Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008592.1 Corchorus capsularis cultivar CVL-1 contig08613, 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: 18737
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:633 original size:6 final size:6
Alignment explanation
Indices: 616--646 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
606 CAAGCAGCAC
*
616 CACAAT CGCAAT CACAAT CACAAT CACAAT C
1 CACAAT CACAAT CACAAT CACAAT CACAAT C
647 TTGCCAACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.45, C:0.35, G:0.03, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:701 original size:38 final size:38
Alignment explanation
Indices: 645--835 Score: 364
Period size: 38 Copynumber: 5.0 Consensus size: 38
635 ACAATCACAA
*
645 TCTTGCCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
683 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
721 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
*
759 TCTTACCATCAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
797 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
835 T
1 T
836 ATGCACAGCC
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 150 1.00
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.22
Consensus pattern (38 bp):
TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
Found at i:2945 original size:20 final size:20
Alignment explanation
Indices: 2912--2949 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2902 AAAAAGAGCA
*
2912 CAATTTGTAAATCAAATGTC
1 CAATTCGTAAATCAAATGTC
*
2932 CAATTCGTACATCAAATG
1 CAATTCGTAAATCAAATG
2950 CCTTGTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (20 bp):
CAATTCGTAAATCAAATGTC
Found at i:3215 original size:180 final size:180
Alignment explanation
Indices: 2913--3275 Score: 726
Period size: 180 Copynumber: 2.0 Consensus size: 180
2903 AAAAGAGCAC
2913 AATTTGTAAATCAAATGTCCAATTCGTACATCAAATGCCTTGTATTTATTTCCAATGTAGCAAAA
1 AATTTGTAAATCAAATGTCCAATTCGTACATCAAATGCCTTGTATTTATTTCCAATGTAGCAAAA
2978 GCATAAGCAAAATGTTGAAATGTAAATAATATGTATGAAACTAAGTATGTAATGCAAAGTGTTAT
66 GCATAAGCAAAATGTTGAAATGTAAATAATATGTATGAAACTAAGTATGTAATGCAAAGTGTTAT
3043 GCTACATTGCCTCAAATTCAAATACTAATATGCTCTTTAACTATGATACT
131 GCTACATTGCCTCAAATTCAAATACTAATATGCTCTTTAACTATGATACT
3093 AATTTGTAAATCAAATGTCCAATTCGTACATCAAATGCCTTGTATTTATTTCCAATGTAGCAAAA
1 AATTTGTAAATCAAATGTCCAATTCGTACATCAAATGCCTTGTATTTATTTCCAATGTAGCAAAA
3158 GCATAAGCAAAATGTTGAAATGTAAATAATATGTATGAAACTAAGTATGTAATGCAAAGTGTTAT
66 GCATAAGCAAAATGTTGAAATGTAAATAATATGTATGAAACTAAGTATGTAATGCAAAGTGTTAT
3223 GCTACATTGCCTCAAATTCAAATACTAATATGCTCTTTAACTATGATACT
131 GCTACATTGCCTCAAATTCAAATACTAATATGCTCTTTAACTATGATACT
3273 AAT
1 AAT
3276 CTAAATGGAC
Statistics
