Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010967.1 Corchorus capsularis cultivar CVL-1 contig10988, 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: 68229
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:57 original size:32 final size:32
Alignment explanation
Indices: 1--133 Score: 126
Period size: 32 Copynumber: 4.1 Consensus size: 32
* * *
1 GCCCCATTGGGGCGGC-CTGCCCATGGTGAAG-C
1 GCCCCAGTGGGGCGGCTCCG-CCACGGT-AAGCC
* * * *
33 GCCCTAATGGGGCGGCTCCGCCATGGTTGAGCC
1 GCCCCAGTGGGGCGGCTCCGCCACGG-TAAGCC
* *
66 TCCCCAGTGGGGCGGCTTCGCCACGGTAAGCC
1 GCCCCAGTGGGGCGGCTCCGCCACGGTAAGCC
* *
98 TCCCCAGTGGGGCGGCTTCGCCACGGTAAGCC
1 GCCCCAGTGGGGCGGCTCCGCCACGGTAAGCC
130 GCCC
1 GCCC
134 TCTTGGGACG
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
32 62 0.71
33 25 0.29
ACGTcount: A:0.12, C:0.37, G:0.35, T:0.16
Consensus pattern (32 bp):
GCCCCAGTGGGGCGGCTCCGCCACGGTAAGCC
Found at i:80 original size:33 final size:32
Alignment explanation
Indices: 40--129 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
30 AGCGCCCTAA
* * *
40 TGGGGCGGCTCCGCCATGGTTGAGCCTCCCCAG
1 TGGGGCGGCTTCGCCACGG-TAAGCCTCCCCAG
73 TGGGGCGGCTTCGCCACGGTAAGCCTCCCCAG
1 TGGGGCGGCTTCGCCACGGTAAGCCTCCCCAG
105 TGGGGCGGCTTCGCCACGGTAAGCC
1 TGGGGCGGCTTCGCCACGGTAAGCC
130 GCCCTCTTGG
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 37 0.69
33 17 0.31
ACGTcount: A:0.11, C:0.36, G:0.37, T:0.17
Consensus pattern (32 bp):
TGGGGCGGCTTCGCCACGGTAAGCCTCCCCAG
Found at i:1506 original size:21 final size:22
Alignment explanation
Indices: 1470--1510 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1460 TTTAAATTTG
*
1470 CTGTCAGAATTATGTTTAATGA
1 CTGTCAGAACTATGTTTAATGA
1492 CTGTCAG-ACTATGTTTAAT
1 CTGTCAGAACTATGTTTAAT
1511 TACTACTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.41
Consensus pattern (22 bp):
CTGTCAGAACTATGTTTAATGA
Found at i:5076 original size:33 final size:33
Alignment explanation
Indices: 5027--5116 Score: 87
Period size: 33 Copynumber: 2.7 Consensus size: 33
5017 CGCGCAACAC
5027 CGGCCACAAGACCGGCCACGCGACAT-GGACATG-T
1 CGGCCAC-A-ACCGGCCACGCGAC-TCGGACATGCT
** *
5061 CCGGCCATC-ACCGGCCAAACGACTCGGCCATGCT
1 -CGGCCA-CAACCGGCCACGCGACTCGGACATGCT
5095 CGGCCACAACCGGCCACGCGAC
1 CGGCCACAACCGGCCACGCGAC
5117 CCTTTGTCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
32 2 0.04
33 36 0.78
34 1 0.02
35 6 0.13
36 1 0.02
ACGTcount: A:0.23, C:0.42, G:0.27, T:0.08
Consensus pattern (33 bp):
CGGCCACAACCGGCCACGCGACTCGGACATGCT
Found at i:8714 original size:36 final size:34
Alignment explanation
Indices: 8665--8783 Score: 129
Period size: 36 Copynumber: 3.4 Consensus size: 34
8655 TCTTTTCTAG
8665 ATTAAGCTCTTTATTGACTTCACTTAATTACCTTGA
1 ATTAAGCTCTTTATTGAC-TCACTTAATTACC-TGA
* *
8701 ATTAAGTTATTTATT--CT-ACTTAATTATCCTGA
1 ATTAAGCTCTTTATTGACTCACTTAATTA-CCTGA
8733 ATTAAGC-CTTTTATTGACCTCACTTAATTACACTGA
1 ATTAAGCTC-TTTATTGA-CTCACTTAATTAC-CTGA
*
8769 ATTAAGTTCTTTATT
1 ATTAAGCTCTTTATT
8784 TTACTTAATT
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
32 24 0.34
33 3 0.04
34 1 0.01
35 3 0.04
36 38 0.54
37 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (34 bp):
ATTAAGCTCTTTATTGACTCACTTAATTACCTGA
Found at i:8722 original size:32 final size:30
Alignment explanation
Indices: 8686--8793 Score: 108
Period size: 32 Copynumber: 3.3 Consensus size: 30
8676 TATTGACTTC
8686 ACTTAATTACCTTGAATTAAGTTATTTATTCT
1 ACTTAATTACC-TGAATTAAGTT-TTTATTCT
*
8718 ACTTAATTATCCTGAATTAAGCCTTTTATTGACCT
1 ACTTAATTA-CCTGAATTAAG-TTTTTATT---CT
*
8753 CACTTAATTACACTGAATTAAGTTCTTTATTTT
1 -ACTTAATTAC-CTGAATTAAGTT-TTTATTCT
8786 ACTTAATT
1 ACTTAATT
8794 TCCTTGCTTG
Statistics
Matches: 65, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
32 32 0.49
