Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012216.1 Corchorus capsularis cultivar CVL-1 contig12237, 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: 28547
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:891 original size:29 final size:29
Alignment explanation
Indices: 827--897 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
817 ACACCGAACC
****
827 GTCAAATAAGCCCCTGAACTATTATTTCG
1 GTCAAATAAGCCCCTGAACTATTAAAAAG
*
856 G-CTAAATAAGCCCCTGAACTCTTAAAAAG
1 GTC-AAATAAGCCCCTGAACTATTAAAAAG
885 GTCAAATAAGCCC
1 GTCAAATAAGCCC
898 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 1 0.03
29 33 0.94
30 1 0.03
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAG
Found at i:1829 original size:8 final size:9
Alignment explanation
Indices: 1793--1826 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
1783 GGGTAACAAA
1793 AAGAAAAAG
1 AAGAAAAAG
*
1802 AAAAAAAAG
1 AAGAAAAAG
1811 AAGAAAAAG
1 AAGAAAAAG
1820 AAGAAAA
1 AAGAAAA
1827 GAATATACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:3150 original size:12 final size:13
Alignment explanation
Indices: 3123--3147 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3113 GTAAGTTAAA
3123 AATAAAATTTTTT
1 AATAAAATTTTTT
3136 AATAAAATTTTT
1 AATAAAATTTTT
3148 AATTTTTAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATAAAATTTTTT
Found at i:3796 original size:2 final size:2
Alignment explanation
Indices: 3759--3784 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3749 TTTTCCAAGC
3759 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
3785 GCTAATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6583 original size:22 final size:22
Alignment explanation
Indices: 6558--6842 Score: 124
Period size: 22 Copynumber: 13.1 Consensus size: 22
6548 GAATTGTCAG
*
6558 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
6580 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
6602 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
6624 TAAATCTTC-CTATGAAATTTTGA
1 T-AATC-ACACTATGAAATTTTGA
* * * *
6647 TAAACCTCCCTATAAAATTTTGA
1 T-AATCACACTATGAAATTTTGA
** * *
6670 TAACTTTC-TTATGAAATCTTG-
1 TAA-TCACACTATGAAATTTTGA
*
6691 --AT-A-ACTA-CAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * **
6708 TAACCTCCCTATGATTTTTTGA
1 TAATCACACTATGAAATTTTGA
* * * *
6730 TAACCTCATTATGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* *
6752 TAATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
6774 T-CTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* * *
6796 TAA-CCCTCTTGTGAAATTTTGA
1 TAATCACAC-TATGAAATTTTGA
* * *
6818 -AAACTAAACTATGAAATTTTTA
1 TAATC-ACACTATGAAATTTTGA
6840 TAA
1 TAA
6843 CCTTCACATA
Statistics
Matches: 199, Mismatches: 47, Indels: 33
0.71 0.17 0.12
Matches are distributed among these distances:
16 7 0.04
17 2 0.01
18 1 0.01
19 2 0.01
21 8 0.04
22 136 0.68
23 41 0.21
24 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:6787 original size:44 final size:44
Alignment explanation
Indices: 6415--6970 Score: 268
Period size: 44 Copynumber: 12.9 Consensus size: 44
6405 AGTTAACCTC
* * * *
6415 GAAATTTTGA-AGACCTCAATATGAAATTTTGATAACTTCCCAAT
1 GAAATTTTGATA-ACATCACTATGAAATTTTGATAACCTCCCTAT
* * * *
6459 GAAATTTTGATAACCAACACTATGAGATGTTGATAACCTCCATAT
1 GAAATTTTGATAA-CATCACTATGAAATTTTGATAACCTCCCTAT
** * * * * *
6504 GGTATATTGATAAC--CACGTTATGAAAATTTAAAAACCTCCATAT
1 GAAATTTTGATAACATCAC--TATGAAATTTTGATAACCTCCCTAT
* * * * * *
6548 G-AATTGTCAGTAATCA-CACTCTGAAATTTTGATAATCACACTAT
