Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011604.1 Corchorus capsularis cultivar CVL-1 contig11625, 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: 52322
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Found at i:1548 original size:33 final size:32
Alignment explanation
Indices: 1475--1582 Score: 110
Period size: 33 Copynumber: 3.3 Consensus size: 32
1465 AGCACTTGTG
*
1475 ACCGGCCACGCGACTTGGAGATGTCC-GCGCAAC
1 ACCGGCCACGCGACTTGGAGATG-CCGGC-CATC
* *
1508 ACTGGCCATGCGACTTGGAGATGCCTGGCCATC
1 ACCGGCCACGCGACTTGGAGATGCC-GGCCATC
* ** *
1541 ACCGGCCACGCGACATGGCCATGCCCGGCCATA
1 ACCGGCCACGCGACTTGGAGATG-CCGGCCATC
1574 ACCGGCCAC
1 ACCGGCCAC
1583 ATGATCCTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
32 2 0.03
33 57 0.90
34 4 0.06
ACGTcount: A:0.20, C:0.38, G:0.29, T:0.13
Consensus pattern (32 bp):
ACCGGCCACGCGACTTGGAGATGCCGGCCATC
Found at i:5669 original size:18 final size:18
Alignment explanation
Indices: 5642--5702 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 18
5632 GATGTGGCAT
5642 TGCCACGTGGCACAAAAA
1 TGCCACGTGGCACAAAAA
* *
5660 TGCCATGTGG--C---AT
1 TGCCACGTGGCACAAAAA
5673 TGCCACGTGGCACAAAAA
1 TGCCACGTGGCACAAAAA
*
5691 TGCCATGTGGCA
1 TGCCACGTGGCA
5703 TTGCCACGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
13 10 0.30
15 1 0.03
16 1 0.03
18 21 0.64
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (18 bp):
TGCCACGTGGCACAAAAA
Found at i:5671 original size:31 final size:31
Alignment explanation
Indices: 5633--5711 Score: 158
Period size: 31 Copynumber: 2.5 Consensus size: 31
5623 TAAGTCGCTG
5633 ATGTGGCATTGCCACGTGGCACAAAAATGCC
1 ATGTGGCATTGCCACGTGGCACAAAAATGCC
5664 ATGTGGCATTGCCACGTGGCACAAAAATGCC
1 ATGTGGCATTGCCACGTGGCACAAAAATGCC
5695 ATGTGGCATTGCCACGT
1 ATGTGGCATTGCCACGT
5712 CAGCGGTTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.22
Consensus pattern (31 bp):
ATGTGGCATTGCCACGTGGCACAAAAATGCC
Found at i:5781 original size:13 final size:13
Alignment explanation
Indices: 5763--5789 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5753 TGGTCTGACA
5763 TGGCAATGCCACG
1 TGGCAATGCCACG
5776 TGGCAATGCCACG
1 TGGCAATGCCACG
5789 T
1 T
5790 CAGCGACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.30, G:0.30, T:0.19
Consensus pattern (13 bp):
TGGCAATGCCACG
Found at i:5869 original size:29 final size:30
Alignment explanation
Indices: 5811--5886 Score: 118
Period size: 29 Copynumber: 2.6 Consensus size: 30
5801 CGGATCCGTT
*
5811 AAGTTGAGGGGGCAAAATGTCCCAAAATTG
1 AAGTTCAGGGGGCAAAATGTCCCAAAATTG
*
5841 AAGTTCAGGGGGCAAAATGT-CCAAGATTG
1 AAGTTCAGGGGGCAAAATGTCCCAAAATTG
*
5870 AAGTTCGGGGGGCAAAA
1 AAGTTCAGGGGGCAAAA
5887 CGTCTAAACG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
29 24 0.56
30 19 0.44
ACGTcount: A:0.36, C:0.13, G:0.33, T:0.18
Consensus pattern (30 bp):
AAGTTCAGGGGGCAAAATGTCCCAAAATTG
Found at i:8801 original size:20 final size:20
Alignment explanation
Indices: 8776--8814 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
8766 CATATAAAAT
*
8776 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
8796 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
8815 TTTAAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:12698 original size:12 final size:12
Alignment explanation