33 4 0.06
35 4 0.06
36 25 0.38
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (30 bp):
ACTTAATTACCTGAATTAAGTTTTTATTCT
Found at i:8750 original size:68 final size:67
Alignment explanation
Indices: 8665--8797 Score: 198
Period size: 68 Copynumber: 2.0 Consensus size: 67
8655 TCTTTTCTAG
*
8665 ATTAAGCTCTTTATTGACTTCACTTAATTAC-CTTGAATTAAGTTATTTATTCTACTTAATTATC
1 ATTAAGCTCTTTATTGACCTCACTTAATTACAC-TGAATTAAGTTATTTATTCTACTTAATT-TC
8729 CTGA
64 CTGA
* *
8733 ATTAAGC-CTTTTATTGACCTCACTTAATTACACTGAATTAAGTTCTTTATTTTACTTAATTTCC
1 ATTAAGCTC-TTTATTGACCTCACTTAATTACACTGAATTAAGTTATTTATTCTACTTAATTTCC
8797 T
65 T
8798 TGCTTGAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
67 5 0.08
68 54 0.90
69 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (67 bp):
ATTAAGCTCTTTATTGACCTCACTTAATTACACTGAATTAAGTTATTTATTCTACTTAATTTCCT
GA
Found at i:8933 original size:107 final size:106
Alignment explanation
Indices: 8822--9178 Score: 450
Period size: 107 Copynumber: 3.3 Consensus size: 106
8812 CCTGTGTCTT
* * * * * *
8822 TTTACTTAATTTCCTTGAAATTAAACCAGTCTTTTCTTTACCTAGTTTCCTCGAAACTAAGCCAG
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTT-TTTACTTAATTTCCTTGAAATTAAGCCAG
* * * *
8887 TCTTTTCTTTACTTAATTTCCTTGGAATTAA-GCTAGTCTATC
65 TCTTTTCTTTACCTAATTTCCTTGAAACTAAGGC-AGTCTTTC
* *
8929 TTTACCTAATTTTCTTGAAATTAAGCCAGTCTTTTATTTAGTTAATTTCCTTGAAATTAAGCCAG
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTT-TTTACTTAATTTCCTTGAAATTAAGCCAG
* *
8994 TCTTTTCTTTACCTAGTTTCTTTGAAACTAAGGCAGTCTTTC
65 TCTTTTCTTTACCTAATTTCCTTGAAACTAAGGCAGTCTTTC
* * *
9036 TTTACCTAGTTTCCTTGAAATTAAGCCAGTCTTTTTTTACTTAATTTCCTTGAAATTAAACTAGT
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTTTTACTTAATTTCCTTGAAATTAAGCCAGT
*
9101 C-TTT-TTTACCTAGTTTCCTTGAAACTAAGGCAGTCTTTTC
66 CTTTTCTTTACCTAATTTCCTTGAAACTAAGGCAGTC-TTTC
* *
9141 TTTCTTACTTAATTTTCTTGAAATTAAGCCAGTCTTTT
1 --T-TTACCTAATTTCCTTGAAATTAAGCCAGTCTTTT
9179 ATCAGTATAA
Statistics
Matches: 221, Mismatches: 24, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
104 30 0.14
105 7 0.03
106 28 0.13
107 123 0.56
108 33 0.15
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (106 bp):
TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTTTTACTTAATTTCCTTGAAATTAAGCCAGT
CTTTTCTTTACCTAATTTCCTTGAAACTAAGGCAGTCTTTC
Found at i:8939 original size:35 final size:36
Alignment explanation
Indices: 8800--9178 Score: 428
Period size: 36 Copynumber: 10.6 Consensus size: 36
8790 AATTTCCTTG
* * * *
8800 CTTGAAATTAAGCCTGTGTCTT-TTTACTTAATTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* *
8835 CTTGAAATTAAACCAGTCTTTTCTTTACCTAGTTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* * *
8871 CTCGAAACTAAGCCAGTCTTTTCTTTACTTAATTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* * * *
8907 CTTGGAATTAAGCTAGTC-TATCTTTACCTAATTTT
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* **
8942 CTTGAAATTAAGCCAGTCTTTTATTTAGTTAATTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
*
8978 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* * * *
9014 TTTGAAACTAAGGCAGTC-TTTCTTTACCTAGTTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
*
9049 CTTGAAATTAAGCCAGTCTTTT-TTTACTTAATTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* * *
9084 CTTGAAATTAAACTAGTC-TTT-TTTACCTAGTTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* * * *
9118 CTTGAAACTAAGGCAGTCTTTTCTTTCTTACTTAATTTT
1 CTTGAAATTAAGCCAGTCTTTTC--T-TTACCTAATTTC
9157 CTTGAAATTAAGCCAGTCTTTT
1 CTTGAAATTAAGCCAGTCTTTT
9179 ATCAGTATAA
Statistics
Matches: 286, Mismatches: 50, Indels: 12
0.82 0.14 0.03
Matches are distributed among these distances:
34 28 0.10
35 110 0.38
36 118 0.41
38 1 0.00
39 29 0.10
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.46