Matches: 183, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 183 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (180 bp):
AATTTGTAAATCAAATGTCCAATTCGTACATCAAATGCCTTGTATTTATTTCCAATGTAGCAAAA
GCATAAGCAAAATGTTGAAATGTAAATAATATGTATGAAACTAAGTATGTAATGCAAAGTGTTAT
GCTACATTGCCTCAAATTCAAATACTAATATGCTCTTTAACTATGATACT
Found at i:3833 original size:12 final size:12
Alignment explanation
Indices: 3816--3911 Score: 64
Period size: 11 Copynumber: 8.2 Consensus size: 12
3806 TTTGCACGTT
*
3816 TTTCTTTTTTCC
1 TTTCTTTTTTTC
3828 TTTC---TTTTC
1 TTTCTTTTTTTC
3837 -TTC-TTTTTTC
1 TTTCTTTTTTTC
3847 TCTTCTTTTTTTTC
1 T-TTC-TTTTTTTC
3861 TTT-TTTTTTTC
1 TTTCTTTTTTTC
3872 TTATCATTTTTTTC
1 TT-TC-TTTTTTTC
*
3886 TTT-TTCTTCTTC
1 TTTCTT-TTTTTC
*
3898 TTT-TCTTTTTC
1 TTTCTTTTTTTC
3909 TTT
1 TTT
3912 TTTCTAAGAC
Statistics
Matches: 70, Mismatches: 4, Indels: 21
0.74 0.04 0.22
Matches are distributed among these distances:
8 3 0.04
9 4 0.06
10 5 0.07
11 20 0.29
12 17 0.24
13 3 0.04
14 18 0.26
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:3842 original size:20 final size:19
Alignment explanation
Indices: 3817--3916 Score: 91
Period size: 20 Copynumber: 5.2 Consensus size: 19
3807 TTGCACGTTT
3817 TTCTTTTTTCCTTTCTTTTC
1 TTCTTTTTT-CTTTCTTTTC
*
3837 TTCTTTTTTCTCTTCTTTTTT
1 TTCTTTTTTCT-TTC-TTTTC
* *
3858 TTCTTTTTTTTTTCTTATC
1 TTCTTTTTTCTTTCTTTTC
*
3877 AT-TTTTTTCTTT-TTCTTC
1 TTCTTTTTTCTTTCTT-TTC
3895 TTCTTTTCTT-TTTCTTTT-
1 TTCTTTT-TTCTTTCTTTTC
3913 TTCT
1 TTCT
3917 AAGACCTACT
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
17 2 0.03
18 16 0.24
19 15 0.23
20 19 0.29
21 14 0.21
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (19 bp):
TTCTTTTTTCTTTCTTTTC
Found at i:3859 original size:24 final size:23
Alignment explanation
Indices: 3814--3916 Score: 90
Period size: 23 Copynumber: 4.6 Consensus size: 23
3804 TATTTGCACG
*
3814 TTTTTCTTTTTTC-C-T-TTCTT
1 TTTTTCTTTTTTCTCTTCTTTTT
*
3834 TTCTTCTTTTTTCTCTTCTTTTT
1 TTTTTCTTTTTTCTCTTCTTTTT
* * **
3857 TTTCTT-TTTTTTTTCTTATCATT
1 TTT-TTCTTTTTTCTCTTCTTTTT
*
3880 TTTTTC-TTTTTCTTCTTCTTTTC
1 TTTTTCTTTTTTC-TCTTCTTTTT
3903 TTTTTCTTTTTTCT
1 TTTTTCTTTTTTCT
3917 AAGACCTACT
Statistics
Matches: 64, Mismatches: 12, Indels: 11
0.74 0.14 0.13
Matches are distributed among these distances:
20 12 0.19
21 1 0.02
22 8 0.12
23 35 0.55
24 8 0.12
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTCTTTTTTCTCTTCTTTTT
Found at i:3881 original size:25 final size:23
Alignment explanation
Indices: 3814--3914 Score: 82
Period size: 25 Copynumber: 4.3 Consensus size: 23
3804 TATTTGCACG
* *
3814 TTTTTCTTTT-TTCCTTTCTTTTC
1 TTTTTTTTTTCTTTCTTT-TTTTC
*
3837 TTCTTTT-TTCTCTTCTTTTTTTTC
1 TTTTTTTTTTCT-TTC-TTTTTTTC
3861 TTTTTTTTTTCTTATCATTTTTTTC
1 TTTTTTTTTTCTT-TC-TTTTTTTC
