Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011957.1 Corchorus olitorius cultivar O-4 contig11990, 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: 30575
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:6052 original size:15 final size:15
Alignment explanation
Indices: 6032--6102 Score: 106
Period size: 15 Copynumber: 4.7 Consensus size: 15
6022 AGGAGTTCGG
6032 GAAGCTCGCTGCTAA
1 GAAGCTCGCTGCTAA
**
6047 GAAGCTCGCTGCTGG
1 GAAGCTCGCTGCTAA
*
6062 GAAGCTCGCTGCTAG
1 GAAGCTCGCTGCTAA
*
6077 GAAGCTCGCTGTTAA
1 GAAGCTCGCTGCTAA
6092 GAAGCTCGCTG
1 GAAGCTCGCTG
6103 ACGCTCGCCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 51 1.00
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.21
Consensus pattern (15 bp):
GAAGCTCGCTGCTAA
Found at i:6868 original size:21 final size:22
Alignment explanation
Indices: 6845--6982 Score: 97
Period size: 22 Copynumber: 6.5 Consensus size: 22
6835 TCGATAAAAA
* * *
6845 TTTGATAACCATATTGTGAAAT
1 TTTGATAACCACACTATGAAAT
*
6867 TTTAATAACCACACTATGAAAT
1 TTTGATAACCACACTATGAAAT
* ** *
6889 TTTGATAACCTCGGTGTGAAAT
1 TTTGATAACCACACTATGAAAT
** *
6911 TTTGATAATCTGC-CTATGAAAA
1 TTTGATAA-CCACACTATGAAAT
**
6933 TTTGATAATGACACTAT-AAA-
1 TTTGATAACCACACTATGAAAT
* *
6953 ATTGGTAACCACACTATG-AA-
1 TTTGATAACCACACTATGAAAT
6973 TTTGATAACC
1 TTTGATAACC
6983 TTCTCACAGA
Statistics
Matches: 90, Mismatches: 23, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
20 23 0.26
21 4 0.04
22 61 0.68
23 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (22 bp):
TTTGATAACCACACTATGAAAT
Found at i:6875 original size:55 final size:56
Alignment explanation
Indices: 6786--6896 Score: 145
Period size: 55 Copynumber: 2.0 Consensus size: 56
6776 TACAACGTAG
* * * *
6786 AAATATTGATAACCATACTGTGGAAATTTGATAACCTCATTATGGAATTTCGATAA
1 AAATATTGATAACCATACTGTGGAAATTTAATAACCACACTATGAAATTTCGATAA
* *
6842 AAAT-TTGATAACCATATTGT-GAAATTTTAATAACCACACTATGAAATTTTGATAA
1 AAATATTGATAACCATACTGTGGAAA-TTTAATAACCACACTATGAAATTTCGATAA
6897 CCTCGGTGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
54 4 0.08
55 40 0.83
56 4 0.08
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (56 bp):
AAATATTGATAACCATACTGTGGAAATTTAATAACCACACTATGAAATTTCGATAA
Found at i:6981 original size:20 final size:20
Alignment explanation
Indices: 6930--6982 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
6920 CTGCCTATGA
**
6930 AAATTTGATAATGACACTAT
1 AAATTTGATAACCACACTAT
* *
6950 AAAATTGGTAACCACACTAT
1 AAATTTGATAACCACACTAT
*
6970 GAATTTGATAACC
1 AAATTTGATAACC
6983 TTCTCACAGA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.30
Consensus pattern (20 bp):
AAATTTGATAACCACACTAT
Found at i:7077 original size:22 final size:22
Alignment explanation
Indices: 7051--7096 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
7041 AATGAAAATA
*
7051 TGATAAACT-CTTCATAAAATTT
1 TGATAAACTCCGT-ATAAAATTT
*
7073 TGATAACCTCCGTATAAAATTT
1 TGATAAACTCCGTATAAAATTT
7095 TG
1 TG
7097 TTAACCTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
TGATAAACTCCGTATAAAATTT
Found at i:7101 original size:22 final size:21
Alignment explanation
Indices: 7064--7165 Score: 69
Period size: 22 Copynumber: 4.5 Consensus size: 21
7054 TAAACTCTTC
*
7064 ATAAAATTTTGATAACCTCCGT
1 ATAAAATTTTGTTAACCTCC-T
*
7086 ATAAAATTTTGTTAACCTTCCC
1 ATAAAATTTTGTTAACC-TCCT
* * *
7108 AGAAAATTTTGATTATCTCCCCCCT