1 GAAATTTTGA-TAA-CATCACTATGAAATTTTGATAACCTCCCTAT
* * * * *
6592 GAAATTGTGATAACCTCGCTATGAAATTTTGATAAATCTTCCTAT
1 GAAATTTTGATAACATCACTATGAAATTTTGAT-AACCTCCCTAT
* * * * * *
6637 GAAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCTTAT
1 GAAATTTTGAT-AACATCACTATGAAATTTTGATAACCTCCCTAT
*
6682 GAAATCTTGATAAC-T-AC----AAATTTTGATAACCTCCCTAT
1 GAAATTTTGATAACATCACTATGAAATTTTGATAACCTCCCTAT
** * * * *
6720 GATTTTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTAT
1 GAAATTTTGATAACATCACTATGAAATTTTGATAACCTCCCTAT
* * *
6764 GAAATTTTGATCTACAT-ACTATGAAATTTTGATAACC-CTCTTGT
1 GAAATTTTGAT-AACATCACTATGAAATTTTGATAACCTC-CCTAT
* * * *
6808 GAAATTTTGAAAAC-TAAACTATGAAATTTTTATAACCTTCAC-AT
1 GAAATTTTGATAACAT-CACTATGAAATTTTGATAACC-TCCCTAT
* * * * *
6852 AAAATTTTGATATCCTC-C-CTG-AATTTTGATATCCT-CCT-T
1 GAAATTTTGATAACATCACTATGAAATTTTGATAACCTCCCTAT
* * * * *
6891 GAAATTTTGATTAC-TC-CATAATAAAAGTTTAATAACCTTCC--T
1 GAAATTTTGATAACATCAC-T-ATGAAATTTTGATAACCTCCCTAT
*
6933 --AA-TTTGATAACCAT-ACTATGAAATTTTGATAACTTCCC
1 GAAATTTTGATAA-CATCACTATGAAATTTTGATAACCTCCC
6971 CAGAAATACC
Statistics
Matches: 390, Mismatches: 89, Indels: 71
0.71 0.16 0.13
Matches are distributed among these distances:
38 32 0.08
39 37 0.09
40 6 0.02
41 14 0.04
42 19 0.05
43 12 0.03
44 164 0.42
45 82 0.21
46 24 0.06
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (44 bp):
GAAATTTTGATAACATCACTATGAAATTTTGATAACCTCCCTAT
Found at i:6907 original size:19 final size:20
Alignment explanation
Indices: 6853--6901 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
6843 CCTTCACATA
6853 AAATTTTGATATCCTCCCTG
1 AAATTTTGATATCCTCCCTG
*
6873 -AATTTTGATATCCTCCTTG
1 AAATTTTGATATCCTCCCTG
6892 AAATTTTGAT
1 AAATTTTGAT
6902 TACTCCATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (20 bp):
AAATTTTGATATCCTCCCTG
Found at i:7033 original size:44 final size:43
Alignment explanation
Indices: 6983--7125 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 43
6973 GAAATACCAC
6983 TATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTTGTAATCACATTTT-AAAATTTGATAACCTCTT
* * * * *
7027 TATGAAA-TTTTGATAACCTC-TTTATAAAATTTTGTTGACCCCTT
1 TATGAAATTTTTG-TAATCACATTT-TAAAA-TTTGATAACCTCTT
* * * * *
7071 TATGAAATTCTTATAATCACATTATTTAATTTTGATAACCTCGCT
1 TATGAAATTTTTGTAATCACATT-TTAAAATTTGATAACCTC-TT
7116 T-TGAAATTTT
1 TATGAAATTTT
7126 GATAACAATG
Statistics
Matches: 76, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
43 12 0.16
44 53 0.70
45 10 0.13
46 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.46
Consensus pattern (43 bp):
TATGAAATTTTTGTAATCACATTTTAAAATTTGATAACCTCTT
Found at i:7078 original size:22 final size:22
Alignment explanation
Indices: 7007--7131 Score: 103
Period size: 22 Copynumber: 5.7 Consensus size: 22
6997 AATCACATTT
* *
7007 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTTTA
*
7029 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTTTA
* * *
7051 TAAAATTTTGTTGACCCCTTTA
1 TGAAATTTTGATAACCCCTTTA
* * *
7073 TGAAATTCTT-ATAATCACATTA
1 TGAAATT-TTGATAACCCCTTTA
**
7095 TTTAATTTTGATAACCTCGC-TT-
1 TGAAATTTTGATAACC-C-CTTTA
7117 TGAAATTTTGATAAC
1 TGAAATTTTGATAAC
7132 AATGCTATGA
Statistics
Matches: 82, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
21 2 0.02
22 75 0.91
23 4 0.05
24 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (22 bp):
TGAAATTTTGATAACCCCTTTA
Found at i:7142 original size:22 final size:23
Alignment explanation
Indices: 7098--7209 Score: 92
Period size: 22 Copynumber: 5.0 Consensus size: 23
