Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020051.1 Corchorus olitorius cultivar O-4 contig20084, 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: 22267
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2578 original size:43 final size:44
Alignment explanation
Indices: 2517--2619 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 44
2507 CATTGTTAGG
* * * * *
2517 TTATCAAAGTTTCTTATGGAATTTATCACAATTTTATA-AGTAA
1 TTATCAAAATTTCATATGGAAGTTATCAAAATTTAATAGAGTAA
* * *
2560 TTATCAAAATTTCATATGGTAGTTATCAAAATTTAATAGGGTAG
1 TTATCAAAATTTCATATGGAAGTTATCAAAATTTAATAGAGTAA
2604 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
2620 AAAATATTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 32 0.63
44 19 0.37
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.42
Consensus pattern (44 bp):
TTATCAAAATTTCATATGGAAGTTATCAAAATTTAATAGAGTAA
Found at i:2586 original size:22 final size:22
Alignment explanation
Indices: 2495--2619 Score: 119
Period size: 22 Copynumber: 5.7 Consensus size: 22
2485 ATAGGAAAGT
* *
2495 TTATTAAAATTTCAT-TGTTAGG
1 TTATCAAAATTTCATATGGTA-G
* * * *
2517 TTATCAAAGTTTCTTATGGAAT
1 TTATCAAAATTTCATATGGTAG
* * * *
2539 TTATCACAATTTTATA-AGTAA
1 TTATCAAAATTTCATATGGTAG
2560 TTATCAAAATTTCATATGGTAG
1 TTATCAAAATTTCATATGGTAG
* *
2582 TTATCAAAATTTAATAGGGTAG
1 TTATCAAAATTTCATATGGTAG
2604 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
2620 AAAATATTCA
Statistics
Matches: 81, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
21 16 0.20
22 62 0.77
23 3 0.04
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCATATGGTAG
Found at i:2608 original size:65 final size:65
Alignment explanation
Indices: 2495--2620 Score: 146
Period size: 65 Copynumber: 1.9 Consensus size: 65
2485 ATAGGAAAGT
* * * ** * * * *
2495 TTATTAAAATTTCATTGTTAGGTTATCAAAGTTTCTTATGGAATTTATCACAATTTTATAAGTAA
1 TTATCAAAATTTCATTGGTAGGTTATCAAAATTTAATAGGGAAGTTATCAAAATTTCATAAGTAA
*
2560 TTATCAAAATTTCATATGGTA-GTTATCAAAATTTAATAGGGTAGTTATCAAAATTTCATAA
1 TTATCAAAATTTCAT-TGGTAGGTTATCAAAATTTAATAGGGAAGTTATCAAAATTTCATAA
2621 AAATATTCAA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
65 46 0.92
66 4 0.08
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (65 bp):
TTATCAAAATTTCATTGGTAGGTTATCAAAATTTAATAGGGAAGTTATCAAAATTTCATAAGTAA
Found at i:3243 original size:36 final size:36
Alignment explanation
Indices: 3198--3283 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
3188 ACGATCAACG
*
3198 TTCTTCATTGCGTGATCTACTCCCATATGGGGAGCA
1 TTCTCCATTGCGTGATCTACTCCCATATGGGGAGCA
* * **
3234 TTCTCCATTGTGCGATCTACTCCTTTATGGGGAGCA
1 TTCTCCATTGCGTGATCTACTCCCATATGGGGAGCA
3270 TTCTCCATT-CGTGA
1 TTCTCCATTGCGTGA
3284 CCTCGGGCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 3 0.07
36 40 0.93
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (36 bp):
TTCTCCATTGCGTGATCTACTCCCATATGGGGAGCA