Indices: 12678--12710 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12668 CTTATAATTA
*
12678 ATTTCAATTTTT
1 ATTTTAATTTTT
12690 ATTTTAATTTTT
1 ATTTTAATTTTT
12702 A-TTTAATTT
1 ATTTTAATTT
12711 AAACATGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTTAATTTTT
Found at i:14347 original size:12 final size:12
Alignment explanation
Indices: 14317--14358 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
14307 TATTAAAGTA
14317 ATATA-TATATAT
1 ATATATTATAT-T
14329 ATATATTATATT
1 ATATATTATATT
14341 ATATATTAT-TT
1 ATATATTATATT
*
14352 TTATATT
1 ATATATT
14359 TTATACCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 8 0.29
12 15 0.54
13 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATATATTATATT
Found at i:14355 original size:18 final size:20
Alignment explanation
Indices: 14320--14363 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
14310 TAAAGTAATA
14320 TATATATATATATATTATAT
1 TATATATATATATATTATAT
*
14340 TATATAT-TAT-TTTTATAT
1 TATATATATATATATTATAT
*
14358 TTTATA
1 TATATA
14364 CCATTTCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 12 0.55
19 3 0.14
20 7 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATATATATATATATTATAT
Found at i:17817 original size:13 final size:13
Alignment explanation
Indices: 17799--17827 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17789 TTGCATAAGC
17799 TCTGGTGTAAATT
1 TCTGGTGTAAATT
17812 TCTGGTGTAAATT
1 TCTGGTGTAAATT
17825 TCT
1 TCT
17828 TGACTGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.48
Consensus pattern (13 bp):
TCTGGTGTAAATT
Found at i:26820 original size:17 final size:17
Alignment explanation
Indices: 26798--26837 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
26788 ATGTAATCTT
* *
26798 TGATCTTGCATCACTGG
1 TGATCTTGAATCACTAG
26815 TGATCTTGAATCACTAG
1 TGATCTTGAATCACTAG
26832 TGATCT
1 TGATCT
26838 GAGGGGTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (17 bp):
TGATCTTGAATCACTAG
Found at i:27812 original size:17 final size:17
Alignment explanation
Indices: 27790--27822 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27780 CGACTTCTCC
27790 AACCGAATAAACCGACA
1 AACCGAATAAACCGACA
*
27807 AACCGAATCAACCGAC
1 AACCGAATAAACCGAC
27823 CCATTTCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.33, G:0.12, T:0.06
Consensus pattern (17 bp):
AACCGAATAAACCGACA
Found at i:35710 original size:53 final size:52
Alignment explanation
Indices: 35639--35773 Score: 173
Period size: 53 Copynumber: 2.6 Consensus size: 52
35629 GACAGTGAAC
* *
35639 ACAGGTTTAATTCGGAGTAATTAACCTAAGCAGTAAAAG-GGAAAGATCAGTAA
1 ACAGGTTTAATTCAGAGTAATTAACCTAAGAAGTAAAAGAGGAAAG--CAGTAA
* * *
35692 ATAGGTTTAATTTAGAGTAATTAACCTAAGAAGTAAAAGCAGTAAAGCAGTAA
1 ACAGGTTTAATTCAGAGTAATTAACCTAAGAAGTAAAAG-AGGAAAGCAGTAA
* *
35745 ACATGTTTAATTCAGAGTAATTAAACTAA
1 ACAGGTTTAATTCAGAGTAATTAACCTAA
35774 AAAGAGTAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
53 66 0.93
55 5 0.07
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.27
Consensus pattern (52 bp):
ACAGGTTTAATTCAGAGTAATTAACCTAAGAAGTAAAAGAGGAAAGCAGTAA
Found at i:35793 original size:29 final size:30
Alignment explanation
Indices: 35760--35824 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
35750 TTTAATTCAG
35760 AGTAATTAAACTAAAAAGAGT-AAAGAAAA
1 AGTAATTAAACTAAAAAGAGTGAAAGAAAA
* * *
35789 AGTAATTAGACTAAAAAGAGTGAAAGGAAG