1 ATAAAATTTTG-TTA---ACCTCCT
* **
7133 ATGAAATTTTGTTAACCTTTTT
1 ATAAAATTTTGTTAACC-TCCT
7155 ATAAAATTTTG
1 ATAAAATTTTG
7166 ATGACCACAT
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
21 2 0.03
22 37 0.61
23 6 0.10
24 3 0.05
25 11 0.18
26 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (21 bp):
ATAAAATTTTGTTAACCTCCT
Found at i:8346 original size:47 final size:47
Alignment explanation
Indices: 8288--8729 Score: 769
Period size: 47 Copynumber: 9.4 Consensus size: 47
8278 TCTCTGTTTA
*
8288 CTTCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
* *
8335 CTTCTTCTTTTACTATTTAGTTTAATTACTCAGAATTAAACTAACCC
1 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
* *
8382 CTTCTTCTTTTACTATTTAGTTTAATTACCCATAATTAAACTAACCC
1 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
*
8429 CTTCTTCTTTTACTACTTAGTTTAATTACCCAGAATTAAACTAACCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
*
8476 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACAT
1 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
*
8523 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACAT
1 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
8570 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
* *
8617 CTTCTTCATTTA-TAATTTAGTTTAATTGCCCAGAATTAAACTAACCT
1 CTTCTTCTTTTACT-ATTTAGTTTAATTACCCAGAATTAAACTAACCT
*
8664 CTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAACTAACCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
8711 CTTCTTCTTTTACTATTTA
1 CTTCTTCTTTTACTATTTA
8730 AACTAACCTC
Statistics
Matches: 377, Mismatches: 16, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
46 1 0.00
47 375 0.99
48 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (47 bp):
CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
Found at i:8425 original size:94 final size:94
Alignment explanation
Indices: 8022--8729 Score: 887
Period size: 94 Copynumber: 7.2 Consensus size: 94
8012 TGCTTACTCT
* *
8022 TTCTTTTACTTTTTAGTTTAATTACCCAGAATTAAACTAACCTCTATTTACTTCTTCTTTTACTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-C-C----T-CTTCTTCTTTTACTA
* *
8087 TTTAGTTTAATTATCTAGAATTAAACTAACCTCTGTTTACTTC
59 TTTAGTTTAATTACCCAGAATTAAACTAA-C-C----T-CTTC
* * * *
8130 TTCTTTTACTCTTTAGTTTAATTACCAAGAATTAAACTAGCTTCTGTTTACTTCTTCTTTTACTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAAC--C----T-CTTCTTCTTTTACTA
* *
8195 TTTAGTCTAATTACCCAGAATTAAACTAGCCTCTGTTTACTTC
59 TTTAGTTTAATTACCCAGAATTAAACTA-AC-C----T-CTTC
* *
8238 TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATCTCTGTTTACTTCTTCTTTTACTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-C-C----T-CTTCTTCTTTTACTA
8303 TTTAGTTTAATTACCCAGAATTAAACTAACCTCTTC
59 TTTAGTTTAATTACCCAGAATTAAACTAACCTCTTC
* *
8339 TTCTTTTACTATTTAGTTTAATTACTCAGAATTAAACTAACCCCTTCTTCTTTTACTATTTAGTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
* *
8404 TAATTACCCATAATTAAACTAACCCCTTC
66 TAATTACCCAGAATTAAACTAACCTCTTC
*
8433 TTCTTTTACTACTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
*
8498 TAATTACCCAGAATTAAACTAACATCTTC
66 TAATTACCCAGAATTAAACTAACCTCTTC
*
8527 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACATCTTCTTCTTTTACTATTTAGTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
8592 TAATTACCCAGAATTAAACTAACCTCTTC
66 TAATTACCCAGAATTAAACTAACCTCTTC
* *
8621 TTCATTTA-TAATTTAGTTTAATTGCCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGT
