Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011224.1 Corchorus capsularis cultivar CVL-1 contig11245, 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: 92773
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:238 original size:30 final size:30
Alignment explanation
Indices: 204--282 Score: 95
Period size: 33 Copynumber: 2.5 Consensus size: 30
194 CAAAACAGAT
**
204 TTATTTTCAATGCTATCAACCAAAATAGGA
1 TTATTTTCAATGCTATCAACCAAAATAAAA
*
234 TTATTTGCAATGCTATGATCAACCAAAATAAAA
1 TTATTTTCAATGC--T-ATCAACCAAAATAAAA
*
267 TTATTTTTAATGCTAT
1 TTATTTTCAATGCTAT
283 GTTCAACCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
30 14 0.34
31 1 0.02
32 1 0.02
33 25 0.61
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (30 bp):
TTATTTTCAATGCTATCAACCAAAATAAAA
Found at i:260 original size:33 final size:33
Alignment explanation
Indices: 218--294 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
208 TTTCAATGCT
**
218 ATCAACCAAAATAGGATTATTTGCAATGCTATG
1 ATCAACCAAAATAAAATTATTTGCAATGCTATG
**
251 ATCAACCAAAATAAAATTATTTTTAATGCTATG
1 ATCAACCAAAATAAAATTATTTGCAATGCTATG
*
284 TTCAACCAAAA
1 ATCAACCAAAA
295 CAGAATTGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (33 bp):
ATCAACCAAAATAAAATTATTTGCAATGCTATG
Found at i:361 original size:33 final size:32
Alignment explanation
Indices: 324--428 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 32
314 ATTAGCATCC
* *
324 AAAACAGATTTAGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTATCATCGCAAACAACA-CT
* * *
357 AAAACAGATTTAATGTCATTGCAAACAACACT
1 AAAACAGATTTAGTATCATCGCAAACAACACT
** *
389 CAAATTAGGTTTAGTATCATCGCAAACAACATCT
1 -AAAACAGATTTAGTATCATCGCAAACAACA-CT
423 AAAACA
1 AAAACA
429 CTCTTTGCAA
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
32 2 0.03
33 54 0.93
34 2 0.03
ACGTcount: A:0.46, C:0.21, G:0.09, T:0.25
Consensus pattern (32 bp):
AAAACAGATTTAGTATCATCGCAAACAACACT
Found at i:2899 original size:33 final size:33
Alignment explanation
Indices: 2857--2919 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
2847 AGCTAAAGGA
2857 TCATGTGGCCGGTTGTGGCCGAGCATGGCCGAG
1 TCATGTGGCCGGTTGTGGCCGAGCATGGCCGAG
*
2890 TCATGTGGCCGGTTGTGGCCGGGCATGGCC
1 TCATGTGGCCGGTTGTGGCCGAGCATGGCC
2920 ATGTCGCATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.10, C:0.25, G:0.43, T:0.22
Consensus pattern (33 bp):
TCATGTGGCCGGTTGTGGCCGAGCATGGCCGAG
Found at i:2932 original size:33 final size:33
Alignment explanation
Indices: 2862--2968 Score: 110
Period size: 33 Copynumber: 3.2 Consensus size: 33
2852 AAGGATCATG
* **
2862 TGGCCGGTTGTGGCCGAGCATGGCCGAGTCATG
1 TGGCCGGTTGTGGCCGGGCATGGCCGAGTCACA
*
2895 TGGCCGGTTGTGGCCGGGCATGGCC-ATGTCGCA
1 TGGCCGGTTGTGGCCGGGCATGGCCGA-GTCACA
** * *
2928 TGGCCGG-TGATGGCCGGGCATCTCCGAGTCGCG
1 TGGCCGGTTG-TGGCCGGGCATGGCCGAGTCACA
2961 TGGCCGGT
1 TGGCCGGT
2969 CTTGTGCCCG
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
32 3 0.05
33 59 0.94
34 1 0.02
ACGTcount: A:0.09, C:0.27, G:0.43, T:0.21
Consensus pattern (33 bp):
TGGCCGGTTGTGGCCGGGCATGGCCGAGTCACA
Found at i:12899 original size:19 final size:18
Alignment explanation
Indices: 12866--12902 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
12856 TTGAAATAAT