1 AGTAATTAAACTAAAAAGAGTGAAAGAAAA
35819 AGTAAT
1 AGTAAT
35825 CAGTAGAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.58, C:0.03, G:0.20, T:0.18
Consensus pattern (30 bp):
AGTAATTAAACTAAAAAGAGTGAAAGAAAA
Found at i:35916 original size:32 final size:34
Alignment explanation
Indices: 35841--35926 Score: 115
Period size: 35 Copynumber: 2.6 Consensus size: 34
35831 AAAGGAGTGA
*
35841 AAAAGTAAAAGAAGTAATCAGCAGTAGAATGAAGT
1 AAAAGTAAAAGAAGTAATCAACAGTAGAA-GAAGT
35876 AAAAGTAAAAGAAGTAATCAACAGT-GTAA-AA-T
1 AAAAGTAAAAGAAGTAATCAACAGTAG-AAGAAGT
*
35908 AAAAGTAAAAGAAGCAATC
1 AAAAGTAAAAGAAGTAATC
35927 TGTAAAAGGA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
32 19 0.40
33 2 0.04
34 1 0.02
35 26 0.54
ACGTcount: A:0.58, C:0.07, G:0.19, T:0.16
Consensus pattern (34 bp):
AAAAGTAAAAGAAGTAATCAACAGTAGAAGAAGT
Found at i:36025 original size:49 final size:49
Alignment explanation
Indices: 35966--36066 Score: 152
Period size: 49 Copynumber: 2.1 Consensus size: 49
35956 AAAAGAGTAA
*
35966 AAGAAAGAGTAA-TCAGCAGA-TAGCTTAATTTAGAGTAATTAAGCTAAAG
1 AAGAAAGAGTAAGT-AGCA-ATTAGCTTAATTCAGAGTAATTAAGCTAAAG
*
36015 AAGAAAGAGTAAGTAGTAATTAGCTTAATTCAGAGTAATTAAGCTAAAG
1 AAGAAAGAGTAAGTAGCAATTAGCTTAATTCAGAGTAATTAAGCTAAAG
36064 AAG
1 AAG
36067 TGAAACGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
48 1 0.02
49 46 0.96
50 1 0.02
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.25
Consensus pattern (49 bp):
AAGAAAGAGTAAGTAGCAATTAGCTTAATTCAGAGTAATTAAGCTAAAG
Found at i:36126 original size:16 final size:16
Alignment explanation
Indices: 36076--36127 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
36066 GTGAAACGAA
36076 AAGTAATCAGTAGAAAG
1 AAGTAATCAGTAG-AAG
* ** *
36093 GAGTGAAAGAGTAAAAG
1 AAGT-AATCAGTAGAAG
36110 AAGTAATCAGTAGAAG
1 AAGTAATCAGTAGAAG
36126 AA
1 AA
36128 AAAGAAGTAA
Statistics
Matches: 26, Mismatches: 8, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
16 11 0.42
17 9 0.35
18 6 0.23
ACGTcount: A:0.54, C:0.04, G:0.27, T:0.15
Consensus pattern (16 bp):
AAGTAATCAGTAGAAG
Found at i:36145 original size:15 final size:15
Alignment explanation
Indices: 36127--36188 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
36117 CAGTAGAAGA
36127 AAAAGAAGTAAGAGT
1 AAAAGAAGTAAGAGT
*
36142 AAAAGAAGTAATCAGT
1 AAAAGAAGTAA-GAGT
* * *
36158 AGAAG-TGAAAGAGT
1 AAAAGAAGTAAGAGT
36172 AAAAGAAG-AAGAAGT
1 AAAAGAAGTAAG-AGT
36187 AA
1 AA
36189 TCAGTAGAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
14 10 0.27
15 20 0.54
16 7 0.19
ACGTcount: A:0.60, C:0.02, G:0.26, T:0.13
Consensus pattern (15 bp):
AAAAGAAGTAAGAGT
Found at i:36184 original size:36 final size:34
Alignment explanation
Indices: 36076--36221 Score: 167
Period size: 37 Copynumber: 4.2 Consensus size: 34
36066 GTGAAACGAA
*
36076 AAGTAATCAGTAG-A-AAGGAGTGAAAGAGTAAAAG
1 AAGTAATCAGTAGAAGAAAGAGT-AAA-AGTAAAAG
*
36110 AAGTAATCAGTAGAAGAAAAAGAAGTAAGAGTAAAAG
1 AAGTAATCAGTAGAAG--AAAG-AGTAAAAGTAAAAG
36147 AAGTAATCAGTAGAAGTGAAAGAGTAAAAG-AAGAAG
1 AAGTAATCAGTAGAA--GAAAGAGTAAAAGTAA-AAG
36183 AAGTAATCAGTAG-A-AAAGAGTAAAAGTAAAAG
1 AAGTAATCAGTAGAAGAAAGAGTAAAAGTAAAAG
36215 AAGTAAT
1 AAGTAAT
36222 TAAGAGTAAA
Statistics
Matches: 100, Mismatches: 3, Indels: 20
0.81 0.02 0.16
Matches are distributed among these distances:
32 22 0.22
33 2 0.02
34 13 0.13
35 4 0.04