7088 CACATTATTT
* *
7098 AATTTTGATAA-CCTCGCTTTGA
1 AATTTTGATAATCATCGCTATGA
7120 AATTTTGATAA-CAAT-GCTATGA
1 AATTTTGATAATC-ATCGCTATGA
* *
7142 AATTTTGACAATCTTC-CTAT-A
1 AATTTTGATAATCATCGCTATGA
*
7163 AATTTTGATAATCCAATCTCTATGA
1 AATTTTGATAAT-C-ATCGCTATGA
* *
7188 AATTTCGATAATCA-CTCTATGA
1 AATTTTGATAATCATCGCTATGA
7210 GATTGGATAA
Statistics
Matches: 76, Mismatches: 7, Indels: 14
0.78 0.07 0.14
Matches are distributed among these distances:
21 12 0.16
22 42 0.55
23 5 0.07
24 5 0.07
25 12 0.16
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (23 bp):
AATTTTGATAATCATCGCTATGA
Found at i:7146 original size:44 final size:45
Alignment explanation
Indices: 7098--7200 Score: 113
Period size: 46 Copynumber: 2.3 Consensus size: 45
7088 CACATTATTT
*
7098 AATTTTGATAA-CCTCGCTTTGAAATTTTGATAA-CAAT-GCTATGA
1 AATTTTGATAATCCTC-CTAT-AAATTTTGATAACCAATCGCTATGA
* * *
7142 AATTTTGACAATCTTCCTATAAATTTTGATAATCCAATCTCTATGA
1 AATTTTGATAATCCTCCTATAAATTTTGATAA-CCAATCGCTATGA
*
7188 AATTTCGATAATC
1 AATTTTGATAATC
7201 ACTCTATGAG
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
43 12 0.24
44 13 0.27
45 7 0.14
46 17 0.35
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (45 bp):
AATTTTGATAATCCTCCTATAAATTTTGATAACCAATCGCTATGA
Found at i:7288 original size:22 final size:23
Alignment explanation
Indices: 7259--7313 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
7249 AAATTGAGAC
* *
7259 TTTT-ATAACCTTCA-TATGAAA
1 TTTTGATAACCTACACTATAAAA
7280 TTTTGATAACC-ACACTATAAAA
1 TTTTGATAACCTACACTATAAAA
7302 TTTTGATAACCT
1 TTTTGATAACCT
7314 CCCCATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (23 bp):
TTTTGATAACCTACACTATAAAA
Found at i:7324 original size:22 final size:22
Alignment explanation
Indices: 7274--7324 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
7264 TAACCTTCAT
*
7274 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACACC
* * *
7296 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCACACC
7318 ATGAAAT
1 ATGAAAT
7325 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:7358 original size:22 final size:22
Alignment explanation
Indices: 7330--7384 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
7320 GAAATATTTA
*
7330 ATGAAATTTTGTTAACC-ACACT
1 ATGAAATTTTGATAACCTA-ACT
*
7352 ATGAAATTCTT-ATAACCTAGCT
1 ATGAAATT-TTGATAACCTAACT
7374 ATGAAATTTTG
1 ATGAAATTTTG
7385 GTAATCTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 2 0.07
22 23 0.82
23 3 0.11
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTAACT
Found at i:7402 original size:56 final size:56
Alignment explanation
Indices: 7274--7380 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
7264 TAACCTTCAT
*
7274 ATGAAATTTTGATAACCACACTATAAAATTTTGATAACCTCCCCATGAAATATTTA
1 ATGAAATTTTGATAACCACACTATAAAATTTTGATAACCTACCCATGAAATATTTA
* * * *
7330 ATGAAATTTTGTTAACCACACTATGAAATTCTT-ATAACCTAGCTATGAAAT
1 ATGAAATTTTGATAACCACACTATAAAATT-TTGATAACCTACCCATGAAAT
7381 TTTGGTAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
56 43 0.96
57 2 0.04
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (56 bp):
ATGAAATTTTGATAACCACACTATAAAATTTTGATAACCTACCCATGAAATATTTA
Found at i:7487 original size:24 final size:22
Alignment explanation
Indices: 7424--7488 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
7414 TTGTGATAAT
*
7424 TAACC-ACCTATGAAATTTCAA
1 TAACCGACCTATGAAATTTTAA
* * *
7445 TAACCGACCTAAGAGATTTTAT
1 TAACCGACCTATGAAATTTTAA
7467 TAACCTGATCCTATGAAATTTT
1 TAACC-GA-CCTATGAAATTTT