12866 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
12884 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
12903 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:26814 original size:26 final size:25
Alignment explanation
Indices: 26781--26829 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
26771 TCCCTCTTTG
* *
26781 AAAAAAAATGAGTGTTAGTAACCTC
1 AAAAAAAAAGAGCGTTAGTAACCTC
*
26806 AAAAGAAAAAGGGCGTTAGTAACC
1 AAAA-AAAAAGAGCGTTAGTAACC
26830 CCTAAATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.18
Consensus pattern (25 bp):
AAAAAAAAAGAGCGTTAGTAACCTC
Found at i:27620 original size:23 final size:23
Alignment explanation
Indices: 27593--27646 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
27583 GCGACATGGG
27593 CGCCCAGCCAGAGTCGGGGGTGC
1 CGCCCAGCCAGAGTCGGGGGTGC
27616 CGCCCAGCCAGAGTCGGGGGTGC
1 CGCCCAGCCAGAGTCGGGGGTGC
27639 CGCCCAGC
1 CGCCCAGC
27647 AGCCACATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.13, C:0.39, G:0.41, T:0.07
Consensus pattern (23 bp):
CGCCCAGCCAGAGTCGGGGGTGC
Found at i:29545 original size:16 final size:18
Alignment explanation
Indices: 29506--29539 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29496 TTTTTAAGTA
*
29506 AAAATATAATATATAAAC
1 AAAATTTAATATATAAAC
29524 AAAATTTAATAT-TAAA
1 AAAATTTAATATATAAA
29540 ATAATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATTTAATATATAAAC
Found at i:32982 original size:11 final size:12
Alignment explanation
Indices: 32966--32997 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
32956 GAAGTTCGTG
32966 TTTGAAGATTA-
1 TTTGAAGATTAT
32977 TTTGAAGA-TAT
1 TTTGAAGATTAT
32988 TTTGAAGATT
1 TTTGAAGATT
32998 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.11
11 16 0.84
12 1 0.05
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (12 bp):
TTTGAAGATTAT
Found at i:34372 original size:6 final size:6
Alignment explanation
Indices: 34361--34391 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
34351 ATAATTGCTA
34361 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
34392 CTTTGCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Found at i:35834 original size:15 final size:15
Alignment explanation
Indices: 35814--35854 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
35804 CCTTGCCAAG
35814 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
35829 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
*
35844 CAAGAAGATGA
1 CCAGAAGATGA
35855 ATAACTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.44, C:0.22, G:0.27, T:0.07
Consensus pattern (15 bp):
CCAGAAGATGAGCCA
Found at i:37506 original size:10 final size:10
Alignment explanation
Indices: 37493--37521 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
37483 CAAAAACGAC
37493 AATGTTGAAG
1 AATGTTGAAG
37503 AATGTTGAAG
1 AATGTTGAAG
37513 AATGTTGAA
1 AATGTTGAA
37522 ATATTGCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (10 bp):
AATGTTGAAG
Found at i:40619 original size:5 final size:5
Alignment explanation
Indices: 40609--40637 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
40599 ATTGCCTTTC
40609 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
40638 AAATTTCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:52613 original size:17 final size:17