* *
3886 TTTTTCTTCTTCTTT-TCTTTTTC
1 TTTTT-TTTTTCTTTCTTTTTTTC
3909 TTTTTT
1 TTTTTT
3915 CTAAGACCTA
Statistics
Matches: 65, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
22 3 0.05
23 18 0.28
24 14 0.22
25 23 0.35
26 7 0.11
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTTTTTCTTTCTTTTTTTC
Found at i:3889 original size:46 final size:47
Alignment explanation
Indices: 3815--3914 Score: 127
Period size: 46 Copynumber: 2.1 Consensus size: 47
3805 ATTTGCACGT
3815 TTTTCTTTTTTCCTTTCTTTTCTTCTTTTT-TCTCTTC-TTT-TTTTTC
1 TTTT-TTTTTTCCTTTCTTTTCTTCTTTTTCT-TCTTCTTTTCTTTTTC
*
3861 TTTTTTTTTT-CTTATCATTTTTTTCTTTTTCTTCTTCTTTTCTTTTTC
1 TTTTTTTTTTCCTT-TC-TTTTCTTCTTTTTCTTCTTCTTTTCTTTTTC
3909 TTTTTT
1 TTTTTT
3915 CTAAGACCTA
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
44 3 0.06
45 8 0.17
46 21 0.44
47 4 0.08
48 12 0.25
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (47 bp):
TTTTTTTTTTCCTTTCTTTTCTTCTTTTTCTTCTTCTTTTCTTTTTC
Found at i:3913 original size:12 final size:11
Alignment explanation
Indices: 3832--3914 Score: 85
Period size: 12 Copynumber: 7.0 Consensus size: 11
3822 TTTTCCTTTC
3832 TTTTCTTCTTTT
1 TTTTCTT-TTTT
*
3844 TTCTCTTCTTTT
1 TTTTCTT-TTTT
3856 TTTTCTTTTTT
1 TTTTCTTTTTT
3867 TTTTCTTATCATTT
1 TTTTCTT-T--TTT
3881 TTTTCTTTTTCT
1 TTTTCTTTTT-T
* *
3893 TCTTCTTTTCT
1 TTTTCTTTTTT
3904 TTTTCTTTTTT
1 TTTTCTTTTTT
3915 CTAAGACCTA
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
11 23 0.38
12 27 0.44
13 1 0.02
14 10 0.16
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:4132 original size:47 final size:47
Alignment explanation
Indices: 3967--4208 Score: 367
Period size: 47 Copynumber: 5.0 Consensus size: 47
3957 GAAACCCGTT
* *
3967 GACCAACTTTGGTCACTAAATTGTAAACTCGCGTGGAAGCGAGAAAGGAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAG--A--AAA
*
4018 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTTGAAGCGAGAGAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGA-AAA
4066 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
* *
4113 GACCATCTTTGGTTACTAAATTGAAAACTCGCGTGGAAACGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
* * *
4160 GACCATCTTTGGTAACTAAATTGTAGACTCGCGTGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
4207 GA
1 GA
4209 TTGCCTGGAT
Statistics
Matches: 181, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
47 93 0.51
48 47 0.26
49 1 0.01
51 40 0.22
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (47 bp):
GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
Found at i:4566 original size:139 final size:139
Alignment explanation
Indices: 4384--4818 Score: 703
Period size: 139 Copynumber: 3.1 Consensus size: 139
4374 ATGGAAAGGT
*