Consensus pattern (36 bp):
CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
Found at i:8974 original size:71 final size:71
Alignment explanation
Indices: 8800--9178 Score: 433
Period size: 71 Copynumber: 5.3 Consensus size: 71
8790 AATTTCCTTG
* * * *
8800 CTTGAAATTAAGCCTGTGTCTTTTTACTTAATTTCCTTGAAATTAAACCAGTCTTTTCTTTACCT
1 CTTGAAATTAAGCCAGTCTTTTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCT
* *
8865 AGTTTC
66 AATTTT
* * * * *
8871 CTCGAAACTAAGCCAGTCTTTTCTTTACTTAATTTCCTTGGAATTAAGCTAGTC-TATCTTTACC
1 CTTGAAATTAAGCCAGTCTTTT-TTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACC
8935 TAATTTT
65 TAATTTT
*
8942 CTTGAAATTAAGCCAGTCTTTTATTTAGTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACC
1 CTTGAAATTAAGCCAGTCTTTT-TTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACC
*
9007 T-AGTTT
65 TAATTTT
* * * * * *
9013 CTTTGAAACTAAGGCAGTCTTTCTTTACCTAGTTTCCTTGAAATTAAGCCAGTCTTTT-TTTACT
1 C-TTGAAATTAAGCCAGTCTTTTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACC
*
9077 TAATTTC
65 TAATTTT
* * * * * *
9084 CTTGAAATTAAACTAGTC-TTTTTTACCTAGTTTCCTTGAAACTAAGGCAGTCTTTTCTTTCTTA
1 CTTGAAATTAAGCCAGTCTTTTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTC--T-TTA
*
9148 CTTAATTTT
63 CCTAATTTT
9157 CTTGAAATTAAGCCAGTCTTTT
1 CTTGAAATTAAGCCAGTCTTTT
9179 ATCAGTATAA
Statistics
Matches: 261, Mismatches: 38, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
69 35 0.13
70 19 0.07
71 120 0.46
72 57 0.22
73 27 0.10
74 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.46
Consensus pattern (71 bp):
CTTGAAATTAAGCCAGTCTTTTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCT
AATTTT
Found at i:9184 original size:11 final size:10
Alignment explanation
Indices: 9170--9409 Score: 54
Period size: 11 Copynumber: 21.7 Consensus size: 10
9160 GAAATTAAGC
9170 CAGTCTTTTAT
1 CAGTCTTTT-T
* *
9181 CAGTATAATTT
1 CAGTCT-TTTT
9192 CAGTCTTCTTT
1 CAGTCTT-TTT
*
9203 CAGTCTGATTT
1 CAGTCT-TTTT
*
9214 CAGT-TTAATAT
1 CAGTCTT--TTT
9225 CAGTCTTTTTT
1 CAGTC-TTTTT
*
9236 CAGTCTATTGT
1 CAGTCT-TTTT
* *
9247 CAGTGTAATTT
1 CAGTCT-TTTT
*
9258 CAGTATTCTTT
1 CAGTCTT-TTT
*
9269 CAGTCTGATTT
1 CAGTCT-TTTT
*
9280 CAGT-TTAATAT
1 CAGTCTT--TTT
*
9291 CAGTCTTATAT
1 CAGTCTT-TTT
* *
9302 CATTCTAATTT
1 CAGTCT-TTTT
* *
9313 CAGTCTAATAT
1 CAGTCT-TTTT
9324 CAGTCTTTTTTT
1 CAGTC--TTTTT
9336 CAGT-TTAATTT
1 CAGTCTT--TTT
*
9347 CAGTCTTCTAT
1 CAGTCTT-TTT
*
9358 CAGTCTAATTT
1 CAGTCT-TTTT
*
9369 CAGTCTTCTAT
1 CAGTCTT-TTT
*
9380 CAGTCTAATTT
1 CAGTCT-TTTT
9391 CAGTCTAATTTT
1 CAGTCT--TTTT
9403 CAGTCTT
1 CAGTCTT
9410 CTTTTCAATC
Statistics
Matches: 172, Mismatches: 34, Indels: 47
0.68 0.13 0.19
Matches are distributed among these distances:
9 2 0.01
10 4 0.02
11 141 0.82
12 22 0.13
13 3 0.02
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.49
Consensus pattern (10 bp):
CAGTCTTTTT
Found at i:9195 original size:22 final size:22
Alignment explanation
Indices: 9170--9396 Score: 185
Period size: 22 Copynumber: 10.3 Consensus size: 22
9160 GAAATTAAGC
*
9170 CAGTCTTTTATCAGTATAATTT
1 CAGTCTTTTATCAGTCTAATTT
*
9192 CAGTCTTCTT-TCAGTCTGATTT
1 CAGTCTT-TTATCAGTCTAATTT
* **
9214 CAGT-TTAATATCAGTCTTTTTT
1 CAGTCTT-TTATCAGTCTAATTT
* * *
9236 CAGTCTATTGTCAGTGTAATTT
1 CAGTCTTTTATCAGTCTAATTT
* *
9258 CAGTATTCTT-TCAGTCTGATTT
1 CAGTCTT-TTATCAGTCTAATTT
* * *
9280 CAGT-TTAATATCAGTCTTATAT
1 CAGTCTT-TTATCAGTCTAATTT
* * *
9302 CATTCTAATT-TCAGTCTAATAT
1 CAGTCT-TTTATCAGTCTAATTT
* *
9324 CAGTCTTTTTTTCAGTTTAATTT
1 CAGTC-TTTTATCAGTCTAATTT
*
9347 CAGTCTTCTATCAGTCTAATTT
1 CAGTCTTTTATCAGTCTAATTT
*
9369 CAGTCTTCTATCAGTCTAATTT
1 CAGTCTTTTATCAGTCTAATTT
9391 CAGTCT
1 CAGTCT
9397 AATTTTCAGT
Statistics