1 TTCTTTTACT-ATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGT
*
8685 TTAATTACCTAGAATTAAACTAACCTCTTC
65 TTAATTACCCAGAATTAAACTAACCTCTTC
8715 TTCTTTTACTATTTA
1 TTCTTTTACTATTTA
8730 AACTAACCTC
Statistics
Matches: 562, Mismatches: 33, Indels: 24
0.91 0.05 0.04
Matches are distributed among these distances:
93 1 0.00
94 327 0.58
95 1 0.00
99 1 0.00
100 1 0.00
101 42 0.07
102 1 0.00
106 1 0.00
107 2 0.00
108 184 0.33
109 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.46
Consensus pattern (94 bp):
TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
TAATTACCCAGAATTAAACTAACCTCTTC
Found at i:8467 original size:141 final size:142
Alignment explanation
Indices: 8022--8729 Score: 852
Period size: 141 Copynumber: 4.8 Consensus size: 142
8012 TGCTTACTCT
* *
8022 TTCTTTTACTTTTTAGTTTAATTACCCAGAATTAAACTAACCTCTATTTACTTCTTCTTTTACTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACC-C------CTTCTTCTTTTACTA
* *
8087 TTTAGTTTAATTATCTAGAATTAAACTAACCTCTGTTTACTTCTTCTTTTACT-CTTTAGTTTAA
59 TTTAGTTTAATTACCCAGAATTAAACTAACC-C------CTTCTTCTTTTACTACTTTAGTTTAA
* *
8151 TTACCAAGAATTAAACTAGCTTCTGTTTACTTC
117 TTACCCAGAATTAAACTAAC--C----T-CTTC
* * * *
8184 TTCTTTTACTCTTTAGTCTAATTACCCAGAATTAAACTAGCCTCTGTTTACTTCTTCTTTTACTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACC-C------CTTCTTCTTTTACTA
*
8249 TTTAGTTTAATTACCCAGAATTAAACTAATCTCTGTTTACTTCTTCTTTTACT-CTTTAGTTTAA
59 TTTAGTTTAATTACCCAGAATTAAACTAA-C-C-----CCTTCTTCTTTTACTACTTTAGTTTAA
8313 TTACCCAGAATTAAACTAACCTCTTC
117 TTACCCAGAATTAAACTAACCTCTTC
*
8339 TTCTTTTACTATTTAGTTTAATTACTCAGAATTAAACTAACCCCTTCTTCTTTTACTATTTAGTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCCCTTCTTCTTTTACTATTTAGTT
*
8404 TAATTACCCATAATTAAACTAACCCCTTCTTCTTTTACTAC-TTAGTTTAATTACCCAGAATTAA
66 TAATTACCCAGAATTAAACTAACCCCTTCTTCTTTTACTACTTTAGTTTAATTACCCAGAATTAA
8468 ACTAACCTCTTC
131 ACTAACCTCTTC
**
8480 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACATCTTCTTCTTTTACTATTTAGTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCCCTTCTTCTTTTACTATTTAGTT
**
8545 TAATTACCCAGAATTAAACTAACATCTTCTTCTTTTACTA-TTTAGTTTAATTACCCAGAATTAA
66 TAATTACCCAGAATTAAACTAACCCCTTCTTCTTTTACTACTTTAGTTTAATTACCCAGAATTAA
8609 ACTAACCTCTTC
131 ACTAACCTCTTC
* * *
8621 TTCATTTA-TAATTTAGTTTAATTGCCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGT
1 TTCTTTTACT-ATTTAGTTTAATTACCCAGAATTAAACTAACCCCTTCTTCTTTTACTATTTAGT
* *
8685 TTAATTACCTAGAATTAAACTAACCTCTTCTTCTTTTACTA-TTTA
65 TTAATTACCCAGAATTAAACTAACCCCTTCTTCTTTTACTACTTTA
8730 AACTAACCTC
Statistics
Matches: 509, Mismatches: 28, Indels: 39
0.88 0.05 0.07
Matches are distributed among these distances:
140 1 0.00
141 285 0.56
142 1 0.00
146 1 0.00
147 1 0.00
148 42 0.08
154 1 0.00
155 42 0.08
156 1 0.00
160 1 0.00
162 130 0.26
163 1 0.00
164 1 0.00
168 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.46
Consensus pattern (142 bp):
TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCCCTTCTTCTTTTACTATTTAGTT
TAATTACCCAGAATTAAACTAACCCCTTCTTCTTTTACTACTTTAGTTTAATTACCCAGAATTAA
ACTAACCTCTTC
Found at i:8731 original size:28 final size:28
Alignment explanation
Indices: 8699--8757 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
8689 TTACCTAGAA
*
8699 TTAAACTAACCTCTTCTTCTTTTACTAT
1 TTAAACTAACCTCCTCTTCTTTTACTAT
8727 TTAAACTAACCTCCTCTTCTTTTACTAT
