among these distances:
28 5 0.05
29 32 0.33
30 9 0.09
31 46 0.47
32 5 0.05
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (30 bp):
TCAAATAAGGGCCTAACGTTTGCAAAATGC
Found at i:29110 original size:31 final size:30
Alignment explanation
Indices: 29075--29179 Score: 108
Period size: 31 Copynumber: 3.5 Consensus size: 30
29065 CGATACCAGG
29075 CCCTTATTTGAGCATTTTGGCAAACGTTAGA
1 CCCTTATTTGAGCATTTT-GCAAACGTTAGA
** * * *
29106 CCCTTATTTG-GTCAAATT--AAAAGATTGGG
1 CCCTTATTTGAG-CATTTTGCAAACG-TTAGA
29135 CCCTTATTTGAGCATTTTAGCAAACGTTAGA
1 CCCTTATTTGAGCATTTT-GCAAACGTTAGA
29166 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
29180 ATTAGCCTTC
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
28 4 0.07
29 17 0.29
30 2 0.03
31 31 0.53
32 4 0.07
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTGCAAACGTTAGA
Found at i:30170 original size:16 final size:16
Alignment explanation
Indices: 30149--30186 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
30139 TTGTGCCAAC
30149 AAGATTGATTCGATAA
1 AAGATTGATTCGATAA
*
30165 AAGATTGCTTCGATAA
1 AAGATTGATTCGATAA
30181 AA-ATTG
1 AAGATTG
30187 TCTAGGTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (16 bp):
AAGATTGATTCGATAA
Found at i:32562 original size:24 final size:24
Alignment explanation
Indices: 32530--32578 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
32520 TAGGAGACTT
32530 ACAGGATATGAATCCATGGAAGGA
1 ACAGGATATGAATCCATGGAAGGA
32554 ACAGGATATGAATCCATGGAAGGA
1 ACAGGATATGAATCCATGGAAGGA
32578 A
1 A
32579 GTACAGGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.29, T:0.16
Consensus pattern (24 bp):
ACAGGATATGAATCCATGGAAGGA
Found at i:32832 original size:51 final size:51
Alignment explanation
Indices: 32756--32858 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
32746 TCCTCTTTCT
32756 TATCCCCTTGAGTTTTAAGAGTTTTAATATCCTCTTTATTACTATCATCCA
1 TATCCCCTTGAGTTTTAAGAGTTTTAATATCCTCTTTATTACTATCATCCA
*
32807 TATCCCCTTGAGTTTTAAGAGTTTTATTATCCTCTTTATTACTATCATCCA
1 TATCCCCTTGAGTTTTAAGAGTTTTAATATCCTCTTTATTACTATCATCCA
32858 T
1 T
32859 GGGAGGCTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.24, C:0.21, G:0.08, T:0.47
Consensus pattern (51 bp):
TATCCCCTTGAGTTTTAAGAGTTTTAATATCCTCTTTATTACTATCATCCA
Found at i:32895 original size:18 final size:18
Alignment explanation
Indices: 32869--32925 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
32859 GGGAGGCTTA
*
32869 GGAGACAGAACAGGAGAT
1 GGAGGCAGAACAGGAGAT
32887 GGAGGCAGAAGC-GGAGAT
1 GGAGGCAGAA-CAGGAGAT
32905 GGAGGCAGAACAGGAGAT
1 GGAGGCAGAACAGGAGAT
32923 GGA
1 GGA
32926 TTCTTATACC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
17 1 0.03
18 34 0.94
19 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.46, T:0.05
Consensus pattern (18 bp):
GGAGGCAGAACAGGAGAT
Done.