Matches: 165, Mismatches: 31, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
21 6 0.04
22 136 0.82
23 23 0.14
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.49
Consensus pattern (22 bp):
CAGTCTTTTATCAGTCTAATTT
Found at i:9208 original size:33 final size:32
Alignment explanation
Indices: 9178--9408 Score: 88
Period size: 33 Copynumber: 6.9 Consensus size: 32
9168 GCCAGTCTTT
* * * *
9178 TATCAGTATAATTTCAGTCTTCTTTCAGTCTGA
1 TATCAGTCTTATTTCAGTC-TATTTCAGTCTAA
* * * *
9211 TTTCAGT-TTAATATCAGTCTTTTTTCAGTCTAT
1 TATCAGTCTT-ATTTCAGTC-TATTTCAGTCTAA
* * * * * *
9244 TGTCAGTGTAATTTCAGTATTCTTTCAGTCTGA
1 TATCAGTCTTATTTCAGT-CTATTTCAGTCTAA
* * * *
9277 TTTCAGT-TTAATATCAGTCTTATATCATTCTAA
1 TATCAGTCTT-ATTTCAGTC-TATTTCAGTCTAA
* * * * *
9310 TTTCAGTCTAATATCAGTCTTTTTTTCAGTTTAA
1 TATCAGTCTTATTTCAGTC--TATTTCAGTCTAA
* * * **
9344 TTTCAGTCTTCTATCAGTCTAATTTCAGTCTTC
1 TATCAGTCTTATTTCAGTCT-ATTTCAGTCTAA
*
9377 TATCAGTCTAATTTCAGTCTAATTTTCAGTCT
1 TATCAGTCTTATTTCAGTCT-A-TTTCAGTCT
9409 TCTTTTCAAT
Statistics
Matches: 153, Mismatches: 36, Indels: 17
0.74 0.17 0.08
Matches are distributed among these distances:
32 3 0.02
33 112 0.73
34 38 0.25
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.49
Consensus pattern (32 bp):
TATCAGTCTTATTTCAGTCTATTTCAGTCTAA
Found at i:9351 original size:56 final size:55
Alignment explanation
Indices: 9235--9408 Score: 127
Period size: 56 Copynumber: 3.1 Consensus size: 55
9225 CAGTCTTTTT
* * * * * *
9235 TCAGTCT-ATTGTCAGTGTAATTTCAGTATTCTTTCAGTCTGATTTCAGTTTAATA
1 TCAGTCTAATT-TCAGTTTAATTTCAGTCTTATATCAGTCTAATTTCAGTCTAATA
* * * ** * *
9290 TCAGTCTTATATCA-TTCTAATTTCAGTCTAATATCAGTCTTTTTTTCAGTTTAATT
1 TCAGTCTAATTTCAGTT-TAATTTCAGTCTTATATCAGTC-TAATTTCAGTCTAATA
** * * * *
9346 TCAGTCTTCTATCAGTCTAATTTCAGTCTTCTATCAGTCTAATTTCAGTCTAATTT
1 TCAGTCTAATTTCAGTTTAATTTCAGTCTTATATCAGTCTAATTTCAGTCTAA-TA
9402 TCAGTCT
1 TCAGTCT
9409 TCTTTTCAAT
Statistics
Matches: 98, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
54 1 0.01
55 39 0.40
56 57 0.58
57 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.48
Consensus pattern (55 bp):
TCAGTCTAATTTCAGTTTAATTTCAGTCTTATATCAGTCTAATTTCAGTCTAATA
Found at i:13560 original size:23 final size:23
Alignment explanation
Indices: 13508--13568 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
13498 TGATCCACTA
* *
13508 GGAAAGTCTACCCTGAGATGCTT
1 GGAAAGTCTGCCCTGAGACGCTT
* *
13531 -GAAAGTCTGCCCTGCGACGTTT
1 GGAAAGTCTGCCCTGAGACGCTT
13553 GGAAAGTCTGCCCTGA
1 GGAAAGTCTGCCCTGA
13569 TCACTCTGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (23 bp):
GGAAAGTCTGCCCTGAGACGCTT
Found at i:17982 original size:36 final size:35
Alignment explanation
Indices: 17942--18051 Score: 115
Period size: 36 Copynumber: 3.2 Consensus size: 35
17932 GATTAAGCCA
17942 TTTATTGACTTCACTTAATTACCTTGAATTAAGTTC
1 TTTATTGAC-TCACTTAATTACCTTGAATTAAGTTC
*
17978 TTTATT--CT-ACTTAATTA-CTCTGAATTAAG-CC
1 TTTATTGACTCACTTAATTACCT-TGAATTAAGTTC
*
18009 TTTTATTGAGCTCACTTGATTACAC-TGAATTAAGTTC
1 -TTTATTGA-CTCACTTAATTAC-CTTGAATTAAGTTC
18046 TTTATT
1 TTTATT
18052 TTACTTAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 18
0.75 0.04 0.22
Matches are distributed among these distances:
31 3 0.05
32 24 0.39
33 1 0.02
34 1 0.02
35 2 0.03
36 29 0.47
37 1 0.02
38 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.47
Consensus pattern (35 bp):
TTTATTGACTCACTTAATTACCTTGAATTAAGTTC
Found at i:17995 original size:32 final size:32
Alignment explanation
Indices: 17954--18067 Score: 108
Period size: 32 Copynumber: 3.4 Consensus size: 32
17944 TATTGACTTC
17954 ACTTAATTACCTTGAATTAAGTTCTTTATTCT
1 ACTTAATTACCTTGAATTAAGTTCTTTATTCT
*
17986 ACTTAATTA-CTCTGAATTAAG-CCTTTTATTGAGCT
1 ACTTAATTACCT-TGAATTAAGTTC-TTTATT---CT
* *