36 23 0.23
37 27 0.27
38 5 0.05
39 4 0.04
ACGTcount: A:0.57, C:0.03, G:0.25, T:0.15
Consensus pattern (34 bp):
AAGTAATCAGTAGAAGAAAGAGTAAAAGTAAAAG
Found at i:36226 original size:25 final size:25
Alignment explanation
Indices: 36198--36246 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
36188 ATCAGTAGAA
36198 AAGAGTAAAAGTAAAAGAAGTAATT
1 AAGAGTAAAAGTAAAAGAAGTAATT
*
36223 AAGAGTAAAAGTAAGAGAAGTAAT
1 AAGAGTAAAAGTAAAAGAAGTAAT
36247 CAGTCAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.18
Consensus pattern (25 bp):
AAGAGTAAAAGTAAAAGAAGTAATT
Found at i:36343 original size:16 final size:17
Alignment explanation
Indices: 36315--36346 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
36305 AAGAAGAAGT
36315 AATCAGTAGAAAGGAGA
1 AATCAGTAGAAAGGAGA
36332 AATCAGTA-AAAGGAG
1 AATCAGTAGAAAGGAG
36347 TAAAAGAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.53, C:0.06, G:0.28, T:0.12
Consensus pattern (17 bp):
AATCAGTAGAAAGGAGA
Found at i:36425 original size:67 final size:67
Alignment explanation
Indices: 36336--36561 Score: 326
Period size: 67 Copynumber: 3.3 Consensus size: 67
36326 AGGAGAAATC
36336 AGTAAAAGGAGTAAAAGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAGTAAA
1 AGTAAAAGGAGTAAAAGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAGTAAA
*
36401 GG
66 GA
* * * *
36403 AGTATAAGGAGTAAATGAAGTAAACAGTAGTAATTAGTTTAATTCAGAGTAATTAAGTTAGTCAA
1 AGTAAAAGGAGTAAAAGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAGTAAA
36468 GA
66 GA
* * * * * *
36470 AGTAAAAGGAGTAAAAGGAAGTAACCAGTAGTAGTTAGCCTAATTTAGAGTAATTAAGTTAATCA
1 AGTAAAAGGAGTAAAA-GAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAGTAA
36535 AGA
65 AGA
*
36538 AGTAAAAGGAATAAAAGGAAGTAA
1 AGTAAAAGGAGTAAAA-GAAGTAA
36562 CCAGAATTTG
Statistics
Matches: 144, Mismatches: 14, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
67 76 0.53
68 68 0.47
ACGTcount: A:0.48, C:0.05, G:0.22, T:0.25
Consensus pattern (67 bp):
AGTAAAAGGAGTAAAAGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAGTAAA
GA
Found at i:36565 original size:68 final size:68
Alignment explanation
Indices: 36336--36561 Score: 339
Period size: 68 Copynumber: 3.4 Consensus size: 68
36326 AGGAGAAATC
*
36336 AGTAAAAGGAGTAAAA-GAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAGTAA
1 AGTAAAAGGAGTAAAAGGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAGTCA
*
36400 AGG
66 AGA
* * *
36403 AGTATAAGGAGT-AAATGAAGTAAACAGTAGTAATTAGTTTAATTCAGAGTAATTAAGTTAGTCA
1 AGTAAAAGGAGTAAAAGGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAGTCA
36467 AGA
66 AGA
* * * * *
36470 AGTAAAAGGAGTAAAAGGAAGTAACCAGTAGTAGTTAGCCTAATTTAGAGTAATTAAGTTAATCA
1 AGTAAAAGGAGTAAAAGGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAGTCA
36535 AGA
66 AGA
*
36538 AGTAAAAGGAATAAAAGGAAGTAA
1 AGTAAAAGGAGTAAAAGGAAGTAA
36562 CCAGAATTTG
Statistics
Matches: 144, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
66 3 0.02
67 70 0.49
68 71 0.49
ACGTcount: A:0.48, C:0.05, G:0.22, T:0.25
Consensus pattern (68 bp):
AGTAAAAGGAGTAAAAGGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAGTCA
AGA
Found at i:42140 original size:44 final size:44
Alignment explanation
Indices: 42088--42330 Score: 362
Period size: 44 Copynumber: 5.5 Consensus size: 44
42078 CAGTAATTTC
*