Found at i:3662 original size:118 final size:118
Alignment explanation
Indices: 3394--3662 Score: 358
Period size: 118 Copynumber: 2.3 Consensus size: 118
3384 TGGGCAAGCG
* * * * * *
3394 TTCTCCTCTCCTTGGGAATCTATGCTTGGCGCTCGGCGAGCATTCTCCACTTGGCACTAGGCAAG
1 TTCTCCTCTCCTTGGGGATCTACGCTTGGCACTAGGCGAGCATTCTCAACTTGGCACTAGACAAG
* * * *
3459 CGTTCTACGCTTCGTGTTTGGCGAGCGTTATCGTTCTCCACTCACGGGGAGCA
66 CGTTCTACGATTCGCGTTCGGCGAGCGTTATCGTTCTCCACTCACGGAGAGCA
* * * * * * *
3512 TTCTCCTTTCTTTTGGGATCTACGCTTAGCACTAGGCGAGCATTTTCAACTTGGCGCTCGACAAG
1 TTCTCCTCTCCTTGGGGATCTACGCTTGGCACTAGGCGAGCATTCTCAACTTGGCACTAGACAAG
*
3577 CGTTCTACGATTCGCGTTCGGCGAGCGTTATCGTTCTCCTCTCACGGAGAGCA
66 CGTTCTACGATTCGCGTTCGGCGAGCGTTATCGTTCTCCACTCACGGAGAGCA
* *
3630 TTCTCCTCTCCTTGGGGATCTCCGCTCGGCACT
1 TTCTCCTCTCCTTGGGGATCTACGCTTGGCACT
3663 CACTCGGCGA
Statistics
Matches: 127, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
118 127 1.00
ACGTcount: A:0.14, C:0.30, G:0.25, T:0.31
Consensus pattern (118 bp):
TTCTCCTCTCCTTGGGGATCTACGCTTGGCACTAGGCGAGCATTCTCAACTTGGCACTAGACAAG
CGTTCTACGATTCGCGTTCGGCGAGCGTTATCGTTCTCCACTCACGGAGAGCA
Found at i:3975 original size:181 final size:181
Alignment explanation
Indices: 3665--4129 Score: 646
Period size: 181 Copynumber: 2.6 Consensus size: 181
3655 TCGGCACTCA
* * **** *
3665 CTCGGCGAGCGTTCTCCGCTTCGCGTTCGGAAAATGTTCTACATATACGATCGGCGATCGCCCTC
1 CTCGACGAGCGTTCTCCGCTTCGCATTCGGAGGGCGTTCTACATTTACGATCGGCGATCGCCCTC
* * * * * **
3730 TTCTCATGTGGAGCATTCTCCTCTCCATGGGATCTACTCTCTTTGGGGATCTACGCTTTGCGCTC
66 CTCTCACGGGGAGCATTCTCCTCTCCATGGGATCTACACTCTTTAGGGATCTACGCGATGCGCTC
*
3795 GGCGAGCGTTCT-TCCCTTGGCACTCACACGGTGAACGTTCTCCACTTGGCG
131 GGCGAGCGTTCTCT-CCTTGGCACTCACACGGCGAACGTTCTCCACTTGGCG
* *
3846 CTCGACGAGCGTTCTCCGCTTCGCATTCGGTGGGCGTTCTACATTTGCGATCGGCGATCGCCCTC
1 CTCGACGAGCGTTCTCCGCTTCGCATTCGGAGGGCGTTCTACATTTACGATCGGCGATCGCCCTC
3911 CTCTCACGGGGAGCATTCTCCTCTCC-TCGGGATCTACACTCTTTAGGGATCTACGCGATGCGCT
66 CTCTCACGGGGAGCATTCTCCTCTCCAT-GGGATCTACACTCTTTAGGGATCTACGCGATGCGCT
* * ** *
3975 CGGCGAGCGTTCTCTGCTTGGCACTCACTCGGCGGGCGTTCTCCGCTTGGCG
130 CGGCGAGCGTTCTCTCCTTGGCACTCACACGGCGAACGTTCTCCACTTGGCG
* * * *
4027 CTCGACGAGCGTTCTCCGCTTCTCATTTGGCGGGCGTTCTACATTTACGATCGGTGATCGCCCTC
1 CTCGACGAGCGTTCTCCGCTTCGCATTCGGAGGGCGTTCTACATTTACGATCGGCGATCGCCCTC
*
4092 CTCTCACGGGGAGCATTCTCCTCTCCTTGGGGATCTAC
66 CTCTCACGGGGAGCATTCTCCTCTCCAT-GGGATCTAC
4130 GCTTTGCGCT
Statistics
Matches: 253, Mismatches: 28, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
180 1 0.00
181 241 0.95
182 11 0.04
ACGTcount: A:0.13, C:0.33, G:0.26, T:0.29
Consensus pattern (181 bp):
CTCGACGAGCGTTCTCCGCTTCGCATTCGGAGGGCGTTCTACATTTACGATCGGCGATCGCCCTC
CTCTCACGGGGAGCATTCTCCTCTCCATGGGATCTACACTCTTTAGGGATCTACGCGATGCGCTC
GGCGAGCGTTCTCTCCTTGGCACTCACACGGCGAACGTTCTCCACTTGGCG
Found at i:4184 original size:29 final size:29
Alignment explanation