18021 CACTTGATTACAC-TGAATTAAGTTCTTTATTTT
1 -ACTTAATTAC-CTTGAATTAAGTTCTTTATTCT
*
18054 ACTTAATTTCCTTG
1 ACTTAATTACCTTG
18068 CTTGAAATTA
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
31 4 0.06
32 34 0.52
33 1 0.02
35 2 0.03
36 23 0.35
37 1 0.02
38 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.09, T:0.47
Consensus pattern (32 bp):
ACTTAATTACCTTGAATTAAGTTCTTTATTCT
Found at i:18014 original size:68 final size:68
Alignment explanation
Indices: 17933--18061 Score: 199
Period size: 68 Copynumber: 1.9 Consensus size: 68
17923 TCTTTTCTAG
17933 ATTAAGCCATTTATTGA-CTTCACTTAATTAC-CTTGAATTAAGTTCTTTATTCTACTTAATTAC
1 ATTAAGCCATTTATTGAGC-TCACTTAATTACAC-TGAATTAAGTTCTTTATTCTACTTAATTAC
17996 TCTGA
64 TCTGA
* * *
18001 ATTAAGCCTTTTATTGAGCTCACTTGATTACACTGAATTAAGTTCTTTATTTTACTTAATT
1 ATTAAGCCATTTATTGAGCTCACTTAATTACACTGAATTAAGTTCTTTATTCTACTTAATT
18062 TCCTTGCTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
68 54 0.96
69 2 0.04
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.47
Consensus pattern (68 bp):
ATTAAGCCATTTATTGAGCTCACTTAATTACACTGAATTAAGTTCTTTATTCTACTTAATTACTC
TGA
Found at i:18139 original size:36 final size:36
Alignment explanation
Indices: 18068--18446 Score: 448
Period size: 36 Copynumber: 10.6 Consensus size: 36
18058 AATTTCCTTG
* * *
18068 CTTGAAATTAAGCCTG-CGTCTT-TTTACTTAATTTC
1 CTTGAAATTAAGCCAGTC-TTTTCTTTACCTAATTTC
* *
18103 CTTGAAATTAAGTCAGTCTTTTCTTTACCTAGTTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* * * *
18139 CTCGAAACTAAGCTAGTCTTTTCTTTACTTAATTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* *
18175 CTTGGAATTAAGCCAGTC-TATCTTTACCTAATTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
**
18210 CTTGAAATTAAGCCAGTCTTTTCTTTAGTTAATTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* *
18246 CTTGAATTTAAGCCAGTCTTTTCTTTACCTAGTTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* * *
18282 TTTGAAACTAAGCCAGT-TTTTCTTTACCTAGTTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
*
18317 CTTGAAATTAAGCCAGTCTTTT-TTTACTTAATTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* *
18352 CTTGAAATTAAACCAGTC--TTCTTTACCTAGTTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* * * *
18386 CTTGAAACTAAGCCAGCCTTTTCTTTCTTACTTAATTTT
1 CTTGAAATTAAGCCAGTCTTTTC--T-TTACCTAATTTC
18425 CTTGAAATTAAGCCAGTCTTTT
1 CTTGAAATTAAGCCAGTCTTTT
18447 ATCAGTATAA
Statistics
Matches: 291, Mismatches: 43, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
33 2 0.01
34 26 0.09
35 110 0.38
36 123 0.42
38 1 0.00
39 29 0.10
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (36 bp):
CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
Found at i:18201 original size:107 final size:107
Alignment explanation
Indices: 18090--18446 Score: 459
Period size: 107 Copynumber: 3.3 Consensus size: 107
18080 CCTGCGTCTT
* * * * * * *
18090 TTTACTTAATTTCCTTGAAATTAAGTCAGTCTTTTCTTTACCTAGTTTCCTCGAAACTAAGCTAG
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACTTAATTTCCTTGAAATTAAGCCAG
* * * *
18155 TCTTTTCTTTACTTAATTTCCTTGGAATTAAGCCAGTCTATC
66 TCTTTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTC
* *
18197 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTAGTTAATTTCCTTGAATTTAAGCCAG
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACTTAATTTCCTTGAAATTAAGCCAG
* * *
18262 TCTTTTCTTTACCTAGTTTCTTTGAAACTAAGCCAGTTTTTC
66 TCTTTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTC
* *
18304 TTTACCTAGTTTCCTTGAAATTAAGCCAGTCTTTT-TTTACTTAATTTCCTTGAAATTAAACCAG
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACTTAATTTCCTTGAAATTAAGCCAG
* *
18368 TC--TTCTTTACCTAGTTTCCTTGAAACTAAGCCAGCCTTTTC
66 TCTTTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTC-TTTC
* *