7489 GGTAAACATA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 5 0.14
22 17 0.49
23 2 0.06
24 11 0.31
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (22 bp):
TAACCGACCTATGAAATTTTAA
Found at i:7530 original size:22 final size:21
Alignment explanation
Indices: 7475--7561 Score: 66
Period size: 22 Copynumber: 4.0 Consensus size: 21
7465 ATTAACCTGA
* *
7475 TCCTATGAAATTTTGGTAAACA
1 TCCTATGAAATTTTGAT-AACC
* *
7497 TACTATGGAATTTTGATAACC
1 TCCTATGAAATTTTGATAACC
* *
7518 TCCTCATGAAATTGTAATAACC
1 TCCT-ATGAAATTTTGATAACC
* * *
7540 ATCTTATAAAATTTTGTTAACC
1 -TCCTATGAAATTTTGATAACC
7562 ACATAGAGAA
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
21 6 0.12
22 41 0.82
23 3 0.06
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (21 bp):
TCCTATGAAATTTTGATAACC
Found at i:7759 original size:19 final size:20
Alignment explanation
Indices: 7728--7766 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
7718 TATTGACATT
7728 TAAAAATTGAAATT-AAAAA
1 TAAAAATTGAAATTCAAAAA
7747 TAAAATATT-AAATTCAAAAA
1 TAAAA-ATTGAAATTCAAAAA
7767 ATAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAA
Found at i:8144 original size:31 final size:31
Alignment explanation
Indices: 8079--8137 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
8069 TGGAAATTTA
8079 GAAATATGTTTTAAAGAAAAGGGTACAACTG
1 GAAATATGTTTTAAAGAAAAGGGTACAACTG
8110 GAAATATGTTTTAAA-AATAAGGGTACAA
1 GAAATATGTTTTAAAGAA-AAGGGTACAA
8138 TCGGAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.27
Consensus pattern (31 bp):
GAAATATGTTTTAAAGAAAAGGGTACAACTG
Found at i:8191 original size:13 final size:13
Alignment explanation
Indices: 8173--8230 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
8163 TTGTACTTTT
8173 ATATATAGTATAG
1 ATATATAGTATAG
**
8186 ATATATAGTGTACTTTT
1 ATATATA--GTA--TAG
8203 ATATATAGTATAG
1 ATATATAGTATAG
*
8216 ATATATAGCATAG
1 ATATATAGTATAG
8229 AT
1 AT
8231 TTATGCTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
13 22 0.61
15 6 0.17
17 8 0.22
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.41
Consensus pattern (13 bp):
ATATATAGTATAG
Found at i:8192 original size:15 final size:15
Alignment explanation
Indices: 8172--8222 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
8162 ATTGTACTTT
8172 TATATATAGTATAGA
1 TATATATAGTATAGA
**
8187 TATATAGT-GTACT-TT
1 TATATA-TAGTA-TAGA
8202 TATATATAGTATAGA
1 TATATATAGTATAGA
8217 TATATA
1 TATATA
8223 GCATAGATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
14 2 0.07
15 24 0.86
16 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (15 bp):
TATATATAGTATAGA
Found at i:8200 original size:30 final size:30
Alignment explanation
Indices: 8164--8223 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
8154 TTCCCCTCAT
8164 TGTACTTTTATATATAGTATAGATATATAG
1 TGTACTTTTATATATAGTATAGATATATAG
8194 TGTACTTTTATATATAGTATAGATATATAG
1 TGTACTTTTATATATAGTATAGATATATAG
8224 CATAGATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (30 bp):
TGTACTTTTATATATAGTATAGATATATAG
Found at i:8234 original size:30 final size:30
Alignment explanation
Indices: 8170--8234 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
8160 TCATTGTACT
** *
8170 TTTATATATAGTATAGATATATAGTGTACT
1 TTTATATATAGTATAGATATATAGCATACA
*
8200 TTTATATATAGTATAGATATATAGCATAGA
1 TTTATATATAGTATAGATATATAGCATACA
8230 TTTAT
1 TTTAT
8235 GCTTTGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.46
Consensus pattern (30 bp):
TTTATATATAGTATAGATATATAGCATACA
Found at i:12361 original size:25 final size:25