Indices: 4146--4223 Score: 138
Period size: 29 Copynumber: 2.7 Consensus size: 29
4136 CGCTCGGCAA
4146 GCGTTCTCCGCTTGGCACTCACTCGGTGG
1 GCGTTCTCCGCTTGGCACTCACTCGGTGG
* *
4175 GCGTTTTCCGCTTGGCACTTACTCGGTGG
1 GCGTTCTCCGCTTGGCACTCACTCGGTGG
4204 GCGTTCTCCGCTTGGCACTC
1 GCGTTCTCCGCTTGGCACTC
4224 GAGGAGCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.06, C:0.33, G:0.29, T:0.31
Consensus pattern (29 bp):
GCGTTCTCCGCTTGGCACTCACTCGGTGG
Found at i:4232 original size:25 final size:25
Alignment explanation
Indices: 4204--4260 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
4194 TACTCGGTGG
*
4204 GCGTTCTCCGCTTGGCACTCGAG-GA
1 GCGTTCTCCGCTTCGCACTC-AGCGA
*
4229 GCGTTCTCCGCTTCGCATTCAGCGA
1 GCGTTCTCCGCTTCGCACTCAGCGA
4254 GCGTTCT
1 GCGTTCT
4261 ATATTGGCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 2 0.07
25 27 0.93
ACGTcount: A:0.11, C:0.33, G:0.28, T:0.28
Consensus pattern (25 bp):
GCGTTCTCCGCTTCGCACTCAGCGA
Found at i:4647 original size:112 final size:110
Alignment explanation
Indices: 4505--4723 Score: 339
Period size: 112 Copynumber: 2.0 Consensus size: 110
4495 TCTGCCGATT
* * *
4505 GGGGGCCATACTAGGTCGAGCTCGGTCTTGCCTGATCGATCGCCTGTTCGCGTTGGGCCCCTTGA
1 GGGGGCCATACTAGGTCGAGCTCGGCCTTGCCTAATCGATCGCCTGTTCGCGTTGGGCCCATTGA
*
4570 GGGCTTCATCATTTCCCATACTCGGTCAGGGATGGTCATTGCCGGTC
66 GGGCTTCATCATTT--CATACTCGGTCAAGGATGGTCATTGCCGGTC
** *
4617 GGGGGCCATACTAGGTCGAGCTCGGCCTTGCCTAATCTCTCGCCTGTTGGCGTTGGGCCCATTGA
1 GGGGGCCATACTAGGTCGAGCTCGGCCTTGCCTAATCGATCGCCTGTTCGCGTTGGGCCCATTGA
* *
4682 GGGCTTCATCATTTCATACTCGGTTAAGGATGGTCCTTGCCG
66 GGGCTTCATCATTTCATACTCGGTCAAGGATGGTCATTGCCG
4724 ATCGCTTGCC
Statistics
Matches: 98, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
110 25 0.26
112 73 0.74
ACGTcount: A:0.13, C:0.28, G:0.31, T:0.28
Consensus pattern (110 bp):
GGGGGCCATACTAGGTCGAGCTCGGCCTTGCCTAATCGATCGCCTGTTCGCGTTGGGCCCATTGA
GGGCTTCATCATTTCATACTCGGTCAAGGATGGTCATTGCCGGTC
Found at i:7470 original size:11 final size:11
Alignment explanation
Indices: 7456--7493 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
7446 ATTCATAACA
7456 AATTTATAATT
1 AATTTATAATT
7467 AATTTATAATT
1 AATTTATAATT
7478 -ATTTGATAATT
1 AATTT-ATAATT
*
7489 TATTT
1 AATTT
7494 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:7821 original size:6 final size:6
Alignment explanation
Indices: 7811--7852 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
7801 TATACAATCT
*
7811 ATATAT ATATAC ATATAC ATATAC ATATAC ATATAC AATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC -ATATA
7853 TTAAAGTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAC
Found at i:9939 original size:12 final size:12
Alignment explanation
Indices: 9922--9952 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
9912 CTTCTCATAT
*
9922 TATATATTGTTA
1 TATATATTGATA
9934 TATATATTGATA
1 TATATATTGATA
9946 TATATAT
1 TATATAT