18409 TTTCTTACTTAATTTTCTTGAAATTAAGCCAGTCTTTT
1 --T-TTACCTAATTTCCTTGAAATTAAGCCAGTCTTTT
18447 ATCAGTATAA
Statistics
Matches: 220, Mismatches: 26, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
104 31 0.14
105 4 0.02
106 28 0.13
107 126 0.57
108 31 0.14
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (107 bp):
TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACTTAATTTCCTTGAAATTAAGCCAG
TCTTTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTC
Found at i:18525 original size:12 final size:11
Alignment explanation
Indices: 18438--18709 Score: 159
Period size: 11 Copynumber: 24.5 Consensus size: 11
18428 GAAATTAAGC
18438 CAGTCT-TTTAT
1 CAGTCTATTT-T
* *
18449 CAGTATAATTT
1 CAGTCTATTTT
18460 CAGTCT-TCTTT
1 CAGTCTAT-TTT
18471 CAGTCTGA-TTT
1 CAGTCT-ATTTT
* * *
18482 CAGTTTAATAT
1 CAGTCTATTTT
*
18493 CAGTCTTTTTT
1 CAGTCTATTTT
18504 CAGTCTATTTT
1 CAGTCTATTTT
* *
18515 CATTCTAATTT
1 CAGTCTATTTT
*
18526 CAGTAT-TCTTT
1 CAGTCTAT-TTT
18537 CAGTCTGA-TTT
1 CAGTCT-ATTTT
* *
18548 CAGTCTAATAT
1 CAGTCTATTTT
*
18559 CAGTCT-TATAT
1 CAGTCTAT-TTT
*
18570 CAGTCTAATTT
1 CAGTCTATTTT
* *
18581 CAGTCTAATAT
1 CAGTCTATTTT
*
18592 CAGTCTTTTTTT
1 CAGTC-TATTTT
* *
18604 AAGTCTAATTT
1 CAGTCTATTTT
18615 CAGTCTAATTTT
1 CAGTCT-ATTTT
*
18627 -AGTCT-TCTAT
1 CAGTCTAT-TTT
*
18637 CAGTCTAATTT
1 CAGTCTATTTT
18648 CAGTCT-TCTTT
1 CAGTCTAT-TTT
*
18659 CAGTCTAATTT
1 CAGTCTATTTT
*
18670 CAGTCT-TCTAT
1 CAGTCTAT-TTT
*
18681 CAGTCTAATTT
1 CAGTCTATTTT
18692 CAGTCTAATTTT
1 CAGTCT-ATTTT
18704 CAGTCT
1 CAGTCT
18710 TCTTTTCAAT
Statistics
Matches: 200, Mismatches: 40, Indels: 41
0.71 0.14 0.15
Matches are distributed among these distances:
9 1 0.00
10 4 0.02
11 172 0.86
12 23 0.12
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (11 bp):
CAGTCTATTTT
Found at i:18702 original size:33 final size:33
Alignment explanation
Indices: 18448--18697 Score: 275
Period size: 33 Copynumber: 7.5 Consensus size: 33
18438 CAGTCTTTTA
* *
18448 TCAGTATAATTTCAGTCTTCTTTCAGTCTGATT
1 TCAGTCTAATTTCAGTCTTCTTTCAGTCTAATT
* * * *
18481 TCAGTTTAATATCAGTCTTTTTTCAGTCTATTT
1 TCAGTCTAATTTCAGTCTTCTTTCAGTCTAATT
* * *
18514 TCATTCTAATTTCAGTATTCTTTCAGTCTGATT
1 TCAGTCTAATTTCAGTCTTCTTTCAGTCTAATT
* * *
18547 TCAGTCTAATATCAGTCTTATATCAGTCTAATT
1 TCAGTCTAATTTCAGTCTTCTTTCAGTCTAATT
* * *
18580 TCAGTCTAATATCAGTCTTTTTTTAAGTCTAATT
1 TCAGTCTAATTTCAGTC-TTCTTTCAGTCTAATT
* *
18614 TCAGTCTAATTTTAGTCTTCTATCAGTCTAATT
1 TCAGTCTAATTTCAGTCTTCTTTCAGTCTAATT
** ** ** *
18647 TCAGTCTTCTTTCAGTCTAATTTCAGTCTTCTA
1 TCAGTCTAATTTCAGTCTTCTTTCAGTCTAATT
18680 TCAGTCTAATTTCAGTCT
1 TCAGTCTAATTTCAGTCT
18698 AATTTTCAGT
Statistics
Matches: 179, Mismatches: 37, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
33 151 0.84
34 28 0.16
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (33 bp):
TCAGTCTAATTTCAGTCTTCTTTCAGTCTAATT
Found at i:18715 original size:12 final size:12
Alignment explanation
Indices: 18645--18726 Score: 64
Period size: 11 Copynumber: 7.2 Consensus size: 12
18635 ATCAGTCTAA
18645 TTTCAGTCTTC-
1 TTTCAGTCTTCT
**
18656 TTTCAGTC-TAA
1 TTTCAGTCTTCT
18667 TTTCAGTCTTC-
1 TTTCAGTCTTCT
* **
18678 TATCAGTC-TAA
1 TTTCAGTCTTCT
**
18689 TTTCAGTCTAAT
1 TTTCAGTCTTCT
18701 TTTCAGTCTTCT
1 TTTCAGTCTTCT
*
18713 TTTCAATCTTCT
1 TTTCAGTCTTCT
18725 TT
1 TT
18727 CTTTTGCCTA
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
10 2 0.04
11 30 0.53
12 25 0.44
ACGTcount: A:0.18, C:0.22, G:0.07, T:0.52
Consensus pattern (12 bp):
TTTCAGTCTTCT
Found at i:30135 original size:108 final size:107
Alignment explanation
Indices: 29945--30144 Score: 265
Period size: 108 Copynumber: 1.9 Consensus size: 107
29935 GATTTGGATA
* * ** *
29945 AAGTCAGATAATTGTCAATTTTCTAATTTTTTTATTGTTTTAATTTTCGTAACCTTTTGTCTGGT