4384 GTTTGGCTTATGGAAAAGCCTCTCTTGCATGGATGGAACCAAAGCTGGATCTGACTCGTGTGGAA
1 GTTTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAACCAAAGCTGGATCTGACTCGTGTGGAA
* *
4449 ATGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTGAAACTATCTCGCG
66 ACGAGTTTGGCTTGTGGAAAAGCTCCTGAATGCTTGGATGGAACCAAATCTGAAACTATCTCGCG
*
4514 TAGAAGCGA
131 TGGAAGCGA
* *
4523 GTTTGGCTTATGGAAAAGCCTCTTTTGCCTGGATGGAACCAAAGCTGGATCTGACTCGTGTGAAA
1 GTTTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAACCAAAGCTGGATCTGACTCGTGTGGAA
* *
4588 ACGGGTTTGGCTTGTGGAAAAGCTCCTGAATGCTTGGATGGAACTAAATCTGAAACTATCTCGCG
66 ACGAGTTTGGCTTGTGGAAAAGCTCCTGAATGCTTGGATGGAACCAAATCTGAAACTATCTCGCG
4653 TGGAAGCGA
131 TGGAAGCGA
* *
4662 GATTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAACCAAAGCTGGATCTGACTCATGTGGAA
1 GTTTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAACCAAAGCTGGATCTGACTCGTGTGGAA
** *
4727 ACGAGTTTGGCTTGTGGAAAAGCTCCTGAATGCTTGGATGGAACCAAGGCT-AAACTGA-CTCGT
66 ACGAGTTTGGCTTGTGGAAAAGCTCCTGAATGCTTGGATGGAACCAAATCTGAAACT-ATCTCGC
*
4790 GTGGAAACGA
130 GTGGAAGCGA
* *
4800 GTTTTGCTTGTGGAAAAGC
1 GTTTGGCTTATGGAAAAGC
4819 TGGAGCATTC
Statistics
Matches: 274, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
138 34 0.12
139 240 0.88
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (139 bp):
GTTTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAACCAAAGCTGGATCTGACTCGTGTGGAA
ACGAGTTTGGCTTGTGGAAAAGCTCCTGAATGCTTGGATGGAACCAAATCTGAAACTATCTCGCG
TGGAAGCGA
Found at i:4697 original size:208 final size:207
Alignment explanation
Indices: 4317--4819 Score: 522
Period size: 208 Copynumber: 2.4 Consensus size: 207
4307 CTCATTGAAC
* *
4317 TTGGCTTATGGAAAAGCC-C-ATGTCGCTTGGATGGAACCAATGCTTGAAT-TGACTCGTATGGA
1 TTGGCTTATGGAAAAGCCTCTAT-T-GCTTGGATGGAACCAAAGC-TGAATCTGACTCGTGTGGA
* * * *
4379 AA-GGTGTTTGGCTTATGGAAAAGCCTCTCTTGCATGGATGGAACCAAAGCTGGATCTGACTCGT
63 AACGG-GTTTGGCTTGTGGAAAAG-CTCTCTTGCATGGATGGAACCAAAGCTGAAACTGACTCGC
* * * * *
4443 GTGGAAATGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTGAAACT-A
126 GTGGAAACGAGATTGGCTTATGGAAAAGCCCCTGAATGCCTGGATGGAACCAAAGCTGAAACTGA
* *
4507 TCTCGCGTAGAAGCGAGT
191 -CTCACGTAGAAACGAGT
* * * *
4525 TTGGCTTATGGAAAAGCCTCTTTTGCCTGGATGGAACCAAAGCTGGATCTGACTCGTGTGAAAAC
1 TTGGCTTATGGAAAAGCCTCTATTGCTTGGATGGAACCAAAGCTGAATCTGACTCGTGTGGAAAC
* * *
4590 GGGTTTGGCTTGTGGAAAAGCTC-CTGAATGCTTGGATGGAACTAAATCTGAAACT-ATCTCGCG
66 GGGTTTGGCTTGTGGAAAAGCTCTCT---TGCATGGATGGAACCAAAGCTGAAACTGA-CTCGCG
* * ** * *
4653 TGGAAGCGAGATTGGCTTATGGAAAAGCCTCT-CTTGCCTGGATGGAACCAAAGCTGGATCTGAC
127 TGGAAACGAGATTGGCTTATGGAAAAGCCCCTGAATGCCTGGATGGAACCAAAGCTGAAACTGAC
* *
4717 TCATGTGGAAACGAGT
192 TCACGTAGAAACGAGT
* * * *
4733 TTGGCTTGTGGAAAAG-CTCCTGAATGCTTGGATGGAACCAAGGCT-AAACTGACTCGTGTGGAA
