Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008132.1 Corchorus capsularis cultivar CVL-1 contig08153, 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: 44745
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:3576 original size:13 final size:13
Alignment explanation
Indices: 3558--3585 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3548 TTAAGTTAAT
3558 TCCATTTGTTTAG
1 TCCATTTGTTTAG
3571 TCCATTTGTTTAG
1 TCCATTTGTTTAG
3584 TC
1 TC
3586 TGTTGGTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.18, G:0.14, T:0.54
Consensus pattern (13 bp):
TCCATTTGTTTAG
Found at i:10096 original size:10 final size:10
Alignment explanation
Indices: 10081--10105 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10071 TTATTGCTAA
10081 TTTTTTCTTT
1 TTTTTTCTTT
10091 TTTTTTCTTT
1 TTTTTTCTTT
10101 TTTTT
1 TTTTT
10106 AGGAATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:10689 original size:10 final size:10
Alignment explanation
Indices: 10676--10705 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
10666 AAAATTTTCA
10676 AAAAATTCCC
1 AAAAATTCCC
*
10686 AAAAATTCTC
1 AAAAATTCCC
10696 AAAAATTCCC
1 AAAAATTCCC
10706 TTTTTCCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAAATTCCC
Found at i:10699 original size:20 final size:21
Alignment explanation
Indices: 10666--10705 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
10656 CGGTCGCCGG
*
10666 AAAATTTTCAAAAAATTCCCA
1 AAAATTCTCAAAAAATTCCCA
10687 AAAATTCTC-AAAAATTCCC
1 AAAATTCTCAAAAAATTCCC
10706 TTTTTCCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATTCTCAAAAAATTCCCA
Found at i:11484 original size:12 final size:12
Alignment explanation
Indices: 11467--11516 Score: 68
Period size: 11 Copynumber: 4.3 Consensus size: 12
11457 TTGGTTTCTT
11467 GTTTTTTTTTAC
1 GTTTTTTTTTAC
11479 GTTTTTTTTTAC
1 GTTTTTTTTTAC
11491 -TTTTTTTTTA-
1 GTTTTTTTTTAC
* *
11501 ATTTTTTATTAC
1 GTTTTTTTTTAC
11513 GTTT
1 GTTT
11517 CTGTTTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 19 0.56
12 15 0.44
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (12 bp):
GTTTTTTTTTAC
Found at i:11485 original size:11 final size:11
Alignment explanation
Indices: 11469--11516 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 11
11459 GGTTTCTTGT
11469 TTTTTTTTACG
1 TTTTTTTTACG
*
11480 TTTTTTTTTACT
1 -TTTTTTTTACG
*
11492 TTTTTTTTA-A
1 TTTTTTTTACG
11502 TTTTTTATTACG
1 TTTTTT-TTACG
11514 TTT
1 TTT
11517 CTGTTTCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 6 0.19
11 12 0.39
12 13 0.42
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.77
Consensus pattern (11 bp):
TTTTTTTTACG
Found at i:12378 original size:38 final size:38
Alignment explanation
Indices: 12322--13053 Score: 671