Alignment explanation
Indices: 52591--52625 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
52581 GACTATTATG
52591 CAATGCAAATGATGGAA
1 CAATGCAAATGATGGAA
52608 CAATGCAAATGATGGAA
1 CAATGCAAATGATGGAA
52625 C
1 C
52626 CTGTCATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.23, T:0.17
Consensus pattern (17 bp):
CAATGCAAATGATGGAA
Found at i:54997 original size:40 final size:40
Alignment explanation
Indices: 54884--54997 Score: 131
Period size: 40 Copynumber: 2.9 Consensus size: 40
54874 ATTAAACCCA
* * *
54884 TTACTGATGACTCCTTTTACTTTTACT-TTTAATTACCAAT
1 TTACTGATTACTTCTTTTACTTTTACTCTTTTA-TACCAAT
* * *
54924 TTACTGATTGCTTCTTTTACTTTTATTCCTTTATACCAAT
1 TTACTGATTACTTCTTTTACTTTTACTCTTTTATACCAAT
* * *
54964 TTTCTGCTTATTTCTTTTACTTTTACTCTTTTAT
1 TTACTGATTACTTCTTTTACTTTTACTCTTTTAT
54998 TGATTACTTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
40 58 0.95
41 3 0.05
ACGTcount: A:0.19, C:0.19, G:0.04, T:0.57
Consensus pattern (40 bp):
TTACTGATTACTTCTTTTACTTTTACTCTTTTATACCAAT
Found at i:55038 original size:17 final size:17
Alignment explanation
Indices: 55016--55103 Score: 58
Period size: 17 Copynumber: 5.4 Consensus size: 17
55006 TCTTTTACTT
55016 TTACTTCATTCTGCTGA
1 TTACTTCATTCTGCTGA
* * *
55033 TTACTTC-TTTTACT-T
1 TTACTTCATTCTGCTGA
* *
55048 TTACTTAACTCTGCTGA
1 TTACTTCATTCTGCTGA
* * *
55065 TTACTTC-TTTTACT-T
1 TTACTTCATTCTGCTGA
* *
55080 TTACTTCACTCTGTTGA
1 TTACTTCATTCTGCTGA
55097 TTACTTC
1 TTACTTC
55104 TTTTACTTTT
Statistics
Matches: 49, Mismatches: 18, Indels: 8
0.65 0.24 0.11
Matches are distributed among these distances:
15 13 0.27
16 16 0.33
17 20 0.41
ACGTcount: A:0.17, C:0.23, G:0.07, T:0.53
Consensus pattern (17 bp):
TTACTTCATTCTGCTGA
Found at i:55039 original size:32 final size:32
Alignment explanation
Indices: 54975--55149 Score: 246
Period size: 32 Copynumber: 5.5 Consensus size: 32
54965 TTCTGCTTAT
* **
54975 TTCTTTTACTTTTAC-TC-TTTTATTGATTAC
1 TTCTTTTACTTTTACTTCATTCTGCTGATTAC
55005 TTCTTTTACTTTTACTTCATTCTGCTGATTAC
1 TTCTTTTACTTTTACTTCATTCTGCTGATTAC
* *
55037 TTCTTTTACTTTTACTTAACTCTGCTGATTAC
1 TTCTTTTACTTTTACTTCATTCTGCTGATTAC
* *
55069 TTCTTTTACTTTTACTTCACTCTGTTGATTAC
1 TTCTTTTACTTTTACTTCATTCTGCTGATTAC
* * *
55101 TTCTTTTACTTTTACTTCATTTTGCTGGTTAT
1 TTCTTTTACTTTTACTTCATTCTGCTGATTAC
55133 TTCTTTTACTTTTACTT
1 TTCTTTTACTTTTACTT
55150 TTACTTTACT
Statistics
Matches: 131, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
30 15 0.11
31 2 0.02
32 114 0.87
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.59
Consensus pattern (32 bp):
TTCTTTTACTTTTACTTCATTCTGCTGATTAC
Found at i:55107 original size:96 final size:94
Alignment explanation
Indices: 54975--55149 Score: 278
Period size: 96 Copynumber: 1.8 Consensus size: 94
54965 TTCTGCTTAT
* *
54975 TTCTTTTACTTTTACTCTTTTATTGATTACTTCTTTTACTTTTACTTCATTCTGCTGATTACTTC
1 TTCTTTTACTTTTACTCCTCTATTGATTACTTCTTTTACTTTTACTTCATTCTGCTGATTACTTC
55040 TTTTACTTTTACTTAACTCTGCTGATTAC
66 TTTTACTTTTACTTAACTCTGCTGATTAC
* * * *
55069 TTCTTTTACTTTTACTTCACTCTGTTGATTACTTCTTTTACTTTTACTTCATTTTGCTGGTTATT
1 TTCTTTTACTTTTAC-TC-CTCTATTGATTACTTCTTTTACTTTTACTTCATTCTGCTGATTACT
55134 TCTTTTACTTTTACTT
64 TCTTTTACTTTTACTT