1 TTGGCTTATGGAAAAGCCT-CT-ATTGCTTGGATGGAACCAAAGCTGAATCTGACTCGTGTGGAA
* *
4796 ACGAGTTTTGCTTGTGGAAAAGCT
64 ACGGGTTTGGCTTGTGGAAAAGCT
4820 GGAGCATTCG
Statistics
Matches: 246, Mismatches: 38, Indels: 22
0.80 0.12 0.07
Matches are distributed among these distances:
206 2 0.01
207 9 0.04
208 156 0.63
209 78 0.32
210 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (207 bp):
TTGGCTTATGGAAAAGCCTCTATTGCTTGGATGGAACCAAAGCTGAATCTGACTCGTGTGGAAAC
GGGTTTGGCTTGTGGAAAAGCTCTCTTGCATGGATGGAACCAAAGCTGAAACTGACTCGCGTGGA
AACGAGATTGGCTTATGGAAAAGCCCCTGAATGCCTGGATGGAACCAAAGCTGAAACTGACTCAC
GTAGAAACGAGT
Found at i:4819 original size:69 final size:70
Alignment explanation
Indices: 4341--4819 Score: 494
Period size: 69 Copynumber: 6.9 Consensus size: 70
4331 AGCCCATGTC
* * * * * * *
4341 GCTTGGATGGAACCAATGCTTGAATTGACTCGTATGGAAAGGTGTTTGGCTTATGGAAAAGCCTC
1 GCTTGGATGGAACCAAAGCTGGAACTGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAG-CTC
4406 TCT--T
65 TCTAAT
* * * *
4410 GCATGGATGGAACCAAAGCTGGATCTGACTCGTGTGGAAATGAGTTTGGCTTGTGGAAAAGC-CC
1 GCTTGGATGGAACCAAAGCTGGAACTGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGCTCT
4474 CTGAAT
66 CT-AAT
* * * * * *
4480 GCTTGGATGGAACCAAATCTGAAACT-ATCTCGCGTAGAAGCGAGTTTGGCTTATGGAAAAGC-C
1 GCTTGGATGGAACCAAAGCTGGAACTGA-CTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGCTC
**
4543 TCTTTT
65 TCTAAT
* * * *
4549 GCCTGGATGGAACCAAAGCTGGATCTGACTCGTGTGAAAACGGGTTTGGCTTGTGGAAAAGCTC-
1 GCTTGGATGGAACCAAAGCTGGAACTGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGCTCT
4613 CTGAAT
66 CT-AAT
* * * * * * *
4619 GCTTGGATGGAACTAAATCTGAAACT-ATCTCGCGTGGAAGCGAGATTGGCTTATGGAAAAGCCT
1 GCTTGGATGGAACCAAAGCTGGAACTGA-CTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAG-CT
4683 CTCT--T
64 CTCTAAT
* * *
4688 GCCTGGATGGAACCAAAGCTGGATCTGACTCATGTGGAAACGAGTTTGGCTTGTGGAAAAGCTC-
1 GCTTGGATGGAACCAAAGCTGGAACTGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGCTCT
4752 CTGAAT
66 CT-AAT
* * *
4758 GCTTGGATGGAACCAAGGCT-AAACTGACTCGTGTGGAAACGAGTTTTGCTTGTGGAAAAGCT
1 GCTTGGATGGAACCAAAGCTGGAACTGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGCT
4820 GGAGCATTCG
Statistics
Matches: 335, Mismatches: 61, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
67 5 0.01
68 4 0.01
69 195 0.58
70 126 0.38
71 3 0.01
72 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (70 bp):
GCTTGGATGGAACCAAAGCTGGAACTGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGCTCT
CTAAT
Found at i:4989 original size:30 final size:30
Alignment explanation
Indices: 4961--5019 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
4951 GTTCTGAATC
4961 TTTGCT-TTCTTGAATTTGCTTCCTTGAATCCT
1 TTTGCTCTTCTTG-ATTTG--TCCTTGAATCCT
*
4993 TTTGTTCTTCTTGATTTGTCCTTGAAT