Period size: 38 Copynumber: 19.3 Consensus size: 38
12312 TTTGGTCGAT
* *
12322 TTTGATAACTGC-TGAAAGAGGACCTTTTTCCAGTCAAC
1 TTTGATAACT-CTTGAAAGATGACCTGTTTCCAGTCAAC
* * *
12360 TTTGATAACTCTTAAAAGATGACCTATTTCCAATCAAC
1 TTTGATAACTCTTGAAAGATGACCTGTTTCCAGTCAAC
* * * *
12398 TTTGATAAC-CTCTAAAAGATGACCTATTTCCAGTCGAT
1 TTTGATAACTCT-TGAAAGATGACCTGTTTCCAGTCAAC
* *
12436 TTTGATGACT-TCTGAAAGATGACATGTTTCCAGTCAAC
1 TTTGATAACTCT-TGAAAGATGACCTGTTTCCAGTCAAC
* * * * *
12474 TTCGATGATTGC-TGAGAGATGACCTTTTTCCAGTCAAC
1 TTTGATAACT-CTTGAAAGATGACCTGTTTCCAGTCAAC
* *
12512 TTGGATAACT-TCTGAAAGATGACCTGTTTCTAGTCAAC
1 TTTGATAACTCT-TGAAAGATGACCTGTTTCCAGTCAAC
* *
12550 TTTGATGATTGC-TGAAAGATGACCTGTTTCCAGTCAAC
1 TTTGATAACT-CTTGAAAGATGACCTGTTTCCAGTCAAC
12588 -TTGATAAACT-TCTGAAAGATGACCTGTTTCCAGTCAAC
1 TTTGAT-AACTCT-TGAAAGATGACCTGTTTCCAGTCAAC
* *
12626 TTTGATAATTGC-TGAAA-AGTGACCTGTTTCCAGTCGA-
1 TTTGATAACT-CTTGAAAGA-TGACCTGTTTCCAGTCAAC
* * * *
12663 TTTCGATAACT-TCTAAAAGATGGCATGTTTCCAGTCGA-
1 TTT-GATAACTCT-TGAAAGATGACCTGTTTCCAGTCAAC
* * *
12701 TTTAGATAAC-CTCTAAAAGATGACCTGTTTCCAGTCGAT
1 TTT-GATAACTCT-TGAAAGATGACCTGTTTCCAGTCAAC
* *
12740 TTTGATGACT-TCTGAAAGATTACCTGTTTCCAGTCAAC
1 TTTGATAACTCT-TGAAAGATGACCTGTTTCCAGTCAAC
* * * * *
12778 TTCGATGATTGC-TGAGAGATGACCTTTTTCCAGTCAAC
1 TTTGATAACT-CTTGAAAGATGACCTGTTTCCAGTCAAC
* *
12816 TTGGATAACT-TCTGAAAGATGACCTGTTTCTAGTCAAC
1 TTTGATAACTCT-TGAAAGATGACCTGTTTCCAGTCAAC
* * *
12854 TTTGATGATTGC-TGAAAGATGACATGTTTCCAGTCAAC
1 TTTGATAACT-CTTGAAAGATGACCTGTTTCCAGTCAAC
12892 -TTGATAAACT-TCTGAAAGATGACCTGTTTCCAGTCAAC
1 TTTGAT-AACTCT-TGAAAGATGACCTGTTTCCAGTCAAC
* *
12930 TTTGAAAACTGC-TGAAAGCTGACCTGTTTCCAGTCAAC
1 TTTGATAACT-CTTGAAAGATGACCTGTTTCCAGTCAAC
* * * *
12968 TTTGATGATTGTTGAAAGATAACCTGTTTCCAGTCAAC
1 TTTGATAACTCTTGAAAGATGACCTGTTTCCAGTCAAC
* *
13006 TTCGATAACTGC-TGAAAGCTGACCTGTTTCCAGTCAAC
1 TTTGATAACT-CTTGAAAGATGACCTGTTTCCAGTCAAC
13044 TTTGATAACT
1 TTTGATAACT
13054 TCTTTGAGTT
Statistics
Matches: 579, Mismatches: 78, Indels: 74
0.79 0.11 0.10
Matches are distributed among these distances:
37 17 0.03
38 549 0.95
39 13 0.02
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (38 bp):
TTTGATAACTCTTGAAAGATGACCTGTTTCCAGTCAAC
Found at i:12454 original size:76 final size:76
Alignment explanation
Indices: 12322--13056 Score: 894
Period size: 76 Copynumber: 9.7 Consensus size: 76
12312 TTTGGTCGAT
* * * *
12322 TTTGATAACTGCTGAAAGAGGACCTTTTTCCAGTCAACTTTGATAAC-TCTTAAAAGATGACCTA
1 TTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTC-TGAAAGATGACCTG
*
12386 TTTCCAATCAAC
65 TTTCCAGTCAAC
* * * * * *
12398 TTTGATAACCT-CTAAAAGATGACCTATTTCCAGTCGATTTTGATGACTTCTGAAAGATGACATG
1 TTTGATAA-CTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTCTGAAAGATGACCTG
12462 TTTCCAGTCAAC
65 TTTCCAGTCAAC
* * * * * *
12474 TTCGATGATTGCTGAGAGATGACCTTTTTCCAGTCAACTTGGATAACTTCTGAAAGATGACCTGT
1 TTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTCTGAAAGATGACCTGT
*
12539 TTCTAGTCAAC
66 TTCCAGTCAAC
* *
12550 TTTGATGATTGCTGAAAGATGACCTGTTTCCAGTCAAC-TTGATAAACTTCTGAAAGATGACCTG
1 TTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGAT-AACTTCTGAAAGATGACCTG
12614 TTTCCAGTCAAC
65 TTTCCAGTCAAC
* * * * *
12626 TTTGATAATTGCTGAAA-AGTGACCTGTTTCCAGTCGA-TTTCGATAACTTCTAAAAGATGGCAT
1 TTTGATAACTGCTGAAAGA-TGACCTGTTTCCAGTCAACTTT-GATAACTTCTGAAAGATGACCT
*
12689 GTTTCCAGTCGA-
64 GTTTCCAGTCAAC
* * * * *
12701 TTTAGATAACCT-CTAAAAGATGACCTGTTTCCAGTCGATTTTGATGACTTCTGAAAGATTACCT
1 TTT-GATAA-CTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTCTGAAAGATGACCT
12765 GTTTCCAGTCAAC
64 GTTTCCAGTCAAC
* * * * * *
12778 TTCGATGATTGCTGAGAGATGACCTTTTTCCAGTCAACTTGGATAACTTCTGAAAGATGACCTGT
1 TTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTCTGAAAGATGACCTGT
*
12843 TTCTAGTCAAC
66 TTCCAGTCAAC
* * *
12854 TTTGATGATTGCTGAAAGATGACATGTTTCCAGTCAAC-TTGATAAACTTCTGAAAGATGACCTG
1 TTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGAT-AACTTCTGAAAGATGACCTG
12918 TTTCCAGTCAAC
65 TTTCCAGTCAAC
* * * * *
12930 TTTGAAAACTGCTGAAAGCTGACCTGTTTCCAGTCAACTTTGATGA-TTGTTGAAAGATAACCTG
1 TTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTT-CTGAAAGATGACCTG
12994 TTTCCAGTCAAC
65 TTTCCAGTCAAC
* *
13006 TTCGATAACTGCTGAAAGCTGACCTGTTTCCAGTCAACTTTGATAACTTCT
1 TTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTCT
13057 TTGAGTTTGA
Statistics
Matches: 571, Mismatches: 71, Indels: 34
0.84 0.11 0.05
Matches are distributed among these distances:
75 16 0.03
76 534 0.94
77 21 0.04
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (76 bp):
TTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTCTGAAAGATGACCTGT
TTCCAGTCAAC
Found at i:12519 original size:114 final size:114
Alignment explanation
Indices: 12322--13052 Score: 813
Period size: 114 Copynumber: 6.4 Consensus size: 114
12312 TTTGGTCGAT
* * * * *
12322 TTTGATAACTGCTGAAAGAGGACCTTTTTCCAGTCAACTTTGATAA-CTCTTAAAAGATGACCTA
1 TTTGATAACTTCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACCTC-TGAAAGATGACCTG
* * * * * *
12386 TTTCCAATCAACTTTGATAACCT-CTAAAAGATGACCTATTTCCAGTCGAT
65 TTTCCAGTCAACTTTGATAA-TTGCTGAAAGATGACCTGTTTCCAGTCAAC
* * * * * * *
12436 TTTGATGACTTCTGAAAGATGACATGTTTCCAGTCAACTTCGATGA-TTGCTGAGAGATGACCTT
1 TTTGATAACTTCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACCT-CTGAAAGATGACCTG
* *
12500 TTTCCAGTCAACTTGGATAACTT-CTGAAAGATGACCTGTTTCTAGTCAAC
65 TTTCCAGTCAACTTTGATAA-TTGCTGAAAGATGACCTGTTTCCAGTCAAC
* *