55150 TTACTTTACT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
94 15 0.21
95 2 0.03
96 56 0.77
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.59
Consensus pattern (94 bp):
TTCTTTTACTTTTACTCCTCTATTGATTACTTCTTTTACTTTTACTTCATTCTGCTGATTACTTC
TTTTACTTTTACTTAACTCTGCTGATTAC
Found at i:62162 original size:14 final size:15
Alignment explanation
Indices: 62143--62172 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
62133 AATTTCCTAG
62143 AAAACTAAAAA-AAA
1 AAAACTAAAAAGAAA
62157 AAAACTAAAAAGAAA
1 AAAACTAAAAAGAAA
62172 A
1 A
62173 TTAGCAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.83, C:0.07, G:0.03, T:0.07
Consensus pattern (15 bp):
AAAACTAAAAAGAAA
Found at i:67728 original size:11 final size:10
Alignment explanation
Indices: 67712--67758 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
67702 CACTTCATCC
67712 TTTTTCTATTT
1 TTTTTCT-TTT
67723 TTTTTCTTCTT
1 TTTTTCTT-TT
*
67734 TTCTTCTTTT
1 TTTTTCTTTT
*
67744 TTTTT-TATT
1 TTTTTCTTTT
67753 TTTTTC
1 TTTTTC
67759 AGAGGGACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
9 8 0.26
10 7 0.23
11 16 0.52
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:67740 original size:22 final size:22
Alignment explanation
Indices: 67715--67758 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
67705 TTCATCCTTT
*
67715 TTCTATTTTTTTTCTTCTTTTC
1 TTCTATTTTTTTTATTCTTTTC
* *
67737 TTCTTTTTTTTTTATTTTTTTC
1 TTCTATTTTTTTTATTCTTTTC
67759 AGAGGGACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (22 bp):
TTCTATTTTTTTTATTCTTTTC
Found at i:69240 original size:25 final size:26
Alignment explanation
Indices: 69212--69263 Score: 61
Period size: 29 Copynumber: 1.9 Consensus size: 26
69202 TGTTGTGTTT
69212 GATC-AAGTGCGGGTTGTGCACTTAG
1 GATCTAAGTGCGGGTTGTGCACTTAG
*
69237 GATCGATTAAGTGCGGGTTTTGCACTT
1 GATC---TAAGTGCGGGTTGTGCACTT
69264 GTTGTTGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 4 0.18
29 18 0.82
ACGTcount: A:0.19, C:0.15, G:0.33, T:0.33
Consensus pattern (26 bp):
GATCTAAGTGCGGGTTGTGCACTTAG
Found at i:73074 original size:33 final size:33
Alignment explanation
Indices: 73037--73121 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
73027 AGCACTAGTG
*
73037 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC
* *
73070 ACCGGCCACGTGACTTGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC
* *
73103 ACCGGCCACTCGACATGGA
1 ACCGGCCACGCGACTTGGA
73122 CATGTCTGGC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.24, C:0.36, G:0.29, T:0.11
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC
Found at i:73133 original size:33 final size:33
Alignment explanation
Indices: 73059--73143 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
73049 ACTTGGAGAA
* *
73059 GCCCGGCCAACACCGGCCACGTGACTTGGAGAT
1 GCCCGGCCAACACCGGCCACGTGACATGGACAT
73092 GCCCGGCCAACACCGGCCAC-TCGACATGGACAT
1 GCCCGGCCAACACCGGCCACGT-GACATGGACAT
* *
73125 GTCTGGCC-ACAACCGGCCA
1 GCCCGGCCAAC-ACCGGCCA
73144 TCGCTTGGCG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
32 3 0.07
33 43 0.93
ACGTcount: A:0.22, C:0.40, G:0.27, T:0.11
Consensus pattern (33 bp):
GCCCGGCCAACACCGGCCACGTGACATGGACAT
Found at i:76458 original size:16 final size:16
Alignment explanation
Indices: 76423--76529 Score: 171