1 TTTGCTCTTCTTGATTTGTCCTTGAAT
5020 TTGTTTCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 9 0.36
32 10 0.40
33 6 0.24
ACGTcount: A:0.12, C:0.19, G:0.14, T:0.56
Consensus pattern (30 bp):
TTTGCTCTTCTTGATTTGTCCTTGAATCCT
Found at i:5099 original size:29 final size:29
Alignment explanation
Indices: 5062--5122 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
5052 TTGCCCCAGA
*
5062 TCTGTCTTGAATAGTATGCTTTGAAAGAT
1 TCTGACTTGAATAGTATGCTTTGAAAGAT
5091 TCTGACTTGAATAGTATGCTTTGAAAGAT
1 TCTGACTTGAATAGTATGCTTTGAAAGAT
5120 TCT
1 TCT
5123 TTTACTGATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (29 bp):
TCTGACTTGAATAGTATGCTTTGAAAGAT
Found at i:5449 original size:50 final size:50
Alignment explanation
Indices: 5370--5476 Score: 135
Period size: 50 Copynumber: 2.1 Consensus size: 50
5360 TAAAATGCCC
* * * * *
5370 TTTGAAAAGTGAATTTTGATCTTGCACTCACAAGTGGAATGCAATCTTAT
1 TTTGAAAAGTGAATCTTGATATTGCACTCACAAATGAAATGCAATCTCAT
* *
5420 TTTGAAAA-TCGAATCTTGATATTGGACTCACAAATGAAATGCCATCTCAT
1 TTTGAAAAGT-GAATCTTGATATTGCACTCACAAATGAAATGCAATCTCAT
5470 TTTGAAA
1 TTTGAAA
5477 CTTCTTGTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
49 1 0.02
50 48 0.98
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (50 bp):
TTTGAAAAGTGAATCTTGATATTGCACTCACAAATGAAATGCAATCTCAT
Found at i:7024 original size:18 final size:19
Alignment explanation
Indices: 6990--7053 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 19
6980 CATCGTTGCT
6990 TTTTTCTCTTTCCTTCCTTTC
1 TTTTT-TCTTT-CTTCCTTTC
*
7011 TTTTTTCTTT-TTCC-ATC
1 TTTTTTCTTTCTTCCTTTC
7028 ATTTTTTCTTTCTT-CTTCTC
1 -TTTTTTCTTTCTTCCTT-TC
7048 TTTTTT
1 TTTTTT
7054 TTCCTTCTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 2 0.05
18 15 0.41
19 8 0.22
20 7 0.19
21 5 0.14
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTTCTTTCTTCCTTTC
Found at i:7039 original size:22 final size:22
Alignment explanation
Indices: 6979--7041 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
6969 TTTTTGAAAA
* * *
6979 CCATCGTTGCTTTTTTCTCTTT
1 CCATCATTTCTTTTTTCTTTTT
* *
7001 CCTTCCTTTCTTTTTTCTTTTT
1 CCATCATTTCTTTTTTCTTTTT
7023 CCATCATTT-TTTCTTTCTT
1 CCATCATTTCTTT-TTTCTT
7042 CTTCTCTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 3 0.09
22 31 0.91
ACGTcount: A:0.05, C:0.27, G:0.03, T:0.65
Consensus pattern (22 bp):
CCATCATTTCTTTTTTCTTTTT
Found at i:12676 original size:21 final size:22
Alignment explanation
Indices: 12631--12677 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
12621 ATTTTCTGAT
* *
12631 TTTTCCATTTTTTCTTTTTTTC
1 TTTTCCATTTCTTCTTTTTTGC
12653 TTTTCC-TTTCTTCTTTTTTGC
1 TTTTCCATTTCTTCTTTTTTGC
12674 TTTT
1 TTTT
12678 TCTTCAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTCCATTTCTTCTTTTTTGC
Done.