9953 ATATAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (12 bp):
TATATATTGATA
Found at i:11223 original size:19 final size:20
Alignment explanation
Indices: 11175--11235 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 20
11165 ATCGTTGCTC
11175 TAATAATCTCATCTGTACAG
1 TAATAATCTCATCTGTACAG
*
11195 TACATAATCTAATCTGTACAG
1 TA-ATAATCTCATCTGTACAG
*
11216 T-GTAATCTCATCTGTACAG
1 TAATAATCTCATCTGTACAG
11235 T
1 T
11236 TGCTAAACAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.46
20 2 0.05
21 18 0.49
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (20 bp):
TAATAATCTCATCTGTACAG
Found at i:11775 original size:2 final size:2
Alignment explanation
Indices: 11768--11797 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11758 GTAATCATAA
11768 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
11798 TGTATAATAA
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:15891 original size:31 final size:31
Alignment explanation
Indices: 15849--16015 Score: 190
Period size: 31 Copynumber: 5.4 Consensus size: 31
15839 GGTGTCCTAC
* *
15849 GTGGCATGCCACGTGTACCAAAAAGCGACAT
1 GTGGCACGCCACGTGTACCAAAAAGTGACAT
*
15880 GTGGCACGCCACATGTACCAAAAAGTGACAT
1 GTGGCACGCCACGTGTACCAAAAAGTGACAT
*
15911 GTGGCACGCCACGTGTATCAAAAAGTGACAT
1 GTGGCACGCCACGTGTACCAAAAAGTGACAT
* ** * **
15942 TTATCACGTCGTGTGTACCAAAAAGTGACAT
1 GTGGCACGCCACGTGTACCAAAAAGTGACAT
* * ** *
15973 GTGGCATGCCATGTGTTTCAAAAAGTGACAC
1 GTGGCACGCCACGTGTACCAAAAAGTGACAT
*
16004 GTGGCATGCCAC
1 GTGGCACGCCAC
16016 ATACACAAAA
Statistics
Matches: 114, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 114 1.00
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (31 bp):
GTGGCACGCCACGTGTACCAAAAAGTGACAT
Found at i:18305 original size:22 final size:22
Alignment explanation
Indices: 18279--18346 Score: 118
Period size: 22 Copynumber: 3.0 Consensus size: 22
18269 GGGTGTAGAA
*
18279 AATTGAAGTATGAAAAGACAAG
1 AATTGAATTATGAAAAGACAAG
18301 AATTGAATTATGAAAAGACAAG
1 AATTGAATTATGAAAAGACAAG
18323 AATTGAATTATGAAAAGGACAAG
1 AATTGAATTATGAAAA-GACAAG
18346 A
1 A
18347 GAATGTAGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 37 0.84
23 7 0.16
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.21
Consensus pattern (22 bp):
AATTGAATTATGAAAAGACAAG
Found at i:20454 original size:35 final size:35
Alignment explanation
Indices: 20408--21073 Score: 827
Period size: 35 Copynumber: 18.7 Consensus size: 35
20398 ATCTTTTGGG
* ** * *
20408 GATCAACTCTGACCATTGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAAGGA
* *
20443 GATCAATTCTGATCATAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCAT-AAAAAACTTCTTGAAAGGA
* *
20479 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAAGGA
* * *
20514 GATCAACTCTAATCAT-CAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAAGGA
** *
20548 -ATCATTTCTGATCATCAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAAGGA
20582 GATCAACTCTGATCATAAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAAGGA
*
20617 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAAGGA
*
20652 GATCAACTCTGATCA-ACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATA-AAAAACTTCTTGAAAGGA
* *
20687 GATCAACTCTGATCATAAAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAAGGA
* * *
20722 AATCAACTCTGATCATCAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAAGGA
* **
20757 GATCAACTCTGATCATAAAAAAAACTCCTTGAACCGA
1 GATCAACTCTGATCAT--AAAAAACTTCTTGAAAGGA
* * *
20794 AATCAACTCTGATAAAAAAAAACCCTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAA--CTTCTTGAAAGGA
*
20831 GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAAGGA
20866 GATCAACTCTGATCATAAAAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCAT--AAAAAACTTCTTGAAAGGA
* * *
20903 GATCAACTCTGATCACAAAAAAAACTTTTTGAAATGA
1 GATCAACTCTGAT--CATAAAAAACTTCTTGAAAGGA
* *
20940 GATCAACTCTAATCA-ACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATA-AAAAACTTCTTGAAAGGA
* *
20975 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAAGGA
* * *
21010 GATCAACTTTGATAATAAAAAAATCTTCTTGAAAAGA
1 GATCAACTCTGATCAT-AAAAAA-CTTCTTGAAAGGA
21047 GATCAACTCTGATCATAAAAAAACTTC
1 GATCAACTCTGATCAT-AAAAAACTTC
21074 ATGGAATGAC
Statistics
Matches: 554, Mismatches: 60, Indels: 33
0.86 0.09 0.05
Matches are distributed among these distances:
33 12 0.02
34 34 0.06
35 314 0.57
36 41 0.07
37 151 0.27
39 2 0.00
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (35 bp):
GATCAACTCTGATCATAAAAAACTTCTTGAAAGGA
Found at i:21279 original size:161 final size:163
Alignment explanation
Indices: 21048--21384 Score: 432
Period size: 161 Copynumber: 2.1 Consensus size: 163
21038 TTGAAAAGAG
* *
21048 ATCAACTCTGATCATAAAAAAACTTCATGGAATGACCGCACCGGTTCATCTGGGGATCAACTCCG
1 ATCAACTCTGATCATAAAAAAACATCATGGAATGACCGCACCGGATCATCTGGGGATCAACTCCG
* *
21113 ATCACTGAAAACTTCTTTTG-AATGATCGCACTGGATCATTTAGGGATCAACTCTGATC--TCTA
66 ATCACTGAAAACTTC--TTGAAATGATCGCACTAGATCATTTAGGGATCAACTCTAATCATTC-A
*
21175 AAACTTATAGGAATGACCGCACTGGGCCATCT-AGA
128 AAACTTATAGGAATGACCGCACTGGACCATCTGAGA
** * * * *
21210 ATCAACTCTGATCA-ACGAAAACATCTTGGAATGACCGTACTGGATCATCTGGGGATCAACTCTG
1 ATCAACTCTGATCATAAAAAAACATCATGGAATGACCGCACCGGATCATCTGGGGATCAACTCCG
* * *
21274 ATCACTGAAAACTTCTTGAAATGATCGCACTATATCATTTGGGGATCAACTCTAATCATTCGAAA
66 ATCACTGAAAACTTCTTGAAATGATCGCACTAGATCATTTAGGGATCAACTCTAATCATTCAAAA
* * * * * *
21339 CTTCTTGGAATGATCTCACTGGACCATCTGGGG
131 CTTATAGGAATGACCGCACTGGACCATCTGAGA
21372 ATCAACTCTGATC
1 ATCAACTCTGATC
21385 TCTAAAAACT
Statistics
Matches: 151, Mismatches: 20, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
159 3 0.02
160 34 0.23
161 84 0.56
162 30 0.20
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (163 bp):
ATCAACTCTGATCATAAAAAAACATCATGGAATGACCGCACCGGATCATCTGGGGATCAACTCCG