Alignment explanation
Indices: 12327--12374 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
12317 CATGTGCCCC
12327 GTTACTAATCAATACTAATTTGTCA
1 GTTACTAATCAATACTAATTTGTCA
12352 GTTACTAATCAATACTAATTTGT
1 GTTACTAATCAATACTAATTTGT
12375 TCAAATGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (25 bp):
GTTACTAATCAATACTAATTTGTCA
Found at i:13078 original size:8 final size:9
Alignment explanation
Indices: 13059--13104 Score: 69
Period size: 8 Copynumber: 5.2 Consensus size: 9
13049 TTGTCGCAAA
13059 ATAGATTAG
1 ATAGATTAG
13068 ATAGA-TAG
1 ATAGATTAG
13076 ATAGA-TAG
1 ATAGATTAG
13084 ATAGATTAG
1 ATAGATTAG
13093 ATTAGATTAG
1 A-TAGATTAG
13103 AT
1 AT
13105 TTATTTATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
8 16 0.46
9 10 0.29
10 9 0.26
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.33
Consensus pattern (9 bp):
ATAGATTAG
Found at i:13105 original size:5 final size:4
Alignment explanation
Indices: 13059--13104 Score: 56
Period size: 4 Copynumber: 10.5 Consensus size: 4
13049 TTGTCGCAAA
13059 ATAG ATTAG ATAG ATAG ATAG ATAG ATAG ATTAG ATTAG ATTAG AT
1 ATAG A-TAG ATAG ATAG ATAG ATAG ATAG A-TAG A-TAG A-TAG AT
13105 TTATTTATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 22 0.55
5 18 0.45
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.33
Consensus pattern (4 bp):
ATAG
Found at i:18507 original size:35 final size:35
Alignment explanation
Indices: 18467--18869 Score: 465
Period size: 35 Copynumber: 11.7 Consensus size: 35
18457 TTAAGTCGAT
* * *
18467 CTTAATTACCCTGACTTAAGTTAACTACTGACTCA
1 CTTAATTACCCTGAATTAAGTTAATTACTGACTTA
* * * *
18502 CTTAATTACACTGAATTAAGTTAACTATTGAATTA
1 CTTAATTACCCTGAATTAAGTTAATTACTGACTTA
* *
18537 CTTAATTACCCTGAATTAAGTTGATTACTGACTCA
1 CTTAATTACCCTGAATTAAGTTAATTACTGACTTA
* *
18572 CTTAATTACCCTGAATTAAGTTGATTACTGAATTA
1 CTTAATTACCCTGAATTAAGTTAATTACTGACTTA
* *
18607 CTTAATTACCCTGAATTAAGTTGATTACTGACTCA
1 CTTAATTACCCTGAATTAAGTTAATTACTGACTTA
* * * *
18642 GTTAATTAACCTGAATTAAGTTGATTACTGAATTA
1 CTTAATTACCCTGAATTAAGTTAATTACTGACTTA
* * *
18677 CTTAATTACCCTGAATTAAGTTGATTATTGACTAA
1 CTTAATTACCCTGAATTAAGTTAATTACTGACTTA
* * **
18712 CTTAATTACCCTGAACTAAGTT-A--CCT-ACTGG
1 CTTAATTACCCTGAATTAAGTTAATTACTGACTTA
* *
18743 CTTAATTACCCTGAATTAAGTTAATTACTAAATTA
1 CTTAATTACCCTGAATTAAGTTAATTACTGACTTA
** *
18778 CTTAATTACCCTGAATTAAGTTACCTA-TTACTTA
1 CTTAATTACCCTGAATTAAGTTAATTACTGACTTA
* * * **
18812 CTTAATTACCCTGAATTAAGTTACTTATTAACACA
1 CTTAATTACCCTGAATTAAGTTAATTACTGACTTA
18847 CTTAATTACCCTGAATTAAGTTA
1 CTTAATTACCCTGAATTAAGTTA
18870 CTTATTACTG
Statistics
Matches: 321, Mismatches: 42, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
31 24 0.07
32 2 0.01
34 34 0.11
35 261 0.81
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (35 bp):
CTTAATTACCCTGAATTAAGTTAATTACTGACTTA
Found at i:18558 original size:70 final size:70
Alignment explanation
Indices: 18467--18869 Score: 521
Period size: 70 Copynumber: 5.8 Consensus size: 70
18457 TTAAGTCGAT
* * * * *
18467 CTTAATTACCCTGACTTAAGTTAACTACTGACTCACTTAATTACACTGAATTAAGTTAACTATTG
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTAACTACTG
18532 AATTA
66 AATTA
* *
18537 CTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTACTG
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTAACTACTG
18602 AATTA
66 AATTA
* * * *
18607 CTTAATTACCCTGAATTAAGTTGATTACTGACTCAGTTAATTAACCTGAATTAAGTTGATTACTG
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTAACTACTG
18672 AATTA
66 AATTA
* * * *