1 TTAAACTAACCTCCTCTTCTTTTACTAT
8755 TTA
1 TTA
8758 GTTTAATTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.49
Consensus pattern (28 bp):
TTAAACTAACCTCCTCTTCTTTTACTAT
Found at i:8775 original size:75 final size:75
Alignment explanation
Indices: 8652--8804 Score: 288
Period size: 75 Copynumber: 2.0 Consensus size: 75
8642 TTGCCCAGAA
* *
8652 TTAAACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAACTAACCTCTTCTT
1 TTAAACTAACCTCCTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTT
8717 CTTTTACTAT
66 CTTTTACTAT
8727 TTAAACTAACCTCCTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTT
1 TTAAACTAACCTCCTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTT
8792 CTTTTACTAT
66 CTTTTACTAT
8802 TTA
1 TTA
8805 GTTTAATTAC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.28, C:0.22, G:0.03, T:0.47
Consensus pattern (75 bp):
TTAAACTAACCTCCTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTT
CTTTTACTAT
Found at i:8796 original size:47 final size:47
Alignment explanation
Indices: 8727--8849 Score: 221
Period size: 47 Copynumber: 2.6 Consensus size: 47
8717 CTTTTACTAT
8727 TTAAACTAACCTCCTCTTCTTTTACTATTTAGTTTAATTACCCAGAA
1 TTAAACTAACCTCCTCTTCTTTTACTATTTAGTTTAATTACCCAGAA
*
8774 TTAAACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAA
1 TTAAACTAACCTCCTCTTCTTTTACTATTTAGTTTAATTACCCAGAA
*
8821 TTAAACTAGCCTCCTCTT-TTTTACTATTT
1 TTAAACTAACCTCCTCTTCTTTTACTATTT
8850 CTCTTACTAT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
46 11 0.15
47 62 0.85
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.46
Consensus pattern (47 bp):
TTAAACTAACCTCCTCTTCTTTTACTATTTAGTTTAATTACCCAGAA
Found at i:8822 original size:122 final size:121
Alignment explanation
Indices: 8605--8849 Score: 411
Period size: 122 Copynumber: 2.0 Consensus size: 121
8595 TTACCCAGAA
* *
8605 TTAAACTAACCTCTTCTTCATTTATAATTTAGTTTAATTGCCCAGAATTAAACTAACCTCTTCTT
1 TTAAACTAACCTCCTCTTCATTTATAATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTT
* *
8670 CTTTTACTATTTAGTTTAATTACCTAGAATTAAACTAACCTCTTCTTCTTTTACTAT
66 CTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCCTCTT-TTTTACTAT
*
8727 TTAAACTAACCTCCTCTTCTTTTACT-ATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCT
1 TTAAACTAACCTCCTCTTCATTTA-TAATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCT
*
8791 TCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAGCCTCCTCTTTTTTACTAT
65 TCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCCTCTTTTTTACTAT
8848 TT
1 TT
8850 CTCTTACTAT
Statistics
Matches: 116, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
121 11 0.09
122 104 0.90
123 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.46
Consensus pattern (121 bp):
TTAAACTAACCTCCTCTTCATTTATAATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTT
CTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCCTCTTTTTTACTAT
Found at i:8926 original size:55 final size:55
Alignment explanation
Indices: 8786--9035 Score: 340
Period size: 55 Copynumber: 4.5 Consensus size: 55
8776 AAACTAACCT
* * **
8786 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAGCCTCCTCTTTTTTA
1 CTTCTTCTTTTACTATTTAGTTTAATTGCCCAGAATTAAACTA-ACT--TCTGCTTTA
* * * *
8844 CTAT-TTCTCTTACTATTTAGTTCAATTGCCCATAATTAAACTAACTTATGCTTTA
1 CT-TCTTCTTTTACTATTTAGTTTAATTGCCCAGAATTAAACTAACTTCTGCTTTA
* *