1 AAGTCAGATAAGTGTCAATTTTCTAATTTTTTTATTGTTTTAATTTCCACAACCTTTTGTCTGAT
*
30010 ATTAGAATTAACCTTTGCTAATATATATATATATATATATAT
66 ATCAGAATTAACCTTTGCTAATATATATATATATATATATAT
* ** * * *
30052 AAGTCATATAAGTGTCCTTTTTCTAATATTTTTTGTTGTTTTCATTTCCACAACTTTTTGTCTGA
1 AAGTCAGATAAGTGTCAATTTTCTAAT-TTTTTTATTGTTTTAATTTCCACAACCTTTTGTCTGA
* *
30117 TATCAGAATTTACGTTTGCTAATATATA
65 TATCAGAATTAACCTTTGCTAATATATA
30145 CAGTAATTCT
Statistics
Matches: 78, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
107 23 0.29
108 55 0.71
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (107 bp):
AAGTCAGATAAGTGTCAATTTTCTAATTTTTTTATTGTTTTAATTTCCACAACCTTTTGTCTGAT
ATCAGAATTAACCTTTGCTAATATATATATATATATATATAT
Found at i:30340 original size:60 final size:60
Alignment explanation
Indices: 30272--30454 Score: 339
Period size: 60 Copynumber: 3.0 Consensus size: 60
30262 ATGTATCTAA
*
30272 TTAAAGTACATTGTAAATAGTTTTTCAGACTATTAATTCAAAAGAAGATAAAACTTCAAT
1 TTAAAGTACATTGTAAATAGTTTTTCAGTCTATTAATTCAAAAGAAGATAAAACTTCAAT
*
30332 TTAAAGTACATTGTAAATAGTTTTTCAGTCTATTAATTCAAAAGAAGATAAAACTTCAAG
1 TTAAAGTACATTGTAAATAGTTTTTCAGTCTATTAATTCAAAAGAAGATAAAACTTCAAT
*
30392 TTAAAGTACATTGTAAATAGTTTTTCAGTCTATTAATTCAAAAGAAGATAAAACTTCAGT
1 TTAAAGTACATTGTAAATAGTTTTTCAGTCTATTAATTCAAAAGAAGATAAAACTTCAAT
30452 TTA
1 TTA
30455 GTTGTCTAAA
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 119 1.00
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (60 bp):
TTAAAGTACATTGTAAATAGTTTTTCAGTCTATTAATTCAAAAGAAGATAAAACTTCAAT
Found at i:30596 original size:34 final size:37
Alignment explanation
Indices: 30558--30644 Score: 117
Period size: 37 Copynumber: 2.4 Consensus size: 37
30548 ATTCTTAGGG
*
30558 GCAGATATATATGTTTTG-TTTTTT-TT-AACATTAA
1 GCAGATATATTTGTTTTGTTTTTTTCTTGAACATTAA
* *
30592 GCAGAAATATTTGTTTTGTTTTTTTCTTGAACATTAG
1 GCAGATATATTTGTTTTGTTTTTTTCTTGAACATTAA
*
30629 GCAGATGTATTTGTTT
1 GCAGATATATTTGTTT
30645 AAAAAGGGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
34 16 0.36
35 6 0.13
36 2 0.04
37 21 0.47
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.52
Consensus pattern (37 bp):
GCAGATATATTTGTTTTGTTTTTTTCTTGAACATTAA
Found at i:33819 original size:33 final size:32
Alignment explanation
Indices: 33777--33894 Score: 155
Period size: 33 Copynumber: 3.6 Consensus size: 32
33767 ATGTGTTCAT
* *
33777 TGAGACACAATATTATTGAGAGCAATCTCATTC
1 TGAGGCACAATATTAGTG-GAGCAATCTCATTC
*
33810 TGAGGCACAATAGTAGTGGGAGCAATCTCATTC
1 TGAGGCACAATATTAGT-GGAGCAATCTCATTC
* * *
33843 TGATGCACAATATCAGTGGCAGCAATCTCATTT
1 TGAGGCACAATATTAGTGG-AGCAATCTCATTC
33876 TGAGGCACAATATTAGTGG
1 TGAGGCACAATATTAGTGG
33895 GAACAATAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
32 2 0.03
33 71 0.96
34 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (32 bp):
TGAGGCACAATATTAGTGGAGCAATCTCATTC
Found at i:34705 original size:11 final size:10
Alignment explanation
Indices: 34687--34720 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
34677 GAAGTTCATG
34687 TTTTGAAGAT
1 TTTTGAAGAT
34697 TTCTTGAAGAT
1 TT-TTGAAGAT
34708 ATTTTGAAGAT
1 -TTTTGAAGAT
34719 TT
1 TT
34721 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:40234 original size:9 final size:9
Alignment explanation
Indices: 40220--40244 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40210 TTATATAGAC
40220 ATAGGTTAT
1 ATAGGTTAT
40229 ATAGGTTAT
1 ATAGGTTAT
40238 ATAGGTT
1 ATAGGTT
40245 TAAAGATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (9 bp):
ATAGGTTAT
Found at i:41574 original size:11 final size:10
Alignment explanation
Indices: 41556--41589 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
41546 GAAGTTTGTG
41556 TTTTGAAGAT
1 TTTTGAAGAT
41566 TTCTTGAAGAT
1 TT-TTGAAGAT
41577 ATTTTGAAGAT