18677 CTTAATTACCCTGAATTAAGTTGATTATTGACTAACTTAATTACCCTGAACTAAGTTACCTACTG
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTAACTACTG
*
18742 ----G
66 AATTA
* * * * * *
18743 CTTAATTACCCTGAATTAAGTTAATTACTAAATTACTTAATTACCCTGAATTAAGTTACCTA-TT
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTAACTACTG
*
18807 ACTTA
66 AATTA
* * *
18812 CTTAATTACCCTGAATTAAGTT-ACTTATTAACACACTTAATTACCCTGAATTAAGTTA
1 CTTAATTACCCTGAATTAAGTTGA-TTACTGACTCACTTAATTACCCTGAATTAAGTTA
18870 CTTATTACTG
Statistics
Matches: 298, Mismatches: 30, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
65 1 0.00
66 56 0.19
68 1 0.00
69 52 0.17
70 188 0.63
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (70 bp):
CTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTAACTACTG
AATTA
Found at i:18768 original size:19 final size:19
Alignment explanation
Indices: 18744--18800 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
18734 ACCTACTGGC
18744 TTAATTACCCTGAATTAAG
1 TTAATTACCCTGAATTAAG
* *
18763 TTAATTA--CTAAATT-AC
1 TTAATTACCCTGAATTAAG
18779 TTAATTACCCTGAATTAAG
1 TTAATTACCCTGAATTAAG
18798 TTA
1 TTA
18801 CCTATTACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 8 0.26
17 6 0.19
18 6 0.19
19 11 0.35
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (19 bp):
TTAATTACCCTGAATTAAG
Found at i:19516 original size:11 final size:10
Alignment explanation
Indices: 19497--19524 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
19487 CTTTTCCTTC
19497 TTCTTTTTTT
1 TTCTTTTTTT
19507 TTCTTTTTTT
1 TTCTTTTTTT
19517 TTCTTTTT
1 TTCTTTTT
19525 CTTCTTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:19523 original size:16 final size:16
Alignment explanation
Indices: 19487--19541 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
19477 CCGTTTTGCC
*
19487 CTTTTCCTTCTTCTTTT
1 CTTTTTCTTCTT-TTTT
*
19504 -TTTTTCTTTTTTTTT
1 CTTTTTCTTCTTTTTT
* *
19519 CTTTTTCTTCTTCTTC
1 CTTTTTCTTCTTTTTT
19535 CTTTTTC
1 CTTTTTC
19542 CTCAGACCTC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
15 4 0.12
16 28 0.88
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
CTTTTTCTTCTTTTTT
Found at i:23255 original size:35 final size:35
Alignment explanation
Indices: 23216--23325 Score: 130
Period size: 35 Copynumber: 3.1 Consensus size: 35
23206 CTACCAAAAT
*
23216 ATTAAACATATGTACTAGCAGCAAGCAAAACCACA
1 ATTAAACCTATGTACTAGCAGCAAGCAAAACCACA
* *** *
23251 ATTAAACCTATGTACGAGCAGCAAATTAAACATACA
1 ATTAAACCTATGTACTAGCAGCAAGCAAAAC-CACA
**
23287 TATTAAACCTATGTACTAGCAATAAGCAAAACCACA
1 -ATTAAACCTATGTACTAGCAGCAAGCAAAACCACA
23323 ATT
1 ATT
23326 CCTACCAAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
35 29 0.48
36 6 0.10
37 25 0.42
ACGTcount: A:0.47, C:0.21, G:0.10, T:0.22
Consensus pattern (35 bp):
ATTAAACCTATGTACTAGCAGCAAGCAAAACCACA
Found at i:26032 original size:12 final size:12
Alignment explanation
Indices: 26015--26042 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
26005 TTACATTTGT
26015 GATTTTTCATTA
1 GATTTTTCATTA
26027 GATTTTTCATTA
1 GATTTTTCATTA
26039 GATT
1 GATT
26043 GATTGAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.57
Consensus pattern (12 bp):
GATTTTTCATTA
Found at i:27108 original size:2 final size:2
Alignment explanation
Indices: 27091--27129 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
27081 AACATCAAAT
* *
27091 TA TA CA TA TT TA 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 TA TA TA TA TA TA T
27130 CAATTAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.