8899 CTTCTTCTTTTACTTTTTAGTTTAATTGCCTAGAATTAAACTAACTTCTGCTTTA
1 CTTCTTCTTTTACTATTTAGTTTAATTGCCCAGAATTAAACTAACTTCTGCTTTA
*
8954 CTTCTTCTTTTACTCTTTAGTTTAATTGCCCAGAATTAAACTAACTTCTGCTTTA
1 CTTCTTCTTTTACTATTTAGTTTAATTGCCCAGAATTAAACTAACTTCTGCTTTA
* *
9009 CTTCTTCTTTTACTCTTCAGTTTAATT
1 CTTCTTCTTTTACTATTTAGTTTAATT
9036 ACCCTGGATT
Statistics
Matches: 173, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
54 1 0.01
55 132 0.76
57 2 0.01
58 37 0.21
59 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.49
Consensus pattern (55 bp):
CTTCTTCTTTTACTATTTAGTTTAATTGCCCAGAATTAAACTAACTTCTGCTTTA
Found at i:9062 original size:55 final size:53
Alignment explanation
Indices: 8741--9039 Score: 261
Period size: 55 Copynumber: 5.5 Consensus size: 53
8731 ACTAACCTCC
* * *
8741 TCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTA-AC--C--T-CT
1 TCTTCTTTTACTCTTCAGTTTAATTACCCAGAATTAAACTATTCTGCTTTACT
* * **
8788 TCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAGCCTCCTCTTTTTTACT
1 TCTTCTTTTACTCTTCAGTTTAATTACCCAGAATTAAACTA---T--TCTGCTTTACT
* * * * * * *
8846 AT-TTCTCTTACTATTTAGTTCAATTGCCCATAATTAAACTAACTTATGCTTTACT
1 -TCTTCTTTTACTCTTCAGTTTAATTACCCAGAATTAAACT-A-TTCTGCTTTACT
* * * *
8901 TCTTCTTTTACTTTTTAGTTTAATTGCCTAGAATTAAACTAACTTCTGCTTTACT
1 TCTTCTTTTACTCTTCAGTTTAATTACCCAGAATTAAACT-A-TTCTGCTTTACT
* *
8956 TCTTCTTTTACTCTTTAGTTTAATTGCCCAGAATTAAACTAACTTCTGCTTTACT
1 TCTTCTTTTACTCTTCAGTTTAATTACCCAGAATTAAACT-A-TTCTGCTTTACT
9011 TCTTCTTTTACTCTTCAGTTTAATTACCC
1 TCTTCTTTTACTCTTCAGTTTAATTACCC
9040 TGGATTAAGT
Statistics
Matches: 219, Mismatches: 19, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
47 41 0.19
53 1 0.00
54 1 0.00
55 135 0.62
57 3 0.01
58 36 0.16
59 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.48
Consensus pattern (53 bp):
TCTTCTTTTACTCTTCAGTTTAATTACCCAGAATTAAACTATTCTGCTTTACT
Found at i:9070 original size:36 final size:37
Alignment explanation
Indices: 9030--9129 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 37
9020 ACTCTTCAGT
*
9030 TTAATTACCCTGGATTAAGTCTTTGACTGC-TTTTAC
1 TTAATTACCCTGAATTAAGTCTTTGACTGCGTTTTAC
9066 TTAATT-CCCTTGAATTAAGTCTTTGACTGCTGGGTTTTAC
1 TTAATTACCC-TGAATTAAGTCTTTGACTGC---GTTTTAC
* *
9106 TTAATTACCATGAATTAAATCTTT
1 TTAATTACCCTGAATTAAGTCTTT
9130 ACTTATGGAT
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
35 3 0.05
36 25 0.45
40 25 0.45
41 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (37 bp):
TTAATTACCCTGAATTAAGTCTTTGACTGCGTTTTAC
Found at i:13054 original size:19 final size:19
Alignment explanation
Indices: 13043--13079 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
13033 AATTTTTAAG
13043 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
13062 TACAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
13080 ATAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:13867 original size:11 final size:11
Alignment explanation
Indices: 13823--13871 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
13813 TTGAAATAAA
13823 TCTTC-AATGG
1 TCTTCAAATGG
13833 TCTTC-AA--G
1 TCTTCAAATGG
*
13841 TCTCCAAATAGG
1 TCTTCAAAT-GG
13853 TCTTCAAATGG
1 TCTTCAAATGG
13864 TCTTCAAA
1 TCTTCAAA
13872 CACGAACTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
8 5 0.15
9 2 0.06
10 7 0.21
11 10 0.30
12 9 0.27
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (11 bp):
TCTTCAAATGG
Done.