12550 TTTGATGA-TTGCTGAAAGATGACCTGTTTCCAGTCAAC-TTGATAAACTTCTGAAAGATGACCT
1 TTTGATAACTT-CTGAAAGATGACCTGTTTCCAGTCAACTTTGAT-AACCTCTGAAAGATGACCT
*
12613 GTTTCCAGTCAACTTTGATAATTGCTGAAA-AGTGACCTGTTTCCAGTCGA-
64 GTTTCCAGTCAACTTTGATAATTGCTGAAAGA-TGACCTGTTTCCAGTCAAC
* * * * *
12663 TTTCGATAACTTCTAAAAGATGGCATGTTTCCAGTCGA-TTTAGATAACCTCTAAAAGATGACCT
1 TTT-GATAACTTCTGAAAGATGACCTGTTTCCAGTCAACTTT-GATAACCTCTGAAAGATGACCT
* * * *
12727 GTTTCCAGTCGATTTTGATGACTT-CTGAAAGATTACCTGTTTCCAGTCAAC
64 GTTTCCAGTCAACTTTGAT-AATTGCTGAAAGATGACCTGTTTCCAGTCAAC
* * * * * *
12778 TTCGATGA-TTGCTGAGAGATGACCTTTTTCCAGTCAACTTGGATAACTTCTGAAAGATGACCTG
1 TTTGATAACTT-CTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACCTCTGAAAGATGACCTG
* * *
12842 TTTCTAGTCAACTTTGATGATTGCTGAAAGATGACATGTTTCCAGTCAAC
65 TTTCCAGTCAACTTTGATAATTGCTGAAAGATGACCTGTTTCCAGTCAAC
* *
12892 -TTGATAAACTTCTGAAAGATGACCTGTTTCCAGTCAACTTTGA-AAACTGCTGAAAGCTGACCT
1 TTTGAT-AACTTCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACCT-CTGAAAGATGACCT
* * *
12955 GTTTCCAGTCAACTTTGATGATTGTTGAAAGATAACCTGTTTCCAGTCAAC
64 GTTTCCAGTCAACTTTGATAATTGCTGAAAGATGACCTGTTTCCAGTCAAC
* * *
13006 TTCGATAACTGCTGAAAGCTGACCTGTTTCCAGTCAACTTTGATAAC
1 TTTGATAACTTCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAAC
13053 TTCTTTGAGT
Statistics
Matches: 523, Mismatches: 73, Indels: 41
0.82 0.11 0.06
Matches are distributed among these distances:
113 23 0.04
114 476 0.91
115 24 0.05
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (114 bp):
TTTGATAACTTCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACCTCTGAAAGATGACCTGT
TTCCAGTCAACTTTGATAATTGCTGAAAGATGACCTGTTTCCAGTCAAC
Found at i:27064 original size:17 final size:17
Alignment explanation
Indices: 27044--27127 Score: 87
Period size: 19 Copynumber: 4.6 Consensus size: 17
27034 TTTCGTTTTT
27044 TTTTTTTTTTACGTTTC
1 TTTTTTTTTTACGTTTC
* *
27061 TTTTTTTTTTACTTTTTT
1 TTTTTTTTTTAC-GTTTC
27079 TTATTTTTTATTACGTTTC
1 TT-TTTTTT-TTACGTTTC
*
27098 ATTTTTTTTTTCACTTTTC
1 -TTTTTTTTTT-ACGTTTC
27117 TGTTTTTTTTT
1 T-TTTTTTTTT
27128 GTTATACGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
17 12 0.21
18 8 0.14
19 30 0.54
20 6 0.11
ACGTcount: A:0.08, C:0.10, G:0.04, T:0.79
Consensus pattern (17 bp):
TTTTTTTTTTACGTTTC
Found at i:27076 original size:23 final size:23
Alignment explanation
Indices: 27033--27076 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
27023 AAAATTTTTG
*
27033 GTTTCGTTTTTTTTTTTTTTTAC
1 GTTTCGTTTTTTTTTTCTTTTAC
27056 GTTTC-TTTTTTTTTTACTTTT
1 GTTTCGTTTTTTTTTT-CTTTT
27077 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.05, C:0.09, G:0.07, T:0.80
Consensus pattern (23 bp):
GTTTCGTTTTTTTTTTCTTTTAC
Found at i:27080 original size:37 final size:39
Alignment explanation