42088 CAGTTGCTCCAAGGAGGGGGCATTTCAACAACTTTTCAGTTTTT
1 CAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTTCAGTTTTT
* *
42132 CAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTACAGTCTTT
1 CAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTTCAGTTTTT
* * * *
42176 CAGTTGCTCCAAGGAAGGTGCATTCCAACAACTTTACAGTCTTT
1 CAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTTCAGTTTTT
* * * *
42220 CAGTTGCTCCAAGGATGGGGCATTCCAACAACTTTTAAATTATT
1 CAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTTCAGTTTTT
* *
42264 CAGTTGTTCCAAAGAGGGGGCATTCCAACAACTTTTCAG-TTTT
1 CAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTTCAGTTTTT
42307 CAGTTGCTCCAAGGAGGGGGCATT
1 CAGTTGCTCCAAGGAGGGGGCATT
42331 GTAGCAGTTT
Statistics
Matches: 179, Mismatches: 20, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
43 25 0.14
44 154 0.86
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (44 bp):
CAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTTCAGTTTTT
Found at i:48980 original size:53 final size:53
Alignment explanation
Indices: 48912--49046 Score: 164
Period size: 53 Copynumber: 2.5 Consensus size: 53
48902 GACAGTGAAC
* * * ** *
48912 ACAGGTTTATTTCAGAGTAATTAACCTAAGCAG-CAAAAGGGGAAGATCAGTAA
1 ACAGGTTTAATTCAGAGTAATTAACCTAAGAAGTAAAAACAGGAA-AGCAGTAA
* *
48965 ATAGGTTTAATTCAGAGTAATTAACCTAAGAAGTAAAAACAGTAAAGCAGTAA
1 ACAGGTTTAATTCAGAGTAATTAACCTAAGAAGTAAAAACAGGAAAGCAGTAA
* *
49018 ACATGTTTAATTCAGAGTAATTAAACTAA
1 ACAGGTTTAATTCAGAGTAATTAACCTAA
49047 AAAGAGGAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
53 63 0.90
54 7 0.10
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (53 bp):
ACAGGTTTAATTCAGAGTAATTAACCTAAGAAGTAAAAACAGGAAAGCAGTAA
Found at i:49066 original size:29 final size:30
Alignment explanation
Indices: 49033--49097 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
49023 TTTAATTCAG
49033 AGTAATTAAACTAAAAAGAG-GAAAGAAAA
1 AGTAATTAAACTAAAAAGAGTGAAAGAAAA
* * *
49062 AGTAATTAGACTAAAAAGAGTGAAAGGAAC
1 AGTAATTAAACTAAAAAGAGTGAAAGAAAA
49092 AGTAAT
1 AGTAAT
49098 CAGTAGAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 19 0.59
30 13 0.41
ACGTcount: A:0.58, C:0.05, G:0.20, T:0.17
Consensus pattern (30 bp):
AGTAATTAAACTAAAAAGAGTGAAAGAAAA
Found at i:49189 original size:32 final size:34
Alignment explanation
Indices: 49114--49201 Score: 128
Period size: 35 Copynumber: 2.6 Consensus size: 34
49104 AAAGGAGTGA
49114 AAAAGTAAAAGAAGTAATCAGCAGTAGAATGAAGT
1 AAAAGTAAAAGAAGTAATCAGCAGTAGAA-GAAGT
49149 AAAAGTAAAAGAAGTAATCAGCAG-AGTAA-AA-T
1 AAAAGTAAAAGAAGTAATCAGCAGTAG-AAGAAGT
*
49181 AAAAGTAAAAGAAGCAATCAG
1 AAAAGTAAAAGAAGTAATCAG
49202 TAAAAGGAAG
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
32 21 0.41
33 2 0.04
34 2 0.04
35 26 0.51
ACGTcount: A:0.58, C:0.07, G:0.20, T:0.15
Consensus pattern (34 bp):
AAAAGTAAAAGAAGTAATCAGCAGTAGAAGAAGT
Found at i:49272 original size:31 final size:29
Alignment explanation
Indices: 49224--49284 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 29
49214 GTTGTCAGTG
*
49224 AAAGTAAAAGAGTAAAAGAAAGGGTAATC
1 AAAGTAAAAGAGTAAAAGAAAGAGTAATC
49253 AAAGTAAAAAGAAGTAAAAGAAAGAGTAATC
1 AAAGT-AAAAG-AGTAAAAGAAAGAGTAATC
49284 A
1 A
49285 GCAGATAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 5 0.17
30 5 0.17
31 19 0.66
ACGTcount: A:0.62, C:0.03, G:0.21, T:0.13
Consensus pattern (29 bp):