ATCACTGAAAACTTCTTGAAATGATCGCACTAGATCATTTAGGGATCAACTCTAATCATTCAAAA
CTTATAGGAATGACCGCACTGGACCATCTGAGA
Found at i:21285 original size:54 final size:54
Alignment explanation
Indices: 21047--21397 Score: 352
Period size: 54 Copynumber: 6.5 Consensus size: 54
21037 CTTGAAAAGA
* * * *
21047 GATCAACTCTGATCA-TAAAAAAACTTCATGGAATGACCGCACCGGTTCATCTGGG
1 GATCAACTCTGATCACT--GAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * * * *
21102 GATCAACTCCGATCACTGAAAACTTCTTTTGAATGATCGCACTGGATCATTTAGG
1 GATCAACTCTGATCACTGAAAACTTC-TTGGAATGACCGCACTGGATCATCTGGG
* * * ** *
21157 GATCAACTCTGATCTCT-AAAACTTATAGGAATGACCGCACTGGGCCATCT-AG
1 GATCAACTCTGATCACTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * *
21209 AATCAACTCTGATCAAC-GAAAACATCTTGGAATGACCGTACTGGATCATCTGGG
1 GATCAACTCTGATC-ACTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * ** *
21263 GATCAACTCTGATCACTGAAAACTTCTTGAAATGATCGCACTATATCATTTGGG
1 GATCAACTCTGATCACTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * * * *
21317 GATCAACTCTAATCATTCG-AAACTTCTTGGAATGATCTCACTGGACCATCTGGG
1 GATCAACTCTGATCACT-GAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* *
21371 GATCAACTCTGATCTCTAAAAACTTCT
1 GATCAACTCTGATCACTGAAAACTTCT
21398 ATGAAAGACA
Statistics
Matches: 240, Mismatches: 48, Indels: 17
0.79 0.16 0.06
Matches are distributed among these distances:
52 14 0.06
53 49 0.20
54 125 0.52
55 51 0.21
56 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (54 bp):
GATCAACTCTGATCACTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
Found at i:21413 original size:108 final size:106
Alignment explanation
Indices: 21093--21432 Score: 323
Period size: 108 Copynumber: 3.2 Consensus size: 106
21083 CCGCACCGGT
* * * * *
21093 TCATCTGGGGATCAACTCCGATCA-CTGAAAACTTCTTTTGAATGATCGCACTGGATCATTTAGG
1 TCATCTGGGGATCAACTCTGATCATC-GAAAACTTC-TTGGAATGATCTCACTGGATCATCTGGG
* * * * *
21157 GATCAACTCTGATCTCTAAAACTTATAGGAATGACCGCACTGGG
64 GATCAACTCTGATCTCTAAAACTTCTATGAAAGA-CGCACTAGA
* * * * * *
21201 CCATCT-AGAATCAACTCTGATCAACGAAAACATCTTGGAATGACCGT-ACTGGATCATCTGGGG
1 TCATCTGGGGATCAACTCTGATCATCGAAAACTTCTTGGAATGATC-TCACTGGATCATCTGGGG
* *
21264 ATCAACTCTGATCACTGAAAACTTCT-TGAAATGATCGCACTATA
65 ATCAACTCTGATCTCT-AAAACTTCTATGAAA-GA-CGCACTAGA
* * *
21308 TCATTTGGGGATCAACTCTAATCATTCG-AAACTTCTTGGAATGATCTCACTGGACCATCTGGGG
1 TCATCTGGGGATCAACTCTGATCA-TCGAAAACTTCTTGGAATGATCTCACTGGATCATCTGGGG
*
21372 ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACACTA-A
65 ATCAACTCTGATCTCT-AAAACTTCTATGAAAGAC-GCACTAGA
**
21415 GTCATCTGAAGATCAACT
1 -TCATCTGGGGATCAACT
21433 TATCTCTGAA
Statistics
Matches: 189, Mismatches: 33, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
106 41 0.22
107 45 0.24
108 96 0.51
109 7 0.04
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (106 bp):
TCATCTGGGGATCAACTCTGATCATCGAAAACTTCTTGGAATGATCTCACTGGATCATCTGGGGA
TCAACTCTGATCTCTAAAACTTCTATGAAAGACGCACTAGA