1 -TTTTGAAGAT
41588 TT
1 TT
41590 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:45312 original size:19 final size:19
Alignment explanation
Indices: 45288--45324 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
45278 CCTATCTATT
*
45288 TGTTGGATTTGAATTCTTC
1 TGTTGGATTTGAAATCTTC
45307 TGTTGGATTTGAAATCTT
1 TGTTGGATTTGAAATCTT
45325 ATTCAAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.08, G:0.22, T:0.51
Consensus pattern (19 bp):
TGTTGGATTTGAAATCTTC
Found at i:49326 original size:25 final size:28
Alignment explanation
Indices: 49279--49329 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
49269 GCTTCGGAAG
*
49279 AAGAAGAAGAAGAAAGAGAAAGGAAATA
1 AAGAAAAAGAAGAAAGAGAAAGGAAATA
49307 AAGAAAAAGAA-AAA-AG-AAGGAAA
1 AAGAAAAAGAAGAAAGAGAAAGGAAA
49330 CGATGTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 2 0.09
27 3 0.14
28 10 0.45
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (28 bp):
AAGAAAAAGAAGAAAGAGAAAGGAAATA
Found at i:50138 original size:37 final size:36
Alignment explanation
Indices: 50097--50242 Score: 134
Period size: 37 Copynumber: 3.9 Consensus size: 36
50087 AAATACAAGT
*
50097 GTTTTCGTTT-TTTTAGAGCAAGGGAAAAATCCCGCTA
1 GTTTTAGTTTCTTTTAG-G-AAGGGAAAAATCCCGCTA
*
50134 GTTTTAGTTTCGTTTTAGGAAGGGAAAGATCCCGCTA
1 GTTTTAGTTTC-TTTTAGGAAGGGAAAAATCCCGCTA
* * * * * *
50171 GTTTTAGTTTCGTCTTAGCACGGGAAGGAATGCCACTA
1 GTTTTAGTTTC-TTTTAGGAAGGGAA-AAATCCCGCTA
*
50209 GTTTTAGTTTCATTTTA-GAAAGGAAAAGATCCCG
1 GTTTTAGTTTC-TTTTAGGAAGGGAAAA-ATCCCG
50243 TCAAAAGTTT
Statistics
Matches: 88, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
36 1 0.01
37 58 0.66
38 23 0.26
39 6 0.07
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (36 bp):
GTTTTAGTTTCTTTTAGGAAGGGAAAAATCCCGCTA
Found at i:50219 original size:38 final size:37
Alignment explanation
Indices: 50113--50241 Score: 141
Period size: 37 Copynumber: 3.5 Consensus size: 37
50103 GTTTTTTTAG
* * *
50113 AGCAAGGGAAAAATCCCGCTAGTTTTAGTTTCGTTTT
1 AGCAAGGGAAAGATCCCACTAGTTTTAGTTTCGTCTT
* *
50150 AGGAAGGGAAAGATCCCGCTAGTTTTAGTTTCGTCTT
1 AGCAAGGGAAAGATCCCACTAGTTTTAGTTTCGTCTT
* * * * *
50187 AGCACGGGAAGGAATGCCACTAGTTTTAGTTTCATTTT
1 AGCAAGGGAAAG-ATCCCACTAGTTTTAGTTTCGTCTT
* *
50225 AGAAAGGAAAAGATCCC
1 AGCAAGGGAAAGATCCC
50242 GTCAAAAGTT
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
37 47 0.62
38 29 0.38
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (37 bp):
AGCAAGGGAAAGATCCCACTAGTTTTAGTTTCGTCTT
Found at i:54857 original size:21 final size:20
Alignment explanation
Indices: 54831--54883 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
54821 GCACTGGAGT
* *
54831 ACATGGGTCGCGAGGCAAACC
1 ACATGGG-CGCCAAGCAAACC
54852 ACATGGAGCGCCAAGCAAACC
1 ACATGG-GCGCCAAGCAAACC
54873 ACATGGGCGCC
1 ACATGGGCGCC
54884 CAACGCTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 5 0.17
21 23 0.79
22 1 0.03
ACGTcount: A:0.30, C:0.32, G:0.30, T:0.08
Consensus pattern (20 bp):
ACATGGGCGCCAAGCAAACC
Found at i:54886 original size:21 final size:21
Alignment explanation
Indices: 54845--54883 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
54835 GGGTCGCGAG
54845 GCAAACCACATGGAGCGCCAA
1 GCAAACCACATGGAGCGCCAA
54866 GCAAACCACATGG-GCGCC
1 GCAAACCACATGGAGCGCC
54884 CAACGCTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.36, G:0.26, T:0.05
Consensus pattern (21 bp):
GCAAACCACATGGAGCGCCAA
Found at i:65018 original size:19 final size:18
Alignment explanation
Indices: 64985--65020 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
64975 TTGAAATAAT
64985 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
65003 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
65021 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.