AAAGTAAAAGAGTAAAAGAAAGAGTAATC
Found at i:49323 original size:49 final size:49
Alignment explanation
Indices: 49270--49370 Score: 152
Period size: 49 Copynumber: 2.1 Consensus size: 49
49260 AAAGAAGTAA
*
49270 AAGAAAGAGTAA-TCAGCAGA-TAGCTTAATTCAGAGTAATTAAGTTAAAG
1 AAGAAAGAGTAAGT-AGCA-ATTAGCTTAATTCAGAGTAATTAAGCTAAAG
*
49319 AAGAAAGAGTAAGTAGTAATTAGCTTAATTCAGAGTAATTAAGCTAAAG
1 AAGAAAGAGTAAGTAGCAATTAGCTTAATTCAGAGTAATTAAGCTAAAG
49368 AAG
1 AAG
49371 TGAAAGGAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
48 1 0.02
49 46 0.96
50 1 0.02
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.25
Consensus pattern (49 bp):
AAGAAAGAGTAAGTAGCAATTAGCTTAATTCAGAGTAATTAAGCTAAAG
Found at i:49444 original size:37 final size:35
Alignment explanation
Indices: 49391--49525 Score: 143
Period size: 37 Copynumber: 3.8 Consensus size: 35
49381 AGTAATCAGT
*
49391 AGAAAGGAGTGAAAGAGTAAAAGAAGTAATCAGTAGA
1 AGAAAAGAGT-AAA-AGTAAAAGAAGTAATCAGTAGA
* *
49428 AGAAAAAGAAGTAAGAGTAAAAGAAGAAATCAGTAGA
1 AG-AAAAG-AGTAAAAGTAAAAGAAGTAATCAGTAGA
* *
49465 AGTGAAAGAGTAAAAG-AAGAAGGAGTAATCAGT---
1 AG-AAAAGAGTAAAAGTAA-AAGAAGTAATCAGTAGA
49498 AGAAAAGAGTAAAAGTAAAAGAAGTAAT
1 AGAAAAGAGTAAAAGTAAAAGAAGTAAT
49526 TAAGAGTAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
32 21 0.25
33 4 0.05
35 2 0.02
36 19 0.23
37 29 0.35
38 6 0.07
39 3 0.04
ACGTcount: A:0.58, C:0.02, G:0.27, T:0.13
Consensus pattern (35 bp):
AGAAAAGAGTAAAAGTAAAAGAAGTAATCAGTAGA
Found at i:49446 original size:21 final size:22
Alignment explanation
Indices: 49409--49452 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
49399 GTGAAAGAGT
*
49409 AAAAGAAGTAATCAGTAGAAGA
1 AAAAGAAGTAATCAGTAAAAGA
*
49431 AAAAGAAGTAA-GAGTAAAAGA
1 AAAAGAAGTAATCAGTAAAAGA
49452 A
1 A
49453 GAAATCAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.64, C:0.02, G:0.23, T:0.11
Consensus pattern (22 bp):
AAAAGAAGTAATCAGTAAAAGA
Found at i:49449 original size:15 final size:16
Alignment explanation
Indices: 49431--49512 Score: 55
Period size: 15 Copynumber: 5.3 Consensus size: 16
49421 CAGTAGAAGA
*
49431 AAAAGAAGTAA-GAGT
1 AAAAGAAGAAAGGAGT
**
49446 AAAAGAAGAAATCAGT
1 AAAAGAAGAAAGGAGT
* *
49462 AGAAG-TGAAA-GAGT
1 AAAAGAAGAAAGGAGT
49476 AAAAGAAG-AAGGAGT
1 AAAAGAAGAAAGGAGT
* * *
49491 AATCAGTAGAAAAGAGT
1 AA-AAGAAGAAAGGAGT
49508 AAAAG
1 AAAAG
49513 TAAAAGAAGT
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
14 9 0.18
15 21 0.41
16 13 0.25
17 8 0.16
ACGTcount: A:0.59, C:0.02, G:0.27, T:0.12
Consensus pattern (16 bp):
AAAAGAAGAAAGGAGT
Found at i:49530 original size:25 final size:25
Alignment explanation
Indices: 49502--49550 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
49492 ATCAGTAGAA
49502 AAGAGTAAAAGTAAAAGAAGTAATT
1 AAGAGTAAAAGTAAAAGAAGTAATT
*
49527 AAGAGTAAAAGTAAGAGAAGTAAT
1 AAGAGTAAAAGTAAAAGAAGTAAT
49551 CAGTCAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.18
Consensus pattern (25 bp):
AAGAGTAAAAGTAAAAGAAGTAATT
Found at i:49700 original size:19 final size:19
Alignment explanation
Indices: 49663--49757 Score: 54
Period size: 19 Copynumber: 4.9 Consensus size: 19
49653 AAAGAAGTAA
49663 ACAGTAGTAATT-AGCTTAAT
1 ACAG-AGTAATTAAG-TTAAT
*
49683 TCAGAGTAATTAAGTTAAT
1 ACAGAGTAATTAAGTTAAT
* * **
49702 AAAGGAATAAAAGAAG-TAA-
1 ACA-GAGT-AATTAAGTTAAT