Indices: 27039--27136 Score: 128
Period size: 37 Copynumber: 2.5 Consensus size: 39
27029 TTTGGTTTCG
27039 TTTTTTTTTTTTTTTACGTTTC-TTTTTTTTTT-ACTTT
1 TTTTTTTTTTTTTTTACGTTTCATTTTTTTTTTCACTTT
* *
27076 TTTTTATTTTTTATTACGTTTCATTTTTTTTTTCACTTT
1 TTTTTTTTTTTTTTTACGTTTCATTTTTTTTTTCACTTT
*
27115 TCTGTTTTTTTTTGTTATACGT
1 T-T-TTTTTTTTT-TTTTACGT
27137 AAGAGAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
37 20 0.39
38 10 0.20
39 6 0.12
40 1 0.02
41 8 0.16
42 6 0.12
ACGTcount: A:0.09, C:0.09, G:0.05, T:0.77
Consensus pattern (39 bp):
TTTTTTTTTTTTTTTACGTTTCATTTTTTTTTTCACTTT
Found at i:28311 original size:13 final size:12
Alignment explanation
Indices: 28288--28330 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
28278 TTAATACAGG
28288 TATCGACGGATA
1 TATCGACGGATA
28300 TATCGAACGGATA
1 TATCG-ACGGATA
*
28313 TATCGATGGATA
1 TATCGACGGATA
28325 TATCGA
1 TATCGA
28331 GGTATCGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 17 0.59
13 12 0.41
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:29787 original size:10 final size:10
Alignment explanation
Indices: 29775--29810 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
29765 AATTTAATAT
*
29775 GGATATTTAT
1 GGATATTTAC
29785 GGATATTTAC
1 GGATATTTAC
29795 GGATATTTAC
1 GGATATTTAC
29805 GGATAT
1 GGATAT
29811 ATCGAGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (10 bp):
GGATATTTAC
Found at i:31633 original size:16 final size:16
Alignment explanation
Indices: 31611--31658 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
31601 AATAATAACT
31611 ATAACCCGAAACCGAC
1 ATAACCCGAAACCGAC
* * *
31627 TTAACCCG-AATCGAG
1 ATAACCCGAAACCGAC
31642 ATAACCCGAAACCGAC
1 ATAACCCGAAACCGAC
31658 A
1 A
31659 AAATCCGATA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.42, C:0.33, G:0.15, T:0.10
Consensus pattern (16 bp):
ATAACCCGAAACCGAC
Found at i:35012 original size:33 final size:31
Alignment explanation
Indices: 34924--35012 Score: 74
Period size: 33 Copynumber: 2.8 Consensus size: 31
34914 ATATATATAG
* **
34924 TGACCCGAATCCGATCT-TATCCGATTTGAAA
1 TGACCCGAACCCGAT-TATATCCGATAAGAAA
* * *
34955 TAACCCGAAACCCG-TTAAACCCGATAAGCATAA
1 TGACCCG-AACCCGATTATATCCGATAAG-A-AA
34988 TGACCCGAACCCGATTATATCCGAT
1 TGACCCGAACCCGATTATATCCGAT
35013 CTGATAAGAC
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
30 1 0.02
31 14 0.32
32 12 0.27
33 17 0.39
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (31 bp):
TGACCCGAACCCGATTATATCCGATAAGAAA
Found at i:36498 original size:30 final size:30
Alignment explanation
Indices: 36472--36542 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
36462 CGTTTGGATG
*
36472 TTTTGCCACCCTGAACT-TCAATTTTGGACA
1 TTTTGCC-CCCTGAACTCCCAATTTTGGACA
*