Period size: 16 Copynumber: 6.8 Consensus size: 16
76413 TTCGGGCGGG
76423 TTCGGGTTCGGGTA-T
1 TTCGGGTTCGGGTATT
76438 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
76454 TTCGGGTTCGGGTAAT
1 TTCGGGTTCGGGTATT
*
76470 TTCGGGTTTGGGTATT
1 TTCGGGTTCGGGTATT
*
76486 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTATT
*
76502 TTCGGGTTCGGATATT
1 TTCGGGTTCGGGTATT
76518 TTCGGGTTCGGG
1 TTCGGGTTCGGG
76530 CTCGGGTCGG
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
15 14 0.17
16 69 0.83
ACGTcount: A:0.07, C:0.12, G:0.38, T:0.43
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:76527 original size:6 final size:6
Alignment explanation
Indices: 76518--76572 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
76508 TTCGGATATT
* * * **
76518 TTCGGG TTCGGG CTCGGG -TCGGG TTCGGG TTTGGA CCCGGG -TCGGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
76564 TTCGGG TTC
1 TTCGGG TTC
76573 ACTTTCGATA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
5 9 0.23
6 30 0.77
ACGTcount: A:0.02, C:0.22, G:0.47, T:0.29
Consensus pattern (6 bp):
TTCGGG
Found at i:76548 original size:23 final size:23
Alignment explanation
Indices: 76518--76572 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
76508 TTCGGATATT
* *
76518 TTCGGGTTCGGGCTCGGGTCGGG
1 TTCGGGTTCGGACCCGGGTCGGG
*
76541 TTCGGGTTTGGACCCGGGTCGGG
1 TTCGGGTTCGGACCCGGGTCGGG
76564 TTCGGGTTC
1 TTCGGGTTC
76573 ACTTTCGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.02, C:0.22, G:0.47, T:0.29
Consensus pattern (23 bp):
TTCGGGTTCGGACCCGGGTCGGG
Found at i:77342 original size:16 final size:16
Alignment explanation
Indices: 77321--77351 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
77311 TCTCGGGTTT
77321 GGGTTCAGGTTCGGGC
1 GGGTTCAGGTTCGGGC
*
77337 GGGTTCGGGTTCGGG
1 GGGTTCAGGTTCGGG
77352 TTGTCTCGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.16, G:0.55, T:0.26
Consensus pattern (16 bp):
GGGTTCAGGTTCGGGC
Found at i:77345 original size:6 final size:6
Alignment explanation
Indices: 77313--77353 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
77303 TATTTTGATC
* *
77313 TCGGGT TTGGGT TCAGGT TCGGG- -CGGGT TCGGGT TCGGGT T
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT T
77354 GTCTCGGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
4 4 0.14
6 25 0.86
ACGTcount: A:0.02, C:0.15, G:0.49, T:0.34
Consensus pattern (6 bp):
TCGGGT
Found at i:77360 original size:16 final size:16
Alignment explanation
Indices: 77341--77385 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
77331 TCGGGCGGGT
77341 TCGGGTTCGGGT-TGTC
1 TCGGGTTCGGGTAT-TC
* *
77357 TCGGATTCGGGTATTT
1 TCGGGTTCGGGTATTC
77373 TCGGGTTCGGGTA
1 TCGGGTTCGGGTA
77386 CGGGCGGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.07, C:0.16, G:0.40, T:0.38
Consensus pattern (16 bp):
TCGGGTTCGGGTATTC
Found at i:83074 original size:25 final size:25
Alignment explanation
Indices: 83040--83087 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
83030 CTCCTTTGAA
*
83040 CTTCTGAGTCCCAGATCGAGAAGAG
1 CTTCAGAGTCCCAGATCGAGAAGAG
* *
83065 CTTCAGAGTCTCAGATTGAGAAG
1 CTTCAGAGTCCCAGATCGAGAAG
83088 GCGAGAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (25 bp):
CTTCAGAGTCCCAGATCGAGAAGAG
Done.