Found at i:21492 original size:106 final size:107
Alignment explanation
Indices: 21372--21569 Score: 301
Period size: 106 Copynumber: 1.9 Consensus size: 107
21362 CCATCTGGGG
*
21372 ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACACTAAGTCATCTGAAGATCAACTT-AT
1 ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACACTAAGTCATCTGAAAATCAACTTAAT
*
21436 CTCTGAAAGCTTCTATGAAAGACCGCACAAGGTCATCTTAAA
66 CTCTGAAAACTTCTATGAAAGACCGCACAAGGTCATCTTAAA
* ** **
21478 ATCAACT-TAGATCTCTGAAAACTTCTATGAAAGACCGCACTGGGTCATCTGAAAATCAACTTAA
1 ATCAACTCT-GATCTCTAAAAACTTCTATGAAAGACAACACTAAGTCATCTGAAAATCAACTT-A
21542 ATCTCTGAAAACTTCTATGAAAGACCGC
64 ATCTCTGAAAACTTCTATGAAAGACCGC
21570 CCAGGGCTTA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
105 1 0.01
106 54 0.66
108 27 0.33
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (107 bp):
ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACACTAAGTCATCTGAAAATCAACTTAAT
CTCTGAAAACTTCTATGAAAGACCGCACAAGGTCATCTTAAA
Found at i:21567 original size:54 final size:53
Alignment explanation
Indices: 21372--21569 Score: 272
Period size: 54 Copynumber: 3.7 Consensus size: 53
21362 CCATCTGGGG
* * ** * *
21372 ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACACTAAGTCATCTGAAG
1 ATCAACT-TAATCTCTGAAAACTTCTATGAAAGACCGCACTAGGTCATCTGAAA
* * *
21426 ATCAACTT-ATCTCTGAAAGCTTCTATGAAAGACCGCACAAGGTCATCTTAAA
1 ATCAACTTAATCTCTGAAAACTTCTATGAAAGACCGCACTAGGTCATCTGAAA
*
21478 ATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCGCACTGGGTCATCTGAAA
1 ATCAACTTA-ATCTCTGAAAACTTCTATGAAAGACCGCACTAGGTCATCTGAAA
21532 ATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGC
1 ATCAACTT-AATCTCTGAAAACTTCTATGAAAGACCGC
21570 CCAGGGCTTA
Statistics
Matches: 129, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
52 44 0.34
53 1 0.01
54 83 0.64
55 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (53 bp):
ATCAACTTAATCTCTGAAAACTTCTATGAAAGACCGCACTAGGTCATCTGAAA
Found at i:21682 original size:92 final size:93
Alignment explanation
Indices: 21493--21683 Score: 253
Period size: 92 Copynumber: 2.1 Consensus size: 93
21483 CTTAGATCTC
**
21493 TGAAAACTTCTATGAAAGACCGCACTGGGTCATCTGAAAATCAACTTAAATCTCTGAAAACTTCT
1 TGAAAACTTCTATGAAAGACCGCAAAGGGTCATCTGAAAATCAACTTAAATCTCTGAAAACTTCT
* * ***
21558 ATGAAAGACCGCCCAGGGCTTAGATCTT
66 ATGAAAGACCACACAGGGCTTAGATAGG
* * *
21586 TGAAAGCTTCTATGAAAGACCGCAAAGGGTC-TCTTAAGATCAACTTAAATCTCTGAAAACTTCT
1 TGAAAACTTCTATGAAAGACCGCAAAGGGTCATCTGAAAATCAACTTAAATCTCTGAAAACTTCT
21650 ATGAAAGACCACACATGGTGCTT-GA-AGG
66 ATGAAAGACCACACA-GG-GCTTAGATAGG
21678 TGAAAA
1 TGAAAA
21684 GATCGCACTG
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
92 49 0.58
93 32 0.38
94 4 0.05
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (93 bp):
TGAAAACTTCTATGAAAGACCGCAAAGGGTCATCTGAAAATCAACTTAAATCTCTGAAAACTTCT
ATGAAAGACCACACAGGGCTTAGATAGG
Done.