36502 TTTTGCCCCATGAACTCCCAATTTTGGACA
1 TTTTGCCCCCTGAACTCCCAATTTTGGACA
36532 TTTTGCCCCCT
1 TTTTGCCCCCT
36543 CTCAAAAGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 8 0.22
30 29 0.78
ACGTcount: A:0.20, C:0.31, G:0.13, T:0.37
Consensus pattern (30 bp):
TTTTGCCCCCTGAACTCCCAATTTTGGACA
Found at i:36900 original size:25 final size:24
Alignment explanation
Indices: 36872--36954 Score: 75
Period size: 25 Copynumber: 3.5 Consensus size: 24
36862 TTTTATTCAA
36872 AATAAATAACTGCCTTTTCCTAATT
1 AATAAATAACT-CCTTTTCCTAATT
* **
36897 AATAGATAACTCACCATT-C-AA--
1 AATAAATAACTC-CTTTTCCTAATT
36918 AATAAATAACTTCCTTTTCCTAATT
1 AATAAATAAC-TCCTTTTCCTAATT
*
36943 AATAGATAACTC
1 AATAAATAACTC
36955 ACCAAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 13
0.69 0.11 0.20
Matches are distributed among these distances:
21 12 0.27
22 3 0.07
23 4 0.09
24 4 0.09
25 22 0.49
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (24 bp):
AATAAATAACTCCTTTTCCTAATT
Found at i:36934 original size:46 final size:46
Alignment explanation
Indices: 36866--36958 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
36856 GAAGTTTTTT
36866 ATTCAAAATAAATAACTGCCTTTTCCTAATTAATAGATAACTCACC
1 ATTCAAAATAAATAACTGCCTTTTCCTAATTAATAGATAACTCACC
*
36912 ATTCAAAATAAATAACTTCCTTTTCCTAATTAATAGATAACTCACC
1 ATTCAAAATAAATAACTGCCTTTTCCTAATTAATAGATAACTCACC
36958 A
1 A
36959 AAAAATATCT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.42, C:0.22, G:0.03, T:0.33
Consensus pattern (46 bp):
ATTCAAAATAAATAACTGCCTTTTCCTAATTAATAGATAACTCACC
Found at i:41581 original size:25 final size:25
Alignment explanation
Indices: 41553--41634 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
41543 CTTTATTCAA
41553 AATAAATAACTTCCTTTTCCTAATT
1 AATAAATAACTTCCTTTTCCTAATT
* **
41578 AATAGATAAC-TCACCATT-C-AA--
1 AATAAATAACTTC-CTTTTCCTAATT
41599 AATAAATAACTTCCTTTTCCTAATT
1 AATAAATAACTTCCTTTTCCTAATT
*
41624 AATAGATAACT
1 AATAAATAACT
41635 CACCAAAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
21 12 0.27
22 3 0.07
23 4 0.09
24 3 0.07
25 22 0.50
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.37
Consensus pattern (25 bp):
AATAAATAACTTCCTTTTCCTAATT
Found at i:41614 original size:46 final size:46
Alignment explanation
Indices: 41547--41639 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
41537 GAAGTTCTTT
41547 ATTCAAAATAAATAACTTCCTTTTCCTAATTAATAGATAACTCACC
1 ATTCAAAATAAATAACTTCCTTTTCCTAATTAATAGATAACTCACC
41593 ATTCAAAATAAATAACTTCCTTTTCCTAATTAATAGATAACTCACC
1 ATTCAAAATAAATAACTTCCTTTTCCTAATTAATAGATAACTCACC
41639 A
1 A
41640 AAAAATACCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.42, C:0.22, G:0.02, T:0.34
Consensus pattern (46 bp):
ATTCAAAATAAATAACTTCCTTTTCCTAATTAATAGATAACTCACC
Done.