49721 ACAGTAGTAATT-AGTTTAAT
1 ACAG-AGTAATTAAG-TTAAT
*
49741 TCAGAGTAATTAAGTTA
1 ACAGAGTAATTAAGTTA
49758 GTCAAGAAGT
Statistics
Matches: 56, Mismatches: 11, Indels: 17
0.67 0.13 0.20
Matches are distributed among these distances:
17 2 0.04
18 3 0.05
19 30 0.54
20 16 0.29
21 5 0.09
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.32
Consensus pattern (19 bp):
ACAGAGTAATTAAGTTAAT
Found at i:49731 original size:58 final size:58
Alignment explanation
Indices: 49644--49847 Score: 239
Period size: 58 Copynumber: 3.3 Consensus size: 58
49634 GAAATCAATA
*
49644 AAAGGAGTAAAAGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAAT
1 AAAGGAATAAAAGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAAT
*
49702 AAAGGAATAAAAGAAGTAAACAGTAGTAATTAGTTTAATTCAGAGTAATTAAGTTAGTCAAGAAG
1 AAAGGAATAAAAGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAG-T--T----AA-
49767 T
58 T
* * *
49768 AAAAGGAGTAAAAGGAAGTAACCAGTTGTAATTAGCTTAATTCAGAGTAATTAAGTTAAT
1 -AAAGGAATAAAA-GAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAAT
* *
49828 CAA-GAAGTAAAAGGAGTAAA
1 AAAGGAA-TAAAAGAAGTAAA
49848 AGGAAGTAAC
Statistics
Matches: 125, Mismatches: 10, Indels: 22
0.80 0.06 0.14
Matches are distributed among these distances:
58 59 0.47
59 8 0.06
60 1 0.01
61 3 0.02
65 3 0.02
66 1 0.01
67 12 0.10
68 38 0.30
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.26
Consensus pattern (58 bp):
AAAGGAATAAAAGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAAT
Found at i:49857 original size:68 final size:68
Alignment explanation
Indices: 49702--49860 Score: 266
Period size: 68 Copynumber: 2.4 Consensus size: 68
49692 TTAAGTTAAT
* * * *
49702 AAAGGAATAAAA-GAAGTAAACAGTAGTAATTAGTTTAATTCAGAGTAATTAAGTTAGTCAAGAA
1 AAAGGAGTAAAAGGAAGTAACCAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAA
49766 GTA
66 GTA
*
49769 AAAGGAGTAAAAGGAAGTAACCAGTTGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAA
1 AAAGGAGTAAAAGGAAGTAACCAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAA
49834 GTA
66 GTA
49837 AAAGGAGTAAAAGGAAGTAACCAG
1 AAAGGAGTAAAAGGAAGTAACCAG
49861 AATTCGAGGT
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
67 11 0.13
68 75 0.87
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.24
Consensus pattern (68 bp):
AAAGGAGTAAAAGGAAGTAACCAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAA
GTA
Found at i:51646 original size:359 final size:354
Alignment explanation
Indices: 50665--52061 Score: 2198
Period size: 353 Copynumber: 4.0 Consensus size: 354
50655 CATTTAGATG
* *
50665 TTTGGACATATAGAGATTTATTCA-ATTGTAATGAAATTTCACAAGTACTTACTC----AAAAAA
1 TTTGGGCATATAGAGATTTATTCAGATTGTAATGAGATTTCACAAGTACTTACTCAAAAAAAAAA
50725 AAACCTTCAAATTAAGTATGGGAAGTTTCAAAGTTGCCTTAGAGAGTGATAAACTCCAGCAATAA
66 AAACCTTCAAATTAAGTATGGGAAGTTTCAAAGTTGCCTTAGAGAGTGATAAACTCCAGCAATAA
* * *
50790 ATTAATCTCAGCAATAATTTCAGTCATCCACAAGAAAAATCAAAGAATAATGAAGGGACAAGAAT
131 ATTAATCTCAGCAATAATTTGAGTCATCCACAAGAAAAATCAAAGAATAATGAAGGGACCAGATT
*
50855 TACGTGGAAAGCCCTCCATTAATATAGAGGGAAAAACCACGGGACAAAATTCGAATAAAATCCAC
196 TACGTGGAAAGCCCTCCATTAATATAGAGGGAAAAACCACGGAACAAAATTCGAATAAAATCCAC
50920 TATCAAATAGACAACTTACAAAGTTCAATATTTCAAACCTTTGCCCCAAGCTAAAAACCATATAA
261 TATCAAATAGACAACTTACAAAGTTCAATATTTCAAACCTTTGCCCCAAGCTAAAAACCATATAA
50985 TAACAAATTGCAGAACACAAGTACATTCC
326 TAACAAATTGCAGAACACAAGTACATTCC
* * * *
51014 TTTGGGCATATAGAGATTTAATCAAATTGTAATGAGATTTCACAAGTATTTACTC-AAAAAAAGA
1 TTTGGGCATATAGAGATTTATTCAGATTGTAATGAGATTTCACAAGTACTTACTCAAAAAAAAAA
* * * * *
51078 AAACATTCATATTAAGTATGGTAAGTTTCAAAGTTGTCTTATAGAGTGATAAACTCCAGCAATAA
66 AAACCTTCAAATTAAGTATGGGAAGTTTCAAAGTTGCCTTAGAGAGTGATAAACTCCAGCAATAA
51143 ATTAATCTCAGCAATAATTTGAGTCATCCACAAGAAAAATCAAAGAATAATGAAGGGACCAGATT
131 ATTAATCTCAGCAATAATTTGAGTCATCCACAAGAAAAATCAAAGAATAATGAAGGGACCAGATT
* * *
51208 TACGTGGAAAGACCTCCATTAATATTGAGGAAAAAACCACGGAACAAAATTCGAATAAAATCCAC
196 TACGTGGAAAGCCCTCCATTAATATAGAGGGAAAAACCACGGAACAAAATTCGAATAAAATCCAC
*
51273 TATCAAATAGACAACTTACAAAGTTCAATATTTCAAACCTTTGCCCCAAGCTAAAAATCATATAA
261 TATCAAATAGACAACTTACAAAGTTCAATATTTCAAACCTTTGCCCCAAGCTAAAAACCATATAA
51338 TAACAAATTGCAGAACACAAGTACATTCC
326 TAACAAATTGCAGAACACAAGTACATTCC
*
51367 TTTGGGCATATAGAGATTTATTCAGATTGTAATGAGATTTCACATGTACTTACTCAAAAAAAAAA
1 TTTGGGCATATAGAGATTTATTCAGATTGTAATGAGATTTCACAAGTACTTACTC----AAAAAA
* *
51432 AAAACAAACCTTCAAATTAAGTATGGGAAGTTTCAAAGTTGCCTTAGAGAGTGAGAAAGTCCAGC
62 AAAA-AAACCTTCAAATTAAGTATGGGAAGTTTCAAAGTTGCCTTAGAGAGTGATAAACTCCAGC
* *
51497 AATAAATTAATCTCAGCAATAATTTGAGTCATGCACAAGAAAAATCAAAGAAAAATGAAGGGACC
126 AATAAATTAATCTCAGCAATAATTTGAGTCATCCACAAGAAAAATCAAAGAATAATGAAGGGACC
* * * * *
51562 AGATTTACGTGGAATGCCCTCCGTCAATATAGAGGGAAAAACCATGGGACAAAATTCGAATAAAA
191 AGATTTACGTGGAAAGCCCTCCATTAATATAGAGGGAAAAACCACGGAACAAAATTCGAATAAAA
* *
51627 TCCACTATCAAATAGACAACTTACAGAGTTCAATATTTCAAACCTTTGCCCCAAGCCAAAAAACC
256 TCCACTATCAAATAGACAACTTACAAAGTTCAATATTTCAAACCTTTGCCCCAAG-CTAAAAACC
51692 ATATAATAACAAATTGTC-GAACACAAGTACATTCC
320 ATATAATAACAAATTG-CAGAACACAAGTACATTCC
* * * *
51727 TTTGGGCATATAGAGATTTATTGAGATTGTAATGAGATTTCACAAGTGCTTACTCATAAAAAAGA
1 TTTGGGCATATAGAGATTTATTCAGATTGTAATGAGATTTCACAAGTACTTACTCAAAAAAAAAA
*
51792 AAACCTTCAAATTAAGTATGGGAAGTTTCAAAGTTGCTTTAGAGAGTGATAAACTCCAGCAATAA
66 AAACCTTCAAATTAAGTATGGGAAGTTTCAAAGTTGCCTTAGAGAGTGATAAACTCCAGCAATAA
*
51857 ATTAATCTCAGCAATAATTTGAGTCATCCACAAGAAAAATCAAAGAATAATGAAGGGATCAGATT
131 ATTAATCTCAGCAATAATTTGAGTCATCCACAAGAAAAATCAAAGAATAATGAAGGGACCAGATT
51922 TACGT-G---G------------A-A-AGGGAAAAACCACGGAACAAAATTCGAATAAAATCCAC
196 TACGTGGAAAGCCCTCCATTAATATAGAGGGAAAAACCACGGAACAAAATTCGAATAAAATCCAC
*
51969 TATTAAATAGACAACTTACAAAGTTCAATATTTCAAACCTTTGCCCC-AGCTAAAAACCATATAA
261 TATCAAATAGACAACTTACAAAGTTCAATATTTCAAACCTTTGCCCCAAGCTAAAAACCATATAA
*
52033 TAACAAATTGCAGAACACAATTACATTCC
326 TAACAAATTGCAGAACACAAGTACATTCC
52062 AATGAAAATC
Statistics
Matches: 975, Mismatches: 60, Indels: 40
0.91 0.06 0.04
Matches are distributed among these distances:
334 1 0.00
335 40 0.04
336 2 0.00
337 81 0.08
338 1 0.00
339 1 0.00
349 22 0.02
350 28 0.03
351 1 0.00
353 332 0.34
354 1 0.00
355 129 0.13
356 8 0.01
358 8 0.01
359 227 0.23
360 92 0.09
361 1 0.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.25
Consensus pattern (354 bp):
TTTGGGCATATAGAGATTTATTCAGATTGTAATGAGATTTCACAAGTACTTACTCAAAAAAAAAA
AAACCTTCAAATTAAGTATGGGAAGTTTCAAAGTTGCCTTAGAGAGTGATAAACTCCAGCAATAA
ATTAATCTCAGCAATAATTTGAGTCATCCACAAGAAAAATCAAAGAATAATGAAGGGACCAGATT
TACGTGGAAAGCCCTCCATTAATATAGAGGGAAAAACCACGGAACAAAATTCGAATAAAATCCAC
TATCAAATAGACAACTTACAAAGTTCAATATTTCAAACCTTTGCCCCAAGCTAAAAACCATATAA
TAACAAATTGCAGAACACAAGTACATTCC
Done.